Skip to content

G
GMatch4py
Commit 0ce8bd23 authored by Fize Jacques's avatar Fize Jacques
Browse files
Options

Add parallelization + prepare test

parent 31bf928c
Hide whitespace changes
Inline Side-by-side
Showing with 225 additions and 136 deletions
gmatch4py/base.pxd
View file @ 0ce8bd23
......@@ -7,9 +7,11 @@ cdef class Base:
## Methods
cpdef np.ndarray compare(self,list graph_list, list selected)
cpdef np.ndarray compare_old(self,list listgs, list selected)
cpdef np.ndarray distance(self, np.ndarray matrix)
cpdef np.ndarray similarity(self, np.ndarray matrix)
cpdef bint isAccepted(self,G,index,selected)
cpdef list get_selected_array(self,selected,size_corpus)
cpdef intersection(G,H)
cpdef union_(G,H)
gmatch4py/base.pyx
View file @ 0ce8bd23
......@@ -136,6 +136,17 @@ cdef class Base:
else:
self.type_alg=type_alg
self.normalized=normalized
cpdef list get_selected_array(self,selected,size_corpus):
cdef list selected_test = [True]*size_corpus
if selected:
selected_test = [False]*size_corpus
for ix in range(len(selected)):
selected_test[ix]=True
return selected
cpdef np.ndarray compare_old(self,list listgs, list selected):
pass
cpdef np.ndarray compare(self,list graph_list, list selected):
"""
Return the similarity/distance matrix using the current algorithm.
......
gmatch4py/ged/abstract_graph_edit_dist.pxd
View file @ 0ce8bd23
......@@ -16,3 +16,4 @@ cdef class AbstractGraphEditDistance(Base):
cdef double insert_cost(self, int i, int j, nodesH, H)
cdef double delete_cost(self, int i, int j, nodesG, G)
cpdef double substitute_cost(self, node1, node2, G, H)
gmatch4py/ged/abstract_graph_edit_dist.pyx
View file @ 0ce8bd23
......@@ -4,14 +4,18 @@ from __future__ import print_function
import sys
import warnings
import numpy as np
cimport numpy as np
try:
from munkres import munkres
except ImportError:
warnings.warn("To obtain optimal results install the Cython 'munkres' module at https://github.com/jfrelinger/cython-munkres-wrapper")
from scipy.optimize import linear_sum_assignment as munkres
cimport numpy as np
from ..base cimport Base
import networkx as nx
from ..helpers.general import parsenx2graph
from cython.parallel cimport prange,parallel
cdef class AbstractGraphEditDistance(Base):
......@@ -90,7 +94,7 @@ cdef class AbstractGraphEditDistance(Base):
cpdef double substitute_cost(self, node1, node2, G, H):
raise NotImplementedError
cpdef np.ndarray compare(self,list listgs, list selected):
cpdef np.ndarray compare_old(self,list listgs, list selected):
cdef int n = len(listgs)
cdef np.ndarray comparison_matrix = np.zeros((n, n)).astype(float)
cdef int i,j
......@@ -105,3 +109,23 @@ cdef class AbstractGraphEditDistance(Base):
#comparison_matrix[j, i] = comparison_matrix[i, j]
np.fill_diagonal(comparison_matrix,0)
return comparison_matrix
cpdef np.ndarray compare(self,list listgs, list selected):
cdef int n = len(listgs)
cdef double[:,:] comparison_matrix = np.zeros((n, n))
listgs=parsenx2graph(listgs)
cdef long[:] n_nodes = np.array([g.size() for g in listgs])
cdef bint[:] selected_test = self.get_selected_array(selected,n)
cdef int i,j
val=np.inf
with nogil, parallel(num_threads=8):
for i in prange(n,schedule='static'):
for j in range(n):
if n_nodes[i]>0 and n_nodes[j]>0 and selected_test[i] :
with gil:
comparison_matrix[i][j] = self.distance_ged(listgs[i],listgs[j])
else:
comparison_matrix[i][j] = 0
#comparison_matrix[j, i] = comparison_matrix[i, j]
return np.array(comparison_matrix)
gmatch4py/ged/bipartite_graph_matching_2.pyx
View file @ 0ce8bd23
......@@ -2,7 +2,8 @@
import numpy as np
