Add initial code for gvmap

diff --git a/cmd/gvmap/DotIO.c b/cmd/gvmap/DotIO.c
new file mode 100644 (file)
index 0000000..8456578
--- /dev/null
+++ b/cmd/gvmap/DotIO.c
@@ -0,0 +1,815 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#define STANDALONE
+#include "general.h"
+#include "DotIO.h"
+#include "clustering.h"
+#include "mq.h"
+#include "spring_electrical.h"
+#include "color_palette.h"
+#include "colorutil.h"
+
+typedef struct {
+    Agrec_t h;
+    unsigned int id;
+} Agnodeinfo_t;
+
+#define ND_id(n)  (((Agnodeinfo_t*)((n)->base.data))->id)
+
+#if 0
+static void
+posStr (char* buf, int dim, real* x, double sc)
+{
+  if (dim== 3){
+    sprintf (buf, "%f,%f,%f", sc*x[0], sc*x[1], sc*x[2]);
+  } else if (dim == 2) {
+    sprintf (buf, "%f,%f", sc*x[0], sc*x[1]);
+  } else if (dim == 1) {
+    sprintf (buf, "%f", sc*x[0]);
+  } else {
+    assert(0);
+  }
+}
+
+static void 
+attach_embedding (Agraph_t* g, int dim, double sc, real *x)
+{
+  Agsym_t* sym = agattr(g, AGNODE, "pos", NULL); 
+  Agnode_t* n;
+  char buf[1024];
+  int i = 0;
+
+  if (!sym)
+    sym = agattr (g, AGNODE, "pos", "");
+
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    assert (i == ND_id(n));
+    posStr (buf, dim, x + i*dim, sc);
+    agxset (n, sym, buf);
+    i++;
+  }
+  
+}
+#endif
+
+/* SparseMatrix_import_dot:
+ * Assumes g is connected and simple, i.e., we can have a->b and b->a
+ * but not a->b and a->b
+ */
+SparseMatrix 
+SparseMatrix_import_dot (Agraph_t* g, int dim, real **label_sizes, real **x, int *n_edge_label_nodes, int **edge_label_nodes, int format, SparseMatrix *D)
+{
+  SparseMatrix A = 0;
+  Agnode_t* n;
+  Agedge_t* e;
+  Agsym_t *sym, *symD = NULL;
+  int nnodes;
+  int nedges;
+  int i, row;
+  int* I;
+  int* J;
+  real *val, *valD = NULL;
+  real v;
+  int type = MATRIX_TYPE_REAL;
+  real padding = 10;
+  int nedge_nodes = 0;
+
+  if (!g) return NULL;
+  nnodes = agnnodes (g);
+  nedges = agnedges (g);
+  if (format != FORMAT_CSR) {
+    fprintf (stderr, "Format %d not supported\n", format);
+    exit (1);
+  }
+
+  /* Assign node ids */
+  i = 0;
+  for (n = agfstnode (g); n; n = agnxtnode (g, n))
+    ND_id(n) = i++;
+
+  I = N_NEW(nedges, int);
+  J = N_NEW(nedges, int);
+  val = N_NEW(nedges, real);
+
+  sym = agattr(g, AGEDGE, "weight", NULL); 
+  if (D) {
+    symD = agattr(g, AGEDGE, "len", NULL); 
+    valD = N_NEW(nedges, real);
+  }
+  i = 0;
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    if (edge_label_nodes && strncmp(agnameof(n), "|edgelabel|",11)==0) nedge_nodes++;
+    row = ND_id(n);
+    for (e = agfstout (g, n); e; e = agnxtout (g, e)) {
+      I[i] = row;
+      J[i] = ND_id(aghead(e));
+
+      /* edge weight */
+      if (sym) {
+        if (sscanf (agxget(e,sym), "%lf", &v) != 1) v = 1;
+      } else {
+        v = 1;
+      }
+      val[i] = v;
+
+      /* edge length */
+      if (symD) {
+        if (sscanf (agxget(e,symD), "%lf", &v) != 1) v = 1;
+       valD[i] = v;
+      }
+
+      i++;
+    }
+  }
+  
+  if (edge_label_nodes) {
+    *edge_label_nodes = MALLOC(sizeof(int)*nedge_nodes);
+    nedge_nodes = 0;
+  }
+
+  *label_sizes = MALLOC(sizeof(real)*2*nnodes);
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    real sz;
+    i = ND_id(n);
+    if (edge_label_nodes && strncmp(agnameof(n), "|edgelabel|",11)==0) {
+      (*edge_label_nodes)[nedge_nodes++] = i;
+    }
+    if (agget(n, "width") && agget(n, "height")){
