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)