diff --git a/Modules/Segmentation/Interactions/mitknnUnetTool.cpp b/Modules/Segmentation/Interactions/mitknnUnetTool.cpp index 9a64f9d539..9ca820f1e5 100644 --- a/Modules/Segmentation/Interactions/mitknnUnetTool.cpp +++ b/Modules/Segmentation/Interactions/mitknnUnetTool.cpp @@ -1,320 +1,313 @@ /*============================================================================ 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()) { 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.svg"); 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 (this->GetMitkTempDir().empty()) + { + this->SetMitkTempDir(IOUtil::CreateTemporaryDirectory("mitk-XXXXXX")); + } 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 = 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/Segmentation/Interactions/mitknnUnetTool.h b/Modules/Segmentation/Interactions/mitknnUnetTool.h index 70f84a68b8..af8f1f6465 100644 --- a/Modules/Segmentation/Interactions/mitknnUnetTool.h +++ b/Modules/Segmentation/Interactions/mitknnUnetTool.h @@ -1,214 +1,214 @@ /*============================================================================ 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 mitknnUnetTool_h #define mitknnUnetTool_h #include "mitkSegWithPreviewTool.h" #include "mitkCommon.h" #include "mitkToolManager.h" #include #include #include #include namespace us { class ModuleResource; } namespace mitk { /** * @brief nnUNet parameter request object holding all model parameters for input. * Also holds output temporary directory path. */ struct ModelParams { std::string task; std::vector folds; std::string model; std::string trainer; std::string planId; std::string outputDir; std::string inputName; std::string timeStamp; size_t generateHash() const { std::string toHash; std::string foldsConcatenated = std::accumulate(folds.begin(), folds.end(), std::string("")); toHash += this->task; toHash += this->model; toHash += this->inputName; toHash += foldsConcatenated; toHash += this->timeStamp; size_t hashVal = std::hash{}(toHash); return hashVal; } }; /** \brief nnUNet segmentation tool. \ingroup Interaction \ingroup ToolManagerEtAl \warning Only to be instantiated by mitk::ToolManager. */ class MITKSEGMENTATION_EXPORT nnUNetTool : public SegWithPreviewTool { public: mitkClassMacro(nnUNetTool, SegWithPreviewTool); itkFactorylessNewMacro(Self); itkCloneMacro(Self); const char **GetXPM() const override; const char *GetName() const override; us::ModuleResource GetIconResource() const override; void Activated() override; itkSetMacro(nnUNetDirectory, std::string); itkGetConstMacro(nnUNetDirectory, std::string); itkSetMacro(ModelDirectory, std::string); itkGetConstMacro(ModelDirectory, std::string); itkSetMacro(PythonPath, std::string); itkGetConstMacro(PythonPath, std::string); itkSetMacro(MitkTempDir, std::string); itkGetConstMacro(MitkTempDir, std::string); itkSetMacro(PostProcessingJsonDirectory, std::string); itkGetConstMacro(PostProcessingJsonDirectory, std::string); itkSetMacro(MixedPrecision, bool); itkGetConstMacro(MixedPrecision, bool); itkBooleanMacro(MixedPrecision); itkSetMacro(Mirror, bool); itkGetConstMacro(Mirror, bool); itkBooleanMacro(Mirror); itkSetMacro(MultiModal, bool); itkGetConstMacro(MultiModal, bool); itkBooleanMacro(MultiModal); itkSetMacro(NoPip, bool); itkGetConstMacro(NoPip, bool); itkBooleanMacro(NoPip); itkSetMacro(Ensemble, bool); itkGetConstMacro(Ensemble, bool); itkBooleanMacro(Ensemble); itkSetMacro(Predict, bool); itkGetConstMacro(Predict, bool); itkBooleanMacro(Predict); itkSetMacro(GpuId, unsigned int); itkGetConstMacro(GpuId, unsigned int); /** * @brief vector of ModelParams. * Size > 1 only for ensemble prediction. */ std::vector m_ParamQ; /** * @brief Holds paths to other input image modalities. * */ std::vector m_OtherModalPaths; mitk::Image::ConstPointer m_InputBuffer; /** * @brief Renders the output LabelSetImage. * To called in the