diff --git a/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.cpp b/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.cpp new file mode 100644 index 0000000000..e2ff6aa6cd --- /dev/null +++ b/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.cpp @@ -0,0 +1,265 @@ +/*============================================================================ + +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 "mitkTotalSegmentatorTool.h" + +#include "mitkIOUtil.h" +#include +#include + +// us +#include +#include +#include +#include +#include + +namespace mitk +{ + MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, TotalSegmentatorTool, "Total Segmentator"); +} + +mitk::TotalSegmentatorTool::~TotalSegmentatorTool() +{ + itksys::SystemTools::RemoveADirectory(this->GetMitkTempDir()); +} + +void mitk::TotalSegmentatorTool::Activated() +{ + Superclass::Activated(); + this->SetLabelTransferMode(LabelTransferMode::AllLabels); +} + +const char **mitk::TotalSegmentatorTool::GetXPM() const +{ + return nullptr; +} + +us::ModuleResource mitk::TotalSegmentatorTool::GetIconResource() const +{ + us::Module *module = us::GetModuleContext()->GetModule(); + us::ModuleResource resource = module->GetResource("AI.svg"); + return resource; +} + +const char *mitk::TotalSegmentatorTool::GetName() const +{ + return "Total Segmentator"; +} + +namespace +{ + void onPythonProcessEvent(itk::Object * /*pCaller*/, const itk::EventObject &e, void *) + { + std::string testCOUT; + std::string testCERR; + const auto *pEvent = dynamic_cast(&e); + + if (pEvent) + { + testCOUT = testCOUT + pEvent->GetOutput(); + MITK_INFO << testCOUT; + } + + const auto *pErrEvent = dynamic_cast(&e); + + if (pErrEvent) + { + testCERR = testCERR + pErrEvent->GetOutput(); + MITK_ERROR << testCERR; + } + } +} // namespace + +void mitk::TotalSegmentatorTool::DoUpdatePreview(const Image *inputAtTimeStep, + const Image * /*oldSegAtTimeStep*/, + LabelSetImage *previewImage, + TimeStepType timeStep) +{ + if (!m_IsMitkTempDirAvailable) // create temp directory if not done already + { + this->SetMitkTempDir(IOUtil::CreateTemporaryDirectory("mitk-XXXXXX")); + m_IsMitkTempDirAvailable = true; + } + this->ParseLabelNames(this->GetLabelMapPath()); + + ProcessExecutor::Pointer spExec = ProcessExecutor::New(); + itk::CStyleCommand::Pointer spCommand = itk::CStyleCommand::New(); + spCommand->SetCallback(&onPythonProcessEvent); + spExec->AddObserver(ExternalProcessOutputEvent(), spCommand); + + std::string inDir, outDir, inputImagePath, outputImagePath, scriptPath; + inDir = IOUtil::CreateTemporaryDirectory("totalseg-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("totalseg-out-XXXXXX", this->GetMitkTempDir()); + outputImagePath = outDir + IOUtil::GetDirectorySeparator() + token + "_000.nii.gz"; + ProcessExecutor::ArgumentListType args; + + IOUtil::Save(inputAtTimeStep, inputImagePath); + + std::string *outArg = &outputImagePath; + bool isSubTask = false; + if (this->GetSubTask() != m_DEFAULT_TOTAL_TASK) + { + isSubTask = true; + outputImagePath = outDir + IOUtil::GetDirectorySeparator() + this->GetSubTask() + ".nii.gz"; + outArg = &outDir; + } + + this->run_totalsegmentator( + spExec, inputImagePath, *outArg, this->GetFast(), !isSubTask, this->GetGpuId(), m_DEFAULT_TOTAL_TASK); + + if (isSubTask) + { + this->run_totalsegmentator( + spExec, inputImagePath, *outArg, !isSubTask, !isSubTask, this->GetGpuId(), this->GetSubTask()); + } + + Image::Pointer outputImage = IOUtil::Load(outputImagePath); + auto outputBuffer = mitk::LabelSetImage::New(); + outputBuffer->InitializeByLabeledImage(outputImage); + outputBuffer->SetGeometry(inputAtTimeStep->GetGeometry()); + this->MapLabelsToSegmentation(outputBuffer, m_LabelMapTotal); + TransferLabelSetImageContent(outputBuffer, previewImage, timeStep); +} + +void mitk::TotalSegmentatorTool::run_totalsegmentator(ProcessExecutor::Pointer spExec, + const std::string &inputImagePath, + const std::string &outputImagePath, + bool isFast, + bool isMultiLabel, + unsigned int gpuId, + const std::string &subTask) +{ + ProcessExecutor::ArgumentListType args; + std::string command = "TotalSegmentator"; +#ifdef _WIN32 + command = "python"; +#else + command = "TotalSegmentator"; +#endif + + args.clear(); + +#ifdef _WIN32 + args.push_back("TotalSegmentator"); +#endif + + args.push_back("-i"); + args.push_back(inputImagePath); + + args.push_back("-o"); + args.push_back(outputImagePath); + + if (subTask != m_DEFAULT_TOTAL_TASK) + { + args.push_back("-ta"); + args.push_back(subTask); + } + + if (isMultiLabel) + { + args.push_back("--ml"); + } + + if (isFast) + { + args.push_back("--fast"); + } + + try + { + std::string cudaEnv = "CUDA_VISIBLE_DEVICES=" + std::to_string(gpuId); + itksys::SystemTools::PutEnv(cudaEnv.c_str()); + + for (auto &arg : args) + MITK_INFO << arg; + MITK_INFO << this->GetPythonPath(); + + spExec->Execute(this->GetPythonPath(), command, args); + } + catch (const mitk::Exception &e) + { + MITK_ERROR << e.GetDescription(); + return; + } +} + +void mitk::TotalSegmentatorTool::ParseLabelNames(const std::string &fileName) +{ + std::fstream newfile; + newfile.open(fileName, ios::in); + std::stringstream buffer; + if (newfile.is_open()) + { + int line = 0; + std::string temp; + while (std::getline(newfile, temp)) + { + if (line > 1 && line < 106) + { + buffer << temp; + } + ++line; + } + } + std::string key, val; + while (std::getline(std::getline(buffer, key, ':'), val, ',')) + { + m_LabelMapTotal[std::stoi(key)] = val; + } +} + +void mitk::TotalSegmentatorTool::MapLabelsToSegmentation(mitk::LabelSetImage::Pointer outputBuffer, + std::map &labelMap) +{ + for (auto const &[key, val] : labelMap) + { + mitk::Label *labelptr = outputBuffer->GetLabel(key, 0); + if (nullptr != labelptr) + { + labelptr->SetName(val); + } + } +} + +std::string mitk::TotalSegmentatorTool::GetLabelMapPath() +{ + std::string pythonFileName; + std::filesystem::path pathToLabelMap(this->GetPythonPath()); + pathToLabelMap = pathToLabelMap.parent_path(); +#ifdef _WIN32 + pythonFileName = pathToLabelMap.string() + "/Lib/site-packages/totalsegmentator/map_to_binary.py"; +#else + pathToLabelMap.append("lib"); + for (auto const &dir_entry : std::filesystem::directory_iterator{pathToLabelMap}) + { + if (dir_entry.is_directory()) + { + auto dirName = dir_entry.path().filename().string(); + if (dirName.rfind("python", 0) == 0) + { + pathToLabelMap.append(dir_entry.path().filename().string()); + break; + } + } + } + pythonFileName = pathToLabelMap.string() + "/site-packages/totalsegmentator/map_to_binary.py"; +#endif + return pythonFileName; +} diff --git a/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.h b/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.h new file mode 100644 index 0000000000..866909c47a --- /dev/null +++ b/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.h @@ -0,0 +1,128 @@ +/*============================================================================ + +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. + +============================================================================*/ +#ifndef MITKTOTALSEGMENTATORTOOL_H +#define MITKTOTALSEGMENTATORTOOL_H + +#include "mitkSegWithPreviewTool.h" +#include +#include "mitkProcessExecutor.h" + + +namespace us +{ + class ModuleResource; +} + +namespace mitk +{ + + /** + \brief TotalSegmentator segmentation tool. + + \ingroup Interaction + \ingroup ToolManagerEtAl + + \warning Only to be instantiated by mitk::ToolManager. + */ + class MITKSEGMENTATION_EXPORT TotalSegmentatorTool : public SegWithPreviewTool + { + public: + mitkClassMacro(TotalSegmentatorTool, SegWithPreviewTool); + itkFactorylessNewMacro(Self); + itkCloneMacro(Self); + + const char *GetName() const override; + const char **GetXPM() const override; + us::ModuleResource GetIconResource() const override; + void Activated() override; + + itkSetMacro(MitkTempDir, std::string); + itkGetConstMacro(MitkTempDir, std::string); + + itkSetMacro(SubTask, std::string); + itkGetConstMacro(SubTask, std::string); + + itkSetMacro(PythonPath, std::string); + itkGetConstMacro(PythonPath, std::string); + + itkSetMacro(GpuId, unsigned int); + itkGetConstMacro(GpuId, unsigned int); + + itkSetMacro(Fast, bool); + itkGetConstMacro(Fast, bool); + itkBooleanMacro(Fast); + + itkSetMacro(IsMitkTempDirAvailable, bool); + itkGetConstMacro(IsMitkTempDirAvailable, bool); + itkBooleanMacro(IsMitkTempDirAvailable); + + protected: + TotalSegmentatorTool() = default; + ~TotalSegmentatorTool(); + + /** + * @brief Overriden method from the tool manager to execute the segmentation + * Implementation: + * 1. Creates temp directory, if not done already. + * 2. Parses Label names from map_to_binary.py for using later on. + * 3. Calls "run_totalsegmentator" method. + * 4. Expects an output image to be saved in the temporary directory by the python proces. Loads it as + * LabelSetImage and sets to previewImage. + * + * @param inputAtTimeStep + * @param oldSegAtTimeStep + * @param previewImage + * @param timeStep + */ + void DoUpdatePreview(const Image* inputAtTimeStep, const Image* oldSegAtTimeStep, LabelSetImage* previewImage, TimeStepType timeStep) override; + + private: + + /** + * @brief Runs Totalsegmentator python process with desired arguments + * + */ + void run_totalsegmentator(ProcessExecutor::Pointer, const std::string &, const std::string &, bool, bool, unsigned int, const std::string &); + + /** + * @brief Applies the m_LabelMapTotal lookup table on the output segmentation LabelSetImage. + * + */ + void MapLabelsToSegmentation(mitk::LabelSetImage::Pointer, std::map&); + + /** + * @brief Parses map_to_binary.py file to extract label ids and names + * and stores as a map for reference in m_LabelMapTotal + * + * @param filePath + */ + void ParseLabelNames(const std::string &); + + /** + * @brief Get the Label Map Path from the virtual environment location + * + * @return std::string + */ + std::string GetLabelMapPath(); + + std::string