Difference between revisions of "Daverage"

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(Created page with " <tt>daverage</tt> is the basic command line option for averaging particles in a data folder using alignment parameters expresed inside a table. == Syntax == The ba...")
 
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=== Options ===
 
=== Options ===
 +
  
 
== Output ==
 
== Output ==
  
 
The output structure has several fields.
 
The output structure has several fields.
 +
*    .average_raw:      <br />  without compensation for overweighting of fourier pixels
 +
 +
*    .average:          <br />  with compensation for the fourier overweighting
 +
 +
*    .fweight:          <br /> map of overrrepresentation of fourier components in  the output property <tt>.average_raw</tt>
 +
 +
*    .fmask:          <br />  binary mask denoting available fourier coefficients
 +
 +
*    .variance:      <br />  variance map
 +
 +
*    .fsc:            <br />  fsc values
 +
 +
*    .fsc_labels:    <br />  useful information to annotate fsc plots
 +
 +
*    .tags:        <br />      list of tags that did actually contribute to the
 +
                        averaging procedure.
 +
*                        This is useful to control which is the final
 +
                        result of confronting which data is available,
 +
                        which tags are marked in the table, and also
 +
                        which particles where excluded.
 +
*    .nanContributions <br />  map with the number of particles that contributed
 +
                        a NaN value for each pixel.
  
  

Revision as of 13:38, 13 October 2017

daverage is the basic command line option for averaging particles in a data folder using alignment parameters expresed inside a table.


Syntax

The basic syntax of the command is:

 output = daverage('myData','t','myTable.tbl');

where output is an structure recording several items (including of course the density map). If you want to use a linux-like notation, you can produce a left-hand-side output wuth the flag ws (short for workspace), i.e.


daverage myData -t myTable.tbl -ws output

Input

Data folder

The location of the particles can be passed through:

Table

A regular Dynamo table, than can be passed as file or numeric matrix.

Options

Output

The output structure has several fields.

  • .average_raw:
    without compensation for overweighting of fourier pixels
  • .average:
    with compensation for the fourier overweighting
  • .fweight:
    map of overrrepresentation of fourier components in the output property .average_raw
  • .fmask:
    binary mask denoting available fourier coefficients
  • .variance:
    variance map
  • .fsc:
    fsc values
  • .fsc_labels:
    useful information to annotate fsc plots
  • .tags:
    list of tags that did actually contribute to the
                       averaging procedure.
  • This is useful to control which is the final
                       result of confronting which data is available,
                       which tags are marked in the table, and also
                       which particles where excluded.
  • .nanContributions
    map with the number of particles that contributed
                       a NaN value for each pixel.


Averaging procedure

Rotation and shift

Normalization

NaN compensation

Missing wedge compensation