def test_box():
ema_logging.log_to_stderr(ema_logging.INFO)
x = np.loadtxt(r'quasiflow x.txt')
y = np.loadtxt(r'quasiflow y.txt')
# prim = prim_box(x, y, pasting=True, threshold = 0, threshold_type = -1)
prim = perform_prim(x, y, pasting=True, threshold = 0, threshold_type =-1)
fig = plt.figure()
ax = fig.add_subplot(111)
ax.scatter(x[:,0], x[:, 1], c=y)
print ' \tmass\tmean'
for i, entry in enumerate(prim[0:-1]):
print 'found box %s:\t%s\t%s' %(i, entry.box_mass, entry.y_mean)
print 'rest box :\t%s\t%s' %(prim[-1].box_mass, prim[-1].y_mean)
colors = graphs.COLOR_LIST
for i, box in enumerate(prim):
box = box.box
# print box
x = np.array([box[0,0], box[1,0], box[1,0], box[0,0], box[0,0]])
y = np.array([box[0,1], box[0,1], box[1,1], box[1,1], box[0,1]])
# print x
# print y
ax.plot(x,y, c=colors[i%len(colors)], lw=4)
plt.show()
def test_optimization():
ema_logging.log_to_stderr(ema_logging.INFO)
model = FluModel(r'..\data', "fluCase")
ensemble = ModelEnsemble()
ensemble.set_model_structure(model)
ensemble.parallel=True
# ensemble.processes = 12
stats, pop = ensemble.perform_outcome_optimization(obj_function = obj_function_multi,
reporting_interval=10,
weights=(MAXIMIZE, MAXIMIZE),
pop_size=100,
nr_of_generations=5,
crossover_rate=0.5,
mutation_rate=0.05)
res = stats.hall_of_fame.keys
x = [entry.values[0] for entry in res]
y = [entry.values[1] for entry in res]
print len(x), len(y)
fig = plt.figure()
ax = fig.add_subplot(111)
ax.scatter(x,y)
ax.set_ylabel("deceased population")
ax.set_xlabel("infected fraction")
plt.show()
def maxmin_optimize():
ema_logging.log_to_stderr(ema_logging.INFO)
model = TestModel("", 'simpleModel') #instantiate the model
ensemble = ModelEnsemble() #instantiate an ensemble
ensemble.set_model_structure(model) #set the model on the ensemble
ensemble.parallel = True
ensemble.processes = 12
def obj_function1(outcomes):
return outcomes['y']
policy_levers = { "L1": (0,1),
"L2": (0,1)}
results = ensemble.perform_maximin_optimization(obj_function1 = obj_function1,
policy_levers = policy_levers,
minimax1='minimize',
nrOfGenerations1=50,
nrOfPopMembers1=200,
minimax2 = "maximize",
nrOfGenerations2 = 50,
nrOfPopMembers2 = 100,
)
graph_errorbars_raw(results['stats'])
plt.show()
def test_save_results():
ema_logging.log_to_stderr(ema_logging.DEBUG)
data = util.load_results("./data/1000 flu cases no policy.cPickle", zip=False)
file_name = "test.bz2"
util.save_results(data, file_name)
os.remove(file_name)
ema_logging.debug("removing " + file_name)
def test_load_results():
data = np.random.rand(1000, 1000)
file_name = "test.bz2"
util.save_results(data, file_name)
ema_logging.log_to_stderr(ema_logging.DEBUG)
util.load_results(file_name)
os.remove(file_name)
ema_logging.debug("removing " + file_name)
def perform_experiments():
ema_logging.log_to_stderr(level=ema_logging.INFO)
model = SalinizationModel(r"C:\workspace\EMA-workbench\models\salinization", "verzilting")
model.step = 4
ensemble = ModelEnsemble()
ensemble.set_model_structure(model)
ensemble.parallel = True
nr_of_experiments = 10000
results = ensemble.perform_experiments(nr_of_experiments)
return results
def test_optimization():
ema_logging.log_to_stderr(ema_logging.INFO)
model = FluModel(r'..\data', "fluCase")
ensemble = ModelEnsemble()
ensemble.set_model_structure(model)
ensemble.parallel=True
stats, pop = ensemble.perform_outcome_optimization(obj_function = obj_function_multi,
reporting_interval=100,
weights=(MAXIMIZE, MAXIMIZE),
pop_size=100,
nr_of_generations=20,
crossover_rate=0.5,
mutation_rate=0.05,
caching=False)
res = stats.hall_of_fame.keys
print len(stats.tried_solutions.values())
def outcome_optimize():
ema_logging.log_to_stderr(ema_logging.INFO)
model = TestModel("", 'simpleModel') #instantiate the model