m_MitkTempDir; + std::string m_PythonPath; + std::string m_SubTask = "total"; + unsigned int m_GpuId; + std::map m_LabelMapTotal; + bool m_Fast; + bool m_IsMitkTempDirAvailable = false; + const std::string m_TEMPLATE_FILENAME = "XXXXXX_000_0000.nii.gz"; + const std::string m_DEFAULT_TOTAL_TASK = "total"; + }; // class +} // namespace +#endif diff --git a/Modules/Segmentation/files.cmake b/Modules/Segmentation/files.cmake index 4520f0edc0..a91d62226e 100644 --- a/Modules/Segmentation/files.cmake +++ b/Modules/Segmentation/files.cmake @@ -1,117 +1,118 @@ set(CPP_FILES Algorithms/mitkCalculateSegmentationVolume.cpp Algorithms/mitkContourModelSetToImageFilter.cpp Algorithms/mitkContourSetToPointSetFilter.cpp Algorithms/mitkContourUtils.cpp Algorithms/mitkCorrectorAlgorithm.cpp Algorithms/mitkDiffImageApplier.cpp Algorithms/mitkDiffSliceOperation.cpp Algorithms/mitkDiffSliceOperationApplier.cpp Algorithms/mitkFeatureBasedEdgeDetectionFilter.cpp Algorithms/mitkGrowCutSegmentationFilter.cpp Algorithms/mitkImageLiveWireContourModelFilter.cpp Algorithms/mitkImageToContourFilter.cpp #Algorithms/mitkImageToContourModelFilter.cpp Algorithms/mitkImageToLiveWireContourFilter.cpp Algorithms/mitkManualSegmentationToSurfaceFilter.cpp Algorithms/mitkOtsuSegmentationFilter.cpp Algorithms/mitkSegmentationHelper.cpp Algorithms/mitkSegmentationObjectFactory.cpp Algorithms/mitkShapeBasedInterpolationAlgorithm.cpp Algorithms/mitkShowSegmentationAsSmoothedSurface.cpp Algorithms/mitkShowSegmentationAsSurface.cpp Algorithms/mitkVtkImageOverwrite.cpp Controllers/mitkSegmentationInterpolationController.cpp Controllers/mitkToolManager.cpp Controllers/mitkSegmentationModuleActivator.cpp Controllers/mitkToolManagerProvider.cpp DataManagement/mitkContour.cpp DataManagement/mitkContourSet.cpp DataManagement/mitkExtrudedContour.cpp Interactions/mitkAddContourTool.cpp Interactions/mitkAutoCropTool.cpp Interactions/mitkSegWithPreviewTool.cpp Interactions/mitkBinaryThresholdBaseTool.cpp Interactions/mitkBinaryThresholdTool.cpp Interactions/mitkBinaryThresholdULTool.cpp Interactions/mitkCloseRegionTool.cpp Interactions/mitkContourModelInteractor.cpp Interactions/mitkContourModelLiveWireInteractor.cpp Interactions/mitkEditableContourTool.cpp Interactions/mitkLiveWireTool2D.cpp Interactions/mitkLassoTool.cpp Interactions/mitkContourTool.cpp Interactions/mitkDrawPaintbrushTool.cpp Interactions/mitkErasePaintbrushTool.cpp Interactions/mitkEraseRegionTool.cpp Interactions/mitkFeedbackContourTool.cpp Interactions/mitkFillRegionBaseTool.cpp Interactions/mitkFillRegionTool.cpp Interactions/mitkGrowCutTool.cpp Interactions/mitkOtsuTool3D.cpp Interactions/mitkPaintbrushTool.cpp Interactions/mitkRegionGrowingTool.cpp Interactions/mitkSegmentationsProcessingTool.cpp Interactions/mitkSegTool2D.cpp Interactions/mitkSubtractContourTool.cpp Interactions/mitkTool.cpp Interactions/mitkToolCommand.cpp Interactions/mitkPickingTool.cpp Interactions/mitknnUnetTool.cpp Interactions/mitkSegmentationInteractor.cpp #SO Interactions/mitkProcessExecutor.cpp + Interactions/mitkTotalSegmentatorTool.cpp Rendering/mitkContourMapper2D.cpp Rendering/mitkContourSetMapper2D.cpp Rendering/mitkContourSetVtkMapper3D.cpp Rendering/mitkContourVtkMapper3D.cpp SegmentationUtilities/BooleanOperations/mitkBooleanOperation.cpp SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.cpp #Added from ML Controllers/mitkSliceBasedInterpolationController.cpp Algorithms/mitkSurfaceStampImageFilter.cpp ) set(RESOURCE_FILES Add.svg Add_Cursor.svg AI.svg AI_Cursor.svg Close.svg Close_Cursor.svg Erase.svg Erase_Cursor.svg Fill.svg Fill_Cursor.svg LiveWire.svg LiveWire_Cursor.svg Lasso.svg GrowCut.svg Lasso_Cursor.svg Otsu.svg Paint.svg Paint_Cursor.svg Picking.svg RegionGrowing.svg RegionGrowing_Cursor.svg Subtract.svg Subtract_Cursor.svg Threshold.svg ULThreshold.svg Wipe.svg Wipe_Cursor.svg Interactions/dummy.xml Interactions/EditableContourTool.xml Interactions/PickingTool.xml Interactions/MouseReleaseOnly.xml Interactions/PressMoveRelease.xml Interactions/PressMoveReleaseAndPointSetting.xml Interactions/PressMoveReleaseWithCTRLInversion.xml Interactions/PressMoveReleaseWithCTRLInversionAllMouseMoves.xml Interactions/SegmentationConfig.xml Interactions/SegmentationInteraction.xml Interactions/SegmentationToolsConfig.xml Interactions/ContourModelModificationConfig.xml Interactions/ContourModelModificationInteractor.xml ) diff --git a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorGUIControls.ui b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorGUIControls.ui new file mode 100644 index 0000000000..a9c32edd1e --- /dev/null +++ b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorGUIControls.ui @@ -0,0 +1,236 @@ + + + QmitkTotalSegmentatorToolGUIControls + + + + 0 + 0 + 699 + 352 + + + + + 0 + 0 + + + + + 100 + 0 + + + + + 100000 + 100000 + + + + QmitkTotalSegmentatorToolWidget + + + + 0 + + + 0 + + + 0 + + + 0 + + + + + + + + 0 + 0 + + + + <html><head/><body><p>Welcome to Total Segmentator tool in MITK. [Experimental]</p><p>Please note that this is only an interface to Total Segmentator. MITK does not ship with Total Segmentator. Make sure to have a working Python environment with TotalSegmentator set up beforehand. Choose that environment in the Python Path before inferencing. </p><p>Refer to <a href="https://github.com/wasserth/TotalSegmentator"><span style=" text-decoration: underline; color:#0000ff;">https://github.com/wasserth/TotalSegmentator</span></a> to learn everything about the Total Segmentator.