def batch_make_measurements(sourcepath, ext = '*.seq', label = 'curated'): """ To update/remake a measurements table, delete the *.npy and *.measurements files in the `sourcepath`. """ warnings.simplefilter("ignore") from glob import glob from ui.whiskerdata import load_trajectories from trace import Load_Whiskers import summary warnings.simplefilter("default") def get_summary_data( filename, whiskers, trajectories ): if os.path.exists(filename): data = numpy.load(filename) else: data = array(list( summary.features(whiskers) )) numpy.save( filename, data ) return data return summary.commit_traj_to_data_table( trajectories, data ) for name in glob( os.path.join( sourcepath, ext ) ): root,ext = os.path.splitext( name ) prefix = root + '[%s]'%label if not os.path.exists( prefix + '.measurements' ): t,tid = load_trajectories( prefix + '.trajectories' ) print prefix print t.keys() w = Load_Whiskers( prefix + '.whiskers' ) data = get_summary_data( prefix + '.npy', w, t ) MeasurementsTable( data ).update_velocities().save( prefix + '.measurements' )
def load(): from ui.whiskerdata import load_whiskers, load_trajectories from ui.genetiff import Reader movie = Reader('../../data/seq/whisker_data_0140.seq', adjuststipple=1) w, wid = load_whiskers('seq-heal.whiskers') t, tid = load_trajectories('seq-heal.trajectories') #w,wid = load_whiskers('whisk-vc/whisk-vc/seq.whiskers') #movie = Reader('../../data/JF8410_041808_001.tif',adjuststipple=1) #w,wid = load_whiskers('test.whiskers') #w,wid = load_whiskers('results/seq-hand.whiskers') #t,tid = load_trajectories('results/seq-hand.trajectories') return w, t, movie
def load(): from ui.whiskerdata import load_whiskers, load_trajectories from ui.genetiff import Reader movie = Reader("../../data/seq/whisker_data_0140.seq", adjuststipple=1) w, wid = load_whiskers("seq-heal.whiskers") t, tid = load_trajectories("seq-heal.trajectories") # w,wid = load_whiskers('whisk-vc/whisk-vc/seq.whiskers') # movie = Reader('../../data/JF8410_041808_001.tif',adjuststipple=1) # w,wid = load_whiskers('test.whiskers') # w,wid = load_whiskers('results/seq-hand.whiskers') # t,tid = load_trajectories('results/seq-hand.trajectories') return w, t, movie
raise IOError, "Could not find destination path %s"%os.path.split(dst)[0] if not all( map( os.path.exists, args )): raise IOError, "Could not find one or more input source files." if all(map( lambda f: os.path.splitext(f)[-1] in ['.trajectories','.whiskers'], args )): if len(args)==1: src = args[0] tfile = None else: src = args[1] #know the order b.c. already sorted by file extenstion tfile = args[0] w = trace.Load_Whiskers( src ) data = numpy.array(list( summary.features(w, options.face) )) if tfile: t,tid = load_trajectories( tfile ) summary.commit_traj_to_data_table( t, data ) elif all(map( lambda f: os.path.splitext(f)[-1] in ['.trajectories','.measurements'], args )): sources = dict( map( lambda f: (os.path.splitext(f)[-1], f), args ) ) try: data = traj.MeasurementsTable( sources['.measurements'] ).asarray() except KeyError: raise UserException, "A .measurements file must be provided as one of the source files." try: t,tid = load_trajectories( sources['.trajectories'] ) summary.commit_traj_to_data_table( t, data ) except KeyError:
if all( map( lambda f: os.path.splitext(f)[-1] in ['.trajectories', '.whiskers'], args)): if len(args) == 1: src = args[0] tfile = None else: src = args[ 1] #know the order b.c. already sorted by file extenstion tfile = args[0] w = trace.Load_Whiskers(src) data = numpy.array(list(summary.features(w, options.face))) if tfile: t, tid = load_trajectories(tfile) summary.commit_traj_to_data_table(t, data) elif all( map( lambda f: os.path.splitext(f)[-1] in ['.trajectories', '.measurements'], args)): sources = dict(map(lambda f: (os.path.splitext(f)[-1], f), args)) try: data = traj.MeasurementsTable(sources['.measurements']).asarray() except KeyError: raise UserException, "A .measurements file must be provided as one of the source files." try: t, tid = load_trajectories(sources['.trajectories'])