+      sscanf(agget(n, "width"), "%lf", &sz);
+      /*      (*label_sizes)[i*2] = POINTS(sz)*.6;*/
+      (*label_sizes)[i*2] = POINTS(sz)*.5 + padding*0.5;
+      sscanf(agget(n, "height"), "%lf", &sz);
+      /*(*label_sizes)[i*2+1] = POINTS(sz)*.6;*/
+      (*label_sizes)[i*2+1] = POINTS(sz)*.5  + padding*0.5;
+    } else {
+      (*label_sizes)[i*2] = 4*POINTS(0.75)*.5;
+      (*label_sizes)[i*2+1] = 4*POINTS(0.5)*.5;
+    }
+ }
+
+  if (x){
+    if (!(*x)) {
+      *x = MALLOC(sizeof(real)*dim*nnodes);
+      assert(*x);
+    }
+    for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+      real xx,yy, zz,ww;
+      int nitems, k;
+      i = ND_id(n);
+      if (agget(n, "pos")){
+       if (dim == 2){
+         nitems = sscanf(agget(n, "pos"), "%lf,%lf", &xx, &yy);
+         if (nitems != 2) return NULL;
+         (*x)[i*dim] = xx;
+         (*x)[i*dim+1] = yy;
+       } else if (dim == 3){
+         nitems = sscanf(agget(n, "pos"), "%lf,%lf,%lf", &xx, &yy, &zz);
+         if (nitems != 3) return NULL;
+         (*x)[i*dim] = xx;
+         (*x)[i*dim+1] = yy;
+         (*x)[i*dim+2] = zz;
+       } else if (dim == 4){
+         nitems = sscanf(agget(n, "pos"), "%lf,%lf,%lf,%lf", &xx, &yy, &zz,&ww);
+         if (nitems != 4) return NULL;
+         (*x)[i*dim] = xx;
+         (*x)[i*dim+1] = yy;
+         (*x)[i*dim+2] = zz;
+         (*x)[i*dim+3] = ww;
+       } else if (dim == 1){
+         nitems = sscanf(agget(n, "pos"), "%lf", &xx);
+         if (nitems != 1) return NULL;
+         (*x)[i*dim] = xx;
+       } else {
+         assert(0);
+       }
+      } else {
+       for (k = 0; k < dim; k++) (*x)[i*dim + k] = 0;
+      }
+    }
+  }
+
+  A = SparseMatrix_from_coordinate_arrays(nedges, nnodes, nnodes, I, J, val, type);
+  if (edge_label_nodes) *n_edge_label_nodes = nedge_nodes;
+
+  if (D) *D = SparseMatrix_from_coordinate_arrays(nedges, nnodes, nnodes, I, J, valD, type);
+
+  FREE(I);
+  FREE(J);
+  FREE(val);
+  if (valD) FREE(valD);
+
+  return A;
+}
+
+
+void dump_coordinates(char *name, int n, int dim, real *x){
+  char fn[1000];
+  FILE *fp;
+  int i, k;
+
+  if (!name){
+    name = "";
+  } else {
+    name = strip_dir(name);
+  }
+  
+  strcpy(fn, name);
+  strcat(fn,".x");
+  fp = fopen(fn,"w");
+  fprintf(fp, "%d %d\n",n, dim);
+  for (i = 0; i < n; i++){
+    for (k = 0; k < dim; k++){
+      fprintf(fp,"%f ",x[i*dim+k]);
+    }
+    fprintf(fp,"\n");
+  }
+  fclose(fp);
+
+}
+
+static Agnode_t*
+mkNode (Agraph_t* g, char* name)
+{
+  Agnode_t* n = agnode(g, name, 1);
+  agbindrec(n, "info", sizeof(Agnodeinfo_t), TRUE);
+  return n;
+}
+
+Agraph_t* 
+makeDotGraph (SparseMatrix A, char *name, int dim, real *x, int with_color, int with_label, int  use_matrix_value)
+{
+  Agraph_t* g;
+  Agnode_t* n;
+  Agnode_t* h;
+  Agedge_t* e;
+  int i, j;
+  char buf[1024], buf2[1024];
+  Agsym_t *sym, *sym2 = NULL, *sym3 = NULL;
+  int* ia=A->ia;
+  int* ja=A->ja;
+  real* val = (real*)(A->a);
+  Agnode_t** arr = N_NEW (A->m, Agnode_t*);
+  real *color = NULL;
+  char cstring[8];
+  char *label_string;
+
+  if (!name){
+    name = "stdin";
+  } else {
+    name = strip_dir(name);
+  }
+  label_string = MALLOC(sizeof(char)*1000);
+
+  if (SparseMatrix_known_undirected(A)){
+    g = agopen ("G", Agundirected, 0);
+  } else {
+    g = agopen ("G", Agdirected, 0);
+  }
+  sprintf (buf, "%f", 1.0);
+
