From aec78a2ca76f4098d867dc30384ce843e7cf027a Mon Sep 17 00:00:00 2001
From: Fize Jacques <jacques.fize@cirad.fr>
Date: Thu, 9 May 2019 14:48:35 +0200
Subject: [PATCH] add edit_path function+ debug graph class + add tqdm progress
bar when using import_dir
---
README.md | 6 +++++-
gmatch4py/ged/abstract_graph_edit_dist.pyx | 20 ++++++++++++++++++++
gmatch4py/graph.pxd | 18 +++++++++---------
gmatch4py/graph.pyx | 22 +++++++++++-----------
gmatch4py/helpers/reader.pyx | 3 ++-
5 files changed, 47 insertions(+), 22 deletions(-)
diff --git a/README.md b/README.md
index 3c7bf65..2d915f9 100644
--- a/README.md
+++ b/README.md
@@ -57,7 +57,6 @@ print(result)
The output is a similarity/distance matrix :
```python
-Out[10]:
array([[0., 14.],
[10., 0.]])
```
@@ -126,6 +125,11 @@ each code is associated with a reference to the original.**
## CHANGELOG
+### 7.05.2019
+
+ * Debug (problems with float edge weight)
+ * Add the `AbstractEditDistance.edit_path(G,H)` method that return the edit path, the cost matrix and the selected cost index in the cost matrix
+ * Add a tqdm progress bar for the `gmatch4py.helpers.reader.import_dir()` function
### 12.03.2019
diff --git a/gmatch4py/ged/abstract_graph_edit_dist.pyx b/gmatch4py/ged/abstract_graph_edit_dist.pyx
index 95ba8d4..b597b13 100644
--- a/gmatch4py/ged/abstract_graph_edit_dist.pyx
+++ b/gmatch4py/ged/abstract_graph_edit_dist.pyx
@@ -51,6 +51,26 @@ cdef class AbstractGraphEditDistance(Base):
cdef list opt_path = self.edit_costs(G,H)
return np.sum(opt_path)
+ def edit_path(self,G,H):
+ """
+ Return the edit path along with the cost matrix and the selected indices from the Munkres Algorithm
+
+ Parameters
+ ----------
+ G : nx.Graph
+ first graph
+ H : nx.Graph
+ second graph
+
+ Returns
+ -------
+ np.array(1D), np.array(2D), (np.array(2D) if munkres) or (np.array(1,2) if scipy)
+ edit_path, cost_matrix, munkres results
+ """
+ cost_matrix = self.create_cost_matrix(G,H).astype(float)
+ index_path= munkres(cost_matrix)
+ return cost_matrix[index_path], cost_matrix, index_path
+
cdef list edit_costs(self, G, H):
"""
diff --git a/gmatch4py/graph.pxd b/gmatch4py/graph.pxd
index e1ef555..d35c42d 100644
--- a/gmatch4py/graph.pxd
+++ b/gmatch4py/graph.pxd
@@ -32,9 +32,9 @@ cdef class Graph:
cdef long[:] nodes_degree # degree list
cdef long[:] nodes_degree_in # in degree list
cdef long[:] nodes_degree_out # out degree list
- cdef long[:] nodes_degree_weighted #weighted vers. of nodes_degree
- cdef long[:] nodes_degree_in_weighted #weighted vers. of nodes_degree_in
- cdef long[:] nodes_degree_out_weighted #weighted vers. of nodes_degree_out
+ cdef double[:] nodes_degree_weighted #weighted vers. of nodes_degree
+ cdef double[:] nodes_degree_in_weighted #weighted vers. of nodes_degree_in
+ cdef double[:] nodes_degree_out_weighted #weighted vers. of nodes_degree_out
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
@@ -97,13 +97,13 @@ cdef class Graph:
# DEGREE FUNCTION
#################
- cpdef int degree(self,str n_id, bint weight=*)
- cpdef int in_degree(self,str n_id, bint weight=*)
- cpdef int out_degree(self,str n_id, bint weight=*)
+ cpdef double degree(self,str n_id, bint weight=*)
+ cpdef double in_degree(self,str n_id, bint weight=*)
+ cpdef double out_degree(self,str n_id, bint weight=*)
- cpdef int in_degree_attr(self,str n_id,str attr_val, bint weight=*)
- cpdef int out_degree_attr(self,str n_id,str attr_val, bint weight=*)
- cpdef int degree_attr(self,str n_id,str attr_val, bint weight=*)
+ cpdef double in_degree_attr(self,str n_id,str attr_val, bint weight=*)
+ cpdef double out_degree_attr(self,str n_id,str attr_val, bint weight=*)
+ cpdef double degree_attr(self,str n_id,str attr_val, bint weight=*)
## GETTER
#########
diff --git a/gmatch4py/graph.pyx b/gmatch4py/graph.pyx
index f3f59c9..1ed87b5 100644
--- a/gmatch4py/graph.pyx
+++ b/gmatch4py/graph.pyx
@@ -108,14 +108,14 @@ cdef class Graph:
self.degree_per_attr_weighted[attr_dict[self.edge_attr_key]][n]["in"]+=1*(attr_dict["weight"] if "weight" in attr_dict else 1 )
