def test_Morris_with_NAN():
'''
Test if morris.analyze raise a ValueError when nan are passed in the Y
values
'''
problem, model_results, param_values = setup_samples()
# Should raise a ValueError type of error
with pytest.raises(ValueError):
morris.analyze(problem, param_values, model_results)
def test_morris_to_df():
params = ['x1', 'x2', 'x3', 'x4', 'x5', 'x6', 'x7', 'x8']
problem = {
'num_vars': 8,
'names': params,
'groups': None,
'bounds': [[0.0, 1.0],
[0.0, 1.0],
[0.0, 1.0],
[0.0, 1.0],
[0.0, 1.0],
[0.0, 1.0],
[0.0, 1.0],
[0.0, 1.0]]
}
param_values = morris_sample.sample(problem, N=1000, num_levels=4,
optimal_trajectories=None)
Y = Sobol_G.evaluate(param_values)
Si = morris.analyze(problem, param_values, Y)
Si_df = Si.to_df()
assert isinstance(Si_df, pd.DataFrame), \
"Morris Si: Expected DataFrame, got {}".format(type(Si_df))
expected_index = set(params)
assert set(Si_df.index) == expected_index, "Incorrect index in DataFrame"
col_names = ['mu', 'mu_star', 'sigma', 'mu_star_conf']
assert set(Si_df.columns) == set(col_names), \
"Unexpected column names in DataFrame. Expected {}, got {}".format(
col_names, Si_df.columns)
def test_regression_morris_optimal(self, set_seed):
'''
Tests the use of optimal trajectories with Morris.
Uses brute force approach
Note that the relative tolerance is set to a very high value
(default is 1e-05) due to the coarse nature of the num_levels.
'''
set_seed
param_file = 'src/SALib/test_functions/params/Ishigami.txt'
problem = read_param_file(param_file)
param_values = sample(problem=problem, N=20,
num_levels=4,
optimal_trajectories=9,
local_optimization=True)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem, param_values, Y,
conf_level=0.95, print_to_console=False,
num_levels=4)
assert_allclose(Si['mu_star'],
[9.786986e+00, 7.875000e+00, 1.388621],
atol=0,
rtol=1e-5)
def test_regression_morris_groups_brute_optim(self, set_seed):
set_seed
param_file = 'src/SALib/test_functions/params/Ishigami_groups.txt'
problem = read_param_file(param_file)
param_values = sample(problem=problem, N=50,
num_levels=4,
optimal_trajectories=6,
local_optimization=False)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem, param_values, Y,
conf_level=0.95, print_to_console=False,
num_levels=4)
assert_allclose(Si['mu'], [9.786986, np.NaN],
atol=0, rtol=1e-5)
assert_allclose(Si['sigma'], [6.453729, np.NaN],
atol=0, rtol=1e-5)
assert_allclose(Si['mu_star'], [9.786986, 7.875],
atol=0, rtol=1e-5)
def test_regression_morris_optimal(self, set_seed):
'''
Tests the use of optimal trajectories with Morris.
Uses brute force approach
Note that the relative tolerance is set to a very high value
(default is 1e-05) due to the coarse nature of the num_levels.
'''
set_seed
param_file = 'src/SALib/test_functions/params/Ishigami.txt'
problem = read_param_file(param_file)
param_values = sample(problem=problem,
N=20,
num_levels=4,
optimal_trajectories=9,
local_optimization=True)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem,
param_values,
Y,
conf_level=0.95,
print_to_console=False,
num_levels=4)
assert_allclose(Si['mu_star'], [9.786986e+00, 7.875000e+00, 1.388621],
atol=0,
rtol=1e-5)
def plot_morris_by_leaf_by_boot(df_out, variable='normalized_audpc',
parameter_range_file='param_range_SA.txt',
input_file='morris_input.txt',
nboots=5, ylims=None):
problem = read_param_file(parameter_range_file)
fig, axs = plt.subplots(6, 2, figsize=(15, 30))
colors = iter(['b', 'g', 'r', 'k', 'm', 'c', 'y'])
colors = {b: next(colors) for b in range(nboots)}
for i, ax in enumerate(axs.flat):
lf = i + 1
for boot in np.unique(df_out['i_boot']):
param_values = np.loadtxt(input_file[:-4] + '_boot' + str(boot) + input_file[-4:])
df = df_out[(df_out['i_boot'] == boot) & (df_out['num_leaf_top'] == lf)]
Y = df[variable]
Si_bt = morris.analyze(problem, param_values, Y, grid_jump=5,
num_levels=10, conf_level=0.95,
print_to_console=False)
for ip, param in enumerate(Si_bt['names']):
ax.plot(Si_bt['mu_star'][ip], Si_bt['sigma'][ip],
color=colors[boot], marker='*')
ax.annotate(param, (Si_bt['mu_star'][ip], Si_bt['sigma'][ip]))
if ylims is not None:
ax.set_ylim(ylims)
ax.set_xlim(ylims)
ax.annotate('Leaf %d' % lf, xy=(0.05, 0.85),
xycoords='axes fraction', fontsize=18)
def gsa_analyse(self):
return [
ma.analyze(self.morris_problem,
self.samples,
np.array(score),
num_levels=4) for score in self.scores
]
def test_regression_morris_groups_brute_optim(self, set_seed):
set_seed
param_file = 'src/SALib/test_functions/params/Ishigami_groups.txt'
problem = read_param_file(param_file)
param_values = sample(problem=problem,
N=50,
num_levels=4,
optimal_trajectories=6,
local_optimization=False)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem,
param_values,
Y,
conf_level=0.95,
print_to_console=False,
num_levels=4)
assert_allclose(Si['mu'], [9.786986, np.NaN], atol=0, rtol=1e-5)
assert_allclose(Si['sigma'], [6.453729, np.NaN], atol=0, rtol=1e-5)
assert_allclose(Si['mu_star'], [9.786986, 7.875], atol=0, rtol=1e-5)
def test_morris_to_df():
params = ['x1', 'x2', 'x3', 'x4', 'x5', 'x6', 'x7', 'x8']
problem = {
'num_vars':
8,
'names':
params,
'groups':
None,
'bounds': [[0.0, 1.0], [0.0, 1.0], [0.0, 1.0], [0.0, 1.0], [0.0, 1.0],
[0.0, 1.0], [0.0, 1.0], [0.0, 1.0]]
}
param_values = morris_sample.sample(problem,
N=1000,
num_levels=4,
optimal_trajectories=None)
Y = Sobol_G.evaluate(param_values)
Si = morris.analyze(problem, param_values, Y)
Si_df = Si.to_df()
assert isinstance(Si_df, pd.DataFrame), \
"Morris Si: Expected DataFrame, got {}".format(type(Si_df))
expected_index = set(params)
assert set(Si_df.index) == expected_index, "Incorrect index in DataFrame"
col_names = ['mu', 'mu_star', 'sigma', 'mu_star_conf']
assert set(Si_df.columns) == set(col_names), \
"Unexpected column names in DataFrame. Expected {}, got {}".format(
col_names, Si_df.columns)
def analyze_morris(self):
# Method of Morris
return morris.analyze(
self.sa_problem,
self.samples_x,
self.samples_y,
conf_level=0.95,
num_levels=4,
print_to_console=self.options["print_to_console"])
def fit(self, X, y):
"""
Fits the regressor to the data `(X, y)` and performs a sensitivity analysis on the result of the regression.
