diff --git a/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.cpp b/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.cpp index a02ce28209..2d8be4d034 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.cpp @@ -1,155 +1,153 @@ /*============================================================================ 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 "QmitkSetupVirtualEnvUtil.h" -#include + +#include "mitkLogMacros.h" #include #include +#include #include -#include "mitkLogMacros.h" QmitkSetupVirtualEnvUtil::QmitkSetupVirtualEnvUtil() { m_BaseDir = QStandardPaths::writableLocation(QStandardPaths::GenericDataLocation) + QDir::separator() + qApp->organizationName() + QDir::separator(); } QmitkSetupVirtualEnvUtil::QmitkSetupVirtualEnvUtil(const QString baseDir) { m_BaseDir = baseDir; } QString QmitkSetupVirtualEnvUtil::GetBaseDir() { return m_BaseDir; } QString QmitkSetupVirtualEnvUtil::GetVirtualEnvPath() { return m_venvPath; } std::map QmitkSetupVirtualEnvUtil::GetInstallParameters( QmitkSetupVirtualEnvUtil::Tool packageName) { std::map parameters; switch (packageName) { case QmitkSetupVirtualEnvUtil::Tool::TOTALSEGMENTATOR: { parameters["venv_name"] = ".totalsegmentator"; parameters["pkg_version"] = "1.5.2"; parameters["pkg_names"] = "Totalsegmentator==1.5.2,scikit-image"; break; } default: { std::runtime_error("Unsupported Tool type"); break; } } return parameters; } - void QmitkSetupVirtualEnvUtil::PrintProcessEvent(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; } } - bool QmitkSetupVirtualEnvUtil::SetupVirtualEnv(QmitkSetupVirtualEnvUtil::Tool packageName) { std::vector packages; std::map params = GetInstallParameters(packageName); std::stringstream pkgs(params["pkg_names"]); while (pkgs.good()) { std::string pkg; std::getline(pkgs, pkg, ','); packages.push_back(pkg); } - QString venvName = QString::fromStdString(params["venv_name"]); QDir folderPath(m_BaseDir); folderPath.mkdir(venvName); if (!folderPath.cd(venvName)) { return false; // Check if directory creation was successful. } mitk::ProcessExecutor::ArgumentListType args; auto spExec = mitk::ProcessExecutor::New(); auto spCommand = itk::CStyleCommand::New(); spCommand->SetCallback(&PrintProcessEvent); spExec->AddObserver(mitk::ExternalProcessOutputEvent(), spCommand); args.push_back("-m"); args.push_back("venv"); args.push_back(venvName.toStdString()); spExec->Execute(m_BaseDir.toStdString(), "/usr/bin/python3", args); // Setup local virtual environment if (folderPath.cd("bin")) { m_venvPath = folderPath.absolutePath(); std::string workingDir = m_venvPath.toStdString(); - for (auto& package : packages) + for (auto &package : packages) { PipInstall(package, workingDir); } std::string pythonCode; // python syntax to check if torch is installed with CUDA. pythonCode.append("import torch;"); pythonCode.append("print('Pytorch installed with CUDA') if torch.cuda.is_available else ValueError('PyTorch " "installed without CUDA');"); ExecutePython(pythonCode, workingDir); return true; - } + } return false; } void QmitkSetupVirtualEnvUtil::PipInstall(const std::string &library, const std::string &workingDir) { mitk::ProcessExecutor::ArgumentListType args; auto spExec = mitk::ProcessExecutor::New(); auto spCommand = itk::CStyleCommand::New(); spCommand->SetCallback(&PrintProcessEvent); spExec->AddObserver(mitk::ExternalProcessOutputEvent(), spCommand); args.push_back("install"); args.push_back(library); spExec->Execute(workingDir, "pip3", args); // Install TotalSegmentator in it. } void QmitkSetupVirtualEnvUtil::ExecutePython(const std::string &pythonCode, const std::string &workingDir) { mitk::ProcessExecutor::ArgumentListType args; auto spExec = mitk::ProcessExecutor::New(); auto spCommand = itk::CStyleCommand::New(); spCommand->SetCallback(&PrintProcessEvent); spExec->AddObserver(mitk::ExternalProcessOutputEvent(), spCommand); args.push_back("-c"); args.push_back(pythonCode); spExec->Execute(workingDir, "python3", args); } diff --git a/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.h b/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.h index 69409e11fb..e87910637d 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.h +++ b/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.h @@ -1,48 +1,48 @@ /*============================================================================ 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 QmitkSetupVirtualEnvUtil_h_Included #define QmitkSetupVirtualEnvUtil_h_Included #include "mitkProcessExecutor.h" #include #include #include "mitkLogMacros.h" /** * @brief Class to ... */ class MITKSEGMENTATIONUI_EXPORT QmitkSetupVirtualEnvUtil { public: enum Tool { TOTALSEGMENTATOR }; QmitkSetupVirtualEnvUtil(const QString baseDir); QmitkSetupVirtualEnvUtil(); bool SetupVirtualEnv(Tool packageName = Tool::TOTALSEGMENTATOR); void PipInstall(const std::string &library, const std::string &workingDir); void ExecutePython(const std::string &args, const std::string &pythonPath); std::map GetInstallParameters(QmitkSetupVirtualEnvUtil::Tool); QString GetBaseDir(); QString GetVirtualEnvPath(); - static void QmitkSetupVirtualEnvUtil::PrintProcessEvent(itk::Object * /*pCaller*/, const itk::EventObject &e, void *); + static void PrintProcessEvent(itk::Object * /*pCaller*/, const itk::EventObject &e, void *); private: QString m_BaseDir; QString m_venvPath; }; #endif \ No newline at end of file diff --git a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp index d5bc19d088..58ae9b8338 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp @@ -1,422 +1,328 @@ #include "QmitkTotalSegmentatorToolGUI.h" #include "mitkProcessExecutor.h" #include "mitkTotalSegmentatorTool.h" #include #include #include #include #include #include #include #include #include MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkTotalSegmentatorToolGUI, "") QmitkTotalSegmentatorToolGUI::QmitkTotalSegmentatorToolGUI() : QmitkMultiLabelSegWithPreviewToolGUIBase(), m_SuperclassEnableConfirmSegBtnFnc(m_EnableConfirmSegBtnFnc) { // Nvidia-smi command returning zero doesn't always imply lack of GPUs. // Pytorch uses its own libraries to communicate to the GPUs. Hence, only a warning can be given. if (m_GpuLoader.GetGPUCount() == 0) { std::string warning = "WARNING: No GPUs were detected on your machine. The TotalSegmentator tool can be very slow."; this->ShowErrorMessage(warning); } m_EnableConfirmSegBtnFnc = [this](bool enabled) { return !m_FirstPreviewComputation ? m_SuperclassEnableConfirmSegBtnFnc(enabled) : false; }; } void QmitkTotalSegmentatorToolGUI::ConnectNewTool(mitk::SegWithPreviewTool *newTool) { Superclass::ConnectNewTool(newTool); newTool->IsTimePointChangeAwareOff(); m_FirstPreviewComputation = true; } void QmitkTotalSegmentatorToolGUI::InitializeUI(QBoxLayout *mainLayout) { m_Controls.setupUi(this); m_Controls.pythonEnvComboBox->addItem("Select"); m_Controls.pythonEnvComboBox->setDuplicatesEnabled(false); + m_Controls.pythonEnvComboBox->setVisible(false); + m_Controls.pythonEnvLabel->setVisible(false); m_Controls.previewButton->setDisabled(true); m_Controls.statusLabel->setTextFormat(Qt::RichText); m_Controls.subtaskComboBox->addItems(m_VALID_TASKS); this->AutoParsePythonPaths(); this->SetGPUInfo(); if (m_GpuLoader.GetGPUCount() != 0) { - WriteStatusMessage(QString("STATUS: Welcome to Total Segmentator tool. You're in luck: " + QString::number(m_GpuLoader.GetGPUCount()) + - " GPU(s) were detected.")); + WriteStatusMessage(QString("STATUS: Welcome to Total Segmentator tool. You're in luck: " + + QString::number(m_GpuLoader.GetGPUCount()) + " GPU(s) were detected.")); } else { - WriteErrorMessage(QString("STATUS: Welcome to Total Segmentator tool. Sorry, " + QString::number(m_GpuLoader.GetGPUCount()) + - " GPUs