print "loading data and tracks from "+prefix+"_TRACKS.npz"
except IOError:
tracksnpz = np.load(locdir+prefix+"_POSITIONS.npz")
print "loading positions data from "+prefix+"_POSITIONS.npz"
data = tracksnpz['data']
if verbose: print "\t...loaded"
try:
cdatanpz = np.load(locdir+prefix+'_CORNER_POSITIONS.npz')
cdata = cdatanpz['data']
if verbose: print "\t...loaded"
except IOError:
print prefix+"_CORNER_POSITIONS.npz file not found, have you run `tracks -lc`?"
if args.orient:
print "calculating orientation data"
from orientation import get_angles_loop
odata, omask = get_angles_loop(data, cdata,
nc=args.ncorners, rc=args.rcorner, drc=args.drcorner)
np.savez(locdir+prefix+'_ORIENTATION.npz',
odata=odata, omask=omask)
if verbose: print '\t...saved'
else:
try:
odatanpz = np.load(locdir+prefix+'_ORIENTATION.npz')
odata = odatanpz['odata']
omask = odatanpz['omask']
except IOError:
print "Cannot find ORIENTATION.npz file, have you run `otracks -o`?"
if args.msd:
msds, msdids = find_msds(dt0, dtau, data, trackids, odata, omask)
elif args.plotmsd:
print "loading msd data from npz files"
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)
else:
trackids = None
if args.orient:
from orientation import get_angles_loop
cfsets = helpy.splitter(cdata, ret_dict=True)
cftrees = { f: KDTree(np.column_stack([cfset['x'], cfset['y']]), leafsize=50)
for f, cfset in cfsets.iteritems() }
meta.update(orient_ncorners=args.ncorners, orient_rcorner=args.rcorner,
orient_drcorner=args.drcorner)
odata, omask = get_angles_loop(pdata, cdata, pfsets, cfsets, cftrees,
nc=args.ncorners, rc=args.rcorner, drc=args.drcorner)
if args.save:
save = absprefix+'_ORIENTATION.npz'
print "saving orientation data to", save
np.savez_compressed(save, odata=odata, omask=omask)
orients = odata['orient']
else:
orients = None
if args.track or args.orient:
data = helpy.initialize_tdata(pdata, trackids, orients)
if args.save:
save = absprefix+"_TRACKS.npz"
print "saving track data to", save
np.savez_compressed(save, data=data)
else:
data = helpy.load_data(absprefix, 'track')
tracksnpz = np.load(locdir + prefix + "_POSITIONS.npz")
print "loading positions data from " + prefix + "_POSITIONS.npz"
data = tracksnpz['data']
if verbose: print "\t...loaded"
try:
cdatanpz = np.load(locdir + prefix + '_CORNER_POSITIONS.npz')
cdata = cdatanpz['data']
if verbose: print "\t...loaded"
except IOError:
print prefix + "_CORNER_POSITIONS.npz file not found, have you run `tracks -lc`?"
if args.orient:
print "calculating orientation data"
from orientation import get_angles_loop
odata, omask = get_angles_loop(data,
cdata,
nc=args.ncorners,
rc=args.rcorner,
drc=args.drcorner)
np.savez(locdir + prefix + '_ORIENTATION.npz',
odata=odata,
omask=omask)
if verbose: print '\t...saved'
else:
try:
odatanpz = np.load(locdir + prefix + '_ORIENTATION.npz')
odata = odatanpz['odata']
omask = odatanpz['omask']
except IOError:
print "Cannot find ORIENTATION.npz file, have you run `otracks -o`?"
if args.msd:
print "loading data and tracks from " + prefix + "_TRACKS.npz"
except IOError:
tracksnpz = np.load(locdir + prefix + "_POSITIONS.npz")
print "loading positions data from " + prefix + "_POSITIONS.npz"
data = tracksnpz['data']
print "\t...loaded"
try:
cdatanpz = np.load(locdir + prefix + '_CORNER_POSITIONS.npz')
cdata = cdatanpz['data']
print "\t...loaded"
except IOError:
print prefix + "_CORNER_POSITIONS.npz file not found, have you run `tracks -lc`?"
if findorient:
print "calculating orientation data"
from orientation import get_angles_loop
odata, omask = get_angles_loop(data, cdata, nc=nc, rc=rc, drc=drc)
np.savez(locdir + prefix + '_ORIENTATION.npz',
odata=odata,
omask=omask)
print '\t...saved'
else:
try:
odatanpz = np.load(locdir + prefix + '_ORIENTATION.npz')
odata = odatanpz['odata']
omask = odatanpz['omask']
except IOError:
print "Cannot find ORIENTATION.npz file, have you run `otracks -o`?"
if findmsd:
msds, msdids = find_msds(dt0, dtau, data, trackids, odata, omask)
elif plotmsd:
print "loading data and tracks from "+prefix+"_TRACKS.npz"
except IOError:
tracksnpz = np.load(locdir+prefix+"_POSITIONS.npz")
print "loading positions data from "+prefix+"_POSITIONS.npz"
data = tracksnpz['data']
print "\t...loaded"
try:
cdatanpz = np.load(locdir+prefix+'_CORNER_POSITIONS.npz')
cdata = cdatanpz['data']
print "\t...loaded"
except IOError:
print prefix+"_CORNER_POSITIONS.npz file not found, have you run `tracks -lc`?"
if findorient:
print "calculating orientation data"
from orientation import get_angles_loop
odata, omask = get_angles_loop(data, cdata, nc=nc, rc=rc, drc=drc)
np.savez(locdir+prefix+'_ORIENTATION.npz',
odata=odata, omask=omask)
print '\t...saved'
else:
try:
odatanpz = np.load(locdir+prefix+'_ORIENTATION.npz')
odata = odatanpz['odata']
omask = odatanpz['omask']
except IOError:
print "Cannot find ORIENTATION.npz file, have you run `otracks -o`?"
if findmsd:
msds, msdids = find_msds(dt0, dtau, data, trackids, odata, omask)
elif plotmsd:
print "loading msd data from npz files"
