def get_probe_flu_at(school, name=None):
return GroupSizeProbe(
name=name or school.name,
queries=[
GroupQry(attr={ 'flu': 's' }, rel={ 'school': school }),
GroupQry(attr={ 'flu': 'i' }, rel={ 'school': school }),
GroupQry(attr={ 'flu': 'r' }, rel={ 'school': school })
],
qry_tot=GroupQry(rel={ 'school': school }),
msg_mode=ProbeMsgMode.DISP
)
def sim_flu_ac_init_get_probe(school, name=None):
return GroupSizeProbe(
name=name or str(school.name),
queries=[
GroupQry(attr={ 'flu': 's' }, rel={ 'school': school }),
GroupQry(attr={ 'flu': 'e' }, rel={ 'school': school }),
GroupQry(attr={ 'flu': 'r' }, rel={ 'school': school })
],
qry_tot=GroupQry(rel={ 'school': school }),
persistance=None, # pp,
var_names=['ps', 'pe', 'pr', 'ns', 'ne', 'nr']
)
def probe_flu_at(school, name=None):
return GroupSizeProbe(
name=name or school.name,
queries=[
GroupQry(attr={ 'flu': 's' }, rel={ 'school': school }),
GroupQry(attr={ 'flu': 'i' }, rel={ 'school': school }),
GroupQry(attr={ 'flu': 'r' }, rel={ 'school': school })
],
qry_tot=GroupQry(rel={ 'school': school }),
persistance=pp,
var_names=['ps', 'pi', 'pr', 'ns', 'ni', 'nr']
)
def probe_grp_size_flu_school(name, school, pp):
return GroupSizeProbe(name=name,
queries=[
GroupQry(attr={'flu': 's'},
rel={'school': school}),
GroupQry(attr={'flu': 'e'},
rel={'school': school}),
GroupQry(attr={'flu': 'r'},
rel={'school': school})
],
qry_tot=GroupQry(rel={'school': school}),
persistence=pp,
var_names=['ps', 'pe', 'pr', 'ns', 'ne', 'nr'])
def probes_ls():
school_l = Site(450149323) # 88% low income students
school_m = Site(450067740) # 7% low income students
return GroupSizeProbe(
name=name or str(school.name),
queries=[
GroupQry(attr={ 'flu': 's' }, rel={ 'school': school }),
GroupQry(attr={ 'flu': 'e' }, rel={ 'school': school }),
GroupQry(attr={ 'flu': 'r' }, rel={ 'school': school })
],
qry_tot=GroupQry(rel={ 'school': school }),
persistance=pp,
var_names=['ps', 'pe', 'pr', 'ns', 'ne', 'nr']
)
probes = [
{ 'name': 'Low-income school', 'inf': '88% low income students', 'persistenceName': 'low-income', 'id': 450149323 },
{ 'name': 'medium-income school', 'inf': '7% low income students', 'persistenceName': 'med-income', 'id': 450067740 }
]
return jsonify({ 'res': True, 'probes': probes })
def sim03(iter_cnt):
sim = (Simulation().add([
ProgressFluIncomeRule(),
GroupSizeProbe(
'flu-income',
[
GroupQry(attr={
'income': 'l',
'flu': 's'
}),
GroupQry(attr={
'income': 'l',
'flu': 'e'
}),
GroupQry(attr={
'income': 'l',
'flu': 'r'
}),
GroupQry(attr={
'income': 'm',
'flu': 's'
}),
GroupQry(attr={
'income': 'm',
'flu': 'e'
}),
GroupQry(attr={
'income': 'm',
'flu': 'r'
})
],
msg_mode=ProbeMsgMode.CUMUL,
),
Group(m=500, attr={'income': 'l'}),
Group(m=500, attr={'income': 'm'})
]).run(iter_cnt))
print(sim.probes[0].get_msg())
print()
s,i,r = state
n = s + i + r
return [
-beta * s * i / n,
beta * s * i / n - gamma * i,
gamma * i
]
# ----------------------------------------------------------------------------------------------------------------------
# (2) Probe:
probe = GroupSizeProbe(
name='flu',
queries=[GroupQry(attr={ 'flu': 's' }), GroupQry(attr={ 'flu': 'i' }), GroupQry(attr={ 'flu': 'r' })],
qry_tot=None,
var_names=['ps', 'pi', 'pr', 'ns', 'ni', 'nr'],
persistence=ProbePersistenceMem(),
msg_mode=ProbeMsgMode.NONE
)
# ----------------------------------------------------------------------------------------------------------------------
# (3) Simulation:
s = (Simulation().
set_pragma_autocompact(True).
