def generate_dep_graphs(topicListFilePath):
topicListFile = open(topicListFilePath, 'r', encoding="utf8")
for topicIndex, topic in enumerate(topicListFile):
topic = topic.replace('\n', '')
print('Processing topic -> [{}]'.format(topic))
outputTopicDepGraphFileDir = '../data/train_data/{}/dep_graphs'.format(
topic)
topicDataFilePath = '../data/train_data/{}/corpus.txt'.format(topic)
corpusDataFile = open(topicDataFilePath, 'r', encoding="utf8")
for docIndex, doc in enumerate(corpusDataFile):
graphOutputFile = '{}/{}.gexf'.format(outputTopicDepGraphFileDir,
docIndex)
if os.path.exists(graphOutputFile):
print(
'Graph`s file for document index -> [{}] is existed, skipping !'
.format(docIndex))
continue
else:
print('Proceed document id: {}'.format(docIndex + 1))
depGraph = depGraphParser.proceed(doc)
if depGraph is not None:
nx.write_gexf(depGraph, graphOutputFile)
def plot_graph(self, name, score):
#Import matplotlib, a library used to produce graphic in python.
import matplotlib.pyplot as plt
from networkx import nx
plt.figure(figsize=(7, 7)) # Adjust the window size
plt.margins(.2, .2) # Adjust margins
#We determine the node position: https://networkx.github.io/documentation/networkx-1.10/reference/generated/networkx.drawing.layout.spring_layout.html
position = nx.spring_layout(self.graph)
nx.draw_networkx(self.graph, with_labels=True, pos=position)
plt.axis('off') # Removing axis
#Weights on edges : solution found on stackoverflow
#https://stackoverflow.com/questions/28372127/add-edge-weights-to-plot-output-in-networkx
labels = nx.get_edge_attributes(self.graph, 'weight')
nx.draw_networkx_edge_labels(self.graph,
pos=position,
edge_labels=labels)
plt.title(
"fasta alignment graph according to a minimum alignment score of "
+ str(score))
plt.savefig(
name +
".png") # Produce a png file with the graph annotated by default
plt.show()
nx.write_gexf(
self.graph, name +
".gexf") # Produce a gexf file that can be annotated with gephi.
return None
def generate_dep_graphs(doc_file_path):
outputDepGraphs = []
outputDocDepGraphFileDir = 'data/test/dep_graphs'
if not os.path.exists(outputDocDepGraphFileDir):
os.mkdir(outputDocDepGraphFileDir)
corpusDataFile = open(doc_file_path, 'r', encoding="utf8")
for docIndex, docContent in enumerate(corpusDataFile):
graphOutputFile = '{}/{}.gexf'.format(outputDocDepGraphFileDir, docIndex)
depGraph = depGraphParser.proceed(docContent)
if depGraph is not None:
outputDepGraphs.append(depGraph)
nx.write_gexf(depGraph, graphOutputFile)
return outputDepGraphs
print len(comms), "communities found"
print "calculating positions via fruchterman reingold"
pos = g.layout_grid_fruchterman_reingold()
print "setting colors and positions on each node"
for i in range(len(comms)):
for n in comms[i]:
color = rgbs[i] if i < len(rgbs) else { "r": 211, "g": 211, "b": 211 }
if len(comms[i]) < 5: color = { "r": 211, "g": 211, "b": 211 }
g.vs[n]['viz'] = str({'color': color, 'position':{'x':pos[n][0], 'y':pos[n][1]}})
g.vs[n]['uid'] = g.vs[n]['name']
g.vs[n]['label'] = mapping[g.vs[n]['uid']]
print "saving to gml"
g.write_gml(open("graph.gml", "w"))
print "read gml file in networkx"
from networkx import nx
G = nx.read_gml('graph.gml')
for node in G.nodes(data=True):
node[1]['viz'] = eval(node[1]['viz'])
print "write to gefx from networkx"
nx.write_gexf(G, './network/data/%s.gexf' % KEYWORD)
config = json.load(open("./network/sample.json"))
config['data'] = 'data/%s.gexf' % KEYWORD
config['logo']['text'] = KEYWORD.title()
config['text']['title'] = ALG
json.dump(config, open('./network/%s.json' % KEYWORD, 'w'))
print "done!"
def map_concept_to_onto_by_topic_name(topic_name):
topicConceptOutputFolder = '../data/cdo_ontology/concepts/{}'.format(
topic_name)
outputTopicConceptFilePath = '../data/train_data/{}/freq_graph.txt'.format(
topic_name)
if not os.path.exists(topicConceptOutputFolder):
os.makedirs(topicConceptOutputFolder)
else:
clear_dir(topicConceptOutputFolder)
conceptDataFile = open(outputTopicConceptFilePath, 'r', encoding="utf8")
vocFile = open(vocFilePath, 'r', encoding="utf8")
relLabelFile = open(relLabelFilePath, 'r', encoding="utf8")
vocList = []
relLabelList = []
for index, line in enumerate(vocFile):
splits = line.split('\t')
vocList.append(splits[1])
for index, line in enumerate(relLabelFile):
splits = line.split('\t')
relLabelList.append(splits[1])
graphBasedConcepts = []
graphCount = 0
verticeList = []
graphBasedConcept = nx.DiGraph()
for index, line in enumerate(conceptDataFile):
splits = line.split(' ')
if splits[0] == 't':
if graphCount > 0:
verticeList = []
graphCount = graphCount + 1
graphBasedConcepts.append(graphBasedConcept)
graphBasedConcept = nx.DiGraph()
else:
graphCount += 1
continue
else:
if splits[0] == 'v':
termLabel = vocList[int(splits[2])].replace('\n', '')
#print(termLabel)
#print(termLabel)
graphBasedConcept.add_node(termLabel)
verticeList.insert(int(splits[1]), termLabel)
elif splits[0] == 'e':
graphBasedConcept.add_edge(
verticeList[int(splits[1])].replace('\n', ''),
verticeList[int(splits[2])].replace('\n', ''),
semantic_label=relLabelList[int(splits[3])].replace(
'\n', ''))
#write concept to file
conceptFileCount = 0
for conceptIndex, concept in enumerate(graphBasedConcepts):
if conceptFileCount < maxNumConceptForEachTopic:
if len(concept.nodes()) > 0:
outputConceptFilePath = '{}/{}.gexf'.format(
topicConceptOutputFolder, conceptFileCount)
nx.write_gexf(concept, outputConceptFilePath)
conceptFileCount += 1
else:
continue
else:
break
print(
'Mapping to topic [{}] of CDO -> total [{}] concepts, get top [{}] concepts.'
.format(topic_name, len(graphBasedConcepts), conceptFileCount))
import sys, json
from networkx import nx
filename = sys.argv[1].split("/")[-1]
G = nx.read_gml(sys.argv[1])
for node in G.nodes(data=True):
node[1]['viz'] = eval(node[1]['viz'].replace("-Inf", "float(\"-inf\")"))
print "write to gefx from networkx"
nx.write_gexf(G, './network/data/%s.gexf' % filename)
config = json.load(open("./network/sample.json"))
config['data'] = 'data/%s.gexf' % filename
config['logo']['text'] = filename.title()
config['text']['title'] = filename.title()
json.dump(config, open('./network/%s.json' % filename, 'w'))