diff --git a/Applications/CoreApp/icons/CoreApp.rc b/Applications/CoreApp/icons/CoreApp.rc new file mode 100644 index 0000000000..bb10963fb3 --- /dev/null +++ b/Applications/CoreApp/icons/CoreApp.rc @@ -0,0 +1 @@ +IDI_ICON1 ICON DISCARDABLE "icon.ico" \ No newline at end of file diff --git a/Applications/CoreApp/icons/icon.icns b/Applications/CoreApp/icons/icon.icns new file mode 100644 index 0000000000..5afc942282 Binary files /dev/null and b/Applications/CoreApp/icons/icon.icns differ diff --git a/Applications/CoreApp/icons/icon.ico b/Applications/CoreApp/icons/icon.ico new file mode 100644 index 0000000000..27d4c9d1b9 Binary files /dev/null and b/Applications/CoreApp/icons/icon.ico differ diff --git a/Applications/CoreApp/icons/icon.png b/Applications/CoreApp/icons/icon.png new file mode 100644 index 0000000000..857e61aef3 Binary files /dev/null and b/Applications/CoreApp/icons/icon.png differ diff --git a/Applications/ExtApp/icons/ExtApp.rc b/Applications/ExtApp/icons/ExtApp.rc new file mode 100644 index 0000000000..bb10963fb3 --- /dev/null +++ b/Applications/ExtApp/icons/ExtApp.rc @@ -0,0 +1 @@ +IDI_ICON1 ICON DISCARDABLE "icon.ico" \ No newline at end of file diff --git a/Applications/ExtApp/icons/icon.icns b/Applications/ExtApp/icons/icon.icns new file mode 100644 index 0000000000..5afc942282 Binary files /dev/null and b/Applications/ExtApp/icons/icon.icns differ diff --git a/Applications/ExtApp/icons/icon.ico b/Applications/ExtApp/icons/icon.ico new file mode 100644 index 0000000000..27d4c9d1b9 Binary files /dev/null and b/Applications/ExtApp/icons/icon.ico differ diff --git a/Applications/ExtApp/icons/icon.png b/Applications/ExtApp/icons/icon.png new file mode 100644 index 0000000000..857e61aef3 Binary files /dev/null and b/Applications/ExtApp/icons/icon.png differ diff --git a/Applications/mitkDiffusion/CMakeLists.txt b/Applications/mitkDiffusion/CMakeLists.txt index 4a0a2467a4..8e414314ab 100644 --- a/Applications/mitkDiffusion/CMakeLists.txt +++ b/Applications/mitkDiffusion/CMakeLists.txt @@ -1,77 +1,74 @@ project(mitkDiffusion) set(DIFFUSIONAPP_NAME mitkDiffusion) set(_app_options) if(MITK_SHOW_CONSOLE_WINDOW) list(APPEND _app_options SHOW_CONSOLE) endif() MITK_USE_MODULE(qtsingleapplication) include_directories(${ALL_INCLUDE_DIRECTORIES}) # Create a cache entry for the provisioning file which is used to export # the file name in the MITKConfig.cmake file. This will keep external projects # which rely on this file happy. set(DIFFUSIONIMAGINGAPP_PROVISIONING_FILE "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${DIFFUSIONAPP_NAME}.provisioning" CACHE INTERNAL "${DIFFUSIONAPP_NAME} provisioning file" FORCE) set(_plugins org.commontk.configadmin org.commontk.eventadmin org.blueberry.osgi org.blueberry.compat org.blueberry.core.runtime org.blueberry.core.expressions org.blueberry.solstice.common org.blueberry.core.commands - org.blueberry.core.jobs org.blueberry.ui org.blueberry.ui.qt org.blueberry.ui.qt.help - org.blueberry.ui.qt.log - org.blueberry.ui.qt.objectinspector org.mitk.core.services org.mitk.gui.common org.mitk.planarfigure org.mitk.core.ext org.mitk.diffusionimaging org.mitk.gui.qt.application org.mitk.gui.qt.ext org.mitk.gui.qt.diffusionimagingapp org.mitk.gui.qt.common org.mitk.gui.qt.stdmultiwidgeteditor org.mitk.gui.qt.common.legacy org.mitk.gui.qt.datamanager org.mitk.gui.qt.measurementtoolbox org.mitk.gui.qt.segmentation org.mitk.gui.qt.volumevisualization org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.imagenavigator org.mitk.gui.qt.moviemaker ) # Plug-ins listed below will not be # - added as a build-time dependency to the executable # - listed in the provisioning file for the executable # - installed if they are external plug-ins set(_exclude_plugins org.blueberry.test org.blueberry.uitest org.mitk.gui.qt.coreapplication org.mitk.gui.qt.extapplication ) FunctionCreateBlueBerryApplication( NAME ${DIFFUSIONAPP_NAME} DESCRIPTION "MITK Diffusion" PLUGINS ${_plugins} EXCLUDE_PLUGINS ${_exclude_plugins} LINK_LIBRARIES ${ALL_LIBRARIES} ${_app_options} ) # Add a build time dependency to legacy BlueBerry bundles. if(MITK_MODULES_ENABLED_PLUGINS) add_dependencies(${DIFFUSIONAPP_NAME} ${MITK_MODULES_ENABLED_PLUGINS}) endif() \ No newline at end of file diff --git a/Applications/mitkDiffusion/icons/icon.icns b/Applications/mitkDiffusion/icons/icon.icns new file mode 100644 index 0000000000..a113602951 Binary files /dev/null and b/Applications/mitkDiffusion/icons/icon.icns differ diff --git a/Applications/mitkDiffusion/icons/icon.ico b/Applications/mitkDiffusion/icons/icon.ico new file mode 100644 index 0000000000..77a2f03ee8 Binary files /dev/null and b/Applications/mitkDiffusion/icons/icon.ico differ diff --git a/Applications/mitkDiffusion/icons/icon.png b/Applications/mitkDiffusion/icons/icon.png new file mode 100644 index 0000000000..48a79b5bfc Binary files /dev/null and b/Applications/mitkDiffusion/icons/icon.png differ diff --git a/Applications/mitkDiffusion/icons/mitkDiffusion.rc b/Applications/mitkDiffusion/icons/mitkDiffusion.rc new file mode 100644 index 0000000000..bb10963fb3 --- /dev/null +++ b/Applications/mitkDiffusion/icons/mitkDiffusion.rc @@ -0,0 +1 @@ +IDI_ICON1 ICON DISCARDABLE "icon.ico" \ No newline at end of file diff --git a/BlueBerry/Bundles/org.blueberry.ui.qt.help/src/internal/berryHelpWebView.cpp b/BlueBerry/Bundles/org.blueberry.ui.qt.help/src/internal/berryHelpWebView.cpp index 93925c4e44..b8d7995cbf 100644 --- a/BlueBerry/Bundles/org.blueberry.ui.qt.help/src/internal/berryHelpWebView.cpp +++ b/BlueBerry/Bundles/org.blueberry.ui.qt.help/src/internal/berryHelpWebView.cpp @@ -1,520 +1,528 @@ /*========================================================================= Program: BlueBerry Platform Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "berryHelpWebView.h" #include "berryHelpPluginActivator.h" #include "berryHelpEditor.h" #include "berryHelpEditorInput.h" #include "berryQHelpEngineWrapper.h" #include #include #include #include #include #include #include #include #include #include #include namespace berry { struct ExtensionMap { const char *extension; const char *mimeType; } extensionMap[] = { { ".bmp", "image/bmp" }, { ".css", "text/css" }, { ".gif", "image/gif" }, { ".html", "text/html" }, { ".htm", "text/html" }, { ".ico", "image/x-icon" }, { ".jpeg", "image/jpeg" }, { ".jpg", "image/jpeg" }, { ".js", "application/x-javascript" }, { ".mng", "video/x-mng" }, { ".pbm", "image/x-portable-bitmap" }, { ".pgm", "image/x-portable-graymap" }, { ".pdf", "application/pdf" }, { ".png", "image/png" }, { ".ppm", "image/x-portable-pixmap" }, { ".rss", "application/rss+xml" }, { ".svg", "image/svg+xml" }, { ".svgz", "image/svg+xml" }, { ".text", "text/plain" }, { ".tif", "image/tiff" }, { ".tiff", "image/tiff" }, { ".txt", "text/plain" }, { ".xbm", "image/x-xbitmap" }, { ".xml", "text/xml" }, { ".xpm", "image/x-xpm" }, { ".xsl", "text/xsl" }, { ".xhtml", "application/xhtml+xml" }, { ".wml", "text/vnd.wap.wml" }, { ".wmlc", "application/vnd.wap.wmlc" }, { "about:blank", 0 }, { 0, 0 } }; const QString HelpWebView::m_PageNotFoundMessage = QCoreApplication::translate("org.blueberry.ui.qt.help", "Error 404...


The page could not be found


'%1'" "

"); class HelpNetworkReply : public QNetworkReply { public: HelpNetworkReply(const QNetworkRequest &request, const QByteArray &fileData, const QString &mimeType); virtual void abort(); virtual qint64 bytesAvailable() const { return data.length() + QNetworkReply::bytesAvailable(); } protected: virtual qint64 readData(char *data, qint64 maxlen); private: QByteArray data; qint64 origLen; }; HelpNetworkReply::HelpNetworkReply(const QNetworkRequest &request, const QByteArray &fileData, const QString& mimeType) : data(fileData), origLen(fileData.length()) { setRequest(request); setOpenMode(QIODevice::ReadOnly); setHeader(QNetworkRequest::ContentTypeHeader, mimeType); setHeader(QNetworkRequest::ContentLengthHeader, QByteArray::number(origLen)); QTimer::singleShot(0, this, SIGNAL(metaDataChanged())); QTimer::singleShot(0, this, SIGNAL(readyRead())); } void HelpNetworkReply::abort() { } qint64 HelpNetworkReply::readData(char *buffer, qint64 maxlen) { qint64 len = qMin(qint64(data.length()), maxlen); if (len) { memcpy(buffer, data.constData(), len); data.remove(0, len); } if (!data.length()) QTimer::singleShot(0, this, SIGNAL(finished())); return len; } class HelpNetworkAccessManager : public QNetworkAccessManager { public: HelpNetworkAccessManager(QObject *parent); protected: virtual QNetworkReply *createRequest(Operation op, const QNetworkRequest &request, QIODevice *outgoingData = 0); }; HelpNetworkAccessManager::HelpNetworkAccessManager(QObject *parent) : QNetworkAccessManager(parent) { } QNetworkReply *HelpNetworkAccessManager::createRequest(Operation /*op*/, const QNetworkRequest &request, QIODevice* /*outgoingData*/) { QString url = request.url().toString(); QHelpEngine& helpEngine = HelpPluginActivator::getInstance()->getQHelpEngine(); // TODO: For some reason the url to load is already wrong (passed from webkit) // though the css file and the references inside should work that way. One // possible problem might be that the css is loaded at the same level as the // html, thus a path inside the css like (../images/foo.png) might cd out of // the virtual folder // if (!helpEngine.findFile(url).isValid()) { // if (url.startsWith(AbstractHelpWebView::DocPath)) { // QUrl newUrl = request.url(); // if (!newUrl.path().startsWith(QLatin1String("/qdoc/"))) { // newUrl.setPath(QLatin1String("qdoc") + newUrl.path()); // url = newUrl.toString(); // } // } // } const QString &mimeType = HelpWebView::mimeFromUrl(url); const QByteArray &data = helpEngine.findFile(url).isValid() ? helpEngine.fileData(url) : HelpWebView::m_PageNotFoundMessage.arg(url).toUtf8(); return new HelpNetworkReply(request, data, mimeType.isEmpty() ? QLatin1String("application/octet-stream") : mimeType); } class HelpPage : public QWebPage { public: HelpPage(IEditorSite::Pointer editorSite, QObject *parent); protected: virtual QWebPage *createWindow(QWebPage::WebWindowType); virtual void triggerAction(WebAction action, bool checked = false); virtual bool acceptNavigationRequest(QWebFrame *frame, const QNetworkRequest &request, NavigationType type); private: IEditorSite::Pointer m_EditorSite; bool m_CloseNewTabIfNeeded; friend class HelpWebView; QUrl m_loadingUrl; Qt::MouseButtons m_pressedButtons; Qt::KeyboardModifiers m_keyboardModifiers; }; HelpPage::HelpPage(IEditorSite::Pointer editorSite, QObject *parent) : QWebPage(parent) , m_EditorSite(editorSite) , m_CloseNewTabIfNeeded(false) , m_pressedButtons(Qt::NoButton) , m_keyboardModifiers(Qt::NoModifier) { } QWebPage *HelpPage::createWindow(QWebPage::WebWindowType type) { IEditorInput::Pointer input(new HelpEditorInput(QUrl())); IEditorPart::Pointer editorPart = m_EditorSite->GetPage()->OpenEditor(input, HelpEditor::EDITOR_ID); HelpEditor::Pointer helpEditor = editorPart.Cast(); HelpPage* newPage = static_cast(helpEditor->GetQWebPage()); if (newPage) newPage->m_CloseNewTabIfNeeded = m_CloseNewTabIfNeeded; m_CloseNewTabIfNeeded = false; return newPage; } void HelpPage::triggerAction(WebAction action, bool checked) { switch (action) { case OpenLinkInNewWindow: m_CloseNewTabIfNeeded = true; default: // fall through QWebPage::triggerAction(action, checked); break; } } bool HelpPage::acceptNavigationRequest(QWebFrame *, const QNetworkRequest &request, QWebPage::NavigationType type) { const bool closeNewTab = m_CloseNewTabIfNeeded; m_CloseNewTabIfNeeded = false; + // open in an external browser if a http link + const QUrl &url = request.url(); + if (url.scheme() == QLatin1String("http")) + { + QDesktopServices::openUrl(url); + return false; + } + // const QUrl &url = request.url(); // if (AbstractHelpWebView::launchWithExternalApp(url)) // { // if (closeNewTab) // QMetaObject::invokeMethod(centralWidget, "closeTab"); // return false; // } // if (type == QWebPage::NavigationTypeLinkClicked // && (m_keyboardModifiers & Qt::ControlModifier // || m_pressedButtons == Qt::MidButton)) // { // if (centralWidget->newEmptyTab()) // centralWidget->setSource(url); // m_pressedButtons = Qt::NoButton; // m_keyboardModifiers = Qt::NoModifier; // return false; // } // m_loadingUrl = url; // because of async page loading, we will hit some kind // of race condition while using a remote command, like a combination of // SetSource; SyncContent. SetSource would be called and SyncContents shortly // afterwards, but the page might not have finished loading and the old url // would be returned. return true; } // -- HelpWebView HelpWebView::HelpWebView(IEditorSite::Pointer editorSite, QWidget *parent, qreal zoom) : QWebView(parent) //, parentWidget(parent) , m_LoadFinished(false) , m_HelpEngine(HelpPluginActivator::getInstance()->getQHelpEngine()) { setAcceptDrops(false); setPage(new HelpPage(editorSite, parent)); page()->setNetworkAccessManager(new HelpNetworkAccessManager(this)); QAction* action = pageAction(QWebPage::OpenLinkInNewWindow); action->setText(tr("Open Link in New Tab")); if (!parent) action->setVisible(false); pageAction(QWebPage::DownloadLinkToDisk)->setVisible(false); pageAction(QWebPage::DownloadImageToDisk)->setVisible(false); pageAction(QWebPage::OpenImageInNewWindow)->setVisible(false); connect(pageAction(QWebPage::Copy), SIGNAL(changed()), this, SLOT(actionChanged())); connect(pageAction(QWebPage::Back), SIGNAL(changed()), this, SLOT(actionChanged())); connect(pageAction(QWebPage::Forward), SIGNAL(changed()), this, SLOT(actionChanged())); connect(page(), SIGNAL(linkHovered(QString,QString,QString)), this, SIGNAL(highlighted(QString))); connect(this, SIGNAL(urlChanged(QUrl)), this, SIGNAL(sourceChanged(QUrl))); connect(this, SIGNAL(loadStarted()), this, SLOT(setLoadStarted())); connect(this, SIGNAL(loadFinished(bool)), this, SLOT(setLoadFinished(bool))); connect(page(), SIGNAL(printRequested(QWebFrame*)), this, SIGNAL(printRequested())); setFont(viewerFont()); setTextSizeMultiplier(zoom == 0.0 ? 1.0 : zoom); } HelpWebView::~HelpWebView() { } QFont HelpWebView::viewerFont() const { //if (m_HelpEngine.usesBrowserFont()) // return m_HelpEngine.browserFont(); QWebSettings *webSettings = QWebSettings::globalSettings(); return QFont(webSettings->fontFamily(QWebSettings::StandardFont), webSettings->fontSize(QWebSettings::DefaultFontSize)); } void HelpWebView::setViewerFont(const QFont &font) { QWebSettings *webSettings = settings(); webSettings->setFontFamily(QWebSettings::StandardFont, font.family()); webSettings->setFontSize(QWebSettings::DefaultFontSize, font.pointSize()); } void HelpWebView::scaleUp() { setTextSizeMultiplier(textSizeMultiplier() + 0.1); } void HelpWebView::scaleDown() { setTextSizeMultiplier(qMax(0.0, textSizeMultiplier() - 0.1)); } void HelpWebView::resetScale() { setTextSizeMultiplier(1.0); } bool HelpWebView::handleForwardBackwardMouseButtons(QMouseEvent *e) { if (e->button() == Qt::XButton1) { triggerPageAction(QWebPage::Back); return true; } if (e->button() == Qt::XButton2) { triggerPageAction(QWebPage::Forward); return true; } return false; } QUrl HelpWebView::source() const { HelpPage *currentPage = static_cast (page()); if (currentPage && !hasLoadFinished()) { // see HelpPage::acceptNavigationRequest(...) return currentPage->m_loadingUrl; } return url(); } void HelpWebView::setSource(const QUrl &url) { if (m_HelpEngine.findFile(url).isValid()) load(url); else setHtml(m_PageNotFoundMessage.arg(url.toString())); } void HelpWebView::wheelEvent(QWheelEvent *e) { if (e->modifiers()& Qt::ControlModifier) { e->accept(); e->delta() > 0 ? scaleUp() : scaleDown(); } else { QWebView::wheelEvent(e); } } void HelpWebView::mouseReleaseEvent(QMouseEvent *e) { #ifndef Q_OS_LINUX if (handleForwardBackwardMouseButtons(e)) return; #endif QWebView::mouseReleaseEvent(e); } void HelpWebView::actionChanged() { QAction *a = qobject_cast(sender()); if (a == pageAction(QWebPage::Copy)) emit copyAvailable(a->isEnabled()); else if (a == pageAction(QWebPage::Back)) emit backwardAvailable(a->isEnabled()); else if (a == pageAction(QWebPage::Forward)) emit forwardAvailable(a->isEnabled()); } void HelpWebView::mousePressEvent(QMouseEvent *event) { #ifdef Q_OS_LINUX if (handleForwardBackwardMouseButtons(event)) return; #endif HelpPage *currentPage = static_cast(page()); if (currentPage) { currentPage->m_pressedButtons = event->buttons(); currentPage->m_keyboardModifiers = event->modifiers(); } QWebView::mousePressEvent(event); } void HelpWebView::setLoadStarted() { m_LoadFinished = false; } void HelpWebView::setLoadFinished(bool ok) { m_LoadFinished = ok; emit sourceChanged(url()); } QString HelpWebView::mimeFromUrl(const QUrl &url) { const QString &path = url.path(); const int index = path.lastIndexOf(QLatin1Char('.')); const QByteArray &ext = path.mid(index).toUtf8().toLower(); const ExtensionMap *e = extensionMap; while (e->extension) { if (ext == e->extension) return QLatin1String(e->mimeType); ++e; } return QLatin1String(""); } bool HelpWebView::canOpenPage(const QString &url) { return !mimeFromUrl(url).isEmpty(); } bool HelpWebView::isLocalUrl(const QUrl &url) { const QString &scheme = url.scheme(); return scheme.isEmpty() || scheme == QLatin1String("file") || scheme == QLatin1String("qrc") || scheme == QLatin1String("data") || scheme == QLatin1String("qthelp") || scheme == QLatin1String("about"); } bool HelpWebView::launchWithExternalApp(const QUrl &url) { if (isLocalUrl(url)) { const QHelpEngine& helpEngine = HelpPluginActivator::getInstance()->getQHelpEngine(); const QUrl &resolvedUrl = helpEngine.findFile(url); if (!resolvedUrl.isValid()) return false; const QString& path = resolvedUrl.path(); if (!canOpenPage(path)) { QTemporaryFile tmpTmpFile; if (!tmpTmpFile.open()) return false; const QString &extension = QFileInfo(path).completeSuffix(); QFile actualTmpFile(tmpTmpFile.fileName() % QLatin1String(".") % extension); if (!actualTmpFile.open(QIODevice::ReadWrite | QIODevice::Truncate)) return false; actualTmpFile.write(helpEngine.fileData(resolvedUrl)); actualTmpFile.close(); return QDesktopServices::openUrl(QUrl(actualTmpFile.fileName())); } } else if (url.scheme() == QLatin1String("http")) { return QDesktopServices::openUrl(url); } return false; } void HelpWebView::home() { setSource(m_HelpEngine.homePage()); } } diff --git a/BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake b/BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake index 8759656417..a906a89e8a 100644 --- a/BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake +++ b/BlueBerry/CMake/FunctionCreateBlueBerryApplication.cmake @@ -1,167 +1,188 @@ #! #! Create a BlueBerry application. #! #! \brif This function will create a BlueBerry application together with all #! necessary provisioning and configuration data and install support. #! #! \param NAME (required) The name of the executable. #! \param DESCRIPTION (optional) A human-readable description of your application. #! The usage depends on the CPack generator (on Windows, this is a descriptive #! text for the created shortcuts). #! \param SOURCES (optional) A list of source files to compile into your executable. Defaults #! to .cpp. #! \param PLUGINS (optional) A list of required plug-ins. Defaults to all known plug-ins. #! \param EXCLUDE_PLUGINS (optional) A list of plug-ins which should not be used. Mainly #! useful if PLUGINS was not used. #! \param LINK_LIBRARIES A list of libraries to be linked with the executable. #! \param SHOW_CONSOLE (option) Show the console output window (on Windows). #! \param NO_PROVISIONING (option) Do not create provisioning files. #! #! Assuming that there exists a file called MyApp.cpp, an example call looks like: #! \code #! FunctionCreateBlueBerryApplication( #! NAME MyApp #! DESCRIPTION "MyApp - New ways to explore medical data" #! EXCLUDE_PLUGINS org.mitk.gui.qt.extapplication #! SHOW_CONSOLE #! ) #! \endcode #! function(FunctionCreateBlueBerryApplication) macro_parse_arguments(_APP "NAME;DESCRIPTION;SOURCES;PLUGINS;EXCLUDE_PLUGINS;LINK_LIBRARIES" "SHOW_CONSOLE;NO_PROVISIONING" ${ARGN}) if(NOT _APP_NAME) message(FATAL_ERROR "NAME argument cannot be empty.") endif() if(NOT _APP_SOURCES) set(_APP_SOURCES ${_APP_NAME}.cpp) endif() if(NOT _APP_PLUGINS) ctkFunctionGetAllPluginTargets(_APP_PLUGINS) else() set(_plugins ${_APP_PLUGINS}) set(_APP_PLUGINS) foreach(_plugin ${_plugins}) string(REPLACE "." "_" _plugin_target ${_plugin}) list(APPEND _APP_PLUGINS ${_plugin_target}) endforeach() # get all plug-in dependencies ctkFunctionGetPluginDependencies(_plugin_deps PLUGINS ${_APP_PLUGINS} ALL) # add the dependencies to the list of application plug-ins list(APPEND _APP_PLUGINS ${_plugin_deps}) endif() #------------------------------------------------------------------------ # Prerequesites #------------------------------------------------------------------------ find_package(MITK REQUIRED) # ----------------------------------------------------------------------- # Set up include and link dirs for the executable # ----------------------------------------------------------------------- include(${QT_USE_FILE}) include_directories( ${org_blueberry_osgi_INCLUDE_DIRS} ${Poco_INCLUDE_DIRS} ${mbilog_INCLUDE_DIRS} ) link_directories(${MITK_LINK_DIRECTORIES}) +# ----------------------------------------------------------------------- +# Add executable icon (Windows) +# ----------------------------------------------------------------------- +set(WINDOWS_ICON_RESOURCE_FILE "") +if(WIN32) + if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/icons/${_APP_NAME}.rc") + set(WINDOWS_ICON_RESOURCE_FILE "${CMAKE_CURRENT_SOURCE_DIR}/icons/${_APP_NAME}.rc") + endif() +endif() + # ----------------------------------------------------------------------- # Create the executable and link libraries # ----------------------------------------------------------------------- if(_APP_SHOW_CONSOLE) - add_executable(${_APP_NAME} MACOSX_BUNDLE ${_APP_SOURCES}) + add_executable(${_APP_NAME} MACOSX_BUNDLE ${_APP_SOURCES} ${WINDOWS_ICON_RESOURCE_FILE}) else() - add_executable(${_APP_NAME} MACOSX_BUNDLE WIN32 ${_APP_SOURCES}) + add_executable(${_APP_NAME} MACOSX_BUNDLE WIN32 ${_APP_SOURCES} ${WINDOWS_ICON_RESOURCE_FILE}) endif() target_link_libraries(${_APP_NAME} org_blueberry_osgi ${_APP_LINK_LIBRARIES}) if(WIN32) target_link_libraries(${_APP_NAME} ${QT_QTCORE_LIBRARY} ${QT_QTMAIN_LIBRARY}) endif() +# ----------------------------------------------------------------------- +# Add executable icon (Mac) +# ----------------------------------------------------------------------- +if(APPLE) + if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/icons/icon.icns") + set_target_properties(${_APP_NAME} PROPERTIES MACOSX_BUNDLE_ICON_FILE "${CMAKE_CURRENT_SOURCE_DIR}/icons/icon.icns") + file(COPY ${MACOSX_BUNDLE_ICON_FILE} DESTINATION "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${_APP_NAME}.app/Contents/Resources/") + file(INSTALL ${MACOSX_BUNDLE_ICON_FILE} DESTINATION "${_APP_NAME}.app/Contents/Resources/") + endif() +endif() + # ----------------------------------------------------------------------- # Set build time dependencies # ----------------------------------------------------------------------- # This ensures that all enabled plug-ins are up-to-date when the # executable is build. if(_APP_PLUGINS) ctkMacroGetAllProjectTargetLibraries("${_APP_PLUGINS}" _project_plugins) if(_APP_EXCLUDE_PLUGINS) set(_exclude_targets) foreach(_exclude_plugin ${_APP_EXCLUDE_PLUGINS}) string(REPLACE "." "_" _exclude_target ${_exclude_plugin}) list(APPEND _exclude_targets ${_exclude_target}) endforeach() list(REMOVE_ITEM _project_plugins ${_exclude_targets}) endif() if(_project_plugins) add_dependencies(${_APP_NAME} ${_project_plugins}) endif() endif() # ----------------------------------------------------------------------- # Additional files needed for the executable # ----------------------------------------------------------------------- if(NOT _APP_NO_PROVISIONING) # Create a provisioning file, listing all plug-ins set(_prov_file "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${_APP_NAME}.provisioning") FunctionCreateProvisioningFile(FILE ${_prov_file} PLUGINS ${_APP_PLUGINS} EXCLUDE_PLUGINS ${_APP_EXCLUDE_PLUGINS} ) endif() # Create a .ini file for initial parameters if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${_APP_NAME}.ini") configure_file(${_APP_NAME}.ini ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${_APP_NAME}.ini) endif() # Create batch files for Windows platforms if(WIN32) foreach(BUILD_TYPE debug release) mitkFunctionCreateWindowsBatchScript(start${_APP_NAME}.bat.in ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/start${_APP_NAME}_${BUILD_TYPE}.bat ${BUILD_TYPE}) endforeach() endif(WIN32) # ----------------------------------------------------------------------- # Install support # ----------------------------------------------------------------------- # This installs all third-party CTK plug-ins FunctionInstallThirdPartyCTKPlugins(${_APP_PLUGINS} EXCLUDE ${_APP_EXCLUDE_PLUGINS}) # Install the executable MITK_INSTALL_TARGETS(EXECUTABLES ${_APP_NAME} GLOB_PLUGINS ) if(NOT _APP_NO_PROVISIONING) # Install the provisioning file mitkFunctionInstallProvisioningFiles(${_prov_file}) endif() # On Linux, create a shell script to start a relocatable application if(UNIX AND NOT APPLE) install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME ${_APP_NAME}.sh) endif() # Tell cpack the executables that you want in the start menu as links set(MITK_CPACK_PACKAGE_EXECUTABLES ${MITK_CPACK_PACKAGE_EXECUTABLES} "${_APP_NAME};${_APP_DESCRIPTION}" CACHE INTERNAL "Collecting windows shortcuts to executables") endfunction() diff --git a/CMake/RunInstalledApp.sh b/CMake/RunInstalledApp.sh index 36f721e68f..b859e80340 100644 --- a/CMake/RunInstalledApp.sh +++ b/CMake/RunInstalledApp.sh @@ -1,6 +1,6 @@ #!/bin/sh -binpath=$(dirname "$(readlink -f $0)") -appname=$(basename $0 .sh) +binpath=$(dirname "$(readlink -f "$0")") +appname=$(basename "$0" .sh) export LD_LIBRARY_PATH="$binpath/bin":"$binpath/bin/plugins":$LD_LIBRARY_PATH cd "$binpath/bin" ./$appname $* diff --git a/CMakeExternals/CTK.cmake b/CMakeExternals/CTK.cmake index 66f047558c..2c4faee1de 100644 --- a/CMakeExternals/CTK.cmake +++ b/CMakeExternals/CTK.cmake @@ -1,67 +1,79 @@ #----------------------------------------------------------------------------- # CTK #----------------------------------------------------------------------------- if(MITK_USE_CTK) # Sanity checks if(DEFINED CTK_DIR AND NOT EXISTS ${CTK_DIR}) message(FATAL_ERROR "CTK_DIR variable is defined but corresponds to non-existing directory") endif() set(proj CTK) set(proj_DEPENDENCIES ) set(CTK_DEPENDS ${proj}) if(NOT DEFINED CTK_DIR) - set(revision_tag 6925794b) - #if(${proj}_REVISION_TAG) - # set(revision_tag ${${proj}_REVISION_TAG}) - #endif() + set(revision_tag 70c0a8d3) + #IF(${proj}_REVISION_TAG) + # SET(revision_tag ${${proj}_REVISION_TAG}) + #ENDIF() set(ctk_optional_cache_args ) if(MITK_USE_Python) list(APPEND ctk_optional_cache_args -DCTK_LIB_Scripting/Python/Widgets:BOOL=ON ) endif() - foreach(type RUNTIME ARCHIVE LIBRARY) - if(DEFINED CTK_PLUGIN_${type}_OUTPUT_DIRECTORY) - list(APPEND mitk_optional_cache_args -DCTK_PLUGIN_${type}_OUTPUT_DIRECTORY:PATH=${CTK_PLUGIN_${type}_OUTPUT_DIRECTORY}) - endif() - endforeach() + + if(MITK_USE_DCMTK) + list(APPEND ctk_optional_cache_args + -DDCMTK_DIR:PATH=${DCMTK_DIR} + ) + list(APPEND proj_DEPENDENCIES DCMTK) + else() + list(APPEND ctk_optional_cache_args + -DDCMTK_URL:STRING=${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/CTK_DCMTK_085525e6.tar.gz + ) + endif() + + FOREACH(type RUNTIME ARCHIVE LIBRARY) + IF(DEFINED CTK_PLUGIN_${type}_OUTPUT_DIRECTORY) + LIST(APPEND mitk_optional_cache_args -DCTK_PLUGIN_${type}_OUTPUT_DIRECTORY:PATH=${CTK_PLUGIN_${type}_OUTPUT_DIRECTORY}) + ENDIF() + ENDFOREACH() ExternalProject_Add(${proj} SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}-src BINARY_DIR ${proj}-build PREFIX ${proj}-cmake URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/CTK_${revision_tag}.tar.gz - URL_MD5 43430cee2dfec2519cbe33cbfebc3eaf + URL_MD5 a3130b2c3e7a1d320740938f61b65840 UPDATE_COMMAND "" INSTALL_COMMAND "" CMAKE_GENERATOR ${gen} CMAKE_ARGS ${ep_common_args} ${ctk_optional_cache_args} -DDESIRED_QT_VERSION:STRING=4 -DQT_QMAKE_EXECUTABLE:FILEPATH=${QT_QMAKE_EXECUTABLE} -DGit_EXECUTABLE:FILEPATH=${GIT_EXECUTABLE} -DGIT_EXECUTABLE:FILEPATH=${GIT_EXECUTABLE} -DCTK_LIB_PluginFramework:BOOL=ON -DCTK_LIB_DICOM/Widgets:BOOL=ON -DCTK_PLUGIN_org.commontk.eventadmin:BOOL=ON -DCTK_PLUGIN_org.commontk.configadmin:BOOL=ON -DCTK_USE_GIT_PROTOCOL:BOOL=OFF -DDCMTK_URL:STRING=${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/CTK_DCMTK_085525e6.tar.gz DEPENDS ${proj_DEPENDENCIES} ) set(CTK_DIR ${CMAKE_CURRENT_BINARY_DIR}/${proj}-build) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif() endif() diff --git a/CMakeExternals/DCMTK.cmake b/CMakeExternals/DCMTK.cmake index 7673a2066e..79661aa4c2 100644 --- a/CMakeExternals/DCMTK.cmake +++ b/CMakeExternals/DCMTK.cmake @@ -1,56 +1,56 @@ #----------------------------------------------------------------------------- # DCMTK #----------------------------------------------------------------------------- if(MITK_USE_DCMTK) # Sanity checks if(DEFINED DCMTK_DIR AND NOT EXISTS ${DCMTK_DIR}) message(FATAL_ERROR "DCMTK_DIR variable is defined but corresponds to non-existing directory") endif() set(proj DCMTK) set(proj_DEPENDENCIES ) set(DCMTK_DEPENDS ${proj}) if(NOT DEFINED DCMTK_DIR) if(UNIX) set(DCMTK_CXX_FLAGS "-fPIC") set(DCMTK_C_FLAGS "-fPIC") endif(UNIX) if(DCMTK_DICOM_ROOT_ID) set(DCMTK_CXX_FLAGS "${DCMTK_CXX_FLAGS} -DSITE_UID_ROOT=\\\"${DCMTK_DICOM_ROOT_ID}\\\"") set(DCMTK_C_FLAGS "${DCMTK_CXX_FLAGS} -DSITE_UID_ROOT=\\\"${DCMTK_DICOM_ROOT_ID}\\\"") endif() ExternalProject_Add(${proj} SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}-src BINARY_DIR ${proj}-build PREFIX ${proj}-cmake - URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/dcmtk-3.6.0.tar.gz - URL_MD5 19409e039e29a330893caea98715390e + URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/dcmtk-3.6.1_20120222.tar.gz + URL_MD5 86fa9e0f91e4e0c6b44d513ea48391d6 INSTALL_DIR ${proj}-install - PATCH_COMMAND ${CMAKE_COMMAND} -DTEMPLATE_FILE:FILEPATH=${MITK_SOURCE_DIR}/CMakeExternals/EmptyFileForPatching.dummy -P ${MITK_SOURCE_DIR}/CMakeExternals/PatchDCMTK-3.6.cmake CMAKE_GENERATOR ${gen} CMAKE_ARGS ${ep_common_args} -DDCMTK_OVERWRITE_WIN32_COMPILER_FLAGS:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=OFF "-DCMAKE_CXX_FLAGS:STRING=${ep_common_CXX_FLAGS} ${DCMTK_CXX_FLAGS}" "-DCMAKE_C_FLAGS:STRING=${ep_common_C_FLAGS} ${DCMTK_C_FLAGS}" -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_BINARY_DIR}/${proj}-install + -DDCMTK_WITH_DOXYGEN:BOOL=OFF -DDCMTK_WITH_ZLIB:BOOL=OFF # see bug #9894 -DDCMTK_WITH_OPENSSL:BOOL=OFF # see bug #9894 -DDCMTK_WITH_PNG:BOOL=OFF # see bug #9894 -DDCMTK_WITH_TIFF:BOOL=OFF # see bug #9894 -DDCMTK_WITH_XML:BOOL=OFF # see bug #9894 -DDCMTK_FORCE_FPIC_ON_UNIX:BOOL=ON DEPENDS ${proj_DEPENDENCIES} ) set(DCMTK_DIR ${CMAKE_CURRENT_BINARY_DIR}/${proj}-install) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif() endif() diff --git a/CMakeExternals/OpenCV.cmake b/CMakeExternals/OpenCV.cmake index 3ac3824748..3b9251b052 100644 --- a/CMakeExternals/OpenCV.cmake +++ b/CMakeExternals/OpenCV.cmake @@ -1,54 +1,63 @@ #----------------------------------------------------------------------------- # OpenCV #----------------------------------------------------------------------------- if(MITK_USE_OpenCV) # Sanity checks if(DEFINED OpenCV_DIR AND NOT EXISTS ${OpenCV_DIR}) message(FATAL_ERROR "OpenCV_DIR variable is defined but corresponds to non-existing directory") endif() set(proj OpenCV) set(proj_DEPENDENCIES) set(OpenCV_DEPENDS ${proj}) if(NOT DEFINED OpenCV_DIR) set(additional_cmake_args ) if(MITK_USE_Python) list(APPEND additional_cmake_args -DBUILD_NEW_PYTHON_SUPPORT:BOOL=ON ) endif() + + # 12-05-02, muellerm, added QT usage by OpenCV if QT is used in MITK + if(MITK_USE_QT) + list(APPEND additional_cmake_args + -DWITH_QT:BOOL=ON + -DWITH_QT_OPENGL:BOOL=OFF + -DQT_QMAKE_EXECUTABLE:FILEPATH=${QT_QMAKE_EXECUTABLE} + ) + endif() set(opencv_url ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/OpenCV-2.3.0.tar.bz2) set(opencv_url_md5 4e353dfb04b53bea37407f397aabf069) ExternalProject_Add(${proj} SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}-src BINARY_DIR ${proj}-build PREFIX ${proj}-cmake URL ${opencv_url} URL_MD5 ${opencv_url_md5} INSTALL_COMMAND "" CMAKE_GENERATOR ${gen} CMAKE_ARGS ${ep_common_args} -DBUILD_DOCS:BOOL=OFF -DBUILD_TESTS:BOOL=OFF -DBUILD_EXAMPLES:BOOL=OFF -DBUILD_DOXYGEN_DOCS:BOOL=OFF ${additional_cmake_args} DEPENDS ${proj_DEPENDENCIES} ) set(OpenCV_DIR ${CMAKE_CURRENT_BINARY_DIR}/${proj}-build) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif() endif() diff --git a/CMakeExternals/PatchDCMTK-3.6.cmake b/CMakeExternals/PatchDCMTK-3.6.cmake deleted file mode 100644 index 775251978f..0000000000 --- a/CMakeExternals/PatchDCMTK-3.6.cmake +++ /dev/null @@ -1,15 +0,0 @@ -# Called by DCMTK.cmake (ExternalProject_Add) as a patch for DCMTK. -# Makes pdf2dcm use "DOC" as modality for Encapsulated PDFs - -#message("Patching dcmdata/apps/pdf2dcm.cc to use modality 'DOC'. Using template ${TEMPLATE_FILE}") - -# read whole file -file(STRINGS dcmdata/apps/pdf2dcm.cc sourceCode NEWLINE_CONSUME) - -# substitute "OT" for "DOC" (only single occurence where modality tag is set) -string(REGEX REPLACE "\"OT\"" "\"DOC\"" sourceCode ${sourceCode}) - -# set variable CONTENTS, which is substituted in TEMPLATE_FILE -set(CONTENTS ${sourceCode}) -configure_file(${TEMPLATE_FILE} dcmdata/apps/pdf2dcm.cc @ONLY) - diff --git a/CMakeExternals/PatchITK-3.20.cmake b/CMakeExternals/PatchITK-3.20.cmake index e0359a2c60..7dd459d922 100644 --- a/CMakeExternals/PatchITK-3.20.cmake +++ b/CMakeExternals/PatchITK-3.20.cmake @@ -1,25 +1,36 @@ # Called by ITK.cmake (ExternalProject_Add) as a patch for ITK to work witk GDCM 2.0.18 # First patch # updates library dependencies # read whole file CMakeLists.txt file(STRINGS CMakeLists.txt sourceCode NEWLINE_CONSUME) # substitute dependency to gdcmMSFF by dependencies for more libraries string(REGEX REPLACE "gdcmMSFF" "gdcmMSFF gdcmDICT gdcmCommon gdcmDSED" sourceCode ${sourceCode}) # set variable CONTENTS, which is substituted in TEMPLATE_FILE set(CONTENTS ${sourceCode}) configure_file(${TEMPLATE_FILE} CMakeLists.txt @ONLY) # second patch # read whole file file(STRINGS Code/Common/itkLandmarkBasedTransformInitializer.h sourceCode2 NEWLINE_CONSUME) -# substitute dependency to gdcmMSFF by dependencies for more libraries +# backported fix from ITK4 string(REGEX REPLACE "typedef typename ParametersType::ValueType +ParameterValueType;" "typedef typename TransformType::ScalarType ParameterValueType;" sourceCode2 ${sourceCode2}) # set variable CONTENTS, which is substituted in TEMPLATE_FILE set(CONTENTS ${sourceCode2}) configure_file(${TEMPLATE_FILE} Code/Common/itkLandmarkBasedTransformInitializer.h @ONLY) +# third patch +# read whole file +file(STRINGS Code/Common/itkImageSource.h sourceCode3 NEWLINE_CONSUME) + +# remove ITK_NO_RETURN since the method sometimes returns which makes clang based builds crash +string(REGEX REPLACE "ITK_NO_RETURN" "" sourceCode3 ${sourceCode3}) + +# set variable CONTENTS, which is substituted in TEMPLATE_FILE +set(CONTENTS ${sourceCode3}) +configure_file(${TEMPLATE_FILE} Code/Common/itkImageSource.h @ONLY) + diff --git a/CMakeExternals/VTK.cmake b/CMakeExternals/VTK.cmake index 0853cf384f..3f905d67b3 100644 --- a/CMakeExternals/VTK.cmake +++ b/CMakeExternals/VTK.cmake @@ -1,87 +1,93 @@ #----------------------------------------------------------------------------- # VTK #----------------------------------------------------------------------------- if(WIN32) option(VTK_USE_SYSTEM_FREETYPE OFF) else(WIN32) option(VTK_USE_SYSTEM_FREETYPE ON) endif(WIN32) # Sanity checks if(DEFINED VTK_DIR AND NOT EXISTS ${VTK_DIR}) message(FATAL_ERROR "VTK_DIR variable is defined but corresponds to non-existing directory") endif() set(proj VTK) set(proj_DEPENDENCIES ) set(VTK_DEPENDS ${proj}) if(NOT DEFINED VTK_DIR) set(additional_cmake_args ) if(MINGW) set(additional_cmake_args -DCMAKE_USE_WIN32_THREADS:BOOL=ON -DCMAKE_USE_PTHREADS:BOOL=OFF -DVTK_USE_VIDEO4WINDOWS:BOOL=OFF # no header files provided by MinGW ) endif() if(MITK_USE_Python) list(APPEND additional_cmake_args -DVTK_WRAP_PYTHON:BOOL=ON -DVTK_USE_TK:BOOL=OFF -DVTK_WINDOWS_PYTHON_DEBUGGABLE:BOOL=OFF ) endif() if(MITK_USE_QT) list(APPEND additional_cmake_args -DDESIRED_QT_VERSION:STRING=4 -DVTK_USE_GUISUPPORT:BOOL=ON -DVTK_USE_QVTK_QTOPENGL:BOOL=ON -DVTK_USE_QT:BOOL=ON -DQT_QMAKE_EXECUTABLE:FILEPATH=${QT_QMAKE_EXECUTABLE} ) endif() option(MITK_USE_VTK_5_8_IN_SUPERBUILD OFF) + if(CMAKE_CXX_COMPILER MATCHES clang) + if(NOT MITK_USE_VTK_5_8_IN_SUPERBUILD) + MESSAGE(STATUS "Forcing VTK 5.8 since we're using clang") + endif() + SET(MITK_USE_VTK_5_8_IN_SUPERBUILD ON CACHE BOOL "Use VTK 5.8 in MITK superbuild" FORCE) + endif() if(MITK_USE_VTK_5_8_IN_SUPERBUILD) set(VTK_URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/vtk-5.8.0.tar.gz) set(VTK_URL_MD5 37b7297d02d647cc6ca95b38174cb41f) else() set(VTK_URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/vtk-5.6.1.tar.gz) set(VTK_URL_MD5 b80a76435207c5d0f74dfcab15b75181) endif() ExternalProject_Add(${proj} SOURCE_DIR ${CMAKE_BINARY_DIR}/${proj}-src BINARY_DIR ${proj}-build PREFIX ${proj}-cmake URL ${VTK_URL} URL_MD5 ${VTK_URL_MD5} INSTALL_COMMAND "" CMAKE_GENERATOR ${gen} CMAKE_ARGS ${ep_common_args} -DVTK_WRAP_TCL:BOOL=OFF -DVTK_WRAP_PYTHON:BOOL=OFF -DVTK_WRAP_JAVA:BOOL=OFF -DBUILD_SHARED_LIBS:BOOL=ON -DVTK_USE_PARALLEL:BOOL=ON -DVTK_USE_CHARTS:BOOL=OFF -DVTK_USE_QTCHARTS:BOOL=ON -DVTK_USE_GEOVIS:BOOL=OFF -DVTK_USE_SYSTEM_FREETYPE:BOOL=${VTK_USE_SYSTEM_FREETYPE} -DVTK_USE_QVTK_QTOPENGL:BOOL=OFF ${additional_cmake_args} DEPENDS ${proj_DEPENDENCIES} ) set(VTK_DIR ${CMAKE_CURRENT_BINARY_DIR}/${proj}-build) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif() diff --git a/CMakeLists.txt b/CMakeLists.txt index 9a384b8aec..2b2529e3ee 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,867 +1,885 @@ -cmake_minimum_required(VERSION 2.8.4) +if(APPLE) + # With XCode 4.3, the SDK location changed. Older CMake + # versions are not able to find it. + cmake_minimum_required(VERSION 2.8.8) +else() + cmake_minimum_required(VERSION 2.8.4) +endif() #----------------------------------------------------------------------------- # Set a default build type if none was specified #----------------------------------------------------------------------------- if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES) message(STATUS "Setting build type to 'Debug' as none was specified.") set(CMAKE_BUILD_TYPE Debug CACHE STRING "Choose the type of build." FORCE) # Set the possible values of build type for cmake-gui set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo") endif() #----------------------------------------------------------------------------- # Superbuild Option - Enabled by default #----------------------------------------------------------------------------- option(MITK_USE_SUPERBUILD "Build MITK and the projects it depends on via SuperBuild.cmake." ON) if(MITK_USE_SUPERBUILD) project(MITK-superbuild) set(MITK_SOURCE_DIR ${PROJECT_SOURCE_DIR}) set(MITK_BINARY_DIR ${PROJECT_BINARY_DIR}) else() project(MITK) endif() #----------------------------------------------------------------------------- # Warn if source or build path is too long #----------------------------------------------------------------------------- if(WIN32) set(_src_dir_length_max 50) set(_bin_dir_length_max 50) if(MITK_USE_SUPERBUILD) set(_src_dir_length_max 43) # _src_dir_length_max - strlen(ITK-src) set(_bin_dir_length_max 40) # _bin_dir_length_max - strlen(MITK-build) endif() string(LENGTH "${MITK_SOURCE_DIR}" _src_n) string(LENGTH "${MITK_BINARY_DIR}" _bin_n) # The warnings should be converted to errors if(_src_n GREATER _src_dir_length_max) message(WARNING "MITK source code directory path length is too long (${_src_n} > ${_src_dir_length_max})." "Please move the MITK source code directory to a directory with a shorter path." ) endif() if(_bin_n GREATER _bin_dir_length_max) message(WARNING "MITK build directory path length is too long (${_bin_n} > ${_bin_dir_length_max})." "Please move the MITK build directory to a directory with a shorter path." ) endif() endif() #----------------------------------------------------------------------------- # See http://cmake.org/cmake/help/cmake-2-8-docs.html#section_Policies for details #----------------------------------------------------------------------------- set(project_policies CMP0001 # NEW: CMAKE_BACKWARDS_COMPATIBILITY should no longer be used. CMP0002 # NEW: Logical target names must be globally unique. CMP0003 # NEW: Libraries linked via full path no longer produce linker search paths. CMP0004 # NEW: Libraries linked may NOT have leading or trailing whitespace. CMP0005 # NEW: Preprocessor definition values are now escaped automatically. CMP0006 # NEW: Installing MACOSX_BUNDLE targets requires a BUNDLE DESTINATION. CMP0007 # NEW: List command no longer ignores empty elements. CMP0008 # NEW: Libraries linked by full-path must have a valid library file name. CMP0009 # NEW: FILE GLOB_RECURSE calls should not follow symlinks by default. CMP0010 # NEW: Bad variable reference syntax is an error. CMP0011 # NEW: Included scripts do automatic cmake_policy PUSH and POP. CMP0012 # NEW: if() recognizes numbers and boolean constants. CMP0013 # NEW: Duplicate binary directories are not allowed. CMP0014 # NEW: Input directories must have CMakeLists.txt ) foreach(policy ${project_policies}) if(POLICY ${policy}) cmake_policy(SET ${policy} NEW) endif() endforeach() #----------------------------------------------------------------------------- # Update CMake module path #------------------------------------------------------------------------------ set(CMAKE_MODULE_PATH ${MITK_SOURCE_DIR}/CMake ${CMAKE_MODULE_PATH} ) #----------------------------------------------------------------------------- # CMake function(s) and macro(s) #----------------------------------------------------------------------------- include(mitkMacroEmptyExternalProject) include(mitkFunctionGenerateProjectXml) include(mitkFunctionSuppressWarnings) SUPPRESS_VC_DEPRECATED_WARNINGS() #----------------------------------------------------------------------------- # Output directories. #----------------------------------------------------------------------------- foreach(type LIBRARY RUNTIME ARCHIVE) # Make sure the directory exists if(DEFINED MITK_CMAKE_${type}_OUTPUT_DIRECTORY AND NOT EXISTS ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}) message("Creating directory MITK_CMAKE_${type}_OUTPUT_DIRECTORY: ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}") file(MAKE_DIRECTORY "${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}") endif() if(MITK_USE_SUPERBUILD) set(output_dir ${MITK_BINARY_DIR}/bin) if(NOT DEFINED MITK_CMAKE_${type}_OUTPUT_DIRECTORY) set(MITK_CMAKE_${type}_OUTPUT_DIRECTORY ${MITK_BINARY_DIR}/MITK-build/bin) endif() else() if(NOT DEFINED MITK_CMAKE_${type}_OUTPUT_DIRECTORY) set(output_dir ${MITK_BINARY_DIR}/bin) else() set(output_dir ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}) endif() endif() set(CMAKE_${type}_OUTPUT_DIRECTORY ${output_dir} CACHE INTERNAL "Single output directory for building all libraries.") mark_as_advanced(CMAKE_${type}_OUTPUT_DIRECTORY) endforeach() #----------------------------------------------------------------------------- # Additional MITK Options (also shown during superbuild) #----------------------------------------------------------------------------- option(BUILD_SHARED_LIBS "Build MITK with shared libraries" ON) option(WITH_COVERAGE "Enable/Disable coverage" OFF) option(BUILD_TESTING "Test the project" ON) option(MITK_BUILD_ALL_APPS "Build all MITK applications" OFF) option(MITK_BUILD_TUTORIAL "Build the MITK tutorial" ON) option(MITK_USE_Boost "Use the Boost C++ library" OFF) option(MITK_USE_BLUEBERRY "Build the BlueBerry platform" ON) option(MITK_USE_CTK "Use CTK in MITK" ${MITK_USE_BLUEBERRY}) option(MITK_USE_QT "Use Nokia's Qt library" ${MITK_USE_CTK}) -option(MITK_USE_DCMTK "EXEPERIMENTAL, superbuild only: Use DCMTK in MITK" OFF) +option(MITK_USE_DCMTK "EXEPERIMENTAL, superbuild only: Use DCMTK in MITK" ${MITK_USE_CTK}) option(MITK_USE_OpenCV "Use Intel's OpenCV library" OFF) option(MITK_USE_Python "Use Python wrapping in MITK" OFF) set(MITK_USE_CableSwig ${MITK_USE_Python}) mark_as_advanced(MITK_BUILD_ALL_APPS MITK_USE_CTK MITK_USE_DCMTK ) if(MITK_USE_Boost) option(MITK_USE_SYSTEM_Boost "Use the system Boost" OFF) set(MITK_USE_Boost_LIBRARIES "" CACHE STRING "A semi-colon separated list of required Boost libraries") endif() if(MITK_USE_BLUEBERRY) option(MITK_BUILD_ALL_PLUGINS "Build all MITK plugins" OFF) mark_as_advanced(MITK_BUILD_ALL_PLUGINS) if(NOT MITK_USE_CTK) message("Forcing MITK_USE_CTK to ON because of MITK_USE_BLUEBERRY") set(MITK_USE_CTK ON CACHE BOOL "Use CTK in MITK" FORCE) endif() endif() -if(MITK_USE_CTK AND NOT MITK_USE_QT) - message("Forcing MITK_USE_QT to ON because of MITK_USE_CTK") - set(MITK_USE_QT ON CACHE BOOL "Use Nokia's Qt library in MITK" FORCE) +if(MITK_USE_CTK) + if(NOT MITK_USE_QT) + message("Forcing MITK_USE_QT to ON because of MITK_USE_CTK") + set(MITK_USE_QT ON CACHE BOOL "Use Nokia's Qt library in MITK" FORCE) + endif() + if(NOT MITK_USE_DCMTK) + message("Setting MITK_USE_DCMTK to ON because DCMTK needs to be build for CTK") + set(MITK_USE_DCMTK ON CACHE BOOL "Use DCMTK in MITK" FORCE) + endif() endif() if(MITK_USE_QT) # find the package at the very beginning, so that QT4_FOUND is available find_package(Qt4 4.6.2 REQUIRED) endif() # Customize the default pixel types for multiplex macros set(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES "int, unsigned int, short, unsigned short, char, unsigned char" CACHE STRING "List of integral pixel types used in AccessByItk and InstantiateAccessFunction macros") set(MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES "double, float" CACHE STRING "List of floating pixel types used in AccessByItk and InstantiateAccessFunction macros") set(MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES "" CACHE STRING "List of composite pixel types used in AccessByItk and InstantiateAccessFunction macros") set(MITK_ACCESSBYITK_DIMENSIONS "2,3" CACHE STRING "List of dimensions used in AccessByItk and InstantiateAccessFunction macros") mark_as_advanced(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES MITK_ACCESSBYITK_DIMENSIONS ) # consistency checks if(NOT MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES) set(MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES "int, unsigned int, short, unsigned short, char, unsigned char" CACHE STRING "List of integral pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE) endif() if(NOT MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES) set(MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES "double, float" CACHE STRING "List of floating pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE) endif() if(NOT MITK_ACCESSBYITK_DIMENSIONS) set(MITK_ACCESSBYITK_DIMENSIONS "2,3" CACHE STRING "List of dimensions used in AccessByItk and InstantiateAccessFunction macros") endif() #----------------------------------------------------------------------------- # Additional CXX/C Flags #----------------------------------------------------------------------------- set(ADDITIONAL_C_FLAGS "" CACHE STRING "Additional C Flags") mark_as_advanced(ADDITIONAL_C_FLAGS) set(ADDITIONAL_CXX_FLAGS "" CACHE STRING "Additional CXX Flags") mark_as_advanced(ADDITIONAL_CXX_FLAGS) #----------------------------------------------------------------------------- # Project.xml #----------------------------------------------------------------------------- # A list of topologically ordered targets set(CTEST_PROJECT_SUBPROJECTS) if(MITK_USE_BLUEBERRY) list(APPEND CTEST_PROJECT_SUBPROJECTS BlueBerry) endif() list(APPEND CTEST_PROJECT_SUBPROJECTS MITK-Core MITK-CoreUI MITK-IGT MITK-ToF MITK-DTI MITK-Registration MITK-Modules # all modules not contained in a specific subproject MITK-Plugins # all plugins not contained in a specific subproject Unlabeled # special "subproject" catching all unlabeled targets and tests ) # Configure CTestConfigSubProject.cmake that could be used by CTest scripts configure_file(${MITK_SOURCE_DIR}/CTestConfigSubProject.cmake.in ${MITK_BINARY_DIR}/CTestConfigSubProject.cmake) if(CTEST_PROJECT_ADDITIONAL_TARGETS) # those targets will be executed at the end of the ctest driver script # and they also get their own subproject label set(subproject_list "${CTEST_PROJECT_SUBPROJECTS};${CTEST_PROJECT_ADDITIONAL_TARGETS}") else() set(subproject_list "${CTEST_PROJECT_SUBPROJECTS}") endif() # Generate Project.xml file expected by the CTest driver script mitkFunctionGenerateProjectXml(${MITK_BINARY_DIR} MITK "${subproject_list}" ${MITK_USE_SUPERBUILD}) #----------------------------------------------------------------------------- # Superbuild script #----------------------------------------------------------------------------- if(MITK_USE_SUPERBUILD) include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake") return() endif() #***************************************************************************** #**************************** END OF SUPERBUILD **************************** #***************************************************************************** #----------------------------------------------------------------------------- # CMake function(s) and macro(s) #----------------------------------------------------------------------------- include(CheckCXXSourceCompiles) include(mitkFunctionCheckCompilerFlags) include(mitkFunctionGetGccVersion) include(MacroParseArguments) include(mitkFunctionSuppressWarnings) # includes several functions include(mitkFunctionOrganizeSources) include(mitkFunctionGetVersion) include(mitkFunctionCreateWindowsBatchScript) include(mitkFunctionInstallProvisioningFiles) include(mitkFunctionCompileSnippets) include(mitkMacroCreateModuleConf) include(mitkMacroCreateModule) include(mitkMacroCheckModule) include(mitkMacroCreateModuleTests) include(mitkFunctionAddCustomModuleTest) include(mitkMacroUseModule) include(mitkMacroMultiplexPicType) include(mitkMacroInstall) include(mitkMacroInstallHelperApp) include(mitkMacroInstallTargets) include(mitkMacroGenerateToolsLibrary) include(mitkMacroGetLinuxDistribution) #----------------------------------------------------------------------------- # Prerequesites #----------------------------------------------------------------------------- find_package(ITK REQUIRED) find_package(VTK REQUIRED) if(ITK_USE_SYSTEM_GDCM) find_package(GDCM PATHS ${ITK_GDCM_DIR} REQUIRED) endif() #----------------------------------------------------------------------------- # Set MITK specific options and variables (NOT available during superbuild) #----------------------------------------------------------------------------- # ASK THE USER TO SHOW THE CONSOLE WINDOW FOR CoreApp and ExtApp option(MITK_SHOW_CONSOLE_WINDOW "Use this to enable or disable the console window when starting MITK GUI Applications" ON) mark_as_advanced(MITK_SHOW_CONSOLE_WINDOW) # TODO: check if necessary option(USE_ITKZLIB "Use the ITK zlib for pic compression." ON) mark_as_advanced(USE_ITKZLIB) if(NOT MITK_FAST_TESTING) if(DEFINED MITK_CTEST_SCRIPT_MODE AND (MITK_CTEST_SCRIPT_MODE STREQUAL "continuous" OR MITK_CTEST_SCRIPT_MODE STREQUAL "experimental") ) set(MITK_FAST_TESTING 1) endif() endif() #----------------------------------------------------------------------------- # Get MITK version info #----------------------------------------------------------------------------- mitkFunctionGetVersion(${MITK_SOURCE_DIR} MITK) #----------------------------------------------------------------------------- # Installation preparation # # These should be set before any MITK install macros are used #----------------------------------------------------------------------------- # on Mac OSX all BlueBerry plugins get copied into every # application bundle (.app directory) specified here -if(APPLE) - if(MITK_BUILD_org.mitk.gui.qt.extapplication) - set(MACOSX_BUNDLE_NAMES ${MACOSX_BUNDLE_NAMES} ExtApp) - endif() - if(MITK_BUILD_org.mitk.gui.qt.application) - set(MACOSX_BUNDLE_NAMES ${MACOSX_BUNDLE_NAMES} CoreApp) - endif() - if(MITK_BUILD_org.mitk.gui.qt.diffusionimagingapp) - set(MACOSX_BUNDLE_NAMES ${MACOSX_BUNDLE_NAMES} mitkDiffusion) - endif() -endif(APPLE) +if(MITK_USE_BLUEBERRY AND APPLE) + + include("${CMAKE_CURRENT_SOURCE_DIR}/Applications/AppList.cmake") + + foreach(mitk_app ${MITK_APPS}) + # extract option_name + string(REPLACE "^^" "\\;" target_info ${mitk_app}) + set(target_info_list ${target_info}) + list(GET target_info_list 1 option_name) + list(GET target_info_list 0 app_name) + # check if the application is enabled + if(${option_name}) + set(MACOSX_BUNDLE_NAMES ${MACOSX_BUNDLE_NAMES} ${app_name}) + endif() + endforeach() + +endif() #----------------------------------------------------------------------------- # Set symbol visibility Flags #----------------------------------------------------------------------------- # MinGW does not export all symbols automatically, so no need to set flags if(CMAKE_COMPILER_IS_GNUCXX AND NOT MINGW) set(VISIBILITY_CXX_FLAGS ) #"-fvisibility=hidden -fvisibility-inlines-hidden") endif() #----------------------------------------------------------------------------- # Set coverage Flags #----------------------------------------------------------------------------- if(WITH_COVERAGE) if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU") set(coverage_flags "-g -fprofile-arcs -ftest-coverage -O0 -DNDEBUG") set(COVERAGE_CXX_FLAGS ${coverage_flags}) set(COVERAGE_C_FLAGS ${coverage_flags}) endif() endif() #----------------------------------------------------------------------------- # MITK C/CXX Flags #----------------------------------------------------------------------------- set(MITK_C_FLAGS "${COVERAGE_C_FLAGS} ${ADDITIONAL_C_FLAGS}") set(MITK_CXX_FLAGS "${VISIBILITY_CXX_FLAGS} ${COVERAGE_CXX_FLAGS} ${ADDITIONAL_CXX_FLAGS}") include(mitkSetupC++0xVariables) set(cflags ) if(WIN32) set(cflags "${cflags} -DPOCO_NO_UNWINDOWS -DWIN32_LEAN_AND_MEAN") endif() if(CMAKE_COMPILER_IS_GNUCXX) set(cflags "${cflags} -Wall -Wextra -Wpointer-arith -Winvalid-pch -Wcast-align -Wwrite-strings -D_FORTIFY_SOURCE=2") mitkFunctionCheckCompilerFlags("-fdiagnostics-show-option" cflags) mitkFunctionCheckCompilerFlags("-Wl,--no-undefined" cflags) mitkFunctionCheckCompilerFlags("-Wl,--as-needed" cflags) if(MITK_USE_C++0x) mitkFunctionCheckCompilerFlags("-std=c++0x" MITK_CXX_FLAGS) endif() mitkFunctionGetGccVersion(${CMAKE_CXX_COMPILER} GCC_VERSION) # With older version of gcc supporting the flag -fstack-protector-all, an extra dependency to libssp.so # is introduced. If gcc is smaller than 4.4.0 and the build type is Release let's not include the flag. # Doing so should allow to build package made for distribution using older linux distro. if(${GCC_VERSION} VERSION_GREATER "4.4.0" OR (CMAKE_BUILD_TYPE STREQUAL "Debug" AND ${GCC_VERSION} VERSION_LESS "4.4.0")) mitkFunctionCheckCompilerFlags("-fstack-protector-all" cflags) endif() if(MINGW) # suppress warnings about auto imported symbols set(MITK_CXX_FLAGS "-Wl,--enable-auto-import ${MITK_CXX_FLAGS}") # we need to define a Windows version set(MITK_CXX_FLAGS "-D_WIN32_WINNT=0x0500 ${MITK_CXX_FLAGS}") endif() #set(MITK_CXX_FLAGS "-Woverloaded-virtual -Wold-style-cast -Wstrict-null-sentinel -Wsign-promo ${MITK_CXX_FLAGS}") set(MITK_CXX_FLAGS "-Woverloaded-virtual -Wstrict-null-sentinel ${MITK_CXX_FLAGS}") endif() set(MITK_C_FLAGS "${cflags} ${MITK_C_FLAGS}") set(MITK_CXX_FLAGS "${cflags} ${MITK_CXX_FLAGS}") #----------------------------------------------------------------------------- # MITK Packages #----------------------------------------------------------------------------- set(MITK_MODULES_PACKAGE_DEPENDS_DIR ${MITK_SOURCE_DIR}/CMake/PackageDepends) set(MODULES_PACKAGE_DEPENDS_DIRS ${MITK_MODULES_PACKAGE_DEPENDS_DIR}) #----------------------------------------------------------------------------- # Testing #----------------------------------------------------------------------------- if(BUILD_TESTING) enable_testing() include(CTest) mark_as_advanced(TCL_TCLSH DART_ROOT) option(MITK_ENABLE_GUI_TESTING OFF "Enable the MITK GUI tests") # Setup file for setting custom ctest vars configure_file( CMake/CTestCustom.cmake.in ${MITK_BINARY_DIR}/CTestCustom.cmake @ONLY ) # Configuration for the CMake-generated test driver set(CMAKE_TESTDRIVER_EXTRA_INCLUDES "#include ") set(CMAKE_TESTDRIVER_BEFORE_TESTMAIN " try {") set(CMAKE_TESTDRIVER_AFTER_TESTMAIN " } catch( std::exception & excp ) { fprintf(stderr,\"%s\\n\",excp.what()); return EXIT_FAILURE; } catch( ... ) { printf(\"Exception caught in the test driver\\n\"); return EXIT_FAILURE; } ") set(MITK_TEST_OUTPUT_DIR "${MITK_BINARY_DIR}/test_output") if(NOT EXISTS ${MITK_TEST_OUTPUT_DIR}) file(MAKE_DIRECTORY ${MITK_TEST_OUTPUT_DIR}) endif() # Test the external project template if(MITK_USE_BLUEBERRY) include(mitkTestProjectTemplate) endif() # Test the package target include(mitkPackageTest) endif() configure_file(mitkTestingConfig.h.in ${MITK_BINARY_DIR}/mitkTestingConfig.h) #----------------------------------------------------------------------------- # MITK_SUPERBUILD_BINARY_DIR #----------------------------------------------------------------------------- # If MITK_SUPERBUILD_BINARY_DIR isn't defined, it means MITK is *NOT* build using Superbuild. # In that specific case, MITK_SUPERBUILD_BINARY_DIR should default to MITK_BINARY_DIR if(NOT DEFINED MITK_SUPERBUILD_BINARY_DIR) set(MITK_SUPERBUILD_BINARY_DIR ${MITK_BINARY_DIR}) endif() #----------------------------------------------------------------------------- # Compile Utilities and set-up MITK variables #----------------------------------------------------------------------------- include(mitkSetupVariables) #----------------------------------------------------------------------------- # Cleanup #----------------------------------------------------------------------------- file(GLOB _MODULES_CONF_FILES ${PROJECT_BINARY_DIR}/${MODULES_CONF_DIRNAME}/*.cmake) if(_MODULES_CONF_FILES) file(REMOVE ${_MODULES_CONF_FILES}) endif() add_subdirectory(Utilities) if(MITK_USE_BLUEBERRY) # We need to hack a little bit because MITK applications may need # to enable certain BlueBerry plug-ins. However, these plug-ins # are validated separately from the MITK plug-ins and know nothing # about potential MITK plug-in dependencies of the applications. Hence # we cannot pass the MITK application list to the BlueBerry # ctkMacroSetupPlugins call but need to extract the BlueBerry dependencies # from the applications and set them explicitly. include("${CMAKE_CURRENT_SOURCE_DIR}/Applications/AppList.cmake") foreach(mitk_app ${MITK_APPS}) # extract target_dir and option_name string(REPLACE "^^" "\\;" target_info ${mitk_app}) set(target_info_list ${target_info}) list(GET target_info_list 0 target_dir) list(GET target_info_list 1 option_name) # check if the application is enabled and if target_libraries.cmake exists if(${option_name} AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/Applications/${target_dir}/target_libraries.cmake") include("${CMAKE_CURRENT_SOURCE_DIR}/Applications/${target_dir}/target_libraries.cmake") foreach(_target_dep ${target_libraries}) if(_target_dep MATCHES org_blueberry_) string(REPLACE _ . _app_bb_dep ${_target_dep}) # explicitly set the build option for the BlueBerry plug-in set(BLUEBERRY_BUILD_${_app_bb_dep} ON CACHE BOOL "Build the ${_app_bb_dep} plug-in") endif() endforeach() endif() endforeach() set(mbilog_DIR "${mbilog_BINARY_DIR}") if(MITK_BUILD_ALL_PLUGINS) set(BLUEBERRY_BUILD_ALL_PLUGINS ON) endif() add_subdirectory(BlueBerry) set(BlueBerry_DIR ${CMAKE_CURRENT_BINARY_DIR}/BlueBerry CACHE PATH "The directory containing a CMake configuration file for BlueBerry" FORCE) include(mitkMacroCreateCTKPlugin) endif() #----------------------------------------------------------------------------- # Set C/CXX Flags for MITK code #----------------------------------------------------------------------------- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MITK_CXX_FLAGS}") set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${MITK_C_FLAGS}") if(MITK_USE_QT) add_definitions(-DQWT_DLL) endif() #----------------------------------------------------------------------------- # Add custom targets representing CDash subprojects #----------------------------------------------------------------------------- foreach(subproject ${CTEST_PROJECT_SUBPROJECTS}) if(NOT TARGET ${subproject} AND NOT subproject MATCHES "Unlabeled") add_custom_target(${subproject}) endif() endforeach() #----------------------------------------------------------------------------- # Add subdirectories #----------------------------------------------------------------------------- link_directories(${MITK_LINK_DIRECTORIES}) add_subdirectory(Core) add_subdirectory(Modules) if(MITK_USE_BLUEBERRY) find_package(BlueBerry REQUIRED) set(MITK_DEFAULT_SUBPROJECTS MITK-Plugins) # Plug-in testing (needs some work to be enabled again) if(BUILD_TESTING) include(berryTestingHelpers) set(BLUEBERRY_UI_TEST_APP "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/CoreApp") get_target_property(_is_macosx_bundle CoreApp MACOSX_BUNDLE) if(APPLE AND _is_macosx_bundle) set(BLUEBERRY_UI_TEST_APP "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/CoreApp.app/Contents/MacOS/CoreApp") endif() set(BLUEBERRY_TEST_APP_ID "org.mitk.qt.coreapplication") endif() include("${CMAKE_CURRENT_SOURCE_DIR}/Plugins/PluginList.cmake") set(mitk_plugins_fullpath ) foreach(mitk_plugin ${MITK_EXT_PLUGINS}) list(APPEND mitk_plugins_fullpath Plugins/${mitk_plugin}) endforeach() if(EXISTS ${MITK_PRIVATE_MODULES}/PluginList.cmake) include(${MITK_PRIVATE_MODULES}/PluginList.cmake) foreach(mitk_plugin ${MITK_PRIVATE_PLUGINS}) list(APPEND mitk_plugins_fullpath ${MITK_PRIVATE_MODULES}/${mitk_plugin}) endforeach() endif() # Specify which plug-ins belong to this project macro(GetMyTargetLibraries all_target_libraries varname) set(re_ctkplugin_mitk "^org_mitk_[a-zA-Z0-9_]+$") set(re_ctkplugin_bb "^org_blueberry_[a-zA-Z0-9_]+$") set(_tmp_list) list(APPEND _tmp_list ${all_target_libraries}) ctkMacroListFilter(_tmp_list re_ctkplugin_mitk re_ctkplugin_bb OUTPUT_VARIABLE ${varname}) endmacro() # Get infos about application directories and build options include("${CMAKE_CURRENT_SOURCE_DIR}/Applications/AppList.cmake") set(mitk_apps_fullpath ) foreach(mitk_app ${MITK_APPS}) list(APPEND mitk_apps_fullpath "${CMAKE_CURRENT_SOURCE_DIR}/Applications/${mitk_app}") endforeach() ctkMacroSetupPlugins(${mitk_plugins_fullpath} BUILD_OPTION_PREFIX MITK_BUILD_ APPS ${mitk_apps_fullpath} BUILD_ALL ${MITK_BUILD_ALL_PLUGINS} COMPACT_OPTIONS) set(MITK_PLUGIN_USE_FILE "${MITK_BINARY_DIR}/MitkPluginUseFile.cmake") if(${PROJECT_NAME}_PLUGIN_LIBRARIES) ctkFunctionGeneratePluginUseFile(${MITK_PLUGIN_USE_FILE}) else() file(REMOVE ${MITK_PLUGIN_USE_FILE}) set(MITK_PLUGIN_USE_FILE ) endif() endif() # Construct a list of paths containing runtime directories # for MITK applications on Windows set(MITK_RUNTIME_PATH "${VTK_LIBRARY_DIRS}/%VS_BUILD_TYPE%;${ITK_LIBRARY_DIRS}/%VS_BUILD_TYPE%;${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/%VS_BUILD_TYPE%" ) if(QT4_FOUND) set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${QT_LIBRARY_DIR}/../bin") endif() if(MITK_USE_BLUEBERRY) set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${CTK_RUNTIME_LIBRARY_DIRS}/%VS_BUILD_TYPE%") if(DEFINED CTK_PLUGIN_RUNTIME_OUTPUT_DIRECTORY) if(IS_ABSOLUTE "${CTK_PLUGIN_RUNTIME_OUTPUT_DIRECTORY}") set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${CTK_PLUGIN_RUNTIME_OUTPUT_DIRECTORY}/%VS_BUILD_TYPE%") else() set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${CTK_PLUGIN_RUNTIME_OUTPUT_DIRECTORY}/%VS_BUILD_TYPE%") endif() else() set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/plugins/%VS_BUILD_TYPE%") endif() endif() if(GDCM_DIR) set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${GDCM_DIR}/bin/%VS_BUILD_TYPE%") endif() if(OpenCV_DIR) set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${OpenCV_DIR}/bin/%VS_BUILD_TYPE%") endif() # DCMTK is statically build #if(DCMTK_DIR) # set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${DCMTK_DIR}/bin/%VS_BUILD_TYPE%") #endif() if(MITK_USE_Boost AND MITK_USE_Boost_LIBRARIES AND NOT MITK_USE_SYSTEM_Boost) set(MITK_RUNTIME_PATH "${MITK_RUNTIME_PATH};${Boost_LIBRARY_DIRS}") endif() #----------------------------------------------------------------------------- # Python Wrapping #----------------------------------------------------------------------------- set(MITK_WRAPPING_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Wrapping) set(MITK_WRAPPING_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/Wrapping) option(MITK_USE_Python "Build cswig Python wrapper support (requires CableSwig)." OFF) if(MITK_USE_Python) add_subdirectory(Wrapping) endif() #----------------------------------------------------------------------------- # Documentation #----------------------------------------------------------------------------- add_subdirectory(Documentation) #----------------------------------------------------------------------------- # Installation #----------------------------------------------------------------------------- # set MITK cpack variables # These are the default variables, which can be overwritten ( see below ) include(mitkSetupCPack) set(use_default_config ON) # MITK_APPS is set in Applications/AppList.cmake (included somewhere above # if MITK_USE_BLUEBERRY is set to ON). if(MITK_APPS) set(activated_apps_no 0) list(LENGTH MITK_APPS app_count) # Check how many apps have been enabled # If more than one app has been activated, the we use the # default CPack configuration. Otherwise that apps configuration # will be used, if present. foreach(mitk_app ${MITK_APPS}) # extract option_name string(REPLACE "^^" "\\;" target_info ${mitk_app}) set(target_info_list ${target_info}) list(GET target_info_list 1 option_name) # check if the application is enabled if(${option_name}) MATH(EXPR activated_apps_no "${activated_apps_no} + 1") endif() endforeach() if(app_count EQUAL 1 AND (activated_apps_no EQUAL 1 OR MITK_BUILD_ALL_APPS)) # Corner case if there is only one app in total set(use_project_cpack ON) elseif(activated_apps_no EQUAL 1 AND NOT MITK_BUILD_ALL_APPS) # Only one app is enabled (no "build all" flag set) set(use_project_cpack ON) else() # Less or more then one app is enabled set(use_project_cpack OFF) endif() foreach(mitk_app ${MITK_APPS}) # extract target_dir and option_name string(REPLACE "^^" "\\;" target_info ${mitk_app}) set(target_info_list ${target_info}) list(GET target_info_list 0 target_dir) list(GET target_info_list 1 option_name) # check if the application is enabled if(${option_name}) # check whether application specific configuration files will be used if(use_project_cpack) # use files if they exist if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/Applications/${target_dir}/CPackOptions.cmake") include("${CMAKE_CURRENT_SOURCE_DIR}/Applications/${target_dir}/CPackOptions.cmake") endif() if(EXISTS "${PROJECT_SOURCE_DIR}/Applications/${target_dir}/CPackConfig.cmake.in") set(CPACK_PROJECT_CONFIG_FILE "${PROJECT_BINARY_DIR}/Applications/${target_dir}/CPackConfig.cmake") configure_file(${PROJECT_SOURCE_DIR}/Applications/${target_dir}/CPackConfig.cmake.in ${CPACK_PROJECT_CONFIG_FILE} @ONLY) set(use_default_config OFF) endif() endif() # add link to the list list(APPEND CPACK_CREATE_DESKTOP_LINKS "${target_dir}") endif() endforeach() endif() # if no application specific configuration file was used, use default if(use_default_config) configure_file(${MITK_SOURCE_DIR}/MITKCPackOptions.cmake.in ${MITK_BINARY_DIR}/MITKCPackOptions.cmake @ONLY) set(CPACK_PROJECT_CONFIG_FILE "${MITK_BINARY_DIR}/MITKCPackOptions.cmake") endif() # include CPack model once all variables are set include(CPack) # Additional installation rules include(mitkInstallRules) #----------------------------------------------------------------------------- # Last configuration steps #----------------------------------------------------------------------------- set(MITK_EXPORTS_FILE "${MITK_BINARY_DIR}/MitkExports.cmake") file(REMOVE ${MITK_EXPORTS_FILE}) if(MITK_USE_BLUEBERRY) # This is for installation support of external projects depending on # MITK plugins. The export file should not be used for linking to MITK # libraries without using LINK_DIRECTORIES, since the exports are incomplete # yet(depending libraries are not exported). if(MITK_PLUGIN_LIBRARIES) export(TARGETS ${MITK_PLUGIN_LIBRARIES} APPEND FILE ${MITK_EXPORTS_FILE}) endif() endif() configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactory.cpp.in ${MITK_BINARY_DIR}/ToolExtensionITKFactory.cpp.in COPYONLY) configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactoryLoader.cpp.in ${MITK_BINARY_DIR}/ToolExtensionITKFactoryLoader.cpp.in COPYONLY) configure_file(${MITK_SOURCE_DIR}/CMake/ToolGUIExtensionITKFactory.cpp.in ${MITK_BINARY_DIR}/ToolGUIExtensionITKFactory.cpp.in COPYONLY) configure_file(mitkVersion.h.in ${MITK_BINARY_DIR}/mitkVersion.h) configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h) set(VECMATH_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/vecmath) set(IPFUNC_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/ipFunc) set(UTILITIES_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities) file(GLOB _MODULES_CONF_FILES RELATIVE ${PROJECT_BINARY_DIR}/${MODULES_CONF_DIRNAME} ${PROJECT_BINARY_DIR}/${MODULES_CONF_DIRNAME}/*.cmake) set(MITK_MODULE_NAMES) foreach(_module ${_MODULES_CONF_FILES}) string(REPLACE Config.cmake "" _module_name ${_module}) list(APPEND MITK_MODULE_NAMES ${_module_name}) endforeach() configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h) configure_file(MITKConfig.cmake.in ${MITK_BINARY_DIR}/MITKConfig.cmake @ONLY) # If we are under Windows, create two batch files which correctly # set up the environment for the application and for Visual Studio if(WIN32) include(mitkFunctionCreateWindowsBatchScript) set(VS_SOLUTION_FILE "${PROJECT_BINARY_DIR}/${PROJECT_NAME}.sln") foreach(VS_BUILD_TYPE debug release) mitkFunctionCreateWindowsBatchScript("${MITK_SOURCE_DIR}/CMake/StartVS.bat.in" ${PROJECT_BINARY_DIR}/StartVS_${VS_BUILD_TYPE}.bat ${VS_BUILD_TYPE}) endforeach() endif(WIN32) #----------------------------------------------------------------------------- # MITK Applications #----------------------------------------------------------------------------- # This must come after MITKConfig.h was generated, since applications # might do a find_package(MITK REQUIRED). add_subdirectory(Applications) diff --git a/Core/Code/Algorithms/itkImportMitkImageContainer.txx b/Core/Code/Algorithms/itkImportMitkImageContainer.txx index e3d85cb1aa..d6c7acb16c 100644 --- a/Core/Code/Algorithms/itkImportMitkImageContainer.txx +++ b/Core/Code/Algorithms/itkImportMitkImageContainer.txx @@ -1,65 +1,65 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 13129 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _itkImportMitkImageContainer_txx #define _itkImportMitkImageContainer_txx #include "itkImportMitkImageContainer.h" namespace itk { template ImportMitkImageContainer ::ImportMitkImageContainer() { } template ImportMitkImageContainer< TElementIdentifier , TElement > ::~ImportMitkImageContainer() { m_ImageDataItem = NULL; } template void ImportMitkImageContainer< TElementIdentifier , TElement > ::SetImageDataItem(mitk::ImageDataItem* imageDataItem) { m_ImageDataItem = imageDataItem; - SetImportPointer( (TElement*) m_ImageDataItem->GetData(), m_ImageDataItem->GetSize()/sizeof(Element), false); + this->SetImportPointer( (TElement*) m_ImageDataItem->GetData(), m_ImageDataItem->GetSize()/sizeof(Element), false); this->Modified(); } template void ImportMitkImageContainer< TElementIdentifier , TElement > ::PrintSelf(std::ostream& os, Indent indent) const { Superclass::PrintSelf(os,indent); os << indent << "ImageDataItem: " << m_ImageDataItem << std::endl; } } // end namespace itk #endif diff --git a/Core/Code/DataManagement/mitkGeometry3D.cpp b/Core/Code/DataManagement/mitkGeometry3D.cpp index 59ce86d746..c98095438a 100644 --- a/Core/Code/DataManagement/mitkGeometry3D.cpp +++ b/Core/Code/DataManagement/mitkGeometry3D.cpp @@ -1,741 +1,741 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ +#include + #include "mitkGeometry3D.h" #include "mitkMatrixConvert.h" #include "mitkRotationOperation.h" #include "mitkRestorePlanePositionOperation.h" #include "mitkPointOperation.h" #include "mitkInteractionConst.h" //#include "mitkStatusBar.h" #include #include // Standard constructor for the New() macro. Sets the geometry to 3 dimensions mitk::Geometry3D::Geometry3D() : m_ParametricBoundingBox(NULL), m_ImageGeometry(false), m_Valid(true), m_FrameOfReferenceID(0), m_IndexToWorldTransformLastModified(0) { FillVector3D(m_FloatSpacing, 1,1,1); m_VtkMatrix = vtkMatrix4x4::New(); m_VtkIndexToWorldTransform = vtkMatrixToLinearTransform::New(); m_VtkIndexToWorldTransform->SetInput(m_VtkMatrix); Initialize(); } mitk::Geometry3D::Geometry3D(const Geometry3D& other) : Superclass(), m_ParametricBoundingBox(other.m_ParametricBoundingBox),m_TimeBounds(other.m_TimeBounds), m_ImageGeometry(other.m_ImageGeometry), m_Valid(other.m_Valid), m_FrameOfReferenceID(other.m_FrameOfReferenceID), m_IndexToWorldTransformLastModified(other.m_IndexToWorldTransformLastModified), m_RotationQuaternion( other.m_RotationQuaternion ) , m_Origin(other.m_Origin) { // AffineGeometryFrame SetBounds(other.GetBounds()); //SetIndexToObjectTransform(other.GetIndexToObjectTransform()); //SetObjectToNodeTransform(other.GetObjectToNodeTransform()); //SetIndexToWorldTransform(other.GetIndexToWorldTransform()); // this is not used in AffineGeometryFrame of ITK, thus there are not Get and Set methods // m_IndexToNodeTransform = other.m_IndexToNodeTransform; // m_InvertedTransform = TransformType::New(); // m_InvertedTransform = TransformType::New(); // m_InvertedTransform->DeepCopy(other.m_InvertedTransform); m_VtkMatrix = vtkMatrix4x4::New(); m_VtkMatrix->DeepCopy(other.m_VtkMatrix); if (other.m_ParametricBoundingBox.IsNotNull()) { m_ParametricBoundingBox = other.m_ParametricBoundingBox->DeepCopy(); } FillVector3D(m_FloatSpacing,other.m_FloatSpacing[0],other.m_FloatSpacing[1],other.m_FloatSpacing[2]); m_VtkIndexToWorldTransform = vtkMatrixToLinearTransform::New(); m_VtkIndexToWorldTransform->DeepCopy(other.m_VtkIndexToWorldTransform); m_VtkIndexToWorldTransform->SetInput(m_VtkMatrix); other.InitializeGeometry(this); } mitk::Geometry3D::~Geometry3D() { m_VtkMatrix->Delete(); m_VtkIndexToWorldTransform->Delete(); } static void CopySpacingFromTransform(mitk::AffineTransform3D* transform, mitk::Vector3D& spacing, float floatSpacing[3]) { mitk::AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = transform->GetMatrix().GetVnlMatrix(); spacing[0]=vnlmatrix.get_column(0).magnitude(); spacing[1]=vnlmatrix.get_column(1).magnitude(); spacing[2]=vnlmatrix.get_column(2).magnitude(); floatSpacing[0]=spacing[0]; floatSpacing[1]=spacing[1]; floatSpacing[2]=spacing[2]; } void mitk::Geometry3D::Initialize() { float b[6] = {0,1,0,1,0,1}; SetFloatBounds(b); m_IndexToObjectTransform = TransformType::New(); m_ObjectToNodeTransform = TransformType::New(); if(m_IndexToWorldTransform.IsNull()) m_IndexToWorldTransform = TransformType::New(); else m_IndexToWorldTransform->SetIdentity(); CopySpacingFromTransform(m_IndexToWorldTransform, m_Spacing, m_FloatSpacing); vtk2itk(m_IndexToWorldTransform->GetOffset(), m_Origin); m_VtkMatrix->Identity(); m_TimeBounds[0]=ScalarTypeNumericTraits::NonpositiveMin(); m_TimeBounds[1]=ScalarTypeNumericTraits::max(); m_FrameOfReferenceID = 0; m_ImageGeometry = false; } void mitk::Geometry3D::TransferItkToVtkTransform() { // copy m_IndexToWorldTransform into m_VtkIndexToWorldTransform TransferItkTransformToVtkMatrix(m_IndexToWorldTransform.GetPointer(), m_VtkMatrix); m_VtkIndexToWorldTransform->Modified(); } void mitk::Geometry3D::TransferVtkToItkTransform() { TransferVtkMatrixToItkTransform(m_VtkMatrix, m_IndexToWorldTransform.GetPointer()); CopySpacingFromTransform(m_IndexToWorldTransform, m_Spacing, m_FloatSpacing); vtk2itk(m_IndexToWorldTransform->GetOffset(), m_Origin); } void mitk::Geometry3D::SetIndexToWorldTransformByVtkMatrix(vtkMatrix4x4* vtkmatrix) { m_VtkMatrix->DeepCopy(vtkmatrix); TransferVtkToItkTransform(); } void mitk::Geometry3D::SetTimeBounds(const TimeBounds& timebounds) { if(m_TimeBounds != timebounds) { m_TimeBounds = timebounds; Modified(); } } void mitk::Geometry3D::SetFloatBounds(const float bounds[6]) { mitk::BoundingBox::BoundsArrayType b; const float *input = bounds; int i=0; for(mitk::BoundingBox::BoundsArrayType::Iterator it = b.Begin(); i < 6 ;++i) *it++ = (mitk::ScalarType)*input++; SetBoundsArray(b, m_BoundingBox); } void mitk::Geometry3D::SetFloatBounds(const double bounds[6]) { mitk::BoundingBox::BoundsArrayType b; const double *input = bounds; int i=0; for(mitk::BoundingBox::BoundsArrayType::Iterator it = b.Begin(); i < 6 ;++i) *it++ = (mitk::ScalarType)*input++; SetBoundsArray(b, m_BoundingBox); } void mitk::Geometry3D::SetParametricBounds(const BoundingBox::BoundsArrayType& bounds) { SetBoundsArray(bounds, m_ParametricBoundingBox); } void mitk::Geometry3D::WorldToIndex(const mitk::Point3D &pt_mm, mitk::Point3D &pt_units) const { BackTransform(pt_mm, pt_units); } void mitk::Geometry3D::IndexToWorld(const mitk::Point3D &pt_units, mitk::Point3D &pt_mm) const { pt_mm = m_IndexToWorldTransform->TransformPoint(pt_units); } void mitk::Geometry3D::WorldToIndex(const mitk::Point3D & /*atPt3d_mm*/, const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const { MITK_WARN<<"Warning! Call of the deprecated function Geometry3D::WorldToIndex(point, vec, vec). Use Geometry3D::WorldToIndex(vec, vec) instead!"; //BackTransform(atPt3d_mm, vec_mm, vec_units); this->WorldToIndex(vec_mm, vec_units); } void mitk::Geometry3D::WorldToIndex( const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const { BackTransform( vec_mm, vec_units); } void mitk::Geometry3D::IndexToWorld(const mitk::Point3D &/*atPt3d_units*/, const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const { MITK_WARN<<"Warning! Call of the deprecated function Geometry3D::IndexToWorld(point, vec, vec). Use Geometry3D::IndexToWorld(vec, vec) instead!"; //vec_mm = m_IndexToWorldTransform->TransformVector(vec_units); this->IndexToWorld(vec_units, vec_mm); } void mitk::Geometry3D::IndexToWorld(const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const { vec_mm = m_IndexToWorldTransform->TransformVector(vec_units); } void mitk::Geometry3D::SetIndexToWorldTransform(mitk::AffineTransform3D* transform) { if(m_IndexToWorldTransform.GetPointer() != transform) { Superclass::SetIndexToWorldTransform(transform); CopySpacingFromTransform(m_IndexToWorldTransform, m_Spacing, m_FloatSpacing); vtk2itk(m_IndexToWorldTransform->GetOffset(), m_Origin); TransferItkToVtkTransform(); Modified(); } } mitk::AffineGeometryFrame3D::Pointer mitk::Geometry3D::Clone() const { Self::Pointer newGeometry = new Self(*this); newGeometry->UnRegister(); return newGeometry.GetPointer(); } /* void mitk::Geometry3D::InitializeGeometry(Geometry3D * newGeometry) const { Superclass::InitializeGeometry(newGeometry); newGeometry->SetTimeBounds(m_TimeBounds); //newGeometry->GetVtkTransform()->SetMatrix(m_VtkIndexToWorldTransform->GetMatrix()); IW //newGeometry->TransferVtkToItkTransform(); //MH newGeometry->SetFrameOfReferenceID(GetFrameOfReferenceID()); newGeometry->m_ImageGeometry = m_ImageGeometry; } */ void mitk::Geometry3D::SetExtentInMM(int direction, ScalarType extentInMM) { ScalarType len = GetExtentInMM(direction); if(fabs(len - extentInMM)>=mitk::eps) { AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = m_IndexToWorldTransform->GetMatrix().GetVnlMatrix(); if(len>extentInMM) vnlmatrix.set_column(direction, vnlmatrix.get_column(direction)/len*extentInMM); else vnlmatrix.set_column(direction, vnlmatrix.get_column(direction)*extentInMM/len); Matrix3D matrix; matrix = vnlmatrix; m_IndexToWorldTransform->SetMatrix(matrix); Modified(); } } mitk::BoundingBox::Pointer mitk::Geometry3D::CalculateBoundingBoxRelativeToTransform(const mitk::AffineTransform3D* transform) const { mitk::BoundingBox::PointsContainer::Pointer pointscontainer=mitk::BoundingBox::PointsContainer::New(); mitk::BoundingBox::PointIdentifier pointid=0; unsigned char i; if(transform!=NULL) { mitk::AffineTransform3D::Pointer inverse = mitk::AffineTransform3D::New(); transform->GetInverse(inverse); for(i=0; i<8; ++i) pointscontainer->InsertElement( pointid++, inverse->TransformPoint( GetCornerPoint(i) )); } else { for(i=0; i<8; ++i) pointscontainer->InsertElement( pointid++, GetCornerPoint(i) ); } mitk::BoundingBox::Pointer result = mitk::BoundingBox::New(); result->SetPoints(pointscontainer); result->ComputeBoundingBox(); return result; } #include void mitk::Geometry3D::ExecuteOperation(Operation* operation) { vtkTransform *vtktransform = vtkTransform::New(); vtktransform->SetMatrix(m_VtkMatrix); switch (operation->GetOperationType()) { case OpNOTHING: break; case OpMOVE: { mitk::PointOperation *pointOp = dynamic_cast(operation); if (pointOp == NULL) { //mitk::StatusBar::GetInstance()->DisplayText("received wrong type of operation!See mitkAffineInteractor.cpp", 10000); return; } mitk::Point3D newPos = pointOp->GetPoint(); ScalarType data[3]; vtktransform->GetPosition(data); vtktransform->PostMultiply(); vtktransform->Translate(newPos[0], newPos[1], newPos[2]); vtktransform->PreMultiply(); break; } case OpSCALE: { mitk::PointOperation *pointOp = dynamic_cast(operation); if (pointOp == NULL) { //mitk::StatusBar::GetInstance()->DisplayText("received wrong type of operation!See mitkAffineInteractor.cpp", 10000); return; } mitk::Point3D newScale = pointOp->GetPoint(); ScalarType data[3]; /* calculate new scale: newscale = oldscale * (oldscale + scaletoadd)/oldscale */ data[0] = 1 + (newScale[0] / GetMatrixColumn(0).magnitude()); data[1] = 1 + (newScale[1] / GetMatrixColumn(1).magnitude()); data[2] = 1 + (newScale[2] / GetMatrixColumn(2).magnitude()); mitk::Point3D center = const_cast(m_BoundingBox.GetPointer())->GetCenter(); ScalarType pos[3]; vtktransform->GetPosition(pos); vtktransform->PostMultiply(); vtktransform->Translate(-pos[0], -pos[1], -pos[2]); vtktransform->Translate(-center[0], -center[1], -center[2]); vtktransform->PreMultiply(); vtktransform->Scale(data[0], data[1], data[2]); vtktransform->PostMultiply(); vtktransform->Translate(+center[0], +center[1], +center[2]); vtktransform->Translate(pos[0], pos[1], pos[2]); vtktransform->PreMultiply(); break; } case OpROTATE: { mitk::RotationOperation *rotateOp = dynamic_cast(operation); if (rotateOp == NULL) { //mitk::StatusBar::GetInstance()->DisplayText("received wrong type of operation!See mitkAffineInteractor.cpp", 10000); return; } Vector3D rotationVector = rotateOp->GetVectorOfRotation(); Point3D center = rotateOp->GetCenterOfRotation(); ScalarType angle = rotateOp->GetAngleOfRotation(); vtktransform->PostMultiply(); vtktransform->Translate(-center[0], -center[1], -center[2]); vtktransform->RotateWXYZ(angle, rotationVector[0], rotationVector[1], rotationVector[2]); vtktransform->Translate(center[0], center[1], center[2]); vtktransform->PreMultiply(); break; } case OpRESTOREPLANEPOSITION: { //Copy necessary to avoid vtk warning vtkMatrix4x4* matrix = vtkMatrix4x4::New(); TransferItkTransformToVtkMatrix(dynamic_cast(operation)->GetTransform().GetPointer(), matrix); vtktransform->SetMatrix(matrix); break; } default: vtktransform->Delete(); return; } m_VtkMatrix->DeepCopy(vtktransform->GetMatrix()); TransferVtkToItkTransform(); Modified(); vtktransform->Delete(); } void mitk::Geometry3D::BackTransform(const mitk::Point3D &in, mitk::Point3D& out) const { ScalarType temp[3]; unsigned int i, j; const TransformType::OffsetType& offset = m_IndexToWorldTransform->GetOffset(); // Remove offset for (j = 0; j < 3; j++) { temp[j] = in[j] - offset[j]; } // Get WorldToIndex transform if (m_IndexToWorldTransformLastModified != m_IndexToWorldTransform->GetMTime()) { m_InvertedTransform = TransformType::New(); if (!m_IndexToWorldTransform->GetInverse( m_InvertedTransform.GetPointer() )) { itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed." ); } m_IndexToWorldTransformLastModified = m_IndexToWorldTransform->GetMTime(); } // Check for valid matrix inversion const TransformType::MatrixType& inverse = m_InvertedTransform->GetMatrix(); if(inverse.GetVnlMatrix().has_nans()) { itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl << m_IndexToWorldTransform->GetMatrix() << "Suggested inverted matrix is:" << std::endl << inverse ); } // Transform point for (i = 0; i < 3; i++) { out[i] = 0.0; for (j = 0; j < 3; j++) { out[i] += inverse[i][j]*temp[j]; } } } void mitk::Geometry3D::BackTransform(const mitk::Point3D &/*at*/, const mitk::Vector3D &in, mitk::Vector3D& out) const { MITK_INFO<<"Warning! Call of the deprecated function Geometry3D::BackTransform(point, vec, vec). Use Geometry3D::BackTransform(vec, vec) instead!"; //// Get WorldToIndex transform //if (m_IndexToWorldTransformLastModified != m_IndexToWorldTransform->GetMTime()) //{ // m_InvertedTransform = TransformType::New(); // if (!m_IndexToWorldTransform->GetInverse( m_InvertedTransform.GetPointer() )) // { // itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed." ); // } // m_IndexToWorldTransformLastModified = m_IndexToWorldTransform->GetMTime(); //} //// Check for valid matrix inversion //const TransformType::MatrixType& inverse = m_InvertedTransform->GetMatrix(); //if(inverse.GetVnlMatrix().has_nans()) //{ // itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl // << m_IndexToWorldTransform->GetMatrix() << "Suggested inverted matrix is:" << std::endl // << inverse ); //} //// Transform vector //for (unsigned int i = 0; i < 3; i++) //{ // out[i] = 0.0; // for (unsigned int j = 0; j < 3; j++) // { // out[i] += inverse[i][j]*in[j]; // } //} this->BackTransform(in, out); } void mitk::Geometry3D::BackTransform(const mitk::Vector3D& in, mitk::Vector3D& out) const { // Get WorldToIndex transform if (m_IndexToWorldTransformLastModified != m_IndexToWorldTransform->GetMTime()) { m_InvertedTransform = TransformType::New(); if (!m_IndexToWorldTransform->GetInverse( m_InvertedTransform.GetPointer() )) { itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed." ); } m_IndexToWorldTransformLastModified = m_IndexToWorldTransform->GetMTime(); } // Check for valid matrix inversion const TransformType::MatrixType& inverse = m_InvertedTransform->GetMatrix(); if(inverse.GetVnlMatrix().has_nans()) { itkExceptionMacro( "Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl << m_IndexToWorldTransform->GetMatrix() << "Suggested inverted matrix is:" << std::endl << inverse ); } // Transform vector for (unsigned int i = 0; i < 3; i++) { out[i] = 0.0; for (unsigned int j = 0; j < 3; j++) { out[i] += inverse[i][j]*in[j]; } } } const float* mitk::Geometry3D::GetFloatSpacing() const { return m_FloatSpacing; } void mitk::Geometry3D::SetSpacing(const mitk::Vector3D& aSpacing) { if(mitk::Equal(m_Spacing, aSpacing) == false) { assert(aSpacing[0]>0 && aSpacing[1]>0 && aSpacing[2]>0); m_Spacing = aSpacing; AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = m_IndexToWorldTransform->GetMatrix().GetVnlMatrix(); mitk::VnlVector col; col = vnlmatrix.get_column(0); col.normalize(); col*=aSpacing[0]; vnlmatrix.set_column(0, col); col = vnlmatrix.get_column(1); col.normalize(); col*=aSpacing[1]; vnlmatrix.set_column(1, col); col = vnlmatrix.get_column(2); col.normalize(); col*=aSpacing[2]; vnlmatrix.set_column(2, col); Matrix3D matrix; matrix = vnlmatrix; AffineTransform3D::Pointer transform = AffineTransform3D::New(); transform->SetMatrix(matrix); transform->SetOffset(m_IndexToWorldTransform->GetOffset()); SetIndexToWorldTransform(transform.GetPointer()); itk2vtk(m_Spacing, m_FloatSpacing); } } void mitk::Geometry3D::SetOrigin(const Point3D & origin) { if(origin!=GetOrigin()) { m_Origin = origin; m_IndexToWorldTransform->SetOffset(m_Origin.GetVectorFromOrigin()); Modified(); TransferItkToVtkTransform(); } } void mitk::Geometry3D::Translate(const Vector3D & vector) { if((vector[0] != 0) || (vector[1] != 0) || (vector[2] != 0)) { m_IndexToWorldTransform->SetOffset(m_IndexToWorldTransform->GetOffset()+vector); TransferItkToVtkTransform(); Modified(); } } void mitk::Geometry3D::SetIdentity() { m_IndexToWorldTransform->SetIdentity(); m_Origin.Fill(0); Modified(); TransferItkToVtkTransform(); } void mitk::Geometry3D::Compose( const mitk::AffineGeometryFrame3D::TransformType * other, bool pre ) { m_IndexToWorldTransform->Compose(other, pre); CopySpacingFromTransform(m_IndexToWorldTransform, m_Spacing, m_FloatSpacing); vtk2itk(m_IndexToWorldTransform->GetOffset(), m_Origin); Modified(); TransferItkToVtkTransform(); } void mitk::Geometry3D::Compose( const vtkMatrix4x4 * vtkmatrix, bool pre ) { mitk::AffineGeometryFrame3D::TransformType::Pointer itkTransform = mitk::AffineGeometryFrame3D::TransformType::New(); TransferVtkMatrixToItkTransform(vtkmatrix, itkTransform.GetPointer()); Compose(itkTransform, pre); } -const char* mitk::Geometry3D::GetTransformAsString( TransformType* transformType ) +const std::string mitk::Geometry3D::GetTransformAsString( TransformType* transformType ) { - static char buffer[255]; - for ( int j=0; j<255; j++) buffer[j] = '\0'; - ostrstream out( buffer, 255 ); + std::ostringstream out; out << '['; for( int i=0; i<3; ++i ) { out << '['; for( int j=0; j<3; ++j ) out << transformType->GetMatrix().GetVnlMatrix().get(i, j) << ' '; out << ']'; } out << "]["; for( int i=0; i<3; ++i ) out << transformType->GetOffset()[i] << ' '; out << "]\0"; - return buffer; + return out.str(); } void mitk::Geometry3D::PrintSelf(std::ostream& os, itk::Indent indent) const { os << indent << " IndexToWorldTransform: "; if(m_IndexToWorldTransform.IsNull()) os << "NULL" << std::endl; else { // from itk::MatrixOffsetTransformBase unsigned int i, j; os << std::endl; os << indent << "Matrix: " << std::endl; for (i = 0; i < 3; i++) { os << indent.GetNextIndent(); for (j = 0; j < 3; j++) { os << m_IndexToWorldTransform->GetMatrix()[i][j] << " "; } os << std::endl; } os << indent << "Offset: " << m_IndexToWorldTransform->GetOffset() << std::endl; os << indent << "Center: " << m_IndexToWorldTransform->GetCenter() << std::endl; os << indent << "Translation: " << m_IndexToWorldTransform->GetTranslation() << std::endl; os << indent << "Inverse: " << std::endl; for (i = 0; i < 3; i++) { os << indent.GetNextIndent(); for (j = 0; j < 3; j++) { os << m_IndexToWorldTransform->GetInverseMatrix()[i][j] << " "; } os << std::endl; } // from itk::ScalableAffineTransform os << indent << "Scale : "; for (i = 0; i < 3; i++) { os << m_IndexToWorldTransform->GetScale()[i] << " "; } os << std::endl; } os << indent << " BoundingBox: "; if(m_BoundingBox.IsNull()) os << "NULL" << std::endl; else { os << indent << "( "; for (unsigned int i=0; i<3; i++) { os << m_BoundingBox->GetBounds()[2*i] << "," << m_BoundingBox->GetBounds()[2*i+1] << " "; } os << " )" << std::endl; } os << indent << " Origin: " << m_Origin << std::endl; os << indent << " ImageGeometry: " << m_ImageGeometry << std::endl; os << indent << " Spacing: " << m_Spacing << std::endl; os << indent << " TimeBounds: " << m_TimeBounds << std::endl; } mitk::Point3D mitk::Geometry3D::GetCornerPoint(int id) const { assert(id >= 0); assert(m_BoundingBox.IsNotNull()); BoundingBox::BoundsArrayType bounds = m_BoundingBox->GetBounds(); Point3D cornerpoint; switch(id) { case 0: FillVector3D(cornerpoint, bounds[0],bounds[2],bounds[4]); break; case 1: FillVector3D(cornerpoint, bounds[0],bounds[2],bounds[5]); break; case 2: FillVector3D(cornerpoint, bounds[0],bounds[3],bounds[4]); break; case 3: FillVector3D(cornerpoint, bounds[0],bounds[3],bounds[5]); break; case 4: FillVector3D(cornerpoint, bounds[1],bounds[2],bounds[4]); break; case 5: FillVector3D(cornerpoint, bounds[1],bounds[2],bounds[5]); break; case 6: FillVector3D(cornerpoint, bounds[1],bounds[3],bounds[4]); break; case 7: FillVector3D(cornerpoint, bounds[1],bounds[3],bounds[5]); break; default: { itkExceptionMacro(<<"A cube only has 8 corners. These are labeled 0-7."); return NULL; } } if(m_ImageGeometry) { // Here i have to adjust the 0.5 offset manually, because the cornerpoint is the corner of the // bounding box. The bounding box itself is no image, so it is corner-based FillVector3D(cornerpoint, cornerpoint[0]-0.5, cornerpoint[1]-0.5, cornerpoint[2]-0.5); } return m_IndexToWorldTransform->TransformPoint(cornerpoint); } mitk::Point3D mitk::Geometry3D::GetCornerPoint(bool xFront, bool yFront, bool zFront) const { assert(m_BoundingBox.IsNotNull()); BoundingBox::BoundsArrayType bounds = m_BoundingBox->GetBounds(); Point3D cornerpoint; cornerpoint[0] = (xFront ? bounds[0] : bounds[1]); cornerpoint[1] = (yFront ? bounds[2] : bounds[3]); cornerpoint[2] = (zFront ? bounds[4] : bounds[5]); if(m_ImageGeometry) { // Here i have to adjust the 0.5 offset manually, because the cornerpoint is the corner of the // bounding box. The bounding box itself is no image, so it is corner-based FillVector3D(cornerpoint, cornerpoint[0]-0.5, cornerpoint[1]-0.5, cornerpoint[2]-0.5); } return m_IndexToWorldTransform->TransformPoint(cornerpoint); } void mitk::Geometry3D::ResetSubTransforms() { } void mitk::Geometry3D::ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry ) { // If Geometry is switched to ImageGeometry, you have to put an offset to the origin, because // imageGeometries origins are pixel-center-based // ... and remove the offset, if you switch an imageGeometry back to a normal geometry // For more information please see the Geometry documentation page if(m_ImageGeometry == isAnImageGeometry) return; const BoundingBox::BoundsArrayType& boundsarray = this->GetBoundingBox()->GetBounds(); Point3D originIndex; FillVector3D(originIndex, boundsarray[0], boundsarray[2], boundsarray[4]); if(isAnImageGeometry == true) FillVector3D( originIndex, originIndex[0] + 0.5, originIndex[1] + 0.5, originIndex[2] + 0.5 ); else FillVector3D( originIndex, originIndex[0] - 0.5, originIndex[1] - 0.5, originIndex[2] - 0.5 ); Point3D originWorld; originWorld = GetIndexToWorldTransform() ->TransformPoint( originIndex ); // instead could as well call IndexToWorld(originIndex,originWorld); SetOrigin(originWorld); this->SetImageGeometry(isAnImageGeometry); } diff --git a/Core/Code/DataManagement/mitkGeometry3D.h b/Core/Code/DataManagement/mitkGeometry3D.h index 46528d5ff1..c7c7decbce 100644 --- a/Core/Code/DataManagement/mitkGeometry3D.h +++ b/Core/Code/DataManagement/mitkGeometry3D.h @@ -1,663 +1,663 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef GEOMETRY3D_H_HEADER_INCLUDED_C1EBD0AD #define GEOMETRY3D_H_HEADER_INCLUDED_C1EBD0AD #include #include #include "mitkVector.h" #include "mitkOperationActor.h" #include #include #include #include class vtkLinearTransform; class vtkMatrixToLinearTransform; class vtkMatrix4x4; namespace mitk { //##Documentation //## @brief Standard 3D-BoundingBox typedef //## //## Standard 3D-BoundingBox typedef to get rid of template arguments (3D, type). typedef itk::BoundingBox BoundingBox; //##Documentation //## @brief Standard typedef for time-bounds typedef itk::FixedArray TimeBounds; typedef itk::FixedArray FixedArrayType; typedef itk::AffineGeometryFrame AffineGeometryFrame3D; //##Documentation //## @brief Describes the geometry of a data object //## //## At least, it can return the bounding box of the data object. //## //## The class holds //## \li a bounding box which is axes-parallel in intrinsic coordinates //## (often integer indices of pixels), to be accessed by //## GetBoundingBox() //## \li a transform to convert intrinsic coordinates into a //## world-coordinate system with coordinates in millimeters //## and milliseconds (all are floating point values), to //## be accessed by GetIndexToWorldTransform() //## \li a life span, i.e. a bounding box in time in ms (with //## start and end time), to be accessed by GetTimeBounds(). //## The default is minus infinity to plus infinity. //## //## Geometry3D and its sub-classes allow converting between //## intrinsic coordinates (called index or unit coordinates) //## and world-coordinates (called world or mm coordinates), //## e.g. WorldToIndex. //## In case you need integer index coordinates, provide an //## mitk::Index3D (or itk::Index) as target variable to //## WorldToIndex, otherwise you will get a continuous index //## (floating point values). //## //## An important sub-class is SlicedGeometry3D, which descibes //## data objects consisting of slices, e.g., objects of type Image. //## Conversions between world coordinates (in mm) and unit coordinates //## (e.g., pixels in the case of an Image) can be performed. //## //## For more information on related classes, see \ref Geometry. //## //## Geometry3D instances referring to an Image need a slightly //## different definition of corners, see SetImageGeometry. This //## is usualy automatically called by Image. //## //## Geometry3D have to be initialized in the method GenerateOutputInformation() //## of BaseProcess (or CopyInformation/ UpdateOutputInformation of BaseData, //## if possible, e.g., by analyzing pic tags in Image) subclasses. See also //## itk::ProcessObject::GenerateOutputInformation(), //## itk::DataObject::CopyInformation() and //## itk::DataObject::UpdateOutputInformation(). //## //## Rule: everything is in mm (ms) if not stated otherwise. //## @ingroup Geometry class MITK_CORE_EXPORT Geometry3D : public AffineGeometryFrame3D, public OperationActor { public: mitkClassMacro(Geometry3D, AffineGeometryFrame3D); typedef itk::QuaternionRigidTransform< ScalarType > QuaternionTransformType; typedef QuaternionTransformType::VnlQuaternionType VnlQuaternionType; /** Method for creation through the object factory. */ itkNewMacro(Self); // a bit of a misuse, but we want only doxygen to see the following: #ifdef DOXYGEN_SKIP //##Documentation //## @brief Get the transformation used to convert from index //## to world coordinates itkGetObjectMacro(IndexToWorldTransform, AffineTransform3D); #endif //## @brief Set the transformation used to convert from index //## to world coordinates virtual void SetIndexToWorldTransform(mitk::AffineTransform3D* transform); //##Documentation //## @brief Convenience method for setting the ITK transform //## (m_IndexToWorldTransform) via an vtkMatrix4x4 //## \sa SetIndexToWorldTransform virtual void SetIndexToWorldTransformByVtkMatrix(vtkMatrix4x4* vtkmatrix); #ifdef DOXYGEN_SKIP //##Documentation //## @brief Get bounding box (in index/unit coordinates) itkGetConstObjectMacro(BoundingBox, BoundingBoxType); //##Documentation //## @brief Get bounding box (in index/unit coordinates) as a BoundsArrayType const BoundsArrayType GetBounds() const { assert(m_BoundingBox.IsNotNull()); return m_BoundingBox->GetBounds(); } //##Documentation //## \brief Set the bounding box (in index/unit coordinates) //## //## Only possible via the BoundsArray to make clear that a //## copy of the bounding-box is stored, not a reference to it. virtual void SetBounds(const BoundsArrayType& bounds); #endif //##Documentation //## @brief Set the bounding box (in index/unit coordinates) via a float array virtual void SetFloatBounds(const float bounds[6]); //##Documentation //## @brief Set the bounding box (in index/unit coordinates) via a double array virtual void SetFloatBounds(const double bounds[6]); //##Documentation //## @brief When switching from an Image Geometry to a normal Geometry (and the other way around), you have to change the origin as well (See Geometry Documentation)! This function will change the "isImageGeometry" bool flag and changes the origin respectively. virtual void ChangeImageGeometryConsideringOriginOffset( const bool isAnImageGeometry ); //##Documentation //## @brief Get the time bounds (in ms) itkGetConstReferenceMacro(TimeBounds, TimeBounds); //##Documentation //## @brief Set the time bounds (in ms) virtual void SetTimeBounds(const TimeBounds& timebounds); //##Documentation //## @brief Get the position of the corner number \a id (in world coordinates) //## //## See SetImageGeometry for how a corner is defined on images. Point3D GetCornerPoint(int id) const; //##Documentation //## @brief Get the position of a corner (in world coordinates) //## //## See SetImageGeometry for how a corner is defined on images. Point3D GetCornerPoint(bool xFront=true, bool yFront=true, bool zFront=true) const; //##Documentation //## @brief Get vector along bounding-box in the specified @a direction in mm //## //## The length of the vector is the size of the bounding-box in the //## specified @a direction in mm //## \sa GetMatrixColumn Vector3D GetAxisVector(unsigned int direction) const { Vector3D frontToBack; frontToBack.Set_vnl_vector(m_IndexToWorldTransform->GetMatrix().GetVnlMatrix().get_column(direction)); frontToBack *= GetExtent(direction); return frontToBack; } //##Documentation //## @brief Get the center of the bounding-box in mm //## Point3D GetCenter() const { assert(m_BoundingBox.IsNotNull()); return m_IndexToWorldTransform->TransformPoint(m_BoundingBox->GetCenter()); } //##Documentation //## @brief Get the squared length of the diagonal of the bounding-box in mm //## double GetDiagonalLength2() const { Vector3D diagonalvector = GetCornerPoint()-GetCornerPoint(false, false, false); return diagonalvector.GetSquaredNorm(); } //##Documentation //## @brief Get the length of the diagonal of the bounding-box in mm //## double GetDiagonalLength() const { return sqrt(GetDiagonalLength2()); } //##Documentation //## @brief Get a VnlVector along bounding-box in the specified //## @a direction, length is spacing //## //## \sa GetAxisVector VnlVector GetMatrixColumn(unsigned int direction) const { return m_IndexToWorldTransform->GetMatrix().GetVnlMatrix().get_column(direction); } #ifdef DOXYGEN_SKIP //##Documentation //## @brief Get the extent of the bounding box (in index/unit coordinates) //## //## To access the extent in mm use GetExtentInMM ScalarType GetExtent(unsigned int direction) const; #endif //##Documentation //## @brief Get the extent of the bounding-box in the specified @a direction in mm //## //## Equals length of GetAxisVector(direction). ScalarType GetExtentInMM(int direction) const { return m_IndexToWorldTransform->GetMatrix().GetVnlMatrix().get_column(direction).magnitude()*GetExtent(direction); } //##Documentation //## @brief Set the extent of the bounding-box in the specified @a direction in mm //## //## @note This changes the matrix in the transform, @a not the bounds, which are given in units! virtual void SetExtentInMM(int direction, ScalarType extentInMM); //##Documentation //## @brief Get the m_IndexToWorldTransform as a vtkLinearTransform vtkLinearTransform* GetVtkTransform() const { return (vtkLinearTransform*)m_VtkIndexToWorldTransform; } //##Documentation //## @brief Set the origin, i.e. the upper-left corner of the plane //## virtual void SetOrigin(const Point3D& origin); //##Documentation //## @brief Translate the origin by a vector //## virtual void Translate(const Vector3D& vector); //##Documentation //## @brief Set the transform to identity //## virtual void SetIdentity(); //##Documentation //## @brief Compose new IndexToWorldTransform with a given transform. //## //## This method composes m_IndexToWorldTransform with another transform, //## modifying self to be the composition of self and other. //## If the argument pre is true, then other is precomposed with self; //## that is, the resulting transformation consists of first applying //## other to the source, followed by self. If pre is false or omitted, //## then other is post-composed with self; that is the resulting //## transformation consists of first applying self to the source, //## followed by other. virtual void Compose( const AffineGeometryFrame3D::TransformType * other, bool pre = 0 ); //##Documentation //## @brief Compose new IndexToWorldTransform with a given vtkMatrix4x4. //## //## Converts the vtkMatrix4x4 into a itk-transform and calls the previous method. virtual void Compose( const vtkMatrix4x4 * vtkmatrix, bool pre = 0 ); //##Documentation //## @brief Get the origin, e.g. the upper-left corner of the plane const Point3D& GetOrigin() const { return m_Origin; } //##Documentation //## @brief Get the origin as VnlVector //## //## \sa GetOrigin VnlVector GetOriginVnl() const { return const_cast(this)->m_Origin.Get_vnl_vector(); } //##Documentation //## @brief Convert world coordinates (in mm) of a \em point to (continuous!) index coordinates //## \warning If you need (discrete) integer index coordinates (e.g., for iterating easily over an image), //## use WorldToIndex(const mitk::Point3D& pt_mm, itk::Index &index). //## For further information about coordinates types, please see the Geometry documentation void WorldToIndex(const mitk::Point3D& pt_mm, mitk::Point3D& pt_units) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em point to world coordinates (in mm) //## For further information about coordinates types, please see the Geometry documentation void IndexToWorld(const mitk::Point3D& pt_units, mitk::Point3D& pt_mm) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## @deprecated First parameter (Point3D) is not used. If possible, please use void WorldToIndex(const mitk::Vector3D& vec_mm, mitk::Vector3D& vec_units) const. //## For further information about coordinates types, please see the Geometry documentation void WorldToIndex(const mitk::Point3D& atPt3d_mm, const mitk::Vector3D& vec_mm, mitk::Vector3D& vec_units) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## For further information about coordinates types, please see the Geometry documentation void WorldToIndex(const mitk::Vector3D& vec_mm, mitk::Vector3D& vec_units) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## @deprecated First parameter (Point3D) is not used. If possible, please use void IndexToWorld(const mitk::Vector3D& vec_units, mitk::Vector3D& vec_mm) const. //## For further information about coordinates types, please see the Geometry documentation void IndexToWorld(const mitk::Point3D& atPt3d_units, const mitk::Vector3D& vec_units, mitk::Vector3D& vec_mm) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## For further information about coordinates types, please see the Geometry documentation void IndexToWorld(const mitk::Vector3D& vec_units, mitk::Vector3D& vec_mm) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em point to (discrete!) index coordinates. //## This method rounds to integer indices! //## For further information about coordinates types, please see the Geometry documentation template void WorldToIndex(const mitk::Point3D& pt_mm, itk::Index &index) const { typedef itk::Index IndexType; mitk::Point3D pt_units; this->WorldToIndex(pt_mm, pt_units); int i, dim=index.GetIndexDimension(); if(dim>3) { index.Fill(0); dim=3; } for(i=0;i( pt_units[i] ); index[i]=itk::Math::RoundHalfIntegerUp( pt_units[i] ); } } //##Documentation //## @brief Deprecated for use with ITK version 3.10 or newer. //## Convert world coordinates (in mm) of a \em point to //## ITK physical coordinates (in mm, but without a possible rotation) //## //## This method is useful if you have want to access an mitk::Image //## via an itk::Image. ITK v3.8 and older did not support rotated (tilted) //## images, i.e., ITK images are always parallel to the coordinate axes. //## When accessing a (possibly rotated) mitk::Image via an itk::Image //## the rotational part of the transformation in the Geometry3D is //## simply discarded; in other word: only the origin and spacing is //## used by ITK, not the complete matrix available in MITK. //## With WorldToItkPhysicalPoint you can convert an MITK world //## coordinate (including the rotation) into a coordinate that //## can be used with the ITK image as a ITK physical coordinate //## (excluding the rotation). template void WorldToItkPhysicalPoint(const mitk::Point3D& pt_mm, itk::Point& itkPhysicalPoint) const { mitk::vtk2itk(pt_mm, itkPhysicalPoint); } //##Documentation //## @brief Deprecated for use with ITK version 3.10 or newer. //## Convert ITK physical coordinates of a \em point (in mm, //## but without a rotation) into MITK world coordinates (in mm) //## //## For more information, see WorldToItkPhysicalPoint. template void ItkPhysicalPointToWorld(const itk::Point& itkPhysicalPoint, mitk::Point3D& pt_mm) const { mitk::vtk2itk(itkPhysicalPoint, pt_mm); } //##Documentation //## @brief Initialize the Geometry3D virtual void Initialize(); //##Documentation //## @brief Is this an ImageGeometry? //## //## For more information, see SetImageGeometry itkGetConstMacro(ImageGeometry, bool); //##Documentation //## @brief Define that this Geometry3D is refering to an Image //## //## A geometry referring to an Image needs a slightly different //## definition of the position of the corners (see GetCornerPoint). //## The position of a voxel is defined by the position of its center. //## If we would use the origin (position of the (center of) the first //## voxel) as a corner and display this point, it would seem to be //## \em not at the corner but a bit within the image. Even worse for //## the opposite corner of the image: here the corner would appear //## outside the image (by half of the voxel diameter). Thus, we have //## to correct for this and to be able to do that, we need to know //## that the Geometry3D is referring to an Image. itkSetMacro(ImageGeometry, bool); itkBooleanMacro(ImageGeometry); //##Documentation //## @brief Is this Geometry3D in a state that is valid? virtual bool IsValid() const { return m_Valid; } //##Documentation //## @brief Test whether the point \a p (world coordinates in mm) is //## inside the bounding box bool IsInside(const mitk::Point3D& p) const { mitk::Point3D index; WorldToIndex(p, index); return IsIndexInside(index); } //##Documentation //## @brief Test whether the point \a p ((continous!)index coordinates in units) is //## inside the bounding box bool IsIndexInside(const mitk::Point3D& index) const { bool inside = false; //if it is an image geometry, we need to convert the index to discrete values //this is done by applying the rounding function also used in WorldToIndex (see line 323) if (m_ImageGeometry) { mitk::Point3D discretIndex; discretIndex[0]=itk::Math::RoundHalfIntegerUp( index[0] ); discretIndex[1]=itk::Math::RoundHalfIntegerUp( index[1] ); discretIndex[2]=itk::Math::RoundHalfIntegerUp( index[2] ); inside = m_BoundingBox->IsInside(discretIndex); //we have to check if the index is at the upper border of each dimension, // because the boundingbox is not centerbased if (inside) { const BoundingBox::BoundsArrayType& bounds = m_BoundingBox->GetBounds(); if((discretIndex[0] == bounds[1]) || (discretIndex[1] == bounds[3]) || (discretIndex[2] == bounds[5])) inside = false; } } else inside = m_BoundingBox->IsInside(index); return inside; } //##Documentation //## @brief Convenience method for working with ITK indices template bool IsIndexInside(const itk::Index &index) const { int i, dim=index.GetIndexDimension(); Point3D pt_index; pt_index.Fill(0); for ( i = 0; i < dim; ++i ) { pt_index[i] = index[i]; } return IsIndexInside(pt_index); } //##Documentation //## @brief Get the spacing (size of a pixel). //## itkGetConstReferenceMacro(Spacing, mitk::Vector3D); //##Documentation //## @brief Get the spacing as a float[3] array. const float* GetFloatSpacing() const; //##Documentation //## @brief Set the spacing (m_Spacing) virtual void SetSpacing(const mitk::Vector3D& aSpacing); //##Documentation //## @brief Get the DICOM FrameOfReferenceID referring to the //## used world coordinate system itkGetConstMacro(FrameOfReferenceID, unsigned int); //##Documentation //## @brief Set the DICOM FrameOfReferenceID referring to the //## used world coordinate system itkSetMacro(FrameOfReferenceID, unsigned int); //##Documentation //## @brief Copy the ITK transform //## (m_IndexToWorldTransform) to the VTK transform //## \sa SetIndexToWorldTransform void TransferItkToVtkTransform(); //##Documentation //## @brief Copy the VTK transform //## to the ITK transform (m_IndexToWorldTransform) //## \sa SetIndexToWorldTransform void TransferVtkToItkTransform(); //##Documentation //## @brief Get the parametric bounding-box //## //## See AbstractTransformGeometry for an example usage of this. itkGetConstObjectMacro(ParametricBoundingBox, BoundingBox); //##Documentation //## @brief Get the parametric bounds //## //## See AbstractTransformGeometry for an example usage of this. const BoundingBox::BoundsArrayType& GetParametricBounds() const { assert(m_ParametricBoundingBox.IsNotNull()); return m_ParametricBoundingBox->GetBounds(); } //##Documentation //## @brief Get the parametric extent //## //## See AbstractTransformGeometry for an example usage of this. mitk::ScalarType GetParametricExtent(int direction) const { assert(direction>=0 && direction<3); assert(m_ParametricBoundingBox.IsNotNull()); BoundingBoxType::BoundsArrayType bounds = m_ParametricBoundingBox->GetBounds(); return bounds[direction*2+1]-bounds[direction*2]; } //##Documentation //## @brief Get the parametric extent in mm //## //## See AbstractTransformGeometry for an example usage of this. virtual mitk::ScalarType GetParametricExtentInMM(int direction) const { return GetExtentInMM(direction); } //##Documentation //## @brief Get the parametric transform //## //## See AbstractTransformGeometry for an example usage of this. virtual const Transform3D* GetParametricTransform() const { return m_IndexToWorldTransform; } //##Documentation //## @brief Calculates a bounding-box around the geometry relative //## to a coordinate system defined by a transform //## mitk::BoundingBox::Pointer CalculateBoundingBoxRelativeToTransform(const mitk::AffineTransform3D* transform) const; //##Documentation //## @brief clones the geometry //## //## Overwrite in all sub-classes. //## Normally looks like: //## \code //## Self::Pointer newGeometry = new Self(*this); //## newGeometry->UnRegister(); //## return newGeometry.GetPointer(); //## \endcode virtual AffineGeometryFrame3D::Pointer Clone() const; //##Documentation //##@brief executes affine operations (translate, rotate, scale) virtual void ExecuteOperation(Operation* operation); protected: Geometry3D(); Geometry3D(const Geometry3D& other); - static const char* GetTransformAsString( TransformType* transformType ); + static const std::string GetTransformAsString( TransformType* transformType ); virtual ~Geometry3D(); virtual void PrintSelf(std::ostream& os, itk::Indent indent) const; virtual void BackTransform(const mitk::Point3D& in, mitk::Point3D& out) const; //##Documentation //## @brief Deprecated virtual void BackTransform(const mitk::Point3D& at, const mitk::Vector3D& in, mitk::Vector3D& out) const; //Without redundant parameter Point3D virtual void BackTransform(const mitk::Vector3D& in, mitk::Vector3D& out) const; //##Documentation //## @brief Set the parametric bounds //## //## Protected in this class, made public in some sub-classes, e.g., //## ExternAbstractTransformGeometry. virtual void SetParametricBounds(const BoundingBox::BoundsArrayType& bounds); /** Resets sub-transforms that compose m_IndexToWorldTransform, by using * the current value of m_IndexToWorldTransform and setting the rotation * component to zero. */ virtual void ResetSubTransforms(); mutable mitk::BoundingBox::Pointer m_ParametricBoundingBox; mutable mitk::TimeBounds m_TimeBounds; vtkMatrix4x4* m_VtkMatrix; bool m_ImageGeometry; //##Documentation //## @brief Spacing of the data. Only significant if the geometry describes //## an Image (m_ImageGeometry==true). mitk::Vector3D m_Spacing; bool m_Valid; unsigned int m_FrameOfReferenceID; static const std::string INDEX_TO_OBJECT_TRANSFORM; static const std::string OBJECT_TO_NODE_TRANSFORM; static const std::string INDEX_TO_NODE_TRANSFORM; static const std::string INDEX_TO_WORLD_TRANSFORM; private: mutable TransformType::Pointer m_InvertedTransform; mutable unsigned long m_IndexToWorldTransformLastModified; VnlQuaternionType m_RotationQuaternion; float m_FloatSpacing[3]; vtkMatrixToLinearTransform* m_VtkIndexToWorldTransform; //##Documentation //## @brief Origin, i.e. upper-left corner of the plane //## Point3D m_Origin; }; } // namespace mitk #endif /* GEOMETRY3D_H_HEADER_INCLUDED_C1EBD0AD */ diff --git a/Core/Code/DataManagement/mitkImage.cpp b/Core/Code/DataManagement/mitkImage.cpp index 6c052b74df..c4e1929abb 100644 --- a/Core/Code/DataManagement/mitkImage.cpp +++ b/Core/Code/DataManagement/mitkImage.cpp @@ -1,1275 +1,1279 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkImage.h" #include "mitkImageStatisticsHolder.h" #include "mitkPixelTypeMultiplex.h" #include #define FILL_C_ARRAY( _arr, _size, _value) for(unsigned int i=0u; i<_size; i++) \ { _arr[i] = _value; } mitk::Image::Image() : m_Dimension(0), m_Dimensions(NULL), m_ImageDescriptor(NULL), m_OffsetTable(NULL), m_CompleteData(NULL), m_ImageStatistics(NULL) { m_Dimensions = new unsigned int[MAX_IMAGE_DIMENSIONS]; FILL_C_ARRAY( m_Dimensions, MAX_IMAGE_DIMENSIONS, 0u); m_Initialized = false; } mitk::Image::Image(const Image &other) : SlicedData(other), m_Dimension(0), m_Dimensions(NULL), m_ImageDescriptor(NULL), m_OffsetTable(NULL), m_CompleteData(NULL), m_ImageStatistics(NULL) { m_Dimensions = new unsigned int[MAX_IMAGE_DIMENSIONS]; FILL_C_ARRAY( m_Dimensions, MAX_IMAGE_DIMENSIONS, 0u); this->Initialize( other.GetPixelType(), other.GetDimension(), other.GetDimensions()); + //Since the above called "Initialize" method doesn't take the geometry into account we need to set it + //here manually + this->SetGeometry(dynamic_cast(other.GetGeometry()->Clone().GetPointer())); + if (this->GetDimension() > 3) { const unsigned int time_steps = this->GetDimension(3); for (unsigned int i = 0u; i < time_steps; ++i) { ImageDataItemPointer volume = const_cast(other).GetVolumeData(i); this->SetVolume(volume->GetData(), i); } } else { ImageDataItemPointer volume = const_cast(other).GetVolumeData(0); this->SetVolume(volume->GetData(), 0); } } mitk::Image::~Image() { Clear(); m_ReferenceCountLock.Lock(); m_ReferenceCount = 3; m_ReferenceCountLock.Unlock(); m_ReferenceCountLock.Lock(); m_ReferenceCount = 0; m_ReferenceCountLock.Unlock(); if(m_OffsetTable != NULL) delete [] m_OffsetTable; if(m_ImageStatistics != NULL) delete m_ImageStatistics; } const mitk::PixelType mitk::Image::GetPixelType(int n) const { return this->m_ImageDescriptor->GetChannelTypeById(n); } unsigned int mitk::Image::GetDimension() const { return m_Dimension; } unsigned int mitk::Image::GetDimension(int i) const { if((i>=0) && (i<(int)m_Dimension)) return m_Dimensions[i]; return 1; } void* mitk::Image::GetData() { if(m_Initialized==false) { if(GetSource().IsNull()) return NULL; if(GetSource()->Updating()==false) GetSource()->UpdateOutputInformation(); } m_CompleteData=GetChannelData(); // update channel's data // if data was not available at creation point, the m_Data of channel descriptor is NULL // if data present, it won't be overwritten m_ImageDescriptor->GetChannelDescriptor(0).SetData(m_CompleteData->GetData()); return m_CompleteData->GetData(); } template void AccessPixel( const mitk::PixelType ptype, void* data, const unsigned int offset, double& value ) { value = 0.0; if( data == NULL ) return; if(ptype.GetBpe() != 24) { value = (double) (((T*) data)[ offset ]); } else { const unsigned int rgboffset = 3 * offset; double returnvalue = (((T*) data)[rgboffset ]); returnvalue += (((T*) data)[rgboffset + 1]); returnvalue += (((T*) data)[rgboffset + 2]); value = returnvalue; } } double mitk::Image::GetPixelValueByIndex(const mitk::Index3D &position, unsigned int timestep) { double value = 0; if (this->GetTimeSteps() < timestep) { timestep = this->GetTimeSteps(); } value = 0.0; const unsigned int* imageDims = this->m_ImageDescriptor->GetDimensions(); const mitk::PixelType ptype = this->m_ImageDescriptor->GetChannelTypeById(0); // Comparison ?>=0 not needed since all position[i] and timestep are unsigned int // (position[0]>=0 && position[1] >=0 && position[2]>=0 && timestep>=0) // && if ( (unsigned int)position[0] < imageDims[0] && (unsigned int)position[1] < imageDims[1] && ( (imageDims[2] == 0) || (unsigned int)position[2] < imageDims[2]) // in case a 2D Image passed in, the third dimension could be set to 0 causing the if() to fail /*&& (unsigned int)timestep < imageDims[3]*/ ) { const unsigned int offset = position[0] + position[1]*imageDims[0] + position[2]*imageDims[0]*imageDims[1] + timestep*imageDims[0]*imageDims[1]*imageDims[2]; mitkPixelTypeMultiplex3( AccessPixel, ptype, this->GetData(), offset, value ); } return value; } double mitk::Image::GetPixelValueByWorldCoordinate(const mitk::Point3D& position, unsigned int timestep) { double value = 0.0; if (this->GetTimeSteps() < timestep) { timestep = this->GetTimeSteps(); } Index3D itkIndex; this->GetGeometry()->WorldToIndex(position, itkIndex); const unsigned int* imageDims = this->m_ImageDescriptor->GetDimensions(); const mitk::PixelType ptype = this->m_ImageDescriptor->GetChannelTypeById(0); //if ( (itkIndex[0]>=0 && itkIndex[1] >=0 && itkIndex[2]>=0 && timestep>=0) // && // lines above taken from comparison since always true due to unsigned type - if((unsigned int)itkIndex[0] < imageDims[0] && + if (((unsigned int)itkIndex[0] < imageDims[0] && (unsigned int)itkIndex[1] < imageDims[1] && - (imageDims[2] == 0) || ((unsigned int)itkIndex[2] < imageDims[2])) // in case a 2D Image passed in, the third dimension could be set to 0 causing the if() to fail + (imageDims[2] == 0) ) || ((unsigned int)itkIndex[2] < imageDims[2])) // in case a 2D Image passed in, the third dimension could be set to 0 causing the if() to fail { const unsigned int offset = itkIndex[0] + itkIndex[1]*imageDims[0] + itkIndex[2]*imageDims[0]*imageDims[1] + timestep*imageDims[0]*imageDims[1]*imageDims[2]; mitkPixelTypeMultiplex3( AccessPixel, ptype, this->GetData(), offset, value ); } return value; } vtkImageData* mitk::Image::GetVtkImageData(int t, int n) { if(m_Initialized==false) { if(GetSource().IsNull()) return NULL; if(GetSource()->Updating()==false) GetSource()->UpdateOutputInformation(); } ImageDataItemPointer volume=GetVolumeData(t, n); if(volume.GetPointer()==NULL || volume->GetVtkImageData() == NULL) return NULL; float *fspacing = const_cast(GetSlicedGeometry(t)->GetFloatSpacing()); double dspacing[3] = {fspacing[0],fspacing[1],fspacing[2]}; volume->GetVtkImageData()->SetSpacing( dspacing ); return volume->GetVtkImageData(); } mitk::Image::ImageDataItemPointer mitk::Image::GetSliceData(int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) { if(IsValidSlice(s,t,n)==false) return NULL; const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); // slice directly available? int pos=GetSliceIndex(s,t,n); if(m_Slices[pos].GetPointer()!=NULL) return m_Slices[pos]; // is slice available as part of a volume that is available? ImageDataItemPointer sl, ch, vol; vol=m_Volumes[GetVolumeIndex(t,n)]; if((vol.GetPointer()!=NULL) && (vol->IsComplete())) { sl=new ImageDataItem(*vol, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*m_OffsetTable[2]*(ptypeSize)); sl->SetComplete(true); return m_Slices[pos]=sl; } // is slice available as part of a channel that is available? ch=m_Channels[n]; if((ch.GetPointer()!=NULL) && (ch->IsComplete())) { sl=new ImageDataItem(*ch, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, (((size_t) s)*m_OffsetTable[2]+((size_t) t)*m_OffsetTable[3])*(ptypeSize)); sl->SetComplete(true); return m_Slices[pos]=sl; } // slice is unavailable. Can we calculate it? if((GetSource().IsNotNull()) && (GetSource()->Updating()==false)) { // ... wir mussen rechnen!!! .... m_RequestedRegion.SetIndex(0, 0); m_RequestedRegion.SetIndex(1, 0); m_RequestedRegion.SetIndex(2, s); m_RequestedRegion.SetIndex(3, t); m_RequestedRegion.SetIndex(4, n); m_RequestedRegion.SetSize(0, m_Dimensions[0]); m_RequestedRegion.SetSize(1, m_Dimensions[1]); m_RequestedRegion.SetSize(2, 1); m_RequestedRegion.SetSize(3, 1); m_RequestedRegion.SetSize(4, 1); m_RequestedRegionInitialized=true; GetSource()->Update(); if(IsSliceSet(s,t,n)) //yes: now we can call ourselves without the risk of a endless loop (see "if" above) return GetSliceData(s,t,n,data,importMemoryManagement); else return NULL; } else { ImageDataItemPointer item = AllocateSliceData(s,t,n,data,importMemoryManagement); item->SetComplete(true); return item; } } mitk::Image::ImageDataItemPointer mitk::Image::GetVolumeData(int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) { if(IsValidVolume(t,n)==false) return NULL; ImageDataItemPointer ch, vol; // volume directly available? int pos=GetVolumeIndex(t,n); vol=m_Volumes[pos]; if((vol.GetPointer()!=NULL) && (vol->IsComplete())) return vol; const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); // is volume available as part of a channel that is available? ch=m_Channels[n]; if((ch.GetPointer()!=NULL) && (ch->IsComplete())) { vol=new ImageDataItem(*ch, m_ImageDescriptor, 3, data, importMemoryManagement == ManageMemory, (((size_t) t)*m_OffsetTable[3])*(ptypeSize)); vol->SetComplete(true); return m_Volumes[pos]=vol; } // let's see if all slices of the volume are set, so that we can (could) combine them to a volume bool complete=true; unsigned int s; for(s=0;sSetComplete(true); } else { mitk::PixelType chPixelType = this->m_ImageDescriptor->GetChannelTypeById(n); vol=m_Volumes[pos]; // ok, let's combine the slices! if(vol.GetPointer()==NULL) vol=new ImageDataItem( chPixelType, 3, m_Dimensions, NULL, true); vol->SetComplete(true); size_t size=m_OffsetTable[2]*(ptypeSize); for(s=0;sGetParent()!=vol) { // copy data of slices in volume size_t offset = ((size_t) s)*size; std::memcpy(static_cast(vol->GetData())+offset, sl->GetData(), size); // FIXME mitkIpPicDescriptor * pic = sl->GetPicDescriptor(); // replace old slice with reference to volume sl=new ImageDataItem(*vol, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*size); sl->SetComplete(true); //mitkIpFuncCopyTags(sl->GetPicDescriptor(), pic); m_Slices[posSl]=sl; } } //if(vol->GetPicDescriptor()->info->tags_head==NULL) // mitkIpFuncCopyTags(vol->GetPicDescriptor(), m_Slices[GetSliceIndex(0,t,n)]->GetPicDescriptor()); } return m_Volumes[pos]=vol; } // volume is unavailable. Can we calculate it? if((GetSource().IsNotNull()) && (GetSource()->Updating()==false)) { // ... wir muessen rechnen!!! .... m_RequestedRegion.SetIndex(0, 0); m_RequestedRegion.SetIndex(1, 0); m_RequestedRegion.SetIndex(2, 0); m_RequestedRegion.SetIndex(3, t); m_RequestedRegion.SetIndex(4, n); m_RequestedRegion.SetSize(0, m_Dimensions[0]); m_RequestedRegion.SetSize(1, m_Dimensions[1]); m_RequestedRegion.SetSize(2, m_Dimensions[2]); m_RequestedRegion.SetSize(3, 1); m_RequestedRegion.SetSize(4, 1); m_RequestedRegionInitialized=true; GetSource()->Update(); if(IsVolumeSet(t,n)) //yes: now we can call ourselves without the risk of a endless loop (see "if" above) return GetVolumeData(t,n,data,importMemoryManagement); else return NULL; } else { ImageDataItemPointer item = AllocateVolumeData(t,n,data,importMemoryManagement); item->SetComplete(true); return item; } } mitk::Image::ImageDataItemPointer mitk::Image::GetChannelData(int n, void *data, ImportMemoryManagementType importMemoryManagement) { if(IsValidChannel(n)==false) return NULL; ImageDataItemPointer ch, vol; ch=m_Channels[n]; if((ch.GetPointer()!=NULL) && (ch->IsComplete())) return ch; // let's see if all volumes are set, so that we can (could) combine them to a channel if(IsChannelSet(n)) { // if there is only one time frame we do not need to combine anything if(m_Dimensions[3]<=1) { vol=GetVolumeData(0,n,data,importMemoryManagement); ch=new ImageDataItem(*vol, m_ImageDescriptor, m_ImageDescriptor->GetNumberOfDimensions(), data, importMemoryManagement == ManageMemory); ch->SetComplete(true); } else { const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); ch=m_Channels[n]; // ok, let's combine the volumes! if(ch.GetPointer()==NULL) ch=new ImageDataItem(this->m_ImageDescriptor, NULL, true); ch->SetComplete(true); size_t size=m_OffsetTable[m_Dimension-1]*(ptypeSize); unsigned int t; ImageDataItemPointerArray::iterator slicesIt = m_Slices.begin()+n*m_Dimensions[2]*m_Dimensions[3]; for(t=0;tGetParent()!=ch) { // copy data of volume in channel size_t offset = ((size_t) t)*m_OffsetTable[3]*(ptypeSize); std::memcpy(static_cast(ch->GetData())+offset, vol->GetData(), size); // REVEIW FIX mitkIpPicDescriptor * pic = vol->GetPicDescriptor(); // replace old volume with reference to channel vol=new ImageDataItem(*ch, m_ImageDescriptor, 3, data, importMemoryManagement == ManageMemory, offset); vol->SetComplete(true); //mitkIpFuncCopyTags(vol->GetPicDescriptor(), pic); m_Volumes[posVol]=vol; // get rid of slices - they may point to old volume ImageDataItemPointer dnull=NULL; for(unsigned int i = 0; i < m_Dimensions[2]; ++i, ++slicesIt) { assert(slicesIt != m_Slices.end()); *slicesIt = dnull; } } } // REVIEW FIX // if(ch->GetPicDescriptor()->info->tags_head==NULL) // mitkIpFuncCopyTags(ch->GetPicDescriptor(), m_Volumes[GetVolumeIndex(0,n)]->GetPicDescriptor()); } return m_Channels[n]=ch; } // channel is unavailable. Can we calculate it? if((GetSource().IsNotNull()) && (GetSource()->Updating()==false)) { // ... wir muessen rechnen!!! .... m_RequestedRegion.SetIndex(0, 0); m_RequestedRegion.SetIndex(1, 0); m_RequestedRegion.SetIndex(2, 0); m_RequestedRegion.SetIndex(3, 0); m_RequestedRegion.SetIndex(4, n); m_RequestedRegion.SetSize(0, m_Dimensions[0]); m_RequestedRegion.SetSize(1, m_Dimensions[1]); m_RequestedRegion.SetSize(2, m_Dimensions[2]); m_RequestedRegion.SetSize(3, m_Dimensions[3]); m_RequestedRegion.SetSize(4, 1); m_RequestedRegionInitialized=true; GetSource()->Update(); // did it work? if(IsChannelSet(n)) //yes: now we can call ourselves without the risk of a endless loop (see "if" above) return GetChannelData(n,data,importMemoryManagement); else return NULL; } else { ImageDataItemPointer item = AllocateChannelData(n,data,importMemoryManagement); item->SetComplete(true); return item; } } bool mitk::Image::IsSliceSet(int s, int t, int n) const { if(IsValidSlice(s,t,n)==false) return false; if(m_Slices[GetSliceIndex(s,t,n)].GetPointer()!=NULL) return true; ImageDataItemPointer ch, vol; vol=m_Volumes[GetVolumeIndex(t,n)]; if((vol.GetPointer()!=NULL) && (vol->IsComplete())) return true; ch=m_Channels[n]; if((ch.GetPointer()!=NULL) && (ch->IsComplete())) return true; return false; } bool mitk::Image::IsVolumeSet(int t, int n) const { if(IsValidVolume(t,n)==false) return false; ImageDataItemPointer ch, vol; // volume directly available? vol=m_Volumes[GetVolumeIndex(t,n)]; if((vol.GetPointer()!=NULL) && (vol->IsComplete())) return true; // is volume available as part of a channel that is available? ch=m_Channels[n]; if((ch.GetPointer()!=NULL) && (ch->IsComplete())) return true; // let's see if all slices of the volume are set, so that we can (could) combine them to a volume unsigned int s; for(s=0;sIsComplete())) return true; // let's see if all volumes are set, so that we can (could) combine them to a channel unsigned int t; for(t=0;t(data), s, t, n, CopyMemory); } bool mitk::Image::SetVolume(const void *data, int t, int n) { // const_cast is no risk for ImportMemoryManagementType == CopyMemory return SetImportVolume(const_cast(data), t, n, CopyMemory); } bool mitk::Image::SetChannel(const void *data, int n) { // const_cast is no risk for ImportMemoryManagementType == CopyMemory return SetImportChannel(const_cast(data), n, CopyMemory); } bool mitk::Image::SetImportSlice(void *data, int s, int t, int n, ImportMemoryManagementType importMemoryManagement) { if(IsValidSlice(s,t,n)==false) return false; ImageDataItemPointer sl; const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); if(IsSliceSet(s,t,n)) { sl=GetSliceData(s,t,n,data,importMemoryManagement); if(sl->GetManageMemory()==false) { sl=AllocateSliceData(s,t,n,data,importMemoryManagement); if(sl.GetPointer()==NULL) return false; } if ( sl->GetData() != data ) std::memcpy(sl->GetData(), data, m_OffsetTable[2]*(ptypeSize)); sl->Modified(); //we have changed the data: call Modified()! Modified(); } else { sl=AllocateSliceData(s,t,n,data,importMemoryManagement); if(sl.GetPointer()==NULL) return false; if ( sl->GetData() != data ) std::memcpy(sl->GetData(), data, m_OffsetTable[2]*(ptypeSize)); //we just added a missing slice, which is not regarded as modification. //Therefore, we do not call Modified()! } return true; } bool mitk::Image::SetImportVolume(void *data, int t, int n, ImportMemoryManagementType importMemoryManagement) { if(IsValidVolume(t,n)==false) return false; const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); ImageDataItemPointer vol; if(IsVolumeSet(t,n)) { vol=GetVolumeData(t,n,data,importMemoryManagement); if(vol->GetManageMemory()==false) { vol=AllocateVolumeData(t,n,data,importMemoryManagement); if(vol.GetPointer()==NULL) return false; } if ( vol->GetData() != data ) std::memcpy(vol->GetData(), data, m_OffsetTable[3]*(ptypeSize)); vol->Modified(); vol->SetComplete(true); //we have changed the data: call Modified()! Modified(); } else { vol=AllocateVolumeData(t,n,data,importMemoryManagement); if(vol.GetPointer()==NULL) return false; if ( vol->GetData() != data ) { std::memcpy(vol->GetData(), data, m_OffsetTable[3]*(ptypeSize)); } vol->SetComplete(true); this->m_ImageDescriptor->GetChannelDescriptor(n).SetData( vol->GetData() ); //we just added a missing Volume, which is not regarded as modification. //Therefore, we do not call Modified()! } return true; } bool mitk::Image::SetImportChannel(void *data, int n, ImportMemoryManagementType importMemoryManagement) { if(IsValidChannel(n)==false) return false; // channel descriptor const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); ImageDataItemPointer ch; if(IsChannelSet(n)) { ch=GetChannelData(n,data,importMemoryManagement); if(ch->GetManageMemory()==false) { ch=AllocateChannelData(n,data,importMemoryManagement); if(ch.GetPointer()==NULL) return false; } if ( ch->GetData() != data ) std::memcpy(ch->GetData(), data, m_OffsetTable[4]*(ptypeSize)); ch->Modified(); ch->SetComplete(true); //we have changed the data: call Modified()! Modified(); } else { ch=AllocateChannelData(n,data,importMemoryManagement); if(ch.GetPointer()==NULL) return false; if ( ch->GetData() != data ) std::memcpy(ch->GetData(), data, m_OffsetTable[4]*(ptypeSize)); ch->SetComplete(true); this->m_ImageDescriptor->GetChannelDescriptor(n).SetData( ch->GetData() ); //we just added a missing Channel, which is not regarded as modification. //Therefore, we do not call Modified()! } return true; } void mitk::Image::Initialize() { ImageDataItemPointerArray::iterator it, end; for( it=m_Slices.begin(), end=m_Slices.end(); it!=end; ++it ) { (*it)=NULL; } for( it=m_Volumes.begin(), end=m_Volumes.end(); it!=end; ++it ) { (*it)=NULL; } for( it=m_Channels.begin(), end=m_Channels.end(); it!=end; ++it ) { (*it)=NULL; } m_CompleteData = NULL; if( m_ImageStatistics == NULL) { m_ImageStatistics = new mitk::ImageStatisticsHolder( this ); } SetRequestedRegionToLargestPossibleRegion(); } void mitk::Image::Initialize(const mitk::ImageDescriptor::Pointer inDesc) { // store the descriptor this->m_ImageDescriptor = inDesc; // initialize image this->Initialize( inDesc->GetChannelDescriptor(0).GetPixelType(), inDesc->GetNumberOfDimensions(), inDesc->GetDimensions(), 1 ); } void mitk::Image::Initialize(const mitk::PixelType& type, unsigned int dimension, const unsigned int *dimensions, unsigned int channels) { Clear(); m_Dimension=dimension; if(!dimensions) itkExceptionMacro(<< "invalid zero dimension image"); unsigned int i; for(i=0;im_ImageDescriptor = mitk::ImageDescriptor::New(); this->m_ImageDescriptor->Initialize( this->m_Dimensions, this->m_Dimension ); for(i=0;i<4;++i) { m_LargestPossibleRegion.SetIndex(i, 0); m_LargestPossibleRegion.SetSize (i, m_Dimensions[i]); } m_LargestPossibleRegion.SetIndex(i, 0); m_LargestPossibleRegion.SetSize(i, channels); if(m_LargestPossibleRegion.GetNumberOfPixels()==0) { delete [] m_Dimensions; m_Dimensions = NULL; return; } for( unsigned int i=0u; im_ImageDescriptor->AddNewChannel( type ); } PlaneGeometry::Pointer planegeometry = PlaneGeometry::New(); planegeometry->InitializeStandardPlane(m_Dimensions[0], m_Dimensions[1]); SlicedGeometry3D::Pointer slicedGeometry = SlicedGeometry3D::New(); slicedGeometry->InitializeEvenlySpaced(planegeometry, m_Dimensions[2]); if(dimension>=4) { TimeBounds timebounds; timebounds[0] = 0.0; timebounds[1] = 1.0; slicedGeometry->SetTimeBounds(timebounds); } TimeSlicedGeometry::Pointer timeSliceGeometry = TimeSlicedGeometry::New(); timeSliceGeometry->InitializeEvenlyTimed(slicedGeometry, m_Dimensions[3]); timeSliceGeometry->ImageGeometryOn(); SetGeometry(timeSliceGeometry); ImageDataItemPointer dnull=NULL; m_Channels.assign(GetNumberOfChannels(), dnull); m_Volumes.assign(GetNumberOfChannels()*m_Dimensions[3], dnull); m_Slices.assign(GetNumberOfChannels()*m_Dimensions[3]*m_Dimensions[2], dnull); ComputeOffsetTable(); Initialize(); m_Initialized = true; } void mitk::Image::Initialize(const mitk::PixelType& type, const mitk::Geometry3D& geometry, unsigned int channels, int tDim ) { unsigned int dimensions[5]; dimensions[0] = (unsigned int)(geometry.GetExtent(0)+0.5); dimensions[1] = (unsigned int)(geometry.GetExtent(1)+0.5); dimensions[2] = (unsigned int)(geometry.GetExtent(2)+0.5); dimensions[3] = 0; dimensions[4] = 0; unsigned int dimension = 2; if ( dimensions[2] > 1 ) dimension = 3; if ( tDim > 0) { dimensions[3] = tDim; } else { const mitk::TimeSlicedGeometry* timeGeometry = dynamic_cast(&geometry); if ( timeGeometry != NULL ) { dimensions[3] = timeGeometry->GetTimeSteps(); } } if ( dimensions[3] > 1 ) dimension = 4; Initialize( type, dimension, dimensions, channels ); SetGeometry(static_cast(geometry.Clone().GetPointer())); mitk::BoundingBox::BoundsArrayType bounds = geometry.GetBoundingBox()->GetBounds(); if( (bounds[0] != 0.0) || (bounds[2] != 0.0) || (bounds[4] != 0.0) ) { SlicedGeometry3D* slicedGeometry = GetSlicedGeometry(0); mitk::Point3D origin; origin.Fill(0.0); slicedGeometry->IndexToWorld(origin, origin); bounds[1]-=bounds[0]; bounds[3]-=bounds[2]; bounds[5]-=bounds[4]; bounds[0] = 0.0; bounds[2] = 0.0; bounds[4] = 0.0; this->m_ImageDescriptor->Initialize( this->m_Dimensions, this->m_Dimension ); slicedGeometry->SetBounds(bounds); slicedGeometry->GetIndexToWorldTransform()->SetOffset(origin.Get_vnl_vector().data_block()); GetTimeSlicedGeometry()->InitializeEvenlyTimed(slicedGeometry, m_Dimensions[3]); } } void mitk::Image::Initialize(const mitk::PixelType& type, int sDim, const mitk::Geometry2D& geometry2d, bool flipped, unsigned int channels, int tDim ) { SlicedGeometry3D::Pointer slicedGeometry = SlicedGeometry3D::New(); slicedGeometry->InitializeEvenlySpaced(static_cast(geometry2d.Clone().GetPointer()), sDim, flipped); Initialize(type, *slicedGeometry, channels, tDim); } void mitk::Image::Initialize(const mitk::Image* image) { Initialize(image->GetPixelType(), *image->GetTimeSlicedGeometry()); } void mitk::Image::Initialize(vtkImageData* vtkimagedata, int channels, int tDim, int sDim) { if(vtkimagedata==NULL) return; m_Dimension=vtkimagedata->GetDataDimension(); unsigned int i, *tmpDimensions=new unsigned int[m_Dimension>4?m_Dimension:4]; for(i=0;iGetDimensions()[i]; if(m_Dimension<4) { unsigned int *p; for(i=0,p=tmpDimensions+m_Dimension;i<4-m_Dimension;++i, ++p) *p=1; } if(sDim>=0) { tmpDimensions[2]=sDim; if(m_Dimension < 3) m_Dimension = 3; } if(tDim>=0) { tmpDimensions[3]=tDim; if(m_Dimension < 4) m_Dimension = 4; } switch ( vtkimagedata->GetScalarType() ) { case VTK_BIT: case VTK_CHAR: //pixelType.Initialize(typeid(char), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_UNSIGNED_CHAR: //pixelType.Initialize(typeid(unsigned char), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_SHORT: //pixelType.Initialize(typeid(short), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_UNSIGNED_SHORT: //pixelType.Initialize(typeid(unsigned short), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_INT: //pixelType.Initialize(typeid(int), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_UNSIGNED_INT: //pixelType.Initialize(typeid(unsigned int), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_LONG: //pixelType.Initialize(typeid(long), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_UNSIGNED_LONG: //pixelType.Initialize(typeid(unsigned long), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_FLOAT: //pixelType.Initialize(typeid(float), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; case VTK_DOUBLE: //pixelType.Initialize(typeid(double), vtkimagedata->GetNumberOfScalarComponents()); Initialize(mitk::MakeScalarPixelType(), m_Dimension, tmpDimensions, channels); break; default: break; } /* Initialize(pixelType, m_Dimension, tmpDimensions, channels); */ const double *spacinglist = vtkimagedata->GetSpacing(); Vector3D spacing; FillVector3D(spacing, spacinglist[0], 1.0, 1.0); if(m_Dimension>=2) spacing[1]=spacinglist[1]; if(m_Dimension>=3) spacing[2]=spacinglist[2]; // access origin of vtkImage Point3D origin; vtkFloatingPointType vtkorigin[3]; vtkimagedata->GetOrigin(vtkorigin); FillVector3D(origin, vtkorigin[0], 0.0, 0.0); if(m_Dimension>=2) origin[1]=vtkorigin[1]; if(m_Dimension>=3) origin[2]=vtkorigin[2]; SlicedGeometry3D* slicedGeometry = GetSlicedGeometry(0); // re-initialize PlaneGeometry with origin and direction PlaneGeometry* planeGeometry = static_cast(slicedGeometry->GetGeometry2D(0)); planeGeometry->SetOrigin(origin); // re-initialize SlicedGeometry3D slicedGeometry->SetOrigin(origin); slicedGeometry->SetSpacing(spacing); GetTimeSlicedGeometry()->InitializeEvenlyTimed(slicedGeometry, m_Dimensions[3]); delete [] tmpDimensions; } bool mitk::Image::IsValidSlice(int s, int t, int n) const { if(m_Initialized) return ((s>=0) && (s<(int)m_Dimensions[2]) && (t>=0) && (t< (int) m_Dimensions[3]) && (n>=0) && (n< (int)GetNumberOfChannels())); else return false; } bool mitk::Image::IsValidVolume(int t, int n) const { if(m_Initialized) return IsValidSlice(0, t, n); else return false; } bool mitk::Image::IsValidChannel(int n) const { if(m_Initialized) return IsValidSlice(0, 0, n); else return false; } void mitk::Image::ComputeOffsetTable() { if(m_OffsetTable!=NULL) delete [] m_OffsetTable; m_OffsetTable=new size_t[m_Dimension>4 ? m_Dimension+1 : 4+1]; unsigned int i; size_t num=1; m_OffsetTable[0] = 1; for (i=0; i < m_Dimension; ++i) { num *= m_Dimensions[i]; m_OffsetTable[i+1] = num; } for (;i < 4; ++i) m_OffsetTable[i+1] = num; } bool mitk::Image::IsValidTimeStep(int t) const { return ( ( m_Dimension >= 4 && t <= (int)m_Dimensions[3] && t > 0 ) || (t == 0) ); } void mitk::Image::Expand(unsigned int timeSteps) { if(timeSteps < 1) itkExceptionMacro(<< "Invalid timestep in Image!"); Superclass::Expand(timeSteps); } int mitk::Image::GetSliceIndex(int s, int t, int n) const { if(IsValidSlice(s,t,n)==false) return false; return ((size_t)s)+((size_t) t)*m_Dimensions[2]+((size_t) n)*m_Dimensions[3]*m_Dimensions[2]; //?? } int mitk::Image::GetVolumeIndex(int t, int n) const { if(IsValidVolume(t,n)==false) return false; return ((size_t)t)+((size_t) n)*m_Dimensions[3]; //?? } mitk::Image::ImageDataItemPointer mitk::Image::AllocateSliceData(int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) { int pos; pos=GetSliceIndex(s,t,n); const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); // is slice available as part of a volume that is available? ImageDataItemPointer sl, ch, vol; vol=m_Volumes[GetVolumeIndex(t,n)]; if(vol.GetPointer()!=NULL) { sl=new ImageDataItem(*vol, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*m_OffsetTable[2]*(ptypeSize)); sl->SetComplete(true); return m_Slices[pos]=sl; } // is slice available as part of a channel that is available? ch=m_Channels[n]; if(ch.GetPointer()!=NULL) { sl=new ImageDataItem(*ch, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, (((size_t) s)*m_OffsetTable[2]+((size_t) t)*m_OffsetTable[3])*(ptypeSize)); sl->SetComplete(true); return m_Slices[pos]=sl; } // allocate new volume (instead of a single slice to keep data together!) m_Volumes[GetVolumeIndex(t,n)]=vol=AllocateVolumeData(t,n,NULL,importMemoryManagement); sl=new ImageDataItem(*vol, m_ImageDescriptor, 2, data, importMemoryManagement == ManageMemory, ((size_t) s)*m_OffsetTable[2]*(ptypeSize)); sl->SetComplete(true); return m_Slices[pos]=sl; ////ALTERNATIVE: //// allocate new slice //sl=new ImageDataItem(*m_PixelType, 2, m_Dimensions); //m_Slices[pos]=sl; //return vol; } mitk::Image::ImageDataItemPointer mitk::Image::AllocateVolumeData(int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) { int pos; pos=GetVolumeIndex(t,n); const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); // is volume available as part of a channel that is available? ImageDataItemPointer ch, vol; ch=m_Channels[n]; if(ch.GetPointer()!=NULL) { vol=new ImageDataItem(*ch, m_ImageDescriptor, 3, data,importMemoryManagement == ManageMemory, (((size_t) t)*m_OffsetTable[3])*(ptypeSize)); return m_Volumes[pos]=vol; } mitk::PixelType chPixelType = this->m_ImageDescriptor->GetChannelTypeById(n); // allocate new volume if(importMemoryManagement == CopyMemory) { vol=new ImageDataItem( chPixelType, 3, m_Dimensions, NULL, true); if(data != NULL) std::memcpy(vol->GetData(), data, m_OffsetTable[3]*(ptypeSize)); } else { vol=new ImageDataItem( chPixelType, 3, m_Dimensions, data, importMemoryManagement == ManageMemory); } m_Volumes[pos]=vol; return vol; } mitk::Image::ImageDataItemPointer mitk::Image::AllocateChannelData(int n, void *data, ImportMemoryManagementType importMemoryManagement) { ImageDataItemPointer ch; // allocate new channel if(importMemoryManagement == CopyMemory) { const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); ch=new ImageDataItem(this->m_ImageDescriptor, NULL, true); if(data != NULL) std::memcpy(ch->GetData(), data, m_OffsetTable[4]*(ptypeSize)); } else { ch=new ImageDataItem(this->m_ImageDescriptor, data, importMemoryManagement == ManageMemory); } m_Channels[n]=ch; return ch; } unsigned int* mitk::Image::GetDimensions() const { return m_Dimensions; } void mitk::Image::Clear() { Superclass::Clear(); delete [] m_Dimensions; m_Dimensions = NULL; } void mitk::Image::SetGeometry(Geometry3D* aGeometry3D) { // Please be aware of the 0.5 offset/pixel-center issue! See Geometry documentation for further information if(aGeometry3D->GetImageGeometry()==false) { MITK_INFO << "WARNING: Applied a non-image geometry onto an image. Please be SURE that this geometry is pixel-center-based! If it is not, you need to call Geometry3D->ChangeImageGeometryConsideringOriginOffset(true) before calling image->setGeometry(..)