Difference between revisions of "Tomogram-table map file"

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(Created page with "A tomogram table map file is a text file with extension <tt>.doc</tt> that shows the names of the tomogram files referred by a table in its column 20. Tomogram <tt>1...")
 
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A tomogram table map file is a text file with extension <tt>.doc</tt> that shows the names of the tomogram files  referred by a [[table]] in its column 20.
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A tomogram table map file is a text file with extension <tt>.doc</tt> that shows the names of the tomogram files  referred by a [[table]] in its column 20 (reserved for this goal).
  
Tomogram 
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An example file could be:
  
 
  <tt>1  /Users/casdanie/test/tomogram_01.mrc </tt>
 
  <tt>1  /Users/casdanie/test/tomogram_01.mrc </tt>
 
  <tt>2  /Users/casdanie/test/tomogram_02.mrc </tt>
 
  <tt>2  /Users/casdanie/test/tomogram_02.mrc </tt>
  <tt>3   /Users/casdanie/test/tomogram_03.mrc </tt>
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  <tt>5   /Users/casdanie/test/tomogram_03.mrc </tt>
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to go along with a table that has only values  1, 2 and 5 in its column 20.
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==Producing tomograp-table map files==
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Such files are created automatically during [[particle extraction]] through the catalogue.  In the [[data folder]] created by ''Dynamo'' as result of an extraction, you should get a file called <tt>indices_column20.doc</tt> with this format.
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They are regular text files and can be normally edited. The only restriction is that they are expected to have the extension <tt>.doc</tt>
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==Using tomograp-table map files==
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These files can be used to directly crop particles from set of tomograms without entering into the catalogue system. You can use the {{docfunction|dynamo_table_crop| dtcrop}}command with the syntax:
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<tt> dtcrop <tomogram-table map file> <table> <sidelength> <target folder> </tt>
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(and the additional flags you may require)

Revision as of 10:56, 23 June 2016

A tomogram table map file is a text file with extension .doc that shows the names of the tomogram files referred by a table in its column 20 (reserved for this goal).

An example file could be:

1   /Users/casdanie/test/tomogram_01.mrc 
2   /Users/casdanie/test/tomogram_02.mrc 
5   /Users/casdanie/test/tomogram_03.mrc 

to go along with a table that has only values 1, 2 and 5 in its column 20.

Producing tomograp-table map files

Such files are created automatically during particle extraction through the catalogue. In the data folder created by Dynamo as result of an extraction, you should get a file called indices_column20.doc with this format.

They are regular text files and can be normally edited. The only restriction is that they are expected to have the extension .doc


Using tomograp-table map files

These files can be used to directly crop particles from set of tomograms without entering into the catalogue system. You can use the dtcropcommand with the syntax:

dtcrop <tomogram-table map file> <sidelength> <target folder> </tt> (and the additional flags you may require)