def save_celltype_graph(self, filename='celltype_conn.gml', format='gml'):
"""
Save the celltype-to-celltype connectivity information in a file.
filename -- path of the file to be saved.
format -- format to save in. Using GML as GraphML support is
not complete in NetworkX.
"""
start = datetime.now()
if format == 'gml':
nx.write_gml(self.__celltype_graph, filename)
elif format == 'yaml':
nx.write_yaml(self.__celltype_graph, filename)
elif format == 'graphml':
nx.write_graphml(self.__celltype_graph, filename)
elif format == 'edgelist':
nx.write_edgelist(self.__celltype_graph, filename)
elif format == 'pickle':
nx.write_gpickle(self.__celltype_graph, filename)
else:
raise Exception(
'Supported formats: gml, graphml, yaml. Received: %s' %
(format))
end = datetime.now()
delta = end - start
config.BENCHMARK_LOGGER.info(
'Saved celltype_graph in file %s of format %s in %g s' %
(filename, format, delta.seconds + delta.microseconds * 1e-6))
print 'Saved celltype connectivity graph in', filename
def save_celltype_graph(self, filename="celltype_conn.gml", format="gml"):
"""
Save the celltype-to-celltype connectivity information in a file.
filename -- path of the file to be saved.
format -- format to save in. Using GML as GraphML support is
not complete in NetworkX.
"""
start = datetime.now()
if format == "gml":
nx.write_gml(self.__celltype_graph, filename)
elif format == "yaml":
nx.write_yaml(self.__celltype_graph, filename)
elif format == "graphml":
nx.write_graphml(self.__celltype_graph, filename)
elif format == "edgelist":
nx.write_edgelist(self.__celltype_graph, filename)
elif format == "pickle":
nx.write_gpickle(self.__celltype_graph, filename)
else:
raise Exception("Supported formats: gml, graphml, yaml. Received: %s" % (format))
end = datetime.now()
delta = end - start
config.BENCHMARK_LOGGER.info(
"Saved celltype_graph in file %s of format %s in %g s"
% (filename, format, delta.seconds + delta.microseconds * 1e-6)
)
print "Saved celltype connectivity graph in", filename
def __update_status(self):
#getting the proportion of non empty feature sets evaluated
self.status_=np.mean([y is not None for x,y in nx.get_node_attributes(self.G,'score').items() if x!=0])
self.leaves_={n:self.G.node[n]['score'] for n,deg in self.G.out_degree if deg==0 and self.G.node[n]['score'] is not None}
nx.write_yaml(self.G,self.file)
#self.verboseprint('Crawler status: progress: {0.status_}, leaves: {0.leaves_}.'.format(self))
return self
def write_graph(graph, filename, file_type=None):
if not file_type:
file_type = get_graph_type(filename)
if not file_type:
raise RuntimeError("Unable to determine graph file type.")
if file_type == "adjlist":
networkx.write_adjlist(graph, filename)
elif file_type == "edgelist":
networkx.write_edgelist(graph, filename)
elif file_type == "gexf":
networkx.write_gexf(graph, filename)
elif file_type == "gml":
networkx.write_gml(graph, filename)
elif file_type == "gpickle":
networkx.write_gpickle(graph, filename)
elif file_type == "graphml":
networkx.write_graphml(graph, filename)
elif file_type == "yaml":
networkx.write_yaml(graph, filename)
elif file_type == "pajek" or file_type == "net":
networkx.write_pajek(graph, filename)
elif file_type == "adjmat":
#sparse_matrix = networkx.adjacency_matrix(graph)
#dense_matrix = sparse_matrix.todense()
#dense_matrix.tofile(filename, sep=",", format="%g")
matrix = networkx.to_numpy_matrix(graph)
numpy.savetxt(filename, matrix, delimiter=",", newline="\n", fmt="%g")
else:
raise RuntimeError("Unrecognized output graph file type.")
def main(inname='submission.yaml'):
try:
submission = nx.read_yaml(inname)
except ScannerError as se:
print(
'Unable to read file: {} Please ensure file has properly formatted YAML.'
.format(inname))
print(se)
sys.exit(125)
# No submission, case of an update to deprecated IDs
if submission is None:
indications = nx.read_yaml('indication_paths.yaml')
indications = filter_deprecated_ids(indications)
nx.write_yaml(indications, 'indication_paths.yaml', indent=4)
print('Paths writen successfully with deprecated IDs removed')
sys.exit(0)
# Prep the submission fixing simple common errors and throwing excptions when not simple fixes
submission = test_and_fix(submission)
# Determine if Update or new submission
has_identifier = ['_id' in rec['graph'].keys() for rec in submission]
if all(has_identifier):
update_existing_records(submission)
elif any(has_identifier):
print('Mixed submissions and updates are not allowed. Please ensure that either all records ' +\
'contain an `_id` feild in the `graph` feild if updating, or none contain the `_id` ' +\
'field if submitting new records')
sys.exit(400)
else:
add_new_submission(submission)
def export_graph(graph, directory):
# write to GraphML file
nx.write_graphml(graph, directory + "/" + prefix + ".graphml")
# write to Yaml file
nx.write_yaml(graph, directory + "/" + prefix + ".yaml")
# write to Gexf file
nx.write_gexf(graph, directory + "/" + prefix + ".gexf")
# write to JSON file
json.dump(json_graph.node_link_data(graph),
open(directory + "/" + prefix + ".json", 'w'),
indent=2)
# write to CSV files
with open(directory + "/" + prefix + '_pages.csv', 'w') as csv_file:
writer = csv.writer(csv_file)
writer.writerow([
'id', 'label', 'title', 'url', 'hub', 'authority', 'pagerank',
'in_degree', 'out_degree', 'closeness', 'betweenness'
])
for node, data in graph.nodes(data=True):
writer.writerow([
node, data['label'], data['title'], data['url'], data['hub'],
data['authority'], data['pagerank'], data['in_degree'],
data['out_degree'], data['closeness'], data['betweenness']
])
with open(directory + "/" + prefix + '_pages_links.csv', 'w') as csv_file:
writer = csv.writer(csv_file)
writer.writerow(['from', 'to'])
for f, t, a in graph.edges(data=True):
writer.writerow([f, t])
def save(G, file_name):
"""Save the graph to .yaml format
.. note::
Yaml was the only format that supported utf-8 attributes and dictionary attributes
"""
import networkx as nx
nx.write_yaml(G, file_name, encoding="utf-8")
def save(self, G, Epoch):
result_dir = './result/'
info = "{}_{}_{}_{}".format(self.network_type, self.player_type,
self.update_rule, Epoch)
Epoch_dir = os.path.join(result_dir, self.dir_str, info)
if not os.path.exists(Epoch_dir):
os.mkdir(Epoch_dir)
graph_path = os.path.join(Epoch_dir, info + "_Graph.yaml")
nx.write_yaml(G, graph_path)
def convert_graph_to_yaml(graph, filename):
"""
convert from a networkX graph object, to yaml format.
