""" NOTEs: - This file is note meant to be run, it's just a collection of functions that are used in the other files. It's just a way to keep the code clean and organized. - Why do I use os.path.join and not the "/"? Because it's more portable, it works on every OS, while "/" works only on Linux and Mac. In windows you would have to change all the "/" with "\". With os.path.join you don't have to worry about it and, as always, f*** Microsoft. """ from multiprocessing import Pool import itertools import os import random import wget import zipfile import pandas as pd import tqdm as tqdm import networkx as nx from typing import Literal from itertools import combinations import plotly.graph_objects as go from collections import Counter import numpy as np import gdown from networkx.utils import py_random_state # ------------------------------------------------------------------------# def download_datasets(): urls = [ ["https://snap.stanford.edu/data/loc-brightkite_edges.txt.gz", "https://snap.stanford.edu/data/loc-brightkite_totalCheckins.txt.gz"], ["https://snap.stanford.edu/data/loc-gowalla_edges.txt.gz", "https://snap.stanford.edu/data/loc-gowalla_totalCheckins.txt.gz"], ["https://drive.google.com/file/d/1PNk3zY8NjLcDiAbzjABzY5FiPAFHq6T8/view?usp=sharing"] ] folders = ["brightkite", "gowalla", "foursquare"] if not os.path.exists("data"): os.mkdir("data") for folder in folders: if not os.path.exists(os.path.join("data", folder)): os.mkdir(os.path.join("data", folder)) # Download every url in their respective folder. For the last one, we have to use gdown, because it's a google drive link. If the file is already downloaded, skip the download for i in range(len(urls)): for url in urls[i]: if not os.path.exists(os.path.join("data", folders[i], url.split("/")[-1])): if i == 2: output = os.path.join("data", folders[i], "something.zip") gdown.download(url, output, quiet=False, fuzzy=True) else: wget.download(url, os.path.join("data", folders[i])) # unzip all the files in the 3 folders. Then remove the .gz or .zip files for folder in folders: for file in os.listdir(os.path.join("data", folder)): print(folder, file) if file.endswith(".gz"): os.system("gunzip {}".format(os.path.join("data", folder, file))) elif file.endswith(".zip"): os.system("unzip {}".format(os.path.join("data", folder, file))) os.remove(os.path.join("data", folder, file)) # take all the .txt files from data/foursquare/dataset_WWW2019 and move them to data/foursquare for file in os.listdir(os.path.join("data", "foursquare", "dataset_WWW2019")): if file.endswith(".txt"): os.rename(os.path.join("data", "foursquare", "dataset_WWW2019", file), os.path.join("data", "foursquare", file)) # remove the dataset_WWW2019 folder, note that is not empty # os.rmdir(os.path.join("data", "foursquare", "dataset_WWW2019")) for file in ["dataset_WWW_friendship_old.txt", "dataset_WWW_readme.txt", "raw_Checkins_anonymized.txt", "raw_POIs.txt"]: os.remove(os.path.join("data", "foursquare", file)) # Now we want to clean our data and rename the files. for file in os.listdir(os.path.join("data", "brightkite")): if file.endswith("_edges.txt"): os.rename(os.path.join("data", "brightkite", file), os.path.join("data", "brightkite", "brightkite_friends_edges.txt")) for file in os.listdir(os.path.join("data", "gowalla")): if file.endswith("_edges.txt"): os.rename(os.path.join("data", "gowalla", file), os.path.join("data", "gowalla", "gowalla_friends_edges.txt")) for file in os.listdir(os.path.join("data", "foursquare")): if file.endswith("dataset_WWW_friendship_new.txt"): os.rename(os.path.join("data", "foursquare", file), os.path.join("data", "foursquare", "foursquare_friends_edges.txt")) # Now we from the _totalCheckins.txt files we want to keep only the first and last column, which are the user ID and the venue ID. We also want to remove the header of the file. for file in os.listdir(os.path.join("data", "brightkite")): if file.endswith("_totalCheckins.txt"): df = pd.read_csv(os.path.join("data", "brightkite", file), sep="\t", header=None, names=["user_id", "check-in time", "latitude", "longitude", "venue_id"]) df["check-in time"] = pd.to_datetime(df["check-in time"]) df = df[df["check-in time"].dt.year == 2010] df = df.drop(["check-in time", "latitude", "longitude"], axis=1) df.to_csv(os.path.join("data", "brightkite", "brightkite_checkins.txt"), sep="\t", header=False, index=False, errors="ignore", encoding="utf-8") os.remove(os.path.join("data", "brightkite", file)) for file in os.listdir(os.path.join("data", "gowalla")): if file.endswith("_totalCheckins.txt"): df = pd.read_csv(os.path.join("data", "gowalla", file), sep="\t", header=None, names=["user_id", "check-in time", "latitude", "longitude", "venue_id"]) df["check-in time"] = pd.to_datetime(df["check-in time"]) df = df[df["check-in time"].dt.year == 2010] df = df.drop(["check-in time", "latitude", "longitude"], axis=1) df.to_csv(os.path.join("data", "gowalla", "gowalla_checkins.txt"), sep="\t", header=False, index=False, errors="ignore", encoding="utf-8") os.remove(os.path.join("data", "gowalla", file)) for file in os.listdir(os.path.join("data", "foursquare")): if file.endswith("dataset_WWW_Checkins_anonymized.txt"): df = pd.read_csv(os.path.join("data", "foursquare", file), sep="\t", header=None) df = df[[0, 1]] df.to_csv(os.path.join("data", "foursquare", "foursquare_checkins.txt"), sep="\t", header=False, index=False, errors="ignore", encoding="utf-8") os.remove(os.path.join("data", "foursquare", file)) # ------------------------------------------------------------------------# def create_graph_from_checkins(dataset: Literal['brightkite', 'gowalla', 'foursquareEU', 'foursquareIT'], create_file = True) -> nx.Graph: """ Create a graph from the checkins of the dataset. The graph is undirected and the nodes are the users and the edges are the checkins in common. Parameters ---------- `dataset` : Literal['brightkite', 'gowalla', 'foursquareEU', 'foursquareIT'] The dataset to use. `create_file` : bool, optional If True, the graph is saved in a file, by default True Returns ------- `G` : networkx.Graph Raises ------ ValueError If the dataset is not valid. """ if dataset not in ['brightkite', 'gowalla', 'foursquareEU', 'foursquareIT']: raise ValueError("Dataset not valid. Please choose between brightkite, gowalla, foursquareEU, foursquareUS, foursquareIT") if dataset in ['brightkite', 'gowalla']: file = os.path.join("data", dataset, dataset + "_checkins.txt") print("\nCreating the graph for the dataset {}...".format(dataset)) df = pd.read_csv(file, sep="\t", header=None, names=["user_id", "venue_id"]) G = nx.Graph() venues_users = df.groupby("venue_id")["user_id"].apply(set) for users in tqdm.tqdm(venues_users): for user1, user2 in combinations(users, 2): G.add_edge(user1, user2) # path to the file where we want to save the graph edges_path = os.path.join("data", dataset , dataset + "_checkins_edges.tsv") print("Done! The graph has {} edges".format(G.number_of_edges()), " and {} nodes".format(G.number_of_nodes())) # delete from memory the dataframe del df if create_file: # save the graph in a file nx.write_edgelist(G, edges_path, data=True, delimiter="\t", encoding="utf-8") return G else: # path to the checkins file and the POIS file path_checkins = os.path.join("data", "foursquare", "foursquare_checkins.txt") path_POIS = os.path.join("data", "foursquare", "raw_POIs.txt") # dataframe with the checkins, we need only the user_id and the venue_id df_all = pd.read_csv(path_checkins, sep="\t", header=None, names=['user_id', 'venue_id', 'time', 'offset']) df_all = df_all[['user_id', 'venue_id']] # dataframe with the POIS, we need only the venue_id and the country code df_POIS = pd.read_csv(path_POIS, sep='\t', header=None, names=['venue_id', 'lat', 'lon', 'category', 'country code']) df_POIS = df_POIS[['venue_id', 'country code']] if dataset == "foursquareIT": venues_array = df_POIS[df_POIS['country code'] == 'IT']['venue_id'].values