</p><p><br/></p></body></html> + + + Qt::RichText + + + true + + + + + + + + 0 + 0 + + + + Python Path: + + + + + + + + + + + 0 + 0 + + + + Task: + + + + + + + + + + + + + 0 + 0 + + + + Advanced + + + true + + + 5 + + + true + + + + + + 0 + + + 0 + + + 0 + + + 0 + + + 6 + + + + + + 0 + 0 + + + + GPU Id: + + + + + + + + + + false + + + + + + + + 0 + 0 + + + + Fast + + + + + + + + + + + + + 0 + 0 + + + + + 100000 + 16777215 + + + + Run Total Segmentator + + + + + + + + 0 + 0 + + + + true + + + + + + + + + ctkComboBox + QComboBox +
ctkComboBox.h
+ 1 + + + ctkCollapsibleGroupBox + QWidget +
ctkCollapsibleGroupBox.h
+ + + ctkCheckBox + QWidget +
ctkCheckBox.h
+ + + + + diff --git a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp new file mode 100644 index 0000000000..82035eff65 --- /dev/null +++ b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp @@ -0,0 +1,285 @@ +#include "QmitkTotalSegmentatorToolGUI.h" + +#include +#include +#include +#include +#include +#include +#include +#include +#include "mitkTotalSegmentatorTool.h" + + +MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkTotalSegmentatorToolGUI, "") + +QmitkTotalSegmentatorToolGUI::QmitkTotalSegmentatorToolGUI() + : QmitkMultiLabelSegWithPreviewToolGUIBase(), m_SuperclassEnableConfirmSegBtnFnc(m_EnableConfirmSegBtnFnc) +{ + // Nvidia-smi command returning zero doesn't always imply lack of GPUs. + // Pytorch uses its own libraries to communicate to the GPUs. Hence, only a warning can be given. + if (m_GpuLoader.GetGPUCount() == 0) + { + std::string warning = "WARNING: No GPUs were detected on your machine. The TotalSegmentator tool can be very slow."; + this->ShowErrorMessage(warning); + } + m_EnableConfirmSegBtnFnc = [this](bool enabled) + { return !m_FirstPreviewComputation ? m_SuperclassEnableConfirmSegBtnFnc(enabled) : false; }; +} + +void QmitkTotalSegmentatorToolGUI::ConnectNewTool(mitk::SegWithPreviewTool *newTool) +{ + Superclass::ConnectNewTool(newTool); + newTool->IsTimePointChangeAwareOff(); + m_FirstPreviewComputation = true; +} + +void QmitkTotalSegmentatorToolGUI::InitializeUI(QBoxLayout *mainLayout) +{ + m_Controls.setupUi(this); + m_Controls.pythonEnvComboBox->addItem("Select"); + m_Controls.previewButton->setDisabled(true); + m_Controls.statusLabel->setTextFormat(Qt::RichText); + m_Controls.subtaskComboBox->addItems(m_VALID_TASKS); + AutoParsePythonPaths(); + SetGPUInfo(); + if (m_GpuLoader.GetGPUCount() != 0) + { + WriteStatusMessage(QString("STATUS: Welcome to Total Segmentator tool. You're in luck: " + QString::number(m_GpuLoader.GetGPUCount()) + + " GPU(s) were detected.")); + } + else + { + WriteErrorMessage(QString("STATUS: Welcome to Total Segmentator tool. Sorry, " + QString::number(m_GpuLoader.GetGPUCount()) + + " GPUs were detected.")); + } + mainLayout->addLayout(m_Controls.verticalLayout); + + connect(m_Controls.previewButton, SIGNAL(clicked()), this, SLOT(OnPreviewBtnClicked())); + connect(m_Controls.pythonEnvComboBox, + SIGNAL(currentTextChanged(const QString &)), + this, + SLOT(OnPythonPathChanged(const QString &))); + + Superclass::InitializeUI(mainLayout); + + QString lastSelectedPyEnv = m_Settings.value("TotalSeg/LastPythonPath").toString(); + m_Controls.pythonEnvComboBox->insertItem(0, lastSelectedPyEnv); +} + +void QmitkTotalSegmentatorToolGUI::EnableWidgets(bool enabled) +{ + Superclass::EnableWidgets(enabled); +} + +void QmitkTotalSegmentatorToolGUI::SetGPUInfo() +{ + std::vector specs = m_GpuLoader.GetAllGPUSpecs(); + for (const QmitkGPUSpec &gpuSpec : specs) + { + m_Controls.gpuComboBox->addItem(QString::number(gpuSpec.id) + ": " + gpuSpec.name + " (" + gpuSpec.memory + ")"); + } + if (specs.empty()) + { + m_Controls.gpuComboBox->setEditable(true); + m_Controls.gpuComboBox->addItem(QString::number(0)); + m_Controls.gpuComboBox->setValidator(new QIntValidator(0, 999, this)); + } +} + +unsigned int QmitkTotalSegmentatorToolGUI::FetchSelectedGPUFromUI() +{ + QString gpuInfo = m_Controls.gpuComboBox->currentText(); + if (m_GpuLoader.GetGPUCount() == 0) + { + return static_cast(gpuInfo.toInt()); + } + else + { + QString gpuId = gpuInfo.split(":", QString::SplitBehavior::SkipEmptyParts).first(); + return static_cast(gpuId.toInt()); + } +} + +void QmitkTotalSegmentatorToolGUI::OnPreviewBtnClicked() +{ + auto tool = this->GetConnectedToolAs(); + if (nullptr == tool) + { + return; + } + QString pythonPathTextItem = ""; + try + { + m_Controls.previewButton->setEnabled(false); + qApp->processEvents(); + if (!this->IsTotalSegmentatorInstalled(m_PythonPath)) + { + throw std::runtime_error(m_WARNING_TOTALSEG_NOT_FOUND); + } + pythonPathTextItem = m_Controls.pythonEnvComboBox->currentText(); + bool isFast = m_Controls.fastBox->isChecked(); + QString subTask = m_Controls.subtaskComboBox->currentText(); + if (subTask != m_VALID_TASKS[0]) + { + isFast = true; + } + tool->SetPythonPath(m_PythonPath.toStdString()); + tool->SetGpuId(FetchSelectedGPUFromUI()); + tool->SetFast(isFast); + tool->SetSubTask(subTask.toStdString()); + this->WriteStatusMessage(QString("STATUS: Starting Segmentation task... This might take a while.")); + tool->UpdatePreview(); + m_Controls.previewButton->setEnabled(true); + } + catch (const std::exception &e) + { + std::stringstream errorMsg; + errorMsg << "STATUS: Error while processing parameters for TotalSegmentator segmentation. Reason: " << e.what(); + this->ShowErrorMessage(errorMsg.str()); + this->WriteErrorMessage(QString::fromStdString(errorMsg.str())); + m_Controls.previewButton->setEnabled(true); + return; + } + catch (...) + { + std::string errorMsg = "Unkown error occured while generation TotalSegmentator segmentation."; + this->ShowErrorMessage(errorMsg); + m_Controls.previewButton->setEnabled(true); + return; + } + this->SetLabelSetPreview(tool->GetPreviewSegmentation()); + tool->IsTimePointChangeAwareOn(); + this->ActualizePreviewLabelVisibility(); + this->WriteStatusMessage("STATUS: Segmentation task finished successfully."); + if (!pythonPathTextItem.isEmpty()) + { // only cache if the prediction ended without errors. + m_Settings.setValue("TotalSeg/LastPythonPath", pythonPathTextItem); + } +} + + +void QmitkTotalSegmentatorToolGUI::ShowErrorMessage(const std::string &message, QMessageBox::Icon icon) +{ + this->setCursor(Qt::ArrowCursor); + QMessageBox *messageBox = new QMessageBox(icon, nullptr, message.c_str()); + messageBox->exec(); + delete messageBox; + MITK_WARN << message; +} + +void QmitkTotalSegmentatorToolGUI::WriteStatusMessage(const QString &message) +{ + m_Controls.statusLabel->setText(message); + m_Controls.statusLabel->setStyleSheet("font-weight: bold; color: white"); +} + +void QmitkTotalSegmentatorToolGUI::WriteErrorMessage(const QString &message) +{ + m_Controls.statusLabel->setText(message); + m_Controls.statusLabel->setStyleSheet("font-weight: bold; color: red"); +} + + +bool QmitkTotalSegmentatorToolGUI::IsTotalSegmentatorInstalled(const QString &pythonPath) +{ + QString fullPath = pythonPath; +#ifdef _WIN32 + if (!(fullPath.endsWith("Scripts", Qt::CaseInsensitive) || fullPath.endsWith("Scripts/", Qt::CaseInsensitive))) + { + fullPath += QDir::separator() + QString("Scripts"); + } +#else + if (!(fullPath.endsWith("bin", Qt::CaseInsensitive) || fullPath.endsWith("bin/", Qt::CaseInsensitive))) + { + fullPath += QDir::separator() + QString("bin"); + } +#endif + fullPath = fullPath.mid(fullPath.indexOf(" ") + 1); + bool isExists = QFile::exists(fullPath + QDir::separator() + QString("TotalSegmentator")) && +#ifdef _WIN32 + QFile::exists(fullPath + QDir::separator() + QString("python.exe")); +#else + QFile::exists(fullPath + QDir::separator() + QString("python3")); +#endif + return isExists; +} + +void QmitkTotalSegmentatorToolGUI::AutoParsePythonPaths() +{ + + QString homeDir = QDir::homePath(); + std::vector searchDirs; +#ifdef _WIN32 + searchDirs.push_back(QString("C:") + QDir::separator() + QString("ProgramData") + QDir::separator() + + QString("anaconda3")); +#else + // Add search locations for possible standard python paths here + searchDirs.push_back(homeDir + QDir::separator() + "environments"); + searchDirs.push_back(homeDir + QDir::separator() + "anaconda3"); + searchDirs.push_back(homeDir + QDir::separator() + "miniconda3"); + searchDirs.push_back(homeDir + QDir::separator() + "opt" + QDir::separator() + "miniconda3"); + searchDirs.push_back(homeDir + QDir::separator() + "opt" + QDir::separator() + "anaconda3"); +#endif + for (QString searchDir : searchDirs) + { + if (searchDir.endsWith("anaconda3", Qt::CaseInsensitive)) + { + if (QDir(searchDir).exists()) + { + m_Controls.pythonEnvComboBox->insertItem(0, "(base): " + searchDir); + searchDir.append((QDir::separator() + QString("envs"))); + } + } + for (QDirIterator subIt(searchDir, QDir::AllDirs, QDirIterator::NoIteratorFlags); subIt.hasNext();) + { + subIt.next(); + QString envName = subIt.fileName(); + if (!envName.startsWith('.')) // Filter out irrelevent hidden folders, if any. + { + m_Controls.pythonEnvComboBox->insertItem(0, "(" + envName + "): " + subIt.filePath()); + } + } + } + m_Controls.pythonEnvComboBox->setCurrentIndex(-1); +} + +void QmitkTotalSegmentatorToolGUI::OnPythonPathChanged(const QString &pyEnv) +{ + if (pyEnv == QString("Select")) + { + QString path = + QFileDialog::getExistingDirectory(m_Controls.pythonEnvComboBox->parentWidget(), "Python Path", "dir"); + if (!path.isEmpty()) + { + this->OnPythonPathChanged(path); // recall same function for new path validation + bool oldState = m_Controls.pythonEnvComboBox->blockSignals(true); // block signal firing while inserting item + m_Controls.pythonEnvComboBox->insertItem(0, path); + m_Controls.pythonEnvComboBox->setCurrentIndex(0); + m_Controls.pythonEnvComboBox->blockSignals(oldState); // unblock signal firing after inserting item. Remove this after Qt6 migration + } + } + else if (!this->IsTotalSegmentatorInstalled(pyEnv)) + { + this->ShowErrorMessage(m_WARNING_TOTALSEG_NOT_FOUND); + m_Controls.previewButton->setDisabled(true); + } + else + { + // Show positive status meeage + m_Controls.previewButton->setDisabled(false); + m_PythonPath = pyEnv.mid(pyEnv.indexOf(" ") + 1); +#ifdef _WIN32 + if (!