New translations graphfiles.py (French)

lang/fr/gklearn/utils/graphfiles.py

@@ -0,0 +1,762 @@
+""" Utilities function to manage graph files
+"""
+from os.path import dirname, splitext
+
+def loadCT(filename):
+	"""load data from a Chemical Table (.ct) file.
+
+	Notes
+	------
+	a typical example of data in .ct is like this:
+
+	3 2  <- number of nodes and edges
+
+	0.0000	0.0000	0.0000 C <- each line describes a node (x,y,z + label)
+
+	0.0000	0.0000	0.0000 C
+
+	0.0000	0.0000	0.0000 O
+
+	1  3  1  1 <- each line describes an edge : to, from, bond type, bond stereo
+
+	2  3  1  1
+	  
+	Check `CTFile Formats file <https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&ved=2ahUKEwivhaSdjsTlAhVhx4UKHczHA8gQFjAJegQIARAC&url=https%3A%2F%2Fwww.daylight.com%2Fmeetings%2Fmug05%2FKappler%2Fctfile.pdf&usg=AOvVaw1cDNrrmMClkFPqodlF2inS>`__
+	for detailed format discription.
+	"""
+	import networkx as nx
+	from os.path import basename
+	g = nx.Graph()
+	with open(filename) as f:
+		content = f.read().splitlines()
+		g = nx.Graph(
+			name = str(content[0]),
+			filename = basename(filename))  # set name of the graph
+		tmp = content[1].split(" ")
+		if tmp[0] == '':
+			nb_nodes = int(tmp[1])  # number of the nodes
+			nb_edges = int(tmp[2])  # number of the edges
+		else:
+			nb_nodes = int(tmp[0])
+			nb_edges = int(tmp[1])
+			# patch for compatibility : label will be removed later
+		for i in range(0, nb_nodes):
+			tmp = content[i + 2].split(" ")
+			tmp = [x for x in tmp if x != '']
+			g.add_node(i, atom=tmp[3].strip(), 
+					   label=[item.strip() for item in tmp[3:]], 
+					   attributes=[item.strip() for item in tmp[0:3]])
+		for i in range(0, nb_edges):
+			tmp = content[i + g.number_of_nodes() + 2].split(" ")
+			tmp = [x for x in tmp if x != '']
+			g.add_edge(int(tmp[0]) - 1, int(tmp[1]) - 1,
+					   bond_type=tmp[2].strip(),
+					   label=[item.strip() for item in tmp[2:]])
+	return g
+
+
+def loadGXL(filename):
+	from os.path import basename
+	import networkx as nx
+	import xml.etree.ElementTree as ET
+
+	tree = ET.parse(filename)
+	root = tree.getroot()
+	index = 0
+	g = nx.Graph(filename=basename(filename), name=root[0].attrib['id'])
+	dic = {}  # used to retrieve incident nodes of edges
+	for node in root.iter('node'):
+		dic[node.attrib['id']] = index
+		labels = {}
+		for attr in node.iter('attr'):
+			labels[attr.attrib['name']] = attr[0].text
+		if 'chem' in labels:
+			labels['label'] = labels['chem']
+			labels['atom'] = labels['chem']
+		g.add_node(index, **labels)
+		index += 1
+
+	for edge in root.iter('edge'):
+		labels = {}
+		for attr in edge.iter('attr'):
+			labels[attr.attrib['name']] = attr[0].text
+		if 'valence' in labels:
+			labels['label'] = labels['valence']
+			labels['bond_type'] = labels['valence']
+		g.add_edge(dic[edge.attrib['from']], dic[edge.attrib['to']], **labels)
+	return g
+
+
+def saveGXL(graph, filename, method='default', node_labels=[], edge_labels=[], node_attrs=[], edge_attrs=[]):
+	if method == 'default':
+		gxl_file = open(filename, 'w')
+		gxl_file.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
+		gxl_file.write("<!DOCTYPE gxl SYSTEM \"http://www.gupro.de/GXL/gxl-1.0.dtd\">\n")
