fontsize='x-large')
if xlim is not None:
plt.xlim(*xlim)
if ylim is not None:
plt.ylim(*ylim)
if show_legend: plt.legend(loc='best')
if save is True:
save = prefix + "_MS{}D.pdf".format('A' if ang else '')
if save:
print "saving to", save
plt.savefig(save)
if show: plt.show()
return [fig] + fig.get_axes() + [taus] + [msd, msd_err] if errorbars else [msd]
if __name__=='__main__':
helpy.save_log_entry(absprefix, 'argv')
meta = helpy.load_meta(absprefix)
if args.load:
datapath = absprefix+'_CORNER'*args.corner+'_POSITIONS.txt'
helpy.txt_to_npz(datapath, verbose=True, compress=True)
if args.orient or args.track:
print 'NOTICE: not tracking, only converting file from txt to npz'
print ' please run again without `-l` to track/orient'
sys.exit()
if args.track or args.orient:
from scipy.spatial import cKDTree as KDTree
if args.track != args.orient and helpy.bool_input("Would you like to "
"simultaneously track and find orientations? (It's faster)\n"):
args.track = args.orient = True
if args.orient:
if not os.path.exists(outdir):
print "Creating new directory", outdir
os.makedirs(outdir)
if args.output.endswith('.gz'):
args.gz = 1
args.output = args.output[:-3]
if args.output.endswith('.txt'):
args.output = args.output[:-4]
if args.output.endswith(suffix):
prefix = args.output[:-len(suffix)]
else:
prefix = args.output
args.output += suffix
outputs = args.output, prefix + '_CORNER' + suffix
helpy.save_log_entry(prefix, argv)
meta = helpy.load_meta(prefix)
imdir = prefix + '_detection'
if not os.path.isdir(imdir):
os.makedirs(imdir)
kern_area = np.pi * args.kern**2
sizes = {
'center': {
'max_ecc': args.ecc,
'min_area': args.min or int(kern_area // 2),
'max_area': args.max or int(kern_area * 2 + 1),
'kern': args.kern,
'thresh': args.thresh
}
if not os.path.exists(outdir):
print "Creating new directory", outdir
os.makedirs(outdir)
if args.output.endswith('.gz'):
args.gz = 1
args.output = args.output[:-3]
if args.output.endswith('.txt'):
args.output = args.output[:-4]
if args.output.endswith(suffix):
prefix = args.output[:-len(suffix)]
else:
prefix = args.output
args.output += suffix
outputs = args.output, prefix + '_CORNER' + suffix
helpy.save_log_entry(prefix, argv)
meta = helpy.load_meta(prefix)
imdir = prefix + '_detection'
if not os.path.isdir(imdir):
os.makedirs(imdir)
kern_area = np.pi*args.kern**2
sizes = {'center': {'max_ecc': args.ecc,
'min_area': args.min or int(kern_area//2),
'max_area': args.max or int(kern_area*2 + 1),
'kern': args.kern,
'thresh': args.thresh}}
if args.ckern:
args.both = True
if args.both:
arg('--noplot', action='store_false', dest='plot',
help="Don't generate (fewer, not none at this point) figures")
arg('-z', '--zoom', metavar="ZOOM", type=float,
help="Factor by which to zoom out (in if ZOOM < 1)")
arg('-v', '--verbose', action='count', help='Be verbose, may repeat: -vv')
args = parser.parse_args()
if not args.verbose:
from warnings import filterwarnings
filterwarnings('ignore', category=RuntimeWarning,
module='numpy|scipy|matplot')
if '*' in args.prefix or '?' in args.prefix:
prefix_pattern = args.prefix
args.prefix = helpy.replace_all(args.prefix, '*?', '') + '_MRG'
helpy.save_log_entry(args.prefix, 'argv')
prefixes = [p[:-9] for p in glob.iglob(
helpy.with_suffix(prefix_pattern, '_MELT.npz'))]
metas, mdatas = zip(*[(helpy.load_meta(prefix),
helpy.load_data(prefix, 'm'))
for prefix in prefixes])
for meta, mdata in zip(metas, mdatas):
mdata['f'] = mdata['f'].astype(int) - int(meta['start_frame'])
mdata = np.concatenate(mdatas)
meta = helpy.merge_meta(metas, excl={'start_frame'},
excl_start=('center', 'corner'))
if args.save:
np.savez_compressed(args.prefix+'_MELT', data=mdata)
helpy.save_meta(args.prefix, meta, merged=prefixes)
print 'merged sets', prefixes, 'saved to', args.prefix
else:
metavar="ZOOM",
type=float,
help="Factor by which to zoom out (in if ZOOM < 1)")
arg('-v', '--verbose', action='count', help='Be verbose, may repeat: -vv')
args = parser.parse_args()
if not args.verbose:
from warnings import filterwarnings
filterwarnings('ignore',
category=RuntimeWarning,
module='numpy|scipy|matplot')
if '*' in args.prefix or '?' in args.prefix:
prefix_pattern = args.prefix
args.prefix = helpy.replace_all(args.prefix, '*?', '') + '_MRG'
helpy.save_log_entry(args.prefix, 'argv')
prefixes = [
p[:-9]
for p in glob.iglob(helpy.with_suffix(prefix_pattern, '_MELT.npz'))
]
metas, mdatas = zip(*[(helpy.load_meta(prefix),
helpy.load_data(prefix, 'm'))
for prefix in prefixes])
for meta, mdata in zip(metas, mdatas):
mdata['f'] = mdata['f'].astype(int) - int(meta['start_frame'])
mdata = np.concatenate(mdatas)
meta = helpy.merge_meta(metas,
excl={'start_frame'},
excl_start=('center', 'corner'))
if args.save:
np.savez_compressed(args.prefix + '_MELT', data=mdata)