\n"; } Superclass::SetGeometry(aGeometry3D); GetTimeSlicedGeometry()->ImageGeometryOn(); } void mitk::Image::PrintSelf(std::ostream& os, itk::Indent indent) const { unsigned char i; if(m_Initialized) { os << indent << " Dimension: " << m_Dimension << std::endl; os << indent << " Dimensions: "; for(i=0; i < m_Dimension; ++i) os << GetDimension(i) << " "; os << std::endl; for(unsigned int ch=0; ch < this->m_ImageDescriptor->GetNumberOfChannels(); ch++) { mitk::PixelType chPixelType = this->m_ImageDescriptor->GetChannelTypeById(ch); os << indent << " Channel: " << this->m_ImageDescriptor->GetChannelName(ch) << std::endl; os << indent << " PixelType: " << chPixelType.GetTypeId().name() << std::endl; os << indent << " BitsPerElement: " << chPixelType.GetSize() << std::endl; os << indent << " NumberOfComponents: " << chPixelType.GetNumberOfComponents() << std::endl; os << indent << " BitsPerComponent: " << chPixelType.GetBitsPerComponent() << std::endl; } } else { os << indent << " Image not initialized: m_Initialized: false" << std::endl; } Superclass::PrintSelf(os,indent); } bool mitk::Image::IsRotated() const { const mitk::Geometry3D* geo = this->GetGeometry(); bool ret = false; if(geo) { const vnl_matrix_fixed & mx = geo->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix(); float ref = 0; for(short k = 0; k < 3; ++k) ref += mx[k][k]; ref/=1000; // Arbitrary value; if a non-diagonal (nd) element is bigger then this, matrix is considered nd. for(short i = 0; i < 3; ++i) { for(short j = 0; j < 3; ++j) { if(i != j) { if(abs(mx[i][j]) > ref) // matrix is nd ret = true; } } } } return ret; } #include "mitkImageStatisticsHolder.h" //##Documentation mitk::ScalarType mitk::Image::GetScalarValueMin(int t) const { return m_ImageStatistics->GetScalarValueMin(t); } //##Documentation //## \brief Get the maximum for scalar images mitk::ScalarType mitk::Image::GetScalarValueMax(int t) const { return m_ImageStatistics->GetScalarValueMax(t); } //##Documentation //## \brief Get the second smallest value for scalar images mitk::ScalarType mitk::Image::GetScalarValue2ndMin(int t) const { return m_ImageStatistics->GetScalarValue2ndMin(t); } mitk::ScalarType mitk::Image::GetScalarValueMinNoRecompute( unsigned int t ) const { return m_ImageStatistics->GetScalarValueMinNoRecompute(t); } mitk::ScalarType mitk::Image::GetScalarValue2ndMinNoRecompute( unsigned int t ) const { return m_ImageStatistics->GetScalarValue2ndMinNoRecompute(t); } mitk::ScalarType mitk::Image::GetScalarValue2ndMax(int t) const { return m_ImageStatistics->GetScalarValue2ndMax(t); } mitk::ScalarType mitk::Image::GetScalarValueMaxNoRecompute( unsigned int t) const { return m_ImageStatistics->GetScalarValueMaxNoRecompute(t); } mitk::ScalarType mitk::Image::GetScalarValue2ndMaxNoRecompute( unsigned int t ) const { return m_ImageStatistics->GetScalarValue2ndMaxNoRecompute(t); } mitk::ScalarType mitk::Image::GetCountOfMinValuedVoxels(int t ) const { return m_ImageStatistics->GetCountOfMinValuedVoxels(t); } mitk::ScalarType mitk::Image::GetCountOfMaxValuedVoxels(int t) const { return m_ImageStatistics->GetCountOfMaxValuedVoxels(t); } unsigned int mitk::Image::GetCountOfMaxValuedVoxelsNoRecompute( unsigned int t ) const { return m_ImageStatistics->GetCountOfMaxValuedVoxelsNoRecompute(t); } unsigned int mitk::Image::GetCountOfMinValuedVoxelsNoRecompute( unsigned int t ) const { return m_ImageStatistics->GetCountOfMinValuedVoxelsNoRecompute(t); } diff --git a/Core/Code/DataManagement/mitkPointSet.cpp b/Core/Code/DataManagement/mitkPointSet.cpp index 2a3828844b..8abce42872 100755 --- a/Core/Code/DataManagement/mitkPointSet.cpp +++ b/Core/Code/DataManagement/mitkPointSet.cpp @@ -1,780 +1,787 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkPointSet.h" #include "mitkPointOperation.h" #include "mitkInteractionConst.h" mitk::PointSet::PointSet() { this->InitializeEmpty(); } -mitk::PointSet::PointSet(const PointSet &other): BaseData(other), -m_PointSetSeries(other.m_PointSetSeries), -m_CalculateBoundingBox(other.m_CalculateBoundingBox) +mitk::PointSet::PointSet(const PointSet &other): BaseData(other) { + this->Expand(other.GetTimeSteps()); + for (int t=0; t < other.GetTimeSteps(); t++) + { + for (int i=0; i< other.GetSize(t); i++) + { + this->InsertPoint(i, other.GetPoint(i,t), t); + } + } + this->SetGeometry(other.GetGeometry()); } mitk::PointSet::~PointSet() { this->ClearData(); } void mitk::PointSet::ClearData() { m_PointSetSeries.clear(); Superclass::ClearData(); } void mitk::PointSet::InitializeEmpty() { m_PointSetSeries.resize( 1 ); m_PointSetSeries[0] = DataType::New(); PointDataContainer::Pointer pointData = PointDataContainer::New(); m_PointSetSeries[0]->SetPointData( pointData ); m_CalculateBoundingBox = false; Superclass::InitializeTimeSlicedGeometry(1); m_Initialized = true; } bool mitk::PointSet::IsEmptyTimeStep(unsigned int t) const { return IsInitialized() && (GetSize(t) == 0); } void mitk::PointSet::Expand( unsigned int timeSteps ) { // Check if the vector is long enough to contain the new element // at the given position. If not, expand it with sufficient pre-initialized // elements. // // NOTE: This method will never REDUCE the vector size; it should only // be used to make sure that the vector has enough elements to include the // specified time step. unsigned int oldSize = m_PointSetSeries.size(); if ( timeSteps > oldSize ) { Superclass::Expand( timeSteps ); m_PointSetSeries.resize( timeSteps ); for ( unsigned int i = oldSize; i < timeSteps; ++i ) { m_PointSetSeries[i] = DataType::New(); PointDataContainer::Pointer pointData = PointDataContainer::New(); m_PointSetSeries[i]->SetPointData( pointData ); } //if the size changes, then compute the bounding box m_CalculateBoundingBox = true; this->InvokeEvent( PointSetExtendTimeRangeEvent() ); } } unsigned int mitk::PointSet::GetPointSetSeriesSize() const { return m_PointSetSeries.size(); } int mitk::PointSet::GetSize( unsigned int t ) const { if ( t < m_PointSetSeries.size() ) { return m_PointSetSeries[t]->GetNumberOfPoints(); } else { return 0; } } mitk::PointSet::DataType::Pointer mitk::PointSet::GetPointSet( int t ) const { if ( t < (int)m_PointSetSeries.size() ) { return m_PointSetSeries[t]; } else { return NULL; } } int mitk::PointSet::SearchPoint( Point3D point, float distance, int t ) const { if ( t >= (int)m_PointSetSeries.size() ) { return -1; } // Out is the point which is checked to be the searched point PointType out; out.Fill( 0 ); PointType indexPoint; this->GetGeometry( t )->WorldToIndex(point, indexPoint); // Searching the first point in the Set, that is +- distance far away fro // the given point unsigned int i; PointsContainer::Iterator it, end; end = m_PointSetSeries[t]->GetPoints()->End(); int bestIndex = -1; distance = distance * distance; // To correct errors from converting index to world and world to index if (distance == 0.0) { distance = 0.000001; } ScalarType bestDist = distance; ScalarType dist, tmp; for ( it = m_PointSetSeries[t]->GetPoints()->Begin(), i = 0; it != end; ++it, ++i ) { bool ok = m_PointSetSeries[t]->GetPoints() ->GetElementIfIndexExists( it->Index(), &out ); if ( !ok ) { return -1; } else if ( indexPoint == out ) //if totally equal { return it->Index(); } //distance calculation tmp = out[0] - indexPoint[0]; dist = tmp * tmp; tmp = out[1] - indexPoint[1]; dist += tmp * tmp; tmp = out[2] - indexPoint[2]; dist += tmp * tmp; if ( dist < bestDist ) { bestIndex = it->Index(); bestDist = dist; } } return bestIndex; } mitk::PointSet::PointType mitk::PointSet::GetPoint( PointIdentifier id, int t ) const { PointType out; out.Fill(0); if ( (unsigned int) t >= m_PointSetSeries.size() ) { return out; } if ( m_PointSetSeries[t]->GetPoints()->IndexExists(id) ) { m_PointSetSeries[t]->GetPoint( id, &out ); this->GetGeometry(t)->IndexToWorld( out, out ); return out; } else { return out; } } bool mitk::PointSet ::GetPointIfExists( PointIdentifier id, PointType* point, int t ) const { if ( (unsigned int) t >= m_PointSetSeries.size() ) { return false; } if ( m_PointSetSeries[t]->GetPoints()->GetElementIfIndexExists(id, point) ) { this->GetGeometry( t )->IndexToWorld( *point, *point ); return true; } else { return false; } } void mitk::PointSet::SetPoint( PointIdentifier id, PointType point, int t ) { // Adapt the size of the data vector if necessary this->Expand( t+1 ); mitk::Point3D indexPoint; this->GetGeometry( t )->WorldToIndex( point, indexPoint ); m_PointSetSeries[t]->SetPoint( id, indexPoint ); PointDataType defaultPointData; defaultPointData.id = id; defaultPointData.selected = false; defaultPointData.pointSpec = mitk::PTUNDEFINED; m_PointSetSeries[t]->SetPointData( id, defaultPointData ); //boundingbox has to be computed anyway m_CalculateBoundingBox = true; this->Modified(); } void mitk::PointSet::SetPoint( PointIdentifier id, PointType point, PointSpecificationType spec, int t ) { // Adapt the size of the data vector if necessary this->Expand( t+1 ); mitk::Point3D indexPoint; this->GetGeometry( t )->WorldToIndex( point, indexPoint ); m_PointSetSeries[t]->SetPoint( id, indexPoint ); PointDataType defaultPointData; defaultPointData.id = id; defaultPointData.selected = false; defaultPointData.pointSpec = spec; m_PointSetSeries[t]->SetPointData( id, defaultPointData ); //boundingbox has to be computed anyway m_CalculateBoundingBox = true; this->Modified(); } void mitk::PointSet::InsertPoint( PointIdentifier id, PointType point, int t ) { if ( (unsigned int) t < m_PointSetSeries.size() ) { mitk::Point3D indexPoint; mitk::Geometry3D* tempGeometry = this->GetGeometry( t ); if (tempGeometry == NULL) { MITK_INFO<< __FILE__ << ", l." << __LINE__ << ": GetGeometry of "<< t <<" returned NULL!" << std::endl; return; } tempGeometry->WorldToIndex( point, indexPoint ); m_PointSetSeries[t]->GetPoints()->InsertElement( id, indexPoint ); PointDataType defaultPointData; defaultPointData.id = id; defaultPointData.selected = false; defaultPointData.pointSpec = mitk::PTUNDEFINED; m_PointSetSeries[t]->GetPointData()->InsertElement(id, defaultPointData); //boundingbox has to be computed anyway m_CalculateBoundingBox = true; this->Modified(); } } void mitk::PointSet::InsertPoint( PointIdentifier id, PointType point, PointSpecificationType spec, int t ) { if ( (unsigned int) t < m_PointSetSeries.size() ) { mitk::Point3D indexPoint; mitk::Geometry3D* tempGeometry = this->GetGeometry( t ); if (tempGeometry == NULL) { MITK_INFO<< __FILE__ << ", l." << __LINE__ << ": GetGeometry of "<< t <<" returned NULL!" << std::endl; return; } tempGeometry->WorldToIndex( point, indexPoint ); m_PointSetSeries[t]->GetPoints()->InsertElement( id, indexPoint ); PointDataType defaultPointData; defaultPointData.id = id; defaultPointData.selected = false; defaultPointData.pointSpec = spec; m_PointSetSeries[t]->GetPointData()->InsertElement(id, defaultPointData); //boundingbox has to be computed anyway m_CalculateBoundingBox = true; this->Modified(); } } bool mitk::PointSet::SwapPointPosition( PointIdentifier id, bool moveUpwards, int t ) { if(IndexExists(id, t) ) { PointType point = GetPoint(id,t); if(moveUpwards) {//up if(IndexExists(id-1,t)) { InsertPoint(id, GetPoint(id - 1, t), t); InsertPoint(id-1,point,t); this->Modified(); return true; } } else {//down if(IndexExists(id+1,t)) { InsertPoint(id, GetPoint(id + 1, t), t); InsertPoint(id+1,point,t); this->Modified(); return true; } } } return false; } bool mitk::PointSet::IndexExists( int position, int t ) const { if ( (unsigned int) t < m_PointSetSeries.size() ) { return m_PointSetSeries[t]->GetPoints()->IndexExists( position ); } else { return false; } } bool mitk::PointSet::GetSelectInfo( int position, int t ) const { if ( this->IndexExists( position, t ) ) { PointDataType pointData = { 0, false, PTUNDEFINED }; m_PointSetSeries[t]->GetPointData( position, &pointData ); return pointData.selected; } else { return false; } } void mitk::PointSet::SetSelectInfo( int position, bool selected, int t ) { if ( this->IndexExists( position, t ) ) { // timeStep to ms ScalarType timeInMS = this->GetTimeSlicedGeometry()->TimeStepToMS( t ); // point Point3D point = this->GetPoint( position, t ); PointOperation* op; if (selected) { op = new mitk::PointOperation(OpSELECTPOINT, timeInMS, point, position ); } else { op = new mitk::PointOperation(OpDESELECTPOINT, timeInMS, point, position ); } this->ExecuteOperation( op ); } } mitk::PointSpecificationType mitk::PointSet::GetSpecificationTypeInfo( int position, int t ) const { if ( this->IndexExists( position, t ) ) { PointDataType pointData = { 0, false, PTUNDEFINED }; m_PointSetSeries[t]->GetPointData( position, &pointData ); return pointData.pointSpec; } else { return PTUNDEFINED; } } int mitk::PointSet::GetNumberOfSelected( int t ) const { if ( (unsigned int) t >= m_PointSetSeries.size() ) { return 0; } int numberOfSelected = 0; PointDataIterator it; for ( it = m_PointSetSeries[t]->GetPointData()->Begin(); it != m_PointSetSeries[t]->GetPointData()->End(); it++ ) { if (it->Value().selected == true) { ++numberOfSelected; } } return numberOfSelected; } int mitk::PointSet::SearchSelectedPoint( int t ) const { if ( (unsigned int) t >= m_PointSetSeries.size() ) { return -1; } PointDataIterator it; for ( it = m_PointSetSeries[t]->GetPointData()->Begin(); it != m_PointSetSeries[t]->GetPointData()->End(); it++ ) { if ( it->Value().selected == true ) { return it->Index(); } } return -1; } void mitk::PointSet::ExecuteOperation( Operation* operation ) { int timeStep = -1; mitkCheckOperationTypeMacro(PointOperation, operation, pointOp); if ( pointOp ) { timeStep = this->GetTimeSlicedGeometry() ->MSToTimeStep( pointOp->GetTimeInMS() ); } if ( timeStep < 0 ) { MITK_ERROR << "Time step (" << timeStep << ") outside of PointSet time bounds" << std::endl; return; } switch (operation->GetOperationType()) { case OpNOTHING: break; case OpINSERT://inserts the point at the given position and selects it. { int position = pointOp->GetIndex(); PointType pt; pt.CastFrom(pointOp->GetPoint()); //transfer from world to index coordinates mitk::Geometry3D* geometry = this->GetGeometry( timeStep ); if (geometry == NULL) { MITK_INFO<<"GetGeometry returned NULL!\n"; return; } geometry->WorldToIndex(pt, pt); m_PointSetSeries[timeStep]->GetPoints()->InsertElement(position, pt); PointDataType pointData = { pointOp->GetIndex(), pointOp->GetSelected(), pointOp->GetPointType() }; m_PointSetSeries[timeStep]->GetPointData() ->InsertElement(position, pointData); this->Modified(); //boundingbox has to be computed m_CalculateBoundingBox = true; this->InvokeEvent( PointSetAddEvent() ); this->OnPointSetChange(); } break; case OpMOVE://moves the point given by index { PointType pt; pt.CastFrom(pointOp->GetPoint()); //transfer from world to index coordinates this->GetGeometry( timeStep )->WorldToIndex(pt, pt); // Copy new point into container m_PointSetSeries[timeStep]->SetPoint(pointOp->GetIndex(), pt); // Insert a default point data object to keep the containers in sync // (if no point data object exists yet) PointDataType pointData; if ( !m_PointSetSeries[timeStep]->GetPointData( pointOp->GetIndex(), &pointData ) ) { m_PointSetSeries[timeStep]->SetPointData( pointOp->GetIndex(), pointData ); } this->OnPointSetChange(); this->Modified(); //boundingbox has to be computed anyway m_CalculateBoundingBox = true; this->InvokeEvent( PointSetMoveEvent() ); } break; case OpREMOVE://removes the point at given by position { m_PointSetSeries[timeStep]->GetPoints()->DeleteIndex((unsigned)pointOp->GetIndex()); m_PointSetSeries[timeStep]->GetPointData()->DeleteIndex((unsigned)pointOp->GetIndex()); this->OnPointSetChange(); this->Modified(); //boundingbox has to be computed anyway m_CalculateBoundingBox = true; this->InvokeEvent( PointSetRemoveEvent() ); } break; case OpSELECTPOINT://select the given point { PointDataType pointData = {0, false, PTUNDEFINED}; m_PointSetSeries[timeStep]->GetPointData(pointOp->GetIndex(), &pointData); pointData.selected = true; m_PointSetSeries[timeStep]->SetPointData(pointOp->GetIndex(), pointData); this->Modified(); } break; case OpDESELECTPOINT://unselect the given point { PointDataType pointData = {0, false, PTUNDEFINED}; m_PointSetSeries[timeStep]->GetPointData(pointOp->GetIndex(), &pointData); pointData.selected = false; m_PointSetSeries[timeStep]->SetPointData(pointOp->GetIndex(), pointData); this->Modified(); } break; case OpSETPOINTTYPE: { PointDataType pointData = {0, false, PTUNDEFINED}; m_PointSetSeries[timeStep]->GetPointData(pointOp->GetIndex(), &pointData); pointData.pointSpec = pointOp->GetPointType(); m_PointSetSeries[timeStep]->SetPointData(pointOp->GetIndex(), pointData); this->Modified(); } break; case OpMOVEPOINTUP: // swap content of point with ID pointOp->GetIndex() with the point preceding it in the container // move point position within the pointset { PointIdentifier currentID = pointOp->GetIndex(); /* search for point with this id and point that precedes this one in the data container */ PointsContainer::STLContainerType points = m_PointSetSeries[timeStep]->GetPoints()->CastToSTLContainer(); PointsContainer::STLContainerType::iterator it = points.find(currentID); if (it == points.end()) // ID not found break; if (it == points.begin()) // we are at the first element, there is no previous element break; /* get and cache current point & pointdata and previous point & pointdata */ --it; PointIdentifier prevID = it->first; if (this->SwapPointContents(prevID, currentID, timeStep) == true) this->Modified(); } break; case OpMOVEPOINTDOWN: // move point position within the pointset { PointIdentifier currentID = pointOp->GetIndex(); /* search for point with this id and point that succeeds this one in the data container */ PointsContainer::STLContainerType points = m_PointSetSeries[timeStep]->GetPoints()->CastToSTLContainer(); PointsContainer::STLContainerType::iterator it = points.find(currentID); if (it == points.end()) // ID not found break; ++it; if (it == points.end()) // ID is already the last element, there is no succeeding element break; /* get and cache current point & pointdata and previous point & pointdata */ PointIdentifier nextID = it->first; if (this->SwapPointContents(nextID, currentID, timeStep) == true) this->Modified(); } break; default: itkWarningMacro("mitkPointSet could not understrand the operation. Please check!"); break; } //to tell the mappers, that the data is modified and has to be updated //only call modified if anything is done, so call in cases //this->Modified(); mitk::OperationEndEvent endevent(operation); ((const itk::Object*)this)->InvokeEvent(endevent); //*todo has to be done here, cause of update-pipeline not working yet // As discussed lately, don't mess with the rendering from inside data structures //mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::PointSet::UpdateOutputInformation() { if ( this->GetSource( ) ) { this->GetSource( )->UpdateOutputInformation( ); } // // first make sure, that the associated time sliced geometry has // the same number of geometry 3d's as PointSets are present // mitk::TimeSlicedGeometry* timeGeometry = GetTimeSlicedGeometry(); if ( timeGeometry->GetTimeSteps() != m_PointSetSeries.size() ) { itkExceptionMacro(<<"timeGeometry->GetTimeSteps() != m_PointSetSeries.size() -- use Initialize(timeSteps) with correct number of timeSteps!"); } // This is needed to detect zero objects mitk::ScalarType nullpoint[]={0,0,0,0,0,0}; BoundingBox::BoundsArrayType itkBoundsNull(nullpoint); // // Iterate over the PointSets and update the Geometry // information of each of the items. // if (m_CalculateBoundingBox) { for ( unsigned int i = 0 ; i < m_PointSetSeries.size() ; ++i ) { const DataType::BoundingBoxType *bb = m_PointSetSeries[i]->GetBoundingBox(); BoundingBox::BoundsArrayType itkBounds = bb->GetBounds(); if ( m_PointSetSeries[i].IsNull() || (m_PointSetSeries[i]->GetNumberOfPoints() == 0) || (itkBounds == itkBoundsNull) ) { itkBounds = itkBoundsNull; continue; } // Ensure minimal bounds of 1.0 in each dimension for ( unsigned int j = 0; j < 3; ++j ) { if ( itkBounds[j*2+1] - itkBounds[j*2] < 1.0 ) { BoundingBox::CoordRepType center = (itkBounds[j*2] + itkBounds[j*2+1]) / 2.0; itkBounds[j*2] = center - 0.5; itkBounds[j*2+1] = center + 0.5; } } this->GetGeometry(i)->SetBounds(itkBounds); } m_CalculateBoundingBox = false; } this->GetTimeSlicedGeometry()->UpdateInformation(); } void mitk::PointSet::SetRequestedRegionToLargestPossibleRegion() { } bool mitk::PointSet::RequestedRegionIsOutsideOfTheBufferedRegion() { return false; } bool mitk::PointSet::VerifyRequestedRegion() { return true; } void mitk::PointSet::SetRequestedRegion( itk::DataObject * ) { } void mitk::PointSet::PrintSelf( std::ostream& os, itk::Indent indent ) const { Superclass::PrintSelf(os, indent); os << indent << "Number timesteps: " << m_PointSetSeries.size() << "\n"; unsigned int i = 0; for (PointSetSeries::const_iterator it = m_PointSetSeries.begin(); it != m_PointSetSeries.end(); ++it) { os << indent << "Timestep " << i++ << ": \n"; MeshType::Pointer ps = *it; itk::Indent nextIndent = indent.GetNextIndent(); ps->Print(os, nextIndent); MeshType::PointsContainer* points = ps->GetPoints(); MeshType::PointDataContainer* datas = ps->GetPointData(); MeshType::PointDataContainer::Iterator dataIterator = datas->Begin(); for (MeshType::PointsContainer::Iterator pointIterator = points->Begin(); pointIterator != points->End(); ++pointIterator, ++dataIterator) { os << nextIndent << "Point " << pointIterator->Index() << ": ["; os << pointIterator->Value().GetElement(0); for (unsigned int i = 1; i < PointType::GetPointDimension(); ++i) { os << ", " << pointIterator->Value().GetElement(i); } os << "]"; os << ", selected: " << dataIterator->Value().selected << ", point spec: " << dataIterator->Value().pointSpec << "\n"; } } } bool mitk::PointSet::SwapPointContents(PointIdentifier id1, PointIdentifier id2, int timeStep) { /* search and cache contents */ PointType p1; if (m_PointSetSeries[timeStep]->GetPoint(id1, &p1) == false) return false; PointDataType data1; if (m_PointSetSeries[timeStep]->GetPointData(id1, &data1) == false) return false; PointType p2; if (m_PointSetSeries[timeStep]->GetPoint(id2, &p2) == false) return false; PointDataType data2; if (m_PointSetSeries[timeStep]->GetPointData(id2, &data2) == false) return false; /* now swap contents */ m_PointSetSeries[timeStep]->SetPoint(id1, p2); m_PointSetSeries[timeStep]->SetPointData(id1, data2); m_PointSetSeries[timeStep]->SetPoint(id2, p1); m_PointSetSeries[timeStep]->SetPointData(id2, data1); return true; } diff --git a/Core/Code/DataManagement/mitkVector.h b/Core/Code/DataManagement/mitkVector.h index e09c49ee0b..c4e3fde5de 100644 --- a/Core/Code/DataManagement/mitkVector.h +++ b/Core/Code/DataManagement/mitkVector.h @@ -1,436 +1,440 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITKVECTOR_H_HEADER_INCLUDED_C1EBD0AD #define MITKVECTOR_H_HEADER_INCLUDED_C1EBD0AD +// this is needed for memcopy in ITK +// can be removed when fixed in ITK +#include + #include #include #include #include #include #include #include #include #include #ifndef DOXYGEN_SKIP namespace mitk { typedef float ScalarType; typedef itk::Matrix Matrix3D; typedef itk::Matrix Matrix4D; typedef vnl_matrix_fixed VnlMatrix3D; typedef itk::Transform Transform3D; typedef vnl_vector VnlVector; typedef vnl_vector_ref VnlVectorRef; typedef itk::Point Point2D; typedef itk::Point Point3D; typedef itk::Point Point4D; typedef itk::Point Point2I; typedef itk::Point Point3I; typedef itk::Point Point4I; typedef itk::Vector Vector2D; typedef itk::Vector Vector3D; typedef itk::Index<3> Index3D; typedef itk::ContinuousIndex ContinuousIndex3D; typedef vnl_quaternion Quaternion; //##Documentation //##@brief enumeration of the type a point can be enum PointSpecificationType { PTUNDEFINED = 0, PTSTART, PTCORNER, PTEDGE, PTEND }; typedef itk::NumericTraits ScalarTypeNumericTraits; MITK_CORE_EXPORT extern const ScalarType eps; MITK_CORE_EXPORT extern const ScalarType sqrteps; MITK_CORE_EXPORT extern const double large; template class VectorTraits { public: typedef T ValueType; }; template <> class VectorTraits { public: typedef ScalarType ValueType; }; template<> class VectorTraits { public: typedef double ValueType; }; template<> class VectorTraits< itk::Index<5> > { public: typedef itk::Index<5>::IndexValueType ValueType; }; template<> class VectorTraits< itk::Index<3> > { public: typedef itk::Index<3>::IndexValueType ValueType; }; template<> class VectorTraits< long int [3]> { public: typedef long int ValueType; }; template<> class VectorTraits< float [3]> { public: typedef float ValueType; }; template<> class VectorTraits< double [3]> { public: typedef double ValueType; }; template<> class VectorTraits< vnl_vector_fixed > { public: typedef ScalarType ValueType; }; template<> class VectorTraits< long unsigned int[3]> { public: typedef long unsigned int ValueType; }; template<> class VectorTraits< unsigned int *> { public: typedef unsigned int ValueType; }; template<> class VectorTraits< ScalarType[4] > { public: typedef ScalarType ValueType; }; template<> class VectorTraits< itk::Vector > { public: typedef float ValueType; }; template<> class VectorTraits< itk::Point > { public: typedef float ValueType; }; template<> class VectorTraits< itk::Point > { public: typedef float ValueType; }; template<> class VectorTraits< itk::Vector > { public: typedef double ValueType; }; template<> class VectorTraits< itk::Point > { public: typedef double ValueType; }; template<> class VectorTraits< itk::Vector > { public: typedef int ValueType; }; template<> class VectorTraits< itk::Point > { public: typedef int ValueType; }; template inline void itk2vtk(const Tin& in, Tout& out) { out[0]=(typename VectorTraits::ValueType)(in[0]); out[1]=(typename VectorTraits::ValueType)(in[1]); out[2]=(typename VectorTraits::ValueType)(in[2]); } template inline void vtk2itk(const Tin& in, Tout& out) { out[0]=(typename VectorTraits::ValueType)(in[0]); out[1]=(typename VectorTraits::ValueType)(in[1]); out[2]=(typename VectorTraits::ValueType)(in[2]); } template inline void FillVector3D(Tout& out, ScalarType x, ScalarType y, ScalarType z) { out[0] = (typename VectorTraits::ValueType)x; out[1] = (typename VectorTraits::ValueType)y; out[2] = (typename VectorTraits::ValueType)z; } template inline void FillVector4D(Tout& out, ScalarType x, ScalarType y, ScalarType z, ScalarType t) { out[0] = (typename VectorTraits::ValueType)x; out[1] = (typename VectorTraits::ValueType)y; out[2] = (typename VectorTraits::ValueType)z; out[3] = (typename VectorTraits::ValueType)t; } template inline void vnl2vtk(const vnl_vector& in, Tout *out) { unsigned int i; for(i=0; i inline void vtk2vnl(const Tin *in, vnl_vector& out) { unsigned int i; for(i=0; i inline void vtk2vnlref(const Tin *in, vnl_vector_ref& out) { unsigned int i; for(i=0; i inline void vnl2vtk(const vnl_vector_fixed& in, Tout *out) { unsigned int i; for(i=0; i inline void vtk2vnl(const Tin *in, vnl_vector_fixed& out) { unsigned int i; for(i=0; i itk::Vector operator+(const itk::Vector &vector, const itk::Point &point) { itk::Vector sub; for( unsigned int i=0; i inline itk::Vector& operator+=(itk::Vector &vector, const itk::Point &point) { for( unsigned int i=0; i itk::Vector operator-(const itk::Vector &vector, const itk::Point &point) { itk::Vector sub; for( unsigned int i=0; i inline itk::Vector& operator-=(itk::Vector &vector, const itk::Point &point) { for( unsigned int i=0; i inline bool MatrixEqualRMS(const vnl_matrix_fixed& matrix1,const vnl_matrix_fixed& matrix2,mitk::ScalarType epsilon=mitk::eps) { if ( (matrix1.rows() == matrix2.rows()) && (matrix1.cols() == matrix2.cols()) ) { vnl_matrix_fixed differenceMatrix = matrix1-matrix2; if (differenceMatrix.rms() inline bool MatrixEqualRMS(const itk::Matrix& matrix1,const itk::Matrix& matrix2,mitk::ScalarType epsilon=mitk::eps) { return mitk::MatrixEqualRMS(matrix1.GetVnlMatrix(),matrix2.GetVnlMatrix(),epsilon); } /*! \brief Check for element-wise matrix equality with a user defined accuracy. \param matrix1 first vnl matrix \param matrix2 second vnl matrix \epsilon user defined accuracy bounds */ template inline bool MatrixEqualElementWise(const vnl_matrix_fixed& matrix1,const vnl_matrix_fixed& matrix2,mitk::ScalarType epsilon=mitk::eps) { if ( (matrix1.rows() == matrix2.rows()) && (matrix1.cols() == matrix2.cols()) ) { for( unsigned int r=0; repsilon) { return false; } } } return true; } else { return false; } } /*! \brief Check for element-wise matrix equality with a user defined accuracy. \param matrix1 first itk matrix \param matrix2 second itk matrix \epsilon user defined accuracy bounds */ template inline bool MatrixEqualElementWise(const itk::Matrix& matrix1,const itk::Matrix& matrix2,mitk::ScalarType epsilon=mitk::eps) { return mitk::MatrixEqualElementWise(matrix1.GetVnlMatrix(),matrix2.GetVnlMatrix(),epsilon); } template inline bool Equal(const itk::Vector& vector1, const itk::Vector& vector2) { typename itk::Vector::VectorType diff = vector1-vector2; return diff.GetSquaredNorm() < mitk::eps; } template inline bool Equal(const itk::Point& vector1, const itk::Point& vector2) { typename itk::Point::VectorType diff = vector1-vector2; return diff.GetSquaredNorm() < mitk::eps; } inline bool Equal(const mitk::VnlVector& vector1, const mitk::VnlVector& vector2) { mitk::VnlVector diff = vector1-vector2; return diff.squared_magnitude() < mitk::eps; } inline bool Equal(double scalar1, double scalar2) { return fabs(scalar1-scalar2) < mitk::eps; } template inline bool Equal(const vnl_vector_fixed & vector1, const vnl_vector_fixed& vector2) { vnl_vector_fixed diff = vector1-vector2; return diff.squared_magnitude() < mitk::eps; } template inline void TransferMatrix(const itk::Matrix& in, itk::Matrix& out) { for (unsigned int i = 0; i < in.RowDimensions; ++i) for (unsigned int j = 0; j < in.ColumnDimensions; ++j) out[i][j] = in[i][j]; } } // namespace mitk #endif //DOXYGEN_SKIP /* * This part of the code has been shifted here to avoid compiler clashes * caused by including before the declaration of * the Equal() methods above. This problem occurs when using MSVC and is * probably related to a compiler bug. */ #include namespace mitk { typedef itk::AffineGeometryFrame::TransformType AffineTransform3D; } #define mitkSetConstReferenceMacro(name,type) \ virtual void Set##name (const type & _arg) \ { \ itkDebugMacro("setting " << #name " to " << _arg ); \ if (this->m_##name != _arg) \ { \ this->m_##name = _arg; \ this->Modified(); \ } \ } #define mitkSetVectorMacro(name,type) \ mitkSetConstReferenceMacro(name,type) #define mitkGetVectorMacro(name,type) \ itkGetConstReferenceMacro(name,type) #endif /* MITKVECTOR_H_HEADER_INCLUDED_C1EBD0AD */ diff --git a/Core/Code/Interactions/mitkStateMachineFactory.cpp b/Core/Code/Interactions/mitkStateMachineFactory.cpp index d528829f9e..324474cf03 100755 --- a/Core/Code/Interactions/mitkStateMachineFactory.cpp +++ b/Core/Code/Interactions/mitkStateMachineFactory.cpp @@ -1,462 +1,462 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkStateMachineFactory.h" #include "mitkGlobalInteraction.h" #include #include #include #include #include /** * @brief This class builds up all the necessary structures for a statemachine. * and stores one start-state for all built statemachines. **/ //mitk::StateMachineFactory::StartStateMap mitk::StateMachineFactory::m_StartStates; //mitk::StateMachineFactory::AllStateMachineMapType mitk::StateMachineFactory::m_AllStateMachineMap; //std::string mitk::StateMachineFactory::s_LastLoadedBehavior; //XML StateMachine const std::string STYLE = "STYLE"; const std::string NAME = "NAME"; const std::string ID = "ID"; const std::string START_STATE = "START_STATE"; const std::string NEXT_STATE_ID = "NEXT_STATE_ID"; const std::string EVENT_ID = "EVENT_ID"; const std::string SIDE_EFFECT_ID = "SIDE_EFFECT_ID"; const std::string ISTRUE = "TRUE"; const std::string ISFALSE = "FALSE"; const std::string STATE_MACHINE = "stateMachine"; const std::string STATE = "state"; const std::string TRANSITION = "transition"; const std::string STATE_MACHINE_NAME = "stateMachine"; const std::string ACTION = "action"; const std::string BOOL_PARAMETER = "boolParameter"; const std::string INT_PARAMETER = "intParameter"; const std::string FLOAT_PARAMETER = "floatParameter"; const std::string DOUBLE_PARAMETER = "doubleParameter"; const std::string STRING_PARAMETER = "stringParameter"; const std::string VALUE = "VALUE"; #include namespace mitk { vtkStandardNewMacro(StateMachineFactory); } mitk::StateMachineFactory::StateMachineFactory() : m_AktStateMachineName(""), m_SkipStateMachine(false) {} mitk::StateMachineFactory::~StateMachineFactory() { //free memory while (!m_AllStateMachineMap.empty()) { StateMachineMapType* temp = m_AllStateMachineMap.begin()->second; m_AllStateMachineMap.erase(m_AllStateMachineMap.begin()); delete temp; } //should not be necessary due to SmartPointers m_StartStates.clear(); //delete WeakPointer if (m_AktTransition) delete m_AktTransition; } /** * @brief Returns NULL if no entry with string type is found. **/ mitk::State* mitk::StateMachineFactory::GetStartState(const char * type) { StartStateMapIter tempState = m_StartStates.find(type); if( tempState != m_StartStates.end() ) return (tempState)->second.GetPointer(); MITK_ERROR << "Error in StateMachineFactory: StartState for pattern \""<< type<< "\"not found! StateMachine might not work!\n"; return NULL; } /** * @brief Loads the xml file filename and generates the necessary instances. **/ bool mitk::StateMachineFactory::LoadBehavior(std::string fileName) { if ( fileName.empty() ) return false; m_LastLoadedBehavior = fileName; this->SetFileName(fileName.c_str()); return this->Parse(); } /** * @brief Loads the xml string and generates the necessary instances. **/ bool mitk::StateMachineFactory::LoadBehaviorString(std::string xmlString) { if ( xmlString.empty() ) return false; m_LastLoadedBehavior = "String"; return ( this->Parse(xmlString.c_str(), xmlString.length()) ); } bool mitk::StateMachineFactory::LoadStandardBehavior() { std::string xmlFileName( mitk::StandardFileLocations::GetInstance()->FindFile("StateMachine.xml", "Core/Code/Interactions") ); if (!xmlFileName.empty()) return this->LoadBehavior(xmlFileName); else return false; } /** * @brief Recursive method, that parses this brand of * the stateMachine; if the history has the same * size at the end, then the StateMachine is correct **/ bool mitk::StateMachineFactory::RParse(mitk::State::StateMap* states, mitk::State::StateMapIter thisState, HistorySet *history) { history->insert((thisState->second)->GetId());//log our path //or thisState->first. but this seems safer std::set nextStatesSet = (thisState->second)->GetAllNextStates(); //remove loops in nextStatesSet; //nether do we have to go there, nor will it clear a deadlock std::set::iterator position = nextStatesSet.find((thisState->second)->GetId());//look for the same state in nextStateSet if (position != nextStatesSet.end()) {//found the same state we are in! nextStatesSet.erase(position);//delete it, cause, we don't have to go there a second time! } //nextStatesSet is empty, so deadlock! if ( nextStatesSet.empty() ) { MITK_INFO<::iterator i = nextStatesSet.begin(); i != nextStatesSet.end(); i++) { if ( history->find(*i) == history->end() )//if we haven't been in this nextstate { mitk::State::StateMapIter nextState = states->find(*i);//search the iterator for our nextState if (nextState == states->end()) { MITK_INFO<size() > 1)//only one state; don't have to be parsed for deadlocks! { //parse all the given states an check for deadlock or not connected states HistorySet *history = new HistorySet; mitk::State::StateMapIter firstState = states->begin(); //parse through all the given states, log the parsed elements in history bool ok = RParse( states, firstState, history); if ( (states->size() == history->size()) && ok ) { delete history; } else //ether !ok or sizeA!=sizeB { delete history; MITK_INFO<begin(); tempState != states->end(); tempState++) { //searched through the States and Connects all Transitions bool tempbool = ( ( tempState->second )->ConnectTransitions( states ) ); if ( tempbool == false ) { MITK_INFO< ok = m_AllStatesOfOneStateMachine.insert(mitk::State::StateMap::value_type(id , m_AktState)); if ( ok.second == false ) { MITK_INFO<AddTransition( m_AktTransition ); } else if ( name == ACTION ) { int actionId = ReadXMLIntegerAttribut( ID, atts ); m_AktAction = Action::New( actionId ); m_AktTransition->AddAction( m_AktAction ); } else if ( name == BOOL_PARAMETER ) { if ( !m_AktAction ) return; bool value = ReadXMLBooleanAttribut( VALUE, atts ); std::string name = ReadXMLStringAttribut( NAME, atts ); m_AktAction->AddProperty( name.c_str(), BoolProperty::New( value ) ); } else if ( name == INT_PARAMETER ) { if ( !m_AktAction ) return; int value = ReadXMLIntegerAttribut( VALUE, atts ); std::string name = ReadXMLStringAttribut( NAME, atts ); m_AktAction->AddProperty( name.c_str(), IntProperty::New( value ) ); } else if ( name == FLOAT_PARAMETER ) { if ( !m_AktAction ) return; float value = ReadXMLIntegerAttribut( VALUE, atts ); std::string name = ReadXMLStringAttribut( NAME, atts ); m_AktAction->AddProperty( name.c_str(), FloatProperty::New( value ) ); } else if ( name == DOUBLE_PARAMETER ) { if ( !m_AktAction ) return; double value = ReadXMLDoubleAttribut( VALUE, atts ); std::string name = ReadXMLStringAttribut( NAME, atts ); m_AktAction->AddProperty( name.c_str(), DoubleProperty::New( value ) ); } else if ( name == STRING_PARAMETER ) { if ( !m_AktAction ) return; std::string value = ReadXMLStringAttribut( VALUE, atts ); std::string name = ReadXMLStringAttribut( NAME, atts ); m_AktAction->AddProperty( name.c_str(), StringProperty::New( value ) ); } } void mitk::StateMachineFactory::EndElement (const char* elementName) { //bool ok = true; std::string name(elementName); //skip the state machine pattern because the name was not unique! if (m_SkipStateMachine && (name != STATE_MACHINE) ) return; if ( name == STATE_MACHINE_NAME ) { if (m_SkipStateMachine) { m_SkipStateMachine = false; return; } /*ok =*/ ConnectStates(&m_AllStatesOfOneStateMachine); m_AllStatesOfOneStateMachine.clear(); } else if ( name == STATE_MACHINE ) { //doesn't have to be done } else if ( name == TRANSITION ) { m_AktTransition = NULL; //pointer stored in its state. memory will be freed in destructor of class state } else if ( name == ACTION ) { m_AktAction = NULL; } else if ( name == STATE ) { m_AktState = NULL; } } std::string mitk::StateMachineFactory::ReadXMLStringAttribut( std::string name, const char** atts ) { if(atts) { const char** attsIter = atts; while(*attsIter) { if ( name == *attsIter ) { attsIter++; return *attsIter; } attsIter++; attsIter++; } } return std::string(); } int mitk::StateMachineFactory::ReadXMLIntegerAttribut( std::string name, const char** atts ) { std::string s = ReadXMLStringAttribut( name, atts ); return atoi( s.c_str() ); } float mitk::StateMachineFactory::ReadXMLFloatAttribut( std::string name, const char** atts ) { std::string s = ReadXMLStringAttribut( name, atts ); return (float) atof( s.c_str() ); } double mitk::StateMachineFactory::ReadXMLDoubleAttribut( std::string name, const char** atts ) { std::string s = ReadXMLStringAttribut( name, atts ); return atof( s.c_str() ); } bool mitk::StateMachineFactory::ReadXMLBooleanAttribut( std::string name, const char** atts ) { std::string s = ReadXMLStringAttribut( name, atts ); if ( s == ISTRUE ) return true; else return false; } mitk::State* mitk::StateMachineFactory::GetState( const char * type, int StateId ) { //check if the state exists AllStateMachineMapType::iterator i = m_AllStateMachineMap.find( type ); if ( i == m_AllStateMachineMap.end() ) - return false; + return NULL; //get the statemachine of the state StateMachineMapType* sm = m_AllStateMachineMap[type]; //get the state from its statemachine if ( sm != NULL ) return (*sm)[StateId].GetPointer(); else return NULL; } bool mitk::StateMachineFactory::AddStateMachinePattern(const char * type, mitk::State* startState, mitk::StateMachineFactory::StateMachineMapType* allStatesOfStateMachine) { if (startState == NULL || allStatesOfStateMachine == NULL) return false; //check if the pattern has already been added StartStateMapIter tempState = m_StartStates.find(type); if( tempState != m_StartStates.end() ) { MITK_WARN << "Pattern " << type << " has already been added!\n"; return false; } //add the start state m_StartStates.insert(StartStateMap::value_type(type, startState)); //add all states of the new pattern to hold their references m_AllStateMachineMap.insert(AllStateMachineMapType::value_type(type, allStatesOfStateMachine)); return true; } diff --git a/Core/Code/Testing/mitkImageTest.cpp b/Core/Code/Testing/mitkImageTest.cpp index 6be4c0b921..3b7fca625f 100644 --- a/Core/Code/Testing/mitkImageTest.cpp +++ b/Core/Code/Testing/mitkImageTest.cpp @@ -1,336 +1,342 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ // mitk includes #include #include #include #include "mitkItkImageFileReader.h" #include #include // itk includes #include #include // stl includes #include // vtk includes #include int mitkImageTest(int argc, char* argv[]) { MITK_TEST_BEGIN(mitkImageTest); //Create Image out of nowhere mitk::Image::Pointer imgMem = mitk::Image::New(); mitk::PixelType pt = mitk::MakeScalarPixelType(); unsigned int dim[]={100,100,20}; MITK_TEST_CONDITION_REQUIRED( imgMem.IsNotNull(), "An image was created. "); // Initialize image imgMem->Initialize( pt, 3, dim); MITK_TEST_CONDITION_REQUIRED( imgMem->IsInitialized(), "Image::IsInitialized() ?"); MITK_TEST_CONDITION_REQUIRED( imgMem->GetPixelType() == pt, "PixelType was set correctly."); int *p = (int*)imgMem->GetData(); MITK_TEST_CONDITION( p != NULL, "GetData() returned not-NULL pointer."); // FIXME: this is directly changing the image data // filling image const unsigned int size = dim[0]*dim[1]*dim[2]; for(unsigned int i=0; iGetData(); MITK_TEST_CONDITION( p2 != NULL, "GetData() returned not-NULL pointer."); bool isEqual = true; for(unsigned int i=0; iGetSliceData(dim[2]/2)->GetData(); MITK_TEST_CONDITION_REQUIRED( p2 != NULL, "Valid slice data returned"); unsigned int xy_size = dim[0]*dim[1]; unsigned int start_mid_slice = (dim[2]/2)*xy_size; isEqual = true; for(unsigned int i=0; i(); imgMem->Initialize( pType , 3, dim); MITK_TEST_CONDITION_REQUIRED(imgMem->GetDimension()== 3, "Testing initialization parameter dimension!"); MITK_TEST_CONDITION_REQUIRED(imgMem->GetPixelType() == pType, "Testing initialization parameter pixeltype!"); MITK_TEST_CONDITION_REQUIRED(imgMem->GetDimension(0) == dim[0] && imgMem->GetDimension(1)== dim[1] && imgMem->GetDimension(2)== dim[2], "Testing initialization of dimensions!"); MITK_TEST_CONDITION( imgMem->IsInitialized(), "Image is initialized."); // Setting volume again: imgMem->SetVolume(imgMem->GetData()); //----------------- // geometry information for image mitk::Point3D origin; mitk::Vector3D right, bottom; mitk::Vector3D spacing; mitk::FillVector3D(origin, 17.0, 19.92, 7.83); mitk::FillVector3D(right, 1.0, 2.0, 3.0); mitk::FillVector3D(bottom, 0.0, -3.0, 2.0); mitk::FillVector3D(spacing, 0.78, 0.91, 2.23); //InitializeStandardPlane(rightVector, downVector, spacing) mitk::PlaneGeometry::Pointer planegeometry = mitk::PlaneGeometry::New(); planegeometry->InitializeStandardPlane(100, 100, right, bottom, &spacing); planegeometry->SetOrigin(origin); // Testing Initialize(const mitk::PixelType& type, const mitk::Geometry3D& geometry, unsigned int slices) with PlaneGeometry and GetData(): "; imgMem->Initialize( mitk::MakePixelType(), *planegeometry); MITK_TEST_CONDITION_REQUIRED( imgMem->GetGeometry()->GetOrigin() == static_cast(planegeometry)->GetOrigin(), "Testing correct setting of geometry via initialize!"); p = (int*)imgMem->GetData(); MITK_TEST_CONDITION_REQUIRED( p!=NULL, "GetData() returned valid pointer."); // Testing Initialize(const mitk::PixelType& type, int sDim, const mitk::PlaneGeometry& geometry) and GetData(): "; imgMem->Initialize( mitk::MakePixelType() , 40, *planegeometry); p = (int*)imgMem->GetData(); MITK_TEST_CONDITION_REQUIRED( p!=NULL, "GetData() returned valid pointer."); //----------------- // testing origin information and methods MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetGeometry()->GetOrigin(), origin), "Testing correctness of origin via GetGeometry()->GetOrigin(): "); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetOrigin(), origin), "Testing correctness of origin via GetTimeSlicedGeometry()->GetOrigin(): "); // Setting origin via SetOrigin(origin): "; mitk::FillVector3D(origin, 37.0, 17.92, 27.83); imgMem->SetOrigin(origin); // Test origin MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetGeometry()->GetOrigin(), origin), "Testing correctness of changed origin via GetGeometry()->GetOrigin(): "); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetOrigin(), origin), "Testing correctness of changed origin via GetTimeSlicedGeometry()->GetOrigin(): "); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetSlicedGeometry()->GetGeometry2D(0)->GetOrigin(), origin), "Testing correctness of changed origin via GetSlicedGeometry()->GetGeometry2D(0)->GetOrigin(): "); //----------------- // testing spacing information and methods MITK_TEST_CONDITION_REQUIRED(mitk::Equal(imgMem->GetGeometry()->GetSpacing(), spacing), "Testing correct spacing from Geometry3D!"); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetSpacing(), spacing), "Testing correctspacing from TimeSlicedGeometry!"); mitk::FillVector3D(spacing, 7.0, 0.92, 1.83); imgMem->SetSpacing(spacing); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetGeometry()->GetSpacing(), spacing), "Testing correctness of changed spacing via GetGeometry()->GetSpacing(): "); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetSpacing(), spacing), "Testing correctness of changed spacing via GetTimeSlicedGeometry()->GetSpacing(): "); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetSlicedGeometry()->GetGeometry2D(0)->GetSpacing(), spacing), "Testing correctness of changed spacing via GetSlicedGeometry()->GetGeometry2D(0)->GetSpacing(): "); mitk::Image::Pointer vecImg = mitk::Image::New(); vecImg->Initialize( imgMem->GetPixelType(), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/ ); vecImg->SetImportChannel(imgMem->GetData(), 0, mitk::Image::CopyMemory ); vecImg->SetImportChannel(imgMem->GetData(), 1, mitk::Image::CopyMemory ); MITK_TEST_CONDITION_REQUIRED(vecImg->GetChannelData(0)->GetData() != NULL && vecImg->GetChannelData(1)->GetData() != NULL, "Testing set and return of channel data!"); MITK_TEST_CONDITION_REQUIRED( vecImg->IsValidSlice(0,0,1) , ""); MITK_TEST_OUTPUT(<< " Testing whether CopyMemory worked"); MITK_TEST_CONDITION_REQUIRED(imgMem->GetData() != vecImg->GetData(), ""); MITK_TEST_OUTPUT(<< " Testing destruction after SetImportChannel"); vecImg = NULL; MITK_TEST_CONDITION_REQUIRED(vecImg.IsNull() , "testing destruction!"); //----------------- MITK_TEST_OUTPUT(<< "Testing initialization via vtkImageData"); MITK_TEST_OUTPUT(<< " Setting up vtkImageData"); vtkImageData* vtkimage = vtkImageData::New(); vtkimage->Initialize(); vtkimage->SetDimensions( 2, 3, 4); double vtkorigin[] = {-350,-358.203, -1363.5}; vtkimage->SetOrigin(vtkorigin); mitk::Point3D vtkoriginAsMitkPoint; mitk::vtk2itk(vtkorigin, vtkoriginAsMitkPoint); double vtkspacing[] = {1.367, 1.367, 2}; vtkimage->SetSpacing(vtkspacing); vtkimage->SetScalarType( VTK_SHORT ); vtkimage->AllocateScalars(); std::cout<<"[PASSED]"<Initialize(vtkimage); MITK_TEST_CONDITION_REQUIRED(mitkByVtkImage->IsInitialized(), ""); vtkimage->Delete(); MITK_TEST_OUTPUT(<< " Testing whether spacing has been correctly initialized from vtkImageData"); mitk::Vector3D spacing2 = mitkByVtkImage->GetGeometry()->GetSpacing(); mitk::Vector3D vtkspacingAsMitkVector; mitk::vtk2itk(vtkspacing, vtkspacingAsMitkVector); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(spacing2,vtkspacingAsMitkVector), ""); MITK_TEST_OUTPUT(<< " Testing whether GetSlicedGeometry(0)->GetOrigin() has been correctly initialized from vtkImageData"); mitk::Point3D origin2 = mitkByVtkImage->GetSlicedGeometry(0)->GetOrigin(); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2,vtkoriginAsMitkPoint), ""); MITK_TEST_OUTPUT(<< " Testing whether GetGeometry()->GetOrigin() has been correctly initialized from vtkImageData"); origin2 = mitkByVtkImage->GetGeometry()->GetOrigin(); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2,vtkoriginAsMitkPoint), ""); MITK_TEST_OUTPUT(<< " Testing whether GetTimeSlicedGeometry()->GetOrigin() has been correctly initialized from vtkImageData"); origin2 = mitkByVtkImage->GetTimeSlicedGeometry()->GetOrigin(); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2,vtkoriginAsMitkPoint), ""); // TODO test the following initializers on channel-incorporation // void mitk::Image::Initialize(const mitk::PixelType& type, unsigned int dimension, unsigned int *dimensions, unsigned int channels) // void mitk::Image::Initialize(const mitk::PixelType& type, int sDim, const mitk::Geometry2D& geometry2d, bool flipped, unsigned int channels, int tDim ) // void mitk::Image::Initialize(const mitk::Image* image) // void mitk::Image::Initialize(const mitkIpPicDescriptor* pic, int channels, int tDim, int sDim) //mitk::Image::Pointer vecImg = mitk::Image::New(); //vecImg->Initialize(PixelType(typeid(float), 6, itk::ImageIOBase::SYMMETRICSECONDRANKTENSOR), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/, false /*shiftBoundingBoxMinimumToZero*/ ); //vecImg->Initialize(PixelType(typeid(itk::Vector)), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/, false /*shiftBoundingBoxMinimumToZero*/ ); // testing access by index coordinates and by world coordinates MITK_TEST_CONDITION_REQUIRED(argc == 2, "Check if test image is accessible!"); const std::string filename = std::string(argv[1]); mitk::ItkImageFileReader::Pointer imageReader = mitk::ItkImageFileReader::New(); try { imageReader->SetFileName(filename); imageReader->Update(); } catch(...) { MITK_TEST_FAILED_MSG(<< "Could not read file for testing: " << filename); return 0; } mitk::Image::Pointer image = imageReader->GetOutput(); // generate a random point in world coordinates mitk::Point3D xMax, yMax, zMax, xMaxIndex, yMaxIndex, zMaxIndex; xMaxIndex.Fill(0.0f); yMaxIndex.Fill(0.0f); zMaxIndex.Fill(0.0f); xMaxIndex[0] = image->GetLargestPossibleRegion().GetSize()[0]; yMaxIndex[1] = image->GetLargestPossibleRegion().GetSize()[1]; zMaxIndex[2] = image->GetLargestPossibleRegion().GetSize()[2]; image->GetGeometry()->IndexToWorld(xMaxIndex, xMax); image->GetGeometry()->IndexToWorld(yMaxIndex, yMax); image->GetGeometry()->IndexToWorld(zMaxIndex, zMax); MITK_INFO << "Origin " << image->GetGeometry()->GetOrigin()[0] << " "<< image->GetGeometry()->GetOrigin()[1] << " "<< image->GetGeometry()->GetOrigin()[2] << ""; MITK_INFO << "MaxExtend " << xMax[0] << " "<< yMax[1] << " "<< zMax[2] << ""; mitk::Point3D point; itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randomGenerator = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); randomGenerator->Initialize( std::rand() ); // initialize with random value, to get sensible random points for the image point[0] = randomGenerator->GetUniformVariate( image->GetGeometry()->GetOrigin()[0], xMax[0]); point[1] = randomGenerator->GetUniformVariate( image->GetGeometry()->GetOrigin()[1], yMax[1]); point[2] = randomGenerator->GetUniformVariate( image->GetGeometry()->GetOrigin()[2], zMax[2]); MITK_INFO << "RandomPoint " << point[0] << " "<< point[1] << " "<< point[2] << ""; // test values and max/min mitk::ScalarType imageMin = image->GetStatistics()->GetScalarValueMin(); mitk::ScalarType imageMax = image->GetStatistics()->GetScalarValueMax(); mitk::ScalarType value = image->GetPixelValueByWorldCoordinate(point); MITK_INFO << imageMin << " "<< imageMax << " "<< value << ""; MITK_TEST_CONDITION( (value >= imageMin && value <= imageMax), "Value returned is between max/min"); + // testing the clone method of mitk::Image mitk::Image::Pointer cloneImage = image->Clone(); MITK_TEST_CONDITION_REQUIRED(cloneImage->GetDimension() == image->GetDimension(), "Clone (testing dimension)"); MITK_TEST_CONDITION_REQUIRED(cloneImage->GetPixelType() == image->GetPixelType(), "Clone (testing pixel type)"); + // After cloning an image the geometry of both images should be equal too + MITK_TEST_CONDITION_REQUIRED(cloneImage->GetGeometry()->GetOrigin() == image->GetGeometry()->GetOrigin(), "Clone (testing origin)"); + MITK_TEST_CONDITION_REQUIRED(cloneImage->GetGeometry()->GetSpacing() == image->GetGeometry()->GetSpacing(), "Clone (testing spacing)"); + MITK_TEST_CONDITION_REQUIRED(mitk::MatrixEqualElementWise(cloneImage->GetGeometry()->GetIndexToWorldTransform()->GetMatrix(), image->GetGeometry()->GetIndexToWorldTransform()->GetMatrix()), + "Clone (testing transformation matrix)"); for (unsigned int i = 0u; i < cloneImage->GetDimension(); ++i) { MITK_TEST_CONDITION_REQUIRED(cloneImage->GetDimension(i) == image->GetDimension(i), "Clone (testing dimension " << i << ")"); } //access via itk if(image->GetDimension()> 3) // CastToItk only works with 3d images so we need to check for 4d images { mitk::ImageTimeSelector::Pointer selector = mitk::ImageTimeSelector::New(); selector->SetTimeNr(0); selector->SetInput(image); selector->Update(); image = selector->GetOutput(); } if(image->GetDimension()==3) { typedef itk::Image ItkFloatImage3D; ItkFloatImage3D::Pointer itkimage; mitk::CastToItkImage(image, itkimage); MITK_TEST_CONDITION_REQUIRED(itkimage.IsNotNull(), "Test conversion to itk::Image!"); mitk::Point3D itkPhysicalPoint; image->GetGeometry()->WorldToItkPhysicalPoint(point, itkPhysicalPoint); MITK_INFO << "ITKPoint " << itkPhysicalPoint[0] << " "<< itkPhysicalPoint[1] << " "<< itkPhysicalPoint[2] << ""; mitk::Point3D backTransformedPoint; image->GetGeometry()->ItkPhysicalPointToWorld(itkPhysicalPoint, backTransformedPoint); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(point,backTransformedPoint), "Testing world->itk-physical->world consistency"); itk::Index<3> idx; bool status = itkimage->TransformPhysicalPointToIndex(itkPhysicalPoint, idx); MITK_INFO << "ITK Index " << idx[0] << " "<< idx[1] << " "<< idx[2] << ""; if(status) { float valByItk = itkimage->GetPixel(idx); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(valByItk, value), "Compare value of pixel returned by mitk in comparison to itk"); } else { MITK_WARN<< "Index is out buffered region!"; } } else { MITK_INFO << "Image does not contain three dimensions, some test cases are skipped!"; } // clone generated 3D image with one slice in z direction (cf. bug 11058) unsigned int* threeDdim = new unsigned int[3]; threeDdim[0] = 100; threeDdim[1] = 200; threeDdim[2] = 1; mitk::Image::Pointer threeDImage = mitk::Image::New(); threeDImage->Initialize(mitk::MakeScalarPixelType(), 3, threeDdim); mitk::Image::Pointer cloneThreeDImage = threeDImage->Clone(); // check that the clone image has the same dimensionality as the source image MITK_TEST_CONDITION_REQUIRED( cloneThreeDImage->GetDimension() == 3, "Testing if the clone image initializes with 3D!"); MITK_TEST_END(); -} \ No newline at end of file +} diff --git a/Core/Code/Testing/mitkPointSetTest.cpp b/Core/Code/Testing/mitkPointSetTest.cpp index d812b356d5..7e8a6cec4f 100644 --- a/Core/Code/Testing/mitkPointSetTest.cpp +++ b/Core/Code/Testing/mitkPointSetTest.cpp @@ -1,610 +1,621 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkTestingMacros.h" #include #include #include #include #include class mitkPointSetTestClass { public: static void TestGetITKPointSet(mitk::PointSet *pointSet) { //try to get the itkPointSet mitk::PointSet::DataType::Pointer itkdata = NULL; itkdata = pointSet->GetPointSet(); MITK_TEST_CONDITION( itkdata.IsNotNull(), "try to get the itkPointSet from a newly created PointSet" ) } static void TestGetSizeIsZero(mitk::PointSet *pointSet) { //fresh PointSet has to be empty! MITK_TEST_CONDITION( pointSet->GetSize() == 0, "check if the PointSet size is 0 " ) } static void TestIsEmpty(mitk::PointSet *pointSet) { MITK_TEST_CONDITION(pointSet->IsEmptyTimeStep(0), "check if the PointSet is empty" ) } static void TestCreateOperationAndAddPoint(mitk::PointSet *pointSet) { int id = 0; mitk::Point3D point; point.Fill(1); mitk::PointOperation* doOp = new mitk::PointOperation(mitk::OpINSERT, point, id); pointSet->ExecuteOperation(doOp); MITK_TEST_CONDITION( pointSet->GetSize()==1 && pointSet->IndexExists(id), "check if added points exists" ) delete doOp; mitk::Point3D tempPoint; tempPoint.Fill(0); tempPoint = pointSet->GetPoint(id); MITK_TEST_CONDITION( point == tempPoint, "check if added point contains real value" ) } static void TestAddSecondPoint(mitk::PointSet *pointSet) { //add a point directly int id=0; mitk::Point3D point; mitk::FillVector3D(point, 1.0, 2.0, 3.0); ++id; pointSet->GetPointSet()->GetPoints()->InsertElement(id, point); MITK_TEST_CONDITION( pointSet->GetSize()==2 ||pointSet->IndexExists(id), "check if added points exists" ) mitk::Point3D tempPoint; tempPoint.Fill(0); tempPoint = pointSet->GetPoint(id); MITK_TEST_CONDITION( point == tempPoint, "check if added point contains real value" ) } static void TestIsNotEmpty(mitk::PointSet *pointSet) { //PointSet can not be empty! MITK_TEST_CONDITION( !pointSet->IsEmptyTimeStep(0), "check if the PointSet is not empty " ) /* std::cout << "check if the PointSet is not empty "; if (pointSet->IsEmpty(0)) { std::cout<<"[FAILED]"<GetPoint(1); pointSet->SwapPointPosition(1, true); tempPoint = pointSet->GetPoint(0); MITK_TEST_CONDITION( point == tempPoint, "check SwapPointPosition upwards" ) /* if(point != tempPoint) { std::cout<<"[FAILED]"<SwapPointPosition(0, true)==false, "check SwapPointPosition upwards not possible" ) /* if(pointSet->SwapPointPosition(0, true)) { std::cout<<"[FAILED]"<GetPoint(0); pointSet->SwapPointPosition(0, false); tempPoint = pointSet->GetPoint(1); MITK_TEST_CONDITION( point == tempPoint, "check SwapPointPosition down" ) /* if(point != tempPoint) { std::cout<<"[FAILED]"<SetPoint(id, point); //Check SwapPointPosition downwards not possible MITK_TEST_CONDITION(!pointSet2->SwapPointPosition(id, false), "check SwapPointPosition downwards not possible" ) /* if(pointSet->SwapPointPosition(1, false)) { std::cout<<"[FAILED]"<ExecuteOperation(doOp); tempPoint = pointSet->GetPoint(id); MITK_TEST_CONDITION(tempPoint == point1 , "check PointOperation OpMove " ) delete doOp; /* if (tempPoint != point1) { std::cout<<"[FAILED]"<GetPoint(id); mitk::PointOperation* doOp = new mitk::PointOperation(mitk::OpREMOVE, point, id); pointSet->ExecuteOperation(doOp); tempPoint = pointSet->GetPoint(id); MITK_TEST_CONDITION(!pointSet->IndexExists(id) , "check PointOperation OpREMOVE " ) delete doOp; /* if(pointSet->IndexExists(id)) { std::cout<<"[FAILED]"<ExecuteOperation(doOp); MITK_TEST_CONDITION(pointSet->GetSelectInfo(4) , "check PointOperation OpSELECTPOINT " ) delete doOp; /* if (!pointSet->GetSelectInfo(4)) { std::cout<<"[FAILED]"<GetNumberOfSelected() == 1 , "check GetNumeberOfSelected " ) /* if(pointSet->GetNumberOfSelected() != 1) { std::cout<<"[FAILED]"<SearchSelectedPoint() == 4 , "check SearchSelectedPoint " ) /* if( pointSet->SearchSelectedPoint() != 4) { std::cout<<"[FAILED]"<ExecuteOperation(doOp); MITK_TEST_CONDITION(!pointSet->GetSelectInfo(4) , "check PointOperation OpDESELECTPOINT " ) MITK_TEST_CONDITION(pointSet->GetNumberOfSelected() == 0 , "check GetNumeberOfSelected " ) delete doOp; /* if (pointSet->GetSelectInfo(4)) { std::cout<<"[FAILED]"<GetNumberOfSelected() != 0) { std::cout<<"[FAILED]"<GetPoint(id); mitk::PointOperation* doOp = new mitk::PointOperation(mitk::OpMOVEPOINTUP, point4, id); pointSet->ExecuteOperation(doOp); tempPoint = pointSet->GetPoint(id-1); MITK_TEST_CONDITION(tempPoint == point , "check PointOperation OpMOVEPOINTUP " ) delete doOp; /* if (tempPoint != point) { std::cout<<"[FAILED]"<GetPoint(id); mitk::PointOperation* doOp = new mitk::PointOperation(mitk::OpMOVEPOINTDOWN, point2, id); pointSet->ExecuteOperation(doOp); tempPoint = pointSet->GetPoint(id+1); MITK_TEST_CONDITION(tempPoint == point , "check PointOperation OpMOVEPOINTDOWN " ) delete doOp; /* if (tempPoint != point) { std::cout<<"[FAILED]"<SetSelectInfo(2, true); MITK_TEST_CONDITION(pointSet->GetSelectInfo(2) , "check SetSelectInfo" ) /* if (!pointSet->GetSelectInfo(2)) { std::cout<<"[FAILED]"<SetPoint(5, point5, mitk::PTEDGE ); tempPoint = pointSet->GetPoint(5); MITK_TEST_CONDITION(tempPoint == point5, "check InsertPoint with PointSpecification" ) /* if (tempPoint != point5) { std::cout<<"[FAILED]"<GetPointIfExists(5, &tmpPoint); MITK_TEST_CONDITION(tmpPoint == point5, "check GetPointIfExists: " ) /* if (tmpPoint != point5) { std::cout<<"[FAILED]"<InsertPoint(10, p10); pointSet->InsertPoint(11, p11); pointSet->InsertPoint(12, p12); MITK_TEST_CONDITION((pointSet->IndexExists(10) == true) || (pointSet->IndexExists(11) == true) || (pointSet->IndexExists(12) == true), "add points with id 10, 11, 12: " ) //check OpREMOVE ExecuteOperation int id = 11; mitk::PointOperation* doOp = new mitk::PointOperation(mitk::OpREMOVE, point, id); pointSet->ExecuteOperation(doOp); MITK_TEST_CONDITION(!pointSet->IndexExists(id), "remove point id 11: ") /* if(pointSet->IndexExists(id)) { std::cout<<"[FAILED]"<ExecuteOperation(doOp); delete doOp; //check OpMOVEPOINTUP ExecuteOperation doOp = new mitk::PointOperation(mitk::OpMOVEPOINTUP, p12, 12); pointSet->ExecuteOperation(doOp); delete doOp; mitk::PointSet::PointType newP10 = pointSet->GetPoint(10); mitk::PointSet::PointType newP12 = pointSet->GetPoint(12); MITK_TEST_CONDITION(((newP10 == p12) && (newP12 == p10)) == true, "check PointOperation OpMOVEPOINTUP for point id 12:" ) //check OpMOVEPOINTDOWN ExecuteOperation doOp = new mitk::PointOperation(mitk::OpMOVEPOINTDOWN, p10, 10); pointSet->ExecuteOperation(doOp); delete doOp; newP10 = pointSet->GetPoint(10); newP12 = pointSet->GetPoint(12); MITK_TEST_CONDITION(((newP10 == p10) && (newP12 == p12)) == true, "check PointOperation OpMOVEPOINTDOWN for point id 10: ") } static void TestOpMovePointUpOnFirstPoint(mitk::PointSet *pointSet) { //check OpMOVEPOINTUP on first point ExecuteOperation mitk::PointSet::PointType p1 = pointSet->GetPoint(1); mitk::PointSet::PointType p2 = pointSet->GetPoint(2); mitk::PointOperation* doOp = new mitk::PointOperation(mitk::OpMOVEPOINTUP, p1, 1); pointSet->ExecuteOperation(doOp); delete doOp; mitk::PointSet::PointType newP1 = pointSet->GetPoint(1); mitk::PointSet::PointType newP2 = pointSet->GetPoint(2); MITK_TEST_CONDITION(((newP1 == p1) && (newP2 == p2)) == true, "check PointOperation OpMOVEPOINTUP for point id 1: ") /* if (((newP1 == p1) && (newP2 == p2)) == false) { std::cout<<"[FAILED]"<GetPointSet()->GetPoints(); mitk::PointSet::PointDataContainer* pd = ps->GetPointSet()->GetPointData(); MITK_TEST_CONDITION_REQUIRED(pc->Size() == pd->Size(), "PointContainer and PointDataContainer have same size"); mitk::PointSet::PointsContainer::ConstIterator pIt = pc->Begin(); mitk::PointSet::PointDataContainer::ConstIterator dIt = pd->Begin(); bool failed = false; for (; pIt != pc->End(); ++pIt, ++dIt) if (pIt->Index() != dIt->Index()) { failed = true; break; } MITK_TEST_CONDITION(failed == false, "Indices in PointContainer and PointDataContainer are equal"); } }; int mitkPointSetTest(int /*argc*/, char* /*argv*/[]) { MITK_TEST_BEGIN("PointSet") //Create PointSet mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); MITK_TEST_CONDITION_REQUIRED(pointSet.IsNotNull(),"Testing instantiation") mitkPointSetTestClass::TestGetITKPointSet(pointSet); mitkPointSetTestClass::TestGetSizeIsZero(pointSet); mitkPointSetTestClass::TestIsEmpty(pointSet); mitkPointSetTestClass::TestCreateOperationAndAddPoint(pointSet); mitk::Point3D point2, point3, point4; point2.Fill(3); point3.Fill(4); point4.Fill(5); pointSet->InsertPoint(2,point2); pointSet->InsertPoint(3,point3); pointSet->InsertPoint(4,point4); mitkPointSetTestClass::TestAddSecondPoint(pointSet); mitkPointSetTestClass::TestIsNotEmpty(pointSet); mitkPointSetTestClass::TestSwapPointPositionUpwards(pointSet); mitkPointSetTestClass::TestSwapPointPositionUpwardsNotPossible(pointSet); mitkPointSetTestClass::TestSwapPointPositionDownwards(pointSet); mitkPointSetTestClass::TestSwapPointPositionDownwardsNotPossible(pointSet); mitkPointSetTestClass::TestPointOperationOpMove(pointSet); mitkPointSetTestClass::TestPointOperationOpRemove(pointSet); mitkPointSetTestClass::TestPointOperationOpSelectPoint(pointSet); mitkPointSetTestClass::TestGetNumberOfSelected(pointSet); mitkPointSetTestClass::TestSearchSelectedPoint(pointSet); mitkPointSetTestClass::TestOpDeselectPoint(pointSet); mitkPointSetTestClass::TestOpMovePointUp(pointSet); mitkPointSetTestClass::TestOpMovePointDown(pointSet); mitkPointSetTestClass::TestSetSelectInfo(pointSet); mitkPointSetTestClass::TestInsertPointWithPointSpecification(pointSet); mitkPointSetTestClass::TestGetPointIfExists(pointSet); mitkPointSetTestClass::TestCreateHoleInThePointIDs(pointSet); mitkPointSetTestClass::TestOpMovePointUpOnFirstPoint(pointSet); MITK_TEST_OUTPUT(<< "Test InsertPoint(), SetPoint() and SwapPointPosition()"); mitk::PointSet::PointType point; mitk::FillVector3D(point, 2.2, 3.3, -4.4); /* call everything that might modify PointContainer and PointDataContainer */ pointSet->InsertPoint(17, point); pointSet->SetPoint(4, point); pointSet->SetPoint(7, point); pointSet->SetPoint(2, point); pointSet->SwapPointPosition(7, true); pointSet->SwapPointPosition(3, true); pointSet->SwapPointPosition(2, false); mitkPointSetTestClass::TestPointContainerPointDataContainer(pointSet); MITK_TEST_OUTPUT(<< "Test OpREMOVE"); mitk::PointOperation op1(mitk::OpREMOVE, mitk::Point3D(), 2); // existing index pointSet->ExecuteOperation(&op1); mitk::PointOperation op1b(mitk::OpREMOVE, mitk::Point3D(), 112); // non existing index pointSet->ExecuteOperation(&op1b); mitkPointSetTestClass::TestPointContainerPointDataContainer(pointSet); MITK_TEST_OUTPUT(<< "Test OpMove"); mitk::PointOperation op2(mitk::OpMOVE, mitk::Point3D(), 4); // existing index pointSet->ExecuteOperation(&op2); mitk::PointOperation op3(mitk::OpMOVE, mitk::Point3D(), 34); // non existing index pointSet->ExecuteOperation(&op3); mitkPointSetTestClass::TestPointContainerPointDataContainer(pointSet); MITK_TEST_OUTPUT(<< "Test OpINSERT"); mitk::PointOperation op4(mitk::OpINSERT, mitk::Point3D(), 38); // non existing index pointSet->ExecuteOperation(&op4); mitk::PointOperation op5(mitk::OpINSERT, mitk::Point3D(), 17); // existing index pointSet->ExecuteOperation(&op5); mitkPointSetTestClass::TestPointContainerPointDataContainer(pointSet); mitk::PointSet::Pointer clonePS = pointSet->Clone(); mitkPointSetTestClass::TestIsNotEmpty(clonePS); MITK_TEST_CONDITION_REQUIRED(clonePS->GetPointSetSeriesSize() == pointSet->GetPointSetSeriesSize(), "Testing cloned point set's size!"); MITK_TEST_CONDITION_REQUIRED(clonePS.GetPointer() != pointSet.GetPointer(), "Testing that the clone is not the source PS!"); MITK_TEST_CONDITION_REQUIRED(clonePS->GetGeometry()->GetCenter() == pointSet->GetGeometry()->GetCenter() , "Testing if the geometry is cloned correctly!"); MITK_TEST_CONDITION_REQUIRED(clonePS->GetPropertyList()->GetMap()->size() == pointSet->GetPropertyList()->GetMap()->size() , "Testing if the property list is cloned correctly!"); + // Also testing, that clone is independent from original + mitk::Point3D p, p2; + p.Fill(42); + p2.Fill(84); + clonePS->InsertPoint(0,p); + pointSet->InsertPoint(0,p2); + p = clonePS->GetPoint(0); + p2 = pointSet->GetPoint(0); + MITK_TEST_CONDITION_REQUIRED(p != p2, "Testing that the clone is independent from source!"); + + MITK_TEST_END(); } diff --git a/Modules/CMakeLists.txt b/Modules/CMakeLists.txt index c9ac643b13..808d527c13 100644 --- a/Modules/CMakeLists.txt +++ b/Modules/CMakeLists.txt @@ -1,52 +1,53 @@ set(LIBPOSTFIX "Ext") # Modules must be listed according to their dependencies set(module_dirs SceneSerializationBase PlanarFigure ImageExtraction ImageStatistics LegacyAdaptors IpPicSupport MitkExt SceneSerialization + Segmentation Qmitk QmitkExt GraphAlgorithms DiffusionImaging GPGPU IGT CameraCalibration IGTUI RigidRegistration RigidRegistrationUI DeformableRegistration DeformableRegistrationUI OpenCVVideoSupport Overlays InputDevices ToFHardware ToFProcessing ToFUI ClippingTools ) set(MITK_DEFAULT_SUBPROJECTS MITK-Modules) foreach(module_dir ${module_dirs}) add_subdirectory(${module_dir}) endforeach() if(MITK_PRIVATE_MODULES) file(GLOB all_subdirs RELATIVE ${MITK_PRIVATE_MODULES} ${MITK_PRIVATE_MODULES}/*) foreach(subdir ${all_subdirs}) string(FIND ${subdir} "." _result) if(_result EQUAL -1) if(EXISTS ${MITK_PRIVATE_MODULES}/${subdir}/CMakeLists.txt) message(STATUS "Found private module ${subdir}") add_subdirectory(${MITK_PRIVATE_MODULES}/${subdir} private_modules/${subdir}) endif() endif() endforeach() endif(MITK_PRIVATE_MODULES) diff --git a/Modules/DiffusionImaging/Algorithms/Connectomics/mitkConnectomicsHistogramCache.cpp b/Modules/DiffusionImaging/Algorithms/Connectomics/mitkConnectomicsHistogramCache.cpp index 183b3b5358..89512a4aef 100644 --- a/Modules/DiffusionImaging/Algorithms/Connectomics/mitkConnectomicsHistogramCache.cpp +++ b/Modules/DiffusionImaging/Algorithms/Connectomics/mitkConnectomicsHistogramCache.cpp @@ -1,84 +1,96 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkConnectomicsHistogramCache.h" mitk::ConnectomicsHistogramCache::ConnectomicsHistogramCache() { } mitk::ConnectomicsHistogramCache::~ConnectomicsHistogramCache() { } mitk::ConnectomicsHistogramsContainer * mitk::ConnectomicsHistogramCache::operator[]( mitk::ConnectomicsNetwork::Pointer sp_NetworkData ) { BaseData *p_BaseData = dynamic_cast< BaseData* >( sp_NetworkData.GetPointer() ); if(!p_BaseData) { MITK_WARN << "ConnectomicsHistogramCache::operator[] with null connectomics network data called"; return 0; } ConnectomicsHistogramsCacheElement *elementToUpdate = 0; - bool first = true; + bool first( true ); + + bool found( false ); for(CacheContainer::iterator iter = cache.begin(); iter != cache.end(); iter++) { ConnectomicsHistogramsCacheElement *e = dynamic_cast(*iter); BaseData *p_tmp = e->baseData.GetPointer(); if(p_tmp == p_BaseData) { if(!first) { cache.erase(iter); cache.push_front(e); } if( p_BaseData->GetMTime() > e->m_LastUpdateTime.GetMTime()) - goto recomputeElement; - + { + // found but needs an update + found = true; + elementToUpdate = e; + break; + } + // found but no update needed return dynamic_cast( e->GetHistograms() ); } first = false; } - if (dynamic_cast(p_BaseData)) + if( !found ) { - elementToUpdate = new ConnectomicsHistogramsCacheElement(); + if (dynamic_cast(p_BaseData)) + { + elementToUpdate = new ConnectomicsHistogramsCacheElement(); + } + else + { + MITK_WARN << "not supported: " << p_BaseData->GetNameOfClass(); + return NULL; + } + + elementToUpdate->baseData = p_BaseData; + cache.push_front(elementToUpdate); + TrimCache(); } - else + + if(elementToUpdate) { - MITK_WARN << "not supported: " << p_BaseData->GetNameOfClass(); - return NULL; + elementToUpdate->ComputeFromBaseData(p_BaseData); + elementToUpdate->m_LastUpdateTime.Modified(); + return dynamic_cast( elementToUpdate->GetHistograms() ); } - - elementToUpdate->baseData = p_BaseData; - cache.push_front(elementToUpdate); - TrimCache(); - - recomputeElement: - - elementToUpdate->ComputeFromBaseData(p_BaseData); - elementToUpdate->m_LastUpdateTime.Modified(); - return dynamic_cast( elementToUpdate->GetHistograms() ); + return NULL; } diff --git a/Modules/DiffusionImaging/Algorithms/Connectomics/mitkConnectomicsSyntheticNetworkGenerator.cpp b/Modules/DiffusionImaging/Algorithms/Connectomics/mitkConnectomicsSyntheticNetworkGenerator.cpp index d71742d711..133cf33333 100644 --- a/Modules/DiffusionImaging/Algorithms/Connectomics/mitkConnectomicsSyntheticNetworkGenerator.cpp +++ b/Modules/DiffusionImaging/Algorithms/Connectomics/mitkConnectomicsSyntheticNetworkGenerator.cpp @@ -1,352 +1,364 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkConnectomicsSyntheticNetworkGenerator.h" #include #include #include "mitkConnectomicsConstantsManager.h" #include //for random number generation #include "vxl/core/vnl/vnl_random.h" #include "vxl/core/vnl/vnl_math.h" mitk::ConnectomicsSyntheticNetworkGenerator::ConnectomicsSyntheticNetworkGenerator() +: m_LastGenerationWasSuccess( false ) { } mitk::ConnectomicsSyntheticNetworkGenerator::~ConnectomicsSyntheticNetworkGenerator() { } mitk::ConnectomicsNetwork::Pointer mitk::ConnectomicsSyntheticNetworkGenerator::CreateSyntheticNetwork(int networkTypeId, int paramterOne, double parameterTwo) { mitk::ConnectomicsNetwork::Pointer network = mitk::ConnectomicsNetwork::New(); + m_LastGenerationWasSuccess = false; // give the network an artificial geometry network->SetGeometry( this->GenerateDefaultGeometry() ); switch (networkTypeId) { case 0: GenerateSyntheticCubeNetwork( network, paramterOne, parameterTwo ); break; case 1: GenerateSyntheticCenterToSurfaceNetwork( network, paramterOne, parameterTwo ); break; case 2: GenerateSyntheticRandomNetwork( network, paramterOne, parameterTwo ); break; case 3: //GenerateSyntheticScaleFreeNetwork( network, 1000 ); break; case 4: //GenerateSyntheticSmallWorldNetwork( network, 1000 ); break; default: MBI_ERROR << "Unrecognized Network ID"; } network->UpdateBounds(); return network; } mitk::Geometry3D::Pointer mitk::ConnectomicsSyntheticNetworkGenerator::GenerateDefaultGeometry() { mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); double zero( 0.0 ); double one( 1.0 ); // origin = {0,0,0} mitk::Point3D origin; origin[0] = zero; origin[1] = zero; origin[2] = zero; geometry->SetOrigin(origin); // spacing = {1,1,1} float spacing[3]; spacing[0] = one; spacing[1] = one; spacing[2] = one; geometry->SetSpacing(spacing); // transform vtkMatrix4x4* transformMatrix = vtkMatrix4x4::New(); transformMatrix->SetElement(0,0,one); transformMatrix->SetElement(1,0,zero); transformMatrix->SetElement(2,0,zero); transformMatrix->SetElement(0,1,zero); transformMatrix->SetElement(1,1,one); transformMatrix->SetElement(2,1,zero); transformMatrix->SetElement(0,2,zero); transformMatrix->SetElement(1,2,zero); transformMatrix->SetElement(2,2,one); transformMatrix->SetElement(0,3,origin[0]); transformMatrix->SetElement(1,3,origin[1]); transformMatrix->SetElement(2,3,origin[2]); transformMatrix->SetElement(3,3,1); geometry->SetIndexToWorldTransformByVtkMatrix( transformMatrix ); geometry->SetImageGeometry(true); return geometry; } void mitk::ConnectomicsSyntheticNetworkGenerator::GenerateSyntheticCubeNetwork( mitk::ConnectomicsNetwork::Pointer network, int cubeExtent, double distance ) { // map for storing the conversion from indices to vertex descriptor std::map< int, mitk::ConnectomicsNetwork::VertexDescriptorType > idToVertexMap; int vertexID(0); for( int loopX( 0 ); loopX < cubeExtent; loopX++ ) { for( int loopY( 0 ); loopY < cubeExtent; loopY++ ) { for( int loopZ( 0 ); loopZ < cubeExtent; loopZ++ ) { std::vector< float > position; std::string label; std::stringstream labelStream; labelStream << vertexID; label = labelStream.str(); position.push_back( loopX * distance ); position.push_back( loopY * distance ); position.push_back( loopZ * distance ); mitk::ConnectomicsNetwork::VertexDescriptorType newVertex = network->AddVertex( vertexID ); network->SetLabel( newVertex, label ); network->SetCoordinates( newVertex, position ); if ( idToVertexMap.count( vertexID ) > 0 ) { MITK_ERROR << "Aborting network creation, duplicate vertex ID generated."; + m_LastGenerationWasSuccess = false; return; } idToVertexMap.insert( std::pair< int, mitk::ConnectomicsNetwork::VertexDescriptorType >( vertexID, newVertex) ); vertexID++; } } } int edgeID(0), edgeSourceID(0), edgeTargetID(0); // uniform weight of one int edgeWeight(1); mitk::ConnectomicsNetwork::VertexDescriptorType source; mitk::ConnectomicsNetwork::VertexDescriptorType target; for( int loopX( 0 ); loopX < cubeExtent; loopX++ ) { for( int loopY( 0 ); loopY < cubeExtent; loopY++ ) { for( int loopZ( 0 ); loopZ < cubeExtent; loopZ++ ) { // to avoid creating an edge twice (this being an undirected graph) we only generate // edges in three directions, the others will be supplied by the corresponding nodes if( loopX != 0 ) { edgeTargetID = edgeSourceID - cubeExtent * cubeExtent; source = idToVertexMap.find( edgeSourceID )->second; target = idToVertexMap.find( edgeTargetID )->second; network->AddEdge( source, target, edgeSourceID, edgeTargetID, edgeWeight); edgeID++; } if( loopY != 0 ) { edgeTargetID = edgeSourceID - cubeExtent; source = idToVertexMap.find( edgeSourceID )->second; target = idToVertexMap.find( edgeTargetID )->second; network->AddEdge( source, target, edgeSourceID, edgeTargetID, edgeWeight); edgeID++; } if( loopZ != 0 ) { edgeTargetID = edgeSourceID - 1; source = idToVertexMap.find( edgeSourceID )->second; target = idToVertexMap.find( edgeTargetID )->second; network->AddEdge( source, target, edgeSourceID, edgeTargetID, edgeWeight); edgeID++; } edgeSourceID++; } // end for( int loopZ( 0 ); loopZ < cubeExtent; loopZ++ ) } // end for( int loopY( 0 ); loopY < cubeExtent; loopY++ ) } // end for( int loopX( 0 ); loopX < cubeExtent; loopX++ ) + m_LastGenerationWasSuccess = true; } void mitk::ConnectomicsSyntheticNetworkGenerator::GenerateSyntheticCenterToSurfaceNetwork( mitk::ConnectomicsNetwork::Pointer network, int numberOfPoints, double radius ) { //the random number generators unsigned int randomOne = (unsigned int) rand(); unsigned int randomTwo = (unsigned int) rand(); vnl_random rng( (unsigned int) rand() ); vnl_random rng2( (unsigned int) rand() ); mitk::ConnectomicsNetwork::VertexDescriptorType centerVertex; int vertexID(0); { //add center vertex std::vector< float > position; std::string label; std::stringstream labelStream; labelStream << vertexID; label = labelStream.str(); position.push_back( 0 ); position.push_back( 0 ); position.push_back( 0 ); centerVertex = network->AddVertex( vertexID ); network->SetLabel( centerVertex, label ); network->SetCoordinates( centerVertex, position ); }//end add center vertex // uniform weight of one int edgeWeight(1); mitk::ConnectomicsNetwork::VertexDescriptorType source; mitk::ConnectomicsNetwork::VertexDescriptorType target; //add vertices on sphere surface for( int loopID( 1 ); loopID < numberOfPoints; loopID++ ) { std::vector< float > position; std::string label; std::stringstream labelStream; labelStream << loopID; label = labelStream.str(); //generate random, uniformly distributed points on a sphere surface const double uVariable = rng.drand64( 0.0 , 1.0); const double vVariable = rng.drand64( 0.0 , 1.0); const double phi = 2 * vnl_math::pi * uVariable; const double theta = std::acos( 2 * vVariable - 1 ); double xpos = radius * std::cos( phi ) * std::sin( theta ); double ypos = radius * std::sin( phi ) * std::sin( theta ); double zpos = radius * std::cos( theta ); position.push_back( xpos ); position.push_back( ypos ); position.push_back( zpos ); mitk::ConnectomicsNetwork::VertexDescriptorType newVertex = network->AddVertex( loopID ); network->SetLabel( newVertex, label ); network->SetCoordinates( newVertex, position ); network->AddEdge( newVertex, centerVertex, loopID, 0, edgeWeight); } + m_LastGenerationWasSuccess = true; } void mitk::ConnectomicsSyntheticNetworkGenerator::GenerateSyntheticRandomNetwork( mitk::ConnectomicsNetwork::Pointer network, int numberOfPoints, double threshold ) { // as the surface is proportional to the square of the radius the density stays the same double radius = 5 * std::sqrt( (float) numberOfPoints ); //the random number generators unsigned int randomOne = (unsigned int) rand(); unsigned int randomTwo = (unsigned int) rand(); vnl_random rng( (unsigned int) rand() ); vnl_random rng2( (unsigned int) rand() ); // map for storing the conversion from indices to vertex descriptor std::map< int, mitk::ConnectomicsNetwork::VertexDescriptorType > idToVertexMap; //add vertices on sphere surface for( int loopID( 0 ); loopID < numberOfPoints; loopID++ ) { std::vector< float > position; std::string label; std::stringstream labelStream; labelStream << loopID; label = labelStream.str(); //generate random, uniformly distributed points on a sphere surface const double uVariable = rng.drand64( 0.0 , 1.0); const double vVariable = rng.drand64( 0.0 , 1.0); const double phi = 2 * vnl_math::pi * uVariable; const double theta = std::acos( 2 * vVariable - 1 ); double xpos = radius * std::cos( phi ) * std::sin( theta ); double ypos = radius * std::sin( phi ) * std::sin( theta ); double zpos = radius * std::cos( theta ); position.push_back( xpos ); position.push_back( ypos ); position.push_back( zpos ); mitk::ConnectomicsNetwork::VertexDescriptorType newVertex = network->AddVertex( loopID ); network->SetLabel( newVertex, label ); network->SetCoordinates( newVertex, position ); if ( idToVertexMap.count( loopID ) > 0 ) { MITK_ERROR << "Aborting network creation, duplicate vertex ID generated."; + m_LastGenerationWasSuccess = false; return; } idToVertexMap.insert( std::pair< int, mitk::ConnectomicsNetwork::VertexDescriptorType >( loopID, newVertex) ); } int edgeID(0); // uniform weight of one int edgeWeight(1); mitk::ConnectomicsNetwork::VertexDescriptorType source; mitk::ConnectomicsNetwork::VertexDescriptorType target; for( int loopID( 0 ); loopID < numberOfPoints; loopID++ ) { // to avoid creating an edge twice (this being an undirected graph) we only // potentially generate edges with all nodes with a bigger ID for( int innerLoopID( loopID ); innerLoopID < numberOfPoints; innerLoopID++ ) { if( rng.drand64( 0.0 , 1.0) > threshold) { // do nothing } else { source = idToVertexMap.find( loopID )->second; target = idToVertexMap.find( innerLoopID )->second; network->AddEdge( source, target, loopID, innerLoopID, edgeWeight); edgeID++; } } // end for( int innerLoopID( loopID ); innerLoopID < numberOfPoints; innerLoopID++ ) } // end for( int loopID( 0 ); loopID < numberOfPoints; loopID++ ) + m_LastGenerationWasSuccess = true; +} + +bool mitk::ConnectomicsSyntheticNetworkGenerator::WasGenerationSuccessfull() +{ + return m_LastGenerationWasSuccess; } \ No newline at end of file diff --git a/Modules/DiffusionImaging/Algorithms/Connectomics/mitkConnectomicsSyntheticNetworkGenerator.h b/Modules/DiffusionImaging/Algorithms/Connectomics/mitkConnectomicsSyntheticNetworkGenerator.h index dca9005c48..c19aa02155 100644 --- a/Modules/DiffusionImaging/Algorithms/Connectomics/mitkConnectomicsSyntheticNetworkGenerator.h +++ b/Modules/DiffusionImaging/Algorithms/Connectomics/mitkConnectomicsSyntheticNetworkGenerator.h @@ -1,83 +1,88 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkConnectomicsSyntheticNetworkGenerator_h #define mitkConnectomicsSyntheticNetworkGenerator_h #include #include #include #include "mitkCommon.h" #include "mitkImage.h" #include "mitkConnectomicsNetwork.h" #include "MitkDiffusionImagingExports.h" namespace mitk { /** * \brief A class to generate synthetic networks */ class MitkDiffusionImaging_EXPORT ConnectomicsSyntheticNetworkGenerator : public itk::Object { public: /** Standard class typedefs. */ /** Method for creation through the object factory. */ mitkClassMacro(ConnectomicsSyntheticNetworkGenerator, itk::Object); itkNewMacro(Self); /** Create Synthetic Networks */ mitk::ConnectomicsNetwork::Pointer CreateSyntheticNetwork(int networkTypeId, int paramterOne, double parameterTwo); + /** Return whether the last attempted network generation was a success*/ + bool WasGenerationSuccessfull(); + protected: //////////////////// Functions /////////////////////// ConnectomicsSyntheticNetworkGenerator(); ~ConnectomicsSyntheticNetworkGenerator(); /** Generate a default geometry for synthetic images */ mitk::Geometry3D::Pointer GenerateDefaultGeometry(); /** Generate a synthetic cube (regular lattice) network */ void GenerateSyntheticCubeNetwork( mitk::ConnectomicsNetwork::Pointer network, int cubeExtent, double distance ); /** Generate a highly heterogenic network * * This is achieved by generating a center vertex and vertices on * a sphere surface, which are all only connected to the center * vertex. */ void GenerateSyntheticCenterToSurfaceNetwork( mitk::ConnectomicsNetwork::Pointer network, int numberOfPoints, double radius ); /** Generate a random network without specific characteristics * * This is achieved by generating vertices and then deciding whether to * specific vertices are connected by comparing a random number to the threshold */ void GenerateSyntheticRandomNetwork( mitk::ConnectomicsNetwork::Pointer network, int numberOfPoints, double threshold ); /////////////////////// Variables //////////////////////// + /** Store whether the network generated last was generated properly */ + bool m_LastGenerationWasSuccess; }; }// end namespace mitk #endif // _mitkConnectomicsSyntheticNetworkGenerator_H_INCLUDED \ No newline at end of file diff --git a/Modules/DiffusionImaging/Algorithms/itkExtractChannelFromRgbaImageFilter.cpp b/Modules/DiffusionImaging/Algorithms/itkExtractChannelFromRgbaImageFilter.cpp index b3d0bc068a..8461b0afd6 100644 --- a/Modules/DiffusionImaging/Algorithms/itkExtractChannelFromRgbaImageFilter.cpp +++ b/Modules/DiffusionImaging/Algorithms/itkExtractChannelFromRgbaImageFilter.cpp @@ -1,159 +1,156 @@ #include "itkExtractChannelFromRgbaImageFilter.h" // VTK #include #include #include // misc #include namespace itk{ - template< class OutputImageType > - ExtractChannelFromRgbaImageFilter< OutputImageType >::ExtractChannelFromRgbaImageFilter(): + template< class ReferenceImageType, class OutputImageType > + ExtractChannelFromRgbaImageFilter< ReferenceImageType, OutputImageType >::ExtractChannelFromRgbaImageFilter(): m_Channel(RED) { } - template< class OutputImageType > - ExtractChannelFromRgbaImageFilter< OutputImageType >::~ExtractChannelFromRgbaImageFilter() + template< class ReferenceImageType, class OutputImageType > + ExtractChannelFromRgbaImageFilter< ReferenceImageType, OutputImageType >::~ExtractChannelFromRgbaImageFilter() { } - template< class OutputImageType > - void ExtractChannelFromRgbaImageFilter< OutputImageType >::GenerateData() + template< class ReferenceImageType, class OutputImageType > + void ExtractChannelFromRgbaImageFilter< ReferenceImageType, OutputImageType >::GenerateData() { typename InputImageType::Pointer rgbaImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) ); typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); typename InputImageType::RegionType region = rgbaImage->GetLargestPossibleRegion(); outputImage->SetSpacing( m_ReferenceImage->GetSpacing() ); // Set the image spacing outputImage->SetOrigin( m_ReferenceImage->GetOrigin() ); // Set the image origin outputImage->SetDirection( m_ReferenceImage->GetDirection() ); // Set the image direction outputImage->SetRegions( m_ReferenceImage->GetLargestPossibleRegion()); outputImage->Allocate(); outputImage->FillBuffer(0); float* outImageBufferPointer = outputImage->GetBufferPointer(); itk::Image< short, 3 >::Pointer counterImage = itk::Image< short, 3 >::New(); counterImage->SetSpacing( m_ReferenceImage->GetSpacing() ); // Set the image spacing counterImage->SetOrigin( m_ReferenceImage->GetOrigin() ); // Set the image origin counterImage->SetDirection( m_ReferenceImage->GetDirection() ); // Set the image direction counterImage->SetRegions( m_ReferenceImage->GetLargestPossibleRegion()); counterImage->Allocate(); counterImage->FillBuffer(0); short* counterImageBufferPointer = counterImage->GetBufferPointer(); int w = m_ReferenceImage->GetLargestPossibleRegion().GetSize().GetElement(0); int h = m_ReferenceImage->GetLargestPossibleRegion().GetSize().GetElement(1); int d = m_ReferenceImage->GetLargestPossibleRegion().GetSize().GetElement(2); typedef ImageRegionConstIterator< InputImageType > InImageIteratorType; InImageIteratorType rgbaIt(rgbaImage, region); rgbaIt.GoToBegin(); while(!rgbaIt.IsAtEnd()){ InPixelType x = rgbaIt.Get(); + ++rgbaIt; itk::Point vertex; itk::Index<3> index = rgbaIt.GetIndex(); rgbaImage->TransformIndexToPhysicalPoint(index, vertex); outputImage->TransformPhysicalPointToIndex(vertex, index); itk::ContinuousIndex contIndex; outputImage->TransformPhysicalPointToContinuousIndex(vertex, contIndex); float frac_x = contIndex[0] - index[0]; float frac_y = contIndex[1] - index[1]; float frac_z = contIndex[2] - index[2]; int px = index[0]; if (frac_x<0) { px -= 1; frac_x += 1; } int py = index[1]; if (frac_y<0) { py -= 1; frac_y += 1; } int pz = index[2]; if (frac_z<0) { pz -= 1; frac_z += 1; } frac_x = 1-frac_x; frac_y = 1-frac_y; frac_z = 1-frac_z; // int coordinates inside image? if (px < 0 || px >= w-1) continue; if (py < 0 || py >= h-1) continue; if (pz < 0 || pz >= d-1) continue; OutPixelType out; switch (m_Channel) { case RED: out = (float)x.GetRed()/255; break; case GREEN: out = (float)x.GetGreen()/255; break; case BLUE: out = (float)x.GetBlue()/255; break; case ALPHA: out = (float)x.GetAlpha()/255; } outImageBufferPointer[( px + w*(py + h*pz ))] += out*( frac_x)*( frac_y)*( frac_z); outImageBufferPointer[( px + w*(py+1+ h*pz ))] += out*( frac_x)*(1-frac_y)*( frac_z); outImageBufferPointer[( px + w*(py + h*pz+h))] += out*( frac_x)*( frac_y)*(1-frac_z); outImageBufferPointer[( px + w*(py+1+ h*pz+h))] += out*( frac_x)*(1-frac_y)*(1-frac_z); outImageBufferPointer[( px+1 + w*(py + h*pz ))] += out*(1-frac_x)*( frac_y)*( frac_z); outImageBufferPointer[( px+1 + w*(py + h*pz+h))] += out*(1-frac_x)*( frac_y)*(1-frac_z); outImageBufferPointer[( px+1 + w*(py+1+ h*pz ))] += out*(1-frac_x)*(1-frac_y)*( frac_z); outImageBufferPointer[( px+1 + w*(py+1+ h*pz+h))] += out*(1-frac_x)*(1-frac_y)*(1-frac_z); counterImageBufferPointer[( px + w*(py + h*pz ))] += 1; counterImageBufferPointer[( px + w*(py+1+ h*pz ))] += 1; counterImageBufferPointer[( px + w*(py + h*pz+h))] += 1; counterImageBufferPointer[( px + w*(py+1+ h*pz+h))] += 1; counterImageBufferPointer[( px+1 + w*(py + h*pz ))] += 1; counterImageBufferPointer[( px+1 + w*(py + h*pz+h))] += 1; counterImageBufferPointer[( px+1 + w*(py+1+ h*pz ))] += 1; counterImageBufferPointer[( px+1 + w*(py+1+ h*pz+h))] += 1; -// outputImage->SetPixel(index, outputImage->GetPixel(index)+out); -// counterImage->SetPixel(index, counterImage->GetPixel(index)+1); - - ++rgbaIt; } typedef ImageRegionIterator< OutputImageType > OutImageIteratorType; OutImageIteratorType outIt(outputImage, outputImage->GetLargestPossibleRegion()); outIt.GoToBegin(); typedef ImageRegionConstIterator< itk::Image< short, 3 > > CountImageIteratorType; CountImageIteratorType counterIt(counterImage, counterImage->GetLargestPossibleRegion()); counterIt.GoToBegin(); while(!outIt.IsAtEnd() && !counterIt.IsAtEnd()){ if (counterIt.Value()>0) outIt.Set(outIt.Value()/counterIt.Value()); ++outIt; ++counterIt; } } } diff --git a/Modules/DiffusionImaging/Algorithms/itkExtractChannelFromRgbaImageFilter.h b/Modules/DiffusionImaging/Algorithms/itkExtractChannelFromRgbaImageFilter.h index e9fdc6e6f4..571b6d8760 100644 --- a/Modules/DiffusionImaging/Algorithms/itkExtractChannelFromRgbaImageFilter.h +++ b/Modules/DiffusionImaging/Algorithms/itkExtractChannelFromRgbaImageFilter.h @@ -1,59 +1,57 @@ #ifndef __itkExtractChannelFromRgbaImageFilter_h__ #define __itkExtractChannelFromRgbaImageFilter_h__ #include #include #include #include namespace itk{ -template< class OutputImageType > +template< class ReferenceImageType, class OutputImageType > class ExtractChannelFromRgbaImageFilter : public ImageToImageFilter< itk::Image,3>, OutputImageType > { public: enum Channel { RED, GREEN, BLUE, ALPHA }; typedef ExtractChannelFromRgbaImageFilter Self; typedef ProcessObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef itk::Image,3> InputImageType; typedef typename OutputImageType::PixelType OutPixelType; typedef typename InputImageType::PixelType InPixelType; - typedef itk::VectorImage< short int, 3 > ReferenceImageType; - itkNewMacro(Self); itkTypeMacro( ExtractChannelFromRgbaImageFilter, ImageSource ); /** Upsampling factor **/ void GenerateData(); itkSetMacro(Channel, Channel) - itkSetMacro(ReferenceImage, ReferenceImageType::Pointer) + itkSetMacro(ReferenceImage, typename ReferenceImageType::Pointer) protected: ExtractChannelFromRgbaImageFilter(); virtual ~ExtractChannelFromRgbaImageFilter(); Channel m_Channel; - ReferenceImageType::Pointer m_ReferenceImage; + typename ReferenceImageType::Pointer m_ReferenceImage; }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkExtractChannelFromRgbaImageFilter.cpp" #endif #endif // __itkExtractChannelFromRgbaImageFilter_h__ diff --git a/Modules/DiffusionImaging/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h b/Modules/DiffusionImaging/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h new file mode 100644 index 0000000000..9ac637a7ba --- /dev/null +++ b/Modules/DiffusionImaging/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h @@ -0,0 +1,237 @@ +/*========================================================================= + +Program: Tensor ToolKit - TTK +Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkTensorImageToDiffusionImageFilter.h $ +Language: C++ +Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $ +Version: $Revision: 68 $ + +Copyright (c) INRIA 2010. All rights reserved. +See LICENSE.txt for details. + +This software is distributed WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR +PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ +#ifndef _itk_TensorReconstructionWithEigenvalueCorrectionFilter_h_ +#define _itk_TensorReconstructionWithEigenvalueCorrectionFilter_h_ + +#include "itkImageToImageFilter.h" +#include +#include +#include + +#include +#include + + +typedef itk::VectorImage ImageType; + + + + +namespace itk +{ + + template + class TensorReconstructionWithEigenvalueCorrectionFilter + : public ImageToImageFilter< itk::Image< TDiffusionPixelType, 3 >, itk::Image,3> > + { + + public: + + typedef TensorReconstructionWithEigenvalueCorrectionFilter Self; + typedef SmartPointer Pointer; + typedef SmartPointer ConstPointer; + typedef ImageToImageFilter< Image< TDiffusionPixelType, 3>, + Image< DiffusionTensor3D< TTensorPixelType >, 3 > > + Superclass; + + /** Method for creation through the object factory. */ + itkNewMacro(Self); + + /** Runtime information support. */ + itkTypeMacro(TensorReconstructionWithEigenvalueCorrectionFilter, ImageToImageFilter); + + typedef TDiffusionPixelType ReferencePixelType; + typedef TDiffusionPixelType GradientPixelType; + typedef DiffusionTensor3D< TTensorPixelType > TensorPixelType; + + + /** Reference image data, This image is aquired in the absence + * of a diffusion sensitizing field gradient */ + typedef typename Superclass::InputImageType ReferenceImageType; + typedef Image< TensorPixelType, 3 > TensorImageType; + typedef TensorImageType OutputImageType; + typedef typename Superclass::OutputImageRegionType + OutputImageRegionType; + + /** Typedef defining one (of the many) gradient images. */ + typedef Image< GradientPixelType, 3 > GradientImageType; + + /** An alternative typedef defining one (of the many) gradient images. + * It will be assumed that the vectorImage has the same dimension as the + * Reference image and a vector length parameter of \c n (number of + * gradient directions) */ + typedef VectorImage< GradientPixelType, 3 > GradientImagesType; + + + + /* + /** Holds the tensor basis coefficients G_k + typedef vnl_matrix_fixed< double, 6, 6 > TensorBasisMatrixType; + + typedef vnl_matrix< double > CoefficientMatrixType; + */ + + /** Holds each magnetic field gradient used to acquire one DWImage */ + typedef vnl_vector_fixed< double, 3 > GradientDirectionType; + + /** Container to hold gradient directions of the 'n' DW measurements */ + typedef VectorContainer< unsigned int, + GradientDirectionType > GradientDirectionContainerType; + + + + /** Another set method to add a gradient directions and its corresponding + * image. The image here is a VectorImage. The user is expected to pass the + * gradient directions in a container. The ith element of the container + * corresponds to the gradient direction of the ith component image the + * VectorImage. For the baseline image, a vector of all zeros + * should be set. */ + void SetGradientImage( GradientDirectionContainerType *, + const GradientImagesType *image); + + /** Set method to set the reference image. */ + void SetReferenceImage( ReferenceImageType *referenceImage ) + { + if( m_GradientImageTypeEnumeration == GradientIsInASingleImage) + { + itkExceptionMacro( << "Cannot call both methods:" + << "AddGradientImage and SetGradientImage. Please call only one of them."); + } + + this->ProcessObject::SetNthInput( 0, referenceImage ); + + m_GradientImageTypeEnumeration = GradientIsInManyImages; + } + + /** Get reference image */ + virtual ReferenceImageType * GetReferenceImage() + { return ( static_cast< ReferenceImageType *>(this->ProcessObject::GetInput(0)) ); } + + /** Return the gradient direction. idx is 0 based */ + virtual GradientDirectionType GetGradientDirection( unsigned int idx) const + { + if( idx >= m_NumberOfGradientDirections ) + { + itkExceptionMacro( << "Gradient direction " << idx << "does not exist" ); + } + return m_GradientDirectionContainer->ElementAt( idx+1 ); + } + + itkSetMacro( BValue, TTensorPixelType); + itkSetMacro( B0Threshold, float); + + itkGetMacro(PseudoInverse, vnl_matrix); + itkGetMacro(H, vnl_matrix); + itkGetMacro(BVec, vnl_vector); + itkGetMacro(B0Mask, vnl_vector); + itkGetMacro(Voxdim, vnl_vector); + + mitk::DiffusionImage::Pointer GetOutputDiffusionImage() + { + return m_OutputDiffusionImage; + } + + ImageType::Pointer GetVectorImage() + { + return m_VectorImage; + } + + itk::Image::Pointer GetMask() + { + return m_MaskImage; + } + + + //itkGetMacro(OutputDiffusionImage, mitk::DiffusionImage) + + //itkGetMacro( GradientDirectionContainer, GradientDirectionContainerType::Pointer); + + protected: + + TensorReconstructionWithEigenvalueCorrectionFilter(); + ~TensorReconstructionWithEigenvalueCorrectionFilter() {}; + + + void GenerateData(); + + + typedef enum + { + GradientIsInASingleImage = 1, + GradientIsInManyImages, + Else + } GradientImageTypeEnumeration; + + + + private: + + void check_the_neighbors(int x, int y, int z,int f, itk::Size<3> size,itk::Index<3> ix, + typename GradientImagesType::Pointer gradientImagePointer,ImageType::IndexType pixelIndex,ImageType::Pointer corrected_diffusion, double &temp_pixel); + + void calculate_attenuation(vnl_vector org_data,vnl_vector< double > b0index, vnl_vector &atten, double mean_b,int nof,int numberb0); + + + void calculate_tensor(vnl_matrix pseudoInverse,vnl_vector atten, vnl_vector &tensor,int nof,int numberb0); + + /** Gradient image was specified in a single image or in multiple images */ + GradientImageTypeEnumeration m_GradientImageTypeEnumeration; + + /** Number of gradient measurements */ + unsigned int m_NumberOfGradientDirections; + + /** container to hold gradient directions */ + GradientDirectionContainerType::Pointer m_GradientDirectionContainer; + + + /** b-value */ + TTensorPixelType m_BValue; + + /** Number of baseline images */ + unsigned int m_NumberOfBaselineImages; + + mitk::DiffusionImage::Pointer m_OutputDiffusionImage; + + ImageType::Pointer m_VectorImage; + + float m_B0Threshold; + + + + itk::Image::Pointer m_MaskImage; + vnl_matrix m_PseudoInverse; + vnl_matrix m_H; + vnl_vector m_BVec; + vnl_vector m_B0Mask; + vnl_vector m_Voxdim; + + }; + + + + + + +} // end of namespace + + +#ifndef ITK_MANUAL_INSTANTIATION +#include "itkTensorReconstructionWithEigenvalueCorrectionFilter.txx" +#endif + + +#endif diff --git a/Modules/DiffusionImaging/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.txx b/Modules/DiffusionImaging/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.txx new file mode 100644 index 0000000000..3b2db6abc6 --- /dev/null +++ b/Modules/DiffusionImaging/Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.txx @@ -0,0 +1,632 @@ +/*========================================================================= + +Program: Tensor ToolKit - TTK +Module: $URL: svn://scm.gforge.inria.fr/svn/ttk/trunk/Algorithms/itkTensorImageToDiffusionImageFilter.txx $ +Language: C++ +Date: $Date: 2010-06-07 13:39:13 +0200 (Mo, 07 Jun 2010) $ +Version: $Revision: 68 $ + +Copyright (c) INRIA 2010. All rights reserved. +See LICENSE.txt for details. + +This software is distributed WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR +PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ +#ifndef _itk_TensorReconstructionWithEigenvalueCorrectionFilter_txx_ +#define _itk_TensorReconstructionWithEigenvalueCorrectioFiltern_txx_ +#endif +#include "itkImageRegionConstIterator.h" +#include +#include + +namespace itk +{ + + + template + TensorReconstructionWithEigenvalueCorrectionFilter + ::TensorReconstructionWithEigenvalueCorrectionFilter() + { + m_B0Threshold = 50.0; + } + + template + void + TensorReconstructionWithEigenvalueCorrectionFilter + ::GenerateData ( ) + { + + typedef ImageRegionConstIterator< GradientImagesType > GradientIteratorType; + typedef typename GradientImagesType::PixelType GradientVectorType; + typename GradientImagesType::Pointer gradientImagePointer = NULL; + + // Would have liked a dynamic_cast here, but seems SGI doesn't like it + // The enum will ensure that an inappropriate cast is not done + gradientImagePointer = static_cast< GradientImagesType * >( + this->ProcessObject::GetInput(0) ); + + // Size of the complete image + typename GradientImagesType::SizeType size = gradientImagePointer->GetLargestPossibleRegion().GetSize(); + + /// First filter + int nof = m_GradientDirectionContainer->Size(); + int numberb0=0; + vnl_vector< double > b0index(nof); + int cnt=0; + + + + for(int i=0; i vec = m_GradientDirectionContainer->ElementAt(i); + + if(vec[0]<0.0001 && vec[1]<0.0001 && vec[2]<0.0001 && vec[0]>-0.001&& vec[1]>-0.001 && vec[2]>-0.001) + { + numberb0++; + } + } + + + itk::Vector spacing_term = gradientImagePointer->GetSpacing(); + itk::Matrix direction_term = gradientImagePointer->GetDirection(); + + vnl_vector spacing_vnl(3); + vnl_matrix dir_vnl (3,3); + + + + for (int i=0;i<3;i++) + { + + spacing_vnl[i]=spacing_term[i]; + + for(int j=0;j<3;j++) + { + dir_vnl[i][j]=direction_term[i][j]; + + } + } + + vnl_matrix vox_dim_step (3,3); + + + for (int i=0;i<3;i++) + { + + for(int j=0;j<3;j++) + { + vox_dim_step[i][j]=spacing_vnl[i]*dir_vnl[i][j]; + + } + } + + vnl_symmetric_eigensystem eigen_spacing(vox_dim_step); + + vnl_vector vox_dim (3); + + vox_dim[0]=eigen_spacing.get_eigenvalue(0); + vox_dim[1]=eigen_spacing.get_eigenvalue(1); + vox_dim[2]=eigen_spacing.get_eigenvalue(2); + + vox_dim=vox_dim/(vox_dim.min_value()); + + + //vnl_matrix directions(nof-numberb0,3); + vnl_matrix directions(nof-numberb0,3); + + for(int i=0; i vec = m_GradientDirectionContainer->ElementAt(i); + + if(vec[0]<0.0001 && vec[1]<0.0001 && vec[2]<0.0001 && vec[0]>-0.001&& vec[1]>-0.001 && vec[2]>-0.001) + { + b0index[i]=5; + } + else + { + b0index[i]=-1; + directions[cnt][0] = vec[0]; + directions[cnt][1] = vec[1]; + directions[cnt][2] = vec[2]; + cnt++; + } + + } + + vnl_matrix dirsTimesDirsTrans = directions*directions.transpose(); + + vnl_vector< double> diagonal(nof-numberb0); + vnl_vector< double> b_vec(nof-numberb0); + vnl_vector< double> temporary(3); + + for (int i=0;i H(nof-numberb0, 6); + vnl_matrix H_org(nof-numberb0, 6); + vnl_matrix temp_3_3(3,3); + vnl_vector pre_tensor(9); + + int etbt[6] = { 0, 4, 8, 1, 5, 2 }; + + for (int i = 0; i < nof-numberb0; i++) + { + for (int j = 0; j < 3; j++) + { + temporary[j] = -directions[i][j]; + } + for (int j = 0; j < 3; j++) + { + for (int k = 0; k < 3; k++) + { + pre_tensor[k + 3 * j] = temporary[k] * directions[i][j]; + } + } + for (int j = 0; j < 6; j++) + { + H[i][j] = pre_tensor[etbt[j]]; + } + for (int j = 0; j < 3; j++) + { + H[i][3 + j] *= 2.0; + } + } + + H_org=H; + + vnl_matrix inputtopseudoinverse=H.transpose()*H; + vnl_symmetric_eigensystem eig( inputtopseudoinverse); + vnl_matrix pseudoInverse = eig.pinverse()*H.transpose(); + + pseudoInverse.print(std::cout); + std::cout << std::endl; + + + double temp_pixel; + + itk::Index<3> ix; + + // declaration of corrected diffusion image/// + ImageType::IndexType start; + start.Fill(0); + + ImageType::RegionType region(start,size); + ImageType::Pointer corrected_diffusion = ImageType::New(); + corrected_diffusion->SetRegions(region); + corrected_diffusion->SetSpacing(gradientImagePointer->GetSpacing()); + corrected_diffusion->SetOrigin(gradientImagePointer->GetOrigin()); + corrected_diffusion->SetVectorLength(nof); + corrected_diffusion->Allocate(); + ImageType::IndexType pixelIndex; + typedef itk::VariableLengthVector VariableVectorType; + VariableVectorType variableLengthVector; + variableLengthVector.SetSize(nof); + + // end of the biggest data structure for this filter + // begining of removing of negative values from the data set + + for ( int x=0;xGetPixel(ix); + for( int f=0;fSetPixel(pixelIndex, variableLengthVector); + } + } + } + + vnl_vector org_data(nof); + vnl_vector atten(nof-numberb0); + double mean_b=0.0; + double pixel=0.0; + vnl_vector tensor (6); + // Declaration of mask-1-good voxel , 0-bad one, initaialy good voxels indicated by 3 + typedef itk::Image ImageType_mask; + ImageType_mask::IndexType start_mask; + start_mask.Fill(0); + ImageType_mask::RegionType region_mask(start_mask,size); + ImageType_mask::Pointer mask = ImageType_mask::New(); + mask->SetRegions(region_mask); + mask->SetSpacing(gradientImagePointer->GetSpacing()); + mask->SetOrigin(gradientImagePointer->GetOrigin()); + mask->Allocate(); + ImageType_mask::IndexType pixelIndex_mask; + + // + int mask_cnt=0; + + // + + // end of mask declaration + // start of filling mask + for(int x=0;xGetPixel(ix); + for (int i=0;i0) + { + mean_b = mean_b + pixel4[i]; + } + } + mean_b=mean_b/numberb0; + if(mean_b>m_B0Threshold) + { + pixel = 3.0; + // + mask_cnt++; + // + } + else + { + pixel=0.0; + } + mask->SetPixel(pixelIndex_mask, pixel); + } + } + } + + // + std::cout << "Number of voxels in mask: " << mask_cnt << std::endl; + // + + // Declaration of tensor image- output of the filter + typedef itk::Image< itk::DiffusionTensor3D, 3 > TensorImageType; + TensorImageType::IndexType start_tensorImg; + start_tensorImg.Fill(0); + TensorImageType::RegionType region_tensorImg(start_tensorImg,size); + TensorImageType::Pointer tensorImg = TensorImageType::New(); + tensorImg->SetRegions(region_tensorImg); + tensorImg->SetSpacing(gradientImagePointer->GetSpacing()); + tensorImg->SetOrigin(gradientImagePointer->GetOrigin()); + tensorImg->Allocate(); + itk::Index<3> pixelIndex_tensorImg; + // end of tensor declaration + // start of the main loop for removing of voxels with negative eigen values tensors + //some important variables + vnl_matrix temp_tensor(3,3); + vnl_vector eigen_vals(3); +// double l1; + // double l2; + //double l3; + int number_of_bads=0; + int old_number_of_bads=10000000000000000; + int diff=1; + + vnl_vector< double> pixel_max(nof); + vnl_vector< double> pixel_min(nof); + + for (int i=1;i0) + { + for (int x=0;xGetPixel(ix); + itk::DiffusionTensor3D ten; + + pixelIndex_tensorImg[0]=x; + pixelIndex_tensorImg[1]=y; + pixelIndex_tensorImg[2]=z; + + if(pixel>2.0) + { + ix[0] = x; + ix[1] = y; + ix[2] = z; + GradientVectorType pt = corrected_diffusion->GetPixel(ix); + mean_b=0.0; + + + for (int i=0;i eigen_tensor(temp_tensor); + + eigen_vals[0]=eigen_tensor.get_eigenvalue(0);eigen_vals[1]=eigen_tensor.get_eigenvalue(1);eigen_vals[2]=eigen_tensor.get_eigenvalue(2); + + + if( eigen_vals[0]>0.0 && eigen_vals[1]>0.0 && eigen_vals[2]>0.0) + { + + + ten(0,0) = tensor[0]; + ten(0,1) = tensor[3]; + ten(0,2) = tensor[5]; + ten(1,1) = tensor[1]; + ten(1,2) = tensor[4]; + ten(2,2) = tensor[2]; + + + if(x==47 && y==69 && z==28) + { + std::cout <<"Joe tensor"<< "\n"; + + std::cout <SetPixel(pixelIndex_tensorImg, ten); + mask->SetPixel(ix,1.0); + }//end of if eigenvalues + else + { + number_of_bads++; + ten.Fill(0.0); + tensorImg->SetPixel(pixelIndex_tensorImg, ten); + + for (int f=0;fpixel_max[f] || pt[f]SetPixel(ix,3.0); + corrected_diffusion->SetPixel(ix, variableLengthVector); + } + }// end of if + + else if(pixel<1.0) + { + ten.Fill(0.0); + tensorImg->SetPixel(pixelIndex_tensorImg, ten); + } + + + }// end of for 3 + } + + }// end of for 1 + diff=old_number_of_bads-number_of_bads; + old_number_of_bads=number_of_bads; + std::cout << "bad voxels: " << number_of_bads << std::endl; + number_of_bads=0; + + + } //while + + this->SetNthOutput(0, tensorImg); + m_VectorImage = corrected_diffusion; + m_MaskImage = mask; + m_PseudoInverse = pseudoInverse; + m_H = H_org; + m_BVec=b_vec; + m_B0Mask=b0index; + m_Voxdim = vox_dim; + + } + + + + template + void + TensorReconstructionWithEigenvalueCorrectionFilter + ::SetGradientImage( GradientDirectionContainerType *gradientDirection, + const GradientImagesType *gradientImage ) + { + // Make sure crazy users did not call both AddGradientImage and + // SetGradientImage + if( m_GradientImageTypeEnumeration == GradientIsInManyImages ) + { + itkExceptionMacro( << "Cannot call both methods:" + << "AddGradientImage and SetGradientImage. Please call only one of them."); + } + + this->m_GradientDirectionContainer = gradientDirection; + + + unsigned int numImages = gradientDirection->Size(); + this->m_NumberOfBaselineImages = 0; + + this->m_NumberOfGradientDirections = numImages - this->m_NumberOfBaselineImages; + + // ensure that the gradient image we received has as many components as + // the number of gradient directions + if( gradientImage->GetVectorLength() != this->m_NumberOfBaselineImages + this->m_NumberOfGradientDirections ) + { + itkExceptionMacro( << this->m_NumberOfGradientDirections << " gradients + " << this->m_NumberOfBaselineImages + << "baselines = " << this->m_NumberOfGradientDirections + this->m_NumberOfBaselineImages + << " directions specified but image has " << gradientImage->GetVectorLength() + << " components."); + } + + this->ProcessObject::SetNthInput( 0, + const_cast< GradientImagesType* >(gradientImage) ); + m_GradientImageTypeEnumeration = GradientIsInASingleImage; + } + + template + void + TensorReconstructionWithEigenvalueCorrectionFilter + ::check_the_neighbors(int x, int y, int z,int f, itk::Size<3> size,itk::Index<3> ix, + typename GradientImagesType::Pointer gradientImagePointer,ImageType::IndexType pixelIndex, + ImageType::Pointer corrected_diffusion,double &temp_pixel) + { + typedef typename GradientImagesType::PixelType GradientVectorType; + + int init_i;int init_j;int init_c;int limit_i;int limit_j;int limit_c; + double tempsum=0.0; + double temp_number=0.0; + + + if(x==0){init_i=x;limit_i=x+2;} + else if(x==size[0]-1){init_i=x-1;limit_i=x+1;} + else{init_i=x-1;limit_i=x+2;} + + for (int i=init_i;iGetPixel(ix); + + if(p[f]<=0.0) + { + tempsum=tempsum + 0; + } + else + { + tempsum=tempsum+p[f]; + + temp_number=temp_number+1; + + } + } + } + }// end of for 1 + if (temp_number==0.0) + { + tempsum=0.0; + } + else + { + tempsum=tempsum/temp_number; + } + + temp_pixel = (short)tempsum; + } + + + template + void + TensorReconstructionWithEigenvalueCorrectionFilter + ::calculate_attenuation(vnl_vector org_data,vnl_vector< double > b0index,vnl_vector &atten, double mean_b,int nof, int numberb0) + { + mean_b=0.0; + + + for (int i=0;i0) + { + mean_b=mean_b+org_data[i]; + } + + } + mean_b=mean_b/numberb0; + int cnt=0; + for (int i=0;i + void + TensorReconstructionWithEigenvalueCorrectionFilter + ::calculate_tensor(vnl_matrix pseudoInverse,vnl_vector atten,vnl_vector &tensor, int nof,int numberb0) + { + for (int i=0;i #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include const char* mitk::FiberBundleX::COLORCODING_ORIENTATION_BASED = "Color_Orient"; //const char* mitk::FiberBundleX::COLORCODING_FA_AS_OPACITY = "Color_Orient_FA_Opacity"; const char* mitk::FiberBundleX::COLORCODING_FA_BASED = "FA_Values"; const char* mitk::FiberBundleX::COLORCODING_CUSTOM = "custom"; const char* mitk::FiberBundleX::FIBER_ID_ARRAY = "Fiber_IDs"; mitk::FiberBundleX::FiberBundleX( vtkPolyData* fiberPolyData ) : m_CurrentColorCoding(NULL) , m_NumFibers(0) { m_FiberPolyData = vtkSmartPointer::New(); if (fiberPolyData != NULL) { vtkSmartPointer cleaner = vtkSmartPointer::New(); cleaner->SetInput(fiberPolyData); cleaner->Update(); fiberPolyData = cleaner->GetOutput(); m_FiberPolyData->DeepCopy(fiberPolyData); this->DoColorCodingOrientationBased(); } if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)) MITK_DEBUG << "ok"; vtkUnsignedCharArray* tmpColors = (vtkUnsignedCharArray*) m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED); if (tmpColors!=NULL) { int tmpColorss = tmpColors->GetNumberOfTuples(); int tmpColorc = tmpColors->GetNumberOfComponents(); } m_NumFibers = m_FiberPolyData->GetNumberOfLines(); this->UpdateFiberGeometry(); this->SetColorCoding(COLORCODING_ORIENTATION_BASED); this->GenerateFiberIds(); } mitk::FiberBundleX::~FiberBundleX() { } mitk::FiberBundleX::Pointer mitk::FiberBundleX::GetDeepCopy() { mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(m_FiberPolyData); if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)) MITK_DEBUG << "ok"; vtkUnsignedCharArray* tmpColors = (vtkUnsignedCharArray*) m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED); int tmpColorss = tmpColors->GetNumberOfTuples(); int tmpColorc = tmpColors->GetNumberOfComponents(); newFib->SetColorCoding(m_CurrentColorCoding); return newFib; } vtkSmartPointer mitk::FiberBundleX::GeneratePolyDataByIds(std::vector fiberIds) { MITK_DEBUG << "\n=====FINAL RESULT: fib_id ======\n"; MITK_DEBUG << "Number of new Fibers: " << fiberIds.size(); // iterate through the vectorcontainer hosting all desired fiber Ids vtkSmartPointer newFiberPolyData = vtkSmartPointer::New(); vtkSmartPointer newLineSet = vtkSmartPointer::New(); vtkSmartPointer newPointSet = vtkSmartPointer::New(); // if FA array available, initialize fa double array // if color orient array is available init color array vtkSmartPointer faValueArray; vtkSmartPointer colorsT; //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; int componentSize = sizeof(rgba); if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_FA_BASED)){ MITK_DEBUG << "FA VALUES AVAILABLE, init array for new fiberbundle"; faValueArray = vtkSmartPointer::New(); } if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){ MITK_DEBUG << "colorValues available, init array for new fiberbundle"; colorsT = vtkUnsignedCharArray::New(); colorsT->SetNumberOfComponents(componentSize); colorsT->SetName(COLORCODING_ORIENTATION_BASED); } std::vector::iterator finIt = fiberIds.begin(); while ( finIt != fiberIds.end() ) { if (*finIt < 0 || *finIt>GetNumFibers()){ MITK_INFO << "FiberID can not be negative or >NumFibers!!! check id Extraction!" << *finIt; break; } vtkSmartPointer fiber = m_FiberIdDataSet->GetCell(*finIt);//->DeepCopy(fiber); vtkSmartPointer fibPoints = fiber->GetPoints(); vtkSmartPointer newFiber = vtkSmartPointer::New(); newFiber->GetPointIds()->SetNumberOfIds( fibPoints->GetNumberOfPoints() ); for(int i=0; iGetNumberOfPoints(); i++) { // MITK_DEBUG << "id: " << fiber->GetPointId(i); // MITK_DEBUG << fibPoints->GetPoint(i)[0] << " | " << fibPoints->GetPoint(i)[1] << " | " << fibPoints->GetPoint(i)[2]; newFiber->GetPointIds()->SetId(i, newPointSet->GetNumberOfPoints()); newPointSet->InsertNextPoint(fibPoints->GetPoint(i)[0], fibPoints->GetPoint(i)[1], fibPoints->GetPoint(i)[2]); if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_FA_BASED)){ // MITK_DEBUG << m_FiberIdDataSet->GetPointData()->GetArray(FA_VALUE_ARRAY)->GetTuple(fiber->GetPointId(i)); } if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){ // MITK_DEBUG << "ColorValue: " << m_FiberIdDataSet->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetTuple(fiber->GetPointId(i))[0]; } } newLineSet->InsertNextCell(newFiber); ++finIt; } newFiberPolyData->SetPoints(newPointSet); newFiberPolyData->SetLines(newLineSet); MITK_DEBUG << "new fiberbundle polydata points: " << newFiberPolyData->GetNumberOfPoints(); MITK_DEBUG << "new fiberbundle polydata lines: " << newFiberPolyData->GetNumberOfLines(); MITK_DEBUG << "=====================\n"; // mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(newFiberPolyData); return newFiberPolyData; } // merge two fiber bundles mitk::FiberBundleX::Pointer mitk::FiberBundleX::AddBundle(mitk::FiberBundleX* fib) { vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); vtkSmartPointer vLines = m_FiberPolyData->GetLines(); vLines->InitTraversal(); // add current fiber bundle int numFibers = GetNumFibers(); for( int i=0; iGetNextCell ( numPoints, points ); vtkSmartPointer container = vtkSmartPointer::New(); for( int j=0; jInsertNextPoint(m_FiberPolyData->GetPoint(points[j])); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } vLines = fib->m_FiberPolyData->GetLines(); vLines->InitTraversal(); // add new fiber bundle numFibers = fib->GetNumFibers(); for( int i=0; iGetNextCell ( numPoints, points ); vtkSmartPointer container = vtkSmartPointer::New(); for( int j=0; jInsertNextPoint(fib->m_FiberPolyData->GetPoint(points[j])); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } // initialize polydata vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(vNewPolyData); return newFib; } // subtract two fiber bundles mitk::FiberBundleX::Pointer mitk::FiberBundleX::SubtractBundle(mitk::FiberBundleX* fib) { vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); vtkSmartPointer vLines = m_FiberPolyData->GetLines(); vLines->InitTraversal(); // iterate over current fibers int numFibers = GetNumFibers(); for( int i=0; iGetNextCell ( numPoints, points ); vtkSmartPointer vLines2 = fib->m_FiberPolyData->GetLines(); vLines2->InitTraversal(); int numFibers2 = fib->GetNumFibers(); bool contained = false; for( int i2=0; i2GetNextCell ( numPoints2, points2 ); // check endpoints itk::Point point_start = GetItkPoint(m_FiberPolyData->GetPoint(points[0])); itk::Point point_end = GetItkPoint(m_FiberPolyData->GetPoint(points[numPoints-1])); itk::Point point2_start = GetItkPoint(fib->m_FiberPolyData->GetPoint(points2[0])); itk::Point point2_end = GetItkPoint(fib->m_FiberPolyData->GetPoint(points2[numPoints2-1])); if (point_start.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps || point_start.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps) { // further checking ??? contained = true; } } // add to result because fiber is not subtracted if (!contained) { vtkSmartPointer container = vtkSmartPointer::New(); for( int j=0; jInsertNextPoint(m_FiberPolyData->GetPoint(points[j])); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } } if(vNewLines->GetNumberOfCells()==0) return NULL; // initialize polydata vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(vNewPolyData); return newFib; } itk::Point mitk::FiberBundleX::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } /* * set polydata (additional flag to recompute fiber geometry, default = true) */ void mitk::FiberBundleX::SetFiberPolyData(vtkSmartPointer fiberPD, bool updateGeometry) { if (fiberPD == NULL) this->m_FiberPolyData = vtkSmartPointer::New(); else { m_FiberPolyData->DeepCopy(fiberPD); DoColorCodingOrientationBased(); } m_NumFibers = m_FiberPolyData->GetNumberOfLines(); if (updateGeometry) UpdateFiberGeometry(); SetColorCoding(COLORCODING_ORIENTATION_BASED); GenerateFiberIds(); } /* * return vtkPolyData */ vtkSmartPointer mitk::FiberBundleX::GetFiberPolyData() { return m_FiberPolyData; } void mitk::FiberBundleX::DoColorCodingOrientationBased() { //===== FOR WRITING A TEST ======================== // colorT size == tupelComponents * tupelElements // compare color results // to cover this code 100% also polydata needed, where colorarray already exists // + one fiber with exactly 1 point // + one fiber with 0 points //================================================= /* make sure that processing colorcoding is only called when necessary */ if ( m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) && m_FiberPolyData->GetNumberOfPoints() == m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetNumberOfTuples() ) { // fiberstructure is already colorcoded MITK_DEBUG << " NO NEED TO REGENERATE COLORCODING! " ; this->ResetFiberOpacity(); this->SetColorCoding(COLORCODING_ORIENTATION_BASED); return; } /* Finally, execute color calculation */ vtkPoints* extrPoints = NULL; extrPoints = m_FiberPolyData->GetPoints(); int numOfPoints = 0; if (extrPoints!=NULL) numOfPoints = extrPoints->GetNumberOfPoints(); //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; // int componentSize = sizeof(rgba); int componentSize = 4; vtkSmartPointer colorsT = vtkUnsignedCharArray::New(); colorsT->Allocate(numOfPoints * componentSize); colorsT->SetNumberOfComponents(componentSize); colorsT->SetName(COLORCODING_ORIENTATION_BASED); /* checkpoint: does polydata contain any fibers */ int numOfFibers = m_FiberPolyData->GetNumberOfLines(); if (numOfFibers < 1) { MITK_DEBUG << "\n ========= Number of Fibers is 0 and below ========= \n"; return; } /* extract single fibers of fiberBundle */ vtkCellArray* fiberList = m_FiberPolyData->GetLines(); fiberList->InitTraversal(); for (int fi=0; fiGetNextCell(pointsPerFiber, idList); // MITK_DEBUG << "Fib#: " << fi << " of " << numOfFibers << " pnts in fiber: " << pointsPerFiber ; /* single fiber checkpoints: is number of points valid */ if (pointsPerFiber > 1) { /* operate on points of single fiber */ for (int i=0; i 0) { /* The color value of the current point is influenced by the previous point and next point. */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); vnl_vector_fixed< double, 3 > diff1; diff1 = currentPntvtk - nextPntvtk; vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; vnl_vector_fixed< double, 3 > diff; diff = (diff1 - diff2) / 2.0; diff.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff[2])); rgba[3] = (unsigned char) (255.0); } else if (i==0) { /* First point has no previous point, therefore only diff1 is taken */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); vnl_vector_fixed< double, 3 > diff1; diff1 = currentPntvtk - nextPntvtk; diff1.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff1[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff1[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff1[2])); rgba[3] = (unsigned char) (255.0); } else if (i==pointsPerFiber-1) { /* Last point has no next point, therefore only diff2 is taken */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; diff2.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff2[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff2[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff2[2])); rgba[3] = (unsigned char) (255.0); } colorsT->InsertTupleValue(idList[i], rgba); } //end for loop } else if (pointsPerFiber == 1) { /* a single point does not define a fiber (use vertex mechanisms instead */ continue; // colorsT->InsertTupleValue(0, rgba); } else { MITK_DEBUG << "Fiber with 0 points detected... please check your tractography algorithm!" ; continue; } }//end for loop m_FiberPolyData->GetPointData()->AddArray(colorsT); /*========================= - this is more relevant for renderer than for fiberbundleX datastructure - think about sourcing this to a explicit method which coordinates colorcoding */ this->SetColorCoding(COLORCODING_ORIENTATION_BASED); // =========================== //mini test, shall be ported to MITK TESTINGS! if (colorsT->GetSize() != numOfPoints*componentSize) MITK_DEBUG << "ALLOCATION ERROR IN INITIATING COLOR ARRAY"; } void mitk::FiberBundleX::DoColorCodingFaBased() { if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED) != 1 ) return; this->SetColorCoding(COLORCODING_FA_BASED); MITK_DEBUG << "FBX: done CC FA based"; this->GenerateFiberIds(); } void mitk::FiberBundleX::DoUseFaFiberOpacity() { if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED) != 1 ) return; if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) != 1 ) return; vtkDoubleArray* FAValArray = (vtkDoubleArray*) m_FiberPolyData->GetPointData()->GetArray(COLORCODING_FA_BASED); vtkUnsignedCharArray* ColorArray = dynamic_cast (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)); for(long i=0; iGetNumberOfTuples(); i++) { double faValue = FAValArray->GetValue(i); faValue = faValue * 255.0; ColorArray->SetComponent(i,3, (unsigned char) faValue ); } this->SetColorCoding(COLORCODING_ORIENTATION_BASED); MITK_DEBUG << "FBX: done CC OPACITY"; this->GenerateFiberIds(); } void mitk::FiberBundleX::ResetFiberOpacity() { vtkUnsignedCharArray* ColorArray = dynamic_cast (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)); for(long i=0; iGetNumberOfTuples(); i++) { ColorArray->SetComponent(i,3, 255.0 ); } } void mitk::FiberBundleX::SetFAMap(mitk::Image::Pointer FAimage) { MITK_DEBUG << "SetFAMap"; vtkSmartPointer faValues = vtkDoubleArray::New(); faValues->SetName(COLORCODING_FA_BASED); faValues->Allocate(m_FiberPolyData->GetNumberOfPoints()); // MITK_DEBUG << faValues->GetNumberOfTuples(); // MITK_DEBUG << faValues->GetSize(); faValues->SetNumberOfValues(m_FiberPolyData->GetNumberOfPoints()); // MITK_DEBUG << faValues->GetNumberOfTuples(); // MITK_DEBUG << faValues->GetSize(); vtkPoints* pointSet = m_FiberPolyData->GetPoints(); for(long i=0; iGetNumberOfPoints(); ++i) { Point3D px; px[0] = pointSet->GetPoint(i)[0]; px[1] = pointSet->GetPoint(i)[1]; px[2] = pointSet->GetPoint(i)[2]; double faPixelValue = 1-FAimage->GetPixelValueByWorldCoordinate(px); // faValues->InsertNextTuple1(faPixelValue); faValues->InsertValue(i, faPixelValue); // MITK_DEBUG << faPixelValue; // MITK_DEBUG << faValues->GetValue(i); } m_FiberPolyData->GetPointData()->AddArray(faValues); this->GenerateFiberIds(); if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED)) MITK_DEBUG << "FA VALUE ARRAY SET"; // vtkDoubleArray* valueArray = (vtkDoubleArray*) m_FiberPolyData->GetPointData()->GetArray(FA_VALUE_ARRAY); // for(long i=0; iGetNumberOfPoints(); i++) // { // MITK_DEBUG << "value at pos "<< i << ": " << valueArray->GetValue(i); // } } void mitk::FiberBundleX::GenerateFiberIds() { if (m_FiberPolyData == NULL) return; vtkSmartPointer idFiberFilter = vtkSmartPointer::New(); idFiberFilter->SetInput(m_FiberPolyData); idFiberFilter->CellIdsOn(); // idFiberFilter->PointIdsOn(); // point id's are not needed idFiberFilter->SetIdsArrayName(FIBER_ID_ARRAY); idFiberFilter->FieldDataOn(); idFiberFilter->Update(); m_FiberIdDataSet = idFiberFilter->GetOutput(); MITK_DEBUG << "Generating Fiber Ids...[done] | " << m_FiberIdDataSet->GetNumberOfCells(); } mitk::FiberBundleX::Pointer mitk::FiberBundleX::ExtractFiberSubset(mitk::PlanarFigure::Pointer pf) { std::vector tmp = ExtractFiberIdSubset(pf); if (tmp.size()<=0) return mitk::FiberBundleX::New(); vtkSmartPointer pTmp = GeneratePolyDataByIds(tmp); return mitk::FiberBundleX::New(pTmp); } std::vector mitk::FiberBundleX::ExtractFiberIdSubset(mitk::PlanarFigure::Pointer pf) { MITK_DEBUG << "Extracting fibers!"; // vector which is returned, contains all extracted FiberIds std::vector FibersInROI; /* Handle type of planarfigure */ // if incoming pf is a pfc mitk::PlanarFigureComposite::Pointer pfcomp= dynamic_cast(pf.GetPointer()); if (!pfcomp.IsNull()) { // process requested boolean operation of PFC switch (pfcomp->getOperationType()) { case 0: { MITK_DEBUG << "AND PROCESSING"; //AND //temporarly store results of the child in this vector, we need that to accumulate the std::vector childResults = this->ExtractFiberIdSubset(pfcomp->getChildAt(0)); MITK_DEBUG << "first roi got fibers in ROI: " << childResults.size(); MITK_DEBUG << "sorting..."; std::sort(childResults.begin(), childResults.end()); MITK_DEBUG << "sorting done"; std::vector AND_Assamblage(childResults.size()); //std::vector AND_Assamblage; fill(AND_Assamblage.begin(), AND_Assamblage.end(), -1); //AND_Assamblage.reserve(childResults.size()); //max size AND can reach anyway std::vector::iterator it; for (int i=1; igetNumberOfChildren(); ++i) { std::vector tmpChild = this->ExtractFiberIdSubset(pfcomp->getChildAt(i)); MITK_DEBUG << "ROI " << i << " has fibers in ROI: " << tmpChild.size(); sort(tmpChild.begin(), tmpChild.end()); it = std::set_intersection(childResults.begin(), childResults.end(), tmpChild.begin(), tmpChild.end(), AND_Assamblage.begin() ); } MITK_DEBUG << "resize Vector"; long i=0; while (i < AND_Assamblage.size() && AND_Assamblage[i] != -1){ //-1 represents a placeholder in the array ++i; } AND_Assamblage.resize(i); MITK_DEBUG << "returning AND vector, size: " << AND_Assamblage.size(); return AND_Assamblage; // break; } case 1: { //OR std::vector OR_Assamblage = this->ExtractFiberIdSubset(pfcomp->getChildAt(0)); std::vector::iterator it; MITK_DEBUG << OR_Assamblage.size(); for (int i=1; igetNumberOfChildren(); ++i) { it = OR_Assamblage.end(); std::vector tmpChild = this->ExtractFiberIdSubset(pfcomp->getChildAt(i)); OR_Assamblage.insert(it, tmpChild.begin(), tmpChild.end()); MITK_DEBUG << "ROI " << i << " has fibers in ROI: " << tmpChild.size() << " OR Assamblage: " << OR_Assamblage.size(); } sort(OR_Assamblage.begin(), OR_Assamblage.end()); it = unique(OR_Assamblage.begin(), OR_Assamblage.end()); OR_Assamblage.resize( it - OR_Assamblage.begin() ); MITK_DEBUG << "returning OR vector, size: " << OR_Assamblage.size(); return OR_Assamblage; } case 2: { //NOT //get IDs of all fibers std::vector childResults; childResults.reserve(this->GetNumFibers()); vtkSmartPointer idSet = m_FiberIdDataSet->GetCellData()->GetArray(FIBER_ID_ARRAY); MITK_DEBUG << "m_NumOfFib: " << this->GetNumFibers() << " cellIdNum: " << idSet->GetNumberOfTuples(); for(long i=0; iGetNumFibers(); i++) { MITK_DEBUG << "i: " << i << " idset: " << idSet->GetTuple(i)[0]; childResults.push_back(idSet->GetTuple(i)[0]); } std::sort(childResults.begin(), childResults.end()); std::vector NOT_Assamblage(childResults.size()); //fill it with -1, otherwise 0 will be stored and 0 can also be an ID of fiber! fill(NOT_Assamblage.begin(), NOT_Assamblage.end(), -1); std::vector::iterator it; for (long i=0; igetNumberOfChildren(); ++i) { std::vector tmpChild = ExtractFiberIdSubset(pfcomp->getChildAt(i)); sort(tmpChild.begin(), tmpChild.end()); it = std::set_difference(childResults.begin(), childResults.end(), tmpChild.begin(), tmpChild.end(), NOT_Assamblage.begin() ); } MITK_DEBUG << "resize Vector"; long i=0; while (NOT_Assamblage[i] != -1){ //-1 represents a placeholder in the array ++i; } NOT_Assamblage.resize(i); return NOT_Assamblage; } default: MITK_DEBUG << "we have an UNDEFINED composition... ERROR" ; break; } } else { mitk::Geometry2D::ConstPointer pfgeometry = pf->GetGeometry2D(); const mitk::PlaneGeometry* planeGeometry = dynamic_cast (pfgeometry.GetPointer()); Vector3D planeNormal = planeGeometry->GetNormal(); planeNormal.Normalize(); Point3D planeOrigin = planeGeometry->GetOrigin(); MITK_DEBUG << "planeOrigin: " << planeOrigin[0] << " | " << planeOrigin[1] << " | " << planeOrigin[2] << endl; MITK_DEBUG << "planeNormal: " << planeNormal[0] << " | " << planeNormal[1] << " | " << planeNormal[2] << endl; std::vector PointsOnPlane; // contains all pointIds which are crossing the cutting plane std::vector PointsInROI; // based on PointsOnPlane, all ROI relevant point IDs are stored here /* Define cutting plane by ROI (PlanarFigure) */ vtkSmartPointer plane = vtkSmartPointer::New(); plane->SetOrigin(planeOrigin[0],planeOrigin[1],planeOrigin[2]); plane->SetNormal(planeNormal[0],planeNormal[1],planeNormal[2]); //same plane but opposite normal direction. so point cloud will be reduced -> better performance // vtkSmartPointer planeR = vtkSmartPointer::New(); //define new origin along the normal but close to the original one // OriginNew = OriginOld + 1*Normal // Vector3D extendedNormal; // int multiplyFactor = 1; // extendedNormal[0] = planeNormal[0] * multiplyFactor; // extendedNormal[1] = planeNormal[1] * multiplyFactor; // extendedNormal[2] = planeNormal[2] * multiplyFactor; // Point3D RplaneOrigin = planeOrigin - extendedNormal; // planeR->SetOrigin(RplaneOrigin[0],RplaneOrigin[1],RplaneOrigin[2]); // planeR->SetNormal(-planeNormal[0],-planeNormal[1],-planeNormal[2]); // MITK_DEBUG << "RPlaneOrigin: " << RplaneOrigin[0] << " | " << RplaneOrigin[1] // << " | " << RplaneOrigin[2]; /* get all points/fibers cutting the plane */ MITK_DEBUG << "start clipping"; vtkSmartPointer clipper = vtkSmartPointer::New(); clipper->SetInput(m_FiberIdDataSet); clipper->SetClipFunction(plane); clipper->GenerateClipScalarsOn(); clipper->GenerateClippedOutputOn(); vtkSmartPointer clipperout = clipper->GetClippedOutput(); MITK_DEBUG << "end clipping"; /* for some reason clipperoutput is not initialized for futher processing * so far only writing out clipped polydata provides requested */ // MITK_DEBUG << "writing clipper output"; // vtkSmartPointer writerC = vtkSmartPointer::New(); // writerC->SetInput(clipperout1); // writerC->SetFileName("/vtkOutput/Clipping.vtk"); // writerC->SetFileTypeToASCII(); // writerC->Write(); // MITK_DEBUG << "writing done"; MITK_DEBUG << "init and update clipperoutput"; clipperout->GetPointData()->Initialize(); clipperout->Update(); MITK_DEBUG << "init and update clipperoutput completed"; // MITK_DEBUG << "start clippingRecursive"; // vtkSmartPointer Rclipper = vtkSmartPointer::New(); // Rclipper->SetInput(clipperout1); // Rclipper->SetClipFunction(planeR); // Rclipper->GenerateClipScalarsOn(); // Rclipper->GenerateClippedOutputOn(); // vtkSmartPointer clipperout = Rclipper->GetClippedOutput(); // MITK_DEBUG << "end clipping recursive"; // MITK_DEBUG << "writing clipper output 2"; // vtkSmartPointer writerC1 = vtkSmartPointer::New(); // writerC1->SetInput(clipperout); // writerC1->SetFileName("/vtkOutput/RClipping.vtk"); // writerC1->SetFileTypeToASCII(); // writerC1->Write(); // MITK_DEBUG << "init and update clipperoutput"; // clipperout->GetPointData()->Initialize(); // clipperout->Update(); // MITK_DEBUG << "init and update clipperoutput completed"; MITK_DEBUG << "STEP 1: find all points which have distance 0 to the given plane"; /*======STEP 1====== * extract all points, which are crossing the plane */ // Scalar values describe the distance between each remaining point to the given plane. Values sorted by point index vtkSmartPointer distanceList = clipperout->GetPointData()->GetScalars(); vtkIdType sizeOfList = distanceList->GetNumberOfTuples(); PointsOnPlane.reserve(sizeOfList); /* use reserve for high-performant push_back, no hidden copy procedures are processed then! * size of list can be optimized by reducing allocation, but be aware of iterator and vector size*/ for (int i=0; iGetTuple(i); // check if point is on plane. // 0.01 due to some approximation errors when calculating distance if (distance[0] >= -0.01 && distance[0] <= 0.01) PointsOnPlane.push_back(i); } // DEBUG print out all interesting points, stop where array starts with value -1. after -1 no more interesting idx are set! // std::vector::iterator rit = PointsOnPlane.begin(); // while (rit != PointsOnPlane.end() ) { // std::cout << "interesting point: " << *rit << " coord: " << clipperout->GetPoint(*rit)[0] << " | " << clipperout->GetPoint(*rit)[1] << " | " << clipperout->GetPoint(*rit)[2] << endl; // rit++; // } MITK_DEBUG << "Num Of points on plane: " << PointsOnPlane.size(); MITK_DEBUG << "Step 2: extract Interesting points with respect to given extraction planarFigure"; PointsInROI.reserve(PointsOnPlane.size()); /*=======STEP 2===== * extract ROI relevant pointIds */ mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New(); mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New(); if ( pf->GetNameOfClass() == circleName->GetNameOfClass() ) { //calculate circle radius mitk::Point3D V1w = pf->GetWorldControlPoint(0); //centerPoint mitk::Point3D V2w = pf->GetWorldControlPoint(1); //radiusPoint double distPF = V1w.EuclideanDistanceTo(V2w); for (int i=0; iGetPoint(PointsOnPlane[i])[0] - V1w[0]) * (clipperout->GetPoint(PointsOnPlane[i])[0] - V1w[0]) + (clipperout->GetPoint(PointsOnPlane[i])[1] - V1w[1]) * (clipperout->GetPoint(PointsOnPlane[i])[1] - V1w[1]) + (clipperout->GetPoint(PointsOnPlane[i])[2] - V1w[2]) * (clipperout->GetPoint(PointsOnPlane[i])[2] - V1w[2])) ; if( XdistPnt <= distPF) PointsInROI.push_back(PointsOnPlane[i]); } } else if ( pf->GetNameOfClass() == polyName->GetNameOfClass() ) { //create vtkPolygon using controlpoints from planarFigure polygon vtkSmartPointer polygonVtk = vtkPolygon::New(); //get the control points from pf and insert them to vtkPolygon unsigned int nrCtrlPnts = pf->GetNumberOfControlPoints(); for (int i=0; iGetPoints()->InsertNextPoint((double)pf->GetWorldControlPoint(i)[0], (double)pf->GetWorldControlPoint(i)[1], (double)pf->GetWorldControlPoint(i)[2] ); } //prepare everything for using pointInPolygon function double n[3]; polygonVtk->ComputeNormal(polygonVtk->GetPoints()->GetNumberOfPoints(), static_cast(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), n); double bounds[6]; polygonVtk->GetPoints()->GetBounds(bounds); for (int i=0; iGetPoint(PointsOnPlane[i])[0], clipperout->GetPoint(PointsOnPlane[i])[1], clipperout->GetPoint(PointsOnPlane[i])[2]}; int isInPolygon = polygonVtk->PointInPolygon(checkIn, polygonVtk->GetPoints()->GetNumberOfPoints() , static_cast(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), bounds, n); if( isInPolygon ) PointsInROI.push_back(PointsOnPlane[i]); } } MITK_DEBUG << "Step3: Identify fibers"; // we need to access the fiberId Array, so make sure that this array is available if (!clipperout->GetCellData()->HasArray(FIBER_ID_ARRAY)) { MITK_DEBUG << "ERROR: FiberID array does not exist, no correlation between points and fiberIds possible! Make sure calling GenerateFiberIds()"; return FibersInROI; // FibersInRoi is empty then } if (PointsInROI.size()<=0) return FibersInROI; // prepare a structure where each point id is represented as an indexId. // vector looks like: | pntId | fiberIdx | std::vector< long > pointindexFiberMap; // walk through the whole subline section and create an vector sorted by point index vtkCellArray *clipperlines = clipperout->GetLines(); clipperlines->InitTraversal(); long numOfLineCells = clipperlines->GetNumberOfCells(); long numofClippedPoints = clipperout->GetNumberOfPoints(); - pointindexFiberMap.reserve(numofClippedPoints); + pointindexFiberMap.resize(numofClippedPoints); //prepare resulting vector FibersInROI.reserve(PointsInROI.size()); MITK_DEBUG << "\n===== Pointindex based structure initialized ======\n"; // go through resulting "sub"lines which are stored as cells, "i" corresponds to current line id. for (int i=0, ic=0 ; iGetCell(ic, npts, pts); // go through point ids in hosting subline, "j" corresponds to current pointindex in current line i. eg. idx[0]=45; idx[1]=46 for (long j=0; jGetCellData()->GetArray(FIBER_ID_ARRAY)->GetTuple(i)[0] << " to pointId: " << pts[j]; pointindexFiberMap[ pts[j] ] = clipperout->GetCellData()->GetArray(FIBER_ID_ARRAY)->GetTuple(i)[0]; // MITK_DEBUG << "in array: " << pointindexFiberMap[ pts[j] ]; } } MITK_DEBUG << "\n===== Pointindex based structure finalized ======\n"; // get all Points in ROI with according fiberID for (long k = 0; k < PointsInROI.size(); k++) { //MITK_DEBUG << "point " << PointsInROI[k] << " belongs to fiber " << pointindexFiberMap[ PointsInROI[k] ]; if (pointindexFiberMap[ PointsInROI[k] ]<=GetNumFibers() && pointindexFiberMap[ PointsInROI[k] ]>=0) FibersInROI.push_back(pointindexFiberMap[ PointsInROI[k] ]); else MITK_INFO << "ERROR in ExtractFiberIdSubset; impossible fiber id detected"; } } // detecting fiberId duplicates MITK_DEBUG << "check for duplicates"; sort(FibersInROI.begin(), FibersInROI.end()); bool hasDuplicats = false; for(long i=0; i::iterator it; it = unique (FibersInROI.begin(), FibersInROI.end()); FibersInROI.resize( it - FibersInROI.begin() ); } return FibersInROI; } void mitk::FiberBundleX::UpdateFiberGeometry() { - if (m_NumFibers<=0) + if (m_NumFibers<=0) // no fibers present; apply default geometry { mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); geometry->SetImageGeometry(true); float b[] = {0, 1, 0, 1, 0, 1}; geometry->SetFloatBounds(b); SetGeometry(geometry); return; } - float min = itk::NumericTraits::min(); + float min = itk::NumericTraits::NonpositiveMin(); float max = itk::NumericTraits::max(); float b[] = {max, min, max, min, max, min}; vtkCellArray* cells = m_FiberPolyData->GetLines(); cells->InitTraversal(); for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int p = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; jGetPoint(j, p); if (p[0]b[1]) b[1]=p[0]; if (p[1]b[3]) b[3]=p[1]; if (p[2]b[5]) b[5]=p[2]; } } - // provide some border margin for(int i=0; i<=4; i+=2) b[i] -=10; for(int i=1; i<=5; i+=2) b[i] +=10; mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); - geometry->SetImageGeometry(true); geometry->SetFloatBounds(b); this->SetGeometry(geometry); } QStringList mitk::FiberBundleX::GetAvailableColorCodings() { QStringList availableColorCodings; int numColors = m_FiberPolyData->GetPointData()->GetNumberOfArrays(); for(int i=0; iGetPointData()->GetArrayName(i)); } //this controlstructure shall be implemented by the calling method if (availableColorCodings.isEmpty()) MITK_DEBUG << "no colorcodings available in fiberbundleX"; // for(int i=0; im_CurrentColorCoding = (char*) COLORCODING_ORIENTATION_BASED; } else if( strcmp (COLORCODING_FA_BASED,requestedColorCoding) == 0 ) { this->m_CurrentColorCoding = (char*) COLORCODING_FA_BASED; } else if( strcmp (COLORCODING_CUSTOM,requestedColorCoding) == 0 ) { this->m_CurrentColorCoding = (char*) COLORCODING_CUSTOM; } else { MITK_DEBUG << "FIBERBUNDLE X: UNKNOWN COLORCODING in FIBERBUNDLEX Datastructure"; this->m_CurrentColorCoding = (char*) COLORCODING_CUSTOM; //will cause blank colorcoding of fibers } } void mitk::FiberBundleX::DoFiberSmoothing(int pointsPerCm) { vtkSmartPointer vtkSmoothPoints = vtkPoints::New(); //in smoothpoints the interpolated points representing a fiber are stored. //in vtkcells all polylines are stored, actually all id's of them are stored vtkSmartPointer vtkSmoothCells = vtkCellArray::New(); //cellcontainer for smoothed lines vtkSmartPointer vLines = m_FiberPolyData->GetLines(); vLines->InitTraversal(); vtkIdType pointHelperCnt = 0; for (int i=0; iGetNextCell ( numPoints, pointIds ); vtkSmartPointer points = vtkSmartPointer::New(); float length = 0; itk::Point lastP; for (int j=0; jGetPoint(pointIds[j]); points->InsertNextPoint(p); if (j>0) length += sqrt(pow(p[0]-lastP[0], 2)+pow(p[1]-lastP[1], 2)+pow(p[2]-lastP[2], 2)); lastP[0] = p[0]; lastP[1] = p[1]; lastP[2] = p[2]; } length /=10; int sampling = pointsPerCm*length; /////PROCESS POLYLINE SMOOTHING///// vtkSmartPointer xSpline = vtkKochanekSpline::New(); vtkSmartPointer ySpline = vtkKochanekSpline::New(); vtkSmartPointer zSpline = vtkKochanekSpline::New(); vtkSmartPointer spline = vtkParametricSpline::New(); spline->SetXSpline(xSpline); spline->SetYSpline(ySpline); spline->SetZSpline(zSpline); spline->SetPoints(points); vtkSmartPointer functionSource = vtkParametricFunctionSource::New(); functionSource->SetParametricFunction(spline); functionSource->SetUResolution(sampling); functionSource->SetVResolution(sampling); functionSource->SetWResolution(sampling); functionSource->Update(); vtkPolyData* outputFunction = functionSource->GetOutput(); vtkPoints* tmpSmoothPnts = outputFunction->GetPoints(); //smoothPoints of current fiber vtkSmartPointer smoothLine = vtkPolyLine::New(); smoothLine->GetPointIds()->SetNumberOfIds(tmpSmoothPnts->GetNumberOfPoints()); for (int j=0; jGetNumberOfPoints(); j++) { smoothLine->GetPointIds()->SetId(j, j+pointHelperCnt); vtkSmoothPoints->InsertNextPoint(tmpSmoothPnts->GetPoint(j)); } vtkSmoothCells->InsertNextCell(smoothLine); pointHelperCnt += tmpSmoothPnts->GetNumberOfPoints(); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkSmoothPoints); m_FiberPolyData->SetLines(vtkSmoothCells); UpdateColorCoding(); UpdateFiberGeometry(); } // Resample fiber to get equidistant points void mitk::FiberBundleX::ResampleFibers(float pointDistance) { vtkSmartPointer newPoly = vtkSmartPointer::New(); vtkSmartPointer newCellArray = vtkSmartPointer::New(); vtkSmartPointer newPoints = vtkSmartPointer::New(); vtkSmartPointer vLines = m_FiberPolyData->GetLines(); vLines->InitTraversal(); int numberOfLines = m_NumFibers; for (int i=0; iGetNextCell ( numPoints, points ); vtkSmartPointer container = vtkSmartPointer::New(); double* point = m_FiberPolyData->GetPoint(points[0]); vtkIdType pointId = newPoints->InsertNextPoint(point); container->GetPointIds()->InsertNextId(pointId); float dtau = 0; int cur_p = 1; itk::Vector dR; float normdR = 0; for (;;) { while (dtau <= pointDistance && cur_p < numPoints) { itk::Vector v1; point = m_FiberPolyData->GetPoint(points[cur_p-1]); v1[0] = point[0]; v1[1] = point[1]; v1[2] = point[2]; itk::Vector v2; point = m_FiberPolyData->GetPoint(points[cur_p]); v2[0] = point[0]; v2[1] = point[1]; v2[2] = point[2]; dR = v2 - v1; normdR = std::sqrt(dR.GetSquaredNorm()); dtau += normdR; cur_p++; } if (dtau >= pointDistance) { itk::Vector v1; point = m_FiberPolyData->GetPoint(points[cur_p-1]); v1[0] = point[0]; v1[1] = point[1]; v1[2] = point[2]; itk::Vector v2 = v1 - dR*( (dtau-pointDistance)/normdR ); pointId = newPoints->InsertNextPoint(v2.GetDataPointer()); container->GetPointIds()->InsertNextId(pointId); } else { point = m_FiberPolyData->GetPoint(points[numPoints-1]); pointId = newPoints->InsertNextPoint(point); container->GetPointIds()->InsertNextId(pointId); break; } dtau = dtau-pointDistance; } newCellArray->InsertNextCell(container); } newPoly->SetPoints(newPoints); newPoly->SetLines(newCellArray); m_FiberPolyData = newPoly; UpdateFiberGeometry(); UpdateColorCoding(); } // reapply selected colorcoding in case polydata structure has changed void mitk::FiberBundleX::UpdateColorCoding() { char* cc = GetCurrentColorCoding(); if( strcmp (COLORCODING_ORIENTATION_BASED,cc) == 0 ) DoColorCodingOrientationBased(); else if( strcmp (COLORCODING_FA_BASED,cc) == 0 ) DoColorCodingFaBased(); } /* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */ void mitk::FiberBundleX::UpdateOutputInformation() { } void mitk::FiberBundleX::SetRequestedRegionToLargestPossibleRegion() { } bool mitk::FiberBundleX::RequestedRegionIsOutsideOfTheBufferedRegion() { return false; } bool mitk::FiberBundleX::VerifyRequestedRegion() { return true; } void mitk::FiberBundleX::SetRequestedRegion( itk::DataObject *data ) { } diff --git a/Modules/DiffusionImaging/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h b/Modules/DiffusionImaging/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h index 3a4cf2dcf9..c6546fd746 100644 --- a/Modules/DiffusionImaging/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h +++ b/Modules/DiffusionImaging/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h @@ -1,305 +1,305 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2009-07-14 19:11:20 +0200 (Tue, 14 Jul 2009) $ Version: $Revision: 18127 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef __itkAnalyticalDiffusionQballReconstructionImageFilter_h_ #define __itkAnalyticalDiffusionQballReconstructionImageFilter_h_ #include "itkImageToImageFilter.h" #include "vnl/vnl_vector_fixed.h" #include "vnl/vnl_matrix.h" #include "vnl/algo/vnl_svd.h" #include "itkVectorContainer.h" #include "itkVectorImage.h" namespace itk{ /** \class AnalyticalDiffusionQballReconstructionImageFilter * \brief This class takes as input one or more reference image (acquired in the * absence of diffusion sensitizing gradients) and 'n' diffusion * weighted images and their gradient directions and computes an image of * orientation distribution function coefficients in a spherical harmonic basis. * * \par Inputs and Usage * \par * When you have the 'n' gradient and one or more reference images in a single * multi-component image (VectorImage), you can specify the images as * \code * filter->SetGradientImage( directionsContainer, vectorImage ); * \endcode * Note that this method is used to specify both the reference and gradient images. * This is convenient when the DWI images are read in using the * NRRD * format. Like the Nrrd format, the reference images are those components of the * vectorImage whose gradient direction is (0,0,0). If more than one reference image * is present, they are averaged prior to the reconstruction. * * \par Outputs * The output image is an image of vectors that must be understood as ODFs: * \code * Image< Vector< TPixelType, OdfNrDirections >, 3 > * \endcode * * \par Parameters * \li Threshold - Threshold on the reference image data. The output ODF will * be a null pdf for pixels in the reference image that have a value less * than this. * \li BValue - See the documentation of SetBValue(). * \li At least 6 gradient images must be specified for the filter to be able * to run. If the input gradient directions g_i are majorly sampled on one half * of the sqhere, then each input image I_i will be duplicated and assign -g_i * in order to guarantee stability of the algorithm. * \li OdfDirections - directions of resulting orientation distribution function * \li EquatorNrSamplingPoints - number of sampling points on equator when * performing Funk Radeon Transform (FRT) * \li BasisFunctionCenters - the centers of the basis functions are used for * the sRBF (spherical radial basis functions interpolation). If not set, they * will be defaulted to equal m_EquatorNrSamplingPoints * * \par Template parameters * The class is templated over * \li the pixel type of the reference and gradient images * (expected to be scalar data types) * \li the internal representation of the ODF pixels (double, float etc). * \li the number of OdfDirections * \li the number of basis function centers for the sRBF * * \par References: * \li[1] * Tuch DS, * "Q-ball imaging", Magn Reson Med. 2004 Dec;52(6):1358-72. * */ template< class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections> class AnalyticalDiffusionQballReconstructionImageFilter : public ImageToImageFilter< Image< TReferenceImagePixelType, 3 >, Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > > { public: enum Normalization { QBAR_STANDARD, QBAR_B_ZERO_B_VALUE, QBAR_B_ZERO, QBAR_NONE, QBAR_ADC_ONLY, QBAR_RAW_SIGNAL, QBAR_SOLID_ANGLE, QBAR_NONNEG_SOLID_ANGLE }; typedef AnalyticalDiffusionQballReconstructionImageFilter Self; typedef SmartPointer Pointer; typedef SmartPointer ConstPointer; typedef ImageToImageFilter< Image< TReferenceImagePixelType, 3>, Image< Vector< TOdfPixelType, NrOdfDirections >, 3 > > Superclass; /** Method for creation through the object factory. */ itkNewMacro(Self); /** Runtime information support. */ itkTypeMacro(AnalyticalDiffusionQballReconstructionImageFilter, ImageToImageFilter); typedef TReferenceImagePixelType ReferencePixelType; typedef TGradientImagePixelType GradientPixelType; typedef Vector< TOdfPixelType, NrOdfDirections > OdfPixelType; typedef TOdfPixelType BZeroPixelType; /** Reference image data, This image is aquired in the absence * of a diffusion sensitizing field gradient */ typedef typename Superclass::InputImageType ReferenceImageType; typedef Image< OdfPixelType, 3 > OdfImageType; typedef OdfImageType OutputImageType; - typedef Image< Vector< TOdfPixelType, (unsigned int)((NOrderL*NOrderL + NOrderL + 2.0)/2.0 + NOrderL) >, 3 > CoefficientImageType; + typedef Image< Vector< TOdfPixelType, (NOrderL*NOrderL + NOrderL + 2)/2 + NOrderL >, 3 > CoefficientImageType; typedef Image< BZeroPixelType, 3 > BZeroImageType; typedef typename Superclass::OutputImageRegionType OutputImageRegionType; /** Typedef defining one (of the many) gradient images. */ typedef Image< GradientPixelType, 3 > GradientImageType; /** An alternative typedef defining one (of the many) gradient images. * It will be assumed that the vectorImage has the same dimension as the * Reference image and a vector length parameter of \c n (number of * gradient directions)*/ typedef VectorImage< GradientPixelType, 3 > GradientImagesType; /** Holds the ODF reconstruction matrix */ typedef vnl_matrix< TOdfPixelType >* OdfReconstructionMatrixType; typedef vnl_matrix< double > CoefficientMatrixType; /** Holds each magnetic field gradient used to acquire one DWImage */ typedef vnl_vector_fixed< double, 3 > GradientDirectionType; /** Container to hold gradient directions of the 'n' DW measurements */ typedef VectorContainer< unsigned int, GradientDirectionType > GradientDirectionContainerType; /** set method to add gradient directions and its corresponding * image. The image here is a VectorImage. The user is expected to pass the * gradient directions in a container. The ith element of the container * corresponds to the gradient direction of the ith component image the * VectorImage. For the baseline image, a vector of all zeros * should be set.