def make_data(fmt):
base_dir = os.path.join(EXAMPLES_DIR, fmt, *RELPATHS[fmt][:-1])
in_fn = os.path.join(base_dir, RELPATHS[fmt][-1])
conf_fn = os.path.join(base_dir, config.RELPATH)
conf = config.get_conf(conf_fn=conf_fn)
reader = readfile.TracksReader(in_fn, conf=conf)
d = {'reader': reader}
for k in 'objects', 'links':
d['%s_path' % k] = os.path.join(base_dir, 'dp', '%s.csv' % k)
return d
def make_data(fmt):
base_dir = os.path.join(EXAMPLES_DIR, fmt, *RELPATHS[fmt][:-1])
dp_dir = os.path.join(base_dir, 'dp')
d = {'dp_dir': dp_dir}
d['obj_df'] = pd.read_csv(os.path.join(dp_dir, 'objects.csv'))
d['links_df'] = pd.read_csv(os.path.join(dp_dir, 'links.csv'))
d['tracks_df'] = pd.read_csv(os.path.join(dp_dir, 'tracks.csv'))
conf_fn = os.path.join(base_dir, config.RELPATH)
d['conf'] = config.get_conf(conf_fn=conf_fn)
return d
def make_data(fmt):
base_dir = os.path.join(EXAMPLES_DIR, fmt, *RELPATHS[fmt][:-1])
exp_dp_dir = os.path.join(base_dir, 'dp')
dp_fn = os.path.join(exp_dp_dir, 'dp.json')
dp = datapackage.DataPackage(dp_fn)
in_fn = os.path.join(base_dir, RELPATHS[fmt][-1])
conf_fn = os.path.join(base_dir, config.RELPATH)
conf = config.get_conf(conf_fn=conf_fn)
reader = readfile.TracksReader(in_fn, conf=conf)
reader.read()
return {'reader': reader, 'dp': dp, 'dp_dir': str(tmpdir)}
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)
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)