ensemble = ModelEnsemble() #instantiate an ensemble
ensemble.set_model_structure(model) #set the model on the ensemble
policy = {"name": "test",
"L1": 1,
"L2": 1}
ensemble.add_policy(policy)
def obj_func(results):
return results['y']
results = ensemble.perform_outcome_optimization(obj_function=obj_func,
minimax = 'minimize',
nrOfGenerations = 1000,
nrOfPopMembers = 10)
graph_errorbars_raw(results['stats'])
plt.show()
def test_tree():
log_to_stderr(level= INFO)
model = FluModel(r'..\..\models\flu', "fluCase")
ensemble = ModelEnsemble()
ensemble.parallel = True
ensemble.set_model_structure(model)
policies = [{'name': 'no policy',
'file': r'\FLUvensimV1basecase.vpm'},
{'name': 'static policy',
'file': r'\FLUvensimV1static.vpm'},
{'name': 'adaptive policy',
'file': r'\FLUvensimV1dynamic.vpm'}
]
ensemble.add_policies(policies)
results = ensemble.perform_experiments(10)
a_tree = tree(results, classify)
def test_feature_selection():
log_to_stderr(level= INFO)
model = FluModel(r'..\..\models\flu', "fluCase")
ensemble = ModelEnsemble()
ensemble.parallel = True
ensemble.set_model_structure(model)
policies = [{'name': 'no policy',
'file': r'\FLUvensimV1basecase.vpm'},
{'name': 'static policy',
'file': r'\FLUvensimV1static.vpm'},
{'name': 'adaptive policy',
'file': r'\FLUvensimV1dynamic.vpm'}
]
ensemble.add_policies(policies)
results = ensemble.perform_experiments(5000)
results = feature_selection(results, classify)
for entry in results:
print entry[0] +"\t" + str(entry[1])
def robust_optimize():
ema_logging.log_to_stderr(ema_logging.INFO)
model = TestModel("", 'simpleModel') #instantiate the model
ensemble = ModelEnsemble() #instantiate an ensemble
ensemble.set_model_structure(model) #set the model on the ensemble
policy_levers = { "L1": (0,1),
"L2": (0,1)}
def obj_func(results):
return np.average(results['y'])
results = ensemble.perform_robust_optimization(cases=1000,
obj_function=obj_func,
policy_levers=policy_levers,
minimax='minimize',
nrOfGenerations=50,
nrOfPopMembers=20 )
graph_errorbars_raw(results['stats'])
plt.show()
def test_optimization():
ema_logging.log_to_stderr(ema_logging.INFO)
model = FluModel(r'../models', "fluCase")
ensemble = ModelEnsemble()
ensemble.set_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)
fn = '../data/test optimization save.bz2'
def perform_loop_knockout():
unique_edges = [['In Goods', 'lost'],
['loss unprofitable extraction capacity', 'decommissioning extraction capacity'],
['production', 'In Goods'],
['production', 'lost'],
['production', 'Supply'],
['Real Annual Demand', 'substitution losses'],
['Real Annual Demand', 'price elasticity of demand losses'],
['Real Annual Demand', 'desired extraction capacity'],
['Real Annual Demand', 'economic demand growth'],
['average recycling cost', 'relative market price'],
['recycling fraction', 'lost'],
['commissioning recycling capacity', 'Recycling Capacity Under Construction'],
['maximum amount recyclable', 'recycling fraction'],
['profitability recycling', 'planned recycling capacity'],
['relative market price', 'price elasticity of demand losses'],
['constrained desired recycling capacity', 'gap between desired and constrained recycling capacity'],
['profitability extraction', 'planned extraction capacity'],
['commissioning extraction capacity', 'Extraction Capacity Under Construction'],
['desired recycling', 'gap between desired and constrained recycling capacity'],
['Installed Recycling Capacity', 'decommissioning recycling capacity'],
['Installed Recycling Capacity', 'loss unprofitable recycling capacity'],
['average extraction costs', 'profitability extraction'],
['average extraction costs', 'relative attractiveness recycling']]
unique_cons_edges = [['recycling', 'recycling'],
['recycling', 'supply demand ratio'],
