diff --git a/Modules/AppUtil/include/mitkBaseApplication.h b/Modules/AppUtil/include/mitkBaseApplication.h index ad11d6f08a..00cca3ef7d 100644 --- a/Modules/AppUtil/include/mitkBaseApplication.h +++ b/Modules/AppUtil/include/mitkBaseApplication.h @@ -1,319 +1,320 @@ /*============================================================================ 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 mitkBaseApplication_h #define mitkBaseApplication_h #include #include #include #include class ctkPluginContext; class ctkPluginFramework; class QCoreApplication; class QTranslator; namespace mitk { /** * A utility class for starting BlueBerry applications. * * In the simplest case, create an instance of this class and call run(). * This will launch a CTK plugin framework instance and execute the * default application registered by a plug-in via the * org.blueberry.osgi.applications extension point. * * This class contains many convenience methods to: * - Put the application in safe mode which catches unhandled * exceptions thrown in the Qt event loop and displays an error * message. * - Put the application in single mode which by default * sends the command line arguments to an already running instance * of the same application instead of creating a second instance. * - Add a list of library names which should be pre-loaded at * application start-up, e.g. to speed up the initial launch during * the caching process of the plug-in meta-data. * - Set a custom provisioning file to start a specific set of CTK * plug-ins during application start-up. * - Set and get CTK plugin framework properties * * The behavior can further be customized by deriving from BaseApplication * and overriding specific methods, such as: * - initializeLibraryPaths() to add specific library / plugin search paths * - defineOptions(Poco::Util::OptionSet&) to define a custom set of * command line options * - getQApplication() to provide a custom QCoreApplication instance * * A simple but complete example: * \code * #include * * int main(int argc, char* argv[]) * { * mitk::BaseApplication app(argc, argv); * app.setApplicationName("MyApp"); * app.setOrganizationName("MyOrganization"); * * // Run the workbench * return app.run(); * } * \endcode */ class MITKAPPUTIL_EXPORT BaseApplication : public Poco::Util::Application { public: // Command line arguments static const QString ARG_APPLICATION; static const QString ARG_CLEAN; static const QString ARG_CONSOLELOG; static const QString ARG_DEBUG; static const QString ARG_FORCE_PLUGIN_INSTALL; static const QString ARG_HOME; static const QString ARG_NEWINSTANCE; static const QString ARG_NO_LAZY_REGISTRY_CACHE_LOADING; static const QString ARG_NO_REGISTRY_CACHE; static const QString ARG_PLUGIN_CACHE; static const QString ARG_PLUGIN_DIRS; static const QString ARG_PRELOAD_LIBRARY; static const QString ARG_PRODUCT; static const QString ARG_PROVISIONING; static const QString ARG_REGISTRY_MULTI_LANGUAGE; static const QString ARG_SPLASH_IMAGE; static const QString ARG_STORAGE_DIR; static const QString ARG_XARGS; static const QString ARG_LOG_QT_MESSAGES; static const QString ARG_SEGMENTATION_LABELSET_PRESET; + static const QString ARG_SEGMENTATION_LABEL_SUGGESTIONS; // BlueBerry specific plugin framework properties static const QString PROP_APPLICATION; static const QString PROP_FORCE_PLUGIN_INSTALL; static const QString PROP_NEWINSTANCE; static const QString PROP_NO_LAZY_REGISTRY_CACHE_LOADING; static const QString PROP_NO_REGISTRY_CACHE; static const QString PROP_PRODUCT; static const QString PROP_REGISTRY_MULTI_LANGUAGE; BaseApplication(int argc, char **argv); ~BaseApplication() override; /** * Initialize the Qt library such that a QCoreApplication * instance is available and e.g. Qt widgets can be created. * * This is usually not called directly by the user. */ void initializeQt(); /** * Launches the BlueBerry framework and runs the default application * or the one specified in the PROP_APPLICATION framework property. * * @return The return code of the application after it was shut down. */ int run() override; void printHelp(const std::string &name, const std::string &value); /** * Set the application name. Same as QCoreApplication::setApplicationName. * @param name The application name. */ void setApplicationName(const QString &name); QString getApplicationName() const; /** * Set the organization name. Same as QCoreApplication::setOrganizationName. * @param name The organization name. */ void setOrganizationName(const QString &name); QString getOrganizationName() const; /** * Set the organization domain. Same as QCoreApplication::setOrganizationDomain. * @param name The organization domain. */ void setOrganizationDomain(const QString &name); QString getOrganizationDomain() const; /** * Put the application in single mode, which by default only allows * a single instance of the application to be created. * * Calling this method after run() has been called has no effect. * * @param singleMode */ void setSingleMode(bool singleMode); bool getSingleMode() const; /** * Put the application in safe mode, catching exceptions from the * Qt event loop. * * @param safeMode */ void setSafeMode(bool safeMode); bool getSafeMode() const; /** * Set a list of library names or absoulte file paths * which should be loaded at application start-up. The name * and file path may contain a library version appended at the * end and separated by a '$' charactger. * * For example liborg_mitk_gui_qt_common$1.0. * Platform specific suffixes are appended automatically. * * @param libraryBaseNames A list of library base names. */ void setPreloadLibraries(const QStringList &libraryBaseNames); /** * Get the list of library base names which should be pre-loaded. * * @return A list of pre-loaded libraries. */ QStringList getPreloadLibraries() const; /** * Set the path to the provisioning file. * * By default a provisioning file located in the same directory * as the executable and named \.provisioning * is loaded if it exists. To disable parsing of provisioning * files, use an empty string as the argument. Use a * null QString (\c QString::null ) to reset to the * default behaviour. * * @param filePath An absolute file path to the provisioning file. */ void setProvisioningFilePath(const QString &filePath); /** * Get the file path to the provisioning file. * @return The provisioning file path. */ QString getProvisioningFilePath() const; void setProperty(const QString &property, const QVariant &value); QVariant getProperty(const QString &property) const; void installTranslator(QTranslator*); bool isRunning(); void sendMessage(const QByteArray); protected: void initialize(Poco::Util::Application &self) override; void uninitialize() override; int getArgc() const; char **getArgv() const; /** * Get the framework storage directory for the CTK plugin * framework. This method is called in the initialize(Poco::Util::Application&) * method. It must not be called without a QCoreApplications instance. * * @return The CTK Plugin Framework storage directory. */ virtual QString getCTKFrameworkStorageDir() const; /** * Initialize the CppMicroServices library. * * The default implementation set the CppMicroServices storage * path to the current ctkPluginConstants::FRAMEWORK_STORAGE property * value. * * This method is called in the initialize(Poco::Util::Application&) * after the CTK Plugin Framework storage directory property * was set. */ virtual void initializeCppMicroServices(); /** * Get the QCoreApplication object. * * This method is called in the initialize(Poco::Util::Application&) * method and must create a QCoreApplication instance if the * global qApp variable is not initialized yet. * * @return The current QCoreApplication instance. This method * never returns null. */ virtual QCoreApplication *getQApplication() const; /** * Add plugin library search paths to the CTK Plugin Framework. * * This method is called in the nitialize(Poco::Util::Application&) * method after getQApplication() was called. */ virtual void initializeLibraryPaths(); /** * Runs the application for which the platform was started. The platform * must be running. *

* The given argument is passed to the application being run. If it is an invalid QVariant * then the command line arguments used in starting the platform, and not consumed * by the platform code, are passed to the application as a QStringList. *

* @param args the argument passed to the application. May be invalid * @return the result of running the application * @throws std::exception if anything goes wrong */ int main(const std::vector &args) override; /** * Define command line arguments * @param options */ void defineOptions(Poco::Util::OptionSet &options) override; QSharedPointer getFramework() const; ctkPluginContext *getFrameworkContext() const; /** * Get the initial properties for the CTK plugin framework. * * The returned map contains the initial framework properties for * initializing the CTK plugin framework. The value of specific * properties may change at runtime and differ from the initial * value. * * @return The initial CTK Plugin Framework properties. */ QHash getFrameworkProperties() const; /* * Initialize and display the splash screen if an image filename is given * */ void initializeSplashScreen(QCoreApplication * application) const; private: struct Impl; Impl* d; }; } #endif // MITKBASEAPPLICATION_H diff --git a/Modules/AppUtil/src/mitkBaseApplication.cpp b/Modules/AppUtil/src/mitkBaseApplication.cpp index 28aa7a35b0..0b8cfb0814 100644 --- a/Modules/AppUtil/src/mitkBaseApplication.cpp +++ b/Modules/AppUtil/src/mitkBaseApplication.cpp @@ -1,880 +1,885 @@ /*============================================================================ 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 #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace { void outputQtMessage(QtMsgType type, const QMessageLogContext&, const QString& msg) { auto message = msg.toStdString(); switch (type) { case QtDebugMsg: MITK_DEBUG << message; break; case QtInfoMsg: MITK_INFO << message; break; case QtWarningMsg: MITK_WARN << message; break; case QtCriticalMsg: MITK_ERROR << message; break; case QtFatalMsg: MITK_ERROR << message; abort(); default: MITK_INFO << message; break; } } } namespace mitk { const QString BaseApplication::ARG_APPLICATION = "BlueBerry.application"; const QString BaseApplication::ARG_CLEAN = "BlueBerry.clean"; const QString BaseApplication::ARG_CONSOLELOG = "BlueBerry.consoleLog"; const QString BaseApplication::ARG_DEBUG = "BlueBerry.debug"; const QString BaseApplication::ARG_FORCE_PLUGIN_INSTALL = "BlueBerry.forcePlugins"; const QString BaseApplication::ARG_HOME = "BlueBerry.home"; const QString BaseApplication::ARG_NEWINSTANCE = "BlueBerry.newInstance"; const QString BaseApplication::ARG_NO_LAZY_REGISTRY_CACHE_LOADING = "BlueBerry.noLazyRegistryCacheLoading"; const QString BaseApplication::ARG_NO_REGISTRY_CACHE = "BlueBerry.noRegistryCache"; const QString BaseApplication::ARG_PLUGIN_CACHE = "BlueBerry.plugin_cache_dir"; const QString BaseApplication::ARG_PLUGIN_DIRS = "BlueBerry.plugin_dirs"; const QString BaseApplication::ARG_PRELOAD_LIBRARY = "BlueBerry.preloadLibrary"; const QString BaseApplication::ARG_PRODUCT = "BlueBerry.product"; const QString BaseApplication::ARG_PROVISIONING = "BlueBerry.provisioning"; const QString BaseApplication::ARG_REGISTRY_MULTI_LANGUAGE = "BlueBerry.registryMultiLanguage"; const QString BaseApplication::ARG_SPLASH_IMAGE = "BlueBerry.splashscreen"; const QString BaseApplication::ARG_STORAGE_DIR = "BlueBerry.storageDir"; const QString BaseApplication::ARG_XARGS = "xargs"; const QString BaseApplication::ARG_LOG_QT_MESSAGES = "Qt.logMessages"; const QString BaseApplication::ARG_SEGMENTATION_LABELSET_PRESET = "Segmentation.labelSetPreset"; + const QString BaseApplication::ARG_SEGMENTATION_LABEL_SUGGESTIONS = "Segmentation.labelSuggestions"; const QString BaseApplication::PROP_APPLICATION = "blueberry.application"; const QString BaseApplication::PROP_FORCE_PLUGIN_INSTALL = BaseApplication::ARG_FORCE_PLUGIN_INSTALL; const QString BaseApplication::PROP_NEWINSTANCE = BaseApplication::ARG_NEWINSTANCE; const QString BaseApplication::PROP_NO_LAZY_REGISTRY_CACHE_LOADING = BaseApplication::ARG_NO_LAZY_REGISTRY_CACHE_LOADING; const QString BaseApplication::PROP_NO_REGISTRY_CACHE = BaseApplication::ARG_NO_REGISTRY_CACHE; const QString BaseApplication::PROP_PRODUCT = "blueberry.product"; const QString BaseApplication::PROP_REGISTRY_MULTI_LANGUAGE = BaseApplication::ARG_REGISTRY_MULTI_LANGUAGE; class SplashCloserCallback : public QRunnable { public: SplashCloserCallback(QSplashScreen* splashscreen) : m_Splashscreen(splashscreen) { } void run() override { this->m_Splashscreen->close(); } private: QSplashScreen *m_Splashscreen; // Owned by BaseApplication::Impl }; struct BaseApplication::Impl { ctkProperties m_FWProps; QCoreApplication *m_QApp; int m_Argc; char **m_Argv; #ifdef Q_OS_MAC std::vector m_Argv_macOS; #endif QString m_AppName; QString m_OrgaName; QString m_OrgaDomain; bool m_SingleMode; bool m_SafeMode; QSplashScreen *m_Splashscreen; SplashCloserCallback *m_SplashscreenClosingCallback; bool m_LogQtMessages; QStringList m_PreloadLibs; QString m_ProvFile; Impl(int argc, char **argv) : m_Argc(argc), m_Argv(argv), #ifdef Q_OS_MAC m_Argv_macOS(), #endif m_SingleMode(false), m_SafeMode(true), m_Splashscreen(nullptr), m_SplashscreenClosingCallback(nullptr), m_LogQtMessages(false) { #ifdef Q_OS_MAC /* On macOS the process serial number is passed as an command line argument (-psn_) in certain circumstances. This option causes a Poco exception. We remove it, if present. */ m_Argv_macOS.reserve(argc + 1); const char psn[] = "-psn"; for (int i = 0; i < argc; ++i) { if (0 == strncmp(argv[i], psn, sizeof(psn) - 1)) continue; m_Argv_macOS.push_back(argv[i]); } m_Argv_macOS.push_back(nullptr); m_Argc = static_cast(m_Argv_macOS.size() - 1); m_Argv = m_Argv_macOS.data(); #endif } ~Impl() { delete m_SplashscreenClosingCallback; delete m_Splashscreen; delete m_QApp; } QVariant getProperty(const QString &property) const { auto iter = m_FWProps.find(property); return m_FWProps.end() != iter ? iter.value() : QVariant(); } void handleBooleanOption(const std::string &name, const std::string &) { if (ARG_LOG_QT_MESSAGES.toStdString() == name) { m_LogQtMessages = true; return; } auto fwKey = QString::fromStdString(name); // Translate some keys to proper framework properties if (ARG_CONSOLELOG == fwKey) fwKey = ctkPluginFrameworkLauncher::PROP_CONSOLE_LOG; // For all other options we use the command line option name as the // framework property key. m_FWProps[fwKey] = true; } void handlePreloadLibraryOption(const std::string &, const std::string &value) { m_PreloadLibs.push_back(QString::fromStdString(value)); } void handleClean(const std::string &, const std::string &) { m_FWProps[ctkPluginConstants::FRAMEWORK_STORAGE_CLEAN] = ctkPluginConstants::FRAMEWORK_STORAGE_CLEAN_ONFIRSTINIT; } void initializeCTKPluginFrameworkProperties(Poco::Util::LayeredConfiguration &configuration) { // Add all configuration key/value pairs as framework properties Poco::Util::LayeredConfiguration::Keys keys; Poco::Util::LayeredConfiguration::Keys keyStack; configuration.keys(keyStack); std::vector keyChain; while (!keyStack.empty()) { const auto currSubKey = keyStack.back(); if (!keyChain.empty() && keyChain.back() == currSubKey) { keyChain.pop_back(); keyStack.pop_back(); continue; } Poco::Util::LayeredConfiguration::Keys subKeys; configuration.keys(currSubKey, subKeys); if (subKeys.empty()) { std::string finalKey; keyStack.pop_back(); for (const auto& key : keyChain) finalKey += key + '.'; finalKey += currSubKey; keys.push_back(finalKey); } else { keyChain.push_back(currSubKey); for (const auto& key : subKeys) keyStack.push_back(key); } } for (const auto& key : keys) { if (configuration.hasProperty(key)) { // .ini and command line options overwrite already inserted keys auto qKey = QString::fromStdString(key); m_FWProps[qKey] = QString::fromStdString(configuration.getString(key)); } } } void parseProvisioningFile(const QString &filePath) { // Skip parsing if the file path is empty if (filePath.isEmpty()) return; auto consoleLog = this->getProperty(ctkPluginFrameworkLauncher::PROP_CONSOLE_LOG).toBool(); // Read initial plugins from a provisioning file QFileInfo provFile(filePath); QStringList pluginsToStart; if (provFile.exists()) { MITK_INFO(consoleLog) << "Using provisioning file: " << qPrintable(provFile.absoluteFilePath()); ProvisioningInfo provInfo(provFile.absoluteFilePath()); // It can still happen that the encoding is not compatible with the fromUtf8 function (i.e. when // manipulating the LANG variable). The QStringList in provInfo is empty then. if (provInfo.getPluginDirs().empty()) { MITK_ERROR << "Cannot search for provisioning file, the retrieved directory list is empty.\n" << "This can happen if there are some special non-ASCII characters in the install path."; } else { for(const auto& pluginPath : provInfo.getPluginDirs()) ctkPluginFrameworkLauncher::addSearchPath(pluginPath); auto pluginUrlsToStart = provInfo.getPluginsToStart(); for (const auto& url : qAsConst(pluginUrlsToStart)) pluginsToStart.push_back(url.toString()); } } else { MITK_INFO(consoleLog) << "Provisionig file does not exist."; } if (!pluginsToStart.isEmpty()) { m_FWProps[ctkPluginFrameworkLauncher::PROP_PLUGINS] = pluginsToStart; // Use transient start with declared activation policy (this helps when the provisioning file // changes and some plug-ins should not be installed in the application any more). ctkPlugin::StartOptions startOptions(ctkPlugin::START_TRANSIENT | ctkPlugin::START_ACTIVATION_POLICY); m_FWProps[ctkPluginFrameworkLauncher::PROP_PLUGINS_START_OPTIONS] = static_cast(startOptions); } } }; BaseApplication::BaseApplication(int argc, char **argv) : Application(), d(new Impl(argc, argv)) { } BaseApplication::~BaseApplication() { delete d; } void BaseApplication::printHelp(const std::string &, const std::string &) { Poco::Util::HelpFormatter help(this->options()); help.setAutoIndent(); help.setCommand(this->commandName()); help.format(std::cout); exit(EXIT_OK); } void BaseApplication::setApplicationName(const QString &name) { if (nullptr != qApp) qApp->setApplicationName(name); d->m_AppName = name; } QString BaseApplication::getApplicationName() const { return nullptr != qApp ? qApp->applicationName() : d->m_AppName; } void BaseApplication::setOrganizationName(const QString &name) { if (nullptr != qApp) qApp->setOrganizationName(name); d->m_OrgaName = name; } QString BaseApplication::getOrganizationName() const { return nullptr != qApp ? qApp->organizationName() : d->m_OrgaName; } void BaseApplication::setOrganizationDomain(const QString &domain) { if (nullptr != qApp) qApp->setOrganizationDomain(domain); d->m_OrgaDomain = domain; } QString BaseApplication::getOrganizationDomain() const { return nullptr != qApp ? qApp->organizationDomain() : d->m_OrgaDomain; } void BaseApplication::setSingleMode(bool singleMode) { if (nullptr != qApp) return; d->m_SingleMode = singleMode; } bool BaseApplication::getSingleMode() const { return d->m_SingleMode; } void BaseApplication::setSafeMode(bool safeMode) { if (nullptr != qApp && nullptr == d->m_QApp) return; d->m_SafeMode = safeMode; nullptr == d->m_QApp && getSingleMode() ? static_cast(d->m_QApp)->setSafeMode(safeMode) : static_cast(d->m_QApp)->setSafeMode(safeMode); } bool BaseApplication::getSafeMode() const { return d->m_SafeMode; } void BaseApplication::setPreloadLibraries(const QStringList &libraryBaseNames) { d->m_PreloadLibs = libraryBaseNames; } QStringList BaseApplication::getPreloadLibraries() const { return d->m_PreloadLibs; } void BaseApplication::setProvisioningFilePath(const QString &filePath) { d->m_ProvFile = filePath; } QString BaseApplication::getProvisioningFilePath() const { auto provFilePath = d->m_ProvFile; // A null QString means look up a default provisioning file if (provFilePath.isNull() && nullptr != qApp) { QFileInfo appFilePath(QCoreApplication::applicationFilePath()); QDir basePath(QCoreApplication::applicationDirPath()); auto provFileName = appFilePath.baseName() + ".provisioning"; QFileInfo provFile(basePath.absoluteFilePath(provFileName)); #ifdef Q_OS_MAC /* * On macOS, if started from the build directory, the .provisioning file is located at: * * The executable path is: * * In this case we have to cdUp threetimes. * * During packaging the MitkWorkbench.provisioning file is placed at the same * level like the executable. Nothing has to be done. */ if (!provFile.exists()) { basePath.cdUp(); basePath.cdUp(); basePath.cdUp(); provFile = basePath.absoluteFilePath(provFileName); } #endif if (provFile.exists()) { provFilePath = provFile.absoluteFilePath(); } #ifdef CMAKE_INTDIR else { basePath.cdUp(); provFile.setFile(basePath.absoluteFilePath(provFileName)); if (provFile.exists()) provFilePath = provFile.absoluteFilePath(); } #endif } return provFilePath; } void BaseApplication::initializeQt() { if (nullptr != qApp) return; // If parameters have been set before, we have to store them to hand them // through to the application auto appName = this->getApplicationName(); auto orgName = this->getOrganizationName(); auto orgDomain = this->getOrganizationDomain(); // Create a QCoreApplication instance this->getQApplication(); // Provide parameters to QCoreApplication this->setApplicationName(appName); this->setOrganizationName(orgName); this->setOrganizationDomain(orgDomain); if (d->m_LogQtMessages) qInstallMessageHandler(outputQtMessage); QWebEngineUrlScheme qtHelpScheme("qthelp"); qtHelpScheme.setFlags(QWebEngineUrlScheme::LocalScheme | QWebEngineUrlScheme::LocalAccessAllowed); QWebEngineUrlScheme::registerScheme(qtHelpScheme); } void BaseApplication::initialize(Poco::Util::Application &self) { // 1. Call the super-class method Poco::Util::Application::initialize(self); // 2. Initialize the Qt framework (by creating a QCoreApplication) this->initializeQt(); // 3. Seed the random number generator, once at startup. QTime time = QTime::currentTime(); qsrand((uint)time.msec()); // 4. Load the "default" configuration, which involves parsing // an optional .ini file and parsing any // command line arguments this->loadConfiguration(); // 5. Add configuration data from the command line and the // optional .ini file as CTK plugin // framework properties. d->initializeCTKPluginFrameworkProperties(this->config()); // 6. Initialize splash screen if an image path is provided // in the .ini file this->initializeSplashScreen(qApp); // 7. Set the custom CTK Plugin Framework storage directory QString storageDir = this->getCTKFrameworkStorageDir(); if (!storageDir.isEmpty()) d->m_FWProps[ctkPluginConstants::FRAMEWORK_STORAGE] = storageDir; // 8. Set the library search paths and the pre-load library property this->initializeLibraryPaths(); auto preloadLibs = this->getPreloadLibraries(); if (!preloadLibs.isEmpty()) d->m_FWProps[ctkPluginConstants::FRAMEWORK_PRELOAD_LIBRARIES] = preloadLibs; // 9. Initialize the CppMicroServices library. // The initializeCppMicroServices() method reuses the // FRAMEWORK_STORAGE property, so we call it after the // getCTKFrameworkStorageDir method. this->initializeCppMicroServices(); // 10. Parse the (optional) provisioning file and set the // correct framework properties. d->parseProvisioningFile(this->getProvisioningFilePath()); // 11. Set the CTK Plugin Framework properties ctkPluginFrameworkLauncher::setFrameworkProperties(d->m_FWProps); } void BaseApplication::uninitialize() { auto pfw = this->getFramework(); if (pfw) { pfw->stop(); // Wait for up to 10 seconds for the CTK plugin framework to stop pfw->waitForStop(10000); } Poco::Util::Application::uninitialize(); } int BaseApplication::getArgc() const { return d->m_Argc; } char **BaseApplication::getArgv() const { return d->m_Argv; } QString BaseApplication::getCTKFrameworkStorageDir() const { QString storageDir; if (this->getSingleMode()) { // This function checks if an instance is already running and either sends a message to // it containing the command line arguments or checks if a new instance was forced by // providing the BlueBerry.newInstance command line argument. In the latter case, a path // to a temporary directory for the new application's storage directory is returned. storageDir = handleNewAppInstance(static_cast(d->m_QApp), d->m_Argc, d->m_Argv, ARG_NEWINSTANCE); } if (storageDir.isEmpty()) { // This is a new instance and no other instance is already running. We specify the // storage directory here (this is the same code as in berryInternalPlatform.cpp) // so that we can re-use the location for the persistent data location of the // the CppMicroServices library. // Append a hash value of the absolute path of the executable to the data location. // This allows to start the same application from different build or install trees. storageDir = QStandardPaths::writableLocation(QStandardPaths::GenericDataLocation) + "/" + this->getOrganizationName() + "/" + this->getApplicationName() + '_'; storageDir += QString::number(qHash(QCoreApplication::applicationDirPath())) + "/"; } return storageDir; } void BaseApplication::initializeCppMicroServices() { auto storageDir = this->getProperty(ctkPluginConstants::FRAMEWORK_STORAGE).toString(); if (!storageDir.isEmpty()) us::ModuleSettings::SetStoragePath((storageDir + "us" + QDir::separator()).toStdString()); } QCoreApplication *BaseApplication::getQApplication() const { if (nullptr == qApp) { vtkOpenGLRenderWindow::SetGlobalMaximumNumberOfMultiSamples(0); auto defaultFormat = QVTKOpenGLNativeWidget::defaultFormat(); defaultFormat.setSamples(0); QSurfaceFormat::setDefaultFormat(defaultFormat); #ifdef Q_OS_OSX QCoreApplication::setAttribute(Qt::AA_DontCreateNativeWidgetSiblings); #endif QCoreApplication::setAttribute(Qt::AA_ShareOpenGLContexts); d->m_QApp = this->getSingleMode() ? static_cast(new QmitkSingleApplication(d->m_Argc, d->m_Argv, this->getSafeMode())) : static_cast(new QmitkSafeApplication(d->m_Argc, d->m_Argv, this->getSafeMode())); } return qApp; } void BaseApplication::initializeLibraryPaths() { QStringList suffixes; suffixes << "plugins"; #ifdef Q_OS_WINDOWS suffixes << "bin/plugins"; #ifdef CMAKE_INTDIR suffixes << "bin/" CMAKE_INTDIR "/plugins"; #endif #else suffixes << "lib/plugins"; #ifdef CMAKE_INTDIR suffixes << "lib/" CMAKE_INTDIR "/plugins"; #endif #endif #ifdef Q_OS_MAC suffixes << "../../plugins"; #endif // We add a couple of standard library search paths for plug-ins QDir appDir(QCoreApplication::applicationDirPath()); // Walk one directory up and add bin and lib sub-dirs; this might be redundant appDir.cdUp(); for (const auto& suffix : qAsConst(suffixes)) ctkPluginFrameworkLauncher::addSearchPath(appDir.absoluteFilePath(suffix)); } int BaseApplication::main(const std::vector &args) { // Start the plugin framework and all installed plug-ins according to their auto-start setting QStringList arguments; for (auto const &arg : args) arguments.push_back(QString::fromStdString(arg)); if (nullptr != d->m_Splashscreen) { // A splash screen is displayed. Create the closing callback. d->m_SplashscreenClosingCallback = new SplashCloserCallback(d->m_Splashscreen); } return ctkPluginFrameworkLauncher::run(d->m_SplashscreenClosingCallback, QVariant::fromValue(arguments)).toInt(); } void BaseApplication::defineOptions(Poco::Util::OptionSet &options) { Poco::Util::Option helpOption("help", "h", "print this help