+  label_string = strcpy(label_string, name);
+  label_string = strcat(label_string, ". ");
+  sprintf (buf, "%d", A->m);
+  label_string = strcat(label_string, buf);
+  label_string = strcat(label_string, " nodes, ");
+  sprintf (buf, "%d", A->nz);
+  label_string = strcat(label_string, buf);
+  /*  label_string = strcat(label_string, " edges. Created by Yifan Hu");*/
+  label_string = strcat(label_string, " edges.");
+
+
+  if (with_label) sym = agattr(g, AGRAPH, "label", label_string); 
+  sym = agattr(g, AGRAPH, "fontcolor", "#808090");
+  if (with_color) sym = agattr(g, AGRAPH, "bgcolor", "black"); 
+  sym = agattr(g, AGRAPH, "outputorder", "edgesfirst"); 
+
+  if (A->m > 100) {
+    /* -Estyle=setlinewidth(0.0)' -Eheadclip=false -Etailclip=false -Nstyle=invis*/
+    agattr(g, AGNODE, "style", "invis"); 
+  } else {
+    /*    width=0, height = 0, label="", style=filled*/
+    agattr(g, AGNODE, "shape", "point"); 
+    if (A->m < 50){
+      agattr(g, AGNODE, "width", "0.03"); 
+    } else {
+      agattr(g, AGNODE, "width", "0"); 
+    }
+    agattr(g, AGNODE, "label", ""); 
+    agattr(g, AGNODE, "style", "filled"); 
+    if (with_color) {
+      agattr(g, AGNODE, "color", "#FF0000"); 
+    } else {
+      agattr(g, AGNODE, "color", "#000000"); 
+    }
+  }
+
+  agattr(g, AGEDGE, "headclip", "false"); 
+  agattr(g, AGEDGE, "tailclip", "false"); 
+  if (A->m < 50){
+    agattr(g, AGEDGE, "style", "setlinewidth(2)"); 
+  } else if (A->m < 500){
+    agattr(g, AGEDGE, "style", "setlinewidth(0.5)"); 
+  } else if (A->m < 5000){
+    agattr(g, AGEDGE, "style", "setlinewidth(0.1)"); 
+  } else {
+    agattr(g, AGEDGE, "style", "setlinewidth(0.0)"); 
+  }
+
+  if (with_color) {
+    sym2 = agattr(g, AGEDGE, "color", ""); 
+    sym3 = agattr(g, AGEDGE, "wt", ""); 
+  }
+  for (i = 0; i < A->m; i++) {
+    sprintf (buf, "%d", i);
+    n = mkNode (g, buf);
+    ND_id(n) = i;
+    arr[i] = n;
+  }
+
+  if (with_color){
+    real maxdist = 0.;
+    real mindist = 0.;
+    int first = TRUE;
+    color = malloc(sizeof(real)*A->nz);
+    for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+      i = ND_id(n);
+      if (A->type != MATRIX_TYPE_REAL || use_matrix_value){
+       for (j = ia[i]; j < ia[i+1]; j++) {
+         color[j] = distance(x, dim, i, ja[j]);
+         if (i != ja[j]){
+           if (first){
+             mindist = color[j];
+             first = FALSE;
+           } else {
+             mindist = MIN(mindist, color[j]);
+           }
+         }
+         maxdist = MAX(color[j], maxdist);
+       }
+      } else {
+       for (j = ia[i]; j < ia[i+1]; j++) {
+         color[j] = ABS(val[j]);
+         if (i != ja[j]){
+           if (first){
+             mindist = color[j];
+             first = FALSE;
+           } else {
+             mindist = MIN(mindist, color[j]);
+           }
+         }
+         maxdist = MAX(color[j], maxdist);
+       }
+      }
+    }
+    for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+      i = ND_id(n);
+      for (j = ia[i]; j < ia[i+1]; j++) {
+       color[j] = ((color[j] - mindist)/MAX(maxdist-mindist, 0.000001));
+      }
+    }
+  }
+
+  i = 0;
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    i = ND_id(n);
+    for (j = ia[i]; j < ia[i+1]; j++) {
+      h = arr [ja[j]];
+      if (val){
+       switch (A->type){
+       case MATRIX_TYPE_REAL:
+         sprintf (buf, "%f", ((real*)A->a)[j]);
+         break;
