diff --git a/Plugins/org.mitk.gui.qt.activelearning/src/internal/QmitkActiveLearning.cpp b/Plugins/org.mitk.gui.qt.activelearning/src/internal/QmitkActiveLearning.cpp index 4ce3dfabd5..3413ae4e52 100644 --- a/Plugins/org.mitk.gui.qt.activelearning/src/internal/QmitkActiveLearning.cpp +++ b/Plugins/org.mitk.gui.qt.activelearning/src/internal/QmitkActiveLearning.cpp @@ -1,977 +1,1057 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. 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 // Qt #include #include #include #include // Qmitk #include "QmitkActiveLearning.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include // ITK #include #include #include #include #include #include #include #include typedef ActiveLearning::FeaturePixelType FeaturePixelType; typedef ActiveLearning::AnnotationPixelType AnnotationPixelType; typedef ActiveLearning::LabelPixelType LabelPixelType; typedef ActiveLearning::FeatureMatrixType FeatureMatrixType; typedef ActiveLearning::LabelVectorType LabelVectorType; // Returns true if list has at least one entry and all entries are valid mitk::Images, otherwise false static bool SelectionAllImages(const QList& nodes) { if (nodes.empty()) { return false; } for (const auto& node : nodes) { if(!(node.IsNotNull() && dynamic_cast(node->GetData()) != nullptr)) return false; } return true; } // QColor to mitk::Color static mitk::Color QColorToMitkColor(const QColor& qcolor) { mitk::Color color; color.SetRed((float)qcolor.red() / 255); color.SetGreen((float)qcolor.green() / 255); color.SetBlue((float)qcolor.blue() / 255); return color; } // For debugging static void PrintAllLabels(mitk::LabelSetImage* image) { for (auto it=image->GetActiveLabelSet()->IteratorBegin(); it!=image->GetActiveLabelSet()->IteratorConstEnd(); ++it) { MITK_INFO << "Key: " << it->first << " - Name: " << it->second->GetName() << " - Value: " << it->second->GetValue() << " - Color: " << it->second->GetColor(); } } // Make values of labels a consistent range static void FillLabelValues(mitk::LabelSetImage* image) { int value(0); for (auto it=image->GetActiveLabelSet()->IteratorBegin(); it!=image->GetActiveLabelSet()->IteratorConstEnd(); ++it) { it->second->SetValue(value); value++; } image->GetActiveLabelSet()->SetActiveLabel(0); } // Fill image with zeros static void FillWithZeros(mitk::Image* image) { unsigned int size = image->GetPixelType().GetSize(); for (unsigned int i=0; iGetDimension(); i++) { size *= image->GetDimension(i); } for (unsigned int t=0; tGetTimeSteps(); t++) { mitk::ImageWriteAccessor accessor(image, image->GetVolumeData(0)); memset(accessor.GetData(), 0, size); } } template static Eigen::Matrix Transform(const std::vector images) { // Find size for output matrix [number of voxels, number of feature images] unsigned int size = images[0]->GetDimension(0); for (unsigned int i=1; i<3; ++i) { size *= images[0]->GetDimension(i); } Eigen::Matrix outputMatrix(size, images.size()); for (unsigned int i=0; i::Pointer imageItk; mitk::CastToItkImage(images[i], imageItk); outputMatrix.col(i) = Eigen::Matrix::Map(imageItk->GetBufferPointer(), size); } return outputMatrix; } template -static mitk::Image::Pointer Transform(const Eigen::Matrix &inputMatrix, const mitk::Image::Pointer referenceImage) +static mitk::Image::Pointer Transform(const Eigen::Matrix &inputMatrix, + const mitk::Image::Pointer referenceImage) { typename itk::Image::Pointer imageItk; auto outputImage = mitk::Image::New(); outputImage->Initialize(mitk::MakeScalarPixelType(), *(referenceImage->GetTimeGeometry()->Clone())); mitk::CastToItkImage(outputImage, imageItk); auto it = itk::ImageRegionIterator>(imageItk, imageItk->GetLargestPossibleRegion()); int i = 0; while (!it.IsAtEnd()) { it.Set(inputMatrix(i, 0)); ++it; ++i; } outputImage = mitk::GrabItkImageMemory(imageItk); return outputImage; } +template +static mitk::Image::Pointer Transform(const Eigen::Matrix &inputMatrix, + const mitk::Image::Pointer referenceImage) +{ + // Create ITK image + typedef itk::VectorImage VectorImageType; + auto imageItk = VectorImageType::New(); + typename VectorImageType::IndexType start; + start.Fill(0); + typename VectorImageType::SizeType size; + for (int i=0; i<3; ++i) + { + size[i] = referenceImage->GetDimension(i); + } + typename VectorImageType::RegionType