def test_createInfectedPersons(helpers):
"""
#create population with 5 people ages [9,19,29,39,49]
#test that each day one of them is getting immuned
"""
helpers.clean_outputs()
#Editig confige file saving is nessery
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
ConfigData = None
#reading the confige file
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
persons_arr = list(map(Person, [9,19,29,39,49,59]))
assert len(persons_arr) == 6
env_arr = []
my_world = World(
all_people = persons_arr,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.run_simulation(7,"test_simulation",datas_to_plot = None,extensionsList = ["ImmuneByAgeExtension","EmptyExtension"] )
cnt = sum([1 for p in persons_arr if p.get_disease_state() == DiseaseState.IMMUNE])
assert cnt == 4
def __init__(self, network, T=5, dt=.001, **kwargs):
"""
Pass in a wc unit, set up recordings, get ready to run.
Args:
sensory_units (SensoryWCUnit): it should already have everything you want connected to it
T (float): T in seconds
dt (float): integration timestep (seconds)
**kwargs:
Derived attributes:
self.tax (numpy.array): time axis
self.ttot (int): total number of time steps
self.t_i (int): the current time step
self.traces (dict): traces
"""
Simulation.__init__(self, T=T, dt=dt, **kwargs)
self.network = network
self.traces = OrderedDict()
# just slap a trace on there?
for unit in self.network.units:
# we'll just staple the traces to the unit, maybe this is wrong but it should make things easier
unit.trace_dict = OrderedDict()
trace_sources = OrderedDict(
FR=unit.r) # , stim=unit.stim, SFA=unit.a
# )
for k, v in trace_sources.items():
self.add_new_trace(unit, source=v, trace_name=k)
current_trace_sources = unit.currents
for k, v in current_trace_sources.items():
self.add_new_current_trace(unit, source=v, trace_name=k)
def __init__(self, sensory_unit=None, T=5, dt=.001, **kwargs):
"""
Pass in a wc unit, set up recordings, get ready to run.
Args:
sensory_unit (SensoryWCUnit): it should already have everything you want connected to it
T (float): T in seconds
dt (float): integration timestep (seconds)
**kwargs:
Derived attributes:
self.tax (numpy.array): time axis
self.ttot (int): total number of time steps
self.t_i (int): the current time step
self.traces (dict): traces
"""
Simulation.__init__(self, T=T, dt=dt, **kwargs)
self.unit = sensory_unit
trace_sources = {
"FR": sensory_unit.r,
"stim": sensory_unit.stim,
"SFA": sensory_unit.a,
# "u1_S": wc_unit.S
}
for k, v in trace_sources.items():
self.add_new_trace(source=v, trace_name=k)
def test_immune_and_get_events1():
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
Expected = -1
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
p = Person(30)
ok , events = p.immune_and_get_events(INITIAL_DATE , timedelta(days = 15), \
((DiseaseState.SUSCEPTIBLE,timedelta(10)),(DiseaseState.IMMUNE,timedelta(21))))
assert len(events) == 2
assert ok
persons_arr = [p]
env_arr = []
small_world = world.World(all_people=persons_arr,
all_environments=env_arr,
generating_city_name="test",
generating_scale=1)
my_simulation = Simulation(world=small_world,
initial_date=INITIAL_DATE,
interventions=[])
for i in range(10):
my_simulation.simulate_day()
events[0].apply(simulation=my_simulation)
assert p.get_disease_state() == DiseaseState.IMMUNE
assert len(p._seir_times) == 3
def __init__(self, network, T=5, dt=.001, **kwargs):
"""
Pass in a wc unit, set up recordings, get ready to run.
