def create_person_callback(mcw, age, gender):
"""
This callback is required by dtk_nodedemographic during population initialization.
It can be named anything as long as it is registered via the appropriate callback.
It takes 3 parameters: monte-carlo weight, age, and sex.
"""
if random.random() <= 0.23:
age = random.randrange(0, ADULT_CHILD_AGE_THRESHOLD)
else:
age = random.randrange(ADULT_CHILD_AGE_THRESHOLD, 36500)
# print("Creating {}.".format("ADULT" if age >= ADULT_CHILD_AGE_THRESHOLD else "CHILD"))
# TODO: move some of this to core.
global human_pop # make sure Python knows to use module-level variable human_pop
#global timestep
global nursery
person = {}
person["mcw"] = mcw
person["age"] = age / 365
person["sex"] = gender
new_id = gi.create(gender, age, mcw)
person["id"] = new_id
human_pop.append(person)
if age == 0:
month_step = int(timestep / 30.0)
#print( "Made a baby on timestep {0}/month {1}.".format( str( timestep ), str( month_step ) ) )
if month_step not in nursery:
nursery[month_step] = (0, 0)
boys = nursery[month_step][0]
girls = nursery[month_step][1]
if gender == 0:
boys += mcw
else:
girls += mcw
nursery[month_step] = (boys, girls)
def perf_bench():
sillypop = []
for _ in range(1000):
sillypop.append( gi.create( ( 1, 1.0, 1.0 ) ) )
start_time = timeit.default_timer()
for t in range(7300):
for human in sillypop:
gi.update( human )
elapsed = timeit.default_timer() - start_time
print( str( elapsed ) )
def create_population(self,
population_count,
age_gaussian_mean=20,
age_gaussian_sigma=7,
probability_male=0.5):
total_population = 0
monte_carlo_weight = 1.0
while total_population < population_count:
sex_draw = random.random()
current_sex = 0
if sex_draw < probability_male:
current_sex = 1
pass
current_age = int(
np.random.normal(loc=age_gaussian_mean,
scale=age_gaussian_sigma) * DAYS_YEAR)
# TODO: It would be nice if I didn't have to talk to numpy here
human = dgi.create((current_sex, current_age, monte_carlo_weight))
self.humans.append(human)
total_population += 1
def create_person_callback(self, mcw, age, gender):
self.humans.append(dgi.create((gender, age, mcw)))
import dtk_generic_intrahost as dgi
people = []
# First, make 100 people. Half men half women, age all 20
for x in range(100):
sex = x%2
person = dgi.create((sex, 7300, 1.0))
people.append(person)
pass
print("Created people.")
# Now, touch each one with an infection before we spin time
for victim in people:
dgi.force_infect(victim)
pass
print("Forced infections.")
for x in range(25):
for person in people:
dgi.update(person)
pass
pass
incubating = 0
infected = 0
for person in people:
if dgi.is_incubating(person):
incubating += 1
pass