def get_saccades(flydra_db_directory, db_group, interval):
with safe_flydra_db_open(flydra_db_directory) as db:
saccades = db.get_table_for_group(db_group, 'saccades')
logger.info('Found %d saccades for group %r.' % (len(saccades), db_group))
if len(saccades) == 0:
raise Exception('No saccades found for group %r.' % db_group)
# make sure we use array
saccades = np.array(saccades)
for s in saccades:
check_saccade_is_well_formed(s)
saccades = add_position_information(saccades) # XXX: using default arena size
def test(saccade):
return (saccade['distance_from_wall'] >= interval[0] and
saccade['distance_from_wall'] <= interval[1])
include = map(test, saccades)
select = saccades[np.array(include)]
logger.info(' of which %d saccades are in interval %g <= d <= %g.' %
(len(select), interval[0], interval[1]))
if len(select) == 0:
raise Exception('No saccades in interval %g <= d <= %g' %
interval )
return select
def detect_angvel(argv):
pdb.set_trace()
np.seterr(all='raise')
parser = LenientOptionParser(usage=usage)
parser.add_option("--db", help="FlydraDB directory.")
parser.add_option(
"--version",
default='smooth',
type='string',
help="[=%default] Which version of the 'rows' table to use.")
parser.add_option("--saccades_table_version",
default='angvel',
type='string',
help='[=%default] Version of output saccades tables.')
parser.add_option("--nocache",
help="Ignores already computed results.",
default=False,
action="store_true")
parser.add_option("--out",
help="Output directory for graphic representation.")
parser.add_option("--fps", help="Recording framerate")
fps = parser.parse_args(args='--fps', type='float')
# detection parameters
dt = 1.0 / 60 # XXX: read from file
warnings.warn('Using fixed dt = %s.' % dt)
parser.add_option("--deltaT_inner_sec",
default=4 * dt,
type='float',
help="Inner interval [= %default]")
parser.add_option("--deltaT_outer_sec",
default=10 * dt,
type='float',
help="Outer interval [= %default]")
parser.add_option("--min_amplitude_deg",
default=25,
type='float',
help="Minimum saccade amplitude (deg) [= %default]")
parser.add_option("--min_linear_velocity",
default=0.1,
type='float',
help="Minimum linear velocity when"
" saccading (m/s) [= %default]")
parser.add_option("--max_linear_acceleration",
default=20,
type='float',
help="Maximum linear acceleration when saccading "
"(m/s^2) [= %default]")
parser.add_option("--max_angular_velocity",
default=8000,
type='float',
help="Maximum angular velocity when saccading"
" (deg/s) [= %default]")
parser.add_option("--max_orientation_dispersion_deg",
default=15,
type='float',
help="Maximum dispersion (deg) [= %default]")
parser.add_option("--minimum_interval_sec",
default=10 * dt,
type='float',
help="Minimum interval between saccades. [= %default]")
(options, args) = parser.parse_args(argv)
if not options.db:
raise Exception('No flydra DB directory specified.')
if args:
raise Exception('Spurious arguments')
# Create processed string
processed = get_computed_string('angvel_saccade_detector', __version__)
rows_table_name = NamingConventions.ROWS_TABLE
rows_table_version = options.version
saccades_table_name = NamingConventions.SACCADES_TABLE
# annotations_table_name = 'annotated'
saccades_table_version = options.saccades_table_version
with safe_flydra_db_open(options.db) as db:
samples = db.list_samples()
for i, sample in enumerate(samples):
already_has = db.has_table(sample, saccades_table_name,
saccades_table_version)
if options.nocache and already_has:
msg = ('Sample %r already has table %s:%s; skipping.' %
(sample, saccades_table_name, saccades_table_version))
logger.info(msg)
continue
if not db.has_table(sample, rows_table_name, rows_table_version):
msg = ('Sample %r does not have table %s:%s.' %
(sample, rows_table_name, rows_table_version))
raise Exception(msg)
with db.safe_get_table(sample, rows_table_name,
rows_table_version) as rows:
rows = np.array(rows[:])
params = {}
# saccades, annotated
data = angvel_saccade_detect(rows, **params)
saccades = data['saccades']
for saccade in saccades:
check_saccade_is_well_formed(saccade)
DT = rows['timestamp'][-1] - rows['timestamp'][0]
logger.info(
"%4d/%d %s: %6d saccades for %6d rows (%6g saccades/s)" %
(i, len(samples), sample, len(saccades), len(rows),
DT / len(saccades)))
if True:
db.set_table(sample=sample,
table=saccades_table_name,
data=saccades,
version=saccades_table_version)
db.set_attr(
sample,
'saccades_%s_processed' % saccades_table_version,
processed)
if options.out is not None:
outdir = os.path.join(options.out, 'angvel_sac_detect')
if not os.path.exists(outdir):
os.makedirs(outdir)
resources = os.path.join(outdir, 'images')
filename = os.path.join(outdir, '%s.html' % sample)
r = Report()
chunks = enumerate_chunks(len(rows), max_chunk_size=300)
for i, select in enumerate(chunks):
rows_i = rows[select]
ri = plot_angvel_saccade_detect_results(rows_i)
ri.nid = 'chunk_%s' % i
r.add_child(ri)
logger.info('Writing to %r.' % filename)
r.to_html(filename, resources_dir=resources)
def detect_angvel(argv):
np.seterr(all='raise')
parser = LenientOptionParser(usage=usage)
parser.add_option("--db", help="FlydraDB directory.")
