microscopium illumination correction script

illumination_correction.py

import os
import re

from microscopium import io
from microscopium.preprocess import correct_multiimage_illumination
from microscopium.preprocess import find_background_illumination


def main():
    IMAGE_FILE_PATH = "/data/"
    OUTPUT_FILE_PATH = "/output/"
    ## get valid filenames and build output filenames
    filenames, names_illum = get_valid_file_names(IMAGE_FILE_PATH, OUTPUT_FILE_PATH)
    for i, directory_files in enumerate(filenames):
        run_illum(directory_files, names_illum[i])
        print("Directory processed: ", directory_files[0])


def get_valid_file_names(input_filepath, output_filepath):
    """
    Get full filenames relative to top level directory for each file in the BBBC trial, and
    construct filenames with paths for saving output

    :param filepath: path to the directory containing folders of images
    :return (valid_filenames, illum_filenames): tuple with lists of filenames for reading and saving
                                                                    images
    """
    filename_reg = r'(^Week._.*)(_..._s._w.)(.*)(\.tif)$'

    valid_filenames = []
    illum_filenames = []

    for root, directories, filenames in os.walk(input_filepath):
        current_subdir = root
        new_subdir = []
        new_subdir_illum = []
        for filename in os.listdir(current_subdir):
            match = re.search(filename_reg, filename)
            if match:
               new_subdir.append(os.path.join(root, match.group(1) + match.group(2) + match.group(3) + match.group(4)))
               new_subdir_illum.append("".join([output_filepath, root[51:]]) + "_" + match.group(1) + match.group(2) + match.group(3) + "_illum" + match.group(4))
        if len(new_subdir) != 0 and len(new_subdir_illum) != 0:
               valid_filenames.append(new_subdir)
               illum_filenames.append(new_subdir_illum)

    return (valid_filenames, illum_filenames)


def run_illum(filenames, names_out):
    """
    Find background illumination and correct all images corresponding to elements in filenames.

    Save corrected images using names_out which includes a relative path from the top level directory.

    :param filenames: list of valid filenames with relative paths from top level directory
    :param names_out: list of valid filenames for saving output with relative paths from top level directory
    """
    illum = find_background_illumination(filenames)
    corrected_images = correct_multiimage_illumination(filenames, illum=illum)
    for (image, name) in zip(corrected_images, names_out):
        io.imsave(name, image)


if __name__=='__main__':
    main()