diff --git a/gmatch4py/base.pxd b/gmatch4py/base.pxd
index f36f2a903ab4a1de9a13f189be4187972bed8903..e3dd39ec7a44d163ec0761eb9f99fb2850fa8141 100644
--- a/gmatch4py/base.pxd
+++ b/gmatch4py/base.pxd
@@ -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)
diff --git a/gmatch4py/base.pyx b/gmatch4py/base.pyx
index f27971f87151c4c67dbc8639a8550dcf8caf3fd7..ac993092459d1027e90a17e8e3106a41a5a30962 100644
--- a/gmatch4py/base.pyx
+++ b/gmatch4py/base.pyx
@@ -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.
diff --git a/gmatch4py/ged/abstract_graph_edit_dist.pxd b/gmatch4py/ged/abstract_graph_edit_dist.pxd
index 9a4b92de1195a188808a4d5223509d59a3be1922..ee01fe9518f21970f26ff2e1a5cba84fca556e8c 100644
--- a/gmatch4py/ged/abstract_graph_edit_dist.pxd
+++ b/gmatch4py/ged/abstract_graph_edit_dist.pxd
@@ -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)
+
diff --git a/gmatch4py/ged/abstract_graph_edit_dist.pyx b/gmatch4py/ged/abstract_graph_edit_dist.pyx
index 141196589418dfac2c4590a380c52ae3d2850e4b..f4b25fde928a0b0c497be35ba9df2bd7a033fbdf 100644
--- a/gmatch4py/ged/abstract_graph_edit_dist.pyx
+++ b/gmatch4py/ged/abstract_graph_edit_dist.pyx
@@ -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)
diff --git a/gmatch4py/ged/bipartite_graph_matching_2.pyx b/gmatch4py/ged/bipartite_graph_matching_2.pyx
index 59e33e08781c00775e36269ca056b48b771f90ca..45fd67f625450c68d0579634de6d652430cfdd14 100644
--- a/gmatch4py/ged/bipartite_graph_matching_2.pyx
+++ b/gmatch4py/ged/bipartite_graph_matching_2.pyx
@@ -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])
diff --git a/gmatch4py/ged/graph_edit_dist.pxd b/gmatch4py/ged/graph_edit_dist.pxd
index 975f39b1ab05df1b55d8d571afc4867d34b63fcf..18020dab052797e7bef10bc24837b4d8802e3f0a 100644
--- a/gmatch4py/ged/graph_edit_dist.pxd
+++ b/gmatch4py/ged/graph_edit_dist.pxd
@@ -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
diff --git a/gmatch4py/ged/graph_edit_dist.pyx b/gmatch4py/ged/graph_edit_dist.pyx
index 331d0bb05fa53831b001f25742bf76818846e21e..3706c283884e6f488124812a0627b8fb5316c16c 100644
--- a/gmatch4py/ged/graph_edit_dist.pyx
+++ b/gmatch4py/ged/graph_edit_dist.pyx
@@ -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:
diff --git a/gmatch4py/ged/graph_edit_dist_2.pyx b/gmatch4py/ged/graph_edit_dist_2.pyx
deleted file mode 100644
index 9120da34ef0d31a70c424bb196a712698ce5d7c1..0000000000000000000000000000000000000000
--- a/gmatch4py/ged/graph_edit_dist_2.pyx
+++ /dev/null
@@ -1,68 +0,0 @@
-# -*- 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
diff --git a/gmatch4py/ged/greedy_edit_distance.pyx b/gmatch4py/ged/greedy_edit_distance.pyx
index b4908cb2337400eec20fa5d20fa6a704b0a61c36..9bdd2c47c9103a2c1a07d5845bbede52beb47b72 100644
--- a/gmatch4py/ged/greedy_edit_distance.pyx
+++ b/gmatch4py/ged/greedy_edit_distance.pyx
@@ -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)):
diff --git a/gmatch4py/ged/hausdorff_edit_distance.pyx b/gmatch4py/ged/hausdorff_edit_distance.pyx
index d2327f6b35da425c0c302eb12b5964a7f9a81450..a83e2a1897bfd9330d2dd9e8beb30d3abd146fa2 100644
--- a/gmatch4py/ged/hausdorff_edit_distance.pyx
+++ b/gmatch4py/ged/hausdorff_edit_distance.pyx
@@ -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])
diff --git a/gmatch4py/graph.pxd b/gmatch4py/graph.pxd
index 4cb6bba0d491f2d1df1f4bcb381f0bb1439f2325..e1ef555680d968f2f84d573b08754cac0749706e 100644
--- a/gmatch4py/graph.pxd
+++ b/gmatch4py/graph.pxd
@@ -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)
diff --git a/gmatch4py/graph.pyx b/gmatch4py/graph.pyx
index 45397f6e07bb1d42c467d9beb672ef50ae1c27c1..4d3b770b1babedcbab3a77c55711ebcff2c20d23 100644
--- a/gmatch4py/graph.pyx
+++ b/gmatch4py/graph.pyx
@@ -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]]
diff --git a/gmatch4py/helpers/general.pyx b/gmatch4py/helpers/general.pyx
new file mode 100644
index 0000000000000000000000000000000000000000..0bb88f726ef6c7f42a80ef923221c0059b4a3417
--- /dev/null
+++ b/gmatch4py/helpers/general.pyx
@@ -0,0 +1,7 @@
+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
diff --git a/gmatch4py/jaccard.pyx b/gmatch4py/jaccard.pyx
index a987192ab183d27f438f1920edaec774830f29a8..99d8b5d03c7fed243a35fd6d56c29e1a80b35710 100644
--- a/gmatch4py/jaccard.pyx
+++ b/gmatch4py/jaccard.pyx
@@ -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)
diff --git a/gmatch4py/mcs.pyx b/gmatch4py/mcs.pyx
index d2742e4f762477587335b3f39021b182a2de4a69..9ad07f06926f3568d3a0afb7bbe290ed70581d00 100644
--- a/gmatch4py/mcs.pyx
+++ b/gmatch4py/mcs.pyx
@@ -1,8 +1,10 @@
# 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):
"""
diff --git a/gmatch4py/vertex_edge_overlap.pyx b/gmatch4py/vertex_edge_overlap.pyx
index 51f365f477ffe9edee3058245ecdbfac912d7ca2..3bbe9c7ee496eb91bb200c046fdc53ec23770664 100644
--- a/gmatch4py/vertex_edge_overlap.pyx
+++ b/gmatch4py/vertex_edge_overlap.pyx
@@ -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:
diff --git a/setup.py b/setup.py
index ecdce15995f8921517ea3ad83a10672aad40fd76..16b9d05a5c4ecb984e4145537bda928a19b553ac 100644
--- a/setup.py
+++ b/setup.py
@@ -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")
diff --git a/gmatch4py/test/test.py b/test/test.py
similarity index 100%
rename from gmatch4py/test/test.py
rename to test/test.py