simple RELION 3.0 to RELION 3.1 data.star conversion

add_optics_block.py

import pandas as pd
import starfile

STAR_FILE = '/path/to/rln30_file.star'

# starfile returns a pandas dataframe for a 'one-block' file
# if you have multiple blocks then
# you get a dictionary of {'block_name': pd.DataFrame)
df = starfile.read(STAR_FILE)

optics_df = pd.DataFrame(
    {
        'rlnOpticsGroup': [1],
        'rlnOpticsGroupName': ['my_optics_group'],
        'rlnImagePixelSize': [1.35],
        'rlnImageSize': [228],
        'rlnImageDimensionality': [3],
        'rlnVoltage': [300],
        'rlnSphericalAberration': [2.7],
    }
)

# add optics group column to rln30 data
df['rlnOpticsGroup'] = 1

# set up and write out output
output_data = {
    'optics': optics_df,
    'particles': df
}

starfile.write(output_data, '/path/to/file/out.star')