diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp index 2c067ea079..ea0b15c38b 100644 --- a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp @@ -1,309 +1,328 @@ /*============================================================================ 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 "mitknnUnetTool.h" #include #include #include #include MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitknnUNetToolGUI, "") QmitknnUNetToolGUI::QmitknnUNetToolGUI() : QmitkAutoMLSegmentationToolGUIBase() { // Nvidia-smi command returning zero doesn't alway mean 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()); this->m_MultiModalPredicate = mitk::NodePredicateAnd::New(imageType, labelSetImageType).GetPointer(); } void QmitknnUNetToolGUI::ConnectNewTool(mitk::AutoSegmentationWithPreviewTool *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(); 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.nopipBox, SIGNAL(stateChanged(int)), this, SLOT(OnCheckBoxChanged(int))); 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.posSpinBox, SIGNAL(valueChanged(int)), this, SLOT(OnModalPositionChanged(int))); connect(m_Controls.pythonEnvComboBox, #if QT_VERSION >= 0x050F00 // 5.15 SIGNAL(textActivated(const QString &)), #elif QT_VERSION >= 0x050C00 // 5.12 SIGNAL(activated(const QString &)), #endif this, SLOT(OnPythonPathChanged(const QString &))); connect(m_Controls.refreshdirectoryBox, SIGNAL(clicked()), this, SLOT(OnRefreshPresssed())); m_Controls.codedirectoryBox->setVisible(false); m_Controls.nnUnetdirLabel->setVisible(false); m_Controls.multiModalSpinBox->setVisible(false); m_Controls.multiModalSpinLabel->setVisible(false); m_Controls.posSpinBoxLabel->setVisible(false); m_Controls.posSpinBox->setVisible(false); m_Controls.previewButton->setEnabled(false); QSize sz(16, 16); m_Controls.stopButton->setVisible(false); QIcon refreshIcon; refreshIcon.addPixmap(style()->standardIcon(QStyle::SP_BrowserReload).pixmap(sz), QIcon::Normal, QIcon::Off); m_Controls.refreshdirectoryBox->setIcon(refreshIcon); m_Controls.refreshdirectoryBox->setEnabled(true); m_Controls.statusLabel->setTextFormat(Qt::RichText); m_Controls.statusLabel->setText("STATUS: Welcome to nnUNet. " + QString::number(m_GpuLoader.GetGPUCount()) + " GPUs were detected."); if (m_GpuLoader.GetGPUCount() != 0) { m_Controls.gpuSpinBox->setMaximum(m_GpuLoader.GetGPUCount() - 1); } mainLayout->addLayout(m_Controls.verticalLayout); Superclass::InitializeUI(mainLayout); m_UI_ROWS = m_Controls.advancedSettingsLayout->rowCount(); // Must do. Row count is correct only here. } void QmitknnUNetToolGUI::OnPreviewRequested() { mitk::nnUNetTool::Pointer tool = this->GetConnectedToolAs(); if (nullptr != tool) { try { 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); } QString pythonPathTextItem = m_Controls.pythonEnvComboBox->currentText(); QString pythonPath = pythonPathTextItem.mid(pythonPathTextItem.indexOf(" ") + 1); bool isNoPip = m_Controls.nopipBox->isChecked(); #ifdef _WIN32 if (!isNoPip && !(pythonPath.endsWith("Scripts", Qt::CaseInsensitive) || pythonPath.endsWith("Scripts/", Qt::CaseInsensitive))) { pythonPath += QDir::separator() + QString("Scripts"); } #else if (!(pythonPath.endsWith("bin", Qt::CaseInsensitive) || pythonPath.endsWith("bin/", Qt::CaseInsensitive))) { pythonPath += QDir::separator() + QString("bin"); } #endif std::string nnUNetDirectory; if (isNoPip) { nnUNetDirectory = m_Controls.codedirectoryBox->directory().toStdString(); } else 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->SetnnUNetDirectory(nnUNetDirectory); 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(isNoPip); tool->SetMultiModal(m_Controls.multiModalBox->isChecked()); // Spinboxes tool->SetGpuId(static_cast(m_Controls.gpuSpinBox->value())); // Multi-Modal tool->MultiModalOff(); if (m_Controls.multiModalBox->isChecked()) { tool->m_OtherModalPaths.clear(); tool->m_OtherModalPaths = FetchMultiModalImagesFromUI(); tool->MultiModalOn(); } tool->m_InputOutputPair = std::make_pair(nullptr, nullptr); m_Controls.statusLabel->setText("STATUS: Starting Segmentation task... This might take a while."); tool->UpdatePreview(); if (tool->GetOutputBuffer() == nullptr) { SegmentationProcessFailed(); } SegmentationResultHandler(tool); tool->PredictOff(); // purposefully placed to make tool->GetMTime different than before. m_Controls.previewButton->setEnabled(true); } catch (const std::exception &e) { std::stringstream errorMsg; errorMsg << "Error while processing parameters for nnUNet segmentation. Reason: " << e.what(); ShowErrorMessage(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; } } } std::vector QmitknnUNetToolGUI::FetchMultiModalImagesFromUI() { std::vector paths; if (m_Controls.multiModalBox->isChecked() && !m_Modalities.empty()) { for (QmitkDataStorageComboBox *modality : m_Modalities) { if (modality->objectName() != "multiModal_0") { paths.push_back(dynamic_cast(modality->GetSelectedNode()->GetData())); } } } return paths; } 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); return QFile::exists(fullPath + QDir::separator() + QString("nnUNet_predict")); } 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::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(); std::vector requestQ; QString ppDirFolderNamePart1 = "ensemble_"; QStringList ppDirFolderNameParts; for (std::unique_ptr &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; // empty vector to consider all folds for inferencing. mitk::ModelParams modelObject = MapToRequest(modelName, taskName, trainer, planId, testfold); requestQ.push_back(modelObject); ppDirFolderNameParts << ppDirFolderName.join(QString("")); } tool->EnsembleOn(); 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()); } else if (QFile(ppJsonFilePossibility2).exists()) { tool->SetPostProcessingJsonDirectory(ppJsonFilePossibility2.toStdString()); } else { // warning message } 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(); 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; +} diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.h index 628033525f..583151c47a 100644 --- a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.h @@ -1,216 +1,222 @@ /*============================================================================ 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 QmitknnUNetToolGUI_h_Included #define QmitknnUNetToolGUI_h_Included #include "QmitkAutoMLSegmentationToolGUIBase.h" #include "QmitknnUNetFolderParser.h" #include "QmitknnUNetGPU.h" #include "mitknnUnetTool.h" #include "ui_QmitknnUNetToolGUIControls.h" #include #include #include #include class MITKSEGMENTATIONUI_EXPORT QmitknnUNetToolGUI : public QmitkAutoMLSegmentationToolGUIBase { Q_OBJECT public: mitkClassMacro(QmitknnUNetToolGUI, QmitkAutoMLSegmentationToolGUIBase); itkFactorylessNewMacro(Self); itkCloneMacro(Self); 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 *); /** * @brief Qt Slot * */ void OnModalitiesNumberChanged(int); /** * @brief Qt Slot * */ void OnPythonPathChanged(const QString &); /** * @brief Qt Slot * */ void OnModalPositionChanged(int); /** * @brief Qt slot * */ void OnRefreshPresssed(); protected: QmitknnUNetToolGUI(); ~QmitknnUNetToolGUI() = default; void ConnectNewTool(mitk::AutoSegmentationWithPreviewTool *newTool) override; void InitializeUI(QBoxLayout *mainLayout) override; void EnableWidgets(bool enabled) override; private: /** * @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 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 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(); /** * @brief Returns all paths from the dynamically generated ctk-path-line-edit boxes. * * @return std::vector */ std::vector FetchMultiModalImagesFromUI(); 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_EnsembleParams; mitk::NodePredicateBase::Pointer m_MultiModalPredicate; /** * @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"}; }; #endif