+       case MATRIX_TYPE_INTEGER:
+         sprintf (buf, "%d", ((int*)A->a)[j]);
+         break;
+       case MATRIX_TYPE_COMPLEX:/* take real part as weight */
+         sprintf (buf, "%f", ((real*)A->a)[2*j]);
+         break;
+       }
+       if (with_color) sprintf (buf2, "%s", hue2rgb(.65*color[j], cstring));
+      } else {
+       sprintf (buf, "%f", 1.);
+       if (with_color) sprintf (buf2, "%s", hue2rgb(.65*color[j], cstring));
+     }
+      e = agedge (g, n, h, NULL, 1);
+      if (with_color) {
+       agxset (e, sym2, buf2);
+       sprintf (buf2, "%f", color[j]);
+       agxset (e, sym3, buf2);
+      }
+    }
+  }
+  
+  FREE(color);
+  FREE (arr);
+  FREE(label_string);
+  return g;
+}
+
+
+char *cat_string(char *s1, char *s2){
+  char *s;
+  s = malloc(sizeof(char)*(strlen(s1)+strlen(s2)+1+1));
+  strcpy(s,s1);
+  strcat(s,"|");
+  strcat(s,s2);
+  return s;
+}
+
+char *cat_string3(char *s1, char *s2, char *s3, int id){
+  char *s;
+  char sid[1000];
+  sprintf(sid,"%d",id);
+  s = malloc(sizeof(char)*(strlen(s1)+strlen(s2)+strlen(s3)+strlen(sid)+1+3));
+  strcpy(s,s1);
+  strcat(s,"|");
+  strcat(s,s2);
+  strcat(s,"|");
+  strcat(s,s3);
+  strcat(s,"|");
+  strcat(s,sid);
+  return s;
+}
+
+
+Agraph_t *convert_edge_labels_to_nodes(Agraph_t* g){
+  Agnode_t *n, *newnode;
+  Agraph_t *dg;
+
+  int nnodes;
+  int nedges;
+
+
+  Agedge_t *ep, *e;
+  int i = 0;
+  Agnode_t **ndmap = NULL;
+  char *s;
+  char *elabel;
+  int id = 0;
+
+  Agsym_t* sym = agattr(g, AGEDGE, "label", NULL);
+
+  dg = agopen("test", g->desc, 0);
+
+  if (!g) return NULL;
+  nnodes = agnnodes (g);
+  nedges = agnedges (g);
+
+  ndmap = malloc(sizeof(Agnode_t *)*nnodes);
+
+  agattr(dg, AGNODE, "label", "\\N"); 
+  agattr(dg, AGNODE, "shape", "ellipse"); 
+  agattr(dg, AGNODE, "width","0.00001");
+  agattr(dg, AGNODE, "height", "0.00001");
+  agattr(dg, AGNODE, "margin","0.");
+  agattr(dg, AGEDGE, "arrowsize", "0.5"); 
+
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    newnode = mkNode(dg, agnameof(n));
+    agset(newnode,"shape","box");
+    ndmap[i] = newnode;
+    ND_id(n) = i++;
+  }
+
+
+  /*
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    for (ep = agfstedge(g, n); ep; ep = agnxtedge(g, ep, n)) {
+      if (agtail(ep) == n) continue;
+      agedge(dg, ndmap[ND_id(agtail(ep))], ndmap[ND_id(aghead(ep))]);
+    }
+  }
+  */
+
+
+
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    for (ep = agfstedge(g, n); ep; ep = agnxtedge(g, ep, n)) {
+      if (agtail(ep) == n && (aghead(ep) != n)) continue;
+      if (sym && (elabel = agxget(ep,sym)) && strcmp(elabel,"") != 0) {
+       s = cat_string3("|edgelabel",agnameof(agtail(ep)), agnameof(aghead(ep)), id++);
+       newnode = mkNode(dg,s);
+       agset(newnode,"label",elabel);
+       agset(newnode,"shape","plaintext");
+       e = agedge(dg, ndmap[ND_id(agtail(ep))], newnode, NULL, 1);
+       agset(e, "arrowsize","0");
+       agedge(dg, newnode, ndmap[ND_id(aghead(ep))], NULL, 1);
+       free(s);
+      } else {
+       agedge(dg, ndmap[ND_id(agtail(ep))], ndmap[ND_id(aghead(ep))], NULL, 1);
+      }
+    }
+  }
+
+  free(ndmap);
+  return dg;
+ }
+
+Agraph_t* assign_random_edge_color(Agraph_t* g){
+  char cstring[8];
+  char buf2[1024];
+  Agsym_t *sym2;
+  Agnode_t* n;
+  Agedge_t *ep;
+
+  sym2 = agattr(g, AGEDGE, "color", ""); 
