diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/Manual.dox b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/Manual.dox index 1a23e3e98a..0c1aedd4f0 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/Manual.dox +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/Manual.dox @@ -1,21 +1,86 @@ /** -\page org_mitk_gui_qt_matchpoint_visualizer The MatchPoint Registration Visualizer View +\page org_mitk_views_matchpoint_visualizer The MatchPoint Registration Visualizer View \imageMacro{map_vis_icon_doc.svg, "Icon of the Registration Visualizer",3} \tableofcontents \section MAP_VIS_Introduction Introduction -This view is in development to offer the user a way to visualize MatchPoint registrations in a MITK scene. +This view is in development to offer the user a way to visualize MatchPoint registrations (so the transformation/deformation field they represent) in a MITK scene. Currently only a simple grid visualization and glyph visualization is implemented.\n -\remark This is an experimental version and work in progress. So please excuse errors or usage issues and report them. This view will be improved and polished with the next releases. - -\section MAP_VIS_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. +\remark This is an experimental version and work in progress. So please excuse errors or usage issues and report them at https://phabricator.mitk.org. \section MAP_VIS_Usage Usage -Oops. Documentation is missing and to be done. -*/ +\imageMacro{map_view_visualizer_example.png, "Example screenshot showing the main elements of the view used to visualize a registration.", 14} +The view has following steps/sections:\n\n +(1) Registration slot: Shows the currently selected registration whose visualization settings should be altered. Click to change.\n\n + +(2) Registration information: General information of the selected registration.\n\n + +(3) Update visual settings: By clicking the button the current settings will be accepted and the visualization of the registration will be updated accordingly.\n\n + +(4) Mapping direction: Allows to select the mapping direction that should be visualized (more details see below \ref MAP_VIS_Direction).\n\n + +(5) Visualization style: Select how the registration should be visualized. Currently two options are available.: +- Grid: Visualize as a wire frame grid that is deformed by the registration. The magnitude of deformation can be encoded in the grid color (cf style example "a)" below). +- Glyph: Visualize as a cloud of arrows that follow the deformation vectors of the registrations. The magnitude of deformation can be encoded in the glyph color (cf style example "f)" below). + +More details can be found in the settings and style section below. + +\imageMacro{map_view_visualizer_style_example.png, "Example of the appearance of different style settings: a) grid style; b) grid with no color interpolation; c) grid in unicolor; d) grid with different grid frequency (frequency=1); e) grid also showing start grid (in gray); f) glyph style.", 14} + +\section MAP_VIS_Settings_vis Visualization settings +\imageMacro{map_view_visualizer_vis_settings.png, "Visualization settings offered by view.", 8} +(6) Color style: The following color styles are available: +- uni color: everything painted in the selected color (cf style example "c)"). Click on the color button to change the used color. +- vector magnitode: the color is depending on the respective vector magnitude of the deformation field (cf style example "a)" and "b)"). See (7) for instructions to change the used color encoding for the magnitude. + +(7) Color coding settings: One can change the color and associated vector length (in mm) for 4 classes of magnitude (negligible, small, medium and large). The color is encoded accordingly.\n\n + +(8) Interpolate colors: By default activated, the colors between to magnitude classes (see (7)) will be linear interpolated (e.g. with the settings given in the example shifts of 5 mm will be yellow, 10 mm will be orange and >=15 mm will be red). If interpolation is deactivated the color of one class is used till a next higher class is reached. Cf style example "a)" and "b)", in "b)" no red color can be seen because no shift was 15 mm or greater (magnitude class "large"). + +\section MAP_VIS_Settings_grid Grid settings +\imageMacro{map_view_visualizer_grid_settings.png, "Grid settings offered by view.", 8} +These are only available for style "grid".\n\n +(9) Grid frequency: Allows to control how spares the grid frame should be. One can also achieve something similar with changing the FOV spacing (see below), but using the frequency allows for a sparse frame and still having a high resolution in the frame deformation. The latter one would loose if just using a low FOV spacing. Style example "a)" and "d)" illustrate different frequency settings and there effect.\n\n + +(10) Start grid: If activated also the start grid of the registration will (for the chosen direction) will be visible. This is another grid specific possibility to illustrate the amount of deformation (cf style example "e)").