Membrane models - Revision history

Daniel Castaño: /* Cropping mesh */

2017-02-28T10:18:39Z

Cropping mesh

Daniel Castaño: /* Through montage viewer */

2017-02-27T16:20:14Z

Through montage viewer

Daniel Castaño at 16:18, 27 February 2017

2017-02-27T16:18:56Z

Daniel Castaño: /* Command line */

2017-02-01T17:07:21Z

Command line

Daniel Castaño at 16:57, 1 February 2017

2017-02-01T16:57:16Z

Daniel Castaño at 16:56, 1 February 2017

2017-02-01T16:56:38Z

Daniel Castaño at 16:53, 1 February 2017

2017-02-01T16:53:49Z

Daniel Castaño at 16:51, 1 February 2017

2017-02-01T16:51:41Z

Daniel Castaño: /* Workflow from the command line */

2017-02-01T16:27:29Z

Workflow from the command line

Daniel Castaño at 16:00, 1 February 2017

2017-02-01T16:00:02Z

@@ Line 65: / Line 65: @@
 # Refine the supporting triangulation one (or more)  step(s) further, or
 # Provide a smaller value for <tt>crop_mesh_parameter</tt>
 ==  Table points ==

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 This procedure works well when you don't need a lot precision when moving to a ''z'' plane to the next one.
-== Through montage viewer ==
+== Through the montage viewer ==
-{{ main | main montage | montage viewer for membrane picking }}
+{{ main | montage viewer for membrane picking | montage viewer for membrane picking}}
 This option is more complicated to learn, but it pays off in several situations:

@@ Line 1: / Line 1: @@
 The input of a membrane model is a set of points defined typically in several z-slices of a tomogram. Through the workflow specific for this model geometry, ''Dynamo'' will create a smooth continuous surface that represents the membrane.
 The output is a set of crop points and orientations. Each orientation will point in the direction of the outwards normal. The membrane model '''needs''' to have a center defined, which is merely used to defined the laterality of the surface (which side is "inward" and which side is "outward" )
 = Workflow description=

@@ Line 45: / Line 45: @@
 = Command line =
 The methods that represent the steps are:
-* <tt>createControl</tt>
+* <tt>controlUpdate</tt>
 *<tt>createMesh</tt>
 *<tt>refineMesh</tt>

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 The original points need to have been picked in the right order on each z-level.<br>
 They are stored in the <tt>crop_points</tt> property of the model.
 == Supporting mesh ==
 The continuous membrane will be represented by a triangulation, stored in the <tt>mesh</tt> property of the model.
 == Refining the supporting mesh==
 Each refinement step subdivides the triangulation stored in the <tt>mesh</tt> property of the model.
 ==  Cropping mesh ==
@@ Line 45: / Line 39: @@
 # Refine the supporting triangulation one (or more)  step(s) further, or
 # Provide a smaller value for <tt>crop_mesh_parameter</tt>
 ==  Table points ==
 This is merely a formatting step. In this point is crucial that the <tt>center</tt> property in the model has been already defined.
 = Command line =

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 # Extraction of the table points.
 The property <tt>center</tt> must have been defined.
-[[File:.png|thumb|center|300px| User points (plot with method <tt>plotPoints</tt>]]
 == Control points==
 Control points are equispaced points distributed along all user points defined for a same level (typically ''z''). They are used as vertices for the initial triangulation that will be used to represent the continuous surface. <br>
 The original points need to have been picked in the right order on each z-level.<br>
 They are stored in the <tt>crop_points</tt> property of the model.
@@ Line 30: / Line 34: @@
 == Supporting mesh ==
 The continuous membrane will be represented by a triangulation, stored in the <tt>mesh</tt> property of the model.
-[[File:.png|thumb|center|300px| Control points]]
 == Refining the supporting mesh==
 Each refinement step subdivides the triangulation stored in the <tt>mesh</tt> property of the model.
-[[File:.png|thumb|center|300px| Control points]]
 ==  Cropping mesh ==
 A new triangulation (property <tt>crop_mesh</tt>) will be defined on top of the membrane defined in the previous step. The final cropping points will be located in the centers of these triangles. The triangulation procedure will try to create these points on a regular distribution with a given average distance. This average distance is provided in pixels as property <tt>crop_mesh_parameter</tt>
@@ Line 39: / Line 45: @@
 # Refine the supporting triangulation one (or more)  step(s) further, or
 # Provide a smaller value for <tt>crop_mesh_parameter</tt>
-[[File:.png|thumb|center|300px| Control points]]
 ==  Table points ==
 This is merely a formatting step. In this point is crucial that the <tt>center</tt> property in the model has been already defined.
-[[File:.png|thumb|center|300px| Control points]]
 = Command line =

@@ Line 36: / Line 36: @@
 *<tt>createMesh</tt>
 *<tt>refineMesh</tt>
-*<tt>createCropMesh</tt>
+*<tt>createCropMesh</tt><br />whose main parameter is <tt>crop_mesh_parameter</tt>
 *<tt>updateCrop</tt>
 An example can be found in [[Example of membrane model workflow through the command line]]