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"