Walkthrough on creation of 3d scenes - Revision history

Raffaele Coray: /* From the Dynamo web */

2025-12-03T15:45:40Z

From the Dynamo web

2024-12-03T12:45:13Z

From the Dynamo web

2024-12-03T12:44:59Z

From the Dynamo web

2024-12-03T12:44:41Z

From the Dynamo web

2024-12-03T12:41:25Z

From the Dynamo web

2024-12-02T12:56:54Z

2017-11-29T10:46:53Z

Template

2017-11-27T22:14:46Z

2017-11-25T15:22:40Z

Depicting a slice of a tomogram

2017-10-31T11:25:52Z

Depicting a slice of a tomogram

@@ Line 21: / Line 21: @@
 <!--<tt>wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/crop.rec </tt>-->
-  <tt>wget  {{Template:DownloadLinkFHV}} </tt>
+  <tt>wget  {{Template:DownloadLinkFHVDrive}} </tt>
 in a linux shell, or through:
   <!--<tt>curl -O  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/crop.rec </tt>-->
-  <tt>curl -O  {{Template:DownloadLinkFHV}} </tt>
+  <tt>curl -O  {{Template:DownloadLinkFHVDrive}} </tt>
 under MacOS.

@@ Line 29: / Line 29: @@
 under MacOS.
-The table, template and membrane model can be fetched similarly with names
+The table, template and membrane model can be fetched similarly with names <br>
   <!--<nowiki>https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/alignmentLocalRefinement.tbl
 https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/averagedLocalRefinement.em

@@ Line 33: / Line 33: @@
 https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/averagedLocalRefinement.em
 https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/membraneModel.omd</nowiki>-->
- <nowiki>{{Template:DownloadLinkFHValignmentLocalRefinement}}
+{{Template:DownloadLinkFHValignmentLocalRefinement}}<br>
-{{Template:DownloadLinkFHVaveragedLocalRefinement}}
+{{Template:DownloadLinkFHVaveragedLocalRefinement}}<br>
-{{Template:DownloadLinkFHVmembraneModel}}</nowiki>
+{{Template:DownloadLinkFHVmembraneModel}}<br>
 === From your previous work ===

@@ Line 30: / Line 30: @@
 The table, template and membrane model can be fetched similarly with names
-  <nowiki>https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/alignmentLocalRefinement.tbl
+  <!--<nowiki>https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/alignmentLocalRefinement.tbl
 https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/averagedLocalRefinement.em
-https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/membraneModel.omd</nowiki>
+https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/membraneModel.omd</nowiki>-->
 === From your previous work ===

@@ Line 19: / Line 19: @@
 The tomogram can get fetched through:
-−
- <tt>wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/crop.rec </tt>
+<!--<tt>wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/crop.rec </tt>-->
 in a linux shell, or through:
-  <tt>curl -O  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/crop.rec </tt>
+  <!--<tt>curl -O  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/crop.rec </tt>-->
 under MacOS.

← Older revision		Revision as of 12:56, 2 December 2024
Line 1:		Line 1:
	[[Category:Walkthroughs]]		[[Category:Walkthroughs]]
		+
	This walkthrough shows how to create graphic depictions of tomogram contents. Those include:		This walkthrough shows how to create graphic depictions of tomogram contents. Those include:

@@ Line 49: / Line 49: @@
 Fetch the last computed average
-  <tt>ddb localizedFullAngle:rt -r a</tt>
+  <tt>ddb localizedFullAngle:a -r a</tt>
 and write it into disk

@@ Line 43: / Line 43: @@
 and write it to a file
-  <tt>dwrite(t,'alignmentLocalRefinement.tbl')</tt>
+  <tt>dwrite(t,'alignmentLocalRefinement.tbl');</tt>
 ==== Template ====
@@ Line 53: / Line 53: @@
 and write it into disk
-  <tt> dwrite(t,'averagedLocalRefinement.tbl'); </tt>
+  <tt> dwrite(a,'averagedLocalRefinement.em'); </tt>
 ==== Membrane model ====

@@ Line 77: / Line 77: @@
 The easiest way is to just use the <tt>dynamo_slice3d</tt> command, which has a simple syntax. For instance,
-  <tt>o = dslice3d(volume,'r',[40,50,67],'normal','y'): </tt>
+  <tt>o = dslice3d(volume,'r',[40,50,67],'normal','y');</tt>
 will create a slice orthogonal to the 'y' direction that cuts the point [40,50,67], and that by definition will have the full extent of the tomogram. This command is  a wrapper around the class <tt>dpktomo.volume.slices.Slice</tt>. The rest of this section explains how to use objects of this class to get a detailed level of control of the depictede slice.

← Older revision		Revision as of 11:25, 31 October 2017
Line 74:		Line 74:

	== Depicting a slice of a tomogram ==		== Depicting a slice of a tomogram ==
		+
		+	The easiest way is to just use the <tt>dynamo_slice3d</tt> command, which has a simple syntax. For instance,
		+
		+	<tt>o = dslice3d(volume,'r',[40,50,67],'normal','y'): </tt>
		+
		+	will create a slice orthogonal to the 'y' direction that cuts the point [40,50,67], and that by definition will have the full extent of the tomogram. This command is a wrapper around the class <tt>dpktomo.volume.slices.Slice</tt>. The rest of this section explains how to use objects of this class to get a detailed level of control of the depictede slice.

	=== The slice object ===		=== The slice object ===