Source code for SALib.analyze.morris

from __future__ import division
from __future__ import print_function

from scipy.stats import norm

import numpy as np

from . import common_args
from ..util import read_param_file, compute_groups_matrix, ResultDict
from ..sample.morris import _compute_delta

[docs]def analyze(problem, X, Y, num_resamples=100, conf_level=0.95, print_to_console=False, num_levels=4, seed=None): """Perform Morris Analysis on model outputs. Returns a dictionary with keys 'mu', 'mu_star', 'sigma', and 'mu_star_conf', where each entry is a list of parameters containing the indices in the same order as the parameter file. Arguments --------- problem : dict The problem definition X : numpy.matrix The NumPy matrix containing the model inputs of dtype=float Y : numpy.array The NumPy array containing the model outputs of dtype=float num_resamples : int The number of resamples used to compute the confidence intervals (default 1000) conf_level : float The confidence interval level (default 0.95) print_to_console : bool Print results directly to console (default False) num_levels : int The number of grid levels, must be identical to the value passed to SALib.sample.morris (default 4) Returns ------- Si : dict 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 References ---------- .. [1] Morris, M. (1991). "Factorial Sampling Plans for Preliminary Computational Experiments." Technometrics, 33(2):161-174, doi:10.1080/00401706.1991.10484804. .. [2] Campolongo, F., J. Cariboni, and A. Saltelli (2007). "An effective screening design for sensitivity analysis of large models." Environmental Modelling & Software, 22(10):1509-1518, doi:10.1016/j.envsoft.2006.10.004. Examples -------- >>> X = morris.sample(problem, 1000, num_levels=4) >>> Y = Ishigami.evaluate(X) >>> Si = morris.analyze(problem, X, Y, conf_level=0.95, >>> print_to_console=True, num_levels=4) """ if seed: np.random.seed(seed) msg = ("dtype of {} array must be 'float', float32 or float64") if X.dtype not in ['float', 'float32', 'float64']: raise ValueError(msg.format('X')) if Y.dtype not in ['float', 'float32', 'float64']: raise ValueError(msg.format('Y')) # Assume that there are no groups groups = None delta = _compute_delta(num_levels) num_vars = problem['num_vars'] if (problem.get('groups') is None) & (Y.size % (num_vars + 1) == 0): num_trajectories = int(Y.size / (num_vars + 1)) elif problem.get('groups') is not None: groups, unique_group_names = compute_groups_matrix( problem['groups']) number_of_groups = len(unique_group_names) num_trajectories = int(Y.size / (number_of_groups + 1)) else: raise ValueError("Number of samples in model output file must be" "a multiple of (D+1), where D is the number of" "parameters (or groups) in your parameter file.") ee = np.zeros((num_vars, num_trajectories)) ee = compute_elementary_effects( X, Y, int(Y.size / num_trajectories), delta) # Output the Mu, Mu*, and Sigma Values. Also return them in case this is # being called from Python Si = ResultDict((k, [None] * num_vars) for k in ['names', 'mu', 'mu_star', 'sigma', 'mu_star_conf']) Si['mu'] = np.average(ee, 1) Si['mu_star'] = np.average(np.abs(ee), 1) Si['sigma'] = np.std(ee, axis=1, ddof=1) Si['names'] = problem['names'] for j in range(num_vars): Si['mu_star_conf'][j] = compute_mu_star_confidence( ee[j, :], num_trajectories, num_resamples, conf_level) if groups is None: if print_to_console: print("{0:<30} {1:>10} {2:>10} {3:>15} {4:>10}".format( "Parameter", "Mu_Star", "Mu", "Mu_Star_Conf", "Sigma") ) for j in list(range(num_vars)): print("{0:30} {1:10.3f} {2:10.3f} {3:15.3f} {4:10.3f}".format( Si['names'][j], Si['mu_star'][j], Si['mu'][j], Si['mu_star_conf'][j], Si['sigma'][j]) ) return Si elif groups is not None: # if there are groups, then the elementary effects returned need to be # computed over the groups of variables, # rather than the individual variables Si_grouped = ResultDict((k, [None] * num_vars) for k in ['mu_star', 'mu_star_conf']) Si_grouped['mu_star'] = compute_grouped_metric(Si['mu_star'], groups) Si_grouped['mu_star_conf'] = compute_grouped_metric(Si['mu_star_conf'], groups) Si_grouped['names'] = unique_group_names Si_grouped['sigma'] = compute_grouped_sigma(Si['sigma'], groups) Si_grouped['mu'] = compute_grouped_sigma(Si['mu'], groups) if print_to_console: print("{0:<30} {1:>10} {2:>10} {3:>15} {4:>10}".format( "Parameter", "Mu_Star", "Mu", "Mu_Star_Conf", "Sigma") ) for j in list(range(number_of_groups)): print("{0:30} {1:10.3f} {2:10.3f} {3:15.3f} {4:10.3f}".format( Si_grouped['names'][j], Si_grouped['mu_star'][j], Si_grouped['mu'][j], Si_grouped['mu_star_conf'][j], Si_grouped['sigma'][j]) ) return Si_grouped else: raise RuntimeError( "Could not determine which parameters should be returned")