Args:
sensory_units (SensoryWCUnit): it should already have everything you want connected to it
T (float): T in seconds
dt (float): integration timestep (seconds)
**kwargs:
Derived attributes:
self.tax (numpy.array): time axis
self.ttot (int): total number of time steps
self.t_i (int): the current time step
self.traces (dict): traces
"""
Simulation.__init__(self, T=T, dt=dt, **kwargs)
self.network = network
self.traces = OrderedDict()
for name, unit in self.network.units.items():
trace_sources = OrderedDict(
FR=unit.r, stim=unit.stim, SFA=unit.a
)
self.traces[unit.name] = OrderedDict()
for k, v in trace_sources.items():
self.add_new_trace(unit, source=v, trace_name=k)
def test_simulation_init():
eps = .000001
sim = Simulation()
assert sim.ttot == 5 / .001
sim2 = Simulation(dt=.05, T=5000)
tax = sim2.tax
assert tax[-1] - tax[-2] - .05 < eps
def test_createInfectedPersonsOredredASCENDING():
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
Expected = -1
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
kids = [0,4,8,12,16]
adults = [25,29,33]
ageList = kids + adults
youngest = Person(21)
Oldest = Person(37)
PersonList = list(map(Person, ageList))
PersonList = PersonList + [youngest , Oldest]
env_arr = []
my_world = World(
all_people = PersonList,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.infect_random_set(num_infected = 0, infection_doc = "", per_to_immune = 0.5,order= ORDER.ASCENDING,city_name = None,min_age=18,people_per_day =1)
my_simulation.simulate_day()
assert youngest.get_disease_state() == DiseaseState.IMMUNE
#Can't check day by day lots of noise with seir times
for _ in range(4):
my_simulation.simulate_day()
cnt_immune =0
for person in my_world.all_people():
if person.get_disease_state() == DiseaseState.IMMUNE:
cnt_immune = cnt_immune + 1
assert cnt_immune <= 5
def test_nested_trace():
# this seems very annoying... TODO: I HATE THIS
sim = Simulation()
sim.traces["foo"] = dict()
src = [0]
trc = Trace(sim, source=src, target=sim.traces["foo"], trace_name="bar")
# print(trc.__dict__.get("source"))
for ind in xrange(5):
src[0] = ind
trc.update_trace()
trc.sim.step()
print(sim.traces["foo"]["bar"].source)
print(sim.traces["foo"]["bar"].trace)
assert len(sim.traces["foo"]["bar"].trace) == sim.ttot
assert sim.traces["foo"]["bar"].source[0] == 4
assert sim.traces["foo"]["bar"].trace[4] == 4
def create_and_run_simulation(self,
outdir,
stop_early,
with_population_caching=True,
verbosity=False):
"""
The main function that handles the run of the simulation by the task.
It updated the params changes, loads or creates the population, initializes the simulation and runs it.
:param outdir: the output directory for the task
:param stop_early: only relevant to R computation, see Simulation doc
:param with_population_caching: bool, if False generates the population, else - tries to use the cache and save time.
:param verbosity: bool, if it's True then additional output logs will be printed to the screen
"""
seed.set_random_seed()
config_path = os.path.join(os.path.dirname(__file__), "config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
citiesDataPath = ConfigData['CitiesFilePath']
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),
paramsDataPath),
override=True)
for param, val in self.params_to_change.items():
Params.loader()[param] = val
DiseaseState.init_infectiousness_list()
citiesDataPath = citiesDataPath
population_loader = PopulationLoader(
citiesDataPath,
added_description=Params.loader().description(),
with_caching=with_population_caching,
verbosity=verbosity)
world = population_loader.get_world(city_name=self.city_name,
scale=self.scale)
sim = Simulation(world,
self.initial_date,
self.interventions,
verbosity=verbosity,
outdir=outdir,
stop_early=stop_early)
self.infection_params.infect_simulation(sim, outdir)
sim.run_simulation(self.days,
self.scenario_name,
datas_to_plot=self.datas_to_plot)
def evaluate(self, individual: Individual) -> Fitness:
"""Evaluate an individual on the proving grounds. Return a fitness of this individual."""
