diff --git a/Modules/Segmentation/Interactions/mitknnUnetTool.cpp b/Modules/Segmentation/Interactions/mitknnUnetTool.cpp index 332713e16c..c6e522a8d4 100644 --- a/Modules/Segmentation/Interactions/mitknnUnetTool.cpp +++ b/Modules/Segmentation/Interactions/mitknnUnetTool.cpp @@ -1,325 +1,320 @@ /*============================================================================ 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 "mitknnUnetTool.h" #include "mitkIOUtil.h" #include "mitkProcessExecutor.h" #include #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, nnUNetTool, "nnUNet tool"); } mitk::nnUNetTool::nnUNetTool() { this->SetMitkTempDir(IOUtil::CreateTemporaryDirectory("mitk-XXXXXX")); } mitk::nnUNetTool::~nnUNetTool() { itksys::SystemTools::RemoveADirectory(this->GetMitkTempDir()); } void mitk::nnUNetTool::Activated() { Superclass::Activated(); this->SetLabelTransferMode(LabelTransferMode::AllLabels); } void mitk::nnUNetTool::RenderOutputBuffer() { if (m_OutputBuffer != nullptr) - { + { try { if (nullptr != this->GetPreviewSegmentationNode()) { - this->GetPreviewSegmentationNode()->SetVisibility(!this->GetSelectedLabels().empty()); - } - if (this->GetSelectedLabels().empty()) - { - this->ResetPreviewNode(); + auto previewImage = this->GetPreviewSegmentation(); + previewImage->InitializeByLabeledImage(m_OutputBuffer); } } catch (const mitk::Exception &e) { MITK_INFO << e.GetDescription(); } } } void mitk::nnUNetTool::SetOutputBuffer(LabelSetImage::Pointer segmentation) { m_OutputBuffer = segmentation; } mitk::LabelSetImage::Pointer mitk::nnUNetTool::GetOutputBuffer() { return m_OutputBuffer; } void mitk::nnUNetTool::ClearOutputBuffer() { m_OutputBuffer = nullptr; } us::ModuleResource mitk::nnUNetTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("AI_48x48.png"); return resource; } const char **mitk::nnUNetTool::GetXPM() const { return nullptr; } const char *mitk::nnUNetTool::GetName() const { return "nnUNet"; } mitk::DataStorage *mitk::nnUNetTool::GetDataStorage() { return this->GetToolManager()->GetDataStorage(); } mitk::DataNode *mitk::nnUNetTool::GetRefNode() { return this->GetToolManager()->GetReferenceData(0); } 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::nnUNetTool::DoUpdatePreview(const Image* inputAtTimeStep, const Image* /*oldSegAtTimeStep*/, LabelSetImage* previewImage, TimeStepType /*timeStep*/) { - if (m_InputBuffer == inputAtTimeStep) - { - return; - } - std::string inDir, outDir, inputImagePath, outputImagePath, scriptPath; ProcessExecutor::Pointer spExec = ProcessExecutor::New(); itk::CStyleCommand::Pointer spCommand = itk::CStyleCommand::New(); spCommand->SetCallback(&onPythonProcessEvent); spExec->AddObserver(ExternalProcessOutputEvent(), spCommand); ProcessExecutor::ArgumentListType args; inDir = IOUtil::CreateTemporaryDirectory("nnunet-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("_")); if (this->GetNoPip()) { scriptPath = this->GetnnUNetDirectory() + IOUtil::GetDirectorySeparator() + "nnunet" + IOUtil::GetDirectorySeparator() + "inference" + IOUtil::GetDirectorySeparator() + "predict_simple.py"; } try { if (this->GetMultiModal()) { const std::string fileFormat(".nii.gz"); const std::string fileNamePart("_000_000"); std::string outModalFile; size_t len = inDir.length() + 1 + token.length() + fileNamePart.length() + 1 + fileFormat.length(); outModalFile.reserve(len); // The 1(s) indicates a directory separator char and an underscore. for (size_t i = 0; i < m_OtherModalPaths.size(); ++i) { mitk::Image::ConstPointer modalImage = m_OtherModalPaths[i]; outModalFile.append(inDir); outModalFile.push_back(IOUtil::GetDirectorySeparator()); outModalFile.append(token); outModalFile.append(fileNamePart); outModalFile.append(std::to_string(i)); outModalFile.append(fileFormat); IOUtil::Save(modalImage.GetPointer(), outModalFile); outModalFile.clear(); } } else { IOUtil::Save(inputAtTimeStep, inputImagePath); } } catch (const mitk::Exception &e) { /* Can't throw mitk exception to the caller. Refer: T28691 */ MITK_ERROR << e.GetDescription(); return; } // Code calls external process std::string command = "nnUNet_predict"; if (this->GetNoPip()) { #ifdef _WIN32 command = "python"; #else command = "python3"; #endif } for (ModelParams &modelparam : m_ParamQ) { outDir = IOUtil::CreateTemporaryDirectory("nnunet-out-XXXXXX", this->GetMitkTempDir()); outputImagePath = outDir + IOUtil::GetDirectorySeparator() + token + "_000.nii.gz"; modelparam.outputDir = outDir; args.clear(); if (this->GetNoPip()) { args.push_back(scriptPath); } args.push_back("-i"); args.push_back(inDir); args.push_back("-o"); args.push_back(outDir); args.push_back("-t"); args.push_back(modelparam.task); if (modelparam.model.find("cascade") != std::string::npos) { args.push_back("-ctr"); } else { args.push_back("-tr"); } args.push_back(modelparam.trainer); args.push_back("-m"); args.push_back(modelparam.model); args.push_back("-p"); args.push_back(modelparam.planId); if (!modelparam.folds.empty()) { args.push_back("-f"); for (auto fold : modelparam.folds) { args.push_back(fold); } } args.push_back("--num_threads_nifti_save"); args.push_back("1"); // fixing to 1 if (!this->GetMirror()) { args.push_back("--disable_tta"); } if (!this->GetMixedPrecision()) { args.push_back("--disable_mixed_precision"); } if (this->GetEnsemble()) { args.push_back("--save_npz"); } try { std::string resultsFolderEnv = "RESULTS_FOLDER=" + this->GetModelDirectory(); itksys::SystemTools::PutEnv(resultsFolderEnv.c_str()); std::string cudaEnv = "CUDA_VISIBLE_DEVICES=" + std::to_string(this->GetGpuId()); itksys::SystemTools::PutEnv(cudaEnv.c_str()); spExec->Execute(this->GetPythonPath(), command, args); } catch (const mitk::Exception &e) { /* Can't throw mitk exception to the caller. Refer: T28691 */ MITK_ERROR << e.GetDescription(); return; } } if (this->GetEnsemble() && !this->GetPostProcessingJsonDirectory().empty()) { args.clear(); command = "nnUNet_ensemble"; outDir = IOUtil::CreateTemporaryDirectory("nnunet-ensemble-out-XXXXXX", this->GetMitkTempDir()); outputImagePath = outDir + IOUtil::GetDirectorySeparator() + token + "_000.nii.gz"; args.push_back("-f"); for (ModelParams &modelparam : m_ParamQ) { args.push_back(modelparam.outputDir); } args.push_back("-o"); args.push_back(outDir); if (!this->GetPostProcessingJsonDirectory().empty()) { args.push_back("-pp"); args.push_back(this->GetPostProcessingJsonDirectory()); } spExec->Execute(this->GetPythonPath(), command, args); } try { Image::Pointer outputImage = IOUtil::Load(outputImagePath); previewImage->InitializeByLabeledImage(outputImage); + previewImage->SetGeometry(inputAtTimeStep->GetGeometry()); m_InputBuffer = inputAtTimeStep; - m_OutputBuffer = previewImage; + m_OutputBuffer = mitk::LabelSetImage::New(); + m_OutputBuffer->InitializeByLabeledImage(outputImage); + m_OutputBuffer->SetGeometry(inputAtTimeStep->GetGeometry()); } catch (const mitk::Exception &e) { /* Can't throw mitk exception to the caller. Refer: T28691 */ MITK_ERROR << e.GetDescription(); return; } } diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetFolderParser.h b/Modules/SegmentationUI/Qmitk/QmitknnUNetFolderParser.h index 50e188bd8f..02eac9ea51 100644 --- a/Modules/SegmentationUI/Qmitk/QmitknnUNetFolderParser.h +++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetFolderParser.h @@ -1,301 +1,301 @@ /*============================================================================ 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.s ============================================================================*/ #ifndef QmitknnUNetFolderParser_h_Included #define QmitknnUNetFolderParser_h_Included #include "QmitknnUNetToolGUI.h" #include #include #include /** * @brief Struct to store each (Folder) Node of the hierarchy tree structure. * */ struct FolderNode { QString name; QString path; // parent std::vector> subFolders; }; /** * @brief Class to store and retreive folder hierarchy information * of RESULTS_FOLDER. Only Root node is explicitly stored in m_RootNode. * No. of sub levels in the hierachry is defined in the LEVEL constant. * */ class MITKSEGMENTATIONUI_EXPORT QmitknnUNetFolderParser { public: /** * @brief Construct a new QmitknnUNetFolderParser object * Initializes root folder node object pointer calls * @param parentFolder */ QmitknnUNetFolderParser(const QString parentFolder) { m_RootNode = std::make_shared(); m_RootNode->path = parentFolder; m_RootNode->name = QString("nnUNet"); m_RootNode->subFolders.clear(); InitDirs(m_RootNode, 0); } /** * @brief Destroy the QmitknnUNetFolderParser object * */ ~QmitknnUNetFolderParser() = default; /*{ DeleteDirs(m_RootNode, LEVEL); }*/ /** * @brief Returns the "Results Folder" string which is parent path of the root node. * * @return QString */ QString getResultsFolder() { return m_RootNode->path; } /** * @brief Returns the Model Names from root node. Template function, * type can be any of stl or Qt containers which supports push_back call. * * @tparam T * @return T (any of stl or Qt containers which supports push_back call) */ template T getModelNames() { auto models = GetSubFolderNamesFromNode(m_RootNode); return models; } /** * @brief Returns the task names for a given model. Template function, * type can be any of stl or Qt containers which supports push_back call. * * @tparam T * @param modelName * @return T (any of stl or Qt containers which supports push_back call) */ template T getTasksForModel(const QString &modelName) { std::shared_ptr modelNode = GetSubNodeMatchingNameCrietria(modelName, m_RootNode); auto tasks = GetSubFolderNamesFromNode(modelNode); return tasks; } /** * @brief Returns the models names for a given task. Template function, * type can be any of stl or Qt containers which supports push_back call. * * @tparam T * @param taskName * @return T (any of stl or Qt containers which supports push_back call) */ template T getModelsForTask(const QString &taskName) { T modelsForTask; auto models = GetSubFolderNamesFromNode(m_RootNode); foreach (QString model, models) { QStringList taskList = getTasksForModel(model); if (taskList.contains(taskName, Qt::CaseInsensitive)) { modelsForTask << model; } } return modelsForTask; } /** * @brief Returns all the task names present in the root node with possible duplicates. * Template function, type can be any of stl or Qt containers which supports push_back call. * - * @tparam T + * @param T * @param taskName * @return T (any of stl or Qt containers which supports push_back call) */ template T getAllTasks() { T allTasks; auto models = GetSubFolderNamesFromNode(m_RootNode); foreach (QString model, models) { allTasks << getTasksForModel(model); } return allTasks; } /** * @brief Returns the trainer / planner names for a given task & model. Template function, * type can be any of stl or Qt containers which supports push_back call. * * @tparam T * @param taskName * @param modelName * @return T (any of stl or Qt containers which supports push_back call) */ template T getTrainerPlannersForTask(const QString &taskName, const QString &modelName) { std::shared_ptr modelNode = GetSubNodeMatchingNameCrietria(modelName, m_RootNode); std::shared_ptr taskNode = GetSubNodeMatchingNameCrietria(taskName, modelNode); auto tps = GetSubFolderNamesFromNode(taskNode); return tps; } /** * @brief Returns the Folds names for a given trainer,planner,task & model name. Template function, * type can be any of stl or Qt containers which supports push_back call. * * @tparam T * @param trainer * @param planner * @param taskName * @param modelName * @return T (any of stl or Qt containers