from scipy.stats import norm
import numpy as np
import pandas as pd
from . import common_args
from ..util import (read_param_file, compute_groups_matrix, ResultDict,
extract_group_names, _check_groups)
from types import MethodType
from multiprocessing import Pool, cpu_count
from functools import partial
from itertools import combinations, zip_longest
[docs]def analyze(problem, Y, calc_second_order=True, num_resamples=100,
conf_level=0.95, print_to_console=False, parallel=False,
n_processors=None, keep_resamples=False, seed=None):
"""Perform Sobol Analysis on model outputs.
Returns a dictionary with keys 'S1', 'S1_conf', 'ST', and 'ST_conf', where
each entry is a list of size D (the number of parameters) containing the
indices in the same order as the parameter file. If calc_second_order is
True, the dictionary also contains keys 'S2' and 'S2_conf'.
Notes
-----
Compatible with:
`saltelli` : :func:`SALib.sample.saltelli.sample`
Parameters
----------
problem : dict
The problem definition
Y : numpy.array
A NumPy array containing the model outputs
calc_second_order : bool
Calculate second-order sensitivities (default True)
num_resamples : int
The number of resamples (default 100)
conf_level : float
The confidence interval level (default 0.95)
print_to_console : bool
Print results directly to console (default False)
keep_resamples : bool
Whether or not to store intermediate resampling results (default False)
References
----------
.. [1] Sobol, I. M. (2001). "Global sensitivity indices for nonlinear
mathematical models and their Monte Carlo estimates." Mathematics
and Computers in Simulation, 55(1-3):271-280,
doi:10.1016/S0378-4754(00)00270-6.
.. [2] Saltelli, A. (2002). "Making best use of model evaluations to
compute sensitivity indices." Computer Physics Communications,
145(2):280-297, doi:10.1016/S0010-4655(02)00280-1.
.. [3] Saltelli, A., P. Annoni, I. Azzini, F. Campolongo, M. Ratto, and
S. Tarantola (2010). "Variance based sensitivity analysis of model
output. Design and estimator for the total sensitivity index."
Computer Physics Communications, 181(2):259-270,
doi:10.1016/j.cpc.2009.09.018.
Examples
--------
>>> X = saltelli.sample(problem, 512)
>>> Y = Ishigami.evaluate(X)
>>> Si = sobol.analyze(problem, Y, print_to_console=True)
"""
if seed:
# Set seed to ensure CIs are the same
rng = np.random.default_rng(seed).integers
else:
rng = np.random.randint
# determining if groups are defined and adjusting the number
# of rows in the cross-sampled matrix accordingly
groups = _check_groups(problem)
if not groups:
D = problem['num_vars']
else:
_, D = extract_group_names(groups)
if calc_second_order and Y.size % (2 * D + 2) == 0:
N = int(Y.size / (2 * D + 2))
elif not calc_second_order and Y.size % (D + 2) == 0:
N = int(Y.size / (D + 2))
else:
raise RuntimeError("""
Incorrect number of samples in model output file.
Confirm that calc_second_order matches option used during sampling.""")
if not 0 < conf_level < 1:
raise RuntimeError("Confidence level must be between 0-1.")
# normalize the model output
Y = (Y - Y.mean()) / Y.std()
A, B, AB, BA = separate_output_values(Y, D, N, calc_second_order)
r = rng(N, size=(N, num_resamples))
Z = norm.ppf(0.5 + conf_level / 2)
if not parallel:
S = create_Si_dict(D, num_resamples, keep_resamples, calc_second_order)
for j in range(D):
S['S1'][j] = first_order(A, AB[:, j], B)
S1_conf_j = first_order(A[r], AB[r, j], B[r])
if keep_resamples:
S['S1_conf_all'][:, j] = S1_conf_j
S['S1_conf'][j] = Z * S1_conf_j.std(ddof=1)
S['ST'][j] = total_order(A, AB[:, j], B)
ST_conf_j = total_order(A[r], AB[r, j], B[r])
if keep_resamples:
S['ST_conf_all'][:, j] = ST_conf_j
S['ST_conf'][j] = Z * ST_conf_j.std(ddof=1)