:param graph: the networkX graph object.
:param filename: the name of the file to write to.
:return:
"""
networkx.write_yaml(graph, filename)
return
def update_existing_records(submission, outname='indication_paths.yaml'):
if submission is not None:
print('Updating Indications...')
indications = nx.read_yaml('indication_paths.yaml')
current_ids = [ind['graph']['_id'] for ind in indications]
submission_prepped = {rec['graph']['_id']: rec for rec in submission}
# Make sure new recrods have unique IDs
if len(submission_prepped) != len(submission):
submitted_id_counts = Counter(
[rec['graph']['_id'] for rec in submission])
duplicated = [k for k, v in submitted_id_counts.items() if v > 1]
print(
'Error, the folling identifiers were used for multiple paths:\n{}'
.format(', '.join(duplicated)))
sys.exit(400)
# Make sure the Updated records exist
diff = set(submission_prepped.keys()) - set(current_ids)
if diff:
print(
"Error, the following path id's submitted for update do not exist:\n{}"
.format(', '.join(diff)))
sys.exit(400)
out = []
errors = []
for ind in indications:
_id = ind['graph']['_id']
if _id in submission_prepped.keys():
# Previous checks will have ensured that the `graph` data matches the `nodes` and `links` data
# To ensure that we're updating the right path we can simply check that the identifier
# is correct for the info found in `graph`
try:
validate_path_id(_id, submission_prepped[_id])
out.append(submission_prepped[_id])
except AssertionError as ae:
errors.append(ae)
else:
out.append(ind)
if errors:
print('Update Unsuccessful')
print('There were {} paths that produced errors'.format(
len(errors)))
print('Please see error messages below\n')
for error in errors:
print(error, end='\n\n')
sys.exit(400)
else:
out = filter_deprecated_ids(out)
print('Update Successful')
nx.write_yaml(out, outname, indent=4)
def convert_graph_to_yaml(graph, filename):
"""
convert from a networkX graph object, to yaml format.
:param graph: the networkX graph object.
:param filename: the name of the file to write to.
:return:
"""
networkx.write_yaml(graph, filename)
return
def write_yaml(self, yaml_file_name):
r"""Export to YAML format
Parameters
----------
yaml_file_name : str
Path to the YAML file
"""
nx.write_yaml(self, yaml_file_name)
def assert_equal(self, G, data=False):
(fd, fname) = tempfile.mkstemp()
nx.write_yaml(G, fname)
Gin = nx.read_yaml(fname)
assert_nodes_equal(list(G), list(Gin))
assert_edges_equal(G.edges(data=data), Gin.edges(data=data))
os.close(fd)
os.unlink(fname)
def assert_equal(self, G, data=False):
(fd, fname) = tempfile.mkstemp()
nx.write_yaml(G, fname)
Gin = nx.read_yaml(fname);
assert_equal(sorted(G.nodes()),sorted(Gin.nodes()))
assert_equal(G.edges(data=data),Gin.edges(data=data))
os.close(fd)
os.unlink(fname)
def main():
G = nx.Graph()
G.add_node("조준영")
G.add_node("김영진")
G.add_edge("조준영","김영진")
nx.write_yaml(G, "data.yml")
nx.draw(G)
plt.show()
def assert_equal(self, G, data=False):
(fd, fname) = tempfile.mkstemp()
nx.write_yaml(G, fname)
Gin = nx.read_yaml(fname)
assert_nodes_equal(list(G), list(Gin))
assert_edges_equal(G.edges(data=data), Gin.edges(data=data))
os.close(fd)
os.unlink(fname)
def combineAll(bucket): bucket=str(bucket) folder='/Users/Ish/Documents/OSM_Files/haiti_earthquake/networks/overlapping_changesets_by_'+bucket+'_hour/' B=nx.Graph() for file in os.listdir(folder): G=nx.read_gml(folder+file) G=nx.Graph(G) B=composeWeights(B,G) #return B nx.write_yaml(B,'../results/'+bucket+'hourBigNetwork.yaml') combineAll(8)
def prune_reconstructed_architectures(archs):
tot_archs = []
# remove the architecture doesn't make any sense
for each_arch in archs:
"""
1: Check if the narrow connection is sane
"""
if not _sane_narrow_connection( \
each_arch, '[0] Embedding', '[12] Sigmoid'): continue
# add the survived ones
tot_archs.append(each_arch)
# end for each...
# check if the store location exists
store_loc = os.path.join(_save_dir, 'architectures')
if not os.path.exists(store_loc): os.makedirs(store_loc)
# store the architecture as a graph and data
options = {
'node_color': 'red',
'node_size': 40,
'width': 1,
'alpha': 0.8,
'arrowstyle': '-|>',
'arrowsize': 8,
'font_size': 10,
}
for aidx, each_arch in enumerate(tot_archs):
# : write the edgelists to a YAML file
nx.write_yaml( \
each_arch, \
os.path.join(store_loc, 'architecture_{}.yaml'.format(aidx)))
# : relabel the node names to include the attribute parameters
new_nodes = {}
for each_node, each_data in each_arch.nodes(data=True):
each_attr = '{}'.format(each_node)
if ('attr_param' in each_data) \
and each_data['attr_param']:
each_attr += ' - {}'.format(each_data['attr_param'])
new_nodes[each_node] = each_attr
new_each_arch = nx.relabel_nodes(each_arch, new_nodes, copy=True)
# : networkx - draw the graphs
nx.draw_networkx(new_each_arch, arrows=True, **options)
plt.savefig(os.path.join(store_loc, 'architecture_{}.pdf'.format(aidx)))
plt.clf()
