diff --git a/Applications/Diffusion/CMakeLists.txt b/Applications/Diffusion/CMakeLists.txt index 5952f3fe15..feeb951778 100644 --- a/Applications/Diffusion/CMakeLists.txt +++ b/Applications/Diffusion/CMakeLists.txt @@ -1,105 +1,109 @@ -if(MITK_USE_Python) - project(MitkDiffusion) set(DIFFUSIONAPP_NAME MitkDiffusion) set(_app_options) if(MITK_SHOW_CONSOLE_WINDOW) list(APPEND _app_options SHOW_CONSOLE) endif() # 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) # should be identical to the list in /CMake/mitkBuildConfigurationmitkDiffusion.cmake # remember to set plugins which should be automatically toggled in target_libraries.cmake set(_plugins org.commontk.configadmin org.commontk.eventadmin org.blueberry.core.runtime org.blueberry.core.expressions org.blueberry.core.commands org.blueberry.ui.qt org.blueberry.ui.qt.log org.blueberry.ui.qt.help org.mitk.core.services org.mitk.gui.common org.mitk.planarfigure org.mitk.core.ext 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.datamanager org.mitk.gui.qt.measurementtoolbox org.mitk.gui.qt.segmentation org.mitk.gui_qt.multilabelsegmentation org.mitk.gui.qt.python org.mitk.gui.qt.volumevisualization org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.diffusionimaging.connectomics org.mitk.gui.qt.diffusionimaging.fiberfox org.mitk.gui.qt.diffusionimaging.fiberprocessing org.mitk.gui.qt.diffusionimaging.ivim org.mitk.gui.qt.diffusionimaging.odfpeaks org.mitk.gui.qt.diffusionimaging.preprocessing org.mitk.gui.qt.diffusionimaging.reconstruction org.mitk.gui.qt.diffusionimaging.tractography org.mitk.gui.qt.diffusionimaging.registration org.mitk.gui.qt.diffusionimaging.python org.mitk.gui.qt.diffusionimaging.denoising org.mitk.gui.qt.diffusionimaging.partialvolume org.mitk.gui.qt.matchpoint.algorithm.browser org.mitk.gui.qt.matchpoint.algorithm.control org.mitk.gui.qt.matchpoint.mapper org.mitk.gui.qt.imagenavigator org.mitk.gui.qt.moviemaker org.mitk.gui.qt.basicimageprocessing org.mitk.gui.qt.properties org.mitk.gui.qt.viewnavigator ) +if(NOT MITK_USE_Python) + list(REMOVE_ITEM _plugins org.mitk.gui.qt.diffusionimaging.python) + list(REMOVE_ITEM _plugins org.mitk.gui.qt.python) +endif() + + + # 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 ) set(_src_files MitkDiffusion.cpp ) qt5_add_resources(_src_files splashscreen.qrc) mitkFunctionCreateBlueBerryApplication( NAME ${DIFFUSIONAPP_NAME} DESCRIPTION "MITK Diffusion" PLUGINS ${_plugins} EXCLUDE_PLUGINS ${_exclude_plugins} SOURCES ${_src_files} ${_app_options} ) mitk_use_modules(TARGET ${DIFFUSIONAPP_NAME} MODULES MitkAppUtil) # Add meta dependencies (e.g. on auto-load modules from depending modules) if(TARGET ${CMAKE_PROJECT_NAME}-autoload) add_dependencies(${DIFFUSIONAPP_NAME} ${CMAKE_PROJECT_NAME}-autoload) endif() # Add a build time dependency to legacy BlueBerry bundles. if(MITK_MODULES_ENABLED_PLUGINS) add_dependencies(${DIFFUSIONAPP_NAME} ${MITK_MODULES_ENABLED_PLUGINS}) endif() -endif() # MITK_USE_PYTHON diff --git a/Applications/Diffusion/target_libraries.cmake b/Applications/Diffusion/target_libraries.cmake index 80346af347..0b880357cb 100644 --- a/Applications/Diffusion/target_libraries.cmake +++ b/Applications/Diffusion/target_libraries.cmake @@ -1,37 +1,42 @@ # A list of plug-in targets which should be automatically enabled # (or be available in external projects) for this application set(target_libraries org_blueberry_ui_qt org_blueberry_ui_qt_help org_mitk_planarfigure org_mitk_gui_qt_diffusionimagingapp org_mitk_gui_qt_ext org_mitk_gui_qt_datamanager org_mitk_gui_qt_segmentation org_mitk_gui_qt_multilabelsegmentation org_mitk_gui_qt_python org_mitk_gui_qt_volumevisualization org_mitk_gui_qt_diffusionimaging org_mitk_gui_qt_diffusionimaging_connectomics org_mitk_gui_qt_diffusionimaging_fiberfox org_mitk_gui_qt_diffusionimaging_fiberprocessing org_mitk_gui_qt_diffusionimaging_ivim org_mitk_gui_qt_diffusionimaging_odfpeaks org_mitk_gui_qt_diffusionimaging_preprocessing org_mitk_gui_qt_diffusionimaging_reconstruction org_mitk_gui_qt_diffusionimaging_tractography org_mitk_gui_qt_diffusionimaging_registration org_mitk_gui_qt_diffusionimaging_python org_mitk_gui_qt_diffusionimaging_denoising org_mitk_gui_qt_diffusionimaging_partialvolume org_mitk_gui_qt_matchpoint_algorithm_browser org_mitk_gui_qt_matchpoint_algorithm_control org_mitk_gui_qt_matchpoint_mapper org_mitk_gui_qt_imagenavigator org_mitk_gui_qt_moviemaker org_mitk_gui_qt_measurementtoolbox org_mitk_gui_qt_basicimageprocessing org_mitk_gui_qt_viewnavigator ) + +if(NOT MITK_USE_Python) + list(REMOVE_ITEM target_libraries org_mitk_gui_qt_diffusionimaging_python) + list(REMOVE_ITEM target_libraries org_mitk_gui_qt_python) +endif() diff --git a/CMake/BuildConfigurations/DiffusionRelease.cmake b/CMake/BuildConfigurations/DiffusionRelease.cmake index 57d55104c6..7de513dd9a 100644 --- a/CMake/BuildConfigurations/DiffusionRelease.cmake +++ b/CMake/BuildConfigurations/DiffusionRelease.cmake @@ -1,42 +1,46 @@ message(STATUS "Configuring MITK Diffusion Release Build") # Enable non-optional external dependencies set(MITK_USE_Vigra ON CACHE BOOL "MITK Use Vigra Library" FORCE) set(MITK_USE_HDF5 ON CACHE BOOL "MITK Use HDF5 Library" FORCE) set(MITK_USE_MatchPoint ON CACHE BOOL "" FORCE) set(MITK_USE_DCMTK ON CACHE BOOL "" FORCE) set(MITK_USE_DCMQI ON CACHE BOOL "" FORCE) set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE) -set(MITK_USE_Python ON CACHE BOOL "" FORCE) +if(UNIX AND NOT APPLE) + set(MITK_USE_Python ON CACHE BOOL "" FORCE) +else() + set(MITK_USE_Python OFF CACHE BOOL "" FORCE) +endif() set(MITK_USE_BetData ON CACHE BOOL "" FORCE) # Disable all apps but MITK Diffusion set(MITK_BUILD_ALL_APPS OFF CACHE BOOL "Build all MITK applications" FORCE) set(MITK_BUILD_APP_CoreApp OFF CACHE BOOL "Build the MITK CoreApp" FORCE) set(MITK_BUILD_APP_Workbench OFF CACHE BOOL "Build the MITK Workbench" FORCE) set(MITK_BUILD_APP_Diffusion ON CACHE BOOL "Build MITK Diffusion" FORCE) # Activate Diffusion Mini Apps set(BUILD_DiffusionFiberProcessingCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber processing" FORCE) set(BUILD_DiffusionFiberfoxCmdApps ON CACHE BOOL "Build commandline tools for diffusion data simulation (Fiberfox)" FORCE) set(BUILD_DiffusionMiscCmdApps ON CACHE BOOL "Build miscellaneous commandline tools for diffusion" FORCE) set(BUILD_DiffusionQuantificationCmdApps ON CACHE BOOL "Build commandline tools for diffusion quantification (IVIM, ADC, ...)" FORCE) set(BUILD_DiffusionTractographyCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography" FORCE) set(BUILD_DiffusionTractographyEvaluationCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography evaluation" FORCE) set(BUILD_DiffusionConnectomicsCmdApps OFF CACHE BOOL "Build commandline tools for diffusion connectomics" FORCE) set(BUILD_DiffusionPythonCmdApps ON CACHE BOOL "Build commandline tools for diffusion with python" FORCE) # Build neither all plugins nor examples set(MITK_BUILD_ALL_PLUGINS OFF CACHE BOOL "Build all MITK plugins" FORCE) set(MITK_BUILD_EXAMPLES OFF CACHE BOOL "Build the MITK examples" FORCE) set(BUILD_TESTING OFF CACHE BOOL "Build the MITK tests" FORCE) # Activate in-application help generation set(MITK_DOXYGEN_GENERATE_QCH_FILES ON CACHE BOOL "Use doxygen to generate Qt compressed help files for MITK docs" FORCE) set(BLUEBERRY_USE_QT_HELP ON CACHE BOOL "Enable support for integrating bundle documentation into Qt Help" FORCE) # Enable console window set(MITK_SHOW_CONSOLE_WINDOW ON CACHE BOOL "Use this to enable or disable the console window when starting MITK GUI Applications" FORCE) set(MITK_VTK_DEBUG_LEAKS OFF CACHE BOOL "" FORCE) set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE) diff --git a/Modules/Chart/include/QmitkChartWidget.h b/Modules/Chart/include/QmitkChartWidget.h index 830f56d8a2..05626cc95d 100644 --- a/Modules/Chart/include/QmitkChartWidget.h +++ b/Modules/Chart/include/QmitkChartWidget.h @@ -1,220 +1,222 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QmitkC3jsWidget_h #define QmitkC3jsWidget_h #include #include #include #include /*! \brief QmitkChartWidget is a widget to display various charts based on the javascript chart library C3js. * \details Data is added via AddData1D() or AddData2D().\n * There can be multiple charts (of different types with different properties) created by calling AddData1D or AddData2D multiple times.\n\n * The following chart types are supported: * * line chart: http://c3js.org/samples/simple_multiple.html * * bar chart: http://c3js.org/samples/chart_bar.html * * spline chart: http://c3js.org/samples/chart_spline.html * * pie chart: http://c3js.org/samples/chart_pie.html * * scatter chart: http://c3js.org/samples/chart_scatter.html * * area chart: http://c3js.org/samples/chart_area.html * * area spline chart: http://c3js.org/samples/chart_area.html * * Technical details: The javascript code is embedded in a QWebEngineView. The actual js code is implemented in resource\Chart.js. * \sa http://c3js.org for further information about the used javaScript library. * \ingroup Modules/Chart */ class MITKCHART_EXPORT QmitkChartWidget : public QWidget { Q_OBJECT public: /*! * \brief enum of diagram types. */ enum class ChartType { bar, /*!< bar chart, see http://c3js.org/samples/chart_bar.html */ line, /*!< line chart, see http://c3js.org/samples/simple_multiple.html */ spline, /*!< spline chart (smoothed line chart), see http://c3js.org/samples/chart_spline.html */ pie, /*!< pie chart, see http://c3js.org/samples/chart_pie.html*/ area, /*!< area chart, see http://c3js.org/samples/chart_area.html*/ area_spline, /*!< area-spline chart, see http://c3js.org/samples/chart_area.html*/ scatter /*!< scatter chart, see http://c3js.org/samples/chart_scatter.html*/ }; /*! * \brief enum of chart style (modifies background and line color). */ enum class ChartStyle { darkstyle, /*!< background color: dark gray, line color: blue */ lightstyle /*!< background color: white, line color: blue */ }; enum class LineStyle { solid, dashed }; enum class AxisScale { linear, log }; /*! * \brief enum of legend position. * See http://c3js.org/reference.html#legend-position */ enum class LegendPosition { bottom, right, inset }; explicit QmitkChartWidget(QWidget* parent = nullptr); //for UnitTests explicit QmitkChartWidget(QWidget *parent, bool unitTest); ~QmitkChartWidget() override; /*! * \brief Adds 1D data to the widget * \details internally, the list is converted to a map with increasing integers keys starting at 0. * \param label the name of the data that is also used as identifier. * \param chartType the chart type that should be used for this data entry * \note the data can be cleared with ClearDiagram() * \note If the label name already exists, the name is replaced with a unique one by concatenating numbers to it. * \warning Pie chart is significantly different than the other chart types. Here, the data given by AddData1D is summed. Each entry represents a different category. */ void AddData1D(const std::vector& data1D, const std::string& label, ChartType chartType = ChartType::bar); /*! * \brief Adds 2D data to the widget. Call repeatedly for displaying multiple charts. * \details each entry represents a data point: key: value --> x-value: y-value. * \param label the name of the data that is also used as identifier. * \param chartType the chart type that should be used for this data entry * \note the data can be cleared with ClearDiagram() * \note If the label name already exists, the name is replaced with a unique one by concatenating numbers to it. * \warning Pie chart is significantly different than the other chart types. Here, the data given by AddData1D is summed. Each entry represents a different category. */ void AddData2D(const std::map& data2D, const std::string& label, ChartType chartType = ChartType::bar); /*! * \brief Removes data from the widget, works for 1D and 2D Data * \param label the name of the data that is also used as identifier. * \note All data can be cleared with ClearDiagram() * \throws Invalid Argument Exception when the label cannot be found */ void RemoveData(const std::string& label); /*! * \brief Sets the color of one data entry (identifier is previously assigned label) * \details the color name can be "red" or a hex number (#FF0000). * \warning Either define all data entries with a color or no data entry. If a mixed approach is used, * C3 choses the color of the data entry (that could be the same as a user defined color). * \note If an unknown label is given, nothing happens. * \sa https://www.w3schools.com/cssref/css_colors.asp */ void SetColor(const std::string& label, const std::string& colorName); /*! * \brief Sets the line style of one data entry (identifier is previously assigned label) * \details two line styles are possible: LineStyle::solid and LineStyle::dashed. * The default line style is solid. * \note If an unknown label is given, nothing happens. * \warning only sets the line style if the current chart type is ChartType::line. * However, the line style remains also if the chart changes (e.g. new chart type) */ void SetLineStyle(const std::string& label, LineStyle style); /*! * \brief Sets the axis scale to either linear (default) or logarithmic. */ void SetYAxisScale(AxisScale scale); void SetXAxisLabel(const std::string& label); void SetYAxisLabel(const std::string& label); /*! * \brief Sets a title for the chart. */ void SetTitle(const std::string &title); /*! * \brief Changes the chart type for all data entries and reloads the chart */ void SetChartTypeForAllDataAndReload(ChartType type); /*! * \brief Sets the chart type for a data entry * \details for available types, see ChartType * \note If an unknown label is given, nothing happens. * \warning Pie chart is significantly different than the other chart types. Here, the data given by AddData1D is summed. Each entry represents a different category. * \sa DiagramType for available types */ void SetChartType(const std::string& label, ChartType type); /*! * \brief Sets the legend position. * \details Default position is bottom. * \sa LegendPosition for available types */ void SetLegendPosition(LegendPosition position); void SetShowLegend(bool show); void SetStackedData(bool stacked); /*! * \brief Displays the chart in the widget * \param showSubChart if a subchart is displayed inside the widget or not (see http://c3js.org/samples/options_subchart.html). * \exception if no data has been provided (\sa AddData1D AddData2D) */ void Show(bool showSubChart=false); /*! * \brief Either displays the dataPoints or not * \param showDataPoints if dataPoints are displayed inside the widget or not. * \details: example for not showing points: http://c3js.org/samples/point_show.html * example for showing the points: http://c3js.org/samples/simple_multiple.html */ void SetShowDataPoints(bool showDataPoints); /*! * \brief Clears all data inside and resets the widget. */ void Clear(); /*! * \brief Changes the theme of the widget. */ void SetTheme(ChartStyle themeEnabled); /*! * \brief Reloads the chart in the widget * \details reloading may be needed to display added data in an existing chart * \param showSubChart if a subchart is displayed inside the widget or not. */ void Reload(bool showSubChart); + QSize sizeHint() const override; + public slots: void OnLoadFinished(bool isLoadSuccessful); signals: void PageSuccessfullyLoaded(); private: class Impl; std::unique_ptr m_Impl; }; #endif diff --git a/Modules/Chart/resource/Chart.js b/Modules/Chart/resource/Chart.js index fac672a8ab..79541bbfc7 100644 --- a/Modules/Chart/resource/Chart.js +++ b/Modules/Chart/resource/Chart.js @@ -1,200 +1,201 @@ document.body.style.backgroundColor = 'rgb(240, 240, 240)'; const minHeight = 255; var chart; var chartData; var xValues=[]; var yValues=[]; var dataLabels=[]; var xs = {}; var dataColors = {}; var chartTypes = {}; var lineStyle = {}; // Important loading function. This will be executed at first in this whole script. // Fetching data from QWebChannel and storing them for display purposes. window.onload = function() { initHeight(); new QWebChannel(qt.webChannelTransport, function(channel) { chartData = channel.objects.chartData; let count = 0; for(let propertyName in channel.objects) { if (propertyName != 'chartData') { let xDataTemp = channel.objects[propertyName].m_XData let yDataTemp = channel.objects[propertyName].m_YData let dataLabel = channel.objects[propertyName].m_Label dataLabels.push(dataLabel) console.log("loading datalabel: "+dataLabel); //add label to x array xDataTemp.unshift('x'+count.toString()) xs[dataLabel] = 'x' + count.toString() xDataTemp.push(null); //append null value, to make sure the last tick on x-axis is displayed correctly yDataTemp.unshift(dataLabel) yDataTemp.push(null); //append null value, to make sure the last tick on y-axis is displayed correctly xValues[count] = xDataTemp yValues[count] = yDataTemp dataColors[dataLabel] = channel.objects[propertyName].m_Color chartTypes[dataLabel] = channel.objects[propertyName].m_ChartType if (channel.objects[propertyName].m_LineStyleName == "solid") { lineStyle[dataLabel] = '' } else { lineStyle[dataLabel] = [{ 'style': 'dashed' }] } count++; } } generateChart(chartData); }); } /** * Inits the height of the chart element to 90% of the full window height. */ function initHeight() { var size = window.innerHeight-(window.innerHeight/100*10); //subtract 10% of height to hide vertical scrool bar let chart = document.getElementById("chart"); chart.style.height = `${size}px`; } function getPlotlyChartType(inputType){ let plotlyType = ""; if (inputType == "line"){ plotlyType = "scatter"; } else if (inputType == "bar"){ plotlyType = "bar"; } return plotlyType; } /** * Here, the chart magic takes place. Plot.ly is called. * * @param {object} chartData - containing the options for plotting, not the actual values */ function generateChart(chartData) { console.log("generate chart"); if (chartData == undefined) { chartData = {} } if (dataLabels == undefined) { dataLabels = [] } //=============================== DATA ======================== let data = []; for (let index = 0; index < dataLabels.length; index++){ let inputType = chartTypes[dataLabels[index]]; let chartType = getPlotlyChartType(inputType); let trace = { x: xValues[index].slice(1), y: yValues[index].slice(1), type: chartType, name: dataLabels[index], }; if (lineStyle[dataLabels[index]]["style"] == "dashed"){ trace["line"]["dash"] = "dot" } data.push(trace) } //=============================== STYLE ======================== let marginTop = chartData.m_diagramTitle == undefined ? 10 : 50; var layout = { title: chartData.m_diagramTitle, xaxis: { title: chartData.m_xAxisLabel }, yaxis: { title: chartData.m_yAxisLabel }, margin: { l: 50, r: 10, b: 50, t: marginTop, pad: 4 }, }; if (chartData.m_YAxisScale){ layout.yaxis["type"] = "log" } if (chartData.m_ShowSubchart){ layout.xaxis.rangeslider = {}; // adds range slider below x axis } Plotly.newPlot('chart', data, layout, {displayModeBar: false, responsive: true}); } /** * Change theme of chart. * * @param {string} color - dark or not dark */ function changeTheme(color) { link = document.getElementsByTagName("link")[0]; if (color == 'dark') { link.href = "Chart_dark.css"; } else { link.href = "Chart.css"; } }; /** * Reload the chart with the given arguments. * * This method is called by C++. Changes on signature with caution. * @param {boolean} showSubchart * @param {string} stackDataString */ -function ReloadChart(showSubchart, stackDataString) +function ReloadChart(showSubchart, stackDataString = false) { chartData.m_ShowSubchart = showSubchart; chartData.m_StackedData = stackDataString; generateChart(chartData); } /** * Transforms the view to another chart type. * * This method is called by C++. Changes on signature with caution. * @param {string} transformTo - 'line' or 'bar' */ function transformView(transformTo) { console.log("transform view"); console.log(transformTo); + chartTypes[dataLabels[0]] = transformTo; // preserve chartType for later updates let plotlyType = getPlotlyChartType(transformTo); let chart = document.getElementById("chart"); let update = {type : plotlyType} Plotly.restyle(chart, update, 0); // updates the given plotly trace at index 0 with an update object built of a standard trace object }; diff --git a/Modules/Chart/src/QmitkChartWidget.cpp b/Modules/Chart/src/QmitkChartWidget.cpp index 0b5673b1f9..58a1e0eb14 100644 --- a/Modules/Chart/src/QmitkChartWidget.cpp +++ b/Modules/Chart/src/QmitkChartWidget.cpp @@ -1,520 +1,535 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include "mitkExceptionMacro.h" #include #include class CustomPage : public QWebEnginePage { public: CustomPage(QObject* parent = 0) : QWebEnginePage(parent) {} virtual void javaScriptConsoleMessage(JavaScriptConsoleMessageLevel /*level*/, const QString &message, int lineNumber, const QString &/*sourceID*/) { MITK_INFO << "JS > " << lineNumber << ": " << message.toStdString(); } }; class QmitkChartWidget::Impl final { public: explicit Impl(QWidget *parent); ~Impl(); Impl(const Impl &) = delete; Impl &operator=(const Impl &) = delete; void AddData1D(const std::vector &data1D, const std::string &label, QmitkChartWidget::ChartType chartType); void AddData2D(const std::map &data2D, const std::string &label, QmitkChartWidget::ChartType chartType); void RemoveData(const std::string &label); void ClearData(); void SetColor(const std::string &label, const std::string &colorName); void SetLineStyle(const std::string &label, LineStyle style); void SetYAxisScale(AxisScale scale); - void SetXAxisLabel(const std::string &label); - void SetYAxisLabel(const std::string &label); + + void SetXAxisLabel(const std::string& label); + + void SetYAxisLabel(const std::string& label); void SetTitle(const std::string &title); void SetChartType(QmitkChartWidget::ChartType chartType); - void SetChartTypeByLabel(const std::string &label, QmitkChartWidget::ChartType chartType); - void SetLegendPosition(LegendPosition position); - void SetShowLegend(bool show); - - void SetStackedData(bool stacked); + void SetChartTypeByLabel(const std::string &label, QmitkChartWidget::ChartType chartType); void Show(bool showSubChart); + void SetShowLegend(bool show); + void SetShowDataPoints(bool showDataPoints = false); + void SetChartType(const std::string& label, QmitkChartWidget::ChartType chartType); + std::string ConvertChartTypeToString(QmitkChartWidget::ChartType chartType) const; void ClearJavaScriptChart(); void InitializeJavaScriptChart(); void CallJavaScriptFuntion(const QString &command); + QSize sizeHint() const; + private: using ChartxyDataVector = std::vector>; - std::string GetUniqueLabelName(const QList &labelList, const std::string &label) const; - QmitkChartxyData *GetDataElementByLabel(const std::string &label) const; - QList GetDataLabels(const ChartxyDataVector &c3xyData) const; + std::string GetUniqueLabelName(const QList& labelList, const std::string& label) const; + QmitkChartxyData* GetDataElementByLabel(const std::string& label) const; + QList GetDataLabels(const ChartxyDataVector& c3xyData) const; void MapTypes(); QWebChannel *m_WebChannel; QWebEngineView *m_WebEngineView; QmitkChartData m_C3Data; ChartxyDataVector m_C3xyData; std::map m_ChartTypeToName; std::map m_LegendPositionToName; std::map m_LineStyleToName; std::map m_AxisScaleToName; }; QmitkChartWidget::Impl::Impl(QWidget *parent) : m_WebChannel(new QWebChannel(parent)), m_WebEngineView(new QWebEngineView(parent)) { // disable context menu for QWebEngineView m_WebEngineView->setContextMenuPolicy(Qt::NoContextMenu); m_WebEngineView->setPage(new CustomPage()); // Set the webengineview to an initial empty page. The actual chart will be loaded once the data is calculated. m_WebEngineView->setUrl(QUrl(QStringLiteral("qrc:///C3js/empty.html"))); m_WebEngineView->page()->setWebChannel(m_WebChannel); m_WebEngineView->settings()->setAttribute(QWebEngineSettings::FocusOnNavigationEnabled, false); connect(m_WebEngineView, SIGNAL(loadFinished(bool)), parent, SLOT(OnLoadFinished(bool))); auto layout = new QGridLayout(parent); layout->setMargin(0); layout->addWidget(m_WebEngineView); - parent->setLayout(layout); - m_ChartTypeToName.emplace(ChartType::bar, "bar"); m_ChartTypeToName.emplace(ChartType::line, "line"); m_ChartTypeToName.emplace(ChartType::spline, "spline"); m_ChartTypeToName.emplace(ChartType::pie, "pie"); m_ChartTypeToName.emplace(ChartType::area, "area"); m_ChartTypeToName.emplace(ChartType::area_spline, "area-spline"); m_ChartTypeToName.emplace(ChartType::scatter, "scatter"); m_LegendPositionToName.emplace(LegendPosition::bottom, "bottom"); m_LegendPositionToName.emplace(LegendPosition::right, "right"); m_LegendPositionToName.emplace(LegendPosition::inset, "inset"); m_LineStyleToName.emplace(LineStyle::solid, "solid"); m_LineStyleToName.emplace(LineStyle::dashed, "dashed"); m_AxisScaleToName.emplace(AxisScale::linear, ""); m_AxisScaleToName.emplace(AxisScale::log, "log"); } -QmitkChartWidget::Impl::~Impl() {} +QmitkChartWidget::Impl::~Impl() +{ +} std::string CheckForCorrectHex(const std::string &colorName) { std::regex rgx("([A-Fa-f0-9]{6}|[A-Fa-f0-9]{3})"); std::smatch match; if (!colorName.empty() && colorName.at(0) != '#' && std::regex_search(colorName.begin(), colorName.end(), match, rgx)) { return "#" + colorName; } else { return colorName; } } -void QmitkChartWidget::Impl::AddData1D(const std::vector &data1D, - const std::string &label, - QmitkChartWidget::ChartType chartType) +void QmitkChartWidget::Impl::AddData1D(const std::vector& data1D, const std::string& label, QmitkChartWidget::ChartType type) { std::map transformedData2D; unsigned int count = 0; // transform the 1D data to 2D data for (const auto &ele : data1D) { transformedData2D[count] = ele; count++; } - AddData2D(transformedData2D, label, chartType); + AddData2D(transformedData2D, label, type); } -void QmitkChartWidget::Impl::AddData2D(const std::map &data2D, - const std::string &label, - QmitkChartWidget::ChartType chartType) +void QmitkChartWidget::Impl::AddData2D(const std::map& data2D, const std::string& label, QmitkChartWidget::ChartType type) { QMap data2DConverted; for (const auto &aValue : data2D) { data2DConverted.insert(aValue.first, aValue.second); } - const std::string chartTypeName(m_ChartTypeToName.at(chartType)); + const std::string chartTypeName(m_ChartTypeToName.at(type)); auto definedLabels = GetDataLabels(m_C3xyData); auto uniqueLabel = GetUniqueLabelName(definedLabels, label); - if (chartType == ChartType::scatter) + if (type == ChartType::scatter) { SetShowDataPoints(true); MITK_INFO << "Enabling data points for all because of scatter plot"; } m_C3xyData.push_back(std::make_unique( data2DConverted, QVariant(QString::fromStdString(uniqueLabel)), QVariant(QString::fromStdString(chartTypeName)))); } void QmitkChartWidget::Impl::RemoveData(const std::string &label) { for (ChartxyDataVector::iterator iter = m_C3xyData.begin(); iter != m_C3xyData.end(); ++iter) { if ((*iter)->GetLabel().toString().toStdString() == label) { m_C3xyData.erase(iter); return; } } throw std::invalid_argument("Cannot Remove Data because the label does not exist."); } void QmitkChartWidget::Impl::ClearData() { - for (auto &xyData : m_C3xyData) + for (auto& xyData : m_C3xyData) { m_WebChannel->deregisterObject(xyData.get()); } m_C3xyData.clear(); } void QmitkChartWidget::Impl::SetColor(const std::string &label, const std::string &colorName) { auto element = GetDataElementByLabel(label); if (element) { auto colorChecked = CheckForCorrectHex(colorName); - element->SetColor(QVariant(QString::fromStdString(colorName))); + element->SetColor(QVariant(QString::fromStdString(colorChecked))); } } void QmitkChartWidget::Impl::SetLineStyle(const std::string &label, LineStyle style) { auto element = GetDataElementByLabel(label); // only has effect with chart type line - if (element && element->GetChartType() == QVariant(QString::fromStdString(ConvertChartTypeToString(ChartType::line)))) + if (element && element->GetChartType()==QVariant(QString::fromStdString(ConvertChartTypeToString(ChartType::line)))) { const std::string lineStyleName(m_LineStyleToName.at(style)); element->SetLineStyle(QVariant(QString::fromStdString(lineStyleName))); } } void QmitkChartWidget::Impl::SetYAxisScale(AxisScale scale) { const std::string axisScaleName(m_AxisScaleToName.at(scale)); m_C3Data.SetYAxisScale(QString::fromStdString(axisScaleName)); } -void QmitkChartWidget::Impl::SetXAxisLabel(const std::string &label) +QmitkChartxyData* QmitkChartWidget::Impl::GetDataElementByLabel(const std::string& label) const +{ + for (const auto &qmitkChartxyData : m_C3xyData) + { + if (qmitkChartxyData->GetLabel().toString() == label.c_str()) + { + return qmitkChartxyData.get(); + } + } + MITK_WARN << "label " << label << " not found in QmitkChartWidget"; + return nullptr; +} + +QList QmitkChartWidget::Impl::GetDataLabels(const ChartxyDataVector& c3xyData) const +{ + QList dataLabels; + for (auto element = c3xyData.begin(); element != c3xyData.end(); ++element) + { + dataLabels.push_back((*element)->GetLabel()); + } + return dataLabels; +} + +void QmitkChartWidget::Impl::SetXAxisLabel(const std::string& label) { m_C3Data.SetXAxisLabel(QString::fromStdString(label)); } void QmitkChartWidget::Impl::SetYAxisLabel(const std::string &label) { m_C3Data.SetYAxisLabel(QString::fromStdString(label)); } void QmitkChartWidget::Impl::SetTitle(const std::string &title) { m_C3Data.SetTitle(QString::fromStdString(title)); } void QmitkChartWidget::Impl::SetChartType(QmitkChartWidget::ChartType chartType) { for (auto iterator = m_C3xyData.begin(); iterator != m_C3xyData.end(); ++iterator) { SetChartTypeByLabel((*iterator)->GetLabel().toString().toStdString(), chartType); } auto chartTypeName = ConvertChartTypeToString(chartType); const QString command = QString::fromStdString("transformView('" + chartTypeName + "')"); CallJavaScriptFuntion(command); } void QmitkChartWidget::Impl::SetChartTypeByLabel(const std::string &label, QmitkChartWidget::ChartType chartType) { auto element = GetDataElementByLabel(label); if (element) { if (chartType == ChartType::scatter) { SetShowDataPoints(true); MITK_INFO << "Enabling data points for all because of scatter plot"; } auto chartTypeName = ConvertChartTypeToString(chartType); element->SetChartType(QVariant(QString::fromStdString(chartTypeName))); } } void QmitkChartWidget::Impl::SetLegendPosition(QmitkChartWidget::LegendPosition legendPosition) { const std::string legendPositionName(m_LegendPositionToName.at(legendPosition)); m_C3Data.SetLegendPosition(QString::fromStdString(legendPositionName)); } -void QmitkChartWidget::Impl::SetShowLegend(bool show) -{ - m_C3Data.SetShowLegend(show); -} - -void QmitkChartWidget::Impl::SetStackedData(bool stacked) -{ - m_C3Data.SetStackedData(stacked); -} - void QmitkChartWidget::Impl::Show(bool showSubChart) { if (m_C3xyData.empty()) { mitkThrow() << "no data available for display in chart"; } m_C3Data.SetAppearance(showSubChart, m_C3xyData.front()->GetChartType() == QVariant("pie")); InitializeJavaScriptChart(); } +void QmitkChartWidget::Impl::SetShowLegend(bool show) +{ + m_C3Data.SetShowLegend(show); +} + void QmitkChartWidget::Impl::SetShowDataPoints(bool showDataPoints) { if (showDataPoints == true) { m_C3Data.SetDataPointSize(3); } else { m_C3Data.SetDataPointSize(0); } } +void QmitkChartWidget::Impl::SetChartType(const std::string& label, QmitkChartWidget::ChartType chartType) +{ + auto element = GetDataElementByLabel(label); + if (element) + { + if (chartType == ChartType::scatter) + { + SetShowDataPoints(true); + MITK_INFO << "Enabling data points for all because of scatter plot"; + } + const std::string chartTypeName(m_ChartTypeToName.at(chartType)); + element->SetChartType(QVariant(QString::fromStdString(chartTypeName))); + } +} + std::string QmitkChartWidget::Impl::ConvertChartTypeToString(QmitkChartWidget::ChartType chartType) const { return m_ChartTypeToName.at(chartType); } +QSize QmitkChartWidget::Impl::sizeHint() const +{ + return QSize(400, 300); +} + +void QmitkChartWidget::Impl::CallJavaScriptFuntion(const QString& command) +{ + m_WebEngineView->page()->runJavaScript(command); +} + void QmitkChartWidget::Impl::ClearJavaScriptChart() { m_WebEngineView->setUrl(QUrl(QStringLiteral("qrc:///C3js/empty.html"))); } void QmitkChartWidget::Impl::InitializeJavaScriptChart() { m_WebChannel->registerObject(QStringLiteral("chartData"), &m_C3Data); unsigned count = 0; - for (auto &xyData : m_C3xyData) + for (auto& xyData : m_C3xyData) { - QString variableName = "xyData" + QString::number(count); - m_WebChannel->registerObject(variableName, xyData.get()); + QString variableName = "xyData" + QString::number(count); + m_WebChannel->registerObject(variableName, xyData.get()); count++; } - m_WebEngineView->load(QUrl(QStringLiteral("qrc:///C3js/QmitkChartWidget.html"))); -} -void QmitkChartWidget::Impl::CallJavaScriptFuntion(const QString &command) -{ - m_WebEngineView->page()->runJavaScript(command); + m_WebEngineView->load(QUrl(QStringLiteral("qrc:///C3js/QmitkChartWidget.html"))); } std::string QmitkChartWidget::Impl::GetUniqueLabelName(const QList &labelList, const std::string &label) const { QString currentLabel = QString::fromStdString(label); int counter = 0; while (labelList.contains(currentLabel)) { currentLabel = QString::fromStdString(label + std::to_string(counter)); counter++; } return currentLabel.toStdString(); } -QmitkChartxyData *QmitkChartWidget::Impl::GetDataElementByLabel(const std::string &label) const -{ - for (const auto &qmitkChartxyData : m_C3xyData) - { - if (qmitkChartxyData->GetLabel().toString() == label.c_str()) - { - return qmitkChartxyData.get(); - } - } - - MITK_WARN << "label " << label << " not found in QmitkChartWidget"; - return nullptr; -} - -QList QmitkChartWidget::Impl::GetDataLabels(const ChartxyDataVector &c3xyData) const -{ - QList dataLabels; - for (auto element = c3xyData.begin(); element != c3xyData.end(); ++element) - { - dataLabels.push_back((*element)->GetLabel()); - } - return dataLabels; -} - QmitkChartWidget::QmitkChartWidget(QWidget *parent) : QWidget(parent), m_Impl(new Impl(this)) {} QmitkChartWidget::~QmitkChartWidget() {} -void QmitkChartWidget::AddData1D(const std::vector &data1D, const std::string &label, ChartType type) -{ - m_Impl->AddData1D(data1D, label, type); -} - void QmitkChartWidget::AddData2D(const std::map &data2D, const std::string &label, ChartType type) { m_Impl->AddData2D(data2D, label, type); } -void QmitkChartWidget::RemoveData(const std::string &label) -{ - m_Impl->RemoveData(label); -} - void QmitkChartWidget::SetColor(const std::string &label, const std::string &colorName) { m_Impl->SetColor(label, colorName); } void QmitkChartWidget::SetLineStyle(const std::string &label, LineStyle style) { m_Impl->SetLineStyle(label, style); } void QmitkChartWidget::SetYAxisScale(AxisScale scale) { m_Impl->SetYAxisScale(scale); } -void QmitkChartWidget::SetXAxisLabel(const std::string &label) +void QmitkChartWidget::AddData1D(const std::vector& data1D, const std::string& label, ChartType type) +{ + m_Impl->AddData1D(data1D, label, type); +} + +void QmitkChartWidget::RemoveData(const std::string& label) +{ + m_Impl->RemoveData(label); +} + +void QmitkChartWidget::SetXAxisLabel(const std::string & label) { m_Impl->SetXAxisLabel(label); } void QmitkChartWidget::SetYAxisLabel(const std::string &label) { m_Impl->SetYAxisLabel(label); } void QmitkChartWidget::SetTitle(const std::string &title) { m_Impl->SetTitle(title); } -void QmitkChartWidget::SetChartTypeForAllDataAndReload(ChartType type) +void QmitkChartWidget::SetShowDataPoints(bool showDataPoints) { - m_Impl->SetChartType(type); + m_Impl->SetShowDataPoints(showDataPoints); } void QmitkChartWidget::SetChartType(const std::string &label, ChartType type) { - m_Impl->SetChartTypeByLabel(label, type); + m_Impl->SetChartType(label, type); } void QmitkChartWidget::SetLegendPosition(LegendPosition position) { m_Impl->SetLegendPosition(position); } void QmitkChartWidget::SetShowLegend(bool show) { m_Impl->SetShowLegend(show); } -void QmitkChartWidget::SetStackedData(bool stacked) -{ - m_Impl->SetStackedData(stacked); -} - void QmitkChartWidget::Show(bool showSubChart) { m_Impl->Show(showSubChart); } -void QmitkChartWidget::SetShowDataPoints(bool showDataPoints) -{ - m_Impl->SetShowDataPoints(showDataPoints); -} - void QmitkChartWidget::Clear() { m_Impl->ClearData(); m_Impl->ClearJavaScriptChart(); } -void QmitkChartWidget::OnLoadFinished(bool isLoadSuccessful) +void QmitkChartWidget::OnLoadFinished(bool isLoadSuccessfull) { - if (isLoadSuccessful) + if(isLoadSuccessfull) { emit PageSuccessfullyLoaded(); } } +void QmitkChartWidget::SetChartTypeForAllDataAndReload(ChartType type) +{ + m_Impl->SetChartType(type); +} + void QmitkChartWidget::SetTheme(ChartStyle themeEnabled) { QString command; if (themeEnabled == ChartStyle::darkstyle) { command = QString("changeTheme('dark')"); } else { command = QString("changeTheme('light')"); } + m_Impl->CallJavaScriptFuntion(command); } void QmitkChartWidget::Reload(bool showSubChart) { QString subChartString; - if (showSubChart) { subChartString = "true"; } else { subChartString = "false"; } const QString command = QString("ReloadChart(" + subChartString + ")"); m_Impl->CallJavaScriptFuntion(command); } + +QSize QmitkChartWidget::sizeHint() const +{ + return m_Impl->sizeHint(); +} diff --git a/Modules/Classification/CLMiniApps/CLPlanarFigureToNrrd.cpp b/Modules/Classification/CLMiniApps/CLPlanarFigureToNrrd.cpp index e87d3065f2..d2f2c005cb 100644 --- a/Modules/Classification/CLMiniApps/CLPlanarFigureToNrrd.cpp +++ b/Modules/Classification/CLMiniApps/CLPlanarFigureToNrrd.cpp @@ -1,145 +1,144 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef mitkCLPolyToNrrd_cpp #define mitkCLPolyToNrrd_cpp #include "time.h" #include #include #include "mitkCommandLineParser.h" #include #include #include #include #include typedef itk::Image< double, 3 > FloatImageType; typedef itk::Image< unsigned char, 3 > MaskImageType; struct MaskParameter { mitk::Image::Pointer mask; unsigned int axis; unsigned int slice; }; template < typename TPixel, unsigned int VImageDimension > void CreateNewMask(const itk::Image< TPixel, VImageDimension > *image, MaskParameter param, mitk::Image::Pointer &output) { int transform[3][2]; transform[0][0] = 1; transform[0][1] = 2; transform[1][0] = 0; transform[1][1] = 2; transform[2][0] = 0; transform[2][1] = 1; typedef itk::Image MaskType; typedef itk::Image Mask2DType; typename Mask2DType::Pointer mask = Mask2DType::New(); mitk::CastToItkImage(param.mask, mask); typename MaskType::Pointer mask3D = MaskType::New(); mask3D->SetRegions(image->GetLargestPossibleRegion()); mask3D->SetSpacing(image->GetSpacing()); mask3D->SetOrigin(image->GetOrigin()); mask3D->Allocate(); itk::ImageRegionIteratorWithIndex iter(mask3D, mask3D->GetLargestPossibleRegion()); while (!iter.IsAtEnd()) { auto index = iter.GetIndex(); iter.Set(0); if (index[param.axis] == param.slice) { Mask2DType::IndexType index2D; index2D[0] = index[transform[param.axis][0]]; index2D[1] = index[transform[param.axis][1]]; auto pixel = mask->GetPixel(index2D); iter.Set(pixel); } ++iter; } mitk::CastToMitkImage(mask3D, output); } int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); // required params parser.addArgument("planar", "p", mitkCommandLineParser::InputDirectory, "Input Polydata", "Path to the input VTK polydata", us::Any(), false); parser.addArgument("image", "i", mitkCommandLineParser::OutputDirectory, "Input Image", "Image which defines the dimensions of the Segmentation", us::Any(), false); parser.addArgument("output", "o", mitkCommandLineParser::InputFile, "Output file", "Output file. ", us::Any(), false); // Miniapp Infos parser.setCategory("Classification Tools"); parser.setTitle("Planar Data to Nrrd Segmentation"); parser.setDescription("Creates a Nrrd segmentation based on a 2d-vtk polydata."); parser.setContributor("MBI"); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) { return EXIT_FAILURE; } if ( parsedArgs.count("help") || parsedArgs.count("h")) { return EXIT_SUCCESS; } try { mitk::BaseData::Pointer data = mitk::IOUtil::Load(parsedArgs["planar"].ToString())[0]; mitk::PlanarFigure::Pointer planar = dynamic_cast(data.GetPointer()); mitk::Image::Pointer image = mitk::IOUtil::Load(parsedArgs["image"].ToString()); mitk::PlanarFigureMaskGenerator::Pointer pfMaskGen = mitk::PlanarFigureMaskGenerator::New(); pfMaskGen->SetPlanarFigure(planar); pfMaskGen->SetTimeStep(0); - pfMaskGen->SetInputImage(image); + pfMaskGen->SetInputImage(image.GetPointer()); mitk::Image::Pointer mask = pfMaskGen->GetMask(); - mitk::Image::Pointer refImage = pfMaskGen->GetReferenceImage(); unsigned int axis = pfMaskGen->GetPlanarFigureAxis(); unsigned int slice = pfMaskGen->GetPlanarFigureSlice(); //itk::Image::IndexType index; mitk::Image::Pointer fullMask; MaskParameter param; param.slice = slice; param.axis = axis; param.mask = mask; AccessByItk_2(image, CreateNewMask, param, fullMask); std::string saveAs = parsedArgs["output"].ToString(); MITK_INFO << "Save as: " << saveAs; mitk::IOUtil::Save(pfMaskGen->GetMask(), saveAs); mitk::IOUtil::Save(fullMask, saveAs); return 0; } catch (...) { return EXIT_FAILURE; } } #endif diff --git a/Modules/Core/files.cmake b/Modules/Core/files.cmake index 2950c63e78..b8e9e5988b 100644 --- a/Modules/Core/files.cmake +++ b/Modules/Core/files.cmake @@ -1,316 +1,315 @@ file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*") set(CPP_FILES mitkCoreActivator.cpp mitkCoreObjectFactoryBase.cpp mitkCoreObjectFactory.cpp mitkCoreServices.cpp mitkException.cpp Algorithms/mitkBaseDataSource.cpp Algorithms/mitkClippedSurfaceBoundsCalculator.cpp Algorithms/mitkCompareImageDataFilter.cpp Algorithms/mitkCompositePixelValueToString.cpp Algorithms/mitkConvert2Dto3DImageFilter.cpp Algorithms/mitkDataNodeSource.cpp Algorithms/mitkExtractSliceFilter.cpp Algorithms/mitkExtractSliceFilter2.cpp Algorithms/mitkHistogramGenerator.cpp Algorithms/mitkImageChannelSelector.cpp Algorithms/mitkImageSliceSelector.cpp Algorithms/mitkImageSource.cpp Algorithms/mitkImageTimeSelector.cpp Algorithms/mitkImageToImageFilter.cpp Algorithms/mitkImageToSurfaceFilter.cpp Algorithms/mitkMultiComponentImageDataComparisonFilter.cpp Algorithms/mitkPlaneGeometryDataToSurfaceFilter.cpp Algorithms/mitkPointSetSource.cpp Algorithms/mitkPointSetToPointSetFilter.cpp Algorithms/mitkRGBToRGBACastImageFilter.cpp Algorithms/mitkSubImageSelector.cpp Algorithms/mitkSurfaceSource.cpp Algorithms/mitkSurfaceToImageFilter.cpp Algorithms/mitkSurfaceToSurfaceFilter.cpp Algorithms/mitkUIDGenerator.cpp Algorithms/mitkVolumeCalculator.cpp Controllers/mitkBaseController.cpp Controllers/mitkCallbackFromGUIThread.cpp Controllers/mitkCameraController.cpp Controllers/mitkCameraRotationController.cpp Controllers/mitkLimitedLinearUndo.cpp Controllers/mitkOperationEvent.cpp Controllers/mitkPlanePositionManager.cpp Controllers/mitkProgressBar.cpp Controllers/mitkRenderingManager.cpp Controllers/mitkSliceNavigationController.cpp Controllers/mitkSlicesCoordinator.cpp Controllers/mitkStatusBar.cpp Controllers/mitkStepper.cpp Controllers/mitkTestManager.cpp Controllers/mitkUndoController.cpp Controllers/mitkVerboseLimitedLinearUndo.cpp Controllers/mitkVtkLayerController.cpp DataManagement/mitkAnatomicalStructureColorPresets.cpp DataManagement/mitkArbitraryTimeGeometry.cpp DataManagement/mitkAbstractTransformGeometry.cpp DataManagement/mitkAnnotationProperty.cpp DataManagement/mitkApplicationCursor.cpp DataManagement/mitkApplyTransformMatrixOperation.cpp DataManagement/mitkBaseData.cpp DataManagement/mitkBaseGeometry.cpp DataManagement/mitkBaseProperty.cpp DataManagement/mitkChannelDescriptor.cpp DataManagement/mitkClippingProperty.cpp DataManagement/mitkColorProperty.cpp DataManagement/mitkDataNode.cpp DataManagement/mitkDataStorage.cpp DataManagement/mitkEnumerationProperty.cpp DataManagement/mitkFloatPropertyExtension.cpp DataManagement/mitkGeometry3D.cpp DataManagement/mitkGeometryData.cpp DataManagement/mitkGeometryTransformHolder.cpp DataManagement/mitkGroupTagProperty.cpp DataManagement/mitkGenericIDRelationRule.cpp DataManagement/mitkIdentifiable.cpp DataManagement/mitkImageAccessorBase.cpp DataManagement/mitkImageCaster.cpp DataManagement/mitkImageCastPart1.cpp DataManagement/mitkImageCastPart2.cpp DataManagement/mitkImageCastPart3.cpp DataManagement/mitkImageCastPart4.cpp DataManagement/mitkImage.cpp DataManagement/mitkImageDataItem.cpp DataManagement/mitkImageDescriptor.cpp DataManagement/mitkImageReadAccessor.cpp DataManagement/mitkImageStatisticsHolder.cpp DataManagement/mitkImageVtkAccessor.cpp DataManagement/mitkImageVtkReadAccessor.cpp DataManagement/mitkImageVtkWriteAccessor.cpp DataManagement/mitkImageWriteAccessor.cpp DataManagement/mitkIntPropertyExtension.cpp DataManagement/mitkIPersistenceService.cpp DataManagement/mitkIPropertyAliases.cpp DataManagement/mitkIPropertyDescriptions.cpp DataManagement/mitkIPropertyExtensions.cpp DataManagement/mitkIPropertyFilters.cpp DataManagement/mitkIPropertyOwner.cpp DataManagement/mitkIPropertyPersistence.cpp DataManagement/mitkIPropertyProvider.cpp DataManagement/mitkLandmarkProjectorBasedCurvedGeometry.cpp DataManagement/mitkLandmarkProjector.cpp DataManagement/mitkLevelWindow.cpp DataManagement/mitkLevelWindowManager.cpp DataManagement/mitkLevelWindowPreset.cpp DataManagement/mitkLevelWindowProperty.cpp DataManagement/mitkLine.cpp DataManagement/mitkLookupTable.cpp DataManagement/mitkLookupTableProperty.cpp DataManagement/mitkLookupTables.cpp # specializations of GenericLookupTable DataManagement/mitkMaterial.cpp DataManagement/mitkMemoryUtilities.cpp DataManagement/mitkModalityProperty.cpp DataManagement/mitkModifiedLock.cpp DataManagement/mitkNodePredicateAnd.cpp DataManagement/mitkNodePredicateBase.cpp DataManagement/mitkNodePredicateCompositeBase.cpp DataManagement/mitkNodePredicateData.cpp DataManagement/mitkNodePredicateDataType.cpp DataManagement/mitkNodePredicateDataUID.cpp DataManagement/mitkNodePredicateDimension.cpp DataManagement/mitkNodePredicateFirstLevel.cpp DataManagement/mitkNodePredicateFunction.cpp DataManagement/mitkNodePredicateGeometry.cpp DataManagement/mitkNodePredicateNot.cpp DataManagement/mitkNodePredicateOr.cpp DataManagement/mitkNodePredicateProperty.cpp DataManagement/mitkNodePredicateDataProperty.cpp DataManagement/mitkNodePredicateSource.cpp - DataManagement/mitkNodePredicateUID.cpp DataManagement/mitkNumericConstants.cpp DataManagement/mitkPlaneGeometry.cpp DataManagement/mitkPlaneGeometryData.cpp DataManagement/mitkPlaneOperation.cpp DataManagement/mitkPlaneOrientationProperty.cpp DataManagement/mitkPointOperation.cpp DataManagement/mitkPointSet.cpp DataManagement/mitkPointSetShapeProperty.cpp DataManagement/mitkProperties.cpp DataManagement/mitkPropertyAliases.cpp DataManagement/mitkPropertyDescriptions.cpp DataManagement/mitkPropertyExtension.cpp DataManagement/mitkPropertyExtensions.cpp DataManagement/mitkPropertyFilter.cpp DataManagement/mitkPropertyFilters.cpp DataManagement/mitkPropertyKeyPath.cpp DataManagement/mitkPropertyList.cpp DataManagement/mitkPropertyListReplacedObserver.cpp DataManagement/mitkPropertyNameHelper.cpp DataManagement/mitkPropertyObserver.cpp DataManagement/mitkPropertyPersistence.cpp DataManagement/mitkPropertyPersistenceInfo.cpp DataManagement/mitkPropertyRelationRuleBase.cpp DataManagement/mitkProportionalTimeGeometry.cpp DataManagement/mitkRenderingModeProperty.cpp DataManagement/mitkResliceMethodProperty.cpp DataManagement/mitkRestorePlanePositionOperation.cpp DataManagement/mitkRotationOperation.cpp DataManagement/mitkScaleOperation.cpp DataManagement/mitkSlicedData.cpp DataManagement/mitkSlicedGeometry3D.cpp DataManagement/mitkSmartPointerProperty.cpp DataManagement/mitkStandaloneDataStorage.cpp DataManagement/mitkStringProperty.cpp DataManagement/mitkSurface.cpp DataManagement/mitkSurfaceOperation.cpp DataManagement/mitkThinPlateSplineCurvedGeometry.cpp DataManagement/mitkTimeGeometry.cpp DataManagement/mitkTransferFunction.cpp DataManagement/mitkTransferFunctionInitializer.cpp DataManagement/mitkTransferFunctionProperty.cpp DataManagement/mitkTemporoSpatialStringProperty.cpp DataManagement/mitkUIDManipulator.cpp DataManagement/mitkVector.cpp DataManagement/mitkVectorProperty.cpp DataManagement/mitkVtkInterpolationProperty.cpp DataManagement/mitkVtkRepresentationProperty.cpp DataManagement/mitkVtkResliceInterpolationProperty.cpp DataManagement/mitkVtkScalarModeProperty.cpp DataManagement/mitkVtkVolumeRenderingProperty.cpp DataManagement/mitkWeakPointerProperty.cpp DataManagement/mitkIPropertyRelations.cpp DataManagement/mitkPropertyRelations.cpp Interactions/mitkAction.cpp Interactions/mitkBindDispatcherInteractor.cpp Interactions/mitkCrosshairPositionEvent.cpp Interactions/mitkDataInteractor.cpp Interactions/mitkDispatcher.cpp Interactions/mitkDisplayCoordinateOperation.cpp Interactions/mitkDisplayInteractor.cpp Interactions/mitkEventConfig.cpp Interactions/mitkEventFactory.cpp Interactions/mitkEventRecorder.cpp Interactions/mitkEventStateMachine.cpp Interactions/mitkInteractionEventConst.cpp Interactions/mitkInteractionEvent.cpp Interactions/mitkInteractionEventHandler.cpp Interactions/mitkInteractionEventObserver.cpp Interactions/mitkInteractionKeyEvent.cpp Interactions/mitkInteractionPositionEvent.cpp Interactions/mitkInternalEvent.cpp Interactions/mitkMouseDoubleClickEvent.cpp Interactions/mitkMouseModeSwitcher.cpp Interactions/mitkMouseMoveEvent.cpp Interactions/mitkMousePressEvent.cpp Interactions/mitkMouseReleaseEvent.cpp Interactions/mitkMouseWheelEvent.cpp Interactions/mitkPointSetDataInteractor.cpp Interactions/mitkSinglePointDataInteractor.cpp Interactions/mitkStateMachineAction.cpp Interactions/mitkStateMachineCondition.cpp Interactions/mitkStateMachineContainer.cpp Interactions/mitkStateMachineState.cpp Interactions/mitkStateMachineTransition.cpp Interactions/mitkVtkEventAdapter.cpp Interactions/mitkVtkInteractorStyle.cxx Interactions/mitkXML2EventParser.cpp IO/mitkAbstractFileIO.cpp IO/mitkAbstractFileReader.cpp IO/mitkAbstractFileWriter.cpp IO/mitkCustomMimeType.cpp IO/mitkFileReader.cpp IO/mitkFileReaderRegistry.cpp IO/mitkFileReaderSelector.cpp IO/mitkFileReaderWriterBase.cpp IO/mitkFileWriter.cpp IO/mitkFileWriterRegistry.cpp IO/mitkFileWriterSelector.cpp IO/mitkGeometry3DToXML.cpp IO/mitkIFileIO.cpp IO/mitkIFileReader.cpp IO/mitkIFileWriter.cpp IO/mitkGeometryDataReaderService.cpp IO/mitkGeometryDataWriterService.cpp IO/mitkImageGenerator.cpp IO/mitkImageVtkLegacyIO.cpp IO/mitkImageVtkXmlIO.cpp IO/mitkIMimeTypeProvider.cpp IO/mitkIOConstants.cpp IO/mitkIOMimeTypes.cpp IO/mitkIOUtil.cpp IO/mitkItkImageIO.cpp IO/mitkItkLoggingAdapter.cpp IO/mitkLegacyFileReaderService.cpp IO/mitkLegacyFileWriterService.cpp IO/mitkLocaleSwitch.cpp IO/mitkLog.cpp IO/mitkMimeType.cpp IO/mitkMimeTypeProvider.cpp IO/mitkOperation.cpp IO/mitkPixelType.cpp IO/mitkPointSetReaderService.cpp IO/mitkPointSetWriterService.cpp IO/mitkProportionalTimeGeometryToXML.cpp IO/mitkRawImageFileReader.cpp IO/mitkStandardFileLocations.cpp IO/mitkSurfaceStlIO.cpp IO/mitkSurfaceVtkIO.cpp IO/mitkSurfaceVtkLegacyIO.cpp IO/mitkSurfaceVtkXmlIO.cpp IO/mitkVtkLoggingAdapter.cpp IO/mitkPreferenceListReaderOptionsFunctor.cpp Rendering/mitkAbstractAnnotationRenderer.cpp Rendering/mitkAnnotationUtils.cpp Rendering/mitkBaseRenderer.cpp #Rendering/mitkGLMapper.cpp Moved to deprecated LegacyGL Module Rendering/mitkGradientBackground.cpp Rendering/mitkImageVtkMapper2D.cpp Rendering/mitkMapper.cpp Rendering/mitkAnnotation.cpp Rendering/mitkPlaneGeometryDataMapper2D.cpp Rendering/mitkPlaneGeometryDataVtkMapper3D.cpp Rendering/mitkPointSetVtkMapper2D.cpp Rendering/mitkPointSetVtkMapper3D.cpp Rendering/mitkRenderWindowBase.cpp Rendering/mitkRenderWindow.cpp Rendering/mitkRenderWindowFrame.cpp #Rendering/mitkSurfaceGLMapper2D.cpp Moved to deprecated LegacyGL Module Rendering/mitkSurfaceVtkMapper2D.cpp Rendering/mitkSurfaceVtkMapper3D.cpp Rendering/mitkVtkEventProvider.cpp Rendering/mitkVtkMapper.cpp Rendering/mitkVtkPropRenderer.cpp Rendering/mitkVtkWidgetRendering.cpp Rendering/vtkMitkLevelWindowFilter.cpp Rendering/vtkMitkRectangleProp.cpp Rendering/vtkMitkRenderProp.cpp Rendering/vtkMitkThickSlicesFilter.cpp Rendering/vtkNeverTranslucentTexture.cpp ) set(RESOURCE_FILES Interactions/globalConfig.xml Interactions/DisplayInteraction.xml Interactions/DisplayConfig.xml Interactions/DisplayConfigPACS.xml Interactions/DisplayConfigPACSPan.xml Interactions/DisplayConfigPACSScroll.xml Interactions/DisplayConfigPACSZoom.xml Interactions/DisplayConfigPACSLevelWindow.xml Interactions/DisplayConfigMITK.xml Interactions/DisplayConfigMITKNoCrosshair.xml Interactions/DisplayConfigMITKRotation.xml Interactions/DisplayConfigMITKRotationUnCoupled.xml Interactions/DisplayConfigMITKSwivel.xml Interactions/DisplayConfigMITKLimited.xml Interactions/PointSet.xml Interactions/Legacy/StateMachine.xml Interactions/Legacy/DisplayConfigMITKTools.xml Interactions/PointSetConfig.xml mitkLevelWindowPresets.xml mitkAnatomicalStructureColorPresets.xml ) diff --git a/Modules/Core/include/mitkDataNode.h b/Modules/Core/include/mitkDataNode.h index 170b1c9747..ad0f520031 100644 --- a/Modules/Core/include/mitkDataNode.h +++ b/Modules/Core/include/mitkDataNode.h @@ -1,618 +1,618 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef DATATREENODE_H_HEADER_INCLUDED_C1E14338 #define DATATREENODE_H_HEADER_INCLUDED_C1E14338 #include "mitkBaseData.h" //#include "mitkMapper.h" #include "mitkDataInteractor.h" #include "mitkIdentifiable.h" #include "mitkIPropertyOwner.h" #ifdef MBI_NO_STD_NAMESPACE #define MBI_STD #include #include #else #define MBI_STD std #include #include #endif #include "mitkColorProperty.h" #include "mitkPropertyList.h" #include "mitkStringProperty.h" //#include "mitkMapper.h" #include "mitkGeometry3D.h" #include "mitkLevelWindow.h" #include #include class vtkLinearTransform; namespace mitk { class BaseRenderer; class Mapper; /** * \brief Class for nodes of the DataTree * * Contains the data (instance of BaseData), a list of mappers, which can * draw the data, a transform (vtkTransform) and a list of properties * (PropertyList). * \ingroup DataManagement * * \todo clean up all the GetProperty methods. There are too many different flavours... Can most probably be reduced * to * bool GetProperty(type&) * * \warning Change in semantics of SetProperty() since Aug 25th 2006. Check your usage of this method if you do * more with properties than just call SetProperty( "key", new SomeProperty("value") ). */ - class MITKCORE_EXPORT DataNode : public itk::DataObject, public Identifiable, public IPropertyOwner + class MITKCORE_EXPORT DataNode : public itk::DataObject, public IPropertyOwner { public: typedef mitk::Geometry3D::Pointer Geometry3DPointer; typedef std::vector> MapperVector; typedef std::map MapOfPropertyLists; typedef std::vector PropertyListKeyNames; typedef std::set GroupTagList; /** * \brief Definition of an itk::Event that is invoked when * a DataInteractor is set on this DataNode. */ itkEventMacro(InteractorChangedEvent, itk::AnyEvent) mitkClassMacroItkParent(DataNode, itk::DataObject) itkFactorylessNewMacro(Self) itkCloneMacro(Self) // IPropertyProvider BaseProperty::ConstPointer GetConstProperty(const std::string &propertyKey, const std::string &contextName = "", bool fallBackOnDefaultContext = true) const override; std::vector GetPropertyKeys(const std::string &contextName = "", bool includeDefaultContext = false) const override; std::vector GetPropertyContextNames() const override; // IPropertyOwner BaseProperty * GetNonConstProperty(const std::string &propertyKey, const std::string &contextName = "", bool fallBackOnDefaultContext = true) override; void SetProperty(const std::string &propertyKey, BaseProperty *property, const std::string &contextName = "", bool fallBackOnDefaultContext = false) override; void RemoveProperty(const std::string &propertyKey, const std::string &contextName = "", bool fallBackOnDefaultContext = false) override; mitk::Mapper *GetMapper(MapperSlotId id) const; /** * \brief Get the data object (instance of BaseData, e.g., an Image) * managed by this DataNode */ BaseData *GetData() const; /** * \brief Get the transformation applied prior to displaying the data as * a vtkTransform * \deprecated use GetData()->GetGeometry()->GetVtkTransform() instead */ vtkLinearTransform *GetVtkTransform(int t = 0) const; /** * \brief Set the data object (instance of BaseData, e.g., an Image) * managed by this DataNode * * Prior set properties are kept if previous data of the node already exists and has the same * type as the new data to be set. Otherwise, the default properties are used. * In case that previous data already exists, the property list of the data node is cleared * before setting new default properties. * * \warning the actor-mode of the vtkInteractor does not work any more, if the transform of the * data-tree-node is connected to the transform of the basedata via vtkTransform->SetInput. */ virtual void SetData(mitk::BaseData *baseData); /** * \brief Set the Interactor. */ virtual void SetDataInteractor(const DataInteractor::Pointer interactor); virtual DataInteractor::Pointer GetDataInteractor() const; mitk::DataNode &operator=(const DataNode &right); mitk::DataNode &operator=(BaseData *right); virtual void SetMapper(MapperSlotId id, mitk::Mapper *mapper); void UpdateOutputInformation() override; void SetRequestedRegionToLargestPossibleRegion() override; bool RequestedRegionIsOutsideOfTheBufferedRegion() override; bool VerifyRequestedRegion() override; void SetRequestedRegion(const itk::DataObject *data) override; void CopyInformation(const itk::DataObject *data) override; /** * \brief The "names" used for (renderer-specific) PropertyLists in GetPropertyList(string). * * All possible values for the "renderer" parameters of * the diverse GetProperty/List() methods. */ PropertyListKeyNames GetPropertyListNames() const; /** * \brief Set the property (instance of BaseProperty) with key \a propertyKey in the PropertyList * of the \a renderer (if nullptr, use BaseRenderer-independent PropertyList). This is set-by-value. * * \warning Change in semantics since Aug 25th 2006. Check your usage of this method if you do * more with properties than just call SetProperty( "key", new SomeProperty("value") ). * * \sa GetProperty * \sa m_PropertyList * \sa m_MapOfPropertyLists */ void SetProperty(const char *propertyKey, BaseProperty *property, const mitk::BaseRenderer *renderer = nullptr); /** * \brief Replace the property (instance of BaseProperty) with key \a propertyKey in the PropertyList * of the \a renderer (if nullptr, use BaseRenderer-independent PropertyList). This is set-by-reference. * * If \a renderer is \a nullptr the property is set in the BaseRenderer-independent * PropertyList of this DataNode. * \sa GetProperty * \sa m_PropertyList * \sa m_MapOfPropertyLists */ void ReplaceProperty(const char *propertyKey, BaseProperty *property, const mitk::BaseRenderer *renderer = nullptr); /** * \brief Add the property (instance of BaseProperty) if it does * not exist (or always if\a overwrite is\a true) * with key \a propertyKey in the PropertyList * of the \a renderer (if nullptr, use BaseRenderer-independent * PropertyList). This is set-by-value. * * For\a overwrite ==\a false the property is\em not changed * if it already exists. For\a overwrite ==\a true the method * is identical to SetProperty. * * \sa SetProperty * \sa GetProperty * \sa m_PropertyList * \sa m_MapOfPropertyLists */ void AddProperty(const char *propertyKey, BaseProperty *property, const mitk::BaseRenderer *renderer = nullptr, bool overwrite = false); /** * \brief Get the PropertyList of the \a renderer. If \a renderer is \a * nullptr, the BaseRenderer-independent PropertyList of this DataNode * is returned. * \sa GetProperty * \sa m_PropertyList * \sa m_MapOfPropertyLists */ mitk::PropertyList *GetPropertyList(const mitk::BaseRenderer *renderer = nullptr) const; mitk::PropertyList *GetPropertyList(const std::string &rendererName) const; /** * \brief Add values from another PropertyList. * * Overwrites values in m_PropertyList only when possible (i.e. when types are compatible). * If you want to allow for object type changes (replacing a "visible":BoolProperty with "visible":IntProperty, * set the \param replace. * * \param replace true: if \param pList contains a property "visible" of type ColorProperty and our m_PropertyList * also has a "visible" property of a different type (e.g. BoolProperty), change the type, i.e. replace the objects * behind the pointer. * * \sa SetProperty * \sa ReplaceProperty * \sa m_PropertyList */ void ConcatenatePropertyList(PropertyList *pList, bool replace = false); /** * \brief Get the property (instance of BaseProperty) with key \a propertyKey from the PropertyList * of the \a renderer, if available there, otherwise use the BaseRenderer-independent PropertyList. * * If \a renderer is \a nullptr or the \a propertyKey cannot be found * in the PropertyList specific to \a renderer or is disabled there, the BaseRenderer-independent * PropertyList of this DataNode is queried. * * If \a fallBackOnDataProperties is true, the data property list is queried as a last resort. * * \sa GetPropertyList * \sa m_PropertyList * \sa m_MapOfPropertyLists */ mitk::BaseProperty *GetProperty(const char *propertyKey, const mitk::BaseRenderer *renderer = nullptr, bool fallBackOnDataProperties = true) const; /** * \brief Get the property of type T with key \a propertyKey from the PropertyList * of the \a renderer, if available there, otherwise use the BaseRenderer-independent PropertyList. * * If \a renderer is \a nullptr or the \a propertyKey cannot be found * in the PropertyList specific to \a renderer or is disabled there, the BaseRenderer-independent * PropertyList of this DataNode is queried. * \sa GetPropertyList * \sa m_PropertyList * \sa m_MapOfPropertyLists */ template bool GetProperty(itk::SmartPointer &property, const char *propertyKey, const mitk::BaseRenderer *renderer = nullptr) const { property = dynamic_cast(GetProperty(propertyKey, renderer)); return property.IsNotNull(); } /** * \brief Get the property of type T with key \a propertyKey from the PropertyList * of the \a renderer, if available there, otherwise use the BaseRenderer-independent PropertyList. * * If \a renderer is \a nullptr or the \a propertyKey cannot be found * in the PropertyList specific to \a renderer or is disabled there, the BaseRenderer-independent * PropertyList of this DataNode is queried. * \sa GetPropertyList * \sa m_PropertyList * \sa m_MapOfPropertyLists */ template bool GetProperty(T *&property, const char *propertyKey, const mitk::BaseRenderer *renderer = nullptr) const { property = dynamic_cast(GetProperty(propertyKey, renderer)); return property != nullptr; } /** * \brief Convenience access method for GenericProperty properties * (T being the type of the second parameter) * \return \a true property was found */ template bool GetPropertyValue(const char *propertyKey, T &value, const mitk::BaseRenderer *renderer = nullptr) const { GenericProperty *gp = dynamic_cast *>(GetProperty(propertyKey, renderer)); if (gp != nullptr) { value = gp->GetValue(); return true; } return false; } /// \brief Get a set of all group tags from this node's property list GroupTagList GetGroupTags() const; /** * \brief Convenience access method for bool properties (instances of * BoolProperty) * \return \a true property was found */ bool GetBoolProperty(const char *propertyKey, bool &boolValue, const mitk::BaseRenderer *renderer = nullptr) const; /** * \brief Convenience access method for int properties (instances of * IntProperty) * \return \a true property was found */ bool GetIntProperty(const char *propertyKey, int &intValue, const mitk::BaseRenderer *renderer = nullptr) const; /** * \brief Convenience access method for float properties (instances of * FloatProperty) * \return \a true property was found */ bool GetFloatProperty(const char *propertyKey, float &floatValue, const mitk::BaseRenderer *renderer = nullptr) const; /** * \brief Convenience access method for double properties (instances of * DoubleProperty) * * If there is no DoubleProperty for the given\c propertyKey argument, the method * looks for a corresponding FloatProperty instance. * * \return \a true property was found */ bool GetDoubleProperty(const char *propertyKey, double &doubleValue, const mitk::BaseRenderer *renderer = nullptr) const; /** * \brief Convenience access method for string properties (instances of * StringProperty) * \return \a true property was found */ bool GetStringProperty(const char *propertyKey, std::string &string, const mitk::BaseRenderer *renderer = nullptr) const; /** * \brief Convenience access method for color properties (instances of * ColorProperty) * \return \a true property was found */ bool GetColor(float rgb[3], const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "color") const; /** * \brief Convenience access method for level-window properties (instances of * LevelWindowProperty) * \return \a true property was found */ bool GetLevelWindow(mitk::LevelWindow &levelWindow, const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "levelwindow") const; /** * \brief set the node as selected */ void SetSelected(bool selected, const mitk::BaseRenderer *renderer = nullptr); /** * \brief set the node as selected * \return \a true node is selected */ bool IsSelected(const mitk::BaseRenderer *renderer = nullptr); /** * \brief Convenience access method for accessing the name of an object (instance of * StringProperty with property-key "name") * \return \a true property was found */ bool GetName(std::string &nodeName, const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "name") const { return GetStringProperty(propertyKey, nodeName, renderer); } /** * \brief Extra convenience access method for accessing the name of an object (instance of * StringProperty with property-key "name"). * * This method does not take the renderer specific * propertylists into account, because the name of an object should never be renderer specific. * \returns a std::string with the name of the object (content of "name" Property). * If there is no "name" Property, an empty string will be returned. */ virtual std::string GetName() const { mitk::StringProperty *sp = dynamic_cast(this->GetProperty("name")); if (sp == nullptr) return ""; return sp->GetValue(); } /** Value constant that is used indicate that node names are not set so far.*/ static std::string NO_NAME_VALUE() { return "No Name!"; } /** * \brief Extra convenience access method to set the name of an object. * * The name will be stored in the non-renderer-specific PropertyList in a StringProperty named "name". */ virtual void SetName(const char *name) { if (name == nullptr) return; this->SetProperty("name", StringProperty::New(name)); } /** * \brief Extra convenience access method to set the name of an object. * * The name will be stored in the non-renderer-specific PropertyList in a StringProperty named "name". */ virtual void SetName(const std::string name) { this->SetName(name.c_str()); } /** * \brief Convenience access method for visibility properties (instances * of BoolProperty with property-key "visible") * \return \a true property was found * \sa IsVisible */ bool GetVisibility(bool &visible, const mitk::BaseRenderer *renderer, const char *propertyKey = "visible") const { return GetBoolProperty(propertyKey, visible, renderer); } /** * \brief Convenience access method for opacity properties (instances of * FloatProperty) * \return \a true property was found */ bool GetOpacity(float &opacity, const mitk::BaseRenderer *renderer, const char *propertyKey = "opacity") const; /** * \brief Convenience access method for boolean properties (instances * of BoolProperty). Return value is the value of the property. If the property is * not found, the value of \a defaultIsOn is returned. * * Thus, the return value has a different meaning than in the * GetBoolProperty method! * \sa GetBoolProperty */ bool IsOn(const char *propertyKey, const mitk::BaseRenderer *renderer, bool defaultIsOn = true) const { if (propertyKey == nullptr) return defaultIsOn; GetBoolProperty(propertyKey, defaultIsOn, renderer); return defaultIsOn; } /** * \brief Convenience access method for visibility properties (instances * of BoolProperty). Return value is the visibility. Default is * visible==true, i.e., true is returned even if the property (\a * propertyKey) is not found. * * Thus, the return value has a different meaning than in the * GetVisibility method! * \sa GetVisibility * \sa IsOn */ bool IsVisible(const mitk::BaseRenderer *renderer, const char *propertyKey = "visible", bool defaultIsOn = true) const { return IsOn(propertyKey, renderer, defaultIsOn); } /** * \brief Convenience method for setting color properties (instances of * ColorProperty) */ void SetColor(const mitk::Color &color, const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "color"); /** * \brief Convenience method for setting color properties (instances of * ColorProperty) */ void SetColor(float red, float green, float blue, const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "color"); /** * \brief Convenience method for setting color properties (instances of * ColorProperty) */ void SetColor(const float rgb[3], const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "color"); /** * \brief Convenience method for setting visibility properties (instances * of BoolProperty) * \param visible If set to true, the data will be rendered. If false, the render will skip this data. * \param renderer Specify a renderer if the visibility shall be specific to a renderer * \param propertykey Can be used to specify a user defined name of the visibility propery. */ void SetVisibility(bool visible, const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "visible"); /** * \brief Convenience method for setting opacity properties (instances of * FloatProperty) */ void SetOpacity(float opacity, const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "opacity"); /** * \brief Convenience method for setting level-window properties * (instances of LevelWindowProperty) */ void SetLevelWindow(mitk::LevelWindow levelWindow, const mitk::BaseRenderer *renderer = nullptr, const char *propertyKey = "levelwindow"); /** * \brief Convenience method for setting int properties (instances of * IntProperty) */ void SetIntProperty(const char *propertyKey, int intValue, const mitk::BaseRenderer *renderer = nullptr); /** * \brief Convenience method for setting boolean properties (instances of * BoolProperty) */ void SetBoolProperty(const char *propertyKey, bool boolValue, const mitk::BaseRenderer *renderer = nullptr); /** * \brief Convenience method for setting float properties (instances of * FloatProperty) */ void SetFloatProperty(const char *propertyKey, float floatValue, const mitk::BaseRenderer *renderer = nullptr); /** * \brief Convenience method for setting double properties (instances of * DoubleProperty) */ void SetDoubleProperty(const char *propertyKey, double doubleValue, const mitk::BaseRenderer *renderer = nullptr); /** * \brief Convenience method for setting string properties (instances of * StringProperty) */ void SetStringProperty(const char *propertyKey, const char *string, const mitk::BaseRenderer *renderer = nullptr); /** * \brief Get the timestamp of the last change of the contents of this node or * the referenced BaseData. */ unsigned long GetMTime() const override; /** * \brief Get the timestamp of the last change of the reference to the * BaseData. */ unsigned long GetDataReferenceChangedTime() const { return m_DataReferenceChangedTime.GetMTime(); } protected: DataNode(); ~DataNode() override; /// Invoked when the property list was modified. Calls Modified() of the DataNode virtual void PropertyListModified(const itk::Object *caller, const itk::EventObject &event); /// \brief Mapper-slots mutable MapperVector m_Mappers; /** * \brief The data object (instance of BaseData, e.g., an Image) managed * by this DataNode */ BaseData::Pointer m_Data; /** * \brief BaseRenderer-independent PropertyList * * Properties herein can be overwritten specifically for each BaseRenderer * by the BaseRenderer-specific properties defined in m_MapOfPropertyLists. */ PropertyList::Pointer m_PropertyList; /// \brief Map associating each BaseRenderer with its own PropertyList mutable MapOfPropertyLists m_MapOfPropertyLists; DataInteractor::Pointer m_DataInteractor; /// \brief Timestamp of the last change of m_Data itk::TimeStamp m_DataReferenceChangedTime; unsigned long m_PropertyListModifiedObserverTag; }; #if (_MSC_VER > 1200) || !defined(_MSC_VER) MITKCORE_EXPORT MBI_STD::istream &operator>>(MBI_STD::istream &i, DataNode::Pointer &dtn); MITKCORE_EXPORT MBI_STD::ostream &operator<<(MBI_STD::ostream &o, DataNode::Pointer &dtn); #endif } // namespace mitk #if ((defined(_MSC_VER)) && (_MSC_VER <= 1200)) MITKCORE_EXPORT MBI_STD::istream &operator>>(MBI_STD::istream &i, mitk::DataNode::Pointer &dtn); MITKCORE_EXPORT MBI_STD::ostream &operator<<(MBI_STD::ostream &o, mitk::DataNode::Pointer &dtn); #endif #endif /* DATATREENODE_H_HEADER_INCLUDED_C1E14338 */ diff --git a/Modules/Core/include/mitkNodePredicateUID.h b/Modules/Core/include/mitkNodePredicateUID.h deleted file mode 100644 index b44164f4b2..0000000000 --- a/Modules/Core/include/mitkNodePredicateUID.h +++ /dev/null @@ -1,48 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef mitkNodePredicateUID_h -#define mitkNodePredicateUID_h - -#include -#include -#include - -namespace mitk -{ - /** - * \brief Predicate that compares the UID of the given DataNode to a specific UID. - * - * \ingroup DataStorage - */ - class MITKCORE_EXPORT NodePredicateUID : public NodePredicateBase - { - public: - mitkClassMacro(NodePredicateUID, NodePredicateBase) - mitkNewMacro1Param(NodePredicateUID, const Identifiable::UIDType &) - - ~NodePredicateUID() override; - - bool CheckNode(const mitk::DataNode *node) const override; - - protected: - explicit NodePredicateUID(const Identifiable::UIDType &uid); - - Identifiable::UIDType m_UID; - }; -} - -#endif diff --git a/Modules/Core/src/DataManagement/mitkPropertyRelationRuleBase.cpp b/Modules/Core/src/DataManagement/mitkPropertyRelationRuleBase.cpp index e753b8310d..41681c0fa5 100644 --- a/Modules/Core/src/DataManagement/mitkPropertyRelationRuleBase.cpp +++ b/Modules/Core/src/DataManagement/mitkPropertyRelationRuleBase.cpp @@ -1,621 +1,672 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkPropertyRelationRuleBase.h" #include #include #include #include #include #include #include bool mitk::PropertyRelationRuleBase::IsAbstract() const { return true; }; bool mitk::PropertyRelationRuleBase::IsSourceCandidate(const IPropertyProvider *owner) const { return owner != nullptr; }; bool mitk::PropertyRelationRuleBase::IsDestinationCandidate(const IPropertyProvider *owner) const { return owner != nullptr; }; mitk::PropertyKeyPath mitk::PropertyRelationRuleBase::GetRootKeyPath() { return PropertyKeyPath().AddElement("MITK").AddElement("Relations"); }; std::string mitk::PropertyRelationRuleBase::GetRIIPropertyRegEx(const std::string propName, const InstanceIDType &instanceID) const { auto path = this->GetRootKeyPath(); if (instanceID.empty()) { path.AddAnyElement(); } else { path.AddElement(instanceID); } auto result = PropertyKeyPathToPropertyRegEx(path) + "\\." + this->GetRuleKeyRegEx(); if (!propName.empty()) { result += "\\."; result += propName; } return result; }; mitk::PropertyRelationRuleBase::RuleIDType mitk::PropertyRelationRuleBase::GetRuleID() const { auto result = GetRuleIDInternal(); PropertyKeyPath path; path.AddAnyElement(); auto regEx = std::regex(PropertyKeyPathToPropertyRegEx(path)); std::smatch instance_matches; if (!std::regex_match(result, regEx)) { mitkThrow() << "Error. RuleID specified by derived class is not valid, because it is not a valid PropertyKeyPath element. Invalid RuleID: "<GetPropertyKeys(); + std::vector keys; + //workaround until T24729 is done. Please remove if T24728 is done + auto sourceCasted = dynamic_cast(owner); + if (sourceCasted) { + auto sourceData = sourceCasted->GetData(); + if (sourceData) { + keys = sourceData->GetPropertyKeys(); + } + else { + keys = sourceCasted->GetPropertyKeys(); + } + } + else { + keys = owner->GetPropertyKeys(); + } + //end workaround for T24729 + auto sourceRegExStr = this->GetRIIPropertyRegEx(); auto regEx = std::regex(sourceRegExStr); for (const auto &key : keys) { std::smatch instance_matches; std::regex_search(key, instance_matches, regEx); if (!instance_matches.empty()) { return true; } } return false; }; mitk::PropertyRelationRuleBase::RelationType mitk::PropertyRelationRuleBase::HasRelation( const IPropertyProvider *source, const IPropertyProvider *destination) const { if (!source) { mitkThrow() << "Error. Passed source pointer is NULL"; } if (!destination) { mitkThrow() << "Error. Passed owner pointer is NULL"; } RelationType result = RelationType::None; if (this->GetInstanceID_IDLayer(source, destination) != NULL_INSTANCE_ID()) { // has relations of type Connected_ID; result = RelationType::Connected_ID; } if (result == RelationType::None) { auto instanceIDs_data = this->GetInstanceID_datalayer(source, destination); if (instanceIDs_data.size() > 1) { MITK_WARN << "Property relation on data level is ambiguous. First relation is used. Instance ID: " << instanceIDs_data.front(); } if (!instanceIDs_data.empty() && instanceIDs_data.front() != NULL_INSTANCE_ID()) { // has relations of type Connected_Data; result = RelationType::Connected_Data; } } if (result == RelationType::None) { if (this->HasImplicitDataRelation(source, destination)) { // has relations of type Connected_Data; result = RelationType::Implicit_Data; } } return result; }; mitk::PropertyRelationRuleBase::RelationUIDVectorType mitk::PropertyRelationRuleBase::GetExistingRelations( const IPropertyProvider *source) const { if (!source) { mitkThrow() << "Error. Passed source pointer is NULL"; } auto relIDRegExStr = this->GetRIIPropertyRegEx("relationUID"); auto regEx = std::regex(relIDRegExStr); const auto keys = source->GetPropertyKeys(); RelationUIDVectorType relationUIDs; for (const auto &key : keys) { if (std::regex_match(key, regEx)) { auto idProp = source->GetConstProperty(key); relationUIDs.push_back(idProp->GetValueAsString()); } } return relationUIDs; }; mitk::PropertyRelationRuleBase::RelationUIDType mitk::PropertyRelationRuleBase::GetRelationUID( const IPropertyProvider *source, const IPropertyProvider *destination) const { if (!source) { mitkThrow() << "Error. Passed source pointer is NULL"; } if (!destination) { mitkThrow() << "Error. Passed destination pointer is NULL"; } RelationUIDType result; auto instanceID = this->GetInstanceID_IDLayer(source, destination); if (instanceID == NULL_INSTANCE_ID()) { auto instanceID_data = this->GetInstanceID_datalayer(source, destination); if (!instanceID_data.empty()) { instanceID = instanceID_data.front(); } if (instanceID_data.size() > 1) { MITK_WARN << "Property relation on data level is ambigious. First relation is used. Instance ID: " << instanceID; } } return this->GetRelationUIDByInstanceID(source, instanceID); }; mitk::PropertyRelationRuleBase::InstanceIDType mitk::PropertyRelationRuleBase::NULL_INSTANCE_ID() { return std::string(); }; mitk::PropertyRelationRuleBase::RelationUIDType mitk::PropertyRelationRuleBase::GetRelationUIDByInstanceID( const IPropertyProvider *source, const InstanceIDType &instanceID) const { RelationUIDType result; if (instanceID != NULL_INSTANCE_ID()) { auto idProp = source->GetConstProperty( PropertyKeyPathToPropertyName(this->GetRuleRootKeyPath().AddElement(instanceID).AddElement("relationUID"))); if (idProp.IsNotNull()) { result = idProp->GetValueAsString(); } } if (result.empty()) { mitkThrowException(NoPropertyRelationException); } return result; }; mitk::PropertyKeyPath mitk::PropertyRelationRuleBase::GetInstanceKeyPathByRelationUID( const IPropertyProvider *source, const RelationUIDType &relationUID) { if (!source) { mitkThrow() << "Error. Passed source pointer is NULL"; } PropertyKeyPath result; auto destRegExStr = PropertyKeyPathToPropertyRegEx(GetRootKeyPath().AddAnyElement().AddAnyElement().AddElement("relationUID")); auto regEx = std::regex(destRegExStr); std::smatch instance_matches; auto keys = source->GetPropertyKeys(); for (const auto &key : keys) { if (std::regex_search(key, instance_matches, regEx)) { auto idProp = source->GetConstProperty(key); if (idProp->GetValueAsString() == relationUID) { if (instance_matches.size()>1) { result = PropertyNameToPropertyKeyPath(key); break; } } } } return result; }; mitk::PropertyRelationRuleBase::InstanceIDType mitk::PropertyRelationRuleBase::GetInstanceID_IDLayer( const IPropertyProvider *source, const IPropertyProvider *destination) const { if (!source) { mitkThrow() << "Error. Passed source pointer is NULL"; } if (!destination) { mitkThrow() << "Error. Passed destination pointer is NULL"; } auto identifiable = dynamic_cast(destination); + if (!identifiable) + { //This check and pass through to data is needed due to solve T25711. See Task for more information. + //This could be removed at the point we can get rid of DataNodes or they get realy transparent. + auto node = dynamic_cast(destination); + if (node && node->GetData()) + { + identifiable = dynamic_cast(node->GetData()); + } + } + std::string result; if (identifiable) { // check for relations of type Connected_ID; auto destRegExStr = PropertyKeyPathToPropertyRegEx(this->GetRuleRootKeyPath().AddAnyElement().AddElement("destinationUID")); auto regEx = std::regex(destRegExStr); std::smatch instance_matches; auto destUID = identifiable->GetUID(); - auto keys = source->GetPropertyKeys(); + std::vector keys; + //workaround until T24729 is done. Please remove if T24728 is done + auto sourceCasted = dynamic_cast(source); + if (sourceCasted) { + auto sourceData = sourceCasted->GetData(); + if (sourceData) { + keys = sourceData->GetPropertyKeys(); + } + else { + keys = sourceCasted->GetPropertyKeys(); + } + } + else { + keys = source->GetPropertyKeys(); + } + //end workaround for T24729 for (const auto &key : keys) { if (std::regex_search(key, instance_matches, regEx)) { auto idProp = source->GetConstProperty(key); if (idProp->GetValueAsString() == destUID) { if (instance_matches.size()>1) { result = instance_matches[1]; break; } } } } } return result; }; void mitk::PropertyRelationRuleBase::Connect(IPropertyOwner *source, const IPropertyProvider *destination) const { if (!source) { mitkThrow() << "Error. Passed source pointer is NULL"; } if (!destination) { mitkThrow() << "Error. Passed destination pointer is NULL"; } InstanceIDType instanceID = this->GetInstanceID_IDLayer(source, destination); bool hasIDlayer = instanceID != NULL_INSTANCE_ID(); auto instanceIDs_data = this->GetInstanceID_datalayer(source, destination); if (instanceIDs_data.size() > 1) { MITK_WARN << "Property relation on data level is ambiguous. First relation is used. Instance ID: " << instanceIDs_data.front(); } bool hasDatalayer = !instanceIDs_data.empty(); if (hasIDlayer && hasDatalayer && instanceID != instanceIDs_data.front()) { mitkThrow() << "Property relation information is in an invalid state. ID and data layer point to different " "relation instances. Rule: " << this->GetRuleID() << "; ID based instance: " << instanceID << "; Data base instance: " << instanceIDs_data.front(); } RelationUIDType relationUID = this->CreateRelationUID(); if (!hasIDlayer) { if (hasDatalayer) { instanceID = instanceIDs_data.front(); } else { instanceID = this->CreateNewRelationInstance(source, relationUID); } } auto relUIDKey = PropertyKeyPathToPropertyName(this->GetRuleRootKeyPath().AddElement(instanceID).AddElement("relationUID")); source->SetProperty(relUIDKey, mitk::StringProperty::New(relationUID)); if (!hasIDlayer) { auto identifiable = dynamic_cast(destination); + if (!identifiable) + { //This check and pass through to data is needed due to solve T25711. See Task for more information. + //This could be removed at the point we can get rid of DataNodes or they get realy transparent. + auto node = dynamic_cast(destination); + if (node && node->GetData()) + { + identifiable = dynamic_cast(node->GetData()); + } + } + if (identifiable) { auto destUIDKey = PropertyKeyPathToPropertyName(this->GetRuleRootKeyPath().AddElement(instanceID).AddElement("destinationUID")); source->SetProperty(destUIDKey, mitk::StringProperty::New(identifiable->GetUID())); } } if (!hasDatalayer) { this->Connect_datalayer(source, destination, instanceID); } }; void mitk::PropertyRelationRuleBase::Disconnect(IPropertyOwner *source, const IPropertyProvider *destination) const { try { this->Disconnect(source, this->GetRelationUID(source, destination)); } catch (const NoPropertyRelationException &) { // nothing to do and no real error in context of disconnect. } }; void mitk::PropertyRelationRuleBase::Disconnect(IPropertyOwner *source, RelationUIDType relationUID) const { auto instancePath = this->GetInstanceKeyPathByRelationUID(source, relationUID); if (!instancePath.IsEmpty()) { auto instanceID = instancePath.GetLastNode().name; this->Disconnect_datalayer(source, instanceID); auto instancePrefix = PropertyKeyPathToPropertyName(this->GetRuleRootKeyPath().AddElement(instanceID)); auto keys = source->GetPropertyKeys(); for (const auto &key : keys) { if (key.find(instancePrefix) == 0) { source->RemoveProperty(key); } } } }; mitk::PropertyRelationRuleBase::RelationUIDType mitk::PropertyRelationRuleBase::CreateRelationUID() { UIDGenerator generator; return generator.GetUID(); }; /**This mutex is used to guard mitk::PropertyRelationRuleBase::CreateNewRelationInstance by a class wide mutex to avoid racing conditions in a scenario where rules are used concurrently. It is not in the class interface itself, because it is an implementation detail. */ std::mutex relationCreationLock; mitk::PropertyRelationRuleBase::InstanceIDType mitk::PropertyRelationRuleBase::CreateNewRelationInstance( IPropertyOwner *source, const RelationUIDType &relationUID) const { std::lock_guard guard(relationCreationLock); ////////////////////////////////////// // Get all existing instanc IDs std::vector instanceIDs; InstanceIDType newID = "1"; auto destRegExStr = PropertyKeyPathToPropertyRegEx(this->GetRootKeyPath().AddAnyElement().AddAnyElement().AddElement("relationUID")); auto regEx = std::regex(destRegExStr); std::smatch instance_matches; auto keys = source->GetPropertyKeys(); for (const auto &key : keys) { if (std::regex_search(key, instance_matches, regEx)) { if (instance_matches.size()>1) { instanceIDs.push_back(std::stoi(instance_matches[1])); } } } ////////////////////////////////////// // Get new ID std::sort(instanceIDs.begin(), instanceIDs.end()); if (!instanceIDs.empty()) { newID = std::to_string(instanceIDs.back() + 1); } ////////////////////////////////////// // reserve new ID auto relUIDKey = PropertyKeyPathToPropertyName(this->GetRootKeyPath().AddElement(newID).AddElement().AddElement("relationUID")); source->SetProperty(relUIDKey, mitk::StringProperty::New(relationUID)); return newID; }; itk::LightObject::Pointer mitk::PropertyRelationRuleBase::InternalClone() const { return Superclass::InternalClone(); }; namespace mitk { /** * \brief Predicate used to wrap rule checks. * * \ingroup DataStorage */ class NodePredicateRuleFunction : public NodePredicateBase { public: using FunctionType = std::function; mitkClassMacro(NodePredicateRuleFunction, NodePredicateBase) mitkNewMacro2Param(NodePredicateRuleFunction, const FunctionType &, PropertyRelationRuleBase::ConstPointer) ~NodePredicateRuleFunction() override = default; bool CheckNode(const mitk::DataNode *node) const override { if (!node) { return false; } return m_Function(node, m_Rule); }; protected: explicit NodePredicateRuleFunction(const FunctionType &function, PropertyRelationRuleBase::ConstPointer rule) : m_Function(function), m_Rule(rule) { }; FunctionType m_Function; PropertyRelationRuleBase::ConstPointer m_Rule; }; } // namespace mitk mitk::NodePredicateBase::ConstPointer mitk::PropertyRelationRuleBase::GetSourceCandidateIndicator() const { auto check = [](const mitk::IPropertyProvider *node, const mitk::PropertyRelationRuleBase *rule) { return rule->IsSourceCandidate(node); }; return NodePredicateRuleFunction::New(check, this).GetPointer(); }; mitk::NodePredicateBase::ConstPointer mitk::PropertyRelationRuleBase::GetDestinationCandidateIndicator() const { auto check = [](const mitk::IPropertyProvider *node, const mitk::PropertyRelationRuleBase *rule) { return rule->IsDestinationCandidate(node); }; return NodePredicateRuleFunction::New(check, this).GetPointer(); }; mitk::NodePredicateBase::ConstPointer mitk::PropertyRelationRuleBase::GetConnectedSourcesDetector() const { auto check = [](const mitk::IPropertyProvider *node, const mitk::PropertyRelationRuleBase *rule) { return rule->IsSource(node); }; return NodePredicateRuleFunction::New(check, this).GetPointer(); }; mitk::NodePredicateBase::ConstPointer mitk::PropertyRelationRuleBase::GetSourcesDetector( const IPropertyProvider *destination, RelationType minimalRelation) const { if (!destination) { mitkThrow() << "Error. Passed destination pointer is NULL"; } auto check = [destination, minimalRelation](const mitk::IPropertyProvider *node, const mitk::PropertyRelationRuleBase *rule) { return rule->HasRelation(node, destination) >= minimalRelation; }; return NodePredicateRuleFunction::New(check, this).GetPointer(); }; mitk::NodePredicateBase::ConstPointer mitk::PropertyRelationRuleBase::GetDestinationsDetector( const IPropertyProvider *source, RelationType minimalRelation) const { if (!source) { mitkThrow() << "Error. Passed source pointer is NULL"; } auto check = [source, minimalRelation](const mitk::IPropertyProvider *node, const mitk::PropertyRelationRuleBase *rule) { return rule->HasRelation(source, node) >= minimalRelation; }; return NodePredicateRuleFunction::New(check, this).GetPointer(); }; mitk::NodePredicateBase::ConstPointer mitk::PropertyRelationRuleBase::GetDestinationDetector( const IPropertyProvider *source, RelationUIDType relationUID) const { if (!source) { mitkThrow() << "Error. Passed source pointer is NULL"; } auto relUIDs = this->GetExistingRelations(source); if (std::find(relUIDs.begin(), relUIDs.end(), relationUID) == relUIDs.end()) { mitkThrow() << "Error. Passed relationUID does not identify a relation instance of the passed source for this rule instance."; }; auto check = [source, relationUID](const mitk::IPropertyProvider *node, const mitk::PropertyRelationRuleBase *rule) { try { return rule->GetRelationUID(source, node) == relationUID; } catch(const NoPropertyRelationException &) { return false; } }; return NodePredicateRuleFunction::New(check, this).GetPointer(); }; diff --git a/Modules/Core/test/mitkPropertyRelationRuleBaseTest.cpp b/Modules/Core/test/mitkPropertyRelationRuleBaseTest.cpp index a2d6c6d1d4..24a1d88c3f 100644 --- a/Modules/Core/test/mitkPropertyRelationRuleBaseTest.cpp +++ b/Modules/Core/test/mitkPropertyRelationRuleBaseTest.cpp @@ -1,641 +1,652 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkPropertyRelationRuleBase.h" #include "mitkDataNode.h" +#include "mitkPointSet.h" #include "mitkStringProperty.h" #include "mitkTestFixture.h" #include "mitkTestingMacros.h" #include /** This class is used to test PropertyRelationRuleBase and get access to internals where needed to test them as well. */ namespace mitk { class TestRule : public mitk::PropertyRelationRuleBase { public: mitkClassMacro(TestRule, mitk::PropertyRelationRuleBase); itkFactorylessNewMacro(Self); itkCloneMacro(Self); using RuleIDType = PropertyRelationRuleBase::RuleIDType; using RelationUIDType = PropertyRelationRuleBase::RelationUIDType; using RelationUIDVectorType = PropertyRelationRuleBase::RelationUIDVectorType; RuleIDType GetRuleID() const override { return "TestRule"; }; std::string GetDisplayName() const override { return "TestDisplayName"; } std::string GetSourceRoleName() const override { return "source role"; } std::string GetDestinationRoleName() const override { return "destination role"; } using Superclass::GetRuleRootKeyPath; protected: TestRule() = default; ~TestRule() override = default; using InstanceIDType = PropertyRelationRuleBase::InstanceIDType; using InstanceIDVectorType = PropertyRelationRuleBase::InstanceIDVectorType; InstanceIDVectorType GetInstanceID_datalayer(const IPropertyProvider *source, const IPropertyProvider *destination) const override { InstanceIDVectorType result; auto destProp = destination->GetConstProperty("name"); if (destProp.IsNotNull()) { auto destRegExStr = PropertyKeyPathToPropertyRegEx(this->GetRuleRootKeyPath().AddAnyElement().AddElement("dataHandle")); auto regEx = std::regex(destRegExStr); std::smatch instance_matches; auto keys = source->GetPropertyKeys(); for (const auto &key : keys) { if (std::regex_search(key, instance_matches, regEx)) { auto sourceProp = source->GetConstProperty(key); if (sourceProp->GetValueAsString() == destProp->GetValueAsString()) { if (instance_matches.size()>1) { result.push_back(instance_matches[1]); } } } } } return result; }; bool HasImplicitDataRelation(const IPropertyProvider *source, const IPropertyProvider *destination) const override { auto destProp = destination->GetConstProperty("name"); auto sourceProp = source->GetConstProperty("referencedName"); return destProp.IsNotNull() && sourceProp.IsNotNull() && destProp->GetValueAsString() == sourceProp->GetValueAsString(); }; void Connect_datalayer(IPropertyOwner *source, const IPropertyProvider *destination, const InstanceIDType &instanceID) const override { auto destProp = destination->GetConstProperty("name"); source->SetProperty("referencedName", StringProperty::New(destProp->GetValueAsString())); source->SetProperty( PropertyKeyPathToPropertyName(this->GetRuleRootKeyPath().AddElement(instanceID).AddElement("dataHandle")), StringProperty::New(destProp->GetValueAsString())); }; void Disconnect_datalayer(IPropertyOwner *source, const InstanceIDType & /*instanceID*/) const override { source->RemoveProperty("referencedName"); }; }; } // namespace mitk class mitkPropertyRelationRuleBaseTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkPropertyRelationRuleBaseTestSuite); MITK_TEST(IsSourceCandidate); MITK_TEST(IsDestinationCandidate); MITK_TEST(IsSource); MITK_TEST(HasRelation); MITK_TEST(GetExistingRelations); MITK_TEST(GetRelationUID); MITK_TEST(GetSourceCandidateIndicator); MITK_TEST(GetDestinationCandidateIndicator); MITK_TEST(GetConnectedSourcesDetector); MITK_TEST(GetSourcesDetector); MITK_TEST(GetDestinationsDetector); MITK_TEST(GetDestinationDetector); MITK_TEST(Connect); MITK_TEST(Disconnect); CPPUNIT_TEST_SUITE_END(); private: mitk::TestRule::Pointer rule; mitk::DataNode::Pointer unRelated; + mitk::PointSet::Pointer unRelated_1_data; + mitk::DataNode::Pointer source_implicit_1; mitk::DataNode::Pointer source_data_1; mitk::DataNode::Pointer source_idOnly_1; mitk::DataNode::Pointer source_1; mitk::DataNode::Pointer source_multi; mitk::DataNode::Pointer source_otherRule; mitk::DataNode::Pointer dest_1; + mitk::PointSet::Pointer dest_1_data; mitk::DataNode::Pointer dest_2; + mitk::PointSet::Pointer dest_2_data; bool hasRelationProperties(mitk::IPropertyProvider *provider, std::string instance = "") const { auto keyPath = rule->GetRuleRootKeyPath(); if (!instance.empty()) { keyPath.AddElement(instance); } auto prefix = mitk::PropertyKeyPathToPropertyName(keyPath); auto keys = provider->GetPropertyKeys(); for (const auto &key : keys) { if (key.find(prefix) == 0) { return true; } } return false; } public: void setUp() override { rule = mitk::TestRule::New(); unRelated = mitk::DataNode::New(); unRelated->SetName("unRelated"); + unRelated_1_data = mitk::PointSet::New(); + unRelated->SetData(unRelated_1_data); dest_1 = mitk::DataNode::New(); dest_1->SetName("dest_1"); + dest_1_data = mitk::PointSet::New(); + dest_1->SetData(dest_1_data); dest_2 = mitk::DataNode::New(); dest_2->SetName("dest_2"); + dest_2_data = mitk::PointSet::New(); + dest_2->SetData(dest_2_data); source_implicit_1 = mitk::DataNode::New(); source_implicit_1->AddProperty("referencedName", mitk::StringProperty::New(dest_1->GetName())); source_idOnly_1 = mitk::DataNode::New(); std::string name = "MITK.Relations." + rule->GetRuleID() + ".1.relationUID"; source_idOnly_1->AddProperty(name.c_str(), mitk::StringProperty::New("uid1")); name = "MITK.Relations." + rule->GetRuleID() + ".1.destinationUID"; - source_idOnly_1->AddProperty(name.c_str(), mitk::StringProperty::New(dest_1->GetUID())); + source_idOnly_1->AddProperty(name.c_str(), mitk::StringProperty::New(dest_1_data->GetUID())); source_data_1 = source_implicit_1->Clone(); name = "MITK.Relations." + rule->GetRuleID() + ".1.relationUID"; source_data_1->AddProperty(name.c_str(), mitk::StringProperty::New("uid2")); name = "MITK.Relations." + rule->GetRuleID() + ".1.dataHandle"; source_data_1->AddProperty(name.c_str(), mitk::StringProperty::New(dest_1->GetName())); source_1 = source_data_1->Clone(); name = "MITK.Relations." + rule->GetRuleID() + ".1.relationUID"; source_1->AddProperty(name.c_str(), mitk::StringProperty::New("uid3"), nullptr, true); name = "MITK.Relations." + rule->GetRuleID() + ".1.destinationUID"; - source_1->AddProperty(name.c_str(), mitk::StringProperty::New(dest_1->GetUID())); + source_1->AddProperty(name.c_str(), mitk::StringProperty::New(dest_1_data->GetUID())); source_multi = source_1->Clone(); name = "MITK.Relations." + rule->GetRuleID() + ".1.relationUID"; source_multi->AddProperty(name.c_str(), mitk::StringProperty::New("uid4"), nullptr, true); name = "MITK.Relations." + rule->GetRuleID() + ".1.destinationUID"; - source_multi->AddProperty(name.c_str(), mitk::StringProperty::New(dest_1->GetUID())); + source_multi->AddProperty(name.c_str(), mitk::StringProperty::New(dest_1_data->GetUID())); name = "MITK.Relations." + rule->GetRuleID() + ".4.relationUID"; source_multi->AddProperty(name.c_str(), mitk::StringProperty::New("uid5")); name = "MITK.Relations." + rule->GetRuleID() + ".4.destinationUID"; - source_multi->AddProperty(name.c_str(), mitk::StringProperty::New(dest_2->GetUID())); + source_multi->AddProperty(name.c_str(), mitk::StringProperty::New(dest_2_data->GetUID())); name = "MITK.Relations." + rule->GetRuleID() + ".2.relationUID"; source_multi->AddProperty(name.c_str(), mitk::StringProperty::New("uid6")); name = "MITK.Relations." + rule->GetRuleID() + ".2.destinationUID"; source_multi->AddProperty(name.c_str(), mitk::StringProperty::New("unknown")); source_otherRule = mitk::DataNode::New(); name = "MITK.Relations.otherRuleID.1.relationUID"; source_otherRule->AddProperty(name.c_str(), mitk::StringProperty::New("uid7")); name = "MITK.Relations.otherRuleID.1.destinationUID"; - source_otherRule->AddProperty(name.c_str(), mitk::StringProperty::New(dest_1->GetUID())); + source_otherRule->AddProperty(name.c_str(), mitk::StringProperty::New(dest_1_data->GetUID())); } void tearDown() override {} void IsSourceCandidate() { CPPUNIT_ASSERT(rule->IsSourceCandidate(mitk::DataNode::New())); CPPUNIT_ASSERT(!rule->IsSourceCandidate(nullptr)); } void IsDestinationCandidate() { CPPUNIT_ASSERT(rule->IsDestinationCandidate(mitk::DataNode::New())); CPPUNIT_ASSERT(!rule->IsDestinationCandidate(nullptr)); } void IsSource() { CPPUNIT_ASSERT_THROW_MESSAGE( "Violated precondition (nullptr) does not throw.", rule->IsSource(nullptr), itk::ExceptionObject); CPPUNIT_ASSERT(!rule->IsSource(unRelated)); CPPUNIT_ASSERT(!rule->IsSource(source_implicit_1)); CPPUNIT_ASSERT(rule->IsSource(source_data_1)); CPPUNIT_ASSERT(rule->IsSource(source_idOnly_1)); CPPUNIT_ASSERT(rule->IsSource(source_1)); CPPUNIT_ASSERT(rule->IsSource(source_multi)); CPPUNIT_ASSERT(!rule->IsSource(source_otherRule)); } void HasRelation() { CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (source is nullptr) does not throw.", rule->HasRelation(nullptr, dest_1), itk::ExceptionObject); CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (destination is nullptr) does not throw.", rule->HasRelation(source_1, nullptr), itk::ExceptionObject); CPPUNIT_ASSERT(rule->HasRelation(source_1, unRelated) == mitk::PropertyRelationRuleBase::RelationType::None); CPPUNIT_ASSERT(rule->HasRelation(unRelated, dest_1) == mitk::PropertyRelationRuleBase::RelationType::None); CPPUNIT_ASSERT(rule->HasRelation(source_otherRule, dest_1) == mitk::PropertyRelationRuleBase::RelationType::None); CPPUNIT_ASSERT(rule->HasRelation(source_implicit_1, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Implicit_Data); CPPUNIT_ASSERT(rule->HasRelation(source_data_1, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Connected_Data); CPPUNIT_ASSERT(rule->HasRelation(source_idOnly_1, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Connected_ID); CPPUNIT_ASSERT(rule->HasRelation(source_1, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Connected_ID); CPPUNIT_ASSERT(rule->HasRelation(source_multi, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Connected_ID); CPPUNIT_ASSERT(rule->HasRelation(source_1, dest_2) == mitk::PropertyRelationRuleBase::RelationType::None); CPPUNIT_ASSERT(rule->HasRelation(source_multi, dest_2) == mitk::PropertyRelationRuleBase::RelationType::Connected_ID); } void GetExistingRelations() { CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (source is nullptr) does not throw.", rule->GetExistingRelations(nullptr), itk::ExceptionObject); CPPUNIT_ASSERT(rule->GetExistingRelations(unRelated).empty()); CPPUNIT_ASSERT(rule->GetExistingRelations(source_otherRule).empty()); CPPUNIT_ASSERT(rule->GetExistingRelations(source_implicit_1).empty()); auto uids = rule->GetExistingRelations(source_idOnly_1); CPPUNIT_ASSERT(uids.size() == 1); CPPUNIT_ASSERT(uids.front() == "uid1"); uids = rule->GetExistingRelations(source_data_1); CPPUNIT_ASSERT(uids.size() == 1); CPPUNIT_ASSERT(uids.front() == "uid2"); uids = rule->GetExistingRelations(source_1); CPPUNIT_ASSERT(uids.size() == 1); CPPUNIT_ASSERT(uids.front() == "uid3"); uids = rule->GetExistingRelations(source_multi); CPPUNIT_ASSERT(uids.size() == 3); CPPUNIT_ASSERT(std::find(uids.begin(), uids.end(), "uid4") != uids.end()); CPPUNIT_ASSERT(std::find(uids.begin(), uids.end(), "uid5") != uids.end()); CPPUNIT_ASSERT(std::find(uids.begin(), uids.end(), "uid6") != uids.end()); } void GetRelationUID() { CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (source is nullptr) does not throw.", rule->GetRelationUID(nullptr, dest_1), itk::ExceptionObject); CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (destination is nullptr) does not throw.", rule->GetRelationUID(source_1, nullptr), itk::ExceptionObject); CPPUNIT_ASSERT_THROW_MESSAGE( "Violated precondition (no relation of connected_data or conncected_ID) does not throw.", rule->GetRelationUID(source_1, unRelated), mitk::NoPropertyRelationException); CPPUNIT_ASSERT_THROW_MESSAGE( "Violated precondition (no relation of connected_data or conncected_ID) does not throw.", rule->GetRelationUID(unRelated, dest_1), mitk::NoPropertyRelationException); CPPUNIT_ASSERT_THROW_MESSAGE( "Violated precondition (no relation of connected_data or conncected_ID) does not throw.", rule->GetRelationUID(source_otherRule, dest_1), mitk::NoPropertyRelationException); CPPUNIT_ASSERT(rule->GetRelationUID(source_idOnly_1, dest_1) == "uid1"); CPPUNIT_ASSERT(rule->GetRelationUID(source_data_1, dest_1) == "uid2"); CPPUNIT_ASSERT(rule->GetRelationUID(source_1, dest_1) == "uid3"); CPPUNIT_ASSERT(rule->GetRelationUID(source_multi, dest_1) == "uid4"); CPPUNIT_ASSERT(rule->GetRelationUID(source_multi, dest_2) == "uid5"); } void GetSourceCandidateIndicator() { auto predicate = rule->GetSourceCandidateIndicator(); CPPUNIT_ASSERT(predicate->CheckNode(mitk::DataNode::New())); CPPUNIT_ASSERT(!predicate->CheckNode(nullptr)); } void GetDestinationCandidateIndicator() { auto predicate = rule->GetDestinationCandidateIndicator(); CPPUNIT_ASSERT(predicate->CheckNode(mitk::DataNode::New())); CPPUNIT_ASSERT(!predicate->CheckNode(nullptr)); } void GetConnectedSourcesDetector() { auto predicate = rule->GetConnectedSourcesDetector(); CPPUNIT_ASSERT(!predicate->CheckNode(nullptr)); CPPUNIT_ASSERT(!predicate->CheckNode(unRelated)); CPPUNIT_ASSERT(!predicate->CheckNode(source_implicit_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_data_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_idOnly_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_multi)); CPPUNIT_ASSERT(!predicate->CheckNode(source_otherRule)); } void GetSourcesDetector() { CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (destination is nullptr) does not throw.", rule->GetSourcesDetector(nullptr), itk::ExceptionObject); auto predicate = rule->GetSourcesDetector(dest_1); CPPUNIT_ASSERT(!predicate->CheckNode(unRelated)); CPPUNIT_ASSERT(!predicate->CheckNode(source_otherRule)); CPPUNIT_ASSERT(predicate->CheckNode(source_implicit_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_data_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_idOnly_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_multi)); predicate = rule->GetSourcesDetector(dest_1, mitk::PropertyRelationRuleBase::RelationType::Connected_Data); CPPUNIT_ASSERT(!predicate->CheckNode(unRelated)); CPPUNIT_ASSERT(!predicate->CheckNode(source_otherRule)); CPPUNIT_ASSERT(!predicate->CheckNode(source_implicit_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_data_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_idOnly_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_multi)); predicate = rule->GetSourcesDetector(dest_1, mitk::PropertyRelationRuleBase::RelationType::Connected_ID); CPPUNIT_ASSERT(!predicate->CheckNode(unRelated)); CPPUNIT_ASSERT(!predicate->CheckNode(source_otherRule)); CPPUNIT_ASSERT(!predicate->CheckNode(source_implicit_1)); CPPUNIT_ASSERT(!predicate->CheckNode(source_data_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_idOnly_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_multi)); predicate = rule->GetSourcesDetector(dest_2, mitk::PropertyRelationRuleBase::RelationType::Implicit_Data); CPPUNIT_ASSERT(!predicate->CheckNode(unRelated)); CPPUNIT_ASSERT(!predicate->CheckNode(source_otherRule)); CPPUNIT_ASSERT(!predicate->CheckNode(source_implicit_1)); CPPUNIT_ASSERT(!predicate->CheckNode(source_data_1)); CPPUNIT_ASSERT(!predicate->CheckNode(source_idOnly_1)); CPPUNIT_ASSERT(!predicate->CheckNode(source_1)); CPPUNIT_ASSERT(predicate->CheckNode(source_multi)); } void GetDestinationsDetector() { CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (source is nullptr) does not throw.", rule->GetDestinationsDetector(nullptr), itk::ExceptionObject); auto predicate = rule->GetDestinationsDetector(source_otherRule); CPPUNIT_ASSERT(!predicate->CheckNode(dest_1)); predicate = rule->GetDestinationsDetector(source_implicit_1); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); predicate = rule->GetDestinationsDetector(source_implicit_1, mitk::PropertyRelationRuleBase::RelationType::Connected_Data); CPPUNIT_ASSERT(!predicate->CheckNode(dest_1)); predicate = rule->GetDestinationsDetector(source_data_1); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); predicate = rule->GetDestinationsDetector(source_data_1, mitk::PropertyRelationRuleBase::RelationType::Connected_Data); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); predicate = rule->GetDestinationsDetector(source_data_1, mitk::PropertyRelationRuleBase::RelationType::Connected_ID); CPPUNIT_ASSERT(!predicate->CheckNode(dest_1)); predicate = rule->GetDestinationsDetector(source_idOnly_1); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); predicate = rule->GetDestinationsDetector(source_idOnly_1, mitk::PropertyRelationRuleBase::RelationType::Connected_Data); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); predicate = rule->GetDestinationsDetector(source_idOnly_1, mitk::PropertyRelationRuleBase::RelationType::Connected_ID); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); predicate = rule->GetDestinationsDetector(source_1); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); CPPUNIT_ASSERT(!predicate->CheckNode(unRelated)); CPPUNIT_ASSERT(!predicate->CheckNode(dest_2)); predicate = rule->GetDestinationsDetector(source_1, mitk::PropertyRelationRuleBase::RelationType::Connected_Data); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); CPPUNIT_ASSERT(!predicate->CheckNode(unRelated)); CPPUNIT_ASSERT(!predicate->CheckNode(dest_2)); predicate = rule->GetDestinationsDetector(source_1, mitk::PropertyRelationRuleBase::RelationType::Connected_ID); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); CPPUNIT_ASSERT(!predicate->CheckNode(unRelated)); CPPUNIT_ASSERT(!predicate->CheckNode(dest_2)); predicate = rule->GetDestinationsDetector(source_multi); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); CPPUNIT_ASSERT(predicate->CheckNode(dest_2)); predicate = rule->GetDestinationsDetector(source_multi, mitk::PropertyRelationRuleBase::RelationType::Connected_Data); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); CPPUNIT_ASSERT(predicate->CheckNode(dest_2)); predicate = rule->GetDestinationsDetector(source_multi, mitk::PropertyRelationRuleBase::RelationType::Connected_ID); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); CPPUNIT_ASSERT(predicate->CheckNode(dest_2)); } void GetDestinationDetector() { CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (source is nullptr) does not throw.", rule->GetDestinationDetector(nullptr, "uid1"), itk::ExceptionObject); CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (relation uid is invalid) does not throw.", rule->GetDestinationDetector(source_1, "invalid uid"), itk::ExceptionObject); auto predicate = rule->GetDestinationDetector(source_1, "uid3"); CPPUNIT_ASSERT(!predicate->CheckNode(unRelated)); CPPUNIT_ASSERT(predicate->CheckNode(dest_1)); CPPUNIT_ASSERT(!predicate->CheckNode(dest_2)); predicate = rule->GetDestinationDetector(source_multi, "uid5"); CPPUNIT_ASSERT(!predicate->CheckNode(unRelated)); CPPUNIT_ASSERT(!predicate->CheckNode(dest_1)); CPPUNIT_ASSERT(predicate->CheckNode(dest_2)); } void Connect() { CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (source is nullptr) does not throw.", rule->Connect(nullptr, dest_1), itk::ExceptionObject); CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (destination is nullptr) does not throw.", rule->Connect(source_1, nullptr), itk::ExceptionObject); // check upgrade of an implicit connection CPPUNIT_ASSERT(rule->HasRelation(source_implicit_1, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Implicit_Data); rule->Connect(source_implicit_1, dest_1); CPPUNIT_ASSERT(rule->HasRelation(source_implicit_1, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Connected_ID); // check upgrade of an data connection CPPUNIT_ASSERT(rule->HasRelation(source_data_1, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Connected_Data); rule->Connect(source_data_1, dest_1); CPPUNIT_ASSERT(rule->HasRelation(source_data_1, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Connected_ID); std::string name = "MITK.Relations." + rule->GetRuleID() + ".1.destinationUID"; auto prop = source_data_1->GetProperty(name.c_str()); CPPUNIT_ASSERT_MESSAGE( "Destination uid was not stored with the correct key. Already existing session should be used.", prop); - CPPUNIT_ASSERT_MESSAGE("Incorrect destination uid was not stored.", prop->GetValueAsString() == dest_1->GetUID()); + CPPUNIT_ASSERT_MESSAGE("Incorrect destination uid was not stored.", prop->GetValueAsString() == dest_1_data->GetUID()); // check actualization of an id only connection rule->Connect(source_idOnly_1, dest_1); CPPUNIT_ASSERT(rule->HasRelation(source_idOnly_1, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Connected_ID); CPPUNIT_ASSERT_MESSAGE("Additional relation was defined instead of updating exting one.", rule->GetExistingRelations(source_1).size() == 1); name = "MITK.Relations." + rule->GetRuleID() + ".1.dataHandle"; prop = source_idOnly_1->GetProperty(name.c_str()); CPPUNIT_ASSERT_MESSAGE( "Data layer information was not stored with the correct key. Already existing session should be used.", prop); CPPUNIT_ASSERT_MESSAGE("Incorrect data layer information was not stored.", prop->GetValueAsString() == dest_1->GetName()); prop = source_idOnly_1->GetProperty("referencedName"); CPPUNIT_ASSERT_MESSAGE( "Data layer information was not stored with the correct key. Already existing session should be used.", prop); CPPUNIT_ASSERT_MESSAGE("Incorrect data layer information was not stored.", prop->GetValueAsString() == dest_1->GetName()); // check actualization of an existing connection rule->Connect(source_1, dest_1); CPPUNIT_ASSERT(rule->HasRelation(source_1, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Connected_ID); CPPUNIT_ASSERT_MESSAGE("Additional relation was defined instead of updating exting one.", rule->GetExistingRelations(source_1).size() == 1); // check new connection rule->Connect(source_multi, unRelated); CPPUNIT_ASSERT(rule->HasRelation(source_multi, unRelated) == mitk::PropertyRelationRuleBase::RelationType::Connected_ID); name = "MITK.Relations." + rule->GetRuleID() + ".5.dataHandle"; prop = source_multi->GetProperty(name.c_str()); CPPUNIT_ASSERT_MESSAGE( "Data layer information was not stored with the correct key. Already existing session should be used.", prop); CPPUNIT_ASSERT_MESSAGE("Incorrect data layer information was not stored.", prop->GetValueAsString() == unRelated->GetName()); prop = source_multi->GetProperty("referencedName"); CPPUNIT_ASSERT_MESSAGE( "Data layer information was not stored with the correct key. Already existing session should be used.", prop); CPPUNIT_ASSERT_MESSAGE("Incorrect data layer information was not stored.", prop->GetValueAsString() == unRelated->GetName()); name = "MITK.Relations." + rule->GetRuleID() + ".5.destinationUID"; prop = source_multi->GetProperty(name.c_str()); CPPUNIT_ASSERT_MESSAGE( "Destination uid was not stored with the correct key. Already existing session should be used.", prop); - CPPUNIT_ASSERT_MESSAGE("Incorrect destination uid was not stored.", prop->GetValueAsString() == unRelated->GetUID()); + CPPUNIT_ASSERT_MESSAGE("Incorrect destination uid was not stored.", prop->GetValueAsString() == unRelated_1_data->GetUID()); } void Disconnect() { CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (source is nullptr) does not throw.", rule->Disconnect(nullptr, dest_1), itk::ExceptionObject); CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (destination is nullptr) does not throw.", rule->Disconnect(source_1, nullptr), itk::ExceptionObject); CPPUNIT_ASSERT_THROW_MESSAGE("Violated precondition (destination is nullptr) does not throw.", rule->Disconnect(nullptr, "uid"), itk::ExceptionObject); CPPUNIT_ASSERT(rule->HasRelation(source_1, unRelated) == mitk::PropertyRelationRuleBase::RelationType::None); rule->Disconnect(source_1, unRelated); CPPUNIT_ASSERT(rule->HasRelation(source_1, unRelated) == mitk::PropertyRelationRuleBase::RelationType::None); CPPUNIT_ASSERT_MESSAGE("Data property was not removed.", !source_1->GetProperty("referencedName")); rule->Disconnect(source_1, dest_2); CPPUNIT_ASSERT(rule->HasRelation(source_1, dest_2) == mitk::PropertyRelationRuleBase::RelationType::None); CPPUNIT_ASSERT(this->hasRelationProperties(source_1)); CPPUNIT_ASSERT(rule->HasRelation(source_1, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Connected_ID); rule->Disconnect(source_1, dest_1); CPPUNIT_ASSERT(rule->HasRelation(source_1, dest_1) == mitk::PropertyRelationRuleBase::RelationType::None); CPPUNIT_ASSERT(!this->hasRelationProperties(source_1)); CPPUNIT_ASSERT(rule->HasRelation(source_multi, dest_1) == mitk::PropertyRelationRuleBase::RelationType::Connected_ID); rule->Disconnect(source_multi, dest_1); CPPUNIT_ASSERT(rule->HasRelation(source_multi, dest_1) == mitk::PropertyRelationRuleBase::RelationType::None); CPPUNIT_ASSERT(!this->hasRelationProperties(source_multi, "1")); CPPUNIT_ASSERT(this->hasRelationProperties(source_multi, "2")); CPPUNIT_ASSERT(this->hasRelationProperties(source_multi, "4")); rule->Disconnect(source_multi, "uid6"); CPPUNIT_ASSERT(!this->hasRelationProperties(source_multi, "1")); CPPUNIT_ASSERT(!this->hasRelationProperties(source_multi, "2")); CPPUNIT_ASSERT(this->hasRelationProperties(source_multi, "4")); rule->Disconnect(source_multi, "unkownRelationUID"); CPPUNIT_ASSERT(!this->hasRelationProperties(source_multi, "1")); CPPUNIT_ASSERT(!this->hasRelationProperties(source_multi, "2")); CPPUNIT_ASSERT(this->hasRelationProperties(source_multi, "4")); } }; MITK_TEST_SUITE_REGISTRATION(mitkPropertyRelationRuleBase) diff --git a/Modules/DicomRT/autoload/IO/mitkDicomRTIOMimeTypes.cpp b/Modules/DicomRT/autoload/IO/mitkDicomRTIOMimeTypes.cpp index 06bda58c5b..5b327e0a78 100644 --- a/Modules/DicomRT/autoload/IO/mitkDicomRTIOMimeTypes.cpp +++ b/Modules/DicomRT/autoload/IO/mitkDicomRTIOMimeTypes.cpp @@ -1,263 +1,266 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkDicomRTIOMimeTypes.h" #include "mitkIOMimeTypes.h" #include "mitkDICOMDCMTKTagScanner.h" #include "mitkDICOMTagPath.h" #include "mitkDICOMTagsOfInterestService.h" #include #include #include #include #include #include #include namespace mitk { std::vector DicomRTIOMimeTypes::Get() { std::vector mimeTypes; // order matters here (descending rank for mime types) mimeTypes.push_back(DICOMRT_DOSE_MIMETYPE().Clone()); mimeTypes.push_back(DICOMRT_PLAN_MIMETYPE().Clone()); mimeTypes.push_back(DICOMRT_STRUCT_MIMETYPE().Clone()); return mimeTypes; } // Mime Types DicomRTIOMimeTypes::RTDoseMimeType::RTDoseMimeType() : CustomMimeType(DICOMRT_DOSE_MIMETYPE_NAME()) { std::string category = "DICOMRT"; this->SetCategory(category); this->SetComment("RTDose"); this->AddExtension("dcm"); } bool DicomRTIOMimeTypes::RTDoseMimeType::AppliesTo(const std::string &path) const { bool canRead( CustomMimeType::AppliesTo(path) ); if (!canRead) { return false; } if (!canReadByDicomFileReader(path)) { return false; } auto modality = GetModality(path); if (modality == "RTDOSE") { return true; } else { return false; } } std::string DicomRTIOMimeTypes::GetModality(const std::string & path) { mitk::IDICOMTagsOfInterest* toiSrv = GetDicomTagsOfInterestService(); auto tagsOfInterest = toiSrv->GetTagsOfInterest(); DICOMTagPathList tagsOfInterestList; for (const auto& tag : tagsOfInterest) { tagsOfInterestList.push_back(tag.first); } mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New(); scanner->SetInputFiles({ path }); scanner->AddTagPaths(tagsOfInterestList); scanner->Scan(); mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList(); + std::string modality = ""; + if (frames.empty()) + return modality; auto findings = frames.front()->GetTagValueAsString(DICOMTagPath(0x0008, 0x0060)); - std::string modality = findings.front().value; + modality = findings.front().value; return modality; } bool DicomRTIOMimeTypes::canReadByDicomFileReader(const std::string & filename) { mitk::DICOMFileReaderSelector::Pointer selector = mitk::DICOMFileReaderSelector::New(); selector->LoadBuiltIn3DConfigs(); selector->SetInputFiles({ filename }); mitk::DICOMFileReader::Pointer reader = selector->GetFirstReaderWithMinimumNumberOfOutputImages(); if (reader.IsNull()) { return false; } else { return true; } } DicomRTIOMimeTypes::RTDoseMimeType* DicomRTIOMimeTypes::RTDoseMimeType::Clone() const { return new RTDoseMimeType(*this); } DicomRTIOMimeTypes::RTStructMimeType::RTStructMimeType() : CustomMimeType(DICOMRT_STRUCT_MIMETYPE_NAME()) { std::string category = "DICOMRT"; this->SetCategory(category); this->SetComment("RTStruct"); this->AddExtension("dcm"); } bool DicomRTIOMimeTypes::RTStructMimeType::AppliesTo(const std::string &path) const { bool canRead(CustomMimeType::AppliesTo(path)); if (!canRead) { return false; } auto modality = GetModality(path); if (modality == "RTSTRUCT") { return true; } else { return false; } } DicomRTIOMimeTypes::RTStructMimeType* DicomRTIOMimeTypes::RTStructMimeType::Clone() const { return new RTStructMimeType(*this); } DicomRTIOMimeTypes::RTPlanMimeType::RTPlanMimeType() : CustomMimeType(DICOMRT_PLAN_MIMETYPE_NAME()) { std::string category = "DICOMRT"; this->SetCategory(category); this->SetComment("RTPLAN"); this->AddExtension("dcm"); } bool DicomRTIOMimeTypes::RTPlanMimeType::AppliesTo(const std::string &path) const { bool canRead(CustomMimeType::AppliesTo(path)); if (!canRead) { return false; } auto modality = GetModality(path); if (modality == "RTPLAN") { return true; } else { return false; } } DicomRTIOMimeTypes::RTPlanMimeType* DicomRTIOMimeTypes::RTPlanMimeType::Clone() const { return new RTPlanMimeType(*this); } DicomRTIOMimeTypes::RTDoseMimeType DicomRTIOMimeTypes::DICOMRT_DOSE_MIMETYPE() { return RTDoseMimeType(); } DicomRTIOMimeTypes::RTStructMimeType DicomRTIOMimeTypes::DICOMRT_STRUCT_MIMETYPE() { return RTStructMimeType(); } DicomRTIOMimeTypes::RTPlanMimeType DicomRTIOMimeTypes::DICOMRT_PLAN_MIMETYPE() { return RTPlanMimeType(); } // Names std::string DicomRTIOMimeTypes::DICOMRT_DOSE_MIMETYPE_NAME() { static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".dicomrt.dose"; return name; } std::string DicomRTIOMimeTypes::DICOMRT_STRUCT_MIMETYPE_NAME() { static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".dicomrt.struct"; return name; } std::string DicomRTIOMimeTypes::DICOMRT_PLAN_MIMETYPE_NAME() { static std::string name = IOMimeTypes::DEFAULT_BASE_NAME() + ".dicomrt.plan"; return name; } // Descriptions std::string DicomRTIOMimeTypes::DICOMRT_DOSE_MIMETYPE_DESCRIPTION() { static std::string description = "RTDOSE reader"; return description; } std::string DicomRTIOMimeTypes::DICOMRT_STRUCT_MIMETYPE_DESCRIPTION() { static std::string description = "RTSTRUCT reader"; return description; } std::string DicomRTIOMimeTypes::DICOMRT_PLAN_MIMETYPE_DESCRIPTION() { static std::string description = "RTPLAN reader"; return description; } mitk::IDICOMTagsOfInterest* DicomRTIOMimeTypes::GetDicomTagsOfInterestService() { mitk::IDICOMTagsOfInterest* result = nullptr; std::vector > toiRegisters = us::GetModuleContext()->GetServiceReferences(); if (!toiRegisters.empty()) { if (toiRegisters.size() > 1) { MITK_WARN << "Multiple DICOM tags of interest services found. Using just one."; } result = us::GetModuleContext()->GetService(toiRegisters.front()); } return result; } } diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp index 26d4854584..3b9f9c10d4 100755 --- a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp @@ -1,253 +1,267 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include "mitkCommandLineParser.h" #include #include #include #include #include using namespace mitk; /*! * \brief Command line interface to Fiberfox. * Simulate a diffusion-weighted image from a tractogram using the specified parameter file. */ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Fiberfox"); parser.setCategory("Diffusion Simulation Tools"); parser.setContributor("MIC"); parser.setDescription("Command line interface to Fiberfox." " Simulate a diffusion-weighted image from a tractogram using the specified parameter file."); parser.setArgumentPrefix("--", "-"); parser.addArgument("", "o", mitkCommandLineParser::OutputFile, "Output root:", "output root", us::Any(), false); parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "Input tractogram or diffusion-weighted image.", us::Any(), false); parser.addArgument("parameters", "p", mitkCommandLineParser::InputFile, "Parameter file:", "fiberfox parameter file (.ffp)", us::Any(), false); parser.addArgument("template", "t", mitkCommandLineParser::String, "Template image:", "Use parameters of the template diffusion-weighted image.", us::Any()); parser.addArgument("verbose", "v", mitkCommandLineParser::Bool, "Output additional images:", "output volume fraction images etc.", us::Any()); + parser.addArgument("dont_apply_direction_matrix", "", mitkCommandLineParser::Bool, "Don't apply direction matrix:", "Don't rotate gradients by image direction matrix.", us::Any()); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) { return EXIT_FAILURE; } std::string outName = us::any_cast(parsedArgs["o"]); std::string paramName = us::any_cast(parsedArgs["parameters"]); std::string input=""; if (parsedArgs.count("i")) input = us::any_cast(parsedArgs["i"]); bool verbose = false; if (parsedArgs.count("verbose")) verbose = us::any_cast(parsedArgs["verbose"]); + bool apply_direction_matrix = true; + if (parsedArgs.count("dont_apply_direction_matrix")) + apply_direction_matrix = false; + FiberfoxParameters parameters; parameters.LoadParameters(paramName); // Test if /path/dir is an existing directory: std::string file_extension = ""; if( itksys::SystemTools::FileIsDirectory( outName ) ) { while( *(--(outName.cend())) == '/') { outName.pop_back(); } outName = outName + '/'; parameters.m_Misc.m_OutputPath = outName; outName = outName + parameters.m_Misc.m_OutputPrefix; // using default m_OutputPrefix as initialized. } else { // outName is NOT an existing directory, so we need to remove all trailing slashes: while( *(--(outName.cend())) == '/') { outName.pop_back(); } // now split up the given outName into directory and (prefix of) filename: if( ! itksys::SystemTools::GetFilenamePath( outName ).empty() && itksys::SystemTools::FileIsDirectory(itksys::SystemTools::GetFilenamePath( outName ) ) ) { parameters.m_Misc.m_OutputPath = itksys::SystemTools::GetFilenamePath( outName ) + '/'; } else { parameters.m_Misc.m_OutputPath = itksys::SystemTools::GetCurrentWorkingDirectory() + '/'; } file_extension = itksys::SystemTools::GetFilenameExtension(outName); if( ! itksys::SystemTools::GetFilenameWithoutExtension( outName ).empty() ) { parameters.m_Misc.m_OutputPrefix = itksys::SystemTools::GetFilenameWithoutExtension( outName ); } else { parameters.m_Misc.m_OutputPrefix = "fiberfox"; } outName = parameters.m_Misc.m_OutputPath + parameters.m_Misc.m_OutputPrefix; } // check if log file already exists and avoid overwriting existing files: std::string NameTest = outName; int c = 0; while( itksys::SystemTools::FileExists( outName + ".log" ) && c <= std::numeric_limits::max() ) { outName = NameTest + "_" + boost::lexical_cast(c); ++c; } mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images", "Fiberbundles"}, {}); mitk::BaseData::Pointer inputData = mitk::IOUtil::Load(input, &functor)[0]; itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); if ( dynamic_cast(inputData.GetPointer()) ) // simulate dataset from fibers { tractsToDwiFilter->SetFiberBundle(dynamic_cast(inputData.GetPointer())); if (parsedArgs.count("template")) { MITK_INFO << "Loading template image"; typedef itk::VectorImage< short, 3 > ItkDwiType; typedef itk::Image< short, 3 > ItkImageType; mitk::BaseData::Pointer templateData = mitk::IOUtil::Load(us::any_cast(parsedArgs["template"]), &functor)[0]; mitk::Image::Pointer template_image = dynamic_cast(templateData.GetPointer()); if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(template_image)) { ItkDwiType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(template_image); parameters.m_SignalGen.m_ImageRegion = itkVectorImagePointer->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkVectorImagePointer->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkVectorImagePointer->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkVectorImagePointer->GetDirection(); parameters.SetBvalue(mitk::DiffusionPropertyHelper::GetReferenceBValue(template_image)); - parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(template_image)); + parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(template_image)); } else { ItkImageType::Pointer itkImagePointer = ItkImageType::New(); mitk::CastToItkImage(template_image, itkImagePointer); parameters.m_SignalGen.m_ImageRegion = itkImagePointer->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkImagePointer->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkImagePointer->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkImagePointer->GetDirection(); } } } else if ( dynamic_cast(inputData.GetPointer()) ) // add artifacts to existing image { typedef itk::VectorImage< short, 3 > ItkDwiType; mitk::Image::Pointer diffImg = dynamic_cast(inputData.GetPointer()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); parameters.m_SignalGen.m_SignalScale = 1; parameters.m_SignalGen.m_ImageRegion = itkVectorImagePointer->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkVectorImagePointer->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkVectorImagePointer->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkVectorImagePointer->GetDirection(); parameters.SetBvalue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); - parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg)); + parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(diffImg)); tractsToDwiFilter->SetInputImage(itkVectorImagePointer); } if (verbose) { MITK_DEBUG << outName << ".ffp"; parameters.SaveParameters(outName+".ffp"); } + + if (apply_direction_matrix) + { + MITK_INFO << "Applying direction matrix to gradient directions."; + parameters.ApplyDirectionMatrix(); + } tractsToDwiFilter->SetParameters(parameters); tractsToDwiFilter->Update(); mitk::Image::Pointer image = mitk::GrabItkImageMemory(tractsToDwiFilter->GetOutput()); - mitk::DiffusionPropertyHelper::SetGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer()); + if (apply_direction_matrix) + mitk::DiffusionPropertyHelper::SetGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer()); + else + mitk::DiffusionPropertyHelper::SetOriginalGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer()); mitk::DiffusionPropertyHelper::SetReferenceBValue(image, parameters.m_SignalGen.GetBvalue()); mitk::DiffusionPropertyHelper::InitializeImage(image); if (file_extension=="") mitk::IOUtil::Save(image, "DWI_NIFTI", outName+".nii.gz"); else if (file_extension==".nii" || file_extension==".nii.gz") mitk::IOUtil::Save(image, "DWI_NIFTI", outName+file_extension); else mitk::IOUtil::Save(image, outName+file_extension); if (verbose) { std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = tractsToDwiFilter->GetVolumeFractions(); for (unsigned int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::IOUtil::Save(image, outName+"_Compartment"+boost::lexical_cast(k+1)+".nii.gz"); } if (tractsToDwiFilter->GetPhaseImage().IsNotNull()) { mitk::Image::Pointer image = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkPhase = tractsToDwiFilter->GetPhaseImage(); image = mitk::GrabItkImageMemory( itkPhase.GetPointer() ); mitk::IOUtil::Save(image, outName+"_Phase.nii.gz"); } if (tractsToDwiFilter->GetKspaceImage().IsNotNull()) { mitk::Image::Pointer image = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkImage = tractsToDwiFilter->GetKspaceImage(); image = mitk::GrabItkImageMemory( itkImage.GetPointer() ); mitk::IOUtil::Save(image, outName+"_kSpace.nii.gz"); } int c = 1; std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_real = tractsToDwiFilter->GetOutputImagesReal(); for (auto real : output_real) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(real.GetPointer()); image->SetVolume(real->GetBufferPointer()); mitk::IOUtil::Save(image, outName+"_Coil-"+boost::lexical_cast(c)+"-real.nii.gz"); ++c; } c = 1; std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_imag = tractsToDwiFilter->GetOutputImagesImag(); for (auto imag : output_imag) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(imag.GetPointer()); image->SetVolume(imag->GetBufferPointer()); mitk::IOUtil::Save(image, outName+"_Coil-"+boost::lexical_cast(c)+"-imag.nii.gz"); ++c; } } return EXIT_SUCCESS; } diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/FiberfoxOptimization.