def wrap_sample_expdata_plot(data_dir, sample, plot_func, function_args):
""" def plot_func(sample, exp_data) """
with safe_flydra_db_open(data_dir) as db:
exp_data = db.get_table(sample, EXP_DATA_TABLE)
result = plot_func(sample, exp_data, **function_args)
db.release_table(exp_data)
return result
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 main():
parser = OptionParser(usage=description)
parser.add_option("--peters_pickle",
help="Peter's pickle file", default='weir.pkl')
parser.add_option("--db", help="FlydraDB directory")
(options, args) = parser.parse_args()
if not options.db:
raise Exception('Please define FlydraDB directory using `--db`.')
if args:
raise Exception('Extraneous arguments: %r.' % args)
if not os.path.exists(options.peters_pickle):
raise Exception('File %r does not exist. ' % options.peters_pickle)
print("Loading file %r ..." % options.peters_pickle)
data = pickle.load(open(options.peters_pickle, 'rb'))
print("...done.")
with safe_flydra_db_open(options.db, create=True) as flydra_db:
for experiment, flies in data.items():
experiment = experiment.replace('/', '')
for fly, fly_data in flies.items():
import_sample(flydra_db, experiment, fly, fly_data)
def get_saccades_for_group(flydra_db_directory, db_group, version):
center = ParamsEstimation.arena_center
radius = ParamsEstimation.arena_radius
warnings.warn('Using hardcoded arena size and position (%s, %s)'
% (center, radius))
with safe_flydra_db_open(flydra_db_directory) as db:
print('Getting all saccades from group %r.' % db_group)
saccades = db.get_table_for_group(group=db_group,
table='saccades',
version=version)
if len(saccades) == 0:
raise Exception('No saccades found for group %r.' % db_group)
print('Checking saccades are well formed.')
for s in saccades:
check_saccade_is_well_formed(s)
print('Adding position information')
saccades = add_position_information(saccades,
arena_radius=radius,
arena_center=center)
return saccades
def main():
parser = OptionParser(usage=description)
parser.add_option("--db", help="FlydraDB directory")
(options, args) = parser.parse_args() # @UnusedVariable
try:
if options.db is None:
raise Exception('Please provide --db option')
if len(args) != 1:
raise Exception('Please provide exactly one argument.')
except Exception as e:
logger.error('Error while parsing configuration.')
logger.error(str(e))
sys.exit(-1)
# detection parameters
directory = args[0]
try:
if not os.path.exists(directory):
raise Exception('Directory %r does not exist.' % directory)
pattern = '*-saccades.h5'
logger.info('Looking for files with pattern %r in directory %r.' %
(pattern, directory))
files = sorted(list(locate(pattern=pattern, root=directory)))
if not files:
raise Exception(
'No files with pattern %r found in directory %r ' %
(pattern, directory))
logger.info('Found %d files.' % len(files))
with flydra_db.safe_flydra_db_open(options.db, create=True) as db:
for i, filename in enumerate(files):
saccades = saccades_read_h5(filename)
saccades['sample_num'] = i
logger.debug('Sample %s: %d saccades.' %
(filename, len(saccades)))
store_sample_in_flydra_db(saccades, db)
except Exception as e:
logger.error('Error while processing. Exception and traceback follow.')
logger.error(str(e))
logger.error(traceback.format_exc())
sys.exit(-2)
def main():
parser = OptionParser(usage=description)
parser.add_option("--db", help="FlydraDB directory")
(options, args) = parser.parse_args() # @UnusedVariable
try:
if options.db is None:
raise Exception('Please provide --db option')
if len(args) != 1:
raise Exception('Please provide exactly one argument.')
except Exception as e:
logger.error('Error while parsing configuration.')
logger.error(str(e))
sys.exit(-1)
# detection parameters
directory = args[0]
try:
if not os.path.exists(directory):
raise Exception('Directory %r does not exist.' % directory)
pattern = '*-saccades.h5'
logger.info('Looking for files with pattern %r in directory %r.' %
(pattern, directory))
files = sorted(list(locate(pattern=pattern, root=directory)))
if not files:
raise Exception('No files with pattern %r found in directory %r ' %
(pattern, directory))
logger.info('Found %d files.' % len(files))
with flydra_db.safe_flydra_db_open(options.db, create=True) as db:
for i, filename in enumerate(files):
saccades = saccades_read_h5(filename)
saccades['sample_num'] = i
logger.debug('Sample %s: %d saccades.' %
(filename, len(saccades)))
store_sample_in_flydra_db(saccades, db)
except Exception as e:
logger.error('Error while processing. Exception and traceback follow.')
logger.error(str(e))
logger.error(traceback.format_exc())
sys.exit(-2)
def wrap_sample_saccades_plot(data_dir, sample, configuration, plot_func, function_args):
""" def plot_func(sample, configuration, exp_data, saccades) """
with safe_flydra_db_open(data_dir) as db:
if db.has_table(sample, EXP_DATA_TABLE):
exp_data = db.get_table(sample, EXP_DATA_TABLE)
else:
exp_data = None
table = db.get_table(sample, table=SACCADES_TABLE, version=configuration)
saccades = numpy.array(table, dtype=table.dtype)
result = plot_func(sample, exp_data, configuration, saccades, **function_args)
db.release_table(table)
if exp_data:
db.release_table(exp_data)
return result
def compute_saccade_stats(flydra_db_directory, samples, image, conditions):
'''
Computes the stats of an image for the saccades that respect a
set of conditions.
db: FlydraDB directory
samples: list of IDs
condition: saccade table -> true/false selector
'''
with safe_flydra_db_open(flydra_db_directory) as db:
progress('Computing stats', (0, 2), 'First pass')
# first compute the mean
group_mean = Expectation()
group_min = None
group_max = None
iter = saccades_iterate_image('computing mean',
db, samples, image, conditions)
for sample, sample_saccades, values in iter: #@UnusedVariable
sample_mean = numpy.mean(values, axis=0)
sample_min = numpy.min(values, axis=0)
sample_max = numpy.max(values, axis=0)
if group_min is None:
group_min = sample_min
group_max = sample_max
else:
group_min = numpy.minimum(sample_min, group_min)
group_max = numpy.maximum(sample_max, group_max)
group_mean.update(sample_mean, len(values))
num_samples = group_mean.num_samples
group_mean = group_mean.get_value()
group_var = Expectation()
progress('Computing stats', (1, 2), 'Second pass')
iter = saccades_iterate_image('computing var',
db, samples, image, conditions)
for sample, sample_saccades, values in iter: #@UnusedVariable
err = values - group_mean
sample_var = numpy.mean(numpy.square(err), axis=0)
group_var.update(sample_var, len(values))
group_var = group_var.get_value()
result = Stats(mean=group_mean, var=group_var,
min=group_min, max=group_max, nsamples=num_samples)
return result
def main():
np.seterr(all='raise')
parser = OptionParser(usage=description)
parser.add_option("--db", help="Main data directory")
parser.add_option("--interactive", action="store_true", default=False,
help="Starts an interactive compmake session.")
parser.add_option("--outdir", help="Output directory")
(options, args) = parser.parse_args() #@UnusedVariable
try:
if args:
raise Exception('Spurious arguments %r.' % args)
if not options.db:
raise Exception('Please provide --db option')
if not options.outdir:
raise Exception('Please provide --outdir option')
except Exception as e:
logger.error('Error while parsing configuration.')
logger.error(str(e))
sys.exit(-1)
try:
compmake_dir = os.path.join(options.outdir, 'compmake')
use_filesystem(compmake_dir)
with safe_flydra_db_open(options.db) as db:
spontaneous_analysis(db, options.outdir)
compmake_console()
except Exception as e:
logger.error('Error while processing. Exception and traceback follow.')
logger.error(str(e))
logger.error(traceback.format_exc())
sys.exit(-2)
def get_group_density_stats(flydra_db_directory, db_group, version, cells):
center = ParamsEstimation.arena_center
radius = ParamsEstimation.arena_radius
warnings.warn('Using hardcoded arena size and position (%s, %s)'
% (center, radius))
with safe_flydra_db_open(flydra_db_directory) as db:
rows = db.get_table_for_group(db_group, table='rows', version=version)
print('Read %d rows' % len(rows))
print('Computing extra information')
rowsp = add_position_information_to_rows(rows,
arena_radius=radius,
arena_center=center)
print('Computing histogram')
stats = compute_histogram(rowsp, cells)
return stats
def wrap_group_plot(data_dir, group, configuration, plot_func, function_args):
""" def plot_func(group, configuration, saccades) """
with safe_flydra_db_open(data_dir) as db:
saccades = get_table_for_group(db, group, SACCADES_TABLE, configuration)
return plot_func(group, configuration, saccades, **function_args)
def flydra_db_detect(args):
np.seterr(all='raise')
parser = LenientOptionParser(usage=usage)
parser.add_option("--db", help="FlydraDB directory.")
parser.add_option("--version",
default=None,
type='string',
help="Which version of the 'rows' table to use.")
parser.add_option("--debug_output",
help="Creates debug figures.",
default=False,
action="store_true")
parser.add_option("--nocache",
help="Ignores already computed results.",
default=False,
action="store_true")
# 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(args)
if not options.db:
raise Exception('No flydra DB directory specified.')
if args:
raise Exception('Spurious arguments')
# Create processed string
processed = get_computed_string('geometric_saccade_detector', __version__)
rows_table_name = 'rows'
rows_table_version = options.version
saccades_table_name = 'saccades'
annotations_table_name = 'annotated'
saccades_table_version = options.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:
params = {
'deltaT_inner_sec': options.deltaT_inner_sec,
'deltaT_outer_sec': options.deltaT_outer_sec,
'min_amplitude_deg': options.min_amplitude_deg,
'max_orientation_dispersion_deg':
options.max_orientation_dispersion_deg,
'minimum_interval_sec': options.minimum_interval_sec,
'max_linear_acceleration': options.max_linear_acceleration,
'min_linear_velocity': options.min_linear_velocity,
'max_angular_velocity': options.max_angular_velocity,
}
rows = np.array(rows[:])
saccades, annotated = geometric_saccade_detect(rows, params)
for saccade in saccades:
check_saccade_is_well_formed(saccade)
dt = 1.0 / 60
logger.info(
"%4d/%d %s: %d saccades for %d rows (%g saccades/s)" %
(i, len(samples), sample, len(saccades), len(rows),
len(rows) * dt / len(saccades)))
db.set_table(sample=sample,
table=saccades_table_name,
data=saccades,
version=saccades_table_version)
db.set_table(sample=sample,
table=annotations_table_name,
data=annotated,
version=saccades_table_version)
db.set_attr(sample,
'saccades_%s_processed' % saccades_table_version,
processed)
# Write debug figures
if options.debug_output:
if not os.path.exists(options.output_dir):
os.makedirs(options.output_dir)
basename = sample
debug_output_dir = os.path.join(options.output_dir, basename)
logger.info("Writing HTML+png to %s" % debug_output_dir)
write_debug_output(debug_output_dir, basename, annotated,
saccades)
def flydra_db_detect(args):
np.seterr(all='raise')
parser = LenientOptionParser(usage=usage)
parser.add_option("--db", help="FlydraDB directory.")
parser.add_option("--version", default=None, type='string',
help="Which version of the 'rows' table to use.")
parser.add_option("--debug_output", help="Creates debug figures.",
default=False, action="store_true")
parser.add_option("--nocache", help="Ignores already computed results.",
default=False, action="store_true")
# 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(args)
if not options.db:
raise Exception('No flydra DB directory specified.')
if args:
raise Exception('Spurious arguments')
# Create processed string
processed = get_computed_string('geometric_saccade_detector', __version__)
rows_table_name = 'rows'
rows_table_version = options.version
saccades_table_name = 'saccades'
annotations_table_name = 'annotated'
saccades_table_version = options.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:
params = {
'deltaT_inner_sec': options.deltaT_inner_sec,
'deltaT_outer_sec': options. deltaT_outer_sec,
'min_amplitude_deg': options.min_amplitude_deg,
'max_orientation_dispersion_deg':
options.max_orientation_dispersion_deg,
'minimum_interval_sec': options.minimum_interval_sec,
'max_linear_acceleration': options.max_linear_acceleration,
'min_linear_velocity': options.min_linear_velocity,
'max_angular_velocity': options.max_angular_velocity,
}
rows = np.array(rows[:])
saccades, annotated = geometric_saccade_detect(rows, params)
for saccade in saccades:
check_saccade_is_well_formed(saccade)
dt = 1.0 / 60
logger.info("%4d/%d %s: %d saccades for %d rows (%g saccades/s)" %
(i, len(samples), sample,
len(saccades), len(rows), len(rows) * dt / len(saccades)))
db.set_table(sample=sample,
table=saccades_table_name,
data=saccades,
version=saccades_table_version)
db.set_table(sample=sample,
table=annotations_table_name,
data=annotated,
version=saccades_table_version)
db.set_attr(sample,
'saccades_%s_processed' % saccades_table_version,
processed)
# Write debug figures
if options.debug_output:
if not os.path.exists(options.output_dir):
os.makedirs(options.output_dir)
basename = sample
debug_output_dir = os.path.join(options.output_dir, basename)
logger.info("Writing HTML+png to %s" % debug_output_dir)
write_debug_output(debug_output_dir, basename,
annotated, saccades)
def compute_stats(flydra_db_directory, samples, image):
'''
Computes the stats of an image.
*db*
FlydraDB directory
*samples*
list of IDs
image: name of a table
'''
with safe_flydra_db_open(flydra_db_directory) as db:
def data_pass(name):
for i, id in enumerate(samples):
progress(name, (i, len(samples)), "Sample %s" % id)
if not (db.has_sample(id) and db.has_table(id, image)):
raise ValueError('No table "%s" for id %s' % (image, id))
rows = db.get_rows(id)
data = db.get_table(id, image)
select = rows[:]['linear_velocity_modulus'] > 0.1
#select = condition(rows)
values = data[select]['value']
yield id, values
db.release_table(data)
db.release_table(rows)
progress('Computing stats', (0, 2), 'First pass')
# first compute the mean
group_mean = Expectation()
group_min = None
group_max = None
for sample, values in data_pass('computing mean'): #@UnusedVariable
sample_mean = numpy.mean(values, axis=0)
sample_min = numpy.min(values, axis=0)
sample_max = numpy.max(values, axis=0)
if group_min is None:
group_min = sample_min
group_max = sample_max
else:
group_min = numpy.minimum(sample_min, group_min)
group_max = numpy.maximum(sample_max, group_max)
group_mean.update(sample_mean, len(values))
num_samples = group_mean.num_samples
group_mean = group_mean.get_value()
group_var = Expectation()
progress('Computing stats', (1, 2), 'Second pass')
for sample, values in data_pass('computing var'): #@UnusedVariable
err = values - group_mean
sample_var = numpy.mean(numpy.square(err), axis=0)
group_var.update(sample_var, len(values))
group_var = group_var.get_value()
return Stats(mean=group_mean, var=group_var,
min=group_min, max=group_max, nsamples=num_samples)
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)
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 bet_on_flies(flydra_db_directory, samples, image, saccades_set):
kernels = {}
for degrees in [15, 30, 45, 60, 90, 180]:
# kernels['mf%d' % degrees] = create_matched_filter(degrees, [-45, 0], False)
kernels['mf%d' % degrees] = create_matched_filter(degrees, [-20, 20], False)
#kernels['pf%d' % degrees] = create_matched_filter(degrees, True)
results = {}
with safe_flydra_db_open(flydra_db_directory) as db:
conditions = [saccades_set.args]
# looking for the optimal dividing plane
ex = {-1: Expectation(), +1: Expectation()}
for sample, sample_saccades, image_values in saccades_iterate_image(#@UnusedVariable
'computing optimal kernel', db, samples, image, conditions):
for s in [-1, +1]:
values = image_values[sample_saccades['sign'] == s]
if len(values) > 0:
ex[s].update(values.mean(axis=0), len(values))
kernels['optimal'] = ex[+1].get_value() - ex[-1].get_value()
dir = '${SNPENV_DATA}/flydra_db/out/saccade_view_joint_analysis/lasvegas/images/'
others = {
'center': 'lasvegas_contrast_w_posts_center:optimal:kernel.pickle',
'border': 'lasvegas_contrast_w_posts_border:optimal:kernel.pickle',
'allsac': 'lasvegas_contrast_w_posts_allsac:optimal:kernel.pickle'
}
for name, f in others.items():
filename = os.path.expandvars(os.path.join(dir, f))
kernel = cPickle.load(open(filename, 'rb'))
#mask_deg = create_matched_filter(75, [-60, 60],True)
mask_deg = create_matched_filter(75, [-90, 90], True)
kernel = kernel * numpy.abs(mask_deg)
kernels['common_%s' % name] = kernel
for i, kernel_name in enumerate(kernels.keys()):
progress('betting', (i, len(kernels)), kernel_name)
kernel = kernels[kernel_name]
signs = []
response = []
overlap = []
for sample, sample_saccades, image_values in saccades_iterate_image(#@UnusedVariable
'computing response', db, samples, image, conditions):
s = sample_saccades[:]['sign']
signs.extend(s)
for i in range(len(image_values)):
response_i = (image_values[i, :] * kernel).sum()
response.append(response_i)
overlap_i = (image_values[i, :] *
numpy.abs(kernel)).sum()
overlap.append(overlap_i)
signs = numpy.array(signs)
response = numpy.array(response)
results[kernel_name] = { 'signs': signs, 'response': response,
'kernel': kernel, 'overlap': overlap}
return results