:param X: Training data
:param y: Target values
:return: `self`
"""
from numpy import argpartition
N = len(X[0])
if (self.domain is None) or (self.probs is None):
self._avg_fucn(X, y)
if self.regressor is None:
from sklearn.svm import SVR
self.regressor = SVR()
self.regressor.fit(self.domain, self.probs)
bounds = [[
min(self.domain[:, idx]) - self.margin,
max(self.domain[:, idx]) + self.margin
] for idx in range(N)]
problem = dict(num_vars=N,
names=['x%d' % idx for idx in range(N)],
bounds=bounds)
res = []
if self.method == 'sobol':
from SALib.sample import saltelli
from SALib.analyze import sobol
param_values = saltelli.sample(problem, self.num_smpl)
y_ = self.regressor.predict(param_values)
res = sobol.analyze(problem, y_)['ST']
self.weights_ = res
elif self.method == 'morris':
from SALib.sample import morris as mrs
from SALib.analyze import morris
param_values = mrs.sample(problem,
self.num_smpl,
num_levels=self.num_levels)
y_ = self.regressor.predict(param_values)
res = morris.analyze(problem,
param_values,
y_,
num_levels=self.num_levels)['mu_star']
self.weights_ = res
elif self.method == 'delta-mmnt':
from SALib.sample import latin
from SALib.analyze import delta
param_values = latin.sample(problem, self.num_smpl)
y_ = self.regressor.predict(param_values)
res = delta.analyze(problem,
param_values,
y_,
num_resamples=self.num_resmpl)['delta']
self.weights_ = res
self.top_features_ = argpartition(
res, -self.n_features_to_select)[-self.n_features_to_select:]
return self
def explain_global(self, name=None):
from SALib.analyze import morris
if name is None:
name = gen_name_from_class(self)
samples = self.sampler.sample()
problem = self.sampler.gen_problem_from_data(self.data,
self.feature_names)
analysis = morris.analyze(problem, samples,
self.predict_fn(samples).astype(float))
mu = analysis["mu"]
mu_star = analysis["mu_star"]
sigma = analysis["sigma"]
mu_star_conf = analysis["mu_star_conf"]
mask = mu_star > 0
convergence_index = np.max(
np.array(mu_star_conf)[mask] / np.array(mu_star)[mask])
overall_data_dict = {
"names": self.feature_names,
"scores": mu_star,
"convergence_index": convergence_index,
}
specific_data_dicts = []
for feat_idx, feature_name in enumerate(self.feature_names):
specific_data_dict = {
"type": "morris",
"mu": mu[feat_idx],
"mu_star": mu_star[feat_idx],
"sigma": sigma[feat_idx],
"mu_star_conf": mu_star_conf[feat_idx],
}
specific_data_dicts.append(specific_data_dict)
internal_obj = {
"overall": overall_data_dict,
"specific": specific_data_dicts
}
global_selector = gen_global_selector(self.data, self.feature_names,
self.feature_types, mu_star)
return MorrisExplanation(
"global",
internal_obj,
feature_names=self.feature_names,
feature_types=self.feature_types,
name=name,
selector=global_selector,
)
def _analyze(*args, **kwargs):
self = args[0]
num_levels = self.getKwarg('num_levels', kwargs)
grid_jump = self.getKwarg('grid_jump', kwargs)
num_resamples = kwargs.get('num_resamples', 1000)
conf_level = kwargs.get('conf_level', 0.95)
print_to_console = kwargs.get('print_to_console', False)
return morris.analyze(self.problem, self.inputs, self.results, num_resamples=num_resamples,
conf_level=conf_level, print_to_console=print_to_console,
grid_jump=grid_jump, num_levels=num_levels)
def _anlzr_salib(método, problema, mstr, simul, ops_método):
'''
Parameters
----------
método: ['morris', 'fast']
lÃms_paráms, mapa_paráms se usan para generar el problema.
mstr: sampled data
simul: simulated model output
ops_método: dict
#{'num_levels': 8, 'grid_jump': 4}
Returns
-------
'''
if isinstance(mstr, list):
mstr = np.asarray(mstr)
if método == 'morris':
if isinstance(simul, list):
simul = np.asarray(simul)
ops = {'X': mstr, 'Y': simul, 'num_levels': 16}
ops.update(ops_método)
mor = {}
Si = morris.analyze(problema, **ops)
mor.update(
{'mu_star': {j: Si['mu_star'][i] for i, j in enumerate(problema['names'])},
'sigma': {j: Si['sigma'][i] for i, j in enumerate(problema['names'])},
# 'sum_sigma': np.sum(Si['sigma'])
})
return mor
elif método == 'fast':
ops = {'Y': simul}
fa = {}
Si = fast.analyze(problema, **ops)
fa.update({'Si': {j: Si['S1'][i] for i, j in enumerate(problema['names'])},
'ST': {j: Si['ST'][i] for i, j in enumerate(problema['names'])},
'St-Si': {j: Si['ST'][i] - Si['S1'][i] for i, j in enumerate(problema['names'])},
# 'sum_s1': np.sum(Si['S1']),
# 'sum_st': np.sum(Si['ST']),
# 'sum_st-s1': np.absolute(np.sum(Si['ST']) - np.sum(Si['S1']))
})
return fa
else:
raise ValueError(_('Algoritmo "{}" no reconocido.').format(método))
def test_analysis_of_morris_results():
'''
Tests a one-dimensional vector of results
Taken from the solution to Exercise 4 (p.138) in Saltelli (2008).
'''
model_input = np.array(
[[0, 1. / 3], [0, 1], [2. / 3, 1], [0, 1. / 3], [2. / 3, 1. / 3],
[2. / 3, 1], [2. / 3, 0], [2. / 3, 2. / 3], [0, 2. / 3], [1. / 3, 1],
[1, 1], [1, 1. / 3], [1. / 3, 1], [1. / 3, 1. / 3], [1, 1. / 3],
[1. / 3, 2. / 3], [1. / 3, 0], [1, 0]],
dtype=float)
model_output = np.array([
0.97, 0.71, 2.39, 0.97, 2.30, 2.39, 1.87, 2.40, 0.87, 2.15, 1.71, 1.54,
2.15, 2.17, 1.54, 2.20, 1.87, 1.0
],
dtype=float)
problem = {
'num_vars': 2,
'names': ['Test 1', 'Test 2'],
'groups': None,
'bounds': [[0.0, 1.0], [0.0, 1.0]]
}
Si = analyze(problem,
model_input,
model_output,
num_resamples=1000,
conf_level=0.95,
print_to_console=False)
desired_mu = np.array([0.66, 0.21])
assert_allclose(Si['mu'],
desired_mu,
rtol=1e-1,
err_msg="The values for mu are incorrect")
desired_mu_star = np.array([1.62, 0.35])
assert_allclose(Si['mu_star'],
desired_mu_star,
rtol=1e-2,
err_msg="The values for mu star are incorrect")
desired_sigma = np.array([1.79, 0.41])
assert_allclose(Si['sigma'],
desired_sigma,
rtol=1e-2,
err_msg="The values for sigma are incorrect")
desired_names = ['Test 1', 'Test 2']
assert_equal(Si['names'],
desired_names,
err_msg="The values for names are incorrect")
def morris():
from SALib.analyze import morris
from SALib.sample.morris import sample
problem = {
'num_vars': 5,
'names': ['HEME', 'K1', 'MPY', 'MPYgu', 'QCC'],
'groups': None,
'bounds': [[.4, .5], [10., 30.], [30., 40.], [15., 25.], [10., 15.]]
