diff --git a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp index d1ebd520f0..1816a3a8fb 100644 --- a/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp +++ b/Modules/Segmentation/Interactions/mitkMonaiLabelTool.cpp @@ -1,387 +1,388 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // MITK #include "mitkMonaiLabelTool.h" // us #include "mitkIOUtil.h" #include #include #include #include #include #include #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, MonaiLabelTool, "MonaiLabel"); } mitk::MonaiLabelTool::MonaiLabelTool() { this->SetMitkTempDir(IOUtil::CreateTemporaryDirectory("mitk-XXXXXX")); } mitk::MonaiLabelTool::~MonaiLabelTool() { itksys::SystemTools::RemoveADirectory(this->GetMitkTempDir()); } void mitk::MonaiLabelTool::Activated() { Superclass::Activated(); - this->SetLabelTransferMode(LabelTransferMode::AllLabels); + this->SetLabelTransferScope(LabelTransferScope::AllLabels); + this->SetLabelTransferMode(LabelTransferMode::AddLabel); } const char **mitk::MonaiLabelTool::GetXPM() const { return nullptr; } us::ModuleResource mitk::MonaiLabelTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("AI.svg"); return resource; } const char *mitk::MonaiLabelTool::GetName() const { return "MonaiLabel"; } bool mitk::MonaiLabelTool::IsMonaiServerOn(std::string &hostName, int &port) { httplib::Client cli(hostName, port); while (cli.is_socket_open()) ; if (auto response = cli.Get("/info/")) { return true; } return false; } void mitk::MonaiLabelTool::DoUpdatePreview(const Image *inputAtTimeStep, const Image * /*oldSegAtTimeStep*/, LabelSetImage *previewImage, TimeStepType timeStep) { std::string &hostName = m_RequestParameters->hostName; int port = m_RequestParameters->port; if (!m_TEST) if (!IsMonaiServerOn(hostName, port)) { mitkThrow() << m_SERVER_503_ERROR_TEXT; } std::string inDir, outDir, inputImagePath, outputImagePath; inDir = IOUtil::CreateTemporaryDirectory("monai-in-XXXXXX", this->GetMitkTempDir()); std::ofstream tmpStream; inputImagePath = IOUtil::CreateTemporaryFile(tmpStream, m_TEMPLATE_FILENAME, inDir + IOUtil::GetDirectorySeparator()); tmpStream.close(); std::size_t found = inputImagePath.find_last_of(IOUtil::GetDirectorySeparator()); std::string fileName = inputImagePath.substr(found + 1); std::string token = fileName.substr(0, fileName.find("_")); outDir = IOUtil::CreateTemporaryDirectory("monai-out-XXXXXX", this->GetMitkTempDir()); outputImagePath = outDir + IOUtil::GetDirectorySeparator() + token + "_000.nii.gz"; try { m_IsLastSuccess = false; if (!m_TEST) { IOUtil::Save(inputAtTimeStep, inputImagePath); PostInferRequest(hostName, port, inputImagePath, outputImagePath); } else { std::string metaData_test = "{\"label_names\":{\"spleen\": 1, \"right kidney\": 2, \"left kidney\": 3, \"liver\": 6, \"stomach\": 7, " "\"aorta\": 8, \"inferior " "vena cava\": 9, \"background\": 0}, \"latencies\": {\"pre\": 0.64, \"infer\": 1.13, \"invert\": 0.03, " "\"post\": 0.06, \"write\": 0.1, \"total\": 1.96, \"transform\": {\"pre\": {\"LoadImaged\": 0.1483, " "\"EnsureChannelFirstd\": 0.0, \"Orientationd\": 0.0, \"ScaleIntensityRanged\": 0.0403, \"Resized\": 0.0401, " "\"DiscardAddGuidanced\": 0.0297, \"EnsureTyped\": 0.3703}, \"post\": {\"EnsureTyped\": 0.0, \"Activationsd\": " "0.0, \"AsDiscreted\": 0.0, \"SqueezeDimd\": 0.0, \"ToNumpyd\": 0.0473, \"Restored\": 0.0001}}}}"; m_ResultMetadata = nlohmann::json::parse(metaData_test); outputImagePath = "C:/DKFZ/MONAI_work/monai_test_python/output.nii.gz"; } Image::Pointer outputImage = IOUtil::Load(outputImagePath); auto outputBuffer = mitk::LabelSetImage::New(); outputBuffer->InitializeByLabeledImage(outputImage); outputBuffer->SetGeometry(inputAtTimeStep->GetGeometry()); std::map labelMap = m_ResultMetadata["label_names"]; MapLabelsToSegmentation(outputBuffer, labelMap); TransferLabelSetImageContent(outputBuffer, previewImage, timeStep); this->SetIsLastSuccess(true); } catch (const mitk::Exception &e) { m_IsLastSuccess = false; MITK_ERROR << e.GetDescription(); mitkThrow() << e.GetDescription(); } } void mitk::MonaiLabelTool::MapLabelsToSegmentation(mitk::LabelSetImage::Pointer outputBuffer, std::map &labelMap) { std::map flippedLabelMap; for (auto const &[key, val] : labelMap) { flippedLabelMap[val] = key; } int labelId = 0; for (auto const &[key, val] : flippedLabelMap) { mitk::Label *labelptr = outputBuffer->GetLabel(labelId, 0); if (nullptr != labelptr) { MITK_INFO << "Replacing label with name: " << labelptr->GetName() << " as " << val; labelptr->SetName(val); } else { MITK_INFO << "nullptr found for " << val; } labelId++; } } void mitk::MonaiLabelTool::GetOverallInfo(std::string &hostName, int &port) { MITK_INFO << "URL..." << hostName << ":" << port; if (!IsMonaiServerOn(hostName, port)) { Tool::ErrorMessage.Send(m_SERVER_503_ERROR_TEXT); mitkThrow() << m_SERVER_503_ERROR_TEXT; } httplib::Client cli(hostName, port); // httplib::Client cli("localhost", 8000); if (auto response = cli.Get("/info/")) { if (response->status == 200) { auto jsonObj = nlohmann::json::parse(response->body); if (jsonObj.is_discarded() || !jsonObj.is_object()) { MITK_ERROR << "Could not parse \"" << /* jsonPath.toStdString() << */ "\" as JSON object!"; return; } m_InfoParameters = DataMapper(jsonObj); if (nullptr != m_InfoParameters) { m_InfoParameters->hostName = hostName; m_InfoParameters->port = port; } } } else { Tool::ErrorMessage.Send(httplib::to_string(response.error()) + " error occured."); } } void mitk::MonaiLabelTool::PostInferRequest(std::string &hostName, int &port, std::string &filePath, std::string &outFile) { // std::string url = "http://localhost:8000/infer/deepedit_seg"; // + m_ModelName; std::string &modelName = m_RequestParameters->model.name; // Get this from args as well. std::string postPath = "/infer/"; // make this separate class of constants postPath.append(modelName); // std::string