def init(self):
if self.config.db is not None and self.config.sample is not None:
db = FlydraDB(self.config.db)
stimulus_xml = db.get_attr(self.config.sample, 'stimulus_xml')
self.arena_info = get_posts_info(stimulus_xml)
else:
self.arena_info = None
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()
class FlydraData(Generator):
''' This block outputs the data from a FlydraDB for
a particular sample. '''
Block.alias('flydra_db_source')
Block.config('db', 'Database directory')
Block.config('sample', 'Sample ID -- such as "DATA20080611_191809".')
for f in fields:
Block.output(f)
Block.output('stimulus_xml')
def init(self):
self.db = FlydraDB(self.config.db, False)
self.rows = self.db.get_rows(self.config.sample)
self.next_index = 0
def update(self):
row = self.rows[self.next_index]
t = row['time']
for field in fields:
self.set_output(field, value=row[field].copy(), timestamp=t)
if self.db.has_attr(self.config.sample, 'stimulus_xml'):
stim_xml = self.db.get_attr(self.config.sample, 'stimulus_xml')
self.set_output('stimulus_xml', stim_xml, timestamp=t)
self.next_index += 1
if self.next_index == len(self.rows):
self.next_index = None
def next_data_status(self):
# TODO: put new interface
if self.next_index is None: # EOF
return (False, None)
else:
return (True, self.rows[self.next_index]['time'])
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()
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():
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)