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/*************************************************************************
* Copyright (c) 2011 AT&T Intellectual Property
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* https://www.eclipse.org/legal/epl-v10.html
*
* Contributors: Details at https://graphviz.org
*************************************************************************/
/************************************************
Functions for computing the high-dimensional
embedding and the PCA projection.
************************************************/
#include <neatogen/dijkstra.h>
#include <neatogen/bfs.h>
#include <neatogen/kkutils.h>
#include <neatogen/embed_graph.h>
#include <stdlib.h>
#include <stdio.h>
#include <time.h>
#include <util/alloc.h>
void embed_graph(vtx_data * graph, int n, int dim, DistType *** Coords,
int reweight_graph)
{
/* Compute 'dim'-dimensional high-dimensional embedding (HDE) for the 'n' nodes
The embedding is based on choosing 'dim' pivots, and associating each
coordinate with a unique pivot, assigning it to the graph-theoretic distances
of all nodes from the pivots
*/
int i, j;
int node;
DistType *storage = gv_calloc(n * dim, sizeof(DistType));
DistType **coords = *Coords;
DistType *dist = gv_calloc(n, sizeof(DistType)); // this vector stores the
// distances of each nodes
// to the selected “pivots”
float *old_weights = graph[0].ewgts;
DistType max_dist = 0;
/* this matrix stores the distance between each node and each "pivot" */
*Coords = coords = gv_calloc(dim, sizeof(DistType *));
for (i = 0; i < dim; i++)
coords[i] = storage + i * n;
if (reweight_graph) {
compute_new_weights(graph, n);
}
/* select the first pivot */
node = rand() % n;
if (reweight_graph) {
ngdijkstra(node, graph, n, coords[0]);
} else {
bfs(node, graph, n, coords[0]);
}
for (i = 0; i < n; i++) {
dist[i] = coords[0][i];
if (dist[i] > max_dist) {
node = i;
max_dist = dist[i];
}
}
/* select other dim-1 nodes as pivots */
for (i = 1; i < dim; i++) {
if (reweight_graph) {
ngdijkstra(node, graph, n, coords[i]);
} else {
bfs(node, graph, n, coords[i]);
}
max_dist = 0;
for (j = 0; j < n; j++) {
dist[j] = MIN(dist[j], coords[i][j]);
if (dist[j] > max_dist) {
node = j;
max_dist = dist[j];
}
}
}
free(dist);
if (reweight_graph) {
restore_old_weights(graph, n, old_weights);
}
}
/* Make each axis centered around 0 */
void center_coordinate(DistType ** coords, int n, int dim)
{
int i, j;
double sum, avg;
for (i = 0; i < dim; i++) {
sum = 0;
for (j = 0; j < n; j++) {
sum += coords[i][j];
}
avg = sum / n;
for (j = 0; j < n; j++) {
coords[i][j] -= (DistType) avg;
}
}
}
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