def main():
set_namespace('env_stats')
parser = OptionParser()
parser.add_option("--db", default='flydra_db', help="FlydraDB directory")
(options, args) = parser.parse_args() #@UnusedVariable
db = FlydraDB(options.db, False)
outdir = os.path.join(options.db, 'out/environment_stats')
images = ["luminance", "contrast", "luminance_w", "contrast_w",
"hluminance_w", "hcontrast_w"]
for image in images:
samples = [x for x in db.list_samples()
if db.get_attr(x, 'stimulus', None) != 'nopost' and
db.has_table(x, image)]
if not samples:
print "No samples for %s" % samples
continue
comp_prefix(image)
data = comp(compute_environment_autocorrelation, options.db, samples, image)
comp(create_report, data, image, outdir)
db.close()
compmake_console()
def main():
parser = OptionParser(usage=description)
parser.add_option("--out", help="Output data directory", default="flydra2ros")
parser.add_option("--db", help="Location of input Flydra db.")
(options, args) = parser.parse_args() # @UnusedVariable
if not options.db:
raise Exception("Please define FlydraDB directory using `--db`.")
verbose = True
def printv(s):
if verbose:
print(s)
db = FlydraDB(options.db, create=False)
configuration = "use_for_report"
for sample in db.list_samples():
if not db.has_table(sample, table=SACCADES_TABLE, version=configuration):
continue
group = guess_group(db, sample)
magno = {}
table = db.get_table(sample, SACCADES_TABLE, configuration)
species = db.get_attr(sample, "species", "Dmelanogaster")
magno["species"] = species
magno["sample"] = sample # _name
if db.has_table(sample, EXP_DATA_TABLE):
exp_data = db.get_table(sample, EXP_DATA_TABLE)
print(exp_data.dtype)
timestamp = exp_data[:]["timestamp"]
else:
timestamp = None
magno["use_for_report"] = convert_saccades_to_ros(table, timestamp)
db.release_table(table)
if timestamp is not None:
db.release_table(exp_data)
output_dir = os.path.join(options.out, group)
filename = os.path.join(output_dir, "magno_%s.mat" % sample)
printv("writing to %s" % filename)
if not os.path.exists(output_dir):
os.makedirs(output_dir)
scipy.io.savemat(filename, {"magno": magno}, oned_as="row")
# put species and sample
print("closing")
db.close()
def main():
parser = OptionParser()
parser.add_option("--db", default='flydra_db', help="FlydraDB directory")
parser.add_option("--nocache", help="Ignores already computed results.",
default=False, action="store_true")
parser.add_option("--sigma", help="Kernel spread (degrees)",
type="float", default=6)
parser.add_option("--source", default='luminance', help="Source table")
parser.add_option("--target", default='contrast', help="Destination table")
(options, args) = parser.parse_args()
kernel = get_contrast_kernel(sigma_deg=options.sigma, eyes_interact=False)
kernel = kernel.astype('float32').copy('C')
db = FlydraDB(options.db, False)
if args:
do_samples = args
else:
do_samples = db.list_samples()
do_samples = filter(lambda x: db.has_table(x, options.source),
do_samples)
if not do_samples:
raise Exception('No samples with table "%s" found. ' % options.source)
for i, sample_id in enumerate(do_samples):
logger.info('Sample %s/%s: %s' % (i + 1, len(do_samples), sample_id))
if not db.has_sample(sample_id):
raise Exception('Sample %s not found in db.' % sample_id)
if not db.has_table(sample_id, options.source):
raise Exception('Sample %s does not have table %s; skipping.' \
% (sample_id, options.source))
if db.has_table(sample_id, options.target) and not options.nocache:
logger.info('Already computed "%s" for %s; skipping' % \
(options.target, sample_id))
continue
luminance = db.get_table(sample_id, options.source)
contrast = compute_contrast_for_table(luminance, kernel)
db.set_table(sample_id, options.target, contrast)
db.release_table(luminance)
db.close()
def main():
parser = OptionParser()
parser.add_option("--db", help="FlydraDB directory")
(options, args) = parser.parse_args() #@UnusedVariable
if not options.db:
raise Exception('Please define the FlydraDB directory using `--db`.')
