diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox
index 08e636a260..78387972f7 100644
--- a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox
+++ b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox
@@ -1,109 +1,194 @@
/**
-\page org_mitk_views_datamanager The DataManager
+\page org_mitk_views_datamanager The Datamanager
-\imageMacro{data-manager.svg,"Icon of the Data Manager",2.00}
+\imageMacro{data-manager.svg,"Icon of the Data Manager", 2.00}
\tableofcontents
-\section QmitkDataManagerIntroduction Introduction
+\section DataManagerIntroduction Introduction
-The Datamanager is the central componenent to manage medical data like images, surfaces, etc..
-After loading one or more data into the Datamanager the data are shown in the four-view window, the so called Standard View.
-The user can now start working on the data by just clicking into the standard view or by using the MITK-modules such as "Segmentation" or "Basic Image Processing".
+The Datamanager is the central component to manage medical data like images, segmentation masks, registrations, surfaces, point sets, annotations, measurements, etc..
+After loading data into the Datamanager the data is shown in the four-view window, the so-called Standard Display.
+The user can now start working on the data by interacting with the data inside the Standard Display,
+by using the MITK-plugins such as Segmentation or Basic Image Processing or by using the context menu inside the data manager.
-\imageMacro{QmitkDatamanager_Overview.png,"How MITK looks when started",16.00}
+\section DataManagerLoadingData Loading Data
+There are several ways of loading data into the Datamanager as so-called data nodes:
-\section QmitkDataManagerLoading Loading Data
-
-There are three ways of loading data into the Datamanager as so called Data-Elements.
-
-The user can just drag and drop data into the Datamanager or directly into one of the four parts of the Standard View.
-He can as well use the Open-Button in the right upper corner. Or he can use the standard "File->Open"-Dialog on the top.
+
+ - drag and drop data (e.g. from a file explorer or desktop) into the Datamanager
+
- drag and drop data (e.g. from a file explorer or desktop) into one of the four windows of the Standard Display
+
- use the keyboard shortcut Ctrl + o
+
- use the Open File Button in the left upper corner and use the Open Dialog
+
- use File -> Open File... from the top menu
+
-A lot of file-formats can be loaded into MITK, for example
+A lot of file-formats can be loaded into MITK, for example:
-- 2D-images/3D-volumes with or without several timesteps (*.dcm, *.ima, *.pic, ...)
-
- Surfaces (*.stl, *.vtk, ...)
-
- Pointsets (*.mps)
-
- ...
+
- 2D-images / 3D-volumes with or without several time steps (*.dcm, *.ima, *.pic, *.nrrd, ...)
+
- Surfaces (*.stl, *.vtk, ...)
+
- Point sets (*.mps)
+
- and many more
The user can also load a series of 2D images (e.g. image001.png, image002.png ...) to a MITK 3D volume.
To do this, just drag and drop one of those 2D data files into the Datamanager by holding the ALT key.
+Note: What really happens is that the data nodes are stored inside a "Data storage" and the Datamanager is just a visual representation of the data inside the "Data storage".
+That's why the documentation sometimes uses the term "Data storage" instead of "Datamanager".
-After loading one or more data into the Datamanager they appear as Data-Elements in a sorted list inside the Datamanager.
-Data-Elements can also be sorted hierarchically as a parent-child-relation.
-For example after using the Segmentation-Module on Data-Element1 the result is created as Data-Element2, which is a child of Data-Element1 (see Screenshot1).
-The order can be changed by drag and drop.
+\section DataManagerSavingData Saving Data
-\imageMacro{QmitkDatamanager_ParentChild.png,"Screenshot1",9.61}
+There are several ways of saving data from the Datamanager:
-The listed Data-Elements are shown in the standard view.
-Here the user can scale or rotate the medical objects or he can change the cutting planes of the object by just using the mouse inside this view.
