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some optimizations to igraph_incuded_subgraph; work in progress
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@ntamas
ntamas committed Sep 1, 2016
1 parent 1bc4a2b commit 32a743f
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Showing 2 changed files with 89 additions and 74 deletions.
119 changes: 45 additions & 74 deletions src/structural_properties.c
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@
#include "igraph_topology.h"
#include "igraph_qsort.h"
#include "config.h"
#include "structural_properties_internal.h"

#include <assert.h>
#include <string.h>
Expand Down Expand Up @@ -1737,17 +1738,6 @@ int igraph_rewire(igraph_t *graph, igraph_integer_t n, igraph_rewiring_t mode) {

}

int igraph_i_subgraph_copy_and_delete(const igraph_t *graph, igraph_t *res,
const igraph_vs_t vids,
igraph_vector_t *map,
igraph_vector_t *invmap);

int igraph_i_subgraph_create_from_scratch(const igraph_t *graph,
igraph_t *res,
const igraph_vs_t vids,
igraph_vector_t *map,
igraph_vector_t *invmap);

/**
* Subgraph creation, old version: it copies the graph and then deletes
* unneeded vertices.
Expand Down Expand Up @@ -1814,8 +1804,9 @@ int igraph_i_subgraph_create_from_scratch(const igraph_t *graph,
igraph_bool_t directed = igraph_is_directed(graph);
long int no_of_nodes = igraph_vcount(graph);
long int no_of_new_nodes = 0;
char* seen_edges = 0;
long int i, j, n;
long int to;
igraph_integer_t eid;
igraph_vector_t vids_old2new, vids_new2old;
igraph_vector_t eids_new2old;
igraph_vector_t nei_edges;
Expand All @@ -1828,15 +1819,15 @@ int igraph_i_subgraph_create_from_scratch(const igraph_t *graph,
* opposite order */
IGRAPH_VECTOR_INIT_FINALLY(&eids_new2old, 0);
if (invmap) {
my_vids_new2old=invmap;
my_vids_new2old = invmap;
igraph_vector_clear(my_vids_new2old);
} else {
IGRAPH_VECTOR_INIT_FINALLY(&vids_new2old, 0);
}
IGRAPH_VECTOR_INIT_FINALLY(&new_edges, 0);
IGRAPH_VECTOR_INIT_FINALLY(&nei_edges, 0);
if (map) {
my_vids_old2new=map;
my_vids_old2new = map;
IGRAPH_CHECK(igraph_vector_resize(map, no_of_nodes));
igraph_vector_null(map);
} else {
Expand All @@ -1863,76 +1854,49 @@ int igraph_i_subgraph_create_from_scratch(const igraph_t *graph,
for (i = 0; i < n; i++) {
long int vid = (long int) VECTOR(nei_edges)[i];
if (VECTOR(*my_vids_old2new)[vid] == 0) {
VECTOR(*my_vids_old2new)[vid] = ++no_of_new_nodes;
IGRAPH_CHECK(igraph_vector_push_back(my_vids_new2old, vid));
no_of_new_nodes++;
VECTOR(*my_vids_old2new)[vid] = no_of_new_nodes;
}
}

/* Allocate some memory for the seen_edges array that avoids processing edges
* twice for undirected graphs */
if (!directed) {
seen_edges = igraph_Calloc(igraph_ecount(graph), char);
if (seen_edges == 0)
IGRAPH_ERROR("cannot calculate subgraph", IGRAPH_ENOMEM);
IGRAPH_FINALLY(igraph_free, seen_edges);
}

/* Calculate the mapping from the new node IDs to the new ones
* and also create the new edge list */
IGRAPH_CHECK(igraph_vector_resize(my_vids_new2old, no_of_new_nodes));
for (i = 0; i < no_of_nodes; i++) {
long int new_vid = (long int) VECTOR(*my_vids_old2new)[i] - 1;
if (new_vid < 0)
continue;

VECTOR(*my_vids_new2old)[new_vid] = i;
/* Create the new edge list */
for (i = 0; i < no_of_new_nodes; i++) {
long int old_vid = (long int) VECTOR(*my_vids_new2old)[i];
long int new_vid = i;

IGRAPH_CHECK(igraph_incident(graph, &nei_edges, (igraph_integer_t) i,
IGRAPH_OUT));
IGRAPH_CHECK(igraph_incident(graph, &nei_edges, old_vid, IGRAPH_OUT));
n = igraph_vector_size(&nei_edges);

if (directed) {
for (j = 0; j < n; j++) {
igraph_integer_t eid = (igraph_integer_t) VECTOR(nei_edges)[j];
long int from, to;

from = (long int) VECTOR(*my_vids_old2new)[
(long int)IGRAPH_FROM(graph, eid) ];
if (!from) continue;
to = (long int) VECTOR(*my_vids_old2new)[
(long int)IGRAPH_TO(graph, eid)];
eid = (igraph_integer_t) VECTOR(nei_edges)[j];

to = (long int) VECTOR(*my_vids_old2new)[ (long int)IGRAPH_TO(graph, eid) ];
if (!to) continue;