['decommissioning recycling capacity', 'recycling fraction'],
['returns to scale', 'relative attractiveness recycling'],
['shortage price effect', 'relative price last year'],
['shortage price effect', 'profitability extraction'],
['loss unprofitable extraction capacity', 'loss unprofitable extraction capacity'],
['production', 'recycling fraction'],
['production', 'constrained desired recycling capacity'],
['production', 'new cumulatively recycled'],
['production', 'effective fraction recycled of supplied'],
['loss unprofitable recycling capacity', 'recycling fraction'],
['average recycling cost', 'loss unprofitable recycling capacity'],
['recycling fraction', 'new cumulatively recycled'],
['substitution losses', 'supply demand ratio'],
['Installed Extraction Capacity', 'Extraction Capacity Under Construction'],
['Installed Extraction Capacity', 'commissioning extraction capacity'],
['Installed Recycling Capacity', 'Recycling Capacity Under Construction'],
['Installed Recycling Capacity', 'commissioning recycling capacity'],
['average extraction costs', 'profitability extraction']]
# CONSTRUCTING THE ENSEMBLE AND SAVING THE RESULTS
ema_logging.log_to_stderr(ema_logging.INFO)
results = load_results(r'base.cPickle')
# GETTING OUT THOSE BEHAVIOURS AND EXPERIMENT SETTINGS
# Indices of a number of examples, these will be looked at.
runs = [526,781,911,988,10,780,740,943,573,991]
VOI = 'relative market price'
results_of_interest = experiment_settings(results,runs,VOI)
cases_of_interest = experiments_to_cases(results_of_interest[0])
behaviour_int = results_of_interest[1][VOI]
# CONSTRUCTING INTERVALS OF ATOMIC BEHAVIOUR PATTERNS
ints = intervals(behaviour_int,False)
# GETTING OUT ONLY THOSE OF MAXIMUM LENGTH PER BEHAVIOUR
max_intervals = intervals_interest(ints)
# THIS HAS TO DO WITH THE MODEL FORMULATION OF THE SWITCHES/VALUES
double_list = [6,9,11,17,19]
indCons = len(unique_edges)
# for elem in unique_cons_edges:
# unique_edges.append(elem)
current = os.getcwd()
for beh_no in range(0,10):
# beh_no = 0 # Varies between 0 and 9, index style.
interval = max_intervals[beh_no]
rmp = behaviour_int[beh_no]
# rmp = rmp[interval[0]:interval[1]]
x = range(0,len(rmp))
fig = plt.figure()
ax = fig.add_subplot(111)
vensim.be_quiet()
# for loop_index in range(7,8):
for loop_index in range(1,len(unique_edges)+1):
if loop_index-indCons > 0:
model_location = current + r'\Models\Consecutive\Metals EMA.vpm'
elif loop_index == 0:
model_location = current + r'\Models\Base\Metals EMA.vpm'
else:
model_location = current + r'\Models\Switches\Metals EMA.vpm'
serie = run_interval(model_location,loop_index,
interval,'relative market price',
unique_edges,indCons,double_list,
cases_of_interest[beh_no])
if serie.shape != rmp.shape:
ema_logging.info('Loop %s created a floating point error' % (loop_index))
ema_logging.info('Caused by trying to switch %s' % (unique_edges[loop_index-1]))
if serie.shape == rmp.shape:
ax.plot(x,serie,'b')
# data = np.zeros(rmp.shape[0])
# data[0:serie.shape[0]] = serie
# ax.plot(x,data,'b')
ax.plot(x,rmp,'r')
ax.axvspan(interval[0]-1,interval[1], facecolor='lightgrey', alpha=0.5)
f_name = 'switched unique edges only'+str(beh_no)
plt.savefig(f_name)
#load the data
experiments, results = load_results(r'1000 flu cases.cPickle')
#transform the results to the required format
newResults = {}
#get time and remove it from the dict
time = results.pop('TIME')
for key, value in results.items():
if key == 'deceased population region 1':
newResults[key] = value[:,-1] #we want the end value
else:
# we want the maximum value of the peak
newResults['max peak'] = np.max(value, axis=1)
# we want the time at which the maximum occurred
# the code here is a bit obscure, I don't know why the transpose
# of value is needed. This however does produce the appropriate results
logicalIndex = value.T==np.max(value, axis=1)