# end for aidx...
return tot_archs
def save_graph(self, filename, fileType):
"""Write graph to GML or Adjacency list or YML format
Args:
filename : File or filename to read
fileType (str): Type of file to write, should be "GML Format" or "Adjacency list"
or "YAML"
"""
if fileType == "GML Format":
nx.write_gml(self.graph, filename + ".gml")
if fileType == "Adjacency list":
nx.write_adjlist(self.graph, filename + ".adjlist")
if fileType == "YAML":
nx.write_yaml(self.graph, filename + ".yaml")
def combineAll(in_folder, out_folder):
#expFolder='/Users/Ish/Dropbox/OSM/results/TwoWeeks/overlapping_changesets/ExpAnnotNets/\
#overlapping_changesets_by_'+bucket+'_hour/'
B = nx.DiGraph()
for file in os.listdir(in_folder):
if file != '.DS_Store': #weird MAC thing
path = in_folder + file
G = getJsonNet(path)
#G=nx.read_gml(path)
G = nx.DiGraph(G)
B = composeWeights(B, G)
#return B
nx.write_yaml(B, out_folder)
def save(self,G,Epoch):
#Save Graph
result_dir = './result/'
info = "{}_{}_{}_{}".format(self.network_type,self.player_type,self.update_rule,Epoch)
Epoch_dir = os.path.join(result_dir,self.dir_str,info)
if not os.path.exists(Epoch_dir):
os.mkdir(Epoch_dir)
graph_path = os.path.join(Epoch_dir,info+"_Graph.yaml")
nx.write_yaml(G,graph_path)
#Save strategy
p_vector = self.get_all_values(G,'p')
q_vector = self.get_all_values(G,'q')
pq_array = np.vstack((p_vector,q_vector))
pq_path = os.path.join(Epoch_dir,info+"_strategy.csv")
pq = pd.DataFrame(data = pq_array)
pq.to_csv(pq_path)
def graph_generator(self, graph_model, graph_param, save_path, file_name):
"""
Create random graph
"""
graph_param[0] = int(graph_param[0])
if graph_model == 'ws':
graph_param[1] = int(graph_param[1])
graph = nx.random_graphs.connected_watts_strogatz_graph(
*graph_param)
elif graph_model == 'er':
graph = nx.random_graphs.erdos_renyi_graph(*graph_param)
elif graph_model == 'ba':
graph_param[1] = int(graph_param[1])
graph = nx.random_graphs.barabasi_albert_graph(*graph_param)
if os.path.isfile(save_path + '/' + file_name + '.yaml') is True:
print('graph loaded')
dgraph = nx.read_yaml(save_path + '/' + file_name + '.yaml')
else:
dgraph = nx.DiGraph()
dgraph.add_nodes_from(graph.nodes)
dgraph.add_edges_from(graph.edges)
dgraph = nx.DiGraph()
dgraph.add_nodes_from(graph.nodes)
dgraph.add_edges_from(graph.edges)
in_node = []
out_node = []
for indeg, outdeg in zip(dgraph.in_degree, dgraph.out_degree):
if indeg[1] == 0:
in_node.append(indeg[0])
elif outdeg[1] == 0:
out_node.append(outdeg[0])
sorted = list(nx.topological_sort(dgraph))
if os.path.isdir(save_path) is False:
os.makedirs(save_path)
if os.path.isfile(save_path + '/' + file_name + '.yaml') is False:
print('graph_saved')
nx.write_yaml(dgraph, save_path + '/' + file_name + '.yaml')
return dgraph, sorted, in_node, out_node
def generate_cpt_graph(self, inputfile):
output = self.config.OUTPUT_DIR
concepts = self.parser.parse_cpt(inputfile)
name = ntpath.basename(inputfile)
graph = nx.MultiDiGraph()
for concept in concepts:
graph.add_node(f"Step:{concept.name}",
smell=False,
smell_names=list())
for i, step in enumerate(concept.steps):
graph.add_node(f"Step:{step}", smell=False, smell_names=list())
graph.add_edge(f"Step:{concept.name}",
f"Step:{step}",
label=i + 1)
nx.write_yaml(graph, f"{output}/{name}.yaml")
return name
def dump_digraph(filename, G):
"""!
Functions writes networkx Digraph as gpickle, adjacency list, gexf and gml file
@param [in] filename as string
@param [in] G as networkX DiGraph
"""
print_info("Dumping digraph to " + filename)
nx.write_gpickle(G, filename + design_name + ".gpickle")
nx.write_adjlist(G, filename + design_name )
nx.write_yaml(G, filename+ ".yaml")
nx.write_gml(G, filename + design_name + ".gml")
nx.write_gexf(G, filename + design_name + ".gexf" , prettyprint=True)
nx.write_gml(G, filename + design_name + ".gml")
return
def draw_graph(node_list, edge_list):
G = nx.Graph()
G.add_nodes_from(node_list)
G.add_edges_from(edge_list)
all_node_degrees = list(G.degree(node_list))
sum_degree = 0
for (u, v) in all_node_degrees:
sum_degree += float(v)
print("Average node degree: {}".format(sum_degree / len(node_list)))
print(len(G))
#nx.draw_shell(G, with_labels=True, node_size=200)
#plt.savefig('apartment_high.png')
#plt.show()
if nx.is_connected(G):
print("graph is being saved")
print(len(G))
nx.write_yaml(G, 'singlehouse_extreme.yaml')
def build_cgraph_lib(ffn_netlist, dir_graph_out=None, ground=0, remove_dummy=False, dir_node_edge_list=None, dir_lib_out=None,
guess_by_name=True, add_edge_annotation=False):
"""
ffn_netlist: full file path of netlist to parse
dir_graph_out: directory path to save the resulting circuit topology graph in yaml format
dir_lib_out: directory path to save circuit topology graph lib in pickle format
remove_dummy: when True, remove dummy mos
guess_by_name: when True, some attributes such as signal type is inferred/guessed from net/instance name
add_edge_annotation: when True, add matching/group edge constraints to the graph
return dict (i.e. {circuit_name:networkx.Graph})
"""
from PySpice.Spice.Parser import SpiceParser
parser = SpiceParser(path=ffn_netlist)
circuit = parser.build_circuit(ground=ground)
cgraph_dict = {}
top_name, ext = os.path.splitext(os.path.basename(ffn_netlist))
G = build_cgraph(circuit, top_name, guess_by_name=guess_by_name, add_edge_annotation=add_edge_annotation)
cgraph_dict[top_name] = G
for c in (circuit.subcircuits):
for e in (c.elements):
G = build_cgraph(c, c.name, guess_by_name=guess_by_name, add_edge_annotation=add_edge_annotation)
cgraph_dict[c.name] = G
for name, G in cgraph_dict.items():
if(dir_graph_out is not None):
nx.write_yaml(G, os.path.join(dir_graph_out, "%s.yaml" % name))
if(dir_node_edge_list is not None):
node_number = {}
with open(os.path.join(dir_node_edge_list, "%s.nodelist" % name), 'w') as f:
for ii, n in enumerate(G.nodes()):
f.write("%s %d\n" % (n, ii))
node_number[n]=ii
with open(os.path.join(dir_node_edge_list, "%s.edgelist" % name), 'w') as f:
for e in G.edges():
f.write('%s %s\n' % (node_number[e[0]], node_number[e[1]]))
if(dir_lib_out is not None):
with open(os.path.join(dir_lib_out, "%s.cgraph.pkl" % top_name), 'wb') as f:
pickle.dump(cgraph_dict, f, -1)
return cgraph_dict
def generate_spec_graph(self, input_file):
filename = ntpath.basename(input_file)
output = self.config.OUTPUT_DIR
scenarios = self.parser.parse_spec(input_file)
graph = nx.MultiDiGraph()
for scenario in scenarios:
graph.add_node(f"Scenario:{scenario.name}",
source_file=scenario.source_file,
smell=False,
smell_names=list())
for i, step in enumerate(scenario.steps):
graph.add_node(f"Step:{step}", smell=False, smell_names=list())
graph.add_edge(f"Scenario:{scenario.name}",
f"Step:{step}",
label=i + 1)
nx.write_yaml(graph, f"{output}/{filename}.yaml")
return filename
def write_graph(graph, filename):
"""Write graph to file, raise IOError if cannot do it."""