# Second order (+conf.)
if calc_second_order:
for j in range(D):
for k in range(j + 1, D):
S['S2'][j, k] = second_order(
A, AB[:, j], AB[:, k], BA[:, j], B)
S['S2_conf'][j, k] = Z * second_order(A[r], AB[r, j],
AB[r, k], BA[r, j],
B[r]).std(ddof=1)
else:
tasks, n_processors = create_task_list(
D, calc_second_order, n_processors)
func = partial(sobol_parallel, Z, A, AB, BA, B, r)
pool = Pool(n_processors)
S_list = pool.map_async(func, tasks)
pool.close()
pool.join()
S = Si_list_to_dict(S_list.get(), D, num_resamples,
keep_resamples, calc_second_order)
# Add problem context and override conversion method for special case
S.problem = problem
S.to_df = MethodType(to_df, S)
# Print results to console
if print_to_console:
res = S.to_df()
for df in res:
print(df)
return S
[docs]def first_order(A, AB, B):
"""
First order estimator following Saltelli et al. 2010 CPC, normalized by
sample variance
"""
return np.mean(B * (AB - A), axis=0) / np.var(np.r_[A, B], axis=0)
[docs]def total_order(A, AB, B):
"""
Total order estimator following Saltelli et al. 2010 CPC, normalized by
sample variance
"""
return 0.5 * np.mean((A - AB) ** 2, axis=0) / np.var(np.r_[A, B], axis=0)
[docs]def second_order(A, ABj, ABk, BAj, B):
"""Second order estimator following Saltelli 2002"""
Vjk = np.mean(BAj * ABk - A * B, axis=0) / np.var(np.r_[A, B], axis=0)
Sj = first_order(A, ABj, B)
Sk = first_order(A, ABk, B)
return Vjk - Sj - Sk
[docs]def create_Si_dict(D: int, num_resamples: int, keep_resamples: bool, calc_second_order: bool):
"""initialize empty dict to store sensitivity indices"""
S = ResultDict((k, np.zeros(D))
for k in ('S1', 'S1_conf', 'ST', 'ST_conf'))
if keep_resamples:
# Create entries to store intermediate resampling results
S['S1_conf_all'] = np.zeros((num_resamples, D))
S['ST_conf_all'] = np.zeros((num_resamples, D))
if calc_second_order:
S['S2'] = np.full((D, D), np.nan)
S['S2_conf'] = np.full((D, D), np.nan)
return S
[docs]def separate_output_values(Y, D, N, calc_second_order):
AB = np.zeros((N, D))
BA = np.zeros((N, D)) if calc_second_order else None
step = 2 * D + 2 if calc_second_order else D + 2
A = Y[0:Y.size:step]
B = Y[(step - 1):Y.size:step]
for j in range(D):
AB[:, j] = Y[(j + 1):Y.size:step]
if calc_second_order:
BA[:, j] = Y[(j + 1 + D):Y.size:step]
return A, B, AB, BA
[docs]def sobol_parallel(Z, A, AB, BA, B, r, tasks):
sobol_indices = []
for d, j, k in tasks:
if d == 'S1':
s = first_order(A, AB[:, j], B)
elif d == 'S1_conf':
s = Z * first_order(A[r], AB[r, j], B[r]).std(ddof=1)
elif d == 'ST':
s = total_order(A, AB[:, j], B)
elif d == 'ST_conf':
s = Z * total_order(A[r], AB[r, j], B[r]).std(ddof=1)
elif d == 'S2':
s = second_order(A, AB[:, j], AB[:, k], BA[:, j], B)
elif d == 'S2_conf':
s = Z * second_order(A[r], AB[r, j], AB[r, k],
BA[r, j], B[r]).std(ddof=1)
sobol_indices.append([d, j, k, s])
return sobol_indices
[docs]def create_task_list(D, calc_second_order, n_processors):
"""
Create list with one entry (key, parameter 1, parameter 2) per sobol
index (+conf.). This is used to supply parallel tasks to
multiprocessing.Pool
"""
tasks_first_order = [[d, j, None] for j in range(
D) for d in ('S1', 'S1_conf', 'ST', 'ST_conf')]
# Add second order (+conf.) to tasks
tasks_second_order = []
if calc_second_order:
tasks_second_order = [[d, j, k] for j in range(D) for k in
range(j + 1, D) for d in ('S2', 'S2_conf')]
if n_processors is None:
n_processors = min(cpu_count(), len(
tasks_first_order) + len(tasks_second_order))
if not calc_second_order:
tasks = np.array_split(tasks_first_order, n_processors)
else:
# merges both lists alternating its elements and splits the
# resulting lists into n_processors sublists
tasks = np.array_split([v for v in sum(
zip_longest(tasks_first_order[::-1], tasks_second_order), ())
if v is not None], n_processors)
return tasks, n_processors
[docs]def Si_list_to_dict(S_list, D: int, num_resamples: int, keep_resamples:bool, calc_second_order: bool):
"""Convert the parallel output into the regular dict format for
printing/returning"""
S = create_Si_dict(D, num_resamples, keep_resamples, calc_second_order)
L = []
for l in S_list: # first reformat to flatten
L += l
for s in L: # First order (+conf.)
