| @@ -35,13 +35,13 @@ def remove_best_graph(ds_name, mpg_options, kernel_options, ged_options, mge_opt | |||
| if save_results: | |||
| # create result files. | |||
| print('creating output files...') | |||
| fn_output_detail, fn_output_summary = __init_output_file(ds_name, kernel_options['name'], mpg_options['fit_method'], dir_save) | |||
| fn_output_detail, fn_output_summary = _init_output_file(ds_name, kernel_options['name'], mpg_options['fit_method'], dir_save) | |||
| else: | |||
| fn_output_detail, fn_output_summary = None, None | |||
| # 2. compute/load Gram matrix a priori. | |||
| print('2. computing/loading Gram matrix...') | |||
| gram_matrix_unnorm_list, time_precompute_gm_list = __get_gram_matrix(load_gm, dir_save, ds_name, kernel_options, datasets) | |||
| gram_matrix_unnorm_list, time_precompute_gm_list = _get_gram_matrix(load_gm, dir_save, ds_name, kernel_options, datasets) | |||
| sod_sm_list = [] | |||
| sod_gm_list = [] | |||
| @@ -82,7 +82,7 @@ def remove_best_graph(ds_name, mpg_options, kernel_options, ged_options, mge_opt | |||
| # 3. get the best graph and remove it from median set. | |||
| print('3. getting and removing the best graph...') | |||
| gram_matrix_unnorm = gram_matrix_unnorm_list[idx - idx_offset] | |||
| best_index, best_dis, best_graph = __get_best_graph([g.copy() for g in dataset.graphs], normalize_gram_matrix(gram_matrix_unnorm.copy())) | |||
| best_index, best_dis, best_graph = _get_best_graph([g.copy() for g in dataset.graphs], normalize_gram_matrix(gram_matrix_unnorm.copy())) | |||
| median_set_new = [dataset.graphs[i] for i in range(len(dataset.graphs)) if i != best_index] | |||
| num_graphs -= 1 | |||
| if num_graphs == 1: | |||
| @@ -294,7 +294,7 @@ def remove_best_graph(ds_name, mpg_options, kernel_options, ged_options, mge_opt | |||
| print('\ncomplete.\n') | |||
| def __get_best_graph(Gn, gram_matrix): | |||
| def _get_best_graph(Gn, gram_matrix): | |||
| k_dis_list = [] | |||
| for idx in range(len(Gn)): | |||
| k_dis_list.append(compute_k_dis(idx, range(0, len(Gn)), [1 / len(Gn)] * len(Gn), gram_matrix, withterm3=False)) | |||
| @@ -313,7 +313,7 @@ def get_relations(sign): | |||
| return 'worse' | |||
| def __get_gram_matrix(load_gm, dir_save, ds_name, kernel_options, datasets): | |||
| def _get_gram_matrix(load_gm, dir_save, ds_name, kernel_options, datasets): | |||
| if load_gm == 'auto': | |||
| gm_fname = dir_save + 'gram_matrix_unnorm.' + ds_name + '.' + kernel_options['name'] + '.gm.npz' | |||
| gmfile_exist = os.path.isfile(os.path.abspath(gm_fname)) | |||
| @@ -325,7 +325,7 @@ def __get_gram_matrix(load_gm, dir_save, ds_name, kernel_options, datasets): | |||
| gram_matrix_unnorm_list = [] | |||
| time_precompute_gm_list = [] | |||
| for dataset in datasets: | |||
| gram_matrix_unnorm, time_precompute_gm = __compute_gram_matrix_unnorm(dataset, kernel_options) | |||
| gram_matrix_unnorm, time_precompute_gm = _compute_gram_matrix_unnorm(dataset, kernel_options) | |||
| gram_matrix_unnorm_list.append(gram_matrix_unnorm) | |||
| time_precompute_gm_list.append(time_precompute_gm) | |||
| np.savez(dir_save + 'gram_matrix_unnorm.' + ds_name + '.' + kernel_options['name'] + '.gm', gram_matrix_unnorm_list=gram_matrix_unnorm_list, run_time_list=time_precompute_gm_list) | |||
| @@ -333,7 +333,7 @@ def __get_gram_matrix(load_gm, dir_save, ds_name, kernel_options, datasets): | |||
| gram_matrix_unnorm_list = [] | |||
| time_precompute_gm_list = [] | |||
| for dataset in datasets: | |||
| gram_matrix_unnorm, time_precompute_gm = __compute_gram_matrix_unnorm(dataset, kernel_options) | |||
| gram_matrix_unnorm, time_precompute_gm = _compute_gram_matrix_unnorm(dataset, kernel_options) | |||
| gram_matrix_unnorm_list.append(gram_matrix_unnorm) | |||
| time_precompute_gm_list.append(time_precompute_gm) | |||
| np.savez(dir_save + 'gram_matrix_unnorm.' + ds_name + '.' + kernel_options['name'] + '.gm', gram_matrix_unnorm_list=gram_matrix_unnorm_list, run_time_list=time_precompute_gm_list) | |||
| @@ -346,7 +346,7 @@ def __get_gram_matrix(load_gm, dir_save, ds_name, kernel_options, datasets): | |||
| return gram_matrix_unnorm_list, time_precompute_gm_list | |||
| def __get_graph_kernel(dataset, kernel_options): | |||
| def _get_graph_kernel(dataset, kernel_options): | |||
| from gklearn.utils.utils import get_graph_kernel_by_name | |||
| graph_kernel = get_graph_kernel_by_name(kernel_options['name'], | |||
| node_labels=dataset.node_labels, | |||
| @@ -358,7 +358,7 @@ def __get_graph_kernel(dataset, kernel_options): | |||
| return graph_kernel | |||
| def __compute_gram_matrix_unnorm(dataset, kernel_options): | |||
| def _compute_gram_matrix_unnorm(dataset, kernel_options): | |||
| from gklearn.utils.utils import get_graph_kernel_by_name | |||
| graph_kernel = get_graph_kernel_by_name(kernel_options['name'], | |||
| node_labels=dataset.node_labels, | |||
| @@ -374,7 +374,7 @@ def __compute_gram_matrix_unnorm(dataset, kernel_options): | |||
| return gram_matrix_unnorm, run_time | |||
| def __init_output_file(ds_name, gkernel, fit_method, dir_output): | |||
| def _init_output_file(ds_name, gkernel, fit_method, dir_output): | |||
| if not os.path.exists(dir_output): | |||
| os.makedirs(dir_output) | |||
| fn_output_detail = 'results_detail.' + ds_name + '.' + gkernel + '.csv' | |||