diff --git a/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.cpp b/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.cpp index 5bd21ddb6c..b45d5fd904 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.cpp @@ -1,221 +1,178 @@ /*============================================================================ 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 "mitkLogMacros.h" -#include -#include #include #include QmitkSetupVirtualEnvUtil::QmitkSetupVirtualEnvUtil() { m_BaseDir = QStandardPaths::writableLocation(QStandardPaths::GenericDataLocation) + QDir::separator() + qApp->organizationName() + QDir::separator(); } -QmitkSetupVirtualEnvUtil::QmitkSetupVirtualEnvUtil(const QString baseDir) +QmitkSetupVirtualEnvUtil::QmitkSetupVirtualEnvUtil(const QString &baseDir) { m_BaseDir = baseDir; } -QString QmitkSetupVirtualEnvUtil::GetBaseDir() +QString& QmitkSetupVirtualEnvUtil::GetBaseDir() { return m_BaseDir; } -QString QmitkSetupVirtualEnvUtil::GetVirtualEnvPath() +QString& QmitkSetupVirtualEnvUtil::GetVirtualEnvPath() { return m_venvPath; } +QString& QmitkSetupVirtualEnvUtil::GetSystemPythonPath() +{ + return m_SysPythonPath; +} + +QString& QmitkSetupVirtualEnvUtil::GetPythonPath() +{ + return m_PythonPath; +} + +QString& QmitkSetupVirtualEnvUtil::GetPipPath() +{ + return m_PipPath; +} + void QmitkSetupVirtualEnvUtil::SetVirtualEnvPath(const QString &path) { m_venvPath = path; } -void QmitkSetupVirtualEnvUtil::SetSystemPythonPath(const QString& path) +void QmitkSetupVirtualEnvUtil::SetPipPath(const QString &path) +{ + m_PipPath = path; +} + +void QmitkSetupVirtualEnvUtil::SetPythonPath(const QString &path) { if (this->IsPythonPath(path)) { - m_SysPythonPath = path; + m_PythonPath = path; } else { - MITK_INFO << "Python was not detected in "+path.toStdString(); + MITK_INFO << "Python was not detected in " + path.toStdString(); } } -std::map QmitkSetupVirtualEnvUtil::GetInstallParameters( - QmitkSetupVirtualEnvUtil::Tool packageName) +void QmitkSetupVirtualEnvUtil::SetSystemPythonPath(const QString &path) { - std::map parameters; - - switch (packageName) + if (this->IsPythonPath(path)) + { + m_SysPythonPath = path; + } + else { - case QmitkSetupVirtualEnvUtil::Tool::TOTALSEGMENTATOR: - { - parameters["venv_name"] = ".totalsegmentator"; - parameters["pkg_version"] = "1.5.3"; - parameters["pkg_names"] = "Totalsegmentator==1.5.3,scipy==1.9.1"; // comma separated string - /*Add other parameters here...*/ - break; - } /*Add more tools here...*/ - default: - { - std::runtime_error("Unsupported Tool type"); - break; - } + MITK_INFO << "Python was not detected in " + path.toStdString(); } - 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) -{ - MITK_INFO << m_SysPythonPath.toStdString(); - if (m_SysPythonPath.isEmpty()) - { - return false; - } - 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()); -#ifdef _WIN32 - QString pythonFile = m_SysPythonPath + QDir::separator() + "python.exe"; - spExec->Execute(m_BaseDir.toStdString(), pythonFile.toStdString(), args); // Setup local virtual environment - QString pythonExeFolder = "Scripts"; -#else - QString pythonFile = m_SysPythonPath + QDir::separator() + "python3"; - spExec->Execute(m_BaseDir.toStdString(), "/usr/bin/python3", args); // Setup local virtual environment - QString pythonExeFolder = "bin"; -#endif - - if (folderPath.cd(pythonExeFolder)) - { - m_venvPath = folderPath.absolutePath(); - std::string workingDir = m_venvPath.toStdString(); - InstallPytorch(workingDir, &PrintProcessEvent); - for (auto &package : packages) - { - PipInstall(package, workingDir, &PrintProcessEvent); - } - std::string pythonCode; // python syntax to check if torch is installed with CUDA. - pythonCode.append("import torch;"); - pythonCode.append("print('Pytorch was installed with CUDA') if torch.cuda.is_available() else print('PyTorch was " - "installed WITHOUT CUDA');"); - ExecutePython(pythonCode, workingDir, &PrintProcessEvent); - return true; - } - return false; -} - void QmitkSetupVirtualEnvUtil::InstallPytorch(const std::string &workingDir, void (*callback)(itk::Object *, const itk::EventObject &, void *)) { mitk::ProcessExecutor::ArgumentListType