def test_update_individual(self):
test = self.namespace_under_test
# self.debug = True
self.create_generic_gene_gina()
curr_expected_gene_age = self.gene['expected']['age']
curr_expected_gina_age = self.gina['expected']['age']
timestep_size = 1 # TODO: figure out how to set / configure this
gene = self.gene['observed']
gina = self.gina['observed']
gina_became_possible_mother = test.is_possible_mother(gina)
gina_ceased_potential_motherhood = False
age_of_potential_motherhood = None
age_of_ceased_motherhood_potential = None
self.assertFalse(gina_became_possible_mother,
"gina should not be a possible mother at creation.")
for x in range(14600):
self.check_property_of_individual('age',
curr_expected_gene_age,
test.get_age(gene),
individual_label="gene")
self.check_property_of_individual('age',
curr_expected_gina_age,
test.get_age(gina),
individual_label="gina")
if not gina_became_possible_mother:
gina_became_possible_mother = test.is_possible_mother(gina)
if gina_became_possible_mother:
age_of_potential_motherhood = curr_expected_gina_age
elif not test.is_possible_mother(
gina) and not gina_ceased_potential_motherhood:
gina_ceased_potential_motherhood = True
age_of_ceased_motherhood_potential = curr_expected_gina_age
test.update(gene)
test.update(gina)
curr_expected_gina_age += timestep_size
curr_expected_gene_age += timestep_size
self.assertTrue(gina_became_possible_mother,
"gina should have become a possible mother.")
if self.debug:
print(
f"gina became a possible mother at age {age_of_potential_motherhood}.\nm"
)
self.assertTrue(gina_ceased_potential_motherhood,
"gina should have ceased being a potential mother.")
if self.debug:
print(
f"gina ceased potential motherhood at age {age_of_ceased_motherhood_potential}.\n"
)
def do_shedding_update(human_pop):
# This is not optimal. Only optimize if it really helps
global fertility
if fertility is None:
config = json.loads(open("nd.json").read())
fertility = config["Enable_Birth"] and config["Enable_Vital_Dynamics"]
stat_pop = 0
for human in human_pop:
hum_id = human["id"]
mcw = gi.get_mcw(hum_id)
#Can we make this conditional on
if fertility:
nd.update_node_stats(
(mcw, 0, gi.is_possible_mother(hum_id),
0)) # mcw, infectiousness, is_poss_mom, is_infected
"""
if gi.is_infected(hum_id):
if gi.has_latent_infection(hum_id):
print( "{0} has latent infection.".format( hum_id ) )
else:
print( "{0} has active infection (I guess).".format( hum_id ) )
else:
print( "{0} has no infection.".format( hum_id ) )
"""
stat_pop += mcw
if gi.is_infected(hum_id):
gi.update1(hum_id) # this should do shedding & vital-dynamics
return stat_pop
def do_shedding_update(human_pop):
for human in human_pop:
hum_id = human["id"]
nd.update_node_stats(
(1.0, 0, gi.is_possible_mother(hum_id),
0)) # mcw, infectiousness, is_poss_mom, is_infected
"""
if gi.is_infected(hum_id):
if gi.has_latent_infection(hum_id):
print( "{0} has latent infection.".format( hum_id ) )
else:
print( "{0} has active infection (I guess).".format( hum_id ) )
else:
print( "{0} has no infection.".format( hum_id ) )
"""
gi.update1(hum_id) # this should do shedding & vital-dynamics
def do_vitaldynamics_update(human_pop,
graveyard,
contagion,
census_cb=None,
death_cb=None):
num_infected = 0
num_incubating = 0
num_active = 0
num_suscept = 0
num_recover = 0
num_people = 0
num_deaths = 0
new_graveyard = []
for human in human_pop:
hum_id = human["id"]
if census_cb != None:
census_cb(hum_id)
gi.update2(
hum_id
) # this should do exposure; possible optimization would be to skip this entirely if zero contagion
mcw = gi.get_mcw(hum_id)
if gi.is_dead(hum_id):
# somebody died
print("{0} is dead.".format(hum_id))
new_graveyard.append(human)
num_deaths += mcw # can't use len(graveyard) coz mcw
if death_cb != None:
death_cb(hum_id)
num_people += mcw
global fertility
if fertility:
ipm = gi.is_possible_mother(hum_id)
ip = gi.is_pregnant(hum_id)
if hum_id == 0:
pdb.set_trace()
age = gi.get_age(hum_id)
#print( "Calling cfp with {0}, {1}, {2}, and {3}.".format( str(ipm), str(ip), str(age), str(hum_id) ) )
