def test_optimization():
if os.name != 'nt':
return
ema_logging.log_to_stderr(ema_logging.INFO)
model = FluModel(r'../models', "fluCase")
ensemble = ModelEnsemble()
ensemble.model_structure = model
ensemble.parallel = True
pop_size = 8
nr_of_generations = 10
eps = np.array([1e-3, 1e6])
stats, pop = ensemble.perform_outcome_optimization(
obj_function=obj_function_multi,
algorithm=epsNSGA2,
reporting_interval=100,
weights=(MAXIMIZE, MAXIMIZE),
pop_size=pop_size,
nr_of_generations=nr_of_generations,
crossover_rate=0.8,
mutation_rate=0.05,
eps=eps)
def test_log_to_stderr(self):
ema_logging._logger = None
logger = ema_logging.log_to_stderr(ema_logging.DEBUG)
self.assertEqual(len(logger.handlers), 2)
self.assertEqual(logger.level, ema_logging.DEBUG)
ema_logging._logger = None
logger = ema_logging.log_to_stderr()
self.assertEqual(len(logger.handlers), 2)
self.assertEqual(logger.level, ema_logging.DEFAULT_LEVEL)
logger = ema_logging.log_to_stderr()
self.assertEqual(len(logger.handlers), 2)
self.assertEqual(logger.level, ema_logging.DEFAULT_LEVEL)
def test_log_messages(self):
ema_logging.log_to_stderr(ema_logging.DEBUG)
with mock.patch('util.ema_logging._logger') as mocked_logger:
message = 'test message'
ema_logging.debug(message)
mocked_logger.debug.assert_called_with(message)
ema_logging.info(message)
mocked_logger.info.assert_called_with(message)
ema_logging.warning(message)
mocked_logger.warning.assert_called_with(message)
ema_logging.error(message)
mocked_logger.error.assert_called_with(message)
ema_logging.exception(message)
mocked_logger.exception.assert_called_with(message)
ema_logging.critical(message)
mocked_logger.critical.assert_called_with(message)
def test_optimization():
if os.name != 'nt':
return
ema_logging.log_to_stderr(ema_logging.INFO)
model = FluModel(r'../models', "fluCase")
ensemble = ModelEnsemble()
ensemble.model_structure = model
ensemble.parallel=True
pop_size = 8
nr_of_generations = 10
eps = np.array([1e-3, 1e6])
stats, pop = ensemble.perform_outcome_optimization(obj_function = obj_function_multi,
algorithm=epsNSGA2,
reporting_interval=100,
weights=(MAXIMIZE, MAXIMIZE),
pop_size=pop_size,
nr_of_generations=nr_of_generations,
crossover_rate=0.8,
mutation_rate=0.05,
eps=eps)
'''
Created on Mar 15, 2012
.. codeauthor:: jhkwakkel <j.h.kwakkel (at) tudelft (dot) nl>
'''
from analysis import clusterer
from util import ema_logging
from core import ModelEnsemble
from test.scarcity_example import ScarcityModel
if __name__ == "__main__":
ema_logging.log_to_stderr(ema_logging.INFO)
model = ScarcityModel(r'..\..\src\test', "fluCase")
ensemble = ModelEnsemble()
ensemble.set_model_structure(model)
ensemble.parallel = True
results = ensemble.perform_experiments(200)
clusterer.cluster(data=results,
outcome='relative market price',
distance='gonenc',
cMethod='maxclust',
cValue=5,
plotDendrogram=False)
'''
Created on May 26, 2015
@author: jhkwakkel
'''
import numpy as np
import matplotlib.pyplot as plt
import analysis.cart as cart
from util import ema_logging
from util.util import load_results
ema_logging.log_to_stderr(level=ema_logging.INFO)
def classify(data):
#get the output for deceased population
result = data['deceased population region 1']
#make an empty array of length equal to number of cases
classes = np.zeros(result.shape[0])
#if deceased population is higher then 1.000.000 people, classify as 1
classes[result[:, -1] > 1000000] = 1
return classes
#load data
fn = r'./data/1000 flu cases.tar.gz'
results = load_results(fn)
experiments, results = results
def obj_func(outcomes):
a = outcomes['a']
b = outcomes['b']
a_mean = np.mean(a)
b_mean = np.mean(b)
if a_mean < 0.5 or b_mean < 0.5:
return (np.inf,) * 2
else:
return a_mean, b_mean
if __name__ == "__main__":
ema_logging.log_to_stderr(ema_logging.INFO)
model = DummyModel(r"", "dummy")
np.random.seed(123456789)
ensemble = ModelEnsemble()
ensemble.set_model_structure(model)
policy_levers = {'Trigger a': {'type':'list', 'values':[0, 0.25, 0.5, 0.75, 1]},
'Trigger b': {'type':'list', 'values':[0, 0.25, 0.5, 0.75, 1]},
'Trigger c': {'type':'list', 'values':[0, 0.25, 0.5, 0.75, 1]}}
cases = ensemble._generate_samples(10, UNION)[0]
ensemble.add_policy({"name":None})
experiments = [entry for entry in ensemble._generate_experiments(cases)]
'''
