def runSimulation(outputPrefix, v, iteration, rng_seed):
# Set up simulator
control = PyController(data_dir="data")
# Load configuration from file
control.loadRunConfig(os.path.join("config", "run_import_default.xml"))
# Set some parameters
if v:
outputPrefix = os.path.join(outputPrefix,
vaccinatedFolder + "_" + str(iteration))
else:
outputPrefix = os.path.join(outputPrefix,
notVaccinatedFolder + "_" + str(iteration))
control.runConfig.setParameter("immunity_profile", "AgeDependent")
control.runConfig.setParameter("immunity_distribution_file",
"data/lower_student_immunity.xml")
control.runConfig.setParameter("immunity_link_probability", 0)
control.runConfig.setParameter("population_file",
"data/2_2_gengeopop.proto")
control.runConfig.setParameter("geopopulation_file",
"data/2_2_gengeopop.proto")
control.runConfig.setParameter("output_prefix", outputPrefix)
control.runConfig.setParameter("rng_seed", rng_seed)
print("config done")
if v:
control.registerCallback(vaccinate, EventType.Stepped)
control.registerCallback(trackCases, EventType.Stepped)
# Run simulation
control.control()
def runSimulation(startDate, transmissionProbability, seed, runID):
control = PyController(data_dir="data")
for paramName, paramValue in getCommonParameters().items():
control.runConfig.setParameter(paramName, paramValue)
control.runConfig.setParameter("transmission_probability", transmissionProbability)
control.runConfig.setParameter("rng_seed", seed)
control.runConfig.setParameter("output_prefix", "TP_" + str(transmissionProbability) + "_START_" + startDate + "_" + str(runID))
control.runConfig.setParameter("start_date", startDate)
control.control()
def runSimulation(R0, scenarioName, seed, extraParams):
control = PyController(data_dir="data")
extraParams.update(getCommonParameters())
for paramName, paramValue in extraParams.items():
control.runConfig.setParameter(paramName, paramValue)
control.runConfig.setParameter(
"output_prefix", scenarioName + "_R0_" + str(R0) + "_" + str(seed))
control.runConfig.setParameter("rng_seed", seed)
control.runConfig.setParameter("r0", R0)
control.control()
def runSimulation(outputPrefix, daycare_fraction, preschool_fraction,
workplace, iteration, rng_seed, days):
print(
f"DC: {daycare_fraction} / PS: {preschool_fraction} - Iteration {iteration}"
)
# Set up simulator
control = PyController(data_dir="data")
# Load configuration from file
control.loadRunConfig(os.path.join("config", "daycare-preschool.xml"))
# Set some parameters
outputPrefix = os.path.join(
outputPrefix,
f"DC-{daycare_fraction}-PS-{preschool_fraction}_{iteration}")
control.runConfig.setParameter("output_prefix", outputPrefix)
control.runConfig.setParameter("rng_seed", rng_seed)
control.runConfig.setParameter("num_days", str(days))
control.runConfig.setParameter("geopop_gen.population_size", "600000")
control.runConfig.setParameter("geopop_gen.participation_preschool",
preschool_fraction)
control.runConfig.setParameter("geopop_gen.participation_daycare",
daycare_fraction)
control.registerCallback(trackCases, EventType.Stepped)
# Run simulation
control.control()
print("Simulation done")
def runSimulation(outputPrefix, fraction, workplace, iteration, rng_seed,
days):
# Set up simulator
control = PyController(data_dir="data")
# Load configuration from file
control.loadRunConfig(os.path.join("config", "workplace.xml"))
# Set some parameters
outputPrefix = os.path.join(
outputPrefix, workplace + str(fraction) + "_" + str(iteration))
control.runConfig.setParameter("seeding_rate", fraction)
control.runConfig.setParameter("disease_config_file",
"disease_influenza.xml")