text"); helpOption.callback(Poco::Util::OptionCallback(this, &BaseApplication::printHelp)); options.addOption(helpOption); Poco::Util::Option newInstanceOption(ARG_NEWINSTANCE.toStdString(), "", "forces a new instance of this application"); newInstanceOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(newInstanceOption); Poco::Util::Option cleanOption(ARG_CLEAN.toStdString(), "", "cleans the plugin cache"); cleanOption.callback(Poco::Util::OptionCallback(d, &Impl::handleClean)); options.addOption(cleanOption); Poco::Util::Option productOption(ARG_PRODUCT.toStdString(), "", "the id of the product to be launched"); productOption.argument("").binding(PROP_PRODUCT.toStdString()); options.addOption(productOption); Poco::Util::Option appOption(ARG_APPLICATION.toStdString(), "", "the id of the application extension to be executed"); appOption.argument("").binding(PROP_APPLICATION.toStdString()); options.addOption(appOption); Poco::Util::Option provOption(ARG_PROVISIONING.toStdString(), "", "the location of a provisioning file"); provOption.argument("").binding(ARG_PROVISIONING.toStdString()); options.addOption(provOption); Poco::Util::Option storageDirOption(ARG_STORAGE_DIR.toStdString(), "", "the location for storing persistent application data"); storageDirOption.argument("").binding(ctkPluginConstants::FRAMEWORK_STORAGE.toStdString()); options.addOption(storageDirOption); Poco::Util::Option consoleLogOption(ARG_CONSOLELOG.toStdString(), "", "log messages to the console"); consoleLogOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(consoleLogOption); Poco::Util::Option debugOption(ARG_DEBUG.toStdString(), "", "enable debug mode"); debugOption.argument("", false).binding(ctkPluginFrameworkLauncher::PROP_DEBUG.toStdString()); options.addOption(debugOption); Poco::Util::Option forcePluginOption(ARG_FORCE_PLUGIN_INSTALL.toStdString(), "", "force installing plug-ins with same symbolic name"); forcePluginOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(forcePluginOption); Poco::Util::Option preloadLibsOption(ARG_PRELOAD_LIBRARY.toStdString(), "", "preload a library"); preloadLibsOption.argument("") .repeatable(true) .callback(Poco::Util::OptionCallback(d, &Impl::handlePreloadLibraryOption)); options.addOption(preloadLibsOption); Poco::Util::Option noRegistryCacheOption(ARG_NO_REGISTRY_CACHE.toStdString(), "", "do not use a cache for the registry"); noRegistryCacheOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(noRegistryCacheOption); Poco::Util::Option noLazyRegistryCacheLoadingOption(ARG_NO_LAZY_REGISTRY_CACHE_LOADING.toStdString(), "", "do not use lazy cache loading for the registry"); noLazyRegistryCacheLoadingOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(noLazyRegistryCacheLoadingOption); Poco::Util::Option registryMultiLanguageOption(ARG_REGISTRY_MULTI_LANGUAGE.toStdString(), "", "enable multi-language support for the registry"); registryMultiLanguageOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(registryMultiLanguageOption); Poco::Util::Option splashScreenOption(ARG_SPLASH_IMAGE.toStdString(), "", "optional picture to use as a splash screen"); splashScreenOption.argument("").binding(ARG_SPLASH_IMAGE.toStdString()); options.addOption(splashScreenOption); Poco::Util::Option xargsOption(ARG_XARGS.toStdString(), "", "Extended argument list"); xargsOption.argument("").binding(ARG_XARGS.toStdString()); options.addOption(xargsOption); Poco::Util::Option logQtMessagesOption(ARG_LOG_QT_MESSAGES.toStdString(), "", "log Qt messages"); logQtMessagesOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(logQtMessagesOption); Poco::Util::Option labelSetPresetOption(ARG_SEGMENTATION_LABELSET_PRESET.toStdString(), "", "use this label set preset for new segmentations"); labelSetPresetOption.argument("").binding(ARG_SEGMENTATION_LABELSET_PRESET.toStdString()); options.addOption(labelSetPresetOption); + Poco::Util::Option labelSuggestionsOption(ARG_SEGMENTATION_LABEL_SUGGESTIONS.toStdString(), "", "use this list of predefined suggestions for segmentation labels"); + labelSuggestionsOption.argument("").binding(ARG_SEGMENTATION_LABEL_SUGGESTIONS.toStdString()); + options.addOption(labelSuggestionsOption); + Poco::Util::Application::defineOptions(options); } QSharedPointer BaseApplication::getFramework() const { return ctkPluginFrameworkLauncher::getPluginFramework(); } ctkPluginContext *BaseApplication::getFrameworkContext() const { auto framework = getFramework(); return framework ? framework->getPluginContext() : nullptr; } void BaseApplication::initializeSplashScreen(QCoreApplication * application) const { auto pixmapFileNameProp = d->getProperty(ARG_SPLASH_IMAGE); if (!pixmapFileNameProp.isNull()) { auto pixmapFileName = pixmapFileNameProp.toString(); QFileInfo checkFile(pixmapFileName); if (checkFile.exists() && checkFile.isFile()) { QPixmap pixmap(checkFile.absoluteFilePath()); d->m_Splashscreen = new QSplashScreen(pixmap, Qt::WindowStaysOnTopHint); d->m_Splashscreen->show(); application->processEvents(); } } } QHash BaseApplication::getFrameworkProperties() const { return d->m_FWProps; } int BaseApplication::run() { this->init(d->m_Argc, d->m_Argv); return Application::run(); } void BaseApplication::setProperty(const QString &property, const QVariant &value) { d->m_FWProps[property] = value; } QVariant BaseApplication::getProperty(const QString &property) const { return d->getProperty(property); } void BaseApplication::installTranslator(QTranslator* translator) { this->getQApplication()->installTranslator(translator); } bool BaseApplication::isRunning() { auto app = dynamic_cast(this->getQApplication()); if (nullptr != app) app->isRunning(); mitkThrow() << "Method not implemented."; } void BaseApplication::sendMessage(const QByteArray msg) { auto app = dynamic_cast(this->getQApplication()); if (nullptr != app) app->sendMessage(msg); mitkThrow() << "Method not implemented."; } } diff --git a/Modules/Core/src/DataManagement/mitkAnatomicalStructureColorPresets.cpp b/Modules/Core/src/DataManagement/mitkAnatomicalStructureColorPresets.cpp index 6ae41cd508..d5d5735216 100644 --- a/Modules/Core/src/DataManagement/mitkAnatomicalStructureColorPresets.cpp +++ b/Modules/Core/src/DataManagement/mitkAnatomicalStructureColorPresets.cpp @@ -1,180 +1,180 @@ /*============================================================================ 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 "mitkAnatomicalStructureColorPresets.h" #include #include "usGetModuleContext.h" #include "usModuleContext.h" #include "usModule.h" #include "usModuleResource.h" #include "usModuleResourceStream.h" namespace mitk { const std::string AnatomicalStructureColorPresets::PRESET = "preset"; const std::string AnatomicalStructureColorPresets::CATEGORY = "category"; const std::string AnatomicalStructureColorPresets::TYPE = "type"; const std::string AnatomicalStructureColorPresets::MODIFIER = "modifier"; const std::string AnatomicalStructureColorPresets::COLOR = "color"; const std::string AnatomicalStructureColorPresets::CODE_VALUE = "code_value"; const std::string AnatomicalStructureColorPresets::CODE_SCHEME = "coding_scheme"; const std::string AnatomicalStructureColorPresets::CODE_NAME = "code_name"; const std::string AnatomicalStructureColorPresets::COLOR_R = "rgb_r"; const std::string AnatomicalStructureColorPresets::COLOR_G = "rgb_g"; const std::string AnatomicalStructureColorPresets::COLOR_B = "rgb_b"; vtkStandardNewMacro(AnatomicalStructureColorPresets); bool AnatomicalStructureColorPresets::LoadPreset() { us::ModuleResource presetResource = us::GetModuleContext()->GetModule()->GetResource("mitkAnatomicalStructureColorPresets.xml"); if (!presetResource) return false; us::ModuleResourceStream presetStream(presetResource); vtkXMLParser::SetStream(&presetStream); if (!vtkXMLParser::Parse()) { #ifdef INTERDEBUG MITK_INFO<<"AnatomicalStructureColorPresets::LoadPreset xml file cannot parse!"< const AnatomicalStructureColorPresets::GetCategoryPresets() { return m_Category; } std::map const AnatomicalStructureColorPresets::GetTypePresets() { return m_Type; } std::map const AnatomicalStructureColorPresets::GetColorPresets() { return m_Color; } void AnatomicalStructureColorPresets::Save() { //Not yet implemented } void AnatomicalStructureColorPresets::NewPresets(std::map& newCategory, std::map& newType, std::map& newColor) { m_Category = newCategory; m_Type = newType; m_Color = newColor; this->Save(); } } diff --git a/Modules/SegmentationUI/Qmitk/QmitkNewSegmentationDialog.cpp b/Modules/SegmentationUI/Qmitk/QmitkNewSegmentationDialog.cpp deleted file mode 100644 index a824e6d94a..0000000000 --- a/Modules/SegmentationUI/Qmitk/QmitkNewSegmentationDialog.cpp +++ /dev/null @@ -1,188 +0,0 @@ -/*============================================================================ - -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 "QmitkNewSegmentationDialog.h" - -#include - -#include -#include -#include -#include -#include -#include -#include - -QmitkNewSegmentationDialog::QmitkNewSegmentationDialog(QWidget *parent) - : QDialog(parent) // true, modal - , selectedOrgan(tr("undefined")) - , newOrganEntry(false) -{ - QDialog::setFixedSize(250, 105); - - QBoxLayout *verticalLayout = new QVBoxLayout(this); - verticalLayout->setMargin(5); - verticalLayout->setSpacing(5); - - // to enter a name for the segmentation - lblPrompt = new QLabel(tr("Name and color of the segmentation"), this); - verticalLayout->addWidget(lblPrompt); - - // to choose a color - m_Color.setRed(255); - m_Color.setGreen(0); - m_Color.setBlue(0); - - btnColor = new QPushButton("", this); - btnColor->setFixedWidth(25); - btnColor->setAutoFillBackground(true); - btnColor->setStyleSheet(QString("background-color:rgb(%1, %2, %3)").arg(m_Color.red()).arg(m_Color.green()).arg(m_Color.blue())); - - connect(btnColor, SIGNAL(clicked()), this, SLOT(onColorBtnClicked())); - - lineEditName = new QLineEdit("", this); - QStringList completionList; - completionList << ""; - completer = new QCompleter(completionList); - completer->setCaseSensitivity(Qt::CaseInsensitive); - lineEditName->setCompleter(completer); - - connect(completer, SIGNAL(activated(const QString &)), this, SLOT(onColorChange(const QString &))); - - QBoxLayout *horizontalLayout2 = new QHBoxLayout(); - verticalLayout->addLayout(horizontalLayout2); - horizontalLayout2->addWidget(btnColor); - horizontalLayout2->addWidget(lineEditName); - - // buttons for closing the dialog - btnOk = new QPushButton(tr("Ok"), this); - btnOk->setDefault(true); - connect(btnOk, SIGNAL(clicked()), this, SLOT(onAcceptClicked())); - - QPushButton *btnCancel = new QPushButton(tr("Cancel"), this); - connect(btnCancel, SIGNAL(clicked()), this, SLOT(reject())); - - QBoxLayout *horizontalLayout = new QHBoxLayout(); - verticalLayout->addLayout(horizontalLayout); - horizontalLayout->setSpacing(5); - horizontalLayout->addStretch(); - horizontalLayout->addWidget(btnOk); - horizontalLayout->addWidget(btnCancel); - - lineEditName->setFocus(); -} - -QmitkNewSegmentationDialog::~QmitkNewSegmentationDialog() -{ -} - -const QString QmitkNewSegmentationDialog::GetSegmentationName() -{ - return m_SegmentationName; -} - -mitk::Color QmitkNewSegmentationDialog::GetColor() -{ - mitk::Color colorProperty; - if (m_Color.isValid()) - { - colorProperty.SetRed(m_Color.redF()); - colorProperty.SetGreen(m_Color.greenF()); - colorProperty.SetBlue(m_Color.blueF()); - } - else - { - colorProperty.SetRed(1); - colorProperty.SetGreen(0); - colorProperty.SetBlue(0); - } - return colorProperty; -} - -const char *QmitkNewSegmentationDialog::GetOrganType() -{ - return selectedOrgan.toLocal8Bit().constData(); -} - -void QmitkNewSegmentationDialog::SetSegmentationName(const QString &segmentationName) -{ - lineEditName->setText(segmentationName); -} - -void QmitkNewSegmentationDialog::SetColor(const mitk::Color &color) -{ - m_Color.setRedF(color.GetRed()); - m_Color.setGreenF(color.GetGreen()); - m_Color.setBlueF(color.GetBlue()); - - btnColor->setStyleSheet(QString("background-color:rgb(%1, %2, %3)").arg(m_Color.red()).arg(m_Color.green()).arg(m_Color.blue())); -} - -void QmitkNewSegmentationDialog::SetSuggestionList(QStringList organColorList) -{ - QStringList::iterator iter; - for (iter = organColorList.begin(); iter != organColorList.end(); ++iter) - { - QString &element = *iter; - QString colorName = element.right(7); - QColor color(colorName); - QString organName = element.left(element.size() - 7); - - organList.push_back(organName); - colorList.push_back(color); - } - - QStringListModel *completeModel = static_cast(completer->model()); - completeModel->setStringList(organList); -} - -void QmitkNewSegmentationDialog::setPrompt(const QString &prompt) -{ - lblPrompt->setText(prompt); -} - -void QmitkNewSegmentationDialog::onAcceptClicked() -{ - m_SegmentationName = lineEditName->text(); - accept(); -} - -void QmitkNewSegmentationDialog::onNewOrganNameChanged(const QString &newText) -{ - if (!newText.isEmpty()) - { - btnOk->setEnabled(true); - } - - selectedOrgan = newText; - SetSegmentationName(newText); -} - -void QmitkNewSegmentationDialog::onColorBtnClicked() -{ - auto selectedColor = QColorDialog::getColor(m_Color); - if (selectedColor.isValid()) - { - m_Color = selectedColor; - btnColor->setStyleSheet(QString("background-color:rgb(%1, %2, %3)").arg(m_Color.red()).arg(m_Color.green()).arg(m_Color.blue())); - } -} - -void QmitkNewSegmentationDialog::onColorChange(const QString &completedWord) -{ - if (organList.contains(completedWord)) - { - int j = organList.indexOf(completedWord); - m_Color = colorList.at(j); - btnColor->setStyleSheet(QString("background-color:rgb(%1, %2, %3)").arg(m_Color.red()).arg(m_Color.green()).arg(m_Color.blue())); - } -} diff --git a/Modules/SegmentationUI/Qmitk/QmitkNewSegmentationDialog.h b/Modules/SegmentationUI/Qmitk/QmitkNewSegmentationDialog.h deleted file mode 100644 index e8559ebd77..0000000000 --- a/Modules/SegmentationUI/Qmitk/QmitkNewSegmentationDialog.h +++ /dev/null @@ -1,93 +0,0 @@ -/*============================================================================ - -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 QmitkNewSegmentationDialog_h_Included -#define QmitkNewSegmentationDialog_h_Included - -#include "mitkColorProperty.h" -#include - -#include - -#include - -class QLabel; -class QLineEdit; -class Q3ListBox; -class QPushButton; - -#include - -/** - \brief Dialog for QmitkInteractiveSegmentation. - - \ingroup ToolManagerEtAl - \ingroup Widgets - - This dialog is used to ask a user about the type of a newly created segmentation and a name for it. -*/ -class MITKSEGMENTATIONUI_EXPORT QmitkNewSegmentationDialog : public QDialog -{ - Q_OBJECT - -public: - QmitkNewSegmentationDialog(QWidget *parent = nullptr); - - ~QmitkNewSegmentationDialog() override; - - const QString GetSegmentationName(); - mitk::Color GetColor(); - const char *GetOrganType(); - - void SetSegmentationName(const QString &segmentationName); - void SetColor(const mitk::Color &color); - void SetSuggestionList(QStringList organColorList); - -signals: - -public slots: - - void setPrompt(const QString &prompt); - -protected slots: - - void onAcceptClicked(); - void onNewOrganNameChanged(const QString &); - void onColorBtnClicked(); - void onColorChange(const QString &completedWord); - -protected: - - QLabel *lblPrompt; - Q3ListBox *lstOrgans; - QLineEdit *lineEditName; - - QPushButton *btnColor; - QPushButton *btnOk; - - QLineEdit *edtNewOrgan; - - QString selectedOrgan; - - bool newOrganEntry; - - QColor m_Color; - - QCompleter *completer; - - QString m_SegmentationName; - - QStringList organList; - QList colorList; -}; - -#endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkSegmentationOrganNamesHandling.cpp b/Modules/SegmentationUI/Qmitk/QmitkSegmentationOrganNamesHandling.cpp deleted file mode 100644 index c027481f2b..0000000000 --- a/Modules/SegmentationUI/Qmitk/QmitkSegmentationOrganNamesHandling.cpp +++ /dev/null @@ -1,62 +0,0 @@ -/*============================================================================ - -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 -#include -#include - -namespace mitk -{ - struct OrganNamesHandling - { - static QStringList GetDefaultOrganColorString() - { - QStringList organColors; - - auto presets = vtkSmartPointer::New(); - presets->LoadPreset(); - - for (const auto& preset : presets->GetColorPresets()) - { - auto organName = preset.first.c_str(); - auto color = QColor(preset.second.GetRed(), preset.second.GetGreen(), preset.second.GetBlue()); - - AppendToOrganList(organColors, organName, color); - } - return organColors; - } - - static void UpdateOrganList(QStringList& organColors, const QString& organname, mitk::Color color) - { - QString listElement(organname + QColor(color.GetRed() * 255, color.GetGreen() * 255, color.GetBlue() * 255).name()); - - // remove previous definition if necessary - int oldIndex = organColors.indexOf(QRegExp(QRegExp::escape(organname) + "#......", Qt::CaseInsensitive)); - if (oldIndex < 0 || organColors.at(oldIndex) != listElement) - { - if (oldIndex >= 0) - { - organColors.removeAt(oldIndex); - } - - // add colored organ name AND sort list - organColors.append(listElement); - organColors.sort(); - } - } - - static void AppendToOrganList(QStringList& organColors, const QString& organname, const QColor& color) - { - organColors.append(organname + color.name()); - } - }; -} diff --git a/Modules/SegmentationUI/files.cmake b/Modules/SegmentationUI/files.cmake index 36584cbe80..54b348aa7c 100644 --- a/Modules/SegmentationUI/files.cmake +++ b/Modules/SegmentationUI/files.cmake @@ -1,87 +1,79 @@ set( CPP_FILES Qmitk/QmitkAdaptiveRegionGrowingToolGUI.cpp Qmitk/QmitkAutoSegmentationToolGUIBase.cpp Qmitk/QmitkAutoMLSegmentationToolGUIBase.cpp Qmitk/QmitkBinaryThresholdToolGUIBase.cpp Qmitk/QmitkBinaryThresholdToolGUI.cpp Qmitk/QmitkBinaryThresholdULToolGUI.cpp Qmitk/QmitkCalculateGrayValueStatisticsToolGUI.cpp Qmitk/QmitkConfirmSegmentationDialog.cpp Qmitk/QmitkCopyToClipBoardDialog.cpp Qmitk/QmitkDrawPaintbrushToolGUI.cpp Qmitk/QmitkErasePaintbrushToolGUI.cpp Qmitk/QmitkLiveWireTool2DGUI.cpp -Qmitk/QmitkNewSegmentationDialog.cpp Qmitk/QmitkOtsuTool3DGUI.cpp Qmitk/QmitkPaintbrushToolGUI.cpp Qmitk/QmitkPickingToolGUI.cpp Qmitk/QmitkPixelManipulationToolGUI.cpp Qmitk/QmitkSlicesInterpolator.cpp Qmitk/QmitkToolGUI.cpp Qmitk/QmitkToolGUIArea.cpp Qmitk/QmitkToolSelectionBox.cpp Qmitk/QmitknnUNetToolGUI.cpp Qmitk/QmitknnUNetToolSlots.cpp -#Added from ML -Qmitk/QmitkLabelSetWidget.cpp Qmitk/QmitkSurfaceStampWidget.cpp Qmitk/QmitkMaskStampWidget.cpp Qmitk/QmitkSliceBasedInterpolatorWidget.cpp Qmitk/QmitkStaticDynamicSegmentationDialog.cpp Qmitk/QmitkSurfaceBasedInterpolatorWidget.cpp Qmitk/QmitkSimpleLabelSetListWidget.cpp ) set(MOC_H_FILES Qmitk/QmitkAdaptiveRegionGrowingToolGUI.h Qmitk/QmitkAutoSegmentationToolGUIBase.h Qmitk/QmitkAutoMLSegmentationToolGUIBase.h Qmitk/QmitkBinaryThresholdToolGUIBase.h Qmitk/QmitkBinaryThresholdToolGUI.h Qmitk/QmitkBinaryThresholdULToolGUI.h Qmitk/QmitkCalculateGrayValueStatisticsToolGUI.h Qmitk/QmitkConfirmSegmentationDialog.h Qmitk/QmitkCopyToClipBoardDialog.h Qmitk/QmitkDrawPaintbrushToolGUI.h Qmitk/QmitkErasePaintbrushToolGUI.h Qmitk/QmitkLiveWireTool2DGUI.h -Qmitk/QmitkNewSegmentationDialog.h Qmitk/QmitkOtsuTool3DGUI.h Qmitk/QmitkPaintbrushToolGUI.h Qmitk/QmitkPickingToolGUI.h Qmitk/QmitkPixelManipulationToolGUI.h Qmitk/QmitkSlicesInterpolator.h Qmitk/QmitkToolGUI.h Qmitk/QmitkToolGUIArea.h Qmitk/QmitkToolSelectionBox.h Qmitk/QmitknnUNetToolGUI.h Qmitk/QmitknnUNetGPU.h Qmitk/QmitknnUNetEnsembleLayout.h Qmitk/QmitknnUNetFolderParser.h -#Added from ML -Qmitk/QmitkLabelSetWidget.h Qmitk/QmitkSurfaceStampWidget.h Qmitk/QmitkMaskStampWidget.h Qmitk/QmitkSliceBasedInterpolatorWidget.h Qmitk/QmitkStaticDynamicSegmentationDialog.h Qmitk/QmitkSurfaceBasedInterpolatorWidget.h Qmitk/QmitkSimpleLabelSetListWidget.h ) set(UI_FILES Qmitk/QmitkAdaptiveRegionGrowingToolGUIControls.ui Qmitk/QmitkConfirmSegmentationDialog.ui Qmitk/QmitkOtsuToolWidgetControls.ui Qmitk/QmitkLiveWireTool2DGUIControls.ui -#Added from ML -Qmitk/QmitkLabelSetWidgetControls.ui Qmitk/QmitkSurfaceStampWidgetGUIControls.ui Qmitk/QmitkMaskStampWidgetGUIControls.ui Qmitk/QmitkSliceBasedInterpolatorWidgetGUIControls.ui Qmitk/QmitkSurfaceBasedInterpolatorWidgetGUIControls.ui Qmitk/QmitknnUNetToolGUIControls.ui ) set(QRC_FILES resources/SegmentationUI.qrc ) diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.multilabelsegmentation/manifest_headers.cmake index 54eb90ad33..97ba4ee1c4 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/manifest_headers.cmake +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/manifest_headers.cmake @@ -1,5 +1,5 @@ set(Plugin-Name "MITK MultiLabelSegmentation") set(Plugin-Version "1.0.0") set(Plugin-Vendor "German Cancer Research Center (DKFZ)") set(Plugin-ContactAddress "http://www.mitk.org") -set(Require-Plugin org.mitk.gui.qt.common org.mitk.gui.qt.datamanager) +set(Require-Plugin org.mitk.gui.qt.common org.mitk.gui.qt.datamanager org.mitk.gui.qt.segmentation) diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui index 1f2ad71121..2d8cf565c5 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui @@ -1,274 +1,274 @@ QmitkImageMaskingWidgetControls 0 0 179 296 2 4 0 Masks 3 4 0 0 Masking Mode Image Masking true Surface Masking Mask make output binary overwrite foreground overwrite background Background Value: Qt::Horizontal 40 20 50 0 50 16777215 0.0 Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter Foreground Value: Qt::Horizontal 40 20 50 0 50 16777215 1.0 Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter Qt::Vertical 20 40 Labels 4 0 0 0 50 Qt::Vertical 20 40 QmitkDataSelectionWidget QWidget
internal/Common/QmitkDataSelectionWidget.h
 QmitkLabelSetWidget QWidget -
Qmitk/QmitkLabelSetWidget.h
+
QmitkLabelSetWidget.h
1 QmitkMaskStampWidget QWidget
QmitkMaskStampWidget.h
1 diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidgetControls.ui b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidgetControls.ui index 976fffbdc3..0e8a3c92b5 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidgetControls.ui +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidgetControls.ui @@ -1,427 +1,427 @@ QmitkMorphologicalOperationsWidgetControls 0 0 155 414 0 0 0 Masks 3 4 0 0 Structuring Element Ball true Cross Radius 1 20 1 Qt::Horizontal 1 20 false 0 0 Dilatation :/SegmentationUtilities/MorphologicalOperations/Dilate_48x48.png:/SegmentationUtilities/MorphologicalOperations/Dilate_48x48.png 32 32 Qt::ToolButtonTextUnderIcon false 0 0 Globally fills holes in segmentation (radius not required) Fill Holes :/SegmentationUtilities/MorphologicalOperations/FillHoles_48x48.png:/SegmentationUtilities/MorphologicalOperations/FillHoles_48x48.png 32 32 Qt::ToolButtonTextUnderIcon false 0 0 Erosion :/SegmentationUtilities/MorphologicalOperations/Erode_48x48.png:/SegmentationUtilities/MorphologicalOperations/Erode_48x48.png 32 32 Qt::ToolButtonTextUnderIcon false 0 0 Closing :/SegmentationUtilities/MorphologicalOperations/Closing_48x48.png:/SegmentationUtilities/MorphologicalOperations/Closing_48x48.png 32 32 Qt::ToolButtonTextUnderIcon false 0 0 Opening :/SegmentationUtilities/MorphologicalOperations/Opening_48x48.png:/SegmentationUtilities/MorphologicalOperations/Opening_48x48.png 32 32 Qt::ToolButtonTextUnderIcon Qt::Vertical 20 40 Labels 3 4 0 0 0 50 0 0 15 0 50 false 0 0 0 15 50 false Qt::Vertical 20 40 QmitkDataSelectionWidget QWidget
internal/Common/QmitkDataSelectionWidget.h
1 QmitkToolSelectionBox QWidget
QmitkToolSelectionBox.h
 QmitkToolGUIArea QWidget
QmitkToolGUIArea.h
 QmitkLabelSetWidget QWidget -
Qmitk/QmitkLabelSetWidget.h
+
QmitkLabelSetWidget.h
1 sliderMorphFactor valueChanged(int) spinBoxMorphFactor setValue(int) 240 27 766 36 spinBoxMorphFactor valueChanged(int) sliderMorphFactor setValue(int) 784 38 657 38 diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidgetControls.ui b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidgetControls.ui index 511fcc381f..52b7fc86e4 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidgetControls.ui +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidgetControls.ui @@ -1,252 +1,252 @@ QmitkSurfaceToImageWidgetControls 0 0 179 183 3 4 0 Masks 3 4 0 0 make output binary overwrite background Background Value: Qt::Horizontal 40 20 50 0 50 16777215 0.0 Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter Foreground Value: Qt::Horizontal 40 20 50 0 50 16777215 1.0 Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter Convert Qt::Vertical 20 40 Labels 2 2 0 0 0 50 0 20 Qt::Vertical 20 40 QmitkDataSelectionWidget QWidget
internal/Common/QmitkDataSelectionWidget.h
1 QmitkLabelSetWidget QWidget -
Qmitk/QmitkLabelSetWidget.h
+
QmitkLabelSetWidget.h
1 QmitkSurfaceStampWidget QWidget
QmitkSurfaceStampWidget.h
1 diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox index 6041c5c04a..a3ef93f2a0 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox @@ -1,394 +1,403 @@ /** \page org_mitk_views_segmentation The Segmentation View \imageMacro{segmentation-dox.svg,"Icon of the segmentation view",2.00} Some of the features described below are closed source additions to the open source toolkit MITK and are not available in every application. \tableofcontents \section org_mitk_views_segmentationoverview Overview Segmentation is the act of partitioning an image into subsets by either manual or automated delineation to create i.e. a distinction between foreground and background. A multilabel segmentation can contain more than one label and more than one layer. This allows you to create different labels for different regions of interest encapsulated in one single image. The difference between labels and layers is that labels on one layer cannot overlap but labels on different layers can. The MITK segmentation plugin allows you to create multilabel segmentations of anatomical and pathological structures in medical images. The plugin consists of two views:
  • Segmentation View: Manual and (semi-)automatic segmentation
  • \subpage org_mitk_views_segmentationutilities : Segmentation post-processing
In this documentation, the features and usage of the segmentation view will be described. For an introduction to the segmentation utilities please be referred to the respective documentation pages. \imageMacro{QmitkSegmentationPlugin_Overview.png,"Segmentation plugin overview", 16.00} \section org_mitk_views_segmentationpreferences Preferences The segmentation plugin offers a number of preferences which can be set via the MITK Workbench application preferences: \imageMacro{QmitkSegmentationPreferences.png,"Segmentation preferences", 10.00}
  • Slim view: Allows to show or hide the tool button description of the segmentation view
  • 2D display: Specify whether the segmentation is drawn as outline or as a transparent overlay
  • Show only selected nodes: Enable if only the selected segmentation and the reference image should be visible
  • Smoothed surface creation: Set certain smoothing parameters for surface creation
  • Default label set preset: Start a new segmentation with this preset instead of a default label +
  • Label creation: Assign default names and colors to new labels or ask users for them +
  • Label suggestions: Specify custom suggestions for label names and colors
\section org_mitk_views_segmentationtechnicalissues Technical issues The segmentation plugin makes a number of assumptions:
  • Images must be 2D, 3D, or 3D+t.
