diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/MFI_DataExport.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/MFI_DataExport.png deleted file mode 100644 index 6caf5dafe0..0000000000 Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/MFI_DataExport.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox index 4abb6951fd..561288c80a 100644 --- a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/Manual.dox @@ -1,78 +1,72 @@ /** -\page org_mitk_gui_qt_fit_inspector The Model Fit Inspector View +\page org_mitk_views_fit_inspector The Model Fit Inspector View \imageMacro{fit_inspector_doc.svg,"Icon of the Model Fit Inspector View",3.0} \tableofcontents \section FIT_INSPECTOR_Introduction Introduction -This view (Model Fit Inspector; MFI) offers the possibility to display the time course of the signal within an individual +The Model Fit Inspector (MFI) View offers the possibility to display the time course of the signal within an individual voxel (with or without fit). -\section FIT_INSPECTOR_Contact Contact information -This plug-in is being developed by the SIDT group (Software development for Integrated Diagnostics -and Therapy) at the German Cancer Research Center (DKFZ). If you have any questions, need support, -find a bug or have a feature request, feel free to contact us at www.mitk.org. - \section FIT_INSPECTOR_Raw Viewing without a model fit \imageMacro{fit_inspect_raw.png, "Example screen shot showing the inspection of raw dynamic data without a fit.", 10} -Open the view and select the dynamic image in the data manager. +Open the view and choose the dynamic image via the Input selection widget from the available data selection in the data manager. The graph plot will show the time course of image intensities (signal) in the selected voxel (cross hair) as red data points. -The blue point indicates the frame currently displayed in the 4-window view. -\section FIT_INSPECTOR_Fit Viewing without a model fit +\section FIT_INSPECTOR_Fit Viewing with a model fit \imageMacro{fit_inspect_fit.png, "Example screen shot showing the inspection of dynamic data and an associated fit.", 10} -Selecting a parameter map of the fit of interest in the Data Manager will display the raw data curve in red dots with -corresponding fit as black line in the selected cross-hair position. If an AIF-based model was used, -the utilized AIF (averaged over AIF mask) is also displayed (default in green). The color of the AIF display can be adjusted. +Selecting a parameter map of interest using the Input selection widget from the data selection available in the data manager will display the raw data curve as red data points along with +the corresponding fit as black line in the selected cross-hair position. If an AIF-based model was used, +the utilized AIF (averaged over AIF mask) is also displayed (default in green). The color of the AIF display can be adjusted (\ref FIT_INSPECTOR_Fit_Settings). For ROI based fits, the MFI will display both the current data curve in the selected voxel (in red) -and the ROI-averaged fitted curve (in dark green, can be adjusted). Scrolling through the individual voxels will change -the current data curve, but the ROI-based curve remains the same. If voxels outside the fitted area defined by the mask +and the ROI-averaged fitted curve (in dark green, color can be adjusted). Scrolling through the individual voxels will change +the current data curve, but the ROI-based curve and the fit remain the same. If voxels outside the fitting mask are selected, the raw data voxel values will be displayed, however no black fit line is visualized. Below the data plot, several options for data visualization can be selected: \subsection FIT_INSPECTOR_Fit_info Fit info tab \imageMacro{fit_inspect_info.png, "Details of the fit info tab.", 5} -The Fit info tab displays meta-data for selected fits performed on the displayed data set. If no fit was performed and only raw data is visualized, the fields are empty. +The Fit info tab displays meta-data for selected fits performed on the displayed data set. If no fit was performed and only raw data is visualized, these fields are empty. \subsection FIT_INSPECTOR_Fit_Parameter Fit parameter tab \imageMacro{fit_inspect_results.png, "Details of the fit parameter tab.", 5} -The "fit parameter" tab shows fit related parameter estimate values, derived parameters, fit criterion values and (optional) debug parameter maps +The Fit parameter tab shows fit related parameter estimates, derived parameters, fit criterion values and (optional) debug parameter maps in the selected voxel (and all inspection positions; see also \ref FIT_INSPECTOR_Inspect "inspection positions") listed as a table. If no fit was performed and only raw data is visualized, the table is empty. -The content of the table may by copied to clipboard or exported as csv file, by clicking the respective button below the table. +The content of the table may be copied to the clipboard or exported as csv file, by clicking the respective button below the table. \subsection FIT_INSPECTOR_Fit_Inspection Inspection positions tab \imageMacro{fit_inspect_positions.png, "Details of the inspection position tab.", 5} -The tab allows to manage inspection positions (see here for more about \ref FIT_INSPECTOR_Inspect "inspection positions"). +The Inspection position tab allows to manage inspection positions (see here for more about \ref FIT_INSPECTOR_Inspect "inspection positions"). - (1) Shows the coordinates of the current selected position in the workbench. -- (2) Press to make the current position a inspected position. It will be added at the bottom of the list (3). +- (2) Click the Add as bookmark button to make the current position an inspected position. It will be added to the bottom of the list (3). - (3) List