def fit_all_case_data(num_procs=4):
pool = multi.Pool(num_procs)
case_counts = parse_tsv()
results = pool.map(fit_one_case_data, list(case_counts.items()))
for k, v in results:
if v is not None:
FIT_CASE_DATA[k] = v
def fit_all_case_data(num_procs=4):
pool = multi.Pool(num_procs)
print(f"Pooling with {num_procs} processors")
case_counts = parse_tsv()
scenario_data = load_population_data()
age_distributions = load_distribution()
params = []
for region in case_counts:
if region in scenario_data:
params.append([
region, case_counts[region],
scenario_data.get(region, None),
age_distributions[scenario_data[region]['ages']], False
])
results = pool.map(fit_population, params)
results_dict = {}
for k, params in results:
if params is None:
results_dict[k] = None
elif np.isfinite(params['logInitial']):
results_dict[k] = params
else:
results_dict[k] = None
return results_dict
def generate(output_json, num_procs=1):
scenario = {}
fit_all_case_data(num_procs)
print("DONE")
print(FIT_CASE_DATA)
print(output_json)
case_counts = parse_tsv()
with open(SCENARIO_POPS, 'r') as fd:
rdr = csv.reader(fd, delimiter='\t')
hdr = next(rdr)
idx = {
'name': hdr.index('name'),
'size': hdr.index('populationServed'),
'ages': hdr.index('ageDistribution'),
'beds': hdr.index('hospitalBeds'),
'icus': hdr.index('ICUBeds'),
'hemisphere': hdr.index('hemisphere')
}
args = ['name', 'ages', 'size', 'beds', 'icus', 'hemisphere']
for region in rdr:
region_name = region[idx['name']]
entry = [region[idx[arg]] for arg in args]
scenario[region_name] = AllParams(*entry)
if region_name in case_counts:
set_mitigation(case_counts[region_name], scenario[region_name])
else:
scenario[region_name].containment.reduction = [
float(x)
for x in scenario[region_name].containment.reduction
]
with open(output_json, "w+") as fd:
marshalJSON(scenario, fd)
def fit_all_case_data():
Params = Fitter()
case_counts = parse_tsv()
for region, data in case_counts.items():
fit = Params.fit(data)
if fit:
FIT_CASE_DATA[region] = fit
def generate(output_json, num_procs=1, recalculate=False):
scenarios = []
fit_fname = os.path.join(BASE_PATH, FIT_PARAMETERS)
if recalculate or (not os.path.isfile(fit_fname)):
fit_all_case_data(num_procs)
with open(fit_fname, 'w') as fh:
json.dump(FIT_CASE_DATA, fh)
else:
with open(fit_fname, 'r') as fh:
tmp = json.load(fh)
for k, v in tmp.items():
FIT_CASE_DATA[k] = v
case_counts = parse_tsv()
with open(SCENARIO_POPS, 'r') as fd:
rdr = csv.reader(fd, delimiter='\t')
hdr = next(rdr)
idx = {
'name': hdr.index('name'),
'size': hdr.index('populationServed'),
'ages': hdr.index('ageDistribution'),
'beds': hdr.index('hospitalBeds'),
'icus': hdr.index('ICUBeds'),
'hemisphere': hdr.index('hemisphere'),
'srcPopulation': hdr.index('srcPopulation'),
'srcHospitalBeds': hdr.index('srcHospitalBeds'),
'srcICUBeds': hdr.index('srcICUBeds')
}
args = [
'name', 'ages', 'size', 'beds', 'icus', 'hemisphere',
'srcPopulation', 'srcHospitalBeds', 'srcICUBeds'
]
for region in rdr:
region_name = region[idx['name']]
entry = [region[idx[arg]] for arg in args]
scenario = AllParams(
*entry, region_name if region_name in case_counts else 'None')
if region_name in case_counts:
set_mitigation(case_counts[region_name], scenario,
FIT_CASE_DATA.get(region_name, None))
else:
scenario.mitigation.mitigation_intervals = []
scenarios.append(ScenarioData(scenario, region_name))
with open(output_json, "w+") as fd:
output = ScenarioArray(scenarios)
output.marshalJSON(fd)
def generate(output_json, num_procs=1, recalculate=False):
scenario = {}
fit_fname = os.path.join(BASE_PATH, FIT_PARAMETERS)
if recalculate or (not os.path.isfile(fit_fname)):
fit_all_case_data(num_procs)
with open(fit_fname, 'w') as fh:
json.dump(FIT_CASE_DATA, fh)
else:
with open(fit_fname, 'r') as fh:
tmp = json.load(fh)
for k, v in tmp.items():
FIT_CASE_DATA[k] = v
print("DONE")
print(FIT_CASE_DATA)
print(output_json)
case_counts = parse_tsv()
with open(SCENARIO_POPS, 'r') as fd:
rdr = csv.reader(fd, delimiter='\t')
hdr = next(rdr)
idx = {
'name': hdr.index('name'),
'size': hdr.index('populationServed'),
'ages': hdr.index('ageDistribution'),