if individual not in self.__score_board:
baits_eaten, steps_used = Simulation(AntStateMachine.from_chromosome(individual.chromosome), self.__grid).run()
fitness = Fitness.from_result(self.__total_baits, baits_eaten, steps_used)
self.__score_board[individual] = fitness
return self.__score_board[individual]
def test_ImmuneGeneralPopulationIntervention():
#pretesting
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
my_intervention = ImmuneGeneralPopulationIntervention(
compliance=1,
start_date=INITIAL_DATE,
duration=daysdelta(40),
people_per_day=1,
min_age=15)
assert my_intervention is not None
persons_arr = list(map(Person, [10, 20, 30]))
assert len(persons_arr) == 3
env_arr = []
small_world = World(all_people=persons_arr,
all_environments=env_arr,
generating_city_name="test",
generating_scale=1)
my_simulation = Simulation(world=small_world,
initial_date=INITIAL_DATE,
interventions=[my_intervention])
#test
lst = my_intervention.generate_events(small_world)
#Assert results
assert lst is not None
assert len(lst) == 2
for i in range(1):
assert isinstance(lst[i], DayEvent)
my_simulation.simulate_day()
cnt_immune = sum([
1 for p in persons_arr if p.get_disease_state() == DiseaseState.IMMUNE
])
assert cnt_immune == 1
my_simulation.simulate_day()
cnt_immune = sum([
1 for p in persons_arr if p.get_disease_state() == DiseaseState.IMMUNE
])
assert cnt_immune == 2
my_simulation.simulate_day()
cnt_immune = sum([
1 for p in persons_arr if p.get_disease_state() == DiseaseState.IMMUNE
])
assert cnt_immune == 2
def __init__(self,
syn_weights=weights,
selectivities=s_units,
stimulus=stim,
**kwargs):
TonotopicNetwork.__init__(self, selectivities, stimulus, **kwargs)
Simulation.__init__(self, **kwargs) # is this black magic?
""" this guy would take a bunch of selectivities and make some units """
self.syn_weights = syn_weights
# now we build us some arrays - we're going to vectorize
self.R_var_array = np.zeros([len(self.units), self.ttot])
self.A_var_array = np.zeros([len(self.units), self.ttot])
self.S_var_array = np.zeros([len(self.units), self.ttot])
# pull out the vars from the vars arrays
self.vars = [
x.split("_")[0] for x in self.__dict__ if x.endswith("_var_array")
]
self.stim_currents = self.build_stimulus_currents()
# list of units
units_array = self.units
self.gstims = np.array(
[x.currents["stim"].weight for x in units_array])
self.i_0s = np.array([x.i_0 for x in units_array])
self.gees = np.array([x.gee for x in units_array])
self.gSFAs = np.array([x.gSFA for x in units_array])
self.Gs = np.array([x.G for x in units_array])
self.taus = np.array([x.tau for x in units_array])
self.tauAs = np.array([x.tauA for x in units_array])
self.tauNMDAs = np.array([x.tauNMDA for x in units_array])
# activation function parameters
self.kes = np.array([x.ke for x in units_array])
self.thes = np.array([x.the for x in units_array])
self.f_e = self.f_activation_builder(self.kes, self.thes)
self.kSs = np.array([x.kS for x in units_array])
self.thSs = np.array([x.thS for x in units_array])
self.f_S = self.f_activation_builder(self.kSs, self.thSs, self.b_00)
# initialize
self.point_wise_Isyn = np.outer(self.syn_weights, self.R_var_array)
def test_SymptomaticIsolationIntervention_Genarete_events(helpers):
#pretesting
helpers.clean_outputs()
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
my_intervention = SymptomaticIsolationIntervention(compliance=1,
start_date=INITIAL_DATE,
duration=daysdelta(40))
assert my_intervention is not None
persons_arr = list(map(Person, [10, 20, 30]))
assert len(persons_arr) == 3
env_arr = []
small_world = World(all_people=persons_arr,
all_environments=env_arr,
generating_city_name="test",
generating_scale=1)
my_simulation = Simulation(world=small_world,
initial_date=INITIAL_DATE,
interventions=[my_intervention])
#test
lst = my_intervention.generate_events(small_world)
#Assert results
assert lst is not None
assert len(lst) == 3
for i in range(1):
assert isinstance(lst[i], DayEvent)