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    for (ep = agfstedge(g, n); ep; ep = agnxtedge(g, ep, n)) {
+      sprintf (buf2, "%s", hue2rgb(0.65*drand(), cstring));
+      agxset (ep, sym2, buf2);
+    }
+  }
+
+  return g;
+ }
+
+void Dot_SetClusterColor(Agraph_t* g, float *rgb_r,  float *rgb_g,  float *rgb_b, int *clusters){
+
+  Agnode_t* n;
+  char scluster[20];
+  int i;
+  Agsym_t* clust_clr_sym = agattr(g, AGNODE, "clustercolor", NULL); 
+
+  if (!clust_clr_sym) clust_clr_sym = agattr(g, AGNODE, "clustercolor", "-1"); 
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    i = ND_id(n);
+    if (rgb_r && rgb_g && rgb_b) {
+      rgb2hex((rgb_r)[(clusters)[i]],(rgb_g)[(clusters)[i]],(rgb_b)[(clusters)[i]], scluster);
+      //sprintf(scluster,"#%2x%2x%2x", (int) (255*((rgb_r)[(clusters)[i]])), (int) (255*((rgb_g)[(clusters)[i]])), (int) (255*((rgb_b)[(clusters)[i]])));
+    }
+    agxset(n,clust_clr_sym,scluster);
+  }
+}
+
+SparseMatrix Import_coord_clusters_from_dot(Agraph_t* g, int maxcluster, int dim, int *nn, real **label_sizes, real **areas, real **x, int **clusters, float **rgb_r,  float **rgb_g,  float **rgb_b,  float **fsz, char ***labels, int default_color_scheme, int clustering_scheme){
+  SparseMatrix A = 0;
+  Agnode_t* n;
+  Agedge_t* e;
+  Agsym_t* sym;
+  Agsym_t* clust_sym;
+  Agsym_t* clust_clr_sym;
+  int nnodes;
+  int nedges;
+  int i, row, ic,nc, j;
+  int* I;
+  int* J;
+  real* val;
+  real v;
+  int type = MATRIX_TYPE_REAL;
+  char scluster[100];
+  float ff;
+  real* areap = NULL;
+
+  int MAX_GRPS, MIN_GRPS, noclusterinfo = FALSE, first = TRUE;
+  float *pal;
+
+  switch (default_color_scheme){
+  case COLOR_SCHEME_BLUE_YELLOW:
+    pal = &(palette_blue_to_yellow[0][0]);
+    break;
+  case COLOR_SCHEME_WHITE_RED:
+    pal = &(palette_white_to_red[0][0]);
+    break;
+  case COLOR_SCHEME_GREY_RED:
+    pal = &(palette_grey_to_red[0][0]);
+    break;
+  case COLOR_SCHEME_GREY:
+    pal = &(palette_grey[0][0]);
+    break;
+  case COLOR_SCHEME_PASTEL:
+    pal = &(palette_pastel[0][0]);
+    break;
+  case COLOR_SCHEME_SEQUENTIAL_SINGLEHUE_RED:
+    fprintf(stderr," HERE!\n");
+    pal = &(palette_sequential_singlehue_red[0][0]);
+    break;
+  case COLOR_SCHEME_SEQUENTIAL_SINGLEHUE_RED_LIGHTER:
+    fprintf(stderr," HERE!\n");
+    pal = &(palette_sequential_singlehue_red_lighter[0][0]);
+    break;
+  case COLOR_SCHEME_PRIMARY:
+    pal = &(palette_primary[0][0]);
+    break;
+  case COLOR_SCHEME_NONE:
+    pal = NULL;
+    break;
+  default:
+    pal = &(palette_pastel[0][0]);
+    break;
+  }
+    
+  if (!g) return NULL;
+  nnodes = agnnodes (g);
+  nedges = agnedges (g);
+  *nn = nnodes;
+
+  /* Assign node ids */
+  i = 0;
+  for (n = agfstnode (g); n; n = agnxtnode (g, n))
+    ND_id(n) = i++;
+
+  /* form matrix */  
+  I = N_NEW(nedges, int);
+  J = N_NEW(nedges, int);
+  val = N_NEW(nedges, real);
+
+  sym = agattr(g, AGEDGE, "weight", NULL); 
+  clust_sym = agattr(g, AGNODE, "cluster", NULL); 
+  clust_clr_sym = agattr(g, AGNODE, "clustercolor", NULL); 
+  //sym = agattr(g, AGEDGE, "wt", NULL); 
+  i = 0;
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    row = ND_id(n);
+    for (e = agfstout (g, n); e; e = agnxtout (g, e)) {
+      I[i] = row;
+      J[i] = ND_id(aghead(e));
+      if (sym) {
+        if (sscanf (agxget(e,sym), "%lf", &v) != 1)
+          v = 1;
+      }
+      else
+        v = 1;
+      val[i] = v;
+      i++;
+    }
+  }