were detected.")); + WriteErrorMessage(QString("STATUS: Welcome to Total Segmentator tool. Sorry, " + + QString::number(m_GpuLoader.GetGPUCount()) + " GPUs were detected.")); } mainLayout->addLayout(m_Controls.verticalLayout); connect(m_Controls.previewButton, SIGNAL(clicked()), this, SLOT(OnPreviewBtnClicked())); connect(m_Controls.installButton, SIGNAL(clicked()), this, SLOT(OnInstallBtnClicked())); // connect(m_Controls.pythonEnvComboBox, // SIGNAL(currentTextChanged(const QString &)), // this, // SLOT(OnPythonPathChanged(const QString &))); Superclass::InitializeUI(mainLayout); QString lastSelectedPyEnv = m_Settings.value("TotalSeg/LastPythonPath").toString(); m_Controls.pythonEnvComboBox->insertItem(0, lastSelectedPyEnv); const QString storageDir = QStandardPaths::writableLocation(QStandardPaths::GenericDataLocation) + QDir::separator() + qApp->organizationName() + QDir::separator() + m_VENV_NAME; m_IsInstalled = this->IsTotalSegmentatorInstalled(storageDir); if (m_IsInstalled) { OnPythonPathChanged(storageDir); this->EnableAll(m_IsInstalled); } } void QmitkTotalSegmentatorToolGUI::EnableWidgets(bool enabled) { Superclass::EnableWidgets(enabled); } void QmitkTotalSegmentatorToolGUI::SetGPUInfo() { std::vector specs = m_GpuLoader.GetAllGPUSpecs(); for (const QmitkGPUSpec &gpuSpec : specs) { m_Controls.gpuComboBox->addItem(QString::number(gpuSpec.id) + ": " + gpuSpec.name + " (" + gpuSpec.memory + ")"); } if (specs.empty()) { m_Controls.gpuComboBox->setEditable(true); m_Controls.gpuComboBox->addItem(QString::number(0)); m_Controls.gpuComboBox->setValidator(new QIntValidator(0, 999, this)); } } unsigned int QmitkTotalSegmentatorToolGUI::FetchSelectedGPUFromUI() { QString gpuInfo = m_Controls.gpuComboBox->currentText(); if (m_GpuLoader.GetGPUCount() == 0) { return static_cast(gpuInfo.toInt()); } else { QString gpuId = gpuInfo.split(":", QString::SplitBehavior::SkipEmptyParts).first(); return static_cast(gpuId.toInt()); } } -//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 QmitkTotalSegmentatorToolGUI::EnableAll(bool isEnable) +void QmitkTotalSegmentatorToolGUI::EnableAll(bool isEnable) { m_Controls.previewButton->setEnabled(isEnable); m_Controls.subtaskComboBox->setEnabled(isEnable); m_Controls.installButton->setEnabled((!isEnable)); } void QmitkTotalSegmentatorToolGUI::OnInstallBtnClicked() { - //const QString storageDir = QStandardPaths::writableLocation(QStandardPaths::GenericDataLocation) + QDir::separator() + - // qApp->organizationName() + QDir::separator(); - //MITK_INFO << storageDir.toStdString(); - bool isInstalled = false; #ifndef _WIN32 - //isInstalled = SetUpTotalSegmentator(storageDir); isInstalled = m_Installer.SetupVirtualEnv(); #endif if (isInstalled) { - // const QString pythonPath = storageDir + m_VENV_NAME; const QString pythonPath = m_Installer.GetVirtualEnvPath(); - MITK_INFO << pythonPath.toStdString(); - OnPythonPathChanged(pythonPath); + this->OnPythonPathChanged(pythonPath); // Bug: isInstalled still true even if totalsegmentator not found this->WriteStatusMessage("Successfully installed TotalSegmentator"); } else { this->WriteErrorMessage("Couldn't find TotalSegmentator"); } this->EnableAll(isInstalled); } - -bool QmitkTotalSegmentatorToolGUI::SetUpTotalSegmentatorWIN(const QString & /*path*/) -{ - return false; -} - -bool QmitkTotalSegmentatorToolGUI::SetUpTotalSegmentator(const QString &path) -{ - auto tool = this->GetConnectedToolAs(); - if (nullptr == tool) - { - return false; - } - bool isInstalled = false; - QDir folderPath(path); - if (this->IsTotalSegmentatorInstalled(folderPath.absoluteFilePath(m_VENV_NAME))) - { - return true; - } - folderPath.mkdir(m_VENV_NAME); - if (!folderPath.cd(m_VENV_NAME)) - { - return false; // Check if directory creation was successful. - } - mitk::ProcessExecutor::ArgumentListType args; - auto spExec = mitk::ProcessExecutor::New(); - auto