for person in persons_arr:
assert len(list(person.state_to_events.keys())) == (1 + 4)
my_simulation.run_simulation(name="test", num_days=60)
def test_createInfectedPersons3():
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
Expected = -1
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
kids = [random.randint(0,17) for i in range(5)]
adults = [random.randint(19,40) for i in range(5)]
ageList = kids + adults
PersonList = list(map(Person, ageList))
env_arr = []
my_world = World(
all_people = PersonList,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.infect_random_set(num_infected = 0, infection_doc = "", per_to_immune = 0.5,Immune_compliance = 0,city_name = None,min_age=18,people_per_day =5)
my_simulation.simulate_day()
#assert events dictionary is not empty
cnt_immune = 0
for person in my_world.all_people():
if person.get_disease_state() == DiseaseState.IMMUNE:
cnt_immune = cnt_immune + 1
assert cnt_immune == 0
def test_createInfectedPersonsBestEffort2():
"""
Test that when the population size is less then the amount of people that had been chosen to be infected,
the simulation doesn't crash
"""
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
ageList = [random.randint(19,40) for i in range(10)]
PersonList = list(map(Person, ageList))
env_arr = []
my_world = World(
all_people = PersonList,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.infect_random_set(num_infected = 0, infection_doc = "", per_to_immune = 2,city_name = None,min_age=18,people_per_day =0)
my_simulation.simulate_day()
cnt_immune = 0
cnt_sick = 0
for person in my_world.all_people():
if person.get_disease_state() == DiseaseState.IMMUNE:
cnt_immune += 1
else:
cnt_sick += 1
assert cnt_immune == 10
assert cnt_sick == 0
def test_trace():
sim = Simulation()
src = [0]
trc = Trace(sim, source=src, target=sim.traces, trace_name="foo")
# print(trc.__dict__.get("source"))
for ind in xrange(5):
src[0] = ind
trc.update_trace()
trc.sim.step()
#print(trc.__dict__)
assert len(trc.trace) == trc.sim.ttot
trc.trace[:5]
assert all(trc.trace[:5] == np.array([0., 1., 2., 3., 4.]))
def test_createInfectedPersonsByHouseHoldBestEffort2():
"""
Test that when the population size is less then the amount of people that had been chosen to be infected by households,
the simulation doesn't crash
"""
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
#create diff enviroments
KidsHouse = Household(city = None,contact_prob_between_each_two_people=1)
AdultsHouse = Household(city = None,contact_prob_between_each_two_people=1)
MixedHouse = Household(city = None,contact_prob_between_each_two_people=1)
kidsAges = [random.randint(0,17) for i in range(4)]
adultsAges = [random.randint(19,40) for i in range(3)]
KidsLst = list(map(Person, kidsAges))
adultsLst = list(map(Person, adultsAges))
persons_arr = KidsLst + adultsLst
#register people to diff env
KidsHouse.sign_up_for_today(KidsLst[0],1)
KidsHouse.sign_up_for_today(KidsLst[1],1)
AdultsHouse.sign_up_for_today(adultsLst[0],1)
AdultsHouse.sign_up_for_today(adultsLst[1],1)
MixedHouse.sign_up_for_today(adultsLst[2],1)
MixedHouse.sign_up_for_today(KidsLst[2],1)
MixedHouse.sign_up_for_today(KidsLst[3],1)
assert len(KidsHouse.get_people()) == 2
assert len(AdultsHouse.get_people()) == 2
assert len(MixedHouse.get_people()) == 3
env_arr = [KidsHouse,AdultsHouse,MixedHouse]
my_world = World(
all_people = persons_arr,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1,)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.immune_households_infect_others(num_infected = 0, infection_doc = "", per_to_immune = 2 ,city_name = None,min_age=18,people_per_day =5)
my_simulation.simulate_day()
cnt_immune = 0
cnt_sick = 0
for person in my_world.all_people():
if person.get_disease_state() == DiseaseState.IMMUNE:
cnt_immune += 1
elif person.get_disease_state() != DiseaseState.SUSCEPTIBLE:
cnt_sick += 1
assert cnt_immune == 3
assert cnt_sick == 0
def test_current_trace():
src = [0]