+  A = SparseMatrix_from_coordinate_arrays(nedges, nnodes, nnodes, I, J, val, type);
+
+  /* get clustering info */
+  nc = 1;
+  MIN_GRPS = 0;
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    i = ND_id(n);
+    if (clust_sym && (sscanf(agxget(n,clust_sym), "%d", &ic)>0)) {
+      nc = MAX(nc, ic);
+      if (first){
+       MIN_GRPS = ic;
+       first = FALSE;
+      } else {
+       MIN_GRPS = MIN(MIN_GRPS, ic);
+      }
+    } else {
+      noclusterinfo = TRUE;
+    }
+  }
+  MAX_GRPS = nc;
+
+  *clusters = MALLOC(sizeof(int)*nnodes);
+
+  if (noclusterinfo) {
+    int use_value = TRUE, flag = 0;
+    real modularity;
+    if (!clust_sym) clust_sym = agattr(g,AGNODE,"cluster","-1");
+
+    if (clustering_scheme == CLUSTERING_MQ){
+      mq_clustering(A, FALSE, maxcluster, use_value,
+                   &nc, clusters, &modularity, &flag);
+    } else if (clustering_scheme == CLUSTERING_MODULARITY){ 
+      modularity_clustering(A, FALSE, maxcluster, use_value,
+                   &nc, clusters, &modularity, &flag);
+    } else {
+      assert(0);
+    }
+    for (i = 0; i < nnodes; i++) (*clusters)[i]++;/* make into 1 based */
+    for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+      i = ND_id(n);
+      sprintf(scluster,"%d",(*clusters)[i]);
+      agxset(n,clust_sym,scluster);
+    }
+    MIN_GRPS = 1;
+    MAX_GRPS = nc;
+    if (Verbose){
+      fprintf(stderr," no complement clustering info in dot file, using modularity clustering. Modularity = %f, ncluster=%d\n",modularity, nc);
+    }
+  }
+
+  *label_sizes = MALLOC(sizeof(real)*dim*nnodes);
+  if (pal){
+    *rgb_r = MALLOC(sizeof(float)*(1+MAX_GRPS));
+    *rgb_g = MALLOC(sizeof(float)*(1+MAX_GRPS));
+    *rgb_b = MALLOC(sizeof(float)*(1+MAX_GRPS));
+  } else {
+    *rgb_r = NULL;
+    *rgb_g = NULL;
+    *rgb_b = NULL;
+  }
+  *fsz = MALLOC(sizeof(float)*nnodes);
+  *labels = MALLOC(sizeof(char*)*nnodes);
+
+  if (areas){
+    *areas = areap = MALLOC(sizeof(real)*nnodes);
+  }
+
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    gvcolor_t color;
+    real sz;
+    i = ND_id(n);
+    if (agget(n, "width") && agget(n, "height")){
+      sscanf(agget(n, "width"), "%lf", &sz);
+      (*label_sizes)[i*2] = POINTS(sz*0.5);
+      sscanf(agget(n, "height"), "%lf", &sz);
+      (*label_sizes)[i*2+1] = POINTS(sz*0.5);
+    } else {
+      (*label_sizes)[i*2] = POINTS(0.75/2);
+      (*label_sizes)[i*2+1] = POINTS(0.5*2);
+    }
+
+    if (areap) {
+      char* s;
+      double d;
+      if ((s = agget(n, "area")) && sscanf(s, "%lf", &d))
+        areap[i] = d;
+      else
+        areap[i] = 1.0;
+    }
+
+    if (!noclusterinfo && (sscanf(agxget(n, clust_sym), "%d", &ic)>0)) {
+      (*clusters)[i] = ic;
+    }
+
+
+   if (agget(n, "fontsize")){
+      sscanf(agget(n, "fontsize"), "%f", &ff);
+      (*fsz)[i] = ff;
+    } else {
+     (*fsz)[i] = 14;
+    }
+
+   if (agget(n, "label") && strcmp(agget(n, "label"), "") != 0 && strcmp(agget(n, "label"), "\\N") != 0){
+     char *lbs;
+     lbs = agget(n, "label");
+      (*labels)[i] = MALLOC(sizeof(char)*(strlen(lbs)+1));
+      strcpy((*labels)[i], lbs);
+    } else {
+     (*labels)[i] = MALLOC(sizeof(char)*(strlen(agnameof(n))+1));
+      strcpy((*labels)[i], agnameof(n));
+    }
+
+
+
+   j = (*clusters)[i];
+   if (MAX_GRPS-MIN_GRPS < MAX_COLOR) {
+     j = (j-MIN_GRPS)*((int)((MAX_COLOR-1)/MAX((MAX_GRPS-MIN_GRPS),1)));