args; auto spExec = mitk::ProcessExecutor::New(); auto spCommand = itk::CStyleCommand::New(); spCommand->SetCallback(callback); spExec->AddObserver(mitk::ExternalProcessOutputEvent(), spCommand); args.push_back("-m"); args.push_back("pip"); args.push_back("install"); args.push_back("light-the-torch"); spExec->Execute(workingDir, "python", args); PipInstall("torch", workingDir, callback, "ltt"); } void QmitkSetupVirtualEnvUtil::PipInstall(const std::string &library, const std::string &workingDir, void (*callback)(itk::Object *, const itk::EventObject &, void *), const std::string &command) { mitk::ProcessExecutor::ArgumentListType args; auto spExec = mitk::ProcessExecutor::New(); auto spCommand = itk::CStyleCommand::New(); spCommand->SetCallback(callback); spExec->AddObserver(mitk::ExternalProcessOutputEvent(), spCommand); args.push_back("install"); args.push_back(library); spExec->Execute(workingDir, command, args); } +void QmitkSetupVirtualEnvUtil::PipInstall(const std::string &library, + void (*callback)(itk::Object*, const itk::EventObject&, void*), + const std::string& command) +{ + this->PipInstall(library, this->GetPipPath().toStdString(), callback, command); +} + void QmitkSetupVirtualEnvUtil::ExecutePython(const std::string &pythonCode, const std::string &workingDir, void (*callback)(itk::Object *, const itk::EventObject &, void *), const std::string &command) { mitk::ProcessExecutor::ArgumentListType args; auto spExec = mitk::ProcessExecutor::New(); auto spCommand = itk::CStyleCommand::New(); spCommand->SetCallback(callback); spExec->AddObserver(mitk::ExternalProcessOutputEvent(), spCommand); args.push_back("-c"); args.push_back(pythonCode); spExec->Execute(workingDir, command, args); } +void QmitkSetupVirtualEnvUtil::ExecutePython(const std::string &args, + void (*callback)(itk::Object *, const itk::EventObject &, void *), + const std::string &command) +{ + this->ExecutePython(args, this->GetPythonPath().toStdString(), callback, command); +} bool QmitkSetupVirtualEnvUtil::IsPythonPath(const QString &pythonPath) { QString fullPath = pythonPath; fullPath = fullPath.mid(fullPath.indexOf(" ") + 1); bool isExists = #ifdef _WIN32 - QFile::exists(fullPath + QDir::separator() + QString("python.exe")); + QFile::exists(fullPath + QDir::separator() + QString("python.exe")); #else - QFile::exists(fullPath + QDir::separator() + QString("python3")); + QFile::exists(fullPath + QDir::separator() + QString("python3")); #endif return isExists; } \ No newline at end of file diff --git a/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.h b/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.h index 808b060ead..1a6ae74dea 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.h +++ b/Modules/SegmentationUI/Qmitk/QmitkSetupVirtualEnvUtil.h @@ -1,63 +1,74 @@ /*============================================================================ 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 "mitkLogMacros.h" #include "mitkProcessExecutor.h" #include #include +#include +#include /** * @brief Class to ... */ class MITKSEGMENTATIONUI_EXPORT QmitkSetupVirtualEnvUtil { public: - enum Tool - { - TOTALSEGMENTATOR - }; - - QmitkSetupVirtualEnvUtil(const QString baseDir); + QmitkSetupVirtualEnvUtil(const QString& baseDir); QmitkSetupVirtualEnvUtil(); - bool SetupVirtualEnv(Tool packageName = Tool::TOTALSEGMENTATOR); + virtual bool SetupVirtualEnv(const QString& venvName) = 0; void PipInstall(const std::string &library, const std::string &workingDir, void (*callback)(itk::Object *, const itk::EventObject &, void *), const std::string &command = "pip3"); + + void PipInstall(const std::string &library, + void (*callback)(itk::Object *, const itk::EventObject &, void *), + const std::string &command = "pip3"); + + void ExecutePython(const std::string &args, const std::string &pythonPath, void (*callback)(itk::Object *, const itk::EventObject &, void *), const std::string &command = "python"); + void ExecutePython(const std::string &args, + void (*callback)(itk::Object *, const itk::EventObject &, void *), + const std::string &command = "python"); + void InstallPytorch(const std::string &workingDir, void (*callback)(itk::Object *, const itk::EventObject &, void *)); - std::map GetInstallParameters(QmitkSetupVirtualEnvUtil::Tool); - QString GetBaseDir(); - QString GetVirtualEnvPath(); + QString& GetBaseDir(); + QString& GetVirtualEnvPath(); + QString& GetSystemPythonPath(); + QString& GetPythonPath(); + QString& GetPipPath(); void SetSystemPythonPath(const QString& path); + void SetPythonPath(const QString& path); + void SetPipPath(const QString& path); void SetVirtualEnvPath(const QString &path); + bool IsPythonPath(const QString &pythonPath); static void PrintProcessEvent(itk::Object * /*pCaller*/, const itk::EventObject &e, void *); private: QString m_PythonPath; QString m_PipPath; QString m_BaseDir; QString m_venvPath; QString m_SysPythonPath; }; - -#endif \ No newline at end of file +#endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp index 47c31e4702..e1b06af105 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp @@ -1,391 +1,450 @@ #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); + this->AutoParsePythonPaths(); #ifndef _WIN32 m_Controls.sysPythonComboBox->addItem("/usr/bin"); #endif m_Controls.sysPythonComboBox->addItem("Select"); - this->AutoParsePythonPaths(); - m_Controls.pythonEnvComboBox->addItem("Select"); m_Controls.pythonEnvComboBox->setDuplicatesEnabled(false); m_Controls.pythonEnvComboBox->setDisabled(true); m_Controls.previewButton->setDisabled(true); m_Controls.statusLabel->setTextFormat(Qt::RichText); m_Controls.subtaskComboBox->addItems(m_VALID_TASKS); QString welcomeText; this->SetGPUInfo(); if (m_GpuLoader.GetGPUCount() != 0) { welcomeText = "STATUS: Welcome to Total Segmentator tool. You're in luck: " + QString::number(m_GpuLoader.GetGPUCount()) + " GPU(s) were detected."; } else { welcomeText = "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.overrideBox, SIGNAL(stateChanged(int)), this, SLOT(OnOverrideChecked(int))); connect(m_Controls.pythonEnvComboBox, QOverload::of(&QComboBox::activated), [=](int index) { OnPythonPathChanged(m_Controls.pythonEnvComboBox->itemText(index)); }); 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; + const QString storageDir = m_Installer.GetVirtualEnvPath(); m_IsInstalled = this->IsTotalSegmentatorInstalled(storageDir); if (m_IsInstalled) { m_PythonPath = GetPythonPathFromUI(storageDir); m_Installer.SetVirtualEnvPath(m_PythonPath); this->EnableAll(m_IsInstalled); - welcomeText += " Totalsegmentator is already found installed"; + welcomeText += " Totalsegmentator is already found installed."; } else { welcomeText += " Totalsegmentator not installed. Please click on \"Install Totalsegmentator\" above."; } this->WriteStatusMessage(welcomeText); } 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()); } } void QmitkTotalSegmentatorToolGUI::EnableAll(bool isEnable) { m_Controls.previewButton->setEnabled(isEnable); m_Controls.subtaskComboBox->setEnabled(isEnable); m_Controls.installButton->setEnabled((!isEnable)); } void QmitkTotalSegmentatorToolGUI::OnInstallBtnClicked() { bool isInstalled = false; MITK_INFO << m_Controls.sysPythonComboBox->currentText().toStdString(); QString systemPython = GetPythonPathFromUI(m_Controls.sysPythonComboBox->currentText()); MITK_INFO << systemPython.toStdString(); if (systemPython.isEmpty()) { this->WriteErrorMessage("Couldn't find Python"); return; } else { m_Installer.SetSystemPythonPath(systemPython); } - isInstalled = m_Installer.SetupVirtualEnv(); + isInstalled = m_Installer.SetupVirtualEnv(m_Installer.m_VENV_NAME); if (isInstalled) { const QString pythonPath = m_Installer.GetVirtualEnvPath(); m_PythonPath = GetPythonPathFromUI(m_Installer.GetVirtualEnvPath()); this->WriteStatusMessage("Successfully installed TotalSegmentator"); } else { this->WriteErrorMessage("Couldn't find TotalSegmentator"); } this->EnableAll(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); } 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. { QString lastSelectedPyEnv = m_Settings.value("TotalSeg/LastPythonPath").toString(); 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; fullPath = fullPath.mid(fullPath.indexOf(" ") + 1); bool isPythonExists = false; #ifdef _WIN32 isPythonExists = QFile::exists(fullPath + QDir::separator() + QString("python.exe")); if (!