  • Images must be single-values, i.e. CT, MRI or "normal" ultrasound. Images from color doppler or photographic (RGB) images are only partially supported (please be aware that some tools might not be compatible with this image type).
  • Segmentations are handled as multilabel images of the same extent as the original image.
\section org_mitk_views_segmentationdataselection Data selection & creating new segmentations To select a reference image for the segmentation, click on the Selected image selection widget and choose a suitable image from the selection available in the data manager. Once an image is selected, a new segmentation can be created on this reference image by clicking the button to the right of the Selected segmentation selection widget. A new multilabel segmentation with an initial label is automatically generated. The new segmentation will be added to the data manager as sub-node of the reference image. This item is then automatically selected in the data selection, which allows to start editing the new segmentation right away. \imageMacro{"QmitkSegmentation_DataSelection.png","Data selection",12} Alternatively to creating a new segmentation, an existing one can be edited as well. If a reference image is selected for which a segmentation already exists in the data manager, the auto selection mode will automatically select a fitting segmentation. Clicking on the segmentation selection widget a drop down list will open, containing all suitable segmentations for the selected reference dataset available in the data manager. \section org_mitk_views_segmentationlayers Segmentation layers For each multilabel segmentation different layers can be added or deleted. The layers can be used independently and layers can be switched using the left and right arrows. A layer is a set of labels that occupy a non-overlapping anatomical space. The best way to describe them is by a real use case: Imagine you are working on a radiotherapy planning application. In the first layer of your segmentation session, you would like to trace the contours of the liver and neighboring organs. You can accommodate all these segmentations in separate labels because they all occupy different anatomical regions and do not overlap. Now say you would like to segment the arteries and veins inside the liver. If you don't trace them in a different layer, you will overwrite the previous ones. You may also need a third layer for segmenting the different irrigation territories in the liver and a fourth layer to contain the lesion you would like to treat. \imageMacro{"QmitkSegmentation_LayerSelection.png","Layer selection",12} \section org_mitk_views_segmentationlabels Segmentation labels For each layer, one or more labels can be added. Pressing the double arrow on the right, all created labels are shown in the 'Label Table'. The following label properties are available:
  • Name:
    • the name of the label. Can be a predefined one or any other.
  • Locked:
    • whether the label is locked or editable. A locked label cannot be overwritten by another.
  • Color:
    • the color of the label.
  • Visible:
    • whether the label is currently visible or hidden.
\imageMacro{"QmitkSegmentation_LabelTable.png","The 'Label Table' shows all labels in the current segmentation session",12} The 'New Label' button can be used to add a new label. This will automatically add a new label with a distinct name and color to the list of available labels.\n In the current implementation of the plugin, the maximum number of labels is restricted to 255. If you need more, you will have to create a new segmentation session. +\subsection org_mitk_views_segmentationlabelsuggestions Label name and color suggestions + +When renaming labels or creating new labels with enforced manual naming in the Segmentation preferences, entering names is supported by auto-completion for common label names. +The list of predefined label names and colors for the auto-completion feature can be either extented or replaced by a custom list of label name and color suggestions. +This custom list must be specified as a JSON file, just containing an array of objects, each with a mandatory "name" string and an optional "color" string. +The JSON file can be set in the Segmentation preferences as well as a few options on how to apply these suggestions. + \subsection org_mitk_views_segmentationlabelpresets Saving and loading label set presets Label set presets are useful to share a certain style or scheme between different segmentation sessions or to provide templates for new segmentation sessions. The properties of all labels in all layers like their names, colors, and visibilities are saved as a label set preset by clicking on the 'Save label set preset' button. Label set presets are applied to any segmentation session by clicking on the 'Load label set preset' button. If a label for a certain value already exists, its properties are overridden by the preset. If a label for a certain value does not yet exist, an empty label with the label properties of the preset is created. The actual segmentations of labels are unaffected as label set presets only store label properties. \subsubsection org_mitk_views_segmentationdefaultlabelpresets Applying label set presets by default If you work on a repetetive segmentation task, manually loading the same label set preset for each and every new segmentation can be tedious. To streamline your workflow, you can set a default label set preset in the Segmentation preferences (Ctrl+P). When set, this label set preset will be applied to all new segmentations instead of creating the default red "New label 1" label. \subsection org_mitk_views_segmentationlabelsearch Searching for a label It may happen that many labels (e.g. > 200) are present in a segmentation session and therefore manual searching can be time-consuming. The 'Label Search' edit box allows for quickly finding a label by providing assistance for label name completion. If the label is found, it will become the active one after pressing 'enter'. To start editing a label needs to be activated by clicking on the corresponding row in the 'Label Table'. Only one label can be active at the time. Then the segmentation tools in the toolbox can be used for mask generation. \subsection org_mitk_views_multilabelsegmentationoperationsonlabels Operations on labels Depending on the selection in the 'Label Table', several actions are offered: \subsubsection org_mitk_views_segmentationoperationssingleselection Operations with single label selection Right-clicking on any label opens a pop-up menu that offers the following actions to be performed on the selected label:
  • Rename...
    • : change the name and / or color of the selected label.
  • Remove...
    • : delete the selected label.
  • Erase...
    • : only clear the contents of the selected label.
  • Merge...
    • : merge two labels by selecting a second label.
  • Random color
    • : assign a random color to the label.
  • View only
    • : make all labels except the current selected label invisible.
  • View/Hide all
    • : make all labels visible / invisible
  • Lock/Unlock all
    • : lock or unlock all labels.
  • Create surface
    • : generate a surface out of the selected label.
  • Create mask
    • : generate a mask out of the selected label. A mask is a binary image with "1" inside and "0" outside.
  • Create cropped mask
    • : generate a binary mask out of the selected label. Crop changes the extent of the resulting image to the extent of the label.
\imageMacro{"QmitkSegmentation_OperationsSingleSelection.png","Context menu for single label selection",12} \subsubsection org_mitk_views_segmentationoperationsmultiselection Operations with multiple label selection Shift-clickink on multiple labels allows to select more than one label. If more than one label is selected, different options will appear in the menu:
  • Merge selection on current label
    • : transfer the contents of the selected labels in the 'Label Table' into the current one.
  • Remove selected labels
    • : delete the selected labels.
  • Erase selected labels
    • : only clear the contents of the selected labels.
\imageMacro{"QmitkSegmentation_OperationsMultiSelection.png","Context menu for multiple label selection",12} \section org_mitk_views_segmentationtooloverview Segmentation tool overview MITK offers a comprehensive set of slice-based 2D and (semi-)automated 3D segmentation tools. The manual 2D tools require some user interaction and can only be applied to a single image slice whereas the 3D tools operate on the whole image. The 3D tools usually only require a small amount of user interaction, i.e. placing seed points or setting / adjusting parameters. You can switch between the different toolsets by selecting the 2D or 3D tab in the segmentation view. \imageMacro{QmitkSegmentation_ToolOverview.png,"An overview of the existing 2D and 3D tools in MITK.",5.50} \section org_mitk_views_segmentation2dsegmentation 2D segmentation tools With 2D manual contouring you define which voxels are part of the segmentation and which are not. This allows you to create segmentations of any structures of interest in an image. You can also use manual contouring to correct segmentations that result from sub-optimal automatic methods. The drawback of manual contouring is that you might need to define contours on many 2D slices. However, this is mitigated by the interpolation feature, which will make suggestions for a segmentation. To start using one of the editing tools, click its button from the displayed toolbox. The selected editing tool will be active and its corresponding button will stay pressed until you click the button again. Selecting a different tool also deactivates the previous one.\n If you have to delineate a lot of images, shortcuts to switch between tools becomes convenient. For that, just hit the first letter of each tool to activate it (A for Add, S for Subtract, etc.). All of the editing tools work by the same principle: using the mouse (left button) to click anywhere in a 2D window (any of the orientations axial, sagittal, or coronal), moving the mouse while holding the mouse button and releasing the button to finish the editing action. Multi-step undo and redo is fully supported by all editing tools by using the application-wide undo / redo buttons in the toolbar. Remark: Clicking and moving the mouse in any of the 2D render windows will move the crosshair that defines what part of the image is displayed. This behavior is disabled as long as any of the manual segmentation tools are active - otherwise you might have a hard time concentrating on the contour you are drawing. \subsection org_mitk_views_segmentationaddsubtracttools Add and subtract tools \imageMacro{QmitkSegmentation_IMGIconAddSubtract.png,"Add and subtract tools",7.70} Use the left mouse button to draw a closed contour. When releasing the mouse button, the contour will be added (Add tool) to or removed (Subtract tool) from the current segmentation. Adding and subtracting voxels can be iteratively repeated for the same segmentation. Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of adding voxels, they will be subtracted). \subsection org_mitk_views_segmentationpaintwipetools Paint and wipe tools \imageMacro{QmitkSegmentation_IMGIconPaintWipe.png,"Paint and wipe tools",7.68} Use the Size slider to change the radius of the round paintbrush tool. Move the mouse in any 2D window and press the left button to draw or erase pixels. Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of painting voxels, they will be wiped). \subsection org_mitk_views_segmentationregiongrowingtool Region growing tool \imageMacro{QmitkSegmentation_IMGIconRegionGrowing.png,"Region growing tool",3.81} Click at one point in a 2D slice widget to add an image region to the segmentation with the region growing tool. Region Growing selects all pixels around the mouse cursor that have a similar gray value as the pixel below the mouse cursor. This allows to quickly create segmentations of structures that have a good contrast to surrounding tissue. The tool operates based on the current level window, so changing the level window to optimize the contrast for the ROI is encouraged. Moving the mouse up / down is different from left / right: Moving up the cursor while holding the left mouse button widens the range for the included grey values; moving it down narrows it. Moving the mouse left and right will shift the range. The tool will select more or less pixels, corresponding to the changing gray value range. \if THISISNOTIMPLEMENTEDATTHEMOMENT A common issue with region growing is the so called "leakage" which happens when the structure of interest is connected to other pixels, of similar gray values, through a narrow "bridge" at the border of the structure. The Region Growing tool comes with a "leakage detection/removal" feature. If leakage happens, you can left-click into the leakage region and the tool will try to automatically remove this region (see illustration below). \imageMacro{QmitkSegmentation_Leakage.png,"Leakage correction feature of the region growing tool",11.28} \endif \subsection org_mitk_views_segmentationfilltool Fill tool \imageMacro{QmitkSegmentation_IMGIconFill.png,"Fill tool",3.81} Left-click inside a segmentation with holes to completely fill all holes. Left-click inside a hole to fill only this specific hole. \subsection org_mitk_views_segmentationerasetool Erase tool \imageMacro{QmitkSegmentation_IMGIconErase.png,"Erase tool",3.79} This tool removes a connected part of pixels that form a segmentation. You may use it to remove single segmentations (left-click on specific segmentation) or to clear a whole slice at once (left-click outside a segmentation). \subsection org_mitk_views_segmentationlivewiretool Live wire tool \imageMacro{QmitkSegmentation_IMGIconLiveWire.png,"Live wire tool",3.01} The Live Wire Tool acts as a magnetic lasso with a contour snapping to edges of objects. \imageMacro{QmitkSegmentation_IMGLiveWireUsage.PNG,"Steps for using the Live Wire Tool",16.00}
  • (1) To start the tool you have to double-click near the edge of the object you want to segment. The initial anchor point will snap to the edge within a 3x3 region.
  • (2) Move the mouse. You don't have trace the edge of the object. The contour will automatically snap to it.
  • (3) To fix a segment you can set anchor points by single left mouse button click.
  • (4) Go on with moving the mouse and setting anchor points.
  • (5) To close the contour double-click on the initial anchor point.
  • (6) After closing, the contour can be edited by moving, inserting and deleting anchor points.
The contour will be transferred to its binary image representation by deactivating the tool. \subsection org_mitk_views_segmentationinterpolation 2D and 3D Interpolation Creating segmentations using 2D manual contouring for large image volumes may be very time-consuming, because structures of interest may cover a large range of slices. Note: Interpolation is currently disabled for segmentations containing more than one label. The segmentation view offers two helpful features to mitigate this drawback:
  • 2D Interpolation
  • 3D Interpolation
The 2D Interpolation creates suggestions for a segmentation whenever you have a slice that
  • has got neighboring slices with segmentations (these do not need to be direct neighbors but could also be a couple of slices away) AND
  • is completely clear of a manual segmentation, i.e. there will be no suggestion if there is even only a single pixel of segmentation in the current slice.
\imageMacro{QmitkSegmentation_2DInterpolation.png,"2D interpolation usage",3.01} Interpolated suggestions are displayed as outlines, until you confirm them as part of the segmentation. To confirm single slices, click the Confirm for single slice button below the toolbox. You may also review the interpolations visually and then accept all of them at once by selecting Confirm for all slices. The 3D interpolation creates suggestions for 3D segmentations. That means if you start contouring, from the second contour onwards, the surface of the segmented area will be interpolated based on the given contour information. The interpolation works with all available manual tools. Please note that this is currently a pure mathematical interpolation, i.e. image intensity information is not taken into account. With each further contour the interpolation result will be improved, but the more contours you provide the longer the recalculation will take. To achieve an optimal interpolation result and in this way a most accurate segmentation you should try to describe the surface with sparse contours by segmenting in arbitrary oriented planes. The 3D interpolation is not meant to be used for parallel slice-wise segmentation, but rather segmentations in i.e. the axial, coronal and sagittal plane. \imageMacro{QmitkSegmentation_3DInterpolationWrongRight.png,"3D interpolation usage",16.00} You can accept the interpolation result by clicking the Confirm-button below the tool buttons. In this case the 3D interpolation will be deactivated automatically so that the result can be post-processed without any interpolation running in the background. Additional to the surface, black contours are shown in the 3D render window, which mark all the drawn contours used for the interpolation. You can navigate between the drawn contours by clicking on the corresponding position nodes in the data manager which are stored as sub-nodes of the selected segmentation. If you do not want to see these nodes just uncheck the Show Position Nodes checkbox and these nodes will be hidden. If you want to delete a drawn contour we recommend to use the Erase-Tool since undo / redo is not yet working for 3D interpolation. The current state of the 3D interpolation can be saved across application restart. For that, just click on save project during the interpolation is active. After restarting the application and load your project you can click on "Reinit Interpolation" within the 3D interpolation GUI area. \section org_mitk_views_segmentation3dsegmentation 3D segmentation tools The 3D tools operate on the whole image and require usually a small amount of interaction like placing seed-points or specifying certain parameters. All 3D tools provide an immediate segmentation feedback, which is displayed as a transparent green overlay. For accepting a preview you have to press the Confirm button of the selected tool. The following 3D tools are available: \subsection org_mitk_views_segmentation3dthresholdtool 3D Threshold tool The thresholding tool simply applies a 3D threshold to the patient image. All pixels with values equal or above the selected threshold are labeled as part of the segmentation. You can change the threshold by either moving the slider of setting a certain value in the spinbox. \imageMacro{QmitkSegmentation_3DThresholdTool.png,"3D Threshold tool",10.00} \subsection org_mitk_views_segmentation3dulthresholdTool 3D upper / lower threshold tool The Upper/Lower Thresholding tool works similar to the simple 3D threshold tool but allows you to define an upper and lower threshold. All pixels with values within this threshold interval will be labeled as part of the segmentation. \imageMacro{QmitkSegmentation_3DULThresholdTool.png,"3D upper / lower threshold tool",10.00} \subsection org_mitk_views_segmentation3dotsutool 3D Otsu tool The 3D Otsu tool provides a more sophisticated thresholding algorithm. It allows you to define a number of regions. Based on the image histogram the pixels will then be divided into different regions. The more regions you define the longer the calculation will take. You can select afterwards which of these regions you want to confirm as segmentation. \imageMacro{QmitkSegmentation_3DOtsuTool.png,"3D Otsu tool",10.00} \subsection org_mitk_views_segmentation3drgtool 3D Region growing tool The 3D Region Growing tool works similar to the 2D pendant. At the beginning you have to place a seedpoint and define a threshold interval. If you press Run Segmentation a preview is calculated. By moving the Adapt region growing slider you can interactively adapt the segmentation result. \imageMacro{QmitkSegmentation_3DRGTool.png,"3D Region growing tool",10.00} \subsection org_mitk_views_segmentationpickingtool Picking Tool The Picking tool offers two modes that allow you to manipulate "islands" within your segmentation. This is especially useful if e.g. a thresholding provided you with several areas within your image but you are just interested in one special region. - Picking mode: Allows you to select certain "islands". When the pick is confirmed, the complete content of the active label will be removed except the pick. This mode is beneficial if you have a lot segmentation noise and want to pick the relevant parts and dismiss the rest. Hint: You can also pick from other labels, but this will only work if these labels are unlocked. - Relabel mode: Allows you to select certain "islands". When the pick is confirmed, it will be relabeled and added to the active label content. Hint: This mode ignores the locks of other labels, hence you do not need to unlock them explicitly. \imageMacro{QmitkSegmentation_PickingTool.png,"Picking tool",10.00} \subsection org_mitk_views_segmentationnnUNetTool nnU-Net Tool (Ubuntu only) \imageMacro{QmitkSegmentation_nnUnetTool.png,"nnUNet tool",10.00} This tool provides a GUI to the deep learning-based segmentation algorithm called the nnUNet. With this tool, you can get a segmentation mask predicted for the loaded image in MITK. Be ready with the pre-trained weights (a.k.a RESULTS_FOLDER) for your organ or task concerned, before using the tool. For a detailed explanation of the parameters and pre-trained weights folder structure etc., please refer to https://github.com/MIC-DKFZ/nnUNet.
Remark: The tool assumes that you have a Python3 environment with nnUNet (pip) installed. Your machine should be also equipped with a CUDA enabled GPU. \subsubsection org_mitk_views_segmentationnnUNetToolWorkflow Workflow: -# Select the "Python Path" drop-down to see if MITK has automatically detected other Python environments. Click on a fitting environment for the nnUNet inference or click "Select" in the dropdown to choose an unlisted python environment. Note that, while selecting an arbitrary environment folder, only select the base folder, e.g. "myenv". No need to select all the way until "../myenv/bin/python", for example. -# Click on the "nnUNet Results Folder" directory icon to navigate to the results folder on your hard disk. This is equivalent to setting the RESULTS_FOLDER environment variable. If your results folder is as per the nnUNet required folder structure, the configuration, trainers, tasks and folds are automatically parsed and correspondingly loaded in the drop-down boxes as shown below. Note that MITK automatically checks for the RESULTS_FOLDER environment variable value and, if found, auto parses that directory when the tool is started. \imageMacro{QmitkSegmentation_nnUNet_Settings.png,"nnUNet Segmentation Settings",10} -# Choose your required Task-Configuration-Trainer-Planner-Fold parameters, sequentially. By default, all entries are selected inside the "Fold" dropdown (shown: "All"). Note that, even if you uncheck all entries from the "Fold" dropdown (shown: "None"), then too, all folds would be considered for inferencing. -# For ensemble predictions, you will get the option to select parameters irrespective on postprocessing files available in the ensembles folder of RESULTS_FOLDER. Note that, if a postprocessing json file exists for the selected combination then it will used for ensembling, by default. To choose not to, uncheck the "Use PostProcessing JSON" in the "Advanced" section. \imageMacro{QmitkSegmentation_nnUNet_ensemble.png,"nnUNet Segmentation Settings",10} -# If your task is trained with multi-modal inputs, then "Multi-Modal" checkbox is checked and the no.of modalities are preloaded in the "No. of Extra Modalities" spinbox. Instantly, as much node selectors with corresponding modality names should appear below to select the Data Manager along including a selector with preselected with the reference node. Now, select the image nodes in the node selectors accordingly for accurate inferencing. \imageMacro{QmitkSegmentation_nnUNet_multimodal.png,"nnUNet Multi Modal Settings",10.00} -# Click on "Preview". -# In the "Advanced" section, you can also activate other options like "Mixed Precision" and "Enable Mirroring" (for test time data augmentation) pertaining to nnUNet. \imageMacro{QmitkSegmentation_nnUNet_Advanced.png,"nnUNet Advanced Settings",10.00} -# Use "Advanced" > "GPU Id" combobox to change the preferred GPU for inferencing. This is internally equivalent to setting the CUDA_VISIBLE_DEVICES environment variable. -# Every inferred segmentation is cached to prevent a redundant computation. In case, a user doesn't wish to cache a Preview, uncheck the "Enable Caching" in the "Advanced" section. This will ensure that the current parameters will neither be checked against the existing cache nor a segmentation be loaded from it when Preview is clicked. -# You may always clear all the cached segmentations by clicking "Clear Cache" button. \subsubsection org_mitk_views_segmentationnnUNetToolMisc Miscellaneous: -# In case you want to reload/reparse the folders in the "nnUNet Results Folder", eg. after adding new tasks into it, you may do so without reselecting the folder again by clicking the "Refresh Results Folder" button. -# The "Advanced" > "GPU Id" combobox lists the Nvidia GPUs available by parsing the nvidia-smi utility output. In case your machine has Nvidia CUDA enabled GPUs but the nvidia-smi fails for some reason, the "GPU Id" combobox will show no entries. In such a situation, it's still possible to execute inferencing by manually entering the preferred GPU Id, eg. 0 in the combobox. -# In the RESULTS_FOLDER directory, inside the trainer-planner folder of every task, MITK keeps a "mitk_export.json" file for fast loading for multi-modal information. It is recommended not to delete this file(s) for a fast responsive UI. Tip: If multi-modal information shown on MITK is not correct for a given task, you may modify this JSON file and try again. \section org_mitk_views_segmentationpostprocessing Additional things you can do with segmentations Segmentations are never an end in themselves. Consequently, the segmentation view adds a couple of "post-processing" actions, accessible through the context-menu of the data manager. \imageMacro{QmitkSegmentation_IMGDataManagerContextMenu.png,"Context menu items for segmentations",10.58}
  • Create polygon %model applies the marching cubes algorithm to the segmentation. This polygon %model can be used for visualization in 3D or other applications such as stereolithography (3D printing).