cimport numpy as np
from ..base cimport Base
from cython.parallel cimport prange,parallel
from ..helpers.general import parsenx2graph
cdef class BP_2(Base):
......@@ -32,7 +33,7 @@ cdef class BP_2(Base):
self.edge_del = edge_del
self.edge_ins = edge_ins
cpdef np.ndarray compare(self,list listgs, list selected):
cpdef np.ndarray compare_old(self,list listgs, list selected):
cdef int n = len(listgs)
cdef np.ndarray comparison_matrix = np.zeros((n, n)).astype(float)
cdef int i,j
......@@ -48,6 +49,27 @@ cdef class BP_2(Base):
return comparison_matrix
cpdef np.ndarray compare(self,list listgs, list selected):
cdef int n = len(listgs)
cdef list new_gs=parsenx2graph(listgs)
cdef double[:,:] comparison_matrix = np.zeros((n, n))
cdef bint[:] selected_test = self.get_selected_array(selected,n)
cdef int i,j
cdef long[:] n_nodes = np.array([g.size() for g in new_gs])
cdef long[:] n_edges = np.array([g.density() for g in new_gs])
with nogil, parallel(num_threads=4):
for i in prange(n,schedule='static'):
for j in range(i,n):
if n_nodes[i] > 0 and n_nodes[j] > 0 and selected_test[i] == True:
with gil:
comparison_matrix[i, j] = self.bp2(new_gs[i], new_gs[j])
else:
comparison_matrix[i, j] = 0
comparison_matrix[j, i] = comparison_matrix[i, j]
return comparison_matrix
cdef double bp2(self, g1, g2):
"""
......@@ -100,8 +122,8 @@ cdef class BP_2(Base):
list containing costs from the optimal edit path
"""
cdef list psi_=[]
cdef list nodes1 = list(g1.nodes)
cdef list nodes2 = list(g2.nodes)
cdef list nodes1 = list(g1.nodes())
cdef list nodes2 = list(g2.nodes())
for u in nodes1:
v=None
for w in nodes2:
......@@ -125,9 +147,9 @@ cdef class BP_2(Base):
:param g2: Second Graph
:return:
"""
cdef np.ndarray min_sum = np.zeros(len(g1))
nodes1 = list(g1.nodes)
nodes2 = list(g2.nodes)
cdef np.ndarray min_sum = np.zeros(g1.size())
nodes1 = list(g1.nodes())
nodes2 = list(g2.nodes())
nodes2.extend([None])
cdef np.ndarray min_i
for i in range(len(nodes1)):
......@@ -178,8 +200,8 @@ cdef class BP_2(Base):
"""
#if isinstance(g1, nx.MultiDiGraph):
cdef list edges1 = list(g1.edges(n1)) if n1 else []
cdef list edges2 = list(g2.edges(n2)) if n2 else []
cdef list edges1 = g1.get_edges_no(n1) if n1 else []
cdef list edges2 = g2.get_edges_no(n2) if n2 else []
cdef np.ndarray min_sum = np.zeros(len(edges1))
edges2.extend([None])
......
gmatch4py/ged/graph_edit_dist.pxd
View file @ 0ce8bd23
......@@ -4,6 +4,7 @@ from .abstract_graph_edit_dist cimport AbstractGraphEditDistance
cdef class GraphEditDistance(AbstractGraphEditDistance):
cpdef object relabel_cost(self, node1, node2, G, H)
cpdef double substitute_cost(self, node1, node2, G, H)
cdef double delete_cost(self, int i, int j, nodesG, G)
cdef double insert_cost(self, int i, int j, nodesH, H)
\ No newline at end of file
gmatch4py/ged/graph_edit_dist.pyx
View file @ 0ce8bd23
......@@ -7,6 +7,7 @@ import numpy as np
cimport numpy as np
from .abstract_graph_edit_dist cimport AbstractGraphEditDistance
from ..base cimport intersection,union_
from ..graph cimport Graph
cdef class GraphEditDistance(AbstractGraphEditDistance):
......@@ -14,52 +15,43 @@ cdef class GraphEditDistance(AbstractGraphEditDistance):
def __init__(self,node_del,node_ins,edge_del,edge_ins,weighted=False):
AbstractGraphEditDistance.__init__(self,node_del,node_ins,edge_del,edge_ins)
self.weighted=weighted
cpdef double substitute_cost(self, node1, node2, G, H):
return self.relabel_cost(node1, node2, G, H)
def add_edges(self,node1,node2,G):
R=nx.create_empty_copy(G)
try:
R.add_edges_from(G.edges(node1,node2))
except Exception as e:
# To counter bug with a None for attribute... weird ??
arr_=G.edges(node1,node2)
new_list=[]
for item in arr_:
new_list.append((item[0],item[1]))
R.add_edges_from(new_list)
return R
def relabel_cost(self, node1, node2, G, H):
cpdef object relabel_cost(self, node1, node2, G, H):
## Si deux noeuds égaux
if node1 == node2 and G.degree(node1) == H.degree(node2):
return 0.0
elif node1 == node2 and G.degree(node1) != H.degree(node2):
R = self.add_edges(node1,node2,G)
R2 = self.add_edges(node1,node2,H)
inter_=intersection(R,R2).number_of_edges()
add_diff=abs(R2.number_of_edges()-inter_)
del_diff=abs(R.number_of_edges()-inter_)
#R = Graph(self.add_edges(node1,node2,G),G.get_node_key(),G.get_egde_key())
#R2 = Graph(self.add_edges(node1,node2,H),H.get_node_key(),H.get_egde_key())
#inter_= R.size_edge_intersect(R2)
R=set(G.get_edges_no(node1))
R2=set(H.get_edges_no(node2))
inter_=R.intersection(R2)
add_diff=abs(len(R2)-len(inter_))#abs(R2.density()-inter_)
del_diff=abs(len(R)-len(inter_))#abs(R.density()-inter_)
return (add_diff*self.edge_ins)+(del_diff*self.edge_del)
#si deux noeuds connectés
if (node1,node2) in G.edges() or (node2,node1) in G.edges():
if G.has_edge(node1,node2) or G.has_edge(node2,node1):
return self.node_ins+self.node_del
if not node2 in G:
nodesH=list(H.nodes())
index=nodesH.index(node2)
if not node2 in G.nodes():
nodesH=H.nodes()
index=list(nodesH).index(node2)
return self.node_del+self.node_ins+self.insert_cost(index,index,nodesH,H)
return sys.maxsize
cdef double delete_cost(self, int i, int j, nodesG, G):
if i == j:
return self.node_del+(G.degree(nodesG[i],weight=("weight" if self.weighted else None))*self.edge_del) # Deleting a node implicate to delete in and out edges
return self.node_del+(G.degree(nodesG[i],weight=True)*self.edge_del) # Deleting a node implicate to delete in and out edges
return sys.maxsize
cdef double insert_cost(self, int i, int j, nodesH, H):
if i == j:
deg=H.degree(nodesH[j],weight=("weight" if self.weighted else None))
deg=H.degree(nodesH[j],weight=True)
if isinstance(deg,dict):deg=0
return self.node_ins+(deg*self.edge_ins)
else:
......
gmatch4py/ged/graph_edit_dist_2.pyx deleted 100644 → 0
View file @ 31bf928c
# -*- coding: UTF-8 -*-
import sys
import networkx as nx
import numpy as np
cimport numpy as np
from .abstract_graph_edit_dist cimport AbstractGraphEditDistance
from ..base cimport intersection,union_
from ..graph cimport Graph
cdef class GraphEditDistance(AbstractGraphEditDistance):
def __init__(self,node_del,node_ins,edge_del,edge_ins,weighted=False):
AbstractGraphEditDistance.__init__(self,node_del,node_ins,edge_del,edge_ins)
self.weighted=weighted
cpdef double substitute_cost(self, node1, node2, G, H):
return self.relabel_cost(node1, node2, G, H)
def add_edges(self,node1,node2,G):
R=nx.create_empty_copy(G.get_nx())
try:
R.add_edges_from(G.edges(node1,node2))
except Exception as e:
# To counter bug with a None for attribute... weird ??
arr_=G.edges(node1,node2)
new_list=[]
for item in arr_:
new_list.append((item[0],item[1]))
R.add_edges_from(new_list)
return R
cpdef relabel_cost(self, node1, node2, G, H):
## Si deux noeuds égaux
if node1 == node2 and G.degree(node1) == H.degree(node2):
return 0.0
elif node1 == node2 and G.degree(node1) != H.degree(node2):
R = Graph(self.add_edges(node1,node2,G),G.get_node_key(),G.get_egde_key())
R2 = Graph(self.add_edges(node1,node2,H),H.get_node_key(),H.get_egde_key())
inter_= R.size_edge_intersect(R2)
add_diff=abs(R2.density()-inter_)
del_diff=abs(R.density()-inter_)
return (add_diff*self.edge_ins)+(del_diff*self.edge_del)
#si deux noeuds connectés
if G.has_edge(*(node1,node2)) or G.has_edge(*(node2,node1)):
return self.node_ins+self.node_del
if not node2 in G:
nodesH=H.nodes()
index=list(nodesH).index(node2)
return self.node_del+self.node_ins+self.insert_cost(index,index,nodesH,H)
return sys.maxsize
cdef double delete_cost(self, int i, int j, nodesG, G):
if i == j:
return self.node_del+(G.degree(nodesG[i],weight=True)*self.edge_del) # Deleting a node implicate to delete in and out edges
return sys.maxsize
cdef double insert_cost(self, int i, int j, nodesH, H):
if i == j:
deg=H.degree(nodesH[j],weight=True)
if isinstance(deg,dict):deg=0
return self.node_ins+(deg*self.edge_ins)
else:
return sys.maxsize
\ No newline at end of file
gmatch4py/ged/greedy_edit_distance.pyx
View file @ 0ce8bd23
......@@ -4,6 +4,7 @@ import sys
from .graph_edit_dist cimport GraphEditDistance
import numpy as np
cimport numpy as np
from cython.parallel cimport prange,parallel
cdef class GreedyEditDistance(GraphEditDistance):
"""
......@@ -20,15 +21,6 @@ cdef class GreedyEditDistance(GraphEditDistance):
cdef list edit_costs(self, G, H):
cdef np.ndarray cost_matrix=self.create_cost_matrix(G,H)
"""
cdef np.ndarray cost_matrix_2=cost_matrix.copy()
cdef list psi=[]
for i in range(len(cost_matrix)):
phi_i=np.argmin((cost_matrix[i]))
cost_matrix=np.delete(cost_matrix,phi_i,1)
psi.append([i,phi_i+i]) #+i to compensate the previous column deletion
return [cost_matrix_2[psi[i][0]][psi[i][1]] for i in range(len(psi))]
"""
cdef np.ndarray cost_matrix_2=cost_matrix.copy().astype(np.double)
cdef list psi=[]
for i in range(len(cost_matrix)):
......
gmatch4py/ged/hausdorff_edit_distance.pyx
View file @ 0ce8bd23
......@@ -3,6 +3,8 @@
import numpy as np
cimport numpy as np
from ..base cimport Base
from cython.parallel cimport prange,parallel
from ..helpers.general import parsenx2graph
cdef class HED(Base):
"""
......@@ -27,7 +29,7 @@ cdef class HED(Base):
self.edge_ins = edge_ins
cpdef np.ndarray compare(self,list listgs, list selected):
cpdef np.ndarray compare_old(self,list listgs, list selected):
cdef int n = len(listgs)
cdef np.ndarray comparison_matrix = np.zeros((n, n)).astype(float)
cdef int i,j
......@@ -42,6 +44,27 @@ cdef class HED(Base):
comparison_matrix[j, i] = comparison_matrix[i, j]
return comparison_matrix
cpdef np.ndarray compare(self,list listgs, list selected):
cdef int n = len(listgs)
cdef list new_gs=parsenx2graph(listgs)
cdef double[:,:] comparison_matrix = np.zeros((n, n))
cdef bint[:] selected_test = self.get_selected_array(selected,n)
cdef int i,j
cdef long[:] n_nodes = np.array([g.size() for g in new_gs])
cdef long[:] n_edges = np.array([g.density() for g in new_gs])