+		gxl_file.write("<gxl xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n")
+		if 'name' in graph.graph:
+			name = str(graph.graph['name'])
+		else:
+			name = 'dummy'
+		gxl_file.write("<graph id=\"" + name + "\" edgeids=\"false\" edgemode=\"undirected\">\n")
+		for v, attrs in graph.nodes(data=True):
+			gxl_file.write("<node id=\"_" + str(v) + "\">")
+			for l_name in node_labels:	
+				gxl_file.write("<attr name=\"" + l_name + "\"><int>" + 
+							   str(attrs[l_name]) + "</int></attr>")
+			for a_name in node_attrs:	
+				gxl_file.write("<attr name=\"" + a_name + "\"><float>" + 
+							   str(attrs[a_name]) + "</float></attr>")
+			gxl_file.write("</node>\n")
+		for v1, v2, attrs in graph.edges(data=True):
+			gxl_file.write("<edge from=\"_" + str(v1) + "\" to=\"_" + str(v2) + "\">")
+			for l_name in edge_labels:	
+				gxl_file.write("<attr name=\"" + l_name + "\"><int>" + 
+							   str(attrs[l_name]) + "</int></attr>")
+			for a_name in edge_attrs:	
+				gxl_file.write("<attr name=\"" + a_name + "\"><float>" + 
+							   str(attrs[a_name]) + "</float></attr>")
+			gxl_file.write("</edge>\n")
+		gxl_file.write("</graph>\n")
+		gxl_file.write("</gxl>")
+		gxl_file.close()
+	elif method == 'benoit':
+		import xml.etree.ElementTree as ET
+		root_node = ET.Element('gxl')
+		attr = dict()
+		attr['id'] = str(graph.graph['name'])
+		attr['edgeids'] = 'true'
+		attr['edgemode'] = 'undirected'
+		graph_node = ET.SubElement(root_node, 'graph', attrib=attr)
+	
+		for v in graph:
+			current_node = ET.SubElement(graph_node, 'node', attrib={'id': str(v)})
+			for attr in graph.nodes[v].keys():
+				cur_attr = ET.SubElement(
+					current_node, 'attr', attrib={'name': attr})
+				cur_value = ET.SubElement(cur_attr,
+										  graph.nodes[v][attr].__class__.__name__)
+				cur_value.text = graph.nodes[v][attr]
+	
+		for v1 in graph:
+			for v2 in graph[v1]:
+				if (v1 < v2):  # Non oriented graphs
+					cur_edge = ET.SubElement(
+						graph_node,
+						'edge',
+						attrib={
+							'from': str(v1),
+							'to': str(v2)
+						})
+					for attr in graph[v1][v2].keys():
+						cur_attr = ET.SubElement(
+							cur_edge, 'attr', attrib={'name': attr})
+						cur_value = ET.SubElement(
+							cur_attr, graph[v1][v2][attr].__class__.__name__)
+						cur_value.text = str(graph[v1][v2][attr])
+	
+		tree = ET.ElementTree(root_node)
+		tree.write(filename)
+	elif method == 'gedlib':
+		# reference: https://github.com/dbblumenthal/gedlib/blob/master/data/generate_molecules.py#L22
+#		pass
+		gxl_file = open(filename, 'w')
+		gxl_file.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
+		gxl_file.write("<!DOCTYPE gxl SYSTEM \"http://www.gupro.de/GXL/gxl-1.0.dtd\">\n")
+		gxl_file.write("<gxl xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n")
+		gxl_file.write("<graph id=\"" + str(graph.graph['name']) + "\" edgeids=\"true\" edgemode=\"undirected\">\n")
+		for v, attrs in graph.nodes(data=True):
+			gxl_file.write("<node id=\"_" + str(v) + "\">")
+			gxl_file.write("<attr name=\"" + "chem" + "\"><int>" + str(attrs['chem']) + "</int></attr>")
+			gxl_file.write("</node>\n")
+		for v1, v2, attrs in graph.edges(data=True):
+			gxl_file.write("<edge from=\"_" + str(v1) + "\" to=\"_" + str(v2) + "\">")
