<?xml version="1.0"?>
<feed xmlns="http://www.w3.org/2005/Atom" xml:lang="en">
	<id>https://www.dynamo-em.org//w/index.php?action=history&amp;feed=atom&amp;title=Linking_surfaces_into_point_models</id>
	<title>Linking surfaces into point models - Revision history</title>
	<link rel="self" type="application/atom+xml" href="https://www.dynamo-em.org//w/index.php?action=history&amp;feed=atom&amp;title=Linking_surfaces_into_point_models"/>
	<link rel="alternate" type="text/html" href="https://www.dynamo-em.org//w/index.php?title=Linking_surfaces_into_point_models&amp;action=history"/>
	<updated>2026-04-14T21:50:08Z</updated>
	<subtitle>Revision history for this page on the wiki</subtitle>
	<generator>MediaWiki 1.34.0</generator>
	<entry>
		<id>https://www.dynamo-em.org//w/index.php?title=Linking_surfaces_into_point_models&amp;diff=1807&amp;oldid=prev</id>
		<title>Daniel Castaño at 13:25, 14 July 2017</title>
		<link rel="alternate" type="text/html" href="https://www.dynamo-em.org//w/index.php?title=Linking_surfaces_into_point_models&amp;diff=1807&amp;oldid=prev"/>
		<updated>2017-07-14T13:25:53Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table class=&quot;diff diff-contentalign-left&quot; data-mw=&quot;interface&quot;&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;tr class=&quot;diff-title&quot; lang=&quot;en&quot;&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;Revision as of 13:25, 14 July 2017&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot; id=&quot;mw-diff-left-l8&quot; &gt;Line 8:&lt;/td&gt;
&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 8:&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;Make certain that &amp;lt;tt&amp;gt;s&amp;lt;/tt&amp;gt; contains already a depiction triangulation. This is created with the black triangle icon in the workflow for surfaces, or with the method &amp;lt;tt&amp;gt;createMesh&amp;lt;/tt&amp;gt; from the command line.&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;Make certain that &amp;lt;tt&amp;gt;s&amp;lt;/tt&amp;gt; contains already a depiction triangulation. This is created with the black triangle icon in the workflow for surfaces, or with the method &amp;lt;tt&amp;gt;createMesh&amp;lt;/tt&amp;gt; from the command line.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt; &lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins style=&quot;font-weight: bold; text-decoration: none;&quot;&gt;&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt; &lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins style=&quot;font-weight: bold; text-decoration: none;&quot;&gt;Note that you can check visually the orientations of the particles in the model through the commands&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt; &lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins style=&quot;font-weight: bold; text-decoration: none;&quot;&gt; &amp;lt;tt&amp;gt;p.plotTableSketch([],'hold_limits',false);&amp;lt;/tt&amp;gt;&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt; &lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins style=&quot;font-weight: bold; text-decoration: none;&quot;&gt;which will show by default orientations pointing upward.&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;You can directly link the mesh inside surface  &amp;lt;tt&amp;gt;s&amp;lt;/tt&amp;gt; into points &amp;lt;tt&amp;gt;p&amp;lt;/tt&amp;gt; by:&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;You can directly link the mesh inside surface  &amp;lt;tt&amp;gt;s&amp;lt;/tt&amp;gt; into points &amp;lt;tt&amp;gt;p&amp;lt;/tt&amp;gt; by:&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt;−&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;  &amp;lt;tt&amp;gt;p.linkedSurface = &lt;del class=&quot;diffchange diffchange-inline&quot;&gt;t&lt;/del&gt;.mesh&lt;del class=&quot;diffchange diffchange-inline&quot;&gt;.triangulation&lt;/del&gt;&amp;lt;/tt&amp;gt;&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;  &amp;lt;tt&amp;gt;p.linkedSurface = &lt;ins class=&quot;diffchange diffchange-inline&quot;&gt;s&lt;/ins&gt;.mesh&amp;lt;/tt&amp;gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;After running this assignment the model &amp;lt;tt&amp;gt;p&amp;lt;/tt&amp;gt; will be able to recompute its &amp;lt;tt&amp;gt;crop_angles&amp;lt;/tt&amp;gt; with reference to its linked surface by:&lt;/div&gt;&lt;/td&gt;&lt;td class='diff-marker'&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;After running this assignment the model &amp;lt;tt&amp;gt;p&amp;lt;/tt&amp;gt; will be able to recompute its &amp;lt;tt&amp;gt;crop_angles&amp;lt;/tt&amp;gt; with reference to its linked surface by:&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>Daniel Castaño</name></author>
		