db = FlydraDB(options.db)
choose = {
'andrea_detector': {
'Dpseudoobscura': 'threshold16',
'Dananassae': 'threshold10',
'Dhydei': 'threshold7',
'Dmelanogaster': 'threshold1',
'Darizonae': 'threshold9',
'Dmojavensis': 'threshold7',
'peter': 'peters_conf',
'mamaramaposts': 'use_for_report',
'mamaramanoposts': 'use_for_report'
},
'ros_detector': {
'Dpseudoobscura': 'filt_kalman-amp_th_10-th_4',
'Dananassae': 'filt_kalman-amp_th_10-th_4',
'Dhydei': 'filt_kalman-amp_th_10-th_4',
'Dmelanogaster': 'filt_kalman-amp_th_10-th_4',
'Darizonae': 'filt_kalman-amp_th_10-th_4',
'Dmojavensis': 'filt_kalman-amp_th_10-th_4'
}
}
for official, choices in choose.items():
for group, version in choices.items():
print("Group %r: %r -> %r" % (group, version, official))
samples = db.list_samples_for_group(group)
for sample in samples:
print(" sample %r" % sample)
table = db.get_table(sample, SACCADES_TABLE, version=version)
copy = numpy.array(table, dtype=table.dtype)
db.set_table(sample=sample, table=SACCADES_TABLE,
version=official, data=copy)
db.release_table(table)
db.close()
def main():
parser = OptionParser(usage=description)
parser.add_option("--saccade_data", help="Main data directory",
default='saccade_data')
parser.add_option("--db", help='Location of output Flydra db.')
(options, args) = parser.parse_args() #@UnusedVariable
if not options.db:
raise Exception('Please define FlydraDB directory using `--db`.')
verbose = True
flydra_db = FlydraDB(options.db, create=True)
matlab_dir = options.saccade_data
for group in os.listdir(matlab_dir):
group_dir = os.path.join(matlab_dir, group)
if not os.path.isdir(group_dir):
continue
if verbose:
print("Opening {0}".format(group))
for file in [file for file in os.listdir(group_dir)
if (file.startswith('magno_')) \
and file.endswith('.mat')]:
sample = file[file.index('_') + 1:file.index('.')]
if verbose:
print(" - Considering sample {0}".format(sample.__repr__()))
if not flydra_db.has_sample(sample):
flydra_db.add_sample(sample)
flydra_db.add_sample_to_group(sample, group)
# flydra_db.add_sample_to_group(sample, 'ros')
filename = os.path.join(group_dir, file)
exp_data, attributes = read_raw_data(filename)
consider_importing_processed(flydra_db, sample, exp_data, attributes)
flydra_db.set_attr(sample, 'species', attributes['species'])
flydra_db.set_attr(sample, 'background', attributes['background'])
flydra_db.set_table(sample, EXP_DATA_TABLE, exp_data)
flydra_db.close()
def compute_environment_autocorrelation(db, samples, image, maxlag=50):
nsensors = 1398
results = numpy.ndarray(shape=(nsensors, 2 * maxlag + 1))
db = FlydraDB(db, create=False)
block_size = 50
num_blocks = int(numpy.ceil(nsensors * 1.0 / block_size))
for b in range(num_blocks):
start = block_size * b
stop = min(start + block_size, nsensors)
progress('Computing autocorrelation', (b, num_blocks))
data = [[] for i in range(nsensors)]
for k, sample in enumerate(samples):
progress('getting data', (k, len(samples)), sample)
table = db.get_table(sample, image)
chunk = (table[:]['value'][:, start:stop]).copy()
for j, i in enumerate(range(start, stop)):
data[i].append(chunk[:, j])
db.release_table(table)
for j, i in enumerate(range(start, stop)):
progress('Computing correlation', (j, stop - start))
x = numpy.concatenate(data[i])
corr, lags = xcorr(x, maxlag=maxlag)
assert(len(lags) == 2 * maxlag + 1)
results[i, :] = corr
db.close()
data = {
'results': results,
'lags': lags
}
return data
def get_all_data_for_signal(db, samples, interval_function,
signal, signal_component):
db = FlydraDB(db, False)
all = []
for id in samples:
if not db.has_rows(id):
logger.warning('Could not find rows table for %s; skipping.' %
(id))
continue
rows_table = db.get_rows(id)
try:
interval = interval_function(db, id, rows_table)
except Exception as e:
logger.warning('Cannot compute interval for sample %s: %s '\