IGRAPH_CHECK(igraph_vector_push_back(&new_edges, from-1));
IGRAPH_CHECK(igraph_vector_push_back(&new_edges, new_vid));
IGRAPH_CHECK(igraph_vector_push_back(&new_edges, to-1));
IGRAPH_CHECK(igraph_vector_push_back(&eids_new2old, eid));
}
} else {
for (j = 0; j < n; j++) {
igraph_integer_t eid = (igraph_integer_t) VECTOR(nei_edges)[j];
long int from, to;

from = (long int) VECTOR(*my_vids_old2new)[
(long int)IGRAPH_FROM(graph, eid)];
if (!from) continue;
to = (long int) VECTOR(*my_vids_old2new)[
(long int)IGRAPH_TO(graph, eid)];
if (!to) continue;
if (seen_edges[(long int)eid])
eid = (igraph_integer_t) VECTOR(nei_edges)[j];

if (IGRAPH_FROM(graph, eid) != old_vid) /* avoid processing edges twice */
continue;

seen_edges[(long int)eid] = 1;
IGRAPH_CHECK(igraph_vector_push_back(&new_edges, from-1));
to = (long int) VECTOR(*my_vids_old2new)[ (long int)IGRAPH_TO(graph, eid) ];
if (!to) continue;

IGRAPH_CHECK(igraph_vector_push_back(&new_edges, new_vid));
IGRAPH_CHECK(igraph_vector_push_back(&new_edges, to-1));
IGRAPH_CHECK(igraph_vector_push_back(&eids_new2old, eid));
}
}
}

/* Get rid of some vectors that are not needed anymore */
if (!directed) {
igraph_free(seen_edges);
IGRAPH_FINALLY_CLEAN(1);
}
if (!map) {
igraph_vector_destroy(&vids_old2new);
IGRAPH_FINALLY_CLEAN(1);
Expand Down Expand Up @@ -2066,27 +2030,34 @@ int igraph_induced_subgraph(const igraph_t *graph, igraph_t *res,
/* invmap= */ 0);
}

igraph_subgraph_implementation_t igraph_i_induced_subgraph_suggest_implementation(
const igraph_t *graph, const igraph_vs_t vids) {
double ratio;
igraph_integer_t num_vs;

if (igraph_vs_is_all(&vids)) {
ratio = 1.0;
} else {
IGRAPH_CHECK(igraph_vs_size(graph, &vids, &num_vs));
ratio = (igraph_real_t) num_vs / igraph_vcount(graph);
}

/* TODO: needs benchmarking; threshold was chosen totally arbitrarily */
if (ratio > 0.5) {
return IGRAPH_SUBGRAPH_COPY_AND_DELETE;
} else {
return IGRAPH_SUBGRAPH_CREATE_FROM_SCRATCH;
}
}

int igraph_induced_subgraph_map(const igraph_t *graph, igraph_t *res,
const igraph_vs_t vids,
igraph_subgraph_implementation_t impl,
igraph_vector_t *map,
igraph_vector_t *invmap) {

if (impl == IGRAPH_SUBGRAPH_AUTO) {
double ratio;

if (igraph_vs_is_all(&vids))
ratio = 1.0;
else {
igraph_integer_t num_vs;
IGRAPH_CHECK(igraph_vs_size(graph, &vids, &num_vs));
ratio = (igraph_real_t) num_vs / igraph_vcount(graph);
}

if (ratio > 0.5)
impl = IGRAPH_SUBGRAPH_COPY_AND_DELETE;
else
impl = IGRAPH_SUBGRAPH_CREATE_FROM_SCRATCH;
impl = igraph_i_induced_subgraph_suggest_implementation(graph, vids);
}

switch (impl) {
Expand Down
44 changes: 44 additions & 0 deletions src/structural_properties_internal.h
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Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
/* -*- mode: C -*- */
/*
IGraph library.
Copyright (C) 2011-2016 Gabor Csardi <csardi.gabor@gmail.com>
334 Harvard st, Cambridge, MA, 02138 USA
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program 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.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
02110-1301 USA
*/

#ifndef STRUCTURAL_PROPERTIES_INTERNAL_H
#define STRUCTURAL_PROPERTIES_INTERNAL_H

#include "igraph_constants.h"
#include "igraph_types.h"

igraph_subgraph_implementation_t igraph_i_induced_subgraph_suggest_implementation(
const igraph_t *graph, const igraph_vs_t vids);

int igraph_i_subgraph_copy_and_delete(const igraph_t *graph, igraph_t *res,
const igraph_vs_t vids,
igraph_vector_t *map,
igraph_vector_t *invmap);

int igraph_i_subgraph_create_from_scratch(const igraph_t *graph,
igraph_t *res,
const igraph_vs_t vids,
igraph_vector_t *map,
igraph_vector_t *invmap);

#endif

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