(fullPath.endsWith("Scripts", Qt::CaseInsensitive) || fullPath.endsWith("Scripts/", Qt::CaseInsensitive))) { fullPath += QDir::separator() + QString("Scripts"); isPythonExists = (!isPythonExists) ? QFile::exists(fullPath + QDir::separator() + QString("python.exe")) : isPythonExists; } #else isPythonExists = QFile::exists(fullPath + QDir::separator() + QString("python3")); if (!(fullPath.endsWith("bin", Qt::CaseInsensitive) || fullPath.endsWith("bin/", Qt::CaseInsensitive))) { fullPath += QDir::separator() + QString("bin"); isPythonExists = (!isPythonExists) ? QFile::exists(fullPath + QDir::separator() + QString("python3")) : isPythonExists; } #endif bool isExists = QFile::exists(fullPath + QDir::separator() + QString("TotalSegmentator")) && isPythonExists; 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.sysPythonComboBox->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.sysPythonComboBox->insertItem(0, "(" + envName + "): " + subIt.filePath()); } } } - m_Controls.sysPythonComboBox->setCurrentIndex(-1); } void QmitkTotalSegmentatorToolGUI::OnPythonPathChanged(const QString &pyEnv) { if (pyEnv == QString("Select")) { m_Controls.previewButton->setDisabled(true); 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 = GetPythonPathFromUI(pyEnv); } } QString QmitkTotalSegmentatorToolGUI::GetPythonPathFromUI(const QString &pyEnv) { QString pythonPath; QString fullPath = pyEnv.mid(pyEnv.indexOf(" ") + 1); + if (fullPath.isEmpty()) + { + return fullPath; + } bool isPythonExists = false; #ifdef _WIN32 isPythonExists = QFile::exists(fullPath + QDir::separator() + QString("python.exe")); if (isPythonExists) { pythonPath = fullPath; } else if (!(fullPath.endsWith("Scripts", Qt::CaseInsensitive) || fullPath.endsWith("Scripts/", Qt::CaseInsensitive))) { fullPath += QDir::separator() + QString("Scripts"); pythonPath = fullPath; } #else isPythonExists = QFile::exists(fullPath + QDir::separator() + QString("python3")); if (isPythonExists) { pythonPath = fullPath; } else if (!(fullPath.endsWith("bin", Qt::CaseInsensitive) || fullPath.endsWith("bin/", Qt::CaseInsensitive))) { fullPath += QDir::separator() + QString("bin"); pythonPath = fullPath; } #endif return pythonPath; } void QmitkTotalSegmentatorToolGUI::OnOverrideChecked(int state) { bool isEnabled = false; if (state == Qt::Checked) { isEnabled = true; m_Controls.previewButton->setDisabled(true); m_PythonPath.clear(); } else { m_PythonPath.clear(); m_Controls.previewButton->setDisabled(true); if (m_IsInstalled) { m_PythonPath = m_Installer.GetVirtualEnvPath(); this->EnableAll(m_IsInstalled); } } m_Controls.pythonEnvComboBox->setEnabled(isEnabled); } + + +bool QmitkTotalSegmentatorToolInstaller::SetupVirtualEnv(const QString& venvName) +{ + MITK_INFO << GetSystemPythonPath().toStdString(); + if (GetSystemPythonPath().isEmpty()) + { + return false; + } + QDir folderPath(GetBaseDir()); + 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()); +#ifdef _WIN32 + QString pythonFile = GetSystemPythonPath() + QDir::separator() + "python.exe"; + spExec->Execute(GetBaseDir().toStdString(), pythonFile.toStdString(), args); // Setup local virtual environment + QString pythonExeFolder = "Scripts"; +#else + QString pythonFile = m_SysPythonPath + QDir::separator() + "python3"; + spExec->Execute(m_BaseDir.toStdString(), "/usr/bin/python3", args); // Setup local virtual environment + QString pythonExeFolder = "bin"; +#endif + + if (folderPath.cd(pythonExeFolder)) + { + SetPythonPath(folderPath.absolutePath()); + SetPipPath(folderPath.absolutePath()); + std::string workingDir = GetPythonPath().toStdString(); + MITK_INFO << "workingDir: " << workingDir; + InstallPytorch(workingDir, &PrintProcessEvent); + for (auto &package : m_PACKAGES) + { + PipInstall(package.toStdString(), &PrintProcessEvent); + } + std::string pythonCode; // python syntax to check if torch is installed with CUDA. + pythonCode.append("import torch;"); + pythonCode.append("print('Pytorch was installed with CUDA') if torch.cuda.is_available() else print('PyTorch was " + "installed WITHOUT CUDA');"); + ExecutePython(pythonCode, &PrintProcessEvent); + return