  • Create smoothed polygon %model uses smoothing in addition to the marching cubes algorithm, which creates models that do not follow the exact outlines of the segmentation, but look smoother.
  • Autocrop can save memory. Manual segmentations have the same extent as the patient image, even if the segmentation comprises only a small sub-volume. This invisible and meaningless margin is removed by autocropping.
\section org_mitk_views_segmentationof3dtimages Segmentation of 3D+t images For segmentation of 3D+t images, some tools give you the option to choose between creating dynamic and static masks.
  • Dynamic masks can be created on each time frame individually.
  • Static masks will be defined on one time frame and will be the same for all other time frames.
In general, segmentation is applied on the time frame that is selected when execution is performed. If you alter the time frame, the segmentation preview is adapted. \section org_mitk_views_segmentationtechnicaldetail Technical information for developers For technical specifications see \subpage QmitkSegmentationTechnicalPage and for information on the extensions of the tools system \subpage toolextensions. */ diff --git a/Plugins/org.mitk.gui.qt.segmentation/files.cmake b/Plugins/org.mitk.gui.qt.segmentation/files.cmake index bb27b67836..584a0cf103 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/files.cmake +++ b/Plugins/org.mitk.gui.qt.segmentation/files.cmake @@ -1,81 +1,87 @@ set(SRC_CPP_FILES QmitkSegmentationPreferencePage.cpp + QmitkNewSegmentationDialog.cpp + QmitkLabelSetWidget.cpp ) set(INTERNAL_CPP_FILES mitkPluginActivator.cpp QmitkSegmentationView.cpp QmitkAutocropAction.cpp QmitkAutocropLabelSetImageAction.cpp QmitkCreatePolygonModelAction.cpp QmitkLoadMultiLabelPresetAction.cpp QmitkSaveMultiLabelPresetAction.cpp Common/QmitkDataSelectionWidget.cpp Common/QmitkLabelsWidget.cpp Common/QmitkLayersWidget.cpp SegmentationUtilities/QmitkSegmentationUtilitiesView.cpp SegmentationUtilities/QmitkSegmentationUtilityWidget.cpp SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.cpp SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidget.cpp SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.cpp ) set(UI_FILES src/QmitkSegmentationPreferencePageControls.ui + src/QmitkNewSegmentationDialog.ui + src/QmitkLabelSetWidgetControls.ui src/internal/QmitkSegmentationViewControls.ui src/internal/Common/QmitkDataSelectionWidgetControls.ui src/internal/Common/QmitkLabelsWidgetControls.ui src/internal/Common/QmitkLayersWidgetControls.ui src/internal/SegmentationUtilities/QmitkSegmentationUtilitiesViewControls.ui src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidgetControls.ui src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidgetControls.ui src/internal/SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidgetControls.ui src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidgetControls.ui ) set(MOC_H_FILES src/QmitkSegmentationPreferencePage.h + src/QmitkNewSegmentationDialog.h + src/QmitkLabelSetWidget.h src/internal/mitkPluginActivator.h src/internal/QmitkSegmentationView.h src/internal/QmitkAutocropAction.h src/internal/QmitkAutocropLabelSetImageAction.h src/internal/QmitkCreatePolygonModelAction.h src/internal/QmitkLoadMultiLabelPresetAction.h src/internal/QmitkSaveMultiLabelPresetAction.h src/internal/Common/QmitkDataSelectionWidget.h src/internal/Common/QmitkLabelsWidget.h src/internal/Common/QmitkLayersWidget.h src/internal/SegmentationUtilities/QmitkSegmentationUtilitiesView.h src/internal/SegmentationUtilities/QmitkSegmentationUtilityWidget.h src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.h src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.h src/internal/SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidget.h src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.h ) set(CACHED_RESOURCE_FILES resources/segmentation.svg resources/segmentation_utilities.svg plugin.xml ) set(QRC_FILES resources/segmentation.qrc resources/SegmentationUtilities.qrc resources/BooleanOperationsWidget.qrc resources/MorphologicalOperationsWidget.qrc ) set(CPP_FILES) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Modules/SegmentationUI/Qmitk/QmitkLabelSetWidget.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkLabelSetWidget.cpp similarity index 98% rename from Modules/SegmentationUI/Qmitk/QmitkLabelSetWidget.cpp rename to Plugins/org.mitk.gui.qt.segmentation/src/QmitkLabelSetWidget.cpp index 032a71aff1..0742129dfa 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkLabelSetWidget.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkLabelSetWidget.cpp @@ -1,1155 +1,1147 @@ /*============================================================================ 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 "QmitkLabelSetWidget.h" // mitk #include #include #include #include #include #include #include #include #include #include #include // Qmitk #include #include #include // Qt #include #include #include #include #include #include #include #include #include // itk #include QmitkLabelSetWidget::QmitkLabelSetWidget(QWidget *parent) : QWidget(parent), m_DataStorage(nullptr), m_Completer(nullptr), m_ToolManager(nullptr), m_ProcessingManualSelection(false) { m_Controls.setupUi(this); m_ColorSequenceRainbow.GoToBegin(); m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); m_Controls.m_LabelSearchBox->setAlwaysShowClearIcon(true); m_Controls.m_LabelSearchBox->setShowSearchIcon(true); QStringList completionList; completionList << ""; m_Completer = new QCompleter(completionList, this); m_Completer->setCaseSensitivity(Qt::CaseInsensitive); m_Controls.m_LabelSearchBox->setCompleter(m_Completer); connect(m_Controls.m_LabelSearchBox, SIGNAL(returnPressed()), this, SLOT(OnSearchLabel())); QStringListModel *completeModel = static_cast(m_Completer->model()); completeModel->setStringList(GetLabelStringList()); m_Controls.m_LabelSearchBox->setEnabled(false); m_Controls.m_lblCaption->setText(""); InitializeTableWidget(); } QmitkLabelSetWidget::~QmitkLabelSetWidget() {} void QmitkLabelSetWidget::OnTableViewContextMenuRequested(const QPoint & /*pos*/) { int pixelValue = GetPixelValueOfSelectedItem(); if (-1 == pixelValue) return; QMenu *menu = new QMenu(m_Controls.m_LabelSetTableWidget); if (m_Controls.m_LabelSetTableWidget->selectedItems().size() > 1) { QAction *mergeAction = new QAction(QIcon(":/Qmitk/MergeLabels.png"), "Merge selection on current label", this); mergeAction->setEnabled(true); QObject::connect(mergeAction, SIGNAL(triggered(bool)), this, SLOT(OnMergeLabels(bool))); menu->addAction(mergeAction); QAction *removeLabelsAction = new QAction(QIcon(":/Qmitk/RemoveLabel.png"), "Remove selected labels", this); removeLabelsAction->setEnabled(true); QObject::connect(removeLabelsAction, SIGNAL(triggered(bool)), this, SLOT(OnRemoveLabels(bool))); menu->addAction(removeLabelsAction); QAction *eraseLabelsAction = new QAction(QIcon(":/Qmitk/EraseLabel.png"), "Erase selected labels", this); eraseLabelsAction->setEnabled(true); QObject::connect(eraseLabelsAction, SIGNAL(triggered(bool)), this, SLOT(OnEraseLabels(bool))); menu->addAction(eraseLabelsAction); } else { QAction *renameAction = new QAction(QIcon(":/Qmitk/RenameLabel.png"), "Rename...", this); renameAction->setEnabled(true); QObject::connect(renameAction, SIGNAL(triggered(bool)), this, SLOT(OnRenameLabel(bool))); menu->addAction(renameAction); QAction *removeAction = new QAction(QIcon(":/Qmitk/RemoveLabel.png"), "Remove...", this); removeAction->setEnabled(true); QObject::connect(removeAction, SIGNAL(triggered(bool)), this, SLOT(OnRemoveLabel(bool))); menu->addAction(removeAction); QAction *eraseAction = new QAction(QIcon(":/Qmitk/EraseLabel.png"), "Erase...", this); eraseAction->setEnabled(true); QObject::connect(eraseAction, SIGNAL(triggered(bool)), this, SLOT(OnEraseLabel(bool))); menu->addAction(eraseAction); QAction *randomColorAction = new QAction(QIcon(":/Qmitk/RandomColor.png"), "Random color", this); randomColorAction->setEnabled(true); QObject::connect(randomColorAction, SIGNAL(triggered(bool)), this, SLOT(OnRandomColor(bool))); menu->addAction(randomColorAction); QAction *viewOnlyAction = new QAction(QIcon(":/Qmitk/visible.png"), "View only", this); viewOnlyAction->setEnabled(true); QObject::connect(viewOnlyAction, SIGNAL(triggered(bool)), this, SLOT(OnSetOnlyActiveLabelVisible(bool))); menu->addAction(viewOnlyAction); QAction *viewAllAction = new QAction(QIcon(":/Qmitk/visible.png"), "View all", this); viewAllAction->setEnabled(true); QObject::connect(viewAllAction, SIGNAL(triggered(bool)), this, SLOT(OnSetAllLabelsVisible(bool))); menu->addAction(viewAllAction); QAction *hideAllAction = new QAction(QIcon(":/Qmitk/invisible.png"), "Hide all", this); hideAllAction->setEnabled(true); QObject::connect(hideAllAction, SIGNAL(triggered(bool)), this, SLOT(OnSetAllLabelsInvisible(bool))); menu->addAction(hideAllAction); QAction *lockAllAction = new QAction(QIcon(":/Qmitk/lock.png"), "Lock all", this); lockAllAction->setEnabled(true); QObject::connect(lockAllAction, SIGNAL(triggered(bool)), this, SLOT(OnLockAllLabels(bool))); menu->addAction(lockAllAction); QAction *unlockAllAction = new QAction(QIcon(":/Qmitk/unlock.png"), "Unlock all", this); unlockAllAction->setEnabled(true); QObject::connect(unlockAllAction, SIGNAL(triggered(bool)), this, SLOT(OnUnlockAllLabels(bool))); menu->addAction(unlockAllAction); QAction *createSurfaceAction = new QAction(QIcon(":/Qmitk/CreateSurface.png"), "Create surface", this); createSurfaceAction->setEnabled(true); createSurfaceAction->setMenu(new QMenu()); QAction *tmp1 = createSurfaceAction->menu()->addAction(QString("Detailed")); QAction *tmp2 = createSurfaceAction->menu()->addAction(QString("Smoothed")); QObject::connect(tmp1, SIGNAL(triggered(bool)), this, SLOT(OnCreateDetailedSurface(bool))); QObject::connect(tmp2, SIGNAL(triggered(bool)), this, SLOT(OnCreateSmoothedSurface(bool))); menu->addAction(createSurfaceAction); QAction *createMaskAction = new QAction(QIcon(":/Qmitk/CreateMask.png"), "Create mask", this); createMaskAction->setEnabled(true); QObject::connect(createMaskAction, SIGNAL(triggered(bool)), this, SLOT(OnCreateMask(bool))); menu->addAction(createMaskAction); QAction *createCroppedMaskAction = new QAction(QIcon(":/Qmitk/CreateMask.png"), "Create cropped mask", this); createCroppedMaskAction->setEnabled(true); QObject::connect(createCroppedMaskAction, SIGNAL(triggered(bool)), this, SLOT(OnCreateCroppedMask(bool))); menu->addAction(createCroppedMaskAction); QSlider *opacitySlider = new QSlider; opacitySlider->setMinimum(0); opacitySlider->setMaximum(100); opacitySlider->setOrientation(Qt::Horizontal); QObject::connect(opacitySlider, SIGNAL(valueChanged(int)), this, SLOT(OnOpacityChanged(int))); QLabel *_OpacityLabel = new QLabel("Opacity: "); QVBoxLayout *_OpacityWidgetLayout = new QVBoxLayout; _OpacityWidgetLayout->setContentsMargins(4, 4, 4, 4); _OpacityWidgetLayout->addWidget(_OpacityLabel); _OpacityWidgetLayout->addWidget(opacitySlider); QWidget *_OpacityWidget = new QWidget; _OpacityWidget->setLayout(_OpacityWidgetLayout); QWidgetAction *OpacityAction = new QWidgetAction(this); OpacityAction->setDefaultWidget(_OpacityWidget); // QObject::connect( m_OpacityAction, SIGNAL( changed() ), this, SLOT( OpacityActionChanged() ) ); auto workingImage = this->GetWorkingImage(); auto activeLayer = workingImage->GetActiveLayer(); auto label = workingImage->GetLabel(pixelValue, activeLayer); if (nullptr != label) { auto opacity = label->GetOpacity(); opacitySlider->setValue(static_cast(opacity * 100)); } menu->addAction(OpacityAction); } menu->popup(QCursor::pos()); } void QmitkLabelSetWidget::OnUnlockAllLabels(bool /*value*/) { GetWorkingImage()->GetActiveLabelSet()->SetAllLabelsLocked(false); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkLabelSetWidget::OnLockAllLabels(bool /*value*/) { GetWorkingImage()->GetActiveLabelSet()->SetAllLabelsLocked(true); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkLabelSetWidget::OnSetAllLabelsVisible(bool /*value*/) { GetWorkingImage()->GetActiveLabelSet()->SetAllLabelsVisible(true); UpdateAllTableWidgetItems(); } void QmitkLabelSetWidget::OnSetAllLabelsInvisible(bool /*value*/) { GetWorkingImage()->GetActiveLabelSet()->SetAllLabelsVisible(false); UpdateAllTableWidgetItems(); } void QmitkLabelSetWidget::OnSetOnlyActiveLabelVisible(bool /*value*/) { mitk::LabelSetImage *workingImage = GetWorkingImage(); int pixelValue = GetPixelValueOfSelectedItem(); workingImage->GetActiveLabelSet()->SetAllLabelsVisible(false); workingImage->GetLabel(pixelValue, workingImage->GetActiveLayer())->SetVisible(true); workingImage->GetActiveLabelSet()->UpdateLookupTable(pixelValue); this->WaitCursorOn(); const mitk::Point3D &pos = workingImage->GetLabel(pixelValue, workingImage->GetActiveLayer())->GetCenterOfMassCoordinates(); this->WaitCursorOff(); if (pos.GetVnlVector().max_value() > 0.0) { emit goToLabel(pos); } UpdateAllTableWidgetItems(); } void QmitkLabelSetWidget::OnEraseLabel(bool /*value*/) { int pixelValue = GetPixelValueOfSelectedItem(); QString question = "Do you really want to erase the contents of label \""; question.append( QString::fromStdString(GetWorkingImage()->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer())->GetName())); question.append("\"?"); QMessageBox::StandardButton answerButton = QMessageBox::question(this, "Erase label", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answerButton == QMessageBox::Yes) { this->WaitCursorOn(); GetWorkingImage()->EraseLabel(pixelValue); this->WaitCursorOff(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkLabelSetWidget::OnRemoveLabel(bool /*value*/) { int pixelValue = GetPixelValueOfSelectedItem(); QString question = "Do you really want to remove label \""; question.append( QString::fromStdString(GetWorkingImage()->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer())->GetName())); question.append("\"?"); QMessageBox::StandardButton answerButton = QMessageBox::question(this, "Remove label", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answerButton == QMessageBox::Yes) { this->WaitCursorOn(); GetWorkingImage()->RemoveLabel(pixelValue, GetWorkingImage()->GetActiveLayer()); this->WaitCursorOff(); } ResetAllTableWidgetItems(); } void QmitkLabelSetWidget::OnRenameLabel(bool /*value*/) { int pixelValue = GetPixelValueOfSelectedItem(); - QmitkNewSegmentationDialog dialog(this); - dialog.setWindowTitle("Rename Label"); - dialog.SetSuggestionList(m_OrganColors); + QmitkNewSegmentationDialog dialog(this, this->GetWorkingImage(), QmitkNewSegmentationDialog::RenameLabel); dialog.SetColor(GetWorkingImage()->GetActiveLabelSet()->GetLabel(pixelValue)->GetColor()); - dialog.SetSegmentationName( - QString::fromStdString(GetWorkingImage()->GetActiveLabelSet()->GetLabel(pixelValue)->GetName())); + dialog.SetName(QString::fromStdString(GetWorkingImage()->GetActiveLabelSet()->GetLabel(pixelValue)->GetName())); if (dialog.exec() == QDialog::Rejected) { return; } - QString segmentationName = dialog.GetSegmentationName(); + QString segmentationName = dialog.GetName(); if (segmentationName.isEmpty()) { segmentationName = "Unnamed"; } GetWorkingImage()->GetActiveLabelSet()->RenameLabel(pixelValue, segmentationName.toStdString(), dialog.GetColor()); GetWorkingImage()->GetActiveLabelSet()->UpdateLookupTable(pixelValue); UpdateAllTableWidgetItems(); } void QmitkLabelSetWidget::OnCombineAndCreateMask(bool /*value*/) { m_Controls.m_LabelSetTableWidget->selectedRanges(); // ...to do... // } void QmitkLabelSetWidget::OnCreateMasks(bool /*value*/) { m_Controls.m_LabelSetTableWidget->selectedRanges(); // ..to do.. // } void QmitkLabelSetWidget::OnCombineAndCreateSurface(bool /*value*/) { m_Controls.m_LabelSetTableWidget->selectedRanges(); // ..to do.. // } void QmitkLabelSetWidget::OnEraseLabels(bool /*value*/) { QString question = "Do you really want to erase the selected labels?"; QMessageBox::StandardButton answerButton = QMessageBox::question( this, "Erase selected labels", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answerButton == QMessageBox::Yes) { QList ranges = m_Controls.m_LabelSetTableWidget->selectedRanges(); if (ranges.isEmpty()) return; std::vector VectorOfLablePixelValues; foreach (QTableWidgetSelectionRange a, ranges) for (int i = a.topRow(); i <= a.bottomRow(); i++) VectorOfLablePixelValues.push_back(m_Controls.m_LabelSetTableWidget->item(i, 0)->data(Qt::UserRole).toInt()); this->WaitCursorOn(); GetWorkingImage()->EraseLabels(VectorOfLablePixelValues); this->WaitCursorOff(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkLabelSetWidget::OnRemoveLabels(bool /*value*/) { QString question = "Do you really want to remove the selected labels?"; QMessageBox::StandardButton answerButton = QMessageBox::question( this, "Remove selected labels", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answerButton == QMessageBox::Yes) { QList ranges = m_Controls.m_LabelSetTableWidget->selectedRanges(); if (ranges.isEmpty()) { return; } std::vector VectorOfLablePixelValues; foreach (QTableWidgetSelectionRange a, ranges) { for (int i = a.topRow(); i <= a.bottomRow(); ++i) { VectorOfLablePixelValues.push_back(m_Controls.m_LabelSetTableWidget->item(i, 0)->data(Qt::UserRole).toInt()); } } this->WaitCursorOn(); GetWorkingImage()->RemoveLabels(VectorOfLablePixelValues, GetWorkingImage()->GetActiveLayer()); this->WaitCursorOff(); } ResetAllTableWidgetItems(); } void QmitkLabelSetWidget::OnMergeLabels(bool /*value*/) { int pixelValue = GetPixelValueOfSelectedItem(); QString question = "Do you really want to merge selected labels into \""; question.append( QString::fromStdString(GetWorkingImage()->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer())->GetName())); question.append("\"?"); QMessageBox::StandardButton answerButton = QMessageBox::question( this, "Merge selected label", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answerButton == QMessageBox::Yes) { QList ranges = m_Controls.m_LabelSetTableWidget->selectedRanges(); if (ranges.isEmpty()) { return; } std::vector vectorOfSourcePixelValues; foreach (QTableWidgetSelectionRange a, ranges) { for (int i = a.topRow(); i <= a.bottomRow(); ++i) { vectorOfSourcePixelValues.push_back(m_Controls.m_LabelSetTableWidget->item(i, 0)->data(Qt::UserRole).toInt()); } } this->WaitCursorOn(); GetWorkingImage()->MergeLabels(pixelValue, vectorOfSourcePixelValues, GetWorkingImage()->GetActiveLayer()); this->WaitCursorOff(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkLabelSetWidget::OnLockedButtonClicked() { int row = -1; for (int i = 0; i < m_Controls.m_LabelSetTableWidget->rowCount(); ++i) { if (sender() == m_Controls.m_LabelSetTableWidget->cellWidget(i, LOCKED_COL)) { row = i; } } if (row >= 0 && row < m_Controls.m_LabelSetTableWidget->rowCount()) { int pixelValue = m_Controls.m_LabelSetTableWidget->item(row, 0)->data(Qt::UserRole).toInt(); GetWorkingImage() ->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer()) ->SetLocked(!GetWorkingImage()->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer())->GetLocked()); } } void QmitkLabelSetWidget::OnVisibleButtonClicked() { int row = -1; for (int i = 0; i < m_Controls.m_LabelSetTableWidget->rowCount(); ++i) { if (sender() == m_Controls.m_LabelSetTableWidget->cellWidget(i, VISIBLE_COL)) { row = i; break; } } if (row >= 0 && row < m_Controls.m_LabelSetTableWidget->rowCount()) { QTableWidgetItem *item = m_Controls.m_LabelSetTableWidget->item(row, 0); int pixelValue = item->data(Qt::UserRole).toInt(); GetWorkingImage() ->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer()) ->SetVisible(!GetWorkingImage()->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer())->GetVisible()); GetWorkingImage()->GetActiveLabelSet()->UpdateLookupTable(pixelValue); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkLabelSetWidget::OnColorButtonClicked() { int row = -1; for (int i = 0; i < m_Controls.m_LabelSetTableWidget->rowCount(); ++i) { if (sender() == m_Controls.m_LabelSetTableWidget->cellWidget(i, COLOR_COL)) { row = i; } } if (row >= 0 && row < m_Controls.m_LabelSetTableWidget->rowCount()) { int pixelValue = m_Controls.m_LabelSetTableWidget->item(row, 0)->data(Qt::UserRole).toInt(); const mitk::Color &color = GetWorkingImage()->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer())->GetColor(); QColor initial(color.GetRed() * 255, color.GetGreen() * 255, color.GetBlue() * 255); QColor qcolor = QColorDialog::getColor(initial, nullptr, QString("Change color")); if (!qcolor.isValid()) { return; } QPushButton *button = static_cast(m_Controls.m_LabelSetTableWidget->cellWidget(row, COLOR_COL)); if (!button) { return; } button->setAutoFillBackground(true); QString styleSheet = "background-color:rgb("; styleSheet.append(QString::number(qcolor.red())); styleSheet.append(","); styleSheet.append(QString::number(qcolor.green())); styleSheet.append(","); styleSheet.append(QString::number(qcolor.blue())); styleSheet.append("); border: 0;"); button->setStyleSheet(styleSheet); mitk::Color newColor; newColor.SetRed(qcolor.red() / 255.0); newColor.SetGreen(qcolor.green() / 255.0); newColor.SetBlue(qcolor.blue() / 255.0); GetWorkingImage()->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer())->SetColor(newColor); GetWorkingImage()->GetActiveLabelSet()->UpdateLookupTable(pixelValue); } } void QmitkLabelSetWidget::OnRandomColor(bool /*value*/) { int pixelValue = GetPixelValueOfSelectedItem(); GetWorkingImage() ->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer()) ->SetColor(m_ColorSequenceRainbow.GetNextColor()); GetWorkingImage()->GetActiveLabelSet()->UpdateLookupTable(pixelValue); UpdateAllTableWidgetItems(); } -void QmitkLabelSetWidget::SetOrganColors(const QStringList &organColors) -{ - m_OrganColors = organColors; -} - void QmitkLabelSetWidget::OnActiveLabelChanged(int pixelValue) { mitk::LabelSetImage *workingImage = GetWorkingImage(); assert(workingImage); workingImage->GetActiveLabelSet()->SetActiveLabel(pixelValue); // MITK_INFO << "Active Label set to << " << pixelValue; mitk::SurfaceBasedInterpolationController *interpolator = mitk::SurfaceBasedInterpolationController::GetInstance(); if (interpolator) { interpolator->SetActiveLabel(pixelValue); } workingImage->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkLabelSetWidget::OnItemClicked(QTableWidgetItem *item) { if (!item) return; int pixelValue = item->data(Qt::UserRole).toInt(); QList ranges = m_Controls.m_LabelSetTableWidget->selectedRanges(); if (!ranges.empty() && ranges.back().rowCount() == 1) { m_ProcessingManualSelection = true; OnActiveLabelChanged(pixelValue); m_ProcessingManualSelection = false; mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkLabelSetWidget::OnItemDoubleClicked(QTableWidgetItem *item) { if (!item) return; int pixelValue = item->data(Qt::UserRole).toInt(); // OnItemClicked(item); <<-- Double click first call OnItemClicked WaitCursorOn(); mitk::LabelSetImage *workingImage = GetWorkingImage(); workingImage->UpdateCenterOfMass(pixelValue, workingImage->GetActiveLayer()); const mitk::Point3D &pos = workingImage->GetLabel(pixelValue, workingImage->GetActiveLayer())->GetCenterOfMassCoordinates(); WaitCursorOff(); if (pos.GetVnlVector().max_value() > 0.0) { emit goToLabel(pos); } workingImage->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkLabelSetWidget::SelectLabelByPixelValue(mitk::Label::PixelType pixelValue) { if (m_ProcessingManualSelection || !GetWorkingImage()->ExistLabel(pixelValue)) return; for (int row = 0; row < m_Controls.m_LabelSetTableWidget->rowCount(); row++) { if (m_Controls.m_LabelSetTableWidget->item(row, 0)->data(Qt::UserRole).toInt() == pixelValue) { m_Controls.m_LabelSetTableWidget->clearSelection(); m_Controls.m_LabelSetTableWidget->selectRow(row); m_Controls.m_LabelSetTableWidget->scrollToItem(m_Controls.m_LabelSetTableWidget->item(row, 0)); return; } } } void QmitkLabelSetWidget::InsertTableWidgetItem(mitk::Label *label) { const mitk::Color &color = label->GetColor(); QString styleSheet = "background-color:rgb("; styleSheet.append(QString::number(color[0] * 255)); styleSheet.append(","); styleSheet.append(QString::number(color[1] * 255)); styleSheet.append(","); styleSheet.append(QString::number(color[2] * 255)); styleSheet.append("); border: 0;"); QTableWidget *tableWidget = m_Controls.m_LabelSetTableWidget; int colWidth = (tableWidget->columnWidth(NAME_COL) < 180) ? 180 : tableWidget->columnWidth(NAME_COL) - 2; QString text = fontMetrics().elidedText(label->GetName().c_str(), Qt::ElideMiddle, colWidth); QTableWidgetItem *nameItem = new QTableWidgetItem(text); nameItem->setTextAlignment(Qt::AlignCenter | Qt::AlignLeft); // ---!--- // IMPORTANT: ADD PIXELVALUE TO TABLEWIDGETITEM.DATA nameItem->setData(Qt::UserRole, QVariant(label->GetValue())); // ---!