PyTom: Create an average

Here, you will learn how to create an average from a particle list with PyTom

Using the UI Server

Not supported yet...

Using a predefined program from pytom/bin

Particle lists are input for the pytom/bin/average.py command

pytom PathToPyTom/bin/average.py -p yourParticleListXML -a pathOfAverage.em

This will generate an average of yourParticleListXML called pathOfAverage.em.

Print all parameters with additional options
pytom PathToPyTom/bin/average.py --help
NAME
    average.py
DESCRIPTION
    Averge a particle. Documentation is available at
	http://www.pytom.org/doc/pytom/average.html
OPTIONS
    -p, --particleList    XML particle list to be averaged. (Is optional: No; Requires arguments: Yes)
    -a, --average    Resulting average filename. (Is optional: No; Requires arguments: Yes)
    --startIndex    Resulting average filename. (Is optional: Yes; Requires arguments: Yes)
    --endIndex    Resulting average filename. (Is optional: Yes; Requires arguments: Yes)
    --infoVolumes    Generate info volumes like wedge volume. (Is optional: Yes; Requires arguments: No)
    --progressbarOff    Display a progressbar. On by default (Is optional: Yes; Requires arguments: No)
    --fromAlignmentList    Average from alignment list XML instead from particleListXML. Optional, off by default. (Is optional: Yes; Requires arguments: Yes)
    --help    Print this help. (Is optional: Yes; Requires arguments: No)
AUTHORS
    Thomas Hrabe
    
Prints all parameters with additional options

Using the PyTom terminal

Using the ipytom command, you can create an average in the terminal:

ipytom
from pytom.basic.structures import ParticleList
pl = ParticleList()
pl.fromXMLFile(yourParticleListXML)
pl.average('averagePath.em')
Will generate an average from a particle list interactively. You can integrate this call into your own scripts.