% (id, e))
db.release_table(rows_table)
continue
rows = rows_table[interval]
s = extract_signal(rows, signal, signal_component)
all.append(s)
db.release_table(rows_table)
db.close()
return numpy.concatenate(all)
def compute_mean_generic(db, samples, image, operator):
'''
db: FlydraDB directory
samples: list of IDs
'''
db = FlydraDB(db, False)
results = { 'samples': {} }
ex = Expectation()
for i, id in enumerate(samples):
progress('Computing mean %s' % image,
(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))
data = db.get_table(id, image)
values = data[:]['value']
this = operator(values)
# print "id: %s len: %d %d" % (id, len(data), len(values))
ex.update(this, len(data))
results['samples'][id] = this
db.release_table(data)
results['all'] = ex.get_value()
db.close()
return results
def main():
parser = OptionParser()
parser.add_option("--db", default='flydra_db', help="FlydraDB directory")
parser.add_option("--nocache", help="Ignores already computed results.",
default=False, action="store_true")
parser.add_option("--compute_mu", help="Computes mu and optic flow.",
default=False, action="store_true")
parser.add_option("--white", help="Computes luminance_w, with the arena"
" painted white.", default=False, action="store_true")
parser.add_option("--host", help="Use a remote rfsee. Otherwise, use local process.",
default=None)
(options, args) = parser.parse_args() #@UnusedVariable
db = FlydraDB(options.db, False)
# look for samples with the rows table
do_samples = db.list_samples()
do_samples = filter(lambda x: db.has_rows(x) and
db.get_attr(x, 'stimulus') == 'nopost',
do_samples)
if not do_samples:
raise Exception('Cannot find samples to hallucinate about.')
print "Summary, including nopost."
for s in sorted(get_db_stimulus_stats(db, include_nopost=True),
key=(lambda x:-x.total_length)):
print "stimulus: {s.stimulus:>10} samples: {s.total_number:>5} "\
" total length: {len:>5} minutes".format(s=s, len=s.total_length / (60 * 60))
stimulus_to_use = list(get_stimulus_to_use(db, len(do_samples)))
for i, sample in enumerate(do_samples):
stimulus = stimulus_to_use[i][0]
print sample, stimulus
if options.white:
target = 'hluminance_w'
else:
target = 'hluminance'
for i, sample_id in enumerate(do_samples):
stimulus = stimulus_to_use[i][0]
stimulus_xml = stimulus_to_use[i][1]
print 'Sample %s/%s: %s' % (i + 1, len(do_samples), sample_id)
if not db.has_sample(sample_id):
raise Exception('Sample %s not found in db.' % sample_id)
if not db.has_rows(sample_id):
raise Exception('Sample %s does not have rows table.' % sample_id)
if options.compute_mu:
if db.has_table(sample_id, 'nearness') and not options.nocache:
logger.info('Already computed nearness for %s; skipping' % sample_id)
continue
else:
if db.has_table(sample_id, target) and not options.nocache:
logger.info('Already computed luminance for %s; skipping' % sample_id)
continue
rows = db.get_rows(sample_id)
results = render(rows, stimulus_xml, host=options.host,
compute_mu=options.compute_mu, white=options.white)
db.set_table(sample_id, target, results['luminance'])
if options.compute_mu:
db.set_table(sample_id, 'hnearness', results['nearness'])
db.set_table(sample_id, 'hretinal_velocities',
results['retinal_velocities'])
db.release_table(rows)
db.close()
def main():
parser = OptionParser(usage=description)
parser.add_option("--db", default='flydra_db', help="FlydraDB directory")
parser.add_option("--nocache", help="Ignores already computed results.",
default=False, action="store_true")
parser.add_option("--white", help="Computes luminance_w, with the arena"
" painted white.", default=False, action="store_true")
parser.add_option("--host", help="Use a remote rfsee. Otherwise,"
"use local process.", default=None)
(options, args) = parser.parse_args()
if options.db is None:
logger.error('Please specify a directory using --db.')