which supports push_back call) */ template T getFoldsForTrainerPlanner(const QString &trainer, const QString &planner, const QString &taskName, const QString &modelName) { std::shared_ptr modelNode = GetSubNodeMatchingNameCrietria(modelName, m_RootNode); std::shared_ptr taskNode = GetSubNodeMatchingNameCrietria(taskName, modelNode); QString trainerPlanner = trainer + QString("__") + planner; std::shared_ptr tpNode = GetSubNodeMatchingNameCrietria(trainerPlanner, taskNode); auto folds = GetSubFolderNamesFromNode(tpNode); return folds; } private: const int m_LEVEL = 4; std::shared_ptr m_RootNode; /** * @brief Iterates through the root node and returns the sub FolderNode object Matching Name Crietria * * @param queryName * @param parentNode * @return std::shared_ptr */ std::shared_ptr GetSubNodeMatchingNameCrietria(const QString &queryName, std::shared_ptr parentNode) { std::shared_ptr retNode; std::vector> subNodes = parentNode->subFolders; for (std::shared_ptr node : subNodes) { if (node->name == queryName) { retNode = node; break; } } return retNode; } /** * @brief Returns the sub folder names for a folder node object. Template function, * type can be any of stl or Qt containers which supports push_back call. * * @tparam T * @param std::shared_ptr * @return T (any of stl or Qt containers which supports push_back call) */ template T GetSubFolderNamesFromNode(const std::shared_ptr parent) { T folders; std::vector> subNodes = parent->subFolders; for (std::shared_ptr folder : subNodes) { folders.push_back(folder->name); } return folders; } /** * @brief Iterates through the sub folder hierarchy upto a level provided * and create a tree structure. * * @param parent * @param level */ void InitDirs(std::shared_ptr parent, int level) { QString searchFolder = parent->path + QDir::separator() + parent->name; auto subFolders = FetchFoldersFromDir(searchFolder); level++; foreach (QString folder, subFolders) { std::shared_ptr fp = std::make_shared(); fp->path = searchFolder; fp->name = folder; if (level < this->m_LEVEL) { InitDirs(fp, level); } parent->subFolders.push_back(fp); } } /** * @brief Iterates through the sub folder hierarchy upto a level provided * and clears the sub folder std::vector from each node. * * @param parent * @param level */ void DeleteDirs(std::shared_ptr parent, int level) { level++; for (std::shared_ptr subFolder : parent->subFolders) { if (level < m_LEVEL) { DeleteDirs(subFolder, level); } parent->subFolders.clear(); } } /** * @brief Template function to fetch all folders inside a given path. * The type can be any of stl or Qt containers which supports push_back call. * * @tparam T * @param path * @return T */ template T FetchFoldersFromDir(const QString &path) { T folders; for (QDirIterator it(path, QDir::AllDirs, QDirIterator::NoIteratorFlags); it.hasNext();) { it.next(); if (!it.fileName().startsWith('.')) { folders.push_back(it.fileName()); } } return folders; } }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp index 60143756e3..f6420e861a 100644 --- a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp @@ -1,578 +1,579 @@ /*============================================================================ 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 "QmitknnUNetToolGUI.h" #include "mitkProcessExecutor.h" #include "mitknnUnetTool.h" #include #include #include #include #include #include #include #include MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitknnUNetToolGUI, "") QmitknnUNetToolGUI::QmitknnUNetToolGUI() : QmitkMultiLabelSegWithPreviewToolGUIBase() { // 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 nnUNet tool might not work."; ShowErrorMessage(warning); } // define predicates for multi modal data selection combobox auto imageType = mitk::TNodePredicateDataType::New(); auto labelSetImageType = mitk::NodePredicateNot::New(mitk::TNodePredicateDataType::New()); m_MultiModalPredicate = mitk::NodePredicateAnd::New(imageType, labelSetImageType).GetPointer(); } void QmitknnUNetToolGUI::ConnectNewTool(mitk::SegWithPreviewTool *newTool) { Superclass::ConnectNewTool(newTool); newTool->IsTimePointChangeAwareOff(); } void QmitknnUNetToolGUI::InitializeUI(QBoxLayout *mainLayout) { m_Controls.setupUi(this); #ifndef _WIN32 m_Controls.pythonEnvComboBox->addItem("/usr/bin"); #endif m_Controls.pythonEnvComboBox->addItem("Select"); AutoParsePythonPaths(); SetGPUInfo(); connect(m_Controls.previewButton, SIGNAL(clicked()), this, SLOT(OnPreviewRequested())); connect(m_Controls.modeldirectoryBox, SIGNAL(directoryChanged(const QString &)), this, SLOT(OnDirectoryChanged(const QString &))); connect( m_Controls.modelBox, SIGNAL(currentTextChanged(const QString &)), this, SLOT(OnModelChanged(const QString &))); connect(m_Controls.taskBox, SIGNAL(currentTextChanged(const QString &)), this, SLOT(OnTaskChanged(const QString &))); connect( m_Controls.plannerBox, SIGNAL(currentTextChanged(const QString &)), this, SLOT(OnTrainerChanged(const QString &))); connect(m_Controls.multiModalBox, SIGNAL(stateChanged(int)), this, SLOT(OnCheckBoxChanged(int))); connect(m_Controls.multiModalSpinBox, SIGNAL(valueChanged(int)), this, SLOT(OnModalitiesNumberChanged(int))); connect(m_Controls.pythonEnvComboBox, #if QT_VERSION >= 0x050F00 // 5.15 SIGNAL(textActivated(const QString &)), #elif QT_VERSION >= 0x050C00 // 5.12 SIGNAL(currentTextChanged(const QString &)), #endif this, SLOT(OnPythonPathChanged(const QString &))); connect(m_Controls.refreshdirectoryBox, SIGNAL(clicked()), this, SLOT(OnRefreshPresssed())); connect(m_Controls.clearCacheButton, SIGNAL(clicked()), this, SLOT(OnClearCachePressed())); m_Controls.multiModalSpinBox->setVisible(false); m_Controls.multiModalSpinBox->setEnabled(false); m_Controls.multiModalSpinLabel->setVisible(false); m_Controls.previewButton->setEnabled(false); QIcon