\n\n + +(11) Start grid color: Select the color that should be used for the start grid. Click on the color button to change the used color. + +\section MAP_VIS_Settings_FOV Field of view (FOV) settings +\imageMacro{map_view_visualizer_grid_settings.png, "FOV settings offered by view.", 8} +The field of view defines the area of space (grid) that should be used for the visualization of the registration.\n\n + +(12) Size: Size of the FOV in mm.\n\n + +(13) Origin: Origin of the FOV in mm.\n\n + +(14) Spacing: Spacing of the FOV in mm. This directly impact the visualization's level of detail. IMPORTANT: Please be careful with setting small spacings, as it can lead to computational very expensive visualizations.\n\n + +(15) Orientation: Orientation matrix of the FOV (only readable).\n\n + +(16) FOV Reference slot: Select an image that should be used to define the geometric properties of the FOV. By default (and available) the target image used to determine the registration will be used. Click slot to change the FOV reference.\n\n + +(17) Relevant FOV reference properties: One can select which properties of the reference image will be used to specify the FOV.\n\n + +\section MAP_VIS_Direction Information regarding the directions + +Registrations can have two supported directions (direct and inverse). The direct kernel maps from the moving space into the target space, so this is the direction that "naively" people assume when they think about registrations. But practically it is only used to map continuous data like point sets. The inverse kernel maps from the target space into the moving space and is used to map images by so called inverse mapping. The effect is most obvious in the glyph style, where the glyphs points from the mapped space to the point in the moving space. + +\section MAP_VIS_image_source Grid settings +The data visible in the visualization styles images is part of the Patient 1 of the DIR_validation_data data set. +For further information: +https://www.creatis.insa-lyon.fr/rio/dir_validation_data + +-------------- + By downloading this data, you agreeing to follow these guidelines. When using any of the data provided for publications, please make reference to: + + The institution from which they were obtained: the Léon Bérard Cancer Center & CREATIS lab, Lyon, France. + The article containing the description of this data: + + J. Vandemeulebroucke, S. Rit, J. Kybic, P. Clarysse, and D. Sarrut. Spatiotemporal motion estimation for respiratory-correlated imaging of the lungs. In Med Phys, 2011, 38(1), 166-178. pdf +--------------- + +*/ \ No newline at end of file diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings.png new file mode 100644 index 0000000000..7de94d99f5 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings.png differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings.svg b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings.svg new file mode 100644 index 0000000000..bf6621589a --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings.svg @@ -0,0 +1,472 @@ + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (12) Setting the size of the visualization + (16) Optional slot of a FOV reference + + (17) Set relevant FOV reference properties + + (13) Setting the origin of the visualization + + (14) Setting the spacing of the visualization + + (15) Displaying the orientation of the visualization + diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings_raw.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings_raw.png new file mode 100644 index 0000000000..2764ba009f Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_FOV_settings_raw.png differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example.png b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example.png new file mode 100644 index 0000000000..cbee7fa9b4 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example.png differ diff --git a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example.svg b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example.svg new file mode 100644 index 0000000000..92c711068f --- /dev/null +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/documentation/UserManual/map_view_visualizer_example.svg @@ -0,0 +1,399 @@ + + + + + + + + image/svg+xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (1) Registration slot + (2) Registation information + (3) Update visual settings + + (4) Selection of mapping direction + + (5) Selection of 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b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.ui index 3c550db5e9..899b10bbc1 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.ui +++ b/Plugins/org.mitk.gui.qt.matchpoint.visualizer/src/internal/QmitkMatchPointRegistrationVisualizer.ui @@ -1,1570 +1,1570 @@ MatchPointRegVisControls 0 0 332 738 5 5 5 5 5 255 0 0 255 0 0 120 120 120 Warning: This plugin is in an experimental state! Registration: 3 0 40 Info: 0 0 0 75 16777215 130 true 0 0 false 5 5 5 5 5 <html><head/><body><p>Updates the visualization with the current settings.