(m_PythonPath.endsWith("Scripts", Qt::CaseInsensitive) || + m_PythonPath.endsWith("Scripts/", Qt::CaseInsensitive))) + { + m_PythonPath += QDir::separator() + QString("Scripts"); + } +#else + if (!(m_PythonPath.endsWith("bin", Qt::CaseInsensitive) || m_PythonPath.endsWith("bin/", Qt::CaseInsensitive))) + { + m_PythonPath += QDir::separator() + QString("bin"); + } +#endif + } +} diff --git a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.h new file mode 100644 index 0000000000..c1ecf08e89 --- /dev/null +++ b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.h @@ -0,0 +1,101 @@ +#ifndef QmitkTotalSegmentatorToolGUI_h_Included +#define QmitkTotalSegmentatorToolGUI_h_Included + +#include "QmitkMultiLabelSegWithPreviewToolGUIBase.h" +#include "ui_QmitkTotalSegmentatorGUIControls.h" +#include +#include +#include "QmitknnUNetGPU.h" +#include + + +class MITKSEGMENTATIONUI_EXPORT QmitkTotalSegmentatorToolGUI : public QmitkMultiLabelSegWithPreviewToolGUIBase +{ + Q_OBJECT + +public: + mitkClassMacro(QmitkTotalSegmentatorToolGUI, QmitkMultiLabelSegWithPreviewToolGUIBase); + itkFactorylessNewMacro(Self); + itkCloneMacro(Self); + +protected slots : + + /** + * @brief Qt Slot + */ + void OnPreviewBtnClicked(); + + /** + * @brief Qt Slot + */ + void OnPythonPathChanged(const QString &); + +protected: + QmitkTotalSegmentatorToolGUI(); + ~QmitkTotalSegmentatorToolGUI() = default; + + void ConnectNewTool(mitk::SegWithPreviewTool* newTool) override; + void InitializeUI(QBoxLayout* mainLayout) override; + + void EnableWidgets(bool enabled) override; + + /** + * @brief Searches and parses paths of python virtual enviroments + * from predefined lookout locations + */ + void AutoParsePythonPaths(); + + /** + * @brief Checks if TotalSegmentator command is valid in the selected python virtual environment. + * + * @return bool + */ + bool IsTotalSegmentatorInstalled(const QString &); + + /** + * @brief Creates a QMessage object and shows on screen. + */ + void ShowErrorMessage(const std::string &, QMessageBox::Icon = QMessageBox::Critical); + + /** + * @brief Writes any message in white on the tool pane. + */ + void WriteStatusMessage(const QString &); + + /** + * @brief Writes any message in red on the tool pane. + */ + void WriteErrorMessage(const QString &); + + /** + * @brief Adds GPU information to the gpu combo box. + * In case, there aren't any GPUs avaialble, the combo box will be + * rendered editable. + */ + void SetGPUInfo(); + + /** + * @brief Returns GPU id of the selected GPU from the Combo box. + * + * @return unsigned int + */ + unsigned int FetchSelectedGPUFromUI(); + + /** + * @brief For storing values like Python path across sessions. + */ + QSettings m_Settings; + + QString m_PythonPath; + QmitkGPULoader m_GpuLoader; + Ui_QmitkTotalSegmentatorToolGUIControls m_Controls; + bool m_FirstPreviewComputation = true; + EnableConfirmSegBtnFunctionType m_SuperclassEnableConfirmSegBtnFnc; + + const std::string m_WARNING_TOTALSEG_NOT_FOUND = "TotalSegmentator is not detected in the selected python environment.Please select a valid " + "python environment or install TotalSegmentator."; + const QStringList m_VALID_TASKS = {"total", "cerebral_bleed", "hip_implant", "coronary_arteries"}; + +}; + +#endif diff --git a/Modules/SegmentationUI/files.cmake b/Modules/SegmentationUI/files.cmake index 08da87a365..60a3005397 100644 --- a/Modules/SegmentationUI/files.cmake +++ b/Modules/SegmentationUI/files.cmake @@ -1,102 +1,105 @@ 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/QmitkSurfaceBasedInterpolatorWidget.cpp Qmitk/QmitkSimpleLabelSetListWidget.cpp Qmitk/QmitkSegmentationTaskListWidget.cpp + Qmitk/QmitkTotalSegmentatorToolGUI.cpp SegmentationUtilities/QmitkBooleanOperationsWidget.cpp SegmentationUtilities/QmitkContourModelToImageWidget.cpp SegmentationUtilities/QmitkImageMaskingWidget.cpp SegmentationUtilities/QmitkMorphologicalOperationsWidget.cpp SegmentationUtilities/QmitkSurfaceToImageWidget.cpp SegmentationUtilities/QmitkSegmentationUtilityWidget.cpp SegmentationUtilities/QmitkDataSelectionWidget.cpp ) 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/QmitkSurfaceBasedInterpolatorWidget.h Qmitk/QmitkSimpleLabelSetListWidget.h Qmitk/QmitkSegmentationTaskListWidget.h + Qmitk/QmitkTotalSegmentatorToolGUI.