epidemiology_tool/scripts/gen_adj_mx.py

from __future__ import absolute_import
from __future__ import division
from __future__ import print_function

import argparse
import numpy as np
import pandas as pd
import pickle


def get_adjacency_matrix(distance_df, sensor_ids):
    """

    :param distance_df: data frame with three columns: [from, to, distance].
    :param sensor_ids: list of sensor ids.
    :param normalized_k: entries that become lower than normalized_k after normalization are set to zero for sparsity.
    :return:
    """
    num_sensors = len(sensor_ids)
    dist_mx = np.zeros((num_sensors, num_sensors), dtype=np.float32)
    # dist_mx[:] = np.inf
    # Builds sensor id to index map.
    sensor_id_to_ind = {}
    for i, sensor_id in enumerate(sensor_ids):
        sensor_id_to_ind[sensor_id] = i

    # Fills cells in the matrix with distances.
    for row in distance_df.values:
        if row[0] not in sensor_id_to_ind or row[1] not in sensor_id_to_ind:
            continue
        dist_mx[sensor_id_to_ind[row[0]], sensor_id_to_ind[row[1]]] = row[2]

    adj_mx = dist_mx

    # calculate diagonal elements
    for i in range(len(adj_mx)):
        adj_mx[i, i] = 1 - np.sum(adj_mx[i])

    # Calculates the standard deviation as theta.
    # distances = dist_mx[~np.isinf(dist_mx)].flatten()
    # std = distances.std()
    # adj_mx = np.exp(-np.square(dist_mx / std))
    #
    # Make the adjacent matrix symmetric by taking the max.
    # adj_mx = np.maximum.reduce([adj_mx, adj_mx.T])
    #
    # Sets entries that lower than a threshold, i.e., k, to zero for sparsity.
    # adj_mx[adj_mx < normalized_k] = 0
    return sensor_ids, sensor_id_to_ind, adj_mx


if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument(
        "--sensor_ids_filename",
        type=str,
        default="../data/sensor_graph/004_ca_commute_flows_nodelist.txt",
        help="File containing sensor ids separated by lines.",
    )
    parser.add_argument(
        "--distances_filename",
        type=str,
        default="../data/sensor_graph/004_ca_commute_flows_edgelist.csv",
        help="CSV file containing sensor distances with three columns: [from, to, distance].",
    )
    # parser.add_argument('--normalized_k', type=float, default=0.0,
    #                     help='Entries that become lower than normalized_k after normalization are set to zero for sparsity.')
    parser.add_argument(
        "--output_pkl_filename",
        type=str,
        default="../data/sensor_graph/adj_mx.pkl",
        help="Path of the output file.",
    )
    args = parser.parse_args()

    with open(args.sensor_ids_filename) as f:
        sensor_ids = f.read().strip().splitlines()
    distance_df = pd.read_csv(
        args.distances_filename,
        dtype={"source_county_fips_code": "str", "target_county_fips_code": "str"},
    )
    _, sensor_id_to_ind, adj_mx = get_adjacency_matrix(distance_df, sensor_ids)
    # Save to pickle file.
    with open(args.output_pkl_filename, "wb") as f:
        pickle.dump([sensor_ids, sensor_id_to_ind, adj_mx], f, protocol=2)