elif dataset == "foursquareEU": # list of the countries in the EU EU_countries = ['AT', 'BE', 'BG', 'CY', 'CZ', 'DE', 'DK', 'EE', 'ES', 'FI', 'FR', 'GR', 'HR', 'HU', 'IE', 'IT', 'LT', 'LU', 'LV', 'MT', 'NL', 'PL', 'PT', 'RO', 'SE', 'SI', 'SK'] venues_array = df_POIS[df_POIS['country code'].isin(EU_countries)]['venue_id'].values print("\nCreating the graph for the dataset {}...".format(dataset)) # we create a dataframe with the checkins in the corresponding country df_country = df_all[df_all['venue_id'].isin(venues_array)] G = nx.Graph() venues_users = df_country.groupby("venue_id")["user_id"].apply(set) for users in tqdm.tqdm(venues_users): for user1, user2 in combinations(users, 2): G.add_edge(user1, user2) # path to the file where we want to save the graph edges_path = os.path.join("data", "foursquare", dataset + "_checkins_edges.tsv") print("Done! The graph has {} edges".format(G.number_of_edges()), " and {} nodes".format(G.number_of_nodes())) # delete from memory the dataframes del df_all, df_POIS, df_country if create_file: # save the graph in a file nx.write_edgelist(G, edges_path, data=True, delimiter="\t", encoding="utf-8") return G # ------------------------------------------------------------------------# def create_friendships_graph(dataset: Literal['brightkite', 'gowalla', 'foursquareEU', 'foursquareIT']) -> nx.Graph: """ Create the graph of friendships for the dataset brightkite, gowalla or foursquare. The graph is saved in a file. Parameters ---------- `dataset` : str The dataset for which we want to create the graph of friendships. Returns ------- `G` : networkx.Graph The graph of friendships. Notes ----- Since we are taking sub-samples of each check-ins dataset, we are also taking sub-samples of the friendship graph. A user is included in the friendship graph if he has at least one check-in in the sub-sample. """ if dataset not in ["brightkite", "gowalla", "foursquareEU", "foursquareIT"]: raise ValueError("The dataset must be brightkite, gowalla or foursquare") if dataset in ["foursquareEU", "foursquareIT"]: file = os.path.join("data", "foursquare", "foursquare_friends_edges.txt") # dataframe with the edges of the graph (friends) df_friends_all = pd.read_csv(file, sep="\t", header=None, names=["node1", "node2"]) # set of the unique users in the graph (friends) unique_friends = set(df_friends_all["node1"].unique()).union(set(df_friends_all["node2"].unique())) # dataframe with the edges of the graph (checkins) df_checkins = pd.read_csv(os.path.join("data", "foursquare", dataset + "_checkins_edges.tsv"), sep="\t", header=None, names=["node1", "node2"]) unique_checkins = set(df_checkins["node1"].unique()).union(set(df_checkins["node2"].unique())) # take the intersection of the two sets unique_users = unique_friends.intersection(unique_checkins) # create a dataframe with the edges of the graph df = df_friends_all[df_friends_all["node1"].isin(unique_users) & df_friends_all["node2"].isin(unique_users)] # create a tsv file with the edges of the graph that ends with _filtered.tsv df.to_csv(os.path.join("data", "foursquare", dataset + "_friends_edges_filtered.tsv"), sep="\t", header=False, index=False) # create the graph G = nx.from_pandas_edgelist(df, "node1", "node2", create_using=nx.Graph()) del df_friends_all, df_checkins, df return G elif dataset in ["brightkite", "gowalla"]: file = os.path.join("data", dataset, dataset + "_friends_edges.txt") df_friends_all = pd.read_csv(file, sep="\t", header=None, names=["node1", "node2"]) unique_friends = set(df_friends_all["node1"].unique()).union(set(df_friends_all["node2"].unique())) df_checkins = pd.read_csv(os.path.join("data", dataset, dataset + "_checkins_edges.tsv"), sep="\t", header=None, names=["node1", "node2"]) unique_checkins = set(df_checkins["node1"].unique()).union(set(df_checkins["node2"].unique())) unique_users = unique_friends.intersection(unique_checkins) df = df_friends_all[df_friends_all["node1"].isin(unique_users) & df_friends_all["node2"].isin(unique_users)] df.to_csv(os.path.join("data", dataset, dataset + "_friends_edges_filtered.tsv"), sep="\t", header=False, index=False) G = nx.from_pandas_edgelist(df, "node1", "node2", create_using=nx.Graph()) del df_friends_all, df_checkins, df return G # ------------------------------------------------------------------------# def degree_distribution(G: nx.Graph, log: bool = True, save: bool = False) -> None: """ This function takes in input a networkx graph object and plots the degree distribution of the graph. Parameters ---------- `G` : networkx graph object The graph object `log` : bool, optional If True, the plot will be in log-log scale, by default True `save` : bool, optional If True, the plot will be saved in the folder "plots", by default False Returns ------- None Notes ----- Due to the characteristics of datasets, not using a log log scale will lead to a un-useful plot. Even if using a log scales alters the power-law distribution, it is still clearly visible and distinguishable from a poisson distribution (witch is what we are interested in in this case) """ degrees = [G.degree(n) for n in G.nodes()] degreeCount = Counter(degrees) fig = go.Figure() fig.add_trace(go.Bar(x=list(degreeCount.keys()), y=list(degreeCount.values()), name='Degree Distribution')) if log: fig.update_layout( title='Degree Distribution (log-log scale) of {}' .format(G.name), xaxis_title='Degree', yaxis_title='Number of Nodes', xaxis_type='log', yaxis_type='log', width=800, height=600, template='plotly_white' ) else: fig.update_layout( title='Degree Distribution of {}' .format(G.name), xaxis_title='Degree', yaxis_title='Number of Nodes', width=800, height=600, template='plotly_white' ) fig.show() if save: fig.write_image("plots/degree_distribution_{}.png".format(G.name)) # ------------------------------------------------------------------------# def chunks(l, n): """ Auxiliary function to divide a list of nodes `l` in `n` chunks Parameters ---------- `l` : list List of nodes `n` : int Number of chunks """ l_c = iter(l) while 1: x = tuple(itertools.islice(l_c, n)) if not x: return yield x # ------------------------------------------------------------------------# def betweenness_centrality_parallel(G, processes=None, k =None) -> dict: """ Compute the betweenness centrality for nodes in a graph using multiprocessing. Parameters ---------- G : graph A networkx graph processes : int, optional The number of processes to use for computation. If `None`, then it sets processes = 1 k : int, optional Percent of nodes to sample. If `None`, then all nodes are used. seed : int, optional Seed for random number generator (default=None). Returns ------- dict Notes ----- Do not use more then 6 process for big graphs, otherwise the memory will be full. Do it only if you have more at least 32 GB of RAM. For small graphs, you can use more processes. """ # if process is None or 1, run the standard algorithm with one process if processes is None or processes == 1: print("\tRunning the networkx approximated algorithm with just one process") G_copy = G.copy() sample = int((k)*G_copy.number_of_nodes()) print("\tNumber of nodes after removing {} % of nodes: {}" .format((k)*100, G_copy.number_of_nodes())) return np.mean(nx.betweenness_centrality(G, k=sample, seed=42).values()) if processes > os.cpu_count(): raise ValueError("The number of processes must be less than the number of cores in the system.") if k is not None: if (k < 0 or k > 1): raise ValueError("k must be between 0 and 1.") else: G_copy = G.copy() G_copy.remove_nodes_from(random.sample(G_copy.nodes(), int((k)*G_copy.number_of_nodes()))) print("\tNumber of nodes after removing {}% of nodes: {}" .format((k)*100, G_copy.number_of_nodes())) print("\tNumber of edges after removing {}% of nodes: {}" .format((k)*100, G_copy.number_of_edges())) p = Pool(processes=processes) node_divisor = len(p._pool) * 4 node_chunks = list(chunks(G_copy.nodes(), G_copy.order() // node_divisor)) num_chunks = len(node_chunks) bt_sc = p.starmap( nx.betweenness_centrality_subset, zip( [G_copy] * num_chunks, # this returns a list of Gs node_chunks, [list(G_copy)] * num_chunks, # this returns a list of lists of nodes [True] * num_chunks, [None] * num_chunks, ), ) # Reduce the partial solutions bt_c = bt_sc[0] for bt in bt_sc[1:]: for n in bt: bt_c[n] += bt[n] return bt_c # ------------------------------------------------------------------------# def average_shortest_path(G: nx.Graph, k=None) -> float: """ This function takes in input a networkx graph and returns the average shortest path length of the graph. This works also for disconnected graphs. Parameters ---------- `G` : networkx graph The graph to compute the average shortest path length of. `k` : int percentage of nodes to remove from the graph. If k is None, the average shortest path length of each connected component is computed using all the nodes of the connected component. Returns ------- float The average shortest path length of the graph. Raises ------ ValueError If k is not between 0 and 1 """ if k is not None and (k < 0 or k > 1): raise ValueError("k must be between 0 and 1") elif k is None: connected_components = list(nx.connected_components(G)) else: G_copy = G.copy() # remove the k% of nodes from G G_copy.remove_nodes_from(random.sample(G_copy.nodes(), int((k)*G_copy.number_of_nodes()))) print("\tNumber of nodes after removing {}% of nodes: {}" .format((k)*100, G_copy.number_of_nodes())) print("\tNumber of edges after removing {}% of nodes: {}" .format((k)*100, G_copy.number_of_edges())) tmp = 0 connected_components = list(nx.connected_components(G_copy)) # remove all the connected components with less than 10 nodes connected_components = [c for c in connected_components if len(c) > 10] print("\tNumber of connected components with more then 10 nodes: {}" .format(len(connected_components)), "\r") for C in (G_copy.subgraph(c).copy() for c in connected_components): print("\tComputing average shortest path length of connected component with {} nodes and {} edges" .format(C.number_of_nodes(), C.number_of_edges()), "\r", end="") tmp += nx.average_shortest_path_length(C) return np.mean(tmp) # ------------------------------------------------------------------------# def average_clustering_coefficient(G: nx.Graph, k=None) -> float: """ This function takes in input a networkx graph and returns the average clustering coefficient of the graph. This works also for disconnected graphs. Parameters ---------- G : networkx graph The graph to compute the average clustering coefficient of. k : int percentage of nodes to remove from the graph. If k is None, the average clustering coefficient of each connected component is computed using all the nodes of the connected component. Returns ------- float The average clustering coefficient of the graph. Raises ------ ValueError If k is not between 0 and 1 """ if k is not None and (k < 0 or k > 1): raise ValueError("k must be between 0 and 1") elif k is None: return nx.average_clustering(G) else: G_copy = G.copy() G_copy.remove_nodes_from(random.sample(list(G_copy.nodes()), int((k)*G_copy.number_of_nodes()))) print("\tNumber of nodes after removing {}% of nodes: {}" .format((k)*100, G_copy.number_of_nodes())) return nx.average_clustering(G_copy) # ------------------------------------------------------------------------# def create_random_graphs(G: nx.Graph, model = None, save = True) -> nx.Graph: """Create a random graphs of the same model of the original graph G. Parameters ---------- G : nx.Graph The original graph. model : str The model to use to generate the random graphs. It can be one of the following: "erdos", "barabasi", "watts_strogatz", "newman_watts_strog save: bool If True, the random graph is saved in the folder data/random/model Returns ------- G_random : nx.Graph """ if model is None: model = "erdos" if model == "erdos": G_random = nx.erdos_renyi_graph(G.number_of_nodes(), nx.density(G)) print("\tNumber