graphkit-learn/gklearn/ged/util/util.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 31 17:06:22 2020

@author: ljia
"""
import numpy as np
from itertools import combinations
import multiprocessing
from multiprocessing import Pool
from functools import partial
import sys
from tqdm import tqdm
import networkx as nx
from gklearn.gedlib import librariesImport, gedlibpy


def compute_ged(g1, g2, options):
	ged_env = gedlibpy.GEDEnv()
	ged_env.set_edit_cost(options['edit_cost'], edit_cost_constant=options['edit_cost_constants'])
	ged_env.add_nx_graph(g1, '')
	ged_env.add_nx_graph(g2, '')
	listID = ged_env.get_all_graph_ids()	
	ged_env.init()
	ged_env.set_method(options['method'], ged_options_to_string(options))
	ged_env.init_method()

	g = listID[0]
	h = listID[1]
	ged_env.run_method(g, h)
	pi_forward = ged_env.get_forward_map(g, h)
	pi_backward = ged_env.get_backward_map(g, h)
	upper = ged_env.get_upper_bound(g, h)	
	dis = upper
			
	# make the map label correct (label remove map as np.inf)
	nodes1 = [n for n in g1.nodes()]
	nodes2 = [n for n in g2.nodes()]
	nb1 = nx.number_of_nodes(g1)
	nb2 = nx.number_of_nodes(g2)
	pi_forward = [nodes2[pi] if pi < nb2 else np.inf for pi in pi_forward]
	pi_backward = [nodes1[pi] if pi < nb1 else np.inf for pi in pi_backward]
#		print(pi_forward)

	return dis, pi_forward, pi_backward


def compute_geds(graphs, options={}, parallel=False):
	# initialize ged env.
	ged_env = gedlibpy.GEDEnv()
	ged_env.set_edit_cost(options['edit_cost'], edit_cost_constant=options['edit_cost_constants'])
	for g in graphs:
		ged_env.add_nx_graph(g, '')
	listID = ged_env.get_all_graph_ids()	
	ged_env.init()
	ged_env.set_method(options['method'], ged_options_to_string(options))
	ged_env.init_method()

	# compute ged.
	neo_options = {'edit_cost': options['edit_cost'], 
				'node_attrs': options['node_attrs'], 'edge_attrs': options['edge_attrs']}
	ged_mat = np.zeros((len(graphs), len(graphs)))
	if parallel:
		len_itr = int(len(graphs) * (len(graphs) - 1) / 2)
		ged_vec = [0 for i in range(len_itr)]
		n_edit_operations = [0 for i in range(len_itr)]
		itr = combinations(range(0, len(graphs)), 2)
		n_jobs = multiprocessing.cpu_count()
		if len_itr < 100 * n_jobs:
			chunksize = int(len_itr / n_jobs) + 1
		else:
			chunksize = 100
		def init_worker(graphs_toshare, ged_env_toshare, listID_toshare):
			global G_graphs, G_ged_env, G_listID
			G_graphs = graphs_toshare
			G_ged_env = ged_env_toshare
			G_listID = listID_toshare
		do_partial = partial(_wrapper_compute_ged_parallel, neo_options)
		pool = Pool(processes=n_jobs, initializer=init_worker, initargs=(graphs, ged_env, listID))
		iterator = tqdm(pool.imap_unordered(do_partial, itr, chunksize),
						desc='computing GEDs', file=sys.stdout)
#		iterator = pool.imap_unordered(do_partial, itr, chunksize)
		for i, j, dis, n_eo_tmp in iterator:
			idx_itr = int(len(graphs) * i + j - (i + 1) * (i + 2) / 2)
			ged_vec[idx_itr] = dis
			ged_mat[i][j] = dis
			ged_mat[j][i] = dis
			n_edit_operations[idx_itr] = n_eo_tmp
#			print('\n-------------------------------------------')
#			print(i, j, idx_itr, dis)
		pool.close()
		pool.join()
		
	else:
		ged_vec = []
		n_edit_operations = []
		for i in tqdm(range(len(graphs)), desc='computing GEDs', file=sys.stdout):
#		for i in range(len(graphs)):
			for j in range(i + 1, len(graphs)):
				dis, pi_forward, pi_backward = _compute_ged(ged_env, listID[i], listID[j], graphs[i], graphs[j])
				ged_vec.append(dis)
				ged_mat[i][j] = dis
				ged_mat[j][i] = dis
				n_eo_tmp = get_nb_edit_operations(graphs[i], graphs[j], pi_forward, pi_backward, **neo_options)
				n_edit_operations.append(n_eo_tmp)
					
	return ged_vec, ged_mat, n_edit_operations


def _wrapper_compute_ged_parallel(options, itr):
	i = itr[0]
	j = itr[1]
	dis, n_eo_tmp = _compute_ged_parallel(G_ged_env, G_listID[i], G_listID[j], G_graphs[i], G_graphs[j], options)
	return i, j, dis, n_eo_tmp


def _compute_ged_parallel(env, gid1, gid2, g1, g2, options):
	dis, pi_forward, pi_backward = _compute_ged(env, gid1, gid2, g1, g2)
	n_eo_tmp = get_nb_edit_operations(g1, g2, pi_forward, pi_backward, **options) # [0,0,0,0,0,0]
	return dis, n_eo_tmp


def _compute_ged(env, gid1, gid2, g1, g2):
	env.run_method(gid1, gid2)
	pi_forward = env.get_forward_map(gid1, gid2)
	pi_backward = env.get_backward_map(gid1, gid2)
	upper = env.get_upper_bound(gid1, gid2)	
	dis = upper
			