self.degree_per_attr_weighted[attr_dict[self.edge_attr_key]][n]["out"]+=1*(attr_dict["weight"] if "weight" in attr_dict else 1 )
-
self.nodes_degree=np.array(degree_all)
self.nodes_degree_in=np.array(degree_in)
self.nodes_degree_out=np.array(degree_out)
- self.nodes_degree_weighted=np.array(degree_all_weighted)
- self.nodes_degree_in_weighted=np.array(degree_in_weighted)
- self.nodes_degree_out_weighted=np.array(degree_out_weighted)
+ self.nodes_degree_weighted=np.array(degree_all_weighted).astype(np.double)
+ self.nodes_degree_in_weighted=np.array(degree_in_weighted).astype(np.double)
+ self.nodes_degree_out_weighted=np.array(degree_out_weighted).astype(np.double)
+
# EDGE INFO INIT
#################
@@ -282,36 +282,36 @@ cdef class Graph:
cpdef int density_attr(self, str attr_val):
return self.number_of_edges_per_attr[attr_val]
- cpdef int degree(self,str n_id, bint weight=False):
+ cpdef double degree(self,str n_id, bint weight=False):
if weight:
return self.nodes_degree_weighted[self.nodes_idx[n_id]]
return self.nodes_degree[self.nodes_idx[n_id]]
- cpdef int in_degree(self,str n_id, bint weight=False):
+ cpdef double in_degree(self,str n_id, bint weight=False):
if weight:
return self.nodes_degree_in_weighted[self.nodes_idx[n_id]]
return self.nodes_degree_in[self.nodes_idx[n_id]]
- cpdef int out_degree(self,str n_id, bint weight=False):
+ cpdef double out_degree(self,str n_id, bint weight=False):
if weight:
return self.nodes_degree_out_weighted[self.nodes_idx[n_id]]
return self.nodes_degree_out[self.nodes_idx[n_id]]
- cpdef int in_degree_attr(self,str n_id,str attr_val, bint weight=False):
+ cpdef double in_degree_attr(self,str n_id,str attr_val, bint weight=False):
if not self.is_edge_attr and not self.is_directed:
raise AttributeError("No edge attribute have been defined")
if weight:
return self.degree_per_attr_weighted[attr_val][n_id]["in"]
return self.degree_per_attr[attr_val][n_id]["in"]
- cpdef int out_degree_attr(self,str n_id,str attr_val, bint weight=False):
+ cpdef double out_degree_attr(self,str n_id,str attr_val, bint weight=False):
if not self.is_edge_attr and not self.is_directed:
raise AttributeError("No edge attribute have been defined")
if weight:
return self.degree_per_attr_weighted[attr_val][n_id]["out"]
return self.degree_per_attr[attr_val][n_id]["out"]
- cpdef int degree_attr(self,str n_id,str attr_val, bint weight=False):
+ cpdef double degree_attr(self,str n_id,str attr_val, bint weight=False):
if not self.is_edge_attr:
raise AttributeError("No edge attribute have been defined")
if not self.is_directed:
@@ -371,7 +371,7 @@ cdef class Graph:
def __init_empty__(self):
self.nodes_list,self.nodes_attr_list,self.nodes_hash,self.nodes_weight,self.attr_nodes=[],[],[],[],[]
- self.nodes_degree,self.nodes_degree_in,self.nodes_degree_out,self.nodes_degree_weighted,self.nodes_degree_in_weighted,self.nodes_degree_out_weighted=np.array([],dtype=np.long),np.array([],dtype=np.long),np.array([],dtype=np.long),np.array([],dtype=np.long),np.array([],dtype=np.long),np.array([],dtype=np.long)
+ self.nodes_degree,self.nodes_degree_in,self.nodes_degree_out,self.nodes_degree_weighted,self.nodes_degree_in_weighted,self.nodes_degree_out_weighted=np.array([],dtype=np.long),np.array([],dtype=np.long),np.array([],dtype=np.long),np.array([],dtype=np.double),np.array([],dtype=np.double),np.array([],dtype=np.double)
self.nodes_idx,self.degree_per_attr,self.degree_per_attr_weighted={},{},{}
self.nodes_hash_set=set([])
self.number_of_nodes = 0
diff --git a/gmatch4py/helpers/reader.pyx b/gmatch4py/helpers/reader.pyx
index ea9b8de..bfc3125 100644
--- a/gmatch4py/helpers/reader.pyx
+++ b/gmatch4py/helpers/reader.pyx
@@ -1,6 +1,7 @@
# coding = utf-8
import sys, os, glob, json, re
import networkx as nx
+from tqdm import tqdm
"""
@@ -66,7 +67,7 @@ def import_dir(directory,format="gexf",numbered=True):
graphs= [nx.Graph()]*(n+1)
association_map, i = {}, 0
- for fn in fns:
+ for fn in tqdm(fns,desc="Loading Graphs from {0}".format(directory)):
if not numbered:
graphs.append(methods_read_graph[format](fn))
association_map[fn]=i
--
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