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/QmitkSurfaceBasedInterpolatorWidgetGUIControls.ui Qmitk/QmitknnUNetToolGUIControls.ui Qmitk/QmitkEditableContourToolGUIControls.ui Qmitk/QmitkSegmentationTaskListWidget.ui + Qmitk/QmitkTotalSegmentatorGUIControls.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 ded0670f04..acc62fcc98 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp @@ -1,1125 +1,1125 @@ /*============================================================================ 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 #include // Qmitk #include #include #include // us #include #include // Qt #include #include #include // vtk #include #include 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"))); m_SegmentationInteractor = mitk::SegmentationInteractor::New(); // add observer for the 'SegmentationInteractionEvent' itk::ReceptorMemberCommand::Pointer geometryNotAlignedCommand = itk::ReceptorMemberCommand::New(); geometryNotAlignedCommand->SetCallbackFunction(this, &QmitkSegmentationView::ValidateRendererGeometry); m_SegmentationInteractor->AddObserver(mitk::SegmentationInteractionEvent(nullptr, true), geometryNotAlignedCommand); m_SegmentationInteractor->Disable(); } QmitkSegmentationView::~QmitkSegmentationView() { if (nullptr != m_Controls) { this->LooseLabelSetConnection(); // 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); } // Disconnect from current label set image this->LooseLabelSetConnection(); // Set new working node m_WorkingNode = selectedWorkingNode; m_ToolManager->SetWorkingData(m_WorkingNode); if (m_WorkingNode.IsNotNull()) { this->ApplySelectionModeOnWorkingNode(); // Connect to new label set image this->EstablishLabelSetConnection(); m_Controls->labelSetWidget->ResetAllTableWidgetItems(); // 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->SetReferenceGeometry(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::LabelSetIOHelper::LoadLabelSetImagePreset(labelSetPreset, newLabelSetImage)) { auto newLabel = mitk::LabelSetImageHelper::CreateNewLabel(newLabelSetImage); if (!m_DefaultLabelNaming) { QmitkNewSegmentationDialog dialog(m_Parent); dialog.SetName(QString::fromStdString(newLabel->GetName())); dialog.SetColor(newLabel->GetColor()); if (QDialog::Rejected == dialog.exec()) return; auto name = dialog.GetName(); if (!name.isEmpty()) newLabel->SetName(name.toStdString()); newLabel->SetColor(dialog.GetColor()); } 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::OnLayersChanged() { this->EstablishLabelSetConnection(); m_Controls->labelSetWidget->ResetAllTableWidgetItems(); } void QmitkSegmentationView::OnShowLabelTable(bool value) { m_Controls->labelSetWidget->setVisible(value); } void QmitkSegmentationView::OnGoToLabel(const mitk::Point3D& pos) { if (m_RenderWindowPart) { m_RenderWindowPart->SetSelectedPosition(pos); } } void QmitkSegmentationView::OnLabelSetWidgetReset() { this->ValidateSelectionInput(); } /**********************************************************************/ /* 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"); + QString segTools3D = tr("Threshold 'UL Threshold' Otsu 'Region Growing 3D' Picking GrowCut 'Total Segmentator'"); #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()); m_Controls->toolSelectionBox2D->SetLayoutColumns(3); 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->toolSelectionBox3D->SetLayoutColumns(3); 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->layersWidget, &QmitkLayersWidget::LayersChanged, this, &QmitkSegmentationView::OnLayersChanged); connect(m_Controls->labelsWidget, &QmitkLabelsWidget::ShowLabelTable, this, &QmitkSegmentationView::OnShowLabelTable); // *------------------------ // * LABELSETWIDGET // *------------------------ connect(m_Controls->labelSetWidget, &QmitkLabelSetWidget::goToLabel, this, &QmitkSegmentationView::OnGoToLabel); connect(m_Controls->labelSetWidget, &QmitkLabelSetWidget::LabelSetWidgetReset, this, &QmitkSegmentationView::OnLabelSetWidgetReset); m_Controls->labelSetWidget->SetDataStorage(this->GetDataStorage()); m_Controls->labelSetWidget->hide(); 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() { auto activeTool = m_ToolManager->GetActiveTool(); if (nullptr == activeTool) { // no tool activated, deactivate the segmentation interactor m_SegmentationInteractor->Disable(); return; } // activate segmentation interactor to get informed about render window entered / left events m_SegmentationInteractor->Enable(); } void QmitkSegmentationView::ValidateRendererGeometry(const itk::EventObject& event) { if (!mitk::SegmentationInteractionEvent().CheckEvent(&event)) { return; } const auto* segmentationInteractionEvent = dynamic_cast(&event); const mitk::BaseRenderer::Pointer sendingRenderer = segmentationInteractionEvent->GetSender(); if (nullptr == sendingRenderer) { return; } bool entered = segmentationInteractionEvent->HasEnteredRenderWindow(); if (entered) { // mouse cursor of tool inside render window // check if tool can be used: reference