control.runConfig.setParameter("output_prefix", outputPrefix)
control.runConfig.setParameter("rng_seed", rng_seed)
control.runConfig.setParameter("num_days", str(days))
control.runConfig.setParameter("geopop_gen.population_size", "600000")
control.runConfig.setParameter("geopop_gen.workplace_distribution_file",
"data/" + workplace)
control.registerCallback(trackCases, EventType.Stepped)
# Run simulation
control.control()
def runSimulation(outputPrefix, fraction, iteration, rng_seed):
# Set up simulator
control = PyController(data_dir="data")
# Load configuration from file
control.loadRunConfig(os.path.join("config", "run_generate_default.xml"))
# Set some parameters
outputPrefix = os.path.join(outputPrefix,
str(fraction) + "_" + str(iteration))
control.runConfig.setParameter("geopop_gen.population_size", 10000)
control.runConfig.setParameter("geopop_gen.participation_college", 0.0)
control.runConfig.setParameter("geopop_gen.particpation_workplace", 1.0)
control.runConfig.setParameter("geopop_gen.fraction_college_commuters",
0.0)
control.runConfig.setParameter("geopop_gen.fraction_workplace_commuters",
fraction)
control.runConfig.setParameter("output_prefix", outputPrefix)
control.runConfig.setParameter("rng_seed", rng_seed)
print("config done")
control.registerCallback(trackCases, EventType.Stepped)
# Run simulation
control.control()
def runSimulation(year, R0, seed):
configFile = os.path.join("config", "ageImmunityShift.xml")
control = PyController(data_dir="data")
control.loadRunConfig(configFile)
control.runConfig.setParameter(
"output_prefix",
str(year) + "_R0_" + str(R0) + "_" + str(seed))
control.runConfig.setParameter("rng_seed", seed)
control.runConfig.setParameter("r0", R0)
control.runConfig.setParameter("immunity_profile", "Random")
control.runConfig.setParameter("immunity_rate", IMMUNITY_RATES[year])
control.registerCallback(registerSusceptibles, EventType.AtStart)
control.registerCallback(trackCases, EventType.Stepped)
control.control()
return
def runSimulation(immunity, outputPrefix):
# Configure simulation
controller = PyController(data_dir="data")
controller.loadRunConfig(
os.path.join("config", "outbreak_2019_estimates.xml"))
controller.runConfig.setParameter("output_prefix",
outputPrefix + "_" + str(immunity))
controller.runConfig.setParameter("immunity_profile", "Random")
controller.runConfig.setParameter("immunity_rate", immunity)
controller.runConfig.setParameter("vaccine_profile", "None")
controller.registerCallback(count, EventType.Stepped)
controller.control()
def runSimulation_vaccination(seed, filename):
# Configure simulation
control = PyController(data_dir="data")
# Load Configuration file:
control.loadRunConfig(os.path.join("config", xmlFile))
control.runConfig.setParameter("rng_seed", seed)
# Register callbacks
control.registerCallback(check_days, EventType.Stepped)
#control.registerCallback(trackCases, [EventType.Stepped, filename])
# Let controller run the simulation
control.control()
return (seed,
control.runner.getSimulator().GetPopulation().GetInfectedCount())
def runSimulation(outputPrefix):
for run in range(0, runs):
print("run number {0} of {1}".format(run+1, runs))
controller = PyController(data_dir="data")
controller.loadRunConfig(os.path.join("config", config))
controller.runConfig.setParameter("num_days", sim_days)
controller.runConfig.setParameter("output_prefix", outputPrefix + "_" + config.split(".")[0])
seed = ""
for _ in range(4):
seed += str(random.randint(1, 999999)) + ","
seed = seed[:-1]
controller.runConfig.setParameter("rng_seed", seed)
controller.registerCallback(trackCases, EventType.Stepped)
