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("--flydra_db", default="saccade_data_flydradb", help="Main data directory") parser.add_option( "--interactive", action="store_true", default=False, help="Starts an interactive compmake session." ) parser.add_option("--report", default="saccade_report", help="Saccade report directory") parser.add_option("--groups", default=None, help="Which groups to consider") parser.add_option("--configurations", default=None, help="Which configurations to consider") parser.add_option("--combid", default=None, help="How to name this combination of groups/configs.") (options, args) = parser.parse_args() # @UnusedVariable if args: raise Exception("Spurious arguments %r." % args) db = FlydraDB(options.flydra_db) robust_split = lambda s: filter(lambda x: x, s.split(",")) if not options.groups in [None, "all"]: groups = robust_split(options.groups) if not groups: raise Exception("No groups specified.") groupset = "_".join(groups) else: groups = db.list_groups() groupset = "all" if not groups: raise Exception("No groups found.") if not options.configurations in [None, "all"]: configurations = robust_split(options.configurations) if not configurations: raise Exception("No configuration specified") confset = "_".join(configurations) else: configurations = db.list_all_versions_for_table(SACCADES_TABLE) confset = "all" configurations = set() for group in groups: configurations.update(db.list_versions_for_table_in_group(group, SACCADES_TABLE)) configurations = natsorted(configurations) if not configurations: raise Exception("No valid versions of table %r found." % SACCADES_TABLE) print ("I will consider the configurations: %r" % configurations) if options.combid is None: combination = "%s_%s" % (groupset, confset) else: combination = options.combid print ("I call this combination %r." % combination) output_dir = os.path.join(options.report, combination) if not os.path.exists(output_dir): os.makedirs(output_dir) set_namespace("master_plot_%s" % combination) # we maintain several indices # key = (group, configuration, plot) index_group_plots = {} # key = (sample, plot) index_sample_expdata_plots = {} # key = (sample, configuration, plot) index_sample_saccades_plots = {} # First we index the DB print ("Looking for data in database...") all_samples = set() group2samples = {} configurations_for_group = {} group_has_exp_data = {} for group in groups: group2samples[group] = db.list_samples_for_group(group) all_samples.update(group2samples[group]) if not group2samples[group]: raise Exception("Empty group %r." % group) available = db.list_versions_for_table_in_group(group=group, table=SACCADES_TABLE) configurations_for_group[group] = set(configurations).intersection(available) if not configurations_for_group[group]: print ("No configurations found for %r; available %r" % (group, available)) group_has_exp_data[group] = db.group_has_table(group, EXP_DATA_TABLE) all_samples = natsorted(all_samples) # print info print ("Summary:") for group in groups: msg = " group {group:>20} samples: {nsamples:3} " " configurations: {nconf:3} raw data? {data}".format( group=group, nsamples=len(group2samples[group]), nconf=len(configurations_for_group[group]), data=group_has_exp_data[group], ) print (msg) # TODO: iterate by sample, not by group for group in groups: for configuration in configurations_for_group[group]: for plot in group_plots: job_id = "%s-%s-%s" % (group, configuration, plot.id) index_group_plots[(group, configuration, plot.id)] = comp( wrap_group_plot, options.flydra_db, group, configuration, plot.command, plot.args, job_id=job_id ) for sample, plot in prod(group2samples[group], sample_saccades_plots): job_id = "%s-%s-%s" % (sample, configuration, plot.id) key = (sample, configuration, plot.id) if key in index_sample_saccades_plots: # we already did it as part of another group continue index_sample_saccades_plots[key] = comp( wrap_sample_saccades_plot, options.flydra_db, sample, configuration, plot.command, plot.args, job_id=job_id, ) if group_has_exp_data[group]: for sample, plot in prod(group2samples[group], sample_expdata_plots): job_id = "%s-%s" % (sample, plot.id) key = (sample, plot.id) if key in index_sample_expdata_plots: # we already did it as part of another group continue index_sample_expdata_plots[key] = comp( wrap_sample_expdata_plot, options.flydra_db, sample, plot.command, plot.args, job_id=job_id ) # now we create the indices # fix configuration, function; iterate groups for configuration, plot in itertools.product(configurations, group_plots): subs = [] descs = [] page_id = "%s.