def gen_no_policy_simulation():
"""
for 500 rounds, run the simulation and update each day ranges according to the global min and max values per state.
"""
consts = Consts.from_file(consts_file)
range_per_day_dict = [
deepcopy(test_states) for _ in range(consts.total_steps)
]
for i in range(500):
print(i)
sm = SimulationManager(supervisable_makers=test_states.keys(),
consts=consts)
sm.run()
for supervisable in sm.supervisor.supervisables:
name = supervisable.name()
val_per_day = supervisable.y
for test_state, val in zip(range_per_day_dict, val_per_day):
test_state[name].update(val)
# translate to dict
for i in range(consts.total_steps):
range_per_day_dict[i] = {
state: val.to_dict()
for state, val in range_per_day_dict[i].items()
}
# dump to json
with open("simulation_test_ranges.json", "w") as f:
json.dump(range_per_day_dict, f)
def __init__(self, consts=Consts()):
self.consts = consts
self.logger = logging.getLogger("simulation")
logging.basicConfig()
self.logger.setLevel(logging.INFO)
self.logger.info("Creating new simulation.")
self.matrix = AffinityMatrix(self.consts.population_size, consts)
self.agents = self.matrix.agents
self.stats_plotter = plotting.StatisticsPlotter()
self.update_matrix_manager = update_matrix.UpdateMatrixManager(self.matrix)
self.infection_manager = infection.InfectionManager(self)
self.step_counter = 0
self.per_generation = {}
self.counters = {}
for state in MedicalState:
self.per_generation[state] = [0] * self.consts.total_steps
self.counters[state] = 0
self.per_generation["total infected"] = [0] * self.consts.total_steps
self.per_generation["total current sick"] = [0] * self.consts.total_steps
self.logger.info("Created new simulation.")
# todo merge sick_agents and sick_agents_vector to one DS
self.sick_agents = set()
self.sick_agent_vector = np.zeros(self.consts.population_size, dtype=bool)
def compare_simulations_example():
sm1 = SimulationManager(
(
Supervisable.Sum(
"Symptomatic", "Asymptomatic", "Latent", "Silent", "ICU", "Hospitalized", "Recovered", "Deceased"
),
"Symptomatic",
"Recovered",
),
consts=Consts(r0=1.5),
)
sm1.run()
sm2 = SimulationManager(
(
Supervisable.Sum(
"Symptomatic", "Asymptomatic", "Latent", "Silent", "ICU", "Hospitalized", "Recovered", "Deceased"
),
"Symptomatic",
"Recovered",
),
consts=Consts(r0=1.8),
)
sm2.run()
def test_no_policy_simulation():
"""
run the simulation with no policy and fixed R0
Ranges for each state was generate from real sim runs, might be flaky.
"""
consts = Consts.from_file(consts_file)
keys = range_per_day_dict[0].keys()
sm = SimulationManager(supervisable_makers=keys, consts=consts)
sm.run()
for supervisable in sm.supervisor.supervisables:
name = supervisable.name()
val_per_day = supervisable.y
# check for each day if value is in range
for test_state, val in zip(range_per_day_dict, val_per_day):
state = test_state[name]
assert state["min"] <= val <= state["max"]
from consts import Consts
from ways import load_map_from_csv
from problems import BusProblem
from path import Path
from matplotlib import pyplot as plt
from ways.draw import plotPath, plotOrders
from ways.tools import compute_distance
import numpy as np
# Read files
roads = load_map_from_csv(Consts.getDataFilePath("israel.csv"))
prob = BusProblem.load(Consts.getDataFilePath("TLV_5.in"))
# Print details of a random order
order = prob.orders[np.random.choice(np.arange(len(prob.orders)))]
print("One of the orders is from junction #{} at ({}, {}) to #{} at ({}, {})".