if filename.endswith('.yaml'):
try:
nx.write_yaml(graph, filename)
except ImportError:
print('E: cannot write graph to file in YAML format.')
print('Please install PyYAML or other similar package '
'to use this functionality.')
raise IOError
else:
print('Write constructed graph to: {0} '
'in YAML format.'.format(filename))
elif filename.endswith('.gml'):
try:
nx.write_gml(graph, filename)
except ImportError:
print('E: cannot write graph to file in GML format.')
print('Please install pyparsing package '
'to use this functionality.')
raise IOError
else:
print('Write constructed graph to: {0} '
'in GML format.'.format(filename))
elif filename.endswith('.net'):
nx.write_pajek(graph, filename)
print('Write constructed graph to: {0} '
'in PAJEK format.'.format(filename))
elif filename.endswith('.gexf'):
graph = exclude_complex_attrs(graph)
nx.write_gexf(graph, filename)
print('Write constructed graph to: {0} '
'in GEXF format.'.format(filename))
elif filename.endswith('.graphml'):
graph = exclude_complex_attrs(graph)
nx.write_graphml(graph, filename)
print('Write constructed graph to: {0} '
'in GraphML format.'.format(filename))
else:
with open(filename, 'wb') as f:
pickle.dump(graph, f, protocol=pickle.HIGHEST_PROTOCOL)
print('Write constructed graph to: {0} '
'in pickle format.'.format(filename))
def write_graph(graph, filename):
"""Write graph to file, raise IOError if cannot do it."""
if filename.endswith('.yaml'):
try:
nx.write_yaml(graph, filename)
except ImportError:
print('E: cannot write graph to file in YAML format.')
print('Please install PyYAML or other similar package '
'to use this functionality.')
raise IOError
else:
print('Write constructed graph to: {0} '
'in YAML format.'.format(filename))
elif filename.endswith('.gml'):
try:
nx.write_gml(graph, filename)
except ImportError:
print('E: cannot write graph to file in GML format.')
print('Please install pyparsing package '
'to use this functionality.')
raise IOError
else:
print('Write constructed graph to: {0} '
'in GML format.'.format(filename))
elif filename.endswith('.net'):
nx.write_pajek(graph, filename)
print('Write constructed graph to: {0} '
'in PAJEK format.'.format(filename))
elif filename.endswith('.gexf'):
graph = exclude_complex_attrs(graph)
nx.write_gexf(graph, filename)
print('Write constructed graph to: {0} '
'in GEXF format.'.format(filename))
elif filename.endswith('.graphml'):
graph = exclude_complex_attrs(graph)
nx.write_graphml(graph, filename)
print('Write constructed graph to: {0} '
'in GraphML format.'.format(filename))
else:
with open(filename, 'wb') as f:
pickle.dump(graph, f, protocol=pickle.HIGHEST_PROTOCOL)
print('Write constructed graph to: {0} '
'in pickle format.'.format(filename))
def save_experiment(self, expr_dir='expr', include_module_classes=False):
'''Save your experiment configurations to yaml files'''
import yaml
# Save locations
if not os.path.exists(expr_dir):
os.mkdir(expr_dir)
loc_file = os.path.join(expr_dir, "locations.yaml")
top_file = os.path.join(expr_dir, 'topology.yaml')
serv_file = os.path.join(expr_dir, 'services.yaml')
self._locs.save_to_yaml(loc_file)
if type(self._top) == dict:
# Save dict
with open(top_file, 'w') as s:
yaml.dump(self._top, s)
else:
# This is networkx file
nx.write_yaml(self._top, top_file)
dump_serv = {}
services = dict()
for k, pt in self._servs.items():
new_pt = pt.config.repr()
if type(pt.service_map) == dict:
serv = dict()
for sk, sc in pt.service_map.items():
if not sc:
serv[sk.__name__] = sc
else:
serv[sk.__name__] = sc.repr()
services[sk.__name__] = sk if include_module_classes else None
else:
serv = tuple(k.__name__ for k in pt.service_map)
if include_module_classes:
services.update({k.__name__: k for k in pt.service_map})
else:
services.update({k.__name__: None for k in pt.service_map})
dump_serv[k] = PeerType(new_pt, serv)
with open(serv_file, 'w') as s:
yaml.dump([dump_serv, services], s)
def write_graph(self, G=None, subgraph_file=None):
if G is None:
G = self.context_graph
if subgraph_file is None:
subgraph_file = self.context_graph_file
logging.info("Writing graph.")
# write the graph out
file_format = subgraph_file.split(".")[-1]
if file_format == "graphml":
nx.write_graphml(G, subgraph_file)
elif file_format == "gml":
nx.write_gml(G, subgraph_file)
elif file_format == "gexf":
nx.write_gexf(G, subgraph_file)
elif file_format == "net":
nx.write_pajek(G, subgraph_file)
elif file_format == "yaml":
nx.write_yaml(G, subgraph_file)
elif file_format == "gpickle":
nx.write_gpickle(G, subgraph_file)
else:
print "File format not found, writing graphml."
nx.write_graphml(G, subgraph_file)
def write_graph(self, G=None, subgraph_file=None):
if G is None:
G = self.context_graph
if subgraph_file is None:
subgraph_file = self.context_graph_file
logging.info("Writing graph.")