*/ void SetGradientImage( GradientDirectionContainerType *, const GradientImagesType *image); /** Get reference image */ virtual ReferenceImageType * GetReferenceImage() { return ( static_cast< ReferenceImageType *>(this->ProcessObject::GetInput(0)) ); } /** Return the gradient direction. idx is 0 based */ virtual GradientDirectionType GetGradientDirection( unsigned int idx) const { if( idx >= m_NumberOfGradientDirections ) { itkExceptionMacro( << "Gradient direction " << idx << "does not exist" ); } return m_GradientDirectionContainer->ElementAt( idx+1 ); } static void tofile2(vnl_matrix *A, std::string fname); static double factorial(int number); static void Cart2Sph(double x, double y, double z, double* cart); static double legendre0(int l); static double spherical_harmonic(int m,int l,double theta,double phi, bool complexPart); static double Yj(int m, int k, double theta, double phi); OdfPixelType Normalize(OdfPixelType odf, typename NumericTraits::AccumulateType b0 ); vnl_vector PreNormalize( vnl_vector vec, typename NumericTraits::AccumulateType b0 ); /** Threshold on the reference image data. The output ODF will be a null * pdf for pixels in the reference image that have a value less than this * threshold. */ itkSetMacro( Threshold, ReferencePixelType ); itkGetMacro( Threshold, ReferencePixelType ); itkSetMacro( NormalizationMethod, Normalization); itkGetMacro( NormalizationMethod, Normalization ); typedef Image FloatImageType; itkGetMacro( BZeroImage, typename BZeroImageType::Pointer); itkGetMacro( ODFSumImage, typename FloatImageType::Pointer); itkGetMacro( CoefficientImage, typename CoefficientImageType::Pointer); itkSetMacro( BValue, TOdfPixelType); #ifdef GetBValue #undef GetBValue #endif itkGetConstReferenceMacro( BValue, TOdfPixelType); itkSetMacro( Lambda, double ); itkGetMacro( Lambda, double ); #ifdef ITK_USE_CONCEPT_CHECKING /** Begin concept checking */ itkConceptMacro(ReferenceEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(TensorEqualityComparableCheck, (Concept::EqualityComparable)); itkConceptMacro(GradientConvertibleToDoubleCheck, (Concept::Convertible)); itkConceptMacro(DoubleConvertibleToTensorCheck, (Concept::Convertible)); itkConceptMacro(GradientReferenceAdditiveOperatorsCheck, (Concept::AdditiveOperators)); itkConceptMacro(ReferenceOStreamWritableCheck, (Concept::OStreamWritable)); itkConceptMacro(TensorOStreamWritableCheck, (Concept::OStreamWritable)); /** End concept checking */ #endif protected: AnalyticalDiffusionQballReconstructionImageFilter(); ~AnalyticalDiffusionQballReconstructionImageFilter() {}; void PrintSelf(std::ostream& os, Indent indent) const; void ComputeReconstructionMatrix(); void BeforeThreadedGenerateData(); void ThreadedGenerateData( const OutputImageRegionType &outputRegionForThread, int); private: OdfReconstructionMatrixType m_ReconstructionMatrix; OdfReconstructionMatrixType m_CoeffReconstructionMatrix; OdfReconstructionMatrixType m_SphericalHarmonicBasisMatrix; /** container to hold gradient directions */ GradientDirectionContainerType::Pointer m_GradientDirectionContainer; /** Number of gradient measurements */ unsigned int m_NumberOfGradientDirections; /** Number of baseline images */ unsigned int m_NumberOfBaselineImages; /** Threshold on the reference image data */ ReferencePixelType m_Threshold; /** LeBihan's b-value for normalizing tensors */ TOdfPixelType m_BValue; typename BZeroImageType::Pointer m_BZeroImage; double m_Lambda; bool m_DirectionsDuplicated; Normalization m_NormalizationMethod; int m_NumberCoefficients; vnl_matrix* m_B_t; vnl_vector* m_LP; FloatImageType::Pointer m_ODFSumImage; typename CoefficientImageType::Pointer m_CoefficientImage; TOdfPixelType m_Delta1; TOdfPixelType m_Delta2; }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkAnalyticalDiffusionQballReconstructionImageFilter.cpp" #endif #endif //__itkAnalyticalDiffusionQballReconstructionImageFilter_h_ diff --git a/Modules/DiffusionImaging/Rendering/mitkFiberBundleXMapper2D.cpp b/Modules/DiffusionImaging/Rendering/mitkFiberBundleXMapper2D.cpp index 6d3115e871..5ac6db6694 100644 --- a/Modules/DiffusionImaging/Rendering/mitkFiberBundleXMapper2D.cpp +++ b/Modules/DiffusionImaging/Rendering/mitkFiberBundleXMapper2D.cpp @@ -1,321 +1,321 @@ /* * mitkFiberBundleMapper2D.cpp * mitk-all * * Created by HAL9000 on 1/17/11. * Copyright 2011 __MyCompanyName__. All rights reserved. * */ #include "mitkFiberBundleXMapper2D.h" #include #include #include #include #include //#include //#include #include #include #include #include #include #include #include #include //#include #include #include #include #include #include #include #include mitk::FiberBundleXMapper2D::FiberBundleXMapper2D() { m_lut = vtkLookupTable::New(); m_lut->Build(); } mitk::FiberBundleXMapper2D::~FiberBundleXMapper2D() { } mitk::FiberBundleX* mitk::FiberBundleXMapper2D::GetInput() { return dynamic_cast< mitk::FiberBundleX * > ( GetData() ); } void mitk::FiberBundleXMapper2D::Update(mitk::BaseRenderer * renderer) { if ( !this->IsVisible( renderer ) ) { return; } - MITK_INFO << "MapperFBX 2D update: "; + MITK_DEBUG << "MapperFBX 2D update: "; // Calculate time step of the input data for the specified renderer (integer value) // this method is implemented in mitkMapper this->CalculateTimeStep( renderer ); //check if updates occured in the node or on the display FBXLocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); const DataNode *node = this->GetDataNode(); if ( (localStorage->m_LastUpdateTime < node->GetMTime()) || (localStorage->m_LastUpdateTime < node->GetPropertyList()->GetMTime()) //was a property modified? || (localStorage->m_LastUpdateTime < node->GetPropertyList(renderer)->GetMTime()) ) { // MITK_INFO << "UPDATE NEEDED FOR _ " << renderer->GetName(); this->GenerateDataForRenderer( renderer ); } if ((localStorage->m_LastUpdateTime < renderer->GetDisplayGeometry()->GetMTime()) ) //was the display geometry modified? e.g. zooming, panning) { this->UpdateShaderParameter(renderer); } } void mitk::FiberBundleXMapper2D::UpdateShaderParameter(mitk::BaseRenderer * renderer) { FBXLocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); //get information about current position of views mitk::SliceNavigationController::Pointer sliceContr = renderer->GetSliceNavigationController(); mitk::PlaneGeometry::ConstPointer planeGeo = sliceContr->GetCurrentPlaneGeometry(); //generate according cutting planes based on the view position float sliceN[3], planeOrigin[3]; // since shader uses camera coordinates, transform origin and normal from worldcoordinates to cameracoordinates planeOrigin[0] = (float) planeGeo->GetOrigin()[0]; planeOrigin[1] = (float) planeGeo->GetOrigin()[1]; planeOrigin[2] = (float) planeGeo->GetOrigin()[2]; sliceN[0] = planeGeo->GetNormal()[0]; sliceN[1] = planeGeo->GetNormal()[1]; sliceN[2] = planeGeo->GetNormal()[2]; float tmp1 = planeOrigin[0] * sliceN[0]; float tmp2 = planeOrigin[1] * sliceN[1]; float tmp3 = planeOrigin[2] * sliceN[2]; float d1 = tmp1 + tmp2 + tmp3; //attention, correct normalvector float plane1[4]; plane1[0] = sliceN[0]; plane1[1] = sliceN[1]; plane1[2] = sliceN[2]; plane1[3] = d1; float thickness = 2.0; if(!this->GetDataNode()->GetPropertyValue("Fiber2DSliceThickness",thickness)) MITK_INFO << "FIBER2D SLICE THICKNESS PROPERTY ERROR"; bool fiberfading = false; if(!this->GetDataNode()->GetPropertyValue("Fiber2DfadeEFX",fiberfading)) MITK_INFO << "FIBER2D SLICE FADE EFX PROPERTY ERROR"; int fiberfading_i = 1; if (!fiberfading) fiberfading_i = 0; // set Opacity float fiberOpacity; this->GetDataNode()->GetOpacity(fiberOpacity, NULL); localStorage->m_PointActor->GetProperty()->AddShaderVariable("slicingPlane",4, plane1); localStorage->m_PointActor->GetProperty()->AddShaderVariable("fiberThickness",1, &thickness); localStorage->m_PointActor->GetProperty()->AddShaderVariable("fiberFadingON",1, &fiberfading_i); localStorage->m_PointActor->GetProperty()->AddShaderVariable("fiberOpacity", 1, &fiberOpacity); } // ALL RAW DATA FOR VISUALIZATION IS GENERATED HERE. // vtkActors and Mappers are feeded here void mitk::FiberBundleXMapper2D::GenerateDataForRenderer(mitk::BaseRenderer *renderer) { //the handler of local storage gets feeded in this method with requested data for related renderwindow FBXLocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); //this procedure is depricated, //not needed after initializaton anymore mitk::DataNode* node = this->GetDataNode(); if ( node == NULL ) { MITK_INFO << "check DATANODE: ....[Fail] "; return; } /////////////////////////////////// ///THIS GET INPUT mitk::FiberBundleX* fbx = this->GetInput(); localStorage->m_PointMapper->ScalarVisibilityOn(); localStorage->m_PointMapper->SetScalarModeToUsePointFieldData(); localStorage->m_PointMapper->SetLookupTable(m_lut); //apply the properties after the slice was set localStorage->m_PointActor->GetProperty()->SetOpacity(0.999); // set color if (fbx->GetCurrentColorCoding() != NULL){ // localStorage->m_PointMapper->SelectColorArray(""); localStorage->m_PointMapper->SelectColorArray(fbx->GetCurrentColorCoding()); MITK_DEBUG << "MapperFBX 2D: " << fbx->GetCurrentColorCoding(); if(fbx->GetCurrentColorCoding() == fbx->COLORCODING_CUSTOM){ float temprgb[3]; this->GetDataNode()->GetColor( temprgb, NULL ); double trgb[3] = { (double) temprgb[0], (double) temprgb[1], (double) temprgb[2] }; localStorage->m_PointActor->GetProperty()->SetColor(trgb); } } localStorage->m_PointMapper->SetInput(fbx->GetFiberPolyData()); localStorage->m_PointActor->SetMapper(localStorage->m_PointMapper); localStorage->m_PointActor->GetProperty()->ShadingOn(); // Applying shading properties { mitk::ShaderRepository::GetGlobalShaderRepository()->ApplyProperties(this->GetDataNode(),localStorage->m_PointActor,renderer, localStorage->m_LastUpdateTime); } this->UpdateShaderParameter(renderer); // We have been modified => save this for next Update() localStorage->m_LastUpdateTime.Modified(); } vtkProp* mitk::FiberBundleXMapper2D::GetVtkProp(mitk::BaseRenderer *renderer) { //MITK_INFO << "FiberBundleMapper2D GetVtkProp(renderer)"; this->Update(renderer); return m_LSH.GetLocalStorage(renderer)->m_PointActor; } void mitk::FiberBundleXMapper2D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite) { //add shader to datano //####### load shader from file ######### QString applicationDir = QCoreApplication::applicationDirPath(); if (applicationDir.endsWith("bin")) applicationDir.append("/"); else if (applicationDir.endsWith("MacOS")) { //on osx, check if path for installer or MITK development is needed applicationDir.append("/"); QFile f( applicationDir+"FiberTrackingLUTBaryCoords.bin" ); if( !f.exists() ) // if file does not exist, then look in MITK development build directory applicationDir.append("../../../"); }else applicationDir.append("\\..\\"); mitk::StandardFileLocations::GetInstance()->AddDirectoryForSearch( applicationDir.toStdString().c_str(), false ); mitk::ShaderRepository::Pointer shaderRepository = mitk::ShaderRepository::GetGlobalShaderRepository(); shaderRepository->LoadShader(mitk::StandardFileLocations::GetInstance()->FindFile("mitkShaderFiberClipping.xml")); //#################################################################### node->SetProperty("shader",mitk::ShaderProperty::New("mitkShaderFiberClipping")); mitk::ShaderRepository::GetGlobalShaderRepository()->AddDefaultProperties(node,renderer,overwrite); //add other parameters to propertylist node->AddProperty( "Fiber2DSliceThickness", mitk::FloatProperty::New(2.0f), renderer, overwrite ); node->AddProperty( "Fiber2DfadeEFX", mitk::BoolProperty::New(true), renderer, overwrite ); Superclass::SetDefaultProperties(node, renderer, overwrite); } // following methods are essential, they actually call the GetVtkProp() method // which returns the desired actors void mitk::FiberBundleXMapper2D::MitkRenderOverlay(BaseRenderer* renderer) { // MITK_INFO << "FiberBundleMapper2D MitkRenderOVerlay(renderer)"; if ( this->IsVisible(renderer)==false ) return; if ( this->GetVtkProp(renderer)->GetVisibility() ) { this->GetVtkProp(renderer)->RenderOverlay(renderer->GetVtkRenderer()); } } void mitk::FiberBundleXMapper2D::MitkRenderOpaqueGeometry(BaseRenderer* renderer) { // MITK_INFO << "FiberBundleMapper2D MitkRenderOpaqueGeometry(renderer)"; if ( this->IsVisible( renderer )==false ) return; if ( this->GetVtkProp(renderer)->GetVisibility() ) this->GetVtkProp(renderer)->RenderOpaqueGeometry( renderer->GetVtkRenderer() ); } void mitk::FiberBundleXMapper2D::MitkRenderTranslucentGeometry(BaseRenderer* renderer) { // MITK_INFO << "FiberBundleMapper2D MitkRenderTranslucentGeometry(renderer)"; if ( this->IsVisible(renderer)==false ) return; //TODO is it possible to have a visible BaseRenderer AND an invisible VtkRenderer??? if ( this->GetVtkProp(renderer)->GetVisibility() ) this->GetVtkProp(renderer)->RenderTranslucentPolygonalGeometry(renderer->GetVtkRenderer()); } void mitk::FiberBundleXMapper2D::MitkRenderVolumetricGeometry(BaseRenderer* renderer) { // MITK_INFO << "FiberBundleMapper2D MitkRenderVolumentricGeometry(renderer)"; if(IsVisible(renderer)==false) return; //TODO is it possible to have a visible BaseRenderer AND an invisible VtkRenderer??? if ( GetVtkProp(renderer)->GetVisibility() ) this->GetVtkProp(renderer)->RenderVolumetricGeometry(renderer->GetVtkRenderer()); } mitk::FiberBundleXMapper2D::FBXLocalStorage::FBXLocalStorage() { m_PointActor = vtkSmartPointer::New(); m_PointMapper = vtkSmartPointer::New(); } diff --git a/Modules/DiffusionImaging/files.cmake b/Modules/DiffusionImaging/files.cmake index 59d5212562..ed47a8eb41 100644 --- a/Modules/DiffusionImaging/files.cmake +++ b/Modules/DiffusionImaging/files.cmake @@ -1,216 +1,218 @@ set(CPP_FILES # DicomImport DicomImport/mitkDicomDiffusionImageReader.cpp DicomImport/mitkGroupDiffusionHeadersFilter.cpp DicomImport/mitkDicomDiffusionImageHeaderReader.cpp DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp # DataStructures IODataStructures/mitkDiffusionImagingObjectFactory.cpp # DataStructures -> DWI IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSource.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageReader.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriter.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageIOFactory.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriterFactory.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSerializer.cpp # DataStructures -> QBall IODataStructures/QBallImages/mitkQBallImageSource.cpp IODataStructures/QBallImages/mitkNrrdQBallImageReader.cpp IODataStructures/QBallImages/mitkNrrdQBallImageWriter.cpp IODataStructures/QBallImages/mitkNrrdQBallImageIOFactory.cpp IODataStructures/QBallImages/mitkNrrdQBallImageWriterFactory.cpp IODataStructures/QBallImages/mitkQBallImage.cpp IODataStructures/QBallImages/mitkQBallImageSerializer.cpp # DataStructures -> Tensor IODataStructures/TensorImages/mitkTensorImageSource.cpp IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp IODataStructures/TensorImages/mitkNrrdTensorImageWriter.cpp IODataStructures/TensorImages/mitkNrrdTensorImageIOFactory.cpp IODataStructures/TensorImages/mitkNrrdTensorImageWriterFactory.cpp IODataStructures/TensorImages/mitkTensorImage.cpp IODataStructures/TensorImages/mitkTensorImageSerializer.cpp # DataStructures -> FiberBundleX IODataStructures/FiberBundleX/mitkFiberBundleX.cpp IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp IODataStructures/FiberBundleX/mitkFiberBundleXIOFactory.cpp IODataStructures/FiberBundleX/mitkFiberBundleXWriterFactory.cpp IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.cpp IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.cpp # DataStructures -> PlanarFigureComposite IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp # DataStructures -> Tbss IODataStructures/TbssImages/mitkTbssImageSource.cpp IODataStructures/TbssImages/mitkTbssRoiImageSource.cpp IODataStructures/TbssImages/mitkNrrdTbssImageReader.cpp IODataStructures/TbssImages/mitkNrrdTbssImageIOFactory.cpp IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.cpp IODataStructures/TbssImages/mitkNrrdTbssRoiImageIOFactory.cpp IODataStructures/TbssImages/mitkTbssImage.cpp IODataStructures/TbssImages/mitkTbssRoiImage.cpp IODataStructures/TbssImages/mitkNrrdTbssImageWriter.cpp IODataStructures/TbssImages/mitkNrrdTbssImageWriterFactory.cpp IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.cpp IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriterFactory.cpp IODataStructures/TbssImages/mitkTbssImporter.cpp # DataStructures Connectomics IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetwork.cpp IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkReader.cpp IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkIOFactory.cpp IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkSerializer.cpp IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkWriter.cpp IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkWriterFactory.cpp IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkDefinitions.cpp IODataStructures/ConnectomicsNetwork/mitkConnectomicsConstantsManager.cpp # Rendering Rendering/vtkMaskedProgrammableGlyphFilter.cpp Rendering/mitkCompositeMapper.cpp Rendering/mitkVectorImageVtkGlyphMapper3D.cpp Rendering/vtkOdfSource.cxx Rendering/vtkThickPlane.cxx Rendering/mitkOdfNormalizationMethodProperty.cpp Rendering/mitkOdfScaleByProperty.cpp Rendering/mitkFiberBundleXMapper2D.cpp Rendering/mitkFiberBundleXMapper3D.cpp Rendering/mitkFiberBundleXThreadMonitorMapper3D.cpp Rendering/mitkTbssImageMapper.cpp Rendering/mitkPlanarCircleMapper3D.cpp Rendering/mitkPlanarPolygonMapper3D.cpp Rendering/mitkConnectomicsNetworkMapper3D.cpp # Interactions Interactions/mitkFiberBundleInteractor.cpp # Algorithms Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp Algorithms/mitkTractAnalyzer.cpp # Algorithms Connectomics Algorithms/Connectomics/mitkConnectomicsNetworkCreator.cpp Algorithms/Connectomics/mitkConnectomicsHistogramBase.cpp Algorithms/Connectomics/mitkConnectomicsDegreeHistogram.cpp Algorithms/Connectomics/mitkConnectomicsShortestPathHistogram.cpp Algorithms/Connectomics/mitkConnectomicsBetweennessHistogram.cpp Algorithms/Connectomics/mitkConnectomicsHistogramCache.cpp Algorithms/Connectomics/mitkConnectomicsSyntheticNetworkGenerator.cpp Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingPermutationBase.cpp Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingManager.cpp Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingCostFunctionBase.cpp Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingCostFunctionModularity.cpp # Tractography Tractography/itkStochasticTractographyFilter.h ) set(H_FILES # Rendering Rendering/mitkDiffusionImageMapper.h Rendering/mitkTbssImageMapper.h Rendering/mitkOdfVtkMapper2D.h Rendering/mitkFiberBundleXMapper3D.h Rendering/mitkFiberBundleXMapper2D.h Rendering/mitkFiberBundleXThreadMonitorMapper3D.h Rendering/mitkPlanarCircleMapper3D.h Rendering/mitkPlanarPolygonMapper3D.h Rendering/mitkConnectomicsNetworkMapper3D.h # Reconstruction Reconstruction/itkDiffusionQballReconstructionImageFilter.h Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h Reconstruction/itkPointShell.h Reconstruction/itkOrientationDistributionFunction.h Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h Reconstruction/itkRegularizedIVIMLocalVariationImageFilter.h Reconstruction/itkRegularizedIVIMReconstructionFilter.h Reconstruction/itkRegularizedIVIMReconstructionSingleIteration.h # IO Datastructures IODataStructures/DiffusionWeightedImages/mitkDiffusionImage.h IODataStructures/TbssImages/mitkTbssImporter.h # DataStructures -> FiberBundleX IODataStructures/FiberBundleX/mitkFiberBundleX.h IODataStructures/FiberBundleX/mitkFiberBundleXWriter.h IODataStructures/FiberBundleX/mitkFiberBundleXReader.h IODataStructures/FiberBundleX/mitkFiberBundleXIOFactory.h IODataStructures/FiberBundleX/mitkFiberBundleXWriterFactory.h IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.h IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.h # Datastructures Connectomics IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetwork.h IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkReader.h IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkIOFactory.h IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkSerializer.h IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkWriter.h IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkWriterFactory.h IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkDefinitions.h IODataStructures/ConnectomicsNetwork/mitkConnectomicsConstantsManager.h # Tractography Tractography/itkGibbsTrackingFilter.h Tractography/itkStochasticTractographyFilter.h # Algorithms Algorithms/itkDiffusionQballGeneralizedFaImageFilter.h Algorithms/itkDiffusionQballPrepareVisualizationImageFilter.h Algorithms/itkTensorDerivedMeasurementsFilter.h Algorithms/itkBrainMaskExtractionImageFilter.h Algorithms/itkB0ImageExtractionImageFilter.h Algorithms/itkTensorImageToDiffusionImageFilter.h Algorithms/itkTensorToL2NormImageFilter.h Algorithms/itkTractDensityImageFilter.h Algorithms/itkTractsToFiberEndingsImageFilter.h Algorithms/itkTractsToRgbaImageFilter.h Algorithms/itkGaussianInterpolateImageFunction.h Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h Algorithms/itkDiffusionTensorPrincipleDirectionImageFilter.h Algorithms/itkCartesianToPolarVectorImageFilter.h Algorithms/itkPolarToCartesianVectorImageFilter.h Algorithms/itkDistanceMapFilter.h Algorithms/itkProjectionFilter.h Algorithms/itkSkeletonizationFilter.h Algorithms/itkReduceDirectionGradientsFilter.h Algorithms/itkResidualImageFilter.h Algorithms/itkExtractChannelFromRgbaImageFilter.h # Algorithms Connectomics Algorithms/Connectomics/mitkConnectomicsNetworkCreator.h Algorithms/Connectomics/mitkConnectomicsHistogramBase.h Algorithms/Connectomics/mitkConnectomicsDegreeHistogram.h Algorithms/Connectomics/mitkConnectomicsShortestPathHistogram.h Algorithms/Connectomics/mitkConnectomicsBetweennessHistogram.h Algorithms/Connectomics/mitkConnectomicsHistogramCache.h Algorithms/Connectomics/mitkConnectomicsSyntheticNetworkGenerator.h Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingPermutationBase.h Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingPermutationModularity.h Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingManager.h Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingCostFunctionBase.h Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h + Algorithms/itkTensorReconstructionWithEigenvalueCorrectionFilter.h + ) set( TOOL_FILES ) if(WIN32) endif(WIN32) #MITK_MULTIPLEX_PICTYPE( Algorithms/mitkImageRegistrationMethod-TYPE.cpp ) diff --git a/Modules/DiffusionImaging/files.cmake~ b/Modules/DiffusionImaging/files.cmake~ index 961349c228..eeb2a72a09 100644 --- a/Modules/DiffusionImaging/files.cmake~ +++ b/Modules/DiffusionImaging/files.cmake~ @@ -1,180 +1,219 @@ -SET(CPP_FILES +set(CPP_FILES # DicomImport DicomImport/mitkDicomDiffusionImageReader.cpp DicomImport/mitkGroupDiffusionHeadersFilter.cpp DicomImport/mitkDicomDiffusionImageHeaderReader.cpp DicomImport/mitkGEDicomDiffusionImageHeaderReader.cpp DicomImport/mitkPhilipsDicomDiffusionImageHeaderReader.cpp DicomImport/mitkSiemensDicomDiffusionImageHeaderReader.cpp DicomImport/mitkSiemensMosaicDicomDiffusionImageHeaderReader.cpp # DataStructures IODataStructures/mitkDiffusionImagingObjectFactory.cpp # DataStructures -> DWI IODataStructures/DiffusionWeightedImages/mitkDiffusionImageHeaderInformation.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSource.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageReader.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriter.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageIOFactory.cpp IODataStructures/DiffusionWeightedImages/mitkNrrdDiffusionImageWriterFactory.cpp IODataStructures/DiffusionWeightedImages/mitkDiffusionImageSerializer.cpp # DataStructures -> QBall IODataStructures/QBallImages/mitkQBallImageSource.cpp IODataStructures/QBallImages/mitkNrrdQBallImageReader.cpp IODataStructures/QBallImages/mitkNrrdQBallImageWriter.cpp IODataStructures/QBallImages/mitkNrrdQBallImageIOFactory.cpp IODataStructures/QBallImages/mitkNrrdQBallImageWriterFactory.cpp IODataStructures/QBallImages/mitkQBallImage.cpp IODataStructures/QBallImages/mitkQBallImageSerializer.cpp # DataStructures -> Tensor IODataStructures/TensorImages/mitkTensorImageSource.cpp IODataStructures/TensorImages/mitkNrrdTensorImageReader.cpp IODataStructures/TensorImages/mitkNrrdTensorImageWriter.cpp IODataStructures/TensorImages/mitkNrrdTensorImageIOFactory.cpp IODataStructures/TensorImages/mitkNrrdTensorImageWriterFactory.cpp IODataStructures/TensorImages/mitkTensorImage.cpp IODataStructures/TensorImages/mitkTensorImageSerializer.cpp - # DataStructures -> FiberBundle - IODataStructures/FiberBundle/mitkFiberBundle.cpp - IODataStructures/FiberBundle/mitkFiberBundleWriter.cpp - IODataStructures/FiberBundle/mitkFiberBundleReader.cpp - IODataStructures/FiberBundle/mitkFiberBundleIOFactory.cpp - IODataStructures/FiberBundle/mitkFiberBundleWriterFactory.cpp - IODataStructures/FiberBundle/mitkFiberBundleSerializer.cpp - IODataStructures/FiberBundle/mitkParticle.cpp - IODataStructures/FiberBundle/mitkParticleGrid.cpp - # DataStructures -> FiberBundleX IODataStructures/FiberBundleX/mitkFiberBundleX.cpp IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp IODataStructures/FiberBundleX/mitkFiberBundleXIOFactory.cpp IODataStructures/FiberBundleX/mitkFiberBundleXWriterFactory.cpp IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.cpp IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.cpp - # DataStructures -> PlanarFigureComposite IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp - # DataStructures -> Tbss IODataStructures/TbssImages/mitkTbssImageSource.cpp IODataStructures/TbssImages/mitkTbssRoiImageSource.cpp IODataStructures/TbssImages/mitkNrrdTbssImageReader.cpp IODataStructures/TbssImages/mitkNrrdTbssImageIOFactory.cpp IODataStructures/TbssImages/mitkNrrdTbssRoiImageReader.cpp IODataStructures/TbssImages/mitkNrrdTbssRoiImageIOFactory.cpp IODataStructures/TbssImages/mitkTbssImage.cpp IODataStructures/TbssImages/mitkTbssRoiImage.cpp IODataStructures/TbssImages/mitkNrrdTbssImageWriter.cpp - IODataStructures/TbssImages/mitkNrrdTbssImageWriterFactory.cpp + IODataStructures/TbssImages/mitkNrrdTbssImageWriterFactory.cpp IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriter.cpp IODataStructures/TbssImages/mitkNrrdTbssRoiImageWriterFactory.cpp IODataStructures/TbssImages/mitkTbssImporter.cpp - + + # DataStructures Connectomics + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetwork.cpp + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkReader.cpp + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkIOFactory.cpp + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkSerializer.cpp + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkWriter.cpp + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkWriterFactory.cpp + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkDefinitions.cpp + IODataStructures/ConnectomicsNetwork/mitkConnectomicsConstantsManager.cpp # Rendering Rendering/vtkMaskedProgrammableGlyphFilter.cpp Rendering/mitkCompositeMapper.cpp Rendering/mitkVectorImageVtkGlyphMapper3D.cpp Rendering/vtkOdfSource.cxx Rendering/vtkThickPlane.cxx Rendering/mitkOdfNormalizationMethodProperty.cpp Rendering/mitkOdfScaleByProperty.cpp - Rendering/mitkFiberBundleMapper2D.cpp - Rendering/mitkFiberBundleMapper3D.cpp Rendering/mitkFiberBundleXMapper2D.cpp Rendering/mitkFiberBundleXMapper3D.cpp Rendering/mitkFiberBundleXThreadMonitorMapper3D.cpp - Rendering/mitkTbssImageMapper.cpp + Rendering/mitkTbssImageMapper.cpp Rendering/mitkPlanarCircleMapper3D.cpp Rendering/mitkPlanarPolygonMapper3D.cpp - + Rendering/mitkConnectomicsNetworkMapper3D.cpp + # Interactions Interactions/mitkFiberBundleInteractor.cpp # Algorithms Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.cpp Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.cpp + Algorithms/mitkTractAnalyzer.cpp + + # Algorithms Connectomics + Algorithms/Connectomics/mitkConnectomicsNetworkCreator.cpp + Algorithms/Connectomics/mitkConnectomicsHistogramBase.cpp + Algorithms/Connectomics/mitkConnectomicsDegreeHistogram.cpp + Algorithms/Connectomics/mitkConnectomicsShortestPathHistogram.cpp + Algorithms/Connectomics/mitkConnectomicsBetweennessHistogram.cpp + Algorithms/Connectomics/mitkConnectomicsHistogramCache.cpp + Algorithms/Connectomics/mitkConnectomicsSyntheticNetworkGenerator.cpp + Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingPermutationBase.cpp + Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingPermutationModularity.cpp + Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingManager.cpp + Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingCostFunctionBase.cpp + Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingCostFunctionModularity.cpp # Tractography Tractography/itkStochasticTractographyFilter.h ) -SET(H_FILES +set(H_FILES # Rendering Rendering/mitkDiffusionImageMapper.h Rendering/mitkTbssImageMapper.h Rendering/mitkOdfVtkMapper2D.h - Rendering/mitkFiberBundleMapper2D.h - Rendering/mitkFiberBundleMapper3D.h Rendering/mitkFiberBundleXMapper3D.h Rendering/mitkFiberBundleXMapper2D.h Rendering/mitkFiberBundleXThreadMonitorMapper3D.h Rendering/mitkPlanarCircleMapper3D.h Rendering/mitkPlanarPolygonMapper3D.h + Rendering/mitkConnectomicsNetworkMapper3D.h # Reconstruction Reconstruction/itkDiffusionQballReconstructionImageFilter.h Reconstruction/mitkTeemDiffusionTensor3DReconstructionImageFilter.h Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.h Reconstruction/itkPointShell.h Reconstruction/itkOrientationDistributionFunction.h Reconstruction/itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h Reconstruction/itkRegularizedIVIMLocalVariationImageFilter.h Reconstruction/itkRegularizedIVIMReconstructionFilter.h Reconstruction/itkRegularizedIVIMReconstructionSingleIteration.h # IO Datastructures IODataStructures/DiffusionWeightedImages/mitkDiffusionImage.h - IODataStructures/FiberBundle/itkSlowPolyLineParametricPath.h + IODataStructures/TbssImages/mitkTbssImporter.h # DataStructures -> FiberBundleX IODataStructures/FiberBundleX/mitkFiberBundleX.h IODataStructures/FiberBundleX/mitkFiberBundleXWriter.h IODataStructures/FiberBundleX/mitkFiberBundleXReader.h IODataStructures/FiberBundleX/mitkFiberBundleXIOFactory.h IODataStructures/FiberBundleX/mitkFiberBundleXWriterFactory.h IODataStructures/FiberBundleX/mitkFiberBundleXSerializer.h IODataStructures/FiberBundleX/mitkFiberBundleXThreadMonitor.h - - + + # Datastructures Connectomics + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetwork.h + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkReader.h + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkIOFactory.h + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkSerializer.h + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkWriter.h + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkWriterFactory.h + IODataStructures/ConnectomicsNetwork/mitkConnectomicsNetworkDefinitions.h + IODataStructures/ConnectomicsNetwork/mitkConnectomicsConstantsManager.h # Tractography Tractography/itkGibbsTrackingFilter.h Tractography/itkStochasticTractographyFilter.h # Algorithms Algorithms/itkDiffusionQballGeneralizedFaImageFilter.h Algorithms/itkDiffusionQballPrepareVisualizationImageFilter.h Algorithms/itkTensorDerivedMeasurementsFilter.h Algorithms/itkBrainMaskExtractionImageFilter.h Algorithms/itkB0ImageExtractionImageFilter.h Algorithms/itkTensorImageToDiffusionImageFilter.h Algorithms/itkTensorToL2NormImageFilter.h - Algorithms/itkTractsToProbabilityImageFilter.h + Algorithms/itkTractDensityImageFilter.h Algorithms/itkTractsToFiberEndingsImageFilter.h + Algorithms/itkTractsToRgbaImageFilter.h Algorithms/itkGaussianInterpolateImageFunction.h Algorithms/mitkPartialVolumeAnalysisHistogramCalculator.h Algorithms/mitkPartialVolumeAnalysisClusteringCalculator.h Algorithms/itkDiffusionTensorPrincipleDirectionImageFilter.h Algorithms/itkCartesianToPolarVectorImageFilter.h Algorithms/itkPolarToCartesianVectorImageFilter.h Algorithms/itkDistanceMapFilter.h Algorithms/itkProjectionFilter.h Algorithms/itkSkeletonizationFilter.h +<<<<<<< HEAD + Algorithms/itkReduceDirectionGradientsFilter.h + Algorithms/itkResidualImageFilter.h + + # Algorithms Connectomics + Algorithms/Connectomics/mitkConnectomicsNetworkCreator.h + Algorithms/Connectomics/mitkConnectomicsHistogramBase.h + Algorithms/Connectomics/mitkConnectomicsDegreeHistogram.h + Algorithms/Connectomics/mitkConnectomicsShortestPathHistogram.h + Algorithms/Connectomics/mitkConnectomicsBetweennessHistogram.h + Algorithms/Connectomics/mitkConnectomicsHistogramCache.h + Algorithms/Connectomics/mitkConnectomicsSyntheticNetworkGenerator.h + Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingPermutationBase.h + Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingPermutationModularity.h + Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingManager.h + Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingCostFunctionBase.h + Algorithms/Connectomics/mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h +======= + Algorithms/itkFreeWaterEliminationFilter.h +>>>>>>> origin/bug-10827-fwe ) -SET( TOOL_FILES +set( TOOL_FILES ) -IF(WIN32) -ENDIF(WIN32) +if(WIN32) +endif(WIN32) #MITK_MULTIPLEX_PICTYPE( Algorithms/mitkImageRegistrationMethod-TYPE.cpp ) diff --git a/Modules/MitkExt/Algorithms/mitkCoreExtObjectFactory.cpp b/Modules/MitkExt/Algorithms/mitkCoreExtObjectFactory.cpp index 4e7c473c4c..a2ee5baa58 100644 --- a/Modules/MitkExt/Algorithms/mitkCoreExtObjectFactory.cpp +++ b/Modules/MitkExt/Algorithms/mitkCoreExtObjectFactory.cpp @@ -1,215 +1,193 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 16916 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkCoreExtObjectFactory.h" #include "mitkProperties.h" #include "mitkBaseRenderer.h" #include "mitkDataNode.h" #include "mitkCoreObjectFactory.h" #include "mitkParRecFileIOFactory.h" #include "mitkObjFileIOFactory.h" #include "mitkVtkUnstructuredGridIOFactory.h" #include "mitkStlVolumeTimeSeriesIOFactory.h" #include "mitkVtkVolumeTimeSeriesIOFactory.h" #include "mitkUnstructuredGridVtkWriterFactory.h" #include "mitkUnstructuredGridVtkWriter.h" #include #include #include #include "mitkCone.h" -#include "mitkContour.h" -#include "mitkContourMapper2D.h" -#include "mitkContourSetMapper2D.h" -#include "mitkContourSetVtkMapper3D.h" -#include "mitkContourVtkMapper3D.h" #include "mitkCuboid.h" #include "mitkCylinder.h" #include "mitkEllipsoid.h" #include "mitkMeshMapper2D.h" #include "mitkMeshVtkMapper3D.h" #include "mitkUnstructuredGridMapper2D.h" #include "mitkEnhancedPointSetVtkMapper3D.h" #include "mitkSeedsImage.h" #include "mitkUnstructuredGrid.h" #include "mitkUnstructuredGridVtkMapper3D.h" #include "mitkPolyDataGLMapper2D.h" #include "mitkGPUVolumeMapper3D.h" #include "mitkVolumeDataVtkMapper3D.h" mitk::CoreExtObjectFactory::CoreExtObjectFactory() :CoreObjectFactoryBase() { static bool alreadyDone = false; if (!alreadyDone) { MITK_DEBUG << "CoreExtObjectFactory c'tor" << std::endl; RegisterIOFactories(); itk::ObjectFactoryBase::RegisterFactory( ParRecFileIOFactory::New() ); itk::ObjectFactoryBase::RegisterFactory( ObjFileIOFactory::New() ); itk::ObjectFactoryBase::RegisterFactory( VtkUnstructuredGridIOFactory::New() ); itk::ObjectFactoryBase::RegisterFactory( StlVolumeTimeSeriesIOFactory::New() ); itk::ObjectFactoryBase::RegisterFactory( VtkVolumeTimeSeriesIOFactory::New() ); mitk::UnstructuredGridVtkWriterFactory::RegisterOneFactory(); m_FileWriters.push_back(mitk::UnstructuredGridVtkWriter::New().GetPointer()); m_FileWriters.push_back(mitk::UnstructuredGridVtkWriter::New().GetPointer()); m_FileWriters.push_back(mitk::UnstructuredGridVtkWriter::New().GetPointer()); CreateFileExtensionsMap(); alreadyDone = true; } } mitk::Mapper::Pointer mitk::CoreExtObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id) { mitk::Mapper::Pointer newMapper=NULL; mitk::BaseData *data = node->GetData(); if ( id == mitk::BaseRenderer::Standard2D ) { if((dynamic_cast(data)!=NULL)) { newMapper = mitk::MeshMapper2D::New(); newMapper->SetDataNode(node); } - else if((dynamic_cast(data)!=NULL)) - { - newMapper = mitk::ContourMapper2D::New(); - newMapper->SetDataNode(node); - } - else if((dynamic_cast(data)!=NULL)) - { - newMapper = mitk::ContourSetMapper2D::New(); - newMapper->SetDataNode(node); - } else if((dynamic_cast(data)!=NULL)) { newMapper = mitk::UnstructuredGridMapper2D::New(); newMapper->SetDataNode(node); } } else if ( id == mitk::BaseRenderer::Standard3D ) { if((dynamic_cast(data) != NULL)) { newMapper = mitk::GPUVolumeMapper3D::New(); newMapper->SetDataNode(node); } else if((dynamic_cast(data)!=NULL)) { newMapper = mitk::MeshVtkMapper3D::New(); newMapper->SetDataNode(node); } - else if((dynamic_cast(data)!=NULL)) - { - newMapper = mitk::ContourVtkMapper3D::New(); - newMapper->SetDataNode(node); - } - else if((dynamic_cast(data)!=NULL)) - { - newMapper = mitk::ContourSetVtkMapper3D::New(); - newMapper->SetDataNode(node); - } else if((dynamic_cast(data)!=NULL)) { newMapper = mitk::UnstructuredGridVtkMapper3D::New(); newMapper->SetDataNode(node); } } return newMapper; } void mitk::CoreExtObjectFactory::SetDefaultProperties(mitk::DataNode* node) { if(node==NULL) return; mitk::DataNode::Pointer nodePointer = node; mitk::Image::Pointer image = dynamic_cast(node->GetData()); if(image.IsNotNull() && image->IsInitialized()) { mitk::GPUVolumeMapper3D::SetDefaultProperties(node); } if (dynamic_cast(node->GetData())) { mitk::UnstructuredGridVtkMapper3D::SetDefaultProperties(node); } } const char* mitk::CoreExtObjectFactory::GetFileExtensions() { std::string fileExtension; this->CreateFileExtensions(m_FileExtensionsMap, fileExtension); return fileExtension.c_str(); }; mitk::CoreObjectFactoryBase::MultimapType mitk::CoreExtObjectFactory::GetFileExtensionsMap() { return m_FileExtensionsMap; } mitk::CoreObjectFactoryBase::MultimapType mitk::CoreExtObjectFactory::GetSaveFileExtensionsMap() { return m_SaveFileExtensionsMap; } void mitk::CoreExtObjectFactory::CreateFileExtensionsMap() { + m_FileExtensionsMap.insert(std::pair("*.mitk", "MITK scene files")); //a better place to add this file ending might be the scene serialization class + //at the moment this is not done because there is a plan to restructure the + //ObjectFactories. When this is done we have to check where we want to add this file ending. m_FileExtensionsMap.insert(std::pair("*.vtu", "VTK Unstructured Grid")); m_FileExtensionsMap.insert(std::pair("*.vtk", "VTK Unstructured Grid")); m_FileExtensionsMap.insert(std::pair("*.pvtu", "VTK Unstructured Grid")); m_SaveFileExtensionsMap.insert(std::pair("*.pvtu", "VTK Parallel XML Unstructured Grid")); m_SaveFileExtensionsMap.insert(std::pair("*.vtu", "VTK XML Unstructured Grid")); m_SaveFileExtensionsMap.insert(std::pair("*.vtk", "VTK Legacy Unstructured Grid")); } const char* mitk::CoreExtObjectFactory::GetSaveFileExtensions() { std::string fileExtension; this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension); return fileExtension.c_str(); } void mitk::CoreExtObjectFactory::RegisterIOFactories() { } void RegisterCoreExtObjectFactory() { static bool oneCoreExtObjectFactoryRegistered = false; if ( ! oneCoreExtObjectFactoryRegistered ) { MITK_DEBUG << "Registering CoreExtObjectFactory..." << std::endl; mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory(mitk::CoreExtObjectFactory::New()); oneCoreExtObjectFactoryRegistered = true; } } diff --git a/Modules/MitkExt/Algorithms/mitkExtractDirectedPlaneImageFilter.cpp.orig b/Modules/MitkExt/Algorithms/mitkExtractDirectedPlaneImageFilter.cpp.orig deleted file mode 100644 index fdc10a7bf1..0000000000 --- a/Modules/MitkExt/Algorithms/mitkExtractDirectedPlaneImageFilter.cpp.orig +++ /dev/null @@ -1,504 +0,0 @@ -/*========================================================================= - -Program: Medical Imaging & Interaction Toolkit -Language: C++ -Date: $Date$ -Version: $Revision: $ - -Copyright (c) German Cancer Research Center, Division of Medical and -Biological Informatics. All rights reserved. -See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. - -This software is distributed WITHOUT ANY WARRANTY; without even -the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR -PURPOSE. See the above copyright notices for more information. - -=========================================================================*/ - - -#include "mitkExtractDirectedPlaneImageFilter.h" -#include "mitkAbstractTransformGeometry.h" - -#include -#include -#include -#include -#include - -#include "pic2vtk.h" -#include "picimage.h" - - - -mitk::ExtractDirectedPlaneImageFilter::ExtractDirectedPlaneImageFilter() -: m_WorldGeometry(NULL) -{ - m_Reslicer = vtkImageReslice::New(); - m_TargetTimestep = 0; - m_InPlaneResampleExtentByGeometry = false; -} - -mitk::ExtractDirectedPlaneImageFilter::~ExtractDirectedPlaneImageFilter() -{ - m_WorldGeometry = NULL; - m_Reslicer->Delete(); -} - -void mitk::ExtractDirectedPlaneImageFilter::GenerateData() -{ - // A world geometry must be set... - if ( m_WorldGeometry == NULL ) - { - itkWarningMacro(<<"No world geometry has been set. Returning."); - return; - } - - Image *input = const_cast< ImageToImageFilter::InputImageType* >( this->GetInput() ); - input->Update(); - - if ( input == NULL ) - { - itkWarningMacro(<<"No input set."); - return; - } - - const TimeSlicedGeometry *inputTimeGeometry = input->GetTimeSlicedGeometry(); - if ( ( inputTimeGeometry == NULL ) - || ( inputTimeGeometry->GetTimeSteps() == 0 ) ) - { - itkWarningMacro(<<"Error reading input image geometry."); - return; - } - - // Get the target timestep; if none is set, use the lowest given. - unsigned int timestep = 0; - if ( ! m_TargetTimestep ) - { - ScalarType time = m_WorldGeometry->GetTimeBounds()[0]; - if ( time > ScalarTypeNumericTraits::NonpositiveMin() ) - { - timestep = inputTimeGeometry->MSToTimeStep( time ); - } - } - else timestep = m_TargetTimestep; - - if ( inputTimeGeometry->IsValidTime( timestep ) == false ) - { - itkWarningMacro(<<"This is not a valid timestep: "<IsVolumeSet( timestep ) ) - { - itkWarningMacro(<<"No volume data existent at given timestep "<GetLargestPossibleRegion(); - requestedRegion.SetIndex( 3, timestep ); - requestedRegion.SetSize( 3, 1 ); - requestedRegion.SetSize( 4, 1 ); - input->SetRequestedRegion( &requestedRegion ); - input->Update(); - - vtkImageData* inputData = input->GetVtkImageData( timestep ); - - if ( inputData == NULL ) - { - itkWarningMacro(<<"Could not extract vtk image data for given timestep"<GetSpacing( spacing ); - - // how big the area is in physical coordinates: widthInMM x heightInMM pixels - mitk::ScalarType widthInMM, heightInMM; - - // where we want to sample - Point3D origin; - Vector3D right, bottom, normal; - Vector3D rightInIndex, bottomInIndex; - - assert( input->GetTimeSlicedGeometry() == inputTimeGeometry ); - - // take transform of input image into account - Geometry3D* inputGeometry = inputTimeGeometry->GetGeometry3D( timestep ); - if ( inputGeometry == NULL ) - { - itkWarningMacro(<<"There is no Geometry3D at given timestep "<( m_WorldGeometry ) != NULL ) - { - const PlaneGeometry *planeGeometry = - static_cast< const PlaneGeometry * >( m_WorldGeometry ); - origin = planeGeometry->GetOrigin(); - right = planeGeometry->GetAxisVector( 0 ); - bottom = planeGeometry->GetAxisVector( 1 ); - normal = planeGeometry->GetNormal(); - - if ( m_InPlaneResampleExtentByGeometry ) - { - // Resampling grid corresponds to the current world geometry. This - // means that the spacing of the output 2D image depends on the - // currently selected world geometry, and *not* on the image itself. - - extent[0] = m_WorldGeometry->GetExtent( 0 ); - extent[1] = m_WorldGeometry->GetExtent( 1 ); - } - else - { - // Resampling grid corresponds to the input geometry. This means that - // the spacing of the output 2D image is directly derived from the - // associated input image, regardless of the currently selected world - // geometry. - inputGeometry->WorldToIndex( origin, right, rightInIndex ); - inputGeometry->WorldToIndex( origin, bottom, bottomInIndex ); - extent[0] = rightInIndex.GetNorm(); - extent[1] = bottomInIndex.GetNorm(); - } - - // Get the extent of the current world geometry and calculate resampling - // spacing therefrom. - widthInMM = m_WorldGeometry->GetExtentInMM( 0 ); - heightInMM = m_WorldGeometry->GetExtentInMM( 1 ); - - mmPerPixel[0] = widthInMM / extent[0]; - mmPerPixel[1] = heightInMM / extent[1]; - - right.Normalize(); - bottom.Normalize(); - normal.Normalize(); - - //origin += right * ( mmPerPixel[0] * 0.5 ); - //origin += bottom * ( mmPerPixel[1] * 0.5 ); - - //widthInMM -= mmPerPixel[0]; - //heightInMM -= mmPerPixel[1]; - - // Use inverse transform of the input geometry for reslicing the 3D image - m_Reslicer->SetResliceTransform( - inputGeometry->GetVtkTransform()->GetLinearInverse() ); - - // Set background level to TRANSLUCENT (see Geometry2DDataVtkMapper3D) - m_Reslicer->SetBackgroundLevel( -32768 ); - - // Check if a reference geometry does exist (as would usually be the case for - // PlaneGeometry). - // Note: this is currently not strictly required, but could facilitate - // correct plane clipping. - if ( m_WorldGeometry->GetReferenceGeometry() ) - { - // Calculate the actual bounds of the transformed plane clipped by the - // dataset bounding box; this is required for drawing the texture at the - // correct position during 3D mapping. - boundsInitialized = this->CalculateClippedPlaneBounds( - m_WorldGeometry->GetReferenceGeometry(), planeGeometry, bounds ); - } - } - - // Do we have an AbstractTransformGeometry? - else if ( dynamic_cast< const AbstractTransformGeometry * >( m_WorldGeometry ) ) - { - const mitk::AbstractTransformGeometry* abstractGeometry = - dynamic_cast< const AbstractTransformGeometry * >(m_WorldGeometry); - - extent[0] = abstractGeometry->GetParametricExtent(0); - extent[1] = abstractGeometry->GetParametricExtent(1); - - widthInMM = abstractGeometry->GetParametricExtentInMM(0); - heightInMM = abstractGeometry->GetParametricExtentInMM(1); - - mmPerPixel[0] = widthInMM / extent[0]; - mmPerPixel[1] = heightInMM / extent[1]; - - origin = abstractGeometry->GetPlane()->GetOrigin(); - - right = abstractGeometry->GetPlane()->GetAxisVector(0); - right.Normalize(); - - bottom = abstractGeometry->GetPlane()->GetAxisVector(1); - bottom.Normalize(); - - normal = abstractGeometry->GetPlane()->GetNormal(); - normal.Normalize(); - - // Use a combination of the InputGeometry *and* the possible non-rigid - // AbstractTransformGeometry for reslicing the 3D Image - vtkGeneralTransform *composedResliceTransform = vtkGeneralTransform::New(); - composedResliceTransform->Identity(); - composedResliceTransform->Concatenate( - inputGeometry->GetVtkTransform()->GetLinearInverse() ); - composedResliceTransform->Concatenate( - abstractGeometry->GetVtkAbstractTransform() - ); - - m_Reslicer->SetResliceTransform( composedResliceTransform ); - - // Set background level to BLACK instead of translucent, to avoid - // boundary artifacts (see Geometry2DDataVtkMapper3D) - m_Reslicer->SetBackgroundLevel( -1023 ); - composedResliceTransform->Delete(); - } - else - { - itkWarningMacro(<<"World Geometry has to be a PlaneGeometry or an AbstractTransformGeometry."); - return; - } - - // Make sure that the image to be resliced has a certain minimum size. - if ( (extent[0] <= 2) && (extent[1] <= 2) ) - { - itkWarningMacro(<<"Image is too small to be resliced..."); - return; - } - - vtkImageChangeInformation * unitSpacingImageFilter = vtkImageChangeInformation::New() ; - unitSpacingImageFilter->SetOutputSpacing( 1.0, 1.0, 1.0 ); - unitSpacingImageFilter->SetInput( inputData ); - - m_Reslicer->SetInput( unitSpacingImageFilter->GetOutput() ); - unitSpacingImageFilter->Delete(); - - //m_Reslicer->SetInput( inputData ); - - m_Reslicer->SetOutputDimensionality( 2 ); - m_Reslicer->SetOutputOrigin( 0.0, 0.0, 0.0 ); - - Vector2D pixelsPerMM; - pixelsPerMM[0] = 1.0 / mmPerPixel[0]; - pixelsPerMM[1] = 1.0 / mmPerPixel[1]; - - //calulate the originArray and the orientations for the reslice-filter - double originArray[3]; - itk2vtk( origin, originArray ); - - m_Reslicer->SetResliceAxesOrigin( originArray ); - - double cosines[9]; - - // direction of the X-axis of the sampled result - vnl2vtk( right.Get_vnl_vector(), cosines ); - - // direction of the Y-axis of the sampled result - vnl2vtk( bottom.Get_vnl_vector(), cosines + 3 ); - - // normal of the plane - vnl2vtk( normal.Get_vnl_vector(), cosines + 6 ); - - m_Reslicer->SetResliceAxesDirectionCosines( cosines ); - - // Determine output extent for reslicing - ScalarType size[2]; - size[0] = (bounds[1] - bounds[0]) / mmPerPixel[0]; - size[1] = (bounds[3] - bounds[2]) / mmPerPixel[1]; - - int xMin, xMax, yMin, yMax; - if ( boundsInitialized ) - { - xMin = static_cast< int >( bounds[0] / mmPerPixel[0] );//+ 0.5 ); - xMax = static_cast< int >( bounds[1] / mmPerPixel[0] );//+ 0.5 ); - yMin = static_cast< int >( bounds[2] / mmPerPixel[1] );//+ 0.5); - yMax = static_cast< int >( bounds[3] / mmPerPixel[1] );//+ 0.5 ); - } - else - { - // If no reference geometry is available, we also don't know about the - // maximum plane size; so the overlap is just ignored - - xMin = yMin = 0; - xMax = static_cast< int >( extent[0] - pixelsPerMM[0] );//+ 0.5 ); - yMax = static_cast< int >( extent[1] - pixelsPerMM[1] );//+ 0.5 ); - } - - m_Reslicer->SetOutputSpacing( mmPerPixel[0], mmPerPixel[1], 1.0 ); - // xMax and yMax are meant exclusive until now, whereas - // SetOutputExtent wants an inclusive bound. Thus, we need - // to subtract 1. - m_Reslicer->SetOutputExtent( xMin, xMax-1, yMin, yMax-1, 0, 1 ); - - // Do the reslicing. Modified() is called to make sure that the reslicer is - // executed even though the input geometry information did not change; this - // is necessary when the input /em data, but not the /em geometry changes. - m_Reslicer->Modified(); - m_Reslicer->ReleaseDataFlagOn(); - - m_Reslicer->Update(); - - // 1. Check the result - vtkImageData* reslicedImage = m_Reslicer->GetOutput(); - - mitkIpPicDescriptor *pic = Pic2vtk::convert( reslicedImage ); - - if((reslicedImage == NULL) || (reslicedImage->GetDataDimension() < 1)) - { - itkWarningMacro(<<"Reslicer returned empty image"); - return; - } - - unsigned int dimensions[2]; - dimensions[0] = (unsigned int)extent[0]; dimensions[1] = (unsigned int)extent[1]; - Vector3D spacingVector; - FillVector3D(spacingVector, mmPerPixel[0], mmPerPixel[1], 1.0); - - mitk::Image::Pointer resultImage = this->GetOutput(); - resultImage->Initialize( pic ); - resultImage->SetSpacing( spacingVector ); - resultImage->SetPicVolume( pic ); - - mitkIpPicFree(pic); - - /*unsigned int dimensions[2]; - dimensions[0] = (unsigned int)extent[0]; dimensions[1] = (unsigned int)extent[1]; - Vector3D spacingVector; - FillVector3D(spacingVector, mmPerPixel[0], mmPerPixel[1], 1.0); - - mitk::Image::Pointer resultImage = this->GetOutput(); - resultImage->Initialize(m_Reslicer->GetOutput()); - resultImage->Initialize(inputImage->GetPixelType(), 2, dimensions); - resultImage->SetSpacing(spacingVector); - resultImage->SetSlice(m_Reslicer->GetOutput());*/ -} - - -void mitk::ExtractDirectedPlaneImageFilter::GenerateOutputInformation() -{ - Superclass::GenerateOutputInformation(); -} - - -bool mitk::ExtractDirectedPlaneImageFilter -::CalculateClippedPlaneBounds( const Geometry3D *boundingGeometry, - const PlaneGeometry *planeGeometry, vtkFloatingPointType *bounds ) -{ - // Clip the plane with the bounding geometry. To do so, the corner points - // of the bounding box are transformed by the inverse transformation - // matrix, and the transformed bounding box edges derived therefrom are - // clipped with the plane z=0. The resulting min/max values are taken as - // bounds for the image reslicer. - const BoundingBox *boundingBox = boundingGeometry->GetBoundingBox(); - - BoundingBox::PointType bbMin = boundingBox->GetMinimum(); - BoundingBox::PointType bbMax = boundingBox->GetMaximum(); - BoundingBox::PointType bbCenter = boundingBox->GetCenter(); - - vtkPoints *points = vtkPoints::New(); - if(boundingGeometry->GetImageGeometry()) - { - points->InsertPoint( 0, bbMin[0]-0.5, bbMin[1]-0.5, bbMin[2]-0.5 ); - points->InsertPoint( 1, bbMin[0]-0.5, bbMin[1]-0.5, bbMax[2]-0.5 ); - points->InsertPoint( 2, bbMin[0]-0.5, bbMax[1]-0.5, bbMax[2]-0.5 ); - points->InsertPoint( 3, bbMin[0]-0.5, bbMax[1]-0.5, bbMin[2]-0.5 ); - points->InsertPoint( 4, bbMax[0]-0.5, bbMin[1]-0.5, bbMin[2]-0.5 ); - points->InsertPoint( 5, bbMax[0]-0.5, bbMin[1]-0.5, bbMax[2]-0.5 ); - points->InsertPoint( 6, bbMax[0]-0.5, bbMax[1]-0.5, bbMax[2]-0.5 ); - points->InsertPoint( 7, bbMax[0]-0.5, bbMax[1]-0.5, bbMin[2]-0.5 ); - } - else - { - points->InsertPoint( 0, bbMin[0], bbMin[1], bbMin[2] ); - points->InsertPoint( 1, bbMin[0], bbMin[1], bbMax[2] ); - points->InsertPoint( 2, bbMin[0], bbMax[1], bbMax[2] ); - points->InsertPoint( 3, bbMin[0], bbMax[1], bbMin[2] ); - points->InsertPoint( 4, bbMax[0], bbMin[1], bbMin[2] ); - points->InsertPoint( 5, bbMax[0], bbMin[1], bbMax[2] ); - points->InsertPoint( 6, bbMax[0], bbMax[1], bbMax[2] ); - points->InsertPoint( 7, bbMax[0], bbMax[1], bbMin[2] ); - } - - vtkPoints *newPoints = vtkPoints::New(); - - vtkTransform *transform = vtkTransform::New(); - transform->Identity(); - transform->Concatenate( - planeGeometry->GetVtkTransform()->GetLinearInverse() - ); - - transform->Concatenate( boundingGeometry->GetVtkTransform() ); - - transform->TransformPoints( points, newPoints ); - transform->Delete(); - - bounds[0] = bounds[2] = 10000000.0; - bounds[1] = bounds[3] = -10000000.0; - bounds[4] = bounds[5] = 0.0; - - this->LineIntersectZero( newPoints, 0, 1, bounds ); - this->LineIntersectZero( newPoints, 1, 2, bounds ); - this->LineIntersectZero( newPoints, 2, 3, bounds ); - this->LineIntersectZero( newPoints, 3, 0, bounds ); - this->LineIntersectZero( newPoints, 0, 4, bounds ); - this->LineIntersectZero( newPoints, 1, 5, bounds ); - this->LineIntersectZero( newPoints, 2, 6, bounds ); - this->LineIntersectZero( newPoints, 3, 7, bounds ); - this->LineIntersectZero( newPoints, 4, 5, bounds ); - this->LineIntersectZero( newPoints, 5, 6, bounds ); - this->LineIntersectZero( newPoints, 6, 7, bounds ); - this->LineIntersectZero( newPoints, 7, 4, bounds ); - - // clean up vtk data - points->Delete(); - newPoints->Delete(); - - if ( (bounds[0] > 9999999.0) || (bounds[2] > 9999999.0) - || (bounds[1] < -9999999.0) || (bounds[3] < -9999999.0) ) - { - return false; - } - else - { - // The resulting bounds must be adjusted by the plane spacing, since we - // we have so far dealt with index coordinates - const float *planeSpacing = planeGeometry->GetFloatSpacing(); - bounds[0] *= planeSpacing[0]; - bounds[1] *= planeSpacing[0]; - bounds[2] *= planeSpacing[1]; - bounds[3] *= planeSpacing[1]; - bounds[4] *= planeSpacing[2]; - bounds[5] *= planeSpacing[2]; - return true; - } -} - -bool mitk::ExtractDirectedPlaneImageFilter -::LineIntersectZero( vtkPoints *points, int p1, int p2, - vtkFloatingPointType *bounds ) -{ - vtkFloatingPointType point1[3]; - vtkFloatingPointType point2[3]; - points->GetPoint( p1, point1 ); - points->GetPoint( p2, point2 ); - - if ( (point1[2] * point2[2] <= 0.0) && (point1[2] != point2[2]) ) - { - double x, y; - x = ( point1[0] * point2[2] - point1[2] * point2[0] ) / ( point2[2] - point1[2] ); - y = ( point1[1] * point2[2] - point1[2] * point2[1] ) / ( point2[2] - point1[2] ); - - if ( x < bounds[0] ) { bounds[0] = x; } - if ( x > bounds[1] ) { bounds[1] = x; } - if ( y < bounds[2] ) { bounds[2] = y; } - if ( y > bounds[3] ) { bounds[3] = y; } - bounds[4] = bounds[5] = 0.0; - return true; - } - return false; -} diff --git a/Modules/MitkExt/Rendering/vtkMitkOpenGLVolumeTextureMapper3D.cpp b/Modules/MitkExt/Rendering/vtkMitkOpenGLVolumeTextureMapper3D.cpp index 13e0609f70..51830c1628 100644 --- a/Modules/MitkExt/Rendering/vtkMitkOpenGLVolumeTextureMapper3D.cpp +++ b/Modules/MitkExt/Rendering/vtkMitkOpenGLVolumeTextureMapper3D.cpp @@ -1,2425 +1,2426 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2009-07-14 19:11:20 +0200 (Tue, 14 Jul 2009) $ Version: $Revision: 18127 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifdef _OPENMP #include #endif #include "vtkWindows.h" #include "vtkMitkOpenGLVolumeTextureMapper3D.h" #include "mitkCommon.h" #define GPU_INFO MITK_INFO("mapper.vr") #define GPU_WARN MITK_WARN("mapper.vr") #include "vtkImageData.h" #include "vtkMatrix4x4.h" +#include "vtkDataArray.h" #include "vtkObjectFactory.h" #include "vtkPlane.h" #include "vtkPlaneCollection.h" #include "vtkPointData.h" #include "vtkRenderWindow.h" #include "vtkRenderer.h" #include "vtkTimerLog.h" #include "vtkVolumeProperty.h" #include "vtkTransform.h" #include "vtkLightCollection.h" #include "vtkLight.h" #include "vtkCamera.h" #include "vtkMath.h" #include "vtkOpenGLExtensionManager.h" #include "vtkgl.h" #include "vtkOpenGLRenderWindow.h" #define myGL_COMPRESSED_RGB_S3TC_DXT1_EXT 0x83F0 #define myGL_COMPRESSED_LUMINANCE_ALPHA_LATC2_EXT 0x8C72 #define myGL_COMPRESSED_RGBA_S3TC_DXT5_EXT 0x83F3 const char *vtkMitkVolumeTextureMapper3D_FourDependentShadeFP = "!!ARBfp1.0\n" //# We need some temporary variables "TEMP index, normal, finalColor;\n" "TEMP temp,temp1, temp2, temp3,temp4; \n" "TEMP sampleColor;\n" "TEMP ndotl, ndoth, ndotv; \n" "TEMP lightInfo, lightResult;\n" //# We are going to use the first //# texture coordinate "ATTRIB tex0 = fragment.texcoord[0];\n" //# This is the lighting information "PARAM lightDirection = program.local[0];\n" "PARAM halfwayVector = program.local[1];\n" "PARAM coefficient = program.local[2];\n" "PARAM lightDiffColor = program.local[3]; \n" "PARAM lightSpecColor = program.local[4]; \n" "PARAM viewVector = program.local[5];\n" "PARAM constants = program.local[6];\n" //# This is our output color "OUTPUT out = result.color;\n" //# Look up the gradient direction //# in the third volume "TEX temp2, tex0, texture[0], 3D;\n" //# This normal is stored 0 to 1, change to -1 to 1 //# by multiplying by 2.0 then adding -1.0. "MAD normal, temp2, constants.x, constants.y;\n" "DP3 temp4, normal, normal;\n" "RSQ temp, temp4.x;\n" "MUL normal, normal, temp;\n" //"RCP temp4,temp.x;\n" //"MUL temp2.w,temp2.w,temp4.x;\n" //"MUL_SAT temp2.w,temp2.w,6.0;\n" "TEX sampleColor, tex0, texture[1], 3D;\n" //# Take the dot product of the light //# direction and the normal "DP3 ndotl, normal, lightDirection;\n" //# Take the dot product of the halfway //# vector and the normal "DP3 ndoth, normal, halfwayVector;\n" "DP3 ndotv, normal, viewVector;\n" //# flip if necessary for two sided lighting "MUL temp3, ndotl, constants.y; \n" "CMP ndotl, ndotv, ndotl, temp3;\n" "MUL temp3, ndoth, constants.y; \n" "CMP ndoth, ndotv, ndoth, temp3;\n" //# put the pieces together for a LIT operation "MOV lightInfo.x, ndotl.x; \n" "MOV lightInfo.y, ndoth.x; \n" "MOV lightInfo.w, coefficient.w; \n" //# compute the lighting "LIT lightResult, lightInfo;\n" //# COLOR FIX "MUL lightResult, lightResult, 4.0;\n" //# This is the ambient contribution "MUL finalColor, coefficient.x, sampleColor;\n" //# This is the diffuse contribution "MUL temp3, lightDiffColor, sampleColor;\n" "MUL temp3, temp3, lightResult.y;\n" "ADD finalColor, finalColor, temp3;\n" //# This is th specular contribution "MUL temp3, lightSpecColor, lightResult.z; \n" //# Add specular into result so far, and replace //# with the original alpha. "ADD out, finalColor, temp3;\n" "MOV out.w, temp2.w;\n" "END\n"; const char *vtkMitkVolumeTextureMapper3D_OneComponentShadeFP = "!!ARBfp1.0\n" //# This is the fragment program for one //# component data with shading //# We need some temporary variables "TEMP index, normal, finalColor;\n" "TEMP temp,temp1, temp2, temp3,temp4; \n" "TEMP sampleColor;\n" "TEMP ndotl, ndoth, ndotv; \n" "TEMP lightInfo, lightResult;\n" //# We are going to use the first //# texture coordinate "ATTRIB tex0 = fragment.texcoord[0];\n" //# This is the lighting information "PARAM lightDirection = program.local[0];\n" "PARAM halfwayVector = program.local[1];\n" "PARAM coefficient = program.local[2];\n" "PARAM lightDiffColor = program.local[3]; \n" "PARAM lightSpecColor = program.local[4]; \n" "PARAM viewVector = program.local[5];\n" "PARAM constants = program.local[6];\n" //# This is our output color "OUTPUT out = result.color;\n" //# Look up the gradient direction //# in the third volume "TEX temp2, tex0, texture[0], 3D;\n" // Gradient Compution //# Look up the scalar value / gradient //# magnitude in the first volume //"TEX temp1, tex0, texture[0], 3D;\n" /* "ADD temp3,tex0,{-0.005,0,0};\n" "TEX temp2,temp3, texture[0], 3D;\n" //"ADD temp3,tex0,{ 0.005,0,0};\n" //"TEX temp1,temp3, texture[0], 3D;\n" "SUB normal.x,temp2.y,temp1.y;\n" "ADD temp3,tex0,{0,-0.005,0};\n" "TEX temp2,temp3, texture[0], 3D;\n" //"ADD temp3,tex0,{0, 0.005,0};\n" //"TEX temp1,temp3, texture[0], 3D;\n" "SUB normal.y,temp2.y,temp1.y;\n" "ADD temp3,tex0,{0,0,-0.005};\n" "TEX temp2,temp3, texture[0], 3D;\n" //"ADD temp3,tex0,{0,0, 0.005};\n" //"TEX temp1,temp3, texture[0], 3D;\n" "SUB normal.z,temp2.y,temp1.y;\n" */ //"MOV normal,{1,1,1};\n" "MOV index.x,temp2.a;\n" //# This normal is stored 0 to 1, change to -1 to 1 //# by multiplying by 2.0 then adding -1.0. "MAD normal, temp2, constants.x, constants.y;\n" //# Swizzle this to use (a,r) as texture //# coordinates //"SWZ index, temp1, a, r, 1, 1;\n" //# Use this coordinate to look up a //# final color in the third texture //# (this is a 2D texture) "DP3 temp4, normal, normal;\n" "RSQ temp, temp4.x;\n" "RCP temp4,temp.x;\n" "MUL normal, normal, temp;\n" "MOV index.y, temp4.x;\n" "TEX sampleColor, index, texture[1], 2D;\n" //"MUL sampleColor.w,sampleColor.w,temp4.x;\n" //# Take the dot product of the light //# direction and the normal "DP3 ndotl, normal, lightDirection;\n" //# Take the dot product of the halfway //# vector and the normal "DP3 ndoth, normal, halfwayVector;\n" "DP3 ndotv, normal, viewVector;\n" //# flip if necessary for two sided lighting "MUL temp3, ndotl, constants.y; \n" "CMP ndotl, ndotv, ndotl, temp3;\n" "MUL temp3, ndoth, constants.y; \n" "CMP ndoth, ndotv, ndoth, temp3;\n" //# put the pieces together for a LIT operation "MOV lightInfo.x, ndotl.x; \n" "MOV lightInfo.y, ndoth.x; \n" "MOV lightInfo.w, coefficient.w; \n" //# compute the lighting "LIT lightResult, lightInfo;\n" //# COLOR FIX "MUL lightResult, lightResult, 4.0;\n" //# This is the ambient contribution "MUL finalColor, coefficient.x, sampleColor;\n" //# This is the diffuse contribution "MUL temp3, lightDiffColor, sampleColor;\n" "MUL temp3, temp3, lightResult.y;\n" "ADD finalColor, finalColor, temp3;\n" //# This is th specular contribution "MUL temp3, lightSpecColor, lightResult.z; \n" //# Add specular into result so far, and replace //# with the original alpha. "ADD out, finalColor, temp3;\n" "MOV out.w, sampleColor.w;\n" "END\n"; //#ifndef VTK_IMPLEMENT_MESA_CXX vtkCxxRevisionMacro(vtkMitkOpenGLVolumeTextureMapper3D, "$Revision: 1.21 $"); vtkStandardNewMacro(vtkMitkOpenGLVolumeTextureMapper3D); //#endif vtkMitkOpenGLVolumeTextureMapper3D::vtkMitkOpenGLVolumeTextureMapper3D() { //GPU_INFO << "vtkMitkOpenGLVolumeTextureMapper3D"; this->Initialized = 0; this->Volume1Index = 0; this->Volume2Index = 0; this->Volume3Index = 0; this->ColorLookupIndex = 0; this->AlphaLookupIndex = 0; this->RenderWindow = NULL; this->SupportsCompressedTexture = false; prgOneComponentShade = 0; prgRGBAShade = 0; } vtkMitkOpenGLVolumeTextureMapper3D::~vtkMitkOpenGLVolumeTextureMapper3D() { //GPU_INFO << "~vtkMitkOpenGLVolumeTextureMapper3D"; if(prgOneComponentShade) vtkgl::DeleteProgramsARB( 1, &prgOneComponentShade ); if(prgRGBAShade) vtkgl::DeleteProgramsARB( 1, &prgRGBAShade ); } // Release the graphics resources used by this texture. void vtkMitkOpenGLVolumeTextureMapper3D::ReleaseGraphicsResources(vtkWindow *renWin) { //GPU_INFO << "ReleaseGraphicsResources"; if (( this->Volume1Index || this->Volume2Index || this->Volume3Index || this->ColorLookupIndex) && renWin) { static_cast(renWin)->MakeCurrent(); #ifdef GL_VERSION_1_1 // free any textures this->DeleteTextureIndex( &this->Volume1Index ); this->DeleteTextureIndex( &this->Volume2Index ); this->DeleteTextureIndex( &this->Volume3Index ); this->DeleteTextureIndex( &this->ColorLookupIndex ); this->DeleteTextureIndex( &this->AlphaLookupIndex ); #endif } this->Volume1Index = 0; this->Volume2Index = 0; this->Volume3Index = 0; this->ColorLookupIndex = 0; this->RenderWindow = NULL; this->SupportsCompressedTexture=false; this->SupportsNonPowerOfTwoTextures=false; this->Modified(); } void vtkMitkOpenGLVolumeTextureMapper3D::Render(vtkRenderer *ren, vtkVolume *vol) { //GPU_INFO << "Render"; ren->GetRenderWindow()->MakeCurrent(); if ( !this->Initialized ) { //this->Initialize(); this->Initialize(ren); } if ( !this->RenderPossible ) { vtkErrorMacro( "required extensions not supported" ); return; } vtkMatrix4x4 *matrix = vtkMatrix4x4::New(); vtkPlaneCollection *clipPlanes; vtkPlane *plane; int numClipPlanes = 0; double planeEquation[4]; // build transformation vol->GetMatrix(matrix); matrix->Transpose(); glPushAttrib(GL_ENABLE_BIT | GL_COLOR_BUFFER_BIT | GL_STENCIL_BUFFER_BIT | GL_DEPTH_BUFFER_BIT | GL_POLYGON_BIT | GL_TEXTURE_BIT); int i; // Use the OpenGL clip planes clipPlanes = this->ClippingPlanes; if ( clipPlanes ) { numClipPlanes = clipPlanes->GetNumberOfItems(); if (numClipPlanes > 6) { vtkErrorMacro(<< "OpenGL guarantees only 6 additional clipping planes"); } for (i = 0; i < numClipPlanes; i++) { glEnable(static_cast(GL_CLIP_PLANE0+i)); plane = static_cast(clipPlanes->GetItemAsObject(i)); planeEquation[0] = plane->GetNormal()[0]; planeEquation[1] = plane->GetNormal()[1]; planeEquation[2] = plane->GetNormal()[2]; planeEquation[3] = -(planeEquation[0]*plane->GetOrigin()[0]+ planeEquation[1]*plane->GetOrigin()[1]+ planeEquation[2]*plane->GetOrigin()[2]); glClipPlane(static_cast(GL_CLIP_PLANE0+i),planeEquation); } } // insert model transformation glMatrixMode( GL_MODELVIEW ); glPushMatrix(); glMultMatrixd(matrix->Element[0]); glColor4f( 1.0, 1.0, 1.0, 1.0 ); // Turn lighting off - the polygon textures already have illumination glDisable( GL_LIGHTING ); vtkGraphicErrorMacro(ren->GetRenderWindow(),"Before actual render method"); this->RenderFP(ren,vol); // pop transformation matrix glMatrixMode( GL_MODELVIEW ); glPopMatrix(); matrix->Delete(); glPopAttrib(); } void vtkMitkOpenGLVolumeTextureMapper3D::RenderFP(vtkRenderer *ren, vtkVolume *vol) { //GPU_INFO << "RenderFP"; /* glAlphaFunc (GL_GREATER, static_cast(1.0/255.0)); glEnable (GL_ALPHA_TEST); */ glEnable( GL_BLEND ); glBlendFunc( GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA ); int components = this->GetInput()->GetNumberOfScalarComponents(); switch ( components ) { case 1: this->RenderOneIndependentShadeFP(ren,vol); break; case 4: this->RenderRGBAShadeFP(ren,vol); break; } vtkgl::ActiveTexture( vtkgl::TEXTURE2); glDisable( GL_TEXTURE_2D ); glDisable( vtkgl::TEXTURE_3D ); vtkgl::ActiveTexture( vtkgl::TEXTURE1); glDisable( GL_TEXTURE_2D ); glDisable( vtkgl::TEXTURE_3D ); vtkgl::ActiveTexture( vtkgl::TEXTURE0); glDisable( GL_TEXTURE_2D ); glDisable( vtkgl::TEXTURE_3D ); glDisable( GL_BLEND ); } void vtkMitkOpenGLVolumeTextureMapper3D::DeleteTextureIndex( GLuint *index ) { //GPU_INFO << "DeleteTextureIndex"; if (glIsTexture(*index)) { GLuint tempIndex; tempIndex = *index; glDeleteTextures(1, &tempIndex); *index = 0; } } void vtkMitkOpenGLVolumeTextureMapper3D::CreateTextureIndex( GLuint *index ) { //GPU_INFO << "CreateTextureIndex"; GLuint tempIndex=0; glGenTextures(1, &tempIndex); *index = static_cast(tempIndex); } void vtkMitkOpenGLVolumeTextureMapper3D::RenderPolygons( vtkRenderer *ren, vtkVolume *vol, int stages[4] ) { //GPU_INFO << "RenderPolygons"; vtkRenderWindow *renWin = ren->GetRenderWindow(); if ( renWin->CheckAbortStatus() ) { return; } double bounds[27][6]; float distance2[27]; int numIterations; int i, j, k; // No cropping case - render the whole thing if ( !this->Cropping ) { // Use the input data bounds - we'll take care of the volume's // matrix during rendering this->GetInput()->GetBounds(bounds[0]); numIterations = 1; } // Simple cropping case - render the subvolume else if ( this->CroppingRegionFlags == 0x2000 ) { this->GetCroppingRegionPlanes(bounds[0]); numIterations = 1; } // Complex cropping case - render each region in back-to-front order else { // Get the camera position double camPos[4]; ren->GetActiveCamera()->GetPosition(camPos); double volBounds[6]; this->GetInput()->GetBounds(volBounds); // Pass camera through inverse volume matrix // so that we are in the same coordinate system vtkMatrix4x4 *volMatrix = vtkMatrix4x4::New(); vol->GetMatrix( volMatrix ); camPos[3] = 1.0; volMatrix->Invert(); volMatrix->MultiplyPoint( camPos, camPos ); volMatrix->Delete(); if ( camPos[3] ) { camPos[0] /= camPos[3]; camPos[1] /= camPos[3]; camPos[2] /= camPos[3]; } // These are the region limits for x (first four), y (next four) and // z (last four). The first region limit is the lower bound for // that axis, the next two are the region planes along that axis, and // the final one in the upper bound for that axis. float limit[12]; for ( i = 0; i < 3; i++ ) { limit[i*4 ] = volBounds[i*2]; limit[i*4+1] = this->CroppingRegionPlanes[i*2]; limit[i*4+2] = this->CroppingRegionPlanes[i*2+1]; limit[i*4+3] = volBounds[i*2+1]; } // For each of the 27 possible regions, find out if it is enabled, // and if so, compute the bounds and the distance from the camera // to the center of the region. int numRegions = 0; int region; for ( region = 0; region < 27; region++ ) { int regionFlag = 1<CroppingRegionFlags & regionFlag ) { // what is the coordinate in the 3x3x3 grid int loc[3]; loc[0] = region%3; loc[1] = (region/3)%3; loc[2] = (region/9)%3; // compute the bounds and center float center[3]; for ( i = 0; i < 3; i++ ) { bounds[numRegions][i*2 ] = limit[4*i+loc[i]]; bounds[numRegions][i*2+1] = limit[4*i+loc[i]+1]; center[i] = (bounds[numRegions][i*2 ] + bounds[numRegions][i*2+1])/2.0; } // compute the distance squared to the center distance2[numRegions] = (camPos[0]-center[0])*(camPos[0]-center[0]) + (camPos[1]-center[1])*(camPos[1]-center[1]) + (camPos[2]-center[2])*(camPos[2]-center[2]); // we've added one region numRegions++; } } // Do a quick bubble sort on distance for ( i = 1; i < numRegions; i++ ) { for ( j = i; j > 0 && distance2[j] > distance2[j-1]; j-- ) { float tmpBounds[6]; float tmpDistance2; for ( k = 0; k < 6; k++ ) { tmpBounds[k] = bounds[j][k]; } tmpDistance2 = distance2[j]; for ( k = 0; k < 6; k++ ) { bounds[j][k] = bounds[j-1][k]; } distance2[j] = distance2[j-1]; for ( k = 0; k < 6; k++ ) { bounds[j-1][k] = tmpBounds[k]; } distance2[j-1] = tmpDistance2; } } numIterations = numRegions; } // loop over all regions we need to render for ( int loop = 0; loop < numIterations; loop++ ) { // Compute the set of polygons for this region // according to the bounds this->ComputePolygons( ren, vol, bounds[loop] ); // Loop over the polygons for ( i = 0; i < this->NumberOfPolygons; i++ ) { if ( renWin->CheckAbortStatus() ) { return; } float *ptr = this->PolygonBuffer + 36*i; glBegin( GL_TRIANGLE_FAN ); for ( j = 0; j < 6; j++ ) { if ( ptr[0] < 0.0 ) { break; } for ( k = 0; k < 4; k++ ) { if ( stages[k] ) { vtkgl::MultiTexCoord3fv( vtkgl::TEXTURE0 + k, ptr ); } } glVertex3fv( ptr+3 ); ptr += 6; } glEnd(); } } } // This method moves the scalars from the input volume into volume1 (and // possibly volume2) which are the 3D texture maps used for rendering. // // In the case where our volume is a power of two, the copy is done // directly. If we need to resample, then trilinear interpolation is used. // // A shift/scale is applied to the input scalar value to produce an 8 bit // value for the texture volume. // // When the input data is one component, the scalar value is placed in the // second component of the two component volume1. The first component is // filled in later with the gradient magnitude. // // When the input data is two component non-independent, the first component // of the input data is placed in the first component of volume1, and the // second component of the input data is placed in the third component of // volume1. Volume1 has three components - the second is filled in later with // the gradient magnitude. // // When the input data is four component non-independent, the first three // components of the input data are placed in volume1 (which has three // components), and the fourth component is placed in the second component // of volume2. The first component of volume2 is later filled in with the // gradient magnitude. template class ScalarGradientCompute { T *dataPtr; unsigned char *tmpPtr; unsigned char *tmpPtr2; int sizeX; int sizeY; int sizeZ; int sizeXY; int sizeXm1; int sizeYm1; int sizeZm1; int fullX; int fullY; int fullZ; int fullXY; int currentChunkStart; int currentChunkEnd; int offZ; float offset; float scale; public: ScalarGradientCompute( T *_dataPtr,unsigned char *_tmpPtr,unsigned char *_tmpPtr2,int _sizeX,int _sizeY,int _sizeZ,int _fullX,int _fullY,int _fullZ,float _offset,float _scale) { dataPtr=_dataPtr; tmpPtr=_tmpPtr; tmpPtr2=_tmpPtr2; sizeX=_sizeX; sizeY=_sizeY; sizeZ=_sizeZ; fullX=_fullX; fullY=_fullY; fullZ=_fullZ; offset=_offset; scale=_scale; sizeXY=sizeX*sizeY; sizeXm1=sizeX-1; sizeYm1=sizeY-1; sizeZm1=sizeZ-1; fullXY=fullX*fullY; } inline float sample(int x,int y,int z) { return float(dataPtr[ x + y * sizeX + z * sizeXY ]); } inline void fill(int x,int y,int z) { int doff = x + y * fullX + (z-offZ) * fullXY; tmpPtr[doff*4+0]= 0; tmpPtr[doff*4+1]= 0; tmpPtr[doff*4+2]= 0; tmpPtr[doff*4+3]= 0; /* tmpPtr2[doff*3+0]= 0; tmpPtr2[doff*3+1]= 0; tmpPtr2[doff*3+2]= 0; */ } inline int clamp(int x) { if(x<0) x=0; else if(x>255) x=255; return x; } inline void write(int x,int y,int z,float grayValue,float gx,float gy,float gz) { /* gx /= aspect[0]; gy /= aspect[1]; gz /= aspect[2]; */ // Compute the gradient magnitude int iGrayValue = static_cast( (grayValue + offset) * scale + 0.5f ); gx *= scale; gy *= scale; gz *= scale; float t = sqrtf( gx*gx + gy*gy + gz*gz ); if ( t > 0.01f ) { if( t < 2.0f ) { float fac = 2.0f/t; gx *= fac; gy *= fac; gz *= fac; } else if( t > 255.0f) { float fac = 255.0f/t; gx *= fac; gy *= fac; gz *= fac; } } else { gx=gy=gz=0.0f; } int nx = static_cast(0.5f*gx+127.5f); int ny = static_cast(0.5f*gy+127.5f); int nz = static_cast(0.5f*gz+127.5f); int doff = x + y * fullX + (z-offZ) * fullXY; //tmpPtr[doff*2+0]= 0; tmpPtr[doff*4+0]= clamp(nx); tmpPtr[doff*4+1]= clamp(ny); tmpPtr[doff*4+2]= clamp(nz); tmpPtr[doff*4+3]= clamp(iGrayValue); /* if( z == fullZ/2 ) if( y == fullY/2 ) MITK_INFO << x << " " << y << " " << z << " : " << iGrayValue << " : " << iGradient; */ } inline void compute(int x,int y,int z) { float grayValue = sample(x,y,z); float gx,gy,gz; gx = sample(x+1,y,z) - sample(x-1,y,z); gy = sample(x,y+1,z) - sample(x,y-1,z); gz = sample(x,y,z+1) - sample(x,y,z-1); write( x, y, z, grayValue, gx, gy, gz ); } inline void computeClamp(int x,int y,int z) { float grayValue = sample(x,y,z); float gx,gy,gz; if(x==0) gx = 2.0f * ( sample(x+1,y,z) - grayValue ); else if(x==sizeXm1) gx = 2.0f * ( grayValue - sample(x-1,y,z) ); else gx = sample(x+1,y,z) - sample(x-1,y,z); if(y==0) gy = 2.0f * ( sample(x,y+1,z) - grayValue ); else if(y==sizeYm1) gy = 2.0f * ( grayValue - sample(x,y-1,z) ); else gy = sample(x,y+1,z) - sample(x,y-1,z); if(z==0) gz = 2.0f * ( sample(x,y,z+1) - grayValue ); else if(z==sizeZm1) gz = 2.0f * ( grayValue - sample(x,y,z-1) ); else gz = sample(x,y,z+1) - sample(x,y,z-1); write( x, y, z, grayValue, gx, gy, gz ); } inline void compute1D(int y,int z) { int x; x=0; computeClamp(x,y,z); x++; while(x=sizeZ) fill2D(z); else compute2D(z); } } }; template void vtkVolumeTextureMapper3DComputeScalars( T *dataPtr, vtkMitkVolumeTextureMapper3D *me, float offset, float scale, GLuint volume1, GLuint /*volume2*/) { T *inPtr; // unsigned char *outPtr, *outPtr2; // int i, j, k; // int idx; int inputDimensions[3]; double inputSpacing[3]; vtkImageData *input = me->GetInput(); input->GetDimensions( inputDimensions ); input->GetSpacing( inputSpacing ); int outputDimensions[3]; float outputSpacing[3]; me->GetVolumeDimensions( outputDimensions ); me->GetVolumeSpacing( outputSpacing ); // int components = input->GetNumberOfScalarComponents(); // double wx, wy, wz; // double fx, fy, fz; // int x, y, z; double sampleRate[3]; sampleRate[0] = outputSpacing[0] / static_cast(inputSpacing[0]); sampleRate[1] = outputSpacing[1] / static_cast(inputSpacing[1]); sampleRate[2] = outputSpacing[2] / static_cast(inputSpacing[2]); int fullX = outputDimensions[0]; int fullY = outputDimensions[1]; int fullZ = outputDimensions[2]; int sizeX = inputDimensions[0]; int sizeY = inputDimensions[1]; int sizeZ = inputDimensions[2]; int chunkSize = 64; if(fullZ < chunkSize) chunkSize=fullZ; int numChunks = ( fullZ + (chunkSize-1) ) / chunkSize; inPtr = dataPtr; unsigned char *tmpPtr = new unsigned char[fullX*fullY*chunkSize*4]; unsigned char *tmpPtr2 = 0;//new unsigned char[fullX*fullY*chunkSize*3]; // For each Chunk { ScalarGradientCompute sgc(dataPtr,tmpPtr,tmpPtr2,sizeX,sizeY,sizeZ,fullX,fullY,fullZ,offset,scale); int currentChunk = 0; while(currentChunk < numChunks) { // MITK_INFO << "processing chunk " << currentChunk; int currentChunkStart = currentChunk * chunkSize; int currentChunkEnd = currentChunkStart + chunkSize - 1 ; if( currentChunkEnd > (fullZ-1) ) currentChunkEnd = (fullZ-1); int currentChunkSize = currentChunkEnd - currentChunkStart + 1; sgc.fillSlices( currentChunkStart , currentChunkEnd ); glBindTexture(vtkgl::TEXTURE_3D, volume1); vtkgl::TexSubImage3D(vtkgl::TEXTURE_3D,0,0,0,currentChunkStart,fullX,fullY,currentChunkSize,GL_RGBA,GL_UNSIGNED_BYTE,tmpPtr); /* glBindTexture(vtkgl::TEXTURE_3D, volume2); vtkgl::TexSubImage3D(vtkgl::TEXTURE_3D,0,0,0,currentChunkStart,fullX,fullY,currentChunkSize,GL_RGB,GL_UNSIGNED_BYTE,tmpPtr2); */ currentChunk ++; } } delete tmpPtr; // delete tmpPtr2; } class RGBACompute { unsigned char *dataPtr; unsigned char *tmpPtr; unsigned char *tmpPtr2; int sizeX; int sizeY; int sizeZ; int sizeXY; int sizeXm1; int sizeYm1; int sizeZm1; int fullX; int fullY; int fullZ; int fullXY; int currentChunkStart; int currentChunkEnd; int offZ; public: RGBACompute( unsigned char *_dataPtr,unsigned char *_tmpPtr,unsigned char *_tmpPtr2,int _sizeX,int _sizeY,int _sizeZ,int _fullX,int _fullY,int _fullZ) { dataPtr=_dataPtr; tmpPtr=_tmpPtr; tmpPtr2=_tmpPtr2; sizeX=_sizeX; sizeY=_sizeY; sizeZ=_sizeZ; fullX=_fullX; fullY=_fullY; fullZ=_fullZ; sizeXY=sizeX*sizeY; sizeXm1=sizeX-1; sizeYm1=sizeY-1; sizeZm1=sizeZ-1; fullXY=fullX*fullY; } inline int sample(int x,int y,int z) { return dataPtr[ ( x + y * sizeX + z * sizeXY ) * 4 +3 ]; } inline void fill(int x,int y,int z) { int doff = x + y * fullX + (z-offZ) * fullXY; tmpPtr[doff*4+0]= 0; tmpPtr[doff*4+1]= 0; tmpPtr[doff*4+2]= 0; tmpPtr[doff*4+3]= 0; tmpPtr2[doff*3+0]= 0; tmpPtr2[doff*3+1]= 0; tmpPtr2[doff*3+2]= 0; } inline int clamp(int x) { if(x<0) x=0; else if(x>255) x=255; return x; } inline void write(int x,int y,int z,int iGrayValue,int gx,int gy,int gz) { /* gx /= aspect[0]; gy /= aspect[1]; gz /= aspect[2]; */ int nx = static_cast(0.5f*gx+127.5f); int ny = static_cast(0.5f*gy+127.5f); int nz = static_cast(0.5f*gz+127.5f); int doff = x + y * fullX + (z-offZ) * fullXY; //tmpPtr[doff*2+0]= 0; tmpPtr[doff*4+0]= clamp(nx); tmpPtr[doff*4+1]= clamp(ny); tmpPtr[doff*4+2]= clamp(nz); tmpPtr[doff*4+3]= clamp(iGrayValue); int soff = x + y * sizeX + z * sizeXY; tmpPtr2[doff*3+0]= dataPtr[soff*4+0]; tmpPtr2[doff*3+1]= dataPtr[soff*4+1]; tmpPtr2[doff*3+2]= dataPtr[soff*4+2]; /* if( z == fullZ/2 ) if( y == fullY/2 ) MITK_INFO << x << " " << y << " " << z << " : " << iGrayValue << " : " << iGradient; */ } inline void compute(int x,int y,int z) { int grayValue = sample(x,y,z); int gx,gy,gz; gx = sample(x+1,y,z) - sample(x-1,y,z); gy = sample(x,y+1,z) - sample(x,y-1,z); gz = sample(x,y,z+1) - sample(x,y,z-1); write( x, y, z, grayValue, gx, gy, gz ); } inline void computeClamp(int x,int y,int z) { int grayValue = sample(x,y,z); int gx,gy,gz; if(x==0) gx = 2 * ( sample(x+1,y,z) - grayValue ); else if(x==sizeXm1) gx = 2 * ( grayValue - sample(x-1,y,z) ); else gx = sample(x+1,y,z) - sample(x-1,y,z); if(y==0) gy = 2 * ( sample(x,y+1,z) - grayValue ); else if(y==sizeYm1) gy = 2 * ( grayValue - sample(x,y-1,z) ); else gy = sample(x,y+1,z) - sample(x,y-1,z); if(z==0) gz = 2 * ( sample(x,y,z+1) - grayValue ); else if(z==sizeZm1) gz = 2 * ( grayValue - sample(x,y,z-1) ); else gz = sample(x,y,z+1) - sample(x,y,z-1); write( x, y, z, grayValue, gx, gy, gz ); } inline void compute1D(int y,int z) { int x=0; computeClamp(x,y,z); x++; while(x=sizeZ) fill2D(z); else compute2D(z); } } }; void vtkVolumeTextureMapper3DComputeRGBA( unsigned char *dataPtr, vtkMitkVolumeTextureMapper3D *me, GLuint volume1, GLuint volume2) { unsigned char *inPtr; // unsigned char *outPtr, *outPtr2; // int i, j, k; // int idx; int inputDimensions[3]; double inputSpacing[3]; vtkImageData *input = me->GetInput(); input->GetDimensions( inputDimensions ); input->GetSpacing( inputSpacing ); int outputDimensions[3]; float outputSpacing[3]; me->GetVolumeDimensions( outputDimensions ); me->GetVolumeSpacing( outputSpacing ); int components = input->GetNumberOfScalarComponents(); MITK_INFO << "components are " << components; // double wx, wy, wz; // double fx, fy, fz; // int x, y, z; double sampleRate[3]; sampleRate[0] = outputSpacing[0] / static_cast(inputSpacing[0]); sampleRate[1] = outputSpacing[1] / static_cast(inputSpacing[1]); sampleRate[2] = outputSpacing[2] / static_cast(inputSpacing[2]); int fullX = outputDimensions[0]; int fullY = outputDimensions[1]; int fullZ = outputDimensions[2]; int sizeX = inputDimensions[0]; int sizeY = inputDimensions[1]; int sizeZ = inputDimensions[2]; int chunkSize = 64; if(fullZ < chunkSize) chunkSize=fullZ; int numChunks = ( fullZ + (chunkSize-1) ) / chunkSize; inPtr = dataPtr; unsigned char *tmpPtr = new unsigned char[fullX*fullY*chunkSize*4]; unsigned char *tmpPtr2 = new unsigned char[fullX*fullY*chunkSize*3]; // For each Chunk { RGBACompute sgc(dataPtr,tmpPtr,tmpPtr2,sizeX,sizeY,sizeZ,fullX,fullY,fullZ); int currentChunk = 0; while(currentChunk < numChunks) { // MITK_INFO << "processing chunk " << currentChunk; int currentChunkStart = currentChunk * chunkSize; int currentChunkEnd = currentChunkStart + chunkSize - 1 ; if( currentChunkEnd > (fullZ-1) ) currentChunkEnd = (fullZ-1); int currentChunkSize = currentChunkEnd - currentChunkStart + 1; sgc.fillSlices( currentChunkStart , currentChunkEnd ); glBindTexture(vtkgl::TEXTURE_3D, volume1); vtkgl::TexSubImage3D(vtkgl::TEXTURE_3D,0,0,0,currentChunkStart,fullX,fullY,currentChunkSize,GL_RGBA,GL_UNSIGNED_BYTE,tmpPtr); glBindTexture(vtkgl::TEXTURE_3D, volume2); vtkgl::TexSubImage3D(vtkgl::TEXTURE_3D,0,0,0,currentChunkStart,fullX,fullY,currentChunkSize,GL_RGB,GL_UNSIGNED_BYTE,tmpPtr2); currentChunk ++; } } delete tmpPtr; delete tmpPtr2; } //----------------------------------------------------------------------------- void vtkMitkOpenGLVolumeTextureMapper3D::ComputeVolumeDimensions() { // Get the image data vtkImageData *input = this->GetInput(); // How big does the Volume need to be? int dim[3]; input->GetDimensions(dim); int powerOfTwoDim[3]; if(this->SupportsNonPowerOfTwoTextures) { for ( int i = 0; i < 3; i++ ) powerOfTwoDim[i]=(dim[i]+1)&~1; // MITK_INFO << "using non-power-two even textures (" << (1.0-double(dim[0]*dim[1]*dim[2])/double(powerOfTwoDim[0]*powerOfTwoDim[1]*powerOfTwoDim[2])) * 100.0 << "% memory wasted)"; } else { for ( int i = 0; i < 3; i++ ) { powerOfTwoDim[i] = 4; while ( powerOfTwoDim[i] < dim[i] ) powerOfTwoDim[i] *= 2; } MITK_WARN << "using power-two textures (" << (1.0-double(dim[0]*dim[1]*dim[2])/double(powerOfTwoDim[0]*powerOfTwoDim[1]*powerOfTwoDim[2])) * 100.0 << "% memory wasted)"; } // Save the volume size this->VolumeDimensions[0] = powerOfTwoDim[0]; this->VolumeDimensions[1] = powerOfTwoDim[1]; this->VolumeDimensions[2] = powerOfTwoDim[2]; // What is the spacing? double spacing[3]; input->GetSpacing(spacing); // Compute the new spacing this->VolumeSpacing[0] = ( dim[0] -1.01)*spacing[0] / static_cast(this->VolumeDimensions[0]-1); this->VolumeSpacing[1] = ( dim[1] -1.01)*spacing[1] / static_cast(this->VolumeDimensions[1]-1); this->VolumeSpacing[2] = ((dim[2])-1.01)*spacing[2] / static_cast(this->VolumeDimensions[2]-1); } //----------------------------------------------------------------------------- bool vtkMitkOpenGLVolumeTextureMapper3D::UpdateVolumes(vtkVolume *vtkNotUsed(vol)) { // Get the image data vtkImageData *input = this->GetInput(); input->Update(); bool needUpdate = false; // Has the volume changed in some way? if ( this->SavedTextureInput != input || this->SavedTextureMTime.GetMTime() < input->GetMTime() ) needUpdate = true; // Do we have any volume on the gpu already? if(!this->Volume1Index) needUpdate = true; if(!needUpdate) return true; ComputeVolumeDimensions(); int components = input->GetNumberOfScalarComponents(); // Find the scalar range double scalarRange[2]; input->GetPointData()->GetScalars()->GetRange(scalarRange, components-1); // Is the difference between max and min less than 4096? If so, and if // the data is not of float or double type, use a simple offset mapping. // If the difference between max and min is 4096 or greater, or the data // is of type float or double, we must use an offset / scaling mapping. // In this case, the array size will be 4096 - we need to figure out the // offset and scale factor. float offset; float scale; int arraySizeNeeded; int scalarType = input->GetScalarType(); if ( scalarType == VTK_FLOAT || scalarType == VTK_DOUBLE || scalarRange[1] - scalarRange[0] > 255 ) { arraySizeNeeded = 256; offset = -scalarRange[0]; scale = 255.0 / (scalarRange[1] - scalarRange[0]); } else { arraySizeNeeded = static_cast(scalarRange[1] - scalarRange[0] + 1); offset = -scalarRange[0]; scale = 1.0; } this->ColorTableSize = arraySizeNeeded; this->ColorTableOffset = offset; this->ColorTableScale = scale; // Allocating volume on gpu { // Deleting old textures this->DeleteTextureIndex(&this->Volume1Index); this->DeleteTextureIndex(&this->Volume2Index); this->DeleteTextureIndex(&this->Volume3Index); this->CreateTextureIndex(&this->Volume1Index); //this->CreateTextureIndex(&this->Volume2Index); int dim[3]; this->GetVolumeDimensions(dim); vtkgl::ActiveTexture( vtkgl::TEXTURE0 ); MITK_INFO << "allocating volume on gpu"; GLint gradientScalarTextureFormat = GL_RGBA8; if(this->UseCompressedTexture && SupportsCompressedTexture) gradientScalarTextureFormat = myGL_COMPRESSED_RGBA_S3TC_DXT5_EXT; glBindTexture(vtkgl::TEXTURE_3D, this->Volume1Index); vtkgl::TexImage3D(vtkgl::TEXTURE_3D,0,gradientScalarTextureFormat,dim[0],dim[1],dim[2],0,GL_RGBA,GL_UNSIGNED_BYTE,0); this->Setup3DTextureParameters( true ); } // Transfer the input volume to the RGBA volume void *dataPtr = input->GetScalarPointer(); switch ( scalarType ) { vtkTemplateMacro( vtkVolumeTextureMapper3DComputeScalars( static_cast(dataPtr), this, offset, scale, this->Volume1Index, this->Volume2Index)); } this->SavedTextureInput = input; this->SavedTextureMTime.Modified(); return true; } //----------------------------------------------------------------------------- bool vtkMitkOpenGLVolumeTextureMapper3D::UpdateVolumesRGBA(vtkVolume *vtkNotUsed(vol)) { // Get the image data vtkImageData *input = this->GetInput(); input->Update(); bool needUpdate = false; // Has the volume changed in some way? if ( this->SavedTextureInput != input || this->SavedTextureMTime.GetMTime() < input->GetMTime() ) needUpdate = true; // Do we have any volume on the gpu already? if(!this->Volume1Index) needUpdate = true; if(!needUpdate) return true; MITK_INFO << "updating rgba volume"; ComputeVolumeDimensions(); // Allocating volume on gpu { // Deleting old textures this->DeleteTextureIndex(&this->Volume1Index); this->DeleteTextureIndex(&this->Volume2Index); this->DeleteTextureIndex(&this->Volume3Index); this->CreateTextureIndex(&this->Volume1Index); this->CreateTextureIndex(&this->Volume2Index); int dim[3]; this->GetVolumeDimensions(dim); MITK_INFO << "allocating volume on gpu"; GLint gradientScalarTextureFormat = GL_RGBA8; GLint colorTextureFormat = GL_RGB8; if(this->UseCompressedTexture && SupportsCompressedTexture) { gradientScalarTextureFormat = myGL_COMPRESSED_RGBA_S3TC_DXT5_EXT; colorTextureFormat = myGL_COMPRESSED_RGB_S3TC_DXT1_EXT; } vtkgl::ActiveTexture( vtkgl::TEXTURE0 ); glBindTexture(vtkgl::TEXTURE_3D, this->Volume1Index); vtkgl::TexImage3D(vtkgl::TEXTURE_3D,0,gradientScalarTextureFormat,dim[0],dim[1],dim[2],0,GL_RGBA,GL_UNSIGNED_BYTE,0); this->Setup3DTextureParameters( true ); glBindTexture(vtkgl::TEXTURE_3D, this->Volume2Index); vtkgl::TexImage3D(vtkgl::TEXTURE_3D,0,colorTextureFormat,dim[0],dim[1],dim[2],0,GL_RGB,GL_UNSIGNED_BYTE,0); this->Setup3DTextureParameters( true ); } // Transfer the input volume to the RGBA volume unsigned char *dataPtr = (unsigned char*)input->GetScalarPointer(); vtkVolumeTextureMapper3DComputeRGBA( dataPtr, this, this->Volume1Index, this->Volume2Index); this->SavedTextureInput = input; this->SavedTextureMTime.Modified(); return true; } void vtkMitkOpenGLVolumeTextureMapper3D::Setup3DTextureParameters( bool linear ) { //GPU_INFO << "Setup3DTextureParameters"; if( linear ) { glTexParameterf( vtkgl::TEXTURE_3D, GL_TEXTURE_MIN_FILTER, GL_LINEAR ); glTexParameterf( vtkgl::TEXTURE_3D, GL_TEXTURE_MAG_FILTER, GL_LINEAR ); } else { glTexParameterf( vtkgl::TEXTURE_3D, GL_TEXTURE_MIN_FILTER, GL_NEAREST ); glTexParameterf( vtkgl::TEXTURE_3D, GL_TEXTURE_MAG_FILTER, GL_NEAREST ); } glTexParameterf( vtkgl::TEXTURE_3D, GL_TEXTURE_WRAP_S, GL_CLAMP ); glTexParameterf( vtkgl::TEXTURE_3D, GL_TEXTURE_WRAP_T, GL_CLAMP ); } void vtkMitkOpenGLVolumeTextureMapper3D::SetupOneIndependentTextures( vtkRenderer *vtkNotUsed(ren), vtkVolume *vol ) { // Update the volume containing the 2 byte scalar / gradient magnitude this->UpdateVolumes( vol ); // Update the dependent 2D color table mapping scalar value and // gradient magnitude to RGBA if ( this->UpdateColorLookup( vol ) || !this->ColorLookupIndex ) { this->DeleteTextureIndex( &this->ColorLookupIndex ); this->DeleteTextureIndex( &this->AlphaLookupIndex ); this->CreateTextureIndex( &this->ColorLookupIndex ); vtkgl::ActiveTexture( vtkgl::TEXTURE1 ); glBindTexture(GL_TEXTURE_2D, this->ColorLookupIndex); glTexParameterf( GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_NEAREST); glTexParameterf( GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_NEAREST ); glTexParameterf( GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP ); glTexParameterf( GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP ); //MITK_INFO << "uploading transferfunction"; GLint colorLookupTextureFormat = GL_RGBA8; if(this->UseCompressedTexture && SupportsCompressedTexture) colorLookupTextureFormat = myGL_COMPRESSED_RGBA_S3TC_DXT5_EXT; glTexImage2D( GL_TEXTURE_2D, 0,colorLookupTextureFormat, 256, 256, 0, GL_RGBA, GL_UNSIGNED_BYTE, this->ColorLookup ); } } void vtkMitkOpenGLVolumeTextureMapper3D::SetupRGBATextures( vtkRenderer *vtkNotUsed(ren), vtkVolume *vol ) { MITK_INFO << "SetupFourDependentTextures"; this->UpdateVolumesRGBA(vol); /* vtkgl::ActiveTexture( vtkgl::TEXTURE0 ); glDisable( GL_TEXTURE_2D ); glEnable( vtkgl::TEXTURE_3D ); vtkgl::ActiveTexture( vtkgl::TEXTURE1 ); glDisable( GL_TEXTURE_2D ); glEnable( vtkgl::TEXTURE_3D ); vtkgl::ActiveTexture( vtkgl::TEXTURE2 ); glDisable( GL_TEXTURE_2D ); glEnable( vtkgl::TEXTURE_3D ); // Update the volume containing the 3 byte scalars / gradient magnitude if ( this->UpdateVolumes( vol ) || !this->Volume1Index || !this->Volume2Index || !this->Volume3Index ) { int dim[3]; this->GetVolumeDimensions(dim); vtkgl::ActiveTexture( vtkgl::TEXTURE0 ); glBindTexture(vtkgl::TEXTURE_3D,0); this->DeleteTextureIndex(&this->Volume1Index); this->CreateTextureIndex(&this->Volume1Index); glBindTexture(vtkgl::TEXTURE_3D, this->Volume1Index); vtkgl::TexImage3D(vtkgl::TEXTURE_3D,0,this->InternalRGB,dim[0],dim[1], dim[2],0,GL_RGB,GL_UNSIGNED_BYTE,this->Volume1); vtkgl::ActiveTexture( vtkgl::TEXTURE1 ); glBindTexture(vtkgl::TEXTURE_3D,0); this->DeleteTextureIndex(&this->Volume2Index); this->CreateTextureIndex(&this->Volume2Index); glBindTexture(vtkgl::TEXTURE_3D, this->Volume2Index); vtkgl::TexImage3D(vtkgl::TEXTURE_3D,0,this->InternalLA,dim[0],dim[1], dim[2],0,GL_LUMINANCE_ALPHA,GL_UNSIGNED_BYTE, this->Volume2); vtkgl::ActiveTexture( vtkgl::TEXTURE2 ); glBindTexture(vtkgl::TEXTURE_3D,0); this->DeleteTextureIndex(&this->Volume3Index); this->CreateTextureIndex(&this->Volume3Index); glBindTexture(vtkgl::TEXTURE_3D, this->Volume3Index); vtkgl::TexImage3D(vtkgl::TEXTURE_3D,0,this->InternalRGB,dim[0],dim[1], dim[2],0,GL_RGB,GL_UNSIGNED_BYTE,this->Volume3); } vtkgl::ActiveTexture( vtkgl::TEXTURE0 ); glBindTexture(vtkgl::TEXTURE_3D, this->Volume1Index); this->Setup3DTextureParameters( true ); vtkgl::ActiveTexture( vtkgl::TEXTURE1 ); glBindTexture(vtkgl::TEXTURE_3D, this->Volume2Index); this->Setup3DTextureParameters( true ); vtkgl::ActiveTexture( vtkgl::TEXTURE2 ); glBindTexture(vtkgl::TEXTURE_3D_EXT, this->Volume3Index); this->Setup3DTextureParameters( true ); vtkgl::ActiveTexture( vtkgl::TEXTURE3 ); glEnable( GL_TEXTURE_2D ); glDisable( vtkgl::TEXTURE_3D ); // Update the dependent 2D table mapping scalar value and // gradient magnitude to opacity if ( this->UpdateColorLookup( vol ) || !this->AlphaLookupIndex ) { this->DeleteTextureIndex(&this->ColorLookupIndex); vtkgl::ActiveTexture( vtkgl::TEXTURE3 ); glBindTexture(GL_TEXTURE_2D,0); this->DeleteTextureIndex(&this->AlphaLookupIndex); this->CreateTextureIndex(&this->AlphaLookupIndex); glBindTexture(GL_TEXTURE_2D, this->AlphaLookupIndex); glTexParameterf( GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_NEAREST); glTexParameterf( GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_NEAREST ); glTexParameterf( GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP ); glTexParameterf( GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP ); //MITK_INFO << "uploading transferfunction"; glTexImage2D(GL_TEXTURE_2D,0,this->InternalAlpha, 256, 256, 0, GL_ALPHA, GL_UNSIGNED_BYTE, this->AlphaLookup ); } vtkgl::ActiveTexture( vtkgl::TEXTURE3 ); glBindTexture(GL_TEXTURE_2D, this->AlphaLookupIndex); */ } void vtkMitkOpenGLVolumeTextureMapper3D::RenderOneIndependentShadeFP( vtkRenderer *ren, vtkVolume *vol ) { //GPU_INFO << "RenderOneIndependentShadeFP"; this->SetupOneIndependentTextures( ren, vol ); glEnable( vtkgl::FRAGMENT_PROGRAM_ARB ); vtkgl::BindProgramARB( vtkgl::FRAGMENT_PROGRAM_ARB, prgOneComponentShade ); this->SetupProgramLocalsForShadingFP( ren, vol ); // Bind Textures { vtkgl::ActiveTexture( vtkgl::TEXTURE0 ); glDisable( GL_TEXTURE_2D ); glEnable( vtkgl::TEXTURE_3D ); glBindTexture(vtkgl::TEXTURE_3D, this->Volume1Index); vtkgl::ActiveTexture( vtkgl::TEXTURE1 ); glEnable( GL_TEXTURE_2D ); glDisable( vtkgl::TEXTURE_3D ); glBindTexture(GL_TEXTURE_2D, this->ColorLookupIndex); vtkgl::ActiveTexture( vtkgl::TEXTURE2 ); glDisable( GL_TEXTURE_2D ); glEnable( vtkgl::TEXTURE_3D ); glBindTexture(vtkgl::TEXTURE_3D, this->Volume2Index); } int stages[4] = {1,1,1,0}; this->RenderPolygons( ren, vol, stages ); glDisable( vtkgl::FRAGMENT_PROGRAM_ARB ); } void vtkMitkOpenGLVolumeTextureMapper3D::RenderRGBAShadeFP( vtkRenderer *ren, vtkVolume *vol ) { this->SetupRGBATextures(ren, vol); glEnable( vtkgl::FRAGMENT_PROGRAM_ARB ); vtkgl::BindProgramARB( vtkgl::FRAGMENT_PROGRAM_ARB, prgRGBAShade ); this->SetupProgramLocalsForShadingFP( ren, vol ); // Bind Textures { vtkgl::ActiveTexture( vtkgl::TEXTURE0 ); glDisable( GL_TEXTURE_2D ); glEnable( vtkgl::TEXTURE_3D ); glBindTexture(vtkgl::TEXTURE_3D, this->Volume1Index); vtkgl::ActiveTexture( vtkgl::TEXTURE1 ); glDisable( GL_TEXTURE_2D ); glEnable( vtkgl::TEXTURE_3D ); glBindTexture(vtkgl::TEXTURE_3D, this->Volume2Index); } int stages[4] = {1,1,1,0}; this->RenderPolygons( ren, vol, stages ); glDisable( vtkgl::FRAGMENT_PROGRAM_ARB ); } void vtkMitkOpenGLVolumeTextureMapper3D::GetLightInformation( vtkRenderer *ren, vtkVolume *vol, GLfloat lightDirection[2][4], GLfloat lightDiffuseColor[2][4], GLfloat lightSpecularColor[2][4], GLfloat halfwayVector[2][4], GLfloat ambientColor[4] ) { //GPU_INFO << "GetLightInformation"; float ambient = vol->GetProperty()->GetAmbient(); float diffuse = vol->GetProperty()->GetDiffuse(); float specular = vol->GetProperty()->GetSpecular(); vtkTransform *volumeTransform = vtkTransform::New(); volumeTransform->SetMatrix( vol->GetMatrix() ); volumeTransform->Inverse(); vtkLightCollection *lights = ren->GetLights(); lights->InitTraversal(); vtkLight *light[2]; light[0] = lights->GetNextItem(); light[1] = lights->GetNextItem(); int lightIndex = 0; double cameraPosition[3]; double cameraFocalPoint[3]; ren->GetActiveCamera()->GetPosition( cameraPosition ); ren->GetActiveCamera()->GetFocalPoint( cameraFocalPoint ); double viewDirection[3]; volumeTransform->TransformPoint( cameraPosition, cameraPosition ); volumeTransform->TransformPoint( cameraFocalPoint, cameraFocalPoint ); viewDirection[0] = cameraFocalPoint[0] - cameraPosition[0]; viewDirection[1] = cameraFocalPoint[1] - cameraPosition[1]; viewDirection[2] = cameraFocalPoint[2] - cameraPosition[2]; vtkMath::Normalize( viewDirection ); ambientColor[0] = 0.0; ambientColor[1] = 0.0; ambientColor[2] = 0.0; ambientColor[3] = 0.0; for ( lightIndex = 0; lightIndex < 2; lightIndex++ ) { float dir[3] = {0,0,0}; float half[3] = {0,0,0}; if ( light[lightIndex] == NULL || light[lightIndex]->GetSwitch() == 0 ) { lightDiffuseColor[lightIndex][0] = 0.0; lightDiffuseColor[lightIndex][1] = 0.0; lightDiffuseColor[lightIndex][2] = 0.0; lightDiffuseColor[lightIndex][3] = 0.0; lightSpecularColor[lightIndex][0] = 0.0; lightSpecularColor[lightIndex][1] = 0.0; lightSpecularColor[lightIndex][2] = 0.0; lightSpecularColor[lightIndex][3] = 0.0; } else { float lightIntensity = light[lightIndex]->GetIntensity(); double lightColor[3]; light[lightIndex]->GetDiffuseColor( lightColor ); double lightPosition[3]; double lightFocalPoint[3]; light[lightIndex]->GetTransformedPosition( lightPosition ); light[lightIndex]->GetTransformedFocalPoint( lightFocalPoint ); volumeTransform->TransformPoint( lightPosition, lightPosition ); volumeTransform->TransformPoint( lightFocalPoint, lightFocalPoint ); dir[0] = lightPosition[0] - lightFocalPoint[0]; dir[1] = lightPosition[1] - lightFocalPoint[1]; dir[2] = lightPosition[2] - lightFocalPoint[2]; vtkMath::Normalize( dir ); lightDiffuseColor[lightIndex][0] = lightColor[0]*diffuse*lightIntensity; lightDiffuseColor[lightIndex][1] = lightColor[1]*diffuse*lightIntensity; lightDiffuseColor[lightIndex][2] = lightColor[2]*diffuse*lightIntensity; lightDiffuseColor[lightIndex][3] = 1.0; lightSpecularColor[lightIndex][0]= lightColor[0]*specular*lightIntensity; lightSpecularColor[lightIndex][1]= lightColor[1]*specular*lightIntensity; lightSpecularColor[lightIndex][2]= lightColor[2]*specular*lightIntensity; lightSpecularColor[lightIndex][3] = 0.0; half[0] = dir[0] - viewDirection[0]; half[1] = dir[1] - viewDirection[1]; half[2] = dir[2] - viewDirection[2]; vtkMath::Normalize( half ); ambientColor[0] += ambient*lightColor[0]; ambientColor[1] += ambient*lightColor[1]; ambientColor[2] += ambient*lightColor[2]; } lightDirection[lightIndex][0] = (dir[0]+1.0)/2.0; lightDirection[lightIndex][1] = (dir[1]+1.0)/2.0; lightDirection[lightIndex][2] = (dir[2]+1.0)/2.0; lightDirection[lightIndex][3] = 0.0; halfwayVector[lightIndex][0] = (half[0]+1.0)/2.0; halfwayVector[lightIndex][1] = (half[1]+1.0)/2.0; halfwayVector[lightIndex][2] = (half[2]+1.0)/2.0; halfwayVector[lightIndex][3] = 0.0; } volumeTransform->Delete(); } void vtkMitkOpenGLVolumeTextureMapper3D::SetupProgramLocalsForShadingFP( vtkRenderer *ren, vtkVolume *vol ) { //GPU_INFO << "SetupProgramLocalsForShadingFP"; GLfloat lightDirection[2][4]; GLfloat lightDiffuseColor[2][4]; GLfloat lightSpecularColor[2][4]; GLfloat halfwayVector[2][4]; GLfloat ambientColor[4]; float ambient = vol->GetProperty()->GetAmbient(); float diffuse = vol->GetProperty()->GetDiffuse(); float specular = vol->GetProperty()->GetSpecular(); float specularPower = vol->GetProperty()->GetSpecularPower(); vtkTransform *volumeTransform = vtkTransform::New(); volumeTransform->SetMatrix( vol->GetMatrix() ); volumeTransform->Inverse(); vtkLightCollection *lights = ren->GetLights(); lights->InitTraversal(); vtkLight *light[2]; light[0] = lights->GetNextItem(); light[1] = lights->GetNextItem(); int lightIndex = 0; double cameraPosition[3]; double cameraFocalPoint[3]; ren->GetActiveCamera()->GetPosition( cameraPosition ); ren->GetActiveCamera()->GetFocalPoint( cameraFocalPoint ); volumeTransform->TransformPoint( cameraPosition, cameraPosition ); volumeTransform->TransformPoint( cameraFocalPoint, cameraFocalPoint ); double viewDirection[4]; viewDirection[0] = cameraFocalPoint[0] - cameraPosition[0]; viewDirection[1] = cameraFocalPoint[1] - cameraPosition[1]; viewDirection[2] = cameraFocalPoint[2] - cameraPosition[2]; viewDirection[3] = 0.0; vtkMath::Normalize( viewDirection ); ambientColor[0] = 0.0; ambientColor[1] = 0.0; ambientColor[2] = 0.0; ambientColor[3] = 0.0; for ( lightIndex = 0; lightIndex < 2; lightIndex++ ) { float dir[3] = {0,0,0}; float half[3] = {0,0,0}; if ( light[lightIndex] == NULL || light[lightIndex]->GetSwitch() == 0 ) { lightDiffuseColor[lightIndex][0] = 0.0; lightDiffuseColor[lightIndex][1] = 0.0; lightDiffuseColor[lightIndex][2] = 0.0; lightDiffuseColor[lightIndex][3] = 0.0; lightSpecularColor[lightIndex][0] = 0.0; lightSpecularColor[lightIndex][1] = 0.0; lightSpecularColor[lightIndex][2] = 0.0; lightSpecularColor[lightIndex][3] = 0.0; } else { float lightIntensity = light[lightIndex]->GetIntensity(); double lightColor[3]; light[lightIndex]->GetDiffuseColor( lightColor ); double lightPosition[3]; double lightFocalPoint[3]; light[lightIndex]->GetTransformedPosition( lightPosition ); light[lightIndex]->GetTransformedFocalPoint( lightFocalPoint ); volumeTransform->TransformPoint( lightPosition, lightPosition ); volumeTransform->TransformPoint( lightFocalPoint, lightFocalPoint ); dir[0] = lightPosition[0] - lightFocalPoint[0]; dir[1] = lightPosition[1] - lightFocalPoint[1]; dir[2] = lightPosition[2] - lightFocalPoint[2]; vtkMath::Normalize( dir ); lightDiffuseColor[lightIndex][0] = lightColor[0]*diffuse*lightIntensity; lightDiffuseColor[lightIndex][1] = lightColor[1]*diffuse*lightIntensity; lightDiffuseColor[lightIndex][2] = lightColor[2]*diffuse*lightIntensity; lightDiffuseColor[lightIndex][3] = 0.0; lightSpecularColor[lightIndex][0]= lightColor[0]*specular*lightIntensity; lightSpecularColor[lightIndex][1]= lightColor[1]*specular*lightIntensity; lightSpecularColor[lightIndex][2]= lightColor[2]*specular*lightIntensity; lightSpecularColor[lightIndex][3] = 0.0; half[0] = dir[0] - viewDirection[0]; half[1] = dir[1] - viewDirection[1]; half[2] = dir[2] - viewDirection[2]; vtkMath::Normalize( half ); ambientColor[0] += ambient*lightColor[0]; ambientColor[1] += ambient*lightColor[1]; ambientColor[2] += ambient*lightColor[2]; } lightDirection[lightIndex][0] = dir[0]; lightDirection[lightIndex][1] = dir[1]; lightDirection[lightIndex][2] = dir[2]; lightDirection[lightIndex][3] = 0.0; halfwayVector[lightIndex][0] = half[0]; halfwayVector[lightIndex][1] = half[1]; halfwayVector[lightIndex][2] = half[2]; halfwayVector[lightIndex][3] = 0.0; } volumeTransform->Delete(); vtkgl::ProgramLocalParameter4fARB( vtkgl::FRAGMENT_PROGRAM_ARB, 0, lightDirection[0][0], lightDirection[0][1], lightDirection[0][2], lightDirection[0][3] ); vtkgl::ProgramLocalParameter4fARB( vtkgl::FRAGMENT_PROGRAM_ARB, 1, halfwayVector[0][0], halfwayVector[0][1], halfwayVector[0][2], halfwayVector[0][3] ); vtkgl::ProgramLocalParameter4fARB( vtkgl::FRAGMENT_PROGRAM_ARB, 2, ambient, diffuse, specular, specularPower ); vtkgl::ProgramLocalParameter4fARB( vtkgl::FRAGMENT_PROGRAM_ARB, 3, lightDiffuseColor[0][0], lightDiffuseColor[0][1], lightDiffuseColor[0][2], lightDiffuseColor[0][3] ); vtkgl::ProgramLocalParameter4fARB( vtkgl::FRAGMENT_PROGRAM_ARB, 4, lightSpecularColor[0][0], lightSpecularColor[0][1], lightSpecularColor[0][2], lightSpecularColor[0][3] ); vtkgl::ProgramLocalParameter4fARB( vtkgl::FRAGMENT_PROGRAM_ARB, 5, viewDirection[0], viewDirection[1], viewDirection[2], viewDirection[3] ); vtkgl::ProgramLocalParameter4fARB( vtkgl::FRAGMENT_PROGRAM_ARB, 6, 2.0, -1.0, 0.0, 0.0 ); } int vtkMitkOpenGLVolumeTextureMapper3D::IsRenderSupported( vtkRenderer *renderer, vtkVolumeProperty *property ) { //GPU_INFO << "IsRenderSupported"; if ( !this->Initialized ) { //this->Initialize(); this->Initialize(renderer); } if ( !this->RenderPossible ) { return 0; } if ( !this->GetInput() ) { return 0; } if ( this->GetInput()->GetNumberOfScalarComponents() > 1 && property->GetIndependentComponents() ) { return 0; } return 1; } void vtkMitkOpenGLVolumeTextureMapper3D::Initialize(vtkRenderer *renderer) { //GPU_INFO << "Initialize"; this->Initialized = 1; // vtkOpenGLExtensionManager * extensions = vtkOpenGLExtensionManager::New(); //extensions->SetRenderWindow(NULL); // set render window to the current one. vtkOpenGLExtensionManager *extensions=static_cast(renderer->GetRenderWindow())->GetExtensionManager(); int supports_texture3D=extensions->ExtensionSupported( "GL_VERSION_1_2" ); if(supports_texture3D) { extensions->LoadExtension("GL_VERSION_1_2"); } else { supports_texture3D=extensions->ExtensionSupported( "GL_EXT_texture3D" ); if(supports_texture3D) { extensions->LoadCorePromotedExtension("GL_EXT_texture3D"); } } int supports_multitexture=extensions->ExtensionSupported( "GL_VERSION_1_3" ); if(supports_multitexture) { extensions->LoadExtension("GL_VERSION_1_3"); } else { supports_multitexture= extensions->ExtensionSupported("GL_ARB_multitexture"); if(supports_multitexture) { extensions->LoadCorePromotedExtension("GL_ARB_multitexture"); } } this->SupportsCompressedTexture=extensions->ExtensionSupported("GL_VERSION_1_3")==1; if(!this->SupportsCompressedTexture) { this->SupportsCompressedTexture= extensions->ExtensionSupported("GL_ARB_texture_compression")==1; if(this->SupportsCompressedTexture) { extensions->LoadCorePromotedExtension("GL_ARB_texture_compression"); } } //GPU_INFO(this->SupportsCompressedTexture) << "supporting compressed textures"; this->SupportsNonPowerOfTwoTextures= extensions->ExtensionSupported("GL_VERSION_2_0") || extensions->ExtensionSupported("GL_ARB_texture_non_power_of_two"); //GPU_INFO << "np2: " << (this->SupportsNonPowerOfTwoTextures?1:0); int supports_GL_ARB_fragment_program = extensions->ExtensionSupported( "GL_ARB_fragment_program" ); if(supports_GL_ARB_fragment_program) { extensions->LoadExtension( "GL_ARB_fragment_program" ); } int supports_GL_ARB_vertex_program = extensions->ExtensionSupported( "GL_ARB_vertex_program" ); if(supports_GL_ARB_vertex_program) { extensions->LoadExtension( "GL_ARB_vertex_program" ); } RenderPossible = 0; if ( supports_texture3D && supports_multitexture && supports_GL_ARB_fragment_program && supports_GL_ARB_vertex_program && vtkgl::TexImage3D && vtkgl::ActiveTexture && vtkgl::MultiTexCoord3fv && vtkgl::GenProgramsARB && vtkgl::DeleteProgramsARB && vtkgl::BindProgramARB && vtkgl::ProgramStringARB && vtkgl::ProgramLocalParameter4fARB ) { RenderPossible = 1; } else { std::string errString = "no gpu-acceleration possible cause following extensions/methods are missing or unsupported:"; if(!supports_texture3D) errString += " EXT_TEXTURE3D"; if(!supports_multitexture) errString += " EXT_MULTITEXTURE"; if(!supports_GL_ARB_fragment_program) errString += " ARB_FRAGMENT_PROGRAM"; if(!supports_GL_ARB_vertex_program) errString += " ARB_VERTEX_PROGRAM"; if(!vtkgl::TexImage3D) errString += " glTexImage3D"; if(!vtkgl::ActiveTexture) errString += " glActiveTexture"; if(!vtkgl::MultiTexCoord3fv) errString += " glMultiTexCoord3fv"; if(!vtkgl::GenProgramsARB) errString += " glGenProgramsARB"; if(!vtkgl::DeleteProgramsARB) errString += " glDeleteProgramsARB"; if(!vtkgl::BindProgramARB) errString += " glBindProgramARB"; if(!vtkgl::ProgramStringARB) errString += " glProgramStringARB"; if(!vtkgl::ProgramLocalParameter4fARB) errString += " glProgramLocalParameter4fARB"; GPU_WARN << errString; }; if(RenderPossible) { vtkgl::GenProgramsARB( 1, &prgOneComponentShade ); vtkgl::BindProgramARB( vtkgl::FRAGMENT_PROGRAM_ARB, prgOneComponentShade ); vtkgl::ProgramStringARB( vtkgl::FRAGMENT_PROGRAM_ARB, vtkgl::PROGRAM_FORMAT_ASCII_ARB, static_cast(strlen(vtkMitkVolumeTextureMapper3D_OneComponentShadeFP)), vtkMitkVolumeTextureMapper3D_OneComponentShadeFP ); vtkgl::GenProgramsARB( 1, &prgRGBAShade ); vtkgl::BindProgramARB( vtkgl::FRAGMENT_PROGRAM_ARB, prgRGBAShade ); vtkgl::ProgramStringARB( vtkgl::FRAGMENT_PROGRAM_ARB, vtkgl::PROGRAM_FORMAT_ASCII_ARB, static_cast(strlen(vtkMitkVolumeTextureMapper3D_FourDependentShadeFP)), vtkMitkVolumeTextureMapper3D_FourDependentShadeFP ); } } // ---------------------------------------------------------------------------- // Print the vtkMitkOpenGLVolumeTextureMapper3D void vtkMitkOpenGLVolumeTextureMapper3D::PrintSelf(ostream& os, vtkIndent indent) { // vtkOpenGLExtensionManager * extensions = vtkOpenGLExtensionManager::New(); // extensions->SetRenderWindow(NULL); // set render window to current render window os << indent << "Initialized " << this->Initialized << endl; /* if ( this->Initialized ) { os << indent << "Supports GL_VERSION_1_2:" << extensions->ExtensionSupported( "GL_VERSION_1_2" ) << endl; os << indent << "Supports GL_EXT_texture3D:" << extensions->ExtensionSupported( "GL_EXT_texture3D" ) << endl; os << indent << "Supports GL_VERSION_1_3:" << extensions->ExtensionSupported( "GL_VERSION_1_3" ) << endl; os << indent << "Supports GL_ARB_multitexture: " << extensions->ExtensionSupported( "GL_ARB_multitexture" ) << endl; os << indent << "Supports GL_NV_texture_shader2: " << extensions->ExtensionSupported( "GL_NV_texture_shader2" ) << endl; os << indent << "Supports GL_NV_register_combiners2: " << extensions->ExtensionSupported( "GL_NV_register_combiners2" ) << endl; os << indent << "Supports GL_ATI_fragment_shader: " << extensions->ExtensionSupported( "GL_ATI_fragment_shader" ) << endl; os << indent << "Supports GL_ARB_fragment_program: " << extensions->ExtensionSupported( "GL_ARB_fragment_program" ) << endl; os << indent << "Supports GL_ARB_texture_compression: " << extensions->ExtensionSupported( "GL_ARB_texture_compression" ) << endl; os << indent << "Supports GL_VERSION_2_0:" << extensions->ExtensionSupported( "GL_VERSION_2_0" ) << endl; os << indent << "Supports GL_ARB_texture_non_power_of_two:" << extensions->ExtensionSupported( "GL_ARB_texture_non_power_of_two" ) << endl; } extensions->Delete(); */ if(this->RenderWindow!=0) { vtkOpenGLExtensionManager *extensions= static_cast(this->RenderWindow)->GetExtensionManager(); if ( this->Initialized ) { os << indent << "Supports GL_VERSION_1_2:" << extensions->ExtensionSupported( "GL_VERSION_1_2" ) << endl; os << indent << "Supports GL_EXT_texture3D:" << extensions->ExtensionSupported( "GL_EXT_texture3D" ) << endl; os << indent << "Supports GL_VERSION_1_3:" << extensions->ExtensionSupported( "GL_VERSION_1_3" ) << endl; os << indent << "Supports GL_ARB_multitexture: " << extensions->ExtensionSupported( "GL_ARB_multitexture" ) << endl; os << indent << "Supports GL_NV_texture_shader2: " << extensions->ExtensionSupported( "GL_NV_texture_shader2" ) << endl; os << indent << "Supports GL_NV_register_combiners2: " << extensions->ExtensionSupported( "GL_NV_register_combiners2" ) << endl; os << indent << "Supports GL_ATI_fragment_shader: " << extensions->ExtensionSupported( "GL_ATI_fragment_shader" ) << endl; os << indent << "Supports GL_ARB_fragment_program: " << extensions->ExtensionSupported( "GL_ARB_fragment_program" ) << endl; os << indent << "Supports GL_ARB_texture_compression: " << extensions->ExtensionSupported( "GL_ARB_texture_compression" ) << endl; os << indent << "Supports GL_VERSION_2_0:" << extensions->ExtensionSupported( "GL_VERSION_2_0" ) << endl; os << indent << "Supports GL_ARB_texture_non_power_of_two:" << extensions->ExtensionSupported( "GL_ARB_texture_non_power_of_two" ) << endl; } } this->Superclass::PrintSelf(os,indent); } diff --git a/Modules/MitkExt/Testing/files.cmake b/Modules/MitkExt/Testing/files.cmake index 529128a720..604b7b6f67 100644 --- a/Modules/MitkExt/Testing/files.cmake +++ b/Modules/MitkExt/Testing/files.cmake @@ -1,41 +1,37 @@ set(MODULE_TESTS mitkAutoCropImageFilterTest.cpp mitkBoundingObjectCutterTest.cpp - mitkContourMapper2DTest.cpp - mitkContourTest.cpp mitkCoreExtObjectFactoryTest mitkDataNodeExtTest.cpp mitkExternalToolsTest.cpp mitkMeshTest.cpp mitkMultiStepperTest.cpp mitkOrganTypePropertyTest.cpp mitkPipelineSmartPointerCorrectnessTest.cpp mitkPlaneFitTest.cpp mitkPointLocatorTest.cpp # mitkSegmentationInterpolationTest.cpp # mitkTestTemplate.cpp - mitkToolManagerTest.cpp mitkUnstructuredGridTest.cpp mitkSimpleHistogramTest.cpp + mitkToolManagerTest.cpp ) set(MODULE_IMAGE_TESTS mitkUnstructuredGridVtkWriterTest.cpp mitkCompressedImageContainerTest.cpp mitkCylindricToCartesianFilterTest.cpp #mitkExtractImageFilterTest.cpp - mitkManualSegmentationToSurfaceFilterTest.cpp - mitkOverwriteSliceImageFilterTest.cpp mitkSurfaceToImageFilterTest.cpp ) set(MODULE_CUSTOM_TESTS mitkLabeledImageToSurfaceFilterTest.cpp ) set(MODULE_TESTIMAGES US4DCyl.nrrd Pic3D.nrrd Pic2DplusT.nrrd BallBinary30x30x30.nrrd Png2D-bw.png binary.stl ball.stl ) diff --git a/Modules/MitkExt/Testing/mitkDataNodeExtTest.cpp b/Modules/MitkExt/Testing/mitkDataNodeExtTest.cpp index 4faeb11b65..72c6289ee3 100644 --- a/Modules/MitkExt/Testing/mitkDataNodeExtTest.cpp +++ b/Modules/MitkExt/Testing/mitkDataNodeExtTest.cpp @@ -1,257 +1,214 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2008-02-25 17:27:17 +0100 (Mo, 25 Feb 2008) $ Version: $Revision: 7837 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkDataNode.h" #include #include "mitkVtkPropRenderer.h" #include "mitkTestingMacros.h" #include "mitkGlobalInteraction.h" #include //Basedata Test -#include -#include #include #include #include #include #include //Mapper Test #include #include #include -#include -#include #include #include #include #include -#include -#include #include #include #include #include //Interactors #include -#include -#include #include #include #include #include //Propertylist Test #include #include #include #include #include #include #include #include #include #include #include /** * Extended test for mitk::DataNode. A number of tests from the core test * mitkDataNodeTest are assumed to pass! */ class mitkDataNodeExtTestClass { public: static void TestDataSetting(mitk::DataNode::Pointer dataNode) { mitk::BaseData::Pointer baseData; //NULL pointer Test dataNode->SetData(baseData); MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a NULL pointer was set correctly" ) - baseData = mitk::Contour::New(); - dataNode->SetData(baseData); - MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a Contour object was set correctly" ) - - baseData = mitk::ContourSet::New(); - dataNode->SetData(baseData); - MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a ContourSet object was set correctly" ) - baseData = mitk::ItkBaseDataAdapter::New(); dataNode->SetData(baseData); MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a ItkBaseDataAdapter object was set correctly" ) baseData = mitk::Mesh::New(); dataNode->SetData(baseData); MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a Mesh object was set correctly" ) baseData = mitk::SeedsImage::New(); dataNode->SetData(baseData); MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a SeedsImage object was set correctly" ) baseData = mitk::BoundingObject::New(); dataNode->SetData(baseData); MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a BoundingObject object was set correctly" ) baseData = mitk::UnstructuredGrid::New(); dataNode->SetData(baseData); MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a UnstructuredGrid object was set correctly" ) } static void TestMapperSetting(mitk::DataNode::Pointer dataNode) { //tests the SetMapper() method //in dataNode is a mapper vector which can be accessed by index //in this test method we use only slot 0 (filled with null) and slot 1 //so we also test the destructor of the mapper classes mitk::Mapper::Pointer mapper; dataNode->SetMapper(0,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(0), "Testing if a NULL pointer was set correctly" ) - mapper = mitk::ContourMapper2D::New(); - dataNode->SetMapper(1,mapper); - MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a ContourMapper2D was set correctly" ) - MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - - mapper = mitk::ContourSetMapper2D::New(); - dataNode->SetMapper(1,mapper); - MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a ContourSetMapper2D was set correctly" ) - MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - mapper = mitk::MeshMapper2D::New(); dataNode->SetMapper(1,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a MeshMapper2D was set correctly" ) MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) mapper = mitk::UnstructuredGridMapper2D::New(); dataNode->SetMapper(1,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a UnstructuredGridMapper2D was set correctly" ) MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) mapper = mitk::LineMapper2D::New(); dataNode->SetMapper(1,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a LineMapper2D was set correctly" ) MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) mapper = mitk::SplineMapper2D::New(); dataNode->SetMapper(1,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a SplineMapper2D was set correctly" ) MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - //3D Mappers - mapper = mitk::ContourSetVtkMapper3D::New(); - dataNode->SetMapper(1,mapper); - MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a ContourSetVtkMapper3D was set correctly" ) - MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - - mapper = mitk::ContourVtkMapper3D::New(); - dataNode->SetMapper(1,mapper); - MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a ContourVtkMapper3D was set correctly" ) - MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - mapper = mitk::MeshVtkMapper3D::New(); dataNode->SetMapper(1,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a MeshVtkMapper3D was set correctly" ) MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) mapper = mitk::UnstructuredGridVtkMapper3D::New(); dataNode->SetMapper(1,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a UnstructuredGridVtkMapper3D was set correctly" ) MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) //linker error //mapper = mitk::LineVtkMapper3D::New(); //dataNode->SetMapper(1,mapper); //MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a LineVtkMapper3D was set correctly" ) //MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) mapper = mitk::SplineVtkMapper3D::New(); dataNode->SetMapper(1,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a SplineVtkMapper3D was set correctly" ) MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) } static void TestInteractorSetting(mitk::DataNode::Pointer dataNode) { //this method tests the SetInteractor() and GetInteractor methods //the Interactor base class calls the DataNode->SetInteractor method mitk::Interactor::Pointer interactor; MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a NULL pointer was set correctly (Interactor)" ) interactor = mitk::ConnectPointsInteractor::New("AffineInteractions click to select", dataNode); MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a ConnectPointsInteractor was set correctly" ) - interactor = mitk::ContourInteractor::New("AffineInteractions click to select", dataNode); - MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a ContourInteractor was set correctly" ) - - interactor = mitk::ExtrudedContourInteractor::New("AffineInteractions click to select", dataNode); - MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a ExtrudedContourInteractor was set correctly" ) - interactor = mitk::PointInteractor::New("AffineInteractions click to select", dataNode); MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a PointInteractor was set correctly" ) interactor = mitk::PointSelectorInteractor::New("AffineInteractions click to select", dataNode); MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a PointSelectorInteractor was set correctly" ) interactor = mitk::SeedsInteractor::New("AffineInteractions click to select", dataNode); MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a SeedsInteractor was set correctly" ) interactor = mitk::DisplayPointSetInteractor::New("AffineInteractions click to select", dataNode); MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a DisplayPointSetInteractor was set correctly" ) } }; int mitkDataNodeExtTest(int /* argc */, char* /*argv*/[]) { // always start with this! MITK_TEST_BEGIN("DataNode") // Global interaction must(!) be initialized mitk::GlobalInteraction::GetInstance()->Initialize("global"); // let's create an object of our class mitk::DataNode::Pointer myDataNode = mitk::DataNode::New(); // first test: did this work? // using MITK_TEST_CONDITION_REQUIRED makes the test stop after failure, since // it makes no sense to continue without an object. MITK_TEST_CONDITION_REQUIRED(myDataNode.IsNotNull(),"Testing instantiation") //test setData() Method mitkDataNodeExtTestClass::TestDataSetting(myDataNode); mitkDataNodeExtTestClass::TestMapperSetting(myDataNode); //note, that no data is set to the dataNode mitkDataNodeExtTestClass::TestInteractorSetting(myDataNode); // write your own tests here and use the macros from mitkTestingMacros.h !!! // do not write to std::cout and do not return from this function yourself! // always end with this! MITK_TEST_END() } diff --git a/Modules/MitkExt/Testing/mitkToolManagerTest.cpp b/Modules/MitkExt/Testing/mitkToolManagerTest.cpp index 21e6cf46db..f8f749f27d 100644 --- a/Modules/MitkExt/Testing/mitkToolManagerTest.cpp +++ b/Modules/MitkExt/Testing/mitkToolManagerTest.cpp @@ -1,94 +1,93 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkTestingMacros.h" #include "mitkToolManager.h" #include "mitkStandaloneDataStorage.h" #include "mitkCoreObjectFactory.h" -#include "mitkAddContourTool.h" #include "mitkGlobalInteraction.h" class mitkToolManagerTestClass { public: static void TestToolManagerWithOutTools(mitk::ToolManager::Pointer toolManager) { MITK_TEST_CONDITION( toolManager->GetTools().size() == 0, "Get empty tool list" ) MITK_TEST_CONDITION( toolManager->GetToolById(0) == NULL, "Get empty tool by id" ) } static void TestToolManagerWithTools(mitk::ToolManager::Pointer toolManager) { MITK_TEST_CONDITION( toolManager->GetTools().size() > 0, "Get tool list with size 1" ) MITK_TEST_CONDITION( toolManager->GetToolById(0) != NULL, "Test GetToolById() method" ) MITK_TEST_CONDITION( toolManager->ActivateTool(0) == true, "Activate tool" ) MITK_TEST_CONDITION( toolManager->GetActiveToolID() == 0, "Check for right tool id" ) mitk::Tool* tool = toolManager->GetActiveTool(); MITK_TEST_CONDITION( tool != NULL, "Check for right tool" ) } static void TestSetterMethods(mitk::ToolManager::Pointer toolManager) { MITK_TEST_CONDITION( toolManager->GetReferenceData().size() == 0, "Get reference data size (0)" ) mitk::DataNode::Pointer nodeEmpty = mitk::DataNode::New(); toolManager->SetReferenceData(nodeEmpty); MITK_TEST_CONDITION( toolManager->GetReferenceData().size() == 1, "Get reference data size (1)" ) MITK_TEST_CONDITION( toolManager->GetReferenceData(0) == nodeEmpty, "Check if it is the right reference data" ) MITK_TEST_CONDITION( toolManager->GetReferenceData()[0] == nodeEmpty, "Check if it is the right reference data vector" ) mitk::DataNode::Pointer nodeEmpty2 = mitk::DataNode::New(); toolManager->SetWorkingData(nodeEmpty2); MITK_TEST_CONDITION( toolManager->GetWorkingData().size() == 1, "Get working data size (1)" ) MITK_TEST_CONDITION( toolManager->GetWorkingData(0) == nodeEmpty2, "Check if it is the right working data" ) MITK_TEST_CONDITION( toolManager->GetWorkingData()[0] == nodeEmpty2, "Check if it is the right working data vector" ) } }; int mitkToolManagerTest(int /* argc */, char* /*argv*/[]) { // always start with this! MITK_TEST_BEGIN("ToolManager") // Global interaction must(!) be initialized if used mitk::GlobalInteraction::GetInstance()->Initialize("global"); // instantiation mitk::StandaloneDataStorage::Pointer dataStorage = mitk::StandaloneDataStorage::New(); mitk::ToolManager::Pointer toolManager = mitk::ToolManager::New(dataStorage.GetPointer()); // first test: did this work? // using MITK_TEST_CONDITION_REQUIRED makes the test stop after failure, since // it makes no sense to continue without an object. MITK_TEST_CONDITION_REQUIRED(toolManager.IsNotNull(),"Testing instantiation") // write your own tests here and use the macros from mitkTestingMacros.h !!! // do not write to std::cout and do not return from this function yourself! //mitkToolManagerTestClass::TestToolManagerWithOutTools(toolManager); //now we add one tool toolManager = mitk::ToolManager::New(dataStorage.GetPointer()); //start test with tool mitkToolManagerTestClass::TestToolManagerWithTools(toolManager); //now the setter methods mitkToolManagerTestClass::TestSetterMethods(toolManager); // always end with this! MITK_TEST_END() } diff --git a/Modules/MitkExt/files.cmake b/Modules/MitkExt/files.cmake index 562eec0b5f..36b48e6c7a 100644 --- a/Modules/MitkExt/files.cmake +++ b/Modules/MitkExt/files.cmake @@ -1,200 +1,152 @@ set(CPP_FILES - Algorithms/mitkImageToContourFilter.cpp - Algorithms/mitkReduceContourSetFilter.cpp - Algorithms/mitkComputeContourSetNormalsFilter.cpp - Algorithms/mitkCreateDistanceImageFromSurfaceFilter.cpp Algorithms/mitkMaskAndCutRoiImageFilter.cpp Algorithms/mitkBoundingObjectToSegmentationFilter.cpp Algorithms/vtkPointSetSlicer.cxx Algorithms/mitkCoreExtObjectFactory.cpp Algorithms/mitkAngleCorrectByPointFilter.cpp Algorithms/mitkAutoCropImageFilter.cpp Algorithms/mitkBoundingObjectCutter.cpp - Algorithms/mitkCalculateSegmentationVolume.cpp - Algorithms/mitkContourSetToPointSetFilter.cpp - Algorithms/mitkContourUtils.cpp - Algorithms/mitkCorrectorAlgorithm.cpp Algorithms/mitkCylindricToCartesianFilter.cpp - Algorithms/mitkDiffImageApplier.cpp Algorithms/mitkDopplerToStrainRateFilter.cpp Algorithms/mitkGeometryClipImageFilter.cpp Algorithms/mitkGeometryDataSource.cpp Algorithms/mitkHeightFieldSurfaceClipImageFilter.cpp Algorithms/mitkImageToLookupTableFilter.cpp Algorithms/mitkImageToSurfaceFilter.cpp Algorithms/mitkInterpolateLinesFilter.cpp Algorithms/mitkLabeledImageToSurfaceFilter.cpp Algorithms/mitkLabeledImageVolumeCalculator.cpp Algorithms/mitkLookupTableSource.cpp - Algorithms/mitkManualSegmentationToSurfaceFilter.cpp Algorithms/mitkMaskImageFilter.cpp Algorithms/mitkMeshSource.cpp Algorithms/mitkNonBlockingAlgorithm.cpp - Algorithms/mitkOverwriteSliceImageFilter.cpp - Algorithms/mitkOverwriteDirectedPlaneImageFilter.cpp Algorithms/mitkPadImageFilter.cpp Algorithms/mitkPlaneCutFilter.cpp Algorithms/mitkPlaneFit.cpp Algorithms/mitkPlanesPerpendicularToLinesFilter.cpp Algorithms/mitkPointLocator.cpp Algorithms/mitkPointSetToCurvedGeometryFilter.cpp Algorithms/mitkPointSetToGeometryDataFilter.cpp Algorithms/mitkPointSetIndexToWorldTransformFilter.cpp Algorithms/mitkSurfaceIndexToWorldTransformFilter.cpp Algorithms/mitkPolygonToRingFilter.cpp Algorithms/mitkProbeFilter.cpp - Algorithms/mitkSegmentationSink.cpp - Algorithms/mitkShapeBasedInterpolationAlgorithm.cpp - Algorithms/mitkShowSegmentationAsSmoothedSurface.cpp - Algorithms/mitkShowSegmentationAsSurface.cpp Algorithms/mitkSimpleHistogram.cpp Algorithms/mitkSimpleUnstructuredGridHistogram.cpp Algorithms/mitkSurfaceToImageFilter.cpp Algorithms/mitkUnstructuredGridHistogram.cpp Algorithms/mitkUnstructuredGridSource.cpp Algorithms/mitkVolumeVisualizationImagePreprocessor.cpp Controllers/mitkMovieGenerator.cpp Controllers/mitkMultiStepper.cpp - Controllers/mitkSegmentationInterpolationController.cpp - Controllers/mitkSurfaceInterpolationController.cpp Controllers/mitkToolManager.cpp DataManagement/mitkAffineTransformationOperation.cpp DataManagement/mitkApplyDiffImageOperation.cpp DataManagement/mitkBoundingObject.cpp DataManagement/mitkBoundingObjectGroup.cpp DataManagement/mitkCellOperation.cpp DataManagement/mitkColorConversions.cpp DataManagement/mitkColorSequence.cpp DataManagement/mitkColorSequenceCycleH.cpp DataManagement/mitkColorSequenceHalfTones.cpp DataManagement/mitkColorSequenceRainbow.cpp DataManagement/mitkCompressedImageContainer.cpp DataManagement/mitkCone.cpp - DataManagement/mitkContour.cpp - DataManagement/mitkContourSet.cpp DataManagement/mitkCuboid.cpp DataManagement/mitkCylinder.cpp DataManagement/mitkDataStorageSelection.cpp DataManagement/mitkDelegateManager.cpp DataManagement/mitkDrawOperation.cpp DataManagement/mitkEllipsoid.cpp DataManagement/mitkExternAbstractTransformGeometry.cpp - DataManagement/mitkExtrudedContour.cpp DataManagement/mitkFrameOfReferenceUIDManager.cpp DataManagement/mitkGridRepresentationProperty.cpp DataManagement/mitkGridVolumeMapperProperty.cpp DataManagement/mitkItkBaseDataAdapter.cpp DataManagement/mitkLabeledImageLookupTable.cpp DataManagement/mitkLineOperation.cpp DataManagement/mitkMesh.cpp DataManagement/mitkObjectSet.cpp DataManagement/mitkOrganTypeProperty.cpp DataManagement/mitkPlaneLandmarkProjector.cpp DataManagement/mitkPlane.cpp DataManagement/mitkPropertyManager.cpp DataManagement/mitkPropertyObserver.cpp DataManagement/mitkSeedsImage.cpp DataManagement/mitkSeedsImageLookupTableSource.cpp DataManagement/mitkSphereLandmarkProjector.cpp # DataManagement/mitkUSLookupTableSource.cpp DataManagement/mitkUnstructuredGrid.cpp DataManagement/mitkVideoSource.cpp DataManagement/vtkObjectSet.cpp IO/mitkObjFileIOFactory.cpp IO/mitkObjFileReader.cpp IO/mitkPACSPlugin.cpp IO/mitkParRecFileIOFactory.cpp IO/mitkParRecFileReader.cpp IO/mitkStlVolumeTimeSeriesIOFactory.cpp IO/mitkStlVolumeTimeSeriesReader.cpp IO/mitkUnstructuredGridVtkWriter.cpp IO/mitkUnstructuredGridVtkWriterFactory.cpp IO/mitkVtkUnstructuredGridIOFactory.cpp IO/mitkVtkUnstructuredGridReader.cpp IO/mitkVtkVolumeTimeSeriesIOFactory.cpp IO/mitkVtkVolumeTimeSeriesReader.cpp - Interactions/mitkAutoSegmentationTool.cpp Interactions/mitkConferenceEventMapper.cpp Interactions/mitkConnectPointsInteractor.cpp - Interactions/mitkContourInteractor.cpp - Interactions/mitkContourTool.cpp #Interactions/mitkCoordinateSupplier.cpp #Interactions/mitkDisplayCoordinateOperation.cpp #Interactions/mitkDisplayInteractor.cpp Interactions/mitkAffineInteractor3D.cpp Interactions/mitkDisplayPointSetInteractor.cpp #Interactions/mitkDisplayVectorInteractor.cpp - Interactions/mitkExtrudedContourInteractor.cpp - Interactions/mitkFeedbackContourTool.cpp Interactions/mitkInteractionDebug.cpp Interactions/mitkInteractionDebugger.cpp - Interactions/mitkPaintbrushTool.cpp Interactions/mitkPointInteractor.cpp Interactions/mitkPointSelectorInteractor.cpp #Interactions/mitkPositionTracker.cpp Interactions/mitkSeedsInteractor.cpp - Interactions/mitkSegTool2D.cpp - Interactions/mitkSegmentationsProcessingTool.cpp - Interactions/mitkSetRegionTool.cpp Interactions/mitkSocketClient.cpp Interactions/mitkSurfaceDeformationInteractor3D.cpp Interactions/mitkSurfaceInteractor.cpp Interactions/mitkTool.cpp - Interactions/mitkAddContourTool.cpp - Interactions/mitkAutoCropTool.cpp - Interactions/mitkBinaryThresholdTool.cpp - Interactions/mitkCalculateGrayValueStatisticsTool.cpp - Interactions/mitkCalculateVolumetryTool.cpp - Interactions/mitkCorrectorTool2D.cpp - Interactions/mitkCreateSurfaceTool.cpp - Interactions/mitkEraseRegionTool.cpp - Interactions/mitkFillRegionTool.cpp - Interactions/mitkRegionGrowingTool.cpp - Interactions/mitkSubtractContourTool.cpp - Interactions/mitkDrawPaintbrushTool.cpp - Interactions/mitkErasePaintbrushTool.cpp +# Interactions/mitkCreateSurfaceTool.cpp Interactions/mitkMorphologicTool.cpp Interactions/mitkErodeTool.cpp Interactions/mitkDilateTool.cpp Interactions/mitkOpeningTool.cpp Interactions/mitkClosingTool.cpp - Interactions/mitkBinaryThresholdULTool.cpp Interactions/mitkPixelManipulationTool.cpp - Interactions/mitkRegionGrow3DTool.cpp - Rendering/mitkContourMapper2D.cpp - Rendering/mitkContourSetMapper2D.cpp - Rendering/mitkContourSetVtkMapper3D.cpp - Rendering/mitkContourVtkMapper3D.cpp Rendering/mitkEnhancedPointSetVtkMapper3D.cpp Rendering/mitkImageBackground2D.cpp Rendering/mitkLineMapper2D.cpp # Rendering/mitkLineVtkMapper3D.cpp Rendering/mitkMeshMapper2D.cpp Rendering/mitkMeshVtkMapper3D.cpp Rendering/mitkNativeRenderWindowInteractor.cpp Rendering/mitkSplineMapper2D.cpp Rendering/mitkSplineVtkMapper3D.cpp Rendering/mitkUnstructuredGridMapper2D.cpp Rendering/mitkUnstructuredGridVtkMapper3D.cpp Rendering/mitkVectorImageMapper2D.cpp Rendering/vtkUnstructuredGridMapper.cpp Rendering/vtkMaskedGlyph2D.cpp Rendering/vtkMaskedGlyph3D.cpp Rendering/vtkMitkVolumeTextureMapper3D.cpp Rendering/vtkMitkOpenGLVolumeTextureMapper3D.cpp Rendering/mitkGPUVolumeMapper3D.cpp Rendering/vtkMitkGPUVolumeRayCastMapper.cpp Rendering/vtkMitkOpenGLGPUVolumeRayCastMapper.cpp Rendering/vtkMitkOpenGLGPUVolumeRayCastMapperShaders.cpp ) if(WIN32 AND NOT MINGW) set(CPP_FILES Controllers/mitkMovieGeneratorWin32.cpp ${CPP_FILES} ) endif(WIN32 AND NOT MINGW) diff --git a/Modules/QmitkExt/CMakeLists.txt b/Modules/QmitkExt/CMakeLists.txt index 5a20a6c175..3153b7f1bd 100644 --- a/Modules/QmitkExt/CMakeLists.txt +++ b/Modules/QmitkExt/CMakeLists.txt @@ -1,6 +1,6 @@ MITK_CREATE_MODULE( QmitkExt INCLUDE_DIRS QmitkApplicationBase QmitkPropertyObservers QmitkFunctionalityComponents - DEPENDS MitkExt IpPicSupport Qmitk qwt qxt PlanarFigure SceneSerialization + DEPENDS MitkExt IpPicSupport Qmitk qwt qxt PlanarFigure SceneSerialization Segmentation QT_MODULE ) diff --git a/Modules/QmitkExt/QmitkApplicationBase/QmitkCommonFunctionality.cpp b/Modules/QmitkExt/QmitkApplicationBase/QmitkCommonFunctionality.cpp index 2b71192769..f3e8769a21 100644 --- a/Modules/QmitkExt/QmitkApplicationBase/QmitkCommonFunctionality.cpp +++ b/Modules/QmitkExt/QmitkApplicationBase/QmitkCommonFunctionality.cpp @@ -1,694 +1,718 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2008-09-18 09:35:44 +0200 (Do, 18 Sep 2008) $ Version: $Revision: 15278 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include #include #include #include #include #include -#include #include "mitkPointSetWriter.h" #include "mitkConfig.h" #include "mitkCoreObjectFactory.h" #include "QmitkCommonFunctionality.h" #include #include #include #include #include #include #include #include +#include +#include #include void CommonFunctionality::SaveToFileWriter( mitk::FileWriterWithInformation::Pointer fileWriter, mitk::BaseData::Pointer data, const char* aFileName, const char* propFileName) { if (! fileWriter->CanWriteBaseDataType(data) ) { QMessageBox::critical(NULL,"ERROR","Could not write file. Invalid data type for file writer."); return; } QString fileName; if (aFileName == NULL) { QString proposedName(""); if(propFileName == NULL) { proposedName.append(fileWriter->GetDefaultFilename()); } else { proposedName.append(propFileName).append(fileWriter->GetDefaultExtension()); } fileName = GetSaveFileNameStartingInLastDirectory("Save file", proposedName,QString::fromAscii(fileWriter->GetFileDialogPattern())); // Check if an extension exists already and if not, append the default extension if ( !fileName.contains( QRegExp("\\.\\w+$") ) ) { fileName.append( fileWriter->GetDefaultExtension() ); } else { std::string extension = itksys::SystemTools::GetFilenameLastExtension( fileName.toLocal8Bit().constData() ); if (!fileWriter->IsExtensionValid(extension)) { QString message; message.append("File extension not suitable for writing given data. Choose one extension of this list: "); message.append(fileWriter->GetPossibleFileExtensionsAsString().c_str()); QMessageBox::critical(NULL,"ERROR",message); return; } } } else fileName = aFileName; if (fileName.isEmpty() == false ) { fileWriter->SetFileName( fileName.toLocal8Bit().constData() ); fileWriter->DoWrite( data ); } } /** * Saves the given mitk::BaseData to a file. The user is prompted to * enter a file name. Currently only mitk::Image, mitk::Surface, mitk::PointSet and * mitk::VesselGraphData are supported. This function is deprecated * until the save-problem is solved by means of a Save-Factory or any * other "nice" mechanism */ void CommonFunctionality::SaveBaseData( mitk::BaseData* data, const char * aFileName ) { //save initial time QDateTime initialTime = QDateTime::currentDateTime(); std::string fileNameUsed; //file name that was actually used by the writer (e.g. after file open dialog) bool writingSuccessful = false; try{ if (data != NULL) { mitk::Image::Pointer image = dynamic_cast(data); QString classname(data->GetNameOfClass()); if ( image.IsNotNull() && (classname.compare("Image")==0 || classname.compare("SeedsImage")==0 ) ) { fileNameUsed = CommonFunctionality::SaveImage(image, aFileName, true); if(!(fileNameUsed.length()>0)){ return; } else { writingSuccessful = true; } } if(!writingSuccessful) { mitk::PointSet::Pointer pointset = dynamic_cast(data); if(pointset.IsNotNull()) { std::string fileName; if(aFileName == NULL) fileName = "PointSet"; else fileName = aFileName; fileName = itksys::SystemTools::GetFilenameWithoutExtension(fileName); QString initialFileName = QString::fromStdString(fileName); QString selected_suffix("MITK Point-Sets (*.mps)"); QString possible_suffixes("MITK Point-Sets (*.mps)"); /*QString qfileName = QFileDialog::getSaveFileName( NULL, "Save image", initialFilename ,mitk::CoreObjectFactory::GetInstance()->GetSaveFileExtensions(),&selected_suffix); */ QString qfileName = GetSaveFileNameStartingInLastDirectory("Save file", initialFileName, possible_suffixes, &selected_suffix); MITK_INFO<IsExtensionValid(extension)) { QString message; message.append("File extension not suitable for writing point set data. Choose one extension of this list: "); message.append(writer->GetPossibleFileExtensionsAsString().c_str()); QMessageBox::critical(NULL,"ERROR",message); return; } if (qfileName.isEmpty() == false ) { writer->SetInput( pointset ); writer->SetFileName( qfileName.toLocal8Bit().constData() ); writer->Update(); fileNameUsed = writer->GetFileName(); writingSuccessful = true; } else { return; } } if(!writingSuccessful) { mitk::Surface::Pointer surface = dynamic_cast(data); if(surface.IsNotNull()) { fileNameUsed = CommonFunctionality::SaveSurface(surface, aFileName); if(!(fileNameUsed.length()>0)){ return; } else { writingSuccessful = true; } } if(!writingSuccessful) { // now try the file writers provided by the CoreObjectFactory mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); bool writerFound = false; for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(data) ) { writerFound = true; SaveToFileWriter(*it, data, NULL, aFileName); fileNameUsed = (*it)->GetFileName(); // correct writer has been found->break if(!(fileNameUsed.length()>0)){ return; } else { writingSuccessful = true; break; } } } if(!writerFound) { // no appropriate writer has been found QMessageBox::critical(NULL,"ERROR","Could not find file writer for this data type"); return; } } } } } else { QMessageBox::critical(NULL,"ERROR","Cannot write data (invalid/empty)"); return; } } catch(itk::ExceptionObject e) { QMessageBox::critical( NULL, "SaveDialog", e.GetDescription(),QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); } //writing is assumed to have been successful //check if file exists, file size >0 and last modified after this function was called try{ QFileInfo* fileInfo = new QFileInfo(QString(fileNameUsed.c_str())); if(!fileInfo->exists()) { QMessageBox::warning(NULL,"WARNING","File was not created or was split into multiple files"); } else if(fileInfo->size()==0) { QMessageBox::warning(NULL,"WARNING","File is empty"); } else if(fileInfo->lastModified()SetFileName( fileName ); factory->Update(); return factory->GetOutput( 0 ); } catch ( itk::ExceptionObject & ex ) { itkGenericOutputMacro( << "Exception during file open: " << ex ); return NULL; } } mitk::DataNode::Pointer CommonFunctionality::FileOpenImageSequence(const QString& aFileName) { return FileOpenImageSequence( aFileName.toLocal8Bit().constData() ); } mitk::DataNode::Pointer CommonFunctionality::FileOpenImageSequence(const char* aFileName) { if(aFileName==NULL) return NULL; mitk::DataNodeFactory::Pointer factory = mitk::DataNodeFactory::New(); QString fileName = aFileName; if (!fileName.contains("dcm") && !fileName.contains("DCM")) { int fnstart = fileName.lastIndexOf( QRegExp("[/\\\\]"), fileName.length() ); if(fnstart<0) fnstart=0; int start = fileName.indexOf( QRegExp("[0-9]"), fnstart ); if(start<0) { return FileOpen(fileName.toLocal8Bit().constData());; } char prefix[1024], pattern[1024]; strncpy(prefix, fileName.toLocal8Bit().constData(), start); prefix[start]=0; int stop=fileName.indexOf( QRegExp("[^0-9]"), start ); sprintf(pattern, "%%s%%0%uu%s",stop-start,fileName.toLocal8Bit().constData()+stop); factory->SetFilePattern( pattern ); factory->SetFilePrefix( prefix ); } else { // factory->SetFileName( fileName ); factory->SetFilePattern( fileName.toLocal8Bit().constData() ); factory->SetFilePrefix( fileName.toLocal8Bit().constData() ); } factory->Update(); return factory->GetOutput( 0 ); } mitk::DataNode::Pointer CommonFunctionality::FileOpenImageSequence() { QString fileName = QFileDialog::getOpenFileName(NULL,mitk::CoreObjectFactory::GetInstance()->GetFileExtensions()); if ( !fileName.isNull() ) { return FileOpenImageSequence(fileName); } else { return NULL; } } mitk::DataNode::Pointer CommonFunctionality::FileOpen() { return CommonFunctionality::FileOpenSpecific( mitk::CoreObjectFactory::GetInstance()->GetFileExtensions() ); } mitk::DataNode::Pointer CommonFunctionality::FileOpenSpecific( const QString& fileExtensions) { return FileOpenSpecific( fileExtensions.toLocal8Bit().constData() ); } mitk::DataNode::Pointer CommonFunctionality::FileOpenSpecific( const char *fileExtensions ) { QString fileName = QFileDialog::getOpenFileName( NULL, fileExtensions ); if ( !fileName.isNull() ) { mitk::DataNode::Pointer result = FileOpen(fileName.toLocal8Bit().constData()); if ( result.IsNull() ) { return FileOpenImageSequence(fileName); } else { return result; } } else { return NULL; } } mitk::DataNode::Pointer CommonFunctionality::OpenVolumeOrSliceStack() { mitk::DataNode::Pointer newNode = NULL; QString fileName = QFileDialog::getOpenFileName(NULL,mitk::CoreObjectFactory::GetInstance()->GetFileExtensions() ); if ( !fileName.isNull() ) { newNode = CommonFunctionality::FileOpen(fileName); if (newNode.IsNotNull()) { mitk::Image::Pointer imageData = dynamic_cast (newNode->GetData()) ; if (imageData.IsNull()) return NULL; if (imageData->GetDimension(2) == 1) { // std::string dir = itksys::SystemTools::GetFilenamePath( std::string(fileName.ascii()) ) newNode = CommonFunctionality::FileOpenImageSequence(fileName); imageData = dynamic_cast (newNode->GetData()); } return newNode; } } { return NULL; } } #include "mitkSurfaceVtkWriter.h" #include #include #include std::string CommonFunctionality::SaveSurface(mitk::Surface* surface, const char* aFileName) { std::string fileName; if(aFileName == NULL) fileName = "Surface"; else fileName = aFileName; std::string selectedItemsName = itksys::SystemTools::GetFilenameWithoutExtension(fileName); //selectedItemsName += ".stl" QString selected_suffix("STL File (*.stl)"); QString possible_suffixes("STL File (*.stl);; VTK File (*.vtk);; VTP File (*.vtp)"); QString qfileName = GetSaveFileNameStartingInLastDirectory("Save surface object", QString::fromStdString(selectedItemsName), possible_suffixes,&selected_suffix); if (qfileName.isEmpty()) return ""; std::string extension = itksys::SystemTools::GetFilenameLastExtension( qfileName.toStdString() ); if (extension == "") // if no extension has been entered manually into the filename { // get from combobox selected file extension extension = itksys::SystemTools::GetFilenameLastExtension( selected_suffix.toLocal8Bit().constData()); extension = extension.substr(0, extension.size()-1); qfileName += QString::fromStdString(extension); } if(extension == ".stl" ) { mitk::SurfaceVtkWriter::Pointer writer=mitk::SurfaceVtkWriter::New(); // check if surface actually consists of triangles; if not, the writer will not do anything; so, convert to triangles... vtkPolyData* polys = surface->GetVtkPolyData(); if( polys->GetNumberOfStrips() > 0 ) { vtkTriangleFilter* triangleFilter = vtkTriangleFilter::New(); triangleFilter->SetInput(polys); triangleFilter->Update(); polys = triangleFilter->GetOutput(); polys->Register(NULL); triangleFilter->Delete(); surface->SetVtkPolyData(polys); } writer->SetInput( surface ); writer->SetFileName(qfileName.toLocal8Bit().constData()); writer->GetVtkWriter()->SetFileTypeToBinary(); writer->Write(); } else if(extension == ".vtp") { mitk::SurfaceVtkWriter::Pointer writer=mitk::SurfaceVtkWriter::New(); writer->SetInput( surface ); writer->SetFileName(qfileName.toLocal8Bit().constData()); writer->GetVtkWriter()->SetDataModeToBinary(); writer->Write(); } else if (extension == ".vtk") { mitk::SurfaceVtkWriter::Pointer writer=mitk::SurfaceVtkWriter::New(); writer->SetInput( surface ); writer->SetFileName(qfileName.toLocal8Bit().constData()); writer->Write(); } else { // file extension not suitable for writing specified data type QMessageBox::critical(NULL,"ERROR","File extension not suitable for writing Surface data. Choose .vtk, .stl or .vtp"); return ""; } return qfileName.toLocal8Bit().constData(); } #include "mitkImageWriter.h" #include void CommonFunctionality::HandleGZExtension(std::string &baseFileName, std::string &extension) { if (extension == ".gz") { std::string filenameWithoutGZ = baseFileName; baseFileName = itksys::SystemTools::GetFilenameWithoutLastExtension( filenameWithoutGZ ); extension = itksys::SystemTools::GetFilenameLastExtension( filenameWithoutGZ ) + ".gz"; } } std::string CommonFunctionality::SaveImage(mitk::Image* image, const char* aFileName, bool askForDifferentFilename) { QString selected_suffix("Nearly Raw Raster Data (*.nrrd)"); + std::string defaultExtension = ".nrrd"; std::string fileName; if(aFileName == NULL || askForDifferentFilename) { QString initialFilename(aFileName); if (initialFilename.isEmpty()) initialFilename = "NewImage.pic"; QString qfileName = GetSaveFileNameStartingInLastDirectory("Save image", initialFilename ,mitk::CoreObjectFactory::GetInstance()->GetSaveFileExtensions(),&selected_suffix); MITK_INFO<IsExtensionValid(extension)) { + // muellerm, 12-05-02, using default file extension + // if no valid extension was given, see bug 11799 + + MITK_WARN << extension << " extension is unknown. Writing image to file " << fileName + << defaultExtension; + extension = defaultExtension; + baseFilename = itksys::SystemTools::GetFilenameName( fileName ); + //MITK_INFO << baseFilename; + + /* QString message; message.append("File extension not suitable for writing image data. Choose one extension of this list: "); message.append(imageWriter->GetPossibleFileExtensionsAsString().c_str()); QMessageBox::critical(NULL,"ERROR",message); return ""; + */ } dir += "/"; dir += baseFilename; + + if( itksys::SystemTools::FileExists( (dir + extension).c_str() ) ) + { + int answer = QMessageBox::question( QApplication::topLevelWidgets().at(0), "Warning", + QString("File %1 already exists. Overwrite?").arg( QString::fromStdString(dir + extension) ), + QMessageBox::Yes, + QMessageBox::No ); + if( answer == QMessageBox::No ) + return ""; + } imageWriter->SetInput(image); imageWriter->SetFileName(dir.c_str()); imageWriter->SetExtension(extension.c_str()); imageWriter->Write(); + fileName = dir + extension; } catch ( itk::ExceptionObject &err) { itkGenericOutputMacro( << "Exception during write: " << err ); QString exceptionString; exceptionString.append("Error during write image: "); exceptionString.append(err.GetDescription()); QMessageBox::critical(NULL,"ERROR",exceptionString); return ""; } catch ( ... ) { itkGenericOutputMacro( << "Unknown type of exception during write" ); QMessageBox::critical(NULL,"ERROR","Error during write image. Possibly no writing permission."); fileName = ""; } return fileName; } std::string CommonFunctionality::SaveScreenshot( vtkRenderWindow* renderWindow , const char* filename ) { // // perform some error checking // if ( ! renderWindow ) { itkGenericOutputMacro( << "render window is NULL!" ); return std::string(""); } if ( ! renderWindow ) { itkGenericOutputMacro( << "Unsupported type of render window! The only supported type is currently QmitkRenderWindow." ); return std::string(""); } // // create the screenshot before the filechooser is opened, // so there the file chooser will not be part of the screenshot // //QPixmap buffer = QPixmap::grabWindow( qtRenderWindow->winId() ); // new Version: //// take screenshot of render window without the coloured frame of 2 pixels by cropping the raw image data vtkWindowToImageFilter* wti = vtkWindowToImageFilter::New(); wti->SetInput( renderWindow ); wti->Update(); vtkImageData* imageData = wti->GetOutput(); int framesize = 5; int* windowSize = renderWindow->GetSize(); int numberOfScalarComponents = imageData->GetNumberOfScalarComponents(); vtkImageData* processedImageData = vtkImageData::New(); processedImageData->SetNumberOfScalarComponents(numberOfScalarComponents); processedImageData->SetExtent(0,windowSize[0]-2*framesize-1,0,windowSize[1]-2*framesize-1,0,0); processedImageData->SetScalarTypeToUnsignedChar(); for (int i=framesize; iSetScalarComponentFromDouble(i-framesize,j-framesize,0,k,imageData->GetScalarComponentAsDouble(i,j,0,k)); } } } // write new image as *.png to file vtkPNGWriter* pngWriter = vtkPNGWriter::New(); // // if the provided filename is empty ask the user // for the name of the file in which the screenshot // should be saved // std::string concreteFilename = ""; if( filename == NULL ) { // // show a file selector with the supported file formats // QString qfileName = GetSaveFileNameStartingInLastDirectory("Save screenshot", QString::fromStdString(""), QString::fromStdString(".png") ); if ( qfileName.isEmpty() ) return ""; concreteFilename = qfileName.toLocal8Bit().constData(); } else concreteFilename = filename; // make sure the filename ends with .png const std::string outFileSuffix("png"); std::string::size_type pos = concreteFilename.rfind('.'); if ( pos == std::string::npos ) concreteFilename = concreteFilename + '.' + outFileSuffix; else { std::string extname = concreteFilename.substr(pos+1); if ( extname.empty() ) concreteFilename += outFileSuffix; // name ended with '.' if ( !(extname == outFileSuffix) ) concreteFilename.replace( pos+1, std::string::npos, "png" ); } // // wait for 500 ms to let the file chooser close itself // // int msecs = 500; // clock_t ticks = ( clock_t )( ( ( ( float ) msecs ) / 1000.0f ) * ( ( float ) CLOCKS_PER_SEC ) ); // clock_t goal = ticks + std::clock(); // while ( goal > std::clock() ); // // // save the screenshot under the given filename // pngWriter->SetInput(processedImageData); //pngWriter->SetInput( wti->GetOutput() ); pngWriter->SetFileName( concreteFilename.c_str() ); pngWriter->Write(); if ( pngWriter->GetErrorCode() != 0 ) QMessageBox::information(NULL, "Save Screenshot...", "The file could not be saved. Please check filename, format and access rights..."); wti->Delete(); pngWriter->Delete(); return concreteFilename; } QString CommonFunctionality::GetSaveFileNameStartingInLastDirectory(QString caption, QString defaultFilename, QString filter, QString* selectedFilter) { QString returnValue = ""; static QString lastDirectory = ""; QString filename = lastDirectory + defaultFilename; returnValue = QFileDialog::getSaveFileName(NULL,caption,filename,filter,selectedFilter); if (returnValue != "") { std::string dir = itksys::SystemTools::GetFilenamePath( returnValue.toStdString() ); dir += Poco::Path::separator(); lastDirectory = dir.c_str(); // remember path for next save dialog } return returnValue; } diff --git a/Modules/MitkExt/Algorithms/itkAdaptiveThresholdIterator.h b/Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator.h similarity index 100% rename from Modules/MitkExt/Algorithms/itkAdaptiveThresholdIterator.h rename to Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator.h diff --git a/Modules/MitkExt/Algorithms/itkAdaptiveThresholdIterator.txx b/Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator.txx similarity index 100% rename from Modules/MitkExt/Algorithms/itkAdaptiveThresholdIterator.txx rename to Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator.txx diff --git a/Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator_Usage.txt b/Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator_Usage.txt new file mode 100644 index 0000000000..9bc242d73c --- /dev/null +++ b/Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator_Usage.txt @@ -0,0 +1,10 @@ +Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator.h:2:#ifndef __itkAdaptiveThresholdIterator_h +Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator.h:3:#define __itkAdaptiveThresholdIterator_h +Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator.h:247:#include "itkAdaptiveThresholdIterator.txx" +Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator.txx:1:#ifndef _itkAdaptiveThresholdIterator_txx +Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator.txx:2:#define _itkAdaptiveThresholdIterator_txx +Modules/Segmentation/Algorithms/itkAdaptiveThresholdIterator.txx:4:#include "itkAdaptiveThresholdIterator.h" +Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter.h:12: * iterator (such as itkAdaptiveThresholdIterator) +Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter.txx:8:#include "itkAdaptiveThresholdIterator.h" +mbi-sb/QFunctionalities/QmitkFailSafeRegionGrowing/QmitkFailSafeRegionGrowing.cpp:78:#include +mbi/Plugins/org.mbi.gui.qt.failsaferegiongrowing/src/internal/QmitkFailSafeRegionGrowing.cpp:75:#include diff --git a/Modules/MitkExt/Algorithms/itkConnectedAdaptiveThresholdImageFilter.h b/Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter.h similarity index 100% rename from Modules/MitkExt/Algorithms/itkConnectedAdaptiveThresholdImageFilter.h rename to Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter.h diff --git a/Modules/MitkExt/Algorithms/itkConnectedAdaptiveThresholdImageFilter.txx b/Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter.txx similarity index 100% rename from Modules/MitkExt/Algorithms/itkConnectedAdaptiveThresholdImageFilter.txx rename to Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter.txx diff --git a/Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter_Usage.txt b/Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter_Usage.txt new file mode 100644 index 0000000000..e4ff16556f --- /dev/null +++ b/Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter_Usage.txt @@ -0,0 +1,16 @@ +Modules/QmitkExt/QmitkAdaptiveRegionGrowingWidget.cpp:33:#include +Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter.h:1:#ifndef __itkConnectedAdaptiveThresholdImageFilter_h +Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter.h:2:#define __itkConnectedAdaptiveThresholdImageFilter_h +Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter.h:117:#include "itkConnectedAdaptiveThresholdImageFilter.txx" +Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter.txx:2:#ifndef _itkConnectedAdaptiveThresholdImageFilter_txx +Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter.txx:3:#define _itkConnectedAdaptiveThresholdImageFilter_txx +Modules/Segmentation/Algorithms/itkConnectedAdaptiveThresholdImageFilter.txx:5:#include "itkConnectedAdaptiveThresholdImageFilter.h" +Modules/Segmentation/Interactions/mitkRegionGrow3DTool.cpp:27:#include "itkConnectedAdaptiveThresholdImageFilter.h" +mbi-sb/BundlesQt/org.mitk.gui.qt.patchproposalplanning/src/internal/QmitkPatchProposalPlanningView.cpp:68:#include +mbi-sb/QApplications/VesselnessTools/RegionGrowPhilipp.cpp:4:#include +mbi-sb/QFunctionalities/QmitkAortaPlanning/QmitkAortaPlanning.cpp:71:#include +mbi-sb/QFunctionalities/QmitkFailSafeRegionGrowing/QmitkFailSafeRegionGrowing.cpp:73:#include +mbi/Modules/LiverSegmentation/mitkVesselSegmentationTool.cpp:11://#include +mbi/Modules/VesselSegmentationUI/Qmitk/QmitkAdaptiveRegionGrowingView.cpp:46:#include +mbi/Modules/VesselSegmentationUI/Qmitk/QmitkBoostVesselTreeSegmentationView.cpp:47:#include +mbi/Plugins/org.mbi.gui.qt.failsaferegiongrowing/src/internal/QmitkFailSafeRegionGrowing.cpp:71:#include diff --git a/Modules/MitkExt/Algorithms/itkContourExtractor2DImageFilter.h b/Modules/Segmentation/Algorithms/itkContourExtractor2DImageFilter.h similarity index 100% rename from Modules/MitkExt/Algorithms/itkContourExtractor2DImageFilter.h rename to Modules/Segmentation/Algorithms/itkContourExtractor2DImageFilter.h diff --git a/Modules/MitkExt/Algorithms/itkContourExtractor2DImageFilter.txx b/Modules/Segmentation/Algorithms/itkContourExtractor2DImageFilter.txx similarity index 100% rename from Modules/MitkExt/Algorithms/itkContourExtractor2DImageFilter.txx rename to Modules/Segmentation/Algorithms/itkContourExtractor2DImageFilter.txx diff --git a/Modules/MitkExt/Algorithms/itkImageToPathFilter.h b/Modules/Segmentation/Algorithms/itkImageToPathFilter.h similarity index 100% rename from Modules/MitkExt/Algorithms/itkImageToPathFilter.h rename to Modules/Segmentation/Algorithms/itkImageToPathFilter.h diff --git a/Modules/MitkExt/Algorithms/itkImageToPathFilter.txx b/Modules/Segmentation/Algorithms/itkImageToPathFilter.txx similarity index 100% rename from Modules/MitkExt/Algorithms/itkImageToPathFilter.txx rename to Modules/Segmentation/Algorithms/itkImageToPathFilter.txx diff --git a/Modules/MitkExt/Algorithms/mitkCalculateSegmentationVolume.cpp b/Modules/Segmentation/Algorithms/mitkCalculateSegmentationVolume.