"fly" does not interpolate clipping plane positions, whereas "view" d…

…oes;

Segmentations tool Settings and other changes in dialog text

docs/user/commands/fly.html

@@ -40,6 +40,9 @@ <h3 class="usage"><a href="usageconventions.html">Usage</a>:
 (start and end) at a time, whereas
 <b>fly</b> can consider multiple views and generate a path that
 visits and leaves intermediate views without discontinuities in motion.
+However, <b>fly</b> does not interpolate
+<a href="clip.html">clipping plane</a> positions, whereas
+<a href="view.html#name"><b>view</b></a> does.
 See also:
 <a href="../movies.html">making movies</a>
 </p><p>
@@ -80,5 +83,5 @@ <h3 class="usage"><a href="usageconventions.html">Usage</a>:
 </p>
 <hr>
 <address>UCSF Resource for Biocomputing, Visualization, and Informatics / 
-March 2021</address>
+November 2023</address>
 </body></html>

docs/user/commands/view.html

@@ -229,6 +229,9 @@ <h3>Named Views and Transitions</h3>
 <a href="fly.html"><b>fly</b></a> command can smoothly traverse a series 
 of multiple views, generating a path that visits and leaves the intermediate 
 views without discontinuities in motion.
+However, an advantage of the <b>view</b>
+command is that it interpolates <a href="clip.html">clipping plane</a>
+positions, but <a href="fly.html"><b>fly</b></a> does not.
 </p>
 
 <a name="scenecoords"></a>
@@ -322,5 +325,5 @@ <h3>Using Transformation Matrices</h3>
 
 <hr>
 <address>UCSF Resource for Biocomputing, Visualization, and Informatics / 
-October 2023</address>
+November 2023</address>
 </body></html>

docs/user/tools/segmentations.html

@@ -76,18 +76,21 @@ <h3><a href="../index.html#tools">Tool</a>: Segmentations</h3>
 <h3>Dialog Settings</h3>
 <p>
 Starting the <b>Segmentations</b> tool automatically sets the view layout
-to four panels: axial, coronal, and sagittal slices along with a 3D rendering
+according to the tool's <a href="#settings-general"><b>General</b> settings</a>.
 </p><p>
-The <b>View Layout</b> can be switched among:
+<a name="layout"></a>
+The <b>View layout</b> can be switched among:
 </p>
 <ul>
-<li><b>4 x 4 (Desktop)</b> 
-&ndash; axial and 3D on the top, coronal and sagittal on the bottom
-<li><b>3D Over Orthoplanes (Desktop)</b>
+<li><b>2 x 2 (desktop)</b> 
+&ndash; axial slice and 3D view on the top, coronal and sagittal slice views
+on the bottom
+<li><b>3D over slices (desktop)</b>
 &ndash; 3D across the top, the three slice views across the bottom
-<li><b>3D Beside Orthoplanes (Desktop)</b>
+<li><b>3D beside slices (desktop)</b>
 &ndash; the three slice views on the left, 3D on the right
-<li><b>3D Only (VR)</b>
+<li><b>3D only (desktop)</b>
+<li><b>3D only (VR)</b>
 </ul>
 <p>
 The <b>Model</b> of interest (the medical image to segment and thus to show
@@ -97,11 +100,12 @@ <h3>Dialog Settings</h3>
 namely the <a href="modelpanel.html"><b>Model Panel</b></a> and/or 
 <a href="../commands/show.html"><b>show/hide</b></a> commands.
 </p><p>
-The <b>Plane Guidelines</b> option controls whether each slice view should
+The <b>Plane guidelines</b> option controls whether each slice view should
 contain crosshairs showing the positions of the other slice views.
 </p><p>
 <a name="range"></a>
-Min and max sliders set the <b>Intensity Range</b> that can be added 
+The <b>Restrict segmentation to intensity range</b> option allows limiting
+the range of data values that can be added
 to a segmentation model during <a href="#editing">interactive editing</a>;
 only those pixels with data values within the specified range will be
 added even when a larger area is swept out by the segmentation cursor.
@@ -126,19 +130,162 @@ <h3>Creating and Editing Segmentations</h3>
 editing the metadata associated with the segmentation model, and <b>Save</b>
 saves it as <a href="../dicom/dicom.html">DICOM</a> with the SEG modality.
 </p><p>
-The segmentation cursor is shown as a red circle; 
+In the slice views, the segmentation cursor is shown as a red circle; 
 left mouse click-drag sweeps out an area in the currently displayed 
 data plane, whereas additionally pressing Shift erases the corresponding area 
 from the segmentation. Shift-scroll adjusts the segmentation cursor size.
 The area swept out by the segmentation cursor in a slice view will be added
 to the current segmentation, unless further restricted by
 <a href="#range">intensity range</a>.
+These slice-view mouse mode assignments are listed in the 
+<a href="#settings-mouse2d"><b>Mouse (2D Slices)</b> settings</a>
+but cannot be changed currently. 
+</p><p>
+Segmentations can also be edited in the desktop 3D view according to the
+<a href="#settings-mouse3d"><b>Mouse (3D)</b> settings</a>
+and in <a href="../vr.html">virtual reality</a> according to the
+<a href="#settings-vr"><b>VR Controller</b> settings</a>
 </p><p>
 Clicking <b>Help</b> opens
 this page in the <a href="helpviewer.html"><b>Help Viewer</b></a>.
 </p>
 
