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'])