--- QPushButton *pbColor = new QPushButton(tableWidget); pbColor->setFixedSize(24, 24); pbColor->setCheckable(false); pbColor->setAutoFillBackground(true); pbColor->setToolTip("Change label color"); pbColor->setStyleSheet(styleSheet); connect(pbColor, SIGNAL(clicked()), this, SLOT(OnColorButtonClicked())); QString transparentStyleSheet = QLatin1String("background-color: transparent; border: 0;"); QPushButton *pbLocked = new QPushButton(tableWidget); pbLocked->setFixedSize(24, 24); QIcon *iconLocked = new QIcon(); auto lockIcon = QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/lock.svg")); auto unlockIcon = QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/unlock.svg")); iconLocked->addPixmap(lockIcon.pixmap(64), QIcon::Normal, QIcon::Off); iconLocked->addPixmap(unlockIcon.pixmap(64), QIcon::Normal, QIcon::On); pbLocked->setIcon(*iconLocked); pbLocked->setIconSize(QSize(24, 24)); pbLocked->setCheckable(true); pbLocked->setToolTip("Lock/unlock label"); pbLocked->setChecked(!label->GetLocked()); pbLocked->setStyleSheet(transparentStyleSheet); connect(pbLocked, SIGNAL(clicked()), this, SLOT(OnLockedButtonClicked())); QPushButton *pbVisible = new QPushButton(tableWidget); pbVisible->setFixedSize(24, 24); pbVisible->setAutoRepeat(false); QIcon *iconVisible = new QIcon(); auto visibleIcon = QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/visible.svg")); auto invisibleIcon = QmitkStyleManager::ThemeIcon(QLatin1String(":/Qmitk/invisible.svg")); iconVisible->addPixmap(visibleIcon.pixmap(64), QIcon::Normal, QIcon::Off); iconVisible->addPixmap(invisibleIcon.pixmap(64), QIcon::Normal, QIcon::On); pbVisible->setIcon(*iconVisible); pbVisible->setIconSize(QSize(24, 24)); pbVisible->setCheckable(true); pbVisible->setToolTip("Show/hide label"); pbVisible->setChecked(!label->GetVisible()); pbVisible->setStyleSheet(transparentStyleSheet); connect(pbVisible, SIGNAL(clicked()), this, SLOT(OnVisibleButtonClicked())); int row = tableWidget->rowCount(); tableWidget->insertRow(row); tableWidget->setRowHeight(row, 24); tableWidget->setItem(row, 0, nameItem); tableWidget->setCellWidget(row, 1, pbLocked); tableWidget->setCellWidget(row, 2, pbColor); tableWidget->setCellWidget(row, 3, pbVisible); tableWidget->selectRow(row); // m_LabelSetImage->SetActiveLabel(label->GetPixelValue()); // m_ToolManager->WorkingDataModified.Send(); // emit activeLabelChanged(label->GetPixelValue()); if (row == 0) { tableWidget->hideRow(row); // hide exterior label } } void QmitkLabelSetWidget::UpdateAllTableWidgetItems() { mitk::LabelSetImage *workingImage = GetWorkingImage(); if (!workingImage) return; // add all labels QTableWidget *tableWidget = m_Controls.m_LabelSetTableWidget; m_LabelStringList.clear(); for (int i = 0; i < tableWidget->rowCount(); ++i) { UpdateTableWidgetItem(tableWidget->item(i, 0)); m_LabelStringList.append(tableWidget->item(i, 0)->text()); } OnLabelListModified(m_LabelStringList); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkLabelSetWidget::UpdateTableWidgetItem(QTableWidgetItem *item) { mitk::LabelSetImage *workingImage = GetWorkingImage(); mitk::Label *label = workingImage->GetLabel(item->data(Qt::UserRole).toInt(), workingImage->GetActiveLayer()); const mitk::Color &color = label->GetColor(); QString styleSheet = "background-color:rgb("; styleSheet.append(QString::number(color[0] * 255)); styleSheet.append(","); styleSheet.append(QString::number(color[1] * 255)); styleSheet.append(","); styleSheet.append(QString::number(color[2] * 255)); styleSheet.append("); border: 0;"); QTableWidget *tableWidget = m_Controls.m_LabelSetTableWidget; int colWidth = (tableWidget->columnWidth(NAME_COL) < 180) ? 180 : tableWidget->columnWidth(NAME_COL) - 2; QString text = fontMetrics().elidedText(label->GetName().c_str(), Qt::ElideMiddle, colWidth); item->setText(text); QPushButton *pbLocked = dynamic_cast(tableWidget->cellWidget(item->row(), 1)); pbLocked->setChecked(!label->GetLocked()); QPushButton *pbColor = dynamic_cast(tableWidget->cellWidget(item->row(), 2)); pbColor->setStyleSheet(styleSheet); QPushButton *pbVisible = dynamic_cast(tableWidget->cellWidget(item->row(), 3)); pbVisible->setChecked(!label->GetVisible()); if (item->row() == 0) { tableWidget->hideRow(item->row()); // hide exterior label } } void QmitkLabelSetWidget::ResetAllTableWidgetItems() { QTableWidget *tableWidget = m_Controls.m_LabelSetTableWidget; // remove all rows while (tableWidget->rowCount()) { tableWidget->removeRow(0); } mitk::DataNode * workingNode = GetWorkingNode(); auto workingImage = dynamic_cast(workingNode->GetData()); if (nullptr == workingImage) { return; } // add all labels m_LabelStringList.clear(); mitk::LabelSet::LabelContainerConstIteratorType it = workingImage->GetActiveLabelSet()->IteratorConstBegin(); mitk::LabelSet::LabelContainerConstIteratorType end = workingImage->GetActiveLabelSet()->IteratorConstEnd(); int pixelValue = -1; while (it != end) { InsertTableWidgetItem(it->second); if (workingImage->GetActiveLabel(workingImage->GetActiveLayer()) == it->second) // get active pixelValue = it->first; m_LabelStringList.append(QString(it->second->GetName().c_str())); it++; } SelectLabelByPixelValue(pixelValue); OnLabelListModified(m_LabelStringList); std::stringstream captionText; captionText << "Number of labels: " << workingImage->GetNumberOfLabels(workingImage->GetActiveLayer()) - 1; m_Controls.m_lblCaption->setText(captionText.str().c_str()); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); emit LabelSetWidgetReset(); } int QmitkLabelSetWidget::GetPixelValueOfSelectedItem() { if (m_Controls.m_LabelSetTableWidget->currentItem()) { return m_Controls.m_LabelSetTableWidget->currentItem()->data(Qt::UserRole).toInt(); } return -1; } QStringList &QmitkLabelSetWidget::GetLabelStringList() { return m_LabelStringList; } void QmitkLabelSetWidget::InitializeTableWidget() { QTableWidget *tableWidget = m_Controls.m_LabelSetTableWidget; tableWidget->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Maximum); tableWidget->setTabKeyNavigation(false); tableWidget->setAlternatingRowColors(false); tableWidget->setFocusPolicy(Qt::NoFocus); tableWidget->setColumnCount(4); tableWidget->resizeColumnToContents(NAME_COL); tableWidget->setColumnWidth(LOCKED_COL, 25); tableWidget->setColumnWidth(COLOR_COL, 25); tableWidget->setColumnWidth(VISIBLE_COL, 25); tableWidget->horizontalHeader()->setSectionResizeMode(0, QHeaderView::Stretch); tableWidget->setContextMenuPolicy(Qt::CustomContextMenu); tableWidget->horizontalHeader()->hide(); tableWidget->setSortingEnabled(false); tableWidget->verticalHeader()->hide(); tableWidget->setEditTriggers(QAbstractItemView::NoEditTriggers); connect(tableWidget, SIGNAL(itemClicked(QTableWidgetItem *)), this, SLOT(OnItemClicked(QTableWidgetItem *))); connect( tableWidget, SIGNAL(itemDoubleClicked(QTableWidgetItem *)), this, SLOT(OnItemDoubleClicked(QTableWidgetItem *))); connect(tableWidget, SIGNAL(customContextMenuRequested(const QPoint &)), this, SLOT(OnTableViewContextMenuRequested(const QPoint &))); } void QmitkLabelSetWidget::OnOpacityChanged(int value) { int pixelValue = GetPixelValueOfSelectedItem(); float opacity = static_cast(value) / 100.0f; GetWorkingImage()->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer())->SetOpacity(opacity); GetWorkingImage()->GetActiveLabelSet()->UpdateLookupTable(pixelValue); } void QmitkLabelSetWidget::setEnabled(bool enabled) { QWidget::setEnabled(enabled); UpdateControls(); } void QmitkLabelSetWidget::SetDataStorage(mitk::DataStorage *storage) { m_DataStorage = storage; } void QmitkLabelSetWidget::OnSearchLabel() { std::string text = m_Controls.m_LabelSearchBox->text().toStdString(); int pixelValue = -1; int row = -1; for (int i = 0; i < m_Controls.m_LabelSetTableWidget->rowCount(); ++i) { if (m_Controls.m_LabelSetTableWidget->item(i, 0)->text().toStdString().compare(text) == 0) { pixelValue = m_Controls.m_LabelSetTableWidget->item(i, 0)->data(Qt::UserRole).toInt(); row = i; break; } } if (pixelValue == -1) { return; } GetWorkingImage()->GetActiveLabelSet()->SetActiveLabel(pixelValue); QTableWidgetItem *nameItem = m_Controls.m_LabelSetTableWidget->item(row, NAME_COL); if (!nameItem) { return; } m_Controls.m_LabelSetTableWidget->clearSelection(); m_Controls.m_LabelSetTableWidget->selectRow(row); m_Controls.m_LabelSetTableWidget->scrollToItem(nameItem); GetWorkingImage()->GetActiveLabelSet()->SetActiveLabel(pixelValue); this->WaitCursorOn(); mitk::Point3D pos = GetWorkingImage()->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer())->GetCenterOfMassCoordinates(); m_ToolManager->WorkingDataChanged(); if (pos.GetVnlVector().max_value() > 0.0) { emit goToLabel(pos); } else { GetWorkingImage()->UpdateCenterOfMass(pixelValue, GetWorkingImage()->GetActiveLayer()); mitk::Point3D pos = GetWorkingImage()->GetLabel(pixelValue, GetWorkingImage()->GetActiveLayer())->GetCenterOfMassCoordinates(); emit goToLabel(pos); } this->WaitCursorOff(); } void QmitkLabelSetWidget::OnLabelListModified(const QStringList &list) { QStringListModel *completeModel = static_cast(m_Completer->model()); completeModel->setStringList(list); } mitk::LabelSetImage *QmitkLabelSetWidget::GetWorkingImage() { mitk::DataNode *workingNode = GetWorkingNode(); mitk::LabelSetImage *workingImage = dynamic_cast(workingNode->GetData()); assert(workingImage); return workingImage; } mitk::DataNode *QmitkLabelSetWidget::GetWorkingNode() { mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); assert(workingNode); return workingNode; } void QmitkLabelSetWidget::UpdateControls() { mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); bool hasWorkingData = (workingNode != nullptr); m_Controls.m_LabelSetTableWidget->setEnabled(hasWorkingData); m_Controls.m_LabelSearchBox->setEnabled(hasWorkingData); if (!hasWorkingData) return; QStringListModel *completeModel = static_cast(m_Completer->model()); completeModel->setStringList(GetLabelStringList()); } void QmitkLabelSetWidget::OnCreateCroppedMask(bool) { m_ToolManager->ActivateTool(-1); mitk::LabelSetImage *workingImage = GetWorkingImage(); mitk::Image::Pointer maskImage; int pixelValue = GetPixelValueOfSelectedItem(); try { this->WaitCursorOn(); mitk::AutoCropImageFilter::Pointer cropFilter = mitk::AutoCropImageFilter::New(); cropFilter->SetInput(workingImage->CreateLabelMask(pixelValue)); cropFilter->SetBackgroundValue(0); cropFilter->SetMarginFactor(1.15); cropFilter->Update(); maskImage = cropFilter->GetOutput(); this->WaitCursorOff(); } catch (mitk::Exception &e) { this->WaitCursorOff(); MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::information(this, "Create Mask", "Could not create a mask out of the selected label.\n"); return; } if (maskImage.IsNull()) { QMessageBox::information(this, "Create Mask", "Could not create a mask out of the selected label.\n"); return; } mitk::DataNode::Pointer maskNode = mitk::DataNode::New(); std::string name = workingImage->GetLabel(pixelValue, workingImage->GetActiveLayer())->GetName(); name += "-mask"; maskNode->SetName(name); maskNode->SetData(maskImage); maskNode->SetBoolProperty("binary", true); maskNode->SetBoolProperty("outline binary", true); maskNode->SetBoolProperty("outline binary shadow", true); maskNode->SetFloatProperty("outline width", 2.0); maskNode->SetColor(workingImage->GetLabel(pixelValue, workingImage->GetActiveLayer())->GetColor()); maskNode->SetOpacity(1.0); m_DataStorage->Add(maskNode, GetWorkingNode()); } void QmitkLabelSetWidget::OnCreateMask(bool /*triggered*/) { m_ToolManager->ActivateTool(-1); mitk::LabelSetImage *workingImage = GetWorkingImage(); mitk::Image::Pointer maskImage; int pixelValue = GetPixelValueOfSelectedItem(); try { this->WaitCursorOn(); maskImage = workingImage->CreateLabelMask(pixelValue); this->WaitCursorOff(); } catch (mitk::Exception &e) { this->WaitCursorOff(); MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::information(this, "Create Mask", "Could not create a mask out of the selected label.\n"); return; } if (maskImage.IsNull()) { QMessageBox::information(this, "Create Mask", "Could not create a mask out of the selected label.\n"); return; } mitk::DataNode::Pointer maskNode = mitk::DataNode::New(); std::string name = workingImage->GetLabel(pixelValue, workingImage->GetActiveLayer())->GetName(); name += "-mask"; maskNode->SetName(name); maskNode->SetData(maskImage); maskNode->SetBoolProperty("binary", true); maskNode->SetBoolProperty("outline binary", true); maskNode->SetBoolProperty("outline binary shadow", true); maskNode->SetFloatProperty("outline width", 2.0); maskNode->SetColor(workingImage->GetLabel(pixelValue, workingImage->GetActiveLayer())->GetColor()); maskNode->SetOpacity(1.0); m_DataStorage->Add(maskNode, GetWorkingNode()); } void QmitkLabelSetWidget::OnToggleOutline(bool value) { mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); assert(workingNode); workingNode->SetBoolProperty("labelset.contour.active", value); workingNode->GetData()->Modified(); // fixme: workaround to force data-type rendering (and not only property-type) mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkLabelSetWidget::OnCreateSmoothedSurface(bool /*triggered*/) { m_ToolManager->ActivateTool(-1); mitk::DataNode::Pointer workingNode = GetWorkingNode(); mitk::LabelSetImage *workingImage = GetWorkingImage(); int pixelValue = GetPixelValueOfSelectedItem(); mitk::LabelSetImageToSurfaceThreadedFilter::Pointer surfaceFilter = mitk::LabelSetImageToSurfaceThreadedFilter::New(); itk::SimpleMemberCommand::Pointer successCommand = itk::SimpleMemberCommand::New(); successCommand->SetCallbackFunction(this, &QmitkLabelSetWidget::OnThreadedCalculationDone); surfaceFilter->AddObserver(mitk::ResultAvailable(), successCommand); itk::SimpleMemberCommand::Pointer errorCommand = itk::SimpleMemberCommand::New(); errorCommand->SetCallbackFunction(this, &QmitkLabelSetWidget::OnThreadedCalculationDone); surfaceFilter->AddObserver(mitk::ProcessingError(), errorCommand); mitk::DataNode::Pointer groupNode = workingNode; surfaceFilter->SetPointerParameter("Group node", groupNode); surfaceFilter->SetPointerParameter("Input", workingImage); surfaceFilter->SetParameter("RequestedLabel", pixelValue); surfaceFilter->SetParameter("Smooth", true); surfaceFilter->SetDataStorage(*m_DataStorage); mitk::StatusBar::GetInstance()->DisplayText("Surface creation is running in background..."); try { surfaceFilter->StartAlgorithm(); } catch (mitk::Exception &e) { MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::information(this, "Create Surface", "Could not create a surface mesh out of the selected label. See error log for details.\n"); } } void QmitkLabelSetWidget::OnCreateDetailedSurface(bool /*triggered*/) { m_ToolManager->ActivateTool(-1); mitk::DataNode::Pointer workingNode = GetWorkingNode(); mitk::LabelSetImage *workingImage = GetWorkingImage(); int pixelValue = GetPixelValueOfSelectedItem(); mitk::LabelSetImageToSurfaceThreadedFilter::Pointer surfaceFilter = mitk::LabelSetImageToSurfaceThreadedFilter::New(); itk::SimpleMemberCommand::Pointer successCommand = itk::SimpleMemberCommand::New(); successCommand->SetCallbackFunction(this, &QmitkLabelSetWidget::OnThreadedCalculationDone); surfaceFilter->AddObserver(mitk::ResultAvailable(), successCommand); itk::SimpleMemberCommand::Pointer errorCommand = itk::SimpleMemberCommand::New(); errorCommand->SetCallbackFunction(this, &QmitkLabelSetWidget::OnThreadedCalculationDone); surfaceFilter->AddObserver(mitk::ProcessingError(), errorCommand); mitk::DataNode::Pointer groupNode = workingNode; surfaceFilter->SetPointerParameter("Group node", groupNode); surfaceFilter->SetPointerParameter("Input", workingImage); surfaceFilter->SetParameter("RequestedLabel", pixelValue); surfaceFilter->SetParameter("Smooth", false); surfaceFilter->SetDataStorage(*m_DataStorage); mitk::StatusBar::GetInstance()->DisplayText("Surface creation is running in background..."); try { surfaceFilter->StartAlgorithm(); } catch (mitk::Exception &e) { MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::information(this, "Create Surface", "Could not create a surface mesh out of the selected label. See error log for details.\n"); } } void QmitkLabelSetWidget::WaitCursorOn() { QApplication::setOverrideCursor(QCursor(Qt::WaitCursor)); } void QmitkLabelSetWidget::WaitCursorOff() { this->RestoreOverrideCursor(); } void QmitkLabelSetWidget::RestoreOverrideCursor() { QApplication::restoreOverrideCursor(); } void QmitkLabelSetWidget::OnThreadedCalculationDone() { mitk::StatusBar::GetInstance()->Clear(); } diff --git a/Modules/SegmentationUI/Qmitk/QmitkLabelSetWidget.h b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkLabelSetWidget.h similarity index 94% rename from Modules/SegmentationUI/Qmitk/QmitkLabelSetWidget.h rename to Plugins/org.mitk.gui.qt.segmentation/src/QmitkLabelSetWidget.h index f5f968b440..9fb7a1c0e8 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkLabelSetWidget.h +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkLabelSetWidget.h @@ -1,167 +1,165 @@ /*============================================================================ 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 QmitkLabelSetWidget_h #define QmitkLabelSetWidget_h -#include "MitkSegmentationUIExports.h" +#include -#include "mitkColorSequenceRainbow.h" -#include "mitkLabel.h" -#include "mitkNumericTypes.h" +#include +#include +#include #include class QmitkDataStorageComboBox; class QCompleter; namespace mitk { class LabelSetImage; class LabelSet; class Label; class DataStorage; class ToolManager; class DataNode; } -class MITKSEGMENTATIONUI_EXPORT QmitkLabelSetWidget : public QWidget +class MITK_QT_SEGMENTATION QmitkLabelSetWidget : public QWidget { Q_OBJECT public: explicit QmitkLabelSetWidget(QWidget *parent = nullptr); ~QmitkLabelSetWidget() override; void SetDataStorage(mitk::DataStorage *storage); - void SetOrganColors(const QStringList &organColors); - void UpdateControls(); virtual void setEnabled(bool enabled); QStringList &GetLabelStringList(); signals: /// \brief Send a signal when it was requested to go to a label. void goToLabel(const mitk::Point3D &); void LabelSetWidgetReset(); public slots: /** * @brief Updates the current labels in the label set widget table. For each label (widget item) the 'UpdateTableWidgetItem' is called. * * Updating means setting the color box of the table, setting the column with and fill it with the label name. * Furthermore the two push buttons for locking and showing/hiding the layer are checked/unchecked. * This functions only changes the appearance of the table widget and no render window update is necessary. */ void UpdateAllTableWidgetItems(); /** * @brief Resets the current labels in the label set widget table. For each label a widget item is inserted into the table. * * Resetting means removing all rows of the widget table and inserting new rows (labels) from the active label set (= layer) of the current working node. * The currently active label is selected and 'Number of labels' is set. * As this function is typically used after one label has been removed or the reference node has been changed (e.g.) the render windows have to be updated. */ void ResetAllTableWidgetItems(); void SelectLabelByPixelValue(mitk::Label::PixelType pixelValue); private slots: // LabelSet dependent void OnOpacityChanged(int); void OnUnlockAllLabels(bool); void OnLockAllLabels(bool); void OnSetAllLabelsVisible(bool); void OnSetAllLabelsInvisible(bool); void OnSetOnlyActiveLabelVisible(bool); void OnRandomColor(bool); void OnRemoveLabel(bool); void OnRemoveLabels(bool); void OnRenameLabel(bool); void OnLockedButtonClicked(); void OnVisibleButtonClicked(); void OnColorButtonClicked(); void OnItemClicked(QTableWidgetItem *item); void OnItemDoubleClicked(QTableWidgetItem *item); void OnTableViewContextMenuRequested(const QPoint &); void InsertTableWidgetItem(mitk::Label *label); void UpdateTableWidgetItem(QTableWidgetItem *item); // reaction to "returnPressed" signal from ... void OnSearchLabel(); // reaction to the button "Change Label" void OnActiveLabelChanged(int pixelValue); // LabelSetImage Dependet void OnCreateDetailedSurface(bool); void OnCreateSmoothedSurface(bool); // reaction to the signal "createMask" from QmitkLabelSetTableWidget void OnCreateMask(bool); void OnCreateMasks(bool); // reaction to the signal "createCroppedMask" from QmitkLabelSetTableWidget void OnCreateCroppedMask(bool); void OnCombineAndCreateMask(bool); void OnCombineAndCreateSurface(bool); void OnEraseLabel(bool); void OnEraseLabels(bool); void OnMergeLabels(bool); // reaction to signal "labelListModified" from QmitkLabelSetTableWidget void OnLabelListModified(const QStringList &list); // reaction to the signal "toggleOutline" from QmitkLabelSetTableWidget void OnToggleOutline(bool); private: enum TableColumns { NAME_COL = 0, LOCKED_COL, COLOR_COL, VISIBLE_COL }; void WaitCursorOn(); void WaitCursorOff(); void RestoreOverrideCursor(); void OnThreadedCalculationDone(); void InitializeTableWidget(); int GetPixelValueOfSelectedItem(); mitk::LabelSetImage *GetWorkingImage(); mitk::DataNode *GetWorkingNode(); Ui::QmitkLabelSetWidgetControls m_Controls; mitk::ColorSequenceRainbow m_ColorSequenceRainbow; mitk::DataStorage *m_DataStorage; QCompleter *m_Completer; mitk::ToolManager *m_ToolManager; QStringList m_OrganColors; QStringList m_LabelStringList; bool m_ProcessingManualSelection; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkLabelSetWidgetControls.ui b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkLabelSetWidgetControls.ui similarity index 100% rename from Modules/SegmentationUI/Qmitk/QmitkLabelSetWidgetControls.ui rename to Plugins/org.mitk.gui.qt.segmentation/src/QmitkLabelSetWidgetControls.ui diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.cpp new file mode 100644 index 0000000000..ddc824a0af --- /dev/null +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.cpp @@ -0,0 +1,325 @@ +/*============================================================================ + +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 "QmitkNewSegmentationDialog.h" +#include + +#include +#include +#include + +#include +#include +#include + +#include +#include + +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace +{ + // Get standard label name and color suggestions from embedded XML preset file for anatomical structures. + QmitkNewSegmentationDialog::SuggestionsType GetStandardSuggestions() + { + QmitkNewSegmentationDialog::SuggestionsType standardSuggestions; + + vtkNew presets; + presets->LoadPreset(); + + for (const auto& preset : presets->GetColorPresets()) + { + auto name = QString::fromStdString(preset.first); + auto color = QColor::fromRgbF(preset.second.GetRed(), preset.second.GetGreen(), preset.second.GetBlue()); + standardSuggestions.emplace(name, color); + } + + return standardSuggestions; + } + + // Parse label name and color suggestions from a JSON file. An array of objects is expected, each consisting + // of a "name" string and an optional "color" string. If present, the "color" string must follow the conventions + // of QColor::setNamedColor(), i.e., #rrggbb or any SVG color keyword name like CornflowerBlue. Everything else + // in the JSON file is simply ignored. In case of any error, an empty map is returned. + QmitkNewSegmentationDialog::SuggestionsType ParseSuggestions(const QString& filename) + { + QmitkNewSegmentationDialog::SuggestionsType parsedSuggestions; + QFile file(filename); + + if (!file.open(QIODevice::ReadOnly)) + { + MITK_ERROR << "Could not open \"" << filename.toStdString() << "\"!"; + return parsedSuggestions; + } + + auto json = file.readAll(); + auto doc = QJsonDocument::fromJson(json); + + if (doc.isNull() || !doc.isArray()) + { + MITK_ERROR << "Could not parse \"" << filename.toStdString() << "\" as JSON array!"; + return parsedSuggestions; + } + + auto array = doc.array(); + + for (auto valueRef : array) + { + if (valueRef.isObject()) + { + auto object = valueRef.toObject(); + + if (object.contains("name") && object["name"].isString()) + { + auto name = object["name"].toString(); + auto color = object.contains("color") && object["color"].isString() + ? QColor(object["color"].toString()) + : QColor(QColor::Invalid); + + parsedSuggestions.emplace(name, color); + } + } + } + + if (parsedSuggestions.empty()) + MITK_WARN << "Could not parse any suggestions from \"" << filename.toStdString() << "\"!"; + + return parsedSuggestions; + } + + struct Preferences + { + QString labelSuggestions; + bool replaceStandardSuggestions; + bool suggestOnce; + }; + + // Get all relevant preferences and consider command-line arguments overrides. + Preferences GetPreferences() + { + auto nodePrefs = berry::Platform::GetPreferencesService()->GetSystemPreferences()->Node("/org.mitk.views.segmentation"); + + Preferences prefs; + + prefs.labelSuggestions = QString::fromStdString(mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABEL_SUGGESTIONS.toStdString(), "")); + + if (prefs.labelSuggestions.isEmpty()) + prefs.labelSuggestions = nodePrefs->Get("label suggestions", ""); + + prefs.replaceStandardSuggestions = nodePrefs->GetBool("replace standard suggestions", true); + prefs.suggestOnce = nodePrefs->GetBool("suggest once", true); + + return prefs; + } + + // Get names of all labels in all layers of a LabelSetImage. + QStringList GetExistingLabelNames(mitk::LabelSetImage* labelSetImage) + { + QStringList existingLabelNames; + existingLabelNames.reserve(labelSetImage->GetTotalNumberOfLabels()); + + const auto numLayers = labelSetImage->GetNumberOfLayers(); + for (std::remove_const_t layerIndex = 0; layerIndex < numLayers; ++layerIndex) + { + const auto* labelSet = labelSetImage->GetLabelSet(layerIndex); + + for (auto labelIter = labelSet->IteratorConstBegin(); labelIter != labelSet->IteratorConstEnd(); ++labelIter) + { + if (0 == labelIter->first) + continue; // Ignore background label + + auto name = QString::fromStdString(labelIter->second->GetName()); + + if (!name.isEmpty()) // Potential duplicates do not matter for our purpose + existingLabelNames.push_back(name); + } + } + + return existingLabelNames; + } + + // Remove blacklisted suggestions. + QmitkNewSegmentationDialog::SuggestionsType FilterSuggestions(const QmitkNewSegmentationDialog::SuggestionsType& suggestions, const QStringList& blacklist) + { + QmitkNewSegmentationDialog::SuggestionsType filteredSuggestions; + + std::remove_copy_if(suggestions.begin(), suggestions.end(), std::inserter(filteredSuggestions, filteredSuggestions.end()), [&blacklist](const auto& suggestion) { + return blacklist.contains(suggestion.first); + }); + + return filteredSuggestions; + } +} + +QmitkNewSegmentationDialog::QmitkNewSegmentationDialog(QWidget *parent, mitk::LabelSetImage* labelSetImage, Mode mode) + : QDialog(parent), + m_Ui(new Ui::QmitkNewSegmentationDialog), + m_SuggestOnce(true), + m_Color(Qt::red) +{ + m_Ui->setupUi(this); + + if (RenameLabel == mode) + { + this->setWindowTitle("Rename Label"); + m_Ui->label->setText("New name and color of the label"); + m_Ui->buttonBox->button(QDialogButtonBox::Ok)->setText("Rename label"); + } + else + { + m_Ui->buttonBox->button(QDialogButtonBox::Ok)->setText("Create label"); + } + + auto* completer = new QCompleter(QStringList()); + completer->setCaseSensitivity(Qt::CaseInsensitive); + + m_Ui->nameLineEdit->setCompleter(completer); + m_Ui->nameLineEdit->setFocus(); + + connect(completer, qOverload(&QCompleter::activated), this, qOverload(&QmitkNewSegmentationDialog::OnSuggestionSelected)); + connect(m_Ui->colorButton, &QToolButton::clicked, this, &QmitkNewSegmentationDialog::OnColorButtonClicked); + connect(m_Ui->buttonBox, &QDialogButtonBox::accepted, this, &QmitkNewSegmentationDialog::OnAccept); + + this->UpdateColorButtonBackground(); + + auto prefs = GetPreferences(); + + if (!prefs.labelSuggestions.isEmpty()) + { + auto suggestions = ParseSuggestions(prefs.labelSuggestions); + this->SetSuggestions(suggestions, prefs.replaceStandardSuggestions && !suggestions.empty()); + } + else + { + this->SetSuggestions(GetStandardSuggestions(), true); + } + + if (nullptr != labelSetImage && prefs.suggestOnce) + { + auto existingLabelNames = GetExistingLabelNames(labelSetImage); + m_Suggestions = FilterSuggestions(m_Suggestions, existingLabelNames); + + this->UpdateCompleterModel(); + } +} + +QmitkNewSegmentationDialog::~QmitkNewSegmentationDialog() +{ +} + +void QmitkNewSegmentationDialog::UpdateColorButtonBackground() +{ + m_Ui->colorButton->setStyleSheet("background-color:" + m_Color.name()); +} + +QString QmitkNewSegmentationDialog::GetName() const +{ + return m_Name; +} + +mitk::Color QmitkNewSegmentationDialog::GetColor() const +{ + mitk::Color color; + + if (m_Color.isValid()) + { + color.SetRed(m_Color.redF()); + color.SetGreen(m_Color.greenF()); + color.SetBlue(m_Color.blueF()); + } + else + { + color.Set(1.0f, 0.0f, 0.0f); + } + + return color; +} + +void QmitkNewSegmentationDialog::SetName(const QString& name) +{ + m_Ui->nameLineEdit->setText(name); +} + +void QmitkNewSegmentationDialog::SetColor(const mitk::Color& color) +{ + m_Color.setRgbF(color.GetRed(), color.GetGreen(), color.GetBlue()); + this->UpdateColorButtonBackground(); +} + +void QmitkNewSegmentationDialog::SetSuggestions(const SuggestionsType& suggestions, bool replaceStandardSuggestions) +{ + if (replaceStandardSuggestions) + { + m_Suggestions = suggestions; + } + else + { + m_Suggestions = GetStandardSuggestions(); + + for (const auto& [name, color] : suggestions) + { + if (m_Suggestions.end() == m_Suggestions.find(name)) + m_Suggestions[name] = color; + } + } + + this->UpdateCompleterModel(); +} + +void QmitkNewSegmentationDialog::UpdateCompleterModel() +{ + QStringList names; + + for (const auto& suggestion : m_Suggestions) + names << suggestion.first; + + auto* completerModel = static_cast(m_Ui->nameLineEdit->completer()->model()); + completerModel->setStringList(names); +} + +void QmitkNewSegmentationDialog::OnAccept() +{ + m_Name = m_Ui->nameLineEdit->text(); + this->accept(); +} + +void QmitkNewSegmentationDialog::OnColorButtonClicked() +{ + auto color = QColorDialog::getColor(m_Color); + + if (color.isValid()) + { + m_Color = color; + this->UpdateColorButtonBackground(); + } +} + +void QmitkNewSegmentationDialog::OnSuggestionSelected(const QString &name) +{ + auto color = m_Suggestions[name]; + + if (color.isValid()) + { + m_Color = color; + this->UpdateColorButtonBackground(); + } +} diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.h b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.h new file mode 100644 index 0000000000..9f188540d1 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.h @@ -0,0 +1,80 @@ +/*============================================================================ + +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 QmitkNewSegmentationDialog_h +#define QmitkNewSegmentationDialog_h + +#include + +#include + +#include + +#include +#include +#include + +namespace mitk +{ + class LabelSetImage; +} + +namespace Ui +{ + class QmitkNewSegmentationDialog; +} + +/** + \brief Dialog for naming labels. +*/ +class MITK_QT_SEGMENTATION QmitkNewSegmentationDialog : public QDialog +{ + Q_OBJECT + +public: + using SuggestionsType = std::map; + + enum Mode + { + NewLabel, + RenameLabel + }; + + explicit QmitkNewSegmentationDialog(QWidget *parent = nullptr, mitk::LabelSetImage* labelSetImage = nullptr, Mode mode = NewLabel); + ~QmitkNewSegmentationDialog() override; + + QString GetName() const; + mitk::Color GetColor() const; + + void SetName(const QString& name); + void SetColor(const mitk::Color& color); + +private: + void OnAccept(); + void OnSuggestionSelected(const QString& name); + void OnColorButtonClicked(); + + void SetSuggestions(const SuggestionsType& suggestions, bool replaceStandardSuggestions = false); + void UpdateColorButtonBackground(); + void UpdateCompleterModel(); + + Ui::QmitkNewSegmentationDialog* m_Ui; + + bool m_SuggestOnce; + + QString m_Name; + QColor m_Color; + + SuggestionsType m_Suggestions; +}; + +#endif diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.ui b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.ui new file mode 100644 index 0000000000..ae71e75c55 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkNewSegmentationDialog.ui @@ -0,0 +1,98 @@ + + + QmitkNewSegmentationDialog + + + + 0 + 0 + 250 + 105 + + + + Create Label + + + + + + + + Name and color of the label + + + + + + + + + + + + + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + Qt::Horizontal + + + QDialogButtonBox::Cancel|QDialogButtonBox::Ok + + + + + + + + + buttonBox + accepted() + QmitkNewSegmentationDialog + accept() + + + 248 + 254 + + + 157 + 274 + + + + + buttonBox + rejected() + QmitkNewSegmentationDialog + reject() + + + 316 + 260 + + + 286 + 274 + + + + + diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.cpp index f77ebd2f21..0ea32131f3 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.cpp @@ -1,135 +1,174 @@ /*============================================================================ 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 "QmitkSegmentationPreferencePage.h" #include #include #include #include #include QmitkSegmentationPreferencePage::QmitkSegmentationPreferencePage() : m_Ui(new Ui::QmitkSegmentationPreferencePageControls), m_Control(nullptr), m_Initializing(false) { } QmitkSegmentationPreferencePage::~QmitkSegmentationPreferencePage() { } void QmitkSegmentationPreferencePage::Init(berry::IWorkbench::Pointer) { } void QmitkSegmentationPreferencePage::CreateQtControl(QWidget* parent) { m_Initializing = true; berry::IPreferencesService* prefService = berry::Platform::GetPreferencesService(); m_SegmentationPreferencesNode = prefService->GetSystemPreferences()->Node("/org.mitk.views.segmentation"); m_Control = new QWidget(parent); m_Ui->setupUi(m_Control); connect(m_Ui->smoothingCheckBox, SIGNAL(stateChanged(int)), this, SLOT(OnSmoothingCheckboxChecked(int))); connect(m_Ui->labelSetPresetToolButton, SIGNAL(clicked()), this, SLOT(OnLabelSetPresetButtonClicked())); + connect(m_Ui->suggestionsToolButton, SIGNAL(clicked()), this, SLOT(OnSuggestionsButtonClicked())); this->Update(); m_Initializing = false; } QWidget* QmitkSegmentationPreferencePage::GetQtControl() const { return m_Control; } bool QmitkSegmentationPreferencePage::PerformOk() { m_SegmentationPreferencesNode->PutBool("slim view", m_Ui->slimViewCheckBox->isChecked()); m_SegmentationPreferencesNode->PutBool("draw outline", m_Ui->outlineRadioButton->isChecked()); m_SegmentationPreferencesNode->PutBool("selection mode", m_Ui->selectionModeCheckBox->isChecked()); m_SegmentationPreferencesNode->PutBool("smoothing hint", m_Ui->smoothingCheckBox->isChecked()); m_SegmentationPreferencesNode->PutDouble("smoothing value", m_Ui->smoothingSpinBox->value()); m_SegmentationPreferencesNode->PutDouble("decimation rate", m_Ui->decimationSpinBox->value()); m_SegmentationPreferencesNode->PutDouble("closing ratio", m_Ui->closingSpinBox->value()); m_SegmentationPreferencesNode->Put("label set preset", m_Ui->labelSetPresetLineEdit->text()); + m_SegmentationPreferencesNode->PutBool("default label naming", m_Ui->defaultNameRadioButton->isChecked()); + m_SegmentationPreferencesNode->Put("label suggestions", m_Ui->suggestionsLineEdit->text()); + m_SegmentationPreferencesNode->PutBool("replace standard suggestions", m_Ui->replaceStandardSuggestionsCheckBox->isChecked()); + m_SegmentationPreferencesNode->PutBool("suggest once", m_Ui->suggestOnceCheckBox->isChecked()); return true; } void QmitkSegmentationPreferencePage::PerformCancel() { } void QmitkSegmentationPreferencePage::Update() { m_Ui->slimViewCheckBox->setChecked(m_SegmentationPreferencesNode->GetBool("slim view", false)); if (m_SegmentationPreferencesNode->GetBool("draw outline", true)) { m_Ui->outlineRadioButton->setChecked(true); } else { m_Ui->overlayRadioButton->setChecked(true); } m_Ui->selectionModeCheckBox->setChecked(m_SegmentationPreferencesNode->GetBool("selection mode", false)); if (m_SegmentationPreferencesNode->GetBool("smoothing hint", true)) { m_Ui->smoothingCheckBox->setChecked(true); m_Ui->smoothingSpinBox->setDisabled(true); } else { m_Ui->smoothingCheckBox->setChecked(false); m_Ui->smoothingSpinBox->setEnabled(true); } m_Ui->smoothingSpinBox->setValue(m_SegmentationPreferencesNode->GetDouble("smoothing value", 1.0)); m_Ui->decimationSpinBox->setValue(m_SegmentationPreferencesNode->GetDouble("decimation rate", 0.5)); m_Ui->closingSpinBox->setValue(m_SegmentationPreferencesNode->GetDouble("closing ratio", 0.0)); auto labelSetPreset = mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABELSET_PRESET.toStdString(), ""); - bool isOverridenByCmdLineArg = !labelSetPreset.empty(); + bool isOverriddenByCmdLineArg = !labelSetPreset.empty(); - if (!isOverridenByCmdLineArg) + if (!isOverriddenByCmdLineArg) labelSetPreset = m_SegmentationPreferencesNode->Get("label set preset", "").toStdString(); - m_Ui->labelSetPresetLineEdit->setDisabled(isOverridenByCmdLineArg); - m_Ui->labelSetPresetToolButton->setDisabled(isOverridenByCmdLineArg); - m_Ui->labelSetPresetCmdLineArgLabel->setVisible(isOverridenByCmdLineArg); + m_Ui->labelSetPresetLineEdit->setDisabled(isOverriddenByCmdLineArg); + m_Ui->labelSetPresetToolButton->setDisabled(isOverriddenByCmdLineArg); + m_Ui->labelSetPresetCmdLineArgLabel->setVisible(isOverriddenByCmdLineArg); m_Ui->labelSetPresetLineEdit->setText(QString::fromStdString(labelSetPreset)); + + if (m_SegmentationPreferencesNode->GetBool("default label naming", true)) + { + m_Ui->defaultNameRadioButton->setChecked(true); + } + else + { + m_Ui->askForNameRadioButton->setChecked(true); + } + + auto labelSuggestions = mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABEL_SUGGESTIONS.toStdString(), ""); + isOverriddenByCmdLineArg = !labelSuggestions.empty(); + + if (!isOverriddenByCmdLineArg) + labelSuggestions = m_SegmentationPreferencesNode->Get("label suggestions", "").toStdString(); + + m_Ui->defaultNameRadioButton->setDisabled(isOverriddenByCmdLineArg); + m_Ui->askForNameRadioButton->setDisabled(isOverriddenByCmdLineArg); + m_Ui->suggestionsLineEdit->setDisabled(isOverriddenByCmdLineArg); + m_Ui->suggestionsToolButton->setDisabled(isOverriddenByCmdLineArg); + m_Ui->suggestionsCmdLineArgLabel->setVisible(isOverriddenByCmdLineArg); + + m_Ui->suggestionsLineEdit->setText(QString::fromStdString(labelSuggestions)); + + m_Ui->replaceStandardSuggestionsCheckBox->setChecked(m_SegmentationPreferencesNode->GetBool("replace standard suggestions", true)); + m_Ui->suggestOnceCheckBox->setChecked(m_SegmentationPreferencesNode->GetBool("suggest once", true)); } void QmitkSegmentationPreferencePage::OnSmoothingCheckboxChecked(int state) { if (state != Qt::Unchecked) m_Ui->smoothingSpinBox->setDisabled(true); else m_Ui->smoothingSpinBox->setEnabled(true); } void QmitkSegmentationPreferencePage::OnLabelSetPresetButtonClicked() { const auto filename = QFileDialog::getOpenFileName(m_Control, QStringLiteral("Load Label Set Preset"), QString(), QStringLiteral("Label set preset (*.lsetp)")); if (!filename.isEmpty()) m_Ui->labelSetPresetLineEdit->setText(filename); } + +void QmitkSegmentationPreferencePage::OnSuggestionsButtonClicked() +{ + const auto filename = QFileDialog::getOpenFileName(m_Control, QStringLiteral("Load Label Suggestions"), QString(), QStringLiteral("Label suggestions (*.json)")); + + if (!filename.isEmpty()) + m_Ui->suggestionsLineEdit->setText(filename); +} diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.h b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.h index fc6406faa2..8c04073a86 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.h +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.h @@ -1,65 +1,66 @@ /*============================================================================ 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 QMITKSEGMENTATIONPREFERENCEPAGE_H #define QMITKSEGMENTATIONPREFERENCEPAGE_H #include "org_mitk_gui_qt_segmentation_Export.h" #include #include class QWidget; namespace Ui { class QmitkSegmentationPreferencePageControls; } class MITK_QT_SEGMENTATION QmitkSegmentationPreferencePage : public QObject, public berry::IQtPreferencePage { Q_OBJECT Q_INTERFACES(berry::IPreferencePage) public: QmitkSegmentationPreferencePage(); ~QmitkSegmentationPreferencePage() override; void Init(berry::IWorkbench::Pointer workbench) override; void CreateQtControl(QWidget* widget) override; QWidget* GetQtControl() const override; bool PerformOk() override; void PerformCancel() override; void Update() override; protected Q_SLOTS: void OnSmoothingCheckboxChecked(int); void OnLabelSetPresetButtonClicked(); + void OnSuggestionsButtonClicked(); protected: Ui::QmitkSegmentationPreferencePageControls* m_Ui; QWidget* m_Control; bool m_Initializing; berry::IPreferences::Pointer m_SegmentationPreferencesNode; }; #endif // QMITKSEGMENTATIONPREFERENCEPAGE_H diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePageControls.ui b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePageControls.ui index 7728e50e20..ee4674f966 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePageControls.ui +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePageControls.ui @@ -1,205 +1,323 @@ QmitkSegmentationPreferencePageControls 0 0 - 640 - 480 + 656 + 779 Form Slim view Hide tool button texts and increase icon size 2D display Draw as outline + + true + + + displayButtonGroup + Draw as transparent overlay + + displayButtonGroup + Data node selection mode If checked the segmentation plugin ensures that only the selected segmentation and the reference image are visible at one time. Show only selected nodes Smoothed surface creation 8 8 Smoothing value (mm) The Smoothing value is used as variance for a gaussian blur. 0.500000000000000 1.000000000000000 Decimation rate Valid range is [0, 1). High values increase decimation, especially when very close to 1. A value of 0 disables decimation. 0.990000000000000 0.100000000000000 0.500000000000000 Closing Ratio Valid range is [0, 1]. Higher values increase closing. A value of 0 disables closing. 1.000000000000000 0.100000000000000 If checked the segmentation plugin ensures that only the selected segmentation and the reference image are visible at one time. Use image spacing as smoothing value hint Default label set preset true ... <html><head/><body><p><span style=" color:#ff0000;">The default label set preset is currently overriden by the </span><span style=" font-family:'Courier New'; color:#ff0000;">Segmentation.labelSetPreset</span><span style=" color:#ff0000;"> command-line argument.</span></p></body></html> Qt::RichText true + + + + Label creation + + + + + + + + + Assign default name and color + + + true + + + labelCreationButtonGroup + + + + + + + Ask for name and color + + + labelCreationButtonGroup + + + + + + + + + Label suggestions + + + + + + + + + true + + + + + + + ... + + + + + + + <html><head/><body><p><span style=" color:#ff0000;">Suggestions are currently enforced by the </span><span style=" font-family:'Courier New'; color:#ff0000;">Segmentation.labelSuggestions</span><span style=" color:#ff0000;"> command-line argument.</span></p></body></html> + + + Qt::RichText + + + true + + + + + + + + + Replace standard organ suggestions + + + true + + + + + + + Suggest once per segmentation + + + true + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkLabelsWidget.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkLabelsWidget.cpp index 3345f642f1..9e354d92ae 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkLabelsWidget.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkLabelsWidget.cpp @@ -1,173 +1,196 @@ /*============================================================================ 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 "QmitkLabelsWidget.h" #include // mitk #include #include #include #include #include // Qmitk #include #include +#include #include "../QmitkSaveMultiLabelPresetAction.h" #include "../QmitkLoadMultiLabelPresetAction.h" // Qt #include QmitkLabelsWidget::QmitkLabelsWidget(QWidget *parent) : QWidget(parent) , m_Controls(new Ui::QmitkLabelsWidgetControls) , m_ToolManager(nullptr) + , m_DefaultLabelNaming(true) { m_Controls->setupUi(this); m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); m_Controls->savePresetButton->setIcon(QmitkStyleManager::ThemeIcon(QStringLiteral(":/org_mitk_icons/icons/awesome/scalable/actions/document-save.svg"))); m_Controls->loadPresetButton->setIcon(QmitkStyleManager::ThemeIcon(QStringLiteral(":/org_mitk_icons/icons/awesome/scalable/actions/document-open.svg"))); connect(m_Controls->newLabelButton, &QToolButton::clicked, this, &QmitkLabelsWidget::OnNewLabel); connect(m_Controls->lockExteriorButton, &QToolButton::toggled, this, &QmitkLabelsWidget::OnLockExterior); connect(m_Controls->savePresetButton, &QToolButton::clicked, this, &QmitkLabelsWidget::OnSavePreset); connect(m_Controls->loadPresetButton, &QToolButton::clicked, this, &QmitkLabelsWidget::OnLoadPreset); connect(m_Controls->showLabelTableButton, &QToolButton::toggled, this, &QmitkLabelsWidget::ShowLabelTable); this->UpdateGUI(); } QmitkLabelsWidget::~QmitkLabelsWidget() { delete m_Controls; } void QmitkLabelsWidget::UpdateGUI() { m_Controls->newLabelButton->setEnabled(false); m_Controls->lockExteriorButton->setEnabled(false); m_Controls->lockExteriorButton->setChecked(false); m_Controls->savePresetButton->setEnabled(false); m_Controls->loadPresetButton->setEnabled(false); m_Controls->showLabelTableButton->setEnabled(false); m_Controls->showLabelTableButton->setChecked(false); mitk::LabelSetImage* workingImage = this->GetWorkingImage(); if (nullptr == workingImage) { return; } int activeLayer = workingImage->GetActiveLayer(); m_Controls->lockExteriorButton->setEnabled(true); m_Controls->lockExteriorButton->setChecked(workingImage->GetLabel(0, activeLayer)->GetLocked()); m_Controls->showLabelTableButton->setEnabled(true); m_Controls->showLabelTableButton->setChecked(true); m_Controls->newLabelButton->setEnabled(true); m_Controls->savePresetButton->setEnabled(true); m_Controls->loadPresetButton->setEnabled(true); } +void QmitkLabelsWidget::SetDefaultLabelNaming(bool defaultLabelNaming) +{ + m_DefaultLabelNaming = defaultLabelNaming; +} + mitk::LabelSetImage* QmitkLabelsWidget::GetWorkingImage() { mitk::DataNode* workingNode = this->GetWorkingNode(); if (nullptr == workingNode) { return nullptr; } auto workingImage = dynamic_cast(workingNode->GetData()); return workingImage; } mitk::DataNode* QmitkLabelsWidget::GetWorkingNode() { mitk::DataNode* referenceNode = m_ToolManager->GetWorkingData(0); return referenceNode; } void QmitkLabelsWidget::OnNewLabel() { m_ToolManager->ActivateTool(-1); mitk::DataNode* workingNode = this->GetWorkingNode(); if (nullptr == workingNode) { return; } auto workingImage = dynamic_cast(workingNode->GetData()); if (nullptr == workingImage) { return; } - this->WaitCursorOn(); mitk::Label::Pointer newLabel = mitk::LabelSetImageHelper::CreateNewLabel(workingImage); + + if (!m_DefaultLabelNaming) + { + QmitkNewSegmentationDialog dialog(this, workingImage); + dialog.SetName(QString::fromStdString(newLabel->GetName())); + dialog.SetColor(newLabel->GetColor()); + + if (QDialog::Rejected == dialog.exec()) + return; + + auto name = dialog.GetName(); + + if (!name.isEmpty()) + newLabel->SetName(name.toStdString()); + + newLabel->SetColor(dialog.GetColor()); + } + workingImage->GetActiveLabelSet()->AddLabel(newLabel); - this->WaitCursorOff(); this->UpdateGUI(); emit LabelsChanged(); } void QmitkLabelsWidget::OnLockExterior(bool checked) { auto workingImage = this->GetWorkingImage(); if (nullptr == workingImage) { return; } workingImage->GetLabel(0)->SetLocked(checked); } void QmitkLabelsWidget::OnSavePreset() { auto workingNode = this->GetWorkingNode(); QmitkAbstractNodeSelectionWidget::NodeList nodes; nodes.append(workingNode); QmitkSaveMultiLabelPresetAction action; action.Run(nodes); } void QmitkLabelsWidget::OnLoadPreset() { auto workingNode = this->GetWorkingNode(); QmitkAbstractNodeSelectionWidget::NodeList nodes; nodes.append(workingNode); QmitkLoadMultiLabelPresetAction action; action.Run(nodes); } void QmitkLabelsWidget::WaitCursorOn() { QApplication::setOverrideCursor(QCursor(Qt::WaitCursor)); } void QmitkLabelsWidget::WaitCursorOff() { this->RestoreOverrideCursor(); } void QmitkLabelsWidget::RestoreOverrideCursor() { QApplication::restoreOverrideCursor(); } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkLabelsWidget.h b/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkLabelsWidget.h index bd74ae2ead..127775d686 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkLabelsWidget.h +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkLabelsWidget.h @@ -1,82 +1,86 @@ /*============================================================================ 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 QMITKLABELSWIDGET_H #define QMITKLABELSWIDGET_H // mitk core #include // Qt #include namespace Ui { class QmitkLabelsWidgetControls; } namespace mitk { class DataNode; class Image; class LabelSetImage; class ToolManager; } class QmitkLabelsWidget : public QWidget { Q_OBJECT public: explicit QmitkLabelsWidget(QWidget* parent = nullptr); ~QmitkLabelsWidget() override; void UpdateGUI(); + void SetDefaultLabelNaming(bool defaultLabelNaming); + Q_SIGNALS: void LabelsChanged(); void ShowLabelTable(bool); private: mitk::LabelSetImage* GetWorkingImage(); mitk::DataNode* GetWorkingNode(); // reaction to button "New Label" void OnNewLabel(); // reaction to the button "Lock exterior" void OnLockExterior(bool); // reaction to button "Save Preset" void OnSavePreset(); // reaction to button "Load Preset" void OnLoadPreset(); void WaitCursorOn(); void WaitCursorOff(); void