+   } else {
+     j = (j-MIN_GRPS)%MAX_COLOR;
+   }
+
+   if (pal){
+     //     assert((*clusters)[i] >= 0 && (*clusters)[i] <= MAX_GRPS);
+     (*rgb_r)[(*clusters)[i]] = pal[3*j+0];
+     (*rgb_g)[(*clusters)[i]] =  pal[3*j+1];
+     (*rgb_b)[(*clusters)[i]] = pal[3*j+2];
+   }
+
+   if (!noclusterinfo && clust_clr_sym && (colorxlate(agxget(n,clust_clr_sym),&color,RGBA_DOUBLE) == COLOR_OK)) {
+     (*rgb_r)[(*clusters)[i]] = color.u.RGBA[0];
+     (*rgb_g)[(*clusters)[i]] = color.u.RGBA[1];
+     (*rgb_b)[(*clusters)[i]] = color.u.RGBA[2];
+   }
+
+
+  }
+
+
+  if (x){
+    *x = MALLOC(sizeof(real)*dim*nnodes);
+    for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+      real xx,yy;
+      i = ND_id(n);
+      if (agget(n, "pos")){
+       sscanf(agget(n, "pos"), "%lf,%lf", &xx, &yy);
+       (*x)[i*dim] = xx;
+       (*x)[i*dim+1] = yy;
+      } else {
+       fprintf(stderr,"WARNING: pos field missing for node %d, set to origin\n",i);
+       (*x)[i*dim] = 0;
+       (*x)[i*dim+1] = 0;
+      }
+    }
+  }
+
+
+  FREE(I);
+  FREE(J);
+  FREE(val);
+
+  return A;
+}
+
+
+void initDotIO (Agraph_t *g)
+{
+  aginit(g, AGNODE, "info", sizeof(Agnodeinfo_t), TRUE);
+}
+

diff --git a/cmd/gvmap/DotIO.h b/cmd/gvmap/DotIO.h
new file mode 100644 (file)
index 0000000..ae24ded
--- /dev/null
+++ b/cmd/gvmap/DotIO.h
@@ -0,0 +1,35 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#ifndef DOTIO_H
+#define DOTIO_H
+
+#include <cgraph.h>
+#include "SparseMatrix.h"
+
+enum {COLOR_SCHEME_NONE, COLOR_SCHEME_PASTEL = 1, COLOR_SCHEME_BLUE_YELLOW, COLOR_SCHEME_WHITE_RED, COLOR_SCHEME_GREY_RED, COLOR_SCHEME_PRIMARY, COLOR_SCHEME_SEQUENTIAL_SINGLEHUE_RED, COLOR_SCHEME_SEQUENTIAL_SINGLEHUE_RED_LIGHTER, COLOR_SCHEME_GREY};
+extern void initDotIO (Agraph_t *g);
+
+/* extern void attach_embedding(Agraph_t *g, int dim, double sc, real *x); */
+extern SparseMatrix SparseMatrix_import_dot(Agraph_t* g, int dim, real **label_sizes, real **x, int *n_edge_label_nodes,
+                                           int **edge_label_nodes, int format, SparseMatrix *D);
+extern Agraph_t* makeDotGraph (SparseMatrix, char *title, int dim, real *x, int with_color, int with_label, int use_matrix_value);
+Agraph_t *convert_edge_labels_to_nodes(Agraph_t* g);
+Agraph_t* assign_random_edge_color(Agraph_t* g);
+void dump_coordinates(char *name, int n, int dim, real *x);
+char * hue2rgb(real hue, char *color);
+
+SparseMatrix Import_coord_clusters_from_dot(Agraph_t* g, int maxcluster, int dim, int *nn, real **label_sizes, real ** areas, real **x, int **clusters, float **rgb_r,  float **rgb_g,  float **rgb_b,  float **fsz, char ***labels, int default_color_scheme, int clustering_scheme);
+
+void Dot_SetClusterColor(Agraph_t* g, float *rgb_r,  float *rgb_g,  float *rgb_b, int *clustering);
+#endif

diff --git a/cmd/gvmap/Makefile.am b/cmd/gvmap/Makefile.am
new file mode 100644 (file)
index 0000000..640fae4
--- /dev/null
+++ b/cmd/gvmap/Makefile.am
@@ -0,0 +1,42 @@
+# $Id$Revision$
+## Process this file with automake to produce Makefile.in
+
+pdfdir = $(pkgdatadir)/doc/pdf
+man_MANS = gvmap.1
+pdf_DATA = gvmap.1.pdf
+
+AM_CPPFLAGS = \
+       -I$(top_srcdir) \
+       -I$(top_srcdir)/lib/common \
+       -I$(top_srcdir)/lib/neatogen \
+       -I$(top_srcdir)/lib/sfdpgen \
+       -I$(top_srcdir)/lib/sparse \
+       -I$(top_srcdir)/lib/cgraph \
+       -I$(top_srcdir)/lib/ingraphs \