refreshIcon = QmitkStyleManager::ThemeIcon(QStringLiteral(":/org_mitk_icons/icons/awesome/scalable/actions/view-refresh.svg")); m_Controls.refreshdirectoryBox->setIcon(refreshIcon); QIcon dirIcon = QmitkStyleManager::ThemeIcon(QStringLiteral(":/org_mitk_icons/icons/awesome/scalable/actions/document-open.svg")); m_Controls.modeldirectoryBox->setIcon(dirIcon); m_Controls.refreshdirectoryBox->setEnabled(true); m_Controls.statusLabel->setTextFormat(Qt::RichText); if (m_GpuLoader.GetGPUCount() != 0) { WriteStatusMessage(QString("STATUS: Welcome to nnUNet. " + QString::number(m_GpuLoader.GetGPUCount()) + " GPUs were detected.")); } else { WriteErrorMessage(QString("STATUS: Welcome to nnUNet. " + QString::number(m_GpuLoader.GetGPUCount()) + " GPUs were detected.")); } mainLayout->addLayout(m_Controls.verticalLayout); Superclass::InitializeUI(mainLayout); m_UI_ROWS = m_Controls.advancedSettingsLayout->rowCount(); // Must do. Row count is correct only here. DisableEverything(); QString lastSelectedPyEnv = m_Settings.value("nnUNet/LastPythonPath").toString(); m_Controls.pythonEnvComboBox->setCurrentText(lastSelectedPyEnv); } void QmitknnUNetToolGUI::OnPreviewRequested() { mitk::nnUNetTool::Pointer tool = this->GetConnectedToolAs(); if (nullptr != tool) { QString pythonPathTextItem = ""; try { size_t hashKey(0); m_Controls.previewButton->setEnabled(false); // To prevent misclicked back2back prediction. qApp->processEvents(); tool->PredictOn(); // purposefully placed to make tool->GetMTime different than before. QString modelName = m_Controls.modelBox->currentText(); if (modelName.startsWith("ensemble", Qt::CaseInsensitive)) { ProcessEnsembleModelsParams(tool); } else { ProcessModelParams(tool); } pythonPathTextItem = m_Controls.pythonEnvComboBox->currentText(); QString pythonPath = m_PythonPath; if (!IsNNUNetInstalled(pythonPath)) { throw std::runtime_error("nnUNet is not detected in the selected python environment. Please select a valid " "python environment or install nnUNet."); } tool->SetPythonPath(pythonPath.toStdString()); tool->SetModelDirectory(m_ParentFolder->getResultsFolder().toStdString()); // checkboxes tool->SetMirror(m_Controls.mirrorBox->isChecked()); tool->SetMixedPrecision(m_Controls.mixedPrecisionBox->isChecked()); tool->SetNoPip(false); bool doCache = m_Controls.enableCachingCheckBox->isChecked(); // Spinboxes tool->SetGpuId(FetchSelectedGPUFromUI()); // Multi-Modal tool->MultiModalOff(); if (m_Controls.multiModalBox->isChecked()) { if (m_Controls.multiModalSpinBox->value() > 0) { tool->m_OtherModalPaths.clear(); tool->m_OtherModalPaths = FetchMultiModalImagesFromUI(); tool->MultiModalOn(); } else { throw std::runtime_error("Please select more than one modalities for a multi-modal task. If you " "would like to use only one modality then uncheck the Multi-Modal option."); } } if (doCache) { hashKey = nnUNetCache::GetUniqueHash(tool->m_ParamQ); if (m_Cache.contains(hashKey)) { tool->PredictOff(); // purposefully placed to make tool->GetMTime different than before. } } if (tool->GetPredict()) { tool->m_InputBuffer = nullptr; WriteStatusMessage(QString("STATUS: Starting Segmentation task... This might take a while.")); tool->UpdatePreview(); if (nullptr == tool->GetOutputBuffer()) { SegmentationProcessFailed(); } else - { + { SegmentationResultHandler(tool); if (doCache) { - AddToCache(hashKey, tool->GetPreviewSegmentation()); + AddToCache(hashKey, tool->GetOutputBuffer()); } + tool->ClearOutputBuffer(); } tool->PredictOff(); // purposefully placed to make tool->GetMTime different than before. } else { MITK_INFO << "won't do segmentation. Key found: " << QString::number(hashKey).toStdString(); if (m_Cache.contains(hashKey)) { nnUNetCache *cacheObject = m_Cache[hashKey]; MITK_INFO << "fetched pointer " << cacheObject->m_SegCache.GetPointer(); tool->SetOutputBuffer(const_cast(cacheObject->m_SegCache.GetPointer())); SegmentationResultHandler(tool, true); } } m_Controls.previewButton->setEnabled(true); } catch (const std::exception &e) { std::stringstream errorMsg; errorMsg << "STATUS: Error while processing parameters for nnUNet segmentation. Reason: " << e.what(); ShowErrorMessage(errorMsg.str()); WriteErrorMessage(QString::fromStdString(errorMsg.str())); m_Controls.previewButton->setEnabled(true); tool->PredictOff(); return; } catch (...) { std::string errorMsg = "Unkown error occured while generation nnUNet segmentation."; ShowErrorMessage(errorMsg); m_Controls.previewButton->setEnabled(true); tool->PredictOff(); return; } if (!pythonPathTextItem.isEmpty()) { // only cache if the prediction ended without errors. m_Settings.setValue("nnUNet/LastPythonPath", pythonPathTextItem); } } } std::vector QmitknnUNetToolGUI::FetchMultiModalImagesFromUI() { std::vector modals; if (m_Controls.multiModalBox->isChecked() && !m_Modalities.empty()) { std::set nodeNames; // set container for keeping names of all nodes to check if they are added twice. for (QmitkDataStorageComboBox *modality : m_Modalities) { if (nodeNames.find(modality->GetSelectedNode()->GetName()) == nodeNames.end()) { modals.push_back(dynamic_cast(modality->GetSelectedNode()->GetData())); nodeNames.insert(modality->GetSelectedNode()->GetName()); } else { throw std::runtime_error("Same modality is selected more than once. Please change your selection."); break; } } } return modals; } bool QmitknnUNetToolGUI::IsNNUNetInstalled(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("nnUNet_predict")) && QFile::exists(fullPath + QDir::separator() + QString("python3")); return isExists; } void QmitknnUNetToolGUI::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 QmitknnUNetToolGUI::WriteStatusMessage(const QString &message) { m_Controls.statusLabel->setText(message); m_Controls.statusLabel->setStyleSheet("font-weight: bold; color: white"); } void QmitknnUNetToolGUI::WriteErrorMessage(const QString &message) { m_Controls.statusLabel->setText(message); m_Controls.statusLabel->setStyleSheet("font-weight: bold; color: red"); } void QmitknnUNetToolGUI::ProcessEnsembleModelsParams(mitk::nnUNetTool::Pointer tool) { if (m_EnsembleParams[0]->modelBox->currentText() == m_EnsembleParams[1]->modelBox->currentText()) { throw std::runtime_error("Both models you have selected for ensembling are the same."); } QString taskName = m_Controls.taskBox->currentText(); bool isPPJson = m_Controls.postProcessingCheckBox->isChecked(); std::vector requestQ; QString ppDirFolderNamePart1 = "ensemble_"; QStringList ppDirFolderNameParts; for (auto &layout : m_EnsembleParams) { QStringList ppDirFolderName; QString modelName = layout->modelBox->currentText(); ppDirFolderName << modelName; ppDirFolderName << "__"; QString trainer = layout->trainerBox->currentText(); ppDirFolderName << trainer; ppDirFolderName << "__"; QString planId = layout->plannerBox->currentText(); ppDirFolderName << planId; if (!IsModelExists(modelName, taskName, QString(trainer + "__" + planId))) { std::string errorMsg = "The configuration " + modelName.toStdString() + " you have selected doesn't exist. Check your Results Folder again."; throw std::runtime_error(errorMsg); } std::vector testfold = FetchSelectedFoldsFromUI(layout->foldBox); mitk::ModelParams modelObject = MapToRequest(modelName, taskName, trainer, planId, testfold); requestQ.push_back(modelObject); ppDirFolderNameParts << ppDirFolderName.join(QString("")); } tool->EnsembleOn(); if (isPPJson) { QString ppJsonFilePossibility1 = QDir::cleanPath( m_ParentFolder->getResultsFolder() + QDir::separator() + "nnUNet" + QDir::separator() + "ensembles" + QDir::separator() + taskName + QDir::separator() + ppDirFolderNamePart1 + ppDirFolderNameParts.first() + "--" + ppDirFolderNameParts.last() + QDir::separator() + "postprocessing.json"); QString ppJsonFilePossibility2 = QDir::cleanPath( m_ParentFolder->getResultsFolder() + QDir::separator() + "nnUNet" + QDir::separator() + "ensembles" + QDir::separator() + taskName + QDir::separator() + ppDirFolderNamePart1 + ppDirFolderNameParts.last() + "--" + ppDirFolderNameParts.first() + QDir::separator() + "postprocessing.json"); if (QFile(ppJsonFilePossibility1).exists()) { tool->SetPostProcessingJsonDirectory(ppJsonFilePossibility1.toStdString()); const QString statusMsg = "Post Processing JSON file found: " + ppJsonFilePossibility1; WriteStatusMessage(statusMsg); } else if (QFile(ppJsonFilePossibility2).exists()) { tool->SetPostProcessingJsonDirectory(ppJsonFilePossibility2.toStdString()); const QString statusMsg = "Post Processing JSON file found:" + ppJsonFilePossibility2; WriteStatusMessage(statusMsg); } else { std::string errorMsg = "No post processing file was found for the selected ensemble combination. Continuing anyway..."; ShowErrorMessage(errorMsg); } } tool->m_ParamQ.clear(); tool->m_ParamQ = requestQ; } void QmitknnUNetToolGUI::ProcessModelParams(mitk::nnUNetTool::Pointer tool) { tool->EnsembleOff(); std::vector requestQ; QString modelName = m_Controls.modelBox->currentText(); QString taskName = m_Controls.taskBox->currentText(); QString trainer = m_Controls.trainerBox->currentText(); QString planId = m_Controls.plannerBox->currentText(); std::vector fetchedFolds = FetchSelectedFoldsFromUI(m_Controls.foldBox); mitk::ModelParams modelObject = MapToRequest(modelName, taskName, trainer, planId, fetchedFolds); requestQ.push_back(modelObject); tool->m_ParamQ.clear(); tool->m_ParamQ = requestQ; } bool QmitknnUNetToolGUI::IsModelExists(const QString &modelName, const QString &taskName, const QString &trainerPlanner) { QString modelSearchPath = QDir::cleanPath(m_ParentFolder->getResultsFolder() + QDir::separator() + "nnUNet" + QDir::separator() + modelName + QDir::separator() + taskName + QDir::separator() + trainerPlanner); if (QDir(modelSearchPath).exists()) { return true; } return false; } void QmitknnUNetToolGUI::CheckAllInCheckableComboBox(ctkCheckableComboBox *foldBox) { // Recalling all added items to check-mark it. const QAbstractItemModel *qaim = foldBox->checkableModel(); auto rows = qaim->rowCount(); for (std::remove_const_t i = 0; i < rows; ++i) { const QModelIndex mi = qaim->index(i, 0); foldBox->setCheckState(mi, Qt::Checked); } } std::pair QmitknnUNetToolGUI::ExtractTrainerPlannerFromString(QStringList trainerPlanners) { QString splitterString = "__"; QStringList trainers, planners; for (const auto &trainerPlanner : trainerPlanners) { trainers << trainerPlanner.split(splitterString, QString::SplitBehavior::SkipEmptyParts).first(); planners << trainerPlanner.split(splitterString, QString::SplitBehavior::SkipEmptyParts).last(); } trainers.removeDuplicates(); planners.removeDuplicates(); return std::make_pair(trainers, planners); } std::vector QmitknnUNetToolGUI::FetchSelectedFoldsFromUI(ctkCheckableComboBox *foldBox) { std::vector folds; if (foldBox->noneChecked()) { CheckAllInCheckableComboBox(foldBox); } QModelIndexList foldList = foldBox->checkedIndexes(); for (const auto &index : foldList) { QString foldQString = foldBox->itemText(index.row()).split("_", QString::SplitBehavior::SkipEmptyParts).last(); folds.push_back(foldQString.toStdString()); } return folds; } void QmitknnUNetToolGUI::OnClearCachePressed() { m_Cache.clear(); UpdateCacheCountOnUI(); } void QmitknnUNetToolGUI::UpdateCacheCountOnUI() { QString cacheText = m_CACHE_COUNT_BASE_LABEL + QString::number(m_Cache.size()); m_Controls.cacheCountLabel->setText(cacheText); } void QmitknnUNetToolGUI::AddToCache(size_t &hashKey, mitk::LabelSetImage::ConstPointer mlPreview) { nnUNetCache *newCacheObj = new nnUNetCache; newCacheObj->m_SegCache = mlPreview; m_Cache.insert(hashKey, newCacheObj); MITK_INFO << "New hash: " << hashKey << " " << newCacheObj->m_SegCache.GetPointer(); UpdateCacheCountOnUI(); } void QmitknnUNetToolGUI::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 QmitknnUNetToolGUI::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()); } } QString QmitknnUNetToolGUI::FetchResultsFolderFromEnv() { const char *pathVal = itksys::SystemTools::GetEnv("RESULTS_FOLDER"); QString retVal; if (pathVal) { retVal = QString::fromUtf8(pathVal); } else { retVal = m_Settings.value("nnUNet/LastRESULTS_FOLDERPath").toString(); } return retVal; } QString QmitknnUNetToolGUI::DumpJSONfromPickle(const QString &parentPath) { const QString picklePath = parentPath + QDir::separator() + QString("plans.pkl"); const QString jsonPath = parentPath + QDir::separator() + QString("mitk_export.json"); if (!QFile::exists(jsonPath)) { mitk::ProcessExecutor::Pointer spExec = mitk::ProcessExecutor::New(); itk::CStyleCommand::Pointer spCommand = itk::CStyleCommand::New(); mitk::ProcessExecutor::ArgumentListType args; args.push_back("-c"); std::string pythonCode; // python syntax to parse plans.pkl file and export as Json file. pythonCode.append("import pickle;"); pythonCode.append("import json;"); pythonCode.append("loaded_pickle = pickle.load(open('"); pythonCode.append(picklePath.toStdString()); pythonCode.append("','rb'));"); pythonCode.append("modal_dict = {key: loaded_pickle[key] for key in loaded_pickle.keys() if key in " "['modalities','num_modalities']};"); pythonCode.append("json.dump(modal_dict, open('"); pythonCode.append(jsonPath.toStdString()); pythonCode.append("', 'w'))"); args.push_back(pythonCode); try { spExec->Execute(m_PythonPath.toStdString(), "python3", args); } catch (const mitk::Exception &e) { MITK_ERROR << "Pickle parsing FAILED!" << e.GetDescription(); // SHOW ERROR WriteStatusMessage( "Parsing failed in backend. Multiple Modalities will now have to be manually entered by the user."); return QString(""); } } return jsonPath; } void QmitknnUNetToolGUI::DisplayMultiModalInfoFromJSON(const QString &jsonPath) { std::ifstream file(jsonPath.toStdString()); if (file.is_open()) { auto jsonObj = nlohmann::json::parse(file, nullptr, false); if (jsonObj.is_discarded() || !jsonObj.is_object()) { MITK_ERROR << "Could not parse \"" << jsonPath.toStdString() << "\" as JSON object!"; return; } auto num_mods = jsonObj["num_modalities"].get(); ClearAllModalLabels(); if (num_mods > 1) { m_Controls.multiModalBox->setChecked(true); m_Controls.multiModalBox->setEnabled(false); m_Controls.multiModalSpinBox->setValue(num_mods - 1); m_Controls.advancedSettingsLayout->update(); auto obj = jsonObj["modalities"]; int count = 0; for (const auto& value : obj) { QLabel *label = new QLabel(QString::fromStdString("" + value.get() + ""), this); m_ModalLabels.push_back(label); m_Controls.advancedSettingsLayout->addWidget(label, m_UI_ROWS + 1 + count, 0); count++; } m_Controls.multiModalSpinBox->setMinimum(num_mods - 1); m_Controls.advancedSettingsLayout->update(); } else { m_Controls.multiModalSpinBox->setMinimum(0); m_Controls.multiModalBox->setChecked(false); } } } diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolSlots.cpp b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolSlots.cpp index 1b1308af45..130c1ef22f 100644 --- a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolSlots.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolSlots.cpp @@ -1,478 +1,479 @@ #include "QmitknnUNetToolGUI.h" #include #include #include #include #include void QmitknnUNetToolGUI::EnableWidgets(bool enabled) { Superclass::EnableWidgets(enabled); } void QmitknnUNetToolGUI::ClearAllModalities() { m_Controls.multiModalSpinBox->setMinimum(0); m_Controls.multiModalBox->setChecked(false); ClearAllModalLabels(); } void QmitknnUNetToolGUI::ClearAllModalLabels() { for (auto modalLabel : m_ModalLabels) { delete modalLabel; // delete the layout item m_ModalLabels.pop_back(); } m_Controls.advancedSettingsLayout->update(); } void QmitknnUNetToolGUI::DisableEverything() { m_Controls.modeldirectoryBox->setEnabled(false); m_Controls.refreshdirectoryBox->setEnabled(false); m_Controls.previewButton->setEnabled(false); m_Controls.multiModalSpinBox->setVisible(false); m_Controls.multiModalBox->setEnabled(false); ClearAllComboBoxes(); ClearAllModalities(); } void QmitknnUNetToolGUI::ClearAllComboBoxes() { m_Controls.modelBox->clear(); m_Controls.taskBox->clear(); m_Controls.foldBox->clear(); m_Controls.trainerBox->clear(); m_Controls.plannerBox->clear(); for (auto &layout : m_EnsembleParams) { layout->modelBox->clear(); layout->trainerBox->clear(); layout->plannerBox->clear(); layout->foldBox->clear(); } } void QmitknnUNetToolGUI::OnRefreshPresssed() { const QString resultsFolder = m_Controls.modeldirectoryBox->directory(); OnDirectoryChanged(resultsFolder); } void QmitknnUNetToolGUI::OnDirectoryChanged(const QString &resultsFolder) { m_Controls.previewButton->setEnabled(false); ClearAllComboBoxes(); ClearAllModalities(); m_ParentFolder = std::make_shared(resultsFolder); auto tasks = m_ParentFolder->getAllTasks(); tasks.removeDuplicates(); std::for_each(tasks.begin(), tasks.end(), [this](QString task) { m_Controls.taskBox->addItem(task); }); m_Settings.setValue("nnUNet/LastRESULTS_FOLDERPath", resultsFolder); } void QmitknnUNetToolGUI::OnModelChanged(const QString &model) { if (model.isEmpty()) { return; } ClearAllModalities(); auto selectedTask = m_Controls.taskBox->currentText(); ctkComboBox *box = qobject_cast(sender()); if (box == m_Controls.modelBox) { if (model == m_VALID_MODELS.last()) { m_Controls.trainerBox->setVisible(false); m_Controls.trainerLabel->setVisible(false); m_Controls.plannerBox->setVisible(false); m_Controls.plannerLabel->setVisible(false); m_Controls.foldBox->setVisible(false); m_Controls.foldLabel->setVisible(false); ShowEnsembleLayout(true); auto