curr = dCurrent(source=src, weight=0.5, target={}, name="foo")
sim = Simulation()
tar = {}
trc = CurrentTrace(sim=sim, source=curr, target=tar, trace_name="foo")
print(tar)
assert isinstance(tar["foo"], CurrentTrace)
for ind in xrange(5):
src[0] = ind
curr.update()
trc.update_trace()
trc.sim.step()
trc.update_trace()
# print trc.trace[:10]
assert trc.trace[4] == src[0] * curr.weight
def main():
simulation = Simulation()
city = City.from_numbers(600, 100).assign_bikes_randomly()
time = time_of_number_of_days(7)
simulation.simulate(city, time)
ResultWriter.write_to_excel(simulation.get_stations_data(),
"stations_states.xlsx")
ResultWriter.write_to_excel(simulation.get_breaking_bikes_data(),
"bikes_breaking.xlsx")
def test_immune_and_get_events5():
"""
Test that a person that is not Susptible nor latent when he should get immuned continues his
usual path to his death
"""
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
Expected = -1
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
p = Person(30)
ok, events = p.immune_and_get_events(INITIAL_DATE , timedelta(days = 20), \
((DiseaseState.SUSCEPTIBLE,timedelta(10)),(DiseaseState.LATENT,timedelta(5)),\
(DiseaseState.ASYMPTOMATICINFECTIOUS,timedelta(5)),(DiseaseState.DECEASED,timedelta(5)),(DiseaseState.DECEASED,None)))
assert len(events) == 4
assert ok == False
persons_arr = [p]
env_arr = []
small_world = world.World(all_people=persons_arr,
all_environments=env_arr,
generating_city_name="test",
generating_scale=1)
my_simulation = Simulation(world=small_world,
initial_date=INITIAL_DATE,
interventions=[])
for i in range(10):
my_simulation.simulate_day()
events[0].apply(simulation=my_simulation)
assert p.get_disease_state() == DiseaseState.LATENT
for i in range(5):
my_simulation.simulate_day()
events[1].apply(simulation=my_simulation)
assert p.get_disease_state() == DiseaseState.ASYMPTOMATICINFECTIOUS
#Because this person was not susptible nor latent he cannot be immuned
for i in range(5):
my_simulation.simulate_day()
events[2].apply(simulation=my_simulation)
assert p.get_disease_state() == DiseaseState.DECEASED
def test_working(self):
city = City.from_numbers(100, 10).assign_bikes_randomly()
time = time_of_number_of_days(3)
simulaiton = Simulation()
simulaiton.simulate(city, time)
broken_bikes = simulaiton.get_breaking_bikes_data()
trips_history = simulaiton.get_stations_data()
res_stations_changes = station_changes.StationChanges(
trips_history).find_stations_changes()
scores = bikes_scoring.BikesScoring(res_stations_changes).score_bikes()
def test_createImmunehouseholds4():
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
#create diff enviroments
KidsHouse = Household(city = None,contact_prob_between_each_two_people=1)
AdultsHouse = Household(city = None,contact_prob_between_each_two_people=1)
MixedHouse = Household(city = None,contact_prob_between_each_two_people=1)
kidsAges = [random.randint(0,17) for i in range(4)]
adultsAges = [random.randint(19,40) for i in range(3)]
KidsLst = list(map(Person, kidsAges))
adultsLst = list(map(Person, adultsAges))
persons_arr = KidsLst + adultsLst
#register people to diff env
KidsHouse.sign_up_for_today(KidsLst[0],1)
KidsHouse.sign_up_for_today(KidsLst[1],1)
AdultsHouse.sign_up_for_today(adultsLst[0],1)
AdultsHouse.sign_up_for_today(adultsLst[1],1)
MixedHouse.sign_up_for_today(adultsLst[2],1)
MixedHouse.sign_up_for_today(KidsLst[2],1)
MixedHouse.sign_up_for_today(KidsLst[3],1)
assert len(KidsHouse.get_people()) == 2
assert len(AdultsHouse.get_people()) == 2
assert len(MixedHouse.get_people()) == 3
env_arr = [KidsHouse,AdultsHouse,MixedHouse]
my_world = World(
all_people = persons_arr,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1,)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.immune_households_infect_others(num_infected = 0, infection_doc = "", per_to_immune = 1,Immune_compliance= 0 ,city_name = None,min_age=18,people_per_day= 3 )
my_simulation.simulate_day()
