#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Mon Mar 16 17:26:40 2020 @author: ljia """ def test_median_graph_estimator(): from gklearn.utils.graphfiles import loadDataset from gklearn.ged.median import MedianGraphEstimator, constant_node_costs from gklearn.gedlib import librariesImport, gedlibpy from gklearn.preimage.utils import get_same_item_indices from gklearn.preimage.ged import convertGraph import multiprocessing # estimator parameters. init_type = 'MEDOID' num_inits = 1 threads = multiprocessing.cpu_count() time_limit = 60000 # algorithm parameters. algo = 'IPFP' initial_solutions = 40 algo_options_suffix = ' --initial-solutions ' + str(initial_solutions) + ' --ratio-runs-from-initial-solutions 1' edit_cost_name = 'LETTER2' edit_cost_constants = [0.02987291, 0.0178211, 0.01431966, 0.001, 0.001] ds_name = 'COIL-DEL' # Load dataset. # dataset = '../../datasets/COIL-DEL/COIL-DEL_A.txt' dataset = '../../../datasets/Letter-high/Letter-high_A.txt' Gn, y_all = loadDataset(dataset) y_idx = get_same_item_indices(y_all) for i, (y, values) in enumerate(y_idx.items()): Gn_i = [Gn[val] for val in values] break # Set up the environment. ged_env = gedlibpy.GEDEnv() # gedlibpy.restart_env() ged_env.set_edit_cost(edit_cost_name, edit_cost_constant=edit_cost_constants) for G in Gn_i: ged_env.add_nx_graph(convertGraph(G, edit_cost_name), '') graph_ids = ged_env.get_all_graph_ids() set_median_id = ged_env.add_graph('set_median') gen_median_id = ged_env.add_graph('gen_median') ged_env.init(init_option='EAGER_WITHOUT_SHUFFLED_COPIES') # Set up the estimator. mge = MedianGraphEstimator(ged_env, constant_node_costs(edit_cost_name)) mge.set_refine_method(algo, '--threads ' + str(threads) + ' --initial-solutions ' + str(initial_solutions) + ' --ratio-runs-from-initial-solutions 1') mge_options = '--time-limit ' + str(time_limit) + ' --stdout 2 --init-type ' + init_type mge_options += ' --random-inits ' + str(num_inits) + ' --seed ' + '1' + ' --refine FALSE'# @todo: std::to_string(rng()) # Select the GED algorithm. algo_options = '--threads ' + str(threads) + algo_options_suffix mge.set_options(mge_options) mge.set_init_method(algo, algo_options) mge.set_descent_method(algo, algo_options) # Run the estimator. mge.run(graph_ids, set_median_id, gen_median_id) # Get SODs. sod_sm = mge.get_sum_of_distances('initialized') sod_gm = mge.get_sum_of_distances('converged') print('sod_sm, sod_gm: ', sod_sm, sod_gm) # Get median graphs. set_median = ged_env.get_nx_graph(set_median_id) gen_median = ged_env.get_nx_graph(gen_median_id) return set_median, gen_median if __name__ == '__main__': set_median, gen_median = test_median_graph_estimator()