controller.control()
def runSimulation(outputPrefix, vaccinationLevel):
# Set up simulator
control = PyController(data_dir="data")
# Load configuration from file
control.loadRunConfig(os.path.join("config", "run_default.xml"))
# Set some parameters
control.runConfig.setParameter("vaccine_rate", vaccinationLevel / 100)
control.runConfig.setParameter("output_cases", "false")
control.runConfig.setParameter("contact_output_file", "false")
control.runConfig.setParameter("output_prefix", outputPrefix + "_" + str(vaccinationLevel))
control.runConfig.setParameter("seeding_rate", 0.00000334) # Seed 2 infected persons in population of 600 000
control.registerCallback(trackCases, EventType.Stepped)
# Run simulation
control.control()
def runRandom():
control = PyController()
setCommonParams(control)
# Output prefix
control.runConfig.setParameter("output_prefix", "Random")
# Immunity profile
control.runConfig.setParameter("immunity_profile", "Random")
control.runConfig.setParameter("immunity_rate", 0.951513)
# Vaccination profile is empty since random immunity was seeded
# through immunity profile
control.runConfig.setParameter("vaccine_profile", "None")
control.registerCallback(getNumSusceptible, EventType.AtStart)
control.registerCallback(trackCases, EventType.Stepped)
control.control()
def runAgeDependent():
control = PyController()
setCommonParams(control)
# Output prefix
control.runConfig.setParameter("output_prefix", "AgeDependent")
# Immunity profile
control.runConfig.setParameter("immunity_link_probability", 0)
control.runConfig.setParameter("immunity_profile", "AgeDependent")
control.runConfig.setParameter("immunity_distribution", "../data/measles_natural_immunity.xml")
# Vaccination profile
control.runConfig.setParameter("vaccine_link_probability", 0)
control.runConfig.setParameter("vaccine_profile", "AgeDependent")
control.runConfig.setParameter("vaccine_distribution", "../data/measles_vaccination.xml")
control.registerCallback(getNumSusceptible, EventType.AtStart)
control.registerCallback(trackCases, EventType.Stepped)
control.control()
def runSimulation(immunity_rate):
# Set up simulator
control = PyController(data_dir="data")
# Load configuration from file
control.loadRunConfig(os.path.join("config",
"outbreak_2019_estimates.xml"))
# Set some parameters
control.runConfig.setParameter("output_prefix",
outputDirectory(immunity_rate))
control.runConfig.setParameter("immunity_profile", "Random")
control.runConfig.setParameter("immunity_rate", immunity_rate / 100)
control.runConfig.setParameter("rng_seed", random.randint(0, 100000000))
control.runConfig.setParameter("vaccine_profile", None)
control.registerCallback(trackCases, EventType.Stepped)
# Run simulation
control.control()
def runSimulation(comuter_fraction, outputPrefix):
tree = ET.parse(os.path.join("config", 'run_generate_default.xml'))
geopop = tree.getroot().find("geopop_gen")
comuters = geopop.find("fraction_workplace_commuters")
comuters.text = str(comuter_fraction)
tree.write(os.path.join("config", "run_generate_default_temp.xml"))
# Configure simulation
controller = PyController(data_dir="data")
controller.loadRunConfig(
os.path.join("config", "run_generate_default_temp.xml"))
controller.runConfig.setParameter("num_days", "400")
controller.runConfig.setParameter(
"output_prefix", outputPrefix + "_" + str(comuter_fraction))
controller.runConfig.setParameter("seeding_rate", 0.00000334)
controller.registerCallback(trackCases, EventType.Stepped)
controller.control()
def runSimulation(output_prefix, immunity_level, rng_seed, iteration=1):
"""Run the simulator, for one immunity level."""
