diff --git a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp index 48482cd677..c2f0324a5e 100644 --- a/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitknnUNetToolGUI.cpp @@ -1,412 +1,412 @@ /*============================================================================ 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 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); } m_SegmentationThread = new QThread(this); m_Worker = new nnUNetSegmentationWorker; m_Worker->moveToThread(m_SegmentationThread); // 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(); } QmitknnUNetToolGUI::~QmitknnUNetToolGUI() { this->m_SegmentationThread->quit(); this->m_SegmentationThread->wait(); } 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(this, &QmitknnUNetToolGUI::Operate, m_Worker, &nnUNetSegmentationWorker::DoWork); connect(m_Worker, &nnUNetSegmentationWorker::Finished, this, &QmitknnUNetToolGUI::SegmentationResultHandler); connect(m_Worker, &nnUNetSegmentationWorker::Failed, this, &QmitknnUNetToolGUI::SegmentationProcessFailed); connect(m_SegmentationThread, &QThread::finished, m_Worker, &QObject::deleteLater); 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.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 { 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_ModelDirectory.left(m_ModelDirectory.lastIndexOf(QDir::separator())).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(); } if (!m_SegmentationThread->isRunning()) { MITK_DEBUG << "Starting thread..."; m_SegmentationThread->start(); } m_Controls.statusLabel->setText("STATUS: Starting Segmentation task... This might take a while."); emit Operate(tool); } catch (const std::exception &e) { std::stringstream errorMsg; errorMsg << "Error while processing parameters for nnUNet segmentation. Reason: " << e.what(); ShowErrorMessage(errorMsg.str()); return; } catch (...) { std::string errorMsg = "Unkown error occured while generation nnUNet segmentation."; ShowErrorMessage(errorMsg); return; } } } /* void QmitknnUNetToolGUI::OnSettingsAccepted() { mitk::nnUNetTool::Pointer tool = this->GetConnectedToolAs(); if (nullptr != tool) { try { QString modelName = m_Controls.modelBox->currentText(); QString taskName = m_Controls.taskBox->currentText(); bool isNoPip = m_Controls.nopipBox->isChecked(); QString pythonPathTextItem = m_Controls.pythonEnvComboBox->currentText(); QString pythonPath = pythonPathTextItem.mid(pythonPathTextItem.indexOf(" ") + 1); #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."); } QString trainerPlanner = m_Controls.trainerBox->currentText(); QString splitterString = "__"; tool->EnsembleOff(); if (modelName.startsWith("ensemble", Qt::CaseInsensitive)) { QString ppJsonFile = QDir::cleanPath(m_ModelDirectory + QDir::separator() + modelName + QDir::separator() + taskName + QDir::separator() + trainerPlanner + QDir::separator() + "postprocessing.json"); if (QFile(ppJsonFile).exists()) { tool->EnsembleOn(); tool->SetPostProcessingJsonDirectory(ppJsonFile.toStdString()); splitterString = "--"; } } QStringList trainerSplitParts = trainerPlanner.split(splitterString, QString::SplitBehavior::SkipEmptyParts); std::vector requestQ; if (tool->GetEnsemble()) { foreach (QString modelSet, trainerSplitParts) { modelSet.remove("ensemble_", Qt::CaseInsensitive); QStringList splitParts = modelSet.split("__", QString::SplitBehavior::SkipEmptyParts); QString modelName = splitParts.first(); QString trainer = splitParts.at(1); QString planId = splitParts.at(2); auto testfold = std::vector(1, "1"); mitk::ModelParams modelObject = MapToRequest(modelName, taskName, trainer, planId, testfold); requestQ.push_back(modelObject); } } else { QString trainer = m_Controls.trainerBox->currentText();//trainerSplitParts.first(); QString planId = m_Controls.plannerBox->currentText(); //trainerSplitParts.last(); 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; tool->SetnnUNetDirectory(nnUNetDirectory); tool->SetPythonPath(pythonPath.toStdString()); tool->SetModelDirectory(m_ModelDirectory.left(m_ModelDirectory.lastIndexOf(QDir::separator())).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(); } if (!m_SegmentationThread->isRunning()) { MITK_DEBUG << "Starting thread..."; m_SegmentationThread->start(); } m_Controls.statusLabel->setText("STATUS: Starting Segmentation task... This might take a while."); emit Operate(tool); } catch (const std::exception &e) { std::stringstream errorMsg; errorMsg << "Error while processing parameters for nnUNet segmentation. Reason: " << e.what(); ShowErrorMessage(errorMsg.str()); return; } catch (...) { std::string errorMsg = "Unkown error occured while generation nnUNet segmentation."; ShowErrorMessage(errorMsg); 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) { QString taskName = m_Controls.taskBox->currentText(); std::vector requestQ; QStringList ppDirFolderName; ppDirFolderName << "ensemble_"; - if (m_EnsembleParams[0]->modelBox->currentText() != m_EnsembleParams[1]->modelBox->currentText()) + 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."); } for (std::unique_ptr &layout : m_EnsembleParams) { QString modelName = layout->modelBox->currentText(); ppDirFolderName << modelName; ppDirFolderName << "__"; QString trainer = layout->trainerBox->currentText(); ppDirFolderName << trainer; ppDirFolderName << "__"; QString planId = layout->plannerBox->currentText(); ppDirFolderName << planId; ppDirFolderName << "--"; auto testfold = std::vector(1, "1"); mitk::ModelParams modelObject = MapToRequest(modelName, taskName, trainer, planId, testfold); requestQ.push_back(modelObject); } tool->EnsembleOn(); QString ppJsonFile = QDir::cleanPath(m_ModelDirectory + QDir::separator() + "ensembles" + QDir::separator() + taskName + QDir::separator() + ppDirFolderName.join(QString("")) + QDir::separator() + "postprocessing.json"); if (QFile(ppJsonFile).exists()) { tool->SetPostProcessingJsonDirectory(ppJsonFile.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; }