main thread. */ void RenderOutputBuffer(); /** * @brief Get the Output Buffer object * * @return LabelSetImage::Pointer */ LabelSetImage::Pointer GetOutputBuffer(); /** * @brief Sets the outputBuffer to nullptr * */ void ClearOutputBuffer(); /** * @brief Returns the DataStorage from the ToolManager */ mitk::DataStorage *GetDataStorage(); mitk::DataNode *GetRefNode(); void SetOutputBuffer(LabelSetImage::Pointer); protected: /** - * @brief Construct a new nnUNet Tool object and temp directory. + * @brief Construct a new nnUNet Tool object. * */ - nnUNetTool(); + nnUNetTool() = default; /** * @brief Destroy the nnUNet Tool object and deletes the temp directory. * */ ~nnUNetTool(); /** * @brief Overriden method from the tool manager to execute the segmentation * Implementation: * 1. Saves the inputAtTimeStep in a temporary directory. * 2. Copies other modalities, renames and saves in the temporary directory, if required. * 3. Sets RESULTS_FOLDER and CUDA_VISIBLE_DEVICES variables in the environment. * 3. Iterates through the parameter queue (m_ParamQ) and executes "nnUNet_predict" command with the parameters * 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: std::string m_MitkTempDir; std::string m_nnUNetDirectory; std::string m_ModelDirectory; std::string m_PythonPath; std::string m_PostProcessingJsonDirectory; // bool m_UseGPU; kept for future // bool m_AllInGPU; bool m_MixedPrecision; bool m_Mirror; bool m_NoPip; bool m_MultiModal; bool m_Ensemble = false; bool m_Predict; LabelSetImage::Pointer m_OutputBuffer; unsigned int m_GpuId; const std::string m_TEMPLATE_FILENAME = "XXXXXX_000_0000.nii.gz"; }; } // namespace mitk #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.cpp b/Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.cpp index d0478d1332..67217dd9ec 100644 --- a/Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetGPU.cpp @@ -1,52 +1,55 @@ /*============================================================================ 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 ============================================================================*/ #include "QmitknnUNetGPU.h" #include QmitkGPULoader::QmitkGPULoader() { QProcess process; process.start("nvidia-smi --query-gpu=name,memory.total --format=csv"); process.waitForFinished(-1); QStringList infoStringList; while (process.canReadLine()) { QString line = process.readLine(); if (!line.startsWith("name")) { infoStringList << line; } } unsigned int count = 0; foreach (QString infoString, infoStringList) { QmitkGPUSpec spec; QStringList gpuDetails; gpuDetails = infoString.split(","); - spec.name = gpuDetails.at(0); - spec.id = count; - spec.memory = gpuDetails.at(1); - this->m_Gpus.push_back(spec); - ++count; + if(gpuDetails.count() == 2) + { + spec.name = gpuDetails.at(0); + spec.id = count; + spec.memory = gpuDetails.at(1); + this->m_Gpus.push_back(spec); + ++count; + } } } int QmitkGPULoader::GetGPUCount() { return static_cast(m_Gpus.size()); } std::vector QmitkGPULoader::GetAllGPUSpecs() { return m_Gpus; } diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp index 5950d12764..1182ce51b0 100644 --- a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp @@ -1,1188 +1,1196 @@ /*============================================================================ 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 #include #include #include #include MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitknnUNetToolGUI, "") QmitknnUNetToolGUI::QmitknnUNetToolGUI() : 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 nnUNet tool might not work."; this->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(); m_nnUNetThread = new QThread(this); m_Worker = new nnUNetDownloadWorker; m_Worker->moveToThread(m_nnUNetThread); m_EnableConfirmSegBtnFnc = [this](bool enabled) { return !m_FirstPreviewComputation ? m_SuperclassEnableConfirmSegBtnFnc(enabled) : false; }; } QmitknnUNetToolGUI::~QmitknnUNetToolGUI() { m_nnUNetThread->quit(); m_nnUNetThread->wait(); } void QmitknnUNetToolGUI::ConnectNewTool(mitk::SegWithPreviewTool *newTool) { Superclass::ConnectNewTool(newTool); newTool->IsTimePointChangeAwareOff(); m_FirstPreviewComputation = true; } 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.