# TBD: Optimization? I happen to know that this is only necessary for females of a
# certain age. But technically that knowledge is for nd.
nd.consider_for_pregnancy((ipm, ip, hum_id, age, 1.0))
#print( str( json.loads(gi.serialize( hum_id ))["individual"]["susceptibility"] ) )
if gi.is_infected(hum_id):
if is_incubating(hum_id):
num_incubating += mcw
else:
num_infected += mcw # TBD: use_mcw
elif gi.get_immunity(hum_id) != 1.0:
num_recover += mcw # TBD: use mcw
else:
num_suscept += mcw # TBD: use mcw
#if gi.has_active_infection( hum_id ):
# num_active += 1
# serialize seems to be broken when you had an intervention (or at least a SimpleVaccine)
#serial_man = gi.serialize( hum_id )
#if hum_id == 1:
#print( json.dumps( json.loads( serial_man ), indent=4 ) )
#print( "infectiousness: " + str( json.loads( serial_man )["individual"]["infectiousness"] ) )
#print( "Updating fertility for this timestep." )
for corpse in new_graveyard:
if corpse in human_pop:
human_pop.pop(human_pop.index(corpse))
else:
print("Exception trying to remove individual from python list: " +
str(ex))
graveyard.extend(new_graveyard)
nd.update_fertility()
exposeds.append(num_incubating)
prevalence.append(num_infected)
active_prevalence.append(num_active)
susceptible.append(num_suscept)
recovered.append(num_recover)
disdeaths.append(num_deaths)
def do_vitaldynamics_update(human_pop,
graveyard,
census_cb=None,
death_cb=None):
num_infected = 0
num_incubating = 0
num_active = 0
num_suscept = 0
num_recover = 0
new_graveyard = []
for human in human_pop:
hum_id = human["id"]
if census_cb != None:
census_cb(hum_id)
gi.update2(hum_id) # this should do exposure
if gi.is_dead(hum_id):
# somebody died
print("{0} is dead.".format(hum_id))
new_graveyard.append(human)
if death_cb != None:
death_cb(hum_id)
# TESTING THIS
ipm = gi.is_possible_mother(hum_id)
ip = gi.is_pregnant(hum_id)
if hum_id == 0:
pdb.set_trace()
age = gi.get_age(hum_id)
#print( "Calling cfp with {0}, {1}, {2}, and {3}.".format( str(ipm), str(ip), str(age), str(hum_id) ) )
nd.consider_for_pregnancy((ipm, ip, hum_id, age, 1.0))
#print( str( json.loads(gi.serialize( hum_id ))["individual"]["susceptibility"] ) )
if gi.is_infected(hum_id):
if is_incubating(hum_id):
num_incubating += 1
else:
num_infected += 1 # TBD: use_mcw
elif gi.get_immunity(hum_id) != 1.0:
num_recover += 1 # TBD: use mcw
else:
num_suscept += 1 # TBD: use mcw
#if gi.has_active_infection( hum_id ):
# num_active += 1
# serialize seems to be broken when you had an intervention (or at least a SimpleVaccine)
#serial_man = gi.serialize( hum_id )
#if hum_id == 1:
#print( json.dumps( json.loads( serial_man ), indent=4 ) )
#print( "infectiousness: " + str( json.loads( serial_man )["individual"]["infectiousness"] ) )
#print( "Updating fertility for this timestep." )
for corpse in new_graveyard:
if corpse in human_pop:
human_pop.pop(human_pop.index(corpse))
else:
print("Exception trying to remove individual from python list: " +
str(ex))
graveyard.extend(new_graveyard)
nd.update_fertility()
exposeds.append(num_incubating)
prevalence.append(num_infected)
active_prevalence.append(num_active)
susceptible.append(num_suscept)
recovered.append(num_recover)
disdeaths.append(len(graveyard))