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:
pdata, cdata = helpy.load_data(absprefix, 'position corner')
else:
pdata = helpy.load_data(absprefix, 'position')
pfsets = helpy.splitter(pdata, ret_dict=True)
pftrees = { f: KDTree(np.column_stack([pfset['x'], pfset['y']]), leafsize=50)
for f, pfset in pfsets.iteritems() }
if args.track:
meta.update(track_sidelength=args.side, track_maxdist=args.maxdist,
track_maxtime=args.giveup, track_stub=args.stub,
track_cut=args.cut)
trackids = find_tracks(pdata, maxdist=args.maxdist, giveup=args.giveup,
n=args.number, cut=args.cut, stub=args.stub)
trackids = remove_duplicates(trackids, data=pdata)
if first.endswith(']'):
first, _, args.slice = first[:-1].rpartition('[')
if os.path.isdir(first):
first = os.path.join(first, '*.tif')
filenames = sorted(glob(first))
if args.slice:
args.slice = helpy.parse_slice(args.slice, len(filenames))
filenames = filenames[args.slice]
filepattern = first
first = filenames[0]
argv = 'argv'
if args.plot > 1:
if len(filenames) > 10:
print "Are you sure you want to make plots for all",
print len(filenames), "frames?",
args.plot -= not helpy.bool_input()
if args.plot > 2 and (not args.save or len(filenames) > 2):
print "Do you want to display all the snapshots without saving?",
args.plot -= not helpy.bool_input()
suffix = '_POSITIONS'
outdir = os.path.abspath(os.path.dirname(args.output))
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):
if first.endswith(']'):
first, _, args.slice = first[:-1].rpartition('[')
if os.path.isdir(first):
first = os.path.join(first, '*.tif')
filenames = sorted(glob(first))
if args.slice:
args.slice = helpy.parse_slice(args.slice, len(filenames))
filenames = filenames[args.slice]
filepattern = first
first = filenames[0]
argv = 'argv'
if args.plot > 1:
if len(filenames) > 10:
print "Are you sure you want to make plots for all",
print len(filenames), "frames?",
args.plot -= not helpy.bool_input()
if args.plot > 2 and (not args.save or len(filenames) > 2):
print "Do you want to display all the snapshots without saving?",
args.plot -= not helpy.bool_input()
suffix = '_POSITIONS'
outdir = os.path.abspath(os.path.dirname(args.output))
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):
from glob import glob
filenames = sorted(glob(first))
filepattern = first
argv = 'argv'
elif len(args.files) > 1:
filenames = sorted(args.files)
filepattern = reduce(helpy.str_union, args.files)
i = sys.argv.index(first)
argv = filter(lambda s: s not in filenames, sys.argv)
argv.insert(i, filepattern)
argv[0] = path.basename(argv[0])
argv = ' '.join(argv)
if args.plot and len(filenames) > 10:
args.plot = helpy.bool_input(
"Are you sure you want to make plots for all {} frames?"
" ".format(len(filenames)))
suffix = '_POSITIONS'
gz = args.gz
output = args.output
outdir = path.abspath(path.dirname(output))
if not path.exists(outdir):
print "Creating new directory", outdir
makedirs(outdir)
if output.endswith('.gz'):
gz = 1
output = output[:-3]
if output.endswith('.txt'):
output = output[:-4]
if output.endswith(suffix):