models = m_ParentFolder->getModelsForTask(m_Controls.taskBox->currentText()); models.removeDuplicates(); models.removeOne(m_VALID_MODELS.last()); for (auto &layout : m_EnsembleParams) { layout->modelBox->clear(); layout->trainerBox->clear(); layout->plannerBox->clear(); std::for_each(models.begin(), models.end(), [&layout, this](QString model) { if (m_VALID_MODELS.contains(model, Qt::CaseInsensitive)) layout->modelBox->addItem(model); }); } m_Controls.previewButton->setEnabled(true); } else { m_Controls.trainerBox->setVisible(true); m_Controls.trainerLabel->setVisible(true); m_Controls.plannerBox->setVisible(true); m_Controls.plannerLabel->setVisible(true); m_Controls.foldBox->setVisible(true); m_Controls.foldLabel->setVisible(true); m_Controls.previewButton->setEnabled(false); ShowEnsembleLayout(false); auto trainerPlanners = m_ParentFolder->getTrainerPlannersForTask(selectedTask, model); QStringList trainers, planners; std::tie(trainers, planners) = ExtractTrainerPlannerFromString(trainerPlanners); m_Controls.trainerBox->clear(); m_Controls.plannerBox->clear(); std::for_each( trainers.begin(), trainers.end(), [this](QString trainer) { m_Controls.trainerBox->addItem(trainer); }); std::for_each( planners.begin(), planners.end(), [this](QString planner) { m_Controls.plannerBox->addItem(planner); }); } } else if (!m_EnsembleParams.empty()) { for (auto &layout : m_EnsembleParams) { if (box == layout->modelBox) { layout->trainerBox->clear(); layout->plannerBox->clear(); auto trainerPlanners = m_ParentFolder->getTrainerPlannersForTask(selectedTask, model); QStringList trainers, planners; std::tie(trainers, planners) = ExtractTrainerPlannerFromString(trainerPlanners); std::for_each(trainers.begin(), trainers.end(), [&layout](const QString &trainer) { layout->trainerBox->addItem(trainer); }); std::for_each(planners.begin(), planners.end(), [&layout](const QString &planner) { layout->plannerBox->addItem(planner); }); break; } } } } void QmitknnUNetToolGUI::OnTaskChanged(const QString &task) { if (task.isEmpty()) { return; } m_Controls.modelBox->clear(); auto models = m_ParentFolder->getModelsForTask(task); models.removeDuplicates(); if (!models.contains(m_VALID_MODELS.last(), Qt::CaseInsensitive)) { models << m_VALID_MODELS.last(); // add ensemble even if folder doesn't exist } std::for_each(models.begin(), models.end(), [this](QString model) { if (m_VALID_MODELS.contains(model, Qt::CaseInsensitive)) m_Controls.modelBox->addItem(model); }); } void QmitknnUNetToolGUI::OnTrainerChanged(const QString &plannerSelected) { if (plannerSelected.isEmpty()) { return; } auto *box = qobject_cast(sender()); if (box == m_Controls.plannerBox) { m_Controls.foldBox->clear(); auto selectedTrainer = m_Controls.trainerBox->currentText(); auto selectedTask = m_Controls.taskBox->currentText(); auto selectedModel = m_Controls.modelBox->currentText(); auto folds = m_ParentFolder->getFoldsForTrainerPlanner( selectedTrainer, plannerSelected, selectedTask, selectedModel); std::for_each(folds.begin(), folds.end(), [this](QString fold) { if (fold.startsWith("fold_", Qt::CaseInsensitive)) // imposed by nnUNet m_Controls.foldBox->addItem(fold); }); if (m_Controls.foldBox->count() != 0) { CheckAllInCheckableComboBox(m_Controls.foldBox); m_Controls.previewButton->setEnabled(true); const QString parentPath = QDir::cleanPath(m_ParentFolder->getResultsFolder() + QDir::separator() + "nnUNet" + QDir::separator() + selectedModel + QDir::separator() + selectedTask + QDir::separator() + selectedTrainer + QString("__") + plannerSelected); const QString jsonPath = this->DumpJSONfromPickle(parentPath); if (!jsonPath.isEmpty()) { this->DisplayMultiModalInfoFromJSON(jsonPath); } } } else if (!m_EnsembleParams.empty()) { for (auto &layout : m_EnsembleParams) { if (box == layout->plannerBox) { layout->foldBox->clear(); auto selectedTrainer = layout->trainerBox->currentText(); auto selectedTask = m_Controls.taskBox->currentText(); auto selectedModel = layout->modelBox->currentText(); auto folds = m_ParentFolder->getFoldsForTrainerPlanner( selectedTrainer, plannerSelected, selectedTask, selectedModel); std::for_each(folds.begin(), folds.end(), [&layout](const QString &fold) { if (fold.startsWith("fold_", Qt::CaseInsensitive)) // imposed by nnUNet layout->foldBox->addItem(fold); }); if (layout->foldBox->count() != 0) { CheckAllInCheckableComboBox(layout->foldBox); m_Controls.previewButton->setEnabled(true); const QString parentPath = QDir::cleanPath( m_ParentFolder->getResultsFolder() + QDir::separator() + "nnUNet" + QDir::separator() + selectedModel + QDir::separator() + selectedTask + QDir::separator() + selectedTrainer + QString("__") + plannerSelected); const QString jsonPath = this->DumpJSONfromPickle(parentPath); if (!jsonPath.isEmpty()) { this->DisplayMultiModalInfoFromJSON(jsonPath); } } break; } } } } void QmitknnUNetToolGUI::OnPythonPathChanged(const QString &pyEnv) { if (pyEnv == QString("Select")) { QString path = QFileDialog::getExistingDirectory(m_Controls.pythonEnvComboBox->parentWidget(), "Python Path", "dir"); if (!path.isEmpty()) { OnPythonPathChanged(path); // recall same function for new path validation m_Controls.pythonEnvComboBox->insertItem(0, path); m_Controls.pythonEnvComboBox->setCurrentIndex(0); } } else if (!IsNNUNetInstalled(pyEnv)) { std::string warning = "WARNING: nnUNet is not detected on the Python environment you selected. Please select another " "environment or create one. For more info refer https://github.com/MIC-DKFZ/nnUNet"; ShowErrorMessage(warning); DisableEverything(); } else { m_Controls.modeldirectoryBox->setEnabled(true); m_Controls.previewButton->setEnabled(true); m_Controls.refreshdirectoryBox->setEnabled(true); m_Controls.multiModalBox->setEnabled(true); QString setVal = FetchResultsFolderFromEnv(); if (!setVal.isEmpty()) { m_Controls.modeldirectoryBox->setDirectory(setVal); } OnRefreshPresssed(); m_PythonPath = pyEnv.mid(pyEnv.indexOf(" ") + 1); if (!