'beds': hdr.index('hospitalBeds'),
'icus': hdr.index('ICUBeds'),
'hemisphere': hdr.index('hemisphere')
}
args = ['name', 'ages', 'size', 'beds', 'icus', 'hemisphere']
for region in rdr:
region_name = region[idx['name']]
entry = [region[idx[arg]] for arg in args]
scenario[region_name] = AllParams(*entry)
if region_name in case_counts:
set_mitigation(case_counts[region_name], scenario[region_name])
else:
scenario[region_name].containment.reduction = [
float(x)
for x in scenario[region_name].containment.reduction
]
with open(output_json, "w+") as fd:
marshalJSON(scenario, fd)
def getRegions():
regions = parse_tsv()
return set(regions.keys())
def generate(output_json, num_procs=1, recalculate=False):
import re
scenarios = []
case_counts = parse_tsv()
scenario_data = load_population_data()
for fname in (FIT_PARAMETERS, 'fit_parameters_1stwave.json'):
first_wave = '1stwave' in fname
print("reading file", fname)
fit_fname = os.path.join(BASE_PATH, fname)
if (recalculate or
(not os.path.isfile(fit_fname))) and (not first_wave):
results = fit_all_case_data(num_procs)
with open(fit_fname, 'w') as fh:
json.dump(results, fh)
else:
with open(fit_fname, 'r') as fh:
results = json.load(fh)
for region in scenario_data:
if region not in results or results[
region] is None or region.startswith('FRA-'):
continue
if first_wave: # skip if a small region or not fit to case data (no 'containment_start')
results[region]['logInitial'] = np.log(
results[region]['initialCases'])
results[region]['tMax'] = '2020-08-31'
results[region]['seroprevalence'] = 0.0
if (re.match('[A-Z][A-Z][A-Z]-', region)
and results[region]['initialCases'] < 100) or (
'containment_start' not in results[region]):
continue
elif np.isnan(results[region]['logInitial']) or np.isinf(
results[region]['logInitial']):
continue
scenario = AllParams(**scenario_data[region],
tMin=results[region]['tMin'],
tMax=results[region]['tMax'],
cases_key=region
if region in case_counts else 'None')
if first_wave:
scenario.mitigation.mitigation_intervals = [
MitigationInterval(
name="Intervention 1",
tMin=datetime.strptime(
results[region]['containment_start'],
'%Y-%m-%d').date(),
id=uuid4(),
tMax=scenario.simulation.simulation_time_range.end +
timedelta(1),
color=mitigation_colors.get("Intervention 1",
"#cccccc"),
mitigationValue=round(100 *
results[region]['efficacy']))
]
elif region in case_counts:
set_mitigation(scenario,
results[region].get('mitigations', []))
else:
scenario.mitigation.mitigation_intervals = []
if len(scenario.mitigation.mitigation_intervals):
scenario.mitigation.mitigation_intervals[
-1].time_range.end = datetime.strptime(
results[region]['tMax'],
'%Y-%m-%d').date() + timedelta(1)
scenario.population.seroprevalence = round(
100 * results[region]['seroprevalence'], 2)
scenario.population.initial_number_of_cases = int(
round(np.exp(results[region]['logInitial'])))
if first_wave:
scenario_name = f"[1st wave] {region}"
else:
scenario_name = region
scenarios.append(ScenarioData(scenario, scenario_name))
with open(output_json, "w+") as fd:
output = ScenarioArray(scenarios)
output.marshalJSON(fd)
scenarios.append(ScenarioData(scenario, scenario_name))
with open(output_json, "w+") as fd:
output = ScenarioArray(scenarios)
output.marshalJSON(fd)
if __name__ == '__main__':
generate('test.json', recalculate=False)
from scripts.test_fitting_procedure import generate_data, check_fit
from scripts.model import trace_ages, get_IFR
from matplotlib import pyplot as plt
case_counts = parse_tsv()
scenario_data = load_population_data()
age_distributions = load_distribution()
# region = 'JPN-Kagawa'
region = 'United States of America'
# region = 'Germany'
region = 'Switzerland'
region = 'USA-Texas'
age_dis = age_distributions[scenario_data[region]['ages']]
region, p, fit_params = fit_population(
(region, case_counts[region], scenario_data[region], age_dis, True))
model_data = generate_data(fit_params)
model_cases = model_data['cases'][7:] - model_data['cases'][:-7]
model_deaths = model_data['deaths'][7:] - model_data['deaths'][:-7]
model_time = fit_params.time[7:]
