create_dpkg.py

# #%L
# Copyright (c) 2016-2017 Cell Migration Standardisation Organization
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"""\
Convert a tracking software output file to a datapackage representation.
"""

import os
import sys
import argparse

# import numpy as np
# import pandas as pd

import biotracks.createdp as createdp
# import biotracks.plot as plot
# import biotracks.pushtopandas as pushtopandas
import biotracks.readfile as readfile
# import biotracks.cmso as cmso
import biotracks.config as config
from biotracks.utils import get_log_level, get_logger


DEFAULT_OUTPUT_BASENAME = 'dp'


def log_level(s):
    try:
        return get_log_level(s)
    except ValueError as e:
        raise argparse.ArgumentTypeError(e.message)


def make_parser():
    parser = argparse.ArgumentParser(description=__doc__)
    parser.add_argument('track_fn', metavar="TRACKING_FILE")
    parser.add_argument("-c", "--config", metavar="FILE", help="config file")
    parser.add_argument("-o", "--out-dir", metavar="DIR", help="output dir")
    parser.add_argument('--log-level', metavar='LEVEL', type=log_level,
                        default='INFO', help='logging level')
    return parser


def main(argv):
    parser = make_parser()
    args = parser.parse_args(argv[1:])
    logger = get_logger('create_dpkg', level=args.log_level, f=sys.stdout)
    input_dir = os.path.dirname(os.path.abspath(args.track_fn))
    if args.out_dir is None:
        args.out_dir = DEFAULT_OUTPUT_BASENAME
    if not args.config:
        args.config = os.path.join(input_dir, config.RELPATH)
        logger.info('Trying default config file location: "%s"', args.config)
    if not os.path.isfile(args.config):
        logger.info('Config file not found, using defaults')
        args.config = None
    conf = config.get_conf(conf_fn=args.config)

    # joint_id = cmso.OBJECT_ID
    # link_id = cmso.LINK_ID
    # track_id = cmso.TRACK_ID

    reader = readfile.TracksReader(
        args.track_fn, conf=conf, log_level=args.log_level
    )
    reader.read()
    createdp.create(reader, args.out_dir, log_level=args.log_level)

    # # push to pandas
    # results_dict = pushtopandas.push_to_pandas(
    #     args.out_dir, joint_id, log_level=args.log_level
    # )
    # logger.debug('Datapackage pushed to pandas')

    # objects = results_dict['objects']
    # links = results_dict['links']
    # tracks = results_dict['tracks']

    # logger.debug('Number of rows: %d', objects.shape[0])
    # logger.debug('Number of columns: %d', objects.shape[1])

    # # aggregation of objects and links for further analytics
    # objects_links = pd.merge(links, objects, how='outer', on=joint_id)
    # # aggregation of tracks as well for further analytics
    # objects_links_tracks = pd.merge(
    #     objects_links, tracks, how='outer', on=link_id
    # )

    # x = cmso.X_COORD
    # y = cmso.Y_COORD
    # frame = cmso.FRAME_ID
    # # basic visualizations
    # objects_links_tracks.sort_values(frame, axis=0, inplace=True)
    # cum_df = plot.compute_cumulative_displacements(
    #     objects_links_tracks, link_id, x, y
    # )
    # plot.plotXY(cum_df, track_id, 'x_cum', 'y_cum')

    # plot.plotXY(cum_df[cum_df[link_id] == 0], track_id, 'x_cum', 'y_cum')
    # plot.plotXY(objects_links_tracks, track_id, x, y)
    # plot.plotXY(objects_links_tracks, link_id, x, y)
    # logger.info(
    #         'normalizing dataset to the origin of the coordinate system...'
    #     )
    # norm = plot.normalize(objects_links_tracks, track_id, x, y)
    # plot.plotXY(norm, track_id, 'x_norm', 'y_norm')
    # plot.plotXY(norm, link_id, 'x_norm', 'y_norm')
    # logger.info('computing displacements in the two directions of motion...')
    # norm = plot.compute_displacements(norm, track_id, x, y)
    # logger.info('computing turning angles...')
    # norm = plot.compute_turning_angle(norm, track_id)
    # theta = pd.DataFrame(norm.ta[~np.isnan(norm.ta)])
    # plot.plot_polar(theta, 10)


if __name__ == "__main__":
    main(sys.argv)