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkCalculateSegmentationVolume.cpp rename to Modules/Segmentation/Algorithms/mitkCalculateSegmentationVolume.cpp diff --git a/Modules/MitkExt/Algorithms/mitkCalculateSegmentationVolume.h b/Modules/Segmentation/Algorithms/mitkCalculateSegmentationVolume.h similarity index 93% rename from Modules/MitkExt/Algorithms/mitkCalculateSegmentationVolume.h rename to Modules/Segmentation/Algorithms/mitkCalculateSegmentationVolume.h index 826a265ddb..6131ea0d04 100644 --- a/Modules/MitkExt/Algorithms/mitkCalculateSegmentationVolume.h +++ b/Modules/Segmentation/Algorithms/mitkCalculateSegmentationVolume.h @@ -1,61 +1,61 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITK_CALCULATE_SEGMENTATION_VOLUME_H_INCLUDET_WAD #define MITK_CALCULATE_SEGMENTATION_VOLUME_H_INCLUDET_WAD #include "mitkSegmentationSink.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkImageCast.h" namespace mitk { -class MitkExt_EXPORT CalculateSegmentationVolume : public SegmentationSink +class Segmentation_EXPORT CalculateSegmentationVolume : public SegmentationSink { public: mitkClassMacro( CalculateSegmentationVolume, SegmentationSink ) mitkAlgorithmNewMacro( CalculateSegmentationVolume ); protected: CalculateSegmentationVolume(); // use smart pointers virtual ~CalculateSegmentationVolume(); virtual bool ReadyToRun(); virtual bool ThreadedUpdateFunction(); // will be called from a thread after calling StartAlgorithm template < typename TPixel, unsigned int VImageDimension > void ItkImageProcessing( itk::Image< TPixel, VImageDimension >* itkImage, TPixel* dummy = NULL ); private: unsigned int m_Volume; Vector3D m_CenterOfMass; Vector3D m_MinIndexOfBoundingBox; Vector3D m_MaxIndexOfBoundingBox; }; } // namespace #endif diff --git a/Modules/MitkExt/Algorithms/mitkComputeContourSetNormalsFilter.cpp b/Modules/Segmentation/Algorithms/mitkComputeContourSetNormalsFilter.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkComputeContourSetNormalsFilter.cpp rename to Modules/Segmentation/Algorithms/mitkComputeContourSetNormalsFilter.cpp diff --git a/Modules/MitkExt/Algorithms/mitkComputeContourSetNormalsFilter.h b/Modules/Segmentation/Algorithms/mitkComputeContourSetNormalsFilter.h similarity index 95% rename from Modules/MitkExt/Algorithms/mitkComputeContourSetNormalsFilter.h rename to Modules/Segmentation/Algorithms/mitkComputeContourSetNormalsFilter.h index b3467bd15f..b9e9366da3 100644 --- a/Modules/MitkExt/Algorithms/mitkComputeContourSetNormalsFilter.h +++ b/Modules/Segmentation/Algorithms/mitkComputeContourSetNormalsFilter.h @@ -1,106 +1,106 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: $ Version: $Revision: $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkComputeContourSetNormalsFilter_h_Included #define mitkComputeContourSetNormalsFilter_h_Included -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkSurfaceToSurfaceFilter.h" #include "mitkProgressBar.h" #include "mitkSurface.h" #include "vtkCellArray.h" #include "vtkPolyData.h" #include "vtkSmartPointer.h" #include "vtkDoubleArray.h" #include "vtkMath.h" #include "vtkCellData.h" #include "vtkLine.h" #include "mitkImage.h" namespace mitk { /** \brief Filter to compute the normales for contours based on vtkPolygons This filter takes a number of extracted contours and computes the normals for each contour edge point. The normals can be accessed by calling: filter->GetOutput(i)->GetVtkPolyData()->GetCellData()->GetNormals(); See also the method GetNormalsAsSurface() Note: If a segmentation binary image is provided this filter assures that the computed normals do not point into the segmentation image $Author: fetzer$ */ -class MitkExt_EXPORT ComputeContourSetNormalsFilter : public SurfaceToSurfaceFilter +class Segmentation_EXPORT ComputeContourSetNormalsFilter : public SurfaceToSurfaceFilter { public: mitkClassMacro(ComputeContourSetNormalsFilter,SurfaceToSurfaceFilter); itkNewMacro(Self); itkSetMacro(SegmentationBinaryImage, mitk::Image::Pointer); /* \brief Returns the computed normals as a surface */ mitk::Surface::Pointer GetNormalsAsSurface(); //Resets the filter, i.e. removes all inputs and outputs void Reset(); void SetMaxSpacing(double); /** \brief Set whether the mitkProgressBar should be used \a Parameter true for using the progress bar, false otherwise */ void SetUseProgressBar(bool); /** \brief Set the stepsize which the progress bar should proceed \a Parameter The stepsize for progressing */ void SetProgressStepSize(unsigned int stepSize); protected: ComputeContourSetNormalsFilter(); virtual ~ComputeContourSetNormalsFilter(); virtual void GenerateData(); virtual void GenerateOutputInformation(); private: //The segmentation out of which the contours were extracted. Can be used to determine the direction of the normals mitk::Image::Pointer m_SegmentationBinaryImage; double m_MaxSpacing; unsigned int m_NegativeNormalCounter; unsigned int m_PositiveNormalCounter; bool m_UseProgressBar; unsigned int m_ProgressStepSize; };//class }//namespace #endif diff --git a/Modules/MitkExt/Algorithms/mitkContourSetToPointSetFilter.cpp b/Modules/Segmentation/Algorithms/mitkContourSetToPointSetFilter.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkContourSetToPointSetFilter.cpp rename to Modules/Segmentation/Algorithms/mitkContourSetToPointSetFilter.cpp diff --git a/Modules/MitkExt/Algorithms/mitkContourSetToPointSetFilter.h b/Modules/Segmentation/Algorithms/mitkContourSetToPointSetFilter.h similarity index 93% rename from Modules/MitkExt/Algorithms/mitkContourSetToPointSetFilter.h rename to Modules/Segmentation/Algorithms/mitkContourSetToPointSetFilter.h index 04bdb21113..37e49036b6 100644 --- a/Modules/MitkExt/Algorithms/mitkContourSetToPointSetFilter.h +++ b/Modules/Segmentation/Algorithms/mitkContourSetToPointSetFilter.h @@ -1,69 +1,69 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _mitkContourSetToPointSetFilter_h__ #define _mitkContourSetToPointSetFilter_h__ #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkPointSet.h" #include "mitkPointSetSource.h" #include "mitkContourSet.h" namespace mitk { /** * * @brief Converts a contour set to a point set. * * The resulting pointset consists of sample points of all the contours * * @ingroup SurfaceFilters * @ingroup Process */ -class MitkExt_EXPORT ContourSetToPointSetFilter : public PointSetSource +class Segmentation_EXPORT ContourSetToPointSetFilter : public PointSetSource { public: mitkClassMacro(ContourSetToPointSetFilter, PointSetSource); itkNewMacro(Self); itkSetMacro(Frequency, unsigned int); itkGetMacro(Frequency, unsigned int); virtual void GenerateOutputInformation(); virtual void GenerateData(); const mitk::ContourSet* GetInput(void); virtual void SetInput(const mitk::ContourSet *contourSet); protected: ContourSetToPointSetFilter(); virtual ~ContourSetToPointSetFilter(); protected: unsigned int m_Frequency; }; } // namespace mitk #endif // _mitkContourSetToPointSetFilter_h__ diff --git a/Modules/MitkExt/Algorithms/mitkContourUtils.cpp b/Modules/Segmentation/Algorithms/mitkContourUtils.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkContourUtils.cpp rename to Modules/Segmentation/Algorithms/mitkContourUtils.cpp diff --git a/Modules/MitkExt/Algorithms/mitkContourUtils.h b/Modules/Segmentation/Algorithms/mitkContourUtils.h similarity index 96% rename from Modules/MitkExt/Algorithms/mitkContourUtils.h rename to Modules/Segmentation/Algorithms/mitkContourUtils.h index 4b49e8ebaa..c40da5ff1e 100644 --- a/Modules/MitkExt/Algorithms/mitkContourUtils.h +++ b/Modules/Segmentation/Algorithms/mitkContourUtils.h @@ -1,79 +1,79 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkContourUtilshIncludett #define mitkContourUtilshIncludett #include "mitkImage.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkContour.h" #include "mitkLegacyAdaptors.h" #include namespace mitk { /** * \brief Helpful methods for working with contours and images * * Originally copied from FeedbackContourTool */ -class MitkExt_EXPORT ContourUtils : public itk::Object +class Segmentation_EXPORT ContourUtils : public itk::Object { public: mitkClassMacro(ContourUtils, itk::Object); itkNewMacro(ContourUtils); /** \brief Projects a contour onto an image point by point. Converts from world to index coordinates. \param correctionForIpSegmentation adds 0.5 to x and y index coordinates (difference between ipSegmentation and MITK contours) */ Contour::Pointer ProjectContourTo2DSlice(Image* slice, Contour* contourIn3D, bool correctionForIpSegmentation, bool constrainToInside); /** \brief Projects a slice index coordinates of a contour back into world coordinates. \param correctionForIpSegmentation subtracts 0.5 to x and y index coordinates (difference between ipSegmentation and MITK contours) */ Contour::Pointer BackProjectContourFrom2DSlice(const Geometry3D* sliceGeometry, Contour* contourIn2D, bool correctionForIpSegmentation = false); /** \brief Fill a contour in a 2D slice with a specified pixel value. */ void FillContourInSlice( Contour* projectedContour, Image* sliceImage, int paintingPixelValue = 1 ); protected: ContourUtils(); virtual ~ContourUtils(); /** \brief Paint a filled contour (e.g. of an ipSegmentation pixel type) into a mitk::Image (or arbitraty pixel type). Will not copy the whole filledContourSlice, but only set those pixels in originalSlice to overwritevalue, where the corresponding pixel in filledContourSlice is non-zero. */ template void ItkCopyFilledContourToSlice( itk::Image* originalSlice, const Image* filledContourSlice, int overwritevalue = 1 ); }; } #endif diff --git a/Modules/MitkExt/Algorithms/mitkCorrectorAlgorithm.cpp b/Modules/Segmentation/Algorithms/mitkCorrectorAlgorithm.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkCorrectorAlgorithm.cpp rename to Modules/Segmentation/Algorithms/mitkCorrectorAlgorithm.cpp diff --git a/Modules/MitkExt/Algorithms/mitkCorrectorAlgorithm.h b/Modules/Segmentation/Algorithms/mitkCorrectorAlgorithm.h similarity index 96% rename from Modules/MitkExt/Algorithms/mitkCorrectorAlgorithm.h rename to Modules/Segmentation/Algorithms/mitkCorrectorAlgorithm.h index 4ae9403074..9b1e48b129 100644 --- a/Modules/MitkExt/Algorithms/mitkCorrectorAlgorithm.h +++ b/Modules/Segmentation/Algorithms/mitkCorrectorAlgorithm.h @@ -1,99 +1,99 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkCorrectorAlgorithmhIncluded #define mitkCorrectorAlgorithmhIncluded #include "mitkImageToImageFilter.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkContour.h" #include "ipSegmentation.h" #include namespace mitk { /** * This class encapsulates an algorithm, which takes a 2D binary image and a contour. * The algorithm tests if the line begins and ends inside or outside a segmentation * and whether areas should be added to or subtracted from the segmentation shape. * * This class has two outputs: * \li a difference image from GetDifferenceImage() * \li the modified input image from GetOutput() * * The difference image is an image of the same dimensions as the input. Each pixel has * one of three values -1, 0, +1 meaning * \li -1 this pixel was foreground in the input image and should be removed from the segmentation * \li 0 this pixel needs no change * \li +1 this pixel was background in the input image and should be added to the segmentation * * The output image is a combination of the original input with the generated difference image. * * \sa CorrectorTool2D */ -class MitkExt_EXPORT CorrectorAlgorithm : public ImageToImageFilter +class Segmentation_EXPORT CorrectorAlgorithm : public ImageToImageFilter { public: mitkClassMacro(CorrectorAlgorithm, ImageToImageFilter); itkNewMacro(CorrectorAlgorithm); /** * \brief User drawn contour */ itkSetMacro(Contour, Contour*); /** * \brief Calculated difference image. */ //itkGetObjectMacro(DifferenceImage, Image); protected: // used by TobiasHeimannCorrectionAlgorithm typedef struct { int lineStart; int lineEnd; bool modified; } TSegData; CorrectorAlgorithm(); virtual ~CorrectorAlgorithm(); // does the actual processing virtual void GenerateData(); void TobiasHeimannCorrectionAlgorithm(mitkIpPicDescriptor* pic); bool modifySegment( int lineStart, int lineEnd, ipMITKSegmentationTYPE state, mitkIpPicDescriptor *pic, int* _ofsArray ); void CalculateDifferenceImage( Image* modifiedImage, Image* originalImage ); template void ItkCalculateDifferenceImage( itk::Image* originalImage, Image* modifiedMITKImage ); Image::Pointer m_WorkingImage; Contour::ConstPointer m_Contour; Image::Pointer m_DifferenceImage; }; } #endif diff --git a/Modules/MitkExt/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.cpp b/Modules/Segmentation/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.cpp rename to Modules/Segmentation/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.cpp diff --git a/Modules/MitkExt/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.h b/Modules/Segmentation/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.h similarity index 97% rename from Modules/MitkExt/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.h rename to Modules/Segmentation/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.h index 3113cd11b9..4486652752 100644 --- a/Modules/MitkExt/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.h +++ b/Modules/Segmentation/Algorithms/mitkCreateDistanceImageFromSurfaceFilter.h @@ -1,159 +1,159 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: $ Version: $Revision: $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkCreateDistanceImageFromSurfaceFilter_h_Included #define mitkCreateDistanceImageFromSurfaceFilter_h_Included -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkImageSource.h" #include "mitkSurface.h" #include "mitkProgressBar.h" #include "vtkSmartPointer.h" #include "vtkDoubleArray.h" #include "vtkCellArray.h" #include "vtkCellData.h" #include "vtkPolyData.h" #include "vnl/vnl_matrix.h" #include "vnl/vnl_vector.h" #include "vnl/vnl_vector_fixed.h" #include "vnl/algo/vnl_qr.h" #include "itkImage.h" #include "itkImageRegionIteratorWithIndex.h" #include "itkNeighborhoodIterator.h" #include namespace mitk { /** \brief This filter interpolates the 3D surface for a segmented area. The basis for the interpolation are the edge-points of contours that are drawn into an image. The interpolation itself is performed via Radial Basis Function Interpolation. ATTENTION: This filter needs beside the edge points of the delineated contours additionally the normals for each edge point. \sa mitkSurfaceInterpolationController Based on the contour edge points and their normal this filter calculates a distance function with the following properties: - Putting a point into the distance function that lies inside the considered surface gives a negativ scalar value - Putting a point into the distance function that lies outside the considered surface gives a positive scalar value - Putting a point into the distance function that lies exactly on the considered surface gives the value zero With this interpolated distance function a distance image will be created. The desired surface can then be extract e.g. with the marching cubes algorithm. (Within the distance image the surface goes exactly where the pixelvalues are zero) Note that the obtained distance image has always an isotropig spacing. The size (in this case volume) of the image can be adjusted by calling SetDistanceImageVolume(unsigned int volume) which specifies the number ob pixels enclosed by the image. \ingroup Process $Author: fetzer$ */ - class MitkExt_EXPORT CreateDistanceImageFromSurfaceFilter : public ImageSource + class Segmentation_EXPORT CreateDistanceImageFromSurfaceFilter : public ImageSource { public: typedef vnl_vector_fixed PointType; typedef std::vector< PointType > NormalList; typedef std::vector< PointType > CenterList; typedef vnl_matrix SolutionMatrix; typedef vnl_vector FunctionValues; typedef vnl_vector InterpolationWeights; typedef std::vector SurfaceList; mitkClassMacro(CreateDistanceImageFromSurfaceFilter,ImageSource); itkNewMacro(Self); //Methods copied from mitkSurfaceToSurfaceFilter virtual void SetInput( const mitk::Surface* surface ); virtual void SetInput( unsigned int idx, const mitk::Surface* surface ); virtual const mitk::Surface* GetInput(); virtual const mitk::Surface* GetInput( unsigned int idx ); virtual void RemoveInputs(mitk::Surface* input); /* \brief Set the size of the output distance image. The size is specified by the image's volume (i.e. in this case how many pixels are enclosed by the image) If non is set, the volume will be 500000 pixels. */ itkSetMacro(DistanceImageVolume, unsigned int); void PrintEquationSystem(); //Resets the filter, i.e. removes all inputs and outputs void Reset(); /** \brief Set whether the mitkProgressBar should be used \a Parameter true for using the progress bar, false otherwise */ void SetUseProgressBar(bool); /** \brief Set the stepsize which the progress bar should proceed \a Parameter The stepsize for progressing */ void SetProgressStepSize(unsigned int stepSize); protected: CreateDistanceImageFromSurfaceFilter(); virtual ~CreateDistanceImageFromSurfaceFilter(); virtual void GenerateData(); virtual void GenerateOutputInformation(); private: void CreateSolutionMatrixAndFunctionValues(); double CalculateDistanceValue(PointType p); void CreateDistanceImage (); //Datastructures for the interpolation CenterList m_Centers; NormalList m_Normals; FunctionValues m_FunctionValues; InterpolationWeights m_Weights; SolutionMatrix m_SolutionMatrix; double m_DistanceImageSpacing; unsigned int m_DistanceImageVolume; bool m_UseProgressBar; unsigned int m_ProgressStepSize; }; }//namespace #endif diff --git a/Modules/MitkExt/Algorithms/mitkDiffImageApplier.cpp b/Modules/Segmentation/Algorithms/mitkDiffImageApplier.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkDiffImageApplier.cpp rename to Modules/Segmentation/Algorithms/mitkDiffImageApplier.cpp diff --git a/Modules/MitkExt/Algorithms/mitkDiffImageApplier.h b/Modules/Segmentation/Algorithms/mitkDiffImageApplier.h similarity index 95% rename from Modules/MitkExt/Algorithms/mitkDiffImageApplier.h rename to Modules/Segmentation/Algorithms/mitkDiffImageApplier.h index e21c7595a8..c72b309ad0 100644 --- a/Modules/MitkExt/Algorithms/mitkDiffImageApplier.h +++ b/Modules/Segmentation/Algorithms/mitkDiffImageApplier.h @@ -1,87 +1,87 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.0 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkDiffImageApplier_h_Included #define mitkDiffImageApplier_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkOperationActor.h" #include "mitkImage.h" #include #include namespace mitk { /** \brief Applies difference images to 3D images. This class is supposed to execute ApplyDiffImageOperations, which contain information about pixel changes within one image slice. Class should be called from the undo stack. At the moment, ApplyDiffImageOperations are only created by OverwriteSliceImageFilter. $Author: maleike $ */ -class MitkExt_EXPORT DiffImageApplier : public itk::Object, public OperationActor +class Segmentation_EXPORT DiffImageApplier : public itk::Object, public OperationActor { public: mitkClassMacro(DiffImageApplier, Object); itkNewMacro(DiffImageApplier); virtual void ExecuteOperation( Operation* operation ); static DiffImageApplier* GetInstanceForUndo(); protected: DiffImageApplier(); // purposely hidden virtual ~DiffImageApplier(); template void ItkImageSwitch2DDiff( itk::Image* image ); template void ItkImageSwitch3DDiff( itk::Image* image ); template void ItkImageProcessing2DDiff( itk::Image* itkImage1, itk::Image* itkImage2 ); template void ItkImageProcessing3DDiff( itk::Image* itkImage1, itk::Image* itkImage2 ); template void ItkInvertPixelValues( itk::Image* itkImage ); Image::Pointer m_Image; Image::ConstPointer m_SliceDifferenceImage; unsigned int m_SliceIndex; unsigned int m_SliceDimension; unsigned int m_TimeStep; unsigned int m_Dimension0; unsigned int m_Dimension1; double m_Factor; }; } // namespace #endif diff --git a/Modules/MitkExt/Algorithms/mitkImageToContourFilter.cpp b/Modules/Segmentation/Algorithms/mitkImageToContourFilter.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkImageToContourFilter.cpp rename to Modules/Segmentation/Algorithms/mitkImageToContourFilter.cpp diff --git a/Modules/MitkExt/Algorithms/mitkImageToContourFilter.h b/Modules/Segmentation/Algorithms/mitkImageToContourFilter.h similarity index 96% rename from Modules/MitkExt/Algorithms/mitkImageToContourFilter.h rename to Modules/Segmentation/Algorithms/mitkImageToContourFilter.h index e7022b7470..4c1895e3fc 100644 --- a/Modules/MitkExt/Algorithms/mitkImageToContourFilter.h +++ b/Modules/Segmentation/Algorithms/mitkImageToContourFilter.h @@ -1,92 +1,92 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: $ Version: $Revision: $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkImageToContourFilter_h_Included #define mitkImageToContourFilter_h_Included //#include "MitkSBExports.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "itkImage.h" #include "mitkImage.h" #include "itkContourExtractor2DImageFilter.h" #include "mitkImageToSurfaceFilter.h" #include "mitkSurface.h" #include "vtkPolyData.h" #include "vtkPolygon.h" #include "vtkCellArray.h" #include "mitkProgressBar.h" namespace mitk { /** \brief A filter that can extract contours out of a 2D binary image This class takes an 2D mitk::Image as input and extracts all contours which are drawn it. The contour extraction is done by using the itk::ContourExtractor2DImageFilter. The output is a mitk::Surface. $Author: fetzer$ */ -class MitkExt_EXPORT ImageToContourFilter : public ImageToSurfaceFilter +class Segmentation_EXPORT ImageToContourFilter : public ImageToSurfaceFilter { public: mitkClassMacro(ImageToContourFilter,ImageToSurfaceFilter); itkNewMacro(Self); /** \brief Set macro for the geometry of the slice. If it is not set explicitly the geometry will be taken from the slice \a Parameter The slice`s geometry */ itkSetMacro(SliceGeometry, Geometry3D*); //typedef unsigned int VDimension; typedef itk::PolyLineParametricPath<2> PolyLineParametricPath2D; typedef PolyLineParametricPath2D::VertexListType ContourPath; /** \brief Set whether the mitkProgressBar should be used \a Parameter true for using the progress bar, false otherwise */ void SetUseProgressBar(bool); /** \brief Set the stepsize which the progress bar should proceed \a Parameter The stepsize for progressing */ void SetProgressStepSize(unsigned int stepSize); protected: ImageToContourFilter(); virtual ~ImageToContourFilter(); virtual void GenerateData(); virtual void GenerateOutputInformation(); private: const Geometry3D* m_SliceGeometry; bool m_UseProgressBar; unsigned int m_ProgressStepSize; template void Itk2DContourExtraction (itk::Image* sliceImage); };//class }//namespace #endif diff --git a/Modules/MitkExt/Algorithms/mitkManualSegmentationToSurfaceFilter.cpp b/Modules/Segmentation/Algorithms/mitkManualSegmentationToSurfaceFilter.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkManualSegmentationToSurfaceFilter.cpp rename to Modules/Segmentation/Algorithms/mitkManualSegmentationToSurfaceFilter.cpp diff --git a/Modules/MitkExt/Algorithms/mitkManualSegmentationToSurfaceFilter.h b/Modules/Segmentation/Algorithms/mitkManualSegmentationToSurfaceFilter.h similarity index 97% rename from Modules/MitkExt/Algorithms/mitkManualSegmentationToSurfaceFilter.h rename to Modules/Segmentation/Algorithms/mitkManualSegmentationToSurfaceFilter.h index 590411d0ea..eb5a5c109b 100644 --- a/Modules/MitkExt/Algorithms/mitkManualSegmentationToSurfaceFilter.h +++ b/Modules/Segmentation/Algorithms/mitkManualSegmentationToSurfaceFilter.h @@ -1,170 +1,170 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _MITKMANUALSEGMENTATIONTISURFACEFILTER_h__ #define _MITKMANUALSEGMENTATIONTISURFACEFILTER_h__ #include -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include #include #include #include namespace mitk { /** * @brief Supplies a 3D surface from pre-processed segmentation. * * The resulting surface depends on a filter pipeline based on vtkMedian (1) and a Gaussian filter with vtkImageGaussianSmooth (2). * All voxel can be changed to an isotropic representation of the * image (ATTANTION: the number of voxels in the will change). The * resulting isotropic image has 1mm isotropic voxel by default. But * can be varied freely. * * @ingroup ImageFilters * @ingroup Process */ - class MitkExt_EXPORT ManualSegmentationToSurfaceFilter : public ImageToSurfaceFilter + class Segmentation_EXPORT ManualSegmentationToSurfaceFilter : public ImageToSurfaceFilter { public: mitkClassMacro(ManualSegmentationToSurfaceFilter,ImageToSurfaceFilter); typedef double vtkDouble; /** * Will pre-process a segmentation voxelwise. The segmentation can use * a hole fill relating a median filter and smooth by a Gaussian * filter. * The image can be interpolated to an isotropic image. * By default every filter is disabled. * This method calls CreateSurface from mitkImageToSurfaceFilter and * does not need a manual call since we use Update(). */ virtual void GenerateData(); itkNewMacro(Self); /** * Supplies a method for setting median filter by a bool value. */ itkSetMacro(MedianFilter3D,bool); /** * Return state if median filter is enabled. */ itkGetConstMacro(MedianFilter3D,bool); /** * Enable the median filter (first filter in pipeline). */ itkBooleanMacro(MedianFilter3D); /** * Supplies a method to enable Interpolation. */ itkSetMacro(Interpolation,bool); /** * Returns activation state of interpolation filter. */ itkGetConstMacro(Interpolation,bool); /** * Enable the interpolation filter (second filter in pipeline) for * isotropic voxel. */ itkBooleanMacro(Interpolation); /** * Supplies a method for Gaussian filter (third filter in pipeline). */ itkSetMacro(UseGaussianImageSmooth,bool); /** * Returns activation state of standard deviation filter. */ itkGetConstMacro(UseGaussianImageSmooth,bool); /** * Enables Gaussian image smooth. As well the threshold for the * CreateSurface() method will raise the threshold to 49 and changes * the image range set from 0 to 100. It is made for reasons in * binary images to prevent conflicts with the used filter. There are * better results for dividing fore- and background. */ itkBooleanMacro(UseGaussianImageSmooth); /** * Set standard deviation for Gaussian Filter. * @param _arg by default 1.5 */ itkSetMacro(GaussianStandardDeviation, double); /** * Returns the standard deviation of the Gaussian filter which will be * used when filter is enabled. */ itkGetConstMacro(GaussianStandardDeviation, double); /** * Set the Kernel for Median3DFilter. By default kernel is set to 3x3x3. * If you choose '1' nothing will be processed in this direction. */ void SetMedianKernelSize(int x, int y, int z); /** * Returns the kernel size in the first direction. */ itkGetConstMacro(MedianKernelSizeX, int); /** * Returns the kernel size in the second direction. */ itkGetConstMacro(MedianKernelSizeY, int); /** * Returns the kernel size in the third direction. */ itkGetConstMacro(MedianKernelSizeZ, int); /** * Set the values for Spacing in X, Y and Z-Dimension */ void SetInterpolation(vtkDouble x, vtkDouble y, vtkDouble z); protected: ManualSegmentationToSurfaceFilter(); virtual ~ManualSegmentationToSurfaceFilter(); bool m_MedianFilter3D; int m_MedianKernelSizeX, m_MedianKernelSizeY, m_MedianKernelSizeZ; bool m_UseGaussianImageSmooth; //Gaussian Filter double m_GaussianStandardDeviation; bool m_Interpolation; vtkDouble m_InterpolationX; vtkDouble m_InterpolationY; vtkDouble m_InterpolationZ; };//namespace } #endif //_MITKMANUALSEGMENTATIONTISURFACEFILTER_h__ diff --git a/Modules/MitkExt/Algorithms/mitkOverwriteDirectedPlaneImageFilter.cpp b/Modules/Segmentation/Algorithms/mitkOverwriteDirectedPlaneImageFilter.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkOverwriteDirectedPlaneImageFilter.cpp rename to Modules/Segmentation/Algorithms/mitkOverwriteDirectedPlaneImageFilter.cpp diff --git a/Modules/MitkExt/Algorithms/mitkOverwriteDirectedPlaneImageFilter.h b/Modules/Segmentation/Algorithms/mitkOverwriteDirectedPlaneImageFilter.h similarity index 97% rename from Modules/MitkExt/Algorithms/mitkOverwriteDirectedPlaneImageFilter.h rename to Modules/Segmentation/Algorithms/mitkOverwriteDirectedPlaneImageFilter.h index 90ca6832ed..e85537156c 100644 --- a/Modules/MitkExt/Algorithms/mitkOverwriteDirectedPlaneImageFilter.h +++ b/Modules/Segmentation/Algorithms/mitkOverwriteDirectedPlaneImageFilter.h @@ -1,119 +1,119 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2010-01-28 18:32:03 +0100 (Do, 28 Jan 2010) $ Version: $Revision: 21147 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkOverwriteDirectedPlaneImageFilter_h_Included #define mitkOverwriteDirectedPlaneImageFilter_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkImageToImageFilter.h" #include namespace mitk { /** \brief Writes a 2D slice into a 3D image. \sa SegTool2D \sa ContourTool \sa ExtractImageFilter \ingroup Process \ingroup Reliver There is a separate page describing the general design of QmitkInteractiveSegmentation: \ref QmitkInteractiveSegmentationTechnicalPage This class takes a 3D mitk::Image as input and tries to replace one slice in it with the second input image, which is specified by calling SetSliceImage with a 2D mitk::Image. Two parameters determine which slice is replaced: the "slice dimension" is that one, which is constant for all points in the plane, e.g. transversal would mean 2. The "slice index" is the slice index in the image direction you specified with "affected dimension". Indices count from zero. This class works with all kind of image types, the only restrictions being that the input is 3D, and the slice image is 2D. If requested by SetCreateUndoInformation(true), this class will create instances of ApplyDiffImageOperation for the undo stack. These operations will (on user request) be executed by DiffImageApplier to perform undo. Last contributor: $Author: maleike $ */ -class MitkExt_EXPORT OverwriteDirectedPlaneImageFilter : public ImageToImageFilter +class Segmentation_EXPORT OverwriteDirectedPlaneImageFilter : public ImageToImageFilter { public: mitkClassMacro(OverwriteDirectedPlaneImageFilter, ImageToImageFilter); itkNewMacro(OverwriteDirectedPlaneImageFilter); /** \brief Which plane to overwrite */ const Geometry3D* GetPlaneGeometry3D() const { return m_PlaneGeometry; } void SetPlaneGeometry3D( const Geometry3D *geometry ) { m_PlaneGeometry = geometry; } /** \brief Time step of the slice to overwrite */ itkSetMacro(TimeStep, unsigned int); itkGetConstMacro(TimeStep, unsigned int); /** \brief Whether to create undo operation in the MITK undo stack */ itkSetMacro(CreateUndoInformation, bool); itkGetConstMacro(CreateUndoInformation, bool); itkSetObjectMacro(SliceImage, Image); const Image* GetSliceImage() { return m_SliceImage.GetPointer(); } const Image* GetLastDifferenceImage() { return m_SliceDifferenceImage.GetPointer(); } protected: OverwriteDirectedPlaneImageFilter(); // purposely hidden virtual ~OverwriteDirectedPlaneImageFilter(); virtual void GenerateData(); template void ItkSliceOverwriting (itk::Image* input3D); template void ItkImageSwitch( itk::Image* image ); template void ItkImageProcessing( itk::Image* itkImage1, itk::Image* itkImage2 ); //std::string EventDescription( unsigned int sliceDimension, unsigned int sliceIndex, unsigned int timeStep ); Image::ConstPointer m_SliceImage; Image::Pointer m_SliceDifferenceImage; const Geometry3D *m_PlaneGeometry; const Geometry3D *m_ImageGeometry3D; unsigned int m_TimeStep; unsigned int m_Dimension0; unsigned int m_Dimension1; bool m_CreateUndoInformation; }; } // namespace #endif diff --git a/Modules/MitkExt/Algorithms/mitkOverwriteSliceImageFilter.cpp b/Modules/Segmentation/Algorithms/mitkOverwriteSliceImageFilter.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkOverwriteSliceImageFilter.cpp rename to Modules/Segmentation/Algorithms/mitkOverwriteSliceImageFilter.cpp diff --git a/Modules/MitkExt/Algorithms/mitkOverwriteSliceImageFilter.h b/Modules/Segmentation/Algorithms/mitkOverwriteSliceImageFilter.h similarity index 97% rename from Modules/MitkExt/Algorithms/mitkOverwriteSliceImageFilter.h rename to Modules/Segmentation/Algorithms/mitkOverwriteSliceImageFilter.h index 5e4366f582..dc7c8f1261 100644 --- a/Modules/MitkExt/Algorithms/mitkOverwriteSliceImageFilter.h +++ b/Modules/Segmentation/Algorithms/mitkOverwriteSliceImageFilter.h @@ -1,124 +1,124 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkOverwriteSliceImageFilter_h_Included #define mitkOverwriteSliceImageFilter_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkImageToImageFilter.h" #include namespace mitk { /** \brief Writes a 2D slice into a 3D image. \sa SegTool2D \sa ContourTool \sa ExtractImageFilter \ingroup Process \ingroup ToolManagerEtAl There is a separate page describing the general design of QmitkInteractiveSegmentation: \ref QmitkInteractiveSegmentationTechnicalPage This class takes a 3D mitk::Image as input and tries to replace one slice in it with the second input image, which is specified by calling SetSliceImage with a 2D mitk::Image. Two parameters determine which slice is replaced: the "slice dimension" is that one, which is constant for all points in the plane, e.g. transversal would mean 2. The "slice index" is the slice index in the image direction you specified with "affected dimension". Indices count from zero. This class works with all kind of image types, the only restrictions being that the input is 3D, and the slice image is 2D. If requested by SetCreateUndoInformation(true), this class will create instances of ApplyDiffImageOperation for the undo stack. These operations will (on user request) be executed by DiffImageApplier to perform undo. Last contributor: $Author$ */ -class MitkExt_EXPORT OverwriteSliceImageFilter : public ImageToImageFilter +class Segmentation_EXPORT OverwriteSliceImageFilter : public ImageToImageFilter { public: mitkClassMacro(OverwriteSliceImageFilter, ImageToImageFilter); itkNewMacro(OverwriteSliceImageFilter); /** \brief Which slice to overwrite (first one has index 0). */ itkSetMacro(SliceIndex, unsigned int); itkGetConstMacro(SliceIndex, unsigned int); /** \brief The orientation of the slice to overwrite. \a Parameter \a SliceDimension Number of the dimension which is constant for all pixels of the desired slices (e.g. 0 for transversal) */ itkSetMacro(SliceDimension, unsigned int); itkGetConstMacro(SliceDimension, unsigned int); /** \brief Time step of the slice to overwrite */ itkSetMacro(TimeStep, unsigned int); itkGetConstMacro(TimeStep, unsigned int); /** \brief Whether to create undo operation in the MITK undo stack */ itkSetMacro(CreateUndoInformation, bool); itkGetConstMacro(CreateUndoInformation, bool); itkSetObjectMacro(SliceImage, Image); const Image* GetSliceImage() { return m_SliceImage.GetPointer(); } const Image* GetLastDifferenceImage() { return m_SliceDifferenceImage.GetPointer(); } protected: OverwriteSliceImageFilter(); // purposely hidden virtual ~OverwriteSliceImageFilter(); virtual void GenerateData(); template void ItkImageSwitch( itk::Image* image ); template void ItkImageProcessing( itk::Image* itkImage1, itk::Image* itkImage2 ); std::string EventDescription( unsigned int sliceDimension, unsigned int sliceIndex, unsigned int timeStep ); Image::ConstPointer m_SliceImage; Image::Pointer m_SliceDifferenceImage; unsigned int m_SliceIndex; unsigned int m_SliceDimension; unsigned int m_TimeStep; unsigned int m_Dimension0; unsigned int m_Dimension1; bool m_CreateUndoInformation; }; } // namespace #endif diff --git a/Modules/MitkExt/Algorithms/mitkReduceContourSetFilter.cpp b/Modules/Segmentation/Algorithms/mitkReduceContourSetFilter.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkReduceContourSetFilter.cpp rename to Modules/Segmentation/Algorithms/mitkReduceContourSetFilter.cpp diff --git a/Modules/MitkExt/Algorithms/mitkReduceContourSetFilter.h b/Modules/Segmentation/Algorithms/mitkReduceContourSetFilter.h similarity index 97% rename from Modules/MitkExt/Algorithms/mitkReduceContourSetFilter.h rename to Modules/Segmentation/Algorithms/mitkReduceContourSetFilter.h index 02b2c5171f..6b19ff5b7b 100644 --- a/Modules/MitkExt/Algorithms/mitkReduceContourSetFilter.h +++ b/Modules/Segmentation/Algorithms/mitkReduceContourSetFilter.h @@ -1,122 +1,122 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: $ Version: $Revision: $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkReduceContourSetFilter_h_Included #define mitkReduceContourSetFilter_h_Included -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkSurfaceToSurfaceFilter.h" #include "mitkSurface.h" #include "mitkProgressBar.h" #include "vtkSmartPointer.h" #include "vtkPolyData.h" #include "vtkPolygon.h" #include "vtkPoints.h" #include "vtkCellArray.h" #include "vtkMath.h" #include namespace mitk { /** \brief A filter that reduces the number of points of contours represented by a mitk::Surface The type of the reduction can be set via SetReductionType. The two ways provided by this filter is the \li NTH_POINT Algorithm which reduces the contours according to a certain stepsize \li DOUGLAS_PEUCKER Algorithm which incorpates an error tolerance into the reduction. Stepsize and error tolerance can be set via SetStepSize and SetTolerance. Additional if more than one input contour is provided this filter tries detect contours which occur just because of an intersection. These intersection contours are eliminated. In oder to ensure a correct elimination the min and max spacing of the original image must be provided. The output is a mitk::Surface. $Author: fetzer$ */ - class MitkExt_EXPORT ReduceContourSetFilter : public SurfaceToSurfaceFilter + class Segmentation_EXPORT ReduceContourSetFilter : public SurfaceToSurfaceFilter { public: enum Reduction_Type { NTH_POINT, DOUGLAS_PEUCKER }; struct LineSegment { unsigned int StartIndex; unsigned int EndIndex; }; mitkClassMacro(ReduceContourSetFilter,SurfaceToSurfaceFilter); itkNewMacro(Self); itkSetMacro(MinSpacing, double); itkSetMacro(MaxSpacing, double); itkSetMacro(ReductionType, Reduction_Type); itkSetMacro(StepSize, unsigned int); itkSetMacro(Tolerance, double); //Resets the filter, i.e. removes all inputs and outputs void Reset(); /** \brief Set whether the mitkProgressBar should be used \a Parameter true for using the progress bar, false otherwise */ void SetUseProgressBar(bool); /** \brief Set the stepsize which the progress bar should proceed \a Parameter The stepsize for progressing */ void SetProgressStepSize(unsigned int stepSize); protected: ReduceContourSetFilter(); virtual ~ReduceContourSetFilter(); virtual void GenerateData(); virtual void GenerateOutputInformation(); private: void ReduceNumberOfPointsByNthPoint (vtkIdType cellSize, vtkIdType* cell, vtkPoints* points, vtkPolygon* reducedPolygon, vtkPoints* reducedPoints); void ReduceNumberOfPointsByDouglasPeucker (vtkIdType cellSize, vtkIdType* cell, vtkPoints* points, vtkPolygon* reducedPolygon, vtkPoints* reducedPoints); bool CheckForIntersection (vtkIdType* currentCell, vtkIdType currentCellSize, vtkPoints* currentPoints, /*vtkIdType numberOfIntersections, vtkIdType* intersectionPoints,*/ unsigned int currentInputIndex); double m_MinSpacing; double m_MaxSpacing; Reduction_Type m_ReductionType; unsigned int m_StepSize; double m_Tolerance; unsigned int m_MaxSegmentLenght; bool m_UseProgressBar; unsigned int m_ProgressStepSize; };//class }//namespace #endif diff --git a/Modules/MitkExt/Algorithms/mitkSegmentationInterpolationAlgorithm.h b/Modules/Segmentation/Algorithms/mitkSegmentationInterpolationAlgorithm.h similarity index 95% rename from Modules/MitkExt/Algorithms/mitkSegmentationInterpolationAlgorithm.h rename to Modules/Segmentation/Algorithms/mitkSegmentationInterpolationAlgorithm.h index d38b0d2dcb..c1f30e6ef2 100644 --- a/Modules/MitkExt/Algorithms/mitkSegmentationInterpolationAlgorithm.h +++ b/Modules/Segmentation/Algorithms/mitkSegmentationInterpolationAlgorithm.h @@ -1,71 +1,71 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 13922 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkSegmentationInterpolationAlgorithm_h_Included #define mitkSegmentationInterpolationAlgorithm_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkImage.h" #include namespace mitk { /** * \brief Interface class for interpolation algorithms * * Interpolation algorithms estimate a binary image (segmentation) given * manual segmentations of neighboring slices. They get the following inputs: * * - slice orientation of given and requested slices (dimension which is constant for all pixels of the meant orientation, e.g. 2 for transversal). * - slice indices of the neighboring slices (for upper and lower slice) * - slice data of the neighboring slices (for upper and lower slice) * - slice index of the requested slice (guaranteed to be between upper and lower index) * - image data of the original patient image that is being segmented (optional, may not be present) * - time step of the requested slice (needed to read out original image data) * * Concrete algorithms can use e.g. itk::ImageSliceConstIteratorWithIndex to * inspect the original patient image at appropriate positions - if they * want to take image data into account. * * All processing is triggered by calling Interpolate(). * * Last contributor: * $Author:$ */ -class MitkExt_EXPORT SegmentationInterpolationAlgorithm : public itk::Object +class Segmentation_EXPORT SegmentationInterpolationAlgorithm : public itk::Object { public: mitkClassMacro(SegmentationInterpolationAlgorithm, itk::Object); virtual Image::Pointer Interpolate(Image::ConstPointer lowerSlice, unsigned int lowerSliceIndex, Image::ConstPointer upperSlice, unsigned int upperSliceIndex, unsigned int requestedIndex, unsigned int sliceDimension, Image::Pointer resultImage, unsigned int timeStep = 0, Image::ConstPointer referenceImage = NULL) = 0; }; } // namespace #endif diff --git a/Modules/Segmentation/Algorithms/mitkSegmentationObjectFactory.cpp b/Modules/Segmentation/Algorithms/mitkSegmentationObjectFactory.cpp new file mode 100644 index 0000000000..403cb2a87e --- /dev/null +++ b/Modules/Segmentation/Algorithms/mitkSegmentationObjectFactory.cpp @@ -0,0 +1,142 @@ +/*========================================================================= + + Program: Medical Imaging & Interaction Toolkit + Language: C++ + Date: $Date$ + Version: $Revision: 16916 $ + + Copyright (c) German Cancer Research Center, Division of Medical and + Biological Informatics. All rights reserved. + See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + + =========================================================================*/ + +#include "mitkSegmentationObjectFactory.h" + +#include "mitkProperties.h" +#include "mitkBaseRenderer.h" +#include "mitkDataNode.h" +#include "mitkCoreObjectFactory.h" + +#include "mitkContour.h" +#include "mitkContourMapper2D.h" +#include "mitkContourSetMapper2D.h" +#include "mitkContourSetVtkMapper3D.h" +#include "mitkContourVtkMapper3D.h" + + +mitk::SegmentationObjectFactory::SegmentationObjectFactory() +:CoreObjectFactoryBase() +{ + static bool alreadyDone = false; + if (!alreadyDone) + { + MITK_DEBUG << "SegmentationObjectFactory c'tor" << std::endl; + + //CreateFileExtensionsMap(); + + alreadyDone = true; + } +} + +mitk::Mapper::Pointer mitk::SegmentationObjectFactory::CreateMapper(mitk::DataNode* node, MapperSlotId id) +{ + mitk::Mapper::Pointer newMapper=NULL; + mitk::BaseData *data = node->GetData(); + + if ( id == mitk::BaseRenderer::Standard2D ) + { + if((dynamic_cast(data)!=NULL)) + { + newMapper = mitk::ContourMapper2D::New(); + newMapper->SetDataNode(node); + } + else if((dynamic_cast(data)!=NULL)) + { + newMapper = mitk::ContourSetMapper2D::New(); + newMapper->SetDataNode(node); + } + } + else if ( id == mitk::BaseRenderer::Standard3D ) + { + if((dynamic_cast(data)!=NULL)) + { + newMapper = mitk::ContourVtkMapper3D::New(); + newMapper->SetDataNode(node); + } + else if((dynamic_cast(data)!=NULL)) + { + newMapper = mitk::ContourSetVtkMapper3D::New(); + newMapper->SetDataNode(node); + } + } + return newMapper; +} + +void mitk::SegmentationObjectFactory::SetDefaultProperties(mitk::DataNode* node) +{ + + if(node==NULL) + return; + + mitk::DataNode::Pointer nodePointer = node; + +// mitk::Image::Pointer image = dynamic_cast(node->GetData()); +// if(image.IsNotNull() && image->IsInitialized()) +// { +// mitk::GPUVolumeMapper3D::SetDefaultProperties(node); +// } +// +// if (dynamic_cast(node->GetData())) +// { +// mitk::UnstructuredGridVtkMapper3D::SetDefaultProperties(node); +// } + +} + +const char* mitk::SegmentationObjectFactory::GetFileExtensions() +{ + std::string fileExtension; + this->CreateFileExtensions(m_FileExtensionsMap, fileExtension); + return fileExtension.c_str(); +}; + +mitk::CoreObjectFactoryBase::MultimapType mitk::SegmentationObjectFactory::GetFileExtensionsMap() +{ + return m_FileExtensionsMap; +} + +mitk::CoreObjectFactoryBase::MultimapType mitk::SegmentationObjectFactory::GetSaveFileExtensionsMap() +{ + return m_SaveFileExtensionsMap; +} + +void mitk::SegmentationObjectFactory::CreateFileExtensionsMap() +{ +} + +const char* mitk::SegmentationObjectFactory::GetSaveFileExtensions() +{ + std::string fileExtension; + this->CreateFileExtensions(m_SaveFileExtensionsMap, fileExtension); + return fileExtension.c_str(); +} + +void mitk::SegmentationObjectFactory::RegisterIOFactories() +{ +} + +void RegisterSegmentationObjectFactory() +{ + static bool oneSegmentationObjectFactoryRegistered = false; + if ( ! oneSegmentationObjectFactoryRegistered ) + { + MITK_DEBUG << "Registering SegmentationObjectFactory..." << std::endl; + mitk::CoreObjectFactory::GetInstance()->RegisterExtraFactory(mitk::SegmentationObjectFactory::New()); + oneSegmentationObjectFactoryRegistered = true; + } +} diff --git a/Modules/Segmentation/Algorithms/mitkSegmentationObjectFactory.h b/Modules/Segmentation/Algorithms/mitkSegmentationObjectFactory.h new file mode 100644 index 0000000000..fe49f1cd7e --- /dev/null +++ b/Modules/Segmentation/Algorithms/mitkSegmentationObjectFactory.h @@ -0,0 +1,51 @@ +/*========================================================================= + + Program: Medical Imaging & Interaction Toolkit + Language: C++ + Date: $Date$ + Version: $Revision: 13129 $ + + Copyright (c) German Cancer Research Center, Division of Medical and + Biological Informatics. All rights reserved. + See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. + + This software is distributed WITHOUT ANY WARRANTY; without even + the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR + PURPOSE. See the above copyright notices for more information. + + =========================================================================*/ + +#ifndef SEGMENTATIONOBJECTFACTORY_H_INCLUDED +#define SEGMENTATIONOBJECTFACTORY_H_INCLUDED + +#include "mitkCoreObjectFactoryBase.h" +#include "SegmentationExports.h" + +namespace mitk { + + class Segmentation_EXPORT SegmentationObjectFactory : public CoreObjectFactoryBase + { + public: + mitkClassMacro(SegmentationObjectFactory,CoreObjectFactoryBase); + itkNewMacro(SegmentationObjectFactory); + virtual Mapper::Pointer CreateMapper(mitk::DataNode* node, MapperSlotId slotId); + virtual void SetDefaultProperties(mitk::DataNode* node); + virtual const char* GetFileExtensions(); + virtual mitk::CoreObjectFactoryBase::MultimapType GetFileExtensionsMap(); + virtual const char* GetSaveFileExtensions(); + virtual mitk::CoreObjectFactoryBase::MultimapType GetSaveFileExtensionsMap(); + void RegisterIOFactories(); + protected: + SegmentationObjectFactory(); + void CreateFileExtensionsMap(); + MultimapType m_FileExtensionsMap; + MultimapType m_SaveFileExtensionsMap; + }; + +} +// global declaration for simple call by +// applications +void Segmentation_EXPORT RegisterSegmentationObjectFactory(); + +#endif + diff --git a/Modules/MitkExt/Algorithms/mitkSegmentationSink.cpp b/Modules/Segmentation/Algorithms/mitkSegmentationSink.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkSegmentationSink.cpp rename to Modules/Segmentation/Algorithms/mitkSegmentationSink.cpp diff --git a/Modules/MitkExt/Algorithms/mitkSegmentationSink.h b/Modules/Segmentation/Algorithms/mitkSegmentationSink.h similarity index 93% rename from Modules/MitkExt/Algorithms/mitkSegmentationSink.h rename to Modules/Segmentation/Algorithms/mitkSegmentationSink.h index e62d80d540..4cddbc7186 100644 --- a/Modules/MitkExt/Algorithms/mitkSegmentationSink.h +++ b/Modules/Segmentation/Algorithms/mitkSegmentationSink.h @@ -1,57 +1,57 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITK_SEGMENTATION_SINK_H_INCLUDET_WAD #define MITK_SEGMENTATION_SINK_H_INCLUDET_WAD #include "mitkNonBlockingAlgorithm.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" namespace mitk { -class MitkExt_EXPORT SegmentationSink : public NonBlockingAlgorithm +class Segmentation_EXPORT SegmentationSink : public NonBlockingAlgorithm { public: mitkClassMacro( SegmentationSink, NonBlockingAlgorithm ) mitkAlgorithmNewMacro( SegmentationSink ); protected: SegmentationSink(); // use smart pointers virtual ~SegmentationSink(); virtual void Initialize(const NonBlockingAlgorithm* other = NULL); virtual bool ReadyToRun(); virtual bool ThreadedUpdateFunction(); // will be called from a thread after calling StartAlgorithm void InsertBelowGroupNode(mitk::DataNode* node); DataNode* LookForPointerTargetBelowGroupNode(const char* name); DataNode* GetGroupNode(); private: }; } // namespace #endif diff --git a/Modules/MitkExt/Algorithms/mitkShapeBasedInterpolationAlgorithm.cpp b/Modules/Segmentation/Algorithms/mitkShapeBasedInterpolationAlgorithm.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkShapeBasedInterpolationAlgorithm.cpp rename to Modules/Segmentation/Algorithms/mitkShapeBasedInterpolationAlgorithm.cpp diff --git a/Modules/MitkExt/Algorithms/mitkShapeBasedInterpolationAlgorithm.h b/Modules/Segmentation/Algorithms/mitkShapeBasedInterpolationAlgorithm.h similarity index 93% rename from Modules/MitkExt/Algorithms/mitkShapeBasedInterpolationAlgorithm.h rename to Modules/Segmentation/Algorithms/mitkShapeBasedInterpolationAlgorithm.h index db3d962233..b7ee495b81 100644 --- a/Modules/MitkExt/Algorithms/mitkShapeBasedInterpolationAlgorithm.h +++ b/Modules/Segmentation/Algorithms/mitkShapeBasedInterpolationAlgorithm.h @@ -1,60 +1,60 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 13922 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkShapeBasedInterpolationAlgorithm_h_Included #define mitkShapeBasedInterpolationAlgorithm_h_Included #include "mitkSegmentationInterpolationAlgorithm.h" #include "mitkLegacyAdaptors.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" namespace mitk { /** * \brief Shape-based binary image interpolation. * * This class uses legacy code from ipSegmentation to implement * the shape-based interpolation algorithm described in * * G.T. Herman, J. Zheng, C.A. Bucholtz: "Shape-based interpolation" * IEEE Computer Graphics & Applications, pp. 69-79,May 1992 * * Last contributor: * $Author:$ */ -class MitkExt_EXPORT ShapeBasedInterpolationAlgorithm : public SegmentationInterpolationAlgorithm +class Segmentation_EXPORT ShapeBasedInterpolationAlgorithm : public SegmentationInterpolationAlgorithm { public: mitkClassMacro(ShapeBasedInterpolationAlgorithm, SegmentationInterpolationAlgorithm); itkNewMacro(ShapeBasedInterpolationAlgorithm); Image::Pointer Interpolate(Image::ConstPointer lowerSlice, unsigned int lowerSliceIndex, Image::ConstPointer upperSlice, unsigned int upperSliceIndex, unsigned int requestedIndex, unsigned int sliceDimension, Image::Pointer resultImage, unsigned int timeStep, Image::ConstPointer referenceImage); }; } // namespace #endif diff --git a/Modules/MitkExt/Algorithms/mitkShowSegmentationAsSmoothedSurface.cpp b/Modules/Segmentation/Algorithms/mitkShowSegmentationAsSmoothedSurface.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkShowSegmentationAsSmoothedSurface.cpp rename to Modules/Segmentation/Algorithms/mitkShowSegmentationAsSmoothedSurface.cpp diff --git a/Modules/MitkExt/Algorithms/mitkShowSegmentationAsSmoothedSurface.h b/Modules/Segmentation/Algorithms/mitkShowSegmentationAsSmoothedSurface.h similarity index 93% rename from Modules/MitkExt/Algorithms/mitkShowSegmentationAsSmoothedSurface.h rename to Modules/Segmentation/Algorithms/mitkShowSegmentationAsSmoothedSurface.h index d2779109b8..db2e56ae61 100644 --- a/Modules/MitkExt/Algorithms/mitkShowSegmentationAsSmoothedSurface.h +++ b/Modules/Segmentation/Algorithms/mitkShowSegmentationAsSmoothedSurface.h @@ -1,46 +1,46 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITK_SHOW_SEGMENTATION_AS_SMOOTHED_SURFACE_H #define MITK_SHOW_SEGMENTATION_AS_SMOOTHED_SURFACE_H #include "mitkSegmentationSink.h" #include namespace mitk { - class MitkExt_EXPORT ShowSegmentationAsSmoothedSurface : public SegmentationSink + class Segmentation_EXPORT ShowSegmentationAsSmoothedSurface : public SegmentationSink { public: mitkClassMacro(ShowSegmentationAsSmoothedSurface, SegmentationSink) mitkAlgorithmNewMacro(ShowSegmentationAsSmoothedSurface) protected: void Initialize(const NonBlockingAlgorithm *other = NULL); bool ReadyToRun(); bool ThreadedUpdateFunction(); void ThreadedUpdateSuccessful(); private: ShowSegmentationAsSmoothedSurface(); ~ShowSegmentationAsSmoothedSurface(); Surface::Pointer m_Surface; }; } #endif diff --git a/Modules/MitkExt/Algorithms/mitkShowSegmentationAsSurface.cpp b/Modules/Segmentation/Algorithms/mitkShowSegmentationAsSurface.cpp similarity index 100% rename from Modules/MitkExt/Algorithms/mitkShowSegmentationAsSurface.cpp rename to Modules/Segmentation/Algorithms/mitkShowSegmentationAsSurface.cpp diff --git a/Modules/MitkExt/Algorithms/mitkShowSegmentationAsSurface.h b/Modules/Segmentation/Algorithms/mitkShowSegmentationAsSurface.h similarity index 93% rename from Modules/MitkExt/Algorithms/mitkShowSegmentationAsSurface.h rename to Modules/Segmentation/Algorithms/mitkShowSegmentationAsSurface.h index c39ce411e7..68eff5cc40 100644 --- a/Modules/MitkExt/Algorithms/mitkShowSegmentationAsSurface.h +++ b/Modules/Segmentation/Algorithms/mitkShowSegmentationAsSurface.h @@ -1,63 +1,63 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITK_SHOW_SEGMENTATION_AS_SURFACE_H_INCLUDET_WAD #define MITK_SHOW_SEGMENTATION_AS_SURFACE_H_INCLUDET_WAD #include "mitkSegmentationSink.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkUIDGenerator.h" #include "mitkSurface.h" namespace mitk { -class MitkExt_EXPORT ShowSegmentationAsSurface : public SegmentationSink +class Segmentation_EXPORT ShowSegmentationAsSurface : public SegmentationSink { public: mitkClassMacro( ShowSegmentationAsSurface, SegmentationSink ) mitkAlgorithmNewMacro( ShowSegmentationAsSurface ); protected: ShowSegmentationAsSurface(); // use smart pointers virtual ~ShowSegmentationAsSurface(); virtual void Initialize(const NonBlockingAlgorithm* other = NULL); virtual bool ReadyToRun(); virtual bool ThreadedUpdateFunction(); // will be called from a thread after calling StartAlgorithm virtual void ThreadedUpdateSuccessful(); // will be called from a thread after calling StartAlgorithm private: UIDGenerator m_UIDGeneratorSurfaces; Surface::Pointer m_Surface; DataNode::Pointer m_Node; bool m_AddToTree; }; } // namespace #endif diff --git a/Modules/Segmentation/CMakeLists.txt b/Modules/Segmentation/CMakeLists.txt new file mode 100644 index 0000000000..133b39a60c --- /dev/null +++ b/Modules/Segmentation/CMakeLists.txt @@ -0,0 +1,10 @@ +#configure_file(${PROJECT_SOURCE_DIR}/CMake/ToolExtensionITKFactory.cpp.in $#{PROJECT_BINARY_DIR}/ToolExtensionITKFactory.cpp.in COPYONLY) +#configure_file(${PROJECT_SOURCE_DIR}/CMake/ToolExtensionITKFactoryLoader.cpp.in $#{PROJECT_BINARY_DIR}/ToolExtensionITKFactoryLoader.cpp.in COPYONLY) +#configure_file(${PROJECT_SOURCE_DIR}/CMake/ToolGUIExtensionITKFactory.cpp.in $#{PROJECT_BINARY_DIR}/ToolGUIExtensionITKFactory.cpp.in COPYONLY) + +MITK_CREATE_MODULE( Segmentation + INCLUDE_DIRS Algorithms Controllers DataManagement Interactions IO Rendering + DEPENDS Mitk ipSegmentation mitkIpFunc MitkExt +) + +add_subdirectory(Testing) \ No newline at end of file diff --git a/Modules/MitkExt/Controllers/mitkSegmentationInterpolationController.cpp b/Modules/Segmentation/Controllers/mitkSegmentationInterpolationController.cpp similarity index 100% rename from Modules/MitkExt/Controllers/mitkSegmentationInterpolationController.cpp rename to Modules/Segmentation/Controllers/mitkSegmentationInterpolationController.cpp diff --git a/Modules/MitkExt/Controllers/mitkSegmentationInterpolationController.h b/Modules/Segmentation/Controllers/mitkSegmentationInterpolationController.h similarity index 97% rename from Modules/MitkExt/Controllers/mitkSegmentationInterpolationController.h rename to Modules/Segmentation/Controllers/mitkSegmentationInterpolationController.h index 0e8a95d503..b4d3a5a8aa 100644 --- a/Modules/MitkExt/Controllers/mitkSegmentationInterpolationController.h +++ b/Modules/Segmentation/Controllers/mitkSegmentationInterpolationController.h @@ -1,203 +1,203 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkSegmentationInterpolationController_h_Included #define mitkSegmentationInterpolationController_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkImage.h" #include #include #include #include namespace mitk { class Image; /** \brief Generates interpolations of 2D slices. \sa QmitkSlicesInterpolator \sa QmitkInteractiveSegmentation \ingroup ToolManagerEtAl There is a separate page describing the general design of QmitkInteractiveSegmentation: \ref QmitkInteractiveSegmentationTechnicalPage This class keeps track of the contents of a 3D segmentation image. \attention mitk::SegmentationInterpolationController assumes that the image contains pixel values of 0 and 1. After you set the segmentation image using SetSegmentationVolume(), the whole image is scanned for pixels other than 0. SegmentationInterpolationController registers as an observer to the segmentation image, and repeats the scan whenvever the image is modified. You can prevent this (time consuming) scan if you do the changes slice-wise and send difference images to SegmentationInterpolationController. For this purpose SetChangedSlice() should be used. mitk::OverwriteImageFilter already does this every time it changes a slice of an image. There is a static method InterpolatorForImage(), which can be used to find out if there already is an interpolator instance for a specified image. OverwriteImageFilter uses this to get to know its interpolator. SegmentationInterpolationController needs to maintain some information about the image slices (in every dimension). This information is stored internally in m_SegmentationCountInSlice, which is basically three std::vectors (one for each dimension). Each item describes one image dimension, each vector item holds the count of pixels in "its" slice. This is perhaps better to understand from the following picture (where red items just mean to symbolize "there is some segmentation" - in reality there is an integer count). \image html slice_based_segmentation_interpolator.png $Author$ */ -class MitkExt_EXPORT SegmentationInterpolationController : public itk::Object +class Segmentation_EXPORT SegmentationInterpolationController : public itk::Object { public: mitkClassMacro(SegmentationInterpolationController, itk::Object); itkNewMacro(SegmentationInterpolationController); /// specify the segmentation image that should be interpolated /** \brief Find interpolator for a given image. \return NULL if there is no interpolator yet. This method is useful if several "clients" modify the same image and want to access the interpolations. Then they can share the same object. */ static SegmentationInterpolationController* InterpolatorForImage(const Image*); /** \brief Block reaction to an images Modified() events. Blocking the scan of the whole image is especially useful when you are about to change a single slice of the image. Then you would send a difference image of this single slice to SegmentationInterpolationController but call image->Modified() anyway. Before calling image->Modified() you should block SegmentationInterpolationController's reactions to this modified by using this method. */ void BlockModified(bool); /** \brief Initialize with a whole volume. Will scan the volume for segmentation pixels (values other than 0) and fill some internal data structures. You don't have to call this method every time something changes, but only when several slices at once change. When you change a single slice, call SetChangedSlice() instead. */ void SetSegmentationVolume( const Image* segmentation ); /** \brief Set a reference image (original patient image) - optional. If this volume is set (must exactly match the dimensions of the segmentation), the interpolation algorithm may consider image content to improve the interpolated (estimated) segmentation. */ void SetReferenceVolume( const Image* segmentation ); /** \brief Update after changing a single slice. \param sliceDiff is a 2D image with the difference image of the slice determined by sliceDimension and sliceIndex. The difference is (pixel value in the new slice minus pixel value in the old slice). \param sliceDimension Number of the dimension which is constant for all pixels of the meant slice. \param sliceIndex Which slice to take, in the direction specified by sliceDimension. Count starts from 0. \param timeStep Which time step is changed */ void SetChangedSlice( const Image* sliceDiff, unsigned int sliceDimension, unsigned int sliceIndex, unsigned int timeStep ); void SetChangedVolume( const Image* sliceDiff, unsigned int timeStep ); /** \brief Generates an interpolated image for the given slice. \param sliceDimension Number of the dimension which is constant for all pixels of the meant slice. \param sliceIndex Which slice to take, in the direction specified by sliceDimension. Count starts from 0. \param timeStep Which time step to use */ Image::Pointer Interpolate( unsigned int sliceDimension, unsigned int sliceIndex, unsigned int timeStep ); void OnImageModified(const itk::EventObject&); protected: /** \brief Protected class of mitk::SegmentationInterpolationController. Don't use (you shouldn't be able to do so)! */ - class MitkExt_EXPORT SetChangedSliceOptions + class Segmentation_EXPORT SetChangedSliceOptions { public: SetChangedSliceOptions( unsigned int sd, unsigned int si, unsigned int d0, unsigned int d1, unsigned int t, void* pixels ) : sliceDimension(sd), sliceIndex(si), dim0(d0), dim1(d1), timeStep(t), pixelData(pixels) { } unsigned int sliceDimension; unsigned int sliceIndex; unsigned int dim0; unsigned int dim1; unsigned int timeStep; void* pixelData; }; typedef std::vector DirtyVectorType; //typedef std::vector< DirtyVectorType[3] > TimeResolvedDirtyVectorType; // cannot work with C++, so next line is used for implementation typedef std::vector< std::vector > TimeResolvedDirtyVectorType; typedef std::map< const Image*, SegmentationInterpolationController* > InterpolatorMapType; SegmentationInterpolationController();// purposely hidden virtual ~SegmentationInterpolationController(); /// internal scan of a single slice template < typename DATATYPE > void ScanChangedSlice( itk::Image*, const SetChangedSliceOptions& options ); template < typename TPixel, unsigned int VImageDimension > void ScanChangedVolume( itk::Image*, unsigned int timeStep ); template < typename DATATYPE > void ScanWholeVolume( itk::Image*, const Image* volume, unsigned int timeStep ); void PrintStatus(); /** An array of flags. One for each dimension of the image. A flag is set, when a slice in a certain dimension has at least one pixel that is not 0 (which would mean that it has to be considered by the interpolation algorithm). E.g. flags for transversal slices are stored in m_SegmentationCountInSlice[0][index]. Enhanced with time steps it is now m_SegmentationCountInSlice[timeStep][0][index] */ TimeResolvedDirtyVectorType m_SegmentationCountInSlice; static InterpolatorMapType s_InterpolatorForImage; Image::ConstPointer m_Segmentation; Image::ConstPointer m_ReferenceImage; bool m_BlockModified; }; } // namespace #endif diff --git a/Modules/MitkExt/Controllers/mitkSurfaceInterpolationController.cpp b/Modules/Segmentation/Controllers/mitkSurfaceInterpolationController.cpp similarity index 100% rename from Modules/MitkExt/Controllers/mitkSurfaceInterpolationController.cpp rename to Modules/Segmentation/Controllers/mitkSurfaceInterpolationController.cpp diff --git a/Modules/MitkExt/Controllers/mitkSurfaceInterpolationController.h b/Modules/Segmentation/Controllers/mitkSurfaceInterpolationController.h similarity index 96% rename from Modules/MitkExt/Controllers/mitkSurfaceInterpolationController.h rename to Modules/Segmentation/Controllers/mitkSurfaceInterpolationController.h index 583eca813f..329cc693de 100644 --- a/Modules/MitkExt/Controllers/mitkSurfaceInterpolationController.h +++ b/Modules/Segmentation/Controllers/mitkSurfaceInterpolationController.h @@ -1,132 +1,132 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkSurfaceInterpolationController_h_Included #define mitkSurfaceInterpolationController_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkRestorePlanePositionOperation.h" #include "mitkSurface.h" #include "mitkInteractionConst.h" #include "mitkColorProperty.h" #include "mitkProperties.h" #include "mitkCreateDistanceImageFromSurfaceFilter.h" #include "mitkReduceContourSetFilter.h" #include "mitkComputeContourSetNormalsFilter.h" #include "mitkDataNode.h" #include "mitkDataStorage.h" #include "mitkWeakPointer.h" #include "vtkPolygon.h" #include "vtkPoints.h" #include "vtkCellArray.h" #include "vtkPolyData.h" #include "vtkSmartPointer.h" #include "vtkAppendPolyData.h" #include "vtkMarchingCubes.h" #include "vtkImageData.h" #include "mitkVtkRepresentationProperty.h" #include "vtkProperty.h" #include "mitkProgressBar.h" namespace mitk { - class MitkExt_EXPORT SurfaceInterpolationController : public itk::Object + class Segmentation_EXPORT SurfaceInterpolationController : public itk::Object { public: mitkClassMacro(SurfaceInterpolationController, itk::Object); itkNewMacro(Self); static SurfaceInterpolationController* GetInstance(); /* * Adds a new extracted contour to the list */ void AddNewContour(Surface::Pointer newContour, RestorePlanePositionOperation *op); /* * Interpolates the 3D surface from the given extracted contours */ void Interpolate (); mitk::Surface::Pointer GetInterpolationResult(); void SetMinSpacing(double minSpacing); void SetMaxSpacing(double maxSpacing); void SetDistanceImageVolume(unsigned int distImageVolume); void SetWorkingImage(Image* workingImage); Surface* GetContoursAsSurface(); void SetDataStorage(DataStorage &ds); unsigned int CreateNewContourList(); void SetCurrentListID (unsigned int ID); mitk::Image* GetImage(); protected: SurfaceInterpolationController(); ~SurfaceInterpolationController(); private: struct ContourPositionPair { Surface::Pointer contour; RestorePlanePositionOperation* position; }; typedef std::vector ContourPositionPairList; ContourPositionPairList::iterator m_Iterator; ReduceContourSetFilter::Pointer m_ReduceFilter; ComputeContourSetNormalsFilter::Pointer m_NormalsFilter; CreateDistanceImageFromSurfaceFilter::Pointer m_InterpolateSurfaceFilter; double m_MinSpacing; double m_MaxSpacing; const Image* m_WorkingImage; Surface::Pointer m_Contours; vtkSmartPointer m_PolyData; unsigned int m_DistImageVolume; mitk::WeakPointer m_DataStorage; std::vector m_ListOfContourLists; unsigned int m_CurrentContourListID; mitk::Surface::Pointer m_InterpolationResult; }; } #endif diff --git a/Modules/MitkExt/DataManagement/mitkContour.cpp b/Modules/Segmentation/DataManagement/mitkContour.cpp similarity index 100% rename from Modules/MitkExt/DataManagement/mitkContour.cpp rename to Modules/Segmentation/DataManagement/mitkContour.cpp diff --git a/Modules/MitkExt/DataManagement/mitkContour.h b/Modules/Segmentation/DataManagement/mitkContour.h similarity index 97% rename from Modules/MitkExt/DataManagement/mitkContour.h rename to Modules/Segmentation/DataManagement/mitkContour.h index 529536bfc1..99d0a8c143 100644 --- a/Modules/MitkExt/DataManagement/mitkContour.h +++ b/Modules/Segmentation/DataManagement/mitkContour.h @@ -1,183 +1,183 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _MITK_CONTOUR_H_ #define _MITK_CONTOUR_H_ #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkBaseData.h" #include #include namespace mitk { /** * This class holds stores vertices for drawing a contour * */ -class MitkExt_EXPORT Contour : public BaseData +class Segmentation_EXPORT Contour : public BaseData { public: mitkClassMacro(Contour, BaseData); itkNewMacro(Self); mitkCloneMacro(Contour); typedef itk::PolyLineParametricPath<3> PathType; typedef PathType::Pointer PathPointer; typedef PathType::ContinuousIndexType ContinuousIndexType; typedef PathType::InputType InputType; typedef PathType::OutputType OutputType; typedef PathType::OffsetType OffsetType; typedef itk::BoundingBox BoundingBoxType; typedef BoundingBoxType::PointsContainer PointsContainer; typedef BoundingBoxType::PointsContainer::Pointer PointsContainerPointer; typedef BoundingBoxType::PointsContainerIterator PointsContainerIterator; /** * sets whether the contour should be closed or open. * by default the contour is closed */ itkSetMacro(Closed, bool); /** * returns if the contour is closed or opened */ itkGetMacro(Closed, bool); itkSetMacro(Selected, bool); itkGetMacro(Selected, bool); itkSetMacro(Width, float); itkGetMacro(Width, float); /** * clean up the contour data */ void Initialize(); /** * add a new vertex to the contour */ void AddVertex(mitk::Point3D newPoint); /** * return an itk parametric path of the contour */ PathPointer GetContourPath() const; /** * set the current render window. This is helpful if one * wants to draw the contour in one special window only. */ void SetCurrentWindow(vtkRenderWindow* rw); /** * returns the points to the current render window */ vtkRenderWindow* GetCurrentWindow() const; /** * returns the number of points stored in the contour */ unsigned int GetNumberOfPoints() const; /** * returns the container of the contour points */ PointsContainerPointer GetPoints() const; /** * set the contour points container. */ void SetPoints(PointsContainerPointer points); /** * intherited from parent */ virtual void UpdateOutputInformation(); /** * intherited from parent */ virtual void SetRequestedRegionToLargestPossibleRegion(); /** * intherited from parent */ virtual bool RequestedRegionIsOutsideOfTheBufferedRegion(); /** * intherited from parent */ virtual bool VerifyRequestedRegion(); /** * intherited from parent */ virtual void SetRequestedRegion(itk::DataObject *data); protected: Contour(); Contour(const Contour & other); virtual ~Contour(); virtual void PrintSelf(std::ostream& os, itk::Indent indent) const; private: /** * parametric path of a contour; */ PathType::Pointer m_ContourPath; /** * the current render window */ vtkRenderWindow* m_CurrentWindow; /** * the bounding box of the contour */ BoundingBoxType::Pointer m_BoundingBox; /** * container for all contour points */ BoundingBoxType::PointsContainer::Pointer m_Vertices; /** * decide whether th contour is open or closed */ bool m_Closed; bool m_Selected; float m_Width; }; } // namespace mitk #endif //_MITK_CONTOUR_H_ diff --git a/Modules/MitkExt/DataManagement/mitkContourSet.cpp b/Modules/Segmentation/DataManagement/mitkContourSet.cpp similarity index 100% rename from Modules/MitkExt/DataManagement/mitkContourSet.cpp rename to Modules/Segmentation/DataManagement/mitkContourSet.cpp diff --git a/Modules/MitkExt/DataManagement/mitkContourSet.h b/Modules/Segmentation/DataManagement/mitkContourSet.h similarity index 96% rename from Modules/MitkExt/DataManagement/mitkContourSet.h rename to Modules/Segmentation/DataManagement/mitkContourSet.h index 6e95508462..408d3ed970 100644 --- a/Modules/MitkExt/DataManagement/mitkContourSet.h +++ b/Modules/Segmentation/DataManagement/mitkContourSet.h @@ -1,115 +1,115 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _MITK_CONTOUR_SET_H_ #define _MITK_CONTOUR_SET_H_ #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkBaseData.h" #include "mitkContour.h" #include namespace mitk { /** * This class holds stores vertices for drawing a contour * */ -class MitkExt_EXPORT ContourSet : public BaseData +class Segmentation_EXPORT ContourSet : public BaseData { public: mitkClassMacro(ContourSet, BaseData); itkNewMacro(Self); typedef std::map ContourVectorType; typedef ContourVectorType::iterator ContourIterator; typedef itk::BoundingBox BoundingBoxType; /** * clean up the contour data */ void Initialize(); /** * add a contour */ void AddContour(unsigned int index, mitk::Contour::Pointer contour); /** * add a contour */ void RemoveContour(unsigned long index); /** * returns the number of points stored in the contour */ unsigned int GetNumberOfContours(); /** * returns the container of the contour points */ ContourVectorType GetContours(); /** * intherited from parent */ virtual void UpdateOutputInformation(); /** * intherited from parent */ virtual void SetRequestedRegionToLargestPossibleRegion(); /** * intherited from parent */ virtual bool RequestedRegionIsOutsideOfTheBufferedRegion(); /** * intherited from parent */ virtual bool VerifyRequestedRegion(); /** * intherited from parent */ virtual void SetRequestedRegion(itk::DataObject *data); protected: ContourSet(); virtual ~ContourSet(); private: /** * the bounding box of the contour */ BoundingBoxType::Pointer m_BoundingBox; ContourVectorType m_ContourVector; unsigned int m_NumberOfContours; }; } // namespace mitk #endif //_MITK_CONTOUR_SET_H_ diff --git a/Modules/MitkExt/DataManagement/mitkExtrudedContour.cpp b/Modules/Segmentation/DataManagement/mitkExtrudedContour.cpp similarity index 100% rename from Modules/MitkExt/DataManagement/mitkExtrudedContour.cpp rename to Modules/Segmentation/DataManagement/mitkExtrudedContour.cpp diff --git a/Modules/MitkExt/DataManagement/mitkExtrudedContour.h b/Modules/Segmentation/DataManagement/mitkExtrudedContour.h similarity index 97% rename from Modules/MitkExt/DataManagement/mitkExtrudedContour.h rename to Modules/Segmentation/DataManagement/mitkExtrudedContour.h index 77854f5438..fcd5bb3266 100644 --- a/Modules/MitkExt/DataManagement/mitkExtrudedContour.h +++ b/Modules/Segmentation/DataManagement/mitkExtrudedContour.h @@ -1,127 +1,127 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITKEXTRUDEDCONTOUR_H_HEADER_INCLUDED #define MITKEXTRUDEDCONTOUR_H_HEADER_INCLUDED #include "mitkBoundingObject.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include #include #include class vtkLinearExtrusionFilter; class vtkPlanes; class vtkClipPolyData; class vtkLinearSubdivisionFilter; class vtkTriangleFilter; class vtkDecimatePro; class vtkPolygon; namespace mitk { //##Documentation //## @brief Data class containing a bounding-object created by //## extruding a Contour along a vector //## //## The m_Contour is extruded in the direction m_Vector until //## reaching m_ClippingGeometry. //## @ingroup Data -class MitkExt_EXPORT ExtrudedContour : public BoundingObject +class Segmentation_EXPORT ExtrudedContour : public BoundingObject { public: mitkClassMacro(ExtrudedContour, BoundingObject); itkNewMacro(Self); virtual mitk::ScalarType GetVolume(); virtual bool IsInside(const Point3D& p) const; virtual void UpdateOutputInformation(); //##Documentation //## @brief Contour to extrude itkGetConstObjectMacro(Contour, mitk::Contour); itkSetObjectMacro(Contour, mitk::Contour); //##Documentation //## @brief Vector to specify the direction of the extrusion mitkGetVectorMacro(Vector, mitk::Vector3D); mitkSetVectorMacro(Vector, mitk::Vector3D); itkGetConstMacro(AutomaticVectorGeneration, bool); itkSetMacro(AutomaticVectorGeneration, bool); itkBooleanMacro(AutomaticVectorGeneration); //##Documentation //## @brief Optional vector to specify the orientation of the bounding-box mitkGetVectorMacro(RightVector, mitk::Vector3D); mitkSetVectorMacro(RightVector, mitk::Vector3D); //##Documentation //## @brief Optional geometry for clipping the extruded contour itkGetConstObjectMacro(ClippingGeometry, mitk::Geometry3D); itkSetObjectMacro(ClippingGeometry, mitk::Geometry3D); virtual unsigned long GetMTime() const; protected: ExtrudedContour(); virtual ~ExtrudedContour(); void BuildSurface(); void BuildGeometry(); mitk::Contour::Pointer m_Contour; mitk::Vector3D m_Vector; mitk::Vector3D m_RightVector; mitk::Geometry3D::Pointer m_ClippingGeometry; bool m_AutomaticVectorGeneration; vtkPolygon* m_Polygon; #if ((VTK_MAJOR_VERSION > 4) || ((VTK_MAJOR_VERSION==4) && (VTK_MINOR_VERSION>=4) )) double m_ProjectedContourBounds[6]; #else float m_ProjectedContourBounds[6]; #endif mitk::PlaneGeometry::Pointer m_ProjectionPlane; //##Documentation //## @brief For fast projection on plane float m_Right[3]; float m_Down[3]; #if ((VTK_MAJOR_VERSION > 4) || ((VTK_MAJOR_VERSION==4) && (VTK_MINOR_VERSION>=4) )) double m_Normal[3]; #else float m_Normal[3]; #endif float m_Origin[3]; vtkLinearExtrusionFilter* m_ExtrusionFilter; vtkTriangleFilter *m_TriangleFilter; vtkDecimatePro* m_Decimate; vtkLinearSubdivisionFilter* m_SubdivisionFilter; vtkPlanes* m_ClippingBox; vtkClipPolyData* m_ClipPolyDataFilter; itk::TimeStamp m_LastCalculateExtrusionTime; }; } #endif /* MITKEXTRUDEDCONTOUR_H_HEADER_INCLUDED */ diff --git a/Modules/MitkExt/Interactions/mitkAddContourTool.cpp b/Modules/Segmentation/Interactions/mitkAddContourTool.cpp similarity index 93% rename from Modules/MitkExt/Interactions/mitkAddContourTool.cpp rename to Modules/Segmentation/Interactions/mitkAddContourTool.cpp index b31a53b7f0..8c5b076001 100644 --- a/Modules/MitkExt/Interactions/mitkAddContourTool.cpp +++ b/Modules/Segmentation/Interactions/mitkAddContourTool.cpp @@ -1,44 +1,44 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkAddContourTool.h" #include "mitkAddContourTool.xpm" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, AddContourTool, "Add tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, AddContourTool, "Add tool"); } mitk::AddContourTool::AddContourTool() :ContourTool(1) { } mitk::AddContourTool::~AddContourTool() { } const char** mitk::AddContourTool::GetXPM() const { return mitkAddContourTool_xpm; } const char* mitk::AddContourTool::GetName() const { return "Add"; } diff --git a/Modules/MitkExt/Interactions/mitkAddContourTool.h b/Modules/Segmentation/Interactions/mitkAddContourTool.h similarity index 94% rename from Modules/MitkExt/Interactions/mitkAddContourTool.h rename to Modules/Segmentation/Interactions/mitkAddContourTool.h index cb31dc4dae..127142b020 100644 --- a/Modules/MitkExt/Interactions/mitkAddContourTool.h +++ b/Modules/Segmentation/Interactions/mitkAddContourTool.h @@ -1,67 +1,67 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkAddContourTool_h_Included #define mitkAddContourTool_h_Included #include "mitkContourTool.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" namespace mitk { /** \brief Fill the inside of a contour with 1 \sa ContourTool \ingroup Interaction \ingroup ToolManagerEtAl Fills a visible contour (from FeedbackContourTool) during mouse dragging. When the mouse button is released, AddContourTool tries to extract a slice from the working image and fill in the (filled) contour as a binary image. All inside pixels are set to 1. While holding the CTRL key, the contour changes color and the pixels on the inside would be filled with 0. \warning Only to be instantiated by mitk::ToolManager. $Author$ */ -class MitkExt_EXPORT AddContourTool : public ContourTool +class Segmentation_EXPORT AddContourTool : public ContourTool { public: mitkClassMacro(AddContourTool, ContourTool); itkNewMacro(AddContourTool); virtual const char** GetXPM() const; virtual const char* GetName() const; protected: AddContourTool(); // purposely hidden virtual ~AddContourTool(); }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkAddContourTool.xpm b/Modules/Segmentation/Interactions/mitkAddContourTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkAddContourTool.xpm rename to Modules/Segmentation/Interactions/mitkAddContourTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkAutoCropTool.cpp b/Modules/Segmentation/Interactions/mitkAutoCropTool.cpp similarity index 96% rename from Modules/MitkExt/Interactions/mitkAutoCropTool.cpp rename to Modules/Segmentation/Interactions/mitkAutoCropTool.cpp index 3ec2e6821a..2db0472109 100644 --- a/Modules/MitkExt/Interactions/mitkAutoCropTool.cpp +++ b/Modules/Segmentation/Interactions/mitkAutoCropTool.cpp @@ -1,89 +1,89 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkAutoCropTool.h" #include "mitkAutoCropTool.xpm" #include "mitkAutoCropImageFilter.h" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, AutoCropImageFilter, "Crop tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, AutoCropImageFilter, "Crop tool"); } mitk::AutoCropTool::AutoCropTool() { } mitk::AutoCropTool::~AutoCropTool() { } const char** mitk::AutoCropTool::GetXPM() const { return mitkAutoCropTool_xpm; } const char* mitk::AutoCropTool::GetName() const { return "Crop"; } std::string mitk::AutoCropTool::GetErrorMessage() { return "Cropping of these nodes failed:"; } bool mitk::AutoCropTool::ProcessOneWorkingData( DataNode* node ) { if (node) { Image::Pointer image = dynamic_cast( node->GetData() ); if (image.IsNull()) return false; // if (image->GetDimension() == 4) // { // Tool::ErrorMessage.Send("Cropping 3D+t segmentations is not implemented. Sorry. Bug #1281"); // return false; // } AutoCropImageFilter::Pointer cropFilter = AutoCropImageFilter::New(); cropFilter->SetInput( image ); cropFilter->SetBackgroundValue( 0 ); try { cropFilter->Update(); image = cropFilter->GetOutput(); if (image.IsNotNull()) { node->SetData( image ); } else { return false; } } catch(...) { return false; } } return true; } diff --git a/Modules/MitkExt/Interactions/mitkAutoCropTool.h b/Modules/Segmentation/Interactions/mitkAutoCropTool.h similarity index 92% rename from Modules/MitkExt/Interactions/mitkAutoCropTool.h rename to Modules/Segmentation/Interactions/mitkAutoCropTool.h index ecd936078f..a223b6c39a 100644 --- a/Modules/MitkExt/Interactions/mitkAutoCropTool.h +++ b/Modules/Segmentation/Interactions/mitkAutoCropTool.h @@ -1,59 +1,59 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.0 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkAutoCropTool_h_Included #define mitkAutoCropTool_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkSegmentationsProcessingTool.h" namespace mitk { /** \brief Crops selected segmentations. \ingroup ToolManagerEtAl \sa mitk::Tool \sa QmitkInteractiveSegmentation Last contributor: $Author$ */ -class MitkExt_EXPORT AutoCropTool : public SegmentationsProcessingTool +class Segmentation_EXPORT AutoCropTool : public SegmentationsProcessingTool { public: mitkClassMacro(AutoCropTool, SegmentationsProcessingTool); itkNewMacro(AutoCropTool); virtual const char** GetXPM() const; virtual const char* GetName() const; protected: virtual bool ProcessOneWorkingData( DataNode* node ); virtual std::string GetErrorMessage(); AutoCropTool(); // purposely hidden virtual ~AutoCropTool(); }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkAutoCropTool.xpm b/Modules/Segmentation/Interactions/mitkAutoCropTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkAutoCropTool.xpm rename to Modules/Segmentation/Interactions/mitkAutoCropTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkAutoSegmentationTool.cpp b/Modules/Segmentation/Interactions/mitkAutoSegmentationTool.cpp similarity index 100% rename from Modules/MitkExt/Interactions/mitkAutoSegmentationTool.cpp rename to Modules/Segmentation/Interactions/mitkAutoSegmentationTool.cpp diff --git a/Modules/MitkExt/Interactions/mitkAutoSegmentationTool.h b/Modules/Segmentation/Interactions/mitkAutoSegmentationTool.h similarity index 92% rename from Modules/MitkExt/Interactions/mitkAutoSegmentationTool.h rename to Modules/Segmentation/Interactions/mitkAutoSegmentationTool.h index 8cdc853940..72c97c441c 100644 --- a/Modules/MitkExt/Interactions/mitkAutoSegmentationTool.h +++ b/Modules/Segmentation/Interactions/mitkAutoSegmentationTool.h @@ -1,50 +1,50 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.0 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkAutoSegmentationTool_h_Included #define mitkAutoSegmentationTool_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkTool.h" namespace mitk { /** \brief Superclass for tool that create a new segmentation without user interaction in render windows This class is undocumented. Ask the creator ($Author$) to supply useful comments. */ -class MitkExt_EXPORT AutoSegmentationTool : public Tool +class Segmentation_EXPORT AutoSegmentationTool : public Tool { public: mitkClassMacro(AutoSegmentationTool, Tool); protected: AutoSegmentationTool(); // purposely hidden virtual ~AutoSegmentationTool(); virtual const char* GetGroup() const; }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkBinaryThresholdTool.cpp b/Modules/Segmentation/Interactions/mitkBinaryThresholdTool.cpp similarity index 99% rename from Modules/MitkExt/Interactions/mitkBinaryThresholdTool.cpp rename to Modules/Segmentation/Interactions/mitkBinaryThresholdTool.cpp index 715e485fcd..94a70f072c 100644 --- a/Modules/MitkExt/Interactions/mitkBinaryThresholdTool.cpp +++ b/Modules/Segmentation/Interactions/mitkBinaryThresholdTool.cpp @@ -1,313 +1,313 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkBinaryThresholdTool.h" #include "mitkBinaryThresholdTool.xpm" #include "mitkToolManager.h" #include "mitkBoundingObjectToSegmentationFilter.h" #include #include "mitkLevelWindowProperty.h" #include "mitkColorProperty.h" #include "mitkProperties.h" #include "mitkOrganTypeProperty.h" #include "mitkVtkResliceInterpolationProperty.h" #include "mitkDataStorage.h" #include "mitkRenderingManager.h" #include "mitkImageCast.h" #include "mitkImageAccessByItk.h" #include "mitkImageTimeSelector.h" #include #include #include "mitkPadImageFilter.h" #include "mitkMaskAndCutRoiImageFilter.h" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, BinaryThresholdTool, "Thresholding tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, BinaryThresholdTool, "Thresholding tool"); } mitk::BinaryThresholdTool::BinaryThresholdTool() :m_SensibleMinimumThresholdValue(-100), m_SensibleMaximumThresholdValue(+100), m_CurrentThresholdValue(0.0), m_IsFloatImage(false) { this->SupportRoiOn(); m_ThresholdFeedbackNode = DataNode::New(); mitk::CoreObjectFactory::GetInstance()->SetDefaultProperties( m_ThresholdFeedbackNode ); m_ThresholdFeedbackNode->SetProperty( "color", ColorProperty::New(1.0, 0.0, 0.0) ); m_ThresholdFeedbackNode->SetProperty( "texture interpolation", BoolProperty::New(false) ); m_ThresholdFeedbackNode->SetProperty( "layer", IntProperty::New( 100 ) ); m_ThresholdFeedbackNode->SetProperty( "levelwindow", LevelWindowProperty::New( LevelWindow(100, 1) ) ); m_ThresholdFeedbackNode->SetProperty( "name", StringProperty::New("Thresholding feedback") ); m_ThresholdFeedbackNode->SetProperty( "opacity", FloatProperty::New(0.3) ); m_ThresholdFeedbackNode->SetProperty( "helper object", BoolProperty::New(true) ); } mitk::BinaryThresholdTool::~BinaryThresholdTool() { } const char** mitk::BinaryThresholdTool::GetXPM() const { return mitkBinaryThresholdTool_xpm; } const char* mitk::BinaryThresholdTool::GetName() const { return "Thresholding"; } void mitk::BinaryThresholdTool::Activated() { m_ToolManager->RoiDataChanged += mitk::MessageDelegate(this, &mitk::BinaryThresholdTool::OnRoiDataChanged); m_OriginalImageNode = m_ToolManager->GetReferenceData(0); m_NodeForThresholding = m_OriginalImageNode; if ( m_NodeForThresholding.IsNotNull() ) { SetupPreviewNodeFor( m_NodeForThresholding ); } else { m_ToolManager->ActivateTool(-1); } } void mitk::BinaryThresholdTool::Deactivated() { m_ToolManager->RoiDataChanged -= mitk::MessageDelegate(this, &mitk::BinaryThresholdTool::OnRoiDataChanged); m_NodeForThresholding = NULL; m_OriginalImageNode = NULL; try { if (DataStorage* storage = m_ToolManager->GetDataStorage()) { storage->Remove( m_ThresholdFeedbackNode ); RenderingManager::GetInstance()->RequestUpdateAll(); } } catch(...) { // don't care } m_ThresholdFeedbackNode->SetData(NULL); } void mitk::BinaryThresholdTool::SetThresholdValue(double value) { if (m_ThresholdFeedbackNode.IsNotNull()) { m_CurrentThresholdValue = value; m_ThresholdFeedbackNode->SetProperty( "levelwindow", LevelWindowProperty::New( LevelWindow(m_CurrentThresholdValue, 1) ) ); RenderingManager::GetInstance()->RequestUpdateAll(); } } void mitk::BinaryThresholdTool::AcceptCurrentThresholdValue(const std::string& organName, const Color& color) { CreateNewSegmentationFromThreshold(m_NodeForThresholding, organName, color ); RenderingManager::GetInstance()->RequestUpdateAll(); m_ToolManager->ActivateTool(-1); } void mitk::BinaryThresholdTool::CancelThresholding() { m_ToolManager->ActivateTool(-1); } void mitk::BinaryThresholdTool::SetupPreviewNodeFor( DataNode* nodeForThresholding ) { if (nodeForThresholding) { Image::Pointer image = dynamic_cast( nodeForThresholding->GetData() ); Image::Pointer originalImage = dynamic_cast (m_OriginalImageNode->GetData()); if (image.IsNotNull()) { // initialize and a new node with the same image as our reference image // use the level window property of this image copy to display the result of a thresholding operation m_ThresholdFeedbackNode->SetData( image ); int layer(50); nodeForThresholding->GetIntProperty("layer", layer); m_ThresholdFeedbackNode->SetIntProperty("layer", layer+1); if (DataStorage* storage = m_ToolManager->GetDataStorage()) { if (storage->Exists(m_ThresholdFeedbackNode)) storage->Remove(m_ThresholdFeedbackNode); storage->Add( m_ThresholdFeedbackNode, m_OriginalImageNode ); } if (image.GetPointer() == originalImage.GetPointer()) { if (originalImage->GetPixelType().GetPixelTypeId() == typeid(float)) m_IsFloatImage = true; else m_IsFloatImage = false; m_SensibleMinimumThresholdValue = static_cast( originalImage->GetScalarValueMin() ); m_SensibleMaximumThresholdValue = static_cast( originalImage->GetScalarValueMax() ); } LevelWindowProperty::Pointer lwp = dynamic_cast( m_ThresholdFeedbackNode->GetProperty( "levelwindow" )); if (lwp && !m_IsFloatImage ) { m_CurrentThresholdValue = static_cast( lwp->GetLevelWindow().GetLevel() ); } else { m_CurrentThresholdValue = (m_SensibleMaximumThresholdValue + m_SensibleMinimumThresholdValue)/2; } IntervalBordersChanged.Send(m_SensibleMinimumThresholdValue, m_SensibleMaximumThresholdValue, m_IsFloatImage); ThresholdingValueChanged.Send(m_CurrentThresholdValue); } } } void mitk::BinaryThresholdTool::CreateNewSegmentationFromThreshold(DataNode* node, const std::string& organName, const Color& color) { if (node) { Image::Pointer image = dynamic_cast( m_NodeForThresholding->GetData() ); if (image.IsNotNull()) { // create a new image of the same dimensions and smallest possible pixel type DataNode::Pointer emptySegmentation = Tool::CreateEmptySegmentationNode( image, organName, color ); if (emptySegmentation) { // actually perform a thresholding and ask for an organ type for (unsigned int timeStep = 0; timeStep < image->GetTimeSteps(); ++timeStep) { try { ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New(); timeSelector->SetInput( image ); timeSelector->SetTimeNr( timeStep ); timeSelector->UpdateLargestPossibleRegion(); Image::Pointer image3D = timeSelector->GetOutput(); AccessFixedDimensionByItk_2( image3D, ITKThresholding, 3, dynamic_cast(emptySegmentation->GetData()), timeStep ); } catch(...) { Tool::ErrorMessage("Error accessing single time steps of the original image. Cannot create segmentation."); } } if (m_OriginalImageNode.GetPointer() != m_NodeForThresholding.GetPointer()) { mitk::PadImageFilter::Pointer padFilter = mitk::PadImageFilter::New(); padFilter->SetInput(0, dynamic_cast (emptySegmentation->GetData())); padFilter->SetInput(1, dynamic_cast (m_OriginalImageNode->GetData())); padFilter->SetBinaryFilter(true); padFilter->SetUpperThreshold(1); padFilter->SetLowerThreshold(1); padFilter->Update(); emptySegmentation->SetData(padFilter->GetOutput()); } if (DataStorage::Pointer storage = m_ToolManager->GetDataStorage()) { storage->Add( emptySegmentation, m_OriginalImageNode ); // add as a child, because the segmentation "derives" from the original } m_ToolManager->SetWorkingData( emptySegmentation ); } } } } template void mitk::BinaryThresholdTool::ITKThresholding( itk::Image* originalImage, Image* segmentation, unsigned int timeStep ) { ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New(); timeSelector->SetInput( segmentation ); timeSelector->SetTimeNr( timeStep ); timeSelector->UpdateLargestPossibleRegion(); Image::Pointer segmentation3D = timeSelector->GetOutput(); typedef itk::Image< Tool::DefaultSegmentationDataType, 3> SegmentationType; // this is sure for new segmentations SegmentationType::Pointer itkSegmentation; CastToItkImage( segmentation3D, itkSegmentation ); // iterate over original and segmentation typedef itk::ImageRegionConstIterator< itk::Image > InputIteratorType; typedef itk::ImageRegionIterator< SegmentationType > SegmentationIteratorType; InputIteratorType inputIterator( originalImage, originalImage->GetLargestPossibleRegion() ); SegmentationIteratorType outputIterator( itkSegmentation, itkSegmentation->GetLargestPossibleRegion() ); inputIterator.GoToBegin(); outputIterator.GoToBegin(); while (!outputIterator.IsAtEnd()) { if ( inputIterator.Get() >= m_CurrentThresholdValue ) outputIterator.Set( 1 ); else outputIterator.Set( 0 ); ++inputIterator; ++outputIterator; } } void mitk::BinaryThresholdTool::OnRoiDataChanged() { mitk::DataNode::Pointer node = m_ToolManager->GetRoiData(0); if (node.IsNotNull()) { mitk::Image::Pointer image = dynamic_cast (m_NodeForThresholding->GetData()); if (image.IsNull()) return; mitk::MaskAndCutRoiImageFilter::Pointer roiFilter = mitk::MaskAndCutRoiImageFilter::New(); roiFilter->SetInput(image); roiFilter->SetRegionOfInterest(node->GetData()); roiFilter->Update(); mitk::DataNode::Pointer tmpNode = mitk::DataNode::New(); mitk::Image::Pointer tmpImage = roiFilter->GetOutput(); tmpNode->SetData(tmpImage); m_SensibleMaximumThresholdValue = static_cast (roiFilter->GetMaxValue()); m_SensibleMinimumThresholdValue = static_cast (roiFilter->GetMinValue()); SetupPreviewNodeFor( tmpNode ); m_NodeForThresholding = tmpNode; return; } else { this->SetupPreviewNodeFor(m_OriginalImageNode); m_NodeForThresholding = m_OriginalImageNode; return; } } diff --git a/Modules/MitkExt/Interactions/mitkBinaryThresholdTool.h b/Modules/Segmentation/Interactions/mitkBinaryThresholdTool.h similarity index 95% rename from Modules/MitkExt/Interactions/mitkBinaryThresholdTool.h rename to Modules/Segmentation/Interactions/mitkBinaryThresholdTool.h index c13f3e58e2..a85541d4c0 100644 --- a/Modules/MitkExt/Interactions/mitkBinaryThresholdTool.h +++ b/Modules/Segmentation/Interactions/mitkBinaryThresholdTool.h @@ -1,89 +1,89 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.0 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkBinaryThresholdTool_h_Included #define mitkBinaryThresholdTool_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkAutoSegmentationTool.h" #include "mitkDataNode.h" #include namespace mitk { /** \brief Calculates the segmented volumes for binary images. \ingroup ToolManagerEtAl \sa mitk::Tool \sa QmitkInteractiveSegmentation Last contributor: $Author$ */ - class MitkExt_EXPORT BinaryThresholdTool : public AutoSegmentationTool + class Segmentation_EXPORT BinaryThresholdTool : public AutoSegmentationTool { public: Message3 IntervalBordersChanged; Message1 ThresholdingValueChanged; mitkClassMacro(BinaryThresholdTool, AutoSegmentationTool); itkNewMacro(BinaryThresholdTool); virtual const char** GetXPM() const; virtual const char* GetName() const; virtual void Activated(); virtual void Deactivated(); virtual void SetThresholdValue(double value); virtual void AcceptCurrentThresholdValue(const std::string& organName, const Color& color); virtual void CancelThresholding(); protected: BinaryThresholdTool(); // purposely hidden virtual ~BinaryThresholdTool(); void SetupPreviewNodeFor( DataNode* nodeForThresholding ); void CreateNewSegmentationFromThreshold(DataNode* node, const std::string& organType, const Color& color); void OnRoiDataChanged(); template void ITKThresholding( itk::Image* originalImage, mitk::Image* segmentation, unsigned int timeStep ); DataNode::Pointer m_ThresholdFeedbackNode; DataNode::Pointer m_OriginalImageNode; DataNode::Pointer m_NodeForThresholding; double m_SensibleMinimumThresholdValue; double m_SensibleMaximumThresholdValue; double m_CurrentThresholdValue; bool m_IsFloatImage; }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkBinaryThresholdTool.xpm b/Modules/Segmentation/Interactions/mitkBinaryThresholdTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkBinaryThresholdTool.xpm rename to Modules/Segmentation/Interactions/mitkBinaryThresholdTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkBinaryThresholdULTool.cpp b/Modules/Segmentation/Interactions/mitkBinaryThresholdULTool.cpp similarity index 99% rename from Modules/MitkExt/Interactions/mitkBinaryThresholdULTool.cpp rename to Modules/Segmentation/Interactions/mitkBinaryThresholdULTool.cpp index 14c785035f..66b2e418e3 100644 --- a/Modules/MitkExt/Interactions/mitkBinaryThresholdULTool.cpp +++ b/Modules/Segmentation/Interactions/mitkBinaryThresholdULTool.cpp @@ -1,320 +1,320 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.0 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkBinaryThresholdULTool.h" #include "mitkBinaryThresholdULTool.xpm" #include "mitkToolManager.h" #include "mitkLevelWindowProperty.h" #include "mitkColorProperty.h" #include "mitkProperties.h" #include "mitkDataStorage.h" #include "mitkRenderingManager.h" #include "mitkImageCast.h" #include "mitkImageAccessByItk.h" #include "mitkImageTimeSelector.h" #include #include #include "mitkMaskAndCutRoiImageFilter.h" #include "mitkPadImageFilter.h" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, BinaryThresholdULTool, "ThresholdingUL tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, BinaryThresholdULTool, "ThresholdingUL tool"); } mitk::BinaryThresholdULTool::BinaryThresholdULTool() :m_SensibleMinimumThresholdValue(-100), m_SensibleMaximumThresholdValue(+100), m_CurrentLowerThresholdValue(1), m_CurrentUpperThresholdValue(1) { this->SupportRoiOn(); m_ThresholdFeedbackNode = DataNode::New(); m_ThresholdFeedbackNode->SetProperty( "color", ColorProperty::New(1.0, 0.0, 0.0) ); m_ThresholdFeedbackNode->SetProperty( "name", StringProperty::New("Thresholding feedback") ); m_ThresholdFeedbackNode->SetProperty( "opacity", FloatProperty::New(0.3) ); m_ThresholdFeedbackNode->SetProperty("binary", BoolProperty::New(true)); m_ThresholdFeedbackNode->SetProperty( "helper object", BoolProperty::New(true) ); } mitk::BinaryThresholdULTool::~BinaryThresholdULTool() { } const char** mitk::BinaryThresholdULTool::GetXPM() const { return mitkBinaryThresholdULTool_xpm; } const char* mitk::BinaryThresholdULTool::GetName() const { return "ThresholdingUL"; } void mitk::BinaryThresholdULTool::Activated() { m_ToolManager->RoiDataChanged += mitk::MessageDelegate(this, &mitk::BinaryThresholdULTool::OnRoiDataChanged); m_OriginalImageNode = m_ToolManager->GetReferenceData(0); m_NodeForThresholding = m_OriginalImageNode; if ( m_NodeForThresholding.IsNotNull() ) { SetupPreviewNode(); } else { m_ToolManager->ActivateTool(-1); } } void mitk::BinaryThresholdULTool::Deactivated() { m_ToolManager->RoiDataChanged -= mitk::MessageDelegate(this, &mitk::BinaryThresholdULTool::OnRoiDataChanged); m_NodeForThresholding = NULL; m_OriginalImageNode = NULL; try { if (DataStorage* storage = m_ToolManager->GetDataStorage()) { storage->Remove( m_ThresholdFeedbackNode ); RenderingManager::GetInstance()->RequestUpdateAll(); } } catch(...) { // don't care } m_ThresholdFeedbackNode->SetData(NULL); } void mitk::BinaryThresholdULTool::SetThresholdValues(int lower, int upper) { if (m_ThresholdFeedbackNode.IsNotNull()) { m_CurrentLowerThresholdValue = lower; m_CurrentUpperThresholdValue = upper; UpdatePreview(); } } void mitk::BinaryThresholdULTool::AcceptCurrentThresholdValue(const std::string& organName, const Color& color) { CreateNewSegmentationFromThreshold(m_NodeForThresholding, organName, color ); RenderingManager::GetInstance()->RequestUpdateAll(); m_ToolManager->ActivateTool(-1); } void mitk::BinaryThresholdULTool::CancelThresholding() { m_ToolManager->ActivateTool(-1); } void mitk::BinaryThresholdULTool::SetupPreviewNode() { if (m_NodeForThresholding.IsNotNull()) { Image::Pointer image = dynamic_cast( m_NodeForThresholding->GetData() ); Image::Pointer originalImage = dynamic_cast (m_OriginalImageNode->GetData()); if (image.IsNotNull()) { // initialize and a new node with the same image as our reference image // use the level window property of this image copy to display the result of a thresholding operation m_ThresholdFeedbackNode->SetData( image ); int layer(50); m_NodeForThresholding->GetIntProperty("layer", layer); m_ThresholdFeedbackNode->SetIntProperty("layer", layer+1); if (DataStorage* ds = m_ToolManager->GetDataStorage()) { if (!ds->Exists(m_ThresholdFeedbackNode)) ds->Add( m_ThresholdFeedbackNode, m_OriginalImageNode ); } if (image.GetPointer() == originalImage.GetPointer()) { m_SensibleMinimumThresholdValue = static_cast( originalImage->GetScalarValueMin() ); m_SensibleMaximumThresholdValue = static_cast( originalImage->GetScalarValueMax() ); } m_CurrentLowerThresholdValue = (m_SensibleMaximumThresholdValue + m_SensibleMinimumThresholdValue) / 3; m_CurrentUpperThresholdValue = 2*m_CurrentLowerThresholdValue; IntervalBordersChanged.Send(m_SensibleMinimumThresholdValue, m_SensibleMaximumThresholdValue); ThresholdingValuesChanged.Send(m_CurrentLowerThresholdValue, m_CurrentUpperThresholdValue); } } } void mitk::BinaryThresholdULTool::CreateNewSegmentationFromThreshold(DataNode* node, const std::string& organName, const Color& color) { if (node) { Image::Pointer image = dynamic_cast( m_NodeForThresholding->GetData() ); if (image.IsNotNull()) { // create a new image of the same dimensions and smallest possible pixel type DataNode::Pointer emptySegmentation = Tool::CreateEmptySegmentationNode( image, organName, color ); if (emptySegmentation) { // actually perform a thresholding and ask for an organ type for (unsigned int timeStep = 0; timeStep < image->GetTimeSteps(); ++timeStep) { try { ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New(); timeSelector->SetInput( image ); timeSelector->SetTimeNr( timeStep ); timeSelector->UpdateLargestPossibleRegion(); Image::Pointer image3D = timeSelector->GetOutput(); AccessFixedDimensionByItk_2( image3D, ITKThresholding, 3, dynamic_cast(emptySegmentation->GetData()), timeStep ); } catch(...) { Tool::ErrorMessage("Error accessing single time steps of the original image. Cannot create segmentation."); } } //since we are maybe working on a smaller image, pad it to the size of the original image if (m_OriginalImageNode.GetPointer() != m_NodeForThresholding.GetPointer()) { mitk::PadImageFilter::Pointer padFilter = mitk::PadImageFilter::New(); padFilter->SetInput(0, dynamic_cast (emptySegmentation->GetData())); padFilter->SetInput(1, dynamic_cast (m_OriginalImageNode->GetData())); padFilter->SetBinaryFilter(true); padFilter->SetUpperThreshold(1); padFilter->SetLowerThreshold(1); padFilter->Update(); emptySegmentation->SetData(padFilter->GetOutput()); } if (DataStorage* ds = m_ToolManager->GetDataStorage()) { ds->Add( emptySegmentation, m_OriginalImageNode ); } m_ToolManager->SetWorkingData( emptySegmentation ); } } } } template void mitk::BinaryThresholdULTool::ITKThresholding( itk::Image* originalImage, Image* segmentation, unsigned int timeStep ) { ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New(); timeSelector->SetInput( segmentation ); timeSelector->SetTimeNr( timeStep ); timeSelector->UpdateLargestPossibleRegion(); Image::Pointer segmentation3D = timeSelector->GetOutput(); typedef itk::Image< Tool::DefaultSegmentationDataType, 3> SegmentationType; // this is sure for new segmentations SegmentationType::Pointer itkSegmentation; CastToItkImage( segmentation3D, itkSegmentation ); // iterate over original and segmentation typedef itk::ImageRegionConstIterator< itk::Image > InputIteratorType; typedef itk::ImageRegionIterator< SegmentationType > SegmentationIteratorType; InputIteratorType inputIterator( originalImage, originalImage->GetLargestPossibleRegion() ); SegmentationIteratorType outputIterator( itkSegmentation, itkSegmentation->GetLargestPossibleRegion() ); inputIterator.GoToBegin(); outputIterator.GoToBegin(); while (!outputIterator.IsAtEnd()) { if ( (signed)inputIterator.Get() >= m_CurrentLowerThresholdValue && (signed)inputIterator.Get() <= m_CurrentUpperThresholdValue ) { outputIterator.Set( 1 ); } else { outputIterator.Set( 0 ); } ++inputIterator; ++outputIterator; } } void mitk::BinaryThresholdULTool::OnRoiDataChanged() { mitk::DataNode::Pointer node = m_ToolManager->GetRoiData(0); if (node.IsNotNull()) { mitk::MaskAndCutRoiImageFilter::Pointer roiFilter = mitk::MaskAndCutRoiImageFilter::New(); mitk::Image::Pointer image = dynamic_cast (m_NodeForThresholding->GetData()); if (image.IsNull()) return; roiFilter->SetInput(image); roiFilter->SetRegionOfInterest(node->GetData()); roiFilter->Update(); mitk::DataNode::Pointer tmpNode = mitk::DataNode::New(); tmpNode->SetData(roiFilter->GetOutput()); m_SensibleMinimumThresholdValue = static_cast( roiFilter->GetMinValue()); m_SensibleMaximumThresholdValue = static_cast( roiFilter->GetMaxValue()); m_NodeForThresholding = tmpNode; } else m_NodeForThresholding = m_OriginalImageNode; this->SetupPreviewNode(); this->UpdatePreview(); } void mitk::BinaryThresholdULTool::UpdatePreview() { typedef itk::Image ImageType; typedef itk::Image SegmentationType; typedef itk::BinaryThresholdImageFilter ThresholdFilterType; mitk::Image::Pointer thresholdimage = dynamic_cast (m_NodeForThresholding->GetData()); if(thresholdimage) { ImageType::Pointer itkImage = ImageType::New(); CastToItkImage(thresholdimage, itkImage); ThresholdFilterType::Pointer filter = ThresholdFilterType::New(); filter->SetInput(itkImage); filter->SetLowerThreshold(m_CurrentLowerThresholdValue); filter->SetUpperThreshold(m_CurrentUpperThresholdValue); filter->SetInsideValue(1); filter->SetOutsideValue(0); filter->Update(); mitk::Image::Pointer new_image = mitk::Image::New(); CastToMitkImage(filter->GetOutput(), new_image); m_ThresholdFeedbackNode->SetData(new_image); } RenderingManager::GetInstance()->RequestUpdateAll(); } diff --git a/Modules/MitkExt/Interactions/mitkBinaryThresholdULTool.h b/Modules/Segmentation/Interactions/mitkBinaryThresholdULTool.h similarity index 96% rename from Modules/MitkExt/Interactions/mitkBinaryThresholdULTool.h rename to Modules/Segmentation/Interactions/mitkBinaryThresholdULTool.h index b5f279b4f4..87653dabc4 100644 --- a/Modules/MitkExt/Interactions/mitkBinaryThresholdULTool.h +++ b/Modules/Segmentation/Interactions/mitkBinaryThresholdULTool.h @@ -1,96 +1,96 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.0 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkBinaryThresholdULTool_h_Included #define mitkBinaryThresholdULTool_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkAutoSegmentationTool.h" #include "mitkDataNode.h" #include #include namespace mitk { /** \brief Calculates the segmented volumes for binary images. \ingroup ToolManagerEtAl \sa mitk::Tool \sa QmitkInteractiveSegmentation Last contributor: $Author$ */ - class MitkExt_EXPORT BinaryThresholdULTool : public AutoSegmentationTool + class Segmentation_EXPORT BinaryThresholdULTool : public AutoSegmentationTool { public: Message2 IntervalBordersChanged; Message2 ThresholdingValuesChanged; mitkClassMacro(BinaryThresholdULTool, AutoSegmentationTool); itkNewMacro(BinaryThresholdULTool); virtual const char** GetXPM() const; virtual const char* GetName() const; virtual void Activated(); virtual void Deactivated(); virtual void SetThresholdValues(int lower, int upper); virtual void AcceptCurrentThresholdValue(const std::string& organName, const Color& color); virtual void CancelThresholding(); protected: BinaryThresholdULTool(); // purposely hidden virtual ~BinaryThresholdULTool(); void SetupPreviewNode(); void CreateNewSegmentationFromThreshold(DataNode* node, const std::string& organType, const Color& color); void OnRoiDataChanged(); void UpdatePreview(); template void ITKThresholding( itk::Image* originalImage, mitk::Image* segmentation, unsigned int timeStep ); DataNode::Pointer m_ThresholdFeedbackNode; DataNode::Pointer m_OriginalImageNode; DataNode::Pointer m_NodeForThresholding; int m_SensibleMinimumThresholdValue; int m_SensibleMaximumThresholdValue; int m_CurrentLowerThresholdValue; int m_CurrentUpperThresholdValue; typedef itk::Image ImageType; typedef itk::Image< Tool::DefaultSegmentationDataType, 3> SegmentationType; // this is sure for new segmentations typedef itk::BinaryThresholdImageFilter ThresholdFilterType; ThresholdFilterType::Pointer m_ThresholdFilter; }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkBinaryThresholdULTool.xpm b/Modules/Segmentation/Interactions/mitkBinaryThresholdULTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkBinaryThresholdULTool.xpm rename to Modules/Segmentation/Interactions/mitkBinaryThresholdULTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkCalculateGrayValueStatisticsTool.cpp b/Modules/Segmentation/Interactions/mitkCalculateGrayValueStatisticsTool.cpp similarity index 99% rename from Modules/MitkExt/Interactions/mitkCalculateGrayValueStatisticsTool.cpp rename to Modules/Segmentation/Interactions/mitkCalculateGrayValueStatisticsTool.cpp index 0f5d664ecc..63ae54cfbe 100644 --- a/Modules/MitkExt/Interactions/mitkCalculateGrayValueStatisticsTool.cpp +++ b/Modules/Segmentation/Interactions/mitkCalculateGrayValueStatisticsTool.cpp @@ -1,341 +1,341 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkCalculateGrayValueStatisticsTool.h" #include "mitkCalculateGrayValueStatisticsTool.xpm" #include "mitkImageAccessByItk.h" #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkImageTimeSelector.h" #include "mitkImageCast.h" #include "mitkToolManager.h" #include #include namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, CalculateGrayValueStatisticsTool, "Statistics tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, CalculateGrayValueStatisticsTool, "Statistics tool"); } mitk::CalculateGrayValueStatisticsTool::CalculateGrayValueStatisticsTool() { } mitk::CalculateGrayValueStatisticsTool::~CalculateGrayValueStatisticsTool() { } const char** mitk::CalculateGrayValueStatisticsTool::GetXPM() const { return mitkCalculateGrayValueStatisticsTool_xpm; } const char* mitk::CalculateGrayValueStatisticsTool::GetName() const { return "Statistics"; } std::string mitk::CalculateGrayValueStatisticsTool::GetErrorMessage() { return "No statistics generated for these segmentations:"; } void mitk::CalculateGrayValueStatisticsTool::StartProcessingAllData() { // clear/prepare report m_CompleteReport.str(""); } bool mitk::CalculateGrayValueStatisticsTool::ProcessOneWorkingData( DataNode* node ) { if (node) { Image::Pointer image = dynamic_cast( node->GetData() ); if (image.IsNull()) return false; DataNode* referencenode = m_ToolManager->GetReferenceData(0); if (!referencenode) return false; try { ProgressBar::GetInstance()->AddStepsToDo(1); // add to report std::string nodename("structure"); node->GetName(nodename); std::string message = "Calculating statistics for "; message += nodename; StatusBar::GetInstance()->DisplayText(message.c_str()); Image::Pointer refImage = dynamic_cast( referencenode->GetData() ); Image::Pointer image = dynamic_cast( node->GetData() ); m_CompleteReport << "======== Gray value analysis of " << nodename << " ========\n"; if (image.IsNotNull() && refImage.IsNotNull() ) { for (unsigned int timeStep = 0; timeStep < image->GetTimeSteps(); ++timeStep) { ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New(); timeSelector->SetInput( refImage ); timeSelector->SetTimeNr( timeStep ); timeSelector->UpdateLargestPossibleRegion(); Image::Pointer refImage3D = timeSelector->GetOutput(); ImageTimeSelector::Pointer timeSelector2 = ImageTimeSelector::New(); timeSelector2->SetInput( image ); timeSelector2->SetTimeNr( timeStep ); timeSelector2->UpdateLargestPossibleRegion(); Image::Pointer image3D = timeSelector2->GetOutput(); if (image3D.IsNotNull() && refImage3D.IsNotNull() ) { m_CompleteReport << "=== " << nodename << ", time step " << timeStep << " ===\n"; AccessFixedDimensionByItk_2( refImage3D, ITKHistogramming, 3, image3D, m_CompleteReport ); } } } m_CompleteReport << "======== End of analysis for " << nodename << " ===========\n\n\n"; ProgressBar::GetInstance()->Progress(); } catch(...) { return false; } } return true; } void mitk::CalculateGrayValueStatisticsTool::FinishProcessingAllData() { SegmentationsProcessingTool::FinishProcessingAllData(); // show/send results StatisticsCompleted.Send(); //MITK_INFO << m_CompleteReport.str() << std::endl; } #define ROUND_P(x) ((int)((x)+0.5)) template void mitk::CalculateGrayValueStatisticsTool::CalculateMinMax( itk::Image* referenceImage, Image* segmentation, TPixel& minimum, TPixel& maximum) { typedef itk::Image ImageType; typedef itk::Image SegmentationType; typename SegmentationType::Pointer segmentationItk; CastToItkImage(segmentation, segmentationItk); typename SegmentationType::RegionType segmentationRegion = segmentationItk->GetLargestPossibleRegion(); segmentationRegion.Crop(referenceImage->GetLargestPossibleRegion()); itk::ImageRegionConstIteratorWithIndex segmentationIterator(segmentationItk, segmentationRegion); itk::ImageRegionConstIteratorWithIndex referenceIterator(referenceImage, segmentationRegion); segmentationIterator.GoToBegin(); referenceIterator.GoToBegin(); minimum = std::numeric_limits::max(); maximum = std::numeric_limits::min(); while (!segmentationIterator.IsAtEnd()) { itk::Point pt; segmentationItk->TransformIndexToPhysicalPoint(segmentationIterator.GetIndex(), pt); typename ImageType::IndexType ind; itk::ContinuousIndex contInd; if (referenceImage->TransformPhysicalPointToContinuousIndex(pt, contInd)) { for (unsigned int i = 0; i < 3; ++i) ind[i] = ROUND_P(contInd[i]); referenceIterator.SetIndex(ind); if (segmentationIterator.Get() > 0) { if (referenceIterator.Get() < minimum) minimum = referenceIterator.Get(); if (referenceIterator.Get() > maximum) maximum = referenceIterator.Get(); } } ++segmentationIterator; } } template void mitk::CalculateGrayValueStatisticsTool::ITKHistogramming( itk::Image* referenceImage, Image* segmentation, std::stringstream& report) { typedef itk::Image ImageType; typedef itk::Image SegmentationType; typename SegmentationType::Pointer segmentationItk; CastToItkImage( segmentation, segmentationItk ); // generate histogram typename SegmentationType::RegionType segmentationRegion = segmentationItk->GetLargestPossibleRegion(); segmentationRegion.Crop( referenceImage->GetLargestPossibleRegion() ); itk::ImageRegionConstIteratorWithIndex< SegmentationType > segmentationIterator( segmentationItk, segmentationRegion); itk::ImageRegionConstIteratorWithIndex< ImageType > referenceIterator( referenceImage, segmentationRegion); segmentationIterator.GoToBegin(); referenceIterator.GoToBegin(); m_ITKHistogram = HistogramType::New(); TPixel minimum = std::numeric_limits::max(); TPixel maximum = std::numeric_limits::min(); CalculateMinMax(referenceImage, segmentation, minimum, maximum); //initialize the histogram to the range of the cropped region HistogramType::SizeType size; #if defined(ITK_USE_REVIEW_STATISTICS) typedef typename HistogramType::SizeType::ValueType HSizeValueType; #else typedef typename HistogramType::SizeType::SizeValueType HSizeValueType; #endif size.Fill(static_cast (maximum - minimum + 1)); HistogramType::MeasurementVectorType lowerBound; HistogramType::MeasurementVectorType upperBound; lowerBound[0] = minimum; upperBound[0] = maximum; m_ITKHistogram->Initialize(size, lowerBound, upperBound); double mean(0.0); double sd(0.0); double voxelCount(0.0); //iterate through the cropped region add the values to the histogram while (!segmentationIterator.IsAtEnd()) { itk::Point< float, 3 > pt; segmentationItk->TransformIndexToPhysicalPoint( segmentationIterator.GetIndex(), pt ); typename ImageType::IndexType ind; itk::ContinuousIndex contInd; if (referenceImage->TransformPhysicalPointToContinuousIndex(pt, contInd)) { for (unsigned int i = 0; i < 3; ++i) ind[i] = ROUND_P(contInd[i]); referenceIterator.SetIndex( ind ); if ( segmentationIterator.Get() > 0 ) { HistogramType::MeasurementVectorType currentMeasurementVector; currentMeasurementVector[0] = static_cast (referenceIterator.Get()); m_ITKHistogram->IncreaseFrequency(currentMeasurementVector, 1); mean = (mean * (static_cast (voxelCount) / static_cast (voxelCount + 1))) // 3 points: old center * 2/3 + currentPoint * 1/3; + static_cast (referenceIterator.Get()) / static_cast (voxelCount + 1); voxelCount += 1.0; } } ++segmentationIterator; } // second pass for SD segmentationIterator.GoToBegin(); referenceIterator.GoToBegin(); while ( !segmentationIterator.IsAtEnd() ) { itk::Point< float, 3 > pt; segmentationItk->TransformIndexToPhysicalPoint( segmentationIterator.GetIndex(), pt ); typename ImageType::IndexType ind; itk::ContinuousIndex contInd; if (referenceImage->TransformPhysicalPointToContinuousIndex(pt, contInd)) { for (unsigned int i = 0; i < 3; ++i) ind[i] = ROUND_P(contInd[i]); referenceIterator.SetIndex( ind ); if ( segmentationIterator.Get() > 0 ) { sd += ((static_cast(referenceIterator.Get() ) - mean)*(static_cast(referenceIterator.Get() ) - mean)); } } ++segmentationIterator; } sd /= static_cast(voxelCount - 1); sd = sqrt( sd ); // generate quantiles TPixel histogramQuantileValues[5]; histogramQuantileValues[0] = m_ITKHistogram->Quantile(0, 0.05); histogramQuantileValues[1] = m_ITKHistogram->Quantile(0, 0.25); histogramQuantileValues[2] = m_ITKHistogram->Quantile(0, 0.50); histogramQuantileValues[3] = m_ITKHistogram->Quantile(0, 0.75); histogramQuantileValues[4] = m_ITKHistogram->Quantile(0, 0.95); // report histogram values std::locale C("C"); std::locale originalLocale = report.getloc(); report.imbue(C); report << " Minimum:" << minimum << "\n 5% quantile: " << histogramQuantileValues[0] << "\n 25% quantile: " << histogramQuantileValues[1] << "\n 50% quantile: " << histogramQuantileValues[2] << "\n 75% quantile: " << histogramQuantileValues[3] << "\n 95% quantile: " << histogramQuantileValues[4] << "\n Maximum: " << maximum << "\n Mean: " << mean << "\n SD: " << sd << "\n"; report.imbue(originalLocale); } std::string mitk::CalculateGrayValueStatisticsTool::GetReport() const { return m_CompleteReport.str(); } mitk::CalculateGrayValueStatisticsTool::HistogramType::ConstPointer mitk::CalculateGrayValueStatisticsTool::GetHistogram() { return m_ITKHistogram.GetPointer(); } diff --git a/Modules/MitkExt/Interactions/mitkCalculateGrayValueStatisticsTool.h b/Modules/Segmentation/Interactions/mitkCalculateGrayValueStatisticsTool.h similarity index 95% rename from Modules/MitkExt/Interactions/mitkCalculateGrayValueStatisticsTool.h rename to Modules/Segmentation/Interactions/mitkCalculateGrayValueStatisticsTool.h index 959cc07a16..a20cc68ec3 100644 --- a/Modules/MitkExt/Interactions/mitkCalculateGrayValueStatisticsTool.h +++ b/Modules/Segmentation/Interactions/mitkCalculateGrayValueStatisticsTool.h @@ -1,102 +1,102 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.0 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkCalculateGrayValueStatisticsTool_h_Included #define mitkCalculateGrayValueStatisticsTool_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkSegmentationsProcessingTool.h" #ifndef __itkHistogram_h #include #endif #include #include namespace mitk { /** \brief Calculates some gray value statistics for segmentations. \ingroup ToolManagerEtAl \sa mitk::Tool \sa QmitkInteractiveSegmentation Last contributor: $Author$ */ -class MitkExt_EXPORT CalculateGrayValueStatisticsTool : public SegmentationsProcessingTool +class Segmentation_EXPORT CalculateGrayValueStatisticsTool : public SegmentationsProcessingTool { public: Message<> StatisticsCompleted; mitkClassMacro(CalculateGrayValueStatisticsTool, SegmentationsProcessingTool); itkNewMacro(CalculateGrayValueStatisticsTool); virtual const char** GetXPM() const; virtual const char* GetName() const; virtual std::string GetReport() const; // // Insight/Code/Review/Algorithms version of Histogram takes // only one template parameter, and the 'release' version // takes 2, but the default value for the second, 1, is what // was specified here. typedef itk::Statistics::Histogram HistogramType; HistogramType::Pointer m_ITKHistogram; HistogramType::ConstPointer GetHistogram(); typedef HistogramType::MeasurementType HistogramMeasurementType; protected: CalculateGrayValueStatisticsTool(); // purposely hidden virtual ~CalculateGrayValueStatisticsTool(); virtual void StartProcessingAllData(); virtual bool ProcessOneWorkingData( DataNode* node ); virtual void FinishProcessingAllData(); virtual std::string GetErrorMessage(); /** Calculates the minimum and maximum of the pixelvalues. They have to be known to initialize the histogram. */ template void CalculateMinMax(itk::Image* referenceImage, Image* segmentation, TPixel& minimum, TPixel& maximum); /** - initializes and fills the histogram - calculates mean, sd and quantiles */ template void ITKHistogramming(itk::Image* referenceImage, Image* segmentation, std::stringstream& report); std::stringstream m_CompleteReport; }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkCalculateGrayValueStatisticsTool.xpm b/Modules/Segmentation/Interactions/mitkCalculateGrayValueStatisticsTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkCalculateGrayValueStatisticsTool.xpm rename to Modules/Segmentation/Interactions/mitkCalculateGrayValueStatisticsTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkCalculateVolumetryTool.cpp b/Modules/Segmentation/Interactions/mitkCalculateVolumetryTool.cpp similarity index 96% rename from Modules/MitkExt/Interactions/mitkCalculateVolumetryTool.cpp rename to Modules/Segmentation/Interactions/mitkCalculateVolumetryTool.cpp index 455d7465c2..97a056a7ce 100644 --- a/Modules/MitkExt/Interactions/mitkCalculateVolumetryTool.cpp +++ b/Modules/Segmentation/Interactions/mitkCalculateVolumetryTool.cpp @@ -1,90 +1,90 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkCalculateVolumetryTool.h" #include "mitkCalculateVolumetryTool.xpm" #include "mitkVolumeCalculator.h" #include "mitkProperties.h" #include "mitkToolManager.h" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, CalculateVolumetryTool, "Volumetry tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, CalculateVolumetryTool, "Volumetry tool"); } mitk::CalculateVolumetryTool::CalculateVolumetryTool() { } mitk::CalculateVolumetryTool::~CalculateVolumetryTool() { } const char** mitk::CalculateVolumetryTool::GetXPM() const { return mitkCalculateVolumetryTool_xpm; } const char* mitk::CalculateVolumetryTool::GetName() const { return "Volumetry"; } std::string mitk::CalculateVolumetryTool::GetErrorMessage() { return "Volume could not be calculated for these nodes:"; } bool mitk::CalculateVolumetryTool::ProcessOneWorkingData( DataNode* node ) { if (node) { Image::Pointer image = dynamic_cast( node->GetData() ); if (image.IsNull()) return false; if (image->GetDimension() == 4) { Tool::ErrorMessage("Volumetry only valid for timestep 0! Bug #1280"); } VolumeCalculator::Pointer volumetryFilter = VolumeCalculator::New(); volumetryFilter->SetImage( image ); volumetryFilter->SetThreshold( 1 ); // comparison is >= try { volumetryFilter->ComputeVolume(); float volumeInTimeStep0 = volumetryFilter->GetVolume(); node->SetProperty( "volume", FloatProperty::New(volumeInTimeStep0) ); } catch(...) { return false; } } return true; } void mitk::CalculateVolumetryTool::FinishProcessingAllData() { Superclass::FinishProcessingAllData(); m_ToolManager->NodePropertiesChanged(); } diff --git a/Modules/MitkExt/Interactions/mitkCalculateVolumetryTool.h b/Modules/Segmentation/Interactions/mitkCalculateVolumetryTool.h similarity index 92% rename from Modules/MitkExt/Interactions/mitkCalculateVolumetryTool.h rename to Modules/Segmentation/Interactions/mitkCalculateVolumetryTool.h index ecec2b89cf..64fd831b18 100644 --- a/Modules/MitkExt/Interactions/mitkCalculateVolumetryTool.h +++ b/Modules/Segmentation/Interactions/mitkCalculateVolumetryTool.h @@ -1,61 +1,61 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.0 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkCalculateVolumetryTool_h_Included #define mitkCalculateVolumetryTool_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkSegmentationsProcessingTool.h" namespace mitk { /** \brief Calculates the segmented volumes for binary images. \ingroup ToolManagerEtAl \sa mitk::Tool \sa QmitkInteractiveSegmentation Last contributor: $Author$ */ -class MitkExt_EXPORT CalculateVolumetryTool : public SegmentationsProcessingTool +class Segmentation_EXPORT CalculateVolumetryTool : public SegmentationsProcessingTool { public: mitkClassMacro(CalculateVolumetryTool, SegmentationsProcessingTool); itkNewMacro(CalculateVolumetryTool); virtual const char** GetXPM() const; virtual const char* GetName() const; protected: virtual bool ProcessOneWorkingData( DataNode* node ); virtual std::string GetErrorMessage(); virtual void FinishProcessingAllData(); CalculateVolumetryTool(); // purposely hidden virtual ~CalculateVolumetryTool(); }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkCalculateVolumetryTool.xpm b/Modules/Segmentation/Interactions/mitkCalculateVolumetryTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkCalculateVolumetryTool.xpm rename to Modules/Segmentation/Interactions/mitkCalculateVolumetryTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkContourInteractor.cpp b/Modules/Segmentation/Interactions/mitkContourInteractor.cpp similarity index 100% rename from Modules/MitkExt/Interactions/mitkContourInteractor.cpp rename to Modules/Segmentation/Interactions/mitkContourInteractor.cpp diff --git a/Modules/MitkExt/Interactions/mitkContourInteractor.h b/Modules/Segmentation/Interactions/mitkContourInteractor.h similarity index 94% rename from Modules/MitkExt/Interactions/mitkContourInteractor.h rename to Modules/Segmentation/Interactions/mitkContourInteractor.h index a18184a080..38fad3ebe1 100644 --- a/Modules/MitkExt/Interactions/mitkContourInteractor.h +++ b/Modules/Segmentation/Interactions/mitkContourInteractor.h @@ -1,66 +1,66 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef __ContourInteractor_H #define __ContourInteractor_H #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include #include namespace mitk { //##Documentation //## @brief Interactor for the creation of an mitk::Contour //## @ingroup Interaction - class MitkExt_EXPORT ContourInteractor : public mitk::Interactor + class Segmentation_EXPORT ContourInteractor : public mitk::Interactor { public: mitkClassMacro(ContourInteractor, Interactor); mitkNewMacro2Param(Self, const char*, DataNode*); protected: ContourInteractor(const char * type, DataNode* dataNode); virtual ~ContourInteractor(); virtual bool ExecuteAction(Action* action, mitk::StateEvent const* stateEvent); /** * entry method for any interaction. Method is called if user * presses the left mouse button down. */ virtual void Press (mitk::Point3D& op); /** * this method is finally called after user release the left mouse button */ virtual void Release (mitk::Point3D& op); /** * method is called when the user moves the mouse with left mouse button down */ virtual void Move (mitk::Point3D& op); protected: bool m_Positive; bool m_Started; }; } #endif //__ContourInteractor_H diff --git a/Modules/MitkExt/Interactions/mitkContourTool.cpp b/Modules/Segmentation/Interactions/mitkContourTool.cpp similarity index 100% rename from Modules/MitkExt/Interactions/mitkContourTool.cpp rename to Modules/Segmentation/Interactions/mitkContourTool.cpp diff --git a/Modules/MitkExt/Interactions/mitkContourTool.h b/Modules/Segmentation/Interactions/mitkContourTool.h similarity index 95% rename from Modules/MitkExt/Interactions/mitkContourTool.h rename to Modules/Segmentation/Interactions/mitkContourTool.h index 1ecc7f73b4..e34b00f79a 100644 --- a/Modules/MitkExt/Interactions/mitkContourTool.h +++ b/Modules/Segmentation/Interactions/mitkContourTool.h @@ -1,78 +1,78 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkContourTool_h_Included #define mitkContourTool_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkFeedbackContourTool.h" namespace mitk { class Image; /** \brief Simple contour filling tool. \sa FeedbackContourTool \sa ExtractImageFilter \sa OverwriteSliceImageFilter \ingroup Interaction \ingroup ToolManagerEtAl Fills a visible contour (from FeedbackContourTool) during mouse dragging. When the mouse button is released, ContourTool tries to extract a slice from the working image and fill in the (filled) contour as a binary image. The painting "color" is defined by m_PaintingPixelValue, which is set in the constructor (by sub-classes) or during some event (e.g. in OnInvertLogic - when CTRL is pressed). \warning Only to be instantiated by mitk::ToolManager. $Author$ */ -class MitkExt_EXPORT ContourTool : public FeedbackContourTool +class Segmentation_EXPORT ContourTool : public FeedbackContourTool { public: mitkClassMacro(ContourTool, FeedbackContourTool); protected: ContourTool(int paintingPixelValue = 1); // purposely hidden virtual ~ContourTool(); virtual void Activated(); virtual void Deactivated(); virtual bool OnMousePressed (Action*, const StateEvent*); virtual bool OnMouseMoved (Action*, const StateEvent*); virtual bool OnMouseReleased(Action*, const StateEvent*); virtual bool OnInvertLogic (Action*, const StateEvent*); int m_PaintingPixelValue; }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkContourTool.xpm b/Modules/Segmentation/Interactions/mitkContourTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkContourTool.xpm rename to Modules/Segmentation/Interactions/mitkContourTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkCorrectorTool2D.cpp b/Modules/Segmentation/Interactions/mitkCorrectorTool2D.cpp similarity index 98% rename from Modules/MitkExt/Interactions/mitkCorrectorTool2D.cpp rename to Modules/Segmentation/Interactions/mitkCorrectorTool2D.cpp index dd1855ed86..9d6ac9d2fb 100644 --- a/Modules/MitkExt/Interactions/mitkCorrectorTool2D.cpp +++ b/Modules/Segmentation/Interactions/mitkCorrectorTool2D.cpp @@ -1,151 +1,151 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkCorrectorTool2D.h" #include "mitkCorrectorAlgorithm.h" #include "mitkToolManager.h" #include "mitkOverwriteSliceImageFilter.h" #include "mitkBaseRenderer.h" #include "mitkRenderingManager.h" #include "mitkCorrectorTool2D.xpm" #include "mitkOverwriteDirectedPlaneImageFilter.h" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, CorrectorTool2D, "Correction tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, CorrectorTool2D, "Correction tool"); } mitk::CorrectorTool2D::CorrectorTool2D(int paintingPixelValue) :FeedbackContourTool("PressMoveRelease"), m_PaintingPixelValue(paintingPixelValue) { GetFeedbackContour()->SetClosed( false ); // don't close the contour to a polygon } mitk::CorrectorTool2D::~CorrectorTool2D() { } const char** mitk::CorrectorTool2D::GetXPM() const { return mitkCorrectorTool2D_xpm; } const char* mitk::CorrectorTool2D::GetName() const { return "Correction"; } void mitk::CorrectorTool2D::Activated() { Superclass::Activated(); } void mitk::CorrectorTool2D::Deactivated() { Superclass::Deactivated(); } bool mitk::CorrectorTool2D::OnMousePressed (Action* action, const StateEvent* stateEvent) { if (!FeedbackContourTool::OnMousePressed( action, stateEvent )) return false; const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return false; Contour* contour = FeedbackContourTool::GetFeedbackContour(); contour->Initialize(); contour->AddVertex( positionEvent->GetWorldPosition() ); FeedbackContourTool::SetFeedbackContourVisible(true); return true; } bool mitk::CorrectorTool2D::OnMouseMoved (Action* action, const StateEvent* stateEvent) { if (!FeedbackContourTool::OnMouseMoved( action, stateEvent )) return false; const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return false; Contour* contour = FeedbackContourTool::GetFeedbackContour(); contour->AddVertex( positionEvent->GetWorldPosition() ); assert( positionEvent->GetSender()->GetRenderWindow() ); mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); return true; } bool mitk::CorrectorTool2D::OnMouseReleased(Action* action, const StateEvent* stateEvent) { // 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's working image corresponds to that FeedbackContourTool::SetFeedbackContourVisible(false); const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return false; assert( positionEvent->GetSender()->GetRenderWindow() ); mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); if (!FeedbackContourTool::OnMouseReleased( action, stateEvent )) return false; DataNode* workingNode( m_ToolManager->GetWorkingData(0) ); if (!workingNode) return false; Image* image = dynamic_cast(workingNode->GetData()); const PlaneGeometry* planeGeometry( dynamic_cast (positionEvent->GetSender()->GetCurrentWorldGeometry2D() ) ); if ( !image || !planeGeometry ) return false; // 2. Slice is known, now we try to get it as a 2D image and project the contour into index coordinates of this slice m_WorkingSlice = FeedbackContourTool::GetAffectedImageSliceAs2DImage( positionEvent, image ); if ( m_WorkingSlice.IsNull() ) { MITK_ERROR << "Unable to extract slice." << std::endl; return false; } CorrectorAlgorithm::Pointer algorithm = CorrectorAlgorithm::New(); algorithm->SetInput( m_WorkingSlice ); algorithm->SetContour( FeedbackContourTool::GetFeedbackContour() ); try { algorithm->UpdateLargestPossibleRegion(); } catch ( std::exception& e ) { MITK_ERROR << "Caught exception '" << e.what() << "'" << std::endl; } mitk::Image::Pointer resultSlice = mitk::Image::New(); resultSlice->Initialize(algorithm->GetOutput()); resultSlice->SetVolume(algorithm->GetOutput()->GetData()); this->WriteBackSegmentationResult(positionEvent, resultSlice); // 6. Make sure the result is drawn again --> is visible then. assert( positionEvent->GetSender()->GetRenderWindow() ); mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); return true; } diff --git a/Modules/MitkExt/Interactions/mitkCorrectorTool2D.h b/Modules/Segmentation/Interactions/mitkCorrectorTool2D.h similarity index 95% rename from Modules/MitkExt/Interactions/mitkCorrectorTool2D.h rename to Modules/Segmentation/Interactions/mitkCorrectorTool2D.h index 0eba6ab07d..f7743d14dd 100644 --- a/Modules/MitkExt/Interactions/mitkCorrectorTool2D.h +++ b/Modules/Segmentation/Interactions/mitkCorrectorTool2D.h @@ -1,81 +1,81 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkCorrectorTool2D_h_Included #define mitkCorrectorTool2D_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkFeedbackContourTool.h" namespace mitk { class Image; /** \brief Corrector tool for 2D binary segmentations \sa FeedbackContourTool \sa ExtractImageFilter \sa OverwriteSliceImageFilter \ingroup Interaction \ingroup ToolManagerEtAl Lets the user draw a (multi-point) line and intelligently decides what to do. The underlying algorithm tests if the line begins and ends inside or outside a segmentation and either adds or subtracts a piece of segmentation. Algorithm is implemented in CorrectorAlgorithm (so that it could be reimplemented in a more modern fashion some time). \warning Only to be instantiated by mitk::ToolManager. $Author$ */ -class MitkExt_EXPORT CorrectorTool2D : public FeedbackContourTool +class Segmentation_EXPORT CorrectorTool2D : public FeedbackContourTool { public: mitkClassMacro(CorrectorTool2D, FeedbackContourTool); itkNewMacro(CorrectorTool2D); virtual const char** GetXPM() const; virtual const char* GetName() const; protected: CorrectorTool2D(int paintingPixelValue = 1); // purposely hidden virtual ~CorrectorTool2D(); virtual void Activated(); virtual void Deactivated(); virtual bool OnMousePressed (Action*, const StateEvent*); virtual bool OnMouseMoved (Action*, const StateEvent*); virtual bool OnMouseReleased(Action*, const StateEvent*); int m_PaintingPixelValue; Image::Pointer m_WorkingSlice; }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkCorrectorTool2D.xpm b/Modules/Segmentation/Interactions/mitkCorrectorTool2D.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkCorrectorTool2D.xpm rename to Modules/Segmentation/Interactions/mitkCorrectorTool2D.xpm diff --git a/Modules/MitkExt/Interactions/mitkCreateSurfaceTool.cpp b/Modules/Segmentation/Interactions/mitkCreateSurfaceTool.cpp similarity index 97% rename from Modules/MitkExt/Interactions/mitkCreateSurfaceTool.cpp rename to Modules/Segmentation/Interactions/mitkCreateSurfaceTool.cpp index a29655c327..153b2d9bfa 100644 --- a/Modules/MitkExt/Interactions/mitkCreateSurfaceTool.cpp +++ b/Modules/Segmentation/Interactions/mitkCreateSurfaceTool.cpp @@ -1,100 +1,100 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkCreateSurfaceTool.h" #include "mitkCreateSurfaceTool.xpm" #include "mitkShowSegmentationAsSurface.h" #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkToolManager.h" #include "itkCommand.h" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, CreateSurfaceTool, "Surface creation tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, CreateSurfaceTool, "Surface creation tool"); } mitk::CreateSurfaceTool::CreateSurfaceTool() { } mitk::CreateSurfaceTool::~CreateSurfaceTool() { } const char** mitk::CreateSurfaceTool::GetXPM() const { return mitkCreateSurfaceTool_xpm; } const char* mitk::CreateSurfaceTool::GetName() const { return "Surface"; } std::string mitk::CreateSurfaceTool::GetErrorMessage() { return "No surfaces created for these segmentations:"; } bool mitk::CreateSurfaceTool::ProcessOneWorkingData( DataNode* node ) { if (node) { Image::Pointer image = dynamic_cast( node->GetData() ); if (image.IsNull()) return false; try { mitk::ShowSegmentationAsSurface::Pointer surfaceFilter = mitk::ShowSegmentationAsSurface::New(); // attach observer to get notified about result itk::SimpleMemberCommand::Pointer goodCommand = itk::SimpleMemberCommand::New(); goodCommand->SetCallbackFunction(this, &CreateSurfaceTool::OnSurfaceCalculationDone); surfaceFilter->AddObserver(mitk::ResultAvailable(), goodCommand); itk::SimpleMemberCommand::Pointer badCommand = itk::SimpleMemberCommand::New(); badCommand->SetCallbackFunction(this, &CreateSurfaceTool::OnSurfaceCalculationDone); surfaceFilter->AddObserver(mitk::ProcessingError(), badCommand); DataNode::Pointer nodepointer = node; surfaceFilter->SetPointerParameter("Input", image); surfaceFilter->SetPointerParameter("Group node", nodepointer); surfaceFilter->SetParameter("Show result", true ); surfaceFilter->SetParameter("Sync visibility", false ); surfaceFilter->SetDataStorage( *m_ToolManager->GetDataStorage() ); ProgressBar::GetInstance()->AddStepsToDo(1); StatusBar::GetInstance()->DisplayText("Surface creation started in background..."); surfaceFilter->StartAlgorithm(); } catch(...) { return false; } } return true; } void mitk::CreateSurfaceTool::OnSurfaceCalculationDone() { ProgressBar::GetInstance()->Progress(); m_ToolManager->NewNodesGenerated(); } diff --git a/Modules/MitkExt/Interactions/mitkCreateSurfaceTool.h b/Modules/Segmentation/Interactions/mitkCreateSurfaceTool.h similarity index 92% rename from Modules/MitkExt/Interactions/mitkCreateSurfaceTool.h rename to Modules/Segmentation/Interactions/mitkCreateSurfaceTool.h index 5589fd1cd2..0c1b57481f 100644 --- a/Modules/MitkExt/Interactions/mitkCreateSurfaceTool.h +++ b/Modules/Segmentation/Interactions/mitkCreateSurfaceTool.h @@ -1,60 +1,60 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.0 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkCreateSurfaceTool_h_Included #define mitkCreateSurfaceTool_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkSegmentationsProcessingTool.h" namespace mitk { /** \brief Creates surface models from segmentations. \ingroup ToolManagerEtAl \sa mitk::Tool \sa QmitkInteractiveSegmentation Last contributor: $Author$ */ -class MitkExt_EXPORT CreateSurfaceTool : public SegmentationsProcessingTool +class Segmentation_EXPORT CreateSurfaceTool : public SegmentationsProcessingTool { public: mitkClassMacro(CreateSurfaceTool, SegmentationsProcessingTool); itkNewMacro(CreateSurfaceTool); virtual const char** GetXPM() const; virtual const char* GetName() const; void OnSurfaceCalculationDone(); protected: virtual bool ProcessOneWorkingData( DataNode* node ); virtual std::string GetErrorMessage(); CreateSurfaceTool(); // purposely hidden virtual ~CreateSurfaceTool(); }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkCreateSurfaceTool.xpm b/Modules/Segmentation/Interactions/mitkCreateSurfaceTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkCreateSurfaceTool.xpm rename to Modules/Segmentation/Interactions/mitkCreateSurfaceTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkDrawPaintbrushTool.cpp b/Modules/Segmentation/Interactions/mitkDrawPaintbrushTool.cpp similarity index 92% rename from Modules/MitkExt/Interactions/mitkDrawPaintbrushTool.cpp rename to Modules/Segmentation/Interactions/mitkDrawPaintbrushTool.cpp index 90fbb8facb..ee95c182b9 100644 --- a/Modules/MitkExt/Interactions/mitkDrawPaintbrushTool.cpp +++ b/Modules/Segmentation/Interactions/mitkDrawPaintbrushTool.cpp @@ -1,44 +1,44 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkDrawPaintbrushTool.h" #include "mitkDrawPaintbrushTool.xpm" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, DrawPaintbrushTool, "Paintbrush drawing tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, DrawPaintbrushTool, "Paintbrush drawing tool"); } mitk::DrawPaintbrushTool::DrawPaintbrushTool() :PaintbrushTool(1) { } mitk::DrawPaintbrushTool::~DrawPaintbrushTool() { } const char** mitk::DrawPaintbrushTool::GetXPM() const { return mitkDrawPaintbrushTool_xpm; } const char* mitk::DrawPaintbrushTool::GetName() const { return "Paint"; } diff --git a/Modules/MitkExt/Interactions/mitkDrawPaintbrushTool.h b/Modules/Segmentation/Interactions/mitkDrawPaintbrushTool.h similarity index 93% rename from Modules/MitkExt/Interactions/mitkDrawPaintbrushTool.h rename to Modules/Segmentation/Interactions/mitkDrawPaintbrushTool.h index e81c07aa3d..642e2e5fe6 100644 --- a/Modules/MitkExt/Interactions/mitkDrawPaintbrushTool.h +++ b/Modules/Segmentation/Interactions/mitkDrawPaintbrushTool.h @@ -1,64 +1,64 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkPaintContourTool_h_Included #define mitkPaintContourTool_h_Included #include "mitkPaintbrushTool.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" namespace mitk { /** \brief Paintbrush tool for InteractiveSegmentation \sa FeedbackContourTool \sa ExtractImageFilter \sa OverwriteSliceImageFilter \ingroup Interaction \ingroup ToolManagerEtAl Simple paintbrush drawing tool. Right now there are only circular pens of varying size. This class specified only the drawing "color" for the super class PaintbrushTool. \warning Only to be instantiated by mitk::ToolManager. $Author: maleike $ */ -class MitkExt_EXPORT DrawPaintbrushTool : public PaintbrushTool +class Segmentation_EXPORT DrawPaintbrushTool : public PaintbrushTool { public: mitkClassMacro(DrawPaintbrushTool, PaintbrushTool); itkNewMacro(DrawPaintbrushTool); virtual const char** GetXPM() const; virtual const char* GetName() const; protected: DrawPaintbrushTool(); // purposely hidden virtual ~DrawPaintbrushTool(); }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkDrawPaintbrushTool.xpm b/Modules/Segmentation/Interactions/mitkDrawPaintbrushTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkDrawPaintbrushTool.xpm rename to Modules/Segmentation/Interactions/mitkDrawPaintbrushTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkErasePaintbrushTool.cpp b/Modules/Segmentation/Interactions/mitkErasePaintbrushTool.cpp similarity index 92% rename from Modules/MitkExt/Interactions/mitkErasePaintbrushTool.cpp rename to Modules/Segmentation/Interactions/mitkErasePaintbrushTool.cpp index af04098073..4ba4b5f6d9 100644 --- a/Modules/MitkExt/Interactions/mitkErasePaintbrushTool.cpp +++ b/Modules/Segmentation/Interactions/mitkErasePaintbrushTool.cpp @@ -1,45 +1,45 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkErasePaintbrushTool.h" #include "mitkErasePaintbrushTool.xpm" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, ErasePaintbrushTool, "Paintbrush erasing tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, ErasePaintbrushTool, "Paintbrush erasing tool"); } mitk::ErasePaintbrushTool::ErasePaintbrushTool() :PaintbrushTool(0) { FeedbackContourTool::SetFeedbackContourColor( 1.0, 0.0, 0.0 ); } mitk::ErasePaintbrushTool::~ErasePaintbrushTool() { } const char** mitk::ErasePaintbrushTool::GetXPM() const { return mitkErasePaintbrushTool_xpm; } const char* mitk::ErasePaintbrushTool::GetName() const { return "Wipe"; } diff --git a/Modules/MitkExt/Interactions/mitkErasePaintbrushTool.h b/Modules/Segmentation/Interactions/mitkErasePaintbrushTool.h similarity index 93% rename from Modules/MitkExt/Interactions/mitkErasePaintbrushTool.h rename to Modules/Segmentation/Interactions/mitkErasePaintbrushTool.h index b1484fccba..09287190c7 100644 --- a/Modules/MitkExt/Interactions/mitkErasePaintbrushTool.h +++ b/Modules/Segmentation/Interactions/mitkErasePaintbrushTool.h @@ -1,64 +1,64 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkErasePaintbrushTool_h_Included #define mitkErasePaintbrushTool_h_Included #include "mitkPaintbrushTool.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" namespace mitk { /** \brief Paintbrush tool for InteractiveSegmentation \sa FeedbackContourTool \sa ExtractImageFilter \sa OverwriteSliceImageFilter \ingroup Interaction \ingroup ToolManagerEtAl Simple paintbrush drawing tool. Right now there are only circular pens of varying size. This class specified only the drawing "color" for the super class PaintbrushTool. \warning Only to be instantiated by mitk::ToolManager. $Author: maleike $ */ -class MitkExt_EXPORT ErasePaintbrushTool : public PaintbrushTool +class Segmentation_EXPORT ErasePaintbrushTool : public PaintbrushTool { public: mitkClassMacro(ErasePaintbrushTool, PaintbrushTool); itkNewMacro(ErasePaintbrushTool); virtual const char** GetXPM() const; virtual const char* GetName() const; protected: ErasePaintbrushTool(); // purposely hidden virtual ~ErasePaintbrushTool(); }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkErasePaintbrushTool.xpm b/Modules/Segmentation/Interactions/mitkErasePaintbrushTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkErasePaintbrushTool.xpm rename to Modules/Segmentation/Interactions/mitkErasePaintbrushTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkEraseRegionTool.cpp b/Modules/Segmentation/Interactions/mitkEraseRegionTool.cpp similarity index 93% rename from Modules/MitkExt/Interactions/mitkEraseRegionTool.cpp rename to Modules/Segmentation/Interactions/mitkEraseRegionTool.cpp index 58ffb471be..e0c3142a13 100644 --- a/Modules/MitkExt/Interactions/mitkEraseRegionTool.cpp +++ b/Modules/Segmentation/Interactions/mitkEraseRegionTool.cpp @@ -1,45 +1,45 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkEraseRegionTool.h" #include "mitkEraseRegionTool.xpm" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, EraseRegionTool, "Erase tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, EraseRegionTool, "Erase tool"); } mitk::EraseRegionTool::EraseRegionTool() :SetRegionTool(0) { FeedbackContourTool::SetFeedbackContourColor( 1.0, 0.0, 0.0 ); } mitk::EraseRegionTool::~EraseRegionTool() { } const char** mitk::EraseRegionTool::GetXPM() const { return mitkEraseRegionTool_xpm; } const char* mitk::EraseRegionTool::GetName() const { return "Erase"; } diff --git a/Modules/MitkExt/Interactions/mitkEraseRegionTool.h b/Modules/Segmentation/Interactions/mitkEraseRegionTool.h similarity index 93% rename from Modules/MitkExt/Interactions/mitkEraseRegionTool.h rename to Modules/Segmentation/Interactions/mitkEraseRegionTool.h index 51e8b65e30..c9e150386b 100644 --- a/Modules/MitkExt/Interactions/mitkEraseRegionTool.h +++ b/Modules/Segmentation/Interactions/mitkEraseRegionTool.h @@ -1,63 +1,63 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkEraseRegionTool_h_Included #define mitkEraseRegionTool_h_Included #include "mitkSetRegionTool.