+<a name="settings"></a>
+<p class="nav">
+[<a href="#top">back to top: Segmentations</a>]
+</p>
+<h3>Segmentations Settings (Preferences)</h3>
+<p>
+<!--
+Choosing <b>Settings...</b> from the
+<a href="#context"><b>Segmentations</b> context menu</a>
+-->
+Clicking the &ldquo;gear&rdquo; icon near the top right corner of
+the <b>Segmentations</b> tool shows its settings in a separate window, 
+with sections:
+</p>
+<ul>
+<li><a href="#settings-general"><b>General</b></a>
+<li><a href="#settings-mouse2d"><b>Mouse (2D Slices)</b></a>
+<li><a href="#settings-mouse3d"><b>Mouse (3D)</b></a>
+<li><a href="#settings-vr"><b>VR Controller</b></a>
+</ul>
+<p>
+<!--
+The settings window can be manipulated like other panels in the
+ChimeraX interface (<a href="../window.html#panels">more...</a>).
+</p><p>
+<b>Save</b> saves the current settings as
+<a href="../preferences.html#other">preferences</a>,
+<b>Reset</b> replaces the current settings with
+the initial &ldquo;factory&rdquo; defaults (values shown in <b>bold</b> below),
+and <b>Restore</b> restores values that were saved previously.
+-->
+Any changes in settings apply to the current session,
+but they are not saved as <a href="../preferences.html#other">preferences</a>
+for future sessions unless <b>OK</b> is clicked. Both <b>OK</b> and 
+<b>Cancel</b> dismiss the dialog, but <b>Cancel</b> does not save the settings.
+</p>
+
+<a name="settings-general"></a>
+<p><a href="#settings" class="nounder"><b>&larr;</b></a>
+<b>General</b> 
+&ndash; tool-associated graphics window and device behaviors
+</p>
+<ul class="none">
+<li><b>Default layout</b>
+&ndash; which of the following <a href="#layout">layouts</a> to use
+when the tool is started:
+  <ul>
+  <li><b>2 x 2 (desktop)</b> (initial default)
+  &ndash; axial slice and 3D view on the top, coronal and sagittal slice views
+  on the bottom
+  <li><b>3D over slices (desktop)</b>
+  &ndash; 3D across the top, the three slice views across the bottom
+  <li><b>3D beside slices (desktop)</b>
+  &ndash; the three slice views on the left, 3D on the right
+  <li><b>3D only (desktop)</b>
+  <li><b>3D only (VR)</b>
+ </ul>
+<li><b>Set 3D mouse modes when the desktop 3D-only layout is chosen</b>
+&ndash; whether to assign mouse buttons automatically according to the
+<a href="#settings-mouse3d"><b>Mouse (3D)</b> settings</a>
+when the desktop 3D-only <a href="#layout">layout</a> is chosen 
+(returning to prior assignments when a different <a href="#layout">layout</a>
+is chosen or the tool is closed)
+<li><b>Start VR when the VR layout is chosen</b>
+&ndash; whether to start <a href="../vr.html">virtual reality</a> mode