RestoreOverrideCursor(); Ui::QmitkLabelsWidgetControls* m_Controls; mitk::ToolManager* m_ToolManager; + bool m_DefaultLabelNaming; + }; #endif diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp index 64a896ca97..98faec74c8 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp @@ -1,963 +1,989 @@ /*============================================================================ 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 "QmitkSegmentationView.h" #include "mitkPluginActivator.h" // blueberry #include // mitk #include #include #include #include #include #include #include #include #include #include #include #include #include // Qmitk #include -#include #include +#include // us #include #include // Qt #include #include #include #include const std::string QmitkSegmentationView::VIEW_ID = "org.mitk.views.segmentation"; QmitkSegmentationView::QmitkSegmentationView() : m_Parent(nullptr) , m_Controls(nullptr) , m_RenderWindowPart(nullptr) , m_ToolManager(nullptr) , m_ReferenceNode(nullptr) , m_WorkingNode(nullptr) , m_DrawOutline(true) , m_SelectionMode(false) , m_MouseCursorSet(false) + , m_DefaultLabelNaming(true) { auto isImage = mitk::TNodePredicateDataType::New(); auto isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); auto isDti = mitk::NodePredicateDataType::New("TensorImage"); auto isOdf = mitk::NodePredicateDataType::New("OdfImage"); auto isSegment = mitk::NodePredicateDataType::New("Segment"); auto validImages = mitk::NodePredicateOr::New(); validImages->AddPredicate(mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isSegment))); validImages->AddPredicate(isDwi); validImages->AddPredicate(isDti); validImages->AddPredicate(isOdf); auto isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); auto isMask = mitk::NodePredicateAnd::New(isBinary, isImage); auto validSegmentations = mitk::NodePredicateOr::New(); validSegmentations->AddPredicate(mitk::TNodePredicateDataType::New()); validSegmentations->AddPredicate(isMask); m_SegmentationPredicate = mitk::NodePredicateAnd::New(); m_SegmentationPredicate->AddPredicate(validSegmentations); m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("hidden object"))); m_ReferencePredicate = mitk::NodePredicateAnd::New(); m_ReferencePredicate->AddPredicate(validImages); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(m_SegmentationPredicate)); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("hidden object"))); } QmitkSegmentationView::~QmitkSegmentationView() { if (nullptr != m_Controls) { OnLooseLabelSetConnection(); // deactivate all tools m_ToolManager->ActivateTool(-1); // removing all observers for (NodeTagMapType::iterator dataIter = m_WorkingDataObserverTags.begin(); dataIter != m_WorkingDataObserverTags.end(); ++dataIter) { (*dataIter).first->GetProperty("visible")->RemoveObserver((*dataIter).second); } m_WorkingDataObserverTags.clear(); mitk::RenderingManager::GetInstance()->RemoveObserver(m_RenderingManagerObserverTag); ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); service->RemoveAllPlanePositions(); context->ungetService(ppmRef); m_ToolManager->SetReferenceData(nullptr); m_ToolManager->SetWorkingData(nullptr); } delete m_Controls; } /**********************************************************************/ /* private Q_SLOTS */ /**********************************************************************/ void QmitkSegmentationView::OnReferenceSelectionChanged(QList nodes) { m_ToolManager->ActivateTool(-1); if (nodes.empty()) { m_Controls->workingNodeSelector->SetNodePredicate(m_SegmentationPredicate); m_ReferenceNode = nullptr; m_ToolManager->SetReferenceData(m_ReferenceNode); this->UpdateGUI(); return; } m_ReferenceNode = nodes.first(); m_ToolManager->SetReferenceData(m_ReferenceNode); if (m_ReferenceNode.IsNotNull()) { // set a predicate such that a segmentation fits the selected reference image geometry auto segPredicate = mitk::NodePredicateAnd::New(m_SegmentationPredicate.GetPointer(), mitk::NodePredicateSubGeometry::New(m_ReferenceNode->GetData()->GetGeometry())); m_Controls->workingNodeSelector->SetNodePredicate(segPredicate); if (m_SelectionMode) { // hide all image nodes to later show only the automatically selected ones mitk::DataStorage::SetOfObjects::ConstPointer imageNodes = this->GetDataStorage()->GetSubset(m_ReferencePredicate); for (mitk::DataStorage::SetOfObjects::const_iterator iter = imageNodes->begin(); iter != imageNodes->end(); ++iter) { (*iter)->SetVisibility(false); } } m_ReferenceNode->SetVisibility(true); } this->UpdateGUI(); } void QmitkSegmentationView::OnSegmentationSelectionChanged(QList nodes) { m_ToolManager->ActivateTool(-1); // Remove observer if one was registered auto finding = m_WorkingDataObserverTags.find(m_WorkingNode); if (finding != m_WorkingDataObserverTags.end()) { m_WorkingNode->GetProperty("visible")->RemoveObserver(m_WorkingDataObserverTags[m_WorkingNode]); m_WorkingDataObserverTags.erase(m_WorkingNode); } if (nodes.empty()) { m_WorkingNode = nullptr; m_ToolManager->SetWorkingData(m_WorkingNode); this->UpdateGUI(); return; } if (m_ReferenceNode.IsNull()) { this->UpdateGUI(); return; } mitk::Image::ConstPointer referenceImage = dynamic_cast(m_ReferenceNode->GetData()); if (referenceImage.IsNull()) { this->UpdateGUI(); return; } m_WorkingNode = nodes.first(); m_ToolManager->SetWorkingData(m_WorkingNode); if (m_WorkingNode.IsNotNull()) { if (m_SelectionMode) { // hide all segmentation nodes to later show only the selected ones mitk::DataStorage::SetOfObjects::ConstPointer segmentationNodes = this->GetDataStorage()->GetSubset(m_SegmentationPredicate); for (mitk::DataStorage::SetOfObjects::const_iterator iter = segmentationNodes->begin(); iter != segmentationNodes->end(); ++iter) { (*iter)->SetVisibility(false); } } m_WorkingNode->SetVisibility(true); this->OnEstablishLabelSetConnection(); m_Controls->labelSetWidget->ResetAllTableWidgetItems(); auto command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::ValidateSelectionInput); m_WorkingDataObserverTags.insert(std::pair(m_WorkingNode, m_WorkingNode->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command))); this->InitializeRenderWindows(referenceImage->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, false); } this->UpdateGUI(); } void QmitkSegmentationView::OnVisibilityShortcutActivated() { if (m_WorkingNode.IsNull()) { return; } bool isVisible = false; m_WorkingNode->GetBoolProperty("visible", isVisible); m_WorkingNode->SetVisibility(!isVisible); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::OnLabelToggleShortcutActivated() { if (m_WorkingNode.IsNull()) { return; } auto workingImage = dynamic_cast(m_WorkingNode->GetData()); if (nullptr == workingImage) { return; } this->WaitCursorOn(); workingImage->GetActiveLabelSet()->SetNextActiveLabel(); workingImage->Modified(); this->WaitCursorOff(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::OnNewSegmentation() { m_ToolManager->ActivateTool(-1); if (m_ReferenceNode.IsNull()) { MITK_ERROR << "'Create new segmentation' button should never be clickable unless a reference image is selected."; return; } mitk::Image::ConstPointer referenceImage = dynamic_cast(m_ReferenceNode->GetData()); if (referenceImage.IsNull()) { QMessageBox::information( m_Parent, "New segmentation", "Please load and select an image before starting some action."); return; } if (referenceImage->GetDimension() <= 1) { QMessageBox::information( m_Parent, "New segmentation", "Segmentation is currently not supported for 2D images"); return; } auto segTemplateImage = referenceImage; if (referenceImage->GetDimension() > 3) { QmitkStaticDynamicSegmentationDialog dialog(m_Parent); dialog.SetReferenceImage(referenceImage.GetPointer()); dialog.exec(); segTemplateImage = dialog.GetSegmentationTemplate(); } mitk::DataNode::Pointer newSegmentationNode; try { this->WaitCursorOn(); newSegmentationNode = mitk::LabelSetImageHelper::CreateNewSegmentationNode(m_ReferenceNode, segTemplateImage); this->WaitCursorOff(); } catch (mitk::Exception& e) { this->WaitCursorOff(); MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::warning(m_Parent, "New segmentation", "Could not create a new segmentation."); return; } auto newLabelSetImage = dynamic_cast(newSegmentationNode->GetData()); if (nullptr == newLabelSetImage) { // something went wrong return; } const auto labelSetPreset = this->GetDefaultLabelSetPreset(); if (labelSetPreset.empty() || !mitk::LabelSetIOHelper::LoadLabelSetImagePreset(labelSetPreset, newLabelSetImage)) { - mitk::Label::Pointer newLabel = mitk::LabelSetImageHelper::CreateNewLabel(newLabelSetImage); + auto newLabel = mitk::LabelSetImageHelper::CreateNewLabel(newLabelSetImage); + + if (!m_DefaultLabelNaming) + { + QmitkNewSegmentationDialog dialog(m_Parent); + dialog.SetName(QString::fromStdString(newLabel->GetName())); + dialog.SetColor(newLabel->GetColor()); + + if (QDialog::Rejected == dialog.exec()) + return; + + auto name = dialog.GetName(); + + if (!name.isEmpty()) + newLabel->SetName(name.toStdString()); + + newLabel->SetColor(dialog.GetColor()); + } + newLabelSetImage->GetActiveLabelSet()->AddLabel(newLabel); } if (!this->GetDataStorage()->Exists(newSegmentationNode)) { this->GetDataStorage()->Add(newSegmentationNode, m_ReferenceNode); } if (m_ToolManager->GetWorkingData(0)) { m_ToolManager->GetWorkingData(0)->SetSelected(false); } newSegmentationNode->SetSelected(true); m_Controls->workingNodeSelector->SetCurrentSelectedNode(newSegmentationNode); } std::string QmitkSegmentationView::GetDefaultLabelSetPreset() const { auto labelSetPreset = mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABELSET_PRESET.toStdString(), ""); if (labelSetPreset.empty()) labelSetPreset = m_LabelSetPresetPreference.toStdString(); return labelSetPreset; } void QmitkSegmentationView::OnManualTool2DSelected(int id) { this->ResetMouseCursor(); mitk::StatusBar::GetInstance()->DisplayText(""); if (id >= 0) { std::string text = "Active Tool: \""; text += m_ToolManager->GetToolById(id)->GetName(); text += "\""; mitk::StatusBar::GetInstance()->DisplayText(text.c_str()); us::ModuleResource resource = m_ToolManager->GetToolById(id)->GetCursorIconResource(); this->SetMouseCursor(resource, 0, 0); } } void QmitkSegmentationView::OnShowMarkerNodes(bool state) { mitk::SegTool2D::Pointer manualSegmentationTool; unsigned int numberOfExistingTools = m_ToolManager->GetTools().size(); for (unsigned int i = 0; i < numberOfExistingTools; i++) { manualSegmentationTool = dynamic_cast(m_ToolManager->GetToolById(i)); if (nullptr == manualSegmentationTool) { continue; } manualSegmentationTool->SetShowMarkerNodes(state); } } void QmitkSegmentationView::OnLayersChanged() { this->OnEstablishLabelSetConnection(); m_Controls->labelSetWidget->ResetAllTableWidgetItems(); } void QmitkSegmentationView::OnShowLabelTable(bool value) { m_Controls->labelSetWidget->setVisible(value); } void QmitkSegmentationView::OnGoToLabel(const mitk::Point3D& pos) { if (m_RenderWindowPart) { m_RenderWindowPart->SetSelectedPosition(pos); } } void QmitkSegmentationView::OnLabelSetWidgetReset() { this->ValidateSelectionInput(); } /**********************************************************************/ /* private */ /**********************************************************************/ void QmitkSegmentationView::CreateQtPartControl(QWidget* parent) { m_Parent = parent; m_Controls = new Ui::QmitkSegmentationViewControls; m_Controls->setupUi(parent); // *------------------------ // * SHORTCUTS // *------------------------ QShortcut* visibilityShortcut = new QShortcut(QKeySequence("CTRL+H"), parent); connect(visibilityShortcut, &QShortcut::activated, this, &QmitkSegmentationView::OnVisibilityShortcutActivated); QShortcut* labelToggleShortcut = new QShortcut(QKeySequence("CTRL+L"), parent); connect(labelToggleShortcut, &QShortcut::activated, this, &QmitkSegmentationView::OnLabelToggleShortcutActivated); // *------------------------ // * DATA SELECTION WIDGETS // *------------------------ m_Controls->referenceNodeSelector->SetDataStorage(GetDataStorage()); m_Controls->referenceNodeSelector->SetNodePredicate(m_ReferencePredicate); m_Controls->referenceNodeSelector->SetInvalidInfo("Select an image"); m_Controls->referenceNodeSelector->SetPopUpTitel("Select an image"); m_Controls->referenceNodeSelector->SetPopUpHint("Select an image that should be used to define the geometry and bounds of the segmentation."); m_Controls->workingNodeSelector->SetDataStorage(GetDataStorage()); m_Controls->workingNodeSelector->SetNodePredicate(m_SegmentationPredicate); m_Controls->workingNodeSelector->SetInvalidInfo("Select a segmentation"); m_Controls->workingNodeSelector->SetPopUpTitel("Select a segmentation"); m_Controls->workingNodeSelector->SetPopUpHint("Select a segmentation that should be modified. Only segmentation with the same geometry and within the bounds of the reference image are selected."); connect(m_Controls->referenceNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkSegmentationView::OnReferenceSelectionChanged); connect(m_Controls->workingNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkSegmentationView::OnSegmentationSelectionChanged); // *------------------------ // * TOOLMANAGER // *------------------------ m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); m_ToolManager->SetDataStorage(*(this->GetDataStorage())); m_ToolManager->InitializeTools(); QString segTools2D = tr("Add Subtract Fill Erase Paint Wipe 'Region Growing' 'Live Wire'"); QString segTools3D = tr("Threshold 'UL Threshold' Otsu 'Region Growing 3D' Picking"); #ifdef __linux__ segTools3D.append(" nnUNet"); // plugin not enabled for MacOS / Windows #endif std::regex extSegTool2DRegEx("SegTool2D$"); std::regex extSegTool3DRegEx("SegTool3D$"); auto tools = m_ToolManager->GetTools(); for (const auto &tool : tools) { if (std::regex_search(tool->GetNameOfClass(), extSegTool2DRegEx)) { segTools2D.append(QString(" '%1'").arg(tool->GetName())); } else if (std::regex_search(tool->GetNameOfClass(), extSegTool3DRegEx)) { segTools3D.append(QString(" '%1'").arg(tool->GetName())); } } // setup 2D tools m_Controls->toolSelectionBox2D->SetToolManager(*m_ToolManager); m_Controls->toolSelectionBox2D->SetGenerateAccelerators(true); m_Controls->toolSelectionBox2D->SetToolGUIArea(m_Controls->toolGUIArea2D); m_Controls->toolSelectionBox2D->SetDisplayedToolGroups(segTools2D.toStdString()); m_Controls->toolSelectionBox2D->SetLayoutColumns(3); m_Controls->toolSelectionBox2D->SetEnabledMode( QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible); connect(m_Controls->toolSelectionBox2D, &QmitkToolSelectionBox::ToolSelected, this, &QmitkSegmentationView::OnManualTool2DSelected); // setup 3D Tools m_Controls->toolSelectionBox3D->SetToolManager(*m_ToolManager); m_Controls->toolSelectionBox3D->SetGenerateAccelerators(true); m_Controls->toolSelectionBox3D->SetToolGUIArea(m_Controls->toolGUIArea3D); m_Controls->toolSelectionBox3D->SetDisplayedToolGroups(segTools3D.toStdString()); m_Controls->toolSelectionBox3D->SetLayoutColumns(3); m_Controls->toolSelectionBox3D->SetEnabledMode( QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible); m_Controls->slicesInterpolator->SetDataStorage(this->GetDataStorage()); // create general signal / slot connections connect(m_Controls->newSegmentationButton, &QToolButton::clicked, this, &QmitkSegmentationView::OnNewSegmentation); connect(m_Controls->slicesInterpolator, &QmitkSlicesInterpolator::SignalShowMarkerNodes, this, &QmitkSegmentationView::OnShowMarkerNodes); connect(m_Controls->layersWidget, &QmitkLayersWidget::LayersChanged, this, &QmitkSegmentationView::OnLayersChanged); connect(m_Controls->labelsWidget, &QmitkLabelsWidget::ShowLabelTable, this, &QmitkSegmentationView::OnShowLabelTable); // *------------------------ // * LABELSETWIDGET // *------------------------ connect(m_Controls->labelSetWidget, &QmitkLabelSetWidget::goToLabel, this, &QmitkSegmentationView::OnGoToLabel); connect(m_Controls->labelSetWidget, &QmitkLabelSetWidget::LabelSetWidgetReset, this, &QmitkSegmentationView::OnLabelSetWidgetReset); m_Controls->labelSetWidget->SetDataStorage(this->GetDataStorage()); - m_Controls->labelSetWidget->SetOrganColors(mitk::OrganNamesHandling::GetDefaultOrganColorString()); m_Controls->labelSetWidget->hide(); auto command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::ValidateSelectionInput); m_RenderingManagerObserverTag = mitk::RenderingManager::GetInstance()->AddObserver(mitk::RenderingManagerViewsInitializedEvent(), command); m_RenderWindowPart = this->GetRenderWindowPart(); if (nullptr != m_RenderWindowPart) { this->RenderWindowPartActivated(m_RenderWindowPart); } // Make sure the GUI notices if appropriate data is already present on creation. // Should be done last, if everything else is configured because it triggers the autoselection of data. m_Controls->referenceNodeSelector->SetAutoSelectNewNodes(true); m_Controls->workingNodeSelector->SetAutoSelectNewNodes(true); this->UpdateGUI(); } void QmitkSegmentationView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { if (m_RenderWindowPart != renderWindowPart) { m_RenderWindowPart = renderWindowPart; } if (nullptr != m_Parent) { m_Parent->setEnabled(true); } if (nullptr == m_Controls) { return; } // tell the interpolation about tool manager, data storage and render window part if (nullptr != m_RenderWindowPart) { QList controllers; controllers.push_back(m_RenderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); controllers.push_back(m_RenderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); controllers.push_back(m_RenderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); m_Controls->slicesInterpolator->Initialize(m_ToolManager, controllers); } } void QmitkSegmentationView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* /*renderWindowPart*/) { m_RenderWindowPart = nullptr; if (nullptr != m_Parent) { m_Parent->setEnabled(false); } } void QmitkSegmentationView::OnPreferencesChanged(const berry::IBerryPreferences* prefs) { + auto labelSuggestions = mitk::BaseApplication::instance().config().getString(mitk::BaseApplication::ARG_SEGMENTATION_LABEL_SUGGESTIONS.toStdString(), ""); + + m_DefaultLabelNaming = labelSuggestions.empty() + ? prefs->GetBool("default label naming", true) + : false; // No default label naming when label suggestions are enforced via command-line argument + if (nullptr != m_Controls) { + m_Controls->labelsWidget->SetDefaultLabelNaming(m_DefaultLabelNaming); + bool slimView = prefs->GetBool("slim view", false); m_Controls->toolSelectionBox2D->SetShowNames(!slimView); m_Controls->toolSelectionBox3D->SetShowNames(!slimView); } m_DrawOutline = prefs->GetBool("draw outline", true); m_SelectionMode = prefs->GetBool("selection mode", false); m_LabelSetPresetPreference = prefs->Get("label set preset", ""); this->ApplyDisplayOptions(); } void QmitkSegmentationView::NodeAdded(const mitk::DataNode* node) { if (m_SegmentationPredicate->CheckNode(node)) { this->ApplyDisplayOptions(const_cast(node)); } } void QmitkSegmentationView::NodeRemoved(const mitk::DataNode* node) { if (!m_SegmentationPredicate->CheckNode(node)) { return; } // remove all possible contour markers of the segmentation mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = this->GetDataStorage()->GetDerivations( node, mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true))); ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); for (mitk::DataStorage::SetOfObjects::ConstIterator it = allContourMarkers->Begin(); it != allContourMarkers->End(); ++it) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1; service->RemovePlanePosition(id); this->GetDataStorage()->Remove(it->Value()); } context->ungetService(ppmRef); service = nullptr; mitk::Image* image = dynamic_cast(node->GetData()); mitk::SurfaceInterpolationController::GetInstance()->RemoveInterpolationSession(image); } void QmitkSegmentationView::OnEstablishLabelSetConnection() { if (m_WorkingNode.IsNull()) { return; } auto workingImage = dynamic_cast(m_WorkingNode->GetData()); if (nullptr == workingImage) { return; } workingImage->GetActiveLabelSet()->AddLabelEvent += mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->RemoveLabelEvent += mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->ModifyLabelEvent += mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->AllLabelsModifiedEvent += mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->ActiveLabelEvent += mitk::MessageDelegate1(m_Controls->labelSetWidget, &QmitkLabelSetWidget::SelectLabelByPixelValue); // Removed in T27851 to have a chance to react to AfterChangeLayerEvent. Did it brake something? // workingImage->BeforeChangeLayerEvent += mitk::MessageDelegate( // this, &QmitkMultiLabelSegmentationView::OnLooseLabelSetConnection); workingImage->AfterChangeLayerEvent += mitk::MessageDelegate( this, &QmitkSegmentationView::UpdateGUI); } void QmitkSegmentationView::OnLooseLabelSetConnection() { if (m_WorkingNode.IsNull()) { return; } auto workingImage = dynamic_cast(m_WorkingNode->GetData()); if (nullptr == workingImage) { return; } // Reset LabelSetWidget Events workingImage->GetActiveLabelSet()->AddLabelEvent -= mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->RemoveLabelEvent -= mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->ModifyLabelEvent -= mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->AllLabelsModifiedEvent -= mitk::MessageDelegate( m_Controls->labelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->ActiveLabelEvent -= mitk::MessageDelegate1(m_Controls->labelSetWidget, &QmitkLabelSetWidget::SelectLabelByPixelValue); // Removed in T27851 to have a chance to react to AfterChangeLayerEvent. Did it brake something? // workingImage->BeforeChangeLayerEvent -= mitk::MessageDelegate( // this, &QmitkMultiLabelSegmentationView::OnLooseLabelSetConnection); workingImage->AfterChangeLayerEvent -= mitk::MessageDelegate( this, &QmitkSegmentationView::UpdateGUI); } void QmitkSegmentationView::ApplyDisplayOptions() { if (nullptr == m_Parent) { return; } if (nullptr == m_Controls) { return; // might happen on initialization (preferences loaded) } mitk::DataStorage::SetOfObjects::ConstPointer allImages = this->GetDataStorage()->GetSubset(m_SegmentationPredicate); for (mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter) { this->ApplyDisplayOptions(*iter); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::ApplyDisplayOptions(mitk::DataNode* node) { if (nullptr == node) { return; } auto labelSetImage = dynamic_cast(node->GetData()); if (nullptr != labelSetImage) { // node is a multi label segmentation // its outline property can be set in the segmentation preference page node->SetProperty("labelset.contour.active", mitk::BoolProperty::New(m_DrawOutline)); // force render window update to show outline node->GetData()->Modified(); } else if (nullptr != node->GetData()) { // node is a legacy binary segmentation bool isBinary = false; node->GetBoolProperty("binary", isBinary); if (isBinary) { node->SetProperty("outline binary", mitk::BoolProperty::New(m_DrawOutline)); node->SetProperty("outline width", mitk::FloatProperty::New(2.0)); // force render window update to show outline node->GetData()->Modified(); } } } void QmitkSegmentationView::OnContourMarkerSelected(const mitk::DataNode* node) { QmitkRenderWindow* selectedRenderWindow = nullptr; auto* renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::OPEN); auto* axialRenderWindow = renderWindowPart->GetQmitkRenderWindow("axial"); auto* sagittalRenderWindow = renderWindowPart->GetQmitkRenderWindow("sagittal"); auto* coronalRenderWindow = renderWindowPart->GetQmitkRenderWindow("coronal"); auto* threeDRenderWindow = renderWindowPart->GetQmitkRenderWindow("3d"); bool PlanarFigureInitializedWindow = false; // find initialized renderwindow if (node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, axialRenderWindow->GetRenderer())) { selectedRenderWindow = axialRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, sagittalRenderWindow->GetRenderer())) { selectedRenderWindow = sagittalRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, coronalRenderWindow->GetRenderer())) { selectedRenderWindow = coronalRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, threeDRenderWindow->GetRenderer())) { selectedRenderWindow = threeDRenderWindow; } // make node visible if (nullptr != selectedRenderWindow) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1; ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); selectedRenderWindow->GetSliceNavigationController()->ExecuteOperation(service->GetPlanePosition(id)); context->ungetService(ppmRef); selectedRenderWindow->GetRenderer()->GetCameraController()->Fit(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkSegmentationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& nodes) { if (0 == nodes.size()) { return; } std::string markerName = "Position"; unsigned int numberOfNodes = nodes.size(); std::string nodeName = nodes.at(0)->GetName(); if ((numberOfNodes == 1) && (nodeName.find(markerName) == 0)) { this->OnContourMarkerSelected(nodes.at(0)); return; } } void QmitkSegmentationView::ResetMouseCursor() { if (m_MouseCursorSet) { mitk::ApplicationCursor::GetInstance()->PopCursor(); m_MouseCursorSet = false; } } void QmitkSegmentationView::SetMouseCursor(const us::ModuleResource& resource, int hotspotX, int hotspotY) { // Remove previously set mouse cursor if (m_MouseCursorSet) { this->ResetMouseCursor(); } if (resource) { us::ModuleResourceStream cursor(resource, std::ios::binary); mitk::ApplicationCursor::GetInstance()->PushCursor(cursor, hotspotX, hotspotY); m_MouseCursorSet = true; } } void QmitkSegmentationView::UpdateGUI() { mitk::DataNode* referenceNode = m_ToolManager->GetReferenceData(0); bool hasReferenceNode = referenceNode != nullptr; mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0); bool hasWorkingNode = workingNode != nullptr; m_Controls->newSegmentationButton->setEnabled(false); if (hasReferenceNode) { m_Controls->newSegmentationButton->setEnabled(true); } if (hasWorkingNode && hasReferenceNode) { int layer = -1; referenceNode->GetIntProperty("layer", layer); workingNode->SetIntProperty("layer", layer + 1); } m_Controls->layersWidget->UpdateGUI(); m_Controls->labelsWidget->UpdateGUI(); this->ValidateSelectionInput(); } void QmitkSegmentationView::ValidateSelectionInput() { this->UpdateWarningLabel(""); m_Controls->layersWidget->setEnabled(false); m_Controls->labelsWidget->setEnabled(false); m_Controls->labelSetWidget->setEnabled(false); // the argument is actually not used // enable status depends on the tool manager selection m_Controls->toolSelectionBox2D->setEnabled(false); m_Controls->toolSelectionBox3D->setEnabled(false); m_Controls->slicesInterpolator->setEnabled(false); m_Controls->interpolatorWarningLabel->hide(); mitk::DataNode* referenceNode = m_Controls->referenceNodeSelector->GetSelectedNode(); mitk::DataNode* workingNode = m_Controls->workingNodeSelector->GetSelectedNode(); if (nullptr == referenceNode) { return; } if (nullptr == workingNode) { return; } mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart(); auto workingNodeIsVisible = renderWindowPart && workingNode->IsVisible(renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderer()); if (!workingNodeIsVisible) { this->UpdateWarningLabel(tr("The selected segmentation is currently not visible!")); return; } /* * Here we check whether the geometry of the selected segmentation image is aligned with the worldgeometry. * At the moment it is not supported to use a geometry different from the selected image for reslicing. * For further information see Bug 16063 */ const mitk::BaseGeometry* workingNodeGeo = workingNode->GetData()->GetGeometry(); const mitk::BaseGeometry* worldGeo = renderWindowPart->GetQmitkRenderWindow("3d")->GetSliceNavigationController()->GetCurrentGeometry3D(); if (nullptr != workingNodeGeo && nullptr != worldGeo) { if (mitk::Equal(*workingNodeGeo->GetBoundingBox(), *worldGeo->GetBoundingBox(), mitk::eps, true)) { m_ToolManager->SetReferenceData(referenceNode); m_ToolManager->SetWorkingData(workingNode); m_Controls->layersWidget->setEnabled(true); m_Controls->labelsWidget->setEnabled(true); m_Controls->labelSetWidget->setEnabled(true); m_Controls->toolSelectionBox2D->setEnabled(true); m_Controls->toolSelectionBox3D->setEnabled(true); auto labelSetImage = dynamic_cast(workingNode->GetData()); if (nullptr != labelSetImage) { int numberOfLabels = labelSetImage->GetNumberOfLabels(labelSetImage->GetActiveLayer()); if (2 == numberOfLabels) // fix for T27319: exterior is label 0, first label is label 1 { m_Controls->slicesInterpolator->setEnabled(true); } else { m_Controls->interpolatorWarningLabel->show(); m_Controls->interpolatorWarningLabel->setText("Interpolation only works for single label segmentations."); } } return; } } m_ToolManager->SetReferenceData(referenceNode); m_ToolManager->SetWorkingData(nullptr); this->UpdateWarningLabel(tr("Please perform a reinit on the segmentation image!")); } void QmitkSegmentationView::UpdateWarningLabel(QString text) { if (text.size() == 0) { m_Controls->selectionWarningLabel->hide(); } else { m_Controls->selectionWarningLabel->show(); m_Controls->selectionWarningLabel->setText("" + text + ""); } } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.h b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.h index 4a9c65a86b..7874805f2d 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.h +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.h @@ -1,152 +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. ============================================================================*/ #ifndef QMITKSEGMENTATIONVIEW_H #define QMITKSEGMENTATIONVIEW_H #include "ui_QmitkSegmentationViewControls.h" #include #include #include /** * @brief The segmentation view provides a set of tool to use different segmentation algorithms. * It provides two selection widgets to load an image node and a segmentation node * on which to perform the segmentation. Creating new segmentation nodes is also possible. * The available segmentation tools are grouped into "2D"- and "3D"-tools. * * Most segmentation tools / algorithms need some kind of user interaction, where the * user is asked to draw something in the image display or set some seed points / start values. * The tools also often provide additional propeties so that a user can modify the * algorithm's behavior. * * This class additionally provides options to work with different layers (create new layers, * switch between layers). * Moreover, a multilabel widget displays all the existing labels of a multilabel segmentation * for the currently active layer. * The multilabel widget allows to control the labels by creatin new one, removing existing ones, * showing / hiding single labels, merging labels, (re-)naming them etc. * * Additionally the view provides an option to create "2D"- and "3D"-interpolations between * neighboring segmentation masks on unsegmented slices. * Interpolation for multilabel segmentations is currently not implemented. */ class QmitkSegmentationView : public QmitkAbstractView, public mitk::IRenderWindowPartListener { Q_OBJECT public: static const std::string VIEW_ID; QmitkSegmentationView(); ~QmitkSegmentationView() override; private Q_SLOTS: // reaction to the selection of a new reference image in the selection widget void OnReferenceSelectionChanged(QList nodes); // reaction to the selection of a new segmentation image in the selection widget void OnSegmentationSelectionChanged(QList nodes); // reaction to the shortcut ("CTRL+H") for toggling the visibility of the working node void OnVisibilityShortcutActivated(); // reaction to the shortcut ("CTRL+L") for iterating over all labels void OnLabelToggleShortcutActivated(); // reaction to the button "New segmentation" void OnNewSegmentation(); void OnManualTool2DSelected(int id); void OnShowMarkerNodes(bool); void OnLayersChanged(); void OnShowLabelTable(bool); void OnGoToLabel(const mitk::Point3D &pos); void OnLabelSetWidgetReset(); private: void CreateQtPartControl(QWidget* parent) override; void SetFocus() override {} void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) override; void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) override; void OnPreferencesChanged(const berry::IBerryPreferences* prefs) override; void NodeAdded(const mitk::DataNode* node) override; void NodeRemoved(const mitk::DataNode* node) override; void OnEstablishLabelSetConnection(); void OnLooseLabelSetConnection(); // make sure all images / segmentations look according to the user preference settings void ApplyDisplayOptions(); // decorates a DataNode according to the user preference settings void ApplyDisplayOptions(mitk::DataNode* node); // If a contourmarker is selected, the plane in the related widget will be reoriented according to the marker`s geometry void OnContourMarkerSelected(const mitk::DataNode* node); void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList &nodes) override; void ResetMouseCursor(); void SetMouseCursor(const us::ModuleResource&, int hotspotX, int hotspotY); void UpdateGUI(); void ValidateSelectionInput(); void UpdateWarningLabel(QString text); std::string GetDefaultLabelSetPreset() const; QWidget* m_Parent; Ui::QmitkSegmentationViewControls* m_Controls; mitk::IRenderWindowPart* m_RenderWindowPart; mitk::ToolManager* m_ToolManager; mitk::DataNode::Pointer m_ReferenceNode; mitk::DataNode::Pointer m_WorkingNode; typedef std::map NodeTagMapType; NodeTagMapType m_WorkingDataObserverTags; unsigned int m_RenderingManagerObserverTag; mitk::NodePredicateAnd::Pointer m_ReferencePredicate; mitk::NodePredicateAnd::Pointer m_SegmentationPredicate; bool m_DrawOutline; bool m_SelectionMode; bool m_MouseCursorSet; QString m_LabelSetPresetPreference; + bool m_DefaultLabelNaming; }; #endif // QMITKSEGMENTATIONVIEW_H diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.semanticrelations/manifest_headers.cmake index 9da36a3fbc..a413decc69 100644 --- a/Plugins/org.mitk.gui.qt.semanticrelations/manifest_headers.cmake +++ b/Plugins/org.mitk.gui.qt.semanticrelations/manifest_headers.cmake @@ -1,5 +1,5 @@ set(Plugin-Name "MITK Semantic relations") set(Plugin-Version "0.1") set(Plugin-Vendor "DKFZ") set(Plugin-ContactAddress "http://www.mitk.org") -set(Require-Plugin org.mitk.gui.qt.common org.mitk.gui.qt.application) +set(Require-Plugin org.mitk.gui.qt.common org.mitk.gui.qt.application org.mitk.gui.qt.segmentation) diff --git a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.cpp b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.cpp index 08102751a3..4570a97efb 100644 --- a/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.cpp +++ b/Plugins/org.mitk.gui.qt.semanticrelations/src/internal/QmitkLesionInfoWidget.cpp @@ -1,495 +1,495 @@ /*============================================================================ 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. ============================================================================*/ // semantic relations plugin #include "QmitkLesionInfoWidget.h" #include "QmitkDataNodeAddToSemanticRelationsAction.h" #include "QmitkFocusOnLesionAction.h" #include "QmitkSemanticRelationsNodeSelectionDialog.h" // semantic relations UI module #include // semantic relations module #include #include #include #include #include // segmentation #include #include // qt #include #include #include #include #include QmitkLesionInfoWidget::QmitkLesionInfoWidget(mitk::DataStorage* dataStorage, berry::IWorkbenchPartSite::Pointer workbenchPartSite, QWidget* parent /*= nullptr*/) : QWidget(parent) , m_DataStorage(dataStorage) , m_WorkbenchPartSite(workbenchPartSite) , m_SemanticRelationsDataStorageAccess(std::make_unique(dataStorage)) , m_SemanticRelationsIntegration(std::make_unique()) { Initialize(); } void QmitkLesionInfoWidget::Initialize() { m_Controls.setupUi(this); m_Controls.lesionTreeView->setAlternatingRowColors(true); m_Controls.lesionTreeView->setSelectionMode(QAbstractItemView::SingleSelection); m_Controls.lesionTreeView->setSelectionBehavior(QAbstractItemView::SelectRows); m_Controls.lesionTreeView->setContextMenuPolicy(Qt::CustomContextMenu); m_StorageModel = new QmitkLesionTreeModel(m_Controls.lesionTreeView); auto dataStorage = m_DataStorage.Lock(); if (dataStorage.IsNull()) { return; } m_StorageModel->SetDataStorage(dataStorage); m_Controls.lesionTreeView->setModel(m_StorageModel); SetUpConnections(); } void QmitkLesionInfoWidget::SetUpConnections() { connect(m_StorageModel, &QmitkLesionTreeModel::ModelUpdated, this, &QmitkLesionInfoWidget::OnModelUpdated); connect(m_Controls.addLesionPushButton, &QPushButton::clicked, this, &QmitkLesionInfoWidget::OnAddLesionButtonClicked); connect(m_Controls.lesionTreeView->selectionModel(), &QItemSelectionModel::currentChanged, this, &QmitkLesionInfoWidget::OnSelectionChanged); connect(m_Controls.lesionTreeView, &QTreeView::customContextMenuRequested, this, &QmitkLesionInfoWidget::OnLesionListContextMenuRequested); } void QmitkLesionInfoWidget::SetCaseID(const mitk::SemanticTypes::CaseID& caseID) { m_CaseID = caseID; m_StorageModel->SetCaseID(caseID); } void QmitkLesionInfoWidget::SetDataNodeSelection(const QList& dataNodeSelection) { m_StorageModel->SetDataNodeSelection(dataNodeSelection); } ////////////////////////////////////////////////////////////////////////// // Implementation of the QT_SLOTS ////////////////////////////////////////////////////////////////////////// void QmitkLesionInfoWidget::OnModelUpdated() { m_Controls.lesionTreeView->expandAll(); int columns = m_Controls.lesionTreeView->model()->columnCount(); for (int i = 0; i < columns; ++i) { m_Controls.lesionTreeView->resizeColumnToContents(i); } } void QmitkLesionInfoWidget::OnAddLesionButtonClicked() { if (m_CaseID.empty()) { QMessageBox msgBox(QMessageBox::Warning, "No case ID set.", "In order to add a lesion, please specify the current case / patient."); msgBox.exec(); return; } mitk::SemanticTypes::Lesion newLesion = mitk::GenerateNewLesion(); try { m_SemanticRelationsIntegration->AddLesion(m_CaseID, newLesion); } catch (mitk::SemanticRelationException& e) { MITK_INFO << "Could not add a new lesion. " << e; } } void QmitkLesionInfoWidget::OnSelectionChanged(const QModelIndex& current, const QModelIndex& /*previous*/) { // only the UID is needed to identify a representing lesion QVariant data = m_StorageModel->data(current, Qt::UserRole); if (!data.canConvert()) { return; } auto lesion = data.value()->GetData().GetLesion(); if (false == mitk::SemanticRelationsInference::InstanceExists(m_CaseID, lesion)) { // no UID of a existing lesion found; cannot create a lesion return; } // if selected data nodes are set, reset to empty list to // hide "selected data nodes presence background highlighting" in the model if (!m_StorageModel->GetSelectedDataNodes().isEmpty()) { m_StorageModel->SetDataNodeSelection(QList()); } emit LesionSelectionChanged(lesion); } void QmitkLesionInfoWidget::OnLesionListContextMenuRequested(const QPoint& pos) { if (nullptr == m_SemanticRelationsIntegration) { return; } if (m_CaseID.empty()) { QMessageBox msgBox(QMessageBox::Warning, "No case ID set.", "In order to access the context menu entries a case ID has to be set."); msgBox.exec(); return; } QModelIndex index = m_Controls.lesionTreeView->indexAt(pos); if (!index.isValid()) { // no item clicked; cannot retrieve the current lesion return; } QVariant data = m_StorageModel->data(index, Qt::UserRole); mitk::SemanticTypes::Lesion selectedLesion; if (data.canConvert()) { selectedLesion = data.value()->GetData().GetLesion(); } else { return; } QMenu* menu = new QMenu(m_Controls.lesionTreeView); QAction* linkToSegmentation = new QAction("Link to segmentation", this); linkToSegmentation->setEnabled(true); connect(linkToSegmentation, &QAction::triggered, [this, selectedLesion] { OnLinkToSegmentation(selectedLesion); }); menu->addAction(linkToSegmentation); QAction* setLesionName = new QAction("Set lesion name", this); setLesionName->setEnabled(true); connect(setLesionName, &QAction::triggered, [this, selectedLesion] { OnSetLesionName(selectedLesion); }); menu->addAction(setLesionName); QAction* setLesionClass = new QAction("Set lesion class", this); setLesionClass->setEnabled(true); connect(setLesionClass, &QAction::triggered, [this, selectedLesion] { OnSetLesionClass(selectedLesion); }); menu->addAction(setLesionClass); QAction* createNewSegmentation = new QAction("Create new lesion", this); createNewSegmentation->setEnabled(true); connect(createNewSegmentation, &QAction::triggered, [this, selectedLesion] { OnCreateNewSegmentation(selectedLesion); }); menu->addAction(createNewSegmentation); QAction* removeLesion = new QAction("Remove lesion", this); removeLesion->setEnabled(true); connect(removeLesion, &QAction::triggered, [this, selectedLesion] { OnRemoveLesion(selectedLesion); }); menu->addAction(removeLesion); auto workbenchPartSite = m_WorkbenchPartSite.Lock(); if (workbenchPartSite.IsNotNull()) { QmitkFocusOnLesionAction* focusOnLesion = new QmitkFocusOnLesionAction(this, workbenchPartSite); focusOnLesion->SetDataStorage(m_DataStorage.Lock()); focusOnLesion->SetSelectedLesion(selectedLesion); menu->addAction(focusOnLesion); } menu->popup(QCursor::pos()); } void QmitkLesionInfoWidget::OnLinkToSegmentation(mitk::SemanticTypes::Lesion selectedLesion) { auto dataStorage = m_DataStorage.Lock(); if (dataStorage.IsNull()) { return; } QmitkSemanticRelationsNodeSelectionDialog* dialog = new QmitkSemanticRelationsNodeSelectionDialog(this, "Select segmentation to link to the selected lesion.", ""); dialog->setWindowTitle("Select segmentation node"); dialog->SetDataStorage(dataStorage); dialog->SetNodePredicate(mitk::NodePredicates::GetSegmentationPredicate()); dialog->SetSelectOnlyVisibleNodes(true); dialog->SetCaseID(m_CaseID); // set the last added segmentation node as pre-selected data node const mitk::DataNode* lastSegmentation = m_StorageModel->GetLastSegmentation(); QList selectedDataNodes; if (nullptr != lastSegmentation) { selectedDataNodes.push_back(const_cast(lastSegmentation)); dialog->SetCurrentSelection(selectedDataNodes); } int dialogReturnValue = dialog->exec(); if (QDialog::Rejected == dialogReturnValue) { return; } mitk::DataNode::Pointer selectedDataNode = nullptr; selectedDataNodes = dialog->GetSelectedNodes(); if (!selectedDataNodes.isEmpty()) { // only single selection allowed selectedDataNode = selectedDataNodes.front(); } if (nullptr == selectedDataNode || false == mitk::NodePredicates::GetSegmentationPredicate()->CheckNode(selectedDataNode)) { QMessageBox msgBox(QMessageBox::Warning, "No valid segmentation node selected.", "In order to link the selected lesion to a segmentation, please specify a valid segmentation node."); msgBox.exec(); return; } mitk::BaseData* baseData = selectedDataNode->GetData(); if (nullptr == baseData) { QMessageBox msgBox(QMessageBox::Warning, "No valid base data.", "In order to link the selected lesion to a segmentation, please specify a valid segmentation node."); msgBox.exec(); return; } LinkSegmentationToLesion(selectedDataNode, selectedLesion); } void QmitkLesionInfoWidget::OnSetLesionName(mitk::SemanticTypes::Lesion selectedLesion) { // use the lesion information to set the input text for the dialog QmitkLesionTextDialog* inputDialog = new QmitkLesionTextDialog(this); inputDialog->setWindowTitle("Set lesion name"); inputDialog->SetLineEditText(selectedLesion.name); int dialogReturnValue = inputDialog->exec(); if (QDialog::Rejected == dialogReturnValue) { return; } selectedLesion.name = inputDialog->GetLineEditText().toStdString(); m_SemanticRelationsIntegration->OverwriteLesion(m_CaseID, selectedLesion); } void QmitkLesionInfoWidget::OnSetLesionClass(mitk::SemanticTypes::Lesion selectedLesion) { // use the lesion information to set the input text for the dialog QmitkLesionTextDialog* inputDialog = new QmitkLesionTextDialog(this); inputDialog->setWindowTitle("Set lesion class"); inputDialog->SetLineEditText(selectedLesion.lesionClass.classType); // prepare the completer for the dialogs input text field mitk::LesionClassVector allLesionClasses = mitk::SemanticRelationsInference::GetAllLesionClassesOfCase(m_CaseID); QStringList wordList; for (const auto& lesionClass : allLesionClasses) { wordList << QString::fromStdString(lesionClass.classType); } QCompleter* completer = new QCompleter(wordList, this); completer->setCaseSensitivity(Qt::CaseInsensitive); inputDialog->GetLineEdit()->setCompleter(completer); int dialogReturnValue = inputDialog->exec(); if (QDialog::Rejected == dialogReturnValue) { return; } // retrieve the new input lesion class type and check for an already existing lesion class types std::string newLesionClassType = inputDialog->GetLineEditText().toStdString(); mitk::SemanticTypes::LesionClass existingLesionClass = mitk::FindExistingLesionClass(m_CaseID, newLesionClassType); if (existingLesionClass.UID.empty()) { // could not find lesion class information for the new lesion class type // create a new lesion class for the selected lesion existingLesionClass = mitk::GenerateNewLesionClass(newLesionClassType); } selectedLesion.lesionClass = existingLesionClass; m_SemanticRelationsIntegration->OverwriteLesion(m_CaseID, selectedLesion); } void QmitkLesionInfoWidget::OnCreateNewSegmentation(mitk::SemanticTypes::Lesion selectedLesion) { auto dataStorage = m_DataStorage.Lock(); if (dataStorage.IsNull()) { return; } QmitkSemanticRelationsNodeSelectionDialog* dialog = new QmitkSemanticRelationsNodeSelectionDialog(this, "Select image to segment lesion on.", ""); dialog->setWindowTitle("Select image node"); dialog->SetDataStorage(dataStorage); dialog->SetNodePredicate(mitk::NodePredicates::GetImagePredicate()); dialog->SetSelectOnlyVisibleNodes(true); dialog->SetCaseID(m_CaseID); dialog->SetLesion(selectedLesion); int dialogReturnValue = dialog->exec(); if (QDialog::Rejected == dialogReturnValue) { return; } auto nodes = dialog->GetSelectedNodes(); mitk::DataNode::Pointer selectedDataNode = nullptr; if (!nodes.isEmpty()) { // only single selection allowed selectedDataNode = nodes.front(); } if (nullptr == selectedDataNode || false == mitk::NodePredicates::GetImagePredicate()->CheckNode(selectedDataNode)) { QMessageBox msgBox(QMessageBox::Warning, "No valid image node selected.", "In order to create a new segmentation, please specify a valid image node."); msgBox.exec(); return; } mitk::Image* selectedImage = dynamic_cast(selectedDataNode->GetData()); if (nullptr == selectedImage) { QMessageBox msgBox(QMessageBox::Warning, "No valid image.", "In order to create a new segmentation, please specify a valid image node."); msgBox.exec(); return; } mitk::LabelSetImage::Pointer segmentation = mitk::LabelSetImage::New(); try { segmentation->Initialize(selectedImage); } catch (mitk::Exception& e) { std::stringstream exceptionMessage; exceptionMessage << e; QMessageBox msgBox(QMessageBox::Warning, "Could not initialize segmentation.", "The segmentation could not be correctly initialized with the selected image geometry.\n" "Reason:\n" + QString::fromStdString(exceptionMessage.str())); msgBox.exec(); return; } auto segmentationDialog = new QmitkNewSegmentationDialog(this); segmentationDialog->setWindowTitle("New lesion segmentation"); dialogReturnValue = segmentationDialog->exec(); if (dialogReturnValue == QDialog::Rejected) { return; } - QString segmentatioName = segmentationDialog->GetSegmentationName(); + QString segmentatioName = segmentationDialog->GetName(); if (segmentatioName.isEmpty()) { segmentatioName = "Unnamed"; } segmentation->GetActiveLabelSet()->AddLabel(segmentatioName.toStdString(), segmentationDialog->GetColor()); mitk::DataNode::Pointer segmentationNode = mitk::DataNode::New(); segmentationNode->SetData(segmentation); segmentationNode->SetName(segmentatioName.toStdString()); dataStorage->Add(segmentationNode, selectedDataNode); LinkSegmentationToLesion(segmentationNode, selectedLesion); } void QmitkLesionInfoWidget::OnRemoveLesion(mitk::SemanticTypes::Lesion selectedLesion) { try { m_SemanticRelationsIntegration->RemoveLesion(m_CaseID, selectedLesion); } catch (const mitk::SemanticRelationException& e) { std::stringstream exceptionMessage; exceptionMessage << e; QMessageBox msgBox(QMessageBox::Warning, "Could not remove the selected lesion.", "The program wasn't able to correctly remove the selected lesion from the semantic relations model.\n" "Reason:\n" + QString::fromStdString(exceptionMessage.str())); msgBox.exec(); } } void QmitkLesionInfoWidget::LinkSegmentationToLesion(const mitk::DataNode* selectedDataNode, mitk::SemanticTypes::Lesion selectedLesion) { auto dataStorage = m_DataStorage.Lock(); if (dataStorage.IsNull()) { return; } // if the segmentation is not contained in the semantic relations, add it if (!mitk::SemanticRelationsInference::InstanceExists(selectedDataNode)) { try { AddToSemanticRelationsAction::Run(dataStorage, selectedDataNode); } catch (const mitk::SemanticRelationException& e) { std::stringstream exceptionMessage; exceptionMessage << e; QMessageBox msgBox(QMessageBox::Warning, "Could not link the selected lesion.", "The program wasn't able to correctly link the selected lesion with the selected segmentation.\n" "Reason:\n" + QString::fromStdString(exceptionMessage.str() + "\n")); msgBox.exec(); } } // link the segmentation try { m_SemanticRelationsIntegration->LinkSegmentationToLesion(selectedDataNode, selectedLesion); } catch (const mitk::SemanticRelationException& e) { std::stringstream exceptionMessage; exceptionMessage << e; QMessageBox msgBox(QMessageBox::Warning, "Could not link the selected lesion.", "The program wasn't able to correctly link the selected lesion with the selected segmentation.\n" "Reason:\n" + QString::fromStdString(exceptionMessage.str())); msgBox.exec(); } }