Difference between revisions of "Table column convention"

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=ftype: #10=
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=col 13: ftype (type of fourier sampling)=
Describes the fraction of the Fourier space covered by the particle.
+
Describes the fraction of the Fourier space covered by the particle. Basically it represents the imaging geometry.
 
0 or 'full'  
 
0 or 'full'  
 
1 or 'single'          beam along z, tilt around y
 
1 or 'single'          beam along z, tilt around y
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7 or 'tilt_x_beam_y'    beam along y, tilt around x
 
7 or 'tilt_x_beam_y'    beam along y, tilt around x
  
=Columns 24-26: position in tomogram =
+
For total characterization of the Fourier components covered by the particle, the information in this column needs to be complemented with other columns [14 to 19] depending on the ftype.
 +
 
 +
=cols 24-26: position in tomogram=
 
Given in pixels.
 
Given in pixels.
 +
 +
=col 34: reference=
 +
This column is written by ''Dynamo'' during the computation of a [[multireference alignment project]]. It marks the reference channel that yielded the highest score for the particle.
 +
A "reference" can be seen as a "class" produced by multireference alignment and classification.
 +
 +
=col 35: subreference=
 +
This column is typically written by ''Dynamo'' while creating averages of the particles assigned to different clusters computed through PCA+Kmeans or Hierarchical Ascending Clustering.
 +
Thus, in ''Dynamo'' jargon, "subreference" can be seen as a "class" produced by classification through PCA+ Kmeans or HAC. The name "subreference" comes from the fact that we frequently use PCA analysis on top of the results attained by Multireference Analysis.
 +
  
 
[[Category:Table]]
 
[[Category:Table]]
 
[[Category:Table rows]]
 
[[Category:Table rows]]

Revision as of 09:09, 8 April 2016


col 1: tag

Identifies the particle number.

col 2: align

0 or 1 Used when a table is fed into Dynamoas initial table for an alignment project. Value 1 tells Dynamo that the particle is to be used during an alignment project, values 0 skips the particle. {T|hola}


col 13: ftype (type of fourier sampling)

Describes the fraction of the Fourier space covered by the particle. Basically it represents the imaging geometry. 0 or 'full' 1 or 'single' beam along z, tilt around y 2 or 'singlex' beam along z, tilt around x 3 or 'cone', beam along z 4 or 'double', 'dual' beam along z, tilts around y and x 5 or 'custom' 6 or 'tilt_z_beam_y' beam along y, tilt around z 7 or 'tilt_x_beam_y' beam along y, tilt around x

For total characterization of the Fourier components covered by the particle, the information in this column needs to be complemented with other columns [14 to 19] depending on the ftype.

cols 24-26: position in tomogram

Given in pixels.

col 34: reference

This column is written by Dynamo during the computation of a multireference alignment project. It marks the reference channel that yielded the highest score for the particle. A "reference" can be seen as a "class" produced by multireference alignment and classification.

col 35: subreference

This column is typically written by Dynamo while creating averages of the particles assigned to different clusters computed through PCA+Kmeans or Hierarchical Ascending Clustering. Thus, in Dynamo jargon, "subreference" can be seen as a "class" produced by classification through PCA+ Kmeans or HAC. The name "subreference" comes from the fact that we frequently use PCA analysis on top of the results attained by Multireference Analysis.