}
parameter_values = sample(problem,
N=10,
num_levels=4,
grid_jump=2,
optimal_trajectories=None)
parameters = assign_parameters()
schedule = get_default_schedule()
y_index = np.argmax(o["Curine"])
ys = []
for inputs in parameter_values:
for i in range(len(problem["names"])):
setattr(parameters, problem["names"][i], inputs[i])
_, __, ___, output = pbpk(parameters, schedule)
ys.append(output["Curine"][y_index])
sis = morris.analyze(problem,
parameter_values,
np.array(ys),
conf_level=0.95,
print_to_console=True,
num_levels=4,
grid_jump=2,
num_resamples=100)
import matplotlib.pyplot as plt
from SALib.plotting.morris import horizontal_bar_plot, covariance_plot, sample_histograms
fig, (ax1, ax2) = plt.subplots(1, 2)
horizontal_bar_plot(ax1, sis, {}, sortby='mu_star', unit=r"mg/g")
covariance_plot(ax2, sis, {}, unit=r"mg/g")
fig2 = plt.figure()
sample_histograms(fig2, parameter_values, problem, {'color': 'y'})
plt.show()
def test_doesnot_raise_error_if_floats():
inputs = np.array([[0, 1. / 3], [0, 1], [2. / 3, 1],
[0, 1. / 3], [2. / 3, 1. / 3], [2. / 3, 1],
[2. / 3, 0], [2. / 3, 2. / 3], [0, 2. / 3],
[1. / 3, 1], [1, 1], [1, 1. / 3],
[1. / 3, 1], [1. / 3, 1. / 3], [1, 1. / 3],
[1. / 3, 2. / 3], [1. / 3, 0], [1, 0]],
dtype=np.float32)
outputs = np.array([0.97, 0.71, 2.39, 0.97, 2.30, 2.39,
1.87, 2.40, 0.87, 2.15, 1.71, 1.54,
2.15, 2.17, 1.54, 2.20, 1.87, 1.0],
dtype=np.float32)
problem = {
'num_vars': 2,
'names': ['Test 1', 'Test 2'],
'groups': None,
'bounds': [[0.0, 1.0], [0.0, 1.0]]
}
analyze(problem, inputs, outputs)
def test_doesnot_raise_error_if_floats():
inputs = np.array(
[[0, 1. / 3], [0, 1], [2. / 3, 1], [0, 1. / 3], [2. / 3, 1. / 3],
[2. / 3, 1], [2. / 3, 0], [2. / 3, 2. / 3], [0, 2. / 3], [1. / 3, 1],
[1, 1], [1, 1. / 3], [1. / 3, 1], [1. / 3, 1. / 3], [1, 1. / 3],
[1. / 3, 2. / 3], [1. / 3, 0], [1, 0]],
dtype=np.float32)
outputs = np.array([
0.97, 0.71, 2.39, 0.97, 2.30, 2.39, 1.87, 2.40, 0.87, 2.15, 1.71, 1.54,
2.15, 2.17, 1.54, 2.20, 1.87, 1.0
],
dtype=np.float32)
problem = {
'num_vars': 2,
'names': ['Test 1', 'Test 2'],
'groups': None,
'bounds': [[0.0, 1.0], [0.0, 1.0]]
}
analyze(problem, inputs, outputs)
def explain_global(self, name=None):
if name is None:
name = gen_name_from_class(self)
samples = self.sampler.sample()
problem = self.sampler.gen_problem_from_data(self.data, self.feature_names)
analysis = morris.analyze(problem, samples, self.predict_fn(samples))
mu = analysis["mu"]
mu_star = analysis["mu_star"]
sigma = analysis["sigma"]
mu_star_conf = analysis["mu_star_conf"]
mask = mu_star > 0
convergence_index = np.max(
np.array(mu_star_conf)[mask] / np.array(mu_star)[mask]
)
overall_data_dict = {
"names": self.feature_names,
"scores": mu_star,
"convergence_index": convergence_index,
}
specific_data_dicts = []
for feat_idx, feature_name in enumerate(self.feature_names):
specific_data_dict = {
"type": "morris",
"mu": mu[feat_idx],
"mu_star": mu_star[feat_idx],
"sigma": sigma[feat_idx],
"mu_star_conf": mu_star_conf[feat_idx],
}
specific_data_dicts.append(specific_data_dict)
internal_obj = {"overall": overall_data_dict, "specific": specific_data_dicts}
global_selector = gen_global_selector(
self.data, self.feature_names, self.feature_types, mu_star
)
return MorrisExplanation(
"global",
internal_obj,
feature_names=self.feature_names,
feature_types=self.feature_types,
name=name,
selector=global_selector,
)
def explain_global(self, name=None):
if name is None:
name = gen_name_from_class(self)
samples = self.sampler.sample()
problem = self.sampler.gen_problem_from_data(self.data,
self.feature_names)
analysis = morris.analyze(problem, samples, self.predict_fn(samples))
mu = analysis['mu']
mu_star = analysis['mu_star']
sigma = analysis['sigma']
mu_star_conf = analysis['mu_star_conf']
mask = mu_star > 0
convergence_index = np.max(
np.array(mu_star_conf)[mask] / np.array(mu_star)[mask])
overall_data_dict = {
'names': self.feature_names,
'scores': mu_star,
'convergence_index': convergence_index,
}
specific_data_dicts = []
for feat_idx, feature_name in enumerate(self.feature_names):
specific_data_dict = {
'type': 'morris',
'mu': mu[feat_idx],
'mu_star': mu_star[feat_idx],
'sigma': sigma[feat_idx],
'mu_star_conf': mu_star_conf[feat_idx],
}
specific_data_dicts.append(specific_data_dict)
internal_obj = {
'overall': overall_data_dict,
'specific': specific_data_dicts,
}
global_selector = gen_global_selector(self.data, self.feature_names,
self.feature_types, mu_star)
return MorrisExplanation('global',
internal_obj,
feature_names=self.feature_names,
feature_types=self.feature_types,
name=name,
selector=global_selector)
def test_regression_morris_vanilla():
param_file = 'SALib/test_functions/params/Ishigami.txt'
problem = read_param_file(param_file)
param_values = sample(problem=problem, N=5000, \
num_levels=10, grid_jump=5, \
optimal_trajectories=None)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem, param_values, Y,
conf_level=0.95, print_to_console=False,
num_levels=10, grid_jump=5)
assert_allclose(Si['mu_star'], [8.1, 2.2, 5.4], atol=0, rtol=5e-1)
def morris_analyze_function(problem, X, Y):
"""
Use the SALib.analyze.morris method to analyze the simulation results.
:param problem: The definition of the problem statement as defined for the sampling method.
:param X: the `X` parameter of the morris method (The NumPy matrix containing the model inputs)
:param Y: The NumPy array containing the model outputs
:param parameters: dictionary containing the key 'num_levels' that is passed on to the
SALib.analyze.morris method parameter of the same name.
:return: returns the result of the SALib.analyze.sobol method (from the documentation: a dictionary with keys
`mu`, `mu_star`, `sigma`, and `mu_star_conf`, where each entry is a list of size D (the number of eters)
containing the indices in the same order as the parameter file.)