# write the graph out
file_format = subgraph_file.split(".")[-1]
if file_format == "graphml":
nx.write_graphml(G, subgraph_file)
elif file_format == "gml":
nx.write_gml(G, subgraph_file)
elif file_format == "gexf":
nx.write_gexf(G, subgraph_file)
elif file_format == "net":
nx.write_pajek(G, subgraph_file)
elif file_format == "yaml":
nx.write_yaml(G, subgraph_file)
elif file_format == "gpickle":
nx.write_gpickle(G, subgraph_file)
else:
print "File format not found, writing graphml."
nx.write_graphml(G, subgraph_file)
def save_cell_graph(self, filename='cell_graph.gml', format='gml'):
"""Save the cell to cell connectivity graph in a file.
"""
start = datetime.now()
if format == 'gml':
nx.write_gml(self.__cell_graph, filename)
elif format == 'pickle':
nx.write_gpickle(self.__cell_graph, filename)
elif format == 'yaml':
nx.write_yaml(self.__cell_graph, filename)
elif format == 'graphml':
nx.write_graphml(self.__cell_graph, filename)
elif format == 'edgelist':
nx.write_edgelist(self.__cell_graph, filename)
else:
raise Exception('Not supported: %s' % (format))
end = datetime.now()
delta = end - start
config.BENCHMARK_LOGGER.info(
'Saved cell graph in file %s of type %s in %g s' %
(filename, format, delta.seconds + 1e-6 * delta.microseconds))
print 'Saved cell-to-cell connectivity data in', filename
def save_cell_graph(self, filename="cell_graph.gml", format="gml"):
"""Save the cell to cell connectivity graph in a file.
"""
start = datetime.now()
if format == "gml":
nx.write_gml(self.__cell_graph, filename)
elif format == "pickle":
nx.write_gpickle(self.__cell_graph, filename)
elif format == "yaml":
nx.write_yaml(self.__cell_graph, filename)
elif format == "graphml":
nx.write_graphml(self.__cell_graph, filename)
elif format == "edgelist":
nx.write_edgelist(self.__cell_graph, filename)
else:
raise Exception("Not supported: %s" % (format))
end = datetime.now()
delta = end - start
config.BENCHMARK_LOGGER.info(
"Saved cell graph in file %s of type %s in %g s"
% (filename, format, delta.seconds + 1e-6 * delta.microseconds)
)
print "Saved cell-to-cell connectivity data in", filename
def main(out_dir, direction, num_graphs, num_nodes, graph_type, graph_params, eta,
require_connected=False, require_invertible=False, require_stationary=False):
graph_params = yaml.safe_load(graph_params)
out_path = Path(out_dir) / graph_type
out_path = out_path / '/'.join([f'{param}_{graph_params[param]}' for param in sorted(graph_params.keys())])
out_path.mkdir(parents=True, exist_ok=True)
graph_params_str = out_path / '/'.join([f'{param}_{graph_params[param]}' for param in sorted(graph_params.keys())])
i = 0
while i < num_graphs:
i_d = str(uuid4())
graph = make_graph(graph_type, graph_params, eta, require_connected=require_connected,
require_invertible=require_invertible, require_stationary=require_stationary)
out_loc = out_path / (graph.graph['id'] + '.yaml')
nx.write_yaml(graph, out_loc)
i+=1
def add_new_submission(submission, outname='indication_paths.yaml'):
if submission is not None:
print('Building Indications...')
indications = nx.read_yaml('indication_paths.yaml')
out = []
# Ensure nothing is duplicated
for path in indications + submission:
# Ensure that we have a list for all references
if path.get('reference'):
path['reference'] = references_to_list(path)
if not is_path_in_paths(path, out):
out.append(path)
out = create_ids(out)
out = filter_deprecated_ids(out)
nx.write_yaml(out, outname, indent=4)
print('Build Successful')
else:
sys.exit(125)
def on_actionYAML_activated(self):
"""
Slot documentation goes here.
"""
if self.network:
nx.write_yaml(self.network.G, self.filename.split('.')[0]+'.yaml')
def to_yaml(self):
"Exports the full graph to yaml"
file_name = raw_input("Save as: ")
nx.write_yaml(self.graph,
file_name+".yaml",
encoding='utf-8')
def save_graph(G, path):
nx.write_yaml(G, os.path.join('./corpus', path))
def genGraphRAMON(token_name, channel, graphType="graphml", xmin=0, xmax=0, ymin=0, ymax=0, zmin=0, zmax=0):
"""Generate the graph based on different inputs"""
# converting all parameters to integers
[xmin, xmax, ymin, ymax, zmin, zmax] = [int(i) for i in [xmin, xmax, ymin, ymax, zmin, zmax]]
proj = NDProject.fromTokenName(token_name)
with closing (ramondb.RamonDB(proj)) as db:
ch = proj.getChannelObj(channel)
resolution = ch.resolution
cubeRestrictions = xmin + xmax + ymin + ymax + zmin + zmax
matrix = []
# assumption that the channel is a neuron channel
if cubeRestrictions != 0:
idslist = getAnnoIds(proj, ch, resolution, xmin, xmax, ymin, ymax, zmin, zmax)
else:
# entire cube
[xmax, ymax, zmax] = proj.datasetcfg.get_imagesize(resolution)
idslist = getAnnoIds(proj, ch, resolution, xmin, xmax, ymin, ymax, zmin, zmax)
if idslist.size == 0:
logger.error("Area specified x:{},{} y:{},{} z:{},{} is empty".format(xmin, xmax, ymin, ymax, zmin, zmax))
raise NDWSError("Area specified x:{},{} y:{},{} z:{},{} is empty".format(xmin, xmax, ymin, ymax, zmin, zmax))
annos = {}
for i in idslist:
tmp = db.getAnnotation(ch, i)
if int(db.annodb.getAnnotationKV(ch, i)['ann_type']) == annotation.ANNO_SYNAPSE:
annos[i]=[int(s) for s in tmp.getField('segments').split(',')]
# create and export graph
outputGraph = nx.Graph()
for key in annos:
outputGraph.add_edges_from([tuple(annos[key])])
try:
f = tempfile.NamedTemporaryFile()
if graphType.upper() == "GRAPHML":
nx.write_graphml(outputGraph, f)
elif graphType.upper() == "ADJLIST":
nx.write_adjlist(outputGraph, f)
elif graphType.upper() == "EDGELIST":
nx.write_edgelist(outputGraph, f)
elif graphType.upper() == "GEXF":
nx.write_gexf(outputGraph, f)
elif graphType.upper() == "GML":
nx.write_gml(outputGraph, f)
elif graphType.upper() == "GPICKLE":
nx.write_gpickle(outputGraph, f)
elif graphType.upper() == "YAML":
nx.write_yaml(outputGraph, f)
elif graphType.upper() == "PAJEK":
nx.write_net(outputGraph, f)
else:
nx.write_graphml(outputGraph, f)
f.flush()
f.seek(0)
except:
logger.error("Internal file error in creating/editing a NamedTemporaryFile")
f.close()
raise NDWSError("Internal file error in creating/editing a NamedTemporaryFile")
return (f, graphType.lower())
def test_all(self):
write_yaml(self.parser.merged_graph, 'target/gaf-graph.yaml')
def _dump_graph_yaml(self, path):
net.write_yaml(self.graph, path)
def mouseReleaseEvent(self,event):
QtGui.QGraphicsItemGroup.mouseReleaseEvent(self,event)
self.node.pos = [self.pos().x(),self.pos().y()]
networkx.write_yaml(self.graph,"/tmp/test.yaml")
def save(self): nx.write_yaml(self.graph,'graph.yaml')
def create_graph():
g = nx.Graph()
xml_docs = Collection()
xml_docs_subset = xml_docs.get_docs(author="Wau Holland")
docs_no = len(xml_docs_subset)
id_dict = dict()
stems_dict = dict()
doc_id = 1
print "Put stems into a dict for each document (with an uniq id) ..."