(m_PythonPath.endsWith("bin", Qt::CaseInsensitive) || m_PythonPath.endsWith("bin/", Qt::CaseInsensitive))) { m_PythonPath += QDir::separator() + QString("bin"); } } } void QmitknnUNetToolGUI::OnCheckBoxChanged(int state) { bool visibility = false; if (state == Qt::Checked) { visibility = true; } ctkCheckBox *box = qobject_cast(sender()); if (box != nullptr) { if (box->objectName() == QString("multiModalBox")) { m_Controls.multiModalSpinLabel->setVisible(visibility); m_Controls.multiModalSpinBox->setVisible(visibility); if (visibility) { QmitkDataStorageComboBox *defaultImage = new QmitkDataStorageComboBox(this, true); defaultImage->setObjectName(QString("multiModal_" + QString::number(0))); defaultImage->SetPredicate(m_MultiModalPredicate); mitk::nnUNetTool::Pointer tool = this->GetConnectedToolAs(); if (tool != nullptr) { defaultImage->SetDataStorage(tool->GetDataStorage()); defaultImage->SetSelectedNode(tool->GetRefNode()); } m_Controls.advancedSettingsLayout->addWidget(defaultImage, m_UI_ROWS + m_Modalities.size() + 1, 1, 1, 3); m_Modalities.push_back(defaultImage); } else { OnModalitiesNumberChanged(0); m_Controls.multiModalSpinBox->setValue(0); delete m_Modalities[0]; m_Modalities.pop_back(); ClearAllModalLabels(); } } } } void QmitknnUNetToolGUI::OnModalitiesNumberChanged(int num) { while (num > static_cast(m_Modalities.size() - 1)) { QmitkDataStorageComboBox *multiModalBox = new QmitkDataStorageComboBox(this, true); mitk::nnUNetTool::Pointer tool = this->GetConnectedToolAs(); multiModalBox->SetDataStorage(tool->GetDataStorage()); multiModalBox->SetPredicate(m_MultiModalPredicate); multiModalBox->setObjectName(QString("multiModal_" + QString::number(m_Modalities.size() + 1))); m_Controls.advancedSettingsLayout->addWidget(multiModalBox, m_UI_ROWS + m_Modalities.size() + 1, 1, 1, 3); m_Modalities.push_back(multiModalBox); } while (num < static_cast(m_Modalities.size() - 1) && !m_Modalities.empty()) { QmitkDataStorageComboBox *child = m_Modalities.back(); if (child->objectName() == "multiModal_0") { std::iter_swap(m_Modalities.end() - 2, m_Modalities.end() - 1); child = m_Modalities.back(); } delete child; // delete the layout item m_Modalities.pop_back(); } m_Controls.advancedSettingsLayout->update(); } void QmitknnUNetToolGUI::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); } mitk::ModelParams QmitknnUNetToolGUI::MapToRequest(const QString &modelName, const QString &taskName, const QString &trainer, const QString &planId, const std::vector &folds) { mitk::ModelParams requestObject; requestObject.model = modelName.toStdString(); requestObject.trainer = trainer.toStdString(); requestObject.planId = planId.toStdString(); requestObject.task = taskName.toStdString(); requestObject.folds = folds; mitk::nnUNetTool::Pointer tool = this->GetConnectedToolAs(); requestObject.inputName = tool->GetRefNode()->GetName(); requestObject.timeStamp = std::to_string(mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint()); return requestObject; } void QmitknnUNetToolGUI::SegmentationProcessFailed() { WriteErrorMessage( "STATUS: Error in the segmentation process.
No resulting segmentation can be loaded.
"); this->setCursor(Qt::ArrowCursor); std::stringstream stream; stream << "Error in the segmentation process. No resulting segmentation can be loaded."; ShowErrorMessage(stream.str()); } void QmitknnUNetToolGUI::SegmentationResultHandler(mitk::nnUNetTool *tool, bool forceRender) { if (forceRender) { tool->RenderOutputBuffer(); } this->SetLabelSetPreview(tool->GetPreviewSegmentation()); WriteStatusMessage("STATUS: Segmentation task finished successfully.
If multiple Preview objects are selected to Confirm, " "they will be merged. Any unselected Preview objects will be lost.
"); + this->ActualizePreviewLabelVisibility(); } void QmitknnUNetToolGUI::ShowEnsembleLayout(bool visible) { if (m_EnsembleParams.empty()) { ctkCollapsibleGroupBox *groupBoxModel1 = new ctkCollapsibleGroupBox(this); auto lay1 = std::make_unique(groupBoxModel1); groupBoxModel1->setObjectName(QString::fromUtf8("model_1_Box")); groupBoxModel1->setTitle(QString::fromUtf8("Model 1")); groupBoxModel1->setMinimumSize(QSize(0, 0)); groupBoxModel1->setCollapsedHeight(5); groupBoxModel1->setCollapsed(false); groupBoxModel1->setFlat(true); groupBoxModel1->setAlignment(Qt::AlignRight); m_Controls.advancedSettingsLayout->addWidget(groupBoxModel1, 5, 0, 1, 2); connect(lay1->modelBox, SIGNAL(currentTextChanged(const QString &)), this, SLOT(OnModelChanged(const QString &))); connect( lay1->plannerBox, SIGNAL(currentTextChanged(const QString &)), this, SLOT(OnTrainerChanged(const QString &))); m_EnsembleParams.push_back(std::move(lay1)); ctkCollapsibleGroupBox *groupBoxModel2 = new ctkCollapsibleGroupBox(this); auto lay2 = std::make_unique(groupBoxModel2); groupBoxModel2->setObjectName(QString::fromUtf8("model_2_Box")); groupBoxModel2->setTitle(QString::fromUtf8("Model 2")); groupBoxModel2->setMinimumSize(QSize(0, 0)); groupBoxModel2->setCollapsedHeight(5); groupBoxModel2->setCollapsed(false); groupBoxModel2->setFlat(true); groupBoxModel2->setAlignment(Qt::AlignLeft); m_Controls.advancedSettingsLayout->addWidget(groupBoxModel2, 5, 2, 1, 2); connect(lay2->modelBox, SIGNAL(currentTextChanged(const QString &)), this, SLOT(OnModelChanged(const QString &))); connect( lay2->plannerBox, SIGNAL(currentTextChanged(const QString &)), this, SLOT(OnTrainerChanged(const QString &))); m_EnsembleParams.push_back(std::move(lay2)); } for (auto &layout : m_EnsembleParams) { layout->setVisible(visible); } }