Difference between revisions of "Daverage"

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<tt> daverage myData -t myTable.tbl -ws output</tt>
+
<tt> daverage myData -t myTable.tbl -ws output</tt>
  
 
== Input==
 
== Input==
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The output structure has several fields.
 
The output structure has several fields.
*   .average_raw:      <br />  without compensation for overweighting of fourier pixels
+
*   <tt> .average_raw:</tt>     <br />  without compensation for overweighting of fourier pixels
 
+
*   <tt> .average: </tt>         <br />  with compensation for the fourier overweighting
*   .average:          <br />  with compensation for the fourier overweighting
+
*   <tt> .fweight:</tt>          <br /> map of overrrepresentation of fourier components in  the output property <tt>.average_raw</tt>
 
+
*   <tt> .fmask: </tt>           <br />  binary mask denoting available fourier coefficients
*   .fweight:         <br /> map of overrrepresentation of fourier components in  the output property <tt>.average_raw</tt>
+
*   <tt> .variance: </tt>       <br />  variance map
 
+
*   <tt> .fsc: </tt>           <br />  fsc values
*   .fmask:          <br />  binary mask denoting available fourier coefficients
+
*   <tt> .fsc_labels: </tt>     <br />  useful information to annotate fsc plots
 
+
*    <tt>.tags:</tt>        <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.
*   .variance:      <br />  variance map
+
*   <tt> .nanContributions <br />  map with the number of particles that contributed a NaN value for each pixel.
 
 
*   .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 13:41, 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===