add([
ODESystemMass(f_sir_model, [DotMap(attr={ 'flu': 's' }), DotMap(attr={ 'flu': 'i' }), DotMap(attr={ 'flu': 'r' })], dt=0.1),
Group(m=950, attr={ 'flu': 's' }),
Group(m= 50, attr={ 'flu': 'i' }),
probe
# ----------------------------------------------------------------------------------------------------------------------
# (1) Simulation (two locations)
loc = [Site('a'), Site('b')]
probe_loc = GroupSizeProbe.by_rel('loc',
Site.AT,
loc,
msg_mode=ProbeMsgMode.DISP)
probe_sim = GroupSizeProbe(name='sim',
queries=[
GroupQry(attr={'team': 'blue'},
rel={Site.AT: loc[0]}),
GroupQry(attr={'team': 'red'},
rel={Site.AT: loc[0]}),
GroupQry(attr={'team': 'blue'},
rel={Site.AT: loc[1]}),
GroupQry(attr={'team': 'red'},
rel={Site.AT: loc[1]})
],
qry_tot=None,
msg_mode=ProbeMsgMode.DISP)
(Simulation().set().pragma_autocompact(True).pragma_live_info(
False).done().add([
SegregationModel('team', len(loc)),
Group(m=200, attr={'team': 'blue'}, rel={Site.AT: loc[0]}),
Group(m=300, attr={'team': 'blue'}, rel={Site.AT: loc[1]}),
Group(m=100, attr={'team': 'red'}, rel={Site.AT: loc[0]}),
Group(m=400, attr={'team': 'red'}, rel={Site.AT: loc[1]}),
# probe_loc # the distribution should tend to 50%-50%
site_home = Site('home')
# ----------------------------------------------------------------------------------------------------------------------
# (2) Probes:
fpath_db_out = os.path.join(os.path.dirname(__file__), 'out.sqlite3')
if os.path.isfile(fpath_db_out):
os.remove(fpath_db_out)
pp = ProbePersistenceDB(fpath_db_out, flush_every=1)
probe_school_pop_size = GroupSizeProbe(
name='school-pop-size',
queries=[GroupQry(rel={Site.AT: s}) for s in sites['school'].values()],
persistence=pp,
var_names=[f'p{i}' for i in range(len(sites['school']))] +
[f'n{i}' for i in range(len(sites['school']))],
memo=f'Population size across all schools')
# ----------------------------------------------------------------------------------------------------------------------
# (3) Simulation:
(Simulation().add_rule(ResetSchoolDayRule(TimePoint(7))).add_rule(
GoToAndBackTimeAtRule(t_at_attr='t@school')).add_probe(
probe_school_pop_size).gen_groups_from_db(
fpath_db_in,
tbl='people',
attr_fix={},
rel_fix={
'home': site_home
i += 1
print(eq * "=", "starting sim {}".format(i), eq * "=")
sim = (Simulation().add([
StartupLocationRule(),
GroupSizeProbe(
'startup-location',
[
GroupQry(attr={
'location': 'usa',
'stage': 'success'
}),
GroupQry(attr={
'location': 'usa',
'stage': 'failure'
}),
GroupQry(attr={
'location': 'others',
'stage': 'success'
}),
GroupQry(attr={
'location': 'others',
'stage': 'failure'
}),
],
msg_mode=ProbeMsgMode.CUMUL,
),
Group(m=10000, attr={'location': 'usa'}),
Group(m=10000, attr={'location': 'others'})
]).run(10))
print(sim.probes[0].get_msg())
print()
p = 0.1
return [
GroupSplitSpec(p=p, attr_set={"form": "c"}),
GroupSplitSpec(p=1 - p)
]
def is_applicable(self, group, iter, t):
return super().is_applicable(
group, iter, t) and group.m > 0 and group.attr['form'] == 's'
#probe including snakes
probe_grp_size_attr = GroupSizeProbe('form', [
GroupQry(attr={'form': 'm'}),
GroupQry(attr={'form': 'h'}),
GroupQry(attr={'form': 's'})
],
msg_mode=ProbeMsgMode.DISP)
#probe not including snakes
#probe_grp_size_attr = GroupSizeProbe('form', [GroupQry(attr={ 'form': 'm' }), GroupQry(attr={ 'form': 'h' })], msg_mode=ProbeMsgMode.DISP)
# 1 carbon => 1 mouse
# 5 carbon => 1 hawk
# 3 carbon => 1 snake
#1750 mice
mice = Group("Mice", 1750)
mice.attr['form'] = "m"
#100 hawks
def main():
# SAMPLE SIMULATION FROM 09-segregation
import os
from pram.data import GroupSizeProbe, ProbeMsgMode, ProbePersistenceDB
from pram.entity import Group, GroupQry, Site, GroupSplitSpec
from pram.rule import SegregationModel
from pram.sim import Simulation
# -----------------------------------------------------------------------------------------------------------------
# (1) Simulation (two locations)
loc = [Site('a'), Site('b')]
def gs(pop, group):
return [
GroupSplitSpec(p=0.7, attr_set={'foobar': 'foo'}),
GroupSplitSpec(p=0.3, attr_set={'foobar': 'bar'})
]
probe_loc = GroupSizeProbe.by_rel('loc',
Site.AT,
loc,
msg_mode=ProbeMsgMode.DISP)
probe_sim = GroupSizeProbe(name='sim',
queries=[
GroupQry(attr={'team': 'blue'},
rel={Site.AT: loc[0]}),
GroupQry(attr={'team': 'red'},
rel={Site.AT: loc[0]}),
GroupQry(attr={'team': 'blue'},
rel={Site.AT: loc[1]}),
GroupQry(attr={'team': 'red'},
rel={Site.AT: loc[1]})
],
qry_tot=None,
persistence=ProbePersistenceDB(),
msg_mode=ProbeMsgMode.DISP)
s = (
Simulation().set().pragma_autocompact(True).pragma_live_info(False).
