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)