parser.add_option("--version", default='smooth', type='string',
help="[=%default] Which version of the 'rows' table to use.")
parser.add_option("--saccades_table_version", default='angvel',
type='string',
help='[=%default] Version of output saccades tables.')
parser.add_option("--nocache", help="Ignores already computed results.",
default=False, action="store_true")
parser.add_option("--out", help="Output directory for graphic representation.")
# detection parameters
dt = 1.0 / 60 # XXX: read from file
warnings.warn('Using fixed dt = %s.' % dt)
parser.add_option("--deltaT_inner_sec", default=4 * dt, type='float',
help="Inner interval [= %default]")
parser.add_option("--deltaT_outer_sec", default=10 * dt, type='float',
help="Outer interval [= %default]")
parser.add_option("--min_amplitude_deg", default=25, type='float',
help="Minimum saccade amplitude (deg) [= %default]")
parser.add_option("--min_linear_velocity", default=0.1, type='float',
help="Minimum linear velocity when"
" saccading (m/s) [= %default]")
parser.add_option("--max_linear_acceleration", default=20, type='float',
help="Maximum linear acceleration when saccading "
"(m/s^2) [= %default]")
parser.add_option("--max_angular_velocity", default=8000, type='float',
help="Maximum angular velocity when saccading"
" (deg/s) [= %default]")
parser.add_option("--max_orientation_dispersion_deg", default=15,
type='float',
help="Maximum dispersion (deg) [= %default]")
parser.add_option("--minimum_interval_sec", default=10 * dt, type='float',
help="Minimum interval between saccades. [= %default]")
(options, args) = parser.parse_args(argv)
if not options.db:
raise Exception('No flydra DB directory specified.')
if args:
raise Exception('Spurious arguments')
# Create processed string
processed = get_computed_string('angvel_saccade_detector', __version__)
rows_table_name = NamingConventions.ROWS_TABLE
rows_table_version = options.version
saccades_table_name = NamingConventions.SACCADES_TABLE
# annotations_table_name = 'annotated'
saccades_table_version = options.saccades_table_version
with safe_flydra_db_open(options.db) as db:
samples = db.list_samples()
for i, sample in enumerate(samples):
already_has = db.has_table(sample, saccades_table_name,
saccades_table_version)
if options.nocache and already_has:
msg = ('Sample %r already has table %s:%s; skipping.' %
(sample, saccades_table_name, saccades_table_version))
logger.info(msg)
continue
if not db.has_table(sample, rows_table_name, rows_table_version):
msg = ('Sample %r does not have table %s:%s.' %
(sample, rows_table_name, rows_table_version))
raise Exception(msg)
with db.safe_get_table(sample, rows_table_name,
rows_table_version) as rows:
rows = np.array(rows[:])
params = {}
# saccades, annotated
data = angvel_saccade_detect(rows, **params)
saccades = data['saccades']
for saccade in saccades:
check_saccade_is_well_formed(saccade)
DT = rows['timestamp'][-1] - rows['timestamp'][0]
logger.info("%4d/%d %s: %6d saccades for %6d rows (%6g saccades/s)" %
(i, len(samples), sample,
len(saccades), len(rows), DT / len(saccades)))
if True:
db.set_table(sample=sample,
table=saccades_table_name,
data=saccades,
version=saccades_table_version)
db.set_attr(sample,
'saccades_%s_processed' % saccades_table_version,
processed)
if options.out is not None:
outdir = os.path.join(options.out, 'angvel_sac_detect')
if not os.path.exists(outdir):
os.makedirs(outdir)
resources = os.path.join(outdir, 'images')
filename = os.path.join(outdir, '%s.html' % sample)
r = Report()
chunks = enumerate_chunks(len(rows), max_chunk_size=300)
for i, select in enumerate(chunks):
rows_i = rows[select]
ri = plot_angvel_saccade_detect_results(rows_i)
ri.nid = 'chunk_%s' % i
r.add_child(ri)
logger.info('Writing to %r.' % filename)
r.to_html(filename, resources_dir=resources)