sys.exit(-1)
db = FlydraDB(options.db)
if args:
do_samples = args
else:
# look for samples with the rows table
all_samples = db.list_samples()
do_samples = filter(lambda x: db.has_saccades(x) and
db.has_attr(x, 'stimulus_xml'),
all_samples)
logger.info('Found %d/%d samples with saccades and stimulus info.' %
(len(do_samples), len(all_samples)))
image = 'luminance_w' if options.white else 'luminance'
target_start = 'saccades_view_start_%s' % image
target_stop = 'saccades_view_stop_%s' % image
target_rstop = 'saccades_view_rstop_%s' % image
target_sstop = 'saccades_view_sstop_%s' % image
target_random = 'saccades_view_random_%s' % image
for i, sample_id in enumerate(do_samples):
logger.info('Sample %s/%s: %s' % (i + 1, len(do_samples), sample_id))
if not db.has_sample(sample_id):
raise Exception('Sample %s not found in db.' % sample_id)
if not db.has_saccades(sample_id):
raise Exception('Sample %s does not have saccades table.' % sample_id)
if not db.has_attr(sample_id, 'stimulus_xml'):
raise Exception('Sample %s does not have the stimulus'
' information ("stimulus_xml")' % sample_id)
# todo: check stale dependencies
if db.has_table(sample_id, target_start) and \
db.has_table(sample_id, target_stop) and \
db.has_table(sample_id, target_rstop) and \
db.has_table(sample_id, target_sstop) and \
db.has_table(sample_id, target_random) and \
not options.nocache:
logger.info('Targets already computed for %s; skipping' % sample_id)
continue
# Get the stimulus description
stimulus_xml = db.get_attr(sample_id, 'stimulus_xml')
saccades = db.get_saccades(sample_id)
view_start, view_stop, view_rstop, view_random, view_sstop = \
render_saccades_view(
saccades=saccades,
stimulus_xml=stimulus_xml,
host=options.host,
white=options.white)
db.set_table(sample_id, target_start, view_start)
db.set_table(sample_id, target_stop, view_stop)
db.set_table(sample_id, target_rstop, view_rstop)
db.set_table(sample_id, target_random, view_random)
db.set_table(sample_id, target_sstop, view_sstop)
db.release_table(saccades)
db.close()
def main():
parser = OptionParser(usage=description)
parser.add_option("--saccade_data", help="Main data directory",
default='saccade_data')
parser.add_option("--db", help="FlydraDB directory")
parser.add_option("--verbose", help='Verbose output',
default=False, action="store_true")
(options, args) = parser.parse_args() #@UnusedVariable
if not options.db:
raise Exception('Please define FlydraDB directory using `--db`.')