"""
assert 'num_levels' in problem, 'morris method requires the `num_levels` parameter to be set (int)'
return morris.analyze(problem, X, Y, num_levels=problem['num_levels'])
def run_salib_morris(target_parameters,
target_output_name,
n_trajectories,
num_levels,
grid_jump,
n_processors=cpu_count() - 1):
num_vars = len(target_parameters)
parameter_names = list(target_parameters.keys())
groups = None
bounds = [target_parameters[name] for name in parameter_names]
problem = {
'num_vars': num_vars,
'names': parameter_names,
'groups': groups,
'bounds': bounds
}
parameter_values = sample(problem,
N=n_trajectories,
num_levels=num_levels,
grid_jump=grid_jump,
optimal_trajectories=None)
ys = None
if n_processors > 1:
chunks = np.array_split(parameter_values, n_processors)
chunks = [(parameter_names, chunk, target_output_name)
for chunk in chunks]
pool = Pool(n_processors)
results = pool.map(hdmpp.generate_outputs, chunks)
ys = np.concatenate(results)
else:
ys = hdmpp.generate_outputs(
(parameter_names, parameter_values, target_output_name))
sis = morris.analyze(problem,
parameter_values,
np.array(ys),
conf_level=0.95,
print_to_console=False,
num_levels=num_levels,
grid_jump=grid_jump,
num_resamples=100)
return problem, parameter_values, sis
def sensiAnal(model_results, Problem):
weather = []
X = []
Y = []
for row in model_results:
weather.append(row[0])
X.append(row[1:len(row) - 2])
Y.append(row[len(row) - 1])
climate = [
'1A', '2A', '2B', '3A', '3B', '3C', '4A', '4B', '4C', '5A', '5B', '6A',
'6B', '7A', '8A'
]
Mu = []
Sigma = []
Name = []
Clim = []
for x in climate:
X_clim = []
Y_clim = []
for ind, val in enumerate(weather):
if val == x:
X_clim.append(X[ind])
Y_clim.append(Y[ind])
for row in Problem:
if row[0] == x:
problem = row[1]
if len(X_clim) > 0:
Si = morris.analyze(problem,
np.array(X_clim),
np.array(Y_clim),
conf_level=0.95,
print_to_console=True,
num_levels=4,
grid_jump=2)
mu_clim = Si['mu_star']
sigma_clim = Si['sigma']
name_clim = Si['names']
Mu.append(mu_clim)
Sigma.append(sigma_clim)
Name.append(name_clim)
Clim.append(x)
return Clim, Name, Mu, Sigma
def _analizar(sÃmismo, vec_res, muestra, ops):
if sÃmismo.método == 'sobol':
return sobol.analyze(problem=sÃmismo.problema, Y=vec_res, **ops)
elif sÃmismo.método == 'fast':
return fast.analyze(problem=sÃmismo.problema, Y=vec_res, **ops)
elif sÃmismo.método == 'morris':
return morris_anlz.analyze(problem=sÃmismo.problema, X=muestra, Y=vec_res, **ops)
elif sÃmismo.método == 'dmim':
return delta.analyze(problem=sÃmismo.problema, X=muestra, Y=vec_res, **ops)
elif sÃmismo.método == 'dgsm':
return dgsm.analyze(problem=sÃmismo.problema, X=muestra, Y=vec_res, **ops)
elif sÃmismo.método == 'ff':
return ff_anlz.analyze(problem=sÃmismo.problema, X=muestra, Y=vec_res, **ops)
else:
raise ValueError('Método de análisis de sensibilidad "{}" no reconocido.'.format(sÃmismo.método))
def morris(self):
"""Morris Method sensitivity of the objective function.
This function estimates the sensitivity with the Morris Method of the
objective function with changes in the parameters using SALib:
https://salib.readthedocs.io/en/latest/api.html#method-of-morris
Returns:
dict: sensitivity values of parameters; dict has keys 'mu',
'mu_star', 'sigma', and 'mu_star_conf'
"""
X, y, problem = self._sensitivity_prep()
n_sample = 2000
param_values = morris.sample(problem, n_sample)
X_s, y_s = self._closest_points(problem, X, y, param_values)
Si = morris.analyze(problem, X_s, y_s)
return Si
def test_regression_morris_groups(self, set_seed):
set_seed
param_file = 'src/SALib/test_functions/params/Ishigami_groups.txt'
problem = read_param_file(param_file)
param_values = sample(problem=problem, N=10000,
num_levels=4,
optimal_trajectories=None)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem, param_values, Y,
conf_level=0.95, print_to_console=False,
num_levels=4)
assert_allclose(Si['mu_star'], [7.610322, 10.197014],
atol=0, rtol=1e-5)
def test_regression_morris_groups(self, set_seed):
set_seed
param_file = 'src/SALib/test_functions/params/Ishigami_groups.txt'
problem = read_param_file(param_file)
param_values = sample(problem=problem, N=10000,
num_levels=4,
optimal_trajectories=None)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem, param_values, Y,
conf_level=0.95, print_to_console=False,
num_levels=4)
assert_allclose(Si['mu_star'], [7.610322, 10.197014],
atol=0, rtol=1e-5)
def test_regression_morris_vanilla(self, set_seed):
"""Note that this is a poor estimate of the Ishigami
function.
"""
set_seed
param_file = 'src/SALib/test_functions/params/Ishigami.txt'
problem = read_param_file(param_file)
param_values = sample(problem, 10000, 4,
optimal_trajectories=None)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem, param_values, Y,
conf_level=0.95, print_to_console=False,
num_levels=4)
assert_allclose(Si['mu_star'], [7.536586, 7.875, 6.308785],
atol=0, rtol=1e-5)
def test_regression_morris_vanilla(self, set_seed):
"""Note that this is a poor estimate of the Ishigami
function.
"""
set_seed
param_file = 'src/SALib/test_functions/params/Ishigami.txt'
problem = read_param_file(param_file)
param_values = sample(problem, 10000, 4,
optimal_trajectories=None)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem, param_values, Y,
conf_level=0.95, print_to_console=False,
num_levels=4)
assert_allclose(Si['mu_star'], [7.536586, 7.875, 6.308785],
atol=0, rtol=1e-5)
def evaluate(self):
"""
:param y: A Numpy array containing the model outputs of dtype=float
:return: A dictionary of sensitivity indices containing the following entries.
- `mu` - the mean elementary effect
- `mu_star` - the absolute of the mean elementary effect
- `sigma` - the standard deviation of the elementary effect
- `mu_star_conf` - the bootstrapped confidence interval
- `names` - the names of the parameters
"""
if self.y is None:
raise NameError('y is not defined. run e+ models first')
self.si = analyze(self.problem,
self.X,
self.y,
num_levels=self.num_levels)
return self.si
def main():
#print param
param = np.array([
["T",0,.75],
["rho",0,1],
["R",10,50],
["D",0,5],
["s",0,.6],
])
np.savetxt('parameters.txt',param,fmt='%s',delimiter=' ')
# Generate samples
param_values = morris_oat.sample(100, "parameters.txt", num_levels=10, grid_jump=5)
# Save the parameter values in a file (they are needed in the analysis)
np.savetxt('model_input.txt', param_values, delimiter=' ')
Y = np.array(POOL.map(measure_tau,param_values))
np.savetxt("model_output.txt", Y, delimiter=' ')
# Perform the sensitivity analysis using the model output
Si = morris.analyze('parameters.txt', 'model_input.txt', 'model_output.txt',
column=0, conf_level=0.95, print_to_console=False)
with open("data.pkle","w") as f:
pkle.dump({"X": param_values, "Y":Y, "Morris":Si},f)
metadata("data.pkle")
plt.scatter(Si["mu_star"],Si["sigma"])
for x,y,s in zip(Si["mu_star"],Si["sigma"],param[:,0]):
plt.annotate(s,(x,y), xytext=(5, 5),textcoords='offset points')
plt.xlabel(r"$\mu^*$")
plt.ylabel(r"$\sigma$")
plt.savefig("sensitivity_with_morris.png")
metadata("sensitivity_with_morris.png")
plt.savefig("sensitivity_with_morris.eps")
metadata("sensitivity_with_morris.eps")
return Si
def test_regression_morris_groups_local_optim(self, set_seed):
set_seed
param_file = 'src/SALib/test_functions/params/Ishigami_groups.txt'
problem = read_param_file(param_file)
param_values = sample(problem=problem, N=500,
num_levels=4,
optimal_trajectories=20,
local_optimization=True)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem, param_values, Y,
conf_level=0.95, print_to_console=False,
num_levels=4)
assert_allclose(Si['mu_star'],
[13.95285, 7.875],
rtol=1e-5)
def test_analysis_of_morris_results():
'''
Tests a one-dimensional vector of results
Taken from the solution to Exercise 4 (p.138) in Saltelli (2008).