print "Create nodes with all the documents' relevant information ..."
pb = ProgressBar(maxval=docs_no).start()
for xml_doc in xml_docs_subset:
pb.update(doc_id)
id_dict[xml_doc.get_xml_filename()] = doc_id
g.add_node(doc_id,
id = xml_doc.get_id(),
rawlen = xml_doc.get_rawlen(),
subj = xml_doc.get_subj(),
author = xml_doc.get_author(),
date = xml_doc.get_date(),
words = xml_doc.get_words(),
uniq_stems = list(xml_doc.get_stems(uniq=True,
relev=True)),
rawcontent = xml_doc.get_rawcontent()
)
doc_id += 1
# It seems sometimes a list (-> set conversion) gets returned
# ... ugly. XXX
stems_dict[doc_id] = set(xml_doc.get_stems(uniq=True, relev=True))
print "Create undirected, weighted graph based on Jaccard similarity ..."
no_of_edges = docs_no * (docs_no - 1) / 2
pb = ProgressBar(maxval=no_of_edges).start()
count = 1
for doc_idx1 in stems_dict.keys():
doc_idx2 = doc_idx1 + 1
# Nothing left to compare
if (doc_idx1 == docs_no):
break
while True:
# print "Comparing: ", doc_idx1, doc_idx2
# Find longer doc
doc1_len, doc2_len = len(stems_dict[doc_idx1]), \
len(stems_dict[doc_idx2])
long_doc_len = max((doc1_len, doc2_len))
short_doc_len = min((doc1_len, doc2_len))
# In case a document has no useful stems to classify
edge_weight = 0
alias_coeff = 0
if long_doc_len == 0 or short_doc_len == 0:
pass
else:
alias_coeff = float(long_doc_len) / short_doc_len
edge_weight = (1 - jaccard_distance(stems_dict[doc_idx1],
stems_dict[doc_idx2])) \
* alias_coeff
print alias_coeff, edge_weight
# Still redundant, only for testing
if (edge_weight > 0.3):
cluster_stems = stems_dict[doc_idx1].intersection(
stems_dict[doc_idx2])
try:
g.node[doc_idx1]['cluster_stems']
except KeyError:
g.node[doc_idx1]['cluster_stems'] = cluster_stems
else:
for stem in cluster_stems:
g.node[doc_idx1]['cluster_stems'].add(stem)
try:
g.node[doc_idx2]['cluster_stems']
except KeyError:
g.node[doc_idx2]['cluster_stems'] = cluster_stems
else:
for stem in cluster_stems:
g.node[doc_idx2]['cluster_stems'].add(stem)
# To be made more flexible
if edge_weight > 0.3:
g.add_edge(doc_idx1, doc_idx2, weight=edge_weight)
doc_idx2 += 1
pb.update(count)
count += 1
if doc_idx2 > docs_no:
break
print "Draw graph showing possible clusters ..."
elarge = [(u,v) for (u,v,d) in g.edges(data=True) if d['weight'] > 0.4]
emedium = [(u,v) for (u,v,d) in g.edges(data=True)
if d['weight'] > 0.2 and d['weight'] < 0.4]
esmall = [(u,v) for (u,v,d) in g.edges(data=True) if d['weight'] <= 0.2]
print "elarge: ", len(elarge)
print "emedium: ", len(emedium)
print "esmall: ", len(esmall)
pos = nx.spring_layout(g, scale=20)
#pos = nx.random_layout(g)
dlarge = [n for n,d in g.degree_iter() if d >= 20]
dmedium = [n for n,d in g.degree_iter() if d > 1 and d < 20]
dsmall = [n for n,d in g.degree_iter() if d == 1]
dnone = [n for n,d in g.degree_iter() if d == 0]
print "dlarge: ", len(dlarge)
print "dmedium: ", len(dmedium)
print "dsmall: ", len(dsmall)
print "dnone: ", len(dnone)
# Draw nodes
# nx.draw_networkx_nodes(g, pos, node_size=5, linewidths=0)
nx.draw_networkx_nodes(g, pos, nodelist=dlarge, node_size=20,
node_color='b',
linewidths=0)
nx.draw_networkx_nodes(g, pos, nodelist=dmedium, node_size=10,
node_color='g',
alpha=0.8,
linewidths=0)
nx.draw_networkx_nodes(g, pos, nodelist=dsmall, node_size=5,
node_color='b',
alpha=0.2,
linewidths=0,
)
nx.draw_networkx_nodes(g, pos, nodelist=dnone, node_size=5,
node_color='b',
alpha=0.2,
linewidths=0)
# Draw edges
nx.draw_networkx_edges(g, pos, edgelist=elarge, width=0.4)
nx.draw_networkx_edges(g, pos, edgelist=emedium, edge_color='g',
alpha=0.8, width=0.2)
nx.draw_networkx_edges(g, pos, edgelist=esmall, width=0.1,
alpha=0.1, edge_color='b')
# Draw labels
# nx.draw_networkx_labels(g, pos, font_size=1, font_family='sans-serif')
plt.axis('off')
plt.figure(1, figsize=(20,20))
"""
print "Print PNG"
plt.savefig("graph.png", dpi=600)
"""
# plt.show()
nx.write_yaml(g, get_graph_file())
d3_js.export_d3_js(g)
def export_yaml(self,fn=None):
if not self._graph:
self.convert()
write_yaml(self._graph, fn)
def write_graph(self, outfile):
nx.write_yaml(self.graph, outfile)
import json
if __name__ == '__main__':
