def run_mother_machine(time=5, out_dir='out'): mother_machine_config = get_mother_machine_config() experiment = mother_machine_experiment(mother_machine_config) # simulate settings = { 'emit_step': 5, 'total_time': time, 'return_raw_data': True} data = simulate_experiment(experiment, settings) # agents plot plot_settings = { 'agents_key': 'agents'} plot_agents_multigen(data, plot_settings, out_dir) # snapshot plot multibody_config = mother_machine_config['environment']['multibody'] agents = {time: time_data['agents'] for time, time_data in data.items()} fields = {time: time_data['fields'] for time, time_data in data.items()} snapshot_data = { 'agents': agents, 'fields': fields, 'config': multibody_config} plot_config = { 'out_dir': out_dir, 'filename': 'snapshots'} plot_snapshots(snapshot_data, plot_config)
def main(): if not os.path.exists(OUT_DIR): os.makedirs(OUT_DIR) data, experiment_config = run_experiment(start_locations=[[0.3, 0.3], [0.5, 0.5]], ) # extract data multibody_config = experiment_config['environment']['multibody'] agents = {time: time_data['agents'] for time, time_data in data.items()} fields = {time: time_data['fields'] for time, time_data in data.items()} # agents plot agents_settings = {'agents_key': 'agents'} plot_agents_multigen(data, agents_settings, OUT_DIR, 'agents') # snapshot plot snapshot_data = { 'agents': agents, 'fields': fields, 'config': multibody_config, } snapshot_config = { 'out_dir': OUT_DIR, 'filename': 'agents_snapshots', } plot_snapshots(snapshot_data, snapshot_config) # Colony Metrics Plot embedded_ts = timeseries_from_data(data) colony_metrics_ts = embedded_ts['colony_global'] colony_metrics_ts['time'] = embedded_ts['time'] path_ts = path_timeseries_from_embedded_timeseries(colony_metrics_ts) fig = plot_colony_metrics(path_ts) fig.savefig(os.path.join(OUT_DIR, 'colonies'))
def run_growth_division(config={}): n_agents = 1 agent_ids = [str(agent_id) for agent_id in range(n_agents)] bounds = [20, 20] settings = { 'growth_rate': 0.02, 'growth_rate_noise': 0.02, 'division_volume': 2.6, 'total_time': 140 } gd_config = { 'agent_shape': config.get('agent_shape', 'segment'), 'animate': True, 'jitter_force': 1e-3, 'bounds': bounds } body_config = {'bounds': bounds, 'agent_ids': agent_ids} gd_config.update(agent_body_config(body_config)) gd_data = simulate_growth_division(gd_config, settings) # snapshots plot agents = { time: time_data['agents'] for time, time_data in gd_data.items() if bool(time_data) } data = {'agents': agents, 'config': gd_config} plot_config = {'out_dir': out_dir, 'filename': 'growth_division_snapshots'} plot_snapshots(data, plot_config)
def run_lattice_experiment(agent_config=get_gd_minimal_config, filename='agents'): n_agents = 1 experiment_config = get_lattice_config() experiment_config['n_agents'] = n_agents experiment_config['agent'] = agent_config() experiment = lattice_experiment(experiment_config) # simulate settings = {'timestep': 1, 'total_time': 200, 'return_raw_data': True} data = simulate_experiment(experiment, settings) # extract data multibody_config = experiment_config['environment']['multibody'] agents = {time: time_data['agents'] for time, time_data in data.items()} fields = {time: time_data['fields'] for time, time_data in data.items()} # agents plot plot_settings = {'agents_key': 'agents'} plot_agents_multigen(data, plot_settings, out_dir, filename) # snapshot plot data = {'agents': agents, 'fields': fields, 'config': multibody_config} plot_config = {'out_dir': out_dir, 'filename': filename + '_snapshots'} plot_snapshots(data, plot_config)
def plot_fields(data, config, out_dir='out', filename='fields'): fields = {time: time_data['fields'] for time, time_data in data.items()} snapshots_data = { 'fields': fields, 'config': config} plot_config = { 'out_dir': out_dir, 'filename': filename} plot_snapshots(snapshots_data, plot_config)
def plot(args): if args.atlas: client = get_atlas_client(SECRETS_PATH) else: client = get_local_client(args.port, args.database_name) data, environment_config = data_from_database(args.experiment_id, client) del data[0] out_dir = os.path.join(OUT_DIR, args.experiment_id) if os.path.exists(out_dir): if not args.force: raise IOError('Directory {} already exists'.format(out_dir)) else: os.makedirs(out_dir) if args.snapshots or args.tags: agents = { time: timepoint['agents'] for time, timepoint in data.items() } fields = { time: timepoint['fields'] for time, timepoint in data.items() } if args.snapshots: snapshots_data = { 'agents': agents, 'fields': fields, 'config': environment_config, } plot_config = { 'out_dir': out_dir, } plot_snapshots(snapshots_data, plot_config) if args.tags is not None: with open(args.tags, 'r') as f: reader = csv.reader(f) molecules = [(store, molecule) for store, molecule in reader] tags_data = { 'agents': agents, 'config': environment_config, } plot_config = { 'out_dir': out_dir, 'tagged_molecules': molecules, } plot_tags(tags_data, plot_config) if args.timeseries: plot_settings = { 'agents_key': 'agents', 'title_size': 10, 'tick_label_size': 10, } plot_agents_multigen(data, plot_settings, out_dir)
def main(): out_dir = os.path.join(COMPARTMENT_OUT_DIR, NAME) if not os.path.exists(out_dir): os.makedirs(out_dir) config = get_lattice_config() data = test_lattice(config, 40) # make snapshot plot agents = {time: time_data['agents'] for time, time_data in data.items()} fields = {time: time_data['fields'] for time, time_data in data.items()} data = {'agents': agents, 'fields': fields, 'config': config} plot_config = {'out_dir': out_dir, 'filename': 'snapshots'} plot_snapshots(data, plot_config)
def plot_experiment_output( data, plot_settings={}, out_dir='out', ): environment_config = plot_settings['environment_config'] agent_type = plot_settings.get('agent_type', 'agent') plot_types = plot_settings['plot_types'] # extract data multibody_config = environment_config['config']['multibody'] agents = {time: time_data['agents'] for time, time_data in data.items()} fields = {time: time_data['fields'] for time, time_data in data.items()} # pass to plots if 'agents' in plot_types: plot_settings = plot_types['agents'] plot_settings['agents_key'] = 'agents' plot_agents_multigen(data, plot_settings, out_dir, agent_type) if 'snapshots' in plot_types: plot_config = plot_types['snapshots'] field_ids = plot_types['snapshots']['fields'] plot_fields = { time: { field_id: field_instance[field_id] for field_id in field_ids} for time, field_instance in fields.items()} data = { 'agents': agents, 'fields': plot_fields, 'config': multibody_config} plot_config.update({ 'out_dir': out_dir, 'filename': agent_type + '_snapshots', }) plot_snapshots(data, plot_config) if 'tags' in plot_types: plot_config = plot_types['tags'] data = { 'agents': agents, 'config': multibody_config} plot_config.update({ 'out_dir': out_dir, 'filename': agent_type + '_tags', }) plot_tags(data, plot_config)
def plot_snapshots(self, data, environment_config, out_dir): agents = { time: timepoint['agents'] for time, timepoint in data.items() } fields = { time: timepoint['fields'] for time, timepoint in data.items() } snapshots_data = { 'agents': agents, 'fields': fields, 'config': environment_config, } plot_config = { 'out_dir': out_dir, } plot_config.update(self.snapshots_config) plot_snapshots(snapshots_data, plot_config)