Filament model - Revision history

Daniel Castaño: /* Types of filaments */

2016-08-15T14:29:56Z

Types of filaments

2016-08-15T14:24:45Z

2016-08-15T14:21:46Z

Types of filaments

2016-08-15T13:54:18Z

Types of filaments

2016-08-15T13:52:49Z

Types of filaments

2016-08-15T13:52:29Z

Geometric computation stage

2016-08-15T12:40:21Z

2016-08-15T12:34:21Z

2016-08-15T12:28:48Z

2016-08-15T11:57:33Z

@@ Line 54: / Line 54: @@
 # randomlly distributed in the tube of the filament.
-[[File:filamentTypes.png|thumb|center|upright|800px|Crop positions generated by the different filament types. The central points are common in all types.]]
+[[File:filamentTypes.png|thumb|center|upright|800px|Crop positions generated by the different filament types. The central points are common in all types. Matlab syntax can be consulted [[Filament types code example here]] ]]
 ====<tt>filamentWithTorsion</tt>====

← Older revision		Revision as of 14:24, 15 August 2016
Line 102:		Line 102:
	: uses the geometrical parameters of the model: <tt>dz</tt>, <tt>dphi</tt>, etc....		: uses the geometrical parameters of the model: <tt>dz</tt>, <tt>dphi</tt>, etc....
	* <tt>saveIntoCatalogue</tt>		* <tt>saveIntoCatalogue</tt>
		+
		+	The syntax for invoking these models can be consulted in this [[Filament types code example \| matlab code example]] .

@@ Line 53: / Line 53: @@
 # in rings orthogonal to the path, pointing outwards.
 # randomlly distributed in the tube of the filament.
 [[File:filamentTypes.png|thumb|center|upright|800px|Crop positions generated by the different filament types. The central points are common in all types.]]
@@ Line 61: / Line 60: @@
 Parameters:
-* <tt>subunits_dz</tt>   distance of the subunits along the backbone (in pixels)
+* <tt>subunits_dz</tt>   distance of the subunits along the backbone (in pixels).
 *<tt> subunits_dphi</tt> torsion between subunits (in degrees).
 ====<tt>filamentSubunitsOnHelix</tt>====
@@ Line 69: / Line 68: @@
 Parameters:
-* <tt>dz</tt>   distance of the subunits along the backbone (in pixels)
+* <tt> subunits_dz </tt>   distance of the subunits along the backbone (in pixels).
-* <tt>dphi</tt> angular distance between the subunits (in degrees)
+* <tt> subunits_dphi </tt> angular distance between the subunits (in degrees) .
-* <tt>radius</tt> distance of the subunits to the backbone (in pixels)
+* <tt>radius</tt> distance of the subunits to the backbone (in pixels).
 === Computation of the particles ===

← Older revision		Revision as of 13:54, 15 August 2016
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−	[[File:filamentTypes.png\|thumb\|upright\|800px\| ~~Opening~~ the ~~model workflow from <tt>dtmslice</tt>~~]]	+	[[File:filamentTypes.png\|thumb\|center\|upright\|800px\|Crop positions generated by the different filament types. The central points are common in all types.]]

	====<tt>filamentWithTorsion</tt>====		====<tt>filamentWithTorsion</tt>====

@@ Line 55: / Line 55: @@
-[File:filamentTypes.png|thumb|upright|800px| Opening the model workflow from <tt>dtmslice</tt>]]
+[[File:filamentTypes.png|thumb|upright|800px| Opening the model workflow from <tt>dtmslice</tt>]]
 ====<tt>filamentWithTorsion</tt>====
@@ Line 72: / Line 72: @@
 * <tt>dphi</tt> angular distance between the subunits (in degrees)
 * <tt>radius</tt> distance of the subunits to the backbone (in pixels)
 === Computation of the particles ===

@@ Line 76: / Line 76: @@
 ==== Using a workflow tool  ====
-The <tt>Active model</tt> option in <tt>dtmslice</tt> includes the option <it>Step-by-step workflow for model</it>.
+The <tt>Active model</tt> option in <tt>dtmslice</tt> includes the option ''Step-by-step workflow for model''.
 {|style="margin: 0 auto;"
@@ Line 84: / Line 84: @@
 ==== Programmatically ====
 The methods used for the processing of a filament objects are typically:
-; <tt>createBackbone</tt>
+* <tt>createBackbone</tt>
-; <tt>updateCrop</tt>
+: derives a smooth backbone that interpolates the <tt>points</tt> introduced by the user.
-; <tt>saveIntoCatalogue</tt>
+: normally does not require to change any parameter.

@@ Line 44: / Line 44: @@
 ==Geometric computation stage==
+The manually introduced points need to be converted into particle points.
 === Types of filaments ===
-Different models are provided to account for different ways of relating particles to the points provided by the user during the input stage.
+Different models are provided to account for different ways of relating particles to the points provided by the user during the input stage:
 ====<tt>filamentWithTorsion</tt>====
@@ Line 76: / Line 80: @@
 {|style="margin: 0 auto;"
 | [[File:filamentSelectWorkflow.png|thumb|upright|400px| Opening the model workflow from <tt>dtmslice</tt>]]
-| [[File:FilamentWorkflowStart.png|thumb|upright|400px| Workflow steps]]
+| [[File:FilamentWorkflowStart.png|thumb|upright|400px| Workflow steps on a workflow GUI opened onto an unprocessed filament model]]
 |}
 ==== Programmatically ====

@@ Line 28: / Line 28: @@
 You can also select a sidelength different to the default value of 32. Here, the units are pixels.
-[[File:filamentControls.png|thumb|right|300px| Control for creating filament sections in <tt>dtmslice</tt>]]
+[[File:filamentControls.png|thumb|center|300px| Control for creating filament sections in <tt>dtmslice</tt>]]
 After clicking the [extract] button, two things will happen:
 # An animation on the <tt>dtmslice</tt> scene will show the sections that will be extracted (using a small cyan rectangle).
 # The sections will appear as a montage in a new window.
-[[File:filamentSliceClickReady.png|thumb|right|300px|Popup window with the created sections.]]
+[[File:filamentSliceClickReady.png|thumb|center|300px|Popup window with the created sections.]]
 ==== Define section centers ====
@@ Line 40: / Line 40: @@
-[[File:filamentUpdatePointsThroughSliceClick.png|thumb|right|300px|Each click on a section in the montage determines a 3d point added to the model.]]
+[[File:filamentUpdatePointsThroughSliceClick.png|thumb|center|300px|Each click on a section in the montage determines a 3d point added to the model.]]
 ==Geometric computation stage==