[docs]def compute_grouped_sigma(ungrouped_sigma, group_matrix): ''' Returns sigma for the groups of parameter values in the argument ungrouped_metric where the group consists of no more than one parameter ''' group_matrix = np.array(group_matrix, dtype=np.bool) sigma_masked = * group_matrix.T, mask=(group_matrix ^ 1).T) sigma_agg =, axis=1) sigma = np.zeros(group_matrix.shape[1], dtype=np.float) np.copyto(sigma, sigma_agg, where=group_matrix.sum(axis=0) == 1) np.copyto(sigma, np.NAN, where=group_matrix.sum(axis=0) != 1) return sigma
[docs]def compute_grouped_metric(ungrouped_metric, group_matrix): ''' Computes the mean value for the groups of parameter values in the argument ungrouped_metric ''' group_matrix = np.array(group_matrix, dtype=np.bool) mu_star_masked = * group_matrix.T, mask=(group_matrix ^ 1).T) mean_of_mu_star =, axis=1) return mean_of_mu_star
[docs]def get_increased_values(op_vec, up, lo): up = np.pad(up, ((0, 0), (1, 0), (0, 0)), 'constant') lo = np.pad(lo, ((0, 0), (0, 1), (0, 0)), 'constant') res = np.einsum('ik,ikj->ij', op_vec, up + lo) return res.T
[docs]def get_decreased_values(op_vec, up, lo): up = np.pad(up, ((0, 0), (0, 1), (0, 0)), 'constant') lo = np.pad(lo, ((0, 0), (1, 0), (0, 0)), 'constant') res = np.einsum('ik,ikj->ij', op_vec, up + lo) return res.T
[docs]def compute_elementary_effects(model_inputs, model_outputs, trajectory_size, delta): ''' Arguments --------- model_inputs : matrix of inputs to the model under analysis. x-by-r where x is the number of variables and r is the number of rows (a function of x and num_trajectories) model_outputs an r-length vector of model outputs trajectory_size a scalar indicating the number of rows in a trajectory delta : float scaling factor computed from `num_levels` Returns --------- ee : np.array Elementary Effects for each parameter ''' num_vars = model_inputs.shape[1] num_rows = model_inputs.shape[0] num_trajectories = int(num_rows / trajectory_size) ee = np.zeros((num_trajectories, num_vars), dtype=np.float) ip_vec = model_inputs.reshape(num_trajectories, trajectory_size, num_vars) ip_cha = np.subtract(ip_vec[:, 1:, :], ip_vec[:, 0:-1, :]) up = (ip_cha > 0) lo = (ip_cha < 0) op_vec = model_outputs.reshape(num_trajectories, trajectory_size) result_up = get_increased_values(op_vec, up, lo) result_lo = get_decreased_values(op_vec, up, lo) ee = np.subtract(result_up, result_lo) np.divide(ee, delta, out=ee) return ee
[docs]def compute_mu_star_confidence(ee, num_trajectories, num_resamples, conf_level): ''' Uses bootstrapping where the elementary effects are resampled with replacement to produce a histogram of resampled mu_star metrics. This resample is used to produce a confidence interval. ''' if not 0 < conf_level < 1: raise ValueError("Confidence level must be between 0-1.") resample_index = np.random.randint( len(ee), size=(num_resamples, num_trajectories)) ee_resampled = ee[resample_index] # Compute average of the absolute values over each of the resamples mu_star_resampled = np.average(np.abs(ee_resampled), axis=1) return norm.ppf(0.5 + conf_level / 2) * mu_star_resampled.std(ddof=1)
[docs]def cli_parse(parser): parser.add_argument('-X', '--model-input-file', type=str, required=True, default=None, help='Model input file') parser.add_argument('-r', '--resamples', type=int, required=False, default=1000, help='Number of bootstrap resamples for Sobol \ confidence intervals') parser.add_argument('-l', '--levels', type=int, required=False, default=4, help='Number of grid levels \ (Morris only)') parser.add_argument('--grid-jump', type=int, required=False, default=2, help='Grid jump size (Morris only)') 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,)) X = np.loadtxt(args.model_input_file, delimiter=args.delimiter, ndmin=2) if len(X.shape) == 1: X = X.reshape((len(X), 1)) analyze(problem, X, Y, num_resamples=args.resamples, print_to_console=True, num_levels=args.levels, seed=args.seed)
if __name__ == "__main__": common_args.run_cli(cli_parse, cli_action)