def plot_chemotaxis_experiment(data, field_config, out_dir):
# multigen agents plot
plot_settings = {
'agents_key':
'agents',
'max_rows':
30,
'skip_paths': [
('boundary', 'mass'),
('boundary', 'length'),
('boundary', 'width'),
('boundary', 'location'),
]
}
plot_agents_multigen(data, plot_settings, out_dir, 'agents')
# trajectory and motility
agents_timeseries = timeseries_from_data(data)
field = make_field(field_config)
trajectory_config = {
'bounds': field_config['bounds'],
'field': field,
'rotate_90': True
}
plot_temporal_trajectory(copy.deepcopy(agents_timeseries),
trajectory_config, out_dir, 'temporal')
plot_agent_trajectory(agents_timeseries, trajectory_config, out_dir,
'trajectory')
try:
plot_motility(agents_timeseries, out_dir, 'motility_analysis')
except:
print('plot_motility failed')
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_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_timeseries(self, data, out_dir):
plot_settings = {
'agents_key': 'agents',
'title_size': 10,
'tick_label_size': 10,
}
plot_settings.update(self.timeseries_config)
plot_agents_multigen(data, plot_settings, out_dir)
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 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)
if not os.path.exists(out_dir):
os.makedirs(out_dir)
agent_id = '0'
compartment = GrowthDivision({'agent_id': agent_id})
# settings for simulation and plot
settings = {
'environment': {
'volume': 1e-6 * units.L, # L
'ports': {
'fields': ('fields', ),
'external': (
'boundary',
'external',
),
'global': ('boundary', ),
'dimensions': ('dimensions', ),
},
},
'outer_path':
('agents', agent_id), # TODO -- need to set the agent_id through here?
'return_raw_data': True,
'timestep': 1,
'total_time': 500
}
output_data = simulate_compartment_in_experiment(compartment, settings)
plot_settings = {}
plot_agents_multigen(output_data, plot_settings, out_dir)