# Set up simulator
control = PyController(data_dir="data")
# Load configuration from file
cfile = os.path.join("config", "outbreak_2019_estimates.xml")
control.loadRunConfig(cfile)
# Set some parameters
control.runConfig.setParameter("immunity_profile", "Random")
control.runConfig.setParameter("immunity_rate", immunity_level / 100)
control.runConfig.setParameter("rng_seed", rng_seed)
control.runConfig.setParameter("vaccine_profile", "None")
outputmap = "{}_{}_{}".format(output_prefix, immunity_level, iteration)
control.runConfig.setParameter("output_prefix", outputmap)
control.registerCallback(trackCases, EventType.Stepped)
# Run simulation
control.control()
def runSimulation(outputPrefix, seed, extraParams={}, callbacks=[]):
control = PyController(data_dir="data")
extraParams.update(getCommonParameters())
for paramName, paramValue in extraParams.items():
control.runConfig.setParameter(paramName, paramValue)
control.runConfig.setParameter("rng_seed", seed)
control.runConfig.setParameter("output_prefix", outputPrefix + "_" + str(seed))
for callbackFunction, callbackEvent in callbacks:
control.registerCallback(callbackFunction, callbackEvent)
control.control()
def runSimulation(level, outputPrefix):
tree = ET.parse(os.path.join("config", config))
geopop = tree.getroot().find("geopop_gen")
comuters = geopop.find(param)
comuters.text = str(level)
tree.write(os.path.join("config", config))
for run in range(0, runs):
print("run number {0} of {1}".format(run + 1, runs))
controller = PyController(data_dir="data")
controller.loadRunConfig(os.path.join("config", config))
controller.runConfig.setParameter("num_days", sim_days)
controller.runConfig.setParameter("output_prefix",
outputPrefix + "_" + str(level))
controller.runConfig.setParameter("seeding_rate", 0.00000334)
seed = ""
for _ in range(4):
seed += str(random.randint(1, 999999999)) + ","
seed = seed[:-1]
controller.runConfig.setParameter("rng_seed", seed)
controller.registerCallback(trackCases, EventType.Stepped)
controller.control()
import pystride
from pystride.PyController import PyController
# Set the workspace (default = .)
pystride.workspace = "pytest_Forker"
# Configure simulation
controller = PyController(config_path="../config/run_default.xml")
controller.runConfig.setParameter("output_prefix", "forks/")
controller.runConfig.setParameter("num_days", 2)
# Create 5 identical forks except for the seed
for index in range(3):
fork = controller.fork("instance" + str(index))
fork.runConfig.setParameter("rng_seed", index)
# Run all forks
controller.controlForks()
from pystride.Event import EventType
from pystride.PyController import PyController
# Callback to check if number of cases produced by sim is acceptable
def checkNumCases(simulator, event):
# Target for total number of cases after simulation
targetCases = 118925
actualCases = simulator.GetPopulation().GetInfectedCount()
# Accept a 10% margin of error
assert (abs(targetCases - actualCases) <=
(targetCases *
0.1)), "Expected value is {} - actual value is {}".format(
targetCases, actualCases)
# Configure simulation
controller = PyController(config_path="../config/run_default.xml")
controller.runConfig.setParameter("output_prefix", "testInfected")
controller.runConfig.setParameter("use_install_dirs", "true")
# Clean up leftover of previous failed testrun
if os.path.isdir("testInfected"):
rmtree("testInfected")
# Register callback
controller.registerCallback(checkNumCases, EventType.AtFinished)
# Let controller run the simulation.
controller.control()
