1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
|
/**
*
* This file is part of Tulip (www.tulip-software.org)
*
* Authors: David Auber and the Tulip development Team
* from LaBRI, University of Bordeaux
*
* Tulip is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Tulip is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
* See the GNU General Public License for more details.
*
*/
#include <deque>
#ifdef _OPENMP
#include <omp.h>
#endif
#include <tulip/ConnectedTest.h>
#include "Eccentricity.h"
PLUGIN(EccentricityMetric)
using namespace std;
using namespace tlp;
namespace {
const char * paramHelp[] = {
// property
HTML_HELP_OPEN() \
HTML_HELP_DEF( "type", "bool" ) \
HTML_HELP_DEF( "values", "[true , false]" ) \
HTML_HELP_DEF( "default", "false" ) \
HTML_HELP_BODY() \
"If true, the closeness centrality is computed (i.e. the average distance from the node to all others)."\
HTML_HELP_CLOSE(),
// norm
HTML_HELP_OPEN() \
HTML_HELP_DEF( "type", "bool" ) \
HTML_HELP_DEF( "values", "[true , false]" ) \
HTML_HELP_DEF( "default", "false" ) \
HTML_HELP_BODY() \
"If true, the returned values are normalized. " \
"For the closeness centrality, the reciprocal of the sum of distances is returned. " \
"The eccentricity values are divided by the graph diameter. " \
"<b> Warning : </b> The normalized eccentricity values sould be computed on a (strongly) connected graph."
HTML_HELP_CLOSE(),
// directed
HTML_HELP_OPEN() \
HTML_HELP_DEF( "type", "bool" ) \
HTML_HELP_DEF( "values", "[true , false]" ) \
HTML_HELP_DEF( "default", "false" ) \
HTML_HELP_BODY() \
"If true, the graph is considered directed."\
HTML_HELP_CLOSE(),
};
}
EccentricityMetric::EccentricityMetric(const tlp::PluginContext* context):DoubleAlgorithm(context), allPaths(false), norm(true), directed(false) {
addInParameter<bool>("closeness centrality",paramHelp[0],"false");
addInParameter<bool>("norm",paramHelp[1],"true");
addInParameter<bool>("directed",paramHelp[2],"false");
}
//====================================================================
EccentricityMetric::~EccentricityMetric() {
}
//====================================================================
double EccentricityMetric::compute(node n) {
MutableContainer<unsigned int> distance;
distance.setAll(0);
double val;
val = directed ?
tlp::maxDistance(graph, n, distance, DIRECTED) :
tlp::maxDistance(graph, n, distance, UNDIRECTED);
if(!allPaths)
return val;
double nbAcc = 0.;
node n2;
val = 0.;
forEach(n2, graph->getNodes()) {
if (distance.get(n2.id) < graph->numberOfNodes()) {
nbAcc += 1.;
if(n2!=n)
val += double(distance.get(n2.id)) ;
}
}
if(nbAcc<2.0) return 0.0;
if (norm) val=1.0/val;
else val/=(nbAcc-1.0);
return val;
}
//====================================================================
bool EccentricityMetric::run() {
allPaths = false;
norm = true;
directed = false;
if (dataSet!=NULL) {
dataSet->get("closeness centrality", allPaths);
dataSet->get("norm", norm);
dataSet->get("directed", directed);
}
node n;
size_t i = 0;
vector<node> vecNodes(graph->numberOfNodes());
vector<double> res(graph->numberOfNodes());
forEach(n, graph->getNodes()) {
vecNodes[i] = n;
++i;
}
// omp_set_num_threads(4);
size_t nbElem = vecNodes.size();
unsigned int nbThreads = 1;
#ifdef _OPENMP
nbThreads = omp_get_num_procs();
#endif
// double t1 = omp_get_wtime();
double diameter = 1.0;
bool stopfor = false;
#ifdef _OPENMP
#pragma omp parallel for
#endif
for (int ni = 0; ni < static_cast<int>(nbElem) ; ++ni) {
if (stopfor) continue;
#ifdef _OPENMP
if (omp_get_thread_num() == 0) {
#endif
if (pluginProgress->progress(ni , graph->numberOfNodes() / nbThreads )!=TLP_CONTINUE) {
#ifdef _OPENMP
#pragma omp critical(STOPFOR)
#endif
stopfor = true;
}
#ifdef _OPENMP
}
#endif
res[ni] = compute(vecNodes[ni]);
if(!allPaths && norm)
#ifdef _OPENMP
#pragma omp critical(DIAMETER)
#endif
{
if(diameter<res[ni])
diameter=res[ni];
}
}
for (size_t ni = 0; ni < nbElem; ++ni) {
if(!allPaths && norm)
result->setNodeValue(vecNodes[ni], res[ni]/diameter);
else
result->setNodeValue(vecNodes[ni], res[ni]);
}
/*
double t2 = omp_get_wtime();
for (size_t ni = 0; ni < nbElem; ++ni) {
double val = compute(vecNodes[ni]);
result->setNodeValue(vecNodes[ni], val);
}
double t3 = omp_get_wtime();
tlp::debug() << "omp : " << t2 - t1 << "s" << endl << flush;
tlp::debug() << "sng : " << t3 - t2 << "s" << endl << flush;
*/
/*
Iterator<node> *itN = graph->getNodes();
for (unsigned int i=0; itN->hasNext(); ++i) {
if (pluginProgress->progress(i, graph->numberOfNodes())!=TLP_CONTINUE) break;
node n = itN->next();
result->setNodeValue(n, compute(n));
}
*/
return pluginProgress->state()!=TLP_CANCEL;
}
|