+automatically when the VR <a href="#layout">layout</a> is chosen 
+<li><b>Set VR controller modes when the VR layout is chosen</b>
+&ndash; whether to assign the <b><i>right</i></b>
+hand-controller buttons automatically
+according to the <a href="#settings-vr"><b>VR Controller</b> settings</a>
+when the VR <a href="#layout">layout</a> is chosen 
+(returning to prior assignments when the tool is closed)
+<li><b>Segmentation opacity</b> (initial default <b>80</b>%)
+&ndash; opacity of segmentation surfaces; transparency = 100% &ndash; opacity
+<li><b>Format for saving segmentations</b> 
+&ndash; file format produced by clicking <b>Save</b> in the tool dialog:
+<!-- <a href="#top"><b>Segmentations</b></a> dialog -->
+  <ul>
+  <li><a href="../dicom/dicom.html"><b>DICOM</b></a> (initial default)
+  with SEG modality
+  <li><a href="https://nifti.nimh.nih.gov/" target="_blank"><b>NIfTI</b></a>
+  <li><a href="https://teem.sourceforge.net/nrrd/" 
+  target="_blank"><b>NRRD</b></a>
+  </ul>
+Formats other than DICOM will not include metadata read from
+the original DICOM file, if any.
+</ul>
+
+<a name="settings-mouse2d"></a>
+<p><a href="#settings" class="nounder"><b>&larr;</b></a>
+<b>Mouse (2D Slices)</b> 
+&ndash; mouse assignments in the axial, coronal, and sagittal slice views.
+<font color="brown">Current limitations</font>: not adjustable, 
+and only the left-mouse assignment works with trackpad.
+</p>
+
+<a name="settings-mouse3d"></a>
+<p><a href="#settings" class="nounder"><b>&larr;</b></a>
+<b>Mouse (3D)</b> 
+&ndash; mouse assignments in the desktop 3D view
+when <a href="#settings-general"><b>Set 3D mouse modes...</b></a> is on
+and the desktop 3D-only <a href="#layout">layout</a> is chosen.
+<font color="brown">Current limitation</font>: does not work with trackpad.
+</p>
+Assignments can be made to each of the following,
+<ul>
+<li>right mouse
+<li>middle mouse + Shift
+<li>scrolling + Shift
+<li>left mouse
+</ul>
+...with available functions:
+<ul>
+<li>none
+<li>add to segmentation
+<li>move sphere
+<li>resize sphere
+</ul>
+
+<a name="settings-vr"></a>
+<p><a href="#settings" class="nounder"><b>&larr;</b></a>
+<b>VR Controller</b> 
+&ndash; assignments to the <b><i>right</i></b> hand controller
+when <a href="#settings-general"><b>Set VR controller modes...</b></a> is on
+and the VR 3D-only <a href="#layout">layout</a> is chosen.
+Available functions:
+<ul>
+<li>none
+<li>resize cursor
+<li>move cursor
+<li>add to segmentation
+<li>erase from segmentation
+</ul>
+
+
 <hr>
 <address>UCSF Resource for Biocomputing, Visualization, and Informatics /
-September 2023</address>
+November 2023</address>
 </body></html>