Created on May 26, 2015
@author: jhkwakkel
'''
import numpy as np
import matplotlib.pyplot as plt
import analysis.cart as cart
from util import ema_logging
from util.util import load_results
ema_logging.log_to_stderr(level=ema_logging.INFO)
def classify(data):
#get the output for deceased population
result = data['deceased population region 1']
#make an empty array of length equal to number of cases
classes = np.zeros(result.shape[0])
#if deceased population is higher then 1.000.000 people, classify as 1
classes[result[:, -1] > 1000000] = 1
return classes
#load data
fn = r'./data/1000 flu cases.tar.gz'
results = load_results(fn)
'''
Created on 20 sep. 2011
.. codeauthor:: jhkwakkel <j.h.kwakkel (at) tudelft (dot) nl>
'''
import numpy as np
import matplotlib.pyplot as plt
from analysis.pairs_plotting import pairs_lines, pairs_scatter, pairs_density
from util.util import load_results
from util import ema_logging
ema_logging.log_to_stderr(level=ema_logging.DEFAULT_LEVEL)
# load the data
fh = r'.\data\1000 flu cases no policy.tar.gz'
experiments, outcomes = load_results(fh)
# transform the results to the required format
# that is, we want to know the max peak and the casualties at the end of the
# run
tr = {}
# get time and remove it from the dict
time = outcomes.pop('TIME')
for key, value in outcomes.items():
if key == 'deceased population region 1':
tr[key] = value[:, -1] #we want the end value
else:
# we want the maximum value of the peak
"""
Created on 20 sep. 2011
.. codeauthor:: jhkwakkel <j.h.kwakkel (at) tudelft (dot) nl>
"""
import numpy as np
import matplotlib.pyplot as plt
from analysis.pairs_plotting import pairs_lines, pairs_scatter, pairs_density
from util.util import load_results
from util import ema_logging
ema_logging.log_to_stderr(level=ema_logging.DEFAULT_LEVEL)
# load the data
fh = r".\data\1000 flu cases no policy.tar.gz"
experiments, outcomes = load_results(fh)
# transform the results to the required format
# that is, we want to know the max peak and the casualties at the end of the
# run
tr = {}
# get time and remove it from the dict
time = outcomes.pop("TIME")
for key, value in outcomes.items():
if key == "deceased population region 1":
tr[key] = value[:, -1] # we want the end value
else:
# we want the maximum value of the peak
speed = kwargs.pop("lookup price substitute speed")
begin = kwargs.pop("lookup price substitute begin")
end = kwargs.pop("lookup price substitute end")
lookup = [self.priceSubstite(x, speed, begin, end) for x in range(0,100, 10)]
kwargs['relative price substitute lookup'] = lookup
scale = kwargs.pop("lookup returns to scale speed")
speed = kwargs.pop("lookup returns to scale scale")
lookup = [self.returnsToScale(x, speed, scale) for x in range(0, 101, 10)]
kwargs['returns to scale lookup'] = lookup
scale = kwargs.pop("lookup approximated learning speed")
speed = kwargs.pop("lookup approximated learning scale")
start = kwargs.pop("lookup approximated learning start")
lookup = [self.approxLearning(x, speed, scale, start) for x in range(0, 101, 10)]
kwargs['approximated learning effect lookup'] = lookup
super(ScarcityModel, self).run_model(kwargs)
if __name__ == "__main__":
ema_logging.log_to_stderr(ema_logging.DEBUG)
model = ScarcityModel(r'./models/scarcity', "scarcity")
ensemble = ModelEnsemble()
ensemble.model_structure = model
ensemble.parallel = True
results = ensemble.perform_experiments(2)
kwargs['relative price substitute lookup'] = lookup
scale = kwargs.pop("lookup returns to scale speed")
speed = kwargs.pop("lookup returns to scale scale")
lookup = [
self.returnsToScale(x, speed, scale) for x in range(0, 101, 10)
]
kwargs['returns to scale lookup'] = lookup
scale = kwargs.pop("lookup approximated learning speed")
speed = kwargs.pop("lookup approximated learning scale")
start = kwargs.pop("lookup approximated learning start")
lookup = [
self.approxLearning(x, speed, scale, start)
for x in range(0, 101, 10)
]
kwargs['approximated learning effect lookup'] = lookup
super(ScarcityModel, self).run_model(kwargs)
if __name__ == "__main__":
ema_logging.log_to_stderr(ema_logging.DEBUG)
model = ScarcityModel(r'./models/scarcity', "scarcity")
ensemble = ModelEnsemble()
ensemble.model_structure = model
ensemble.parallel = True
results = ensemble.perform_experiments(2)