import sys
import itertools
import os
import pystride
from pystride.Event import EventType
from pystride.PyController import PyController
# callback functions
from outputUtil import getSummary, getCases, parseLogfile
# Set the workspace (default = .)
pystride.workspace = "sim_output"
# Configure simulation
controller = PyController(config_path="./config/run_default.xml",
data_dir="./data")
controller.runConfig.setParameter("vaccine_profile", "None")
controller.runConfig.setParameter("num_days", 18)
controller.runConfig.setParameter("num_participants_survey", 10)
controller.runConfig.setParameter("contact_log_level", "Transmissions")
controller.runConfig.setParameter("track_index_case", "true")
controller.runConfig.setParameter("seeding_rate", "0.000002")
controller.runConfig.setParameter("output_summary", "true")
# Design of Experiement: parameter values
rng_opt = range(1)
r0_opt = [14]
# Create forks with varying parameters
f_id = 0 # fork id
for r0, rng_seed in list(itertools.product(r0_opt, rng_opt)):
def runSimulation(year, R0, numDays, seed, trackIndexCase):
configFile = os.path.join("config", "ageImmunityShift.xml")
control = PyController(data_dir="data")
control.loadRunConfig(configFile)
control.runConfig.setParameter(
"output_prefix",
str(year) + "_R0_" + str(R0) + "_" + str(seed))
control.runConfig.setParameter("rng_seed", seed)
control.runConfig.setParameter("r0", R0)
control.runConfig.setParameter("num_days", numDays)
control.runConfig.setParameter("immunity_link_probability", 0)
control.runConfig.setParameter("immunity_profile", "AgeDependent")
control.runConfig.setParameter(
"immunity_distribution_file",
os.path.join("data",
str(year) + "_measles_immunity.xml"))
if trackIndexCase:
control.runConfig.setParameter("track_index_case", "true")
control.registerCallback(registerSusceptibles, EventType.AtStart)
control.registerCallback(trackCases, EventType.Stepped)
control.registerCallback(registerAgesInfected, EventType.AtFinished)
control.control()
return
import sys
import pystride
from pystride.Event import EventType
from pystride.PyController import PyController
def printInfected(simulator, event):
day = event.timestep
print("Infected at day {}: {}".format(
day,
simulator.GetPopulation().GetInfectedCount()))
sys.stdout.flush()
# Configure Simulation
controller = PyController(config_path="../config/run_default.xml")
controller.runConfig.setParameter("population_file", "pop_antwerp.csv")
controller.runConfig.setParameter("num_days", 10)
controller.runConfig.setParameter("output_prefix", "pytest_Print/")
# Register callback
controller.registerCallback(printInfected, EventType.Stepped)
# Let controller run the simulation
controller.control()
import pystride
from pystride.Event import EventType
from pystride.PyController import PyController
def vaccinate(simulator, event):
if event.timestep == 20:
pop = simulator.GetPopulation()
for pIndex in range(pop.size()):
if pop[pIndex].GetHealth().IsSusceptible():
pop[pIndex].GetHealth().SetImmune()
def check(simulator, event):
if event.timestep == 20:
check.value = getattr(check, 'value', 0)
check.value = simulator.GetPopulation().GetInfectedCount()
if event.timestep > 20:
assert(simulator.GetPopulation().GetInfectedCount() == check.value), "Infection count still changing on day {}".format(event.timestep)
# Configure simulation
controller = PyController(config_path="../config/run_default.xml")
# Register callbacks
controller.registerCallback(vaccinate, EventType.Stepped)
controller.registerCallback(check, EventType.Stepped)
# Let controller run the simulation
controller.control()
import pystride
from pystride.PyController import PyController
# Configure simulation
controller = PyController(config_path="../config/run_default.xml")
controller.runConfig.setParameter("output_prefix", "pytest_Smoke/")
# Let controller run the simulation
controller.control()
import pystride
from pystride.Event import EventType
from pystride.PyController import PyController
def printInfected(simulator, event):
day = event.timestep
print("Infected at day {}: {}".format(
day,
simulator.GetPopulation().GetInfectedCount()))
sys.stdout.flush()
# Set the workspace (default = .)
pystride.workspace = "experiment"
# Configure simulation
controller = PyController("../config/run_default.xml")
controller.runConfig.setParameter("num_days", 2)
# Create forks with varying parameters
for r0, ir in list(itertools.product([10.0, 25.0], [0.4, 0.01])):
# Create fork
fork = controller.fork("r0_" + str(r0) + "-ir_" + str(ir))
fork.runConfig.setParameter("r0", r0)
fork.runConfig.setParameter("immunity_rate", ir)
fork.registerCallback(printInfected, EventType.Stepped)
# Run all forks
controller.controlForks()