format(order[0], roads[order[0]].lat, roads[order[0]].lon, order[1],
roads[order[1]].lat, roads[order[1]].lon))
print(
"A lower bound on the distance we need to drive for this order is: {:.2f}km"
.format(
compute_distance(roads[order[0]].coordinates,
roads[order[1]].coordinates) / 1000))
# Create hard coded example path
examplePath = Path(roads, [
2744, 2745, 2746, 2747, 85561, 62583, 46937, 42405, 19096, 17273, 46582,
43933, 465367, 57190, 819204, 819205, 47816, 16620, 819206, 465324, 3421,
819207, 19950, 819208, 529485, 646688, 646689, 646690, 646691, 646692,
646693, 646694, 47335, 646695, 646696, 522500, 646680, 646681, 646682,
646683, 7372, 867063, 867064, 867065, 867066, 867067, 867068, 867069,
def __init__(
self,
supervisable_makers: Iterable[Union[str, Supervisable, Callable]],
population_data: PopulationData,
matrix_data: MatrixData,
inital_agent_constraints: InitialAgentsConstraints,
run_args,
consts: Consts = Consts(),
):
# setting logger
self.logger = logging.getLogger("simulation")
logging.basicConfig()
self.logger.setLevel(logging.INFO)
self.logger.info("Creating a new simulation.")
# unpacking data from generation
self.initial_agent_constraints = inital_agent_constraints
self.agents = population_data.agents
self.geographic_circles = population_data.geographic_circles
self.social_circles_by_connection_type = population_data.social_circles_by_connection_type
self.geographic_circle_by_agent_index = population_data.geographic_circle_by_agent_index
self.social_circles_by_agent_index = population_data.social_circles_by_agent_index
self.matrix_type = matrix_data.matrix_type
self.matrix = matrix_data.matrix
self.depth = matrix_data.depth
self.run_args = run_args
# setting up medical things
self.consts = consts
self.medical_machine = consts.medical_state_machine()
initial_state = self.medical_machine.initial
self.pending_transfers = PendingTransfers()
# the manager holds the vector, but the agents update it
self.contagiousness_vector = np.zeros(len(
self.agents), dtype=float) # how likely to infect others
self.susceptible_vector = np.zeros(len(self.agents),
dtype=bool) # can get infected
# healthcare related data
self.living_agents_vector = np.ones(len(self.agents), dtype=bool)
self.test_willingness_vector = np.zeros(len(self.agents), dtype=float)
self.tested_vector = np.zeros(len(self.agents), dtype=bool)
self.tested_positive_vector = np.zeros(len(self.agents), dtype=bool)
self.ever_tested_positive_vector = np.zeros(len(self.agents),
dtype=bool)
self.date_of_last_test = np.zeros(len(self.agents), dtype=int)
self.pending_test_results = PendingTestResults()
# initializing agents to current simulation
for agent in self.agents:
agent.add_to_simulation(self, initial_state)
initial_state.add_many(self.agents)
# initializing simulation modules
self.simulation_progression = SimulationProgression(
[Supervisable.coerce(a, self) for a in supervisable_makers], self)
self.update_matrix_manager = update_matrix.UpdateMatrixManager(self)
self.infection_manager = infection.InfectionManager(self)
self.healthcare_manager = healthcare.HealthcareManager(self)
self.medical_state_manager = MedicalStateManager(self)
self.policy_manager = PolicyManager(self)
self.current_step = 0
# initializing data for supervising
# dict(day:int -> message:string) saving policies messages
self.policies_messages = defaultdict(str)
self.sick_agents = SickAgents()
self.new_sick_counter = 0
self.new_detected_daily = 0
self.logger.info("Created new simulation.")