#assert events dictionary is not empty
cnt_immune = 0
for person in my_world.all_people():
if person.get_disease_state() == DiseaseState.IMMUNE:
cnt_immune = cnt_immune + 1
assert cnt_immune == 0
def perturbation_simulation():
# the main function for perturbation simulation
# initial parameters
# initial total balance of the system
total_balance = 1000000000000
# the block reward for a single round
block_reward = 0.000035 * total_balance
# the expected mining expense for a single bidder
mining_expense = 0.000006 * total_balance
# the transaction fees of the first round
transaction_fees = 0.00006 * total_balance
# the number of bid winners
bid_winner = 10
# if simulation needs to be traced in console
trace_tag = True
# True if use C-prop, False to use C-const
update_mining_cost_tag = False
# True if use R-prop, False to use R-const
update_block_reward_tag = False
# perturbation type decides which kind of perturbation will be deployed
# 1 indicates instant increase/decrease in total supply
# 2 indicates instant increase/decrease in fisher coefficient
# else for doing nothing
perturbation_type = 1
# the simulation object
simulation = Simulation(total_balance, block_reward, mining_expense,
bid_winner, transaction_fees, trace_tag,
update_mining_cost_tag, update_block_reward_tag,
perturbation_type)
# simulate round by round
total_round = 500000
for i in range(total_round):
simulation.single_round()
simulation.draw_time_series()
def test_CreateDeltaFile(helpers):
helpers.clean_outputs()
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
ageList = [random.randint(0, 40) for i in range(10)]
PersonList = list(map(Person, ageList))
events_acc = []
for person in PersonList:
states_table = ((DiseaseState.LATENT, daysdelta(3)),
(DiseaseState.ASYMPTOMATICINFECTIOUS,
daysdelta(3)), (DiseaseState.IMMUNE, daysdelta(3)),
(DiseaseState.IMMUNE, None))
events = person.gen_and_register_events_from_seir_times(
date=INITIAL_DATE, states_and_times=states_table)
events_acc += events
# person.set_disease_state(DiseaseState.LATENT)
env_arr = []
my_world = World(all_people=PersonList,
all_environments=env_arr,
generating_city_name="test",
generating_scale=1)
my_simulation = Simulation(world=my_world, initial_date=INITIAL_DATE)
my_simulation.register_events(events_acc)
my_simulation.run_simulation(num_days=10, name="test")
#assert events dictionary is not empty
txt = my_simulation.stats.get_state_stratified_summary_table(
table_format=TableFormat.CSV)
test_data = StringIO(txt)
tbl = pd.read_csv(test_data)
assert len(tbl) == 7
print(tbl)
assert tbl.iloc[0, DiseaseState.SUSCEPTIBLE.value] == 10
assert tbl.iloc[3, DiseaseState.ASYMPTOMATICINFECTIOUS.value] == 10
assert tbl.iloc[6, DiseaseState.IMMUNE.value] == 10
def test_createImmunehouseholds2():
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
#create diff enviroments
house1 = Household(city = None,contact_prob_between_each_two_people=1)
house2 = Household(city = None,contact_prob_between_each_two_people=1)
house1Ages = [98,93,5]
house2Ages = [94,6]
house1Lst = list(map(Person, house1Ages))
house2Lst = list(map(Person, house2Ages))
persons_arr = house1Lst + house2Lst
#register people to diff env
house1.sign_up_for_today(house1Lst[0],1)
house1.sign_up_for_today(house1Lst[1],1)
house1.sign_up_for_today(house1Lst[2],1)
house2.sign_up_for_today(house2Lst[0],1)
house2.sign_up_for_today(house2Lst[1],1)
assert len(house1.get_people()) == 3
assert len(house2.get_people()) == 2
env_arr = [house1,house2]
my_world = World(
all_people = persons_arr,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1,)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.immune_households_infect_others(num_infected = 0, infection_doc = "", per_to_immune = 0.6,Sort_order=ORDER.DESCENDING ,city_name = None,min_age=18,people_per_day= 3 )
my_simulation.simulate_day()
#assert events dictionary is not empty
cnt_immune = 0
for person in my_world.all_people():