'''
model_input = np.array([[0, 1. / 3], [0, 1], [2. / 3, 1],
[0, 1. / 3], [2. / 3, 1. / 3], [2. / 3, 1],
[2. / 3, 0], [2. / 3, 2. / 3], [0, 2. / 3],
[1. / 3, 1], [1, 1], [1, 1. / 3],
[1. / 3, 1], [1. / 3, 1. / 3], [1, 1. / 3],
[1. / 3, 2. / 3], [1. / 3, 0], [1, 0]],
dtype=np.float)
model_output = np.array([0.97, 0.71, 2.39, 0.97, 2.30, 2.39,
1.87, 2.40, 0.87, 2.15, 1.71, 1.54,
2.15, 2.17, 1.54, 2.20, 1.87, 1.0],
dtype=np.float)
problem = {
'num_vars': 2,
'names': ['Test 1', 'Test 2'],
'groups': None,
'bounds': [[0.0, 1.0], [0.0, 1.0]]
}
Si = analyze(problem, model_input, model_output,
num_resamples=1000,
conf_level=0.95,
print_to_console=False)
desired_mu = np.array([0.66, 0.21])
assert_allclose(Si['mu'], desired_mu, rtol=1e-1,
err_msg="The values for mu are incorrect")
desired_mu_star = np.array([1.62, 0.35])
assert_allclose(Si['mu_star'], desired_mu_star, rtol=1e-2,
err_msg="The values for mu star are incorrect")
desired_sigma = np.array([1.79, 0.41])
assert_allclose(Si['sigma'], desired_sigma, rtol=1e-2,
err_msg="The values for sigma are incorrect")
desired_names = ['Test 1', 'Test 2']
assert_equal(Si['names'], desired_names,
err_msg="The values for names are incorrect")
def test_regression_morris_groups_local_optim(self, set_seed):
set_seed
param_file = 'src/SALib/test_functions/params/Ishigami_groups.txt'
problem = read_param_file(param_file)
param_values = sample(problem=problem, N=500,
num_levels=4,
optimal_trajectories=20,
local_optimization=True)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem, param_values, Y,
conf_level=0.95, print_to_console=False,
num_levels=4)
assert_allclose(Si['mu_star'],
[13.95285, 7.875],
rtol=1e-5)
def test_regression_morris_optimal():
'''
Tests the use of optimal trajectories with Morris.
Note that the relative tolerance is set to a very high value (default is 1e-05)
due to the coarse nature of the num_levels and grid_jump.
'''
param_file = 'SALib/test_functions/params/Ishigami.txt'
problem = read_param_file(param_file)
param_values = sample(problem=problem, N=20, \
num_levels=4, grid_jump=2, \
optimal_trajectories=9)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem, param_values, Y,
conf_level=0.95, print_to_console=False,
num_levels=4, grid_jump=2)
assert_allclose(Si['mu_star'], [8.1, 2.2, 5.4], rtol=10)
def plot_morris_by_leaf_by_boot(df_out,
variable='normalized_audpc',
parameter_range_file='param_range_SA.txt',
input_file='morris_input.txt',
nboots=5,
ylims=None):
problem = read_param_file(parameter_range_file)
fig, axs = plt.subplots(6, 2, figsize=(15, 30))
colors = iter(['b', 'g', 'r', 'k', 'm', 'c', 'y'])
colors = {b: next(colors) for b in range(nboots)}
for i, ax in enumerate(axs.flat):
lf = i + 1
for boot in np.unique(df_out['i_boot']):
param_values = np.loadtxt(input_file[:-4] + '_boot' + str(boot) +
input_file[-4:])
df = df_out[(df_out['i_boot'] == boot)
& (df_out['num_leaf_top'] == lf)]
Y = df[variable]
Si_bt = morris.analyze(problem,
param_values,
Y,
grid_jump=5,
num_levels=10,
conf_level=0.95,
print_to_console=False)
for ip, param in enumerate(Si_bt['names']):
ax.plot(Si_bt['mu_star'][ip],
Si_bt['sigma'][ip],
color=colors[boot],
marker='*')
ax.annotate(param, (Si_bt['mu_star'][ip], Si_bt['sigma'][ip]))
if ylims is not None:
ax.set_ylim(ylims)
ax.set_xlim(ylims)
ax.annotate('Leaf %d' % lf,
xy=(0.05, 0.85),
xycoords='axes fraction',
fontsize=18)
def test_regression_morris_vanilla(self, set_seed):
set_seed
param_file = 'SALib/test_functions/params/Ishigami.txt'
problem = read_param_file(param_file)
param_values = sample(problem=problem,
N=10000,
num_levels=4,
grid_jump=2,
optimal_trajectories=None)
Y = Ishigami.evaluate(param_values)
Si = morris.analyze(problem,
param_values,
Y,
conf_level=0.95,
print_to_console=False,
num_levels=4,
grid_jump=2)
assert_allclose(Si['mu_star'], [7.701555, 7.875, 6.288788],
atol=0,
rtol=1e-5)
# }
# Files with a 4th column for "group name" will be detected automatically, e.g.:
# param_file = '../../SALib/test_functions/params/Ishigami_groups.txt'
# Generate samples
param_values = sample(problem, N=1000, num_levels=4, grid_jump=2, \
optimal_trajectories=None)
# To use optimized trajectories (brute force method), give an integer value for optimal_trajectories
# Run the "model" -- this will happen offline for external models
Y = Sobol_G.evaluate(param_values)
# Perform the sensitivity analysis using the model output
# Specify which column of the output file to analyze (zero-indexed)
Si = morris.analyze(problem, param_values, Y, conf_level=0.95,
print_to_console=True,
num_levels=4, grid_jump=2, num_resamples=100)
# Returns a dictionary with keys 'mu', 'mu_star', 'sigma', and 'mu_star_conf'
# e.g. Si['mu_star'] contains the mu* value for each parameter, in the
# same order as the parameter file
fig, (ax1, ax2) = plt.subplots(1, 2)
horizontal_bar_plot(ax1, Si,{}, sortby='mu_star', unit=r"tCO$_2$/year")
covariance_plot(ax2, Si, {}, unit=r"tCO$_2$/year")
fig2 = plt.figure()
sample_histograms(fig2, param_values, problem, {'color':'y'})
plt.show()
