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(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()