+			gxl_file.write("<attr name=\"valence\"><int>" + str(attrs['valence']) + "</int></attr>")
+#			gxl_file.write("<attr name=\"valence\"><int>" + "1" + "</int></attr>")
+			gxl_file.write("</edge>\n")
+		gxl_file.write("</graph>\n")
+		gxl_file.write("</gxl>")
+		gxl_file.close()
+	elif method == 'gedlib-letter':
+		# reference: https://github.com/dbblumenthal/gedlib/blob/master/data/generate_molecules.py#L22
+		# and https://github.com/dbblumenthal/gedlib/blob/master/data/datasets/Letter/HIGH/AP1_0000.gxl
+		gxl_file = open(filename, 'w')
+		gxl_file.write("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n")
+		gxl_file.write("<!DOCTYPE gxl SYSTEM \"http://www.gupro.de/GXL/gxl-1.0.dtd\">\n")
+		gxl_file.write("<gxl xmlns:xlink=\"http://www.w3.org/1999/xlink\">\n")
+		gxl_file.write("<graph id=\"" + str(graph.graph['name']) + "\" edgeids=\"false\" edgemode=\"undirected\">\n")
+		for v, attrs in graph.nodes(data=True):
+			gxl_file.write("<node id=\"_" + str(v) + "\">")
+			gxl_file.write("<attr name=\"x\"><float>" + str(attrs['attributes'][0]) + "</float></attr>")
+			gxl_file.write("<attr name=\"y\"><float>" + str(attrs['attributes'][1]) + "</float></attr>")
+			gxl_file.write("</node>\n")
+		for v1, v2, attrs in graph.edges(data=True):
+			gxl_file.write("<edge from=\"_" + str(v1) + "\" to=\"_" + str(v2) + "\"/>\n")
+		gxl_file.write("</graph>\n")
+		gxl_file.write("</gxl>")
+		gxl_file.close()
+
+
+def loadSDF(filename):
+	"""load data from structured data file (.sdf file).
+
+	Notes
+	------
+	A SDF file contains a group of molecules, represented in the similar way as in MOL format.
+	Check `here <http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx>`__ for detailed structure.
+	"""
+	import networkx as nx
+	from os.path import basename
+	from tqdm import tqdm
+	import sys
+	data = []
+	with open(filename) as f:
+		content = f.read().splitlines()
+		index = 0
+		pbar = tqdm(total=len(content) + 1, desc='load SDF', file=sys.stdout)
+		while index < len(content):
+			index_old = index
+
+			g = nx.Graph(name=content[index].strip())  # set name of the graph
+
+			tmp = content[index + 3]
+			nb_nodes = int(tmp[:3])  # number of the nodes
+			nb_edges = int(tmp[3:6])  # number of the edges
+
+			for i in range(0, nb_nodes):
+				tmp = content[i + index + 4]
+				g.add_node(i, atom=tmp[31:34].strip())
+
+			for i in range(0, nb_edges):
+				tmp = content[i + index + g.number_of_nodes() + 4]
+				tmp = [tmp[i:i + 3] for i in range(0, len(tmp), 3)]
+				g.add_edge(
+					int(tmp[0]) - 1, int(tmp[1]) - 1, bond_type=tmp[2].strip())
+
+			data.append(g)
+
+			index += 4 + g.number_of_nodes() + g.number_of_edges()
+			while content[index].strip() != '$$$$':  # seperator
+				index += 1
+			index += 1
+
+			pbar.update(index - index_old)
+		pbar.update(1)
+		pbar.close()
+
+	return data
+
+
+def loadMAT(filename, extra_params):
+	"""Load graph data from a MATLAB (up to version 7.1) .mat file.
+
+	Notes
+	------
+	A MAT file contains a struct array containing graphs, and a column vector lx containing a class label for each graph.
+	Check README in `downloadable file <http://mlcb.is.tuebingen.mpg.de/Mitarbeiter/Nino/WL/>`__ for detailed structure.