graph = nx.read_edgelist('input/example_graph.edgelist', nodetype=int, data=(('weight', float),))
assert isinstance(graph, nx.Graph)
print 'edges:', graph.edges()
# raw
nx.write_adjlist(graph, 'output_raw/example_graph.adjlist')
nx.write_multiline_adjlist(graph, 'output_raw/example_graph.multiline_adjlist')
nx.write_edgelist(graph, 'output_raw/example_graph.edgelist')
# better serialization
nx.write_gpickle(graph, 'output_serialization/example_graph.pickle')
nx.write_yaml(graph, 'output_serialization/example_graph.yaml')
nx.write_graph6(graph, 'output_serialization/example_graph.graph6')
# xml
nx.write_gexf(graph, 'output_xml/example_graph.gexf')
nx.write_graphml(graph, 'output_xml/example_graph.graphml')
# json
with open('output_json/node_link.json', 'w') as outfile:
json.dump(json_graph.node_link_data(graph), outfile, indent=2)
with open('output_json/adjacency.json', 'w') as outfile:
json.dump(json_graph.adjacency_data(graph), outfile, indent=2)
# other
nx.write_gml(graph, 'output_other/example_graph.gml')
def gen_data(graph_path, lda_path, user_lim=200, user_wb_lim=200):
import jieba
import jieba.posseg as pseg
jieba.load_userdict(u"/etc/jieba/jieba.dic")
G = nx.Graph()
ldaf = open(lda_path, 'w')
ldaf.write("%d\n" % user_lim)
ucnt = 0
for item in Weibo.objects.values('owner').annotate(cnt=Count('owner')):
if item['cnt']>450:
user = Account.objects.get(id=item['owner'])
logging.info(u'%5d Dealing with %s' % (ucnt, user))
logging.info(u'Current graph:%d nodes and %d edges' % (G.number_of_nodes(), G.number_of_edges()))
user_words = []
for wb in user.ownweibo.order_by("-created_at").all()[:user_wb_lim]:
#filter(retweeted_status__exact=None).all():
text = wb.text.lower()
#TODO
#if wb.retweeted_status:
# text = wb.retweeted_status.text.lower() + text
text = re.sub("@[^\s@:]+", "", text)
text = re.sub(u"http://t.cn[^ ]*", u"", text)
text = re.sub(u"\[[^ ]{1,3}\]", u"", text)
for word in re.findall(u"【.+?】|#.+?#|《.+?》|“.+?”|\".+?\"", text):
for w in pseg.cut(word):
if len(w.word)<2 or w.word in Config.STOP_WORDS or 'n' not in w.flag:
continue
wd = w.word.encode('utf-8')
if G.has_node(wd) and 'weight' in G.node[wd]:
G.node[wd]['weight'] += 1.0
else:
G.add_node(wd, weight=1.0)
wb_words = []
for w in pseg.cut(text):
if len(w.word)>1 and 'n' in w.flag and w.word not in Config.STOP_WORDS:
wb_words.append(w.word.encode('utf-8'))
if not wb_words:
continue
for w1, w2, w3 in zip(wb_words[:-2], wb_words[1:-1], wb_words[2:]):
if not G.has_edge(w1, w2):
G.add_edge(w1, w2, weight=1.0)
else:
G[w1][w2]['weight'] += 1.0
if not G.has_edge(w1, w3):
G.add_edge(w1, w3, weight=1.0)
else:
G[w1][w3]['weight'] += 1.0
user_words.extend(wb_words)
if not user_words:
continue
ldaf.write(' '.join(user_words)+'\n')
ucnt += 1
if ucnt>=user_lim:
break
if ucnt<user_lim:
logging.error("no enough docs, %d/%d" % (ucnt, user_lim))
if graph_path:
nx.write_yaml(G, graph_path, encoding='UTF-8')
ldaf.close()
return G
def write_graph_file(self):
'''
Write the graph file to disk.
'''
networkx.write_yaml(self.graph, GRAPH_FILE)
def saveUrlGraph(self):
filefloder = r'../data/'
filename = filefloder + 'whutgraph.yaml'
nx.write_yaml(self.DG,filename)
nx.draw(self.DG)
plt.savefig("whutnetwork.png")
def saveGraph(self, filename):
"""Saves the graph as a YAML file
"""
nx.write_yaml(self.G,filename)
def save(self):
nx.write_yaml(self.graph, "graph.yaml")
pass
try:
g.write_picklez("user user org.picz")
except:
pass
g.write_adjacency("user user org.adj")
g.write_svg("user user org.svg")
"""
print('initialising module .. reading graph')
# g=Graph.Read_Pickle("user user org.pic")
# g2=nx.Graph()
# g3=nx.read_gpickle("user user org.pic")
g=nx.read_gpickle("user user org.pic")
# print g2
g=nx.convert_node_labels_to_integers(g)
print 'writing pajek'
# nx.write_pajek(g,"org_mem.net")
nx.write_adjlist(g,"org_mem.adj")
nx.write_yaml(g,"org_mem.yaml")
# plt.show()
# print('reading graph done.. layout graph initilaizing')
# layout = g.layout("")
# print('done.. strting to plot graph')
# plot(g, layout = layout)
# print 'plot done :D'
else:
wot_file = open(args.wot_file, "rb")
else:
wot_file = latest_wot()
logging.info("Parsing files...")