newResults['time of max'] = time[logicalIndex.T]
results = (experiments, newResults)
scatter3d(results, outcomes=newResults.keys())
if __name__ == '__main__':
log_to_stderr(level= INFO)
# test_envelopes3d()
# test_envelopes3d_group_by()
# test_lines3d()
# test_scatter3d()
'''
Created on Sep 8, 2011
@author: gonengyucel, jhkwakkel
'''
import matplotlib.pyplot as plt
from analysis.clusterer import cluster
from expWorkbench import load_results
from expWorkbench import ema_logging
ema_logging.log_to_stderr(ema_logging.INFO)
#load the data
data = load_results(r'..\gallery\data\100 flu cases no policy.cPickle')
# specify the number of desired clusters
# note: the meaning of cValue is tied to the value for cMethod
cValue = 5
#perform cluster analysis
dist, clusteraloc, runlog, z = cluster(data=data,
outcome='deceased population region 1',
distance='gonenc',
interClusterDistance='complete',
cMethod = 'maxclust',
cValue = cValue,
plotDendrogram=False,
plotClusters=False,
groupPlot=False,
uncs = [ParameterUncertainty((0,1), "a"),
ParameterUncertainty((0,1), "b")]
outcomes = [Outcome("test 1", time=True),
Outcome("test 2", time=True)]
callback = DefaultCallback(uncs, outcomes, nr_experiments=nr_experiments)
policy = {"name": "none"}
name = "test"
for i in range(nr_experiments):
if i % 2 == 0:
case = {uncs[0].name: random.random()}
result = {outcomes[0].name: np.random.rand(10)}
else:
case = {uncs[1].name: random.random()}
result = {outcomes[1].name: np.random.rand(10)}
callback(case, policy, name, result)
results = callback.get_results()
debug("\n"+str(results[0]))
for key, value in results[1].iteritems():
debug("\n" + str(key) + "\n" + str(value))
if __name__ == "__main__":
ema_logging.log_to_stderr(ema_logging.DEBUG)
# test_callback_initalization()
test_callback_store_results()
# test_callback_call_intersection()
# test_callback_call_union()
'''
self.uncertainties.append(LookupUncertainty([(0, 5), (-1, 2), (0, 1.5), (0, 1.5), (0, 1), (0.5, 1.5)], "TF", 'hearne', self, 0, 2))
#self.uncertainties.pop()
self.uncertainties.append(LookupUncertainty([(0, 4), (1, 5), (1, 5), (0, 2), (0, 2)], "TF2", 'approximation', self, 0, 10))
#self.uncertainties.pop()
self.uncertainties.append(ParameterUncertainty((0.02, 0.08), "rate1"))
self.uncertainties.append(ParameterUncertainty((0.02, 0.08), "rate2"))
self.uncertainties.append(LookupUncertainty([[(0.0, 0.05), (0.25, 0.15), (0.5, 0.4), (0.75, 1), (1, 1.25)],
[(0.0, 0.1), (0.25, 0.25), (0.5, 0.75), (1, 1.25)],
[(0.0, 0.0), (0.1, 0.2), (0.3, 0.6), (0.6, 0.9), (1, 1.25)]], "TF3", 'categories', self, 0, 2))
#self.uncertainties.pop()
self.delete_lookup_uncertainties()
if __name__ == "__main__":
logger = logging.log_to_stderr(logging.INFO)
model = lookup_model(r'..\lookups', "sampleModel")
#model.step = 4 #reduce data to be stored
ensemble = ModelEnsemble()
ensemble.set_model_structure(model)
#turn on parallel
ensemble.parallel = False
#run policy with old cases
results = ensemble.perform_experiments(10)
save_results(results, 'lookup_3methods.cpickle')
results = load_results('lookup_3methods.cpickle')
outcomes =['TF', 'TF2', 'TF3', 'flow1']
'''
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 expWorkbench.util import load_results
from expWorkbench import ema_logging
ema_logging.log_to_stderr(level=ema_logging.DEFAULT_LEVEL)
#load the data
experiments, outcomes = load_results(r'.\data\100 flu cases no policy.bz2')
#transform the results to the required format
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
tr['max peak'] = np.max(value, axis=1)
# we want the time at which the maximum occurred
See flu_example.py for the code. The dataset was generated using 32 bit Python.