+	"""
+	from scipy.io import loadmat
+	import numpy as np
+	import networkx as nx
+	data = []
+	content = loadmat(filename)
+	order = extra_params['am_sp_al_nl_el']
+	# print(content)
+	# print('----')
+	for key, value in content.items():
+		if key[0] == 'l':  # class label
+			y = np.transpose(value)[0].tolist()
+			# print(y)
+		elif key[0] != '_':
+			# print(value[0][0][0])
+			# print()
+			# print(value[0][0][1])
+			# print()
+			# print(value[0][0][2])
+			# print()
+			# if len(value[0][0]) > 3:
+			#	 print(value[0][0][3])
+			# print('----')
+			# if adjacency matrix is not compressed / edge label exists
+			if order[1] == 0:
+				for i, item in enumerate(value[0]):
+					# print(item)
+					# print('------')
+					g = nx.Graph(name=i)  # set name of the graph
+					nl = np.transpose(item[order[3]][0][0][0])  # node label
+					# print(item[order[3]])
+					# print()
+					for index, label in enumerate(nl[0]):
+						g.add_node(index, atom=str(label))
+					el = item[order[4]][0][0][0]  # edge label
+					for edge in el:
+						g.add_edge(
+							edge[0] - 1, edge[1] - 1, bond_type=str(edge[2]))
+					data.append(g)
+			else:
+				from scipy.sparse import csc_matrix
+				for i, item in enumerate(value[0]):
+					# print(item)
+					# print('------')
+					g = nx.Graph(name=i)  # set name of the graph
+					nl = np.transpose(item[order[3]][0][0][0])  # node label
+					# print(nl)
+					# print()
+					for index, label in enumerate(nl[0]):
+						g.add_node(index, atom=str(label))
+					sam = item[order[0]]  # sparse adjacency matrix
+					index_no0 = sam.nonzero()
+					for col, row in zip(index_no0[0], index_no0[1]):
+						# print(col)
+						# print(row)
+						g.add_edge(col, row)
+					data.append(g)
+					# print(g.edges(data=True))
+	return data, y
+
+
+def loadTXT(filename):
+	"""Load graph data from a .txt file.
+
+	Notes
+	------
+	The graph data is loaded from separate files.
+	Check README in `downloadable file <http://tiny.cc/PK_MLJ_data>`__, 2018 for detailed structure.
+	"""
+#	import numpy as np
+	import networkx as nx
+	from os import listdir
+	from os.path import dirname, basename
+	
+	
+	def get_label_names(frm):
+		"""Get label names from DS_label_readme.txt file.
+		"""
+		
+		def get_names_from_line(line):
+			"""Get names of labels/attributes from a line.
+			"""
+			str_names = line.split('[')[1].split(']')[0]
+			names = str_names.split(',')
+			names = [attr.strip() for attr in names]
+			return names
+
+
+		label_names = {'node_labels': [], 'node_attrs': [], 
+					   'edge_labels': [], 'edge_attrs': []}
+		content_rm = open(frm).read().splitlines()
+		for line in content_rm:
+			line = line.strip()
+			if line.startswith('Node labels:'):
+				label_names['node_labels'] = get_names_from_line(line)
+			elif line.startswith('Node attributes:'):
+				label_names['node_attrs'] = get_names_from_line(line)
+			elif line.startswith('Edge labels:'):
+				label_names['edge_labels'] = get_names_from_line(line)
+			elif line.startswith('Edge attributes:'):
+				label_names['edge_attrs'] = get_names_from_line(line)
+		return label_names
+
+	
+	# get dataset name.
+	dirname_dataset = dirname(filename)
+	filename = basename(filename)
+	fn_split = filename.split('_A')
+	ds_name = fn_split[0].strip()
+	
+	# load data file names
+	for name in listdir(dirname_dataset):
+		if ds_name + '_A' in name:
+			fam = dirname_dataset + '/' + name
+		elif ds_name + '_graph_indicator' in name:
+			fgi = dirname_dataset + '/' + name
+		elif ds_name + '_graph_labels' in name:
+			fgl = dirname_dataset + '/' + name
+		elif ds_name + '_node_labels' in name:
+			fnl = dirname_dataset + '/' + name
+		elif ds_name + '_edge_labels' in name:
+			fel = dirname_dataset + '/' + name
+		elif ds_name + '_edge_attributes' in name:
+			fea = dirname_dataset + '/' + name
+		elif ds_name + '_node_attributes' in name:
+			fna = dirname_dataset + '/' + name
+		elif ds_name + '_graph_attributes' in name:
+			fga = dirname_dataset + '/' + name
+		elif ds_name + '_label_readme' in name:
+			frm = dirname_dataset + '/' + name
+		# this is supposed to be the node attrs, make sure to put this as the last 'elif'
+		elif ds_name + '_attributes' in name:
+			fna = dirname_dataset + '/' + name
+			
+	# get labels and attributes names.