with nogil, parallel(num_threads=4):
for i in prange(n,schedule='static'):
for j in range(i,n):
if n_nodes[i] > 0 and n_nodes[j] > 0 and selected_test[i] == True:
with gil:
comparison_matrix[i, j] = self.hed(new_gs[i], new_gs[j])
else:
comparison_matrix[i, j] = 0
comparison_matrix[j, i] = comparison_matrix[i, j]
return comparison_matrix
cdef float hed(self, g1, g2):
......@@ -61,8 +84,8 @@ cdef class HED(Base):
:return:
"""
cdef np.ndarray min_sum = np.zeros(len(g1))
nodes1 = list(g1.nodes)
nodes2 = list(g2.nodes)
nodes1 = list(g1.nodes())
nodes2 = list(g2.nodes())
nodes2.extend([None])
cdef np.ndarray min_i
for i in range(len(nodes1)):
......@@ -113,8 +136,8 @@ cdef class HED(Base):
"""
#if isinstance(g1, nx.MultiDiGraph):
cdef list edges1 = list(g1.edges(n1)) if n1 else []
cdef list edges2 = list(g2.edges(n2)) if n2 else []
cdef list edges1 = g1.get_edges_no(n1) if n1 else []
cdef list edges2 = g2.get_edges_no(n2) if n2 else []
cdef np.ndarray min_sum = np.zeros(len(edges1))
edges2.extend([None])
......
gmatch4py/graph.pxd
View file @ 0ce8bd23
......@@ -38,6 +38,7 @@ cdef class Graph:
cdef dict degree_per_attr # degree information per attr val
cdef dict degree_per_attr_weighted # degree information per attr val
cdef list attr_nodes # list of attr(dict) values for each node
cdef dict edges_of_nodes # list of egdes connected to each node
# EDGES ATTRIBUTES
##################
......@@ -107,7 +108,8 @@ cdef class Graph:
## GETTER
#########
cpdef list get_edges_(self,e1,e2)
cpdef list get_edges_ed(self,str e1, str e2)
cpdef list get_edges_no(self,str n)
cpdef set get_edges_hash(self)
cpdef set get_nodes_hash(self)
......
gmatch4py/graph.pyx
View file @ 0ce8bd23
......@@ -59,7 +59,9 @@ cdef class Graph:
self.degree_per_attr_weighted={attr_v:{n:{"in":0,"out":0} for n in self.nodes_list} for attr_v in self.unique_edge_attr_vals}
# Retrieving Degree Information
self.edges_of_nodes={}
for n in self.nodes_list:
self.edges_of_nodes[n]=[self.hash_edge_attr(e1,e2,attr_dict[self.edge_attr_key]) if self.is_edge_attr else self.hash_edge(e1,e2) for e1,e2,attr_dict in G.edges(n,data=True)]
degree_all.append(G.degree(n))
degree_all_weighted.append(G.degree(n,weight="weight"))
if self.is_directed:
......@@ -161,12 +163,12 @@ cdef class Graph:
cpdef bint has_edge(self,str n_id1,str n_id2):
if self.is_directed:
if n_id1 in self.edges_hash_map and n_id2 in self.edges_hash_map[n_id1][n_id2]:
if n_id1 in self.edges_hash_map and n_id2 in self.edges_hash_map[n_id1]:
return True
else:
if n_id1 in self.edges_hash_map and n_id2 in self.edges_hash_map[n_id1][n_id2]:
if n_id1 in self.edges_hash_map and n_id2 in self.edges_hash_map[n_id1]:
return True
if n_id2 in self.edges_hash_map and n_id1 in self.edges_hash_map[n_id2][n_id1]:
if n_id2 in self.edges_hash_map and n_id1 in self.edges_hash_map[n_id2]:
return True
return False
......@@ -199,12 +201,14 @@ cdef class Graph:
else:
return self.edges_list
cpdef list get_edges_(self,e1,e2):
cpdef list get_edges_ed(self,str e1,str e2):
if self.is_edge_attr:
hashes=self.edges_hash_map[e1][e2]
return [(e1,e2,self.edges_attr_list[self.edges_hash_idx[hash_]])for hash_ in hashes]
else:
return [(e1,e2,None)]
cpdef list get_edges_no(self,str n):
return self.edges_of_nodes[n]
cpdef dict get_edge_attr(self,edge_hash):
return self.edges_attr_list[self.edges_hash_idx[edge_hash]]
......