def printv(s):
if options.verbose:
print(s)
flydra_db = FlydraDB(options.db, create=True)
matlab_dir = options.saccade_data
for group in os.listdir(matlab_dir):
group_dir = os.path.join(matlab_dir, group)
if not os.path.isdir(group_dir):
continue
printv("Opening {0}".format(group))
#
#
# exp_data, attributes = read_raw_data(filename)
#
# consider_importing_processed(flydra_db, sample, exp_data, attributes)
#
# flydra_db.set_attr(sample, 'species', attributes['species'])
# flydra_db.set_attr(sample, 'background', attributes['background'])
#
# flydra_db.set_table(sample, EXP_DATA_TABLE, exp_data)
# flydra_db.add_sample_to_group(sample, group)
# flydra_db.add_sample_to_group(sample, 'ros')
#
processed_dir = os.path.join(group_dir, 'processed')
if not os.path.exists(processed_dir):
printv("No processed data found for group %r." % group)
continue
for conf in os.listdir(processed_dir):
# first look for saccades.mat
saccades_file = os.path.join(processed_dir, conf, 'saccades.mat')
if os.path.exists(saccades_file):
printv('Loading from file %r.' % saccades_file)
saccades = saccades_read_mat(saccades_file)
samples = numpy.unique(saccades['sample'])
for sample in samples:
if not flydra_db.has_sample(sample):
flydra_db.add_sample(sample)
flydra_db.add_sample_to_group(sample, group)
sample_saccades = saccades[saccades[:]['sample'] == sample]
flydra_db.set_table(sample=sample, table=SACCADES_TABLE,
version=conf, data=sample_saccades)
# else:
# prefix = 'data_'
# suffix = '.mat'
# for file in [file for file in os.listdir(group_dir)
# if (file.startswith(prefix)) and file.endswith(suffix)]:
#
# sample = file[len(prefix):file.index('.')]
#
# if verbose:
# print(" - Considering sample {0}".format(sample.__repr__()))
#
# if not flydra_db.has_sample(sample):
# flydra_db.add_sample(sample)
#
# filename = os.path.join(group_dir, file)
#
#
#
# else:
# for conf in os.listdir(processed_dir):
# saccades = os.path.join(processed_dir, conf, 'saccades.mat')
# if os.path.exists(saccades):
# group_record.configurations[conf] = saccades
# # add to general list
# self.configurations.add(conf)
## else:
## conf_dir = os.path.join(processed_dir, conf)
## for file in [file for file in os.listdir(conf_dir)
## if file.startswith('processed_data_') and file.endswith('.mat')]:
## id = file[5:-7]
#
# # if we don't have exp data, get list of samples from
# # processed data
# if group_record.configurations and \
# not group_record.has_experimental_data:
# saccades = saccades_read_mat(saccades)
# group_record.samples = set(numpy.unique(saccades['sample']))
# for sample in group_record.samples:
# self.sample2group[sample] = group
#
# if len(group_record.samples)> 0:
# self.groups[group] = group_record
#
# print "has it", group, group_record.has_experimental_data
#
flydra_db.close()
def main():
parser = OptionParser()
parser.add_option("--db", default='flydra_db', help="FlydraDB directory")
parser.add_option("--nocache", help="Ignores already computed results.",
default=False, action="store_true")
parser.add_option("--compute_mu", help="Computes mu and optic flow.",
default=False, action="store_true")
parser.add_option("--white", help="Computes luminance_w, with the arena"
" painted white.", default=False, action="store_true")
parser.add_option("--host", help="Use a remote rfsee. Otherwise, use local process.",
default=None)
(options, args) = parser.parse_args()
db = FlydraDB(options.db, False)
if args:
do_samples = args
else:
# look for samples with the rows table
do_samples = db.list_samples()
do_samples = filter(lambda x: db.has_rows(x), do_samples)
if options.white:
target = 'luminance_w'
else:
target = 'luminance'
for i, sample_id in enumerate(do_samples):
print 'Sample %s/%s: %s' % (i + 1, len(do_samples), sample_id)
if not db.has_sample(sample_id):
raise Exception('Sample %r not found in db.' % sample_id)
if not db.has_rows(sample_id):
raise Exception('Sample %r does not have rows table.' % sample_id)
if not db.has_attr(sample_id, 'stimulus_xml'):
raise Exception('Sample %r does not have the "stimulus_xml" attribute.'
