Source code for SALib.analyze.sobol

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)