""" 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 import shutil # ------------------------------------------------------------------------# def download_datasets(): """ Download the datasets from the web and unzip them. The datasets are downloaded from the SNAP website and from a Google Drive folder. Parameters ---------- None Returns ------- None Notes ----- The datasets are downloaded in the "data" folder. If the folder doesn't exist, it will be created. If the dataset is already downloaded, it will be skipped. The files are renamed to make them more readable. """ dict = { "brightkite": ["https://snap.stanford.edu/data/loc-brightkite_edges.txt.gz", "https://snap.stanford.edu/data/loc-brightkite_totalCheckins.txt.gz"], "gowalla": ["https://snap.stanford.edu/data/loc-gowalla_edges.txt.gz", "https://snap.stanford.edu/data/loc-gowalla_totalCheckins.txt.gz"], "foursquare": ["https://drive.google.com/file/d/1PNk3zY8NjLcDiAbzjABzY5FiPAFHq6T8/view?usp=sharing"] } if not os.path.exists("data"): os.mkdir("data") print("Created data folder") for folder in dict.keys(): if not os.path.exists(os.path.join("data", folder)): os.mkdir(os.path.join("data", folder)) print("Created {} folder".format(folder)) ## DOWNLOADING ## for folder in dict.keys(): for url in dict[folder]: if folder == "foursquare": if not os.path.exists(os.path.join("data", folder, "foursquare_full.zip")): output = os.path.join("data", folder, "foursquare_full.zip") gdown.download(url, output, quiet=False, fuzzy=True) else : print("{} already downloaded".format(url)) else: if not os.path.exists(os.path.join("data", folder, url.split("/")[-1])): print("Downloading {}...".format(url)) wget.download(url, os.path.join("data", folder)) else : print("{} already downloaded".format(url)) ## UNZIPPING ## for folder in dict.keys(): for file in os.listdir(os.path.join("data", folder)): if file.endswith(".gz"): print("Unzipping {}...".format(file)) os.system("gunzip {}".format(os.path.join("data", folder, file))) elif file.endswith(".zip"): print("Unzipping {}...".format(file)) os.system("unzip -o {} -d {}".format(os.path.join("data", folder, file), os.path.join("data", folder))) os.remove(os.path.join("data", folder, file)) ## FOURSQUARE CLEANING ## 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)) for file in ["dataset_WWW_friendship_old.txt", "dataset_WWW_readme.txt", "raw_Checkins_anonymized.txt"]: os.remove(os.path.join("data", "foursquare", file)) shutil.rmtree(os.path.join("data", "foursquare", "dataset_WWW2019")) shutil.rmtree(os.path.join("data", "foursquare", "__MACOSX")) os.rename(os.path.join("data", "foursquare", "dataset_WWW_friendship_new.txt"), os.path.join("data", "foursquare", "foursquare_friends_edges.txt")) os.rename(os.path.join("data", "foursquare", "dataset_WWW_Checkins_anonymized.txt"), os.path.join("data", "foursquare", "foursquare_checkins.txt")) ## BRIGHTKITE CLEANING ## os.rename(os.path.join("data", "brightkite", "loc-brightkite_totalCheckins.txt"), os.path.join("data", "brightkite", "brightkite_checkins.txt")) os.rename(os.path.join("data", "brightkite", "loc-brightkite_edges.txt"), os.path.join("data", "brightkite", "brightkite_friends_edges.txt")) ## GOWALLA CLEANING ## os.rename(os.path.join("data", "gowalla", "loc-gowalla_totalCheckins.txt"), os.path.join("data", "gowalla", "gowalla_checkins.txt")) os.rename(os.path.join("data", "gowalla", "loc-gowalla_edges.txt"), os.path.join("data", "gowalla", "gowalla_friends_edges.txt")) # ------------------------------------------------------------------------# 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', 'foursquare'] 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', 'foursquare']: raise ValueError("Dataset not valid. Please choose between brightkite, gowalla, foursquare") 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"], engine='pyarrow') 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 # ------------------------------------------------------------------------# 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", "foursquare"]: raise ValueError("The dataset must be brightkite, gowalla or foursquare") file = os.path.join("data", dataset, dataset + "_friends_edges.txt") df_friends_all = pd.read_csv(file, sep="\t", header=None, names=["node1", "node2"], engine='pyarrow') 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())) if k is None: G_copy = G.copy() 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: G_copy = G.copy() 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 generalized_average_clustering_coefficient(G: nx.Graph) -> float: """ Generalized definition of the average clustering coefficient of a graph. It better applies to small world networks and it's way more efficient than the average_clustering_coefficient function with the standard definition of the clustering coefficient. Parameters ---------- G : networkx graph The graph to compute the generalized average clustering coefficient of. Returns ------- float The generalized average clustering coefficient of the graph. """ C = 0 for node in G.nodes(): k = G.degree(node) C += (3*(k-1))/(2*(2*k - 1)) return C/G.number_of_nodes() # ------------------------------------------------------------------------# 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", "watts_strogatz" 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_renyi" if model == "erdos_renyi": G_random = nx.erdos_renyi_graph(G.number_of_nodes(), nx.density(G)) print("Creating a random graph with the Erdos-Renyi model {}" .format(G.name)) print("Number of edges in the original graph: {}" .format(G.number_of_edges())) print("Number of edges in the random graph: {}" .format(G_random.number_of_edges())) G_random.name = G.name + " Erdos-Renyi" 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("Number of edges in the original graph: {}" .format(G.number_of_edges())) print("Number 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