Convert Class Average MRC File to PNGs

mrc_to_pngs.py

import imageio
import mrcfile
import os
import sys

def make_photos(basename, working_directory="."):
    """
    Convert MRC file with stack of classes to series of scaled PNGs for web viewing.
    Args:
        basename (str): name of desired folder within class_images - usually the same name as the mrc file.
        working_directory (str): the base directory where :py:mod:`live_2d` is working.
    Returns:
        str: Directory path with new PNGs written out.
    """

    if not os.path.isdir(os.path.join(working_directory, "class_images")):
        os.mkdir(os.path.join(working_directory, "class_images"))
    if not os.path.isdir(os.path.join(working_directory, "class_images", basename)):
        os.mkdir(os.path.join(working_directory, "class_images", basename))
    photo_dir = os.path.join(working_directory, "class_images", basename)
    with mrcfile.open(os.path.join(working_directory, "{}.mrc".format(basename)), "r") as stack:
        for index, item in enumerate(stack.data):
            imageio.imwrite(os.path.join(photo_dir, "{}.png".format(index+1)), item)
    return photo_dir

if __name__ == "__main__":
  filename = sys.argv[1]
  assert(filename[-4:] == ".mrc")
  basename = filename[:-4]
  print(make_photos(basename))