region(start, size); + imageItk->SetRegions(region); + imageItk->SetVectorLength(inputMatrix.cols()); + imageItk->Allocate(); + + auto outputImage = mitk::Image::New(); + + auto it = itk::ImageRegionIterator>(imageItk, imageItk->GetLargestPossibleRegion()); + int i = 0; + while (!it.IsAtEnd()) + { + itk::VariableLengthVector pixel; + pixel.SetSize(inputMatrix.cols()); + for (int j=0; j(inputMatrix(i, j)); + } + it.Set(pixel); + ++it; + ++i; + } + + outputImage = mitk::ImportItkImage(imageItk); + outputImage->SetClonedTimeGeometry(referenceImage->GetTimeGeometry()); + return outputImage; +} + template -static void PrintMatrix(const Eigen::Matrix dataMatrix, int maxRows = 0) +static void PrintMatrix(const Eigen::Matrix dataMatrix, + int maxRows = 0) { if (maxRows == 0 || maxRows > dataMatrix.rows()) maxRows = dataMatrix.rows(); MITK_INFO << "---------------------"; for (int i=0; i -static void PrintMatrix(const Eigen::Matrix dataMatrix, const Eigen::Matrix labelMatrix, int maxRows = 0) +static void PrintMatrix(const Eigen::Matrix dataMatrix, + const Eigen::Matrix labelMatrix, + int maxRows = 0) { if (labelMatrix.rows() < dataMatrix.rows()) return; if (maxRows == 0 || maxRows > dataMatrix.rows()) maxRows = dataMatrix.rows(); MITK_INFO << "---------------------"; for (int i=0; i -static void GaussianSmoothing(const itk::Image* inputImage, const double sigma, mitk::Image::Pointer outputImage) +static void GaussianSmoothing(const itk::Image* inputImage, + const double sigma, mitk::Image::Pointer outputImage) { typedef itk::Image ImageType; typedef itk::Image FeatureImageType; auto filter = itk::DiscreteGaussianImageFilter::New(); filter->SetInput(inputImage); filter->SetVariance(sigma*sigma); filter->Update(); mitk::GrabItkImageMemory(filter->GetOutput(), outputImage); } template -static void GaussianGradientMagnitude(const itk::Image* inputImage, const double sigma, mitk::Image::Pointer outputImage) +static void GaussianGradientMagnitude(const itk::Image* inputImage, + const double sigma, mitk::Image::Pointer outputImage) { typedef itk::Image ImageType; typedef itk::Image FeatureImageType; auto filter = itk::GradientMagnitudeRecursiveGaussianImageFilter::New(); filter->SetInput(inputImage); filter->SetSigma(sigma); filter->Update(); mitk::GrabItkImageMemory(filter->GetOutput(), outputImage); } template -static void LaplacianOfGaussian(const itk::Image* inputImage, const double sigma, mitk::Image::Pointer outputImage) +static void LaplacianOfGaussian(const itk::Image* inputImage, + const double sigma, mitk::Image::Pointer outputImage) { typedef itk::Image ImageType; typedef itk::Image FeatureImageType; auto filter = itk::LaplacianRecursiveGaussianImageFilter::New(); filter->SetInput(inputImage); filter->SetSigma(sigma); filter->Update(); mitk::GrabItkImageMemory(filter->GetOutput(), outputImage); } //template -//static void StructureTensorEigenvalues(const itk::Image* inputImage, float sigma, std::vector outputImages) +//static void StructureTensorEigenvalues(const itk::Image* inputImage, +// float sigma, std::vector outputImages) //{ // typedef itk::Image ImageType; // auto filter = itk::StructureTensorEigenvalueImageFilter::New(); // filter->SetInput(inputImage); // filter->SetInnerScale(sigma); // filter->SetOuterScale(sigma); // filter->Update(); // for (unsigned int i=0; iGetNumberOfOutputs(); i++) // { // mitk::GrabItkImageMemory(filter->GetOutput(i), outputImages[i]); // } //} //template -//static void HessianEigenvalues(const itk::Image* inputImage, float sigma, std::vector outputImages) +//static void HessianEigenvalues(const itk::Image* inputImage, +// float sigma, std::vector outputImages) //{ // typedef itk::Image ImageType; // typedef itk::Image, imageDimension> TensorImageType; // auto filter = itk::HessianRecursiveGaussianImageFilter::New(); // ImageType::Pointer o1, o2, o3; // o1->Allocate(); // o2->Allocate(); // o3->Allocate(); // filter->SetInput(inputImage); // filter->SetSigma(sigma); // filter->Update(); // TensorImageType::Pointer tensorImage = filter->GetOutput(); // itk::ImageRegionIterator tensorIt(tensorImage, tensorImage->GetLargestPossibleRegion()); // itk::ImageRegionIterator o1It(o1, o1->GetLargestPossibleRegion()); // itk::ImageRegionIterator o2It(o2, o2->GetLargestPossibleRegion()); // itk::ImageRegionIterator o3It(o3, o3->GetLargestPossibleRegion()); // while (!tensorIt.IsAtEnd()) // { // itk::SymmetricSecondRankTensor::EigenValue // for (unsigned int i=0; iGetNumberOfOutputs(); i++) // { // mitk::GrabItkImageMemory(filter->GetOutput(i), outputImages[i]); // } //} /* ================================================================== * PUBLIC SLOTS * =============================================================== */ void ActiveLearning::Initialize() { // Get selected nodes and check again if these are all images m_Nodes = this->GetDataManagerSelection(); if (!SelectionAllImages(m_Nodes)) return; m_Controls.m_InitializePushButton->setDisabled(true); // Set names to the label (again) QString nameList = QString::fromStdString(m_Nodes[0]->GetName()); if (m_Nodes.length() >= 2) { for (int i=1; i"); nameList += QString::fromStdString(m_Nodes[i]->GetName()); } } m_Controls.m_InitializeLabel->setText(nameList); // ======================================= // PREDICTION IMAGE // ======================================= m_PredictionImage = mitk::Image::New(); try { mitk::Image::Pointer referenceImage = dynamic_cast(m_Nodes[0]->GetData()); m_PredictionImage->Initialize(referenceImage); } catch (mitk::Exception& e) { MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::information(m_Parent, "Error", "Could not initialize prediction image"); return; } FillWithZeros(m_PredictionImage); m_PredictionNode = mitk::DataNode::New(); m_PredictionNode->SetData(m_PredictionImage); m_PredictionNode->SetName("Predictions"); m_PredictionNode->SetColor(1., 1. ,1.); m_PredictionNode->SetBoolProperty("binary", false); m_PredictionNode->SetProperty("opacity", mitk::FloatProperty::New(0.0f)); // m_PredictionNode->SetBoolProperty("helper object", true); this->GetDataStorage()->Add(m_PredictionNode, m_Nodes[0]); // ======================================= // SEGMENTATION IMAGE // ======================================= m_SegmentationImage = mitk::Image::New(); try { mitk::Image::Pointer referenceImage = dynamic_cast(m_Nodes[0]->GetData()); m_SegmentationImage->Initialize(mitk::MakeScalarPixelType(), *(referenceImage->GetTimeGeometry()->Clone())); } catch (mitk::Exception& e) { MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::information(m_Parent, "Error", "Could not initialize segmentation image"); return; } FillWithZeros(m_SegmentationImage); m_SegmentationNode = mitk::DataNode::New(); m_SegmentationNode->SetData(m_SegmentationImage); m_SegmentationNode->SetName("Segmentation"); m_SegmentationNode->SetColor(1., 1., 1.); m_SegmentationNode->SetBoolProperty("binary", false); // m_PredictionNode->SetBoolProperty("helper object", true); this->GetDataStorage()->Add(m_SegmentationNode, m_Nodes[0]); // ======================================= // ANNOTATION IMAGE // ======================================= m_AnnotationImage = mitk::Image::New(); try { mitk::Image::Pointer referenceImage = dynamic_cast(m_Nodes[0]->GetData()); m_AnnotationImage->Initialize(mitk::MakeScalarPixelType(), *(referenceImage->GetTimeGeometry()->Clone())); } catch (mitk::Exception& e) { MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::information(m_Parent, "Error", "Could not initialize annotation image"); return; } FillWithZeros(m_AnnotationImage); m_AnnotationNode = mitk::DataNode::New(); m_AnnotationNode->SetData(m_AnnotationImage); m_AnnotationNode->SetName("Labels"); m_AnnotationNode->SetColor(1., 1., 1.); m_AnnotationNode->SetBoolProperty("binary", false); m_AnnotationNode->SetProperty("opacity", mitk::FloatProperty::New(1.0f)); // m_AnnotationNode->SetBoolProperty("helper object", true); this->GetDataStorage()->Add(m_AnnotationNode, m_Nodes[0]); // Convert input images to FeaturePixelType for (auto node : m_Nodes) { mitk::Image::Pointer image = dynamic_cast(node->GetData()); auto itkImage = itk::Image::New(); mitk::CastToItkImage(image, itkImage); image = mitk::GrabItkImageMemory(itkImage); node->SetData(image); } // Calculate features for (const auto node : m_Nodes) { mitk::Image::Pointer currentImage = dynamic_cast(node->GetData()); QFuture>> future; future = QtConcurrent::run(this, &ActiveLearning::CalculateFeatures, currentImage); auto futureWatcher = new QFutureWatcher>>(); futureWatcher->setFuture(future); connect(futureWatcher, SIGNAL(finished()), this, SLOT(OnInitializationFinished())); m_FeatureCalculationWatchers.push_back(futureWatcher); } // Interactor auto activeLearningLib = us::ModuleRegistry::GetModule("MitkCLActiveLearning"); m_Interactor = mitk::ActiveLearningInteractor::New(); m_Interactor->LoadStateMachine("Paint.xml", activeLearningLib); m_Interactor->SetEventConfig("PaintConfig.xml", activeLearningLib); m_Interactor->SetDataNode(m_AnnotationNode); // Automatically add first label OnAddLabelPushButtonClicked(); m_Active = true; } /* ================================================================== * PUBLIC * =============================================================== */ ActiveLearning::ActiveLearning() : m_Parent(nullptr), m_AnnotationImage(nullptr), m_AnnotationNode(nullptr), m_PredictionImage(nullptr), m_PredictionNode(nullptr), m_SegmentationImage(nullptr), m_SegmentationNode(nullptr), m_Active(false), m_NumberOfTrees(50), m_MaximumTreeDepth(10), m_SamplesPerTree(0.66), m_PredictionMatrix(nullptr) { } ActiveLearning::~ActiveLearning() { } void ActiveLearning::CreateQtPartControl( QWidget *parent ) { m_Controls.setupUi(parent); m_Parent = parent; // Label model m_LabelListModel = new QStandardItemModel(0, 3, this); m_Controls.m_LabelTableView->setModel(m_LabelListModel); m_Controls.m_LabelTableView->horizontalHeader()->setDefaultSectionSize(20); m_Controls.m_LabelTableView->verticalHeader()->setDefaultSectionSize(20); NotEditableDelegate* itemDelegate = new NotEditableDelegate(parent); m_Controls.m_LabelTableView->setItemDelegateForColumn(1, itemDelegate); connect(m_Controls.m_LabelTableView, SIGNAL(doubleClicked(QModelIndex)), this, SLOT(OnColorIconDoubleClicked(QModelIndex))); connect(m_Controls.m_LabelTableView->selectionModel(), SIGNAL(selectionChanged(QItemSelection, QItemSelection)), this, SLOT(OnLabelListSelectionChanged(QItemSelection, QItemSelection))); connect(m_LabelListModel, SIGNAL(dataChanged(QModelIndex, QModelIndex)), this, SLOT(OnLabelNameChanged(QModelIndex, QModelIndex))); // Buttons connect(m_Controls.m_InitializePushButton, SIGNAL(clicked()), this, SLOT(Initialize())); connect(m_Controls.m_AddLabelPushButton, SIGNAL(clicked()), this, SLOT(OnAddLabelPushButtonClicked())); connect(m_Controls.m_RemoveLabelPushButton, SIGNAL(clicked()), this, SLOT(OnRemoveLabelPushButtonClicked())); connect(m_Controls.m_PaintToolButton, SIGNAL(clicked()), this, SLOT(OnPaintToolButtonClicked())); connect(m_Controls.m_EraseToolButton, SIGNAL(clicked()), this, SLOT(OnEraseToolButtonClicked())); connect(m_Controls.m_UpdatePredictionsPushButton, SIGNAL(clicked()), this, SLOT(OnUpdatePredictionsPushButtonClicked())); - connect(m_PredictionCalculationWatcher, SIGNAL(finished()), - this, SLOT(OnPredictionCalculationFinished())); - // Set start configuration m_Controls.m_LabelControlsFrame->setVisible(false); SetInitializeReady(false); } void ActiveLearning::ResetLabels() { for (int i=0; irowCount(); i++) { m_LabelListModel->item(i, 1)->setText(QString::number(i + 1)); } } std::vector > ActiveLearning::CalculateFeatures(const mitk::Image::Pointer inputImage) { std::vector> result; // TODO: Get features from preference page std::vector sigmas = {0.7, 1.6}; for (auto sigma : sigmas) { std::stringstream ss; auto gaussImage = mitk::Image::New(); AccessByItk_n(inputImage, GaussianSmoothing, (sigma, gaussImage)); ss << "GaussianSmoothing (" << std::fixed << std::setprecision(2) << sigma << ")"; result.push_back(std::pair(gaussImage, ss.str())); ss.str(""); auto gradMagImage = mitk::Image::New(); AccessByItk_n(inputImage, GaussianGradientMagnitude, (sigma, gradMagImage)); ss << "GaussianGradientMagnitude (" << std::fixed << std::setprecision(2) << sigma << ")"; result.push_back(std::pair(gradMagImage, ss.str())); ss.str(""); auto logImage = mitk::Image::New(); AccessByItk_n(inputImage, LaplacianOfGaussian, (sigma, logImage)); ss << "LaplacianOfGaussian (" << std::fixed << std::setprecision(2) << sigma << ")"; result.push_back(std::pair(logImage, ss.str())); ss.str(""); // auto structImage1 = mitk::Image::New(); // auto structImage2 = mitk::Image::New(); // auto structImage3 = mitk::Image::New(); // std::vector structImages = {structImage1, structImage2, structImage3}; // AccessByItk_n(inputImage, StructureTensorEigenvalues, (sigma, structImages)); // ss << "StructureTensorEigenvalue1 (" << std::fixed << std::setprecision(2) << sigma << ")"; // result.push_back(std::pair(structImage1, ss.str())); // ss.str(""); // ss << "StructureTensorEigenvalue2 (" << std::fixed << std::setprecision(2) << sigma << ")"; // result.push_back(std::pair(structImage2, ss.str())); // ss.str(""); // if (inputImage->GetDimension() == 3) // { // ss << "StructureTensorEigenvalue3 (" << std::fixed << std::setprecision(2) << sigma << ")"; // result.push_back(std::pair(structImage3, ss.str())); // ss.str(""); // } // auto hessianImage1 = mitk::Image::New(); // auto hessianImage2 = mitk::Image::New(); // auto hessianImage3 = mitk::Image::New(); // std::vector hessianImages = {hessianImage1, hessianImage2, hessianImage3}; // AccessByItk_n(inputImage, HessianEigenvalues, (sigma, hessianImages)); // ss << "HessianEigenvalue1 (" << std::fixed << std::setprecision(2) << sigma << ")"; // result.push_back(std::pair(hessianImage1, ss.str())); // ss.str(""); // ss << "HessianEigenvalue2 (" << std::fixed << std::setprecision(2) << sigma << ")"; // result.push_back(std::pair(hessianImage2, ss.str())); // ss.str(""); // if (inputImage->GetDimension() == 3) // { // ss << "HessianEigenvalue3 (" << std::fixed << std::setprecision(2) << sigma << ")"; // result.push_back(std::pair(hessianImage3, ss.str())); // ss.str(""); // } } return result; } -std::pair, std::shared_ptr> ActiveLearning::GetTrainingData(const mitk::Image::Pointer annotationImage, const std::vector featureImageVector) +std::pair ActiveLearning::CalculatePrediction(const mitk::Image::Pointer annotationImage, + const std::vector &featureImageVector, + const mitk::Image::Pointer referenceImage, + mitk::AbstractClassifier* classifier, + std::shared_ptr predictionMatrix) +{ + // Create prediction matrix if necessary + if (predictionMatrix == nullptr) + { + FeatureMatrixType mat = Transform(featureImageVector); + predictionMatrix = std::make_shared(mat); + } + + // Get training data and train + auto training = GetTrainingData(annotationImage, featureImageVector); + classifier->Train(*training.second, *training.first); + + // Get result + LabelVectorType segmentation = classifier->Predict(*predictionMatrix); + FeatureMatrixType prediction = classifier->GetPointWiseProbabilities(); + mitk::Image::Pointer segmentationImage = Transform(segmentation, referenceImage); + mitk::Image::Pointer predictionImage = Transform(prediction, referenceImage); + + std::pair result = std::make_pair(segmentationImage, predictionImage); + return result; +} + +std::pair, std::shared_ptr> ActiveLearning::GetTrainingData(const mitk::Image::Pointer annotationImage, + const std::vector &featureImageVector) { // Get indices and labels std::vector> indices; std::vector labels; itk::Image::Pointer annotationImageItk; mitk::CastToItkImage(annotationImage, annotationImageItk); itk::ImageRegionIteratorWithIndex> it(annotationImageItk, annotationImageItk->GetLargestPossibleRegion()); while (!it.IsAtEnd()) { if (it.Get() != 0) { indices.push_back(it.GetIndex()); labels.push_back(it.Get()); } ++it; } FeatureMatrixType trainingData(indices.size(), featureImageVector.size()); LabelVectorType trainingLabels = LabelVectorType::Map(labels.data(), labels.size()); int j = 0; for (mitk::Image::Pointer feature : featureImageVector) { int i = 0; mitk::ImagePixelReadAccessor access(feature, feature->GetVolumeData()); for (auto index : indices) { trainingData(i, j) = access.GetPixelByIndexSafe(index); i++; } j++; } auto trainingLabelsPtr = std::make_shared(trainingLabels); auto trainingDataPtr = std::make_shared(trainingData); std::pair, std::shared_ptr> result = std::make_pair(trainingLabelsPtr, trainingDataPtr); return result; } void ActiveLearning::UpdateLookupTables() { // Create new lookup table from list // Annotation type is int, but we only use a ushort lookup table auto lut = vtkSmartPointer::New(); int lowlim = std::numeric_limits::min(); int uplim = std::numeric_limits::max(); lut->SetNumberOfTableValues(uplim - lowlim + 1); lut->SetTableRange(lowlim, uplim); for (long i=0; i<(uplim-lowlim+1); ++i) { lut->SetTableValue(i, 0.0, 0.0, 0.0, 0.0); } for (int j=0; jrowCount(); ++j) { int value = m_LabelListModel->item(j, 1)->text().toInt(); const QColor color = m_LabelListModel->item(j, 0)->background().color(); lut->SetTableValue(value, color.redF(), color.greenF(), color.blueF(), 1.0); } auto lutMitk = mitk::LookupTable::New(); lutMitk->SetVtkLookupTable(lut); // Set to annotation image and segmentation image auto * lut_prop = dynamic_cast(m_AnnotationNode->GetProperty("LookupTable")); lut_prop->SetLookupTable(lutMitk); m_AnnotationNode->SetProperty("Image Rendering.Mode", mitk::RenderingModeProperty::New(mitk::RenderingModeProperty::LOOKUPTABLE_COLOR)); lut_prop = dynamic_cast(m_SegmentationNode->GetProperty("LookupTable")); lut_prop->SetLookupTable(lutMitk); m_SegmentationNode->SetProperty("Image Rendering.Mode", mitk::RenderingModeProperty::New(mitk::RenderingModeProperty::LOOKUPTABLE_COLOR)); } const std::string ActiveLearning::VIEW_ID = "org.mitk.views.activelearning"; /* ================================================================== * PROTECTED SLOTS * =============================================================== */ void ActiveLearning::OnAddLabelPushButtonClicked() { QString labelName = QString("Label ") + QString::number(m_LabelListModel->rowCount() + 1); QColor labelColor = Qt::GlobalColor(m_LabelListModel->rowCount() % 12 + 7); // We only want Qt default colors 7 to 18 // Create icon QStandardItem* colorSquare = new QStandardItem; colorSquare->setBackground(labelColor); colorSquare->setEditable(false); QPixmap colorPixmap(20, 20); colorPixmap.fill(labelColor); colorSquare->setIcon(QIcon(colorPixmap)); // Key is the highest existing key + 1 int value = 1; if (m_LabelListModel->rowCount() >= 1) { value = m_LabelListModel->item(m_LabelListModel->rowCount() - 1, 1)->text().toInt() + 1; } QStandardItem* valueItem = new QStandardItem; valueItem->setText(QString::number(value)); // Create label item QStandardItem* label = new QStandardItem(labelName); // Make list and insert QList list; list.append(colorSquare); list.append(valueItem); list.append(label); m_LabelListModel->appendRow(list); // If this is the first label, we activate the paint button // We also have to set the data node color for this one, because for 1 values that color seems to define the rendered color if (m_LabelListModel->rowCount() == 1) { OnPaintToolButtonClicked(); } // Update colors UpdateLookupTables(); } void ActiveLearning::OnRemoveLabelPushButtonClicked() { // STILL NEED TO REMOVE ANNOTATIONS QItemSelectionModel* selection = m_Controls.m_LabelTableView->selectionModel(); if (selection->hasSelection()) { unsigned int removeIndex = selection->selectedRows().first().row(); QString removeMessage = QString("Remove label '") + m_LabelListModel->item(removeIndex, 2)->text() + QString("'?"); QMessageBox::StandardButton removeReply; removeReply = QMessageBox::question(m_Parent, "Remove Label", removeMessage, QMessageBox::Yes | QMessageBox::No); if (removeReply == QMessageBox::Yes) { m_LabelListModel->removeRow(removeIndex); if (!m_Interactor->IsUsed()) ResetLabels(); } } } void ActiveLearning::OnPaintToolButtonClicked() { m_Controls.m_PaintToolButton->setChecked(true); QItemSelectionModel* selection = m_Controls.m_LabelTableView->selectionModel(); int row(0); if (selection->hasSelection()) { row = selection->selectedRows().first().row(); } else { m_Controls.m_LabelTableView->selectRow(0); } m_Interactor->SetPaintingPixelValue(m_LabelListModel->item(row, 1)->text().toInt()); } void ActiveLearning::OnEraseToolButtonClicked() { m_Controls.m_EraseToolButton->setChecked(true); m_Interactor->SetPaintingPixelValue(0); } void ActiveLearning::OnActivateGuidancePushButtonToggled(bool toggled) { } void ActiveLearning::OnSaveSegmentationPushButtonClicked() { } void ActiveLearning::OnSavePredictionsPushButtonClicked() { } void ActiveLearning::OnExportSegmentationPushButtonClicked() { } void ActiveLearning::OnExportPredictionsPushButtonClicked() { } void ActiveLearning::OnColorIconDoubleClicked(const QModelIndex& index) { // Check if click is really from color icon if (index.column() != 0) { return; } else { // Color change dialog QColor setColor = QColorDialog::getColor(m_LabelListModel->itemFromIndex(index)->background().color(), m_Parent, "Select Label Color"); if (setColor.isValid()) { m_LabelListModel->itemFromIndex(index)->setBackground(setColor); QPixmap colorPixmap(20, 20); colorPixmap.fill(setColor); m_LabelListModel->itemFromIndex(index)->setIcon(QIcon(colorPixmap)); UpdateLookupTables(); } } } -void ActiveLearning::OnLabelListSelectionChanged(const QItemSelection& selected, const QItemSelection& /*deselected*/) +void ActiveLearning::OnLabelListSelectionChanged(const QItemSelection& selected, + const QItemSelection& /*deselected*/) { if (selected.empty()) return; if (m_Controls.m_EraseToolButton->isChecked()) return; // This assumes that only one item can be selected (single selection table view) try { int labelValue = m_LabelListModel->item(selected.indexes()[0].row(), 1)->text().toInt(); m_Interactor->SetPaintingPixelValue(labelValue); } catch (...) { m_Interactor->SetPaintingPixelValue(-1); } } void ActiveLearning::OnLabelNameChanged(const QModelIndex& topLeft, const QModelIndex& /*bottomRight*/) { } void ActiveLearning::OnInitializationFinished() { // Check if all futures are finished for (auto watcher : m_FeatureCalculationWatchers) { if (watcher->isFinished() == false) {return;} } // Empty feature vector m_FeatureImageVector.clear(); // Insert features into feature vector and data storage for (unsigned int i=0; iresult(); for (unsigned int j=0; jSetData(result[j].first); node->SetName(result[j].second); node->SetBoolProperty("helper object", true); node->SetVisibility(false); this->GetDataStorage()->Add(node, m_Nodes[i]); } } // Show controls m_Controls.m_LabelControlsFrame->setVisible(true); m_Controls.m_InitializePushButton->setHidden(true); // Delete watchers for (auto watcher : m_FeatureCalculationWatchers) { delete watcher; } m_FeatureCalculationWatchers.clear(); } void ActiveLearning::OnUpdatePredictionsPushButtonClicked() { - if (m_PredictionMatrix == nullptr) - { - FeatureMatrixType mat = Transform(m_FeatureImageVector); - m_PredictionMatrix = std::make_shared(mat); - } + m_Controls.m_UpdatePredictionsPushButton->setDisabled(true); // Classifier m_Classifier = mitk::VigraRandomForestClassifier::New(); m_Classifier->SetTreeCount(m_NumberOfTrees); m_Classifier->SetMaximumTreeDepth(m_MaximumTreeDepth); m_Classifier->SetSamplesPerTree(m_SamplesPerTree); - auto training = GetTrainingData(m_AnnotationImage, m_FeatureImageVector); - m_Classifier->Train(*training.second, *training.first); - - LabelVectorType prediction = m_Classifier->Predict(*m_PredictionMatrix); mitk::Image::Pointer referenceImage = dynamic_cast(m_Nodes[0]->GetData()); + QFuture> future; + future = QtConcurrent::run(this, &ActiveLearning::CalculatePrediction, m_AnnotationImage, m_FeatureImageVector, referenceImage, m_Classifier, m_PredictionMatrix); + m_PredictionCalculationWatcher = new QFutureWatcher>(); + m_PredictionCalculationWatcher->setFuture(future); - m_SegmentationImage = Transform(prediction, referenceImage); - m_SegmentationImage->Modified(); - m_SegmentationNode->SetData(m_SegmentationImage); - m_SegmentationNode->Modified(); - -// this->RequestRenderWindowUpdate(); + connect(m_PredictionCalculationWatcher, SIGNAL(finished()), + this, SLOT(OnPredictionCalculationFinished())); } void ActiveLearning::OnPredictionCalculationFinished() { + auto result = m_PredictionCalculationWatcher->result(); + + m_SegmentationImage = result.first; + m_SegmentationImage->Modified(); + m_SegmentationNode->SetData(m_SegmentationImage); + m_SegmentationNode->Modified(); + + m_PredictionImage = result.second; + m_PredictionImage->Modified(); + m_PredictionNode->SetData(m_PredictionImage); + m_PredictionNode->Modified(); + m_Controls.m_UpdatePredictionsPushButton->setEnabled(true); } /* ================================================================== * PROTECTED * =============================================================== */ void ActiveLearning::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList& nodes) { if (!SelectionAllImages(nodes)) { SetInitializeReady(false); return; } if (nodes.length() >= 2) { // First selection is the reference (could be any other) mitk::Image::Pointer referenceImage = dynamic_cast(nodes[0]->GetData()); mitk::BaseGeometry* referenceGeometry = referenceImage->GetTimeGeometry()->GetGeometryForTimeStep(0); // Adjust for multiple timesteps for (int i=1; i(nodes[i]->GetData()); mitk::BaseGeometry* currentGeometry = currentImage->GetTimeGeometry()->GetGeometryForTimeStep(0); // Adjust for multiple timesteps if (!mitk::Equal(*currentGeometry, *referenceGeometry, mitk::eps, true)) { SetInitializeReady(false); return; } } } // All nodes have the same geometry, allow init SetInitializeReady(true); } void ActiveLearning::SetFocus() { } /* ================================================================== * PRIVATE * =============================================================== */ void ActiveLearning::SetInitializeReady(bool