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" namespace mitk { /** \brief Fill the inside of a contour with 1 \sa SetRegionTool \ingroup Interaction \ingroup ToolManagerEtAl Finds the outer contour of a shape in 2D (possibly including holes) and sets all the inside pixels to 0 (erasing a segmentation). \warning Only to be instantiated by mitk::ToolManager. $Author$ */ -class MitkExt_EXPORT EraseRegionTool : public SetRegionTool +class Segmentation_EXPORT EraseRegionTool : public SetRegionTool { public: mitkClassMacro(EraseRegionTool, SetRegionTool); itkNewMacro(EraseRegionTool); virtual const char** GetXPM() const; virtual const char* GetName() const; protected: EraseRegionTool(); // purposely hidden virtual ~EraseRegionTool(); }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkEraseRegionTool.xpm b/Modules/Segmentation/Interactions/mitkEraseRegionTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkEraseRegionTool.xpm rename to Modules/Segmentation/Interactions/mitkEraseRegionTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkExtrudedContourInteractor.cpp b/Modules/Segmentation/Interactions/mitkExtrudedContourInteractor.cpp similarity index 100% rename from Modules/MitkExt/Interactions/mitkExtrudedContourInteractor.cpp rename to Modules/Segmentation/Interactions/mitkExtrudedContourInteractor.cpp diff --git a/Modules/MitkExt/Interactions/mitkExtrudedContourInteractor.h b/Modules/Segmentation/Interactions/mitkExtrudedContourInteractor.h similarity index 94% rename from Modules/MitkExt/Interactions/mitkExtrudedContourInteractor.h rename to Modules/Segmentation/Interactions/mitkExtrudedContourInteractor.h index 1deaf74afd..be8c3a7be2 100644 --- a/Modules/MitkExt/Interactions/mitkExtrudedContourInteractor.h +++ b/Modules/Segmentation/Interactions/mitkExtrudedContourInteractor.h @@ -1,73 +1,73 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef __ExtrudedContourInteractor_H #define __ExtrudedContourInteractor_H #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include #include #include #include namespace mitk { //##Documentation //## @brief Interactor for the creation of an mitk::Contour //## @ingroup Interaction - class MitkExt_EXPORT ExtrudedContourInteractor : public mitk::Interactor + class Segmentation_EXPORT ExtrudedContourInteractor : public mitk::Interactor { public: mitkClassMacro(ExtrudedContourInteractor, Interactor); mitkNewMacro2Param(Self, const char*, DataNode*); itkGetObjectMacro(Contour, mitk::Contour); itkGetObjectMacro(ContourNode, mitk::DataNode); protected: ExtrudedContourInteractor(const char * type, DataNode* dataNode); virtual ~ExtrudedContourInteractor(); virtual bool ExecuteAction(Action* action, mitk::StateEvent const* stateEvent); /** * entry method for any interaction. Method is called if user * presses the left mouse button down. */ virtual void Press (mitk::Point3D& op); /** * this method is finally called after user release the left mouse button */ virtual void Release (mitk::Point3D& op); /** * method is called when the user moves the mouse with left mouse button down */ virtual void Move (mitk::Point3D& op); protected: bool m_Positive; bool m_Started; mitk::Contour::Pointer m_Contour; mitk::DataNode::Pointer m_ContourNode; }; } #endif //__ExtrudedContourInteractor_H diff --git a/Modules/MitkExt/Interactions/mitkFeedbackContourTool.cpp b/Modules/Segmentation/Interactions/mitkFeedbackContourTool.cpp similarity index 100% rename from Modules/MitkExt/Interactions/mitkFeedbackContourTool.cpp rename to Modules/Segmentation/Interactions/mitkFeedbackContourTool.cpp diff --git a/Modules/MitkExt/Interactions/mitkFeedbackContourTool.h b/Modules/Segmentation/Interactions/mitkFeedbackContourTool.h similarity index 97% rename from Modules/MitkExt/Interactions/mitkFeedbackContourTool.h rename to Modules/Segmentation/Interactions/mitkFeedbackContourTool.h index 0291f7ea9e..2eb88d73ee 100644 --- a/Modules/MitkExt/Interactions/mitkFeedbackContourTool.h +++ b/Modules/Segmentation/Interactions/mitkFeedbackContourTool.h @@ -1,107 +1,107 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.0 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkFeedbackContourTool_h_Included #define mitkFeedbackContourTool_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkSegTool2D.h" #include "mitkContour.h" #include "mitkContourUtils.h" #include "mitkImage.h" #include "mitkDataNode.h" #include "mitkImageCast.h" namespace mitk { /** \brief Base class for tools that use a contour for feedback \sa Tool \sa Contour \ingroup Interaction \ingroup ToolManagerEtAl Implements helper methods, that might be of use to all kind of 2D segmentation tools that use a contour for user feedback. - Providing a feedback contour that might be added or removed from the visible scene (SetFeedbackContourVisible). - Filling of a contour into a 2D slice These helper methods are actually implemented in ContourUtils now. FeedbackContourTool only forwards such requests. \warning Only to be instantiated by mitk::ToolManager. $Author: nolden $ */ -class MitkExt_EXPORT FeedbackContourTool : public SegTool2D +class Segmentation_EXPORT FeedbackContourTool : public SegTool2D { public: mitkClassMacro(FeedbackContourTool, SegTool2D); protected: FeedbackContourTool(); // purposely hidden FeedbackContourTool(const char*); // purposely hidden virtual ~FeedbackContourTool(); Contour* GetFeedbackContour(); void SetFeedbackContour(Contour&); void Disable3dRendering(); void SetFeedbackContourVisible(bool); /// Provide values from 0.0 (black) to 1.0 (full color) void SetFeedbackContourColor( float r, float g, float b ); void SetFeedbackContourColorDefault(); /** \brief Projects a contour onto an image point by point. Converts from world to index coordinates. \param correctionForIpSegmentation adds 0.5 to x and y index coordinates (difference between ipSegmentation and MITK contours) */ Contour::Pointer ProjectContourTo2DSlice(Image* slice, Contour* contourIn3D, bool correctionForIpSegmentation = false, bool constrainToInside = true); /** \brief Projects a slice index coordinates of a contour back into world coordinates. \param correctionForIpSegmentation subtracts 0.5 to x and y index coordinates (difference between ipSegmentation and MITK contours) */ Contour::Pointer BackProjectContourFrom2DSlice(const Geometry3D* sliceGeometry, Contour* contourIn2D, bool correctionForIpSegmentation = false); /** \brief Fill a contour in a 2D slice with a specified pixel value. */ void FillContourInSlice( Contour* projectedContour, Image* sliceImage, int paintingPixelValue = 1 ); private: Contour::Pointer m_FeedbackContour; DataNode::Pointer m_FeedbackContourNode; bool m_FeedbackContourVisible; ContourUtils::Pointer m_ContourUtils; }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkFillRegionTool.cpp b/Modules/Segmentation/Interactions/mitkFillRegionTool.cpp similarity index 93% rename from Modules/MitkExt/Interactions/mitkFillRegionTool.cpp rename to Modules/Segmentation/Interactions/mitkFillRegionTool.cpp index 2968c23e5e..dea2ca010a 100644 --- a/Modules/MitkExt/Interactions/mitkFillRegionTool.cpp +++ b/Modules/Segmentation/Interactions/mitkFillRegionTool.cpp @@ -1,44 +1,44 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkFillRegionTool.h" #include "mitkFillRegionTool.xpm" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, FillRegionTool, "Fill tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, FillRegionTool, "Fill tool"); } mitk::FillRegionTool::FillRegionTool() :SetRegionTool(1) { } mitk::FillRegionTool::~FillRegionTool() { } const char** mitk::FillRegionTool::GetXPM() const { return mitkFillRegionTool_xpm; } const char* mitk::FillRegionTool::GetName() const { return "Fill"; } diff --git a/Modules/MitkExt/Interactions/mitkFillRegionTool.h b/Modules/Segmentation/Interactions/mitkFillRegionTool.h similarity index 93% rename from Modules/MitkExt/Interactions/mitkFillRegionTool.h rename to Modules/Segmentation/Interactions/mitkFillRegionTool.h index e3c7e2722f..9809e9b8fb 100644 --- a/Modules/MitkExt/Interactions/mitkFillRegionTool.h +++ b/Modules/Segmentation/Interactions/mitkFillRegionTool.h @@ -1,62 +1,62 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkFillRegionTool_h_Included #define mitkFillRegionTool_h_Included #include "mitkSetRegionTool.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" namespace mitk { /** \brief Fill the inside of a contour with 1 \sa SetRegionTool \ingroup Interaction \ingroup ToolManagerEtAl Finds the outer contour of a shape in 2D (possibly including holes) and sets all the inside pixels to 1, filling holes in a segmentation. \warning Only to be instantiated by mitk::ToolManager. $Author$ */ -class MitkExt_EXPORT FillRegionTool : public SetRegionTool +class Segmentation_EXPORT FillRegionTool : public SetRegionTool { public: mitkClassMacro(FillRegionTool, SetRegionTool); itkNewMacro(FillRegionTool); virtual const char** GetXPM() const; virtual const char* GetName() const; protected: FillRegionTool(); // purposely hidden virtual ~FillRegionTool(); }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkFillRegionTool.xpm b/Modules/Segmentation/Interactions/mitkFillRegionTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkFillRegionTool.xpm rename to Modules/Segmentation/Interactions/mitkFillRegionTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkPaintbrushTool.cpp b/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp similarity index 98% rename from Modules/MitkExt/Interactions/mitkPaintbrushTool.cpp rename to Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp index dbb9eeb2b1..ade53e541f 100644 --- a/Modules/MitkExt/Interactions/mitkPaintbrushTool.cpp +++ b/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp @@ -1,379 +1,377 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkPaintbrushTool.h" #include "mitkToolManager.h" #include "mitkOverwriteSliceImageFilter.h" #include "mitkBaseRenderer.h" #include "mitkImageDataItem.h" #include "ipSegmentation.h" #include "mitkLevelWindowProperty.h" #define ROUND(a) ((a)>0 ? (int)((a)+0.5) : -(int)(0.5-(a))) int mitk::PaintbrushTool::m_Size = 1; mitk::PaintbrushTool::PaintbrushTool(int paintingPixelValue) :FeedbackContourTool("PressMoveReleaseWithCTRLInversionAllMouseMoves"), m_PaintingPixelValue(paintingPixelValue), m_LastContourSize(0) // other than initial mitk::PaintbrushTool::m_Size (around l. 28) { m_MasterContour = Contour::New(); m_MasterContour->Initialize(); m_CurrentPlane = NULL; m_WorkingNode = DataNode::New(); m_WorkingNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( mitk::LevelWindow(0, 1) ) ); m_WorkingNode->SetProperty( "binary", mitk::BoolProperty::New(true) ); } mitk::PaintbrushTool::~PaintbrushTool() { } void mitk::PaintbrushTool::Activated() { Superclass::Activated(); FeedbackContourTool::SetFeedbackContourVisible(true); SizeChanged.Send(m_Size); } void mitk::PaintbrushTool::Deactivated() { FeedbackContourTool::SetFeedbackContourVisible(false); if (m_ToolManager->GetDataStorage()->Exists(m_WorkingNode)) m_ToolManager->GetDataStorage()->Remove(m_WorkingNode); Superclass::Deactivated(); } void mitk::PaintbrushTool::SetSize(int value) { m_Size = value; } void mitk::PaintbrushTool::UpdateContour(const StateEvent* stateEvent) { //MITK_INFO<<"Update..."; // examine stateEvent and create a contour that matches the pixel mask that we are going to draw const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return; // create a copy of this slice (at least match the pixel sizes/spacings), // then draw the desired mask on it and create a contour from it // Convert to ipMITKSegmentationTYPE (because getting pixels relys on that data type) itk::Image< ipMITKSegmentationTYPE, 2 >::Pointer correctPixelTypeImage; CastToItkImage(m_WorkingSlice/*dynamic_cast(m_WorkingNode->GetData())*/, correctPixelTypeImage ); assert (correctPixelTypeImage.IsNotNull() ); itk::Image< ipMITKSegmentationTYPE, 2 >::DirectionType imageDirection; imageDirection.SetIdentity(); correctPixelTypeImage->SetDirection(imageDirection); Image::Pointer temporarySlice = Image::New(); CastToMitkImage( correctPixelTypeImage, temporarySlice ); //mitkIpPicDescriptor* stupidClone = mitkIpPicClone( temporarySlice->GetSliceData()->GetPicDescriptor() ); mitkIpPicDescriptor* stupidClone = mitkIpPicNew(); CastToIpPicDescriptor( temporarySlice->GetSliceData(), stupidClone ); unsigned int pixelWidth = m_Size + 1; unsigned int pixelHeight = m_Size + 1; if ( stupidClone->n[0] <= pixelWidth || stupidClone->n[1] <= pixelHeight ) { MITK_INFO << "Brush size is bigger than your working image. Reconsider this...\n" "(Or tell your progammer until (s)he fixes this message.)" << std::endl; mitkIpPicFree( stupidClone ); return; } unsigned int lineLength( stupidClone->n[0] ); unsigned int oneContourOffset(0); float circleCenterX = (float)m_Size / 2.0; float circleCenterY = (float)m_Size / 2.0; for (unsigned int x = 0; x <= pixelWidth; ++x) { for (unsigned int y = 0; y <= pixelHeight; ++y) { unsigned int offset = lineLength * y + x; ipMITKSegmentationTYPE* current = (ipMITKSegmentationTYPE*)stupidClone->data + offset; float pixelCenterX = x + 0.5; float pixelCenterY = y + 0.5; float xoff = pixelCenterX - circleCenterX; float yoff = pixelCenterY - circleCenterY; bool inside = xoff * xoff + yoff * yoff < (m_Size * m_Size) / 4.0; // no idea, if this would work for ellipses if (inside) { *current = 1; oneContourOffset = offset; } else { *current = 0; } } } int numberOfContourPoints( 0 ); int newBufferSize( 0 ); float* contourPoints = ipMITKSegmentationGetContour8N( stupidClone, oneContourOffset, numberOfContourPoints, newBufferSize ); // memory allocated with malloc if (!contourPoints) { mitkIpPicFree( stupidClone ); return; } // copy point from float* to mitk::Contour Contour::Pointer contourInImageIndexCoordinates = Contour::New(); contourInImageIndexCoordinates->Initialize(); Point3D newPoint; //ipMITKSegmentationGetContour8N returns all points, which causes vtk warnings, since the first and the last points are coincident. //leaving the last point out, the contour is still drawn correctly for (int index = 0; index < numberOfContourPoints-1; ++index) { newPoint[0] = contourPoints[ 2 * index + 0 ] - circleCenterX; // master contour should be centered around (0,0) newPoint[1] = contourPoints[ 2 * index + 1] - circleCenterY; newPoint[2] = 0.0; MITK_DEBUG << "Point [" << index << "] (" << newPoint[0] << ", " << newPoint[1] << ")" << std::endl; contourInImageIndexCoordinates->AddVertex( newPoint ); } free(contourPoints); m_MasterContour = contourInImageIndexCoordinates; // The PicDescriptor is only REFERENCING(!) the data, the temporarySlice takes care of deleting the data also the descriptor is pointing on // because they got allocated by the ImageDataItem, not the descriptor. stupidClone->data = NULL; mitkIpPicFree( stupidClone ); } /** Just show the contour, get one point as the central point and add surrounding points to the contour. */ bool mitk::PaintbrushTool::OnMousePressed (Action* action, const StateEvent* stateEvent) { return this->OnMouseMoved(action, stateEvent); } /** Insert the point to the feedback contour,finish to build the contour and at the same time the painting function */ bool mitk::PaintbrushTool::OnMouseMoved (Action* itkNotUsed(action), const StateEvent* stateEvent) { const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return false; CheckIfCurrentSliceHasChanged(positionEvent); if ( m_LastContourSize != m_Size ) { UpdateContour( stateEvent ); m_LastContourSize = m_Size; } bool leftMouseButtonPressed( stateEvent->GetId() == 530 || stateEvent->GetId() == 534 || stateEvent->GetId() == 1 || stateEvent->GetId() == 5 ); Point3D worldCoordinates = positionEvent->GetWorldPosition(); Point3D indexCoordinates; m_WorkingSlice->GetGeometry()->WorldToIndex( worldCoordinates, indexCoordinates ); MITK_DEBUG << "Mouse at W " << worldCoordinates << std::endl; MITK_DEBUG << "Mouse at I " << indexCoordinates << std::endl; // round to nearest voxel center (abort if this hasn't changed) if ( m_Size % 2 == 0 ) // even { indexCoordinates[0] = ROUND( indexCoordinates[0] /*+ 0.5*/) + 0.5; indexCoordinates[1] = ROUND( indexCoordinates[1] /*+ 0.5*/ ) + 0.5; } else // odd { indexCoordinates[0] = ROUND( indexCoordinates[0] ) ; indexCoordinates[1] = ROUND( indexCoordinates[1] ) ; } static Point3D lastPos; // uninitialized: if somebody finds out how this can be initialized in a one-liner, tell me static bool lastLeftMouseButtonPressed(false); if ( fabs(indexCoordinates[0] - lastPos[0]) > mitk::eps || fabs(indexCoordinates[1] - lastPos[1]) > mitk::eps || fabs(indexCoordinates[2] - lastPos[2]) > mitk::eps || leftMouseButtonPressed != lastLeftMouseButtonPressed ) { lastPos = indexCoordinates; lastLeftMouseButtonPressed = leftMouseButtonPressed; } else { MITK_DEBUG << "." << std::flush; return false; } MITK_DEBUG << "Mouse at C " << indexCoordinates; Contour::Pointer contour = Contour::New(); contour->Initialize(); for (unsigned int index = 0; index < m_MasterContour->GetNumberOfPoints(); ++index) { Point3D point = m_MasterContour->GetPoints()->ElementAt(index); point[0] += indexCoordinates[ 0 ]; point[1] += indexCoordinates[ 1 ]; MITK_DEBUG << "Contour point [" << index << "] :" << point; contour->AddVertex( point ); } if (leftMouseButtonPressed) { FeedbackContourTool::FillContourInSlice( contour, m_WorkingSlice, m_PaintingPixelValue ); m_WorkingNode->SetData(m_WorkingSlice); m_WorkingNode->Modified(); } // visualize contour Contour::Pointer displayContour = Contour::New(); displayContour->Initialize(); //for (unsigned int index = 0; index < contour->GetNumberOfPoints(); ++index) //{ // Point3D point = contour->GetPoints()->ElementAt(index); // if ( m_Size % 2 == 0 ) // even // { // point[0] += 0.5; // point[1] += 0.5; // } // displayContour->AddVertex( point ); //} displayContour = FeedbackContourTool::BackProjectContourFrom2DSlice( m_WorkingSlice->GetGeometry(), /*displayContour*/contour ); SetFeedbackContour( *displayContour ); assert( positionEvent->GetSender()->GetRenderWindow() ); RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); return true; } bool mitk::PaintbrushTool::OnMouseReleased(Action* /*action*/, const StateEvent* stateEvent) { //When mouse is released write segmentationresult back into image const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return false; this->WriteBackSegmentationResult(positionEvent, m_WorkingSlice); // FeedbackContourTool::SetFeedbackContourVisible(false); return true; } /** Called when the CTRL key is pressed. Will change the painting pixel value from 0 to 1 or from 1 to 0. */ bool mitk::PaintbrushTool::OnInvertLogic(Action* action, const StateEvent* stateEvent) { if (!FeedbackContourTool::OnInvertLogic(action, stateEvent)) return false; // Inversion only for 0 and 1 as painting values if (m_PaintingPixelValue == 1) { m_PaintingPixelValue = 0; FeedbackContourTool::SetFeedbackContourColor( 1.0, 0.0, 0.0 ); } else if (m_PaintingPixelValue == 0) { m_PaintingPixelValue = 1; FeedbackContourTool::SetFeedbackContourColorDefault(); } return true; } void mitk::PaintbrushTool::CheckIfCurrentSliceHasChanged(const PositionEvent *event) { const PlaneGeometry* planeGeometry( dynamic_cast (event->GetSender()->GetCurrentWorldGeometry2D() ) ); DataNode* workingNode( m_ToolManager->GetWorkingData(0) ); if (!workingNode) return; Image::Pointer image = dynamic_cast(workingNode->GetData()); if ( !image || !planeGeometry ) return; if(m_CurrentPlane.IsNull()) { m_CurrentPlane = const_cast(planeGeometry); m_WorkingSlice = SegTool2D::GetAffectedImageSliceAs2DImage(event, image)->Clone(); m_WorkingNode->ReplaceProperty( "color", workingNode->GetProperty("color") ); m_WorkingNode->SetData(m_WorkingSlice); } else { bool isSameSlice (false); isSameSlice = mitk::MatrixEqualElementWise(planeGeometry->GetIndexToWorldTransform()->GetMatrix(),m_CurrentPlane->GetIndexToWorldTransform()->GetMatrix()); isSameSlice = mitk::Equal(planeGeometry->GetIndexToWorldTransform()->GetOffset(),m_CurrentPlane->GetIndexToWorldTransform()->GetOffset()); if (!isSameSlice) { m_ToolManager->GetDataStorage()->Remove(m_WorkingNode); m_CurrentPlane = NULL; m_WorkingSlice = NULL; m_WorkingNode = NULL; m_CurrentPlane = const_cast(planeGeometry); m_WorkingSlice = SegTool2D::GetAffectedImageSliceAs2DImage(event, image)->Clone(); m_WorkingNode = mitk::DataNode::New(); m_WorkingNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( mitk::LevelWindow(0, 1) ) ); m_WorkingNode->SetProperty( "binary", mitk::BoolProperty::New(true) ); m_WorkingNode->SetData(m_WorkingSlice); } } if(!m_ToolManager->GetDataStorage()->Exists(m_WorkingNode)) { m_WorkingNode->SetProperty( "outline binary", mitk::BoolProperty::New(true) ); m_WorkingNode->SetProperty( "color", workingNode->GetProperty("color") ); - m_WorkingNode->SetProperty( "texture interpolation", mitk::BoolProperty::New(true) ); - m_WorkingNode->SetProperty( "layer", mitk::IntProperty::New( 100 ) ); m_WorkingNode->SetProperty( "name", mitk::StringProperty::New("Paintbrush_Node") ); m_WorkingNode->SetProperty( "helper object", mitk::BoolProperty::New(true) ); m_WorkingNode->SetProperty( "opacity", mitk::FloatProperty::New(0.8) ); m_WorkingNode->SetProperty( "includeInBoundingBox", mitk::BoolProperty::New(false)); m_ToolManager->GetDataStorage()->Add(m_WorkingNode); } } diff --git a/Modules/MitkExt/Interactions/mitkPaintbrushTool.h b/Modules/Segmentation/Interactions/mitkPaintbrushTool.h similarity index 96% rename from Modules/MitkExt/Interactions/mitkPaintbrushTool.h rename to Modules/Segmentation/Interactions/mitkPaintbrushTool.h index 997f0c97c6..30887b73df 100644 --- a/Modules/MitkExt/Interactions/mitkPaintbrushTool.h +++ b/Modules/Segmentation/Interactions/mitkPaintbrushTool.h @@ -1,97 +1,97 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkPaintbrushTool_h_Included #define mitkPaintbrushTool_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkFeedbackContourTool.h" #include "mitkPointSet.h" #include "mitkPointOperation.h" #include "mitkLegacyAdaptors.h" namespace mitk { /** \brief Paintbrush tool for InteractiveSegmentation \sa FeedbackContourTool \sa ExtractImageFilter \sa OverwriteSliceImageFilter \ingroup Interaction \ingroup ToolManagerEtAl Simple paintbrush drawing tool. Right now there are only circular pens of varying size. \todo Bug #1727: Should be modified, so that the contour is always visible, i.e.without pressing a mouse button. \warning Only to be instantiated by mitk::ToolManager. $Author: maleike $ */ -class MitkExt_EXPORT PaintbrushTool : public FeedbackContourTool +class Segmentation_EXPORT PaintbrushTool : public FeedbackContourTool { public: // sent when the pen size is changed or should be updated in a GUI. Message1 SizeChanged; mitkClassMacro(PaintbrushTool, FeedbackContourTool); void SetSize(int value); protected: PaintbrushTool(int paintingPixelValue = 1); // purposely hidden virtual ~PaintbrushTool(); virtual void Activated(); virtual void Deactivated(); virtual bool OnMousePressed (Action*, const StateEvent*); virtual bool OnMouseMoved (Action*, const StateEvent*); virtual bool OnMouseReleased(Action*, const StateEvent*); virtual bool OnInvertLogic (Action*, const StateEvent*); /** * \todo This is a possible place where to introduce * different types of pens */ void UpdateContour(const StateEvent* stateEvent); /** * Checks if the current slice has changed */ void CheckIfCurrentSliceHasChanged(const PositionEvent* event); int m_PaintingPixelValue; static int m_Size; Contour::Pointer m_MasterContour; int m_LastContourSize; Image::Pointer m_WorkingSlice; PlaneGeometry::Pointer m_CurrentPlane; DataNode::Pointer m_WorkingNode; }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkRegionGrow3DTool.cpp b/Modules/Segmentation/Interactions/mitkRegionGrow3DTool.cpp similarity index 99% rename from Modules/MitkExt/Interactions/mitkRegionGrow3DTool.cpp rename to Modules/Segmentation/Interactions/mitkRegionGrow3DTool.cpp index e4a0b9e01d..83fd12b4f6 100644 --- a/Modules/MitkExt/Interactions/mitkRegionGrow3DTool.cpp +++ b/Modules/Segmentation/Interactions/mitkRegionGrow3DTool.cpp @@ -1,442 +1,442 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 28959 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkRegionGrow3DTool.h" #include "mitkToolManager.h" #include "mitkRenderingManager.h" #include "mitkLevelWindowProperty.h" #include "mitkPointSetInteractor.h" #include "mitkGlobalInteraction.h" #include "mitkITKImageImport.h" #include "itkImage.h" #include "itkBinaryThresholdImageFilter.h" #include "itkConnectedAdaptiveThresholdImageFilter.h" #include "mitkImageCast.h" #include "mitkImageAccessByItk.h" #include "mitkMaskAndCutRoiImageFilter.h" #include "mitkPadImageFilter.h" #include "mitkRegionGrow3DTool.xpm" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, RegionGrow3DTool, "RegionGrower 3D"); + MITK_TOOL_MACRO(Segmentation_EXPORT, RegionGrow3DTool, "RegionGrower 3D"); } mitk::RegionGrow3DTool::RegionGrow3DTool(): Tool("PressMoveRelease"), m_LowerThreshold(-5000), m_UpperThreshold(5000), m_CurrentRGDirectionIsUpwards(false) { CONNECT_ACTION( 42, OnMouseReleased ); this->SupportRoiOn(); m_FeedbackNode = DataNode::New(); m_FeedbackNode->SetProperty( "color", ColorProperty::New(1.0, 0.0, 0.0) ); m_FeedbackNode->SetProperty( "texture interpolation", BoolProperty::New(false) ); m_FeedbackNode->SetProperty( "layer", IntProperty::New( 100 ) ); m_FeedbackNode->SetProperty( "levelwindow", LevelWindowProperty::New( LevelWindow(100, 1) ) ); m_FeedbackNode->SetProperty( "name", StringProperty::New("failsafe region grow feedback") ); m_FeedbackNode->SetProperty( "opacity", FloatProperty::New(0.3) ); m_FeedbackNode->SetProperty( "helper object", BoolProperty::New(true) ); m_FeedbackNode->SetVisibility(false); m_PointSetNode = mitk::DataNode::New(); m_PointSetNode->SetName("regiongrow3d pointset"); m_PointSetNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_PointSetNode->SetProperty("layer", mitk::IntProperty::New(2)); mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); m_PointSetNode->SetData(pointSet); } mitk::RegionGrow3DTool::~RegionGrow3DTool() { } bool mitk::RegionGrow3DTool::OnMouseReleased(Action*, const StateEvent* stateEvent) { mitk::PointSetInteractor::Pointer interactor = dynamic_cast (m_PointSetNode->GetInteractor()); if (interactor.IsNotNull()) { mitk::PointSet::Pointer pointSet = dynamic_cast (m_PointSetNode->GetData()); if (pointSet.IsNotNull()) { if (pointSet->GetSize() == 1) { //check if we have a valid picture this->RunSegmentation(); SeedButtonToggled.Send(false); } } } return true; } void mitk::RegionGrow3DTool::Activated() { if (m_ToolManager) { m_ToolManager->RoiDataChanged += mitk::MessageDelegate(this, &mitk::RegionGrow3DTool::UpdatePreview); m_OriginalImageNode = m_ToolManager->GetReferenceData(0); m_NodeToProceed = m_OriginalImageNode; if (m_NodeToProceed.IsNotNull()) { SetupPreviewNodeFor(m_NodeToProceed); mitk::Image::Pointer image = dynamic_cast (m_OriginalImageNode->GetData()); if (image.IsNotNull()) { m_RoiMin = image->GetScalarValueMin(); m_RoiMax = image->GetScalarValueMax(); } } else m_ToolManager->ActivateTool(-1); } } void mitk::RegionGrow3DTool::Deactivated() { m_ToolManager->RoiDataChanged -= mitk::MessageDelegate(this, &mitk::RegionGrow3DTool::UpdatePreview); if (mitk::DataStorage* ds = m_ToolManager->GetDataStorage()) { ds->Remove(m_PointSetNode); ds->Remove(m_FeedbackNode); } m_FeedbackNode->SetData(NULL); m_FeedbackNode->SetLevelWindow(NULL); m_FeedbackNode->SetVisibility(false); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } const char* mitk::RegionGrow3DTool::GetName() const { return "RegionGrower 3D"; } const char** mitk::RegionGrow3DTool::GetXPM() const { return mitkRegionGrow3DTool_xpm; } void mitk::RegionGrow3DTool::SetSeedPoint(bool toggled) { if (!m_ToolManager->GetDataStorage()->Exists(m_PointSetNode)) //no pointSet present m_ToolManager->GetDataStorage()->Add(m_PointSetNode, m_OriginalImageNode); //add Interactor if there is none and add it to GlobalInteraction if (toggled == true) // button is down { mitk::PointSetInteractor::Pointer interactor = dynamic_cast (m_PointSetNode->GetInteractor()); if (interactor.IsNull()) { //create a new interactor and add it to node interactor = mitk::PointSetInteractor::New("singlepointinteractorwithoutshiftclick", m_PointSetNode, 1); } mitk::GlobalInteraction::GetInstance()->AddInteractor(interactor); } else { mitk::PointSetInteractor::Pointer interactor = dynamic_cast (m_PointSetNode->GetInteractor()); if (interactor.IsNotNull()) { m_PointSetNode->SetInteractor(NULL); mitk::GlobalInteraction::GetInstance()->RemoveInteractor(interactor); } } } void mitk::RegionGrow3DTool::RunSegmentation() { //safety if no pointSet or pointSet empty mitk::PointSet::Pointer seedPointSet = dynamic_cast (m_PointSetNode->GetData()); if (seedPointSet.IsNull()) { return; } if (!(seedPointSet->GetSize() > 0)) { return; } mitk::PointSet::PointType seedPoint = seedPointSet->GetPointSet()->GetPoints()->Begin().Value(); mitk::Image::Pointer image = dynamic_cast (m_NodeToProceed->GetData()); if (image.IsNotNull()) { m_LowerThreshold = static_cast (m_RoiMin); m_UpperThreshold = static_cast (m_RoiMax); AccessByItk_2(image, StartRegionGrowing, image->GetGeometry(), seedPoint); } } template void mitk::RegionGrow3DTool::StartRegionGrowing(itk::Image* itkImage, mitk::Geometry3D* imageGeometry, mitk::PointSet::PointType seedPoint) { typedef itk::Image InputImageType; typedef typename InputImageType::IndexType IndexType; typedef itk::ConnectedAdaptiveThresholdImageFilter RegionGrowingFilterType; typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New(); if ( !imageGeometry->IsInside(seedPoint) ) { return; } IndexType seedIndex; imageGeometry->WorldToIndex( seedPoint, seedIndex);// convert world coordinates to image indices //int seedValue = itkImage->GetPixel(seedIndex); regionGrower->SetInput( itkImage ); regionGrower->AddSeed( seedIndex ); regionGrower->SetLower( m_LowerThreshold ); regionGrower->SetUpper( m_UpperThreshold ); regionGrower->SetGrowingDirectionIsUpwards( m_CurrentRGDirectionIsUpwards ); try { regionGrower->Update(); } catch( ... ) { MITK_ERROR << "Something went wrong!" << endl; return; } m_SeedpointValue = regionGrower->GetSeedpointValue(); //initialize slider if(m_CurrentRGDirectionIsUpwards) { UpperThresholdValueChanged.Send(m_UpperThreshold); LowerThresholdValueChanged.Send(m_SeedpointValue); } else { UpperThresholdValueChanged.Send(m_SeedpointValue); LowerThresholdValueChanged.Send(m_LowerThreshold); } m_DetectedLeakagePoint = regionGrower->GetLeakagePoint(); mitk::Image::Pointer resultImage = mitk::ImportItkImage( regionGrower->GetOutput() ); m_FeedbackNode->SetData( resultImage ); m_FeedbackNode->SetVisibility(true); InitializeLevelWindow(); } void mitk::RegionGrow3DTool::InitializeLevelWindow() { mitk::LevelWindow tempLevelWindow; m_FeedbackNode->GetLevelWindow(tempLevelWindow, NULL, "levelWindow"); mitk::ScalarType* level = new mitk::ScalarType(0.5); mitk::ScalarType* window = new mitk::ScalarType(1); int upper; if (m_CurrentRGDirectionIsUpwards) { upper = m_UpperThreshold - m_SeedpointValue; } else { upper = m_SeedpointValue - m_LowerThreshold; } tempLevelWindow.SetRangeMinMax(mitk::ScalarType(0), mitk::ScalarType(upper)); tempLevelWindow.SetLevelWindow(*level, *window); m_FeedbackNode->SetLevelWindow(tempLevelWindow, NULL, "levelWindow"); //get the suggested threshold from the detected leakage-point and adjust the slider if (m_CurrentRGDirectionIsUpwards) { SliderValueChanged.Send(m_SeedpointValue + m_DetectedLeakagePoint -1); } else { SliderValueChanged.Send(m_SeedpointValue - m_DetectedLeakagePoint +1); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::RegionGrow3DTool::ChangeLevelWindow(int value) { if (m_FeedbackNode.IsNull()) return; mitk::LevelWindow tempLevelWindow; m_FeedbackNode->GetLevelWindow(tempLevelWindow, NULL, "levelWindow"); //get the levelWindow associated with the preview mitk::ScalarType level;// = this->m_UPPERTHRESHOLD - newValue + 0.5; mitk::ScalarType* window = new mitk::ScalarType(1); //adjust the levelwindow according to the position of the slider (newvalue) if (m_CurrentRGDirectionIsUpwards) { level = m_UpperThreshold - value + 0.5; tempLevelWindow.SetLevelWindow(level, *window); } else { level = value - m_LowerThreshold +0.5; tempLevelWindow.SetLevelWindow(level, *window); } m_FeedbackNode->SetLevelWindow(tempLevelWindow, NULL, "levelWindow"); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::RegionGrow3DTool::ConfirmSegmentation( std::string name, mitk::Color color) { mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetColor(color); new_node->SetName(name); new_node->SetProperty("binary", mitk::BoolProperty::New("true")); mitk::Image* image = dynamic_cast (m_FeedbackNode->GetData()); mitk::LevelWindow tempLevelWindow; m_FeedbackNode->GetLevelWindow( tempLevelWindow, NULL, "levelWindow"); int upperThresholdLabeledImage = (short int) tempLevelWindow.GetRangeMax(); int lowerThresholdLabeledImage = (short int) tempLevelWindow.GetLowerWindowBound() + 1; typedef itk::Image InputImageType; typedef itk::Image SegmentationType; typedef itk::BinaryThresholdImageFilter ThresholdFilterType; ThresholdFilterType::Pointer filter = ThresholdFilterType::New(); InputImageType::Pointer itkImage; mitk::CastToItkImage(image, itkImage); filter->SetInput(itkImage); filter->SetInsideValue(1); filter->SetOutsideValue(0); filter->SetUpperThreshold(upperThresholdLabeledImage); filter->SetLowerThreshold(lowerThresholdLabeledImage); filter->Update(); mitk::Image::Pointer new_image = mitk::Image::New(); mitk::CastToMitkImage(filter->GetOutput(), new_image); //pad to original size if (m_OriginalImageNode.GetPointer() != m_NodeToProceed.GetPointer()) { mitk::PadImageFilter::Pointer padFilter = mitk::PadImageFilter::New(); padFilter->SetInput(0, new_image); padFilter->SetInput(1, dynamic_cast (m_OriginalImageNode->GetData())); padFilter->SetBinaryFilter(true); padFilter->SetUpperThreshold(1); padFilter->SetLowerThreshold(1); padFilter->Update(); new_image = padFilter->GetOutput(); } new_node->SetData(new_image); m_ToolManager->GetDataStorage()->Add(new_node); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); m_ToolManager->ActivateTool(-1); } void mitk::RegionGrow3DTool::CancelSegmentation() { m_ToolManager->ActivateTool(-1); } void mitk::RegionGrow3DTool::SetupPreviewNodeFor( DataNode* nodeToProceed) { if (nodeToProceed) { Image::Pointer image = dynamic_cast( nodeToProceed->GetData() ); if (image.IsNotNull()) { m_FeedbackNode->SetData( image ); int layer(50); nodeToProceed->GetIntProperty("layer", layer); m_FeedbackNode->SetIntProperty("layer", layer+1); m_FeedbackNode->SetLevelWindow(NULL); if (DataStorage* storage = m_ToolManager->GetDataStorage()) { if (storage->Exists(m_FeedbackNode)) storage->Remove(m_FeedbackNode); storage->Add( m_FeedbackNode, nodeToProceed ); } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::RegionGrow3DTool::UpdatePreview() { typedef itk::Image ItkImageType; typedef itk::Image ItkMaskType; mitk::DataNode::Pointer node = m_ToolManager->GetRoiData(0); if (node.IsNull()) { this->SetupPreviewNodeFor(m_OriginalImageNode); m_NodeToProceed = m_OriginalImageNode; mitk::Image::Pointer image = dynamic_cast (m_OriginalImageNode->GetData()); if (image.IsNotNull()) { m_RoiMin = image->GetScalarValueMin(); m_RoiMax = image->GetScalarValueMax(); } return; } mitk::MaskAndCutRoiImageFilter::Pointer roiFilter = mitk::MaskAndCutRoiImageFilter::New(); roiFilter->SetInput(dynamic_cast (m_NodeToProceed->GetData())); roiFilter->SetRegionOfInterest(node->GetData()); roiFilter->Update(); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); mitk::Image::Pointer tmpImage = roiFilter->GetOutput(); new_node->SetData(tmpImage); m_RoiMax = roiFilter->GetMaxValue(); m_RoiMin = roiFilter->GetMinValue(); this->SetupPreviewNodeFor(new_node); m_NodeToProceed = new_node; //this->RunSegmentation(); } void mitk::RegionGrow3DTool::SetCurrentRGDirectionIsUpwards(bool flag) { m_CurrentRGDirectionIsUpwards = flag; } diff --git a/Modules/MitkExt/Interactions/mitkRegionGrow3DTool.h b/Modules/Segmentation/Interactions/mitkRegionGrow3DTool.h similarity index 96% rename from Modules/MitkExt/Interactions/mitkRegionGrow3DTool.h rename to Modules/Segmentation/Interactions/mitkRegionGrow3DTool.h index 85c9420576..50cea8a508 100644 --- a/Modules/MitkExt/Interactions/mitkRegionGrow3DTool.h +++ b/Modules/Segmentation/Interactions/mitkRegionGrow3DTool.h @@ -1,83 +1,83 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 28959 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITKREGIONGROW3DTOOL_H #define MITKREGIONGROW3DTOOL_H #include "mitkTool.h" #include "mitkPointSet.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkStateEvent.h" #include "itkImage.h" namespace mitk{ - class MitkExt_EXPORT RegionGrow3DTool : public Tool + class Segmentation_EXPORT RegionGrow3DTool : public Tool { public: mitkClassMacro(RegionGrow3DTool, Tool); itkNewMacro(RegionGrow3DTool); mitk::Message1 UpperThresholdValueChanged; mitk::Message1 LowerThresholdValueChanged; mitk::Message1 SliderValueChanged; mitk::Message1 SeedButtonToggled; virtual const char* GetName() const; virtual const char** GetXPM() const; virtual void Activated(); virtual void Deactivated(); void RunSegmentation(); void ConfirmSegmentation(std::string name, mitk::Color color); void CancelSegmentation(); void InitializeLevelWindow(); void ChangeLevelWindow(int); void SetSeedPoint(bool); void SetCurrentRGDirectionIsUpwards(bool); protected: RegionGrow3DTool(); virtual ~RegionGrow3DTool(); void SetupPreviewNodeFor(mitk::DataNode* nodeToProceed); void UpdatePreview(); template < typename TPixel, unsigned int VImageDimension > void StartRegionGrowing( itk::Image< TPixel, VImageDimension >* itkImage, mitk::Geometry3D* imageGeometry, mitk::PointSet::PointType seedPoint ); bool OnMouseReleased(Action*, const StateEvent*); int m_SeedpointValue; mitk::ScalarType m_RoiMax; mitk::ScalarType m_RoiMin; int m_LowerThreshold; int m_UpperThreshold; int m_DetectedLeakagePoint; bool m_CurrentRGDirectionIsUpwards; mitk::DataNode::Pointer m_PointSetNode; mitk::DataNode::Pointer m_FeedbackNode; mitk::DataNode::Pointer m_NodeToProceed; mitk::DataNode::Pointer m_OriginalImageNode; };//class }//namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkRegionGrow3DTool.xpm b/Modules/Segmentation/Interactions/mitkRegionGrow3DTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkRegionGrow3DTool.xpm rename to Modules/Segmentation/Interactions/mitkRegionGrow3DTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkRegionGrowingTool.cpp b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp similarity index 99% rename from Modules/MitkExt/Interactions/mitkRegionGrowingTool.cpp rename to Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp index dc3d2c7696..3758bd04f5 100644 --- a/Modules/MitkExt/Interactions/mitkRegionGrowingTool.cpp +++ b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp @@ -1,661 +1,661 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkRegionGrowingTool.h" #include "mitkToolManager.h" #include "mitkOverwriteSliceImageFilter.h" #include "mitkImageDataItem.h" #include "mitkBaseRenderer.h" #include "mitkRenderingManager.h" #include "mitkApplicationCursor.h" #include "ipSegmentation.h" #include "mitkRegionGrowingTool.xpm" #include "mitkOverwriteDirectedPlaneImageFilter.h" #include "mitkExtractDirectedPlaneImageFilterNew.h" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, RegionGrowingTool, "Region growing tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, RegionGrowingTool, "Region growing tool"); } #define ROUND(a) ((a)>0 ? (int)((a)+0.5) : -(int)(0.5-(a))) mitk::RegionGrowingTool::RegionGrowingTool() :FeedbackContourTool("PressMoveRelease"), m_LowerThreshold(200), m_UpperThreshold(200), m_InitialLowerThreshold(200), m_InitialUpperThreshold(200), m_ScreenYDifference(0), m_OriginalPicSlice(NULL), m_SeedPointMemoryOffset(0), m_VisibleWindow(0), m_DefaultWindow(0), m_MouseDistanceScaleFactor(0.5), m_LastWorkingSeed(-1), m_FillFeedbackContour(true) { } mitk::RegionGrowingTool::~RegionGrowingTool() { } const char** mitk::RegionGrowingTool::GetXPM() const { return mitkRegionGrowingTool_xpm; } const char* mitk::RegionGrowingTool::GetName() const { return "Region Growing"; } void mitk::RegionGrowingTool::Activated() { Superclass::Activated(); } void mitk::RegionGrowingTool::Deactivated() { Superclass::Deactivated(); } /** 1 Determine which slice is clicked into 2 Determine if the user clicked inside or outside of the segmentation 3 Depending on the pixel value under the mouse click position, two different things happen: (separated out into OnMousePressedInside and OnMousePressedOutside) 3.1 Create a skeletonization of the segmentation and try to find a nice cut 3.1.1 Call a ipSegmentation algorithm to create a nice cut 3.1.2 Set the result of this algorithm as the feedback contour 3.2 Initialize region growing 3.2.1 Determine memory offset inside the original image 3.2.2 Determine initial region growing parameters from the level window settings of the image 3.2.3 Perform a region growing (which generates a new feedback contour) */ bool mitk::RegionGrowingTool::OnMousePressed (Action* action, const StateEvent* stateEvent) { //ToolLogger::SetVerboseness(3); MITK_DEBUG << "OnMousePressed" << std::endl; if (FeedbackContourTool::OnMousePressed( action, stateEvent )) { MITK_DEBUG << "OnMousePressed: FeedbackContourTool says ok" << std::endl; // 1. Find out which slice the user clicked, find out which slice of the toolmanager's reference and working image corresponds to that const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (positionEvent) { MITK_DEBUG << "OnMousePressed: got positionEvent" << std::endl; m_ReferenceSlice = FeedbackContourTool::GetAffectedReferenceSlice( positionEvent ); m_WorkingSlice = FeedbackContourTool::GetAffectedWorkingSlice( positionEvent ); if ( m_WorkingSlice.IsNotNull() ) // can't do anything without the segmentation { MITK_DEBUG << "OnMousePressed: got working slice" << std::endl; // 2. Determine if the user clicked inside or outside of the segmentation const Geometry3D* workingSliceGeometry = m_WorkingSlice->GetGeometry(); Point3D mprojectedPointIn2D; workingSliceGeometry->WorldToIndex( positionEvent->GetWorldPosition(), mprojectedPointIn2D); itk::Index<2> projectedPointInWorkingSlice2D; projectedPointInWorkingSlice2D[0] = static_cast( mprojectedPointIn2D[0] - 0.5 ); projectedPointInWorkingSlice2D[1] = static_cast( mprojectedPointIn2D[1] - 0.5 ); if ( workingSliceGeometry->IsIndexInside( projectedPointInWorkingSlice2D ) ) { MITK_DEBUG << "OnMousePressed: point " << positionEvent->GetWorldPosition() << " (index coordinates " << projectedPointInWorkingSlice2D << ") IS in working slice" << std::endl; // Convert to ipMITKSegmentationTYPE (because getting pixels relys on that data type) itk::Image< ipMITKSegmentationTYPE, 2 >::Pointer correctPixelTypeImage; CastToItkImage( m_WorkingSlice, correctPixelTypeImage ); assert (correctPixelTypeImage.IsNotNull() ); // possible bug in CastToItkImage ? // direction maxtrix is wrong/broken/not working after CastToItkImage, leading to a failed assertion in // mitk/Core/DataStructures/mitkSlicedGeometry3D.cpp, 479: // virtual void mitk::SlicedGeometry3D::SetSpacing(const mitk::Vector3D&): Assertion `aSpacing[0]>0 && aSpacing[1]>0 && aSpacing[2]>0' failed // solution here: we overwrite it with an unity matrix itk::Image< ipMITKSegmentationTYPE, 2 >::DirectionType imageDirection; imageDirection.SetIdentity(); correctPixelTypeImage->SetDirection(imageDirection); Image::Pointer temporarySlice = Image::New(); // temporarySlice = ImportItkImage( correctPixelTypeImage ); CastToMitkImage( correctPixelTypeImage, temporarySlice ); mitkIpPicDescriptor* workingPicSlice = mitkIpPicNew(); CastToIpPicDescriptor(temporarySlice, workingPicSlice); int initialWorkingOffset = projectedPointInWorkingSlice2D[1] * workingPicSlice->n[0] + projectedPointInWorkingSlice2D[0]; if ( initialWorkingOffset < static_cast( workingPicSlice->n[0] * workingPicSlice->n[1] ) && initialWorkingOffset >= 0 ) { // 3. determine the pixel value under the last click bool inside = static_cast(workingPicSlice->data)[initialWorkingOffset] != 0; m_PaintingPixelValue = inside ? 0 : 1; // if inside, we want to remove a part, otherwise we want to add something if ( m_LastWorkingSeed >= static_cast( workingPicSlice->n[0] * workingPicSlice->n[1] ) || m_LastWorkingSeed < 0 ) { inside = false; } if ( m_ReferenceSlice.IsNotNull() ) { MITK_DEBUG << "OnMousePressed: got reference slice" << std::endl; m_OriginalPicSlice = mitkIpPicNew(); CastToIpPicDescriptor(m_ReferenceSlice, m_OriginalPicSlice); // 3.1. Switch depending on the pixel value if (inside) { OnMousePressedInside(action, stateEvent, workingPicSlice, initialWorkingOffset); } else { OnMousePressedOutside(action, stateEvent); } } } } } } } MITK_DEBUG << "end OnMousePressed" << std::endl; return true; } /** 3.1 Create a skeletonization of the segmentation and try to find a nice cut 3.1.1 Call a ipSegmentation algorithm to create a nice cut 3.1.2 Set the result of this algorithm as the feedback contour */ bool mitk::RegionGrowingTool::OnMousePressedInside(Action* itkNotUsed( action ), const StateEvent* stateEvent, mitkIpPicDescriptor* workingPicSlice, int initialWorkingOffset) { const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); // checked in OnMousePressed // 3.1.1. Create a skeletonization of the segmentation and try to find a nice cut // apply the skeletonization-and-cut algorithm // generate contour to remove // set m_ReferenceSlice = NULL so nothing will happen during mouse move // remember to fill the contour with 0 in mouserelease mitkIpPicDescriptor* segmentationHistory = ipMITKSegmentationCreateGrowerHistory( workingPicSlice, m_LastWorkingSeed, NULL ); // free again if (segmentationHistory) { tCutResult cutContour = ipMITKSegmentationGetCutPoints( workingPicSlice, segmentationHistory, initialWorkingOffset ); // tCutResult is a ipSegmentation type mitkIpPicFree( segmentationHistory ); if (cutContour.cutIt) { // 3.1.2 copy point from float* to mitk::Contour Contour::Pointer contourInImageIndexCoordinates = Contour::New(); contourInImageIndexCoordinates->Initialize(); Point3D newPoint; for (int index = 0; index < cutContour.deleteSize; ++index) { newPoint[0] = cutContour.deleteCurve[ 2 * index + 0 ]; newPoint[1] = cutContour.deleteCurve[ 2 * index + 1 ]; newPoint[2] = 0.0; contourInImageIndexCoordinates->AddVertex( newPoint - 0.5 ); } free(cutContour.traceline); free(cutContour.deleteCurve); // perhaps visualize this for fun? free(cutContour.onGradient); Contour::Pointer contourInWorldCoordinates = FeedbackContourTool::BackProjectContourFrom2DSlice( m_WorkingSlice->GetGeometry(), contourInImageIndexCoordinates, true ); // true: sub 0.5 for ipSegmentation correction FeedbackContourTool::SetFeedbackContour( *contourInWorldCoordinates ); FeedbackContourTool::SetFeedbackContourVisible(true); mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); m_FillFeedbackContour = true; } else { m_FillFeedbackContour = false; } } else { m_FillFeedbackContour = false; } m_ReferenceSlice = NULL; return true; } /** 3.2 Initialize region growing 3.2.1 Determine memory offset inside the original image 3.2.2 Determine initial region growing parameters from the level window settings of the image 3.2.3 Perform a region growing (which generates a new feedback contour) */ bool mitk::RegionGrowingTool::OnMousePressedOutside(Action* itkNotUsed( action ), const StateEvent* stateEvent) { const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); // checked in OnMousePressed // 3.2 If we have a reference image, then perform an initial region growing, considering the reference image's level window // if click was outside the image, don't continue const Geometry3D* sliceGeometry = m_ReferenceSlice->GetGeometry(); Point3D mprojectedPointIn2D; sliceGeometry->WorldToIndex( positionEvent->GetWorldPosition(), mprojectedPointIn2D ); itk::Index<2> projectedPointIn2D; projectedPointIn2D[0] = static_cast( mprojectedPointIn2D[0] - 0.5 ); projectedPointIn2D[1] = static_cast( mprojectedPointIn2D[1] - 0.5 ); if ( sliceGeometry->IsIndexInside( mprojectedPointIn2D ) ) { MITK_DEBUG << "OnMousePressed: point " << positionEvent->GetWorldPosition() << " (index coordinates " << mprojectedPointIn2D << ") IS in reference slice" << std::endl; // 3.2.1 Remember Y cursor position and initial seed point //m_ScreenYPositionAtStart = static_cast(positionEvent->GetDisplayPosition()[1]); m_LastScreenPosition = ApplicationCursor::GetInstance()->GetCursorPosition(); m_ScreenYDifference = 0; m_SeedPointMemoryOffset = projectedPointIn2D[1] * m_OriginalPicSlice->n[0] + projectedPointIn2D[0]; m_LastWorkingSeed = m_SeedPointMemoryOffset; // remember for skeletonization if ( m_SeedPointMemoryOffset < static_cast( m_OriginalPicSlice->n[0] * m_OriginalPicSlice->n[1] ) && m_SeedPointMemoryOffset >= 0 ) { // 3.2.2 Get level window from reference DataNode // Use some logic to determine initial gray value bounds LevelWindow lw(0, 500); m_ToolManager->GetReferenceData(0)->GetLevelWindow(lw); // will fill lw if levelwindow property is present, otherwise won't touch it. ScalarType currentVisibleWindow = lw.GetWindow(); if (!mitk::Equal(currentVisibleWindow, m_VisibleWindow)) { m_InitialLowerThreshold = currentVisibleWindow / 20.0; m_InitialUpperThreshold = currentVisibleWindow / 20.0; m_LowerThreshold = m_InitialLowerThreshold; m_UpperThreshold = m_InitialUpperThreshold; // 3.2.3. Actually perform region growing mitkIpPicDescriptor* result = PerformRegionGrowingAndUpdateContour(); ipMITKSegmentationFree( result); // display the contour FeedbackContourTool::SetFeedbackContourVisible(true); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); m_FillFeedbackContour = true; } } return true; } return false; } /** If in region growing mode (m_ReferenceSlice != NULL), then 1. Calculate the new thresholds from mouse position (relative to first position) 2. Perform a new region growing and update the feedback contour */ bool mitk::RegionGrowingTool::OnMouseMoved(Action* action, const StateEvent* stateEvent) { if (FeedbackContourTool::OnMouseMoved( action, stateEvent )) { if ( m_ReferenceSlice.IsNotNull() && m_OriginalPicSlice ) { const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (positionEvent) { ApplicationCursor* cursor = ApplicationCursor::GetInstance(); if (!cursor) return false; m_ScreenYDifference += cursor->GetCursorPosition()[1] - m_LastScreenPosition[1]; cursor->SetCursorPosition( m_LastScreenPosition ); m_LowerThreshold = std::max(0.0, m_InitialLowerThreshold - m_ScreenYDifference * m_MouseDistanceScaleFactor); m_UpperThreshold = std::max(0.0, m_InitialUpperThreshold - m_ScreenYDifference * m_MouseDistanceScaleFactor); // 2. Perform region growing again and show the result mitkIpPicDescriptor* result = PerformRegionGrowingAndUpdateContour(); ipMITKSegmentationFree( result ); // 3. Update the contour mitk::RenderingManager::GetInstance()->ForceImmediateUpdate(positionEvent->GetSender()->GetRenderWindow()); } } } return true; } /** If the feedback contour should be filled, then it is done here. (Contour is NOT filled, when skeletonization is done but no nice cut was found) */ bool mitk::RegionGrowingTool::OnMouseReleased(Action* action, const StateEvent* stateEvent) { if (FeedbackContourTool::OnMouseReleased( action, stateEvent )) { // 1. If we have a working slice, use the contour to fill a new piece on segmentation on it (or erase a piece that was selected by ipMITKSegmentationGetCutPoints) if ( m_WorkingSlice.IsNotNull() && m_OriginalPicSlice ) { const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (positionEvent) { // remember parameters for next time m_InitialLowerThreshold = m_LowerThreshold; m_InitialUpperThreshold = m_UpperThreshold; if (m_FillFeedbackContour) { // 3. use contour to fill a region in our working slice Contour* feedbackContour( FeedbackContourTool::GetFeedbackContour() ); if (feedbackContour) { Contour::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice( m_WorkingSlice, feedbackContour, false, false ); // false: don't add any 0.5 // false: don't constrain the contour to the image's inside if (projectedContour.IsNotNull()) { FeedbackContourTool::FillContourInSlice( projectedContour, m_WorkingSlice, m_PaintingPixelValue ); const PlaneGeometry* planeGeometry( dynamic_cast (positionEvent->GetSender()->GetCurrentWorldGeometry2D() ) ); //MITK_DEBUG << "OnMouseReleased: writing back to dimension " << affectedDimension << ", slice " << affectedSlice << " in working image" << std::endl; // 4. write working slice back into image volume this->WriteBackSegmentationResult(positionEvent, m_WorkingSlice); } } } FeedbackContourTool::SetFeedbackContourVisible(false); mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); } } } m_ReferenceSlice = NULL; // don't leak m_WorkingSlice = NULL; m_OriginalPicSlice = NULL; return true; } /** Uses ipSegmentation algorithms to do the actual region growing. The result (binary image) is first smoothed by a 5x5 circle mask, then its contour is extracted and converted to MITK coordinates. */ mitkIpPicDescriptor* mitk::RegionGrowingTool::PerformRegionGrowingAndUpdateContour() { // 1. m_OriginalPicSlice and m_SeedPointMemoryOffset are set to sensitive values, as well as m_LowerThreshold and m_UpperThreshold assert (m_OriginalPicSlice); if (m_OriginalPicSlice->n[0] != 256 || m_OriginalPicSlice->n[1] != 256) // ??? assert( (m_SeedPointMemoryOffset < static_cast( m_OriginalPicSlice->n[0] * m_OriginalPicSlice->n[1] )) && (m_SeedPointMemoryOffset >= 0) ); // inside the image // 2. ipSegmentation is used to perform region growing float ignored; int oneContourOffset( 0 ); mitkIpPicDescriptor* regionGrowerResult = ipMITKSegmentationGrowRegion4N( m_OriginalPicSlice, m_SeedPointMemoryOffset, // seed point true, // grayvalue interval relative to seed point gray value? m_LowerThreshold, m_UpperThreshold, 0, // continue until done (maxIterations == 0) NULL, // allocate new memory (only this time, on mouse move we'll reuse the old buffer) oneContourOffset, // a pixel that is near the resulting contour ignored // ignored by us ); if (!regionGrowerResult || oneContourOffset == -1) { Contour::Pointer dummyContour = Contour::New(); dummyContour->Initialize(); FeedbackContourTool::SetFeedbackContour( *dummyContour ); if (regionGrowerResult) ipMITKSegmentationFree(regionGrowerResult); return NULL; } // 3. We smooth the result a little to reduce contour complexity bool smoothResult( true ); // currently fixed, perhaps remove else block mitkIpPicDescriptor* smoothedRegionGrowerResult; if (smoothResult) { // Smooth the result (otherwise very detailed contour) smoothedRegionGrowerResult = SmoothIPPicBinaryImage( regionGrowerResult, oneContourOffset ); ipMITKSegmentationFree( regionGrowerResult ); } else { smoothedRegionGrowerResult = regionGrowerResult; } // 4. convert the result of region growing into a mitk::Contour // At this point oneContourOffset could be useless, if smoothing destroyed a thin bridge. In these // cases, we have two or more unconnected segmentation regions, and we don't know, which one is touched by oneContourOffset. // In the bad case, the contour is not the one around our seedpoint, so the result looks very strange to the user. // -> we remove the point where the contour started so far. Then we look from the bottom of the image for the first segmentation pixel // and start another contour extraction from there. This is done, until the seedpoint is inside the contour int numberOfContourPoints( 0 ); int newBufferSize( 0 ); float* contourPoints = ipMITKSegmentationGetContour8N( smoothedRegionGrowerResult, oneContourOffset, numberOfContourPoints, newBufferSize ); // memory allocated with malloc if (contourPoints) { while ( !ipMITKSegmentationIsInsideContour( contourPoints, // contour numberOfContourPoints, // points in contour m_SeedPointMemoryOffset % smoothedRegionGrowerResult->n[0], // test point x m_SeedPointMemoryOffset / smoothedRegionGrowerResult->n[0] // test point y ) ) { // we decide that this cannot be part of the segmentation because the seedpoint is not contained in the contour (fill the 4-neighborhood with 0) ipMITKSegmentationReplaceRegion4N( smoothedRegionGrowerResult, oneContourOffset, 0 ); // move the contour offset to the last row (x position of the seed point) int rowLength = smoothedRegionGrowerResult->n[0]; // number of pixels in a row oneContourOffset = m_SeedPointMemoryOffset % smoothedRegionGrowerResult->n[0] // x of seed point + rowLength*(smoothedRegionGrowerResult->n[1]-1); // y of last row while ( oneContourOffset >=0 && (*(static_cast(smoothedRegionGrowerResult->data) + oneContourOffset) == 0) ) { oneContourOffset -= rowLength; // if pixel at data+oneContourOffset is 0, then move up one row } if ( oneContourOffset < 0 ) { break; // just use the last contour we found } free(contourPoints); // release contour memory contourPoints = ipMITKSegmentationGetContour8N( smoothedRegionGrowerResult, oneContourOffset, numberOfContourPoints, newBufferSize ); // memory allocated with malloc } // copy point from float* to mitk::Contour Contour::Pointer contourInImageIndexCoordinates = Contour::New(); contourInImageIndexCoordinates->Initialize(); Point3D newPoint; for (int index = 0; index < numberOfContourPoints; ++index) { newPoint[0] = contourPoints[ 2 * index + 0 ]; newPoint[1] = contourPoints[ 2 * index + 1 ]; newPoint[2] = 0; contourInImageIndexCoordinates->AddVertex( newPoint - 0.5); } free(contourPoints); Contour::Pointer contourInWorldCoordinates = FeedbackContourTool::BackProjectContourFrom2DSlice( m_ReferenceSlice->GetGeometry(), contourInImageIndexCoordinates, true ); // true: sub 0.5 for ipSegmentation correctio FeedbackContourTool::SetFeedbackContour( *contourInWorldCoordinates ); } // 5. Result HAS TO BE freed by caller, contains the binary region growing result return smoothedRegionGrowerResult; } /** Helper method for SmoothIPPicBinaryImage. Smoothes a given part of and image. \param sourceImage The original binary image. \param dest The smoothed image (will be written without bounds checking). \param contourOfs One offset of the contour. Is updated if a pixel is changed (which might change the contour). \param maskOffsets Memory offsets that describe the smoothing mask. \param maskSize Entries of the mask. \param startOffset First pixel that should be smoothed using this mask. \param endOffset Last pixel that should be smoothed using this mask. */ void mitk::RegionGrowingTool::SmoothIPPicBinaryImageHelperForRows( mitkIpPicDescriptor* sourceImage, mitkIpPicDescriptor* dest, int &contourOfs, int* maskOffsets, int maskSize, int startOffset, int endOffset ) { // work on the very first row ipMITKSegmentationTYPE* current; ipMITKSegmentationTYPE* source = ((ipMITKSegmentationTYPE*)sourceImage->data) + startOffset; // + 1! don't read at start-1 ipMITKSegmentationTYPE* end = ((ipMITKSegmentationTYPE*)dest->data) + endOffset; int ofs = startOffset; int minority = (maskSize - 1) / 2; for (current = ((ipMITKSegmentationTYPE*)dest->data) + startOffset; current minority) { *current = 1; contourOfs = ofs; } else { *current = 0; } ++source; ++ofs; } } /** Smoothes a binary ipPic image with a 5x5 mask. The image borders (some first and last rows) are treated differently. */ mitkIpPicDescriptor* mitk::RegionGrowingTool::SmoothIPPicBinaryImage( mitkIpPicDescriptor* image, int &contourOfs, mitkIpPicDescriptor* dest ) { if (!image) return NULL; // Original code from /trunk/mbi-qm/Qmitk/Qmitk2DSegTools/RegionGrowerTool.cpp (first version by T. Boettger?). Reformatted and documented and restructured. #define MSK_SIZE5x5 21 #define MSK_SIZE3x3 5 #define MSK_SIZE3x1 3 // mask is an array of coordinates that form a rastered circle like this // // OOO // OOOOO // OOOOO // OOOOO // OOO // // int mask5x5[MSK_SIZE5x5][2] = { /******/ {-1,-2}, {0,-2}, {1,-2}, /*****/ {-2,-1}, {-1,-1}, {0,-1}, {1,-1}, {2,-1}, {-2, 0}, {-1, 0}, {0, 0}, {1, 0}, {2, 0}, {-2, 1}, {-1, 1}, {0, 1}, {1, 1}, {2, 1}, /******/ {-1, 2}, {0, 2}, {1, 2} /*****/ }; int mask3x3[MSK_SIZE3x3][2] = { /******/ {0,-1}, /*****/ {-1, 0}, {0, 0}, {1, 0}, /******/ {0, 1} /*****/ }; int mask3x1[MSK_SIZE3x1][2] = { {-1, 0}, {0, 0}, {1, 0} }; // The following lines iterate over all the pixels of a (sliced) image (except the first and last three rows). // For each pixel, all the coordinates around it (according to mask) are evaluated (this means 21 pixels). // If more than 10 of the evaluated pixels are non-zero, then the central pixel is set to 1, else to 0. // This is determining a majority. If there is no clear majority, then the central pixel itself "decides". int maskOffset5x5[MSK_SIZE5x5]; int line = image->n[0]; for (int i=0; in[0]; int spareOut1Rows = 1*image->n[0]; if ( image->n[1] > 0 ) SmoothIPPicBinaryImageHelperForRows( image, dest, contourOfs, maskOffset3x1, MSK_SIZE3x1, 1, dest->n[0] ); if ( image->n[1] > 3 ) SmoothIPPicBinaryImageHelperForRows( image, dest, contourOfs, maskOffset3x3, MSK_SIZE3x3, spareOut1Rows, dest->n[0]*3 ); if ( image->n[1] > 6 ) SmoothIPPicBinaryImageHelperForRows( image, dest, contourOfs, maskOffset5x5, MSK_SIZE5x5, spareOut3Rows, dest->n[0]*dest->n[1] - spareOut3Rows ); if ( image->n[1] > 8 ) SmoothIPPicBinaryImageHelperForRows( image, dest, contourOfs, maskOffset3x3, MSK_SIZE3x3, dest->n[0]*dest->n[1] -spareOut3Rows, dest->n[0]*dest->n[1] - spareOut1Rows ); if ( image->n[1] > 10) SmoothIPPicBinaryImageHelperForRows( image, dest, contourOfs, maskOffset3x1, MSK_SIZE3x1, dest->n[0]*dest->n[1] -spareOut1Rows, dest->n[0]*dest->n[1] - 1 ); // correction for first pixel (sorry for the ugliness) if ( *((ipMITKSegmentationTYPE*)(dest->data)+1) == 1 ) { *((ipMITKSegmentationTYPE*)(dest->data)+0) = 1; } if (dest->n[0] * dest->n[1] > 2) { // correction for last pixel if ( *((ipMITKSegmentationTYPE*)(dest->data)+dest->n[0]*dest->n[1]-2) == 1 ) { *((ipMITKSegmentationTYPE*)(dest->data)+dest->n[0]*dest->n[1]-1) = 1; } } return dest; } diff --git a/Modules/MitkExt/Interactions/mitkRegionGrowingTool.h b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.h similarity index 97% rename from Modules/MitkExt/Interactions/mitkRegionGrowingTool.h rename to Modules/Segmentation/Interactions/mitkRegionGrowingTool.h index c01334b366..ee9a8690c9 100644 --- a/Modules/MitkExt/Interactions/mitkRegionGrowingTool.h +++ b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.h @@ -1,115 +1,115 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkRegionGrowingTool_h_Included #define mitkRegionGrowingTool_h_Included #include "mitkFeedbackContourTool.h" #include "mitkLegacyAdaptors.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" struct mitkIpPicDescriptor; namespace mitk { /** \brief A slice based region growing tool. \sa FeedbackContourTool \ingroup Interaction \ingroup ToolManagerEtAl When the user presses the mouse button, RegionGrowingTool will use the gray values at that position to initialize a region growing algorithm (in the affected 2D slice). By moving the mouse up and down while the button is still pressed, the user can change the parameters of the region growing algorithm (selecting more or less of an object). The current result of region growing will always be shown as a contour to the user. After releasing the button, the current result of the region growing algorithm will be written to the working image of this tool's ToolManager. If the first click is inside a segmentation that was generated by region growing (recently), the tool will try to cut off a part of the segmentation. For this reason a skeletonization of the segmentation is generated and the optimal cut point is determined. \warning Only to be instantiated by mitk::ToolManager. $Author$ */ -class MitkExt_EXPORT RegionGrowingTool : public FeedbackContourTool +class Segmentation_EXPORT RegionGrowingTool : public FeedbackContourTool { public: mitkClassMacro(RegionGrowingTool, FeedbackContourTool); itkNewMacro(RegionGrowingTool); virtual const char** GetXPM() const; virtual const char* GetName() const; protected: RegionGrowingTool(); // purposely hidden virtual ~RegionGrowingTool(); virtual void Activated(); virtual void Deactivated(); virtual bool OnMousePressed (Action*, const StateEvent*); virtual bool OnMousePressedInside (Action*, const StateEvent*, mitkIpPicDescriptor* workingPicSlice, int initialWorkingOffset); virtual bool OnMousePressedOutside (Action*, const StateEvent*); virtual bool OnMouseMoved (Action*, const StateEvent*); virtual bool OnMouseReleased(Action*, const StateEvent*); mitkIpPicDescriptor* PerformRegionGrowingAndUpdateContour(); Image::Pointer m_ReferenceSlice; Image::Pointer m_WorkingSlice; ScalarType m_LowerThreshold; ScalarType m_UpperThreshold; ScalarType m_InitialLowerThreshold; ScalarType m_InitialUpperThreshold; Point2I m_LastScreenPosition; int m_ScreenYDifference; private: mitkIpPicDescriptor* SmoothIPPicBinaryImage( mitkIpPicDescriptor* image, int &contourOfs, mitkIpPicDescriptor* dest = NULL ); void SmoothIPPicBinaryImageHelperForRows( mitkIpPicDescriptor* source, mitkIpPicDescriptor* dest, int &contourOfs, int* maskOffsets, int maskSize, int startOffset, int endOffset ); mitkIpPicDescriptor* m_OriginalPicSlice; int m_SeedPointMemoryOffset; ScalarType m_VisibleWindow; ScalarType m_DefaultWindow; ScalarType m_MouseDistanceScaleFactor; int m_PaintingPixelValue; int m_LastWorkingSeed; bool m_FillFeedbackContour; }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkRegionGrowingTool.xpm b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkRegionGrowingTool.xpm rename to Modules/Segmentation/Interactions/mitkRegionGrowingTool.xpm diff --git a/Modules/MitkExt/Interactions/mitkSegTool2D.cpp b/Modules/Segmentation/Interactions/mitkSegTool2D.cpp similarity index 100% rename from Modules/MitkExt/Interactions/mitkSegTool2D.cpp rename to Modules/Segmentation/Interactions/mitkSegTool2D.cpp diff --git a/Modules/MitkExt/Interactions/mitkSegTool2D.h b/Modules/Segmentation/Interactions/mitkSegTool2D.h similarity index 98% rename from Modules/MitkExt/Interactions/mitkSegTool2D.h rename to Modules/Segmentation/Interactions/mitkSegTool2D.h index cc126bc16e..b2b3482014 100644 --- a/Modules/MitkExt/Interactions/mitkSegTool2D.h +++ b/Modules/Segmentation/Interactions/mitkSegTool2D.h @@ -1,136 +1,136 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkSegTool2D_h_Included #define mitkSegTool2D_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkTool.h" #include "mitkImage.h" #include "mitkStateEvent.h" #include "mitkPositionEvent.h" #include "mitkPlanePositionManager.h" #include "mitkRestorePlanePositionOperation.h" #include "mitkInteractionConst.h" namespace mitk { class BaseRenderer; /** \brief Abstract base class for segmentation tools. \sa Tool \ingroup Interaction \ingroup ToolManagerEtAl Implements 2D segmentation specific helper methods, that might be of use to all kind of 2D segmentation tools. At the moment these are: - Determination of the slice where the user paints upon (DetermineAffectedImageSlice) - Projection of a 3D contour onto a 2D plane/slice SegTool2D tries to structure the interaction a bit. If you pass "PressMoveRelease" as the interaction type of your derived tool, you might implement the methods OnMousePressed, OnMouseMoved, and OnMouseReleased. Yes, your guess about when they are called is correct. \warning Only to be instantiated by mitk::ToolManager. $Author$ */ -class MitkExt_EXPORT SegTool2D : public Tool +class Segmentation_EXPORT SegTool2D : public Tool { public: mitkClassMacro(SegTool2D, Tool); /** \brief Calculates for a given Image and PlaneGeometry, which slice of the image (in index corrdinates) is meant by the plane. \return false, if no slice direction seems right (e.g. rotated planes) \param affectedDimension The image dimension, which is constant for all points in the plane, e.g. Transversal --> 2 \param affectedSlice The index of the image slice */ static bool DetermineAffectedImageSlice( const Image* image, const PlaneGeometry* plane, int& affectedDimension, int& affectedSlice ); void SetShowMarkerNodes(bool); void Enable3DInterpolation(bool); protected: SegTool2D(); // purposely hidden SegTool2D(const char*); // purposely hidden virtual ~SegTool2D(); virtual bool OnMousePressed (Action*, const StateEvent*); virtual bool OnMouseMoved (Action*, const StateEvent*); virtual bool OnMouseReleased(Action*, const StateEvent*); virtual bool OnInvertLogic (Action*, const StateEvent*); /** \brief Extract the slice of an image that the user just scribbles on. \return NULL if SegTool2D is either unable to determine which slice was affected, or if there was some problem getting the image data at that position. */ Image::Pointer GetAffectedImageSliceAs2DImage(const PositionEvent*, const Image* image); /** \brief Extract the slice of the currently selected working image that the user just scribbles on. \return NULL if SegTool2D is either unable to determine which slice was affected, or if there was some problem getting the image data at that position, or just no working image is selected. */ Image::Pointer GetAffectedWorkingSlice(const PositionEvent*); /** \brief Extract the slice of the currently selected reference image that the user just scribbles on. \return NULL if SegTool2D is either unable to determine which slice was affected, or if there was some problem getting the image data at that position, or just no reference image is selected. */ Image::Pointer GetAffectedReferenceSlice(const PositionEvent*); void WriteBackSegmentationResult (const PositionEvent*, Image*); /** \brief Adds a new node called Contourmarker to the datastorage which holds a mitk::PlanarFigure. By selecting this node the slicestack will be reoriented according to the PlanarFigure's Geometry */ unsigned int AddContourmarker ( const PositionEvent* ); void InteractiveSegmentationBugMessage( const std::string& message ); private: BaseRenderer* m_LastEventSender; unsigned int m_LastEventSlice; //The prefix of the contourmarkername. Suffix is a consecutive number const std::string m_Contourmarkername; bool m_ShowMarkerNodes; bool m_3DInterpolationEnabled; }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkSegmentationsProcessingTool.cpp b/Modules/Segmentation/Interactions/mitkSegmentationsProcessingTool.cpp similarity index 100% rename from Modules/MitkExt/Interactions/mitkSegmentationsProcessingTool.cpp rename to Modules/Segmentation/Interactions/mitkSegmentationsProcessingTool.cpp diff --git a/Modules/MitkExt/Interactions/mitkSegmentationsProcessingTool.h b/Modules/Segmentation/Interactions/mitkSegmentationsProcessingTool.h similarity index 96% rename from Modules/MitkExt/Interactions/mitkSegmentationsProcessingTool.h rename to Modules/Segmentation/Interactions/mitkSegmentationsProcessingTool.h index 99cffcdf07..04f7e2d198 100644 --- a/Modules/MitkExt/Interactions/mitkSegmentationsProcessingTool.h +++ b/Modules/Segmentation/Interactions/mitkSegmentationsProcessingTool.h @@ -1,102 +1,102 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.0 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkSegmentationsProcessingTool_h_Included #define mitkSegmentationsProcessingTool_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkTool.h" #include "mitkDataNode.h" namespace mitk { /** \brief Batch processing of all selected segmentations/data This class is undocumented. Ask the creator ($Author$) to supply useful comments. */ -class MitkExt_EXPORT SegmentationsProcessingTool : public Tool +class Segmentation_EXPORT SegmentationsProcessingTool : public Tool { public: mitkClassMacro(SegmentationsProcessingTool, Tool); protected: SegmentationsProcessingTool(); // purposely hidden virtual ~SegmentationsProcessingTool(); virtual const char* GetGroup() const; /** \brief Called when the tool gets activated Will just call ProcessAllObjects and then deactivate this tool again. */ virtual void Activated(); virtual void Deactivated(); /** \brief Loop over all working data items Will call the following methods in turn - StartProcessingAllData - ProcessOneWorkingData(DataNode*) for each node in the working data list of our tool manager - FinishProcessingAllData Subclasses should override these methods as needed and provide meaningful implementations. */ virtual void ProcessAllObjects(); /** \brief Subclasses should override this method \sa ProcessAllObjects */ virtual void StartProcessingAllData(); /** \brief Subclasses should override this method \sa ProcessAllObjects */ virtual bool ProcessOneWorkingData( DataNode* node ); /** \brief Subclasses should override this method \sa ProcessAllObjects */ virtual void FinishProcessingAllData(); /** \brief Sends an error message if there was an error during processing. */ virtual void SendErrorMessageIfAny(); /** \brief Describes the error (if one occurred during processing). */ virtual std::string GetErrorMessage(); std::string m_FailedNodes; }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkSetRegionTool.cpp b/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp similarity index 100% rename from Modules/MitkExt/Interactions/mitkSetRegionTool.cpp rename to Modules/Segmentation/Interactions/mitkSetRegionTool.cpp diff --git a/Modules/MitkExt/Interactions/mitkSetRegionTool.h b/Modules/Segmentation/Interactions/mitkSetRegionTool.h similarity index 94% rename from Modules/MitkExt/Interactions/mitkSetRegionTool.h rename to Modules/Segmentation/Interactions/mitkSetRegionTool.h index 8ab316636c..b36385f262 100644 --- a/Modules/MitkExt/Interactions/mitkSetRegionTool.h +++ b/Modules/Segmentation/Interactions/mitkSetRegionTool.h @@ -1,78 +1,78 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkSetRegionTool_h_Included #define mitkSetRegionTool_h_Included #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkFeedbackContourTool.h" namespace mitk { class Image; /** \brief Fills or erases a 2D region \sa FeedbackContourTool \sa ExtractImageFilter \sa OverwriteSliceImageFilter \ingroup Interaction \ingroup ToolManagerEtAl Finds the outer contour of a shape in 2D (possibly including holes) and sets all the inside pixels to a specified value. This might fill holes or erase segmentations. \warning Only to be instantiated by mitk::ToolManager. $Author$ */ -class MitkExt_EXPORT SetRegionTool : public FeedbackContourTool +class Segmentation_EXPORT SetRegionTool : public FeedbackContourTool { public: mitkClassMacro(SetRegionTool, FeedbackContourTool); protected: SetRegionTool(int paintingPixelValue = 1); // purposely hidden virtual ~SetRegionTool(); virtual void Activated(); virtual void Deactivated(); virtual bool OnMousePressed (Action*, const StateEvent*); virtual bool OnMouseReleased(Action*, const StateEvent*); virtual bool OnInvertLogic (Action*, const StateEvent*); int m_PaintingPixelValue; bool m_FillContour; bool m_StatusFillWholeSlice; Contour::Pointer m_SegmentationContourInWorldCoordinates; Contour::Pointer m_WholeImageContourInWorldCoordinates; }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkSubtractContourTool.cpp b/Modules/Segmentation/Interactions/mitkSubtractContourTool.cpp similarity index 93% rename from Modules/MitkExt/Interactions/mitkSubtractContourTool.cpp rename to Modules/Segmentation/Interactions/mitkSubtractContourTool.cpp index c8fbd4bca2..4d6af47257 100644 --- a/Modules/MitkExt/Interactions/mitkSubtractContourTool.cpp +++ b/Modules/Segmentation/Interactions/mitkSubtractContourTool.cpp @@ -1,45 +1,45 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkSubtractContourTool.h" #include "mitkSubtractContourTool.xpm" namespace mitk { - MITK_TOOL_MACRO(MitkExt_EXPORT, SubtractContourTool, "Subtract tool"); + MITK_TOOL_MACRO(Segmentation_EXPORT, SubtractContourTool, "Subtract tool"); } mitk::SubtractContourTool::SubtractContourTool() :ContourTool(0) { FeedbackContourTool::SetFeedbackContourColor( 1.0, 0.0, 0.0 ); } mitk::SubtractContourTool::~SubtractContourTool() { } const char** mitk::SubtractContourTool::GetXPM() const { return mitkSubtractContourTool_xpm; } const char* mitk::SubtractContourTool::GetName() const { return "Subtract"; } diff --git a/Modules/MitkExt/Interactions/mitkSubtractContourTool.h b/Modules/Segmentation/Interactions/mitkSubtractContourTool.h similarity index 94% rename from Modules/MitkExt/Interactions/mitkSubtractContourTool.h rename to Modules/Segmentation/Interactions/mitkSubtractContourTool.h index 372b5cb6b4..529c893d3b 100644 --- a/Modules/MitkExt/Interactions/mitkSubtractContourTool.h +++ b/Modules/Segmentation/Interactions/mitkSubtractContourTool.h @@ -1,68 +1,68 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef mitkSubtractContourTool_h_Included #define mitkSubtractContourTool_h_Included #include "mitkContourTool.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" namespace mitk { /** \brief Fill the inside of a contour with 1 \sa ContourTool \ingroup Interaction \ingroup ToolManagerEtAl Fills a visible contour (from FeedbackContourTool) during mouse dragging. When the mouse button is released, SubtractContourTool tries to extract a slice from the working image and fill in the (filled) contour as a binary image. All inside pixels are set to 0. While holding the CTRL key, the contour changes color and the pixels on the inside would be filled with 1. \warning Only to be instantiated by mitk::ToolManager. $Author$ */ -class MitkExt_EXPORT SubtractContourTool : public ContourTool +class Segmentation_EXPORT SubtractContourTool : public ContourTool { public: mitkClassMacro(SubtractContourTool, ContourTool); itkNewMacro(SubtractContourTool); virtual const char** GetXPM() const; virtual const char* GetName() const; protected: SubtractContourTool(); // purposely hidden virtual ~SubtractContourTool(); }; } // namespace #endif diff --git a/Modules/MitkExt/Interactions/mitkSubtractContourTool.xpm b/Modules/Segmentation/Interactions/mitkSubtractContourTool.xpm similarity index 100% rename from Modules/MitkExt/Interactions/mitkSubtractContourTool.xpm rename to Modules/Segmentation/Interactions/mitkSubtractContourTool.xpm diff --git a/Modules/MitkExt/Rendering/mitkContourMapper2D.cpp b/Modules/Segmentation/Rendering/mitkContourMapper2D.cpp similarity index 100% rename from Modules/MitkExt/Rendering/mitkContourMapper2D.cpp rename to Modules/Segmentation/Rendering/mitkContourMapper2D.cpp diff --git a/Modules/MitkExt/Rendering/mitkContourMapper2D.h b/Modules/Segmentation/Rendering/mitkContourMapper2D.h similarity index 93% rename from Modules/MitkExt/Rendering/mitkContourMapper2D.h rename to Modules/Segmentation/Rendering/mitkContourMapper2D.h index 4bc7ce4eef..97fda995ab 100644 --- a/Modules/MitkExt/Rendering/mitkContourMapper2D.h +++ b/Modules/Segmentation/Rendering/mitkContourMapper2D.h @@ -1,66 +1,66 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITK_CONTOUR_MAPPER_2D_H_ #define MITK_CONTOUR_MAPPER_2D_H_ #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkGLMapper2D.h" namespace mitk { class BaseRenderer; class Contour; /** * @brief OpenGL-based mapper to display a mitk::Contour object in a 2D render window * * * @ingroup Mapper */ -class MitkExt_EXPORT ContourMapper2D : public GLMapper2D +class Segmentation_EXPORT ContourMapper2D : public GLMapper2D { public: mitkClassMacro(ContourMapper2D, Mapper2D); itkNewMacro(Self); /** * reimplemented from Baseclass */ virtual void Paint(BaseRenderer * renderer); /** * return a refernce of the rendered data object */ const Contour* GetInput(void); protected: ContourMapper2D(); virtual ~ContourMapper2D(); }; } // namespace mitk #endif /* MITKContourMapper2D_H_HEADER_INCLUDED */ diff --git a/Modules/MitkExt/Rendering/mitkContourSetMapper2D.cpp b/Modules/Segmentation/Rendering/mitkContourSetMapper2D.cpp similarity index 100% rename from Modules/MitkExt/Rendering/mitkContourSetMapper2D.cpp rename to Modules/Segmentation/Rendering/mitkContourSetMapper2D.cpp diff --git a/Modules/MitkExt/Rendering/mitkContourSetMapper2D.h b/Modules/Segmentation/Rendering/mitkContourSetMapper2D.h similarity index 93% rename from Modules/MitkExt/Rendering/mitkContourSetMapper2D.h rename to Modules/Segmentation/Rendering/mitkContourSetMapper2D.h index 3f71393784..d494839a0f 100644 --- a/Modules/MitkExt/Rendering/mitkContourSetMapper2D.h +++ b/Modules/Segmentation/Rendering/mitkContourSetMapper2D.h @@ -1,66 +1,66 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITK_CONTOUR_SET_MAPPER_2D_H_ #define MITK_CONTOUR_SET_MAPPER_2D_H_ #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkGLMapper2D.h" namespace mitk { class BaseRenderer; class ContourSet; class BaseRenderer; /** * @brief OpenGL-based mapper to display a mitk::Contour object in a 2D render window * * * @ingroup Mapper */ -class MitkExt_EXPORT ContourSetMapper2D : public GLMapper2D +class Segmentation_EXPORT ContourSetMapper2D : public GLMapper2D { public: mitkClassMacro(ContourSetMapper2D, Mapper2D); itkNewMacro(Self); /** * reimplemented from Baseclass */ virtual void Paint(mitk::BaseRenderer * renderer); /** * return a refernce of the rendered data object */ const mitk::ContourSet * GetInput(void); protected: ContourSetMapper2D(); virtual ~ContourSetMapper2D(); }; } // namespace mitk #endif /* MITK_CONTOUR_SET_MAPPER_2D_H_ */ diff --git a/Modules/MitkExt/Rendering/mitkContourSetVtkMapper3D.cpp b/Modules/Segmentation/Rendering/mitkContourSetVtkMapper3D.cpp similarity index 100% rename from Modules/MitkExt/Rendering/mitkContourSetVtkMapper3D.cpp rename to Modules/Segmentation/Rendering/mitkContourSetVtkMapper3D.cpp diff --git a/Modules/MitkExt/Rendering/mitkContourSetVtkMapper3D.h b/Modules/Segmentation/Rendering/mitkContourSetVtkMapper3D.h similarity index 94% rename from Modules/MitkExt/Rendering/mitkContourSetVtkMapper3D.h rename to Modules/Segmentation/Rendering/mitkContourSetVtkMapper3D.h index c1d21e9c4e..ef8cd4ae77 100644 --- a/Modules/MitkExt/Rendering/mitkContourSetVtkMapper3D.h +++ b/Modules/Segmentation/Rendering/mitkContourSetVtkMapper3D.h @@ -1,70 +1,70 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITK_CONTOUR_SET_VTK_MAPPER_3D_H #define MITK_CONTOUR_SET_VTK_MAPPER_3D_H #include "mitkCommon.h" -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkVtkMapper3D.h" #include "mitkContourSet.h" #include "mitkBaseRenderer.h" #include class vtkPolyDataMapper; class vtkAppendPolyData; class vtkActor; class vtkTubeFilter; namespace mitk { //##Documentation //## @brief Vtk-based mapper for mitk::Contour //## @ingroup Mapper -class MitkExt_EXPORT ContourSetVtkMapper3D : public VtkMapper3D +class Segmentation_EXPORT ContourSetVtkMapper3D : public VtkMapper3D { public: mitkClassMacro(ContourSetVtkMapper3D, VtkMapper3D); itkNewMacro(Self); virtual const mitk::ContourSet* GetInput(); virtual vtkProp* GetVtkProp(mitk::BaseRenderer* renderer); protected: ContourSetVtkMapper3D(); virtual ~ContourSetVtkMapper3D(); virtual void GenerateDataForRenderer(mitk::BaseRenderer* renderer); vtkPolyDataMapper* m_VtkPolyDataMapper; vtkTubeFilter* m_TubeFilter; vtkPolyData *m_ContourSet; vtkActor *m_Actor; }; } // namespace mitk #endif // MITK_CONTOUR_VTK_MAPPER_3D_H diff --git a/Modules/MitkExt/Rendering/mitkContourVtkMapper3D.cpp b/Modules/Segmentation/Rendering/mitkContourVtkMapper3D.cpp similarity index 100% rename from Modules/MitkExt/Rendering/mitkContourVtkMapper3D.cpp rename to Modules/Segmentation/Rendering/mitkContourVtkMapper3D.cpp diff --git a/Modules/MitkExt/Rendering/mitkContourVtkMapper3D.h b/Modules/Segmentation/Rendering/mitkContourVtkMapper3D.h similarity index 94% rename from Modules/MitkExt/Rendering/mitkContourVtkMapper3D.h rename to Modules/Segmentation/Rendering/mitkContourVtkMapper3D.h index cef2d7200e..d149d2522d 100644 --- a/Modules/MitkExt/Rendering/mitkContourVtkMapper3D.h +++ b/Modules/Segmentation/Rendering/mitkContourVtkMapper3D.h @@ -1,69 +1,69 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITK_CONTOUR_VTK_MAPPER_3D_H #define MITK_CONTOUR_VTK_MAPPER_3D_H -#include "MitkExtExports.h" +#include "SegmentationExports.h" #include "mitkVtkMapper3D.h" #include #include class vtkPolyDataMapper; class vtkAppendPolyData; class vtkActor; class vtkTubeFilter; namespace mitk { class BaseRenderer; class Contour; /** @brief Vtk-based mapper for mitk::Contour @ingroup Mapper */ -class MitkExt_EXPORT ContourVtkMapper3D : public VtkMapper3D +class Segmentation_EXPORT ContourVtkMapper3D : public VtkMapper3D { public: mitkClassMacro(ContourVtkMapper3D, VtkMapper3D); itkNewMacro(Self); virtual const mitk::Contour* GetInput(); virtual vtkProp* GetVtkProp(mitk::BaseRenderer* renderer); protected: ContourVtkMapper3D(); virtual ~ContourVtkMapper3D(); virtual void GenerateDataForRenderer(mitk::BaseRenderer* renderer); vtkSmartPointer m_VtkPolyDataMapper; vtkSmartPointer m_TubeFilter; vtkSmartPointer m_VtkPointList; vtkSmartPointer m_Contour; vtkSmartPointer m_Actor; }; } // namespace mitk #endif // MITK_CONTOUR_VTK_MAPPER_3D_H diff --git a/Modules/Segmentation/Testing/CMakeLists.txt b/Modules/Segmentation/Testing/CMakeLists.txt new file mode 100644 index 0000000000..e69de29bb2 diff --git a/Modules/Segmentation/Testing/Data/img.nrrd b/Modules/Segmentation/Testing/Data/img.nrrd new file mode 100644 index 0000000000..04a51b53cb --- /dev/null +++ b/Modules/Segmentation/Testing/Data/img.nrrd @@ -0,0 +1,17 @@ +NRRD0004 +# Complete NRRD file format specification at: +# http://teem.sourceforge.net/nrrd/format.html +content: SomeIDNumber42 +type: short +dimension: 3 +space: right-anterior-superior +sizes: 3 3 1 +thicknesses: 1 1 1 +space directions: (1,0,0) (0,1,0) (0,0,1) +centerings: cell cell cell +kinds: space space space +encoding: ASCII +space units: "mm" "mm" "mm" +space origin: (0,0,0) + +1 2 3 4 5 6 7 8 9 diff --git a/Modules/Segmentation/Testing/Data/lungs.vtk b/Modules/Segmentation/Testing/Data/lungs.vtk new file mode 100644 index 0000000000..5b0f7f17ac --- /dev/null +++ b/Modules/Segmentation/Testing/Data/lungs.vtk @@ -0,0 +1,18985 @@ +# vtk DataFile Version 3.0 +vtk output +ASCII +DATASET POLYDATA +POINTS 7860 float +59 174 77.8 95 170 80.2059 55 171 80.2222 +56 171 79.2353 56 172 78.5806 57 172 78.1765 +58 173 78.2 59 173 78.6923 61 173 79.6452 +87 173 80.4194 88 173 79.8 89 173 79.4571 +91 173 80.4706 58 174 78.5172 60 174 78.1765 +89 174 80.4706 91 174 80.8235 59 175 78.5172 +60 175 78.0909 63 175 79.4571 88 175 80.5588 +64 176 80.1429 63 177 80.2059 65 177 80.2059 +67 177 80.1429 81 177 80.4706 82 177 79.8 +84 177 79.8 62 177.087 81 64 177.5 81 +68 178 80.2059 80 178 80.2059 82 178 80.2059 +69 179 79.8529 77 179 80.2059 79 179 79.8 +80 179 80.2059 81 179 80.8235 70 180 80.5455 +74 180 80.4706 114 150 83.4706 113 151 83.4706 +112.739 151 84 114 152 82.8529 39 155 83.8 +38.6667 155 84 113 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-0.0394837 0.217662 0.976024 0 +-0.78792 0.597133 -0.150381 -0.738577 0.656931 -0.151476 0.335756 0.93732 -0.0932657 +0.325028 0.941474 -0.0893519 0.319809 0.940182 -0.117386 -0.312036 0.934975 -0.168689 +0.0745504 0.984242 -0.160342 0.158075 0.973779 -0.163606 0.0663259 0.99153 -0.111663 +0 0.995211 -0.0977514 0.0882513 0.992617 -0.0832084 0.254057 0.962565 -0.0944677 + diff --git a/Modules/Segmentation/Testing/Data/testNrrd.ascii b/Modules/Segmentation/Testing/Data/testNrrd.ascii new file mode 100644 index 0000000000..f78381e84b --- /dev/null +++ b/Modules/Segmentation/Testing/Data/testNrrd.ascii @@ -0,0 +1,8 @@ +2 2 +2 2 +2 2 +2 2 +1 1 +1 1 +1 1 +1 1 \ No newline at end of file diff --git a/Modules/Segmentation/Testing/Data/testNrrd.nhdr b/Modules/Segmentation/Testing/Data/testNrrd.nhdr new file mode 100644 index 0000000000..d62bdcaba6 --- /dev/null +++ b/Modules/Segmentation/Testing/Data/testNrrd.nhdr @@ -0,0 +1,20 @@ +NRRD0005 +content: SomeIDNumber42 +type: short +dimension: 4 +space: right-anterior-superior +sizes: 2 2 2 2 +thicknesses: NaN NaN 2.5 NaN +space directions: (2,0,0) (0,2.5,0) (0,0,2) none +centerings: cell cell cell none +kinds: space space space list +endian: little +encoding: ascii +space units: "mm" "mm" "mm" +space origin: (0,0,0) +data file: testNrrd.ascii +measurement frame: (1,0,0) (0,0,1) (0,1,0) +modality:=DWMRI +DWMRI_b-value:=1000 +DWMRI_gradient_0000:= 0 0 0 +DWMRI_gradient_0001:= 1 0 1 \ No newline at end of file diff --git a/Modules/Segmentation/Testing/Data/testimage.dcm b/Modules/Segmentation/Testing/Data/testimage.dcm new file mode 100644 index 0000000000..ecf7b12d33 Binary files /dev/null and b/Modules/Segmentation/Testing/Data/testimage.dcm differ diff --git a/Modules/Segmentation/Testing/Data/vtkUnstructuredGrid.vtk b/Modules/Segmentation/Testing/Data/vtkUnstructuredGrid.vtk new file mode 100644 index 0000000000..392ef94c61 Binary files /dev/null and b/Modules/Segmentation/Testing/Data/vtkUnstructuredGrid.vtk differ diff --git a/Modules/Segmentation/Testing/files.cmake b/Modules/Segmentation/Testing/files.cmake new file mode 100644 index 0000000000..2f9a9aa8a0 --- /dev/null +++ b/Modules/Segmentation/Testing/files.cmake @@ -0,0 +1,22 @@ +set(MODULE_TESTS + mitkContourMapper2DTest.cpp + mitkContourTest.cpp + mitkDataNodeSegmentationTest.cpp +# mitkSegmentationInterpolationTest.cpp +) + +set(MODULE_IMAGE_TESTS + mitkManualSegmentationToSurfaceFilterTest.cpp + mitkOverwriteSliceImageFilterTest.cpp +) +set(MODULE_CUSTOM_TESTS +) +set(MODULE_TESTIMAGES + US4DCyl.nrrd + Pic3D.nrrd + Pic2DplusT.nrrd + BallBinary30x30x30.nrrd + Png2D-bw.png + binary.stl + ball.stl +) diff --git a/Modules/MitkExt/Testing/mitkCompareImageSliceTestHelper.h b/Modules/Segmentation/Testing/mitkCompareImageSliceTestHelper.h similarity index 100% rename from Modules/MitkExt/Testing/mitkCompareImageSliceTestHelper.h rename to Modules/Segmentation/Testing/mitkCompareImageSliceTestHelper.h diff --git a/Modules/MitkExt/Testing/mitkContourMapper2DTest.cpp b/Modules/Segmentation/Testing/mitkContourMapper2DTest.cpp similarity index 100% rename from Modules/MitkExt/Testing/mitkContourMapper2DTest.cpp rename to Modules/Segmentation/Testing/mitkContourMapper2DTest.cpp diff --git a/Modules/MitkExt/Testing/mitkContourTest.cpp b/Modules/Segmentation/Testing/mitkContourTest.cpp similarity index 100% rename from Modules/MitkExt/Testing/mitkContourTest.cpp rename to Modules/Segmentation/Testing/mitkContourTest.cpp diff --git a/Modules/MitkExt/Testing/mitkDataNodeExtTest.cpp b/Modules/Segmentation/Testing/mitkDataNodeSegmentationTest.cpp similarity index 54% copy from Modules/MitkExt/Testing/mitkDataNodeExtTest.cpp copy to Modules/Segmentation/Testing/mitkDataNodeSegmentationTest.cpp index 4faeb11b65..150220120e 100644 --- a/Modules/MitkExt/Testing/mitkDataNodeExtTest.cpp +++ b/Modules/Segmentation/Testing/mitkDataNodeSegmentationTest.cpp @@ -1,257 +1,165 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2008-02-25 17:27:17 +0100 (Mo, 25 Feb 2008) $ Version: $Revision: 7837 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkDataNode.h" #include #include "mitkVtkPropRenderer.h" #include "mitkTestingMacros.h" #include "mitkGlobalInteraction.h" #include //Basedata Test #include #include #include -#include -#include -#include -#include //Mapper Test #include #include #include #include #include -#include -#include -#include -#include #include #include -#include -#include -#include -#include //Interactors #include #include #include -#include -#include -#include -#include //Propertylist Test #include #include #include #include #include #include #include #include #include #include #include /** * Extended test for mitk::DataNode. A number of tests from the core test * mitkDataNodeTest are assumed to pass! */ -class mitkDataNodeExtTestClass { public: +class mitkDataNodeSegmentationTestClass { public: static void TestDataSetting(mitk::DataNode::Pointer dataNode) { mitk::BaseData::Pointer baseData; //NULL pointer Test dataNode->SetData(baseData); MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a NULL pointer was set correctly" ) baseData = mitk::Contour::New(); dataNode->SetData(baseData); MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a Contour object was set correctly" ) baseData = mitk::ContourSet::New(); dataNode->SetData(baseData); MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a ContourSet object was set correctly" ) - - baseData = mitk::ItkBaseDataAdapter::New(); - dataNode->SetData(baseData); - MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a ItkBaseDataAdapter object was set correctly" ) - - baseData = mitk::Mesh::New(); - dataNode->SetData(baseData); - MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a Mesh object was set correctly" ) - - baseData = mitk::SeedsImage::New(); - dataNode->SetData(baseData); - MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a SeedsImage object was set correctly" ) - - baseData = mitk::BoundingObject::New(); - dataNode->SetData(baseData); - MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a BoundingObject object was set correctly" ) - - baseData = mitk::UnstructuredGrid::New(); - dataNode->SetData(baseData); - MITK_TEST_CONDITION( baseData == dataNode->GetData(), "Testing if a UnstructuredGrid object was set correctly" ) } static void TestMapperSetting(mitk::DataNode::Pointer dataNode) { //tests the SetMapper() method //in dataNode is a mapper vector which can be accessed by index //in this test method we use only slot 0 (filled with null) and slot 1 //so we also test the destructor of the mapper classes mitk::Mapper::Pointer mapper; dataNode->SetMapper(0,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(0), "Testing if a NULL pointer was set correctly" ) mapper = mitk::ContourMapper2D::New(); dataNode->SetMapper(1,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a ContourMapper2D was set correctly" ) MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) mapper = mitk::ContourSetMapper2D::New(); dataNode->SetMapper(1,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a ContourSetMapper2D was set correctly" ) MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - mapper = mitk::MeshMapper2D::New(); - dataNode->SetMapper(1,mapper); - MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a MeshMapper2D was set correctly" ) - MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - - mapper = mitk::UnstructuredGridMapper2D::New(); - dataNode->SetMapper(1,mapper); - MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a UnstructuredGridMapper2D was set correctly" ) - MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - - mapper = mitk::LineMapper2D::New(); - dataNode->SetMapper(1,mapper); - MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a LineMapper2D was set correctly" ) - MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - - mapper = mitk::SplineMapper2D::New(); - dataNode->SetMapper(1,mapper); - MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a SplineMapper2D was set correctly" ) - MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - //3D Mappers mapper = mitk::ContourSetVtkMapper3D::New(); dataNode->SetMapper(1,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a ContourSetVtkMapper3D was set correctly" ) MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) mapper = mitk::ContourVtkMapper3D::New(); dataNode->SetMapper(1,mapper); MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a ContourVtkMapper3D was set correctly" ) MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - - mapper = mitk::MeshVtkMapper3D::New(); - dataNode->SetMapper(1,mapper); - MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a MeshVtkMapper3D was set correctly" ) - MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - - mapper = mitk::UnstructuredGridVtkMapper3D::New(); - dataNode->SetMapper(1,mapper); - MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a UnstructuredGridVtkMapper3D was set correctly" ) - MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - - //linker error - //mapper = mitk::LineVtkMapper3D::New(); - //dataNode->SetMapper(1,mapper); - //MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a LineVtkMapper3D was set correctly" ) - //MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) - - mapper = mitk::SplineVtkMapper3D::New(); - dataNode->SetMapper(1,mapper); - MITK_TEST_CONDITION( mapper == dataNode->GetMapper(1), "Testing if a SplineVtkMapper3D was set correctly" ) - MITK_TEST_CONDITION( dataNode == mapper->GetDataNode(), "Testing if the mapper returns the right DataNode" ) } static void TestInteractorSetting(mitk::DataNode::Pointer dataNode) { //this method tests the SetInteractor() and GetInteractor methods //the Interactor base class calls the DataNode->SetInteractor method mitk::Interactor::Pointer interactor; MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a NULL pointer was set correctly (Interactor)" ) - - interactor = mitk::ConnectPointsInteractor::New("AffineInteractions click to select", dataNode); - MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a ConnectPointsInteractor was set correctly" ) - + interactor = mitk::ContourInteractor::New("AffineInteractions click to select", dataNode); MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a ContourInteractor was set correctly" ) interactor = mitk::ExtrudedContourInteractor::New("AffineInteractions click to select", dataNode); MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a ExtrudedContourInteractor was set correctly" ) - - interactor = mitk::PointInteractor::New("AffineInteractions click to select", dataNode); - MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a PointInteractor was set correctly" ) - - interactor = mitk::PointSelectorInteractor::New("AffineInteractions click to select", dataNode); - MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a PointSelectorInteractor was set correctly" ) - - interactor = mitk::SeedsInteractor::New("AffineInteractions click to select", dataNode); - MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a SeedsInteractor was set correctly" ) - - interactor = mitk::DisplayPointSetInteractor::New("AffineInteractions click to select", dataNode); - MITK_TEST_CONDITION( interactor == dataNode->GetInteractor(), "Testing if a DisplayPointSetInteractor was set correctly" ) } }; int mitkDataNodeExtTest(int /* argc */, char* /*argv*/[]) { // always start with this! MITK_TEST_BEGIN("DataNode") // Global interaction must(!) be initialized mitk::GlobalInteraction::GetInstance()->Initialize("global"); // let's create an object of our class mitk::DataNode::Pointer myDataNode = mitk::DataNode::New(); // first test: did this work? // using MITK_TEST_CONDITION_REQUIRED makes the test stop after failure, since // it makes no sense to continue without an object. MITK_TEST_CONDITION_REQUIRED(myDataNode.IsNotNull(),"Testing instantiation") //test setData() Method mitkDataNodeExtTestClass::TestDataSetting(myDataNode); mitkDataNodeExtTestClass::TestMapperSetting(myDataNode); //note, that no data is set to the dataNode mitkDataNodeExtTestClass::TestInteractorSetting(myDataNode); // write your own tests here and use the macros from mitkTestingMacros.h !!! // do not write to std::cout and do not return from this function yourself! // always end with this! MITK_TEST_END() } diff --git a/Modules/MitkExt/Testing/mitkManualSegmentationToSurfaceFilterTest.cpp b/Modules/Segmentation/Testing/mitkManualSegmentationToSurfaceFilterTest.cpp similarity index 100% rename from Modules/MitkExt/Testing/mitkManualSegmentationToSurfaceFilterTest.cpp rename to Modules/Segmentation/Testing/mitkManualSegmentationToSurfaceFilterTest.cpp diff --git a/Modules/MitkExt/Testing/mitkOverwriteSliceImageFilterTest.cpp b/Modules/Segmentation/Testing/mitkOverwriteSliceImageFilterTest.cpp similarity index 100% rename from Modules/MitkExt/Testing/mitkOverwriteSliceImageFilterTest.cpp rename to Modules/Segmentation/Testing/mitkOverwriteSliceImageFilterTest.cpp diff --git a/Modules/MitkExt/Testing/mitkSegmentationInterpolationTest.cpp b/Modules/Segmentation/Testing/mitkSegmentationInterpolationTest.cpp similarity index 98% rename from Modules/MitkExt/Testing/mitkSegmentationInterpolationTest.cpp rename to Modules/Segmentation/Testing/mitkSegmentationInterpolationTest.cpp index 68f470689c..ef0950dfd3 100644 --- a/Modules/MitkExt/Testing/mitkSegmentationInterpolationTest.cpp +++ b/Modules/Segmentation/Testing/mitkSegmentationInterpolationTest.cpp @@ -1,366 +1,366 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkSegmentationInterpolationController.h" #include "mitkCoreObjectFactory.h" #include "mitkStandardFileLocations.h" #include "mitkDataNodeFactory.h" #include "ipSegmentation.h" -#include "mitkCompareImageSliceTestHelper.h" +#include "mitkCompareImageSliceTestHelper.h"s class mitkSegmentationInterpolationTestClass { public: mitkSegmentationInterpolationTestClass() {} ~mitkSegmentationInterpolationTestClass() {} bool Test() { return CreateNewInterpolator() && CreateSegmentation() && ClearSegmentation() && CreateTwoSlices(2) && TestInterpolation(2) && ClearSegmentation() && CreateTwoSlices(1) && TestInterpolation(1) && ClearSegmentation() && CreateTwoSlices(0) && TestInterpolation(0) && DeleteInterpolator() && CreateNewInterpolator() && LoadTestImages() && CompareInterpolationsToDefinedReference(); } protected: bool CreateNewInterpolator(); bool CreateSegmentation(); bool ClearSegmentation(); bool CreateTwoSlices(int); bool TestInterpolation(int); bool DeleteInterpolator(); bool LoadTestImages(); bool CompareInterpolationsToDefinedReference(); mitk::Image::Pointer LoadImage(const std::string& filename); mitk::SegmentationInterpolationController::Pointer m_Interpolator; mitk::Image::Pointer m_Image; mitk::Image::Pointer m_ManualSlices; mitk::Image::Pointer m_InterpolatedSlices; unsigned int dim[3]; int pad[3]; }; bool mitkSegmentationInterpolationTestClass::CreateNewInterpolator() { std::cout << "Instantiation" << std::endl; // instantiation m_Interpolator = mitk::SegmentationInterpolationController::New(); if (m_Interpolator.IsNotNull()) { std::cout << " (II) Instantiation works." << std::endl; } else { std::cout << " Instantiation test failed!" << std::endl; return false; } return true; } bool mitkSegmentationInterpolationTestClass::CreateSegmentation() { m_Image = mitk::Image::New(); dim[0]=15; dim[1]=20; dim[2]=25; pad[0]=2; pad[1]=3; pad[2]=4; - m_Image->Initialize(mitk::PixelType(typeid(int)), 3, dim); + m_Image->Initialize( mitk::MakeScalarPixelType(), 3, dim); return true; } bool mitkSegmentationInterpolationTestClass::ClearSegmentation() { int* p = (int*)m_Image->GetData(); // pointer to pixel data int size = dim[0]*dim[1]*dim[2]; for(int i=0; iGetData(); // pointer to pixel data int size = dim[0]*dim[1]*dim[2]; for(int i=0; i= pad[xdim]) && (x < ( (signed) dim[xdim]-pad[xdim])) && (y >= pad[ydim]) && (y < ( (signed) dim[ydim]-pad[ydim])) ) { *p = 1; } else { *p = 0; } } m_Interpolator->SetSegmentationVolume( m_Image ); std::cout << " (II) SetSegmentationVolume works (slicedim " << slicedim << ")" << std::endl; return true; } /** * Checks if interpolation would create a square in slice 1 */ bool mitkSegmentationInterpolationTestClass::TestInterpolation(int slicedim) { int slice = 1; mitk::Image::Pointer interpolated = m_Interpolator->Interpolate( slicedim, slice, 0 ); // interpolate second slice transversal if (interpolated.IsNull()) { std::cerr << " (EE) Interpolation did not return anything for slicedim == " << slicedim << " (although it should)." << std::endl; return false; } int xdim,ydim; switch (slicedim) { case 0: xdim = 1; ydim = 2; // different than above! break; case 1: xdim = 0; ydim = 2; break; case 2: default: xdim = 0; ydim = 1; break; } ipMITKSegmentationTYPE* p = (ipMITKSegmentationTYPE*)interpolated->GetData(); // pointer to pixel data int size = dim[xdim]*dim[ydim]; if ( (signed) interpolated->GetDimension(0) * (signed) interpolated->GetDimension(1) != size ) { std::cout << " (EE) Size of interpolated image differs from original segmentation..." << std::endl; return false; } for(int i=0; i= pad[xdim]) && (x < ((signed) dim[xdim]-pad[xdim])) && (y >= pad[ydim]) && (y < ((signed) dim[ydim]-pad[ydim])) && (value != 1) ) { std::cout << " (EE) Interpolation of a square figure failed" << std::endl; std::cout << " Value at " << x << " " << y << ": " << (int)value << std::endl; return false; } } std::cout << " (II) Interpolation of a square figure works like expected (slicedim " << slicedim << ")" << std::endl; return true; } bool mitkSegmentationInterpolationTestClass::DeleteInterpolator() { std::cout << "Object destruction" << std::endl; // freeing m_Interpolator = NULL; std::cout << " (II) Freeing works." << std::endl; return true; } bool mitkSegmentationInterpolationTestClass::LoadTestImages() { std::string filename1 = mitk::StandardFileLocations::GetInstance()->FindFile("interpolation_test_manual.pic.gz", "../mitk/Core/Testing/Data/"); if ( filename1.empty() ) { filename1 = mitk::StandardFileLocations::GetInstance()->FindFile("interpolation_test_manual.pic.gz", "Testing/Data/"); } std::cout << "Found test image (manual slices) in '" << filename1 << "'" << std::endl; std::string filename2 = mitk::StandardFileLocations::GetInstance()->FindFile("interpolation_test_result.pic.gz", "../mitk/Core/Testing/Data/"); if ( filename2.empty() ) { filename2 = mitk::StandardFileLocations::GetInstance()->FindFile("interpolation_test_result.pic.gz", "Testing/Data/"); } std::cout << "Found test image (reference for interpolation) in '" << filename2 << "'" << std::endl; if ( filename1.empty() || filename2.empty() ) { return false; } else { m_ManualSlices = LoadImage( filename1 ); m_InterpolatedSlices = LoadImage( filename2 ); return ( m_ManualSlices.IsNotNull() && m_InterpolatedSlices.IsNotNull() ); } return true; } mitk::Image::Pointer mitkSegmentationInterpolationTestClass::LoadImage(const std::string& filename) { mitk::Image::Pointer image = NULL; mitk::DataNodeFactory::Pointer factory = mitk::DataNodeFactory::New(); try { factory->SetFileName( filename ); factory->Update(); if(factory->GetNumberOfOutputs()<1) { std::cerr<<"File " << filename << " could not be loaded [FAILED]"<GetOutput( 0 ); image = dynamic_cast(node->GetData()); if(image.IsNull()) { std::cout<<"File " << filename << " is not an image! [FAILED]"<SetSegmentationVolume( m_ManualSlices ); std::cout << "OK" << std::endl; std::cout << " (II) Testing interpolation result for slice " << std::flush; for (unsigned int slice = 1; slice < 98; ++slice) { if (slice % 2 == 0) continue; // these were manually drawn, no interpolation possible std::cout << slice << " " << std::flush; mitk::Image::Pointer interpolation = m_Interpolator->Interpolate( 2, slice, 0 ); if ( interpolation.IsNull() ) { std::cerr << " (EE) Interpolated image is NULL." << std::endl; return false; } if ( !CompareImageSliceTestHelper::CompareSlice( m_InterpolatedSlices, 2, slice, interpolation ) ) { std::cerr << " (EE) interpolated image is not identical to reference in slice " << slice << std::endl; return false; } } std::cout << std::endl; std::cout << " (II) Interpolations are the same as the saved references." << std::endl; return true; } /// ctest entry point int mitkSegmentationInterpolationTest(int /*argc*/, char* /*argv*/[]) { // one big variable to tell if anything went wrong std::cout << "Creating CoreObjectFactory" << std::endl; itk::ObjectFactoryBase::RegisterFactory(mitk::CoreObjectFactory::New()); mitkSegmentationInterpolationTestClass test; if ( test.Test() ) { std::cout << "[PASSED]" << std::endl; return EXIT_SUCCESS; } else { std::cout << "[FAILED]" << std::endl; return EXIT_FAILURE; } } diff --git a/Modules/Segmentation/files.cmake b/Modules/Segmentation/files.cmake new file mode 100644 index 0000000000..9911599184 --- /dev/null +++ b/Modules/Segmentation/files.cmake @@ -0,0 +1,53 @@ +set(CPP_FILES +Algorithms/mitkCalculateSegmentationVolume.cpp +Algorithms/mitkComputeContourSetNormalsFilter.cpp +Algorithms/mitkContourSetToPointSetFilter.cpp +Algorithms/mitkContourUtils.cpp +Algorithms/mitkCorrectorAlgorithm.cpp +Algorithms/mitkCreateDistanceImageFromSurfaceFilter.cpp +Algorithms/mitkDiffImageApplier.cpp +Algorithms/mitkImageToContourFilter.cpp +Algorithms/mitkManualSegmentationToSurfaceFilter.cpp +Algorithms/mitkOverwriteDirectedPlaneImageFilter.cpp +Algorithms/mitkOverwriteSliceImageFilter.cpp +Algorithms/mitkReduceContourSetFilter.cpp +Algorithms/mitkSegmentationObjectFactory.cpp +Algorithms/mitkSegmentationSink.cpp +Algorithms/mitkShapeBasedInterpolationAlgorithm.cpp +Algorithms/mitkShowSegmentationAsSmoothedSurface.cpp +Algorithms/mitkShowSegmentationAsSurface.cpp +Controllers/mitkSegmentationInterpolationController.cpp +Controllers/mitkSurfaceInterpolationController.cpp +# DataManagement/mitkApplyDiffImageOperation.cpp +DataManagement/mitkContour.cpp +DataManagement/mitkContourSet.cpp +DataManagement/mitkExtrudedContour.cpp +Interactions/mitkAddContourTool.cpp +Interactions/mitkAutoCropTool.cpp +Interactions/mitkAutoSegmentationTool.cpp +Interactions/mitkBinaryThresholdTool.cpp +Interactions/mitkBinaryThresholdULTool.cpp +Interactions/mitkCalculateGrayValueStatisticsTool.cpp +Interactions/mitkCalculateVolumetryTool.cpp +Interactions/mitkContourInteractor.cpp +Interactions/mitkContourTool.cpp +Interactions/mitkCorrectorTool2D.cpp +Interactions/mitkCreateSurfaceTool.cpp +Interactions/mitkDrawPaintbrushTool.cpp +Interactions/mitkErasePaintbrushTool.cpp +Interactions/mitkEraseRegionTool.cpp +Interactions/mitkExtrudedContourInteractor.cpp +Interactions/mitkFeedbackContourTool.cpp +Interactions/mitkFillRegionTool.cpp +Interactions/mitkPaintbrushTool.cpp +Interactions/mitkRegionGrow3DTool.cpp +Interactions/mitkRegionGrowingTool.cpp +Interactions/mitkSegmentationsProcessingTool.cpp +Interactions/mitkSetRegionTool.cpp +Interactions/mitkSegTool2D.cpp +Interactions/mitkSubtractContourTool.cpp +Rendering/mitkContourMapper2D.cpp +Rendering/mitkContourSetMapper2D.cpp +Rendering/mitkContourSetVtkMapper3D.cpp +Rendering/mitkContourVtkMapper3D.cpp +) diff --git a/Plugins/PluginList.cmake b/Plugins/PluginList.cmake index de27ac4b0d..67b5e41db5 100644 --- a/Plugins/PluginList.cmake +++ b/Plugins/PluginList.cmake @@ -1,40 +1,41 @@ # Plug-ins must be ordered according to their dependencies set(MITK_EXT_PLUGINS org.mitk.core.services:ON org.mitk.gui.common:ON org.mitk.planarfigure:ON org.mitk.core.ext:OFF org.mitk.core.jobs:OFF org.mitk.diffusionimaging:OFF org.mitk.gui.qt.application:ON org.mitk.gui.qt.coreapplication:OFF org.mitk.gui.qt.ext:OFF org.mitk.gui.qt.extapplication:OFF org.mitk.gui.qt.common:ON org.mitk.gui.qt.stdmultiwidgeteditor:ON org.mitk.gui.qt.common.legacy:OFF org.mitk.gui.qt.diffusionimagingapp:OFF org.mitk.gui.qt.datamanager:ON org.mitk.gui.qt.basicimageprocessing:OFF org.mitk.gui.qt.diffusionimaging:OFF org.mitk.gui.qt.dtiatlasapp:OFF org.mitk.gui.qt.examples:OFF org.mitk.gui.qt.examplesopencv:OFF org.mitk.gui.qt.igtexamples:OFF org.mitk.gui.qt.igttracking:OFF org.mitk.gui.qt.imagecropper:OFF org.mitk.gui.qt.imagenavigator:ON org.mitk.gui.qt.materialeditor:OFF org.mitk.gui.qt.measurementtoolbox:OFF + org.mitk.gui.qt.meshdecimation:OFF org.mitk.gui.qt.moviemaker:OFF org.mitk.gui.qt.pointsetinteraction:OFF org.mitk.gui.qt.python.console:OFF org.mitk.gui.qt.registration:OFF org.mitk.gui.qt.segmentation:OFF org.mitk.gui.qt.toftutorial:OFF org.mitk.gui.qt.tofutil:OFF org.mitk.gui.qt.ugvisualization:OFF org.mitk.gui.qt.volumevisualization:OFF -) \ No newline at end of file +) diff --git a/Plugins/org.mitk.gui.qt.common/src/QmitkAbstractView.cpp b/Plugins/org.mitk.gui.qt.common/src/QmitkAbstractView.cpp index 423053e073..c230739aae 100644 --- a/Plugins/org.mitk.gui.qt.common/src/QmitkAbstractView.cpp +++ b/Plugins/org.mitk.gui.qt.common/src/QmitkAbstractView.cpp @@ -1,561 +1,559 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkAbstractView.h" #include "QmitkDataNodeSelectionProvider.h" #include "internal/QmitkCommonActivator.h" #include "internal/QmitkDataNodeItemModel.h" // mitk Includes #include #include #include #include #include #include // berry Includes #include #include #include // CTK Includes #include // Qt Includes #include #include #include #include #include class QmitkAbstractViewPrivate { public: QmitkAbstractViewPrivate(QmitkAbstractView* qq) : q(qq) , m_PrefServiceTracker(QmitkCommonActivator::GetContext()) , m_DataStorageServiceTracker(QmitkCommonActivator::GetContext()) , m_Parent(0) , m_DataNodeItemModel(new QmitkDataNodeItemModel) , m_DataNodeSelectionModel(new QItemSelectionModel(m_DataNodeItemModel)) , m_InDataStorageChanged(false) { m_PrefServiceTracker.open(); m_DataStorageServiceTracker.open(); } ~QmitkAbstractViewPrivate() { delete m_DataNodeSelectionModel; delete m_DataNodeItemModel; m_PrefServiceTracker.close(); m_DataStorageServiceTracker.close(); } /** * Called when a DataStorage Add Event was thrown. Sets * m_InDataStorageChanged to true and calls NodeAdded afterwards. * \see m_InDataStorageChanged */ void NodeAddedProxy(const mitk::DataNode* node) { // garantuee no recursions when a new node event is thrown in NodeAdded() if(!m_InDataStorageChanged) { m_InDataStorageChanged = true; q->NodeAdded(node); q->DataStorageModified(); m_InDataStorageChanged = false; } } /** * Called when a DataStorage remove event was thrown. Sets * m_InDataStorageChanged to true and calls NodeRemoved afterwards. * \see m_InDataStorageChanged */ void NodeRemovedProxy(const mitk::DataNode* node) { // garantuee no recursions when a new node event is thrown in NodeAdded() if(!m_InDataStorageChanged) { m_InDataStorageChanged = true; q->NodeRemoved(node); q->DataStorageModified(); m_InDataStorageChanged = false; } } /** * Called when a DataStorage changed event was thrown. Sets * m_InDataStorageChanged to true and calls NodeChanged afterwards. * \see m_InDataStorageChanged */ void NodeChangedProxy(const mitk::DataNode* node) { // garantuee no recursions when a new node event is thrown in NodeAdded() if(!m_InDataStorageChanged) { m_InDataStorageChanged = true; q->NodeChanged(node); q->DataStorageModified(); m_InDataStorageChanged = false; } } /** - * reactions to selection events from data manager (and potential other senders) + * reactions to selection events from views */ void BlueBerrySelectionChanged(berry::IWorkbenchPart::Pointer sourcepart, berry::ISelection::ConstPointer selection) { - if(sourcepart.IsNull() || sourcepart->GetSite()->GetId() != "org.mitk.views.datamanager") + if(sourcepart.IsNull() || sourcepart.GetPointer() == static_cast(q)) return; mitk::DataNodeSelection::ConstPointer _DataNodeSelection = selection.Cast(); q->OnSelectionChanged(sourcepart, this->DataNodeSelectionToQList(_DataNodeSelection)); } /** * Converts a mitk::DataNodeSelection to a QList (possibly empty) */ QList DataNodeSelectionToQList(mitk::DataNodeSelection::ConstPointer currentSelection) const; QmitkAbstractView* const q; ctkServiceTracker m_PrefServiceTracker; ctkServiceTracker m_DataStorageServiceTracker; /** * Saves the parent of this view (this is the scrollarea created in CreatePartControl(void*) * \see CreatePartControl(void*) */ QWidget* m_Parent; /** * Holds the current selection (selection made by this View !!!) */ QmitkDataNodeSelectionProvider::Pointer m_SelectionProvider; /** * Holds a helper model for firing selection events. */ QmitkDataNodeItemModel* m_DataNodeItemModel; /** * The selection model for the QmitkDataNodeItemModel; */ QItemSelectionModel* m_DataNodeSelectionModel; /** * object to observe BlueBerry selections */ berry::ISelectionListener::Pointer m_BlueBerrySelectionListener; /** * Saves if this class is currently working on DataStorage changes. * This is a protector variable to avoid recursive calls on event listener functions. */ bool m_InDataStorageChanged; }; QmitkAbstractView::QmitkAbstractView() : d(new QmitkAbstractViewPrivate(this)) { } void QmitkAbstractView::CreatePartControl(void* parent) { // scrollArea QScrollArea* scrollArea = new QScrollArea; //QVBoxLayout* scrollAreaLayout = new QVBoxLayout(scrollArea); scrollArea->setFrameShadow(QFrame::Plain); scrollArea->setFrameShape(QFrame::NoFrame); scrollArea->setHorizontalScrollBarPolicy(Qt::ScrollBarAsNeeded); scrollArea->setVerticalScrollBarPolicy(Qt::ScrollBarAsNeeded); // m_Parent d->m_Parent = new QWidget; //m_Parent->setSizePolicy(QSizePolicy(QSizePolicy::MinimumExpanding, QSizePolicy::MinimumExpanding)); this->CreateQtPartControl(d->m_Parent); //scrollAreaLayout->addWidget(m_Parent); //scrollArea->setLayout(scrollAreaLayout); // set the widget now scrollArea->setWidgetResizable(true); scrollArea->setWidget(d->m_Parent); // add the scroll area to the real parent (the view tabbar) QWidget* parentQWidget = static_cast(parent); QVBoxLayout* parentLayout = new QVBoxLayout(parentQWidget); parentLayout->setMargin(0); parentLayout->setSpacing(0); parentLayout->addWidget(scrollArea); // finally set the layout containing the scroll area to the parent widget (= show it) parentQWidget->setLayout(parentLayout); this->AfterCreateQtPartControl(); } void QmitkAbstractView::AfterCreateQtPartControl() { this->SetSelectionProvider(); // REGISTER DATASTORAGE LISTENER this->GetDataStorage()->AddNodeEvent.AddListener( mitk::MessageDelegate1 ( d.data(), &QmitkAbstractViewPrivate::NodeAddedProxy ) ); this->GetDataStorage()->ChangedNodeEvent.AddListener( mitk::MessageDelegate1 ( d.data(), &QmitkAbstractViewPrivate::NodeChangedProxy ) ); this->GetDataStorage()->RemoveNodeEvent.AddListener( mitk::MessageDelegate1 ( d.data(), &QmitkAbstractViewPrivate::NodeRemovedProxy ) ); // REGISTER PREFERENCES LISTENER berry::IBerryPreferences::Pointer prefs = this->GetPreferences().Cast(); if(prefs.IsNotNull()) prefs->OnChanged.AddListener( berry::MessageDelegate1(this, &QmitkAbstractView::OnPreferencesChanged)); // REGISTER FOR WORKBENCH SELECTION EVENTS d->m_BlueBerrySelectionListener = berry::ISelectionListener::Pointer( new berry::SelectionChangedAdapter(d.data(), &QmitkAbstractViewPrivate::BlueBerrySelectionChanged)); - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ d->m_BlueBerrySelectionListener); + this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(d->m_BlueBerrySelectionListener); // EMULATE INITIAL SELECTION EVENTS // send the current selection berry::IWorkbenchPart::Pointer activePart = this->GetSite()->GetPage()->GetActivePart(); if (activePart.IsNotNull()) { this->OnSelectionChanged(activePart, this->GetCurrentSelection()); } // send preferences changed event this->OnPreferencesChanged(this->GetPreferences().Cast().GetPointer()); } QmitkAbstractView::~QmitkAbstractView() { this->Register(); this->GetDataStorage()->AddNodeEvent.RemoveListener( mitk::MessageDelegate1 ( d.data(), &QmitkAbstractViewPrivate::NodeAddedProxy ) ); this->GetDataStorage()->RemoveNodeEvent.RemoveListener( mitk::MessageDelegate1 ( d.data(), &QmitkAbstractViewPrivate::NodeRemovedProxy) ); this->GetDataStorage()->ChangedNodeEvent.RemoveListener( mitk::MessageDelegate1 ( d.data(), &QmitkAbstractViewPrivate::NodeChangedProxy ) ); berry::IBerryPreferences::Pointer prefs = this->GetPreferences().Cast(); if(prefs.IsNotNull()) { prefs->OnChanged.RemoveListener( berry::MessageDelegate1(this, &QmitkAbstractView::OnPreferencesChanged)); // flush the preferences here (disabled, everyone should flush them by themselves at the right moment) // prefs->Flush(); } // REMOVE SELECTION PROVIDER this->GetSite()->SetSelectionProvider(berry::ISelectionProvider::Pointer(NULL)); berry::ISelectionService* s = GetSite()->GetWorkbenchWindow()->GetSelectionService(); if(s) { s->RemovePostSelectionListener(d->m_BlueBerrySelectionListener); } this->UnRegister(false); } void QmitkAbstractView::SetSelectionProvider() { // REGISTER A SELECTION PROVIDER d->m_SelectionProvider = QmitkDataNodeSelectionProvider::Pointer(new QmitkDataNodeSelectionProvider); d->m_SelectionProvider->SetItemSelectionModel(GetDataNodeSelectionModel()); this->GetSite()->SetSelectionProvider(berry::ISelectionProvider::Pointer(d->m_SelectionProvider)); } QItemSelectionModel *QmitkAbstractView::GetDataNodeSelectionModel() const { return d->m_DataNodeSelectionModel; } void QmitkAbstractView::OnPreferencesChanged( const berry::IBerryPreferences* ) { } void QmitkAbstractView::DataStorageModified() { } void QmitkAbstractView::DataStorageChanged(mitk::IDataStorageReference::Pointer /*dsRef*/) { } mitk::IRenderWindowPart* QmitkAbstractView::GetRenderWindowPart( IRenderWindowPartStrategies strategies ) const { berry::IWorkbenchPage::Pointer page = this->GetSite()->GetPage(); // Return the active editor if it implements mitk::IRenderWindowPart mitk::IRenderWindowPart* renderPart = dynamic_cast(page->GetActiveEditor().GetPointer()); if (renderPart) return renderPart; // No suitable active editor found, check visible editors std::list editors = page->GetEditorReferences(); for (std::list::iterator i = editors.begin(); i != editors.end(); ++i) { berry::IWorkbenchPart::Pointer part = (*i)->GetPart(false); if (page->IsPartVisible(part)) { renderPart = dynamic_cast(part.GetPointer()); if (renderPart) return renderPart; } } // No suitable visible editor found, check visible views std::vector views = page->GetViewReferences(); for(std::vector::iterator i = views.begin(); i != views.end(); ++i) { berry::IWorkbenchPart::Pointer part = (*i)->GetPart(false); if (page->IsPartVisible(part)) { renderPart = dynamic_cast(part.GetPointer()); if (renderPart) return renderPart; } } // No strategies given if (strategies == NONE) return 0; mitk::DataStorageEditorInput::Pointer input(new mitk::DataStorageEditorInput(GetDataStorageReference())); bool activate = false; if(strategies & ACTIVATE) { activate = true; } berry::IEditorPart::Pointer editorPart; if(strategies & OPEN) { // This will create a default editor for the given input. If an editor // with that input is already open, the editor is brought to the front. editorPart = mitk::WorkbenchUtil::OpenEditor(page, input, activate); } else if (activate || (strategies & BRING_TO_FRONT)) { // check if a suitable editor is already opened editorPart = page->FindEditor(input); if (activate) { page->Activate(editorPart); } else { page->BringToTop(editorPart); } } return dynamic_cast(editorPart.GetPointer()); } void QmitkAbstractView::RequestRenderWindowUpdate(mitk::RenderingManager::RequestType requestType) { mitk::IRenderWindowPart* renderPart = this->GetRenderWindowPart(); if (renderPart == 0) return; if (mitk::IRenderingManager* renderingManager = renderPart->GetRenderingManager()) { renderingManager->RequestUpdateAll(requestType); } else { renderPart->RequestUpdate(requestType); } } void QmitkAbstractView::HandleException( const char* str, QWidget* parent, bool showDialog ) const { //itkGenericOutputMacro( << "Exception caught: " << str ); MITK_ERROR << str; if ( showDialog ) { QMessageBox::critical ( parent, "Exception caught!", str ); } } void QmitkAbstractView::HandleException( std::exception& e, QWidget* parent, bool showDialog ) const { HandleException( e.what(), parent, showDialog ); } void QmitkAbstractView::WaitCursorOn() { QApplication::setOverrideCursor( QCursor(Qt::WaitCursor) ); } void QmitkAbstractView::BusyCursorOn() { QApplication::setOverrideCursor( QCursor(Qt::BusyCursor) ); } void QmitkAbstractView::WaitCursorOff() { this->RestoreOverrideCursor(); } void QmitkAbstractView::BusyCursorOff() { this->RestoreOverrideCursor(); } void QmitkAbstractView::RestoreOverrideCursor() { QApplication::restoreOverrideCursor(); } berry::IPreferences::Pointer QmitkAbstractView::GetPreferences() const { berry::IPreferencesService* prefService = d->m_PrefServiceTracker.getService(); // const_cast workaround for bad programming: const uncorrectness this->GetViewSite() should be const std::string id = "/" + (const_cast(this))->GetViewSite()->GetId(); return prefService ? prefService->GetSystemPreferences()->Node(id): berry::IPreferences::Pointer(0); } mitk::DataStorage::Pointer QmitkAbstractView::GetDataStorage() const { mitk::IDataStorageService* dsService = d->m_DataStorageServiceTracker.getService(); if (dsService != 0) { return dsService->GetDataStorage()->GetDataStorage(); } return 0; } mitk::IDataStorageReference::Pointer QmitkAbstractView::GetDataStorageReference() const { mitk::IDataStorageService* dsService = d->m_DataStorageServiceTracker.getService(); if (dsService != 0) { return dsService->GetDataStorage(); } return mitk::IDataStorageReference::Pointer(0); } QList QmitkAbstractView::GetCurrentSelection() const { berry::ISelection::ConstPointer selection( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection()); - // buffer for the data manager selection mitk::DataNodeSelection::ConstPointer currentSelection = selection.Cast(); return d->DataNodeSelectionToQList(currentSelection); } QList QmitkAbstractView::GetDataManagerSelection() const { berry::ISelection::ConstPointer selection( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); - // buffer for the data manager selection mitk::DataNodeSelection::ConstPointer currentSelection = selection.Cast(); return d->DataNodeSelectionToQList(currentSelection); } void QmitkAbstractView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& /*nodes*/) { } QList QmitkAbstractViewPrivate::DataNodeSelectionToQList(mitk::DataNodeSelection::ConstPointer currentSelection) const { QList selectedNodes; if(currentSelection.IsNull()) return selectedNodes; mitk::DataNodeObject::Pointer _DataNodeObject; mitk::DataNode::Pointer _DataNode; for(mitk::DataNodeSelection::iterator it = currentSelection->Begin(); it != currentSelection->End(); ++it) { _DataNodeObject = it->Cast(); if(_DataNodeObject.IsNotNull()) { _DataNode = _DataNodeObject->GetDataNode(); if(_DataNode.IsNotNull()) selectedNodes << _DataNode; } } return selectedNodes; } void QmitkAbstractView::NodeAdded( const mitk::DataNode* /*node*/ ) { } void QmitkAbstractView::NodeRemoved( const mitk::DataNode* /*node*/ ) { } void QmitkAbstractView::NodeChanged( const mitk::DataNode* /*node*/ ) { } void QmitkAbstractView::FireNodeSelected( mitk::DataNode::Pointer node ) { QList nodes; nodes << node; this->FireNodesSelected(nodes); } void QmitkAbstractView::FireNodesSelected( const QList& nodes ) { if (nodes.empty()) { d->m_DataNodeSelectionModel->clearSelection(); d->m_DataNodeItemModel->clear(); return; } // The helper data node model is just used for sending selection events. // We add the to be selected nodes and set the selection range to everything. d->m_DataNodeItemModel->clear(); foreach(mitk::DataNode::Pointer node, nodes) { d->m_DataNodeItemModel->AddDataNode(node); } d->m_DataNodeSelectionModel->select(QItemSelection(d->m_DataNodeItemModel->index(0,0), d->m_DataNodeItemModel->index(nodes.size(), 0)), QItemSelectionModel::ClearAndSelect); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkBrainNetworkAnalysis.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkBrainNetworkAnalysis.dox index 47b688052a..81963a008a 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkBrainNetworkAnalysis.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkBrainNetworkAnalysis.dox @@ -1,61 +1,69 @@ /** \page org_brainnetworkanalysis The Brain Network Analysis Module \image html QmitkBrainNetworkAnalysisViewIcon_64.png "Icon of the Module" \section QmitkBrainNetworkAnalysisUserManualSummary Summary This module can be used to create a network from a parcellation and a fiber image as well as to calculate and display network statistics. This document will tell you how to use this module, but it is assumed that you already know how to use MITK in general. Please see \ref QmitkBrainNetworkAnalysisUserManualDetails for more detailed information on usage and supported filters. If you encounter problems using the module, please have a look at the \ref QmitkBrainNetworkAnalysisUserManualTrouble page. \section QmitkBrainNetworkAnalysisUserManualDetails Details Manual sections: - \ref QmitkBrainNetworkAnalysisUserManualOverview - \ref QmitkBrainNetworkAnalysisUserManualUsage - \ref QmitkBrainNetworkAnalysisUserManualTrouble \section QmitkBrainNetworkAnalysisUserManualOverview Overview This module is currently under heavy development and as such the interface as well as the capabilities are likely to change significantly between different versions. This documentation describes the features of this current version. \image html QmitkBrainNetworkAnalysisInterface.png "The interface" \section QmitkBrainNetworkAnalysisUserManualUsage Usage To create a network select first a parcellation of the brain (e.g. as provided by freesurfer ) by CTRL+Leftclick and secondly a fiber image ( as created using tractography module). Then click on the "Create Network" button. To calculate network statistics select a network in the datamanager. At this time the following statistics are calculated for the entire network:
  • The number of vertices in the network
  • The number of edges in the network
  • The number of edges which have the same vertex as beginning and end point
  • The average degree of the nodes in the network
  • The connection density the network (the number of edges divided by the number of possible edges)
  • The unweighted efficiency of the network ( 1 divided by average path length, this is zero for disconnected graphs) +
  • The global clustering
Furthermore some statistics are calculated on a per node basis and displayed as histograms:
  • The degree of each node
  • The (unweighted) betweenness centrality of each node
  • The spread of shortest paths between each pair of nodes (For disconnected graphs the shortest paths with infinite length are omitted for readability)
+Additionally you have the option to create artificial networks, for testing purposes. Currently choices are: +
    +
  • A regular lattice, where each node is placed in a cubic pattern and only connected to its neighbours +
  • A heterogenic sphere, where one node is placed in the center and connected to all nodes on the shell +
  • A random network, where nodes are randomly placed on a spherical shell and randomly connected +
+ \section QmitkBrainNetworkAnalysisUserManualTrouble Troubleshooting No known problems. All other problems.
Please report to the MITK mailing list. See http://www.mitk.org/wiki/Mailinglist on how to do this. */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkBrainNetworkAnalysisInterface.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkBrainNetworkAnalysisInterface.png index f6ef05bdb9..40d69844a5 100644 Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkBrainNetworkAnalysisInterface.png and b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkBrainNetworkAnalysisInterface.png differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingUserManual.dox index 252dc1d22c..d39b26362c 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkDiffusionImagingUserManual.dox @@ -1,124 +1,122 @@ /** \bundlemainpage{org_diffusion} MITK Diffusion Imaging (MITK-DI) This module provides means to diffusion weighted image reconstruction, visualization and quantification. Diffusion tensors as well as different q-ball reconstruction schemes are supported. Q-ball imaging aims at recovering more detailed information about the orientations of fibers from diffusion MRI measurements and, in particular, to resolve the orientations of crossing fibers. Available sections: - \ref QmitkDiffusionImagingUserManualIssues - \ref QmitkDiffusionImagingUserManualPreprocessing - \ref QmitkDiffusionImagingUserManualTensorReconstruction - \ref QmitkDiffusionImagingUserManualQBallReconstruction - \ref QmitkDiffusionImagingUserManualDicomImport - \ref QmitkDiffusionImagingUserManualQuantification - \ref QmitkDiffusionImagingUserManualVisualizationSettings - \ref QmitkDiffusionImagingUserManualReferences - \ref QmitkDiffusionImagingUserManualTechnicalDetail - \ref QmitkDiffusionImagingUserManualSubManuals -\image html overview.png The MITK Diffusion Imaging Module - \section QmitkDiffusionImagingUserManualIssues Known Issues \li Dicom Import: The dicom import has so far only been implemented for Siemens dicom images. MITK-DI is capable of reading the nrrd format, which is documented elsewhere [1, 2]. These files can be created by combining the raw image data with a corresponding textual header file. The file extension should be changed from *.nrrd to *.dwi or from *.nhdr to *.hdwi respectively in order to let MITK-DI recognize the diffusion related header information provided in the files. \section QmitkDiffusionImagingUserManualPreprocessing Preprocessing -The preprocessing view gives an overview over the important features of a diffusion weighted image like the number of gradient directions, b-value and the measurement frame. Additionally it allows the extraction of the B0 image and the generation of a binary brain mask. The image volume can be modified by applying a new mesurement frame, which is useful if the measurement frame is not set correctly in the image header, or by averaging redundant gradient directions. +The preprocessing view gives an overview over the important features of a diffusion weighted image like the number of gradient directions, b-value and the measurement frame. Additionally it allows the extraction of the B0 image, reduction of gradient directions and the generation of a binary brain mask. The image volume can be modified by applying a new mesurement frame, which is useful if the measurement frame is not set correctly in the image header, or by averaging redundant gradient directions. \image html prepro1.png Preprocessing \section QmitkDiffusionImagingUserManualTensorReconstruction Tensor Reconstruction The tensor reconstruction view allows ITK based tensor reconstruction [3]. The advanced settings for ITK reconstruction let you configure a manual threshold on the non-diffusion weighted image. All voxels below this threshold will not be reconstructed and left blank. It is also possible to check for negative eigenvalues. The according voxels are also left blank. \image html tensor1.png ITK tensor reconstruction A few seconds (depending on the image size) after the reconstruction button is hit, a colored image should appear in the main window. \image html tensor4.png Tensor image after reconstruction The view also allows the generation of artificial diffusion weighted or Q-Ball images from the selected tensor image. The ODFs of the Q-Ball image are directly initialized from the tensor values and afterwards normalized. The diffusion weighted image is estimated using the l2-norm image of the tensor image as B0. The gradient images are afterwards generated using the standard tensor equation. \section QmitkDiffusionImagingUserManualQBallReconstruction Q-Ball Reconstruction The q-ball reonstruction bundle implements a variety of reconstruction methods. The different reconstruction methods are described in the following: \li Numerical: The original, numerical q-ball reconstruction presented by Tuch et al. [5] \li Standard (SH): Descoteaux's reconstruction based on spherical harmonic basis functions [6] \li Solid Angle (SH): Aganj's reconstruction with solid angle consideration [7] \li ADC-profile only: The ADC-profile reconstructed with spherical harmonic basis functions \li Raw signal only: The raw signal reconstructed with spherical harmonic basis functions \image html qballs1.png The q-ball resonstruction view B0 threshold works the same as in tensor reconstruction. The maximum l-level configures the size of the spherical harmonics basis. Larger l-values (e.g. l=8) allow higher levels of detail, lower levels are more stable against noise (e.g. l=4). Lambda is a regularisation parameter. Set it to 0 for no regularisation. lambda = 0.006 has proven to be a stable choice under various settings. \image html qballs2.png Advanced q-ball reconstruction settings This is how a q-ball image should initially look after reconstruction. Standard q-balls feature a relatively low GFA and thus appear rather dark. Adjust the level-window to solve this. \image html qballs3.png q-ball image after reconstruction \section QmitkDiffusionImagingUserManualDicomImport Dicom Import The dicom import does not cover all hardware manufacturers but only Siemens dicom images. MITK-DI is also capable of reading the nrrd format, which is documented elsewhere [1, 2]. These files can be created by combining the raw image data with a corresponding textual header file. The file extension should be changed from *.nrrd to *.dwi or from *.nhdr to *.hdwi respectively in order to let MITK-DI recognize the diffusion related header information provided in the files. In case your dicom images are readable by MITK-DI, select one or more input dicom folders and click import. Each input folder must only contain DICOM-images that can be combined into one vector-valued 3D output volume. Different patients must be loaded from different input-folders. The folders must not contain other acquisitions (e.g. T1,T2,localizer). In case many imports are performed at once, it is recommended to set the the optional output folder argument. This prevents the images from being kept in memory. \image html dicom1.png Dicom import The option "Average duplicate gradients" accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "blur radius" > 0 is configured. \section QmitkDiffusionImagingUserManualQuantification Quantification The quantification view allows the derivation of different scalar anisotropy measures for the reconstructed tensors (Fractional Anisotropy, Relative Anisotropy, Axial Diffusivity, Radial Diffusivity) or q-balls (Generalized Fractional Anisotropy). \image html quantification.png Anisotropy quantification \section QmitkDiffusionImagingUserManualVisualizationSettings ODF Visualization Setting In this small view, the visualization of ODFs and diffusion images can be configured. Depending on the selected image in the data storage, different options are shown here. For tensor or q-ball images, the visibility of glyphs in the different render windows (T)ransversal, (S)agittal, and (C)oronal can be configured here. The maximal number of glyphs to display can also be configured here for. This is usefull to keep the system response time during rendering feasible. The other options configure normalization and scaling of the glyphs. In diffusion images, a slider lets you choose the desired image channel from the vector of images (each gradient direction one image) for rendering. Furthermore reinit can be performed and texture interpolation toggled. This is how a visualization with activated glyphs should look like: \image html visualization3.png Q-ball image with ODF glyph visibility toggled ON \section QmitkDiffusionImagingUserManualReferences References 1. http://teem.sourceforge.net/nrrd/format.html 2. http://www.cmake.org/Wiki/Getting_Started_with_the_NRRD_Format 3. C.F.Westin, S.E.Maier, H.Mamata, A.Nabavi, F.A.Jolesz, R.Kikinis, "Processing and visualization for Diffusion tensor MRI", Medical image Analysis, 2002, pp 93-108 5. Tuch, D.S., 2004. Q-ball imaging. Magn Reson Med 52, 1358-1372. 6. Descoteaux, M., Angelino, E., Fitzgibbons, S., Deriche, R., 2007. Regularized, fast, and robust analytical Q-ball imaging. Magn Reson Med 58, 497-510. 7. Aganj, I., Lenglet, C., Sapiro, G., 2009. ODF reconstruction in q-ball imaging with solid angle consideration. Proceedings of the Sixth IEEE International Symposium on Biomedical Imaging Boston, MA. 8. Goh, A., Lenglet, C., Thompson, P.M., Vidal, R., 2009. Estimating Orientation Distribution Functions with Probability Density Constraints and Spatial Regularity. Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv LNCS 5761, 877 ff. \section QmitkDiffusionImagingUserManualTechnicalDetail Technical Information for Developers The diffusion imaging module uses additional properties beside the ones in use in other modules, for further information see \subpage DiffusionImagingPropertiesPage . \section QmitkDiffusionImagingUserManualSubManuals Manuals of componentes The MITK Diffusion tools consist of further components, which have their own documentation, see: \li \subpage org_fiberprocessing \li \subpage org_gibbstracking \li \subpage org_odfdetails \li \subpage org_pvanalysis \li \subpage screenshot_maker \li \subpage org_stochastictracking \li \subpage org_ivim \li \subpage org_brainnetworkanalysis - + \li \subpage org_tractbasedspatialstatistics */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox index a93e08af92..9c1e982b69 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkFiberProcessingViewUserManual.dox @@ -1,25 +1,23 @@ /** \page org_fiberprocessing Fiber Processing View This view provides everything needed to process fiber bundles. -Available sections: - - \ref QmitkFiberProcessingUserManualFiberManpulation - - \ref QmitkFiberProcessingUserManualFiberProcessing - \image html fiberprocessing.png The Fiber Processing View -\section QmitkFiberProcessingUserManualFiberManpulation Fiber Bundle Manipulation - Fiber extraction: -Place ROIs in the 2D render widgets (cricles or polygons) and extract fibers from the bundle that pass through these ROIs by selecting the according ROI and fiber bundle in the datamanger and starting the extraction. The ROIs can be combined via logical operations. All fibers that pass through the thus generated composite ROI are extracted. +Place ROIs in the 2D render widgets (cricles or polygons) and extract fibers from the bundle that pass through these ROIs by selecting the according ROI and fiber bundle in the datamanger and starting the extraction. The ROIs can be combined via logical operations. All fibers that pass through the thus generated composite ROI are extracted. The extraction can also be performed using 3D ROIs represented as closed surface meshes. In this extraction method, the logical operations are not implemented at the moment. -\section QmitkFiberProcessingUserManualFiberProcessing Generation of additional information from fiber bundles +The selected fiber bundle can be smoothed by interpolating the fiber points using Kochanek splines with the specified number of points per cm. +If a float image with pixel values between 0 and 1 is selcted, the fiber bundle can be colored according to the pixel values. + +Generation of additional data from fiber bundles: \li Tract density image: generate a 2D heatmap from a fiber bundle \li Binary envelope: generate a binary image from a fiber bundle \li Fiber bundle image: generate a 2D rgba image representation of the fiber bundle \li Fiber endings image: generate a 2D binary image showing the locations of fiber endpoints \li Fiber endings pointset: generate a poinset containing the locations of fiber endpoints + */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox index e4d56d33b5..433c4e7775 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkGibbsTrackingViewUserManual.dox @@ -1,40 +1,44 @@ /** \page org_gibbstracking Gibbs Tracking View This view provides the user interface for the Gibbs Tracking algorithm, a global fiber tracking algorithm, originally proposed by Reisert et.al. [1]. Available sections: - \ref QmitkGibbsTrackingUserManualInputData - \ref QmitkGibbsTrackingUserManualParameters - \ref QmitkGibbsTrackingUserManualTrackingSurveillance - \ref QmitkGibbsTrackingUserManualReferences \image html gibbstrackingview.png The Gibbs Tracking View \section QmitkGibbsTrackingUserManualInputData Input Data Mandatory Input: \li One Q-Ball image selected in the datamanager Optional Input: \li Mask Image: Float image used as probability mask for the generation of fiber segments. Usually used as binary brain mask to reduce the searchspace of the algorithm and to avoid fibers resulting from noise outside of the brain. -\li GFA Image: Float image used to automatically determine the "particle weight" parameter. \section QmitkGibbsTrackingUserManualParameters Q-Ball Reconstruction \li Number of iterations: More iterations causes the algorithm to be more stable but also to take longer to finish the tracking. Rcommended: 10â·-10â¹ iterations. \li Particle length/width/weight controlling the contribution of each particle to the model M \li Start and end temperature controlling how fast the process reaches a stable state. (usually no change needed) \li Weighting between the internal (affinity of the model to long and straigt fibers) and external energy (affinity of the model towards the data). (usually no change needed). -\li Minimum fiber length constraint. Fibers containing less segments are discarded after the tracking. (usually no change needed) +\li Minimum fiber length constraint (in mm). Shorter fibers are discarded after the tracking. + +The automatic selection of parameters for the particle length/width and weight are determined directly from the input image using information about the image spacing and GFA. + +\image html gibbstrackingviewadvanced.png Advanced Tracking Parameters \section QmitkGibbsTrackingUserManualTrackingSurveillance Surveilance of the tracking process -Once started, the tracking can be monitored via the textual output that informs about the tracking progress and several stats of the current state of the algorithm. If enabled, the intermediate tracking results are displayed in the renderwindows each second. This live visualization should usually be disabled for performance reasons. It can be turned on and off during the tracking process via the according checkbox. +Once started, the tracking can be monitored via the textual output that informs about the tracking progress and several stats of the current state of the algorithm. +If enabled, the intermediate tracking results are displayed in the renderwindows each second. This live visualization should usually be disabled for performance reasons. It can be turned on and off during the tracking process via the according checkbox. The button next to this checkbox allows the visualization of only the next iteration step. \section QmitkGibbsTrackingUserManualReferences References [1] Reisert, M., Mader, I., Anastasopoulos, C., Weigel, M., Schnell, S., Kiselev, V.: Global fiber reconstruction becomes practical. Neuroimage 54 (2011) 955-962 */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox index e7098f064f..7885ebd5dc 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkOdfDetailsViewUserManual.dox @@ -1,11 +1,8 @@ /** \page org_odfdetails ODF Details View -This view provides detailed information about the orentation distribution function at the current crosshair position (if a Q-Ball image is selected). A visualization of the ODF as well as the ODF values and according statistical information are displayed. +This view provides detailed information about the orentation distribution function at the current crosshair position (if a Tensor/Q-Ball image is selected). A visualization of the ODF as well as statistical information are displayed. \image html odfdetails.png The Gibbs Tracking View -\section QmitkOdfDetailsUserManualInputData Issues -At the moment this view can opnly process Q-Ball images but not tensor images. Also the normalization properties etc. of the image as well as the correct rotation of the ODF are currently not incorporated into the views visualization. - */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox index 7f899fc34a..7573738c5e 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkStochasticTrackingViewUserManual.dox @@ -1,36 +1,31 @@ /** \page org_stochastictracking Stochastic Tracking View This view provides the user interface for the Stochastic Fibertracking algorithm, proposed by Ngo [1]. Available sections: - \ref QmitkStochasticTrackingUserManualInputData - \ref QmitkStochasticTrackingUserManualParameters - \ref QmitkStochasticTrackingUserManualReferences \image html stochastictrackingview.png Stochastic Tracking View -\image html segmentationview.png Segmentation View to define ROIs - \section QmitkStochasticTrackingUserManualInputData Input Data Mandatory Input: -\li For a successful execution of the stochastic tractography filter, a DWI input and a binary image defining the desired ROI are required. The ROI serves as the origin from where on the fibers are beeing tracked. Both, DWI and ROI data can be imported via drag nÕ drop or via the opening dialog box provided by MITK. Alternatively, the segmentation view offers tools for generating ROI data. \li One DWI Image image selected in the datamanager \li One or more ROIs selected in the datamanager +For a successful execution of the stochastic tractography filter, a DWI input and a binary image defining the desired ROI are required. The ROI serves as the origin from where on the fibers are beeing tracked. To generate the seed ROI the segmentation view in the quantification perspective can be used or a binary image can be loaded. \section QmitkStochasticTrackingUserManualParameters Input Parameters - -\li Parameters such as max. tract length (Tract_len), number of total tracts per voxel (TotalTracts) and likelihood cache size in MB (Lkhd chache) are individually set by the user. - +\li Parameters such as max. tract length, number of seeds per voxel and likelihood cache size in MB can be controlled individually. \li After successfully setting necessary Input and Parameter, pressing the command button executes the algorithm. - \section QmitkStochasticTrackingUserManualReferences References [1] Tri M. Ngo, Polina Golland, and Tri M. Ngo. A stochastic tractography system and applications, 2007 */ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkTbssViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkTbssViewUserManual.dox index e213b09d22..26b49bbb0a 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkTbssViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/QmitkTbssViewUserManual.dox @@ -1,61 +1,59 @@ /** -\bundlemainpage{org.mitk.views.tractbasedspatialstatistics} The TBSS Module +\page org_tractbasedspatialstatistics The TBSS Module \image html tbss.png "Icon of the Module" \section QmitkTractbasedSpatialStatistics Summary This module can be used to locally explore data resulting from preprocessing with the TBSS module of FSL This document will tell you how to use this module, but it is assumed that you already know how to use MITK in general and how to work with the TBSS module of FSL. If you encounter problems using the module, please have a look at the \ref QmitkTractbasedSpatialStatisticsUserManualTrouble page. Sections: - \ref QmitkTractbasedSpatialStatisticsUserManualOverview - \ref QmitkTractbasedSpatialStatisticsUserManualFSLImport - \ref QmitkTractbasedSpatialStatisticsUserManualRois - \ref QmitkTractbasedSpatialStatisticsUserManualProfiles - \ref QmitkTractbasedSpatialStatisticsUserManualTroubleshooting - \ref QmitkTractbasedSpatialStatisticsUserManualReferences \section QmitkTractbasedSpatialStatisticsUserManualOverview Overview This module is currently under development and as such the interface as well as the capabilities are likely to change significantly between different versions. This documentation describes the features of this current version. \section QmitkTractbasedSpatialStatisticsUserManualFSLImport FSL Import The FSL import allows to import data that has been preprocessed by FSL. FSL creates output images that typically have names like all_FA_skeletonized.nii.gz that are 4-dimensional images that contain registered images of all subjects. By loading this 4D image into the datamanager and listing the groups with the correct number of subjects, in the order of occurrence in the 4D image, in the TBSS-View using the Add button and clicking the import subject data a TBSS file is created that contains all the information needed for tract analysis. The diffusion measure of the image can be set as well. \image html fslimport.png "FSL Import" \section QmitkTractbasedSpatialStatisticsUserManualRois Regions of Interest (ROIs) To create a ROI the mean FA skeleton (typically called mean_FA_skeleton.nii.gz) that is created by FSL should be loaded in to the datamanager and selected. By using the Pointlistwidget points should be set on the skeleton (make sure to select points with relatively high FA values). Points are set by first selecting the button with the '+' and than shift-leftclick in the image. When the correct image is selected in the datamanager the Create ROI button is enabled. Clicking this will create a region of interest that passes through the previously selected points. The roi appears in the datamanager. Before doing so, the name of the roi and the information on the structure on which the ROI lies can be set. This will be saved as extra information in the roi-image. Before the ROI is calculated, a pop-up window will ask the user to provide a threshold value. This should be the same threshold that was previously used in FSL to create a binary mask of the FA skeleton. When this is not done correctly, the region of interest will possible contain zero-valued voxels. \image html tbssRoi.png "Regions of Interest (ROIs)" \section QmitkTractbasedSpatialStatisticsUserManualProfiles y selecting a tbss image with group information and a region of interest image (as was created in a previous stap). A profile plot is drawn in the plot canvas. By clicking in the graph the crosshairs jump to the corresponding location in the image. \image html profiles.png "Profile plots" \section QmitkTractbasedSpatialStatisticsUserManualTroubleshooting Troubleshooting -No known problems. - -All other problems.