if s[2] is None:
S[s[0]][s[1]] = s[3]
else:
S[s[0]][s[1], s[2]] = s[3]
return S
[docs]def Si_to_pandas_dict(S_dict):
"""Convert Si information into Pandas DataFrame compatible dict.
Parameters
----------
S_dict : ResultDict
Sobol sensitivity indices
See Also
----------
Si_list_to_dict
Returns
----------
tuple : of total, first, and second order sensitivities.
Total and first order are dicts.
Second order sensitivities contain a tuple of parameter name
combinations for use as the DataFrame index and second order
sensitivities.
If no second order indices found, then returns tuple of
(None, None)
Examples
--------
>>> X = saltelli.sample(problem, 512)
>>> Y = Ishigami.evaluate(X)
>>> Si = sobol.analyze(problem, Y, print_to_console=True)
>>> T_Si, first_Si, (idx, second_Si) = sobol.Si_to_pandas_dict(Si, problem)
"""
problem = S_dict.problem
total_order = {
'ST': S_dict['ST'],
'ST_conf': S_dict['ST_conf']
}
first_order = {
'S1': S_dict['S1'],
'S1_conf': S_dict['S1_conf']
}
idx = None
second_order = None
if 'S2' in S_dict:
groups = _check_groups(problem)
if groups:
names, _ = extract_group_names(groups)
else:
names = problem.get('names')
if len(names) > 2:
idx = list(combinations(names, 2))
else:
idx = (names, )
second_order = {
'S2': [S_dict['S2'][names.index(i[0]), names.index(i[1])]
for i in idx],
'S2_conf': [S_dict['S2_conf'][names.index(i[0]), names.index(i[1])]
for i in idx]
}
return total_order, first_order, (idx, second_order)
[docs]def to_df(self):
'''Conversion method to Pandas DataFrame. To be attached to ResultDict.
Returns
--------
List : of Pandas DataFrames in order of Total, First, Second
Example
-------
>>> Si = sobol.analyze(problem, Y, print_to_console=True)
>>> total_Si, first_Si, second_Si = Si.to_df()
'''
total, first, (idx, second) = Si_to_pandas_dict(self)
problem = self.problem
groups = _check_groups(problem)
if not groups:
names = problem.get('names')
else:
names, _ = extract_group_names(groups)
ret = [pd.DataFrame(total, index=names),
pd.DataFrame(first, index=names)]
if second:
ret += [pd.DataFrame(second, index=idx)]
return ret
[docs]def cli_parse(parser):
parser.add_argument('--max-order', type=int, required=False, default=2,
choices=[1, 2],
help='Maximum order of sensitivity indices to '
'calculate')
parser.add_argument('-r', '--resamples', type=int, required=False,
default=100,
help='Number of bootstrap resamples for Sobol '
'confidence intervals')
parser.add_argument('--parallel', action='store_true', help='Makes '
'use of parallelization.',
dest='parallel')
parser.add_argument('--processors', type=int, required=False,
default=None,
help='Number of processors to be used with the ' +
'parallel option.', dest='n_processors')
return parser
[docs]def cli_action(args):
problem = read_param_file(args.paramfile)
Y = np.loadtxt(args.model_output_file, delimiter=args.delimiter,
usecols=(args.column,))
analyze(problem, Y, (args.max_order == 2),
num_resamples=args.resamples, print_to_console=True,
parallel=args.parallel, n_processors=args.n_processors,
seed=args.seed)
if __name__ == "__main__":
common_args.run_cli(cli_parse, cli_action)