fides/run.py at master · Entropy5/fides · GitHub

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"""
pipeline control
usage: CMD python run.py data/7cell0303/
force stop docker with CTRL <
@author: micsla
"""
import logging
import multiprocessing
import platform
import sys
from datetime import datetime

import datasets
from datasets import Datasets

from esimclasses.anomalies import Protrusion, ContractileRing

L = [
    # *Datasets.zygo01,
    # *Datasets.zygo02,
    # *Datasets.zygo03,
    # *Datasets.zygo01b,  # ruffles
    # *Datasets.zygo06,   # ruffles
    # *Datasets.zygo07,   # ruffles
    # *Datasets.old2to4,
    *Datasets.old7cellseries,
    *Datasets.wt02,
    *Datasets.wt07,
    *Datasets.wt08,
    *Datasets.wt08b,
    *Datasets.crm,
    *Datasets.crmb,
]

name_option = None
# name_option = "crm0440"
if len(sys.argv) == 2:
    name_option = sys.argv[1]
if name_option is not None:
    L = [line for line in L if name_option in line[0]]

# L = [["wt/02/wt0204", "wild", 2.8]]
# L = [["7cellseries/7cell0106", "wild", 8.5]]
# L = [["synthetic/syn4loosehullb", "syn", 4, []]]
# L = [["synthetic/syn7realb", "syn", 7.8]]


def run(order):  # check mesh_utils for rotation
    if len(order) == 4:
        ds, series, stage, ano = order  # embryo set, wild type, cell stage, anomalies
    else:
        ds, series, stage = order  # use default anomalies for this stage
        ano = datasets.default_anomalies(stage)

    folder = f'data/{ds}/'
    print(f"Run processing {folder}")
    try:
        if "Linux" in platform.system():
            # from esim import pics  # pics import seems to break optimize
            # pics.process(folder)
            # pics.is_done(folder)
            # from esim import solve_shape
            # solve_shape.optimize(folder, ano)
            pass

        else:
            # from xu import xu_measure, xu_solve, tangent_solve
            # xu_measure.main(folder, stage)
            # xu_solve.main(folder, series, stage)
            # tangent_solve.main(folder, series, stage)
            # from gastru import tissue_solve
            # tissue_solve.main(folder, series, stage)
            # from esim import plot_optimization
            # plot_optimization.plot_opt(folder)
            pass

    except Exception as e:
        logging.exception(e)  # prints stacktrace
        return ds
    return 0


if __name__ == '__main__':
    # res = multiprocessing.Pool(10).map(run, L)  # multithreaded
    res = [run(line) for line in L]  # singlethreaded
    success = sum([r == 0 for r in res])
    problems = [r for r in res if r != 0]

    # from aggregate import aggregate
    # aggregate.datacoverage(L)  # plot embryos and frames
    # df, df_p, df_r = aggregate.summarize(L)  # make dataframes
    # from tests import compare_xu_sim
    # compare_xu_sim.compare(L)
    from gastru import gastru_xu
    gastru_xu.visualize(L)

    print(f"\n--- Run Done - {datetime.utcnow().hour + 2}:{datetime.utcnow().minute} - Processed {success} ---")
    if len(problems) > 0:
        print(f"Something went wrong in {problems}")