# Files with a 4th column for "group name" will be detected automatically, e.g.
# param_file = '../../SALib/test_functions/params/Ishigami_groups.txt'
# Generate samples
param_values = sample(problem, N=1000, num_levels=4,
optimal_trajectories=None)
# To use optimized trajectories (brute force method),
# give an integer value for optimal_trajectories
# Run the "model" -- this will happen offline for external models
Y = Sobol_G.evaluate(param_values)
# Perform the sensitivity analysis using the model output
# Specify which column of the output file to analyze (zero-indexed)
Si = morris.analyze(problem, param_values, Y, conf_level=0.95,
print_to_console=True,
num_levels=4, num_resamples=100)
# Returns a dictionary with keys 'mu', 'mu_star', 'sigma', and 'mu_star_conf'
# e.g. Si['mu_star'] contains the mu* value for each parameter, in the
# same order as the parameter file
fig, (ax1, ax2) = plt.subplots(1, 2)
horizontal_bar_plot(ax1, Si, {}, sortby='mu_star', unit=r"tCO$_2$/year")
covariance_plot(ax2, Si, {}, unit=r"tCO$_2$/year")
fig2 = plt.figure()
sample_histograms(fig2, param_values, problem, {'color': 'y'})
plt.show()
partial_order = {}
mu_st, sigma_dt = {}, {}
rank_low_dt, rank_up_dt = {}, {}
n_start, n_end, n_step = 20, 120, 10
x_large_size = sample_morris.sample(problem, n_end, num_levels=4)
for i in range(n_start, n_end, n_step):
# partial ordering
x_morris = x_large_size[:i * (len_params + 1)]
if i == n_start:
y_morris = evaluate(x_morris, a)
else:
y_eval = evaluate(x_morris[-(len_params + 1) * n_step:], a)
y_morris = np.append(y_morris, y_eval)
sa_dict = analyze_morris.analyze(problem,
x_morris,
y_morris,
num_resamples=1000,
conf_level=0.95,
seed=123)
mu_star_rank_dict = sa_dict['mu_star'].argsort().argsort()
# use toposort to find parameter sa block
conf_low = sa_dict['mu_star_rank_conf'][0]
conf_up = sa_dict['mu_star_rank_conf'][1]
abs_sort = partial_rank(len_params, conf_low, conf_up)
rank_list = list(toposort(abs_sort))
key = 'result_' + str(i)
partial_order[key] = {
j: list(rank_list[j])
for j in range(len(rank_list))
}
#save results returned from Morris if needed
def sa(model, response, policy={}, method="sobol", nsamples=1000, **kwargs):
if len(model.uncertainties) == 0:
raise ValueError("no uncertainties defined in model")
problem = {
'num_vars': len(model.uncertainties),
'names': model.uncertainties.keys(),
'bounds': [[0.0, 1.0] for u in model.uncertainties],
'groups': kwargs.get("groups", None)
}
# estimate the argument N passed to the sampler that produces the requested
# number of samples
N = _predict_N(method, nsamples, problem["num_vars"], kwargs)
# generate the samples
if method == "sobol":
samples = saltelli.sample(problem, N,
**_cleanup_kwargs(saltelli.sample, kwargs))
elif method == "morris":
samples = morris_sampler.sample(
problem, N, **_cleanup_kwargs(morris_sampler.sample, kwargs))
elif method == "fast":
samples = fast_sampler.sample(
problem, N, **_cleanup_kwargs(fast_sampler.sample, kwargs))
elif method == "ff":
samples = ff_sampler.sample(
problem, **_cleanup_kwargs(ff_sampler.sample, kwargs))
elif method == "dgsm":
samples = finite_diff.sample(
problem, N, **_cleanup_kwargs(finite_diff.sample, kwargs))
elif method == "delta":
if "samples" in kwargs:
samples = kwargs["samples"]
else:
samples = latin.sample(problem, N,
**_cleanup_kwargs(latin.sample, kwargs))
# convert from samples in [0, 1] to uncertainty domain
for i, u in enumerate(model.uncertainties):
samples[:, i] = u.ppf(samples[:, i])
# run the model and collect the responses
responses = np.empty(samples.shape[0])
for i in range(samples.shape[0]):
sample = {k: v for k, v in zip(model.uncertainties.keys(), samples[i])}
responses[i] = evaluate(model, overwrite(sample, policy))[response]
# run the sensitivity analysis method
if method == "sobol":
result = sobol.analyze(problem, responses,
**_cleanup_kwargs(sobol.analyze, kwargs))
elif method == "morris":
result = morris_analyzer.analyze(
problem, samples, responses,
**_cleanup_kwargs(morris_analyzer.analyze, kwargs))
elif method == "fast":
result = fast.analyze(problem, responses,
**_cleanup_kwargs(fast.analyze, kwargs))
elif method == "ff":
result = ff_analyzer.analyze(
problem, samples, responses,
**_cleanup_kwargs(ff_analyzer.analyze, kwargs))
elif method == "dgsm":
result = dgsm.analyze(problem, samples, responses,
**_cleanup_kwargs(dgsm.analyze, kwargs))
elif method == "delta":
result = delta.analyze(problem, samples, responses,
**_cleanup_kwargs(delta.analyze, kwargs))
# convert the SALib results into a form allowing pretty printing and
# lookups using the parameter name
pretty_result = SAResult(
list(result["names"] if "names" in result else problem["names"]))
if "S1" in result:
pretty_result["S1"] = {
k: float(v)
for k, v in zip(problem["names"], result["S1"])
}
if "S1_conf" in result:
pretty_result["S1_conf"] = {
k: float(v)
for k, v in zip(problem["names"], result["S1_conf"])
}
if "ST" in result:
pretty_result["ST"] = {
k: float(v)
for k, v in zip(problem["names"], result["ST"])
}
if "ST_conf" in result:
pretty_result["ST_conf"] = {
k: float(v)
for k, v in zip(problem["names"], result["ST_conf"])
}
if "S2" in result:
pretty_result["S2"] = _S2_to_dict(result["S2"], problem)
if "S2_conf" in result:
pretty_result["S2_conf"] = _S2_to_dict(result["S2_conf"], problem)
if "delta" in result:
pretty_result["delta"] = {
k: float(v)
for k, v in zip(problem["names"], result["delta"])
}
if "delta_conf" in result:
pretty_result["delta_conf"] = {
k: float(v)
for k, v in zip(problem["names"], result["delta_conf"])
}
if "vi" in result:
pretty_result["vi"] = {
k: float(v)
for k, v in zip(problem["names"], result["vi"])
}
if "vi_std" in result:
pretty_result["vi_std"] = {
k: float(v)
for k, v in zip(problem["names"], result["vi_std"])
}
if "dgsm" in result:
pretty_result["dgsm"] = {
k: float(v)
for k, v in zip(problem["names"], result["dgsm"])
}
if "dgsm_conf" in result:
pretty_result["dgsm_conf"] = {
k: float(v)
for k, v in zip(problem["names"], result["dgsm_conf"])
}
if "mu" in result:
pretty_result["mu"] = {
k: float(v)
for k, v in zip(result["names"], result["mu"])
}
if "mu_star" in result:
pretty_result["mu_star"] = {
k: float(v)
for k, v in zip(result["names"], result["mu_star"])
}
if "mu_star_conf" in result:
pretty_result["mu_star_conf"] = {
k: float(v)
for k, v in zip(result["names"], result["mu_star_conf"])
}
if "sigma" in result:
pretty_result["sigma"] = {
k: float(v)
for k, v in zip(result["names"], result["sigma"])
}
return pretty_result
def plot_morris_one_leaf(df_out, problem, leaf=1, ax=None,
variable='normalized_audpc',
input_file='morris_input.txt',
folder='septoria',
nboots=5, ylims=None, force_rename={},
markers_SA={}, add_legend=True, colored=False,
annotation_suffix='', markersize=8, return_legend=False):
if ax is None:
fig, ax = plt.subplots()
df_mu_lf = pd.DataFrame()
df_sigma_lf = pd.DataFrame()
for boot in np.unique(df_out['i_boot']):
param_values = np.loadtxt('./' + folder + '/' + input_file[:-4] + '_boot' + str(boot) + input_file[-4:])
df = df_out[(df_out['i_boot'] == boot) & (df_out['num_leaf_top'] == leaf)]
Y = df[variable]
Si_bt = morris.analyze(problem, param_values, Y, grid_jump=5,
num_levels=10, conf_level=0.95,