+	if 'frm' in locals():
+		label_names = get_label_names(frm)
+	else:
+		label_names = {'node_labels': [], 'node_attrs': [], 
+					   'edge_labels': [], 'edge_attrs': []}
+
+	content_gi = open(fgi).read().splitlines()  # graph indicator
+	content_am = open(fam).read().splitlines()  # adjacency matrix
+	content_gl = open(fgl).read().splitlines()  # graph labels
+
+	# create graphs and add nodes
+	data = [nx.Graph(name=str(i), 
+					 node_labels=label_names['node_labels'],
+					 node_attrs=label_names['node_attrs'],
+					 edge_labels=label_names['edge_labels'],
+					 edge_attrs=label_names['edge_attrs']) for i in range(0, len(content_gl))]
+	if 'fnl' in locals():
+		content_nl = open(fnl).read().splitlines()  # node labels
+		for idx, line in enumerate(content_gi):
+			# transfer to int first in case of unexpected blanks
+			data[int(line) - 1].add_node(idx)
+			labels = [l.strip() for l in content_nl[idx].split(',')]
+			data[int(line) - 1].nodes[idx]['atom'] = str(int(labels[0])) # @todo: this should be removed after.
+			if data[int(line) - 1].graph['node_labels'] == []:
+				for i, label in enumerate(labels):
+					l_name = 'label_' + str(i)
+					data[int(line) - 1].nodes[idx][l_name] = label
+					data[int(line) - 1].graph['node_labels'].append(l_name)
+			else:
+				for i, l_name in enumerate(data[int(line) - 1].graph['node_labels']):
+					data[int(line) - 1].nodes[idx][l_name] = labels[i]
+	else:
+		for i, line in enumerate(content_gi):
+			data[int(line) - 1].add_node(i)
+			
+	# add edges
+	for line in content_am:
+		tmp = line.split(',')
+		n1 = int(tmp[0]) - 1
+		n2 = int(tmp[1]) - 1
+		# ignore edge weight here.
+		g = int(content_gi[n1]) - 1
+		data[g].add_edge(n1, n2)
+
+	# add edge labels
+	if 'fel' in locals():
+		content_el = open(fel).read().splitlines()
+		for idx, line in enumerate(content_el):
+			labels = [l.strip() for l in line.split(',')]
+			n = [int(i) - 1 for i in content_am[idx].split(',')]
+			g = int(content_gi[n[0]]) - 1
+			data[g].edges[n[0], n[1]]['bond_type'] = labels[0] # @todo: this should be removed after.
+			if data[g].graph['edge_labels'] == []:
+				for i, label in enumerate(labels):
+					l_name = 'label_' + str(i)
+					data[g].edges[n[0], n[1]][l_name] = label
+					data[g].graph['edge_labels'].append(l_name)
+			else:
+				for i, l_name in enumerate(data[g].graph['edge_labels']):
+					data[g].edges[n[0], n[1]][l_name] = labels[i]
+
+	# add node attributes
+	if 'fna' in locals():
+		content_na = open(fna).read().splitlines()
+		for idx, line in enumerate(content_na):
+			attrs = [a.strip() for a in line.split(',')]
+			g = int(content_gi[idx]) - 1
+			data[g].nodes[idx]['attributes'] = attrs # @todo: this should be removed after.
+			if data[g].graph['node_attrs'] == []:
+				for i, attr in enumerate(attrs):
+					a_name = 'attr_' + str(i)
+					data[g].nodes[idx][a_name] = attr
+					data[g].graph['node_attrs'].append(a_name)
+			else:
+				for i, a_name in enumerate(data[g].graph['node_attrs']):
+					data[g].nodes[idx][a_name] = attrs[i]
+
+	# add edge attributes
+	if 'fea' in locals():
+		content_ea = open(fea).read().splitlines()
+		for idx, line in enumerate(content_ea):
+			attrs = [a.strip() for a in line.split(',')]
+			n = [int(i) - 1 for i in content_am[idx].split(',')]
+			g = int(content_gi[n[0]]) - 1
+			data[g].edges[n[0], n[1]]['attributes'] = attrs # @todo: this should be removed after.