fn_group_setup(gs).done().add([
SegregationModel('team', len(loc)),
# TranslateEverything(),
# LambdasAndArguments(),
Group(m=200,
attr={'team': 'blue'},
rel={
Site.AT: loc[0],
'origin': loc[0]
}),
Group(m=300,
attr={'team': 'blue'},
rel={
Site.AT: loc[1],
'origin': loc[1]
}),
Group(m=100,
attr={'team': 'red'},
rel={
Site.AT: loc[0],
'origin': loc[0]
}),
Group(m=400,
attr={'team': 'red'},
rel={
Site.AT: loc[1],
'origin': loc[1]
}),
probe_loc, # the distribution should tend to 50%-50%
probe_sim # mass should tend to move towards two of the four sites
# fixed naming issue in pram/sim.py line 815
]))
pram2mesa(s, 'TestSimultaneousGrammar')
from pram.sim import Simulation
from pram.entity import AttrFluStage, GroupQry, GroupSplitSpec
from pram.data import GroupSizeProbe, ProbeMsgMode, ProbePersistenceDB
from pram.rule import Rule, TimeInt
from rules import ProgressFluRule
# ----------------------------------------------------------------------------------------------------------------------
rand_seed = 1928
dpath_cwd = os.path.dirname(__file__)
fpath_db = os.path.join(dpath_cwd, f'sim.sqlite3')
if os.path.isfile(fpath_db):
os.remove(fpath_db)
probe = GroupSizeProbe(name='flu',
queries=[
GroupQry(attr={'flu-stage': AttrFluStage.NO}),
GroupQry(attr={'flu-stage': AttrFluStage.ASYMPT}),
GroupQry(attr={'flu-stage': AttrFluStage.SYMPT})
],
qry_tot=None,
var_names=['pn', 'pa', 'ps', 'nn', 'na', 'ns'],
persistence=ProbePersistenceDB(fpath_db))
(Simulation(6, 1, 16, rand_seed=rand_seed).add_rule(
ProgressFluRule()).add_probe(probe).new_group('0', 1000).set_attr(
'flu-stage', AttrFluStage.NO).commit().run())
'work' : Site.gen_from_db(fpath_db, 'workplaces', 'sp_id', 'work', [])
},
pragma_live_info=pragma_live_info,
pragma_live_info_ts=pragma_live_info_ts
)
site_home = Site('home')
# ----------------------------------------------------------------------------------------------------------------------
# (2) Probes:
n_schools = 8
few_schools = [sites['school'][k] for k in list(sites['school'].keys())[:n_schools]]
probe_grp_size_schools = GroupSizeProbe('school', [GroupQry(rel={ Site.AT: s }) for s in few_schools], msg_mode=ProbeMsgMode.DISP)
fpath_db = os.path.join(os.path.dirname(__file__), 'out-test-03c.sqlite3')
if os.path.isfile(fpath_db):
os.remove(fpath_db)
pp = ProbePersistenceDB(fpath_db)
# ----------------------------------------------------------------------------------------------------------------------
# (3) Simulation:
(Simulation().
set().
rand_seed(rand_seed).