true; + } + return false; +} + +QString QmitkTotalSegmentatorToolInstaller::GetVirtualEnvPath() +{ + return m_STORAGE_DIR + m_VENV_NAME; +} \ No newline at end of file diff --git a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.h index 9e0dbcd558..b9d41f1a06 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.h @@ -1,126 +1,139 @@ #ifndef QmitkTotalSegmentatorToolGUI_h_Included #define QmitkTotalSegmentatorToolGUI_h_Included #include "QmitkMultiLabelSegWithPreviewToolGUIBase.h" +#include "QmitkSetupVirtualEnvUtil.h" +#include "QmitknnUNetGPU.h" #include "ui_QmitkTotalSegmentatorGUIControls.h" #include #include -#include "QmitknnUNetGPU.h" #include -#include "QmitkSetupVirtualEnvUtil.h" +#include +class QmitkTotalSegmentatorToolInstaller : public QmitkSetupVirtualEnvUtil +{ +public: + const QString m_VENV_NAME = ".totalsegmentator"; + const QString m_TOTALSEGMENTATOR_VERSION = "1.5.3"; + const std::vector m_PACKAGES = {QString("Totalsegmentator==") + m_TOTALSEGMENTATOR_VERSION, + QString("scipy==1.9.1")}; + const QString m_STORAGE_DIR; + inline QmitkTotalSegmentatorToolInstaller( + const QString baseDir = QStandardPaths::writableLocation(QStandardPaths::GenericDataLocation) + QDir::separator() + + qApp->organizationName() + QDir::separator()) + : QmitkSetupVirtualEnvUtil(baseDir), m_STORAGE_DIR(baseDir){}; + bool SetupVirtualEnv(const QString &) override; + QString GetVirtualEnvPath(); +}; class MITKSEGMENTATIONUI_EXPORT QmitkTotalSegmentatorToolGUI : public QmitkMultiLabelSegWithPreviewToolGUIBase { Q_OBJECT public: mitkClassMacro(QmitkTotalSegmentatorToolGUI, QmitkMultiLabelSegWithPreviewToolGUIBase); itkFactorylessNewMacro(Self); itkCloneMacro(Self); -protected slots : - +protected slots: + /** * @brief Qt Slot */ void OnPreviewBtnClicked(); /** * @brief Qt Slot */ void OnPythonPathChanged(const QString &); /** * @brief Qt Slot */ void OnInstallBtnClicked(); /** - * @brief Qt Slot + * @brief Qt Slot */ void OnOverrideChecked(int); protected: QmitkTotalSegmentatorToolGUI(); ~QmitkTotalSegmentatorToolGUI() = default; - void ConnectNewTool(mitk::SegWithPreviewTool* newTool) override; - void InitializeUI(QBoxLayout* mainLayout) override; + void ConnectNewTool(mitk::SegWithPreviewTool *newTool) override; + void InitializeUI(QBoxLayout *mainLayout) override; void EnableWidgets(bool enabled) override; /** * @brief Enable (or Disable) GUI elements. */ void EnableAll(bool); /** * @brief Searches and parses paths of python virtual enviroments * from predefined lookout locations - */ + */ void AutoParsePythonPaths(); - + /** * @brief Checks if TotalSegmentator command is valid in the selected python virtual environment. * * @return bool */ bool IsTotalSegmentatorInstalled(const QString &); /** * @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 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 Returns GPU id of the selected GPU from the Combo box. * * @return unsigned int */ unsigned int FetchSelectedGPUFromUI(); bool SetUpTotalSegmentator(const QString &); bool SetUpTotalSegmentatorWIN(const QString &); QString GetPythonPathFromUI(const QString &pyEnv); - /** * @brief For storing values like Python path across sessions. */ QSettings m_Settings; QString m_PythonPath; - QmitkSetupVirtualEnvUtil m_Installer; QmitkGPULoader m_GpuLoader; Ui_QmitkTotalSegmentatorToolGUIControls m_Controls; bool m_FirstPreviewComputation = true; bool m_IsInstalled = false; EnableConfirmSegBtnFunctionType m_SuperclassEnableConfirmSegBtnFnc; - const std::string m_WARNING_TOTALSEG_NOT_FOUND = "TotalSegmentator is not detected in the selected python environment.Please select a valid " - "python environment or install TotalSegmentator."; + const std::string m_WARNING_TOTALSEG_NOT_FOUND = + "TotalSegmentator is not detected in the selected python environment.Please select a valid " + "python environment or install TotalSegmentator."; const QStringList m_VALID_TASKS = {"total", "cerebral_bleed", "hip_implant", "coronary_arteries"}; - const QString m_VENV_NAME = ".totalsegmentator"; - const std::string m_TOTALSEGMENTATOR_VERSION = "1.5.2"; + QmitkTotalSegmentatorToolInstaller m_Installer; }; - #endif