if (person.get_age() in [94,93,98]) and (person.get_disease_state() == DiseaseState.IMMUNE):
cnt_immune = cnt_immune + 1
assert cnt_immune == 3
def simulate(self, individual):
self.robot.client.display_activation(False)
simulation = Simulation(self.robot.client)
simulation.start()
self.robot.init_stream()
time.sleep(0.1)
start = self.robot.position
for move in individual.moves:
self.robot.pause(True)
self.robot.wrist = math.radians(move.x())
self.robot.elbow = math.radians(move.y())
self.robot.shoulder = math.radians(move.z())
self.robot.pause(False)
self.robot.wait()
end = self.robot.position
simulation.stop()
time.sleep(0.1)
return euclidean_distance(start, end)
def test_CreateDeltaFileAtlit(helpers):
helpers.clean_outputs()
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
citiesDataPath = ConfigData['CitiesFilePath']
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
Params.loader()["person"]["state_macine_type"] = "SIR"
DiseaseState.init_infectiousness_list()
pop = population_loader.PopulationLoader(citiesDataPath)
my_world = pop.get_world(city_name='Atlit', scale=1, is_smart=False)
sim = Simulation(world=my_world, initial_date=INITIAL_DATE)
sim.infect_random_set(num_infected=500, infection_doc="")
sim.run_simulation(num_days=180, name="test")
#assert events dictionary is not empty
txt = sim.stats.get_state_stratified_summary_table(
table_format=TableFormat.CSV)
test_data = StringIO(txt)
tbl = pd.read_csv(test_data)
cnt_start = tbl.iloc[0, DiseaseState.SUSCEPTIBLE.value] + tbl.iloc[
0, DiseaseState.LATENT.value]
cnt_end = 0
for i in range(len(tbl)):
cnt_end = cnt_end + tbl.iloc[i, DiseaseState.IMMUNE.value] + tbl.iloc[
i, DiseaseState.DECEASED.value]
plug_number = len([
p for p in sim._world.all_people()
if p.get_disease_state() == DiseaseState.SUSCEPTIBLE
])
assert cnt_start >= cnt_end + plug_number
print "Connection failed!"
exit(1)
print client.id
robot = Robot(client)
if not robot.load():
print "Robot initialization failed!"
exit(1)
client.synchronous_mode()
random.seed()
for i in range(0, 3):
# Wait until the robot is settled to the default position
print "----- Simulation started -----"
simulation = Simulation(client)
simulation.start()
# client.display_activation(False)
robot.init_stream()
start = robot.position
# client.display_activation(False)
# Make the robot move randomly five times
for j in range(0, 20):
# Generating random positions for the motors
awrist = random.randint(0, 300)
aelbow = random.randint(0, 300)
ashoulder = random.randint(0, 300)
robot.pause(True)
robot.wrist = math.radians(awrist)
def test_count_infected_in_hood():
'''
Test that we gather the right data about the infected persons
in each neighborhood.
'''
config_path = os.path.join(os.path.dirname(__file__),"..","src","config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__),"..","src", paramsDataPath), override=True)
Params.loader()["person"]["state_macine_type"] = "SIR"
DiseaseState.init_infectiousness_list()
#create diff enviroments
house1 = Household(city = None,contact_prob_between_each_two_people=1)
house2 = Household(city = None,contact_prob_between_each_two_people=1)
house1Ages = [98,95,5]
house2Ages = [94,6]
house1Lst = list(map(Person, house1Ages))
house2Lst = list(map(Person, house2Ages))
#register people to diff env
house1.sign_up_for_today(house1Lst[0],1)
house1.sign_up_for_today(house1Lst[1],1)
house1.sign_up_for_today(house1Lst[2],1)
house2.sign_up_for_today(house2Lst[0],1)
house2.sign_up_for_today(house2Lst[1],1)
assert len(house1.get_people()) == 3
assert len(house2.get_people()) == 2
n1 = NeighborhoodCommunity(city= None,contact_prob_between_each_two_people= 1)
n2 = NeighborhoodCommunity(city= None,contact_prob_between_each_two_people= 1)
states_table1 = ((DiseaseState.LATENT,daysdelta(3)),
(DiseaseState.ASYMPTOMATICINFECTIOUS,daysdelta(3)),
(DiseaseState.IMMUNE, daysdelta(3)),
(DiseaseState.IMMUNE, None))
states_table2 = ((DiseaseState.IMMUNE, daysdelta(3)),
(DiseaseState.IMMUNE, None))
