Script to generate a single star file from mod files

mod2star.py

from pathlib import Path
import imodmodel
import starfile
import pandas as pd
import numpy as np

# Create optics dataframe
df_optics = pd.DataFrame({
    'rlnOpticsGroup': [1],
    'rlnOpticsGroupName': ["OpticsGroup1"],
    'rlnSphericalAberration': [2.7],
    'rlnVoltage': [300],
    'rlnImagePixelSize': [5.8],
    'rlnImageDimensionality': [3]
})

# Initialize empty lists to store particle data
micrograph_names = []
x_coords = []
y_coords = []
z_coords = []
optics_groups = []
class_numbers = []

# Process each .mod file
mods = Path("./").glob("*.mod")
for mod in mods:
    # Read the model file
    mod_df = imodmodel.read(mod)

    # Get number of points in this model
    n_points = len(mod_df)

    # Extend all lists with data
    micrograph_names.extend([mod.stem.replace("_5.80Apx", "")] * n_points)
    x_coords.extend(mod_df['x'].tolist())
    y_coords.extend(mod_df['y'].tolist())
    z_coords.extend(mod_df['z'].tolist())
    optics_groups.extend([1] * n_points)
    class_numbers.extend([1] * n_points)

# Create particles dataframe
df_particles = pd.DataFrame({
    "rlnMicrographName": micrograph_names,
    "rlnCoordinateX": x_coords,
    "rlnCoordinateY": y_coords,
    "rlnCoordinateZ": z_coords,
    "rlnOpticsGroup": optics_groups,
    "rlnClassNumber": class_numbers
})

# Prepare star data dictionary
star_data = {
    'optics': df_optics,
    'particles': df_particles
}

# Write the STAR file
starfile.write(star_data, "output.star", overwrite=True)

print(f"Processed {len(micrograph_names)} particles from {len(set(micrograph_names))} micrographs.")