Please report to the MITK mailing list. See http://www.mitk.org/wiki/Mailinglist on how to do this. \section QmitkTractbasedSpatialStatisticsUserManualReferences References 1. S.M. Smith, M. Jenkinson, H. Johansen-Berg, D. Rueckert, T.E. Nichols, C.E. Mackay, K.E. Watkins, O. Ciccarelli, M.Z. Cader, P.M. Matthews, and T.E.J. Behrens. Tract-based spatial statistics: Voxelwise analysis of multi-subject diffusion data. NeuroImage, 31:1487-1505, 2006. -2. S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004. \ No newline at end of file +2. S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-219, 2004. +*/ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/fiberprocessing.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/fiberprocessing.png index 595de7ff23..bc8e88b655 100644 Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/fiberprocessing.png and b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/fiberprocessing.png differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/gibbstrackingview.png b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/gibbstrackingview.png index 3e20911bed..e30a8b2059 100644 Binary files a/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/gibbstrackingview.png and b/Plugins/org.mitk.gui.qt.diffusionimaging/documentation/UserManual/gibbstrackingview.png differ diff --git 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b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkODFDetailsWidget.cpp index 3cc2bbfd30..faf92ede4a 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkODFDetailsWidget.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/QmitkODFDetailsWidget.cpp @@ -1,64 +1,64 @@ /*========================================================================= Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkODFDetailsWidget.h" #include QmitkODFDetailsWidget::QmitkODFDetailsWidget( QWidget * parent ) : QmitkPlotWidget(parent) { m_Plot->setCanvasLineWidth(0); m_Plot->setMargin(0); QwtLinearScaleEngine* scale = new QwtLinearScaleEngine(); m_Plot->setAxisScaleEngine(0, scale); m_Plot->setAxisScale ( 0, -0.5, 0.5 ); } QmitkODFDetailsWidget::~QmitkODFDetailsWidget() { } void QmitkODFDetailsWidget::SetParameters( itk::OrientationDistributionFunction odf ) { this->Clear(); std::vector xVals; std::vector yVals; - float max = itk::NumericTraits::min(); + float max = itk::NumericTraits::NonpositiveMin(); float min = itk::NumericTraits::max(); for (int i=0; imax) max = odf[i]; if (odf[i]0) m_Plot->setAxisScale ( 0, 0, max ); else m_Plot->setAxisScale ( 0, min, max ); int curveId = this->InsertCurve( "ODF Values" ); this->SetCurveData( curveId, xVals, yVals ); this->SetCurvePen( curveId, QPen(Qt::blue, 0.5, Qt::SolidLine, Qt::RoundCap, Qt::RoundJoin) ); QwtLegend* legend = new QwtLegend(); //m_Plot->insertLegend(legend, QwtPlot::BottomLegend); this->Replot(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkBrainNetworkAnalysisView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkBrainNetworkAnalysisView.cpp index e8e6630bcb..bf4b45eab5 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkBrainNetworkAnalysisView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkBrainNetworkAnalysisView.cpp @@ -1,549 +1,678 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ // ####### Blueberry includes ####### #include #include // ####### Qmitk includes ####### #include "QmitkBrainNetworkAnalysisView.h" #include "QmitkStdMultiWidget.h" // ####### Qt includes ####### #include // ####### ITK includes ####### #include // ####### MITK includes ####### #include #include "mitkConnectomicsSyntheticNetworkGenerator.h" #include "mitkConnectomicsSimulatedAnnealingManager.h" #include "mitkConnectomicsSimulatedAnnealingPermutationModularity.h" #include "mitkConnectomicsSimulatedAnnealingCostFunctionModularity.h" // Includes for image casting between ITK and MITK #include "mitkImageCast.h" #include "mitkITKImageImport.h" #include "mitkImageAccessByItk.h" const std::string QmitkBrainNetworkAnalysisView::VIEW_ID = "org.mitk.views.brainnetworkanalysis"; QmitkBrainNetworkAnalysisView::QmitkBrainNetworkAnalysisView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_ConnectomicsNetworkCreator( mitk::ConnectomicsNetworkCreator::New() ) , m_demomode( false ) , m_currentIndex( 0 ) { } QmitkBrainNetworkAnalysisView::~QmitkBrainNetworkAnalysisView() { } void QmitkBrainNetworkAnalysisView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkBrainNetworkAnalysisViewControls; m_Controls->setupUi( parent ); QObject::connect( m_Controls->convertToRGBAImagePushButton, SIGNAL(clicked()), this, SLOT(OnConvertToRGBAImagePushButtonClicked()) ); QObject::connect( m_Controls->networkifyPushButton, SIGNAL(clicked()), this, SLOT(OnNetworkifyPushButtonClicked()) ); QObject::connect( m_Controls->syntheticNetworkCreationPushButton, SIGNAL(clicked()), this, SLOT(OnSyntheticNetworkCreationPushButtonClicked()) ); QObject::connect( (QObject*)( m_Controls->syntheticNetworkComboBox ), SIGNAL(currentIndexChanged (int)), this, SLOT(OnSyntheticNetworkComboBoxCurrentIndexChanged(int)) ); QObject::connect( (QObject*)( m_Controls->modularizePushButton ), SIGNAL(clicked()), this, SLOT(OnModularizePushButtonClicked()) ); } // GUI is different for developer and demo mode m_demomode = false; if( m_demomode ) { this->m_Controls->convertToRGBAImagePushButton->hide(); this->m_Controls->networkifyPushButton->show(); this->m_Controls->networkifyPushButton->setText( "Create Network" ); this->m_Controls->modularizePushButton->hide(); this->m_Controls->syntheticNetworkOptionsGroupBox->show(); //--------------------------- fill comboBox--------------------------- this->m_Controls->syntheticNetworkComboBox->insertItem(0,"Regular lattice"); this->m_Controls->syntheticNetworkComboBox->insertItem(1,"Heterogenic sphere"); this->m_Controls->syntheticNetworkComboBox->insertItem(2,"Random network"); } else { this->m_Controls->convertToRGBAImagePushButton->show(); this->m_Controls->networkifyPushButton->show(); this->m_Controls->networkifyPushButton->setText( "Networkify" ); this->m_Controls->modularizePushButton->show(); this->m_Controls->syntheticNetworkOptionsGroupBox->show(); //--------------------------- fill comboBox--------------------------- this->m_Controls->syntheticNetworkComboBox->insertItem(0,"Regular lattice"); this->m_Controls->syntheticNetworkComboBox->insertItem(1,"Heterogenic sphere"); this->m_Controls->syntheticNetworkComboBox->insertItem(2,"Random network"); this->m_Controls->syntheticNetworkComboBox->insertItem(3,"Scale free network"); this->m_Controls->syntheticNetworkComboBox->insertItem(4,"Small world network"); } + + this->WipeDisplay(); } void QmitkBrainNetworkAnalysisView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkBrainNetworkAnalysisView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkBrainNetworkAnalysisView::WipeDisplay() { + m_Controls->lblWarning->setVisible( true ); + m_Controls->inputImageOneNameLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH ); + m_Controls->inputImageOneNameLabel->setVisible( false ); + m_Controls->inputImageOneLabel->setVisible( false ); + m_Controls->inputImageTwoNameLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH ); + m_Controls->inputImageTwoNameLabel->setVisible( false ); + m_Controls->inputImageTwoLabel->setVisible( false ); m_Controls->numberOfVerticesLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH ); m_Controls->numberOfEdgesLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH ); m_Controls->numberOfSelfLoopsLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH ); m_Controls->averageDegreeLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH ); m_Controls->connectionDensityLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH ); m_Controls->efficiencyLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH ); m_Controls->globalClusteringLabel->setText( mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_DASH ); m_Controls->betweennessNetworkHistogramCanvas->SetHistogram( NULL ); m_Controls->degreeNetworkHistogramCanvas->SetHistogram( NULL ); m_Controls->shortestPathNetworkHistogramCanvas->SetHistogram( NULL ); m_Controls->betweennessNetworkHistogramCanvas->update(); m_Controls->degreeNetworkHistogramCanvas->update(); m_Controls->shortestPathNetworkHistogramCanvas->update(); + m_Controls->betweennessNetworkHistogramCanvas->Clear(); + m_Controls->degreeNetworkHistogramCanvas->Clear(); + m_Controls->shortestPathNetworkHistogramCanvas->Clear(); + m_Controls->betweennessNetworkHistogramCanvas->Replot(); + m_Controls->degreeNetworkHistogramCanvas->Replot(); + m_Controls->shortestPathNetworkHistogramCanvas->Replot(); } void QmitkBrainNetworkAnalysisView::OnSelectionChanged( std::vector nodes ) { this->WipeDisplay(); + // Valid options are either + // 1 image (parcellation) + // + // 1 image (parcellation) + // 1 fiber bundle + // + // 1 network + if( nodes.size() > 2 ) + { + return; + } + + bool alreadyFiberBundleSelected( false ), alreadyImageSelected( false ), currentFormatUnknown( true ); // iterate all selected objects, adjust warning visibility for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; + currentFormatUnknown = true; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { + currentFormatUnknown = false; + if( alreadyImageSelected ) + { + this->WipeDisplay(); + return; + } + alreadyImageSelected = true; m_Controls->lblWarning->setVisible( false ); - return; + m_Controls->inputImageOneNameLabel->setText(node->GetName().c_str()); + m_Controls->inputImageOneNameLabel->setVisible( true ); + m_Controls->inputImageOneLabel->setVisible( true ); } + if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { + currentFormatUnknown = false; + // a fiber bundle has to be in conjunction with a parcellation + if( nodes.size() != 2 || alreadyFiberBundleSelected ) + { + this->WipeDisplay(); + return; + } + alreadyFiberBundleSelected = true; + m_Controls->lblWarning->setVisible( false ); + m_Controls->inputImageTwoNameLabel->setText(node->GetName().c_str()); + m_Controls->inputImageTwoNameLabel->setVisible( true ); + m_Controls->inputImageTwoLabel->setVisible( true ); + } + + { // network section mitk::ConnectomicsNetwork* network = dynamic_cast( node->GetData() ); if( node.IsNotNull() && network ) { + currentFormatUnknown = false; + if( nodes.size() != 1 ) + { + // only valid option is a single network + this->WipeDisplay(); + return; + } m_Controls->lblWarning->setVisible( false ); + m_Controls->inputImageOneNameLabel->setText(node->GetName().c_str()); + m_Controls->inputImageOneNameLabel->setVisible( true ); + m_Controls->inputImageOneLabel->setVisible( true ); int noVertices = network->GetNumberOfVertices(); int noEdges = network->GetNumberOfEdges(); int noSelfLoops = network->GetNumberOfSelfLoops(); double averageDegree = network->GetAverageDegree(); double connectionDensity = network->GetConnectionDensity(); double globalClustering = network->GetGlobalClusteringCoefficient(); m_Controls->numberOfVerticesLabel->setText( QString::number( noVertices ) ); m_Controls->numberOfEdgesLabel->setText( QString::number( noEdges ) ); m_Controls->numberOfSelfLoopsLabel->setText( QString::number( noSelfLoops ) ); m_Controls->averageDegreeLabel->setText( QString::number( averageDegree ) ); m_Controls->connectionDensityLabel->setText( QString::number( connectionDensity ) ); m_Controls->globalClusteringLabel->setText( QString::number( globalClustering ) ); mitk::ConnectomicsNetwork::Pointer connectomicsNetwork( network ); mitk::ConnectomicsHistogramsContainer *histogramContainer = histogramCache[ connectomicsNetwork ]; - m_Controls->betweennessNetworkHistogramCanvas->SetHistogram( histogramContainer->GetBetweennessHistogram() ); - m_Controls->degreeNetworkHistogramCanvas->SetHistogram( histogramContainer->GetDegreeHistogram() ); - m_Controls->shortestPathNetworkHistogramCanvas->SetHistogram( histogramContainer->GetShortestPathHistogram() ); - m_Controls->betweennessNetworkHistogramCanvas->DrawProfiles(); - m_Controls->degreeNetworkHistogramCanvas->DrawProfiles(); - m_Controls->shortestPathNetworkHistogramCanvas->DrawProfiles(); - - double efficiency = histogramContainer->GetShortestPathHistogram()->GetEfficiency(); + if(histogramContainer) + { + m_Controls->betweennessNetworkHistogramCanvas->SetHistogram( histogramContainer->GetBetweennessHistogram() ); + m_Controls->degreeNetworkHistogramCanvas->SetHistogram( histogramContainer->GetDegreeHistogram() ); + m_Controls->shortestPathNetworkHistogramCanvas->SetHistogram( histogramContainer->GetShortestPathHistogram() ); + m_Controls->betweennessNetworkHistogramCanvas->DrawProfiles(); + m_Controls->degreeNetworkHistogramCanvas->DrawProfiles(); + m_Controls->shortestPathNetworkHistogramCanvas->DrawProfiles(); - m_Controls->efficiencyLabel->setText( QString::number( efficiency ) ); + double efficiency = histogramContainer->GetShortestPathHistogram()->GetEfficiency(); - return; + m_Controls->efficiencyLabel->setText( QString::number( efficiency ) ); + } } - } - } + } // end network section - m_Controls->lblWarning->setVisible( true ); + if ( currentFormatUnknown ) + { + this->WipeDisplay(); + return; + } + } // end for loop } void QmitkBrainNetworkAnalysisView::OnSyntheticNetworkComboBoxCurrentIndexChanged(int currentIndex) { m_currentIndex = currentIndex; switch (m_currentIndex) { case 0: this->m_Controls->parameterOneLabel->setText( "Nodes per side" ); this->m_Controls->parameterTwoLabel->setText( "Internode distance" ); this->m_Controls->parameterOneSpinBox->setEnabled( true ); this->m_Controls->parameterOneSpinBox->setValue( 5 ); this->m_Controls->parameterTwoDoubleSpinBox->setEnabled( true ); this->m_Controls->parameterTwoDoubleSpinBox->setMaximum( 999.999 ); this->m_Controls->parameterTwoDoubleSpinBox->setValue( 10.0 ); break; case 1: this->m_Controls->parameterOneLabel->setText( "Number of nodes" ); this->m_Controls->parameterTwoLabel->setText( "Radius" ); this->m_Controls->parameterOneSpinBox->setEnabled( true ); this->m_Controls->parameterOneSpinBox->setValue( 1000 ); this->m_Controls->parameterTwoDoubleSpinBox->setEnabled( true ); this->m_Controls->parameterTwoDoubleSpinBox->setMaximum( 999.999 ); this->m_Controls->parameterTwoDoubleSpinBox->setValue( 50.0 ); break; case 2: this->m_Controls->parameterOneLabel->setText( "Number of nodes" ); this->m_Controls->parameterTwoLabel->setText( "Edge percentage" ); this->m_Controls->parameterOneSpinBox->setEnabled( true ); this->m_Controls->parameterOneSpinBox->setValue( 100 ); this->m_Controls->parameterTwoDoubleSpinBox->setEnabled( true ); this->m_Controls->parameterTwoDoubleSpinBox->setMaximum( 1.0 ); this->m_Controls->parameterTwoDoubleSpinBox->setValue( 0.5 ); break; case 3: //GenerateSyntheticScaleFreeNetwork( network, 1000 ); break; case 4: //GenerateSyntheticSmallWorldNetwork( network, 1000 ); break; default: this->m_Controls->parameterOneLabel->setText( "Parameter 1" ); this->m_Controls->parameterTwoLabel->setText( "Paramater 2" ); this->m_Controls->parameterOneSpinBox->setEnabled( false ); this->m_Controls->parameterOneSpinBox->setValue( 0 ); this->m_Controls->parameterTwoDoubleSpinBox->setEnabled( false ); this->m_Controls->parameterTwoDoubleSpinBox->setValue( 0.0 ); } } void QmitkBrainNetworkAnalysisView::OnSyntheticNetworkCreationPushButtonClicked() { + // warn if trying to create a very big network + // big network is a network with > 5000 nodes (estimate) + // this might fill up the memory to the point it freezes + int numberOfNodes( 0 ); + switch (m_currentIndex) { + case 0: + numberOfNodes = this->m_Controls->parameterOneSpinBox->value() + * this->m_Controls->parameterOneSpinBox->value() + * this->m_Controls->parameterOneSpinBox->value(); + break; + case 1: + numberOfNodes = this->m_Controls->parameterOneSpinBox->value(); + break; + case 2: + numberOfNodes = this->m_Controls->parameterOneSpinBox->value(); + break; + case 3: + // not implemented yet + break; + case 4: + // not implemented yet + break; + default: + break; + + } + + if( numberOfNodes > 5000 ) + { + QMessageBox msgBox; + msgBox.setText("Trying to generate very large network."); + msgBox.setIcon( QMessageBox::Warning ); + msgBox.setInformativeText("You are trying to generate a network with more than 5000 nodes, this is very resource intensive and might lead to program instability. Proceed with network generation?"); + msgBox.setStandardButtons(QMessageBox::Yes | QMessageBox::No); + msgBox.setDefaultButton(QMessageBox::No); + int ret = msgBox.exec(); + + switch (ret) { + case QMessageBox::Yes: + // continue + break; + case QMessageBox::No: + // stop + return; + break; + + default: + // should never be reached + break; + } + } + + // proceed mitk::ConnectomicsSyntheticNetworkGenerator::Pointer generator = mitk::ConnectomicsSyntheticNetworkGenerator::New(); mitk::DataNode::Pointer networkNode = mitk::DataNode::New(); int parameterOne = this->m_Controls->parameterOneSpinBox->value(); double parameterTwo = this->m_Controls->parameterTwoDoubleSpinBox->value(); ////add network to datastorage networkNode->SetData( generator->CreateSyntheticNetwork( m_currentIndex, parameterOne, parameterTwo ) ); networkNode->SetName( mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_CNF_NAME ); - this->GetDefaultDataStorage()->Add( networkNode ); + if( generator->WasGenerationSuccessfull() ) + { + this->GetDefaultDataStorage()->Add( networkNode ); + } + else + { + MITK_WARN << "Problem occured during synthetic network generation."; + } return; } void QmitkBrainNetworkAnalysisView::OnConvertToRGBAImagePushButtonClicked() { std::vector nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataNode* node = nodes.front(); if (!node) { // Nothing selected. Inform the user and return QMessageBox::information( NULL, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS_CREATION, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_SELECTION_WARNING); return; } // here we have a valid mitk::DataNode // a node itself is not very useful, we need its data item (the image) mitk::BaseData* data = node->GetData(); if (data) { // test if this data item is an image or not (could also be a surface or something totally different) mitk::Image* image = dynamic_cast( data ); if (image) { std::stringstream message; std::string name; message << mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_PERFORMING_IMAGE_PROCESSING_FOR_IMAGE; if (node->GetName(name)) { // a property called "name" was found for this DataNode message << "'" << name << "'"; } message << "."; MITK_INFO << message.str(); // Convert to RGBA AccessByItk( image, TurnIntoRGBA ); this->GetDefaultDataStorage()->GetNamedNode( mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_RGBA_NAME )->GetData()->SetGeometry( node->GetData()->GetGeometry() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } template < typename TPixel, unsigned int VImageDimension > void QmitkBrainNetworkAnalysisView::TurnIntoRGBA( itk::Image* inputImage) { typedef itk::RGBAPixel< unsigned char > RGBAPixelType; typedef itk::Image< TPixel, VImageDimension > TemplateImageType; typedef itk::Image< RGBAPixelType, VImageDimension > RGBAImageType; itk::ImageRegionIterator it_inputImage(inputImage, inputImage->GetLargestPossibleRegion()); TPixel minimumValue, maximumValue; it_inputImage.GoToBegin(); maximumValue = minimumValue = it_inputImage.Value(); for(it_inputImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage) { if ( it_inputImage.Value() < minimumValue ) { minimumValue = it_inputImage.Value(); } else { if ( it_inputImage.Value() > maximumValue ) { maximumValue = it_inputImage.Value(); } } } int range = int ( maximumValue - minimumValue ); //needs to be castable to int int offset = int ( minimumValue ); if ( range < 0 ) //error { return; } std::vector< unsigned int > histogram; histogram.resize( range + 1, 0 ); for(it_inputImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage) { histogram[ int ( it_inputImage.Value() ) - offset ] += 1; } int gapCounter = 0; //this variable will be used to count the empty labels //stores how much has to be subtracted from the image to remove gaps std::vector< TPixel > subtractionStorage; subtractionStorage.resize( range + 1, 0 ); for( int index = 0; index <= range; index++ ) { if( histogram[ index ] == 0 ) { gapCounter++; //if the label is empty, increase gapCounter } else { subtractionStorage[ index ] = TPixel ( gapCounter ); } } //remove gaps from label image for(it_inputImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage) { it_inputImage.Value() = it_inputImage.Value() - subtractionStorage[ int ( it_inputImage.Value() ) ]; } // create colour vector std::vector< RGBAPixelType > lookupTable; { RGBAPixelType backgroundColour; for( int elementIndex = 0; elementIndex < 4; ++elementIndex ) { backgroundColour.SetElement( elementIndex, 0 ); } lookupTable.push_back( backgroundColour ); for(int colourNumber = 0; colourNumber < range ; ++colourNumber) { RGBAPixelType colour; for( int elementIndex = 0; elementIndex < 3; ++elementIndex ) { colour.SetElement( elementIndex, rand() % 256 ); } colour.SetAlpha( 255 ); lookupTable.push_back( colour ); } } // create RGBA image typename RGBAImageType::Pointer rgbaImage = RGBAImageType::New(); rgbaImage->SetRegions(inputImage->GetLargestPossibleRegion().GetSize()); rgbaImage->SetSpacing(inputImage->GetSpacing()); rgbaImage->SetOrigin(inputImage->GetOrigin()); rgbaImage->Allocate(); //fill with appropriate colours itk::ImageRegionIterator it_rgbaImage(rgbaImage, rgbaImage->GetLargestPossibleRegion()); for(it_inputImage.GoToBegin(), it_rgbaImage.GoToBegin(); !it_inputImage.IsAtEnd(); ++it_inputImage, ++it_rgbaImage) { it_rgbaImage.Value() = lookupTable[ int ( it_inputImage.Value() ) ]; } mitk::Image::Pointer mitkRGBAImage = mitk::ImportItkImage( rgbaImage ); mitk::DataNode::Pointer rgbaImageNode = mitk::DataNode::New(); rgbaImageNode->SetData(mitkRGBAImage); rgbaImageNode->SetProperty(mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_NAME, mitk::StringProperty::New(mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_RGBA_NAME)); rgbaImageNode->SetBoolProperty( mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_VOLUMERENDERING, true); this->GetDefaultDataStorage()->Add( rgbaImageNode ); } void QmitkBrainNetworkAnalysisView::OnNetworkifyPushButtonClicked() { std::vector nodes = this->GetDataManagerSelection(); if ( nodes.empty() ) { QMessageBox::information( NULL, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS_CREATION, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_SELECTION_WARNING); return; } if (! ( nodes.size() == 2 ) ) { QMessageBox::information( NULL, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS_CREATION, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_SELECTION_WARNING); return; } mitk::DataNode* firstNode = nodes.front(); mitk::DataNode* secondNode = nodes.at(1); if (!firstNode) { // Nothing selected. Inform the user and return QMessageBox::information( NULL, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_CONNECTOMICS_CREATION, mitk::ConnectomicsConstantsManager::CONNECTOMICS_GUI_SELECTION_WARNING); return; } // here we have a valid mitk::DataNode // a node itself is not very useful, we need its data item (the image) mitk::BaseData* firstData = firstNode->GetData(); mitk::BaseData* secondData = secondNode->GetData(); if (firstData && secondData) { // test if this data item is an image or not (could also be a surface or something totally different) mitk::Image* image = dynamic_cast( firstData ); mitk::FiberBundleX* fiberBundle = dynamic_cast( secondData ); // check whether order was switched if (! (image && fiberBundle) ) { image = dynamic_cast( secondData ); fiberBundle = dynamic_cast( firstData ); } if (image && fiberBundle) { m_ConnectomicsNetworkCreator->SetSegmentation( image ); m_ConnectomicsNetworkCreator->SetFiberBundle( fiberBundle ); m_ConnectomicsNetworkCreator->CreateNetworkFromFibersAndSegmentation(); mitk::DataNode::Pointer networkNode = mitk::DataNode::New(); ////add network to datastorage networkNode->SetData( m_ConnectomicsNetworkCreator->GetNetwork() ); networkNode->SetName( mitk::ConnectomicsConstantsManager::CONNECTOMICS_PROPERTY_DEFAULT_CNF_NAME ); this->GetDefaultDataStorage()->Add( networkNode ); } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkBrainNetworkAnalysisView::OnModularizePushButtonClicked() { std::vector nodes = this->GetDataManagerSelection(); if ( nodes.empty() ) { QMessageBox::information( NULL, "Modularization calculation", "Please select exactly one network."); return; } for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { return; } { mitk::ConnectomicsNetwork* network = dynamic_cast( node->GetData() ); if( node.IsNotNull() && network ) { typedef mitk::ConnectomicsSimulatedAnnealingPermutationModularity::ToModuleMapType MappingType; int depthOfModuleRecursive( 2 ); double startTemperature( 2.0 ); double stepSize( 4.0 ); mitk::ConnectomicsNetwork::Pointer connectomicsNetwork( network ); mitk::ConnectomicsSimulatedAnnealingManager::Pointer manager = mitk::ConnectomicsSimulatedAnnealingManager::New(); mitk::ConnectomicsSimulatedAnnealingPermutationModularity::Pointer permutation = mitk::ConnectomicsSimulatedAnnealingPermutationModularity::New(); mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::Pointer costFunction = mitk::ConnectomicsSimulatedAnnealingCostFunctionModularity::New(); permutation->SetCostFunction( costFunction.GetPointer() ); permutation->SetNetwork( connectomicsNetwork ); permutation->SetDepth( depthOfModuleRecursive ); permutation->SetStepSize( stepSize ); manager->SetPermutation( permutation.GetPointer() ); manager->RunSimulatedAnnealing( startTemperature, stepSize ); MappingType mapping = permutation->GetMapping(); MappingType::iterator iter = mapping.begin(); MappingType::iterator end = mapping.end(); int loop( 0 ); while( iter != end ) { MBI_DEBUG << "Vertex " << iter->first << " belongs to module " << iter->second ; MBI_INFO << "Vertex " << iter->first << " belongs to module " << iter->second ; iter++; } MBI_DEBUG << "Overall number of modules is " << permutation->getNumberOfModules( &mapping ) ; MBI_DEBUG << "Cost is " << costFunction->Evaluate( network, &mapping ) ; MBI_INFO << "Overall number of modules is " << permutation->getNumberOfModules( &mapping ) ; MBI_INFO << "Cost is " << costFunction->Evaluate( network, &mapping ) ; return; } } } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkBrainNetworkAnalysisViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkBrainNetworkAnalysisViewControls.ui index d92a3700de..497e043298 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkBrainNetworkAnalysisViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/Connectomics/QmitkBrainNetworkAnalysisViewControls.ui @@ -1,318 +1,363 @@ QmitkBrainNetworkAnalysisViewControls 0 0 227 - 941 + 1012 0 0 QmitkTemplate - - - QLabel { color: rgb(255, 0, 0) } - - - Please select data! + + + Data + + + + + QLabel { color: rgb(255, 0, 0) } + + + Please select data! + + + + + + + + + Image 1: + + + + + + + - + + + + + + + + + + + Image 2: + + + + + + + - + + + + + + Convert the selected image to RGBA format Convert to RGBA Create a network from a parcellation and a fiber image Networkify Create Synthetic Networks Divide in Modules Qt::Vertical 20 40 true Synthetic Network Options Parameter 1 false 9999 Parameter 2 false 3 999.899999999999977 Network Statistics # of vertices: # of edges: - - # of self loops: - average degree - connection density - efficiency - global clustering - Histograms 0 0 50 150 50 150 50 150 Qt::Vertical 20 40 QmitkNetworkHistogramCanvas QWidget
internal/Connectomics/QmitkNetworkHistogramCanvas.h
1 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp index fdcf725c3f..52114cd27b 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp @@ -1,755 +1,737 @@ /*========================================================================= Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkDiffusionDicomImportView.h" // qt includes #include // itk includes #include "itkTimeProbesCollectorBase.h" #include "itkGDCMSeriesFileNames.h" #include "itksys/SystemTools.hxx" // mitk includes #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkProperties.h" #include "mitkRenderingManager.h" #include "mitkMemoryUtilities.h" // diffusion module includes #include "mitkDicomDiffusionImageHeaderReader.h" #include "mitkGroupDiffusionHeadersFilter.h" #include "mitkDicomDiffusionImageReader.h" #include "mitkDiffusionImage.h" #include "mitkNrrdDiffusionImageWriter.h" #include "gdcmDirectory.h" #include "gdcmScanner.h" #include "gdcmSorter.h" #include "gdcmIPPSorter.h" #include "gdcmAttribute.h" #include "gdcmVersion.h" #include const std::string QmitkDiffusionDicomImport::VIEW_ID = "org.mitk.views.diffusiondicomimport"; QmitkDiffusionDicomImport::QmitkDiffusionDicomImport(QObject* /*parent*/, const char* /*name*/) : QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL), m_OutputFolderName(""), m_OutputFolderNameSet(false) { } QmitkDiffusionDicomImport::QmitkDiffusionDicomImport(const QmitkDiffusionDicomImport& other) { Q_UNUSED(other) throw std::runtime_error("Copy constructor not implemented"); } QmitkDiffusionDicomImport::~QmitkDiffusionDicomImport() {} void QmitkDiffusionDicomImport::CreateQtPartControl(QWidget *parent) { m_Parent = parent; if (m_Controls == NULL) { m_Controls = new Ui::QmitkDiffusionDicomImportControls; m_Controls->setupUi(parent); this->CreateConnections(); m_Controls->m_DicomLoadRecursiveCheckbox->setChecked(true); m_Controls->m_DicomLoadAverageDuplicatesCheckbox->setChecked(false); m_Controls->m_DicomLoadRecursiveCheckbox->setVisible(false); AverageClicked(); - AdvancedCheckboxClicked(); } } void QmitkDiffusionDicomImport::CreateConnections() { if ( m_Controls ) { connect( m_Controls->m_AddFoldersButton, SIGNAL(clicked()), this, SLOT(DicomLoadAddFolderNames()) ); connect( m_Controls->m_DeleteFoldersButton, SIGNAL(clicked()), this, SLOT(DicomLoadDeleteFolderNames()) ); connect( m_Controls->m_DicomLoadStartLoadButton, SIGNAL(clicked()), this, SLOT(DicomLoadStartLoad()) ); connect( m_Controls->m_DicomLoadAverageDuplicatesCheckbox, SIGNAL(clicked()), this, SLOT(AverageClicked()) ); connect( m_Controls->m_OutputSetButton, SIGNAL(clicked()), this, SLOT(OutputSet()) ); connect( m_Controls->m_OutputClearButton, SIGNAL(clicked()), this, SLOT(OutputClear()) ); - connect( m_Controls->m_Advanced, SIGNAL(clicked()), this, SLOT(AdvancedCheckboxClicked()) ); connect( m_Controls->m_Remove, SIGNAL(clicked()), this, SLOT(Remove()) ); } } void QmitkDiffusionDicomImport::Remove() { int i = m_Controls->listWidget->currentRow(); m_Controls->listWidget->takeItem(i); } -void QmitkDiffusionDicomImport::AdvancedCheckboxClicked() -{ - bool check = m_Controls-> - m_Advanced->isChecked(); - - m_Controls->m_AdvancedFrame->setVisible(check); -} - void QmitkDiffusionDicomImport::OutputSet() { // SELECT FOLDER DIALOG QFileDialog* w = new QFileDialog( m_Parent, QString("Select folders containing DWI data") ); w->setFileMode( QFileDialog::Directory ); // RETRIEVE SELECTION if ( w->exec() != QDialog::Accepted ) return; m_OutputFolderName = w->selectedFiles()[0]; m_OutputFolderNameSet = true; m_Controls->m_OutputLabel->setText(m_OutputFolderName); } void QmitkDiffusionDicomImport::OutputClear() { m_OutputFolderName = ""; m_OutputFolderNameSet = false; m_Controls->m_OutputLabel->setText("... optional out-folder ..."); } void QmitkDiffusionDicomImport::AverageClicked() { m_Controls->m_Blur->setEnabled(m_Controls->m_DicomLoadAverageDuplicatesCheckbox->isChecked()); } void QmitkDiffusionDicomImport::Activated() { QmitkFunctionality::Activated(); } void QmitkDiffusionDicomImport::DicomLoadDeleteFolderNames() { m_Controls->listWidget->clear(); } void QmitkDiffusionDicomImport::DicomLoadAddFolderNames() { // SELECT FOLDER DIALOG QFileDialog* w = new QFileDialog( m_Parent, QString("Select folders containing DWI data") ); w->setFileMode( QFileDialog::Directory ); // RETRIEVE SELECTION if ( w->exec() != QDialog::Accepted ) return; m_Controls->listWidget->addItems(w->selectedFiles()); } bool SortBySeriesUID(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 ) { gdcm::Attribute<0x0020,0x000e> at1; at1.Set( ds1 ); gdcm::Attribute<0x0020,0x000e> at2; at2.Set( ds2 ); return at1 < at2; } bool SortByAcquisitionNumber(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 ) { gdcm::Attribute<0x0020,0x0012> at1; at1.Set( ds1 ); gdcm::Attribute<0x0020,0x0012> at2; at2.Set( ds2 ); return at1 < at2; } bool SortBySeqName(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 ) { gdcm::Attribute<0x0018, 0x0024> at1; at1.Set( ds1 ); gdcm::Attribute<0x0018, 0x0024> at2; at2.Set( ds2 ); std::string str1 = at1.GetValue().Trim(); std::string str2 = at2.GetValue().Trim(); return std::lexicographical_compare(str1.begin(), str1.end(), str2.begin(), str2.end() ); } void QmitkDiffusionDicomImport::Status(QString status) { mitk::StatusBar::GetInstance()->DisplayText(status.toAscii()); MITK_INFO << status.toStdString().c_str(); } void QmitkDiffusionDicomImport::Status(std::string status) { mitk::StatusBar::GetInstance()->DisplayText(status.c_str()); MITK_INFO << status.c_str(); } void QmitkDiffusionDicomImport::Status(const char* status) { mitk::StatusBar::GetInstance()->DisplayText(status); MITK_INFO << status; } void QmitkDiffusionDicomImport::Error(QString status) { mitk::StatusBar::GetInstance()->DisplayErrorText(status.toAscii()); MITK_ERROR << status.toStdString().c_str(); } void QmitkDiffusionDicomImport::Error(std::string status) { mitk::StatusBar::GetInstance()->DisplayErrorText(status.c_str()); MITK_ERROR << status.c_str(); } void QmitkDiffusionDicomImport::Error(const char* status) { mitk::StatusBar::GetInstance()->DisplayErrorText(status); MITK_ERROR << status; } void QmitkDiffusionDicomImport::PrintMemoryUsage() { size_t processSize = mitk::MemoryUtilities::GetProcessMemoryUsage(); size_t totalSize = mitk::MemoryUtilities::GetTotalSizeOfPhysicalRam(); float percentage = ( (float) processSize / (float) totalSize ) * 100.0; MITK_INFO << "Current memory usage: " << GetMemoryDescription( processSize, percentage ); } std::string QmitkDiffusionDicomImport::FormatMemorySize( size_t size ) { double val = size; std::string descriptor("B"); if ( val >= 1000.0 ) { val /= 1024.0; descriptor = "KB"; } if ( val >= 1000.0 ) { val /= 1024.0; descriptor = "MB"; } if ( val >= 1000.0 ) { val /= 1024.0; descriptor = "GB"; } std::ostringstream str; str << std::fixed << std::setprecision(2) << val << " " << descriptor; return str.str(); } std::string QmitkDiffusionDicomImport::FormatPercentage( double val ) { std::ostringstream str; str << std::fixed << std::setprecision(2) << val << " " << "%"; return str.str(); } std::string QmitkDiffusionDicomImport::GetMemoryDescription( size_t processSize, float percentage ) { std::ostringstream str; str << FormatMemorySize(processSize) << " (" << FormatPercentage( percentage ) <<")" ; return str.str(); } void QmitkDiffusionDicomImport::DicomLoadStartLoad() { itk::TimeProbesCollectorBase clock; bool imageSuccessfullySaved = true; try { const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, NULL ); if ( locale.compare(currLocale)!=0 ) { try { MITK_INFO << " ** Changing locale from " << setlocale(LC_ALL, NULL) << " to '" << locale << "'"; setlocale(LC_ALL, locale.c_str()); } catch(...) { MITK_INFO << "Could not set locale " << locale; } } int nrFolders = m_Controls->listWidget->count(); if(!nrFolders) { Error(QString("No input folders were selected. ABORTING.")); return; } Status(QString("GDCM %1 used for DICOM parsing and sorting!").arg(gdcm::Version::GetVersion())); PrintMemoryUsage(); QString status; mitk::DataNode::Pointer node; mitk::ProgressBar::GetInstance()->AddStepsToDo(2*nrFolders); std::string folder = m_Controls->m_OutputLabel->text().toStdString(); if(berry::Platform::IsWindows()) { folder.append("\\import.log"); } else { folder.append("/import.log"); } ofstream logfile; if(m_OutputFolderNameSet) logfile.open(folder.c_str()); while(m_Controls->listWidget->count()) { // RETREIVE FOLDERNAME QListWidgetItem * item = m_Controls->listWidget->takeItem(0); QString folderName = item->text(); if(m_OutputFolderNameSet) logfile << "Reading " << folderName.toStdString() << '\n'; // PARSING DIRECTORY PrintMemoryUsage(); clock.Start(folderName.toAscii()); std::vector seriesUIDs(0); std::vector > seriesFilenames(0); Status("== Initial Directory Scan =="); if(m_OutputFolderNameSet) logfile << "== Initial Directory Scan ==\n"; gdcm::Directory d; d.Load( folderName.toStdString().c_str(), true ); // recursive ! const gdcm::Directory::FilenamesType &l1 = d.GetFilenames(); const unsigned int ntotalfiles = l1.size(); Status(QString(" ... found %1 different files").arg(ntotalfiles)); if(m_OutputFolderNameSet)logfile << "...found " << ntotalfiles << " different files\n"; Status("Scanning Headers"); if(m_OutputFolderNameSet) logfile << "Scanning Headers\n"; gdcm::Scanner s; const gdcm::Tag t1(0x0020,0x000d); // Study Instance UID const gdcm::Tag t2(0x0020,0x000e); // Series Instance UID const gdcm::Tag t5(0x0028, 0x0010); // number rows const gdcm::Tag t6(0x0028, 0x0011); // number cols s.AddTag( t1 ); s.AddTag( t2 ); s.AddTag( t5 ); s.AddTag( t6 ); bool b = s.Scan( d.GetFilenames() ); if( !b ) { Error("Scanner failed"); if(m_OutputFolderNameSet )logfile << "ERROR: scanner failed\n"; continue; } // Only get the DICOM files: gdcm::Directory::FilenamesType l2 = s.GetKeys(); const int nfiles = l2.size(); if(nfiles < 1) { Error("No DICOM files found"); if(m_OutputFolderNameSet)logfile << "ERROR: No DICOM files found\n"; continue; } Status(QString(" ... successfully scanned %1 headers.").arg(nfiles)); if(m_OutputFolderNameSet) logfile << "...succesfully scanned " << nfiles << " headers\n"; Status("Sorting"); if(m_OutputFolderNameSet) logfile << "Sorting\n"; const gdcm::Scanner::ValuesType &values1 = s.GetValues(t1); int nvalues; if(m_Controls->m_DuplicateID->isChecked()) { nvalues = 1; } else { nvalues = values1.size(); } if(nvalues>1) { Error("Multiple sSeries tudies found. Please limit to 1 study per folder"); if(m_OutputFolderNameSet) logfile << "Multiple series found. Limit to one. If you are convinced this is an error use the merge duplicate study IDs option \n"; continue; } const gdcm::Scanner::ValuesType &values5 = s.GetValues(t5); const gdcm::Scanner::ValuesType &values6 = s.GetValues(t6); if(values5.size()>1 || values6.size()>1) { Error("Folder contains images of unequal dimensions that cannot be combined in one 3d volume. ABORTING."); if(m_OutputFolderNameSet) logfile << "Folder contains images of unequal dimensions that cannot be combined in one 3d volume. ABORTING\n."; continue; } const gdcm::Scanner::ValuesType &values2 = s.GetValues(t2); int nSeries; if(m_Controls->m_DuplicateID->isChecked()) { nSeries = 1; } else { nSeries = values2.size(); } gdcm::Directory::FilenamesType files; if(nSeries > 1) { gdcm::Sorter sorter; sorter.SetSortFunction( SortBySeriesUID ); sorter.StableSort( l2 ); files = sorter.GetFilenames(); } else { files = l2; } unsigned int nTotalAcquis = 0; if(nfiles % nSeries != 0) { Error("Number of files in series not equal, ABORTING"); if(m_OutputFolderNameSet) logfile << "Number of files in series not equal, Some volumes are probably incomplete. ABORTING \n"; continue; } int filesPerSeries = nfiles / nSeries; gdcm::Scanner::ValuesType::const_iterator it2 = values2.begin(); for(int i=0; i & list = ippsorter.GetFilenames(); seriesFilenames.push_back(list); seriesUIDs.push_back(identifier.c_str()); } ++it2; } if(nfiles % nTotalAcquis != 0) { Error("Number of files per acquisition differs between series, ABORTING"); if(m_OutputFolderNameSet) logfile << "Number of files per acquisition differs between series, ABORTING \n"; continue; } int slices = nfiles/nTotalAcquis; Status(QString("Series is composed of %1 different 3D volumes with %2 slices.").arg(nTotalAcquis).arg(slices)); if(m_OutputFolderNameSet) logfile << "Series is composed of " << nTotalAcquis << " different 3D volumes with " << slices << " slices\n"; // READING HEADER-INFOS PrintMemoryUsage(); Status(QString("Reading Headers %1").arg(folderName)); if(m_OutputFolderNameSet) logfile << "Reading Headers "<< folderName.toStdString() << "\n"; mitk::DicomDiffusionImageHeaderReader::Pointer headerReader; mitk::GroupDiffusionHeadersFilter::InputType inHeaders; unsigned int size2 = seriesUIDs.size(); for ( unsigned int i = 0 ; i < size2 ; ++i ) { Status(QString("Reading header image #%1/%2").arg(i+1).arg(size2)); headerReader = mitk::DicomDiffusionImageHeaderReader::New(); headerReader->SetSeriesDicomFilenames(seriesFilenames[i]); headerReader->Update(); inHeaders.push_back(headerReader->GetOutput()); //Status(std::endl; } mitk::ProgressBar::GetInstance()->Progress(); // // GROUP HEADERS // mitk::GroupDiffusionHeadersFilter::Pointer grouper // = mitk::GroupDiffusionHeadersFilter::New(); // mitk::GroupDiffusionHeadersFilter::OutputType outHeaders; // grouper->SetInput(inHeaders); // grouper->Update(); // outHeaders = grouper->GetOutput(); // READ VOLUMES PrintMemoryUsage(); if(m_OutputFolderNameSet) logfile << "Loading volumes\n"; Status(QString("Loading Volumes %1").arg(folderName)); typedef short PixelValueType; typedef mitk::DicomDiffusionImageReader< PixelValueType, 3 > VolumesReader; VolumesReader::Pointer vReader = VolumesReader::New(); VolumesReader::HeaderContainer hc = inHeaders; // hc.insert(hc.end(), outHeaders[1].begin(), outHeaders[1].end() ); // hc.insert(hc.end(), outHeaders[2].begin(), outHeaders[2].end() ); if(hc.size()>1) { vReader->SetHeaders(hc); vReader->Update(); VolumesReader::OutputImageType::Pointer vecImage; vecImage = vReader->GetOutput(); Status(QString("Volumes Loaded (%1)").arg(folderName)); // CONSTRUCT CONTAINER WITH DIRECTIONS typedef vnl_vector_fixed< double, 3 > GradientDirectionType; typedef itk::VectorContainer< unsigned int, GradientDirectionType > GradientDirectionContainerType; GradientDirectionContainerType::Pointer directions = GradientDirectionContainerType::New(); std::vector b_vals; double maxb = 0; for(unsigned int i=0; ibValue; if(maxb vect = hc[i]->DiffusionVector; vect.normalize(); vect *= sqrt(b_vals[i]/maxb); directions->push_back(vect); } // DWI TO DATATREE PrintMemoryUsage(); Status(QString("Initializing Diffusion Image")); if(m_OutputFolderNameSet) logfile << "Initializing Diffusion Image\n"; typedef mitk::DiffusionImage DiffVolumesType; DiffVolumesType::Pointer diffImage = DiffVolumesType::New(); diffImage->SetDirections(directions); diffImage->SetOriginalDirections(directions); - if(m_Controls->m_DicomLoadDKFZ->isChecked()) - { - diffImage->CorrectDKFZBrokenGradientScheme(m_Controls->m_Blur->value()); - } diffImage->SetVectorImage(vecImage); diffImage->SetB_Value(maxb); diffImage->InitializeFromVectorImage(); Status(QString("Diffusion Image initialized")); if(m_OutputFolderNameSet) logfile << "Diffusion Image initialized\n"; if(m_Controls->m_DicomLoadAverageDuplicatesCheckbox->isChecked()) { PrintMemoryUsage(); Status(QString("Averaging gradient directions")); logfile << "Averaging gradient directions\n"; diffImage->AverageRedundantGradients(m_Controls->m_Blur->value()); } - //if(m_Controls->m_DicomLoadDuplicateIfSingleSliceCheckbox->isChecked()) - // diffVolumes->DuplicateIfSingleSlice(); - QString descr = QString("%1_%2_%3") .arg(((inHeaders)[0])->seriesDescription.c_str()) .arg(((inHeaders)[0])->seriesNumber) .arg(((inHeaders)[0])->patientName.c_str()); descr = descr.trimmed(); descr = descr.replace(" ", "_"); if(!m_OutputFolderNameSet) { node=mitk::DataNode::New(); node->SetData( diffImage ); GetDefaultDataStorage()->Add(node); SetDwiNodeProperties(node, descr.toStdString().c_str()); Status(QString("Image %1 added to datastorage").arg(descr)); } else { typedef mitk::NrrdDiffusionImageWriter WriterType; WriterType::Pointer writer = WriterType::New(); QString fullpath = QString("%1/%2.dwi") .arg(m_OutputFolderName) .arg(descr); - //std::string pathstring = itksys::SystemTools::ConvertToOutputPath(fullpath.toStdString().c_str()); writer->SetFileName(fullpath.toStdString()); writer->SetInput(diffImage); try { writer->Update(); } catch (itk::ExceptionObject &ex) { imageSuccessfullySaved = false; Error(QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription())); logfile << QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription()).toStdString() << "\n"; node=mitk::DataNode::New(); node->SetData( diffImage ); GetDefaultDataStorage()->Add(node); SetDwiNodeProperties(node, descr.toStdString().c_str()); Status(QString("Image %1 added to datastorage").arg(descr)); logfile << "Image " << descr.toStdString() << " added to datastorage\n"; continue ; } Status(QString("Image %1 written to disc (%1)").arg(fullpath.toStdString().c_str())); logfile << "Image " << fullpath.toStdString() << "\n"; } } else { Status(QString("No diffusion information found (%1)").arg(folderName)); if(m_OutputFolderNameSet) logfile << "No diffusion information found "<< folderName.toStdString(); } Status(QString("Finished processing %1 with memory:").arg(folderName)); if(m_OutputFolderNameSet) logfile << "Finished processing " << folderName.toStdString() << "\n"; PrintMemoryUsage(); clock.Stop(folderName.toAscii()); mitk::ProgressBar::GetInstance()->Progress(); int lwidget = m_Controls->listWidget->count(); std::cout << lwidget <GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeSlicedGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); try { MITK_INFO << " ** Changing locale back from " << setlocale(LC_ALL, NULL) << " to '" << currLocale << "'"; setlocale(LC_ALL, currLocale.c_str()); } catch(...) { MITK_INFO << "Could not reset locale " << currLocale; } } catch (itk::ExceptionObject &ex) { Error(QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription())); return ; } if (!imageSuccessfullySaved) QMessageBox::warning(NULL,"WARNING","One or more files could not be saved! The according files where moved to the datastorage."); Status(QString("Finished import with memory:")); PrintMemoryUsage(); } void QmitkDiffusionDicomImport::SetDwiNodeProperties(mitk::DataNode::Pointer node, std::string name) { node->SetProperty( "IsDWIRawVolume", mitk::BoolProperty::New( true ) ); // set foldername as string property mitk::StringProperty::Pointer nameProp = mitk::StringProperty::New( name ); node->SetProperty( "name", nameProp ); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.h index b7dcb07d03..87aceb3cab 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.h @@ -1,119 +1,112 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-05 11:31:02 +0200 (Di, 05 Mai 2009) $ Version: $Revision: 10185 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef QmitkDiffusionDicomImportView_H__INCLUDED #define QmitkDiffusionDicomImportView_H__INCLUDED #include "QmitkFunctionality.h" #include "ui_QmitkDiffusionDicomImportViewControls.h" /*! -\brief QmitkDiffusionDicomImport +\brief QmitkDiffusionDicomImport \sa QmitkFunctionality \ingroup Functionalities */ class QmitkDiffusionDicomImport : public QmitkFunctionality -{ +{ Q_OBJECT -public: +public: static const std::string VIEW_ID; - /*! + /*! \ Convenient typedefs */ typedef mitk::DataStorage::SetOfObjects ConstVector; typedef ConstVector::ConstPointer ConstVectorPointer; typedef ConstVector::ConstIterator ConstVectorIterator; - /*! - \brief default constructor - */ + /*! + \brief default constructor + */ QmitkDiffusionDicomImport(QObject *parent=0, const char *name=0); QmitkDiffusionDicomImport(const QmitkDiffusionDicomImport& other); - /*! - \brief default destructor - */ + /*! + \brief default destructor + */ virtual ~QmitkDiffusionDicomImport(); - /*! - \brief method for creating the widget containing the application controls, like sliders, buttons etc. - */ + /*! + \brief method for creating the widget containing the application controls, like sliders, buttons etc. + */ virtual void CreateQtPartControl(QWidget *parent); - /*! - \brief method for creating the connections of main and control widget - */ + /*! + \brief method for creating the connections of main and control widget + */ virtual void CreateConnections(); virtual void Activated(); void SetDwiNodeProperties(mitk::DataNode::Pointer node, std::string name); protected slots: void DicomLoadAddFolderNames(); - void DicomLoadDeleteFolderNames(); - void DicomLoadStartLoad() ; - void AverageClicked(); - void OutputSet(); void OutputClear(); - - void AdvancedCheckboxClicked(); - void Remove(); -protected: +protected: void Status(QString status); void Status(std::string status); void Status(const char* status); void Error(QString status); void Error(std::string status); void Error(const char* status); void PrintMemoryUsage(); std::string FormatMemorySize( size_t size ); std::string FormatPercentage( double val ); std::string GetMemoryDescription( size_t processSize, float percentage ); - /*! - * controls containing sliders for scrolling through the slices - */ + /*! + * controls containing sliders for scrolling through the slices + */ Ui::QmitkDiffusionDicomImportControls *m_Controls; QmitkStdMultiWidget* m_MultiWidget; QWidget *m_Parent; QString m_OutputFolderName; bool m_OutputFolderNameSet; }; #endif // !defined(QmitkDiffusionDicomImport_H__INCLUDED) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportViewControls.ui index 3e096d8494..02cbb86b1e 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportViewControls.ui @@ -1,330 +1,313 @@ QmitkDiffusionDicomImportControls 0 0 - 313 + 338 498 0 0 true QmitkDiffusionDicomImport 16777215 70 QFrame::NoFrame QFrame::Plain 0 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Ubuntu'; font-size:11pt; font-weight:400; font-style:normal;"> <table border="0" style="-qt-table-type: root; margin-top:4px; margin-bottom:4px; margin-left:4px; margin-right:4px;"> <tr> <td style="border: none;"> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans'; font-size:10pt;">Each input folder must only contain DICOM-images that can be combined into one vector-valued 3D output volume. Different patients must be loaded from different input-folders. The folders must not contain other acquisitions (e.g. T1,T2,localizer).</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'Sans'; font-size:10pt;"></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Sans'; font-size:10pt;">In case many imports are performed at once, it is recommended to set the the optional output folder argument. This prevents the images from being kept in memory.</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'Sans'; font-size:10pt;"></p></td></tr></table></body></html> 0 0 QFrame::NoFrame QFrame::Raised 0 0 Add Input Folders Remove Clear 0 0 0 70 QFrame::Box QFrame::Plain 1 0 Qt::ScrollBarAsNeeded Qt::ScrollBarAlwaysOn QListView::Adjust true QFrame::StyledPanel QFrame::Raised Recursive + + Multiple acquistions of one gradient direction can be averaged. Due to rounding errors, similar gradients often differ in the last decimal positions. The Merge radius allows to average them anyway by taking into account all directions within a certain radius. + QFrame::NoFrame QFrame::Raised 0 - Avg. dupl. grad., blur= + Merge duplicate gradients: false + + + - 6 + 4 2.000000000000000 0.000100000000000 0.001000000000000 - + + + Select this option if you are sure that your DICOM dataset contains multiple Study Instance UID or Series Instance UID. It will ignore that fact and attempt to import all images as one. + - Advanced + Merge duplicate study IDs - - - - QFrame::StyledPanel - - - QFrame::Raised - - - - - - Correct DKFZ Gradient Scheme - - - - - - - Select this option if you are sure that your DICOM dataset contains multiple Study Instance UID or Series Instance UID. It will ignore that fact and attempt to import all images as one. - - - merge duplicate study IDs - - - - - - QFrame::NoFrame QFrame::Raised 0 40 25 30 16777215 + + Files are automaticall saved to disc. If the files can not be written, they are added to the data manager. + Set ... optional out-folder ... false true 50 25 30 16777215 Clear Import DICOM as *.dwi Qt::Vertical 20 0 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.cpp index 0030b57e25..198577bba2 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.cpp @@ -1,665 +1,573 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkDiffusionQuantificationView.h" #include "mitkDiffusionImagingConfigure.h" #include "itkTimeProbe.h" #include "itkImage.h" #include "mitkNodePredicateDataType.h" #include "mitkDataNodeObject.h" #include "mitkQBallImage.h" +#include #include "mitkImageCast.h" #include "mitkStatusBar.h" #include "itkDiffusionQballGeneralizedFaImageFilter.h" #include "itkShiftScaleImageFilter.h" #include "itkTensorFractionalAnisotropyImageFilter.h" #include "itkTensorRelativeAnisotropyImageFilter.h" #include "itkTensorDerivedMeasurementsFilter.h" #include "QmitkDataStorageComboBox.h" #include "QmitkStdMultiWidget.h" #include #include "berryIWorkbenchWindow.h" #include "berryISelectionService.h" const std::string QmitkDiffusionQuantificationView::VIEW_ID = "org.mitk.views.diffusionquantification"; -using namespace berry; -struct DqSelListener : ISelectionListener -{ - - berryObjectMacro(DqSelListener); - - DqSelListener(QmitkDiffusionQuantificationView* view) - { - m_View = view; - } - - void DoSelectionChanged(ISelection::ConstPointer selection) - { - // save current selection in member variable - m_View->m_CurrentSelection = selection.Cast(); - - // do something with the selected items - if(m_View->m_CurrentSelection) - { - bool foundQBIVolume = false; - bool foundTensorVolume = false; - - // iterate selection - for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); - i != m_View->m_CurrentSelection->End(); ++i) - { - - // extract datatree node - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - - // only look at interesting types - // process only on valid nodes - const mitk::BaseData* nodeData = node->GetData(); - if(nodeData) - { - if(QString("QBallImage").compare(nodeData->GetNameOfClass())==0) - { - foundQBIVolume = true; - } - - if(QString("TensorImage").compare(nodeData->GetNameOfClass())==0) - { - foundTensorVolume = true; - } - } - } - } - - m_View->m_Controls->m_GFAButton->setEnabled(foundQBIVolume); - m_View->m_Controls->m_CurvatureButton->setEnabled(foundQBIVolume); - - m_View->m_Controls->m_FAButton->setEnabled(foundTensorVolume); - m_View->m_Controls->m_RAButton->setEnabled(foundTensorVolume); - m_View->m_Controls->m_ADButton->setEnabled(foundTensorVolume); - m_View->m_Controls->m_RDButton->setEnabled(foundTensorVolume); - m_View->m_Controls->m_MDButton->setEnabled(foundTensorVolume); - m_View->m_Controls->m_ClusteringAnisotropy->setEnabled(foundTensorVolume); - } - } - - void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) - { - // check, if selection comes from datamanager - if (part) - { - QString partname(part->GetPartName().c_str()); - if(partname.compare("Datamanager")==0) - { - - // apply selection - DoSelectionChanged(selection); - - } - } - } - - QmitkDiffusionQuantificationView* m_View; -}; QmitkDiffusionQuantificationView::QmitkDiffusionQuantificationView() -: QmitkFunctionality(), -m_Controls(NULL), -m_MultiWidget(NULL) + : QmitkFunctionality(), + m_Controls(NULL), + m_MultiWidget(NULL) { + m_QBallImages = mitk::DataStorage::SetOfObjects::New(); + m_TensorImages = mitk::DataStorage::SetOfObjects::New(); } QmitkDiffusionQuantificationView::QmitkDiffusionQuantificationView(const QmitkDiffusionQuantificationView& other) { Q_UNUSED(other) throw std::runtime_error("Copy constructor not implemented"); } QmitkDiffusionQuantificationView::~QmitkDiffusionQuantificationView() { - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); + } void QmitkDiffusionQuantificationView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkDiffusionQuantificationViewControls; m_Controls->setupUi(parent); this->CreateConnections(); GFACheckboxClicked(); #ifndef DIFFUSION_IMAGING_EXTENDED m_Controls->m_StandardGFACheckbox->setVisible(false); m_Controls->frame_3->setVisible(false); m_Controls->m_CurvatureButton->setVisible(false); #endif } - - m_SelListener = berry::ISelectionListener::Pointer(new DqSelListener(this)); - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); - berry::ISelection::ConstPointer sel( - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); - m_CurrentSelection = sel.Cast(); - m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkDiffusionQuantificationView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkDiffusionQuantificationView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkDiffusionQuantificationView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_StandardGFACheckbox), SIGNAL(clicked()), this, SLOT(GFACheckboxClicked()) ); connect( (QObject*)(m_Controls->m_GFAButton), SIGNAL(clicked()), this, SLOT(GFA()) ); connect( (QObject*)(m_Controls->m_CurvatureButton), SIGNAL(clicked()), this, SLOT(Curvature()) ); connect( (QObject*)(m_Controls->m_FAButton), SIGNAL(clicked()), this, SLOT(FA()) ); connect( (QObject*)(m_Controls->m_RAButton), SIGNAL(clicked()), this, SLOT(RA()) ); connect( (QObject*)(m_Controls->m_ADButton), SIGNAL(clicked()), this, SLOT(AD()) ); connect( (QObject*)(m_Controls->m_RDButton), SIGNAL(clicked()), this, SLOT(RD()) ); connect( (QObject*)(m_Controls->m_MDButton), SIGNAL(clicked()), this, SLOT(MD()) ); connect( (QObject*)(m_Controls->m_ClusteringAnisotropy), SIGNAL(clicked()), this, SLOT(ClusterAnisotropy()) ); } } +void QmitkDiffusionQuantificationView::OnSelectionChanged( std::vector nodes ) +{ + if (!m_Visible) + return; + + m_QBallImages = mitk::DataStorage::SetOfObjects::New(); + m_TensorImages = mitk::DataStorage::SetOfObjects::New(); + bool foundQBIVolume = false; + bool foundTensorVolume = false; + mitk::DataNode::Pointer selNode = NULL; + + int c=0; + for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) + { + mitk::DataNode::Pointer node = *it; + + if( node.IsNotNull() && dynamic_cast(node->GetData()) ) + { + foundQBIVolume = true; + m_QBallImages->push_back(node); + selNode = node; + c++; + } + else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) + { + foundTensorVolume = true; + m_TensorImages->push_back(node); + selNode = node; + c++; + } + } + + m_Controls->m_GFAButton->setEnabled(foundQBIVolume); + m_Controls->m_CurvatureButton->setEnabled(foundQBIVolume); + + if (c>0) + m_Controls->m_InputImageLabel->setText(selNode->GetName().c_str()); + else + m_Controls->m_InputImageLabel->setText("-"); + + m_Controls->m_FAButton->setEnabled(foundTensorVolume); + m_Controls->m_RAButton->setEnabled(foundTensorVolume); + m_Controls->m_ADButton->setEnabled(foundTensorVolume); + m_Controls->m_RDButton->setEnabled(foundTensorVolume); + m_Controls->m_MDButton->setEnabled(foundTensorVolume); + m_Controls->m_ClusteringAnisotropy->setEnabled(foundTensorVolume); +} + void QmitkDiffusionQuantificationView::Activated() { - berry::ISelection::ConstPointer sel( - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); - m_CurrentSelection = sel.Cast(); - m_SelListener.Cast()->DoSelectionChanged(sel); QmitkFunctionality::Activated(); } void QmitkDiffusionQuantificationView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkDiffusionQuantificationView::GFACheckboxClicked() { - m_Controls->frame_2->setVisible(m_Controls-> - m_StandardGFACheckbox->isChecked()); + m_Controls->frame_2->setVisible(m_Controls->m_StandardGFACheckbox->isChecked()); } void QmitkDiffusionQuantificationView::GFA() { if(m_Controls->m_StandardGFACheckbox->isChecked()) { QBIQuantify(13); } else { QBIQuantify(0); } } void QmitkDiffusionQuantificationView::Curvature() { QBIQuantify(12); } void QmitkDiffusionQuantificationView::FA() { TensorQuantify(0); } void QmitkDiffusionQuantificationView::RA() { TensorQuantify(1); } void QmitkDiffusionQuantificationView::AD() { TensorQuantify(2); } void QmitkDiffusionQuantificationView::RD() { TensorQuantify(3); } void QmitkDiffusionQuantificationView::ClusterAnisotropy() { TensorQuantify(4); } void QmitkDiffusionQuantificationView::MD() { TensorQuantify(5); } void QmitkDiffusionQuantificationView::QBIQuantify(int method) { - if (m_CurrentSelection) - { - mitk::DataStorage::SetOfObjects::Pointer set = - mitk::DataStorage::SetOfObjects::New(); - - int at = 0; - for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); - i != m_CurrentSelection->End(); - ++i) - { - - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - if(QString("QBallImage").compare(node->GetData()->GetNameOfClass())==0) - { - set->InsertElement(at++, node); - } - } - } - - QBIQuantification(set, method); - - } + QBIQuantification(m_QBallImages, method); } void QmitkDiffusionQuantificationView::TensorQuantify(int method) { - if (m_CurrentSelection) - { - mitk::DataStorage::SetOfObjects::Pointer set = - mitk::DataStorage::SetOfObjects::New(); - - int at = 0; - for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); - i != m_CurrentSelection->End(); - ++i) - { - - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - // process only on valid nodes - mitk::BaseData* nodeData = node->GetData(); - if(nodeData) - { - if(QString("TensorImage").compare(nodeData->GetNameOfClass())==0) - { - set->InsertElement(at++, node); - } - } - } - } - - TensorQuantification(set, method); - - } + TensorQuantification(m_TensorImages, method); } void QmitkDiffusionQuantificationView::QBIQuantification( mitk::DataStorage::SetOfObjects::Pointer inImages, int method) { itk::TimeProbe clock; QString status; int nrFiles = inImages->size(); if (!nrFiles) return; mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { typedef float TOdfPixelType; const int odfsize = QBALL_ODFSIZE; typedef itk::Vector OdfVectorType; typedef itk::Image OdfVectorImgType; mitk::Image* vol = - static_cast((*itemiter)->GetData()); + static_cast((*itemiter)->GetData()); OdfVectorImgType::Pointer itkvol = OdfVectorImgType::New(); mitk::CastToItkImage(vol, itkvol); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); ++itemiter; float p1 = m_Controls->m_ParamKEdit->text().toFloat(); float p2 = m_Controls->m_ParamPEdit->text().toFloat(); // COMPUTE RA clock.Start(); MBI_INFO << "Computing GFA "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( - "Computing GFA for %s", nodename.c_str()).toAscii()); + "Computing GFA for %s", nodename.c_str()).toAscii()); typedef OdfVectorType::ValueType RealValueType; typedef itk::Image< RealValueType, 3 > RAImageType; typedef itk::DiffusionQballGeneralizedFaImageFilter - GfaFilterType; + GfaFilterType; GfaFilterType::Pointer gfaFilter = GfaFilterType::New(); gfaFilter->SetInput(itkvol); gfaFilter->SetNumberOfThreads(8); double scale = 1; std::string newname; newname.append(nodename); switch(method) { case 0: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD); newname.append("GFA"); break; } case 1: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILES_HIGH_LOW); newname.append("01"); break; } case 2: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILE_HIGH); newname.append("02"); break; } case 3: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_MAX_ODF_VALUE); newname.append("03"); break; } case 4: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_DECONVOLUTION_COEFFS); newname.append("04"); break; } case 5: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_MIN_MAX_NORMALIZED_STANDARD); newname.append("05"); break; } case 6: - { - gfaFilter->SetComputationMethod(GfaFilterType::GFA_NORMALIZED_ENTROPY); - newname.append("06"); - break; - } + { + gfaFilter->SetComputationMethod(GfaFilterType::GFA_NORMALIZED_ENTROPY); + newname.append("06"); + break; + } case 7: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_NEMATIC_ORDER_PARAMETER); newname.append("07"); break; } case 8: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILES_LOW_HIGH); newname.append("08"); break; } case 9: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILE_LOW); newname.append("09"); break; } case 10: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_MIN_ODF_VALUE); newname.append("10"); break; } case 11: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_STD_BY_MAX); newname.append("11"); break; } case 12: { p1 = m_Controls->MinAngle->text().toFloat(); p2 = m_Controls->MaxAngle->text().toFloat(); gfaFilter->SetComputationMethod(GfaFilterType::GFA_PRINCIPLE_CURVATURE); QString paramString; paramString = paramString.append("PC%1-%2").arg(p1).arg(p2); newname.append(paramString.toAscii()); gfaFilter->SetParam1(p1); gfaFilter->SetParam2(p2); break; } case 13: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_GENERALIZED_GFA); QString paramString; paramString = paramString.append("GFAK%1P%2").arg(p1).arg(p2); newname.append(paramString.toAscii()); gfaFilter->SetParam1(p1); gfaFilter->SetParam2(p2); break; } default: { newname.append("0"); gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD); } } gfaFilter->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s."; typedef itk::Image ImgType; ImgType::Pointer img = ImgType::New(); img->SetSpacing( gfaFilter->GetOutput()->GetSpacing() ); // Set the image spacing img->SetOrigin( gfaFilter->GetOutput()->GetOrigin() ); // Set the image origin img->SetDirection( gfaFilter->GetOutput()->GetDirection() ); // Set the image direction img->SetLargestPossibleRegion( gfaFilter->GetOutput()->GetLargestPossibleRegion()); img->SetBufferedRegion( gfaFilter->GetOutput()->GetLargestPossibleRegion() ); img->Allocate(); itk::ImageRegionIterator ot (img, img->GetLargestPossibleRegion() ); ot = ot.Begin(); itk::ImageRegionConstIterator it - (gfaFilter->GetOutput(), gfaFilter->GetOutput()->GetLargestPossibleRegion() ); + (gfaFilter->GetOutput(), gfaFilter->GetOutput()->GetLargestPossibleRegion() ); it = it.Begin(); for (it = it.Begin(); !it.IsAtEnd(); ++it) { GfaFilterType::OutputImageType::PixelType val = it.Get(); ot.Set(val * m_Controls->m_ScaleImageValuesBox->value()); ++ot; } // GFA TO DATATREE mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( img.GetPointer() ); image->SetVolume( img->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); node->SetProperty( "name", mitk::StringProperty::New(newname) ); nodes.push_back(node); mitk::StatusBar::GetInstance()->DisplayText("Computation complete."); } std::vector::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); m_MultiWidget->RequestUpdate(); } void QmitkDiffusionQuantificationView::TensorQuantification( mitk::DataStorage::SetOfObjects::Pointer inImages, int method) { itk::TimeProbe clock; QString status; int nrFiles = inImages->size(); if (!nrFiles) return; mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { typedef float TTensorPixelType; typedef itk::DiffusionTensor3D< TTensorPixelType > TensorPixelType; typedef itk::Image< TensorPixelType, 3 > TensorImageType; mitk::Image* vol = - static_cast((*itemiter)->GetData()); + static_cast((*itemiter)->GetData()); TensorImageType::Pointer itkvol = TensorImageType::New(); mitk::CastToItkImage(vol, itkvol); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); ++itemiter; // COMPUTE FA clock.Start(); MBI_INFO << "Computing FA "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( - "Computing FA for %s", nodename.c_str()).toAscii()); + "Computing FA for %s", nodename.c_str()).toAscii()); typedef itk::Image< TTensorPixelType, 3 > FAImageType; typedef itk::ShiftScaleImageFilter - ShiftScaleFilterType; + ShiftScaleFilterType; ShiftScaleFilterType::Pointer multi = - ShiftScaleFilterType::New(); + ShiftScaleFilterType::New(); multi->SetShift(0.0); multi->SetScale(m_Controls->m_ScaleImageValuesBox->value());//itk::NumericTraits::max() typedef itk::TensorDerivedMeasurementsFilter MeasurementsType; if(method == 0) //FA { - /* typedef itk::TensorFractionalAnisotropyImageFilter< + /* typedef itk::TensorFractionalAnisotropyImageFilter< TensorImageType, FAImageType > FilterType; FilterType::Pointer anisotropyFilter = FilterType::New(); anisotropyFilter->SetInput( itkvol.GetPointer() ); anisotropyFilter->Update(); multi->SetInput(anisotropyFilter->GetOutput()); nodename = QString(nodename.c_str()).append("_FA").toStdString();*/ MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); measurementsCalculator->SetMeasure(MeasurementsType::FA); measurementsCalculator->Update(); multi->SetInput(measurementsCalculator->GetOutput()); nodename = QString(nodename.c_str()).append("_FA").toStdString(); } else if(method == 1) //RA { /*typedef itk::TensorRelativeAnisotropyImageFilter< TensorImageType, FAImageType > FilterType; FilterType::Pointer anisotropyFilter = FilterType::New(); anisotropyFilter->SetInput( itkvol.GetPointer() ); anisotropyFilter->Update(); multi->SetInput(anisotropyFilter->GetOutput()); nodename = QString(nodename.c_str()).append("_RA").toStdString();*/ MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); measurementsCalculator->SetMeasure(MeasurementsType::RA); measurementsCalculator->Update(); multi->SetInput(measurementsCalculator->GetOutput()); nodename = QString(nodename.c_str()).append("_RA").toStdString(); } else if(method == 2) // AD (Axial diffusivity) { MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); measurementsCalculator->SetMeasure(MeasurementsType::AD); measurementsCalculator->Update(); multi->SetInput(measurementsCalculator->GetOutput()); nodename = QString(nodename.c_str()).append("_AD").toStdString(); } else if(method == 3) // RD (Radial diffusivity, (Lambda2+Lambda3)/2 { MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); measurementsCalculator->SetMeasure(MeasurementsType::RD); measurementsCalculator->Update(); multi->SetInput(measurementsCalculator->GetOutput()); nodename = QString(nodename.c_str()).append("_RD").toStdString(); } else if(method == 4) // 1-(Lambda2+Lambda3)/(2*Lambda1) { MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); measurementsCalculator->SetMeasure(MeasurementsType::CA); measurementsCalculator->Update(); multi->SetInput(measurementsCalculator->GetOutput()); nodename = QString(nodename.c_str()).append("_CA").toStdString(); } else if(method == 5) // MD (Mean Diffusivity, (Lambda1+Lambda2+Lambda3)/3 ) { MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); measurementsCalculator->SetMeasure(MeasurementsType::MD); measurementsCalculator->Update(); multi->SetInput(measurementsCalculator->GetOutput()); nodename = QString(nodename.c_str()).append("_MD").toStdString(); } multi->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s."; // FA TO DATATREE mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( multi->GetOutput() ); image->SetVolume( multi->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); node->SetProperty( "name", mitk::StringProperty::New(nodename) ); nodes.push_back(node); mitk::StatusBar::GetInstance()->DisplayText("Computation complete."); } std::vector::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); m_MultiWidget->RequestUpdate(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.h index cb98ea5a5c..3e8c319f7b 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.h @@ -1,108 +1,104 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ -Version: $Revision: 17495 $ - +Version: $Revision: 17495 $ + Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _QMITKDIFFUSIONQUANTIFICATIONVIEW_H_INCLUDED #define _QMITKDIFFUSIONQUANTIFICATIONVIEW_H_INCLUDED #include #include -#include "berryISelectionListener.h" -#include "berryIStructuredSelection.h" - #include "ui_QmitkDiffusionQuantificationViewControls.h" - - - /*! * \ingroup org_mitk_gui_qt_diffusionquantification_internal * * \brief QmitkDiffusionQuantificationView * * Document your class here. * * \sa QmitkFunctionality */ class QmitkDiffusionQuantificationView : public QmitkFunctionality { friend struct DqSelListener; // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; QmitkDiffusionQuantificationView(); QmitkDiffusionQuantificationView(const QmitkDiffusionQuantificationView& other); virtual ~QmitkDiffusionQuantificationView(); virtual void CreateQtPartControl(QWidget *parent); /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); protected slots: void GFACheckboxClicked(); - + void GFA(); void Curvature(); void FA(); void RA(); void AD(); void RD(); void ClusterAnisotropy(); void MD(); void QBIQuantify(int method); - void QBIQuantification(mitk::DataStorage::SetOfObjects::Pointer inImages, + void QBIQuantification(mitk::DataStorage::SetOfObjects::Pointer inImages, int method) ; void TensorQuantify(int method); - void TensorQuantification(mitk::DataStorage::SetOfObjects::Pointer inImages, + void TensorQuantification(mitk::DataStorage::SetOfObjects::Pointer inImages, int method) ; protected: + /// \brief called by QmitkFunctionality when DataManager's selection has changed + virtual void OnSelectionChanged( std::vector nodes ); + Ui::QmitkDiffusionQuantificationViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; - - berry::ISelectionListener::Pointer m_SelListener; - berry::IStructuredSelection::ConstPointer m_CurrentSelection; + mitk::DataStorage::SetOfObjects::Pointer m_QBallImages; + mitk::DataStorage::SetOfObjects::Pointer m_TensorImages; static const float m_ScaleDAIValues; }; #endif // _QMITKDIFFUSIONQUANTIFICATIONVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationViewControls.ui index fc834371ea..46d6099700 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationViewControls.ui @@ -1,280 +1,300 @@ QmitkDiffusionQuantificationViewControls 0 0 343 - 553 + 543 0 0 QmitkTemplate - General Parameters + Data - + - Scale values by: + Tensor/Q-Ball Image: - - - All tensor or Q-Ball derived quantities are scaled by this value. + + + - + + + + + + + + + General Parameters + + + + + + Scale Image Values: + + + + + 100.000000000000000 1.000000000000000 Q-Ball Imaging QFrame::NoFrame QFrame::Raised 0 Generalized GFA QFrame::NoFrame QFrame::Raised 0 true k true true p true false GFA QFrame::NoFrame QFrame::Raised 0 Min. angle Max. angle false Curvature Tensor Imaging false FA (Fractional Anisotropy) false RA (Relative Anisotropy) false AD (Axial Diffusivity) false RD (Radial Diffusivity) false MD (Mean Diffusivity) false 1-(λ2+λ3)/(2*λ1) Qt::Vertical QSizePolicy::Expanding 20 220 QmitkDataStorageComboBox.h diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp index 2dde0a992c..204f17b3ff 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp @@ -1,1759 +1,1767 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $ Version: $Revision: 21975 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkFiberProcessingView.h" #include // Qt #include // MITK #include #include #include #include #include #include #include #include #include #include #include // ITK #include #include #include #include #include #include #include #include const std::string QmitkFiberProcessingView::VIEW_ID = "org.mitk.views.fiberprocessing"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace mitk; QmitkFiberProcessingView::QmitkFiberProcessingView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_EllipseCounter(0) , m_PolygonCounter(0) , m_UpsamplingFactor(5) { } // Destructor QmitkFiberProcessingView::~QmitkFiberProcessingView() { } void QmitkFiberProcessingView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberProcessingViewControls; m_Controls->setupUi( parent ); m_Controls->doExtractFibersButton->setDisabled(true); m_Controls->PFCompoANDButton->setDisabled(true); m_Controls->PFCompoORButton->setDisabled(true); m_Controls->PFCompoNOTButton->setDisabled(true); m_Controls->m_PlanarFigureButtonsFrame->setEnabled(false); m_Controls->m_RectangleButton->setVisible(false); connect( m_Controls->doExtractFibersButton, SIGNAL(clicked()), this, SLOT(DoFiberExtraction()) ); connect( m_Controls->m_CircleButton, SIGNAL( clicked() ), this, SLOT( OnDrawCircle() ) ); connect( m_Controls->m_PolygonButton, SIGNAL( clicked() ), this, SLOT( OnDrawPolygon() ) ); connect(m_Controls->PFCompoANDButton, SIGNAL(clicked()), this, SLOT(GenerateAndComposite()) ); connect(m_Controls->PFCompoORButton, SIGNAL(clicked()), this, SLOT(GenerateOrComposite()) ); connect(m_Controls->PFCompoNOTButton, SIGNAL(clicked()), this, SLOT(GenerateNotComposite()) ); connect(m_Controls->m_JoinBundles, SIGNAL(clicked()), this, SLOT(JoinBundles()) ); connect(m_Controls->m_SubstractBundles, SIGNAL(clicked()), this, SLOT(SubstractBundles()) ); connect(m_Controls->m_GenerateRoiImage, SIGNAL(clicked()), this, SLOT(GenerateRoiImage()) ); connect(m_Controls->m_Extract3dButton, SIGNAL(clicked()), this, SLOT(Extract3d())); connect( m_Controls->m_ProcessFiberBundleButton, SIGNAL(clicked()), this, SLOT(ProcessSelectedBundles()) ); connect( m_Controls->m_ResampleFibersButton, SIGNAL(clicked()), this, SLOT(ResampleSelectedBundles()) ); connect(m_Controls->m_FaColorFibersButton, SIGNAL(clicked()), this, SLOT(DoFaColorCoding())); } } void QmitkFiberProcessingView::Extract3d() { std::vector nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::FiberBundleX::Pointer fib = mitk::FiberBundleX::New(); mitk::Surface::Pointer roi = mitk::Surface::New(); bool fibB = false; bool roiB = false; for (int i=0; i(nodes.at(i)->GetData())) { fib = dynamic_cast(nodes.at(i)->GetData()); fibB = true; } else if (dynamic_cast(nodes.at(i)->GetData())) { roi = dynamic_cast(nodes.at(i)->GetData()); roiB = true; } } if (!fibB) return; if (!roiB) return; vtkSmartPointer polyRoi = roi->GetVtkPolyData(); vtkSmartPointer polyFib = fib->GetFiberPolyData(); vtkSmartPointer selectEnclosedPoints = vtkSmartPointer::New(); selectEnclosedPoints->SetInput(polyFib); selectEnclosedPoints->SetSurface(polyRoi); selectEnclosedPoints->Update(); vtkSmartPointer newPoly = vtkSmartPointer::New(); vtkSmartPointer newCellArray = vtkSmartPointer::New(); vtkSmartPointer newPoints = vtkSmartPointer::New(); vtkSmartPointer newPolyComplement = vtkSmartPointer::New(); vtkSmartPointer newCellArrayComplement = vtkSmartPointer::New(); vtkSmartPointer newPointsComplement = vtkSmartPointer::New(); vtkSmartPointer vLines = polyFib->GetLines(); vLines->InitTraversal(); int numberOfLines = vLines->GetNumberOfCells(); // each line for (int j=0; jGetNextCell ( numPoints, points ); bool isPassing = false; // each point of this line for (int k=0; kIsInside(points[k])) { isPassing = true; // fill new polydata vtkSmartPointer container = vtkSmartPointer::New(); for (int k=0; kGetPoint(points[k]); vtkIdType pointId = newPoints->InsertNextPoint(point); container->GetPointIds()->InsertNextId(pointId); } newCellArray->InsertNextCell(container); break; } } if (!isPassing) { vtkSmartPointer container = vtkSmartPointer::New(); for (int k=0; kGetPoint(points[k]); vtkIdType pointId = newPointsComplement->InsertNextPoint(point); container->GetPointIds()->InsertNextId(pointId); } newCellArrayComplement->InsertNextCell(container); } } newPoly->SetPoints(newPoints); newPoly->SetLines(newCellArray); mitk::FiberBundleX::Pointer fb = mitk::FiberBundleX::New(newPoly); DataNode::Pointer newNode = DataNode::New(); newNode->SetData(fb); newNode->SetName("passing surface"); GetDefaultDataStorage()->Add(newNode); newPolyComplement->SetPoints(newPointsComplement); newPolyComplement->SetLines(newCellArrayComplement); mitk::FiberBundleX::Pointer fbComplement = mitk::FiberBundleX::New(newPolyComplement); DataNode::Pointer newNodeComplement = DataNode::New(); newNodeComplement->SetData(fbComplement); newNodeComplement->SetName("not passing surface"); GetDefaultDataStorage()->Add(newNodeComplement); } void QmitkFiberProcessingView::GenerateRoiImage(){ if (m_SelectedPF.empty()) return; mitk::Geometry3D::Pointer geometry; - if (m_SelectedImage.IsNotNull()) - geometry = m_SelectedImage->GetGeometry(); - else if (!m_SelectedFB.empty()) + if (!m_SelectedFB.empty()) { mitk::FiberBundleX::Pointer fib = dynamic_cast(m_SelectedFB.front()->GetData()); geometry = fib->GetGeometry(); } else return; + mitk::Vector3D spacing = geometry->GetSpacing(); + spacing /= m_UpsamplingFactor; + + mitk::Point3D newOrigin = geometry->GetOrigin(); + mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds(); + newOrigin[0] += bounds.GetElement(0); + newOrigin[1] += bounds.GetElement(2); + newOrigin[2] += bounds.GetElement(4); + itk::Matrix direction; itk::ImageRegion<3> imageRegion; for (int i=0; i<3; i++) for (int j=0; j<3; j++) - direction[j][i] = geometry->GetMatrixColumn(i)[j]; + direction[j][i] = geometry->GetMatrixColumn(i)[j]/spacing[j]; imageRegion.SetSize(0, geometry->GetExtent(0)*m_UpsamplingFactor); imageRegion.SetSize(1, geometry->GetExtent(1)*m_UpsamplingFactor); imageRegion.SetSize(2, geometry->GetExtent(2)*m_UpsamplingFactor); m_PlanarFigureImage = itkUCharImageType::New(); - m_PlanarFigureImage->SetSpacing( geometry->GetSpacing() ); // Set the image spacing - m_PlanarFigureImage->SetOrigin( geometry->GetOrigin() ); // Set the image origin + m_PlanarFigureImage->SetSpacing( spacing ); // Set the image spacing + m_PlanarFigureImage->SetOrigin( newOrigin ); // Set the image origin m_PlanarFigureImage->SetDirection( direction ); // Set the image direction m_PlanarFigureImage->SetRegions( imageRegion ); m_PlanarFigureImage->Allocate(); m_PlanarFigureImage->FillBuffer( 0 ); Image::Pointer tmpImage = Image::New(); tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer()); tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer()); for (int i=0; iInitializeByItk(m_PlanarFigureImage.GetPointer()); tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer()); node->SetData(tmpImage); node->SetName("ROI Image"); this->GetDefaultDataStorage()->Add(node); } void QmitkFiberProcessingView::CompositeExtraction(mitk::DataNode::Pointer node, mitk::Image* image) { if (dynamic_cast(node.GetPointer()->GetData()) && !dynamic_cast(node.GetPointer()->GetData())) { m_PlanarFigure = dynamic_cast(node.GetPointer()->GetData()); AccessFixedDimensionByItk_2( image, InternalReorientImagePlane, 3, m_PlanarFigure->GetGeometry(), -1); // itk::Image< unsigned char, 3 >::Pointer outimage = itk::Image< unsigned char, 3 >::New(); // outimage->SetSpacing( m_PlanarFigure->GetGeometry()->GetSpacing()/m_UpsamplingFactor ); // Set the image spacing // mitk::Point3D origin = m_PlanarFigure->GetGeometry()->GetOrigin(); // mitk::Point3D indexOrigin; // m_PlanarFigure->GetGeometry()->WorldToIndex(origin, indexOrigin); // indexOrigin[0] = indexOrigin[0] - .5 * (1.0-1.0/m_UpsamplingFactor); // indexOrigin[1] = indexOrigin[1] - .5 * (1.0-1.0/m_UpsamplingFactor); // indexOrigin[2] = indexOrigin[2] - .5 * (1.0-1.0/m_UpsamplingFactor); // mitk::Point3D newOrigin; // m_PlanarFigure->GetGeometry()->IndexToWorld(indexOrigin, newOrigin); // outimage->SetOrigin( newOrigin ); // Set the image origin // itk::Matrix matrix; // for (int i=0; i<3; i++) // for (int j=0; j<3; j++) // matrix[j][i] = m_PlanarFigure->GetGeometry()->GetMatrixColumn(i)[j]/m_PlanarFigure->GetGeometry()->GetSpacing().GetElement(i); // outimage->SetDirection( matrix ); // Set the image direction // itk::ImageRegion<3> upsampledRegion; // upsampledRegion.SetSize(0, m_PlanarFigure->GetGeometry()->GetParametricExtentInMM(0)/m_PlanarFigure->GetGeometry()->GetSpacing()[0]); // upsampledRegion.SetSize(1, m_PlanarFigure->GetGeometry()->GetParametricExtentInMM(1)/m_PlanarFigure->GetGeometry()->GetSpacing()[1]); // upsampledRegion.SetSize(2, 1); // typename itk::Image< unsigned char, 3 >::RegionType::SizeType upsampledSize = upsampledRegion.GetSize(); // for (unsigned int n = 0; n < 2; n++) // { // upsampledSize[n] = upsampledSize[n] * m_UpsamplingFactor; // } // upsampledRegion.SetSize( upsampledSize ); // outimage->SetRegions( upsampledRegion ); // outimage->Allocate(); // this->m_InternalImage = mitk::Image::New(); // this->m_InternalImage->InitializeByItk( outimage.GetPointer() ); // this->m_InternalImage->SetVolume( outimage->GetBufferPointer() ); AccessFixedDimensionByItk_2( m_InternalImage, InternalCalculateMaskFromPlanarFigure, 3, 2, node->GetName() ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkFiberProcessingView::InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > *image, mitk::Geometry3D* planegeo3D, int additionalIndex ) { MITK_INFO << "InternalReorientImagePlane() start"; typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::Image< float, VImageDimension > FloatImageType; typedef itk::ResampleImageFilter ResamplerType; typename ResamplerType::Pointer resampler = ResamplerType::New(); mitk::PlaneGeometry* planegeo = dynamic_cast(planegeo3D); float upsamp = m_UpsamplingFactor; float gausssigma = 0.5; // Spacing typename ResamplerType::SpacingType spacing = planegeo->GetSpacing(); spacing[0] = image->GetSpacing()[0] / upsamp; spacing[1] = image->GetSpacing()[1] / upsamp; spacing[2] = image->GetSpacing()[2]; resampler->SetOutputSpacing( spacing ); // Size typename ResamplerType::SizeType size; size[0] = planegeo->GetParametricExtentInMM(0) / spacing[0]; size[1] = planegeo->GetParametricExtentInMM(1) / spacing[1]; size[2] = 1; resampler->SetSize( size ); // Origin typename mitk::Point3D orig = planegeo->GetOrigin(); typename mitk::Point3D corrorig; planegeo3D->WorldToIndex(orig,corrorig); corrorig[0] += 0.5/upsamp; corrorig[1] += 0.5/upsamp; corrorig[2] += 0; planegeo3D->IndexToWorld(corrorig,corrorig); resampler->SetOutputOrigin(corrorig ); // Direction typename ResamplerType::DirectionType direction; typename mitk::AffineTransform3D::MatrixType matrix = planegeo->GetIndexToWorldTransform()->GetMatrix(); for(int c=0; cSetOutputDirection( direction ); // Gaussian interpolation if(gausssigma != 0) { double sigma[3]; for( unsigned int d = 0; d < 3; d++ ) { sigma[d] = gausssigma * image->GetSpacing()[d]; } double alpha = 2.0; typedef itk::GaussianInterpolateImageFunction GaussianInterpolatorType; typename GaussianInterpolatorType::Pointer interpolator = GaussianInterpolatorType::New(); interpolator->SetInputImage( image ); interpolator->SetParameters( sigma, alpha ); resampler->SetInterpolator( interpolator ); } else { // typedef typename itk::BSplineInterpolateImageFunction // InterpolatorType; typedef typename itk::LinearInterpolateImageFunction InterpolatorType; typename InterpolatorType::Pointer interpolator = InterpolatorType::New(); interpolator->SetInputImage( image ); resampler->SetInterpolator( interpolator ); } // Other resampling options resampler->SetInput( image ); resampler->SetDefaultPixelValue(0); MITK_INFO << "Resampling requested image plane ... "; resampler->Update(); MITK_INFO << " ... done"; if(additionalIndex < 0) { this->m_InternalImage = mitk::Image::New(); this->m_InternalImage->InitializeByItk( resampler->GetOutput() ); this->m_InternalImage->SetVolume( resampler->GetOutput()->GetBufferPointer() ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkFiberProcessingView::InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string nodeName ) { MITK_INFO << "InternalCalculateMaskFromPlanarFigure() start"; typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::CastImageFilter< ImageType, itkUCharImageType > CastFilterType; // Generate mask image as new image with same header as input image and // initialize with "1". itkUCharImageType::Pointer newMaskImage = itkUCharImageType::New(); newMaskImage->SetSpacing( image->GetSpacing() ); // Set the image spacing newMaskImage->SetOrigin( image->GetOrigin() ); // Set the image origin newMaskImage->SetDirection( image->GetDirection() ); // Set the image direction newMaskImage->SetRegions( image->GetLargestPossibleRegion() ); newMaskImage->Allocate(); newMaskImage->FillBuffer( 1 ); // Generate VTK polygon from (closed) PlanarFigure polyline // (The polyline points are shifted by -0.5 in z-direction to make sure // that the extrusion filter, which afterwards elevates all points by +0.5 // in z-direction, creates a 3D object which is cut by the the plane z=0) const Geometry2D *planarFigureGeometry2D = m_PlanarFigure->GetGeometry2D(); const PlanarFigure::PolyLineType planarFigurePolyline = m_PlanarFigure->GetPolyLine( 0 ); const Geometry3D *imageGeometry3D = m_InternalImage->GetGeometry( 0 ); vtkPolyData *polyline = vtkPolyData::New(); polyline->Allocate( 1, 1 ); // Determine x- and y-dimensions depending on principal axis int i0, i1; switch ( axis ) { case 0: i0 = 1; i1 = 2; break; case 1: i0 = 0; i1 = 2; break; case 2: default: i0 = 0; i1 = 1; break; } // Create VTK polydata object of polyline contour vtkPoints *points = vtkPoints::New(); PlanarFigure::PolyLineType::const_iterator it; std::vector indices; unsigned int numberOfPoints = 0; for ( it = planarFigurePolyline.begin(); it != planarFigurePolyline.end(); ++it ) { Point3D point3D; // Convert 2D point back to the local index coordinates of the selected // image Point2D point2D = it->Point; planarFigureGeometry2D->WorldToIndex(point2D, point2D); point2D[0] -= 0.5/m_UpsamplingFactor; point2D[1] -= 0.5/m_UpsamplingFactor; planarFigureGeometry2D->IndexToWorld(point2D, point2D); planarFigureGeometry2D->Map( point2D, point3D ); // Polygons (partially) outside of the image bounds can not be processed // further due to a bug in vtkPolyDataToImageStencil if ( !imageGeometry3D->IsInside( point3D ) ) { float bounds[2] = {0,0}; bounds[0] = this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i0); bounds[1] = this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i1); imageGeometry3D->WorldToIndex( point3D, point3D ); // if (point3D[i0]<0) // point3D[i0] = 0.5; // else if (point3D[i0]>bounds[0]) // point3D[i0] = bounds[0]-0.5; // if (point3D[i1]<0) // point3D[i1] = 0.5; // else if (point3D[i1]>bounds[1]) // point3D[i1] = bounds[1]-0.5; if (point3D[i0]<0) point3D[i0] = 0.0; else if (point3D[i0]>bounds[0]) point3D[i0] = bounds[0]-0.001; if (point3D[i1]<0) point3D[i1] = 0.0; else if (point3D[i1]>bounds[1]) point3D[i1] = bounds[1]-0.001; points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 ); numberOfPoints++; } else { imageGeometry3D->WorldToIndex( point3D, point3D ); // Add point to polyline array points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 ); numberOfPoints++; } } polyline->SetPoints( points ); points->Delete(); vtkIdType *ptIds = new vtkIdType[numberOfPoints]; for ( vtkIdType i = 0; i < numberOfPoints; ++i ) { ptIds[i] = i; } polyline->InsertNextCell( VTK_POLY_LINE, numberOfPoints, ptIds ); // Extrude the generated contour polygon vtkLinearExtrusionFilter *extrudeFilter = vtkLinearExtrusionFilter::New(); extrudeFilter->SetInput( polyline ); extrudeFilter->SetScaleFactor( 1 ); extrudeFilter->SetExtrusionTypeToNormalExtrusion(); extrudeFilter->SetVector( 0.0, 0.0, 1.0 ); // Make a stencil from the extruded polygon vtkPolyDataToImageStencil *polyDataToImageStencil = vtkPolyDataToImageStencil::New(); polyDataToImageStencil->SetInput( extrudeFilter->GetOutput() ); // Export from ITK to VTK (to use a VTK filter) typedef itk::VTKImageImport< itkUCharImageType > ImageImportType; typedef itk::VTKImageExport< itkUCharImageType > ImageExportType; typename ImageExportType::Pointer itkExporter = ImageExportType::New(); itkExporter->SetInput( newMaskImage ); vtkImageImport *vtkImporter = vtkImageImport::New(); this->ConnectPipelines( itkExporter, vtkImporter ); vtkImporter->Update(); // Apply the generated image stencil to the input image vtkImageStencil *imageStencilFilter = vtkImageStencil::New(); imageStencilFilter->SetInputConnection( vtkImporter->GetOutputPort() ); imageStencilFilter->SetStencil( polyDataToImageStencil->GetOutput() ); imageStencilFilter->ReverseStencilOff(); imageStencilFilter->SetBackgroundValue( 0 ); imageStencilFilter->Update(); // Export from VTK back to ITK vtkImageExport *vtkExporter = vtkImageExport::New(); vtkExporter->SetInputConnection( imageStencilFilter->GetOutputPort() ); vtkExporter->Update(); typename ImageImportType::Pointer itkImporter = ImageImportType::New(); this->ConnectPipelines( vtkExporter, itkImporter ); itkImporter->Update(); // calculate cropping bounding box m_InternalImageMask3D = itkImporter->GetOutput(); m_InternalImageMask3D->SetDirection(image->GetDirection()); itk::ImageRegionConstIterator itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion()); itk::ImageRegionIterator itimage(image, image->GetLargestPossibleRegion()); itmask = itmask.Begin(); itimage = itimage.Begin(); typename ImageType::SizeType lowersize = {{9999999999,9999999999,9999999999}}; typename ImageType::SizeType uppersize = {{0,0,0}}; while( !itmask.IsAtEnd() ) { if(itmask.Get() == 0) { itimage.Set(0); } else { typename ImageType::IndexType index = itimage.GetIndex(); typename ImageType::SizeType signedindex; signedindex[0] = index[0]; signedindex[1] = index[1]; signedindex[2] = index[2]; lowersize[0] = signedindex[0] < lowersize[0] ? signedindex[0] : lowersize[0]; lowersize[1] = signedindex[1] < lowersize[1] ? signedindex[1] : lowersize[1]; lowersize[2] = signedindex[2] < lowersize[2] ? signedindex[2] : lowersize[2]; uppersize[0] = signedindex[0] > uppersize[0] ? signedindex[0] : uppersize[0]; uppersize[1] = signedindex[1] > uppersize[1] ? signedindex[1] : uppersize[1]; uppersize[2] = signedindex[2] > uppersize[2] ? signedindex[2] : uppersize[2]; } ++itmask; ++itimage; } typename ImageType::IndexType index; index[0] = lowersize[0]; index[1] = lowersize[1]; index[2] = lowersize[2]; typename ImageType::SizeType size; size[0] = uppersize[0] - lowersize[0] + 1; size[1] = uppersize[1] - lowersize[1] + 1; size[2] = uppersize[2] - lowersize[2] + 1; itk::ImageRegion<3> cropRegion = itk::ImageRegion<3>(index, size); // crop internal mask typedef itk::RegionOfInterestImageFilter< itkUCharImageType, itkUCharImageType > ROIMaskFilterType; typename ROIMaskFilterType::Pointer roi2 = ROIMaskFilterType::New(); roi2->SetRegionOfInterest(cropRegion); roi2->SetInput(m_InternalImageMask3D); roi2->Update(); m_InternalImageMask3D = roi2->GetOutput(); Image::Pointer tmpImage = Image::New(); tmpImage->InitializeByItk(m_InternalImageMask3D.GetPointer()); tmpImage->SetVolume(m_InternalImageMask3D->GetBufferPointer()); Image::Pointer tmpImage2 = Image::New(); tmpImage2->InitializeByItk(m_PlanarFigureImage.GetPointer()); const Geometry3D *pfImageGeometry3D = tmpImage2->GetGeometry( 0 ); const Geometry3D *intImageGeometry3D = tmpImage->GetGeometry( 0 ); typedef itk::ImageRegionIteratorWithIndex IteratorType; IteratorType imageIterator (m_InternalImageMask3D, m_InternalImageMask3D->GetRequestedRegion()); imageIterator.GoToBegin(); while ( !imageIterator.IsAtEnd() ) { unsigned char val = imageIterator.Value(); if (val>0) { itk::Index<3> index = imageIterator.GetIndex(); Point3D point; point[0] = index[0]; point[1] = index[1]; point[2] = index[2]; intImageGeometry3D->IndexToWorld(point, point); pfImageGeometry3D->WorldToIndex(point, point); point[i0] += 0.5; point[i1] += 0.5; index[0] = point[0]; index[1] = point[1]; index[2] = point[2]; - m_PlanarFigureImage->SetPixel(index, 1); + if (pfImageGeometry3D->IsIndexInside(index)) + m_PlanarFigureImage->SetPixel(index, 1); } ++imageIterator; } // Clean up VTK objects polyline->Delete(); extrudeFilter->Delete(); polyDataToImageStencil->Delete(); vtkImporter->Delete(); imageStencilFilter->Delete(); //vtkExporter->Delete(); // TODO: crashes when outcommented; memory leak?? delete[] ptIds; } void QmitkFiberProcessingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkFiberProcessingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } /* OnSelectionChanged is registered to SelectionService, therefore no need to implement SelectionService Listener explicitly */ void QmitkFiberProcessingView::UpdateGui() { // are fiber bundles selected? if ( m_SelectedFB.empty() ) { m_Controls->m_JoinBundles->setEnabled(false); m_Controls->m_SubstractBundles->setEnabled(false); m_Controls->m_ProcessFiberBundleButton->setEnabled(false); m_Controls->doExtractFibersButton->setEnabled(false); m_Controls->m_Extract3dButton->setEnabled(false); m_Controls->m_ResampleFibersButton->setEnabled(false); m_Controls->m_PlanarFigureButtonsFrame->setEnabled(false); m_Controls->m_FaColorFibersButton->setEnabled(false); } else { m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true); m_Controls->m_ProcessFiberBundleButton->setEnabled(true); m_Controls->m_ResampleFibersButton->setEnabled(true); if (m_Surfaces.size()>0) m_Controls->m_Extract3dButton->setEnabled(true); // one bundle and one planar figure needed to extract fibers if (!m_SelectedPF.empty()) m_Controls->doExtractFibersButton->setEnabled(true); // more than two bundles needed to join/subtract if (m_SelectedFB.size() > 1) { m_Controls->m_JoinBundles->setEnabled(true); m_Controls->m_SubstractBundles->setEnabled(true); } else { m_Controls->m_JoinBundles->setEnabled(false); m_Controls->m_SubstractBundles->setEnabled(false); } if (m_SelectedImage.IsNotNull()) m_Controls->m_FaColorFibersButton->setEnabled(true); } // are planar figures selected? if ( m_SelectedPF.empty() ) { m_Controls->doExtractFibersButton->setEnabled(false); m_Controls->PFCompoANDButton->setEnabled(false); m_Controls->PFCompoORButton->setEnabled(false); m_Controls->PFCompoNOTButton->setEnabled(false); m_Controls->m_GenerateRoiImage->setEnabled(false); } else { - if ( m_SelectedImage.IsNotNull() || !m_SelectedFB.empty() ) + if ( !m_SelectedFB.empty() ) m_Controls->m_GenerateRoiImage->setEnabled(true); else m_Controls->m_GenerateRoiImage->setEnabled(false); if (m_SelectedPF.size() > 1) { m_Controls->PFCompoANDButton->setEnabled(true); m_Controls->PFCompoORButton->setEnabled(true); m_Controls->PFCompoNOTButton->setEnabled(false); } else { m_Controls->PFCompoANDButton->setEnabled(false); m_Controls->PFCompoORButton->setEnabled(false); m_Controls->PFCompoNOTButton->setEnabled(true); } } } void QmitkFiberProcessingView::OnSelectionChanged( std::vector nodes ) { if ( !this->IsVisible() ) return; //reset existing Vectors containing FiberBundles and PlanarFigures from a previous selection m_SelectedFB.clear(); m_SelectedPF.clear(); m_Surfaces.clear(); m_SelectedImage = NULL; for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( dynamic_cast(node->GetData()) ) m_SelectedFB.push_back(node); else if (dynamic_cast(node->GetData())) m_SelectedPF.push_back(node); else if (dynamic_cast(node->GetData())) m_SelectedImage = dynamic_cast(node->GetData()); else if (dynamic_cast(node->GetData())) m_Surfaces.push_back(dynamic_cast(node->GetData())); } UpdateGui(); GenerateStats(); } void QmitkFiberProcessingView::OnDrawPolygon() { // bool checked = m_Controls->m_PolygonButton->isChecked(); // if(!this->AssertDrawingIsPossible(checked)) // return; mitk::PlanarPolygon::Pointer figure = mitk::PlanarPolygon::New(); figure->ClosedOn(); this->AddFigureToDataStorage(figure, QString("Polygon%1").arg(++m_PolygonCounter)); MITK_INFO << "PlanarPolygon created ..."; mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll(); mitk::DataNode* node = 0; mitk::PlanarFigureInteractor::Pointer figureInteractor = 0; mitk::PlanarFigure* figureP = 0; for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End() ; it++) { node = const_cast(it->Value().GetPointer()); figureP = dynamic_cast(node->GetData()); if(figureP) { figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); } } } void QmitkFiberProcessingView::OnDrawCircle() { //bool checked = m_Controls->m_CircleButton->isChecked(); //if(!this->AssertDrawingIsPossible(checked)) // return; mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New(); this->AddFigureToDataStorage(figure, QString("Circle%1").arg(++m_EllipseCounter)); this->GetDataStorage()->Modified(); MITK_INFO << "PlanarCircle created ..."; //call mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll(); mitk::DataNode* node = 0; mitk::PlanarFigureInteractor::Pointer figureInteractor = 0; mitk::PlanarFigure* figureP = 0; for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End() ; it++) { node = const_cast(it->Value().GetPointer()); figureP = dynamic_cast(node->GetData()); if(figureP) { figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); } } } void QmitkFiberProcessingView::Activated() { MITK_INFO << "FB OPerations ACTIVATED()"; /* mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll(); mitk::DataNode* node = 0; mitk::PlanarFigureInteractor::Pointer figureInteractor = 0; mitk::PlanarFigure* figure = 0; for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End() ; it++) { node = const_cast(it->Value().GetPointer()); figure = dynamic_cast(node->GetData()); if(figure) { figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); } } */ } void QmitkFiberProcessingView::AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char *propertyKey, mitk::BaseProperty *property ) { // initialize figure's geometry with empty geometry mitk::PlaneGeometry::Pointer emptygeometry = mitk::PlaneGeometry::New(); figure->SetGeometry2D( emptygeometry ); //set desired data to DataNode where Planarfigure is stored mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetName(name.toStdString()); newNode->SetData(figure); newNode->AddProperty( "planarfigure.default.line.color", mitk::ColorProperty::New(1.0,0.0,0.0)); newNode->AddProperty( "planarfigure.line.width", mitk::FloatProperty::New(2.0)); newNode->AddProperty( "planarfigure.drawshadow", mitk::BoolProperty::New(true)); newNode->AddProperty( "selected", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.ishovering", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.drawoutline", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.drawquantities", mitk::BoolProperty::New(false) ); newNode->AddProperty( "planarfigure.drawshadow", mitk::BoolProperty::New(true) ); newNode->AddProperty( "planarfigure.line.width", mitk::FloatProperty::New(3.0) ); newNode->AddProperty( "planarfigure.shadow.widthmodifier", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.outline.width", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.helperline.width", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.line.color", mitk::ColorProperty::New(1.0,1.0,1.0) ); newNode->AddProperty( "planarfigure.default.line.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.default.outline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.default.helperline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.markerline.color", mitk::ColorProperty::New(0.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.default.markerline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.default.marker.color", mitk::ColorProperty::New(1.0,1.0,1.0) ); newNode->AddProperty( "planarfigure.default.marker.opacity",mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.line.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.line.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.outline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.helperline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.markerline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.markerline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.hover.marker.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.hover.marker.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.line.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.line.opacity",mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.outline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.outline.opacity", mitk::FloatProperty::New(2.0)); newNode->AddProperty( "planarfigure.selected.helperline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.helperline.opacity",mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.markerline.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.markerline.opacity", mitk::FloatProperty::New(2.0) ); newNode->AddProperty( "planarfigure.selected.marker.color", mitk::ColorProperty::New(1.0,0.0,0.0) ); newNode->AddProperty( "planarfigure.selected.marker.opacity",mitk::FloatProperty::New(2.0)); // figure drawn on the topmost layer / image newNode->SetColor(1.0,1.0,1.0); newNode->SetOpacity(0.8); GetDataStorage()->Add(newNode ); std::vector selectedNodes = GetDataManagerSelection(); for(unsigned int i = 0; i < selectedNodes.size(); i++) { selectedNodes[i]->SetSelected(false); } newNode->SetSelected(true); } void QmitkFiberProcessingView::DoFiberExtraction() { if ( m_SelectedFB.empty() ){ QMessageBox::information( NULL, "Warning", "No fibe bundle selected!"); MITK_WARN("QmitkFiberProcessingView") << "no fibe bundle selected"; return; } for (int i=0; i(m_SelectedFB.at(i)->GetData()); mitk::PlanarFigure::Pointer roi = dynamic_cast (m_SelectedPF.at(0)->GetData()); mitk::FiberBundleX::Pointer extFB = fib->ExtractFiberSubset(roi); if (extFB->GetNumFibers()<=0) continue; mitk::DataNode::Pointer node; node = mitk::DataNode::New(); node->SetData(extFB); QString name(m_SelectedFB.at(i)->GetName().c_str()); name += "_"; name += m_SelectedPF.at(0)->GetName().c_str(); node->SetName(name.toStdString()); GetDataStorage()->Add(node); m_SelectedFB.at(i)->SetVisibility(false); } } void QmitkFiberProcessingView::GenerateAndComposite() { mitk::PlanarFigureComposite::Pointer PFCAnd = mitk::PlanarFigureComposite::New(); mitk::PlaneGeometry* currentGeometry2D = dynamic_cast( const_cast(GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D())); PFCAnd->SetGeometry2D(currentGeometry2D); PFCAnd->setOperationType(mitk::PFCOMPOSITION_AND_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; mitk::PlanarFigure::Pointer tmpPF = dynamic_cast( nodePF->GetData() ); PFCAnd->addPlanarFigure( tmpPF ); PFCAnd->addDataNode( nodePF ); PFCAnd->setDisplayName("AND_COMPO"); } AddCompositeToDatastorage(PFCAnd, NULL); } void QmitkFiberProcessingView::GenerateOrComposite() { mitk::PlanarFigureComposite::Pointer PFCOr = mitk::PlanarFigureComposite::New(); mitk::PlaneGeometry* currentGeometry2D = dynamic_cast( const_cast(GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D())); PFCOr->SetGeometry2D(currentGeometry2D); PFCOr->setOperationType(mitk::PFCOMPOSITION_OR_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; mitk::PlanarFigure::Pointer tmpPF = dynamic_cast( nodePF->GetData() ); PFCOr->addPlanarFigure( tmpPF ); PFCOr->addDataNode( nodePF ); PFCOr->setDisplayName("OR_COMPO"); } AddCompositeToDatastorage(PFCOr, NULL); } void QmitkFiberProcessingView::GenerateNotComposite() { mitk::PlanarFigureComposite::Pointer PFCNot = mitk::PlanarFigureComposite::New(); mitk::PlaneGeometry* currentGeometry2D = dynamic_cast( const_cast(GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderer()->GetCurrentWorldGeometry2D())); PFCNot->SetGeometry2D(currentGeometry2D); PFCNot->setOperationType(mitk::PFCOMPOSITION_NOT_OPERATION); for( std::vector::iterator it = m_SelectedPF.begin(); it != m_SelectedPF.end(); ++it ) { mitk::DataNode::Pointer nodePF = *it; mitk::PlanarFigure::Pointer tmpPF = dynamic_cast( nodePF->GetData() ); PFCNot->addPlanarFigure( tmpPF ); PFCNot->addDataNode( nodePF ); PFCNot->setDisplayName("NOT_COMPO"); } AddCompositeToDatastorage(PFCNot, NULL); } /* CLEANUP NEEDED */ void QmitkFiberProcessingView::AddCompositeToDatastorage(mitk::PlanarFigureComposite::Pointer pfcomp, mitk::DataNode::Pointer parentDataNode ) { mitk::DataNode::Pointer newPFCNode; newPFCNode = mitk::DataNode::New(); newPFCNode->SetName( pfcomp->getDisplayName() ); newPFCNode->SetData(pfcomp); newPFCNode->SetVisibility(true); switch (pfcomp->getOperationType()) { case 0: { if (!parentDataNode.IsNull()) { GetDataStorage()->Add(newPFCNode, parentDataNode); } else { GetDataStorage()->Add(newPFCNode); } //iterate through its childs for(int i=0; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if ( !pfcompcast.IsNull() ) { // child is of type planar Figure composite // make new node of the child, cuz later the child has to be removed of its old position in datamanager // feed new dataNode with information of the savedDataNode, which is gonna be removed soon mitk::DataNode::Pointer newChildPFCNode; newChildPFCNode = mitk::DataNode::New(); newChildPFCNode->SetData(tmpPFchild); newChildPFCNode->SetName( savedPFchildNode->GetName() ); pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user //update inside vector the dataNodePointer pfcomp->replaceDataNodeAt(i, newChildPFCNode); AddCompositeToDatastorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent // remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager // without having its parent anymore //GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_INFO << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " still exists"; } } else { // child is not of type PlanarFigureComposite, so its one of the planarFigures // create new dataNode containing the data of the old dataNode, but position in dataManager will be // modified cuz we re setting a (new) parent. mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New(); newPFchildNode->SetName(savedPFchildNode->GetName() ); newPFchildNode->SetData(tmpPFchild); newPFchildNode->SetVisibility(true); // replace the dataNode in PFComp DataNodeVector pfcomp->replaceDataNodeAt(i, newPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; } else { MITK_INFO << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " still exists"; } MITK_INFO << "adding " << newPFchildNode->GetName() << " to " << newPFCNode->GetName(); //add new child to datamanager with its new position as child of newPFCNode parent GetDataStorage()->Add(newPFchildNode, newPFCNode); } } GetDataStorage()->Modified(); break; } case 1: { if (!parentDataNode.IsNull()) { MITK_INFO << "adding " << newPFCNode->GetName() << " to " << parentDataNode->GetName() ; GetDataStorage()->Add(newPFCNode, parentDataNode); } else { MITK_INFO << "adding " << newPFCNode->GetName(); GetDataStorage()->Add(newPFCNode); } for(int i=0; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if ( !pfcompcast.IsNull() ) { // child is of type planar Figure composite // make new node of the child, cuz later the child has to be removed of its old position in datamanager // feed new dataNode with information of the savedDataNode, which is gonna be removed soon mitk::DataNode::Pointer newChildPFCNode; newChildPFCNode = mitk::DataNode::New(); newChildPFCNode->SetData(tmpPFchild); newChildPFCNode->SetName( savedPFchildNode->GetName() ); pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user //update inside vector the dataNodePointer pfcomp->replaceDataNodeAt(i, newChildPFCNode); AddCompositeToDatastorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent // remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager // without having its parent anymore //GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_INFO << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " still exists"; } } else { // child is not of type PlanarFigureComposite, so its one of the planarFigures // create new dataNode containing the data of the old dataNode, but position in dataManager will be // modified cuz we re setting a (new) parent. mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New(); newPFchildNode->SetName(savedPFchildNode->GetName() ); newPFchildNode->SetData(tmpPFchild); newPFchildNode->SetVisibility(true); // replace the dataNode in PFComp DataNodeVector pfcomp->replaceDataNodeAt(i, newPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_INFO << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " still exists"; } MITK_INFO << "adding " << newPFchildNode->GetName() << " to " << newPFCNode->GetName(); //add new child to datamanager with its new position as child of newPFCNode parent GetDataStorage()->Add(newPFchildNode, newPFCNode); } } GetDataStorage()->Modified(); break; } case 2: { if (!parentDataNode.IsNull()) { MITK_INFO << "adding " << newPFCNode->GetName() << " to " << parentDataNode->GetName() ; GetDataStorage()->Add(newPFCNode, parentDataNode); } else { MITK_INFO << "adding " << newPFCNode->GetName(); GetDataStorage()->Add(newPFCNode); } //iterate through its childs for(int i=0; igetNumberOfChildren(); ++i) { mitk::PlanarFigure::Pointer tmpPFchild = pfcomp->getChildAt(i); mitk::DataNode::Pointer savedPFchildNode = pfcomp->getDataNodeAt(i); mitk::PlanarFigureComposite::Pointer pfcompcast= dynamic_cast(tmpPFchild.GetPointer()); if ( !pfcompcast.IsNull() ) { // child is of type planar Figure composite // makeRemoveBundle new node of the child, cuz later the child has to be removed of its old position in datamanager // feed new dataNode with information of the savedDataNode, which is gonna be removed soon mitk::DataNode::Pointer newChildPFCNode; newChildPFCNode = mitk::DataNode::New(); newChildPFCNode->SetData(tmpPFchild); newChildPFCNode->SetName( savedPFchildNode->GetName() ); pfcompcast->setDisplayName( savedPFchildNode->GetName() ); //name might be changed in DataManager by user //update inside vector the dataNodePointer pfcomp->replaceDataNodeAt(i, newChildPFCNode); AddCompositeToDatastorage(pfcompcast, newPFCNode); //the current PFCNode becomes the childs parent // remove savedNode here, cuz otherwise its children will change their position in the dataNodeManager // without having its parent anymore //GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_INFO << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " still exists"; } } else { // child is not of type PlanarFigureComposite, so its one of the planarFigures // create new dataNode containing the data of the old dataNode, but position in dataManager will be // modified cuz we re setting a (new) parent. mitk::DataNode::Pointer newPFchildNode = mitk::DataNode::New(); newPFchildNode->SetName(savedPFchildNode->GetName() ); newPFchildNode->SetData(tmpPFchild); newPFchildNode->SetVisibility(true); // replace the dataNode in PFComp DataNodeVector pfcomp->replaceDataNodeAt(i, newPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " exists in DS...trying to remove it"; }else{ MITK_INFO << "[ERROR] does NOT exist, but can I read its Name? " << savedPFchildNode->GetName(); } // remove old child position in dataStorage GetDataStorage()->Remove(savedPFchildNode); if ( GetDataStorage()->Exists(savedPFchildNode)) { MITK_INFO << savedPFchildNode->GetName() << " still exists"; } MITK_INFO << "adding " << newPFchildNode->GetName() << " to " << newPFCNode->GetName(); //add new child to datamanager with its new position as child of newPFCNode parent GetDataStorage()->Add(newPFchildNode, newPFCNode); } } GetDataStorage()->Modified(); break; } default: MITK_INFO << "we have an UNDEFINED composition... ERROR" ; break; } } void QmitkFiberProcessingView::JoinBundles() { if ( m_SelectedFB.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedFB.begin(); mitk::FiberBundleX::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (it; it!=m_SelectedFB.end(); ++it) { newBundle = newBundle->AddBundle(dynamic_cast((*it)->GetData())); name += "+"+QString((*it)->GetName().c_str()); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); } void QmitkFiberProcessingView::SubstractBundles() { if ( m_SelectedFB.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedFB.begin(); mitk::FiberBundleX::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (it; it!=m_SelectedFB.end(); ++it) { newBundle = newBundle->SubtractBundle(dynamic_cast((*it)->GetData())); if (newBundle.IsNull()) break; name += "-"+QString((*it)->GetName().c_str()); } if (newBundle.IsNull()) { QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers. Did you select the fiber bundles in the correct order? X-Y is not equal to Y-X!"); return; } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); } void QmitkFiberProcessingView::GenerateStats() { if ( m_SelectedFB.empty() ) return; QString stats(""); for( int i=0; i(node->GetData())) { if (i>0) stats += "\n-----------------------------\n"; stats += QString(node->GetName().c_str()) + "\n"; mitk::FiberBundleX::Pointer fib = dynamic_cast(node->GetData()); vtkSmartPointer fiberPolyData = fib->GetFiberPolyData(); vtkSmartPointer vLines = fiberPolyData->GetLines(); vLines->InitTraversal(); int numberOfLines = vLines->GetNumberOfCells(); stats += "Number of fibers: "+ QString::number(numberOfLines) + "\n"; float length = 0; std::vector lengths; for (int i=0; iGetNextCell ( numPoints, points ); float l=0; for (unsigned int j=0; j p1; itk::Point p2; fiberPolyData->GetPoint(points[j], p1.GetDataPointer()); fiberPolyData->GetPoint(points[j+1], p2.GetDataPointer()); float dist = p1.EuclideanDistanceTo(p2); length += dist; l += dist; } itk::Point p2; fiberPolyData->GetPoint(points[numPoints-1], p2.GetDataPointer()); lengths.push_back(l); } std::sort(lengths.begin(), lengths.end()); if (numberOfLines>0) length /= numberOfLines; float dev=0; int count = 0; vLines->InitTraversal(); for (int i=0; iGetNextCell ( numPoints, points ); float l=0; for (unsigned int j=0; j p1; itk::Point p2; fiberPolyData->GetPoint(points[j], p1.GetDataPointer()); fiberPolyData->GetPoint(points[j+1], p2.GetDataPointer()); float dist = p1.EuclideanDistanceTo(p2); l += dist; } dev += (length-l)*(length-l); count++; } if (numberOfLines>1) dev /= (numberOfLines-1); else dev = 0; stats += "Min. length: "+ QString::number(lengths.front(),'f',1) + " mm\n"; stats += "Max. length: "+ QString::number(lengths.back(),'f',1) + " mm\n"; stats += "Mean length: "+ QString::number(length,'f',1) + " mm\n"; stats += "Median length: "+ QString::number(lengths.at(lengths.size()/2),'f',1) + " mm\n"; stats += "Standard deviation: "+ QString::number(sqrt(dev),'f',1) + " mm\n"; } } this->m_Controls->m_StatsTextEdit->setText(stats); } void QmitkFiberProcessingView::ProcessSelectedBundles() { if ( m_SelectedFB.empty() ){ QMessageBox::information( NULL, "Warning", "No fibe bundle selected!"); MITK_WARN("QmitkFiberProcessingView") << "no fibe bundle selected"; return; } int generationMethod = m_Controls->m_GenerationBox->currentIndex(); for( int i=0; i(node->GetData())) { mitk::FiberBundleX::Pointer fib = dynamic_cast(node->GetData()); QString name(node->GetName().c_str()); DataNode::Pointer newNode = NULL; switch(generationMethod){ case 0: newNode = GenerateTractDensityImage(fib, false); name += "_TDI"; break; case 1: newNode = GenerateTractDensityImage(fib, true); name += "_envelope"; break; case 2: newNode = GenerateColorHeatmap(fib); break; case 3: newNode = GenerateFiberEndingsImage(fib); name += "_fiber_endings"; break; case 4: newNode = GenerateFiberEndingsPointSet(fib); name += "_fiber_endings"; break; } if (newNode.IsNotNull()) { newNode->SetName(name.toStdString()); GetDataStorage()->Add(newNode); } } } } // generate pointset displaying the fiber endings mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateFiberEndingsPointSet(mitk::FiberBundleX::Pointer fib) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); vtkSmartPointer fiberPolyData = fib->GetFiberPolyData(); vtkSmartPointer vLines = fiberPolyData->GetLines(); vLines->InitTraversal(); int count = 0; int numFibers = fib->GetNumFibers(); for( int i=0; iGetNextCell ( numPoints, points ); if (numPoints>0) { double* point = fiberPolyData->GetPoint(points[0]); itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; pointSet->InsertPoint(count, itkPoint); count++; } if (numPoints>2) { double* point = fiberPolyData->GetPoint(points[numPoints-1]); itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; pointSet->InsertPoint(count, itkPoint); count++; } } mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( pointSet ); return node; } // generate image displaying the fiber endings mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateFiberEndingsImage(mitk::FiberBundleX::Pointer fib) { typedef unsigned char OutPixType; typedef itk::Image OutImageType; typedef itk::TractsToFiberEndingsImageFilter< OutImageType > ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); generator->SetFiberBundle(fib); generator->SetInvertImage(m_Controls->m_InvertCheckbox->isChecked()); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { OutImageType::Pointer itkImage = OutImageType::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image OutImageType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } // generate rgba heatmap from fiber bundle mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateColorHeatmap(mitk::FiberBundleX::Pointer fib) { typedef itk::RGBAPixel OutPixType; typedef itk::Image OutImageType; typedef itk::TractsToRgbaImageFilter< OutImageType > ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); generator->SetFiberBundle(fib); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { itk::Image::Pointer itkImage = itk::Image::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } // generate tract density image from fiber bundle mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateTractDensityImage(mitk::FiberBundleX::Pointer fib, bool binary) { typedef float OutPixType; typedef itk::Image OutImageType; itk::TractDensityImageFilter< OutImageType >::Pointer generator = itk::TractDensityImageFilter< OutImageType >::New(); generator->SetFiberBundle(fib); generator->SetBinaryOutput(binary); generator->SetInvertImage(m_Controls->m_InvertCheckbox->isChecked()); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { OutImageType::Pointer itkImage = OutImageType::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } void QmitkFiberProcessingView::ResampleSelectedBundles() { int factor = this->m_Controls->m_ResampleFibersSpinBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); fib->DoFiberSmoothing(factor); } } void QmitkFiberProcessingView::DoFaColorCoding() { if (m_SelectedImage.IsNull()) return; // mitk::PixelType pType = mitk::MakeScalarPixelType(); // if (m_SelectedImage->GetPixelType()!=pType) // { // //mitk::Image bla; bla.GetPixelType().GetNameOfClass() // MITK_INFO << m_SelectedImage->GetPixelType().GetNameOfClass(); // QMessageBox::warning(NULL, "Wrong Image Type", "FA/GFA image should be of type float"); //// return; // } for( int i=0; i(m_SelectedFB.at(i)->GetData()); fib->SetFAMap(m_SelectedImage); fib->SetColorCoding(mitk::FiberBundleX::COLORCODING_FA_BASED); fib->DoColorCodingFaBased(); } if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui index c1cf883f2d..e907ff8063 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingViewControls.ui @@ -1,683 +1,683 @@ QmitkFiberProcessingViewControls 0 0 665 587 Form 0 9 3 9 3 Fiber Bundle Modification 0 0 200 0 16777215 60 QFrame::NoFrame QFrame::Raised 0 30 30 Draw circular ROI. Select reference fiber bundle to execute. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true 30 30 Draw rectangular ROI. Select reference fiber bundle to execute. :/QmitkDiffusionImaging/rectangle.png:/QmitkDiffusionImaging/rectangle.png 32 32 true true 30 30 Draw polygonal ROI. Select reference fiber bundle to execute. :/QmitkDiffusionImaging/polygon.png:/QmitkDiffusionImaging/polygon.png 32 32 true true Qt::Horizontal 40 20 QFrame::NoFrame QFrame::Raised 0 false 0 0 200 16777215 11 Extract fibers passing through selected ROI or composite ROI. Select ROI and fiber bundle to execute. Extract false 0 0 200 16777215 11 Returns all fibers contained in bundle X that are not contained in bundle Y (not commutative!). Select at least two fiber bundles to execute. Substract false 0 0 200 16777215 11 Merge selected fiber bundles. Select at least two fiber bundles to execute. Join Qt::Horizontal 40 20 false 0 0 200 16777215 11 Extract fibers passing through selected surface mesh. Select surface mesh and fiber bundle to execute. Extract 3D false 0 0 16777215 16777215 11 Generate a binary image containing all selected ROIs. Select at least one ROI (planar figure) and a reference fiber bundle or image. ROI Image 0 0 200 0 16777215 60 QFrame::NoFrame QFrame::Raised 0 Qt::Horizontal 40 20 false 60 16777215 Create AND composition with selected ROIs. AND false 60 16777215 Create OR composition with selected ROIs. OR false 60 16777215 Create NOT composition from selected ROI. NOT Fiber Bundle Processing 0 0 Tract Density Image (TDI) Binary Envelope Fiber Bundle Image Fiber Endings Image Fiber Endings Pointset Upsampling factor 1 10 2 false 0 0 200 16777215 11 Perform selected operation on all selected fiber bundles. Generate If selected operation generates an image, the inverse image is returned. Invert false 0 0 200 16777215 11 Resample fibers using a Kochanek spline interpolation. Smooth Fibers Points per cm 1 50 10 false 0 0 200 16777215 11 - Resample fibers using a Kochanek spline interpolation. + Apply float image values (0-1) as color coding to the selected fiber bundle. - FA Color Coding + Color By Scalar Map Fiber Bundle Statistics Courier 10 Pitch false true Qt::Vertical 20 40 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkIVIMView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkIVIMView.cpp index 4ca5b1f513..17eb182803 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkIVIMView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkIVIMView.cpp @@ -1,842 +1,814 @@ /*========================================================================= Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkIVIMView.h" #include "QmitkStdMultiWidget.h" // qt #include "qmessagebox.h" #include "qclipboard.h" // mitk #include "mitkDiffusionImage.h" #include "mitkImageCast.h" // itk #include "itkScalarImageToHistogramGenerator.h" #include "itkRegionOfInterestImageFilter.h" #include "itkImageRegionConstIteratorWithIndex.h" // itk/mitk #include "itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h" #include "itkRegularizedIVIMReconstructionFilter.h" #include "mitkImageCast.h" const std::string QmitkIVIMView::VIEW_ID = "org.mitk.views.ivim"; QmitkIVIMView::QmitkIVIMView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_Active(false) , m_SliceObserverTag1(0), m_SliceObserverTag2(0), m_SliceObserverTag3(0) + , m_DiffusionImageNode(NULL) + , m_MaskImageNode(NULL) { } QmitkIVIMView::~QmitkIVIMView() { QmitkStdMultiWidget* MultiWidget = this->GetActiveStdMultiWidget(false); if(MultiWidget) { //unregister observers when view is destroyed if( MultiWidget->mitkWidget1 != NULL && m_SliceObserverTag1 != 0) { mitk::SliceNavigationController* slicer = MultiWidget->mitkWidget1->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag1 ); } if( MultiWidget->mitkWidget2 != NULL && m_SliceObserverTag2 != 0) { mitk::SliceNavigationController* slicer = MultiWidget->mitkWidget2->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag2 ); } if( MultiWidget->mitkWidget3!= NULL && m_SliceObserverTag3 != 0) { mitk::SliceNavigationController* slicer = MultiWidget->mitkWidget3->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag3 ); } } } void QmitkIVIMView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkIVIMViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_ButtonStart, SIGNAL(clicked()), this, SLOT(FittIVIMStart()) ); connect( m_Controls->m_ButtonAutoThres, SIGNAL(clicked()), this, SLOT(AutoThreshold()) ); connect( m_Controls->m_MethodCombo, SIGNAL(currentIndexChanged(int)), this, SLOT(MethodCombo(int)) ); connect( m_Controls->m_DStarSlider, SIGNAL(valueChanged(int)), this, SLOT(DStarSlider(int)) ); connect( m_Controls->m_BThreshSlider, SIGNAL(valueChanged(int)), this, SLOT(BThreshSlider(int)) ); connect( m_Controls->m_S0ThreshSlider, SIGNAL(valueChanged(int)), this, SLOT(S0ThreshSlider(int)) ); connect( m_Controls->m_NumItSlider, SIGNAL(valueChanged(int)), this, SLOT(NumItsSlider(int)) ); connect( m_Controls->m_LambdaSlider, SIGNAL(valueChanged(int)), this, SLOT(LambdaSlider(int)) ); connect( m_Controls->m_DisplayResultsCheckbox, SIGNAL(clicked()), this, SLOT(Checkbox()) ); connect( m_Controls->m_CheckDStar, SIGNAL(clicked()), this, SLOT(Checkbox()) ); connect( m_Controls->m_CheckD, SIGNAL(clicked()), this, SLOT(Checkbox()) ); connect( m_Controls->m_Checkf, SIGNAL(clicked()), this, SLOT(Checkbox()) ); connect( m_Controls->m_ChooseMethod, SIGNAL(clicked()), this, SLOT(ChooseMethod()) ); connect( m_Controls->m_CurveClipboard, SIGNAL(clicked()), this, SLOT(ClipboardCurveButtonClicked()) ); connect( m_Controls->m_ValuesClipboard, SIGNAL(clicked()), this, SLOT(ClipboardStatisticsButtonClicked()) ); } QString dstar = QString::number(m_Controls->m_DStarSlider->value()/1000.0); m_Controls->m_DStarLabel->setText(dstar); QString bthresh = QString::number(m_Controls->m_BThreshSlider->value()*5.0); m_Controls->m_BThreshLabel->setText(bthresh); QString s0thresh = QString::number(m_Controls->m_S0ThreshSlider->value()*0.5); m_Controls->m_S0ThreshLabel->setText(s0thresh); QString numits = QString::number(m_Controls->m_NumItSlider->value()); m_Controls->m_NumItsLabel->setText(numits); QString lambda = QString::number(m_Controls->m_LambdaSlider->value()*.00001); m_Controls->m_LambdaLabel->setText(lambda); m_Controls->m_VisualizeResultsWidget->setVisible(m_Controls->m_DisplayResultsCheckbox->isChecked()); m_Controls->m_MethodCombo->setVisible(m_Controls->m_ChooseMethod->isChecked()); - -// m_Controls->m_ADCBValues->setVisible(m_Controls->m_CheckADC->isChecked()); + m_Controls->m_Warning->setVisible(false); MethodCombo(m_Controls->m_MethodCombo->currentIndex()); } void QmitkIVIMView::Checkbox() { m_Controls->m_VisualizeResultsWidget->setVisible(m_Controls->m_DisplayResultsCheckbox->isChecked()); // m_Controls->m_ADCBValues->setVisible(m_Controls->m_CheckADC->isChecked()); itk::StartEvent dummy; OnSliceChanged(dummy); } void QmitkIVIMView::MethodCombo(int val) { switch(val) { case 0: - m_Controls->dstar->setVisible(false); - m_Controls->thres->setVisible(false); - m_Controls->thres_2->setVisible(true); - m_Controls->m_RegFrame->setVisible(false); + m_Controls->m_DstarFrame->setVisible(false); + m_Controls->m_NeglSiFrame->setVisible(true); + m_Controls->m_NeglBframe->setVisible(false); + m_Controls->m_IterationsFrame->setVisible(false); + m_Controls->m_LambdaFrame->setVisible(false); break; case 1: - m_Controls->dstar->setVisible(true); - m_Controls->thres->setVisible(false); - m_Controls->thres_2->setVisible(true); - m_Controls->m_RegFrame->setVisible(false); + m_Controls->m_DstarFrame->setVisible(true); + m_Controls->m_NeglSiFrame->setVisible(true); + m_Controls->m_NeglBframe->setVisible(false); + m_Controls->m_IterationsFrame->setVisible(false); + m_Controls->m_LambdaFrame->setVisible(false); break; case 2: - m_Controls->dstar->setVisible(false); - m_Controls->thres->setVisible(true); - m_Controls->thres_2->setVisible(true); - m_Controls->m_RegFrame->setVisible(false); + m_Controls->m_DstarFrame->setVisible(false); + m_Controls->m_NeglSiFrame->setVisible(true); + m_Controls->m_NeglBframe->setVisible(true); + m_Controls->m_IterationsFrame->setVisible(false); + m_Controls->m_LambdaFrame->setVisible(false); break; case 3: - m_Controls->dstar->setVisible(false); - m_Controls->thres->setVisible(true); - m_Controls->thres_2->setVisible(true); - m_Controls->m_RegFrame->setVisible(false); + m_Controls->m_DstarFrame->setVisible(false); + m_Controls->m_NeglSiFrame->setVisible(true); + m_Controls->m_NeglBframe->setVisible(true); + m_Controls->m_IterationsFrame->setVisible(false); + m_Controls->m_LambdaFrame->setVisible(false); break; case 4: - m_Controls->dstar->setVisible(false); - m_Controls->thres->setVisible(true); - m_Controls->thres_2->setVisible(true); - m_Controls->m_RegFrame->setVisible(true); + m_Controls->m_DstarFrame->setVisible(false); + m_Controls->m_NeglSiFrame->setVisible(false); + m_Controls->m_NeglBframe->setVisible(false); + m_Controls->m_IterationsFrame->setVisible(false); + m_Controls->m_LambdaFrame->setVisible(false); break; } itk::StartEvent dummy; OnSliceChanged(dummy); } void QmitkIVIMView::DStarSlider (int val) { QString sval = QString::number(val/1000.0); m_Controls->m_DStarLabel->setText(sval); itk::StartEvent dummy; OnSliceChanged(dummy); } void QmitkIVIMView::BThreshSlider (int val) { QString sval = QString::number(val*5.0); m_Controls->m_BThreshLabel->setText(sval); itk::StartEvent dummy; OnSliceChanged(dummy); } void QmitkIVIMView::S0ThreshSlider (int val) { QString sval = QString::number(val*0.5); m_Controls->m_S0ThreshLabel->setText(sval); itk::StartEvent dummy; OnSliceChanged(dummy); } void QmitkIVIMView::NumItsSlider (int val) { QString sval = QString::number(val); m_Controls->m_NumItsLabel->setText(sval); itk::StartEvent dummy; OnSliceChanged(dummy); } void QmitkIVIMView::LambdaSlider (int val) { QString sval = QString::number(val*.00001); m_Controls->m_LambdaLabel->setText(sval); itk::StartEvent dummy; OnSliceChanged(dummy); } void QmitkIVIMView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget1->GetSliceNavigationController(); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkIVIMView::OnSliceChanged ); m_SliceObserverTag1 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(NULL, 0), command ); } { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget2->GetSliceNavigationController(); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkIVIMView::OnSliceChanged ); m_SliceObserverTag2 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(NULL, 0), command ); } { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget3->GetSliceNavigationController(); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkIVIMView::OnSliceChanged ); m_SliceObserverTag3 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(NULL, 0), command ); } } void QmitkIVIMView::StdMultiWidgetNotAvailable() { { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget1->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag1 ); } { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget2->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag2 ); } { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget3->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag3 ); } m_MultiWidget = NULL; } void QmitkIVIMView::OnSelectionChanged( std::vector nodes ) { bool foundOneDiffusionImage = false; + m_Controls->m_DiffusionImageLabel->setText("-"); + m_Controls->m_MaskImageLabel->setText("-"); + m_MaskImageNode = NULL; + m_DiffusionImageNode = NULL; // iterate all selected objects, adjust warning visibility - for( std::vector::iterator it = nodes.begin(); - it != nodes.end(); - ++it ) + for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; - if( node.IsNotNull() ) + if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { - mitk::DiffusionImage* img = dynamic_cast*>(node->GetData()); - if( img ) + if( dynamic_cast*>(node->GetData()) ) { - if(!foundOneDiffusionImage ) - { - foundOneDiffusionImage = true; - } - else + m_DiffusionImageNode = node; + foundOneDiffusionImage = true; + m_Controls->m_DiffusionImageLabel->setText(node->GetName().c_str()); + } + else + { + bool isBinary = false; + node->GetPropertyValue("binary", isBinary); + if (isBinary) { - foundOneDiffusionImage = false; + m_MaskImageNode = node; + m_Controls->m_MaskImageLabel->setText(node->GetName().c_str()); } } } } -// m_Controls->m_ADCBValues->setVisible( foundOneDiffusionImage && m_Controls->m_CheckADC->isChecked() ); - m_Controls->m_ButtonStart->setEnabled( foundOneDiffusionImage ); m_Controls->m_ButtonAutoThres->setEnabled( foundOneDiffusionImage ); m_Controls->m_ControlsFrame->setEnabled( foundOneDiffusionImage ); m_Controls->m_BottomControlsFrame->setEnabled( foundOneDiffusionImage ); itk::StartEvent dummy; OnSliceChanged(dummy); } void QmitkIVIMView::AutoThreshold() { std::vector nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; if (!nodes.front()) { // Nothing selected. Inform the user and return QMessageBox::information( NULL, "Template", "Please load and select a diffusion image before starting image processing."); return; } typedef mitk::DiffusionImage DiffImgType; DiffImgType* dimg = dynamic_cast(nodes.front()->GetData()); if (!dimg) { // Nothing selected. Inform the user and return QMessageBox::information( NULL, "Template", "No valid diffusion image was found."); return; } // find bzero index int index = -1; DiffImgType::GradientDirectionContainerType::Pointer directions = dimg->GetDirections(); for(DiffImgType::GradientDirectionContainerType::ConstIterator it = directions->Begin(); it != directions->End(); ++it) { index++; DiffImgType::GradientDirectionType g = it.Value(); if(g[0] == 0 && g[1] == 0 && g[2] == 0 ) break; } typedef itk::VectorImage VecImgType; VecImgType::Pointer vecimg = dimg->GetVectorImage(); int vecLength = vecimg->GetVectorLength(); index = index > vecLength-1 ? vecLength-1 : index; MITK_INFO << "Performing Histogram Analysis on Channel" << index; typedef itk::Image ImgType; ImgType::Pointer img = ImgType::New(); mitk::CastToItkImage(dimg, img); itk::ImageRegionIterator itw (img, img->GetLargestPossibleRegion() ); itw = itw.Begin(); itk::ImageRegionConstIterator itr (vecimg, vecimg->GetLargestPossibleRegion() ); itr = itr.Begin(); while(!itr.IsAtEnd()) { itw.Set(itr.Get().GetElement(index)); ++itr; ++itw; } typedef itk::Statistics::ScalarImageToHistogramGenerator< ImgType > HistogramGeneratorType; typedef HistogramGeneratorType::HistogramType HistogramType; HistogramGeneratorType::Pointer histogramGenerator = HistogramGeneratorType::New(); histogramGenerator->SetInput( img ); histogramGenerator->SetMarginalScale( 10 ); // Defines y-margin width of histogram histogramGenerator->SetNumberOfBins( 100 ); // CT range [-1024, +2048] --> bin size 4 values histogramGenerator->SetHistogramMin( dimg->GetScalarValueMin() ); histogramGenerator->SetHistogramMax( dimg->GetScalarValueMax() * .5 ); histogramGenerator->Compute(); HistogramType::ConstIterator iter = histogramGenerator->GetOutput()->Begin(); float maxFreq = 0; float maxValue = 0; while ( iter != histogramGenerator->GetOutput()->End() ) { if(iter.GetFrequency() > maxFreq) { maxFreq = iter.GetFrequency(); maxValue = iter.GetMeasurementVector()[0]; } ++iter; } maxValue *= 2; int sliderPos = maxValue * 2; m_Controls->m_S0ThreshSlider->setValue(sliderPos); S0ThreshSlider(sliderPos); } void QmitkIVIMView::FittIVIMStart() { std::vector nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; if (!nodes.front()) { // Nothing selected. Inform the user and return QMessageBox::information( NULL, "Template", "Please load and select a diffusion image before starting image processing."); return; } mitk::DiffusionImage* img = dynamic_cast*>( nodes.front()->GetData()); if (!img) { // Nothing selected. Inform the user and return QMessageBox::information( NULL, "Template", "No valid diffusion image was found."); return; } typedef itk::VectorImage VecImgType; VecImgType::Pointer vecimg = img->GetVectorImage(); OutImgType::IndexType dummy; FittIVIM(vecimg, img->GetDirections(), img->GetB_Value(), true, dummy); OutputToDatastorage(nodes); } void QmitkIVIMView::OnSliceChanged(const itk::EventObject& /*e*/) { - if(!m_Controls) + m_Controls->m_Warning->setVisible(false); + if(!m_Controls || m_DiffusionImageNode.IsNull()) return; - m_Controls->m_Warning->setVisible(false); - if(!m_Active) - return; +// if(!m_Active) +// return; m_Controls->m_VisualizeResultsWidget->setVisible(false); if(!m_Controls->m_DisplayResultsCheckbox->isChecked()) return; - std::vector nodes = this->GetDataManagerSelection(); - if (nodes.empty()) return; - if (!nodes.front()) return; - if (nodes.size()>2) return; - - mitk::DiffusionImage* diffusionImg = 0; - mitk::DiffusionImage* img1 = - dynamic_cast*>( - nodes.front()->GetData()); - - mitk::DiffusionImage* img2 = 0; - mitk::Image* maskImg = 0; - if(nodes.size()>1) - { - if(img1) - { - if(strcmp(nodes.at(1)->GetData()->GetNameOfClass(), "Image") != 0 ) - return; - - maskImg = dynamic_cast( - nodes.at(1)->GetData()); - - diffusionImg = img1; - } - else - { - if(strcmp(nodes.front()->GetData()->GetNameOfClass(), "Image") != 0 ) - return; - - maskImg = dynamic_cast( - nodes.front()->GetData()); - - diffusionImg = dynamic_cast*>( - nodes.at(1)->GetData()); - } - } - else - { - diffusionImg = img1; - } - if (nodes.size()==2 && (!diffusionImg || !maskImg || m_Controls->m_MethodCombo->currentIndex() == 4 )) return; - if (nodes.size()==1 && !diffusionImg) return; + mitk::DiffusionImage::Pointer diffusionImg = dynamic_cast*>(m_DiffusionImageNode->GetData()); + mitk::Image::Pointer maskImg = NULL; + if (m_MaskImageNode.IsNotNull()) + maskImg = dynamic_cast(m_MaskImageNode->GetData()); IVIMFilterType::GradientDirectionContainerType::ConstIterator gdcit = diffusionImg->GetDirections()->Begin(); bool foundB0 = false; while( gdcit != diffusionImg->GetDirections()->End() ) { if(gdcit.Value().one_norm() <= 0.0) foundB0 = true; ++gdcit; } if(!foundB0) { m_Controls->m_Warning->setText(QString("No baseline (non diffusion-weighted) image found.. aborting:(")); m_Controls->m_Warning->setVisible(true); } else { m_Controls->m_Warning->setVisible(false); } if (!m_MultiWidget) return; m_Controls->m_VisualizeResultsWidget->setVisible(true); typedef itk::VectorImage VecImgType; VecImgType::Pointer vecimg = (VecImgType*)diffusionImg->GetVectorImage().GetPointer(); VecImgType::Pointer roiImage = VecImgType::New(); - if(maskImg == 0) + if(maskImg.IsNull()) { int roisize = 0; if(m_Controls->m_MethodCombo->currentIndex() == 4) roisize = 5; mitk::Point3D pos = m_MultiWidget->GetCrossPosition(); VecImgType::IndexType crosspos; diffusionImg->GetTimeSlicedGeometry()->WorldToIndex(pos, crosspos); VecImgType::IndexType index; index[0] = crosspos[0] - roisize; index[0] = index[0] < 0 ? 0 : index[0]; index[1] = crosspos[1] - roisize; index[1] = index[1] < 0 ? 0 : index[1]; index[2] = crosspos[2] - roisize; index[2] = index[2] < 0 ? 0 : index[2]; VecImgType::SizeType size; size[0] = roisize*2+1; size[1] = roisize*2+1; size[2] = roisize*2+1; VecImgType::SizeType maxSize = vecimg->GetLargestPossibleRegion().GetSize(); size[0] = index[0]+size[0] > maxSize[0] ? maxSize[0]-index[0] : size[0]; size[1] = index[1]+size[1] > maxSize[1] ? maxSize[1]-index[1] : size[1]; size[2] = index[2]+size[2] > maxSize[2] ? maxSize[2]-index[2] : size[2]; VecImgType::RegionType region; region.SetSize( size ); region.SetIndex( index ); vecimg->SetRequestedRegion( region ); VecImgType::IndexType newstart; newstart.Fill(0); VecImgType::RegionType newregion; newregion.SetSize( size ); newregion.SetIndex( newstart ); roiImage->CopyInformation( vecimg ); roiImage->SetRegions( newregion ); roiImage->SetOrigin( pos ); roiImage->Allocate(); roiImage->SetPixel(newstart, vecimg->GetPixel(index)); FittIVIM(roiImage, diffusionImg->GetDirections(), diffusionImg->GetB_Value(), false, crosspos); } else { typedef itk::Image MaskImgType; MaskImgType::Pointer maskItk; CastToItkImage( maskImg, maskItk ); mitk::Point3D pos; pos[0] = 0; pos[1] = 0; pos[2] = 0; VecImgType::IndexType index; index[0] = 0; index[1] = 0; index[2] = 0; VecImgType::SizeType size; size[0] = 1; size[1] = 1; size[2] = 1; VecImgType::RegionType region; region.SetSize( size ); region.SetIndex( index ); vecimg->SetRequestedRegion( region ); // iterators over output and input itk::ImageRegionConstIteratorWithIndex vecit(vecimg, vecimg->GetLargestPossibleRegion()); itk::VariableLengthVector avg(vecimg->GetVectorLength()); avg.Fill(0); float numPixels = 0; while ( ! vecit.IsAtEnd() ) { VecImgType::PointType point; vecimg->TransformIndexToPhysicalPoint(vecit.GetIndex(), point); MaskImgType::IndexType index; maskItk->TransformPhysicalPointToIndex(point, index); if(maskItk->GetPixel(index) != 0) { avg += vecit.Get(); numPixels += 1.0; } // update iterators ++vecit; } avg /= numPixels; m_Controls->m_Warning->setText(QString("Averaging ")+QString::number((int)numPixels)+QString(" voxels!")); m_Controls->m_Warning->setVisible(true); roiImage->CopyInformation( vecimg ); roiImage->SetRegions( region ); roiImage->SetOrigin( pos ); roiImage->Allocate(); roiImage->SetPixel(index, avg); FittIVIM(roiImage, diffusionImg->GetDirections(), diffusionImg->GetB_Value(), false, index); } vecimg->SetRegions( vecimg->GetLargestPossibleRegion() ); m_Controls->m_VisualizeResultsWidget->SetParameters(m_Snap); } void QmitkIVIMView::FittIVIM(itk::VectorImage* vecimg, DirContainerType* dirs, float bval, bool multivoxel, OutImgType::IndexType &crosspos) { IVIMFilterType::Pointer filter = IVIMFilterType::New(); filter->SetInput(vecimg); filter->SetGradientDirections(dirs); filter->SetBValue(bval); switch(m_Controls->m_MethodCombo->currentIndex()) { case 0: filter->SetMethod(IVIMFilterType::IVIM_FIT_ALL); filter->SetS0Thres(m_Controls->m_S0ThreshLabel->text().toDouble()); break; case 1: filter->SetMethod(IVIMFilterType::IVIM_DSTAR_FIX); filter->SetDStar(m_Controls->m_DStarLabel->text().toDouble()); filter->SetS0Thres(m_Controls->m_S0ThreshLabel->text().toDouble()); break; case 2: filter->SetMethod(IVIMFilterType::IVIM_D_THEN_DSTAR); filter->SetBThres(m_Controls->m_BThreshLabel->text().toDouble()); filter->SetS0Thres(m_Controls->m_S0ThreshLabel->text().toDouble()); filter->SetFitDStar(m_Controls->m_CheckDStar->isChecked()); break; case 3: filter->SetMethod(IVIMFilterType::IVIM_LINEAR_D_THEN_F); filter->SetBThres(m_Controls->m_BThreshLabel->text().toDouble()); filter->SetS0Thres(m_Controls->m_S0ThreshLabel->text().toDouble()); filter->SetFitDStar(m_Controls->m_CheckDStar->isChecked()); break; case 4: filter->SetMethod(IVIMFilterType::IVIM_REGULARIZED); filter->SetBThres(m_Controls->m_BThreshLabel->text().toDouble()); filter->SetS0Thres(m_Controls->m_S0ThreshLabel->text().toDouble()); filter->SetNumberIterations(m_Controls->m_NumItsLabel->text().toInt()); filter->SetLambda(m_Controls->m_LambdaLabel->text().toDouble()); filter->SetFitDStar(m_Controls->m_CheckDStar->isChecked()); break; } if(!multivoxel) { filter->SetFitDStar(true); } filter->SetNumberOfThreads(1); filter->SetVerbose(multivoxel); filter->SetCrossPosition(crosspos); filter->Update(); m_Snap = filter->GetSnapshot(); m_DStarMap = filter->GetOutput(2); m_DMap = filter->GetOutput(1); m_fMap = filter->GetOutput(0); } void QmitkIVIMView::OutputToDatastorage(std::vector nodes) { // Outputs to Datastorage QString basename(nodes.front()->GetName().c_str()); if(m_Controls->m_CheckDStar->isChecked()) { mitk::Image::Pointer dstarimage = mitk::Image::New(); dstarimage->InitializeByItk(m_DStarMap.GetPointer()); dstarimage->SetVolume(m_DStarMap->GetBufferPointer()); QString newname2 = basename; newname2 = newname2.append("_DStarMap%1").arg(m_Controls->m_MethodCombo->currentIndex()); mitk::DataNode::Pointer node2=mitk::DataNode::New(); node2->SetData( dstarimage ); node2->SetName(newname2.toAscii()); GetDefaultDataStorage()->Add(node2); } if(m_Controls->m_CheckD->isChecked()) { mitk::Image::Pointer dimage = mitk::Image::New(); dimage->InitializeByItk(m_DMap.GetPointer()); dimage->SetVolume(m_DMap->GetBufferPointer()); QString newname1 = basename; newname1 = newname1.append("_DMap%1").arg(m_Controls->m_MethodCombo->currentIndex()); mitk::DataNode::Pointer node1=mitk::DataNode::New(); node1->SetData( dimage ); node1->SetName(newname1.toAscii()); GetDefaultDataStorage()->Add(node1); } if(m_Controls->m_Checkf->isChecked()) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(m_fMap.GetPointer()); image->SetVolume(m_fMap->GetBufferPointer()); QString newname0 = basename; newname0 = newname0.append("_fMap%1").arg(m_Controls->m_MethodCombo->currentIndex()); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); node->SetName(newname0.toAscii()); GetDefaultDataStorage()->Add(node); } m_MultiWidget->RequestUpdate(); } void QmitkIVIMView::ChooseMethod() { m_Controls->m_MethodCombo->setVisible(m_Controls->m_ChooseMethod->isChecked()); } void QmitkIVIMView::ClipboardCurveButtonClicked() { if(true) { QString clipboard("Measurement Points\n"); for ( int i=0; isetText( clipboard, QClipboard::Clipboard ); } else { QApplication::clipboard()->clear(); } } void QmitkIVIMView::ClipboardStatisticsButtonClicked() { if ( true ) { QString clipboard( "f \t D \t D* \n" ); clipboard = clipboard.append( "%L1 \t %L2 \t %L3" ) .arg( m_Snap.currentF, 0, 'f', 10 ) .arg( m_Snap.currentD, 0, 'f', 10 ) .arg( m_Snap.currentDStar, 0, 'f', 10 ) ; QApplication::clipboard()->setText( clipboard, QClipboard::Clipboard ); } else { QApplication::clipboard()->clear(); } } void QmitkIVIMView::Activated() { m_Active = true; } void QmitkIVIMView::Deactivated() { m_Active = false; } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkIVIMView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkIVIMView.h index f3e407e1c1..c06c29d8de 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkIVIMView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkIVIMView.h @@ -1,112 +1,115 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $ -Version: $Revision: 21975 $ +Version: $Revision: 21975 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _QMITKIVIMVIEW_H_INCLUDED #define _QMITKIVIMVIEW_H_INCLUDED #include #include #include "ui_QmitkIVIMViewControls.h" #include "itkVectorImage.h" #include "itkImage.h" #include "mitkDiffusionImage.h" #include "itkDiffusionIntravoxelIncoherentMotionReconstructionImageFilter.h" /*! \brief QmitkIVIMView \warning This application module is not yet documented. Use "svn blame/praise/annotate" and ask the author to provide basic documentation. \sa QmitkFunctionality \ingroup Functionalities */ class QmitkIVIMView : public QmitkFunctionality -{ +{ // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; QmitkIVIMView(); virtual ~QmitkIVIMView(); typedef mitk::DiffusionImage::GradientDirectionContainerType DirContainerType; typedef itk::DiffusionIntravoxelIncoherentMotionReconstructionImageFilter IVIMFilterType; typedef itk::Image OutImgType; virtual void CreateQtPartControl(QWidget *parent); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); void OnSliceChanged(const itk::EventObject& e); void OutputToDatastorage(std::vector nodes); void FittIVIM(itk::VectorImage* vecimg, DirContainerType* dirs, float bval, bool multivoxel, OutImgType::IndexType &crosspos); void Activated(); void Deactivated(); protected slots: - + /// \brief Called when the user clicks the GUI button void FittIVIMStart(); void AutoThreshold(); void MethodCombo(int val); void Checkbox(); void DStarSlider(int val); void BThreshSlider(int val); void S0ThreshSlider(int val); void NumItsSlider(int val); void LambdaSlider(int val); void ChooseMethod(); void ClipboardStatisticsButtonClicked(); void ClipboardCurveButtonClicked(); protected: /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( std::vector nodes ); Ui::QmitkIVIMViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; int m_SliceObserverTag1; int m_SliceObserverTag2; int m_SliceObserverTag3; OutImgType::Pointer m_DStarMap; OutImgType::Pointer m_DMap; OutImgType::Pointer m_fMap; IVIMFilterType::IVIMSnapshot m_Snap; + mitk::DataNode::Pointer m_DiffusionImageNode; + mitk::DataNode::Pointer m_MaskImageNode; + bool m_Active; }; #endif // _QMITKIVIMVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkIVIMViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkIVIMViewControls.ui index 49d20b570b..0967ddb8ae 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkIVIMViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkIVIMViewControls.ui @@ -1,631 +1,803 @@ QmitkIVIMViewControls 0 0 - 307 - 790 + 360 + 922 0 0 QmitkTemplate - 0 + 9 Intra Voxel Incoherent Motion Estimation 0 9 0 0 - - - QFrame::NoFrame + + + Data - - QFrame::Raised + + + + + Diffusion Image: + + + + + + + - + + + + + + + Mask Image: + + + + + + + - + + + + + + + + + + Parameters - - - 0 + + + 9 - - + + QFrame::NoFrame QFrame::Raised - + 0 - + + 0 + + 80 16777215 D* - + 100 60 Qt::Horizontal - + 51 16777215 200 + + Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter + - - + + QFrame::NoFrame QFrame::Raised - + 0 - + + 0 + + 80 16777215 neglect b< - + 250 34 Qt::Horizontal - + 51 16777215 46.5 + + Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter + - - + + QFrame::NoFrame - QFrame::Raised + QFrame::Plain - + 0 - + + 0 + + 80 16777215 neglect Si< - + 100 0 Qt::Horizontal - - + + + + + 0 + 0 + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + + + + 0 + 0 + + + + + 30 + 16777215 + + + + TextLabel + + + Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter + + + + + + + + 15 + 16777215 + + + + * + + + + + + + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + - 30 + 80 16777215 - TextLabel + #iterations - - + + + + 100 + + + 10 + + + Qt::Horizontal + + + + + - 15 + 30 16777215 - * + TextLabel + + + Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter - - + + QFrame::NoFrame QFrame::Raised - + 0 - - - - QFrame::NoFrame + + 0 + + + + + + 80 + 16777215 + - - QFrame::Raised + + lambda - - - 0 - - - - - - 80 - 16777215 - - - - #iterations - - - - - - - 100 - - - 10 - - - Qt::Horizontal - - - - - - - - 30 - 16777215 - - - - TextLabel - - - - - - + + + + 1000 + + + 10 + + + Qt::Horizontal + + + + + + + + 0 + 0 + + QFrame::NoFrame QFrame::Raised - + 0 - - - - - 80 - 16777215 - - - - lambda - - - - - - - 1000 - - - 10 - - - Qt::Horizontal - - - - + + 0 + + + + + 0 + 0 + + 30 16777215 TextLabel + + Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter + - + 15 16777215 * + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + + QFrame::NoFrame QFrame::Raised 0 80 0 Output Images f true D false D* false Generate Output Images color: rgb(255, 0, 0); font: 75 14pt "Ubuntu"; - Bla bla bla + warning display Qt::RichText display voxel-wise results true QFrame::StyledPanel QFrame::Raised 0 0 true 0 0 0 400 0 QFrame::NoFrame QFrame::Raised 0 QFrame::NoFrame QFrame::Raised 0 QFrame::NoFrame QFrame::Raised 0 Curve to Clipboard Values to Clipboard Choose Method 2 3 Param. Fit Fit D & f with fixed D* value Fit D & f (high b), then fit D* Linearly fit D & f (high b), then fit D* Regularized Qt::Vertical QSizePolicy::Expanding 20 220 QmitkIVIMWidget QWidget
QmitkIVIMWidget.h