	# make the map label correct (label remove map as np.inf)
	nodes1 = [n for n in g1.nodes()]
	nodes2 = [n for n in g2.nodes()]
	nb1 = nx.number_of_nodes(g1)
	nb2 = nx.number_of_nodes(g2)
	pi_forward = [nodes2[pi] if pi < nb2 else np.inf for pi in pi_forward]
	pi_backward = [nodes1[pi] if pi < nb1 else np.inf for pi in pi_backward]

	return dis, pi_forward, pi_backward


def get_nb_edit_operations(g1, g2, forward_map, backward_map, edit_cost=None, **kwargs):
	if edit_cost == 'LETTER' or edit_cost == 'LETTER2':
		return get_nb_edit_operations_letter(g1, g2, forward_map, backward_map)
	elif edit_cost == 'NON_SYMBOLIC':
		node_attrs = kwargs.get('node_attrs', [])
		edge_attrs = kwargs.get('edge_attrs', [])
		return get_nb_edit_operations_nonsymbolic(g1, g2, forward_map, backward_map, 
											node_attrs=node_attrs, edge_attrs=edge_attrs)
	else: 
		return get_nb_edit_operations_symbolic(g1, g2, forward_map, backward_map)
	

def get_nb_edit_operations_symbolic(g1, g2, forward_map, backward_map):
	"""Compute the number of each edit operations.
	"""
	n_vi = 0
	n_vr = 0
	n_vs = 0
	n_ei = 0
	n_er = 0
	n_es = 0
	
	nodes1 = [n for n in g1.nodes()]
	for i, map_i in enumerate(forward_map):
		if map_i == np.inf:
			n_vr += 1
		elif g1.node[nodes1[i]]['atom'] != g2.node[map_i]['atom']:
			n_vs += 1
	for map_i in backward_map:
		if map_i == np.inf:
			n_vi += 1
	
#	idx_nodes1 = range(0, len(node1))
	
	edges1 = [e for e in g1.edges()]
	nb_edges2_cnted = 0
	for n1, n2 in edges1:
		idx1 = nodes1.index(n1)
		idx2 = nodes1.index(n2)
		# one of the nodes is removed, thus the edge is removed.
		if forward_map[idx1] == np.inf or forward_map[idx2] == np.inf:
			n_er += 1
		# corresponding edge is in g2.
		elif (forward_map[idx1], forward_map[idx2]) in g2.edges():
			nb_edges2_cnted += 1
			# edge labels are different.
			if g2.edges[((forward_map[idx1], forward_map[idx2]))]['bond_type'] \
				!= g1.edges[(n1, n2)]['bond_type']:
					n_es += 1
		elif (forward_map[idx2], forward_map[idx1]) in g2.edges():
			nb_edges2_cnted += 1
			# edge labels are different.
			if g2.edges[((forward_map[idx2], forward_map[idx1]))]['bond_type'] \
				!= g1.edges[(n1, n2)]['bond_type']:
					n_es += 1				
		# corresponding nodes are in g2, however the edge is removed.
		else:
			n_er += 1
	n_ei = nx.number_of_edges(g2) - nb_edges2_cnted
	
	return n_vi, n_vr, n_vs, n_ei, n_er, n_es


def get_nb_edit_operations_letter(g1, g2, forward_map, backward_map):
	"""Compute the number of each edit operations.
	"""
	n_vi = 0
	n_vr = 0
	n_vs = 0
	sod_vs = 0
	n_ei = 0
	n_er = 0
	
	nodes1 = [n for n in g1.nodes()]
	for i, map_i in enumerate(forward_map):
		if map_i == np.inf:
			n_vr += 1
		else:
			n_vs += 1
			diff_x = float(g1.nodes[nodes1[i]]['x']) - float(g2.nodes[map_i]['x'])
			diff_y = float(g1.nodes[nodes1[i]]['y']) - float(g2.nodes[map_i]['y'])
			sod_vs += np.sqrt(np.square(diff_x) + np.square(diff_y))
	for map_i in backward_map:
		if map_i == np.inf:
			n_vi += 1
	