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/FiberfoxOptimization.cpp index bc0c8bedd0..dc4547ce02 100644 --- a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/FiberfoxOptimization.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/FiberfoxOptimization.cpp @@ -1,849 +1,849 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include "mitkCommandLineParser.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include using namespace mitk; double CalcErrorSignal(const std::vector& histo_mod, itk::VectorImage< short, 3 >* reference, itk::VectorImage< short, 3 >* simulation, itk::Image< unsigned char,3 >::ConstPointer mask, itk::Image< double,3 >::ConstPointer fa) { typedef itk::Image< double, 3 > DoubleImageType; typedef itk::VectorImage< short, 3 > DwiImageType; if (fa.IsNotNull()) { itk::ImageRegionIterator< DwiImageType > it1(reference, reference->GetLargestPossibleRegion()); itk::ImageRegionIterator< DwiImageType > it2(simulation, simulation->GetLargestPossibleRegion()); itk::ImageRegionConstIterator< DoubleImageType > it3(fa, fa->GetLargestPossibleRegion()); unsigned int count = 0; double error = 0; while(!it1.IsAtEnd()) { if (mask.IsNull() || (mask.IsNotNull() && mask->GetLargestPossibleRegion().IsInside(it1.GetIndex()) && mask->GetPixel(it1.GetIndex())>0) ) { double fa = it3.Get(); if (fa>0) { double mod = 1.0; for (int i=histo_mod.size()-1; i>=0; --i) if (fa >= (double)i/histo_mod.size()) { mod = histo_mod.at(i); break; } for (unsigned int i=0; iGetVectorLength(); ++i) { if (it1.Get()[i]>0) { double diff = (double)it2.Get()[i]/it1.Get()[i] - 1.0; error += std::pow(mod, 4) * fabs(diff); count++; } } } } ++it1; ++it2; ++it3; } return error/count; } else { itk::ImageRegionIterator< DwiImageType > it1(reference, reference->GetLargestPossibleRegion()); itk::ImageRegionIterator< DwiImageType > it2(simulation, simulation->GetLargestPossibleRegion()); unsigned int count = 0; double error = 0; while(!it1.IsAtEnd()) { if (mask.IsNull() || (mask.IsNotNull() && mask->GetLargestPossibleRegion().IsInside(it1.GetIndex()) && mask->GetPixel(it1.GetIndex())>0) ) { for (unsigned int i=0; iGetVectorLength(); ++i) { if (it1.Get()[i]>0) { double diff = (double)it2.Get()[i]/it1.Get()[i] - 1.0; error += fabs(diff); count++; } } } ++it1; ++it2; } return error/count; } return -1; } double CalcErrorFA(const std::vector& histo_mod, mitk::Image::Pointer dwi1, const itk::VectorImage< short, 3 >* dwi2, itk::Image< unsigned char,3 >::ConstPointer mask, itk::Image< double,3 >::ConstPointer fa1, itk::Image< double,3 >::ConstPointer md1, bool b0_contrast) { typedef itk::TensorDerivedMeasurementsFilter MeasurementsType; typedef itk::Image< double, 3 > DoubleImageType; typedef itk::VectorImage< short, 3 > DwiType; DwiType::Pointer dwi1_itk = mitk::DiffusionPropertyHelper::GetItkVectorImage(dwi1); typedef itk::DiffusionTensor3DReconstructionImageFilter TensorReconstructionImageFilterType; DoubleImageType::Pointer fa2; { mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientContainerCopy = mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::New(); for(auto it = mitk::DiffusionPropertyHelper::GetGradientContainer(dwi1)->Begin(); it != mitk::DiffusionPropertyHelper::GetGradientContainer(dwi1)->End(); it++) gradientContainerCopy->push_back(it.Value()); typename itk::ImageDuplicator>::Pointer duplicator = itk::ImageDuplicator>::New(); duplicator->SetInputImage(dwi2); duplicator->Update(); auto working_dwi = duplicator->GetOutput(); TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter = TensorReconstructionImageFilterType::New(); tensorReconstructionFilter->SetBValue( mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi1) ); tensorReconstructionFilter->SetGradientImage(gradientContainerCopy, working_dwi ); tensorReconstructionFilter->Update(); MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput( tensorReconstructionFilter->GetOutput() ); measurementsCalculator->SetMeasure(MeasurementsType::FA); measurementsCalculator->Update(); fa2 = measurementsCalculator->GetOutput(); } DoubleImageType::Pointer md2; if (md1.IsNotNull()) { typename itk::ImageDuplicator>::Pointer duplicator = itk::ImageDuplicator>::New(); duplicator->SetInputImage(dwi2); duplicator->Update(); auto working_dwi = duplicator->GetOutput(); typedef itk::AdcImageFilter< short, double > AdcFilterType; AdcFilterType::Pointer filter = AdcFilterType::New(); filter->SetInput( working_dwi ); filter->SetGradientDirections( mitk::DiffusionPropertyHelper::GetGradientContainer(dwi1) ); filter->SetB_value( mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi1) ); filter->SetFitSignal(false); filter->Update(); md2 = filter->GetOutput(); } itk::ImageRegionConstIterator< DoubleImageType > it1(fa1, fa1->GetLargestPossibleRegion()); itk::ImageRegionConstIterator< DoubleImageType > it2(fa2, fa2->GetLargestPossibleRegion()); itk::ImageRegionConstIterator< itk::VectorImage< short, 3 > > it_diff1(dwi1_itk, dwi1_itk->GetLargestPossibleRegion()); itk::ImageRegionConstIterator< itk::VectorImage< short, 3 > > it_diff2(dwi2, dwi2->GetLargestPossibleRegion()); unsigned int count = 0; double error = 0; if (md1.IsNotNull() && md2.IsNotNull()) { itk::ImageRegionConstIterator< DoubleImageType > it3(md1, md1->GetLargestPossibleRegion()); itk::ImageRegionConstIterator< DoubleImageType > it4(md2, md2->GetLargestPossibleRegion()); while(!it1.IsAtEnd()) { if (mask.IsNull() || (mask.IsNotNull() && mask->GetLargestPossibleRegion().IsInside(it1.GetIndex()) && mask->GetPixel(it1.GetIndex())>0) ) { double fa = it1.Get(); if (fa>0 && it3.Get()>0) { double mod = 1.0; for (int i=histo_mod.size()-1; i>=0; --i) if (fa >= (double)i/histo_mod.size()) { mod = histo_mod.at(i); break; } double fa_diff = std::fabs(it2.Get()/fa - 1.0); double md_diff = std::fabs(it4.Get()/it3.Get() - 1.0); error += mod * (fa_diff + md_diff); count += 2; if (b0_contrast && it_diff1.Get()[0]>0) { double b0_diff = (double)it_diff2.Get()[0]/it_diff1.Get()[0] - 1.0; error += std::fabs(b0_diff); ++count; } } } ++it1; ++it2; ++it3; ++it4; ++it_diff1; ++it_diff2; } } else { unsigned int count = 0; double error = 0; while(!it1.IsAtEnd()) { if (mask.IsNull() || (mask.IsNotNull() && mask->GetLargestPossibleRegion().IsInside(it1.GetIndex()) && mask->GetPixel(it1.GetIndex())>0) ) { double fa = it1.Get(); if (fa>0) { double mod = 1.0; for (int i=histo_mod.size()-1; i>=0; --i) if (fa >= (double)i/histo_mod.size()) { mod = histo_mod.at(i); break; } double fa_diff = fabs(it2.Get()/fa - 1.0); error += mod * fa_diff; ++count; if (b0_contrast && it_diff1.Get()[0]>0) { double b0_diff = (double)it_diff2.Get()[0]/it_diff1.Get()[0] - 1.0; error += std::fabs(b0_diff); ++count; } } } ++it1; ++it2; ++it_diff1; ++it_diff2; } } return error/count; } FiberfoxParameters MakeProposalScale(FiberfoxParameters old_params, double temperature) { FiberfoxParameters new_params(old_params); std::random_device r; std::default_random_engine randgen(r()); std::normal_distribution normal_dist(0, new_params.m_SignalGen.m_SignalScale*0.1*temperature); double add = 0; while (add == 0) add = normal_dist(randgen); new_params.m_SignalGen.m_SignalScale += add; MITK_INFO << "Proposal Signal Scale: " << new_params.m_SignalGen.m_SignalScale << " (" << add << ")"; return new_params; } FiberfoxParameters MakeProposalRelaxation(FiberfoxParameters old_params, double temperature) { FiberfoxParameters new_params(old_params); std::random_device r; std::default_random_engine randgen(r()); std::uniform_int_distribution uint1(0, 3); int prop = uint1(randgen); switch(prop) { case 0: { int model_index = rand()%new_params.m_NonFiberModelList.size(); double t2 = new_params.m_NonFiberModelList[model_index]->GetT2(); std::normal_distribution normal_dist(0, t2*0.1*temperature); double add = 0; while (add == 0) add = normal_dist(randgen); if ( (t2+add)*1.5 > new_params.m_NonFiberModelList[model_index]->GetT1() ) add = -add; t2 += add; new_params.m_NonFiberModelList[model_index]->SetT2(t2); MITK_INFO << "Proposal T2 (Non-Fiber " << model_index << "): " << t2 << " (" << add << ")"; break; } case 1: { int model_index = rand()%new_params.m_FiberModelList.size(); double t2 = new_params.m_FiberModelList[model_index]->GetT2(); std::normal_distribution normal_dist(0, t2*0.1*temperature); double add = 0; while (add == 0) add = normal_dist(randgen); if ( (t2+add)*1.5 > new_params.m_FiberModelList[model_index]->GetT1() ) add = -add; t2 += add; new_params.m_FiberModelList[model_index]->SetT2(t2); MITK_INFO << "Proposal T2 (Fiber " << model_index << "): " << t2 << " (" << add << ")"; break; } case 2: { int model_index = rand()%new_params.m_NonFiberModelList.size(); double t1 = new_params.m_NonFiberModelList[model_index]->GetT1(); std::normal_distribution normal_dist(0, t1*0.1*temperature); double add = 0; while (add == 0) add = normal_dist(randgen); if ( t1+add < new_params.m_NonFiberModelList[model_index]->GetT2() * 1.5 ) add = -add; t1 += add; new_params.m_NonFiberModelList[model_index]->SetT1(t1); MITK_INFO << "Proposal T1 (Non-Fiber " << model_index << "): " << t1 << " (" << add << ")"; break; } case 3: { int model_index = rand()%new_params.m_FiberModelList.size(); double t1 = new_params.m_FiberModelList[model_index]->GetT1(); std::normal_distribution normal_dist(0, t1*0.1*temperature); double add = 0; while (add == 0) add = normal_dist(randgen); if ( t1+add < new_params.m_FiberModelList[model_index]->GetT2() * 1.5 ) add = -add; t1 += add; new_params.m_FiberModelList[model_index]->SetT1(t1); MITK_INFO << "Proposal T1 (Fiber " << model_index << "): " << t1 << " (" << add << ")"; break; } } return new_params; } double UpdateDiffusivity(double d, double temperature) { std::random_device r; std::default_random_engine randgen(r()); std::normal_distribution normal_dist(0, d*0.1*temperature); double add = 0; while (add == 0) add = normal_dist(randgen); if (d+add > 0.0025) d -= add; else if ( d+add < 0.0 ) d -= add; else d += add; return d; } void ProposeDiffusivities(mitk::DiffusionSignalModel<>* signalModel, double temperature) { if (dynamic_cast*>(signalModel)) { mitk::StickModel<>* m = dynamic_cast*>(signalModel); double new_d = UpdateDiffusivity(m->GetDiffusivity(), temperature); MITK_INFO << "d: " << new_d << " (" << new_d-m->GetDiffusivity() << ")"; m->SetDiffusivity(new_d); } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel<>* m = dynamic_cast*>(signalModel); double new_d1 = UpdateDiffusivity(m->GetDiffusivity1(), temperature); double new_d2 = UpdateDiffusivity(m->GetDiffusivity2(), temperature); while (new_d1GetDiffusivity2(), temperature); MITK_INFO << "d1: " << new_d1 << " (" << new_d1-m->GetDiffusivity1() << ")"; MITK_INFO << "d2: " << new_d2 << " (" << new_d2-m->GetDiffusivity2() << ")"; m->SetDiffusivity1(new_d1); m->SetDiffusivity2(new_d2); m->SetDiffusivity3(new_d2); } else if (dynamic_cast*>(signalModel)) { mitk::BallModel<>* m = dynamic_cast*>(signalModel); double new_d = UpdateDiffusivity(m->GetDiffusivity(), temperature); MITK_INFO << "d: " << new_d << " (" << new_d-m->GetDiffusivity() << ")"; m->SetDiffusivity(new_d); } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel<>* m = dynamic_cast*>(signalModel); double new_d = UpdateDiffusivity(m->GetDiffusivity(), temperature); MITK_INFO << "d: " << new_d << " (" << new_d-m->GetDiffusivity() << ")"; m->SetDiffusivity(new_d); } } FiberfoxParameters MakeProposalDiff(FiberfoxParameters old_params, double temperature) { FiberfoxParameters new_params(old_params); std::random_device r; std::default_random_engine randgen(r()); std::uniform_int_distribution uint1(0, new_params.m_FiberModelList.size() - 1); unsigned int prop = uint1(randgen); MITK_INFO << "Proposal D (Fiber " << prop << ")"; ProposeDiffusivities( new_params.m_FiberModelList[prop], temperature ); return new_params; } FiberfoxParameters MakeProposalVolume(double old_tdi_thr, double old_sqrt, double& new_tdi_thr, double& new_sqrt, FiberfoxParameters old_params, std::vector< itk::Image< double, 3 >::Pointer > frac, double temperature) { FiberfoxParameters new_params(old_params); MITK_INFO << "Proposal Volume"; std::random_device r; std::default_random_engine randgen(r()); { std::normal_distribution normal_dist(0, old_tdi_thr*0.1*temperature); new_tdi_thr = old_tdi_thr + normal_dist(randgen); while (new_tdi_thr<=0.01) { new_tdi_thr = old_tdi_thr + normal_dist(randgen); } } { std::normal_distribution normal_dist(0, old_sqrt*0.1*temperature); new_sqrt = old_sqrt + normal_dist(randgen); while (new_sqrt<=0.01) { new_sqrt = old_sqrt + normal_dist(randgen); } } itk::TdiToVolumeFractionFilter< double >::Pointer fraction_generator = itk::TdiToVolumeFractionFilter< double >::New(); fraction_generator->SetTdiThreshold(new_tdi_thr); fraction_generator->SetSqrt(new_sqrt); fraction_generator->SetInput(0, frac.at(0)); fraction_generator->SetInput(1, frac.at(1)); fraction_generator->SetInput(2, frac.at(2)); fraction_generator->SetInput(3, frac.at(3)); fraction_generator->SetInput(4, frac.at(4)); fraction_generator->Update(); new_params.m_FiberModelList[0]->SetVolumeFractionImage(fraction_generator->GetOutput(0)); new_params.m_FiberModelList[1]->SetVolumeFractionImage(fraction_generator->GetOutput(1)); new_params.m_NonFiberModelList[0]->SetVolumeFractionImage(fraction_generator->GetOutput(2)); new_params.m_NonFiberModelList[1]->SetVolumeFractionImage(fraction_generator->GetOutput(3)); MITK_INFO << "TDI Threshold: " << new_tdi_thr << " (" << new_tdi_thr-old_tdi_thr << ")"; MITK_INFO << "SQRT: " << new_sqrt << " (" << new_sqrt-old_sqrt << ")"; return new_params; } /*! * \brief Command line interface to optimize Fiberfox parameters. */ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("FiberfoxOptimization"); parser.setCategory("Optimize Fiberfox Parameters"); parser.setContributor("MIC"); parser.setArgumentPrefix("--", "-"); parser.beginGroup("1. Mandatory Input:"); parser.addArgument("parameters", "p", mitkCommandLineParser::InputFile, "Parameter File:", "fiberfox parameter file (.ffp)", us::Any(), false); parser.addArgument("tracts", "t", mitkCommandLineParser::String, "Input Tractogram:", "Input tractogram.", us::Any(), false); parser.addArgument("", "o", mitkCommandLineParser::String, "Output Folder:", "", us::Any(), false); parser.addArgument("dmri", "d", mitkCommandLineParser::String, "Target image:", "Target dMRI to approximate.", us::Any(), false); parser.addArgument("mask", "", mitkCommandLineParser::InputFile, "Mask image:", "Error is only calculated inside the mask image", false); parser.endGroup(); parser.beginGroup("2. Parameters to optimize:"); parser.addArgument("no_diff", "", mitkCommandLineParser::Bool, "Don't optimize diffusivities:", "Don't optimize diffusivities"); parser.addArgument("no_relax", "", mitkCommandLineParser::Bool, "Don't optimize relaxation times:", "Don't optimize relaxation times"); parser.addArgument("no_scale", "", mitkCommandLineParser::Bool, "Don't optimize signal scale:", "Don't optimize global signal scale"); parser.endGroup(); parser.beginGroup("3. Error measure:"); parser.addArgument("fa_error", "", mitkCommandLineParser::Bool, "Optimize FA", "Optimize FA instead of raw signal. Requires FA image."); parser.addArgument("fa_image", "", mitkCommandLineParser::InputFile, "FA image:", "Weight error by FA histogram. Always necessary with option fa_error!"); parser.addArgument("md_image", "", mitkCommandLineParser::InputFile, "MD image:", "Optimize MD in conjunction with FA (recommended when optimizing FA)."); parser.addArgument("use_histo", "", mitkCommandLineParser::Bool, "Use histogram modifiers:", "Modify error per voxel by corresponding FA frequency."); parser.addArgument("raise_histo", "", mitkCommandLineParser::Float, "Raise histogram modifiers:", "Raise histogram modifiers by the specified power.", 1.0); parser.endGroup(); parser.beginGroup("4. Optimization of volume fraction maps:"); parser.addArgument("tdi", "", mitkCommandLineParser::InputFile, "TDI:", "tract density image"); parser.addArgument("wm", "", mitkCommandLineParser::InputFile, "WM:", "white matter volume fraction image"); parser.addArgument("gm", "", mitkCommandLineParser::InputFile, "GM:", "gray matter volume fraction image"); parser.addArgument("dgm", "", mitkCommandLineParser::InputFile, "DGM:", "subcortical gray matter volume fraction image"); parser.addArgument("csf", "", mitkCommandLineParser::InputFile, "CSF:", "CSF volume fraction image"); parser.addArgument("tdi_threshold", "", mitkCommandLineParser::Float, "", "", 0.75); parser.addArgument("sqrt", "", mitkCommandLineParser::Float, "", "", 1.0); parser.endGroup(); parser.beginGroup("5. General parameters:"); parser.addArgument("iterations", "", mitkCommandLineParser::Int, "Iterations:", "Number of optimizations steps", 1000); parser.addArgument("start_temp", "", mitkCommandLineParser::Float, "Start temperature:", "Higher temperature means larger parameter change proposals", 1.0); parser.addArgument("end_temp", "", mitkCommandLineParser::Float, "End temperature:", "Higher temperature means larger parameter change proposals", 0.1); parser.endGroup(); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; std::string paramName = us::any_cast(parsedArgs["parameters"]); std::string out_folder = us::any_cast(parsedArgs["o"]); std::string tract_file = us::any_cast(parsedArgs["tracts"]); MITK_INFO << "Loading target dMRI and parameters"; FiberfoxParameters parameters; parameters.LoadParameters(paramName); typedef itk::VectorImage< short, 3 > ItkDwiType; mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images", "Fiberbundles"}, {}); mitk::Image::Pointer dwi = mitk::IOUtil::Load(us::any_cast(parsedArgs["dmri"]), &functor); ItkDwiType::Pointer reference = mitk::DiffusionPropertyHelper::GetItkVectorImage(dwi); parameters.m_SignalGen.m_ImageRegion = reference->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = reference->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = reference->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = reference->GetDirection(); parameters.SetBvalue(mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi)); parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(dwi)); auto tracts = mitk::IOUtil::Load(tract_file, &functor); int iterations=1000; if (parsedArgs.count("iterations")) iterations = us::any_cast(parsedArgs["iterations"]); float start_temp=1.0; if (parsedArgs.count("start_temp")) start_temp = us::any_cast(parsedArgs["start_temp"]); float end_temp=0.1; if (parsedArgs.count("end_temp")) end_temp = us::any_cast(parsedArgs["end_temp"]); float tdi_threshold=0.75; if (parsedArgs.count("tdi_threshold")) tdi_threshold = us::any_cast(parsedArgs["tdi_threshold"]); float raise_histo=1.0; if (parsedArgs.count("raise_histo")) raise_histo = us::any_cast(parsedArgs["raise_histo"]); float sqrt=1.0; if (parsedArgs.count("sqrt")) sqrt = us::any_cast(parsedArgs["sqrt"]); bool fa_error=false; if (parsedArgs.count("fa_error")) fa_error = true; bool use_histo=false; if (parsedArgs.count("use_histo")) use_histo = true; std::string fa_file = ""; if (parsedArgs.count("fa_image")) fa_file = us::any_cast(parsedArgs["fa_image"]); std::string md_file = ""; if (parsedArgs.count("md_image")) md_file = us::any_cast(parsedArgs["md_image"]); std::vector< int > possible_proposals; if (!parsedArgs.count("no_diff")) { MITK_INFO << "Optimizing diffusivities"; possible_proposals.push_back(0); } if (!parsedArgs.count("no_relax")) { MITK_INFO << "Optimizing relaxation constants"; possible_proposals.push_back(1); } if (!parsedArgs.count("no_scale")) { MITK_INFO << "Optimizing global signal scale"; possible_proposals.push_back(2); } mitk::LocaleSwitch localeSwitch("C"); itk::ImageFileReader< itk::Image< unsigned char, 3 > >::Pointer reader = itk::ImageFileReader< itk::Image< unsigned char, 3 > >::New(); reader->SetFileName( us::any_cast(parsedArgs["mask"]) ); reader->Update(); itk::Image< unsigned char,3 >::ConstPointer mask = reader->GetOutput(); std::vector< itk::Image< double, 3 >::Pointer > fracs; if ( parsedArgs.count("tdi")>0 && parsedArgs.count("wm")>0 && parsedArgs.count("gm")>0 && parsedArgs.count("dgm")>0 && parsedArgs.count("csf")>0 ) { MITK_INFO << "Optimizing volume fractions"; { itk::ImageFileReader< itk::Image< double, 3 > >::Pointer reader = itk::ImageFileReader< itk::Image< double, 3 > >::New(); reader->SetFileName( us::any_cast(parsedArgs["tdi"]) ); reader->Update(); fracs.push_back(reader->GetOutput()); } { itk::ImageFileReader< itk::Image< double, 3 > >::Pointer reader = itk::ImageFileReader< itk::Image< double, 3 > >::New(); reader->SetFileName( us::any_cast(parsedArgs["wm"]) ); reader->Update(); fracs.push_back(reader->GetOutput()); } { itk::ImageFileReader< itk::Image< double, 3 > >::Pointer reader = itk::ImageFileReader< itk::Image< double, 3 > >::New(); reader->SetFileName( us::any_cast(parsedArgs["gm"]) ); reader->Update(); fracs.push_back(reader->GetOutput()); } { itk::ImageFileReader< itk::Image< double, 3 > >::Pointer reader = itk::ImageFileReader< itk::Image< double, 3 > >::New(); reader->SetFileName( us::any_cast(parsedArgs["dgm"]) ); reader->Update(); fracs.push_back(reader->GetOutput()); } { itk::ImageFileReader< itk::Image< double, 3 > >::Pointer reader = itk::ImageFileReader< itk::Image< double, 3 > >::New(); reader->SetFileName( us::any_cast(parsedArgs["csf"]) ); reader->Update(); fracs.push_back(reader->GetOutput()); } MITK_INFO << "Initial sqrt: " << sqrt; MITK_INFO << "Initial TDI threshold: " << tdi_threshold; possible_proposals.push_back(3); } std::vector< double > histogram_modifiers; itk::Image< double,3 >::ConstPointer fa_image = nullptr; if (fa_file.compare("")!=0) { itk::ImageFileReader< itk::Image< double, 3 > >::Pointer reader = itk::ImageFileReader< itk::Image< double, 3 > >::New(); reader->SetFileName( fa_file ); reader->Update(); fa_image = reader->GetOutput(); if (use_histo) { int binsPerDimension = 10; using ImageToHistogramFilterType = itk::Statistics::MaskedImageToHistogramFilter< itk::Image< double,3 >, itk::Image< unsigned char,3 > >; ImageToHistogramFilterType::HistogramType::MeasurementVectorType lowerBound(binsPerDimension); lowerBound.Fill(0.0); ImageToHistogramFilterType::HistogramType::MeasurementVectorType upperBound(binsPerDimension); upperBound.Fill(1.0); ImageToHistogramFilterType::HistogramType::SizeType size(1); size.Fill(binsPerDimension); ImageToHistogramFilterType::Pointer imageToHistogramFilter = ImageToHistogramFilterType::New(); imageToHistogramFilter->SetInput( fa_image ); imageToHistogramFilter->SetHistogramBinMinimum( lowerBound ); imageToHistogramFilter->SetHistogramBinMaximum( upperBound ); imageToHistogramFilter->SetHistogramSize( size ); imageToHistogramFilter->SetMaskImage(mask); imageToHistogramFilter->SetMaskValue(1); imageToHistogramFilter->Update(); ImageToHistogramFilterType::HistogramType* histogram = imageToHistogramFilter->GetOutput(); unsigned int max = 0; for(unsigned int i = 0; i < histogram->GetSize()[0]; ++i) { if (histogram->GetFrequency(i)>max) max = histogram->GetFrequency(i); } MITK_INFO << "FA histogram modifiers:"; for(unsigned int i = 0; i < histogram->GetSize()[0]; ++i) { histogram_modifiers.push_back( std::pow(1.0 - (double)histogram->GetFrequency(i)/(double)max, raise_histo) ); MITK_INFO << histogram_modifiers.back(); } } if (fa_error) MITK_INFO << "Using FA error measure."; } itk::Image< double,3 >::ConstPointer md_image = nullptr; if (md_file.compare("")!=0) { itk::ImageFileReader< itk::Image< double, 3 > >::Pointer reader = itk::ImageFileReader< itk::Image< double, 3 > >::New(); reader->SetFileName( md_file ); reader->Update(); md_image = reader->GetOutput(); if (fa_error) MITK_INFO << "Using MD error measure."; } if (fa_error && fa_image.IsNull()) { MITK_INFO << "Incompatible options. Need FA image to calculate FA error."; return EXIT_FAILURE; } if (possible_proposals.empty()) { MITK_INFO << "Incompatible options. Nothing to optimize."; return EXIT_FAILURE; } itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); tractsToDwiFilter->SetFiberBundle(tracts); tractsToDwiFilter->SetParameters(parameters); tractsToDwiFilter->Update(); ItkDwiType::Pointer sim = tractsToDwiFilter->GetOutput(); { mitk::Image::Pointer image = mitk::GrabItkImageMemory( tractsToDwiFilter->GetOutput() ); - mitk::DiffusionPropertyHelper::SetGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer()); + mitk::DiffusionPropertyHelper::SetOriginalGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer()); mitk::DiffusionPropertyHelper::SetReferenceBValue(image, parameters.m_SignalGen.GetBvalue()); mitk::DiffusionPropertyHelper::InitializeImage( image ); mitk::IOUtil::Save(image, out_folder + "/initial.dwi"); } double old_tdi_thr = tdi_threshold; double old_sqrt = sqrt; double new_tdi_thr = old_tdi_thr; double new_sqrt = old_sqrt; MITK_INFO << "\n\n"; MITK_INFO << "Iterations: " << iterations; MITK_INFO << "start_temp: " << start_temp; MITK_INFO << "end_temp: " << end_temp; double alpha = log(end_temp/start_temp); int accepted = 0; double last_error = 9999999; if (fa_error) { MITK_INFO << "Calculating FA error"; last_error = CalcErrorFA(histogram_modifiers, dwi, sim, mask, fa_image, md_image, true); } else { MITK_INFO << "Calculating raw-image error"; last_error = CalcErrorSignal(histogram_modifiers, reference, sim, mask, fa_image); } MITK_INFO << "Initial E = " << last_error; MITK_INFO << "\n\n**************************************************************************************"; std::random_device r; std::default_random_engine randgen(r()); std::uniform_int_distribution uint1(0, possible_proposals.size()-1); for (int i=0; i::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); tractsToDwiFilter->SetFiberBundle(dynamic_cast(tracts.GetPointer())); tractsToDwiFilter->SetParameters(proposal); tractsToDwiFilter->Update(); ItkDwiType::Pointer sim = tractsToDwiFilter->GetOutput(); std::cout.rdbuf (old); // <-- restore double new_error = 9999999; if (fa_error && fa_image.IsNotNull()) new_error = CalcErrorFA(histogram_modifiers, dwi, sim, mask, fa_image, md_image, true); else new_error = CalcErrorSignal(histogram_modifiers, reference, sim, mask, fa_image); MITK_INFO << "E = " << new_error << "(" << new_error-last_error << ")"; if (last_errorGetOutput() ); - mitk::DiffusionPropertyHelper::SetGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer()); + mitk::DiffusionPropertyHelper::SetOriginalGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer()); mitk::DiffusionPropertyHelper::SetReferenceBValue(image, parameters.m_SignalGen.GetBvalue()); mitk::DiffusionPropertyHelper::InitializeImage( image ); mitk::IOUtil::Save(image, out_folder + "/optimized.dwi"); proposal.SaveParameters(out_folder + "/optimized.ffp"); std::cout.rdbuf (old); // <-- restore accepted++; old_tdi_thr = new_tdi_thr; old_sqrt = new_sqrt; MITK_INFO << "Accepted (acc. rate " << (float)accepted/(i+1) << ")"; parameters = FiberfoxParameters(proposal); last_error = new_error; } MITK_INFO << "\n\n\n"; } return EXIT_SUCCESS; } diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/RandomFiberPhantom.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/RandomFiberPhantom.cpp index 2d311b9b09..13b019f8b3 100755 --- a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/RandomFiberPhantom.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/RandomFiberPhantom.cpp @@ -1,169 +1,172 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include "mitkCommandLineParser.h" #include #include #include #include #include -/*! -\brief Join multiple tractograms -*/ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Random Fiber Phantom"); parser.setCategory("Diffusion Simulation Tools"); parser.setContributor("MIC"); parser.setDescription("Create Random Fiber Configurations"); parser.setArgumentPrefix("--", "-"); parser.addArgument("num_bundles", "", mitkCommandLineParser::Int, "", "", 50); parser.addArgument("min_density", "", mitkCommandLineParser::Int, "", "", 50); parser.addArgument("max_density", "", mitkCommandLineParser::Int, "", "", 200); parser.addArgument("size_x", "", mitkCommandLineParser::Int, "", "", 250); parser.addArgument("size_y", "", mitkCommandLineParser::Int, "", "", 250); parser.addArgument("size_z", "", mitkCommandLineParser::Int, "", "", 250); parser.addArgument("min_stepsize", "", mitkCommandLineParser::Int, "", "", 15); parser.addArgument("max_stepsize", "", mitkCommandLineParser::Int, "", "", 30); parser.addArgument("min_curve", "", mitkCommandLineParser::Int, "", "", 5); parser.addArgument("max_curve", "", mitkCommandLineParser::Int, "", "", 45); parser.addArgument("min_radius", "", mitkCommandLineParser::Int, "", "", 5); parser.addArgument("max_radius", "", mitkCommandLineParser::Int, "", "", 25); parser.addArgument("min_twist", "", mitkCommandLineParser::Int, "", "", 15); parser.addArgument("max_twist", "", mitkCommandLineParser::Int, "", "", 30); parser.addArgument("compress", "", mitkCommandLineParser::Float, "Compress:", "Compress fiber using the given error threshold (in mm)", 0.1); parser.addArgument("", "o", mitkCommandLineParser::String, "Output folder:", "output folder", us::Any(), false); + parser.addArgument("fix_seed", "", mitkCommandLineParser::Bool, "Fix random seed:", "Produce same random values on each run.", us::Any()); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; std::string out_folder = us::any_cast(parsedArgs["o"]); float compress=0.1; if (parsedArgs.count("compress")) compress = us::any_cast(parsedArgs["compress"]); int num_bundles=50; if (parsedArgs.count("num_bundles")) num_bundles = us::any_cast(parsedArgs["num_bundles"]); int min_density=50; if (parsedArgs.count("min_density")) min_density = us::any_cast(parsedArgs["min_density"]); int max_density=200; if (parsedArgs.count("max_density")) max_density = us::any_cast(parsedArgs["max_density"]); int size_x=250; if (parsedArgs.count("size_x")) size_x = us::any_cast(parsedArgs["size_x"]); int size_y=250; if (parsedArgs.count("size_y")) size_y = us::any_cast(parsedArgs["size_y"]); int size_z=250; if (parsedArgs.count("size_z")) size_z = us::any_cast(parsedArgs["size_z"]); int min_stepsize=15; if (parsedArgs.count("min_stepsize")) min_stepsize = us::any_cast(parsedArgs["min_stepsize"]); int max_stepsize=30; if (parsedArgs.count("max_stepsize")) max_stepsize = us::any_cast(parsedArgs["max_stepsize"]); int min_curve=5; if (parsedArgs.count("min_curve")) min_curve = us::any_cast(parsedArgs["min_curve"]); int max_curve=45; if (parsedArgs.count("max_curve")) max_curve = us::any_cast(parsedArgs["max_curve"]); int min_radius=5; if (parsedArgs.count("min_radius")) min_radius = us::any_cast(parsedArgs["min_radius"]); int max_radius=25; if (parsedArgs.count("max_radius")) max_radius = us::any_cast(parsedArgs["max_radius"]); int min_twist=15; if (parsedArgs.count("min_twist")) min_twist = us::any_cast(parsedArgs["min_twist"]); int max_twist=30; if (parsedArgs.count("max_twist")) max_twist = us::any_cast(parsedArgs["max_twist"]); + bool fix_seed = false; + if (parsedArgs.count("fix_seed")) + fix_seed = us::any_cast(parsedArgs["fix_seed"]); + try { itk::RandomPhantomFilter::Pointer filter = itk::RandomPhantomFilter::New(); - filter->SetNumTracts(num_bundles); - filter->setMinStreamlineDensity(min_density); - filter->setMaxStreamlineDensity(max_density); + filter->SetNumTracts(static_cast(num_bundles)); + filter->SetMinStreamlineDensity(static_cast(min_density)); + filter->SetMaxStreamlineDensity(static_cast(max_density)); mitk::Vector3D vol; vol[0] = size_x; vol[1] = size_y; vol[2] = size_z; - filter->setVolumeSize(vol); - filter->setStepSizeMin(min_stepsize); - filter->setStepSizeMax(max_stepsize); - filter->setCurvynessMin(min_curve); - filter->setCurvynessMax(max_curve); - filter->setStartRadiusMin(min_radius); - filter->setStartRadiusMax(max_radius); - filter->setMinTwist(min_twist); - filter->setMaxTwist(max_twist); + filter->SetVolumeSize(vol); + filter->SetStepSizeMin(static_cast(min_stepsize)); + filter->SetStepSizeMax(static_cast(max_stepsize)); + filter->SetCurvynessMin(static_cast(min_curve)); + filter->SetCurvynessMax(static_cast(max_curve)); + filter->SetStartRadiusMin(static_cast(min_radius)); + filter->SetStartRadiusMax(static_cast(max_radius)); + filter->SetMinTwist(static_cast(min_twist)); + filter->SetMaxTwist(static_cast(max_twist)); + filter->SetFixSeed(fix_seed); filter->Update(); auto fibs = filter->GetFiberBundles(); std::vector< mitk::DataNode::Pointer > fiber_nodes; int c = 1; for (auto fib : fibs) { if (compress>0) fib->Compress(compress); mitk::IOUtil::Save(fib, out_folder + "Bundle_" + boost::lexical_cast(c) + ".fib"); ++c; } } catch (itk::ExceptionObject e) { std::cout << e; return EXIT_FAILURE; } catch (std::exception e) { std::cout << e.what(); return EXIT_FAILURE; } catch (...) { std::cout << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } diff --git a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp index a6fd6c1555..2a1e93df86 100644 --- a/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp +++ b/Modules/DiffusionImaging/DiffusionCore/src/IODataStructures/Properties/mitkDiffusionPropertyHelper.cpp @@ -1,615 +1,615 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkDiffusionPropertyHelper.h" #include #include #include #include #include #include #include #include #include const std::string mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME = "DWMRI.GradientDirections"; const std::string mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME = "DWMRI.OriginalGradientDirections"; const std::string mitk::DiffusionPropertyHelper::MEASUREMENTFRAMEPROPERTYNAME = "DWMRI.MeasurementFrame"; const std::string mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME = "DWMRI.ReferenceBValue"; const std::string mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME = "DWMRI.BValueMap"; const std::string mitk::DiffusionPropertyHelper::MODALITY = "DWMRI.Modality"; const std::string mitk::DiffusionPropertyHelper::KEEP_ORIGINAL_DIRECTIONS = "DWMRI.KeepOriginalDirections"; mitk::DiffusionPropertyHelper::DiffusionPropertyHelper() { } mitk::DiffusionPropertyHelper::~DiffusionPropertyHelper() { } mitk::DiffusionPropertyHelper::ImageType::Pointer mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk::Image* image) { ImageType::Pointer vectorImage = ImageType::New(); mitk::CastToItkImage(image, vectorImage); return vectorImage; } mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer mitk::DiffusionPropertyHelper::CalcAveragedDirectionSet(double precision, GradientDirectionsContainerType::Pointer directions) { // save old and construct new direction container GradientDirectionsContainerType::Pointer newDirections = GradientDirectionsContainerType::New(); // fill new direction container for(GradientDirectionsContainerType::ConstIterator gdcitOld = directions->Begin(); gdcitOld != directions->End(); ++gdcitOld) { // already exists? bool found = false; for(GradientDirectionsContainerType::ConstIterator gdcitNew = newDirections->Begin(); gdcitNew != newDirections->End(); ++gdcitNew) { if(AreAlike(gdcitNew.Value(), gdcitOld.Value(), precision)) { found = true; break; } } // if not found, add it to new container if(!found) { newDirections->push_back(gdcitOld.Value()); } } return newDirections; } void mitk::DiffusionPropertyHelper::AverageRedundantGradients(mitk::Image* image, double precision) { GradientDirectionsContainerType::Pointer oldDirs = GetOriginalGradientContainer(image); GradientDirectionsContainerType::Pointer newDirs = CalcAveragedDirectionSet(precision, oldDirs); // if sizes equal, we do not need to do anything in this function if(oldDirs->size() == newDirs->size()) return; // new image ImageType::Pointer oldImage = ImageType::New(); mitk::CastToItkImage( image, oldImage); ImageType::Pointer newITKImage = ImageType::New(); newITKImage->SetSpacing( oldImage->GetSpacing() ); // Set the image spacing newITKImage->SetOrigin( oldImage->GetOrigin() ); // Set the image origin newITKImage->SetDirection( oldImage->GetDirection() ); // Set the image direction newITKImage->SetLargestPossibleRegion( oldImage->GetLargestPossibleRegion() ); newITKImage->SetVectorLength( newDirs->size() ); newITKImage->SetBufferedRegion( oldImage->GetLargestPossibleRegion() ); newITKImage->Allocate(); // average image data that corresponds to identical directions itk::ImageRegionIterator< ImageType > newIt(newITKImage, newITKImage->GetLargestPossibleRegion()); newIt.GoToBegin(); itk::ImageRegionIterator< ImageType > oldIt(oldImage, oldImage->GetLargestPossibleRegion()); oldIt.GoToBegin(); // initial new value of voxel ImageType::PixelType newVec; newVec.SetSize(newDirs->size()); newVec.AllocateElements(newDirs->size()); // find which gradients should be averaged GradientDirectionsContainerType::Pointer oldDirections = oldDirs; std::vector > dirIndices; for(GradientDirectionsContainerType::ConstIterator gdcitNew = newDirs->Begin(); gdcitNew != newDirs->End(); ++gdcitNew) { dirIndices.push_back(std::vector(0)); for(GradientDirectionsContainerType::ConstIterator gdcitOld = oldDirs->Begin(); gdcitOld != oldDirections->End(); ++gdcitOld) { if(AreAlike(gdcitNew.Value(), gdcitOld.Value(), precision)) { //MITK_INFO << gdcitNew.Value() << " " << gdcitOld.Value(); dirIndices[gdcitNew.Index()].push_back(gdcitOld.Index()); } } } //int ind1 = -1; while(!newIt.IsAtEnd()) { // init new vector with zeros newVec.Fill(0.0); // the old voxel value with duplicates ImageType::PixelType oldVec = oldIt.Get(); for(unsigned int i=0; iGetProperty(mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str()).IsNull() ) { return; } GradientDirectionsContainerType::Pointer originalDirections = GetOriginalGradientContainer(image); MeasurementFrameType measurementFrame = GetMeasurementFrame(image); mitk::Vector3D s = image->GetGeometry()->GetSpacing(); mitk::VnlVector c0 = image->GetGeometry()->GetMatrixColumn(0)/s[0]; mitk::VnlVector c1 = image->GetGeometry()->GetMatrixColumn(1)/s[1]; mitk::VnlVector c2 = image->GetGeometry()->GetMatrixColumn(2)/s[2]; MeasurementFrameType imageRotationMatrix; imageRotationMatrix[0][0] = c0[0]; imageRotationMatrix[1][0] = c0[1]; imageRotationMatrix[2][0] = c0[2]; imageRotationMatrix[0][1] = c1[0]; imageRotationMatrix[1][1] = c1[1]; imageRotationMatrix[2][1] = c1[2]; imageRotationMatrix[0][2] = c2[0]; imageRotationMatrix[1][2] = c2[1]; imageRotationMatrix[2][2] = c2[2]; GradientDirectionsContainerType::Pointer directions = GradientDirectionsContainerType::New(); if( originalDirections.IsNull() || ( originalDirections->size() == 0 ) ) { // original direction container was not set return; } bool keep_originals = false; image->GetPropertyList()->GetBoolProperty(mitk::DiffusionPropertyHelper::KEEP_ORIGINAL_DIRECTIONS.c_str(), keep_originals); -// if (!keep_originals) -// { -// MITK_INFO << "Applying measurement frame to diffusion-gradient directions:"; -// std::cout << measurementFrame << std::endl; -// MITK_INFO << "Applying image rotation to diffusion-gradient directions:"; -// std::cout << imageRotationMatrix << std::endl; -// } + if (!keep_originals) + { + MITK_INFO << "Applying measurement frame to diffusion-gradient directions:"; + std::cout << measurementFrame << std::endl; + MITK_INFO << "Applying image rotation to diffusion-gradient directions:"; + std::cout << imageRotationMatrix << std::endl; + } int c = 0; for(GradientDirectionsContainerType::ConstIterator gdcit = originalDirections->Begin(); gdcit != originalDirections->End(); ++gdcit) { vnl_vector vec = gdcit.Value(); if (!keep_originals) { vec = vec.pre_multiply(measurementFrame); vec = vec.pre_multiply(imageRotationMatrix); } directions->InsertElement(c, vec); c++; } SetGradientContainer(image, directions); } void mitk::DiffusionPropertyHelper::UnApplyMeasurementFrameAndRotationMatrix(mitk::Image* image) { if( image->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).IsNull() ) { return; } GradientDirectionsContainerType::Pointer modifiedDirections = GetGradientContainer(image); MeasurementFrameType measurementFrame = GetMeasurementFrame(image); measurementFrame = vnl_matrix_inverse(measurementFrame).pinverse(); mitk::Vector3D s = image->GetGeometry()->GetSpacing(); mitk::VnlVector c0 = image->GetGeometry()->GetMatrixColumn(0)/s[0]; mitk::VnlVector c1 = image->GetGeometry()->GetMatrixColumn(1)/s[1]; mitk::VnlVector c2 = image->GetGeometry()->GetMatrixColumn(2)/s[2]; MeasurementFrameType imageRotationMatrix; imageRotationMatrix[0][0] = c0[0]; imageRotationMatrix[1][0] = c0[1]; imageRotationMatrix[2][0] = c0[2]; imageRotationMatrix[0][1] = c1[0]; imageRotationMatrix[1][1] = c1[1]; imageRotationMatrix[2][1] = c1[2]; imageRotationMatrix[0][2] = c2[0]; imageRotationMatrix[1][2] = c2[1]; imageRotationMatrix[2][2] = c2[2]; imageRotationMatrix = vnl_matrix_inverse(imageRotationMatrix).pinverse(); GradientDirectionsContainerType::Pointer directions = GradientDirectionsContainerType::New(); if( modifiedDirections.IsNull() || ( modifiedDirections->size() == 0 ) ) { // original direction container was not set return; } bool keep_originals = false; image->GetPropertyList()->GetBoolProperty(mitk::DiffusionPropertyHelper::KEEP_ORIGINAL_DIRECTIONS.c_str(), keep_originals); -// if (!keep_originals) -// { -// MITK_INFO << "Reverting image rotation to diffusion-gradient directions:"; -// std::cout << imageRotationMatrix << std::endl; -// MITK_INFO << "Reverting measurement frame to diffusion-gradient directions:"; -// std::cout << measurementFrame << std::endl; -// } + if (!keep_originals) + { + MITK_INFO << "Reverting image rotation to diffusion-gradient directions:"; + std::cout << imageRotationMatrix << std::endl; + MITK_INFO << "Reverting measurement frame to diffusion-gradient directions:"; + std::cout << measurementFrame << std::endl; + } int c = 0; for(GradientDirectionsContainerType::ConstIterator gdcit = modifiedDirections->Begin(); gdcit != modifiedDirections->End(); ++gdcit) { vnl_vector vec = gdcit.Value(); if (!keep_originals) { vec = vec.pre_multiply(imageRotationMatrix); vec = vec.pre_multiply(measurementFrame); } directions->InsertElement(c, vec); c++; } SetOriginalGradientContainer(image, directions); } void mitk::DiffusionPropertyHelper::ClearMeasurementFrameAndRotationMatrixFromGradients(mitk::Image* image) { GradientDirectionsContainerType::Pointer originalDirections = GetOriginalGradientContainer(image); GradientDirectionsContainerType::Pointer directions = GradientDirectionsContainerType::New(); if(originalDirections.IsNull() || originalDirections->size()==0) return; int c = 0; for(GradientDirectionsContainerType::ConstIterator gdcit = originalDirections->Begin(); gdcit != originalDirections->End(); ++gdcit) { vnl_vector vec = gdcit.Value(); directions->InsertElement(c, vec); c++; } image->GetPropertyList()->ReplaceProperty( mitk::DiffusionPropertyHelper::KEEP_ORIGINAL_DIRECTIONS.c_str(), mitk::BoolProperty::New(true) ); SetGradientContainer(image, directions); } void mitk::DiffusionPropertyHelper::UpdateBValueMap(mitk::Image* image) { BValueMapType b_ValueMap; if(image->GetProperty(mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME.c_str()).IsNotNull()) b_ValueMap = GetBValueMap(image); if(!b_ValueMap.empty()) b_ValueMap.clear(); if(GetGradientContainer(image).IsNotNull()) { GradientDirectionsContainerType::Pointer directions = GetGradientContainer(image); for(auto gdcit = directions->Begin(); gdcit!=directions->End(); ++gdcit) { b_ValueMap[GetB_Value(image, gdcit.Index())].push_back(gdcit.Index()); } } SetBValueMap(image, b_ValueMap); } bool mitk::DiffusionPropertyHelper::AreAlike(GradientDirectionType g1, GradientDirectionType g2, double precision) { GradientDirectionType diff = g1 - g2; GradientDirectionType diff2 = g1 + g2; return diff.two_norm() < precision || diff2.two_norm() < precision; } float mitk::DiffusionPropertyHelper::GetB_Value(const mitk::Image* image, unsigned int i) { GradientDirectionsContainerType::Pointer directions = GetGradientContainer(image); float b_value = GetReferenceBValue(image); if(i > directions->Size()-1) return -1; if(directions->ElementAt(i).one_norm() <= 0.0) { return 0; } else { double twonorm = directions->ElementAt(i).two_norm(); double bval = b_value*twonorm*twonorm; if (bval<0) bval = ceil(bval - 0.5); else bval = floor(bval + 0.5); return bval; } } void mitk::DiffusionPropertyHelper::CopyProperties(mitk::Image* source, mitk::Image* target, bool ignore_original_gradients) { mitk::PropertyList::Pointer props = source->GetPropertyList()->Clone(); if (ignore_original_gradients) props->RemoveProperty(mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME); target->SetPropertyList(props); } void mitk::DiffusionPropertyHelper::InitializeImage(mitk::Image* image) { if ( image->GetProperty(mitk::DiffusionPropertyHelper::KEEP_ORIGINAL_DIRECTIONS.c_str()).IsNull() ) image->SetProperty( mitk::DiffusionPropertyHelper::KEEP_ORIGINAL_DIRECTIONS.c_str(), mitk::BoolProperty::New(false) ); if( image->GetProperty(mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str()).IsNull() ) { // we don't have the original gradient directions. Therefore use the modified directions and roatate them back. UnApplyMeasurementFrameAndRotationMatrix(image); } else ApplyMeasurementFrameAndRotationMatrix(image); UpdateBValueMap(image); // initialize missing properties mitk::MeasurementFrameProperty::Pointer mf = dynamic_cast( image->GetProperty(MEASUREMENTFRAMEPROPERTYNAME.c_str()).GetPointer()); if( mf.IsNull() ) { //no measurement frame present, identity is assumed MeasurementFrameType identity; identity.set_identity(); image->GetPropertyList()->ReplaceProperty( mitk::DiffusionPropertyHelper::MEASUREMENTFRAMEPROPERTYNAME.c_str(), mitk::MeasurementFrameProperty::New( identity )); } } bool mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(const mitk::DataNode* node) { if ( node==nullptr ) return false; if ( node->GetData()==nullptr ) return false; return IsDiffusionWeightedImage(dynamic_cast(node->GetData())); } bool mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(const mitk::Image * image) { bool isDiffusionWeightedImage( true ); if( image == nullptr ) { isDiffusionWeightedImage = false; } if( isDiffusionWeightedImage ) { mitk::FloatProperty::Pointer referenceBValue = dynamic_cast(image->GetProperty(REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer()); if( referenceBValue.IsNull() ) { isDiffusionWeightedImage = false; } } unsigned int gradientDirections( 0 ); if( isDiffusionWeightedImage ) { mitk::GradientDirectionsProperty::Pointer gradientDirectionsProperty = dynamic_cast(image->GetProperty(GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer()); if( gradientDirectionsProperty.IsNull() ) { isDiffusionWeightedImage = false; } else { gradientDirections = gradientDirectionsProperty->GetGradientDirectionsContainer()->size(); } } if( isDiffusionWeightedImage ) { unsigned int components = image->GetPixelType().GetNumberOfComponents(); if( components != gradientDirections ) { isDiffusionWeightedImage = false; } } return isDiffusionWeightedImage; } const mitk::DiffusionPropertyHelper::BValueMapType & mitk::DiffusionPropertyHelper::GetBValueMap(const mitk::Image *image) { return dynamic_cast(image->GetProperty(BVALUEMAPPROPERTYNAME.c_str()).GetPointer())->GetBValueMap(); } std::vector< int > mitk::DiffusionPropertyHelper::GetBValueVector(const mitk::Image* image) { auto gcon = mitk::DiffusionPropertyHelper::GetGradientContainer(image); float b_value = mitk::DiffusionPropertyHelper::GetReferenceBValue(image); std::vector< int > bvalues; for (unsigned int i=0; iSize(); ++i) { double twonorm = gcon->ElementAt(i).two_norm(); double bval = b_value*twonorm*twonorm; if (bval<0) bval = ceil(bval - 0.5); else bval = floor(bval + 0.5); bvalues.push_back(bval); } return bvalues; } float mitk::DiffusionPropertyHelper::GetReferenceBValue(const mitk::Image *image) { return dynamic_cast(image->GetProperty(REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer())->GetValue(); } const mitk::DiffusionPropertyHelper::MeasurementFrameType & mitk::DiffusionPropertyHelper::GetMeasurementFrame(const mitk::Image *image) { mitk::MeasurementFrameProperty::Pointer mf = dynamic_cast( image->GetProperty(MEASUREMENTFRAMEPROPERTYNAME.c_str()).GetPointer()); if( mf.IsNull() ) { //no measurement frame present, identity is assumed MeasurementFrameType identity; identity.set_identity(); mf = mitk::MeasurementFrameProperty::New( identity ); } return mf->GetMeasurementFrame(); } mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(const mitk::Image *image) { return dynamic_cast(image->GetProperty(ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer())->GetGradientDirectionsContainer(); } mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer mitk::DiffusionPropertyHelper::GetGradientContainer(const mitk::Image *image) { return dynamic_cast(image->GetProperty(GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer())->GetGradientDirectionsContainer(); } void mitk::DiffusionPropertyHelper::SetReferenceBValue(mitk::Image* image, float b_value) { image->GetPropertyList()->ReplaceProperty(REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New(b_value)); } void mitk::DiffusionPropertyHelper::SetBValueMap(mitk::Image* image, BValueMapType map) { image->GetPropertyList()->ReplaceProperty( mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME.c_str(), mitk::BValueMapProperty::New(map)); } void mitk::DiffusionPropertyHelper::SetOriginalGradientContainer(mitk::Image* image, GradientDirectionsContainerType::Pointer g_cont) { image->GetPropertyList()->ReplaceProperty(ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New(g_cont)); } void mitk::DiffusionPropertyHelper::SetGradientContainer(mitk::Image* image, GradientDirectionsContainerType::Pointer g_cont) { image->GetPropertyList()->ReplaceProperty(GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New(g_cont)); } void mitk::DiffusionPropertyHelper::SetMeasurementFrame(mitk::Image* image, MeasurementFrameType mf) { image->GetPropertyList()->ReplaceProperty( MEASUREMENTFRAMEPROPERTYNAME.c_str(), mitk::MeasurementFrameProperty::New( mf ) ); } void mitk::DiffusionPropertyHelper::RotateGradients(mitk::Image* image, vnl_matrix_fixed rotation_matrix, bool normalize_columns) { if (normalize_columns) rotation_matrix = rotation_matrix.normalize_columns(); int c = 0; auto new_gradients = GradientDirectionsContainerType::New(); auto old_gradients = GetGradientContainer(image); for(auto gdcit = old_gradients->Begin(); gdcit != old_gradients->End(); ++gdcit) { vnl_vector vec = gdcit.Value(); vec = vec.pre_multiply(rotation_matrix); new_gradients->InsertElement(c, vec); c++; } SetGradientContainer(image, new_gradients); } void mitk::DiffusionPropertyHelper::RotateOriginalGradients(mitk::Image* image, vnl_matrix_fixed rotation_matrix, bool normalize_columns) { if (normalize_columns) rotation_matrix = rotation_matrix.normalize_columns(); int c = 0; auto new_gradients = GradientDirectionsContainerType::New(); auto old_gradients = GetOriginalGradientContainer(image); for(auto gdcit = old_gradients->Begin(); gdcit != old_gradients->End(); ++gdcit) { vnl_vector vec = gdcit.Value(); vec = vec.pre_multiply(rotation_matrix); new_gradients->InsertElement(c, vec); c++; } SetOriginalGradientContainer(image, new_gradients); } void mitk::DiffusionPropertyHelper::SetupProperties() { //register relevant properties //non-persistent properties mitk::CoreServices::GetPropertyDescriptions()->AddDescription(mitk::DiffusionPropertyHelper::BVALUEMAPPROPERTYNAME, "This map stores which b values belong to which gradients."); mitk::CoreServices::GetPropertyDescriptions()->AddDescription(mitk::DiffusionPropertyHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME, "The original gradients used during acquisition. This property may be empty."); //persistent properties mitk::CoreServices::GetPropertyDescriptions()->AddDescription(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME, "The reference b value the gradients are normalized to."); mitk::CoreServices::GetPropertyDescriptions()->AddDescription(mitk::DiffusionPropertyHelper::MEASUREMENTFRAMEPROPERTYNAME, "The measurment frame used during acquisition."); mitk::CoreServices::GetPropertyDescriptions()->AddDescription(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME, "The gradients after applying measurement frame and image matrix."); mitk::CoreServices::GetPropertyDescriptions()->AddDescription(mitk::DiffusionPropertyHelper::MODALITY, "Defines the modality used for acquisition. DWMRI signifies diffusion weighted images."); mitk::PropertyPersistenceInfo::Pointer PPI_referenceBValue = mitk::PropertyPersistenceInfo::New(); PPI_referenceBValue->SetNameAndKey(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME, "DWMRI_b-value"); mitk::PropertyPersistenceInfo::Pointer PPI_measurementFrame = mitk::PropertyPersistenceInfo::New(); PPI_measurementFrame->SetNameAndKey(mitk::DiffusionPropertyHelper::MEASUREMENTFRAMEPROPERTYNAME, "measurement frame"); mitk::PropertyPersistenceInfo::Pointer PPI_gradientContainer = mitk::PropertyPersistenceInfo::New(); PPI_gradientContainer->SetNameAndKey(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME, "DWMRI_gradient"); mitk::PropertyPersistenceInfo::Pointer PPI_modality = mitk::PropertyPersistenceInfo::New(); PPI_modality->SetNameAndKey(mitk::DiffusionPropertyHelper::MODALITY, "modality"); mitk::CoreServices::GetPropertyPersistence()->AddInfo(PPI_referenceBValue.GetPointer() , true); mitk::CoreServices::GetPropertyPersistence()->AddInfo(PPI_measurementFrame.GetPointer(), true); mitk::CoreServices::GetPropertyPersistence()->AddInfo(PPI_gradientContainer.GetPointer(), true); mitk::CoreServices::GetPropertyPersistence()->AddInfo(PPI_modality.GetPointer(), true); } diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.cpp index be51ca4621..a96514f0ef 100644 --- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.cpp @@ -1,239 +1,248 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __itkibersFromPlanarFiguresFilter_cpp #define __itkibersFromPlanarFiguresFilter_cpp #include "itkFibersFromPlanarFiguresFilter.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace itk{ FibersFromPlanarFiguresFilter::FibersFromPlanarFiguresFilter() + : m_FixSeed(false) { } FibersFromPlanarFiguresFilter::~FibersFromPlanarFiguresFilter() { } void FibersFromPlanarFiguresFilter::GeneratePoints() { Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New(); - randGen->SetSeed((unsigned int)0); + if (m_FixSeed) + randGen->SetSeed(0); + else + randGen->SetSeed(); m_2DPoints.clear(); unsigned int count = 0; while (count < m_Parameters.m_Density) { mitk::Vector2D p; switch (m_Parameters.m_Distribution) { case FiberGenerationParameters::DISTRIBUTE_GAUSSIAN: p[0] = randGen->GetNormalVariate(0, m_Parameters.m_Variance); p[1] = randGen->GetNormalVariate(0, m_Parameters.m_Variance); break; default: p[0] = randGen->GetUniformVariate(-1, 1); p[1] = randGen->GetUniformVariate(-1, 1); } if (sqrt(p[0]*p[0]+p[1]*p[1]) <= 1) { m_2DPoints.push_back(p); count++; } } } +void FibersFromPlanarFiguresFilter::SetFixSeed(bool FixSeed) +{ + m_FixSeed = FixSeed; +} + void FibersFromPlanarFiguresFilter::GenerateData() { // check if enough fiducials are available for (unsigned int i=0; i m_VtkCellArray = vtkSmartPointer::New(); vtkSmartPointer m_VtkPoints = vtkSmartPointer::New(); std::vector< mitk::PlanarEllipse::Pointer > bundle = m_Parameters.m_Fiducials.at(i); std::vector< unsigned int > fliplist; if (i container = vtkSmartPointer::New(); mitk::PlanarEllipse::Pointer figure = bundle.at(0); mitk::Point2D p0 = figure->GetControlPoint(0); mitk::Point2D p1 = figure->GetControlPoint(1); mitk::Point2D p2 = figure->GetControlPoint(2); mitk::Point2D p3 = figure->GetControlPoint(3); double r1 = p0.EuclideanDistanceTo(p1); double r2 = p0.EuclideanDistanceTo(p2); mitk::Vector2D eDir = p1-p0; eDir.Normalize(); mitk::Vector2D tDir = p3-p0; tDir.Normalize(); // apply twist vnl_matrix_fixed tRot; tRot[0][0] = tDir[0]; tRot[1][1] = tRot[0][0]; tRot[1][0] = sin(acos(tRot[0][0])); tRot[0][1] = -tRot[1][0]; if (tDir[1]<0) tRot.inplace_transpose(); m_2DPoints[j].SetVnlVector(tRot*m_2DPoints[j].GetVnlVector()); // apply new ellipse shape vnl_vector_fixed< double, 2 > newP; newP[0] = m_2DPoints.at(j)[0]; newP[1] = m_2DPoints.at(j)[1]; double alpha = acos(eDir[0]); if (eDir[1]>0) alpha = 2*itk::Math::pi-alpha; vnl_matrix_fixed eRot; eRot[0][0] = cos(alpha); eRot[1][1] = eRot[0][0]; eRot[1][0] = sin(alpha); eRot[0][1] = -eRot[1][0]; newP = eRot*newP; newP[0] *= r1; newP[1] *= r2; newP = eRot.transpose()*newP; p0[0] += newP[0]; p0[1] += newP[1]; const mitk::PlaneGeometry* planeGeo = figure->GetPlaneGeometry(); mitk::Point3D w, wc; planeGeo->Map(p0, w); wc = figure->GetWorldControlPoint(0); vtkIdType id = m_VtkPoints->InsertNextPoint(w.GetDataPointer()); container->GetPointIds()->InsertNextId(id); vnl_vector_fixed< double, 3 > n = planeGeo->GetNormalVnl(); for (unsigned int k=1; kGetControlPoint(0); p1 = figure->GetControlPoint(1); p2 = figure->GetControlPoint(2); p3 = figure->GetControlPoint(3); r1 = p0.EuclideanDistanceTo(p1); r2 = p0.EuclideanDistanceTo(p2); eDir = p1-p0; eDir.Normalize(); mitk::Vector2D tDir2 = p3-p0; tDir2.Normalize(); mitk::Vector2D temp; temp.Fill(0); temp.SetVnlVector(tRot.transpose() * tDir2.GetVnlVector()); // apply twist tRot[0][0] = tDir[0]*tDir2[0] + tDir[1]*tDir2[1]; if (tRot[0][0]>1.0) tRot[0][0] = 1.0; tRot[1][1] = tRot[0][0]; tRot[1][0] = sin(acos(tRot[0][0])); tRot[0][1] = -tRot[1][0]; if (temp[1]<0) tRot.inplace_transpose(); m_2DPoints[j].SetVnlVector(tRot*m_2DPoints[j].GetVnlVector()); tDir = tDir2; // apply new ellipse shape newP[0] = m_2DPoints.at(j)[0]; newP[1] = m_2DPoints.at(j)[1]; // calculate normal mitk::PlaneGeometry* planeGeo = const_cast(figure->GetPlaneGeometry()); mitk::Vector3D perp = wc-planeGeo->ProjectPointOntoPlane(wc); perp.Normalize(); vnl_vector_fixed< double, 3 > n2 = planeGeo->GetNormalVnl(); wc = figure->GetWorldControlPoint(0); // is flip needed? if (dot_product(perp.GetVnlVector(),n2)>0 && dot_product(n,n2)<=0.00001) newP[0] *= -1; if (fliplist.at(k)>0) newP[0] *= -1; n = n2; alpha = acos(eDir[0]); if (eDir[1]>0) alpha = 2*itk::Math::pi-alpha; eRot[0][0] = cos(alpha); eRot[1][1] = eRot[0][0]; eRot[1][0] = sin(alpha); eRot[0][1] = -eRot[1][0]; newP = eRot*newP; newP[0] *= r1; newP[1] *= r2; newP = eRot.transpose()*newP; p0[0] += newP[0]; p0[1] += newP[1]; mitk::Point3D w; planeGeo->Map(p0, w); vtkIdType id = m_VtkPoints->InsertNextPoint(w.GetDataPointer()); container->GetPointIds()->InsertNextId(id); } m_VtkCellArray->InsertNextCell(container); } vtkSmartPointer fiberPolyData = vtkSmartPointer::New(); fiberPolyData->SetPoints(m_VtkPoints); fiberPolyData->SetLines(m_VtkCellArray); mitk::FiberBundle::Pointer mitkFiberBundle = mitk::FiberBundle::New(fiberPolyData); mitkFiberBundle->ResampleSpline(m_Parameters.m_Sampling, m_Parameters.m_Tension, m_Parameters.m_Continuity, m_Parameters.m_Bias); m_FiberBundles.push_back(mitkFiberBundle); } } } #endif // __itkFibersFromPlanarFiguresFilter_cpp diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.h index 22693e1730..ea1445b073 100644 --- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkFibersFromPlanarFiguresFilter.h @@ -1,85 +1,88 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef itkFibersFromPlanarFiguresFilter_h #define itkFibersFromPlanarFiguresFilter_h // MITK #include #include #include // ITK #include // VTK #include #include #include #include #include namespace itk{ /** * \brief Generates artificial fibers distributed in and interpolated between the input planar figures. */ class FibersFromPlanarFiguresFilter : public ProcessObject { public: typedef FibersFromPlanarFiguresFilter Self; typedef ProcessObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef mitk::FiberBundle::Pointer FiberType; typedef std::vector< mitk::FiberBundle::Pointer > FiberContainerType; itkFactorylessNewMacro(Self) itkCloneMacro(Self) itkTypeMacro( FibersFromPlanarFiguresFilter, ProcessObject ) void Update() override{ this->GenerateData(); } // input void SetParameters( FiberGenerationParameters param ) ///< Simulation parameters. { m_Parameters = param; } // output FiberContainerType GetFiberBundles(){ return m_FiberBundles; } + void SetFixSeed(bool FixSeed); + protected: void GenerateData() override; FibersFromPlanarFiguresFilter(); ~FibersFromPlanarFiguresFilter() override; void GeneratePoints(); FiberContainerType m_FiberBundles; ///< container for the output fiber bundles std::vector< mitk::Vector2D > m_2DPoints; ///< container for the 2D fiber waypoints FiberGenerationParameters m_Parameters; + bool m_FixSeed; }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkFibersFromPlanarFiguresFilter.cpp" #endif #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.cpp index e774d4f4ba..ee9d8df5fd 100644 --- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.cpp @@ -1,450 +1,457 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ //#ifndef __itkRandomPhantomFilter_cpp //#define __itkRandomPhantomFilter_cpp #include "itkRandomPhantomFilter.h" -#include #include #include namespace itk{ RandomPhantomFilter::RandomPhantomFilter() : m_NumTracts(1) , m_MinStreamlineDensity(25) , m_MaxStreamlineDensity(200) , m_StartRadiusMin(5) , m_StartRadiusMax(30) , m_CurvynessMin(10) , m_CurvynessMax(45) , m_StepSizeMin(15) , m_StepSizeMax(30) , m_MinTwist(10) , m_MaxTwist(30) + , m_FixSeed(false) { m_VolumeSize[0] = 500; m_VolumeSize[1] = 500; m_VolumeSize[2] = 500; } RandomPhantomFilter::~RandomPhantomFilter() { } void RandomPhantomFilter::TransformPlanarFigure(mitk::PlanarEllipse* pe, mitk::Vector3D translation, mitk::Vector3D rotation, double twistangle, double radius1, double radius2) { mitk::BaseGeometry* geom = pe->GetGeometry(); // translate geom->Translate(translation); // calculate rotation matrix double x = rotation[0]*itk::Math::pi/180; double y = rotation[1]*itk::Math::pi/180; double z = rotation[2]*itk::Math::pi/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); // adjust control points auto p0 = pe->GetControlPoint(0); auto p1 = pe->GetControlPoint(1); auto p2 = pe->GetControlPoint(2); auto p3 = pe->GetControlPoint(3); auto v1 = p1 - p0; auto v2 = p2 - p0; auto dot = std::cos(itk::Math::pi*twistangle/180.0); vnl_matrix_fixed tRot; tRot[0][0] = dot; tRot[1][1] = tRot[0][0]; tRot[1][0] = sin(acos(tRot[0][0])); tRot[0][1] = -tRot[1][0]; if (twistangle<0) tRot = tRot.transpose(); vnl_vector_fixed vt; vt[0]=1; vt[1]=0; vnl_vector_fixed v3 = tRot*vt; v1.Normalize(); v2.Normalize(); p1 = p0 + radius1; p2 = p0 + radius2; p3 = p0 + mitk::Vector2D(v3); pe->SetControlPoint(1, p1); pe->SetControlPoint(2, p2); pe->SetControlPoint(3, p3); pe->Modified(); } mitk::PlanarEllipse::Pointer RandomPhantomFilter::CreatePlanarFigure() { mitk::PlaneGeometry::Pointer pl = mitk::PlaneGeometry::New(); pl->SetIdentity(); // mitk::Point3D o; o.Fill(10.0); // pl->SetOrigin(o); mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New(); figure->ResetNumberOfControlPoints(0); figure->SetPlaneGeometry(pl); mitk::Point2D p0; p0.Fill(0.0); mitk::Point2D p1; p1.Fill(0.0); p1[0] = 1; mitk::Point2D p2; p2.Fill(0.0); p2[1] = 1; figure->PlaceFigure(p0); figure->AddControlPoint(p0); figure->AddControlPoint(p1); figure->AddControlPoint(p2); figure->AddControlPoint(p2); figure->SetProperty("initiallyplaced", mitk::BoolProperty::New(true)); return figure; } void RandomPhantomFilter::SetNumTracts(unsigned int NumTracts) { m_NumTracts = NumTracts; } void RandomPhantomFilter::GetPfOnBoundingPlane(mitk::Vector3D& pos, mitk::Vector3D& rot) { - Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New(); - randGen->SetSeed(); - int plane = randGen->GetIntegerVariate(5) + 1; + auto plane = randGen->GetIntegerVariate(5) + 1; MITK_INFO << "Plane: " << plane; switch(plane) { case 1: { pos[0] = randGen->GetUniformVariate(0, m_VolumeSize[0]); pos[1] = randGen->GetUniformVariate(0, m_VolumeSize[1]); pos[2] = 0; rot[0] = 0; rot[1] = 0; rot[2] = 0; break; } case 2: { pos[0] = 0; pos[1] = randGen->GetUniformVariate(0, m_VolumeSize[1]); pos[2] = randGen->GetUniformVariate(0, m_VolumeSize[2]); rot[0] = 0; rot[1] = 90; rot[2] = 0; break; } case 3: { pos[0] = randGen->GetUniformVariate(0, m_VolumeSize[0]); pos[1] = 0; pos[2] = randGen->GetUniformVariate(0, m_VolumeSize[2]); rot[0] = -90; rot[1] = 0; rot[2] = 0; break; } case 4: { pos[0] = randGen->GetUniformVariate(0, m_VolumeSize[0]); pos[1] = m_VolumeSize[1]; pos[2] = randGen->GetUniformVariate(0, m_VolumeSize[2]); rot[0] = 90; rot[1] = 0; rot[2] = 0; break; } case 5: { pos[0] = m_VolumeSize[0]; pos[1] = randGen->GetUniformVariate(0, m_VolumeSize[1]); pos[2] = randGen->GetUniformVariate(0, m_VolumeSize[2]); rot[0] = 0; rot[1] = -90; rot[2] = 0; break; } case 6: { pos[0] = randGen->GetUniformVariate(0, m_VolumeSize[0]); pos[1] = randGen->GetUniformVariate(0, m_VolumeSize[1]); pos[2] = m_VolumeSize[2]; rot[0] = 180; rot[1] = 0; rot[2] = 0; break; } } } bool RandomPhantomFilter::IsInVolume(mitk::Vector3D pos) { if (pos[0]>=0 && pos[0]<=m_VolumeSize[0] && pos[1]>=0 && pos[1]<=m_VolumeSize[1] && pos[2]>=0 && pos[2]<=m_VolumeSize[2]) return true; return false; } -void RandomPhantomFilter::setMinTwist(unsigned int MinTwist) +void RandomPhantomFilter::SetFixSeed(bool FixSeed) +{ + m_FixSeed = FixSeed; +} + +void RandomPhantomFilter::SetMinTwist(unsigned int MinTwist) { m_MinTwist = MinTwist; } -void RandomPhantomFilter::setMaxStreamlineDensity(unsigned int MaxStreamlineDensity) +void RandomPhantomFilter::SetMaxStreamlineDensity(unsigned int MaxStreamlineDensity) { m_MaxStreamlineDensity = MaxStreamlineDensity; } -void RandomPhantomFilter::setMinStreamlineDensity(unsigned int MinStreamlinDensity) +void RandomPhantomFilter::SetMinStreamlineDensity(unsigned int MinStreamlinDensity) { m_MinStreamlineDensity = MinStreamlinDensity; } -void RandomPhantomFilter::setMaxTwist(unsigned int MaxTwist) +void RandomPhantomFilter::SetMaxTwist(unsigned int MaxTwist) { m_MaxTwist = MaxTwist; } -void RandomPhantomFilter::setVolumeSize(const mitk::Vector3D &VolumeSize) +void RandomPhantomFilter::SetVolumeSize(const mitk::Vector3D &VolumeSize) { m_VolumeSize = VolumeSize; } -void RandomPhantomFilter::setStepSizeMax(unsigned int StepSizeMax) +void RandomPhantomFilter::SetStepSizeMax(unsigned int StepSizeMax) { m_StepSizeMax = StepSizeMax; } -void RandomPhantomFilter::setStepSizeMin(unsigned int StepSizeMin) +void RandomPhantomFilter::SetStepSizeMin(unsigned int StepSizeMin) { m_StepSizeMin = StepSizeMin; } -void RandomPhantomFilter::setCurvynessMax(unsigned int CurvynessMax) +void RandomPhantomFilter::SetCurvynessMax(unsigned int CurvynessMax) { m_CurvynessMax = CurvynessMax; } -void RandomPhantomFilter::setCurvynessMin(unsigned int CurvynessMin) +void RandomPhantomFilter::SetCurvynessMin(unsigned int CurvynessMin) { m_CurvynessMin = CurvynessMin; } -void RandomPhantomFilter::setStartRadiusMax(unsigned int StartRadiusMax) +void RandomPhantomFilter::SetStartRadiusMax(unsigned int StartRadiusMax) { m_StartRadiusMax = StartRadiusMax; } -void RandomPhantomFilter::setStartRadiusMin(unsigned int StartRadiusMin) +void RandomPhantomFilter::SetStartRadiusMin(unsigned int StartRadiusMin) { m_StartRadiusMin = StartRadiusMin; } void RandomPhantomFilter::GenerateData() { - Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New(); - randGen->SetSeed(); + randGen = Statistics::MersenneTwisterRandomVariateGenerator::New(); + if (m_FixSeed) + randGen->SetSeed(42); + else + randGen->SetSeed(); for (unsigned int i=0; i bundle_waypoints; double curvyness = randGen->GetUniformVariate(m_CurvynessMin, m_CurvynessMax); int twistdir = static_cast(randGen->GetIntegerVariate(2)) - 1; double dtwist = randGen->GetUniformVariate(m_MinTwist, m_MaxTwist); mitk::Vector3D pos; pos.Fill(0.0); mitk::Vector3D rot; rot.Fill(0.0); double twist = 0; double radius1 = randGen->GetUniformVariate(m_StartRadiusMin, m_StartRadiusMax); double radius2 = randGen->GetUniformVariate(m_StartRadiusMin, m_StartRadiusMax); GetPfOnBoundingPlane(pos, rot); rot[0] += randGen->GetUniformVariate(-curvyness, curvyness); rot[1] += randGen->GetUniformVariate(-curvyness, curvyness); rot[2] += randGen->GetUniformVariate(-curvyness, curvyness); mitk::PlanarEllipse::Pointer start = CreatePlanarFigure(); TransformPlanarFigure(start, pos, rot, twist, radius1, radius2); bundle_waypoints.push_back(start); double c_area = itk::Math::pi*radius1*radius2; int sizestrategy = static_cast(randGen->GetIntegerVariate(2)) - 1; MITK_INFO << "Twist: " << dtwist; MITK_INFO << "Twist direction: " << twistdir; MITK_INFO << "Curvyness: " << curvyness; MITK_INFO << "Size strategy: " << sizestrategy; int c = 1; while(IsInVolume(pos)) { pos += bundle_waypoints.at(c-1)->GetPlaneGeometry()->GetNormal() * randGen->GetUniformVariate(m_StepSizeMin, m_StepSizeMax); rot[0] += randGen->GetUniformVariate(-curvyness, curvyness); rot[1] += randGen->GetUniformVariate(-curvyness, curvyness); rot[2] += randGen->GetUniformVariate(-curvyness, curvyness); twist += dtwist * twistdir; if (randGen->GetUniformVariate(0.0, 1.0) < 0.25) { int temp = static_cast(randGen->GetIntegerVariate(2)) - 1; if (temp!=twistdir) { twistdir = temp; MITK_INFO << "Twist direction change: " << twistdir; } } if (randGen->GetUniformVariate(0.0, 1.0) < 0.25) { int temp = static_cast(randGen->GetIntegerVariate(2)) - 1; if (temp!=sizestrategy) { sizestrategy = temp; MITK_INFO << "Size strategy change: " << sizestrategy; } } double dsize = 3.0; double minradius = 5.0; double maxradius = 2.0*m_StartRadiusMax; if (sizestrategy==0) { radius1 += randGen->GetUniformVariate(-dsize, dsize); radius2 += randGen->GetUniformVariate(-dsize, dsize); while (radius1 < 5) radius1 += randGen->GetUniformVariate(-dsize, dsize); while (radius2 < 5) radius2 += randGen->GetUniformVariate(-dsize, dsize); } else if (sizestrategy==1) { radius1 += randGen->GetUniformVariate(0, dsize); radius2 += randGen->GetUniformVariate(0, dsize); if (radius1 > maxradius) { radius1 = maxradius; sizestrategy = static_cast(randGen->GetIntegerVariate(1)) - 1; } if (radius2 > maxradius) { radius2 = maxradius; sizestrategy = static_cast(randGen->GetIntegerVariate(1)) - 1; } } else if (sizestrategy==-1) { radius1 += randGen->GetUniformVariate(-dsize, 0); radius2 += randGen->GetUniformVariate(-dsize, 0); if (radius1 < minradius) { radius1 = minradius; sizestrategy = static_cast(randGen->GetIntegerVariate(1)); } if (radius2 < minradius) { radius2 = minradius; sizestrategy = static_cast(randGen->GetIntegerVariate(1)); } } c_area += itk::Math::pi*radius1*radius2; mitk::PlanarEllipse::Pointer pf = CreatePlanarFigure(); TransformPlanarFigure(pf, pos, rot, twist, radius1, radius2); bundle_waypoints.push_back(pf); ++c; } c_area /= c; c_area /= 100; MITK_INFO << "Average crossectional area: " << c_area << "cm²"; fiber_params.m_Fiducials.push_back(bundle_waypoints); auto density = randGen->GetUniformVariate(m_MinStreamlineDensity, m_MaxStreamlineDensity); MITK_INFO << "Density: " << density; MITK_INFO << "Num. fibers: " << fiber_params.m_Density; fiber_params.m_Density = static_cast(std::ceil(c_area*density)); if (randGen->GetIntegerVariate(1)==0) { fiber_params.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; MITK_INFO << "Distribution: uniform"; } else { fiber_params.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN; MITK_INFO << "Distribution: Gaussian"; } MITK_INFO << "Num. fiducials: " << c; MITK_INFO << "------------\n"; std::streambuf *old = cout.rdbuf(); // <-- save std::stringstream ss; std::cout.rdbuf (ss.rdbuf()); // <-- redirect itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); filter->SetParameters(fiber_params); + filter->SetFixSeed(m_FixSeed); filter->Update(); m_FiberBundles.push_back(filter->GetFiberBundles().at(0)); std::cout.rdbuf (old); // <-- restore } } } //#endif // __itkRandomPhantomFilter_cpp diff --git a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.h b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.h index 6d0cdf079a..3078b41ee6 100644 --- a/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Fiberfox/itkRandomPhantomFilter.h @@ -1,109 +1,114 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef itkRandomPhantomFilter_h #define itkRandomPhantomFilter_h // MITK #include #include #include // ITK #include +#include namespace itk{ /** * \brief */ class RandomPhantomFilter : public ProcessObject { public: typedef RandomPhantomFilter Self; typedef ProcessObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef mitk::FiberBundle::Pointer FiberType; typedef std::vector< mitk::FiberBundle::Pointer > FiberContainerType; itkFactorylessNewMacro(Self) itkCloneMacro(Self) itkTypeMacro( RandomPhantomFilter, ProcessObject ) void Update() override{ this->GenerateData(); } // output FiberContainerType GetFiberBundles(){ return m_FiberBundles; } void SetNumTracts(unsigned int NumTracts); - void setStartRadiusMin(unsigned int StartRadiusMin); + void SetStartRadiusMin(unsigned int StartRadiusMin); - void setStartRadiusMax(unsigned int StartRadiusMax); + void SetStartRadiusMax(unsigned int StartRadiusMax); - void setCurvynessMin(unsigned int CurvynessMin); + void SetCurvynessMin(unsigned int CurvynessMin); - void setCurvynessMax(unsigned int CurvynessMax); + void SetCurvynessMax(unsigned int CurvynessMax); - void setStepSizeMin(unsigned int StepSizeMin); + void SetStepSizeMin(unsigned int StepSizeMin); - void setStepSizeMax(unsigned int StepSizeMax); + void SetStepSizeMax(unsigned int StepSizeMax); - void setVolumeSize(const mitk::Vector3D &VolumeSize); + void SetVolumeSize(const mitk::Vector3D &VolumeSize); - void setMaxTwist(unsigned int MaxTwist); + void SetMaxTwist(unsigned int MaxTwist); - void setMinStreamlineDensity(unsigned int MinStreamlinDensity); + void SetMinStreamlineDensity(unsigned int MinStreamlinDensity); - void setMaxStreamlineDensity(unsigned int MaxStreamlineDensity); + void SetMaxStreamlineDensity(unsigned int MaxStreamlineDensity); - void setMinTwist(unsigned int MinTwist); + void SetMinTwist(unsigned int MinTwist); + + void SetFixSeed(bool FixSeed); protected: void GenerateData() override; RandomPhantomFilter(); ~RandomPhantomFilter() override; void TransformPlanarFigure(mitk::PlanarEllipse* pe, mitk::Vector3D translation, mitk::Vector3D rotation, double twistangle, double radius1, double radius2); mitk::PlanarEllipse::Pointer CreatePlanarFigure(); void GetPfOnBoundingPlane(mitk::Vector3D& pos, mitk::Vector3D& rot); bool IsInVolume(mitk::Vector3D pos); FiberContainerType m_FiberBundles; ///< container for the output fiber bundles unsigned int m_NumTracts; unsigned int m_MinStreamlineDensity; unsigned int m_MaxStreamlineDensity; unsigned int m_StartRadiusMin; unsigned int m_StartRadiusMax; unsigned int m_CurvynessMin; unsigned int m_CurvynessMax; unsigned int m_StepSizeMin; unsigned int m_StepSizeMax; unsigned int m_MinTwist; unsigned int m_MaxTwist; mitk::Vector3D m_VolumeSize; + bool m_FixSeed; + Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen; }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkRandomPhantomFilter.cpp" #endif #endif diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp index 0790febc01..a0d157612d 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp @@ -1,1044 +1,1068 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #define RAPIDXML_NO_EXCEPTIONS #include #include #include #include #include #include #include #include #include mitk::FiberfoxParameters::FiberfoxParameters() : m_NoiseModel(nullptr) { mitk::StickModel* model_aniso = new mitk::StickModel(); model_aniso->m_CompartmentId = 1; m_FiberModelList.push_back(model_aniso); mitk::BallModel* model_iso = new mitk::BallModel(); model_iso->m_CompartmentId = 3; m_NonFiberModelList.push_back(model_iso); } mitk::FiberfoxParameters::FiberfoxParameters(const mitk::FiberfoxParameters& params) : m_NoiseModel(nullptr) { m_FiberGen = params.m_FiberGen; m_SignalGen = params.m_SignalGen; m_Misc = params.m_Misc; if (params.m_NoiseModel!=nullptr) { if (dynamic_cast*>(params.m_NoiseModel.get())) m_NoiseModel = std::make_shared< mitk::RicianNoiseModel<> >(); else if (dynamic_cast*>(params.m_NoiseModel.get())) m_NoiseModel = std::make_shared< mitk::ChiSquareNoiseModel<> >(); m_NoiseModel->SetNoiseVariance(params.m_NoiseModel->GetNoiseVariance()); } for (unsigned int i=0; i* outModel = nullptr; mitk::DiffusionSignalModel<>* signalModel = nullptr; if (i*>(signalModel)) outModel = new mitk::StickModel<>(dynamic_cast*>(signalModel)); else if (dynamic_cast*>(signalModel)) outModel = new mitk::TensorModel<>(dynamic_cast*>(signalModel)); else if (dynamic_cast*>(signalModel)) outModel = new mitk::RawShModel<>(dynamic_cast*>(signalModel)); else if (dynamic_cast*>(signalModel)) outModel = new mitk::BallModel<>(dynamic_cast*>(signalModel)); else if (dynamic_cast*>(signalModel)) outModel = new mitk::AstroStickModel<>(dynamic_cast*>(signalModel)); else if (dynamic_cast*>(signalModel)) outModel = new mitk::DotModel<>(dynamic_cast*>(signalModel)); if (i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*itk::Math::pi); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i mitk::SignalGenerationParameters::GetBaselineIndices() { std::vector< int > result; for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) result.push_back(i); return result; } unsigned int mitk::SignalGenerationParameters::GetFirstBaselineIndex() { for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) return i; return -1; } bool mitk::SignalGenerationParameters::IsBaselineIndex(unsigned int idx) { if (m_GradientDirections.size()>idx && m_GradientDirections.at(idx).GetNorm()<0.0001) return true; return false; } unsigned int mitk::SignalGenerationParameters::GetNumWeightedVolumes() { return m_NumGradients; } unsigned int mitk::SignalGenerationParameters::GetNumBaselineVolumes() { return m_NumBaseline; } unsigned int mitk::SignalGenerationParameters::GetNumVolumes() { return m_GradientDirections.size(); } mitk::SignalGenerationParameters::GradientListType mitk::SignalGenerationParameters::GetGradientDirections() { return m_GradientDirections; } mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer mitk::SignalGenerationParameters::GetItkGradientContainer() { int c = 0; mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer out = mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::New(); for (auto g : m_GradientDirections) { mitk::DiffusionPropertyHelper::GradientDirectionType vnl_dir; vnl_dir[0] = g[0]; vnl_dir[1] = g[1]; vnl_dir[2] = g[2]; out->InsertElement(c, vnl_dir); ++c; } return out; } mitk::SignalGenerationParameters::GradientType mitk::SignalGenerationParameters::GetGradientDirection(unsigned int i) { return m_GradientDirections.at(i); } void mitk::SignalGenerationParameters::SetNumWeightedVolumes(int numGradients) { m_NumGradients = numGradients; GenerateGradientHalfShell(); } std::vector< int > mitk::SignalGenerationParameters::GetBvalues() { std::vector< int > bVals; for( GradientType g : m_GradientDirections) { float norm = g.GetNorm(); int bVal = std::round(norm*norm*m_Bvalue); if ( std::find(bVals.begin(), bVals.end(), bVal) == bVals.end() ) bVals.push_back(bVal); } return bVals; } double mitk::SignalGenerationParameters::GetBvalue() { return m_Bvalue; } void mitk::SignalGenerationParameters::SetGradienDirections(GradientListType gradientList) { m_GradientDirections = gradientList; m_NumGradients = 0; m_NumBaseline = 0; for( unsigned int i=0; im_GradientDirections.size(); i++) { float norm = m_GradientDirections.at(i).GetNorm(); if (norm>0.0001) m_NumGradients++; else m_NumBaseline++; } } void mitk::SignalGenerationParameters::SetGradienDirections(mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList) { m_NumGradients = 0; m_NumBaseline = 0; m_GradientDirections.clear(); for( unsigned int i=0; iSize(); i++) { GradientType g; g[0] = gradientList->at(i)[0]; g[1] = gradientList->at(i)[1]; g[2] = gradientList->at(i)[2]; m_GradientDirections.push_back(g); float norm = m_GradientDirections.at(i).GetNorm(); if (norm>0.0001) m_NumGradients++; else m_NumBaseline++; } } +void mitk::SignalGenerationParameters::ApplyDirectionMatrix() +{ + auto imageRotationMatrix = m_ImageDirection.GetVnlMatrix(); + + GradientListType rotated_gradients; + for(auto g : m_GradientDirections) + { + vnl_vector vec = g.GetVnlVector(); + vec = vec.pre_multiply(imageRotationMatrix); + + GradientType g2; + g2[0] = vec[0]; + g2[1] = vec[1]; + g2[2] = vec[2]; + rotated_gradients.push_back(g2); + } + m_GradientDirections = rotated_gradients; +} + +void mitk::FiberfoxParameters::ApplyDirectionMatrix() +{ + m_SignalGen.ApplyDirectionMatrix(); + UpdateSignalModels(); +} void mitk::FiberfoxParameters::SaveParameters(std::string filename) { if(filename.empty()) return; if(".ffp"!=filename.substr(filename.size()-4, 4)) filename += ".ffp"; const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, nullptr ); if ( locale.compare(currLocale)!=0 ) { try { setlocale(LC_ALL, locale.c_str()); } catch(...) { MITK_INFO << "Could not set locale " << locale; } } boost::property_tree::ptree parameters; // fiber generation parameters parameters.put("fiberfox.fibers.distribution", m_FiberGen.m_Distribution); parameters.put("fiberfox.fibers.variance", m_FiberGen.m_Variance); parameters.put("fiberfox.fibers.density", m_FiberGen.m_Density); parameters.put("fiberfox.fibers.spline.sampling", m_FiberGen.m_Sampling); parameters.put("fiberfox.fibers.spline.tension", m_FiberGen.m_Tension); parameters.put("fiberfox.fibers.spline.continuity", m_FiberGen.m_Continuity); parameters.put("fiberfox.fibers.spline.bias", m_FiberGen.m_Bias); parameters.put("fiberfox.fibers.rotation.x", m_FiberGen.m_Rotation[0]); parameters.put("fiberfox.fibers.rotation.y", m_FiberGen.m_Rotation[1]); parameters.put("fiberfox.fibers.rotation.z", m_FiberGen.m_Rotation[2]); parameters.put("fiberfox.fibers.translation.x", m_FiberGen.m_Translation[0]); parameters.put("fiberfox.fibers.translation.y", m_FiberGen.m_Translation[1]); parameters.put("fiberfox.fibers.translation.z", m_FiberGen.m_Translation[2]); parameters.put("fiberfox.fibers.scale.x", m_FiberGen.m_Scale[0]); parameters.put("fiberfox.fibers.scale.y", m_FiberGen.m_Scale[1]); parameters.put("fiberfox.fibers.scale.z", m_FiberGen.m_Scale[2]); // image generation parameters parameters.put("fiberfox.image.basic.size.x", m_SignalGen.m_ImageRegion.GetSize(0)); parameters.put("fiberfox.image.basic.size.y", m_SignalGen.m_ImageRegion.GetSize(1)); parameters.put("fiberfox.image.basic.size.z", m_SignalGen.m_ImageRegion.GetSize(2)); parameters.put("fiberfox.image.basic.spacing.x", m_SignalGen.m_ImageSpacing[0]); parameters.put("fiberfox.image.basic.spacing.y", m_SignalGen.m_ImageSpacing[1]); parameters.put("fiberfox.image.basic.spacing.z", m_SignalGen.m_ImageSpacing[2]); parameters.put("fiberfox.image.basic.origin.x", m_SignalGen.m_ImageOrigin[0]); parameters.put("fiberfox.image.basic.origin.y", m_SignalGen.m_ImageOrigin[1]); parameters.put("fiberfox.image.basic.origin.z", m_SignalGen.m_ImageOrigin[2]); parameters.put("fiberfox.image.basic.direction.d1", m_SignalGen.m_ImageDirection[0][0]); parameters.put("fiberfox.image.basic.direction.d2", m_SignalGen.m_ImageDirection[0][1]); parameters.put("fiberfox.image.basic.direction.d3", m_SignalGen.m_ImageDirection[0][2]); parameters.put("fiberfox.image.basic.direction.d4", m_SignalGen.m_ImageDirection[1][0]); parameters.put("fiberfox.image.basic.direction.d5", m_SignalGen.m_ImageDirection[1][1]); parameters.put("fiberfox.image.basic.direction.d6", m_SignalGen.m_ImageDirection[1][2]); parameters.put("fiberfox.image.basic.direction.d7", m_SignalGen.m_ImageDirection[2][0]); parameters.put("fiberfox.image.basic.direction.d8", m_SignalGen.m_ImageDirection[2][1]); parameters.put("fiberfox.image.basic.direction.d9", m_SignalGen.m_ImageDirection[2][2]); mitk::gradients::WriteBvalsBvecs(filename+".bvals", filename+".bvecs", m_SignalGen.GetItkGradientContainer(), m_SignalGen.m_Bvalue); parameters.put("fiberfox.image.acquisitiontype", m_SignalGen.m_AcquisitionType); parameters.put("fiberfox.image.coilsensitivityprofile", m_SignalGen.m_CoilSensitivityProfile); parameters.put("fiberfox.image.numberofcoils", m_SignalGen.m_NumberOfCoils); parameters.put("fiberfox.image.reversephase", m_SignalGen.m_ReversePhase); parameters.put("fiberfox.image.partialfourier", m_SignalGen.m_PartialFourier); parameters.put("fiberfox.image.noisevariance", m_SignalGen.m_NoiseVariance); parameters.put("fiberfox.image.trep", m_SignalGen.m_tRep); parameters.put("fiberfox.image.signalScale", m_SignalGen.m_SignalScale); parameters.put("fiberfox.image.tEcho", m_SignalGen.m_tEcho); parameters.put("fiberfox.image.tLine", m_SignalGen.m_tLine); parameters.put("fiberfox.image.tInhom", m_SignalGen.m_tInhom); parameters.put("fiberfox.image.simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition); parameters.put("fiberfox.image.axonRadius", m_SignalGen.m_AxonRadius); parameters.put("fiberfox.image.doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation); parameters.put("fiberfox.image.doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume); parameters.put("fiberfox.image.artifacts.spikesnum", m_SignalGen.m_Spikes); parameters.put("fiberfox.image.artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude); parameters.put("fiberfox.image.artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset); parameters.put("fiberfox.image.artifacts.eddyStrength", m_SignalGen.m_EddyStrength); parameters.put("fiberfox.image.artifacts.eddyTau", m_SignalGen.m_Tau); parameters.put("fiberfox.image.artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor); parameters.put("fiberfox.image.artifacts.drift", m_SignalGen.m_Drift); parameters.put("fiberfox.image.artifacts.doAddMotion", m_SignalGen.m_DoAddMotion); parameters.put("fiberfox.image.artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion); parameters.put("fiberfox.image.artifacts.translation0", m_SignalGen.m_Translation[0]); parameters.put("fiberfox.image.artifacts.translation1", m_SignalGen.m_Translation[1]); parameters.put("fiberfox.image.artifacts.translation2", m_SignalGen.m_Translation[2]); parameters.put("fiberfox.image.artifacts.rotation0", m_SignalGen.m_Rotation[0]); parameters.put("fiberfox.image.artifacts.rotation1", m_SignalGen.m_Rotation[1]); parameters.put("fiberfox.image.artifacts.rotation2", m_SignalGen.m_Rotation[2]); parameters.put("fiberfox.image.artifacts.motionvolumes", m_Misc.m_MotionVolumesBox); parameters.put("fiberfox.image.artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging); parameters.put("fiberfox.image.artifacts.addnoise", m_Misc.m_DoAddNoise); parameters.put("fiberfox.image.artifacts.addghosts", m_Misc.m_DoAddGhosts); parameters.put("fiberfox.image.artifacts.addaliasing", m_Misc.m_DoAddAliasing); parameters.put("fiberfox.image.artifacts.addspikes", m_Misc.m_DoAddSpikes); parameters.put("fiberfox.image.artifacts.addeddycurrents", m_Misc.m_DoAddEddyCurrents); parameters.put("fiberfox.image.artifacts.doAddDistortions", m_Misc.m_DoAddDistortions); parameters.put("fiberfox.image.artifacts.doAddDrift", m_SignalGen.m_DoAddDrift); parameters.put("fiberfox.image.outputvolumefractions", m_Misc.m_CheckOutputVolumeFractionsBox); parameters.put("fiberfox.image.showadvanced", m_Misc.m_CheckAdvancedSignalOptionsBox); parameters.put("fiberfox.image.signalmodelstring", m_Misc.m_SignalModelString); parameters.put("fiberfox.image.artifactmodelstring", m_Misc.m_ArtifactModelString); parameters.put("fiberfox.image.outpath", m_Misc.m_OutputPath); parameters.put("fiberfox.fibers.realtime", m_Misc.m_CheckRealTimeFibersBox); parameters.put("fiberfox.fibers.showadvanced", m_Misc.m_CheckAdvancedFiberOptionsBox); parameters.put("fiberfox.fibers.constantradius", m_Misc.m_CheckConstantRadiusBox); parameters.put("fiberfox.fibers.includeFiducials", m_Misc.m_CheckIncludeFiducialsBox); if (m_NoiseModel!=nullptr) { parameters.put("fiberfox.image.artifacts.noisevariance", m_NoiseModel->GetNoiseVariance()); if (dynamic_cast*>(m_NoiseModel.get())) parameters.put("fiberfox.image.artifacts.noisetype", "rice"); else if (dynamic_cast*>(m_NoiseModel.get())) parameters.put("fiberfox.image.artifacts.noisetype", "chisquare"); } for (std::size_t i=0; i* signalModel = nullptr; if (i(i)+".type", "fiber"); } else { signalModel = m_NonFiberModelList.at(i-m_FiberModelList.size()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".type", "non-fiber"); } if (dynamic_cast*>(signalModel)) { mitk::StickModel<>* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".model", "stick"); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".t1", model->GetT1()); } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel<>* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".model", "tensor"); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".d1", model->GetDiffusivity1()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".d2", model->GetDiffusivity2()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".d3", model->GetDiffusivity3()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".t1", model->GetT1()); } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".model", "prototype"); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".minFA", model->GetFaRange().first); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".maxFA", model->GetFaRange().second); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".minADC", model->GetAdcRange().first); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".maxADC", model->GetAdcRange().second); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".maxNumSamples", model->GetMaxNumKernels()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".numSamples", model->GetNumberOfKernels()); int shOrder = model->GetShOrder(); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".numCoeffs", (shOrder*shOrder + shOrder + 2)/2 + shOrder); for (unsigned int j=0; jGetNumberOfKernels(); j++) { vnl_vector< double > coeffs = model->GetCoefficients(j); for (unsigned int k=0; k(i)+".kernels."+boost::lexical_cast(j)+".coeffs."+boost::lexical_cast(k), coeffs[k]); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".kernels."+boost::lexical_cast(j)+".B0", model->GetBaselineSignal(j)); } } else if (dynamic_cast*>(signalModel)) { mitk::BallModel<>* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".model", "ball"); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".t1", model->GetT1()); } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel<>* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".model", "astrosticks"); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".t1", model->GetT1()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".randomize", model->GetRandomizeSticks()); } else if (dynamic_cast*>(signalModel)) { mitk::DotModel<>* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".model", "dot"); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".t1", model->GetT1()); } if (signalModel!=nullptr) { parameters.put("fiberfox.image.compartments.c"+boost::lexical_cast(i)+".ID", signalModel->m_CompartmentId); if (signalModel->GetVolumeFractionImage().IsNotNull()) { try{ itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); writer->SetFileName(filename+"_VOLUME"+boost::lexical_cast(signalModel->m_CompartmentId)+".nii.gz"); writer->SetInput(signalModel->GetVolumeFractionImage()); writer->Update(); MITK_INFO << "Volume fraction image for compartment "+boost::lexical_cast(signalModel->m_CompartmentId)+" saved."; } catch(...) { } } } } boost::property_tree::xml_writer_settings writerSettings(' ', 2); boost::property_tree::xml_parser::write_xml(filename, parameters, std::locale(), writerSettings); try{ itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); writer->SetFileName(filename+"_FMAP.nii.gz"); writer->SetInput(m_SignalGen.m_FrequencyMap); writer->Update(); } catch(...) { MITK_INFO << "No frequency map saved."; } try{ itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); writer->SetFileName(filename+"_MASK.nii.gz"); writer->SetInput(m_SignalGen.m_MaskImage); writer->Update(); } catch(...) { MITK_INFO << "No mask image saved."; } setlocale(LC_ALL, currLocale.c_str()); } template< class ParameterType > ParameterType mitk::FiberfoxParameters::ReadVal(boost::property_tree::ptree::value_type const& v, std::string tag, ParameterType defaultValue, bool essential) { try { return v.second.get(tag); } catch (...) { if (essential) { mitkThrow() << "Parameter file corrupted. Essential tag is missing: '" << tag << "'"; } if (tag!="artifacts.noisetype") { MITK_INFO << "Tag '" << tag << "' not found. Using default value '" << defaultValue << "'."; m_MissingTags += "\n- "; m_MissingTags += tag; } return defaultValue; } } void mitk::FiberfoxParameters::UpdateSignalModels() { for (mitk::DiffusionSignalModel<>* m : m_FiberModelList) { m->SetGradientList(m_SignalGen.m_GradientDirections); m->SetBvalue(m_SignalGen.m_Bvalue); } for (mitk::DiffusionSignalModel<>* m : m_NonFiberModelList) { m->SetGradientList(m_SignalGen.m_GradientDirections); m->SetBvalue(m_SignalGen.m_Bvalue); } } void mitk::FiberfoxParameters::SetNumWeightedVolumes(int numGradients) { m_SignalGen.SetNumWeightedVolumes(numGradients); UpdateSignalModels(); } void mitk::FiberfoxParameters::SetGradienDirections(mitk::SignalGenerationParameters::GradientListType gradientList) { m_SignalGen.SetGradienDirections(gradientList); UpdateSignalModels(); } void mitk::FiberfoxParameters::SetGradienDirections(mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList) { m_SignalGen.SetGradienDirections(gradientList); UpdateSignalModels(); } void mitk::FiberfoxParameters::SetBvalue(double Bvalue) { m_SignalGen.m_Bvalue = Bvalue; UpdateSignalModels(); } void mitk::FiberfoxParameters::GenerateGradientHalfShell() { m_SignalGen.GenerateGradientHalfShell(); UpdateSignalModels(); } void mitk::FiberfoxParameters::LoadParameters(std::string filename) { srand(time(0)); m_MissingTags = ""; if(filename.empty()) { return; } const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, nullptr ); if ( locale.compare(currLocale)!=0 ) { try { setlocale(LC_ALL, locale.c_str()); } catch(...) { MITK_INFO << "Could not set locale " << locale; } } boost::property_tree::ptree parameterTree; boost::property_tree::xml_parser::read_xml( filename, parameterTree ); m_FiberModelList.clear(); m_NonFiberModelList.clear(); if (m_NoiseModel) { m_NoiseModel = nullptr; } BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameterTree.get_child("fiberfox") ) { if( v1.first == "fibers" ) { m_Misc.m_CheckRealTimeFibersBox = ReadVal(v1,"realtime", m_Misc.m_CheckRealTimeFibersBox); m_Misc.m_CheckAdvancedFiberOptionsBox = ReadVal(v1,"showadvanced", m_Misc.m_CheckAdvancedFiberOptionsBox); m_Misc.m_CheckConstantRadiusBox = ReadVal(v1,"constantradius", m_Misc.m_CheckConstantRadiusBox); m_Misc.m_CheckIncludeFiducialsBox = ReadVal(v1,"includeFiducials", m_Misc.m_CheckIncludeFiducialsBox); switch (ReadVal(v1,"distribution", 0)) { case 0: m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; break; case 1: m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN; break; default: m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; } m_FiberGen.m_Variance = ReadVal(v1,"variance", m_FiberGen.m_Variance); m_FiberGen.m_Density = ReadVal(v1,"density", m_FiberGen.m_Density); m_FiberGen.m_Sampling = ReadVal(v1,"spline.sampling", m_FiberGen.m_Sampling); m_FiberGen.m_Tension = ReadVal(v1,"spline.tension", m_FiberGen.m_Tension); m_FiberGen.m_Continuity = ReadVal(v1,"spline.continuity", m_FiberGen.m_Continuity); m_FiberGen.m_Bias = ReadVal(v1,"spline.bias", m_FiberGen.m_Bias); m_FiberGen.m_Rotation[0] = ReadVal(v1,"rotation.x", m_FiberGen.m_Rotation[0]); m_FiberGen.m_Rotation[1] = ReadVal(v1,"rotation.y", m_FiberGen.m_Rotation[1]); m_FiberGen.m_Rotation[2] = ReadVal(v1,"rotation.z", m_FiberGen.m_Rotation[2]); m_FiberGen.m_Translation[0] = ReadVal(v1,"translation.x", m_FiberGen.m_Translation[0]); m_FiberGen.m_Translation[1] = ReadVal(v1,"translation.y", m_FiberGen.m_Translation[1]); m_FiberGen.m_Translation[2] = ReadVal(v1,"translation.z", m_FiberGen.m_Translation[2]); m_FiberGen.m_Scale[0] = ReadVal(v1,"scale.x", m_FiberGen.m_Scale[0]); m_FiberGen.m_Scale[1] = ReadVal(v1,"scale.y", m_FiberGen.m_Scale[1]); m_FiberGen.m_Scale[2] = ReadVal(v1,"scale.z", m_FiberGen.m_Scale[2]); } else if ( v1.first == "image" ) { m_Misc.m_SignalModelString = ReadVal(v1,"signalmodelstring", m_Misc.m_SignalModelString); m_Misc.m_ArtifactModelString = ReadVal(v1,"artifactmodelstring", m_Misc.m_ArtifactModelString); m_Misc.m_OutputPath = ReadVal(v1,"outpath", m_Misc.m_OutputPath); m_Misc.m_CheckOutputVolumeFractionsBox = ReadVal(v1,"outputvolumefractions", m_Misc.m_CheckOutputVolumeFractionsBox); m_Misc.m_CheckAdvancedSignalOptionsBox = ReadVal(v1,"showadvanced", m_Misc.m_CheckAdvancedSignalOptionsBox); m_Misc.m_DoAddDistortions = ReadVal(v1,"artifacts.doAddDistortions", m_Misc.m_DoAddDistortions); m_Misc.m_DoAddNoise = ReadVal(v1,"artifacts.addnoise", m_Misc.m_DoAddNoise); m_Misc.m_DoAddGhosts = ReadVal(v1,"artifacts.addghosts", m_Misc.m_DoAddGhosts); m_Misc.m_DoAddAliasing = ReadVal(v1,"artifacts.addaliasing", m_Misc.m_DoAddAliasing); m_Misc.m_DoAddSpikes = ReadVal(v1,"artifacts.addspikes", m_Misc.m_DoAddSpikes); m_Misc.m_DoAddEddyCurrents = ReadVal(v1,"artifacts.addeddycurrents", m_Misc.m_DoAddEddyCurrents); m_SignalGen.m_ImageRegion.SetSize(0, ReadVal(v1,"basic.size.x",m_SignalGen.m_ImageRegion.GetSize(0))); m_SignalGen.m_ImageRegion.SetSize(1, ReadVal(v1,"basic.size.y",m_SignalGen.m_ImageRegion.GetSize(1))); m_SignalGen.m_ImageRegion.SetSize(2, ReadVal(v1,"basic.size.z",m_SignalGen.m_ImageRegion.GetSize(2))); m_SignalGen.m_ImageSpacing[0] = ReadVal(v1,"basic.spacing.x",m_SignalGen.m_ImageSpacing[0]); m_SignalGen.m_ImageSpacing[1] = ReadVal(v1,"basic.spacing.y",m_SignalGen.m_ImageSpacing[1]); m_SignalGen.m_ImageSpacing[2] = ReadVal(v1,"basic.spacing.z",m_SignalGen.m_ImageSpacing[2]); m_SignalGen.m_ImageOrigin[0] = ReadVal(v1,"basic.origin.x",m_SignalGen.m_ImageOrigin[0]); m_SignalGen.m_ImageOrigin[1] = ReadVal(v1,"basic.origin.y",m_SignalGen.m_ImageOrigin[1]); m_SignalGen.m_ImageOrigin[2] = ReadVal(v1,"basic.origin.z",m_SignalGen.m_ImageOrigin[2]); int i = 0; int j = 0; for(auto v : v1.second.get_child("basic.direction")) { m_SignalGen.m_ImageDirection[i][j] = boost::lexical_cast(v.second.data()); ++j; if (j==3) { j = 0; ++i; } } m_SignalGen.m_AcquisitionType = (SignalGenerationParameters::AcquisitionType)ReadVal(v1,"acquisitiontype", m_SignalGen.m_AcquisitionType); m_SignalGen.m_CoilSensitivityProfile = (SignalGenerationParameters::CoilSensitivityProfile)ReadVal(v1,"coilsensitivityprofile", m_SignalGen.m_CoilSensitivityProfile); m_SignalGen.m_NumberOfCoils = ReadVal(v1,"numberofcoils", m_SignalGen.m_NumberOfCoils); m_SignalGen.m_ReversePhase = ReadVal(v1,"reversephase", m_SignalGen.m_ReversePhase); m_SignalGen.m_PartialFourier = ReadVal(v1,"partialfourier", m_SignalGen.m_PartialFourier); m_SignalGen.m_NoiseVariance = ReadVal(v1,"noisevariance", m_SignalGen.m_NoiseVariance); m_SignalGen.m_tRep = ReadVal(v1,"trep", m_SignalGen.m_tRep); m_SignalGen.m_SignalScale = ReadVal(v1,"signalScale", m_SignalGen.m_SignalScale); m_SignalGen.m_tEcho = ReadVal(v1,"tEcho", m_SignalGen.m_tEcho); m_SignalGen.m_tLine = ReadVal(v1,"tLine", m_SignalGen.m_tLine); m_SignalGen.m_tInhom = ReadVal(v1,"tInhom", m_SignalGen.m_tInhom); m_SignalGen.m_SimulateKspaceAcquisition = ReadVal(v1,"simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition); m_SignalGen.m_AxonRadius = ReadVal(v1,"axonRadius", m_SignalGen.m_AxonRadius); m_SignalGen.m_Spikes = ReadVal(v1,"artifacts.spikesnum", m_SignalGen.m_Spikes); m_SignalGen.m_SpikeAmplitude = ReadVal(v1,"artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude); m_SignalGen.m_KspaceLineOffset = ReadVal(v1,"artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset); m_SignalGen.m_EddyStrength = ReadVal(v1,"artifacts.eddyStrength", m_SignalGen.m_EddyStrength); m_SignalGen.m_Tau = ReadVal(v1,"artifacts.eddyTau", m_SignalGen.m_Tau); m_SignalGen.m_CroppingFactor = ReadVal(v1,"artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor); m_SignalGen.m_Drift = ReadVal(v1,"artifacts.drift", m_SignalGen.m_Drift); m_SignalGen.m_DoAddGibbsRinging = ReadVal(v1,"artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging); m_SignalGen.m_DoSimulateRelaxation = ReadVal(v1,"doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation); m_SignalGen.m_DoDisablePartialVolume = ReadVal(v1,"doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume); m_SignalGen.m_DoAddMotion = ReadVal(v1,"artifacts.doAddMotion", m_SignalGen.m_DoAddMotion); m_SignalGen.m_DoRandomizeMotion = ReadVal(v1,"artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion); m_SignalGen.m_DoAddDrift = ReadVal(v1,"artifacts.doAddDrift", m_SignalGen.m_DoAddDrift); m_SignalGen.m_Translation[0] = ReadVal(v1,"artifacts.translation0", m_SignalGen.m_Translation[0]); m_SignalGen.m_Translation[1] = ReadVal(v1,"artifacts.translation1", m_SignalGen.m_Translation[1]); m_SignalGen.m_Translation[2] = ReadVal(v1,"artifacts.translation2", m_SignalGen.m_Translation[2]); m_SignalGen.m_Rotation[0] = ReadVal(v1,"artifacts.rotation0", m_SignalGen.m_Rotation[0]); m_SignalGen.m_Rotation[1] = ReadVal(v1,"artifacts.rotation1", m_SignalGen.m_Rotation[1]); m_SignalGen.m_Rotation[2] = ReadVal(v1,"artifacts.rotation2", m_SignalGen.m_Rotation[2]); if (itksys::SystemTools::FileExists(filename+".bvals") && itksys::SystemTools::FileExists(filename+".bvecs")) { m_Misc.m_BvalsFile = filename+".bvals"; m_Misc.m_BvecsFile = filename+".bvecs"; m_SignalGen.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Misc.m_BvalsFile, m_Misc.m_BvecsFile, m_SignalGen.m_Bvalue) ); } else { m_SignalGen.m_Bvalue = ReadVal(v1,"bvalue", m_SignalGen.m_Bvalue); SignalGenerationParameters::GradientListType gradients; try { BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("gradients") ) { SignalGenerationParameters::GradientType g; g[0] = ReadVal(v2,"x",0); g[1] = ReadVal(v2,"y",0); g[2] = ReadVal(v2,"z",0); gradients.push_back(g); } } catch(...) { MITK_INFO << "WARNING: Fiberfox parameters without any gradient directions loaded."; } m_SignalGen.SetGradienDirections(gradients); } m_Misc.m_MotionVolumesBox = ReadVal(v1,"artifacts.motionvolumes", m_Misc.m_MotionVolumesBox); m_SignalGen.m_MotionVolumes.clear(); if ( m_Misc.m_MotionVolumesBox == "random" ) { m_SignalGen.m_MotionVolumes.push_back(0); for ( size_t i=1; i < m_SignalGen.GetNumVolumes(); ++i ) { m_SignalGen.m_MotionVolumes.push_back( bool( rand()%2 ) ); } MITK_DEBUG << "mitkFiberfoxParameters.cpp: Case m_Misc.m_MotionVolumesBox == \"random\"."; } else if ( ! m_Misc.m_MotionVolumesBox.empty() ) { std::stringstream stream( m_Misc.m_MotionVolumesBox ); std::vector numbers; int nummer = std::numeric_limits::max(); while( stream >> nummer ) { if( nummer < std::numeric_limits::max() ) { numbers.push_back( nummer ); } } // If a list of negative numbers is given: if( *(std::min_element( numbers.begin(), numbers.end() )) < 0 && *(std::max_element( numbers.begin(), numbers.end() )) <= 0 ) // cave: -0 == +0 { for ( size_t i=0; i(m_SignalGen.GetNumVolumes()) && -number >= 0 ) m_SignalGen.m_MotionVolumes.at(-number) = false; } MITK_DEBUG << "mitkFiberfoxParameters.cpp: Case list of negative numbers."; } // If a list of positive numbers is given: else if( *(std::min_element( numbers.begin(), numbers.end() )) >= 0 && *(std::max_element( numbers.begin(), numbers.end() )) >= 0 ) { for ( size_t i=0; i(m_SignalGen.GetNumVolumes()) && number >= 0) m_SignalGen.m_MotionVolumes.at(number) = true; } MITK_DEBUG << "mitkFiberfoxParameters.cpp: Case list of positive numbers."; } else { MITK_WARN << "mitkFiberfoxParameters.cpp: Inconsistent list of numbers in m_MotionVolumesBox."; break; } } else { MITK_WARN << "mitkFiberfoxParameters.cpp: Cannot make sense of string in m_MotionVolumesBox."; break; } try { if (ReadVal(v1,"artifacts.noisetype","")=="rice") { m_NoiseModel = std::make_shared< mitk::RicianNoiseModel<> >(); m_NoiseModel->SetNoiseVariance(ReadVal(v1,"artifacts.noisevariance",m_NoiseModel->GetNoiseVariance())); } } catch(...) { MITK_DEBUG << "mitkFiberfoxParameters.cpp: caught some error while trying m_NoiseModel->SetNoiseVariance()"; // throw; } try { if (ReadVal(v1,"artifacts.noisetype","")=="chisquare") { m_NoiseModel = std::make_shared< mitk::ChiSquareNoiseModel<> >(); m_NoiseModel->SetNoiseVariance(ReadVal(v1,"artifacts.noisevariance",m_NoiseModel->GetNoiseVariance())); } } catch(...) { MITK_DEBUG << "mitkFiberfoxParameters.cpp: caught some error while trying m_NoiseModel->SetNoiseVariance()"; // throw; } BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("compartments") ) { mitk::DiffusionSignalModel<>* signalModel = nullptr; std::string model = ReadVal(v2,"model","",true); if (model=="stick") { mitk::StickModel<>* model = new mitk::StickModel<>(); model->SetDiffusivity(ReadVal(v2,"d",model->GetDiffusivity())); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); model->SetBvalue(m_SignalGen.m_Bvalue); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="tensor") { mitk::TensorModel<>* model = new mitk::TensorModel<>(); model->SetDiffusivity1(ReadVal(v2,"d1",model->GetDiffusivity1())); model->SetDiffusivity2(ReadVal(v2,"d2",model->GetDiffusivity2())); model->SetDiffusivity3(ReadVal(v2,"d3",model->GetDiffusivity3())); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); model->SetBvalue(m_SignalGen.m_Bvalue); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="ball") { mitk::BallModel<>* model = new mitk::BallModel<>(); model->SetDiffusivity(ReadVal(v2,"d",model->GetDiffusivity())); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); model->SetBvalue(m_SignalGen.m_Bvalue); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="astrosticks") { mitk::AstroStickModel<>* model = new AstroStickModel<>(); model->SetDiffusivity(ReadVal(v2,"d",model->GetDiffusivity())); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); model->SetBvalue(m_SignalGen.m_Bvalue); model->SetRandomizeSticks(ReadVal(v2,"randomize",model->GetRandomizeSticks())); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="dot") { mitk::DotModel<>* model = new mitk::DotModel<>(); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="prototype") { mitk::RawShModel<>* model = new mitk::RawShModel<>(); model->SetMaxNumKernels(ReadVal(v2,"maxNumSamples",model->GetMaxNumKernels())); model->SetFaRange(ReadVal(v2,"minFA",model->GetFaRange().first), ReadVal(v2,"maxFA",model->GetFaRange().second)); model->SetAdcRange(ReadVal(v2,"minADC",model->GetAdcRange().first), ReadVal(v2,"maxADC",model->GetAdcRange().second)); model->m_CompartmentId = ReadVal(v2,"ID",0,true); unsigned int numCoeffs = ReadVal(v2,"numCoeffs",0,true); unsigned int numSamples = ReadVal(v2,"numSamples",0,true); for (unsigned int j=0; j coeffs(numCoeffs); for (unsigned int k=0; k(v2,"kernels."+boost::lexical_cast(j)+".coeffs."+boost::lexical_cast(k),0,true); } model->SetShCoefficients( coeffs, ReadVal(v2,"kernels."+boost::lexical_cast(j)+".B0",0,true) ); } if (ReadVal(v2,"type","",true)=="fiber") { m_FiberModelList.push_back(model); } else if (ReadVal(v2,"type","",true)=="non-fiber") { m_NonFiberModelList.push_back(model); } // else ? signalModel = model; } if (signalModel!=nullptr) { try { itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); if ( itksys::SystemTools::FileExists(filename+"_VOLUME"+ReadVal(v2,"ID","")+".nii.gz") ) reader->SetFileName(filename+"_VOLUME"+ReadVal(v2,"ID","")+".nii.gz"); else if ( itksys::SystemTools::FileExists(filename+"_VOLUME"+ReadVal(v2,"ID","")+".nii") ) reader->SetFileName(filename+"_VOLUME"+ReadVal(v2,"ID","")+".nii"); else reader->SetFileName(filename+"_VOLUME"+ReadVal(v2,"ID","")+".nrrd"); reader->Update(); signalModel->SetVolumeFractionImage(reader->GetOutput()); MITK_INFO << "Volume fraction image loaded for compartment " << signalModel->m_CompartmentId; } catch(...) { MITK_INFO << "No volume fraction image found for compartment " << signalModel->m_CompartmentId; } } } } else { } } UpdateSignalModels(); try { itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); reader->SetFileName(filename+"_FMAP.nrrd"); if ( itksys::SystemTools::FileExists(filename+"_FMAP.nii.gz") ) reader->SetFileName(filename+"_FMAP.nii.gz"); else if ( itksys::SystemTools::FileExists(filename+"_FMAP.nii") ) reader->SetFileName(filename+"_FMAP.nii"); else reader->SetFileName(filename+"_FMAP.nrrd"); reader->Update(); m_SignalGen.m_FrequencyMap = reader->GetOutput(); MITK_INFO << "Frequency map loaded."; } catch(...) { MITK_INFO << "No frequency map found."; } try { itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); if ( itksys::SystemTools::FileExists(filename+"_MASK.nii.gz") ) reader->SetFileName(filename+"_MASK.nii.gz"); else if ( itksys::SystemTools::FileExists(filename+"_MASK.nii") ) reader->SetFileName(filename+"_MASK.nii"); else reader->SetFileName(filename+"_MASK.nrrd"); reader->Update(); m_SignalGen.m_MaskImage = reader->GetOutput(); m_SignalGen.m_ImageRegion = m_SignalGen.m_MaskImage->GetLargestPossibleRegion(); m_SignalGen.m_ImageSpacing = m_SignalGen.m_MaskImage->GetSpacing(); m_SignalGen.m_ImageOrigin = m_SignalGen.m_MaskImage->GetOrigin(); m_SignalGen.m_ImageDirection = m_SignalGen.m_MaskImage->GetDirection(); MITK_INFO << "Mask image loaded."; } catch(...) { MITK_INFO << "No mask image found."; } setlocale(LC_ALL, currLocale.c_str()); } void mitk::FiberfoxParameters::PrintSelf() { MITK_INFO << "Not implemented :("; } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h index 2ca404962e..5ea3d0b7f0 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h @@ -1,326 +1,328 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef _MITK_FiberfoxParameters_H #define _MITK_FiberfoxParameters_H #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace mitk { class MITKFIBERTRACKING_EXPORT FiberfoxParameters; /** Signal generation */ class MITKFIBERTRACKING_EXPORT SignalGenerationParameters { friend FiberfoxParameters; public: typedef itk::Image ItkFloatImgType; typedef itk::Image ItkUcharImgType; typedef itk::Vector GradientType; typedef std::vector GradientListType; enum CoilSensitivityProfile : int { COIL_CONSTANT, COIL_LINEAR, COIL_EXPONENTIAL }; enum AcquisitionType : int { SingleShotEpi, SpinEcho }; SignalGenerationParameters() : m_AcquisitionType(SignalGenerationParameters::SingleShotEpi) , m_SignalScale(100) , m_tEcho(100) , m_tRep(4000) , m_tLine(1) , m_tInhom(50) , m_ReversePhase(false) , m_PartialFourier(1.0) , m_NoiseVariance(0.001) , m_NumberOfCoils(1) , m_CoilSensitivityProfile(SignalGenerationParameters::COIL_CONSTANT) , m_SimulateKspaceAcquisition(false) , m_AxonRadius(0) , m_DoDisablePartialVolume(false) , m_Spikes(0) , m_SpikeAmplitude(1) , m_KspaceLineOffset(0) , m_EddyStrength(300) , m_Tau(70) , m_CroppingFactor(1) , m_Drift(0.06) , m_DoAddGibbsRinging(false) , m_DoSimulateRelaxation(true) , m_DoAddMotion(false) , m_DoRandomizeMotion(true) , m_DoAddDrift(false) , m_FrequencyMap(nullptr) , m_MaskImage(nullptr) , m_Bvalue(1000) { m_ImageRegion.SetSize(0, 12); m_ImageRegion.SetSize(1, 12); m_ImageRegion.SetSize(2, 3); m_ImageSpacing.Fill(2.0); m_ImageOrigin.Fill(0.0); m_ImageDirection.SetIdentity(); m_Translation.Fill(0.0); m_Rotation.Fill(0.0); SetNumWeightedVolumes(6); } /** input/output image specifications */ itk::ImageRegion<3> m_CroppedRegion; ///< Image size with reduced FOV. itk::ImageRegion<3> m_ImageRegion; ///< Image size. itk::Vector m_ImageSpacing; ///< Image voxel size. itk::Point m_ImageOrigin; ///< Image origin. itk::Matrix m_ImageDirection; ///< Image rotation matrix. /** Other acquisitions parameters */ AcquisitionType m_AcquisitionType; ///< determines k-space trajectory and maximum echo position(s) float m_SignalScale; ///< Scaling factor for output signal (before noise is added). float m_tEcho; ///< Echo time TE. float m_tRep; ///< Echo time TR. float m_tLine; ///< k-space line readout time (dwell time). float m_tInhom; ///< T2' bool m_ReversePhase; ///< If true, the phase readout direction will be inverted (-y instead of y) float m_PartialFourier; ///< Partial fourier factor (0.5-1) float m_NoiseVariance; ///< Variance of complex gaussian noise int m_NumberOfCoils; ///< Number of coils in multi-coil acquisition CoilSensitivityProfile m_CoilSensitivityProfile; ///< Choose between constant, linear or exponential sensitivity profile of the used coils bool m_SimulateKspaceAcquisition;///< Flag to enable/disable k-space acquisition simulation double m_AxonRadius; ///< Determines compartment volume fractions (0 == automatic axon radius estimation) bool m_DoDisablePartialVolume; ///< Disable partial volume effects. Each voxel is either all fiber or all non-fiber. /** Artifacts and other effects */ unsigned int m_Spikes; ///< Number of spikes randomly appearing in the image float m_SpikeAmplitude; ///< amplitude of spikes relative to the largest signal intensity (magnitude of complex) float m_KspaceLineOffset; ///< Causes N/2 ghosts. Larger offset means stronger ghost. float m_EddyStrength; ///< Strength of eddy current induced gradients in mT/m. float m_Tau; ///< Eddy current decay constant (in ms) float m_CroppingFactor; ///< FOV size in y-direction is multiplied by this factor. Causes aliasing artifacts. float m_Drift; ///< Global signal decrease by the end of the acquisition. bool m_DoAddGibbsRinging; ///< Add Gibbs ringing artifact bool m_DoSimulateRelaxation; ///< Add T2 relaxation effects bool m_DoAddMotion; ///< Enable motion artifacts. bool m_DoRandomizeMotion; ///< Toggles between random and linear motion. bool m_DoAddDrift; ///< Add quadratic signal drift. std::vector< bool > m_MotionVolumes; ///< Indicates the image volumes that are affected by motion ///< with positive numbers, inverted logic with negative numbers. itk::Vector m_Translation; ///< Maximum translational motion. itk::Vector m_Rotation; ///< Maximum rotational motion. ItkFloatImgType::Pointer m_FrequencyMap; ///< If != nullptr, distortions are added to the image using this frequency map. ItkUcharImgType::Pointer m_MaskImage; ///< Signal is only genrated inside of the mask image. std::vector< int > GetBaselineIndices(); ///< Returns list of nun-diffusion-weighted image volume indices unsigned int GetFirstBaselineIndex(); ///< Returns index of first non-diffusion-weighted image volume bool IsBaselineIndex(unsigned int idx); ///< Checks if image volume with given index is non-diffusion-weighted volume or not. unsigned int GetNumWeightedVolumes(); ///< Get number of diffusion-weighted image volumes unsigned int GetNumBaselineVolumes(); ///< Get number of non-diffusion-weighted image volumes unsigned int GetNumVolumes(); ///< Get number of baseline and diffusion-weighted image volumes GradientListType GetGradientDirections(); ///< Return gradient direction container mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer GetItkGradientContainer(); GradientType GetGradientDirection(unsigned int i); std::vector< int > GetBvalues(); ///< Returns a vector with all unique b-values (determined by the gradient magnitudes) double GetBvalue(); + void ApplyDirectionMatrix(); protected: unsigned int m_NumGradients; ///< Number of diffusion-weighted image volumes. unsigned int m_NumBaseline; ///< Number of non-diffusion-weighted image volumes. GradientListType m_GradientDirections; ///< Total number of image volumes. double m_Bvalue; ///< Acquisition b-value void SetNumWeightedVolumes(int numGradients); ///< Automaticall calls GenerateGradientHalfShell() afterwards. void SetGradienDirections(GradientListType gradientList); void SetGradienDirections(mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList); void GenerateGradientHalfShell(); ///< Generates half shell of gradient directions (with m_NumGradients non-zero directions) }; /** Fiber generation */ class MITKFIBERTRACKING_EXPORT FiberGenerationParameters { public: enum FiberDistribution { DISTRIBUTE_UNIFORM, // distribute fibers uniformly in the ROIs DISTRIBUTE_GAUSSIAN // distribute fibers using a 2D gaussian }; typedef std::vector< std::vector< mitk::PlanarEllipse::Pointer > > FiducialListType; typedef std::vector< std::vector< unsigned int > > FlipListType; FiberGenerationParameters() : m_Distribution(DISTRIBUTE_UNIFORM) , m_Density(100) , m_Variance(100) , m_Sampling(1) , m_Tension(0) , m_Continuity(0) , m_Bias(0) { m_Rotation.Fill(0.0); m_Translation.Fill(0.0); m_Scale.Fill(1.0); } FiberDistribution m_Distribution; unsigned int m_Density; double m_Variance; double m_Sampling; double m_Tension; double m_Continuity; double m_Bias; mitk::Vector3D m_Rotation; mitk::Vector3D m_Translation; mitk::Vector3D m_Scale; FlipListType m_FlipList; ///< contains flags indicating a flip of the 2D fiber x-coordinates (needed to resolve some unwanted fiber twisting) FiducialListType m_Fiducials; ///< container of the planar ellipses used as fiducials for the fiber generation process }; /** GUI persistence, input, output, ... */ class MITKFIBERTRACKING_EXPORT MiscFiberfoxParameters { public: MiscFiberfoxParameters() : m_ResultNode(DataNode::New()) , m_ParentNode(nullptr) , m_SignalModelString("") , m_ArtifactModelString("") , m_OutputPath("/tmp/") , m_OutputPrefix("fiberfox") , m_AfterSimulationMessage("") , m_BvalsFile("") , m_BvecsFile("") , m_CheckOutputVolumeFractionsBox(false) , m_CheckAdvancedSignalOptionsBox(false) , m_DoAddNoise(false) , m_DoAddGhosts(false) , m_DoAddAliasing(false) , m_DoAddSpikes(false) , m_DoAddEddyCurrents(false) , m_DoAddDistortions(false) , m_MotionVolumesBox("random") , m_CheckRealTimeFibersBox(true) , m_CheckAdvancedFiberOptionsBox(false) , m_CheckConstantRadiusBox(false) , m_CheckIncludeFiducialsBox(true) {} DataNode::Pointer m_ResultNode; ///< Stores resulting image. DataNode::Pointer m_ParentNode; ///< Parent node of result node. std::string m_SignalModelString; ///< Appendet to the name of the result node std::string m_ArtifactModelString; ///< Appendet to the name of the result node std::string m_OutputPath; ///< Image is automatically saved to the specified folder after simulation is finished. std::string m_OutputPrefix; /** Prefix for filename of output files and logfile. */ std::string m_AfterSimulationMessage; ///< Store messages that are displayed after the simulation has finished (e.g. warnings, automatic parameter adjustments etc.) std::string m_BvalsFile; std::string m_BvecsFile; /** member variables that store the check-state of GUI checkboxes */ // image generation bool m_CheckOutputVolumeFractionsBox; bool m_CheckAdvancedSignalOptionsBox; bool m_DoAddNoise; bool m_DoAddGhosts; bool m_DoAddAliasing; bool m_DoAddSpikes; bool m_DoAddEddyCurrents; bool m_DoAddDistortions; std::string m_MotionVolumesBox; // fiber generation bool m_CheckRealTimeFibersBox; bool m_CheckAdvancedFiberOptionsBox; bool m_CheckConstantRadiusBox; bool m_CheckIncludeFiducialsBox; }; /** * \brief Datastructure to manage the Fiberfox signal generation parameters. * */ class MITKFIBERTRACKING_EXPORT FiberfoxParameters { public: typedef itk::Image ItkFloatImgType; typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; typedef DiffusionSignalModel DiffusionModelType; typedef std::vector< DiffusionModelType* > DiffusionModelListType; typedef DiffusionNoiseModel NoiseModelType; FiberfoxParameters(); FiberfoxParameters(const FiberfoxParameters ¶ms); ~FiberfoxParameters(); /** Not templated parameters */ FiberGenerationParameters m_FiberGen; ///< Fiber generation parameters SignalGenerationParameters m_SignalGen; ///< Signal generation parameters MiscFiberfoxParameters m_Misc; ///< GUI realted and I/O parameters /** Templated parameters */ DiffusionModelListType m_FiberModelList; ///< Intra- and inter-axonal compartments. DiffusionModelListType m_NonFiberModelList; ///< Extra-axonal compartments. std::shared_ptr< NoiseModelType > m_NoiseModel; ///< If != nullptr, noise is added to the image. void GenerateGradientHalfShell(); void SetNumWeightedVolumes(int numGradients); ///< Automaticall calls GenerateGradientHalfShell() afterwards. void SetGradienDirections(mitk::SignalGenerationParameters::GradientListType gradientList); void SetGradienDirections(mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList); void SetBvalue(double Bvalue); void UpdateSignalModels(); void ClearFiberParameters(); void ClearSignalParameters(); + void ApplyDirectionMatrix(); void PrintSelf(); ///< Print parameters to stdout. void SaveParameters(std::string filename); ///< Save image generation parameters to .ffp file. void LoadParameters(std::string filename); ///< Load image generation parameters from .ffp file. template< class ParameterType > ParameterType ReadVal(boost::property_tree::ptree::value_type const& v, std::string tag, ParameterType defaultValue, bool essential=false); std::string m_MissingTags; }; } #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp index 0f667d9f6c..b754986684 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp @@ -1,80 +1,81 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include /**Documentation * Test if fiber transfortaiom methods work correctly */ int mitkFiberGenerationTest(int argc, char* argv[]) { omp_set_num_threads(1); MITK_TEST_BEGIN("mitkFiberGenerationTest"); MITK_TEST_CONDITION_REQUIRED(argc==6,"check for input data") try{ mitk::PlanarEllipse::Pointer pf1 = mitk::IOUtil::Load(argv[1]); mitk::PlanarEllipse::Pointer pf2 = mitk::IOUtil::Load(argv[2]); mitk::PlanarEllipse::Pointer pf3 = mitk::IOUtil::Load(argv[3]); mitk::FiberBundle::Pointer uniform = mitk::IOUtil::Load(argv[4]); mitk::FiberBundle::Pointer gaussian = mitk::IOUtil::Load(argv[5]); FiberGenerationParameters parameters; std::vector< mitk::PlanarEllipse::Pointer > fid; fid.push_back(pf1); fid.push_back(pf2); fid.push_back(pf3); std::vector< unsigned int > flip; flip.push_back(0); flip.push_back(0); flip.push_back(0); parameters.m_Fiducials.push_back(fid); parameters.m_FlipList.push_back(flip); parameters.m_Density = 50; parameters.m_Tension = 0; parameters.m_Continuity = 0; parameters.m_Bias = 0; parameters.m_Sampling = 1; parameters.m_Variance = 0.1; // check uniform fiber distribution { itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); parameters.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; filter->SetParameters(parameters); + filter->SetFixSeed(true); filter->Update(); std::vector< mitk::FiberBundle::Pointer > fiberBundles = filter->GetFiberBundles(); MITK_TEST_CONDITION_REQUIRED(uniform->Equals(fiberBundles.at(0)),"check uniform bundle") } // check gaussian fiber distribution { itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); parameters.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN; filter->SetParameters(parameters); - filter->SetParameters(parameters); + filter->SetFixSeed(true); filter->Update(); std::vector< mitk::FiberBundle::Pointer > fiberBundles = filter->GetFiberBundles(); MITK_TEST_CONDITION_REQUIRED(gaussian->Equals(fiberBundles.at(0)),"check gaussian bundle") } } catch(...) { return EXIT_FAILURE; } // always end with this! MITK_TEST_END(); } diff --git a/Modules/ImageStatistics/Testing/files.cmake b/Modules/ImageStatistics/Testing/files.cmake index 41431d2af0..2be45c6a95 100644 --- a/Modules/ImageStatistics/Testing/files.cmake +++ b/Modules/ImageStatistics/Testing/files.cmake @@ -1,11 +1,12 @@ set(MODULE_TESTS mitkImageStatisticsCalculatorTest.cpp mitkPointSetStatisticsCalculatorTest.cpp mitkPointSetDifferenceStatisticsCalculatorTest.cpp mitkImageStatisticsTextureAnalysisTest.cpp + mitkImageStatisticsContainerManagerTest.cpp ) set(MODULE_CUSTOM_TESTS mitkImageStatisticsHotspotTest.cpp # mitkMultiGaussianTest.cpp # TODO: activate test to generate new test cases for mitkImageStatisticsHotspotTest ) diff --git a/Modules/ImageStatistics/Testing/mitkImageStatisticsCalculatorTest.cpp b/Modules/ImageStatistics/Testing/mitkImageStatisticsCalculatorTest.cpp index 4efe996173..f4695678ee 100644 --- a/Modules/ImageStatistics/Testing/mitkImageStatisticsCalculatorTest.cpp +++ b/Modules/ImageStatistics/Testing/mitkImageStatisticsCalculatorTest.cpp @@ -1,1767 +1,1836 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkImageStatisticsCalculator.h" #include #include #include #include #include #include #include #include #include #include #include +#include /** * \brief Test class for mitkImageStatisticsCalculator * * This test covers: * - instantiation of an ImageStatisticsCalculator class * - correctness of statistics when using PlanarFigures for masking */ class mitkImageStatisticsCalculatorTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkImageStatisticsCalculatorTestSuite); MITK_TEST(TestUninitializedImage); MITK_TEST(TestCase1); MITK_TEST(TestCase2); MITK_TEST(TestCase3); MITK_TEST(TestCase4); MITK_TEST(TestCase5); MITK_TEST(TestCase6); MITK_TEST(TestCase7); MITK_TEST(TestCase8); MITK_TEST(TestCase9); MITK_TEST(TestCase10); MITK_TEST(TestCase11); MITK_TEST(TestCase12); MITK_TEST(TestImageMaskingEmpty); MITK_TEST(TestImageMaskingNonEmpty); MITK_TEST(TestRecomputeOnModifiedMask); MITK_TEST(TestPic3DStatistics); MITK_TEST(TestPic3DAxialPlanarFigureMaskStatistics); MITK_TEST(TestPic3DSagittalPlanarFigureMaskStatistics); MITK_TEST(TestPic3DCoronalPlanarFigureMaskStatistics); MITK_TEST(TestPic3DImageMaskStatistics_label1); MITK_TEST(TestPic3DImageMaskStatistics_label2); MITK_TEST(TestPic3DIgnorePixelValueMaskStatistics); MITK_TEST(TestPic3DSecondaryMaskStatistics); MITK_TEST(TestUS4DCylStatistics_time1); MITK_TEST(TestUS4DCylAxialPlanarFigureMaskStatistics_time1); MITK_TEST(TestUS4DCylSagittalPlanarFigureMaskStatistics_time1); MITK_TEST(TestUS4DCylCoronalPlanarFigureMaskStatistics_time1); MITK_TEST(TestUS4DCylImageMaskStatistics_time1_label_1); MITK_TEST(TestUS4DCylImageMaskStatistics_time2_label_1); MITK_TEST(TestUS4DCylImageMaskStatistics_time1_label_2); MITK_TEST(TestUS4DCylIgnorePixelValueMaskStatistics_time1); MITK_TEST(TestUS4DCylSecondaryMaskStatistics_time1); CPPUNIT_TEST_SUITE_END(); public: void setUp() override; void tearDown() override; void TestUninitializedImage(); void TestCase1(); void TestCase2(); void TestCase3(); void TestCase4(); void TestCase5(); void TestCase6(); void TestCase7(); void TestCase8(); void TestCase9(); void TestCase10(); void TestCase11(); void TestCase12(); void TestImageMaskingEmpty(); void TestImageMaskingNonEmpty(); void TestRecomputeOnModifiedMask(); void TestPic3DStatistics(); void TestPic3DAxialPlanarFigureMaskStatistics(); void TestPic3DSagittalPlanarFigureMaskStatistics(); void TestPic3DCoronalPlanarFigureMaskStatistics(); void TestPic3DImageMaskStatistics_label1(); void TestPic3DImageMaskStatistics_label2(); void TestPic3DIgnorePixelValueMaskStatistics(); void TestPic3DSecondaryMaskStatistics(); void TestUS4DCylStatistics_time1(); void TestUS4DCylAxialPlanarFigureMaskStatistics_time1(); void TestUS4DCylSagittalPlanarFigureMaskStatistics_time1(); void TestUS4DCylCoronalPlanarFigureMaskStatistics_time1(); void TestUS4DCylImageMaskStatistics_time1_label_1(); void TestUS4DCylImageMaskStatistics_time2_label_1(); void TestUS4DCylImageMaskStatistics_time1_label_2(); void TestUS4DCylIgnorePixelValueMaskStatistics_time1(); void TestUS4DCylSecondaryMaskStatistics_time1(); void TestDifferentNBinsForHistogramStatistics(); void TestDifferentBinSizeForHistogramStatistic(); void TestSwitchFromBinSizeToNBins(); void TestSwitchFromNBinsToBinSize(); private: - mitk::Image::Pointer m_TestImage; + mitk::Image::ConstPointer m_TestImage; - mitk::Image::Pointer m_Pic3DImage; + mitk::Image::ConstPointer m_Pic3DImage; mitk::Image::Pointer m_Pic3DImageMask; mitk::Image::Pointer m_Pic3DImageMask2; mitk::PlanarFigure::Pointer m_Pic3DPlanarFigureAxial; mitk::PlanarFigure::Pointer m_Pic3DPlanarFigureSagittal; mitk::PlanarFigure::Pointer m_Pic3DPlanarFigureCoronal; - mitk::Image::Pointer m_US4DImage; + mitk::Image::ConstPointer m_US4DImage; mitk::Image::Pointer m_US4DImageMask; mitk::Image::Pointer m_US4DImageMask2; mitk::PlanarFigure::Pointer m_US4DPlanarFigureAxial; mitk::PlanarFigure::Pointer m_US4DPlanarFigureSagittal; mitk::PlanarFigure::Pointer m_US4DPlanarFigureCoronal; mitk::PlaneGeometry::Pointer m_Geometry; // calculate statistics for the given image and planarpolygon - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer ComputeStatistics( mitk::Image::Pointer image, + const mitk::ImageStatisticsContainer::Pointer ComputeStatistics( mitk::Image::ConstPointer image, mitk::PlanarFigure::Pointer polygon ); // calculate statistics for the given image and mask - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer ComputeStatistics( mitk::Image::Pointer image, + const mitk::ImageStatisticsContainer::Pointer ComputeStatistics(mitk::Image::ConstPointer image, mitk::Image::Pointer image_mask ); // universal function to calculate statistics - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer ComputeStatisticsNew(mitk::Image::Pointer image, - int timeStep=0, + const mitk::ImageStatisticsContainer::Pointer ComputeStatisticsNew(mitk::Image::ConstPointer image, mitk::MaskGenerator::Pointer maskGen=nullptr, mitk::MaskGenerator::Pointer secondardMaskGen=nullptr, unsigned short label=1); - void VerifyStatistics(mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer stats, + void VerifyStatistics(mitk::ImageStatisticsContainer::StatisticsObject stats, double testMean, double testSD, double testMedian=0); - void VerifyStatistics(mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer stats, - long N, + void VerifyStatistics(mitk::ImageStatisticsContainer::StatisticsObject stats, + unsigned long N, double mean, double MPP, double median, double skewness, double kurtosis, double uniformity, double UPP, double variance, double stdev, double min, double max, double RMS, double entropy, vnl_vector minIndex, vnl_vector maxIndex); }; void mitkImageStatisticsCalculatorTestSuite::tearDown() { m_TestImage = nullptr; m_Pic3DImage = nullptr; m_Pic3DImageMask = nullptr; m_Pic3DImageMask2 = nullptr; m_Pic3DPlanarFigureAxial = nullptr; m_Pic3DPlanarFigureSagittal = nullptr; m_Pic3DPlanarFigureCoronal = nullptr; m_US4DImage = nullptr; m_US4DImageMask = nullptr; m_US4DImageMask2 = nullptr; m_US4DPlanarFigureAxial = nullptr; m_US4DPlanarFigureSagittal = nullptr; m_US4DPlanarFigureCoronal = nullptr; m_Geometry = nullptr; } void mitkImageStatisticsCalculatorTestSuite::setUp() { std::string filename = this->GetTestDataFilePath("ImageStatisticsTestData/testimage.dcm"); std::string Pic3DFile = this->GetTestDataFilePath("Pic3D.nrrd"); std::string Pic3DImageMaskFile = this->GetTestDataFilePath("ImageStatisticsTestData/Pic3D-labels.nrrd"); std::string Pic3DImageMaskFile2 = this->GetTestDataFilePath("ImageStatisticsTestData/Pic3D-labels2.nrrd"); std::string Pic3DAxialPlanarFigureFile = this->GetTestDataFilePath("ImageStatisticsTestData/Pic3DAxialPlanarFigure.pf"); std::string Pic3DSagittalPlanarFigureFile = this->GetTestDataFilePath("ImageStatisticsTestData/Pic3DSagittalPlanarFigure.pf"); std::string Pic3DCoronalPlanarFigureFile = this->GetTestDataFilePath("ImageStatisticsTestData/Pic3DCoronalPlanarFigure.pf"); std::string US4DFile = this->GetTestDataFilePath("US4DCyl.nrrd"); std::string US4DImageMaskFile = this->GetTestDataFilePath("ImageStatisticsTestData/US4D-labels.nrrd"); std::string US4DImageMaskFile2 = this->GetTestDataFilePath("ImageStatisticsTestData/US4D-labels2.nrrd"); std::string US4DAxialPlanarFigureFile = this->GetTestDataFilePath("ImageStatisticsTestData/US4DAxialPlanarFigure.pf"); std::string US4DSagittalPlanarFigureFile = this->GetTestDataFilePath("ImageStatisticsTestData/US4DSagittalPlanarFigure.pf"); std::string US4DCoronalPlanarFigureFile = this->GetTestDataFilePath("ImageStatisticsTestData/US4DCoronalPlanarFigure.pf"); if (filename.empty() || Pic3DFile.empty() || Pic3DImageMaskFile.empty() || Pic3DAxialPlanarFigureFile.empty() || Pic3DSagittalPlanarFigureFile.empty() || Pic3DCoronalPlanarFigureFile.empty() || US4DFile.empty() || US4DImageMaskFile.empty() || US4DAxialPlanarFigureFile.empty() || US4DSagittalPlanarFigureFile.empty() || US4DCoronalPlanarFigureFile.empty()) { MITK_TEST_FAILED_MSG( << "Could not find test file" ) } MITK_TEST_OUTPUT(<< "Loading test image '" << filename << "'") m_TestImage = mitk::IOUtil::Load(filename); MITK_TEST_CONDITION_REQUIRED( m_TestImage.IsNotNull(), "Loaded an mitk::Image" ); m_Geometry = m_TestImage->GetSlicedGeometry()->GetPlaneGeometry(0); MITK_TEST_CONDITION_REQUIRED( m_Geometry.IsNotNull(), "Getting image geometry" ); m_Pic3DImage = mitk::IOUtil::Load(Pic3DFile); MITK_TEST_CONDITION_REQUIRED( m_Pic3DImage.IsNotNull(), "Loaded Pic3D" ); m_Pic3DImageMask = mitk::IOUtil::Load(Pic3DImageMaskFile); MITK_TEST_CONDITION_REQUIRED( m_Pic3DImageMask.IsNotNull(), "Loaded Pic3D image mask" ); m_Pic3DImageMask2 = mitk::IOUtil::Load(Pic3DImageMaskFile2); MITK_TEST_CONDITION_REQUIRED( m_Pic3DImageMask2.IsNotNull(), "Loaded Pic3D image secondary mask" ); m_Pic3DPlanarFigureAxial = mitk::IOUtil::Load(Pic3DAxialPlanarFigureFile); MITK_TEST_CONDITION_REQUIRED( m_Pic3DPlanarFigureAxial.IsNotNull(), "Loaded Pic3D axial planarFigure" ); m_Pic3DPlanarFigureSagittal = mitk::IOUtil::Load(Pic3DSagittalPlanarFigureFile); MITK_TEST_CONDITION_REQUIRED( m_Pic3DPlanarFigureSagittal.IsNotNull(), "Loaded Pic3D sagittal planarFigure" ); m_Pic3DPlanarFigureCoronal = mitk::IOUtil::Load(Pic3DCoronalPlanarFigureFile); MITK_TEST_CONDITION_REQUIRED( m_Pic3DPlanarFigureCoronal.IsNotNull(), "Loaded Pic3D coronal planarFigure" ); m_US4DImage = mitk::IOUtil::Load(US4DFile); MITK_TEST_CONDITION_REQUIRED( m_US4DImage.IsNotNull(), "Loaded US4D" ); m_US4DImageMask = mitk::IOUtil::Load(US4DImageMaskFile); MITK_TEST_CONDITION_REQUIRED( m_US4DImageMask.IsNotNull(), "Loaded US4D image mask" ); m_US4DImageMask2 = mitk::IOUtil::Load(US4DImageMaskFile2); MITK_TEST_CONDITION_REQUIRED( m_US4DImageMask2.IsNotNull(), "Loaded US4D image mask2" ); m_US4DPlanarFigureAxial = mitk::IOUtil::Load(US4DAxialPlanarFigureFile); MITK_TEST_CONDITION_REQUIRED( m_US4DPlanarFigureAxial.IsNotNull(), "Loaded US4D axial planarFigure" ); m_US4DPlanarFigureSagittal = mitk::IOUtil::Load(US4DSagittalPlanarFigureFile); MITK_TEST_CONDITION_REQUIRED( m_US4DPlanarFigureSagittal.IsNotNull(), "Loaded US4D sagittal planarFigure" ); m_US4DPlanarFigureCoronal = mitk::IOUtil::Load(US4DCoronalPlanarFigureFile); MITK_TEST_CONDITION_REQUIRED( m_US4DPlanarFigureCoronal.IsNotNull(), "Loaded US4D coronal planarFigure" ); } void mitkImageStatisticsCalculatorTestSuite::TestCase1() { /***************************** * one whole white pixel * -> mean of 255 expected ******************************/ MITK_INFO << std::endl << "Test case 1:-----------------------------------------------------------------------------------"; mitk::PlanarPolygon::Pointer figure1 = mitk::PlanarPolygon::New(); figure1->SetPlaneGeometry( m_Geometry ); mitk::Point2D pnt1; pnt1[0] = 10.5 ; pnt1[1] = 3.5; figure1->PlaceFigure( pnt1 ); mitk::Point2D pnt2; pnt2[0] = 9.5; pnt2[1] = 3.5; figure1->SetControlPoint( 1, pnt2, true ); mitk::Point2D pnt3; pnt3[0] = 9.5; pnt3[1] = 4.5; figure1->SetControlPoint( 2, pnt3, true ); mitk::Point2D pnt4; pnt4[0] = 10.5; pnt4[1] = 4.5; figure1->SetControlPoint( 3, pnt4, true ); figure1->GetPolyLine(0); - this->VerifyStatistics(ComputeStatistics(m_TestImage, figure1.GetPointer()), 255.0, 0.0, 255.0); + auto statisticsContainer = ComputeStatistics(m_TestImage, figure1.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 255.0, 0.0, 255.0); } void mitkImageStatisticsCalculatorTestSuite::TestCase2() { /***************************** * half pixel in x-direction (white) * -> mean of 255 expected ******************************/ MITK_INFO << std::endl << "Test case 2:-----------------------------------------------------------------------------------"; mitk::PlanarPolygon::Pointer figure1 = mitk::PlanarPolygon::New(); figure1->SetPlaneGeometry( m_Geometry ); mitk::Point2D pnt1; pnt1[0] = 10.0 ; pnt1[1] = 3.5; figure1->PlaceFigure( pnt1 ); mitk::Point2D pnt2; pnt2[0] = 9.5; pnt2[1] = 3.5; figure1->SetControlPoint( 1, pnt2, true ); mitk::Point2D pnt3; pnt3[0] = 9.5; pnt3[1] = 4.5; figure1->SetControlPoint( 2, pnt3, true ); mitk::Point2D pnt4; pnt4[0] = 10.0; pnt4[1] = 4.5; figure1->SetControlPoint( 3, pnt4, true ); figure1->GetPolyLine(0); - this->VerifyStatistics(ComputeStatistics(m_TestImage, figure1.GetPointer()), 255.0, 0.0, 255.0); + auto statisticsContainer = ComputeStatistics(m_TestImage, figure1.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 255.0, 0.0, 255.0); } void mitkImageStatisticsCalculatorTestSuite::TestCase3() { /***************************** * half pixel in diagonal-direction (white) * -> mean of 255 expected ******************************/ MITK_INFO << std::endl << "Test case 3:-----------------------------------------------------------------------------------"; mitk::PlanarPolygon::Pointer figure1 = mitk::PlanarPolygon::New(); figure1->SetPlaneGeometry( m_Geometry ); mitk::Point2D pnt1; pnt1[0] = 10.5 ; pnt1[1] = 3.5; figure1->PlaceFigure( pnt1 ); mitk::Point2D pnt2; pnt2[0] = 9.5; pnt2[1] = 3.5; figure1->SetControlPoint( 1, pnt2, true ); mitk::Point2D pnt3; pnt3[0] = 9.5; pnt3[1] = 4.5; figure1->SetControlPoint( 2, pnt3, true ); figure1->GetPolyLine(0); - this->VerifyStatistics(ComputeStatistics(m_TestImage, figure1.GetPointer()), 255.0, 0.0, 255.0); + auto statisticsContainer = ComputeStatistics(m_TestImage, figure1.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 255.0, 0.0, 255.0); } void mitkImageStatisticsCalculatorTestSuite::TestCase4() { /***************************** * one pixel (white) + 2 half pixels (white) + 1 half pixel (black) * -> mean of 191.25 expected ******************************/ MITK_INFO << std::endl << "Test case 4:-----------------------------------------------------------------------------------"; mitk::PlanarPolygon::Pointer figure1 = mitk::PlanarPolygon::New(); figure1->SetPlaneGeometry( m_Geometry ); mitk::Point2D pnt1; pnt1[0] = 1.1; pnt1[1] = 1.1; figure1->PlaceFigure( pnt1 ); mitk::Point2D pnt2; pnt2[0] = 2.0; pnt2[1] = 2.0; figure1->SetControlPoint( 1, pnt2, true ); mitk::Point2D pnt3; pnt3[0] = 3.0; pnt3[1] = 1.0; figure1->SetControlPoint( 2, pnt3, true ); mitk::Point2D pnt4; pnt4[0] = 2.0; pnt4[1] = 0.0; figure1->SetControlPoint( 3, pnt4, true ); figure1->GetPolyLine(0); - this->VerifyStatistics(ComputeStatistics(m_TestImage, figure1.GetPointer()), 191.25, 110.41, 242.250); + auto statisticsContainer = ComputeStatistics(m_TestImage, figure1.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 191.25, 110.41, 242.250); } void mitkImageStatisticsCalculatorTestSuite::TestCase5() { /***************************** * whole pixel (white) + half pixel (gray) in x-direction * -> mean of 191.5 expected ******************************/ MITK_INFO << std::endl << "Test case 5:-----------------------------------------------------------------------------------"; mitk::PlanarPolygon::Pointer figure1 = mitk::PlanarPolygon::New(); figure1->SetPlaneGeometry( m_Geometry ); mitk::Point2D pnt1; pnt1[0] = 11.0; pnt1[1] = 3.5; figure1->PlaceFigure( pnt1 ); mitk::Point2D pnt2; pnt2[0] = 9.5; pnt2[1] = 3.5; figure1->SetControlPoint( 1, pnt2, true ); mitk::Point2D pnt3; pnt3[0] = 9.5; pnt3[1] = 4.5; figure1->SetControlPoint( 2, pnt3, true ); mitk::Point2D pnt4; pnt4[0] = 11.0; pnt4[1] = 4.5; figure1->SetControlPoint( 3, pnt4, true ); figure1->GetPolyLine(0); - this->VerifyStatistics(ComputeStatistics(m_TestImage, figure1.GetPointer()), 191.50, 63.50, 134.340); + auto statisticsContainer = ComputeStatistics(m_TestImage, figure1.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 191.50, 63.50, 134.340); } void mitkImageStatisticsCalculatorTestSuite::TestCase6() { /***************************** * quarter pixel (black) + whole pixel (white) + half pixel (gray) in x-direction * -> mean of 191.5 expected ******************************/ MITK_INFO << std::endl << "Test case 6:-----------------------------------------------------------------------------------"; mitk::PlanarPolygon::Pointer figure1 = mitk::PlanarPolygon::New(); figure1->SetPlaneGeometry( m_Geometry ); mitk::Point2D pnt1; pnt1[0] = 11.0; pnt1[1] = 3.5; figure1->PlaceFigure( pnt1 ); mitk::Point2D pnt2; pnt2[0] = 9.25; pnt2[1] = 3.5; figure1->SetControlPoint( 1, pnt2, true ); mitk::Point2D pnt3; pnt3[0] = 9.25; pnt3[1] = 4.5; figure1->SetControlPoint( 2, pnt3, true ); mitk::Point2D pnt4; pnt4[0] = 11.0; pnt4[1] = 4.5; figure1->SetControlPoint( 3, pnt4, true ); figure1->GetPolyLine(0); - this->VerifyStatistics(ComputeStatistics(m_TestImage, figure1.GetPointer()), 191.5, 63.50, 134.340); + auto statisticsContainer = ComputeStatistics(m_TestImage, figure1.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 191.5, 63.50, 134.340); } void mitkImageStatisticsCalculatorTestSuite::TestCase7() { /***************************** * half pixel (black) + whole pixel (white) + half pixel (gray) in x-direction * -> mean of 127.66 expected ******************************/ MITK_INFO << std::endl << "Test case 7:-----------------------------------------------------------------------------------"; mitk::PlanarPolygon::Pointer figure1 = mitk::PlanarPolygon::New(); figure1->SetPlaneGeometry( m_Geometry ); mitk::Point2D pnt1; pnt1[0] = 11.0; pnt1[1] = 3.5; figure1->PlaceFigure( pnt1 ); mitk::Point2D pnt2; pnt2[0] = 9.0; pnt2[1] = 3.5; figure1->SetControlPoint( 1, pnt2, true ); mitk::Point2D pnt3; pnt3[0] = 9.0; pnt3[1] = 4.0; figure1->SetControlPoint( 2, pnt3, true ); mitk::Point2D pnt4; pnt4[0] = 11.0; pnt4[1] = 4.0; figure1->SetControlPoint( 3, pnt4, true ); figure1->GetPolyLine(0); - this->VerifyStatistics(ComputeStatistics(m_TestImage, figure1.GetPointer()), 127.66, 104.1, 140.250); + auto statisticsContainer = ComputeStatistics(m_TestImage, figure1.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 127.66, 104.1, 140.250); } void mitkImageStatisticsCalculatorTestSuite::TestCase8() { /***************************** * whole pixel (gray) * -> mean of 128 expected ******************************/ MITK_INFO << std::endl << "Test case 8:-----------------------------------------------------------------------------------"; mitk::PlanarPolygon::Pointer figure2 = mitk::PlanarPolygon::New(); figure2->SetPlaneGeometry( m_Geometry ); mitk::Point2D pnt1; pnt1[0] = 11.5; pnt1[1] = 10.5; figure2->PlaceFigure( pnt1 ); mitk::Point2D pnt2; pnt2[0] = 11.5; pnt2[1] = 11.5; figure2->SetControlPoint( 1, pnt2, true ); mitk::Point2D pnt3; pnt3[0] = 12.5; pnt3[1] = 11.5; figure2->SetControlPoint( 2, pnt3, true ); mitk::Point2D pnt4; pnt4[0] = 12.5; pnt4[1] = 10.5; figure2->SetControlPoint( 3, pnt4, true ); figure2->GetPolyLine(0); - this->VerifyStatistics(ComputeStatistics(m_TestImage, figure2.GetPointer()), 128.0, 0.0, 128.0); + auto statisticsContainer = ComputeStatistics(m_TestImage, figure2.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 128.0, 0.0, 128.0); } void mitkImageStatisticsCalculatorTestSuite::TestCase9() { /***************************** * whole pixel (gray) + half pixel (white) in y-direction * -> mean of 191.5 expected ******************************/ MITK_INFO << std::endl << "Test case 9:-----------------------------------------------------------------------------------"; mitk::PlanarPolygon::Pointer figure2 = mitk::PlanarPolygon::New(); figure2->SetPlaneGeometry( m_Geometry ); mitk::Point2D pnt1; pnt1[0] = 11.5; pnt1[1] = 10.5; figure2->PlaceFigure( pnt1 ); mitk::Point2D pnt2; pnt2[0] = 11.5; pnt2[1] = 12.0; figure2->SetControlPoint( 1, pnt2, true ); mitk::Point2D pnt3; pnt3[0] = 12.5; pnt3[1] = 12.0; figure2->SetControlPoint( 2, pnt3, true ); mitk::Point2D pnt4; pnt4[0] = 12.5; pnt4[1] = 10.5; figure2->SetControlPoint( 3, pnt4, true ); figure2->GetPolyLine(0); - this->VerifyStatistics(ComputeStatistics(m_TestImage, figure2.GetPointer()), 191.5, 63.50, 134.340); + auto statisticsContainer = ComputeStatistics(m_TestImage, figure2.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 191.5, 63.50, 134.340); } void mitkImageStatisticsCalculatorTestSuite::TestCase10() { /***************************** * 2 whole pixel (white) + 2 whole pixel (black) in y-direction * -> mean of 127.66 expected ******************************/ MITK_INFO << std::endl << "Test case 10:-----------------------------------------------------------------------------------"; mitk::PlanarPolygon::Pointer figure2 = mitk::PlanarPolygon::New(); figure2->SetPlaneGeometry( m_Geometry ); mitk::Point2D pnt1; pnt1[0] = 11.5; pnt1[1] = 10.5; figure2->PlaceFigure( pnt1 ); mitk::Point2D pnt2; pnt2[0] = 11.5; pnt2[1] = 13.5; figure2->SetControlPoint( 1, pnt2, true ); mitk::Point2D pnt3; pnt3[0] = 12.5; pnt3[1] = 13.5; figure2->SetControlPoint( 2, pnt3, true ); mitk::Point2D pnt4; pnt4[0] = 12.5; pnt4[1] = 10.5; figure2->SetControlPoint( 3, pnt4, true ); figure2->GetPolyLine(0); - this->VerifyStatistics(ComputeStatistics(m_TestImage, figure2.GetPointer()), 127.66, 104.1, 140.250); + auto statisticsContainer = ComputeStatistics(m_TestImage, figure2.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 127.66, 104.1, 140.250); } void mitkImageStatisticsCalculatorTestSuite::TestCase11() { /***************************** * 9 whole pixels (white) + 3 half pixels (white) * + 3 whole pixel (black) [ + 3 slightly less than half pixels (black)] * -> mean of 204.0 expected ******************************/ MITK_INFO << std::endl << "Test case 11:-----------------------------------------------------------------------------------"; mitk::PlanarPolygon::Pointer figure2 = mitk::PlanarPolygon::New(); figure2->SetPlaneGeometry( m_Geometry ); mitk::Point2D pnt1; pnt1[0] = 0.5; pnt1[1] = 0.5; figure2->PlaceFigure( pnt1 ); mitk::Point2D pnt2; pnt2[0] = 3.5; pnt2[1] = 3.5; figure2->SetControlPoint( 1, pnt2, true ); mitk::Point2D pnt3; pnt3[0] = 8.4999; pnt3[1] = 3.5; figure2->SetControlPoint( 2, pnt3, true ); mitk::Point2D pnt4; pnt4[0] = 5.4999; pnt4[1] = 0.5; figure2->SetControlPoint( 3, pnt4, true ); figure2->GetPolyLine(0); - this->VerifyStatistics(ComputeStatistics(m_TestImage, figure2.GetPointer()), 204.0, 102.00, 242.250); + auto statisticsContainer = ComputeStatistics(m_TestImage, figure2.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 204.0, 102.00, 242.250); } void mitkImageStatisticsCalculatorTestSuite::TestCase12() { /***************************** * half pixel (white) + whole pixel (white) + half pixel (black) * -> mean of 212.66 expected ******************************/ MITK_INFO << std::endl << "Test case 12:-----------------------------------------------------------------------------------"; mitk::PlanarPolygon::Pointer figure2 = mitk::PlanarPolygon::New(); figure2->SetPlaneGeometry( m_Geometry ); mitk::Point2D pnt1; pnt1[0] = 9.5; pnt1[1] = 0.5; figure2->PlaceFigure( pnt1 ); mitk::Point2D pnt2; pnt2[0] = 9.5; pnt2[1] = 2.5; figure2->SetControlPoint( 1, pnt2, true ); mitk::Point2D pnt3; pnt3[0] = 11.5; pnt3[1] = 2.5; figure2->SetControlPoint( 2, pnt3, true ); figure2->GetPolyLine(0); - this->VerifyStatistics(ComputeStatistics(m_TestImage, figure2.GetPointer()), 212.66, 59.860, 248.640); + auto statisticsContainer = ComputeStatistics(m_TestImage, figure2.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 212.66, 59.860, 248.640); } void mitkImageStatisticsCalculatorTestSuite::TestImageMaskingEmpty() { MITK_INFO << std::endl << "TestImageMaskingEmpty:-----------------------------------------------------------------------------------"; - mitk::Image::Pointer mask_image = mitk::ImageGenerator::GenerateImageFromReference( m_TestImage, 0 ); + mitk::Image::Pointer mask_image = mitk::ImageGenerator::GenerateImageFromReference( m_TestImage->Clone(), 0 ); - this->VerifyStatistics( ComputeStatistics( m_TestImage, mask_image ), -21474836.480, -21474836.480, -21474836.480); // empty statisticsContainer (default values) + auto statisticsContainer = ComputeStatistics( m_TestImage, mask_image ); + // test if no statisticsContainer for timestep 0 exists + MITK_TEST_CONDITION(!statisticsContainer->TimeStepExists(0), "No statistics for TimeStep 0 does exist."); + MITK_TEST_FOR_EXCEPTION(mitk::Exception, statisticsContainer->GetStatisticsForTimeStep(0)); } void mitkImageStatisticsCalculatorTestSuite::TestImageMaskingNonEmpty() { MITK_INFO << std::endl << "TestImageMaskingNonEmpty:-----------------------------------------------------------------------------------"; - mitk::Image::Pointer mask_image = mitk::ImageGenerator::GenerateImageFromReference( m_TestImage, 0 ); + mitk::Image::Pointer mask_image = mitk::ImageGenerator::GenerateImageFromReference( m_TestImage->Clone(), 0 ); // activate voxel in the mask image if (mask_image->GetDimension() == 3) { std::vector< itk::Index<3U> > activated_indices; itk::Index<3U> index = { { 10, 8, 0 } }; activated_indices.push_back(index); index[0] = 9; index[1] = 8; index[2] = 0; activated_indices.push_back(index); index[0] = 9; index[1] = 7; index[2] = 0; activated_indices.push_back(index); index[0] = 10; index[1] = 7; index[2] = 0; activated_indices.push_back(index); std::vector< itk::Index<3U> >::const_iterator indexIter = activated_indices.begin(); mitk::ImagePixelWriteAccessor< unsigned char, 3> writeAccess(mask_image); while (indexIter != activated_indices.end()) { writeAccess.SetPixelByIndex((*indexIter++), 1); } } if (mask_image->GetDimension() == 4) { std::vector< itk::Index<4U> > activated_indices; itk::Index<4U> index = { { 10, 8, 0, 0 } }; activated_indices.push_back(index); index[0] = 9; index[1] = 8; index[2] = 0; index[3] = 0; activated_indices.push_back(index); index[0] = 9; index[1] = 7; index[2] = 0; index[3] = 0; activated_indices.push_back(index); index[0] = 10; index[1] = 7; index[2] = 0; index[3] = 0; activated_indices.push_back(index); std::vector< itk::Index<4U> >::const_iterator indexIter = activated_indices.begin(); mitk::ImagePixelWriteAccessor< unsigned char, 4> writeAccess(mask_image); while (indexIter != activated_indices.end()) { writeAccess.SetPixelByIndex((*indexIter++), 1); } } - this->VerifyStatistics( ComputeStatistics( m_TestImage, mask_image ), 127.5, 127.5, 12.750); + auto statisticsContainer = ComputeStatistics(m_TestImage, mask_image); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + + this->VerifyStatistics(statisticsObjectTimestep0, 127.5, 127.5, 12.750); } void mitkImageStatisticsCalculatorTestSuite::TestRecomputeOnModifiedMask() { MITK_INFO << std::endl << "TestRecomputeOnModifiedMask:-----------------------------------------------------------------------------------"; - mitk::Image::Pointer mask_image = mitk::ImageGenerator::GenerateImageFromReference( m_TestImage, 0 ); + mitk::Image::Pointer mask_image = mitk::ImageGenerator::GenerateImageFromReference( m_TestImage->Clone(), 0 ); mitk::ImageStatisticsCalculator::Pointer statisticsCalculator = mitk::ImageStatisticsCalculator::New(); statisticsCalculator->SetInputImage( m_TestImage ); mitk::ImageMaskGenerator::Pointer imgMaskGen = mitk::ImageMaskGenerator::New(); imgMaskGen->SetImageMask(mask_image); statisticsCalculator->SetMask(imgMaskGen.GetPointer()); - this->VerifyStatistics( statisticsCalculator->GetStatistics(), -21474836.480, -21474836.480, -21474836.480); + auto statisticsContainer = statisticsCalculator->GetStatistics(); + + // test if no statisticsContainer for timestep 0 exists + MITK_TEST_CONDITION(!statisticsContainer->TimeStepExists(0), "No statistics for TimeStep 0 does exist."); + MITK_TEST_FOR_EXCEPTION(mitk::Exception, statisticsContainer->GetStatisticsForTimeStep(0)); // activate voxel in the mask image if (mask_image->GetDimension() == 3) { itk::Index<3U> test_index = { { 11, 8, 0 } }; mitk::ImagePixelWriteAccessor< unsigned char, 3> writeAccess(mask_image); writeAccess.SetPixelByIndex(test_index, 1); } if (mask_image->GetDimension() == 4) { itk::Index<4U> test_index = { { 11, 8, 0, 0 } }; mitk::ImagePixelWriteAccessor< unsigned char, 4> writeAccess(mask_image); writeAccess.SetPixelByIndex(test_index, 1); } + //Delete if T25625 has been resolved + imgMaskGen->Modified(); - mask_image->Modified(); + statisticsContainer = statisticsCalculator->GetStatistics(); - mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer stat = statisticsCalculator->GetStatistics(); - - this->VerifyStatistics( stat, 128.0, 0.0, 128.0); - MITK_TEST_CONDITION( stat->GetN() == 1, "Calculated mask voxel count '" << stat->GetN() << "' is equal to the desired value '" << 1 << "'" ); + MITK_TEST_CONDITION(statisticsContainer->TimeStepExists(0), "Statistics for TimeStep 0 does exist."); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); + this->VerifyStatistics(statisticsObjectTimestep0, 128.0, 0.0, 128.0); + auto numberOfVoxels = statisticsObjectTimestep0.GetValueConverted( + mitk::ImageStatisticsConstants::NUMBEROFVOXELS()); + MITK_TEST_CONDITION(numberOfVoxels == 1, "Calculated mask voxel count '" << numberOfVoxels << "' is equal to the desired value '" << 1 << "'" ); } void mitkImageStatisticsCalculatorTestSuite::TestPic3DStatistics() { MITK_INFO << std::endl << "Test plain Pic3D:-----------------------------------------------------------------------------------"; - long expected_N = 3211264; + unsigned long expected_N = 3211264; double expected_mean = -365.80015345982144; double expected_MPP = 111.80226129535752; double expected_median = -105.16000366210938; double expected_skewness = -0.26976612134147004; double expected_kurtosis = 1.4655017209571437; double expected_uniformity = 0.06087994379480554; double expected_UPP = 0.011227934437026977; double expected_variance = 224036.80150510342; double expected_standarddev = 473.32525973700518; double expected_min = -1023; double expected_max = 1361; double expected_RMS = 598.20276978323352; double expected_entropy = 4.6727423654570357; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 0; expected_minIndex[1] = 0; expected_minIndex[2] = 0; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 139; expected_maxIndex[1] = 182; expected_maxIndex[2] = 43; - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_Pic3DImage, 0); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_Pic3DImage); + auto statisticsObject = statisticsContainer->GetStatisticsForTimeStep(0); - VerifyStatistics(result, + VerifyStatistics(statisticsObject, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestPic3DAxialPlanarFigureMaskStatistics() { MITK_INFO << std::endl << "Test Pic3D axial pf:-----------------------------------------------------------------------------------"; double expected_entropy = 5.6719817476387417; double expected_kurtosis = 5.8846935191205221; double expected_MPP = 230.43933685003768; double expected_max = 1206; double expected_mean = 182.30282131661443; double expected_median = 95.970001220703125; double expected_min = -156; - long expected_N = 3190; + unsigned long expected_N = 3190; double expected_RMS = 301.93844376702253; double expected_skewness = 1.6400489794326298; double expected_standarddev = 240.69172225993557; double expected_UPP = 0.024889790784288681; double expected_uniformity = 0.027579917650180332; double expected_variance = 57932.505164453964; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 156; expected_minIndex[1] = 133; expected_minIndex[2] = 24; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 125; expected_maxIndex[1] = 167; expected_maxIndex[2] = 24; mitk::PlanarFigureMaskGenerator::Pointer pfMaskGen = mitk::PlanarFigureMaskGenerator::New(); pfMaskGen->SetInputImage(m_Pic3DImage); pfMaskGen->SetPlanarFigure(m_Pic3DPlanarFigureAxial); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_Pic3DImage, 0, pfMaskGen.GetPointer()); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_Pic3DImage, pfMaskGen.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep0, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestPic3DSagittalPlanarFigureMaskStatistics() { MITK_INFO << std::endl << "Test Pic3D sagittal pf:-----------------------------------------------------------------------------------"; double expected_entropy = 5.6051911962074286; double expected_kurtosis = 6.5814062739142338; double expected_MPP = 249.03202846975088; double expected_max = 1240; double expected_mean = 233.93602693602693; double expected_median = 174.9849853515625; double expected_min = -83; - long expected_N = 1188; + unsigned long expected_N = 1188; double expected_RMS = 332.03230188484594; double expected_skewness = 1.7489809015501814; double expected_standarddev = 235.62551813489128; double expected_UPP = 0.026837539253364174; double expected_uniformity = 0.027346982734188126; double expected_variance = 55519.384796335973; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 128; expected_minIndex[1] = 119; expected_minIndex[2] = 22; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 128; expected_maxIndex[1] = 167; expected_maxIndex[2] = 22; mitk::PlanarFigureMaskGenerator::Pointer pfMaskGen = mitk::PlanarFigureMaskGenerator::New(); pfMaskGen->SetInputImage(m_Pic3DImage); pfMaskGen->SetPlanarFigure(m_Pic3DPlanarFigureSagittal); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_Pic3DImage, 0, pfMaskGen.GetPointer()); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_Pic3DImage, pfMaskGen.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep0, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestPic3DCoronalPlanarFigureMaskStatistics() { MITK_INFO << std::endl << "Test Pic3D coronal pf:-----------------------------------------------------------------------------------"; double expected_entropy = 6.0677398647867449; double expected_kurtosis = 1.6242929941303372; double expected_MPP = 76.649350649350652; double expected_max = 156; double expected_mean = -482.14807692307693; double expected_median = -660.07501220703125; double expected_min = -897; - long expected_N = 520; + unsigned long expected_N = 520; double expected_RMS = 595.09446729069839; double expected_skewness = 0.51691492278851858; double expected_standarddev = 348.81321207686312; double expected_UPP = 0.0021560650887573964; double expected_uniformity = 0.020295857988165685; double expected_variance = 121670.6569193787; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 217; expected_minIndex[1] = 127; expected_minIndex[2] = 43; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 209; expected_maxIndex[1] = 127; expected_maxIndex[2] = 39; mitk::PlanarFigureMaskGenerator::Pointer pfMaskGen = mitk::PlanarFigureMaskGenerator::New(); pfMaskGen->SetInputImage(m_Pic3DImage); pfMaskGen->SetPlanarFigure(m_Pic3DPlanarFigureCoronal); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_Pic3DImage, 0, pfMaskGen.GetPointer()); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_Pic3DImage, pfMaskGen.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep0, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestPic3DImageMaskStatistics_label1() { MITK_INFO << std::endl << "Test Pic3D image mask label 1 pf:-----------------------------------------------------------------------------------"; double expected_entropy = 5.695858251095868; double expected_kurtosis = 4.2728827997815717; double expected_MPP = 413.52408256880733; double expected_max = 1206; double expected_mean = 413.52408256880733; double expected_median = 324; double expected_min = 6; - long expected_N = 872; + unsigned long expected_N = 872; double expected_RMS = 472.02024695145235; double expected_skewness = 1.3396074364415382; double expected_standarddev = 227.59821323493802; double expected_UPP = 0.029758648261930806; double expected_uniformity = 0.029758648261930806; double expected_variance = 51800.946667736309; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 135; expected_minIndex[1] = 158; expected_minIndex[2] = 24; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 125; expected_maxIndex[1] = 167; expected_maxIndex[2] = 24; mitk::ImageMaskGenerator::Pointer imgMaskGen = mitk::ImageMaskGenerator::New(); imgMaskGen->SetImageMask(m_Pic3DImageMask); imgMaskGen->SetInputImage(m_Pic3DImage); imgMaskGen->SetTimeStep(0); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_Pic3DImage, 0, imgMaskGen.GetPointer(), nullptr, 1); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_Pic3DImage, imgMaskGen.GetPointer(), nullptr, 1); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep0, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestPic3DImageMaskStatistics_label2() { MITK_INFO << std::endl << "Test Pic3D image mask label 2 pf:-----------------------------------------------------------------------------------"; double expected_entropy = 4.3685781901212764; double expected_kurtosis = 9.7999112757587934; double expected_MPP = -nan(""); double expected_max = -145; double expected_mean = -897.92833876221493; double expected_median = -969.16499900817871; double expected_min = -1008; - long expected_N = 307; + unsigned long expected_N = 307; double expected_RMS = 913.01496468179471; double expected_skewness = 2.6658524648889736; double expected_standarddev = 165.29072623903585; double expected_UPP = 0; double expected_uniformity = 0.087544695434434425; double expected_variance = 27321.024180627897; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 170; expected_minIndex[1] = 60; expected_minIndex[2] = 24; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 173; expected_maxIndex[1] = 57; expected_maxIndex[2] = 24; mitk::ImageMaskGenerator::Pointer imgMaskGen = mitk::ImageMaskGenerator::New(); imgMaskGen->SetImageMask(m_Pic3DImageMask); imgMaskGen->SetInputImage(m_Pic3DImage); imgMaskGen->SetTimeStep(0); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_Pic3DImage, 0, imgMaskGen.GetPointer(), nullptr, 2); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_Pic3DImage, imgMaskGen.GetPointer(), nullptr, 2); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep0, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestPic3DIgnorePixelValueMaskStatistics() { MITK_INFO << std::endl << "Test Pic3D ignore zero pixels:-----------------------------------------------------------------------------------"; double expected_entropy = 4.671045011438645; double expected_kurtosis = 1.4638176488404484; double expected_MPP = 111.80226129535752; double expected_max = 1361; double expected_mean = -366.48547402877585; double expected_median = -105.16000366210938; double expected_min = -1023; - long expected_N = 3205259; + unsigned long expected_N = 3205259; double expected_RMS = 598.76286909522139; double expected_skewness = -0.26648854845130782; double expected_standarddev = 473.50329537717545; double expected_UPP = 0.011270044547276429; double expected_uniformity = 0.061029773286547614; double expected_variance = 224205.37073304466; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 0; expected_minIndex[1] = 0; expected_minIndex[2] = 0; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 139; expected_maxIndex[1] = 182; expected_maxIndex[2] = 43; mitk::IgnorePixelMaskGenerator::Pointer ignPixelValMask = mitk::IgnorePixelMaskGenerator::New(); ignPixelValMask->SetInputImage(m_Pic3DImage); ignPixelValMask->SetIgnoredPixelValue(0); ignPixelValMask->SetTimeStep(0); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_Pic3DImage, 0, ignPixelValMask.GetPointer()); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_Pic3DImage, ignPixelValMask.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep0, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestPic3DSecondaryMaskStatistics() { MITK_INFO << std::endl << "Test Pic3D ignore zero pixels AND Image mask 2:-----------------------------------------------------------------------------------"; double expected_entropy = 5.9741637167320176; double expected_kurtosis = 3.490663358061596; double expected_MPP = 332.43534482758622; double expected_max = 1206; double expected_mean = 320.63333333333333; double expected_median = 265.06500244140625; double expected_min = -57; - long expected_N = 720; + unsigned long expected_N = 720; double expected_RMS = 433.57749531594055; double expected_skewness = 1.1047775627624981; double expected_standarddev = 291.86248474238687; double expected_UPP = 0.020628858024691339; double expected_uniformity = 0.021377314814814797; double expected_variance = 85183.710000000006; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 116; expected_minIndex[1] = 170; expected_minIndex[2] = 24; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 125; expected_maxIndex[1] = 167; expected_maxIndex[2] = 24; mitk::IgnorePixelMaskGenerator::Pointer ignPixelValMask = mitk::IgnorePixelMaskGenerator::New(); ignPixelValMask->SetInputImage(m_Pic3DImage); ignPixelValMask->SetIgnoredPixelValue(0); ignPixelValMask->SetTimeStep(0); mitk::ImageMaskGenerator::Pointer imgMaskGen2 = mitk::ImageMaskGenerator::New(); imgMaskGen2->SetImageMask(m_Pic3DImageMask2); imgMaskGen2->SetInputImage(m_Pic3DImage); imgMaskGen2->SetTimeStep(0); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_Pic3DImage, 0, imgMaskGen2.GetPointer(), ignPixelValMask.GetPointer()); - //std::cout << result->GetAsString(); + auto statisticsContainer = + ComputeStatisticsNew(m_Pic3DImage, imgMaskGen2.GetPointer(), ignPixelValMask.GetPointer()); + auto statisticsObjectTimestep0 = statisticsContainer->GetStatisticsForTimeStep(0); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep0, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestUS4DCylStatistics_time1() { MITK_INFO << std::endl << "Test plain US4D timeStep1:-----------------------------------------------------------------------------------"; double expected_entropy = 4.8272774900452502; double expected_kurtosis = 6.1336513352934432; double expected_MPP = 53.395358640738536; double expected_max = 199; double expected_mean = 35.771298153622375; double expected_median = 20.894999504089355; double expected_min = 0; - long expected_N = 3409920; + unsigned long expected_N = 3409920; double expected_RMS = 59.244523377028408; double expected_skewness = 1.8734292240015058; double expected_standarddev = 47.226346233600559; double expected_UPP = 0.12098731125004937; double expected_uniformity = 0.12098731125004937; double expected_variance = 2230.3277785759178; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 0; expected_minIndex[1] = 0; expected_minIndex[2] = 0; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 268; expected_maxIndex[1] = 101; expected_maxIndex[2] = 0; - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_US4DImage, 1); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_US4DImage); + auto statisticsObjectTimestep1 = statisticsContainer->GetStatisticsForTimeStep(1); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep1, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestUS4DCylAxialPlanarFigureMaskStatistics_time1() { MITK_INFO << std::endl << "Test US4D axial pf timeStep1:-----------------------------------------------------------------------------------"; double expected_entropy = 6.218151288002292; double expected_kurtosis = 1.7322676370242023; double expected_MPP = 121.11663807890223; double expected_max = 199; double expected_mean = 121.11663807890223; double expected_median = 120.14999771118164; double expected_min = 9; - long expected_N = 2332; + unsigned long expected_N = 2332; double expected_RMS = 134.41895158590751; double expected_skewness = -0.1454808104597369; double expected_standarddev = 58.30278317472294; double expected_UPP = 0.021354765820606133; double expected_uniformity = 0.021354765820606133; double expected_variance = 3399.214525918756; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 129; expected_minIndex[1] = 131; expected_minIndex[2] = 19; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 126; expected_maxIndex[1] = 137; expected_maxIndex[2] = 19; mitk::PlanarFigureMaskGenerator::Pointer pfMaskGen = mitk::PlanarFigureMaskGenerator::New(); pfMaskGen->SetInputImage(m_US4DImage); pfMaskGen->SetPlanarFigure(m_US4DPlanarFigureAxial); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_US4DImage, 1, pfMaskGen.GetPointer()); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_US4DImage, pfMaskGen.GetPointer()); + auto statisticsObjectTimestep1 = statisticsContainer->GetStatisticsForTimeStep(1); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep1, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestUS4DCylSagittalPlanarFigureMaskStatistics_time1() { MITK_INFO << std::endl << "Test US4D sagittal pf timeStep1:-----------------------------------------------------------------------------------"; double expected_entropy = 5.2003987046387508; double expected_kurtosis = 2.7574491062430142; double expected_MPP = 26.212534059945504; double expected_max = 59; double expected_mean = 26.176870748299319; double expected_median = 26.254999160766602; double expected_min = 0; - long expected_N = 735; + unsigned long expected_N = 735; double expected_RMS = 28.084905283121476; double expected_skewness = 0.18245181360752327; double expected_standarddev = 10.175133541567705; double expected_UPP = 0.032921467906890628; double expected_uniformity = 0.032921467906890628; double expected_variance = 103.53334258873615; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 147; expected_minIndex[1] = 94; expected_minIndex[2] = 21; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 147; expected_maxIndex[1] = 77; expected_maxIndex[2] = 24; mitk::PlanarFigureMaskGenerator::Pointer pfMaskGen = mitk::PlanarFigureMaskGenerator::New(); pfMaskGen->SetInputImage(m_US4DImage); pfMaskGen->SetPlanarFigure(m_US4DPlanarFigureSagittal); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_US4DImage, 1, pfMaskGen.GetPointer()); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_US4DImage, pfMaskGen.GetPointer()); + auto statisticsObjectTimestep1 = statisticsContainer->GetStatisticsForTimeStep(1); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep1, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestUS4DCylCoronalPlanarFigureMaskStatistics_time1() { MITK_INFO << std::endl << "Test US4D coronal pf timeStep1:-----------------------------------------------------------------------------------"; double expected_entropy = 5.8892941136639161; double expected_kurtosis = 4.6434920707409564; double expected_MPP = 55.486426346239433; double expected_max = 199; double expected_mean = 55.118479221927501; double expected_median = 36.815000534057617; double expected_min = 0; - long expected_N = 2262; + unsigned long expected_N = 2262; double expected_RMS = 71.98149752438627; double expected_skewness = 1.4988288344523237; double expected_standarddev = 46.29567187238105; double expected_UPP = 0.023286748110675673; double expected_uniformity = 0.023286748110675673; double expected_variance = 2143.2892341151742; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 214; expected_minIndex[1] = 169; expected_minIndex[2] = 10; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 99; expected_maxIndex[1] = 169; expected_maxIndex[2] = 17; mitk::PlanarFigureMaskGenerator::Pointer pfMaskGen = mitk::PlanarFigureMaskGenerator::New(); pfMaskGen->SetInputImage(m_US4DImage); pfMaskGen->SetPlanarFigure(m_US4DPlanarFigureCoronal); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_US4DImage, 1, pfMaskGen.GetPointer()); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_US4DImage, pfMaskGen.GetPointer()); + auto statisticsObjectTimestep1 = statisticsContainer->GetStatisticsForTimeStep(1); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep1, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestUS4DCylImageMaskStatistics_time1_label_1() { MITK_INFO << std::endl << "Test US4D image mask time 1 label 1:-----------------------------------------------------------------------------------"; double expected_entropy = 5.0082903903398677; double expected_kurtosis = 3.6266994778237809; double expected_MPP = 169.58938547486034; double expected_max = 199; double expected_mean = 169.58938547486034; double expected_median = 187.44000244140625; double expected_min = 63; - long expected_N = 716; + unsigned long expected_N = 716; double expected_RMS = 173.09843164831432; double expected_skewness = -1.2248969838579555; double expected_standarddev = 34.677188083311712; double expected_UPP = 0.076601073624418703; double expected_uniformity = 0.076601073624418703; double expected_variance = 1202.5073733653758; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 82; expected_minIndex[1] = 158; expected_minIndex[2] = 19; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 126; expected_maxIndex[1] = 140; expected_maxIndex[2] = 19; mitk::ImageMaskGenerator::Pointer imgMask1 = mitk::ImageMaskGenerator::New(); imgMask1->SetInputImage(m_US4DImage); imgMask1->SetImageMask(m_US4DImageMask); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_US4DImage, 1, imgMask1.GetPointer(), nullptr, 1); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_US4DImage, imgMask1.GetPointer(), nullptr, 1); + auto statisticsObjectTimestep1 = statisticsContainer->GetStatisticsForTimeStep(1); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep1, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestUS4DCylImageMaskStatistics_time2_label_1() { MITK_INFO << std::endl << "Test US4D image mask time 2 label 1:-----------------------------------------------------------------------------------"; double expected_entropy = 5.1857604214916506; double expected_kurtosis = 3.0692303858330683; double expected_MPP = 167.97194163860831; double expected_max = 199; double expected_mean = 167.97194163860831; double expected_median = 184.39499664306641; double expected_min = 72; - long expected_N = 891; + unsigned long expected_N = 891; double expected_RMS = 171.67986611998634; double expected_skewness = -1.1221651136259736; double expected_standarddev = 35.488071983870803; double expected_UPP = 0.063124070232188439; double expected_uniformity = 0.063124070232188439; double expected_variance = 1259.4032531323958; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 103; expected_minIndex[1] = 212; expected_minIndex[2] = 19; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 102; expected_maxIndex[1] = 168; expected_maxIndex[2] = 19; mitk::ImageMaskGenerator::Pointer imgMask1 = mitk::ImageMaskGenerator::New(); imgMask1->SetInputImage(m_US4DImage); imgMask1->SetImageMask(m_US4DImageMask); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_US4DImage, 2, imgMask1.GetPointer(), nullptr, 1); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_US4DImage, imgMask1.GetPointer(), nullptr, 1); + auto statisticsObjectTimestep2 = statisticsContainer->GetStatisticsForTimeStep(2); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep2, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestUS4DCylImageMaskStatistics_time1_label_2() { MITK_INFO << std::endl << "Test US4D image mask time 1 label 2:-----------------------------------------------------------------------------------"; double expected_entropy = 5.0822234230119001; double expected_kurtosis = 2.4346603343623747; double expected_MPP = 20.733626373626375; double expected_max = 46; double expected_mean = 20.624836029733274; double expected_median = 20.010000228881836; double expected_min = 0; - long expected_N = 2287; + unsigned long expected_N = 2287; double expected_RMS = 22.508347574573804; double expected_skewness = 0.13837218490626488; double expected_standarddev = 9.0134260569684965; double expected_UPP = 0.034783970308787; double expected_uniformity = 0.034783970308787; double expected_variance = 81.241849284438644; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 178; expected_minIndex[1] = 76; expected_minIndex[2] = 19; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 198; expected_maxIndex[1] = 90; expected_maxIndex[2] = 19; mitk::ImageMaskGenerator::Pointer imgMask1 = mitk::ImageMaskGenerator::New(); imgMask1->SetInputImage(m_US4DImage); imgMask1->SetImageMask(m_US4DImageMask); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_US4DImage, 1, imgMask1.GetPointer(), nullptr, 2); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_US4DImage, imgMask1.GetPointer(), nullptr, 2); + auto statisticsObjectTimestep1 = statisticsContainer->GetStatisticsForTimeStep(1); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep1, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestUS4DCylIgnorePixelValueMaskStatistics_time1() { MITK_INFO << std::endl << "Test US4D ignore zero pixels:-----------------------------------------------------------------------------------"; double expected_entropy = 5.8609813848087962; double expected_kurtosis = 4.7556214582883651; double expected_MPP = 53.395358640738536; double expected_max = 199; double expected_mean = 53.395358640738536; double expected_median = 35.649999618530273; double expected_min = 1; - long expected_N = 2284417; + unsigned long expected_N = 2284417; double expected_RMS = 72.382339046507084; double expected_skewness = 1.588289859859108; double expected_standarddev = 48.868585834566694; double expected_UPP = 0.023927063695115193; double expected_uniformity = 0.023927063695115193; double expected_variance = 2388.1386814704128; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 187; expected_minIndex[1] = 19; expected_minIndex[2] = 0; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 268; expected_maxIndex[1] = 101; expected_maxIndex[2] = 0; mitk::IgnorePixelMaskGenerator::Pointer ignPixelValMask = mitk::IgnorePixelMaskGenerator::New(); ignPixelValMask->SetInputImage(m_US4DImage); ignPixelValMask->SetIgnoredPixelValue(0); ignPixelValMask->SetTimeStep(1); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_US4DImage, 1, ignPixelValMask.GetPointer()); - //std::cout << result->GetAsString(); + auto statisticsContainer = ComputeStatisticsNew(m_US4DImage, ignPixelValMask.GetPointer()); + auto statisticsObjectTimestep1 = statisticsContainer->GetStatisticsForTimeStep(1); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep1, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } void mitkImageStatisticsCalculatorTestSuite::TestUS4DCylSecondaryMaskStatistics_time1() { MITK_INFO << std::endl << "Test US4d ignore zero pixels AND Image mask 2:-----------------------------------------------------------------------------------"; double expected_entropy = 4.9955858614274558; double expected_kurtosis = 17.471042803365179; double expected_MPP = 32.791403286978507; double expected_max = 199; double expected_mean = 32.791403286978507; double expected_median = 25.75; double expected_min = 1; - long expected_N = 17402; + unsigned long expected_N = 17402; double expected_RMS = 42.776697859745241; double expected_skewness = 3.3991813038552596; double expected_standarddev = 27.469433016621732; double expected_UPP = 0.043040554251756687; double expected_uniformity = 0.043040554251756687; double expected_variance = 754.56975025466807; vnl_vector expected_minIndex; expected_minIndex.set_size(3); expected_minIndex[0] = 177; expected_minIndex[1] = 27; expected_minIndex[2] = 36; vnl_vector expected_maxIndex; expected_maxIndex.set_size(3); expected_maxIndex[0] = 109; expected_maxIndex[1] = 116; expected_maxIndex[2] = 36; mitk::IgnorePixelMaskGenerator::Pointer ignPixelValMask = mitk::IgnorePixelMaskGenerator::New(); ignPixelValMask->SetInputImage(m_US4DImage); ignPixelValMask->SetIgnoredPixelValue(0); mitk::ImageMaskGenerator::Pointer imgMaskGen2 = mitk::ImageMaskGenerator::New(); imgMaskGen2->SetImageMask(m_US4DImageMask2); imgMaskGen2->SetInputImage(m_US4DImage); - const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result = ComputeStatisticsNew(m_US4DImage, 1, imgMaskGen2.GetPointer(), ignPixelValMask.GetPointer()); - //std::cout << result->GetAsString(); + auto statisticsContainer = + ComputeStatisticsNew(m_US4DImage, imgMaskGen2.GetPointer(), ignPixelValMask.GetPointer()); + auto statisticsObjectTimestep1 = statisticsContainer->GetStatisticsForTimeStep(1); - VerifyStatistics(result, + VerifyStatistics(statisticsObjectTimestep1, expected_N, expected_mean, expected_MPP, expected_median, expected_skewness, expected_kurtosis, expected_uniformity, expected_UPP, expected_variance, expected_standarddev, expected_min, expected_max, expected_RMS, expected_entropy, expected_minIndex, expected_maxIndex); } -const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer -mitkImageStatisticsCalculatorTestSuite::ComputeStatistics( mitk::Image::Pointer image, mitk::PlanarFigure::Pointer polygon ) +const mitk::ImageStatisticsContainer::Pointer mitkImageStatisticsCalculatorTestSuite::ComputeStatistics( mitk::Image::ConstPointer image, mitk::PlanarFigure::Pointer polygon ) { mitk::ImageStatisticsCalculator::Pointer statisticsCalculator = mitk::ImageStatisticsCalculator::New(); statisticsCalculator->SetInputImage( image ); statisticsCalculator->SetNBinsForHistogramStatistics(10); mitk::PlanarFigureMaskGenerator::Pointer planFigMaskGen = mitk::PlanarFigureMaskGenerator::New(); planFigMaskGen->SetInputImage(image); planFigMaskGen->SetPlanarFigure(polygon); statisticsCalculator->SetMask(planFigMaskGen.GetPointer()); try { return statisticsCalculator->GetStatistics(); } catch( ... ) { + return nullptr; } - - return mitk::ImageStatisticsCalculator::StatisticsContainer::New(); } -const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer -mitkImageStatisticsCalculatorTestSuite::ComputeStatistics(mitk::Image::Pointer image, mitk::Image::Pointer image_mask ) +const mitk::ImageStatisticsContainer::Pointer +mitkImageStatisticsCalculatorTestSuite::ComputeStatistics(mitk::Image::ConstPointer image, mitk::Image::Pointer image_mask ) { mitk::ImageStatisticsCalculator::Pointer statisticsCalculator = mitk::ImageStatisticsCalculator::New(); statisticsCalculator->SetInputImage(image); statisticsCalculator->SetNBinsForHistogramStatistics(10); mitk::ImageMaskGenerator::Pointer imgMaskGen = mitk::ImageMaskGenerator::New(); imgMaskGen->SetImageMask(image_mask); statisticsCalculator->SetMask(imgMaskGen.GetPointer()); return statisticsCalculator->GetStatistics(); } -const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer -mitkImageStatisticsCalculatorTestSuite::ComputeStatisticsNew(mitk::Image::Pointer image, - int timeStep, +const mitk::ImageStatisticsContainer::Pointer +mitkImageStatisticsCalculatorTestSuite::ComputeStatisticsNew(mitk::Image::ConstPointer image, mitk::MaskGenerator::Pointer maskGen, mitk::MaskGenerator::Pointer secondardMaskGen, unsigned short label) { mitk::ImageStatisticsCalculator::Pointer imgStatCalc = mitk::ImageStatisticsCalculator::New(); imgStatCalc->SetInputImage(image); if (maskGen.IsNotNull()) { imgStatCalc->SetMask(maskGen.GetPointer()); if (secondardMaskGen.IsNotNull()) { imgStatCalc->SetSecondaryMask(secondardMaskGen.GetPointer()); } } - return imgStatCalc->GetStatistics(timeStep, label); + return imgStatCalc->GetStatistics(label); } -void mitkImageStatisticsCalculatorTestSuite::VerifyStatistics(mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer stats, +void mitkImageStatisticsCalculatorTestSuite::VerifyStatistics(mitk::ImageStatisticsContainer::StatisticsObject stats, double testMean, double testSD, double testMedian) { - int tmpMean = stats->GetMean() * 100; + auto mean = stats.GetValueConverted(mitk::ImageStatisticsConstants::MEAN()); + int tmpMean = mean * 100; double calculatedMean = tmpMean / 100.0; MITK_TEST_CONDITION( calculatedMean == testMean, "Calculated mean grayvalue '" << calculatedMean << "' is equal to the desired value '" << testMean << "'" ); - int tmpSD = stats->GetStd() * 100; + auto standardDeviation = stats.GetValueConverted(mitk::ImageStatisticsConstants::STANDARDDEVIATION()); + int tmpSD = standardDeviation * 100; double calculatedSD = tmpSD / 100.0; MITK_TEST_CONDITION( calculatedSD == testSD, "Calculated grayvalue sd '" << calculatedSD << "' is equal to the desired value '" << testSD <<"'" ); - int tmpMedian = stats->GetMedian() * 100; + auto median = stats.GetValueConverted(mitk::ImageStatisticsConstants::MEDIAN()); + int tmpMedian = median * 100; double calculatedMedian = tmpMedian / 100.0; MITK_TEST_CONDITION( testMedian == calculatedMedian, "Calculated median grayvalue '" << calculatedMedian << "' is equal to the desired value '" << testMedian << "'"); } -void mitkImageStatisticsCalculatorTestSuite::VerifyStatistics(mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer stats, - long N, +void mitkImageStatisticsCalculatorTestSuite::VerifyStatistics(mitk::ImageStatisticsContainer::StatisticsObject stats, + unsigned long N, double mean, double MPP, double median, double skewness, double kurtosis, double uniformity, double UPP, double variance, double stdev, double min, double max, double RMS, double entropy, vnl_vector minIndex, vnl_vector maxIndex) { - MITK_TEST_CONDITION(std::abs(stats->GetN() - N) < mitk::eps, "calculated N: " << stats->GetN() << " expected N: " << N); - MITK_TEST_CONDITION(std::abs(stats->GetMean() - mean) < mitk::eps, "calculated mean: " << stats->GetMean() << " expected mean: " << mean); + auto numberOfVoxelsObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::NUMBEROFVOXELS()); + auto meanObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::MEAN()); + auto mppObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::MPP()); + auto medianObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::MEDIAN()); + auto skewnessObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::SKEWNESS()); + auto kurtosisObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::KURTOSIS()); + auto uniformityObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::UNIFORMITY()); + auto uppObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::UPP()); + auto varianceObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::VARIANCE()); + auto standardDeviationObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::STANDARDDEVIATION()); + auto minObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::MINIMUM()); + auto maxObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::MAXIMUM()); + auto rmsObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::RMS()); + auto entropyObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::ENTROPY()); + auto minIndexObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::MINIMUMPOSITION()); + auto maxIndexObject = stats.GetValueConverted(mitk::ImageStatisticsConstants::MAXIMUMPOSITION()); + + MITK_TEST_CONDITION(numberOfVoxelsObject - N == 0, "calculated N: " << numberOfVoxelsObject << " expected N: " << N); + MITK_TEST_CONDITION(std::abs(meanObject - mean) < mitk::eps, "calculated mean: " << meanObject << " expected mean: " << mean); // in one test case MPP is None because the roi has no positive pixels - if (!std::isnan(stats->GetMPP())) + if (!std::isnan(mppObject)) { - MITK_TEST_CONDITION(std::abs(stats->GetMPP() - MPP) < mitk::eps, "calculated MPP: " << stats->GetMPP() << " expected MPP: " << MPP); + MITK_TEST_CONDITION(std::abs(mppObject - MPP) < mitk::eps, "calculated MPP: " << mppObject << " expected MPP: " << MPP); } - MITK_TEST_CONDITION(std::abs(stats->GetMedian() - median) < mitk::eps, "calculated median: " << stats->GetMedian() << " expected median: " << median); - MITK_TEST_CONDITION(std::abs(stats->GetSkewness() - skewness) < mitk::eps, "calculated skewness: " << stats->GetSkewness() << " expected skewness: " << skewness); - MITK_TEST_CONDITION(std::abs(stats->GetKurtosis() - kurtosis) < mitk::eps, "calculated kurtosis: " << stats->GetKurtosis() << " expected kurtosis: " << kurtosis); - MITK_TEST_CONDITION(std::abs(stats->GetUniformity() - uniformity) < mitk::eps, "calculated uniformity: " << stats->GetUniformity() << " expected uniformity: " << uniformity); - MITK_TEST_CONDITION(std::abs(stats->GetUPP() - UPP) < mitk::eps, "calculated UPP: " << stats->GetUPP() << " expected UPP: " << UPP); - MITK_TEST_CONDITION(std::abs(stats->GetVariance() - variance) < mitk::eps, "calculated variance: " << stats->GetVariance() << " expected variance: " << variance); - MITK_TEST_CONDITION(std::abs(stats->GetStd() - stdev) < mitk::eps, "calculated stdev: " << stats->GetStd() << " expected stdev: " << stdev); - MITK_TEST_CONDITION(std::abs(stats->GetMin() - min) < mitk::eps, "calculated min: " << stats->GetMin() << " expected min: " << min); - MITK_TEST_CONDITION(std::abs(stats->GetMax() - max) < mitk::eps, "calculated max: " << stats->GetMax() << " expected max: " << max); - MITK_TEST_CONDITION(std::abs(stats->GetRMS() - RMS) < mitk::eps, "calculated RMS: " << stats->GetRMS() << " expected RMS: " << RMS); - MITK_TEST_CONDITION(std::abs(stats->GetEntropy() - entropy) < mitk::eps, "calculated entropy: " << stats->GetEntropy() << " expected entropy: " << entropy); + MITK_TEST_CONDITION(std::abs(medianObject - median) < mitk::eps, "calculated median: " << medianObject << " expected median: " << median); + MITK_TEST_CONDITION(std::abs(skewnessObject - skewness) < mitk::eps, "calculated skewness: " << skewnessObject << " expected skewness: " << skewness); + MITK_TEST_CONDITION(std::abs(kurtosisObject - kurtosis) < mitk::eps, "calculated kurtosis: " << kurtosisObject << " expected kurtosis: " << kurtosis); + MITK_TEST_CONDITION(std::abs(uniformityObject - uniformity) < mitk::eps, "calculated uniformity: " << uniformityObject << " expected uniformity: " << uniformity); + MITK_TEST_CONDITION(std::abs(uppObject - UPP) < mitk::eps, "calculated UPP: " << uppObject << " expected UPP: " << UPP); + MITK_TEST_CONDITION(std::abs(varianceObject - variance) < mitk::eps, "calculated variance: " << varianceObject << " expected variance: " << variance); + MITK_TEST_CONDITION(std::abs(standardDeviationObject - stdev) < mitk::eps, "calculated stdev: " << standardDeviationObject << " expected stdev: " << stdev); + MITK_TEST_CONDITION(std::abs(minObject - min) < mitk::eps, "calculated min: " << minObject << " expected min: " << min); + MITK_TEST_CONDITION(std::abs(maxObject - max) < mitk::eps, "calculated max: " << maxObject << " expected max: " << max); + MITK_TEST_CONDITION(std::abs(rmsObject - RMS) < mitk::eps, "calculated RMS: " << rmsObject << " expected RMS: " << RMS); + MITK_TEST_CONDITION(std::abs(entropyObject - entropy) < mitk::eps, "calculated entropy: " << entropyObject << " expected entropy: " << entropy); for (unsigned int i = 0; i < minIndex.size(); ++i) { - MITK_TEST_CONDITION(std::abs(stats->GetMinIndex()[i] - minIndex[i]) < mitk::eps, "minIndex [" << i << "] = " << stats->GetMinIndex()[i] << " expected: " << minIndex[i]); + MITK_TEST_CONDITION(std::abs(minIndexObject[i] - minIndex[i]) < mitk::eps, "minIndex [" << i << "] = " << minIndexObject[i] << " expected: " << minIndex[i]); } for (unsigned int i = 0; i < maxIndex.size(); ++i) { - MITK_TEST_CONDITION(std::abs(stats->GetMaxIndex()[i] - maxIndex[i]) < mitk::eps, "maxIndex [" << i << "] = " << stats->GetMaxIndex()[i] << " expected: " << maxIndex[i]); + MITK_TEST_CONDITION(std::abs(maxIndexObject[i] - maxIndex[i]) < mitk::eps, "maxIndex [" << i << "] = " << maxIndexObject[i] << " expected: " << maxIndex[i]); } } void mitkImageStatisticsCalculatorTestSuite::TestUninitializedImage() { /***************************** * loading uninitialized image to datastorage ******************************/ MITK_INFO << std::endl << "Test uninitialized image: -----------------------------------------------------------------------------------"; MITK_TEST_FOR_EXCEPTION_BEGIN(mitk::Exception) mitk::Image::Pointer image = mitk::Image::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(image); mitk::ImageStatisticsCalculator::Pointer is = mitk::ImageStatisticsCalculator::New(); is->GetStatistics(); MITK_TEST_FOR_EXCEPTION_END(mitk::Exception) } MITK_TEST_SUITE_REGISTRATION(mitkImageStatisticsCalculator) diff --git a/Modules/ImageStatistics/Testing/mitkImageStatisticsContainerManagerTest.cpp b/Modules/ImageStatistics/Testing/mitkImageStatisticsContainerManagerTest.cpp new file mode 100644 index 0000000000..5ff94409cb --- /dev/null +++ b/Modules/ImageStatistics/Testing/mitkImageStatisticsContainerManagerTest.cpp @@ -0,0 +1,251 @@ +/*=================================================================== +The Medical Imaging Interaction Toolkit (MITK) +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. +See LICENSE.txt or http://www.mitk.org for details. +===================================================================*/ +// Testing +#include "mitkTestingMacros.h" +#include "mitkTestFixture.h" + +//MITK includes +#include +#include +#include +#include +#include +#include +#include +#include +#include + +class mitkImageStatisticsContainerManagerTestSuite : public mitk::TestFixture +{ + CPPUNIT_TEST_SUITE(mitkImageStatisticsContainerManagerTestSuite); + MITK_TEST(GetImageStatisticsNoRules); + MITK_TEST(GetImageStatisticsWithImageConnected); + MITK_TEST(GetImageStatisticsWithImageNotConnected); + MITK_TEST(GetImageStatisticsWithImageAndMaskConnected); + MITK_TEST(GetImageStatisticsWithImageAndMaskNotConnected); + MITK_TEST(GetImageStatisticsInvalid); + CPPUNIT_TEST_SUITE_END(); + +private: + mitk::ImageStatisticsContainer::Pointer m_statisticsContainer, m_statisticsContainer2, m_statisticsContainer3; + mitk::Image::Pointer m_image, m_image2; + mitk::Image::Pointer m_mask, m_mask2; + mitk::PlanarFigure::Pointer m_planarFigure, m_planarFigure2; + +public: + void setUp() override + { + m_statisticsContainer = mitk::ImageStatisticsContainer::New(); + m_statisticsContainer2 = mitk::ImageStatisticsContainer::New(); + m_statisticsContainer3 = mitk::ImageStatisticsContainer::New(); + m_image = mitk::Image::New(); + m_image2 = mitk::Image::New(); + m_mask = mitk::Image::New(); + m_mask2 = mitk::Image::New(); + m_planarFigure = mitk::PlanarCircle::New().GetPointer(); + m_planarFigure2 = mitk::PlanarCircle::New().GetPointer(); + } + + void tearDown() override + { + } + + void CreateNodeRelationImage(mitk::BaseData::Pointer statistics, mitk::BaseData::ConstPointer image) + { + auto rule = mitk::StatisticsToImageRelationRule::New(); + rule->Connect(statistics, image); + } + + void CreateNodeRelationMask(mitk::BaseData::Pointer statistics, mitk::BaseData::ConstPointer image) + { + auto rule = mitk::StatisticsToMaskRelationRule::New(); + rule->Connect(statistics, image); + } + + void GetImageStatisticsNoRules() { + auto statisticsNode = mitk::CreateImageStatisticsNode(m_statisticsContainer, "testStatistics"); + auto standaloneDataStorage = mitk::StandaloneDataStorage::New(); + standaloneDataStorage->Add(statisticsNode); + + //no rules + 1 image --> test return nullptr + mitk::ImageStatisticsContainer::ConstPointer emptyStatistic; + CPPUNIT_ASSERT_NO_THROW(emptyStatistic = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer())); + CPPUNIT_ASSERT_EQUAL(emptyStatistic.IsNull(), true); + + //no rules + 1 image + 1 mask --> test return nullptr + CPPUNIT_ASSERT_NO_THROW(emptyStatistic = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_mask.GetPointer())); + CPPUNIT_ASSERT_EQUAL(emptyStatistic.IsNull(), true); + + //no rules + 1 image + 1 planarFigure --> test return nullptr + CPPUNIT_ASSERT_NO_THROW(emptyStatistic = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_planarFigure.GetPointer())); + CPPUNIT_ASSERT_EQUAL(emptyStatistic.IsNull(), true); + } + + void GetImageStatisticsWithImageConnected() + { + //create rules connection + auto statisticsNode = mitk::CreateImageStatisticsNode(m_statisticsContainer, "testStatistics"); + CreateNodeRelationImage(m_statisticsContainer.GetPointer(), m_image.GetPointer()); + auto standaloneDataStorage = mitk::StandaloneDataStorage::New(); + standaloneDataStorage->Add(statisticsNode); + + //rule: (image-->statistics), 1 connected image --> test return image statistics + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImage; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImage = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImage->GetUID(), m_statisticsContainer->GetUID()); + + //new rule: (image2-->statistics2 AND mask --> statistics2) + CreateNodeRelationImage(m_statisticsContainer2.GetPointer(), m_image2.GetPointer()); + CreateNodeRelationMask(m_statisticsContainer2.GetPointer(), m_mask.GetPointer()); + + auto statisticsNode2 = mitk::CreateImageStatisticsNode(m_statisticsContainer2, "testStatistics2"); + standaloneDataStorage->Add(statisticsNode2); + + //--> test return (still) image statistics (!= statistics2) + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAgain; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAgain = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAgain->GetUID(), m_statisticsContainer->GetUID()); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAgain->GetUID() != m_statisticsContainer2->GetUID(), true); + + //--> test return image statistics 2 + CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAgain = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer(), m_mask.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAgain->GetUID(), m_statisticsContainer2->GetUID()); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAgain->GetUID() != m_statisticsContainer->GetUID(), true); + + //add another newer statistic: should return this newer one + auto statisticsContainerNew = mitk::ImageStatisticsContainer::New(); + CreateNodeRelationImage(statisticsContainerNew.GetPointer(), m_image.GetPointer()); + + auto statisticsNodeNew = mitk::CreateImageStatisticsNode(statisticsContainerNew, "testStatisticsNew"); + standaloneDataStorage->Add(statisticsNodeNew); + statisticsContainerNew->Modified(); + + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageNew; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImageNew = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageNew->GetUID(), statisticsContainerNew->GetUID()); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageNew->GetUID() != m_statisticsContainer->GetUID(), true); + } + + void GetImageStatisticsWithImageNotConnected() { + //create rules connection + auto statisticsNode = mitk::CreateImageStatisticsNode(m_statisticsContainer, "testStatistics"); + CreateNodeRelationImage(m_statisticsContainer.GetPointer(), m_image.GetPointer()); + auto standaloneDataStorage = mitk::StandaloneDataStorage::New(); + standaloneDataStorage->Add(statisticsNode); + + //rule: (image-->statistics), 1 unconnected image --> test return nullptr + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImage; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImage = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImage.IsNull(), true); + + //rule: (image-->statistics), 1 connected image + 1 unconnected mask --> test return nullptr + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndMask; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndMask = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_mask.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMask.IsNull(), true); + + //rule: (image-->statistics), 1 connected image + 1 unconnected planar figure --> test return nullptr + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndPlanarFigure; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndPlanarFigure = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_planarFigure.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndPlanarFigure.IsNull(), true); + } + + void GetImageStatisticsWithImageAndMaskConnected() + { + //create rules connection + add statistics to dataStorage + auto statisticsNode = mitk::CreateImageStatisticsNode(m_statisticsContainer, "testStatistics"); + + CreateNodeRelationImage(m_statisticsContainer.GetPointer(), m_image.GetPointer()); + CreateNodeRelationMask(m_statisticsContainer.GetPointer(), m_mask.GetPointer()); + auto standaloneDataStorage = mitk::StandaloneDataStorage::New(); + standaloneDataStorage->Add(statisticsNode); + + //rule: (image-->statistics, mask-->statistics), 1 connected image, 1 connected mask --> test return statistics + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndMask; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndMask = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_mask.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMask.IsNull(), false); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMask->GetUID(), m_statisticsContainer->GetUID()); + + //new rule: (image-->statistics2) --> returns statistic because statistic2 has no mask connection + CreateNodeRelationImage(m_statisticsContainer2.GetPointer(), m_image.GetPointer()); + + auto statisticsNode2 = mitk::CreateImageStatisticsNode(m_statisticsContainer2, "testStatistics2"); + standaloneDataStorage->Add(statisticsNode2); + + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndMaskAgain; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndMaskAgain = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_mask.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMaskAgain->GetUID(), m_statisticsContainer->GetUID()); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMaskAgain->GetUID() != m_statisticsContainer2->GetUID(), true); + + //add another newer statistic: should return this newer one + auto statisticsContainerNew = mitk::ImageStatisticsContainer::New(); + + mitk::PropertyRelations::RuleResultVectorType rules4; + CreateNodeRelationImage(statisticsContainerNew.GetPointer(), m_image.GetPointer()); + CreateNodeRelationMask(statisticsContainerNew.GetPointer(), m_mask.GetPointer()); + auto statisticsNodeNew = mitk::CreateImageStatisticsNode(statisticsContainerNew, "testStatisticsNew"); + standaloneDataStorage->Add(statisticsNodeNew); + + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndMaskNew; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndMaskNew = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_mask.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsContainerNew->GetUID(), statisticsWithImageAndMaskNew->GetUID()); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMaskNew->GetUID() != m_statisticsContainer->GetUID(), true); + } + + void GetImageStatisticsWithImageAndMaskNotConnected() + { + //create rules connection + add statistics to dataStorage + auto statisticsNode = mitk::CreateImageStatisticsNode(m_statisticsContainer, "testStatistics"); + CreateNodeRelationImage(m_statisticsContainer.GetPointer(), m_image.GetPointer()); + CreateNodeRelationMask(m_statisticsContainer.GetPointer(), m_mask.GetPointer()); + auto standaloneDataStorage = mitk::StandaloneDataStorage::New(); + standaloneDataStorage->Add(statisticsNode); + + //rule: (image-->statistics, mask-->statistics), 1 connected image --> test return nullptr + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImage; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImage = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImage.IsNull(), true); + + //rule: (image-->statistics, mask-->statistics), 1 unconnected image, 1 unconnected mask --> test return nullptr + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageNotConnectedAndMaskNotConnected; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImageNotConnectedAndMaskNotConnected = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer(), m_mask2.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageNotConnectedAndMaskNotConnected.IsNull(), true); + + //rule: (image-->statistics, mask-->statistics), 1 unconnected image, 1 connected mask --> test return nullptr + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndMaskNotConnected; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndMaskNotConnected = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer(), m_mask.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndMaskNotConnected.IsNull(), true); + + //rule: (image-->statistics, mask-->statistics), 1 connected image, 1 unconnected planarFigure --> test return nullptr + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageAndPlanarFigureNotConnected; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndPlanarFigureNotConnected = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image.GetPointer(), m_planarFigure.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndPlanarFigureNotConnected.IsNull(), true); + + //rule: (image-->statistics, mask-->statistics), 1 unconnected image, 1 unconnected planarFigure --> test return nullptr + mitk::ImageStatisticsContainer::ConstPointer statisticsWithImageNotConnectedAndPlanarFigureNotConnected; + CPPUNIT_ASSERT_NO_THROW(statisticsWithImageAndPlanarFigureNotConnected = mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), m_image2.GetPointer(), m_planarFigure.GetPointer())); + CPPUNIT_ASSERT_EQUAL(statisticsWithImageAndPlanarFigureNotConnected.IsNull(), true); + } + + void GetImageStatisticsInvalid() + { + CreateNodeRelationImage(m_statisticsContainer.GetPointer(), m_image.GetPointer()); + + CPPUNIT_ASSERT_THROW(mitk::ImageStatisticsContainerManager::GetImageStatistics(nullptr, m_image.GetPointer()), mitk::Exception); + + auto standaloneDataStorage = mitk::StandaloneDataStorage::New(); + + CPPUNIT_ASSERT_THROW(mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), nullptr), mitk::Exception); + CPPUNIT_ASSERT_THROW(mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), nullptr, m_mask.GetPointer()), mitk::Exception); + CPPUNIT_ASSERT_THROW(mitk::ImageStatisticsContainerManager::GetImageStatistics(standaloneDataStorage.GetPointer(), nullptr, m_planarFigure.GetPointer()), mitk::Exception); + } + +}; +MITK_TEST_SUITE_REGISTRATION(mitkImageStatisticsContainerManager) \ No newline at end of file diff --git a/Modules/ImageStatistics/Testing/mitkImageStatisticsHotspotTest.cpp b/Modules/ImageStatistics/Testing/mitkImageStatisticsHotspotTest.cpp index c417798f23..925f2f6210 100644 --- a/Modules/ImageStatistics/Testing/mitkImageStatisticsHotspotTest.cpp +++ b/Modules/ImageStatistics/Testing/mitkImageStatisticsHotspotTest.cpp @@ -1,651 +1,653 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkImageStatisticsCalculator.h" #include "itkMultiGaussianImageSource.h" #include "mitkTestingMacros.h" #include "mitkImageCast.h" #include #include #include #include #include #include #include /** \section hotspotCalculationTestCases Testcases To see the different Hotspot-Testcases have a look at the \ref hotspottestdoc. Note from an intensive session of checking the test results: - itk::MultiGaussianImageSource needs a review - the test idea is ok, but the combination of XML files for parameters and MultiGaussianImageSource has serious flaws - the XML file should contain exactly the parameters that MultiGaussianImageSource requires - in contrast, now the XML file mentions index coordinates for gaussian centers while the MultiGaussianImageSource expects world coordinates - this requires a transformation (index * spacing assuming no rotation) that was actually broken until recently */ struct mitkImageStatisticsHotspotTestClass { /** \brief Test parameters for one test case. Describes all aspects of a single test case: - parameters to generate a test image - parameters of a ROI that describes where to calculate statistics - expected statistics results */ struct Parameters { public: // XML-Tag /** \brief XML-Tag "image-rows": size of x-dimension */ int m_ImageRows; /** \brief XML-Tag "image-columns": size of y-dimension */ int m_ImageColumns; /** \brief XML-Tag "image-slices": size of z-dimension */ int m_ImageSlices; /** \brief XML-Tag "numberOfGaussians": number of used gauss-functions */ int m_NumberOfGaussian; /** \brief XML-Tags "spacingX", "spacingY", "spacingZ": spacing of image in every direction */ double m_Spacing[3]; /** \brief XML-Tag "entireHotSpotInImage" */ unsigned int m_EntireHotspotInImage; // XML-Tag /** \brief XML-Tag "centerIndexX: gaussian parameter \warning This parameter READS the centerIndexX parameter from file and is THEN MISUSED to calculate some position in world coordinates, so we require double. */ std::vector m_CenterX; /** \brief XML-Tag "centerIndexY: gaussian parameter \warning This parameter READS the centerIndexX parameter from file and is THEN MISUSED to calculate some position in world coordinates, so we require double. */ std::vector m_CenterY; /** \brief XML-Tag "centerIndexZ: gaussian parameter \warning This parameter READS the centerIndexX parameter from file and is THEN MISUSED to calculate some position in world coordinates, so we require double. */ std::vector m_CenterZ; /** \brief XML-Tag "deviationX: gaussian parameter */ std::vector m_SigmaX; /** \brief XML-Tag "deviationY: gaussian parameter */ std::vector m_SigmaY; /** \brief XML-Tag "deviationZ: gaussian parameter */ std::vector m_SigmaZ; /** \brief XML-Tag "altitude: gaussian parameter */ std::vector m_Altitude; // XML-Tag /** \brief XML-Tag "numberOfLabels": number of different labels which appear in the mask */ unsigned int m_NumberOfLabels; /** \brief XML-Tag "hotspotRadiusInMM": radius of hotspot */ double m_HotspotRadiusInMM; // XML-Tag /** \brief XML-Tag "maximumSizeX": maximum position of ROI in x-dimension */ vnl_vector m_MaxIndexX; /** \brief XML-Tag "minimumSizeX": minimum position of ROI in x-dimension */ vnl_vector m_MinIndexX; /** \brief XML-Tag "maximumSizeX": maximum position of ROI in y-dimension */ vnl_vector m_MaxIndexY; /** \brief XML-Tag "minimumSizeX": minimum position of ROI in y-dimension */ vnl_vector m_MinIndexY; /** \brief XML-Tag "maximumSizeX": maximum position of ROI in z-dimension */ vnl_vector m_MaxIndexZ; /** \brief XML-Tag "minimumSizeX": minimum position of ROI in z-dimension */ vnl_vector m_MinIndexZ; /** \brief XML-Tag "label": value of label */ vnl_vector m_Label; //XML-Tag /** \brief XML-Tag "minimum": minimum inside hotspot */ vnl_vector m_HotspotMin; /** \brief XML-Tag "maximum": maximum inside hotspot */ vnl_vector m_HotspotMax; /** \brief XML-Tag "mean": mean value of hotspot */ vnl_vector m_HotspotMean; /** \brief XML-Tag "maximumIndexX": x-coordinate of maximum-location inside hotspot */ vnl_vector m_HotspotMaxIndexX; /** \brief XML-Tag "maximumIndexX": y-coordinate of maximum-location inside hotspot */ vnl_vector m_HotspotMaxIndexY; /** \brief XML-Tag "maximumIndexX": z-coordinate of maximum-location inside hotspot */ vnl_vector m_HotspotMaxIndexZ; /** \brief XML-Tag "maximumIndexX": x-coordinate of maximum-location inside hotspot */ vnl_vector m_HotspotMinIndexX; /** \brief XML-Tag "maximumIndexX": y-coordinate of maximum-location inside hotspot */ vnl_vector m_HotspotMinIndexY; /** \brief XML-Tag "maximumIndexX": z-coordinate of maximum-location inside hotspot */ vnl_vector m_HotspotMinIndexZ; /** \brief XML-Tag "maximumIndexX": x-coordinate of hotspot-location */ vnl_vector m_HotspotIndexX; /** \brief XML-Tag "maximumIndexX": y-coordinate of hotspot-location */ vnl_vector m_HotspotIndexY; /** \brief XML-Tag "maximumIndexX": z-coordinate of hotspot-location */ vnl_vector m_HotspotIndexZ; }; /** \brief Find/Convert integer attribute in itk::DOMNode. */ static int GetIntegerAttribute(itk::DOMNode* domNode, const std::string& tag) { assert(domNode); MITK_TEST_CONDITION_REQUIRED( domNode->HasAttribute(tag), "Tag '" << tag << "' is defined in test parameters" ); std::string attributeValue = domNode->GetAttribute(tag); int resultValue; try { //MITK_TEST_OUTPUT( << "Converting tag value '" << attributeValue << "' for tag '" << tag << "' to integer"); std::stringstream(attributeValue) >> resultValue; return resultValue; } catch(std::exception& /*e*/) { MITK_TEST_CONDITION_REQUIRED(false, "Convert tag value '" << attributeValue << "' for tag '" << tag << "' to integer"); return 0; // just to satisfy compiler } } /** \brief Find/Convert double attribute in itk::DOMNode. */ static double GetDoubleAttribute(itk::DOMNode* domNode, const std::string& tag) { assert(domNode); MITK_TEST_CONDITION_REQUIRED( domNode->HasAttribute(tag), "Tag '" << tag << "' is defined in test parameters" ); std::string attributeValue = domNode->GetAttribute(tag); double resultValue; try { //MITK_TEST_OUTPUT( << "Converting tag value '" << attributeValue << "' for tag '" << tag << "' to double"); std::stringstream(attributeValue) >> resultValue; return resultValue; } catch(std::exception& /*e*/) { MITK_TEST_CONDITION_REQUIRED(false, "Convert tag value '" << attributeValue << "' for tag '" << tag << "' to double"); return 0.0; // just to satisfy compiler } } /** \brief Read XML file describing the test parameters. Reads XML file given in first commandline parameter in order to construct a Parameters structure. The XML file should be structurs as the following example, i.e. we describe the three test aspects of Parameters in four different tags, with all the details described as tag attributes. */ /** \verbatim \endverbatim */ static Parameters ParseParameters(int argc, char* argv[]) { MITK_TEST_CONDITION_REQUIRED(argc == 2, "Test is invoked with exactly 1 parameter (XML parameters file)"); MITK_INFO << "Reading parameters from file '" << argv[1] << "'"; std::string filename = argv[1]; Parameters result; itk::DOMNodeXMLReader::Pointer xmlReader = itk::DOMNodeXMLReader::New(); xmlReader->SetFileName( filename ); try { xmlReader->Update(); itk::DOMNode::Pointer domRoot = xmlReader->GetOutput(); typedef std::vector NodeList; NodeList testimages; domRoot->GetChildren("testimage", testimages); MITK_TEST_CONDITION_REQUIRED( testimages.size() == 1, "One test image defined" ) itk::DOMNode* testimage = testimages[0]; result.m_ImageRows = GetIntegerAttribute( testimage, "image-rows" ); result.m_ImageColumns = GetIntegerAttribute( testimage, "image-columns" ); result.m_ImageSlices = GetIntegerAttribute( testimage, "image-slices" ); result.m_NumberOfGaussian = GetIntegerAttribute( testimage, "numberOfGaussians" ); result.m_Spacing[0] = GetDoubleAttribute(testimage, "spacingX"); result.m_Spacing[1] = GetDoubleAttribute(testimage, "spacingY"); result.m_Spacing[2] = GetDoubleAttribute(testimage, "spacingZ"); result.m_EntireHotspotInImage = GetIntegerAttribute( testimage, "entireHotSpotInImage" ); MITK_TEST_OUTPUT( << "Read size parameters (x,y,z): " << result.m_ImageRows << "," << result.m_ImageColumns << "," << result.m_ImageSlices); MITK_TEST_OUTPUT( << "Read spacing parameters (x,y,z): " << result.m_Spacing[0] << "," << result.m_Spacing[1] << "," << result.m_Spacing[2]); NodeList gaussians; testimage->GetChildren("gaussian", gaussians); MITK_TEST_CONDITION_REQUIRED( gaussians.size() >= 1, "At least one gaussian is defined" ) result.m_CenterX.resize(result.m_NumberOfGaussian); result.m_CenterY.resize(result.m_NumberOfGaussian); result.m_CenterZ.resize(result.m_NumberOfGaussian); result.m_SigmaX.resize(result.m_NumberOfGaussian); result.m_SigmaY.resize(result.m_NumberOfGaussian); result.m_SigmaZ.resize(result.m_NumberOfGaussian); result.m_Altitude.resize(result.m_NumberOfGaussian); for(int i = 0; i < result.m_NumberOfGaussian ; ++i) { itk::DOMNode* gaussian = gaussians[i]; result.m_CenterX[i] = GetIntegerAttribute(gaussian, "centerIndexX"); result.m_CenterY[i] = GetIntegerAttribute(gaussian, "centerIndexY"); result.m_CenterZ[i] = GetIntegerAttribute(gaussian, "centerIndexZ"); result.m_SigmaX[i] = GetDoubleAttribute(gaussian, "deviationX"); result.m_SigmaY[i] = GetDoubleAttribute(gaussian, "deviationY"); result.m_SigmaZ[i] = GetDoubleAttribute(gaussian, "deviationZ"); result.m_Altitude[i] = GetDoubleAttribute(gaussian, "altitude"); result.m_CenterX[i] = result.m_CenterX[i] * result.m_Spacing[0]; result.m_CenterY[i] = result.m_CenterY[i] * result.m_Spacing[1]; result.m_CenterZ[i] = result.m_CenterZ[i] * result.m_Spacing[2]; result.m_SigmaX[i] = result.m_SigmaX[i] * result.m_Spacing[0]; result.m_SigmaY[i] = result.m_SigmaY[i] * result.m_Spacing[1]; result.m_SigmaZ[i] = result.m_SigmaZ[i] * result.m_Spacing[2]; } NodeList segmentations; domRoot->GetChildren("segmentation", segmentations); MITK_TEST_CONDITION_REQUIRED( segmentations.size() == 1, "One segmentation defined"); itk::DOMNode* segmentation = segmentations[0]; result.m_NumberOfLabels = GetIntegerAttribute(segmentation, "numberOfLabels"); result.m_HotspotRadiusInMM = GetDoubleAttribute(segmentation, "hotspotRadiusInMM"); // read ROI parameters, fill result structure NodeList rois; segmentation->GetChildren("roi", rois); MITK_TEST_CONDITION_REQUIRED( rois.size() >= 1, "At least one ROI defined" ) result.m_MaxIndexX.set_size(result.m_NumberOfLabels); result.m_MinIndexX.set_size(result.m_NumberOfLabels); result.m_MaxIndexY.set_size(result.m_NumberOfLabels); result.m_MinIndexY.set_size(result.m_NumberOfLabels); result.m_MaxIndexZ.set_size(result.m_NumberOfLabels); result.m_MinIndexZ.set_size(result.m_NumberOfLabels); result.m_Label.set_size(result.m_NumberOfLabels); for(unsigned int i = 0; i < rois.size(); ++i) { result.m_MaxIndexX[i] = GetIntegerAttribute(rois[i], "maximumIndexX"); result.m_MinIndexX[i] = GetIntegerAttribute(rois[i], "minimumIndexX"); result.m_MaxIndexY[i] = GetIntegerAttribute(rois[i], "maximumIndexY"); result.m_MinIndexY[i] = GetIntegerAttribute(rois[i], "minimumIndexY"); result.m_MaxIndexZ[i] = GetIntegerAttribute(rois[i], "maximumIndexZ"); result.m_MinIndexZ[i] = GetIntegerAttribute(rois[i], "minimumIndexZ"); result.m_Label[i] = GetIntegerAttribute(rois[i], "label"); } // read statistic parameters, fill result structure NodeList statistics; domRoot->GetChildren("statistic", statistics); MITK_TEST_CONDITION_REQUIRED( statistics.size() >= 1 , "At least one statistic defined" ) MITK_TEST_CONDITION_REQUIRED( statistics.size() == rois.size(), "Same number of rois and corresponding statistics defined"); result.m_HotspotMin.set_size(statistics.size()); result.m_HotspotMax.set_size(statistics.size()); result.m_HotspotMean.set_size(statistics.size()); result.m_HotspotMinIndexX.set_size(statistics.size()); result.m_HotspotMinIndexY.set_size(statistics.size()); result.m_HotspotMinIndexZ.set_size(statistics.size()); result.m_HotspotMaxIndexX.set_size(statistics.size()); result.m_HotspotMaxIndexY.set_size(statistics.size()); result.m_HotspotMaxIndexZ.set_size(statistics.size()); result.m_HotspotIndexX.set_size(statistics.size()); result.m_HotspotIndexY.set_size(statistics.size()); result.m_HotspotIndexZ.set_size(statistics.size()); for(unsigned int i = 0; i < statistics.size(); ++i) { result.m_HotspotMin[i] = GetDoubleAttribute(statistics[i], "minimum"); result.m_HotspotMax[i] = GetDoubleAttribute(statistics[i], "maximum"); result.m_HotspotMean[i] = GetDoubleAttribute(statistics[i], "mean"); result.m_HotspotMinIndexX[i] = GetIntegerAttribute(statistics[i], "minimumIndexX"); result.m_HotspotMinIndexY[i] = GetIntegerAttribute(statistics[i], "minimumIndexY"); result.m_HotspotMinIndexZ[i] = GetIntegerAttribute(statistics[i], "minimumIndexZ"); result.m_HotspotMaxIndexX[i] = GetIntegerAttribute(statistics[i], "maximumIndexX"); result.m_HotspotMaxIndexY[i] = GetIntegerAttribute(statistics[i], "maximumIndexY"); result.m_HotspotMaxIndexZ[i] = GetIntegerAttribute(statistics[i], "maximumIndexZ"); result.m_HotspotIndexX[i] = GetIntegerAttribute(statistics[i], "hotspotIndexX"); result.m_HotspotIndexY[i] = GetIntegerAttribute(statistics[i], "hotspotIndexY"); result.m_HotspotIndexZ[i] = GetIntegerAttribute(statistics[i], "hotspotIndexZ"); } } catch (std::exception& e) { MITK_TEST_CONDITION_REQUIRED(false, "Reading test parameters from XML file. Error message: " << e.what()); } return result; } /** \brief Generate an image that contains a couple of 3D gaussian distributions. Uses the given parameters to produce a test image using class MultiGaussianImageSource. */ static mitk::Image::Pointer BuildTestImage(const Parameters& testParameters) { mitk::Image::Pointer result; typedef double PixelType; const int Dimension = 3; typedef itk::Image ImageType; ImageType::Pointer image = ImageType::New(); typedef itk::MultiGaussianImageSource< ImageType > MultiGaussianImageSource; MultiGaussianImageSource::Pointer gaussianGenerator = MultiGaussianImageSource::New(); ImageType::SizeValueType size[3]; size[0] = testParameters.m_ImageColumns; size[1] = testParameters.m_ImageRows; size[2] = testParameters.m_ImageSlices; itk::MultiGaussianImageSource::VectorType centerXVec, centerYVec, centerZVec, sigmaXVec, sigmaYVec, sigmaZVec, altitudeVec; for(int i = 0; i < testParameters.m_NumberOfGaussian; ++i) { centerXVec.push_back(testParameters.m_CenterX[i]); centerYVec.push_back(testParameters.m_CenterY[i]); centerZVec.push_back(testParameters.m_CenterZ[i]); sigmaXVec.push_back(testParameters.m_SigmaX[i]); sigmaYVec.push_back(testParameters.m_SigmaY[i]); sigmaZVec.push_back(testParameters.m_SigmaZ[i]); altitudeVec.push_back(testParameters.m_Altitude[i]); } ImageType::SpacingType spacing; for( int i = 0; i < Dimension; ++i ) spacing[i] = testParameters.m_Spacing[i]; gaussianGenerator->SetSize( size ); gaussianGenerator->SetSpacing( spacing ); gaussianGenerator->SetRadius(testParameters.m_HotspotRadiusInMM); gaussianGenerator->SetNumberOfGausssians(testParameters.m_NumberOfGaussian); gaussianGenerator->AddGaussian(centerXVec, centerYVec, centerZVec, sigmaXVec, sigmaYVec, sigmaZVec, altitudeVec); gaussianGenerator->Update(); image = gaussianGenerator->GetOutput(); mitk::CastToMitkImage(image, result); return result; } /** \brief Calculates hotspot statistics for given test image and ROI parameters. Uses ImageStatisticsCalculator to find a hotspot in a defined ROI within the given image. */ - static mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer CalculateStatistics(mitk::Image* image, const Parameters& testParameters, unsigned int label) + static mitk::ImageStatisticsContainer::StatisticsObject CalculateStatistics(mitk::Image* image, const Parameters& testParameters, unsigned int label) { - mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer result; const unsigned int Dimension = 3; typedef itk::Image MaskImageType; MaskImageType::Pointer mask = MaskImageType::New(); MaskImageType::SizeType size; MaskImageType::SpacingType spacing; MaskImageType::IndexType start; mitk::ImageStatisticsCalculator::Pointer statisticsCalculator = mitk::ImageStatisticsCalculator::New(); statisticsCalculator->SetInputImage(image); mitk::Image::Pointer mitkMaskImage; if((testParameters.m_MaxIndexX[label] > testParameters.m_MinIndexX[label] && testParameters.m_MinIndexX[label] >= 0) && (testParameters.m_MaxIndexY[label] > testParameters.m_MinIndexY[label] && testParameters.m_MinIndexY[label] >= 0) && (testParameters.m_MaxIndexZ[label] > testParameters.m_MinIndexZ[label] && testParameters.m_MinIndexZ[label] >= 0)) { for(unsigned int i = 0; i < Dimension; ++i) { start[i] = 0; spacing[i] = testParameters.m_Spacing[i]; } size[0] = testParameters.m_ImageColumns; size[1] = testParameters.m_ImageRows; size[2] = testParameters.m_ImageSlices; MaskImageType::RegionType region; region.SetIndex(start); region.SetSize(size); mask->SetSpacing(spacing); mask->SetRegions(region); mask->Allocate(); typedef itk::ImageRegionIteratorWithIndex MaskImageIteratorType; MaskImageIteratorType maskIt(mask, region); for(maskIt.GoToBegin(); !maskIt.IsAtEnd(); ++maskIt) { maskIt.Set(0); } for(unsigned int i = 0; i < testParameters.m_NumberOfLabels; ++i) { for(maskIt.GoToBegin(); !maskIt.IsAtEnd(); ++maskIt) { MaskImageType::IndexType index = maskIt.GetIndex(); if((index[0] >= testParameters.m_MinIndexX[i] && index[0] <= testParameters.m_MaxIndexX[i] ) && (index[1] >= testParameters.m_MinIndexY[i] && index[1] <= testParameters.m_MaxIndexY[i] ) && (index[2] >= testParameters.m_MinIndexZ[i] && index[2] <= testParameters.m_MaxIndexZ[i] )) { maskIt.Set(testParameters.m_Label[i]); } } } mitk::CastToMitkImage(mask, mitkMaskImage); mitk::ImageMaskGenerator::Pointer imgMaskGen = mitk::ImageMaskGenerator::New(); imgMaskGen->SetImageMask(mitkMaskImage); mitk::HotspotMaskGenerator::Pointer hotspotMaskGen = mitk::HotspotMaskGenerator::New(); hotspotMaskGen->SetInputImage(image); hotspotMaskGen->SetLabel(testParameters.m_Label[label]); hotspotMaskGen->SetMask(imgMaskGen.GetPointer()); hotspotMaskGen->SetHotspotRadiusInMM(testParameters.m_HotspotRadiusInMM); if(testParameters.m_EntireHotspotInImage == 1) { MITK_INFO << "Hotspot must be completly inside image"; hotspotMaskGen->SetHotspotMustBeCompletelyInsideImage(true); } else { MITK_INFO << "Hotspot must not be completly inside image"; hotspotMaskGen->SetHotspotMustBeCompletelyInsideImage(false); } statisticsCalculator->SetMask(hotspotMaskGen.GetPointer()); MITK_DEBUG << "Masking is set to hotspot+image mask"; } else { mitk::HotspotMaskGenerator::Pointer hotspotMaskGen = mitk::HotspotMaskGenerator::New(); hotspotMaskGen->SetInputImage(image); hotspotMaskGen->SetHotspotRadiusInMM(testParameters.m_HotspotRadiusInMM); if(testParameters.m_EntireHotspotInImage == 1) { MITK_INFO << "Hotspot must be completly inside image"; hotspotMaskGen->SetHotspotMustBeCompletelyInsideImage(true); } else { MITK_INFO << "Hotspot must not be completly inside image"; hotspotMaskGen->SetHotspotMustBeCompletelyInsideImage(false); } MITK_DEBUG << "Masking is set to hotspot only"; } - result = statisticsCalculator->GetStatistics(0); - return result; + return statisticsCalculator->GetStatistics()->GetStatisticsForTimeStep(0); } static void ValidateStatisticsItem(const std::string& label, double testvalue, double reference, double tolerance) { double diff = ::fabs(reference - testvalue); MITK_TEST_CONDITION( diff < tolerance, "'" << label << "' value close enough to reference value " "(value=" << testvalue << ", reference=" << reference << ", diff=" << diff << ")" ); } static void ValidateStatisticsItem(const std::string& label, const vnl_vector& testvalue, const vnl_vector& reference) { double diffX = ::fabs(double(testvalue[0] - reference[0])); double diffY = ::fabs(double(testvalue[1] - reference[1])); double diffZ = ::fabs(double(testvalue[2] - reference[2])); std::stringstream testPosition; testPosition << testvalue[0] << "," << testvalue[1] << "," << testvalue[2]; std::stringstream referencePosition; referencePosition << reference[0] << "," << reference[1] << "," << reference[2]; MITK_TEST_CONDITION( diffX < mitk::eps && diffY < mitk::eps && diffZ < mitk::eps, "'" << label << "' close enough to reference value " << "(value=[" << testPosition.str() << "]," << " reference=[" << referencePosition.str() << "]"); } /** \brief Compares calculated against actual statistics values. Checks validness of all statistics aspects. Lets test fail if any aspect is not sufficiently equal. */ - static void ValidateStatistics(const mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer hotspotStatistics, const Parameters& testParameters, unsigned int label) + static void ValidateStatistics(const mitk::ImageStatisticsContainer::StatisticsObject hotspotStatistics, const Parameters& testParameters, unsigned int label) { // check all expected test result against actual results double eps = 0.25; // value above the largest tested difference - ValidateStatisticsItem("Hotspot mean", hotspotStatistics->GetMean(), testParameters.m_HotspotMean[label], eps); - ValidateStatisticsItem("Hotspot maximum", hotspotStatistics->GetMax(), testParameters.m_HotspotMax[label], eps); - ValidateStatisticsItem("Hotspot minimum", hotspotStatistics->GetMin(), testParameters.m_HotspotMin[label], eps); + auto mean = hotspotStatistics.GetValueConverted(mitk::ImageStatisticsConstants::MEAN()); + auto max = hotspotStatistics.GetValueConverted(mitk::ImageStatisticsConstants::MAXIMUM()); + auto min = hotspotStatistics.GetValueConverted(mitk::ImageStatisticsConstants::MINIMUM()); + + ValidateStatisticsItem("Hotspot mean", mean, testParameters.m_HotspotMean[label], eps); + ValidateStatisticsItem("Hotspot maximum", max, testParameters.m_HotspotMax[label], eps); + ValidateStatisticsItem("Hotspot minimum", min, testParameters.m_HotspotMin[label], eps); vnl_vector referenceHotspotCenterIndex; referenceHotspotCenterIndex.set_size(3); referenceHotspotCenterIndex[0] = testParameters.m_HotspotIndexX[label]; referenceHotspotCenterIndex[1] = testParameters.m_HotspotIndexY[label]; referenceHotspotCenterIndex[2] = testParameters.m_HotspotIndexZ[label]; // ValidateStatisticsItem("Hotspot center position", statistics.GetHotspotStatistics().GetHotspotIndex(), referenceHotspotCenterIndex); TODO: new image statistics calculator does not give hotspot position // TODO we do not test minimum/maximum positions within the peak/hotspot region, because // these positions are not unique, i.e. there are multiple valid minima/maxima positions. // One solution would be to modify the test cases in order to achive clear positions. // The BETTER/CORRECT solution would be to change the singular position into a set of positions / a region } }; /** \brief Verifies that hotspot statistics part of ImageStatisticsCalculator. The test reads parameters from an XML-file to generate a test-image, calculates the hotspot statistics of the image and checks if the calculated statistics are the same as the specified values of the XML-file. */ int mitkImageStatisticsHotspotTest(int argc, char* argv[]) { MITK_TEST_BEGIN("mitkImageStatisticsHotspotTest") try { mitkImageStatisticsHotspotTestClass::Parameters parameters = mitkImageStatisticsHotspotTestClass::ParseParameters(argc,argv); mitk::Image::Pointer image = mitkImageStatisticsHotspotTestClass::BuildTestImage(parameters); MITK_TEST_CONDITION_REQUIRED( image.IsNotNull(), "Generate test image" ); for(unsigned int label = 0; label < parameters.m_NumberOfLabels; ++label) { - mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer statistics = mitkImageStatisticsHotspotTestClass::CalculateStatistics(image, parameters, label); + mitk::ImageStatisticsContainer::StatisticsObject statistics = mitkImageStatisticsHotspotTestClass::CalculateStatistics(image, parameters, label); mitkImageStatisticsHotspotTestClass::ValidateStatistics(statistics, parameters, label); std::cout << std::endl; } } catch (std::exception& e) { std::cout << "Error: " << e.what() << std::endl; MITK_TEST_CONDITION_REQUIRED( false, "Exception occurred during test execution: " << e.what() ); } catch(...) { MITK_TEST_CONDITION_REQUIRED( false, "Exception occurred during test execution." ); } MITK_TEST_END() } diff --git a/Modules/ImageStatistics/files.cmake b/Modules/ImageStatistics/files.cmake index 5904c1fdfb..d41c612329 100644 --- a/Modules/ImageStatistics/files.cmake +++ b/Modules/ImageStatistics/files.cmake @@ -1,33 +1,47 @@ set(CPP_FILES mitkImageStatisticsCalculator.cpp + mitkImageStatisticsContainer.cpp mitkPointSetStatisticsCalculator.cpp mitkPointSetDifferenceStatisticsCalculator.cpp mitkIntensityProfile.cpp mitkHotspotMaskGenerator.cpp mitkMaskGenerator.cpp mitkPlanarFigureMaskGenerator.cpp mitkMultiLabelMaskGenerator.cpp mitkImageMaskGenerator.cpp mitkHistogramStatisticsCalculator.cpp mitkMaskUtilities.cpp mitkIgnorePixelMaskGenerator.cpp + mitkImageStatisticsPredicateHelper.cpp + mitkImageStatisticsContainerNodeHelper.cpp + mitkImageStatisticsContainerManager.cpp + mitkStatisticsToImageRelationRule.cpp + mitkStatisticsToMaskRelationRule.cpp + mitkImageStatisticsConstants.cpp ) set(H_FILES mitkImageStatisticsCalculator.h + mitkImageStatisticsContainer.h mitkPointSetDifferenceStatisticsCalculator.h mitkPointSetStatisticsCalculator.h mitkExtendedStatisticsImageFilter.h mitkExtendedLabelStatisticsImageFilter.h mitkHotspotMaskGenerator.h mitkMaskGenerator.h mitkPlanarFigureMaskGenerator.h mitkMultiLabelMaskGenerator.h mitkImageMaskGenerator.h mitkHistogramStatisticsCalculator.h mitkMaskUtilities.h mitkitkMaskImageFilter.h mitkIgnorePixelMaskGenerator.h mitkMinMaxImageFilterWithIndex.h mitkMinMaxLabelmageFilterWithIndex.h + mitkImageStatisticsPredicateHelper.h + mitkImageStatisticsContainerNodeHelper.h + mitkImageStatisticsContainerManager.h + mitkStatisticsToImageRelationRule.h + mitkStatisticsToMaskRelationRule.h + mitkImageStatisticsConstants.h ) diff --git a/Modules/ImageStatistics/mitkImageStatisticsCalculator.cpp b/Modules/ImageStatistics/mitkImageStatisticsCalculator.cpp index ff59624466..771e715948 100644 --- a/Modules/ImageStatistics/mitkImageStatisticsCalculator.cpp +++ b/Modules/ImageStatistics/mitkImageStatisticsCalculator.cpp @@ -1,630 +1,564 @@ +/*=================================================================== -#include -#include - -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include - -#include +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include "mitkImageStatisticsCalculator.h" +#include +#include #include -#include #include -#include -#include -#include +#include +#include #include +#include +#include #include #include #include -#include - - - -#include - -#include "itkImageFileWriter.h" namespace mitk { - - void ImageStatisticsCalculator::SetInputImage(mitk::Image::Pointer image) + void ImageStatisticsCalculator::SetInputImage(mitk::Image::ConstPointer image) + { + if (image != m_Image) { - if (image != m_Image) - { - m_Image = image; - m_StatisticsByTimeStep.resize(m_Image->GetTimeSteps()); - m_StatisticsUpdateTimePerTimeStep.resize(m_Image->GetTimeSteps()); - std::fill(m_StatisticsUpdateTimePerTimeStep.begin(), m_StatisticsUpdateTimePerTimeStep.end(), 0); - this->Modified(); - } + m_Image = image; + this->Modified(); } + } - void ImageStatisticsCalculator::SetMask(mitk::MaskGenerator::Pointer mask) + void ImageStatisticsCalculator::SetMask(mitk::MaskGenerator::Pointer mask) + { + if (mask != m_MaskGenerator) { - - if (mask != m_MaskGenerator) - { - m_MaskGenerator = mask; - this->Modified(); - } - + m_MaskGenerator = mask; + this->Modified(); } + } - void ImageStatisticsCalculator::SetSecondaryMask(mitk::MaskGenerator::Pointer mask) + void ImageStatisticsCalculator::SetSecondaryMask(mitk::MaskGenerator::Pointer mask) + { + if (mask != m_SecondaryMaskGenerator) { + m_SecondaryMaskGenerator = mask; + this->Modified(); + } + } - if (mask != m_SecondaryMaskGenerator) - { - m_SecondaryMaskGenerator = mask; - this->Modified(); - } - + void ImageStatisticsCalculator::SetNBinsForHistogramStatistics(unsigned int nBins) + { + if (nBins != m_nBinsForHistogramStatistics) + { + m_nBinsForHistogramStatistics = nBins; + this->Modified(); + this->m_UseBinSizeOverNBins = false; } + if (m_UseBinSizeOverNBins) + { + this->Modified(); + this->m_UseBinSizeOverNBins = false; + } + } + unsigned int ImageStatisticsCalculator::GetNBinsForHistogramStatistics() const + { + return m_nBinsForHistogramStatistics; + } - void ImageStatisticsCalculator::SetNBinsForHistogramStatistics(unsigned int nBins) + void ImageStatisticsCalculator::SetBinSizeForHistogramStatistics(double binSize) + { + if (binSize != m_binSizeForHistogramStatistics) { - if (nBins != m_nBinsForHistogramStatistics) - { - m_nBinsForHistogramStatistics = nBins; - this->Modified(); - this->m_UseBinSizeOverNBins = false; - } - if (m_UseBinSizeOverNBins) - { - this->Modified(); - this->m_UseBinSizeOverNBins = false; - } + m_binSizeForHistogramStatistics = binSize; + this->Modified(); + this->m_UseBinSizeOverNBins = true; } - - unsigned int ImageStatisticsCalculator::GetNBinsForHistogramStatistics() const + if (!m_UseBinSizeOverNBins) { - return m_nBinsForHistogramStatistics; + this->Modified(); + this->m_UseBinSizeOverNBins = true; } + } + + double ImageStatisticsCalculator::GetBinSizeForHistogramStatistics() const { return m_binSizeForHistogramStatistics; } - void ImageStatisticsCalculator::SetBinSizeForHistogramStatistics(double binSize) + mitk::ImageStatisticsContainer::Pointer ImageStatisticsCalculator::GetStatistics(LabelIndex label) + { + if (m_Image.IsNull()) { - if (binSize != m_binSizeForHistogramStatistics) - { - m_binSizeForHistogramStatistics = binSize; - this->Modified(); - this->m_UseBinSizeOverNBins = true; - } - if (!m_UseBinSizeOverNBins) - { - this->Modified(); - this->m_UseBinSizeOverNBins = true; - } + mitkThrow() << "no image"; } - double ImageStatisticsCalculator::GetBinSizeForHistogramStatistics() const + if (!m_Image->IsInitialized()) { - return m_binSizeForHistogramStatistics; + mitkThrow() << "Image not initialized!"; } - ImageStatisticsCalculator::StatisticsContainer::Pointer ImageStatisticsCalculator::GetStatistics(unsigned int timeStep, unsigned int label) + if (IsUpdateRequired(label)) { - - if (timeStep >= m_StatisticsByTimeStep.size()) + // auto aStatisticContainer = ImageStatisticsContainer::New(); + auto timeGeometry = m_Image->GetTimeGeometry(); + // aStatisticContainer->SetTimeGeometry(timeGeometry); + // always compute statistics on all timesteps + for (unsigned int timeStep = 0; timeStep < m_Image->GetTimeSteps(); timeStep++) + { + if (m_MaskGenerator.IsNotNull()) { - mitkThrow() << "invalid timeStep in ImageStatisticsCalculator_v2::GetStatistics"; + m_MaskGenerator->SetTimeStep(timeStep); + //See T25625: otherwise, the mask is not computed again after setting a different time step + m_MaskGenerator->Modified(); + m_InternalMask = m_MaskGenerator->GetMask(); + if (m_MaskGenerator->GetReferenceImage().IsNotNull()) + { + m_InternalImageForStatistics = m_MaskGenerator->GetReferenceImage(); + } + else + { + m_InternalImageForStatistics = m_Image; + } } - - if (m_Image.IsNull()) + else { - mitkThrow() << "no image"; + m_InternalImageForStatistics = m_Image; } - if (!m_Image->IsInitialized()) + if (m_SecondaryMaskGenerator.IsNotNull()) { - mitkThrow() << "Image not initialized!"; + m_SecondaryMaskGenerator->SetTimeStep(timeStep); + m_SecondaryMask = m_SecondaryMaskGenerator->GetMask(); } - if (IsUpdateRequired(timeStep)) + ImageTimeSelector::Pointer imgTimeSel = ImageTimeSelector::New(); + imgTimeSel->SetInput(m_InternalImageForStatistics); + imgTimeSel->SetTimeNr(timeStep); + imgTimeSel->UpdateLargestPossibleRegion(); + imgTimeSel->Update(); + m_ImageTimeSlice = imgTimeSel->GetOutput(); + + // Calculate statistics with/without mask + if (m_MaskGenerator.IsNull() && m_SecondaryMaskGenerator.IsNull()) { - if (m_MaskGenerator.IsNotNull()) - { - m_MaskGenerator->SetTimeStep(timeStep); - m_InternalMask = m_MaskGenerator->GetMask(); - if (m_MaskGenerator->GetReferenceImage().IsNotNull()) - { - m_InternalImageForStatistics = m_MaskGenerator->GetReferenceImage(); - } - else - { - m_InternalImageForStatistics = m_Image; - } - } - else - { - m_InternalImageForStatistics = m_Image; - } - - if (m_SecondaryMaskGenerator.IsNotNull()) - { - m_SecondaryMaskGenerator->SetTimeStep(timeStep); - m_SecondaryMask = m_SecondaryMaskGenerator->GetMask(); - } - - ImageTimeSelector::Pointer imgTimeSel = ImageTimeSelector::New(); - imgTimeSel->SetInput(m_InternalImageForStatistics); - imgTimeSel->SetTimeNr(timeStep); - imgTimeSel->UpdateLargestPossibleRegion(); - m_ImageTimeSlice = imgTimeSel->GetOutput(); - - - // Calculate statistics with/without mask - if (m_MaskGenerator.IsNull() && m_SecondaryMaskGenerator.IsNull()) - { - // 1) calculate statistics unmasked: - AccessByItk_1(m_ImageTimeSlice, InternalCalculateStatisticsUnmasked, timeStep) - - } - else - { - // 2) calculate statistics masked - AccessByItk_1(m_ImageTimeSlice, InternalCalculateStatisticsMasked, timeStep) - } - - - //this->Modified(); + // 1) calculate statistics unmasked: + AccessByItk_2(m_ImageTimeSlice, InternalCalculateStatisticsUnmasked, timeGeometry, timeStep) } - - m_StatisticsUpdateTimePerTimeStep[timeStep] = m_StatisticsByTimeStep[timeStep][m_StatisticsByTimeStep[timeStep].size()-1]->GetMTime(); - - for (auto it = m_StatisticsByTimeStep[timeStep].begin(); it != m_StatisticsByTimeStep[timeStep].end(); ++it) + else { - StatisticsContainer::Pointer statCont = *it; - if (statCont->GetLabel() == label) - { - return statCont->Clone(); - } + // 2) calculate statistics masked + AccessByItk_2(m_ImageTimeSlice, InternalCalculateStatisticsMasked, timeGeometry, timeStep) } - // these lines will ony be executed if the requested label could not be found! - MITK_WARN << "Invalid label: " << label << " in time step: " << timeStep; - return StatisticsContainer::New(); + // this->Modified(); + } } - template < typename TPixel, unsigned int VImageDimension > void ImageStatisticsCalculator::InternalCalculateStatisticsUnmasked( - typename itk::Image< TPixel, VImageDimension >* image, unsigned int timeStep) + auto it = m_StatisticContainers.find(label); + if (it != m_StatisticContainers.end()) { - typedef typename itk::Image< TPixel, VImageDimension > ImageType; - typedef typename itk::ExtendedStatisticsImageFilter ImageStatisticsFilterType; - typedef typename itk::MinMaxImageFilterWithIndex MinMaxFilterType; - - StatisticsContainer::Pointer statisticsResult = StatisticsContainer::New(); + return it->second; + } + else + { + mitkThrow() << "unknown label"; + return nullptr; + } + } + + template + void ImageStatisticsCalculator::InternalCalculateStatisticsUnmasked( + typename itk::Image *image, const TimeGeometry *timeGeometry, TimeStepType timeStep) + { + typedef typename itk::Image ImageType; + typedef typename itk::ExtendedStatisticsImageFilter ImageStatisticsFilterType; + typedef typename itk::MinMaxImageFilterWithIndex MinMaxFilterType; + + // reset statistics container if exists + ImageStatisticsContainer::Pointer statisticContainerForImage; + LabelIndex labelNoMask = 1; + auto it = m_StatisticContainers.find(labelNoMask); + if (it != m_StatisticContainers.end()) + { + statisticContainerForImage = it->second; + // statisticContainerForImage->Reset(); + // statisticContainerForImage->SetTimeGeometry(timeGeometry); + } + else + { + statisticContainerForImage = ImageStatisticsContainer::New(); + statisticContainerForImage->SetTimeGeometry(const_cast(timeGeometry)); + m_StatisticContainers.emplace(labelNoMask, statisticContainerForImage); + } - typename ImageStatisticsFilterType::Pointer statisticsFilter = ImageStatisticsFilterType::New(); - statisticsFilter->SetInput(image); - statisticsFilter->SetCoordinateTolerance(0.001); - statisticsFilter->SetDirectionTolerance(0.001); + auto statObj = ImageStatisticsContainer::StatisticsObject(); - // TODO: this is single threaded. Implement our own image filter that does this multi threaded -// typename itk::MinimumMaximumImageCalculator::Pointer imgMinMaxFilter = itk::MinimumMaximumImageCalculator::New(); -// imgMinMaxFilter->SetImage(image); -// imgMinMaxFilter->Compute(); - vnl_vector minIndex, maxIndex; + typename ImageStatisticsFilterType::Pointer statisticsFilter = ImageStatisticsFilterType::New(); + statisticsFilter->SetInput(image); + statisticsFilter->SetCoordinateTolerance(0.001); + statisticsFilter->SetDirectionTolerance(0.001); - typename MinMaxFilterType::Pointer minMaxFilter = MinMaxFilterType::New(); - minMaxFilter->SetInput(image); - minMaxFilter->UpdateLargestPossibleRegion(); - typename ImageType::PixelType minval = minMaxFilter->GetMin(); - typename ImageType::PixelType maxval = minMaxFilter->GetMax(); + // TODO: this is single threaded. Implement our own image filter that does this multi threaded + // typename itk::MinimumMaximumImageCalculator::Pointer imgMinMaxFilter = + // itk::MinimumMaximumImageCalculator::New(); imgMinMaxFilter->SetImage(image); + // imgMinMaxFilter->Compute(); + vnl_vector minIndex, maxIndex; - typename ImageType::IndexType tmpMinIndex = minMaxFilter->GetMinIndex(); - typename ImageType::IndexType tmpMaxIndex = minMaxFilter->GetMaxIndex(); + typename MinMaxFilterType::Pointer minMaxFilter = MinMaxFilterType::New(); + minMaxFilter->SetInput(image); + minMaxFilter->UpdateLargestPossibleRegion(); + typename ImageType::PixelType minval = minMaxFilter->GetMin(); + typename ImageType::PixelType maxval = minMaxFilter->GetMax(); -// typename ImageType::IndexType tmpMinIndex = imgMinMaxFilter->GetIndexOfMinimum(); -// typename ImageType::IndexType tmpMaxIndex = imgMinMaxFilter->GetIndexOfMaximum(); + typename ImageType::IndexType tmpMinIndex = minMaxFilter->GetMinIndex(); + typename ImageType::IndexType tmpMaxIndex = minMaxFilter->GetMaxIndex(); - minIndex.set_size(tmpMaxIndex.GetIndexDimension()); - maxIndex.set_size(tmpMaxIndex.GetIndexDimension()); + // typename ImageType::IndexType tmpMinIndex = imgMinMaxFilter->GetIndexOfMinimum(); + // typename ImageType::IndexType tmpMaxIndex = imgMinMaxFilter->GetIndexOfMaximum(); - for (unsigned int i=0; i < tmpMaxIndex.GetIndexDimension(); i++) - { - minIndex[i] = tmpMinIndex[i]; - maxIndex[i] = tmpMaxIndex[i]; - } + minIndex.set_size(tmpMaxIndex.GetIndexDimension()); + maxIndex.set_size(tmpMaxIndex.GetIndexDimension()); - statisticsResult->SetMinIndex(minIndex); - statisticsResult->SetMaxIndex(maxIndex); + for (unsigned int i = 0; i < tmpMaxIndex.GetIndexDimension(); i++) + { + minIndex[i] = tmpMinIndex[i]; + maxIndex[i] = tmpMaxIndex[i]; + } - //convert m_binSize in m_nBins if necessary - unsigned int nBinsForHistogram; - if (m_UseBinSizeOverNBins) - { - nBinsForHistogram = std::max(static_cast(std::ceil(maxval - minval)) / m_binSizeForHistogramStatistics, 10.); // do not allow less than 10 bins - } - else - { - nBinsForHistogram = m_nBinsForHistogramStatistics; - } + statObj.AddStatistic(mitk::ImageStatisticsConstants::MINIMUMPOSITION(), minIndex); + statObj.AddStatistic(mitk::ImageStatisticsConstants::MAXIMUMPOSITION(), maxIndex); - statisticsFilter->SetHistogramParameters(nBinsForHistogram, minval, maxval); + // convert m_binSize in m_nBins if necessary + unsigned int nBinsForHistogram; + if (m_UseBinSizeOverNBins) + { + nBinsForHistogram = std::max(static_cast(std::ceil(maxval - minval)) / m_binSizeForHistogramStatistics, + 10.); // do not allow less than 10 bins + } + else + { + nBinsForHistogram = m_nBinsForHistogramStatistics; + } - try - { - statisticsFilter->Update(); - } - catch (const itk::ExceptionObject& e) - { - mitkThrow() << "Image statistics calculation failed due to following ITK Exception: \n " << e.what(); - } + statisticsFilter->SetHistogramParameters(nBinsForHistogram, minval, maxval); - // no mask, therefore just one label = the whole image - m_StatisticsByTimeStep[timeStep].resize(1); - statisticsResult->SetLabel(1); - statisticsResult->SetN(image->GetLargestPossibleRegion().GetNumberOfPixels()); - statisticsResult->SetMean(statisticsFilter->GetMean()); - statisticsResult->SetMin(statisticsFilter->GetMinimum()); - statisticsResult->SetMax(statisticsFilter->GetMaximum()); - statisticsResult->SetVariance(statisticsFilter->GetVariance()); - statisticsResult->SetStd(statisticsFilter->GetSigma()); - statisticsResult->SetSkewness(statisticsFilter->GetSkewness()); - statisticsResult->SetKurtosis(statisticsFilter->GetKurtosis()); - statisticsResult->SetRMS(std::sqrt(std::pow(statisticsFilter->GetMean(), 2.) + statisticsFilter->GetVariance())); // variance = sigma^2 - statisticsResult->SetMPP(statisticsFilter->GetMPP()); - - statisticsResult->SetEntropy(statisticsFilter->GetEntropy()); - statisticsResult->SetMedian(statisticsFilter->GetMedian()); - statisticsResult->SetUniformity(statisticsFilter->GetUniformity()); - statisticsResult->SetUPP(statisticsFilter->GetUPP()); - statisticsResult->SetHistogram(statisticsFilter->GetHistogram()); - - m_StatisticsByTimeStep[timeStep][0] = statisticsResult; - } - - - template < typename TPixel, unsigned int VImageDimension > void ImageStatisticsCalculator::InternalCalculateStatisticsMasked( - typename itk::Image< TPixel, VImageDimension >* image, - unsigned int timeStep) - { - typedef itk::Image< TPixel, VImageDimension > ImageType; - typedef itk::Image< MaskPixelType, VImageDimension > MaskType; - typedef typename MaskType::PixelType LabelPixelType; - typedef itk::ExtendedLabelStatisticsImageFilter< ImageType, MaskType > ImageStatisticsFilterType; - typedef MaskUtilities< TPixel, VImageDimension > MaskUtilType; - typedef typename itk::MinMaxLabelImageFilterWithIndex MinMaxLabelFilterType; - typedef typename ImageType::PixelType InputImgPixelType; - - // workaround: if m_SecondaryMaskGenerator ist not null but m_MaskGenerator is! (this is the case if we request a 'ignore zuero valued pixels' - // mask in the gui but do not define a primary mask) - bool swapMasks = false; - if (m_SecondaryMask.IsNotNull() && m_InternalMask.IsNull()) - { - m_InternalMask = m_SecondaryMask; - m_SecondaryMask = nullptr; - swapMasks = true; - } + try + { + statisticsFilter->Update(); + } + catch (const itk::ExceptionObject &e) + { + mitkThrow() << "Image statistics calculation failed due to following ITK Exception: \n " << e.what(); + } - // maskImage has to have the same dimension as image - typename MaskType::Pointer maskImage = MaskType::New(); - try { - // try to access the pixel values directly (no copying or casting). Only works if mask pixels are of pixelType unsigned short - maskImage = ImageToItkImage< MaskPixelType, VImageDimension >(m_InternalMask); - } - catch (const itk::ExceptionObject &) + auto voxelVolume = GetVoxelVolume(image); + + auto numberOfPixels = image->GetLargestPossibleRegion().GetNumberOfPixels(); + auto volume = static_cast(numberOfPixels) * voxelVolume; + auto variance = statisticsFilter->GetSigma() * statisticsFilter->GetSigma(); + auto rms = + std::sqrt(std::pow(statisticsFilter->GetMean(), 2.) + statisticsFilter->GetVariance()); // variance = sigma^2 + + statObj.AddStatistic(mitk::ImageStatisticsConstants::NUMBEROFVOXELS(), + static_cast(numberOfPixels)); + statObj.AddStatistic(mitk::ImageStatisticsConstants::VOLUME(), volume); + statObj.AddStatistic(mitk::ImageStatisticsConstants::MEAN(), statisticsFilter->GetMean()); + statObj.AddStatistic(mitk::ImageStatisticsConstants::MINIMUM(), + static_cast(statisticsFilter->GetMinimum())); + statObj.AddStatistic(mitk::ImageStatisticsConstants::MAXIMUM(), + static_cast(statisticsFilter->GetMaximum())); + statObj.AddStatistic(mitk::ImageStatisticsConstants::STANDARDDEVIATION(), statisticsFilter->GetSigma()); + statObj.AddStatistic(mitk::ImageStatisticsConstants::VARIANCE(), variance); + statObj.AddStatistic(mitk::ImageStatisticsConstants::SKEWNESS(), statisticsFilter->GetSkewness()); + statObj.AddStatistic(mitk::ImageStatisticsConstants::KURTOSIS(), statisticsFilter->GetKurtosis()); + statObj.AddStatistic(mitk::ImageStatisticsConstants::RMS(), rms); + statObj.AddStatistic(mitk::ImageStatisticsConstants::MPP(), statisticsFilter->GetMPP()); + statObj.AddStatistic(mitk::ImageStatisticsConstants::ENTROPY(), statisticsFilter->GetEntropy()); + statObj.AddStatistic(mitk::ImageStatisticsConstants::MEDIAN(), statisticsFilter->GetMedian()); + statObj.AddStatistic(mitk::ImageStatisticsConstants::UNIFORMITY(), statisticsFilter->GetUniformity()); + statObj.AddStatistic(mitk::ImageStatisticsConstants::UPP(), statisticsFilter->GetUPP()); + statObj.m_Histogram = statisticsFilter->GetHistogram().GetPointer(); + statisticContainerForImage->SetStatisticsForTimeStep(timeStep, statObj); + } + + template + double ImageStatisticsCalculator::GetVoxelVolume(typename itk::Image *image) const + { + auto spacing = image->GetSpacing(); + double voxelVolume = 1.; + for (unsigned int i = 0; i < image->GetImageDimension(); i++) + { + voxelVolume *= spacing[i]; + } + return voxelVolume; + } + + template + void ImageStatisticsCalculator::InternalCalculateStatisticsMasked(typename itk::Image *image, + const TimeGeometry *timeGeometry, + unsigned int timeStep) + { + typedef itk::Image ImageType; + typedef itk::Image MaskType; + typedef typename MaskType::PixelType LabelPixelType; + typedef itk::ExtendedLabelStatisticsImageFilter ImageStatisticsFilterType; + typedef MaskUtilities MaskUtilType; + typedef typename itk::MinMaxLabelImageFilterWithIndex MinMaxLabelFilterType; + typedef typename ImageType::PixelType InputImgPixelType; + + // workaround: if m_SecondaryMaskGenerator ist not null but m_MaskGenerator is! (this is the case if we request a + // 'ignore zuero valued pixels' mask in the gui but do not define a primary mask) + bool swapMasks = false; + if (m_SecondaryMask.IsNotNull() && m_InternalMask.IsNull()) + { + m_InternalMask = m_SecondaryMask; + m_SecondaryMask = nullptr; + swapMasks = true; + } - { - // if the pixel type of the mask is not short, then we have to make a copy of m_InternalMask (and cast the values) - CastToItkImage(m_InternalMask, maskImage); - } + // maskImage has to have the same dimension as image + typename MaskType::Pointer maskImage = MaskType::New(); + try + { + // try to access the pixel values directly (no copying or casting). Only works if mask pixels are of pixelType + // unsigned short + maskImage = ImageToItkImage(m_InternalMask); + } + catch (const itk::ExceptionObject &) - // if we have a secondary mask (say a ignoreZeroPixelMask) we need to combine the masks (corresponds to AND) - if (m_SecondaryMask.IsNotNull()) - { - // dirty workaround for a bug when pf mask + any other mask is used in conjunction. We need a proper fix for this (Fabian Isensee is responsible and probably working on it!) - if (m_InternalMask->GetDimension() == 2 && (m_SecondaryMask->GetDimension() == 3 || m_SecondaryMask->GetDimension() == 4)) - { - mitk::Image::Pointer old_img = m_SecondaryMaskGenerator->GetReferenceImage(); - m_SecondaryMaskGenerator->SetInputImage(m_MaskGenerator->GetReferenceImage()); - m_SecondaryMask = m_SecondaryMaskGenerator->GetMask(); - m_SecondaryMaskGenerator->SetInputImage(old_img); - } - typename MaskType::Pointer secondaryMaskImage = MaskType::New(); - secondaryMaskImage = ImageToItkImage< MaskPixelType, VImageDimension >(m_SecondaryMask); - - // secondary mask should be a ignore zero value pixel mask derived from image. it has to be cropped to the mask region (which may be planar or simply smaller) - typename MaskUtilities::Pointer secondaryMaskMaskUtil = MaskUtilities::New(); - secondaryMaskMaskUtil->SetImage(secondaryMaskImage.GetPointer()); - secondaryMaskMaskUtil->SetMask(maskImage.GetPointer()); - typename MaskType::Pointer adaptedSecondaryMaskImage = secondaryMaskMaskUtil->ExtractMaskImageRegion(); - - typename itk::MaskImageFilter2::Pointer maskFilter = itk::MaskImageFilter2::New(); - maskFilter->SetInput1(maskImage); - maskFilter->SetInput2(adaptedSecondaryMaskImage); - maskFilter->SetMaskingValue(1); // all pixels of maskImage where secondaryMaskImage==1 will be kept, all the others are set to 0 - maskFilter->UpdateLargestPossibleRegion(); - maskImage = maskFilter->GetOutput(); - } + { + // if the pixel type of the mask is not short, then we have to make a copy of m_InternalMask (and cast the values) + CastToItkImage(m_InternalMask, maskImage); + } - typename MaskUtilType::Pointer maskUtil = MaskUtilType::New(); - maskUtil->SetImage(image); - maskUtil->SetMask(maskImage.GetPointer()); + // if we have a secondary mask (say a ignoreZeroPixelMask) we need to combine the masks (corresponds to AND) + if (m_SecondaryMask.IsNotNull()) + { + // dirty workaround for a bug when pf mask + any other mask is used in conjunction. We need a proper fix for this + // (Fabian Isensee is responsible and probably working on it!) + if (m_InternalMask->GetDimension() == 2 && + (m_SecondaryMask->GetDimension() == 3 || m_SecondaryMask->GetDimension() == 4)) + { + mitk::Image::ConstPointer old_img = m_SecondaryMaskGenerator->GetReferenceImage(); + m_SecondaryMaskGenerator->SetInputImage(m_MaskGenerator->GetReferenceImage()); + m_SecondaryMask = m_SecondaryMaskGenerator->GetMask(); + m_SecondaryMaskGenerator->SetInputImage(old_img); + } + typename MaskType::Pointer secondaryMaskImage = MaskType::New(); + secondaryMaskImage = ImageToItkImage(m_SecondaryMask); + + // secondary mask should be a ignore zero value pixel mask derived from image. it has to be cropped to the mask + // region (which may be planar or simply smaller) + typename MaskUtilities::Pointer secondaryMaskMaskUtil = + MaskUtilities::New(); + secondaryMaskMaskUtil->SetImage(secondaryMaskImage.GetPointer()); + secondaryMaskMaskUtil->SetMask(maskImage.GetPointer()); + typename MaskType::Pointer adaptedSecondaryMaskImage = secondaryMaskMaskUtil->ExtractMaskImageRegion(); + + typename itk::MaskImageFilter2::Pointer maskFilter = + itk::MaskImageFilter2::New(); + maskFilter->SetInput1(maskImage); + maskFilter->SetInput2(adaptedSecondaryMaskImage); + maskFilter->SetMaskingValue( + 1); // all pixels of maskImage where secondaryMaskImage==1 will be kept, all the others are set to 0 + maskFilter->UpdateLargestPossibleRegion(); + maskImage = maskFilter->GetOutput(); + } - // if mask is smaller than image, extract the image region where the mask is - typename ImageType::Pointer adaptedImage = ImageType::New(); + typename MaskUtilType::Pointer maskUtil = MaskUtilType::New(); + maskUtil->SetImage(image); + maskUtil->SetMask(maskImage.GetPointer()); - adaptedImage = maskUtil->ExtractMaskImageRegion(); // this also checks mask sanity + // if mask is smaller than image, extract the image region where the mask is + typename ImageType::Pointer adaptedImage = ImageType::New(); - // find min, max, minindex and maxindex - typename MinMaxLabelFilterType::Pointer minMaxFilter = MinMaxLabelFilterType::New(); - minMaxFilter->SetInput(adaptedImage); - minMaxFilter->SetLabelInput(maskImage); - minMaxFilter->UpdateLargestPossibleRegion(); + adaptedImage = maskUtil->ExtractMaskImageRegion(); // this also checks mask sanity - // set histogram parameters for each label individually (min/max may be different for each label) - typedef typename std::map MapType; - typedef typename std::pair PairType; + // find min, max, minindex and maxindex + typename MinMaxLabelFilterType::Pointer minMaxFilter = MinMaxLabelFilterType::New(); + minMaxFilter->SetInput(adaptedImage); + minMaxFilter->SetLabelInput(maskImage); + minMaxFilter->UpdateLargestPossibleRegion(); - std::vector relevantLabels = minMaxFilter->GetRelevantLabels(); - MapType minVals; - MapType maxVals; - std::map nBins; + // set histogram parameters for each label individually (min/max may be different for each label) + typedef typename std::map MapType; + typedef typename std::pair PairType; - for (LabelPixelType label:relevantLabels) - { - minVals.insert(PairType(label, minMaxFilter->GetMin(label))); - maxVals.insert(PairType(label, minMaxFilter->GetMax(label))); - - unsigned int nBinsForHistogram; - if (m_UseBinSizeOverNBins) - { - nBinsForHistogram = std::max(static_cast(std::ceil(minMaxFilter->GetMax(label) - minMaxFilter->GetMin(label))) / m_binSizeForHistogramStatistics, 10.); // do not allow less than 10 bins - } - else - { - nBinsForHistogram = m_nBinsForHistogramStatistics; - } - - nBins.insert(typename std::pair(label, nBinsForHistogram)); - } + std::vector relevantLabels = minMaxFilter->GetRelevantLabels(); + MapType minVals; + MapType maxVals; + std::map nBins; - typename ImageStatisticsFilterType::Pointer imageStatisticsFilter = ImageStatisticsFilterType::New(); - imageStatisticsFilter->SetDirectionTolerance(0.001); - imageStatisticsFilter->SetCoordinateTolerance(0.001); - imageStatisticsFilter->SetInput(adaptedImage); - imageStatisticsFilter->SetLabelInput(maskImage); - imageStatisticsFilter->SetHistogramParametersForLabels(nBins, minVals, maxVals); - imageStatisticsFilter->Update(); + for (LabelPixelType label : relevantLabels) + { + minVals.insert(PairType(label, minMaxFilter->GetMin(label))); + maxVals.insert(PairType(label, minMaxFilter->GetMax(label))); + + unsigned int nBinsForHistogram; + if (m_UseBinSizeOverNBins) + { + nBinsForHistogram = + std::max(static_cast(std::ceil(minMaxFilter->GetMax(label) - minMaxFilter->GetMin(label))) / + m_binSizeForHistogramStatistics, + 10.); // do not allow less than 10 bins + } + else + { + nBinsForHistogram = m_nBinsForHistogramStatistics; + } + + nBins.insert(typename std::pair(label, nBinsForHistogram)); + } - std::list labels = imageStatisticsFilter->GetRelevantLabels(); - auto it = labels.begin(); - m_StatisticsByTimeStep[timeStep].resize(0); + typename ImageStatisticsFilterType::Pointer imageStatisticsFilter = ImageStatisticsFilterType::New(); + imageStatisticsFilter->SetDirectionTolerance(0.001); + imageStatisticsFilter->SetCoordinateTolerance(0.001); + imageStatisticsFilter->SetInput(adaptedImage); + imageStatisticsFilter->SetLabelInput(maskImage); + imageStatisticsFilter->SetHistogramParametersForLabels(nBins, minVals, maxVals); + imageStatisticsFilter->Update(); - while(it != labels.end()) - { - StatisticsContainer::Pointer statisticsResult = StatisticsContainer::New(); - - // find min, max, minindex and maxindex - // make sure to only look in the masked region, use a masker for this - - vnl_vector minIndex, maxIndex; - mitk::Point3D worldCoordinateMin; - mitk::Point3D worldCoordinateMax; - mitk::Point3D indexCoordinateMin; - mitk::Point3D indexCoordinateMax; - m_InternalImageForStatistics->GetGeometry()->IndexToWorld(minMaxFilter->GetMinIndex(*it), worldCoordinateMin); - m_InternalImageForStatistics->GetGeometry()->IndexToWorld(minMaxFilter->GetMaxIndex(*it), worldCoordinateMax); - m_Image->GetGeometry()->WorldToIndex(worldCoordinateMin, indexCoordinateMin); - m_Image->GetGeometry()->WorldToIndex(worldCoordinateMax, indexCoordinateMax); - - minIndex.set_size(3); - maxIndex.set_size(3); - - //for (unsigned int i=0; i < tmpMaxIndex.GetIndexDimension(); i++) - for (unsigned int i=0; i < 3; i++) - { - minIndex[i] = indexCoordinateMin[i]; - maxIndex[i] = indexCoordinateMax[i]; - } - - statisticsResult->SetMinIndex(minIndex); - statisticsResult->SetMaxIndex(maxIndex); - - assert(std::abs(minMaxFilter->GetMax(*it) - imageStatisticsFilter->GetMaximum(*it)) < mitk::eps); - assert(std::abs(minMaxFilter->GetMin(*it) - imageStatisticsFilter->GetMinimum(*it)) < mitk::eps); - - - statisticsResult->SetN(imageStatisticsFilter->GetSum(*it) / (double) imageStatisticsFilter->GetMean(*it)); - statisticsResult->SetMean(imageStatisticsFilter->GetMean(*it)); - statisticsResult->SetMin(imageStatisticsFilter->GetMinimum(*it)); - statisticsResult->SetMax(imageStatisticsFilter->GetMaximum(*it)); - statisticsResult->SetVariance(imageStatisticsFilter->GetVariance(*it)); - statisticsResult->SetStd(imageStatisticsFilter->GetSigma(*it)); - statisticsResult->SetSkewness(imageStatisticsFilter->GetSkewness(*it)); - statisticsResult->SetKurtosis(imageStatisticsFilter->GetKurtosis(*it)); - statisticsResult->SetRMS(std::sqrt(std::pow(imageStatisticsFilter->GetMean(*it), 2.) + imageStatisticsFilter->GetVariance(*it))); // variance = sigma^2 - statisticsResult->SetMPP(imageStatisticsFilter->GetMPP(*it)); - statisticsResult->SetLabel(*it); - - statisticsResult->SetEntropy(imageStatisticsFilter->GetEntropy(*it)); - statisticsResult->SetMedian(imageStatisticsFilter->GetMedian(*it)); - statisticsResult->SetUniformity(imageStatisticsFilter->GetUniformity(*it)); - statisticsResult->SetUPP(imageStatisticsFilter->GetUPP(*it)); - statisticsResult->SetHistogram(imageStatisticsFilter->GetHistogram(*it)); - - m_StatisticsByTimeStep[timeStep].push_back(statisticsResult); - ++it; - } + std::list labels = imageStatisticsFilter->GetRelevantLabels(); + auto it = labels.begin(); - // swap maskGenerators back - if (swapMasks) - { - m_SecondaryMask = m_InternalMask; - m_InternalMask = nullptr; - } + while (it != labels.end()) + { + ImageStatisticsContainer::Pointer statisticContainerForLabelImage; + auto labelIt = m_StatisticContainers.find(*it); + // reset if statisticContainer already exist + if (labelIt != m_StatisticContainers.end()) + { + statisticContainerForLabelImage = labelIt->second; + // statisticContainerForLabelImage->Reset(); + // statisticContainerForLabelImage->SetTimeGeometry(timeGeometry); + } + // create new statisticContainer + else + { + statisticContainerForLabelImage = ImageStatisticsContainer::New(); + statisticContainerForLabelImage->SetTimeGeometry(const_cast(timeGeometry)); + // link label (*it) to statisticContainer + m_StatisticContainers.emplace(*it, statisticContainerForLabelImage); + } + + ImageStatisticsContainer::StatisticsObject statObj; + + // find min, max, minindex and maxindex + // make sure to only look in the masked region, use a masker for this + + vnl_vector minIndex, maxIndex; + mitk::Point3D worldCoordinateMin; + mitk::Point3D worldCoordinateMax; + mitk::Point3D indexCoordinateMin; + mitk::Point3D indexCoordinateMax; + m_InternalImageForStatistics->GetGeometry()->IndexToWorld(minMaxFilter->GetMinIndex(*it), worldCoordinateMin); + m_InternalImageForStatistics->GetGeometry()->IndexToWorld(minMaxFilter->GetMaxIndex(*it), worldCoordinateMax); + m_Image->GetGeometry()->WorldToIndex(worldCoordinateMin, indexCoordinateMin); + m_Image->GetGeometry()->WorldToIndex(worldCoordinateMax, indexCoordinateMax); + + minIndex.set_size(3); + maxIndex.set_size(3); + + // for (unsigned int i=0; i < tmpMaxIndex.GetIndexDimension(); i++) + for (unsigned int i = 0; i < 3; i++) + { + minIndex[i] = indexCoordinateMin[i]; + maxIndex[i] = indexCoordinateMax[i]; + } + + statObj.AddStatistic(mitk::ImageStatisticsConstants::MINIMUMPOSITION(), minIndex); + statObj.AddStatistic(mitk::ImageStatisticsConstants::MAXIMUMPOSITION(), maxIndex); + + assert(std::abs(minMaxFilter->GetMax(*it) - imageStatisticsFilter->GetMaximum(*it)) < mitk::eps); + assert(std::abs(minMaxFilter->GetMin(*it) - imageStatisticsFilter->GetMinimum(*it)) < mitk::eps); + + auto voxelVolume = GetVoxelVolume(image); + auto numberOfVoxels = + static_cast(imageStatisticsFilter->GetSum(*it) / (double)imageStatisticsFilter->GetMean(*it)); + auto volume = static_cast(numberOfVoxels) * voxelVolume; + auto rms = std::sqrt(std::pow(imageStatisticsFilter->GetMean(*it), 2.) + + imageStatisticsFilter->GetVariance(*it)); // variance = sigma^2 + auto variance = imageStatisticsFilter->GetSigma(*it) * imageStatisticsFilter->GetSigma(*it); + + statObj.AddStatistic(mitk::ImageStatisticsConstants::NUMBEROFVOXELS(), numberOfVoxels); + statObj.AddStatistic(mitk::ImageStatisticsConstants::VOLUME(), volume); + statObj.AddStatistic(mitk::ImageStatisticsConstants::MEAN(), imageStatisticsFilter->GetMean(*it)); + statObj.AddStatistic(mitk::ImageStatisticsConstants::MINIMUM(), imageStatisticsFilter->GetMinimum(*it)); + statObj.AddStatistic(mitk::ImageStatisticsConstants::MAXIMUM(), imageStatisticsFilter->GetMaximum(*it)); + statObj.AddStatistic(mitk::ImageStatisticsConstants::STANDARDDEVIATION(), imageStatisticsFilter->GetSigma(*it)); + statObj.AddStatistic(mitk::ImageStatisticsConstants::VARIANCE(), variance); + statObj.AddStatistic(mitk::ImageStatisticsConstants::SKEWNESS(), imageStatisticsFilter->GetSkewness(*it)); + statObj.AddStatistic(mitk::ImageStatisticsConstants::KURTOSIS(), imageStatisticsFilter->GetKurtosis(*it)); + statObj.AddStatistic(mitk::ImageStatisticsConstants::RMS(), rms); + statObj.AddStatistic(mitk::ImageStatisticsConstants::MPP(), imageStatisticsFilter->GetMPP(*it)); + statObj.AddStatistic(mitk::ImageStatisticsConstants::ENTROPY(), imageStatisticsFilter->GetEntropy(*it)); + statObj.AddStatistic(mitk::ImageStatisticsConstants::MEDIAN(), imageStatisticsFilter->GetMedian(*it)); + statObj.AddStatistic(mitk::ImageStatisticsConstants::UNIFORMITY(), imageStatisticsFilter->GetUniformity(*it)); + statObj.AddStatistic(mitk::ImageStatisticsConstants::UPP(), imageStatisticsFilter->GetUPP(*it)); + statObj.m_Histogram = imageStatisticsFilter->GetHistogram(*it).GetPointer(); + + statisticContainerForLabelImage->SetStatisticsForTimeStep(timeStep, statObj); + ++it; } - bool ImageStatisticsCalculator::IsUpdateRequired(unsigned int timeStep) const + // swap maskGenerators back + if (swapMasks) { - unsigned long thisClassTimeStamp = this->GetMTime(); - unsigned long inputImageTimeStamp = m_Image->GetMTime(); - unsigned long statisticsTimeStamp = m_StatisticsUpdateTimePerTimeStep[timeStep]; - - if (thisClassTimeStamp > statisticsTimeStamp) // inputs have changed - { - return true; - } - - if (inputImageTimeStamp > statisticsTimeStamp) // image has changed - { - return true; - } - - if (m_MaskGenerator.IsNotNull()) - { - unsigned long maskGeneratorTimeStamp = m_MaskGenerator->GetMTime(); - if (maskGeneratorTimeStamp > statisticsTimeStamp) // there is a mask generator and it has changed - { - return true; - } - } + m_SecondaryMask = m_InternalMask; + m_InternalMask = nullptr; + } + } - if (m_SecondaryMaskGenerator.IsNotNull()) - { - unsigned long maskGeneratorTimeStamp = m_SecondaryMaskGenerator->GetMTime(); - if (maskGeneratorTimeStamp > statisticsTimeStamp) // there is a secondary mask generator and it has changed - { - return true; - } - } + bool ImageStatisticsCalculator::IsUpdateRequired(LabelIndex label) const + { + unsigned long thisClassTimeStamp = this->GetMTime(); + unsigned long inputImageTimeStamp = m_Image->GetMTime(); - return false; - } - - - ImageStatisticsCalculator::StatisticsContainer::StatisticsContainer(): - m_N(0), - m_Mean(nan("")), - m_Min(nan("")), - m_Max(nan("")), - m_Std(nan("")), - m_Variance(nan("")), - m_Skewness(nan("")), - m_Kurtosis(nan("")), - m_RMS(nan("")), - m_MPP(nan("")), - m_Median(nan("")), - m_Uniformity(nan("")), - m_UPP(nan("")), - m_Entropy(nan("")), - m_Label(0) - { - m_minIndex.set_size(0); - m_maxIndex.set_size(0); - } - - ImageStatisticsCalculator::statisticsMapType ImageStatisticsCalculator::StatisticsContainer::GetStatisticsAsMap() - { - ImageStatisticsCalculator::statisticsMapType statisticsAsMap; - - statisticsAsMap["N"] = m_N; - statisticsAsMap["Mean"] = m_Mean; - statisticsAsMap["Min"] = m_Min; - statisticsAsMap["Max"] = m_Max; - statisticsAsMap["StandardDeviation"] = m_Std; - statisticsAsMap["Variance"] = m_Variance; - statisticsAsMap["Skewness"] = m_Skewness; - statisticsAsMap["Kurtosis"] = m_Kurtosis; - statisticsAsMap["RMS"] = m_RMS; - statisticsAsMap["MPP"] = m_MPP; - statisticsAsMap["Median"] = m_Median; - statisticsAsMap["Uniformity"] = m_Uniformity; - statisticsAsMap["UPP"] = m_UPP; - statisticsAsMap["Entropy"] = m_Entropy; - statisticsAsMap["Label"] = m_Label; - - return statisticsAsMap; - } - - - void ImageStatisticsCalculator::StatisticsContainer::Reset() - { - m_N = 0; - m_Mean = nan(""); - m_Min = nan(""); - m_Max = nan(""); - m_Std = nan(""); - m_Variance = nan(""); - m_Skewness = nan(""); - m_Kurtosis = nan(""); - m_RMS = nan(""); - m_MPP = nan(""); - m_Median = nan(""); - m_Uniformity = nan(""); - m_UPP = nan(""); - m_Entropy = nan(""); - m_Histogram = HistogramType::New(); - m_minIndex.set_size(0); - m_maxIndex.set_size(0); - m_Label = 0; - } - - void ImageStatisticsCalculator::StatisticsContainer::Print() - { - ImageStatisticsCalculator::statisticsMapType statMap = this->GetStatisticsAsMap(); - // print all map key value pairs - // const auto& val:statMap - for (auto it = statMap.begin(); it != statMap.end(); ++it) - { - std::cout << it->first << ": " << it->second << std::endl; - } + auto it = m_StatisticContainers.find(label); + if (it == m_StatisticContainers.end()) + { + return true; + } - // print the min and max index - std::cout << "Min Index:" << std::endl; - for (auto it = this->GetMinIndex().begin(); it != this->GetMinIndex().end(); ++it) - { - std::cout << *it << " "; - } - std::cout << std::endl; + unsigned long statisticsTimeStamp = it->second->GetMTime(); - // print the min and max index - std::cout << "Max Index:" << std::endl; - for (auto it = this->GetMaxIndex().begin(); it != this->GetMaxIndex().end(); ++it) - { - std::cout << *it << " "; - } - std::cout << std::endl; + if (thisClassTimeStamp > statisticsTimeStamp) // inputs have changed + { + return true; } - std::string ImageStatisticsCalculator::StatisticsContainer::GetAsString() + if (inputImageTimeStamp > statisticsTimeStamp) // image has changed { - std::string res = ""; - ImageStatisticsCalculator::statisticsMapType statMap = this->GetStatisticsAsMap(); - // print all map key value pairs - // const auto& val:statMap - for (auto it = statMap.begin(); it != statMap.end(); ++it) - { - res += std::string(it->first) + ": " + std::to_string(it->second) + "\n"; - } - - // print the min and max index - res += "Min Index:" + std::string("\n"); - for (auto it = this->GetMinIndex().begin(); it != this->GetMinIndex().end(); it++) - { - res += std::to_string(*it) + std::string(" "); - } - res += "\n"; + return true; + } - // print the min and max index - res += "Max Index:" + std::string("\n"); - for (auto it = this->GetMaxIndex().begin(); it != this->GetMaxIndex().end(); it++) - { - res += std::to_string(*it) + " "; - } - res += "\n"; - return res; + if (m_MaskGenerator.IsNotNull()) + { + unsigned long maskGeneratorTimeStamp = m_MaskGenerator->GetMTime(); + if (maskGeneratorTimeStamp > statisticsTimeStamp) // there is a mask generator and it has changed + { + return true; + } } + if (m_SecondaryMaskGenerator.IsNotNull()) + { + unsigned long maskGeneratorTimeStamp = m_SecondaryMaskGenerator->GetMTime(); + if (maskGeneratorTimeStamp > statisticsTimeStamp) // there is a secondary mask generator and it has changed + { + return true; + } + } -} + return false; + } +} // namespace mitk diff --git a/Modules/ImageStatistics/mitkImageStatisticsCalculator.h b/Modules/ImageStatistics/mitkImageStatisticsCalculator.h index 7a8f23403c..78f07aae14 100644 --- a/Modules/ImageStatistics/mitkImageStatisticsCalculator.h +++ b/Modules/ImageStatistics/mitkImageStatisticsCalculator.h @@ -1,414 +1,128 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + #ifndef MITKIMAGESTATISTICSCALCULATOR #define MITKIMAGESTATISTICSCALCULATOR #include #include #include +#include #include -#include #include -#include namespace mitk { class MITKIMAGESTATISTICS_EXPORT ImageStatisticsCalculator: public itk::Object { public: /** Standard Self typedef */ typedef ImageStatisticsCalculator Self; typedef itk::Object Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkNewMacro(Self) /** Runtime information support. */ itkTypeMacro(ImageStatisticsCalculator_v2, itk::Object) typedef double statisticsValueType; typedef std::map statisticsMapType; typedef itk::Statistics::Histogram HistogramType; typedef unsigned short MaskPixelType; - - /**Documentation - @brief Container class for storing the computed image statistics. - - Container class for storing the computed image statistics. Stored statistics are: - - N: number of voxels - - Mean - - MPP (Mean of positive pixels) - - Median - - Skewness - - Kurtosis - - Uniformity - - UPP (Uniformity of positive pixels) - - Variance - - Std (Standard Deviation) - - Min - - Max - - RMS (Root Mean Square) - - Label (if applicable, the label (unsigned short) of the mask the statistics belong to) - - Entropy - - It furthermore stores the following: - - MinIndex (Index of Image where the Minimum is located) - - MaxIndex (Index of Image where the Maximum is located) - - Histogram of Pixel Values*/ - class MITKIMAGESTATISTICS_EXPORT StatisticsContainer : public itk::Object - { - public: - /** Standard Self typedef */ - typedef StatisticsContainer Self; - typedef itk::Object Superclass; - typedef itk::SmartPointer< Self > Pointer; - typedef itk::SmartPointer< const Self > ConstPointer; - - /** Method for creation through the object factory. */ - itkNewMacro(Self) - - /** Runtime information support. */ - itkTypeMacro(StatisticsContainer, itk::Object) - - typedef double RealType; - - /**Documentation - @brief Returns a std::map containing all real valued statistics stored in this class (= all statistics except minIndex, maxIndex and the histogram)*/ - statisticsMapType GetStatisticsAsMap(); - - /**Documentation - @brief Deletes all stored values*/ - void Reset(); - - void SetN(long n) - { - m_N = n; - } - - const long& GetN() const - { - return m_N; - } - - void SetMean(RealType mean) - { - m_Mean = mean; - } - - const RealType& GetMean() const - { - return m_Mean; - } - - void SetVariance(RealType variance) - { - m_Variance = variance; - } - - const RealType& GetVariance() const - { - return m_Variance; - } - - void SetStd(RealType std) - { - m_Std = std; - } - - const RealType& GetStd() const - { - return m_Std; - } - - void SetMin(RealType minVal) - { - m_Min = minVal; - } - - const RealType& GetMin() const - { - return m_Min; - } - - void SetMax(RealType maxVal) - { - m_Max = maxVal; - } - - const RealType& GetMax() const - { - return m_Max; - } - - void SetRMS(RealType rms) - { - m_RMS = rms; - } - - const RealType& GetRMS() const - { - return m_RMS; - } - - void SetSkewness(RealType skewness) - { - m_Skewness = skewness; - } - - const RealType& GetSkewness() const - { - return m_Skewness; - } - - void SetKurtosis(RealType kurtosis) - { - m_Kurtosis = kurtosis; - } - - const RealType& GetKurtosis() const - { - return m_Kurtosis; - } - - void SetMPP(RealType mpp) - { - m_MPP = mpp; - } - - const RealType& GetMPP() const - { - return m_MPP; - } - - void SetLabel(unsigned int label) - { - m_Label = label; - } - - const unsigned int& GetLabel() const - { - return m_Label; - } - - void SetMinIndex(vnl_vector minIndex) - { - m_minIndex = minIndex; - } - - vnl_vector GetMinIndex() const - { - return m_minIndex; - } - - void SetMaxIndex(vnl_vector maxIndex) - { - m_maxIndex = maxIndex; - } - - vnl_vector GetMaxIndex() const - { - return m_maxIndex; - } - - void SetHistogram(HistogramType::Pointer hist) - { - if (m_Histogram != hist) - { - m_Histogram = hist; - } - } - - const HistogramType::Pointer GetHistogram() const - { - return m_Histogram; - } - - void SetEntropy(RealType entropy) - { - m_Entropy = entropy; - } - - const RealType & GetEntropy() const - { - return m_Entropy; - } - - void SetMedian(RealType median) - { - m_Median = median; - } - - const RealType & GetMedian() const - { - return m_Median; - } - - void SetUniformity(RealType uniformity) - { - m_Uniformity = uniformity; - } - - const RealType & GetUniformity() const - { - return m_Uniformity; - } - - void SetUPP(RealType upp) - { - m_UPP = upp; - } - - const RealType & GetUPP() const - { - return m_UPP; - } - - /**Documentation - @brief Creates a StatisticsMapType containing all real valued statistics stored in this class (= all statistics except minIndex, maxIndex and the histogram) and prints its contents to std::cout*/ - void Print(); - - /**Documentation - @brief Generates a string that contains all real valued statistics stored in this class (= all statistics except minIndex, maxIndex and the histogram)*/ - std::string GetAsString(); - - - protected: - StatisticsContainer(); - - private: - itk::LightObject::Pointer InternalClone() const override - { - itk::LightObject::Pointer ioPtr = Superclass::InternalClone(); - Self::Pointer rval = dynamic_cast(ioPtr.GetPointer()); - if (rval.IsNull()) - { - itkExceptionMacro(<< "downcast to type " - << "StatisticsContainer" - << " failed."); - } - - rval->SetEntropy(this->GetEntropy()); - rval->SetKurtosis(this->GetKurtosis()); - rval->SetLabel(this->GetLabel()); - rval->SetMax(this->GetMax()); - rval->SetMin(this->GetMin()); - rval->SetMean(this->GetMean()); - rval->SetMedian(this->GetMedian()); - rval->SetMPP(this->GetMPP()); - rval->SetN(this->GetN()); - rval->SetRMS(this->GetRMS()); - rval->SetSkewness(this->GetSkewness()); - rval->SetStd(this->GetStd()); - rval->SetUniformity(this->GetUniformity()); - rval->SetUPP(this->GetUPP()); - rval->SetVariance(this->GetVariance()); - rval->SetHistogram(this->GetHistogram()); - rval->SetMinIndex(this->GetMinIndex()); - rval->SetMaxIndex(this->GetMaxIndex()); - return ioPtr; - } - - // not pretty, is temporary - long m_N; - RealType m_Mean, m_Min, m_Max, m_Std, m_Variance; - RealType m_Skewness; - RealType m_Kurtosis; - RealType m_RMS; - RealType m_MPP; - vnl_vector m_minIndex, m_maxIndex; - RealType m_Median; - RealType m_Uniformity; - RealType m_UPP; - RealType m_Entropy; - unsigned int m_Label; - HistogramType::Pointer m_Histogram; - - }; + using LabelIndex = ImageStatisticsContainer::LabelIndex; /**Documentation @brief Set the image for which the statistics are to be computed.*/ - void SetInputImage(mitk::Image::Pointer image); + void SetInputImage(mitk::Image::ConstPointer image); /**Documentation @brief Set the mask generator that creates the mask which is to be used to calculate statistics. If no more mask is desired simply set @param mask to nullptr*/ void SetMask(mitk::MaskGenerator::Pointer mask); /**Documentation @brief Set this if more than one mask should be applied (for instance if a IgnorePixelValueMask were to be used alongside with a segmentation). Both masks are combined using pixel wise AND operation. The secondary mask does not have to be the same size than the primary but they need to have some overlap*/ void SetSecondaryMask(mitk::MaskGenerator::Pointer mask); /**Documentation @brief Set number of bins to be used for histogram statistics. If Bin size is set after number of bins, bin size will be used instead!*/ void SetNBinsForHistogramStatistics(unsigned int nBins); /**Documentation @brief Retrieve the number of bins used for histogram statistics. Careful: The return value does not indicate whether NBins or BinSize is used. That solely depends on which parameter has been set last.*/ unsigned int GetNBinsForHistogramStatistics() const; /**Documentation @brief Set bin size to be used for histogram statistics. If nbins is set after bin size, nbins will be used instead!*/ void SetBinSizeForHistogramStatistics(double binSize); /**Documentation @brief Retrieve the bin size for histogram statistics. Careful: The return value does not indicate whether NBins or BinSize is used. That solely depends on which parameter has been set last.*/ double GetBinSizeForHistogramStatistics() const; /**Documentation - @brief Returns the statistics for label @a label and timeStep @a timeStep. If these requested statistics are not computed yet the computation is done as well. + @brief Returns the statistics for label @a label. If these requested statistics are not computed yet the computation is done as well. For performance reasons, statistics for all labels in the image are computed at once. */ - StatisticsContainer::Pointer GetStatistics(unsigned int timeStep=0, unsigned int label=1); + ImageStatisticsContainer::Pointer GetStatistics(LabelIndex label=1); protected: ImageStatisticsCalculator(){ m_nBinsForHistogramStatistics = 100; m_binSizeForHistogramStatistics = 10; m_UseBinSizeOverNBins = false; }; private: + //Calculates statistics for each timestep for image template < typename TPixel, unsigned int VImageDimension > void InternalCalculateStatisticsUnmasked( - typename itk::Image< TPixel, VImageDimension >* image, - unsigned int timeStep); - - template < typename TPixel, unsigned int VImageDimension > typename HistogramType::Pointer InternalCalculateHistogramUnmasked( - typename itk::Image< TPixel, VImageDimension >* image, - double minVal, - double maxVal); + typename itk::Image< TPixel, VImageDimension >* image, const TimeGeometry* timeGeometry, TimeStepType timeStep); template < typename TPixel, unsigned int VImageDimension > void InternalCalculateStatisticsMasked( - typename itk::Image< TPixel, VImageDimension >* image, + typename itk::Image< TPixel, VImageDimension >* image, const TimeGeometry* timeGeometry, unsigned int timeStep); - bool IsUpdateRequired(unsigned int timeStep) const; + template < typename TPixel, unsigned int VImageDimension > + double GetVoxelVolume(typename itk::Image* image) const; - std::string GetNameOfClass() - { - return std::string("ImageStatisticsCalculator_v2"); - } + bool IsUpdateRequired(LabelIndex label) const; - mitk::Image::Pointer m_Image; + mitk::Image::ConstPointer m_Image; mitk::Image::Pointer m_ImageTimeSlice; - mitk::Image::Pointer m_InternalImageForStatistics; + mitk::Image::ConstPointer m_InternalImageForStatistics; mitk::MaskGenerator::Pointer m_MaskGenerator; mitk::Image::Pointer m_InternalMask; mitk::MaskGenerator::Pointer m_SecondaryMaskGenerator; mitk::Image::Pointer m_SecondaryMask; unsigned int m_nBinsForHistogramStatistics; double m_binSizeForHistogramStatistics; bool m_UseBinSizeOverNBins; - std::vector> m_StatisticsByTimeStep; - std::vector m_StatisticsUpdateTimePerTimeStep; + std::map m_StatisticContainers; }; } #endif // MITKIMAGESTATISTICSCALCULATOR diff --git a/Modules/ImageStatistics/mitkImageStatisticsConstants.cpp b/Modules/ImageStatistics/mitkImageStatisticsConstants.cpp new file mode 100644 index 0000000000..a1909086b8 --- /dev/null +++ b/Modules/ImageStatistics/mitkImageStatisticsConstants.cpp @@ -0,0 +1,69 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include "mitkImageStatisticsConstants.h" + +const std::string mitk::ImageStatisticsConstants::MEAN() { + return "Mean"; +} +const std::string mitk::ImageStatisticsConstants::MEDIAN() { + return "Median"; +} +const std::string mitk::ImageStatisticsConstants::STANDARDDEVIATION() { + return "StandardDeviation"; +} +const std::string mitk::ImageStatisticsConstants::VARIANCE() { + return "Variance"; +} +const std::string mitk::ImageStatisticsConstants::RMS() { + return "RMS"; +} +const std::string mitk::ImageStatisticsConstants::MAXIMUM() { + return "Max"; +} +const std::string mitk::ImageStatisticsConstants::MAXIMUMPOSITION() { + return "MaxPosition"; +} +const std::string mitk::ImageStatisticsConstants::MINIMUM() { + return "Min"; +} +const std::string mitk::ImageStatisticsConstants::MINIMUMPOSITION() { + return "MinPosition"; +} +const std::string mitk::ImageStatisticsConstants::NUMBEROFVOXELS() { + return "#Voxel"; +} +const std::string mitk::ImageStatisticsConstants::VOLUME() { + return "Volume [mm^3]"; +} +const std::string mitk::ImageStatisticsConstants::SKEWNESS() { + return "Skewness"; +} +const std::string mitk::ImageStatisticsConstants::KURTOSIS() { + return "Kurtosis"; +} +const std::string mitk::ImageStatisticsConstants::UNIFORMITY() { + return "Uniformity"; +} +const std::string mitk::ImageStatisticsConstants::ENTROPY() { + return "Entropy"; +} +const std::string mitk::ImageStatisticsConstants::MPP() { + return "MPP"; +} +const std::string mitk::ImageStatisticsConstants::UPP() { + return "UPP"; +} diff --git a/Modules/ImageStatistics/mitkImageStatisticsConstants.h b/Modules/ImageStatistics/mitkImageStatisticsConstants.h new file mode 100644 index 0000000000..29fee6265c --- /dev/null +++ b/Modules/ImageStatistics/mitkImageStatisticsConstants.h @@ -0,0 +1,60 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#ifndef _MITK_IMAGE_STATISTICS_CONSTANTS_H_ +#define _MITK_IMAGE_STATISTICS_CONSTANTS_H_ + +#include + +#include + +#ifdef _MSC_VER +# pragma warning(push) +# pragma warning(disable:4251) +#endif + +namespace mitk +{ + + struct MITKIMAGESTATISTICS_EXPORT ImageStatisticsConstants + + { + static const std::string MEAN(); + static const std::string MEDIAN(); + static const std::string STANDARDDEVIATION(); + static const std::string VARIANCE(); + static const std::string RMS(); + static const std::string MAXIMUM(); + static const std::string MAXIMUMPOSITION(); + static const std::string MINIMUM(); + static const std::string MINIMUMPOSITION(); + static const std::string NUMBEROFVOXELS(); + static const std::string VOLUME(); + static const std::string SKEWNESS(); + static const std::string KURTOSIS(); + static const std::string UNIFORMITY(); + static const std::string ENTROPY(); + static const std::string MPP(); + static const std::string UPP(); + + }; +} + +#ifdef _MSC_VER +# pragma warning(pop) +#endif + +#endif diff --git a/Modules/ImageStatistics/mitkImageStatisticsContainer.cpp b/Modules/ImageStatistics/mitkImageStatisticsContainer.cpp new file mode 100644 index 0000000000..2bc4794ec2 --- /dev/null +++ b/Modules/ImageStatistics/mitkImageStatisticsContainer.cpp @@ -0,0 +1,210 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ +#include + +#include + +namespace mitk +{ + ImageStatisticsContainer::ImageStatisticsContainer() + { + this->Reset(); + } + + //The order is derived from the old (<2018) image statistics plugin. + const ImageStatisticsContainer::StatisticsObject::StatisticNameVector ImageStatisticsContainer::StatisticsObject::m_DefaultNames = { + ImageStatisticsConstants::MEAN(), + ImageStatisticsConstants::MEDIAN(), + ImageStatisticsConstants::STANDARDDEVIATION(), + ImageStatisticsConstants::RMS(), + ImageStatisticsConstants::MAXIMUM(), + ImageStatisticsConstants::MAXIMUMPOSITION(), + ImageStatisticsConstants::MINIMUM(), + ImageStatisticsConstants::MINIMUMPOSITION(), + ImageStatisticsConstants::NUMBEROFVOXELS(), + ImageStatisticsConstants::VOLUME(), + ImageStatisticsConstants::SKEWNESS(), + ImageStatisticsConstants::KURTOSIS(), + ImageStatisticsConstants::UNIFORMITY(), + ImageStatisticsConstants::ENTROPY(), + ImageStatisticsConstants::MPP(), + ImageStatisticsConstants::UPP() }; + + ImageStatisticsContainer::StatisticsObject::StatisticsObject() { + Reset(); + } + + void ImageStatisticsContainer::StatisticsObject::AddStatistic(const std::string& key, StatisticsVariantType value) + { + m_Statistics.emplace(key, value); + + if (std::find(std::cbegin(m_DefaultNames), std::cend(m_DefaultNames), key)==std::cend(m_DefaultNames)) + { + if (std::find(std::cbegin(m_CustomNames), std::cend(m_CustomNames), key) == std::cend(m_CustomNames)) + { + m_CustomNames.emplace_back(key); + } + } + } + + const ImageStatisticsContainer::StatisticsObject::StatisticNameVector& ImageStatisticsContainer::StatisticsObject::GetDefaultStatisticNames() + { + return m_DefaultNames; + }; + + const ImageStatisticsContainer::StatisticsObject::StatisticNameVector& ImageStatisticsContainer::StatisticsObject::GetCustomStatisticNames() const + { + return m_CustomNames; + } + + ImageStatisticsContainer::StatisticsObject::StatisticNameVector ImageStatisticsContainer::StatisticsObject::GetAllStatisticNames() const + { + StatisticNameVector names = GetDefaultStatisticNames(); + names.insert(std::end(names),std::cbegin(m_CustomNames), std::cend(m_CustomNames)); + + return names; + } + + bool ImageStatisticsContainer::StatisticsObject::HasStatistic(const std::string& name) const + { + return m_Statistics.find(name)!=std::cend(m_Statistics); + } + + ImageStatisticsContainer::StatisticsVariantType ImageStatisticsContainer::StatisticsObject::GetValueNonConverted(const std::string& name) const + { + if (HasStatistic(name)) { + return m_Statistics.find(name)->second; + } + else { + mitkThrow() << "invalid statistic key, could not find"; + } + } + + void ImageStatisticsContainer::StatisticsObject::Reset() + { + m_Statistics.clear(); + m_CustomNames.clear(); + } + + bool ImageStatisticsContainer::TimeStepExists(TimeStepType timeStep) const { + return m_TimeStepMap.find(timeStep) != m_TimeStepMap.end(); + } + + const ImageStatisticsContainer::StatisticsObject& ImageStatisticsContainer::GetStatisticsForTimeStep(TimeStepType timeStep) const { + auto it = m_TimeStepMap.find(timeStep); + if (it != m_TimeStepMap.end()) { + return it->second; + } + mitkThrow() << "StatisticsObject for timeStep " << timeStep << " not found!"; + } + + void ImageStatisticsContainer::SetStatisticsForTimeStep(TimeStepType timeStep, StatisticsObject statistics) { + if (timeStep < this->GetTimeSteps()) { + m_TimeStepMap.emplace(timeStep, statistics); + this->Modified(); + } + else { + mitkThrow() << "Given timeStep " << timeStep << " out of timeStep geometry bounds. TimeSteps in geometry: " << this->GetTimeSteps(); + } + } + + void ImageStatisticsContainer::PrintSelf(std::ostream &os, itk::Indent indent) const + { + Superclass::PrintSelf(os, indent); + for (unsigned int i = 0; i < this->GetTimeSteps(); i++) { + auto statisticsValues = GetStatisticsForTimeStep(i); + os << std::endl << indent << "Statistics instance for timeStep " << i << ":"; + auto statisticKeys = statisticsValues.GetAllStatisticNames(); + os << std::endl << indent << "Number of entries: " << statisticKeys.size(); + for (const auto& aKey : statisticKeys) { + os << std::endl << indent.GetNextIndent() << aKey << ": " << statisticsValues.GetValueNonConverted(aKey); + } + } + } + + unsigned int ImageStatisticsContainer::GetNumberOfTimeSteps()const { + return this->GetTimeSteps(); + } + + void ImageStatisticsContainer::Reset() + { + for (auto iter = m_TimeStepMap.begin(); iter != m_TimeStepMap.end(); iter++) { + iter->second.Reset(); + } + } + + itk::LightObject::Pointer ImageStatisticsContainer::InternalClone() const + { + itk::LightObject::Pointer ioPtr = Superclass::InternalClone(); + Self::Pointer rval = dynamic_cast(ioPtr.GetPointer()); + if (rval.IsNull()) + { + itkExceptionMacro(<< "downcast to type " + << "StatisticsContainer" + << " failed."); + } + + rval->SetTimeStepMap(m_TimeStepMap); + rval->SetTimeGeometry(this->GetTimeGeometry()->Clone()); + + return ioPtr; + } + + void ImageStatisticsContainer::SetTimeStepMap(TimeStepMapType map) { + m_TimeStepMap = map; + } + + ImageStatisticsContainer::StatisticsObject::StatisticNameVector + GetAllStatisticNames(const ImageStatisticsContainer* container) + { + ImageStatisticsContainer::StatisticsObject::StatisticNameVector names = ImageStatisticsContainer::StatisticsObject::GetDefaultStatisticNames(); + + if (container) + { + std::set customKeys; + + for (unsigned int i = 0; i < container->GetTimeSteps(); i++) { + auto statisticKeys = container->GetStatisticsForTimeStep(i).GetCustomStatisticNames(); + customKeys.insert(std::cbegin(statisticKeys), std::cend(statisticKeys)); + } + + names.insert(std::end(names), std::begin(customKeys), std::end(customKeys)); + } + + return names; + }; + + ImageStatisticsContainer::StatisticsObject::StatisticNameVector + GetAllStatisticNames(std::vector containers) + { + ImageStatisticsContainer::StatisticsObject::StatisticNameVector names = ImageStatisticsContainer::StatisticsObject::GetDefaultStatisticNames(); + + std::set customKeys; + + for (auto container : containers) + { + for (unsigned int i = 0; i < container->GetTimeSteps(); i++) { + auto statisticKeys = container->GetStatisticsForTimeStep(i).GetCustomStatisticNames(); + customKeys.insert(std::cbegin(statisticKeys), std::cend(statisticKeys)); + } + } + + names.insert(std::end(names), std::begin(customKeys), std::end(customKeys)); + + return names; + }; + +} diff --git a/Modules/ImageStatistics/mitkImageStatisticsContainer.h b/Modules/ImageStatistics/mitkImageStatisticsContainer.h new file mode 100644 index 0000000000..591928490b --- /dev/null +++ b/Modules/ImageStatistics/mitkImageStatisticsContainer.h @@ -0,0 +1,163 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#ifndef MITKIMAGESTATISTICSCONTAINER +#define MITKIMAGESTATISTICSCONTAINER + +#include +#include +#include +#include + +#include + +namespace mitk +{ + /** + @brief Container class for storing a StatisticsObject for each timestep. + + Stored statistics are: + - for the defined statistics, see GetAllStatisticNames + - Histogram of Pixel Values*/ + class MITKIMAGESTATISTICS_EXPORT ImageStatisticsContainer : public mitk::BaseData + { + public: + mitkClassMacro(ImageStatisticsContainer, mitk::BaseData) + itkFactorylessNewMacro(Self) + itkCloneMacro(Self) + + using HistogramType = itk::Statistics::Histogram; + using RealType = double; + using LabelIndex = unsigned int; + using IndexType = vnl_vector; + using VoxelCountType = unsigned long; + using StatisticsVariantType = boost::variant; + using StatisticsMapType = std::map < std::string, StatisticsVariantType>; + using StatisticsKeyType = std::string; + + virtual void SetRequestedRegionToLargestPossibleRegion() override {}; + + virtual bool RequestedRegionIsOutsideOfTheBufferedRegion() override { return false; }; + + virtual bool VerifyRequestedRegion() override { return true; }; + + virtual void SetRequestedRegion(const itk::DataObject*) override {}; + + /** + @brief Container class for storing the computed image statistics. + @details The statistics are stored in a map with value as boost::variant. + The type used to create the boost::variant is important as only this type can be recovered lateron. + */ + class MITKIMAGESTATISTICS_EXPORT StatisticsObject { + public: + StatisticsObject(); + /** + @brief Adds a statistic to the statistics object + @details if already a statistic with that name is included, it is overwritten + */ + void AddStatistic(const std::string& key, StatisticsVariantType value); + + using StatisticNameVector = std::vector; + + /** + @brief Returns the names of the default statistics + @details The order is derived from the image statistics plugin. + */ + static const StatisticNameVector& GetDefaultStatisticNames(); + + /** + @brief Returns the names of all custom statistics (defined at runtime and no default names). + */ + const StatisticNameVector& GetCustomStatisticNames() const; + + /** + @brief Returns the names of all statistics (default and custom defined) + Additional custom keys are added at the end in a sorted order. + */ + StatisticNameVector GetAllStatisticNames() const; + + bool HasStatistic(const std::string& name) const; + + /** + @brief Converts the requested value to the defined type + @param name defined string on creation (AddStatistic) + @exception if no statistics with key name was found. + */ + template + TType GetValueConverted(const std::string& name) const + { + auto value = GetValueNonConverted(name); + return boost::get(value); + }; + + /** + @brief Returns the requested value + @exception if no statistics with key name was found. + */ + StatisticsVariantType GetValueNonConverted(const std::string& name) const; + + void Reset(); + + HistogramType::ConstPointer m_Histogram=nullptr; + private: + StatisticsMapType m_Statistics; + StatisticNameVector m_CustomNames; + static const StatisticNameVector m_DefaultNames; + }; + + using TimeStepMapType = std::map; + + unsigned int GetNumberOfTimeSteps() const; + + /** + @brief Deletes all stored values*/ + void Reset(); + + /** + @brief Returns the statisticObject for the given Timestep + @pre timeStep must be valid + */ + const StatisticsObject& GetStatisticsForTimeStep(TimeStepType timeStep) const; + + /** + @brief Sets the statisticObject for the given Timestep + @pre timeStep must be valid + */ + void SetStatisticsForTimeStep(TimeStepType timeStep, StatisticsObject statistics); + + /** + @brief Checks if the Time step exists + @pre timeStep must be valid + */ + bool TimeStepExists(TimeStepType timeStep) const; + + protected: + ImageStatisticsContainer(); + virtual void PrintSelf(std::ostream &os, itk::Indent indent) const override; + + private: + itk::LightObject::Pointer InternalClone() const override; + + void SetTimeStepMap(TimeStepMapType map); + + TimeStepMapType m_TimeStepMap; + }; + + MITKIMAGESTATISTICS_EXPORT ImageStatisticsContainer::StatisticsObject::StatisticNameVector GetAllStatisticNames(const ImageStatisticsContainer* container); + MITKIMAGESTATISTICS_EXPORT ImageStatisticsContainer::StatisticsObject::StatisticNameVector GetAllStatisticNames(std::vector containers); + +} +#endif // MITKIMAGESTATISTICSCONTAINER diff --git a/Modules/ImageStatistics/mitkImageStatisticsContainerManager.cpp b/Modules/ImageStatistics/mitkImageStatisticsContainerManager.cpp new file mode 100644 index 0000000000..847916deca --- /dev/null +++ b/Modules/ImageStatistics/mitkImageStatisticsContainerManager.cpp @@ -0,0 +1,94 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include "mitkImageStatisticsContainerManager.h" + +#include "mitkNodePredicateAnd.h" +#include "mitkNodePredicateOr.h" +#include "mitkNodePredicateDataType.h" +#include "mitkNodePredicateNot.h" +#include "mitkStatisticsToImageRelationRule.h" +#include "mitkStatisticsToMaskRelationRule.h" + +mitk::ImageStatisticsContainer::ConstPointer mitk::ImageStatisticsContainerManager::GetImageStatistics(const mitk::DataStorage* dataStorage, const mitk::BaseData* image, const mitk::BaseData* mask) +{ + if (!dataStorage) { + mitkThrow() << "data storage is nullptr!"; + } + if (!image) { + mitkThrow() << "Image is nullptr"; + } + + mitk::NodePredicateBase::ConstPointer predicate = GetPredicateForSources(image, mask);; + + if (predicate) { + auto nodePredicateImageStatisticsContainer = mitk::NodePredicateDataType::New(ImageStatisticsContainer::GetStaticNameOfClass()); + predicate = mitk::NodePredicateAnd::New(predicate, nodePredicateImageStatisticsContainer); + + auto statisticContainerCandidateNodes = dataStorage->GetSubset(predicate); + mitk::DataStorage::SetOfObjects::Pointer statisticContainerCandidateNodesFiltered; + + statisticContainerCandidateNodesFiltered = mitk::DataStorage::SetOfObjects::New(); + for (const auto& node : *statisticContainerCandidateNodes) { + statisticContainerCandidateNodesFiltered->push_back(node); + } + + if (statisticContainerCandidateNodesFiltered->empty()) { + return nullptr; + } + + auto newestElement = statisticContainerCandidateNodesFiltered->front(); + if (statisticContainerCandidateNodesFiltered->size() > 1) { + //in case of multiple found statistics, return only newest one + auto newestIter = std::max_element(std::begin(*statisticContainerCandidateNodesFiltered), std::end(*statisticContainerCandidateNodesFiltered), [](mitk::DataNode::Pointer a, mitk::DataNode::Pointer b) { + return a->GetData()->GetMTime() < b->GetData()->GetMTime(); + }); + newestElement = *newestIter; + MITK_WARN << "multiple statistics (" << statisticContainerCandidateNodesFiltered->size() << ") for image/mask found. Returning only newest one."; + for (const auto& node : *statisticContainerCandidateNodesFiltered) { + MITK_DEBUG << node->GetName() << ", timestamp: " << node->GetData()->GetMTime(); + } + } + return dynamic_cast(newestElement->GetData()); + } + else { + return nullptr; + } +} + +mitk::NodePredicateBase::ConstPointer mitk::ImageStatisticsContainerManager::GetPredicateForSources(const mitk::BaseData* image, const mitk::BaseData* mask) +{ + if (!image) { + mitkThrow() << "Image is nullptr"; + } + + auto imageRule = mitk::StatisticsToImageRelationRule::New(); + mitk::NodePredicateBase::ConstPointer predicate = imageRule->GetSourcesDetector(image); + + auto maskRule = mitk::StatisticsToMaskRelationRule::New(); + if (mask) + { + auto maskPredicate = maskRule->GetSourcesDetector(mask); + predicate = mitk::NodePredicateAnd::New(predicate, maskPredicate); + } + else + { + auto maskPredicate = mitk::NodePredicateNot::New(maskRule->GetConnectedSourcesDetector()); + predicate = mitk::NodePredicateAnd::New(predicate, maskPredicate); + } + + return predicate; +} diff --git a/Modules/ImageStatistics/mitkImageStatisticsContainerManager.h b/Modules/ImageStatistics/mitkImageStatisticsContainerManager.h new file mode 100644 index 0000000000..9f1b7ccfa6 --- /dev/null +++ b/Modules/ImageStatistics/mitkImageStatisticsContainerManager.h @@ -0,0 +1,49 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ +#ifndef QmitkImageStatisticsContainerManager_H__INCLUDED +#define QmitkImageStatisticsContainerManager_H__INCLUDED + +#include "MitkImageStatisticsExports.h" + +#include +#include +#include +#include +#include +#include + +namespace mitk +{ + /** + \brief Returns the StatisticsContainer that was computed on given input (image/mask/planar figure) and is added as DataNode in a DataStorage + */ + class MITKIMAGESTATISTICS_EXPORT ImageStatisticsContainerManager + { + public: + /**Documentation + @brief Returns the StatisticContainer for the given image and mask + @return a valid StatisticsContainer or nullptr if no StatisticContainer is found or no rules have been defined + @details if more than one StatisticsContainer is found, only the newest (ModifiedTime) is returned + @pre Datastorage must point to a valid instance. + @pre image must Point to a valid instance. + */ + static mitk::ImageStatisticsContainer::ConstPointer GetImageStatistics(const mitk::DataStorage* dataStorage, const mitk::BaseData* image, const mitk::BaseData* mask=nullptr); + + protected: + static mitk::NodePredicateBase::ConstPointer GetPredicateForSources(const mitk::BaseData* image, const mitk::BaseData* mask = nullptr); + }; +} +#endif diff --git a/Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp b/Modules/ImageStatistics/mitkImageStatisticsContainerNodeHelper.cpp similarity index 52% copy from Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp copy to Modules/ImageStatistics/mitkImageStatisticsContainerNodeHelper.cpp index a57ee8aa83..90904c20fd 100644 --- a/Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp +++ b/Modules/ImageStatistics/mitkImageStatisticsContainerNodeHelper.cpp @@ -1,34 +1,29 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ +#include "mitkImageStatisticsContainerNodeHelper.h" -#include -#include +#include -mitk::NodePredicateUID::NodePredicateUID(const Identifiable::UIDType &uid) - : m_UID(uid) +namespace mitk { -} - -mitk::NodePredicateUID::~NodePredicateUID() -{ -} - -bool mitk::NodePredicateUID::CheckNode(const mitk::DataNode *node) const -{ - return nullptr != node - ? node->GetUID() == m_UID - : false; + DataNode::Pointer CreateImageStatisticsNode(ImageStatisticsContainer::Pointer statistic, const std::string& name) { + auto statisticsNode = mitk::DataNode::New(); + statisticsNode->SetName(name); + statisticsNode->SetData(statistic); + statisticsNode->SetProperty("helper object", mitk::BoolProperty::New(true)); + return statisticsNode; + } } diff --git a/Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp b/Modules/ImageStatistics/mitkImageStatisticsContainerNodeHelper.h similarity index 57% copy from Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp copy to Modules/ImageStatistics/mitkImageStatisticsContainerNodeHelper.h index a57ee8aa83..9c5bf00fb0 100644 --- a/Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp +++ b/Modules/ImageStatistics/mitkImageStatisticsContainerNodeHelper.h @@ -1,34 +1,30 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ -#include -#include +#ifndef MITKIMAGESTATISTICSCONTAINERNODEHELPER +#define MITKIMAGESTATISTICSCONTAINERNODEHELPER -mitk::NodePredicateUID::NodePredicateUID(const Identifiable::UIDType &uid) - : m_UID(uid) -{ -} +#include -mitk::NodePredicateUID::~NodePredicateUID() -{ -} +#include +#include -bool mitk::NodePredicateUID::CheckNode(const mitk::DataNode *node) const +namespace mitk { - return nullptr != node - ? node->GetUID() == m_UID - : false; + MITKIMAGESTATISTICS_EXPORT DataNode::Pointer CreateImageStatisticsNode(ImageStatisticsContainer::Pointer statistic, const std::string& name = "statistics"); } +#endif // MITKIMAGESTATISTICSCONTAINERNODEHELPER + diff --git a/Modules/ImageStatistics/mitkImageStatisticsPredicateHelper.cpp b/Modules/ImageStatistics/mitkImageStatisticsPredicateHelper.cpp new file mode 100644 index 0000000000..d40d6cf33c --- /dev/null +++ b/Modules/ImageStatistics/mitkImageStatisticsPredicateHelper.cpp @@ -0,0 +1,83 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include "mitkImageStatisticsPredicateHelper.h" + +#include +#include +#include +#include +#include + +namespace mitk +{ + + mitk::NodePredicateBase::Pointer GetNoHelperObjectPredicate() + { + auto hasHelperObjectProperty = mitk::NodePredicateProperty::New("helper object", nullptr); + auto isNoHelperObject = mitk::NodePredicateNot::New(hasHelperObjectProperty); + return isNoHelperObject.GetPointer(); + } + + mitk::NodePredicateBase::Pointer GetImageStatisticsImagePredicate() + { + auto isImage = mitk::NodePredicateDataType::New("Image"); + auto hasBinaryProperty = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); + auto isNotBinary = mitk::NodePredicateNot::New(hasBinaryProperty); + auto isNotBinaryImage = mitk::NodePredicateAnd::New(isImage, isNotBinary); + auto isNoHelperObjectPredicate = GetNoHelperObjectPredicate(); + + auto isImageForImageStatistics = mitk::NodePredicateAnd::New(isNotBinaryImage, isNoHelperObjectPredicate); + return isImageForImageStatistics.GetPointer(); + } + + mitk::NodePredicateBase::Pointer GetImageStatisticsMaskPredicate() + { + auto isImage = mitk::NodePredicateDataType::New("Image"); + auto isLabelSetImage = mitk::NodePredicateDataType::New("LabelSetImage"); + auto hasBinaryProperty = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); + auto isBinaryImage = mitk::NodePredicateAnd::New(isImage, hasBinaryProperty); + auto isNoHelperObjectPredicate = GetNoHelperObjectPredicate(); + + auto isLabelSetOrBinaryImage = mitk::NodePredicateOr::New(isLabelSetImage, isBinaryImage); + auto isMaskForImageStatistics = mitk::NodePredicateAnd::New(isLabelSetOrBinaryImage, isNoHelperObjectPredicate); + return isMaskForImageStatistics.GetPointer(); + } + + mitk::NodePredicateBase::Pointer GetImageStatisticsPlanarFigurePredicate() + { + auto isPlanarCircle = mitk::NodePredicateDataType::New("PlanarCircle"); + auto isPlanarRectangle = mitk::NodePredicateDataType::New("PlanarRectangle"); + auto isPlanarEllipse = mitk::NodePredicateDataType::New("PlanarEllipse"); + auto isPlanarDoubleEllipse = mitk::NodePredicateDataType::New("PlanarDoubleEllipse"); + auto isPlanarPolygon = mitk::NodePredicateDataType::New("PlanarPolygon"); + auto isPlanarSubdivisionPolygon = mitk::NodePredicateDataType::New("PlanarSubdivisionPolygon"); + auto isPlanarBezierCurve = mitk::NodePredicateDataType::New("PlanarBezierCurve"); + auto isPlanarLine = mitk::NodePredicateDataType::New("PlanarLine"); + auto isNoHelperObjectPredicate = GetNoHelperObjectPredicate(); + + auto isPlanarFigureForImageStatistics = mitk::NodePredicateOr::New(isPlanarCircle, isPlanarEllipse); + isPlanarFigureForImageStatistics = mitk::NodePredicateOr::New(isPlanarFigureForImageStatistics, isPlanarRectangle); + isPlanarFigureForImageStatistics = mitk::NodePredicateOr::New(isPlanarFigureForImageStatistics, isPlanarDoubleEllipse); + isPlanarFigureForImageStatistics = mitk::NodePredicateOr::New(isPlanarFigureForImageStatistics, isPlanarPolygon); + isPlanarFigureForImageStatistics = mitk::NodePredicateOr::New(isPlanarFigureForImageStatistics, isPlanarSubdivisionPolygon); + isPlanarFigureForImageStatistics = mitk::NodePredicateOr::New(isPlanarFigureForImageStatistics, isPlanarBezierCurve); + isPlanarFigureForImageStatistics = mitk::NodePredicateOr::New(isPlanarFigureForImageStatistics, isPlanarLine); + auto isPlanarFigureAndNoHelperForImageStatistics = mitk::NodePredicateAnd::New(isPlanarFigureForImageStatistics, isNoHelperObjectPredicate); + + return isPlanarFigureAndNoHelperForImageStatistics.GetPointer(); + } +} diff --git a/Modules/ImageStatistics/mitkImageStatisticsPredicateHelper.h b/Modules/ImageStatistics/mitkImageStatisticsPredicateHelper.h new file mode 100644 index 0000000000..5fe1a47245 --- /dev/null +++ b/Modules/ImageStatistics/mitkImageStatisticsPredicateHelper.h @@ -0,0 +1,44 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#ifndef MITKPREDICATEHELPER_H +#define MITKPREDICATEHELPER_H + +#include +#include + +namespace mitk +{ + /** + @brief Gets a predicate for the ImageStatistics plugin input image + @details Predicate: DataType:Image && !(Property:binary) && !(Property:helper object) + */ + mitk::NodePredicateBase::Pointer MITKIMAGESTATISTICS_EXPORT GetImageStatisticsImagePredicate(); + /** + @brief Gets a predicate for the ImageStatistics plugin input mask + @details Predicate: ((DataType:Image && Property:binary) || DataType:LabelSetImage) && !(Property:helper object) + */ + mitk::NodePredicateBase::Pointer MITKIMAGESTATISTICS_EXPORT GetImageStatisticsMaskPredicate(); + /** + @brief Gets a predicate for the ImageStatistics plugin planar figure + @details Predicate: (DataType:PlanarCircle || DataType:PlanarRectangle || DataType:PlanarEllipse + DataType:PlanarDoubleEllipse || DataType:PlanarPolygon || DataType:PlanarSubdivisionPolygon || + DataType:PlanarBezierCurve || DataType:PlanarLine) && !(Property:helper object) + */ + mitk::NodePredicateBase::Pointer MITKIMAGESTATISTICS_EXPORT GetImageStatisticsPlanarFigurePredicate(); +} + +#endif diff --git a/Modules/ImageStatistics/mitkIntensityProfile.cpp b/Modules/ImageStatistics/mitkIntensityProfile.cpp index 0a75482d2e..fc72f28352 100644 --- a/Modules/ImageStatistics/mitkIntensityProfile.cpp +++ b/Modules/ImageStatistics/mitkIntensityProfile.cpp @@ -1,380 +1,382 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include +#include #include "mitkIntensityProfile.h" using namespace mitk; template static void ReadPixel(const PixelType&, Image::Pointer image, const itk::Index<3>& index, ScalarType* returnValue) { switch (image->GetDimension()) { case 2: { ImagePixelReadAccessor readAccess(image, image->GetSliceData(0)); *returnValue = readAccess.GetPixelByIndex(reinterpret_cast&>(index)); break; } case 3: { ImagePixelReadAccessor readAccess(image, image->GetVolumeData(0)); *returnValue = readAccess.GetPixelByIndex(index); break; } default: *returnValue = 0; break; } } static IntensityProfile::Pointer ComputeIntensityProfile(Image::Pointer image, itk::PolyLineParametricPath<3>::Pointer path) { IntensityProfile::Pointer intensityProfile = IntensityProfile::New(); itk::PolyLineParametricPath<3>::InputType input = path->StartOfInput(); BaseGeometry* imageGeometry = image->GetGeometry(); const PixelType pixelType = image->GetPixelType(); IntensityProfile::MeasurementVectorType measurementVector; itk::PolyLineParametricPath<3>::OffsetType offset; Point3D worldPoint; itk::Index<3> index; do { imageGeometry->IndexToWorld(path->Evaluate(input), worldPoint); imageGeometry->WorldToIndex(worldPoint, index); mitkPixelTypeMultiplex3(ReadPixel, pixelType, image, index, measurementVector.GetDataPointer()); intensityProfile->PushBack(measurementVector); offset = path->IncrementInput(input); } while ((offset[0] | offset[1] | offset[2]) != 0); return intensityProfile; } template static typename itk::InterpolateImageFunction::Pointer CreateInterpolateImageFunction(InterpolateImageFunction::Enum interpolator) { switch (interpolator) { case InterpolateImageFunction::NearestNeighbor: return itk::NearestNeighborInterpolateImageFunction::New().GetPointer(); case InterpolateImageFunction::Linear: return itk::LinearInterpolateImageFunction::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Blackman_3: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Blackman_4: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Blackman_5: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Cosine_3: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Cosine_4: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Cosine_5: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Hamming_3: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Hamming_4: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Hamming_5: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Lanczos_3: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Lanczos_4: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Lanczos_5: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Welch_3: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Welch_4: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Welch_5: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); default: return itk::NearestNeighborInterpolateImageFunction::New().GetPointer(); } } template static void ComputeIntensityProfile(itk::Image* image, itk::PolyLineParametricPath<3>::Pointer path, unsigned int numSamples, InterpolateImageFunction::Enum interpolator, IntensityProfile::Pointer intensityProfile) { typename itk::InterpolateImageFunction >::Pointer interpolateImageFunction = CreateInterpolateImageFunction >(interpolator); interpolateImageFunction->SetInputImage(image); const itk::PolyLineParametricPath<3>::InputType startOfInput = path->StartOfInput(); const itk::PolyLineParametricPath<3>::InputType delta = 1.0 / (numSamples - 1); IntensityProfile::MeasurementVectorType measurementVector; for (unsigned int i = 0; i < numSamples; ++i) { measurementVector[0] = interpolateImageFunction->EvaluateAtContinuousIndex(path->Evaluate(startOfInput + i * delta)); intensityProfile->PushBack(measurementVector); } } static IntensityProfile::Pointer ComputeIntensityProfile(Image::Pointer image, itk::PolyLineParametricPath<3>::Pointer path, unsigned int numSamples, InterpolateImageFunction::Enum interpolator) { IntensityProfile::Pointer intensityProfile = IntensityProfile::New(); AccessFixedDimensionByItk_n(image, ComputeIntensityProfile, 3, (path, numSamples, interpolator, intensityProfile)); return intensityProfile; } class AddPolyLineElementToPath { public: AddPolyLineElementToPath(const PlaneGeometry* planarFigureGeometry, const BaseGeometry* imageGeometry, itk::PolyLineParametricPath<3>::Pointer path) : m_PlanarFigureGeometry(planarFigureGeometry), m_ImageGeometry(imageGeometry), m_Path(path) { } void operator()(const PlanarFigure::PolyLineElement& polyLineElement) { m_PlanarFigureGeometry->Map(polyLineElement, m_WorldPoint); m_ImageGeometry->WorldToIndex(m_WorldPoint, m_ContinuousIndexPoint); m_Vertex.CastFrom(m_ContinuousIndexPoint); m_Path->AddVertex(m_Vertex); } private: const PlaneGeometry* m_PlanarFigureGeometry; const BaseGeometry* m_ImageGeometry; itk::PolyLineParametricPath<3>::Pointer m_Path; Point3D m_WorldPoint; Point3D m_ContinuousIndexPoint; itk::PolyLineParametricPath<3>::ContinuousIndexType m_Vertex; }; static itk::PolyLineParametricPath<3>::Pointer CreatePathFromPlanarFigure(BaseGeometry* imageGeometry, PlanarFigure* planarFigure) { itk::PolyLineParametricPath<3>::Pointer path = itk::PolyLineParametricPath<3>::New(); const PlanarFigure::PolyLineType polyLine = planarFigure->GetPolyLine(0); std::for_each(polyLine.begin(), polyLine.end(), AddPolyLineElementToPath(planarFigure->GetPlaneGeometry(), imageGeometry, path)); return path; } static void AddPointToPath(const BaseGeometry* imageGeometry, const Point3D& point, itk::PolyLineParametricPath<3>::Pointer path) { Point3D continuousIndexPoint; imageGeometry->WorldToIndex(point, continuousIndexPoint); itk::PolyLineParametricPath<3>::ContinuousIndexType vertex; vertex.CastFrom(continuousIndexPoint); path->AddVertex(vertex); } static itk::PolyLineParametricPath<3>::Pointer CreatePathFromPoints(BaseGeometry* imageGeometry, const Point3D& startPoint, const Point3D& endPoint) { itk::PolyLineParametricPath<3>::Pointer path = itk::PolyLineParametricPath<3>::New(); AddPointToPath(imageGeometry, startPoint, path); AddPointToPath(imageGeometry, endPoint, path); return path; } IntensityProfile::Pointer mitk::ComputeIntensityProfile(Image::Pointer image, PlanarFigure::Pointer planarFigure) { return ::ComputeIntensityProfile(image, CreatePathFromPlanarFigure(image->GetGeometry(), planarFigure)); } IntensityProfile::Pointer mitk::ComputeIntensityProfile(Image::Pointer image, PlanarLine::Pointer planarLine, unsigned int numSamples, InterpolateImageFunction::Enum interpolator) { return ::ComputeIntensityProfile(image, CreatePathFromPlanarFigure(image->GetGeometry(), planarLine.GetPointer()), numSamples, interpolator); } IntensityProfile::Pointer mitk::ComputeIntensityProfile(Image::Pointer image, const Point3D& startPoint, const Point3D& endPoint, unsigned int numSamples, InterpolateImageFunction::Enum interpolator) { return ::ComputeIntensityProfile(image, CreatePathFromPoints(image->GetGeometry(), startPoint, endPoint), numSamples, interpolator); } IntensityProfile::InstanceIdentifier mitk::ComputeGlobalMaximum(IntensityProfile::ConstPointer intensityProfile, IntensityProfile::MeasurementType &max) { max = -vcl_numeric_limits::min(); IntensityProfile::InstanceIdentifier maxIndex = 0; IntensityProfile::ConstIterator end = intensityProfile->End(); IntensityProfile::MeasurementType measurement; for (IntensityProfile::ConstIterator it = intensityProfile->Begin(); it != end; ++it) { measurement = it.GetMeasurementVector()[0]; if (measurement > max) { max = measurement; maxIndex = it.GetInstanceIdentifier(); } } return maxIndex; } IntensityProfile::InstanceIdentifier mitk::ComputeGlobalMinimum(IntensityProfile::ConstPointer intensityProfile, IntensityProfile::MeasurementType &min) { min = vcl_numeric_limits::max(); IntensityProfile::InstanceIdentifier minIndex = 0; IntensityProfile::ConstIterator end = intensityProfile->End(); IntensityProfile::MeasurementType measurement; for (IntensityProfile::ConstIterator it = intensityProfile->Begin(); it != end; ++it) { measurement = it.GetMeasurementVector()[0]; if (measurement < min) { min = measurement; minIndex = it.GetInstanceIdentifier(); } } return minIndex; } IntensityProfile::InstanceIdentifier mitk::ComputeCenterOfMaximumArea(IntensityProfile::ConstPointer intensityProfile, IntensityProfile::InstanceIdentifier radius) { //const IntensityProfile::MeasurementType min = intensityProfile->GetMeasurementVector(ComputeGlobalMinimum(intensityProfile))[0]; IntensityProfile::MeasurementType min; ComputeGlobalMinimum(intensityProfile, min); const IntensityProfile::InstanceIdentifier areaWidth = 1 + 2 * radius; IntensityProfile::MeasurementType maxArea = 0; for (IntensityProfile::InstanceIdentifier i = 0; i < areaWidth; ++i) maxArea += intensityProfile->GetMeasurementVector(i)[0] - min; const IntensityProfile::InstanceIdentifier lastIndex = intensityProfile->Size() - areaWidth; IntensityProfile::InstanceIdentifier centerOfMaxArea = radius; IntensityProfile::MeasurementType area = maxArea; for (IntensityProfile::InstanceIdentifier i = 1; i <= lastIndex; ++i) { area += intensityProfile->GetMeasurementVector(i + areaWidth - 1)[0] - min; area -= intensityProfile->GetMeasurementVector(i - 1)[0] - min; if (area > maxArea) { maxArea = area; centerOfMaxArea = i + radius; // TODO: If multiple areas in the neighborhood have the same intensity chose the middle one instead of the first one. } } return centerOfMaxArea; } std::vector mitk::CreateVectorFromIntensityProfile(IntensityProfile::ConstPointer intensityProfile) { std::vector result; result.reserve(intensityProfile->Size()); IntensityProfile::ConstIterator end = intensityProfile->End(); for (IntensityProfile::ConstIterator it = intensityProfile->Begin(); it != end; ++it) result.push_back(it.GetMeasurementVector()[0]); return result; } IntensityProfile::Pointer mitk::CreateIntensityProfileFromVector(const std::vector& vector) { const IntensityProfile::InstanceIdentifier size = vector.size(); IntensityProfile::Pointer result = IntensityProfile::New(); result->Resize(size); for (IntensityProfile::InstanceIdentifier i = 0; i < size; ++i) result->SetMeasurement(i, 0, vector[i]); return result; } -void mitk::ComputeIntensityProfileStatistics(IntensityProfile::ConstPointer intensityProfile, ImageStatisticsCalculator::StatisticsContainer::Pointer stats) +void mitk::ComputeIntensityProfileStatistics(IntensityProfile::ConstPointer intensityProfile, ImageStatisticsContainer::StatisticsObject& stats) { typedef std::vector StatsVecType; StatsVecType statsVec = mitk::CreateVectorFromIntensityProfile( intensityProfile ); IntensityProfile::MeasurementType min; IntensityProfile::MeasurementType max; mitk::ComputeGlobalMinimum( intensityProfile, min ); mitk::ComputeGlobalMaximum( intensityProfile, max ); - StatsVecType::size_type numSamples = statsVec.size(); + auto numSamples = static_cast(statsVec.size()); double mean = 0.0; double rms = 0.0; for ( StatsVecType::const_iterator it = statsVec.begin(); it != statsVec.end(); ++it ) { double val = *it; mean += val; rms += val*val; } - mean /= numSamples; - rms /= numSamples; + mean /= static_cast(numSamples); + rms /= static_cast(numSamples); double var = 0.0; for ( StatsVecType::const_iterator it = statsVec.begin(); it != statsVec.end(); ++it ) { double diff = *it - mean; var += diff*diff; } - var /= ( numSamples - 1 ); + var /= (static_cast(numSamples) - 1 ); rms = sqrt( rms ); - stats->SetMin( static_cast( min ) ); - stats->SetMax( static_cast( max ) ); - stats->SetN( numSamples ); - stats->SetMean( mean ); - stats->SetVariance( var ); - stats->SetRMS( rms ); + stats.AddStatistic(mitk::ImageStatisticsConstants::MINIMUM(), min); + stats.AddStatistic(mitk::ImageStatisticsConstants::MAXIMUM(), max); + stats.AddStatistic(mitk::ImageStatisticsConstants::NUMBEROFVOXELS(), numSamples); + stats.AddStatistic(mitk::ImageStatisticsConstants::MEAN(), mean); + stats.AddStatistic(mitk::ImageStatisticsConstants::STANDARDDEVIATION(), sqrt(var)); + stats.AddStatistic(mitk::ImageStatisticsConstants::VARIANCE(), var); + stats.AddStatistic(mitk::ImageStatisticsConstants::RMS(), rms); } diff --git a/Modules/ImageStatistics/mitkIntensityProfile.h b/Modules/ImageStatistics/mitkIntensityProfile.h index 95022ab617..82d5787a09 100644 --- a/Modules/ImageStatistics/mitkIntensityProfile.h +++ b/Modules/ImageStatistics/mitkIntensityProfile.h @@ -1,137 +1,137 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef mitkIntensityProfile_h #define mitkIntensityProfile_h #include #include #include #include #include namespace mitk { typedef itk::Statistics::ListSample::MeasurementVectorType> IntensityProfile; /** \brief Compute intensity profile of an image for each pixel along the first PolyLine of a given planar figure. * * \param[in] image A two or three-dimensional image which consists of single component pixels. * \param[in] planarFigure A planar figure from which the first PolyLine is used to evaluate the intensity profile. * * \return The computed intensity profile. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::Pointer ComputeIntensityProfile(Image::Pointer image, PlanarFigure::Pointer planarFigure); namespace InterpolateImageFunction { enum Enum { NearestNeighbor, Linear, WindowedSinc_Blackman_3, WindowedSinc_Blackman_4, WindowedSinc_Blackman_5, WindowedSinc_Cosine_3, WindowedSinc_Cosine_4, WindowedSinc_Cosine_5, WindowedSinc_Hamming_3, WindowedSinc_Hamming_4, WindowedSinc_Hamming_5, WindowedSinc_Lanczos_3, WindowedSinc_Lanczos_4, WindowedSinc_Lanczos_5, WindowedSinc_Welch_3, WindowedSinc_Welch_4, WindowedSinc_Welch_5 }; } /** \brief Compute intensity profile of an image for each sample along a planar line. * * \param[in] image A three-dimensional image which consists of single component pixels. * \param[in] planarLine A planar line along which the intensity profile will be evaluated. * \param[in] numSamples Number of samples along the planar line (must be at least 2). * \param[in] interpolator Image interpolation function which is used to read each sample. * * \return The computed intensity profile. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::Pointer ComputeIntensityProfile(Image::Pointer image, PlanarLine::Pointer planarLine, unsigned int numSamples, InterpolateImageFunction::Enum interpolator = InterpolateImageFunction::NearestNeighbor); /** \brief Compute intensity profile of an image for each sample between two points. * * \param[in] image A three-dimensional image which consists of single component pixels. * \param[in] startPoint A point at which the first sample is to be read. * \param[in] endPoint A point at which the last sample is to be read. * \param[in] numSamples Number of samples between startPoint and endPoint (must be at least 2). * \param[in] interpolator Image interpolation function which is used to read each sample. * * \return The computed intensity profile. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::Pointer ComputeIntensityProfile(Image::Pointer image, const Point3D& startPoint, const Point3D& endPoint, unsigned int numSamples, InterpolateImageFunction::Enum interpolator = InterpolateImageFunction::NearestNeighbor); /** \brief Compute global maximum of an intensity profile. * * \param[in] intensityProfile An intensity profile. * * \return Index of the global maximum. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::InstanceIdentifier ComputeGlobalMaximum(IntensityProfile::ConstPointer intensityProfile, IntensityProfile::MeasurementType &max); /** \brief Compute global minimum of an intensity profile. * * \param[in] intensityProfile An intensity profile. * * \return Index of the global minimum. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::InstanceIdentifier ComputeGlobalMinimum(IntensityProfile::ConstPointer intensityProfile, IntensityProfile::MeasurementType &min); /** \brief Compute statistics of an intensity profile. * * \param[in] intensityProfile An intensity profile. * * \param[in] stats An ImageStatisticsCalculator::Statistics object to hold the calculated statistics. * */ - MITKIMAGESTATISTICS_EXPORT void ComputeIntensityProfileStatistics(IntensityProfile::ConstPointer intensityProfile, ImageStatisticsCalculator::StatisticsContainer::Pointer stats); + MITKIMAGESTATISTICS_EXPORT void ComputeIntensityProfileStatistics(IntensityProfile::ConstPointer intensityProfile, ImageStatisticsContainer::StatisticsObject& stats); /** \brief Compute center of maximum area under the curve of an intensity profile. * * \param[in] intensityProfile An intensity profile. * \param[in] radius Radius of the area (width of area equals 1 + 2 * radius). * * \return Index of the maximum area center. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::InstanceIdentifier ComputeCenterOfMaximumArea(IntensityProfile::ConstPointer intensityProfile, IntensityProfile::InstanceIdentifier radius); /** \brief Convert an intensity profile to a standard library vector. * * \param[in] intensityProfile An intensity profile. * * \return Standard library vector which contains the input intensity profile measurements. */ MITKIMAGESTATISTICS_EXPORT std::vector CreateVectorFromIntensityProfile(IntensityProfile::ConstPointer intensityProfile); /** \brief Convert a standard library vector to an intensity profile. * * \param[in] vector An standard library vector which contains intensity profile measurements. * * \return An intensity profile. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::Pointer CreateIntensityProfileFromVector(const std::vector& vector); } #endif diff --git a/Modules/ImageStatistics/mitkMaskGenerator.cpp b/Modules/ImageStatistics/mitkMaskGenerator.cpp index 37374d440f..611e0fb7aa 100644 --- a/Modules/ImageStatistics/mitkMaskGenerator.cpp +++ b/Modules/ImageStatistics/mitkMaskGenerator.cpp @@ -1,51 +1,52 @@ #include namespace mitk { MaskGenerator::MaskGenerator(): m_TimeStep(0) { m_inputImage = nullptr; } mitk::Image::Pointer MaskGenerator::GetMask() { - return mitk::Image::New(); + return mitk::Image::New(); } + //typename itk::Region<3>::Pointer MaskGenerator::GetImageRegionOfMask(Image::Pointer image) //{ // if (m_InternalMask.IsNull() || m_Modified) // { // MITK_ERROR << "Update MaskGenerator first!"; // } // mitk::BaseGeometry::Pointer imageGeometry = image->GetGeometry(); // mitk::BaseGeometry::Pointer maskGeometry = m_InternalMask->GetGeometry(); //} void MaskGenerator::SetTimeStep(unsigned int timeStep) { if (timeStep != m_TimeStep) { m_TimeStep = timeStep; } } -void MaskGenerator::SetInputImage(mitk::Image::Pointer inputImg) +void MaskGenerator::SetInputImage(mitk::Image::ConstPointer inputImg) { if (inputImg != m_inputImage) { m_inputImage = inputImg; this->Modified(); } } -mitk::Image::Pointer MaskGenerator::GetReferenceImage() +mitk::Image::ConstPointer MaskGenerator::GetReferenceImage() { return m_inputImage; } } diff --git a/Modules/ImageStatistics/mitkMaskGenerator.h b/Modules/ImageStatistics/mitkMaskGenerator.h index 3fced6ef46..112e669e37 100644 --- a/Modules/ImageStatistics/mitkMaskGenerator.h +++ b/Modules/ImageStatistics/mitkMaskGenerator.h @@ -1,66 +1,66 @@ #ifndef MITKMASKGENERATOR #define MITKMASKGENERATOR #include #include #include #include #include namespace mitk { /** * \class MaskGenerator * \brief Base Class for all Mask Generators. Mask generators are classes that provide functionality for the * creation of binary (or unsigned short) masks that can be applied to an image. See dervied classes for more * information. */ class MITKIMAGESTATISTICS_EXPORT MaskGenerator: public itk::Object { public: /** Standard Self typedef */ typedef MaskGenerator Self; typedef itk::Object Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkNewMacro(Self) /** Runtime information support. */ itkTypeMacro(MaskGenerator, itk::Object) //~MaskGenerator(); /** * @brief GetMask must be overridden by derived classes. * @return mitk::Image::Pointer of generated mask */ virtual mitk::Image::Pointer GetMask(); /** * @brief GetReferenceImage per default returns the inputImage (as set by SetInputImage). If no input image is set it will return a nullptr. */ - virtual mitk::Image::Pointer GetReferenceImage(); + virtual mitk::Image::ConstPointer GetReferenceImage(); /** * @brief SetInputImage is used to set the input image to the mask generator. Some subclasses require an input image, others don't. See the documentation of the specific Mask Generator for more information. */ - void SetInputImage(mitk::Image::Pointer inputImg); + void SetInputImage(mitk::Image::ConstPointer inputImg); virtual void SetTimeStep(unsigned int timeStep); protected: MaskGenerator(); unsigned int m_TimeStep; mitk::Image::Pointer m_InternalMask; - mitk::Image::Pointer m_inputImage; + mitk::Image::ConstPointer m_inputImage; private: }; } #endif // MITKMASKGENERATOR diff --git a/Modules/ImageStatistics/mitkPlanarFigureMaskGenerator.cpp b/Modules/ImageStatistics/mitkPlanarFigureMaskGenerator.cpp index a2cc97da19..f80ec0bdc8 100644 --- a/Modules/ImageStatistics/mitkPlanarFigureMaskGenerator.cpp +++ b/Modules/ImageStatistics/mitkPlanarFigureMaskGenerator.cpp @@ -1,530 +1,528 @@ #include #include #include #include "mitkImageAccessByItk.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace mitk { void PlanarFigureMaskGenerator::SetPlanarFigure(mitk::PlanarFigure::Pointer planarFigure) { if ( planarFigure.IsNull() ) { throw std::runtime_error( "Error: planar figure empty!" ); } const PlaneGeometry *planarFigurePlaneGeometry = planarFigure->GetPlaneGeometry(); if ( planarFigurePlaneGeometry == nullptr ) { throw std::runtime_error( "Planar-Figure not yet initialized!" ); } const auto *planarFigureGeometry = dynamic_cast< const PlaneGeometry * >( planarFigurePlaneGeometry ); if ( planarFigureGeometry == nullptr ) { throw std::runtime_error( "Non-planar planar figures not supported!" ); } if (planarFigure != m_PlanarFigure) { this->Modified(); m_PlanarFigure = planarFigure; } } -mitk::Image::Pointer PlanarFigureMaskGenerator::GetReferenceImage() +mitk::Image::ConstPointer PlanarFigureMaskGenerator::GetReferenceImage() { if (IsUpdateRequired()) { this->CalculateMask(); } return m_ReferenceImage; } template < typename TPixel, unsigned int VImageDimension > void PlanarFigureMaskGenerator::InternalCalculateMaskFromPlanarFigure( const itk::Image< TPixel, VImageDimension > *image, unsigned int axis ) { typedef itk::Image< unsigned short, 2 > MaskImage2DType; typename MaskImage2DType::Pointer maskImage = MaskImage2DType::New(); maskImage->SetOrigin(image->GetOrigin()); maskImage->SetSpacing(image->GetSpacing()); maskImage->SetLargestPossibleRegion(image->GetLargestPossibleRegion()); maskImage->SetBufferedRegion(image->GetBufferedRegion()); maskImage->SetDirection(image->GetDirection()); maskImage->SetNumberOfComponentsPerPixel(image->GetNumberOfComponentsPerPixel()); maskImage->Allocate(); maskImage->FillBuffer(1); // all PolylinePoints of the PlanarFigure are stored in a vtkPoints object. // These points are used by the vtkLassoStencilSource to create // a vtkImageStencil. const mitk::PlaneGeometry *planarFigurePlaneGeometry = m_PlanarFigure->GetPlaneGeometry(); const typename PlanarFigure::PolyLineType planarFigurePolyline = m_PlanarFigure->GetPolyLine( 0 ); const mitk::BaseGeometry *imageGeometry3D = m_inputImage->GetGeometry( 0 ); // If there is a second poly line in a closed planar figure, treat it as a hole. PlanarFigure::PolyLineType planarFigureHolePolyline; if (m_PlanarFigure->GetPolyLinesSize() == 2) planarFigureHolePolyline = m_PlanarFigure->GetPolyLine(1); // Determine x- and y-dimensions depending on principal axis // TODO use plane geometry normal to determine that automatically, then check whether the PF is aligned with one of the three 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; } // store the polyline contour as vtkPoints object bool outOfBounds = false; vtkSmartPointer points = vtkSmartPointer::New(); typename PlanarFigure::PolyLineType::const_iterator it; for ( it = planarFigurePolyline.begin(); it != planarFigurePolyline.end(); ++it ) { Point3D point3D; // Convert 2D point back to the local index coordinates of the selected // image // Fabian: From PlaneGeometry documentation: // Converts a 2D point given in mm (pt2d_mm) relative to the upper-left corner of the geometry into the corresponding world-coordinate (a 3D point in mm, pt3d_mm). // To convert a 2D point given in units (e.g., pixels in case of an image) into a 2D point given in mm (as required by this method), use IndexToWorld. planarFigurePlaneGeometry->Map( *it, point3D ); // Polygons (partially) outside of the image bounds can not be processed // further due to a bug in vtkPolyDataToImageStencil if ( !imageGeometry3D->IsInside( point3D ) ) { outOfBounds = true; } imageGeometry3D->WorldToIndex( point3D, point3D ); points->InsertNextPoint( point3D[i0], point3D[i1], 0 ); } vtkSmartPointer holePoints = nullptr; if (!planarFigureHolePolyline.empty()) { holePoints = vtkSmartPointer::New(); Point3D point3D; PlanarFigure::PolyLineType::const_iterator end = planarFigureHolePolyline.end(); for (it = planarFigureHolePolyline.begin(); it != end; ++it) { // Fabian: same as above planarFigurePlaneGeometry->Map(*it, point3D); imageGeometry3D->WorldToIndex(point3D, point3D); holePoints->InsertNextPoint(point3D[i0], point3D[i1], 0); } } // mark a malformed 2D planar figure ( i.e. area = 0 ) as out of bounds // this can happen when all control points of a rectangle lie on the same line = two of the three extents are zero double bounds[6] = {0, 0, 0, 0, 0, 0}; points->GetBounds( bounds ); bool extent_x = (fabs(bounds[0] - bounds[1])) < mitk::eps; bool extent_y = (fabs(bounds[2] - bounds[3])) < mitk::eps; bool extent_z = (fabs(bounds[4] - bounds[5])) < mitk::eps; // throw an exception if a closed planar figure is deformed, i.e. has only one non-zero extent if ( m_PlanarFigure->IsClosed() && ((extent_x && extent_y) || (extent_x && extent_z) || (extent_y && extent_z))) { mitkThrow() << "Figure has a zero area and cannot be used for masking."; } if ( outOfBounds ) { throw std::runtime_error( "Figure at least partially outside of image bounds!" ); } // create a vtkLassoStencilSource and set the points of the Polygon vtkSmartPointer lassoStencil = vtkSmartPointer::New(); lassoStencil->SetShapeToPolygon(); lassoStencil->SetPoints( points ); vtkSmartPointer holeLassoStencil = nullptr; if (holePoints.GetPointer() != nullptr) { holeLassoStencil = vtkSmartPointer::New(); holeLassoStencil->SetShapeToPolygon(); holeLassoStencil->SetPoints(holePoints); } // Export from ITK to VTK (to use a VTK filter) typedef itk::VTKImageImport< MaskImage2DType > ImageImportType; typedef itk::VTKImageExport< MaskImage2DType > ImageExportType; typename ImageExportType::Pointer itkExporter = ImageExportType::New(); itkExporter->SetInput( maskImage ); // itkExporter->SetInput( castFilter->GetOutput() ); vtkSmartPointer vtkImporter = vtkSmartPointer::New(); this->ConnectPipelines( itkExporter, vtkImporter ); // Apply the generated image stencil to the input image vtkSmartPointer imageStencilFilter = vtkSmartPointer::New(); imageStencilFilter->SetInputConnection( vtkImporter->GetOutputPort() ); imageStencilFilter->SetStencilConnection(lassoStencil->GetOutputPort()); imageStencilFilter->ReverseStencilOff(); imageStencilFilter->SetBackgroundValue( 0 ); imageStencilFilter->Update(); vtkSmartPointer holeStencilFilter = nullptr; if (holeLassoStencil.GetPointer() != nullptr) { holeStencilFilter = vtkSmartPointer::New(); holeStencilFilter->SetInputConnection(imageStencilFilter->GetOutputPort()); holeStencilFilter->SetStencilConnection(holeLassoStencil->GetOutputPort()); holeStencilFilter->ReverseStencilOn(); holeStencilFilter->SetBackgroundValue(0); holeStencilFilter->Update(); } // Export from VTK back to ITK vtkSmartPointer vtkExporter = vtkSmartPointer::New(); vtkExporter->SetInputConnection( holeStencilFilter.GetPointer() == nullptr ? imageStencilFilter->GetOutputPort() : holeStencilFilter->GetOutputPort()); vtkExporter->Update(); typename ImageImportType::Pointer itkImporter = ImageImportType::New(); this->ConnectPipelines( vtkExporter, itkImporter ); itkImporter->Update(); typedef itk::ImageDuplicator< ImageImportType::OutputImageType > DuplicatorType; DuplicatorType::Pointer duplicator = DuplicatorType::New(); duplicator->SetInputImage( itkImporter->GetOutput() ); duplicator->Update(); // Store mask m_InternalITKImageMask2D = duplicator->GetOutput(); } template < typename TPixel, unsigned int VImageDimension > void PlanarFigureMaskGenerator::InternalCalculateMaskFromOpenPlanarFigure( const itk::Image< TPixel, VImageDimension > *image, unsigned int axis ) { typedef itk::Image< unsigned short, 2 > MaskImage2DType; typedef itk::LineIterator< MaskImage2DType > LineIteratorType; typedef MaskImage2DType::IndexType IndexType2D; typedef std::vector< IndexType2D > IndexVecType; typename MaskImage2DType::Pointer maskImage = MaskImage2DType::New(); maskImage->SetOrigin(image->GetOrigin()); maskImage->SetSpacing(image->GetSpacing()); maskImage->SetLargestPossibleRegion(image->GetLargestPossibleRegion()); maskImage->SetBufferedRegion(image->GetBufferedRegion()); maskImage->SetDirection(image->GetDirection()); maskImage->SetNumberOfComponentsPerPixel(image->GetNumberOfComponentsPerPixel()); maskImage->Allocate(); maskImage->FillBuffer(0); // all PolylinePoints of the PlanarFigure are stored in a vtkPoints object. const mitk::PlaneGeometry *planarFigurePlaneGeometry = m_PlanarFigure->GetPlaneGeometry(); const typename PlanarFigure::PolyLineType planarFigurePolyline = m_PlanarFigure->GetPolyLine( 0 ); const mitk::BaseGeometry *imageGeometry3D = m_inputImage->GetGeometry( 0 ); // Determine x- and y-dimensions depending on principal axis // TODO use plane geometry normal to determine that automatically, then check whether the PF is aligned with one of the three 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; } int numPolyLines = m_PlanarFigure->GetPolyLinesSize(); for ( int lineId = 0; lineId < numPolyLines; ++lineId ) { // store the polyline contour as vtkPoints object bool outOfBounds = false; IndexVecType pointIndices; typename PlanarFigure::PolyLineType::const_iterator it; for ( it = planarFigurePolyline.begin(); it != planarFigurePolyline.end(); ++it ) { Point3D point3D; planarFigurePlaneGeometry->Map( *it, point3D ); if ( !imageGeometry3D->IsInside( point3D ) ) { outOfBounds = true; } imageGeometry3D->WorldToIndex( point3D, point3D ); IndexType2D index2D; index2D[0] = point3D[i0]; index2D[1] = point3D[i1]; pointIndices.push_back( index2D ); } if ( outOfBounds ) { throw std::runtime_error( "Figure at least partially outside of image bounds!" ); } for ( IndexVecType::const_iterator it = pointIndices.begin(); it != pointIndices.end()-1; ++it ) { IndexType2D ind1 = *it; IndexType2D ind2 = *(it+1); LineIteratorType lineIt( maskImage, ind1, ind2 ); while ( !lineIt.IsAtEnd() ) { lineIt.Set( 1 ); ++lineIt; } } } // Store mask m_InternalITKImageMask2D = maskImage; } bool PlanarFigureMaskGenerator::GetPrincipalAxis( const BaseGeometry *geometry, Vector3D vector, unsigned int &axis ) { vector.Normalize(); for ( unsigned int i = 0; i < 3; ++i ) { Vector3D axisVector = geometry->GetAxisVector( i ); axisVector.Normalize(); if ( fabs( fabs( axisVector * vector ) - 1.0) < mitk::eps ) { axis = i; return true; } } return false; } void PlanarFigureMaskGenerator::CalculateMask() { if (m_inputImage.IsNull()) { MITK_ERROR << "Image is not set."; } if (m_PlanarFigure.IsNull()) { MITK_ERROR << "PlanarFigure is not set."; } if (m_TimeStep != 0) { MITK_WARN << "Multiple TimeSteps are not supported in PlanarFigureMaskGenerator (yet)."; } const BaseGeometry *imageGeometry = m_inputImage->GetGeometry(); if ( imageGeometry == nullptr ) { throw std::runtime_error( "Image geometry invalid!" ); } if (m_inputImage->GetTimeSteps() > 0) { mitk::ImageTimeSelector::Pointer imgTimeSel = mitk::ImageTimeSelector::New(); imgTimeSel->SetInput(m_inputImage); imgTimeSel->SetTimeNr(m_TimeStep); imgTimeSel->UpdateLargestPossibleRegion(); m_InternalTimeSliceImage = imgTimeSel->GetOutput(); } else { m_InternalTimeSliceImage = m_inputImage; } m_InternalITKImageMask2D = nullptr; const PlaneGeometry *planarFigurePlaneGeometry = m_PlanarFigure->GetPlaneGeometry(); const auto *planarFigureGeometry = dynamic_cast< const PlaneGeometry * >( planarFigurePlaneGeometry ); //const BaseGeometry *imageGeometry = m_inputImage->GetGeometry(); // Find principal direction of PlanarFigure in input image unsigned int axis; if ( !this->GetPrincipalAxis( imageGeometry, planarFigureGeometry->GetNormal(), axis ) ) { throw std::runtime_error( "Non-aligned planar figures not supported!" ); } m_PlanarFigureAxis = axis; // Find slice number corresponding to PlanarFigure in input image itk::Image< unsigned short, 3 >::IndexType index; imageGeometry->WorldToIndex( planarFigureGeometry->GetOrigin(), index ); unsigned int slice = index[axis]; m_PlanarFigureSlice = slice; // extract image slice which corresponds to the planarFigure and store it in m_InternalImageSlice - mitk::Image::Pointer inputImageSlice = extract2DImageSlice(axis, slice); + mitk::Image::ConstPointer inputImageSlice = extract2DImageSlice(axis, slice); //mitk::IOUtil::Save(inputImageSlice, "/home/fabian/inputSliceImage.nrrd"); // Compute mask from PlanarFigure // rastering for open planar figure: if ( !m_PlanarFigure->IsClosed() ) { AccessFixedDimensionByItk_1(inputImageSlice, InternalCalculateMaskFromOpenPlanarFigure, 2, axis) } else//for closed planar figure { AccessFixedDimensionByItk_1(inputImageSlice, InternalCalculateMaskFromPlanarFigure, 2, axis) } //convert itk mask to mitk::Image::Pointer and return it mitk::Image::Pointer planarFigureMaskImage; planarFigureMaskImage = mitk::GrabItkImageMemory(m_InternalITKImageMask2D); //mitk::IOUtil::Save(planarFigureMaskImage, "/home/fabian/planarFigureMaskImage.nrrd"); //Convert2Dto3DImageFilter::Pointer sliceTo3DImageConverter = Convert2Dto3DImageFilter::New(); //sliceTo3DImageConverter->SetInput(planarFigureMaskImage); //sliceTo3DImageConverter->Update(); //mitk::IOUtil::Save(sliceTo3DImageConverter->GetOutput(), "/home/fabian/3DsliceImage.nrrd"); m_ReferenceImage = inputImageSlice; //mitk::IOUtil::Save(m_ReferenceImage, "/home/fabian/referenceImage.nrrd"); m_InternalMask = planarFigureMaskImage; } void PlanarFigureMaskGenerator::SetTimeStep(unsigned int timeStep) { if (timeStep != m_TimeStep) { m_TimeStep = timeStep; } } mitk::Image::Pointer PlanarFigureMaskGenerator::GetMask() { if (IsUpdateRequired()) { this->CalculateMask(); this->Modified(); } m_InternalMaskUpdateTime = this->GetMTime(); return m_InternalMask; } -mitk::Image::Pointer PlanarFigureMaskGenerator::extract2DImageSlice(unsigned int axis, unsigned int slice) +mitk::Image::ConstPointer PlanarFigureMaskGenerator::extract2DImageSlice(unsigned int axis, unsigned int slice) { // Extract slice with given position and direction from image unsigned int dimension = m_InternalTimeSliceImage->GetDimension(); - mitk::Image::Pointer imageSlice = mitk::Image::New(); if (dimension == 3) { ExtractImageFilter::Pointer imageExtractor = ExtractImageFilter::New(); imageExtractor->SetInput( m_InternalTimeSliceImage ); imageExtractor->SetSliceDimension( axis ); imageExtractor->SetSliceIndex( slice ); imageExtractor->Update(); - imageSlice = imageExtractor->GetOutput(); + return imageExtractor->GetOutput(); } else if(dimension == 2) { - imageSlice = m_InternalTimeSliceImage; + return m_InternalTimeSliceImage; } else { - MITK_ERROR << "Unsupported image dimension. Dimension is: " << dimension << ". Only 2D and 3D images are supported."; + MITK_ERROR << "Unsupported image dimension. Dimension is: " << dimension << ". Only 2D and 3D images are supported."; + return nullptr; } - - return imageSlice; } bool PlanarFigureMaskGenerator::IsUpdateRequired() const { unsigned long thisClassTimeStamp = this->GetMTime(); unsigned long internalMaskTimeStamp = m_InternalMask->GetMTime(); unsigned long planarFigureTimeStamp = m_PlanarFigure->GetMTime(); unsigned long inputImageTimeStamp = m_inputImage->GetMTime(); if (thisClassTimeStamp > m_InternalMaskUpdateTime) // inputs have changed { return true; } if (m_InternalMaskUpdateTime < planarFigureTimeStamp || m_InternalMaskUpdateTime < inputImageTimeStamp) // mask image has changed outside of this class { return true; } if (internalMaskTimeStamp > m_InternalMaskUpdateTime) // internal mask has been changed outside of this class { return true; } return false; } } diff --git a/Modules/ImageStatistics/mitkPlanarFigureMaskGenerator.h b/Modules/ImageStatistics/mitkPlanarFigureMaskGenerator.h index 3598e7d533..6d5c632109 100644 --- a/Modules/ImageStatistics/mitkPlanarFigureMaskGenerator.h +++ b/Modules/ImageStatistics/mitkPlanarFigureMaskGenerator.h @@ -1,133 +1,133 @@ #ifndef MITKPLANARFIGUREMASKGENERATOR #define MITKPLANARFIGUREMASKGENERATOR #include #include #include #include #include #include #include #include #include #include namespace mitk { /** * \class PlanarFigureMaskGenerator * \brief Derived from MaskGenerator. This class is used to convert a mitk::PlanarFigure into a binary image mask */ class MITKIMAGESTATISTICS_EXPORT PlanarFigureMaskGenerator : public MaskGenerator { public: /** Standard Self typedef */ typedef PlanarFigureMaskGenerator Self; typedef MaskGenerator Superclass; typedef itk::SmartPointer Pointer; typedef itk::SmartPointer ConstPointer; /** Method for creation through the object factory. */ itkNewMacro(Self) /** Runtime information support. */ itkTypeMacro(PlanarFigureMaskGenerator, MaskGenerator) /** * @brief GetMask Computes and returns the mask * @return mitk::Image::Pointer of the generated mask */ mitk::Image::Pointer GetMask() override; void SetPlanarFigure(mitk::PlanarFigure::Pointer planarFigure); - mitk::Image::Pointer GetReferenceImage() override; + mitk::Image::ConstPointer GetReferenceImage() override; /** * @brief SetTimeStep is used to set the time step for which the mask is to be generated * @param timeStep */ void SetTimeStep(unsigned int timeStep) override; itkGetConstMacro(PlanarFigureAxis, unsigned int); itkGetConstMacro(PlanarFigureSlice, unsigned int); protected: PlanarFigureMaskGenerator() : Superclass(), m_ReferenceImage(nullptr), m_PlanarFigureAxis(0), m_InternalMaskUpdateTime(0), m_PlanarFigureSlice(0) { m_InternalMask = mitk::Image::New(); } private: void CalculateMask(); template void InternalCalculateMaskFromPlanarFigure(const itk::Image *image, unsigned int axis); template void InternalCalculateMaskFromOpenPlanarFigure(const itk::Image *image, unsigned int axis); - mitk::Image::Pointer extract2DImageSlice(unsigned int axis, unsigned int slice); + mitk::Image::ConstPointer extract2DImageSlice(unsigned int axis, unsigned int slice); bool GetPrincipalAxis(const BaseGeometry *geometry, Vector3D vector, unsigned int &axis); /** Connection from ITK to VTK */ template void ConnectPipelines(ITK_Exporter exporter, vtkSmartPointer importer) { importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback()); importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback()); importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback()); importer->SetSpacingCallback(exporter->GetSpacingCallback()); importer->SetOriginCallback(exporter->GetOriginCallback()); importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback()); importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback()); importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback()); importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback()); importer->SetDataExtentCallback(exporter->GetDataExtentCallback()); importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()); importer->SetCallbackUserData(exporter->GetCallbackUserData()); } /** Connection from VTK to ITK */ template void ConnectPipelines(vtkSmartPointer exporter, ITK_Importer importer) { importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback()); importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback()); importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback()); importer->SetSpacingCallback(exporter->GetSpacingCallback()); importer->SetOriginCallback(exporter->GetOriginCallback()); importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback()); importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback()); importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback()); importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback()); importer->SetDataExtentCallback(exporter->GetDataExtentCallback()); importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()); importer->SetCallbackUserData(exporter->GetCallbackUserData()); } bool IsUpdateRequired() const; mitk::PlanarFigure::Pointer m_PlanarFigure; itk::Image::Pointer m_InternalITKImageMask2D; - mitk::Image::Pointer m_InternalTimeSliceImage; - mitk::Image::Pointer m_ReferenceImage; + mitk::Image::ConstPointer m_InternalTimeSliceImage; + mitk::Image::ConstPointer m_ReferenceImage; unsigned int m_PlanarFigureAxis; unsigned long m_InternalMaskUpdateTime; unsigned int m_PlanarFigureSlice; }; } // namespace mitk #endif // MITKPLANARFIGUREMASKGENERATOR diff --git a/Modules/ImageStatistics/mitkPointSetDifferenceStatisticsCalculator.cpp b/Modules/ImageStatistics/mitkPointSetDifferenceStatisticsCalculator.cpp index 221b97c69e..f28d1163df 100644 --- a/Modules/ImageStatistics/mitkPointSetDifferenceStatisticsCalculator.cpp +++ b/Modules/ImageStatistics/mitkPointSetDifferenceStatisticsCalculator.cpp @@ -1,216 +1,215 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkPointSetDifferenceStatisticsCalculator.h" +#include "mitkImageStatisticsConstants.h" mitk::PointSetDifferenceStatisticsCalculator::PointSetDifferenceStatisticsCalculator() : m_StatisticsCalculated(false) { - m_Statistics = ImageStatisticsCalculator::StatisticsContainer::New(); m_PointSet1 = mitk::PointSet::New(); m_PointSet2 = mitk::PointSet::New(); //m_Statistics.Reset(); } mitk::PointSetDifferenceStatisticsCalculator::PointSetDifferenceStatisticsCalculator(mitk::PointSet::Pointer pSet1, mitk::PointSet::Pointer pSet2) { - m_Statistics = ImageStatisticsCalculator::StatisticsContainer::New(); m_PointSet1 = pSet1; m_PointSet2 = pSet2; m_StatisticsCalculated = false; //m_Statistics.Reset(); } mitk::PointSetDifferenceStatisticsCalculator::~PointSetDifferenceStatisticsCalculator() { } void mitk::PointSetDifferenceStatisticsCalculator::SetPointSets(mitk::PointSet::Pointer pSet1, mitk::PointSet::Pointer pSet2) { if (pSet1.IsNotNull()) { m_PointSet1 = pSet1; } if (pSet2.IsNotNull()) { m_PointSet2 = pSet2; } m_StatisticsCalculated = false; //m_Statistics.Reset(); } std::vector mitk::PointSetDifferenceStatisticsCalculator::GetDifferences() { if (!m_StatisticsCalculated) { this->ComputeStatistics(); } return m_DifferencesVector; } std::vector mitk::PointSetDifferenceStatisticsCalculator::GetSquaredDifferences() { if (!m_StatisticsCalculated) { this->ComputeStatistics(); } return m_SquaredDifferencesVector; } double mitk::PointSetDifferenceStatisticsCalculator::GetMean() { if (!m_StatisticsCalculated) { this->ComputeStatistics(); } - return m_Statistics->GetMean(); + return m_Statistics.GetValueConverted(mitk::ImageStatisticsConstants::MEAN()); } double mitk::PointSetDifferenceStatisticsCalculator::GetSD() { if (!m_StatisticsCalculated) { this->ComputeStatistics(); } - return m_Statistics->GetStd(); + return m_Statistics.GetValueConverted(mitk::ImageStatisticsConstants::STANDARDDEVIATION()); } double mitk::PointSetDifferenceStatisticsCalculator::GetVariance() { if (!m_StatisticsCalculated) { this->ComputeStatistics(); } - return m_Statistics->GetVariance(); + return m_Statistics.GetValueConverted(mitk::ImageStatisticsConstants::VARIANCE()); } double mitk::PointSetDifferenceStatisticsCalculator::GetRMS() { if (!m_StatisticsCalculated) { this->ComputeStatistics(); } - return m_Statistics->GetRMS(); + return m_Statistics.GetValueConverted(mitk::ImageStatisticsConstants::RMS()); } double mitk::PointSetDifferenceStatisticsCalculator::GetMedian() { if (!m_StatisticsCalculated) { this->ComputeStatistics(); } - return m_Statistics->GetMedian(); + return m_Statistics.GetValueConverted(mitk::ImageStatisticsConstants::MEDIAN()); } double mitk::PointSetDifferenceStatisticsCalculator::GetMax() { if (!m_StatisticsCalculated) { this->ComputeStatistics(); } - return m_Statistics->GetMax(); + return m_Statistics.GetValueConverted(mitk::ImageStatisticsConstants::MAXIMUM()); } double mitk::PointSetDifferenceStatisticsCalculator::GetMin() { if (!m_StatisticsCalculated) { this->ComputeStatistics(); } - return m_Statistics->GetMin(); + return m_Statistics.GetValueConverted(mitk::ImageStatisticsConstants::MINIMUM()); } double mitk::PointSetDifferenceStatisticsCalculator::GetNumberOfPoints() { if (!m_StatisticsCalculated) { this->ComputeStatistics(); } - return m_Statistics->GetN(); + return m_Statistics.GetValueConverted(mitk::ImageStatisticsConstants::NUMBEROFVOXELS()); } void mitk::PointSetDifferenceStatisticsCalculator::ComputeStatistics() { if ((m_PointSet1.IsNull())||(m_PointSet2.IsNull())) { itkExceptionMacro("Point sets specified are not valid. Please specify correct Point sets"); } else if (m_PointSet1->GetSize()!=m_PointSet2->GetSize()) { itkExceptionMacro("PointSets are not equal. Please make sure that your PointSets have the same size and hold corresponding points."); } else if (m_PointSet1->GetSize()==0) { itkExceptionMacro("There are no points in the PointSets. Please make sure that the PointSets contain points"); } else { double mean = 0.0; double sd = 0.0; double rms= 0.0; std::vector differencesVector; mitk::Point3D point1; mitk::Point3D point2; - int numberOfPoints = m_PointSet1->GetSize(); + auto numberOfPoints = static_cast(m_PointSet1->GetSize()); //Iterate over both pointsets in order to compare all points pair-wise mitk::PointSet::PointsIterator end = m_PointSet1->End(); for( mitk::PointSet::PointsIterator pointSetIterator = m_PointSet1->Begin(), pointSetIterator2 = m_PointSet2->Begin(); pointSetIterator != end; ++pointSetIterator, ++pointSetIterator2) //iterate simultaneously over both sets { point1 = pointSetIterator.Value(); point2 = pointSetIterator2.Value(); double squaredDistance = point1.SquaredEuclideanDistanceTo(point2); mean+=sqrt(squaredDistance); rms+=squaredDistance; this->m_SquaredDifferencesVector.push_back(squaredDistance); differencesVector.push_back(sqrt(squaredDistance)); } m_DifferencesVector = differencesVector; - mean = mean/numberOfPoints; - rms = sqrt(rms/numberOfPoints); + mean = mean/static_cast(numberOfPoints); + rms = sqrt(rms/ static_cast(numberOfPoints)); for (std::vector::size_type i=0; i(numberOfPoints); sd = sqrt(variance); std::sort(differencesVector.begin(),differencesVector.end()); double median = 0.0; if (numberOfPoints%2 == 0) { median = (differencesVector.at(numberOfPoints/2)+differencesVector.at(numberOfPoints/2-1))/2; } else { median = differencesVector.at((numberOfPoints-1)/2+1); } - m_Statistics->SetMean(mean); - m_Statistics->SetStd(sd); - m_Statistics->SetVariance(variance); - m_Statistics->SetRMS(rms); - m_Statistics->SetMin(differencesVector.at(0)); - m_Statistics->SetMax(differencesVector.at(numberOfPoints-1)); - m_Statistics->SetMedian(median); - m_Statistics->SetN(numberOfPoints); + m_Statistics.AddStatistic(mitk::ImageStatisticsConstants::MEAN(), mean); + m_Statistics.AddStatistic(mitk::ImageStatisticsConstants::STANDARDDEVIATION(), sd); + m_Statistics.AddStatistic(mitk::ImageStatisticsConstants::VARIANCE(), sd*sd); + m_Statistics.AddStatistic(mitk::ImageStatisticsConstants::RMS(), rms); + m_Statistics.AddStatistic(mitk::ImageStatisticsConstants::MINIMUM(), differencesVector.at(0)); + m_Statistics.AddStatistic(mitk::ImageStatisticsConstants::MAXIMUM(), differencesVector.at(numberOfPoints - 1)); + m_Statistics.AddStatistic(mitk::ImageStatisticsConstants::MEDIAN(), median); + m_Statistics.AddStatistic(mitk::ImageStatisticsConstants::NUMBEROFVOXELS(), numberOfPoints); m_StatisticsCalculated = true; } } diff --git a/Modules/ImageStatistics/mitkPointSetDifferenceStatisticsCalculator.h b/Modules/ImageStatistics/mitkPointSetDifferenceStatisticsCalculator.h index 5f26224dde..8d0b1589fa 100644 --- a/Modules/ImageStatistics/mitkPointSetDifferenceStatisticsCalculator.h +++ b/Modules/ImageStatistics/mitkPointSetDifferenceStatisticsCalculator.h @@ -1,110 +1,110 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef _MITK_PointSetDifferenceStatisticsCalculator_H #define _MITK_PointSetDifferenceStatisticsCalculator_H #include #include #include "mitkImageStatisticsCalculator.h" #include namespace mitk { /** * \brief Class for calculating the difference between two corresponding point sets. * The user can access the single distances between corresponding points as well as a complete statistic (mean, sd, rms, median, max, min) * The point sets must be of equal size! */ class MITKIMAGESTATISTICS_EXPORT PointSetDifferenceStatisticsCalculator : public itk::Object { public: mitkClassMacroItkParent( PointSetDifferenceStatisticsCalculator, itk::Object ); itkFactorylessNewMacro(Self) itkCloneMacro(Self) mitkNewMacro2Param(PointSetDifferenceStatisticsCalculator,mitk::PointSet::Pointer,mitk::PointSet::Pointer); /*! \brief set point sets to be compared */ void SetPointSets(mitk::PointSet::Pointer pSet1, mitk::PointSet::Pointer pSet2); /*! \brief returns a vector holding the differences between the corresponding points of the point sets */ std::vector GetDifferences(); /*! \brief returns a vector holding the squared differences between the corresponding points of the point sets */ std::vector GetSquaredDifferences(); /*! \brief returns the mean distance of all corresponding points of the point sets */ double GetMean(); /*! \brief returns the standard deviation of the distances between all corresponding points of the point sets */ double GetSD(); /*! \brief returns the variance of the distances between all corresponding points of the point sets */ double GetVariance(); /*! \brief returns the root mean squared distance of all corresponding points of the point sets */ double GetRMS(); /*! \brief returns the median distance of all corresponding points of the point sets */ double GetMedian(); /*! \brief returns the maximal distance of all corresponding points of the point sets */ double GetMax(); /*! \brief returns the minimal distance of all corresponding points of the point sets */ double GetMin(); /*! \brief returns the total number of corresponding points of the point sets */ double GetNumberOfPoints(); protected: PointSetDifferenceStatisticsCalculator(); PointSetDifferenceStatisticsCalculator(mitk::PointSet::Pointer,mitk::PointSet::Pointer); ~PointSetDifferenceStatisticsCalculator() override; /*! \brief Method for computing the complete statistics of the differences between the given point sets. */ void ComputeStatistics(); - mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer m_Statistics; ///< struct holding the statistics + mitk::ImageStatisticsContainer::StatisticsObject m_Statistics; ///< struct holding the statistics std::vector m_DifferencesVector; ///< vector holding the differences between the corresponding points std::vector m_SquaredDifferencesVector; ///< vector holding the squared differences between the corresponding points mitk::PointSet::Pointer m_PointSet1; ///< first point set used for comparison mitk::PointSet::Pointer m_PointSet2; ///< second point set used for comparison bool m_StatisticsCalculated; ///< flag indicating whether statistics are already calculated or not. }; } #endif // #define _MITK_PointSetDifferenceStatisticsCalculator_H diff --git a/Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp b/Modules/ImageStatistics/mitkStatisticsToImageRelationRule.cpp similarity index 59% copy from Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp copy to Modules/ImageStatistics/mitkStatisticsToImageRelationRule.cpp index a57ee8aa83..97969d183e 100644 --- a/Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp +++ b/Modules/ImageStatistics/mitkStatisticsToImageRelationRule.cpp @@ -1,34 +1,21 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ -#include -#include +#include "mitkStatisticsToImageRelationRule.h" -mitk::NodePredicateUID::NodePredicateUID(const Identifiable::UIDType &uid) - : m_UID(uid) -{ -} - -mitk::NodePredicateUID::~NodePredicateUID() -{ -} - -bool mitk::NodePredicateUID::CheckNode(const mitk::DataNode *node) const -{ - return nullptr != node - ? node->GetUID() == m_UID - : false; +mitk::StatisticsToImageRelationRule::StatisticsToImageRelationRule() : + GenericIDRelationRule("statisticsToImage", "relation between ImageStatisticsContainer and Image that was used as computation input", "ImageStatisticsContainer", "Image"){ } diff --git a/Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp b/Modules/ImageStatistics/mitkStatisticsToImageRelationRule.h similarity index 51% copy from Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp copy to Modules/ImageStatistics/mitkStatisticsToImageRelationRule.h index a57ee8aa83..20325c7e3f 100644 --- a/Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp +++ b/Modules/ImageStatistics/mitkStatisticsToImageRelationRule.h @@ -1,34 +1,36 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ -#include -#include +#ifndef mitkStatisticsToImageRelationRule_h +#define mitkStatisticsToImageRelationRule_h -mitk::NodePredicateUID::NodePredicateUID(const Identifiable::UIDType &uid) - : m_UID(uid) -{ -} +#include +#include "mitkGenericIDRelationRule.h" -mitk::NodePredicateUID::~NodePredicateUID() +namespace mitk { + class MITKIMAGESTATISTICS_EXPORT StatisticsToImageRelationRule : public mitk::GenericIDRelationRule + { + public: + mitkClassMacroItkParent(StatisticsToImageRelationRule, mitk::GenericIDRelationRule) + itkNewMacro(Self) + + protected: + StatisticsToImageRelationRule(); + }; } -bool mitk::NodePredicateUID::CheckNode(const mitk::DataNode *node) const -{ - return nullptr != node - ? node->GetUID() == m_UID - : false; -} +#endif diff --git a/Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp b/Modules/ImageStatistics/mitkStatisticsToMaskRelationRule.cpp similarity index 59% copy from Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp copy to Modules/ImageStatistics/mitkStatisticsToMaskRelationRule.cpp index a57ee8aa83..79f5245814 100644 --- a/Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp +++ b/Modules/ImageStatistics/mitkStatisticsToMaskRelationRule.cpp @@ -1,34 +1,21 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ -#include -#include +#include "mitkStatisticsToMaskRelationRule.h" -mitk::NodePredicateUID::NodePredicateUID(const Identifiable::UIDType &uid) - : m_UID(uid) -{ -} - -mitk::NodePredicateUID::~NodePredicateUID() -{ -} - -bool mitk::NodePredicateUID::CheckNode(const mitk::DataNode *node) const -{ - return nullptr != node - ? node->GetUID() == m_UID - : false; +mitk::StatisticsToMaskRelationRule::StatisticsToMaskRelationRule() : + GenericIDRelationRule("statisticsToMask", "relation between ImageStatisticsContainer and Mask that was used as computation input", "ImageStatisticsContainer", "Mask") { } diff --git a/Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp b/Modules/ImageStatistics/mitkStatisticsToMaskRelationRule.h similarity index 52% rename from Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp rename to Modules/ImageStatistics/mitkStatisticsToMaskRelationRule.h index a57ee8aa83..1bee1304df 100644 --- a/Modules/Core/src/DataManagement/mitkNodePredicateUID.cpp +++ b/Modules/ImageStatistics/mitkStatisticsToMaskRelationRule.h @@ -1,34 +1,36 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ -#include -#include +#ifndef mitkStatisticsToMaskRelationRule_h +#define mitkStatisticsToMaskRelationRule_h -mitk::NodePredicateUID::NodePredicateUID(const Identifiable::UIDType &uid) - : m_UID(uid) -{ -} +#include +#include "mitkGenericIDRelationRule.h" -mitk::NodePredicateUID::~NodePredicateUID() +namespace mitk { + class MITKIMAGESTATISTICS_EXPORT StatisticsToMaskRelationRule : public mitk::GenericIDRelationRule + { + public: + mitkClassMacroItkParent(StatisticsToMaskRelationRule, mitk::GenericIDRelationRule) + itkNewMacro(Self) + + protected: + StatisticsToMaskRelationRule(); + }; } -bool mitk::NodePredicateUID::CheckNode(const mitk::DataNode *node) const -{ - return nullptr != node - ? node->GetUID() == m_UID - : false; -} +#endif diff --git a/Modules/ImageStatisticsUI/CMakeLists.txt b/Modules/ImageStatisticsUI/CMakeLists.txt new file mode 100644 index 0000000000..8c9069b05f --- /dev/null +++ b/Modules/ImageStatisticsUI/CMakeLists.txt @@ -0,0 +1,5 @@ +MITK_CREATE_MODULE( + INCLUDE_DIRS Qmitk + DEPENDS MitkCore MitkChart MitkImageStatistics MitkQtWidgets + PACKAGE_DEPENDS PRIVATE Qt5|WebEngineWidgets +) \ No newline at end of file diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.cpp b/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.cpp new file mode 100644 index 0000000000..507ecd6e43 --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.cpp @@ -0,0 +1,144 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include "QmitkHistogramVisualizationWidget.h" + +#include + +QmitkHistogramVisualizationWidget::QmitkHistogramVisualizationWidget(QWidget* parent) : QWidget(parent) +{ + m_Controls.setupUi(this); + m_Controls.checkBoxShowSubchart->setChecked(false); + m_Controls.spinBoxNBins->setValue(m_DefaultNBins); + m_Controls.spinBoxNBins->setMinimum(m_MinNBins); + m_Controls.spinBoxNBins->setMaximum(m_MaxNBins); + + CreateConnections(); +} + +void QmitkHistogramVisualizationWidget::SetHistogram(itk::Statistics::Histogram::ConstPointer histogram, const std::string& dataLabel) +{ + if (histogram == nullptr) + return; + + m_Histogram = histogram; + m_Controls.chartWidget->AddData2D(ConvertHistogramToMap(m_Histogram), dataLabel); + m_Controls.chartWidget->SetChartType(dataLabel, QmitkChartWidget::ChartType::bar); + m_Controls.chartWidget->SetXAxisLabel("Gray value"); + m_Controls.chartWidget->SetYAxisLabel("Frequency"); + m_Controls.chartWidget->Show(m_Controls.checkBoxShowSubchart->isChecked()); + SetGUIElementsEnabled(true); +} + +void QmitkHistogramVisualizationWidget::Reset() +{ + m_Controls.chartWidget->Clear(); + SetGUIElementsEnabled(false); +} + +void QmitkHistogramVisualizationWidget::SetTheme(QmitkChartWidget::ChartStyle style) +{ + m_ChartStyle = style; +} + +void QmitkHistogramVisualizationWidget::CreateConnections() +{ + connect(m_Controls.buttonCopyHistogramToClipboard, &QPushButton::clicked, this, &QmitkHistogramVisualizationWidget::OnClipboardButtonClicked); + connect(m_Controls.checkBoxUseDefaultNBins, &QCheckBox::clicked, this, &QmitkHistogramVisualizationWidget::OnDefaultNBinsCheckBoxChanged); + connect(m_Controls.spinBoxNBins, &QSpinBox::editingFinished, this, &QmitkHistogramVisualizationWidget::OnNBinsSpinBoxValueChanged); + connect(m_Controls.checkBoxShowSubchart, &QCheckBox::clicked, this, &QmitkHistogramVisualizationWidget::OnShowSubchartCheckBoxChanged); + connect(m_Controls.chartWidget, &QmitkChartWidget::PageSuccessfullyLoaded, this, &QmitkHistogramVisualizationWidget::OnPageSuccessfullyLoaded); +} + +void QmitkHistogramVisualizationWidget::SetGUIElementsEnabled(bool enabled) +{ + this->setEnabled(enabled); + m_Controls.groupBoxPlot->setEnabled(enabled); + m_Controls.checkBoxShowSubchart->setEnabled(enabled); + m_Controls.checkBoxUseDefaultNBins->setEnabled(enabled); + m_Controls.spinBoxNBins->setEnabled(!m_Controls.checkBoxUseDefaultNBins->isChecked()); + m_Controls.buttonCopyHistogramToClipboard->setEnabled(enabled); +} + +std::map QmitkHistogramVisualizationWidget::ConvertHistogramToMap(itk::Statistics::Histogram::ConstPointer histogram) const +{ + std::map histogramMap; + if (histogram) + { + auto endIt = histogram->End(); + auto it = histogram->Begin(); + + // generating Lists of measurement and frequencies + for (; it != endIt; ++it) + { + double frequency = it.GetFrequency(); + double measurement = it.GetMeasurementVector()[0]; + histogramMap.emplace(measurement, frequency); + } + + } + return histogramMap; +} + +void QmitkHistogramVisualizationWidget::OnClipboardButtonClicked() +{ + if (m_Histogram) + { + QApplication::clipboard()->clear(); + QString clipboard("Measurement \t Frequency\n"); + auto iter = m_Histogram->Begin(); + auto iterEnd = m_Histogram->End(); + for (; iter != iterEnd; ++iter) + { + clipboard = clipboard.append("%L1 \t %L2\n") + .arg(iter.GetMeasurementVector()[0], 0, 'f', 2) + .arg(iter.GetFrequency()); + } + + QApplication::clipboard()->setText(clipboard, QClipboard::Clipboard); + } +} + +void QmitkHistogramVisualizationWidget::OnDefaultNBinsCheckBoxChanged() +{ + if (m_Controls.checkBoxUseDefaultNBins->isChecked()) + { + m_Controls.spinBoxNBins->setEnabled(false); + if (m_Controls.spinBoxNBins->value() != static_cast(m_DefaultNBins) ) { + m_Controls.spinBoxNBins->setValue(m_DefaultNBins); + OnNBinsSpinBoxValueChanged(); + } + } + else + { + m_Controls.spinBoxNBins->setEnabled(true); + } +} + +void QmitkHistogramVisualizationWidget::OnNBinsSpinBoxValueChanged() +{ + emit RequestHistogramUpdate(m_Controls.spinBoxNBins->value()); +} + +void QmitkHistogramVisualizationWidget::OnShowSubchartCheckBoxChanged() +{ + m_Controls.chartWidget->Show(m_Controls.checkBoxShowSubchart->isChecked()); +} + +void QmitkHistogramVisualizationWidget::OnPageSuccessfullyLoaded() +{ + m_Controls.chartWidget->SetTheme(m_ChartStyle); +} diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.h b/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.h new file mode 100644 index 0000000000..aac9fdf1c3 --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.h @@ -0,0 +1,75 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ +#ifndef QmitkHistogramVisualizationWidget_H__INCLUDED +#define QmitkHistogramVisualizationWidget_H__INCLUDED + +#include +#include + +//itk +#include + +/** +* \brief Widget for displaying Histograms. +*/ + +class MITKIMAGESTATISTICSUI_EXPORT QmitkHistogramVisualizationWidget : public QWidget +{ + Q_OBJECT + +public: + QmitkHistogramVisualizationWidget(QWidget* parent = nullptr); + /** \brief Draws the histogram and enables the GUI elements. */ + void SetHistogram(itk::Statistics::Histogram::ConstPointer histogram, const std::string& dataLabel); + /** \brief Clears the histogram and disables all GUI elements. */ + void Reset(); + /** \brief Sets the theme (either dark or light) */ + void SetTheme(QmitkChartWidget::ChartStyle style); + +signals: + /** \brief Signal to be emitted when the number of bins is changed by the user. The HistogramCalculator should connect to this signal and recalculate the data accordingly. */ + void RequestHistogramUpdate(unsigned int nBins); + +private: + + void CreateConnections(); + + void SetGUIElementsEnabled(bool enabled); + /** \brief Helper function to convert the histogram in order to forward it to the ChartWidget. */ + std::map ConvertHistogramToMap(itk::Statistics::Histogram::ConstPointer histogram) const; + +//slots + /** \brief Saves the histogram to the clipboard. */ + void OnClipboardButtonClicked(); + /** \brief Enables / Disables SpinBox to change the number of bins. */ + void OnDefaultNBinsCheckBoxChanged(); + /** \brief Emits the signal RequestHistogramUpdate(unsigned int nBins) with the updated value. */ + void OnNBinsSpinBoxValueChanged(); + /** \brief Shows / Hides the subchart. */ + void OnShowSubchartCheckBoxChanged(); + void OnPageSuccessfullyLoaded(); + +private: + Ui::QmitkHistogramVisualizationControls m_Controls; + const unsigned int m_DefaultNBins = 100; + const unsigned int m_MinNBins = 10; + const unsigned int m_MaxNBins = 10000; + + itk::Statistics::Histogram::ConstPointer m_Histogram; + QmitkChartWidget::ChartStyle m_ChartStyle = QmitkChartWidget::ChartStyle::darkstyle; +}; + +#endif //QmitkHistogramVisualizationWidget_H__INCLUDED \ No newline at end of file diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.ui b/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.ui new file mode 100644 index 0000000000..22c9133f14 --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.ui @@ -0,0 +1,193 @@ + + + QmitkHistogramVisualizationControls + + + + 0 + 0 + 540 + 394 + + + + Form + + + + + + false + + + + 0 + 0 + + + + + 0 + 0 + + + + + 16777215 + 16777215 + + + + Plot + + + + + + Show Subchart + + + true + + + + + + + Use default #bins + + + true + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + + + + 60 + 0 + + + + + 100 + 16777215 + + + + # bins: + + + + + + + false + + + Press enter to recalculate statistics with new bin size. + + + 1 + + + 10000 + + + 100 + + + + + + + + + + + + + + + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + + + + 0 + 0 + + + + Copy to Clipboard + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + + + + QmitkChartWidget + QWidget +
QmitkChartWidget.h
+ + + + + diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsCalculationThread.cpp b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.cpp similarity index 67% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsCalculationThread.cpp rename to Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.cpp index 536d6dcdbc..3cc5603737 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsCalculationThread.cpp +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.cpp @@ -1,242 +1,246 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ -#include "QmitkImageStatisticsCalculationThread.h" +#include "QmitkImageStatisticsCalculationJob.h" -//QT headers -#include -#include +#include "mitkImageStatisticsCalculator.h" #include #include #include -QmitkImageStatisticsCalculationThread::QmitkImageStatisticsCalculationThread() +QmitkImageStatisticsCalculationJob::QmitkImageStatisticsCalculationJob() : QThread() , m_StatisticsImage(nullptr) , m_BinaryMask(nullptr) , m_PlanarFigureMask(nullptr) , m_TimeStep(0) , m_IgnoreZeros(false) , m_HistogramNBins(100) , m_StatisticChanged(false) , m_CalculationSuccessful(false) { } -QmitkImageStatisticsCalculationThread::~QmitkImageStatisticsCalculationThread() +QmitkImageStatisticsCalculationJob::~QmitkImageStatisticsCalculationJob() { } -void QmitkImageStatisticsCalculationThread::Initialize( mitk::Image::Pointer image, mitk::Image::Pointer binaryImage, mitk::PlanarFigure::Pointer planarFig ) +void QmitkImageStatisticsCalculationJob::Initialize( mitk::Image::ConstPointer image, mitk::Image::ConstPointer binaryImage, mitk::PlanarFigure::ConstPointer planarFig ) { // reset old values if( this->m_StatisticsImage.IsNotNull() ) this->m_StatisticsImage = nullptr; - if( this->m_BinaryMask.IsNotNull() ) this->m_BinaryMask = nullptr; - if( this->m_PlanarFigureMask.IsNotNull()) this->m_PlanarFigureMask = nullptr; // set new values if passed in if(image.IsNotNull()) - this->m_StatisticsImage = image->Clone(); + this->m_StatisticsImage = image; if(binaryImage.IsNotNull()) - this->m_BinaryMask = binaryImage->Clone(); + this->m_BinaryMask = binaryImage; if(planarFig.IsNotNull()) - this->m_PlanarFigureMask = planarFig->Clone(); + this->m_PlanarFigureMask = planarFig; } -void QmitkImageStatisticsCalculationThread::SetTimeStep( int times ) +void QmitkImageStatisticsCalculationJob::SetTimeStep( int times ) { this->m_TimeStep = times; } -int QmitkImageStatisticsCalculationThread::GetTimeStep() +int QmitkImageStatisticsCalculationJob::GetTimeStep() const { return this->m_TimeStep; } -std::vector QmitkImageStatisticsCalculationThread::GetStatisticsData() +mitk::ImageStatisticsContainer::ConstPointer QmitkImageStatisticsCalculationJob::GetStatisticsData() const { - return this->m_StatisticsVector; + mitk::ImageStatisticsContainer::ConstPointer constContainer = this->m_StatisticsContainer.GetPointer(); + return constContainer; } -mitk::Image::Pointer QmitkImageStatisticsCalculationThread::GetStatisticsImage() +mitk::Image::ConstPointer QmitkImageStatisticsCalculationJob::GetStatisticsImage() const { return this->m_StatisticsImage; } -void QmitkImageStatisticsCalculationThread::SetIgnoreZeroValueVoxel(bool _arg) +mitk::Image::ConstPointer QmitkImageStatisticsCalculationJob::GetMaskImage() const +{ + return this->m_BinaryMask; +} + +mitk::PlanarFigure::ConstPointer QmitkImageStatisticsCalculationJob::GetPlanarFigure() const +{ + return this->m_PlanarFigureMask; +} + +void QmitkImageStatisticsCalculationJob::SetIgnoreZeroValueVoxel(bool _arg) { this->m_IgnoreZeros = _arg; } -bool QmitkImageStatisticsCalculationThread::GetIgnoreZeroValueVoxel() +bool QmitkImageStatisticsCalculationJob::GetIgnoreZeroValueVoxel() const { return this->m_IgnoreZeros; } -void QmitkImageStatisticsCalculationThread::SetHistogramNBins(unsigned int nbins) +void QmitkImageStatisticsCalculationJob::SetHistogramNBins(unsigned int nbins) { this->m_HistogramNBins = nbins; } -unsigned int QmitkImageStatisticsCalculationThread::GetHistogramNBins() const +unsigned int QmitkImageStatisticsCalculationJob::GetHistogramNBins() const { return this->m_HistogramNBins; } -std::string QmitkImageStatisticsCalculationThread::GetLastErrorMessage() +std::string QmitkImageStatisticsCalculationJob::GetLastErrorMessage() const { return m_message; } -QmitkImageStatisticsCalculationThread::HistogramType::Pointer -QmitkImageStatisticsCalculationThread::GetTimeStepHistogram(unsigned int t) +QmitkImageStatisticsCalculationJob::HistogramType::ConstPointer +QmitkImageStatisticsCalculationJob::GetTimeStepHistogram(unsigned int t) const { if (t >= this->m_HistogramVector.size()) return nullptr; return this->m_HistogramVector[t]; } -bool QmitkImageStatisticsCalculationThread::GetStatisticsChangedFlag() +bool QmitkImageStatisticsCalculationJob::GetStatisticsChangedFlag() const { return m_StatisticChanged; } -bool QmitkImageStatisticsCalculationThread::GetStatisticsUpdateSuccessFlag() +bool QmitkImageStatisticsCalculationJob::GetStatisticsUpdateSuccessFlag() const { return m_CalculationSuccessful; } -void QmitkImageStatisticsCalculationThread::run() +void QmitkImageStatisticsCalculationJob::run() { bool statisticCalculationSuccessful = true; mitk::ImageStatisticsCalculator::Pointer calculator = mitk::ImageStatisticsCalculator::New(); if(this->m_StatisticsImage.IsNotNull()) { calculator->SetInputImage(m_StatisticsImage); } else { statisticCalculationSuccessful = false; } // Bug 13416 : The ImageStatistics::SetImageMask() method can throw exceptions, i.e. when the dimensionality // of the masked and input image differ, we need to catch them and mark the calculation as failed // the same holds for the ::SetPlanarFigure() try { if(this->m_BinaryMask.IsNotNull()) { mitk::ImageMaskGenerator::Pointer imgMask = mitk::ImageMaskGenerator::New(); - imgMask->SetImageMask(m_BinaryMask); + imgMask->SetImageMask(m_BinaryMask->Clone()); calculator->SetMask(imgMask.GetPointer()); } if(this->m_PlanarFigureMask.IsNotNull()) { mitk::PlanarFigureMaskGenerator::Pointer pfMaskGen = mitk::PlanarFigureMaskGenerator::New(); pfMaskGen->SetInputImage(m_StatisticsImage); - pfMaskGen->SetPlanarFigure(m_PlanarFigureMask); + pfMaskGen->SetPlanarFigure(m_PlanarFigureMask->Clone()); calculator->SetMask(pfMaskGen.GetPointer()); } } catch (const mitk::Exception& e) { MITK_ERROR << "MITK Exception: " << e.what(); m_message = e.what(); statisticCalculationSuccessful = false; } catch( const itk::ExceptionObject& e) { MITK_ERROR << "ITK Exception:" << e.what(); m_message = e.what(); statisticCalculationSuccessful = false; } catch ( const std::runtime_error &e ) { MITK_ERROR<< "Runtime Exception: " << e.what(); m_message = e.what(); statisticCalculationSuccessful = false; } catch ( const std::exception &e ) { MITK_ERROR<< "Standard Exception: " << e.what(); m_message = e.what(); statisticCalculationSuccessful = false; } bool statisticChanged = false; if (this->m_IgnoreZeros) { mitk::IgnorePixelMaskGenerator::Pointer ignorePixelValueMaskGen = mitk::IgnorePixelMaskGenerator::New(); ignorePixelValueMaskGen->SetIgnoredPixelValue(0); ignorePixelValueMaskGen->SetInputImage(m_StatisticsImage); calculator->SetSecondaryMask(ignorePixelValueMaskGen.GetPointer()); } else { calculator->SetSecondaryMask(nullptr); } calculator->SetNBinsForHistogramStatistics(m_HistogramNBins); - for (unsigned int i = 0; i < m_StatisticsImage->GetTimeSteps(); i++) - { try { - calculator->GetStatistics(i); + calculator->GetStatistics(); } catch ( mitk::Exception& e) { m_message = e.GetDescription(); MITK_ERROR<< "MITK Exception: " << e.what(); statisticCalculationSuccessful = false; } catch ( const std::runtime_error &e ) { m_message = "Failure: " + std::string(e.what()); MITK_ERROR<< "Runtime Exception: " << e.what(); statisticCalculationSuccessful = false; } catch ( const std::exception &e ) { m_message = "Failure: " + std::string(e.what()); MITK_ERROR<< "Standard Exception: " << e.what(); statisticCalculationSuccessful = false; } - } this->m_StatisticChanged = statisticChanged; this->m_CalculationSuccessful = statisticCalculationSuccessful; if(statisticCalculationSuccessful) { - this->m_StatisticsVector.clear(); + m_StatisticsContainer = calculator->GetStatistics(); this->m_HistogramVector.clear(); for (unsigned int i = 0; i < m_StatisticsImage->GetTimeSteps(); i++) { - this->m_StatisticsVector.push_back(calculator->GetStatistics(i)); - this->m_HistogramVector.push_back((HistogramType*)this->m_StatisticsVector[i]->GetHistogram()); + this->m_HistogramVector.push_back(calculator->GetStatistics()->GetStatisticsForTimeStep(i).m_Histogram); } + } } diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsCalculationThread.h b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.h similarity index 63% rename from Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsCalculationThread.h rename to Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.h index 0f547ce224..66769171b1 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsCalculationThread.h +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.h @@ -1,112 +1,116 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QMITKIMAGESTATISTICSCALCULATIONTHREAD_H_INCLUDED #define QMITKIMAGESTATISTICSCALCULATIONTHREAD_H_INCLUDED //QT headers #include -#include + //mitk headers #include "mitkImage.h" #include "mitkPlanarFigure.h" -#include "mitkImageStatisticsCalculator.h" +#include "mitkImageStatisticsContainer.h" +#include // itk headers #ifndef __itkHistogram_h #include #endif /** /brief This class is executed as background thread for image statistics calculation. * Documentation: This class is derived from QThread and is intended to be used by QmitkImageStatisticsView to run the image statistics calculation in a background thread keepung the gui usable. - * \ingroup Plugins/MeasurementToolbox */ -class QmitkImageStatisticsCalculationThread : public QThread +class MITKIMAGESTATISTICSUI_EXPORT QmitkImageStatisticsCalculationJob : public QThread { Q_OBJECT public: typedef itk::Statistics::Histogram HistogramType; /*! /brief standard constructor. */ - QmitkImageStatisticsCalculationThread(); + QmitkImageStatisticsCalculationJob(); /*! /brief standard destructor. */ - ~QmitkImageStatisticsCalculationThread(); + ~QmitkImageStatisticsCalculationJob(); /*! /brief Initializes the object with necessary data. */ - void Initialize( mitk::Image::Pointer image, mitk::Image::Pointer binaryImage, mitk::PlanarFigure::Pointer planarFig ); + void Initialize( mitk::Image::ConstPointer image, mitk::Image::ConstPointer binaryImage, mitk::PlanarFigure::ConstPointer planarFig ); /*! /brief returns the calculated image statistics. */ - std::vector GetStatisticsData(); - /*! - /brief */ - mitk::Image::Pointer GetStatisticsImage(); + mitk::ImageStatisticsContainer::ConstPointer GetStatisticsData() const; + + mitk::Image::ConstPointer GetStatisticsImage() const; + mitk::Image::ConstPointer GetMaskImage() const; + mitk::PlanarFigure::ConstPointer GetPlanarFigure() const; + + //T25568: can be removed when deprecated image statistics plugin is removed /*! /brief Set the time step of the image you want to process. */ void SetTimeStep( int times ); /*! /brief Get the time step of the image you want to process. */ - int GetTimeStep(); + int GetTimeStep() const; /*! /brief Set flag to ignore zero valued voxels */ void SetIgnoreZeroValueVoxel( bool _arg ); /*! /brief Get status of zero value voxel ignoring. */ - bool GetIgnoreZeroValueVoxel(); + bool GetIgnoreZeroValueVoxel() const; /*! /brief Set bin size for histogram resolution.*/ void SetHistogramNBins( unsigned int nbins); /*! /brief Get bin size for histogram resolution.*/ unsigned int GetHistogramNBins() const; /*! /brief Returns the histogram of the currently selected time step. */ - HistogramType::Pointer GetTimeStepHistogram(unsigned int t = 0); + HistogramType::ConstPointer GetTimeStepHistogram(unsigned int t = 0) const; /*! /brief Returns a flag indicating if the statistics have changed during calculation */ - bool GetStatisticsChangedFlag(); + bool GetStatisticsChangedFlag() const; /*! /brief Returns a flag the indicates if the statistics are updated successfully */ - bool GetStatisticsUpdateSuccessFlag(); + bool GetStatisticsUpdateSuccessFlag() const; /*! /brief Method called once the thread is executed. */ void run() override; - std::string GetLastErrorMessage(); + std::string GetLastErrorMessage() const; private: //member declaration - mitk::Image::Pointer m_StatisticsImage; ///< member variable holds the input image for which the statistics need to be calculated. - mitk::Image::Pointer m_BinaryMask; ///< member variable holds the binary mask image for segmentation image statistics calculation. - mitk::PlanarFigure::Pointer m_PlanarFigureMask; ///< member variable holds the planar figure for segmentation image statistics calculation. - std::vector m_StatisticsVector; ///< member variable holds the result structs. + mitk::Image::ConstPointer m_StatisticsImage; ///< member variable holds the input image for which the statistics need to be calculated. + mitk::Image::ConstPointer m_BinaryMask; ///< member variable holds the binary mask image for segmentation image statistics calculation. + mitk::PlanarFigure::ConstPointer m_PlanarFigureMask; ///< member variable holds the planar figure for segmentation image statistics calculation. + mitk::ImageStatisticsContainer::Pointer m_StatisticsContainer; + //T25568: can be removed when deprecated image statistics plugin is removed int m_TimeStep; ///< member variable holds the time step for statistics calculation bool m_IgnoreZeros; ///< member variable holds flag to indicate if zero valued voxel should be suppressed unsigned int m_HistogramNBins; ///< member variable holds the bin size for histogram resolution. bool m_StatisticChanged; ///< flag set if statistics have changed bool m_CalculationSuccessful; ///< flag set if statistics calculation was successful - std::vector m_HistogramVector; ///< member holds the histograms of all time steps. + std::vector m_HistogramVector; ///< member holds the histograms of all time steps. std::string m_message; }; #endif // QMITKIMAGESTATISTICSCALCULATIONTHREAD_H_INCLUDED diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsTableModel.cpp b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsTableModel.cpp new file mode 100644 index 0000000000..641b9f87c4 --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsTableModel.cpp @@ -0,0 +1,323 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include "QmitkImageStatisticsTableModel.h" +#include "mitkProportionalTimeGeometry.h" +#include "mitkStatisticsToImageRelationRule.h" +#include "mitkImageStatisticsContainerManager.h" +#include "itkMutexLockHolder.h" +#include "itkSimpleFastMutexLock.h" + + +QmitkImageStatisticsTableModel::QmitkImageStatisticsTableModel(QObject *parent) : + QmitkAbstractDataStorageModel(parent) +{} + +QmitkImageStatisticsTableModel +::~QmitkImageStatisticsTableModel() +{ + // set data storage to nullptr so that the event listener gets removed + this->SetDataStorage(nullptr); +}; + +void QmitkImageStatisticsTableModel::DataStorageChanged() +{ + emit beginResetModel(); + UpdateByDataStorage(); + emit endResetModel(); +} + +void QmitkImageStatisticsTableModel::NodePredicateChanged() +{ + emit beginResetModel(); + UpdateByDataStorage(); + emit endResetModel(); +} + + +int QmitkImageStatisticsTableModel::rowCount(const QModelIndex &parent) const +{ + if (parent.isValid()) + { + return 0; + } + return m_StatisticNames.size(); +} + +int QmitkImageStatisticsTableModel::columnCount(const QModelIndex &parent) const +{ + if (parent.isValid()) + return 0; + + if (m_ViewMode == ViewMode::imageXStatistic) + { + return static_cast(m_TimeStepResolvedImageNodes.size()); + } + else + { + mitkThrow() << "View mode ImageXMask is not implemented yet"; + } +} + +std::pair QmitkImageStatisticsTableModel::GetRelevantStatsticsByIndex(const QModelIndex &index) const +{ + auto result = std::make_pair(nullptr, 0); + + if (m_ViewMode == ViewMode::imageXStatistic) + { + if (index.column() < static_cast(m_TimeStepResolvedImageNodes.size())) + { + auto selectedImage = m_TimeStepResolvedImageNodes.at(static_cast(index.column())); + + //get the right statistic + auto rule = mitk::StatisticsToImageRelationRule::New(); + for (mitk::ImageStatisticsContainer::ConstPointer container : m_Statistics) + { + if (rule->HasRelation(container, selectedImage.first->GetData()) >= mitk::PropertyRelationRuleBase::RelationType::Connected_Data) + { + return std::make_pair(container, selectedImage.second); + } + } + } + } + else + { + mitkThrow() << "View mode ImageXMask is not implemented yet"; + } + + return result; +} + +QVariant QmitkImageStatisticsTableModel::data(const QModelIndex &index, int role) const +{ + if (!index.isValid()) + return QVariant(); + + QVariant result; + if (m_ViewMode == ViewMode::imageXStatistic) { + + auto containerInfo = GetRelevantStatsticsByIndex(index); + + if (containerInfo.first.IsNotNull() && index.row() < rowCount(QModelIndex())) + { + if (Qt::DisplayRole == role) + { + auto statsObj = containerInfo.first->GetStatisticsForTimeStep(containerInfo.second); + auto statisticKey = m_StatisticNames.at(index.row()); + std::stringstream ss; + if (statsObj.HasStatistic(statisticKey)) + { + ss << statsObj.GetValueNonConverted(statisticKey); + } + else + { + ss << "N/A"; + } + result = QVariant(QString::fromStdString(ss.str())); + } + else if (Qt::UserRole == role) + { + result = QVariant(index.row()); + } + + } + } + + return result; +} + +QModelIndex QmitkImageStatisticsTableModel::index(int row, int column, const QModelIndex &parent) const +{ + bool hasIndex = this->hasIndex(row, column, parent); + if (hasIndex) + { + return this->createIndex(row, column); + } + + return QModelIndex(); +} + +QModelIndex QmitkImageStatisticsTableModel::parent(const QModelIndex &/*child*/) const +{ + return QModelIndex(); +} + + +Qt::ItemFlags QmitkImageStatisticsTableModel::flags(const QModelIndex &index) const +{ + Qt::ItemFlags flags = QAbstractItemModel::flags(index); + + return flags; +} + +QVariant QmitkImageStatisticsTableModel::headerData(int section, Qt::Orientation orientation, int role) const +{ + if ((Qt::DisplayRole == role) && (Qt::Horizontal == orientation)) + { + if (!m_TimeStepResolvedImageNodes.empty()) { + if (m_ViewMode == ViewMode::imageXStatistic) { + std::stringstream ss; + auto imageInfo = m_TimeStepResolvedImageNodes.at(section); + ss << imageInfo.first->GetName(); + if (imageInfo.first->GetData() && imageInfo.first->GetData()->GetTimeSteps() > 1) + { + ss << " #" << imageInfo.second; + } + if (!m_MaskNodes.empty() && m_MaskNodes.size() == m_ImageNodes.size()) { + auto maskInfo = m_TimeStepResolvedMaskNodes.at(section); + ss << " / " << maskInfo.first->GetName(); + } + return QVariant(ss.str().c_str()); + } + } + } + else if ((Qt::DisplayRole == role) && (Qt::Vertical == orientation)) { + if (m_ViewMode == ViewMode::imageXStatistic) { + return QVariant(m_StatisticNames.at(section).c_str()); + } + } + return QVariant(); +} + +void QmitkImageStatisticsTableModel::SetImageNodes(const std::vector& nodes) +{ + std::vector > tempNodes; + for (const auto& node: nodes) + { + auto data = node->GetData(); + if (data) + { + auto timeSteps = data->GetTimeSteps(); + for (unsigned int i = 0; i < timeSteps; i++) + { + tempNodes.push_back(std::make_pair(node, i)); + } + } + } + + emit beginResetModel(); + m_TimeStepResolvedImageNodes = std::move(tempNodes); + m_ImageNodes = nodes; + UpdateByDataStorage(); + emit endResetModel(); +} + +void QmitkImageStatisticsTableModel::SetMaskNodes(const std::vector& nodes) +{ + std::vector> tempNodes; + for (const auto &node : nodes) + { + auto data = node->GetData(); + if (data) + { + auto timeSteps = data->GetTimeSteps(); + //special case: apply one mask to each timestep of an 4D image + if (timeSteps == 1 && m_TimeStepResolvedImageNodes.size() > 1) + { + timeSteps = m_TimeStepResolvedImageNodes.size(); + } + for (unsigned int i = 0; i < timeSteps; i++) + { + tempNodes.push_back(std::make_pair(node, i)); + } + } + } + + emit beginResetModel(); + m_TimeStepResolvedMaskNodes = std::move(tempNodes); + m_MaskNodes = nodes; + UpdateByDataStorage(); + emit endResetModel(); +} + +void QmitkImageStatisticsTableModel::SetViewMode(ViewMode m) +{ + emit beginResetModel(); + m_ViewMode = m; + emit endResetModel(); +} + +void QmitkImageStatisticsTableModel::Clear() +{ + emit beginResetModel(); + m_Statistics.clear(); + m_ImageNodes.clear(); + m_TimeStepResolvedImageNodes.clear(); + m_MaskNodes.clear(); + m_StatisticNames.clear(); + emit endResetModel(); +} + +void QmitkImageStatisticsTableModel::UpdateByDataStorage() +{ + StatisticsContainerVector newStatistics; + + auto datamanager = m_DataStorage.Lock(); + + if (datamanager.IsNotNull()) + { + for (const auto& image : m_ImageNodes) + { + if (m_MaskNodes.empty()) + { + auto stats = mitk::ImageStatisticsContainerManager::GetImageStatistics(datamanager, image->GetData()); + if (stats.IsNotNull()) + { + newStatistics.emplace_back(stats); + } + } + else + { + for (const auto& mask : m_MaskNodes) + { + auto stats = mitk::ImageStatisticsContainerManager::GetImageStatistics(datamanager, image->GetData(), mask->GetData()); + if (stats.IsNotNull()) + { + newStatistics.emplace_back(stats); + } + } + } + } + } + + { + itk::MutexLockHolder locked(m_Mutex); + m_Statistics = newStatistics; + } + + m_StatisticNames = mitk::GetAllStatisticNames(m_Statistics); +} + +void QmitkImageStatisticsTableModel::NodeRemoved(const mitk::DataNode *) +{ + emit beginResetModel(); + UpdateByDataStorage(); + emit endResetModel(); +} + +void QmitkImageStatisticsTableModel::NodeAdded(const mitk::DataNode *) +{ + emit beginResetModel(); + UpdateByDataStorage(); + emit endResetModel(); +} + +void QmitkImageStatisticsTableModel::NodeChanged(const mitk::DataNode *) +{ + emit beginResetModel(); + UpdateByDataStorage(); + emit endResetModel(); +} diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsTableModel.h b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsTableModel.h new file mode 100644 index 0000000000..cd35e5798b --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsTableModel.h @@ -0,0 +1,112 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + + +#ifndef QmitkImageStatisticsTableModel_h +#define QmitkImageStatisticsTableModel_h + +#include "itkSimpleFastMutexLock.h" + +#include "QmitkAbstractDataStorageModel.h" + +//MITK +#include +#include "mitkImageStatisticsContainer.h" +#include "mitkDataNode.h" +#include "mitkDataStorage.h" + +/*! +\class QmitkImageStatisticsTableModel +Model that takes a mitk::ImageStatisticsContainer and represents it as model in context of the QT view-model-concept. +*/ +class MITKIMAGESTATISTICSUI_EXPORT QmitkImageStatisticsTableModel : public QmitkAbstractDataStorageModel +{ + Q_OBJECT + +public: + enum class ViewMode { + imageXStatistic, + imageXMask + }; + + QmitkImageStatisticsTableModel(QObject *parent = nullptr); + virtual ~QmitkImageStatisticsTableModel(); + + void SetImageNodes(const std::vector& nodes); + void SetMaskNodes(const std::vector& nodes); + void SetViewMode(ViewMode m); + void Clear(); + + virtual Qt::ItemFlags flags(const QModelIndex &index) const override; + virtual QVariant data(const QModelIndex &index, int role) const override; + virtual QVariant headerData(int section, Qt::Orientation orientation, int role) const override; + virtual int rowCount(const QModelIndex &parent = QModelIndex()) const override; + virtual int columnCount(const QModelIndex &parent = QModelIndex()) const override; + + QModelIndex index(int row, int column, const QModelIndex &parent = QModelIndex()) const override; + QModelIndex parent(const QModelIndex &child) const override; + +protected: + /* + * @brief See 'QmitkAbstractDataStorageModel' + */ + void DataStorageChanged() override; + /* + * @brief See 'QmitkAbstractDataStorageModel' + */ + void NodePredicateChanged() override; + /* + * @brief See 'QmitkAbstractDataStorageModel' + */ + void NodeAdded(const mitk::DataNode *node) override; + /* + * @brief See 'QmitkAbstractDataStorageModel' + */ + void NodeChanged(const mitk::DataNode *node) override; + /* + * @brief See 'QmitkAbstractDataStorageModel' + */ + void NodeRemoved(const mitk::DataNode *node) override; + +private: + void UpdateByDataStorage(); + + using StatisticsContainerVector = std::vector; + /* the function returns the statistic container and the time point indicated by the index. + If the index is not valid result.first will point to a nullptr.*/ + std::pair GetRelevantStatsticsByIndex(const QModelIndex &index) const; + + StatisticsContainerVector m_Statistics; + + /** Relevant images set by the user.*/ + std::vector m_ImageNodes; + /** Helper that is constructed when m_ImageNodes is set. It has the same order + like m_ImageNodes, but each image is represented n times, while n is the number + of time steps the respective image has. This structure makes the business logic + to select the correct image given a QIndex much simpler and therfore easy to + understand/maintaine. */ + std::vector > m_TimeStepResolvedImageNodes; + /** relevant masks set by the user.*/ + std::vector m_MaskNodes; + /** @sa m_TimeStepResolvedImageNodes */ + std::vector> m_TimeStepResolvedMaskNodes; + std::vector m_StatisticNames; + ViewMode m_ViewMode = ViewMode::imageXStatistic; + + itk::SimpleFastMutexLock m_Mutex; +}; + +#endif // mitkQmitkImageStatisticsTableModel_h diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsWidget.cpp b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsWidget.cpp new file mode 100644 index 0000000000..be83f69c06 --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsWidget.cpp @@ -0,0 +1,72 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include "QmitkImageStatisticsWidget.h" + +#include "QmitkTableModelToStringConverter.h" + +#include +#include + +QmitkImageStatisticsWidget::QmitkImageStatisticsWidget(QWidget* parent) : QWidget(parent) +{ + m_Controls.setupUi(this); + m_imageStatisticsModel = new QmitkImageStatisticsTableModel(parent); + //temporarily disabled because 4D clipboard functionality is not implemented yet + m_Controls.checkBox4dCompleteTable->setVisible(false); + CreateConnections(); + m_ProxyModel = new QSortFilterProxyModel(this); + m_Controls.tableViewStatistics->setModel(m_ProxyModel); + m_ProxyModel->setSourceModel(m_imageStatisticsModel); +} + +void QmitkImageStatisticsWidget::SetDataStorage(mitk::DataStorage* newDataStorage) +{ + m_imageStatisticsModel->SetDataStorage(newDataStorage); + m_Controls.tableViewStatistics->resizeColumnsToContents(); // should call data in table model + m_Controls.tableViewStatistics->resizeRowsToContents(); +} + +void QmitkImageStatisticsWidget::SetImageNodes(const std::vector& nodes) +{ + m_imageStatisticsModel->SetImageNodes(nodes); +} + +void QmitkImageStatisticsWidget::SetMaskNodes(const std::vector& nodes) +{ + m_imageStatisticsModel->SetMaskNodes(nodes); +} + +void QmitkImageStatisticsWidget::Reset() +{ + m_imageStatisticsModel->Clear(); +} + +void QmitkImageStatisticsWidget::CreateConnections() +{ + connect(m_Controls.buttonCopyImageStatisticsToClipboard, &QPushButton::clicked, this, &QmitkImageStatisticsWidget::OnClipboardButtonClicked); +} + +void QmitkImageStatisticsWidget::OnClipboardButtonClicked() +{ + QmitkTableModelToStringConverter converter; + converter.SetTableModel(m_imageStatisticsModel); + converter.SetIncludeHeaderData(true); + converter.SetColumnDelimiter('\t'); + + QString clipboardAsString = converter.GetString(); + QApplication::clipboard()->setText(clipboardAsString, QClipboard::Clipboard); +} diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsWidget.h b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsWidget.h new file mode 100644 index 0000000000..bdd716c09b --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsWidget.h @@ -0,0 +1,58 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ +#ifndef QmitkImageStatisticsWidget_H__INCLUDED +#define QmitkImageStatisticsWidget_H__INCLUDED + +#include + +#include +#include +#include + +class QSortFilterProxyModel; + +//Qt +#include + +class MITKIMAGESTATISTICSUI_EXPORT QmitkImageStatisticsWidget : public QWidget +{ + Q_OBJECT + +public: + QmitkImageStatisticsWidget(QWidget* parent = nullptr); + + /**Documentation + Set the data storage the model should fetch its statistic objects from. + @pre data storage must be valid + */ + void SetDataStorage(mitk::DataStorage* newDataStorage); + + void SetImageNodes(const std::vector& nodes); + void SetMaskNodes(const std::vector& nodes); + void Reset(); + +private: + void CreateConnections(); + + /** \brief Saves the image statistics to the clipboard */ + void OnClipboardButtonClicked(); + +private: + Ui::QmitkImageStatisticsControls m_Controls; + QmitkImageStatisticsTableModel* m_imageStatisticsModel; + QSortFilterProxyModel* m_ProxyModel; +}; +#endif // QmitkImageStatisticsWidget_H__INCLUDED diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsWidget.ui b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsWidget.ui new file mode 100644 index 0000000000..2db3a52e73 --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsWidget.ui @@ -0,0 +1,140 @@ + + + QmitkImageStatisticsControls + + + + 0 + 0 + 395 + 366 + + + + + 0 + 0 + + + + Form + + + + 2 + + + 2 + + + 2 + + + 2 + + + + + + 0 + 0 + + + + + 0 + 150 + + + + QAbstractItemView::NoEditTriggers + + + true + + + false + + + + + + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + + + false + + + + 0 + 0 + + + + Copy to Clipboard + + + + + + + Qt::Horizontal + + + QSizePolicy::Fixed + + + + 20 + 20 + + + + + + + + false + + + copy complete table + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + + + + diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.cpp b/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.cpp new file mode 100644 index 0000000000..9905339eef --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.cpp @@ -0,0 +1,135 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include "QmitkIntensityProfileVisualizationWidget.h" + +#include + +QmitkIntensityProfileVisualizationWidget::QmitkIntensityProfileVisualizationWidget(QWidget* parent) : QWidget(parent) +{ + m_Controls.setupUi(this); + #if QT_VERSION < QT_VERSION_CHECK(5, 10, 0) + WarnQtVersionTooLow(); + #else + m_Controls.labelIntensityProfileIsInvisibleWarning->setVisible(false); + m_Controls.checkBoxShowSubchart->setChecked(false); + #endif + CreateConnections(); +} + + + +void QmitkIntensityProfileVisualizationWidget::SetIntensityProfile(mitk::IntensityProfile::ConstPointer intensityProfile, const std::string& dataLabel) +{ + if (intensityProfile == nullptr) + return; + + m_IntensityProfileList = mitk::CreateVectorFromIntensityProfile(intensityProfile); + if (m_IntensityProfileList.empty()) + return; + + m_Controls.chartWidget->AddData1D(m_IntensityProfileList, dataLabel); + m_Controls.chartWidget->SetChartType(dataLabel, QmitkChartWidget::ChartType::line); + m_Controls.chartWidget->SetXAxisLabel("Distance"); + m_Controls.chartWidget->SetYAxisLabel("Intensity"); + #if QT_VERSION >= QT_VERSION_CHECK(5, 10, 0) + m_Controls.chartWidget->Show(m_Controls.checkBoxShowSubchart->isChecked()); + #endif + SetGUIElementsEnabled(true); +} + +void QmitkIntensityProfileVisualizationWidget::Reset() +{ + #if QT_VERSION >= QT_VERSION_CHECK(5, 10, 0) + m_Controls.chartWidget->Clear(); + #endif + SetGUIElementsEnabled(false); + m_IntensityProfileList.clear(); +} + +void QmitkIntensityProfileVisualizationWidget::SetTheme(QmitkChartWidget::ChartStyle style) +{ + m_ChartStyle = style; +} + +void QmitkIntensityProfileVisualizationWidget::CreateConnections() +{ + connect(m_Controls.checkBoxShowSubchart, &QCheckBox::clicked, this, &QmitkIntensityProfileVisualizationWidget::OnShowSubchartCheckBoxChanged); + connect(m_Controls.buttonCopyToClipboard, &QPushButton::clicked, this, &QmitkIntensityProfileVisualizationWidget::OnClipboardButtonClicked); + connect(m_Controls.chartWidget, &QmitkChartWidget::PageSuccessfullyLoaded, this, &QmitkIntensityProfileVisualizationWidget::OnPageSuccessfullyLoaded); +} + +void QmitkIntensityProfileVisualizationWidget::SetGUIElementsEnabled(bool enabled) +{ + this->setEnabled(enabled); + m_Controls.groupBoxIntensityProfile->setEnabled(enabled); + m_Controls.groupBoxPlot->setEnabled(enabled); + m_Controls.buttonCopyToClipboard->setEnabled(enabled); + m_Controls.checkBoxShowSubchart->setEnabled(enabled); + m_Controls.chartWidget->setEnabled(enabled); + m_Controls.labelIntensityProfileIsInvisibleWarning->setEnabled(enabled); + m_Controls.labelInfo->setEnabled(enabled); +} + +std::vector QmitkIntensityProfileVisualizationWidget::ConvertIntensityProfileToVector(mitk::IntensityProfile::ConstPointer intensityProfile) const +{ + std::vector intensityProfileList; + if (intensityProfile != nullptr) + { + auto end = intensityProfile->End(); + + for (auto it = intensityProfile->Begin(); it != end; ++it) + { + intensityProfileList.push_back(it.GetMeasurementVector()[0]); + } + } + return intensityProfileList; +} + +void QmitkIntensityProfileVisualizationWidget::OnClipboardButtonClicked() +{ + if (m_IntensityProfileList.empty()) + return; + + QApplication::clipboard()->clear(); + + QString clipboard("Pixel \t Intensity\n"); + for (unsigned int i = 0; i < m_IntensityProfileList.size(); i++) + { + clipboard = clipboard.append("%L1 \t %L2\n") + .arg(QString::number(i)) + .arg(QString::number(m_IntensityProfileList.at(i))); + } + QApplication::clipboard()->setText(clipboard, QClipboard::Clipboard); +} + +void QmitkIntensityProfileVisualizationWidget::OnShowSubchartCheckBoxChanged() +{ + m_Controls.chartWidget->Show(m_Controls.checkBoxShowSubchart->isChecked()); +} + +void QmitkIntensityProfileVisualizationWidget::OnPageSuccessfullyLoaded() +{ + m_Controls.chartWidget->SetTheme(m_ChartStyle); +} + +void QmitkIntensityProfileVisualizationWidget::WarnQtVersionTooLow() +{ + m_Controls.labelIntensityProfileIsInvisibleWarning->setVisible(true); + m_Controls.labelIntensityProfileIsInvisibleWarning->setText("Intensity profile is not visible because Qt 5.10 is required for MitkChart. You can use the button Copy to Clipboard below to retrieve values.< / font>"); + m_Controls.groupBoxPlot->setVisible(false); + m_Controls.chartWidget->setVisible(false); +} diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.h b/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.h new file mode 100644 index 0000000000..22687716e9 --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.h @@ -0,0 +1,69 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ +#ifndef QmitkIntensityProfileVisualizationWidget_H__INCLUDED +#define QmitkIntensityProfileVisualizationWidget_H__INCLUDED + +//Qt +#include + +#include +#include + +//mitk +#include + +/** +* \brief Widget for displaying intensity profiles. +*/ + +class MITKIMAGESTATISTICSUI_EXPORT QmitkIntensityProfileVisualizationWidget : public QWidget +{ + Q_OBJECT + +public: + QmitkIntensityProfileVisualizationWidget(QWidget* parent = nullptr); + + void SetIntensityProfile(mitk::IntensityProfile::ConstPointer intensityProfile, const std::string& dataLabel); + /** \brief Clears the intensity profile and disables all GUI elements. */ + void Reset(); + + void SetTheme(QmitkChartWidget::ChartStyle style); + +private: + + void CreateConnections(); + + void SetGUIElementsEnabled(bool enabled); + + std::vector ConvertIntensityProfileToVector(mitk::IntensityProfile::ConstPointer intensityProfile) const; + + /** \brief Saves the intensity profile to the clipboard. */ + void OnClipboardButtonClicked(); + /** \brief Shows / Hides the subchart. */ + void OnShowSubchartCheckBoxChanged(); + + void OnPageSuccessfullyLoaded(); + +private: + void WarnQtVersionTooLow(); + + Ui::QmitkIntensityProfileControls m_Controls; + QmitkChartWidget::ChartStyle m_ChartStyle = QmitkChartWidget::ChartStyle::darkstyle; + + std::vector m_IntensityProfileList; +}; + +#endif //QmitkIntensityProfileVisualizationWidget_H__INCLUDED \ No newline at end of file diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.ui b/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.ui new file mode 100644 index 0000000000..d49f3477a8 --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.ui @@ -0,0 +1,241 @@ + + + QmitkIntensityProfileControls + + + + 0 + 0 + 540 + 468 + + + + Form + + + + + + false + + + + + + false + + + + + + false + + + + + + + + 255 + 0 + 0 + + + + + + + 255 + 0 + 0 + + + + + + + 255 + 0 + 0 + + + + + + + + + 255 + 0 + 0 + + + + + + + 255 + 0 + 0 + + + + + + + 255 + 0 + 0 + + + + + + + + + 120 + 120 + 120 + + + + + + + 120 + 120 + 120 + + + + + + + 120 + 120 + 120 + + + + + + + + + + + + + + + false + + + + 0 + 0 + + + + + 0 + 0 + + + + + 16777215 + 16777215 + + + + Plot + + + + + + Show Subchart + + + true + + + + + + + + + + + + + + + + + + + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + + + + 0 + 0 + + + + Copy to Clipboard + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + + + + + + + QmitkChartWidget + QWidget +
QmitkChartWidget.h
+ + + + + diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkTableModelToStringConverter.cpp b/Modules/ImageStatisticsUI/Qmitk/QmitkTableModelToStringConverter.cpp new file mode 100644 index 0000000000..9d7a9a7dff --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkTableModelToStringConverter.cpp @@ -0,0 +1,127 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include "QmitkTableModelToStringConverter.h" + +#include + +QmitkTableModelToStringConverter::QmitkTableModelToStringConverter() +{ +} + +void QmitkTableModelToStringConverter::SetTableModel(QAbstractItemModel* model) +{ + m_tableModel = model; +} + +QString QmitkTableModelToStringConverter::GetString() const +{ + if (m_tableModel == nullptr) { + mitkThrow() << "Cannot convert TableModel to String: TableModel is nullptr"; + } + + if (m_transposeOutput) { + return GetStringTransposed(); + } + else { + return GetStringNonTransposed(); + } +} + +void QmitkTableModelToStringConverter::SetTransposeOutput(bool transposeOutput) +{ + m_transposeOutput = transposeOutput; +} + +void QmitkTableModelToStringConverter::SetLineDelimiter(QChar lineDelimiter) +{ + m_lineDelimiter = lineDelimiter; +} + +void QmitkTableModelToStringConverter::SetColumnDelimiter(QChar columnDelimiter) +{ + m_columnDelimiterWithSpace = columnDelimiter + QString(" "); +} + +void QmitkTableModelToStringConverter::SetIncludeHeaderData(bool includeHeaderData) +{ + m_includeHeaderData = includeHeaderData; +} + +QString QmitkTableModelToStringConverter::GetStringTransposed() const +{ + QString textData; + int rows = m_tableModel->rowCount(); + int columns = m_tableModel->columnCount(); + + if (m_includeHeaderData) { + textData += " "; + for (int i = 0; i < rows; i++) { + textData += m_columnDelimiterWithSpace; + textData += m_tableModel->headerData(i, Qt::Vertical).toString(); + } + textData += m_lineDelimiter; + } + + for (int i = 0; i < columns; i++) { + if (i > 0) { + textData += m_lineDelimiter; + } + if (m_includeHeaderData) { + textData += m_tableModel->headerData(i, Qt::Horizontal).toString() + m_columnDelimiterWithSpace; + } + for (int j = 0; j < rows; j++) { + if (j > 0) { + textData += m_columnDelimiterWithSpace; + } + textData += m_tableModel->data(m_tableModel->index(j, i)).toString(); + MITK_WARN << i << " " << j; + } + } + return textData; +} + +QString QmitkTableModelToStringConverter::GetStringNonTransposed() const +{ + QString textData; + int rows = m_tableModel->rowCount(); + int columns = m_tableModel->columnCount(); + + if (m_includeHeaderData) { + textData += " "; + for (int i = 0; i < columns; i++) { + textData += m_columnDelimiterWithSpace; + textData += m_tableModel->headerData(i, Qt::Horizontal).toString(); + } + textData += m_lineDelimiter; + } + + for (int i = 0; i < rows; i++) { + if (i > 0) { + textData += m_lineDelimiter; + } + if (m_includeHeaderData) { + textData += m_tableModel->headerData(i, Qt::Vertical).toString() + m_columnDelimiterWithSpace; + } + for (int j = 0; j < columns; j++) { + if (j > 0) { + textData += m_columnDelimiterWithSpace; + } + textData += m_tableModel->data(m_tableModel->index(i, j)).toString(); + } + } + return textData; +} diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkTableModelToStringConverter.h b/Modules/ImageStatisticsUI/Qmitk/QmitkTableModelToStringConverter.h new file mode 100644 index 0000000000..69be6b605b --- /dev/null +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkTableModelToStringConverter.h @@ -0,0 +1,67 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ +#ifndef QmitkTableModelToQString_H__INCLUDED +#define QmitkTableModelToQString_H__INCLUDED + +#include +#include + +/** +\brief Converts the content of a table model to a string + +\details +The content of a table model is converted (as-is or transposed) to a string. Each cell of the table +is converted to a string. Default oder: iteration over rows. The line separation delimiter (default: +'\n' and the column separation delimiter (default: ',') can be chosen. It also can be chosen if +the (colum/row) headers should be exported to the string. + +By default, the produced string is csv conform +*/ + +class MITKIMAGESTATISTICSUI_EXPORT QmitkTableModelToStringConverter +{ + +public: + QmitkTableModelToStringConverter(); + + void SetTableModel(QAbstractItemModel* model); + /** + \brief Returns the string + \exception throws exception if model is nullptr + */ + QString GetString() const; + /** + \brief If the table should be transposed (iterate over columns instead of rows) + */ + void SetTransposeOutput(bool transposeOutput); + void SetLineDelimiter(QChar lineDelimiter); + void SetColumnDelimiter(QChar columnDelimiter); + /** + \brief If header data (column/row captions) are exported + */ + void SetIncludeHeaderData(bool includeHeaderData); + +private: + QString GetStringTransposed() const; + QString GetStringNonTransposed() const; + + QAbstractItemModel* m_tableModel=nullptr; + bool m_transposeOutput=false; + QChar m_lineDelimiter = '\n'; + bool m_includeHeaderData = false; + QString m_columnDelimiterWithSpace = ", "; +}; +#endif // QmitkTableModelToQString_H__INCLUDED diff --git a/Modules/ImageStatisticsUI/files.cmake b/Modules/ImageStatisticsUI/files.cmake new file mode 100644 index 0000000000..e6faafc5b1 --- /dev/null +++ b/Modules/ImageStatisticsUI/files.cmake @@ -0,0 +1,29 @@ +set(CPP_FILES + Qmitk/QmitkHistogramVisualizationWidget.cpp + Qmitk/QmitkIntensityProfileVisualizationWidget.cpp + Qmitk/QmitkImageStatisticsTableModel.cpp + Qmitk/QmitkImageStatisticsCalculationJob.cpp + Qmitk/QmitkTableModelToStringConverter.cpp + Qmitk/QmitkImageStatisticsWidget.cpp +) + +set(H_FILES + Qmitk/QmitkTableModelToStringConverter.h +) + +set(TPP_FILES +) + +set(UI_FILES + Qmitk/QmitkHistogramVisualizationWidget.ui + Qmitk/QmitkIntensityProfileVisualizationWidget.ui + Qmitk/QmitkImageStatisticsWidget.ui +) + +set(MOC_H_FILES + Qmitk/QmitkHistogramVisualizationWidget.h + Qmitk/QmitkIntensityProfileVisualizationWidget.h + Qmitk/QmitkImageStatisticsTableModel.h + Qmitk/QmitkImageStatisticsCalculationJob.h + Qmitk/QmitkImageStatisticsWidget.h +) diff --git a/Modules/ModuleList.cmake b/Modules/ModuleList.cmake index e34b1219a1..2db311b104 100644 --- a/Modules/ModuleList.cmake +++ b/Modules/ModuleList.cmake @@ -1,83 +1,84 @@ # The entries in the mitk_modules list must be # ordered according to their dependencies. set(MITK_MODULES Core CommandLine AppUtil RDF LegacyIO DataTypesExt Annotation LegacyGL AlgorithmsExt MapperExt DICOMReader DICOMReaderServices DICOMQI DICOMTesting SceneSerializationBase PlanarFigure ImageDenoising ImageExtraction SceneSerialization Gizmo GraphAlgorithms Multilabel + Chart ImageStatistics ContourModel SurfaceInterpolation Segmentation PlanarFigureSegmentation QtWidgets QtWidgetsExt - Chart + ImageStatisticsUI SegmentationUI MatchPointRegistration MatchPointRegistrationUI Classification GPGPU OpenIGTLink IGTBase IGT CameraCalibration OpenCL OpenCVVideoSupport QtOverlays ToFHardware ToFProcessing ToFUI PhotoacousticsHardware PhotoacousticsAlgorithms PhotoacousticsLib US USUI DicomUI Remeshing Python QtPython Persistence OpenIGTLinkUI IGTUI DicomRT RTUI IOExt XNAT TubeGraph BiophotonicsHardware DiffusionImaging TumorInvasionAnalysis BoundingShape RenderWindowManager RenderWindowManagerUI CEST BasicImageProcessing ModelFit ModelFitUI Pharmacokinetics PharmacokineticsUI ) if(MITK_ENABLE_PIC_READER) list(APPEND MITK_MODULES IpPicSupportIO) endif() diff --git a/Modules/Segmentation/Algorithms/mitkFeatureBasedEdgeDetectionFilter.cpp b/Modules/Segmentation/Algorithms/mitkFeatureBasedEdgeDetectionFilter.cpp index 623e1b17cc..3d7c1fd877 100644 --- a/Modules/Segmentation/Algorithms/mitkFeatureBasedEdgeDetectionFilter.cpp +++ b/Modules/Segmentation/Algorithms/mitkFeatureBasedEdgeDetectionFilter.cpp @@ -1,198 +1,199 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkFeatureBasedEdgeDetectionFilter.h" #include #include #include #include #include #include #include #include #include #include +#include #include #include #include #include #include #include mitk::FeatureBasedEdgeDetectionFilter::FeatureBasedEdgeDetectionFilter() { this->SetNumberOfRequiredInputs(1); this->SetNumberOfIndexedOutputs(1); } mitk::FeatureBasedEdgeDetectionFilter::~FeatureBasedEdgeDetectionFilter() { } void mitk::FeatureBasedEdgeDetectionFilter::GenerateData() { - mitk::Image::Pointer image = ImageToUnstructuredGridFilter::GetInput(); + mitk::Image::ConstPointer image = ImageToUnstructuredGridFilter::GetInput(); if (m_SegmentationMask.IsNull()) { MITK_WARN << "Please set a segmentation mask first" << std::endl; return; } // First create a threshold segmentation of the image. The threshold is determined // by the mean +/- stddev of the pixel values that are covered by the segmentation mask // Compute mean and stdDev based on the current segmentation mitk::ImageStatisticsCalculator::Pointer statCalc = mitk::ImageStatisticsCalculator::New(); statCalc->SetInputImage(image); mitk::ImageMaskGenerator::Pointer imgMask = mitk::ImageMaskGenerator::New(); imgMask->SetImageMask(m_SegmentationMask); - mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer stats = statCalc->GetStatistics(); - double mean = stats->GetMean(); - double stdDev = stats->GetStd(); + auto stats = statCalc->GetStatistics()->GetStatisticsForTimeStep(0); + double mean = stats.GetValueConverted(mitk::ImageStatisticsConstants::MEAN()); + double stdDev = stats.GetValueConverted(mitk::ImageStatisticsConstants::STANDARDDEVIATION()); double upperThreshold = mean + stdDev; double lowerThreshold = mean - stdDev; // Perform thresholding mitk::Image::Pointer thresholdImage = mitk::Image::New(); AccessByItk_3(image.GetPointer(), ITKThresholding, lowerThreshold, upperThreshold, thresholdImage) mitk::ProgressBar::GetInstance() ->Progress(2); // Postprocess threshold segmentation // First a closing will be executed mitk::Image::Pointer closedImage = mitk::Image::New(); AccessByItk_1(thresholdImage, ThreadedClosing, closedImage); // Then we will holes that might exist mitk::MorphologicalOperations::FillHoles(closedImage); mitk::ProgressBar::GetInstance()->Progress(); // Extract the binary edges of the resulting segmentation mitk::Image::Pointer edgeImage = mitk::Image::New(); AccessByItk_1(closedImage, ContourSearch, edgeImage); // Convert the edge image into an unstructured grid mitk::ImageToUnstructuredGridFilter::Pointer i2UFilter = mitk::ImageToUnstructuredGridFilter::New(); i2UFilter->SetInput(edgeImage); i2UFilter->SetThreshold(1.0); i2UFilter->Update(); m_PointGrid = this->GetOutput(); if (m_PointGrid.IsNull()) m_PointGrid = mitk::UnstructuredGrid::New(); m_PointGrid->SetVtkUnstructuredGrid(i2UFilter->GetOutput()->GetVtkUnstructuredGrid()); mitk::ProgressBar::GetInstance()->Progress(); } template void mitk::FeatureBasedEdgeDetectionFilter::ThreadedClosing(itk::Image *originalImage, mitk::Image::Pointer &result) { typedef itk::BinaryBallStructuringElement myKernelType; myKernelType ball; ball.SetRadius(1); ball.CreateStructuringElement(); typedef typename itk::Image ImageType; typename itk::DilateObjectMorphologyImageFilter::Pointer dilationFilter = itk::DilateObjectMorphologyImageFilter::New(); dilationFilter->SetInput(originalImage); dilationFilter->SetKernel(ball); dilationFilter->Update(); typename itk::Image::Pointer dilatedImage = dilationFilter->GetOutput(); typename itk::ErodeObjectMorphologyImageFilter::Pointer erodeFilter = itk::ErodeObjectMorphologyImageFilter::New(); erodeFilter->SetInput(dilatedImage); erodeFilter->SetKernel(ball); erodeFilter->Update(); mitk::GrabItkImageMemory(erodeFilter->GetOutput(), result); } template void mitk::FeatureBasedEdgeDetectionFilter::ContourSearch(itk::Image *originalImage, mitk::Image::Pointer &result) { typedef itk::Image ImageType; typedef itk::BinaryContourImageFilter binaryContourImageFilterType; typename binaryContourImageFilterType::Pointer binaryContourFilter = binaryContourImageFilterType::New(); binaryContourFilter->SetInput(originalImage); binaryContourFilter->SetForegroundValue(1); binaryContourFilter->SetBackgroundValue(0); binaryContourFilter->Update(); typename itk::Image::Pointer itkImage = itk::Image::New(); itkImage->Graft(binaryContourFilter->GetOutput()); mitk::GrabItkImageMemory(itkImage, result); } template -void mitk::FeatureBasedEdgeDetectionFilter::ITKThresholding(itk::Image *originalImage, +void mitk::FeatureBasedEdgeDetectionFilter::ITKThresholding(const itk::Image *originalImage, double lower, double upper, mitk::Image::Pointer &result) { typedef itk::Image ImageType; typedef itk::Image SegmentationType; typedef itk::BinaryThresholdImageFilter ThresholdFilterType; if (typeid(TPixel) != typeid(float) && typeid(TPixel) != typeid(double)) { // round the thresholds if we have nor a float or double image lower = std::floor(lower + 0.5); upper = std::floor(upper - 0.5); } if (lower >= upper) { upper = lower; } typename ThresholdFilterType::Pointer filter = ThresholdFilterType::New(); filter->SetInput(originalImage); filter->SetLowerThreshold(lower); filter->SetUpperThreshold(upper); filter->SetInsideValue(1); filter->SetOutsideValue(0); filter->Update(); mitk::GrabItkImageMemory(filter->GetOutput(), result); } void mitk::FeatureBasedEdgeDetectionFilter::SetSegmentationMask(mitk::Image::Pointer segmentation) { this->m_SegmentationMask = segmentation; } void mitk::FeatureBasedEdgeDetectionFilter::GenerateOutputInformation() { Superclass::GenerateOutputInformation(); } diff --git a/Modules/Segmentation/Algorithms/mitkFeatureBasedEdgeDetectionFilter.h b/Modules/Segmentation/Algorithms/mitkFeatureBasedEdgeDetectionFilter.h index 8d481aa1dd..adb0a80903 100644 --- a/Modules/Segmentation/Algorithms/mitkFeatureBasedEdgeDetectionFilter.h +++ b/Modules/Segmentation/Algorithms/mitkFeatureBasedEdgeDetectionFilter.h @@ -1,78 +1,78 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef mitkFeatureBasedEdgeDetectionFilter_h_Included #define mitkFeatureBasedEdgeDetectionFilter_h_Included #include #include namespace mitk { /** * @brief Calculates edges and extracts them as an UnstructuredGrid with respect * to the given segmentation. * * At first the statistic of the grey values within the segmentation is * calculated. Based on this statistic a thresholding is executed. The * thresholded image will be processed by morphological filters. The resulting * image will be used for masking the input image. The masked image is used as * input for the ImageToPointCloudFilter, which output is an UnstructuredGrid. */ class MITKSEGMENTATION_EXPORT FeatureBasedEdgeDetectionFilter : public ImageToUnstructuredGridFilter { public: mitkClassMacro(FeatureBasedEdgeDetectionFilter, ImageToUnstructuredGridFilter) itkFactorylessNewMacro(Self) /** Sets the segmentation for calculating the statistics within that */ void SetSegmentationMask(mitk::Image::Pointer); protected: /** This method is called by Update(). */ void GenerateData() override; /** Initializes the output information */ void GenerateOutputInformation() override; /** Constructor */ FeatureBasedEdgeDetectionFilter(); /** Destructor */ ~FeatureBasedEdgeDetectionFilter() override; /** Execute a thresholding filter with the given lower and upper bound */ template - void ITKThresholding(itk::Image *originalImage, + void ITKThresholding(const itk::Image *originalImage, double lower, double upper, mitk::Image::Pointer &result); template void ContourSearch(itk::Image *originalImage, mitk::Image::Pointer &result); template void ThreadedClosing(itk::Image *originalImage, mitk::Image::Pointer &result); private: mitk::UnstructuredGrid::Pointer m_PointGrid; /** The used mask given by the segmentation*/ mitk::Image::Pointer m_SegmentationMask; }; } #endif diff --git a/Modules/SurfaceInterpolation/mitkImageToPointCloudFilter.cpp b/Modules/SurfaceInterpolation/mitkImageToPointCloudFilter.cpp index 8497ab49a5..49a0fb4845 100644 --- a/Modules/SurfaceInterpolation/mitkImageToPointCloudFilter.cpp +++ b/Modules/SurfaceInterpolation/mitkImageToPointCloudFilter.cpp @@ -1,166 +1,167 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkImageToPointCloudFilter.h" #include #include #include #include #include #include #include #include #include +#include mitk::ImageToPointCloudFilter::ImageToPointCloudFilter() : m_Geometry(nullptr) { m_Method = DetectionMethod(0); this->SetNumberOfRequiredInputs(1); this->SetNumberOfIndexedOutputs(1); } mitk::ImageToPointCloudFilter::~ImageToPointCloudFilter() { } void mitk::ImageToPointCloudFilter::GenerateData() { mitk::Image::ConstPointer image = ImageToUnstructuredGridFilter::GetInput(); m_Geometry = image->GetGeometry(); if (image.IsNull()) { MITK_ERROR << "mitk::ImageToContourFilter: No input available. " "Please set the input!" << std::endl; return; } mitk::Image::Pointer notConstImage = const_cast(image.GetPointer()); switch (m_Method) { case 0: AccessByItk_1(notConstImage.GetPointer(), StdDeviations, 2) break; case 1: AccessByItk_1(notConstImage.GetPointer(), StdDeviations, 3) break; case 2: AccessByItk_1(notConstImage.GetPointer(), StdDeviations, 4) break; default: AccessByItk_1(notConstImage.GetPointer(), StdDeviations, 2) break; } } template void mitk::ImageToPointCloudFilter::StdDeviations(itk::Image *image, int amount) { typedef itk::Image InputImageType; typedef itk::CastImageFilter ImagePTypeToFloatPTypeCasterType; typedef itk::LaplacianImageFilter LaplacianFilterType; typename LaplacianFilterType::Pointer lapFilter = LaplacianFilterType::New(); typename ImagePTypeToFloatPTypeCasterType::Pointer caster = ImagePTypeToFloatPTypeCasterType::New(); caster->SetInput(image); caster->Update(); FloatImageType::Pointer fImage = caster->GetOutput(); lapFilter->SetInput(fImage); lapFilter->UpdateLargestPossibleRegion(); - mitk::Image::Pointer edgeImage = mitk::ImportItkImage(lapFilter->GetOutput()); + auto edgeImage = mitk::ImportItkImage(lapFilter->GetOutput()); mitk::ImageStatisticsCalculator::Pointer statCalc = mitk::ImageStatisticsCalculator::New(); - statCalc->SetInputImage(edgeImage); - mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer stats = statCalc->GetStatistics(); - double mean = stats->GetMean(); - double stdDev = stats->GetStd(); + statCalc->SetInputImage(edgeImage.GetPointer()); + auto stats = statCalc->GetStatistics()->GetStatisticsForTimeStep(0); + auto mean = stats.GetValueConverted(mitk::ImageStatisticsConstants::MEAN()); + auto stdDev = stats.GetValueConverted(mitk::ImageStatisticsConstants::STANDARDDEVIATION()); double upperThreshold = mean + stdDev * amount; double lowerThreshold = mean - stdDev * amount; typename itk::ImageRegionIterator it(lapFilter->GetOutput(), lapFilter->GetOutput()->GetRequestedRegion()); vtkSmartPointer points = vtkSmartPointer::New(); double greatX = 0, greatY = 0, greatZ = 0; it.GoToBegin(); while (!it.IsAtEnd()) { if (it.Get() > lowerThreshold && it.Get() < upperThreshold) { it.Set(0); } else { it.Set(1); mitk::Point3D imagePoint; mitk::Point3D worldPoint; imagePoint[0] = it.GetIndex()[0]; imagePoint[1] = it.GetIndex()[1]; imagePoint[2] = it.GetIndex()[2]; m_Geometry->IndexToWorld(imagePoint, worldPoint); if (worldPoint[0] > greatX) greatX = worldPoint[0]; if (worldPoint[1] > greatY) greatY = worldPoint[1]; if (worldPoint[2] > greatZ) greatZ = worldPoint[2]; points->InsertNextPoint(worldPoint[0], worldPoint[1], worldPoint[2]); m_NumberOfExtractedPoints++; } ++it; } /*need to build the UnstructuredGrid with at least one vertex otherwise its not visible*/ vtkSmartPointer verts = vtkSmartPointer::New(); verts->GetPointIds()->SetNumberOfIds(m_NumberOfExtractedPoints); for (int i = 0; i < m_NumberOfExtractedPoints; i++) { verts->GetPointIds()->SetId(i, i); } vtkSmartPointer uGrid = vtkSmartPointer::New(); uGrid->Allocate(1); uGrid->InsertNextCell(verts->GetCellType(), verts->GetPointIds()); uGrid->SetPoints(points); mitk::UnstructuredGrid::Pointer outputGrid = mitk::UnstructuredGrid::New(); outputGrid->SetVtkUnstructuredGrid(uGrid); this->SetNthOutput(0, outputGrid); } void mitk::ImageToPointCloudFilter::GenerateOutputInformation() { Superclass::GenerateOutputInformation(); } diff --git a/Plugins/org.mitk.gui.qt.cest/CMakeLists.txt b/Plugins/org.mitk.gui.qt.cest/CMakeLists.txt index e566584d43..02e76db46f 100644 --- a/Plugins/org.mitk.gui.qt.cest/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.cest/CMakeLists.txt @@ -1,7 +1,7 @@ project(org_mitk_gui_qt_cest) mitk_create_plugin( EXPORT_DIRECTIVE CEST_EXPORT EXPORTED_INCLUDE_SUFFIXES src - MODULE_DEPENDS MitkQtWidgetsExt MitkImageStatistics MitkPlanarFigure MitkCEST + MODULE_DEPENDS MitkQtWidgetsExt MitkImageStatistics MitkImageStatisticsUI MitkPlanarFigure MitkCEST ) diff --git a/Plugins/org.mitk.gui.qt.cest/files.cmake b/Plugins/org.mitk.gui.qt.cest/files.cmake index 54f1352424..67dcc599ba 100644 --- a/Plugins/org.mitk.gui.qt.cest/files.cmake +++ b/Plugins/org.mitk.gui.qt.cest/files.cmake @@ -1,47 +1,45 @@ set(SRC_CPP_FILES - QmitkImageStatisticsCalculationThread.cpp ) set(INTERNAL_CPP_FILES org_mitk_gui_qt_cest_Activator.cpp QmitkCESTStatisticsView.cpp QmitkCESTNormalizeView.cpp ) set(UI_FILES src/internal/QmitkCESTStatisticsViewControls.ui src/internal/QmitkCESTNormalizeViewControls.ui ) set(MOC_H_FILES src/internal/org_mitk_gui_qt_cest_Activator.h src/internal/QmitkCESTStatisticsView.h src/internal/QmitkCESTNormalizeView.h - src/QmitkImageStatisticsCalculationThread.h ) # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench set(CACHED_RESOURCE_FILES resources/icon.svg resources/icon_norm.png plugin.xml ) # list of Qt .qrc files which contain additional resources # specific to this plugin 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.cest/src/QmitkImageStatisticsCalculationThread.cpp b/Plugins/org.mitk.gui.qt.cest/src/QmitkImageStatisticsCalculationThread.cpp deleted file mode 100644 index c065e8d218..0000000000 --- a/Plugins/org.mitk.gui.qt.cest/src/QmitkImageStatisticsCalculationThread.cpp +++ /dev/null @@ -1,266 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include "QmitkImageStatisticsCalculationThread.h" - -//QT headers -#include -#include -#include -#include -#include - -QmitkImageStatisticsCalculationThread::QmitkImageStatisticsCalculationThread():QThread(), - m_StatisticsImage(nullptr), m_BinaryMask(nullptr), m_PlanarFigureMask(nullptr), m_TimeStep(0), - m_IgnoreZeros(false), m_CalculationSuccessful(false), m_StatisticChanged(false), m_HistogramBinSize(10.0), m_UseDefaultNBins(true), m_nBinsForHistogramStatistics(100), m_prioritizeNBinsOverBinSize(true) -{ -} - -QmitkImageStatisticsCalculationThread::~QmitkImageStatisticsCalculationThread() -{ -} - -void QmitkImageStatisticsCalculationThread::Initialize( mitk::Image::Pointer image, mitk::Image::Pointer binaryImage, mitk::PlanarFigure::Pointer planarFig ) -{ - // reset old values - if( this->m_StatisticsImage.IsNotNull() ) - this->m_StatisticsImage = nullptr; - - if( this->m_BinaryMask.IsNotNull() ) - this->m_BinaryMask = nullptr; - - if( this->m_PlanarFigureMask.IsNotNull()) - this->m_PlanarFigureMask = nullptr; - - // set new values if passed in - if(image.IsNotNull()) - this->m_StatisticsImage = image->Clone(); - if(binaryImage.IsNotNull()) - this->m_BinaryMask = binaryImage->Clone(); - if(planarFig.IsNotNull()) - this->m_PlanarFigureMask = planarFig->Clone(); -} - -void QmitkImageStatisticsCalculationThread::SetUseDefaultNBins(bool useDefault) -{ - m_UseDefaultNBins = useDefault; -} - -void QmitkImageStatisticsCalculationThread::SetTimeStep( int times ) -{ - this->m_TimeStep = times; -} - -int QmitkImageStatisticsCalculationThread::GetTimeStep() -{ - return this->m_TimeStep; -} - -std::vector QmitkImageStatisticsCalculationThread::GetStatisticsData() -{ - return this->m_StatisticsVector; -} - -mitk::Image::Pointer QmitkImageStatisticsCalculationThread::GetStatisticsImage() -{ - return this->m_StatisticsImage; -} - -void QmitkImageStatisticsCalculationThread::SetIgnoreZeroValueVoxel(bool _arg) -{ - this->m_IgnoreZeros = _arg; -} - -bool QmitkImageStatisticsCalculationThread::GetIgnoreZeroValueVoxel() -{ - return this->m_IgnoreZeros; -} - -void QmitkImageStatisticsCalculationThread::SetHistogramBinSize(double size) -{ - this->m_HistogramBinSize = size; - this->m_prioritizeNBinsOverBinSize = false; -} - -double QmitkImageStatisticsCalculationThread::GetHistogramBinSize() const -{ - return this->m_HistogramBinSize; -} - -void QmitkImageStatisticsCalculationThread::SetHistogramNBins(double size) -{ - this->m_nBinsForHistogramStatistics = size; - this->m_prioritizeNBinsOverBinSize = true; -} - -double QmitkImageStatisticsCalculationThread::GetHistogramNBins() const -{ - return this->m_nBinsForHistogramStatistics; -} - -std::string QmitkImageStatisticsCalculationThread::GetLastErrorMessage() -{ - return m_message; -} - -QmitkImageStatisticsCalculationThread::HistogramType::Pointer -QmitkImageStatisticsCalculationThread::GetTimeStepHistogram(unsigned int t) -{ - if (t >= this->m_HistogramVector.size()) - return nullptr; - - return this->m_HistogramVector[t]; -} - -bool QmitkImageStatisticsCalculationThread::GetStatisticsChangedFlag() -{ - return m_StatisticChanged; -} - -bool QmitkImageStatisticsCalculationThread::GetStatisticsUpdateSuccessFlag() -{ - return m_CalculationSuccessful; -} - -void QmitkImageStatisticsCalculationThread::run() -{ - bool statisticCalculationSuccessful = true; - mitk::ImageStatisticsCalculator::Pointer calculator = mitk::ImageStatisticsCalculator::New(); - - if(this->m_StatisticsImage.IsNotNull()) - { - calculator->SetInputImage(m_StatisticsImage); - } - else - { - statisticCalculationSuccessful = false; - } - - // Bug 13416 : The ImageStatistics::SetImageMask() method can throw exceptions, i.e. when the dimensionality - // of the masked and input image differ, we need to catch them and mark the calculation as failed - // the same holds for the ::SetPlanarFigure() - try - { - if(this->m_BinaryMask.IsNotNull()) - { - mitk::ImageMaskGenerator::Pointer imgMask = mitk::ImageMaskGenerator::New(); - imgMask->SetImageMask(m_BinaryMask); - calculator->SetMask(imgMask.GetPointer()); - } - if(this->m_PlanarFigureMask.IsNotNull()) - { - mitk::PlanarFigureMaskGenerator::Pointer pfMaskGen = mitk::PlanarFigureMaskGenerator::New(); - pfMaskGen->SetInputImage(m_StatisticsImage); - pfMaskGen->SetPlanarFigure(m_PlanarFigureMask); - calculator->SetMask(pfMaskGen.GetPointer()); - } - } - catch (const mitk::Exception& e) - { - MITK_ERROR << "MITK Exception: " << e.what(); - statisticCalculationSuccessful = false; - } - catch (const itk::ExceptionObject& e) - { - MITK_ERROR << "ITK Exception:" << e.what(); - statisticCalculationSuccessful = false; - } - catch ( const std::runtime_error &e ) - { - MITK_ERROR<< "Runtime Exception: " << e.what(); - statisticCalculationSuccessful = false; - } - catch ( const std::exception &e ) - { - //m_message = "Failure: " + std::string(e.what()); - MITK_ERROR<< "Standard Exception: " << e.what(); - statisticCalculationSuccessful = false; - } - - bool statisticChanged = false; - - if (this->m_IgnoreZeros) - { - mitk::IgnorePixelMaskGenerator::Pointer ignorePixelValueMaskGen = mitk::IgnorePixelMaskGenerator::New(); - ignorePixelValueMaskGen->SetIgnoredPixelValue(0); - ignorePixelValueMaskGen->SetInputImage(m_StatisticsImage); - calculator->SetSecondaryMask(ignorePixelValueMaskGen.GetPointer()); - } - else - { - calculator->SetSecondaryMask(nullptr); - } - - if (m_UseDefaultNBins) - { - calculator->SetNBinsForHistogramStatistics(100); - } - else - { - if (!m_prioritizeNBinsOverBinSize) - { - calculator->SetBinSizeForHistogramStatistics(m_HistogramBinSize); - } - else - { - calculator->SetNBinsForHistogramStatistics(100); - } - } - - //calculator->SetHistogramBinSize( m_HistogramBinSize ); - //calculator->SetUseDefaultBinSize( m_UseDefaultBinSize ); - - for (unsigned int i = 0; i < m_StatisticsImage->GetTimeSteps(); i++) - { - try - { - calculator->GetStatistics(i); - } - catch ( mitk::Exception& e) - { - //m_message = e.GetDescription(); - MITK_ERROR<< "MITK Exception: " << e.what(); - statisticCalculationSuccessful = false; - } - catch ( const std::runtime_error &e ) - { - //m_message = "Failure: " + std::string(e.what()); - MITK_ERROR<< "Runtime Exception: " << e.what(); - statisticCalculationSuccessful = false; - } - catch ( const std::exception &e ) - { - //m_message = "Failure: " + std::string(e.what()); - MITK_ERROR<< "Standard Exception: " << e.what(); - statisticCalculationSuccessful = false; - } - } - - this->m_StatisticChanged = statisticChanged; - this->m_CalculationSuccessful = statisticCalculationSuccessful; - - if(statisticCalculationSuccessful) - { - this->m_StatisticsVector.clear(); - this->m_HistogramVector.clear(); - - for (unsigned int i = 0; i < m_StatisticsImage->GetTimeSteps(); i++) - { - this->m_StatisticsVector.push_back(calculator->GetStatistics(i)); - this->m_HistogramVector.push_back((HistogramType*)this->m_StatisticsVector[i]->GetHistogram()); - } - } -} diff --git a/Plugins/org.mitk.gui.qt.cest/src/QmitkImageStatisticsCalculationThread.h b/Plugins/org.mitk.gui.qt.cest/src/QmitkImageStatisticsCalculationThread.h deleted file mode 100644 index ab02f7d5af..0000000000 --- a/Plugins/org.mitk.gui.qt.cest/src/QmitkImageStatisticsCalculationThread.h +++ /dev/null @@ -1,123 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ -#ifndef QMITKIMAGESTATISTICSCALCULATIONTHREAD_H_INCLUDED -#define QMITKIMAGESTATISTICSCALCULATIONTHREAD_H_INCLUDED - -//QT headers -#include -#include - -//mitk headers -#include "mitkImage.h" -#include "mitkPlanarFigure.h" -#include "mitkImageStatisticsCalculator.h" - -// itk headers -#ifndef __itkHistogram_h -#include -#endif - - -/** /brief This class is executed as background thread for image statistics calculation. - * Documentation: This class is derived from QThread and is intended to be used by QmitkImageStatisticsView - to run the image statistics calculation in a background thread keepung the gui usable. - * \ingroup Plugins/MeasurementToolbox - */ - -class QmitkImageStatisticsCalculationThread : public QThread -{ - Q_OBJECT - -public: - - typedef itk::Statistics::Histogram HistogramType; - - /*! - /brief standard constructor. */ - QmitkImageStatisticsCalculationThread(); - /*! - /brief standard destructor. */ - ~QmitkImageStatisticsCalculationThread(); - /*! - *\brief Automatically calculate bin size to obtain 200 bins. */ - void SetUseDefaultNBins(bool useDefault); - /*! - /brief Initializes the object with necessary data. */ - void Initialize( mitk::Image::Pointer image, mitk::Image::Pointer binaryImage, mitk::PlanarFigure::Pointer planarFig ); - /*! - /brief returns the calculated image statistics. */ - std::vector GetStatisticsData(); - /*! - /brief */ - mitk::Image::Pointer GetStatisticsImage(); - /*! - /brief Set the time step of the image you want to process. */ - void SetTimeStep( int times ); - /*! - /brief Get the time step of the image you want to process. */ - int GetTimeStep(); - /*! - /brief Set flag to ignore zero valued voxels */ - void SetIgnoreZeroValueVoxel( bool _arg ); - /*! - /brief Get status of zero value voxel ignoring. */ - bool GetIgnoreZeroValueVoxel(); - /*! - /brief Set bin size for histogram resolution.*/ - void SetHistogramBinSize( double size); - /*! - /brief Get bin size for histogram resolution.*/ - double GetHistogramBinSize() const; - /*! - /brief Set bin size for histogram resolution.*/ - void SetHistogramNBins( double size); - /*! - /brief Get bin size for histogram resolution.*/ - double GetHistogramNBins() const; - /*! - /brief Returns the histogram of the currently selected time step. */ - HistogramType::Pointer GetTimeStepHistogram(unsigned int t = 0); - /*! - /brief Returns a flag indicating if the statistics have changed during calculation */ - bool GetStatisticsChangedFlag(); - /*! - /brief Returns a flag the indicates if the statistics are updated successfully */ - bool GetStatisticsUpdateSuccessFlag(); - /*! - /brief Method called once the thread is executed. */ - void run() override; - - std::string GetLastErrorMessage(); - -private: - //member declaration - - mitk::Image::Pointer m_StatisticsImage; ///< member variable holds the input image for which the statistics need to be calculated. - mitk::Image::Pointer m_BinaryMask; ///< member variable holds the binary mask image for segmentation image statistics calculation. - mitk::PlanarFigure::Pointer m_PlanarFigureMask; ///< member variable holds the planar figure for segmentation image statistics calculation. - std::vector m_StatisticsVector; ///< member variable holds the result structs. - int m_TimeStep; ///< member variable holds the time step for statistics calculation - bool m_IgnoreZeros; ///< member variable holds flag to indicate if zero valued voxel should be suppressed - bool m_CalculationSuccessful; ///< flag set if statistics calculation was successful - bool m_StatisticChanged; ///< flag set if statistics have changed - double m_HistogramBinSize; ///< member variable holds the bin size for histogram resolution. - std::vector m_HistogramVector; ///< member holds the histograms of all time steps. - std::string m_message; - bool m_UseDefaultNBins; - unsigned int m_nBinsForHistogramStatistics; - bool m_prioritizeNBinsOverBinSize; -}; -#endif // QMITKIMAGESTATISTICSCALCULATIONTHREAD_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsView.cpp b/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsView.cpp index b3d856c624..2de9dfc5cd 100644 --- a/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsView.cpp @@ -1,896 +1,822 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ -//itk +// itk #include "itksys/SystemTools.hxx" #include #include // Blueberry #include #include // Qmitk #include "QmitkCESTStatisticsView.h" // Qt #include #include // qwt #include // mitk #include #include #include #include #include #include +#include #include +#include +#include +#include #include #include -#include // boost -#include #include +#include -//stl -#include -#include -#include +// stl #include +#include #include +#include +#include #include namespace { template void GetSortPermutation(std::vector &out, const std::vector &determiningVector, Compare compare = std::less()) { out.resize(determiningVector.size()); std::iota(out.begin(), out.end(), 0); std::sort(out.begin(), out.end(), [&](unsigned i, unsigned j) { return compare(determiningVector[i], determiningVector[j]); }); } template void ApplyPermutation(const std::vector &order, std::vector &vectorToSort) { assert(order.size() == vectorToSort.size()); std::vector tempVector(vectorToSort.size()); for (unsigned i = 0; i < vectorToSort.size(); i++) { tempVector[i] = vectorToSort[order[i]]; } vectorToSort = tempVector; } template void ApplyPermutation(const std::vector &order, std::vector ¤tVector, std::vector &... remainingVectors) { ApplyPermutation(order, currentVector); ApplyPermutation(order, remainingVectors...); } template void SortVectors(const std::vector &orderDeterminingVector, Compare comparison, std::vector &... vectorsToBeSorted) { std::vector order; GetSortPermutation(order, orderDeterminingVector, comparison); ApplyPermutation(order, vectorsToBeSorted...); } -} +} // namespace const std::string QmitkCESTStatisticsView::VIEW_ID = "org.mitk.views.ceststatistics"; static const int STAT_TABLE_BASE_HEIGHT = 180; -QmitkCESTStatisticsView::QmitkCESTStatisticsView(QObject* /*parent*/, const char* /*name*/) +QmitkCESTStatisticsView::QmitkCESTStatisticsView(QObject * /*parent*/, const char * /*name*/) { - this->m_CalculatorThread = new QmitkImageStatisticsCalculationThread; + this->m_CalculatorJob = new QmitkImageStatisticsCalculationJob(); m_currentSelectedPosition.Fill(0.0); m_currentSelectedTimeStep = 0; m_CrosshairPointSet = mitk::PointSet::New(); } QmitkCESTStatisticsView::~QmitkCESTStatisticsView() { - while (this->m_CalculatorThread->isRunning()) // wait until thread has finished + while (this->m_CalculatorJob->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } - delete this->m_CalculatorThread; + delete this->m_CalculatorJob; } void QmitkCESTStatisticsView::SetFocus() { m_Controls.threeDimToFourDimPushButton->setFocus(); } -void QmitkCESTStatisticsView::CreateQtPartControl( QWidget *parent ) +void QmitkCESTStatisticsView::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file - m_Controls.setupUi( parent ); - connect(m_Controls.threeDimToFourDimPushButton, SIGNAL(clicked()), this, SLOT(OnThreeDimToFourDimPushButtonClicked())); - connect((QObject*) this->m_CalculatorThread, SIGNAL(finished()), this, SLOT(OnThreadedStatisticsCalculationEnds()), Qt::QueuedConnection); - connect((QObject*)(this->m_Controls.m_CopyStatisticsToClipboardPushButton), SIGNAL(clicked()), (QObject*) this, SLOT(OnCopyStatisticsToClipboardPushButtonClicked())); - connect((QObject*)(this->m_Controls.fixedRangeCheckBox), SIGNAL(toggled(bool)), (QObject*) this, SLOT(OnFixedRangeCheckBoxToggled(bool))); - connect((QObject*)(this->m_Controls.fixedRangeLowerDoubleSpinBox), SIGNAL(editingFinished()), (QObject*) this, SLOT(OnFixedRangeDoubleSpinBoxChanged())); - connect((QObject*)(this->m_Controls.fixedRangeUpperDoubleSpinBox), SIGNAL(editingFinished()), (QObject*) this, SLOT(OnFixedRangeDoubleSpinBoxChanged())); + m_Controls.setupUi(parent); + connect( + m_Controls.threeDimToFourDimPushButton, SIGNAL(clicked()), this, SLOT(OnThreeDimToFourDimPushButtonClicked())); + connect((QObject *)this->m_CalculatorJob, + SIGNAL(finished()), + this, + SLOT(OnThreadedStatisticsCalculationEnds()), + Qt::QueuedConnection); + connect((QObject *)(this->m_Controls.fixedRangeCheckBox), + SIGNAL(toggled(bool)), + (QObject *)this, + SLOT(OnFixedRangeCheckBoxToggled(bool))); + connect((QObject *)(this->m_Controls.fixedRangeLowerDoubleSpinBox), + SIGNAL(editingFinished()), + (QObject *)this, + SLOT(OnFixedRangeDoubleSpinBoxChanged())); + connect((QObject *)(this->m_Controls.fixedRangeUpperDoubleSpinBox), + SIGNAL(editingFinished()), + (QObject *)this, + SLOT(OnFixedRangeDoubleSpinBoxChanged())); m_Controls.threeDimToFourDimPushButton->setEnabled(false); + m_Controls.widget_statistics->SetDataStorage(this->GetDataStorage()); + this->m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); } -void QmitkCESTStatisticsView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) +void QmitkCESTStatisticsView::RenderWindowPartActivated(mitk::IRenderWindowPart *renderWindowPart) { this->m_SliceChangeListener.RenderWindowPartActivated(renderWindowPart); } -void QmitkCESTStatisticsView::RenderWindowPartDeactivated( - mitk::IRenderWindowPart* renderWindowPart) +void QmitkCESTStatisticsView::RenderWindowPartDeactivated(mitk::IRenderWindowPart *renderWindowPart) { this->m_SliceChangeListener.RenderWindowPartDeactivated(renderWindowPart); } -void QmitkCESTStatisticsView::OnSelectionChanged( berry::IWorkbenchPart::Pointer /*source*/, - const QList& nodes ) +void QmitkCESTStatisticsView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, + const QList &nodes) { if (nodes.empty()) { std::stringstream message; message << "Please select an image."; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); this->Clear(); return; } // iterate all selected objects bool atLeastOneWasCESTImage = false; - foreach( mitk::DataNode::Pointer node, nodes ) + foreach (mitk::DataNode::Pointer node, nodes) { if (node.IsNull()) { continue; } - if( dynamic_cast(node->GetData()) != nullptr ) + if (dynamic_cast(node->GetData()) != nullptr) { - m_Controls.labelWarning->setVisible( false ); + m_Controls.labelWarning->setVisible(false); - bool zSpectrumSet = - SetZSpectrum(dynamic_cast(node->GetData()->GetProperty(mitk::CustomTagParser::m_OffsetsPropertyName.c_str()).GetPointer())); + bool zSpectrumSet = SetZSpectrum(dynamic_cast( + node->GetData()->GetProperty(mitk::CustomTagParser::m_OffsetsPropertyName.c_str()).GetPointer())); atLeastOneWasCESTImage = atLeastOneWasCESTImage || zSpectrumSet; if (zSpectrumSet) { - m_ZImage = dynamic_cast(node->GetData()); + m_ZImage = dynamic_cast(node->GetData()); + m_Controls.widget_statistics->SetImageNodes({node.GetPointer()}); } else { - m_MaskImage = dynamic_cast(node->GetData()); + m_MaskImage = dynamic_cast(node->GetData()); + m_Controls.widget_statistics->SetMaskNodes({node.GetPointer()}); } } - if (dynamic_cast(node->GetData()) != nullptr) + if (dynamic_cast(node->GetData()) != nullptr) { - m_MaskPlanarFigure = dynamic_cast(node->GetData()); + m_MaskPlanarFigure = dynamic_cast(node->GetData()); + m_Controls.widget_statistics->SetMaskNodes({node.GetPointer()}); } - if (dynamic_cast(node->GetData()) != nullptr) + if (dynamic_cast(node->GetData()) != nullptr) { - m_PointSet = dynamic_cast(node->GetData()); + m_PointSet = dynamic_cast(node->GetData()); } } // We only want to offer normalization or timestep copying if one object is selected if (nodes.size() == 1) { - if (dynamic_cast(nodes.front()->GetData()) ) + if (dynamic_cast(nodes.front()->GetData())) { m_Controls.threeDimToFourDimPushButton->setDisabled(atLeastOneWasCESTImage); } else { m_Controls.threeDimToFourDimPushButton->setEnabled(false); std::stringstream message; message << "The selected node is not an image."; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); } this->Clear(); return; } - - // we always need a mask, either image or planar figure as well as an image for further processing if (nodes.size() != 2) { this->Clear(); return; } m_Controls.threeDimToFourDimPushButton->setEnabled(false); if (!atLeastOneWasCESTImage) { std::stringstream message; message << "None of the selected data nodes contains required CEST meta information"; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); this->Clear(); return; } bool bothAreImages = (m_ZImage.GetPointer() != nullptr) && (m_MaskImage.GetPointer() != nullptr); if (bothAreImages) { - bool geometriesMatch = mitk::Equal(*(m_ZImage->GetTimeGeometry()), *(m_MaskImage->GetTimeGeometry()), mitk::eps, false); + bool geometriesMatch = + mitk::Equal(*(m_ZImage->GetTimeGeometry()), *(m_MaskImage->GetTimeGeometry()), mitk::eps, false); if (!geometriesMatch) { std::stringstream message; message << "The selected images have different geometries."; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); this->Clear(); return; } } if (!this->DataSanityCheck()) { this->Clear(); return; } if (m_PointSet.IsNull()) { // initialize thread and trigger it - this->m_CalculatorThread->SetIgnoreZeroValueVoxel(false); - this->m_CalculatorThread->Initialize(m_ZImage, m_MaskImage, m_MaskPlanarFigure); + this->m_CalculatorJob->SetIgnoreZeroValueVoxel(false); + this->m_CalculatorJob->Initialize(m_ZImage.GetPointer(), m_MaskImage.GetPointer(), m_MaskPlanarFigure.GetPointer()); std::stringstream message; message << "Calculating statistics..."; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); try { // Compute statistics - this->m_CalculatorThread->start(); + this->m_CalculatorJob->start(); } - catch (const mitk::Exception& e) + catch (const mitk::Exception &e) { std::stringstream message; message << "" << e.GetDescription() << ""; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); } catch (const std::runtime_error &e) { // In case of exception, print error message on GUI std::stringstream message; message << "" << e.what() << ""; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); } 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! Unequal Dimensions of Image and Segmentation. No recompute possible "; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); } - while (this->m_CalculatorThread->isRunning()) // wait until thread has finished + while (this->m_CalculatorJob->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } } if (m_PointSet.IsNotNull()) { if (m_ZImage->GetDimension() == 4) { AccessFixedDimensionByItk(m_ZImage, PlotPointSet, 4); } else { MITK_WARN << "Expecting a 4D image."; } } } void QmitkCESTStatisticsView::OnThreadedStatisticsCalculationEnds() { this->m_Controls.m_DataViewWidget->SetAxisTitle(QwtPlot::Axis::xBottom, "delta w"); this->m_Controls.m_DataViewWidget->SetAxisTitle(QwtPlot::Axis::yLeft, "z"); - const std::vector &statistics = - this->m_CalculatorThread->GetStatisticsData(); + if (this->m_CalculatorJob->GetStatisticsUpdateSuccessFlag()) + { + auto statistics = this->m_CalculatorJob->GetStatisticsData(); - QmitkPlotWidget::DataVector::size_type numberOfSpectra = this->m_zSpectrum.size(); + auto statisticNonConst = statistics->Clone(); + std::string statisticsNodeName = "CEST_statistics"; + auto statisticsNode = mitk::CreateImageStatisticsNode(statisticNonConst, statisticsNodeName); + auto imageRule = mitk::StatisticsToImageRelationRule::New(); + imageRule->Connect(statisticNonConst.GetPointer(), m_CalculatorJob->GetStatisticsImage().GetPointer()); - QmitkPlotWidget::DataVector means(numberOfSpectra); - QmitkPlotWidget::DataVector stdevs(numberOfSpectra); + if (m_CalculatorJob->GetMaskImage()) + { + auto maskRule = mitk::StatisticsToMaskRelationRule::New(); + maskRule->Connect(statisticNonConst.GetPointer(), m_CalculatorJob->GetMaskImage().GetPointer()); + } + else if (m_CalculatorJob->GetPlanarFigure()) + { + auto planarFigureRule = mitk::StatisticsToMaskRelationRule::New(); + planarFigureRule->Connect(statisticNonConst.GetPointer(), m_CalculatorJob->GetPlanarFigure().GetPointer()); + } - for (unsigned int index = 0; index < numberOfSpectra; ++index) - { - means[index] = statistics[index]->GetMean(); - stdevs[index] = statistics[index]->GetStd(); - } + this->GetDataStorage()->Add(statisticsNode); - QmitkPlotWidget::DataVector xValues = this->m_zSpectrum; + QmitkPlotWidget::DataVector::size_type numberOfSpectra = this->m_zSpectrum.size(); - RemoveMZeros(xValues, means, stdevs); - ::SortVectors(xValues, std::less(), xValues, means, stdevs); + QmitkPlotWidget::DataVector means(numberOfSpectra); + QmitkPlotWidget::DataVector stdevs(numberOfSpectra); - unsigned int curveId = this->m_Controls.m_DataViewWidget->InsertCurve("Spectrum"); - this->m_Controls.m_DataViewWidget->SetCurveData(curveId, xValues, means, stdevs, stdevs); - this->m_Controls.m_DataViewWidget->SetErrorPen(curveId, QPen(Qt::blue)); - QwtSymbol* blueSymbol = new QwtSymbol(QwtSymbol::Rect, QColor(Qt::blue), QColor(Qt::blue), - QSize(8, 8)); - this->m_Controls.m_DataViewWidget->SetCurveSymbol(curveId, blueSymbol); - this->m_Controls.m_DataViewWidget->SetLegendAttribute(curveId, QwtPlotCurve::LegendShowSymbol); + for (unsigned int index = 0; index < numberOfSpectra; ++index) + { + means[index] = + statistics->GetStatisticsForTimeStep(index).GetValueConverted( + mitk::ImageStatisticsConstants::MEAN()); + stdevs[index] = + statistics->GetStatisticsForTimeStep(index).GetValueConverted( + mitk::ImageStatisticsConstants::STANDARDDEVIATION()); + } - QwtLegend* legend = new QwtLegend(); - legend->setFrameShape(QFrame::Box); - legend->setFrameShadow(QFrame::Sunken); - legend->setLineWidth(1); - this->m_Controls.m_DataViewWidget->SetLegend(legend, QwtPlot::BottomLegend); + QmitkPlotWidget::DataVector xValues = this->m_zSpectrum; - m_Controls.m_DataViewWidget->GetPlot()->axisScaleEngine(QwtPlot::Axis::xBottom)->setAttributes(QwtScaleEngine::Inverted); + RemoveMZeros(xValues, means, stdevs); + ::SortVectors(xValues, std::less(), xValues, means, stdevs); - this->m_Controls.m_DataViewWidget->Replot(); - m_Controls.labelWarning->setVisible(false); + unsigned int curveId = this->m_Controls.m_DataViewWidget->InsertCurve("Spectrum"); + this->m_Controls.m_DataViewWidget->SetCurveData(curveId, xValues, means, stdevs, stdevs); + this->m_Controls.m_DataViewWidget->SetErrorPen(curveId, QPen(Qt::blue)); + QwtSymbol *blueSymbol = new QwtSymbol(QwtSymbol::Rect, QColor(Qt::blue), QColor(Qt::blue), QSize(8, 8)); + this->m_Controls.m_DataViewWidget->SetCurveSymbol(curveId, blueSymbol); + this->m_Controls.m_DataViewWidget->SetLegendAttribute(curveId, QwtPlotCurve::LegendShowSymbol); - if (this->m_Controls.fixedRangeCheckBox->isChecked()) - { - this->m_Controls.m_DataViewWidget->GetPlot()->setAxisAutoScale(2, false); - this->m_Controls.m_DataViewWidget->GetPlot()->setAxisScale(2, this->m_Controls.fixedRangeLowerDoubleSpinBox->value(), this->m_Controls.fixedRangeUpperDoubleSpinBox->value()); - } - else - { - this->m_Controls.m_DataViewWidget->GetPlot()->setAxisAutoScale(2, true); - } + QwtLegend *legend = new QwtLegend(); + legend->setFrameShape(QFrame::Box); + legend->setFrameShadow(QFrame::Sunken); + legend->setLineWidth(1); + this->m_Controls.m_DataViewWidget->SetLegend(legend, QwtPlot::BottomLegend); - if(this->DataSanityCheck()) - { - this->FillStatisticsTableView(this->m_CalculatorThread->GetStatisticsData(), this->m_CalculatorThread->GetStatisticsImage()); + m_Controls.m_DataViewWidget->GetPlot() + ->axisScaleEngine(QwtPlot::Axis::xBottom) + ->setAttributes(QwtScaleEngine::Inverted); + + this->m_Controls.m_DataViewWidget->Replot(); + m_Controls.labelWarning->setVisible(false); + + m_Controls.m_StatisticsGroupBox->setEnabled(true); + m_Controls.m_StatisticsGroupBox->setEnabled(true); + + if (this->m_Controls.fixedRangeCheckBox->isChecked()) + { + this->m_Controls.m_DataViewWidget->GetPlot()->setAxisAutoScale(2, false); + this->m_Controls.m_DataViewWidget->GetPlot()->setAxisScale( + 2, + this->m_Controls.fixedRangeLowerDoubleSpinBox->value(), + this->m_Controls.fixedRangeUpperDoubleSpinBox->value()); + } + else + { + this->m_Controls.m_DataViewWidget->GetPlot()->setAxisAutoScale(2, true); + } } else { + m_Controls.labelWarning->setText(m_CalculatorJob->GetLastErrorMessage().c_str()); + m_Controls.labelWarning->setVisible(true); this->Clear(); } } void QmitkCESTStatisticsView::OnFixedRangeDoubleSpinBoxChanged() { if (this->m_Controls.fixedRangeCheckBox->isChecked()) { this->m_Controls.m_DataViewWidget->GetPlot()->setAxisAutoScale(2, false); - this->m_Controls.m_DataViewWidget->GetPlot()->setAxisScale(2, this->m_Controls.fixedRangeLowerDoubleSpinBox->value(), this->m_Controls.fixedRangeUpperDoubleSpinBox->value()); + this->m_Controls.m_DataViewWidget->GetPlot()->setAxisScale(2, + this->m_Controls.fixedRangeLowerDoubleSpinBox->value(), + this->m_Controls.fixedRangeUpperDoubleSpinBox->value()); } this->m_Controls.m_DataViewWidget->Replot(); } template -void QmitkCESTStatisticsView::PlotPointSet(itk::Image* image) +void QmitkCESTStatisticsView::PlotPointSet(itk::Image *image) { this->m_Controls.m_DataViewWidget->SetAxisTitle(QwtPlot::Axis::xBottom, "delta w"); this->m_Controls.m_DataViewWidget->SetAxisTitle(QwtPlot::Axis::yLeft, "z"); QmitkPlotWidget::DataVector::size_type numberOfSpectra = this->m_zSpectrum.size(); mitk::PointSet::Pointer internalPointset; if (m_PointSet.IsNotNull()) { internalPointset = m_PointSet; } else { internalPointset = m_CrosshairPointSet; } if (internalPointset.IsNull()) { return; } if (!this->DataSanityCheck()) { m_Controls.labelWarning->setText("Data can not be plotted, internally inconsistent."); m_Controls.labelWarning->show(); return; } auto maxIndex = internalPointset->GetMaxId().Index(); for (std::size_t number = 0; number < maxIndex + 1; ++number) { mitk::PointSet::PointType point; if (!internalPointset->GetPointIfExists(number, &point)) { continue; } if (!this->m_ZImage->GetGeometry()->IsInside(point)) { continue; } itk::Index<3> itkIndex; this->m_ZImage->GetGeometry()->WorldToIndex(point, itkIndex); itk::Index itkIndexTime; itkIndexTime[0] = itkIndex[0]; itkIndexTime[1] = itkIndex[1]; itkIndexTime[2] = itkIndex[2]; QmitkPlotWidget::DataVector values(numberOfSpectra); for (std::size_t step = 0; step < numberOfSpectra; ++step) { - if( VImageDimension == 4 ) + if (VImageDimension == 4) { itkIndexTime[3] = step; } values[step] = image->GetPixel(itkIndexTime); } std::stringstream name; name << "Point " << number; // Qcolor enums go from 0 to 19, but 19 is transparent and 0,1 are for bitmaps // 3 is white and thus not visible QColor color(static_cast(number % 17 + 4)); QmitkPlotWidget::DataVector xValues = this->m_zSpectrum; RemoveMZeros(xValues, values); ::SortVectors(xValues, std::less(), xValues, values); unsigned int curveId = this->m_Controls.m_DataViewWidget->InsertCurve(name.str().c_str()); this->m_Controls.m_DataViewWidget->SetCurveData(curveId, xValues, values); this->m_Controls.m_DataViewWidget->SetCurvePen(curveId, QPen(color)); - QwtSymbol* symbol = new QwtSymbol(QwtSymbol::Rect, color, color, - QSize(8, 8)); + QwtSymbol *symbol = new QwtSymbol(QwtSymbol::Rect, color, color, QSize(8, 8)); this->m_Controls.m_DataViewWidget->SetCurveSymbol(curveId, symbol); this->m_Controls.m_DataViewWidget->SetLegendAttribute(curveId, QwtPlotCurve::LegendShowSymbol); } if (this->m_Controls.fixedRangeCheckBox->isChecked()) { this->m_Controls.m_DataViewWidget->GetPlot()->setAxisAutoScale(2, false); - this->m_Controls.m_DataViewWidget->GetPlot()->setAxisScale(2, this->m_Controls.fixedRangeLowerDoubleSpinBox->value(), this->m_Controls.fixedRangeUpperDoubleSpinBox->value()); + this->m_Controls.m_DataViewWidget->GetPlot()->setAxisScale(2, + this->m_Controls.fixedRangeLowerDoubleSpinBox->value(), + this->m_Controls.fixedRangeUpperDoubleSpinBox->value()); } else { this->m_Controls.m_DataViewWidget->GetPlot()->setAxisAutoScale(2, true); } - QwtLegend* legend = new QwtLegend(); + QwtLegend *legend = new QwtLegend(); legend->setFrameShape(QFrame::Box); legend->setFrameShadow(QFrame::Sunken); legend->setLineWidth(1); this->m_Controls.m_DataViewWidget->SetLegend(legend, QwtPlot::BottomLegend); - m_Controls.m_DataViewWidget->GetPlot()->axisScaleEngine(QwtPlot::Axis::xBottom)->setAttributes(QwtScaleEngine::Inverted); + m_Controls.m_DataViewWidget->GetPlot() + ->axisScaleEngine(QwtPlot::Axis::xBottom) + ->setAttributes(QwtScaleEngine::Inverted); this->m_Controls.m_DataViewWidget->Replot(); m_Controls.labelWarning->setVisible(false); - } void QmitkCESTStatisticsView::OnFixedRangeCheckBoxToggled(bool state) { this->m_Controls.fixedRangeLowerDoubleSpinBox->setEnabled(state); this->m_Controls.fixedRangeUpperDoubleSpinBox->setEnabled(state); } -void QmitkCESTStatisticsView::RemoveMZeros(QmitkPlotWidget::DataVector& xValues, QmitkPlotWidget::DataVector& yValues) +void QmitkCESTStatisticsView::RemoveMZeros(QmitkPlotWidget::DataVector &xValues, QmitkPlotWidget::DataVector &yValues) { QmitkPlotWidget::DataVector tempX; QmitkPlotWidget::DataVector tempY; for (std::size_t index = 0; index < xValues.size(); ++index) { if ((xValues.at(index) < -299) || (xValues.at(index)) > 299) { // do not include } else { tempX.push_back(xValues.at(index)); tempY.push_back(yValues.at(index)); } } xValues = tempX; yValues = tempY; } -void QmitkCESTStatisticsView::RemoveMZeros(QmitkPlotWidget::DataVector& xValues, QmitkPlotWidget::DataVector& yValues, QmitkPlotWidget::DataVector& stdDevs) +void QmitkCESTStatisticsView::RemoveMZeros(QmitkPlotWidget::DataVector &xValues, + QmitkPlotWidget::DataVector &yValues, + QmitkPlotWidget::DataVector &stdDevs) { QmitkPlotWidget::DataVector tempX; QmitkPlotWidget::DataVector tempY; QmitkPlotWidget::DataVector tempDevs; for (std::size_t index = 0; index < xValues.size(); ++index) { if ((xValues.at(index) < -299) || (xValues.at(index)) > 299) { // do not include } else { tempX.push_back(xValues.at(index)); tempY.push_back(yValues.at(index)); tempDevs.push_back(stdDevs.at(index)); } } xValues = tempX; yValues = tempY; stdDevs = tempDevs; } void QmitkCESTStatisticsView::OnThreeDimToFourDimPushButtonClicked() { QList nodes = this->GetDataManagerSelection(); - if (nodes.empty()) return; + if (nodes.empty()) + return; - mitk::DataNode* node = nodes.front(); + mitk::DataNode *node = nodes.front(); if (!node) { // Nothing selected. Inform the user and return - QMessageBox::information( nullptr, "CEST View", "Please load and select an image before starting image processing."); + QMessageBox::information(nullptr, "CEST View", "Please load and select an image before starting image processing."); 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(); + 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 ); + mitk::Image *image = dynamic_cast(data); if (image) { if (image->GetDimension() == 4) { AccessFixedDimensionByItk(image, CopyTimesteps, 4); } this->Clear(); } } } template -void QmitkCESTStatisticsView::CopyTimesteps(itk::Image* image) +void QmitkCESTStatisticsView::CopyTimesteps(itk::Image *image) { - typedef itk::Image ImageType; - //typedef itk::PasteImageFilter PasteImageFilterType; + typedef itk::Image ImageType; + // typedef itk::PasteImageFilter PasteImageFilterType; unsigned int numberOfTimesteps = image->GetLargestPossibleRegion().GetSize(3); typename ImageType::RegionType sourceRegion = image->GetLargestPossibleRegion(); sourceRegion.SetSize(3, 1); typename ImageType::RegionType targetRegion = image->GetLargestPossibleRegion(); targetRegion.SetSize(3, 1); for (unsigned int timestep = 1; timestep < numberOfTimesteps; ++timestep) { targetRegion.SetIndex(3, timestep); itk::ImageRegionConstIterator sourceIterator(image, sourceRegion); itk::ImageRegionIterator targetIterator(image, targetRegion); while (!sourceIterator.IsAtEnd()) { targetIterator.Set(sourceIterator.Get()); ++sourceIterator; ++targetIterator; } } } -bool QmitkCESTStatisticsView::SetZSpectrum(mitk::StringProperty* zSpectrumProperty) +bool QmitkCESTStatisticsView::SetZSpectrum(mitk::StringProperty *zSpectrumProperty) { if (zSpectrumProperty == nullptr) { return false; } mitk::LocaleSwitch localeSwitch("C"); std::string zSpectrumString = zSpectrumProperty->GetValueAsString(); std::istringstream iss(zSpectrumString); std::vector zSpectra; - std::copy(std::istream_iterator(iss), - std::istream_iterator(), - std::back_inserter(zSpectra)); + std::copy( + std::istream_iterator(iss), std::istream_iterator(), std::back_inserter(zSpectra)); m_zSpectrum.clear(); m_zSpectrum.resize(0); for (auto const &spectrumString : zSpectra) { m_zSpectrum.push_back(std::stod(spectrumString)); } return (m_zSpectrum.size() > 0); } -void QmitkCESTStatisticsView::FillStatisticsTableView( - const std::vector &s, - const mitk::Image *image) -{ - this->m_Controls.m_StatisticsTable->setColumnCount(image->GetTimeSteps()); - this->m_Controls.m_StatisticsTable->horizontalHeader()->setVisible(image->GetTimeSteps() > 1); - - int decimals = 2; - - mitk::PixelType doublePix = mitk::MakeScalarPixelType< double >(); - mitk::PixelType floatPix = mitk::MakeScalarPixelType< float >(); - if (image->GetPixelType() == doublePix || image->GetPixelType() == floatPix) - { - decimals = 5; - } - - for (unsigned int t = 0; t < image->GetTimeSteps(); t++) - { - this->m_Controls.m_StatisticsTable->setHorizontalHeaderItem(t, - new QTableWidgetItem(QString::number(m_zSpectrum[t]))); - - this->m_Controls.m_StatisticsTable->setItem(0, t, new QTableWidgetItem( - QString("%1").arg(s[t]->GetMean(), 0, 'f', decimals))); - this->m_Controls.m_StatisticsTable->setItem(1, t, new QTableWidgetItem( - QString("%1").arg(s[t]->GetStd(), 0, 'f', decimals))); - - this->m_Controls.m_StatisticsTable->setItem(2, t, new QTableWidgetItem( - QString("%1").arg(s[t]->GetRMS(), 0, 'f', decimals))); - - QString max; max.append(QString("%1").arg(s[t]->GetMax(), 0, 'f', decimals)); - max += " ("; - for (unsigned int i = 0; iGetMaxIndex().size(); i++) - { - max += QString::number(s[t]->GetMaxIndex()[i]); - if (iGetMaxIndex().size() - 1) - max += ","; - } - max += ")"; - this->m_Controls.m_StatisticsTable->setItem(3, t, new QTableWidgetItem(max)); - - QString min; min.append(QString("%1").arg(s[t]->GetMin(), 0, 'f', decimals)); - min += " ("; - for (unsigned int i = 0; iGetMinIndex().size(); i++) - { - min += QString::number(s[t]->GetMinIndex()[i]); - if (iGetMinIndex().size() - 1) - min += ","; - } - min += ")"; - this->m_Controls.m_StatisticsTable->setItem(4, t, new QTableWidgetItem(min)); - - this->m_Controls.m_StatisticsTable->setItem(5, t, new QTableWidgetItem( - QString("%1").arg(s[t]->GetN()))); - - const mitk::BaseGeometry *geometry = image->GetGeometry(); - if (geometry != nullptr) - { - const mitk::Vector3D &spacing = image->GetGeometry()->GetSpacing(); - double volume = spacing[0] * spacing[1] * spacing[2] * (double)s[t]->GetN(); - this->m_Controls.m_StatisticsTable->setItem(6, t, new QTableWidgetItem( - QString("%1").arg(volume, 0, 'f', decimals))); - } - else - { - this->m_Controls.m_StatisticsTable->setItem(6, t, new QTableWidgetItem( - "NA")); - } - } - - this->m_Controls.m_StatisticsTable->resizeColumnsToContents(); - int height = STAT_TABLE_BASE_HEIGHT; - - if (this->m_Controls.m_StatisticsTable->horizontalHeader()->isVisible()) - height += this->m_Controls.m_StatisticsTable->horizontalHeader()->height(); - - //if (this->m_Controls.m_StatisticsTable->horizontalScrollBar()->isVisible()) - // height += this->m_Controls.m_StatisticsTable->horizontalScrollBar()->height(); - - this->m_Controls.m_StatisticsTable->setMinimumHeight(height); - this->m_Controls.m_StatisticsGroupBox->setEnabled(true); - this->m_Controls.m_StatisticsTable->setEnabled(true); -} - -void QmitkCESTStatisticsView::InvalidateStatisticsTableView() -{ - this->m_Controls.m_StatisticsTable->horizontalHeader()->setVisible(false); - this->m_Controls.m_StatisticsTable->setColumnCount(1); - - for (int i = 0; i < this->m_Controls.m_StatisticsTable->rowCount(); ++i) - { - { - this->m_Controls.m_StatisticsTable->setItem(i, 0, new QTableWidgetItem("NA")); - } - } - - this->m_Controls.m_StatisticsTable->setMinimumHeight(STAT_TABLE_BASE_HEIGHT); - this->m_Controls.m_StatisticsTable->setEnabled(false); -} - bool QmitkCESTStatisticsView::DataSanityCheck() { QmitkPlotWidget::DataVector::size_type numberOfSpectra = m_zSpectrum.size(); // if we do not have a spectrum, the data can not be processed if (numberOfSpectra == 0) { return false; } // if we do not have CEST image data, the data can not be processed if (m_ZImage.IsNull()) { return false; } // if the CEST image data and the meta information do not match, the data can not be processed if (numberOfSpectra != m_ZImage->GetTimeSteps()) { MITK_INFO << "CEST meta information and number of volumes does not match."; return false; } // if we have neither a mask image, a point set nor a mask planar figure, we can not do statistics // statistics on the whole image would not make sense if (m_MaskImage.IsNull() && m_MaskPlanarFigure.IsNull() && m_PointSet.IsNull() && m_CrosshairPointSet->IsEmpty()) { return false; } // if we have a mask image and a mask planar figure, we can not do statistics // we do not know which one to use if (m_MaskImage.IsNotNull() && m_MaskPlanarFigure.IsNotNull()) { return false; } return true; } void QmitkCESTStatisticsView::Clear() { this->m_zSpectrum.clear(); this->m_zSpectrum.resize(0); this->m_ZImage = nullptr; this->m_MaskImage = nullptr; this->m_MaskPlanarFigure = nullptr; this->m_PointSet = nullptr; this->m_Controls.m_DataViewWidget->Clear(); - this->InvalidateStatisticsTableView(); this->m_Controls.m_StatisticsGroupBox->setEnabled(false); -} - -void QmitkCESTStatisticsView::OnCopyStatisticsToClipboardPushButtonClicked() -{ - QLocale tempLocal; - QLocale::setDefault(QLocale(QLocale::English, QLocale::UnitedStates)); - - const std::vector &statistics = - this->m_CalculatorThread->GetStatisticsData(); - - QmitkPlotWidget::DataVector::size_type size = m_zSpectrum.size(); - - QString clipboard("delta_w \t Mean \t StdDev \t RMS \t Max \t Min \t N\n"); - for (QmitkPlotWidget::DataVector::size_type index = 0; index < size; ++index) - { - // Copy statistics to clipboard ("%Ln" will use the default locale for - // number formatting) - clipboard = clipboard.append("%L1 \t %L2 \t %L3 \t %L4 \t %L5 \t %L6 \t %L7\n") - .arg(m_zSpectrum[index], 0, 'f', 10) - .arg(statistics[index]->GetMean(), 0, 'f', 10) - .arg(statistics[index]->GetStd(), 0, 'f', 10) - .arg(statistics[index]->GetRMS(), 0, 'f', 10) - .arg(statistics[index]->GetMax(), 0, 'f', 10) - .arg(statistics[index]->GetMin(), 0, 'f', 10) - .arg(statistics[index]->GetN()); - } - - QApplication::clipboard()->setText( - clipboard, QClipboard::Clipboard); - - QLocale::setDefault(tempLocal); + this->m_Controls.widget_statistics->SetImageNodes({}); + this->m_Controls.widget_statistics->SetMaskNodes({}); } void QmitkCESTStatisticsView::OnSliceChanged() { mitk::Point3D currentSelectedPosition = this->GetRenderWindowPart()->GetSelectedPosition(nullptr); - unsigned int currentSelectedTimeStep = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos(); + unsigned int currentSelectedTimeStep = + this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos(); - if (m_currentSelectedPosition != currentSelectedPosition - || m_currentSelectedTimeStep != currentSelectedTimeStep) - //|| m_selectedNodeTime > m_currentPositionTime) + if (m_currentSelectedPosition != currentSelectedPosition || m_currentSelectedTimeStep != currentSelectedTimeStep) + //|| m_selectedNodeTime > m_currentPositionTime) { - //the current position has been changed or the selected node has been changed since the last position validation -> check position + // the current position has been changed or the selected node has been changed since the last position validation -> + // check position m_currentSelectedPosition = currentSelectedPosition; m_currentSelectedTimeStep = currentSelectedTimeStep; m_currentPositionTime.Modified(); m_CrosshairPointSet->Clear(); m_CrosshairPointSet->SetPoint(0, m_currentSelectedPosition); QList nodes = this->GetDataManagerSelection(); - if (nodes.empty() || nodes.size() > 1) return; + if (nodes.empty() || nodes.size() > 1) + return; - mitk::DataNode* node = nodes.front(); + mitk::DataNode *node = nodes.front(); if (!node) { return; } if (dynamic_cast(node->GetData()) != nullptr) { m_Controls.labelWarning->setVisible(false); bool zSpectrumSet = SetZSpectrum(dynamic_cast( node->GetData()->GetProperty(mitk::CustomTagParser::m_OffsetsPropertyName.c_str()).GetPointer())); if (zSpectrumSet) { m_ZImage = dynamic_cast(node->GetData()); } else { return; } } else { return; } this->m_Controls.m_DataViewWidget->Clear(); AccessFixedDimensionByItk(m_ZImage, PlotPointSet, 4); - } } diff --git a/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsView.h b/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsView.h index d402f9ac14..e9c29ccd3e 100644 --- a/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsView.h +++ b/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsView.h @@ -1,150 +1,139 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QmitkCESTStatisticsView_h #define QmitkCESTStatisticsView_h #include #include #include #include "ui_QmitkCESTStatisticsViewControls.h" -#include +#include #include #include /** \brief QmitkCESTStatisticsView \warning Basic statistics view for CEST data. \sa QmitkAbstractView \ingroup ${plugin_target}_internal */ class QmitkCESTStatisticsView : public QmitkAbstractView, public mitk::IRenderWindowPartListener { // 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; /*! \brief default constructor */ QmitkCESTStatisticsView(QObject *parent = nullptr, const char *name = nullptr); /*! \brief default destructor */ virtual ~QmitkCESTStatisticsView(); protected slots: /// \brief Called when the user clicks the GUI button void OnThreeDimToFourDimPushButtonClicked(); /// \brief takes care of processing the computed data void OnThreadedStatisticsCalculationEnds(); - /// \brief copy statistics to clipboard - void OnCopyStatisticsToClipboardPushButtonClicked(); - /// \brief Toggle whether or not the plot uses a fixed x range void OnFixedRangeCheckBoxToggled(bool state); /// \brief Adapt axis scale when manual ranges are set void OnFixedRangeDoubleSpinBoxChanged(); /// \brief What to do if the crosshair moves void OnSliceChanged(); protected: virtual void CreateQtPartControl(QWidget *parent) override; virtual void SetFocus() override; virtual void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart); virtual void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart); /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged( berry::IWorkbenchPart::Pointer source, const QList& nodes ) override; - /** \brief Writes the calculated statistics to the GUI */ - void FillStatisticsTableView(const std::vector &s, - const mitk::Image *image); - - - /** \brief Removes statistics from the GUI */ - void InvalidateStatisticsTableView(); - /// parse string and set data vector returns true if succesfull bool SetZSpectrum(mitk::StringProperty* zSpectrumProperty); /** Checks whether the currently set data appears reasonable */ bool DataSanityCheck(); /** Fills the plot based on a point set * * This will only use the first timestep */ template void PlotPointSet(itk::Image* image); /** Deletes all data */ void Clear(); /** Remove MZeros * * Will remove the data for the M0 images from the given input */ void RemoveMZeros(QmitkPlotWidget::DataVector& xValues, QmitkPlotWidget::DataVector& yValues); void RemoveMZeros(QmitkPlotWidget::DataVector& xValues, QmitkPlotWidget::DataVector& yValues, QmitkPlotWidget::DataVector& stdDevs); /** Copies the first timestep of a segmentation to all others */ template void CopyTimesteps(itk::Image* image); Ui::QmitkCESTStatisticsViewControls m_Controls; - QmitkImageStatisticsCalculationThread* m_CalculatorThread; + QmitkImageStatisticsCalculationJob* m_CalculatorJob; QmitkPlotWidget::DataVector m_zSpectrum; mitk::Image::Pointer m_ZImage; mitk::Image::Pointer m_MaskImage; mitk::PlanarFigure::Pointer m_MaskPlanarFigure; mitk::PointSet::Pointer m_PointSet; mitk::PointSet::Pointer m_CrosshairPointSet; QmitkSliceNavigationListener m_SliceChangeListener; itk::TimeStamp m_selectedNodeTime; itk::TimeStamp m_currentPositionTime; /** @brief currently valid selected position in the inspector*/ mitk::Point3D m_currentSelectedPosition; /** @brief indicates if the currently selected position is valid for the currently selected fit. * This it is within the input image */ unsigned int m_currentSelectedTimeStep; }; #endif // QmitkCESTStatisticsView_h diff --git a/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsViewControls.ui b/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsViewControls.ui index 6ecd840443..dc3bc4b724 100644 --- a/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsViewControls.ui +++ b/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsViewControls.ui @@ -1,373 +1,314 @@ QmitkCESTStatisticsViewControls 0 0 696 963 0 0 QmitkTemplate QLabel { color: rgb(255, 0, 0) } Please select an image! Do image processing Copy first time step to rest false + + + 0 + 200 + + Statistics 9 9 9 - - - false - - - - 100 - 180 - - - - - 16777215 - 16777215 - - - - Qt::ScrollBarAsNeeded - - - Qt::ScrollBarAsNeeded - - - true + + + + + + + + 255 + 0 + 0 + + + + + + + 255 + 0 + 0 + + + + + + + 255 + 0 + 0 + + + + + + + + + 255 + 0 + 0 + + + + + + + 255 + 0 + 0 + + + + + + + 255 + 0 + 0 + + + + + + + + + 120 + 120 + 120 + + + + + + + 120 + 120 + 120 + + + + + + + 120 + 120 + 120 + + + + + - - QAbstractItemView::NoEditTriggers - - - true - - - true - - - Qt::DotLine - - - false - - - 7 - - - false - - - false - - - 80 - - - true - - - 80 - - - false - - - true - - - true - - - false - - - 25 - - - 25 - - - false - - - false - - - - Mean - - - - - StdDev - - - - - RMS - - - - - Max - - - - - Min - - - - - N - - - - - V (mm³) - - - - - 0 - - - - - - - - - 0 - - - 0 - - - 0 - - - 0 - - - 0 - - - - - Copy to Clipboard - - - - - - - Qt::Horizontal - - - - 40 - 20 - - - - - QLayout::SetDefaultConstraint 0 0 Define manual range Qt::Horizontal 40 20 Lower limit false -299.899999999999977 299.990000000000009 Upper limit false 2 -299.899999999999977 299.990000000000009 Qt::Horizontal 40 20 Plot 0 0 0 400 Qt::Vertical QSizePolicy::Expanding 20 220 QmitkPlotWidget QWidget
QmitkPlotWidget.h
1 + + QmitkImageStatisticsWidget + QWidget +
QmitkImageStatisticsWidget.h
+ 1 + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingView.cpp index ec81a1398f..fb9f58de2e 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingView.cpp @@ -1,233 +1,232 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkDenoisingView.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include const std::string QmitkDenoisingView::VIEW_ID = "org.mitk.views.denoisingview"; QmitkDenoisingView::QmitkDenoisingView() : QmitkAbstractView() , m_Controls( 0 ) , m_ImageNode(nullptr) { } QmitkDenoisingView::~QmitkDenoisingView() { } void QmitkDenoisingView::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::QmitkDenoisingViewControls; m_Controls->setupUi( parent ); connect( (QObject*)(m_Controls->m_ApplyButton), SIGNAL(clicked()), this, SLOT(StartDenoising())); connect( (QObject*)(m_Controls->m_SelectFilterComboBox), SIGNAL(activated(int)), this, SLOT(UpdateGui())); connect( (QObject*)(m_Controls->m_InputImageBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui())); m_Controls->m_InputImageBox->SetDataStorage(this->GetDataStorage()); mitk::NodePredicateIsDWI::Pointer isImagePredicate = mitk::NodePredicateIsDWI::New(); m_Controls->m_InputImageBox->SetPredicate( isImagePredicate ); UpdateGui(); } } void QmitkDenoisingView::SetFocus() { m_Controls->m_SelectFilterComboBox->setFocus(); } void QmitkDenoisingView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& ) { } void QmitkDenoisingView::StartDenoising() { typedef itk::DiscreteGaussianImageFilter < DwiVolumeType, DwiVolumeType > GaussianFilterType; typedef itk::PatchBasedDenoisingImageFilter < DwiVolumeType, DwiVolumeType > NlmFilterType; typedef itk::VectorImageToImageFilter < DiffusionPixelType > ExtractFilterType; typedef itk::ComposeImageFilter < itk::Image > ComposeFilterType; m_ImageNode = m_Controls->m_InputImageBox->GetSelectedNode(); mitk::Image::Pointer input_image = dynamic_cast(m_ImageNode->GetData()); if (!mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(input_image)) { QMessageBox::warning(nullptr, "Image not processed", "Input is not a diffusion-weighted image!"); return; } DwiImageType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(input_image); mitk::Image::Pointer denoised_image = nullptr; mitk::DataNode::Pointer denoised_image_node = mitk::DataNode::New(); switch (m_Controls->m_SelectFilterComboBox->currentIndex()) { case 0: { ComposeFilterType::Pointer composer = ComposeFilterType::New(); for (unsigned int i=0; iGetVectorLength(); ++i) { ExtractFilterType::Pointer extractor = ExtractFilterType::New(); extractor->SetInput( itkVectorImagePointer ); extractor->SetIndex( i ); extractor->Update(); DwiVolumeType::Pointer gradient_volume = extractor->GetOutput(); itk::TotalVariationDenoisingImageFilter< DwiVolumeType, DwiVolumeType >::Pointer filter = itk::TotalVariationDenoisingImageFilter< DwiVolumeType, DwiVolumeType >::New(); filter->SetInput(gradient_volume); filter->SetLambda(m_Controls->m_TvLambdaBox->value()); filter->SetNumberIterations(m_Controls->m_TvIterationsBox->value()); filter->Update(); composer->SetInput(i, filter->GetOutput()); } composer->Update(); denoised_image = mitk::GrabItkImageMemory(composer->GetOutput()); denoised_image_node->SetName( "TotalVariation" ); break; } case 1: { ExtractFilterType::Pointer extractor = ExtractFilterType::New(); extractor->SetInput( itkVectorImagePointer ); ComposeFilterType::Pointer composer = ComposeFilterType::New(); for (unsigned int i = 0; i < itkVectorImagePointer->GetVectorLength(); ++i) { extractor->SetIndex(i); extractor->Update(); GaussianFilterType::Pointer filter = GaussianFilterType::New(); filter->SetVariance(m_Controls->m_GaussVarianceBox->value()); filter->SetInput(extractor->GetOutput()); filter->Update(); composer->SetInput(i, filter->GetOutput()); } composer->Update(); denoised_image = mitk::GrabItkImageMemory(composer->GetOutput()); denoised_image_node->SetName( "Gauss" ); break; } case 2: { typedef itk::Statistics::GaussianRandomSpatialNeighborSubsampler< NlmFilterType::PatchSampleType, DwiVolumeType::RegionType > SamplerType; // sampling the image to find similar patches SamplerType::Pointer sampler = SamplerType::New(); sampler->SetRadius( m_Controls->m_NlmSearchRadiusBox->value() ); sampler->SetVariance( m_Controls->m_NlmSearchRadiusBox->value()*m_Controls->m_NlmSearchRadiusBox->value() ); sampler->SetNumberOfResultsRequested( m_Controls->m_NlmNumPatchesBox->value() ); MITK_INFO << "Starting NLM denoising"; ExtractFilterType::Pointer extractor = ExtractFilterType::New(); extractor->SetInput( itkVectorImagePointer ); ComposeFilterType::Pointer composer = ComposeFilterType::New(); for (unsigned int i = 0; i < itkVectorImagePointer->GetVectorLength(); ++i) { extractor->SetIndex(i); extractor->Update(); NlmFilterType::Pointer filter = NlmFilterType::New(); filter->SetInput(extractor->GetOutput()); filter->SetPatchRadius(m_Controls->m_NlmPatchSizeBox->value()); filter->SetNoiseModel(NlmFilterType::RICIAN); filter->UseSmoothDiscPatchWeightsOn(); filter->UseFastTensorComputationsOn(); filter->SetNumberOfIterations(m_Controls->m_NlmIterationsBox->value()); filter->SetSmoothingWeight( 1 ); filter->SetKernelBandwidthEstimation(true); filter->SetSampler( sampler ); filter->Update(); composer->SetInput(i, filter->GetOutput()); MITK_INFO << "Gradient " << i << " finished"; } composer->Update(); denoised_image = mitk::GrabItkImageMemory(composer->GetOutput()); denoised_image_node->SetName( "NLM" ); break; } } - mitk::DiffusionPropertyHelper::SetGradientContainer(denoised_image, mitk::DiffusionPropertyHelper::GetGradientContainer(input_image) ); - mitk::DiffusionPropertyHelper::SetReferenceBValue(denoised_image, mitk::DiffusionPropertyHelper::GetReferenceBValue(input_image) ); - mitk::DiffusionPropertyHelper::InitializeImage(denoised_image); + mitk::DiffusionPropertyHelper::CopyProperties(input_image, denoised_image, true); + mitk::DiffusionPropertyHelper::InitializeImage( denoised_image ); denoised_image_node->SetData( denoised_image ); GetDataStorage()->Add(denoised_image_node, m_ImageNode); } void QmitkDenoisingView::UpdateGui() { m_Controls->m_ApplyButton->setEnabled(false); m_Controls->m_TvFrame->setVisible(false); m_Controls->m_NlmFrame->setVisible(false); m_Controls->m_GaussFrame->setVisible(false); switch (m_Controls->m_SelectFilterComboBox->currentIndex()) { case 0: { m_Controls->m_TvFrame->setVisible(true); break; } case 1: { m_Controls->m_GaussFrame->setVisible(true); break; } case 2: { m_Controls->m_NlmFrame->setVisible(true); break; } } if (m_Controls->m_InputImageBox->GetSelectedNode().IsNotNull()) m_Controls->m_ApplyButton->setEnabled(true); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationView.cpp index dc37d11497..8b517283c0 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationView.cpp @@ -1,1165 +1,1165 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkFiberGenerationView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #define RAPIDXML_NO_EXCEPTIONS #include #include #include #include #include "usModuleRegistry.h" #include #include #include #include #include #include #include #include #include #include #include "mitkNodePredicateDataType.h" #include #include #include #include #define _USE_MATH_DEFINES #include const std::string QmitkFiberGenerationView::VIEW_ID = "org.mitk.views.fibergenerationview"; QmitkFiberGenerationView::QmitkFiberGenerationView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImageNode( nullptr ) { } // Destructor QmitkFiberGenerationView::~QmitkFiberGenerationView() { } void QmitkFiberGenerationView::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::QmitkFiberGenerationViewControls; m_Controls->setupUi( parent ); m_ParameterFile = QDir::currentPath()+"/param.ffp"; connect(static_cast(m_Controls->m_RandomPhantomButton), SIGNAL(clicked()), static_cast(this), SLOT(RandomPhantom())); connect(static_cast(m_Controls->m_GenerateFibersButton), SIGNAL(clicked()), static_cast(this), SLOT(GenerateFibers())); connect(static_cast(m_Controls->m_CircleButton), SIGNAL(clicked()), static_cast(this), SLOT(OnDrawROI())); connect(static_cast(m_Controls->m_FlipButton), SIGNAL(clicked()), static_cast(this), SLOT(OnFlipButton())); connect(static_cast(m_Controls->m_JoinBundlesButton), SIGNAL(clicked()), static_cast(this), SLOT(JoinBundles())); connect(static_cast(m_Controls->m_VarianceBox), SIGNAL(valueChanged(double)), static_cast(this), SLOT(OnVarianceChanged(double))); connect(static_cast(m_Controls->m_DistributionBox), SIGNAL(currentIndexChanged(int)), static_cast(this), SLOT(OnDistributionChanged(int))); connect(static_cast(m_Controls->m_FiberDensityBox), SIGNAL(valueChanged(int)), static_cast(this), SLOT(OnFiberDensityChanged(int))); connect(static_cast(m_Controls->m_FiberSamplingBox), SIGNAL(valueChanged(double)), static_cast(this), SLOT(OnFiberSamplingChanged(double))); connect(static_cast(m_Controls->m_TensionBox), SIGNAL(valueChanged(double)), static_cast(this), SLOT(OnTensionChanged(double))); connect(static_cast(m_Controls->m_ContinuityBox), SIGNAL(valueChanged(double)), static_cast(this), SLOT(OnContinuityChanged(double))); connect(static_cast(m_Controls->m_BiasBox), SIGNAL(valueChanged(double)), static_cast(this), SLOT(OnBiasChanged(double))); connect(static_cast(m_Controls->m_ConstantRadiusBox), SIGNAL(stateChanged(int)), static_cast(this), SLOT(OnConstantRadius(int))); connect(static_cast(m_Controls->m_CopyBundlesButton), SIGNAL(clicked()), static_cast(this), SLOT(CopyBundles())); connect(static_cast(m_Controls->m_TransformBundlesButton), SIGNAL(clicked()), static_cast(this), SLOT(ApplyTransform())); connect(static_cast(m_Controls->m_AlignOnGrid), SIGNAL(clicked()), static_cast(this), SLOT(AlignOnGrid())); connect(static_cast(m_Controls->m_FidAxis1), SIGNAL(editingFinished()), static_cast(this), SLOT(UpdateFiducialPosition())); connect(static_cast(m_Controls->m_FidAxis2), SIGNAL(editingFinished()), static_cast(this), SLOT(UpdateFiducialPosition())); connect(static_cast(m_Controls->m_FidPosX), SIGNAL(editingFinished()), static_cast(this), SLOT(UpdateFiducialPosition())); connect(static_cast(m_Controls->m_FidPosY), SIGNAL(editingFinished()), static_cast(this), SLOT(UpdateFiducialPosition())); connect(static_cast(m_Controls->m_FidPosZ), SIGNAL(editingFinished()), static_cast(this), SLOT(UpdateFiducialPosition())); connect(static_cast(m_Controls->m_FidTwist), SIGNAL(editingFinished()), static_cast(this), SLOT(UpdateFiducialPosition())); connect(static_cast(m_Controls->m_AdvancedOptionsBox), SIGNAL( stateChanged(int)), static_cast(this), SLOT(ShowAdvancedOptions(int))); connect(static_cast(m_Controls->m_SaveParametersButton), SIGNAL(clicked()), static_cast(this), SLOT(SaveParameters())); connect(static_cast(m_Controls->m_LoadParametersButton), SIGNAL(clicked()), static_cast(this), SLOT(LoadParameters())); OnDistributionChanged(0); } UpdateGui(); } void QmitkFiberGenerationView::RandomPhantom() { itk::RandomPhantomFilter::Pointer filter = itk::RandomPhantomFilter::New(); filter->SetNumTracts(m_Controls->m_NumBundlesBox->value()); - filter->setMinStreamlineDensity(m_Controls->m_MinDensityBox->value()); - filter->setMaxStreamlineDensity(m_Controls->m_MaxDensityBox->value()); + filter->SetMinStreamlineDensity(m_Controls->m_MinDensityBox->value()); + filter->SetMaxStreamlineDensity(m_Controls->m_MaxDensityBox->value()); mitk::Vector3D vol; vol[0] = m_Controls->m_VolumeSizeX->value(); vol[1] = m_Controls->m_VolumeSizeY->value(); vol[2] = m_Controls->m_VolumeSizeZ->value(); - filter->setVolumeSize(vol); - filter->setStepSizeMin(m_Controls->m_StepSizeMinBox->value()); - filter->setStepSizeMax(m_Controls->m_StepSizeMaxBox->value()); - filter->setCurvynessMin(m_Controls->m_CurvyMinBox->value()); - filter->setCurvynessMax(m_Controls->m_CurvyMaxBox->value()); - filter->setStartRadiusMin(m_Controls->m_SizeMinBox->value()); - filter->setStartRadiusMax(m_Controls->m_SizeMaxBox->value()); - filter->setMinTwist(m_Controls->m_MinTwistBox->value()); - filter->setMaxTwist(m_Controls->m_MaxTwistBox->value()); + filter->SetVolumeSize(vol); + filter->SetStepSizeMin(m_Controls->m_StepSizeMinBox->value()); + filter->SetStepSizeMax(m_Controls->m_StepSizeMaxBox->value()); + filter->SetCurvynessMin(m_Controls->m_CurvyMinBox->value()); + filter->SetCurvynessMax(m_Controls->m_CurvyMaxBox->value()); + filter->SetStartRadiusMin(m_Controls->m_SizeMinBox->value()); + filter->SetStartRadiusMax(m_Controls->m_SizeMaxBox->value()); + filter->SetMinTwist(m_Controls->m_MinTwistBox->value()); + filter->SetMaxTwist(m_Controls->m_MaxTwistBox->value()); filter->Update(); auto fibs = filter->GetFiberBundles(); std::vector< mitk::DataNode::Pointer > fiber_nodes; int c = 1; for (auto fib : fibs) { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( fib ); node->SetName("Bundle_" + boost::lexical_cast(c)); GetDataStorage()->Add(node); fiber_nodes.push_back(node); ++c; } // mitk::RenderingManager::GetInstance()->RequestUpdateAll(); mitk::RenderingManager::GetInstance()->InitializeViews(GetDataStorage()->ComputeVisibleBoundingGeometry3D()); } void QmitkFiberGenerationView::UpdateParametersFromGui() { m_Parameters.ClearFiberParameters(); m_Parameters.m_Misc.m_CheckAdvancedFiberOptionsBox = m_Controls->m_AdvancedOptionsBox->isChecked(); switch(m_Controls->m_DistributionBox->currentIndex()) { case 0: m_Parameters.m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; break; case 1: m_Parameters.m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN; break; default: m_Parameters.m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; } m_Parameters.m_FiberGen.m_Variance = m_Controls->m_VarianceBox->value(); m_Parameters.m_FiberGen.m_Density = m_Controls->m_FiberDensityBox->value(); m_Parameters.m_FiberGen.m_Sampling = m_Controls->m_FiberSamplingBox->value(); m_Parameters.m_FiberGen.m_Tension = m_Controls->m_TensionBox->value(); m_Parameters.m_FiberGen.m_Continuity = m_Controls->m_ContinuityBox->value(); m_Parameters.m_FiberGen.m_Bias = m_Controls->m_BiasBox->value(); m_Parameters.m_FiberGen.m_Rotation[0] = m_Controls->m_XrotBox->value(); m_Parameters.m_FiberGen.m_Rotation[1] = m_Controls->m_YrotBox->value(); m_Parameters.m_FiberGen.m_Rotation[2] = m_Controls->m_ZrotBox->value(); m_Parameters.m_FiberGen.m_Translation[0] = m_Controls->m_XtransBox->value(); m_Parameters.m_FiberGen.m_Translation[1] = m_Controls->m_YtransBox->value(); m_Parameters.m_FiberGen.m_Translation[2] = m_Controls->m_ZtransBox->value(); m_Parameters.m_FiberGen.m_Scale[0] = m_Controls->m_XscaleBox->value(); m_Parameters.m_FiberGen.m_Scale[1] = m_Controls->m_YscaleBox->value(); m_Parameters.m_FiberGen.m_Scale[2] = m_Controls->m_ZscaleBox->value(); m_Parameters.m_Misc.m_CheckRealTimeFibersBox = m_Controls->m_RealTimeFibers->isChecked(); m_Parameters.m_Misc.m_CheckAdvancedFiberOptionsBox = m_Controls->m_AdvancedOptionsBox->isChecked(); m_Parameters.m_Misc.m_CheckIncludeFiducialsBox = m_Controls->m_IncludeFiducials->isChecked(); m_Parameters.m_Misc.m_CheckConstantRadiusBox = m_Controls->m_ConstantRadiusBox->isChecked(); } void QmitkFiberGenerationView::SaveParameters(QString filename) { UpdateParametersFromGui(); m_Parameters.SaveParameters(filename.toStdString()); m_ParameterFile = filename; } void QmitkFiberGenerationView::SaveParameters() { QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), m_ParameterFile, tr("Fiberfox Parameters (*.ffp)") ); SaveParameters(filename); } void QmitkFiberGenerationView::LoadParameters() { QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QString(itksys::SystemTools::GetFilenamePath(m_ParameterFile.toStdString()).c_str()), tr("Fiberfox Parameters (*.ffp)") ); if(filename.isEmpty() || filename.isNull()) return; m_ParameterFile = filename; m_Parameters.LoadParameters(filename.toStdString()); if (m_Parameters.m_MissingTags.size()>0) { QString missing("Parameter file might be corrupted. The following parameters could not be read: "); missing += QString(m_Parameters.m_MissingTags.c_str()); missing += "\nDefault values have been assigned to the missing parameters."; QMessageBox::information( nullptr, "Warning!", missing); } m_Controls->m_RealTimeFibers->setChecked(m_Parameters.m_Misc.m_CheckRealTimeFibersBox); m_Controls->m_AdvancedOptionsBox->setChecked(m_Parameters.m_Misc.m_CheckAdvancedFiberOptionsBox); m_Controls->m_IncludeFiducials->setChecked(m_Parameters.m_Misc.m_CheckIncludeFiducialsBox); m_Controls->m_ConstantRadiusBox->setChecked(m_Parameters.m_Misc.m_CheckConstantRadiusBox); m_Controls->m_DistributionBox->setCurrentIndex(m_Parameters.m_FiberGen.m_Distribution); m_Controls->m_VarianceBox->setValue(m_Parameters.m_FiberGen.m_Variance); m_Controls->m_FiberDensityBox->setValue(m_Parameters.m_FiberGen.m_Density); m_Controls->m_FiberSamplingBox->setValue(m_Parameters.m_FiberGen.m_Sampling); m_Controls->m_TensionBox->setValue(m_Parameters.m_FiberGen.m_Tension); m_Controls->m_ContinuityBox->setValue(m_Parameters.m_FiberGen.m_Continuity); m_Controls->m_BiasBox->setValue(m_Parameters.m_FiberGen.m_Bias); m_Controls->m_XrotBox->setValue(m_Parameters.m_FiberGen.m_Rotation[0]); m_Controls->m_YrotBox->setValue(m_Parameters.m_FiberGen.m_Rotation[1]); m_Controls->m_ZrotBox->setValue(m_Parameters.m_FiberGen.m_Rotation[2]); m_Controls->m_XtransBox->setValue(m_Parameters.m_FiberGen.m_Translation[0]); m_Controls->m_YtransBox->setValue(m_Parameters.m_FiberGen.m_Translation[1]); m_Controls->m_ZtransBox->setValue(m_Parameters.m_FiberGen.m_Translation[2]); m_Controls->m_XscaleBox->setValue(m_Parameters.m_FiberGen.m_Scale[0]); m_Controls->m_YscaleBox->setValue(m_Parameters.m_FiberGen.m_Scale[1]); m_Controls->m_ZscaleBox->setValue(m_Parameters.m_FiberGen.m_Scale[2]); } void QmitkFiberGenerationView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox->setChecked(true); } else { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox->setChecked(false); } } void QmitkFiberGenerationView::OnConstantRadius(int value) { if (value>0 && m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberGenerationView::OnDistributionChanged(int value) { if (value==1) m_Controls->m_VarianceBox->setVisible(true); else m_Controls->m_VarianceBox->setVisible(false); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberGenerationView::OnVarianceChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberGenerationView::OnFiberDensityChanged(int) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberGenerationView::OnFiberSamplingChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberGenerationView::OnTensionChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberGenerationView::OnContinuityChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberGenerationView::OnBiasChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberGenerationView::UpdateFiducialPosition() { if (m_SelectedFiducials.size()!=1) return; mitk::PlanarEllipse* pe = dynamic_cast(m_SelectedFiducials.at(0)->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Point3D origin; origin[0] = m_Controls->m_FidPosX->value(); origin[1] = m_Controls->m_FidPosY->value(); origin[2] = m_Controls->m_FidPosZ->value(); // transform control point coordinate into geometry translation auto p0 = pe->GetControlPoint(0); auto p1 = pe->GetControlPoint(1); auto p2 = pe->GetControlPoint(2); auto p3 = pe->GetControlPoint(3); auto v1 = p1 - p0; auto v2 = p2 - p0; auto angle_deg = m_Controls->m_FidTwist->value(); auto dot = std::cos(itk::Math::pi*angle_deg/180.0); vnl_matrix_fixed tRot; tRot[0][0] = dot; tRot[1][1] = tRot[0][0]; tRot[1][0] = sin(acos(tRot[0][0])); tRot[0][1] = -tRot[1][0]; if (angle_deg<0) tRot = tRot.transpose(); vnl_vector_fixed vt; vt[0]=1; vt[1]=0; vnl_vector_fixed v3 = tRot*vt; if (v1.GetNorm()<0.0001 || v2.GetNorm()<0.0001) { QMessageBox::information( nullptr, "", "Please select exactly one fiducial."); return; } v1.Normalize(); v2.Normalize(); p1 = p0 + v1*m_Controls->m_FidAxis1->value(); p2 = p0 + v2*m_Controls->m_FidAxis2->value(); p3 = p0 + mitk::Vector2D(v3); pe->SetControlPoint(1, p1); pe->SetControlPoint(2, p2); pe->SetControlPoint(3, p3); geom->SetOrigin(origin); pe->Modified(); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); UpdateGui(); } void QmitkFiberGenerationView::AlignOnGrid() { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it ) { mitk::DataNode::Pointer pFibNode = *it; if ( pFibNode.IsNotNull() && dynamic_cast(pFibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(pImgNode->GetData()); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); break; } } break; } } } for(unsigned int i=0; iGetSources(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it ) { mitk::DataNode::Pointer imgNode = *it; if ( imgNode.IsNotNull() && dynamic_cast(imgNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Image::Pointer img = dynamic_cast(imgNode->GetData()); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } break; } } } for(unsigned int i=0; i(m_SelectedImages.at(i)->GetData()); mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberGenerationView::OnFlipButton() { if (m_SelectedFiducial.IsNull()) return; std::map::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; data.m_Flipped += 1; data.m_Flipped %= 2; } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberGenerationView::OnAddBundle() { if (m_SelectedImageNode.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImageNode); mitk::FiberBundle::Pointer bundle = mitk::FiberBundle::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( bundle ); QString name = QString("Bundle_%1").arg(children->size()); node->SetName(name.toStdString()); m_SelectedBundles.push_back(node); UpdateGui(); GetDataStorage()->Add(node, m_SelectedImageNode); } void QmitkFiberGenerationView::OnDrawROI() { if (m_SelectedBundles.empty()) OnAddBundle(); if (m_SelectedBundles.empty()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(0)); mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( figure ); node->SetBoolProperty("planarfigure.3drendering", true); node->SetBoolProperty("planarfigure.3drendering.fill", true); QList nodes = this->GetDataManagerSelection(); for( int i=0; iSetSelected(false); m_SelectedFiducial = node; QString name = QString("Fiducial_%1").arg(children->size()); node->SetName(name.toStdString()); node->SetSelected(true); this->DisableCrosshairNavigation(); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( node ); } UpdateGui(); GetDataStorage()->Add(node, m_SelectedBundles.at(0)); } bool QmitkFiberGenerationView::CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j) { int li = -1; i->GetPropertyValue("layer", li); int lj = -1; j->GetPropertyValue("layer", lj); return liGetSources(m_SelectedFiducial); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) if(dynamic_cast((*it)->GetData())) m_SelectedBundles.push_back(*it); if (m_SelectedBundles.empty()) return; } UpdateParametersFromGui(); for (unsigned int i=0; iGetDerivations(m_SelectedBundles.at(i)); std::vector< mitk::DataNode::Pointer > childVector; for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it ) childVector.push_back(*it); std::sort(childVector.begin(), childVector.end(), CompareLayer); std::vector< mitk::PlanarEllipse::Pointer > fib; std::vector< unsigned int > flip; float radius = 1; int count = 0; for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::PlanarEllipse* ellipse = dynamic_cast(node->GetData()); if (m_Controls->m_ConstantRadiusBox->isChecked()) { ellipse->SetTreatAsCircle(true); mitk::Point2D c = ellipse->GetControlPoint(0); mitk::Point2D p = ellipse->GetControlPoint(1); mitk::Vector2D v = p-c; if (count==0) { radius = v.GetVnlVector().magnitude(); ellipse->SetControlPoint(1, p); ellipse->Modified(); } else { v.Normalize(); v *= radius; ellipse->SetControlPoint(1, c+v); ellipse->Modified(); } } fib.push_back(ellipse); std::map::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; flip.push_back(data.m_Flipped); } else flip.push_back(0); } count++; } if (fib.size()>1) { m_Parameters.m_FiberGen.m_Fiducials.push_back(fib); m_Parameters.m_FiberGen.m_FlipList.push_back(flip); } else if (fib.size()>0) m_SelectedBundles.at(i)->SetData( mitk::FiberBundle::New() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); filter->SetParameters(m_Parameters.m_FiberGen); filter->Update(); std::vector< mitk::FiberBundle::Pointer > fiberBundles = filter->GetFiberBundles(); for (unsigned int i=0; iSetData( fiberBundles.at(i) ); if (fiberBundles.at(i)->GetNumFibers()>50000) m_SelectedBundles.at(i)->SetVisibility(false); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberGenerationView::ApplyTransform() { std::vector< mitk::DataNode::Pointer > selectedBundles; for(unsigned int i=0; iGetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) selectedBundles.push_back(fibNode); } } if (selectedBundles.empty()) selectedBundles = m_SelectedBundles2; if (!selectedBundles.empty()) { for (std::vector::const_iterator it = selectedBundles.begin(); it!=selectedBundles.end(); ++it) { mitk::FiberBundle::Pointer fib = dynamic_cast((*it)->GetData()); fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value()); fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value()); fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value()); // handle child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse* pe = dynamic_cast(fiducialNode->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*itk::Math::pi/180; double y = m_Controls->m_YrotBox->value()*itk::Math::pi/180; double z = m_Controls->m_ZrotBox->value()*itk::Math::pi/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); // implicit translation mitk::Vector3D trans; trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0]; trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1]; trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2]; mitk::Vector3D newWc = rot*trans; newWc = newWc-trans; geom->Translate(newWc); pe->Modified(); } } } } } else { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*itk::Math::pi/180; double y = m_Controls->m_YrotBox->value()*itk::Math::pi/180; double z = m_Controls->m_ZrotBox->value()*itk::Math::pi/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); pe->Modified(); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberGenerationView::CopyBundles() { if ( m_SelectedBundles.size()<1 ){ QMessageBox::information( nullptr, "Warning", "Select at least one fiber bundle!"); MITK_WARN("QmitkFiberGenerationView") << "Select at least one fiber bundle!"; return; } for (std::vector::const_iterator it = m_SelectedBundles.begin(); it!=m_SelectedBundles.end(); ++it) { // find parent image mitk::DataNode::Pointer parentNode; mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { parentNode = pImgNode; break; } } mitk::FiberBundle::Pointer fib = dynamic_cast((*it)->GetData()); mitk::FiberBundle::Pointer newBundle = fib->GetDeepCopy(); QString name((*it)->GetName().c_str()); name += "_copy"; mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); if (parentNode.IsNotNull()) GetDataStorage()->Add(fbNode, parentNode); else GetDataStorage()->Add(fbNode); // copy child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData())->Clone(); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pe); newNode->SetName(fiducialNode->GetName()); newNode->SetBoolProperty("planarfigure.3drendering", true); GetDataStorage()->Add(newNode, fbNode); } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberGenerationView::JoinBundles() { if ( m_SelectedBundles.size()<2 ){ QMessageBox::information( nullptr, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberGenerationView") << "Select at least two fiber bundles!"; return; } std::vector< mitk::FiberBundle::Pointer > to_add; std::vector::const_iterator it = m_SelectedBundles.begin(); (*it)->SetVisibility(false); mitk::FiberBundle::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (; it!=m_SelectedBundles.end(); ++it) { (*it)->SetVisibility(false); to_add.push_back(dynamic_cast((*it)->GetData())); } newBundle = newBundle->AddBundles(to_add); mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName("Joined"); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberGenerationView::UpdateGui() { m_Controls->m_FiberGenMessage->setVisible(true); m_Controls->m_TransformBundlesButton->setEnabled(false); m_Controls->m_CopyBundlesButton->setEnabled(false); m_Controls->m_GenerateFibersButton->setEnabled(false); m_Controls->m_FlipButton->setEnabled(false); m_Controls->m_CircleButton->setEnabled(false); m_Controls->m_JoinBundlesButton->setEnabled(false); m_Controls->m_AlignOnGrid->setEnabled(false); m_Controls->m_FiducialAttributeBox->setEnabled(false); // Fiber generation gui if (m_SelectedFiducial.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_FlipButton->setEnabled(true); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_SelectedFiducials.size()==1) { m_Controls->m_FiducialAttributeBox->setEnabled(true); mitk::PlanarEllipse* pe = dynamic_cast(m_SelectedFiducials.at(0)->GetData()); auto origin = pe->GetGeometry()->GetOrigin(); m_Controls->m_FidPosX->setValue(origin[0]); m_Controls->m_FidPosY->setValue(origin[1]); m_Controls->m_FidPosZ->setValue(origin[2]); auto p0 = pe->GetControlPoint(0); auto p1 = pe->GetControlPoint(1); auto p2 = pe->GetControlPoint(2); auto p3 = pe->GetControlPoint(3); auto v1 = p1 - p0; auto v2 = p2 - p0; m_Controls->m_FidAxis1->setValue(v1.GetNorm()); m_Controls->m_FidAxis2->setValue(v2.GetNorm()); vnl_vector_fixed vt; vt[0]=1; vt[1]=0; auto v3 = p3-p0; v3.Normalize(); auto angle = dot_product(vt, v3.GetVnlVector()); angle = std::acos(angle)*180.0/itk::Math::pi; if (v3[1]<0) angle *= -1; m_Controls->m_FidTwist->setValue(angle); } else { m_Controls->m_FidPosX->setValue(0); m_Controls->m_FidPosY->setValue(0); m_Controls->m_FidPosZ->setValue(0); m_Controls->m_FidAxis1->setValue(1); m_Controls->m_FidAxis2->setValue(1); m_Controls->m_FidTwist->setValue(0); } if (m_SelectedImageNode.IsNotNull() || !m_SelectedBundles.empty()) { m_Controls->m_CircleButton->setEnabled(true); m_Controls->m_FiberGenMessage->setVisible(false); } if (m_SelectedImageNode.IsNotNull() && !m_SelectedBundles.empty()) m_Controls->m_AlignOnGrid->setEnabled(true); if (!m_SelectedBundles.empty()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_CopyBundlesButton->setEnabled(true); m_Controls->m_GenerateFibersButton->setEnabled(true); if (m_SelectedBundles.size()>1) m_Controls->m_JoinBundlesButton->setEnabled(true); } } void QmitkFiberGenerationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList& nodes) { m_SelectedBundles2.clear(); m_SelectedImages.clear(); m_SelectedFiducials.clear(); m_SelectedFiducial = nullptr; m_SelectedBundles.clear(); m_SelectedImageNode = nullptr; // iterate all selected objects, adjust warning visibility for( int i=0; i(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImageNode = node; } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedBundles2.push_back(node); if (m_Controls->m_RealTimeFibers->isChecked()) { m_SelectedBundles.push_back(node); mitk::FiberBundle::Pointer newFib = dynamic_cast(node->GetData()); if (newFib->GetNumFibers()!=static_cast(m_Controls->m_FiberDensityBox->value())) GenerateFibers(); } else m_SelectedBundles.push_back(node); } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedFiducials.push_back(node); m_SelectedFiducial = node; m_SelectedBundles.clear(); mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) { mitk::DataNode::Pointer pNode = *it; if ( pNode.IsNotNull() && dynamic_cast(pNode->GetData()) ) m_SelectedBundles.push_back(pNode); } } } UpdateGui(); } void QmitkFiberGenerationView::EnableCrosshairNavigation() { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberGenerationView::DisableCrosshairNavigation() { } void QmitkFiberGenerationView::NodeRemoved(const mitk::DataNode* node) { mitk::DataNode* nonConstNode = const_cast(node); std::map::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode); if (dynamic_cast(node->GetData())) { m_SelectedBundles.clear(); m_SelectedBundles2.clear(); } else if (dynamic_cast(node->GetData())) m_SelectedImages.clear(); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; // remove observers data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag ); data.m_Figure->RemoveObserver( data.m_SelectObserverTag ); data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag ); data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag ); m_DataNodeToPlanarFigureData.erase( it ); } } void QmitkFiberGenerationView::NodeAdded( const mitk::DataNode* node ) { // add observer for selection in renderwindow mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); bool isPositionMarker (false); node->GetBoolProperty("isContourMarker", isPositionMarker); if( figure && !isPositionMarker ) { MITK_DEBUG << "figure added. will add interactor if needed."; mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); mitk::DataNode* nonConstNode = const_cast( node ); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode( nonConstNode ); } MITK_DEBUG << "will now add observers for planarfigure"; QmitkPlanarFigureData data; data.m_Figure = figure; // // add observer for event when figure has been placed typedef itk::SimpleMemberCommand< QmitkFiberGenerationView > SimpleCommandType; // SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New(); // initializationCommand->SetCallbackFunction( this, &QmitkFiberGenerationView::PlanarFigureInitialized ); // data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand ); // add observer for event when figure is picked (selected) typedef itk::MemberCommand< QmitkFiberGenerationView > MemberCommandType; MemberCommandType::Pointer selectCommand = MemberCommandType::New(); selectCommand->SetCallbackFunction( this, &QmitkFiberGenerationView::PlanarFigureSelected ); data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New(); startInteractionCommand->SetCallbackFunction( this, &QmitkFiberGenerationView::DisableCrosshairNavigation); data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New(); endInteractionCommand->SetCallbackFunction( this, &QmitkFiberGenerationView::EnableCrosshairNavigation); data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand ); m_DataNodeToPlanarFigureData[nonConstNode] = data; } } void QmitkFiberGenerationView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& ) { mitk::TNodePredicateDataType::Pointer isPf = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer allPfs = this->GetDataStorage()->GetSubset( isPf ); for ( mitk::DataStorage::SetOfObjects::const_iterator it = allPfs->begin(); it!=allPfs->end(); ++it) { mitk::DataNode* node = *it; if( node->GetData() == object ) { node->SetSelected(true); m_SelectedFiducial = node; } else node->SetSelected(false); } UpdateGui(); this->RequestRenderWindowUpdate(); } void QmitkFiberGenerationView::SetFocus() { m_Controls->m_CircleButton->setFocus(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp index a1bbc8189a..b5bde54f56 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp @@ -1,2125 +1,2127 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkFiberfoxView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #define RAPIDXML_NO_EXCEPTIONS #include #include #include #include #include "usModuleRegistry.h" #include #include #include #include #include #include #include #include #include #include "mitkNodePredicateDataType.h" #include #include #include #include #define _USE_MATH_DEFINES #include QmitkFiberfoxWorker::QmitkFiberfoxWorker(QmitkFiberfoxView* view) : m_View(view) { } void QmitkFiberfoxWorker::run() { try{ m_View->m_TractsToDwiFilter->Update(); } catch( ... ) { } m_View->m_Thread.quit(); } const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImageNode( nullptr ) , m_Worker(this) , m_ThreadIsRunning(false) { m_Worker.moveToThread(&m_Thread); connect(&m_Thread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_Thread, SIGNAL(started()), &m_Worker, SLOT(run())); connect(&m_Thread, SIGNAL(finished()), this, SLOT(AfterThread())); // connect(&m_Thread, SIGNAL(terminated()), this, SLOT(AfterThread())); m_SimulationTimer = new QTimer(this); } void QmitkFiberfoxView::KillThread() { MITK_INFO << "Aborting DWI simulation."; m_TractsToDwiFilter->SetAbortGenerateData(true); m_Controls->m_AbortSimulationButton->setEnabled(false); m_Controls->m_AbortSimulationButton->setText("Aborting simulation ..."); } void QmitkFiberfoxView::BeforeThread() { m_SimulationTime = QTime::currentTime(); m_SimulationTimer->start(100); m_Controls->m_AbortSimulationButton->setVisible(true); m_Controls->m_GenerateImageButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(true); m_ThreadIsRunning = true; } void QmitkFiberfoxView::AfterThread() { UpdateSimulationStatus(); m_SimulationTimer->stop(); m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_AbortSimulationButton->setEnabled(true); m_Controls->m_AbortSimulationButton->setText("Abort simulation"); m_Controls->m_GenerateImageButton->setVisible(true); m_ThreadIsRunning = false; QString statusText; FiberfoxParameters parameters; mitk::Image::Pointer mitkImage = mitk::Image::New(); statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); if (m_TractsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_TractsToDwiFilter->GetParameters(); mitkImage = mitk::GrabItkImageMemory( m_TractsToDwiFilter->GetOutput() ); mitk::DiffusionPropertyHelper::SetGradientContainer(mitkImage, parameters.m_SignalGen.GetItkGradientContainer()); mitk::DiffusionPropertyHelper::SetReferenceBValue(mitkImage, parameters.m_SignalGen.GetBvalue()); mitk::DiffusionPropertyHelper::InitializeImage( mitkImage ); parameters.m_Misc.m_ResultNode->SetData( mitkImage ); GetDataStorage()->Add(parameters.m_Misc.m_ResultNode, parameters.m_Misc.m_ParentNode); parameters.m_Misc.m_ResultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(m_TractsToDwiFilter->GetLevelWindow()) ); if (m_Controls->m_VolumeFractionsBox->isChecked()) { if (m_TractsToDwiFilter->GetPhaseImage().IsNotNull()) { mitk::Image::Pointer phaseImage = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkPhase = m_TractsToDwiFilter->GetPhaseImage(); phaseImage = mitk::GrabItkImageMemory( itkPhase.GetPointer() ); mitk::DataNode::Pointer phaseNode = mitk::DataNode::New(); phaseNode->SetData( phaseImage ); phaseNode->SetName("Phase Image"); GetDataStorage()->Add(phaseNode, parameters.m_Misc.m_ResultNode); } if (m_TractsToDwiFilter->GetKspaceImage().IsNotNull()) { mitk::Image::Pointer image = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkImage = m_TractsToDwiFilter->GetKspaceImage(); image = mitk::GrabItkImageMemory( itkImage.GetPointer() ); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("k-Space"); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); } { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_TractsToDwiFilter->GetCoilPointset()); node->SetName("Coil Positions"); node->SetProperty("pointsize", mitk::FloatProperty::New(parameters.m_SignalGen.m_ImageSpacing[0]/4)); node->SetProperty("color", mitk::ColorProperty::New(0, 1, 0)); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); } int c = 1; std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_real = m_TractsToDwiFilter->GetOutputImagesReal(); for (auto real : output_real) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(real.GetPointer()); image->SetVolume(real->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Coil-"+QString::number(c).toStdString()+"-real"); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); ++c; } c = 1; std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_imag = m_TractsToDwiFilter->GetOutputImagesImag(); for (auto imag : output_imag) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(imag.GetPointer()); image->SetVolume(imag->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Coil-"+QString::number(c).toStdString()+"-imag"); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); ++c; } std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = m_TractsToDwiFilter->GetVolumeFractions(); for (unsigned int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("CompartmentVolume-"+QString::number(k).toStdString()); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); } } m_TractsToDwiFilter = nullptr; if (parameters.m_Misc.m_AfterSimulationMessage.size()>0) QMessageBox::information( nullptr, "Warning", parameters.m_Misc.m_AfterSimulationMessage.c_str()); mitk::BaseData::Pointer basedata = parameters.m_Misc.m_ResultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } if (!parameters.m_Misc.m_OutputPath.empty()) { try{ QString outputFileName(parameters.m_Misc.m_OutputPath.c_str()); outputFileName += parameters.m_Misc.m_ResultNode->GetName().c_str(); outputFileName.replace(QString("."), QString("_")); SaveParameters(outputFileName+".ffp"); outputFileName += ".dwi"; QString status("Saving output image to "); status += outputFileName; m_Controls->m_SimulationStatusText->append(status); mitk::IOUtil::Save(mitkImage, outputFileName.toStdString()); m_Controls->m_SimulationStatusText->append("File saved successfully."); } catch (itk::ExceptionObject &e) { QString status("Exception during DWI writing: "); status += e.GetDescription(); m_Controls->m_SimulationStatusText->append(status); } catch (...) { m_Controls->m_SimulationStatusText->append("Unknown exception during DWI writing!"); } } parameters.m_SignalGen.m_FrequencyMap = nullptr; } void QmitkFiberfoxView::UpdateSimulationStatus() { QString statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); if (QString::compare(m_SimulationStatusText,statusText)!=0) { m_Controls->m_SimulationStatusText->clear(); m_Controls->m_SimulationStatusText->setText(statusText); QScrollBar *vScrollBar = m_Controls->m_SimulationStatusText->verticalScrollBar(); vScrollBar->triggerAction(QScrollBar::SliderToMaximum); } } // Destructor QmitkFiberfoxView::~QmitkFiberfoxView() { delete m_SimulationTimer; } void QmitkFiberfoxView::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::QmitkFiberfoxViewControls; m_Controls->setupUi( parent ); m_Controls->m_StickWidget1->setVisible(true); m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_BallWidget1->setVisible(true); m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_BallWidget2->SetT1(4500); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->SetT1(4500); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_DotWidget2->SetT1(4500); m_Controls->m_PrototypeWidget1->setVisible(false); m_Controls->m_PrototypeWidget2->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_PrototypeWidget3->SetMinFa(0.0); m_Controls->m_PrototypeWidget3->SetMaxFa(0.15); m_Controls->m_PrototypeWidget4->SetMinFa(0.0); m_Controls->m_PrototypeWidget4->SetMaxFa(0.15); m_Controls->m_PrototypeWidget3->SetMinAdc(0.0); m_Controls->m_PrototypeWidget3->SetMaxAdc(0.001); m_Controls->m_PrototypeWidget4->SetMinAdc(0.003); m_Controls->m_PrototypeWidget4->SetMaxAdc(0.004); m_Controls->m_Comp2FractionFrame->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_NoiseFrame->setVisible(false); m_Controls->m_GhostFrame->setVisible(false); m_Controls->m_DistortionsFrame->setVisible(false); m_Controls->m_EddyFrame->setVisible(false); m_Controls->m_SpikeFrame->setVisible(false); m_Controls->m_AliasingFrame->setVisible(false); m_Controls->m_MotionArtifactFrame->setVisible(false); m_Controls->m_DriftFrame->setVisible(false); m_ParameterFile = QDir::currentPath()+"/param.ffp"; m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(false); m_Controls->m_FrequencyMapBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp1VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp2VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp3VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp4VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_MaskComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TemplateComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_FiberBundleComboBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isFiberBundle = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateIsDWI::Pointer isDwi = mitk::NodePredicateIsDWI::New( ); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("Odfmage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isOdf); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer isNonDiffMitkImage = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer isBinaryMitkImage = mitk::NodePredicateAnd::New( isNonDiffMitkImage, isBinaryPredicate ); m_Controls->m_FrequencyMapBox->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp1VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp1VolumeFraction->SetZeroEntryText("--"); m_Controls->m_Comp2VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp2VolumeFraction->SetZeroEntryText("--"); m_Controls->m_Comp3VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp3VolumeFraction->SetZeroEntryText("--"); m_Controls->m_Comp4VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp4VolumeFraction->SetZeroEntryText("--"); m_Controls->m_MaskComboBox->SetPredicate(isBinaryMitkImage); m_Controls->m_MaskComboBox->SetZeroEntryText("--"); m_Controls->m_TemplateComboBox->SetPredicate(isMitkImage); m_Controls->m_TemplateComboBox->SetZeroEntryText("--"); m_Controls->m_FiberBundleComboBox->SetPredicate(isFiberBundle); m_Controls->m_FiberBundleComboBox->SetZeroEntryText("--"); QFont font; font.setFamily("Courier"); font.setStyleHint(QFont::Monospace); font.setFixedPitch(true); font.setPointSize(7); m_Controls->m_SimulationStatusText->setFont(font); connect( m_SimulationTimer, SIGNAL(timeout()), this, SLOT(UpdateSimulationStatus()) ); connect((QObject*) m_Controls->m_AbortSimulationButton, SIGNAL(clicked()), (QObject*) this, SLOT(KillThread())); connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage())); connect((QObject*) m_Controls->m_AddNoise, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddNoise(int))); connect((QObject*) m_Controls->m_AddGhosts, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGhosts(int))); connect((QObject*) m_Controls->m_AddDistortions, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDistortions(int))); connect((QObject*) m_Controls->m_AddEddy, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddEddy(int))); connect((QObject*) m_Controls->m_AddSpikes, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddSpikes(int))); connect((QObject*) m_Controls->m_AddAliasing, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddAliasing(int))); connect((QObject*) m_Controls->m_AddMotion, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddMotion(int))); connect((QObject*) m_Controls->m_AddDrift, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDrift(int))); connect((QObject*) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp1ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp2ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp3ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp4ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_UseBvalsBvecsBox, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(OnBvalsBvecsCheck(int))); connect((QObject*) m_Controls->m_SaveParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(SaveParameters())); connect((QObject*) m_Controls->m_LoadParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(LoadParameters())); connect((QObject*) m_Controls->m_OutputPathButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetOutputPath())); connect((QObject*) m_Controls->m_LoadBvalsButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetBvalsEdit())); connect((QObject*) m_Controls->m_LoadBvecsButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetBvecsEdit())); connect((QObject*) m_Controls->m_MaskComboBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnMaskSelected(int))); connect((QObject*) m_Controls->m_TemplateComboBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnTemplateSelected(int))); connect((QObject*) m_Controls->m_FiberBundleComboBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnFibSelected(int))); } UpdateGui(); } void QmitkFiberfoxView::OnMaskSelected(int ) { UpdateGui(); } void QmitkFiberfoxView::OnTemplateSelected(int ) { UpdateGui(); } void QmitkFiberfoxView::OnFibSelected(int ) { UpdateGui(); } void QmitkFiberfoxView::OnBvalsBvecsCheck(int ) { UpdateGui(); } void QmitkFiberfoxView::UpdateParametersFromGui() { m_Parameters.ClearSignalParameters(); m_Parameters.m_Misc.m_CheckAdvancedSignalOptionsBox = m_Controls->m_AdvancedOptionsBox_2->isChecked(); m_Parameters.m_Misc.m_CheckOutputVolumeFractionsBox = m_Controls->m_VolumeFractionsBox->isChecked(); std::string outputPath = m_Controls->m_SavePathEdit->text().toStdString(); if (outputPath.compare("-")!=0) { m_Parameters.m_Misc.m_OutputPath = outputPath; m_Parameters.m_Misc.m_OutputPath += "/"; } if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer mitkMaskImage = dynamic_cast(m_Controls->m_MaskComboBox->GetSelectedNode()->GetData()); mitk::CastToItkImage(mitkMaskImage, m_Parameters.m_SignalGen.m_MaskImage); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(m_Parameters.m_SignalGen.m_MaskImage); duplicator->Update(); m_Parameters.m_SignalGen.m_MaskImage = duplicator->GetOutput(); } if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( m_Controls->m_TemplateComboBox->GetSelectedNode())) // use parameters of selected DWI { mitk::Image::Pointer dwi = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(dwi, itkVectorImagePointer); m_Parameters.m_SignalGen.m_ImageRegion = itkVectorImagePointer->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = itkVectorImagePointer->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = itkVectorImagePointer->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = itkVectorImagePointer->GetDirection(); m_Parameters.SetBvalue(mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi)); - m_Parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(dwi)); + m_Parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(dwi)); } else if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()) // use geometry of selected image { mitk::Image::Pointer img = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New(); CastToItkImage< itk::Image< float, 3 > >(img, itkImg); m_Parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); if (m_Controls->m_UseBvalsBvecsBox->isChecked()) { double bval; m_Parameters.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Controls->m_LoadBvalsEdit->text().toStdString(), m_Controls->m_LoadBvecsEdit->text().toStdString(), bval) ); m_Parameters.SetBvalue(bval); } else { m_Parameters.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); m_Parameters.SetBvalue(m_Controls->m_BvalueBox->value()); m_Parameters.GenerateGradientHalfShell(); } } else if (m_Parameters.m_SignalGen.m_MaskImage.IsNotNull()) // use geometry of mask image { ItkUcharImgType::Pointer itkImg = m_Parameters.m_SignalGen.m_MaskImage; m_Parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); if (m_Controls->m_UseBvalsBvecsBox->isChecked()) { double bval; m_Parameters.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Controls->m_LoadBvalsEdit->text().toStdString(), m_Controls->m_LoadBvecsEdit->text().toStdString(), bval) ); m_Parameters.SetBvalue(bval); } else { m_Parameters.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); m_Parameters.SetBvalue(m_Controls->m_BvalueBox->value()); m_Parameters.GenerateGradientHalfShell(); } } else // use GUI parameters { m_Parameters.m_SignalGen.m_ImageRegion.SetSize(0, m_Controls->m_SizeX->value()); m_Parameters.m_SignalGen.m_ImageRegion.SetSize(1, m_Controls->m_SizeY->value()); m_Parameters.m_SignalGen.m_ImageRegion.SetSize(2, m_Controls->m_SizeZ->value()); m_Parameters.m_SignalGen.m_ImageSpacing[0] = m_Controls->m_SpacingX->value(); m_Parameters.m_SignalGen.m_ImageSpacing[1] = m_Controls->m_SpacingY->value(); m_Parameters.m_SignalGen.m_ImageSpacing[2] = m_Controls->m_SpacingZ->value(); m_Parameters.m_SignalGen.m_ImageOrigin[0] = m_Parameters.m_SignalGen.m_ImageSpacing[0]/2; m_Parameters.m_SignalGen.m_ImageOrigin[1] = m_Parameters.m_SignalGen.m_ImageSpacing[1]/2; m_Parameters.m_SignalGen.m_ImageOrigin[2] = m_Parameters.m_SignalGen.m_ImageSpacing[2]/2; m_Parameters.m_SignalGen.m_ImageDirection.SetIdentity(); if (m_Controls->m_UseBvalsBvecsBox->isChecked()) { double bval; m_Parameters.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Controls->m_LoadBvalsEdit->text().toStdString(), m_Controls->m_LoadBvecsEdit->text().toStdString(), bval) ); m_Parameters.SetBvalue(bval); } else { m_Parameters.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); m_Parameters.SetBvalue(m_Controls->m_BvalueBox->value()); m_Parameters.GenerateGradientHalfShell(); } } // signal relaxation m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; if (m_Controls->m_RelaxationBox->isChecked()) { m_Parameters.m_SignalGen.m_DoSimulateRelaxation = true; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(true)); m_Parameters.m_Misc.m_ArtifactModelString += "_RELAX"; } m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = m_Parameters.m_SignalGen.m_DoSimulateRelaxation; // N/2 ghosts m_Parameters.m_Misc.m_DoAddGhosts = m_Controls->m_AddGhosts->isChecked(); m_Parameters.m_SignalGen.m_KspaceLineOffset = m_Controls->m_kOffsetBox->value(); if (m_Controls->m_AddGhosts->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_GHOST"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(m_Parameters.m_SignalGen.m_KspaceLineOffset)); } // Aliasing m_Parameters.m_Misc.m_DoAddAliasing = m_Controls->m_AddAliasing->isChecked(); m_Parameters.m_SignalGen.m_CroppingFactor = (100-m_Controls->m_WrapBox->value())/100; if (m_Controls->m_AddAliasing->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_ALIASING"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value())); } // Spikes m_Parameters.m_Misc.m_DoAddSpikes = m_Controls->m_AddSpikes->isChecked(); m_Parameters.m_SignalGen.m_Spikes = m_Controls->m_SpikeNumBox->value(); m_Parameters.m_SignalGen.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value(); if (m_Controls->m_AddSpikes->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_SPIKES"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(m_Parameters.m_SignalGen.m_Spikes)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(m_Parameters.m_SignalGen.m_SpikeAmplitude)); } // Drift m_Parameters.m_SignalGen.m_DoAddDrift = m_Controls->m_AddDrift->isChecked(); m_Parameters.m_SignalGen.m_Drift = m_Controls->m_DriftFactor->value()/100; if (m_Controls->m_AddDrift->isChecked()) { m_Parameters.m_Misc.m_ArtifactModelString += "_DRIFT"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Drift", FloatProperty::New(m_Parameters.m_SignalGen.m_Drift)); } // gibbs ringing m_Parameters.m_SignalGen.m_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); if (m_Controls->m_AddGibbsRinging->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true)); m_Parameters.m_Misc.m_ArtifactModelString += "_RINGING"; } // add distortions m_Parameters.m_Misc.m_DoAddDistortions = m_Controls->m_AddDistortions->isChecked(); if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); mitk::Image* img = dynamic_cast(fMapNode->GetData()); ItkFloatImgType::Pointer itkImg = ItkFloatImgType::New(); CastToItkImage< ItkFloatImgType >(img, itkImg); if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNull()) // use geometry of frequency map { m_Parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); } m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(itkImg); duplicator->Update(); m_Parameters.m_SignalGen.m_FrequencyMap = duplicator->GetOutput(); m_Parameters.m_Misc.m_ArtifactModelString += "_DISTORTED"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true)); } m_Parameters.m_SignalGen.m_EddyStrength = m_Controls->m_EddyGradientStrength->value(); m_Parameters.m_Misc.m_DoAddEddyCurrents = m_Controls->m_AddEddy->isChecked(); if (m_Controls->m_AddEddy->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_EDDY"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(m_Parameters.m_SignalGen.m_EddyStrength)); } // Motion m_Parameters.m_SignalGen.m_DoAddMotion = false; m_Parameters.m_SignalGen.m_DoRandomizeMotion = m_Controls->m_RandomMotion->isChecked(); m_Parameters.m_SignalGen.m_Translation[0] = m_Controls->m_MaxTranslationBoxX->value(); m_Parameters.m_SignalGen.m_Translation[1] = m_Controls->m_MaxTranslationBoxY->value(); m_Parameters.m_SignalGen.m_Translation[2] = m_Controls->m_MaxTranslationBoxZ->value(); m_Parameters.m_SignalGen.m_Rotation[0] = m_Controls->m_MaxRotationBoxX->value(); m_Parameters.m_SignalGen.m_Rotation[1] = m_Controls->m_MaxRotationBoxY->value(); m_Parameters.m_SignalGen.m_Rotation[2] = m_Controls->m_MaxRotationBoxZ->value(); m_Parameters.m_SignalGen.m_MotionVolumes.clear(); m_Parameters.m_Misc.m_MotionVolumesBox = m_Controls->m_MotionVolumesBox->text().toStdString(); if ( m_Controls->m_AddMotion->isChecked()) { m_Parameters.m_SignalGen.m_DoAddMotion = true; m_Parameters.m_Misc.m_ArtifactModelString += "_MOTION"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(m_Parameters.m_SignalGen.m_DoRandomizeMotion)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(m_Parameters.m_SignalGen.m_Translation[0])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(m_Parameters.m_SignalGen.m_Translation[1])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(m_Parameters.m_SignalGen.m_Translation[2])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(m_Parameters.m_SignalGen.m_Rotation[0])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(m_Parameters.m_SignalGen.m_Rotation[1])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(m_Parameters.m_SignalGen.m_Rotation[2])); if ( m_Parameters.m_Misc.m_MotionVolumesBox == "random" ) { for ( size_t i=0; i < m_Parameters.m_SignalGen.GetNumVolumes(); ++i ) { m_Parameters.m_SignalGen.m_MotionVolumes.push_back( bool( rand()%2 ) ); } MITK_DEBUG << "QmitkFiberfoxView.cpp: Case m_Misc.m_MotionVolumesBox == \"random\"."; } else if ( ! m_Parameters.m_Misc.m_MotionVolumesBox.empty() ) { std::stringstream stream( m_Parameters.m_Misc.m_MotionVolumesBox ); std::vector numbers; int number = std::numeric_limits::max(); while( stream >> number ) { if( number < std::numeric_limits::max() ) { numbers.push_back( number ); } } // If a list of negative numbers is given: if( *(std::min_element( numbers.begin(), numbers.end() )) < 0 && *(std::max_element( numbers.begin(), numbers.end() )) <= 0 ) // cave: -0 == +0 { for ( size_t i=0; i < m_Parameters.m_SignalGen.GetNumVolumes(); ++i ) { m_Parameters.m_SignalGen.m_MotionVolumes.push_back( true ); } // set all true except those given. for( auto iter = std::begin( numbers ); iter != std::end( numbers ); ++iter ) { if ( -(*iter) < (int)m_Parameters.m_SignalGen.GetNumVolumes() && -(*iter) >= 0 ) { m_Parameters.m_SignalGen.m_MotionVolumes.at( -(*iter) ) = false; } } MITK_DEBUG << "QmitkFiberfoxView.cpp: Case list of negative numbers."; } // If a list of positive numbers is given: else if( *(std::min_element( numbers.begin(), numbers.end() )) >= 0 && *(std::max_element( numbers.begin(), numbers.end() )) >= 0 ) { for ( size_t i=0; i < m_Parameters.m_SignalGen.GetNumVolumes(); ++i ) { m_Parameters.m_SignalGen.m_MotionVolumes.push_back( false ); } // set all false except those given. for( auto iter = std::begin( numbers ); iter != std::end( numbers ); ++iter ) { if ( *iter < (int)m_Parameters.m_SignalGen.GetNumVolumes() && *iter >= 0 ) { m_Parameters.m_SignalGen.m_MotionVolumes.at( *iter ) = true; } } MITK_DEBUG << "QmitkFiberfoxView.cpp: Case list of positive numbers."; } else { MITK_ERROR << "QmitkFiberfoxView.cpp: Inconsistent list of numbers in m_MotionVolumesBox."; } } else { MITK_WARN << "QmitkFiberfoxView.cpp: Unrecognised parameters.m_Misc.m_MotionVolumesBox: " << m_Parameters.m_Misc.m_MotionVolumesBox; m_Parameters.m_Misc.m_MotionVolumesBox = "random"; // set default. for (unsigned int i=0; im_AcquisitionTypeBox->currentIndex(); m_Parameters.m_SignalGen.m_CoilSensitivityProfile = (SignalGenerationParameters::CoilSensitivityProfile)m_Controls->m_CoilSensBox->currentIndex(); m_Parameters.m_SignalGen.m_NumberOfCoils = m_Controls->m_NumCoilsBox->value(); m_Parameters.m_SignalGen.m_PartialFourier = m_Controls->m_PartialFourier->value(); m_Parameters.m_SignalGen.m_ReversePhase = m_Controls->m_ReversePhaseBox->isChecked(); m_Parameters.m_SignalGen.m_tLine = m_Controls->m_LineReadoutTimeBox->value(); m_Parameters.m_SignalGen.m_tInhom = m_Controls->m_T2starBox->value(); m_Parameters.m_SignalGen.m_tEcho = m_Controls->m_TEbox->value(); m_Parameters.m_SignalGen.m_tRep = m_Controls->m_TRbox->value(); m_Parameters.m_SignalGen.m_DoDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked(); m_Parameters.m_SignalGen.m_AxonRadius = m_Controls->m_FiberRadius->value(); m_Parameters.m_SignalGen.m_SignalScale = m_Controls->m_SignalScaleBox->value(); double voxelVolume = m_Parameters.m_SignalGen.m_ImageSpacing[0] * m_Parameters.m_SignalGen.m_ImageSpacing[1] * m_Parameters.m_SignalGen.m_ImageSpacing[2]; if ( m_Parameters.m_SignalGen.m_SignalScale*voxelVolume > itk::NumericTraits::max()*0.75 ) { m_Parameters.m_SignalGen.m_SignalScale = itk::NumericTraits::max()*0.75/voxelVolume; m_Controls->m_SignalScaleBox->setValue(m_Parameters.m_SignalGen.m_SignalScale); QMessageBox::information( nullptr, "Warning", "Maximum signal exceeding data type limits. Automatically adjusted to " + QString::number(m_Parameters.m_SignalGen.m_SignalScale) + " to obtain a maximum signal of 75% of the data type maximum." " Relaxation and other effects that affect the signal intensities are not accounted for."); } // Noise m_Parameters.m_Misc.m_DoAddNoise = m_Controls->m_AddNoise->isChecked(); m_Parameters.m_SignalGen.m_NoiseVariance = m_Controls->m_NoiseLevel->value(); if (m_Controls->m_AddNoise->isChecked()) { switch (m_Controls->m_NoiseDistributionBox->currentIndex()) { case 0: { if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_COMPLEX-GAUSSIAN-"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Complex Gaussian")); } break; } case 1: { if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_NoiseModel = std::make_shared< mitk::RicianNoiseModel >(); m_Parameters.m_Misc.m_ArtifactModelString += "_RICIAN-"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); m_Parameters.m_NoiseModel->SetNoiseVariance(m_Parameters.m_SignalGen.m_NoiseVariance); } break; } case 2: { if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_NoiseModel = std::make_shared< mitk::ChiSquareNoiseModel >(); m_Parameters.m_Misc.m_ArtifactModelString += "_CHISQUARED-"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared")); m_Parameters.m_NoiseModel->SetNoiseVariance(m_Parameters.m_SignalGen.m_NoiseVariance); } break; } default: { if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_COMPLEX-GAUSSIAN-"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Complex Gaussian")); } break; } } if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_Misc.m_ArtifactModelString += QString::number(m_Parameters.m_SignalGen.m_NoiseVariance).toStdString(); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(m_Parameters.m_SignalGen.m_NoiseVariance)); } } // signal models { // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: { mitk::StickModel* model = new mitk::StickModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_StickWidget1->GetD()); model->SetT2(m_Controls->m_StickWidget1->GetT2()); model->SetT1(m_Controls->m_StickWidget1->GetT1()); model->m_CompartmentId = 1; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Stick"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 1: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); model->SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); model->SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); model->SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); model->SetT1(m_Controls->m_ZeppelinWidget1->GetT1()); model->m_CompartmentId = 1; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Zeppelin"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); model->SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); model->SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); model->SetT2(m_Controls->m_TensorWidget1->GetT2()); model->SetT1(m_Controls->m_TensorWidget1->GetT1()); model->m_CompartmentId = 1; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Tensor"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::RawShModel* model = new mitk::RawShModel(); m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetMaxNumKernels(m_Controls->m_PrototypeWidget1->GetNumberOfSamples()); model->SetFaRange(m_Controls->m_PrototypeWidget1->GetMinFa(), m_Controls->m_PrototypeWidget1->GetMaxFa()); model->SetAdcRange(m_Controls->m_PrototypeWidget1->GetMinAdc(), m_Controls->m_PrototypeWidget1->GetMaxAdc()); model->m_CompartmentId = 1; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Prototype"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Prototype") ); break; } } if (m_Controls->m_Comp1VolumeFraction->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp1VolumeFraction->GetSelectedNode(); ItkDoubleImgType::Pointer comp1VolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, comp1VolumeImage); m_Parameters.m_FiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage); } // compartment 2 switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: { mitk::StickModel* model = new mitk::StickModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_StickWidget2->GetD()); model->SetT2(m_Controls->m_StickWidget2->GetT2()); model->SetT1(m_Controls->m_StickWidget2->GetT1()); model->m_CompartmentId = 2; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Stick"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); model->SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); model->SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); model->SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); model->SetT1(m_Controls->m_ZeppelinWidget2->GetT1()); model->m_CompartmentId = 2; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Zeppelin"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); model->SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); model->SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); model->SetT2(m_Controls->m_TensorWidget2->GetT2()); model->SetT1(m_Controls->m_TensorWidget2->GetT1()); model->m_CompartmentId = 2; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Tensor"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } } if (m_Controls->m_Comp2VolumeFraction->GetSelectedNode().IsNotNull() && m_Parameters.m_FiberModelList.size()==2) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp2VolumeFraction->GetSelectedNode(); ItkDoubleImgType::Pointer comp1VolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, comp1VolumeImage); m_Parameters.m_FiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage); } // compartment 3 switch (m_Controls->m_Compartment3Box->currentIndex()) { case 0: { mitk::BallModel* model = new mitk::BallModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_BallWidget1->GetD()); model->SetT2(m_Controls->m_BallWidget1->GetT2()); model->SetT1(m_Controls->m_BallWidget1->GetT1()); model->m_CompartmentId = 3; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Ball"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); break; } case 1: { mitk::AstroStickModel* model = new mitk::AstroStickModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); model->SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); model->SetT1(m_Controls->m_AstrosticksWidget1->GetT1()); model->SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); model->m_CompartmentId = 3; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Astrosticks"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); break; } case 2: { mitk::DotModel* model = new mitk::DotModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetT2(m_Controls->m_DotWidget1->GetT2()); model->SetT1(m_Controls->m_DotWidget1->GetT1()); model->m_CompartmentId = 3; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Dot"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::RawShModel* model = new mitk::RawShModel(); m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetMaxNumKernels(m_Controls->m_PrototypeWidget3->GetNumberOfSamples()); model->SetFaRange(m_Controls->m_PrototypeWidget3->GetMinFa(), m_Controls->m_PrototypeWidget3->GetMaxFa()); model->SetAdcRange(m_Controls->m_PrototypeWidget3->GetMinAdc(), m_Controls->m_PrototypeWidget3->GetMaxAdc()); model->m_CompartmentId = 3; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Prototype"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Prototype") ); break; } } if (m_Controls->m_Comp3VolumeFraction->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp3VolumeFraction->GetSelectedNode(); ItkDoubleImgType::Pointer comp1VolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, comp1VolumeImage); m_Parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage); } switch (m_Controls->m_Compartment4Box->currentIndex()) { case 0: break; case 1: { mitk::BallModel* model = new mitk::BallModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_BallWidget2->GetD()); model->SetT2(m_Controls->m_BallWidget2->GetT2()); model->SetT1(m_Controls->m_BallWidget2->GetT1()); model->m_CompartmentId = 4; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Ball"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::AstroStickModel* model = new mitk::AstroStickModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); model->SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); model->SetT1(m_Controls->m_AstrosticksWidget2->GetT1()); model->SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); model->m_CompartmentId = 4; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Astrosticks"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); break; } case 3: { mitk::DotModel* model = new mitk::DotModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetT2(m_Controls->m_DotWidget2->GetT2()); model->SetT1(m_Controls->m_DotWidget2->GetT1()); model->m_CompartmentId = 4; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Dot"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); break; } case 4: { mitk::RawShModel* model = new mitk::RawShModel(); m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetMaxNumKernels(m_Controls->m_PrototypeWidget4->GetNumberOfSamples()); model->SetFaRange(m_Controls->m_PrototypeWidget4->GetMinFa(), m_Controls->m_PrototypeWidget4->GetMaxFa()); model->SetAdcRange(m_Controls->m_PrototypeWidget4->GetMinAdc(), m_Controls->m_PrototypeWidget4->GetMaxAdc()); model->m_CompartmentId = 4; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Prototype"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Prototype") ); break; } } if (m_Controls->m_Comp4VolumeFraction->GetSelectedNode().IsNotNull() && m_Parameters.m_NonFiberModelList.size()==2) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode(); ItkDoubleImgType::Pointer compVolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, compVolumeImage); m_Parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(compVolumeImage); } } m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(m_Parameters.m_SignalGen.m_SignalScale)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(m_Parameters.m_SignalGen.m_AxonRadius)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(m_Parameters.m_SignalGen.m_tInhom)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(m_Parameters.m_SignalGen.m_tLine)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(m_Parameters.m_SignalGen.m_tEcho)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(m_Parameters.m_SignalGen.GetBvalue())); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(m_Parameters.m_SignalGen.m_DoDisablePartialVolume)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(m_Parameters.m_SignalGen.m_DoSimulateRelaxation)); m_Parameters.m_Misc.m_ResultNode->AddProperty("binary", BoolProperty::New(false)); } void QmitkFiberfoxView::SaveParameters(QString filename) { UpdateParametersFromGui(); std::vector< int > bVals = m_Parameters.m_SignalGen.GetBvalues(); std::cout << "b-values: "; for (auto v : bVals) std::cout << v << " "; std::cout << std::endl; bool ok = true; bool first = true; bool dosampling = false; mitk::Image::Pointer diffImg = nullptr; itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = nullptr; const int shOrder = 2; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; QballFilterType::CoefficientImageType::Pointer itkFeatureImage = nullptr; ItkDoubleImgType::Pointer adcImage = nullptr; for (unsigned int i=0; i* model = nullptr; if (i* >(m_Parameters.m_FiberModelList.at(i)); } else { model = dynamic_cast< mitk::RawShModel<>* >(m_Parameters.m_NonFiberModelList.at(i-m_Parameters.m_FiberModelList.size())); } if ( model!=nullptr && model->GetNumberOfKernels() <= 0 ) { if (first==true) { if ( QMessageBox::question(nullptr, "Prototype signal sampling", "Do you want to sample prototype signals from the selected diffusion-weighted imag and save them?", QMessageBox::Yes, QMessageBox::No) == QMessageBox::Yes ) dosampling = true; first = false; if ( dosampling && (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNull() || !mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()) ) ) ) { QMessageBox::information(nullptr, "Parameter file not saved", "No diffusion-weighted image selected to sample signal from."); return; } else if (dosampling) { diffImg = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); filter->Update(); tensorImage = filter->GetOutput(); QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput( itkVectorImagePointer ); adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg)); adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); adcFilter->Update(); adcImage = adcFilter->GetOutput(); } } typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); filter->Update(); tensorImage = filter->GetOutput(); QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput( itkVectorImagePointer ); adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg)); adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); adcFilter->Update(); adcImage = adcFilter->GetOutput(); if (dosampling && diffImg.IsNotNull()) { ok = model->SampleKernels(diffImg, m_Parameters.m_SignalGen.m_MaskImage, tensorImage, itkFeatureImage, adcImage); if (!ok) { QMessageBox::information( nullptr, "Parameter file not saved", "No valid prototype signals could be sampled."); return; } } } } m_Parameters.SaveParameters(filename.toStdString()); m_ParameterFile = filename; } void QmitkFiberfoxView::SaveParameters() { QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), m_ParameterFile, tr("Fiberfox Parameters (*.ffp)") ); SaveParameters(filename); } void QmitkFiberfoxView::LoadParameters() { QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QString(itksys::SystemTools::GetFilenamePath(m_ParameterFile.toStdString()).c_str()), tr("Fiberfox Parameters (*.ffp)") ); if(filename.isEmpty() || filename.isNull()) return; m_ParameterFile = filename; m_Parameters.LoadParameters(filename.toStdString()); if (m_Parameters.m_MissingTags.size()>0) { QString missing("Parameter file might be corrupted. The following parameters could not be read: "); missing += QString(m_Parameters.m_MissingTags.c_str()); missing += "\nDefault values have been assigned to the missing parameters."; QMessageBox::information( nullptr, "Warning!", missing); } // image generation parameters m_Controls->m_SizeX->setValue(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0)); m_Controls->m_SizeY->setValue(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)); m_Controls->m_SizeZ->setValue(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(2)); m_Controls->m_SpacingX->setValue(m_Parameters.m_SignalGen.m_ImageSpacing[0]); m_Controls->m_SpacingY->setValue(m_Parameters.m_SignalGen.m_ImageSpacing[1]); m_Controls->m_SpacingZ->setValue(m_Parameters.m_SignalGen.m_ImageSpacing[2]); m_Controls->m_NumGradientsBox->setValue(m_Parameters.m_SignalGen.GetNumWeightedVolumes()); m_Controls->m_BvalueBox->setValue(m_Parameters.m_SignalGen.GetBvalue()); m_Controls->m_SignalScaleBox->setValue(m_Parameters.m_SignalGen.m_SignalScale); m_Controls->m_TEbox->setValue(m_Parameters.m_SignalGen.m_tEcho); m_Controls->m_LineReadoutTimeBox->setValue(m_Parameters.m_SignalGen.m_tLine); m_Controls->m_T2starBox->setValue(m_Parameters.m_SignalGen.m_tInhom); m_Controls->m_FiberRadius->setValue(m_Parameters.m_SignalGen.m_AxonRadius); m_Controls->m_RelaxationBox->setChecked(m_Parameters.m_SignalGen.m_DoSimulateRelaxation); m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(m_Parameters.m_SignalGen.m_DoDisablePartialVolume); m_Controls->m_ReversePhaseBox->setChecked(m_Parameters.m_SignalGen.m_ReversePhase); m_Controls->m_PartialFourier->setValue(m_Parameters.m_SignalGen.m_PartialFourier); m_Controls->m_TRbox->setValue(m_Parameters.m_SignalGen.m_tRep); m_Controls->m_NumCoilsBox->setValue(m_Parameters.m_SignalGen.m_NumberOfCoils); m_Controls->m_CoilSensBox->setCurrentIndex(m_Parameters.m_SignalGen.m_CoilSensitivityProfile); m_Controls->m_AcquisitionTypeBox->setCurrentIndex(m_Parameters.m_SignalGen.m_AcquisitionType); if (!m_Parameters.m_Misc.m_BvalsFile.empty()) { m_Controls->m_UseBvalsBvecsBox->setChecked(true); m_Controls->m_LoadBvalsEdit->setText(QString(m_Parameters.m_Misc.m_BvalsFile.c_str())); } else m_Controls->m_LoadBvalsEdit->setText("-"); if (!m_Parameters.m_Misc.m_BvecsFile.empty()) { m_Controls->m_UseBvalsBvecsBox->setChecked(true); m_Controls->m_LoadBvecsEdit->setText(QString(m_Parameters.m_Misc.m_BvecsFile.c_str())); } else m_Controls->m_LoadBvecsEdit->setText("-"); if (m_Parameters.m_NoiseModel!=nullptr) { m_Controls->m_AddNoise->setChecked(m_Parameters.m_Misc.m_DoAddNoise); if (dynamic_cast*>(m_Parameters.m_NoiseModel.get())) { m_Controls->m_NoiseDistributionBox->setCurrentIndex(0); } else if (dynamic_cast*>(m_Parameters.m_NoiseModel.get())) { m_Controls->m_NoiseDistributionBox->setCurrentIndex(1); } m_Controls->m_NoiseLevel->setValue(m_Parameters.m_NoiseModel->GetNoiseVariance()); } else { m_Controls->m_AddNoise->setChecked(m_Parameters.m_Misc.m_DoAddNoise); m_Controls->m_NoiseLevel->setValue(m_Parameters.m_SignalGen.m_NoiseVariance); } m_Controls->m_VolumeFractionsBox->setChecked(m_Parameters.m_Misc.m_CheckOutputVolumeFractionsBox); m_Controls->m_AdvancedOptionsBox_2->setChecked(m_Parameters.m_Misc.m_CheckAdvancedSignalOptionsBox); m_Controls->m_AddGhosts->setChecked(m_Parameters.m_Misc.m_DoAddGhosts); m_Controls->m_AddAliasing->setChecked(m_Parameters.m_Misc.m_DoAddAliasing); m_Controls->m_AddDistortions->setChecked(m_Parameters.m_Misc.m_DoAddDistortions); m_Controls->m_AddSpikes->setChecked(m_Parameters.m_Misc.m_DoAddSpikes); m_Controls->m_AddEddy->setChecked(m_Parameters.m_Misc.m_DoAddEddyCurrents); m_Controls->m_AddDrift->setChecked(m_Parameters.m_SignalGen.m_DoAddDrift); m_Controls->m_kOffsetBox->setValue(m_Parameters.m_SignalGen.m_KspaceLineOffset); m_Controls->m_WrapBox->setValue(100*(1-m_Parameters.m_SignalGen.m_CroppingFactor)); m_Controls->m_DriftFactor->setValue(100*m_Parameters.m_SignalGen.m_Drift); m_Controls->m_SpikeNumBox->setValue(m_Parameters.m_SignalGen.m_Spikes); m_Controls->m_SpikeScaleBox->setValue(m_Parameters.m_SignalGen.m_SpikeAmplitude); m_Controls->m_EddyGradientStrength->setValue(m_Parameters.m_SignalGen.m_EddyStrength); m_Controls->m_AddGibbsRinging->setChecked(m_Parameters.m_SignalGen.m_DoAddGibbsRinging); m_Controls->m_AddMotion->setChecked(m_Parameters.m_SignalGen.m_DoAddMotion); m_Controls->m_RandomMotion->setChecked(m_Parameters.m_SignalGen.m_DoRandomizeMotion); m_Controls->m_MotionVolumesBox->setText(QString(m_Parameters.m_Misc.m_MotionVolumesBox.c_str())); m_Controls->m_MaxTranslationBoxX->setValue(m_Parameters.m_SignalGen.m_Translation[0]); m_Controls->m_MaxTranslationBoxY->setValue(m_Parameters.m_SignalGen.m_Translation[1]); m_Controls->m_MaxTranslationBoxZ->setValue(m_Parameters.m_SignalGen.m_Translation[2]); m_Controls->m_MaxRotationBoxX->setValue(m_Parameters.m_SignalGen.m_Rotation[0]); m_Controls->m_MaxRotationBoxY->setValue(m_Parameters.m_SignalGen.m_Rotation[1]); m_Controls->m_MaxRotationBoxZ->setValue(m_Parameters.m_SignalGen.m_Rotation[2]); m_Controls->m_Compartment1Box->setCurrentIndex(0); m_Controls->m_Compartment2Box->setCurrentIndex(0); m_Controls->m_Compartment3Box->setCurrentIndex(0); m_Controls->m_Compartment4Box->setCurrentIndex(0); for (unsigned int i=0; i* signalModel = nullptr; if (iGetVolumeFractionImage().IsNotNull() ) { compVolNode = mitk::DataNode::New(); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(signalModel->GetVolumeFractionImage().GetPointer()); image->SetVolume(signalModel->GetVolumeFractionImage()->GetBufferPointer()); compVolNode->SetData( image ); compVolNode->SetName("Compartment volume "+QString::number(signalModel->m_CompartmentId).toStdString()); GetDataStorage()->Add(compVolNode); } switch (signalModel->m_CompartmentId) { case 1: { if (compVolNode.IsNotNull()) m_Controls->m_Comp1VolumeFraction->SetSelectedNode(compVolNode); if (dynamic_cast*>(signalModel)) { mitk::StickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_StickWidget1->SetT2(model->GetT2()); m_Controls->m_StickWidget1->SetT1(model->GetT1()); m_Controls->m_StickWidget1->SetD(model->GetDiffusivity()); m_Controls->m_Compartment1Box->setCurrentIndex(0); break; } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_TensorWidget1->SetT2(model->GetT2()); m_Controls->m_TensorWidget1->SetT1(model->GetT1()); m_Controls->m_TensorWidget1->SetD1(model->GetDiffusivity1()); m_Controls->m_TensorWidget1->SetD2(model->GetDiffusivity2()); m_Controls->m_TensorWidget1->SetD3(model->GetDiffusivity3()); m_Controls->m_Compartment1Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget1->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget1->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget1->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget1->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget1->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment1Box->setCurrentIndex(3); break; } break; } case 2: { if (compVolNode.IsNotNull()) m_Controls->m_Comp2VolumeFraction->SetSelectedNode(compVolNode); if (dynamic_cast*>(signalModel)) { mitk::StickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_StickWidget2->SetT2(model->GetT2()); m_Controls->m_StickWidget2->SetT1(model->GetT1()); m_Controls->m_StickWidget2->SetD(model->GetDiffusivity()); m_Controls->m_Compartment2Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_TensorWidget2->SetT2(model->GetT2()); m_Controls->m_TensorWidget2->SetT1(model->GetT1()); m_Controls->m_TensorWidget2->SetD1(model->GetDiffusivity1()); m_Controls->m_TensorWidget2->SetD2(model->GetDiffusivity2()); m_Controls->m_TensorWidget2->SetD3(model->GetDiffusivity3()); m_Controls->m_Compartment2Box->setCurrentIndex(3); break; } break; } case 3: { if (compVolNode.IsNotNull()) m_Controls->m_Comp3VolumeFraction->SetSelectedNode(compVolNode); if (dynamic_cast*>(signalModel)) { mitk::BallModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_BallWidget1->SetT2(model->GetT2()); m_Controls->m_BallWidget1->SetT1(model->GetT1()); m_Controls->m_BallWidget1->SetD(model->GetDiffusivity()); m_Controls->m_Compartment3Box->setCurrentIndex(0); break; } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_AstrosticksWidget1->SetT2(model->GetT2()); m_Controls->m_AstrosticksWidget1->SetT1(model->GetT1()); m_Controls->m_AstrosticksWidget1->SetD(model->GetDiffusivity()); m_Controls->m_AstrosticksWidget1->SetRandomizeSticks(model->GetRandomizeSticks()); m_Controls->m_Compartment3Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::DotModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_DotWidget1->SetT2(model->GetT2()); m_Controls->m_DotWidget1->SetT1(model->GetT1()); m_Controls->m_Compartment3Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget3->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget3->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget3->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget3->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget3->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment3Box->setCurrentIndex(3); break; } break; } case 4: { if (compVolNode.IsNotNull()) m_Controls->m_Comp4VolumeFraction->SetSelectedNode(compVolNode); if (dynamic_cast*>(signalModel)) { mitk::BallModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_BallWidget2->SetT2(model->GetT2()); m_Controls->m_BallWidget2->SetT1(model->GetT1()); m_Controls->m_BallWidget2->SetD(model->GetDiffusivity()); m_Controls->m_Compartment4Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_AstrosticksWidget2->SetT2(model->GetT2()); m_Controls->m_AstrosticksWidget2->SetT1(model->GetT1()); m_Controls->m_AstrosticksWidget2->SetD(model->GetDiffusivity()); m_Controls->m_AstrosticksWidget2->SetRandomizeSticks(model->GetRandomizeSticks()); m_Controls->m_Compartment4Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::DotModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_DotWidget2->SetT2(model->GetT2()); m_Controls->m_DotWidget2->SetT1(model->GetT1()); m_Controls->m_Compartment4Box->setCurrentIndex(3); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget4->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget4->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget4->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget4->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget4->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment4Box->setCurrentIndex(4); break; } break; } } } if ( m_Parameters.m_SignalGen.m_MaskImage ) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(m_Parameters.m_SignalGen.m_MaskImage.GetPointer()); image->SetVolume(m_Parameters.m_SignalGen.m_MaskImage->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Tissue mask"); GetDataStorage()->Add(node); m_Controls->m_MaskComboBox->SetSelectedNode(node); } if ( m_Parameters.m_SignalGen.m_FrequencyMap ) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(m_Parameters.m_SignalGen.m_FrequencyMap.GetPointer()); image->SetVolume(m_Parameters.m_SignalGen.m_FrequencyMap->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Frequency map"); GetDataStorage()->Add(node); m_Controls->m_FrequencyMapBox->SetSelectedNode(node); } } void QmitkFiberfoxView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox_2->setChecked(false); } } void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index) { m_Controls->m_StickWidget1->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_PrototypeWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_StickWidget1->setVisible(true); break; case 1: m_Controls->m_ZeppelinWidget1->setVisible(true); break; case 2: m_Controls->m_TensorWidget1->setVisible(true); break; case 3: m_Controls->m_PrototypeWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index) { m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_Comp2FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); m_Controls->m_Comp2FractionFrame->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); m_Controls->m_Comp2FractionFrame->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->setVisible(true); m_Controls->m_Comp2FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index) { m_Controls->m_BallWidget1->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); switch (index) { case 0: m_Controls->m_BallWidget1->setVisible(true); break; case 1: m_Controls->m_AstrosticksWidget1->setVisible(true); break; case 2: m_Controls->m_DotWidget1->setVisible(true); break; case 3: m_Controls->m_PrototypeWidget3->setVisible(true); break; } } void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index) { m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_BallWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 2: m_Controls->m_AstrosticksWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 3: m_Controls->m_DotWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 4: m_Controls->m_PrototypeWidget4->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::OnAddMotion(int value) { if (value>0) m_Controls->m_MotionArtifactFrame->setVisible(true); else m_Controls->m_MotionArtifactFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDrift(int value) { if (value>0) m_Controls->m_DriftFrame->setVisible(true); else m_Controls->m_DriftFrame->setVisible(false); } void QmitkFiberfoxView::OnAddAliasing(int value) { if (value>0) m_Controls->m_AliasingFrame->setVisible(true); else m_Controls->m_AliasingFrame->setVisible(false); } void QmitkFiberfoxView::OnAddSpikes(int value) { if (value>0) m_Controls->m_SpikeFrame->setVisible(true); else m_Controls->m_SpikeFrame->setVisible(false); } void QmitkFiberfoxView::OnAddEddy(int value) { if (value>0) m_Controls->m_EddyFrame->setVisible(true); else m_Controls->m_EddyFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDistortions(int value) { if (value>0) m_Controls->m_DistortionsFrame->setVisible(true); else m_Controls->m_DistortionsFrame->setVisible(false); } void QmitkFiberfoxView::OnAddGhosts(int value) { if (value>0) m_Controls->m_GhostFrame->setVisible(true); else m_Controls->m_GhostFrame->setVisible(false); } void QmitkFiberfoxView::OnAddNoise(int value) { if (value>0) m_Controls->m_NoiseFrame->setVisible(true); else m_Controls->m_NoiseFrame->setVisible(false); } QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints) { NPoints *= 2; GradientListType pointshell; int numB0 = NPoints/20; if (numB0==0) numB0=1; GradientType g; g.Fill(0.0); for (int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*itk::Math::pi); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); 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); } return retval; } void QmitkFiberfoxView::GenerateImage() { if (m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNull() && !mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( m_Controls->m_TemplateComboBox->GetSelectedNode())) { mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage( m_Controls->m_SizeX->value(), m_Controls->m_SizeY->value(), m_Controls->m_SizeZ->value(), m_Controls->m_SpacingX->value(), m_Controls->m_SpacingY->value(), m_Controls->m_SpacingZ->value()); mitk::Point3D origin; origin[0] = m_Controls->m_SpacingX->value()/2; origin[1] = m_Controls->m_SpacingY->value()/2; origin[2] = m_Controls->m_SpacingZ->value()/2; image->SetOrigin(origin); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); unsigned int window = m_Controls->m_SizeX->value()*m_Controls->m_SizeY->value()*m_Controls->m_SizeZ->value(); unsigned int level = window/2; mitk::LevelWindow lw; lw.SetLevelWindow(level, window); node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) ); GetDataStorage()->Add(node); m_SelectedImageNode = node; mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } UpdateGui(); QMessageBox::information(nullptr, "Template image generated", "You have selected no fiber bundle or diffusion-weighted image, which can be used to simulate a new diffusion-weighted image. A template image with the specified geometry has been generated that can be used to draw artificial fibers (see view 'Fiber Generator')."); } else if (m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNotNull()) SimulateImageFromFibers(m_Controls->m_FiberBundleComboBox->GetSelectedNode()); else if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( m_Controls->m_TemplateComboBox->GetSelectedNode()) ) SimulateForExistingDwi(m_Controls->m_TemplateComboBox->GetSelectedNode()); else QMessageBox::information(nullptr, "No image generated", "You have selected no fiber bundle or diffusion-weighted image, which can be used to simulate a new diffusion-weighted image."); } void QmitkFiberfoxView::SetFocus() { } void QmitkFiberfoxView::SimulateForExistingDwi(mitk::DataNode* imageNode) { bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(imageNode->GetData())) ); if ( !isDiffusionImage ) { return; } UpdateParametersFromGui(); mitk::Image::Pointer diffImg = dynamic_cast(imageNode->GetData()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); m_Parameters.m_Misc.m_ParentNode = imageNode; m_Parameters.m_SignalGen.m_SignalScale = 1; m_Parameters.m_Misc.m_ResultNode->SetName(m_Parameters.m_Misc.m_ParentNode->GetName() +"_D"+QString::number(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0)).toStdString() +"-"+QString::number(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)).toStdString() +"-"+QString::number(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(2)).toStdString() +"_S"+QString::number(m_Parameters.m_SignalGen.m_ImageSpacing[0]).toStdString() +"-"+QString::number(m_Parameters.m_SignalGen.m_ImageSpacing[1]).toStdString() +"-"+QString::number(m_Parameters.m_SignalGen.m_ImageSpacing[2]).toStdString() +"_b"+QString::number(m_Parameters.m_SignalGen.GetBvalue()).toStdString() +"_"+m_Parameters.m_Misc.m_SignalModelString +m_Parameters.m_Misc.m_ArtifactModelString); + m_Parameters.ApplyDirectionMatrix(); m_TractsToDwiFilter->SetParameters(m_Parameters); m_TractsToDwiFilter->SetInputImage(itkVectorImagePointer); m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::SimulateImageFromFibers(mitk::DataNode* fiberNode) { mitk::FiberBundle::Pointer fiberBundle = dynamic_cast(fiberNode->GetData()); if (fiberBundle->GetNumFibers()<=0) { return; } UpdateParametersFromGui(); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); m_Parameters.m_Misc.m_ParentNode = fiberNode; m_Parameters.m_Misc.m_ResultNode->SetName(m_Parameters.m_Misc.m_ParentNode->GetName() +"_D"+QString::number(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0)).toStdString() +"-"+QString::number(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)).toStdString() +"-"+QString::number(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(2)).toStdString() +"_S"+QString::number(m_Parameters.m_SignalGen.m_ImageSpacing[0]).toStdString() +"-"+QString::number(m_Parameters.m_SignalGen.m_ImageSpacing[1]).toStdString() +"-"+QString::number(m_Parameters.m_SignalGen.m_ImageSpacing[2]).toStdString() +"_b"+QString::number(m_Parameters.m_SignalGen.GetBvalue()).toStdString() +"_"+m_Parameters.m_Misc.m_SignalModelString +m_Parameters.m_Misc.m_ArtifactModelString); if ( m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast (m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()) ) ) { bool first = true; bool ok = true; mitk::Image::Pointer diffImg = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = nullptr; const int shOrder = 2; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; QballFilterType::CoefficientImageType::Pointer itkFeatureImage = nullptr; ItkDoubleImgType::Pointer adcImage = nullptr; for (unsigned int i=0; i* model = nullptr; if (i* >(m_Parameters.m_FiberModelList.at(i)); else model = dynamic_cast< mitk::RawShModel<>* >(m_Parameters.m_NonFiberModelList.at(i-m_Parameters.m_FiberModelList.size())); if (model!=0 && model->GetNumberOfKernels()<=0) { if (first==true) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); filter->Update(); tensorImage = filter->GetOutput(); QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput( itkVectorImagePointer ); adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg)); adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); adcFilter->Update(); adcImage = adcFilter->GetOutput(); } ok = model->SampleKernels(diffImg, m_Parameters.m_SignalGen.m_MaskImage, tensorImage, itkFeatureImage, adcImage); if (!ok) break; } } if (!ok) { QMessageBox::information( nullptr, "Simulation cancelled", "No valid prototype signals could be sampled."); return; } } else if ( m_Controls->m_Compartment1Box->currentIndex()==3 || m_Controls->m_Compartment3Box->currentIndex()==3 || m_Controls->m_Compartment4Box->currentIndex()==4 ) { QMessageBox::information( nullptr, "Simulation cancelled", "Prototype signal but no diffusion-weighted image selected to sample signal from."); return; } + m_Parameters.ApplyDirectionMatrix(); m_TractsToDwiFilter->SetParameters(m_Parameters); m_TractsToDwiFilter->SetFiberBundle(fiberBundle); m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::SetBvalsEdit() { // SELECT FOLDER DIALOG std::string filename; filename = QFileDialog::getOpenFileName(nullptr, "Select bvals file", QString(filename.c_str())).toStdString(); if (filename.empty()) m_Controls->m_LoadBvalsEdit->setText("-"); else m_Controls->m_LoadBvalsEdit->setText(QString(filename.c_str())); } void QmitkFiberfoxView::SetBvecsEdit() { // SELECT FOLDER DIALOG std::string filename; filename = QFileDialog::getOpenFileName(nullptr, "Select bvecs file", QString(filename.c_str())).toStdString(); if (filename.empty()) m_Controls->m_LoadBvecsEdit->setText("-"); else m_Controls->m_LoadBvecsEdit->setText(QString(filename.c_str())); } void QmitkFiberfoxView::SetOutputPath() { // SELECT FOLDER DIALOG std::string outputPath; outputPath = QFileDialog::getExistingDirectory(nullptr, "Save images to...", QString(outputPath.c_str())).toStdString(); if (outputPath.empty()) m_Controls->m_SavePathEdit->setText("-"); else { outputPath += "/"; m_Controls->m_SavePathEdit->setText(QString(outputPath.c_str())); } } void QmitkFiberfoxView::UpdateGui() { m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_LoadGradientsFrame->setVisible(false); m_Controls->m_GenerateGradientsFrame->setVisible(false); if (m_Controls->m_UseBvalsBvecsBox->isChecked()) m_Controls->m_LoadGradientsFrame->setVisible(true); else m_Controls->m_GenerateGradientsFrame->setVisible(true); // Signal generation gui if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull() || m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()) { m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if ( m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()) ) ) { m_Controls->m_DiffusionPropsMessage->setVisible(true); m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); m_Controls->m_LoadGradientsFrame->setVisible(false); m_Controls->m_GenerateGradientsFrame->setVisible(false); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp index fd6a354556..e89d4822a2 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp @@ -1,1850 +1,1940 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ //#define MBILOG_ENABLE_DEBUG #include "QmitkPreprocessingView.h" #include "mitkDiffusionImagingConfigure.h" // qt includes #include // itk includes #include "itkTimeProbe.h" #include "itkB0ImageExtractionImageFilter.h" #include "itkB0ImageExtractionToSeparateImageFilter.h" #include "itkBrainMaskExtractionImageFilter.h" #include "itkCastImageFilter.h" #include "itkVectorContainer.h" #include #include #include #include #include #include // Multishell includes #include // Multishell Functors #include #include #include #include // mitk includes #include "QmitkDataStorageComboBox.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 #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 const std::string QmitkPreprocessingView::VIEW_ID = "org.mitk.views.diffusionpreprocessing"; #define DI_INFO MITK_INFO("DiffusionImaging") typedef float TTensorPixelType; QmitkPreprocessingView::QmitkPreprocessingView() : QmitkAbstractView(), m_Controls(nullptr) { } QmitkPreprocessingView::~QmitkPreprocessingView() { } 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()->setSectionResizeMode(QHeaderView::Stretch); m_Controls->m_MeasurementFrameTable->verticalHeader()->setSectionResizeMode(QHeaderView::Stretch); m_Controls->m_DirectionMatrixTable->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch); m_Controls->m_DirectionMatrixTable->verticalHeader()->setSectionResizeMode(QHeaderView::Stretch); } } void QmitkPreprocessingView::SetFocus() { m_Controls->m_MirrorGradientToHalfSphereButton->setFocus(); } void QmitkPreprocessingView::CreateConnections() { if ( m_Controls ) { m_Controls->m_NormalizationMaskBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_SelctedImageComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_MergeDwiBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_AlignImageBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isOdf, isDti); mitk::NodePredicateAnd::Pointer noDiffusionImage = mitk::NodePredicateAnd::New(isMitkImage, mitk::NodePredicateNot::New(isDiffusionImage)); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer binaryNoDiffusionImage = mitk::NodePredicateAnd::New(noDiffusionImage, isBinaryPredicate); m_Controls->m_NormalizationMaskBox->SetPredicate(binaryNoDiffusionImage); m_Controls->m_SelctedImageComboBox->SetPredicate(isMitkImage); m_Controls->m_MergeDwiBox->SetPredicate(isMitkImage); m_Controls->m_AlignImageBox->SetPredicate(isMitkImage); m_Controls->m_ExtractBrainMask->setVisible(false); m_Controls->m_BrainMaskIterationsBox->setVisible(false); m_Controls->m_ResampleIntFrame->setVisible(false); 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_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()) ); connect( (QObject*)(m_Controls->m_MergeDwisButton), SIGNAL(clicked()), this, SLOT(MergeDwis()) ); connect( (QObject*)(m_Controls->m_ProjectSignalButton), SIGNAL(clicked()), this, SLOT(DoProjectSignal()) ); connect( (QObject*)(m_Controls->m_B_ValueMap_Rounder_SpinBox), SIGNAL(valueChanged(int)), this, SLOT(UpdateDwiBValueMapRounder(int))); connect( (QObject*)(m_Controls->m_CreateLengthCorrectedDwi), SIGNAL(clicked()), this, SLOT(DoLengthCorrection()) ); connect( (QObject*)(m_Controls->m_NormalizeImageValuesButton), SIGNAL(clicked()), this, SLOT(DoDwiNormalization()) ); connect( (QObject*)(m_Controls->m_ResampleImageButton), SIGNAL(clicked()), this, SLOT(DoResampleImage()) ); connect( (QObject*)(m_Controls->m_ResampleTypeBox), SIGNAL(currentIndexChanged(int)), this, SLOT(DoUpdateInterpolationGui(int)) ); connect( (QObject*)(m_Controls->m_CropImageButton), SIGNAL(clicked()), this, SLOT(DoCropImage()) ); connect( (QObject*)(m_Controls->m_RemoveGradientButton), SIGNAL(clicked()), this, SLOT(DoRemoveGradient()) ); connect( (QObject*)(m_Controls->m_ExtractGradientButton), SIGNAL(clicked()), this, SLOT(DoExtractGradient()) ); connect( (QObject*)(m_Controls->m_FlipAxis), SIGNAL(clicked()), this, SLOT(DoFlipAxis()) ); connect( (QObject*)(m_Controls->m_FlipGradientsButton), SIGNAL(clicked()), this, SLOT(DoFlipGradientDirections()) ); connect( (QObject*)(m_Controls->m_ClearRotationButton), SIGNAL(clicked()), this, SLOT(DoClearRotationOfGradients()) ); connect( (QObject*)(m_Controls->m_ModifyHeader), SIGNAL(clicked()), this, SLOT(DoApplyHeader()) ); connect( (QObject*)(m_Controls->m_AlignImageButton), SIGNAL(clicked()), this, SLOT(DoAlignImages()) ); connect( (QObject*)(m_Controls->m_SelctedImageComboBox), SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnImageSelectionChanged()) ); m_Controls->m_NormalizationMaskBox->SetZeroEntryText("--"); } } void QmitkPreprocessingView::DoAlignImages() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } mitk::DataNode::Pointer target_node = m_Controls->m_AlignImageBox->GetSelectedNode(); if (target_node.IsNull()) { return; } mitk::Image::Pointer target_image = dynamic_cast(target_node->GetData()); if ( target_image == nullptr ) { return; } image->SetOrigin(target_image->GetGeometry()->GetOrigin()); mitk::RenderingManager::GetInstance()->InitializeViews( image->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoFlipAxis() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(node) ); if (isDiffusionImage) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); itk::FixedArray flipAxes; flipAxes[0] = m_Controls->m_FlipX->isChecked(); flipAxes[1] = m_Controls->m_FlipY->isChecked(); flipAxes[2] = m_Controls->m_FlipZ->isChecked(); itk::FlipImageFilter< ItkDwiType >::Pointer flipper = itk::FlipImageFilter< ItkDwiType >::New(); flipper->SetInput(itkVectorImagePointer); flipper->SetFlipAxes(flipAxes); flipper->Update(); auto oldGradients = PropHelper::GetGradientContainer(image); auto newGradients = GradProp::GradientDirectionsContainerType::New(); for (unsigned int i=0; iSize(); i++) { GradProp::GradientDirectionType g = oldGradients->GetElement(i); GradProp::GradientDirectionType newG = g; if (flipAxes[0]) { newG[0] *= -1; } if (flipAxes[1]) { newG[1] *= -1; } if (flipAxes[2]) { newG[2] *= -1; } newGradients->InsertElement(i, newG); } mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( flipper->GetOutput() ); PropHelper::CopyProperties(image, newImage, true); PropHelper::SetGradientContainer(newImage, newGradients); PropHelper::InitializeImage(newImage); newImage->GetGeometry()->SetOrigin(image->GetGeometry()->GetOrigin()); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_flipped").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else if( image->GetPixelType().GetNumberOfComponents() == 1 ) { AccessFixedDimensionByItk(image, TemplatedFlipAxis,3); } else { QMessageBox::warning(nullptr,"Warning", QString("Operation not supported in multi-component images") ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedFlipAxis(itk::Image* itkImage) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } itk::FixedArray flipAxes; flipAxes[0] = m_Controls->m_FlipX->isChecked(); flipAxes[1] = m_Controls->m_FlipY->isChecked(); flipAxes[2] = m_Controls->m_FlipZ->isChecked(); typename itk::FlipImageFilter< itk::Image >::Pointer flipper = itk::FlipImageFilter< itk::Image >::New(); flipper->SetInput(itkImage); flipper->SetFlipAxes(flipAxes); flipper->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( flipper->GetOutput() ); newImage->GetGeometry()->SetOrigin(image->GetGeometry()->GetOrigin()); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_flipped").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoRemoveGradient() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } std::vector< unsigned int > channelsToRemove; channelsToRemove.push_back(m_Controls->m_RemoveGradientBox->value()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); itk::RemoveDwiChannelFilter< short >::Pointer filter = itk::RemoveDwiChannelFilter< short >::New(); filter->SetInput(itkVectorImagePointer); filter->SetChannelIndices(channelsToRemove); filter->SetDirections(PropHelper::GetGradientContainer(image)); filter->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::CopyProperties(image, newImage, true); PropHelper::SetGradientContainer(newImage, filter->GetNewDirections()); PropHelper::InitializeImage( newImage ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_removedgradients").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoExtractGradient() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); unsigned int channel = m_Controls->m_ExtractGradientBox->value(); itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); filter->SetInput( itkVectorImagePointer); filter->SetChannelIndex(channel); filter->Update(); mitk::Image::Pointer newImage = mitk::Image::New(); newImage->InitializeByItk( filter->GetOutput() ); newImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName( (name+"_direction-"+QString::number(channel)).toStdString().c_str() ); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); } void QmitkPreprocessingView::DoCropImage() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( isDiffusionImage ) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); ItkDwiType::SizeType lower; ItkDwiType::SizeType upper; lower[0] = m_Controls->m_XstartBox->value(); lower[1] = m_Controls->m_YstartBox->value(); lower[2] = m_Controls->m_ZstartBox->value(); upper[0] = m_Controls->m_XendBox->value(); upper[1] = m_Controls->m_YendBox->value(); upper[2] = m_Controls->m_ZendBox->value(); itk::CropImageFilter< ItkDwiType, ItkDwiType >::Pointer cropper = itk::CropImageFilter< ItkDwiType, ItkDwiType >::New(); cropper->SetLowerBoundaryCropSize(lower); cropper->SetUpperBoundaryCropSize(upper); cropper->SetInput( itkVectorImagePointer ); cropper->Update(); ItkDwiType::Pointer itkOutImage = cropper->GetOutput(); ItkDwiType::DirectionType dir = itkOutImage->GetDirection(); itk::Point origin = itkOutImage->GetOrigin(); itk::Point t; t[0] = lower[0]*itkOutImage->GetSpacing()[0]; t[1] = lower[1]*itkOutImage->GetSpacing()[1]; t[2] = lower[2]*itkOutImage->GetSpacing()[2]; t= dir*t; origin[0] += t[0]; origin[1] += t[1]; origin[2] += t[2]; itkOutImage->SetOrigin(origin); mitk::Image::Pointer newimage = mitk::GrabItkImageMemory( itkOutImage ); PropHelper::CopyProperties(image, newimage, false); PropHelper::InitializeImage( newimage ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newimage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_cropped").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else if( image->GetPixelType().GetNumberOfComponents() ) { AccessFixedDimensionByItk(image, TemplatedCropImage,3); } else { QMessageBox::warning(nullptr,"Warning", QString("Operation not supported in multi-component images") ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedCropImage( itk::Image* itkImage) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } ItkDwiType::SizeType lower; ItkDwiType::SizeType upper; lower[0] = m_Controls->m_XstartBox->value(); lower[1] = m_Controls->m_YstartBox->value(); lower[2] = m_Controls->m_ZstartBox->value(); upper[0] = m_Controls->m_XendBox->value(); upper[1] = m_Controls->m_YendBox->value(); upper[2] = m_Controls->m_ZendBox->value(); typedef itk::Image ImageType; typename itk::CropImageFilter< ImageType, ImageType >::Pointer cropper = itk::CropImageFilter< ImageType, ImageType >::New(); cropper->SetLowerBoundaryCropSize(lower); cropper->SetUpperBoundaryCropSize(upper); cropper->SetInput(itkImage); cropper->Update(); typename ImageType::Pointer itkOutImage = cropper->GetOutput(); typename ImageType::DirectionType dir = itkOutImage->GetDirection(); itk::Point origin = itkOutImage->GetOrigin(); itk::Point t; t[0] = lower[0]*itkOutImage->GetSpacing()[0]; t[1] = lower[1]*itkOutImage->GetSpacing()[1]; t[2] = lower[2]*itkOutImage->GetSpacing()[2]; t= dir*t; origin[0] += t[0]; origin[1] += t[1]; origin[2] += t[2]; itkOutImage->SetOrigin(origin); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( itkOutImage.GetPointer() ); image->SetVolume( itkOutImage->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_cropped").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoUpdateInterpolationGui(int i) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } switch (i) { case 0: { m_Controls->m_ResampleIntFrame->setVisible(false); m_Controls->m_ResampleDoubleFrame->setVisible(true); break; } case 1: { m_Controls->m_ResampleIntFrame->setVisible(false); m_Controls->m_ResampleDoubleFrame->setVisible(true); mitk::BaseGeometry* geom = image->GetGeometry(); m_Controls->m_ResampleDoubleX->setValue(geom->GetSpacing()[0]); m_Controls->m_ResampleDoubleY->setValue(geom->GetSpacing()[1]); m_Controls->m_ResampleDoubleZ->setValue(geom->GetSpacing()[2]); break; } case 2: { m_Controls->m_ResampleIntFrame->setVisible(true); m_Controls->m_ResampleDoubleFrame->setVisible(false); mitk::BaseGeometry* geom = image->GetGeometry(); m_Controls->m_ResampleIntX->setValue(geom->GetExtent(0)); m_Controls->m_ResampleIntY->setValue(geom->GetExtent(1)); m_Controls->m_ResampleIntZ->setValue(geom->GetExtent(2)); break; } default: { m_Controls->m_ResampleIntFrame->setVisible(false); m_Controls->m_ResampleDoubleFrame->setVisible(true); } } } void QmitkPreprocessingView::DoExtractBrainMask() { } void QmitkPreprocessingView::DoResampleImage() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( isDiffusionImage ) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); typedef itk::ResampleDwiImageFilter< short > ResampleFilter; ResampleFilter::Pointer resampler = ResampleFilter::New(); resampler->SetInput( itkVectorImagePointer ); switch (m_Controls->m_ResampleTypeBox->currentIndex()) { case 0: { itk::Vector< double, 3 > samplingFactor; samplingFactor[0] = m_Controls->m_ResampleDoubleX->value(); samplingFactor[1] = m_Controls->m_ResampleDoubleY->value(); samplingFactor[2] = m_Controls->m_ResampleDoubleZ->value(); resampler->SetSamplingFactor(samplingFactor); break; } case 1: { itk::Vector< double, 3 > newSpacing; newSpacing[0] = m_Controls->m_ResampleDoubleX->value(); newSpacing[1] = m_Controls->m_ResampleDoubleY->value(); newSpacing[2] = m_Controls->m_ResampleDoubleZ->value(); resampler->SetNewSpacing(newSpacing); break; } case 2: { itk::ImageRegion<3> newRegion; newRegion.SetSize(0, m_Controls->m_ResampleIntX->value()); newRegion.SetSize(1, m_Controls->m_ResampleIntY->value()); newRegion.SetSize(2, m_Controls->m_ResampleIntZ->value()); resampler->SetNewImageSize(newRegion); break; } default: { MITK_WARN << "Unknown resampling parameters!"; return; } } QString outAdd; switch (m_Controls->m_InterpolatorBox->currentIndex()) { case 0: { resampler->SetInterpolation(ResampleFilter::Interpolate_NearestNeighbour); outAdd = "NearestNeighbour"; break; } case 1: { resampler->SetInterpolation(ResampleFilter::Interpolate_Linear); outAdd = "Linear"; break; } case 2: { resampler->SetInterpolation(ResampleFilter::Interpolate_BSpline); outAdd = "BSpline"; break; } case 3: { resampler->SetInterpolation(ResampleFilter::Interpolate_WindowedSinc); outAdd = "WindowedSinc"; break; } default: { resampler->SetInterpolation(ResampleFilter::Interpolate_NearestNeighbour); outAdd = "NearestNeighbour"; } } resampler->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( resampler->GetOutput() ); PropHelper::CopyProperties(image, newImage, false); PropHelper::InitializeImage( newImage ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_resampled_"+outAdd).toStdString().c_str()); imageNode->SetVisibility(false); GetDataStorage()->Add(imageNode, node); } else if( image->GetPixelType().GetNumberOfComponents() ) { AccessFixedDimensionByItk(image, TemplatedResampleImage,3); } else { QMessageBox::warning(nullptr,"Warning", QString("Operation not supported in multi-component images") ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedResampleImage( itk::Image* itkImage) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } itk::Vector< double, 3 > newSpacing; itk::ImageRegion<3> newRegion; switch (m_Controls->m_ResampleTypeBox->currentIndex()) { case 0: { itk::Vector< double, 3 > sampling; sampling[0] = m_Controls->m_ResampleDoubleX->value(); sampling[1] = m_Controls->m_ResampleDoubleY->value(); sampling[2] = m_Controls->m_ResampleDoubleZ->value(); newSpacing = itkImage->GetSpacing(); newSpacing[0] /= sampling[0]; newSpacing[1] /= sampling[1]; newSpacing[2] /= sampling[2]; newRegion = itkImage->GetLargestPossibleRegion(); newRegion.SetSize(0, newRegion.GetSize(0)*sampling[0]); newRegion.SetSize(1, newRegion.GetSize(1)*sampling[1]); newRegion.SetSize(2, newRegion.GetSize(2)*sampling[2]); break; } case 1: { newSpacing[0] = m_Controls->m_ResampleDoubleX->value(); newSpacing[1] = m_Controls->m_ResampleDoubleY->value(); newSpacing[2] = m_Controls->m_ResampleDoubleZ->value(); itk::Vector< double, 3 > oldSpacing = itkImage->GetSpacing(); itk::Vector< double, 3 > sampling; sampling[0] = oldSpacing[0]/newSpacing[0]; sampling[1] = oldSpacing[1]/newSpacing[1]; sampling[2] = oldSpacing[2]/newSpacing[2]; newRegion = itkImage->GetLargestPossibleRegion(); newRegion.SetSize(0, newRegion.GetSize(0)*sampling[0]); newRegion.SetSize(1, newRegion.GetSize(1)*sampling[1]); newRegion.SetSize(2, newRegion.GetSize(2)*sampling[2]); break; } case 2: { newRegion.SetSize(0, m_Controls->m_ResampleIntX->value()); newRegion.SetSize(1, m_Controls->m_ResampleIntY->value()); newRegion.SetSize(2, m_Controls->m_ResampleIntZ->value()); itk::ImageRegion<3> oldRegion = itkImage->GetLargestPossibleRegion(); itk::Vector< double, 3 > sampling; sampling[0] = (double)newRegion.GetSize(0)/oldRegion.GetSize(0); sampling[1] = (double)newRegion.GetSize(1)/oldRegion.GetSize(1); sampling[2] = (double)newRegion.GetSize(2)/oldRegion.GetSize(2); newSpacing = itkImage->GetSpacing(); newSpacing[0] /= sampling[0]; newSpacing[1] /= sampling[1]; newSpacing[2] /= sampling[2]; break; } default: { MITK_WARN << "Unknown resampling parameters!"; return; } } itk::Point origin = itkImage->GetOrigin(); origin[0] -= itkImage->GetSpacing()[0]/2; origin[1] -= itkImage->GetSpacing()[1]/2; origin[2] -= itkImage->GetSpacing()[2]/2; origin[0] += newSpacing[0]/2; origin[1] += newSpacing[1]/2; origin[2] += newSpacing[2]/2; typedef itk::Image ImageType; typename ImageType::Pointer outImage = ImageType::New(); outImage->SetSpacing( newSpacing ); outImage->SetOrigin( origin ); outImage->SetDirection( itkImage->GetDirection() ); outImage->SetLargestPossibleRegion( newRegion ); outImage->SetBufferedRegion( newRegion ); outImage->SetRequestedRegion( newRegion ); outImage->Allocate(); typedef itk::ResampleImageFilter ResampleFilter; typename ResampleFilter::Pointer resampler = ResampleFilter::New(); resampler->SetInput(itkImage); resampler->SetOutputParametersFromImage(outImage); QString outAdd; switch (m_Controls->m_InterpolatorBox->currentIndex()) { case 0: { typename itk::NearestNeighborInterpolateImageFunction::Pointer interp = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "NearestNeighbour"; break; } case 1: { typename itk::LinearInterpolateImageFunction::Pointer interp = itk::LinearInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "Linear"; break; } case 2: { typename itk::BSplineInterpolateImageFunction::Pointer interp = itk::BSplineInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "BSpline"; break; } case 3: { typename itk::WindowedSincInterpolateImageFunction::Pointer interp = itk::WindowedSincInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "WindowedSinc"; break; } default: { typename itk::NearestNeighborInterpolateImageFunction::Pointer interp = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "NearestNeighbour"; } } resampler->Update(); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( resampler->GetOutput() ); image->SetVolume( resampler->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_resampled_"+outAdd).toStdString().c_str()); GetDataStorage()->Add(imageNode, node); } void QmitkPreprocessingView::DoApplyHeader() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); bool isDti = false; bool isOdf = false; bool isPeak = false; if (!isDiffusionImage) { if ( dynamic_cast(node->GetData()) ) isDti = true; else if ( dynamic_cast(node->GetData()) ) isOdf = true; else if ( dynamic_cast(node->GetData()) ) isPeak = true; } mitk::Image::Pointer newImage = image->Clone(); mitk::Vector3D spacing; spacing[0] = m_Controls->m_HeaderSpacingX->value(); spacing[1] = m_Controls->m_HeaderSpacingY->value(); spacing[2] = m_Controls->m_HeaderSpacingZ->value(); newImage->GetGeometry()->SetSpacing( spacing ); mitk::Point3D origin; origin[0] = m_Controls->m_HeaderOriginX->value(); origin[1] = m_Controls->m_HeaderOriginY->value(); origin[2] = m_Controls->m_HeaderOriginZ->value(); newImage->GetGeometry()->SetOrigin(origin); vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New(); matrix->SetElement(0,3,newImage->GetGeometry()->GetOrigin()[0]); matrix->SetElement(1,3,newImage->GetGeometry()->GetOrigin()[1]); matrix->SetElement(2,3,newImage->GetGeometry()->GetOrigin()[2]); for (int r=0; r<3; r++) { for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item(r,c); if (!item) continue; matrix->SetElement(r,c,item->text().toDouble()); } } newImage->GetGeometry()->SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(matrix); if ( isDiffusionImage ) { 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) continue; mf[r][c] = item->text().toDouble(); } } PropHelper::SetMeasurementFrame(newImage, mf); PropHelper::InitializeImage( newImage ); } mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); if (isOdf) { mitk::OdfImage::ItkOdfImageType::Pointer itk_img = mitk::OdfImage::ItkOdfImageType::New(); mitk::CastToItkImage(newImage, itk_img); mitk::Image::Pointer odfImage = dynamic_cast(mitk::OdfImage::New().GetPointer()); mitk::CastToMitkImage(itk_img, odfImage); odfImage->SetVolume(itk_img->GetBufferPointer()); imageNode->SetData( odfImage ); } else if (isDti) { mitk::TensorImage::ItkTensorImageType::Pointer itk_img = mitk::ImageToItkImage(newImage); mitk::Image::Pointer tensorImage = dynamic_cast(mitk::TensorImage::New().GetPointer()); mitk::CastToMitkImage(itk_img, tensorImage); tensorImage->SetVolume(itk_img->GetBufferPointer()); imageNode->SetData( tensorImage ); } else if (isPeak) { mitk::PeakImage::ItkPeakImageType::Pointer itk_img = mitk::ImageToItkImage(newImage); mitk::Image::Pointer peakImage = dynamic_cast(mitk::PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_img, peakImage); peakImage->SetVolume(itk_img->GetBufferPointer()); imageNode->SetData( peakImage ); } else imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_newheader").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoProjectSignal() { switch(m_Controls->m_ProjectionMethodBox->currentIndex()) { case 0: DoADCAverage(); break; case 1: DoAKCFit(); break; case 2: DoBiExpFit(); break; default: DoADCAverage(); } } void QmitkPreprocessingView::DoDwiNormalization() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) { return; } auto gradientContainer = PropHelper::GetGradientContainer(image); int b0Index = -1; for (unsigned int i=0; isize(); i++) { GradientDirectionType g = gradientContainer->GetElement(i); if (g.magnitude()<0.001) { b0Index = i; break; } } if (b0Index==-1) { return; } typedef itk::DwiNormilzationFilter FilterType; ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkVectorImagePointer ); filter->SetGradientDirections(PropHelper::GetGradientContainer(image)); filter->SetNewMean(m_Controls->m_NewMean->value()); filter->SetNewStdev(m_Controls->m_NewStdev->value()); UcharImageType::Pointer itkImage = nullptr; if (m_Controls->m_NormalizationMaskBox->GetSelectedNode().IsNotNull()) { itkImage = UcharImageType::New(); if ( dynamic_cast(m_Controls->m_NormalizationMaskBox->GetSelectedNode()->GetData()) != nullptr ) { mitk::CastToItkImage( dynamic_cast(m_Controls->m_NormalizationMaskBox->GetSelectedNode()->GetData()), itkImage ); } filter->SetMaskImage(itkImage); } filter->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::CopyProperties(image, newImage, false); PropHelper::InitializeImage( newImage ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_normalized").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); } void QmitkPreprocessingView::DoLengthCorrection() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) return; mitk::Image::Pointer image = dynamic_cast(node->GetData()); if (image == nullptr ) return; if (!PropHelper::IsDiffusionWeightedImage(image)) return; typedef itk::DwiGradientLengthCorrectionFilter FilterType; ItkDwiType::Pointer itkVectorImagePointer = PropHelper::GetItkVectorImage(image); FilterType::Pointer filter = FilterType::New(); filter->SetRoundingValue( m_Controls->m_B_ValueMap_Rounder_SpinBox->value()); filter->SetReferenceBValue(PropHelper::GetReferenceBValue(image)); filter->SetReferenceGradientDirectionContainer(PropHelper::GetGradientContainer(image)); filter->Update(); mitk::Image::Pointer newImage = mitk::Image::New(); newImage->InitializeByItk( itkVectorImagePointer.GetPointer() ); newImage->SetImportVolume( itkVectorImagePointer->GetBufferPointer(), 0, 0, mitk::Image::CopyMemory); itkVectorImagePointer->GetPixelContainer()->ContainerManageMemoryOff(); PropHelper::CopyProperties(image, newImage, true); PropHelper::SetGradientContainer(newImage, filter->GetOutputGradientDirectionContainer()); PropHelper::SetReferenceBValue(newImage, filter->GetNewBValue()); PropHelper::InitializeImage( newImage ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_rounded").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); } void QmitkPreprocessingView::UpdateDwiBValueMapRounder(int i) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(node) ); if ( ! isDiffusionImage ) { return; } UpdateBValueTableWidget(i); + UpdateGradientDetails(); } void QmitkPreprocessingView:: CallMultishellToSingleShellFilter( itk::DWIVoxelFunctor * functor, mitk::Image::Pointer image, QString imageName, mitk::DataNode* parent ) { typedef itk::RadialMultishellToSingleshellImageFilter FilterType; // filter input parameter const mitk::BValueMapProperty::BValueMap& originalShellMap = PropHelper::GetBValueMap(image); ItkDwiType::Pointer itkVectorImagePointer = PropHelper::GetItkVectorImage(image); ItkDwiType* vectorImage = itkVectorImagePointer.GetPointer(); const GradProp::GradientDirectionsContainerType::Pointer gradientContainer = PropHelper::GetGradientContainer(image); const unsigned int& bValue = PropHelper::GetReferenceBValue(image); mitk::DataNode::Pointer imageNode = 0; // filter call FilterType::Pointer filter = FilterType::New(); filter->SetInput(vectorImage); filter->SetOriginalGradientDirections(gradientContainer); filter->SetOriginalBValueMap(originalShellMap); filter->SetOriginalBValue(bValue); filter->SetFunctor(functor); filter->Update(); // create new DWI image mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::CopyProperties(image, outImage, true); PropHelper::SetGradientContainer(outImage, filter->GetTargetGradientDirections()); PropHelper::SetReferenceBValue(outImage, m_Controls->m_targetBValueSpinBox->value()); PropHelper::InitializeImage( outImage ); imageNode = mitk::DataNode::New(); imageNode->SetData( outImage ); imageNode->SetName(imageName.toStdString().c_str()); GetDataStorage()->Add(imageNode, parent); } void QmitkPreprocessingView::DoBiExpFit() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) { return; } itk::BiExpFitFunctor::Pointer functor = itk::BiExpFitFunctor::New(); QString name(node->GetName().c_str()); const mitk::BValueMapProperty::BValueMap& originalShellMap = PropHelper::GetBValueMap(image); mitk::BValueMapProperty::BValueMap::const_iterator it = originalShellMap.begin(); ++it;/* skip b=0*/ unsigned int s = 0; /*shell index */ vnl_vector bValueList(originalShellMap.size()-1); while( it != originalShellMap.end() ) { bValueList.put(s++,(it++)->first); } const double targetBValue = m_Controls->m_targetBValueSpinBox->value(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); CallMultishellToSingleShellFilter(functor,image,name + "_BiExp", node); } void QmitkPreprocessingView::DoAKCFit() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) { return; } itk::KurtosisFitFunctor::Pointer functor = itk::KurtosisFitFunctor::New(); QString name(node->GetName().c_str()); const mitk::BValueMapProperty::BValueMap& originalShellMap = PropHelper::GetBValueMap(image); mitk::BValueMapProperty::BValueMap::const_iterator it = originalShellMap.begin(); ++it;/* skip b=0*/ unsigned int s = 0; /*shell index */ vnl_vector bValueList(originalShellMap.size()-1); while(it != originalShellMap.end()) bValueList.put(s++,(it++)->first); const double targetBValue = m_Controls->m_targetBValueSpinBox->value(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); CallMultishellToSingleShellFilter(functor,image,name + "_AKC", node); } void QmitkPreprocessingView::DoADCFit() { // later } void QmitkPreprocessingView::DoADCAverage() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) return; itk::ADCAverageFunctor::Pointer functor = itk::ADCAverageFunctor::New(); QString name(node->GetName().c_str()); const mitk::BValueMapProperty::BValueMap &originalShellMap = PropHelper::GetBValueMap(image); mitk::BValueMapProperty::BValueMap::const_iterator it = originalShellMap.begin(); ++it;/* skip b=0*/ unsigned int s = 0; /*shell index */ vnl_vector bValueList(originalShellMap.size()-1); while(it != originalShellMap.end()) bValueList.put(s++,(it++)->first); const double targetBValue = m_Controls->m_targetBValueSpinBox->value(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); CallMultishellToSingleShellFilter(functor,image,name + "_ADC", node); } void QmitkPreprocessingView::CleanBValueTableWidget() { m_Controls->m_B_ValueMap_TableWidget->clear(); m_Controls->m_B_ValueMap_TableWidget->setRowCount(1); QStringList headerList; headerList << "b-Value" << "Number of gradients"; m_Controls->m_B_ValueMap_TableWidget->setHorizontalHeaderLabels(headerList); m_Controls->m_B_ValueMap_TableWidget->setItem(0,0,new QTableWidgetItem("-")); m_Controls->m_B_ValueMap_TableWidget->setItem(0,1,new QTableWidgetItem("-")); } +void QmitkPreprocessingView::UpdateGradientDetails() +{ + mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); + mitk::Image::Pointer image = dynamic_cast(node->GetData()); + if ( image == nullptr ) { return; } + + bool isDiffusionImage(false); + + isDiffusionImage = PropHelper::IsDiffusionWeightedImage(image); + + if ( ! isDiffusionImage ) + { + m_Controls->m_WorkingGradientsText->clear(); + m_Controls->m_OriginalGradientsText->clear(); + return; + } + + auto gradientContainer = PropHelper::GetGradientContainer(image); + QString text = ""; + for (unsigned int j=0; jSize(); j++) + { + auto g = gradientContainer->at(j); + g = g.normalize(); + text += QString::number(g[0]); + if (jSize()-1) + text += " "; + else + text += "\n"; + } + for (unsigned int j=0; jSize(); j++) + { + auto g = gradientContainer->at(j); + g = g.normalize(); + text += QString::number(g[1]); + if (jSize()-1) + text += " "; + else + text += "\n"; + } + for (unsigned int j=0; jSize(); j++) + { + auto g = gradientContainer->at(j); + g = g.normalize(); + text += QString::number(g[2]); + if (jSize()-1) + text += " "; + else + text += "\n"; + } + + m_Controls->m_WorkingGradientsText->setPlainText(text); + + gradientContainer = PropHelper::GetOriginalGradientContainer(image); + text = ""; + for (unsigned int j=0; jSize(); j++) + { + auto g = gradientContainer->at(j); + g = g.normalize(); + text += QString::number(g[0]); + if (jSize()-1) + text += " "; + else + text += "\n"; + } + for (unsigned int j=0; jSize(); j++) + { + auto g = gradientContainer->at(j); + g = g.normalize(); + text += QString::number(g[1]); + if (jSize()-1) + text += " "; + else + text += "\n"; + } + for (unsigned int j=0; jSize(); j++) + { + auto g = gradientContainer->at(j); + g = g.normalize(); + text += QString::number(g[2]); + if (jSize()-1) + text += " "; + else + text += "\n"; + } + m_Controls->m_OriginalGradientsText->setPlainText(text); +} + void QmitkPreprocessingView::UpdateBValueTableWidget(int) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { CleanBValueTableWidget(); return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage(false); isDiffusionImage = PropHelper::IsDiffusionWeightedImage(image); if ( ! isDiffusionImage ) { CleanBValueTableWidget(); } else { typedef mitk::BValueMapProperty::BValueMap BValueMap; typedef mitk::BValueMapProperty::BValueMap::iterator BValueMapIterator; BValueMapIterator it; BValueMap roundedBValueMap = PropHelper::GetBValueMap(image); m_Controls->m_B_ValueMap_TableWidget->clear(); m_Controls->m_B_ValueMap_TableWidget->setRowCount(roundedBValueMap.size() ); QStringList headerList; headerList << "b-Value" << "Number of gradients"; m_Controls->m_B_ValueMap_TableWidget->setHorizontalHeaderLabels(headerList); int i = 0 ; for(it = roundedBValueMap.begin() ;it != roundedBValueMap.end(); it++) { m_Controls->m_B_ValueMap_TableWidget->setItem(i,0,new QTableWidgetItem(QString::number(it->first))); QTableWidgetItem* item = m_Controls->m_B_ValueMap_TableWidget->item(i,0); item->setFlags(item->flags() & ~Qt::ItemIsEditable); m_Controls->m_B_ValueMap_TableWidget->setItem(i,1,new QTableWidgetItem(QString::number(it->second.size()))); i++; } } } void QmitkPreprocessingView::OnSelectionChanged(berry::IWorkbenchPart::Pointer , const QList& nodes) { (void) nodes; this->OnImageSelectionChanged(); } void QmitkPreprocessingView::OnImageSelectionChanged() { 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 ); } { QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item( r, c ); delete item; item = new QTableWidgetItem(); m_Controls->m_DirectionMatrixTable->setItem( r, c, item ); } } bool foundImageVolume = true; mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } bool foundDwiVolume( PropHelper::IsDiffusionWeightedImage( node ) ); mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool multiComponentVolume = (image->GetPixelType().GetNumberOfComponents() > 1); bool threeDplusTVolume = (image->GetTimeSteps() > 1); m_Controls->m_ButtonAverageGradients->setEnabled(foundDwiVolume); m_Controls->m_ButtonExtractB0->setEnabled(foundDwiVolume); m_Controls->m_CheckExtractAll->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); m_Controls->m_MergeDwisButton->setEnabled(foundDwiVolume); m_Controls->m_B_ValueMap_Rounder_SpinBox->setEnabled(foundDwiVolume); m_Controls->m_ProjectSignalButton->setEnabled(foundDwiVolume); m_Controls->m_CreateLengthCorrectedDwi->setEnabled(foundDwiVolume); m_Controls->m_targetBValueSpinBox->setEnabled(foundDwiVolume); m_Controls->m_NormalizeImageValuesButton->setEnabled(foundDwiVolume); m_Controls->m_RemoveGradientButton->setEnabled(foundDwiVolume); m_Controls->m_ExtractGradientButton->setEnabled(foundDwiVolume); m_Controls->m_FlipGradientsButton->setEnabled(foundDwiVolume); m_Controls->m_ClearRotationButton->setEnabled(foundDwiVolume); m_Controls->m_DirectionMatrixTable->setEnabled(foundImageVolume); m_Controls->m_ModifyHeader->setEnabled(foundImageVolume); m_Controls->m_AlignImageBox->setEnabled(foundImageVolume); // we do not support multi-component and 3D+t images for certain operations bool foundSingleImageVolume = foundDwiVolume || (foundImageVolume && !(multiComponentVolume || threeDplusTVolume)); m_Controls->m_FlipAxis->setEnabled(foundSingleImageVolume); m_Controls->m_CropImageButton->setEnabled(foundSingleImageVolume); m_Controls->m_ExtractBrainMask->setEnabled(foundSingleImageVolume); m_Controls->m_ResampleImageButton->setEnabled(foundSingleImageVolume); // reset sampling frame to 1 and update all ealted components m_Controls->m_B_ValueMap_Rounder_SpinBox->setValue(1); UpdateBValueTableWidget(m_Controls->m_B_ValueMap_Rounder_SpinBox->value()); DoUpdateInterpolationGui(m_Controls->m_ResampleTypeBox->currentIndex()); + UpdateGradientDetails(); m_Controls->m_HeaderSpacingX->setValue(image->GetGeometry()->GetSpacing()[0]); m_Controls->m_HeaderSpacingY->setValue(image->GetGeometry()->GetSpacing()[1]); m_Controls->m_HeaderSpacingZ->setValue(image->GetGeometry()->GetSpacing()[2]); m_Controls->m_HeaderOriginX->setValue(image->GetGeometry()->GetOrigin()[0]); m_Controls->m_HeaderOriginY->setValue(image->GetGeometry()->GetOrigin()[1]); m_Controls->m_HeaderOriginZ->setValue(image->GetGeometry()->GetOrigin()[2]); m_Controls->m_XstartBox->setMaximum(image->GetGeometry()->GetExtent(0)-1); m_Controls->m_YstartBox->setMaximum(image->GetGeometry()->GetExtent(1)-1); m_Controls->m_ZstartBox->setMaximum(image->GetGeometry()->GetExtent(2)-1); m_Controls->m_XendBox->setMaximum(image->GetGeometry()->GetExtent(0)-1); m_Controls->m_YendBox->setMaximum(image->GetGeometry()->GetExtent(1)-1); m_Controls->m_ZendBox->setMaximum(image->GetGeometry()->GetExtent(2)-1); for (int r=0; r<3; r++) for (int c=0; c<3; c++) { // Direction matrix QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item( r, c ); delete item; item = new QTableWidgetItem(); item->setTextAlignment(Qt::AlignCenter | Qt::AlignVCenter); double val = image->GetGeometry()->GetVtkMatrix()->GetElement(r,c)/image->GetGeometry()->GetSpacing()[c]; item->setText(QString::number(val)); m_Controls->m_DirectionMatrixTable->setItem( r, c, item ); } if (foundDwiVolume) { m_Controls->m_InputData->setTitle("Input Data"); vnl_matrix_fixed< double, 3, 3 > mf = PropHelper::GetMeasurementFrame(image); for (int r=0; r<3; r++) for (int c=0; c<3; c++) { // Measurement frame 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 ); } //calculate target bValue for MultishellToSingleShellfilter const mitk::BValueMapProperty::BValueMap & bValMap = PropHelper::GetBValueMap(image); mitk::BValueMapProperty::BValueMap::const_iterator it = bValMap.begin(); unsigned int targetBVal = 0; while(it != bValMap.end()) { targetBVal += (it++)->first; } targetBVal /= (float)bValMap.size()-1; m_Controls->m_targetBValueSpinBox->setValue(targetBVal); m_Controls->m_RemoveGradientBox->setMaximum(PropHelper::GetGradientContainer(image)->Size()-1); m_Controls->m_ExtractGradientBox->setMaximum(PropHelper::GetGradientContainer(image)->Size()-1); } } void QmitkPreprocessingView::Activated() { } void QmitkPreprocessingView::Deactivated() { OnImageSelectionChanged(); } void QmitkPreprocessingView::Visible() { OnImageSelectionChanged(); } void QmitkPreprocessingView::Hidden() { } void QmitkPreprocessingView::DoClearRotationOfGradients() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) return; mitk::Image::Pointer image = dynamic_cast(node->GetData()); if (image == nullptr) return; if(!PropHelper::IsDiffusionWeightedImage(image)) return; mitk::Image::Pointer newDwi = image->Clone(); PropHelper::InitializeImage( newDwi ); PropHelper::ClearMeasurementFrameAndRotationMatrixFromGradients(newDwi); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = node->GetName().c_str(); imageNode->SetName( (name+"_OriginalGradients").toStdString().c_str() ); GetDataStorage()->Add( imageNode, node ); } void QmitkPreprocessingView::DoFlipGradientDirections() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } mitk::Image::Pointer newDwi = image->Clone(); auto gradientContainer = PropHelper::GetGradientContainer(newDwi); for (unsigned int j=0; jSize(); j++) { if (m_Controls->m_FlipGradBoxX->isChecked()) { gradientContainer->at(j)[0] *= -1; } if (m_Controls->m_FlipGradBoxY->isChecked()) { gradientContainer->at(j)[1] *= -1; } if (m_Controls->m_FlipGradBoxZ->isChecked()) { gradientContainer->at(j)[2] *= -1; } } PropHelper::CopyProperties(image, newDwi, true); PropHelper::SetGradientContainer(newDwi, gradientContainer); PropHelper::InitializeImage( newDwi ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = node->GetName().c_str(); imageNode->SetName( (name+"_GradientFlip").toStdString().c_str() ); GetDataStorage()->Add( imageNode, node ); } void QmitkPreprocessingView::DoHalfSphereGradientDirections() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } mitk::Image::Pointer newDwi = image->Clone(); auto gradientContainer = PropHelper::GetGradientContainer(newDwi); for (unsigned int j=0; jSize(); j++) { if (gradientContainer->at(j)[0]<0) { gradientContainer->at(j) = -gradientContainer->at(j); } } PropHelper::CopyProperties(image, newDwi, true); PropHelper::SetGradientContainer(newDwi, gradientContainer); PropHelper::InitializeImage( newDwi ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = node->GetName().c_str(); imageNode->SetName( (name+"_halfsphere").toStdString().c_str() ); GetDataStorage()->Add( imageNode, node ); } void QmitkPreprocessingView::DoShowGradientDirections() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } int maxIndex = 0; unsigned int maxSize = image->GetDimension(0); if (maxSizeGetDimension(1)) { maxSize = image->GetDimension(1); maxIndex = 1; } if (maxSizeGetDimension(2)) { maxSize = image->GetDimension(2); maxIndex = 2; } mitk::Point3D origin = image->GetGeometry()->GetOrigin(); mitk::PointSet::Pointer originSet = mitk::PointSet::New(); typedef mitk::BValueMapProperty::BValueMap BValueMap; typedef mitk::BValueMapProperty::BValueMap::iterator BValueMapIterator; BValueMap bValMap = PropHelper::GetBValueMap(image); auto gradientContainer = PropHelper::GetGradientContainer(image); mitk::BaseGeometry::Pointer geometry = image->GetGeometry(); int shellCount = 1; for(BValueMapIterator it = bValMap.begin(); it!=bValMap.end(); ++it) { mitk::PointSet::Pointer pointset = mitk::PointSet::New(); for (unsigned int j=0; jsecond.size(); j++) { mitk::Point3D ip; vnl_vector_fixed< double, 3 > v = gradientContainer->at(it->second[j]); if (v.magnitude()>mitk::eps) { ip[0] = v[0]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[0]-0.5*geometry->GetSpacing()[0] + geometry->GetSpacing()[0]*image->GetDimension(0)/2; ip[1] = v[1]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[1]-0.5*geometry->GetSpacing()[1] + geometry->GetSpacing()[1]*image->GetDimension(1)/2; ip[2] = v[2]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[2]-0.5*geometry->GetSpacing()[2] + geometry->GetSpacing()[2]*image->GetDimension(2)/2; pointset->InsertPoint(j, ip); } else if (originSet->IsEmpty()) { ip[0] = v[0]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[0]-0.5*geometry->GetSpacing()[0] + geometry->GetSpacing()[0]*image->GetDimension(0)/2; ip[1] = v[1]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[1]-0.5*geometry->GetSpacing()[1] + geometry->GetSpacing()[1]*image->GetDimension(1)/2; ip[2] = v[2]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[2]-0.5*geometry->GetSpacing()[2] + geometry->GetSpacing()[2]*image->GetDimension(2)/2; originSet->InsertPoint(j, ip); } } if ( it->first < mitk::eps ) { continue; } // add shell to datastorage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pointset); QString name = node->GetName().c_str(); name += "_Shell_"; name += QString::number( it->first ); newNode->SetName( name.toStdString().c_str() ); newNode->SetProperty( "pointsize", mitk::FloatProperty::New((float)maxSize / 50) ); int b0 = shellCount % 2; int b1 = 0; int b2 = 0; if (shellCount>4) { b2 = 1; } if (shellCount%4 >= 2) { b1 = 1; } newNode->SetProperty("color", mitk::ColorProperty::New( b2, b1, b0 )); GetDataStorage()->Add( newNode, node ); shellCount++; } // add origin to datastorage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(originSet); QString name = node->GetName().c_str(); name += "_Origin"; newNode->SetName(name.toStdString().c_str()); newNode->SetProperty("pointsize", mitk::FloatProperty::New((float)maxSize/50)); newNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); GetDataStorage()->Add(newNode, node); } void QmitkPreprocessingView::DoReduceGradientDirections() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } typedef itk::ElectrostaticRepulsionDiffusionGradientReductionFilter FilterType; typedef mitk::BValueMapProperty::BValueMap BValueMap; // GetShellSelection from GUI BValueMap shellSlectionMap; BValueMap originalShellMap = PropHelper::GetBValueMap(image); std::vector newNumGradientDirections; int shellCounter = 0; QString name = node->GetName().c_str(); for (int i=0; im_B_ValueMap_TableWidget->rowCount(); i++) { double BValue = m_Controls->m_B_ValueMap_TableWidget->item(i,0)->text().toDouble(); shellSlectionMap[BValue] = originalShellMap[BValue]; unsigned int num = m_Controls->m_B_ValueMap_TableWidget->item(i,1)->text().toUInt(); newNumGradientDirections.push_back(num); name += "_"; name += QString::number(num); shellCounter++; } if (newNumGradientDirections.empty()) { return; } auto gradientContainer = PropHelper::GetGradientContainer(image); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkVectorImagePointer ); filter->SetOriginalGradientDirections(gradientContainer); filter->SetNumGradientDirections(newNumGradientDirections); filter->SetOriginalBValueMap(originalShellMap); filter->SetShellSelectionBValueMap(shellSlectionMap); filter->SetUseFirstN(m_Controls->m_KeepFirstNBox->isChecked()); filter->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::CopyProperties(image, newImage, true); PropHelper::SetGradientContainer(newImage, filter->GetGradientDirections()); PropHelper::InitializeImage(newImage); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); imageNode->SetName(name.toStdString().c_str()); GetDataStorage()->Add(imageNode, node); // update the b-value widget to remove the modified number of gradients used for extraction this->CleanBValueTableWidget(); this->UpdateBValueTableWidget(0); + this->UpdateGradientDetails(); } void QmitkPreprocessingView::MergeDwis() { typedef GradProp::GradientDirectionsContainerType GradientContainerType; mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } mitk::DataNode::Pointer node2 = m_Controls->m_MergeDwiBox->GetSelectedNode(); if (node2.IsNull()) { return; } mitk::Image::Pointer image2 = dynamic_cast(node2->GetData()); if ( image2 == nullptr ) { return; } typedef itk::VectorImage DwiImageType; typedef std::vector< DwiImageType::Pointer > DwiImageContainerType; typedef std::vector< GradientContainerType::Pointer > GradientListContainerType; DwiImageContainerType imageContainer; GradientListContainerType gradientListContainer; std::vector< double > bValueContainer; QString name = ""; { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); imageContainer.push_back( itkVectorImagePointer ); gradientListContainer.push_back(PropHelper::GetGradientContainer(image)); bValueContainer.push_back(PropHelper::GetReferenceBValue(image)); name += node->GetName().c_str(); } { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image2, itkVectorImagePointer); imageContainer.push_back( itkVectorImagePointer ); gradientListContainer.push_back(PropHelper::GetGradientContainer(image2)); bValueContainer.push_back(PropHelper::GetReferenceBValue(image2)); name += "+"; name += node2->GetName().c_str(); } typedef itk::MergeDiffusionImagesFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetImageVolumes(imageContainer); filter->SetGradientLists(gradientListContainer); filter->SetBValues(bValueContainer); filter->Update(); vnl_matrix_fixed< double, 3, 3 > mf; mf.set_identity(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::SetGradientContainer(newImage, filter->GetOutputGradients()); PropHelper::SetMeasurementFrame(newImage, mf); PropHelper::SetReferenceBValue(newImage, filter->GetB_Value()); PropHelper::InitializeImage( newImage ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); imageNode->SetName(name.toStdString().c_str()); GetDataStorage()->Add(imageNode); } void QmitkPreprocessingView::ExtractB0() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } // call the extraction withou averaging if the check-box is checked if( this->m_Controls->m_CheckExtractAll->isChecked() ) { DoExtractBOWithoutAveraging(); return; } ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); // Extract image using found index typedef itk::B0ImageExtractionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkVectorImagePointer ); filter->SetDirections(PropHelper::GetGradientContainer(image)); filter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( filter->GetOutput() ); mitkImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer newNode=mitk::DataNode::New(); newNode->SetData( mitkImage ); newNode->SetProperty( "name", mitk::StringProperty::New(node->GetName() + "_B0")); GetDataStorage()->Add(newNode, node); } void QmitkPreprocessingView::DoExtractBOWithoutAveraging() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } // typedefs typedef itk::B0ImageExtractionToSeparateImageFilter< short, short> FilterType; ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); // Extract image using found index FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkVectorImagePointer ); filter->SetDirections(PropHelper::GetGradientContainer(image)); filter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( filter->GetOutput() ); mitkImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer newNode=mitk::DataNode::New(); newNode->SetData( mitkImage ); newNode->SetProperty( "name", mitk::StringProperty::New(node->GetName() + "_B0_ALL")); GetDataStorage()->Add(newNode, node); /*A reinitialization is needed to access the time channels via the ImageNavigationController The Global-Geometry can not recognize the time channel without a re-init. (for a new selection in datamanger a automatically updated of the Global-Geometry should be done - if it contains the time channel)*/ mitk::RenderingManager::GetInstance()->InitializeViews( newNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); } void QmitkPreprocessingView::AverageGradients() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) return; mitk::Image::Pointer newDwi = image->Clone(); PropHelper::AverageRedundantGradients(newDwi, m_Controls->m_Blur->value()); PropHelper::InitializeImage(newDwi); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_averaged").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.h index a196f9b798..eb6690bf5b 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.h @@ -1,158 +1,159 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef _QMITKPREPROCESSINGVIEW_H_INCLUDED #define _QMITKPREPROCESSINGVIEW_H_INCLUDED #include #include #include "ui_QmitkPreprocessingViewControls.h" // st includes #include // itk includes #include #include // mitk includes #include #include "itkDWIVoxelFunctor.h" #include #include #include #include #include typedef short DiffusionPixelType; struct PrpSelListener; /*! * \ingroup org_mitk_gui_qt_preprocessing_internal * * \brief Viewing and modifying diffusion weighted images (gradient reduction, resampling, b-value projection, ...) * */ class QmitkPreprocessingView : public QmitkAbstractView, public mitk::ILifecycleAwarePart { 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 mitk::DiffusionPropertyHelper::GradientDirectionType GradientDirectionType; typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType; typedef itk::VectorImage< short, 3 > ItkDwiType; typedef itk::Image< unsigned char, 3 > UcharImageType; typedef itk::Image< double, 3 > ItkDoubleImageType; typedef mitk::DiffusionPropertyHelper PropHelper; typedef mitk::GradientDirectionsProperty GradProp; QmitkPreprocessingView(); virtual ~QmitkPreprocessingView(); virtual void CreateQtPartControl(QWidget *parent) override; /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); virtual void Activated() override; virtual void Deactivated() override; virtual void Visible() override; virtual void Hidden() override; /// /// Sets the focus to an internal widget. /// virtual void SetFocus() override; static const int nrconvkernels; protected slots: void AverageGradients(); void ExtractB0(); void MergeDwis(); void DoApplyHeader(); void DoReduceGradientDirections(); void DoShowGradientDirections(); void DoHalfSphereGradientDirections(); void UpdateDwiBValueMapRounder(int i); void DoLengthCorrection(); void DoDwiNormalization(); void DoProjectSignal(); void DoExtractBrainMask(); void DoResampleImage(); void DoCropImage(); void DoUpdateInterpolationGui(int i); void DoRemoveGradient(); void DoExtractGradient(); void DoFlipAxis(); void OnImageSelectionChanged(); void DoFlipGradientDirections(); void DoClearRotationOfGradients(); void DoAlignImages(); protected: void DoADCFit(); void DoAKCFit(); void DoBiExpFit(); void DoADCAverage(); template < typename TPixel, unsigned int VImageDimension > void TemplatedFlipAxis( itk::Image* itkImage); template < typename TPixel, unsigned int VImageDimension > void TemplatedCropImage( itk::Image* itkImage); template < typename TPixel, unsigned int VImageDimension > void TemplatedResampleImage( itk::Image* itkImage); /** Called by ExtractB0 if check-box activated, extracts all b0 images without averaging */ void DoExtractBOWithoutAveraging(); void UpdateBValueTableWidget(int); + void UpdateGradientDetails(); /// \brief called by QmitkAbstractView when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; Ui::QmitkPreprocessingViewControls* m_Controls; void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name); void CallMultishellToSingleShellFilter( itk::DWIVoxelFunctor * functor, mitk::Image::Pointer ImPtr, QString imageName, mitk::DataNode* parent ); void CleanBValueTableWidget(); }; #endif // _QMITKPREPROCESSINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingViewControls.ui index f1e9f15e88..dbcdfbf628 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingViewControls.ui @@ -1,1748 +1,1807 @@ QmitkPreprocessingViewControls 0 0 503 1001 0 0 false QmitkPreprocessingViewControls true QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; } 25 Please Select Input Data 6 6 6 6 Image: QComboBox::AdjustToMinimumContentsLength 0 Gradients 25 - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - 0 - 0 - - - - Qt::ScrollBarAsNeeded - - - Qt::ScrollBarAlwaysOff + + + + Remove or extract gradient volumes - - true - - - 100 - - - true - - - false - - - true - - - - b-Value + + + 6 - - - - Number of gradients + + 6 - + + 6 + + + 6 + + + 6 + + + 6 + + + + + false + + + Remove gradient volume + + + + + + + + + + false + + + Extract gradient volume + + + + + + + QFrame::NoFrame QFrame::Raised 0 0 0 0 6 <html><head/><body><p>Define the sampling frame the b-Values are rounded with.</p></body></html> Sampling frame: false <html><head/><body><p>Round b-values to nearest multiple of this value (click &quot;Round b-value&quot; to create new image with these values).</p></body></html> QAbstractSpinBox::CorrectToNearestValue 1 10000 10 false Sometimes the gradient directions are not located on one half sphere. Mirror gradients to half sphere false Generate pointset displaying the gradient vectors (applied measurement frame). Show gradients false Generate pointset displaying the gradient vectors (applied measurement frame). Flip gradients false Retain only the specified number of gradient directions and according image volumes. The retained directions are spread equally over the half sphere using an iterative energy repulsion strategy. Reduce number of gradients QFrame::NoFrame QFrame::Plain 0 0 0 0 0 x y z false Round b-values false By default, the image matrix is applied to the image gradients. This button removes this additional rotation. Clear rotation of gradients Don't optimize gradients to retain, simply keep first n gradients per b-value. first n - - - - Remove or extract gradient volumes + + + + 0 - - - 6 - - - 6 - - - 6 - - - 6 - - - 6 + + + Original Gradients + + + + + + Qt::ScrollBarAsNeeded + + + Qt::ScrollBarAsNeeded + + + QAbstractScrollArea::AdjustIgnored + + + QPlainTextEdit::NoWrap + + + true + + + + + + + + Working Gradients + + + + + + Qt::ScrollBarAsNeeded + + + Qt::ScrollBarAsNeeded + + + QAbstractScrollArea::AdjustIgnored + + + QPlainTextEdit::NoWrap + + + true + + + + + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + 0 + 0 + + + + Qt::ScrollBarAsNeeded + + + Qt::ScrollBarAlwaysOff + + + true + + + 100 + + + true + + + false + + + true + + + + b-Value - - 6 + + + + Number of gradients - - - - false - - - Remove gradient volume - - - - - - - - - - false - - - Extract gradient volume - - - - - - - + Image Values 25 Qt::Vertical 20 40 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 QFrame::NoFrame QFrame::Raised 0 0 0 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 Merges selected DWIs of same dimension. If several b-values are present, the resulting image will contain multiple b-shells. Merge selected DWIs false Normalizes the diffusion-weighted image values across all weighted volumes to the given mean and standard deviation. Normalize image values QFrame::NoFrame QFrame::Raised 0 0 0 0 0 false Target b-value 100000 500 Select projection method. QComboBox::AdjustToMinimumContentsLength ADC Average AKC Bi-Exponential false 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 by taking all directions within a certain radius into account. Average repetitions false Project image values onto one b-shell. Project onto shell QFrame::NoFrame QFrame::Raised 0 0 0 0 0 true New stdev 100000 100 500 Select binary mask image. The mask is used to calculate the old mean and standard deviation. QComboBox::AdjustToMinimumContentsLength true New mean value 100000 100 1000 false Merges selected DWIs of same dimension. If several b-values are present, the resulting image will contain multiple b-shells. Flip axis QFrame::NoFrame QFrame::Raised 0 0 0 0 Y Qt::Horizontal 40 20 X Z Axis: QComboBox::AdjustToMinimumContentsLength Resample image 6 6 6 6 6 QFrame::NoFrame QFrame::Raised 0 0 0 0 0 0.010000000000000 2.000000000000000 0.010000000000000 2.000000000000000 0.010000000000000 2.000000000000000 Sampling factor New image spacing New image size QFrame::NoFrame QFrame::Raised 0 0 0 0 0 Interpolator: Nearest neighbour Linear B-spline Windowed sinc false Resample image QFrame::NoFrame QFrame::Raised 0 0 0 0 0 1 10000 1 10000 1 10000 Crop Image 6 6 6 6 6 x: y: z: Crop Image Header 25 Voxel size 6 6 6 6 4 0.000000000000000 99.989999999999995 4 4 false Apply new header information Direction matrix 6 6 6 6 false 0 0 0 0 IBeamCursor true Qt::ScrollBarAlwaysOff Qt::ScrollBarAlwaysOff true false false true true 0 false true true New Row New Row New Row New Column New Column New Column Qt::Horizontal 40 20 0 0 Measurment frame 6 6 6 6 false 0 0 0 0 IBeamCursor true Qt::ScrollBarAlwaysOff Qt::ScrollBarAlwaysOff true false false true true 0 false true true New Row New Row New Row New Column New Column New Column Qt::Horizontal 40 20 Qt::Vertical 20 40 Origin 6 6 6 6 4 -999999999.000000000000000 999999999.000000000000000 4 -99999999.000000000000000 999999999.000000000000000 4 -999999999.000000000000000 999999999.000000000000000 Align origins 6 6 6 6 QComboBox::AdjustToMinimumContentsLength Align to Other false If multiple baseline acquisitions are present, the default behaviour is to output an averaged image. Estimate binary brain mask Maximum number of iterations. 10000 10000 Qt::Vertical 20 40 false If multiple baseline acquisitions are present, the default behaviour is to output an averaged image. Extract baseline image Create a 3D+t data set containing all b0 images as timesteps Disable averaging QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkDataStorageComboBoxWithSelectNone QComboBox
QmitkDataStorageComboBoxWithSelectNone.h
 m_SelctedImageComboBox tabWidget m_B_ValueMap_TableWidget m_CreateLengthCorrectedDwi m_B_ValueMap_Rounder_SpinBox m_FlipGradientsButton m_FlipGradBoxX m_FlipGradBoxY m_FlipGradBoxZ m_ShowGradientsButton m_MirrorGradientToHalfSphereButton m_ReduceGradientsButton m_ClearRotationButton m_RemoveGradientButton m_RemoveGradientBox m_ExtractGradientButton m_ExtractGradientBox m_ButtonAverageGradients m_Blur m_ProjectSignalButton m_targetBValueSpinBox m_ProjectionMethodBox m_NormalizeImageValuesButton m_NewMean m_NewStdev m_NormalizationMaskBox m_FlipAxis m_FlipX m_FlipY m_FlipZ m_MergeDwisButton m_MergeDwiBox m_ResampleTypeBox m_ResampleDoubleX m_ResampleDoubleY m_ResampleDoubleZ m_ResampleIntX m_ResampleIntY m_ResampleIntZ m_InterpolatorBox m_ResampleImageButton m_XstartBox m_XendBox m_YstartBox m_YendBox m_ZstartBox m_ZendBox m_CropImageButton m_ModifyHeader m_HeaderOriginX m_HeaderOriginY m_HeaderOriginZ m_HeaderSpacingX m_HeaderSpacingY m_HeaderSpacingZ m_DirectionMatrixTable m_MeasurementFrameTable m_ButtonExtractB0 m_CheckExtractAll m_ExtractBrainMask m_BrainMaskIterationsBox diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.cpp index 15933e1b06..e28dd5db5e 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.cpp @@ -1,396 +1,403 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ //misc #define _USE_MATH_DEFINES #include // Blueberry #include #include // Qmitk #include "QmitkSimpleRegistrationView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include // Qt #include #define _USE_MATH_DEFINES #include const std::string QmitkSimpleRegistrationView::VIEW_ID = "org.mitk.views.simpleregistrationview"; QmitkSimpleRegistrationView::QmitkSimpleRegistrationView() : QmitkAbstractView() , m_Controls( 0 ) , m_RegistrationType(0) { } // Destructor QmitkSimpleRegistrationView::~QmitkSimpleRegistrationView() { } void QmitkSimpleRegistrationView::StartRegistration() { QmitkRegistrationJob* pJob; if (m_Controls->m_RegBox->currentIndex()==0) { mitk::MultiModalRigidDefaultRegistrationAlgorithm< ItkFloatImageType >::Pointer algo = mitk::MultiModalRigidDefaultRegistrationAlgorithm< ItkFloatImageType >::New(); pJob = new QmitkRegistrationJob(algo); m_RegistrationType = 0; } else { mitk::MultiModalAffineDefaultRegistrationAlgorithm< ItkFloatImageType >::Pointer algo = mitk::MultiModalAffineDefaultRegistrationAlgorithm< ItkFloatImageType >::New(); pJob = new QmitkRegistrationJob(algo); m_RegistrationType = 1; } pJob->setAutoDelete(true); m_MovingImageNode = m_Controls->m_MovingImageBox->GetSelectedNode(); mitk::Image::Pointer movingImage = dynamic_cast(m_MovingImageNode->GetData()); if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(movingImage)) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(movingImage, itkVectorImagePointer); itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); filter->SetInput( itkVectorImagePointer); filter->SetChannelIndex(m_Controls->m_MovingChannelBox->value()); filter->Update(); mitk::Image::Pointer newImage = mitk::Image::New(); newImage->InitializeByItk( filter->GetOutput() ); newImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); pJob->m_spMovingData = newImage; } else pJob->m_spMovingData = movingImage; mitk::Image::Pointer fixedImage = dynamic_cast(m_Controls->m_FixedImageBox->GetSelectedNode()->GetData()); if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(fixedImage)) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(fixedImage, itkVectorImagePointer); itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); filter->SetInput( itkVectorImagePointer); filter->SetChannelIndex(m_Controls->m_MovingChannelBox->value()); filter->Update(); mitk::Image::Pointer newImage = mitk::Image::New(); newImage->InitializeByItk( filter->GetOutput() ); newImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); pJob->m_spTargetData = newImage; } else pJob->m_spTargetData = fixedImage; pJob->m_TargetDataUID = mitk::EnsureUID(m_Controls->m_FixedImageBox->GetSelectedNode()->GetData()); pJob->m_MovingDataUID = mitk::EnsureUID(m_Controls->m_MovingImageBox->GetSelectedNode()->GetData()); connect(pJob, SIGNAL(RegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer, const QmitkRegistrationJob*)), this, SLOT(OnRegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer, const QmitkRegistrationJob*)), Qt::BlockingQueuedConnection); QThreadPool* threadPool = QThreadPool::globalInstance(); threadPool->start(pJob); m_Controls->m_RegistrationStartButton->setEnabled(false); m_Controls->m_RegistrationStartButton->setText("Registration in progress ..."); } void QmitkSimpleRegistrationView::OnRegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer spResultRegistration, const QmitkRegistrationJob* job) { mitk::Image::Pointer movingImage = dynamic_cast(m_MovingImageNode->GetData()); mitk::Image::Pointer image; if (m_RegistrationType==0 && !m_Controls->m_ResampleBox->isChecked()) { image = mitk::ImageMappingHelper::refineGeometry(movingImage, spResultRegistration, true); + + mitk::DiffusionPropertyHelper::CopyProperties(movingImage, image, true); + auto reg = spResultRegistration->GetRegistration(); + typedef mitk::DiffusionImageCorrectionFilter CorrectionFilterType; + CorrectionFilterType::Pointer corrector = CorrectionFilterType::New(); + corrector->SetImage( image ); + corrector->CorrectDirections( mitk::MITKRegistrationHelper::getAffineMatrix(reg, false)->GetMatrix().GetVnlMatrix() ); } else { if (!mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(movingImage)) { image = mitk::ImageMappingHelper::map(movingImage, spResultRegistration, false, 0, job->m_spTargetData->GetGeometry(), false, 0, mitk::ImageMappingInterpolator::BSpline_3); } else { typedef itk::ComposeImageFilter < ITKDiffusionVolumeType > ComposeFilterType; ComposeFilterType::Pointer composer = ComposeFilterType::New(); ItkDwiType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(movingImage); for (unsigned int i=0; iGetVectorLength(); ++i) { itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); filter->SetInput( itkVectorImagePointer); filter->SetChannelIndex(i); filter->Update(); mitk::Image::Pointer gradientVolume = mitk::Image::New(); gradientVolume->InitializeByItk( filter->GetOutput() ); gradientVolume->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); mitk::Image::Pointer registered_mitk_image = mitk::ImageMappingHelper::map(gradientVolume, spResultRegistration, false, 0, job->m_spTargetData->GetGeometry(), false, 0, mitk::ImageMappingInterpolator::BSpline_3); ITKDiffusionVolumeType::Pointer registered_itk_image = ITKDiffusionVolumeType::New(); mitk::CastToItkImage(registered_mitk_image, registered_itk_image); composer->SetInput(i, registered_itk_image); } composer->Update(); image = mitk::GrabItkImageMemory( composer->GetOutput() ); mitk::DiffusionPropertyHelper::CopyProperties(movingImage, image, true); auto reg = spResultRegistration->GetRegistration(); typedef mitk::DiffusionImageCorrectionFilter CorrectionFilterType; CorrectionFilterType::Pointer corrector = CorrectionFilterType::New(); corrector->SetImage( image ); corrector->CorrectDirections( mitk::MITKRegistrationHelper::getAffineMatrix(reg, false)->GetMatrix().GetVnlMatrix() ); } } if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image)) mitk::DiffusionPropertyHelper::InitializeImage( image ); mitk::DataNode::Pointer resultNode = mitk::DataNode::New(); resultNode->SetData(image); if (m_MovingImageNode.IsNotNull()) { m_MovingImageNode->SetVisibility(false); QString name = m_MovingImageNode->GetName().c_str(); if (m_RegistrationType==0) resultNode->SetName((name+"_registered (rigid)").toStdString().c_str()); else resultNode->SetName((name+"_registered (affine)").toStdString().c_str()); } else { if (m_RegistrationType==0) resultNode->SetName("Registered (rigid)"); else resultNode->SetName("Registered (affine)"); } // resultNode->SetOpacity(0.6); // resultNode->SetColor(0.0, 0.0, 1.0); GetDataStorage()->Add(resultNode); mitk::RenderingManager::GetInstance()->InitializeViews( resultNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); if (m_Controls->m_RegOutputBox->isChecked()) { mitk::DataNode::Pointer registration_node = mitk::DataNode::New(); registration_node->SetData(spResultRegistration); if (m_RegistrationType==0) registration_node->SetName("Registration Object (rigid)"); else registration_node->SetName("Registration Object (affine)"); GetDataStorage()->Add(registration_node, resultNode); } this->GetRenderWindowPart()->RequestUpdate(); m_Controls->m_RegistrationStartButton->setEnabled(true); m_Controls->m_RegistrationStartButton->setText("Start Registration"); m_MovingImageNode = nullptr; TractoChanged(); } void QmitkSimpleRegistrationView::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::QmitkSimpleRegistrationViewControls; m_Controls->setupUi( parent ); m_Controls->m_FixedImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_MovingImageBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isImagePredicate = mitk::TNodePredicateDataType::New(); m_Controls->m_FixedImageBox->SetPredicate(isImagePredicate); m_Controls->m_MovingImageBox->SetPredicate(isImagePredicate); mitk::TNodePredicateDataType::Pointer isFib = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isReg = mitk::TNodePredicateDataType::New(); m_Controls->m_TractoBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_RegObjectBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TractoBox->SetPredicate(isFib); m_Controls->m_RegObjectBox->SetPredicate(isReg); connect( m_Controls->m_FixedImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(FixedImageChanged()) ); connect( m_Controls->m_MovingImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(MovingImageChanged()) ); connect( m_Controls->m_TractoBox, SIGNAL(currentIndexChanged(int)), this, SLOT(TractoChanged()) ); connect( m_Controls->m_RegObjectBox, SIGNAL(currentIndexChanged(int)), this, SLOT(TractoChanged()) ); connect( m_Controls->m_RegistrationStartButton, SIGNAL(clicked()), this, SLOT(StartRegistration()) ); connect( m_Controls->m_TractoRegistrationStartButton, SIGNAL(clicked()), this, SLOT(StartTractoRegistration()) ); FixedImageChanged(); MovingImageChanged(); TractoChanged(); } } void QmitkSimpleRegistrationView::StartTractoRegistration() { mitk::FiberBundle::Pointer fib = dynamic_cast(m_Controls->m_TractoBox->GetSelectedNode()->GetData()); mitk::MAPRegistrationWrapper::Pointer reg = dynamic_cast(m_Controls->m_RegObjectBox->GetSelectedNode()->GetData()); mitk::MITKRegistrationHelper::Affine3DTransformType::Pointer affine = mitk::MITKRegistrationHelper::getAffineMatrix(reg, false); mitk::FiberBundle::Pointer fib_copy = fib->GetDeepCopy(); fib_copy->TransformFibers(affine); mitk::DataNode::Pointer registration_node = mitk::DataNode::New(); registration_node->SetData(fib_copy); QString name = m_Controls->m_TractoBox->GetSelectedNode()->GetName().c_str(); registration_node->SetName((name+"_registered").toStdString().c_str()); GetDataStorage()->Add(registration_node, m_Controls->m_TractoBox->GetSelectedNode()); } void QmitkSimpleRegistrationView::TractoChanged() { if (m_Controls->m_RegObjectBox->GetSelectedNode().IsNotNull() && m_Controls->m_TractoBox->GetSelectedNode().IsNotNull()) m_Controls->m_TractoRegistrationStartButton->setEnabled(true); else m_Controls->m_TractoRegistrationStartButton->setEnabled(false); } void QmitkSimpleRegistrationView::FixedImageChanged() { if (m_Controls->m_FixedImageBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer image = dynamic_cast(m_Controls->m_FixedImageBox->GetSelectedNode()->GetData()); int channels = image->GetNumberOfChannels(); int dims = image->GetDimension(); int fourth_dim_size = image->GetTimeSteps(); bool isdiff = mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image); if (dims==4 || channels>1) { m_Controls->m_FixedChannelBox->setEnabled(false); m_Controls->m_RegistrationStartButton->setEnabled(false); } if (isdiff) { m_Controls->m_FixedChannelBox->setEnabled(true); if (fourth_dim_size>1) m_Controls->m_FixedChannelBox->setMaximum(fourth_dim_size-1); else if (isdiff) m_Controls->m_FixedChannelBox->setMaximum(mitk::DiffusionPropertyHelper::GetGradientContainer(image)->Size()-1); } else { m_Controls->m_FixedChannelBox->setEnabled(false); } m_Controls->m_RegistrationStartButton->setEnabled(true); } else { m_Controls->m_FixedChannelBox->setEnabled(false); m_Controls->m_RegistrationStartButton->setEnabled(false); } } void QmitkSimpleRegistrationView::MovingImageChanged() { if (m_Controls->m_MovingImageBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer image = dynamic_cast(m_Controls->m_MovingImageBox->GetSelectedNode()->GetData()); int channels = image->GetNumberOfChannels(); int dims = image->GetDimension(); int fourth_dim_size = image->GetTimeSteps(); bool isdiff = mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image); if (dims==4 || channels>1) { m_Controls->m_MovingChannelBox->setEnabled(false); m_Controls->m_RegistrationStartButton->setEnabled(false); } if (isdiff) { m_Controls->m_MovingChannelBox->setEnabled(true); if (fourth_dim_size>1) m_Controls->m_MovingChannelBox->setMaximum(fourth_dim_size-1); else if (isdiff) m_Controls->m_MovingChannelBox->setMaximum(mitk::DiffusionPropertyHelper::GetGradientContainer(image)->Size()-1); } else { m_Controls->m_MovingChannelBox->setEnabled(false); } m_Controls->m_RegistrationStartButton->setEnabled(true); } else { m_Controls->m_MovingChannelBox->setEnabled(false); m_Controls->m_RegistrationStartButton->setEnabled(false); } } void QmitkSimpleRegistrationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList& ) { FixedImageChanged(); MovingImageChanged(); TractoChanged(); } void QmitkSimpleRegistrationView::SetFocus() { m_Controls->m_RegistrationStartButton->setFocus(); FixedImageChanged(); MovingImageChanged(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp index 988d1a641b..7de96cb900 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp @@ -1,1000 +1,1000 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include #include // Qmitk #include "QmitkStreamlineTrackingView.h" #include "QmitkStdMultiWidget.h" // Qt #include // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include // VTK #include #include #include #include #include #include #include #include #include #include const std::string QmitkStreamlineTrackingView::VIEW_ID = "org.mitk.views.streamlinetracking"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace berry; QmitkStreamlineTrackingWorker::QmitkStreamlineTrackingWorker(QmitkStreamlineTrackingView* view) : m_View(view) { } void QmitkStreamlineTrackingWorker::run() { m_View->m_Tracker->Update(); m_View->m_TrackingThread.quit(); } QmitkStreamlineTrackingView::QmitkStreamlineTrackingView() : m_TrackingWorker(this) , m_Controls(nullptr) , m_FirstTensorProbRun(true) , m_FirstInteractiveRun(true) , m_TrackingHandler(nullptr) , m_ThreadIsRunning(false) , m_DeleteTrackingHandler(false) , m_Visible(false) - , m_LastPrior("") + , m_LastPrior(nullptr) , m_TrackingPriorHandler(nullptr) { m_TrackingWorker.moveToThread(&m_TrackingThread); connect(&m_TrackingThread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_TrackingThread, SIGNAL(started()), &m_TrackingWorker, SLOT(run())); connect(&m_TrackingThread, SIGNAL(finished()), this, SLOT(AfterThread())); m_TrackingTimer = new QTimer(this); } // Destructor QmitkStreamlineTrackingView::~QmitkStreamlineTrackingView() { if (m_Tracker.IsNull()) return; m_Tracker->SetStopTracking(true); m_TrackingThread.wait(); } void QmitkStreamlineTrackingView::CreateQtPartControl( QWidget *parent ) { if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkStreamlineTrackingViewControls; m_Controls->setupUi( parent ); m_Controls->m_FaImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_SeedImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_MaskImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_TargetImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_PriorImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_StopImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_ForestSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_ExclusionImageSelectionWidget->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isPeakImagePredicate = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isImagePredicate = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isTractographyForest = mitk::TNodePredicateDataType::New(); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateNot::Pointer isNotBinaryPredicate = mitk::NodePredicateNot::New( isBinaryPredicate ); mitk::NodePredicateAnd::Pointer isNotABinaryImagePredicate = mitk::NodePredicateAnd::New( isImagePredicate, isNotBinaryPredicate ); mitk::NodePredicateDimension::Pointer dimensionPredicate = mitk::NodePredicateDimension::New(3); m_Controls->m_ForestSelectionWidget->SetNodePredicate(isTractographyForest); m_Controls->m_FaImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, dimensionPredicate) ); m_Controls->m_FaImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_FaImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_SeedImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_SeedImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_SeedImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_MaskImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_MaskImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_MaskImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_StopImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_StopImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_StopImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_TargetImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_TargetImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_TargetImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_PriorImageSelectionWidget->SetNodePredicate( isPeakImagePredicate ); m_Controls->m_PriorImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_PriorImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_ExclusionImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_ExclusionImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_ExclusionImageSelectionWidget->SetSelectionIsOptional(true); connect( m_TrackingTimer, SIGNAL(timeout()), this, SLOT(TimerUpdate()) ); connect( m_Controls->commandLinkButton_2, SIGNAL(clicked()), this, SLOT(StopTractography()) ); connect( m_Controls->commandLinkButton, SIGNAL(clicked()), this, SLOT(DoFiberTracking()) ); connect( m_Controls->m_InteractiveBox, SIGNAL(stateChanged(int)), this, SLOT(ToggleInteractive()) ); connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()) ); connect( m_Controls->m_FaImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(DeleteTrackingHandler()) ); connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(DeleteTrackingHandler()) ); connect( m_Controls->m_OutputProbMap, SIGNAL(stateChanged(int)), this, SLOT(OutputStyleSwitched()) ); connect( m_Controls->m_SeedImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_StopImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_TargetImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_PriorImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_ExclusionImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_MaskImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FaImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_ForestSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(ForestSwitched()) ); connect( m_Controls->m_ForestSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_SeedsPerVoxelBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_NumFibersBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_ScalarThresholdBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_OdfCutoffBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_StepSizeBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_SamplingDistanceBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_AngularThresholdBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_MinTractLengthBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_fBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_gBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_NumSamplesBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_SeedRadiusBox, SIGNAL(editingFinished()), this, SLOT(InteractiveSeedChanged()) ); connect( m_Controls->m_NumSeedsBox, SIGNAL(editingFinished()), this, SLOT(InteractiveSeedChanged()) ); connect( m_Controls->m_OutputProbMap, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_SharpenOdfsBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_InterpolationBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_MaskInterpolationBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FlipXBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FlipYBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FlipZBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FrontalSamplesBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_StopVotesBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_LoopCheckBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_TrialsPerSeedBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_EpConstraintsBox, SIGNAL(currentIndexChanged(int)), this, SLOT(OnParameterChanged()) ); m_Controls->m_SeedsPerVoxelBox->editingFinished(); m_Controls->m_NumFibersBox->editingFinished(); m_Controls->m_ScalarThresholdBox->editingFinished(); m_Controls->m_OdfCutoffBox->editingFinished(); m_Controls->m_StepSizeBox->editingFinished(); m_Controls->m_SamplingDistanceBox->editingFinished(); m_Controls->m_AngularThresholdBox->editingFinished(); m_Controls->m_MinTractLengthBox->editingFinished(); m_Controls->m_fBox->editingFinished(); m_Controls->m_gBox->editingFinished(); m_Controls->m_NumSamplesBox->editingFinished(); m_Controls->m_SeedRadiusBox->editingFinished(); m_Controls->m_NumSeedsBox->editingFinished(); m_Controls->m_LoopCheckBox->editingFinished(); m_Controls->m_TrialsPerSeedBox->editingFinished(); StartStopTrackingGui(false); } UpdateGui(); } void QmitkStreamlineTrackingView::StopTractography() { if (m_Tracker.IsNull()) return; m_Tracker->SetStopTracking(true); } void QmitkStreamlineTrackingView::TimerUpdate() { if (m_Tracker.IsNull()) return; QString status_text(m_Tracker->GetStatusText().c_str()); m_Controls->m_StatusTextBox->setText(status_text); } void QmitkStreamlineTrackingView::BeforeThread() { m_TrackingTimer->start(1000); } void QmitkStreamlineTrackingView::AfterThread() { m_TrackingTimer->stop(); if (!m_Tracker->GetUseOutputProbabilityMap()) { vtkSmartPointer fiberBundle = m_Tracker->GetFiberPolyData(); if (!m_Controls->m_InteractiveBox->isChecked() && fiberBundle->GetNumberOfLines() == 0) { QMessageBox warnBox; warnBox.setWindowTitle("Warning"); warnBox.setText("No fiberbundle was generated!"); warnBox.setDetailedText("No fibers were generated using the chosen parameters. Typical reasons are:\n\n- Cutoff too high. Some images feature very low FA/GFA/peak size. Try to lower this parameter.\n- Angular threshold too strict. Try to increase this parameter.\n- A small step sizes also means many steps to go wrong. Especially in the case of probabilistic tractography. Try to adjust the angular threshold."); warnBox.setIcon(QMessageBox::Warning); warnBox.exec(); if (m_InteractivePointSetNode.IsNotNull()) m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); StartStopTrackingGui(false); if (m_DeleteTrackingHandler) DeleteTrackingHandler(); UpdateGui(); return; } mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(fiberBundle); fib->SetReferenceGeometry(dynamic_cast(m_ParentNode->GetData())->GetGeometry()); if (m_Controls->m_ResampleFibersBox->isChecked() && fiberBundle->GetNumberOfLines()>0) fib->Compress(m_Controls->m_FiberErrorBox->value()); fib->ColorFibersByOrientation(); m_Tracker->SetDicomProperties(fib); if (m_Controls->m_InteractiveBox->isChecked()) { if (m_InteractiveNode.IsNull()) { m_InteractiveNode = mitk::DataNode::New(); QString name("Interactive"); m_InteractiveNode->SetName(name.toStdString()); GetDataStorage()->Add(m_InteractiveNode); } m_InteractiveNode->SetData(fib); m_InteractiveNode->SetFloatProperty("Fiber2DSliceThickness", m_Tracker->GetMinVoxelSize()/2); if (auto renderWindowPart = this->GetRenderWindowPart()) renderWindowPart->RequestUpdate(); } else { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(fib); QString name("FiberBundle_"); name += m_ParentNode->GetName().c_str(); name += "_Streamline"; node->SetName(name.toStdString()); node->SetFloatProperty("Fiber2DSliceThickness", m_Tracker->GetMinVoxelSize()/2); GetDataStorage()->Add(node, m_ParentNode); } } else { TrackerType::ItkDoubleImgType::Pointer outImg = m_Tracker->GetOutputProbabilityMap(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); if (m_Controls->m_InteractiveBox->isChecked()) { if (m_InteractiveNode.IsNull()) { m_InteractiveNode = mitk::DataNode::New(); QString name("Interactive"); m_InteractiveNode->SetName(name.toStdString()); GetDataStorage()->Add(m_InteractiveNode); } m_InteractiveNode->SetData(img); mitk::LookupTable::Pointer lut = mitk::LookupTable::New(); lut->SetType(mitk::LookupTable::JET_TRANSPARENT); mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New(); lut_prop->SetLookupTable(lut); m_InteractiveNode->SetProperty("LookupTable", lut_prop); m_InteractiveNode->SetProperty("opacity", mitk::FloatProperty::New(0.5)); m_InteractiveNode->SetFloatProperty("Fiber2DSliceThickness", m_Tracker->GetMinVoxelSize()/2); if (auto renderWindowPart = this->GetRenderWindowPart()) renderWindowPart->RequestUpdate(); } else { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); QString name("ProbabilityMap_"); name += m_ParentNode->GetName().c_str(); node->SetName(name.toStdString()); mitk::LookupTable::Pointer lut = mitk::LookupTable::New(); lut->SetType(mitk::LookupTable::JET_TRANSPARENT); mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New(); lut_prop->SetLookupTable(lut); node->SetProperty("LookupTable", lut_prop); node->SetProperty("opacity", mitk::FloatProperty::New(0.5)); GetDataStorage()->Add(node, m_ParentNode); } } if (m_InteractivePointSetNode.IsNotNull()) m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); StartStopTrackingGui(false); if (m_DeleteTrackingHandler) DeleteTrackingHandler(); UpdateGui(); } void QmitkStreamlineTrackingView::InteractiveSeedChanged(bool posChanged) { if(!CheckAndStoreLastParams(sender()) && !posChanged) return; if (m_ThreadIsRunning || !m_Visible) return; if (!posChanged && (!m_Controls->m_InteractiveBox->isChecked() || !m_Controls->m_ParamUpdateBox->isChecked()) ) return; std::srand(std::time(0)); m_SeedPoints.clear(); itk::Point world_pos = this->GetRenderWindowPart()->GetSelectedPosition(); m_SeedPoints.push_back(world_pos); float radius = m_Controls->m_SeedRadiusBox->value(); int num = m_Controls->m_NumSeedsBox->value(); mitk::PointSet::Pointer pointset = mitk::PointSet::New(); pointset->InsertPoint(0, world_pos); m_InteractivePointSetNode->SetProperty("pointsize", mitk::FloatProperty::New(radius*2)); m_InteractivePointSetNode->SetProperty("point 2D size", mitk::FloatProperty::New(radius*2)); m_InteractivePointSetNode->SetData(pointset); for (int i=1; i p; p[0] = rand()%1000-500; p[1] = rand()%1000-500; p[2] = rand()%1000-500; p.Normalize(); p *= radius; m_SeedPoints.push_back(world_pos+p); } m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,0,0)); DoFiberTracking(); } bool QmitkStreamlineTrackingView::CheckAndStoreLastParams(QObject* obj) { if (obj!=nullptr) { std::string new_val = ""; if(qobject_cast(obj)!=nullptr) new_val = boost::lexical_cast(qobject_cast(obj)->value()); else if (qobject_cast(obj)!=nullptr) new_val = boost::lexical_cast(qobject_cast(obj)->value()); else return true; if (m_LastTractoParams.find(obj->objectName())==m_LastTractoParams.end()) { m_LastTractoParams[obj->objectName()] = new_val; return false; } else if (m_LastTractoParams.at(obj->objectName()) != new_val) { m_LastTractoParams[obj->objectName()] = new_val; return true; } else if (m_LastTractoParams.at(obj->objectName()) == new_val) return false; } return true; } void QmitkStreamlineTrackingView::OnParameterChanged() { UpdateGui(); if(!CheckAndStoreLastParams(sender())) return; if (m_Controls->m_InteractiveBox->isChecked() && m_Controls->m_ParamUpdateBox->isChecked()) DoFiberTracking(); } void QmitkStreamlineTrackingView::ToggleInteractive() { UpdateGui(); m_Controls->m_SeedsPerVoxelBox->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); m_Controls->m_SeedsPerVoxelLabel->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); m_Controls->m_SeedImageSelectionWidget->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); m_Controls->label_6->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); if ( m_Controls->m_InteractiveBox->isChecked() ) { if (m_FirstInteractiveRun) { QMessageBox::information(nullptr, "Information", "Place and move a spherical seed region anywhere in the image by left-clicking and dragging. If the seed region is colored red, tracking is in progress. If the seed region is colored white, tracking is finished.\nPlacing the seed region for the first time in a newly selected dataset might cause a short delay, since the tracker needs to be initialized."); m_FirstInteractiveRun = false; } QApplication::setOverrideCursor(Qt::PointingHandCursor); QApplication::processEvents(); m_InteractivePointSetNode = mitk::DataNode::New(); m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); m_InteractivePointSetNode->SetName("InteractiveSeedRegion"); mitk::PointSetShapeProperty::Pointer shape_prop = mitk::PointSetShapeProperty::New(); shape_prop->SetValue(mitk::PointSetShapeProperty::PointSetShape::CIRCLE); m_InteractivePointSetNode->SetProperty("Pointset.2D.shape", shape_prop); GetDataStorage()->Add(m_InteractivePointSetNode); m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); } else { QApplication::restoreOverrideCursor(); QApplication::processEvents(); m_InteractiveNode = nullptr; m_InteractivePointSetNode = nullptr; m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); disconnect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); } } void QmitkStreamlineTrackingView::Activated() { } void QmitkStreamlineTrackingView::Deactivated() { } void QmitkStreamlineTrackingView::Visible() { m_Visible = true; } void QmitkStreamlineTrackingView::Hidden() { m_Visible = false; m_Controls->m_InteractiveBox->setChecked(false); ToggleInteractive(); } void QmitkStreamlineTrackingView::OnSliceChanged() { InteractiveSeedChanged(true); } void QmitkStreamlineTrackingView::SetFocus() { } void QmitkStreamlineTrackingView::DeleteTrackingHandler() { if (!m_ThreadIsRunning && m_TrackingHandler != nullptr) { if (m_TrackingPriorHandler != nullptr) { delete m_TrackingPriorHandler; m_TrackingPriorHandler = nullptr; } delete m_TrackingHandler; m_TrackingHandler = nullptr; m_DeleteTrackingHandler = false; - m_LastPrior = ""; + m_LastPrior = nullptr; } else if (m_ThreadIsRunning) { m_DeleteTrackingHandler = true; } } void QmitkStreamlineTrackingView::ForestSwitched() { DeleteTrackingHandler(); } void QmitkStreamlineTrackingView::OutputStyleSwitched() { if (m_InteractiveNode.IsNotNull()) GetDataStorage()->Remove(m_InteractiveNode); m_InteractiveNode = nullptr; } void QmitkStreamlineTrackingView::OnSelectionChanged( berry::IWorkbenchPart::Pointer , const QList& nodes ) { std::vector< mitk::DataNode::Pointer > last_nodes = m_InputImageNodes; m_InputImageNodes.clear(); m_AdditionalInputImages.clear(); bool retrack = false; for( auto node : nodes ) { if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { if( dynamic_cast(node->GetData()) || dynamic_cast(node->GetData()) || dynamic_cast(node->GetData()) || dynamic_cast(node->GetData()) || mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(node->GetData()))) { m_InputImageNodes.push_back(node); retrack = true; } else { mitk::Image* img = dynamic_cast(node->GetData()); if (img!=nullptr && img->GetDimension()==3) m_AdditionalInputImages.push_back(dynamic_cast(node->GetData())); } } } // sometimes the OnSelectionChanged event is sent twice and actually no selection has changed for the first event. We need to catch that. if (last_nodes.size() == m_InputImageNodes.size()) { bool same_nodes = true; for (unsigned int i=0; im_TensorImageLabel->setText("select in data-manager"); m_Controls->m_fBox->setEnabled(false); m_Controls->m_fLabel->setEnabled(false); m_Controls->m_gBox->setEnabled(false); m_Controls->m_gLabel->setEnabled(false); m_Controls->m_FaImageSelectionWidget->setEnabled(true); m_Controls->mFaImageLabel->setEnabled(true); m_Controls->m_OdfCutoffBox->setEnabled(false); m_Controls->m_OdfCutoffLabel->setEnabled(false); m_Controls->m_SharpenOdfsBox->setEnabled(false); m_Controls->m_ForestSelectionWidget->setVisible(false); m_Controls->m_ForestLabel->setVisible(false); m_Controls->commandLinkButton->setEnabled(false); m_Controls->m_TrialsPerSeedBox->setEnabled(false); m_Controls->m_TrialsPerSeedLabel->setEnabled(false); m_Controls->m_TargetImageSelectionWidget->setEnabled(false); m_Controls->m_TargetImageLabel->setEnabled(false); if (m_Controls->m_InteractiveBox->isChecked()) { m_Controls->m_InteractiveSeedingFrame->setVisible(true); m_Controls->m_StaticSeedingFrame->setVisible(false); m_Controls->commandLinkButton_2->setVisible(false); m_Controls->commandLinkButton->setVisible(false); } else { m_Controls->m_InteractiveSeedingFrame->setVisible(false); m_Controls->m_StaticSeedingFrame->setVisible(true); m_Controls->commandLinkButton_2->setVisible(m_ThreadIsRunning); m_Controls->commandLinkButton->setVisible(!m_ThreadIsRunning); } if (m_Controls->m_EpConstraintsBox->currentIndex()>0) { m_Controls->m_TargetImageSelectionWidget->setEnabled(true); m_Controls->m_TargetImageLabel->setEnabled(true); } // trials per seed are only important for probabilistic tractography if (m_Controls->m_ModeBox->currentIndex()==1) { m_Controls->m_TrialsPerSeedBox->setEnabled(true); m_Controls->m_TrialsPerSeedLabel->setEnabled(true); } if(!m_InputImageNodes.empty()) { if (m_InputImageNodes.size()>1) m_Controls->m_TensorImageLabel->setText( ( std::to_string(m_InputImageNodes.size()) + " images selected").c_str() ); else m_Controls->m_TensorImageLabel->setText(m_InputImageNodes.at(0)->GetName().c_str()); m_Controls->commandLinkButton->setEnabled(!m_Controls->m_InteractiveBox->isChecked() && !m_ThreadIsRunning); m_Controls->m_ScalarThresholdBox->setEnabled(true); m_Controls->m_FaThresholdLabel->setEnabled(true); if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) ) { m_Controls->m_fBox->setEnabled(true); m_Controls->m_fLabel->setEnabled(true); m_Controls->m_gBox->setEnabled(true); m_Controls->m_gLabel->setEnabled(true); } else if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) || dynamic_cast(m_InputImageNodes.at(0)->GetData())) { m_Controls->m_OdfCutoffBox->setEnabled(true); m_Controls->m_OdfCutoffLabel->setEnabled(true); m_Controls->m_SharpenOdfsBox->setEnabled(true); } else if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_InputImageNodes.at(0)->GetData())) ) { m_Controls->m_ForestSelectionWidget->setVisible(true); m_Controls->m_ForestLabel->setVisible(true); m_Controls->m_ScalarThresholdBox->setEnabled(false); m_Controls->m_FaThresholdLabel->setEnabled(false); } } } void QmitkStreamlineTrackingView::StartStopTrackingGui(bool start) { m_ThreadIsRunning = start; if (!m_Controls->m_InteractiveBox->isChecked()) { m_Controls->commandLinkButton_2->setVisible(start); m_Controls->commandLinkButton->setVisible(!start); m_Controls->m_InteractiveBox->setEnabled(!start); m_Controls->m_StatusTextBox->setVisible(start); } } void QmitkStreamlineTrackingView::DoFiberTracking() { if (m_InputImageNodes.empty()) { QMessageBox::information(nullptr, "Information", "Please select an input image in the datamaneger (tensor, ODF, peak or dMRI image)!"); return; } if (m_ThreadIsRunning || !m_Visible) return; if (m_Controls->m_InteractiveBox->isChecked() && m_SeedPoints.empty()) return; StartStopTrackingGui(true); m_Tracker = TrackerType::New(); if( dynamic_cast(m_InputImageNodes.at(0)->GetData()) ) { if (m_Controls->m_ModeBox->currentIndex()==1) { if (m_InputImageNodes.size()>1) { QMessageBox::information(nullptr, "Information", "Probabilistic tensor tractography is only implemented for single-tensor mode!"); StartStopTrackingGui(false); return; } if (m_TrackingHandler==nullptr) { m_TrackingHandler = new mitk::TrackingHandlerOdf(); typedef itk::TensorImageToOdfImageFilter< float, float > FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput( mitk::convert::GetItkTensorFromTensorImage(dynamic_cast(m_InputImageNodes.at(0)->GetData())) ); filter->Update(); dynamic_cast(m_TrackingHandler)->SetOdfImage(filter->GetOutput()); if (m_Controls->m_FaImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_FaImageSelectionWidget->GetSelectedNode()->GetData()), itkImg); dynamic_cast(m_TrackingHandler)->SetGfaImage(itkImg); } } dynamic_cast(m_TrackingHandler)->SetGfaThreshold(static_cast(m_Controls->m_ScalarThresholdBox->value())); dynamic_cast(m_TrackingHandler)->SetOdfThreshold(0); dynamic_cast(m_TrackingHandler)->SetSharpenOdfs(true); dynamic_cast(m_TrackingHandler)->SetIsOdfFromTensor(true); } else { if (m_TrackingHandler==nullptr) { m_TrackingHandler = new mitk::TrackingHandlerTensor(); for (unsigned int i=0; i(m_TrackingHandler)->AddTensorImage(mitk::convert::GetItkTensorFromTensorImage(dynamic_cast(m_InputImageNodes.at(i)->GetData())).GetPointer()); if (m_Controls->m_FaImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_FaImageSelectionWidget->GetSelectedNode()->GetData()), itkImg); dynamic_cast(m_TrackingHandler)->SetFaImage(itkImg); } } dynamic_cast(m_TrackingHandler)->SetFaThreshold(static_cast(m_Controls->m_ScalarThresholdBox->value())); dynamic_cast(m_TrackingHandler)->SetF(static_cast(m_Controls->m_fBox->value())); dynamic_cast(m_TrackingHandler)->SetG(static_cast(m_Controls->m_gBox->value())); } } else if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) || dynamic_cast(m_InputImageNodes.at(0)->GetData())) { if (m_TrackingHandler==nullptr) { m_TrackingHandler = new mitk::TrackingHandlerOdf(); if (dynamic_cast(m_InputImageNodes.at(0)->GetData())) dynamic_cast(m_TrackingHandler)->SetOdfImage(mitk::convert::GetItkOdfFromShImage(dynamic_cast(m_InputImageNodes.at(0)->GetData()))); else dynamic_cast(m_TrackingHandler)->SetOdfImage(mitk::convert::GetItkOdfFromOdfImage(dynamic_cast(m_InputImageNodes.at(0)->GetData()))); if (m_Controls->m_FaImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_FaImageSelectionWidget->GetSelectedNode()->GetData()), itkImg); dynamic_cast(m_TrackingHandler)->SetGfaImage(itkImg); } } dynamic_cast(m_TrackingHandler)->SetGfaThreshold(static_cast(m_Controls->m_ScalarThresholdBox->value())); dynamic_cast(m_TrackingHandler)->SetOdfThreshold(static_cast(m_Controls->m_OdfCutoffBox->value())); dynamic_cast(m_TrackingHandler)->SetSharpenOdfs(m_Controls->m_SharpenOdfsBox->isChecked()); } else if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_InputImageNodes.at(0)->GetData())) ) { if ( m_Controls->m_ForestSelectionWidget->GetSelectedNode().IsNull() ) { QMessageBox::information(nullptr, "Information", "Not random forest for machine learning based tractography (raw dMRI tractography) selected. Did you accidentally select the raw diffusion-weighted image in the datamanager?"); StartStopTrackingGui(false); return; } if (m_TrackingHandler==nullptr) { mitk::TractographyForest::Pointer forest = dynamic_cast(m_Controls->m_ForestSelectionWidget->GetSelectedNode()->GetData()); mitk::Image::Pointer dwi = dynamic_cast(m_InputImageNodes.at(0)->GetData()); std::vector< std::vector< ItkFloatImageType::Pointer > > additionalFeatureImages; additionalFeatureImages.push_back(std::vector< ItkFloatImageType::Pointer >()); for (auto img : m_AdditionalInputImages) { ItkFloatImageType::Pointer itkimg = ItkFloatImageType::New(); mitk::CastToItkImage(img, itkimg); additionalFeatureImages.at(0).push_back(itkimg); } bool forest_valid = false; if (forest->GetNumFeatures()>=100) { unsigned int num_previous_directions = static_cast((forest->GetNumFeatures() - (100 + additionalFeatureImages.at(0).size()))/3); m_TrackingHandler = new mitk::TrackingHandlerRandomForest<6, 100>(); dynamic_cast*>(m_TrackingHandler)->AddDwi(dwi); dynamic_cast*>(m_TrackingHandler)->SetAdditionalFeatureImages(additionalFeatureImages); dynamic_cast*>(m_TrackingHandler)->SetForest(forest); dynamic_cast*>(m_TrackingHandler)->SetNumPreviousDirections(num_previous_directions); forest_valid = dynamic_cast*>(m_TrackingHandler)->IsForestValid(); } else { unsigned int num_previous_directions = static_cast((forest->GetNumFeatures() - (28 + additionalFeatureImages.at(0).size()))/3); m_TrackingHandler = new mitk::TrackingHandlerRandomForest<6, 28>(); dynamic_cast*>(m_TrackingHandler)->AddDwi(dwi); dynamic_cast*>(m_TrackingHandler)->SetAdditionalFeatureImages(additionalFeatureImages); dynamic_cast*>(m_TrackingHandler)->SetForest(forest); dynamic_cast*>(m_TrackingHandler)->SetNumPreviousDirections(num_previous_directions); forest_valid = dynamic_cast*>(m_TrackingHandler)->IsForestValid(); } if (!forest_valid) { QMessageBox::information(nullptr, "Information", "Random forest is invalid. The forest signatue does not match the parameters of TrackingHandlerRandomForest."); StartStopTrackingGui(false); return; } } } else { if (m_Controls->m_ModeBox->currentIndex()==1) { QMessageBox::information(nullptr, "Information", "Probabilstic tractography is not implemented for peak images."); StartStopTrackingGui(false); return; } if (m_TrackingHandler==nullptr) { m_TrackingHandler = new mitk::TrackingHandlerPeaks(); dynamic_cast(m_TrackingHandler)->SetPeakImage(mitk::convert::GetItkPeakFromPeakImage(dynamic_cast(m_InputImageNodes.at(0)->GetData()))); } dynamic_cast(m_TrackingHandler)->SetPeakThreshold(static_cast(m_Controls->m_ScalarThresholdBox->value())); } m_TrackingHandler->SetFlipX(m_Controls->m_FlipXBox->isChecked()); m_TrackingHandler->SetFlipY(m_Controls->m_FlipYBox->isChecked()); m_TrackingHandler->SetFlipZ(m_Controls->m_FlipZBox->isChecked()); m_TrackingHandler->SetInterpolate(m_Controls->m_InterpolationBox->isChecked()); switch (m_Controls->m_ModeBox->currentIndex()) { case 0: m_TrackingHandler->SetMode(mitk::TrackingDataHandler::MODE::DETERMINISTIC); break; case 1: m_TrackingHandler->SetMode(mitk::TrackingDataHandler::MODE::PROBABILISTIC); break; default: m_TrackingHandler->SetMode(mitk::TrackingDataHandler::MODE::DETERMINISTIC); } if (m_Controls->m_InteractiveBox->isChecked()) { m_Tracker->SetSeedPoints(m_SeedPoints); } else if (m_Controls->m_SeedImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_SeedImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetSeedImage(mask); } if (m_Controls->m_MaskImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_MaskImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetMaskImage(mask); } if (m_Controls->m_StopImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_StopImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetStoppingRegions(mask); } if (m_Controls->m_TargetImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_TargetImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetTargetRegions(mask); } if (m_Controls->m_PriorImageSelectionWidget->GetSelectedNode().IsNotNull()) { - if (m_LastPrior!=m_Controls->m_PriorImageSelectionWidget->GetSelectedNode()->GetUID() || m_TrackingPriorHandler==nullptr) + if (m_LastPrior!=m_Controls->m_PriorImageSelectionWidget->GetSelectedNode() || m_TrackingPriorHandler==nullptr) { typedef mitk::ImageToItk< mitk::TrackingHandlerPeaks::PeakImgType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(dynamic_cast(m_Controls->m_PriorImageSelectionWidget->GetSelectedNode()->GetData())); caster->SetCopyMemFlag(true); caster->Update(); mitk::TrackingHandlerPeaks::PeakImgType::Pointer itkImg = caster->GetOutput(); m_TrackingPriorHandler = new mitk::TrackingHandlerPeaks(); dynamic_cast(m_TrackingPriorHandler)->SetPeakImage(itkImg); dynamic_cast(m_TrackingPriorHandler)->SetPeakThreshold(0.0); - m_LastPrior = m_Controls->m_PriorImageSelectionWidget->GetSelectedNode()->GetUID(); + m_LastPrior = m_Controls->m_PriorImageSelectionWidget->GetSelectedNode(); } m_TrackingPriorHandler->SetInterpolate(m_Controls->m_InterpolationBox->isChecked()); m_TrackingPriorHandler->SetMode(mitk::TrackingDataHandler::MODE::DETERMINISTIC); m_Tracker->SetTrackingPriorHandler(m_TrackingPriorHandler); m_Tracker->SetTrackingPriorWeight(m_Controls->m_PriorWeightBox->value()); m_Tracker->SetTrackingPriorAsMask(m_Controls->m_PriorAsMaskBox->isChecked()); m_Tracker->SetIntroduceDirectionsFromPrior(m_Controls->m_NewDirectionsFromPriorBox->isChecked()); } else if (m_Controls->m_PriorImageSelectionWidget->GetSelectedNode().IsNull()) m_Tracker->SetTrackingPriorHandler(nullptr); if (m_Controls->m_ExclusionImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_ExclusionImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetExclusionRegions(mask); } // Endpoint constraints switch (m_Controls->m_EpConstraintsBox->currentIndex()) { case 0: m_Tracker->SetEndpointConstraint(itk::StreamlineTrackingFilter::EndpointConstraints::NONE); m_Tracker->SetTargetRegions(nullptr); break; case 1: m_Tracker->SetEndpointConstraint(itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET); break; case 2: m_Tracker->SetEndpointConstraint(itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET_LABELDIFF); break; case 3: m_Tracker->SetEndpointConstraint(itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET); break; case 4: m_Tracker->SetEndpointConstraint(itk::StreamlineTrackingFilter::EndpointConstraints::MIN_ONE_EP_IN_TARGET); break; case 5: m_Tracker->SetEndpointConstraint(itk::StreamlineTrackingFilter::EndpointConstraints::ONE_EP_IN_TARGET); break; case 6: m_Tracker->SetEndpointConstraint(itk::StreamlineTrackingFilter::EndpointConstraints::NO_EP_IN_TARGET); break; } if (m_Tracker->GetEndpointConstraint()!=itk::StreamlineTrackingFilter::EndpointConstraints::NONE && m_Controls->m_TargetImageSelectionWidget->GetSelectedNode().IsNull()) { QMessageBox::information(nullptr, "Error", "Endpoint constraints are used but no target image is set!"); StartStopTrackingGui(false); return; } else if (m_Tracker->GetEndpointConstraint()==itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET && (m_Controls->m_SeedImageSelectionWidget->GetSelectedNode().IsNull()|| m_Controls->m_TargetImageSelectionWidget->GetSelectedNode().IsNull()) ) { QMessageBox::information(nullptr, "Error", "Endpoint constraint EPS_IN_SEED_AND_TARGET is used but no target or no seed image is set!"); StartStopTrackingGui(false); return; } m_Tracker->SetInterpolateMasks(m_Controls->m_MaskInterpolationBox->isChecked()); m_Tracker->SetVerbose(!m_Controls->m_InteractiveBox->isChecked()); m_Tracker->SetSeedsPerVoxel(m_Controls->m_SeedsPerVoxelBox->value()); m_Tracker->SetStepSize(m_Controls->m_StepSizeBox->value()); m_Tracker->SetSamplingDistance(m_Controls->m_SamplingDistanceBox->value()); m_Tracker->SetUseStopVotes(m_Controls->m_StopVotesBox->isChecked()); m_Tracker->SetOnlyForwardSamples(m_Controls->m_FrontalSamplesBox->isChecked()); m_Tracker->SetTrialsPerSeed(m_Controls->m_TrialsPerSeedBox->value()); m_Tracker->SetMaxNumTracts(m_Controls->m_NumFibersBox->value()); m_Tracker->SetNumberOfSamples(m_Controls->m_NumSamplesBox->value()); m_Tracker->SetTrackingHandler(m_TrackingHandler); m_Tracker->SetLoopCheck(m_Controls->m_LoopCheckBox->value()); m_Tracker->SetAngularThreshold(m_Controls->m_AngularThresholdBox->value()); m_Tracker->SetMinTractLength(m_Controls->m_MinTractLengthBox->value()); m_Tracker->SetUseOutputProbabilityMap(m_Controls->m_OutputProbMap->isChecked()); m_ParentNode = m_InputImageNodes.at(0); m_TrackingThread.start(QThread::LowestPriority); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.h index fce481227b..f2d3bcb433 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.h @@ -1,154 +1,154 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QmitkStreamlineTrackingView_h #define QmitkStreamlineTrackingView_h #include #include "ui_QmitkStreamlineTrackingViewControls.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include class QmitkStreamlineTrackingView; class QmitkStreamlineTrackingWorker : public QObject { Q_OBJECT public: QmitkStreamlineTrackingWorker(QmitkStreamlineTrackingView* view); public slots: void run(); private: QmitkStreamlineTrackingView* m_View; }; /*! \brief View for tensor based deterministic streamline fiber tracking. */ class QmitkStreamlineTrackingView : public QmitkAbstractView, public mitk::ILifecycleAwarePart { // 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; typedef itk::Image< unsigned int, 3 > ItkUintImgType; typedef itk::Image< unsigned char, 3 > ItkUCharImageType; typedef itk::Image< float, 3 > ItkFloatImageType; typedef itk::StreamlineTrackingFilter TrackerType; QmitkStreamlineTrackingView(); virtual ~QmitkStreamlineTrackingView(); virtual void CreateQtPartControl(QWidget *parent) override; /// /// Sets the focus to an internal widget. /// virtual void SetFocus() override; TrackerType::Pointer m_Tracker; QmitkStreamlineTrackingWorker m_TrackingWorker; QThread m_TrackingThread; virtual void Activated() override; virtual void Deactivated() override; virtual void Visible() override; virtual void Hidden() override; protected slots: void DoFiberTracking(); ///< start fiber tracking void UpdateGui(); void ToggleInteractive(); void DeleteTrackingHandler(); void OnParameterChanged(); void InteractiveSeedChanged(bool posChanged=false); void ForestSwitched(); void OutputStyleSwitched(); void AfterThread(); ///< update gui etc. after tracking has finished void BeforeThread(); ///< start timer etc. void TimerUpdate(); void StopTractography(); void OnSliceChanged(); protected: /// \brief called by QmitkAbstractView when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; Ui::QmitkStreamlineTrackingViewControls* m_Controls; protected slots: private: bool CheckAndStoreLastParams(QObject* obj); void StartStopTrackingGui(bool start); std::vector< itk::Point > m_SeedPoints; mitk::DataNode::Pointer m_ParentNode; mitk::DataNode::Pointer m_InteractiveNode; mitk::DataNode::Pointer m_InteractivePointSetNode; std::vector< mitk::DataNode::Pointer > m_InputImageNodes; ///< input image nodes std::vector< mitk::Image::ConstPointer > m_AdditionalInputImages; bool m_FirstTensorProbRun; bool m_FirstInteractiveRun; mitk::TrackingDataHandler* m_TrackingHandler; bool m_ThreadIsRunning; QTimer* m_TrackingTimer; bool m_DeleteTrackingHandler; QmitkSliceNavigationListener m_SliceChangeListener; bool m_Visible; - mitk::Identifiable::UIDType m_LastPrior; + mitk::DataNode::Pointer m_LastPrior; mitk::TrackingDataHandler* m_TrackingPriorHandler; - std::map< QString, std::string > m_LastTractoParams; + std::map< QString, std::string > m_LastTractoParams; }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.cpp b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.cpp index a59fcc3f39..2280d46dba 100644 --- a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.cpp +++ b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropper.cpp @@ -1,578 +1,579 @@ /*========================================================================= 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 "QmitkImageCropper.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // Includes for image casting between ITK and MITK: added after using Plugin Generator #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include const std::string QmitkImageCropper::VIEW_ID = "org.mitk.views.qmitkimagecropper"; QmitkImageCropper::QmitkImageCropper(QObject *) : m_ParentWidget(0), m_ImageNode(nullptr), m_CroppingObject(nullptr), m_CroppingObjectNode(nullptr), m_BoundingShapeInteractor(nullptr), m_CropOutsideValue(0), m_Advanced(0), m_Active(0), m_ScrollEnabled(true) { CreateBoundingShapeInteractor(false); } QmitkImageCropper::~QmitkImageCropper() { //delete pointer objects m_CroppingObjectNode = nullptr; m_CroppingObject = nullptr; //disable interactor if (m_BoundingShapeInteractor != nullptr) { m_BoundingShapeInteractor->SetDataNode(nullptr); m_BoundingShapeInteractor->EnableInteraction(false); } } void QmitkImageCropper::SetFocus() { m_Controls.buttonCreateNewBoundingBox->setFocus(); } void QmitkImageCropper::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Controls.boundingShapeSelector->SetDataStorage(this->GetDataStorage()); m_Controls.boundingShapeSelector->SetPredicate(mitk::NodePredicateAnd::New( mitk::TNodePredicateDataType::New(), mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")))); m_CroppingObjectNode = m_Controls.boundingShapeSelector->GetSelectedNode(); connect(m_Controls.buttonCropping, SIGNAL(clicked()), this, SLOT(DoCropping())); connect(m_Controls.buttonMasking, SIGNAL(clicked()), this, SLOT(DoMasking())); connect(m_Controls.boundingShapeSelector, SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnDataSelectionChanged(const mitk::DataNode*))); connect(m_Controls.buttonCreateNewBoundingBox, SIGNAL(clicked()), this, SLOT(DoCreateNewBoundingObject())); connect(m_Controls.buttonAdvancedSettings, SIGNAL(clicked()), this, SLOT(OnAdvancedSettingsButtonToggled())); connect(m_Controls.spinBoxOutsidePixelValue, SIGNAL(valueChanged(int)), this, SLOT(OnSliderValueChanged(int))); setDefaultGUI(); m_Controls.labelWarningRotation->setVisible(false); m_Advanced = false; this->OnAdvancedSettingsButtonToggled(); m_ParentWidget = parent; } void QmitkImageCropper::OnDataSelectionChanged(const mitk::DataNode*) { m_Controls.boundingShapeSelector->setEnabled(true); m_CroppingObjectNode = m_Controls.boundingShapeSelector->GetSelectedNode(); if (m_CroppingObjectNode.IsNotNull() && dynamic_cast(this->m_CroppingObjectNode->GetData())) { m_Controls.buttonAdvancedSettings->setEnabled(true); + m_Controls.groupImageSettings->setEnabled(true); m_Controls.labelWarningBB->setVisible(false); m_CroppingObject = dynamic_cast(m_CroppingObjectNode->GetData()); m_Advanced = true; m_BoundingShapeInteractor->EnableInteraction(true); m_BoundingShapeInteractor->SetDataNode(m_CroppingObjectNode); mitk::RenderingManager::GetInstance()->InitializeViews(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else { setDefaultGUI(); m_CroppingObject = nullptr; m_BoundingShapeInteractor->EnableInteraction(false); m_BoundingShapeInteractor->SetDataNode(nullptr); m_Advanced = false; this->OnAdvancedSettingsButtonToggled(); } } void QmitkImageCropper::OnAdvancedSettingsButtonToggled() { m_Controls.groupImageSettings->setVisible(m_Advanced); m_Advanced = !m_Advanced; } void QmitkImageCropper::CreateBoundingShapeInteractor(bool rotationEnabled) { if (m_BoundingShapeInteractor.IsNull()) { m_BoundingShapeInteractor = mitk::BoundingShapeInteractor::New(); m_BoundingShapeInteractor->LoadStateMachine("BoundingShapeInteraction.xml", us::ModuleRegistry::GetModule("MitkBoundingShape")); m_BoundingShapeInteractor->SetEventConfig("BoundingShapeMouseConfig.xml", us::ModuleRegistry::GetModule("MitkBoundingShape")); } m_BoundingShapeInteractor->SetRotationEnabled(rotationEnabled); } mitk::Geometry3D::Pointer QmitkImageCropper::InitializeWithImageGeometry(mitk::BaseGeometry::Pointer geometry) { // convert a basegeometry into a Geometry3D (otherwise IO is not working properly) if (geometry == nullptr) mitkThrow() << "Geometry is not valid."; auto boundingGeometry = mitk::Geometry3D::New(); boundingGeometry->SetBounds(geometry->GetBounds()); boundingGeometry->SetImageGeometry(geometry->GetImageGeometry()); boundingGeometry->SetOrigin(geometry->GetOrigin()); boundingGeometry->SetSpacing(geometry->GetSpacing()); boundingGeometry->SetIndexToWorldTransform(geometry->GetIndexToWorldTransform()); boundingGeometry->Modified(); return boundingGeometry; } QString QmitkImageCropper::AdaptBoundingObjectName(const QString& name) const { unsigned int counter = 2; QString newName = QString("%1 %2").arg(name).arg(counter); while (nullptr != this->GetDataStorage()->GetNode(mitk::NodePredicateFunction::New([&newName](const mitk::DataNode *node) { return 0 == node->GetName().compare(newName.toStdString()); }))) { newName = QString("%1 %2").arg(name).arg(++counter); } return newName; } void QmitkImageCropper::DoCreateNewBoundingObject() { if (!m_ImageNode.IsExpired()) { auto imageNode = m_ImageNode.Lock(); QString name = QString::fromStdString(imageNode->GetName() + " Bounding Shape"); auto boundingShape = this->GetDataStorage()->GetNode(mitk::NodePredicateFunction::New([&name](const mitk::DataNode *node) { return 0 == node->GetName().compare(name.toStdString()); })); if (nullptr != boundingShape) name = this->AdaptBoundingObjectName(name); m_Controls.buttonCropping->setEnabled(true); m_Controls.buttonMasking->setEnabled(true); m_Controls.boundingShapeSelector->setEnabled(true); m_Controls.groupImageSettings->setEnabled(true); // get current timestep to support 3d+t images auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN); int timeStep = renderWindowPart->GetTimeNavigationController()->GetTime()->GetPos(); mitk::BaseGeometry::Pointer imageGeometry = static_cast(imageNode->GetData()->GetGeometry(timeStep)); m_CroppingObject = mitk::GeometryData::New(); m_CroppingObject->SetGeometry(static_cast(this->InitializeWithImageGeometry(imageGeometry))); m_CroppingObjectNode = mitk::DataNode::New(); m_CroppingObjectNode->SetData(m_CroppingObject); m_CroppingObjectNode->SetProperty("name", mitk::StringProperty::New(name.toStdString())); m_CroppingObjectNode->SetProperty("color", mitk::ColorProperty::New(1.0, 1.0, 1.0)); m_CroppingObjectNode->SetProperty("opacity", mitk::FloatProperty::New(0.6)); m_CroppingObjectNode->SetProperty("layer", mitk::IntProperty::New(99)); m_CroppingObjectNode->AddProperty("handle size factor", mitk::DoubleProperty::New(1.0 / 40.0)); m_CroppingObjectNode->SetBoolProperty("pickable", true); if (!this->GetDataStorage()->Exists(m_CroppingObjectNode)) { GetDataStorage()->Add(m_CroppingObjectNode, imageNode); m_Controls.boundingShapeSelector->SetSelectedNode(m_CroppingObjectNode); m_CroppingObjectNode->SetVisibility(true); m_BoundingShapeInteractor->EnableInteraction(true); m_BoundingShapeInteractor->SetDataNode(this->m_CroppingObjectNode); this->OnDataSelectionChanged(m_CroppingObjectNode); } } // Adjust coordinate system by doing a reinit on auto tempDataStorage = mitk::DataStorage::SetOfObjects::New(); tempDataStorage->InsertElement(0, m_CroppingObjectNode); //// initialize the views to the bounding geometry //mitk::TimeGeometry::Pointer bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(tempDataStorage); //mitk::RenderingManager::GetInstance()->InitializeViews(bounds); //mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkImageCropper::setDefaultGUI() { m_Controls.labelWarningImage->setStyleSheet(" QLabel { color: rgb(255, 0, 0) }"); m_Controls.labelWarningImage->setText(QString::fromStdString("Select an image.")); m_Controls.labelWarningImage->setVisible(true); m_Controls.labelWarningBB->setStyleSheet(" QLabel { color: rgb(255, 0, 0) }"); m_Controls.labelWarningBB->setText(QString::fromStdString("Create a bounding shape below.")); m_Controls.labelWarningBB->setVisible(true); m_Controls.buttonCreateNewBoundingBox->setEnabled(false); m_Controls.labelWarningRotation->setVisible(false); m_Controls.buttonCropping->setEnabled(false); m_Controls.buttonMasking->setEnabled(false); m_Controls.boundingShapeSelector->setEnabled(false); m_Controls.buttonAdvancedSettings->setEnabled(false); m_Controls.groupImageSettings->setEnabled(false); m_Controls.checkOverwriteImage->setChecked(false); m_Controls.checkBoxCropTimeStepOnly->setChecked(false); } void QmitkImageCropper::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& nodes) { bool rotationEnabled = false; if (nodes.empty()) { setDefaultGUI(); return; } m_ParentWidget->setEnabled(true); foreach(mitk::DataNode::Pointer node, nodes) { if (node.IsNotNull() && dynamic_cast(node->GetData())) { m_ImageNode = nodes[0]; m_Controls.groupBoundingObject->setEnabled(true); m_Controls.labelWarningImage->setStyleSheet(""); m_Controls.labelWarningImage->setText(QString::fromStdString("Selected image: " + nodes[0]->GetName())); m_Controls.buttonCreateNewBoundingBox->setEnabled(true); mitk::Image::Pointer image = dynamic_cast(nodes[0]->GetData()); if (image != nullptr) { if (image->GetDimension() < 3) { QMessageBox::warning(nullptr, tr("Invalid image selected"), tr("ImageCropper only works with 3 or more dimensions."), QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); setDefaultGUI(); return; } vtkSmartPointer imageMat = image->GetGeometry()->GetVtkMatrix(); // check whether the image geometry is rotated, if so, no pixel aligned cropping or masking can be performed if ((imageMat->GetElement(1, 0) == 0.0) && (imageMat->GetElement(0, 1) == 0.0) && (imageMat->GetElement(1, 2) == 0.0) && (imageMat->GetElement(2, 1) == 0.0) && (imageMat->GetElement(2, 0) == 0.0) && (imageMat->GetElement(0, 2) == 0.0)) { rotationEnabled = false; m_Controls.labelWarningRotation->setVisible(false); } else { rotationEnabled = true; m_Controls.labelWarningRotation->setStyleSheet(" QLabel { color: rgb(255, 0, 0) }"); m_Controls.labelWarningRotation->setVisible(true); } this->CreateBoundingShapeInteractor(rotationEnabled); m_CroppingObjectNode = m_Controls.boundingShapeSelector->GetSelectedNode(); if (m_CroppingObjectNode != nullptr) { this->OnDataSelectionChanged(m_CroppingObjectNode); m_BoundingShapeInteractor->EnableInteraction(true); m_BoundingShapeInteractor->SetDataNode(this->m_CroppingObjectNode); m_Controls.boundingShapeSelector->setEnabled(true); } if (image->GetPixelType().GetPixelType() == itk::ImageIOBase::SCALAR) { // Might be changed with the upcoming new image statistics plugin //(recomputation might be very expensive for large images ;) ) auto statistics = image->GetStatistics(); auto minPixelValue = statistics->GetScalarValueMin(); auto maxPixelValue = statistics->GetScalarValueMax(); if (minPixelValue < std::numeric_limits::min()) { minPixelValue = std::numeric_limits::min(); } if (maxPixelValue > std::numeric_limits::max()) { maxPixelValue = std::numeric_limits::max(); } m_Controls.spinBoxOutsidePixelValue->setEnabled(true); m_Controls.spinBoxOutsidePixelValue->setMaximum(static_cast(maxPixelValue)); m_Controls.spinBoxOutsidePixelValue->setMinimum(static_cast(minPixelValue)); m_Controls.spinBoxOutsidePixelValue->setValue(static_cast(minPixelValue)); } else { m_Controls.spinBoxOutsidePixelValue->setEnabled(false); } unsigned int dim = image->GetDimension(); if (dim < 2 || dim > 4) { m_Controls.labelWarningImage->setStyleSheet(" QLabel { color: rgb(255, 0, 0) }"); m_Controls.labelWarningImage->setText(QString::fromStdString("Select an image.")); m_ParentWidget->setEnabled(false); } if (m_CroppingObjectNode != nullptr) { m_Controls.buttonCropping->setEnabled(true); m_Controls.buttonMasking->setEnabled(true); m_Controls.boundingShapeSelector->setEnabled(true); m_Controls.labelWarningBB->setVisible(false); } else { m_Controls.buttonCropping->setEnabled(false); m_Controls.buttonMasking->setEnabled(false); m_Controls.boundingShapeSelector->setEnabled(false); m_Controls.labelWarningBB->setVisible(true); } return; } // iterate all selected objects, adjust warning visibility setDefaultGUI(); m_ParentWidget->setEnabled(true); m_Controls.labelWarningRotation->setVisible(false); } } } void QmitkImageCropper::OnComboBoxSelectionChanged(const mitk::DataNode* node) { mitk::DataNode* selectedNode = const_cast(node); if (selectedNode != nullptr) { if (!m_ImageNode.IsExpired()) selectedNode->SetDataInteractor(m_ImageNode.Lock()->GetDataInteractor()); // m_ImageNode->GetDataInteractor()->SetDataNode(selectedNode); m_ImageNode = selectedNode; } } void QmitkImageCropper::OnSliderValueChanged(int slidervalue) { m_CropOutsideValue = slidervalue; } void QmitkImageCropper::DoMasking() { this->ProcessImage(true); } void QmitkImageCropper::DoCropping() { this->ProcessImage(false); } void QmitkImageCropper::ProcessImage(bool mask) { // cropping only possible if valid bounding shape as well as a valid image are loaded QList nodes = this->GetDataManagerSelection(); auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN); int timeStep = renderWindowPart->GetTimeNavigationController()->GetTime()->GetPos(); if (nodes.empty()) return; mitk::DataNode* node = nodes[0]; if (node == nullptr) { QMessageBox::information(nullptr, "Warning", "Please load and select an image before starting image processing."); return; } if (m_CroppingObject == nullptr) { QMessageBox::information(nullptr, "Warning", "Please load and select a cropping object before starting image processing."); return; } mitk::BaseData* data = node->GetData(); //get data from node if (data != nullptr) { QString imageName; if (mask) { imageName = QString::fromStdString(node->GetName() + "_" + m_CroppingObjectNode->GetName() + "_masked"); } else { imageName = QString::fromStdString(node->GetName() + "_" + m_CroppingObjectNode->GetName() + "_cropped"); } if (m_Controls.checkBoxCropTimeStepOnly->isChecked()) { imageName = imageName + "_T" + QString::number(timeStep); } // image and bounding shape ok, set as input auto croppedImageNode = mitk::DataNode::New(); auto cutter = mitk::BoundingShapeCropper::New(); cutter->SetGeometry(m_CroppingObject); // adjustable in advanced settings cutter->SetUseWholeInputRegion(mask); //either mask (mask=true) or crop (mask=false) cutter->SetOutsideValue(m_CropOutsideValue); cutter->SetUseCropTimeStepOnly(m_Controls.checkBoxCropTimeStepOnly->isChecked()); cutter->SetCurrentTimeStep(timeStep); // TODO: Add support for MultiLayer (right now only Mulitlabel support) mitk::LabelSetImage* labelsetImageInput = dynamic_cast(data); if (labelsetImageInput != nullptr) { cutter->SetInput(labelsetImageInput); // do the actual cutting try { cutter->Update(); } catch (const itk::ExceptionObject& e) { std::string message = std::string("The Cropping filter could not process because of: \n ") + e.GetDescription(); QMessageBox::warning(nullptr, tr("Cropping not possible!"), tr(message.c_str()), QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); return; } auto labelSetImage = mitk::LabelSetImage::New(); labelSetImage->InitializeByLabeledImage(cutter->GetOutput()); for (unsigned int i = 0; i < labelsetImageInput->GetNumberOfLayers(); i++) { labelSetImage->AddLabelSetToLayer(i, labelsetImageInput->GetLabelSet(i)); } croppedImageNode->SetData(labelSetImage); croppedImageNode->SetProperty("name", mitk::StringProperty::New(imageName.toStdString())); //add cropping result to the current data storage as child node to the image node if (!m_Controls.checkOverwriteImage->isChecked()) { if (!this->GetDataStorage()->Exists(croppedImageNode)) { this->GetDataStorage()->Add(croppedImageNode, m_ImageNode.Lock()); } } else // original image will be overwritten by the result image and the bounding box of the result is adjusted { node->SetData(labelSetImage); node->Modified(); // Adjust coordinate system by doing a reinit on auto tempDataStorage = mitk::DataStorage::SetOfObjects::New(); tempDataStorage->InsertElement(0, node); // initialize the views to the bounding geometry auto bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(tempDataStorage); mitk::RenderingManager::GetInstance()->InitializeViews(bounds); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } else { mitk::Image::Pointer imageInput = dynamic_cast(data); if (imageInput != nullptr) { cutter->SetInput(imageInput); // do the actual cutting try { cutter->Update(); } catch (const itk::ExceptionObject& e) { std::string message = std::string("The Cropping filter could not process because of: \n ") + e.GetDescription(); QMessageBox::warning(nullptr, tr("Cropping not possible!"), tr(message.c_str()), QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); return; } //add cropping result to the current data storage as child node to the image node if (!m_Controls.checkOverwriteImage->isChecked()) { croppedImageNode->SetData(cutter->GetOutput()); croppedImageNode->SetProperty("name", mitk::StringProperty::New(imageName.toStdString())); croppedImageNode->SetProperty("color", mitk::ColorProperty::New(1.0, 1.0, 1.0)); croppedImageNode->SetProperty("layer", mitk::IntProperty::New(99)); // arbitrary, copied from segmentation functionality if (!this->GetDataStorage()->Exists(croppedImageNode)) { this->GetDataStorage()->Add(croppedImageNode, m_ImageNode.Lock()); } } else // original image will be overwritten by the result image and the bounding box of the result is adjusted { node->SetData(cutter->GetOutput()); node->Modified(); // Adjust coordinate system by doing a reinit on auto tempDataStorage = mitk::DataStorage::SetOfObjects::New(); tempDataStorage->InsertElement(0, node); // initialize the views to the bounding geometry auto bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(tempDataStorage); mitk::RenderingManager::GetInstance()->InitializeViews(bounds); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } } else { QMessageBox::information(nullptr, "Warning", "Please load and select an image before starting image processing."); } } diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/CMakeLists.txt b/Plugins/org.mitk.gui.qt.measurementtoolbox/CMakeLists.txt index 9af2e00fda..8403f27fb6 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/CMakeLists.txt @@ -1,9 +1,9 @@ # The project name must correspond to the directory name of your plug-in # and must not contain periods. project(org_mitk_gui_qt_measurementtoolbox) mitk_create_plugin( EXPORT_DIRECTIVE MITK_QT_MEASUREMENTTOOLBOX EXPORTED_INCLUDE_SUFFIXES src - MODULE_DEPENDS MitkQtWidgetsExt MitkImageStatistics MitkPlanarFigure MitkChart -) + MODULE_DEPENDS MitkQtWidgetsExt MitkImageStatistics MitkImageStatisticsUI MitkPlanarFigure MitkChart +) \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatisticsReloaded.dox b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatisticsReloaded.dox new file mode 100644 index 0000000000..0de797abdb --- /dev/null +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/documentation/UserManual/QmitkImageStatisticsReloaded.dox @@ -0,0 +1,54 @@ +/** +\page org_mitk_views_imagestatistics The Image Statistics View + +\imageMacro{bar-chart.svg,"Icon of the Image Statistics View",2.00} + +\section QmitkImageStatisticsUserManualSummary Summary + +This view provides an easy interface to quickly compute some features of a whole image or a region of interest. + +This document will tell you how to use this view, but it is assumed that you already know how to use MITK in general. + +Please see \ref QmitkImageStatisticsUserManualDetails for more detailed information on usage and supported filters. +If you encounter problems using the view, please have a look at the \ref QmitkImageStatisticsUserManualTrouble page. + +\section QmitkImageStatisticsUserManualDetails Details + +Manual sections: + +- \ref QmitkImageStatisticsUserManualOverview +- \ref QmitkImageStatisticsUserManualUsage +- \ref QmitkImageStatisticsUserManualTrouble + +\section QmitkImageStatisticsUserManualOverview Overview + +This view provides an easy interface to quickly compute some features of a whole image or a region of interest. + +\imageMacro{QmitkMeasurementToolbox_Interface.png,"The interface",9.10} + +\section QmitkImageStatisticsUserManualUsage Usage + +After selection of an image or a binary mask of an image in the datamanager, the Image Statistics view shows some statistical information. If a mask is selected, the name of the mask and the name of the image, to which the mask is applied, are shown at the top. For time data the current time step is used for the selected mask and the selected image. If the total number of time steps on the selected mask is less than the current time step, the last time step of the mask is used. If a mask is selected, its used time step will be displayed next to its name like this: (t=0). + +Check "Ignore zero-valued voxels" to hide voxels with grayvalue zero. + +Below it is the statistics window which displays the calculated statistical features (such as mean, standard deviation...). + +Beneath the statistics window is the histogram window, which shows the histogram of the current selection. + +At top of the histogram window are two radiobuttons. Toggle one of them to either show the histogram as a barchart or as a lineplot. + +Use mousewheel to zoom in and out the histogram. With the left mouse button the histogram is pannable in zoomed state. + +If the histogram is displayed as a barchart a tooltip is available by hovering over one of the bins. A tooltip is also available, if an intesity profile is created for a path element as mask. + +At the bottom of each view is one button. They copy their respective data in csv format to the clipboard. + +\section QmitkImageStatisticsUserManualTrouble 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.measurementtoolbox/files.cmake b/Plugins/org.mitk.gui.qt.measurementtoolbox/files.cmake index 2e7ff6628c..c6751d8b7a 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/files.cmake +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/files.cmake @@ -1,57 +1,56 @@ set(SRC_CPP_FILES ) set(INTERNAL_CPP_FILES QmitkMeasurementView.cpp - QmitkPlanarFiguresTableModel.cpp QmitkImageStatisticsView.cpp - QmitkImageStatisticsCalculationThread.cpp + QmitkImageStatisticsReloadedView.cpp mitkPluginActivator.cpp ) set(UI_FILES + src/internal/QmitkImageStatisticsReloadedViewControls.ui src/internal/QmitkImageStatisticsViewControls.ui ) set(MOC_H_FILES src/internal/QmitkMeasurementView.h - src/internal/QmitkPlanarFiguresTableModel.h src/internal/QmitkImageStatisticsView.h - src/internal/QmitkImageStatisticsCalculationThread.h + src/internal/QmitkImageStatisticsReloadedView.h src/internal/mitkPluginActivator.h - ) set(CACHED_RESOURCE_FILES resources/angle.png resources/arrow.png resources/circle.png resources/four-point-angle.png resources/lena.xpm resources/line.png resources/measurement.svg resources/path.png resources/polygon.png resources/rectangle.png resources/stats.png resources/text.png resources/bar-chart.svg + resources/bar-chart2.svg plugin.xml ) set(QRC_FILES resources/measurement.qrc resources/QmitkImageStatisticsView.qrc ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/plugin.xml b/Plugins/org.mitk.gui.qt.measurementtoolbox/plugin.xml index 5b85110301..2e69a3ef29 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/plugin.xml +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/plugin.xml @@ -1,42 +1,53 @@ Measure distance and areas in the image - Calculate the statistic of image regions + DEPRECATED: Calculate the statistic of image regions + + + + Calculate the statistic of image regions + + + diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/resources/bar-chart2.svg b/Plugins/org.mitk.gui.qt.measurementtoolbox/resources/bar-chart2.svg new file mode 100644 index 0000000000..6173a2c58d --- /dev/null +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/resources/bar-chart2.svg @@ -0,0 +1,75 @@ + + + + + + image/svg+xml + + + + + + + + + + diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsReloadedView.cpp b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsReloadedView.cpp new file mode 100644 index 0000000000..672bb2b976 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsReloadedView.cpp @@ -0,0 +1,414 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include "QmitkImageStatisticsReloadedView.h" + +#include + +// berry includes +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include "mitkImageStatisticsContainerManager.h" + + +const std::string QmitkImageStatisticsReloadedView::VIEW_ID = "org.mitk.views.imagestatisticsReloaded"; + +QmitkImageStatisticsReloadedView::QmitkImageStatisticsReloadedView(QObject* /*parent*/, const char* /*name*/) +{ + this->m_CalculationThread = new QmitkImageStatisticsCalculationJob(); +} + +QmitkImageStatisticsReloadedView::~QmitkImageStatisticsReloadedView() +{ + if (m_selectedPlanarFigure) + m_selectedPlanarFigure->RemoveObserver(m_PlanarFigureObserverTag); +} + +void QmitkImageStatisticsReloadedView::CreateQtPartControl(QWidget *parent) +{ + m_Controls.setupUi(parent); + m_Controls.widget_histogram->SetTheme(this->GetColorTheme()); + m_Controls.widget_intensityProfile->SetTheme(this->GetColorTheme()); + m_Controls.groupBox_histogram->setVisible(true); + m_Controls.groupBox_intensityProfile->setVisible(false); + m_Controls.label_currentlyComputingStatistics->setVisible(false); + m_Controls.sliderWidget_histogram->setPrefix("Time: "); + m_Controls.sliderWidget_histogram->setDecimals(0); + m_Controls.sliderWidget_histogram->setVisible(false); + + PrepareDataStorageComboBoxes(); + m_Controls.widget_statistics->SetDataStorage(this->GetDataStorage()); + CreateConnections(); +} + +void QmitkImageStatisticsReloadedView::CreateConnections() +{ + connect(this->m_CalculationThread, &QmitkImageStatisticsCalculationJob::finished, this, &QmitkImageStatisticsReloadedView::OnStatisticsCalculationEnds, Qt::QueuedConnection); + connect(this->m_Controls.checkBox_ignoreZero, &QCheckBox::stateChanged, this, &QmitkImageStatisticsReloadedView::OnCheckBoxIgnoreZeroStateChanged); + connect(this->m_Controls.sliderWidget_histogram, &ctkSliderWidget::valueChanged, this, &QmitkImageStatisticsReloadedView::OnSliderWidgetHistogramChanged); + connect(this->m_Controls.imageSelector, static_cast(&QComboBox::currentIndexChanged), this, &QmitkImageStatisticsReloadedView::OnImageSelectorChanged); + connect(this->m_Controls.maskImageSelector, static_cast(&QComboBox::currentIndexChanged), this, &QmitkImageStatisticsReloadedView::OnMaskSelectorChanged); +} + +void QmitkImageStatisticsReloadedView::OnCheckBoxIgnoreZeroStateChanged(int state) +{ + m_ForceRecompute = true; + if (state != Qt::Unchecked) + { + this->m_CalculationThread->SetIgnoreZeroValueVoxel(true); + } + else + { + this->m_CalculationThread->SetIgnoreZeroValueVoxel(false); + } + CalculateOrGetStatistics(); +} + +void QmitkImageStatisticsReloadedView::OnSliderWidgetHistogramChanged(double value) +{ + unsigned int timeStep = static_cast(value); + auto mask = m_selectedMaskNode ? m_selectedMaskNode->GetData() : nullptr; + auto imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(this->GetDataStorage(), m_selectedImageNode->GetData(), mask); + HistogramType::ConstPointer histogram = imageStatistics->GetStatisticsForTimeStep(timeStep).m_Histogram; + + if (histogram.IsNotNull() && this->m_CalculationThread->GetStatisticsUpdateSuccessFlag()) + { + this->FillHistogramWidget({ histogram }, { m_selectedImageNode->GetName() }); + } +} + +void QmitkImageStatisticsReloadedView::PartClosed(const berry::IWorkbenchPartReference::Pointer&) +{ +} + +void QmitkImageStatisticsReloadedView::FillHistogramWidget(const std::vector& histogram, const std::vector& dataLabels) +{ + m_Controls.groupBox_histogram->setVisible(true); + m_Controls.widget_histogram->SetTheme(this->GetColorTheme()); + m_Controls.widget_histogram->Reset(); + m_Controls.widget_histogram->SetHistogram(histogram.front(), dataLabels.front()); + connect(m_Controls.widget_histogram, &QmitkHistogramVisualizationWidget::RequestHistogramUpdate, this, &QmitkImageStatisticsReloadedView::OnRequestHistogramUpdate); +} + +QmitkChartWidget::ChartStyle QmitkImageStatisticsReloadedView::GetColorTheme() const +{ + ctkPluginContext* context = berry::WorkbenchPlugin::GetDefault()->GetPluginContext(); + ctkServiceReference styleManagerRef = context->getServiceReference(); + if (styleManagerRef) + { + auto styleManager = context->getService(styleManagerRef); + if (styleManager->GetStyle().name == "Dark") { + return QmitkChartWidget::ChartStyle::darkstyle; + } + else { + return QmitkChartWidget::ChartStyle::lightstyle; + } + } + return QmitkChartWidget::ChartStyle::darkstyle; +} + +void QmitkImageStatisticsReloadedView::OnImageSelectorChanged() +{ + auto selectedImageNode = m_Controls.imageSelector->GetSelectedNode(); + if (selectedImageNode != m_selectedImageNode) + { + m_selectedImageNode = selectedImageNode; + if (m_selectedImageNode.IsNotNull()) { + auto isPlanarFigurePredicate = mitk::GetImageStatisticsPlanarFigurePredicate(); + auto isMaskPredicate = mitk::GetImageStatisticsMaskPredicate(); + auto hasSameGeometry = mitk::NodePredicateGeometry::New(m_selectedImageNode->GetData()->GetGeometry()); + hasSameGeometry->SetCheckPrecision(1e-10); + auto isMaskWithGeometryPredicate = mitk::NodePredicateAnd::New(isMaskPredicate, hasSameGeometry); + auto isMaskOrPlanarFigureWithGeometryPredicate = mitk::NodePredicateOr::New(isPlanarFigurePredicate, isMaskWithGeometryPredicate); + //prevent triggering of computation as the predicate triggers a signalChanged event + m_Controls.maskImageSelector->disconnect(); + m_Controls.maskImageSelector->SetPredicate(isMaskOrPlanarFigureWithGeometryPredicate); + m_Controls.maskImageSelector->SetZeroEntryText(""); + CalculateOrGetStatistics(); + m_Controls.widget_statistics->SetImageNodes({ m_selectedImageNode.GetPointer() }); + connect(this->m_Controls.maskImageSelector, + static_cast(&QComboBox::currentIndexChanged), + this, + &QmitkImageStatisticsReloadedView::OnMaskSelectorChanged); + } + else + { + m_Controls.widget_statistics->SetImageNodes({}); + } + } +} + +void QmitkImageStatisticsReloadedView::OnMaskSelectorChanged() +{ + auto selectedMaskNode = m_Controls.maskImageSelector->GetSelectedNode(); + if (selectedMaskNode != m_selectedMaskNode) + { + m_selectedMaskNode = selectedMaskNode; + if (m_selectedMaskNode.IsNotNull()) + { + m_Controls.widget_statistics->SetMaskNodes({ m_selectedMaskNode.GetPointer() }); + } + else + { + m_Controls.widget_statistics->SetMaskNodes({}); + } + CalculateOrGetStatistics(); + } +} + +void QmitkImageStatisticsReloadedView::CalculateOrGetStatistics() +{ + if (this->m_selectedPlanarFigure) + { + this->m_selectedPlanarFigure->RemoveObserver(this->m_PlanarFigureObserverTag); + this->m_selectedPlanarFigure = nullptr; + } + + m_Controls.groupBox_intensityProfile->setVisible(false); + m_Controls.widget_statistics->setEnabled(m_selectedImageNode.IsNotNull()); + + if (m_selectedImageNode != nullptr) { + auto image = dynamic_cast(m_selectedImageNode->GetData()); + mitk::Image::Pointer mask = nullptr; + mitk::PlanarFigure::Pointer maskPlanarFigure = nullptr; + + if (image->GetDimension() == 4) { + m_Controls.sliderWidget_histogram->setVisible(true); + unsigned int maxTimestep = image->GetTimeSteps(); + m_Controls.sliderWidget_histogram->setMaximum(maxTimestep - 1); + } + else { + m_Controls.sliderWidget_histogram->setVisible(false); + } + + if (m_selectedMaskNode != nullptr) { + mask = dynamic_cast(m_selectedMaskNode->GetData()); + if (mask == nullptr) { + maskPlanarFigure = dynamic_cast(m_selectedMaskNode->GetData()); + } + } + + mitk::ImageStatisticsContainer::ConstPointer imageStatistics; + if (mask) { + auto imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(this->GetDataStorage(), image, mask.GetPointer()); + } + else if (maskPlanarFigure) { + m_selectedPlanarFigure = maskPlanarFigure; + ITKCommandType::Pointer changeListener = ITKCommandType::New(); + changeListener->SetCallbackFunction(this, &QmitkImageStatisticsReloadedView::CalculateOrGetStatistics); + this->m_PlanarFigureObserverTag = + m_selectedPlanarFigure->AddObserver(mitk::EndInteractionPlanarFigureEvent(), changeListener); + if (!maskPlanarFigure->IsClosed()) { + ComputeAndDisplayIntensityProfile(image, maskPlanarFigure); + } + imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(this->GetDataStorage(), image, maskPlanarFigure.GetPointer()); + } + else { + imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(this->GetDataStorage(),image); + } + + bool imageStatisticsOlderThanInputs = false; + if (imageStatistics && (imageStatistics->GetMTime() < image->GetMTime() || + (mask && imageStatistics->GetMTime() < mask->GetMTime()) || + (maskPlanarFigure && imageStatistics->GetMTime() < maskPlanarFigure->GetMTime()))) { + imageStatisticsOlderThanInputs = true; + } + + //statistics need to be computed + if (!imageStatistics || imageStatisticsOlderThanInputs || m_ForceRecompute) { + CalculateStatistics(image, mask.GetPointer(), maskPlanarFigure.GetPointer()); + } + //statistics already computed + else { + if (!(maskPlanarFigure && maskPlanarFigure->IsClosed())) { + if (imageStatistics->TimeStepExists(0)) { + auto histogram = imageStatistics->GetStatisticsForTimeStep(0).m_Histogram.GetPointer(); + std::string imageNodeName = m_selectedImageNode->GetName(); + this->FillHistogramWidget({histogram}, {imageNodeName }); + } + } + } + + } + else { + ResetGUI(); + } + m_ForceRecompute = false; +} + +void QmitkImageStatisticsReloadedView::ComputeAndDisplayIntensityProfile(mitk::Image * image, mitk::PlanarFigure::Pointer maskPlanarFigure) +{ + auto intensityProfile = mitk::ComputeIntensityProfile(image, maskPlanarFigure); + //Don't show histogram for intensity profiles + m_Controls.groupBox_histogram->setVisible(false); + m_Controls.groupBox_intensityProfile->setVisible(true); + m_Controls.widget_intensityProfile->Reset(); + m_Controls.widget_intensityProfile->SetIntensityProfile(intensityProfile.GetPointer(), "Intensity Profile of " + m_selectedImageNode->GetName()); +} + +void QmitkImageStatisticsReloadedView::ResetGUI() +{ + m_Controls.widget_statistics->Reset(); + //m_Controls.widget_statistics->setEnabled(false); + m_Controls.widget_histogram->Reset(); + m_Controls.widget_histogram->setEnabled(false); +} + +void QmitkImageStatisticsReloadedView::OnStatisticsCalculationEnds() +{ + mitk::StatusBar::GetInstance()->Clear(); + + if (this->m_CalculationThread->GetStatisticsUpdateSuccessFlag()) { + auto statistic = m_CalculationThread->GetStatisticsData(); + mitk::PropertyRelations::RuleResultVectorType rulesForCurrentStatistic; + auto statisticNonConst = statistic->Clone(); + auto statisticsNodeName = m_selectedImageNode->GetName(); + if (m_selectedMaskNode) { + statisticsNodeName += "_" + m_selectedMaskNode->GetName(); + } + statisticsNodeName += "_statistics"; + auto statisticsNode = mitk::CreateImageStatisticsNode(statisticNonConst, statisticsNodeName); + auto imageRule = mitk::StatisticsToImageRelationRule::New(); + imageRule->Connect(statisticNonConst.GetPointer(), m_CalculationThread->GetStatisticsImage().GetPointer()); + rulesForCurrentStatistic.push_back(imageRule.GetPointer()); + + if (m_CalculationThread->GetMaskImage()) { + auto maskRule = mitk::StatisticsToMaskRelationRule::New(); + maskRule->Connect(statisticNonConst.GetPointer(), m_CalculationThread->GetMaskImage().GetPointer()); + rulesForCurrentStatistic.push_back(maskRule.GetPointer()); + } + else if (m_CalculationThread->GetPlanarFigure()) { + auto planarFigureRule = mitk::StatisticsToMaskRelationRule::New(); + planarFigureRule->Connect(statisticNonConst.GetPointer(), m_CalculationThread->GetPlanarFigure().GetPointer()); + rulesForCurrentStatistic.push_back(planarFigureRule.GetPointer()); + } + + m_statisticContainerRules.push_back(rulesForCurrentStatistic); + + this->GetDataStorage()->Add(statisticsNode); + + if (!m_selectedPlanarFigure || m_selectedPlanarFigure->IsClosed()) { + this->FillHistogramWidget({ m_CalculationThread->GetTimeStepHistogram() }, { m_selectedImageNode->GetName() }); + } + } + else { + mitk::StatusBar::GetInstance()->DisplayErrorText(m_CalculationThread->GetLastErrorMessage().c_str()); + m_Controls.widget_histogram->setEnabled(false); + } + m_Controls.label_currentlyComputingStatistics->setVisible(false); +} + +void QmitkImageStatisticsReloadedView::OnRequestHistogramUpdate(unsigned int nBins) +{ + m_CalculationThread->SetHistogramNBins(nBins); + m_CalculationThread->start(); +} + +void QmitkImageStatisticsReloadedView::CalculateStatistics(mitk::Image::ConstPointer image, mitk::Image::ConstPointer mask, mitk::PlanarFigure::ConstPointer maskPlanarFigure) +{ + this->m_StatisticsUpdatePending = true; + auto renderPart = this->GetRenderWindowPart(); + unsigned int timeStep = renderPart->GetTimeNavigationController()->GetTime()->GetPos(); + this->m_CalculationThread->Initialize(image, mask, maskPlanarFigure); + this->m_CalculationThread->SetTimeStep(timeStep); + + try + { + // Compute statistics + this->m_CalculationThread->start(); + m_Controls.label_currentlyComputingStatistics->setVisible(true); + } + catch (const mitk::Exception& e) + { + mitk::StatusBar::GetInstance()->DisplayErrorText(e.GetDescription()); + this->m_StatisticsUpdatePending = false; + m_Controls.label_currentlyComputingStatistics->setVisible(false); + } + catch (const std::runtime_error &e) + { + mitk::StatusBar::GetInstance()->DisplayErrorText(e.what()); + this->m_StatisticsUpdatePending = false; + m_Controls.label_currentlyComputingStatistics->setVisible(false); + } + catch (const std::exception &e) + { + mitk::StatusBar::GetInstance()->DisplayErrorText(e.what()); + this->m_StatisticsUpdatePending = false; + m_Controls.label_currentlyComputingStatistics->setVisible(false); + } +} + +void QmitkImageStatisticsReloadedView::OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList &nodes) +{ + Q_UNUSED(part); + Q_UNUSED(nodes); +} + +void QmitkImageStatisticsReloadedView::PrepareDataStorageComboBoxes() +{ + auto isPlanarFigurePredicate = mitk::GetImageStatisticsPlanarFigurePredicate(); + auto isMaskPredicate = mitk::GetImageStatisticsMaskPredicate(); + auto isImagePredicate = mitk::GetImageStatisticsImagePredicate(); + auto isMaskOrPlanarFigurePredicate = mitk::NodePredicateOr::New(isPlanarFigurePredicate, isMaskPredicate); + + m_Controls.imageSelector->SetDataStorage(GetDataStorage()); + m_Controls.imageSelector->SetPredicate(isImagePredicate); + + m_Controls.maskImageSelector->SetDataStorage(GetDataStorage()); + + m_Controls.maskImageSelector->SetPredicate(isMaskOrPlanarFigurePredicate); + m_Controls.maskImageSelector->SetZeroEntryText(""); +} + +void QmitkImageStatisticsReloadedView::Activated() +{ +} + +void QmitkImageStatisticsReloadedView::Deactivated() +{ +} + +void QmitkImageStatisticsReloadedView::Visible() +{ + connect(this->m_Controls.imageSelector, static_cast(&QComboBox::currentIndexChanged), this, &QmitkImageStatisticsReloadedView::OnImageSelectorChanged); + connect(this->m_Controls.maskImageSelector, static_cast(&QComboBox::currentIndexChanged), this, &QmitkImageStatisticsReloadedView::OnMaskSelectorChanged); + OnImageSelectorChanged(); + OnMaskSelectorChanged(); +} + +void QmitkImageStatisticsReloadedView::Hidden() +{ + m_Controls.imageSelector->disconnect(); + m_Controls.maskImageSelector->disconnect(); +} + +void QmitkImageStatisticsReloadedView::SetFocus() +{ +} diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsReloadedView.h b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsReloadedView.h new file mode 100644 index 0000000000..d4fafae072 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsReloadedView.h @@ -0,0 +1,112 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#ifndef QmitkImageStatisticsReloadedView_H__INCLUDED +#define QmitkImageStatisticsReloadedView_H__INCLUDED + +#include "ui_QmitkImageStatisticsReloadedViewControls.h" + +// Qmitk includes +#include +#include +#include + +#include +#include +#include + +/*! +\brief QmitkImageStatisticsView is a bundle that allows statistics calculation from images. Three modes +are supported: 1. Statistics of one image, 2. Statistics of an image and a segmentation, 3. Statistics +of an image and a Planar Figure. The statistics calculation is realized in a separate thread to keep the +gui accessible during calculation. + +\ingroup Plugins/org.mitk.gui.qt.measurementtoolbox +*/ +class QmitkImageStatisticsReloadedView : public QmitkAbstractView, public mitk::ILifecycleAwarePart, public berry::IPartListener +{ + Q_OBJECT + +public: + using HistogramType = mitk::ImageStatisticsContainer::HistogramType; + + /*! + \brief default constructor */ + QmitkImageStatisticsReloadedView(QObject *parent = nullptr, const char *name = nullptr); + /*! + \brief default destructor */ + virtual ~QmitkImageStatisticsReloadedView(); + /*! + \brief method for creating the widget containing the application controls, like sliders, buttons etc. */ + virtual void CreateQtPartControl(QWidget *parent) override; + /*! + \brief method for creating the connections of main and control widget */ + virtual void CreateConnections(); + /*! + \brief Is called from the selection mechanism once the data manager selection has changed*/ + void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList &selectedNodes) override; + + void PrepareDataStorageComboBoxes(); + + static const std::string VIEW_ID; + + void FillHistogramWidget(const std::vector& histogram, const std::vector& dataLabels); + QmitkChartWidget::ChartStyle GetColorTheme() const; +protected: + virtual void Activated() override; + virtual void Deactivated() override; + virtual void Visible() override; + virtual void Hidden() override; + + virtual void SetFocus() override; + + /** \brief Is called right before the view closes (before the destructor) */ + virtual void PartClosed(const berry::IWorkbenchPartReference::Pointer&) override; + + /** \brief Required for berry::IPartListener */ + virtual Events::Types GetPartEventTypes() const override { return Events::CLOSED; } + + void OnImageSelectorChanged(); + void OnMaskSelectorChanged(); + + void CalculateOrGetStatistics(); + + void ComputeAndDisplayIntensityProfile(mitk::Image * image, mitk::PlanarFigure::Pointer maskPlanarFigure); + + void ResetGUI(); + + void OnStatisticsCalculationEnds(); + void OnRequestHistogramUpdate(unsigned int nBins); + void OnCheckBoxIgnoreZeroStateChanged(int state); + void OnSliderWidgetHistogramChanged(double value); + + void CalculateStatistics(mitk::Image::ConstPointer image, mitk::Image::ConstPointer mask=nullptr, mitk::PlanarFigure::ConstPointer maskPlanarFigure = nullptr); + + // member variables + Ui::QmitkImageStatisticsReloadedViewControls m_Controls; + +private: + typedef itk::SimpleMemberCommand< QmitkImageStatisticsReloadedView > ITKCommandType; + QmitkImageStatisticsCalculationJob * m_CalculationThread = nullptr; + bool m_StatisticsUpdatePending=false; + mitk::DataNode::ConstPointer m_selectedImageNode = nullptr, m_selectedMaskNode = nullptr; + + std::vector m_statisticContainerRules; + mitk::PlanarFigure::Pointer m_selectedPlanarFigure=nullptr; + long m_PlanarFigureObserverTag; + bool m_ForceRecompute = false; +}; +#endif // QmitkImageStatisticsView_H__INCLUDED diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsReloadedViewControls.ui b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsReloadedViewControls.ui new file mode 100644 index 0000000000..dfd1df3073 --- /dev/null +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsReloadedViewControls.ui @@ -0,0 +1,469 @@ + + + QmitkImageStatisticsReloadedViewControls + + + true + + + + 0 + 0 + 419 + 1016 + + + + Form + + + + + + QLayout::SetMinimumSize + + + 4 + + + + + + 0 + 0 + + + + false + + + + + + + + + + + + 255 + 0 + 0 + + + + + + + 0 + 0 + 0 + + + + + + + + + 255 + 0 + 0 + + + + + + + 0 + 0 + 0 + + + + + + + + + 120 + 120 + 120 + + + + + + + 120 + 120 + 120 + + + + + + + + Calculating statistics... + + + + + + + + 0 + 0 + + + + + + + + + 0 + 0 + 0 + + + + + + + + + 0 + 0 + 0 + + + + + + + + + 120 + 120 + 120 + + + + + + + + Mask image: + + + + + + + + 0 + 0 + + + + + + + + + 0 + 0 + 0 + + + + + + + + + 0 + 0 + 0 + + + + + + + + + 120 + 120 + 120 + + + + + + + + Image: + + + + + + + + 0 + 0 + + + + false + + + + + + + Ignore zero-valued voxels + + + + + + + + + + 0 + 200 + + + + Statistics + + + + 3 + + + 3 + + + 3 + + + 3 + + + + + + + + + + 255 + 0 + 0 + + + + + + + 255 + 0 + 0 + + + + + + + 255 + 0 + 0 + + + + + + + + + 255 + 0 + 0 + + + + + + + 255 + 0 + 0 + + + + + + + 255 + 0 + 0 + + + + + + + + + 120 + 120 + 120 + + + + + + + 120 + 120 + 120 + + + + + + + 120 + 120 + 120 + + + + + + + + + + + + + + + + 0 + 200 + + + + Histogram + + + + + + + + + + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + + + + + + + + 0 + 200 + + + + Intensity Profile + + + + + + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + + QmitkDataStorageComboBox + QComboBox +