%sample_id)
if options.compute_mu:
if db.has_table(sample_id, 'nearness') and not options.nocache:
logger.info('Already computed nearness for %r; skipping' % sample_id)
continue
else:
if db.has_table(sample_id, target) and not options.nocache:
logger.info('Already computed luminance for %r; skipping' % sample_id)
continue
rows = db.get_rows(sample_id)
stimulus_xml = db.get_attr(sample_id, 'stimulus_xml')
results = render(rows, stimulus_xml, host=options.host,
compute_mu=options.compute_mu, white=options.white)
db.set_table(sample_id, target, results['luminance'])
if options.compute_mu:
db.set_table(sample_id, 'nearness', results['nearness'])
db.set_table(sample_id, 'retinal_velocities',
results['retinal_velocities'])
db.release_table(rows)
db.close()
def main_filter(args):
parser = LenientOptionParser()
parser.add_option("--db", default='flydra_db', help="FlydraDB directory")
parser.add_option("--min_frames_per_track", default=400,
help="Minimum number of frames per track [= %default]")
parser.add_option("--confirm_problems",
help="Stop interactively on problems with log files'\
'(e.g.: cannot find valid obj_ids) [default: %default]",
default=False, action="store_true")
parser.add_option("--dynamic_model_name",
help="Smoothing dynamical model [default: %default]",
default="mamarama, units: mm")
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")
parser.add_option("--smoothing", help="Uses Kalman-smoothed data.",
default=False, action="store_true")
(options, args) = parser.parse_args(args)
table_name = 'rows' # TODO: use constant
table_version = "smooth" if options.smoothing else "kf"
if not args:
raise UserError('No files or directories specified.')
if not os.path.exists(options.db):
os.makedirs(options.db)
db = FlydraDB(options.db)
good_files = get_good_files(where=args, pattern="*.kh5",
confirm_problems=options.confirm_problems)
if len(good_files) == 0:
logger.error("No good files to process")
sys.exit(1)
n = len(good_files)
for i in range(n):
(filename, obj_ids, stim_fname) = good_files[i]
logger.info('Sample %s/%s: %s' % (i + 1, n, filename))
# only maintain basename
stim = os.path.splitext(os.path.basename(stim_fname))[0]
sample_id = os.path.splitext(os.path.basename(filename))[0]
logger.info("File %d/%d %s %s %s " %
(i, n, str(filename), str(obj_ids), stim_fname))
if (db.has_sample(sample_id)
and db.has_table(sample_id, table_name, table_version)
and not options.nocache):
logger.info('Sample %r already computed; skipping.'
' (use --nocache to ignore)' % sample_id)
continue
all_data = []
for obj_id, rows in get_good_smoothed_tracks(#@UnusedVariable
filename=filename,
obj_ids=obj_ids,
min_frames_per_track=options.min_frames_per_track,
dynamic_model_name=options.dynamic_model_name,
use_smoothing=options.smoothing):
filtered = filter_rows(rows, options)
all_data.append(filtered)
if not all_data:
logger.info('Not enough data found for %r; skipping.' % sample_id)
continue
if not db.has_sample(sample_id):
db.add_sample(sample_id)
db.set_attr(sample_id, 'stim_fname', stim_fname)
db.set_attr(sample_id, 'stimulus', stim)
stim_xml = open(stim_fname).read()
db.set_attr(sample_id, 'stimulus_xml', stim_xml)
geometry = get_posts_info(stim_xml)
print(geometry)
db.set_attr(sample_id, 'posts', geometry['posts'])
if 'arena' in geometry:
db.set_attr(sample_id, 'arena', geometry['arena'])
db.add_sample_to_group(sample_id, stim)
if stim != 'nopost':
db.add_sample_to_group(sample_id, 'posts')
rows = numpy.concatenate(all_data)
db.set_table(sample=sample_id,
table=table_name,
data=rows,
version=table_version)
db.set_attr(sample_id, 'filter_time', datetime.now().strftime("%Y%m%d_%H%M%S"))
db.set_attr(sample_id, 'filter_host', platform.node())
db.set_attr(sample_id, 'filter_user', get_user())
db.set_attr(sample_id, 'filter_python_version', platform.python_version())
db.set_attr(sample_id, 'filter_numpy_version', numpy.version.version)
db.close()
def main():
parser = OptionParser(usage=description)
parser.add_option("--db", default='flydra_db', help="Data directory")
parser.add_option("--interactive", default=False, action="store_true",
help="Start a compmake interactive session."