filePath = "C:/DKFZ/MONAI_work/monai_test_python/la_030.nii.gz"; std::ifstream input(filePath, std::ios::binary); if (!input) { MITK_WARN << "could not read file to POST"; } std::stringstream buffer_lf_img; buffer_lf_img << input.rdbuf(); input.close(); httplib::MultipartFormDataItems items = { {"file", buffer_lf_img.str(), "post_from_mitk.nii.gz", "application/octet-stream"}}; // httplib::MultipartFormDataMap itemMap = {{"file", {"file", buffer_lf_img.str(), "spleen_58.nii.gz", // "application/octet-stream"}}}; httplib::Client cli(hostName, port); cli.set_read_timeout(60); // arbitary 1 minute time-out to avoid corner cases. if (auto response = cli.Post(postPath, items)) // cli.Post("/infer/deepedit_seg", items); { if (response->status == 200) { // Find boundary httplib::Headers headers = response->headers; std::string contentType = headers.find("content-type")->second; std::string delimiter = "boundary="; std::string boundaryString = contentType.substr(contentType.find(delimiter) + delimiter.length(), std::string::npos); boundaryString.insert(0, "--"); MITK_INFO << "boundary hash: " << boundaryString; // Parse metadata JSON std::string resBody = response->body; std::vector multiPartResponse = this->getPartsBetweenBoundary(resBody, boundaryString); std::string metaData = multiPartResponse[0]; std::string contentTypeJson = "Content-Type: application/json"; size_t ctPos = metaData.find(contentTypeJson) + contentTypeJson.length(); std::string metaDataPart = metaData.substr(ctPos); MITK_INFO << metaDataPart; auto jsonObj = nlohmann::json::parse(metaDataPart); if (jsonObj.is_discarded() || !jsonObj.is_object()) { MITK_ERROR << "Could not parse \"" << /* jsonPath.toStdString() << */ "\" as JSON object!"; return; } else // use the metadata { m_ResultMetadata = jsonObj; } // Parse response image string std::string imagePart = multiPartResponse[1]; std::string contentTypeStream = "Content-Type: application/octet-stream"; ctPos = imagePart.find(contentTypeStream) + contentTypeStream.length(); std::string imageDataPart = imagePart.substr(ctPos); MITK_INFO << imageDataPart.substr(0, 50); std::string whitespaces = " \n\r"; imageDataPart.erase(0, imageDataPart.find_first_not_of(whitespaces)); // clean up std::ofstream output(outFile, std::ios::out | std::ios::app | std::ios::binary); output << imageDataPart; output.unsetf(std::ios::skipws); output.flush(); output.close(); // necessary to close? RAII } else { auto err = response.error(); MITK_ERROR << "An HTTP POST error: " << httplib::to_string(err) << " occured."; mitkThrow() << "An HTTP POST error: " << httplib::to_string(err) << " occured."; } } } std::vector mitk::MonaiLabelTool::getPartsBetweenBoundary(const std::string &body, const std::string &boundary) { std::vector retVal; std::string master = body; size_t found = master.find(boundary); size_t beginPos = 0; while (found != std::string::npos) { std::string part = master.substr(beginPos, found); if (!part.empty()) { retVal.push_back(part); } master.erase(beginPos, found + boundary.length()); found = master.find(boundary); } return retVal; } std::unique_ptr mitk::MonaiLabelTool::DataMapper(nlohmann::json &jsonObj) { auto object = std::make_unique(); object->name = jsonObj["name"].get(); object->description = jsonObj["description"].get(); object->labels = jsonObj["labels"].get>(); auto modelJsonMap = jsonObj["models"].get>(); for (const auto &[_name, _jsonObj] : modelJsonMap) { if (_jsonObj.is_discarded() || !_jsonObj.is_object()) { MITK_ERROR << "Could not parse JSON object."; } MonaiModelInfo modelInfo; modelInfo.name = _name; try { auto labels = _jsonObj["labels"].get>(); modelInfo.labels = labels; } catch (const std::exception &) { auto labels = _jsonObj["labels"].get>(); for (const auto &label : labels) { modelInfo.labels[label] = -1; // Hardcode -1 as label id } } modelInfo.type = _jsonObj["type"].get(); modelInfo.dimension = _jsonObj["dimension"].get(); modelInfo.description = _jsonObj["description"].get(); object->models.push_back(modelInfo); } return object; } std::vector mitk::MonaiLabelTool::GetAutoSegmentationModels() { std::vector autoModels; if (nullptr != m_InfoParameters) { for (mitk::MonaiModelInfo &model : m_InfoParameters->models) { if (m_AUTO_SEG_TYPE_NAME.find(model.type) != m_AUTO_SEG_TYPE_NAME.end()) { autoModels.push_back(model); } } } return autoModels; } std::vector mitk::MonaiLabelTool::GetInteractiveSegmentationModels() { std::vector interactiveModels; if (nullptr != m_InfoParameters) { for (mitk::MonaiModelInfo &model : m_InfoParameters->models) { if (m_INTERACTIVE_SEG_TYPE_NAME.find(model.type) != m_INTERACTIVE_SEG_TYPE_NAME.end()) { interactiveModels.push_back(model); } } } return interactiveModels; } std::vector mitk::MonaiLabelTool::GetScribbleSegmentationModels() { std::vector scribbleModels; if (nullptr != m_InfoParameters) { for (mitk::MonaiModelInfo &model : m_InfoParameters->models) { if (m_SCRIBBLE_SEG_TYPE_NAME.find(model.type) != m_SCRIBBLE_SEG_TYPE_NAME.end()) { scribbleModels.push_back(model); } } } return scribbleModels; } diff --git a/Modules/SegmentationUI/files.cmake b/Modules/SegmentationUI/files.cmake index 1bb88a8336..dd90c58132 100644 --- a/Modules/SegmentationUI/files.cmake +++ b/Modules/SegmentationUI/files.cmake @@ -1,122 +1,124 @@ set(CPP_FILES Qmitk/QmitkSegWithPreviewToolGUIBase.cpp Qmitk/QmitkMultiLabelSegWithPreviewToolGUIBase.cpp Qmitk/QmitkBinaryThresholdToolGUIBase.cpp Qmitk/QmitkBinaryThresholdToolGUI.cpp Qmitk/QmitkBinaryThresholdULToolGUI.cpp Qmitk/QmitkConfirmSegmentationDialog.cpp Qmitk/QmitkCopyToClipBoardDialog.cpp Qmitk/QmitkDrawPaintbrushToolGUI.cpp Qmitk/QmitkErasePaintbrushToolGUI.cpp Qmitk/QmitkEditableContourToolGUIBase.cpp Qmitk/QmitkGrowCutToolGUI.cpp Qmitk/QmitkLiveWireTool2DGUI.cpp Qmitk/QmitkLassoToolGUI.cpp Qmitk/QmitkOtsuTool3DGUI.cpp Qmitk/QmitkPaintbrushToolGUI.cpp