+
+ - use the keyboard shortcut Ctrl + s on a single data node
+
- use the keyboard shortcut Ctrl + s on multiple data nodes
+
- use the context menu right-click -> Save on a single data node
+
- use the context menu right-click -> Save on multiple data nodes
+
- use File -> Save... from the top menu on a single data node
+
- use File -> Save... from the top menu on multiple data nodes
+
-\section QmitkDataManagerSaving Saving Data
+\section DataManagerWorking Working with the Datamanager
-There are two ways of saving data from the Datamanger. The user can either save the whole project with all Data-Elements by clicking on "File"->"Save Project"
-or he can save single Data-Elements by right-clicking->"Save", directly on a Data-Element.
-When saving the whole project, the sorting of Data-Elements is saved as well. By contrast the sorting is lost, when saving a single Data-Element.
+After loading data into the Datamanager the data appears as data nodes in a sorted list inside the Datamanager.
+The user can change the order of the data nodes manually by dragging one or multiple data nodes and dropping them at any position inside the Datamanager.
+Data nodes can also be sorted hierarchically as a parent-child-relation.
+For example after using the Segmentation-Plugin to create a segmentation on DataNode, the result is created as ChildNode,
+which is a child of DataNode (see \ref ParentChild "Parent-Child-Relation" screenshot).
+A parent-child-relation can be changed by dragging a child of a data node and dropping it onto another data node.
+For this the Property Allow changing of parent nodes needs to be enabled (see \ref DataManagerPreferences "Preferences").
-\section QmitkDataManagerProperties Working with the Datamanager
+\anchor ParentChild
+\imageMacro{QmitkDatamanager_ParentChild.png, "Parent-Child-Relation", 16.00}
-\subsection QmitkDataManagerPropertiesList List of Data-Elements
+\subsection DataManagerNodeVisibility Visibility of data nodes
-The Data-Elements are listed in the Datamanager.
-As described above the elements can be sorted hierarchically as a parent-child-relation.
-For example after using the Segmentation-Module on Data-Element1 the result is created as Data-Element2, which is a child of Data-Element1 (see Screenshot1).
-By drag and drop the sorting of Data-Elements and their hierarchical relation can be changed.
+By default all loaded data nodes are visible in the Standard Display. The visibility is indicated by the checkbox in front of the data node name in the Datamanager.
+If a data node is visible, the checkbox is filled - an empty checkbox indicates a hidden data node (see \ref ParentChild "Parent-Child-Relation" screenshot).
+Hint: The data nodes are rendered on top of each other, such that the topmost visible data node is always displayed on top of other data nodes. By hiding
+the topmost visible data node the next data node becomes the topmost visible data node and the hidden data node is not rendered anymore.
+Note: "Visible" does not mean that the node is correctly displayed inside the render windows. The user might have to re-initialize a data node to have it correctly displayed.
-\subsection QmitkDataManagerPropertiesVisibility Visibility of Data-Elements
+\subsection DataManagerNodeSelection Selection of data nodes
-By default all loaded Data-Elements are visible in the standard view.
-The visibility can be changed by right-clicking on the Data-Element and then choosing "Toogle visibility".
-The box in front of the Data-Element in the Datamanager shows the visibility.
-A green-filled box means a visible Data-Element, an empty box means an invisible Data-Element (see Screenshot1).
+Some MITK-plugins contain widgets to control the data nodes that are used for plugin-specific data processing. These widgets can be configured such that they listen to
+the current selection of the Datamanager. Having such a plugin active each selection change of data nodes inside the data manager will change the respective selection of
+the plugin. The data node selection widgets can have specific node predicates, which means that only specific data nodes can be controlled by the widgets. It might happen
+that a selected data node will not be represented in such a selection widget or that the selection widget will be emptied.
-\subsection QmitkDataManagerPropertiesRepresentation Representation of Data-Elements
+\subsection DataManagerNodeRenaming Renaming data nodes
-There are different types of representations how to show the Data-Element inside the standard view. By right-clicking on the Data-Element all options are listed (see Screenshot2 and Screenshot 3).