of edges in the original graph: {}" .format(G.number_of_edges())) print("\tNumber of edges in the random graph: {}" .format(G_random.number_of_edges())) G_random.name = G.name + " erdos" if save: # check if the folder exists, otherwise create it if not os.path.exists(os.path.join('data', 'random', 'erdos')): os.makedirs(os.path.join('data', 'random', 'erdos')) nx.write_gpickle(G_random, os.path.join('data', 'random', 'erdos', "erdos_" + str(G.number_of_nodes()) + "_" + str(G_random.number_of_edges()) + ".gpickle")) print("\tThe file graph has been saved in the folder data/random/erdos with the syntax erdos_n_nodes_n_edges.gpickle") return G_random elif model == "watts_strogatz": p = G.number_of_edges() / (G.number_of_nodes()) avg_degree = int(np.mean([d for n, d in G.degree()])) G_random = nx.watts_strogatz_graph(G.number_of_nodes(), avg_degree, p) print("\tNumber of edges in the original graph: {}" .format(G.number_of_edges())) print("\tNumber of edges in the random graph: {}" .format(G_random.number_of_edges())) G_random.name = G.name + " watts_strogatz" if save: # check if the folder exists, otherwise create it if not os.path.exists(os.path.join('data', 'random', 'watts_strogatz')): os.makedirs(os.path.join('data', 'random', 'watts_strogatz')) nx.write_gpickle(G_random, os.path.join('data', 'random', 'watts_strogatz', "watts_strogatz_" + str(G.number_of_nodes()) + "_" + str(G_random.number_of_edges()) + ".gpickle")) print("\tThe file graph has been saved in the folder data/random/watts_strogatz with the syntax watts_strogatz_n_nodes_n_edges.gpickle") return G_random # elif model == "regular": # G_random = nx.random_regular_graph(1, G.number_of_nodes()) # print("\tNumber of edges in the original graph: {}" .format(G.number_of_edges())) # print("\tNumber of edges in the random graph: {}" .format(G_random.number_of_edges())) # G_random.name = G.name + "regular" # if save: # # check if the folder exists, otherwise create it # if not os.path.exists(os.path.join('data', 'random', 'regular')): # os.makedirs(os.path.join('data', 'random', 'regular')) # nx.write_gpickle(G_random, os.path.join('data', 'random', 'regular', "regular_" + str(G.number_of_nodes()) + "_" + str(G_random.number_of_edges()) + ".gpickle")) # print("\tThe file graph has been saved in the folder data/random/regular with the syntax regular_n_nodes_n_edges.gpickle") # return G_random # elif model == "reference": # G_random = nx.random_reference(G) # print("\tNumber of edges in the original graph: {}" .format(G.number_of_edges())) # print("\tNumber of edges in the random graph: {}" .format(G_random.number_of_edges())) # G_random.name = G.name + "reference" # if save: # # check if the folder exists, otherwise create it # if not os.path.exists(os.path.join('data', 'random', 'reference')): # os.makedirs(os.path.join('data', 'random', 'reference')) # nx.write_gpickle(G_random, os.path.join('data', 'random', 'reference', "reference_" + str(G.number_of_nodes()) + "_" + str(G_random.number_of_edges()) + ".gpickle")) # print("\tThe file graph has been saved in the folder data/random/reference with the syntax reference_n_nodes_n_edges.gpickle") # return G_random # #lattice # elif model == "lattice": # G_random = nx.lattice_reference(G, 1) # print("\tNumber of edges in the original graph: {}" .format(G.number_of_edges())) # print("\tNumber of edges in the random graph: {}" .format(G_random.number_of_edges())) # G_random.name = G.name + "lattice" # if save: # # check if the folder exists, otherwise create it # if not os.path.exists(os.path.join('data', 'random', 'lattice')): # os.makedirs(os.path.join('data', 'random', 'lattice')) # nx.write_gpickle(G_random, os.path.join('data', 'random', 'lattice', "lattice_" + str(G.number_of_nodes()) + "_" + str(G_random.number_of_edges()) + ".gpickle")) # print("\tThe file graph has been saved in the folder data/random/lattice with the syntax lattice_n_nodes_n_edges.gpickle") # return G_random