self.simulation_progression.snapshot(self)
def run_simulation(args):
matrix_data = MatrixData.import_matrix_data(args.matrix_data)
population_data = PopulationData.import_population_data(args.population_data)
initial_agent_constraints = InitialAgentsConstraints(args.agent_constraints_path)
if args.simulation_parameters_path:
consts = Consts.from_file(args.simulation_parameters_path)
else:
consts = Consts()
set_seeds(args.seed)
sm = SimulationManager(
(
# "Latent",
Supervisable.State.AddedPerDay("Asymptomatic"),
Supervisable.State.Current("Asymptomatic"),
Supervisable.State.TotalSoFar("Asymptomatic"),
# "Silent",
# "Asymptomatic",
# "Symptomatic",
# "Deceased",
# "Hospitalized",
# "ICU",
# "Susceptible",
# "Recovered",
Supervisable.Sum(
"Latent",
"Latent-Asymp",
"Latent-Presymp",
"Asymptomatic",
"Pre-Symptomatic",
"Mild-Condition",
"NeedOfCloseMedicalCare",
"NeedICU",
"ImprovingHealth",
"PreRecovered",
name="currently sick"
),
# LambdaValueSupervisable("ever hospitalized", lambda manager: len(manager.medical_machine["Hospitalized"].ever_visited)),
LambdaValueSupervisable(
"was ever sick",
lambda manager: len(manager.agents) - manager.medical_machine["Susceptible"].agent_count,
),
Supervisable.NewCasesCounter(),
Supervisable.Wrappers.Growth(Supervisable.NewCasesCounter(), 1),
Supervisable.Wrappers.RunningAverage(Supervisable.Wrappers.Growth(Supervisable.NewCasesCounter()), 7),
Supervisable.Wrappers.Growth(Supervisable.NewCasesCounter(), 7),
# Supervisable.GrowthFactor(
# Supervisable.Sum("Symptomatic", "Asymptomatic", "Latent", "Silent", "ICU", "Hospitalized"),
# LambdaValueSupervisable("Detected Daily", lambda manager: manager.new_detected_daily),
# LambdaValueSupervisable("Current Confirmed Cases", lambda manager: sum(manager.tested_positive_vector)),
# Supervisable.R0(),
# Supervisable.Delayed("Symptomatic", 3),
),
population_data,
matrix_data,
initial_agent_constraints,
run_args=args,
consts=consts,
)
print(sm)
sm.run()
df: pd.DataFrame = sm.dump(filename=args.output)
df.plot()
if args.figure_path:
if not os.path.splitext(args.figure_path)[1]:
args.figure_path = args.figure_path+'.png'
plt.savefig(args.figure_path)
else:
plt.show()
def monte_carlo_state_machine_analysis(configuration: Dict) -> Dict:
"""
:param configuration: Dictionary with configuration for the mc run
configuration must contain:
* population_size for the mc
configuration might contain:
* consts_file - For loading Consts()
* circle_consts file - for loading CircleConsts
:return: Dictionary with statistics of the run:
* population_size
* days_passed - time it took to all the agents to recover/die
* time_in_each_state - for each state, total number of days all agents were in it
* visitors_in_each_state - Number of agents that visited each state
* average_duration_in_state - Empirical mean time to stay
at state conditioned that we enter it
* state_duration_expected_time - Empirical mean to stay in state, not conditioned
* average_time_to_terminal -Empirical mean time until death/recovery
"""
if 'consts_file' in configuration:
consts = Consts.from_file(configuration['consts_file'])
else:
consts = Consts()
if "circle_consts_file" in configuration:
circle_const = CirclesConsts.from_file(
configuration['circle_consts_file'])
else:
circle_const = CirclesConsts()
population_size = configuration["monte_carlo_size"]
medical_state_machine = consts.medical_state_machine()
medical_machine_manager = MedicalStateManager(
medical_state_machine=medical_state_machine)
agents_list = _generate_agents_randomly(population_size=population_size,
circle_consts=circle_const)
_infect_all_agents(agents_list, medical_machine_manager,
medical_state_machine)
medical_states = medical_state_machine.states
terminal_states = list(filter(_is_terminal_state, medical_states))
state_counter = Counter({m.name: m.agent_count for m in medical_states})
sum_days_to_terminal = 0
days_passed = 1
number_terminals_agents = 0
while number_terminals_agents != population_size:
# No manager so we don't update it
previous_terminal_agents = sum(
[m.agent_count for m in terminal_states])
medical_machine_manager.step(list())
number_terminals_agents = sum([m.agent_count for m in terminal_states])
new_terminals = number_terminals_agents - previous_terminal_agents
for m in medical_states:
state_counter[m.name] += m.agent_count
days_passed += 1
sum_days_to_terminal += days_passed * new_terminals
average_state_time_duration, state_duration_expected_time = _get_empirical_state_times(
medical_state_machine, population_size, state_counter)
return dict(population_size=population_size,
days_passed=days_passed,
time_in_each_state=dict(state_counter),
visitors_in_each_state={
m.name: len(m.ever_visited)
for m in medical_state_machine.states
},
average_duration_in_state=average_state_time_duration,
state_duration_expected_time=state_duration_expected_time,
average_time_to_terminal=sum_days_to_terminal /
population_size)