Qmitk/QmitkPickingToolGUI.cpp Qmitk/QmitkSlicesInterpolator.cpp Qmitk/QmitkToolGUI.cpp Qmitk/QmitkToolGUIArea.cpp Qmitk/QmitkToolSelectionBox.cpp Qmitk/QmitknnUNetFolderParser.cpp Qmitk/QmitknnUNetToolGUI.cpp Qmitk/QmitknnUNetWorker.cpp Qmitk/QmitknnUNetGPU.cpp Qmitk/QmitkSurfaceStampWidget.cpp Qmitk/QmitkMaskStampWidget.cpp Qmitk/QmitkStaticDynamicSegmentationDialog.cpp Qmitk/QmitkSimpleLabelSetListWidget.cpp Qmitk/QmitkSegmentationTaskListWidget.cpp Qmitk/QmitkTotalSegmentatorToolGUI.cpp Qmitk/QmitkSetupVirtualEnvUtil.cpp Qmitk/QmitkMultiLabelInspector.cpp Qmitk/QmitkMultiLabelManager.cpp Qmitk/QmitkMultiLabelTreeModel.cpp Qmitk/QmitkMultiLabelTreeView.cpp Qmitk/QmitkMultiLabelPresetHelper.cpp Qmitk/QmitkLabelColorItemDelegate.cpp Qmitk/QmitkLabelToggleItemDelegate.cpp + Qmitk/QmitkMonaiLabelToolGUI.cpp SegmentationUtilities/QmitkBooleanOperationsWidget.cpp SegmentationUtilities/QmitkContourModelToImageWidget.cpp SegmentationUtilities/QmitkImageMaskingWidget.cpp SegmentationUtilities/QmitkMorphologicalOperationsWidget.cpp SegmentationUtilities/QmitkSurfaceToImageWidget.cpp SegmentationUtilities/QmitkSegmentationUtilityWidget.cpp SegmentationUtilities/QmitkDataSelectionWidget.cpp ) set(H_FILES Qmitk/QmitkMultiLabelPresetHelper.h ) set(MOC_H_FILES Qmitk/QmitkSegWithPreviewToolGUIBase.h Qmitk/QmitkMultiLabelSegWithPreviewToolGUIBase.h Qmitk/QmitkBinaryThresholdToolGUIBase.h Qmitk/QmitkBinaryThresholdToolGUI.h Qmitk/QmitkBinaryThresholdULToolGUI.h Qmitk/QmitkConfirmSegmentationDialog.h Qmitk/QmitkCopyToClipBoardDialog.h Qmitk/QmitkDrawPaintbrushToolGUI.h Qmitk/QmitkErasePaintbrushToolGUI.h Qmitk/QmitkEditableContourToolGUIBase.h Qmitk/QmitkGrowCutToolGUI.h Qmitk/QmitkLiveWireTool2DGUI.h Qmitk/QmitkLassoToolGUI.h Qmitk/QmitkOtsuTool3DGUI.h Qmitk/QmitkPaintbrushToolGUI.h Qmitk/QmitkPickingToolGUI.h Qmitk/QmitkSlicesInterpolator.h Qmitk/QmitkToolGUI.h Qmitk/QmitkToolGUIArea.h Qmitk/QmitkToolSelectionBox.h Qmitk/QmitknnUNetFolderParser.h Qmitk/QmitknnUNetToolGUI.h Qmitk/QmitknnUNetGPU.h Qmitk/QmitknnUNetWorker.h Qmitk/QmitknnUNetEnsembleLayout.h Qmitk/QmitkSurfaceStampWidget.h Qmitk/QmitkMaskStampWidget.h Qmitk/QmitkStaticDynamicSegmentationDialog.h Qmitk/QmitkSimpleLabelSetListWidget.h Qmitk/QmitkSegmentationTaskListWidget.h Qmitk/QmitkTotalSegmentatorToolGUI.h Qmitk/QmitkSetupVirtualEnvUtil.h Qmitk/QmitkMultiLabelInspector.h Qmitk/QmitkMultiLabelManager.h Qmitk/QmitkMultiLabelTreeModel.h Qmitk/QmitkMultiLabelTreeView.h Qmitk/QmitkLabelColorItemDelegate.h Qmitk/QmitkLabelToggleItemDelegate.h + Qmitk/QmitkMonaiLabelToolGUI.h SegmentationUtilities/QmitkBooleanOperationsWidget.h SegmentationUtilities/QmitkContourModelToImageWidget.h SegmentationUtilities/QmitkImageMaskingWidget.h SegmentationUtilities/QmitkMorphologicalOperationsWidget.h SegmentationUtilities/QmitkSurfaceToImageWidget.h SegmentationUtilities/QmitkSegmentationUtilityWidget.h SegmentationUtilities/QmitkDataSelectionWidget.h ) set(UI_FILES Qmitk/QmitkConfirmSegmentationDialog.ui Qmitk/QmitkGrowCutToolWidgetControls.ui Qmitk/QmitkOtsuToolWidgetControls.ui Qmitk/QmitkSurfaceStampWidgetGUIControls.ui Qmitk/QmitkMaskStampWidgetGUIControls.ui Qmitk/QmitknnUNetToolGUIControls.ui Qmitk/QmitkEditableContourToolGUIControls.ui Qmitk/QmitkSegmentationTaskListWidget.ui Qmitk/QmitkTotalSegmentatorGUIControls.ui Qmitk/QmitkMultiLabelInspectorControls.ui Qmitk/QmitkMultiLabelManagerControls.ui SegmentationUtilities/QmitkBooleanOperationsWidgetControls.ui SegmentationUtilities/QmitkContourModelToImageWidgetControls.ui SegmentationUtilities/QmitkImageMaskingWidgetControls.ui SegmentationUtilities/QmitkMorphologicalOperationsWidgetControls.ui SegmentationUtilities/QmitkSurfaceToImageWidgetControls.ui SegmentationUtilities/QmitkDataSelectionWidgetControls.ui ) set(QRC_FILES resources/SegmentationUI.qrc ) diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp index 182470da6c..8a8e62bb17 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp @@ -1,1031 +1,1031 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkSegmentationView.h" #include "mitkPluginActivator.h" // blueberry #include // mitk #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // Qmitk #include #include #include #include // us #include #include // Qt #include #include #include // vtk #include #include namespace { QList Get2DWindows(const QList allWindows) { QList all2DWindows; for (auto* window : allWindows) { if (window->GetRenderer()->GetMapperID() == mitk::BaseRenderer::Standard2D) { all2DWindows.append(window); } } return all2DWindows; } } const std::string QmitkSegmentationView::VIEW_ID = "org.mitk.views.segmentation"; QmitkSegmentationView::QmitkSegmentationView() : m_Parent(nullptr) , m_Controls(nullptr) , m_RenderWindowPart(nullptr) , m_ToolManager(nullptr) , m_ReferenceNode(nullptr) , m_WorkingNode(nullptr) , m_DrawOutline(true) , m_SelectionMode(false) , m_MouseCursorSet(false) , m_DefaultLabelNaming(true) , m_SelectionChangeIsAlreadyBeingHandled(false) { auto isImage = mitk::TNodePredicateDataType::New(); auto isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); auto isDti = mitk::NodePredicateDataType::New("TensorImage"); auto isOdf = mitk::NodePredicateDataType::New("OdfImage"); auto isSegment = mitk::NodePredicateDataType::New("Segment"); auto validImages = mitk::NodePredicateOr::New(); validImages->AddPredicate(mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isSegment))); validImages->AddPredicate(isDwi); validImages->AddPredicate(isDti); validImages->AddPredicate(isOdf); m_SegmentationPredicate = mitk::NodePredicateAnd::New(); m_SegmentationPredicate->AddPredicate(mitk::TNodePredicateDataType::New()); m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("hidden object"))); m_ReferencePredicate = mitk::NodePredicateAnd::New(); m_ReferencePredicate->AddPredicate(validImages); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(m_SegmentationPredicate)); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("hidden object"))); } QmitkSegmentationView::~QmitkSegmentationView() { if (nullptr != m_Controls) { // deactivate all tools m_ToolManager->ActivateTool(-1); // removing all observers from working data for (NodeTagMapType::iterator dataIter = m_WorkingDataObserverTags.begin(); dataIter != m_WorkingDataObserverTags.end(); ++dataIter) { (*dataIter).first->GetProperty("visible")->RemoveObserver((*dataIter).second); } m_WorkingDataObserverTags.clear(); // removing all observers from reference data for (NodeTagMapType::iterator dataIter = m_ReferenceDataObserverTags.begin(); dataIter != m_ReferenceDataObserverTags.end(); ++dataIter) { (*dataIter).first->GetProperty("visible")->RemoveObserver((*dataIter).second); } m_ReferenceDataObserverTags.clear(); mitk::RenderingManager::GetInstance()->RemoveObserver(m_RenderingManagerObserverTag); ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); service->RemoveAllPlanePositions(); context->ungetService(ppmRef); m_ToolManager->SetReferenceData(nullptr); m_ToolManager->SetWorkingData(nullptr); } m_ToolManager->ActiveToolChanged -= mitk::MessageDelegate(this, &QmitkSegmentationView::ActiveToolChanged); delete m_Controls; } /**********************************************************************/ /* private Q_SLOTS */ /**********************************************************************/ void QmitkSegmentationView::OnReferenceSelectionChanged(QList) { this->OnAnySelectionChanged(); } void QmitkSegmentationView::OnSegmentationSelectionChanged(QList) { this->OnAnySelectionChanged(); } void QmitkSegmentationView::OnAnySelectionChanged() { // When only a segmentation has been selected and the method is then called by a reference image selection, // the already selected segmentation may not match the geometry predicate of the new reference image anymore. // This will trigger a recursive call of this method further below. While it would be resolved gracefully, we // can spare the extra call with an early-out. The original call of this method will handle the segmentation // selection change afterwards anyway. if (m_SelectionChangeIsAlreadyBeingHandled) return; auto selectedReferenceNode = m_Controls->referenceNodeSelector->GetSelectedNode(); bool referenceNodeChanged = false; m_ToolManager->ActivateTool(-1); if (m_ReferenceNode != selectedReferenceNode) { referenceNodeChanged = true; // Remove visibility observer for the current reference node if (m_ReferenceDataObserverTags.find(m_ReferenceNode) != m_ReferenceDataObserverTags.end()) { m_ReferenceNode->GetProperty("visible")->RemoveObserver(m_ReferenceDataObserverTags[m_ReferenceNode]); m_ReferenceDataObserverTags.erase(m_ReferenceNode); } // Set new reference node m_ReferenceNode = selectedReferenceNode; m_ToolManager->SetReferenceData(m_ReferenceNode); // Prepare for a potential recursive call when changing node predicates of the working node selector m_SelectionChangeIsAlreadyBeingHandled = true; if (m_ReferenceNode.IsNull()) { // Without a reference image, allow all segmentations to be selected m_Controls->workingNodeSelector->SetNodePredicate(m_SegmentationPredicate); m_SelectionChangeIsAlreadyBeingHandled = false; } else { // With a reference image, only allow segmentations that fit the geometry of the reference image to be selected. m_Controls->workingNodeSelector->SetNodePredicate(mitk::NodePredicateAnd::New( mitk::NodePredicateSubGeometry::New(m_ReferenceNode->GetData()->GetGeometry()), m_SegmentationPredicate.GetPointer())); m_SelectionChangeIsAlreadyBeingHandled = false; this->ApplySelectionModeOnReferenceNode(); // Add visibility observer for the new reference node auto command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::ValidateSelectionInput); m_ReferenceDataObserverTags[m_ReferenceNode] = m_ReferenceNode->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command); } } auto selectedWorkingNode = m_Controls->workingNodeSelector->GetSelectedNode(); bool workingNodeChanged = false; if (m_WorkingNode != selectedWorkingNode) { workingNodeChanged = true; // Remove visibility observer for the current working node if (m_WorkingDataObserverTags.find(m_WorkingNode) != m_WorkingDataObserverTags.end()) { m_WorkingNode->GetProperty("visible")->RemoveObserver(m_WorkingDataObserverTags[m_WorkingNode]); m_WorkingDataObserverTags.erase(m_WorkingNode); } // Set new working node m_WorkingNode = selectedWorkingNode; m_ToolManager->SetWorkingData(m_WorkingNode); if (m_WorkingNode.IsNotNull()) { this->ApplySelectionModeOnWorkingNode(); // Add visibility observer for the new segmentation node auto command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::ValidateSelectionInput); m_WorkingDataObserverTags[m_WorkingNode] = m_WorkingNode->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command); } } // Reset camera if any selection changed but only if both reference node and working node are set if ((referenceNodeChanged || workingNodeChanged) && (m_ReferenceNode.IsNotNull() && m_WorkingNode.IsNotNull())) { if (nullptr != m_RenderWindowPart) { m_RenderWindowPart->InitializeViews(m_ReferenceNode->GetData()->GetTimeGeometry(), false); } } this->UpdateGUI(); } void QmitkSegmentationView::OnVisibilityShortcutActivated() { if (m_WorkingNode.IsNull()) { return; } bool isVisible = false; m_WorkingNode->GetBoolProperty("visible", isVisible); m_WorkingNode->SetVisibility(!isVisible); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::OnLabelToggleShortcutActivated() { if (m_WorkingNode.IsNull()) { return; } auto workingImage = dynamic_cast(m_WorkingNode->GetData()); if (nullptr == workingImage) { return; } this->WaitCursorOn(); workingImage->GetActiveLabelSet()->SetNextActiveLabel(); workingImage->Modified(); this->WaitCursorOff(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::OnNewSegmentation() { m_ToolManager->ActivateTool(-1); if (m_ReferenceNode.IsNull()) { MITK_ERROR << "'Create new segmentation' button should never be clickable unless a reference image is selected."; return; } mitk::Image::ConstPointer referenceImage = dynamic_cast(m_ReferenceNode->GetData()); if (referenceImage.IsNull()) { QMessageBox::information( m_Parent, "New segmentation", "Please load and select an image before starting some action."); return; } if (referenceImage->GetDimension() <= 1) { QMessageBox::information( m_Parent, "New segmentation", "Segmentation is currently not supported for 2D images"); return; } auto segTemplateImage = referenceImage; if (referenceImage->GetDimension() > 3) { QmitkStaticDynamicSegmentationDialog dialog(m_Parent); dialog.SetReferenceImage(referenceImage.GetPointer()); dialog.exec(); segTemplateImage = dialog.GetSegmentationTemplate(); } mitk::DataNode::Pointer newSegmentationNode; try { this->WaitCursorOn(); newSegmentationNode = mitk::LabelSetImageHelper::CreateNewSegmentationNode(m_ReferenceNode, segTemplateImage); this->WaitCursorOff(); } catch (mitk::Exception& e) { this->WaitCursorOff(); MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::warning(m_Parent, "New segmentation", "Could not create a new segmentation."); return; } auto newLabelSetImage = dynamic_cast(newSegmentationNode->GetData()); if (nullptr == newLabelSetImage) { // something went wrong return; } const auto labelSetPreset = this->GetDefaultLabelSetPreset(); if (labelSetPreset.empty() || !mitk::MultiLabelIOHelper::LoadLabelSetImagePreset(labelSetPreset, newLabelSetImage)) { auto newLabel = mitk::LabelSetImageHelper::CreateNewLabel(newLabelSetImage); if (!m_DefaultLabelNaming) QmitkNewSegmentationDialog::DoRenameLabel(newLabel, nullptr, m_Parent); newLabelSetImage->GetActiveLabelSet()->AddLabel(newLabel); } if (!this->GetDataStorage()->Exists(newSegmentationNode)) { this->GetDataStorage()->Add(newSegmentationNode, m_ReferenceNode); } if (m_ToolManager->GetWorkingData(0)) { m_ToolManager->GetWorkingData(0)->SetSelected(false); } newSegmentationNode->SetSelected(true); m_Controls->workingNodeSelector->SetCurrentSelectedNode(newSegmentationNode); } std::string QmitkSegmentationView::GetDefaultLabelSetPreset() const { auto labelSetPreset = mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABELSET_PRESET.toStdString(), ""); if (labelSetPreset.empty()) labelSetPreset = m_LabelSetPresetPreference.toStdString(); return labelSetPreset; } void QmitkSegmentationView::OnManualTool2DSelected(int id) { this->ResetMouseCursor(); mitk::StatusBar::GetInstance()->DisplayText(""); if (id >= 0) { std::string text = "Active Tool: \""; text += m_ToolManager->GetToolById(id)->GetName(); text += "\""; mitk::StatusBar::GetInstance()->DisplayText(text.c_str()); us::ModuleResource resource = m_ToolManager->GetToolById(id)->GetCursorIconResource(); this->SetMouseCursor(resource, 0, 0); } } void QmitkSegmentationView::OnShowMarkerNodes(bool state) { mitk::SegTool2D::Pointer manualSegmentationTool; unsigned int numberOfExistingTools = m_ToolManager->GetTools().size(); for (unsigned int i = 0; i < numberOfExistingTools; i++) { manualSegmentationTool = dynamic_cast(m_ToolManager->GetToolById(i)); if (nullptr == manualSegmentationTool) { continue; } manualSegmentationTool->SetShowMarkerNodes(state); } } void QmitkSegmentationView::OnCurrentLabelSelectionChanged(QmitkMultiLabelManager::LabelValueVectorType labels) { auto segmentation = this->GetCurrentSegmentation(); const auto labelValue = labels.front(); const auto groupID = segmentation->GetGroupIndexOfLabel(labelValue); if (groupID != segmentation->GetActiveLayer()) segmentation->SetActiveLayer(groupID); if (labelValue != segmentation->GetActiveLabelSet()->GetActiveLabel()->GetValue()) segmentation->GetActiveLabelSet()->SetActiveLabel(labelValue); segmentation->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::OnGoToLabel(mitk::LabelSetImage::LabelValueType /*label*/, const mitk::Point3D& pos) { if (m_RenderWindowPart) { m_RenderWindowPart->SetSelectedPosition(pos); } } void QmitkSegmentationView::OnLabelRenameRequested(mitk::Label* label, bool rename) const { auto segmentation = this->GetCurrentSegmentation(); if (rename) { QmitkNewSegmentationDialog::DoRenameLabel(label, segmentation, this->m_Parent, QmitkNewSegmentationDialog::Mode::RenameLabel); return; } QmitkNewSegmentationDialog::DoRenameLabel(label, nullptr, this->m_Parent, QmitkNewSegmentationDialog::Mode::NewLabel); } mitk::LabelSetImage* QmitkSegmentationView::GetCurrentSegmentation() const { auto workingNode = m_Controls->workingNodeSelector->GetSelectedNode(); if (workingNode.IsNull()) mitkThrow() << "Segmentation view is in an invalid state. Working node is null, but a label selection change has been triggered."; auto segmentation = dynamic_cast(workingNode->GetData()); if (nullptr == segmentation) mitkThrow() << "Segmentation view is in an invalid state. Working node contains no segmentation, but a label selection change has been triggered."; return segmentation; } /**********************************************************************/ /* private */ /**********************************************************************/ void QmitkSegmentationView::CreateQtPartControl(QWidget* parent) { m_Parent = parent; m_Controls = new Ui::QmitkSegmentationViewControls; m_Controls->setupUi(parent); // *------------------------ // * SHORTCUTS // *------------------------ QShortcut* visibilityShortcut = new QShortcut(QKeySequence(Qt::CTRL | Qt::Key::Key_H), parent); connect(visibilityShortcut, &QShortcut::activated, this, &QmitkSegmentationView::OnVisibilityShortcutActivated); QShortcut* labelToggleShortcut = new QShortcut(QKeySequence(Qt::CTRL | Qt::Key::Key_L, Qt::CTRL | Qt::Key::Key_I), parent); connect(labelToggleShortcut, &QShortcut::activated, this, &QmitkSegmentationView::OnLabelToggleShortcutActivated); // *------------------------ // * DATA SELECTION WIDGETS // *------------------------ m_Controls->referenceNodeSelector->SetDataStorage(GetDataStorage()); m_Controls->referenceNodeSelector->SetNodePredicate(m_ReferencePredicate); m_Controls->referenceNodeSelector->SetInvalidInfo("Select an image"); m_Controls->referenceNodeSelector->SetPopUpTitel("Select an image"); m_Controls->referenceNodeSelector->SetPopUpHint("Select an image that should be used to define the geometry and bounds of the segmentation."); m_Controls->workingNodeSelector->SetDataStorage(GetDataStorage()); m_Controls->workingNodeSelector->SetNodePredicate(m_SegmentationPredicate); m_Controls->workingNodeSelector->SetInvalidInfo("Select a segmentation"); m_Controls->workingNodeSelector->SetPopUpTitel("Select a segmentation"); m_Controls->workingNodeSelector->SetPopUpHint("Select a segmentation that should be modified. Only segmentation with the same geometry and within the bounds of the reference image are selected."); connect(m_Controls->referenceNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkSegmentationView::OnReferenceSelectionChanged); connect(m_Controls->workingNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkSegmentationView::OnSegmentationSelectionChanged); // *------------------------ // * TOOLMANAGER // *------------------------ m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); m_ToolManager->SetDataStorage(*(this->GetDataStorage())); m_ToolManager->InitializeTools(); QString segTools2D = tr("Add Subtract Lasso Fill Erase Close Paint Wipe 'Region Growing' 'Live Wire'"); - QString segTools3D = tr("Threshold 'UL Threshold' Otsu 'Region Growing 3D' Picking GrowCut TotalSegmentator"); + QString segTools3D = tr("Threshold 'UL Threshold' Otsu 'Region Growing 3D' Picking GrowCut TotalSegmentator MonaiLabel"); #ifdef __linux__ segTools3D.append(" nnUNet"); // plugin not enabled for MacOS / Windows #endif std::regex extSegTool2DRegEx("SegTool2D$"); std::regex extSegTool3DRegEx("SegTool3D$"); auto tools = m_ToolManager->GetTools(); for (const auto &tool : tools) { if (std::regex_search(tool->GetNameOfClass(), extSegTool2DRegEx)) { segTools2D.append(QString(" '%1'").arg(tool->GetName())); } else if (std::regex_search(tool->GetNameOfClass(), extSegTool3DRegEx)) { segTools3D.append(QString(" '%1'").arg(tool->GetName())); } } // setup 2D tools m_Controls->toolSelectionBox2D->SetToolManager(*m_ToolManager); m_Controls->toolSelectionBox2D->SetGenerateAccelerators(true); m_Controls->toolSelectionBox2D->SetToolGUIArea(m_Controls->toolGUIArea2D); m_Controls->toolSelectionBox2D->SetDisplayedToolGroups(segTools2D.toStdString()); connect(m_Controls->toolSelectionBox2D, &QmitkToolSelectionBox::ToolSelected, this, &QmitkSegmentationView::OnManualTool2DSelected); // setup 3D Tools m_Controls->toolSelectionBox3D->SetToolManager(*m_ToolManager); m_Controls->toolSelectionBox3D->SetGenerateAccelerators(true); m_Controls->toolSelectionBox3D->SetToolGUIArea(m_Controls->toolGUIArea3D); m_Controls->toolSelectionBox3D->SetDisplayedToolGroups(segTools3D.toStdString()); m_Controls->slicesInterpolator->SetDataStorage(this->GetDataStorage()); // create general signal / slot connections connect(m_Controls->newSegmentationButton, &QToolButton::clicked, this, &QmitkSegmentationView::OnNewSegmentation); connect(m_Controls->slicesInterpolator, &QmitkSlicesInterpolator::SignalShowMarkerNodes, this, &QmitkSegmentationView::OnShowMarkerNodes); connect(m_Controls->multiLabelWidget, &QmitkMultiLabelManager::CurrentSelectionChanged, this, &QmitkSegmentationView::OnCurrentLabelSelectionChanged); connect(m_Controls->multiLabelWidget, &QmitkMultiLabelManager::GoToLabel, this, &QmitkSegmentationView::OnGoToLabel); connect(m_Controls->multiLabelWidget, &QmitkMultiLabelManager::LabelRenameRequested, this, &QmitkSegmentationView::OnLabelRenameRequested); auto command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::ValidateSelectionInput); m_RenderingManagerObserverTag = mitk::RenderingManager::GetInstance()->AddObserver(mitk::RenderingManagerViewsInitializedEvent(), command); m_RenderWindowPart = this->GetRenderWindowPart(); if (nullptr != m_RenderWindowPart) { this->RenderWindowPartActivated(m_RenderWindowPart); } // Make sure the GUI notices if appropriate data is already present on creation. // Should be done last, if everything else is configured because it triggers the autoselection of data. m_Controls->referenceNodeSelector->SetAutoSelectNewNodes(true); m_Controls->workingNodeSelector->SetAutoSelectNewNodes(true); this->UpdateGUI(); } void QmitkSegmentationView::ActiveToolChanged() { if (nullptr == m_RenderWindowPart) { return; } mitk::TimeGeometry* interactionReferenceGeometry = nullptr; auto activeTool = m_ToolManager->GetActiveTool(); if (nullptr != activeTool && m_ReferenceNode.IsNotNull()) { mitk::Image::ConstPointer referenceImage = dynamic_cast(m_ReferenceNode->GetData()); if (referenceImage.IsNotNull()) { // tool activated, reference image available: set reference geometry interactionReferenceGeometry = m_ReferenceNode->GetData()->GetTimeGeometry(); } } // set the interaction reference geometry for the render window part (might be nullptr) m_RenderWindowPart->SetInteractionReferenceGeometry(interactionReferenceGeometry); } void QmitkSegmentationView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { if (m_RenderWindowPart != renderWindowPart) { m_RenderWindowPart = renderWindowPart; } if (nullptr != m_Parent) { m_Parent->setEnabled(true); } if (nullptr == m_Controls) { return; } if (nullptr != m_RenderWindowPart) { auto all2DWindows = Get2DWindows(m_RenderWindowPart->GetQmitkRenderWindows().values()); m_Controls->slicesInterpolator->Initialize(m_ToolManager, all2DWindows); if (!m_RenderWindowPart->HasCoupledRenderWindows()) { // react if the active tool changed, only if a render window part with decoupled render windows is used m_ToolManager->ActiveToolChanged += mitk::MessageDelegate(this, &QmitkSegmentationView::ActiveToolChanged); } } } void QmitkSegmentationView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* /*renderWindowPart*/) { m_RenderWindowPart = nullptr; if (nullptr != m_Parent) { m_Parent->setEnabled(false); } // remove message-connection to make sure no message is processed if no render window part is available m_ToolManager->ActiveToolChanged -= mitk::MessageDelegate(this, &QmitkSegmentationView::ActiveToolChanged); m_Controls->slicesInterpolator->Uninitialize(); } void QmitkSegmentationView::RenderWindowPartInputChanged(mitk::IRenderWindowPart* /*renderWindowPart*/) { if (nullptr == m_RenderWindowPart) { return; } m_Controls->slicesInterpolator->Uninitialize(); auto all2DWindows = Get2DWindows(m_RenderWindowPart->GetQmitkRenderWindows().values()); m_Controls->slicesInterpolator->Initialize(m_ToolManager, all2DWindows); } void QmitkSegmentationView::OnPreferencesChanged(const mitk::IPreferences* prefs) { auto labelSuggestions = mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABEL_SUGGESTIONS.toStdString(), ""); m_DefaultLabelNaming = labelSuggestions.empty() ? prefs->GetBool("default label naming", true) : false; // No default label naming when label suggestions are enforced via command-line argument if (nullptr != m_Controls) { m_Controls->multiLabelWidget->SetDefaultLabelNaming(m_DefaultLabelNaming); bool compactView = prefs->GetBool("compact view", false); int numberOfColumns = compactView ? 6 : 4; m_Controls->toolSelectionBox2D->SetLayoutColumns(numberOfColumns); m_Controls->toolSelectionBox2D->SetShowNames(!compactView); m_Controls->toolSelectionBox3D->SetLayoutColumns(numberOfColumns); m_Controls->toolSelectionBox3D->SetShowNames(!compactView); } m_DrawOutline = prefs->GetBool("draw outline", true); m_SelectionMode = prefs->GetBool("selection mode", false); m_LabelSetPresetPreference = QString::fromStdString(prefs->Get("label set preset", "")); this->ApplyDisplayOptions(); this->ApplySelectionMode(); } void QmitkSegmentationView::NodeAdded(const mitk::DataNode* node) { if (m_SegmentationPredicate->CheckNode(node)) this->ApplyDisplayOptions(const_cast(node)); this->ApplySelectionMode(); } void QmitkSegmentationView::NodeRemoved(const mitk::DataNode* node) { if (!m_SegmentationPredicate->CheckNode(node)) { return; } // remove all possible contour markers of the segmentation mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = this->GetDataStorage()->GetDerivations( node, mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true))); ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); for (mitk::DataStorage::SetOfObjects::ConstIterator it = allContourMarkers->Begin(); it != allContourMarkers->End(); ++it) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1; service->RemovePlanePosition(id); this->GetDataStorage()->Remove(it->Value()); } context->ungetService(ppmRef); service = nullptr; mitk::Image* image = dynamic_cast(node->GetData()); mitk::SurfaceInterpolationController::GetInstance()->RemoveInterpolationSession(image); } void QmitkSegmentationView::ApplyDisplayOptions() { if (nullptr == m_Parent) { return; } if (nullptr == m_Controls) { return; // might happen on initialization (preferences loaded) } mitk::DataStorage::SetOfObjects::ConstPointer allImages = this->GetDataStorage()->GetSubset(m_SegmentationPredicate); for (mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter) { this->ApplyDisplayOptions(*iter); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::ApplyDisplayOptions(mitk::DataNode* node) { if (nullptr == node) { return; } auto labelSetImage = dynamic_cast(node->GetData()); if (nullptr == labelSetImage) { return; } // the outline property can be set in the segmentation preference page node->SetProperty("labelset.contour.active", mitk::BoolProperty::New(m_DrawOutline)); // force render window update to show outline mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::ApplySelectionMode() { if (!m_SelectionMode) return; this->ApplySelectionModeOnReferenceNode(); this->ApplySelectionModeOnWorkingNode(); } void QmitkSegmentationView::ApplySelectionModeOnReferenceNode() { this->ApplySelectionMode(m_ReferenceNode, m_ReferencePredicate); } void QmitkSegmentationView::ApplySelectionModeOnWorkingNode() { this->ApplySelectionMode(m_WorkingNode, m_SegmentationPredicate); } void QmitkSegmentationView::ApplySelectionMode(mitk::DataNode* node, mitk::NodePredicateBase* predicate) { if (!m_SelectionMode || node == nullptr || predicate == nullptr) return; auto nodes = this->GetDataStorage()->GetSubset(predicate); for (auto iter = nodes->begin(); iter != nodes->end(); ++iter) (*iter)->SetVisibility(*iter == node); } void QmitkSegmentationView::OnContourMarkerSelected(const mitk::DataNode* node) { QmitkRenderWindow* selectedRenderWindow = nullptr; auto* renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN); auto* axialRenderWindow = renderWindowPart->GetQmitkRenderWindow("axial"); auto* sagittalRenderWindow = renderWindowPart->GetQmitkRenderWindow("sagittal"); auto* coronalRenderWindow = renderWindowPart->GetQmitkRenderWindow("coronal"); auto* threeDRenderWindow = renderWindowPart->GetQmitkRenderWindow("3d"); bool PlanarFigureInitializedWindow = false; // find initialized renderwindow if (node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, axialRenderWindow->GetRenderer())) { selectedRenderWindow = axialRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, sagittalRenderWindow->GetRenderer())) { selectedRenderWindow = sagittalRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, coronalRenderWindow->GetRenderer())) { selectedRenderWindow = coronalRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, threeDRenderWindow->GetRenderer())) { selectedRenderWindow = threeDRenderWindow; } // make node visible if (nullptr != selectedRenderWindow) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1; ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); selectedRenderWindow->GetSliceNavigationController()->ExecuteOperation(service->GetPlanePosition(id)); context->ungetService(ppmRef); selectedRenderWindow->GetRenderer()->GetCameraController()->Fit(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkSegmentationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& nodes) { if (0 == nodes.size()) { return; } std::string markerName = "Position"; unsigned int numberOfNodes = nodes.size(); std::string nodeName = nodes.at(0)->GetName(); if ((numberOfNodes == 1) && (nodeName.find(markerName) == 0)) { this->OnContourMarkerSelected(nodes.at(0)); return; } } void QmitkSegmentationView::ResetMouseCursor() { if (m_MouseCursorSet) { mitk::ApplicationCursor::GetInstance()->PopCursor(); m_MouseCursorSet = false; } } void QmitkSegmentationView::SetMouseCursor(const us::ModuleResource& resource, int hotspotX, int hotspotY) { // Remove previously set mouse cursor if (m_MouseCursorSet) { this->ResetMouseCursor(); } if (resource) { us::ModuleResourceStream cursor(resource, std::ios::binary); mitk::ApplicationCursor::GetInstance()->PushCursor(cursor, hotspotX, hotspotY); m_MouseCursorSet = true; } } void QmitkSegmentationView::UpdateGUI() { mitk::DataNode* referenceNode = m_ToolManager->GetReferenceData(0); bool hasReferenceNode = referenceNode != nullptr; mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0); bool hasWorkingNode = workingNode != nullptr; m_Controls->newSegmentationButton->setEnabled(false); if (hasReferenceNode) { m_Controls->newSegmentationButton->setEnabled(true); } if (hasWorkingNode && hasReferenceNode) { int layer = -1; referenceNode->GetIntProperty("layer", layer); workingNode->SetIntProperty("layer", layer + 1); } this->ValidateSelectionInput(); } void QmitkSegmentationView::ValidateSelectionInput() { auto referenceNode = m_Controls->referenceNodeSelector->GetSelectedNode(); auto workingNode = m_Controls->workingNodeSelector->GetSelectedNode(); bool hasReferenceNode = referenceNode.IsNotNull(); bool hasWorkingNode = workingNode.IsNotNull(); bool hasBothNodes = hasReferenceNode && hasWorkingNode; QString warning; bool toolSelectionBoxesEnabled = hasReferenceNode && hasWorkingNode; unsigned int numberOfLabels = 0; m_Controls->multiLabelWidget->setEnabled(hasWorkingNode); m_Controls->toolSelectionBox2D->setEnabled(hasBothNodes); m_Controls->toolSelectionBox3D->setEnabled(hasBothNodes); m_Controls->slicesInterpolator->setEnabled(false); m_Controls->interpolatorWarningLabel->hide(); if (hasReferenceNode) { if (nullptr != m_RenderWindowPart && m_RenderWindowPart->HasCoupledRenderWindows() && !referenceNode->IsVisible(nullptr)) { warning += tr("The selected reference image is currently not visible!"); toolSelectionBoxesEnabled = false; } } if (hasWorkingNode) { if (nullptr != m_RenderWindowPart && m_RenderWindowPart->HasCoupledRenderWindows() && !workingNode->IsVisible(nullptr)) { warning += (!warning.isEmpty() ? "
" : "") + tr("The selected segmentation is currently not visible!"); toolSelectionBoxesEnabled = false; } m_ToolManager->SetReferenceData(referenceNode); m_ToolManager->SetWorkingData(workingNode); m_Controls->multiLabelWidget->setEnabled(true); m_Controls->toolSelectionBox2D->setEnabled(true); m_Controls->toolSelectionBox3D->setEnabled(true); auto labelSetImage = dynamic_cast(workingNode->GetData()); auto activeLayer = labelSetImage->GetActiveLayer(); numberOfLabels = labelSetImage->GetNumberOfLabels(activeLayer); if (numberOfLabels > 0) m_Controls->slicesInterpolator->setEnabled(true); m_Controls->multiLabelWidget->SetMultiLabelSegmentation(dynamic_cast(workingNode->GetData())); } else { m_Controls->multiLabelWidget->SetMultiLabelSegmentation(nullptr); } toolSelectionBoxesEnabled &= numberOfLabels > 0; // Here we need to check whether the geometry of the selected segmentation image (working image geometry) // is aligned with the geometry of the 3D render window. // It is not allowed to use a geometry different from the working image geometry for segmenting. // We only need to this if the tool selection box would be enabled without this check. // Additionally this check only has to be performed for render window parts with coupled render windows. // For different render window parts the user is given the option to reinitialize each render window individually // (see QmitkRenderWindow::ShowOverlayMessage). if (toolSelectionBoxesEnabled && nullptr != m_RenderWindowPart && m_RenderWindowPart->HasCoupledRenderWindows()) { const mitk::BaseGeometry* workingNodeGeometry = workingNode->GetData()->GetGeometry(); const mitk::BaseGeometry* renderWindowGeometry = m_RenderWindowPart->GetQmitkRenderWindow("3d")->GetSliceNavigationController()->GetCurrentGeometry3D(); if (nullptr != workingNodeGeometry && nullptr != renderWindowGeometry) { if (!mitk::Equal(*workingNodeGeometry->GetBoundingBox(), *renderWindowGeometry->GetBoundingBox(), mitk::eps, true)) { warning += (!warning.isEmpty() ? "
" : "") + tr("Please reinitialize the selected segmentation image!"); toolSelectionBoxesEnabled = false; } } } m_Controls->toolSelectionBox2D->setEnabled(toolSelectionBoxesEnabled); m_Controls->toolSelectionBox3D->setEnabled(toolSelectionBoxesEnabled); this->UpdateWarningLabel(warning); m_ToolManager->SetReferenceData(referenceNode); m_ToolManager->SetWorkingData(workingNode); } void QmitkSegmentationView::UpdateWarningLabel(QString text) { if (text.isEmpty()) { m_Controls->selectionWarningLabel->hide(); } else { m_Controls->selectionWarningLabel->setText("" + text + ""); m_Controls->selectionWarningLabel->show(); } }