diff --git a/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.cpp b/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.cpp index e2ff6aa6cd..c26e3457b1 100644 --- a/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.cpp +++ b/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.cpp @@ -1,265 +1,262 @@ /*============================================================================ 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. ============================================================================*/ // MITK #include "mitkTotalSegmentatorTool.h" #include "mitkIOUtil.h" -#include #include +#include // us #include #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, TotalSegmentatorTool, "Total Segmentator"); } mitk::TotalSegmentatorTool::~TotalSegmentatorTool() { itksys::SystemTools::RemoveADirectory(this->GetMitkTempDir()); } void mitk::TotalSegmentatorTool::Activated() { Superclass::Activated(); this->SetLabelTransferMode(LabelTransferMode::AllLabels); } const char **mitk::TotalSegmentatorTool::GetXPM() const { return nullptr; } us::ModuleResource mitk::TotalSegmentatorTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("AI.svg"); return resource; } const char *mitk::TotalSegmentatorTool::GetName() const { return "Total Segmentator"; } -namespace +void mitk::TotalSegmentatorTool::onPythonProcessEvent(itk::Object * /*pCaller*/, const itk::EventObject &e, void *) { - void onPythonProcessEvent(itk::Object * /*pCaller*/, const itk::EventObject &e, void *) - { - std::string testCOUT; - std::string testCERR; - const auto *pEvent = dynamic_cast(&e); + std::string testCOUT; + std::string testCERR; + const auto *pEvent = dynamic_cast(&e); - if (pEvent) - { - testCOUT = testCOUT + pEvent->GetOutput(); - MITK_INFO << testCOUT; - } + if (pEvent) + { + testCOUT = testCOUT + pEvent->GetOutput(); + MITK_INFO << testCOUT; + } - const auto *pErrEvent = dynamic_cast(&e); + const auto *pErrEvent = dynamic_cast(&e); - if (pErrEvent) - { - testCERR = testCERR + pErrEvent->GetOutput(); - MITK_ERROR << testCERR; - } + if (pErrEvent) + { + testCERR = testCERR + pErrEvent->GetOutput(); + MITK_ERROR << testCERR; } -} // namespace +} void mitk::TotalSegmentatorTool::DoUpdatePreview(const Image *inputAtTimeStep, const Image * /*oldSegAtTimeStep*/, LabelSetImage *previewImage, TimeStepType timeStep) { if (!m_IsMitkTempDirAvailable) // create temp directory if not done already { this->SetMitkTempDir(IOUtil::CreateTemporaryDirectory("mitk-XXXXXX")); m_IsMitkTempDirAvailable = true; } this->ParseLabelNames(this->GetLabelMapPath()); ProcessExecutor::Pointer spExec = ProcessExecutor::New(); itk::CStyleCommand::Pointer spCommand = itk::CStyleCommand::New(); spCommand->SetCallback(&onPythonProcessEvent); spExec->AddObserver(ExternalProcessOutputEvent(), spCommand); - + std::string inDir, outDir, inputImagePath, outputImagePath, scriptPath; inDir = IOUtil::CreateTemporaryDirectory("totalseg-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("_")); outDir = IOUtil::CreateTemporaryDirectory("totalseg-out-XXXXXX", this->GetMitkTempDir()); outputImagePath = outDir + IOUtil::GetDirectorySeparator() + token + "_000.nii.gz"; ProcessExecutor::ArgumentListType args; IOUtil::Save(inputAtTimeStep, inputImagePath); std::string *outArg = &outputImagePath; bool isSubTask = false; if (this->GetSubTask() != m_DEFAULT_TOTAL_TASK) { isSubTask = true; outputImagePath = outDir + IOUtil::GetDirectorySeparator() + this->GetSubTask() + ".nii.gz"; outArg = &outDir; } this->run_totalsegmentator( - spExec, inputImagePath, *outArg, this->GetFast(), !isSubTask, this->GetGpuId(), m_DEFAULT_TOTAL_TASK); + spExec, inputImagePath, *outArg, this->GetFast(), !isSubTask, this->GetGpuId(), m_DEFAULT_TOTAL_TASK); if (isSubTask) { this->run_totalsegmentator( spExec, inputImagePath, *outArg, !isSubTask, !isSubTask, this->GetGpuId(), this->GetSubTask()); } Image::Pointer outputImage = IOUtil::Load(outputImagePath); auto outputBuffer = mitk::LabelSetImage::New(); outputBuffer->InitializeByLabeledImage(outputImage); outputBuffer->SetGeometry(inputAtTimeStep->GetGeometry()); this->MapLabelsToSegmentation(outputBuffer, m_LabelMapTotal); TransferLabelSetImageContent(outputBuffer, previewImage, timeStep); } void mitk::TotalSegmentatorTool::run_totalsegmentator(ProcessExecutor::Pointer spExec, const std::string &inputImagePath, const std::string &outputImagePath, bool isFast, bool isMultiLabel, unsigned int gpuId, const std::string &subTask) { ProcessExecutor::ArgumentListType args; std::string command = "TotalSegmentator"; #ifdef _WIN32 command = "python"; #else command = "TotalSegmentator"; #endif args.clear(); #ifdef _WIN32 args.push_back("TotalSegmentator"); #endif args.push_back("-i"); args.push_back(inputImagePath); args.push_back("-o"); args.push_back(outputImagePath); if (subTask != m_DEFAULT_TOTAL_TASK) { args.push_back("-ta"); args.push_back(subTask); } if (isMultiLabel) { args.push_back("--ml"); } if (isFast) { args.push_back("--fast"); } try { std::string cudaEnv = "CUDA_VISIBLE_DEVICES=" + std::to_string(gpuId); itksys::SystemTools::PutEnv(cudaEnv.c_str()); for (auto &arg : args) MITK_INFO << arg; MITK_INFO << this->GetPythonPath(); spExec->Execute(this->GetPythonPath(), command, args); } catch (const mitk::Exception &e) { MITK_ERROR << e.GetDescription(); return; } } void mitk::TotalSegmentatorTool::ParseLabelNames(const std::string &fileName) { std::fstream newfile; newfile.open(fileName, ios::in); std::stringstream buffer; if (newfile.is_open()) { int line = 0; std::string temp; while (std::getline(newfile, temp)) { if (line > 1 && line < 106) { buffer << temp; } ++line; } } std::string key, val; while (std::getline(std::getline(buffer, key, ':'), val, ',')) { m_LabelMapTotal[std::stoi(key)] = val; } } void mitk::TotalSegmentatorTool::MapLabelsToSegmentation(mitk::LabelSetImage::Pointer outputBuffer, std::map &labelMap) { for (auto const &[key, val] : labelMap) { mitk::Label *labelptr = outputBuffer->GetLabel(key, 0); if (nullptr != labelptr) { labelptr->SetName(val); } } } std::string mitk::TotalSegmentatorTool::GetLabelMapPath() { std::string pythonFileName; std::filesystem::path pathToLabelMap(this->GetPythonPath()); pathToLabelMap = pathToLabelMap.parent_path(); #ifdef _WIN32 pythonFileName = pathToLabelMap.string() + "/Lib/site-packages/totalsegmentator/map_to_binary.py"; #else pathToLabelMap.append("lib"); for (auto const &dir_entry : std::filesystem::directory_iterator{pathToLabelMap}) { if (dir_entry.is_directory()) { auto dirName = dir_entry.path().filename().string(); if (dirName.rfind("python", 0) == 0) { pathToLabelMap.append(dir_entry.path().filename().string()); break; } } } pythonFileName = pathToLabelMap.string() + "/site-packages/totalsegmentator/map_to_binary.py"; #endif return pythonFileName; } diff --git a/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.h b/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.h index 866909c47a..7553739a8c 100644 --- a/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.h +++ b/Modules/Segmentation/Interactions/mitkTotalSegmentatorTool.h @@ -1,128 +1,130 @@ /*============================================================================ 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 MITKTOTALSEGMENTATORTOOL_H #define MITKTOTALSEGMENTATORTOOL_H #include "mitkSegWithPreviewTool.h" #include #include "mitkProcessExecutor.h" namespace us { class ModuleResource; } namespace mitk { /** \brief TotalSegmentator segmentation tool. \ingroup Interaction \ingroup ToolManagerEtAl \warning Only to be instantiated by mitk::ToolManager. */ class MITKSEGMENTATION_EXPORT TotalSegmentatorTool : public SegWithPreviewTool { public: mitkClassMacro(TotalSegmentatorTool, SegWithPreviewTool); itkFactorylessNewMacro(Self); itkCloneMacro(Self); const char *GetName() const override; const char **GetXPM() const override; us::ModuleResource GetIconResource() const override; void Activated() override; itkSetMacro(MitkTempDir, std::string); itkGetConstMacro(MitkTempDir, std::string); itkSetMacro(SubTask, std::string); itkGetConstMacro(SubTask, std::string); itkSetMacro(PythonPath, std::string); itkGetConstMacro(PythonPath, std::string); itkSetMacro(GpuId, unsigned int); itkGetConstMacro(GpuId, unsigned int); itkSetMacro(Fast, bool); itkGetConstMacro(Fast, bool); itkBooleanMacro(Fast); itkSetMacro(IsMitkTempDirAvailable, bool); itkGetConstMacro(IsMitkTempDirAvailable, bool); itkBooleanMacro(IsMitkTempDirAvailable); + static void onPythonProcessEvent(itk::Object * /*pCaller*/, const itk::EventObject &e, void *); + protected: TotalSegmentatorTool() = default; ~TotalSegmentatorTool(); /** * @brief Overriden method from the tool manager to execute the segmentation * Implementation: * 1. Creates temp directory, if not done already. * 2. Parses Label names from map_to_binary.py for using later on. * 3. Calls "run_totalsegmentator" method. * 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: /** * @brief