" Otherwise run in batch mode")
parser.add_option("--empty_group_ok",
default=False, action="store_true",
help="do not give up if one group does not have samples ")
(options, args) = parser.parse_args() #@UnusedVariable
if options.db is None:
logger.error('Please specify a directory using --db.')
sys.exit(-1)
outdir = os.path.join(options.db, 'out/saccade_view_joint_analysis')
db = FlydraDB(options.db, False)
set_namespace('saccade_view_joint_analysis')
# for each image we do a different report
data = {}
for image in images:
# For each image we have different tables
tables = ["saccades_view_%s_%s" % (view.id, image.id) for view in views]
all_available = [x for x in db.list_samples() if db.has_saccades(x) and
all([db.has_table(x, table) for table in tables])]
# We further divide these in post and nopost
groups_samples = {
'posts':
filter(lambda s: db.get_attr(s, 'stimulus') != 'nopost', all_available),
'noposts':
filter(lambda s: db.get_attr(s, 'stimulus') == 'nopost', all_available)
}
# now, for each group
for group in groups:
is_hallucination = image.id.startswith('h')
white_arena = image.id.endswith('_w')
if (not is_hallucination) and white_arena and (group.id == 'noposts'):
# if there are not posts, it's useless
continue
samples = groups_samples[group.id]
if not samples:
print "Warning: no samples for %s/%s" % (image.id, group.id)
continue
# global statistics
key = (group.id, image.id)
job_id = "%s-%s" % key
data[key] = comp(compute_stats, options.db,
samples, image.id, job_id=job_id)
for saccades_set, direction in prod(saccades_sets, dirs):
view2result = {}
for i, view in enumerate(views):
table = tables[i]
key = Exp(image=image.id, group=group.id,
view=view.id, dir=direction.id,
saccades_set=saccades_set.id)
job_id = "%s-%s-%s-%s-%s" % key
result = comp(compute_saccade_stats, options.db,
samples, table,
[direction.args, saccades_set.args],
job_id=job_id)
data[key] = result
view2result[view.id] = result
page_id = make_page_id(image=image.id, group=group.id,
dir=direction.id, saccades_set=saccades_set.id)
comp(render_page, view2result, outdir, page_id, job_id=page_id)
for saccades_set in saccades_sets:
table = "saccades_view_start_%s" % (image.id)
exp_id = '%s_%s_%s' % (image.id, group.id, saccades_set.id)
results = comp(bet_on_flies, options.db, samples, table, saccades_set,
job_id='lasvegas-' + exp_id + '-bet')
page_id = exp_id
comp(las_vegas_report, os.path.join(outdir, 'lasvegas'), page_id, results,
job_id='lasvegas-' + exp_id + '-report')
db.close()
comp(add_comparisons, data, outdir)
filename = os.path.join(outdir, 'gui.html')
comp(create_gui_new, filename, menus)
if options.interactive:
# start interactive session
compmake_console()
else:
# batch mode
# try to do everything
batch_command('make all')
# exit with error if we are not done
# (that is, make all failed for some reason)
todo = list(parse_job_list('todo'))
if todo:
logger.info('Still %d jobs to do.' % len(todo))
sys.exit(-2)