%s" % (configuration, plot.id) for group, group_desc in order_groups(groups): if not configuration in configurations_for_group[group]: continue descs.append(group_desc) subs.append(index_group_plots[(group, configuration, plot.id)]) if not subs: raise Exception("no groups for configuration %r." % configuration) job_id = page_id comp(combine_reports, subs, descs, page_id, output_dir, job_id=job_id) comp( create_gui, filename=os.path.join(output_dir, "group_plots.html"), menus=[ ("Detector", configurations, configurations), ("Plot/table", map(lambda x: x.id, group_plots), map(lambda x: x.description, group_plots)), ], job_id="gui-group_plots", ) # fix group, function; iterate samples for group in groups: if not group_has_exp_data[group]: continue for plot in sample_expdata_plots: subs = [] descs = [] for sample in group2samples[group]: descs.append(sample) subs.append(index_sample_expdata_plots[(sample, plot.id)]) page_id = "%s.%s" % (group, plot.id) job_id = page_id comp(combine_reports, subs, descs, page_id, output_dir, job_id=job_id) # get the ordered group lists and desc ordered_groups = map(lambda t: t[0], order_groups(groups)) ordered_groups_desc = map(lambda t: t[1], order_groups(groups)) comp( create_gui, filename=os.path.join(output_dir, "expdata_plots.html"), menus=[ ("Group", ordered_groups, ordered_groups_desc), ( "Plot/table", map(lambda x: x.id, sample_expdata_plots), map(lambda x: x.description, sample_expdata_plots), ), ], job_id="gui-expdata_plots", ) # fix configuration, group, function; iterate samples for group in groups: for configuration in configurations: if not configuration in configurations_for_group[group]: for plot in sample_saccades_plots: page_id = "%s.%s.%s" % (configuration, group, plot.id) comp( write_empty, page_id, output_dir, "Group %r has not been processed with algorithm %r." % (group, configuration), job_id=page_id, ) continue for plot in sample_saccades_plots: subs = [] descs = [] for sample in group2samples[group]: descs.append(sample) r = index_sample_saccades_plots[(sample, configuration, plot.id)] subs.append(r) page_id = "%s.%s.%s" % (configuration, group, plot.id) job_id = page_id comp(combine_reports, subs, descs, page_id, output_dir, job_id=job_id) comp( create_gui, filename=os.path.join(output_dir, "saccade_plots.html"), menus=[ ("Detector", configurations, configurations), ("Group", ordered_groups, ordered_groups_desc), ( "Plot/table", map(lambda x: x.id, sample_saccades_plots), map(lambda x: x.description, sample_saccades_plots), ), ], job_id="gui-saccade_plots", ) # fix configuration, sample; plot fullsscreen for group in groups: for configuration in configurations: for sample in group2samples[group]: # XXX make it clenaer if not configuration in configurations_for_group[group]: for plot in sample_fullscreen_plots: page_id = "%s.%s.%s" % (sample, configuration, plot.id) comp( write_empty, page_id, output_dir, 'Group %s has not been processed with algorithm "%s".' % (group, configuration), job_id=page_id, ) # print "skipping sample %s group %s config %s" %\ # (sample,group, configuration) continue if not group_has_exp_data[group]: for plot in sample_fullscreen_plots: page_id = "%s.%s.%s" % (sample, configuration, plot.id) comp( write_empty, page_id, output_dir, "Group %r does not have raw experimental data." % (group), job_id=page_id, ) continue for plot in sample_fullscreen_plots: job_id = "%s-%s-%s" % (sample, configuration, plot.id) # FIXME: error if sample in 2 groups job = comp( wrap_sample_saccades_plot, options.flydra_db, sample, configuration, plot.command, plot.args, job_id=job_id, ) page_id = "%s.%s.%s" % (sample, configuration, plot.id) comp(write_report, job, output_dir, page_id, job_id=job_id + "-write_report") comp( create_gui, filename=os.path.join(output_dir, "sample_fullscreen_plots.html"), menus=[ ("Sample", all_samples, all_samples), ("Detector", configurations, configurations), ( "Plot/table", map(lambda x: x.id, sample_fullscreen_plots), map(lambda x: x.description, sample_fullscreen_plots), ), ], job_id="gui-sample_fullscreen_plots", ) tabs = [ ( "group_plots", "By group", "This set displays one plot/table for each group of samples. " "You have the further choice of detection algorithm and plot/table to display.", ), ( "saccade_plots", "By sample", "This set displays one plot/table for each individual sample. " "You have the further choice of which group to consider, which " "detection algorithm, and which plot/table to display.", ), ( "expdata_plots", "By sample (raw)", "This set displays one plot/table for each individual sample, " " produced from the raw data (no saccade detection, so no choice of detector). " "You have the further choice of which group to consider, " "and which plot/table to display." " Note that some samples might be missing; for example, we don't use " " raw orientation data for the Mamarama samples.", ), ( "sample_fullscreen_plots", "By sample, single page", "This set displays one entire page for each sample. " "You have the further choice of sample, " "detection algorithm, and which plot/table to display.", ), ] comp(create_main_gui, tabs, filename=os.path.join(output_dir, "main.html"), job_id="gui-main") 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: print ("Still %d jobs to do." % len(todo)) sys.exit(-2)