1 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsView.cpp index 8cda17993f..c13bd7be11 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsView.cpp @@ -1,308 +1,323 @@ /*========================================================================= Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkODFDetailsView.h" #include #include #include #include #include #include #include #include #include #include #include const std::string QmitkODFDetailsView::VIEW_ID = "org.mitk.views.odfdetails"; QmitkODFDetailsView::QmitkODFDetailsView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_OdfNormalization(0) - , m_SelectedNode(NULL) + , m_ImageNode(NULL) { m_VtkActor = vtkActor::New(); m_VtkMapper = vtkPolyDataMapper::New(); m_Renderer = vtkRenderer::New(); m_VtkRenderWindow = vtkRenderWindow::New(); m_RenderWindowInteractor = vtkRenderWindowInteractor::New(); m_Camera = vtkCamera::New(); m_VtkRenderWindow->SetSize(300,300); } QmitkODFDetailsView::~QmitkODFDetailsView() { QmitkStdMultiWidget* MultiWidget = this->GetActiveStdMultiWidget(false); if(MultiWidget) { //unregister observers when view is destroyed if( MultiWidget->mitkWidget1 != NULL && m_SliceObserverTag1 != 0) { mitk::SliceNavigationController* slicer = MultiWidget->mitkWidget1->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag1 ); } if( MultiWidget->mitkWidget2 != NULL && m_SliceObserverTag2 != 0) { mitk::SliceNavigationController* slicer = MultiWidget->mitkWidget2->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag2 ); } if( MultiWidget->mitkWidget3!= NULL && m_SliceObserverTag3 != 0) { mitk::SliceNavigationController* slicer = MultiWidget->mitkWidget3->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag3 ); } } } void QmitkODFDetailsView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkODFDetailsViewControls; m_Controls->setupUi( parent ); m_Controls->m_OdfBox->setVisible(false); m_Controls->m_ODFRenderWidget->setVisible(false); } } void QmitkODFDetailsView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget1->GetSliceNavigationController(); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkODFDetailsView::OnSliceChanged ); m_SliceObserverTag1 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(NULL, 0), command ); } { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget2->GetSliceNavigationController(); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkODFDetailsView::OnSliceChanged ); m_SliceObserverTag2 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(NULL, 0), command ); } { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget3->GetSliceNavigationController(); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkODFDetailsView::OnSliceChanged ); m_SliceObserverTag3 = slicer->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(NULL, 0), command ); } - } void QmitkODFDetailsView::StdMultiWidgetNotAvailable() { { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget1->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag1 ); } { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget2->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag2 ); } { mitk::SliceNavigationController* slicer = m_MultiWidget->mitkWidget3->GetSliceNavigationController(); slicer->RemoveObserver( m_SliceObserverTag3 ); } m_MultiWidget = NULL; } void QmitkODFDetailsView::OnSelectionChanged( std::vector nodes ) { - if (m_SelectedNode.IsNotNull()) - m_SelectedNode->RemoveObserver( m_PropertyObserverTag ); + if (m_ImageNode.IsNotNull()) + m_ImageNode->RemoveObserver( m_PropertyObserverTag ); + + m_ImageNode = NULL; + m_Controls->m_InputImageLabel->setText("-"); + // iterate selection + for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) + { + mitk::DataNode::Pointer node = *it; + + if( node.IsNotNull() && (dynamic_cast(node->GetData()) || dynamic_cast(node->GetData())) ) + { + m_Controls->m_InputImageLabel->setText(node->GetName().c_str()); + m_ImageNode = node; + } + } + UpdateOdf(); - if (m_SelectedNode.IsNotNull()) + if (m_ImageNode.IsNotNull()) { itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkODFDetailsView::OnSliceChanged ); - m_PropertyObserverTag = m_SelectedNode->AddObserver( itk::ModifiedEvent(), command ); + m_PropertyObserverTag = m_ImageNode->AddObserver( itk::ModifiedEvent(), command ); } } void QmitkODFDetailsView::UpdateOdf() { + try { m_Values.clear(); - std::vector nodes = this->GetDataManagerSelection(); - if (nodes.empty()) return; - if (!nodes.front()) return; - m_SelectedNode = nodes.front(); - - mitk::Image::Pointer img = dynamic_cast(nodes.front()->GetData()); - - if (!img) return; - if (!m_MultiWidget) return; + m_Controls->m_OverviewBox->setVisible(true); + if (m_ImageNode.IsNull() || !m_MultiWidget) + { + m_Controls->m_ODFRenderWidget->setVisible(false); + m_Controls->m_OdfBox->setVisible(false); + m_Controls->m_OverviewBox->setVisible(false); + return; + } // ODF Normalization Property - mitk::OdfNormalizationMethodProperty* nmp = dynamic_cast(nodes.front()->GetProperty( "Normalization" )); + mitk::OdfNormalizationMethodProperty* nmp = dynamic_cast(m_ImageNode->GetProperty( "Normalization" )); if(nmp) m_OdfNormalization = nmp->GetNormalization(); m_TemplateOdf = itk::OrientationDistributionFunction::GetBaseMesh(); m_OdfTransform = vtkSmartPointer::New(); m_OdfTransform->Identity(); m_OdfVals = vtkSmartPointer::New(); m_OdfSource = vtkSmartPointer::New(); itk::OrientationDistributionFunction odf; mitk::Point3D world = m_MultiWidget->GetCrossPosition(); mitk::Point3D index; + mitk::Image::Pointer img = dynamic_cast(m_ImageNode->GetData()); img->GetTimeSlicedGeometry()->WorldToIndex(world, index); float sum = 0; - float max = itk::NumericTraits::min(); + float max = itk::NumericTraits::NonpositiveMin(); float min = itk::NumericTraits::max(); QString values; QString overviewText; + // check if dynamic_cast successfull and if the crosshair position is inside of the geometry of the ODF data // otherwise possible crash for a scenario with multiple nodes - if (dynamic_cast(nodes.front()->GetData()) && ( nodes.front()->GetData()->GetGeometry()->IsInside(world) ) ) + if (dynamic_cast(m_ImageNode->GetData()) && ( m_ImageNode->GetData()->GetGeometry()->IsInside(world) ) ) { m_Controls->m_ODFRenderWidget->setVisible(true); m_Controls->m_OdfBox->setVisible(true); OdfVectorImgType::Pointer itkQBallImage = OdfVectorImgType::New(); - mitk::CastToItkImage(dynamic_cast(nodes.front()->GetData()), itkQBallImage); - + mitk::CastToItkImage(dynamic_cast(m_ImageNode->GetData()), itkQBallImage); OdfVectorImgType::IndexType ind; ind[0] = (int)(index[0]+0.5); ind[1] = (int)(index[1]+0.5); ind[2] = (int)(index[2]+0.5); OdfVectorImgType::PixelType pixel = itkQBallImage->GetPixel(ind); for (int i=0; imax) max = val; if (val pd = odf.GetDirection(odf.GetPrincipleDiffusionDirection()); overviewText += "Main Diffusion:\n "+QString::number(pd[0])+"\n "+QString::number(pd[1])+"\n "+QString::number(pd[2])+"\n"; m_Controls->m_OdfValuesTextEdit->setText(values); } - else if (dynamic_cast(nodes.front()->GetData())) + else if (dynamic_cast(m_ImageNode->GetData())) { m_Controls->m_ODFRenderWidget->setVisible(true); m_Controls->m_OdfBox->setVisible(false); TensorImageType::Pointer itkQBallImage = TensorImageType::New(); - mitk::CastToItkImage(dynamic_cast(nodes.front()->GetData()), itkQBallImage); + mitk::CastToItkImage(dynamic_cast(m_ImageNode->GetData()), itkQBallImage); TensorImageType::IndexType ind; ind[0] = (int)(index[0]+0.5); ind[1] = (int)(index[1]+0.5); ind[2] = (int)(index[2]+0.5); TensorImageType::PixelType pixel = itkQBallImage->GetPixel(ind); float tensorelems[6] = { (float)pixel[0], (float)pixel[1], (float)pixel[2], (float)pixel[3], (float)pixel[4], (float)pixel[5], }; itk::DiffusionTensor3D tensor(tensorelems); odf.InitFromTensor(tensor); /** Array of eigen-values. */ typedef itk::FixedArray EigenValuesArrayType; /** Matrix of eigen-vectors. */ typedef itk::Matrix MatrixType; typedef itk::Matrix EigenVectorsMatrixType; EigenValuesArrayType eigenValues; EigenVectorsMatrixType eigenVectors; QString pos = QString::number(ind[0])+", "+QString::number(ind[1])+", "+QString::number(ind[2]); overviewText += "Coordinates: "+pos+"\n"; overviewText += "FA: "+QString::number(tensor.GetFractionalAnisotropy())+"\n"; overviewText += "RA: "+QString::number(tensor.GetRelativeAnisotropy())+"\n"; overviewText += "Trace: "+QString::number(tensor.GetTrace())+"\n"; tensor.ComputeEigenAnalysis(eigenValues,eigenVectors); overviewText += "Eigenvalues:\n "+QString::number(eigenValues[2])+"\n "+QString::number(eigenValues[1])+"\n "+QString::number(eigenValues[0])+"\n"; overviewText += "Main Diffusion:\n "+QString::number(eigenVectors[0][0])+"\n "+QString::number(eigenVectors[1][0])+"\n "+QString::number(eigenVectors[2][0])+"\n"; overviewText += "Values:\n "+QString::number(tensorelems[0])+"\n "+QString::number(tensorelems[1])+"\n "+QString::number(tensorelems[2])+"\n "+QString::number(tensorelems[3])+"\n "+QString::number(tensorelems[4])+"\n "+QString::number(tensorelems[5])+"\n "+"\n"; } else { m_Controls->m_ODFRenderWidget->setVisible(false); m_Controls->m_OdfBox->setVisible(false); - overviewText += "Please select a Q-Ball or tensor image\n"; + overviewText += "Please reinit image geometry.\n"; } m_Controls->m_ODFDetailsWidget->SetParameters(odf); switch(m_OdfNormalization) { case 0: odf = odf.MinMaxNormalize(); break; case 1: odf = odf.MaxNormalize(); break; case 2: odf = odf.MaxNormalize(); break; default: odf = odf.MinMaxNormalize(); } m_Controls->m_ODFRenderWidget->GenerateODF(odf); m_Controls->m_OverviewTextEdit->setText(overviewText.toStdString().c_str()); } catch(...) { QMessageBox::critical(0, "Error", "Data could not be analyzed. The image might be corrupted."); } } void QmitkODFDetailsView::OnSliceChanged(const itk::EventObject& /*e*/) { UpdateOdf(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsView.h index a935492329..37162c8af2 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsView.h @@ -1,114 +1,115 @@ /*========================================================================= Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _QMITKQmitkODFDetailsView_H_INCLUDED #define _QMITKQmitkODFDetailsView_H_INCLUDED #include #include #include "ui_QmitkODFDetailsViewControls.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include /*! \brief QmitkODFDetailsView \warning This application module is not yet documented. Use "svn blame/praise/annotate" and ask the author to provide basic documentation. \sa QmitkFunctionality \ingroup Functionalities */ class QmitkODFDetailsView : public QmitkFunctionality { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; QmitkODFDetailsView(); QmitkODFDetailsView(const QmitkODFDetailsView& other) { Q_UNUSED(other) throw std::runtime_error("Copy constructor not implemented"); } virtual ~QmitkODFDetailsView(); typedef float TOdfPixelType; typedef itk::Vector OdfVectorType; typedef itk::Image OdfVectorImgType; typedef itk::DiffusionTensor3D< TOdfPixelType > TensorPixelType; typedef itk::Image< TensorPixelType, 3 > TensorImageType; virtual void CreateQtPartControl(QWidget *parent); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); void OnSliceChanged(const itk::EventObject& e); protected slots: protected: /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( std::vector nodes ); void UpdateOdf(); Ui::QmitkODFDetailsViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; int m_SliceObserverTag1; int m_SliceObserverTag2; int m_SliceObserverTag3; int m_PropertyObserverTag; vtkPolyData* m_TemplateOdf; vtkSmartPointer m_OdfTransform; vtkSmartPointer m_OdfVals; vtkSmartPointer m_OdfSource; vtkActor* m_VtkActor; vtkPolyDataMapper* m_VtkMapper; vtkRenderer* m_Renderer; vtkRenderWindow* m_VtkRenderWindow; vtkRenderWindowInteractor* m_RenderWindowInteractor; vtkCamera* m_Camera; - mitk::DataNode::Pointer m_SelectedNode; std::vector m_Values; int m_OdfNormalization; + + mitk::DataNode::Pointer m_ImageNode; }; #endif // _QmitkODFDetailsView_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsViewControls.ui index 895117622a..b3705a1f4d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkODFDetailsViewControls.ui @@ -1,191 +1,205 @@ QmitkODFDetailsViewControls 0 0 351 734 0 0 QmitkTemplate - 0 + 6 - - 4 - - - 0 - - - 0 - - - 0 + + 9 - + + + Data + + + + + + Tensor/Q-Ball Image: + + + + + + + - + + + + + + + + Overview 0 9 0 0 0 0 0 0 true 0 0 200 200 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 ODF Values true 0 0 0 200 Qt::Vertical QSizePolicy::Expanding 20 220 QmitkODFDetailsWidget QWidget
QmitkODFDetailsWidget.h
1 QmitkODFRenderWidget QWidget
QmitkODFRenderWidget.h
1 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPartialVolumeAnalysisView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPartialVolumeAnalysisView.cpp index 52ea734ec8..560405779d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPartialVolumeAnalysisView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPartialVolumeAnalysisView.cpp @@ -1,2169 +1,2139 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2009-05-22 11:00:35 +0200 (Fr, 22 Mai 2009) $ Version: $Revision: 10185 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkPartialVolumeAnalysisView.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include "QmitkStdMultiWidget.h" +#include "QmitkStdMultiWidgetEditor.h" #include "QmitkSliderNavigatorWidget.h" +#include #include "mitkNodePredicateDataType.h" #include "mitkNodePredicateOr.h" #include "mitkImageTimeSelector.h" #include "mitkProperties.h" #include "mitkProgressBar.h" #include "mitkImageCast.h" #include "mitkImageToItk.h" #include "mitkITKImageImport.h" #include "mitkDataNodeObject.h" #include "mitkNodePredicateData.h" #include "mitkPlanarFigureInteractor.h" #include "mitkGlobalInteraction.h" #include "mitkTensorImage.h" #include "mitkPlanarCircle.h" #include "mitkPlanarRectangle.h" #include "mitkPlanarPolygon.h" #include "mitkPartialVolumeAnalysisClusteringCalculator.h" #include "mitkDiffusionImage.h" #include #include "itkTensorDerivedMeasurementsFilter.h" #include "itkDiffusionTensor3D.h" #include "itkCartesianToPolarVectorImageFilter.h" #include "itkPolarToCartesianVectorImageFilter.h" #include "itkBinaryThresholdImageFilter.h" #include "itkMaskImageFilter.h" #include "itkCastImageFilter.h" #include "itkImageMomentsCalculator.h" #include #include #include #include #define _USE_MATH_DEFINES #include #define PVA_PI M_PI const std::string QmitkPartialVolumeAnalysisView::VIEW_ID = -"org.mitk.views.partialvolumeanalysisview"; + "org.mitk.views.partialvolumeanalysisview"; class QmitkRequestStatisticsUpdateEvent : public QEvent { public: enum Type { StatisticsUpdateRequest = QEvent::MaxUser - 1025 - }; + }; QmitkRequestStatisticsUpdateEvent() : QEvent( (QEvent::Type) StatisticsUpdateRequest ) {}; }; typedef itk::Image ImageType; typedef itk::Image FloatImageType; typedef itk::Image, 3> VectorImageType; inline bool my_isnan(float x) { volatile float d = x; if(d!=d) return true; if(d==d) return false; return d != d; } QmitkPartialVolumeAnalysisView::QmitkPartialVolumeAnalysisView(QObject * /*parent*/, const char * /*name*/) - : QmitkFunctionality(), - m_Controls( NULL ), - m_TimeStepperAdapter( NULL ), - m_MeasurementInfoRenderer(0), - m_MeasurementInfoAnnotation(0), - m_SelectedImageNodes( ), - m_SelectedImage( NULL ), - m_SelectedMaskNode( NULL ), - m_SelectedImageMask( NULL ), - m_SelectedPlanarFigureNodes(0), - m_SelectedPlanarFigure( NULL ), - m_IsTensorImage(false), - m_FAImage(0), - m_RDImage(0), - m_ADImage(0), - m_MDImage(0), - m_CAImage(0), - // m_DirectionImage(0), - m_DirectionComp1Image(0), - m_DirectionComp2Image(0), - m_AngularErrorImage(0), - m_SelectedRenderWindow(NULL), - m_LastRenderWindow(NULL), - m_ImageObserverTag( -1 ), - m_ImageMaskObserverTag( -1 ), - m_PlanarFigureObserverTag( -1 ), - m_CurrentStatisticsValid( false ), - m_StatisticsUpdatePending( false ), - m_GaussianSigmaChangedSliding(false), - m_NumberBinsSliding(false), - m_UpsamplingChangedSliding(false), - m_ClusteringResult(NULL), - m_EllipseCounter(0), - m_RectangleCounter(0), - m_PolygonCounter(0), - m_CurrentFigureNodeInitialized(false), - m_QuantifyClass(2), - m_IconTexOFF(new QIcon(":/QmitkPartialVolumeAnalysisView/texIntOFFIcon.png")), - m_IconTexON(new QIcon(":/QmitkPartialVolumeAnalysisView/texIntONIcon.png")), - m_TexIsOn(true) + : //QmitkFunctionality(), + m_Controls( NULL ), + m_TimeStepperAdapter( NULL ), + m_MeasurementInfoRenderer(0), + m_MeasurementInfoAnnotation(0), + m_SelectedImageNodes( ), + m_SelectedImage( NULL ), + m_SelectedMaskNode( NULL ), + m_SelectedImageMask( NULL ), + m_SelectedPlanarFigureNodes(0), + m_SelectedPlanarFigure( NULL ), + m_IsTensorImage(false), + m_FAImage(0), + m_RDImage(0), + m_ADImage(0), + m_MDImage(0), + m_CAImage(0), + // m_DirectionImage(0), + m_DirectionComp1Image(0), + m_DirectionComp2Image(0), + m_AngularErrorImage(0), + m_SelectedRenderWindow(NULL), + m_LastRenderWindow(NULL), + m_ImageObserverTag( -1 ), + m_ImageMaskObserverTag( -1 ), + m_PlanarFigureObserverTag( -1 ), + m_CurrentStatisticsValid( false ), + m_StatisticsUpdatePending( false ), + m_GaussianSigmaChangedSliding(false), + m_NumberBinsSliding(false), + m_UpsamplingChangedSliding(false), + m_ClusteringResult(NULL), + m_EllipseCounter(0), + m_RectangleCounter(0), + m_PolygonCounter(0), + m_CurrentFigureNodeInitialized(false), + m_QuantifyClass(2), + m_IconTexOFF(new QIcon(":/QmitkPartialVolumeAnalysisView/texIntOFFIcon.png")), + m_IconTexON(new QIcon(":/QmitkPartialVolumeAnalysisView/texIntONIcon.png")), + m_TexIsOn(true), + m_Visible(false) { } QmitkPartialVolumeAnalysisView::~QmitkPartialVolumeAnalysisView() { if ( m_SelectedImage.IsNotNull() ) m_SelectedImage->RemoveObserver( m_ImageObserverTag ); if ( m_SelectedImageMask.IsNotNull() ) m_SelectedImageMask->RemoveObserver( m_ImageMaskObserverTag ); if ( m_SelectedPlanarFigure.IsNotNull() ) { m_SelectedPlanarFigure->RemoveObserver( m_PlanarFigureObserverTag ); m_SelectedPlanarFigure->RemoveObserver( m_InitializedObserverTag ); } - this->GetDefaultDataStorage()->AddNodeEvent -= mitk::MessageDelegate1( this, &QmitkPartialVolumeAnalysisView::NodeAddedInDataStorage ); + this->GetDataStorage()->AddNodeEvent -= mitk::MessageDelegate1( this, &QmitkPartialVolumeAnalysisView::NodeAddedInDataStorage ); m_SelectedPlanarFigureNodes->NodeChanged.RemoveListener( mitk::MessageDelegate1( this, &QmitkPartialVolumeAnalysisView::NodeChanged ) ); m_SelectedPlanarFigureNodes->NodeRemoved.RemoveListener( mitk::MessageDelegate1( this, &QmitkPartialVolumeAnalysisView::NodeRemoved ) ); m_SelectedPlanarFigureNodes->PropertyChanged.RemoveListener( mitk::MessageDelegate2( this, &QmitkPartialVolumeAnalysisView::PropertyChanged ) ); m_SelectedImageNodes->NodeChanged.RemoveListener( mitk::MessageDelegate1( this, &QmitkPartialVolumeAnalysisView::NodeChanged ) ); m_SelectedImageNodes->NodeRemoved.RemoveListener( mitk::MessageDelegate1( this, &QmitkPartialVolumeAnalysisView::NodeRemoved ) ); m_SelectedImageNodes->PropertyChanged.RemoveListener( mitk::MessageDelegate2( this, &QmitkPartialVolumeAnalysisView::PropertyChanged ) ); } void QmitkPartialVolumeAnalysisView::CreateQtPartControl(QWidget *parent) { if (m_Controls == NULL) { m_Controls = new Ui::QmitkPartialVolumeAnalysisViewControls; m_Controls->setupUi(parent); this->CreateConnections(); - - m_Controls->m_ErrorMessageLabel->hide(); } SetHistogramVisibility(); m_Controls->m_TextureIntON->setIcon(*m_IconTexON); m_Controls->m_SimilarAnglesFrame->setVisible(false); m_Controls->m_SimilarAnglesLabel->setVisible(false); vtkTextProperty *textProp = vtkTextProperty::New(); textProp->SetColor(1.0, 1.0, 1.0); m_MeasurementInfoAnnotation = vtkCornerAnnotation::New(); m_MeasurementInfoAnnotation->SetMaximumFontSize(12); m_MeasurementInfoAnnotation->SetTextProperty(textProp); m_MeasurementInfoRenderer = vtkRenderer::New(); m_MeasurementInfoRenderer->AddActor(m_MeasurementInfoAnnotation); - m_SelectedPlanarFigureNodes = mitk::DataStorageSelection::New(this->GetDefaultDataStorage(), false); + m_SelectedPlanarFigureNodes = mitk::DataStorageSelection::New(this->GetDataStorage(), false); m_SelectedPlanarFigureNodes->NodeChanged.AddListener( mitk::MessageDelegate1( this, &QmitkPartialVolumeAnalysisView::NodeChanged ) ); m_SelectedPlanarFigureNodes->NodeRemoved.AddListener( mitk::MessageDelegate1( this, &QmitkPartialVolumeAnalysisView::NodeRemoved ) ); m_SelectedPlanarFigureNodes->PropertyChanged.AddListener( mitk::MessageDelegate2( this, &QmitkPartialVolumeAnalysisView::PropertyChanged ) ); - m_SelectedImageNodes = mitk::DataStorageSelection::New(this->GetDefaultDataStorage(), false); + m_SelectedImageNodes = mitk::DataStorageSelection::New(this->GetDataStorage(), false); m_SelectedImageNodes->PropertyChanged.AddListener( mitk::MessageDelegate2( this, &QmitkPartialVolumeAnalysisView::PropertyChanged ) ); m_SelectedImageNodes->NodeChanged.AddListener( mitk::MessageDelegate1( this, &QmitkPartialVolumeAnalysisView::NodeChanged ) ); m_SelectedImageNodes->NodeRemoved.AddListener( mitk::MessageDelegate1( this, &QmitkPartialVolumeAnalysisView::NodeRemoved ) ); - this->GetDefaultDataStorage()->AddNodeEvent.AddListener( mitk::MessageDelegate1( this, &QmitkPartialVolumeAnalysisView::NodeAddedInDataStorage ) ); + this->GetDataStorage()->AddNodeEvent.AddListener( mitk::MessageDelegate1( this, &QmitkPartialVolumeAnalysisView::NodeAddedInDataStorage ) ); Select(NULL,true,true); SetAdvancedVisibility(); } void QmitkPartialVolumeAnalysisView::SetHistogramVisibility() { m_Controls->m_HistogramWidget->setVisible(m_Controls->m_DisplayHistogramCheckbox->isChecked()); } void QmitkPartialVolumeAnalysisView::SetAdvancedVisibility() { m_Controls->frame_7->setVisible(m_Controls->m_AdvancedCheckbox->isChecked()); } void QmitkPartialVolumeAnalysisView::CreateConnections() { if ( m_Controls ) { connect( m_Controls->m_DisplayHistogramCheckbox, SIGNAL( clicked() ) , this, SLOT( SetHistogramVisibility() ) ); connect( m_Controls->m_AdvancedCheckbox, SIGNAL( clicked() ) , this, SLOT( SetAdvancedVisibility() ) ); connect( m_Controls->m_NumberBinsSlider, SIGNAL( sliderReleased () ), this, SLOT( NumberBinsReleasedSlider( ) ) ); connect( m_Controls->m_UpsamplingSlider, SIGNAL( sliderReleased( ) ), this, SLOT( UpsamplingReleasedSlider( ) ) ); connect( m_Controls->m_GaussianSigmaSlider, SIGNAL( sliderReleased( ) ), this, SLOT( GaussianSigmaReleasedSlider( ) ) ); connect( m_Controls->m_SimilarAnglesSlider, SIGNAL( sliderReleased( ) ), this, SLOT( SimilarAnglesReleasedSlider( ) ) ); connect( m_Controls->m_NumberBinsSlider, SIGNAL( valueChanged (int) ), this, SLOT( NumberBinsChangedSlider( int ) ) ); connect( m_Controls->m_UpsamplingSlider, SIGNAL( valueChanged( int ) ), this, SLOT( UpsamplingChangedSlider( int ) ) ); connect( m_Controls->m_GaussianSigmaSlider, SIGNAL( valueChanged( int ) ), this, SLOT( GaussianSigmaChangedSlider( int ) ) ); connect( m_Controls->m_SimilarAnglesSlider, SIGNAL( valueChanged( int ) ), this, SLOT( SimilarAnglesChangedSlider(int) ) ); connect( m_Controls->m_OpacitySlider, SIGNAL( valueChanged( int ) ), this, SLOT( OpacityChangedSlider(int) ) ); connect( (QObject*)(m_Controls->m_ButtonCopyHistogramToClipboard), SIGNAL(clicked()),(QObject*) this, SLOT(ToClipBoard())); connect( m_Controls->m_CircleButton, SIGNAL( clicked() ) , this, SLOT( ActionDrawEllipseTriggered() ) ); connect( m_Controls->m_RectangleButton, SIGNAL( clicked() ) , this, SLOT( ActionDrawRectangleTriggered() ) ); connect( m_Controls->m_PolygonButton, SIGNAL( clicked() ) , this, SLOT( ActionDrawPolygonTriggered() ) ); connect( m_Controls->m_GreenRadio, SIGNAL( clicked(bool) ) , this, SLOT( GreenRadio(bool) ) ); connect( m_Controls->m_PartialVolumeRadio, SIGNAL( clicked(bool) ) , this, SLOT( PartialVolumeRadio(bool) ) ); connect( m_Controls->m_BlueRadio, SIGNAL( clicked(bool) ) , this, SLOT( BlueRadio(bool) ) ); connect( m_Controls->m_AllRadio, SIGNAL( clicked(bool) ) , this, SLOT( AllRadio(bool) ) ); connect( m_Controls->m_EstimateCircle, SIGNAL( clicked() ) , this, SLOT( EstimateCircle() ) ); connect( (QObject*)(m_Controls->m_TextureIntON), SIGNAL(clicked()), this, SLOT(TextIntON()) ); connect( m_Controls->m_ExportClusteringResultsButton, SIGNAL(clicked()), this, SLOT(ExportClusteringResults())); } } void QmitkPartialVolumeAnalysisView::ExportClusteringResults() { if (m_ClusteringResult.IsNull() || m_SelectedImage.IsNull()) return; - mitk::DiffusionImage::Pointer diffusionImage = NULL; - if (dynamic_cast*>(m_SelectedImage.GetPointer())) - diffusionImage = dynamic_cast*>(m_SelectedImage.GetPointer()); - else - return; + mitk::Geometry3D* geometry = m_SelectedImage->GetGeometry(); + + itk::Image< short, 3>::Pointer referenceImage = itk::Image< short, 3>::New(); + + mitk::Vector3D newSpacing = geometry->GetSpacing(); + mitk::Point3D newOrigin = geometry->GetOrigin(); + mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds(); + newOrigin[0] += bounds.GetElement(0); + newOrigin[1] += bounds.GetElement(2); + newOrigin[2] += bounds.GetElement(4); + itk::Matrix newDirection; + itk::ImageRegion<3> imageRegion; + for (int i=0; i<3; i++) + for (int j=0; j<3; j++) + newDirection[j][i] = geometry->GetMatrixColumn(i)[j]/newSpacing[j]; + imageRegion.SetSize(0, geometry->GetExtent(0)); + imageRegion.SetSize(1, geometry->GetExtent(1)); + imageRegion.SetSize(2, geometry->GetExtent(2)); + + // apply new image parameters + referenceImage->SetSpacing( newSpacing ); + referenceImage->SetOrigin( newOrigin ); + referenceImage->SetDirection( newDirection ); + referenceImage->SetRegions( imageRegion ); + referenceImage->Allocate(); typedef itk::Image< float, 3 > OutType; mitk::Image::Pointer mitkInImage = dynamic_cast(m_ClusteringResult->GetData()); - typedef itk::ExtractChannelFromRgbaImageFilter< OutType > ExtractionFilterType; typedef itk::Image< itk::RGBAPixel, 3 > ItkRgbaImageType; typedef mitk::ImageToItk< ItkRgbaImageType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(mitkInImage); caster->Update(); ItkRgbaImageType::Pointer itkInImage = caster->GetOutput(); + typedef itk::ExtractChannelFromRgbaImageFilter< itk::Image< short, 3>, OutType > ExtractionFilterType; ExtractionFilterType::Pointer filter = ExtractionFilterType::New(); filter->SetInput(itkInImage); filter->SetChannel(ExtractionFilterType::ALPHA); - filter->SetReferenceImage(diffusionImage->GetVectorImage()); + filter->SetReferenceImage(referenceImage); filter->Update(); - OutType::Pointer outImg = filter->GetOutput(); -// mitk::Geometry3D* geometry = m_SelectedImage->GetGeometry(); -// itk::Matrix direction; -// itk::ImageRegion<3> imageRegion; -// for (int i=0; i<3; i++) -// for (int j=0; j<3; j++) -// direction[j][i] = geometry->GetMatrixColumn(i)[j]; -// imageRegion.SetSize(0, geometry->GetExtent(0)); -// imageRegion.SetSize(1, geometry->GetExtent(1)); -// imageRegion.SetSize(2, geometry->GetExtent(2)); -// typedef itk::ResampleImageFilter ResamplerType; -// ResamplerType::Pointer resampler = ResamplerType::New(); -// resampler->SetOutputSpacing( geometry->GetSpacing() ); -// resampler->SetOutputOrigin( geometry->GetOrigin() ); -// resampler->SetOutputDirection( direction ); -// resampler->SetSize( imageRegion.GetSize() ); -// resampler->SetInput( outImg ); -// const itk::Transform* trafo = geometry->GetParametricTransform(); -// itk::Transform::InverseTransformBasePointer t = trafo->GetInverseTransform(); -// itk::Transform* invTrafo = dynamic_cast*>(t.GetPointer()); -// resampler->SetTransform(invTrafo); - -//// double gausssigma = 10; -//// double sigma[3]; -//// for( unsigned int d = 0; d < 3; d++ ) -//// sigma[d] = gausssigma * geometry->GetSpacing()[d]; -//// double alpha = 2.0; -//// typedef itk::GaussianInterpolateImageFunction InterpolatorType; -//// typedef itk::NearestNeighborInterpolateImageFunction InterpolatorType; -//// typename InterpolatorType::Pointer interpolator = InterpolatorType::New(); -//// interpolator->SetInputImage( outImg ); -//// interpolator->SetParameters( sigma, alpha ); -//// resampler->SetInterpolator( interpolator ); - -// resampler->Update(); -// outImg = resampler->GetOutput(); - - mitk::Image::Pointer img = mitk::Image::New(); - img->InitializeByItk(outImg.GetPointer()); + mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); node->SetName("Clustering Result"); GetDataStorage()->Add(node); } void QmitkPartialVolumeAnalysisView::EstimateCircle() { typedef itk::Image SegImageType; SegImageType::Pointer mask_itk = SegImageType::New(); typedef mitk::ImageToItk CastType; CastType::Pointer caster = CastType::New(); caster->SetInput(m_SelectedImageMask); caster->Update(); typedef itk::ImageMomentsCalculator< SegImageType > MomentsType; MomentsType::Pointer momentsCalc = MomentsType::New(); momentsCalc->SetImage(caster->GetOutput()); momentsCalc->Compute(); MomentsType::VectorType cog = momentsCalc->GetCenterOfGravity(); MomentsType::MatrixType axes = momentsCalc->GetPrincipalAxes(); MomentsType::VectorType moments = momentsCalc->GetPrincipalMoments(); // moments-coord conversion // third coordinate min oder max? // max-min = extent MomentsType::AffineTransformPointer trafo = momentsCalc->GetPhysicalAxesToPrincipalAxesTransform(); itk::ImageRegionIterator itimage(caster->GetOutput(), caster->GetOutput()->GetLargestPossibleRegion()); itimage = itimage.Begin(); double max = -9999999999.0; double min = 9999999999.0; while( !itimage.IsAtEnd() ) { if(itimage.Get()) { ImageType::IndexType index = itimage.GetIndex(); itk::Point point; caster->GetOutput()->TransformIndexToPhysicalPoint(index,point); itk::Point newPoint; newPoint = trafo->TransformPoint(point); if(newPoint[2]max) max = newPoint[2]; } ++itimage; } double extent = max - min; MITK_INFO << "EXTENT = " << extent; mitk::Point3D origin; mitk::Vector3D right, bottom, normal; double factor = 1000.0; mitk::FillVector3D(origin, cog[0]-factor*axes[1][0]-factor*axes[2][0], cog[1]-factor*axes[1][1]-factor*axes[2][1], cog[2]-factor*axes[1][2]-factor*axes[2][2]); // mitk::FillVector3D(normal, axis[0][0],axis[0][1],axis[0][2]); mitk::FillVector3D(bottom, 2*factor*axes[1][0], 2*factor*axes[1][1], 2*factor*axes[1][2]); mitk::FillVector3D(right, 2*factor*axes[2][0], 2*factor*axes[2][1], 2*factor*axes[2][2]); mitk::PlaneGeometry::Pointer planegeometry = mitk::PlaneGeometry::New(); planegeometry->InitializeStandardPlane(right.Get_vnl_vector(), bottom.Get_vnl_vector()); planegeometry->SetOrigin(origin); double len1 = sqrt(axes[1][0]*axes[1][0] + axes[1][1]*axes[1][1] + axes[1][2]*axes[1][2]); double len2 = sqrt(axes[2][0]*axes[2][0] + axes[2][1]*axes[2][1] + axes[2][2]*axes[2][2]); mitk::Point2D point1; point1[0] = factor*len1; point1[1] = factor*len2; mitk::Point2D point2; point2[0] = factor*len1+extent*.5; point2[1] = factor*len2; mitk::PlanarCircle::Pointer circle = mitk::PlanarCircle::New(); circle->SetGeometry2D(planegeometry); circle->PlaceFigure( point1 ); circle->SetControlPoint(0,point1); circle->SetControlPoint(1,point2); //circle->SetCurrentControlPoint( point2 ); mitk::PlanarFigure::PolyLineType polyline = circle->GetPolyLine( 0 ); MITK_INFO << "SIZE of planar figure polyline: " << polyline.size(); AddFigureToDataStorage(circle, "Circle"); } -void QmitkPartialVolumeAnalysisView::StdMultiWidgetAvailable( QmitkStdMultiWidget& stdMultiWidget ) -{ - QmitkFunctionality::StdMultiWidgetAvailable(stdMultiWidget); -} - bool QmitkPartialVolumeAnalysisView::AssertDrawingIsPossible(bool checked) { if (m_SelectedImageNodes->GetNode().IsNull()) { checked = false; - this->HandleException("Please select an image!", this->m_Parent, true); + this->HandleException("Please select an image!", dynamic_cast(this->parent()), true); return false; } //this->GetActiveStdMultiWidget()->SetWidgetPlanesVisibility(false); return checked; } void QmitkPartialVolumeAnalysisView::ActionDrawEllipseTriggered() { bool checked = m_Controls->m_CircleButton->isChecked(); if(!this->AssertDrawingIsPossible(checked)) return; mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New(); this->AddFigureToDataStorage(figure, QString("Circle%1").arg(++m_EllipseCounter)); MITK_INFO << "PlanarCircle created ..."; } void QmitkPartialVolumeAnalysisView::ActionDrawRectangleTriggered() { bool checked = m_Controls->m_RectangleButton->isChecked(); if(!this->AssertDrawingIsPossible(checked)) return; mitk::PlanarRectangle::Pointer figure = mitk::PlanarRectangle::New(); this->AddFigureToDataStorage(figure, QString("Rectangle%1").arg(++m_RectangleCounter)); MITK_INFO << "PlanarRectangle created ..."; } void QmitkPartialVolumeAnalysisView::ActionDrawPolygonTriggered() { bool checked = m_Controls->m_PolygonButton->isChecked(); if(!this->AssertDrawingIsPossible(checked)) return; mitk::PlanarPolygon::Pointer figure = mitk::PlanarPolygon::New(); figure->ClosedOn(); this->AddFigureToDataStorage(figure, QString("Polygon%1").arg(++m_PolygonCounter)); MITK_INFO << "PlanarPolygon created ..."; } void QmitkPartialVolumeAnalysisView::AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, - const char *propertyKey, mitk::BaseProperty *property ) + const char *propertyKey, mitk::BaseProperty *property ) { mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetName(name.toStdString()); newNode->SetData(figure); // Add custom property, if available if ( (propertyKey != NULL) && (property != NULL) ) { newNode->AddProperty( propertyKey, property ); } // figure drawn on the topmost layer / image this->GetDataStorage()->Add(newNode, m_SelectedImageNodes->GetNode() ); - std::vector selectedNodes = GetDataManagerSelection(); + QList selectedNodes = this->GetDataManagerSelection(); for(unsigned int i = 0; i < selectedNodes.size(); i++) { selectedNodes[i]->SetSelected(false); } - selectedNodes = m_SelectedPlanarFigureNodes->GetNodes(); - for(unsigned int i = 0; i < selectedNodes.size(); i++) + + std::vector selectedPFNodes = m_SelectedPlanarFigureNodes->GetNodes(); + for(unsigned int i = 0; i < selectedPFNodes.size(); i++) { - selectedNodes[i]->SetSelected(false); + selectedPFNodes[i]->SetSelected(false); } newNode->SetSelected(true); Select(newNode); } void QmitkPartialVolumeAnalysisView::PlanarFigureInitialized() { if(m_SelectedPlanarFigureNodes->GetNode().IsNull()) return; m_CurrentFigureNodeInitialized = true; this->Select(m_SelectedPlanarFigureNodes->GetNode()); m_Controls->m_CircleButton->setChecked(false); m_Controls->m_RectangleButton->setChecked(false); m_Controls->m_PolygonButton->setChecked(false); //this->GetActiveStdMultiWidget()->SetWidgetPlanesVisibility(true); this->RequestStatisticsUpdate(); } void QmitkPartialVolumeAnalysisView::PlanarFigureFocus(mitk::DataNode* node) { mitk::PlanarFigure* _PlanarFigure = 0; _PlanarFigure = dynamic_cast (node->GetData()); if (_PlanarFigure) { FindRenderWindow(node); const mitk::PlaneGeometry * _PlaneGeometry = dynamic_cast (_PlanarFigure->GetGeometry2D()); // make node visible if (m_SelectedRenderWindow) { mitk::Point3D centerP = _PlaneGeometry->GetOrigin(); m_SelectedRenderWindow->GetSliceNavigationController()->ReorientSlices( - centerP, _PlaneGeometry->GetNormal()); + centerP, _PlaneGeometry->GetNormal()); m_SelectedRenderWindow->GetSliceNavigationController()->SelectSliceByPoint( - centerP); + centerP); } } } void QmitkPartialVolumeAnalysisView::FindRenderWindow(mitk::DataNode* node) { - - if(node) + if (node && dynamic_cast (node->GetData())) { - mitk::PlanarFigure* _PlanarFigure = 0; - _PlanarFigure = dynamic_cast (node->GetData()); + m_SelectedRenderWindow = 0; + bool PlanarFigureInitializedWindow = false; - if (_PlanarFigure) + foreach(QmitkRenderWindow * window, this->GetRenderWindowPart()->GetRenderWindows().values()) { - m_SelectedRenderWindow = 0; - QmitkRenderWindow* RenderWindow1 = - this->GetActiveStdMultiWidget()->GetRenderWindow1(); - QmitkRenderWindow* RenderWindow2 = - this->GetActiveStdMultiWidget()->GetRenderWindow2(); - QmitkRenderWindow* RenderWindow3 = - this->GetActiveStdMultiWidget()->GetRenderWindow3(); - QmitkRenderWindow* RenderWindow4 = - this->GetActiveStdMultiWidget()->GetRenderWindow4(); - - bool PlanarFigureInitializedWindow = false; - - // find initialized renderwindow - if (node->GetBoolProperty("PlanarFigureInitializedWindow", - PlanarFigureInitializedWindow, RenderWindow1->GetRenderer())) + if (!m_SelectedRenderWindow && node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, window->GetRenderer())) { - m_SelectedRenderWindow = RenderWindow1; + m_SelectedRenderWindow = window; } - - if (!m_SelectedRenderWindow && node->GetBoolProperty( - "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, - RenderWindow2->GetRenderer())) - { - m_SelectedRenderWindow = RenderWindow2; - } - - if (!m_SelectedRenderWindow && node->GetBoolProperty( - "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, - RenderWindow3->GetRenderer())) - { - m_SelectedRenderWindow = RenderWindow3; - } - - if (!m_SelectedRenderWindow && node->GetBoolProperty( - "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, - RenderWindow4->GetRenderer())) - { - m_SelectedRenderWindow = RenderWindow4; - } - } } } -void QmitkPartialVolumeAnalysisView::OnSelectionChanged( std::vector nodes ) + +void QmitkPartialVolumeAnalysisView::OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList &nodes) { - if ( !this->IsVisible() ) + if ( !m_Visible ) { return; } if ( nodes.empty() || nodes.size() > 1 ) { // Nothing to do: invalidate image, clear statistics, histogram, and GUI return; } Select(nodes.front()); } void QmitkPartialVolumeAnalysisView::Select( mitk::DataNode::Pointer node, bool clearMaskOnFirstArgNULL, bool clearImageOnFirstArgNULL ) { // Clear any unreferenced images this->RemoveOrphanImages(); bool somethingChanged = false; if(node.IsNull()) { somethingChanged = true; if(clearMaskOnFirstArgNULL) { if ( (m_SelectedImageMask.IsNotNull()) && (m_ImageMaskObserverTag >= 0) ) { m_SelectedImageMask->RemoveObserver( m_ImageMaskObserverTag ); m_ImageMaskObserverTag = -1; } if ( (m_SelectedPlanarFigure.IsNotNull()) && (m_PlanarFigureObserverTag >= 0) ) { m_SelectedPlanarFigure->RemoveObserver( m_PlanarFigureObserverTag ); m_PlanarFigureObserverTag = -1; } if ( (m_SelectedPlanarFigure.IsNotNull()) && (m_InitializedObserverTag >= 0) ) { m_SelectedPlanarFigure->RemoveObserver( m_InitializedObserverTag ); m_InitializedObserverTag = -1; } m_SelectedPlanarFigure = NULL; m_SelectedPlanarFigureNodes->RemoveAllNodes(); m_CurrentFigureNodeInitialized = false; m_SelectedRenderWindow = 0; m_SelectedMaskNode = NULL; m_SelectedImageMask = NULL; } if(clearImageOnFirstArgNULL) { if ( (m_SelectedImage.IsNotNull()) && (m_ImageObserverTag >= 0) ) { m_SelectedImage->RemoveObserver( m_ImageObserverTag ); m_ImageObserverTag = -1; } m_SelectedImageNodes->RemoveAllNodes(); m_SelectedImage = NULL; m_IsTensorImage = false; m_FAImage = NULL; m_RDImage = NULL; m_ADImage = NULL; m_MDImage = NULL; m_CAImage = NULL; m_DirectionComp1Image = NULL; m_DirectionComp2Image = NULL; m_AngularErrorImage = NULL; m_Controls->m_SimilarAnglesFrame->setVisible(false); m_Controls->m_SimilarAnglesLabel->setVisible(false); } } else { typedef itk::SimpleMemberCommand< QmitkPartialVolumeAnalysisView > ITKCommandType; ITKCommandType::Pointer changeListener; changeListener = ITKCommandType::New(); changeListener->SetCallbackFunction( this, &QmitkPartialVolumeAnalysisView::RequestStatisticsUpdate ); // Get selected element mitk::TensorImage *selectedTensorImage = dynamic_cast< mitk::TensorImage * >( node->GetData() ); mitk::Image *selectedImage = dynamic_cast< mitk::Image * >( node->GetData() ); mitk::PlanarFigure *selectedPlanar = dynamic_cast< mitk::PlanarFigure * >( node->GetData() ); bool isMask = false; bool isImage = false; bool isPlanar = false; bool isTensorImage = false; if (selectedTensorImage != NULL) { isTensorImage = true; } else if(selectedImage != NULL) { node->GetPropertyValue("binary", isMask); isImage = !isMask; } else if ( (selectedPlanar != NULL) ) { isPlanar = true; } // image if(isImage && selectedImage->GetDimension()==3) { if(selectedImage != m_SelectedImage.GetPointer()) { somethingChanged = true; if ( (m_SelectedImage.IsNotNull()) && (m_ImageObserverTag >= 0) ) { m_SelectedImage->RemoveObserver( m_ImageObserverTag ); m_ImageObserverTag = -1; } *m_SelectedImageNodes = node; m_SelectedImage = selectedImage; m_IsTensorImage = false; m_FAImage = NULL; m_RDImage = NULL; m_ADImage = NULL; m_MDImage = NULL; m_CAImage = NULL; m_DirectionComp1Image = NULL; m_DirectionComp2Image = NULL; m_AngularErrorImage = NULL; // Add change listeners to selected objects m_ImageObserverTag = m_SelectedImage->AddObserver( - itk::ModifiedEvent(), changeListener ); + itk::ModifiedEvent(), changeListener ); m_Controls->m_SimilarAnglesFrame->setVisible(false); m_Controls->m_SimilarAnglesLabel->setVisible(false); m_Controls->m_SelectedImageLabel->setText( m_SelectedImageNodes->GetNode()->GetName().c_str() ); } } //planar if(isPlanar) { if(selectedPlanar != m_SelectedPlanarFigure.GetPointer()) { MITK_INFO << "Planar selection changed"; somethingChanged = true; // Possibly previous change listeners if ( (m_SelectedPlanarFigure.IsNotNull()) && (m_PlanarFigureObserverTag >= 0) ) { m_SelectedPlanarFigure->RemoveObserver( m_PlanarFigureObserverTag ); m_PlanarFigureObserverTag = -1; } if ( (m_SelectedPlanarFigure.IsNotNull()) && (m_InitializedObserverTag >= 0) ) { m_SelectedPlanarFigure->RemoveObserver( m_InitializedObserverTag ); m_InitializedObserverTag = -1; } m_SelectedPlanarFigure = selectedPlanar; *m_SelectedPlanarFigureNodes = node; m_CurrentFigureNodeInitialized = selectedPlanar->IsPlaced(); m_SelectedMaskNode = NULL; m_SelectedImageMask = NULL; m_PlanarFigureObserverTag = m_SelectedPlanarFigure->AddObserver( - mitk::EndInteractionPlanarFigureEvent(), changeListener ); + mitk::EndInteractionPlanarFigureEvent(), changeListener ); if(!m_CurrentFigureNodeInitialized) { typedef itk::SimpleMemberCommand< QmitkPartialVolumeAnalysisView > ITKCommandType; ITKCommandType::Pointer initializationCommand; initializationCommand = ITKCommandType::New(); // set the callback function of the member command initializationCommand->SetCallbackFunction( this, &QmitkPartialVolumeAnalysisView::PlanarFigureInitialized ); // add an observer m_InitializedObserverTag = selectedPlanar->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand ); } m_Controls->m_SelectedMaskLabel->setText( m_SelectedPlanarFigureNodes->GetNode()->GetName().c_str() ); PlanarFigureFocus(node); } } //mask if(isMask && selectedImage->GetDimension()==3) { if(selectedImage != m_SelectedImage.GetPointer()) { somethingChanged = true; if ( (m_SelectedImageMask.IsNotNull()) && (m_ImageMaskObserverTag >= 0) ) { m_SelectedImageMask->RemoveObserver( m_ImageMaskObserverTag ); m_ImageMaskObserverTag = -1; } m_SelectedMaskNode = node; m_SelectedImageMask = selectedImage; m_SelectedPlanarFigure = NULL; m_SelectedPlanarFigureNodes->RemoveAllNodes(); m_ImageMaskObserverTag = m_SelectedImageMask->AddObserver( - itk::ModifiedEvent(), changeListener ); + itk::ModifiedEvent(), changeListener ); m_Controls->m_SelectedMaskLabel->setText( m_SelectedMaskNode->GetName().c_str() ); } } //tensor image if(isTensorImage && selectedTensorImage->GetDimension()==3) { if(selectedImage != m_SelectedImage.GetPointer()) { somethingChanged = true; if ( (m_SelectedImage.IsNotNull()) && (m_ImageObserverTag >= 0) ) { m_SelectedImage->RemoveObserver( m_ImageObserverTag ); m_ImageObserverTag = -1; } *m_SelectedImageNodes = node; m_SelectedImage = selectedImage; m_IsTensorImage = true; ExtractTensorImages(selectedImage); // Add change listeners to selected objects m_ImageObserverTag = m_SelectedImage->AddObserver( - itk::ModifiedEvent(), changeListener ); + itk::ModifiedEvent(), changeListener ); m_Controls->m_SimilarAnglesFrame->setVisible(true); m_Controls->m_SimilarAnglesLabel->setVisible(true); m_Controls->m_SelectedImageLabel->setText( m_SelectedImageNodes->GetNode()->GetName().c_str() ); } } } if(somethingChanged) { this->SetMeasurementInfoToRenderWindow(""); if(m_SelectedPlanarFigure.IsNull() && m_SelectedImageMask.IsNull() ) { - m_Controls->m_SelectedMaskLabel->setText( "None" ); + m_Controls->m_SelectedMaskLabel->setText( "-" ); m_Controls->m_ResampleOptionsFrame->setEnabled(false); m_Controls->m_HistogramWidget->setEnabled(false); m_Controls->m_ClassSelector->setEnabled(false); m_Controls->m_DisplayHistogramCheckbox->setEnabled(false); m_Controls->m_AdvancedCheckbox->setEnabled(false); m_Controls->frame_7->setEnabled(false); } else { m_Controls->m_ResampleOptionsFrame->setEnabled(true); m_Controls->m_HistogramWidget->setEnabled(true); m_Controls->m_ClassSelector->setEnabled(true); m_Controls->m_DisplayHistogramCheckbox->setEnabled(true); m_Controls->m_AdvancedCheckbox->setEnabled(true); m_Controls->frame_7->setEnabled(true); } // Clear statistics / histogram GUI if nothing is selected if ( m_SelectedImage.IsNull() ) { m_Controls->m_PlanarFigureButtonsFrame->setEnabled(false); m_Controls->m_OpacityFrame->setEnabled(false); - m_Controls->m_SelectedImageLabel->setText( "None" ); + m_Controls->m_SelectedImageLabel->setText( "-" ); } else { m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true); m_Controls->m_OpacityFrame->setEnabled(true); } if( m_SelectedImage.IsNull() - || (m_SelectedPlanarFigure.IsNull() && m_SelectedImageMask.IsNull()) ) - { + || (m_SelectedPlanarFigure.IsNull() && m_SelectedImageMask.IsNull()) ) + { m_Controls->m_HistogramWidget->ClearItemModel(); m_CurrentStatisticsValid = false; - m_Controls->m_ErrorMessageLabel->hide(); } else { this->RequestStatisticsUpdate(); } } } void QmitkPartialVolumeAnalysisView::ShowClusteringResults() { typedef itk::Image MaskImageType; mitk::Image::Pointer mask = 0; MaskImageType::Pointer itkmask = 0; if(m_IsTensorImage && m_Controls->m_SimilarAnglesSlider->value() != 0) { typedef itk::Image AngularErrorImageType; typedef mitk::ImageToItk CastType; CastType::Pointer caster = CastType::New(); caster->SetInput(m_AngularErrorImage); caster->Update(); typedef itk::BinaryThresholdImageFilter< AngularErrorImageType, MaskImageType > ThreshType; ThreshType::Pointer thresh = ThreshType::New(); thresh->SetUpperThreshold((90-m_Controls->m_SimilarAnglesSlider->value())*(PVA_PI/180.0)); thresh->SetInsideValue(1.0); thresh->SetInput(caster->GetOutput()); thresh->Update(); itkmask = thresh->GetOutput(); mask = mitk::Image::New(); mask->InitializeByItk(itkmask.GetPointer()); mask->SetVolume(itkmask->GetBufferPointer()); // GetDefaultDataStorage()->Remove(m_newnode); // m_newnode = mitk::DataNode::New(); // m_newnode->SetData(mask); // m_newnode->SetName("masking node"); // m_newnode->SetIntProperty( "layer", 1002 ); // GetDefaultDataStorage()->Add(m_newnode, m_SelectedImageNodes->GetNode()); } mitk::Image::Pointer clusteredImage; ClusteringType::Pointer clusterer = ClusteringType::New(); if(m_QuantifyClass==3) { if(m_IsTensorImage) { double *green_fa, *green_rd, *green_ad, *green_md; //double *greengray_fa, *greengray_rd, *greengray_ad, *greengray_md; double *gray_fa, *gray_rd, *gray_ad, *gray_md; //double *redgray_fa, *redgray_rd, *redgray_ad, *redgray_md; double *red_fa, *red_rd, *red_ad, *red_md; mitk::Image* tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(0); mitk::Image::ConstPointer imgToCluster = tmpImg; red_fa = clusterer->PerformQuantification(imgToCluster, m_CurrentRGBClusteringResults->rgbChannels->r, mask); green_fa = clusterer->PerformQuantification(imgToCluster, m_CurrentRGBClusteringResults->rgbChannels->g, mask); gray_fa = clusterer->PerformQuantification(imgToCluster, m_CurrentRGBClusteringResults->rgbChannels->b, mask); tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(3); mitk::Image::ConstPointer imgToCluster3 = tmpImg; red_rd = clusterer->PerformQuantification(imgToCluster3, m_CurrentRGBClusteringResults->rgbChannels->r, mask); green_rd = clusterer->PerformQuantification(imgToCluster3, m_CurrentRGBClusteringResults->rgbChannels->g, mask); gray_rd = clusterer->PerformQuantification(imgToCluster3, m_CurrentRGBClusteringResults->rgbChannels->b, mask); tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(4); mitk::Image::ConstPointer imgToCluster4 = tmpImg; red_ad = clusterer->PerformQuantification(imgToCluster4, m_CurrentRGBClusteringResults->rgbChannels->r, mask); green_ad = clusterer->PerformQuantification(imgToCluster4, m_CurrentRGBClusteringResults->rgbChannels->g, mask); gray_ad = clusterer->PerformQuantification(imgToCluster4, m_CurrentRGBClusteringResults->rgbChannels->b, mask); tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(5); mitk::Image::ConstPointer imgToCluster5 = tmpImg; red_md = clusterer->PerformQuantification(imgToCluster5, m_CurrentRGBClusteringResults->rgbChannels->r, mask); green_md = clusterer->PerformQuantification(imgToCluster5, m_CurrentRGBClusteringResults->rgbChannels->g, mask); gray_md = clusterer->PerformQuantification(imgToCluster5, m_CurrentRGBClusteringResults->rgbChannels->b, mask); // clipboard QString clipboardText("FA\t%1\t%2\t\t%3\t%4\t\t%5\t%6\t"); clipboardText = clipboardText - .arg(red_fa[0]).arg(red_fa[1]) - .arg(gray_fa[0]).arg(gray_fa[1]) - .arg(green_fa[0]).arg(green_fa[1]); + .arg(red_fa[0]).arg(red_fa[1]) + .arg(gray_fa[0]).arg(gray_fa[1]) + .arg(green_fa[0]).arg(green_fa[1]); QString clipboardText3("RD\t%1\t%2\t\t%3\t%4\t\t%5\t%6\t"); clipboardText3 = clipboardText3 - .arg(red_rd[0]).arg(red_rd[1]) - .arg(gray_rd[0]).arg(gray_rd[1]) - .arg(green_rd[0]).arg(green_rd[1]); + .arg(red_rd[0]).arg(red_rd[1]) + .arg(gray_rd[0]).arg(gray_rd[1]) + .arg(green_rd[0]).arg(green_rd[1]); QString clipboardText4("AD\t%1\t%2\t\t%3\t%4\t\t%5\t%6\t"); clipboardText4 = clipboardText4 - .arg(red_ad[0]).arg(red_ad[1]) - .arg(gray_ad[0]).arg(gray_ad[1]) - .arg(green_ad[0]).arg(green_ad[1]); + .arg(red_ad[0]).arg(red_ad[1]) + .arg(gray_ad[0]).arg(gray_ad[1]) + .arg(green_ad[0]).arg(green_ad[1]); QString clipboardText5("MD\t%1\t%2\t\t%3\t%4\t\t%5\t%6"); clipboardText5 = clipboardText5 - .arg(red_md[0]).arg(red_md[1]) - .arg(gray_md[0]).arg(gray_md[1]) - .arg(green_md[0]).arg(green_md[1]); + .arg(red_md[0]).arg(red_md[1]) + .arg(gray_md[0]).arg(gray_md[1]) + .arg(green_md[0]).arg(green_md[1]); QApplication::clipboard()->setText(clipboardText+clipboardText3+clipboardText4+clipboardText5, QClipboard::Clipboard); // now paint infos also on renderwindow QString plainInfoText("%1 %2 %3 \n"); plainInfoText = plainInfoText - .arg("Red ", 20) - .arg("Gray ", 20) - .arg("Green", 20); + .arg("Red ", 20) + .arg("Gray ", 20) + .arg("Green", 20); QString plainInfoText0("FA:%1 ± %2%3 ± %4%5 ± %6\n"); plainInfoText0 = plainInfoText0 - .arg(red_fa[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(red_fa[1], -10, 'g', 2, QLatin1Char( ' ' )) - .arg(gray_fa[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(gray_fa[1], -10, 'g', 2, QLatin1Char( ' ' )) - .arg(green_fa[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(green_fa[1], -10, 'g', 2, QLatin1Char( ' ' )); + .arg(red_fa[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(red_fa[1], -10, 'g', 2, QLatin1Char( ' ' )) + .arg(gray_fa[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(gray_fa[1], -10, 'g', 2, QLatin1Char( ' ' )) + .arg(green_fa[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(green_fa[1], -10, 'g', 2, QLatin1Char( ' ' )); QString plainInfoText3("RDx10³:%1 ± %2%3 ± %4%5 ± %6\n"); plainInfoText3 = plainInfoText3 - .arg(1000.0 * red_rd[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_rd[1], -10, 'g', 2, QLatin1Char( ' ' )) - .arg(1000.0 * gray_rd[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * gray_rd[1], -10, 'g', 2, QLatin1Char( ' ' )) - .arg(1000.0 * green_rd[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * green_rd[1], -10, 'g', 2, QLatin1Char( ' ' )); + .arg(1000.0 * red_rd[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_rd[1], -10, 'g', 2, QLatin1Char( ' ' )) + .arg(1000.0 * gray_rd[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * gray_rd[1], -10, 'g', 2, QLatin1Char( ' ' )) + .arg(1000.0 * green_rd[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * green_rd[1], -10, 'g', 2, QLatin1Char( ' ' )); QString plainInfoText4("ADx10³:%1 ± %2%3 ± %4%5 ± %6\n"); plainInfoText4 = plainInfoText4 - .arg(1000.0 * red_ad[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_ad[1], -10, 'g', 2, QLatin1Char( ' ' )) - .arg(1000.0 * gray_ad[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * gray_ad[1], -10, 'g', 2, QLatin1Char( ' ' )) - .arg(1000.0 * green_ad[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * green_ad[1], -10, 'g', 2, QLatin1Char( ' ' )); + .arg(1000.0 * red_ad[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_ad[1], -10, 'g', 2, QLatin1Char( ' ' )) + .arg(1000.0 * gray_ad[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * gray_ad[1], -10, 'g', 2, QLatin1Char( ' ' )) + .arg(1000.0 * green_ad[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * green_ad[1], -10, 'g', 2, QLatin1Char( ' ' )); QString plainInfoText5("MDx10³:%1 ± %2%3 ± %4%5 ± %6"); plainInfoText5 = plainInfoText5 - .arg(1000.0 * red_md[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_md[1], -10, 'g', 2, QLatin1Char( ' ' )) - .arg(1000.0 * gray_md[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * gray_md[1], -10, 'g', 2, QLatin1Char( ' ' )) - .arg(1000.0 * green_md[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * green_md[1], -10, 'g', 2, QLatin1Char( ' ' )); + .arg(1000.0 * red_md[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_md[1], -10, 'g', 2, QLatin1Char( ' ' )) + .arg(1000.0 * gray_md[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * gray_md[1], -10, 'g', 2, QLatin1Char( ' ' )) + .arg(1000.0 * green_md[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * green_md[1], -10, 'g', 2, QLatin1Char( ' ' )); this->SetMeasurementInfoToRenderWindow(plainInfoText+plainInfoText0+plainInfoText3+plainInfoText4+plainInfoText5); } else { double* green; double* gray; double* red; mitk::Image* tmpImg = m_CurrentStatisticsCalculator->GetInternalImage(); mitk::Image::ConstPointer imgToCluster = tmpImg; red = clusterer->PerformQuantification(imgToCluster, m_CurrentRGBClusteringResults->rgbChannels->r); green = clusterer->PerformQuantification(imgToCluster, m_CurrentRGBClusteringResults->rgbChannels->g); gray = clusterer->PerformQuantification(imgToCluster, m_CurrentRGBClusteringResults->rgbChannels->b); // clipboard QString clipboardText("%1\t%2\t\t%3\t%4\t\t%5\t%6"); clipboardText = clipboardText.arg(red[0]).arg(red[1]) - .arg(gray[0]).arg(gray[1]) - .arg(green[0]).arg(green[1]); + .arg(gray[0]).arg(gray[1]) + .arg(green[0]).arg(green[1]); QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard); // now paint infos also on renderwindow QString plainInfoText("Red: %1 ± %2\nGray: %3 ± %4\nGreen: %5 ± %6"); plainInfoText = plainInfoText.arg(red[0]).arg(red[1]) - .arg(gray[0]).arg(gray[1]) - .arg(green[0]).arg(green[1]); + .arg(gray[0]).arg(gray[1]) + .arg(green[0]).arg(green[1]); this->SetMeasurementInfoToRenderWindow(plainInfoText); } clusteredImage = m_CurrentRGBClusteringResults->rgb; } else { if(m_IsTensorImage) { double *red_fa, *red_rd, *red_ad, *red_md; mitk::Image* tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(0); mitk::Image::ConstPointer imgToCluster = tmpImg; red_fa = clusterer->PerformQuantification(imgToCluster, m_CurrentPerformClusteringResults->clusteredImage, mask); tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(3); mitk::Image::ConstPointer imgToCluster3 = tmpImg; red_rd = clusterer->PerformQuantification(imgToCluster3, m_CurrentPerformClusteringResults->clusteredImage, mask); tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(4); mitk::Image::ConstPointer imgToCluster4 = tmpImg; red_ad = clusterer->PerformQuantification(imgToCluster4, m_CurrentPerformClusteringResults->clusteredImage, mask); tmpImg = m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(5); mitk::Image::ConstPointer imgToCluster5 = tmpImg; red_md = clusterer->PerformQuantification(imgToCluster5, m_CurrentPerformClusteringResults->clusteredImage, mask); // clipboard QString clipboardText("FA\t%1\t%2\t"); clipboardText = clipboardText - .arg(red_fa[0]).arg(red_fa[1]); + .arg(red_fa[0]).arg(red_fa[1]); QString clipboardText3("RD\t%1\t%2\t"); clipboardText3 = clipboardText3 - .arg(red_rd[0]).arg(red_rd[1]); + .arg(red_rd[0]).arg(red_rd[1]); QString clipboardText4("AD\t%1\t%2\t"); clipboardText4 = clipboardText4 - .arg(red_ad[0]).arg(red_ad[1]); + .arg(red_ad[0]).arg(red_ad[1]); QString clipboardText5("MD\t%1\t%2\t"); clipboardText5 = clipboardText5 - .arg(red_md[0]).arg(red_md[1]); + .arg(red_md[0]).arg(red_md[1]); QApplication::clipboard()->setText(clipboardText+clipboardText3+clipboardText4+clipboardText5, QClipboard::Clipboard); // now paint infos also on renderwindow QString plainInfoText("%1 \n"); plainInfoText = plainInfoText - .arg("Red ", 20); + .arg("Red ", 20); QString plainInfoText0("FA:%1 ± %2\n"); plainInfoText0 = plainInfoText0 - .arg(red_fa[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(red_fa[1], -10, 'g', 2, QLatin1Char( ' ' )); + .arg(red_fa[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(red_fa[1], -10, 'g', 2, QLatin1Char( ' ' )); QString plainInfoText3("RDx10³:%1 ± %2\n"); plainInfoText3 = plainInfoText3 - .arg(1000.0 * red_rd[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_rd[1], -10, 'g', 2, QLatin1Char( ' ' )); + .arg(1000.0 * red_rd[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_rd[1], -10, 'g', 2, QLatin1Char( ' ' )); QString plainInfoText4("ADx10³:%1 ± %2\n"); plainInfoText4 = plainInfoText4 - .arg(1000.0 * red_ad[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_ad[1], -10, 'g', 2, QLatin1Char( ' ' )); + .arg(1000.0 * red_ad[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_ad[1], -10, 'g', 2, QLatin1Char( ' ' )); QString plainInfoText5("MDx10³:%1 ± %2"); plainInfoText5 = plainInfoText5 - .arg(1000.0 * red_md[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_md[1], -10, 'g', 2, QLatin1Char( ' ' )); + .arg(1000.0 * red_md[0], 10, 'g', 2, QLatin1Char( ' ' )).arg(1000.0 * red_md[1], -10, 'g', 2, QLatin1Char( ' ' )); this->SetMeasurementInfoToRenderWindow(plainInfoText+plainInfoText0+plainInfoText3+plainInfoText4+plainInfoText5); } else { double* quant; mitk::Image* tmpImg = m_CurrentStatisticsCalculator->GetInternalImage(); mitk::Image::ConstPointer imgToCluster = tmpImg; quant = clusterer->PerformQuantification(imgToCluster, m_CurrentPerformClusteringResults->clusteredImage); // clipboard QString clipboardText("%1\t%2"); clipboardText = clipboardText.arg(quant[0]).arg(quant[1]); QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard); // now paint infos also on renderwindow QString plainInfoText("Measurement: %1 ± %2"); plainInfoText = plainInfoText.arg(quant[0]).arg(quant[1]); this->SetMeasurementInfoToRenderWindow(plainInfoText); } clusteredImage = m_CurrentPerformClusteringResults->displayImage; } if(mask.IsNotNull()) { typedef itk::Image,3> RGBImageType; typedef mitk::ImageToItk ClusterCasterType; ClusterCasterType::Pointer clCaster = ClusterCasterType::New(); clCaster->SetInput(clusteredImage); clCaster->Update(); clCaster->GetOutput(); typedef itk::MaskImageFilter< RGBImageType, MaskImageType, RGBImageType > MaskType; MaskType::Pointer masker = MaskType::New(); masker->SetInput1(clCaster->GetOutput()); masker->SetInput2(itkmask); masker->Update(); clusteredImage = mitk::Image::New(); clusteredImage->InitializeByItk(masker->GetOutput()); clusteredImage->SetVolume(masker->GetOutput()->GetBufferPointer()); } if(m_ClusteringResult.IsNotNull()) { - GetDefaultDataStorage()->Remove(m_ClusteringResult); + this->GetDataStorage()->Remove(m_ClusteringResult); } m_ClusteringResult = mitk::DataNode::New(); m_ClusteringResult->SetBoolProperty("helper object", true); m_ClusteringResult->SetIntProperty( "layer", 1000 ); m_ClusteringResult->SetBoolProperty("texture interpolation", m_TexIsOn); m_ClusteringResult->SetData(clusteredImage); m_ClusteringResult->SetName("Clusterprobs"); - GetDefaultDataStorage()->Add(m_ClusteringResult, m_SelectedImageNodes->GetNode()); + this->GetDataStorage()->Add(m_ClusteringResult, m_SelectedImageNodes->GetNode()); if(m_SelectedPlanarFigure.IsNotNull() && m_SelectedPlanarFigureNodes->GetNode().IsNotNull()) { m_SelectedPlanarFigureNodes->GetNode()->SetIntProperty( "layer", 1001 ); } - GetActiveStdMultiWidget()->RequestUpdate(); + this->RequestRenderWindowUpdate(); } void QmitkPartialVolumeAnalysisView::UpdateStatistics() { MITK_INFO << "UpdateStatistics()"; if(!m_CurrentFigureNodeInitialized && m_SelectedPlanarFigure.IsNotNull()) { MITK_INFO << "Selected planar figure not initialized. No stats calculation performed."; return; } // Remove any cached images that are no longer referenced elsewhere this->RemoveOrphanImages(); - QmitkStdMultiWidget *multiWidget = this->GetActiveStdMultiWidget(); + + QmitkStdMultiWidget *multiWidget = 0; + QmitkStdMultiWidgetEditor * multiWidgetEdit = 0; + + multiWidgetEdit = dynamic_cast(this->GetRenderWindowPart()); + if(multiWidgetEdit){ + multiWidget = multiWidgetEdit->GetStdMultiWidget(); + } + if ( multiWidget == NULL ) { return; } if ( m_SelectedImage.IsNotNull() ) { // Check if a the selected image is a multi-channel image. If yes, statistics // cannot be calculated currently. if ( !m_IsTensorImage && m_SelectedImage->GetPixelType().GetNumberOfComponents() > 1 ) { - std::stringstream message; - message << "Non-tensor multi-component images not supported."; - m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); - m_Controls->m_ErrorMessageLabel->show(); + QMessageBox::information( NULL, "Warning", "Non-tensor multi-component images not supported."); m_Controls->m_HistogramWidget->ClearItemModel(); m_CurrentStatisticsValid = false; return; } // Retrieve HistogramStatisticsCalculator from has map (or create a new one // for this image if non-existant) PartialVolumeAnalysisMapType::iterator it = m_PartialVolumeAnalysisMap.find( m_SelectedImage ); if ( it != m_PartialVolumeAnalysisMap.end() ) { m_CurrentStatisticsCalculator = it->second; MITK_INFO << "Retrieving StatisticsCalculator"; } else { m_CurrentStatisticsCalculator = mitk::PartialVolumeAnalysisHistogramCalculator::New(); m_CurrentStatisticsCalculator->SetPlanarFigureThickness(m_Controls->m_PlanarFiguresThickness->value()); if(m_IsTensorImage) { m_CurrentStatisticsCalculator->SetImage( m_CAImage ); m_CurrentStatisticsCalculator->AddAdditionalResamplingImage( m_FAImage ); m_CurrentStatisticsCalculator->AddAdditionalResamplingImage( m_DirectionComp1Image ); m_CurrentStatisticsCalculator->AddAdditionalResamplingImage( m_DirectionComp2Image ); m_CurrentStatisticsCalculator->AddAdditionalResamplingImage( m_RDImage ); m_CurrentStatisticsCalculator->AddAdditionalResamplingImage( m_ADImage ); m_CurrentStatisticsCalculator->AddAdditionalResamplingImage( m_MDImage ); } else { m_CurrentStatisticsCalculator->SetImage( m_SelectedImage ); } m_PartialVolumeAnalysisMap[m_SelectedImage] = m_CurrentStatisticsCalculator; MITK_INFO << "Creating StatisticsCalculator"; } std::string maskName; std::string maskType; unsigned int maskDimension; if ( m_SelectedImageMask.IsNotNull() ) { mitk::PixelType pixelType = m_SelectedImageMask->GetPixelType(); std::cout << pixelType.GetItkTypeAsString() << std::endl; if(pixelType.GetBitsPerComponent() == 16) { //convert from short to uchar typedef itk::Image ShortImageType; typedef itk::Image CharImageType; CharImageType::Pointer charImage; ShortImageType::Pointer shortImage; mitk::CastToItkImage(m_SelectedImageMask, shortImage); typedef itk::CastImageFilter ImageCasterType; ImageCasterType::Pointer caster = ImageCasterType::New(); caster->SetInput( shortImage ); caster->Update(); charImage = caster->GetOutput(); mitk::CastToMitkImage(charImage, m_SelectedImageMask); } m_CurrentStatisticsCalculator->SetImageMask( m_SelectedImageMask ); m_CurrentStatisticsCalculator->SetMaskingModeToImage(); maskName = m_SelectedMaskNode->GetName(); maskType = m_SelectedImageMask->GetNameOfClass(); maskDimension = 3; std::stringstream maskLabel; maskLabel << maskName; if ( maskDimension > 0 ) { maskLabel << " [" << maskDimension << "D " << maskType << "]"; } m_Controls->m_SelectedMaskLabel->setText( maskLabel.str().c_str() ); } else if ( m_SelectedPlanarFigure.IsNotNull() && m_SelectedPlanarFigureNodes->GetNode().IsNotNull()) { m_CurrentStatisticsCalculator->SetPlanarFigure( m_SelectedPlanarFigure ); m_CurrentStatisticsCalculator->SetMaskingModeToPlanarFigure(); maskName = m_SelectedPlanarFigureNodes->GetNode()->GetName(); maskType = m_SelectedPlanarFigure->GetNameOfClass(); maskDimension = 2; } else { m_CurrentStatisticsCalculator->SetMaskingModeToNone(); - maskName = "None"; + maskName = "-"; maskType = ""; maskDimension = 0; } bool statisticsChanged = false; bool statisticsCalculationSuccessful = false; // Initialize progress bar mitk::ProgressBar::GetInstance()->AddStepsToDo( 100 ); // Install listener for progress events and initialize progress bar typedef itk::SimpleMemberCommand< QmitkPartialVolumeAnalysisView > ITKCommandType; ITKCommandType::Pointer progressListener; progressListener = ITKCommandType::New(); progressListener->SetCallbackFunction( this, &QmitkPartialVolumeAnalysisView::UpdateProgressBar ); unsigned long progressObserverTag = m_CurrentStatisticsCalculator - ->AddObserver( itk::ProgressEvent(), progressListener ); + ->AddObserver( itk::ProgressEvent(), progressListener ); ClusteringType::ParamsType *cparams = 0; ClusteringType::ClusterResultType *cresult = 0; ClusteringType::HistType *chist = 0; try { m_CurrentStatisticsCalculator->SetNumberOfBins(m_Controls->m_NumberBins->text().toInt()); m_CurrentStatisticsCalculator->SetUpsamplingFactor(m_Controls->m_Upsampling->text().toDouble()); m_CurrentStatisticsCalculator->SetGaussianSigma(m_Controls->m_GaussianSigma->text().toDouble()); // Compute statistics statisticsChanged = m_CurrentStatisticsCalculator->ComputeStatistics( ); mitk::Image* tmpImg = m_CurrentStatisticsCalculator->GetInternalImage(); mitk::Image::ConstPointer imgToCluster = tmpImg; if(imgToCluster.IsNotNull()) { // perform clustering const HistogramType *histogram = m_CurrentStatisticsCalculator->GetHistogram( ); if(histogram != NULL) { ClusteringType::Pointer clusterer = ClusteringType::New(); clusterer->SetStepsNumIntegration(200); clusterer->SetMaxIt(1000); mitk::Image::Pointer pFiberImg; if(m_QuantifyClass==3) { if(m_Controls->m_Quantiles->isChecked()) { m_CurrentRGBClusteringResults = clusterer->PerformRGBQuantiles(imgToCluster, histogram, m_Controls->m_q1->value(),m_Controls->m_q2->value()); } else { m_CurrentRGBClusteringResults = clusterer->PerformRGBClustering(imgToCluster, histogram); } pFiberImg = m_CurrentRGBClusteringResults->rgbChannels->r; cparams = m_CurrentRGBClusteringResults->params; cresult = m_CurrentRGBClusteringResults->result; chist = m_CurrentRGBClusteringResults->hist; } else { if(m_Controls->m_Quantiles->isChecked()) { m_CurrentPerformClusteringResults = clusterer->PerformQuantiles(imgToCluster, histogram, m_Controls->m_q1->value(),m_Controls->m_q2->value()); } else { m_CurrentPerformClusteringResults = - clusterer->PerformClustering(imgToCluster, histogram, m_QuantifyClass); + clusterer->PerformClustering(imgToCluster, histogram, m_QuantifyClass); } pFiberImg = m_CurrentPerformClusteringResults->clusteredImage; cparams = m_CurrentPerformClusteringResults->params; cresult = m_CurrentPerformClusteringResults->result; chist = m_CurrentPerformClusteringResults->hist; } if(m_IsTensorImage) { m_AngularErrorImage = clusterer->CaculateAngularErrorImage( - m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(1), - m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(2), - pFiberImg); + m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(1), + m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(2), + pFiberImg); // GetDefaultDataStorage()->Remove(m_newnode2); // m_newnode2 = mitk::DataNode::New(); // m_newnode2->SetData(m_AngularErrorImage); // m_newnode2->SetName(("AngularError")); // m_newnode2->SetIntProperty( "layer", 1003 ); // GetDefaultDataStorage()->Add(m_newnode2, m_SelectedImageNodes->GetNode()); // newnode = mitk::DataNode::New(); // newnode->SetData(m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(1)); // newnode->SetName(("Comp1")); // GetDefaultDataStorage()->Add(newnode, m_SelectedImageNodes->GetNode()); // newnode = mitk::DataNode::New(); // newnode->SetData(m_CurrentStatisticsCalculator->GetInternalAdditionalResampledImage(2)); // newnode->SetName(("Comp2")); // GetDefaultDataStorage()->Add(newnode, m_SelectedImageNodes->GetNode()); } ShowClusteringResults(); } } statisticsCalculationSuccessful = true; } catch ( const std::runtime_error &e ) { - // In case of exception, print error message on GUI - std::stringstream message; - message << e.what(); - m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); - m_Controls->m_ErrorMessageLabel->show(); + QMessageBox::information( NULL, "Warning", e.what()); } catch ( const std::exception &e ) { MITK_ERROR << "Caught exception: " << e.what(); - // In case of exception, print error message on GUI - std::stringstream message; - message << "Error in calculating histogram: " << e.what(); - m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); - m_Controls->m_ErrorMessageLabel->show(); + QMessageBox::information( NULL, "Warning", e.what()); } m_CurrentStatisticsCalculator->RemoveObserver( progressObserverTag ); // Make sure that progress bar closes mitk::ProgressBar::GetInstance()->Progress( 100 ); if ( statisticsCalculationSuccessful ) { if ( statisticsChanged ) { // Do not show any error messages - m_Controls->m_ErrorMessageLabel->hide(); - m_CurrentStatisticsValid = true; } // m_Controls->m_HistogramWidget->SetHistogramModeToDirectHistogram(); m_Controls->m_HistogramWidget->SetParameters( - cparams, cresult, chist ); + cparams, cresult, chist ); // m_Controls->m_HistogramWidget->UpdateItemModelFromHistogram(); } else { - m_Controls->m_SelectedMaskLabel->setText( "None" ); + m_Controls->m_SelectedMaskLabel->setText( "-" ); // Clear statistics and histogram m_Controls->m_HistogramWidget->ClearItemModel(); m_CurrentStatisticsValid = false; // If a (non-closed) PlanarFigure is selected, display a line profile widget if ( m_SelectedPlanarFigure.IsNotNull() ) { // TODO: enable line profile widget //m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 1 ); //m_Controls->m_LineProfileWidget->SetImage( m_SelectedImage ); //m_Controls->m_LineProfileWidget->SetPlanarFigure( m_SelectedPlanarFigure ); //m_Controls->m_LineProfileWidget->UpdateItemModelFromPath(); } } } } void QmitkPartialVolumeAnalysisView::SetMeasurementInfoToRenderWindow(const QString& text) { FindRenderWindow(m_SelectedPlanarFigureNodes->GetNode()); if(m_LastRenderWindow != m_SelectedRenderWindow) { if(m_LastRenderWindow) { QObject::disconnect( m_LastRenderWindow, SIGNAL( destroyed(QObject*) ) , this, SLOT( OnRenderWindowDelete(QObject*) ) ); } m_LastRenderWindow = m_SelectedRenderWindow; if(m_LastRenderWindow) { QObject::connect( m_LastRenderWindow, SIGNAL( destroyed(QObject*) ) , this, SLOT( OnRenderWindowDelete(QObject*) ) ); } } if(m_LastRenderWindow && m_SelectedPlanarFigureNodes->GetNode().IsNotNull()) { if (!text.isEmpty()) { m_MeasurementInfoAnnotation->SetText(1, text.toLatin1().data()); mitk::VtkLayerController::GetInstance(m_LastRenderWindow->GetRenderWindow())->InsertForegroundRenderer( - m_MeasurementInfoRenderer, true); + m_MeasurementInfoRenderer, true); } else { if (mitk::VtkLayerController::GetInstance( - m_LastRenderWindow->GetRenderWindow()) ->IsRendererInserted( - m_MeasurementInfoRenderer)) + m_LastRenderWindow->GetRenderWindow()) ->IsRendererInserted( + m_MeasurementInfoRenderer)) mitk::VtkLayerController::GetInstance(m_LastRenderWindow->GetRenderWindow())->RemoveRenderer( - m_MeasurementInfoRenderer); + m_MeasurementInfoRenderer); } } else { + QmitkStdMultiWidget *multiWidget = 0; + QmitkStdMultiWidgetEditor * multiWidgetEdit = 0; + + multiWidgetEdit = dynamic_cast(this->GetRenderWindowPart()); + if(multiWidgetEdit){ + multiWidget = multiWidgetEdit->GetStdMultiWidget(); + } + + if ( multiWidget == NULL ) + { + return; + } + if (!text.isEmpty()) { m_MeasurementInfoAnnotation->SetText(1, text.toLatin1().data()); - mitk::VtkLayerController::GetInstance(this->GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderWindow())->InsertForegroundRenderer( - m_MeasurementInfoRenderer, true); + mitk::VtkLayerController::GetInstance(multiWidget->GetRenderWindow1()->GetRenderWindow())->InsertForegroundRenderer( + m_MeasurementInfoRenderer, true); } else { if (mitk::VtkLayerController::GetInstance( - this->GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderWindow()) ->IsRendererInserted( - m_MeasurementInfoRenderer)) - mitk::VtkLayerController::GetInstance(this->GetActiveStdMultiWidget()->GetRenderWindow1()->GetRenderWindow())->RemoveRenderer( - m_MeasurementInfoRenderer); + multiWidget->GetRenderWindow1()->GetRenderWindow()) ->IsRendererInserted( + m_MeasurementInfoRenderer)) + mitk::VtkLayerController::GetInstance(multiWidget->GetRenderWindow1()->GetRenderWindow())->RemoveRenderer( + m_MeasurementInfoRenderer); } } } void QmitkPartialVolumeAnalysisView::UpdateProgressBar() { mitk::ProgressBar::GetInstance()->Progress(); } void QmitkPartialVolumeAnalysisView::RequestStatisticsUpdate() { if ( !m_StatisticsUpdatePending ) { QApplication::postEvent( this, new QmitkRequestStatisticsUpdateEvent ); m_StatisticsUpdatePending = true; } } void QmitkPartialVolumeAnalysisView::RemoveOrphanImages() { PartialVolumeAnalysisMapType::iterator it = m_PartialVolumeAnalysisMap.begin(); while ( it != m_PartialVolumeAnalysisMap.end() ) { mitk::Image *image = it->first; mitk::PartialVolumeAnalysisHistogramCalculator *calculator = it->second; ++it; mitk::NodePredicateData::Pointer hasImage = mitk::NodePredicateData::New( image ); - if ( this->GetDefaultDataStorage()->GetNode( hasImage ) == NULL ) + if ( this->GetDataStorage()->GetNode( hasImage ) == NULL ) { if ( m_SelectedImage == image ) { m_SelectedImage = NULL; m_SelectedImageNodes->RemoveAllNodes(); } if ( m_CurrentStatisticsCalculator == calculator ) { m_CurrentStatisticsCalculator = NULL; } m_PartialVolumeAnalysisMap.erase( image ); it = m_PartialVolumeAnalysisMap.begin(); } } } void QmitkPartialVolumeAnalysisView::ExtractTensorImages( mitk::Image::ConstPointer tensorimage) { typedef itk::Image< itk::DiffusionTensor3D, 3> TensorImageType; typedef mitk::ImageToItk CastType; CastType::Pointer caster = CastType::New(); caster->SetInput(tensorimage); caster->Update(); TensorImageType::Pointer image = caster->GetOutput(); typedef itk::TensorDerivedMeasurementsFilter MeasurementsType; MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(image ); measurementsCalculator->SetMeasure(MeasurementsType::FA); measurementsCalculator->Update(); MeasurementsType::OutputImageType::Pointer fa = measurementsCalculator->GetOutput(); m_FAImage = mitk::Image::New(); m_FAImage->InitializeByItk(fa.GetPointer()); m_FAImage->SetVolume(fa->GetBufferPointer()); // mitk::DataNode::Pointer node = mitk::DataNode::New(); // node->SetData(m_FAImage); // GetDefaultDataStorage()->Add(node); measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(image ); measurementsCalculator->SetMeasure(MeasurementsType::CA); measurementsCalculator->Update(); MeasurementsType::OutputImageType::Pointer ca = measurementsCalculator->GetOutput(); m_CAImage = mitk::Image::New(); m_CAImage->InitializeByItk(ca.GetPointer()); m_CAImage->SetVolume(ca->GetBufferPointer()); // node = mitk::DataNode::New(); // node->SetData(m_CAImage); // GetDefaultDataStorage()->Add(node); measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(image ); measurementsCalculator->SetMeasure(MeasurementsType::RD); measurementsCalculator->Update(); MeasurementsType::OutputImageType::Pointer rd = measurementsCalculator->GetOutput(); m_RDImage = mitk::Image::New(); m_RDImage->InitializeByItk(rd.GetPointer()); m_RDImage->SetVolume(rd->GetBufferPointer()); // node = mitk::DataNode::New(); // node->SetData(m_CAImage); // GetDefaultDataStorage()->Add(node); measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(image ); measurementsCalculator->SetMeasure(MeasurementsType::AD); measurementsCalculator->Update(); MeasurementsType::OutputImageType::Pointer ad = measurementsCalculator->GetOutput(); m_ADImage = mitk::Image::New(); m_ADImage->InitializeByItk(ad.GetPointer()); m_ADImage->SetVolume(ad->GetBufferPointer()); // node = mitk::DataNode::New(); // node->SetData(m_CAImage); // GetDefaultDataStorage()->Add(node); measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(image ); measurementsCalculator->SetMeasure(MeasurementsType::RA); measurementsCalculator->Update(); MeasurementsType::OutputImageType::Pointer md = measurementsCalculator->GetOutput(); m_MDImage = mitk::Image::New(); m_MDImage->InitializeByItk(md.GetPointer()); m_MDImage->SetVolume(md->GetBufferPointer()); // node = mitk::DataNode::New(); // node->SetData(m_CAImage); // GetDefaultDataStorage()->Add(node); typedef DirectionsFilterType::OutputImageType DirImageType; DirectionsFilterType::Pointer dirFilter = DirectionsFilterType::New(); dirFilter->SetInput(image ); dirFilter->Update(); itk::ImageRegionIterator itd(dirFilter->GetOutput(), dirFilter->GetOutput()->GetLargestPossibleRegion()); itd = itd.Begin(); while( !itd.IsAtEnd() ) { DirImageType::PixelType direction = itd.Get(); direction[0] = fabs(direction[0]); direction[1] = fabs(direction[1]); direction[2] = fabs(direction[2]); itd.Set(direction); ++itd; } typedef itk::CartesianToPolarVectorImageFilter< DirImageType, DirImageType, true> C2PFilterType; C2PFilterType::Pointer cpFilter = C2PFilterType::New(); cpFilter->SetInput(dirFilter->GetOutput()); cpFilter->Update(); DirImageType::Pointer dir = cpFilter->GetOutput(); typedef itk::Image CompImageType; CompImageType::Pointer comp1 = CompImageType::New(); comp1->SetSpacing( dir->GetSpacing() ); // Set the image spacing comp1->SetOrigin( dir->GetOrigin() ); // Set the image origin comp1->SetDirection( dir->GetDirection() ); // Set the image direction comp1->SetRegions( dir->GetLargestPossibleRegion() ); comp1->Allocate(); CompImageType::Pointer comp2 = CompImageType::New(); comp2->SetSpacing( dir->GetSpacing() ); // Set the image spacing comp2->SetOrigin( dir->GetOrigin() ); // Set the image origin comp2->SetDirection( dir->GetDirection() ); // Set the image direction comp2->SetRegions( dir->GetLargestPossibleRegion() ); comp2->Allocate(); itk::ImageRegionConstIterator it(dir, dir->GetLargestPossibleRegion()); itk::ImageRegionIterator it1(comp1, comp1->GetLargestPossibleRegion()); itk::ImageRegionIterator it2(comp2, comp2->GetLargestPossibleRegion()); it = it.Begin(); it1 = it1.Begin(); it2 = it2.Begin(); while( !it.IsAtEnd() ) { it1.Set(it.Get()[1]); it2.Set(it.Get()[2]); ++it; ++it1; ++it2; } m_DirectionComp1Image = mitk::Image::New(); m_DirectionComp1Image->InitializeByItk(comp1.GetPointer()); m_DirectionComp1Image->SetVolume(comp1->GetBufferPointer()); m_DirectionComp2Image = mitk::Image::New(); m_DirectionComp2Image->InitializeByItk(comp2.GetPointer()); m_DirectionComp2Image->SetVolume(comp2->GetBufferPointer()); } void QmitkPartialVolumeAnalysisView::OnRenderWindowDelete(QObject * obj) { if(obj == m_LastRenderWindow) m_LastRenderWindow = 0; if(obj == m_SelectedRenderWindow) m_SelectedRenderWindow = 0; } bool QmitkPartialVolumeAnalysisView::event( QEvent *event ) { if ( event->type() == (QEvent::Type) QmitkRequestStatisticsUpdateEvent::StatisticsUpdateRequest ) { // Update statistics m_StatisticsUpdatePending = false; this->UpdateStatistics(); return true; } return false; } -void QmitkPartialVolumeAnalysisView::Visible() -{ - this->OnSelectionChanged( this->GetDataManagerSelection() ); -} bool QmitkPartialVolumeAnalysisView::IsExclusiveFunctionality() const { return true; } void QmitkPartialVolumeAnalysisView::Activated() { - this->GetActiveStdMultiWidget()->SetWidgetPlanesVisibility(false); + + MITK_INFO << "QmitkPartialVolumeAnalysisView:Activated"; + + //this->GetActiveStdMultiWidget()->SetWidgetPlanesVisibility(false); //this->GetActiveStdMultiWidget()->GetRenderWindow1()->FullScreenMode(true); - mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll(); + mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDataStorage()->GetAll(); mitk::DataNode* node = 0; mitk::PlanarFigure* figure = 0; mitk::PlanarFigureInteractor::Pointer figureInteractor = 0; // finally add all nodes to the model for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End() - ; it++) - { + ; it++) + { node = const_cast(it->Value().GetPointer()); figure = dynamic_cast(node->GetData()); if(figure) { figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", node); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); } } m_Visible = true; } void QmitkPartialVolumeAnalysisView::Deactivated() { - this->GetActiveStdMultiWidget()->SetWidgetPlanesVisibility(true); - //this->GetActiveStdMultiWidget()->GetRenderWindow1()->FullScreenMode(false); + MITK_INFO << "QmitkPartialVolumeAnalysisView:Deactivated"; +} + +void QmitkPartialVolumeAnalysisView::ActivatedZombieView(berry::IWorkbenchPartReference::Pointer reference) +{ + MITK_INFO << "QmitkPartialVolumeAnalysisView:ActivatedZombieView"; + + //this->GetActiveStdMultiWidget()->SetWidgetPlanesVisibility(true); this->SetMeasurementInfoToRenderWindow(""); - mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDefaultDataStorage()->GetAll(); + mitk::DataStorage::SetOfObjects::ConstPointer _NodeSet = this->GetDataStorage()->GetAll(); mitk::DataNode* node = 0; mitk::PlanarFigure* figure = 0; mitk::PlanarFigureInteractor::Pointer figureInteractor = 0; // finally add all nodes to the model for(mitk::DataStorage::SetOfObjects::ConstIterator it=_NodeSet->Begin(); it!=_NodeSet->End() - ; it++) - { + ; it++) + { node = const_cast(it->Value().GetPointer()); figure = dynamic_cast(node->GetData()); if(figure) { figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor) mitk::GlobalInteraction::GetInstance()->RemoveInteractor(figureInteractor); } } - m_Visible = false; } +void QmitkPartialVolumeAnalysisView::Hidden() +{ + +} + +void QmitkPartialVolumeAnalysisView::Visible() +{ + //this->OnSelectionChanged( this->Get, this->GetDataManagerSelection() ); +} + +void QmitkPartialVolumeAnalysisView::SetFocus() +{ + +} + + void QmitkPartialVolumeAnalysisView::GreenRadio(bool checked) { if(checked) { m_Controls->m_PartialVolumeRadio->setChecked(false); m_Controls->m_BlueRadio->setChecked(false); m_Controls->m_AllRadio->setChecked(false); m_Controls->m_ExportClusteringResultsButton->setEnabled(true); } m_QuantifyClass = 0; RequestStatisticsUpdate(); } void QmitkPartialVolumeAnalysisView::PartialVolumeRadio(bool checked) { if(checked) { m_Controls->m_GreenRadio->setChecked(false); m_Controls->m_BlueRadio->setChecked(false); m_Controls->m_AllRadio->setChecked(false); m_Controls->m_ExportClusteringResultsButton->setEnabled(true); } m_QuantifyClass = 1; RequestStatisticsUpdate(); } void QmitkPartialVolumeAnalysisView::BlueRadio(bool checked) { if(checked) { m_Controls->m_PartialVolumeRadio->setChecked(false); m_Controls->m_GreenRadio->setChecked(false); m_Controls->m_AllRadio->setChecked(false); m_Controls->m_ExportClusteringResultsButton->setEnabled(true); } m_QuantifyClass = 2; RequestStatisticsUpdate(); } void QmitkPartialVolumeAnalysisView::AllRadio(bool checked) { if(checked) { m_Controls->m_BlueRadio->setChecked(false); m_Controls->m_PartialVolumeRadio->setChecked(false); m_Controls->m_GreenRadio->setChecked(false); m_Controls->m_ExportClusteringResultsButton->setEnabled(false); } m_QuantifyClass = 3; RequestStatisticsUpdate(); } void QmitkPartialVolumeAnalysisView::NumberBinsChangedSlider(int v ) { m_Controls->m_NumberBins->setText(QString("%1").arg(m_Controls->m_NumberBinsSlider->value()*5.0)); } void QmitkPartialVolumeAnalysisView::UpsamplingChangedSlider( int v) { m_Controls->m_Upsampling->setText(QString("%1").arg(m_Controls->m_UpsamplingSlider->value()/10.0)); } void QmitkPartialVolumeAnalysisView::GaussianSigmaChangedSlider(int v ) { m_Controls->m_GaussianSigma->setText(QString("%1").arg(m_Controls->m_GaussianSigmaSlider->value()/100.0)); } void QmitkPartialVolumeAnalysisView::SimilarAnglesChangedSlider(int v ) { m_Controls->m_SimilarAngles->setText(QString("%1°").arg(90-m_Controls->m_SimilarAnglesSlider->value())); ShowClusteringResults(); } void QmitkPartialVolumeAnalysisView::OpacityChangedSlider(int v ) { if(m_SelectedImageNodes->GetNode().IsNotNull()) { float opacImag = 1.0f-(v-5)/5.0f; opacImag = opacImag < 0 ? 0 : opacImag; m_SelectedImageNodes->GetNode()->SetFloatProperty("opacity", opacImag); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } if(m_ClusteringResult.IsNotNull()) { float opacClust = v/5.0f; opacClust = opacClust > 1 ? 1 : opacClust; m_ClusteringResult->SetFloatProperty("opacity", opacClust); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkPartialVolumeAnalysisView::NumberBinsReleasedSlider( ) { RequestStatisticsUpdate(); } void QmitkPartialVolumeAnalysisView::UpsamplingReleasedSlider( ) { RequestStatisticsUpdate(); } void QmitkPartialVolumeAnalysisView::GaussianSigmaReleasedSlider( ) { RequestStatisticsUpdate(); } void QmitkPartialVolumeAnalysisView::SimilarAnglesReleasedSlider( ) { } void QmitkPartialVolumeAnalysisView::ToClipBoard() { std::vector* > vals = m_Controls->m_HistogramWidget->m_Vals; QString clipboardText; for (std::vector* >::iterator it = vals.begin(); it - != vals.end(); ++it) + != vals.end(); ++it) { for (std::vector::iterator it2 = (**it).begin(); it2 != (**it).end(); ++it2) { clipboardText.append(QString("%1 \t").arg(*it2)); } clipboardText.append(QString("\n")); } QApplication::clipboard()->setText(clipboardText, QClipboard::Clipboard); } void QmitkPartialVolumeAnalysisView::PropertyChanged(const mitk::DataNode* /*node*/, const mitk::BaseProperty* /*prop*/) { } void QmitkPartialVolumeAnalysisView::NodeChanged(const mitk::DataNode* /*node*/) { } void QmitkPartialVolumeAnalysisView::NodeRemoved(const mitk::DataNode* node) { if (dynamic_cast(node->GetData())) - GetDefaultDataStorage()->Remove(m_ClusteringResult); + this->GetDataStorage()->Remove(m_ClusteringResult); if( node == m_SelectedPlanarFigureNodes->GetNode().GetPointer() - || node == m_SelectedMaskNode.GetPointer() ) - { + || node == m_SelectedMaskNode.GetPointer() ) + { this->Select(NULL,true,false); SetMeasurementInfoToRenderWindow(""); } if( node == m_SelectedImageNodes->GetNode().GetPointer() ) { this->Select(NULL,false,true); SetMeasurementInfoToRenderWindow(""); } } void QmitkPartialVolumeAnalysisView::NodeAddedInDataStorage(const mitk::DataNode* node) { if(!m_Visible) return; mitk::DataNode* nonConstNode = const_cast(node); mitk::PlanarFigure* figure = dynamic_cast(nonConstNode->GetData()); if(figure) { // set interactor for new node (if not already set) mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetInteractor()); if(figureInteractor.IsNull()) figureInteractor = mitk::PlanarFigureInteractor::New("PlanarFigureInteractor", nonConstNode); mitk::GlobalInteraction::GetInstance()->AddInteractor(figureInteractor); // remove uninitialized old planars if( m_SelectedPlanarFigureNodes->GetNode().IsNotNull() && m_CurrentFigureNodeInitialized == false ) { mitk::Interactor::Pointer oldInteractor = m_SelectedPlanarFigureNodes->GetNode()->GetInteractor(); if(oldInteractor.IsNotNull()) mitk::GlobalInteraction::GetInstance()->RemoveInteractor(oldInteractor); - this->GetDefaultDataStorage()->Remove(m_SelectedPlanarFigureNodes->GetNode()); + this->GetDataStorage()->Remove(m_SelectedPlanarFigureNodes->GetNode()); } } } void QmitkPartialVolumeAnalysisView::TextIntON() { if(m_ClusteringResult.IsNotNull()) { if(m_TexIsOn) { m_Controls->m_TextureIntON->setIcon(*m_IconTexOFF); } else { m_Controls->m_TextureIntON->setIcon(*m_IconTexON); } m_ClusteringResult->SetBoolProperty("texture interpolation", !m_TexIsOn); m_TexIsOn = !m_TexIsOn; - GetActiveStdMultiWidget()->RequestUpdate(); + this->RequestRenderWindowUpdate(); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPartialVolumeAnalysisView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPartialVolumeAnalysisView.h index bbae16184c..df2d207363 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPartialVolumeAnalysisView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPartialVolumeAnalysisView.h @@ -1,270 +1,281 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2009-05-28 20:08:26 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 10185 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #if !defined(QmitkPartialVolumeAnalysisView_H__INCLUDED) #define QmitkPartialVolumeAnalysisView_H__INCLUDED -#include "QmitkFunctionality.h" +//#include "QmitkFunctionality.h" #include "ui_QmitkPartialVolumeAnalysisViewControls.h" +#include +#include +#include // berry #include #include // itk #include #include "itkDiffusionTensorPrincipleDirectionImageFilter.h" #include // qmitk #include "QmitkStepperAdapter.h" #include "QmitkRenderWindow.h" // mitk #include "mitkPartialVolumeAnalysisHistogramCalculator.h" #include "mitkPlanarLine.h" #include #include "mitkDataStorageSelection.h" #include // vtk #include #include #include //#include "itkProcessObject.h" /*! \brief QmitkPartialVolumeAnalysis \sa QmitkFunctionality \ingroup Functionalities */ -class QmitkPartialVolumeAnalysisView : public QmitkFunctionality//, public itk::ProcessObject +class QmitkPartialVolumeAnalysisView : public QmitkAbstractView, public mitk::IZombieViewPart//, public itk::ProcessObject { Q_OBJECT public: /*! \ Convenient typedefs */ typedef mitk::DataStorage::SetOfObjects ConstVector; typedef ConstVector::ConstPointer ConstVectorPointer; typedef ConstVector::ConstIterator ConstVectorIterator; typedef mitk::PartialVolumeAnalysisHistogramCalculator HistogramCalculatorType; typedef HistogramCalculatorType::HistogramType HistogramType; typedef mitk::PartialVolumeAnalysisClusteringCalculator ClusteringType; typedef itk::DiffusionTensorPrincipleDirectionImageFilter DirectionsFilterType; /*! \brief default constructor */ QmitkPartialVolumeAnalysisView(QObject *parent=0, const char *name=0); /*! \brief default destructor */ virtual ~QmitkPartialVolumeAnalysisView(); /*! \brief method for creating the widget containing the application controls, like sliders, buttons etc. */ virtual void CreateQtPartControl(QWidget *parent); /*! \brief method for creating the connections of main and control widget */ virtual void CreateConnections(); bool IsExclusiveFunctionality() const; virtual bool event( QEvent *event ); - void OnSelectionChanged( std::vector nodes ); + virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList &nodes); virtual void Activated(); virtual void Deactivated(); + virtual void ActivatedZombieView(berry::IWorkbenchPartReference::Pointer reference); + + virtual void Hidden(); + + virtual void Visible(); + + virtual void SetFocus(); + bool AssertDrawingIsPossible(bool checked); virtual void NodeChanged(const mitk::DataNode* node); virtual void PropertyChanged(const mitk::DataNode* node, const mitk::BaseProperty* prop); virtual void NodeRemoved(const mitk::DataNode* node); virtual void NodeAddedInDataStorage(const mitk::DataNode* node); virtual void AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char *propertyKey = NULL, mitk::BaseProperty *property = NULL ); void PlanarFigureInitialized(); void PlanarFigureFocus(mitk::DataNode* node); void ShowClusteringResults(); static const std::string VIEW_ID; protected slots: void EstimateCircle(); void SetHistogramVisibility(); void SetAdvancedVisibility(); void NumberBinsChangedSlider(int v ); void UpsamplingChangedSlider( int v ); void GaussianSigmaChangedSlider( int v ); void SimilarAnglesChangedSlider(int v ); void OpacityChangedSlider(int v ); void NumberBinsReleasedSlider( ); void UpsamplingReleasedSlider( ); void GaussianSigmaReleasedSlider( ); void SimilarAnglesReleasedSlider( ); void ActionDrawEllipseTriggered(); void ActionDrawRectangleTriggered(); void ActionDrawPolygonTriggered(); void ToClipBoard(); void GreenRadio(bool checked); void PartialVolumeRadio(bool checked); void BlueRadio(bool checked); void AllRadio(bool checked); void OnRenderWindowDelete(QObject * obj); void TextIntON(); void ExportClusteringResults(); protected: - void StdMultiWidgetAvailable( QmitkStdMultiWidget& stdMultiWidget ); + //void StdMultiWidgetAvailable( QmitkStdMultiWidget& stdMultiWidget ); /** \brief Issues a request to update statistics by sending an event to the * Qt event processing queue. * * Statistics update should only be executed after program execution returns * to the Qt main loop. This mechanism also prevents multiple execution of * updates where only one is required.*/ void RequestStatisticsUpdate(); /** \brief Recalculate statistics for currently selected image and mask and * update the GUI. */ void UpdateStatistics(); /** \brief Listener for progress events to update progress bar. */ void UpdateProgressBar(); /** \brief Removes any cached images which are no longer referenced elsewhere. */ void RemoveOrphanImages(); void Select( mitk::DataNode::Pointer node, bool clearMaskOnFirstArgNULL=false, bool clearImageOnFirstArgNULL=false ); - void Visible( ); - void SetMeasurementInfoToRenderWindow(const QString& text); void FindRenderWindow(mitk::DataNode* node); void ExtractTensorImages( mitk::Image::ConstPointer tensorimage); typedef std::map< mitk::Image *, mitk::PartialVolumeAnalysisHistogramCalculator::Pointer > PartialVolumeAnalysisMapType; /*! * controls containing sliders for scrolling through the slices */ Ui::QmitkPartialVolumeAnalysisViewControls *m_Controls; QmitkStepperAdapter* m_TimeStepperAdapter; unsigned int m_CurrentTime; QString m_Clipboard; // result text rendering vtkRenderer * m_MeasurementInfoRenderer; vtkCornerAnnotation *m_MeasurementInfoAnnotation; // Image and mask data mitk::DataStorageSelection::Pointer m_SelectedImageNodes; mitk::Image::Pointer m_SelectedImage; mitk::DataNode::Pointer m_SelectedMaskNode; mitk::Image::Pointer m_SelectedImageMask; mitk::DataStorageSelection::Pointer m_SelectedPlanarFigureNodes; mitk::PlanarFigure::Pointer m_SelectedPlanarFigure; bool m_IsTensorImage; mitk::Image::Pointer m_FAImage; mitk::Image::Pointer m_CAImage; mitk::Image::Pointer m_RDImage; mitk::Image::Pointer m_ADImage; mitk::Image::Pointer m_MDImage; // mitk::Image::Pointer m_DirectionImage; mitk::Image::Pointer m_DirectionComp1Image; mitk::Image::Pointer m_DirectionComp2Image; mitk::Image::Pointer m_AngularErrorImage; QmitkRenderWindow* m_SelectedRenderWindow; QmitkRenderWindow* m_LastRenderWindow; long m_ImageObserverTag; long m_ImageMaskObserverTag; long m_PlanarFigureObserverTag; // Hash map for associating one image statistics calculator with each iamge // (so that previously calculated histograms / statistics can be recovered // if a recalculation is not required) PartialVolumeAnalysisMapType m_PartialVolumeAnalysisMap; HistogramCalculatorType::Pointer m_CurrentStatisticsCalculator; bool m_CurrentStatisticsValid; bool m_StatisticsUpdatePending; bool m_GaussianSigmaChangedSliding; bool m_NumberBinsSliding; bool m_UpsamplingChangedSliding; + bool m_Visible; + mitk::DataNode::Pointer m_ClusteringResult; int m_EllipseCounter; int m_RectangleCounter; int m_PolygonCounter; unsigned int m_InitializedObserverTag; bool m_CurrentFigureNodeInitialized; int m_QuantifyClass; ClusteringType::HelperStructPerformRGBClusteringRetval* m_CurrentRGBClusteringResults; ClusteringType::HelperStructPerformClusteringRetval *m_CurrentPerformClusteringResults; // mitk::DataNode::Pointer m_newnode; // mitk::DataNode::Pointer m_newnode2; QIcon* m_IconTexOFF; QIcon* m_IconTexON; bool m_TexIsOn; }; #endif // !defined(QmitkPartialVolumeAnalysis_H__INCLUDED) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPartialVolumeAnalysisViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPartialVolumeAnalysisViewControls.ui index ef60ffb5a4..ab458e8f78 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPartialVolumeAnalysisViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPartialVolumeAnalysisViewControls.ui @@ -1,793 +1,797 @@ QmitkPartialVolumeAnalysisViewControls true 0 0 - 343 - 470 + 360 + 528 Form 0 - - 0 + + 9 + + + 3 + + + 9 + + + 3 - - - false + + + Data - - true + + + + + + 0 + 0 + + + + Tensor/Scalar Image: + + + + + + + + 0 + 0 + + + + Mask Image: + + + + + + + - + + + + + + + - + + + + + + + + + + Parameters QFrame::NoFrame QFrame::Raised 0 QFrame::NoFrame QFrame::Raised 0 0 - - - - QFrame::NoFrame - - - QFrame::Raised - - - - 6 - - - 0 - - - 0 - - - 0 - - - 9 - - - 0 - - - - - - 0 - 0 - - - - Image: - - - - - - - false - - - true - - - - - - - - 0 - 0 - - - - Mask: - - - - - - - false - - - true - - - - - - QFrame::NoFrame QFrame::Raised 0 30 30 + + Draw circular ROI + :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 true true 30 30 + + Draw quadratic ROI + :/QmitkDiffusionImaging/rectangle.png:/QmitkDiffusionImaging/rectangle.png 32 32 true true 30 30 + + Draw polygonal ROI + :/QmitkDiffusionImaging/polygon.png:/QmitkDiffusionImaging/polygon.png 32 32 true true + + + + Qt::Horizontal + + + + 40 + 20 + + + + true QFrame::NoFrame QFrame::Raised + + QFormLayout::AllNonFixedFieldsGrow + 0 Upsampling QFrame::NoFrame QFrame::Raised 0 1 50 1 25 Qt::Horizontal 50 0 2.5 Similar angles QFrame::NoFrame 0 90 0 Qt::Horizontal QSlider::NoTicks 50 0 90° QFrame::NoFrame QFrame::Raised 0 0 display histogram true 0 0 QFrame::NoFrame QFrame::Raised 0 QFrame::NoFrame QFrame::Raised 0 20 20 true true Green Partial Volume Partial Volume Partial Volume Partial Volume PV Red true All Export clustering result as float image. ... :/org.mitk.gui.qt.diffusionimaging/resources/arrow.png:/org.mitk.gui.qt.diffusionimaging/resources/arrow.png QFrame::NoFrame 0 Opacity 10 5 Qt::Horizontal QSlider::TicksBelow Histogram to Clipboard Advanced Qt::Vertical QSizePolicy::Preferred 10 1 QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 0 Blurring QFrame::NoFrame QFrame::Raised 0 200 1 0 Qt::Horizontal 50 0 0.0 # Bins QFrame::NoFrame 0 1 100 10 Qt::Horizontal QSlider::NoTicks 50 0 50 quantiles QFrame::StyledPanel QFrame::Raised 0 1.000000000000000 0.010000000000000 0.250000000000000 1.000000000000000 0.010000000000000 0.750000000000000 Estimate circle from binary image "Thick" PFs Qt::Vertical 20 40 QmitkPartialVolumeAnalysisWidget QWidget
QmitkPartialVolumeAnalysisWidget.h
1 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp index c6302d1b44..e5d7925b30 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp @@ -1,561 +1,388 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ //#define MBILOG_ENABLE_DEBUG #include "QmitkPreprocessingView.h" #include "mitkDiffusionImagingConfigure.h" // qt includes #include // itk includes #include "itkTimeProbe.h" #include "itkB0ImageExtractionImageFilter.h" #include "itkBrainMaskExtractionImageFilter.h" #include "itkCastImageFilter.h" #include "itkVectorContainer.h" #include // mitk includes #include "QmitkDataStorageComboBox.h" #include "QmitkStdMultiWidget.h" #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkNodePredicateDataType.h" #include "mitkProperties.h" #include "mitkVtkResliceInterpolationProperty.h" #include "mitkLookupTable.h" #include "mitkLookupTableProperty.h" #include "mitkTransferFunction.h" #include "mitkTransferFunctionProperty.h" #include "mitkDataNodeObject.h" #include "mitkOdfNormalizationMethodProperty.h" #include "mitkOdfScaleByProperty.h" #include -#include "berryIStructuredSelection.h" -#include "berryIWorkbenchWindow.h" -#include "berryISelectionService.h" - #include #include const std::string QmitkPreprocessingView::VIEW_ID = "org.mitk.views.preprocessing"; #define DI_INFO MITK_INFO("DiffusionImaging") typedef float TTensorPixelType; -using namespace berry; - -struct PrpSelListener : ISelectionListener -{ - - berryObjectMacro(PrpSelListener); - - PrpSelListener(QmitkPreprocessingView* view) - { - m_View = view; - } - - void DoSelectionChanged(ISelection::ConstPointer selection) - { - // save current selection in member variable - m_View->m_CurrentSelection = selection.Cast(); - - // do something with the selected items - if(m_View->m_CurrentSelection) - { - bool foundDwiVolume = false; - m_View->m_DiffusionImage = NULL; - - // iterate selection - for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); - i != m_View->m_CurrentSelection->End(); ++i) - { - - // extract datatree node - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - - // process only on valid nodes - mitk::BaseData* nodeData = node->GetData(); - if(nodeData) - { - // only look at interesting types - if(QString("DiffusionImage").compare(nodeData->GetNameOfClass())==0) - { - foundDwiVolume = true; - m_View->m_DiffusionImage = dynamic_cast*>(nodeData); - } - } - } - } - - m_View->m_Controls->m_ButtonBrainMask->setEnabled(foundDwiVolume); - m_View->m_Controls->m_ButtonAverageGradients->setEnabled(foundDwiVolume); - m_View->m_Controls->m_ButtonExtractB0->setEnabled(foundDwiVolume); - m_View->m_Controls->m_ModifyMeasurementFrame->setEnabled(foundDwiVolume); - m_View->m_Controls->m_MeasurementFrameTable->setEnabled(foundDwiVolume); - m_View->m_Controls->m_ReduceGradientsButton->setEnabled(foundDwiVolume); - m_View->m_Controls->m_ShowGradientsButton->setEnabled(foundDwiVolume); - m_View->m_Controls->m_MirrorGradientToHalfSphereButton->setEnabled(foundDwiVolume); - - if (foundDwiVolume) - { - vnl_matrix_fixed< double, 3, 3 > mf = m_View->m_DiffusionImage->GetMeasurementFrame(); - for (int r=0; r<3; r++) - for (int c=0; c<3; c++) - { - QTableWidgetItem* item = m_View->m_Controls->m_MeasurementFrameTable->item(r,c); - delete item; - item = new QTableWidgetItem(); - item->setTextAlignment(Qt::AlignCenter | Qt::AlignVCenter); - item->setText(QString::number(mf.get(r,c))); - m_View->m_Controls->m_MeasurementFrameTable->setItem(r,c,item); - } - m_View->m_Controls->m_GradientsLabel->setText(QString::number(m_View->m_DiffusionImage->GetNumDirections())); - - if (m_View->m_DiffusionImage->IsMultiBval()) - m_View->m_Controls->m_BvalLabel->setText("Acquisition with multiple b-values!"); - else - m_View->m_Controls->m_BvalLabel->setText(QString::number(m_View->m_DiffusionImage->GetB_Value())); - } - else - { - for (int r=0; r<3; r++) - for (int c=0; c<3; c++) - { - QTableWidgetItem* item = m_View->m_Controls->m_MeasurementFrameTable->item(r,c); - delete item; - item = new QTableWidgetItem(); - m_View->m_Controls->m_MeasurementFrameTable->setItem(r,c,item); - } - m_View->m_Controls->m_GradientsLabel->setText("-"); - m_View->m_Controls->m_BvalLabel->setText("-"); - } - } - } - - void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) - { - // check, if selection comes from datamanager - if (part) - { - QString partname(part->GetPartName().c_str()); - if(partname.compare("Datamanager")==0) - { - - // apply selection - DoSelectionChanged(selection); - - } - } - } - - QmitkPreprocessingView* m_View; -}; QmitkPreprocessingView::QmitkPreprocessingView() : QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL), m_DiffusionImage(NULL) { } QmitkPreprocessingView::QmitkPreprocessingView(const QmitkPreprocessingView& other) { Q_UNUSED(other) throw std::runtime_error("Copy constructor not implemented"); } QmitkPreprocessingView::~QmitkPreprocessingView() { - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); + } void QmitkPreprocessingView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkPreprocessingViewControls; m_Controls->setupUi(parent); this->CreateConnections(); m_Controls->m_MeasurementFrameTable->horizontalHeader()->setResizeMode(QHeaderView::Stretch); m_Controls->m_MeasurementFrameTable->verticalHeader()->setResizeMode(QHeaderView::Stretch); } - - m_SelListener = berry::ISelectionListener::Pointer(new PrpSelListener(this)); - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); - berry::ISelection::ConstPointer sel( - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); - m_CurrentSelection = sel.Cast(); - m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkPreprocessingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkPreprocessingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkPreprocessingView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_ButtonAverageGradients), SIGNAL(clicked()), this, SLOT(AverageGradients()) ); connect( (QObject*)(m_Controls->m_ButtonExtractB0), SIGNAL(clicked()), this, SLOT(ExtractB0()) ); connect( (QObject*)(m_Controls->m_ButtonBrainMask), SIGNAL(clicked()), this, SLOT(BrainMask()) ); connect( (QObject*)(m_Controls->m_ModifyMeasurementFrame), SIGNAL(clicked()), this, SLOT(DoApplyMesurementFrame()) ); connect( (QObject*)(m_Controls->m_ReduceGradientsButton), SIGNAL(clicked()), this, SLOT(DoReduceGradientDirections()) ); connect( (QObject*)(m_Controls->m_ShowGradientsButton), SIGNAL(clicked()), this, SLOT(DoShowGradientDirections()) ); connect( (QObject*)(m_Controls->m_MirrorGradientToHalfSphereButton), SIGNAL(clicked()), this, SLOT(DoHalfSphereGradientDirections()) ); } } +void QmitkPreprocessingView::OnSelectionChanged( std::vector nodes ) +{ + bool foundDwiVolume = false; + m_DiffusionImage = NULL; + m_SelectedDiffusionNodes = mitk::DataStorage::SetOfObjects::New(); + + // iterate selection + for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) + { + mitk::DataNode::Pointer node = *it; + + if( node.IsNotNull() && dynamic_cast*>(node->GetData()) ) + { + foundDwiVolume = true; + m_DiffusionImage = dynamic_cast*>(node->GetData()); + m_Controls->m_DiffusionImageLabel->setText(node->GetName().c_str()); + m_SelectedDiffusionNodes->push_back(node); + } + } + + m_Controls->m_ButtonBrainMask->setEnabled(foundDwiVolume); + m_Controls->m_ButtonAverageGradients->setEnabled(foundDwiVolume); + m_Controls->m_ButtonExtractB0->setEnabled(foundDwiVolume); + m_Controls->m_ModifyMeasurementFrame->setEnabled(foundDwiVolume); + m_Controls->m_MeasurementFrameTable->setEnabled(foundDwiVolume); + m_Controls->m_ReduceGradientsButton->setEnabled(foundDwiVolume); + m_Controls->m_ShowGradientsButton->setEnabled(foundDwiVolume); + m_Controls->m_MirrorGradientToHalfSphereButton->setEnabled(foundDwiVolume); + + if (foundDwiVolume) + { + vnl_matrix_fixed< double, 3, 3 > mf = m_DiffusionImage->GetMeasurementFrame(); + for (int r=0; r<3; r++) + for (int c=0; c<3; c++) + { + QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c); + delete item; + item = new QTableWidgetItem(); + item->setTextAlignment(Qt::AlignCenter | Qt::AlignVCenter); + item->setText(QString::number(mf.get(r,c))); + m_Controls->m_MeasurementFrameTable->setItem(r,c,item); + } + m_Controls->m_GradientsLabel->setText(QString::number(m_DiffusionImage->GetNumDirections())); + + if (m_DiffusionImage->IsMultiBval()) + m_Controls->m_BvalLabel->setText("Acquisition with multiple b-values!"); + else + m_Controls->m_BvalLabel->setText(QString::number(m_DiffusionImage->GetB_Value())); + } + else + { + for (int r=0; r<3; r++) + for (int c=0; c<3; c++) + { + QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c); + delete item; + item = new QTableWidgetItem(); + m_Controls->m_MeasurementFrameTable->setItem(r,c,item); + } + m_Controls->m_GradientsLabel->setText("-"); + m_Controls->m_BvalLabel->setText("-"); + m_Controls->m_DiffusionImageLabel->setText("-"); + } +} + void QmitkPreprocessingView::Activated() { QmitkFunctionality::Activated(); - - berry::ISelection::ConstPointer sel( - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); - m_CurrentSelection = sel.Cast(); - m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkPreprocessingView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkPreprocessingView::DoHalfSphereGradientDirections() { if (m_DiffusionImage.IsNull()) return; GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetOriginalDirections(); for (int j=0; jSize(); j++) if (gradientContainer->at(j)[0]<0) gradientContainer->at(j) = -gradientContainer->at(j); } void QmitkPreprocessingView::DoApplyMesurementFrame() { if (m_DiffusionImage.IsNull()) return; vnl_matrix_fixed< double, 3, 3 > mf; for (int r=0; r<3; r++) for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c); if (!item) return; mf[r][c] = item->text().toDouble(); } m_DiffusionImage->SetMeasurementFrame(mf); } void QmitkPreprocessingView::DoShowGradientDirections() { if (m_DiffusionImage.IsNull()) return; GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetOriginalDirections(); mitk::PointSet::Pointer pointset = mitk::PointSet::New(); for (int j=0; jSize(); j++) { mitk::Point3D p; vnl_vector_fixed< double, 3 > v = gradientContainer->at(j); if (fabs(v[0])>0.001 || fabs(v[1])>0.001 || fabs(v[2])>0.001) { p[0] = v[0]; p[1] = v[1]; p[2] = v[2]; pointset->InsertPoint(j, p); } } mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(pointset); node->SetName("gradient directions"); node->SetProperty("pointsize", mitk::FloatProperty::New(0.05)); node->SetProperty("color", mitk::ColorProperty::New(1,0,0)); GetDefaultDataStorage()->Add(node); } void QmitkPreprocessingView::DoReduceGradientDirections() { if (m_DiffusionImage.IsNull()) return; typedef mitk::DiffusionImage DiffusionImageType; typedef itk::ReduceDirectionGradientsFilter FilterType; GradientDirectionContainerType::Pointer gradientContainer = m_DiffusionImage->GetOriginalDirections(); FilterType::Pointer filter = FilterType::New(); filter->SetInput(m_DiffusionImage->GetVectorImage()); filter->SetOriginalGradientDirections(gradientContainer); filter->SetNumGradientDirections(m_Controls->m_ReduceGradientsBox->value()); filter->Update(); DiffusionImageType::Pointer image = DiffusionImageType::New(); image->SetVectorImage( filter->GetOutput() ); image->SetB_Value(m_DiffusionImage->GetB_Value()); image->SetDirections(filter->GetGradientDirections()); image->SetOriginalDirections(filter->GetGradientDirections()); image->SetMeasurementFrame(m_DiffusionImage->GetMeasurementFrame()); image->InitializeFromVectorImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); imageNode->SetName("reduced_image"); GetDefaultDataStorage()->Add(imageNode); } void QmitkPreprocessingView::ExtractB0() -{ - - if (m_CurrentSelection) - { - mitk::DataStorage::SetOfObjects::Pointer set = - mitk::DataStorage::SetOfObjects::New(); - - int at = 0; - for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); - i != m_CurrentSelection->End(); - ++i) - { - - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - - // process only on valid nodes - const mitk::BaseData* nodeData = node->GetData(); - if(nodeData) - { - if(QString("DiffusionImage").compare(nodeData->GetNameOfClass())==0) - { - set->InsertElement(at++, node); - } - } - } - } - - DoExtractB0(set); - - } -} - -void QmitkPreprocessingView::DoExtractB0 -(mitk::DataStorage::SetOfObjects::Pointer inImages) { typedef mitk::DiffusionImage DiffusionImageType; typedef DiffusionImageType::GradientDirectionContainerType GradientContainerType; - int nrFiles = inImages->size(); + int nrFiles = m_SelectedDiffusionNodes->size(); if (!nrFiles) return; - mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); - mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); + mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes->begin() ); + mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { DiffusionImageType* vols = static_cast( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); // Extract image using found index typedef itk::B0ImageExtractionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput(vols->GetVectorImage()); filter->SetDirections(vols->GetDirections()); filter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( filter->GetOutput() ); mitkImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( mitkImage ); node->SetProperty( "name", mitk::StringProperty::New(nodename + "_B0")); GetDefaultDataStorage()->Add(node); ++itemiter; } - - } void QmitkPreprocessingView::AverageGradients() { - - if (m_CurrentSelection) - { - mitk::DataStorage::SetOfObjects::Pointer set = - mitk::DataStorage::SetOfObjects::New(); - - int at = 0; - for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); - i != m_CurrentSelection->End(); - ++i) - { - - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - // process only on valid nodes - const mitk::BaseData* nodeData = node->GetData(); - - if(nodeData) - { - if(QString("DiffusionImage").compare(nodeData->GetNameOfClass())==0) - { - set->InsertElement(at++, node); - } - } - } - } - - DoAverageGradients(set); - - } - -} - -void QmitkPreprocessingView::DoAverageGradients -(mitk::DataStorage::SetOfObjects::Pointer inImages) -{ - int nrFiles = inImages->size(); + int nrFiles = m_SelectedDiffusionNodes->size(); if (!nrFiles) return; - mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); - mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); + mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes->begin() ); + mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); vols->AverageRedundantGradients(m_Controls->m_Blur->value()); ++itemiter; } } void QmitkPreprocessingView::BrainMask() { - - if (m_CurrentSelection) - { - mitk::DataStorage::SetOfObjects::Pointer set = - mitk::DataStorage::SetOfObjects::New(); - - int at = 0; - for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); - i != m_CurrentSelection->End(); - ++i) - { - - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - // process only on valid nodes - const mitk::BaseData* nodeData = node->GetData(); - - if(nodeData) - { - if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) - { - set->InsertElement(at++, node); - } - } - } - } - - DoBrainMask(set); - - } - -} - -void QmitkPreprocessingView::DoBrainMask -(mitk::DataStorage::SetOfObjects::Pointer inImages) -{ - int nrFiles = inImages->size(); + int nrFiles = m_SelectedDiffusionNodes->size(); if (!nrFiles) return; - mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); - mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); + mitk::DataStorage::SetOfObjects::const_iterator itemiter( m_SelectedDiffusionNodes->begin() ); + mitk::DataStorage::SetOfObjects::const_iterator itemiterend( m_SelectedDiffusionNodes->end() ); while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); // Extract image using found index typedef itk::B0ImageExtractionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput(vols->GetVectorImage()); filter->SetDirections(vols->GetDirections()); typedef itk::CastImageFilter, itk::Image > CastFilterType; CastFilterType::Pointer castfilter = CastFilterType::New(); castfilter->SetInput(filter->GetOutput()); typedef itk::BrainMaskExtractionImageFilter MaskFilterType; MaskFilterType::Pointer maskfilter = MaskFilterType::New(); maskfilter->SetInput(castfilter->GetOutput()); maskfilter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( maskfilter->GetOutput() ); mitkImage->SetVolume( maskfilter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( mitkImage ); node->SetProperty( "name", mitk::StringProperty::New(nodename + "_Mask")); GetDefaultDataStorage()->Add(node); ++itemiter; } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h index 3577677361..1c449b4fa2 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h @@ -1,114 +1,107 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _QMITKPREPROCESSINGVIEW_H_INCLUDED #define _QMITKPREPROCESSINGVIEW_H_INCLUDED #include #include #include "ui_QmitkPreprocessingViewControls.h" #include "mitkDiffusionImage.h" -#include -#include -#include - typedef short DiffusionPixelType; struct PrpSelListener; /*! * \ingroup org_mitk_gui_qt_preprocessing_internal * * \brief QmitkPreprocessingView * * Document your class here. * * \sa QmitkFunctionality */ class QmitkPreprocessingView : public QmitkFunctionality { friend struct PrpSelListener; // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; typedef vnl_vector_fixed< double, 3 > GradientDirectionType; typedef itk::VectorContainer< unsigned int, GradientDirectionType > GradientDirectionContainerType; QmitkPreprocessingView(); QmitkPreprocessingView(const QmitkPreprocessingView& other); virtual ~QmitkPreprocessingView(); virtual void CreateQtPartControl(QWidget *parent); /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); static const int nrconvkernels; protected slots: void AverageGradients(); - void DoAverageGradients(mitk::DataStorage::SetOfObjects::Pointer inImages); - void ExtractB0(); - void DoExtractB0(mitk::DataStorage::SetOfObjects::Pointer inImages); - void BrainMask(); - void DoBrainMask(mitk::DataStorage::SetOfObjects::Pointer inImages); void DoApplyMesurementFrame(); void DoReduceGradientDirections(); void DoShowGradientDirections(); void DoHalfSphereGradientDirections(); protected: + /// \brief called by QmitkFunctionality when DataManager's selection has changed + virtual void OnSelectionChanged( std::vector nodes ); + Ui::QmitkPreprocessingViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name); - berry::ISelectionListener::Pointer m_SelListener; - berry::IStructuredSelection::ConstPointer m_CurrentSelection; mitk::DiffusionImage::Pointer m_DiffusionImage; + mitk::DataStorage::SetOfObjects::Pointer m_SelectedDiffusionNodes; }; #endif // _QMITKPREPROCESSINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui index 104e53d529..fd89ef86d2 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingViewControls.ui @@ -1,496 +1,519 @@ QmitkPreprocessingViewControls 0 0 389 913 0 0 true QmitkPreprocessingViewControls + + + + Data + + + + + + Diffusion Image: + + + + + + + - + + + + + + Info QFormLayout::AllNonFixedFieldsGrow Number of Gradients: - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter + Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter b-Value: - - Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter + Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter false - + Generate pointset displaying the gradient vectors. Show gradients Reduce size 0 70 Multiple acquistions of one gradient direction can be averaged. Due to rounding errors, similar gradients often differ in the last decimal positions. The Merge radius allows to average them anyway by taking into account all directions within a certain radius. true QFrame::NoFrame QFrame::Raised 0 Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. 6 2.000000000000000 0.000100000000000 0.001000000000000 Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Accumulates the information that was acquired with multiple repetitions for one gradient. Vectors do not have to be precisely equal in order to be merged, if a "Merge radius" > 0 is configured. Merge radius false Average redundant gradients false - + Mirror all gradients around one axis. Mirror gradients to half sphere Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 0 0 New number of gradients: 1 30 false - + Retain only the specified number of gradient directions and according image volumes. The retained directions are spread equally over the half sphere. Reduce number of gradients Non diffusion weighted image 0 30 Average and extract all images that were acquired without diffusion weighting. true false Extract B0 Brain mask false Estimate binary brain mask 0 0 Measurment frame Qt::Horizontal 40 20 false 0 0 10 10 IBeamCursor true Qt::ScrollBarAlwaysOff Qt::ScrollBarAlwaysOff true false false true true false true true New Row New Row New Row New Column New Column New Column false Apply new mesurement frame Qt::Vertical 20 40 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.cpp index 331a9f2616..7edbd04136 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.cpp @@ -1,801 +1,796 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ //#define MBILOG_ENABLE_DEBUG #include "QmitkQBallReconstructionView.h" #include "mitkDiffusionImagingConfigure.h" // qt includes #include // itk includes #include "itkTimeProbe.h" // mitk includes #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkNodePredicateDataType.h" #include "QmitkDataStorageComboBox.h" #include "QmitkStdMultiWidget.h" #include "itkDiffusionQballReconstructionImageFilter.h" #include "itkAnalyticalDiffusionQballReconstructionImageFilter.h" #include "itkVectorContainer.h" #include "mitkQBallImage.h" #include "mitkProperties.h" #include "mitkVtkResliceInterpolationProperty.h" #include "mitkLookupTable.h" #include "mitkLookupTableProperty.h" #include "mitkTransferFunction.h" #include "mitkTransferFunctionProperty.h" #include "mitkDataNodeObject.h" #include "mitkOdfNormalizationMethodProperty.h" #include "mitkOdfScaleByProperty.h" #include "berryIStructuredSelection.h" #include "berryIWorkbenchWindow.h" #include "berryISelectionService.h" #include const std::string QmitkQBallReconstructionView::VIEW_ID = "org.mitk.views.qballreconstruction"; #define DI_INFO MITK_INFO("DiffusionImaging") typedef float TTensorPixelType; const int QmitkQBallReconstructionView::nrconvkernels = 252; using namespace berry; struct QbrSelListener : ISelectionListener { berryObjectMacro(QbrSelListener); QbrSelListener(QmitkQBallReconstructionView* view) { m_View = view; } void DoSelectionChanged(ISelection::ConstPointer selection) { // save current selection in member variable m_View->m_CurrentSelection = selection.Cast(); // do something with the selected items if(m_View->m_CurrentSelection) { bool foundDwiVolume = false; + m_View->m_Controls->m_DiffusionImageLabel->setText("-"); // iterate selection for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); i != m_View->m_CurrentSelection->End(); ++i) { // extract datatree node if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - // check if node valid - const mitk::BaseData* nodeData = node->GetData(); - - if(nodeData) + // only look at interesting types + if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) { - // only look at interesting types - if(QString("DiffusionImage").compare(nodeData->GetNameOfClass())==0) - { - foundDwiVolume = true; - } + foundDwiVolume = true; + m_View->m_Controls->m_DiffusionImageLabel->setText(node->GetName().c_str()); } } } m_View->m_Controls->m_ButtonStandard->setEnabled(foundDwiVolume); } } void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) { // check, if selection comes from datamanager if (part) { QString partname(part->GetPartName().c_str()); if(partname.compare("Datamanager")==0) { // apply selection DoSelectionChanged(selection); } } } QmitkQBallReconstructionView* m_View; }; QmitkQBallReconstructionView::QmitkQBallReconstructionView() : QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL) { } QmitkQBallReconstructionView::QmitkQBallReconstructionView(const QmitkQBallReconstructionView& other) { Q_UNUSED(other); throw std::runtime_error("Copy constructor not implemented"); } //void QmitkQBallReconstructionView::OpactiyChanged(int value) //{ // if (m_CurrentSelection) // { // if (mitk::DataNodeObject::Pointer nodeObj = m_CurrentSelection->Begin()->Cast()) // { // mitk::DataNode::Pointer node = nodeObj->GetDataNode(); // if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) // { // node->SetIntProperty("DisplayChannel", value); // mitk::RenderingManager::GetInstance()->RequestUpdateAll(); // } // } // } //} // //void QmitkQBallReconstructionView::OpactiyActionChanged() //{ // if (m_CurrentSelection) // { // if (mitk::DataNodeObject::Pointer nodeObj = m_CurrentSelection->Begin()->Cast()) // { // mitk::DataNode::Pointer node = nodeObj->GetDataNode(); // if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) // { // int displayChannel = 0.0; // if(node->GetIntProperty("DisplayChannel", displayChannel)) // { // m_OpacitySlider->setValue(displayChannel); // } // } // } // } // // MITK_INFO << "changed"; //} QmitkQBallReconstructionView::~QmitkQBallReconstructionView() { this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); } void QmitkQBallReconstructionView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkQBallReconstructionViewControls; m_Controls->setupUi(parent); this->CreateConnections(); QStringList items; items << "2" << "4" << "6" << "8" << "10" << "12"; m_Controls->m_QBallReconstructionMaxLLevelComboBox->addItems(items); m_Controls->m_QBallReconstructionMaxLLevelComboBox->setCurrentIndex(1); MethodChoosen(m_Controls->m_QBallReconstructionMethodComboBox->currentIndex()); #ifndef DIFFUSION_IMAGING_EXTENDED m_Controls->m_QBallReconstructionMethodComboBox->removeItem(3); #endif AdvancedCheckboxClicked(); // define data type for combobox //m_Controls->m_ImageSelector->SetDataStorage( this->GetDefaultDataStorage() ); //m_Controls->m_ImageSelector->SetPredicate( mitk::NodePredicateDataType::New("DiffusionImage") ); } m_SelListener = berry::ISelectionListener::Pointer(new QbrSelListener(this)); this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkQBallReconstructionView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkQBallReconstructionView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkQBallReconstructionView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_ButtonStandard), SIGNAL(clicked()), this, SLOT(ReconstructStandard()) ); connect( (QObject*)(m_Controls->m_AdvancedCheckbox), SIGNAL(clicked()), this, SLOT(AdvancedCheckboxClicked()) ); connect( (QObject*)(m_Controls->m_QBallReconstructionMethodComboBox), SIGNAL(currentIndexChanged(int)), this, SLOT(MethodChoosen(int)) ); } } +void QmitkQBallReconstructionView::OnSelectionChanged( std::vector nodes ) +{ + +} + void QmitkQBallReconstructionView::Activated() { QmitkFunctionality::Activated(); berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkQBallReconstructionView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkQBallReconstructionView::ReconstructStandard() { int index = m_Controls->m_QBallReconstructionMethodComboBox->currentIndex(); #ifndef DIFFUSION_IMAGING_EXTENDED if(index>=3) { index = index + 1; } #endif switch(index) { case 0: { // Numerical Reconstruct(0,0); break; } case 1: { // Standard Reconstruct(1,0); break; } case 2: { // Solid Angle Reconstruct(1,6); break; } case 3: { // Constrained Solid Angle Reconstruct(1,7); break; } case 4: { // ADC Reconstruct(1,4); break; } case 5: { // Raw Signal Reconstruct(1,5); break; } } } void QmitkQBallReconstructionView::MethodChoosen(int method) { switch(method) { case 0: m_Controls->m_Description->setText("Numerical recon. (Tuch2004)"); break; case 1: m_Controls->m_Description->setText("Spherical harmonics recon. (Descoteaux2007)"); break; case 2: m_Controls->m_Description->setText("SH recon. with solid angle consideration (Aganj2009)"); break; case 3: m_Controls->m_Description->setText("SH solid angle with non-neg. constraint (Goh2009)"); break; case 4: m_Controls->m_Description->setText("SH recon. of the plain ADC-profiles"); break; case 5: m_Controls->m_Description->setText("SH recon. of the raw diffusion signal"); break; } } void QmitkQBallReconstructionView::AdvancedCheckboxClicked() { bool check = m_Controls-> m_AdvancedCheckbox->isChecked(); m_Controls->m_QBallReconstructionMaxLLevelTextLabel_2->setVisible(check); m_Controls->m_QBallReconstructionMaxLLevelComboBox->setVisible(check); m_Controls->m_QBallReconstructionLambdaTextLabel_2->setVisible(check); m_Controls->m_QBallReconstructionLambdaLineEdit->setVisible(check); m_Controls->m_QBallReconstructionThresholdLabel_2->setVisible(check); m_Controls->m_QBallReconstructionThreasholdEdit->setVisible(check); m_Controls->m_OutputB0Image->setVisible(check); m_Controls->label_2->setVisible(check); //m_Controls->textLabel1_2->setVisible(check); //m_Controls->m_QBallReconstructionLambdaStepLineEdit->setVisible(check); //m_Controls->textLabel1_3->setVisible(check); m_Controls->frame_2->setVisible(check); } void QmitkQBallReconstructionView::Reconstruct(int method, int normalization) { if (m_CurrentSelection) { mitk::DataStorage::SetOfObjects::Pointer set = mitk::DataStorage::SetOfObjects::New(); int at = 0; for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); i != m_CurrentSelection->End(); ++i) { if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - - // check if node's data valid - const mitk::BaseData* nodeData = node->GetData(); - if(nodeData) - { - if(QString("DiffusionImage").compare(nodeData->GetNameOfClass())==0) + if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) { set->InsertElement(at++, node); } - } } } if(method == 0) { NumericalQBallReconstruction(set, normalization); } else { #if BOOST_VERSION / 100000 > 0 #if BOOST_VERSION / 100 % 1000 > 34 if(method == 1) { AnalyticalQBallReconstruction(set, normalization); } #else std::cout << "ERROR: Boost 1.35 minimum required" << std::endl; QMessageBox::warning(NULL,"ERROR","Boost 1.35 minimum required"); #endif #else std::cout << "ERROR: Boost 1.35 minimum required" << std::endl; QMessageBox::warning(NULL,"ERROR","Boost 1.35 minimum required"); #endif } } } void QmitkQBallReconstructionView::NumericalQBallReconstruction (mitk::DataStorage::SetOfObjects::Pointer inImages, int normalization) { try { itk::TimeProbe clock; int nrFiles = inImages->size(); if (!nrFiles) return; QString status; mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); ++itemiter; // QBALL RECONSTRUCTION clock.Start(); MBI_INFO << "QBall reconstruction "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( "QBall reconstruction for %s", nodename.c_str()).toAscii()); typedef itk::DiffusionQballReconstructionImageFilter QballReconstructionImageFilterType; QballReconstructionImageFilterType::Pointer filter = QballReconstructionImageFilterType::New(); filter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() ); filter->SetBValue(vols->GetB_Value()); filter->SetThreshold( m_Controls->m_QBallReconstructionThreasholdEdit->text().toFloat() ); switch(normalization) { case 0: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD); break; } case 1: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_B_ZERO_B_VALUE); break; } case 2: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_B_ZERO); break; } case 3: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_NONE); break; } default: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD); } } filter->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s." ; // ODFs TO DATATREE mitk::QBallImage::Pointer image = mitk::QBallImage::New(); image->InitializeByItk( filter->GetOutput() ); //image->SetImportVolume( filter->GetOutput()->GetBufferPointer(), 0, 0, mitk::Image::ImportMemoryManagementType::ManageMemory ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); QString newname; newname = newname.append(nodename.c_str()); newname = newname.append("_QN%1").arg(normalization); SetDefaultNodeProperties(node, newname.toStdString()); nodes.push_back(node); // B-Zero TO DATATREE if(m_Controls->m_OutputB0Image->isChecked()) { mitk::Image::Pointer image4 = mitk::Image::New(); image4->InitializeByItk( filter->GetBZeroImage().GetPointer() ); image4->SetVolume( filter->GetBZeroImage()->GetBufferPointer() ); mitk::DataNode::Pointer node4=mitk::DataNode::New(); node4->SetData( image4 ); node4->SetProperty( "name", mitk::StringProperty::New( QString(nodename.c_str()).append("_b0").toStdString()) ); nodes.push_back(node4); } mitk::ProgressBar::GetInstance()->Progress(); } std::vector::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); m_MultiWidget->RequestUpdate(); } catch (itk::ExceptionObject &ex) { MBI_INFO << ex ; return ; } } void QmitkQBallReconstructionView::AnalyticalQBallReconstruction( mitk::DataStorage::SetOfObjects::Pointer inImages, int normalization) { try { itk::TimeProbe clock; int nrFiles = inImages->size(); if (!nrFiles) return; std::vector lambdas; float minLambda = m_Controls->m_QBallReconstructionLambdaLineEdit->text().toFloat(); lambdas.push_back(minLambda); int nLambdas = lambdas.size(); QString status; mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles*nLambdas); mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector* nodes = new std::vector(); while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name",nodename); itemiter++; // QBALL RECONSTRUCTION clock.Start(); MBI_INFO << "QBall reconstruction "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( "QBall reconstruction for %s", nodename.c_str()).toAscii()); for(int i=0; im_QBallReconstructionMaxLLevelComboBox->currentIndex()) { case 0: { TemplatedAnalyticalQBallReconstruction<2>(vols, currentLambda, nodename, nodes, normalization); break; } case 1: { TemplatedAnalyticalQBallReconstruction<4>(vols, currentLambda, nodename, nodes, normalization); break; } case 2: { TemplatedAnalyticalQBallReconstruction<6>(vols, currentLambda, nodename, nodes, normalization); break; } case 3: { TemplatedAnalyticalQBallReconstruction<8>(vols, currentLambda, nodename, nodes, normalization); break; } case 4: { TemplatedAnalyticalQBallReconstruction<10>(vols, currentLambda, nodename, nodes, normalization); break; } case 5: { TemplatedAnalyticalQBallReconstruction<12>(vols, currentLambda, nodename, nodes, normalization); break; } } clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s." ; mitk::ProgressBar::GetInstance()->Progress(); } } std::vector::iterator nodeIt; for(nodeIt = nodes->begin(); nodeIt != nodes->end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); m_MultiWidget->RequestUpdate(); mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); } catch (itk::ExceptionObject &ex) { MBI_INFO << ex ; return ; } } template void QmitkQBallReconstructionView::TemplatedAnalyticalQBallReconstruction( mitk::DiffusionImage* vols, float lambda, std::string nodename, std::vector* nodes, int normalization) { typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; typename FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() ); filter->SetBValue(vols->GetB_Value()); filter->SetThreshold( m_Controls->m_QBallReconstructionThreasholdEdit->text().toFloat() ); filter->SetLambda(lambda); switch(normalization) { case 0: { filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); break; } case 1: { filter->SetNormalizationMethod(FilterType::QBAR_B_ZERO_B_VALUE); break; } case 2: { filter->SetNormalizationMethod(FilterType::QBAR_B_ZERO); break; } case 3: { filter->SetNormalizationMethod(FilterType::QBAR_NONE); break; } case 4: { filter->SetNormalizationMethod(FilterType::QBAR_ADC_ONLY); break; } case 5: { filter->SetNormalizationMethod(FilterType::QBAR_RAW_SIGNAL); break; } case 6: { filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); break; } case 7: { filter->SetNormalizationMethod(FilterType::QBAR_NONNEG_SOLID_ANGLE); break; } default: { filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); } } filter->Update(); // ODFs TO DATATREE mitk::QBallImage::Pointer image = mitk::QBallImage::New(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); QString newname; newname = newname.append(nodename.c_str()); newname = newname.append("_QA%1").arg(normalization); SetDefaultNodeProperties(node, newname.toStdString()); nodes->push_back(node); // mitk::Image::Pointer image5 = mitk::Image::New(); // image5->InitializeByItk( filter->GetODFSumImage().GetPointer() ); // image5->SetVolume( filter->GetODFSumImage()->GetBufferPointer() ); // mitk::DataNode::Pointer node5=mitk::DataNode::New(); // node5->SetData( image5 ); // node5->SetProperty( "name", mitk::StringProperty::New( // QString(nodename.c_str()).append("_ODF").toStdString()) ); // nodes->push_back(node5); // B-Zero TO DATATREE if(m_Controls->m_OutputB0Image->isChecked()) { mitk::Image::Pointer image4 = mitk::Image::New(); image4->InitializeByItk( filter->GetBZeroImage().GetPointer() ); image4->SetVolume( filter->GetBZeroImage()->GetBufferPointer() ); mitk::DataNode::Pointer node4=mitk::DataNode::New(); node4->SetData( image4 ); node4->SetProperty( "name", mitk::StringProperty::New( QString(nodename.c_str()).append("_b0").toStdString()) ); nodes->push_back(node4); } } void QmitkQBallReconstructionView::SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name) { node->SetProperty( "ShowMaxNumber", mitk::IntProperty::New( 500 ) ); node->SetProperty( "Scaling", mitk::FloatProperty::New( 1.0 ) ); node->SetProperty( "Normalization", mitk::OdfNormalizationMethodProperty::New()); node->SetProperty( "ScaleBy", mitk::OdfScaleByProperty::New()); node->SetProperty( "IndexParam1", mitk::FloatProperty::New(2)); node->SetProperty( "IndexParam2", mitk::FloatProperty::New(1)); node->SetProperty( "visible", mitk::BoolProperty::New( true ) ); node->SetProperty( "VisibleOdfs", mitk::BoolProperty::New( false ) ); node->SetProperty ("layer", mitk::IntProperty::New(100)); node->SetProperty( "DoRefresh", mitk::BoolProperty::New( true ) ); //node->SetProperty( "opacity", mitk::FloatProperty::New(1.0f) ); node->SetProperty( "name", mitk::StringProperty::New(name) ); } //node->SetProperty( "volumerendering", mitk::BoolProperty::New( false ) ); //node->SetProperty( "use color", mitk::BoolProperty::New( true ) ); //node->SetProperty( "texture interpolation", mitk::BoolProperty::New( true ) ); //node->SetProperty( "reslice interpolation", mitk::VtkResliceInterpolationProperty::New() ); //node->SetProperty( "layer", mitk::IntProperty::New(0)); //node->SetProperty( "in plane resample extent by geometry", mitk::BoolProperty::New( false ) ); //node->SetOpacity(1.0f); //node->SetColor(1.0,1.0,1.0); //node->SetVisibility(true); //node->SetProperty( "IsQBallVolume", mitk::BoolProperty::New( true ) ); //mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New(); //mitk::LevelWindow levelwindow; //// levelwindow.SetAuto( image ); //levWinProp->SetLevelWindow( levelwindow ); //node->GetPropertyList()->SetProperty( "levelwindow", levWinProp ); //// add a default rainbow lookup table for color mapping //if(!node->GetProperty("LookupTable")) //{ // mitk::LookupTable::Pointer mitkLut = mitk::LookupTable::New(); // vtkLookupTable* vtkLut = mitkLut->GetVtkLookupTable(); // vtkLut->SetHueRange(0.6667, 0.0); // vtkLut->SetTableRange(0.0, 20.0); // vtkLut->Build(); // mitk::LookupTableProperty::Pointer mitkLutProp = mitk::LookupTableProperty::New(); // mitkLutProp->SetLookupTable(mitkLut); // node->SetProperty( "LookupTable", mitkLutProp ); //} //if(!node->GetProperty("binary")) // node->SetProperty( "binary", mitk::BoolProperty::New( false ) ); //// add a default transfer function //mitk::TransferFunction::Pointer tf = mitk::TransferFunction::New(); //node->SetProperty ( "TransferFunction", mitk::TransferFunctionProperty::New ( tf.GetPointer() ) ); //// set foldername as string property //mitk::StringProperty::Pointer nameProp = mitk::StringProperty::New( name ); //node->SetProperty( "name", nameProp ); diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.h index bfc262add3..9843de4102 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.h @@ -1,119 +1,122 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ -Version: $Revision: 17495 $ - +Version: $Revision: 17495 $ + Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _QMITKQBALLRECONSTRUCTIONVIEW_H_INCLUDED #define _QMITKQBALLRECONSTRUCTIONVIEW_H_INCLUDED #include #include #include "ui_QmitkQBallReconstructionViewControls.h" #include "mitkDiffusionImage.h" #include #include #include typedef short DiffusionPixelType; struct QbrSelListener; /*! * \ingroup org_mitk_gui_qt_qballreconstruction_internal * * \brief QmitkQBallReconstructionView * * Document your class here. * * \sa QmitkFunctionality */ class QmitkQBallReconstructionView : public QmitkFunctionality { friend struct QbrSelListener; // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; QmitkQBallReconstructionView(); QmitkQBallReconstructionView(const QmitkQBallReconstructionView& other); virtual ~QmitkQBallReconstructionView(); virtual void CreateQtPartControl(QWidget *parent); /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); static const int nrconvkernels; protected slots: void ReconstructStandard(); //void ReconstructNormalized1(); //void ReconstructNormalized2(); //void ReconstructNonNormalized(); //void AnalyticallyReconstructStandard(); //void AnalyticallyReconstructSolidAngle(); //void AnalyticallyReconstructNonNegSolidAngle(); //void AnalyticallyReconstructAdc(); //void AnalyticallyReconstructRaw(); - + void AdvancedCheckboxClicked(); void MethodChoosen(int method); - + void Reconstruct(int method, int normalization); - + void NumericalQBallReconstruction(mitk::DataStorage::SetOfObjects::Pointer inImages, int normalization); void AnalyticalQBallReconstruction(mitk::DataStorage::SetOfObjects::Pointer inImages, int normalization); protected: + /// \brief called by QmitkFunctionality when DataManager's selection has changed + virtual void OnSelectionChanged( std::vector nodes ); + Ui::QmitkQBallReconstructionViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; template - void TemplatedAnalyticalQBallReconstruction(mitk::DiffusionImage* vols, + void TemplatedAnalyticalQBallReconstruction(mitk::DiffusionImage* vols, float lambda, std::string nodename, std::vector* nodes, int normalization); void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name); berry::ISelectionListener::Pointer m_SelListener; berry::IStructuredSelection::ConstPointer m_CurrentSelection; }; #endif // _QMITKQBALLRECONSTRUCTIONVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionViewControls.ui index ce29e09017..f436cbda5a 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionViewControls.ui @@ -1,230 +1,253 @@ QmitkQBallReconstructionViewControls 0 0 350 385 0 0 true QmitkQBallReconstructionViewControls + + + + Data + + + + + + Diffusion Image: + + + + + + + - + + + + + + Reconstruction Advanced Settings QFrame::StyledPanel QFrame::Raised QFormLayout::AllNonFixedFieldsGrow true B0 Threshold false true 0 true Output B0-Image true Spherical Harmonics: true Maximum l-Level false true -1 true Regularization Parameter Lambda false true 0.006 2 Numerical Standard (SH) Solid Angle (SH) Constraint Solid Angle (SH) ADC-Profile only (SH) Raw Signal only (SH) TextLabel false Start Reconstruction Qt::Vertical 20 0 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStochasticFiberTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStochasticFiberTrackingView.cpp index 2db143d7d3..6b079cbe23 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStochasticFiberTrackingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStochasticFiberTrackingView.cpp @@ -1,272 +1,280 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $ Version: $Revision: 21975 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ // Blueberry #include #include #include // Qmitk #include "QmitkStochasticFiberTrackingView.h" #include "QmitkStdMultiWidget.h" // Qt #include // MITK #include #include // VTK #include #include #include #include #include #include const std::string QmitkStochasticFiberTrackingView::VIEW_ID = "org.mitk.views.stochasticfibertracking"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace berry; QmitkStochasticFiberTrackingView::QmitkStochasticFiberTrackingView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_DiffusionImage( NULL ) , m_SeedRoi( NULL ) { } // Destructor QmitkStochasticFiberTrackingView::~QmitkStochasticFiberTrackingView() { } void QmitkStochasticFiberTrackingView::CreateQtPartControl( QWidget *parent ) { if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkStochasticFiberTrackingViewControls; m_Controls->setupUi( parent ); connect( m_Controls->commandLinkButton, SIGNAL(clicked()), this, SLOT(DoFiberTracking()) ); connect( m_Controls->m_SeedsPerVoxelSlider, SIGNAL(valueChanged(int)), this, SLOT(OnSeedsPerVoxelChanged(int)) ); connect( m_Controls->m_MaxCacheSizeSlider, SIGNAL(valueChanged(int)), this, SLOT(OnMaxCacheSizeChanged(int)) ); connect( m_Controls->m_MaxTractLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(OnMaxTractLengthChanged(int)) ); } } void QmitkStochasticFiberTrackingView::OnSeedsPerVoxelChanged(int value) { m_Controls->m_SeedsPerVoxelLabel->setText(QString("Seeds per Voxel: ")+QString::number(value)); } void QmitkStochasticFiberTrackingView::OnMaxTractLengthChanged(int value) { m_Controls->m_MaxTractLengthLabel->setText(QString("Max. Tract Length: ")+QString::number(value)); } void QmitkStochasticFiberTrackingView::OnMaxCacheSizeChanged(int value) { m_Controls->m_MaxCacheSizeLabel->setText(QString("Max. Cache Size: ")+QString::number(value)+"GB"); } void QmitkStochasticFiberTrackingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkStochasticFiberTrackingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkStochasticFiberTrackingView::OnSelectionChanged( std::vector nodes ) { + m_DiffusionImageNode = NULL; m_DiffusionImage = NULL; m_SeedRoi = NULL; m_Controls->m_DiffusionImageLabel->setText("-"); m_Controls->m_RoiImageLabel->setText("-"); if(nodes.empty()) return; for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { if( dynamic_cast*>(node->GetData()) ) { + m_DiffusionImageNode = node; m_DiffusionImage = dynamic_cast*>(node->GetData()); m_Controls->m_DiffusionImageLabel->setText(node->GetName().c_str()); } else { bool isBinary = false; node->GetPropertyValue("binary", isBinary); if (isBinary) { m_SeedRoi = dynamic_cast(node->GetData()); m_Controls->m_RoiImageLabel->setText(node->GetName().c_str()); } } } } if(m_DiffusionImage.IsNotNull() && m_SeedRoi.IsNotNull()) m_Controls->commandLinkButton->setEnabled(true); else m_Controls->commandLinkButton->setEnabled(false); } void QmitkStochasticFiberTrackingView::DoFiberTracking() { /* get Gradients/Direction of dwi */ itk::VectorContainer< unsigned int, vnl_vector_fixed >::Pointer Pdir = m_DiffusionImage->GetDirections(); /* bValueContainer, Container includes b-values according to corresponding gradient-direction*/ PTFilterType::bValueContainerType::Pointer vecCont = PTFilterType::bValueContainerType::New(); /* for each gradient set b-Value; for 0-gradient set b-value eq. 0 */ for ( int i=0; i<(int)Pdir->size(); ++i) { vnl_vector_fixed valsGrad = Pdir->at(i); if (valsGrad.get(0) == 0 && valsGrad.get(1) == 0 && valsGrad.get(2) == 0) { //set 0-Gradient to bValue 0 vecCont->InsertElement(i,0); }else{ vecCont->InsertElement(i,m_DiffusionImage->GetB_Value()); } } /* define measurement frame (identity-matrix 3x3) */ PTFilterType::MeasurementFrameType measurement_frame = m_DiffusionImage->GetMeasurementFrame(); /* generate white matterImage (dummy?)