ready) { if (ready) { // get selection, check again just to be sure auto nodes = this->GetDataManagerSelection(); if (!SelectionAllImages(nodes)) return; m_Controls.m_InitializePushButton->setEnabled(true); if (!m_Active) { QString nameList = QString::fromStdString(nodes[0]->GetName()); if (nodes.length() >= 2) { for (int i=1; i"); nameList += QString::fromStdString(nodes[i]->GetName()); } } m_Controls.m_InitializeLabel->setText(nameList); } } else { m_Controls.m_InitializePushButton->setDisabled(true); if (!m_Active) { m_Controls.m_InitializeLabel->setText("Selected images must have matching geometries"); } } } diff --git a/Plugins/org.mitk.gui.qt.activelearning/src/internal/QmitkActiveLearning.h b/Plugins/org.mitk.gui.qt.activelearning/src/internal/QmitkActiveLearning.h index 0f1791583a..04dd476249 100644 --- a/Plugins/org.mitk.gui.qt.activelearning/src/internal/QmitkActiveLearning.h +++ b/Plugins/org.mitk.gui.qt.activelearning/src/internal/QmitkActiveLearning.h @@ -1,172 +1,177 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. 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 ActiveLearning_h #define ActiveLearning_h #include #include #include "ui_QmitkActiveLearningControls.h" // Qt #include #include #include #include // MITK #include #include #include #include /** \brief ActiveLearning \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation. \sa QmitkAbstractView \ingroup ${plugin_target}_internal */ + + // Just a helper class class NotEditableDelegate : public QItemDelegate { Q_OBJECT public: explicit NotEditableDelegate(QObject* parent = nullptr) : QItemDelegate(parent) {} protected: QWidget* createEditor(QWidget*, const QStyleOptionViewItem&, const QModelIndex&) const {return Q_NULLPTR;} }; + + class ActiveLearning : public QmitkAbstractView { Q_OBJECT public slots: void Initialize(); public: typedef unsigned short AnnotationPixelType; typedef double FeaturePixelType; typedef int LabelPixelType; typedef Eigen::Matrix FeatureMatrixType; typedef Eigen::Matrix LabelVectorType; ActiveLearning(); ~ActiveLearning(); void CreateQtPartControl(QWidget *parent) override; std::vector> CalculateFeatures(const mitk::Image::Pointer inputImage); std::pair CalculatePrediction(const mitk::Image::Pointer annotationImage, const std::vector &featureImageVector, const mitk::Image::Pointer referenceImage, + mitk::AbstractClassifier *classifier, std::shared_ptr predictionMatrix); std::pair, std::shared_ptr > GetTrainingData(const mitk::Image::Pointer annotationImage, const std::vector &featureImageVector); void UpdateLookupTables(); static const std::string VIEW_ID; protected slots: void OnAddLabelPushButtonClicked(); void OnRemoveLabelPushButtonClicked(); void OnPaintToolButtonClicked(); void OnEraseToolButtonClicked(); void OnActivateGuidancePushButtonToggled(bool toggled); void OnSaveSegmentationPushButtonClicked(); void OnSavePredictionsPushButtonClicked(); void OnExportSegmentationPushButtonClicked(); void OnExportPredictionsPushButtonClicked(); void OnColorIconDoubleClicked(const QModelIndex& index); void OnLabelListSelectionChanged(const QItemSelection& selected, const QItemSelection& /*deselected*/); void OnLabelNameChanged(const QModelIndex& topLeft, const QModelIndex& /*bottomRight*/); void OnUpdatePredictionsPushButtonClicked(); void OnPredictionCalculationFinished(); void OnInitializationFinished(); protected: void OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList& nodes) override; void SetFocus() override; void ResetLabels(); void SetInitializeReady(bool ready); Ui::ActiveLearningControls m_Controls; QWidget* m_Parent; mitk::Image::Pointer m_AnnotationImage; mitk::DataNode::Pointer m_AnnotationNode; mitk::Image::Pointer m_PredictionImage; mitk::DataNode::Pointer m_PredictionNode; mitk::Image::Pointer m_SegmentationImage; mitk::DataNode::Pointer m_SegmentationNode; std::vector m_FeatureImageVector; std::vector>>*> m_FeatureCalculationWatchers; - QFutureWatcher* m_PredictionCalculationWatcher; + QFutureWatcher>* m_PredictionCalculationWatcher; QStandardItemModel* m_LabelListModel; mitk::ActiveLearningInteractor::Pointer m_Interactor; QList m_Nodes; mitk::VigraRandomForestClassifier::Pointer m_Classifier; private: bool m_Active; int m_NumberOfTrees; int m_MaximumTreeDepth; float m_SamplesPerTree; std::shared_ptr m_PredictionMatrix; }; #endif // ActiveLearning_h