sites = {'home': Site('home')}
for s in school_specs:
# Site:
site_name = f'school-{s.name}'
site = Site(site_name)
sites[site_name] = site
# Probe:
probes_grp_size_flu_school.append(
GroupSizeProbe(name=f'flu-{s.name}',
queries=[
GroupQry(attr={'flu': 's'}, rel={'school': site}),
GroupQry(attr={'flu': 'i'}, rel={'school': site}),
GroupQry(attr={'flu': 'r'}, rel={'school': site})
],
qry_tot=GroupQry(rel={'school': site}),
var_names=['ps', 'pi', 'pr', 'ns', 'ni', 'nr'],
persistence=probe_persistence,
memo=f'Flu at school {s.name.upper()}'))
probe_grp_size_flu = GroupSizeProbe.by_attr(
'flu',
'flu', ['s', 'i', 'r'],
msg_mode=ProbeMsgMode.DISP,
memo='Mass distribution across flu stages')
probe_grp_size_site = GroupSizeProbe.by_rel(
'site',
Site.AT,
sites.values(),
msg_mode=ProbeMsgMode.DISP,
if os.path.isfile(fpath_db_out):
os.remove(fpath_db_out)
pp = ProbePersistenceDB(fpath_db_out)
home = Site('home')
school_l = Site('school-l')
school_m = Site('school-m')
probe_grp_size_flu_school_l = GroupSizeProbe(
name='flu-school-l',
queries=[
GroupQry(attr={ 'flu': 's' }, rel={ 'school': school_l }),
GroupQry(attr={ 'flu': 'e' }, rel={ 'school': school_l }),
GroupQry(attr={ 'flu': 'r' }, rel={ 'school': school_l })
],
qry_tot=GroupQry(rel={ 'school': school_l }),
persistence=pp,
var_names=['ps', 'pe', 'pr', 'ns', 'ne', 'nr'],
memo='Population size across flu states for low-income school'
)
probe_grp_size_flu_school_m = GroupSizeProbe(
name='flu-school-m',
queries=[
GroupQry(attr={ 'flu': 's' }, rel={ 'school': school_m }),
GroupQry(attr={ 'flu': 'e' }, rel={ 'school': school_m }),
GroupQry(attr={ 'flu': 'r' }, rel={ 'school': school_m })
],
qry_tot=GroupQry(rel={ 'school': school_m }),
persistence=pp,
],
rel_at='home')
print('done.')
print('Saving groups... ', end='')
with gzip.GzipFile(fpath_groups, 'wb') as f:
pickle.dump(groups, f)
print('done.')
inf('groups', groups, do_calc_size_groups)
# groups: 164,459 (175.2M)
# file 5.1M
# ----------------------------------------------------------------------------------------------------------------------
# (3) Simulation:
n_schools = 8
few_schools = [
sites['school'][k] for k in list(sites['school'].keys())[:n_schools]
]
probe_grp_size_schools = GroupSizeProbe(
'school', [GroupQry(rel={Site.AT: v}) for v in few_schools])
# sys.exit(0)
(Simulation(6, 1, 16, rand_seed=rand_seed).add_groups(groups).add_rule(
ResetDayRule(TimePoint(7))).add_rule(
AttendSchoolRule()).add_probe(probe_grp_size_schools).run())
'''
A simulation implementing the flu progression model. This version tests probe database persistence.
'''
from pram.sim import Simulation
from pram.entity import GroupQry, GroupSplitSpec
from pram.data import GroupSizeProbe, ProbeMsgMode, ProbePersistenceDB
from pram.rule import Rule, TimeInt
from rules import ProgressFluRule
# ----------------------------------------------------------------------------------------------------------------------
dpath_cwd = os.path.dirname(__file__)
fpath_db = os.path.join(dpath_cwd, f'sim.sqlite3')
if os.path.isfile(fpath_db):
os.remove(fpath_db)
probe = GroupSizeProbe(name='flu',
queries=[
GroupQry(attr={'flu': 's'}),
GroupQry(attr={'flu': 'i'}),
GroupQry(attr={'flu': 'r'})
],
qry_tot=None,
var_names=['pn', 'pa', 'ps', 'nn', 'na', 'ns'],
persistence=ProbePersistenceDB(fpath_db))
(Simulation().add_rule(ProgressFluRule()).add_probe(probe).new_group(
'0', 1000).set_attr('flu', 's').done().run(16))
def f_decay_a(t, state):
n1, n2 = state
return [-l_a * n1, l_a * n1]
def f_decay_b(t, state):
n1, n2 = state
return [-l_b * n1, l_b * n1]
# ----------------------------------------------------------------------------------------------------------------------
# (2) Probe:
probe_u = GroupSizeProbe(
name='sub', # substance
queries=[GroupQry(attr={ 'sub-a': 'u' }), GroupQry(attr={ 'sub-b': 'u' })],
qry_tot=None,
var_names=['pau', 'pbu', 'nau', 'nbu'], # pau - proportion of substance A undecayed, etc.
persistence=ProbePersistenceMem(),
msg_mode=ProbeMsgMode.NONE
)
probe_d = GroupSizeProbe(
name='sub', # substance
queries=[GroupQry(attr={ 'sub-a': 'd' }), GroupQry(attr={ 'sub-b': 'd' })],
qry_tot=None,
var_names=['pad', 'pbd', 'nad', 'nbd'], # pad - proportion of substance A decayed, etc.
persistence=ProbePersistenceMem(),
msg_mode=ProbeMsgMode.NONE
)
# ----------------------------------------------------------------------------------------------------------------------
