Average subtomograms - SBC-Utrecht/PyTom GitHub Wiki

Create an average

Average using average.py

After reconstructing the subtomogram it may be handy to average them, in particular if they are aligned to some extent. To this end you can use the following command:
pytom PathToPyTom/bin/average.py -p yourParticleListXML -a pathOfAverage.em
This will generate an average of yourParticleListXML called pathOfAverage.em. Here are the possible parameters: 
NAME
    average.py
DESCRIPTION
    Average 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
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