Postprocessing plugins - Revision history

Daniel Castaño at 17:07, 9 March 2017

2017-03-09T17:07:30Z

2017-03-03T16:33:24Z

Applications of plugins

2017-03-03T16:31:40Z

2017-03-03T15:37:41Z

2017-03-03T13:12:11Z

2017-03-03T12:56:10Z

2017-03-03T12:54:42Z

2017-03-03T12:42:22Z

2017-03-03T11:35:39Z

2017-03-03T11:28:55Z

@@ Line 120: / Line 120: @@
 and put it inside your matlab path.
-<nowiki>
+ <nowiki>
 function dynamo_plugin_post_frozenTemplate(file_card);

@@ Line 6: / Line 6: @@
 * [Simple] Online definition of mask, depending on the average computed in the iteration.
-* [Simple] Online definition of symmetrization operator.
+* [Simple] Taylored definition of [[Example of post processing plugin with template update | symmetrization operator]].
 * [Simple] User-defined thresholding for subtomograms from different tomograms.
 * [Medium] Resolution dependent scanning of angular scan parameters.
 * [Medium] Customization of golden-standard policy.
 * [Advanced] Fine tuning of [[MRA]] policy by PCA classification after each iteration.
 == Naming of a plugin script==

@@ Line 82: / Line 82: @@
 * <tt>refined_table</tt>
 * <tt>average</tt>
 They represent the results of the iteration in course. Also, they are passed to the next iteration to produce the starting positions and reference for the next computation.
@@ Line 97: / Line 96: @@
 </nowiki>
+Nopte that you can get  the indices of the references that are still alive in the current iteraration by:
 ==== In a non-matlab executable ====

@@ Line 93: / Line 93: @@
   <nowiki>
-fileTable   =
+fileTable   =  dynamo_database_locate('refine_table',vpr,'ite',1,'ref',1);
-fileAverage =
+fileAverage =  dynamo_database_locate('average',vpr,'ite',1,'ref',1);
 </nowiki>
@@ Line 119: / Line 119: @@
 and put it inside your matlab path.
 <nowiki>
@@ Line 154: / Line 152: @@
 backUpLocation=dynamo_database_locate('average',vpr,'ite',...
          ite,'ref',ref,'prepend','OLD');
 % nwo we set our own file in the database position for the result of the

@@ Line 50: / Line 50: @@
   <tt>function dynamo_plugin_post_example(iterationCard);
 ===Location of iteration and round ===
@@ Line 91: / Line 89: @@
 Both <tt>refined_table</tt> and <tt>average</tt> are identified by iteration and reference number (in case you have a multireference project);
 ==== In a non-matlab executable ====
@@ Line 103: / Line 110: @@
 ==Example script==

@@ Line 3: / Line 3: @@
 ==Applications of plugins==
-Users have reported the use of plugins in very different scenarios and with very different levels of complexity. Here some examples:
+Users have devised the use of plugins in very different scenarios and with very different levels of complexity. We just mention below some some examples. In square bracket we describe the difficulty of the writing the interface between the plugin and ''Dynamo'', not the complexity of the plugin itself.
-* Online definition of mask, depending on the average computed in the iteration.
+* [Simple] Online definition of mask, depending on the average computed in the iteration.
-* Online definition of symmetrization operator;
+* [Simple] Online definition of symmetrization operator;
-* Customization of golden-standard policy.
+* [Simple] User-defined thresholding for subtomograms from different tomograms.
-* Fine tuning of [[MRA]] policy by PCA classification after each iteration.
+* [Medium ]Customization of golden-standard policy.
 ==Naming of a plugin script==

@@ Line 74: / Line 74: @@
 ===The project database===
 ==== In Matlab====
 ==== In a non-matlab executable ====
@@ Line 82: / Line 95: @@
 # providing the right paths for all project items
 # using their own IO tools to read and write map and table files.
 ==Example script==

← Older revision		Revision as of 11:28, 3 March 2017
Line 50:		Line 50:

	===Location of iteration and round ===		===Location of iteration and round ===
		+
		+	<nowiki>
		+	scard=dynamo_read(iterationCard);
		+
		+	% 1 from which iteration it is being executed:
		+	ite = scard.database_ite;
		+
		+	% 2 from which project it is being invoked
		+	name_projec t= scard.name_project;
		+
		+	% 3 we read the corresponding virtual project
		+	vpr=dynamo_vpr_load(name_project)
		+	</nowiki>

	===The project database===		===The project database===