import logging import numpy as np import os import pickle import scipy.sparse as sp import sys import tensorflow as tf import random from scipy.sparse import linalg class DataLoader(object): def __init__( self, xs, ys, x0s, batch_size, pad_with_last_sample=True, shuffle=False ): """ :param xs: :param ys: :param x0s: (starting point) :param batch_size: :param pad_with_last_sample: pad with the last sample to make number of samples divisible to batch_size. """ self.batch_size = batch_size self.current_ind = 0 if pad_with_last_sample: num_padding = (batch_size - (len(xs) % batch_size)) % batch_size x_padding = np.repeat(xs[-1:], num_padding, axis=0) y_padding = np.repeat(ys[-1:], num_padding, axis=0) x0_padding = np.repeat(x0s[-1:], num_padding, axis=0) xs = np.concatenate([xs, x_padding], axis=0) ys = np.concatenate([ys, y_padding], axis=0) x0s = np.concatenate([x0s, x0_padding], axis=0) self.size = len(xs) self.num_batch = int(self.size // self.batch_size) if shuffle: permutation = np.random.permutation(self.size) xs, ys, x0s = xs[permutation], ys[permutation], x0s[permutation] self.xs = xs self.ys = ys self.x0s = x0s def get_iterator(self): self.current_ind = 0 def _wrapper(): while self.current_ind < self.num_batch: start_ind = self.batch_size * self.current_ind end_ind = min(self.size, self.batch_size * (self.current_ind + 1)) x_i = self.xs[start_ind:end_ind, ...] y_i = self.ys[start_ind:end_ind, ...] x0_i = self.x0s[start_ind:end_ind, ...] yield (x_i, y_i, x0_i) self.current_ind += 1 return _wrapper() def add_simple_summary(writer, names, values, global_step): """ Writes summary for a list of scalars. :param writer: :param names: :param values: :param global_step: :return: """ for name, value in zip(names, values): summary = tf.Summary() summary_value = summary.value.add() summary_value.simple_value = value summary_value.tag = name writer.add_summary(summary, global_step) def calculate_normalized_laplacian(adj): """ # L = D^-1/2 (D-A) D^-1/2 = I - D^-1/2 A D^-1/2 # D = diag(A 1) :param adj: :return: """ adj = sp.coo_matrix(adj) d = np.array(adj.sum(1)) d_inv_sqrt = np.power(d, -0.5).flatten() d_inv_sqrt[np.isinf(d_inv_sqrt)] = 0.0 d_mat_inv_sqrt = sp.diags(d_inv_sqrt) normalized_laplacian = ( sp.eye(adj.shape[0]) - adj.dot(d_mat_inv_sqrt).transpose().dot(d_mat_inv_sqrt).tocoo() ) return normalized_laplacian def calculate_random_walk_matrix(adj_mx): adj_mx = sp.coo_matrix(adj_mx) d = np.array(adj_mx.sum(1)) d_inv = np.power(d, -1).flatten() d_inv[np.isinf(d_inv)] = 0.0 d_mat_inv = sp.diags(d_inv) random_walk_mx = d_mat_inv.dot(adj_mx).tocoo() return random_walk_mx def calculate_reverse_random_walk_matrix(adj_mx): return calculate_random_walk_matrix(np.transpose(adj_mx)) def calculate_scaled_laplacian(adj_mx, lambda_max=2, undirected=True): if undirected: adj_mx = np.maximum.reduce([adj_mx, adj_mx.T]) L = calculate_normalized_laplacian(adj_mx) if lambda_max is None: lambda_max, _ = linalg.eigsh(L, 1, which="LM") lambda_max = lambda_max[0] L = sp.csr_matrix(L) M, _ = L.shape I = sp.identity(M, format="csr", dtype=L.dtype) L = (2 / lambda_max * L) - I return L.astype(np.float32) def config_logging(log_dir, log_filename="info.log", level=logging.INFO): # Add file handler and stdout handler formatter = logging.Formatter( "%(asctime)s - %(name)s - %(levelname)s - %(message)s" ) # Create the log directory if necessary. try: os.makedirs(log_dir) except OSError: pass file_handler = logging.FileHandler(os.path.join(log_dir, log_filename)) file_handler.setFormatter(formatter) file_handler.setLevel(level=level) # Add console handler. console_formatter = logging.Formatter("%(asctime)s - %(levelname)s - %(message)s") console_handler = logging.StreamHandler(sys.stdout) console_handler.setFormatter(console_formatter) console_handler.setLevel(level=level) logging.basicConfig(handlers=[file_handler, console_handler], level=level) def get_logger(log_dir, name, log_filename="info.log", level=logging.INFO): logger = logging.getLogger(name) logger.setLevel(level) logger.handlers = [] # Add file handler and stdout handler formatter = logging.Formatter( "%(asctime)s - %(name)s - %(levelname)s - %(message)s" ) file_handler = logging.FileHandler(os.path.join(log_dir, log_filename)) file_handler.setFormatter(formatter) # Add console handler. console_formatter = logging.Formatter("%(asctime)s - %(levelname)s - %(message)s") console_handler = logging.StreamHandler(sys.stdout) console_handler.setFormatter(console_formatter) logger.addHandler(file_handler) logger.addHandler(console_handler) # Add google cloud log handler logger.info("Log directory: %s", log_dir) return logger def get_total_trainable_parameter_size(): """ Calculates the total number of trainable parameters in the current graph. :return: """ total_parameters = 0 for variable in tf.trainable_variables(): # shape is an array of tf.Dimension total_parameters += np.product([x.value for x in variable.get_shape()]) return total_parameters def generate_new_trainset( selected_data, previous_data, dataset_dir, batch_size, test_batch_size=None, **kwargs ): selected_x = np.concatenate(selected_data["x"], 0) selected_y = np.concatenate(selected_data["y"], 0) data1 = previous_data data1["x_train"] = np.concatenate([previous_data["x_train"], selected_x], 0) data1["y_train"] = np.concatenate([previous_data["y_train"], selected_y[:, 1:]], 0) data1["x0_train"] = np.concatenate([previous_data["x0_train"], selected_y[:, 0]], 0) data1["train_loader"] = DataLoader( data1["x_train"], data1["y_train"], data1["x0_train"], batch_size, shuffle=True ) return data1 def load_dataset(dataset_dir, batch_size, test_batch_size=None, **kwargs): data_list = [] data = {} for category in ["train", "val", "test"]: cat_data = np.load(os.path.join(dataset_dir, category + ".npz")) data["x_" + category] = cat_data["x"] # normalize data data["y_" + category] = np.log(cat_data["y"] + 1.0) # # load scenario index # scenario_array = np.load(os.path.join(dataset_dir, 'train_scenario_array.npy'),allow_pickle=True) # x_scenario_list = [] # y_scenario_list = [] # data['x_train'] = data['x_train'].reshape(9,1848,28, 58, 10) # data['y_train'] = data['y_train'].reshape(9,1848, 29, 24) # for i in range(len(scenario_array)): # indices = np.array(scenario_array[i]) # scenario_x = data['x_train'][:,indices] # scenario_y = data['y_train'][:,indices] # x_scenario_list.append(scenario_x) # y_scenario_list.append(scenario_y) # # delet original train data # del data['x_train'] # del data['y_train'] # # generate training data for initial case # data['x_train'] = np.concatenate([x_scenario_list[12].reshape(-1,28, 58, 10),x_scenario_list[16].reshape(-1,28, 58, 10), # x_scenario_list[20].reshape(-1,28, 58, 10),x_scenario_list[24].reshape(-1,28, 58, 10),x_scenario_list[28].reshape(-1,28, 58, 10)],0) # data['y_train'] = np.concatenate([y_scenario_list[12].reshape(-1,29, 24),y_scenario_list[16].reshape(-1,29, 24), # y_scenario_list[20].reshape(-1,29, 24),y_scenario_list[24].reshape(-1,29, 24),y_scenario_list[28].reshape(-1,29, 24)],0) # # search data # # search_data_list_x = list(x_scenario_list[:23] + x_scenario_list[24:]) # # search_data_list_y = list(y_scenario_list[:23] + y_scenario_list[24:]) # search_data_list_x = list(x_scenario_list[:12] + x_scenario_list[13:16] + # x_scenario_list[17:20] + x_scenario_list[21:24] + x_scenario_list[25:28] + x_scenario_list[29:]) # search_data_list_y = list(y_scenario_list[:12] + y_scenario_list[13:16] + # y_scenario_list[17:20] + y_scenario_list[21:24] + y_scenario_list[25:28] + y_scenario_list[29:]) # # flatten list # search_data_x = [item for sublist in search_data_list_x for item in sublist] # search_data_y = [item for sublist in search_data_list_y for item in sublist] # Data format (train data modified) data1 = {} for category in ["train", "val", "test"]: data1["x_" + category] = data["x_" + category] data1["y_" + category] = data["y_" + category][:, 1:] data1["x0_" + category] = data["y_" + category][:, 0] data1["train_loader"] = DataLoader( data1["x_train"], data1["y_train"], data1["x0_train"], batch_size, shuffle=True ) data1["val_loader"] = DataLoader( data1["x_val"], data1["y_val"], data1["x0_val"], test_batch_size, shuffle=False ) data1["test_loader"] = DataLoader( data1["x_test"], data1["y_test"], data1["x0_test"], test_batch_size, shuffle=False, ) return data1 def load_graph_data(pkl_filename): sensor_ids, sensor_id_to_ind, adj_mx = load_pickle(pkl_filename) return sensor_ids, sensor_id_to_ind, adj_mx def load_pickle(pickle_file): try: with open(pickle_file, "rb") as f: pickle_data = pickle.load(f) except UnicodeDecodeError as e: with open(pickle_file, "rb") as f: pickle_data = pickle.load(f, encoding="latin1") except Exception as e: print("Unable to load data ", pickle_file, ":", e) raise return pickle_data