print_to_console=False)
for ip, param in enumerate(Si_bt['names']):
if param != 'proba_main_nff':
df_mu_lf.loc[boot, param] = Si_bt['mu_star'][ip]
df_sigma_lf.loc[boot, param] = Si_bt['sigma'][ip]
mu_star = df_mu_lf.mean().values
mu_star_conf = df_mu_lf.apply(conf_int).values
sigma = df_sigma_lf.mean().values
sigma_conf = df_sigma_lf.apply(conf_int).values
# ax.errorbar(mu_star, sigma, yerr=sigma_conf, xerr=mu_star_conf,
# color='b', marker='*', linestyle='')
tags = iter(df_mu_lf.columns)
markers = itertools.cycle(['o', '^', 'v', 's', 'p', '*', 'd', 'D', '<', '>'])
colors = itertools.cycle(['b', 'g', 'r', 'k', 'm', 'c'])
labels = []
proxys = []
for x, y in zip(mu_star, sigma):
tag = tags.next()
if tag in markers_SA:
marker = markers_SA[tag]
else:
marker = markers.next()
if tag in force_rename:
tag = force_rename[tag]
if colored == True:
color = next(colors)
else:
color = 'k'
ax.plot(x, y, color=color, marker=marker, markersize=markersize)
# ax.annotate(tag, (x,y))
labels += [tag]
proxys += [plt.Line2D((0, 1), (0, 0), color=color,
marker=marker, markersize=markersize, linestyle='None')]
if ylims is not None:
ax.set_ylim(ylims)
ax.set_xlim(ylims)
else:
ylims = [min([ax.get_xlim()[0], ax.get_xlim()[0]]),
max([max(mu_star), max(sigma)]) * 1.05]
ax.set_ylim(ylims)
ax.set_xlim(ylims)
ax.annotate('Leaf %d ' % leaf + annotation_suffix, xy=(0.05, 0.85),
xycoords='axes fraction', fontsize=24)
ax.set_ylabel(r"$\sigma$", fontsize=36)
ax.set_xlabel(r"$\mu^\ast$", fontsize=36)
ax.tick_params(axis='both', labelsize=24)
if add_legend:
lgd = ax.legend(proxys, labels, numpoints=1,
bbox_to_anchor=(1.01, 1.), loc=2, borderaxespad=0., fontsize=28)
plt.rcParams['text.usetex'] = False
if return_legend:
return lgd
import sys
sys.path.append('../..')
from SALib.sample import morris_oat
from SALib.analyze import morris
from SALib.test_functions import Ishigami
import numpy as np
# Read the parameter range file and generate samples
param_file = '../../SALib/test_functions/params/Ishigami.txt'
# Generate samples
param_values = morris_oat.sample(1000, param_file, num_levels=10, grid_jump=5)
# Save the parameter values in a file (they are needed in the analysis)
np.savetxt('model_input.txt', param_values, delimiter=' ')
# Run the "model" and save the output in a text file
# This will happen offline for external models
Y = Ishigami.evaluate(param_values)
np.savetxt("model_output.txt", Y, delimiter=' ')
# Perform the sensitivity analysis using the model output
# Specify which column of the output file to analyze (zero-indexed)
Si = morris.analyze(param_file, 'model_input.txt', 'model_output.txt',
column=0, conf_level=0.95, print_to_console=False)
# Returns a dictionary with keys 'mu', 'mu_star', 'sigma', and 'mu_star_conf'
# e.g. Si['mu_star'] contains the mu* value for each parameter, in the
# same order as the parameter file
def sa(model, response, policy={}, method="sobol", nsamples=1000, **kwargs):
if len(model.uncertainties) == 0:
raise ValueError("no uncertainties defined in model")
problem = { 'num_vars' : len(model.uncertainties),
'names' : model.uncertainties.keys(),
'bounds' : [[0.0, 1.0] for u in model.uncertainties],
'groups' : kwargs.get("groups", None) }
# estimate the argument N passed to the sampler that produces the requested
# number of samples
N = _predict_N(method, nsamples, problem["num_vars"], kwargs)
# generate the samples
if method == "sobol":
samples = saltelli.sample(problem, N, **_cleanup_kwargs(saltelli.sample, kwargs))
elif method == "morris":
samples = morris_sampler.sample(problem, N, **_cleanup_kwargs(morris_sampler.sample, kwargs))
elif method == "fast":
samples = fast_sampler.sample(problem, N, **_cleanup_kwargs(fast_sampler.sample, kwargs))
elif method == "ff":
samples = ff_sampler.sample(problem, **_cleanup_kwargs(ff_sampler.sample, kwargs))
elif method == "dgsm":
samples = finite_diff.sample(problem, N, **_cleanup_kwargs(finite_diff.sample, kwargs))
elif method == "delta":
if "samples" in kwargs:
samples = kwargs["samples"]
else:
samples = latin.sample(problem, N, **_cleanup_kwargs(latin.sample, kwargs))
# convert from samples in [0, 1] to uncertainty domain
for i, u in enumerate(model.uncertainties):
samples[:,i] = u.ppf(samples[:,i])
# run the model and collect the responses
responses = np.empty(samples.shape[0])
for i in range(samples.shape[0]):
sample = {k : v for k, v in zip(model.uncertainties.keys(), samples[i])}
responses[i] = evaluate(model, overwrite(sample, policy))[response]
# run the sensitivity analysis method
if method == "sobol":
result = sobol.analyze(problem, responses, **_cleanup_kwargs(sobol.analyze, kwargs))
elif method == "morris":
result = morris_analyzer.analyze(problem, samples, responses, **_cleanup_kwargs(morris_analyzer.analyze, kwargs))
elif method == "fast":
result = fast.analyze(problem, responses, **_cleanup_kwargs(fast.analyze, kwargs))
elif method == "ff":
result = ff_analyzer.analyze(problem, samples, responses, **_cleanup_kwargs(ff_analyzer.analyze, kwargs))
elif method == "dgsm":
result = dgsm.analyze(problem, samples, responses, **_cleanup_kwargs(dgsm.analyze, kwargs))
elif method == "delta":
result = delta.analyze(problem, samples, responses, **_cleanup_kwargs(delta.analyze, kwargs))
# convert the SALib results into a form allowing pretty printing and
# lookups using the parameter name
pretty_result = SAResult(result["names"] if "names" in result else problem["names"])
if "S1" in result:
pretty_result["S1"] = {k : float(v) for k, v in zip(problem["names"], result["S1"])}
if "S1_conf" in result:
pretty_result["S1_conf"] = {k : float(v) for k, v in zip(problem["names"], result["S1_conf"])}
if "ST" in result:
pretty_result["ST"] = {k : float(v) for k, v in zip(problem["names"], result["ST"])}
if "ST_conf" in result:
pretty_result["ST_conf"] = {k : float(v) for k, v in zip(problem["names"], result["ST_conf"])}
if "S2" in result:
pretty_result["S2"] = _S2_to_dict(result["S2"], problem)
if "S2_conf" in result:
pretty_result["S2_conf"] = _S2_to_dict(result["S2_conf"], problem)
if "delta" in result:
pretty_result["delta"] = {k : float(v) for k, v in zip(problem["names"], result["delta"])}
if "delta_conf" in result:
pretty_result["delta_conf"] = {k : float(v) for k, v in zip(problem["names"], result["delta_conf"])}
if "vi" in result:
pretty_result["vi"] = {k : float(v) for k, v in zip(problem["names"], result["vi"])}
if "vi_std" in result:
pretty_result["vi_std"] = {k : float(v) for k, v in zip(problem["names"], result["vi_std"])}
if "dgsm" in result:
pretty_result["dgsm"] = {k : float(v) for k, v in zip(problem["names"], result["dgsm"])}
if "dgsm_conf" in result:
pretty_result["dgsm_conf"] = {k : float(v) for k, v in zip(problem["names"], result["dgsm_conf"])}
if "mu" in result:
pretty_result["mu"] = {k : float(v) for k, v in zip(result["names"], result["mu"])}
if "mu_star" in result:
pretty_result["mu_star"] = {k : float(v) for k, v in zip(result["names"], result["mu_star"])}
if "mu_star_conf" in result:
pretty_result["mu_star_conf"] = {k : float(v) for k, v in zip(result["names"], result["mu_star_conf"])}
if "sigma" in result:
pretty_result["sigma"] = {k : float(v) for k, v in zip(result["names"], result["sigma"])}