G = read_wot(wot_file)
logging.info("Read {0} keys, {1} signatures".format(nx.number_of_nodes(G),
nx.number_of_edges(G)))
logging.info("Filtering...")
if args.mutual:
G = G.to_undirected(reciprocal=True)
G = nx.connected_component_subgraphs(G)[0]
if args.key:
G = nx.ego_graph(G, args.key, radius=args.radius, undirected=True)
logging.info("Writing output file...")
if args.output:
outfile = open(args.output, "wb")
else:
outfile = sys.stdout.buffer
if args.file_format == "gexf":
nx.write_gexf(G, outfile)
elif args.file_format == "graphml":
nx.write_graphml(G, outfile)
elif args.file_format == "yaml":
nx.write_yaml(G, outfile)
#data['pwy'] = ','.join(sorted(set(data['pwy'])))
for nA,nB,data in G.edges(data=True):
w = data['weight']
occA = G.node[nA]['occ']
occB = G.node[nB]['occ']
print(nA, nB, occA, occB, w)
data['nw'] = w ** 2 / (occA + occB - w)
data['stanza'] = '/'.join(data['stanza'])
nx.write_gml(G, 'R_shijing.gml')
nx.write_yaml(G, 'R_shijing.yaml')
import html.parser
with open('R_shijing.gml') as f:
shijing = f.read()
with open('R_shijing.gml', 'w') as f:
f.write(html.parser.unescape(shijing))
# get chars which are unresolved
M = {}
for k in wl:
ocbsyun = wl[k,'ocbsyun']
rid = wl[k,'rhymeid']
char = wl[k,'character']
def genGraphRAMON(database, project, channel, graphType="graphml", Xmin=0, Xmax=0, Ymin=0, Ymax=0, Zmin=0, Zmax=0,):
cubeRestrictions = int(Xmin) + int(Xmax) + int(Ymin) + int(Ymax) + int(Zmin) + int(Zmax)
conn = MySQLdb.connect(host=settings.DATABASES['default']['HOST'], user=settings.DATABASES['default']['USER'], passwd=settings.DATABASES['default']['PASSWORD'], db=project.getProjectName())
matrix = []
if cubeRestrictions != 0:
idslist = getAnnoIds(project, channel, Xmin, Xmax, Ymin, Ymax, Zmin, Zmax)
if (idslist.size) == 0:
logger.warning("Area specified is empty")
raise OCPCAError("Area specified is empty")
with closing(conn.cursor()) as cursor:
for i in range(idslist.size):
cursor.execute(("select kv_value from {} where kv_key = 'synapse_segments' and annoid = {};").format(
channel.getKVTable(""), idslist[i]))
matrix.append(cursor.fetchall()[0])
else:
with closing(conn.cursor()) as cursor:
cursor.execute(("select kv_value from {} where kv_key = 'synapse_segments';").format(
channel.getKVTable("")))
matrix = cursor.fetchall()
synapses = np.empty(shape=(len(matrix), 2))
rawstring = (matrix[0])[0]
splitString = rawstring.split(",")
if len(splitString) == 2:
# For kv pairs with 127:0, 13:0 (for example)
for i in range(len(matrix)):
# Get raw from matrix
rawstring = (matrix[i])[0]
splitString = rawstring.split(",")
# Split and cast the raw string
synapses[i] = [int((splitString[0].split(":"))[0]), int((splitString[1].split(":"))[0])]
else:
# for kv pairs with just 4:5
for i in range(len(matrix)):
# Get raw from matrix
rawstring = (matrix[i])[0]
# Split and cast the raw string
synapses[i] = rawstring.split(":")
# Create and export graph
outputGraph = nx.Graph()
outputGraph.add_edges_from(synapses)
if graphType.upper() == "GRAPHML":
nx.write_graphml(outputGraph, ("/tmp/{}_{}.graphml").format(
project.getProjectName(), channel.getChannelName()))
return ("/tmp/{}_{}.graphml").format(project.getProjectName(), channel.getChannelName())
elif graphType.upper() == "ADJLIST":
nx.write_adjlist(outputGraph, ("/tmp/{}_{}.adjlist").format(
project.getProjectName(), channel.getChannelName()))
return ("/tmp/{}_{}.adjlist").format(project.getProjectName(), channel.getChannelName())
elif graphType.upper() == "EDGELIST":
nx.write_edgelist(outputGraph, ("/tmp/{}_{}.edgelist").format(
project.getProjectName(), channel.getChannelName()))
return ("/tmp/{}_{}.edgelist").format(project.getProjectName(), channel.getChannelName())
elif graphType.upper() == "GEXF":
nx.write_gexf(outputGraph, ("/tmp/{}_{}.gexf").format(
project.getProjectName(), channel.getChannelName()))
return ("/tmp/{}_{}.gexf").format(project.getProjectName(), channel.getChannelName())
elif graphType.upper() == "GML":
nx.write_gml(outputGraph, ("/tmp/{}_{}.gml").format(
project.getProjectName(), channel.getChannelName()))
return ("/tmp/{}_{}.gml").format(project.getProjectName(), channel.getChannelName())
elif graphType.upper() == "GPICKLE":
nx.write_gpickle(outputGraph, ("/tmp/{}_{}.gpickle").format(
project.getProjectName(), channel.getChannelName()))
return ("/tmp/{}_{}.gpickle").format(project.getProjectName(), channel.getChannelName())
elif graphType.upper() == "YAML":
nx.write_yaml(outputGraph, ("/tmp/{}_{}.yaml").format(
project.getProjectName(), channel.getChannelName()))
return ("/tmp/{}_{}.yaml").format(project.getProjectName(), channel.getChannelName())
elif graphType.upper() == "PAJEK":
nx.write_net(outputGraph, ("/tmp/{}_{}.net").format(
project.getProjectName(), channel.getChannelName()))
return ("/tmp/{}_{}.net").format(project.getProjectName(), channel.getChannelName())
else:
nx.write_graphml(outputGraph, ("/tmp/{}_{}.graphml").format(
project.getProjectName(), channel.getChannelName()))
return ("/tmp/{}_{}.graphml").format(project.getProjectName(), channel.getChannelName())
for node,data in _G.nodes(data=True):
G.add_vertex(name=node, **data)
for nodeA, nodeB, data in _G.edges(data=True):
G.add_edge(nodeA, nodeB, **data)
# do the same for the N graph
_N = igraph.Graph()
for node,data in N.nodes(data=True):
_N.add_vertex(name=node, **data)
for nodeA, nodeB, data in N.edges(data=True):
if data['occurrence'] >= 10:
_N.add_edge(nodeA, nodeB, **data)
nx.write_yaml(N, 'R_rime_graph.yaml')
if 'communities' in argv:
C = _N.community_infomap(
edge_weights = 'occurrence',
vertex_weights = 'occurrence'
)
for community,name in zip(C.membership, _N.vs['name']):
N.node[name]['infomap'] = community
print('[i] Calculated communities for rhyme groups')
# check statistics, for example, get
C = G.community_infomap(