289 lines
7.5 KiB
Python
289 lines
7.5 KiB
Python
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# -*- coding: UTF-8 -*-
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import itertools
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import sys
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sys.path.insert(0, '/usr/local/lib/python2.7/dist-packages/')
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import networkx as nx
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#import numpy as np
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from subprocess import Popen, PIPE
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import pdb
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import os
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import re,mmap
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#from graph_edit_new import *
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class raw_graph:
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def __init__(self, funcname, g, func_f):
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#print "create"
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self.funcname = funcname
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self.old_g = g[0]
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self.g = nx.DiGraph()
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self.entry = g[1]
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self.fun_features = func_f
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self.attributing()
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def __len__(self):
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return len(self.g)
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def attributing(self):
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self.obtainOffsprings(self.old_g)
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for node in self.old_g:
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fvector = self.retrieveVec(node, self.old_g)
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self.g.add_node(node)
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self.g.node[node]['v'] = fvector
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for edge in self.old_g.edges():
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node1 = edge[0]
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node2 = edge[1]
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self.g.add_edge(node1, node2)
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def obtainOffsprings(self,g):
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nodes = g.nodes()
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for node in nodes:
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offsprings = {}
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self.getOffsprings(g, node, offsprings)
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g.node[node]['offs'] = len(offsprings)
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return g
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def getOffsprings(self, g, node, offsprings):
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node_offs = 0
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sucs = g.successors(node)
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for suc in sucs:
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if suc not in offsprings:
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offsprings[suc] = 1
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self.getOffsprings(g, suc, offsprings)
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def retrieveVec(self, id_, g):
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feature_vec = []
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#numC0
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numc = g.node[id_]['consts']
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feature_vec.append(numc)
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#nums1
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nums = g.node[id_]['strings']
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feature_vec.append(nums)
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#offsprings2
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offs = g.node[id_]['offs']
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feature_vec.append(offs)
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#numAs3
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numAs = g.node[id_]['numAs']
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feature_vec.append(numAs)
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# of calls4
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calls = g.node[id_]['numCalls']
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feature_vec.append(calls)
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# of insts5
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insts = g.node[id_]['numIns']
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feature_vec.append(insts)
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# of LIs6
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insts = g.node[id_]['numLIs']
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feature_vec.append(insts)
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# of TIs7
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insts = g.node[id_]['numTIs']
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feature_vec.append(insts)
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return feature_vec
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def enumerating(self, n):
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subgs = []
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#pdb.set_trace()
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for sub_nodes in itertools.combinations(self.g.nodes(), n):
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subg = self.g.subgraph(sub_nodes)
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u_subg = subg.to_undirected()
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if nx.is_connected(u_subg):
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subgs.append(subg)
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return subgs
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def genMotifs(self, n):
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motifs = {}
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subgs = enumerating(n)
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for subg in subgs:
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if len(motifs) == 0:
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motifs[subg] = [subg]
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else:
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nomatch = True
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for mt in motifs:
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if nx.is_isomorphic(mt, subg):
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motifs[mt].append(subg)
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nomatch = False
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if nomatch:
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motifs[subg] = [subg]
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return motifs
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def enumerating_efficient(self, n):
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#pdb.set_trace()
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if len(self.g) >= 200:
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return []
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with open('/home/qian/workspace/gEnding/gencoding/encoding/labeled/data/preprocessing/OUTPUT.txt','wb') as f:
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nx.write_edgelist(self.g,f,data=False)
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#pdb.set_trace()
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process = Popen(["/home/qian/workspace/FANMOD-command_line-source/executables/./fanmod_command_line_linux", str(n), "100000", "1", "/home/qian/workspace/gEnding/gencoding/encoding/labeled/data/preprocessing/OUTPUT.txt", "1", "0", "0", "2", "0", "0", "0", "1000", "3", "3", "/home/qian/workspace/gEnding/gencoding/encoding/labeled/data/preprocessing/MotifCount.txt", "0", "1"], stdout=PIPE, stderr=PIPE)
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stdout, stderr = process.communicate()
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if process.returncode >= 0:
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#os.system("/home/qian/software/FANMOD-command_line-source/executables/./fanmod_command_line_linux " +str(n) + " 100000 1 /home/qian/workspace/gEnding/gencoding/encoding/labeled/data/preprocessing/OUTPUT.txt 1 0 0 2 0 0 0 1000 3 3 /home/qian/workspace/gEnding/gencoding/encoding/labeled/data/preprocessing/MotifCount.txt 0 1")
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#pdb.set_trace()
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#pdb.set_trace()
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subgs = self.parseOutput("/home/qian/workspace/gEnding/gencoding/encoding/labeled/data/preprocessing/MotifCount.txt.dump", n)
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#pdb.set_trace()
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os.remove("/home/qian/workspace/gEnding/gencoding/encoding/labeled/data/preprocessing/MotifCount.txt.dump")
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return subgs
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return []
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def parseOutput(self, path, n):
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pattern = re.compile('[0-9]+\,[0-9]+\,[0-9]+\,[0-9]+')
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subgraphs = []
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with open(path,'r') as f:
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data = mmap.mmap(f.fileno(), 0, prot=mmap.PROT_READ)