of all inspection positions - (4) Toggle adding mode on/off. If on, you can add new positions by clicking into render windows with "SHIFT + left mouse button". - (5) Manually adding inspection positions by entering the coordinates. - (6) Remove the selected inspection positions. (Hot key: Del) - (7) Move the selected inspection position up in the list (3). - (8) Move the selected inspection position down in the list (3). - (9) Save inspection points to a file. - (10) Load inspection points from a file. \subsection FIT_INSPECTOR_Fit_Settings Settings tab \imageMacro{fit_inspect_settings.png, "Details of the settings tab.", 5} -The View settings tab is used to adjust the plot display, namely, x and y axis scales and colors of displayed data plots (i.e. AIF). +The View settings tab is used to adjust the plot display, namely, x and y axis scaling and colors of displayed data plots (i.e. AIF). \subsection FIT_INSPECTOR_Fit_Export Plot data export tab -\imageMacro{fit_inspect_export.png, "Details of the plot data export tab.", 5} -Displays voxel data (input image) and corresponding time grid together with model fit values and additional curves (like AIF values) for each time point. -The table will contain the position depended values of the current selected position as well as of all inspection positions (see also \ref FIT_INSPECTOR_Inspect "inspection positions"). +\imageMacro{fit_inspect_plotDataExport.png, "Details of the plot data export tab.", 5} +The Plot data export displays voxel data (Sample) and corresponding time grid (Time [s]) together with model fit values (Signal) and additional curves (like AIF values) for each time point. +The table will contain the values of the current selected position as well as of all inspection positions (see also \ref FIT_INSPECTOR_Inspect "inspection positions"). The data in the table can also be copied to clipboard or exported to csv files, by clicking the respective button below the table. \section FIT_INSPECTOR_Inspect Inspection positions -\imageMacro{fit_inspect_positions_example.png, "Example of the usage of inspection positions.", 5} +\imageMacro{fit_inspect_positions_example.png, "Example usage of inspection positions.", 5} The fit inspector allows to define positions in the world coordinate system that will be constantly displayed in addition to the current selected position. These inspected position will be shown in the following parts of the view: -- The plot windows. See example image above; the plot shows the current position (raw data: red dots, fit: black line) and an additional inspection position (green). -- The fit parameter tab (see example image above) -- The plot data export tab. +- The plot window. See example image above; the plot shows the current position (raw data: red dots, fit: black line) and an additional inspection position (turquoise). +- The Fit parameter tab (see example image above). +- The plot data export tab. It will work with dynamic data with and without an model fit. See the \ref FIT_INSPECTOR_Fit_Inspection "inspection positions tab section" for more details on how to manage inspection positions. */ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_export.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_export.png deleted file mode 100644 index c6e28b8504..0000000000 Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_export.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_fit.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_fit.png index 39135d7a61..904edd93fe 100644 Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_fit.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_fit.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_info.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_info.png index db85415509..dd80bd85f8 100644 Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_info.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_info.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_plotDataExport.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_plotDataExport.png new file mode 100644 index 0000000000..77eddfcc4b Binary files /dev/null and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_plotDataExport.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.png index 6d5c46c456..630665a304 100644 Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions_example.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions_example.png index ddfef4b2c1..c851ab7cfe 100644 Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions_example.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_positions_example.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_raw.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_raw.png index c333213f75..cf3213c9a3 100644 Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_raw.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_raw.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_results.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_results.png index 49a74507ce..65154c8600 100644 Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_results.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_results.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_settings.png b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_settings.png index ffedbddbfe..69cb6065b4 100644 Binary files a/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_settings.png and b/Plugins/org.mitk.gui.qt.fit.inspector/documentation/UserManual/fit_inspect_settings.png differ diff --git a/Plugins/org.mitk.gui.qt.fit.inspector/plugin.xml b/Plugins/org.mitk.gui.qt.fit.inspector/plugin.xml index 3a24f2ddb5..69d4996bf2 100644 --- a/Plugins/org.mitk.gui.qt.fit.inspector/plugin.xml +++ b/Plugins/org.mitk.gui.qt.fit.inspector/plugin.xml @@ -1,12 +1,12 @@ -