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())); connect(m_Controls.startDownloadButton, SIGNAL(clicked()), this, SLOT(OnDownloadModel())); connect(m_Controls.stopDownloadButton, SIGNAL(clicked()), this, SLOT(OnStopDownload())); // Qthreads qRegisterMetaType(); qRegisterMetaType(); connect(this, &QmitknnUNetToolGUI::Operate, m_Worker, &nnUNetDownloadWorker::DoWork); connect(m_Worker, &nnUNetDownloadWorker::Exit, this, &QmitknnUNetToolGUI::OnDownloadWorkerExit); connect(m_nnUNetThread, &QThread::finished, m_Worker, &QObject::deleteLater); m_Controls.multiModalValueLabel->setStyleSheet("font-weight: bold; color: white"); m_Controls.multiModalValueLabel->setVisible(false); m_Controls.requiredModalitiesLabel->setVisible(false); m_Controls.stopDownloadButton->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); QIcon stopIcon = QmitkStyleManager::ThemeIcon(QStringLiteral(":/org_mitk_icons/icons/awesome/scalable/status/dialog-error.svg")); m_Controls.stopDownloadButton->setIcon(stopIcon); 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. this->DisableEverything(); QString lastSelectedPyEnv = m_Settings.value("nnUNet/LastPythonPath").toString(); m_Controls.pythonEnvComboBox->setCurrentText(lastSelectedPyEnv); } void QmitknnUNetToolGUI::EnableWidgets(bool enabled) { Superclass::EnableWidgets(enabled); } void QmitknnUNetToolGUI::ClearAllModalities() { m_Controls.multiModalBox->setChecked(false); this->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.multiModalValueLabel->setVisible(false); m_Controls.multiModalBox->setEnabled(false); this->ClearAllComboBoxes(); this->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(); } } 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()) + for (QmitkSingleNodeSelectionWidget *modality : m_Modalities) + { + mitk::DataNode::Pointer node = modality->GetSelectedNode(); + if (nodeNames.find(node->GetName()) == nodeNames.end()) { - modals.push_back(dynamic_cast(modality->GetSelectedNode()->GetData())); - nodeNames.insert(modality->GetSelectedNode()->GetName()); + modals.push_back(dynamic_cast(node->GetData())); + nodeNames.insert(node->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 (!this->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; this->WriteStatusMessage(statusMsg); } else if (QFile(ppJsonFilePossibility2).exists()) { tool->SetPostProcessingJsonDirectory(ppJsonFilePossibility2.toStdString()); const QString statusMsg = "Post Processing JSON file found:" + ppJsonFilePossibility2; this->WriteStatusMessage(statusMsg); } else { std::string errorMsg = "No post processing file was found for the selected ensemble combination. Continuing anyway..."; this->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 = this->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()) { this->CheckAllInCheckableComboBox(foldBox); } QModelIndexList foldList = foldBox->checkedIndexes(); for (const auto &index : foldList) { QString foldQString = foldBox->itemText(index.row()); if(foldQString != "dummy_element_that_nobody_can_see") { foldQString = foldQString.split("_", QString::SplitBehavior::SkipEmptyParts).last(); folds.push_back(foldQString.toStdString()); } else { throw std::runtime_error("Folds are not recognized. Please check if your nnUNet results folder structure is legitimate"); } } return folds; } 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(); this->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; } void QmitknnUNetToolGUI::DumpJSONfromPickle(const QString &picklePath) { const QString pickleFile = picklePath + QDir::separator() + m_PICKLE_FILENAME; const QString jsonFile = picklePath + QDir::separator() + m_MITK_EXPORT_JSON_FILENAME; if (!QFile::exists(jsonFile)) { mitk::ProcessExecutor::Pointer spExec = mitk::ProcessExecutor::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(pickleFile.