+There are two ways of changing the name of a data node inside the Datamanager:
-- An arbitrary color can be chosen
-
- The opacity can be changed with a slide control
-
- In case of images a texture interpolation can be switched on or off. The texture interpolation smoothes the image, so that no single pixels are visible anymore.
-
- In case of surfaces the surface representation can be changed between points, wireframe or surface.
-
- Global reinit updates all windows to contain all the current data:
+
- use the F2 key on a single data node
+
- double-click on a single data node
+
- - The orientation of the worldgeometry, which basically defines the rendering space, is set to the standard coordinate system, i.e. [(0,0,1);(0,1,0);(0,0,1)]
- - The size of the worldgeometry is calculated, so that it includes all loaded data (depends on size and position of your data)
- - The spacing is set to the smallest existing spacing regarding your data
+In both cases the new name can be accepted by hitting Enter or by clicking somewhere else.
- Reinit updates a single data item and fits the windows to contain only this data item:
+\section DataManagerContextMenu Context Menu
- - The orientation of the worldgeometry, is aligned according to the orientation of the currently selected datanode
- - The size of the worldgeometry is set to the size of the currently selected datanode
- - The spacing is set to the spacing of the currently selected datanode
+The Datamanager provides a context menu for each data node that can be opened by right-clicking on a data node.
+An example of the context-menu can be seen in the \ref ContextMenu "Context menu" screenshot.
+The context menu allows to quickly perform common actions on data nodes. These actions differ according to the data type. Some of these actions are described here.
+For more actions see the respective modules and plugins (e.g. QmitkCreatePolygonModelAction inside the org_mitk_gui_qt_segmentation-plugin.
+
+ - Global Reinit: Re-initializes the render windows to the common bounding box of all data nodes of the data storage that
+
+ - have not set "includeInBoundingBox" to false
+
- are "visible".
+
+ In this case it does not matter on which node this action is performed.
+ - Reinit: Re-initializes the render windows to the common bounding box of all selected data nodes of the data storage that
+
+ - have not set "includeInBoundingBox" to false
+
- are "visible".
+
+ - Save: see \ref DataManagerSavingData "Saving Data" section
+
- Remove: Removes all selected data nodes from the data storage.
+
- Show only selected nodes: Enables the visibility of all selected data nodes and hides all other data nodes.
+
- Toggle visibility: Shows / hides each selected data node according to each node's current visibility state.
+
- Show details: Opens a pop-up window with detailed information about each node, like data type, geometry, DICOM information, file path etc.
+
- Opacity: Sets the opacity via a slider for the rendering of the selected data node.
+
- Color: Opens a pop-up window that allows to pick an arbitrary color for the rendering of all selected data nodes.
+
- Colormap: Opens another submenu with a list of different colormaps that can be chosen for the rendering of all selected data nodes.
+
- Component: Sets the currently visible data component for the rendering of this particular component of the selected data node.
+
- Texture Interpolation: Smooths the data visualization for rendering of a selected data node.
+
- Surface Representation: Opens another submenu with the following entries:
+
+ - Points: Visually represents a surface (a data type) as a set of points.
+
- Wireframe: Visually represents a surface (a data type) as a wireframe model.
+
- Surface: Visually represents a surface (a data type) as a solid surface.
+
-\imageMacro{QmitkDatamanager_ImageProperties.png,"Screenshot2: Properties for images",10.56}
-\imageMacro{QmitkDatamanager_SurfaceProperties.png,"Screenshot3: Properties for surfaces",11.01}
+As the description of the actions showed, it is possible to open / use the context menu with a single data node or with a set of selected data nodes.
+If the data types of multiple selected data nodes differ, the actions might not appear / work as expected. Also some actions are not available for a set of selected data nodes.