Therefore, this example will not work if you are running 64 bit Python.
.. codeauthor:: jhkwakkel <j.h.kwakkel (at) tudelft (dot) nl>
chamarat <c.hamarat (at) tudelft (dot) nl>
'''
import numpy as np
import matplotlib.pyplot as plt
import analysis.prim as prim
from expWorkbench import load_results, ema_logging
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
results = load_results(r'./data/1000 flu cases.bz2')
import numpy as np
import matplotlib.pyplot as plt
import analysis.prim as prim
from expWorkbench import load_results
import expWorkbench.ema_logging as ema_logging
#perform_prim logs information to the logger
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
results = load_results(r'../../../src/analysis/1000 flu cases.cPickle',
zipped=False)
experiments, results = results
#extract results for 1 policy
# if len(activationTimeStep) > 0:
# activationTimeStep = activationTimeStep[0]
# else:
# activationTimeStep = np.array([0])
## if activationTimeStep.shape[0] > 0:
## activationTimeStep = activationTimeStep
## else:
## activationTimeStep = np.array([0])
# results[output.name] = activationTimeStep
self.output = results
if error:
raise CaseError("run not completed", case)
if __name__ == "__main__":
logger = logging.log_to_stderr(logging.INFO)
model = EnergyTrans(r'..\..\models\CANER\CESUN', "ESDMAElecTrans")
model.step = 4 #reduce data to be stored
ensemble = SimpleModelEnsemble()
ensemble.set_model_structure(model)
ensemble.parallel = True
policies = [
{
'name': 'No Policy',
'file': r'\CESUN_no.vpm'
},
{
'name': 'Basic Policy',
'file': r'\CESUN_basic.vpm'
},
{
results[output.name] = activationTimeStep
self.output = results
if error:
raise CaseError("run not completed", case)
def obj_func(outcomes):
outcome = outcomes['total fraction new technologies']
zeros = np.zeros((outcome.shape[0], 1))
zeros[outcome[:,-1]>0.6] = 1
value = np.sum(zeros)/zeros.shape[0]
return value,
if __name__ == "__main__":
ema_logging.log_to_stderr(ema_logging.INFO)
model = EnergyTrans(r"..\data", "ESDMAElecTrans")
ensemble = ModelEnsemble()
ensemble.set_model_structure(model)
ensemble.parallel = True
policy_levers = {'Trigger subsidy T2': {'type':'range', 'values':(0,1)},
'Trigger subsidy T3': {'type':'range', 'values':(0,1)},
'Trigger subsidy T4': {'type':'range', 'values':(0,1)},
'Trigger addnewcom': {'type':'list', 'values':[0, 0.25, 0.5, 0.75, 1]}}
stats_callback, pop = ensemble.perform_robust_optimization(cases=10,
reporting_interval=100,
obj_function=obj_func,
policy_levers=policy_levers,
susceptible_population_region_1 = susceptible_population_region_1_NEXT
susceptible_population_region_2 = susceptible_population_region_2_NEXT
immune_population_region_1 = immune_population_region_1_NEXT
immune_population_region_2 = immune_population_region_2_NEXT
deceased_population_region_1.append(deceased_population_region_1_NEXT)
deceased_population_region_2.append(deceased_population_region_2_NEXT)
#End of main code
return (runTime, deceased_population_region_1) #, Max_infected, Max_time)
if __name__ == "__main__":
import expWorkbench.ema_logging as logging
np.random.seed(150) #set the seed for replication purposes
logging.log_to_stderr(logging.INFO)
fluModel = MexicanFlu(None, "mexicanFluExample")
ensemble = ModelEnsemble()
ensemble.parallel = True
ensemble.set_model_structure(fluModel)
nr_experiments = 500
results = ensemble.perform_experiments(nr_experiments, reporting_interval=100)
lines(results, outcomes_to_show="deceased_population_region_1",
show_envelope=True, density=KDE, titles=None,
experiments_to_show=np.arange(0, nr_experiments, 10)
)
plt.show()