QmitkDataStorageComboBox.h
+ + + QmitkHistogramVisualizationWidget + QWidget +
QmitkHistogramVisualizationWidget.h
+ 1 + + + QmitkImageStatisticsWidget + QWidget +
QmitkImageStatisticsWidget.h
+ 1 + + + QmitkDataStorageComboBoxWithSelectNone + QComboBox +
QmitkDataStorageComboBoxWithSelectNone.h
+ + + QmitkIntensityProfileVisualizationWidget + QWidget +
QmitkIntensityProfileVisualizationWidget.h
+ 1 + + + ctkSliderWidget + QWidget +
ctkSliderWidget.h
+ 1 + + + + + diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp index bcf8c0a50f..e778e73bdc 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp @@ -1,1266 +1,1297 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkImageStatisticsView.h" // Qt includes #include #include #include // berry includes #include // mitk includes #include #include #include #include #include #include #include #include +#include // itk includes #include "itksys/SystemTools.hxx" #include "itkImageRegionConstIteratorWithIndex.h" #include //blueberry includes #include #include const std::string QmitkImageStatisticsView::VIEW_ID = "org.mitk.views.imagestatistics"; const int QmitkImageStatisticsView::STAT_TABLE_BASE_HEIGHT = 180; QmitkImageStatisticsView::QmitkImageStatisticsView(QObject* /*parent*/, const char* /*name*/) -: m_Controls( nullptr ), - m_SelectedImage( nullptr ), - m_SelectedImageMask( nullptr ), - m_SelectedPlanarFigure( nullptr ), - m_ImageObserverTag( -1 ), - m_ImageMaskObserverTag( -1 ), - m_PlanarFigureObserverTag( -1 ), - m_TimeObserverTag( -1 ), - m_CurrentStatisticsValid( false ), - m_StatisticsUpdatePending( false ), - m_DataNodeSelectionChanged ( false ), + : m_Controls(nullptr), + m_SelectedImage(nullptr), + m_SelectedImageMask(nullptr), + m_SelectedPlanarFigure(nullptr), + m_ImageObserverTag(-1), + m_ImageMaskObserverTag(-1), + m_PlanarFigureObserverTag(-1), + m_TimeObserverTag(-1), + m_CurrentStatisticsValid(false), + m_StatisticsUpdatePending(false), + m_DataNodeSelectionChanged(false), m_Visible(false) { - this->m_CalculationThread = new QmitkImageStatisticsCalculationThread; + this->m_CalculationThread = new QmitkImageStatisticsCalculationJob; } QmitkImageStatisticsView::~QmitkImageStatisticsView() { - if ( m_SelectedImage != nullptr ) - m_SelectedImage->RemoveObserver( m_ImageObserverTag ); - if ( m_SelectedImageMask != nullptr ) - m_SelectedImageMask->RemoveObserver( m_ImageMaskObserverTag ); - if ( m_SelectedPlanarFigure != nullptr ) - m_SelectedPlanarFigure->RemoveObserver( m_PlanarFigureObserverTag ); - - while(this->m_CalculationThread->isRunning()) // wait until thread has finished + if (m_SelectedImage != nullptr) + m_SelectedImage->RemoveObserver(m_ImageObserverTag); + if (m_SelectedImageMask != nullptr) + m_SelectedImageMask->RemoveObserver(m_ImageMaskObserverTag); + if (m_SelectedPlanarFigure != nullptr) + m_SelectedPlanarFigure->RemoveObserver(m_PlanarFigureObserverTag); + + while (this->m_CalculationThread->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } delete this->m_CalculationThread; } void QmitkImageStatisticsView::CreateQtPartControl(QWidget *parent) { if (m_Controls == nullptr) { m_Controls = new Ui::QmitkImageStatisticsViewControls; m_Controls->setupUi(parent); CreateConnections(); m_Controls->m_ErrorMessageLabel->hide(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_Controls->m_BinSizeFrame->setEnabled(false); } } void QmitkImageStatisticsView::OnPageSuccessfullyLoaded() { berry::IPreferencesService* prefService = berry::WorkbenchPlugin::GetDefault()->GetPreferencesService(); m_StylePref = prefService->GetSystemPreferences()->Node(berry::QtPreferences::QT_STYLES_NODE); QString styleName = m_StylePref->Get(berry::QtPreferences::QT_STYLE_NAME, ""); if (styleName == ":/org.blueberry.ui.qt/darkstyle.qss") { this->m_Controls->m_JSHistogram->SetTheme(QmitkChartWidget::ChartStyle::darkstyle); } else { this->m_Controls->m_JSHistogram->SetTheme(QmitkChartWidget::ChartStyle::lightstyle); } } void QmitkImageStatisticsView::CreateConnections() { - if ( m_Controls ) + if (m_Controls) { - connect( (QObject*)(this->m_Controls->m_ButtonCopyHistogramToClipboard), SIGNAL(clicked()),(QObject*) this, SLOT(OnClipboardHistogramButtonClicked()) ); - connect( (QObject*)(this->m_Controls->m_ButtonCopyStatisticsToClipboard), SIGNAL(clicked()),(QObject*) this, SLOT(OnClipboardStatisticsButtonClicked()) ); - connect( (QObject*)(this->m_Controls->m_IgnoreZerosCheckbox), SIGNAL(clicked()),(QObject*) this, SLOT(OnIgnoreZerosCheckboxClicked()) ); - connect( (QObject*) this->m_CalculationThread, SIGNAL(finished()),this, SLOT( OnThreadedStatisticsCalculationEnds()),Qt::QueuedConnection); - connect( (QObject*) this, SIGNAL(StatisticsUpdate()),this, SLOT( RequestStatisticsUpdate()), Qt::QueuedConnection); - connect( (QObject*) this->m_Controls->m_StatisticsTable, SIGNAL(cellDoubleClicked(int,int)),this, SLOT( JumpToCoordinates(int,int)) ); + connect((QObject*)(this->m_Controls->m_ButtonCopyHistogramToClipboard), SIGNAL(clicked()), (QObject*)this, SLOT(OnClipboardHistogramButtonClicked())); + connect((QObject*)(this->m_Controls->m_ButtonCopyStatisticsToClipboard), SIGNAL(clicked()), (QObject*)this, SLOT(OnClipboardStatisticsButtonClicked())); + connect((QObject*)(this->m_Controls->m_IgnoreZerosCheckbox), SIGNAL(clicked()), (QObject*)this, SLOT(OnIgnoreZerosCheckboxClicked())); + connect((QObject*)this->m_CalculationThread, SIGNAL(finished()), this, SLOT(OnThreadedStatisticsCalculationEnds()), Qt::QueuedConnection); + connect((QObject*)this, SIGNAL(StatisticsUpdate()), this, SLOT(RequestStatisticsUpdate()), Qt::QueuedConnection); + connect((QObject*)this->m_Controls->m_StatisticsTable, SIGNAL(cellDoubleClicked(int, int)), this, SLOT(JumpToCoordinates(int, int))); connect((QObject*)(this->m_Controls->m_barRadioButton), SIGNAL(clicked()), (QObject*)(this), SLOT(OnBarRadioButtonSelected())); connect((QObject*)(this->m_Controls->m_lineRadioButton), SIGNAL(clicked()), (QObject*)(this), SLOT(OnLineRadioButtonSelected())); - connect( (QObject*) (this->m_Controls->m_HistogramNBinsSpinbox), SIGNAL(editingFinished()), this, SLOT(OnHistogramNBinsCheckBoxValueChanged())); - connect((QObject*)(this->m_Controls->m_UseDefaultNBinsCheckBox), SIGNAL(clicked()), (QObject*) this, SLOT(OnDefaultNBinsSpinBoxChanged())); - connect((QObject*)(this->m_Controls->m_ShowSubchartCheckBox), SIGNAL(clicked()), (QObject*) this, SLOT(OnShowSubchartBoxChanged())); - connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnPageSuccessfullyLoaded())); + connect((QObject*)(this->m_Controls->m_HistogramNBinsSpinbox), SIGNAL(editingFinished()), this, SLOT(OnHistogramNBinsCheckBoxValueChanged())); + connect((QObject*)(this->m_Controls->m_UseDefaultNBinsCheckBox), SIGNAL(clicked()), (QObject*)this, SLOT(OnDefaultNBinsSpinBoxChanged())); + connect((QObject*)(this->m_Controls->m_ShowSubchartCheckBox), SIGNAL(clicked()), (QObject*)this, SLOT(OnShowSubchartBoxChanged())); + connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*)this, SLOT(OnPageSuccessfullyLoaded())); } } void QmitkImageStatisticsView::OnDefaultNBinsSpinBoxChanged() { if (this->m_Controls->m_UseDefaultNBinsCheckBox->isChecked()) { m_Controls->m_HistogramNBinsSpinbox->setValue(100); this->m_CalculationThread->SetHistogramNBins(m_Controls->m_HistogramNBinsSpinbox->value()); m_HistogramNBins = m_Controls->m_HistogramNBinsSpinbox->value(); } m_Controls->m_BinSizeFrame->setEnabled(!m_Controls->m_UseDefaultNBinsCheckBox->isChecked()); this->UpdateStatistics(); } void QmitkImageStatisticsView::OnShowSubchartBoxChanged() { bool showSubchart = this->m_Controls->m_ShowSubchartCheckBox->isChecked(); this->m_Controls->m_JSHistogram->Reload(showSubchart); } void QmitkImageStatisticsView::OnBarRadioButtonSelected() { this->m_Controls->m_JSHistogram->SetChartTypeForAllDataAndReload(QmitkChartWidget::ChartType::bar); } void QmitkImageStatisticsView::OnLineRadioButtonSelected() { this->m_Controls->m_JSHistogram->SetChartTypeForAllDataAndReload(QmitkChartWidget::ChartType::line); } -void QmitkImageStatisticsView::PartClosed(const berry::IWorkbenchPartReference::Pointer& ) +void QmitkImageStatisticsView::PartClosed(const berry::IWorkbenchPartReference::Pointer&) { } void QmitkImageStatisticsView::OnTimeChanged(const itk::EventObject& e) { if (this->m_SelectedDataNodes.isEmpty() || this->m_SelectedImage == nullptr) return; const mitk::SliceNavigationController::GeometryTimeEvent* timeEvent = - dynamic_cast(&e); + dynamic_cast(&e); assert(timeEvent != nullptr); int timestep = timeEvent->GetPos(); if (this->m_SelectedImage->GetTimeSteps() > 1) { for (int x = 0; x < this->m_Controls->m_StatisticsTable->columnCount(); x++) { for (int y = 0; y < this->m_Controls->m_StatisticsTable->rowCount(); y++) { QTableWidgetItem* item = this->m_Controls->m_StatisticsTable->item(y, x); if (item == nullptr) break; if (x == timestep) { item->setBackgroundColor(Qt::yellow); } else { if (y % 2 == 0) item->setBackground(this->m_Controls->m_StatisticsTable->palette().base()); else item->setBackground(this->m_Controls->m_StatisticsTable->palette().alternateBase()); } } } this->m_Controls->m_StatisticsTable->viewport()->update(); } if ((this->m_SelectedImage->GetTimeSteps() == 1 && timestep == 0) || - this->m_SelectedImage->GetTimeSteps() > 1) + this->m_SelectedImage->GetTimeSteps() > 1) { m_Controls->m_JSHistogram->Clear(); - QmitkImageStatisticsCalculationThread::HistogramType::ConstPointer histogram = - (QmitkImageStatisticsCalculationThread::HistogramType::ConstPointer)this->m_CalculationThread->GetTimeStepHistogram(timestep); + QmitkImageStatisticsCalculationJob::HistogramType::ConstPointer histogram = + (QmitkImageStatisticsCalculationJob::HistogramType::ConstPointer)this->m_CalculationThread->GetTimeStepHistogram(timestep); if (histogram.IsNotNull()) { bool statisticsUpdateSuccessful = this->m_CalculationThread->GetStatisticsUpdateSuccessFlag(); if (statisticsUpdateSuccessful) { auto imageNameLabel = m_Controls->m_SelectedFeatureImageLabel->text().toStdString(); this->m_Controls->m_JSHistogram->AddData2D(ConvertHistogramToMap(histogram), imageNameLabel); if (this->m_Controls->m_lineRadioButton->isChecked()) { this->m_Controls->m_JSHistogram->SetChartType(imageNameLabel, QmitkChartWidget::ChartType::line); } else { this->m_Controls->m_JSHistogram->SetChartType(imageNameLabel, QmitkChartWidget::ChartType::bar); } this->m_Controls->m_JSHistogram->SetXAxisLabel("Grey value"); this->m_Controls->m_JSHistogram->SetYAxisLabel("Frequency"); this->m_Controls->m_JSHistogram->Show(this->m_Controls->m_ShowSubchartCheckBox->isChecked()); } } } } -void QmitkImageStatisticsView::JumpToCoordinates(int row ,int col) +void QmitkImageStatisticsView::JumpToCoordinates(int row, int col) { - if(m_SelectedDataNodes.isEmpty()) + if (m_SelectedDataNodes.isEmpty()) { - MITK_WARN("QmitkImageStatisticsView") << "No data node selected for statistics calculation." ; + MITK_WARN("QmitkImageStatisticsView") << "No data node selected for statistics calculation."; return; } mitk::Point3D world; - if (row==5 && !m_WorldMinList.empty()) + if (row == 5 && !m_WorldMinList.empty()) world = m_WorldMinList[col]; - else if (row==4 && !m_WorldMaxList.empty()) + else if (row == 4 && !m_WorldMaxList.empty()) world = m_WorldMaxList[col]; else return; mitk::IRenderWindowPart* part = this->GetRenderWindowPart(); if (part) { part->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SelectSliceByPoint(world); part->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()->SelectSliceByPoint(world); part->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()->SelectSliceByPoint(world); mitk::SliceNavigationController::GeometryTimeEvent timeEvent(this->m_SelectedImage->GetTimeGeometry(), col); part->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SetGeometryTime(timeEvent); } } void QmitkImageStatisticsView::OnIgnoreZerosCheckboxClicked() { emit StatisticsUpdate(); } void QmitkImageStatisticsView::OnClipboardHistogramButtonClicked() { if (!m_CurrentStatisticsValid) { QApplication::clipboard()->clear(); } if (m_SelectedPlanarFigure == nullptr) { const unsigned int t = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos(); typedef mitk::ImageStatisticsCalculator::HistogramType HistogramType; const HistogramType *histogram = this->m_CalculationThread->GetTimeStepHistogram(t).GetPointer(); QString clipboard("Measurement \t Frequency\n"); for (HistogramType::ConstIterator it = histogram->Begin(); it != histogram->End(); ++it) { clipboard = clipboard.append("%L1 \t %L2\n") .arg(it.GetMeasurementVector()[0], 0, 'f', 2) .arg(it.GetFrequency()); } QApplication::clipboard()->setText( clipboard, QClipboard::Clipboard); } //If a (non-closed) PlanarFigure is selected, display a line profile widget else if (m_SelectedPlanarFigure != nullptr) { QString clipboard("Pixel \t Intensity\n"); for (unsigned int i = 0; i < m_IntensityProfileList.size(); i++) { clipboard = clipboard.append("%L1 \t %L2\n").arg(QString::number(i)).arg(QString::number(m_IntensityProfileList.at(i))); } QApplication::clipboard()->setText(clipboard, QClipboard::Clipboard); } } void QmitkImageStatisticsView::OnClipboardStatisticsButtonClicked() { QLocale tempLocal; QLocale::setDefault(QLocale(QLocale::English, QLocale::UnitedStates)); - if ( m_CurrentStatisticsValid && !( m_SelectedPlanarFigure != nullptr)) - { - const std::vector &statistics = + if (m_CurrentStatisticsValid && !(m_SelectedPlanarFigure != nullptr)) + { + const auto &statistics = this->m_CalculationThread->GetStatisticsData(); // Set time borders for for loop ;) unsigned int startT, endT; - if(this->m_Controls->m_CheckBox4dCompleteTable->checkState()==Qt::CheckState::Unchecked) + if (this->m_Controls->m_CheckBox4dCompleteTable->checkState() == Qt::CheckState::Unchecked) { - startT = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()-> - GetPos(); - endT = startT+1; + startT = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()-> + GetPos(); + endT = startT + 1; } else { - startT = 0; - endT = statistics.size(); + startT = 0; + endT = statistics->GetNumberOfTimeSteps(); } QVector< QVector > statisticsTable; QStringList headline{ "Timestep", "Mean", "Median", "StdDev", "RMS", "Max", "Min", "NumberOfVoxels", "Skewness", "Kurtosis", "Uniformity", "Entropy", "MPP", "UPP", "V [mm³]" }; - for(int i=0;i row; - row.append(headline.at(i)); - statisticsTable.append(row); + QVector row; + row.append(headline.at(i)); + statisticsTable.append(row); } // Fill Table - for(unsigned int t=startT;tGetMean()) - << QString::number(statistics[t]->GetMedian()) - << QString::number(statistics[t]->GetStd()) - << QString::number(statistics[t]->GetRMS()) - << QString::number(statistics[t]->GetMax()) - << QString::number(statistics[t]->GetMin()) - << QString::number(statistics[t]->GetN()) - << QString::number(statistics[t]->GetSkewness()) - << QString::number(statistics[t]->GetKurtosis()) - << QString::number(statistics[t]->GetUniformity()) - << QString::number(statistics[t]->GetEntropy()) - << QString::number(statistics[t]->GetMPP()) - << QString::number(statistics[t]->GetUPP()) - << QString::number(m_Controls->m_StatisticsTable->item(7, 0)->data(Qt::DisplayRole).toDouble()); - - for(int z=0;zGetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::MEAN())) + << QString::number(statistics->GetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::MEDIAN())) + << QString::number(statistics->GetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::STANDARDDEVIATION())) + << QString::number(statistics->GetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::RMS())) + << QString::number(statistics->GetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::MAXIMUM())) + << QString::number(statistics->GetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::MINIMUM())) + << QString::number(statistics->GetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::NUMBEROFVOXELS())) + << QString::number(statistics->GetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::SKEWNESS())) + << QString::number(statistics->GetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::KURTOSIS())) + << QString::number(statistics->GetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::UNIFORMITY())) + << QString::number(statistics->GetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::ENTROPY())) + << QString::number(statistics->GetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::MPP())) + << QString::number(statistics->GetStatisticsForTimeStep(t).GetValueConverted(mitk::ImageStatisticsConstants::UPP())) + << QString::number(m_Controls->m_StatisticsTable->item(7, 0)->data(Qt::DisplayRole).toDouble()); + + for (int z = 0; z < value.size(); z++) + { + statisticsTable[z].append(value.at(z)); + } } // Create output string QString clipboard; - for(int i=0;isetText(clipboard, QClipboard::Clipboard); } else { QApplication::clipboard()->clear(); } QLocale::setDefault(tempLocal); } -void QmitkImageStatisticsView::OnSelectionChanged( berry::IWorkbenchPart::Pointer /*part*/, - const QList &nodes ) +void QmitkImageStatisticsView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, + const QList &nodes) { if (this->m_Visible) { - this->SelectionChanged( nodes ); + this->SelectionChanged(nodes); } else { this->m_DataNodeSelectionChanged = true; } } void QmitkImageStatisticsView::SelectionChanged(const QList &selectedNodes) { m_Controls->m_JSHistogram->Clear(); - if( this->m_StatisticsUpdatePending ) + if (this->m_StatisticsUpdatePending) { this->m_DataNodeSelectionChanged = true; return; // not ready for new data now! } if (selectedNodes.size() == this->m_SelectedDataNodes.size()) { int i = 0; for (; i < selectedNodes.size(); ++i) { if (selectedNodes.at(i) != this->m_SelectedDataNodes.at(i)) { break; } } // node selection did not change if (i == selectedNodes.size()) return; } //reset the feature image and image mask field m_Controls->m_SelectedFeatureImageLabel->setText("None"); m_Controls->m_SelectedMaskLabel->setText("None"); this->ReinitData(); if (selectedNodes.isEmpty()) { DisableHistogramGUIElements(); } else { EnableHistogramGUIElements(); ResetHistogramGUIElementsToDefault(); } - if(selectedNodes.size() == 1 || selectedNodes.size() == 2) + if (selectedNodes.size() == 1 || selectedNodes.size() == 2) { bool isBinary = false; - selectedNodes.value(0)->GetBoolProperty("binary",isBinary); + selectedNodes.value(0)->GetBoolProperty("binary", isBinary); mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage"); isBinary |= isLabelSet->CheckNode(selectedNodes.value(0)); - if(isBinary) + if (isBinary) { EnableHistogramGUIElements(); m_Controls->m_InfoLabel->setText(""); } - for (int i= 0; i< selectedNodes.size(); ++i) + for (int i = 0; i < selectedNodes.size(); ++i) { this->m_SelectedDataNodes.push_back(selectedNodes.at(i)); } this->m_DataNodeSelectionChanged = false; - this->m_Controls->m_ErrorMessageLabel->setText( "" ); + this->m_Controls->m_ErrorMessageLabel->setText(""); this->m_Controls->m_ErrorMessageLabel->hide(); emit StatisticsUpdate(); } else { this->m_DataNodeSelectionChanged = false; } } void QmitkImageStatisticsView::DisableHistogramGUIElements() { m_Controls->m_InfoLabel->setText(""); m_Controls->groupBox_histogram->setEnabled(false); m_Controls->groupBox_statistics->setEnabled(false); } void QmitkImageStatisticsView::ResetHistogramGUIElementsToDefault() { m_Controls->m_barRadioButton->setChecked(true); m_Controls->m_HistogramNBinsSpinbox->setValue(100); m_HistogramNBins = m_Controls->m_HistogramNBinsSpinbox->value(); m_Controls->m_UseDefaultNBinsCheckBox->setChecked(true); m_Controls->m_ShowSubchartCheckBox->setChecked(true); m_Controls->m_BinSizeFrame->setEnabled(false); m_Controls->m_barRadioButton->setEnabled(true); m_Controls->m_lineRadioButton->setEnabled(true); m_Controls->m_HistogramNBinsSpinbox->setEnabled(true); this->m_CalculationThread->SetHistogramNBins(m_Controls->m_HistogramNBinsSpinbox->value()); } void QmitkImageStatisticsView::EnableHistogramGUIElements() { m_Controls->groupBox_histogram->setEnabled(true); m_Controls->groupBox_plot->setEnabled(true); m_Controls->groupBox_statistics->setEnabled(true); } void QmitkImageStatisticsView::ReinitData() { - while( this->m_CalculationThread->isRunning()) // wait until thread has finished + while (this->m_CalculationThread->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } - if(this->m_SelectedImage != nullptr) + if (this->m_SelectedImage != nullptr) { - this->m_SelectedImage->RemoveObserver( this->m_ImageObserverTag); + this->m_SelectedImage->RemoveObserver(this->m_ImageObserverTag); this->m_SelectedImage = nullptr; } - if(this->m_SelectedImageMask != nullptr) + if (this->m_SelectedImageMask != nullptr) { - this->m_SelectedImageMask->RemoveObserver( this->m_ImageMaskObserverTag); + this->m_SelectedImageMask->RemoveObserver(this->m_ImageMaskObserverTag); this->m_SelectedImageMask = nullptr; } - if(this->m_SelectedPlanarFigure != nullptr) + if (this->m_SelectedPlanarFigure != nullptr) { - this->m_SelectedPlanarFigure->RemoveObserver( this->m_PlanarFigureObserverTag); + this->m_SelectedPlanarFigure->RemoveObserver(this->m_PlanarFigureObserverTag); this->m_SelectedPlanarFigure = nullptr; } this->m_SelectedDataNodes.clear(); this->m_StatisticsUpdatePending = false; - m_Controls->m_ErrorMessageLabel->setText( "" ); + m_Controls->m_ErrorMessageLabel->setText(""); m_Controls->m_ErrorMessageLabel->hide(); this->InvalidateStatisticsTableView(); - m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); + m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); } void QmitkImageStatisticsView::OnThreadedStatisticsCalculationEnds() { m_Controls->m_ErrorMessageLabel->setText(""); m_Controls->m_ErrorMessageLabel->hide(); this->WriteStatisticsToGUI(); } void QmitkImageStatisticsView::UpdateStatistics() { mitk::IRenderWindowPart* renderPart = this->GetRenderWindowPart(); - if ( renderPart == nullptr ) + if (renderPart == nullptr) { - this->m_StatisticsUpdatePending = false; + this->m_StatisticsUpdatePending = false; return; } m_WorldMinList.clear(); m_WorldMaxList.clear(); // classify selected nodes mitk::NodePredicateDataType::Pointer isImage = mitk::NodePredicateDataType::New("Image"); mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage"); mitk::NodePredicateOr::Pointer imagePredicate = mitk::NodePredicateOr::New(isImage, isLabelSet); std::string maskName; std::string maskType; std::string featureImageName; unsigned int maskDimension = 0; // reset data from last run ITKCommandType::Pointer changeListener = ITKCommandType::New(); - changeListener->SetCallbackFunction( this, &QmitkImageStatisticsView::SelectedDataModified ); + changeListener->SetCallbackFunction(this, &QmitkImageStatisticsView::SelectedDataModified); mitk::DataNode::Pointer planarFigureNode; - for( int i= 0 ; i < this->m_SelectedDataNodes.size(); ++i) + for (int i = 0; i < this->m_SelectedDataNodes.size(); ++i) { mitk::PlanarFigure::Pointer planarFig = dynamic_cast(this->m_SelectedDataNodes.at(i)->GetData()); - if( imagePredicate->CheckNode(this->m_SelectedDataNodes.at(i)) ) + if (imagePredicate->CheckNode(this->m_SelectedDataNodes.at(i))) { bool isMask = false; this->m_SelectedDataNodes.at(i)->GetPropertyValue("binary", isMask); isMask |= isLabelSet->CheckNode(this->m_SelectedDataNodes.at(i)); - if( this->m_SelectedImageMask == nullptr && isMask) + if (this->m_SelectedImageMask == nullptr && isMask) { this->m_SelectedImageMask = dynamic_cast(this->m_SelectedDataNodes.at(i)->GetData()); this->m_ImageMaskObserverTag = this->m_SelectedImageMask->AddObserver(itk::ModifiedEvent(), changeListener); maskName = this->m_SelectedDataNodes.at(i)->GetName(); maskType = m_SelectedImageMask->GetNameOfClass(); maskDimension = 3; } - else if( !isMask ) + else if (!isMask) { - if(this->m_SelectedImage == nullptr) + if (this->m_SelectedImage == nullptr) { this->m_SelectedImage = static_cast(this->m_SelectedDataNodes.at(i)->GetData()); this->m_ImageObserverTag = this->m_SelectedImage->AddObserver(itk::ModifiedEvent(), changeListener); } featureImageName = this->m_SelectedDataNodes.at(i)->GetName(); } } else if (planarFig.IsNotNull()) { - if(this->m_SelectedPlanarFigure == nullptr) + if (this->m_SelectedPlanarFigure == nullptr) { this->m_SelectedPlanarFigure = planarFig; - this->m_PlanarFigureObserverTag = - this->m_SelectedPlanarFigure->AddObserver(mitk::EndInteractionPlanarFigureEvent(), changeListener); + this->m_PlanarFigureObserverTag = + this->m_SelectedPlanarFigure->AddObserver(mitk::EndInteractionPlanarFigureEvent(), changeListener); maskName = this->m_SelectedDataNodes.at(i)->GetName(); maskType = this->m_SelectedPlanarFigure->GetNameOfClass(); maskDimension = 2; planarFigureNode = m_SelectedDataNodes.at(i); } } else { m_Controls->m_ErrorMessageLabel->setText("Invalid data node type!"); m_Controls->m_ErrorMessageLabel->show(); } } - if(maskName == "") + if (maskName == "") { maskName = "None"; maskType = ""; maskDimension = 0; } - if(featureImageName == "") + if (featureImageName == "") { featureImageName = "None"; } if (m_SelectedPlanarFigure != nullptr && m_SelectedImage == nullptr) { mitk::DataStorage::SetOfObjects::ConstPointer parentSet = this->GetDataStorage()->GetSources(planarFigureNode); - for (unsigned int i=0; iSize(); i++) + for (unsigned int i = 0; i < parentSet->Size(); i++) { mitk::DataNode::Pointer node = parentSet->ElementAt(i); - if( imagePredicate->CheckNode(node) ) + if (imagePredicate->CheckNode(node)) { bool isMask = false; node->GetPropertyValue("binary", isMask); isMask |= isLabelSet->CheckNode(node); - if( !isMask ) + if (!isMask) { - if(this->m_SelectedImage == nullptr) + if (this->m_SelectedImage == nullptr) { this->m_SelectedImage = static_cast(node->GetData()); this->m_ImageObserverTag = this->m_SelectedImage->AddObserver(itk::ModifiedEvent(), changeListener); } } } } } unsigned int timeStep = renderPart->GetTimeNavigationController()->GetTime()->GetPos(); - if ( m_SelectedImage != nullptr && m_SelectedImage->IsInitialized()) + if (m_SelectedImage != nullptr && m_SelectedImage->IsInitialized()) { // Check if a the selected image is a multi-channel image. If yes, statistics // cannot be calculated currently. - if ( m_SelectedImage->GetPixelType().GetNumberOfComponents() > 1 ) + if (m_SelectedImage->GetPixelType().GetNumberOfComponents() > 1) { - m_Controls->m_ErrorMessageLabel->setText( "Multi-component images not supported." ); + m_Controls->m_ErrorMessageLabel->setText("Multi-component images not supported."); m_Controls->m_ErrorMessageLabel->show(); this->InvalidateStatisticsTableView(); - m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); + m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_CurrentStatisticsValid = false; this->m_StatisticsUpdatePending = false; this->DisableHistogramGUIElements(); m_Controls->m_InfoLabel->setText(""); return; } std::stringstream maskLabel; maskLabel << maskName; - if ( maskDimension > 0 ) + if (maskDimension > 0) { maskLabel << " [" << maskDimension << "D " << maskType << "]"; } - m_Controls->m_SelectedMaskLabel->setText( maskLabel.str().c_str() ); + m_Controls->m_SelectedMaskLabel->setText(maskLabel.str().c_str()); m_Controls->m_SelectedFeatureImageLabel->setText(featureImageName.c_str()); // check time step validity - if(m_SelectedImage->GetDimension() <= 3 && timeStep > m_SelectedImage->GetDimension(3)-1) + if (m_SelectedImage->GetDimension() <= 3 && timeStep > m_SelectedImage->GetDimension(3) - 1) { - timeStep = m_SelectedImage->GetDimension(3)-1; + timeStep = m_SelectedImage->GetDimension(3) - 1; } // Add the used mask time step to the mask label so the user knows which mask time step was used // if the image time step is bigger than the total number of mask time steps (see // ImageStatisticsCalculator::ExtractImageAndMask) if (m_SelectedImageMask != nullptr) { unsigned int maskTimeStep = timeStep; if (maskTimeStep >= m_SelectedImageMask->GetTimeSteps()) { maskTimeStep = m_SelectedImageMask->GetTimeSteps() - 1; } m_Controls->m_SelectedMaskLabel->setText(m_Controls->m_SelectedMaskLabel->text() + - QString(" (t=") + - QString::number(maskTimeStep) + - QString(")")); + QString(" (t=") + + QString::number(maskTimeStep) + + QString(")")); } // check if the segmentation mask is empty if (m_SelectedImageMask != nullptr) { auto maskStatistics = m_SelectedImageMask->GetStatistics(); mitk::ScalarType maskMaxValue = maskStatistics->GetScalarValueMax(0); if (m_SelectedImageMask->GetDimension() == 4) { for (unsigned int curTimestep = 1; curTimestep < m_SelectedImageMask->GetTimeSteps(); curTimestep++) { maskMaxValue = std::max(maskStatistics->GetScalarValueMax(curTimestep), maskMaxValue); } } bool segmentationIsEmpty = maskMaxValue == 0; if (segmentationIsEmpty) { - m_Controls->m_ErrorMessageLabel->setText( "Empty segmentation mask selected..." ); + m_Controls->m_ErrorMessageLabel->setText("Empty segmentation mask selected..."); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; return; } } //// initialize thread and trigger it - this->m_CalculationThread->SetIgnoreZeroValueVoxel( m_Controls->m_IgnoreZerosCheckbox->isChecked() ); - this->m_CalculationThread->Initialize( m_SelectedImage, m_SelectedImageMask, m_SelectedPlanarFigure ); - this->m_CalculationThread->SetTimeStep( timeStep ); + this->m_CalculationThread->SetIgnoreZeroValueVoxel(m_Controls->m_IgnoreZerosCheckbox->isChecked()); + this->m_CalculationThread->Initialize(m_SelectedImage, m_SelectedImageMask, m_SelectedPlanarFigure); + this->m_CalculationThread->SetTimeStep(timeStep); m_Controls->m_ErrorMessageLabel->setText("Calculating statistics..."); m_Controls->m_ErrorMessageLabel->show(); try { // Compute statistics this->m_CalculationThread->start(); } - catch ( const mitk::Exception& e) + catch (const mitk::Exception& e) { m_Controls->m_ErrorMessageLabel->setText("" + QString(e.GetDescription()) + ""); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } - catch ( const std::runtime_error &e ) + catch (const std::runtime_error &e) { // In case of exception, print error message on GUI m_Controls->m_ErrorMessageLabel->setText("" + QString(e.what()) + ""); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } - catch ( const std::exception &e ) + catch (const std::exception &e) { MITK_ERROR << "Caught exception: " << e.what(); // In case of exception, print error message on GUI m_Controls->m_ErrorMessageLabel->setText("" + QString(e.what()) + ""); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } } else { this->m_StatisticsUpdatePending = false; } } void QmitkImageStatisticsView::SelectedDataModified() { - if( !m_StatisticsUpdatePending ) + if (!m_StatisticsUpdatePending) { emit StatisticsUpdate(); } } void QmitkImageStatisticsView::NodeRemoved(const mitk::DataNode *node) { - while(this->m_CalculationThread->isRunning()) // wait until thread has finished + while (this->m_CalculationThread->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } if (node->GetData() == m_SelectedImage) { m_SelectedImage = nullptr; } } void QmitkImageStatisticsView::RequestStatisticsUpdate() { - if ( !m_StatisticsUpdatePending ) + if (!m_StatisticsUpdatePending) { - if(this->m_DataNodeSelectionChanged) + if (this->m_DataNodeSelectionChanged) { this->SelectionChanged(this->GetCurrentSelection()); } else { this->m_StatisticsUpdatePending = true; this->UpdateStatistics(); } } if (this->GetRenderWindowPart()) this->GetRenderWindowPart()->RequestUpdate(); } void QmitkImageStatisticsView::OnHistogramNBinsCheckBoxValueChanged() { - if (static_cast(m_Controls->m_HistogramNBinsSpinbox->value()) != m_HistogramNBins) - { - m_HistogramNBins = m_Controls->m_HistogramNBinsSpinbox->value(); - this->m_CalculationThread->SetHistogramNBins(m_Controls->m_HistogramNBinsSpinbox->value()); - this->UpdateStatistics(); - } + if (static_cast(m_Controls->m_HistogramNBinsSpinbox->value()) != m_HistogramNBins) + { + m_HistogramNBins = m_Controls->m_HistogramNBinsSpinbox->value(); + this->m_CalculationThread->SetHistogramNBins(m_Controls->m_HistogramNBinsSpinbox->value()); + this->UpdateStatistics(); + } } void QmitkImageStatisticsView::WriteStatisticsToGUI() { m_Controls->m_JSHistogram->Clear(); m_IntensityProfileList.clear(); //Disconnect OnLineRadioButtonSelected() to prevent reloading chart when radiobutton is checked programmatically disconnect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), 0, 0); - connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnPageSuccessfullyLoaded())); + connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*)this, SLOT(OnPageSuccessfullyLoaded())); m_Controls->m_InfoLabel->setText(""); if (m_DataNodeSelectionChanged) { this->m_StatisticsUpdatePending = false; this->RequestStatisticsUpdate(); return; // stop visualization of results and calculate statistics of new selection } if (this->m_CalculationThread->GetStatisticsUpdateSuccessFlag()) { if (this->m_CalculationThread->GetStatisticsChangedFlag()) { // Do not show any error messages m_Controls->m_ErrorMessageLabel->hide(); m_CurrentStatisticsValid = true; } if (m_SelectedImage != nullptr) { //all statistics are now computed also on planar figures (lines, paths...)! // If a (non-closed) PlanarFigure is selected, display a line profile widget if (m_SelectedPlanarFigure != nullptr && !m_SelectedPlanarFigure->IsClosed()) { // check whether PlanarFigure is initialized const mitk::PlaneGeometry *planarFigurePlaneGeometry = m_SelectedPlanarFigure->GetPlaneGeometry(); if (planarFigurePlaneGeometry != nullptr) { unsigned int timeStep = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos(); mitk::Image::Pointer image; if (this->m_CalculationThread->GetStatisticsImage()->GetDimension() == 4) { mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(this->m_CalculationThread->GetStatisticsImage()); timeSelector->SetTimeNr(timeStep); timeSelector->Update(); image = timeSelector->GetOutput(); } else { - image = this->m_CalculationThread->GetStatisticsImage(); + image = this->m_CalculationThread->GetStatisticsImage()->Clone(); } mitk::IntensityProfile::ConstPointer intensityProfile = (mitk::IntensityProfile::ConstPointer)mitk::ComputeIntensityProfile(image, m_SelectedPlanarFigure); m_IntensityProfileList = ConvertIntensityProfileToVector(intensityProfile); auto lineDataLabel = "Intensity profile " + m_Controls->m_SelectedMaskLabel->text().toStdString(); m_Controls->m_JSHistogram->SetChartType(lineDataLabel, QmitkChartWidget::ChartType::line); m_Controls->m_JSHistogram->AddData1D(m_IntensityProfileList, lineDataLabel); m_Controls->m_JSHistogram->SetXAxisLabel("Distance"); m_Controls->m_JSHistogram->SetYAxisLabel("Intensity"); m_Controls->m_JSHistogram->Show(m_Controls->m_ShowSubchartCheckBox->isChecked()); m_Controls->m_lineRadioButton->setChecked(true); m_Controls->m_lineRadioButton->setEnabled(false); m_Controls->m_barRadioButton->setEnabled(false); m_Controls->m_HistogramNBinsSpinbox->setEnabled(false); m_Controls->m_BinSizeFrame->setEnabled(false); m_Controls->m_UseDefaultNBinsCheckBox->setEnabled(false); //Reconnect OnLineRadioButtonSelected() - connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnLineRadioButtonSelected())); - auto statisticsVector = this->m_CalculationThread->GetStatisticsData(); + connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*)this, SLOT(OnLineRadioButtonSelected())); + auto statisticsContainer = this->m_CalculationThread->GetStatisticsData(); //only one entry (current timestep) - this->FillLinearProfileStatisticsTableView(statisticsVector.front().GetPointer(), this->m_CalculationThread->GetStatisticsImage()); + this->FillLinearProfileStatisticsTableView(statisticsContainer, this->m_CalculationThread->GetStatisticsImage()); QString message("Only linegraph available for an intensity profile!"); if (this->m_CalculationThread->GetStatisticsImage()->GetDimension() == 4) { message += "Only current timestep displayed!"; } message += ""; m_Controls->m_InfoLabel->setText(message); m_CurrentStatisticsValid = true; } else { // Clear statistics, histogram, and GUI this->InvalidateStatisticsTableView(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_CurrentStatisticsValid = false; m_Controls->m_ErrorMessageLabel->hide(); m_Controls->m_SelectedMaskLabel->setText("None"); this->m_StatisticsUpdatePending = false; m_Controls->m_InfoLabel->setText(""); return; } } else { m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); auto histogram = this->m_CalculationThread->GetTimeStepHistogram(this->m_CalculationThread->GetTimeStep()).GetPointer(); auto imageLabelName = m_Controls->m_SelectedFeatureImageLabel->text().toStdString(); m_Controls->m_JSHistogram->AddData2D(ConvertHistogramToMap(histogram), imageLabelName); m_Controls->m_JSHistogram->SetChartType(imageLabelName, QmitkChartWidget::ChartType::bar); this->m_Controls->m_JSHistogram->SetXAxisLabel("Gray value"); this->m_Controls->m_JSHistogram->SetYAxisLabel("Frequency"); m_Controls->m_UseDefaultNBinsCheckBox->setEnabled(true); m_Controls->m_JSHistogram->Show(this->m_Controls->m_ShowSubchartCheckBox->isChecked()); this->FillStatisticsTableView(this->m_CalculationThread->GetStatisticsData(), this->m_CalculationThread->GetStatisticsImage()); + + auto aStatistic = this->m_CalculationThread->GetStatisticsData(); + auto statisticsNode = mitk::DataNode::New(); + statisticsNode->SetName(m_Controls->m_SelectedFeatureImageLabel->text().toStdString()); + statisticsNode->SetData(aStatistic->Clone()); + statisticsNode->SetProperty("helper object", mitk::BoolProperty::New(true)); + this->GetDataStorage()->Add(statisticsNode); + } m_CurrentStatisticsValid = true; } } else { m_Controls->m_SelectedMaskLabel->setText("None"); m_Controls->m_ErrorMessageLabel->setText(m_CalculationThread->GetLastErrorMessage().c_str()); m_Controls->m_ErrorMessageLabel->show(); // Clear statistics and histogram this->InvalidateStatisticsTableView(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0); m_CurrentStatisticsValid = false; } berry::IPreferencesService* prefService = berry::WorkbenchPlugin::GetDefault()->GetPreferencesService(); m_StylePref = prefService->GetSystemPreferences()->Node(berry::QtPreferences::QT_STYLES_NODE); this->m_StatisticsUpdatePending = false; } void QmitkImageStatisticsView::FillStatisticsTableView( - const std::vector &statistics, - const mitk::Image *image ) + mitk::ImageStatisticsContainer::ConstPointer statistics, + const mitk::Image *image) { this->m_Controls->m_StatisticsTable->setColumnCount(image->GetTimeSteps()); this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(image->GetTimeSteps() > 1); // Set Checkbox for complete copy of statistic table - if(image->GetTimeSteps()>1) + if (image->GetTimeSteps() > 1) { this->m_Controls->m_CheckBox4dCompleteTable->setEnabled(true); } else { this->m_Controls->m_CheckBox4dCompleteTable->setEnabled(false); this->m_Controls->m_CheckBox4dCompleteTable->setChecked(false); } for (unsigned int t = 0; t < image->GetTimeSteps(); t++) { this->m_Controls->m_StatisticsTable->setHorizontalHeaderItem(t, - new QTableWidgetItem(QString::number(t))); + new QTableWidgetItem(QString::number(t))); + + auto minIndex = statistics->GetStatisticsForTimeStep(t).GetValueConverted( + mitk::ImageStatisticsConstants::MINIMUMPOSITION()); + auto maxIndex = statistics->GetStatisticsForTimeStep(t).GetValueConverted( + mitk::ImageStatisticsConstants::MAXIMUMPOSITION()); - if (statistics.at(t)->GetMaxIndex().size()==3) + if (maxIndex.size() == 3) { + mitk::Point3D index, max, min; - index[0] = statistics.at(t)->GetMaxIndex()[0]; - index[1] = statistics.at(t)->GetMaxIndex()[1]; - index[2] = statistics.at(t)->GetMaxIndex()[2]; + index[0] = maxIndex[0]; + index[1] = maxIndex[1]; + index[2] = maxIndex[2]; m_SelectedImage->GetGeometry()->IndexToWorld(index, max); this->m_WorldMaxList.push_back(max); - index[0] = statistics.at(t)->GetMinIndex()[0]; - index[1] = statistics.at(t)->GetMinIndex()[1]; - index[2] = statistics.at(t)->GetMinIndex()[2]; + index[0] = minIndex[0]; + index[1] = minIndex[1]; + index[2] = minIndex[2]; m_SelectedImage->GetGeometry()->IndexToWorld(index, min); this->m_WorldMinList.push_back(min); } - auto statisticsVector = AssembleStatisticsIntoVector(statistics.at(t).GetPointer(), image); + auto statisticsVector = AssembleStatisticsIntoVector(statistics, image); unsigned int count = 0; for (const auto& entry : statisticsVector) { auto item = new QTableWidgetItem(entry); this->m_Controls->m_StatisticsTable->setItem(count, t, item); count++; } - } + } this->m_Controls->m_StatisticsTable->resizeColumnsToContents(); int height = STAT_TABLE_BASE_HEIGHT; if (this->m_Controls->m_StatisticsTable->horizontalHeader()->isVisible()) height += this->m_Controls->m_StatisticsTable->horizontalHeader()->height(); if (this->m_Controls->m_StatisticsTable->horizontalScrollBar()->isVisible()) height += this->m_Controls->m_StatisticsTable->horizontalScrollBar()->height(); this->m_Controls->m_StatisticsTable->setMinimumHeight(height); // make sure the current timestep's column is highlighted (and the correct histogram is displayed) unsigned int t = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()-> - GetPos(); + GetPos(); mitk::SliceNavigationController::GeometryTimeEvent timeEvent(this->m_SelectedImage->GetTimeGeometry(), - t); + t); this->OnTimeChanged(timeEvent); t = std::min(image->GetTimeSteps() - 1, t); // See bug 18340 /*QString hotspotMean; hotspotMean.append(QString("%1").arg(s[t].GetHotspotStatistics().GetMean(), 0, 'f', decimals)); hotspotMean += " ("; for (int i=0; im_Controls->m_StatisticsTable->setItem( 7, t, new QTableWidgetItem( hotspotMean ) ); QString hotspotMax; hotspotMax.append(QString("%1").arg(s[t].GetHotspotStatistics().GetMax(), 0, 'f', decimals)); hotspotMax += " ("; for (int i=0; im_Controls->m_StatisticsTable->setItem( 8, t, new QTableWidgetItem( hotspotMax ) ); QString hotspotMin; hotspotMin.append(QString("%1").arg(s[t].GetHotspotStatistics().GetMin(), 0, 'f', decimals)); hotspotMin += " ("; for (int i=0; im_Controls->m_StatisticsTable->setItem( 9, t, new QTableWidgetItem( hotspotMin ) );*/ } -std::vector QmitkImageStatisticsView::AssembleStatisticsIntoVector(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics, mitk::Image::ConstPointer image, bool noVolumeDefined) const +std::vector QmitkImageStatisticsView::AssembleStatisticsIntoVector(mitk::ImageStatisticsContainer::ConstPointer statistics, mitk::Image::ConstPointer image, bool noVolumeDefined) const { std::vector result; unsigned int decimals = 2; //statistics of higher order should have 5 decimal places because they used to be very small unsigned int decimalsHigherOrderStatistics = 5; if (image->GetPixelType().GetComponentType() == itk::ImageIOBase::DOUBLE || image->GetPixelType().GetComponentType() == itk::ImageIOBase::FLOAT) { decimals = 5; } - - result.push_back(GetFormattedString(statistics->GetMean(), decimals)); - result.push_back(GetFormattedString(statistics->GetMedian(), decimals)); - result.push_back(GetFormattedString(statistics->GetStd(), decimals)); - result.push_back(GetFormattedString(statistics->GetRMS(), decimals)); - result.push_back(GetFormattedString(statistics->GetMax(), decimals) + " " + GetFormattedIndex(statistics->GetMaxIndex())); - result.push_back(GetFormattedString(statistics->GetMin(), decimals) + " " + GetFormattedIndex(statistics->GetMinIndex())); + auto statistic = statistics->GetStatisticsForTimeStep(0); + result.push_back(GetFormattedString( + statistic.GetValueConverted(mitk::ImageStatisticsConstants::MEAN()), decimals)); + result.push_back(GetFormattedString( + statistic.GetValueConverted(mitk::ImageStatisticsConstants::MEDIAN()), decimals)); + result.push_back(GetFormattedString( + statistic.GetValueConverted(mitk::ImageStatisticsConstants::STANDARDDEVIATION()), decimals)); + result.push_back(GetFormattedString( + statistic.GetValueConverted(mitk::ImageStatisticsConstants::RMS()), decimals)); + result.push_back(GetFormattedString( + statistic.GetValueConverted(mitk::ImageStatisticsConstants::MAXIMUM()), decimals) + + " " + GetFormattedIndex(statistic.GetValueConverted(mitk::ImageStatisticsConstants::MAXIMUMPOSITION()))); + result.push_back(GetFormattedString( + statistic.GetValueConverted(mitk::ImageStatisticsConstants::MINIMUM()), decimals) + + " " + GetFormattedIndex(statistic.GetValueConverted(mitk::ImageStatisticsConstants::MINIMUMPOSITION()))); + + auto numberVoxels = statistic.GetValueConverted(mitk::ImageStatisticsConstants::NUMBEROFVOXELS()); //to prevent large negative values of empty image statistics - if (statistics->GetN() != std::numeric_limits::min()) { - result.push_back(GetFormattedString(statistics->GetN(), 0)); + if (numberVoxels != std::numeric_limits::min()) { + result.push_back(GetFormattedString(numberVoxels, 0)); const mitk::BaseGeometry *geometry = image->GetGeometry(); if (geometry != NULL && !noVolumeDefined) - { + { const mitk::Vector3D &spacing = image->GetGeometry()->GetSpacing(); - double volume = spacing[0] * spacing[1] * spacing[2] * static_cast(statistics->GetN()); + double volume = spacing[0] * spacing[1] * spacing[2] * static_cast(numberVoxels); result.push_back(GetFormattedString(volume, decimals)); - } + } else { result.push_back("NA"); - } + } } else { result.push_back("NA"); result.push_back("NA"); } - result.push_back(GetFormattedString(statistics->GetSkewness(), decimalsHigherOrderStatistics)); - result.push_back(GetFormattedString(statistics->GetKurtosis(), decimalsHigherOrderStatistics)); - result.push_back(GetFormattedString(statistics->GetUniformity(), decimalsHigherOrderStatistics)); - result.push_back(GetFormattedString(statistics->GetEntropy(), decimalsHigherOrderStatistics)); - result.push_back(GetFormattedString(statistics->GetMPP(), decimals)); - result.push_back(GetFormattedString(statistics->GetUPP(), decimalsHigherOrderStatistics)); + result.push_back( + GetFormattedString(statistic.GetValueConverted(mitk::ImageStatisticsConstants::SKEWNESS()), decimalsHigherOrderStatistics)); + result.push_back( + GetFormattedString(statistic.GetValueConverted(mitk::ImageStatisticsConstants::KURTOSIS()), decimalsHigherOrderStatistics)); + result.push_back( + GetFormattedString(statistic.GetValueConverted(mitk::ImageStatisticsConstants::UNIFORMITY()), decimalsHigherOrderStatistics)); + result.push_back( + GetFormattedString(statistic.GetValueConverted(mitk::ImageStatisticsConstants::ENTROPY()), decimalsHigherOrderStatistics)); + result.push_back( + GetFormattedString(statistic.GetValueConverted(mitk::ImageStatisticsConstants::MPP()), decimals)); + result.push_back( + GetFormattedString(statistic.GetValueConverted(mitk::ImageStatisticsConstants::UPP()), decimalsHigherOrderStatistics)); return result; } -void QmitkImageStatisticsView::FillLinearProfileStatisticsTableView(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics, +void QmitkImageStatisticsView::FillLinearProfileStatisticsTableView(mitk::ImageStatisticsContainer::ConstPointer statistics, const mitk::Image *image) { this->m_Controls->m_StatisticsTable->setColumnCount(1); this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(false); m_PlanarFigureStatistics = this->AssembleStatisticsIntoVector(statistics, image, true); - for (unsigned int i = 0; i< m_PlanarFigureStatistics.size(); i++) + for (unsigned int i = 0; i < m_PlanarFigureStatistics.size(); i++) { - this->m_Controls->m_StatisticsTable->setItem( i, 0, new QTableWidgetItem(m_PlanarFigureStatistics[i] )); + this->m_Controls->m_StatisticsTable->setItem(i, 0, new QTableWidgetItem(m_PlanarFigureStatistics[i])); } this->m_Controls->m_StatisticsTable->resizeColumnsToContents(); int height = STAT_TABLE_BASE_HEIGHT; if (this->m_Controls->m_StatisticsTable->horizontalHeader()->isVisible()) height += this->m_Controls->m_StatisticsTable->horizontalHeader()->height(); if (this->m_Controls->m_StatisticsTable->horizontalScrollBar()->isVisible()) height += this->m_Controls->m_StatisticsTable->horizontalScrollBar()->height(); this->m_Controls->m_StatisticsTable->setMinimumHeight(height); } void QmitkImageStatisticsView::InvalidateStatisticsTableView() { this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(false); this->m_Controls->m_StatisticsTable->setColumnCount(1); - for ( int i = 0; i < this->m_Controls->m_StatisticsTable->rowCount(); ++i ) + for (int i = 0; i < this->m_Controls->m_StatisticsTable->rowCount(); ++i) { { - this->m_Controls->m_StatisticsTable->setItem( i, 0, new QTableWidgetItem( "NA" ) ); + this->m_Controls->m_StatisticsTable->setItem(i, 0, new QTableWidgetItem("NA")); } } this->m_Controls->m_StatisticsTable->setMinimumHeight(STAT_TABLE_BASE_HEIGHT); } void QmitkImageStatisticsView::Activated() { } void QmitkImageStatisticsView::Deactivated() { } void QmitkImageStatisticsView::Visible() { m_Visible = true; mitk::IRenderWindowPart* renderWindow = GetRenderWindowPart(); if (renderWindow) { itk::ReceptorMemberCommand::Pointer cmdTimeEvent = - itk::ReceptorMemberCommand::New(); + itk::ReceptorMemberCommand::New(); cmdTimeEvent->SetCallbackFunction(this, &QmitkImageStatisticsView::OnTimeChanged); // It is sufficient to add the observer to the axial render window since the GeometryTimeEvent // is always triggered by all views. m_TimeObserverTag = renderWindow->GetQmitkRenderWindow("axial")-> - GetSliceNavigationController()-> - AddObserver(mitk::SliceNavigationController::GeometryTimeEvent(nullptr, 0), cmdTimeEvent); + GetSliceNavigationController()-> + AddObserver(mitk::SliceNavigationController::GeometryTimeEvent(nullptr, 0), cmdTimeEvent); } if (m_DataNodeSelectionChanged) { if (this->IsCurrentSelectionValid()) { this->SelectionChanged(this->GetCurrentSelection()); } else { this->SelectionChanged(this->GetDataManagerSelection()); } m_DataNodeSelectionChanged = false; } } void QmitkImageStatisticsView::Hidden() { m_Visible = false; // The slice navigation controller observer is removed here instead of in the destructor. // If it was called in the destructor, the application would freeze because the view's // destructor gets called after the render windows have been destructed. - if ( m_TimeObserverTag != 0 ) + if (m_TimeObserverTag != 0) { mitk::IRenderWindowPart* renderWindow = GetRenderWindowPart(); if (renderWindow) { renderWindow->GetQmitkRenderWindow("axial")->GetSliceNavigationController()-> - RemoveObserver( m_TimeObserverTag ); + RemoveObserver(m_TimeObserverTag); } m_TimeObserverTag = 0; } } void QmitkImageStatisticsView::SetFocus() { } std::map QmitkImageStatisticsView::ConvertHistogramToMap(itk::Statistics::Histogram::ConstPointer histogram) const { std::map histogramMap; auto endIt = histogram->End(); auto it = histogram->Begin(); // generating Lists of measurement and frequencies for (; it != endIt; ++it) { double frequency = it.GetFrequency(); double measurement = it.GetMeasurementVector()[0]; histogramMap.emplace(measurement, frequency); } return histogramMap; } std::vector QmitkImageStatisticsView::ConvertIntensityProfileToVector(mitk::IntensityProfile::ConstPointer intensityProfile) const { std::vector intensityProfileList; auto end = intensityProfile->End(); for (auto it = intensityProfile->Begin(); it != end; ++it) { intensityProfileList.push_back(it.GetMeasurementVector()[0]); } return intensityProfileList; } QString QmitkImageStatisticsView::GetFormattedString(double value, unsigned int decimals) const { - typedef mitk::ImageStatisticsCalculator::StatisticsContainer::RealType RealType; + typedef mitk::ImageStatisticsContainer::RealType RealType; RealType maxVal = std::numeric_limits::max(); if (value == maxVal) { return QString("NA"); } else { return QString("%1").arg(value, 0, 'f', decimals); } } QString QmitkImageStatisticsView::GetFormattedIndex(const vnl_vector& vector) const { if (vector.empty()) { return QString(); } QString formattedIndex("("); for (const auto& entry : vector) { formattedIndex += QString::number(entry); formattedIndex += ","; } formattedIndex.chop(1); formattedIndex += ")"; return formattedIndex; } diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h index 8543970725..e49ee842d2 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h @@ -1,191 +1,191 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QmitkImageStatisticsView_H__INCLUDED #define QmitkImageStatisticsView_H__INCLUDED #include "ui_QmitkImageStatisticsViewControls.h" // Qmitk includes #include #include -#include "QmitkImageStatisticsCalculationThread.h" +#include #include // mitk includes #include #include #include #include /*! \brief QmitkImageStatisticsView is a bundle that allows statistics calculation from images. Three modes are supported: 1. Statistics of one image, 2. Statistics of an image and a segmentation, 3. Statistics of an image and a Planar Figure. The statistics calculation is realized in a separate thread to keep the gui accessible during calculation. \ingroup Plugins/org.mitk.gui.qt.measurementtoolbox */ class QmitkImageStatisticsView : public QmitkAbstractView, public mitk::ILifecycleAwarePart, public berry::IPartListener { Q_OBJECT private: /*! \ Convenient typedefs */ typedef QList SelectedDataNodeVectorType; typedef itk::SimpleMemberCommand< QmitkImageStatisticsView > ITKCommandType; std::map ConvertHistogramToMap(itk::Statistics::Histogram::ConstPointer histogram) const; std::vector ConvertIntensityProfileToVector(mitk::IntensityProfile::ConstPointer intensityProfile) const; - std::vector AssembleStatisticsIntoVector(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics, mitk::Image::ConstPointer image, bool noVolumeDefined=false) const; + std::vector AssembleStatisticsIntoVector(mitk::ImageStatisticsContainer::ConstPointer statistics, mitk::Image::ConstPointer image, bool noVolumeDefined=false) const; QString GetFormattedIndex(const vnl_vector& vector) const; QString GetFormattedString(double value, unsigned int decimals) const; public: /*! \brief default constructor */ QmitkImageStatisticsView(QObject *parent = nullptr, const char *name = nullptr); /*! \brief default destructor */ virtual ~QmitkImageStatisticsView(); /*! \brief method for creating the widget containing the application controls, like sliders, buttons etc. */ virtual void CreateQtPartControl(QWidget *parent) override; /*! \brief method for creating the connections of main and control widget */ virtual void CreateConnections(); /*! \brief Is called from the selection mechanism once the data manager selection has changed*/ void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList &selectedNodes) override; static const std::string VIEW_ID; static const int STAT_TABLE_BASE_HEIGHT; public slots: /** \brief Called when the statistics update is finished, sets the results to GUI.*/ void OnThreadedStatisticsCalculationEnds(); /** \brief Update bin size for histogram resolution. */ void OnHistogramNBinsCheckBoxValueChanged(); protected slots: /** \brief Saves the histogram to the clipboard */ void OnClipboardHistogramButtonClicked(); /** \brief Saves the statistics to the clipboard */ void OnClipboardStatisticsButtonClicked(); /** \brief Indicates if zeros should be excluded from statistics calculation */ void OnIgnoreZerosCheckboxClicked(); /** \brief Checks if update is possible and calls StatisticsUpdate() possible */ void RequestStatisticsUpdate(); /** \brief Jump to coordinates stored in the double clicked cell */ void JumpToCoordinates(int row, int col); /** \brief Toogle GUI elements if histogram default bin size checkbox value changed. */ void OnDefaultNBinsSpinBoxChanged(); void OnShowSubchartBoxChanged(); void OnBarRadioButtonSelected(); void OnLineRadioButtonSelected(); void OnPageSuccessfullyLoaded(); signals: /** \brief Method to set the data to the member and start the threaded statistics update */ void StatisticsUpdate(); protected: /** \brief Writes the calculated statistics to the GUI */ - void FillStatisticsTableView(const std::vector &statistics, + void FillStatisticsTableView(mitk::ImageStatisticsContainer::ConstPointer statistics, const mitk::Image *image); - void FillLinearProfileStatisticsTableView(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics, const mitk::Image *image); + void FillLinearProfileStatisticsTableView(mitk::ImageStatisticsContainer::ConstPointer statistics, const mitk::Image *image); /** \brief Removes statistics from the GUI */ void InvalidateStatisticsTableView(); /** \brief Recalculate statistics for currently selected image and mask and * update the GUI. */ void UpdateStatistics(); virtual void Activated() override; virtual void Deactivated() override; virtual void Visible() override; virtual void Hidden() override; virtual void SetFocus() override; /** \brief Method called when itkModifiedEvent is called by selected data. */ void SelectedDataModified(); /** \brief Method called when the data manager selection changes */ void SelectionChanged(const QList &selectedNodes); void DisableHistogramGUIElements(); void ResetHistogramGUIElementsToDefault(); void EnableHistogramGUIElements(); /** \brief Method called to remove old selection when a new selection is present */ void ReinitData(); /** \brief writes the statistics to the gui*/ void WriteStatisticsToGUI(); void NodeRemoved(const mitk::DataNode *node) override; /** \brief Is called right before the view closes (before the destructor) */ virtual void PartClosed(const berry::IWorkbenchPartReference::Pointer&) override; /** \brief Is called from the image navigator once the time step has changed */ void OnTimeChanged(const itk::EventObject&); /** \brief Required for berry::IPartListener */ virtual Events::Types GetPartEventTypes() const override { return Events::CLOSED; } // member variables Ui::QmitkImageStatisticsViewControls *m_Controls; // if you have a planar figure selected, the statistics values will be saved in this one. std::vector m_PlanarFigureStatistics; - QmitkImageStatisticsCalculationThread* m_CalculationThread; + QmitkImageStatisticsCalculationJob* m_CalculationThread; // Image and mask data mitk::Image* m_SelectedImage; mitk::Image* m_SelectedImageMask; mitk::PlanarFigure* m_SelectedPlanarFigure; // observer tags long m_ImageObserverTag; long m_ImageMaskObserverTag; long m_PlanarFigureObserverTag; long m_TimeObserverTag; SelectedDataNodeVectorType m_SelectedDataNodes; bool m_CurrentStatisticsValid; bool m_StatisticsUpdatePending; bool m_DataNodeSelectionChanged; bool m_Visible; unsigned int m_HistogramNBins; std::vector m_WorldMinList; std::vector m_WorldMaxList; std::vector m_IntensityProfileList; berry::IPreferences::Pointer m_StylePref; }; #endif // QmitkImageStatisticsView_H__INCLUDED diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsViewControls.ui b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsViewControls.ui index 7475b0623e..d0171ca775 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsViewControls.ui +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsViewControls.ui @@ -1,649 +1,747 @@ QmitkImageStatisticsViewControls true 0 0 548 812 Form + + + + + + + + + 255 + 0 + 4 + + + + + + + 255 + 0 + 4 + + + + + + + 255 + 0 + 4 + + + + + + + + + 255 + 0 + 4 + + + + + + + 255 + 0 + 4 + + + + + + + 255 + 0 + 4 + + + + + + + + + 120 + 120 + 120 + + + + + + + 120 + 120 + 120 + + + + + + + 120 + 120 + 120 + + + + + + + + This plugin is deprecated. Consider using the new image statistics plugin (icon with star). + + + 0 0 Qt::LeftToRight Feature Image: 0 0 None 0 0 Mask: 0 0 None -1 0 0 color: rgb(255, 0, 0); Error Message Qt::AutoText Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter Ignore zero-valued voxels false Statistics 9 9 9 100 180 16777215 16777215 Qt::ScrollBarAsNeeded Qt::ScrollBarAsNeeded true QAbstractItemView::NoEditTriggers true true Qt::DotLine false 14 1 false false 80 true 80 false true true false 25 25 false false Mean Median StdDev RMS Max Min N V (mm³) Skewness Kurtosis Uniformity Entropy MPP UPP 0 0 0 0 0 0 Copy to Clipboard Qt::Horizontal QSizePolicy::Fixed 20 20 false copy complete table Qt::Horizontal 40 20 false 400 450 Histogram false false 0 0 0 0 16777215 16777215 Plot 0 0 Barchart true 0 0 0 0 Linegraph Qt::Horizontal 40 20 Show Subchart true Use default #bins true QFrame::NoFrame QFrame::Raised 0 0 0 0 0 60 0 100 16777215 # bins: false Press enter to recalculate statistics with new bin size. 1 10000 100 0 0 0 0 0 0 0 0 0 0 0 0 Copy to Clipboard Qt::Horizontal 40 20 Qt::Vertical 20 40 QmitkChartWidget QWidget
QmitkChartWidget.h
 diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkPlanarFiguresTableModel.cpp b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkPlanarFiguresTableModel.cpp deleted file mode 100644 index 26414a03d0..0000000000 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkPlanarFiguresTableModel.cpp +++ /dev/null @@ -1,124 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include "QmitkPlanarFiguresTableModel.h" -#include -#include -#include - -QmitkPlanarFiguresTableModel::QmitkPlanarFiguresTableModel( mitk::DataStorage::Pointer _DataStorage, mitk::NodePredicateBase* _Predicate, QObject* parent ) -: QmitkDataStorageTableModel(_DataStorage, _Predicate, parent) -{ - -} - -QmitkPlanarFiguresTableModel::~QmitkPlanarFiguresTableModel() -{ - -} - -QVariant QmitkPlanarFiguresTableModel::headerData( int section, Qt::Orientation orientation, int role ) const -{ - QVariant headerData; - - // show only horizontal header - if ( role == Qt::DisplayRole ) - { - if( orientation == Qt::Horizontal ) - { - // first column: "Name" - if(section == 0) - headerData = "Name"; - else if(section == 1) - headerData = "Info"; - } - else if( orientation == Qt::Vertical ) - { - // show numbers for rows - headerData = section+1; - } - } - - return headerData; -} - -Qt::ItemFlags QmitkPlanarFiguresTableModel::flags( const QModelIndex &index ) const -{ - // name & visibility is editable - if (index.column() == 0) - return Qt::ItemIsEnabled | Qt::ItemIsSelectable | Qt::ItemIsEditable; - else - return Qt::ItemIsEnabled | Qt::ItemIsSelectable; -} - -int QmitkPlanarFiguresTableModel::columnCount( const QModelIndex & ) const -{ - return 2; -} - -QVariant QmitkPlanarFiguresTableModel::data( const QModelIndex &index, int role ) const -{ - QVariant data; - if(!index.isValid()) - return data; - mitk::DataNode::Pointer node = this->m_NodeSet.at(index.row()); - - if(!node) - return data; - - if(index.column() == 0 && role == Qt::DecorationRole) - { - if(node) - { - QmitkNodeDescriptor* nodeDescriptor - = QmitkNodeDescriptorManager::GetInstance()->GetDescriptor(node); - data = nodeDescriptor->GetIcon(node); - } - } - else if(index.column() == 1) - { - if(role == Qt::DisplayRole || role == Qt::ToolTipRole) - { - QString info; - mitk::PlanarFigure* planarFigure = dynamic_cast(node->GetData()); - if(!planarFigure) - return data; - - mitk::PlanarAngle* planarAngle = dynamic_cast(planarFigure); - double featureQuantity; - for(unsigned int i=0; iGetNumberOfFeatures(); ++i) - { - featureQuantity = planarFigure->GetQuantity(i); - if(planarAngle && i == planarAngle->FEATURE_ID_ANGLE) - featureQuantity = featureQuantity * 180 / vnl_math::pi; - - //std::ostringstream s; s.precision(2); s << featureQuantity; - info.append(QString("%1: %2 %3") - .arg(QString(planarFigure->GetFeatureName(i))) - .arg(featureQuantity, 0, 'f', 2) - .arg(QString(planarFigure->GetFeatureUnit(i)))); - if((i+1) != planarFigure->GetNumberOfFeatures()) - info.append(", "); - - data = info; - } - } - } - else - return QmitkDataStorageTableModel::data(index, role); - - return data; -} diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkPlanarFiguresTableModel.h b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkPlanarFiguresTableModel.h deleted file mode 100644 index 01dfc33d1c..0000000000 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkPlanarFiguresTableModel.h +++ /dev/null @@ -1,75 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#ifndef QmitkPlanarFiguresTableModel_h -#define QmitkPlanarFiguresTableModel_h - -/// Toolkit includes. -#include - -/// Forward declarations. - -/// -/// \class QmitkPlanarFiguresTableModel -/// -/// \brief A table model for a set of DataNodes defined by a predicate. -/// \TODO make columns interchangeable, select which properties to show as columns -/// -class QmitkPlanarFiguresTableModel : public QmitkDataStorageTableModel -{ - Q_OBJECT - - //#Ctors/Dtor -public: - /// - /// Constructs a new QmitkPlanarFiguresTableModel and sets a predicate that defines - /// this list. - /// \see setPredicate() - /// - QmitkPlanarFiguresTableModel(mitk::DataStorage::Pointer _DataStorage, mitk::NodePredicateBase* _Predicate = nullptr - , QObject* parent = nullptr ); - - /// - /// Standard dtor. Delete predicate, disconnect from DataStorage. - /// - virtual ~QmitkPlanarFiguresTableModel(); - - //# Public GETTER -public: - /// - /// Overridden from QAbstractTableModel. Returns the header data at section - /// for given orientation and role. - /// - QVariant headerData(int section, Qt::Orientation orientation, - int role) const override; - /// - /// Overridden from QAbstractTableModel. Returns what can be done - /// with an item. - /// - Qt::ItemFlags flags(const QModelIndex &index) const override; - /// - /// Overridden from QAbstractTableModel. Returns the number of features (columns) to display. - /// - int columnCount(const QModelIndex &parent) const override; - /// - /// Overridden from QAbstractTableModel. Returns the data at index for given role. - /// - QVariant data(const QModelIndex &index, int role) const override; - -}; - -#endif - diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/mitkPluginActivator.cpp b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/mitkPluginActivator.cpp index a48d1c5ae9..259a13aeeb 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/mitkPluginActivator.cpp +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/mitkPluginActivator.cpp @@ -1,39 +1,41 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkPluginActivator.h" #include "QmitkMeasurementView.h" #include "QmitkImageStatisticsView.h" +#include "QmitkImageStatisticsReloadedView.h" ctkPluginContext* mitk::PluginActivator::m_Context = nullptr; ctkPluginContext* mitk::PluginActivator::GetContext() { return m_Context; } void mitk::PluginActivator::start(ctkPluginContext* context) { BERRY_REGISTER_EXTENSION_CLASS(QmitkMeasurementView, context) BERRY_REGISTER_EXTENSION_CLASS(QmitkImageStatisticsView, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkImageStatisticsReloadedView, context) m_Context = context; } void mitk::PluginActivator::stop(ctkPluginContext* context) { Q_UNUSED(context) m_Context = nullptr; } diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/src/internal/QmitkPointSetInteractionView.cpp b/Plugins/org.mitk.gui.qt.pointsetinteraction/src/internal/QmitkPointSetInteractionView.cpp index 83e9bf97a5..85a41651a3 100755 --- a/Plugins/org.mitk.gui.qt.pointsetinteraction/src/internal/QmitkPointSetInteractionView.cpp +++ b/Plugins/org.mitk.gui.qt.pointsetinteraction/src/internal/QmitkPointSetInteractionView.cpp @@ -1,142 +1,148 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Qmitk related includes #include "QmitkPointSetInteractionView.h" #include "ui_QmitkPointSetInteractionViewControls.h" #include #include #include #include #include #include #include #include const std::string QmitkPointSetInteractionView::VIEW_ID = "org.mitk.views.pointsetinteraction"; QmitkPointSetInteractionView::QmitkPointSetInteractionView( QObject* /*parent*/ ) : m_Controls(0) { } QmitkPointSetInteractionView::~QmitkPointSetInteractionView() { } void QmitkPointSetInteractionView::CreateQtPartControl( QWidget *parent ) { m_Controls = new Ui::QmitkPointSetInteractionControls; m_Controls->setupUi(parent); m_Controls->m_PbAddPointSet->connect( m_Controls->m_PbAddPointSet, SIGNAL( clicked() ) , this, SLOT( OnAddPointSetClicked() ) ); + + if (mitk::IRenderWindowPart *renderWindowPart = GetRenderWindowPart()) + { + // let the point set widget know about the render window part (crosshair updates) + RenderWindowPartActivated(renderWindowPart); + } } void QmitkPointSetInteractionView::SetFocus() { m_Controls->m_PbAddPointSet->setFocus(); } void QmitkPointSetInteractionView::OnAddPointSetClicked() { //Ask for the name of the point set bool ok = false; QString name = QInputDialog::getText( QApplication::activeWindow() , tr("Add point set..."), tr("Enter name for the new point set"), QLineEdit::Normal, tr("PointSet"), &ok ); if ( ! ok || name.isEmpty() ) return; // //Create a new empty pointset // mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); // // Create a new data tree node // mitk::DataNode::Pointer pointSetNode = mitk::DataNode::New(); // // fill the data tree node with the appropriate information // pointSetNode->SetData( pointSet ); pointSetNode->SetProperty( "name", mitk::StringProperty::New( name.toStdString() ) ); pointSetNode->SetProperty( "opacity", mitk::FloatProperty::New( 1 ) ); pointSetNode->SetColor( 1.0, 1.0, 0.0 ); // // add the node to the ds // this->GetDataStorage()->Add(pointSetNode); // make new selection and emulate selection for this berry::IWorkbenchPart::Pointer nullPart; QList selection; selection.push_back(pointSetNode); this->OnSelectionChanged(nullPart, selection); } void QmitkPointSetInteractionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList& nodes) { mitk::DataNode::Pointer selectedNode; if(!nodes.empty()) selectedNode = nodes.front(); mitk::PointSet::Pointer pointSet; if(selectedNode.IsNotNull()) pointSet = dynamic_cast(selectedNode->GetData()); if (pointSet.IsNotNull()) { m_SelectedPointSetNode = selectedNode; m_Controls->m_CurrentPointSetLabel->setText(QString::fromStdString(selectedNode->GetName())); m_Controls->m_PointListWidget->SetPointSetNode(selectedNode); } else { m_Controls->m_CurrentPointSetLabel->setText(tr("None")); m_Controls->m_PointListWidget->SetPointSetNode(nullptr); } } void QmitkPointSetInteractionView::NodeChanged( const mitk::DataNode* node ) { if(node == m_SelectedPointSetNode && m_Controls->m_CurrentPointSetLabel->text().toStdString() != node->GetName()) { m_Controls->m_CurrentPointSetLabel->setText(QString::fromStdString(node->GetName())); } } void QmitkPointSetInteractionView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { if(m_Controls) { m_Controls->m_PointListWidget->AddSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); m_Controls->m_PointListWidget->AddSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); m_Controls->m_PointListWidget->AddSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); } } void QmitkPointSetInteractionView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) { if(m_Controls) { m_Controls->m_PointListWidget->RemoveSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); m_Controls->m_PointListWidget->RemoveSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); m_Controls->m_PointListWidget->RemoveSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); } } diff --git a/Plugins/org.mitk.gui.qt.python/CMakeLists.txt b/Plugins/org.mitk.gui.qt.python/CMakeLists.txt index 42115978c2..3a784c3ba4 100644 --- a/Plugins/org.mitk.gui.qt.python/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.python/CMakeLists.txt @@ -1,6 +1,10 @@ +if(MITK_USE_Python) + project(org_mitk_gui_qt_python) mitk_create_plugin( EXPORT_DIRECTIVE org_mitk_gui_qt_python_EXPORT EXPORTED_INCLUDE_SUFFIXES src MODULE_DEPENDS MitkQtWidgetsExt MitkPython MitkQtPython) + +endif() diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp index df5c59d6b8..0a35eace89 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp @@ -1,1128 +1,1128 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include "mitkProperties.h" #include "mitkSegTool2D.h" #include "mitkStatusBar.h" #include "QmitkNewSegmentationDialog.h" #include #include #include #include "QmitkSegmentationView.h" #include #include "mitkVtkResliceInterpolationProperty.h" #include "mitkApplicationCursor.h" #include "mitkSegmentationObjectFactory.h" #include "mitkPluginActivator.h" #include "mitkCameraController.h" #include "mitkLabelSetImage.h" #include #include "usModuleResource.h" #include "usModuleResourceStream.h" //micro service to get the ToolManager instance #include "mitkToolManagerProvider.h" #include const std::string QmitkSegmentationView::VIEW_ID = "org.mitk.views.segmentation"; QmitkSegmentationView::QmitkSegmentationView() : m_Parent(nullptr) , m_Controls(nullptr) , m_RenderWindowPart(nullptr) , m_MouseCursorSet(false) , m_DataSelectionChanged(false) , m_AutoSelectionEnabled(false) { mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage"); auto isSegment = mitk::NodePredicateDataType::New("Segment"); mitk::NodePredicateOr::Pointer validImages = mitk::NodePredicateOr::New(); validImages->AddPredicate(mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isSegment))); validImages->AddPredicate(isDwi); validImages->AddPredicate(isDti); validImages->AddPredicate(isOdf); m_IsNotAHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true))); m_IsOfTypeImagePredicate = mitk::NodePredicateAnd::New(validImages, m_IsNotAHelperObject); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateNot::Pointer isNotBinaryPredicate = mitk::NodePredicateNot::New(isBinaryPredicate); mitk::NodePredicateAnd::Pointer isABinaryImagePredicate = mitk::NodePredicateAnd::New(m_IsOfTypeImagePredicate, isBinaryPredicate); mitk::NodePredicateAnd::Pointer isNotABinaryImagePredicate = mitk::NodePredicateAnd::New(m_IsOfTypeImagePredicate, isNotBinaryPredicate); m_IsASegmentationImagePredicate = mitk::NodePredicateOr::New(isABinaryImagePredicate, mitk::TNodePredicateDataType::New()); m_IsAPatientImagePredicate = mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, mitk::NodePredicateNot::New(mitk::TNodePredicateDataType::New())); } QmitkSegmentationView::~QmitkSegmentationView() { if (m_Controls) { SetToolSelectionBoxesEnabled(false); // deactivate all tools mitk::ToolManagerProvider::GetInstance()->GetToolManager()->ActivateTool(-1); // removing all observers for (NodeTagMapType::iterator dataIter = m_WorkingDataObserverTags.begin(); dataIter != m_WorkingDataObserverTags.end(); ++dataIter) { (*dataIter).first->GetProperty("visible")->RemoveObserver((*dataIter).second); } m_WorkingDataObserverTags.clear(); for (NodeTagMapType::iterator dataIter = m_BinaryPropertyObserverTags.begin(); dataIter != m_BinaryPropertyObserverTags.end(); ++dataIter) { (*dataIter).first->GetProperty("binary")->RemoveObserver((*dataIter).second); } m_BinaryPropertyObserverTags.clear(); mitk::RenderingManager::GetInstance()->RemoveObserver(m_RenderingManagerObserverTag); ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); service->RemoveAllPlanePositions(); context->ungetService(ppmRef); SetToolManagerSelection(0, 0); } delete m_Controls; } void QmitkSegmentationView::NewNodesGenerated() { MITK_WARN << "Use of deprecated function: NewNodesGenerated!! This function is empty and will be removed in the next time!"; } void QmitkSegmentationView::NewNodeObjectsGenerated(mitk::ToolManager::DataVectorType* nodes) { if (!nodes) return; mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->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::Visible() { } void QmitkSegmentationView::Hidden() { } void QmitkSegmentationView::Activated() { } void QmitkSegmentationView::Deactivated() { } void QmitkSegmentationView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { if (m_RenderWindowPart != renderWindowPart) { m_RenderWindowPart = renderWindowPart; } if (m_Parent) { m_Parent->setEnabled(true); } // tell the interpolation about tool manager, data storage and render window part if (m_Controls) { mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); m_Controls->m_SlicesInterpolator->SetDataStorage(this->GetDataStorage()); QList controllers; controllers.push_back(renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); controllers.push_back(renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); controllers.push_back(renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); m_Controls->m_SlicesInterpolator->Initialize(toolManager, controllers); } } void QmitkSegmentationView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* /*renderWindowPart*/) { m_RenderWindowPart = nullptr; if (m_Parent) { m_Parent->setEnabled(false); } } void QmitkSegmentationView::OnPreferencesChanged(const berry::IBerryPreferences* prefs) { if (m_Controls != nullptr) { bool slimView = prefs->GetBool("slim view", false); m_Controls->m_ManualToolSelectionBox2D->SetShowNames(!slimView); m_Controls->m_ManualToolSelectionBox3D->SetShowNames(!slimView); m_Controls->btnNewSegmentation->setToolButtonStyle(slimView ? Qt::ToolButtonIconOnly : Qt::ToolButtonTextOnly); } m_AutoSelectionEnabled = prefs->GetBool("auto selection", false); this->ForceDisplayPreferencesUponAllImages(); } void QmitkSegmentationView::CreateNewSegmentation() { mitk::DataNode::Pointer node = mitk::ToolManagerProvider::GetInstance()->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 QStringList organColors = mitk::OrganNamesHandling::GetDefaultOrganColorString();; dialog->SetSuggestionList(organColors); int dialogReturnValue = dialog->exec(); if (dialogReturnValue == QDialog::Rejected) { // user clicked cancel or pressed Esc or something similar return; } // 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 = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); mitk::Tool* firstTool = toolManager->GetToolById(0); if (firstTool) { try { std::string newNodeName = dialog->GetSegmentationName().toStdString(); if (newNodeName.empty()) { newNodeName = "no_name"; } mitk::DataNode::Pointer emptySegmentation = firstTool->CreateEmptySegmentationNode(image, newNodeName, dialog->GetColor()); // 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 } mitk::OrganNamesHandling::UpdateOrganList(organColors, dialog->GetSegmentationName(), dialog->GetColor()); // escape ';' here (replace by '\;'), see longer comment above QString stringForStorage = organColors.replaceInStrings(";", "\\;").join(";"); MITK_DEBUG << "Will store: " << stringForStorage; this->GetPreferences()->Put("Organ-Color-List", stringForStorage); this->GetPreferences()->Flush(); if (mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0)) { mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0)->SetSelected(false); } emptySegmentation->SetSelected(true); this->GetDataStorage()->Add(emptySegmentation, node); // add as a child, because the segmentation "derives" from the original this->FireNodeSelected(emptySegmentation); this->OnSelectionChanged(emptySegmentation); m_Controls->segImageSelector->SetSelectedNode(emptySegmentation); mitk::RenderingManager::GetInstance()->InitializeViews(emptySegmentation->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); } catch (const std::bad_alloc&) { QMessageBox::warning(nullptr, tr("Create new segmentation"), tr("Could not allocate memory for new segmentation")); } } } else { QMessageBox::information(nullptr, tr("Segmentation"), tr("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::OnVisiblePropertyChanged() { mitk::DataNode* selectedNode = m_Controls->segImageSelector->GetSelectedNode(); if ( !selectedNode ) { this->SetToolSelectionBoxesEnabled(false); return; } mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart(); bool selectedNodeIsVisible = renderWindowPart && selectedNode->IsVisible(renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderer()); if (!selectedNodeIsVisible) { this->SetToolSelectionBoxesEnabled(false); this->UpdateWarningLabel(tr("The selected segmentation is currently not visible!")); } else { this->SetToolSelectionBoxesEnabled(true); this->UpdateWarningLabel(""); } } void QmitkSegmentationView::OnBinaryPropertyChanged() { mitk::DataStorage::SetOfObjects::ConstPointer patImages = m_Controls->patImageSelector->GetNodes(); for (mitk::DataStorage::SetOfObjects::ConstIterator it = patImages->Begin(); it != patImages->End(); ++it) { const mitk::DataNode* node = it->Value(); if(m_IsASegmentationImagePredicate->CheckNode(node)) { m_Controls->patImageSelector->RemoveNode(node); m_Controls->segImageSelector->AddNode(node); this->SetToolManagerSelection(nullptr,nullptr); return; } } mitk::DataStorage::SetOfObjects::ConstPointer segImages = m_Controls->segImageSelector->GetNodes(); for (mitk::DataStorage::SetOfObjects::ConstIterator it = segImages->Begin(); it != segImages->End(); ++it) { const mitk::DataNode* node = it->Value(); if(!m_IsASegmentationImagePredicate->CheckNode(node)) { m_Controls->segImageSelector->RemoveNode(node); m_Controls->patImageSelector->AddNode(node); if (mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0) == node) { mitk::ToolManagerProvider::GetInstance()->GetToolManager()->SetWorkingData(nullptr); } return; } } } void QmitkSegmentationView::NodeAdded(const mitk::DataNode *node) { if (!m_IsOfTypeImagePredicate->CheckNode(node)) { return; } itk::SimpleMemberCommand::Pointer command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::OnVisiblePropertyChanged); m_WorkingDataObserverTags.insert(std::pair(const_cast(node), node->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command))); itk::SimpleMemberCommand::Pointer command2 = itk::SimpleMemberCommand::New(); command2->SetCallbackFunction(this, &QmitkSegmentationView::OnBinaryPropertyChanged); m_BinaryPropertyObserverTags.insert(std::pair(const_cast(node), node->GetProperty("binary")->AddObserver(itk::ModifiedEvent(), command2))); ApplyDisplayOptions(const_cast(node)); } void QmitkSegmentationView::NodeRemoved(const mitk::DataNode* node) { if (m_IsASegmentationImagePredicate->CheckNode(node)) { //First of all remove all possible contour markers of the segmentation mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = this->GetDataStorage()->GetDerivations(node, mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true))); ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); for (mitk::DataStorage::SetOfObjects::ConstIterator it = allContourMarkers->Begin(); it != allContourMarkers->End(); ++it) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1; service->RemovePlanePosition(id); this->GetDataStorage()->Remove(it->Value()); } context->ungetService(ppmRef); service = nullptr; if ((mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0) == node) && m_Controls->patImageSelector->GetSelectedNode().IsNotNull()) { this->SetToolManagerSelection(mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetReferenceData(0), nullptr); this->UpdateWarningLabel(tr("Select or create a segmentation")); } mitk::Image* image = dynamic_cast(node->GetData()); mitk::SurfaceInterpolationController::GetInstance()->RemoveInterpolationSession(image); } mitk::DataNode* tempNode = const_cast(node); //Since the binary property could be changed during runtime by the user if (m_IsOfTypeImagePredicate->CheckNode(node)) { node->GetProperty("visible")->RemoveObserver(m_WorkingDataObserverTags[tempNode]); m_WorkingDataObserverTags.erase(tempNode); node->GetProperty("binary")->RemoveObserver(m_BinaryPropertyObserverTags[tempNode]); m_BinaryPropertyObserverTags.erase(tempNode); } if (mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetReferenceData(0) == node) { //as we don't know which node was actually removed e.g. our reference node, disable 'New Segmentation' button. //consider the case that there is no more image in the datastorage this->SetToolManagerSelection(nullptr, nullptr); this->SetToolSelectionBoxesEnabled(false); } } void QmitkSegmentationView::OnPatientComboBoxSelectionChanged( const mitk::DataNode* node ) { //mitk::DataNode* selectedNode = const_cast(node); if( node != nullptr ) { this->UpdateWarningLabel(""); mitk::DataNode* segNode = m_Controls->segImageSelector->GetSelectedNode(); if (segNode) { mitk::DataStorage::SetOfObjects::ConstPointer possibleParents = this->GetDataStorage()->GetSources(segNode, m_IsAPatientImagePredicate); bool isSourceNode(false); for (mitk::DataStorage::SetOfObjects::ConstIterator it = possibleParents->Begin(); it != possibleParents->End(); it++) { if (it.Value() == node) isSourceNode = true; } if ( !isSourceNode && (!this->CheckForSameGeometry(segNode, node) || possibleParents->Size() > 0 )) { this->SetToolManagerSelection(node, nullptr); this->SetToolSelectionBoxesEnabled( false ); this->UpdateWarningLabel(tr("The selected patient image does not match with the selected segmentation!")); } else if ((!isSourceNode && this->CheckForSameGeometry(segNode, node)) || isSourceNode ) { this->SetToolManagerSelection(node, segNode); //Doing this we can assure that the segmenation is always visible if the segmentation and the patient image are //loaded separately int layer(10); node->GetIntProperty("layer", layer); layer++; segNode->SetProperty("layer", mitk::IntProperty::New(layer)); //this->UpdateWarningLabel(""); RenderingManagerReinitialized(); } } else { this->SetToolManagerSelection(node, nullptr); this->SetToolSelectionBoxesEnabled( false ); this->UpdateWarningLabel(tr("Select or create a segmentation")); } } else { - this->UpdateWarningLabel(tr("Please load an image!")); + this->UpdateWarningLabel(tr("Please select an image!")); this->SetToolSelectionBoxesEnabled( false ); } } void QmitkSegmentationView::OnSegmentationComboBoxSelectionChanged(const mitk::DataNode *node) { if (node == nullptr) { this->UpdateWarningLabel(tr("Select or create a segmentation")); this->SetToolSelectionBoxesEnabled( false ); return; } mitk::DataNode* refNode = m_Controls->patImageSelector->GetSelectedNode(); RenderingManagerReinitialized(); if ( m_Controls->lblSegmentationWarnings->isVisible()) // "RenderingManagerReinitialized()" caused a warning. we do not need to go any further return; if (m_AutoSelectionEnabled) { this->OnSelectionChanged(const_cast(node)); } else { mitk::DataStorage::SetOfObjects::ConstPointer possibleParents = this->GetDataStorage()->GetSources(node, m_IsAPatientImagePredicate); if ( possibleParents->Size() == 1 ) { mitk::DataNode* parentNode = possibleParents->ElementAt(0); if (parentNode != refNode) { this->UpdateWarningLabel(tr("The selected segmentation does not match with the selected patient image!")); this->SetToolSelectionBoxesEnabled( false ); this->SetToolManagerSelection(nullptr, node); } else { this->UpdateWarningLabel(""); this->SetToolManagerSelection(refNode, node); } } else if (refNode && this->CheckForSameGeometry(node, refNode)) { this->UpdateWarningLabel(""); this->SetToolManagerSelection(refNode, node); } else if (!refNode || !this->CheckForSameGeometry(node, refNode)) { - this->UpdateWarningLabel(tr("Please select or load the according patient image!")); + this->UpdateWarningLabel(tr("Please select the matching patient image!")); } } mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart(); if (!renderWindowPart || !node->IsVisible(renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderer())) { this->UpdateWarningLabel(tr("The selected segmentation is currently not visible!")); this->SetToolSelectionBoxesEnabled( false ); } } void QmitkSegmentationView::OnShowMarkerNodes (bool state) { mitk::SegTool2D::Pointer manualSegmentationTool; unsigned int numberOfExistingTools = mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetTools().size(); for(unsigned int i = 0; i < numberOfExistingTools; i++) { manualSegmentationTool = dynamic_cast(mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetToolById(i)); if (manualSegmentationTool) { if(state == true) { manualSegmentationTool->SetShowMarkerNodes( true ); } else { manualSegmentationTool->SetShowMarkerNodes( false ); } } } } void QmitkSegmentationView::OnSelectionChanged(mitk::DataNode* node) { berry::IWorkbenchPart::Pointer nullPart; QList nodes; nodes.push_back(node); this->OnSelectionChanged(nullPart, nodes); } void QmitkSegmentationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& nodes) { if (nodes.size() != 0) { std::string markerName = "Position"; unsigned int numberOfNodes = nodes.size(); std::string nodeName = nodes.at(0)->GetName(); if ((numberOfNodes == 1) && (nodeName.find(markerName) == 0)) { OnContourMarkerSelected(nodes.at(0)); return; } } if (m_AutoSelectionEnabled) { if (nodes.size() == 0 && m_Controls->patImageSelector->GetSelectedNode().IsNull()) { SetToolManagerSelection(nullptr, nullptr); } else if (nodes.size() == 1) { mitk::DataNode::Pointer selectedNode = nodes.at(0); if (selectedNode.IsNull()) { return; } mitk::Image::Pointer selectedImage = dynamic_cast(selectedNode->GetData()); if (selectedImage.IsNull()) { SetToolManagerSelection(nullptr, nullptr); return; } if (m_IsASegmentationImagePredicate->CheckNode(selectedNode)) { // set all nodes to invisible mitk::DataStorage::SetOfObjects::ConstPointer allImages = GetDataStorage()->GetSubset(m_IsNotAHelperObject); for (mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter) { (*iter)->SetVisibility(false); } // if a segmentation is selected find a possible patient image (a parent node) mitk::DataStorage::SetOfObjects::ConstPointer sources = GetDataStorage()->GetSources(selectedNode, m_IsAPatientImagePredicate); mitk::DataNode::Pointer sourceNode; if (sources->Size() != 0) { // found one or more sources - use the first one sourceNode = sources->ElementAt(0); sourceNode->SetVisibility(true); selectedNode->SetVisibility(true); SetToolManagerSelection(sourceNode, selectedNode); // set all child nodes of the segmentation to visible mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(selectedNode, m_IsNotAHelperObject, false); for (mitk::DataStorage::SetOfObjects::const_iterator iter = derivations->begin(); iter != derivations->end(); ++iter) { (*iter)->SetVisibility(true); } } else { // did not find a source / patient image, check all images and compare geometry mitk::DataStorage::SetOfObjects::ConstPointer possiblePatientImages = GetDataStorage()->GetSubset(m_IsAPatientImagePredicate); for (mitk::DataStorage::SetOfObjects::ConstIterator iter = possiblePatientImages->Begin(); iter != possiblePatientImages->End(); ++iter) { sourceNode = iter->Value(); if (CheckForSameGeometry(selectedNode, iter->Value())) { sourceNode->SetVisibility(true); selectedNode->SetVisibility(true); SetToolManagerSelection(sourceNode, selectedNode); // set all child nodes of the segmentation to visible mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(selectedNode, m_IsNotAHelperObject, false); for (mitk::DataStorage::SetOfObjects::const_iterator iter = derivations->begin(); iter != derivations->end(); ++iter) { (*iter)->SetVisibility(true); } // doing this we can assure that the segmentation is always visible if the segmentation and the patient image are at the // same level in the data manager int layer(10); sourceNode->GetIntProperty("layer", layer); layer++; selectedNode->SetProperty("layer", mitk::IntProperty::New(layer)); return; } } // did not find a source / patient image with the same geometry SetToolManagerSelection(nullptr, selectedNode); } mitk::RenderingManager::GetInstance()->InitializeViews(selectedNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); } else { if (mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetReferenceData(0) != selectedNode) { SetToolManagerSelection(selectedNode, nullptr); // may be a bug in the selection services. A node which is deselected will be passed as selected node to the OnSelectionChanged function mitk::IRenderWindowPart* renderWindowPart = GetRenderWindowPart(); if (renderWindowPart && !selectedNode->IsVisible(renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderer())) { selectedNode->SetVisibility(true); } UpdateWarningLabel(tr("The selected patient image does not match with the selected segmentation!")); SetToolSelectionBoxesEnabled(false); } } } if (m_Controls->lblSegmentationWarnings->isVisible()) // "RenderingManagerReinitialized()" caused a warning. we do not need to go any further { return; } RenderingManagerReinitialized(); } } void QmitkSegmentationView::OnContourMarkerSelected(const mitk::DataNode *node) { QmitkRenderWindow* selectedRenderWindow = 0; QmitkRenderWindow* axialRenderWindow = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("axial"); QmitkRenderWindow* sagittalRenderWindow = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("sagittal"); QmitkRenderWindow* coronalRenderWindow = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("coronal"); QmitkRenderWindow* _3DRenderWindow = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("3d"); bool PlanarFigureInitializedWindow = false; // find initialized renderwindow if (node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, axialRenderWindow->GetRenderer())) { selectedRenderWindow = axialRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, sagittalRenderWindow->GetRenderer())) { selectedRenderWindow = sagittalRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, coronalRenderWindow->GetRenderer())) { selectedRenderWindow = coronalRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, _3DRenderWindow->GetRenderer())) { selectedRenderWindow = _3DRenderWindow; } // 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; { ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); selectedRenderWindow->GetSliceNavigationController()->ExecuteOperation(service->GetPlanePosition(id)); context->ungetService(ppmRef); } selectedRenderWindow->GetRenderer()->GetCameraController()->Fit(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkSegmentationView::OnTabWidgetChanged(int id) { //always disable tools on tab changed mitk::ToolManagerProvider::GetInstance()->GetToolManager()->ActivateTool(-1); //2D Tab ID = 0 //3D Tab ID = 1 if (id == 0) { //Hide 3D selection box, show 2D selection box m_Controls->m_ManualToolSelectionBox3D->hide(); m_Controls->m_ManualToolSelectionBox2D->show(); //Deactivate possible active tool //TODO Remove possible visible interpolations -> Maybe changes in SlicesInterpolator } else { //Hide 3D selection box, show 2D selection box m_Controls->m_ManualToolSelectionBox2D->hide(); m_Controls->m_ManualToolSelectionBox3D->show(); //Deactivate possible active tool } } void QmitkSegmentationView::InitToolManagerSelection(const mitk::DataNode* referenceData, const mitk::DataNode* workingData) { // initial tool manager selection, called from 'CreateQtPartControl' mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); toolManager->SetReferenceData(const_cast(referenceData)); toolManager->SetWorkingData(const_cast(workingData)); // check original image m_Controls->btnNewSegmentation->setEnabled(referenceData != nullptr); if (referenceData) { UpdateWarningLabel(""); } } 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 = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); toolManager->SetReferenceData(const_cast(referenceData)); toolManager->SetWorkingData(const_cast(workingData)); // check original image m_Controls->btnNewSegmentation->setEnabled(referenceData != nullptr); if (referenceData) { UpdateWarningLabel(""); disconnect(m_Controls->patImageSelector, SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnPatientComboBoxSelectionChanged(const mitk::DataNode*))); m_Controls->patImageSelector->setCurrentIndex(m_Controls->patImageSelector->Find(referenceData)); connect(m_Controls->patImageSelector, SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnPatientComboBoxSelectionChanged(const mitk::DataNode*))); // check segmentation if (workingData) { //FireNodeSelected(const_cast(workingData)); disconnect(m_Controls->segImageSelector, SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnSegmentationComboBoxSelectionChanged(const mitk::DataNode*))); m_Controls->segImageSelector->setCurrentIndex(m_Controls->segImageSelector->Find(workingData)); connect(m_Controls->segImageSelector, SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnSegmentationComboBoxSelectionChanged(const mitk::DataNode*))); } } } void QmitkSegmentationView::ForceDisplayPreferencesUponAllImages() { if (!m_Parent) { 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, nullptr parent)) // if no segmentation is selected, do nothing if (!m_Controls) { return; // might happen on initialization (preferences loaded) } mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); mitk::DataNode::Pointer referenceData = toolManager->GetReferenceData(0); mitk::DataNode::Pointer workingData = toolManager->GetWorkingData(0); // 1. if (referenceData.IsNotNull()) { // iterate all images mitk::DataStorage::SetOfObjects::ConstPointer allImages = this->GetDataStorage()->GetSubset(m_IsASegmentationImagePredicate); for ( mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter) { mitk::DataNode* node = *iter; // apply display preferences ApplyDisplayOptions(node); // set visibility node->SetVisibility(node == referenceData); } } // 2. if (workingData.IsNotNull()) workingData->SetVisibility(true); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::ApplyDisplayOptions(mitk::DataNode* node) { if (!node) { return; } mitk::BoolProperty::Pointer drawOutline = mitk::BoolProperty::New(GetPreferences()->GetBool("draw outline", true)); mitk::BoolProperty::Pointer volumeRendering = mitk::BoolProperty::New(GetPreferences()->GetBool("volume rendering", false)); mitk::LabelSetImage* labelSetImage = dynamic_cast(node->GetData()); if (nullptr != labelSetImage) { // node is actually a multi label segmentation, // but its outline property can be set in the 'single label' segmentation preference page as well node->SetProperty("labelset.contour.active", drawOutline); node->SetProperty("opacity", mitk::FloatProperty::New(drawOutline->GetValue() ? 1.0f : 0.3f)); node->SetProperty("volumerendering", volumeRendering); // force render window update to show outline node->GetData()->Modified(); } else { // node is a 'single label' segmentation bool isBinary = false; node->GetBoolProperty("binary", isBinary); if (isBinary) { node->SetProperty("outline binary", drawOutline); node->SetProperty("outline width", mitk::FloatProperty::New(2.0)); node->SetProperty("opacity", mitk::FloatProperty::New(drawOutline->GetValue() ? 1.0f : 0.3f)); node->SetProperty("volumerendering", volumeRendering); // force render window update to show outline node->GetData()->Modified(); } } } void QmitkSegmentationView::RenderingManagerReinitialized() { if (!this->GetRenderWindowPart()) { return; } /* * Here we check whether the geometry of the selected segmentation image if aligned with the worldgeometry * At the moment it is not supported to use a geometry different from the selected image for reslicing. * For further information see Bug 16063 */ mitk::DataNode* workingNode = m_Controls->segImageSelector->GetSelectedNode(); const mitk::BaseGeometry* worldGeo = this->GetRenderWindowPart()->GetQmitkRenderWindow("3d")->GetSliceNavigationController()->GetCurrentGeometry3D(); if (workingNode && worldGeo) { const mitk::BaseGeometry* workingNodeGeo = workingNode->GetData()->GetGeometry(); const mitk::BaseGeometry* worldGeo = this->GetRenderWindowPart()->GetQmitkRenderWindow("3d")->GetSliceNavigationController()->GetCurrentGeometry3D(); if (mitk::Equal(*workingNodeGeo->GetBoundingBox(), *worldGeo->GetBoundingBox(), mitk::eps, true)) { this->SetToolManagerSelection(m_Controls->patImageSelector->GetSelectedNode(), workingNode); this->SetToolSelectionBoxesEnabled(true); this->UpdateWarningLabel(""); } else { this->SetToolManagerSelection(m_Controls->patImageSelector->GetSelectedNode(), nullptr); this->SetToolSelectionBoxesEnabled(false); this->UpdateWarningLabel(tr("Please perform a reinit on the segmentation image!")); } } } bool QmitkSegmentationView::CheckForSameGeometry(const mitk::DataNode *node1, const mitk::DataNode *node2) const { bool isSameGeometry(true); mitk::Image* image1 = dynamic_cast(node1->GetData()); mitk::Image* image2 = dynamic_cast(node2->GetData()); if (image1 && image2) { mitk::BaseGeometry* geo1 = image1->GetGeometry(); mitk::BaseGeometry* geo2 = image2->GetGeometry(); isSameGeometry = isSameGeometry && mitk::Equal(geo1->GetOrigin(), geo2->GetOrigin()); isSameGeometry = isSameGeometry && mitk::Equal(geo1->GetExtent(0), geo2->GetExtent(0)); isSameGeometry = isSameGeometry && mitk::Equal(geo1->GetExtent(1), geo2->GetExtent(1)); isSameGeometry = isSameGeometry && mitk::Equal(geo1->GetExtent(2), geo2->GetExtent(2)); isSameGeometry = isSameGeometry && mitk::Equal(geo1->GetSpacing(), geo2->GetSpacing()); isSameGeometry = isSameGeometry && mitk::MatrixEqualElementWise(geo1->GetIndexToWorldTransform()->GetMatrix(), geo2->GetIndexToWorldTransform()->GetMatrix()); return isSameGeometry; } else { return false; } } void QmitkSegmentationView::UpdateWarningLabel(QString text) { if (text.size() == 0) m_Controls->lblSegmentationWarnings->hide(); else m_Controls->lblSegmentationWarnings->show(); - m_Controls->lblSegmentationWarnings->setText(text); + m_Controls->lblSegmentationWarnings->setText("" + text + ""); } 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->patImageSelector->SetDataStorage(GetDataStorage()); m_Controls->patImageSelector->SetPredicate(m_IsAPatientImagePredicate); - UpdateWarningLabel(tr("Please load an image")); + UpdateWarningLabel(tr("Please select an image")); if (m_Controls->patImageSelector->GetSelectedNode().IsNotNull()) { UpdateWarningLabel(tr("Select or create a new segmentation")); } m_Controls->segImageSelector->SetDataStorage(GetDataStorage()); m_Controls->segImageSelector->SetPredicate(m_IsASegmentationImagePredicate); if (m_Controls->segImageSelector->GetSelectedNode().IsNotNull()) { UpdateWarningLabel(""); } mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); assert(toolManager); toolManager->SetDataStorage(*(GetDataStorage())); toolManager->InitializeTools(); // all part of open source MITK m_Controls->m_ManualToolSelectionBox2D->setEnabled(true); m_Controls->m_ManualToolSelectionBox2D->SetGenerateAccelerators(true); m_Controls->m_ManualToolSelectionBox2D->SetToolGUIArea( m_Controls->m_ManualToolGUIContainer2D ); m_Controls->m_ManualToolSelectionBox2D->SetDisplayedToolGroups(tr("Add Subtract Correction Paint Wipe 'Region Growing' Fill Erase 'Live Wire' '2D Fast Marching'").toStdString()); m_Controls->m_ManualToolSelectionBox2D->SetLayoutColumns(3); m_Controls->m_ManualToolSelectionBox2D->SetEnabledMode( QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible ); connect( m_Controls->m_ManualToolSelectionBox2D, SIGNAL(ToolSelected(int)), this, SLOT(OnManualTool2DSelected(int)) ); //setup 3D Tools m_Controls->m_ManualToolSelectionBox3D->setEnabled(true); m_Controls->m_ManualToolSelectionBox3D->SetGenerateAccelerators(true); m_Controls->m_ManualToolSelectionBox3D->SetToolGUIArea( m_Controls->m_ManualToolGUIContainer3D ); //specify tools to be added to 3D Tool area m_Controls->m_ManualToolSelectionBox3D->SetDisplayedToolGroups(tr("Threshold 'UL Threshold' Otsu 'Fast Marching 3D' 'Region Growing 3D' Watershed Picking").toStdString()); m_Controls->m_ManualToolSelectionBox3D->SetLayoutColumns(3); m_Controls->m_ManualToolSelectionBox3D->SetEnabledMode( QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible ); //Hide 3D selection box, show 2D selection box m_Controls->m_ManualToolSelectionBox3D->hide(); m_Controls->m_ManualToolSelectionBox2D->show(); // update the list of segmentations toolManager->NewNodesGenerated += mitk::MessageDelegate(this, &QmitkSegmentationView::NewNodesGenerated); // update the list of segmentations toolManager->NewNodeObjectsGenerated += mitk::MessageDelegate1(this, &QmitkSegmentationView::NewNodeObjectsGenerated); // create signal/slot connections connect(m_Controls->patImageSelector, SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnPatientComboBoxSelectionChanged(const mitk::DataNode*))); connect(m_Controls->segImageSelector, SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnSegmentationComboBoxSelectionChanged(const mitk::DataNode*))); connect(m_Controls->btnNewSegmentation, SIGNAL(clicked()), this, SLOT(CreateNewSegmentation())); connect(m_Controls->tabWidgetSegmentationTools, SIGNAL(currentChanged(int)), this, SLOT(OnTabWidgetChanged(int))); connect(m_Controls->m_SlicesInterpolator, SIGNAL(SignalShowMarkerNodes(bool)), this, SLOT(OnShowMarkerNodes(bool))); mitk::DataStorage::SetOfObjects::ConstPointer patientImages = GetDataStorage()->GetSubset(m_IsAPatientImagePredicate); if (!patientImages->empty()) { OnSelectionChanged(*patientImages->begin()); } // set callback function for already existing nodes (images & segmentations) mitk::DataStorage::SetOfObjects::ConstPointer allImages = GetDataStorage()->GetSubset(m_IsOfTypeImagePredicate); for (mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter) { mitk::DataNode* node = *iter; itk::SimpleMemberCommand::Pointer command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::OnVisiblePropertyChanged); m_WorkingDataObserverTags.insert(std::pair(node, node->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command))); itk::SimpleMemberCommand::Pointer command2 = itk::SimpleMemberCommand::New(); command2->SetCallbackFunction(this, &QmitkSegmentationView::OnBinaryPropertyChanged); m_BinaryPropertyObserverTags.insert(std::pair(node, node->GetProperty("binary")->AddObserver(itk::ModifiedEvent(), command2))); } itk::SimpleMemberCommand::Pointer command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::RenderingManagerReinitialized); m_RenderingManagerObserverTag = mitk::RenderingManager::GetInstance()->AddObserver(mitk::RenderingManagerViewsInitializedEvent(), command); InitToolManagerSelection(m_Controls->patImageSelector->GetSelectedNode(), m_Controls->segImageSelector->GetSelectedNode()); m_RenderWindowPart = GetRenderWindowPart(); if (m_RenderWindowPart) { RenderWindowPartActivated(m_RenderWindowPart); } } void QmitkSegmentationView::SetFocus() { m_Controls->btnNewSegmentation->setFocus(); } void QmitkSegmentationView::OnManualTool2DSelected(int id) { if (id >= 0) { std::string text = "Active Tool: \""; mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); text += toolManager->GetToolById(id)->GetName(); text += "\""; mitk::StatusBar::GetInstance()->DisplayText(text.c_str()); us::ModuleResource resource = toolManager->GetToolById(id)->GetCursorIconResource(); this->SetMouseCursor(resource, 0, 0); } else { this->ResetMouseCursor(); mitk::StatusBar::GetInstance()->DisplayText(""); } } void QmitkSegmentationView::ResetMouseCursor() { if ( m_MouseCursorSet ) { mitk::ApplicationCursor::GetInstance()->PopCursor(); m_MouseCursorSet = false; } } void QmitkSegmentationView::SetMouseCursor( const us::ModuleResource& resource, int hotspotX, int hotspotY ) { if (!resource) return; // Remove previously set mouse cursor if ( m_MouseCursorSet ) { mitk::ApplicationCursor::GetInstance()->PopCursor(); } us::ModuleResourceStream cursor(resource, std::ios::binary); mitk::ApplicationCursor::GetInstance()->PushCursor( cursor, hotspotX, hotspotY ); m_MouseCursorSet = true; } void QmitkSegmentationView::SetToolSelectionBoxesEnabled(bool status) { if (status) { m_Controls->m_ManualToolSelectionBox2D->RecreateButtons(); m_Controls->m_ManualToolSelectionBox3D->RecreateButtons(); } m_Controls->m_ManualToolSelectionBox2D->setEnabled(status); m_Controls->m_ManualToolSelectionBox3D->setEnabled(status); m_Controls->m_SlicesInterpolator->setEnabled(status); }