	</entry>
	<entry>
		<id>https://www.dynamo-em.org//w/index.php?title=Linking_surfaces_into_point_models&amp;diff=1806&amp;oldid=prev</id>
		<title>Daniel Castaño: Created page with &quot; Linking surfaces with point models is an useful way to get initial orientations of particles. The idea is to assign to each &lt;tt&gt;crop_point&lt;/tt&gt; in the general model a &lt;tt&gt;cro...&quot;</title>
		<link rel="alternate" type="text/html" href="https://www.dynamo-em.org//w/index.php?title=Linking_surfaces_into_point_models&amp;diff=1806&amp;oldid=prev"/>
		<updated>2017-07-14T10:36:02Z</updated>

		<summary type="html">&lt;p&gt;Created page with &amp;quot; Linking surfaces with point models is an useful way to get initial orientations of particles. The idea is to assign to each &amp;lt;tt&amp;gt;crop_point&amp;lt;/tt&amp;gt; in the general model a &amp;lt;tt&amp;gt;cro...&amp;quot;&lt;/p&gt;
&lt;p&gt;&lt;b&gt;New page&lt;/b&gt;&lt;/p&gt;&lt;div&gt;&lt;br /&gt;
Linking surfaces with point models is an useful way to get initial orientations of particles. The idea is to assign to each &amp;lt;tt&amp;gt;crop_point&amp;lt;/tt&amp;gt; in the general model a &amp;lt;tt&amp;gt;crop_angle&amp;lt;/tt&amp;gt; that is defined with reference to the support surface. Mathematically, ''Dynamo'' locates the closest triangle in the triangulation of the supporting surface, reads the normal, and formats it to provide the three euler angles needed to crop a particle.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Command line==&lt;br /&gt;
&lt;br /&gt;
Let's assume you have to models in your workspace: &amp;lt;tt&amp;gt;p&amp;lt;/tt&amp;gt; is a general point model, and &amp;lt;tt&amp;gt;s&amp;lt;/tt&amp;gt; is a surface model (for instance of class &amp;lt;tt&amp;gt;membraneByLevels&amp;lt;/tt&amp;gt;)&lt;br /&gt;
&lt;br /&gt;
Make certain that &amp;lt;tt&amp;gt;s&amp;lt;/tt&amp;gt; contains already a depiction triangulation. This is created with the black triangle icon in the workflow for surfaces, or with the method &amp;lt;tt&amp;gt;createMesh&amp;lt;/tt&amp;gt; from the command line.&lt;br /&gt;
&lt;br /&gt;
You can directly link the mesh inside surface  &amp;lt;tt&amp;gt;s&amp;lt;/tt&amp;gt; into points &amp;lt;tt&amp;gt;p&amp;lt;/tt&amp;gt; by:&lt;br /&gt;
&lt;br /&gt;
 &amp;lt;tt&amp;gt;p.linkedSurface = t.mesh.triangulation&amp;lt;/tt&amp;gt;&lt;br /&gt;
&lt;br /&gt;
After running this assignment the model &amp;lt;tt&amp;gt;p&amp;lt;/tt&amp;gt; will be able to recompute its &amp;lt;tt&amp;gt;crop_angles&amp;lt;/tt&amp;gt; with reference to its linked surface by:&lt;br /&gt;
&lt;br /&gt;
 &amp;lt;tt&amp;gt;p.cropAnglesFromLinkedSurface();&amp;lt;/tt&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Linking filaments ===&lt;br /&gt;
This technique can also be used to set orientations defined as normals from a filament. In this case, for a filament model &amp;lt;tt&amp;gt;f&amp;lt;/tt&amp;gt;, the linkage is performed through:&lt;br /&gt;
&lt;br /&gt;
 &amp;lt;tt&amp;gt;p.linkedBackbone = f.backbone&amp;lt;/tt&amp;gt;&lt;/div&gt;</summary>
		<author><name>Daniel Castaño</name></author>
		
	</entry>
</feed>