<?xml version="1.0" encoding="utf-8"?>
<executable>
  <category>Informatics</category>
  <title>Markups</title>
  <description><![CDATA[Create and edit markups, supplementary information associated with a scene. Currently supported markups are lists of fiducial points. Fiducials can be placed using the mouse mode tool bar. Once fiducial place mode has been entered, a new fiducial can be placed under the current mouse position by pressing the p key. Right mouse button click will exit persistent place mode.]]></description>
  <documentation-url>http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.4/Modules/Markups</documentation-url>
  <license>slicer4</license>
  <contributor>Nicole Aucoin (SPL, BWH)</contributor>
  <acknowledgements><![CDATA[This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149.]]></acknowledgements>
  <parameters>
    <label>Markups List</label>
    <description>Top level Markups list with some often used options.</description>
    <parameter>
      <label>List</label>
      <description><![CDATA[Select a Markups fiducial node from the scene to populate the GUI and allow modifications. One option is to create a new node with the display properties of the current list.]]></description>
    </parameter>
    <parameter>
      <label>Visibility</label>
      <description><![CDATA[Toggle the list visibility, which will override the individual markup visibility settings. If the eye icon is open, the list is visible, and pressing it will make it invisible. If the eye icon is closed, the list is invisible and pressing the button will make it visible.]]></description>
    </parameter>
    <parameter>
      <label>Locked</label>
      <description><![CDATA[Toggle the list lock state (if it can be moved by mouse interactions in the viewers), which will override the individual markup lock settings. If the lock icon is open, the list is unlocked, and pressing it will lock it. If the lock icon is closed, the list is locked and pressing the button will unlock it. When the list is locked, the table is disabled so no changes can be made to fiducial positions there.]]></description>
    </parameter>
    <parameter>
      <label>Scale</label>
      <description><![CDATA[Set both the glyph and text size to the same value for all markups in the list.]]></description>
    </parameter>
    <parameter>
      <label>Click to Jump Slices</label>
      <description><![CDATA[If checked, click in name column to jump slices to that point. The radio buttons control if the slice is centered on the markup or not after the jump. Right click in the table allows jumping 2D slices to a highlighted fiducial (uses the center/offset radio button settings). Once checked, arrow keys moving the highlighted row will also jump slice viewers to that markup position.]]></description>
    </parameter>
  </parameters>
  <parameters>
    <label>Buttons</label>
    <description>These buttons apply changes to markups in the selected list.</description>
    <parameter>
      <label>Toggle visibility flag</label>
      <description><![CDATA[Toggle visibility flag on all markups in list. Use the drop down menu to set all to visible or invisible.]]></description>
    </parameter>
    <parameter>
      <label>Toggle selected flag</label>
      <description><![CDATA[Toggle selected flag on all markups in list. Use the drop down menu to set all to selected or deselected. Only selected markups will be passed to command line modules.]]></description>
    </parameter>
    <parameter>
      <label>Toggle lock flag</label>
      <description><![CDATA[Toggle lock flag on all markups in list, use drop down menu to set all to locked or unlocked.]]></description>
    </parameter>
    <parameter>
      <label>Delete the highlighted markups from the active list</label>
      <description><![CDATA[After highlighting rows in the table to select markups, press this button to delete them from the list.]]></description>
    </parameter>
    <parameter>
      <label>Remove all markups from the active list</label>
      <description><![CDATA[Pressing this button will delete all of the markups in the active list, leaving it with a list length of 0.]]></description>
    </parameter>
  </parameters>
  <parameters>
    <label>Checkboxes</label>
    <description>These check boxes change how the markups in the selected list are displayed.</description>
    <parameter>
      <label>Transformed</label>
      <description><![CDATA[Check to show the transformed coordinates in the table. This will apply any transform nodes to the points in the list and show that result. Keep unchecked to show the raw RAS values that are stored in MRML. If you harden the transform the transformed coordinates will be the same as the non transformed coordinates.]]></description>
    </parameter>
    <parameter>
      <label>Hide RAS</label>
      <description><![CDATA[Check to hide the coordinate columns in the table and uncheck to show them. Right click in rows to see coordinates.]]></description>
    </parameter>
  </parameters>
  <parameters>
    <label>Markups Table</label>
    <description><![CDATA[Right click on rows in the table to bring up a context menu to show the full precision coordinates, distance between multiple highlighted fiducials, delete the highlighted markup, jump slice viewers to that location, refocus 3D viewers to that location, or if there are other lists, to copy or move the markup to another list.]]></description>
    <parameter>
      <label>Selected</label>
      <description><![CDATA[A check box is shown in this column, it's check state depends on if the markup is selected or not. Click to toggle the selected state. Only selected markups will be passed to command line modules.]]></description>
    </parameter>
    <parameter>
      <label>Locked</label>