+			if data[g].graph['edge_attrs'] == []:
+				for i, attr in enumerate(attrs):
+					a_name = 'attr_' + str(i)
+					data[g].edges[n[0], n[1]][a_name] = attr
+					data[g].graph['edge_attrs'].append(a_name)
+			else:
+				for i, a_name in enumerate(data[g].graph['edge_attrs']):
+					data[g].edges[n[0], n[1]][a_name] = attrs[i]
+
+	# load y
+	y = [int(i) for i in content_gl]
+
+	return data, y
+
+
+def loadDataset(filename, filename_y=None, extra_params=None):
+	"""Read graph data from filename and load them as NetworkX graphs.
+
+	Parameters
+	----------
+	filename : string
+		The name of the file from where the dataset is read.
+	filename_y : string
+		The name of file of the targets corresponding to graphs.
+	extra_params : dict
+		Extra parameters only designated to '.mat' format.
+
+	Return
+	------
+	data : List of NetworkX graph.
+
+	y : List
+
+	Targets corresponding to graphs.
+		
+	Notes
+	-----
+	This function supports following graph dataset formats:
+
+	'ds': load data from .ds file. See comments of function loadFromDS for a example.
+
+	'cxl': load data from Graph eXchange Language file (.cxl file). See 
+	`here <http://www.gupro.de/GXL/Introduction/background.html>`__ for detail.
+
+	'sdf': load data from structured data file (.sdf file). See 
+	`here <http://www.nonlinear.com/progenesis/sdf-studio/v0.9/faq/sdf-file-format-guidance.aspx>`__
+	for details.
+
+	'mat': Load graph data from a MATLAB (up to version 7.1) .mat file. See
+	README in `downloadable file <http://mlcb.is.tuebingen.mpg.de/Mitarbeiter/Nino/WL/>`__
+	for details.
+
+	'txt': Load graph data from a special .txt file. See
+	`here <https://ls11-www.cs.tu-dortmund.de/staff/morris/graphkerneldatasets>`__
+	for details. Note here filename is the name of either .txt file in
+	the dataset directory.
+	"""
+	extension = splitext(filename)[1][1:]
+	if extension == "ds":
+		data, y = loadFromDS(filename, filename_y)
+	elif extension == "cxl":
+		import xml.etree.ElementTree as ET
+		
+		dirname_dataset = dirname(filename)
+		tree = ET.parse(filename)
+		root = tree.getroot()
+		data = []
+		y = []
+		for graph in root.iter('graph'):
+			mol_filename = graph.attrib['file']
+			mol_class = graph.attrib['class']
+			data.append(loadGXL(dirname_dataset + '/' + mol_filename))
+			y.append(mol_class)
+	elif extension == 'xml':
+		data, y = loadFromXML(filename, extra_params)
+	elif extension == "sdf":
+#		import numpy as np
+		from tqdm import tqdm
+		import sys
+
+		data = loadSDF(filename)
+
+		y_raw = open(filename_y).read().splitlines()
+		y_raw.pop(0)
+		tmp0 = []
+		tmp1 = []
+		for i in range(0, len(y_raw)):
+			tmp = y_raw[i].split(',')
+			tmp0.append(tmp[0])
+			tmp1.append(tmp[1].strip())
+
+		y = []
+		for i in tqdm(range(0, len(data)), desc='ajust data', file=sys.stdout):
+			try:
+				y.append(tmp1[tmp0.index(data[i].name)].strip())
+			except ValueError:  # if data[i].name not in tmp0
+				data[i] = []
+		data = list(filter(lambda a: a != [], data))
+	elif extension == "mat":
+		data, y = loadMAT(filename, extra_params)
+	elif extension == 'txt':
+		data, y = loadTXT(filename)
+		# print(len(y))
+		# print(y)
+		# print(data[0].nodes(data=True))
+		# print('----')
+		# print(data[0].edges(data=True))
+		# for g in data:
+		#	 print(g.nodes(data=True))
+		#	 print('----')
+		#	 print(g.edges(data=True))
+
+	return data, y
+
+
+def loadFromXML(filename, extra_params):
+	import xml.etree.ElementTree as ET
+	
+	if extra_params:
+		dirname_dataset = extra_params
+	else:
+		dirname_dataset = dirname(filename)
+	tree = ET.parse(filename)
+	root = tree.getroot()
+	data = []
+	y = []
+	for graph in root.iter('graph'):
+		mol_filename = graph.attrib['file']
+		mol_class = graph.attrib['class']
+		data.append(loadGXL(dirname_dataset + '/' + mol_filename))
+		y.append(mol_class)
+		
+	return data, y
+			
+
+def loadFromDS(filename, filename_y):
+	"""Load data from .ds file.