events_acc = []
for person in house1.get_people():
person.add_environment(n1)
events = person.gen_and_register_events_from_seir_times(date = INITIAL_DATE,states_and_times= states_table1)
events_acc += events
for person in house2.get_people():
person.add_environment(n2)
events = person.gen_and_register_events_from_seir_times(date = INITIAL_DATE,states_and_times= states_table2)
events_acc += events
env_arr = [house1,house2,n1,n2]
persons_arr = []
persons_arr += house1Lst
persons_arr += house2Lst
my_world = World(
all_people = persons_arr,
all_environments=env_arr,
generating_city_name = "test",
generating_scale = 1,)
my_simulation = Simulation(world = my_world, initial_date= INITIAL_DATE)
my_simulation.register_events(events_acc)
for i in range(4):
d1 = my_simulation.stats.get_neiborhood_data(INITIAL_DATE + daysdelta(i),n1.get_neighborhood_id())
d2 = my_simulation.stats.get_neiborhood_data(INITIAL_DATE + daysdelta(i),n2.get_neighborhood_id())
assert d1 == 0 , "Day:" + str(i)
assert d2 == 0 , "Day:" + str(i)
my_simulation.simulate_day()
for i in range(3):
d1 = my_simulation.stats.get_neiborhood_data(INITIAL_DATE + daysdelta(i+3),n1.get_neighborhood_id())
d2 = my_simulation.stats.get_neiborhood_data(INITIAL_DATE + daysdelta(i+3),n2.get_neighborhood_id())
assert d1 == 3 , "Day:" + str(3 + i)
assert d2 == 0 , "Day:" + str(3 + i)
my_simulation.simulate_day()
for i in range(3):
d1 = my_simulation.stats.get_neiborhood_data(INITIAL_DATE,n1.get_neighborhood_id())
d2 = my_simulation.stats.get_neiborhood_data(INITIAL_DATE,n2.get_neighborhood_id())
assert d1 == 0 , "Day:" + str(6 + i)
assert d2 == 0 , "Day:" + str(6 + i)
my_simulation.simulate_day()
def test_ImmuneByHouseholdIntervention():
#pretesting
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
my_intervention = ImmuneByHouseholdIntervention(compliance=1,
start_date=INITIAL_DATE,
duration=daysdelta(40),
houses_per_day=1,
min_age=18)
assert my_intervention is not None
config_path = os.path.join(os.path.dirname(__file__), "..", "src",
"config.json")
with open(config_path) as json_data_file:
ConfigData = json.load(json_data_file)
paramsDataPath = ConfigData['ParamsFilePath']
Params.load_from(os.path.join(os.path.dirname(__file__), "..", "src",
paramsDataPath),
override=True)
#create diff enviroments
KidsHouse = Household(city=None, contact_prob_between_each_two_people=1)
AdultsHouse = Household(city=None, contact_prob_between_each_two_people=1)
MixedHouse = Household(city=None, contact_prob_between_each_two_people=1)
kidsAges = [random.randint(0, 17) for i in range(4)]
adultsAges = [random.randint(19, 40) for i in range(3)]
KidsLst = list(map(Person, kidsAges))
adultsLst = list(map(Person, adultsAges))
persons_arr = KidsLst + adultsLst
#register people to diff env
KidsHouse.sign_up_for_today(KidsLst[0], 1)
KidsHouse.sign_up_for_today(KidsLst[1], 1)
AdultsHouse.sign_up_for_today(adultsLst[0], 1)
AdultsHouse.sign_up_for_today(adultsLst[1], 1)
MixedHouse.sign_up_for_today(adultsLst[2], 1)
MixedHouse.sign_up_for_today(KidsLst[2], 1)
MixedHouse.sign_up_for_today(KidsLst[3], 1)
assert len(KidsHouse.get_people()) == 2
assert len(AdultsHouse.get_people()) == 2
assert len(MixedHouse.get_people()) == 3
env_arr = [KidsHouse, AdultsHouse, MixedHouse]
my_world = World(
all_people=persons_arr,
all_environments=env_arr,
generating_city_name="test",
generating_scale=1,
)
my_simulation = Simulation(world=my_world,
initial_date=INITIAL_DATE,
interventions=[my_intervention])
#test
lst = my_intervention.generate_events(my_world)
#Assert results
assert lst is not None
assert len(lst) == 5
for i in range(1):
assert isinstance(lst[i], DayEvent)
my_simulation.simulate_day()
cnt_immune = sum([
1 for p in persons_arr if p.get_disease_state() == DiseaseState.IMMUNE
])
assert cnt_immune <= 3
my_simulation.simulate_day()
cnt_immune = sum([
1 for p in persons_arr if p.get_disease_state() == DiseaseState.IMMUNE
])
assert cnt_immune == 5
my_simulation.simulate_day()