      <description><![CDATA[An open or closed padlock is shown in this column, depending on if the markup is unlocked or locked. Click it to toggle the locked state.]]></description>
    </parameter>
    <parameter>
      <label>Visibility</label>
      <description><![CDATA[An open or closed eye icon is shown in this column, depending on if the markup is visible or not. Click it to toggle the visibility state.]]></description>
    </parameter>
    <parameter>
      <label>Name</label>
      <description><![CDATA[A short name for this markup, displayed in the viewers as text next to the glyphs.]]></description>
    </parameter>
    <parameter>
      <label>Description</label>
      <description><![CDATA[A longer description for this markup, not displayed in the viewers.]]></description>
    </parameter>
    <parameter>
      <label>X, Y, Z</label>
      <description><![CDATA[The RAS coordinates of this markup, 3 places of precision are shown.]]></description>
    </parameter>
  </parameters>
  <parameters>
    <label>Advanced: Buttons</label>
    <parameter>
      <label>Move Up</label>
      <description><![CDATA[Move a highlighted markup up one spot in the list.]]></description>
    </parameter>
    <parameter>
      <label>Move Down</label>
      <description><![CDATA[Move a highlighted markup down one spot in the list.]]></description>
    </parameter>
    <parameter>
      <label>Add Markup</label>
      <description><![CDATA[Add a new markup to the selected list, placing it at the origin]]></description>
    </parameter>
  </parameters>
  <parameters>
    <label>Advanced: Naming</label>
    <parameter>
      <label>Name Format</label>
      <description><![CDATA[Format for creating names of new markups, using sprintf format style. %N is replaced by the list name, %d by an integer.]]></description>
    </parameter>
    <parameter>
      <label>Apply</label>
      <description><![CDATA[Rename all markups in this list according to the current name format, trying to preserve numbers. A quick way to re-number all the fiducials according to their index is to use a name format with no number in it, rename, then add the number format specifier %d to the format and rename one more time.]]></description>
    </parameter>
    <parameter>
      <label>Reset</label>
      <description><![CDATA[Rest the name format field to the default value, %N-%d.]]></description>
    </parameter>
  </parameters>
  <parameters>
    <label>Advanced: Conversion</label>
    <parameter>
      <label>Convert Annotation Fiducials to Markups Fiducial Lists</label>
      <description><![CDATA[Uses annotation fiduical hierarchies to make markup lists. Removes the annotations once they've been moved.]]></description>
    </parameter>
  </parameters>
  <parameters>
    <label>Advanced: Display Properties</label>
    <parameter>
      <label>Glyph Type</label>
	  <description><![CDATA[Select the symbol that will be used to mark each location. Default is the Sphere3D.]]></description>
	</parameter>
	<parameter>
	  <label>Selected Color</label>
	  <description><![CDATA[Select the color that will be used to display the glyph and text when the markup is marked as selected.]]></description>
	</parameter>
	<parameter>
	  <label>Unselected Color</label>
	  <description><![CDATA[Select the color that will be used to display the glyph and text when the markup is not marked as selected.]]></description>
	</parameter>
	<parameter>
	  <label>Glyph Scale</label>
	  <description><![CDATA[Pick the relative size of the glyph used to mark the points.]]></description>
	</parameter>
	<parameter>
	  <label>Text Scale</label>
	  <description><![CDATA[Pick the relative size of the text shown beside each glyph. Select 0 to turn off text.]]></description>
	</parameter>
	<parameter>
	  <label>Opacity</label>
	  <description><![CDATA[Pick the opacity used for the glyph and text, select 0 for invisible, 1 for fully visible.]]></description>
	</parameter>
	<parameter>
	  <label>Reset to Defaults</label>
	  <description><![CDATA[Reset the display properties of this markups node to the system defaults.]]></description>
	</parameter>
	<parameter>
	  <label>Save to Defaults</label>
	  <description><![CDATA[Save the display properties of this markups node to be the new system defaults.]]></description>
	</parameter>
  </parameters>
  <parameters>
    <label>Advanced: Display Properties: Fiducuial Projection</label>
    <description><![CDATA[A widget that controls the projection of the fiducials in the 2D viewers onto slices around the one on which the fiducial has been placed.]]></description>
    <parameter>
      <label>2D Projection</label>
      <description><![CDATA[Toggle the eye icon open or closed to enable or disable visualization of projectied fiducial on 2D viewers.]]></description>
    </parameter>
    <parameter>
      <label>Use Fiducial Color</label>
      <description><![CDATA[If checked, color the projections the same color as the fiducials.]]></description>
    </parameter>
    <parameter>
      <label>Projection Color</label>
      <description><![CDATA[If not using fiducial color for the projection, use this color.]]></description>
    </parameter>
    <parameter>
      <label>Outlined Behind Slice Plane</label>
      <description><![CDATA[Fiducial projection is displayed filled (opacity = Projection Opacity) when on top of slice plane, outlined when behind, and with full opacity when in the plane. Outline isn't used for some glyphs (Dash2D, Cross2D, Starburst).]]></description>
    </parameter>
    <parameter>
      <label>Projection Opacity</label>
      <description><![CDATA[A value between 0 (invisible) and 1 (fully visible) for displaying the fiducial projection.]]></description>
    </parameter>
  </parameters>
</executable>