</p></body></html> Update visualization false Show mapping direction: <html><head/><body><p>Select the direction/kernel of the registration you want to visualize:</p><p>- &quot;direct&quot;: select to show the direct mapping kernel (used for continuous spaced data like point sets).</p><p>- &quot;inverse&quot;: select to show the inverse mapping kernel (used for discrete spaced data like voxel images).</p><p><br/></p><p>If the selected registration does not support a direction, you cannot select it.</p></body></html> Direct Inverse 0 0 0 30 5 0 5 0 5 <html><head/><body><p>Select to vizualize registration via grid(s).</p></body></html> Grid true true true true Select to vizualize registration via glyphs. Glyph true true false Select to vizualize registration via a pointset selected from the data manager... Points true true 2 Visualization 5 5 5 Color style: uni color: false 60 0 false Qt::Horizontal 40 20 vector magnitude: Color coding: 0 0 7 3 Qt::Horizontal 40 20 Qt::Horizontal 40 20 Qt::Horizontal 40 20 Qt::Horizontal 40 20 mm small: medium: 30 16777215 > Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter 999.000000000000000 0.100000000000000 999.000000000000000 large: 30 16777215 > Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter mm 999.000000000000000 mm 30 16777215 > Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter negligible: 50 0 40 16777215 50 0 40 16777215 50 0 40 16777215 50 0 40 16777215 interpolate colors Qt::Vertical 20 40 true Grid <html><head/><body><p>General grid visualization settings.</p></body></html> 5 5 5 5 5 QFormLayout::AllNonFixedFieldsGrow 5 5 Grid frequency: <html><head/><body><p>Indicate the frequency of visible gridlines used for visualization.</p><p>e.g. 1: every line of the grid is visible; 2: only every second line is visible ...</p></body></html> 200 50 false <html><head/><body><p>Allows that pixels may not be defined in the mapped image because they are outside of the field of view of the used input image.</p><p>The pixels will be marked with the given padding value.</p><p>If unchecked the mapping will be aborted in a case of undefined pixels.</p></body></html> Show start grid false true false 11 5 11 5 Color 60 0 false Qt::Horizontal 40 20 Qt::Vertical QSizePolicy::Expanding 20 300 FOV <html><head/><body><p>Field of view settings (FOV) for vizualizing the grid correctly (its origin, size and orientation).</p></body></html> 5 5 5 5 5 Size (in mm): 0 0 0 x: 0 0 10 0 50 16777215 <html><head/><body><p>Indicate the size (in mm) of the grid in the x direction.</p></body></html> 2 0.010000000000000 9999.000000000000000 y: Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter 0 0 10 0 50 16777215 <html><head/><body><p>Indicate the size (in mm) of the grid in the y direction.</p></body></html> 2 0.010000000000000 9999.000000000000000 z: Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter 0 0 10 0 50 16777215 <html><head/><body><p>Indicate the size (in mm) of the grid in the z direction.</p></body></html> 2 0.010000000000000 9999.000000000000000 Origin (in mm): 0 0 0 x: 0 0 10 0 50 16777215 <html><head/><body><p>Indicate the origin (in mm) of the grid in the x direction.</p></body></html> -99999.000000000000000 99999.000000000000000 y: Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter 0 0 10 0 50 16777215 <html><head/><body><p>Indicate the origin (in mm) of the grid in the y direction.</p></body></html> -99999.000000000000000 99999.000000000000000 z: Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter 0 0 10 0 50 16777215 <html><head/><body><p>Indicate the origin (in mm) of the grid in the z direction.</p></body></html> -99999.000000000000000 99999.000000000000000 0.000000000000000 Spacing (in mm): 0 0 0 x: 0 0 10 0 50 16777215 <html><head/><body><p>Indicate the spacing/resolution of the grid in the x direction.</p></body></html> 0.010000000000000 9999.000000000000000 0.010000000000000 y: Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter 0 0 10 0 50 16777215 <html><head/><body><p>Indicate the spacing/resolution of the grid in the y direction.</p></body></html> 0.010000000000000 9999.000000000000000 0.010000000000000 z: Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter 0 0 10 0 50 16777215 <html><head/><body><p>Indicate the spacing/resolution of the grid in the z direction.</p></body></html> 0.010000000000000 9999.000000000000000 0.010000000000000 Orientation: true 0 0 160 50 7 false false false false false 20 50 false 20 R1 R2 R3 C1 C2 C3 0 ItemIsEnabled 0 ItemIsEnabled 0 ItemIsEnabled 0 ItemIsEnabled 0 ItemIsEnabled 0 ItemIsEnabled 0 ItemIsEnabled 0 ItemIsEnabled 0 ItemIsEnabled - FOV Reverence: + FOV Reference: 3 0 40 size true origin true spacing true orientation true Qt::Vertical 20 40 Qt::Vertical 20 40 QmitkSingleNodeSelectionWidget QWidget
QmitkSingleNodeSelectionWidget.h
1
ctkColorPickerButton QPushButton
ctkColorPickerButton.h
5 5 true true true