def main(): parser = OptionParser() parser.add_option("--db", default='flydra_db', help="Data directory") parser.add_option("--image", default="luminance", help="Rendered image to use -- " " corresponding to image 'saccades_view_{start,stop}_X'") parser.add_option("--interactive", help="Start an interactive compmake session." " Otherwise run in batch mode. ", default=False, action="store_true") (options, args) = parser.parse_args() #@UnusedVariable if options.db is None: logger.error('Please specify a directory using --db.') sys.exit(-1) view_start = 'saccades_view_start_%s' % options.image view_stop = 'saccades_view_stop_%s' % options.image view_rstop = 'saccades_view_rstop_%s' % options.image db = FlydraDB(options.db, False) # all samples with enough data all_available = lambda x: db.has_saccades(x) and \ db.has_table(x, view_start) and \ db.has_table(x, view_stop) and \ db.has_table(x, view_rstop) samples = filter(all_available, db.list_samples()) set_namespace('saccade_view_show_%s' % options.image) for sample in samples: comp_prefix(sample) comp(create_and_write_report, options.db, sample, options.image) if options.interactive: # start interactive session compmake_console() else: # batch mode # try to do everything batch_command('make all') # start the console 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)
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("--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)