+\anchor ContextMenu
+\imageMacro{QmitkDatamanager_ContextMenu.png, "Context menu", 16.00}
-\subsection QmitkDataManagerPropertiesPreferences Preferences
+\section DataManagerPreferences Preferences
-For the datamanager there are already some default hotkeys like the del-key for deleting a Data-Element. The whole list is seen in Screenshot4.
-From here the Hotkeys can also be changed. The preference page is found in "Window"->"Preferences".
+The MITK Workbench provides a preference page for specific plugins. The preference page provided for the Datamanager can be seen in the \ref PreferencePage "Preference page" screenshot.
+The user can open the preference page by
+
+ - using the keyboard shortcut Ctrl + p
+
- using Window -> Preferences... from the top menu.
+
+
+It allows to set the following preferences for the Datamanager, which define the behavior of the Datamanager:
+
+ - Place new nodes on top: If enabled, newly added data nodes will be inserted at the top of the list of data nodes inside the Datamanager.
+ If disabled, newly added nodes will be inserted at the bottom of the list.
+
- Show helper objects: If enabled, data nodes that have set "helper object" to true will be displayed in the Datamanager.
+ If disabled, data nodes that have set "helper object" to true will not be visible in the Datamanager.
+
- Show nodes containing no data: If enabled, data nodes that have no underlying base data defined will be displayed in the Datamanager.
+ If disabled, data nodes that have no underlying base data defined will not be visible in the Datamanager.
+
- Use surface decimation: If enabled, a newly created surface will be decimated to reduce the number of triangles in the triangle mesh.
+ Such a surface can be created as a polygon model from a segmentation (see \ref DataManagerContextMenu "Context Menu").
+ If disabled, the surface will have its original number of triangles in the triangle mesh.
+
- Allow changing of parent node: If enabled, the user can change the hierarchy of the data nodes manually by dragging one or multiple data nodes and
+ dropping them at any position inside the Datamanager (see \ref DataManagerWorking "Working with the Datamanager") for changing the order of the data nodes manually).
+
-\imageMacro{QmitkDatamanager_Preferences.png,"Screenshot4",16.00}
+\anchor PreferencePage
+\imageMacro{QmitkDatamanager_PreferencePage.png, "Preference page", 16.00}
-\section QmitkDataManagerPropertyList Property List
+\section DataManagerHotkeys Hotkeys
-The Property List displays all the properties the currently selected Data-Element has. Which properties these are depends on the Data-Element. Examples are opacity, shader, visibility. These properties can be changed by clicking on the appropriate field in the "value" column.
+The MITK Workbench provides hotkeys for specific plugins. The hotkeys provided for the Datamanager can be seen in the \ref Hotkeys "Hotkeys" screenshot.
+They allow to expedite common operations in relation to data nodes or the Datamanager.
+The user can customize the hotkeys by accessing the preference page:
+
+ - using the keyboard shortcut Ctrl + p
+
- useing Window -> Preferences... from the top menu
+
-\imageMacro{QmitkDatamanager_PropertyList.png,"Screenshot5: Property List",7.85}
+
+ - Delete selected nodes Removes all selected data nodes from the data storage.
+
- Global reinit Re-initializes the render windows to the common bounding box of all data nodes of the data storage that
+
+ - have not set "includeInBoundingBox" to false
+
- are "visible"
+
+ In this case it does not matter on which node this action is performed.
+ - Make all nodes invisible Hides all data nodes of the data storage.
+
- Reinit selected nodes Re-initializes the render windows to the common bounding box of all selected data nodes of the data storage that
+
+ - have not set "includeInBoundingBox" to false
+
- are "visible"
+
+ - Show node information Opens a pop-up window with detailed information about each node, like data type, geometry, DICOM information, file path etc.
+
- Toggle visibility of selected nodes: Shows / hides each selected data node according to each node's current visibility state.
+
+\anchor Hotkeys
+\imageMacro{QmitkDatamanager_Hotkeys.png, "Hotkeys", 16.00}
*/
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