spCommand = itk::CStyleCommand::New(); - spCommand->SetCallback(tool->onPythonProcessEvent); - spExec->AddObserver(mitk::ExternalProcessOutputEvent(), spCommand); - - args.push_back("-m"); - args.push_back("venv"); - args.push_back(m_VENV_NAME.toStdString()); - spExec->Execute(path.toStdString(), "/usr/bin/python3", args);// Setup local virtual environment - - if (folderPath.cd("bin")) - { - std::string workingDir; - workingDir = folderPath.absolutePath().toStdString(); - args.clear(); - args.push_back("install"); - args.push_back("Totalsegmentator==" + m_TOTALSEGMENTATOR_VERSION); - spExec->Execute(workingDir, "pip3", args); // Install TotalSegmentator in it. - - args.clear(); - args.push_back("install"); - args.push_back("scikit-image"); - spExec->Execute(workingDir, "pip3", args); // Install TotalSegmentator in it. - - if (this->IsTotalSegmentatorInstalled(folderPath.absolutePath())) - { - isInstalled = true; // Check if installation was successful - } - - args.clear(); - args.push_back("-c"); - std::string pythonCode; // python syntax to check if torch is installed with CUDA. - pythonCode.append("import torch;"); - pythonCode.append("print('Pytorch installed with CUDA') if torch.cuda.is_available else ValueError('PyTorch installed without CUDA');"); - args.push_back(pythonCode); - spExec->Execute(workingDir, "python3", args); - } - return isInstalled; -} - void QmitkTotalSegmentatorToolGUI::OnPreviewBtnClicked() { auto tool = this->GetConnectedToolAs(); if (nullptr == tool) { return; } QString pythonPathTextItem = ""; try { m_Controls.previewButton->setEnabled(false); qApp->processEvents(); if (!this->IsTotalSegmentatorInstalled(m_PythonPath)) { throw std::runtime_error(m_WARNING_TOTALSEG_NOT_FOUND); } - //pythonPathTextItem = m_Controls.pythonEnvComboBox->currentText(); + // pythonPathTextItem = m_Controls.pythonEnvComboBox->currentText(); bool isFast = m_Controls.fastBox->isChecked(); QString subTask = m_Controls.subtaskComboBox->currentText(); if (subTask != m_VALID_TASKS[0]) { isFast = true; } tool->SetPythonPath(m_PythonPath.toStdString()); tool->SetGpuId(FetchSelectedGPUFromUI()); tool->SetFast(isFast); tool->SetSubTask(subTask.toStdString()); this->WriteStatusMessage(QString("STATUS: Starting Segmentation task... This might take a while.")); tool->UpdatePreview(); m_Controls.previewButton->setEnabled(true); } catch (const std::exception &e) { std::stringstream errorMsg; errorMsg << "STATUS: Error while processing parameters for TotalSegmentator segmentation. Reason: " << e.what(); this->ShowErrorMessage(errorMsg.str()); this->WriteErrorMessage(QString::fromStdString(errorMsg.str())); m_Controls.previewButton->setEnabled(true); return; } catch (...) { std::string errorMsg = "Unkown error occured while generation TotalSegmentator segmentation."; this->ShowErrorMessage(errorMsg); m_Controls.previewButton->setEnabled(true); return; } this->SetLabelSetPreview(tool->GetPreviewSegmentation()); tool->IsTimePointChangeAwareOn(); this->ActualizePreviewLabelVisibility(); this->WriteStatusMessage("STATUS: Segmentation task finished successfully."); - if (!pythonPathTextItem.isEmpty())// only cache if the prediction ended without errors. - { + if (!pythonPathTextItem.isEmpty()) // only cache if the prediction ended without errors. + { QString lastSelectedPyEnv = m_Settings.value("TotalSeg/LastPythonPath").toString(); - if (lastSelectedPyEnv != pythonPathTextItem) + if (lastSelectedPyEnv != pythonPathTextItem) { m_Settings.setValue("TotalSeg/LastPythonPath", pythonPathTextItem); } } } void QmitkTotalSegmentatorToolGUI::ShowErrorMessage(const std::string &message, QMessageBox::Icon icon) { this->setCursor(Qt::ArrowCursor); QMessageBox *messageBox = new QMessageBox(icon, nullptr, message.c_str()); messageBox->exec(); delete messageBox; MITK_WARN << message; } void QmitkTotalSegmentatorToolGUI::WriteStatusMessage(const QString &message) { m_Controls.statusLabel->setText(message); m_Controls.statusLabel->setStyleSheet("font-weight: bold; color: white"); } void QmitkTotalSegmentatorToolGUI::WriteErrorMessage(const QString &message) { m_Controls.statusLabel->setText(message); m_Controls.statusLabel->setStyleSheet("font-weight: bold; color: red"); } bool QmitkTotalSegmentatorToolGUI::IsTotalSegmentatorInstalled(const QString &pythonPath) { QString fullPath = pythonPath; #ifdef _WIN32 if (!