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mo = re.findall(pattern, data)
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if mo:
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results = [map(int, v.split(',')[1:]) for v in mo]
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subgraphs = self.createGraphDirectly(results)
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return subgraphs
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def parseOutputByconditions(self, path, n):
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pattern = re.compile('[0-9]+\,[0-9]+\,[0-9]+\,[0-9]+')
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subgraphs = []
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with open(path,'r') as f:
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data = mmap.mmap(f.fileno(), 0, prot=mmap.PROT_READ)
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mo = re.findall(pattern, data)
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if mo:
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results = [map(int, v.split(',')[1:]) for v in mo]
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subgraphs = self.create_Graphbycondition_Directly(results)
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return subgraphs
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def create_Graphbycondition_Directly(self, results):
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subgs = []
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for indexes in results:
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tg = template_graph()
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subg = self.g.subgraph(indexes)
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tg.updateG(subg)
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subgs.append(tg)
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del tg
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return subgs
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def createGraphDirectly(self, results):
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#pdb.set_trace()
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#subgs = [self.g.subgraph(indexes) for indexes in results]
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subgs = []
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for indexes in results:
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tg = template_graph()
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subg = self.g.subgraph(indexes)
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tg.updateG(subg)
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subgs.append(tg)
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del tg
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return subgs
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def createGraph(self, results, n):
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binary_value = int(results[0],2)
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indexes = [int(v) for v in results[1:]]
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fang = self.createG(results[0], n)
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if fang:
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tg = template_graph(binary_value)
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tg.updateG(fang, indexes, self.g)
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return tg
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pdb.set_trace()
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print "there is g which is none"
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def createG(self, binary_str, n):
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g = nx.DiGraph()
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l = [int(v) for v in binary_str]
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#pdb.set_trace()
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shape = (n, n)
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data = np.array(l)
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ad_matrix = data.reshape(shape)
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for i in xrange(n):
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for j in xrange(n):
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if ad_matrix[i][j] == 1:
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g.add_edge(i, j)
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return g
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class raw_graphs: #创建空的list，然后存储raw_graphs类的instance
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def __init__(self, binary_name):
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self.binary_name = binary_name
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self.raw_graph_list = []
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def append(self, raw_g):
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self.raw_graph_list.append(raw_g)
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def __len__(self):
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return len(self.raw_graph_list)
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class graphlets:
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def __init__(self, funcname):
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self.funcname = funcname
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self.graphlets_list = []
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self.binary_name = None
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def updateBN(self, binary_name):
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self.binary_name = binary_name
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def append(self, subg):
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self.graphlets_list.append(subg)
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def appendSet(self, subgs):
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self.graphlets_list += subgs
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def __len__(self):
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return len(self.graphlets_list)
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class template_graph:
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def __init__(self, value=None):
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self.value = value
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self.g = None
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def updateG(self,g):
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self.g = g
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#def updateIndexes(self, indexes):
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# self.indexes = indexes
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#def updateAttributes(self, pg, indexes, maing):
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# for id_ in xrange(len(indexes)):
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# index = indexes[id_]
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# gnode = self.findNode(index, maing)
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# self.g.node[gnode] = pg.node[index]
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class template_graphs:
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def __init__(self, size):
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self.size = size
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self.gs = []
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self.bit_len = None
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def enumeratingAll(self):
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subgs = []
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binary_value = self.genBinValue()
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for i in xrange(binary_value):
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if i == 0 :
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continue
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g = self.createG(i)
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if g:
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tg = template_graph(i)
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tg.updateG(g)
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self.gs.append(tg)
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def genBinValue(self):
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n = self.size
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self.bit_len = n*n
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return 2**(self.bit_len)
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def createG(self, i):
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g = nx.DiGraph()
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l = self.genArray(i)
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#pdb.set_trace()
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shape = (self.size, self.size)
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data = np.array(l)
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ad_matrix = data.reshape(shape)
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for i in xrange(self.size):
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for j in xrange(self.size):
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if ad_matrix[i][j] == 1:
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g.add_edge(i, j)
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u_g = g.to_undirected()
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if len(g) == self.size and nx.is_connected(u_g):
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return g
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return False
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def genArray(self, i):
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l = [int(x) for x in bin(i)[2:]]
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x = [0 for v in xrange(self.bit_len - len(l))]
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return x + l
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