Runs Totalsegmentator python process with desired arguments * */ void run_totalsegmentator(ProcessExecutor::Pointer, const std::string &, const std::string &, bool, bool, unsigned int, const std::string &); /** * @brief Applies the m_LabelMapTotal lookup table on the output segmentation LabelSetImage. * */ void MapLabelsToSegmentation(mitk::LabelSetImage::Pointer, std::map&); /** * @brief Parses map_to_binary.py file to extract label ids and names * and stores as a map for reference in m_LabelMapTotal * * @param filePath */ void ParseLabelNames(const std::string &); /** * @brief Get the Label Map Path from the virtual environment location * * @return std::string */ std::string GetLabelMapPath(); std::string m_MitkTempDir; std::string m_PythonPath; std::string m_SubTask = "total"; unsigned int m_GpuId; std::map m_LabelMapTotal; bool m_Fast; bool m_IsMitkTempDirAvailable = false; const std::string m_TEMPLATE_FILENAME = "XXXXXX_000_0000.nii.gz"; const std::string m_DEFAULT_TOTAL_TASK = "total"; }; // class } // namespace #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp index fe633d2649..97a85f4ad1 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.cpp @@ -1,391 +1,407 @@ #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.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.")); } else { 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) + "/" + qApp->organizationName() + "/"; MITK_INFO << storageDir.toStdString(); - this->ToggleEnableEverything(false); - if (this->IsTotalSegmentatorInstalled(storageDir + QDir::separator() + m_VENV_NAME)) - { - this->ToggleEnableEverything(true); - } + m_IsInstalled = this->IsTotalSegmentatorInstalled(storageDir + QDir::separator() + m_VENV_NAME); + 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 +//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::ToggleEnableEverything(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) + "/" + qApp->organizationName() + "/"; MITK_INFO << storageDir.toStdString(); - bool isSuccess = false; + bool isInstalled = false; #ifndef _WIN32 isSuccess = SetUpTotalSegmentator(storageDir); #endif - if (isSuccess) + if (isInstalled) { - this->ToggleEnableEverything(true); + this->EnableAll(true); this->WriteStatusMessage("Successfully installed TotalSegmentator"); } else { this->WriteErrorMessage("Couldn't find TotalSegmentator"); } } + +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(); - itk::CStyleCommand::Pointer spCommand = itk::CStyleCommand::New(); - spCommand->SetCallback(&onPythonProcessEvent); + 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/python", 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"); + args.push_back("Totalsegmentator==" + m_TOTALSEGMENTATOR_VERSION); 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("if not torch.cuda.is_available: raise 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(); 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; #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 } } diff --git a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.h index 02ccfed186..2bb4860607 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkTotalSegmentatorToolGUI.h @@ -1,111 +1,113 @@ #ifndef QmitkTotalSegmentatorToolGUI_h_Included #define QmitkTotalSegmentatorToolGUI_h_Included #include "QmitkMultiLabelSegWithPreviewToolGUIBase.h" #include "ui_QmitkTotalSegmentatorGUIControls.h" #include #include #include "QmitknnUNetGPU.h" #include class MITKSEGMENTATIONUI_EXPORT QmitkTotalSegmentatorToolGUI : public QmitkMultiLabelSegWithPreviewToolGUIBase { Q_OBJECT public: mitkClassMacro(QmitkTotalSegmentatorToolGUI, QmitkMultiLabelSegWithPreviewToolGUIBase); itkFactorylessNewMacro(Self); itkCloneMacro(Self); protected slots : /** * @brief Qt Slot */ void OnPreviewBtnClicked(); /** * @brief Qt Slot */ void OnPythonPathChanged(const QString &); /** @brief Qt Slot */ void OnInstallBtnClicked(); protected: QmitkTotalSegmentatorToolGUI(); ~QmitkTotalSegmentatorToolGUI() = default; void ConnectNewTool(mitk::SegWithPreviewTool* newTool) override; void InitializeUI(QBoxLayout* mainLayout) override; void EnableWidgets(bool enabled) override; - void ToggleEnableEverything(bool); + 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 &); /** * @brief For storing values like Python path across sessions. */ QSettings m_Settings; QString m_PythonPath; 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 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"; }; #endif