(fullPath.endsWith("Scripts", Qt::CaseInsensitive) || fullPath.endsWith("Scripts/", Qt::CaseInsensitive))) { fullPath += QDir::separator() + QString("Scripts"); } #else if (!(fullPath.endsWith("bin", Qt::CaseInsensitive) || fullPath.endsWith("bin/", Qt::CaseInsensitive))) { fullPath += QDir::separator() + QString("bin"); } #endif fullPath = fullPath.mid(fullPath.indexOf(" ") + 1); bool isExists = QFile::exists(fullPath + QDir::separator() + QString("TotalSegmentator")) && #ifdef _WIN32 QFile::exists(fullPath + QDir::separator() + QString("python.exe")); #else QFile::exists(fullPath + QDir::separator() + QString("python3")); #endif return isExists; } void QmitkTotalSegmentatorToolGUI::AutoParsePythonPaths() { QString homeDir = QDir::homePath(); std::vector searchDirs; #ifdef _WIN32 searchDirs.push_back(QString("C:") + QDir::separator() + QString("ProgramData") + QDir::separator() + QString("anaconda3")); #else // Add search locations for possible standard python paths here searchDirs.push_back(homeDir + QDir::separator() + "environments"); searchDirs.push_back(homeDir + QDir::separator() + "anaconda3"); searchDirs.push_back(homeDir + QDir::separator() + "miniconda3"); searchDirs.push_back(homeDir + QDir::separator() + "opt" + QDir::separator() + "miniconda3"); searchDirs.push_back(homeDir + QDir::separator() + "opt" + QDir::separator() + "anaconda3"); #endif for (QString searchDir : searchDirs) { if (searchDir.endsWith("anaconda3", Qt::CaseInsensitive)) { if (QDir(searchDir).exists()) { m_Controls.pythonEnvComboBox->insertItem(0, "(base): " + searchDir); searchDir.append((QDir::separator() + QString("envs"))); } } for (QDirIterator subIt(searchDir, QDir::AllDirs, QDirIterator::NoIteratorFlags); subIt.hasNext();) { subIt.next(); QString envName = subIt.fileName(); if (!envName.startsWith('.')) // Filter out irrelevent hidden folders, if any. { m_Controls.pythonEnvComboBox->insertItem(0, "(" + envName + "): " + subIt.filePath()); } } } m_Controls.pythonEnvComboBox->setCurrentIndex(-1); } void QmitkTotalSegmentatorToolGUI::OnPythonPathChanged(const QString &pyEnv) { if (pyEnv == QString("Select")) { QString path = QFileDialog::getExistingDirectory(m_Controls.pythonEnvComboBox->parentWidget(), "Python Path", "dir"); if (!path.isEmpty()) { this->OnPythonPathChanged(path); // recall same function for new path validation bool oldState = m_Controls.pythonEnvComboBox->blockSignals(true); // block signal firing while inserting item m_Controls.pythonEnvComboBox->insertItem(0, path); m_Controls.pythonEnvComboBox->setCurrentIndex(0); m_Controls.pythonEnvComboBox->blockSignals( oldState); // unblock signal firing after inserting item. Remove this after Qt6 migration } } else if (!this->IsTotalSegmentatorInstalled(pyEnv)) { this->ShowErrorMessage(m_WARNING_TOTALSEG_NOT_FOUND); m_Controls.previewButton->setDisabled(true); } else { // Show positive status meeage m_Controls.previewButton->setDisabled(false); m_PythonPath = pyEnv.mid(pyEnv.indexOf(" ") + 1); #ifdef _WIN32 if (!(m_PythonPath.endsWith("Scripts", Qt::CaseInsensitive) || m_PythonPath.endsWith("Scripts/", Qt::CaseInsensitive))) { m_PythonPath += QDir::separator() + QString("Scripts"); } #else if (!(m_PythonPath.endsWith("bin", Qt::CaseInsensitive) || m_PythonPath.endsWith("bin/", Qt::CaseInsensitive))) { m_PythonPath += QDir::separator() + QString("bin"); } #endif } }