*/ FloatImageType::Pointer wmImage = FloatImageType::New(); wmImage->SetSpacing( m_DiffusionImage->GetVectorImage()->GetSpacing() ); wmImage->SetOrigin( m_DiffusionImage->GetVectorImage()->GetOrigin() ); wmImage->SetDirection( m_DiffusionImage->GetVectorImage()->GetDirection() ); wmImage->SetLargestPossibleRegion( m_DiffusionImage->GetVectorImage()->GetLargestPossibleRegion() ); wmImage->SetBufferedRegion( wmImage->GetLargestPossibleRegion() ); wmImage->SetRequestedRegion( wmImage->GetLargestPossibleRegion() ); wmImage->Allocate(); itk::ImageRegionIterator ot(wmImage, wmImage->GetLargestPossibleRegion() ); while (!ot.IsAtEnd()) { ot.Set(1); ++ot; } /* init TractographyFilter */ PTFilterType::Pointer trackingFilter = PTFilterType::New(); trackingFilter->SetInput(m_DiffusionImage->GetVectorImage().GetPointer()); trackingFilter->SetbValues(vecCont); trackingFilter->SetGradients(Pdir); trackingFilter->SetMeasurementFrame(measurement_frame); trackingFilter->SetWhiteMatterProbabilityImageInput(wmImage); trackingFilter->SetTotalTracts(m_Controls->m_SeedsPerVoxelSlider->value()); trackingFilter->SetMaxLikelihoodCacheSize(m_Controls->m_MaxCacheSizeSlider->value()*1000); trackingFilter->SetMaxTractLength(m_Controls->m_MaxTractLengthSlider->value()); m_tractcontainer = PTFilterType::TractContainerType::New(); //itk::Image< char, 3 > mitk::ImageToItk< itk::Image< unsigned char, 3 > >::Pointer binaryImageToItk1 = mitk::ImageToItk< itk::Image< unsigned char, 3 > >::New(); binaryImageToItk1->SetInput( m_SeedRoi ); binaryImageToItk1->Update(); + vtkSmartPointer vPoints = vtkSmartPointer::New(); + vtkSmartPointer vCellArray = vtkSmartPointer::New(); + itk::ImageRegionConstIterator< BinaryImageType > it(binaryImageToItk1->GetOutput(), binaryImageToItk1->GetOutput()->GetRequestedRegion()); it.Begin(); + mitk::Geometry3D* geom = m_DiffusionImage->GetGeometry(); while(!it.IsAtEnd()) { itk::ImageConstIterator::PixelType tmpPxValue = it.Get(); if(tmpPxValue != 0){ + mitk::Point3D point; itk::ImageRegionConstIterator< BinaryImageType >::IndexType seedIdx = it.GetIndex(); trackingFilter->SetSeedIndex(seedIdx); trackingFilter->Update(); /* get results from Filter */ /* write each single tract into member container */ PTFilterType::TractContainerType::Pointer container_tmp = trackingFilter->GetOutputTractContainer(); PTFilterType::TractContainerType::Iterator elIt = container_tmp->Begin(); PTFilterType::TractContainerType::Iterator end = container_tmp->End(); + bool addTract = true; while( elIt != end ){ - PTFilterType::TractContainerType::Element tract_tmp = elIt.Value(); - m_tractcontainer->InsertElement(m_tractcontainer->Size(),tract_tmp); - ++elIt; - } - } - ++it; - } - - /* allocate the VTK Polydata to output the tracts */ - vtkSmartPointer vPoints = vtkSmartPointer::New(); - vtkSmartPointer vCellArray = vtkSmartPointer::New(); - - for( int i=0; i<(int)m_tractcontainer->Size(); i++ ) - { - mitk::Point3D point; + PTFilterType::TractContainerType::Element tract = elIt.Value(); + PTFilterType::TractContainerType::Element::ObjectType::VertexListType::ConstPointer vertexlist = tract->GetVertexList(); - PTFilterType::TractContainerType::Element tract = m_tractcontainer->GetElement(i); - PTFilterType::TractContainerType::Element::ObjectType::VertexListType::ConstPointer vertexlist = tract->GetVertexList(); - - vtkSmartPointer vPolyLine = vtkSmartPointer::New(); - for( int j=0; j<(int)vertexlist->Size(); j++) - { - PTFilterType::TractContainerType::Element::ObjectType::VertexListType::Element vertex = vertexlist->GetElement(j); - mitk::Point3D index; - index[0] = (float)vertex[0]; - index[1] = (float)vertex[1]; - index[2] = (float)vertex[2]; + vtkSmartPointer vPolyLine = vtkSmartPointer::New(); + for( int j=0; j<(int)vertexlist->Size(); j++) + { + PTFilterType::TractContainerType::Element::ObjectType::VertexListType::Element vertex = vertexlist->GetElement(j); + mitk::Point3D index; + index[0] = (float)vertex[0]; + index[1] = (float)vertex[1]; + index[2] = (float)vertex[2]; + + if (geom->IsIndexInside(index)) + { + geom->IndexToWorld(index, point); + vtkIdType id = vPoints->InsertNextPoint(point.GetDataPointer()); + vPolyLine->GetPointIds()->InsertNextId(id); + } + else + { + addTract = false; + break; + } + } - m_DiffusionImage->GetGeometry()->IndexToWorld(index, point); + if (addTract) + vCellArray->InsertNextCell(vPolyLine); - vtkIdType id = vPoints->InsertNextPoint(point.GetDataPointer()); - vPolyLine->GetPointIds()->InsertNextId(id); + ++elIt; + } } - vCellArray->InsertNextCell(vPolyLine); + ++it; } vtkSmartPointer fiberPolyData = vtkSmartPointer::New(); fiberPolyData->SetPoints(vPoints); fiberPolyData->SetLines(vCellArray); mitk::FiberBundleX::Pointer fib = mitk::FiberBundleX::New(fiberPolyData); mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(fib); - fbNode->SetName("GroupFinberBundle"); + QString name(m_DiffusionImageNode->GetName().c_str()); + name += "_FiberBundle"; + fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStochasticFiberTrackingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStochasticFiberTrackingView.h index 34f31895ba..d6857a757b 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStochasticFiberTrackingView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStochasticFiberTrackingView.h @@ -1,102 +1,103 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2010-03-31 16:40:27 +0200 (Mi, 31 Mrz 2010) $ Version: $Revision: 21975 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef QmitkStochasticFiberTrackingView_h #define QmitkStochasticFiberTrackingView_h #include #include #include #include "ui_QmitkStochasticFiberTrackingViewControls.h" #include #include #include #include #include #include #include #include //define the input/output types typedef itk::VectorImage< short int, 3 > DWIVectorImageType; typedef itk::Image< float, 3 > FloatImageType; typedef itk::Image< unsigned int, 3 > CImageType; typedef itk::StochasticTractographyFilter< DWIVectorImageType, FloatImageType, CImageType > PTFilterType; typedef itk::DTITubeSpatialObject<3> DTITubeType; typedef itk::DTITubeSpatialObjectPoint<3> DTITubePointType; typedef itk::SceneSpatialObject<3> SceneSpatialObjectType; /*! \brief QmitkFiberTrackingView \warning This application module is not yet documented. Use "svn blame/praise/annotate" and ask the author to provide basic documentation. \sa QmitkFunctionality \ingroup Functionalities */ class QmitkStochasticFiberTrackingView : public QmitkFunctionality { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; QmitkStochasticFiberTrackingView(); virtual ~QmitkStochasticFiberTrackingView(); virtual void CreateQtPartControl(QWidget *parent); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); protected slots: void DoFiberTracking(); protected: /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( std::vector nodes ); Ui::QmitkStochasticFiberTrackingViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; protected slots: void OnSeedsPerVoxelChanged(int value); void OnMaxTractLengthChanged(int value); void OnMaxCacheSizeChanged(int value); private: mitk::Image::Pointer m_SeedRoi; mitk::DiffusionImage::Pointer m_DiffusionImage; + mitk::DataNode::Pointer m_DiffusionImageNode; typedef itk::Image< unsigned char, 3 > BinaryImageType; PTFilterType::TractContainerType::Pointer m_tractcontainer; }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.cpp index fbe44bf130..12d4575f1f 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.cpp @@ -1,1377 +1,1339 @@ -/*========================================================================= + /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkTensorReconstructionView.h" #include "mitkDiffusionImagingConfigure.h" // qt includes #include #include #include #include #include // itk includes #include "itkTimeProbe.h" //#include "itkTensor.h" // mitk includes #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkNodePredicateDataType.h" #include "QmitkDataStorageComboBox.h" #include "QmitkStdMultiWidget.h" #include "mitkTeemDiffusionTensor3DReconstructionImageFilter.h" #include "itkDiffusionTensor3DReconstructionImageFilter.h" #include "itkTensorImageToDiffusionImageFilter.h" #include "itkPointShell.h" #include "itkVector.h" #include "itkB0ImageExtractionImageFilter.h" +#include "itkTensorReconstructionWithEigenvalueCorrectionFilter.h" +//#include "itkFreeWaterEliminationFilter.h" #include "mitkProperties.h" #include "mitkDataNodeObject.h" #include "mitkOdfNormalizationMethodProperty.h" #include "mitkOdfScaleByProperty.h" #include "mitkDiffusionImageMapper.h" #include "mitkLookupTableProperty.h" #include "mitkLookupTable.h" #include "mitkImageStatisticsHolder.h" -#include "berryIStructuredSelection.h" -#include "berryIWorkbenchWindow.h" -#include "berryISelectionService.h" - #include #include const std::string QmitkTensorReconstructionView::VIEW_ID = "org.mitk.views.tensorreconstruction"; #define DI_INFO MITK_INFO("DiffusionImaging") typedef float TTensorPixelType; typedef itk::DiffusionTensor3D< TTensorPixelType > TensorPixelType; typedef itk::Image< TensorPixelType, 3 > TensorImageType; using namespace berry; struct TrSelListener : ISelectionListener { berryObjectMacro(TrSelListener); TrSelListener(QmitkTensorReconstructionView* view) { m_View = view; } void DoSelectionChanged(ISelection::ConstPointer selection) { + /* // if(!m_View->IsVisible()) // return; // save current selection in member variable m_View->m_CurrentSelection = selection.Cast(); // do something with the selected items if(m_View->m_CurrentSelection) { bool foundDwiVolume = false; bool foundTensorVolume = false; // iterate selection for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); i != m_View->m_CurrentSelection->End(); ++i) { // extract datatree node if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - mitk::BaseData* nodeData = node->GetData(); - if( nodeData != NULL ) + // only look at interesting types + if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) { - // only look at interesting types - if(QString("DiffusionImage").compare(nodeData->GetNameOfClass())==0) - { - foundDwiVolume = true; - } + foundDwiVolume = true; + } - // only look at interesting types - if(QString("TensorImage").compare(nodeData->GetNameOfClass())==0) - { - foundTensorVolume = true; - } + // only look at interesting types + if(QString("TensorImage").compare(node->GetData()->GetNameOfClass())==0) + { + foundTensorVolume = true; } } } m_View->m_Controls->m_ItkReconstruction->setEnabled(foundDwiVolume); m_View->m_Controls->m_TeemReconstruction->setEnabled(foundDwiVolume); + m_View->m_Controls->m_ReconstructionWithCorrection->setEnabled(foundDwiVolume); m_View->m_Controls->m_TensorsToDWIButton->setEnabled(foundTensorVolume); m_View->m_Controls->m_TensorsToQbiButton->setEnabled(foundTensorVolume); m_View->m_Controls->m_ResidualButton->setEnabled(foundDwiVolume && foundTensorVolume); m_View->m_Controls->m_PercentagesOfOutliers->setEnabled(foundDwiVolume && foundTensorVolume); m_View->m_Controls->m_PerSliceView->setEnabled(foundDwiVolume && foundTensorVolume); } + */ } void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) { // check, if selection comes from datamanager if (part) { QString partname(part->GetPartName().c_str()); if(partname.compare("Datamanager")==0) { // apply selection DoSelectionChanged(selection); } } } QmitkTensorReconstructionView* m_View; }; + QmitkTensorReconstructionView::QmitkTensorReconstructionView() -: QmitkFunctionality(), -m_Controls(NULL), -m_MultiWidget(NULL) + : QmitkFunctionality(), + m_Controls(NULL), + m_MultiWidget(NULL) { - - if(m_CurrentSelection) - { - mitk::DataStorage::SetOfObjects::Pointer set = - mitk::DataStorage::SetOfObjects::New(); - - mitk::DiffusionImage::Pointer diffImage - = mitk::DiffusionImage::New(); - - - TensorImageType::Pointer tensorImage; - - std::string nodename; - - - for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); - i != m_CurrentSelection->End(); - ++i) - { - - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - - mitk::BaseData* nodeData = node->GetData(); - if(nodeData) - { - if(QString("DiffusionImage").compare(nodeData->GetNameOfClass())==0) - { - diffImage = static_cast*>((node)->GetData()); - } - else if((QString("TensorImage").compare(nodeData->GetNameOfClass())==0)) - { - mitk::TensorImage* mitkVol; - mitkVol = static_cast((node)->GetData()); - mitk::CastToItkImage(mitkVol, tensorImage); - node->GetStringProperty("name", nodename); - } - } - } - } - - } - - + m_DiffusionImages = mitk::DataStorage::SetOfObjects::New(); + m_TensorImages = mitk::DataStorage::SetOfObjects::New(); } QmitkTensorReconstructionView::QmitkTensorReconstructionView(const QmitkTensorReconstructionView& other) { Q_UNUSED(other) throw std::runtime_error("Copy constructor not implemented"); } QmitkTensorReconstructionView::~QmitkTensorReconstructionView() { - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); + } void QmitkTensorReconstructionView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkTensorReconstructionViewControls; m_Controls->setupUi(parent); this->CreateConnections(); QStringList items; items << "LLS (Linear Least Squares)" - << "MLE (Maximum Likelihood)" - << "NLS (Nonlinear Least Squares)" - << "WLS (Weighted Least Squares)"; + << "MLE (Maximum Likelihood)" + << "NLS (Nonlinear Least Squares)" + << "WLS (Weighted Least Squares)"; m_Controls->m_TensorEstimationTeemEstimationMethodCombo->addItems(items); m_Controls->m_TensorEstimationTeemEstimationMethodCombo->setCurrentIndex(0); m_Controls->m_TensorEstimationManualThreashold->setChecked(false); m_Controls->m_TensorEstimationTeemSigmaEdit->setText("NaN"); m_Controls->m_TensorEstimationTeemNumItsSpin->setValue(1); m_Controls->m_TensorEstimationTeemFuzzyEdit->setText("0.0"); m_Controls->m_TensorEstimationTeemMinValEdit->setText("1.0"); m_Controls->m_TensorEstimationTeemNumItsLabel_2->setEnabled(true); m_Controls->m_TensorEstimationTeemNumItsSpin->setEnabled(true); m_Controls->m_TensorsToDWIBValueEdit->setText("1000"); Advanced1CheckboxClicked(); Advanced2CheckboxClicked(); + Advanced3CheckboxClicked(); TeemCheckboxClicked(); #ifndef DIFFUSION_IMAGING_EXTENDED m_Controls->m_TeemToggle->setVisible(false); #endif // define data type for combobox //m_Controls->m_ImageSelector->SetDataStorage( this->GetDefaultDataStorage() ); //m_Controls->m_ImageSelector->SetPredicate( mitk::NodePredicateDataType::New("DiffusionImage") ); } - - m_SelListener = berry::ISelectionListener::Pointer(new TrSelListener(this)); - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); - berry::ISelection::ConstPointer sel( - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); - m_CurrentSelection = sel.Cast(); - m_SelListener.Cast()->DoSelectionChanged(sel); - - - - - - } void QmitkTensorReconstructionView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { - berry::ISelection::ConstPointer sel( - this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); - m_CurrentSelection = sel.Cast(); - m_SelListener.Cast()->DoSelectionChanged(sel); m_MultiWidget = &stdMultiWidget; } void QmitkTensorReconstructionView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkTensorReconstructionView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_TeemToggle), SIGNAL(clicked()), this, SLOT(TeemCheckboxClicked()) ); connect( (QObject*)(m_Controls->m_ItkReconstruction), SIGNAL(clicked()), this, SLOT(ItkReconstruction()) ); connect( (QObject*)(m_Controls->m_TeemReconstruction), SIGNAL(clicked()), this, SLOT(TeemReconstruction()) ); + connect( (QObject*)(m_Controls->m_ReconstructionWithCorrection), SIGNAL(clicked()), this, SLOT(ReconstructionWithCorrection()) ); connect( (QObject*)(m_Controls->m_TensorEstimationTeemEstimationMethodCombo), SIGNAL(currentIndexChanged(int)), this, SLOT(MethodChoosen(int)) ); connect( (QObject*)(m_Controls->m_Advanced1), SIGNAL(clicked()), this, SLOT(Advanced1CheckboxClicked()) ); connect( (QObject*)(m_Controls->m_Advanced2), SIGNAL(clicked()), this, SLOT(Advanced2CheckboxClicked()) ); + connect( (QObject*)(m_Controls->m_Advanced3), SIGNAL(clicked()), this, SLOT(Advanced3CheckboxClicked()) ); connect( (QObject*)(m_Controls->m_TensorEstimationManualThreashold), SIGNAL(clicked()), this, SLOT(ManualThresholdClicked()) ); connect( (QObject*)(m_Controls->m_TensorsToDWIButton), SIGNAL(clicked()), this, SLOT(TensorsToDWI()) ); connect( (QObject*)(m_Controls->m_TensorsToQbiButton), SIGNAL(clicked()), this, SLOT(TensorsToQbi()) ); connect( (QObject*)(m_Controls->m_ResidualButton), SIGNAL(clicked()), this, SLOT(ResidualCalculation()) ); connect( (QObject*)(m_Controls->m_PerSliceView), SIGNAL(pointSelected(int, int)), this, SLOT(ResidualClicked(int, int)) ); } } void QmitkTensorReconstructionView::ResidualClicked(int slice, int volume) { // Use image coord to reset crosshair // Find currently selected diffusion image // Update Label // to do: This position should be modified in order to skip B0 volumes that are not taken into account // when calculating residuals // Find the diffusion image mitk::DiffusionImage* diffImage; - - mitk::DataNodeObject::Pointer nodeObj; mitk::DataNode::Pointer correctNode; mitk::Geometry3D* geometry; - for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); - i != m_CurrentSelection->End(); - ++i) + if (m_DiffusionImage.IsNotNull()) { - if (nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - // process only on valid nodes - mitk::BaseData* nodeData = node->GetData(); - if(nodeData) - { - if(QString("DiffusionImage").compare(nodeData->GetNameOfClass())==0) - { - diffImage = static_cast*>(nodeData); + diffImage = static_cast*>(m_DiffusionImage->GetData()); - geometry = diffImage->GetGeometry(); + geometry = diffImage->GetGeometry(); - // Remember the node whose display index must be updated - correctNode = mitk::DataNode::New(); - correctNode = node; - } - } - } + // Remember the node whose display index must be updated + correctNode = mitk::DataNode::New(); + correctNode = m_DiffusionImage; } if(diffImage != NULL) { typedef vnl_vector_fixed< double, 3 > GradientDirectionType; typedef itk::VectorContainer< unsigned int, - GradientDirectionType > GradientDirectionContainerType; + GradientDirectionType > GradientDirectionContainerType; GradientDirectionContainerType::Pointer dirs = diffImage->GetDirections(); - - for(int i=0; iSize() && i<=volume; i++) { GradientDirectionType grad = dirs->ElementAt(i); // check if image is b0 weighted if(fabs(grad[0]) < 0.001 && fabs(grad[1]) < 0.001 && fabs(grad[2]) < 0.001) { volume++; } } - QString pos = "Volume: "; pos.append(QString::number(volume)); pos.append(", Slice: "); pos.append(QString::number(slice)); m_Controls->m_PositionLabel->setText(pos); - - - if(correctNode) { - int oldDisplayVal; correctNode->GetIntProperty("DisplayChannel", oldDisplayVal); std::string oldVal = QString::number(oldDisplayVal).toStdString(); std::string newVal = QString::number(volume).toStdString(); - correctNode->SetIntProperty("DisplayChannel",volume); - correctNode->SetSelected(true); - this->FirePropertyChanged("DisplayChannel", oldVal, newVal); - - correctNode->UpdateOutputInformation(); mitk::Point3D p3 = m_MultiWidget->GetCrossPosition(); itk::Index<3> ix; geometry->WorldToIndex(p3, ix); - // ix[2] = slice; + // ix[2] = slice; mitk::Vector3D vec; vec[0] = ix[0]; vec[1] = ix[1]; vec[2] = slice; - mitk::Vector3D v3New; geometry->IndexToWorld(vec, v3New); - - mitk::Point3D origin = geometry->GetOrigin(); - mitk::Point3D p3New; p3New[0] = v3New[0] + origin[0]; p3New[1] = v3New[1] + origin[1]; p3New[2] = v3New[2] + origin[2]; - - m_MultiWidget->MoveCrossToPosition(p3New); - - m_MultiWidget->RequestUpdate(); - - } - - - } - } void QmitkTensorReconstructionView::TeemCheckboxClicked() { m_Controls->groupBox_3->setVisible(m_Controls-> - m_TeemToggle->isChecked()); + m_TeemToggle->isChecked()); } void QmitkTensorReconstructionView::Advanced1CheckboxClicked() { bool check = m_Controls-> - m_Advanced1->isChecked(); + m_Advanced1->isChecked(); m_Controls->frame->setVisible(check); } void QmitkTensorReconstructionView::Advanced2CheckboxClicked() { bool check = m_Controls-> - m_Advanced2->isChecked(); + m_Advanced2->isChecked(); m_Controls->frame_2->setVisible(check); } +void QmitkTensorReconstructionView::Advanced3CheckboxClicked() +{ + bool check = m_Controls-> + m_Advanced3->isChecked(); + + m_Controls->frame_6->setVisible(check); +} + void QmitkTensorReconstructionView::ManualThresholdClicked() { m_Controls->m_TensorReconstructionThreasholdEdit_2->setEnabled( - m_Controls->m_TensorEstimationManualThreashold->isChecked()); + m_Controls->m_TensorEstimationManualThreashold->isChecked()); } void QmitkTensorReconstructionView::Activated() { QmitkFunctionality::Activated(); } void QmitkTensorReconstructionView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkTensorReconstructionView::MethodChoosen(int method) { m_Controls->m_TensorEstimationTeemNumItsLabel_2->setEnabled(method==3); m_Controls->m_TensorEstimationTeemNumItsSpin->setEnabled(method==3); } void QmitkTensorReconstructionView::ResidualCalculation() { // Extract dwi and dti from current selection // In case of multiple selections, take the first one, since taking all combinations is not meaningful - - - if(m_CurrentSelection) - { - mitk::DataStorage::SetOfObjects::Pointer set = + mitk::DataStorage::SetOfObjects::Pointer set = mitk::DataStorage::SetOfObjects::New(); - mitk::DiffusionImage::Pointer diffImage - = mitk::DiffusionImage::New(); + mitk::DiffusionImage::Pointer diffImage + = mitk::DiffusionImage::New(); - TensorImageType::Pointer tensorImage; - - std::string nodename; - - - for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); - i != m_CurrentSelection->End(); - ++i) - { - - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - - // process only on valid nodes - mitk::BaseData* nodeData = node->GetData(); - if(nodeData) - { - if(QString("DiffusionImage").compare(nodeData->GetNameOfClass())==0) - { - diffImage = static_cast*>((node)->GetData()); - } - else if((QString("TensorImage").compare(nodeData->GetNameOfClass())==0)) - { - mitk::TensorImage* mitkVol; - mitkVol = static_cast(nodeData); - mitk::CastToItkImage(mitkVol, tensorImage); - node->GetStringProperty("name", nodename); - } - } - } - } + TensorImageType::Pointer tensorImage; + std::string nodename; + if(m_DiffusionImage.IsNotNull()) + { + diffImage = static_cast*>(m_DiffusionImage->GetData()); + } + else + return; + if(m_TensorImage.IsNotNull()) + { + mitk::TensorImage* mitkVol; + mitkVol = static_cast(m_TensorImage->GetData()); + mitk::CastToItkImage(mitkVol, tensorImage); + m_TensorImage->GetStringProperty("name", nodename); + } + else + return; - typedef itk::TensorImageToDiffusionImageFilter< + typedef itk::TensorImageToDiffusionImageFilter< TTensorPixelType, DiffusionPixelType > FilterType; - FilterType::GradientListType gradientList; - mitk::DiffusionImage::GradientDirectionContainerType* gradients - = diffImage->GetDirections(); + FilterType::GradientListType gradientList; + mitk::DiffusionImage::GradientDirectionContainerType* gradients + = diffImage->GetDirections(); - // Copy gradients vectors from gradients to gradientList - for(int i=0; iSize(); i++) - { - mitk::DiffusionImage::GradientDirectionType vec = gradients->at(i); - itk::Vector grad; + // Copy gradients vectors from gradients to gradientList + for(int i=0; iSize(); i++) + { + mitk::DiffusionImage::GradientDirectionType vec = gradients->at(i); + itk::Vector grad; - grad[0] = vec[0]; - grad[1] = vec[1]; - grad[2] = vec[2]; + grad[0] = vec[0]; + grad[1] = vec[1]; + grad[2] = vec[2]; - gradientList.push_back(grad); - } + gradientList.push_back(grad); + } - // Find the min and the max values from a baseline image - mitk::ImageStatisticsHolder *stats = diffImage->GetStatistics(); + // Find the min and the max values from a baseline image + mitk::ImageStatisticsHolder *stats = diffImage->GetStatistics(); - //Initialize filter that calculates the modeled diffusion weighted signals - FilterType::Pointer filter = FilterType::New(); - filter->SetInput( tensorImage ); - filter->SetBValue(diffImage->GetB_Value()); - filter->SetGradientList(gradientList); - filter->SetMin(stats->GetScalarValueMin()); - filter->SetMax(500); - filter->Update(); + //Initialize filter that calculates the modeled diffusion weighted signals + FilterType::Pointer filter = FilterType::New(); + filter->SetInput( tensorImage ); + filter->SetBValue(diffImage->GetB_Value()); + filter->SetGradientList(gradientList); + filter->SetMin(stats->GetScalarValueMin()); + filter->SetMax(500); + filter->Update(); - // TENSORS TO DATATREE - mitk::DiffusionImage::Pointer image = mitk::DiffusionImage::New(); - image->SetVectorImage( filter->GetOutput() ); - image->SetB_Value(diffImage->GetB_Value()); - image->SetDirections(gradientList); - image->SetOriginalDirections(gradientList); - image->InitializeFromVectorImage(); - mitk::DataNode::Pointer node = mitk::DataNode::New(); - node->SetData( image ); - mitk::DiffusionImageMapper::SetDefaultProperties(node); + // TENSORS TO DATATREE + mitk::DiffusionImage::Pointer image = mitk::DiffusionImage::New(); + image->SetVectorImage( filter->GetOutput() ); + image->SetB_Value(diffImage->GetB_Value()); + image->SetDirections(gradientList); + image->SetOriginalDirections(gradientList); + image->InitializeFromVectorImage(); + mitk::DataNode::Pointer node = mitk::DataNode::New(); + node->SetData( image ); + mitk::DiffusionImageMapper::SetDefaultProperties(node); - QString newname; - newname = newname.append(nodename.c_str()); - newname = newname.append("_dwi"); - node->SetName(newname.toAscii()); + QString newname; + newname = newname.append(nodename.c_str()); + newname = newname.append("_dwi"); + node->SetName(newname.toAscii()); - GetDefaultDataStorage()->Add(node); + GetDefaultDataStorage()->Add(node); - std::vector b0Indices = image->GetB0Indices(); + std::vector b0Indices = image->GetB0Indices(); - typedef itk::ResidualImageFilter ResidualImageFilterType; + typedef itk::ResidualImageFilter ResidualImageFilterType; - ResidualImageFilterType::Pointer residualFilter = ResidualImageFilterType::New(); - residualFilter->SetInput(diffImage->GetVectorImage()); - residualFilter->SetSecondDiffusionImage(image->GetVectorImage()); - residualFilter->SetGradients(gradients); - residualFilter->SetB0Index(b0Indices[0]); - residualFilter->SetB0Threshold(30); - residualFilter->Update(); + ResidualImageFilterType::Pointer residualFilter = ResidualImageFilterType::New(); + residualFilter->SetInput(diffImage->GetVectorImage()); + residualFilter->SetSecondDiffusionImage(image->GetVectorImage()); + residualFilter->SetGradients(gradients); + residualFilter->SetB0Index(b0Indices[0]); + residualFilter->SetB0Threshold(30); + residualFilter->Update(); - itk::Image::Pointer residualImage = itk::Image::New(); - residualImage = residualFilter->GetOutput(); + itk::Image::Pointer residualImage = itk::Image::New(); + residualImage = residualFilter->GetOutput(); - mitk::Image::Pointer mitkResImg = mitk::Image::New(); + mitk::Image::Pointer mitkResImg = mitk::Image::New(); - mitk::CastToMitkImage(residualImage, mitkResImg); + mitk::CastToMitkImage(residualImage, mitkResImg); - stats = mitkResImg->GetStatistics(); - float min = stats->GetScalarValueMin(); - float max = stats->GetScalarValueMax(); + stats = mitkResImg->GetStatistics(); + float min = stats->GetScalarValueMin(); + float max = stats->GetScalarValueMax(); - mitk::LookupTableProperty::Pointer lutProp = mitk::LookupTableProperty::New(); - mitk::LookupTable::Pointer lut = mitk::LookupTable::New(); + mitk::LookupTableProperty::Pointer lutProp = mitk::LookupTableProperty::New(); + mitk::LookupTable::Pointer lut = mitk::LookupTable::New(); - vtkSmartPointer lookupTable = - vtkSmartPointer::New(); + vtkSmartPointer lookupTable = + vtkSmartPointer::New(); - lookupTable->SetTableRange(min, max); + lookupTable->SetTableRange(min, max); - // If you don't want to use the whole color range, you can use - // SetValueRange, SetHueRange, and SetSaturationRange - lookupTable->Build(); + // If you don't want to use the whole color range, you can use + // SetValueRange, SetHueRange, and SetSaturationRange + lookupTable->Build(); - int size = lookupTable->GetTable()->GetSize(); + int size = lookupTable->GetTable()->GetSize(); - vtkSmartPointer reversedlookupTable = - vtkSmartPointer::New(); - reversedlookupTable->SetTableRange(min+1, max); - reversedlookupTable->Build(); + vtkSmartPointer reversedlookupTable = + vtkSmartPointer::New(); + reversedlookupTable->SetTableRange(min+1, max); + reversedlookupTable->Build(); - for(int i=0; i<256; i++) - { - double* rgba = reversedlookupTable->GetTableValue(255-i); + for(int i=0; i<256; i++) + { + double* rgba = reversedlookupTable->GetTableValue(255-i); - lookupTable->SetTableValue(i, rgba[0], rgba[1], rgba[2], rgba[3]); - } + lookupTable->SetTableValue(i, rgba[0], rgba[1], rgba[2], rgba[3]); + } - lut->SetVtkLookupTable(lookupTable); - lutProp->SetLookupTable(lut); + lut->SetVtkLookupTable(lookupTable); + lutProp->SetLookupTable(lut); - // Create lookuptable + // Create lookuptable - mitk::DataNode::Pointer resNode=mitk::DataNode::New(); - resNode->SetData( mitkResImg ); - resNode->SetName("Residual Image"); + mitk::DataNode::Pointer resNode=mitk::DataNode::New(); + resNode->SetData( mitkResImg ); + resNode->SetName("Residual Image"); - resNode->SetProperty("LookupTable", lutProp); + resNode->SetProperty("LookupTable", lutProp); - bool b; - resNode->GetBoolProperty("use color", b); - resNode->SetBoolProperty("use color", false); + bool b; + resNode->GetBoolProperty("use color", b); + resNode->SetBoolProperty("use color", false); - GetDefaultDataStorage()->Add(resNode); + GetDefaultDataStorage()->Add(resNode); - m_MultiWidget->RequestUpdate(); + m_MultiWidget->RequestUpdate(); - // Draw Graph - std::vector means = residualFilter->GetMeans(); - std::vector q1s = residualFilter->GetQ1(); - std::vector q3s = residualFilter->GetQ3(); - std::vector percentagesOfOUtliers = residualFilter->GetPercentagesOfOutliers(); + // Draw Graph + std::vector means = residualFilter->GetMeans(); + std::vector q1s = residualFilter->GetQ1(); + std::vector q3s = residualFilter->GetQ3(); + std::vector percentagesOfOUtliers = residualFilter->GetPercentagesOfOutliers(); - m_Controls->m_ResidualAnalysis->SetMeans(means); - m_Controls->m_ResidualAnalysis->SetQ1(q1s); - m_Controls->m_ResidualAnalysis->SetQ3(q3s); - m_Controls->m_ResidualAnalysis->SetPercentagesOfOutliers(percentagesOfOUtliers); + m_Controls->m_ResidualAnalysis->SetMeans(means); + m_Controls->m_ResidualAnalysis->SetQ1(q1s); + m_Controls->m_ResidualAnalysis->SetQ3(q3s); + m_Controls->m_ResidualAnalysis->SetPercentagesOfOutliers(percentagesOfOUtliers); - if(m_Controls->m_PercentagesOfOutliers->isChecked()) - { - m_Controls->m_ResidualAnalysis->DrawPercentagesOfOutliers(); - } - else - { - m_Controls->m_ResidualAnalysis->DrawMeans(); - } + if(m_Controls->m_PercentagesOfOutliers->isChecked()) + { + m_Controls->m_ResidualAnalysis->DrawPercentagesOfOutliers(); + } + else + { + m_Controls->m_ResidualAnalysis->DrawMeans(); + } - // Draw Graph for volumes per slice in the QGraphicsView - std::vector< std::vector > outliersPerSlice = residualFilter->GetOutliersPerSlice(); - int xSize = outliersPerSlice.size(); - if(xSize == 0) - { - return; - } - int ySize = outliersPerSlice[0].size(); + // Draw Graph for volumes per slice in the QGraphicsView + std::vector< std::vector > outliersPerSlice = residualFilter->GetOutliersPerSlice(); + int xSize = outliersPerSlice.size(); + if(xSize == 0) + { + return; + } + int ySize = outliersPerSlice[0].size(); - // Find maximum in outliersPerSlice - double maxOutlier= 0.0; - for(int i=0; imaxOutlier) { - if(outliersPerSlice[i][j]>maxOutlier) - { - maxOutlier = outliersPerSlice[i][j]; - } + maxOutlier = outliersPerSlice[i][j]; } } + } - // Create some QImage - QImage qImage(xSize, ySize, QImage::Format_RGB32); - QImage legend(1, 256, QImage::Format_RGB32); - QRgb value; + // Create some QImage + QImage qImage(xSize, ySize, QImage::Format_RGB32); + QImage legend(1, 256, QImage::Format_RGB32); + QRgb value; - vtkSmartPointer lookup = - vtkSmartPointer::New(); + vtkSmartPointer lookup = + vtkSmartPointer::New(); - lookup->SetTableRange(0.0, maxOutlier); - lookup->Build(); + lookup->SetTableRange(0.0, maxOutlier); + lookup->Build(); - reversedlookupTable->SetTableRange(0, maxOutlier); - reversedlookupTable->Build(); + reversedlookupTable->SetTableRange(0, maxOutlier); + reversedlookupTable->Build(); - for(int i=0; i<256; i++) - { - double* rgba = reversedlookupTable->GetTableValue(255-i); - lookup->SetTableValue(i, rgba[0], rgba[1], rgba[2], rgba[3]); - } + for(int i=0; i<256; i++) + { + double* rgba = reversedlookupTable->GetTableValue(255-i); + lookup->SetTableValue(i, rgba[0], rgba[1], rgba[2], rgba[3]); + } - // Fill qImage - for(int i=0; iMapValue(out); - int r, g, b; - r = _rgba[0]; - g = _rgba[1]; - b = _rgba[2]; + double out = outliersPerSlice[i][j]; - value = qRgb(r, g, b); - - qImage.setPixel(i,j,value); - - } - } - - for(int i=0; i<256; i++) - { - double* rgba = lookup->GetTableValue(i); + unsigned char *_rgba = lookup->MapValue(out); int r, g, b; - r = rgba[0]*255; - g = rgba[1]*255; - b = rgba[2]*255; + r = _rgba[0]; + g = _rgba[1]; + b = _rgba[2]; + value = qRgb(r, g, b); - legend.setPixel(0,255-i,value); - } - QString upper = QString::number(maxOutlier, 'g', 3); - upper.append(" %"); - QString lower = QString::number(0.0); - lower.append(" %"); - m_Controls->m_UpperLabel->setText(upper); - m_Controls->m_LowerLabel->setText(lower); + qImage.setPixel(i,j,value); - QGraphicsScene* scene = new QGraphicsScene; - QGraphicsScene* scene2 = new QGraphicsScene; + } + } + for(int i=0; i<256; i++) + { + double* rgba = lookup->GetTableValue(i); + int r, g, b; + r = rgba[0]*255; + g = rgba[1]*255; + b = rgba[2]*255; + value = qRgb(r, g, b); + legend.setPixel(0,255-i,value); + } - QPixmap pixmap(QPixmap::fromImage(qImage)); - QGraphicsPixmapItem *item = new QGraphicsPixmapItem( pixmap, 0, scene); - item->scale(10.0, 3.0); + QString upper = QString::number(maxOutlier, 'g', 3); + upper.append(" %"); + QString lower = QString::number(0.0); + lower.append(" %"); + m_Controls->m_UpperLabel->setText(upper); + m_Controls->m_LowerLabel->setText(lower); - QPixmap pixmap2(QPixmap::fromImage(legend)); - QGraphicsPixmapItem *item2 = new QGraphicsPixmapItem( pixmap2, 0, scene2); - item2->scale(20.0, 1.0); + QGraphicsScene* scene = new QGraphicsScene; + QGraphicsScene* scene2 = new QGraphicsScene; - m_Controls->m_PerSliceView->SetResidualPixmapItem(item); + QPixmap pixmap(QPixmap::fromImage(qImage)); + QGraphicsPixmapItem *item = new QGraphicsPixmapItem( pixmap, 0, scene); + item->scale(10.0, 3.0); + QPixmap pixmap2(QPixmap::fromImage(legend)); + QGraphicsPixmapItem *item2 = new QGraphicsPixmapItem( pixmap2, 0, scene2); + item2->scale(20.0, 1.0); - m_Controls->m_PerSliceView->setScene(scene); - m_Controls->m_LegendView->setScene(scene2); - m_Controls->m_PerSliceView->show(); - m_Controls->m_PerSliceView->repaint(); + m_Controls->m_PerSliceView->SetResidualPixmapItem(item); - m_Controls->m_LegendView->setHorizontalScrollBarPolicy ( Qt::ScrollBarAlwaysOff ); - m_Controls->m_LegendView->setVerticalScrollBarPolicy ( Qt::ScrollBarAlwaysOff ); - m_Controls->m_LegendView->show(); - m_Controls->m_LegendView->repaint(); - } + m_Controls->m_PerSliceView->setScene(scene); + m_Controls->m_LegendView->setScene(scene2); + m_Controls->m_PerSliceView->show(); + m_Controls->m_PerSliceView->repaint(); + m_Controls->m_LegendView->setHorizontalScrollBarPolicy ( Qt::ScrollBarAlwaysOff ); + m_Controls->m_LegendView->setVerticalScrollBarPolicy ( Qt::ScrollBarAlwaysOff ); + m_Controls->m_LegendView->show(); + m_Controls->m_LegendView->repaint(); } void QmitkTensorReconstructionView::ItkReconstruction() { Reconstruct(0); } void QmitkTensorReconstructionView::TeemReconstruction() { Reconstruct(1); } +void QmitkTensorReconstructionView::ReconstructionWithCorrection() +{ + Reconstruct(2); +} + void QmitkTensorReconstructionView::Reconstruct(int method) { - if (m_CurrentSelection) + if(method == 0) + ItkTensorReconstruction(m_DiffusionImages); + + + if(method == 1) + TeemTensorReconstruction(m_DiffusionImages); + + if(method == 2) { - mitk::DataStorage::SetOfObjects::Pointer set = - mitk::DataStorage::SetOfObjects::New(); + TensorReconstructionWithCorr(m_DiffusionImages); + } - int at = 0; - for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); - i != m_CurrentSelection->End(); - ++i) - { + +} - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) - { - set->InsertElement(at++, node); - } - } - } +void QmitkTensorReconstructionView::TensorReconstructionWithCorr +(mitk::DataStorage::SetOfObjects::Pointer inImages) +{ + try + { + itk::TimeProbe clock; - if(method == 0) - { - ItkTensorReconstruction(set); - } + int nrFiles = inImages->size(); + if (!nrFiles) return; + + QString status; + mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); - if(method == 1) + mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); + mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); + + std::vector nodes; + while ( itemiter != itemiterend ) // for all items { - TeemTensorReconstruction(set); + + mitk::DiffusionImage* vols = + static_cast*>( + (*itemiter)->GetData()); + + std::string nodename; + (*itemiter)->GetStringProperty("name", nodename); + ++itemiter; + + // TENSOR RECONSTRUCTION + clock.Start(); + MBI_INFO << "Tensor reconstruction with correction for negative eigenvalues"; + mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( + "Tensor reconstruction for %s", nodename.c_str()).toAscii()); + + typedef itk::TensorReconstructionWithEigenvalueCorrectionFilter< + DiffusionPixelType, TTensorPixelType > ReconstructionFilter; + + float b0Threshold = m_Controls->m_ReconstructionThreshold->text().toFloat(); + + ReconstructionFilter::Pointer reconFilter = ReconstructionFilter::New(); + reconFilter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() ); + reconFilter->SetBValue(vols->GetB_Value()); + reconFilter->SetB0Threshold(b0Threshold); + reconFilter->Update(); + + itk::Image,3>::Pointer outputTensorImg = reconFilter->GetOutput(); + + + mitk::TensorImage::Pointer image = mitk::TensorImage::New(); + image->InitializeByItk( outputTensorImg.GetPointer() ); + image->SetVolume( outputTensorImg->GetBufferPointer() ); + mitk::DataNode::Pointer node=mitk::DataNode::New(); + node->SetData( image ); + + QString newname; + newname = newname.append(nodename.c_str()); + newname = newname.append("_dti"); + + SetDefaultNodeProperties(node, newname.toStdString()); + nodes.push_back(node); + + + mitk::ProgressBar::GetInstance()->Progress(); + } + std::vector::iterator nodeIt; + for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) + GetDefaultDataStorage()->Add(*nodeIt); + + mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); + m_MultiWidget->RequestUpdate(); + + } + catch (itk::ExceptionObject &ex) + { + MBI_INFO << ex ; + return ; } + } void QmitkTensorReconstructionView::ItkTensorReconstruction (mitk::DataStorage::SetOfObjects::Pointer inImages) { try { itk::TimeProbe clock; int nrFiles = inImages->size(); if (!nrFiles) return; QString status; mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = - static_cast*>( - (*itemiter)->GetData()); + static_cast*>( + (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); ++itemiter; // TENSOR RECONSTRUCTION clock.Start(); MBI_INFO << "Tensor reconstruction "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( - "Tensor reconstruction for %s", nodename.c_str()).toAscii()); + "Tensor reconstruction for %s", nodename.c_str()).toAscii()); typedef itk::DiffusionTensor3DReconstructionImageFilter< - DiffusionPixelType, DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType; + DiffusionPixelType, DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter = - TensorReconstructionImageFilterType::New(); - - - mitk::DiffusionImage::GradientDirectionContainerType::Pointer dirs = vols->GetDirections(); - itk::VectorImage::Pointer img = vols->GetVectorImage(); - + TensorReconstructionImageFilterType::New(); tensorReconstructionFilter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() ); tensorReconstructionFilter->SetBValue(vols->GetB_Value()); tensorReconstructionFilter->SetThreshold( m_Controls->m_TensorReconstructionThreasholdEdit->text().toFloat() ); tensorReconstructionFilter->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s."; // TENSORS TO DATATREE mitk::TensorImage::Pointer image = mitk::TensorImage::New(); typedef itk::Image, 3> TensorImageType; TensorImageType::Pointer tensorImage; tensorImage = tensorReconstructionFilter->GetOutput(); // Check the tensor for negative eigenvalues if(m_Controls->m_CheckNegativeEigenvalues->isChecked()) { typedef itk::ImageRegionIterator TensorImageIteratorType; TensorImageIteratorType tensorIt(tensorImage, tensorImage->GetRequestedRegion()); tensorIt.GoToBegin(); while(!tensorIt.IsAtEnd()) { typedef itk::DiffusionTensor3D TensorType; //typedef itk::Tensor TensorType2; TensorType tensor = tensorIt.Get(); - // TensorType2 tensor2; + // TensorType2 tensor2; /* for(int i=0; i SymEigenSystemType; SymEigenSystemType eig (tensor2.GetVnlMatrix()); for(unsigned int i=0; iInitializeByItk( tensorImage.GetPointer() ); image->SetVolume( tensorReconstructionFilter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); QString newname; newname = newname.append(nodename.c_str()); newname = newname.append("_dti"); SetDefaultNodeProperties(node, newname.toStdString()); nodes.push_back(node); mitk::ProgressBar::GetInstance()->Progress(); } std::vector::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); m_MultiWidget->RequestUpdate(); } catch (itk::ExceptionObject &ex) { MBI_INFO << ex ; return ; } } void QmitkTensorReconstructionView::TeemTensorReconstruction (mitk::DataStorage::SetOfObjects::Pointer inImages) { try { itk::TimeProbe clock; int nrFiles = inImages->size(); if (!nrFiles) return; QString status; mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = - static_cast*>( - (*itemiter)->GetData()); + static_cast*>( + (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); ++itemiter; // TENSOR RECONSTRUCTION clock.Start(); MBI_INFO << "Teem Tensor reconstruction "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( - "Teem Tensor reconstruction for %s", nodename.c_str()).toAscii()); + "Teem Tensor reconstruction for %s", nodename.c_str()).toAscii()); typedef mitk::TeemDiffusionTensor3DReconstructionImageFilter< - DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType; + DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter = - TensorReconstructionImageFilterType::New(); + TensorReconstructionImageFilterType::New(); tensorReconstructionFilter->SetInput( vols ); if(!m_Controls->m_TensorEstimationTeemSigmaEdit->text().contains(QString("NaN"))) tensorReconstructionFilter->SetSigma( m_Controls->m_TensorEstimationTeemSigmaEdit->text().toFloat() ); switch(m_Controls->m_TensorEstimationTeemEstimationMethodCombo->currentIndex()) { - // items << "LLS (Linear Least Squares)" - //<< "MLE (Maximum Likelihood)" - //<< "NLS (Nonlinear Least Squares)" - //<< "WLS (Weighted Least Squares)"; + // items << "LLS (Linear Least Squares)" + //<< "MLE (Maximum Likelihood)" + //<< "NLS (Nonlinear Least Squares)" + //<< "WLS (Weighted Least Squares)"; case 0: tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsLLS); break; case 1: tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsMLE); break; case 2: tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsNLS); break; case 3: tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsWLS); break; default: tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsLLS); } tensorReconstructionFilter->SetNumIterations( m_Controls->m_TensorEstimationTeemNumItsSpin->value() ); if(m_Controls->m_TensorEstimationManualThreashold->isChecked()) tensorReconstructionFilter->SetConfidenceThreshold( m_Controls->m_TensorReconstructionThreasholdEdit_2->text().toDouble() ); tensorReconstructionFilter->SetConfidenceFuzzyness( m_Controls->m_TensorEstimationTeemFuzzyEdit->text().toFloat() ); tensorReconstructionFilter->SetMinPlausibleValue( m_Controls->m_TensorEstimationTeemMinValEdit->text().toDouble() ); tensorReconstructionFilter->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s." ; // TENSORS TO DATATREE mitk::DataNode::Pointer node2=mitk::DataNode::New(); node2->SetData( tensorReconstructionFilter->GetOutputItk() ); QString newname; newname = newname.append(nodename.c_str()); newname = newname.append("_dtix"); SetDefaultNodeProperties(node2, newname.toStdString()); nodes.push_back(node2); mitk::ProgressBar::GetInstance()->Progress(); } std::vector::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); m_MultiWidget->RequestUpdate(); } catch (itk::ExceptionObject &ex) { MBI_INFO << ex ; return ; } } void QmitkTensorReconstructionView::SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name) { node->SetProperty( "ShowMaxNumber", mitk::IntProperty::New( 500 ) ); node->SetProperty( "Scaling", mitk::FloatProperty::New( 1.0 ) ); node->SetProperty( "Normalization", mitk::OdfNormalizationMethodProperty::New()); node->SetProperty( "ScaleBy", mitk::OdfScaleByProperty::New()); node->SetProperty( "IndexParam1", mitk::FloatProperty::New(2)); node->SetProperty( "IndexParam2", mitk::FloatProperty::New(1)); node->SetProperty( "visible", mitk::BoolProperty::New( true ) ); node->SetProperty( "VisibleOdfs", mitk::BoolProperty::New( false ) ); node->SetProperty ("layer", mitk::IntProperty::New(100)); node->SetProperty( "DoRefresh", mitk::BoolProperty::New( true ) ); //node->SetProperty( "opacity", mitk::FloatProperty::New(1.0f) ); node->SetProperty( "name", mitk::StringProperty::New(name) ); } //node->SetProperty( "volumerendering", mitk::BoolProperty::New( false ) ); //node->SetProperty( "use color", mitk::BoolProperty::New( true ) ); //node->SetProperty( "texture interpolation", mitk::BoolProperty::New( true ) ); //node->SetProperty( "reslice interpolation", mitk::VtkResliceInterpolationProperty::New() ); //node->SetProperty( "layer", mitk::IntProperty::New(0)); //node->SetProperty( "in plane resample extent by geometry", mitk::BoolProperty::New( false ) ); //node->SetOpacity(1.0f); //node->SetColor(1.0,1.0,1.0); //node->SetVisibility(true); //node->SetProperty( "IsTensorVolume", mitk::BoolProperty::New( true ) ); //mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New(); //mitk::LevelWindow levelwindow; //// levelwindow.SetAuto( image ); //levWinProp->SetLevelWindow( levelwindow ); //node->GetPropertyList()->SetProperty( "levelwindow", levWinProp ); //// add a default rainbow lookup table for color mapping //if(!node->GetProperty("LookupTable")) //{ // mitk::LookupTable::Pointer mitkLut = mitk::LookupTable::New(); // vtkLookupTable* vtkLut = mitkLut->GetVtkLookupTable(); // vtkLut->SetHueRange(0.6667, 0.0); // vtkLut->SetTableRange(0.0, 20.0); // vtkLut->Build(); // mitk::LookupTableProperty::Pointer mitkLutProp = mitk::LookupTableProperty::New(); // mitkLutProp->SetLookupTable(mitkLut); // node->SetProperty( "LookupTable", mitkLutProp ); //} //if(!node->GetProperty("binary")) // node->SetProperty( "binary", mitk::BoolProperty::New( false ) ); //// add a default transfer function //mitk::TransferFunction::Pointer tf = mitk::TransferFunction::New(); //node->SetProperty ( "TransferFunction", mitk::TransferFunctionProperty::New ( tf.GetPointer() ) ); //// set foldername as string property //mitk::StringProperty::Pointer nameProp = mitk::StringProperty::New( name ); //node->SetProperty( "name", nameProp ); void QmitkTensorReconstructionView::TensorsToDWI() { - if (m_CurrentSelection) - { - mitk::DataStorage::SetOfObjects::Pointer set = - mitk::DataStorage::SetOfObjects::New(); - - int at = 0; - for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); - i != m_CurrentSelection->End(); - ++i) - { - - if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) - { - mitk::DataNode::Pointer node = nodeObj->GetDataNode(); - // process only on valid nodes - const mitk::BaseData* nodeData = node->GetData(); - if(nodeData) - { - if(QString("TensorImage").compare(nodeData->GetNameOfClass())==0) - { - set->InsertElement(at++, node); - } - } - } - } - - DoTensorsToDWI(set); - } + DoTensorsToDWI(m_TensorImages); } void QmitkTensorReconstructionView::TensorsToQbi() { - std::vector nodes = this->GetDataManagerSelection(); - for (int i=0; isize(); i++) { - mitk::DataNode::Pointer tensorImageNode = nodes.at(i); + mitk::DataNode::Pointer tensorImageNode = m_TensorImages->at(i); MITK_INFO << "starting Q-Ball estimation"; typedef float TTensorPixelType; typedef itk::DiffusionTensor3D< TTensorPixelType > TensorPixelType; typedef itk::Image< TensorPixelType, 3 > TensorImageType; TensorImageType::Pointer itkvol = TensorImageType::New(); mitk::CastToItkImage(dynamic_cast(tensorImageNode->GetData()), itkvol); typedef itk::TensorImageToQBallImageFilter< TTensorPixelType, TTensorPixelType > FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkvol ); filter->Update(); typedef itk::Vector OutputPixelType; typedef itk::Image OutputImageType; mitk::QBallImage::Pointer image = mitk::QBallImage::New(); OutputImageType::Pointer outimg = filter->GetOutput(); image->InitializeByItk( outimg.GetPointer() ); image->SetVolume( outimg->GetBufferPointer() ); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); QString newname; newname = newname.append(tensorImageNode->GetName().c_str()); newname = newname.append("_qbi"); node->SetName(newname.toAscii()); GetDefaultDataStorage()->Add(node); } } void QmitkTensorReconstructionView::OnSelectionChanged( std::vector nodes ) { if ( !this->IsVisible() ) return; + m_DiffusionImages = mitk::DataStorage::SetOfObjects::New(); + m_TensorImages = mitk::DataStorage::SetOfObjects::New(); + bool foundDwiVolume = false; + bool foundTensorVolume = false; + m_Controls->m_DiffusionImageLabel->setText("-"); + m_Controls->m_TensorImageLabel->setText("-"); + m_DiffusionImage = NULL; + m_TensorImage = NULL; + + // iterate selection + for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) + { + mitk::DataNode::Pointer node = *it; + if (node.IsNull()) + continue; + + // only look at interesting types + if(dynamic_cast*>(node->GetData())) + { + foundDwiVolume = true; + m_Controls->m_DiffusionImageLabel->setText(node->GetName().c_str()); + m_DiffusionImages->push_back(node); + m_DiffusionImage = node; + } + else if(dynamic_cast(node->GetData())) + { + foundTensorVolume = true; + m_Controls->m_TensorImageLabel->setText(node->GetName().c_str()); + m_TensorImages->push_back(node); + m_TensorImage = node; + } + } + + m_Controls->m_ItkReconstruction->setEnabled(foundDwiVolume); + m_Controls->m_TeemReconstruction->setEnabled(foundDwiVolume); + + m_Controls->m_TensorsToDWIButton->setEnabled(foundTensorVolume); + m_Controls->m_TensorsToQbiButton->setEnabled(foundTensorVolume); + + + m_Controls->m_ResidualButton->setEnabled(foundDwiVolume && foundTensorVolume); + m_Controls->m_PercentagesOfOutliers->setEnabled(foundDwiVolume && foundTensorVolume); + m_Controls->m_PerSliceView->setEnabled(foundDwiVolume && foundTensorVolume); } template std::vector > QmitkTensorReconstructionView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = - itk::PointShell >::DistributePointShell(); + itk::PointShell >::DistributePointShell(); for(int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } // Add 0 vector for B0 itk::Vector v; v.Fill(0.0); retval.push_back(v); return retval; } void QmitkTensorReconstructionView::DoTensorsToDWI (mitk::DataStorage::SetOfObjects::Pointer inImages) { try { itk::TimeProbe clock; int nrFiles = inImages->size(); if (!nrFiles) return; QString status; mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { std::string nodename; (*itemiter)->GetStringProperty("name", nodename); mitk::TensorImage* vol = - static_cast((*itemiter)->GetData()); + static_cast((*itemiter)->GetData()); ++itemiter; typedef float TTensorPixelType; typedef itk::DiffusionTensor3D< TTensorPixelType > TensorPixelType; typedef itk::Image< TensorPixelType, 3 > TensorImageType; TensorImageType::Pointer itkvol = TensorImageType::New(); mitk::CastToItkImage(vol, itkvol); typedef itk::TensorImageToDiffusionImageFilter< - TTensorPixelType, DiffusionPixelType > FilterType; + TTensorPixelType, DiffusionPixelType > FilterType; FilterType::GradientListType gradientList; switch(m_Controls->m_TensorsToDWINumDirsSelect->currentIndex()) { case 0: gradientList = MakeGradientList<12>(); break; case 1: gradientList = MakeGradientList<42>(); break; case 2: gradientList = MakeGradientList<92>(); break; case 3: gradientList = MakeGradientList<162>(); break; case 4: gradientList = MakeGradientList<252>(); break; case 5: gradientList = MakeGradientList<362>(); break; case 6: gradientList = MakeGradientList<492>(); break; case 7: gradientList = MakeGradientList<642>(); break; case 8: gradientList = MakeGradientList<812>(); break; case 9: gradientList = MakeGradientList<1002>(); break; default: gradientList = MakeGradientList<92>(); } double bVal = m_Controls->m_TensorsToDWIBValueEdit->text().toDouble(); // DWI ESTIMATION clock.Start(); MBI_INFO << "DWI Estimation "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( - "DWI Estimation for %s", nodename.c_str()).toAscii()); + "DWI Estimation for %s", nodename.c_str()).toAscii()); FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkvol ); filter->SetBValue(bVal); filter->SetGradientList(gradientList); //filter->SetNumberOfThreads(1); filter->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s."; // TENSORS TO DATATREE mitk::DiffusionImage::Pointer image = mitk::DiffusionImage::New(); image->SetVectorImage( filter->GetOutput() ); image->SetB_Value(bVal); image->SetDirections(gradientList); image->SetOriginalDirections(gradientList); image->InitializeFromVectorImage(); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); mitk::DiffusionImageMapper::SetDefaultProperties(node); QString newname; newname = newname.append(nodename.c_str()); newname = newname.append("_dwi"); node->SetName(newname.toAscii()); nodes.push_back(node); mitk::ProgressBar::GetInstance()->Progress(); } std::vector::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); m_MultiWidget->RequestUpdate(); } catch (itk::ExceptionObject &ex) { MBI_INFO << ex ; return ; } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.h index 8afe39952d..afbe6f821d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.h @@ -1,125 +1,127 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _QMITKTENSORRECONSTRUCTIONVIEW_H_INCLUDED #define _QMITKTENSORRECONSTRUCTIONVIEW_H_INCLUDED #include #include #include "ui_QmitkTensorReconstructionViewControls.h" #include #include -#include -#include -#include - typedef short DiffusionPixelType; struct TrSelListener; /*! * \ingroup org_mitk_gui_qt_tensorreconstruction_internal * * \brief QmitkTensorReconstructionView * * Document your class here. * * \sa QmitkFunctionality */ class QmitkTensorReconstructionView : public QmitkFunctionality { friend struct TrSelListener; // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; QmitkTensorReconstructionView(); QmitkTensorReconstructionView(const QmitkTensorReconstructionView& other); virtual ~QmitkTensorReconstructionView(); virtual void CreateQtPartControl(QWidget *parent); /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); static const int nrconvkernels; protected slots: void TensorsToQbi(); void TensorsToDWI(); void DoTensorsToDWI(mitk::DataStorage::SetOfObjects::Pointer inImages); void TeemCheckboxClicked(); void Advanced1CheckboxClicked(); void Advanced2CheckboxClicked(); + void Advanced3CheckboxClicked(); void ManualThresholdClicked(); void MethodChoosen(int method); void Reconstruct(int method); void TeemReconstruction(); void ItkReconstruction(); + void ReconstructionWithCorrection(); void ResidualCalculation(); void ResidualClicked(int slice, int volume); protected: void ItkTensorReconstruction (mitk::DataStorage::SetOfObjects::Pointer inImages); void TeemTensorReconstruction + (mitk::DataStorage::SetOfObjects::Pointer inImages); + void TensorReconstructionWithCorr (mitk::DataStorage::SetOfObjects::Pointer inImages); void OnSelectionChanged( std::vector nodes ); Ui::QmitkTensorReconstructionViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; template std::vector > MakeGradientList() ; template void TemplatedAnalyticalTensorReconstruction(mitk::DiffusionImage* vols, float lambda, std::string nodename, std::vector* nodes, int normalization); void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name); - berry::ISelectionListener::Pointer m_SelListener; - berry::IStructuredSelection::ConstPointer m_CurrentSelection; + mitk::DataNode::Pointer m_DiffusionImage; + mitk::DataNode::Pointer m_TensorImage; + mitk::DataStorage::SetOfObjects::Pointer m_DiffusionImages; + mitk::DataStorage::SetOfObjects::Pointer m_TensorImages; }; #endif // _QMITKTENSORRECONSTRUCTIONVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionViewControls.ui index 23f2ebb31f..323796533b 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionViewControls.ui @@ -1,696 +1,790 @@ QmitkTensorReconstructionViewControls 0 0 - 345 + 363 1303 0 0 true QmitkTensorReconstructionViewControls - + + + + + Data: + + + + + + Diffusion Image: + + + + + + + - + + + + + + + Tensor Image: + + + + + + + - + + + + + + ITK Reconstruction Advanced Settings false QFrame::StyledPanel QFrame::Raised QFormLayout::AllNonFixedFieldsGrow B0 Threshold false 0 Check for negative eigenvalues QFrame::StyledPanel QFrame::Raised false ITK Tensor Reconstruction Estimate Diffusion Image from Tensors QFrame::StyledPanel QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 6 9 how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0" how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0" how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0" B-Value false 0 0 how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0" how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0" how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0" # Gradient Directions 3 12 42 92 162 252 362 492 642 812 1002 false Diffusion Image Estimation Estimate Q-Ball Image from Tensors false Calculate ODF value as tensor value in the according direction Q-Ball Image Estimation + + + + Tensor reconstruction correction + + + + + + Advanced Settings + + + false + + + + + + + QFrame::StyledPanel + + + QFrame::Raised + + + + QFormLayout::AllNonFixedFieldsGrow + + + + + B0 Threshold + + + false + + + + + + + 50 + + + + + + + + + + false + + + + + + + + + + + + Reconstruction with correction + + + + + + true Teem Reconstruction true Teem Reconstruction Advanced Settings QFrame::StyledPanel QFrame::Raised QFormLayout::AllNonFixedFieldsGrow important in case of method wls # Iterations false how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0" how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0" how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0" Fuzzy confidence false 0 0 how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0" how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0" how fuzzy the confidence boundary should be. By default, confidence boundary is perfectly sharp (float); default: "0" minimum plausible value (especially important for linear least squares estimation) (double); default: "1.0" minimum plausible value (especially important for linear least squares estimation) (double); default: "1.0" minimum plausible value (especially important for linear least squares estimation) (double); default: "1.0" Min plausible value false Rician noise parameter (float) Rician noise parameter (float) Rician noise parameter (float) Sigma false 0 0 minimum plausible value (especially important for linear least squares estimation) (double); default: "1.0" minimum plausible value (especially important for linear least squares estimation) (double); default: "1.0" minimum plausible value (especially important for linear least squares estimation) (double); default: "1.0" 0 0 Rician noise parameter (float) Rician noise parameter (float) Rician noise parameter (float) Method B0-Threshold false 0 false Teem Tensor Reconstruction Residuals false false QFrame::StyledPanel QFrame::Raised false Calculate the residual from a dti and a dwi iimage Residual Image Calculation 1 Per volume 200 300 Per slice outliers per slice QFrame::StyledPanel QFrame::Raised 300 400 QFrame::StyledPanel QFrame::Raised 20 255 Volume: .., Slice:.. false percentages of error - - - - Qt::Vertical - - - - 20 - 1150 - - - - QmitkResidualAnalysisWidget QWidget
QmitkResidualAnalysisWidget.h
1 QmitkResidualViewWidget QGraphicsView
QmitkResidualViewWidget.h
 diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.diffusionimagingapp/manifest_headers.cmake index 3474a73b0d..6f2d820686 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/manifest_headers.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimagingapp/manifest_headers.cmake @@ -1,8 +1,8 @@ set(Plugin-Name "MITK Diffusion") set(Plugin-Version "1.0") set(Plugin-Vendor "DKFZ, Medical and Biological Informatics") set(Plugin-ContactAddress "http://www.mitk.org") -set(Require-Plugin org.mitk.gui.qt.ext org.mitk.gui.qt.stdmultiwidgeteditor) +set(Require-Plugin org.mitk.gui.qt.ext) set(Plugin-Activator QmitkDiffusionImagingAppApplicationPlugin) diff --git a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.cpp b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.cpp index f6d2bccbc0..c12bf82cdf 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimagingapp/src/internal/QmitkDiffusionImagingAppIntroPart.cpp @@ -1,184 +1,212 @@ /*========================================================================= Program: BlueBerry Platform Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkDiffusionImagingAppIntroPart.h" #include "mitkNodePredicateDataType.h" #include #include #include #include #include #include + #include +#include + +#include +#include #include #include #include #include #ifdef QT_WEBKIT #include #include #endif #include #include #include #include #include #include -#include "QmitkStdMultiWidget.h" -#include "QmitkStdMultiWidgetEditor.h" #include "QmitkDiffusionApplicationPlugin.h" #include "mitkDataStorageEditorInput.h" +#include #include "mitkBaseDataIOFactory.h" #include "mitkSceneIO.h" #include "mitkProgressBar.h" #include "mitkDataNodeFactory.h" #include "mitkNodePredicateNot.h" #include "mitkNodePredicateProperty.h" QmitkDiffusionImagingAppIntroPart::QmitkDiffusionImagingAppIntroPart() : m_Controls(NULL) { berry::IPreferences::Pointer workbenchPrefs = QmitkDiffusionApplicationPlugin::GetDefault()->GetPreferencesService()->GetSystemPreferences(); workbenchPrefs->PutBool(berry::WorkbenchPreferenceConstants::SHOW_INTRO, true); workbenchPrefs->Flush(); } QmitkDiffusionImagingAppIntroPart::~QmitkDiffusionImagingAppIntroPart() { // if the workbench is not closing (that means, welcome screen was closed explicitly), set "Show_intro" false if (!this->GetIntroSite()->GetPage()->GetWorkbenchWindow()->GetWorkbench()->IsClosing()) { berry::IPreferences::Pointer workbenchPrefs = QmitkDiffusionApplicationPlugin::GetDefault()->GetPreferencesService()->GetSystemPreferences(); workbenchPrefs->PutBool(berry::WorkbenchPreferenceConstants::SHOW_INTRO, false); workbenchPrefs->Flush(); } else { berry::IPreferences::Pointer workbenchPrefs = QmitkDiffusionApplicationPlugin::GetDefault()->GetPreferencesService()->GetSystemPreferences(); workbenchPrefs->PutBool(berry::WorkbenchPreferenceConstants::SHOW_INTRO, true); workbenchPrefs->Flush(); } // if workbench is not closing (Just welcome screen closing), open last used perspective if (this->GetIntroSite()->GetPage()->GetPerspective()->GetId() == "org.mitk.diffusionimagingapp.perspectives.welcome" && !this->GetIntroSite()->GetPage()->GetWorkbenchWindow()->GetWorkbench()->IsClosing()) { berry::IPerspectiveDescriptor::Pointer perspective = this->GetIntroSite()->GetWorkbenchWindow()->GetWorkbench()->GetPerspectiveRegistry()->FindPerspectiveWithId("org.mitk.diffusionimagingapp.perspectives.diffusionimagingapp"); if (perspective) { this->GetIntroSite()->GetPage()->SetPerspective(perspective); } } } void QmitkDiffusionImagingAppIntroPart::CreateQtPartControl(QWidget* parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkWelcomeScreenViewControls; m_Controls->setupUi(parent); #ifdef QT_WEBKIT // create a QWebView as well as a QWebPage and QWebFrame within the QWebview m_view = new QWebView(parent); m_view->page()->setLinkDelegationPolicy(QWebPage::DelegateAllLinks); QUrl urlQtResource(QString("qrc:/org.mitk.gui.qt.welcomescreen/mitkdiffusionimagingappwelcomeview.html"), QUrl::TolerantMode ); m_view->load( urlQtResource ); // adds the webview as a widget parent->layout()->addWidget(m_view); this->CreateConnections(); #else parent->layout()->addWidget(new QLabel("

Please install Qt with the WebKit option to see cool pictures!

")); #endif } } #ifdef QT_WEBKIT void QmitkDiffusionImagingAppIntroPart::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_view->page()), SIGNAL(linkClicked(const QUrl& )), this, SLOT(DelegateMeTo(const QUrl& )) ); } } void QmitkDiffusionImagingAppIntroPart::DelegateMeTo(const QUrl& showMeNext) { QString scheme = showMeNext.scheme(); QByteArray urlHostname = showMeNext.encodedHost(); QByteArray urlPath = showMeNext.encodedPath(); QByteArray dataset = showMeNext.encodedQueryItemValue("dataset"); QByteArray clear = showMeNext.encodedQueryItemValue("clear"); if (scheme.isEmpty()) MITK_INFO << " empty scheme of the to be delegated link" ; // if the scheme is set to mitk, it is to be tested which action should be applied if (scheme.contains(QString("mitk")) ) { if(urlPath.isEmpty() ) MITK_INFO << " mitk path is empty " ; // searching for the perspective keyword within the host name if(urlHostname.contains(QByteArray("perspectives")) ) { // the simplified method removes every whitespace // ( whitespace means any character for which the standard C++ isspace() method returns true) urlPath = urlPath.simplified(); QString tmpPerspectiveId(urlPath.data()); tmpPerspectiveId.replace(QString("/"), QString("") ); std::string perspectiveId = tmpPerspectiveId.toStdString(); // is working fine as long as the perspective id is valid, if not the application crashes GetIntroSite()->GetWorkbenchWindow()->GetWorkbench()->ShowPerspective(perspectiveId, GetIntroSite()->GetWorkbenchWindow() ); + + // search the Workbench for opened StdMultiWidgets to ensure the focus does not stay on the welcome screen and is switched to + // an StdMultiWidget if one available + mitk::IDataStorageService::Pointer service = + berry::Platform::GetServiceRegistry().GetServiceById(mitk::IDataStorageService::ID); + berry::IEditorInput::Pointer editorInput; + editorInput = new mitk::DataStorageEditorInput( service->GetActiveDataStorage() ); + + // the solution is not clean, but the dependency to the StdMultiWidget was removed in order to fix a crash problem + // as described in Bug #11715 + // This is the correct way : use the static string ID variable + // berry::IEditorPart::Pointer editor = GetIntroSite()->GetPage()->FindEditors( editorInput, QmitkStdMultiWidgetEditor::EDITOR_ID ); + // QuickFix: we use the same string for an local variable + const std::string stdEditorID = "org.mitk.editors.stdmultiwidget"; + + // search for opened StdMultiWidgetEditors + std::vector editorList = GetIntroSite()->GetPage()->FindEditors( editorInput, stdEditorID, 1 ); + + // if an StdMultiWidgetEditor open was found, give focus to it + if(editorList.size()) + { + GetIntroSite()->GetPage()->Activate( editorList[0]->GetPart(true) ); + } + } } // if the scheme is set to http, by default no action is performed, if an external webpage needs to be // shown it should be implemented below else if (scheme.contains(QString("http")) ) { QDesktopServices::openUrl(showMeNext); // m_view->load( ) ; } else if(scheme.contains("qrc")) { m_view->load(showMeNext); } } #endif void QmitkDiffusionImagingAppIntroPart::StandbyStateChanged(bool standby) { } void QmitkDiffusionImagingAppIntroPart::SetFocus() { } diff --git a/Plugins/org.mitk.gui.qt.ext/src/QmitkExtWorkbenchWindowAdvisor.cpp b/Plugins/org.mitk.gui.qt.ext/src/QmitkExtWorkbenchWindowAdvisor.cpp index 5ba07d39aa..f1c849dc34 100644 --- a/Plugins/org.mitk.gui.qt.ext/src/QmitkExtWorkbenchWindowAdvisor.cpp +++ b/Plugins/org.mitk.gui.qt.ext/src/QmitkExtWorkbenchWindowAdvisor.cpp @@ -1,1148 +1,1148 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkExtWorkbenchWindowAdvisor.h" #include "QmitkExtActionBarAdvisor.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // UGLYYY #include "internal/QmitkExtWorkbenchWindowAdvisorHack.h" #include "internal/QmitkCommonExtPlugin.h" #include "mitkUndoController.h" #include "mitkVerboseLimitedLinearUndo.h" #include #include #include #include QmitkExtWorkbenchWindowAdvisorHack * QmitkExtWorkbenchWindowAdvisorHack::undohack = new QmitkExtWorkbenchWindowAdvisorHack(); QString QmitkExtWorkbenchWindowAdvisor::QT_SETTINGS_FILENAME = "QtSettings.ini"; class PartListenerForTitle: public berry::IPartListener { public: PartListenerForTitle(QmitkExtWorkbenchWindowAdvisor* wa) : windowAdvisor(wa) { } Events::Types GetPartEventTypes() const { return Events::ACTIVATED | Events::BROUGHT_TO_TOP | Events::CLOSED | Events::HIDDEN | Events::VISIBLE; } void PartActivated(berry::IWorkbenchPartReference::Pointer ref) { if (ref.Cast ()) { windowAdvisor->UpdateTitle(false); } } void PartBroughtToTop(berry::IWorkbenchPartReference::Pointer ref) { if (ref.Cast ()) { windowAdvisor->UpdateTitle(false); } } void PartClosed(berry::IWorkbenchPartReference::Pointer /*ref*/) { windowAdvisor->UpdateTitle(false); } void PartHidden(berry::IWorkbenchPartReference::Pointer ref) { if (!windowAdvisor->lastActiveEditor.Expired() && ref->GetPart(false) == windowAdvisor->lastActiveEditor.Lock()) { windowAdvisor->UpdateTitle(true); } } void PartVisible(berry::IWorkbenchPartReference::Pointer ref) { if (!windowAdvisor->lastActiveEditor.Expired() && ref->GetPart(false) == windowAdvisor->lastActiveEditor.Lock()) { windowAdvisor->UpdateTitle(false); } } private: QmitkExtWorkbenchWindowAdvisor* windowAdvisor; }; class PartListenerForImageNavigator: public berry::IPartListener { public: PartListenerForImageNavigator(QAction* act) : imageNavigatorAction(act) { } Events::Types GetPartEventTypes() const { return Events::OPENED | Events::CLOSED | Events::HIDDEN | Events::VISIBLE; } void PartOpened(berry::IWorkbenchPartReference::Pointer ref) { if (ref->GetId()=="org.mitk.views.imagenavigator") { imageNavigatorAction->setChecked(true); } } void PartClosed(berry::IWorkbenchPartReference::Pointer ref) { if (ref->GetId()=="org.mitk.views.imagenavigator") { imageNavigatorAction->setChecked(false); } } void PartVisible(berry::IWorkbenchPartReference::Pointer ref) { if (ref->GetId()=="org.mitk.views.imagenavigator") { imageNavigatorAction->setChecked(true); } } void PartHidden(berry::IWorkbenchPartReference::Pointer ref) { if (ref->GetId()=="org.mitk.views.imagenavigator") { imageNavigatorAction->setChecked(false); } } private: QAction* imageNavigatorAction; }; class PerspectiveListenerForTitle: public berry::IPerspectiveListener { public: PerspectiveListenerForTitle(QmitkExtWorkbenchWindowAdvisor* wa) : windowAdvisor(wa), perspectivesClosed(false) { } Events::Types GetPerspectiveEventTypes() const { return Events::ACTIVATED | Events::SAVED_AS | Events::DEACTIVATED // remove the following line when command framework is finished | Events::CLOSED | Events::OPENED; } void PerspectiveActivated(berry::IWorkbenchPage::Pointer /*page*/, berry::IPerspectiveDescriptor::Pointer /*perspective*/) { windowAdvisor->UpdateTitle(false); } void PerspectiveSavedAs(berry::IWorkbenchPage::Pointer /*page*/, berry::IPerspectiveDescriptor::Pointer /*oldPerspective*/, berry::IPerspectiveDescriptor::Pointer /*newPerspective*/) { windowAdvisor->UpdateTitle(false); } void PerspectiveDeactivated(berry::IWorkbenchPage::Pointer /*page*/, berry::IPerspectiveDescriptor::Pointer /*perspective*/) { windowAdvisor->UpdateTitle(false); } void PerspectiveOpened(berry::IWorkbenchPage::Pointer /*page*/, berry::IPerspectiveDescriptor::Pointer /*perspective*/) { if (perspectivesClosed) { QListIterator i(windowAdvisor->viewActions); while (i.hasNext()) { i.next()->setEnabled(true); } windowAdvisor->fileSaveProjectAction->setEnabled(true); windowAdvisor->closeProjectAction->setEnabled(true); windowAdvisor->undoAction->setEnabled(true); windowAdvisor->redoAction->setEnabled(true); windowAdvisor->imageNavigatorAction->setEnabled(true); windowAdvisor->resetPerspAction->setEnabled(true); if( windowAdvisor->GetShowClosePerspectiveMenuItem() ) { windowAdvisor->closePerspAction->setEnabled(true); } } perspectivesClosed = false; } void PerspectiveClosed(berry::IWorkbenchPage::Pointer /*page*/, berry::IPerspectiveDescriptor::Pointer /*perspective*/) { berry::IWorkbenchWindow::Pointer wnd = windowAdvisor->GetWindowConfigurer()->GetWindow(); bool allClosed = true; if (wnd->GetActivePage()) { std::vector perspectives(wnd->GetActivePage()->GetOpenPerspectives()); allClosed = perspectives.empty(); } if (allClosed) { perspectivesClosed = true; QListIterator i(windowAdvisor->viewActions); while (i.hasNext()) { i.next()->setEnabled(false); } windowAdvisor->fileSaveProjectAction->setEnabled(false); windowAdvisor->closeProjectAction->setEnabled(false); windowAdvisor->undoAction->setEnabled(false); windowAdvisor->redoAction->setEnabled(false); windowAdvisor->imageNavigatorAction->setEnabled(false); windowAdvisor->resetPerspAction->setEnabled(false); if( windowAdvisor->GetShowClosePerspectiveMenuItem() ) { windowAdvisor->closePerspAction->setEnabled(false); } } } private: QmitkExtWorkbenchWindowAdvisor* windowAdvisor; bool perspectivesClosed; }; class PerspectiveListenerForMenu: public berry::IPerspectiveListener { public: PerspectiveListenerForMenu(QmitkExtWorkbenchWindowAdvisor* wa) : windowAdvisor(wa) { } Events::Types GetPerspectiveEventTypes() const { return Events::ACTIVATED | Events::DEACTIVATED; } void PerspectiveActivated(berry::IWorkbenchPage::Pointer /*page*/, berry::IPerspectiveDescriptor::Pointer perspective) { QAction* action = windowAdvisor->mapPerspIdToAction[perspective->GetId()]; if (action) { action->setChecked(true); } } void PerspectiveDeactivated(berry::IWorkbenchPage::Pointer /*page*/, berry::IPerspectiveDescriptor::Pointer perspective) { QAction* action = windowAdvisor->mapPerspIdToAction[perspective->GetId()]; if (action) { action->setChecked(false); } } private: QmitkExtWorkbenchWindowAdvisor* windowAdvisor; }; QmitkExtWorkbenchWindowAdvisor::QmitkExtWorkbenchWindowAdvisor(berry::WorkbenchAdvisor* wbAdvisor, berry::IWorkbenchWindowConfigurer::Pointer configurer) : berry::WorkbenchWindowAdvisor(configurer), lastInput(0), wbAdvisor(wbAdvisor), showViewToolbar(true), showPerspectiveToolbar(false), showVersionInfo(true), showMitkVersionInfo(true), showViewMenuItem(true), -showNewWindowMenuItem(true), +showNewWindowMenuItem(false), showClosePerspectiveMenuItem(true), dropTargetListener(new QmitkDefaultDropTargetListener) { productName = berry::Platform::GetConfiguration().getString("application.baseName"); } berry::ActionBarAdvisor::Pointer QmitkExtWorkbenchWindowAdvisor::CreateActionBarAdvisor( berry::IActionBarConfigurer::Pointer configurer) { berry::ActionBarAdvisor::Pointer actionBarAdvisor( new QmitkExtActionBarAdvisor(configurer)); return actionBarAdvisor; } void* QmitkExtWorkbenchWindowAdvisor::CreateEmptyWindowContents(void* parent) { QWidget* parentWidget = static_cast(parent); QLabel* label = new QLabel(parentWidget); label->setText("No perspectives are open. Open a perspective in the Window->Open Perspective menu."); label->setContentsMargins(10,10,10,10); label->setAlignment(Qt::AlignTop); label->setEnabled(false); parentWidget->layout()->addWidget(label); return label; } void QmitkExtWorkbenchWindowAdvisor::ShowClosePerspectiveMenuItem(bool show) { showClosePerspectiveMenuItem = show; } bool QmitkExtWorkbenchWindowAdvisor::GetShowClosePerspectiveMenuItem() { return showClosePerspectiveMenuItem; } void QmitkExtWorkbenchWindowAdvisor::ShowNewWindowMenuItem(bool show) { showNewWindowMenuItem = show; } void QmitkExtWorkbenchWindowAdvisor::ShowViewToolbar(bool show) { showViewToolbar = show; } void QmitkExtWorkbenchWindowAdvisor::ShowViewMenuItem(bool show) { showViewMenuItem = show; } void QmitkExtWorkbenchWindowAdvisor::ShowPerspectiveToolbar(bool show) { showPerspectiveToolbar = show; } void QmitkExtWorkbenchWindowAdvisor::ShowVersionInfo(bool show) { showVersionInfo = show; } void QmitkExtWorkbenchWindowAdvisor::ShowMitkVersionInfo(bool show) { showMitkVersionInfo = show; } void QmitkExtWorkbenchWindowAdvisor::SetProductName(const std::string& product) { productName = product; } void QmitkExtWorkbenchWindowAdvisor::SetWindowIcon(const std::string& wndIcon) { windowIcon = wndIcon; } void QmitkExtWorkbenchWindowAdvisor::PostWindowCreate() { // very bad hack... berry::IWorkbenchWindow::Pointer window = this->GetWindowConfigurer()->GetWindow(); QMainWindow* mainWindow = static_cast (window->GetShell()->GetControl()); if (!windowIcon.empty()) { mainWindow->setWindowIcon(QIcon(QString::fromStdString(windowIcon))); } mainWindow->setContextMenuPolicy(Qt::PreventContextMenu); /*mainWindow->setStyleSheet("color: white;" "background-color: #808080;" "selection-color: #659EC7;" "selection-background-color: #808080;" " QMenuBar {" "background-color: #808080; }");*/ // ==== Application menu ============================ QMenuBar* menuBar = mainWindow->menuBar(); menuBar->setContextMenuPolicy(Qt::PreventContextMenu); QMenu* fileMenu = menuBar->addMenu("&File"); fileMenu->setObjectName("FileMenu"); QAction* fileOpenAction = new QmitkFileOpenAction(QIcon(":/org.mitk.gui.qt.ext/Load_48.png"), window); fileMenu->addAction(fileOpenAction); fileSaveProjectAction = new QmitkExtFileSaveProjectAction(window); fileSaveProjectAction->setIcon(QIcon(":/org.mitk.gui.qt.ext/Save_48.png")); fileMenu->addAction(fileSaveProjectAction); closeProjectAction = new QmitkCloseProjectAction(window); closeProjectAction->setIcon(QIcon(":/org.mitk.gui.qt.ext/Remove_48.png")); fileMenu->addAction(closeProjectAction); fileMenu->addSeparator(); QAction* fileExitAction = new QmitkFileExitAction(window); fileExitAction->setObjectName("QmitkFileExitAction"); fileMenu->addAction(fileExitAction); berry::IViewRegistry* viewRegistry = berry::PlatformUI::GetWorkbench()->GetViewRegistry(); const std::vector& viewDescriptors = viewRegistry->GetViews(); // another bad hack to get an edit/undo menu... QMenu* editMenu = menuBar->addMenu("&Edit"); undoAction = editMenu->addAction(QIcon(":/org.mitk.gui.qt.ext/Undo_48.png"), "&Undo", QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onUndo()), QKeySequence("CTRL+Z")); undoAction->setToolTip("Undo the last action (not supported by all modules)"); redoAction = editMenu->addAction(QIcon(":/org.mitk.gui.qt.ext/Redo_48.png") , "&Redo", QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onRedo()), QKeySequence("CTRL+Y")); redoAction->setToolTip("execute the last action that was undone again (not supported by all modules)"); imageNavigatorAction = new QAction(QIcon(":/org.mitk.gui.qt.ext/Slider.png"), "&Image Navigator", NULL); bool imageNavigatorViewFound = window->GetWorkbench()->GetViewRegistry()->Find("org.mitk.views.imagenavigator"); if (imageNavigatorViewFound) { QObject::connect(imageNavigatorAction, SIGNAL(triggered(bool)), QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onImageNavigator())); imageNavigatorAction->setCheckable(true); // add part listener for image navigator imageNavigatorPartListener = new PartListenerForImageNavigator(imageNavigatorAction); window->GetPartService()->AddPartListener(imageNavigatorPartListener); berry::IViewPart::Pointer imageNavigatorView = window->GetActivePage()->FindView("org.mitk.views.imagenavigator"); imageNavigatorAction->setChecked(false); if (imageNavigatorView) { bool isImageNavigatorVisible = window->GetActivePage()->IsPartVisible(imageNavigatorView); if (isImageNavigatorVisible) imageNavigatorAction->setChecked(true); } imageNavigatorAction->setToolTip("Open image navigator for navigating through image"); } // toolbar for showing file open, undo, redo and other main actions QToolBar* mainActionsToolBar = new QToolBar; mainActionsToolBar->setContextMenuPolicy(Qt::PreventContextMenu); #ifdef __APPLE__ mainActionsToolBar->setToolButtonStyle ( Qt::ToolButtonTextUnderIcon ); #else mainActionsToolBar->setToolButtonStyle ( Qt::ToolButtonTextBesideIcon ); #endif mainActionsToolBar->addAction(fileOpenAction); mainActionsToolBar->addAction(fileSaveProjectAction); mainActionsToolBar->addAction(closeProjectAction); mainActionsToolBar->addAction(undoAction); mainActionsToolBar->addAction(redoAction); if (imageNavigatorViewFound) { mainActionsToolBar->addAction(imageNavigatorAction); } mainWindow->addToolBar(mainActionsToolBar); #ifdef __APPLE__ mainWindow->setUnifiedTitleAndToolBarOnMac(true); #endif // ==== Window Menu ========================== QMenu* windowMenu = menuBar->addMenu("Window"); if (showNewWindowMenuItem) { windowMenu->addAction("&New Window", QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onNewWindow())); windowMenu->addSeparator(); } QMenu* perspMenu = windowMenu->addMenu("&Open Perspective"); QMenu* viewMenu; if (showViewMenuItem) { viewMenu = windowMenu->addMenu("Show &View"); viewMenu->setObjectName("Show View"); } windowMenu->addSeparator(); resetPerspAction = windowMenu->addAction("&Reset Perspective", QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onResetPerspective())); if(showClosePerspectiveMenuItem) closePerspAction = windowMenu->addAction("&Close Perspective", QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onClosePerspective())); windowMenu->addSeparator(); windowMenu->addAction("&Preferences...", QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onEditPreferences()), QKeySequence("CTRL+P")); // fill perspective menu berry::IPerspectiveRegistry* perspRegistry = window->GetWorkbench()->GetPerspectiveRegistry(); QActionGroup* perspGroup = new QActionGroup(menuBar); std::vector perspectives( perspRegistry->GetPerspectives()); bool skip = false; for (std::vector::iterator perspIt = perspectives.begin(); perspIt != perspectives.end(); ++perspIt) { // if perspectiveExcludeList is set, it contains the id-strings of perspectives, which // should not appear as an menu-entry in the perspective menu if (perspectiveExcludeList.size() > 0) { for (unsigned int i=0; iGetId()) { skip = true; break; } } if (skip) { skip = false; continue; } } QAction* perspAction = new berry::QtOpenPerspectiveAction(window, *perspIt, perspGroup); mapPerspIdToAction.insert(std::make_pair((*perspIt)->GetId(), perspAction)); } perspMenu->addActions(perspGroup->actions()); // sort elements (converting vector to map...) std::vector::const_iterator iter; std::map VDMap; skip = false; for (iter = viewDescriptors.begin(); iter != viewDescriptors.end(); ++iter) { // if viewExcludeList is set, it contains the id-strings of view, which // should not appear as an menu-entry in the menu if (viewExcludeList.size() > 0) { for (unsigned int i=0; iGetId()) { skip = true; break; } } if (skip) { skip = false; continue; } } if ((*iter)->GetId() == "org.blueberry.ui.internal.introview") continue; if ((*iter)->GetId() == "org.mitk.views.imagenavigator") continue; std::pair p( (*iter)->GetLabel(), (*iter)); VDMap.insert(p); } // ================================================== // ==== Perspective Toolbar ================================== QToolBar* qPerspectiveToolbar = new QToolBar; if (showPerspectiveToolbar) { qPerspectiveToolbar->addActions(perspGroup->actions()); mainWindow->addToolBar(qPerspectiveToolbar); } else delete qPerspectiveToolbar; // ==== View Toolbar ================================== QToolBar* qToolbar = new QToolBar; std::map::const_iterator MapIter; for (MapIter = VDMap.begin(); MapIter != VDMap.end(); ++MapIter) { berry::QtShowViewAction* viewAction = new berry::QtShowViewAction(window, (*MapIter).second); viewActions.push_back(viewAction); if(showViewMenuItem) viewMenu->addAction(viewAction); if (showViewToolbar) { qToolbar->addAction(viewAction); } } if (showViewToolbar) { mainWindow->addToolBar(qToolbar); } else delete qToolbar; QSettings settings(GetQSettingsFile(), QSettings::IniFormat); mainWindow->restoreState(settings.value("ToolbarPosition").toByteArray()); // ==================================================== // ===== Help menu ==================================== QMenu* helpMenu = menuBar->addMenu("Help"); helpMenu->addAction("&Welcome",this, SLOT(onIntro())); helpMenu->addAction("&Contents", this, SLOT(onHelpContents())); helpMenu->addAction("Context &Help",this, SLOT(onHelp()), QKeySequence("F1")); helpMenu->addAction("&About",this, SLOT(onAbout())); // ===================================================== QStatusBar* qStatusBar = new QStatusBar(); //creating a QmitkStatusBar for Output on the QStatusBar and connecting it with the MainStatusBar QmitkStatusBar *statusBar = new QmitkStatusBar(qStatusBar); //disabling the SizeGrip in the lower right corner statusBar->SetSizeGripEnabled(false); QmitkProgressBar *progBar = new QmitkProgressBar(); qStatusBar->addPermanentWidget(progBar, 0); progBar->hide(); // progBar->AddStepsToDo(2); // progBar->Progress(1); mainWindow->setStatusBar(qStatusBar); QmitkMemoryUsageIndicatorView* memoryIndicator = new QmitkMemoryUsageIndicatorView(); qStatusBar->addPermanentWidget(memoryIndicator, 0); } void QmitkExtWorkbenchWindowAdvisor::PreWindowOpen() { berry::IWorkbenchWindowConfigurer::Pointer configurer = GetWindowConfigurer(); // show the shortcut bar and progress indicator, which are hidden by // default //configurer->SetShowPerspectiveBar(true); //configurer->SetShowFastViewBars(true); //configurer->SetShowProgressIndicator(true); // // add the drag and drop support for the editor area // configurer.addEditorAreaTransfer(EditorInputTransfer.getInstance()); // configurer.addEditorAreaTransfer(ResourceTransfer.getInstance()); // configurer.addEditorAreaTransfer(FileTransfer.getInstance()); // configurer.addEditorAreaTransfer(MarkerTransfer.getInstance()); // configurer.configureEditorAreaDropListener(new EditorAreaDropAdapter( // configurer.getWindow())); this->HookTitleUpdateListeners(configurer); menuPerspectiveListener = new PerspectiveListenerForMenu(this); configurer->GetWindow()->AddPerspectiveListener(menuPerspectiveListener); configurer->AddEditorAreaTransfer(QStringList("text/uri-list")); configurer->ConfigureEditorAreaDropListener(dropTargetListener); } void QmitkExtWorkbenchWindowAdvisor::onIntro() { QmitkExtWorkbenchWindowAdvisorHack::undohack->onIntro(); } void QmitkExtWorkbenchWindowAdvisor::onHelp() { QmitkExtWorkbenchWindowAdvisorHack::undohack->onHelp(); } void QmitkExtWorkbenchWindowAdvisor::onHelpContents() { QmitkExtWorkbenchWindowAdvisorHack::undohack->onHelpContents(); } void QmitkExtWorkbenchWindowAdvisor::onAbout() { QmitkExtWorkbenchWindowAdvisorHack::undohack->onAbout(); } //-------------------------------------------------------------------------------- // Ugly hack from here on. Feel free to delete when command framework // and undo buttons are done. //-------------------------------------------------------------------------------- QmitkExtWorkbenchWindowAdvisorHack::QmitkExtWorkbenchWindowAdvisorHack() : QObject() { } QmitkExtWorkbenchWindowAdvisorHack::~QmitkExtWorkbenchWindowAdvisorHack() { } void QmitkExtWorkbenchWindowAdvisorHack::onUndo() { mitk::UndoModel* model = mitk::UndoController::GetCurrentUndoModel(); if (model) { if (mitk::VerboseLimitedLinearUndo* verboseundo = dynamic_cast( model )) { mitk::VerboseLimitedLinearUndo::StackDescription descriptions = verboseundo->GetUndoDescriptions(); if (descriptions.size() >= 1) { MITK_INFO << "Undo " << descriptions.front().second; } } model->Undo(); } else { MITK_ERROR << "No undo model instantiated"; } } void QmitkExtWorkbenchWindowAdvisorHack::onRedo() { mitk::UndoModel* model = mitk::UndoController::GetCurrentUndoModel(); if (model) { if (mitk::VerboseLimitedLinearUndo* verboseundo = dynamic_cast( model )) { mitk::VerboseLimitedLinearUndo::StackDescription descriptions = verboseundo->GetRedoDescriptions(); if (descriptions.size() >= 1) { MITK_INFO << "Redo " << descriptions.front().second; } } model->Redo(); } else { MITK_ERROR << "No undo model instantiated"; } } void QmitkExtWorkbenchWindowAdvisorHack::onImageNavigator() { // get ImageNavigatorView berry::IViewPart::Pointer imageNavigatorView = berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetActivePage()->FindView("org.mitk.views.imagenavigator"); if (imageNavigatorView) { bool isImageNavigatorVisible = berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetActivePage()->IsPartVisible(imageNavigatorView); if (isImageNavigatorVisible) { berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetActivePage()->HideView(imageNavigatorView); return; } } berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetActivePage()->ShowView("org.mitk.views.imagenavigator"); //berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetActivePage()->ResetPerspective(); } void QmitkExtWorkbenchWindowAdvisorHack::onEditPreferences() { QmitkPreferencesDialog _PreferencesDialog(QApplication::activeWindow()); _PreferencesDialog.exec(); } void QmitkExtWorkbenchWindowAdvisorHack::onQuit() { berry::PlatformUI::GetWorkbench()->Close(); } void QmitkExtWorkbenchWindowAdvisorHack::onResetPerspective() { berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetActivePage()->ResetPerspective(); } void QmitkExtWorkbenchWindowAdvisorHack::onClosePerspective() { berry::IWorkbenchPage::Pointer page = berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetActivePage(); page->ClosePerspective(page->GetPerspective(), true, true); } void QmitkExtWorkbenchWindowAdvisorHack::onNewWindow() { berry::PlatformUI::GetWorkbench()->OpenWorkbenchWindow(0); } void QmitkExtWorkbenchWindowAdvisorHack::onIntro() { bool hasIntro = berry::PlatformUI::GetWorkbench()->GetIntroManager()->HasIntro(); if (!hasIntro) { QRegExp reg("(.*)(\\n)*"); QRegExp reg2("(\\n)*(.*)"); QFile file(":/org.mitk.gui.qt.ext/index.html"); file.open(QIODevice::ReadOnly | QIODevice::Text); // Als Text-Datei nur zum Lesen öffnen QString text = QString(file.readAll()); file.close(); QString title = text; title.replace(reg, ""); title.replace(reg2, ""); std::cout << title.toStdString() << std::endl; QMessageBox::information(NULL, title, text, "Close"); } else { berry::PlatformUI::GetWorkbench()->GetIntroManager()->ShowIntro( berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow(), false); } } void QmitkExtWorkbenchWindowAdvisorHack::onHelp() { ctkPluginContext* context = QmitkCommonExtPlugin::getContext(); if (context == 0) { MITK_WARN << "Plugin context not set, unable to open context help"; return; } // Check if the org.blueberry.ui.qt.help plug-in is installed and started QList > plugins = context->getPlugins(); foreach(QSharedPointer p, plugins) { if (p->getSymbolicName() == "org.blueberry.ui.qt.help") { if (p->getState() != ctkPlugin::ACTIVE) { // try to activate the plug-in explicitly try { p->start(ctkPlugin::START_TRANSIENT); } catch (const ctkPluginException& pe) { MITK_ERROR << "Activating org.blueberry.ui.qt.help failed: " << pe.what(); return; } } } } ctkServiceReference eventAdminRef = context->getServiceReference(); ctkEventAdmin* eventAdmin = 0; if (eventAdminRef) { eventAdmin = context->getService(eventAdminRef); } if (eventAdmin == 0) { MITK_WARN << "ctkEventAdmin service not found. Unable to open context help"; } else { ctkEvent ev("org/blueberry/ui/help/CONTEXTHELP_REQUESTED"); eventAdmin->postEvent(ev); } } void QmitkExtWorkbenchWindowAdvisorHack::onHelpContents() { berry::PlatformUI::GetWorkbench()->ShowPerspective("org.blueberry.perspectives.help", berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()); } void QmitkExtWorkbenchWindowAdvisorHack::onAbout() { QmitkAboutDialog* aboutDialog = new QmitkAboutDialog(QApplication::activeWindow(),NULL); aboutDialog->open(); } void QmitkExtWorkbenchWindowAdvisor::HookTitleUpdateListeners( berry::IWorkbenchWindowConfigurer::Pointer configurer) { // hook up the listeners to update the window title titlePartListener = new PartListenerForTitle(this); titlePerspectiveListener = new PerspectiveListenerForTitle(this); editorPropertyListener = new berry::PropertyChangeIntAdapter< QmitkExtWorkbenchWindowAdvisor>(this, &QmitkExtWorkbenchWindowAdvisor::PropertyChange); // configurer.getWindow().addPageListener(new IPageListener() { // public void pageActivated(IWorkbenchPage page) { // updateTitle(false); // } // // public void pageClosed(IWorkbenchPage page) { // updateTitle(false); // } // // public void pageOpened(IWorkbenchPage page) { // // do nothing // } // }); configurer->GetWindow()->AddPerspectiveListener(titlePerspectiveListener); configurer->GetWindow()->GetPartService()->AddPartListener(titlePartListener); } std::string QmitkExtWorkbenchWindowAdvisor::ComputeTitle() { berry::IWorkbenchWindowConfigurer::Pointer configurer = GetWindowConfigurer(); berry::IWorkbenchPage::Pointer currentPage = configurer->GetWindow()->GetActivePage(); berry::IEditorPart::Pointer activeEditor; if (currentPage) { activeEditor = lastActiveEditor.Lock(); } std::string title; //TODO Product // IProduct product = Platform.getProduct(); // if (product != null) { // title = product.getName(); // } // instead of the product name, we use a custom variable for now title = productName; if(showMitkVersionInfo) { title += std::string(" ") + MITK_VERSION_STRING; } if (showVersionInfo) { // add version informatioin QString versions = QString(" (ITK %1.%2.%3 VTK %4.%5.%6 Qt %7 MITK %8)") .arg(ITK_VERSION_MAJOR).arg(ITK_VERSION_MINOR).arg(ITK_VERSION_PATCH) .arg(VTK_MAJOR_VERSION).arg(VTK_MINOR_VERSION).arg(VTK_BUILD_VERSION) .arg(QT_VERSION_STR) .arg(MITK_VERSION_STRING); title += versions.toStdString(); } if (currentPage) { if (activeEditor) { lastEditorTitle = activeEditor->GetTitleToolTip(); if (!lastEditorTitle.empty()) title = lastEditorTitle + " - " + title; } berry::IPerspectiveDescriptor::Pointer persp = currentPage->GetPerspective(); std::string label = ""; if (persp) { label = persp->GetLabel(); } berry::IAdaptable* input = currentPage->GetInput(); if (input && input != wbAdvisor->GetDefaultPageInput()) { label = currentPage->GetLabel(); } if (!label.empty()) { title = label + " - " + title; } } title += " (Not for use in diagnosis or treatment of patients)"; return title; } void QmitkExtWorkbenchWindowAdvisor::RecomputeTitle() { berry::IWorkbenchWindowConfigurer::Pointer configurer = GetWindowConfigurer(); std::string oldTitle = configurer->GetTitle(); std::string newTitle = ComputeTitle(); if (newTitle != oldTitle) { configurer->SetTitle(newTitle); } } void QmitkExtWorkbenchWindowAdvisor::UpdateTitle(bool editorHidden) { berry::IWorkbenchWindowConfigurer::Pointer configurer = GetWindowConfigurer(); berry::IWorkbenchWindow::Pointer window = configurer->GetWindow(); berry::IEditorPart::Pointer activeEditor; berry::IWorkbenchPage::Pointer currentPage = window->GetActivePage(); berry::IPerspectiveDescriptor::Pointer persp; berry::IAdaptable* input = 0; if (currentPage) { activeEditor = currentPage->GetActiveEditor(); persp = currentPage->GetPerspective(); input = currentPage->GetInput(); } if (editorHidden) { activeEditor = 0; } // Nothing to do if the editor hasn't changed if (activeEditor == lastActiveEditor.Lock() && currentPage == lastActivePage.Lock() && persp == lastPerspective.Lock() && input == lastInput) { return; } if (!lastActiveEditor.Expired()) { lastActiveEditor.Lock()->RemovePropertyListener(editorPropertyListener); } lastActiveEditor = activeEditor; lastActivePage = currentPage; lastPerspective = persp; lastInput = input; if (activeEditor) { activeEditor->AddPropertyListener(editorPropertyListener); } RecomputeTitle(); } void QmitkExtWorkbenchWindowAdvisor::PropertyChange(berry::Object::Pointer /*source*/, int propId) { if (propId == berry::IWorkbenchPartConstants::PROP_TITLE) { if (!lastActiveEditor.Expired()) { std::string newTitle = lastActiveEditor.Lock()->GetPartName(); if (lastEditorTitle != newTitle) { RecomputeTitle(); } } } } void QmitkExtWorkbenchWindowAdvisor::SetPerspectiveExcludeList(std::vector v) { this->perspectiveExcludeList = v; } std::vector QmitkExtWorkbenchWindowAdvisor::GetPerspectiveExcludeList() { return this->perspectiveExcludeList; } void QmitkExtWorkbenchWindowAdvisor::SetViewExcludeList(std::vector v) { this->viewExcludeList = v; } std::vector QmitkExtWorkbenchWindowAdvisor::GetViewExcludeList() { return this->viewExcludeList; } void QmitkExtWorkbenchWindowAdvisor::PostWindowClose() { berry::IWorkbenchWindow::Pointer window = this->GetWindowConfigurer()->GetWindow(); QMainWindow* mainWindow = static_cast (window->GetShell()->GetControl()); QSettings settings(GetQSettingsFile(), QSettings::IniFormat); settings.setValue("ToolbarPosition", mainWindow->saveState()); } QString QmitkExtWorkbenchWindowAdvisor::GetQSettingsFile() const { QFileInfo settingsInfo = QmitkCommonExtPlugin::getContext()->getDataFile(QT_SETTINGS_FILENAME); return settingsInfo.canonicalFilePath(); } diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/CMakeLists.txt b/Plugins/org.mitk.gui.qt.meshdecimation/CMakeLists.txt new file mode 100644 index 0000000000..514256f123 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.meshdecimation/CMakeLists.txt @@ -0,0 +1,8 @@ +PROJECT(org_mitk_gui_qt_meshdecimation) + +MACRO_CREATE_MITK_CTK_PLUGIN( + EXPORT_DIRECTIVE MESHDECIMATION_EXPORT + EXPORTED_INCLUDE_SUFFIXES src + MODULE_DEPENDENCIES QmitkExt +) + diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation-manual.dox b/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation-manual.dox new file mode 100644 index 0000000000..33ead4ba4d --- /dev/null +++ b/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation-manual.dox @@ -0,0 +1,33 @@ +/** + +\bundlemainpage{org_meshdecimation} The Mesh Decimation Module + +\image html meshdecimation.png "Icon of the Module" + +Available sections: + - \ref meshdecimationOverview + - \ref meshdecimationFeatures + - \ref meshdecimationUsage + +\section meshdecimationOverview Overview + +MeshDecimation is a user friendly tool to decimate a MITK surface. + +\section meshdecimationFeatures Features + +The module offers two basic procedures to decimate surfaces: One that reduces a surface with a possible loss of topology (quality), but with a garuanteed reduction rate that is expressed in terms of percent of the original mesh. The other variant preserves the topology and stops decimating when it detects heavy topological changes. + +\section meshdecimationUsage Usage + +\image html meshdecimation-ui.png "The user interface of the Mesh Decimation Module" + +The usage of the module should be straightforward, as shown in the screenshot. To decimate a MITK surface do the following: +- Select a surface in the datamanager +- Enter a target reduction rate +- Select a decimation method (\ref meshdecimationFeatures) +- Press the "Decimate" button +- Repeat the process until you are satisfied with the decimation +- Save the surface to disk + +*/ + diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation-ui.png b/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation-ui.png new file mode 100644 index 0000000000..97b45078fe Binary files /dev/null and b/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation-ui.png differ diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation.png b/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation.png new file mode 100644 index 0000000000..8ba6124527 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.meshdecimation/documentation/Manual/meshdecimation.png differ diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/documentation/doxygen/modules.dox b/Plugins/org.mitk.gui.qt.meshdecimation/documentation/doxygen/modules.dox new file mode 100644 index 0000000000..8c37f6ce32 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.meshdecimation/documentation/doxygen/modules.dox @@ -0,0 +1,8 @@ +/** + \defgroup org_mbi_gui_qt_meshdecimation org.mbi.gui.qt.meshdecimation Plugin + \ingroup MBIPlugins + + \brief The plugin is a user friendly tool to decimate a mesh. + + It has no public API and uses VTK filters internally to decimate MITK Surfaces. Please refer to the user manual for usage information. +*/ diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/files.cmake b/Plugins/org.mitk.gui.qt.meshdecimation/files.cmake new file mode 100644 index 0000000000..6db717a8e8 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.meshdecimation/files.cmake @@ -0,0 +1,37 @@ +SET(SRC_CPP_FILES + +) + +SET(INTERNAL_CPP_FILES + QmitkMeshDecimationView.cpp + mitkPluginActivator.cpp +) + +SET(UI_FILES + src/internal/QmitkMeshDecimationView.ui +) + +SET(MOC_H_FILES + src/internal/QmitkMeshDecimationView.h + src/internal/mitkPluginActivator.h +) + +SET(CACHED_RESOURCE_FILES + resources/meshdecimation.png + plugin.xml +) + +SET(QRC_FILES + +) + +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/Plugins/org.mitk.gui.qt.meshdecimation/manifest_headers.cmake b/Plugins/org.mitk.gui.qt.meshdecimation/manifest_headers.cmake new file mode 100644 index 0000000000..824126c979 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.meshdecimation/manifest_headers.cmake @@ -0,0 +1,5 @@ +set(Plugin-Name "Mesh Decimation") +set(Plugin-Version "0.1") +set(Plugin-Vendor "DKFZ, Medical and Biological Informatics") +set(Plugin-ContactAddress "http://www.mitk.org") +set(Require-Plugin org.mitk.gui.qt.common) diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/plugin.xml b/Plugins/org.mitk.gui.qt.meshdecimation/plugin.xml new file mode 100644 index 0000000000..13005afb6a --- /dev/null +++ b/Plugins/org.mitk.gui.qt.meshdecimation/plugin.xml @@ -0,0 +1,12 @@ + + + + + + + + + \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/resources/meshdecimation.png b/Plugins/org.mitk.gui.qt.meshdecimation/resources/meshdecimation.png new file mode 100644 index 0000000000..8ba6124527 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.meshdecimation/resources/meshdecimation.png differ diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/QmitkMeshDecimationView.cpp b/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/QmitkMeshDecimationView.cpp new file mode 100644 index 0000000000..44d8642dac --- /dev/null +++ b/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/QmitkMeshDecimationView.cpp @@ -0,0 +1,232 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date$ +Version: $Revision$ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. + +This software is distributed WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR +PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +// Blueberry +#include +#include + +// Qmitk +#include "QmitkMeshDecimationView.h" +#include "QmitkStdMultiWidget.h" + +// Qt +#include +#include +#include + +// mitk +#include +#include +#include + +// VTK +#include +#include +#include + +const std::string QmitkMeshDecimationView::VIEW_ID = "org.mitk.views.meshdecimation"; + +QmitkMeshDecimationView::QmitkMeshDecimationView() +: QmitkAbstractView() +, m_Controls( 0 ) +, m_MessageBox( 0 ) +, m_MessageBoxDisplayTime( 5 ) +, m_MessageBoxTimer( new QTimer(this) ) +{ + m_MessageBoxTimer->setInterval(1000); + connect(m_MessageBoxTimer, SIGNAL(timeout()), this, SLOT(MessageBoxTimer())); +} + +QmitkMeshDecimationView::~QmitkMeshDecimationView() +{ +} + +void QmitkMeshDecimationView::CreateQtPartControl( QWidget *parent ) +{ + // build up qt view, unless already done + if ( !m_Controls ) + { + // create GUI widgets from the Qt Designer's .ui file + m_Controls = new Ui::QmitkMeshDecimationView; + m_Controls->setupUi( parent ); + + connect((QObject*)(m_Controls->Decimate), SIGNAL(clicked()), this, SLOT(Decimate())); + } +} + +void QmitkMeshDecimationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList& nodes) +{ + this->m_Node = 0; + this->DisableGui(); + + for( int i=0; iGetData(); + if( dynamic_cast( baseData ) != 0 ) + { + this->m_Node = nodes.at(i); + this->m_Controls->NodeLabel->setEnabled( true ); + this->m_Controls->TargetReduction->setEnabled( true ); + this->m_Controls->Decimate->setEnabled( true ); + this->m_Controls->DecimationType->setEnabled( true ); + break; + } + } + this->UpdateNodeLabel(); +} + +void QmitkMeshDecimationView::SetFocus() +{ + m_Controls->NodeLabel->setFocus(); +} + +void QmitkMeshDecimationView::DisableGui() +{ + this->m_Controls->NodeLabel->setEnabled( false ); + this->m_Controls->TargetReduction->setEnabled( false ); + this->m_Controls->Decimate->setEnabled( false ); + this->m_Controls->DecimationType->setEnabled( false ); +} + +void QmitkMeshDecimationView::UpdateNodeLabel() +{ + QString nodeLabel = "none selected"; + if (this->m_Node.IsNotNull()) + { + vtkPolyData* polyData = static_cast(this->m_Node->GetData())->GetVtkPolyData(); + nodeLabel = QString::fromStdString( this->m_Node->GetName() ); + nodeLabel.append(" ("); + nodeLabel.append( QString("%1").arg( polyData->GetNumberOfCells() ) ); + nodeLabel.append(" cells)"); + } + this->m_Controls->NodeLabel->setText( nodeLabel ); +} + +void QmitkMeshDecimationView::Decimate() +{ + if (this->m_Node.IsNotNull()) + { + this->WaitCursorOn(); + QString error; + try + { + vtkPolyData* polyData = static_cast(this->m_Node->GetData())->GetVtkPolyData(); + int startingNumberOfCells = polyData->GetNumberOfCells(); + if( startingNumberOfCells == 0 ) + throw std::logic_error("Could not reduce Mesh since it is already empty."); + + + double targetReduction = static_cast(this->m_Controls->TargetReduction->value()) / 100.0; + + vtkPolyData* newPolyData = 0; + if( this->m_Controls->DecimationType->currentText() == "DecimatePro" ) + { + vtkSmartPointer decimator = vtkDecimatePro::New(); + decimator->SetInput( polyData ); + decimator->SetTargetReduction( targetReduction ); + decimator->SetPreserveTopology( 1 ); + decimator->Update(); + newPolyData = decimator->GetOutput(); + } + else + { + vtkSmartPointer decimator = vtkQuadricDecimation::New(); + decimator->SetInput( polyData ); + decimator->SetTargetReduction( targetReduction ); + decimator->Update(); + newPolyData = decimator->GetOutput(); + } + + if( newPolyData != 0 ) + { + static_cast(this->m_Node->GetData())->SetVtkPolyData(newPolyData); + this->m_Node->Update(); + this->UpdateNodeLabel(); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + } + + int endingNumberOfCells = newPolyData->GetNumberOfCells(); + int reducedCells = startingNumberOfCells - endingNumberOfCells; + + QString message; + if( reducedCells == 0 ) + message = "Decimation was not able to reduce any more cells from Mesh."; + else + message = QString("Decimation successful. %1 cells removed").arg(reducedCells); + + this->WaitCursorOff(); + this->ShowAutoCloseMessageDialog(message); + } + catch(std::exception& e) + { + this->WaitCursorOff(); + error = QString::fromStdString(e.what()); + } + catch(...) + { + this->WaitCursorOff(); + error = "An unknown error occured. Please report error at bugs.mitk.org."; + } + if( !error.isEmpty() ) + this->ShowAutoCloseErrorDialog(error); + } + else + this->DisableGui(); +} + +void QmitkMeshDecimationView::MessageBoxTimer() +{ + m_MessageBoxDisplayTime--; + QString text = m_MessageBoxText; + text.append( QString(" (Will close in %1 seconds)").arg(m_MessageBoxDisplayTime) ); + m_MessageBox->setText( text ); + + if( m_MessageBoxDisplayTime == 0 ) + { + m_MessageBox->accept(); + } +} + +void QmitkMeshDecimationView::ShowAutoCloseErrorDialog( const QString& error ) +{ + m_MessageBox = new QMessageBox(QMessageBox::Warning, "Warning", error, QMessageBox::Ok ); + m_MessageBoxDisplayTime = 5; + m_MessageBoxText = error; + + this->MessageBoxTimer(); + m_MessageBoxTimer->start(); + m_MessageBox->exec(); + m_MessageBoxTimer->stop(); + + delete m_MessageBox; + m_MessageBox = 0; +} + +void QmitkMeshDecimationView::ShowAutoCloseMessageDialog( const QString& message ) +{ + m_MessageBox = new QMessageBox(QMessageBox::Information, "Information", message, QMessageBox::Ok ); + m_MessageBoxDisplayTime = 5; + m_MessageBoxText = message; + + this->MessageBoxTimer(); + m_MessageBoxTimer->start(); + m_MessageBox->exec(); + m_MessageBoxTimer->stop(); + + delete m_MessageBox; + m_MessageBox = 0; +} diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/QmitkMeshDecimationView.h b/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/QmitkMeshDecimationView.h new file mode 100644 index 0000000000..e333577be4 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/QmitkMeshDecimationView.h @@ -0,0 +1,72 @@ +/*========================================================================= + +Program: Medical Imaging & Interaction Toolkit +Language: C++ +Date: $Date$ +Version: $Revision$ + +Copyright (c) German Cancer Research Center, Division of Medical and +Biological Informatics. All rights reserved. +See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. + +This software is distributed WITHOUT ANY WARRANTY; without even +the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR +PURPOSE. See the above copyright notices for more information. + +=========================================================================*/ + +#ifndef QmitkMeshDecimationView_h +#define QmitkMeshDecimationView_h + +#include +#include +#include +#include +#include +#include "ui_QmitkMeshDecimationView.h" + +/*! + \brief QmitkMeshDecimationView + + \warning This application module is not yet documented. Use "svn blame/praise/annotate" and ask the author to provide basic documentation. + + \sa QmitkFunctionality + \ingroup Functionalities +*/ +class QmitkMeshDecimationView : public QmitkAbstractView +{ +// this is needed for all Qt objects that should have a Qt meta-object +// (everything that derives from QObject and wants to have signal/slots) +Q_OBJECT +public: + static const std::string VIEW_ID; + + QmitkMeshDecimationView(); + virtual ~QmitkMeshDecimationView(); + + virtual void CreateQtPartControl(QWidget *parent); + virtual void SetFocus(); + + virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList&); +protected slots: + void Decimate(); + void MessageBoxTimer(); +protected: + void DisableGui(); + void UpdateNodeLabel(); + void ShowAutoCloseErrorDialog( const QString& error ); + void ShowAutoCloseMessageDialog( const QString& message ); + + Ui::QmitkMeshDecimationView* m_Controls; + mitk::WeakPointer m_Node; + QWidget* m_Parent; + QMessageBox* m_MessageBox; + int m_MessageBoxDisplayTime; + QString m_MessageBoxText; + QTimer *m_MessageBoxTimer; +}; + + + +#endif // _QMITKMESHSMOOTHINGVIEW_H_INCLUDED + diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/QmitkMeshDecimationView.ui b/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/QmitkMeshDecimationView.ui new file mode 100644 index 0000000000..23d2dcd7f1 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/QmitkMeshDecimationView.ui @@ -0,0 +1,145 @@ + + + QmitkMeshDecimationView + + + + 0 + 0 + 389 + 811 + + + + + 0 + 0 + + + + QmitkTemplate + + + + + + + + Selected node: + + + + + + + none selected + + + + + + + + 132 + 0 + + + + Target reduction [percent]: + + + + + + + false + + + 1 + + + 100 + + + 50 + + + + + + + Decimation Type*: + + + true + + + + + + + false + + + + DecimatePro + + + + + Quadric + + + + + + + + + + <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> +<html><head><meta name="qrichtext" content="1" /><style type="text/css"> +p, li { white-space: pre-wrap; } +</style></head><body style=" font-family:'MS Shell Dlg 2'; font-size:8.25pt; font-weight:400; font-style:normal;"> +<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:8pt;">* Quadric Decimation reduces the mesh without accounting much for its topology. DecimatePro preserves topology best but does not garantuee the target reduction rate.</span></p></body></html> + + + true + + + + + + + false + + + Do image processing + + + Decimate + + + + + + + Qt::Vertical + + + QSizePolicy::Expanding + + + + 20 + 220 + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/mitkPluginActivator.cpp new file mode 100644 index 0000000000..0995ef5ffe --- /dev/null +++ b/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/mitkPluginActivator.cpp @@ -0,0 +1,22 @@ +#include "mitkPluginActivator.h" + +#include + +#include "QmitkMeshDecimationView.h" + +namespace mitk { + +void PluginActivator::start(ctkPluginContext* context) +{ + BERRY_REGISTER_EXTENSION_CLASS(QmitkMeshDecimationView, context) + //BERRY_REGISTER_EXTENSION_CLASS(QmitkHexVolumeMesherView, context) +} + +void PluginActivator::stop(ctkPluginContext* context) +{ + Q_UNUSED(context) +} + +} + +Q_EXPORT_PLUGIN2(org_mbi_gui_qt_meshdecimation, mitk::PluginActivator) diff --git a/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/mitkPluginActivator.h b/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/mitkPluginActivator.h new file mode 100644 index 0000000000..a34be34be4 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.meshdecimation/src/internal/mitkPluginActivator.h @@ -0,0 +1,23 @@ +#ifndef MITKPLUGINACTIVATOR_H +#define MITKPLUGINACTIVATOR_H + +#include + +namespace mitk { + +class PluginActivator : + public QObject, public ctkPluginActivator +{ + Q_OBJECT + Q_INTERFACES(ctkPluginActivator) + +public: + + void start(ctkPluginContext* context); + void stop(ctkPluginContext* context); + +}; // PluginActivator + +} + +#endif // MITKPLUGINACTIVATOR_H diff --git a/Plugins/org.mitk.gui.qt.segmentation/CMakeLists.txt b/Plugins/org.mitk.gui.qt.segmentation/CMakeLists.txt index 4cf6b1231e..c0878bf72f 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.segmentation/CMakeLists.txt @@ -1,7 +1,7 @@ project(org_mitk_gui_qt_segmentation) MACRO_CREATE_MITK_CTK_PLUGIN( EXPORT_DIRECTIVE MITK_QT_SEGMENTATION EXPORTED_INCLUDE_SUFFIXES src - MODULE_DEPENDENCIES QmitkExt ClippingTools + MODULE_DEPENDENCIES QmitkExt ClippingTools Segmentation ) 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 2b2701c80d..39be172557 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp @@ -1,1227 +1,1230 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision: 1.12 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkDataNodeObject.h" #include "mitkProperties.h" #include "mitkSegTool2D.h" #include "mitkGlobalInteraction.h" #include "QmitkStdMultiWidget.h" #include "QmitkNewSegmentationDialog.h" #include #include #include "QmitkSegmentationView.h" #include "QmitkSegmentationPostProcessing.h" #include "QmitkSegmentationOrganNamesHandling.cpp" #include #include //For Segmentation in rotated slices //TODO clean up includes #include "mitkVtkResliceInterpolationProperty.h" #include "mitkPlanarCircle.h" #include "mitkGetModuleContext.h" #include "mitkModule.h" #include "mitkModuleRegistry.h" +#include "mitkSegmentationObjectFactory.h" + const std::string QmitkSegmentationView::VIEW_ID = "org.mitk.views.segmentation"; // public methods QmitkSegmentationView::QmitkSegmentationView() :m_Parent(NULL) ,m_Controls(NULL) ,m_MultiWidget(NULL) ,m_RenderingManagerObserverTag(0) { + RegisterSegmentationObjectFactory(); } QmitkSegmentationView::~QmitkSegmentationView() { // delete m_PostProcessing; delete m_Controls; } void QmitkSegmentationView::NewNodesGenerated() { // ForceDisplayPreferencesUponAllImages(); } void QmitkSegmentationView::NewNodeObjectsGenerated(mitk::ToolManager::DataVectorType* nodes) { if (!nodes) return; mitk::ToolManager* toolManager = m_Controls->m_ManualToolSelectionBox->GetToolManager(); if (!toolManager) return; for (mitk::ToolManager::DataVectorType::iterator iter = nodes->begin(); iter != nodes->end(); ++iter) { this->FireNodeSelected( *iter ); // only last iteration meaningful, multiple generated objects are not taken into account here } } void QmitkSegmentationView::Activated() { // should be moved to ::BecomesVisible() or similar if( m_Controls ) { m_Controls->m_ManualToolSelectionBox->setEnabled( true ); m_Controls->m_OrganToolSelectionBox->setEnabled( true ); m_Controls->m_LesionToolSelectionBox->setEnabled( true ); m_Controls->m_SlicesInterpolator->Enable3DInterpolation( m_Controls->widgetStack->currentWidget() == m_Controls->pageManual ); //TODO Remove Observer itk::ReceptorMemberCommand::Pointer command1 = itk::ReceptorMemberCommand::New(); command1->SetCallbackFunction( this, &QmitkSegmentationView::RenderingManagerReinitialized ); m_RenderingManagerObserverTag = mitk::RenderingManager::GetInstance()->AddObserver( mitk::RenderingManagerViewsInitializedEvent(), command1 ); //Adding observers for node visibility to existing segmentations mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateProperty::Pointer isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer isSegmentation = mitk::NodePredicateAnd::New( isImage, isBinary ); mitk::DataStorage::SetOfObjects::ConstPointer segmentations = this->GetDefaultDataStorage()->GetSubset( isSegmentation ); for ( mitk::DataStorage::SetOfObjects::const_iterator iter = segmentations->begin(); iter != segmentations->end(); ++iter) { mitk::DataNode* node = *iter; itk::SimpleMemberCommand::Pointer command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::OnWorkingNodeVisibilityChanged); m_WorkingDataObserverTags.insert( std::pair( node, node->GetProperty("visible")->AddObserver( itk::ModifiedEvent(), command ) ) ); } if(segmentations->Size() > 0) { FireNodeSelected(segmentations->ElementAt(0)); segmentations->ElementAt(0)->GetProperty("visible")->Modified(); } } } void QmitkSegmentationView::Deactivated() { if( m_Controls ) { mitk::RenderingManager::GetInstance()->RemoveObserver( m_RenderingManagerObserverTag ); m_Controls->m_ManualToolSelectionBox->setEnabled( false ); //deactivate all tools m_Controls->m_ManualToolSelectionBox->GetToolManager()->ActivateTool(-1); m_Controls->m_OrganToolSelectionBox->setEnabled( false ); m_Controls->m_LesionToolSelectionBox->setEnabled( false ); m_Controls->m_SlicesInterpolator->EnableInterpolation( false ); //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(); // gets the context of the "Mitk" (Core) module (always has id 1) // TODO Workaround until CTL plugincontext is available mitk::ModuleContext* context = mitk::ModuleRegistry::GetModule(1)->GetModuleContext(); // Workaround end mitk::ServiceReference serviceRef = context->GetServiceReference(); //mitk::ServiceReference serviceRef = mitk::GetModuleContext()->GetServiceReference(); mitk::PlanePositionManagerService* service = dynamic_cast(context->GetService(serviceRef)); service->RemoveAllPlanePositions(); } } void QmitkSegmentationView::StdMultiWidgetAvailable( QmitkStdMultiWidget& stdMultiWidget ) { SetMultiWidget(&stdMultiWidget); } void QmitkSegmentationView::StdMultiWidgetNotAvailable() { SetMultiWidget(NULL); } void QmitkSegmentationView::StdMultiWidgetClosed( QmitkStdMultiWidget& /*stdMultiWidget*/ ) { SetMultiWidget(NULL); } void QmitkSegmentationView::SetMultiWidget(QmitkStdMultiWidget* multiWidget) { if (m_MultiWidget) { mitk::SlicesCoordinator* coordinator = m_MultiWidget->GetSlicesRotator(); if (coordinator) { coordinator->RemoveObserver( m_SlicesRotationObserverTag1 ); } coordinator = m_MultiWidget->GetSlicesSwiveller(); if (coordinator) { coordinator->RemoveObserver( m_SlicesRotationObserverTag2 ); } } // save the current multiwidget as the working widget m_MultiWidget = multiWidget; //TODO Remove Observers if (m_MultiWidget) { mitk::SlicesCoordinator* coordinator = m_MultiWidget->GetSlicesRotator(); if (coordinator) { itk::ReceptorMemberCommand::Pointer command2 = itk::ReceptorMemberCommand::New(); command2->SetCallbackFunction( this, &QmitkSegmentationView::SliceRotation ); m_SlicesRotationObserverTag1 = coordinator->AddObserver( mitk::SliceRotationEvent(), command2 ); } coordinator = m_MultiWidget->GetSlicesSwiveller(); if (coordinator) { itk::ReceptorMemberCommand::Pointer command2 = itk::ReceptorMemberCommand::New(); command2->SetCallbackFunction( this, &QmitkSegmentationView::SliceRotation ); m_SlicesRotationObserverTag2 = coordinator->AddObserver( mitk::SliceRotationEvent(), command2 ); } } //TODO End Remove Observers if (m_Parent) { m_Parent->setEnabled(m_MultiWidget); } // tell the interpolation about toolmanager and multiwidget (and data storage) if (m_Controls && m_MultiWidget) { mitk::ToolManager* toolManager = m_Controls->m_ManualToolSelectionBox->GetToolManager(); m_Controls->m_SlicesInterpolator->SetDataStorage( *(this->GetDefaultDataStorage())); m_Controls->m_SlicesInterpolator->Initialize( toolManager, m_MultiWidget ); } } void QmitkSegmentationView::OnPreferencesChanged(const berry::IBerryPreferences*) { ForceDisplayPreferencesUponAllImages(); } //TODO remove function void QmitkSegmentationView::RenderingManagerReinitialized(const itk::EventObject&) { CheckImageAlignment(); } //TODO remove function void QmitkSegmentationView::SliceRotation(const itk::EventObject&) { CheckImageAlignment(); } // protected slots void QmitkSegmentationView::CreateNewSegmentation() { mitk::DataNode::Pointer node = m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetReferenceData(0); if (node.IsNotNull()) { mitk::Image::Pointer image = dynamic_cast( node->GetData() ); if (image.IsNotNull()) { if (image->GetDimension()>1) { // ask about the name and organ type of the new segmentation QmitkNewSegmentationDialog* dialog = new QmitkNewSegmentationDialog( m_Parent ); // needs a QWidget as parent, "this" is not QWidget QString storedList = QString::fromStdString( this->GetPreferences()->GetByteArray("Organ-Color-List","") ); QStringList organColors; if (storedList.isEmpty()) { organColors = GetDefaultOrganColorString(); } else { /* a couple of examples of how organ names are stored: a simple item is built up like 'name#AABBCC' where #AABBCC is the hexadecimal notation of a color as known from HTML items are stored separated by ';' this makes it necessary to escape occurrences of ';' in name. otherwise the string "hugo;ypsilon#AABBCC;eugen#AABBCC" could not be parsed as two organs but we would get "hugo" and "ypsilon#AABBCC" and "eugen#AABBCC" so the organ name "hugo;ypsilon" is stored as "hugo\;ypsilon" and must be unescaped after loading the following lines could be one split with Perl's negative lookbehind */ // recover string list from BlueBerry view's preferences QString storedString = QString::fromStdString( this->GetPreferences()->GetByteArray("Organ-Color-List","") ); MITK_DEBUG << "storedString: " << storedString.toStdString(); // match a string consisting of any number of repetitions of either "anything but ;" or "\;". This matches everything until the next unescaped ';' QRegExp onePart("(?:[^;]|\\\\;)*"); MITK_DEBUG << "matching " << onePart.pattern().toStdString(); int count = 0; int pos = 0; while( (pos = onePart.indexIn( storedString, pos )) != -1 ) { ++count; int length = onePart.matchedLength(); if (length == 0) break; QString matchedString = storedString.mid(pos, length); MITK_DEBUG << " Captured length " << length << ": " << matchedString.toStdString(); pos += length + 1; // skip separating ';' // unescape possible occurrences of '\;' in the string matchedString.replace("\\;", ";"); // add matched string part to output list organColors << matchedString; } MITK_DEBUG << "Captured " << count << " organ name/colors"; } dialog->SetSuggestionList( organColors ); int dialogReturnValue = dialog->exec(); if ( dialogReturnValue == QDialog::Rejected ) return; // user clicked cancel or pressed Esc or something similar // ask the user about an organ type and name, add this information to the image's (!) propertylist // create a new image of the same dimensions and smallest possible pixel type mitk::ToolManager* toolManager = m_Controls->m_ManualToolSelectionBox->GetToolManager(); mitk::Tool* firstTool = toolManager->GetToolById(0); if (firstTool) { try { mitk::DataNode::Pointer emptySegmentation = firstTool->CreateEmptySegmentationNode( image, dialog->GetSegmentationName().toStdString(), dialog->GetColor() ); //Here we change the reslice interpolation mode for a segmentation, so that contours in rotated slice can be shown correctly emptySegmentation->SetProperty( "reslice interpolation", mitk::VtkResliceInterpolationProperty::New(VTK_RESLICE_LINEAR) ); // initialize showVolume to false to prevent recalculating the volume while working on the segmentation emptySegmentation->SetProperty( "showVolume", mitk::BoolProperty::New( false ) ); if (!emptySegmentation) return; // could be aborted by user UpdateOrganList( organColors, dialog->GetSegmentationName(), dialog->GetColor() ); /* escape ';' here (replace by '\;'), see longer comment above */ std::string stringForStorage = organColors.replaceInStrings(";","\\;").join(";").toStdString(); MITK_DEBUG << "Will store: " << stringForStorage; this->GetPreferences()->PutByteArray("Organ-Color-List", stringForStorage ); this->GetPreferences()->Flush(); if(m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetWorkingData(0)) { m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetWorkingData(0)->SetSelected(false); } emptySegmentation->SetSelected(true); this->GetDefaultDataStorage()->Add( emptySegmentation, node ); // add as a child, because the segmentation "derives" from the original this->FireNodeSelected( emptySegmentation ); this->OnSelectionChanged( emptySegmentation ); this->SetToolManagerSelection(node, emptySegmentation); } catch (std::bad_alloc) { QMessageBox::warning(NULL,"Create new segmentation","Could not allocate memory for new segmentation"); } } } else { QMessageBox::information(NULL,"Segmentation","Segmentation is currently not supported for 2D images"); } } } else { MITK_ERROR << "'Create new segmentation' button should never be clickable unless a patient image is selected..."; } } void QmitkSegmentationView::OnWorkingNodeVisibilityChanged(/*const itk::Object* caller, const itk::EventObject& e*/) { if (!m_Parent || !m_Parent->isVisible()) return; // The new selection behaviour is: // // When clicking on the checkbox of a segmentation the node will e selected and its reference node either // The previous selected segmentation (if there is one) will be deselected. Additionally a reinit on the // selected segmenation will be performed. // If more than one segmentation is selected the tools will be disabled. if (!m_Controls) return; // might happen on initialization (preferences loaded) mitk::DataNode::Pointer referenceDataNew = mitk::DataNode::New(); mitk::DataNode::Pointer workingData; bool workingNodeIsVisible (true); unsigned int numberOfSelectedSegmentations (0); // iterate all images mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer allImages = this->GetDefaultDataStorage()->GetSubset( isImage ); for ( mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter) { mitk::DataNode* node = *iter; // apply display preferences ApplyDisplayOptions(node); bool isSegmentation(false); node->GetBoolProperty("binary", isSegmentation); if (node->IsSelected() && isSegmentation) { workingNodeIsVisible = node->IsVisible(mitk::BaseRenderer::GetInstance( mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget1"))); if (!workingNodeIsVisible) return; numberOfSelectedSegmentations++; workingData = node; if (this->GetDefaultDataStorage()->GetSources(node)->Size() != 0) { referenceDataNew = this->GetDefaultDataStorage()->GetSources(node)->ElementAt(0); } bool isBinary(false); //Find topmost source or first source which is no binary image while (referenceDataNew && this->GetDefaultDataStorage()->GetSources(referenceDataNew)->Size() != 0) { referenceDataNew = this->GetDefaultDataStorage()->GetSources(referenceDataNew)->ElementAt(0); referenceDataNew->GetBoolProperty("binary",isBinary); if (!isBinary) break; } if (workingNodeIsVisible && referenceDataNew) { //Since the binary property of a segmentation can be set to false and afterwards you can create a new segmentation out of it //->could lead to a deadloop NodeTagMapType::iterator searchIter = m_WorkingDataObserverTags.find( referenceDataNew ); if ( searchIter != m_WorkingDataObserverTags.end()) { referenceDataNew->GetProperty("visible")->RemoveObserver( (*searchIter).second ); } referenceDataNew->SetVisibility(true); } //set comboBox to reference image disconnect( m_Controls->refImageSelector, SIGNAL( OnSelectionChanged( const mitk::DataNode* ) ), this, SLOT( OnComboBoxSelectionChanged( const mitk::DataNode* ) ) ); m_Controls->refImageSelector->setCurrentIndex( m_Controls->refImageSelector->Find(referenceDataNew) ); connect( m_Controls->refImageSelector, SIGNAL( OnSelectionChanged( const mitk::DataNode* ) ), this, SLOT( OnComboBoxSelectionChanged( const mitk::DataNode* ) ) ); continue; } if (workingData.IsNull() || (workingNodeIsVisible && node != referenceDataNew)) { node->SetVisibility((false)); } } if(numberOfSelectedSegmentations == 1) SetToolManagerSelection(referenceDataNew, workingData); mitk::DataStorage::SetOfObjects::Pointer temp = mitk::DataStorage::SetOfObjects::New(); temp->InsertElement(0,workingData); mitk::TimeSlicedGeometry::Pointer bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(temp); // initialize the views to the bounding geometry /*mitk::RenderingManager::GetInstance()->InitializeViews(bounds); mitk::RenderingManager::GetInstance()->RequestUpdateAll();*/ } void QmitkSegmentationView::NodeRemoved(const mitk::DataNode* node) { bool isSeg(false); bool isHelperObject(false); node->GetBoolProperty("helper object", isHelperObject); node->GetBoolProperty("binary", isSeg); if(isSeg && !isHelperObject) { mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = this->GetDataStorage()->GetDerivations(node, mitk::NodePredicateProperty::New("isContourMarker" , mitk::BoolProperty::New(true))); // gets the context of the "Mitk" (Core) module (always has id 1) // TODO Workaround until CTL plugincontext is available mitk::ModuleContext* context = mitk::ModuleRegistry::GetModule(1)->GetModuleContext(); // Workaround end mitk::ServiceReference serviceRef = context->GetServiceReference(); //mitk::ServiceReference serviceRef = mitk::GetModuleContext()->GetServiceReference(); mitk::PlanePositionManagerService* service = dynamic_cast(context->GetService(serviceRef)); 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()); } mitk::DataNode* tempNode = const_cast(node); node->GetProperty("visible")->RemoveObserver( m_WorkingDataObserverTags[tempNode] ); m_WorkingDataObserverTags.erase(tempNode); this->SetToolManagerSelection(NULL, NULL); } } void QmitkSegmentationView::CreateSegmentationFromSurface() { mitk::DataNode::Pointer surfaceNode = m_Controls->MaskSurfaces->GetSelectedNode(); mitk::Surface::Pointer surface(0); if(surfaceNode.IsNotNull()) surface = dynamic_cast ( surfaceNode->GetData() ); if(surface.IsNull()) { this->HandleException( "No surface selected.", m_Parent, true); return; } mitk::DataNode::Pointer imageNode = m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetReferenceData(0); mitk::Image::Pointer image(0); if (imageNode.IsNotNull()) image = dynamic_cast( imageNode->GetData() ); if(image.IsNull()) { this->HandleException( "No image selected.", m_Parent, true); return; } mitk::SurfaceToImageFilter::Pointer s2iFilter = mitk::SurfaceToImageFilter::New(); s2iFilter->MakeOutputBinaryOn(); s2iFilter->SetInput(surface); s2iFilter->SetImage(image); s2iFilter->Update(); mitk::DataNode::Pointer resultNode = mitk::DataNode::New(); std::string nameOfResultImage = imageNode->GetName(); nameOfResultImage.append(surfaceNode->GetName()); resultNode->SetProperty("name", mitk::StringProperty::New(nameOfResultImage) ); resultNode->SetProperty("binary", mitk::BoolProperty::New(true) ); resultNode->SetData( s2iFilter->GetOutput() ); this->GetDataStorage()->Add(resultNode, imageNode); } void QmitkSegmentationView::ManualToolSelected(int id) { // disable crosshair movement when a manual drawing tool is active (otherwise too much visual noise) if (m_MultiWidget) { if (id >= 0) { m_MultiWidget->DisableNavigationControllerEventListening(); } else { m_MultiWidget->EnableNavigationControllerEventListening(); } } } void QmitkSegmentationView::ToolboxStackPageChanged(int id) { // interpolation only with manual tools visible m_Controls->m_SlicesInterpolator->EnableInterpolation( id == 0 ); if( id == 0 ) { mitk::DataNode::Pointer workingData = m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetWorkingData(0); if( workingData.IsNotNull() ) { m_Controls->lblSegmentation->setText( workingData->GetName().c_str() ); m_Controls->lblSegImage->show(); m_Controls->lblSegmentation->show(); } } else { m_Controls->lblSegImage->hide(); m_Controls->lblSegmentation->hide(); } // this is just a workaround, should be removed when all tools support 3D+t if (id==2) // lesions { mitk::DataNode::Pointer node = m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetReferenceData(0); if (node.IsNotNull()) { mitk::Image::Pointer image = dynamic_cast( node->GetData() ); if (image.IsNotNull()) { if (image->GetDimension()>3) { m_Controls->widgetStack->setCurrentIndex(0); QMessageBox::information(NULL,"Segmentation","Lesion segmentation is currently not supported for 4D images"); } } } } } // protected void QmitkSegmentationView::OnComboBoxSelectionChanged( const mitk::DataNode* node ) { mitk::DataNode* selectedNode = const_cast(node); if( selectedNode != NULL ) { m_Controls->refImageSelector->show(); m_Controls->lblReferenceImageSelectionWarning->hide(); bool isBinary(false); selectedNode->GetBoolProperty("binary", isBinary); if ( isBinary ) { FireNodeSelected(selectedNode); selectedNode->SetVisibility(true); } else if (node != m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetReferenceData(0)) { if (m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetReferenceData(0)) m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetReferenceData(0)->SetVisibility(false); if (m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetWorkingData(0)) { m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetWorkingData(0)->SetVisibility(false); } FireNodeSelected(selectedNode); selectedNode->SetVisibility(true); SetToolManagerSelection(selectedNode, NULL); } } else { m_Controls->refImageSelector->hide(); m_Controls->lblReferenceImageSelectionWarning->show(); } } void QmitkSegmentationView::OnShowMarkerNodes (bool state) { mitk::SegTool2D::Pointer manualSegmentationTool; unsigned int numberOfExistingTools = m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetTools().size(); for(unsigned int i = 0; i < numberOfExistingTools; i++) { manualSegmentationTool = dynamic_cast(m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetToolById(i)); if (manualSegmentationTool) { if(state == true) { manualSegmentationTool->SetShowMarkerNodes( true ); } else { manualSegmentationTool->SetShowMarkerNodes( false ); } } } } void QmitkSegmentationView::On3DInterpolationEnabled (bool state) { mitk::SegTool2D::Pointer manualSegmentationTool; unsigned int numberOfExistingTools = m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetTools().size(); for(unsigned int i = 0; i < numberOfExistingTools; i++) { manualSegmentationTool = dynamic_cast(m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetToolById(i)); if (manualSegmentationTool) { manualSegmentationTool->Enable3DInterpolation( state ); } } } void QmitkSegmentationView::OnSelectionChanged(mitk::DataNode* node) { std::vector nodes; nodes.push_back( node ); this->OnSelectionChanged( nodes ); } void QmitkSegmentationView::OnSurfaceSelectionChanged() { // if Image and Surface are selected, enable button if ( (m_Controls->refImageSelector->GetSelectedNode().IsNull()) || (m_Controls->MaskSurfaces->GetSelectedNode().IsNull())) m_Controls->CreateSegmentationFromSurface->setEnabled(false); else m_Controls->CreateSegmentationFromSurface->setEnabled(true); } void QmitkSegmentationView::OnSelectionChanged(std::vector nodes) { // if the selected node is a contourmarker if ( !nodes.empty() ) { 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 ) ); } } // if Image and Surface are selected, enable button if ( (m_Controls->refImageSelector->GetSelectedNode().IsNull()) || (m_Controls->MaskSurfaces->GetSelectedNode().IsNull())) m_Controls->CreateSegmentationFromSurface->setEnabled(false); else m_Controls->CreateSegmentationFromSurface->setEnabled(true); if (!m_Parent || !m_Parent->isVisible()) return; // reaction to BlueBerry selection events // this method will try to figure out if a relevant segmentation and its corresponding original image were selected // a warning is issued if the selection is invalid // appropriate reactions are triggered otherwise mitk::DataNode::Pointer referenceData = FindFirstRegularImage( nodes ); //m_Controls->refImageSelector->GetSelectedNode(); //FindFirstRegularImage( nodes ); mitk::DataNode::Pointer workingData = FindFirstSegmentation( nodes ); if(referenceData.IsNull() && workingData.IsNull()) return; bool invalidSelection( !nodes.empty() && ( nodes.size() > 2 || // maximum 2 selected nodes (nodes.size() == 2 && (workingData.IsNull() || referenceData.IsNull()) ) || // with two nodes, one must be the original image, one the segmentation ( workingData.GetPointer() == referenceData.GetPointer() ) //one node is selected as reference and working image // one item is always ok (might be working or reference or nothing ) ); if (invalidSelection) { // TODO visible warning when two images are selected MITK_ERROR << "WARNING: No image, too many (>2) or two equal images were selected."; workingData = NULL; if( m_Controls->refImageSelector->GetSelectedNode().IsNull() ) referenceData = NULL; } if ( workingData.IsNotNull() && referenceData.IsNull() ) { // find the DataStorage parent of workingData // try to find a "normal image" parent, select this as reference image mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateProperty::Pointer isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateNot::Pointer isNotBinary = mitk::NodePredicateNot::New( isBinary ); mitk::NodePredicateAnd::Pointer isNormalImage = mitk::NodePredicateAnd::New( isImage, isNotBinary ); mitk::DataStorage::SetOfObjects::ConstPointer possibleParents = this->GetDefaultDataStorage()->GetSources( workingData, isNormalImage ); if (possibleParents->size() > 0) { if (possibleParents->size() > 1) { // TODO visible warning for this rare case MITK_ERROR << "Selected binary image has multiple parents. Using arbitrary first one for segmentation."; } referenceData = (*possibleParents)[0]; } NodeTagMapType::iterator searchIter = m_WorkingDataObserverTags.find( workingData ); if ( searchIter == m_WorkingDataObserverTags.end() ) { //MITK_INFO<<"Creating new observer"; itk::SimpleMemberCommand::Pointer command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::OnWorkingNodeVisibilityChanged); m_WorkingDataObserverTags.insert( std::pair( workingData, workingData->GetProperty("visible")->AddObserver( itk::ModifiedEvent(), command ) ) ); workingData->GetProperty("visible")->Modified(); return; } if(workingData->IsVisible(mitk::BaseRenderer::GetInstance( mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget1")))) { //set comboBox to reference image disconnect( m_Controls->refImageSelector, SIGNAL( OnSelectionChanged( const mitk::DataNode* ) ), this, SLOT( OnComboBoxSelectionChanged( const mitk::DataNode* ) ) ); m_Controls->refImageSelector->setCurrentIndex( m_Controls->refImageSelector->Find(workingData) ); connect( m_Controls->refImageSelector, SIGNAL( OnSelectionChanged( const mitk::DataNode* ) ), this, SLOT( OnComboBoxSelectionChanged( const mitk::DataNode* ) ) ); // if Image and Surface are selected, enable button if ( (m_Controls->refImageSelector->GetSelectedNode().IsNull()) || (m_Controls->MaskSurfaces->GetSelectedNode().IsNull()) || (!referenceData)) m_Controls->CreateSegmentationFromSurface->setEnabled(false); else m_Controls->CreateSegmentationFromSurface->setEnabled(true); SetToolManagerSelection(referenceData, workingData); FireNodeSelected(workingData); } else { SetToolManagerSelection(NULL, NULL); FireNodeSelected(workingData); } } else { //set comboBox to reference image disconnect( m_Controls->refImageSelector, SIGNAL( OnSelectionChanged( const mitk::DataNode* ) ), this, SLOT( OnComboBoxSelectionChanged( const mitk::DataNode* ) ) ); m_Controls->refImageSelector->setCurrentIndex( m_Controls->refImageSelector->Find(referenceData) ); connect( m_Controls->refImageSelector, SIGNAL( OnSelectionChanged( const mitk::DataNode* ) ), this, SLOT( OnComboBoxSelectionChanged( const mitk::DataNode* ) ) ); // if Image and Surface are selected, enable button if ( (m_Controls->refImageSelector->GetSelectedNode().IsNull()) || (m_Controls->MaskSurfaces->GetSelectedNode().IsNull()) || (!referenceData)) m_Controls->CreateSegmentationFromSurface->setEnabled(false); else m_Controls->CreateSegmentationFromSurface->setEnabled(true); SetToolManagerSelection(referenceData, workingData); FireNodeSelected(referenceData); } } void QmitkSegmentationView::OnContourMarkerSelected(const mitk::DataNode *node) { //TODO renderWindow anders bestimmen, siehe CheckAlignment QmitkRenderWindow* selectedRenderWindow = 0; QmitkRenderWindow* RenderWindow1 = this->GetActiveStdMultiWidget()->GetRenderWindow1(); QmitkRenderWindow* RenderWindow2 = this->GetActiveStdMultiWidget()->GetRenderWindow2(); QmitkRenderWindow* RenderWindow3 = this->GetActiveStdMultiWidget()->GetRenderWindow3(); QmitkRenderWindow* RenderWindow4 = this->GetActiveStdMultiWidget()->GetRenderWindow4(); bool PlanarFigureInitializedWindow = false; // find initialized renderwindow if (node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, RenderWindow1->GetRenderer())) { selectedRenderWindow = RenderWindow1; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, RenderWindow2->GetRenderer())) { selectedRenderWindow = RenderWindow2; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, RenderWindow3->GetRenderer())) { selectedRenderWindow = RenderWindow3; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, RenderWindow4->GetRenderer())) { selectedRenderWindow = RenderWindow4; } // make node visible if (selectedRenderWindow) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t+1).c_str())-1; // gets the context of the "Mitk" (Core) module (always has id 1) // TODO Workaround until CTL plugincontext is available mitk::ModuleContext* context = mitk::ModuleRegistry::GetModule(1)->GetModuleContext(); // Workaround end mitk::ServiceReference serviceRef = context->GetServiceReference(); //mitk::ServiceReference serviceRef = mitk::GetModuleContext()->GetServiceReference(); mitk::PlanePositionManagerService* service = dynamic_cast(context->GetService(serviceRef)); selectedRenderWindow->GetSliceNavigationController()->ExecuteOperation(service->GetPlanePosition(id)); selectedRenderWindow->GetRenderer()->GetDisplayGeometry()->Fit(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } mitk::DataNode::Pointer QmitkSegmentationView::FindFirstRegularImage( std::vector nodes ) { if (nodes.empty()) return NULL; for(unsigned int i = 0; i < nodes.size(); ++i) { //mitk::DataNode::Pointer node = i.value() bool isImage(false); if (nodes.at(i)->GetData()) { isImage = dynamic_cast(nodes.at(i)->GetData()) != NULL; } // make sure this is not a binary image bool isSegmentation(false); nodes.at(i)->GetBoolProperty("binary", isSegmentation); // return first proper mitk::Image if (isImage && !isSegmentation) return nodes.at(i); } return NULL; } mitk::DataNode::Pointer QmitkSegmentationView::FindFirstSegmentation( std::vector nodes ) { if (nodes.empty()) return NULL; for(unsigned int i = 0; i < nodes.size(); ++i) { bool isImage(false); if (nodes.at(i)->GetData()) { isImage = dynamic_cast(nodes.at(i)->GetData()) != NULL; } bool isSegmentation(false); nodes.at(i)->GetBoolProperty("binary", isSegmentation); // return first proper binary mitk::Image if (isImage && isSegmentation) { return nodes.at(i); } } return NULL; } void QmitkSegmentationView::SetToolManagerSelection(const mitk::DataNode* referenceData, const mitk::DataNode* workingData) { // called as a result of new BlueBerry selections // tells the ToolManager for manual segmentation about new selections // updates GUI information about what the user should select mitk::ToolManager* toolManager = m_Controls->m_ManualToolSelectionBox->GetToolManager(); toolManager->SetReferenceData(const_cast(referenceData)); toolManager->SetWorkingData( const_cast(workingData)); // check original image m_Controls->btnNewSegmentation->setEnabled(referenceData != NULL); if (referenceData) { m_Controls->lblReferenceImageSelectionWarning->hide(); } else { m_Controls->lblReferenceImageSelectionWarning->show(); m_Controls->lblWorkingImageSelectionWarning->hide(); m_Controls->lblSegImage->hide(); m_Controls->lblSegmentation->hide(); } //TODO remove statement // check, wheter reference image is aligned like render windows. Otherwise display a visible warning (because 2D tools will probably not work) CheckImageAlignment(); // check segmentation if (referenceData) { if (!workingData) { m_Controls->lblWorkingImageSelectionWarning->show(); if( m_Controls->widgetStack->currentIndex() == 0 ) { m_Controls->lblSegImage->hide(); m_Controls->lblSegmentation->hide(); } } else { m_Controls->lblWorkingImageSelectionWarning->hide(); this->FireNodeSelected(const_cast(workingData)); if( m_Controls->widgetStack->currentIndex() == 0 ) { m_Controls->lblSegmentation->setText( workingData->GetName().c_str() ); m_Controls->lblSegmentation->show(); m_Controls->lblSegImage->show(); } } } } //TODO remove function void QmitkSegmentationView::CheckImageAlignment() { bool wrongAlignment(true); mitk::DataNode::Pointer node = m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetReferenceData(0); if (node.IsNotNull()) { mitk::Image::Pointer image = dynamic_cast( node->GetData() ); if (image.IsNotNull() && m_MultiWidget) { wrongAlignment = !( IsRenderWindowAligned(m_MultiWidget->GetRenderWindow1(), image ) && IsRenderWindowAligned(m_MultiWidget->GetRenderWindow2(), image ) && IsRenderWindowAligned(m_MultiWidget->GetRenderWindow3(), image ) ); } if (wrongAlignment) { m_Controls->lblAlignmentWarning->show(); } } } //TODO remove function bool QmitkSegmentationView::IsRenderWindowAligned(QmitkRenderWindow* renderWindow, mitk::Image* image) { if (!renderWindow) return false; // for all 2D renderwindows of m_MultiWidget check alignment mitk::PlaneGeometry::ConstPointer displayPlane = dynamic_cast( renderWindow->GetRenderer()->GetCurrentWorldGeometry2D() ); if (displayPlane.IsNull()) return false; int affectedDimension(-1); int affectedSlice(-1); return mitk::SegTool2D::DetermineAffectedImageSlice( image, displayPlane, affectedDimension, affectedSlice ); } //TODO remove function void QmitkSegmentationView::ForceDisplayPreferencesUponAllImages() { if (!m_Parent || !m_Parent->isVisible()) return; // check all images and segmentations in DataStorage: // (items in brackets are implicitly done by previous steps) // 1. // if a reference image is selected, // show the reference image // and hide all other images (orignal and segmentation), // (and hide all segmentations of the other original images) // and show all the reference's segmentations // if no reference image is selected, do do nothing // // 2. // if a segmentation is selected, // show it // (and hide all all its siblings (childs of the same parent, incl, NULL parent)) // if no segmentation is selected, do nothing if (!m_Controls) return; // might happen on initialization (preferences loaded) mitk::DataNode::Pointer referenceData = m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetReferenceData(0); mitk::DataNode::Pointer workingData = m_Controls->m_ManualToolSelectionBox->GetToolManager()->GetWorkingData(0); // 1. if (referenceData.IsNotNull()) { // iterate all images mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer allImages = this->GetDefaultDataStorage()->GetSubset( isImage ); //mitk::DataStorage::SetOfObjects::ConstPointer allSegmentationChilds = this->GetDefaultDataStorage()->GetDerivations(referenceData, isImage ); for ( mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter) { mitk::DataNode* node = *iter; // apply display preferences ApplyDisplayOptions(node); // set visibility if(!node->IsSelected() || (node->IsSelected() && !node->IsVisible(mitk::BaseRenderer::GetInstance( mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget1"))))) node->SetVisibility((node == referenceData) || node->IsSelected() ); } } // 2. //if (workingData.IsNotNull() && !workingData->IsSelected()) //{ // workingData->SetVisibility(true); //} mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::ApplyDisplayOptions(mitk::DataNode* node) { if (!node) return; bool isBinary(false); node->GetPropertyValue("binary", isBinary); if (isBinary) { node->SetProperty( "outline binary", mitk::BoolProperty::New( this->GetPreferences()->GetBool("draw outline", true)) ); node->SetProperty( "outline width", mitk::FloatProperty::New( 2.0 ) ); node->SetProperty( "opacity", mitk::FloatProperty::New( this->GetPreferences()->GetBool("draw outline", true) ? 1.0 : 0.3 ) ); node->SetProperty( "volumerendering", mitk::BoolProperty::New( this->GetPreferences()->GetBool("volume rendering", false) ) ); } } void QmitkSegmentationView::CreateQtPartControl(QWidget* parent) { // setup the basic GUI of this view m_Parent = parent; m_Controls = new Ui::QmitkSegmentationControls; m_Controls->setupUi(parent); m_Controls->lblWorkingImageSelectionWarning->hide(); m_Controls->lblAlignmentWarning->hide(); m_Controls->lblSegImage->hide(); m_Controls->lblSegmentation->hide(); m_Controls->refImageSelector->SetDataStorage(this->GetDefaultDataStorage()); m_Controls->refImageSelector->SetPredicate(mitk::NodePredicateDataType::New("Image")); if( m_Controls->refImageSelector->GetSelectedNode().IsNotNull() ) m_Controls->lblReferenceImageSelectionWarning->hide(); else m_Controls->refImageSelector->hide(); mitk::ToolManager* toolManager = m_Controls->m_ManualToolSelectionBox->GetToolManager(); toolManager->SetDataStorage( *(this->GetDefaultDataStorage()) ); assert ( toolManager ); // all part of open source MITK m_Controls->m_ManualToolSelectionBox->SetGenerateAccelerators(true); m_Controls->m_ManualToolSelectionBox->SetToolGUIArea( m_Controls->m_ManualToolGUIContainer ); m_Controls->m_ManualToolSelectionBox->SetDisplayedToolGroups("Add Subtract Paint Wipe 'Region Growing' Correction Fill Erase"); m_Controls->m_ManualToolSelectionBox->SetEnabledMode( QmitkToolSelectionBox::EnabledWithReferenceAndWorkingData ); // available only in the 3M application if ( !m_Controls->m_OrganToolSelectionBox->children().count() ) { m_Controls->widgetStack->setItemEnabled( 1, false ); } m_Controls->m_OrganToolSelectionBox->SetToolManager( *toolManager ); m_Controls->m_OrganToolSelectionBox->SetToolGUIArea( m_Controls->m_OrganToolGUIContainer ); m_Controls->m_OrganToolSelectionBox->SetDisplayedToolGroups("'Hippocampus left' 'Hippocampus right' 'Lung left' 'Lung right' 'Liver' 'Heart LV' 'Endocard LV' 'Epicard LV' 'Prostate'"); m_Controls->m_OrganToolSelectionBox->SetEnabledMode( QmitkToolSelectionBox::EnabledWithReferenceData ); // available only in the 3M application if ( !m_Controls->m_LesionToolSelectionBox->children().count() ) { m_Controls->widgetStack->setItemEnabled( 2, false ); } m_Controls->m_LesionToolSelectionBox->SetToolManager( *toolManager ); m_Controls->m_LesionToolSelectionBox->SetToolGUIArea( m_Controls->m_LesionToolGUIContainer ); m_Controls->m_LesionToolSelectionBox->SetDisplayedToolGroups("'Lymph Node'"); m_Controls->m_LesionToolSelectionBox->SetEnabledMode( QmitkToolSelectionBox::EnabledWithReferenceData ); toolManager->NewNodesGenerated += mitk::MessageDelegate( this, &QmitkSegmentationView::NewNodesGenerated ); // update the list of segmentations toolManager->NewNodeObjectsGenerated += mitk::MessageDelegate1( this, &QmitkSegmentationView::NewNodeObjectsGenerated ); // update the list of segmentations // create signal/slot connections connect( m_Controls->refImageSelector, SIGNAL( OnSelectionChanged( const mitk::DataNode* ) ), this, SLOT( OnComboBoxSelectionChanged( const mitk::DataNode* ) ) ); connect( m_Controls->btnNewSegmentation, SIGNAL(clicked()), this, SLOT(CreateNewSegmentation()) ); connect( m_Controls->CreateSegmentationFromSurface, SIGNAL(clicked()), this, SLOT(CreateSegmentationFromSurface()) ); connect( m_Controls->m_ManualToolSelectionBox, SIGNAL(ToolSelected(int)), this, SLOT(ManualToolSelected(int)) ); connect( m_Controls->widgetStack, SIGNAL(currentChanged(int)), this, SLOT(ToolboxStackPageChanged(int)) ); connect(m_Controls->MaskSurfaces, SIGNAL( OnSelectionChanged( const mitk::DataNode* ) ), this, SLOT( OnSurfaceSelectionChanged( ) ) ); connect(m_Controls->MaskSurfaces, SIGNAL( OnSelectionChanged( const mitk::DataNode* ) ), this, SLOT( OnSurfaceSelectionChanged( ) ) ); connect(m_Controls->m_SlicesInterpolator, SIGNAL(SignalShowMarkerNodes(bool)), this, SLOT(OnShowMarkerNodes(bool))); connect(m_Controls->m_SlicesInterpolator, SIGNAL(Signal3DInterpolationEnabled(bool)), this, SLOT(On3DInterpolationEnabled(bool))); m_Controls->MaskSurfaces->SetDataStorage(this->GetDefaultDataStorage()); m_Controls->MaskSurfaces->SetPredicate(mitk::NodePredicateDataType::New("Surface")); //// create helper class to provide context menus for segmentations in data manager // m_PostProcessing = new QmitkSegmentationPostProcessing(this->GetDefaultDataStorage(), this, m_Parent); } //void QmitkSegmentationView::OnPlaneModeChanged(int i) //{ // //if plane mode changes, disable all tools // if (m_MultiWidget) // { // mitk::ToolManager* toolManager = m_Controls->m_ManualToolSelectionBox->GetToolManager(); // // if (toolManager) // { // if (toolManager->GetActiveToolID() >= 0) // { // toolManager->ActivateTool(-1); // } // else // { // m_MultiWidget->EnableNavigationControllerEventListening(); // } // } // } //} // ATTENTION some methods for handling the known list of (organ names, colors) are defined in QmitkSegmentationOrganNamesHandling.cpp diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkThresholdAction.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkThresholdAction.cpp index 2cb05d7528..17cefd99c8 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkThresholdAction.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkThresholdAction.cpp @@ -1,99 +1,100 @@ #include "QmitkThresholdAction.h" // MITK #include #include #include // Qt #include #include +#include using namespace berry; using namespace mitk; using namespace std; QmitkThresholdAction::QmitkThresholdAction() : m_ThresholdingDialog(NULL) { } QmitkThresholdAction::~QmitkThresholdAction() { } void QmitkThresholdAction::Run(const QList &selectedNodes) { m_ThresholdingToolManager = ToolManager::New(m_DataStorage); m_ThresholdingToolManager->RegisterClient(); m_ThresholdingToolManager->ActiveToolChanged += mitk::MessageDelegate(this, &QmitkThresholdAction::OnThresholdingToolManagerToolModified); - m_ThresholdingDialog = new QDialog; + m_ThresholdingDialog = new QDialog(QApplication::activeWindow()); connect(m_ThresholdingDialog, SIGNAL(finished(int)), this, SLOT(ThresholdingDone(int))); QVBoxLayout *layout = new QVBoxLayout; layout->setContentsMargins(0, 0, 0, 0); Tool *binaryThresholdTool = m_ThresholdingToolManager->GetToolById(m_ThresholdingToolManager->GetToolIdByToolType()); if (binaryThresholdTool != NULL) { QmitkToolGUI *gui = dynamic_cast(binaryThresholdTool->GetGUI("Qmitk", "GUI").GetPointer()); if (gui != NULL) { gui->SetTool(binaryThresholdTool); gui->setParent(m_ThresholdingDialog); layout->addWidget(gui); m_ThresholdingDialog->setLayout(layout); m_ThresholdingDialog->setFixedSize(300, 80); m_ThresholdingDialog->open(); } m_ThresholdingToolManager->SetReferenceData(selectedNodes[0]); m_ThresholdingToolManager->ActivateTool(m_ThresholdingToolManager->GetToolIdByToolType()); } } void QmitkThresholdAction::ThresholdingDone(int result) { if (result == QDialog::Rejected) m_ThresholdingToolManager->ActivateTool(-1); m_ThresholdingDialog->deleteLater(); m_ThresholdingDialog = NULL; m_ThresholdingToolManager->SetReferenceData(NULL); m_ThresholdingToolManager->SetWorkingData(NULL); RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkThresholdAction::OnThresholdingToolManagerToolModified() { if (m_ThresholdingToolManager.IsNotNull()) if (m_ThresholdingToolManager->GetActiveToolID() < 0) if (m_ThresholdingDialog != NULL) m_ThresholdingDialog->accept(); } void QmitkThresholdAction::SetDataStorage(DataStorage *dataStorage) { m_DataStorage = dataStorage; } void QmitkThresholdAction::SetSmoothed(bool) { } void QmitkThresholdAction::SetDecimated(bool) { } void QmitkThresholdAction::SetFunctionality(QtViewPart* /*functionality*/) { } diff --git a/SuperBuild.cmake b/SuperBuild.cmake index 9273d6c61b..333dc51aff 100644 --- a/SuperBuild.cmake +++ b/SuperBuild.cmake @@ -1,309 +1,309 @@ #----------------------------------------------------------------------------- # Convenient macro allowing to download a file #----------------------------------------------------------------------------- macro(downloadFile url dest) file(DOWNLOAD ${url} ${dest} STATUS status) list(GET status 0 error_code) list(GET status 1 error_msg) if(error_code) message(FATAL_ERROR "error: Failed to download ${url} - ${error_msg}") endif() endmacro() #----------------------------------------------------------------------------- # MITK Prerequisites #----------------------------------------------------------------------------- if(UNIX AND NOT APPLE) #----------------------------- libxt-dev -------------------- include(${CMAKE_ROOT}/Modules/CheckIncludeFile.cmake) set(CMAKE_REQUIRED_INCLUDES "/usr/include/X11/") CHECK_INCLUDE_FILE("StringDefs.h" STRING_DEFS_H) if(NOT STRING_DEFS_H) message(FATAL_ERROR "error: could not find StringDefs.h provided by libxt-dev") endif() set(CMAKE_REQUIRED_INCLUDES "/usr/include/") CHECK_INCLUDE_FILE("tiff.h" TIFF_H) if(NOT TIFF_H) message(FATAL_ERROR "error: could not find tiff.h - libtiff4-dev needs to be installed") endif() CHECK_INCLUDE_FILE("tcpd.h" LIB_WRAP) if(NOT LIB_WRAP) - message(FATAL_ERROR "error: could not find tcpd.h - libwrap0-dev needs to be installed") + message(STATUS "Could not find tcpd.h - if this is missing in the build libwrap0-dev needs to be installed") endif() endif() #----------------------------------------------------------------------------- # ExternalProjects #----------------------------------------------------------------------------- set(external_projects VTK GDCM CableSwig ITK Boost DCMTK CTK OpenCV MITKData ) set(MITK_USE_CableSwig ${MITK_USE_Python}) set(MITK_USE_GDCM 1) set(MITK_USE_ITK 1) set(MITK_USE_VTK 1) foreach(proj VTK GDCM CableSwig ITK DCMTK CTK OpenCV) if(MITK_USE_${proj}) set(EXTERNAL_${proj}_DIR "${${proj}_DIR}" CACHE PATH "Path to ${proj} build directory") mark_as_advanced(EXTERNAL_${proj}_DIR) if(EXTERNAL_${proj}_DIR) set(${proj}_DIR ${EXTERNAL_${proj}_DIR}) endif() endif() endforeach() if(MITK_USE_Boost) set(EXTERNAL_BOOST_ROOT "${BOOST_ROOT}" CACHE PATH "Path to Boost directory") mark_as_advanced(EXTERNAL_BOOST_ROOT) if(EXTERNAL_BOOST_ROOT) set(BOOST_ROOT ${EXTERNAL_BOOST_ROOT}) endif() endif() if(BUILD_TESTING) set(EXTERNAL_MITK_DATA_DIR "${MITK_DATA_DIR}" CACHE PATH "Path to the MITK data directory") mark_as_advanced(EXTERNAL_MITK_DATA_DIR) if(EXTERNAL_MITK_DATA_DIR) set(MITK_DATA_DIR ${EXTERNAL_MITK_DATA_DIR}) endif() endif() # Look for git early on, if needed if((BUILD_TESTING AND NOT EXTERNAL_MITK_DATA_DIR) OR (MITK_USE_CTK AND NOT EXTERNAL_CTK_DIR)) find_package(Git REQUIRED) endif() #----------------------------------------------------------------------------- # External project settings #----------------------------------------------------------------------------- include(ExternalProject) set(ep_base "${CMAKE_BINARY_DIR}/CMakeExternals") set_property(DIRECTORY PROPERTY EP_BASE ${ep_base}) set(ep_install_dir ${ep_base}/Install) #set(ep_build_dir ${ep_base}/Build) set(ep_source_dir ${ep_base}/Source) #set(ep_parallelism_level) set(ep_build_shared_libs ON) set(ep_build_testing OFF) if(NOT MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL) set(MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL http://mitk.org/download/thirdparty) endif() # Compute -G arg for configuring external projects with the same CMake generator: if(CMAKE_EXTRA_GENERATOR) set(gen "${CMAKE_EXTRA_GENERATOR} - ${CMAKE_GENERATOR}") else() set(gen "${CMAKE_GENERATOR}") endif() # Use this value where semi-colons are needed in ep_add args: set(sep "^^") ## if(MSVC90 OR MSVC10) set(ep_common_C_FLAGS "${CMAKE_C_FLAGS} /bigobj /MP") set(ep_common_CXX_FLAGS "${CMAKE_CXX_FLAGS} /bigobj /MP") else() set(ep_common_C_FLAGS "${CMAKE_C_FLAGS} -DLINUX_EXTRA") set(ep_common_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DLINUX_EXTRA") endif() set(ep_common_args -DBUILD_TESTING:BOOL=${ep_build_testing} -DCMAKE_INSTALL_PREFIX:PATH=${ep_install_dir} -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE} -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER} -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER} -DCMAKE_C_FLAGS:STRING=${ep_common_C_FLAGS} -DCMAKE_CXX_FLAGS:STRING=${ep_common_CXX_FLAGS} #debug flags -DCMAKE_CXX_FLAGS_DEBUG:STRING=${CMAKE_CXX_FLAGS_DEBUG} -DCMAKE_C_FLAGS_DEBUG:STRING=${CMAKE_C_FLAGS_DEBUG} #release flags -DCMAKE_CXX_FLAGS_RELEASE:STRING=${CMAKE_CXX_FLAGS_RELEASE} -DCMAKE_C_FLAGS_RELEASE:STRING=${CMAKE_C_FLAGS_RELEASE} #relwithdebinfo -DCMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -DCMAKE_C_FLAGS_RELWITHDEBINFO:STRING=${CMAKE_C_FLAGS_RELWITHDEBINFO} ) # Include external projects foreach(p ${external_projects}) include(CMakeExternals/${p}.cmake) endforeach() #----------------------------------------------------------------------------- # Set superbuild boolean args #----------------------------------------------------------------------------- set(mitk_cmake_boolean_args BUILD_SHARED_LIBS WITH_COVERAGE BUILD_TESTING MITK_USE_QT MITK_BUILD_ALL_PLUGINS MITK_BUILD_ALL_APPS MITK_BUILD_TUTORIAL MITK_USE_Boost MITK_USE_SYSTEM_Boost MITK_USE_BLUEBERRY MITK_USE_CTK MITK_USE_DCMTK MITK_USE_OpenCV MITK_USE_Python ) #----------------------------------------------------------------------------- # Create the final variable containing superbuild boolean args #----------------------------------------------------------------------------- set(mitk_superbuild_boolean_args) foreach(mitk_cmake_arg ${mitk_cmake_boolean_args}) list(APPEND mitk_superbuild_boolean_args -D${mitk_cmake_arg}:BOOL=${${mitk_cmake_arg}}) endforeach() if(MITK_BUILD_ALL_PLUGINS) list(APPEND mitk_superbuild_boolean_args -DBLUEBERRY_BUILD_ALL_PLUGINS:BOOL=ON) endif() #----------------------------------------------------------------------------- # MITK Utilities #----------------------------------------------------------------------------- set(proj MITK-Utilities) ExternalProject_Add(${proj} DOWNLOAD_COMMAND "" CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" DEPENDS # Mandatory dependencies ${VTK_DEPENDS} ${ITK_DEPENDS} # Optionnal dependencies ${Boost_DEPENDS} ${CTK_DEPENDS} ${DCMTK_DEPENDS} ${OpenCV_DEPENDS} ${MITK-Data_DEPENDS} ) #----------------------------------------------------------------------------- # MITK Configure #----------------------------------------------------------------------------- if(MITK_INITIAL_CACHE_FILE) set(mitk_initial_cache_arg -C "${MITK_INITIAL_CACHE_FILE}") endif() set(mitk_optional_cache_args ) foreach(type RUNTIME ARCHIVE LIBRARY) if(DEFINED CTK_PLUGIN_${type}_OUTPUT_DIRECTORY) list(APPEND mitk_optional_cache_args -DCTK_PLUGIN_${type}_OUTPUT_DIRECTORY:PATH=${CTK_PLUGIN_${type}_OUTPUT_DIRECTORY}) endif() endforeach() set(proj MITK-Configure) ExternalProject_Add(${proj} LIST_SEPARATOR ^^ DOWNLOAD_COMMAND "" CMAKE_GENERATOR ${gen} CMAKE_CACHE_ARGS ${ep_common_args} ${mitk_superbuild_boolean_args} ${mitk_optional_cache_args} -DMITK_USE_SUPERBUILD:BOOL=OFF -DMITK_CMAKE_LIBRARY_OUTPUT_DIRECTORY:PATH=${MITK_CMAKE_LIBRARY_OUTPUT_DIRECTORY} -DMITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY:PATH=${MITK_CMAKE_RUNTIME_OUTPUT_DIRECTORY} -DMITK_CMAKE_ARCHIVE_OUTPUT_DIRECTORY:PATH=${MITK_CMAKE_ARCHIVE_OUTPUT_DIRECTORY} -DCTEST_USE_LAUNCHERS:BOOL=${CTEST_USE_LAUNCHERS} -DMITK_CTEST_SCRIPT_MODE:STRING=${MITK_CTEST_SCRIPT_MODE} -DMITK_SUPERBUILD_BINARY_DIR:PATH=${MITK_BINARY_DIR} -DQT_QMAKE_EXECUTABLE:FILEPATH=${QT_QMAKE_EXECUTABLE} -DMITK_KWSTYLE_EXECUTABLE:FILEPATH=${MITK_KWSTYLE_EXECUTABLE} -DMITK_MODULES_TO_BUILD:INTERNAL=${MITK_MODULES_TO_BUILD} -DCTK_DIR:PATH=${CTK_DIR} -DDCMTK_DIR:PATH=${DCMTK_DIR} -DVTK_DIR:PATH=${VTK_DIR} # FindVTK expects VTK_DIR -DITK_DIR:PATH=${ITK_DIR} # FindITK expects ITK_DIR -DOpenCV_DIR:PATH=${OpenCV_DIR} -DGDCM_DIR:PATH=${GDCM_DIR} -DBOOST_ROOT:PATH=${BOOST_ROOT} -DMITK_USE_Boost_LIBRARIES:STRING=${MITK_USE_Boost_LIBRARIES} -DMITK_DATA_DIR:PATH=${MITK_DATA_DIR} -DMITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES} -DMITK_ACCESSBYITK_FLOATING_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES} -DMITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES:STRING=${MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES} -DMITK_ACCESSBYITK_DIMENSIONS:STRING=${MITK_ACCESSBYITK_DIMENSIONS} CMAKE_ARGS ${mitk_initial_cache_arg} SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR} BINARY_DIR ${CMAKE_BINARY_DIR}/MITK-build BUILD_COMMAND "" INSTALL_COMMAND "" DEPENDS MITK-Utilities ) #----------------------------------------------------------------------------- # MITK #----------------------------------------------------------------------------- if(CMAKE_GENERATOR MATCHES ".*Makefiles.*") set(mitk_build_cmd "$(MAKE)") else() set(mitk_build_cmd ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/MITK-build --config ${CMAKE_CFG_INTDIR}) endif() if(NOT DEFINED SUPERBUILD_EXCLUDE_MITKBUILD_TARGET OR NOT SUPERBUILD_EXCLUDE_MITKBUILD_TARGET) set(MITKBUILD_TARGET_ALL_OPTION "ALL") else() set(MITKBUILD_TARGET_ALL_OPTION "") endif() add_custom_target(MITK-build ${MITKBUILD_TARGET_ALL_OPTION} COMMAND ${mitk_build_cmd} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/MITK-build DEPENDS MITK-Configure ) #----------------------------------------------------------------------------- # Custom target allowing to drive the build of the MITK project itself #----------------------------------------------------------------------------- add_custom_target(MITK COMMAND ${mitk_build_cmd} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/MITK-build ) diff --git a/Utilities/Poco/Foundation/include/Poco/Hash.h b/Utilities/Poco/Foundation/include/Poco/Hash.h index 99b1aa9d90..3f4b98881b 100755 --- a/Utilities/Poco/Foundation/include/Poco/Hash.h +++ b/Utilities/Poco/Foundation/include/Poco/Hash.h @@ -1,127 +1,127 @@ // // Hash.h // // $Id$ // // Library: Foundation // Package: Hashing // Module: Hash // // Definition of the Hash class. // // Copyright (c) 2006, Applied Informatics Software Engineering GmbH. // and Contributors. // // Permission is hereby granted, free of charge, to any person or organization // obtaining a copy of the software and accompanying documentation covered by // this license (the "Software") to use, reproduce, display, distribute, // execute, and transmit the Software, and to prepare derivative works of the // Software, and to permit third-parties to whom the Software is furnished to // do so, all subject to the following: // // The copyright notices in the Software and this entire statement, including // the above license grant, this restriction and the following disclaimer, // must be included in all copies of the Software, in whole or in part, and // all derivative works of the Software, unless such copies or derivative // works are solely in the form of machine-executable object code generated by // a source language processor. // // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, // FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT // SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE // FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, // ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER // DEALINGS IN THE SOFTWARE. // #ifndef Foundation_Hash_INCLUDED #define Foundation_Hash_INCLUDED #include "Poco/Foundation.h" #include namespace Poco { +std::size_t Foundation_API hash(Int8 n); +std::size_t Foundation_API hash(UInt8 n); +std::size_t Foundation_API hash(Int16 n); +std::size_t Foundation_API hash(UInt16 n); +std::size_t Foundation_API hash(Int32 n); +std::size_t Foundation_API hash(UInt32 n); +std::size_t Foundation_API hash(Int64 n); +std::size_t Foundation_API hash(UInt64 n); +std::size_t Foundation_API hash(const std::string& str); + template struct Hash /// A generic hash function. { std::size_t operator () (T value) const /// Returns the hash for the given value. { return hash(value); } }; -std::size_t Foundation_API hash(Int8 n); -std::size_t Foundation_API hash(UInt8 n); -std::size_t Foundation_API hash(Int16 n); -std::size_t Foundation_API hash(UInt16 n); -std::size_t Foundation_API hash(Int32 n); -std::size_t Foundation_API hash(UInt32 n); -std::size_t Foundation_API hash(Int64 n); -std::size_t Foundation_API hash(UInt64 n); -std::size_t Foundation_API hash(const std::string& str); - // // inlines // inline std::size_t hash(Int8 n) { return static_cast(n)*2654435761U; } inline std::size_t hash(UInt8 n) { return static_cast(n)*2654435761U; } inline std::size_t hash(Int16 n) { return static_cast(n)*2654435761U; } inline std::size_t hash(UInt16 n) { return static_cast(n)*2654435761U; } inline std::size_t hash(Int32 n) { return static_cast(n)*2654435761U; } inline std::size_t hash(UInt32 n) { return static_cast(n)*2654435761U; } inline std::size_t hash(Int64 n) { return static_cast(n)*2654435761U; } inline std::size_t hash(UInt64 n) { return static_cast(n)*2654435761U; } } // namespace Poco #endif // Foundation_Hash_INCLUDED