+
+	Possible graph formats include:
+
+	'.ct': see function loadCT for detail.
+
+	'.gxl': see dunction loadGXL for detail.
+
+	Note these graph formats are checked automatically by the extensions of 
+	graph files.
+	"""
+	dirname_dataset = dirname(filename)
+	data = []
+	y = []
+	content = open(filename).read().splitlines()
+	extension = splitext(content[0].split(' ')[0])[1][1:]
+	if filename_y is None or filename_y == '':
+		if extension == 'ct': 
+			for i in range(0, len(content)):
+				tmp = content[i].split(' ')
+				# remove the '#'s in file names
+				data.append(
+					loadCT(dirname_dataset + '/' + tmp[0].replace('#', '', 1)))
+				y.append(float(tmp[1]))
+		elif extension == 'gxl':
+			for i in range(0, len(content)):
+				tmp = content[i].split(' ')
+				# remove the '#'s in file names
+				data.append(
+					loadGXL(dirname_dataset + '/' + tmp[0].replace('#', '', 1)))
+				y.append(float(tmp[1]))
+	else:  # y in a seperate file
+		if extension == 'ct':
+			for i in range(0, len(content)):
+				tmp = content[i]
+				# remove the '#'s in file names
+				data.append(
+					loadCT(dirname_dataset + '/' + tmp.replace('#', '', 1)))
+		elif extension == 'gxl':
+			for i in range(0, len(content)):
+				tmp = content[i]
+				# remove the '#'s in file names
+				data.append(
+					loadGXL(dirname_dataset + '/' + tmp.replace('#', '', 1)))													   
+															   
+		content_y = open(filename_y).read().splitlines()
+		# assume entries in filename and filename_y have the same order.
+		for item in content_y:
+			tmp = item.split(' ')
+			# assume the 3rd entry in a line is y (for Alkane dataset)
+			y.append(float(tmp[2]))
+			
+	return data, y
+				
+
+def saveDataset(Gn, y, gformat='gxl', group=None, filename='gfile', xparams=None):
+	"""Save list of graphs.
+	"""
+	import os
+	dirname_ds = os.path.dirname(filename)
+	if dirname_ds != '':
+		dirname_ds += '/'
+		if not os.path.exists(dirname_ds) :
+			os.makedirs(dirname_ds)
+				
+	if xparams is not None and 'graph_dir' in xparams:
+		graph_dir = xparams['graph_dir'] + '/'
+		if not os.path.exists(graph_dir):
+			os.makedirs(graph_dir)
+	else:
+		graph_dir = dirname_ds 
+			
+	if group == 'xml' and gformat == 'gxl':
+		kwargs = {'method': xparams['method']} if xparams is not None else {}
+		with open(filename + '.xml', 'w') as fgroup:
+			fgroup.write("<?xml version=\"1.0\"?>")
+			fgroup.write("\n<!DOCTYPE GraphCollection SYSTEM \"http://www.inf.unibz.it/~blumenthal/dtd/GraphCollection.dtd\">")
+			fgroup.write("\n<GraphCollection>")
+			for idx, g in enumerate(Gn):
+				fname_tmp = "graph" + str(idx) + ".gxl"
+				saveGXL(g, graph_dir + fname_tmp, **kwargs)
+				fgroup.write("\n\t<graph file=\"" + fname_tmp + "\" class=\"" + str(y[idx]) + "\"/>")
+			fgroup.write("\n</GraphCollection>")
+			fgroup.close()
+			
+			
+if __name__ == '__main__':	
+#	### Load dataset from .ds file.