geometry needs to be aligned with renderer geometry const auto* referenceDataNode = m_ToolManager->GetReferenceData(0); if (nullptr != referenceDataNode) { const auto workingImage = dynamic_cast(referenceDataNode->GetData()); if (nullptr != workingImage) { const mitk::TimeGeometry* workingImageGeometry = workingImage->GetTimeGeometry(); if (nullptr != workingImageGeometry) { bool isGeometryAligned = false; try { isGeometryAligned = mitk::BaseRendererHelper::IsRendererAlignedWithSegmentation(sendingRenderer, workingImageGeometry); } catch (const mitk::Exception& e) { MITK_ERROR << "Unable to validate renderer geometry\n" << "Reason: " << e.GetDescription(); this->ShowRenderWindowWarning(sendingRenderer, true); this->UpdateWarningLabel( tr("Unable to validate renderer geometry. Please see log!")); return; } if (!isGeometryAligned) { this->ShowRenderWindowWarning(sendingRenderer, true); this->UpdateWarningLabel( tr("Please perform a reinit on the segmentation image inside the entered Render Window!")); return; } } } } } this->ShowRenderWindowWarning(sendingRenderer, false); this->UpdateWarningLabel(tr("")); } void QmitkSegmentationView::ShowRenderWindowWarning(mitk::BaseRenderer* baseRenderer, bool show) { const auto* rendererName = baseRenderer->GetName(); auto* renderWindow = m_RenderWindowPart->GetQmitkRenderWindow(rendererName); renderWindow->ShowOverlayMessage(show); } 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) { // tell the interpolation about tool manager, data storage and render window part QList controllers; controllers.push_back(m_RenderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); controllers.push_back(m_RenderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); controllers.push_back(m_RenderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); m_Controls->slicesInterpolator->Initialize(m_ToolManager, controllers); 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::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->labelsWidget->SetDefaultLabelNaming(m_DefaultLabelNaming); bool slimView = prefs->GetBool("slim view", false); m_Controls->toolSelectionBox2D->SetShowNames(!slimView); m_Controls->toolSelectionBox3D->SetShowNames(!slimView); } 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::EstablishLabelSetConnection() { if (m_WorkingNode.IsNull()) return; auto workingImage = dynamic_cast(m_WorkingNode->GetData()); if (nullptr == workingImage) return; workingImage->GetActiveLabelSet()->AddLabelEvent += mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->RemoveLabelEvent += mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->ModifyLabelEvent += mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->AllLabelsModifiedEvent += mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->ActiveLabelEvent += mitk::MessageDelegate1(m_Controls->labelSetWidget, &QmitkLabelSetWidget::SelectLabelByPixelValue); workingImage->AfterChangeLayerEvent += mitk::MessageDelegate( this, &QmitkSegmentationView::UpdateGUI); } void QmitkSegmentationView::LooseLabelSetConnection() { if (m_WorkingNode.IsNull()) return; auto workingImage = dynamic_cast(m_WorkingNode->GetData()); if (nullptr == workingImage) return; workingImage->GetActiveLabelSet()->AddLabelEvent -= mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->RemoveLabelEvent -= mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->ModifyLabelEvent -= mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->AllLabelsModifiedEvent -= mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->ActiveLabelEvent -= mitk::MessageDelegate1(m_Controls->labelSetWidget, &QmitkLabelSetWidget::SelectLabelByPixelValue); workingImage->AfterChangeLayerEvent -= mitk::MessageDelegate( this, &QmitkSegmentationView::UpdateGUI); } 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); } m_Controls->layersWidget->UpdateGUI(); m_Controls->labelsWidget->UpdateGUI(); 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->layersWidget->setEnabled(hasWorkingNode); m_Controls->labelsWidget->setEnabled(hasWorkingNode); m_Controls->labelSetWidget->setEnabled(hasWorkingNode); m_Controls->toolSelectionBox2D->setEnabled(hasBothNodes); m_Controls->toolSelectionBox3D->setEnabled(hasBothNodes); m_Controls->slicesInterpolator->setEnabled(false); m_Controls->interpolatorWarningLabel->hide(); if (hasReferenceNode) { if (!referenceNode->IsVisible(nullptr)) { warning += tr("The selected reference image is currently not visible!"); toolSelectionBoxesEnabled = false; } } if (hasWorkingNode) { if (!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->layersWidget->setEnabled(true); m_Controls->labelsWidget->setEnabled(true); m_Controls->labelSetWidget->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 > 1) m_Controls->slicesInterpolator->setEnabled(true); } toolSelectionBoxesEnabled &= numberOfLabels > 1; // 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. 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(); } } \ No newline at end of file