live_tiffs_generator_.py

"""
Live tiffs generator
====================

Simulation of microscope acquisition. This code generates time series tiffs in
an output directory (must be supplied by the user).
"""


import os
import sys
import time
import argparse

import numpy as np
from skimage import data
import tifffile


parser = argparse.ArgumentParser()
parser.add_argument('outdir', help='output directory for tiffs')
parser.add_argument(
    '--sleep-time',
    help='how long to sleep between volumes, in seconds',
    type=float,
    default=1.0,
)
parser.add_argument(
    '-n', help='total number of volumes', type=int, default=100
)


def main(argv=sys.argv[1:]):
    args = parser.parse_args(argv)
    outdir = args.outdir
    sleep_time = args.sleep_time
    n = args.n
    fractions = np.linspace(0.05, 0.5, n)
    os.makedirs(outdir, exist_ok=True)
    for i, f in enumerate(fractions):
        # We are using skimage binary_blobs which generate's synthetic binary
        # image with several rounded blob-like objects and write them into files.
        curr_vol = 255 * data.binary_blobs(
            length=128, blob_size_fraction=0.05, n_dim=3, volume_fraction=f
        ).astype(np.uint8)
        tifffile.imwrite(
            os.path.join(outdir, f'{i}.tiff'), curr_vol, compress=6
        )
        time.sleep(sleep_time)
    # create a final.log file as an indicator for end of acquisition
    final_file = open(os.path.join(outdir, 'final.log'), 'w')
    final_file.close()


if __name__ == '__main__':
    main()