+#	# .ct files.
+#	ds = {'name': 'Alkane', 'dataset': '../../datasets/Alkane/dataset.ds',
+#		'dataset_y': '../../datasets/Alkane/dataset_boiling_point_names.txt'}
+#	Gn, y = loadDataset(ds['dataset'], filename_y=ds['dataset_y'])
+##	ds = {'name': 'Acyclic', 'dataset': '../../datasets/acyclic/dataset_bps.ds'}  # node symb
+##	Gn, y = loadDataset(ds['dataset'])
+##	ds = {'name': 'MAO', 'dataset': '../../datasets/MAO/dataset.ds'} # node/edge symb
+##	Gn, y = loadDataset(ds['dataset'])
+##	ds = {'name': 'PAH', 'dataset': '../../datasets/PAH/dataset.ds'} # unlabeled
+##	Gn, y = loadDataset(ds['dataset'])
+#	print(Gn[1].nodes(data=True))
+#	print(Gn[1].edges(data=True))
+#	print(y[1])
+	
+#	# .gxl file.
+#	ds = {'name': 'monoterpenoides', 
+#		  'dataset': '../../datasets/monoterpenoides/dataset_10+.ds'}  # node/edge symb
+#	Gn, y = loadDataset(ds['dataset'])
+#	print(Gn[1].nodes(data=True))
+#	print(Gn[1].edges(data=True))
+#	print(y[1])
+	
+#	### Convert graph from one format to another.
+#	# .gxl file.
+#	import networkx as nx
+#	ds = {'name': 'monoterpenoides', 
+#		  'dataset': '../../datasets/monoterpenoides/dataset_10+.ds'}  # node/edge symb
+#	Gn, y = loadDataset(ds['dataset'])
+#	y = [int(i) for i in y]
+#	print(Gn[1].nodes(data=True))
+#	print(Gn[1].edges(data=True))
+#	print(y[1])
+#	# Convert a graph to the proper NetworkX format that can be recognized by library gedlib.
+#	Gn_new = []
+#	for G in Gn:
+#		G_new = nx.Graph()
+#		for nd, attrs in G.nodes(data=True):
+#			G_new.add_node(str(nd), chem=attrs['atom'])
+#		for nd1, nd2, attrs in G.edges(data=True):
+#			G_new.add_edge(str(nd1), str(nd2), valence=attrs['bond_type'])
+##			G_new.add_edge(str(nd1), str(nd2))
+#		Gn_new.append(G_new)
+#	print(Gn_new[1].nodes(data=True))
+#	print(Gn_new[1].edges(data=True))
+#	print(Gn_new[1])
+#	filename = '/media/ljia/DATA/research-repo/codes/others/gedlib/tests_linlin/generated_datsets/monoterpenoides/gxl/monoterpenoides'
+#	xparams = {'method': 'gedlib'}
+#	saveDataset(Gn, y, gformat='gxl', group='xml', filename=filename, xparams=xparams)
+	
+	# save dataset.
+#	ds = {'name': 'MUTAG', 'dataset': '../../datasets/MUTAG/MUTAG.mat',
+#		  'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}  # node/edge symb
+#	Gn, y = loadDataset(ds['dataset'], extra_params=ds['extra_params'])
+#	saveDataset(Gn, y, group='xml', filename='temp/temp')
+	
+	# test - new way to add labels and attributes.
+#	dataset = '../../datasets/SYNTHETICnew/SYNTHETICnew_A.txt'
+#	dataset = '../../datasets/Fingerprint/Fingerprint_A.txt'
+#	dataset = '../../datasets/Letter-med/Letter-med_A.txt'
+#	dataset = '../../datasets/AIDS/AIDS_A.txt'
+#	dataset = '../../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'
+#	Gn, y_all = loadDataset(dataset)
+	pass