calculate_proximity.py

import argparse, os
import network_utilities, wrappers

def main():                         
    parser = argparse.ArgumentParser()
    parser.add_argument('-e', '--network_file') #, required=True) 
    parser.add_argument('-s', '--nodes_from') #, required=True) 
    parser.add_argument('-t', '--nodes_to') #, required=True) 
    parser.add_argument('-o', '--out_file') #, required=True)
    parser.add_argument('-n', '--n_random', type=int, default=1000) 
    parser.add_argument('-m', '--min_bin_size', type=int, default=100) 
    parser.add_argument('-x', '--n_seed', type=int, default=452456) 
    parser.add_argument('-f', '--parameter_file', type=str, default=None) 
    parser.add_argument('-p', '--parameter_file_prefix', type=str, default=None) 
    parser.add_argument('-i', '--parameter_file_start_index', type=int, default=None) 
    parser.add_argument('-j', '--parameter_file_end_index', type=int, default=None) 
    args = parser.parse_args()
    # Run more than once for given input files
    if args.parameter_file_prefix is not None:
	parameter_file_prefix = args.parameter_file_prefix
	i_start = args.parameter_file_start_index
	i_end = args.parameter_file_end_index
	calculate_proximity_multiple(parameter_file_prefix, i_start, i_end)
	return
    # Run from input parameter file
    elif args.parameter_file is not None:
	network_file, nodes_from, nodes_to, out_file, min_bin_size, n_random, n_seed = get_parameters_from_file(parameter_file_prefix + "%s.txt" % n)
    # Run once with provided arguments
    else:
	nodes_from = args.nodes_from.split(",")
	nodes_to = args.nodes_to.split(",")
	network_file = args.network_file
	n_random = args.n_random
	min_bin_size = args.min_bin_size
	n_seed = args.n_seed
	out_file = args.out_file
	network = network_utilities.create_network_from_sif_file(network_file, use_edge_data = False, delim = None, include_unconnected=True)
    #print args
    print network_file, nodes_from, nodes_to, n_random, min_bin_size, n_seed, out_file
    values = wrappers.calculate_proximity(network, nodes_from = nodes_from, nodes_to = nodes_to, n_random = n_random, min_bin_size = min_bin_size, seed = n_seed)
    if values is not None: # not in network
	d, z, (m, s) = values
	#print z, d, (m, s)
	open(out_file, 'w').write("%f %f %f %f\n" % (z, d, m, s))
    return


def calculate_proximity_multiple(parameter_file_prefix, i_start, i_end):
    network_file, nodes_from, nodes_to, out_file, min_bin_size, n_random, n_seed = get_parameters_from_file(parameter_file_prefix + "%s.txt" % i_start)
    network = network_utilities.create_network_from_sif_file(network_file, use_edge_data = False, delim = None, include_unconnected=True)
    bins = network_utilities.get_degree_binning(network, min_bin_size, lengths=None)
    for i in xrange(i_start, i_end):
	if not os.path.exists(parameter_file_prefix + "%s.txt" % i):
	    print "File does not exists for index (aborting):", i
	    break
	network_file, nodes_from, nodes_to, out_file, min_bin_size, n_random, n_seed = get_parameters_from_file(parameter_file_prefix + "%s.txt" % i)
	if os.path.exists(out_file):
	    print "Skipping existing file for index:", i
	    continue
	print network_file, nodes_from, nodes_to, n_random, min_bin_size, n_seed, out_file
	values = wrappers.calculate_proximity(network, nodes_from = nodes_from, nodes_to = nodes_to, bins = bins, n_random = n_random, min_bin_size = min_bin_size, seed = n_seed)
	if values is not None: # not in network
	    d, z, (m, s) = values
	    #print z, d, (m, s)
	    open(out_file, 'w').write("%f %f %f %f\n" % (z, d, m, s))
    return


def get_parameters_from_file(file_name):
    network_file = None 
    nodes_from = None
    nodes_to = None
    out_file = None
    min_bin_size = None
    n_random = None
    n_seed = None
    arguments = open(file_name).read().split()
    #print arguments
    i = 0
    if arguments[0] == "":
	i = 1
    while i < len(arguments):
	if arguments[i] == "-e":
	    network_file = arguments[i+1]
	if arguments[i] == "-s":
	    nodes_from = arguments[i+1].split(",")
	if arguments[i] == "-t":
	    nodes_to = arguments[i+1].split(",")
	if arguments[i] == "-o":
	    out_file = arguments[i+1]
	if arguments[i] == "-m":
	    min_bin_size = int(arguments[i+1])
	if arguments[i] == "-n":
	    n_random = int(arguments[i+1])
	if arguments[i] == "-x":
	    n_seed = int(arguments[i+1])
	#print arguments[i], arguments[i+1]
	i += 2
    return network_file, nodes_from, nodes_to, out_file, min_bin_size, n_random, n_seed

if __name__ == "__main__":
    main()