for ido

for_ido.py

from pathlib import Path

import numpy as np
import pandas as pd

import starfile
# generate fake data


a = np.random.uniform(0, 200, size=(100, 3))
for f in '123':
    filename = f'data/{f}.csv'
    np.savetxt(filename, a, fmt='%.2f', delimiter=',')

# use pandas to read in text files
# - add tilt series id column
# - give columns meaningful names
dfs = []

files = list(Path('data').glob('*.csv'))

for csv_file in files:
    df = pd.read_csv(csv_file, header=None)
    df = df.rename(columns={0: 'z', 1: 'y', 2: 'x'})
    df['tilt_series_id'] = csv_file.name
    dfs.append(df)

# make one big dataframe
df = pd.concat(dfs)
print(df.columns, df.shape)

# some operation on the cooordinate values
df[['x', 'y', 'z']] = df[['x', 'y', 'z']].to_numpy() * 8

df = df.rename(
    columns={
        'x': 'rlnCoordinateX',
        'y': 'rlnCoordinateY',
        'z': 'rlnCoordinateZ',
        'tilt_series_id': 'rlnTomoName',
    }
)

starfile.write({'particles': df}, 'test.star', overwrite=True)