return pretty_result
sample
# ### Factor Prioritisation
#
# We'll run a sensitivity analysis to see which is the most influential parameter.
#
# The results parameters are called **mu**, **sigma** and **mu_star**.
#
# * **Mu** is the mean effect caused by the input parameter being moved over its range.
# * **Sigma** is the standard deviation of the mean effect.
# * **Mu_star** is the mean absolute effect.
# In[21]:
Si = ma.analyze(morris_problem, sample, output, print_to_console=False)
print("{:20s} {:>7s} {:>7s} {:>7s}".format("Name", "mu", "mu_star", "sigma"))
for name, s1, st, mean in zip(morris_problem['names'], Si['mu'], Si['mu_star'], Si['sigma']):
print("{:20s} {:=7.2f} {:=7.2f} {:=7.2f}".format(name, s1, st, mean))
# We can plot the results
# In[22]:
fig, (ax1, ax2) = plt.subplots(1,2)
mp.horizontal_bar_plot(ax1, Si, param_dict={})
mp.covariance_plot(ax2, Si, {})
# ## Sanity check
def sensitivity_main(locator, weather_path, gv, output_parameters, groups_var, num_samples, method):
"""
This function creates the sensitivity analysis problem for either sobol or morris methods.
It calculates the number of samples for the analysis and calls the CEA to run every sample.
:param locator: locator class
:param weather_path: path to weather file
:param gv: global variables class
:param output_parameters: list of output parameters to analyse
:param groups_var: list of names of groups of variables to analyse. Possible values are:
'THERMAL', 'ARCHITECTURE', 'INDOOR_COMFORT', 'INTERNAL_LOADS'. This list links to the probability density functions
of the variables contained in locator.get_uncertainty_db().
:param num_samples: number of samples to calculate
:param method: 'morris' or 'sobol' method
:return: .xls file stored in locator.get_sensitivity_output(). every spreadsheet of the workbook
stores a matrix whose content is the output of one sensitivity parameter and one output_parameter:
- columns: groups of variables to anlyse.
- rows: number of buildings of the case study under analysis.
- content: sensitivity parameter per output parameter
every sensitivity parameter depends on the method:
- sobol: S1, ST and ST_conf >>for more information refereto SaBil documentation
- morris: mu_star, sigma and mu_star_conf >> for more information refereto SaBil documentation
"""
t0 = time.clock()
# Model constants
gv.multiprocessing = False # false to deactivate the multiprocessing in the demand algorithm
# write only monthly instead of hourly values
gv.demand_writer = cea.demand.demand_writers.MonthlyDemandWriter(gv)
# Define the model inputs
pdf = pd.concat([pd.read_excel(locator.get_uncertainty_db(), group, axis=1) for group in groups_var])
num_vars = pdf.name.count() # integer with number of variables
names = pdf.name.values # [,,] with names of each variable
bounds = []
for var in range(num_vars):
limits = [pdf.loc[var, 'min'], pdf.loc[var, 'max']]
bounds.append(limits)
# define the problem
problem = {'num_vars': num_vars, 'names': names, 'bounds': bounds, 'groups': None}
# create samples (combinations of variables)
if method is 'sobol':
second_order = False
samples = sampler_sobol(problem, N=num_samples, calc_second_order=second_order)
else:
grid = 2
levels = 4
optimal_trajects = int(0.04 * num_samples)
samples = sampler_morris(problem, N=num_samples, grid_jump=grid, num_levels=levels)
#optimal_trajectories=optimal_trajects, local_optimization=True)
gv.log('Sampling done, time elapsed: %(time_elapsed).2f seconds', time_elapsed=time.clock() - t0)
gv.log('Running %i samples' %len(samples))
#call the CEA for building demand and store the results of every sample in a vector
simulations = screening_cea_multiprocessing(samples, names, output_parameters, locator, weather_path, gv)
gv.log('Simulations done - time elapsed: %(time_elapsed).2f seconds', time_elapsed=time.clock() - t0)
#do morris analysis and output to excel
buildings_num = simulations[0].shape[0]
writer = pd.ExcelWriter(locator.get_sensitivity_output(method, num_samples))
for parameter in output_parameters:
results_1 = []
results_2 = []
results_3 = []
for building in range(buildings_num):
simulations_parameter = np.array([x.loc[building, parameter] for x in simulations])
if method is 'sobol':
VAR1, VAR2, VAR3 = 'S1', 'ST', 'ST_conf'
sobol_result = sobol.analyze(problem, simulations_parameter, calc_second_order=second_order)
results_1.append(sobol_result['S1'])
results_2.append(sobol_result['ST'])
results_3.append(sobol_result['ST_conf'])
else:
VAR1, VAR2, VAR3 = 'mu_star', 'sigma', 'mu_star_conf'
morris_result = morris.analyze(problem, samples, simulations_parameter, grid_jump=grid, num_levels=levels)
results_1.append(morris_result['mu_star'])
results_2.append(morris_result['sigma'])
results_3.append(morris_result['mu_star_conf'])
pd.DataFrame(results_1, columns=problem['names']).to_excel(writer, parameter + VAR1)
pd.DataFrame(results_2, columns=problem['names']).to_excel(writer, parameter + VAR2)
pd.DataFrame(results_3, columns=problem['names']).to_excel(writer, parameter + VAR3)
writer.save()
gv.log('Sensitivity analysis done - time elapsed: %(time_elapsed).2f seconds', time_elapsed=time.clock() - t0)