gmatch4py/helpers/general.pyx 0 → 100644
View file @ 0ce8bd23
from ..graph cimport Graph
import networkx as nx
def parsenx2graph(list_gs):
new_gs=[nx.relabel_nodes(g,{node:str(node) for node in list(g.nodes)},copy=True) for g in list_gs]
new_gs=[Graph(g) for g in new_gs]
return new_gs
gmatch4py/jaccard.pyx
View file @ 0ce8bd23
......@@ -5,14 +5,16 @@ cimport numpy as np
from .base cimport Base
from .base cimport intersection,union_
from ..helpers.general import parsenx2graph
from cython.parallel cimport prange,parallel
cdef class Jaccard(Base):
def __init__(self):
Base.__init__(self,0,True)
cpdef np.ndarray compare(self,list listgs, list selected):
cpdef np.ndarray compare_old(self,list listgs, list selected):
cdef int n = len(listgs)
cdef np.ndarray comparison_matrix = np.zeros((n, n))
cdef int i,j
......@@ -37,5 +39,38 @@ cdef class Jaccard(Base):
return comparison_matrix
cpdef np.ndarray compare(self,list listgs, list selected):
cdef int n = len(listgs)
cdef list new_gs=parsenx2graph(listgs)
cdef double[:,:] comparison_matrix = np.zeros((n, n))
cdef long[:] n_nodes = np.array([g.size() for g in new_gs])
cdef long[:] n_edges = np.array([g.density() for g in new_gs])
cdef int i,j
cdef bint[:] selected_test = self.get_selected_array(selected,n)
cdef double[:,:] intersect_len_nodes = np.zeros((n, n))
cdef double[:,:] intersect_len_edges = np.zeros((n, n))
cdef double[:,:] union_len_nodes = np.zeros((n, n))
cdef double[:,:] union_len_edges = np.zeros((n, n))
for i in range(n):
for j in range(i,n):
intersect_len_nodes[i][j]=new_gs[i].size_node_intersect(new_gs[j])
intersect_len_edges[i][j]=new_gs[i].size_edge_intersect(new_gs[j])#len(set(hash_edges[i]).intersection(hash_edges[j]))
union_len_nodes[i][j]=new_gs[i].size_node_union(new_gs[j])
union_len_edges[i][j]=new_gs[i].size_node_union(new_gs[j])
with nogil, parallel(num_threads=4):
for i in prange(n,schedule='static'):
for j in range(i,n):
if n_nodes[i] > 0 and n_nodes[j] > 0 and selected_test[i]:
if union_len_edges[i][j] >0 and union_len_nodes[i][j] >0:
comparison_matrix[i][j]= \
(intersect_len_edges[i][j]/union_len_edges[i][j])*\
(intersect_len_nodes[i][j]/union_len_nodes[i][j])
else:
comparison_matrix[i][j] = 0.
comparison_matrix[j][i] = comparison_matrix[i][j]
return np.array(comparison_matrix)
gmatch4py/mcs.pyx
View file @ 0ce8bd23
# coding = utf-8
import numpy as np
cimport numpy as np
from .graph cimport Graph
from .base cimport Base
from cython.parallel cimport prange,parallel
from ..helpers.general import parsenx2graph
cdef class MCS(Base):
"""
......@@ -12,7 +14,7 @@ cdef class MCS(Base):
def __init__(self):
Base.__init__(self,0,True)
cpdef np.ndarray compare(self,list listgs, list selected):
cpdef np.ndarray compare_old(self,list listgs, list selected):
cdef int n = len(listgs)
cdef np.ndarray comparison_matrix = np.zeros((n, n))
for i in range(n):
......@@ -25,6 +27,28 @@ cdef class MCS(Base):
comparison_matrix[i, j] = 0.