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(jsonFile.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(); this->WriteStatusMessage( "Parsing failed in backend. Multiple Modalities will now have to be manually entered by the user."); } } } void QmitknnUNetToolGUI::ExportAvailableModelsAsJSON(const QString &resultsFolder) { const QString jsonPath = resultsFolder + QDir::separator() + m_AVAILABLE_MODELS_JSON_FILENAME; if (!QFile::exists(jsonPath)) { auto spExec = mitk::ProcessExecutor::New(); mitk::ProcessExecutor::ArgumentListType args; args.push_back("--export"); args.push_back(resultsFolder.toStdString()); try { spExec->Execute(m_PythonPath.toStdString(), "nnUNet_print_available_pretrained_models", args); } catch (const mitk::Exception &e) { MITK_ERROR << "Exporting information FAILED." << e.GetDescription(); this->WriteStatusMessage("Exporting information FAILED."); } } } 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(); this->ClearAllModalLabels(); if (num_mods > 1) { m_Controls.multiModalBox->setChecked(true); m_Controls.multiModalBox->setEnabled(false); m_Controls.multiModalValueLabel->setText(QString::number(num_mods)); OnModalitiesNumberChanged(num_mods); 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.advancedSettingsLayout->update(); } else { m_Controls.multiModalBox->setChecked(false); } } } void QmitknnUNetToolGUI::FillAvailableModelsInfoFromJSON(const QString &jsonPath) { std::ifstream file(jsonPath.toStdString()); if (file.is_open() && m_Controls.availableBox->count() < 1) { 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; } for (const auto &obj : jsonObj.items()) { m_Controls.availableBox->addItem(QString::fromStdString(obj.key())); } } } 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::SetComboBoxToNone(ctkCheckableComboBox* comboBox) { comboBox->clear(); comboBox->addItem("dummy_element_that_nobody_can_see"); qobject_cast(comboBox->view())->setRowHidden(0, true); // For the cosmetic purpose of showing "None" on the combobox. } /* ---------------------SLOTS---------------------------------------*/ 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)) { this->ProcessEnsembleModelsParams(tool); } else { this->ProcessModelParams(tool); } pythonPathTextItem = m_Controls.pythonEnvComboBox->currentText(); QString pythonPath = m_PythonPath; if (!this->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()) { tool->m_OtherModalPaths.clear(); tool->m_OtherModalPaths = FetchMultiModalImagesFromUI(); tool->MultiModalOn(); } 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; this->WriteStatusMessage( QString("STATUS: Starting Segmentation task... This might take a while.")); tool->UpdatePreview(); if (nullptr == tool->GetOutputBuffer()) { this->SegmentationProcessFailed(); } else { this->SegmentationResultHandler(tool); if (doCache) { this->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())); this->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(); this->ShowErrorMessage(errorMsg.str()); this->WriteErrorMessage(QString::fromStdString(errorMsg.str())); m_Controls.previewButton->setEnabled(true); tool->PredictOff(); return; } catch (...) { std::string errorMsg = "Unkown error occured while generation nnUNet segmentation."; this->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); } } } void QmitknnUNetToolGUI::OnRefreshPresssed() { const QString resultsFolder = m_Controls.modeldirectoryBox->directory(); this->OnDirectoryChanged(resultsFolder); } void QmitknnUNetToolGUI::OnDirectoryChanged(const QString &resultsFolder) { m_IsResultsFolderValid = false; m_Controls.previewButton->setEnabled(false); this->ClearAllComboBoxes(); this->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; } this->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); m_Controls.previewButton->setEnabled(false); this->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); }); } } 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); this->ShowEnsembleLayout(false); m_Controls.trainerBox->clear(); m_Controls.plannerBox->clear(); auto trainerPlanners = m_ParentFolder->getTrainerPlannersForTask(selectedTask, model); if(trainerPlanners.isEmpty()) { this->ShowErrorMessage("No plans.pkl found for "+model.toStdString()+". Check your directory or download the task again."); this->SetComboBoxToNone(m_Controls.foldBox); return; } QStringList trainers, planners; std::tie(trainers, planners) = ExtractTrainerPlannerFromString(trainerPlanners); 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()) { m_Controls.previewButton->setEnabled(false); for (auto &layout : m_EnsembleParams) { if (box == layout->modelBox) { layout->trainerBox->clear(); layout->plannerBox->clear(); auto trainerPlanners = m_ParentFolder->getTrainerPlannersForTask(selectedTask, model); if(trainerPlanners.isEmpty()) { this->ShowErrorMessage("No plans.pkl found for "+model.toStdString()+". Check your directory or download the task again."); this->SetComboBoxToNone(layout->foldBox); return; } 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; } m_IsResultsFolderValid = false; QString parentPath; 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); if(folds.isEmpty()) { this->ShowErrorMessage("No valid folds found. Check your directory or download the task again."); this->SetComboBoxToNone(m_Controls.foldBox); return; } 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) { m_IsResultsFolderValid = true; this->CheckAllInCheckableComboBox(m_Controls.foldBox); auto tempPath = QStringList() << m_ParentFolder->getResultsFolder() << "nnUNet" << selectedModel << selectedTask << QString("%1__%2").arg(selectedTrainer, plannerSelected); parentPath = QDir::cleanPath(tempPath.join(QDir::separator())); } } 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); if(folds.isEmpty()) { this->ShowErrorMessage("No valid folds found. Check your directory."); this->SetComboBoxToNone(layout->foldBox); return; } 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) { this->CheckAllInCheckableComboBox(layout->foldBox); m_IsResultsFolderValid = true; auto tempPath = QStringList() << m_ParentFolder->getResultsFolder() << "nnUNet" << selectedModel << selectedTask << QString("%1__%2").arg(selectedTrainer, plannerSelected); parentPath = QDir::cleanPath(tempPath.join(QDir::separator())); } break; } } } if (m_IsResultsFolderValid) { m_Controls.previewButton->setEnabled(true); const QString mitkJsonFile = parentPath + QDir::separator() + m_MITK_EXPORT_JSON_FILENAME; this->DumpJSONfromPickle(parentPath); if (QFile::exists(mitkJsonFile)) { this->DisplayMultiModalInfoFromJSON(mitkJsonFile); } } } void QmitknnUNetToolGUI::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 m_Controls.pythonEnvComboBox->insertItem(0, path); m_Controls.pythonEnvComboBox->setCurrentIndex(0); } } else if (!this->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"; this->ShowErrorMessage(warning); this->DisableEverything(); m_Controls.availableBox->clear(); } else { m_Controls.modeldirectoryBox->setEnabled(true); m_Controls.refreshdirectoryBox->setEnabled(true); m_Controls.multiModalBox->setEnabled(true); QString setVal = this->FetchResultsFolderFromEnv(); if (!setVal.isEmpty()) { m_Controls.modeldirectoryBox->setDirectory(setVal); } this->OnRefreshPresssed(); 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 // Export available model info as json and fill them for Download QString tempPath = QString::fromStdString(mitk::IOUtil::GetTempPath()); this->ExportAvailableModelsAsJSON(tempPath); const QString jsonPath = tempPath + QDir::separator() + m_AVAILABLE_MODELS_JSON_FILENAME; if (QFile::exists(jsonPath)) { this->FillAvailableModelsInfoFromJSON(jsonPath); } } } 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.requiredModalitiesLabel->setVisible(visibility); m_Controls.multiModalValueLabel->setVisible(visibility); if (!visibility) { this->OnModalitiesNumberChanged(0); m_Controls.multiModalValueLabel->setText("0"); this->ClearAllModalLabels(); } } } } void QmitknnUNetToolGUI::OnModalitiesNumberChanged(int num) { while (num > static_cast(m_Modalities.size())) { - QmitkDataStorageComboBox *multiModalBox = new QmitkDataStorageComboBox(this, true); + QmitkSingleNodeSelectionWidget *multiModalBox = new QmitkSingleNodeSelectionWidget(this); mitk::nnUNetTool::Pointer tool = this->GetConnectedToolAs(); multiModalBox->SetDataStorage(tool->GetDataStorage()); - multiModalBox->SetPredicate(m_MultiModalPredicate); + multiModalBox->SetInvalidInfo("Select corresponding modalities"); + multiModalBox->SetNodePredicate(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()) && !m_Modalities.empty()) { - QmitkDataStorageComboBox *child = m_Modalities.back(); + QmitkSingleNodeSelectionWidget *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); } void QmitknnUNetToolGUI::SegmentationProcessFailed() { this->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."; this->ShowErrorMessage(stream.str()); } void QmitknnUNetToolGUI::SegmentationResultHandler(mitk::nnUNetTool *tool, bool forceRender) { if (forceRender) { tool->RenderOutputBuffer(); } m_FirstPreviewComputation = false; this->SetLabelSetPreview(tool->GetPreviewSegmentation()); this->WriteStatusMessage("STATUS: Segmentation task finished successfully."); 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); } } void QmitknnUNetToolGUI::OnDownloadModel() { auto selectedTask = m_Controls.availableBox->currentText(); if(!selectedTask.isEmpty()) { auto spExec = mitk::ProcessExecutor::New(); mitk::ProcessExecutor::ArgumentListType args; args.push_back(selectedTask.toStdString()); this->WriteStatusMessage( "Downloading the requested task in to the selected Results Folder. This might take some time " "depending on your internet connection..."); m_Processes["DOWNLOAD"] = spExec; if (!m_nnUNetThread->isRunning()) { MITK_DEBUG << "Starting thread..."; m_nnUNetThread->start(); } QString resultsFolder = m_ParentFolder->getResultsFolder(); emit Operate(resultsFolder, m_PythonPath, spExec, args); m_Controls.stopDownloadButton->setVisible(true); m_Controls.startDownloadButton->setVisible(false); } } void QmitknnUNetToolGUI::OnDownloadWorkerExit(const bool isSuccess, const QString message) { if (isSuccess) { this->WriteStatusMessage(message + QString(" Click Refresh Results Folder to use the new Task.")); } else { MITK_ERROR << "Download FAILED! " << message.toStdString(); this->WriteStatusMessage(QString("Download failed. Check your internet connection. " + message)); } m_Controls.stopDownloadButton->setVisible(false); m_Controls.startDownloadButton->setVisible(true); } void QmitknnUNetToolGUI::OnStopDownload() { mitk::ProcessExecutor::Pointer spExec = m_Processes["DOWNLOAD"]; spExec->KillProcess(); this->WriteStatusMessage("Download Killed by the user."); m_Controls.stopDownloadButton->setVisible(false); m_Controls.startDownloadButton->setVisible(true); } void QmitknnUNetToolGUI::OnClearCachePressed() { m_Cache.clear(); this->UpdateCacheCountOnUI(); } diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.h index b590ac2f82..0d4f016f35 100644 --- a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.h @@ -1,405 +1,405 @@ /*============================================================================ 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 QmitknnUNetToolGUI_h #define QmitknnUNetToolGUI_h #include "QmitkMultiLabelSegWithPreviewToolGUIBase.h" #include "QmitknnUNetFolderParser.h" #include "QmitknnUNetGPU.h" #include "QmitknnUNetWorker.h" #include "mitkProcessExecutor.h" #include "mitknnUnetTool.h" #include "ui_QmitknnUNetToolGUIControls.h" #include #include #include #include #include -#include +#include #include #include #include class nnUNetCache { public: mitk::LabelSetImage::ConstPointer m_SegCache; static size_t GetUniqueHash(std::vector &requestQ) { size_t hashCode = 0; for (mitk::ModelParams &request : requestQ) { boost::hash_combine(hashCode, request.generateHash()); } return hashCode; } }; class MITKSEGMENTATIONUI_EXPORT QmitknnUNetToolGUI : public QmitkMultiLabelSegWithPreviewToolGUIBase { Q_OBJECT public: mitkClassMacro(QmitknnUNetToolGUI, QmitkMultiLabelSegWithPreviewToolGUIBase); itkFactorylessNewMacro(Self); itkCloneMacro(Self); QCache m_Cache; /** * @brief The hash map stores all bifurcating processes' ID. * */ std::unordered_map m_Processes; protected slots: /** * @brief Qt slot * */ void OnPreviewRequested(); /** * @brief Qt slot * */ void OnDirectoryChanged(const QString&); /** * @brief Qt slot * */ void OnModelChanged(const QString&); /** * @brief Qt slot * */ void OnTaskChanged(const QString &); /** * @brief Qt slot * */ void OnTrainerChanged(const QString&); /** * @brief Qt slot * */ void OnCheckBoxChanged(int); /** * @brief Qthread slot to capture failures from thread worker and * shows error message * */ void SegmentationProcessFailed(); /** * @brief Qthread to capture sucessfull nnUNet segmentation. * Further, renders the LabelSet image */ void SegmentationResultHandler(mitk::nnUNetTool *, bool forceRender = false); /** * @brief Qt Slot * */ void OnModalitiesNumberChanged(int); /** * @brief Qt Slot * */ void OnPythonPathChanged(const QString&); /** * @brief Qt slot * */ void OnRefreshPresssed(); /** * @brief Qt slot * */ void OnClearCachePressed(); /** * @brief Qt slot * */ void OnDownloadModel(); /** * @brief Qt slot * */ void OnDownloadWorkerExit(bool, const QString); /** * @brief Qt slot * */ void OnStopDownload(); signals: /** * @brief signal for starting the segmentation which is caught by a worker thread. */ void Operate(QString, QString, mitk::ProcessExecutor::Pointer, mitk::ProcessExecutor::ArgumentListType); protected: QmitknnUNetToolGUI(); ~QmitknnUNetToolGUI(); void ConnectNewTool(mitk::SegWithPreviewTool* newTool) override; void InitializeUI(QBoxLayout* mainLayout) override; void EnableWidgets(bool enabled) override; private: /** * @brief Adds an element and hides it so that the ctkCheckableComboBox shows "None". */ void SetComboBoxToNone(ctkCheckableComboBox*); /** * @brief Parses the available_models.json file from RESULTS_FOLDER and loads * the task names to the Download combobox in Advanced. */ void FillAvailableModelsInfoFromJSON(const QString&); /** * @brief Exports available models to download from nnUNet_print_available_pretrained_models * output. */ void ExportAvailableModelsAsJSON(const QString&); /** * @brief Clears all displayed modal labels and widgets from GUI. * */ void ClearAllModalities(); /** * @brief Parses Json file containing modality info and populates * labels and selection widgets accordingly on the GUI. */ void DisplayMultiModalInfoFromJSON(const QString&); /** * @brief Clears all modality labels previously populated from GUI. * */ void ClearAllModalLabels(); /** * @brief Runs a set of python commands to read "plans.pkl" and extract * modality information required for inferencing. This information is exported * as json file : "mitk_export.json". * * @return QString */ void DumpJSONfromPickle(const QString&); /** * @brief Searches RESULTS_FOLDER environment variable. If not found, * returns from the QSettings stored last used path value. * @return QString */ QString FetchResultsFolderFromEnv(); /** * @brief Returns GPU id of the selected GPU from the Combo box. * * @return unsigned int */ unsigned int FetchSelectedGPUFromUI(); /** * @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 Inserts the hash and segmentation into cache and * updates count on UI. */ void AddToCache(size_t&, mitk::LabelSetImage::ConstPointer); /** * @brief Checks all the entries of the ctkCheckableComboBox ui widget. * This feature is not present in ctkCheckableComboBox API. */ void CheckAllInCheckableComboBox(ctkCheckableComboBox*); /** * @brief Parses the folder names containing trainer and planner together and, * returns it as separate lists. * @return std::pair */ std::pair ExtractTrainerPlannerFromString(QStringList); /** * @brief Parses the ensemble UI elements and sets to nnUNetTool object pointer. * */ void ProcessEnsembleModelsParams(mitk::nnUNetTool::Pointer); /** * @brief Parses the UI elements and sets to nnUNetTool object pointer. * */ void ProcessModelParams(mitk::nnUNetTool::Pointer); /** * @brief Creates and renders QmitknnUNetTaskParamsUITemplate layout for ensemble input. */ void ShowEnsembleLayout(bool visible = true); /** * @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 Searches and parses paths of python virtual enviroments * from predefined lookout locations */ void AutoParsePythonPaths(); /** * @brief Check if pretrained model sub folder inside RESULTS FOLDER exist. */ bool IsModelExists(const QString&, const QString&, const QString&); /** * @brief Clears all combo boxes * Any new combo box added in the future can be featured here for clearance. * */ void ClearAllComboBoxes(); /** * @brief Disable/deactivates the nnUNet GUI. * Clears any multi modal labels and selection widgets, as well. */ void DisableEverything(); /** * @brief Checks if nnUNet_predict command is valid in the selected python virtual environment. * * @return bool */ bool IsNNUNetInstalled(const QString&); /** * @brief Mapper function to map QString entries from UI to ModelParam attributes. * * @return mitk::ModelParams */ mitk::ModelParams MapToRequest( const QString&, const QString&, const QString&, const QString&, const std::vector&); /** * @brief Returns checked fold names from the ctk-Checkable-ComboBox. * * @return std::vector */ std::vector FetchSelectedFoldsFromUI(ctkCheckableComboBox*); /** * @brief Returns all paths from the dynamically generated ctk-path-line-edit boxes. * * @return std::vector */ std::vector FetchMultiModalImagesFromUI(); /** * @brief Updates cache count on UI. * */ void UpdateCacheCountOnUI(); Ui_QmitknnUNetToolGUIControls m_Controls; QmitkGPULoader m_GpuLoader; /** * @brief Stores all dynamically added ctk-path-line-edit UI elements. * */ - std::vector m_Modalities; + std::vector m_Modalities; std::vector m_ModalLabels; std::vector> m_EnsembleParams; mitk::NodePredicateBase::Pointer m_MultiModalPredicate; QString m_PythonPath; /** * @brief Stores row count of the "advancedSettingsLayout" layout element. This value helps dynamically add * ctk-path-line-edit UI elements at the right place. Forced to initialize in the InitializeUI method since there is * no guarantee of retrieving exact row count anywhere else. * */ int m_UI_ROWS; /** * @brief Stores path of the model director (RESULTS_FOLDER appended by "nnUNet"). * */ std::shared_ptr m_ParentFolder = nullptr; /** * @brief Valid list of models supported by nnUNet * */ const QStringList m_VALID_MODELS = {"2d", "3d_lowres", "3d_fullres", "3d_cascade_fullres", "ensembles"}; const QString m_CACHE_COUNT_BASE_LABEL = "Cached Items: "; const QString m_MITK_EXPORT_JSON_FILENAME = "mitk_export.json"; const QString m_AVAILABLE_MODELS_JSON_FILENAME = "available_models.json"; const QString m_PICKLE_FILENAME = "plans.pkl"; /** * @brief For storing values across sessions. Currently, RESULTS_FOLDER value is cached using this. */ QSettings m_Settings; bool m_IsResultsFolderValid = false; QThread* m_nnUNetThread; nnUNetDownloadWorker* m_Worker; bool m_FirstPreviewComputation = true; EnableConfirmSegBtnFunctionType m_SuperclassEnableConfirmSegBtnFnc; }; #endif