#	idx_nodes1 = range(0, len(node1))
	
	edges1 = [e for e in g1.edges()]
	nb_edges2_cnted = 0
	for n1, n2 in edges1:
		idx1 = nodes1.index(n1)
		idx2 = nodes1.index(n2)
		# one of the nodes is removed, thus the edge is removed.
		if forward_map[idx1] == np.inf or forward_map[idx2] == np.inf:
			n_er += 1
		# corresponding edge is in g2. Edge label is not considered.
		elif (forward_map[idx1], forward_map[idx2]) in g2.edges() or \
			(forward_map[idx2], forward_map[idx1]) in g2.edges():
				nb_edges2_cnted += 1
		# corresponding nodes are in g2, however the edge is removed.
		else:
			n_er += 1
	n_ei = nx.number_of_edges(g2) - nb_edges2_cnted
	
	return n_vi, n_vr, n_vs, sod_vs, n_ei, n_er


def get_nb_edit_operations_nonsymbolic(g1, g2, forward_map, backward_map,
									   node_attrs=[], edge_attrs=[]):
	"""Compute the number of each edit operations.
	"""
	n_vi = 0
	n_vr = 0
	n_vs = 0
	sod_vs = 0
	n_ei = 0
	n_er = 0
	n_es = 0
	sod_es = 0
	
	nodes1 = [n for n in g1.nodes()]
	for i, map_i in enumerate(forward_map):
		if map_i == np.inf:
			n_vr += 1
		else:
			n_vs += 1
			sum_squares = 0
			for a_name in node_attrs:
				diff = float(g1.nodes[nodes1[i]][a_name]) - float(g2.nodes[map_i][a_name])
				sum_squares += np.square(diff)
			sod_vs += np.sqrt(sum_squares)
	for map_i in backward_map:
		if map_i == np.inf:
			n_vi += 1
	
#	idx_nodes1 = range(0, len(node1))
	
	edges1 = [e for e in g1.edges()]
	for n1, n2 in edges1:
		idx1 = nodes1.index(n1)
		idx2 = nodes1.index(n2)
		n1_g2 = forward_map[idx1]
		n2_g2 = forward_map[idx2]
		# one of the nodes is removed, thus the edge is removed.
		if n1_g2 == np.inf or n2_g2 == np.inf:
			n_er += 1
		# corresponding edge is in g2.
		elif (n1_g2, n2_g2) in g2.edges():
			n_es += 1
			sum_squares = 0
			for a_name in edge_attrs:
				diff = float(g1.edges[n1, n2][a_name]) - float(g2.edges[n1_g2, n2_g2][a_name])
				sum_squares += np.square(diff)
			sod_es += np.sqrt(sum_squares)
		elif (n2_g2, n1_g2) in g2.edges():
			n_es += 1
			sum_squares = 0
			for a_name in edge_attrs:
				diff = float(g1.edges[n2, n1][a_name]) - float(g2.edges[n2_g2, n1_g2][a_name])
				sum_squares += np.square(diff)
			sod_es += np.sqrt(sum_squares)
		# corresponding nodes are in g2, however the edge is removed.
		else:
			n_er += 1
	n_ei = nx.number_of_edges(g2) - n_es
		
	return n_vi, n_vr, sod_vs, n_ei, n_er, sod_es


def ged_options_to_string(options):
	opt_str = ' '
	for key, val in options.items():
		if key == 'initialization_method':
			opt_str += '--initialization-method ' + str(val) + ' '
		elif key == 'initialization_options':
			opt_str += '--initialization-options ' + str(val) + ' '
		elif key == 'lower_bound_method':
			opt_str += '--lower-bound-method ' + str(val) + ' '
		elif key == 'random_substitution_ratio':
			opt_str += '--random-substitution-ratio ' + str(val) + ' '
		elif key == 'initial_solutions':
 			opt_str += '--initial-solutions ' + str(val) + ' '
		elif key == 'ratio_runs_from_initial_solutions':
 			opt_str += '--ratio-runs-from-initial-solutions ' + str(val) + ' '
		elif key == 'threads':
			opt_str += '--threads ' + str(val) + ' '
		elif key == 'num_randpost_loops':
			opt_str += '--num-randpost-loops ' + str(val) + ' '
		elif key == 'max_randpost_retrials':
			opt_str += '--maxrandpost-retrials ' + str(val) + ' '
		elif key == 'randpost_penalty':
			opt_str += '--randpost-penalty ' + str(val) + ' '
		elif key == 'randpost_decay':
			opt_str += '--randpost-decay ' + str(val) + ' '
		elif key == 'log':
			opt_str += '--log ' + str(val) + ' '
		elif key == 'randomness':
			opt_str += '--randomness ' + str(val) + ' '
			
# 		if not isinstance(val, list):
# 			opt_str += '--' + key.replace('_', '-') + ' '
# 			if val == False:
# 	 			val_str = 'FALSE'
# 			else:
# 	 			val_str = str(val)
# 			opt_str += val_str + ' '

	return opt_str