comparison_matrix[j, i] = comparison_matrix[i, j]
return comparison_matrix
cpdef np.ndarray compare(self,list listgs, list selected):
cdef int n = len(listgs)
cdef double [:,:] comparison_matrix = np.zeros((n, n))
cdef bint[:] selected_test = self.get_selected_array(selected,n)
cdef list new_gs=parsenx2graph(listgs)
cdef long[:] n_nodes = np.array([g.size() for g in new_gs])
cdef double [:,:] intersect_len_nodes = np.zeros((n, n))
cdef int i,j
for i in range(n):
for j in range(i,n):
intersect_len_nodes[i][j]=new_gs[i].size_node_intersect(new_gs[j])
with nogil, parallel(num_threads=4):
for i in prange(n,schedule='static'):
for j in range(i, n):
if n_nodes[i] > 0 and n_nodes[j] > 0 and selected_test[i]:
comparison_matrix[i][j] = intersect_len_nodes[i][j]/max(n_nodes[i],n_nodes[j])
else:
comparison_matrix[i][j] = 0.
comparison_matrix[j][i] = comparison_matrix[i][j]
return np.array(comparison_matrix)
def s_mcs(self,G, H):
"""
......
gmatch4py/vertex_edge_overlap.pyx
View file @ 0ce8bd23
......@@ -5,6 +5,7 @@ cimport numpy as np
from .base cimport Base,intersection
from .graph cimport Graph
from cython.parallel cimport prange,parallel
from ..helpers.general import parsenx2graph
cdef class VertexEdgeOverlap(Base):
......@@ -18,19 +19,35 @@ cdef class VertexEdgeOverlap(Base):
def __init__(self):
Base.__init__(self,0,True)
cpdef np.ndarray compare_old(self,list listgs, list selected):
n = len(listgs)
cdef np.ndarray comparison_matrix = np.zeros((n, n))
cdef list inter_ver,inter_ed
cdef int denom,i,j
for i in range(n):
for j in range(i,n):
g1,g2 = listgs[i],listgs[j]
f=self.isAccepted(g1,i,selected)
if f:
inter_g= intersection(g1,g2)
denom=g1.number_of_nodes()+g2.number_of_nodes()+\
g1.number_of_edges()+g2.number_of_edges()
if denom == 0:
continue
comparison_matrix[i,j]=(2*(inter_g.number_of_nodes()
+inter_g.number_of_edges()))/denom # Data = True --> For nx.MultiDiGraph
comparison_matrix[j, i] = comparison_matrix[i, j]
return comparison_matrix
cpdef np.ndarray compare(self,list listgs, list selected):
cdef int n = len(listgs)
cdef list new_gs=[Graph(g) for g in listgs]
cdef list new_gs=parsenx2graph(listgs)
cdef double[:,:] comparison_matrix = np.zeros((n, n))
cdef list inter_ver,inter_ed
cdef int denom,i,j
cdef bint f
cdef long[:] n_nodes = np.array([g.size() for g in new_gs])
cdef long[:] n_edges = np.array([g.density() for g in new_gs])
#print(type(test[0,0]))
#cdef str[:,:] hash_edges = test
cdef bint[:] selected_test
cdef bint[:] selected_test = self.get_selected_array(selected,n)
cdef double[:,:] intersect_len_nodes = np.zeros((n, n))
cdef double[:,:] intersect_len_edges = np.zeros((n, n))
......@@ -42,7 +59,7 @@ cdef class VertexEdgeOverlap(Base):
with nogil, parallel(num_threads=4):
for i in prange(n,schedule='static'):
for j in range(i,n):
if n_nodes[i] > 0 and n_nodes[j] > 0 :
if n_nodes[i] > 0 and n_nodes[j] > 0 and selected_test[i] == True:
denom=n_nodes[i]+n_nodes[j]+\
n_edges[i]+n_edges[j]
if denom == 0:
......
setup.py
View file @ 0ce8bd23
......@@ -70,7 +70,7 @@ setup(
cmdclass={'build_ext': build_ext},
setup_requires=["numpy","networkx","scipy",'scikit-learn'],
install_requires=["numpy","networkx","scipy",'scikit-learn'],
version="0.2.2",
version="0.2.2alpha",
classifiers=[
"Programming Language :: Python :: 3",
"License :: OSI Approved :: MIT License",
......@@ -78,7 +78,7 @@ setup(
]
)
#Clean cpp and compiled file
f=False
f=True
if f:
if os.path.exists("build"):
shutil.rmtree("build")
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment