Volume list file - Revision history

AlisterBurt: /* Advanced syntax */

2020-04-10T14:24:33Z

Advanced syntax

2019-02-06T11:37:53Z

2019-02-06T11:35:15Z

2019-02-06T11:32:57Z

Creating catalogues

2018-05-03T16:05:23Z

Tomogram numbering

2018-05-03T12:37:08Z

Tomogram numbering

2018-05-03T12:34:22Z

2017-02-23T15:17:54Z

From lists of models

2017-02-23T15:13:34Z

Creating volume list files

2017-02-23T14:57:18Z

@@ Line 22: / Line 22: @@
 # <nowiki>*</nowiki>  Parameter assignation (ftype,ytilt, etc)
 #: * label = testCatalogue_2
-#:* index = 2
+#: * index = 2
 #: * ftype =  1
 #: * xtilt =  -60 60
@@ Line 29: / Line 29: @@
 #: * apix =   1.20
 #: * defocus =   2.40
 #<nowiki>></nowiki>  Crop particles from this source
 #<nowiki>!</nowiki>  Import models from this source

@@ Line 98: / Line 98: @@
 here, {{t|somelist.vll}} can contain [[#Syntax|just tomogram names]] or also  [[#Advanced syntax|attributes]] of each tomogram.
-You can also add a set of new files to a catalogue through this flag, i.e.:
+You can also add a set of new files to a catalogue through the flag <tt>addvll</tt>.:
 <tt>
@@ Line 104: / Line 104: @@
 </tt>
-Here <tt>-c</tt> simply stands for the name of the catalogue into which you want to add new tomograms.
+Here <tt>-c</tt> simply stands for the name of the catalogue into which you want to add new tomograms. Do '''not''' use the  <tt>.ctlg</tt> of the catalogue file.
 == Creating volume list files ==

@@ Line 101: / Line 101: @@
 <tt>
-dcm -c oldCatalogue -fromvll somelist.vll
+dcm -c oldCatalogue -addvll somelist.vll
 </tt>
-Here <tt>-c</tt> simply stands
+Here <tt>-c</tt> simply stands for the name of the catalogue into which you want to add new tomograms.
 == Creating volume list files ==

← Older revision		Revision as of 11:32, 6 February 2019
Line 97:		Line 97:

	here, {{t\|somelist.vll}} can contain [[#Syntax\|just tomogram names]] or also [[#Advanced syntax\|attributes]] of each tomogram.		here, {{t\|somelist.vll}} can contain [[#Syntax\|just tomogram names]] or also [[#Advanced syntax\|attributes]] of each tomogram.
		+
		+	You can also add a set of new files to a catalogue through this flag, i.e.:
		+
		+	<tt>
		+	dcm -c oldCatalogue -fromvll somelist.vll
		+	</tt>
		+
		+	Here <tt>-c</tt> simply stands

	== Creating volume list files ==		== Creating volume list files ==

@@ Line 73: / Line 73: @@
   <nowiki>
 myTomogram1.mrc
-# index 1
+* index = 1
 > myTable1.tbl
 myTomogram2.mrc
-# index 2
+* index = 2
 > myTable2.tbl
 </nowiki>
 </tt>
-The reason is that models are naturally bound to catalogues, and can remember the number that the respective tomogram had in the indexing of a particular catalogue. With tables, the assumption is that the user created them independently from the catalogue, and the column 20 (which represents a volume number) does not necessarily contain a catalogue-aware indexing.
+The reason is that models are naturally bound to catalogues, and can remember the number that the respective tomogram had in the indexing of a particular catalogue. With tables, it is a frequent scenario that the the user created them independently from the catalogue. Thus, the column 20 (which represents a volume number) in a general table does not necessarily contain a catalogue-aware indexing. In such a case, the user does not need to manually edit the 20th column on each table of interest, but can impose independently a tomogram number  with the syntax <tt>* index = 1</tt> like in example above.
 === Through the catalogue ===

@@ Line 68: / Line 68: @@
 ==== Tomogram numbering ====
-It is convenient to make certain that particles from different tomograms remember from which tomogram they were cropped.  This happens automatically when particles are cropped through the catalogue GUI or when the source files indicated with <tt> > </tt> are model files  (with .omd extension).  When the sources are table files, one needs to enforce the tomogram number manually.
+It is convenient to make certain that particles from different tomograms remember from which tomogram they were cropped.  This happens automatically when particles are cropped through the catalogue GUI or when the source files indicated with <tt> > </tt> are model files  (with .omd extension).  When the sources are table files, if volume information is not available one needs to enforce the tomogram number manually.
 <tt>
@@ Line 82: / Line 82: @@
 </tt>
 === Through the catalogue ===

@@ Line 66: / Line 66: @@
 ''Dynamo'' will use {{t|myTable1.tbl}} to crop particles (with a sidelength of 64) from {{t|myTomogram1.mrc}}. For the next volume {{t|myTomogram2.mrc}}It will generate internally a table out of model {{t|myModel_imported.omd}} and use those positions and angles together with the ones in {{t|myTable2.tbl}}.
 The particles will land in a [[data folder]] called {{t|mydata}}, which will include a ''single'' [[cropping table]] that will represent positions and angles merged from {{t|myTable1.tbl}},  {{t|myModel_imported.omd}} and  {{t|myTable2.tbl}}.
 === Through the catalogue ===

@@ Line 95: / Line 95: @@
 After this operation, you can crop particles from the tomograms referred by the models through the command:
   <tt>dtcrop myList.vll reorder 64 myDataFolder </tt>
 ==== By the GUIs ====

← Older revision		Revision as of 14:57, 23 February 2017
Line 80:		Line 80:

	here, {{t\|somelist.vll}} can contain [[#Syntax\|just tomogram names]] or also [[#Advanced syntax\|attributes]] of each tomogram.		here, {{t\|somelist.vll}} can contain [[#Syntax\|just tomogram names]] or also [[#Advanced syntax\|attributes]] of each tomogram.
		+
		+	== Creating volume list files ==
		+
		+	=== From lists of models ===
		+
		+	==== Manually ====
		+
		+	==== By the GUIs ====