+       -I$(top_srcdir)/lib/cdt
+
+bin_PROGRAMS = gvmap
+
+noinst_HEADERS = make_map.h power.h country_graph_coloring.h DotIO.h \
+       colorutil.h color_palette.h mq.h clustering.h
+
+gvmap_SOURCES = gvmap.c make_map.c power.c country_graph_coloring.c DotIO.c \
+       colorutil.c mq.c clustering.c
+
+gvmap_CPPFLAGS = $(AM_CPPFLAGS)
+gvmap_LDADD = \
+       $(top_builddir)/lib/sfdpgen/libsfdpgen_C.la \
+       $(top_builddir)/lib/neatogen/libneatogen_C.la \
+       $(top_builddir)/lib/sparse/libsparse_C.la \
+       $(top_builddir)/lib/rbtree/librbtree_C.la \
+       $(top_builddir)/lib/ingraphs/libingraphs_C.la \
+       $(top_builddir)/lib/common/libcommon_C.la \
+       $(top_builddir)/lib/cgraph/libcgraph.la \
+       $(GTS_LIBS)
+
+gvmap.1.pdf: $(srcdir)/gvmap.1
+       - @GROFF@ -Tps -man $(srcdir)/gvmap.1 | @PS2PDF@ - - >gvmap.1.pdf
+
+EXTRA_DIST = $(man_MANS) $(pdf_DATA) # gvmap.vcproj
+
+DISTCLEANFILES = $(pdf_DATA)

diff --git a/cmd/gvmap/clustering.c b/cmd/gvmap/clustering.c
new file mode 100644 (file)
index 0000000..caf702e
--- /dev/null
+++ b/cmd/gvmap/clustering.c
@@ -0,0 +1,338 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#define STANDALONE
+#include "general.h"
+#include "SparseMatrix.h"
+#include "clustering.h"
+
+Multilevel_Modularity_Clustering Multilevel_Modularity_Clustering_init(SparseMatrix A, int level){
+  Multilevel_Modularity_Clustering grid;
+  int n = A->n, i, j;
+
+  assert(A->type == MATRIX_TYPE_REAL);
+  assert(SparseMatrix_is_symmetric(A, FALSE));
+
+  if (!A) return NULL;
+  assert(A->m == n);
+  grid = MALLOC(sizeof(struct Multilevel_Modularity_Clustering_struct));
+  grid->level = level;
+  grid->n = n;
+  grid->A = A;
+  grid->P = NULL;
+  grid->R = NULL;
+  grid->next = NULL;
+  grid->prev = NULL;
+  grid->delete_top_level_A = FALSE;
+  grid->matching = MALLOC(sizeof(real)*(n));
+  grid->deg = NULL;
+
+  if (level == 0){
+    real modularity = 0;
+    int *ia = A->ia, *ja = A->ja, n = A->n;
+    real deg_total = 0;
+    real *deg, *a = (real*) (A->a);
+    real *indeg;
+
+    grid->deg_total = 0.;
+    grid->deg = MALLOC(sizeof(real)*(n));
+    deg = grid->deg;
+
+    indeg = MALLOC(sizeof(real)*n);
+    for (i = 0; i < n; i++){
+      deg[i] = 0;
+      indeg[i] = 0.;
+      for (j = ia[i]; j < ia[i+1]; j++){
+       deg[i] += a[j];
+       if (ja[j] == i) indeg[i] = a[j];
+      }
+      deg_total += deg[i];
+    }
+    if (deg_total == 0) deg_total = 1;
+    for (i = 0; i < n; i++){
+      modularity += (indeg[i] - deg[i]*deg[i]/deg_total)/deg_total;
+    }
+    grid->deg_total = deg_total;
+    grid->deg = deg;
+    grid->modularity = modularity;
+    FREE(indeg);
+  }
+
+
+  return grid;
+} 
+
+void Multilevel_Modularity_Clustering_delete(Multilevel_Modularity_Clustering grid){
+  if (!grid) return;
+  if (grid->A){
+    if (grid->level == 0) {
+      if (grid->delete_top_level_A) SparseMatrix_delete(grid->A);
+    } else {
+      SparseMatrix_delete(grid->A);
+    }
+  }
+  SparseMatrix_delete(grid->P);
+  SparseMatrix_delete(grid->R);
+  FREE(grid->matching);
+  FREE(grid->deg);
+
+  Multilevel_Modularity_Clustering_delete(grid->next);
+  FREE(grid);
+}
+
+Multilevel_Modularity_Clustering Multilevel_Modularity_Clustering_establish(Multilevel_Modularity_Clustering grid, int maxcluster){
+  int *matching = grid->matching;
+  SparseMatrix A = grid->A;
+  int n = grid->n, level = grid->level, nc = 0;
+  real modularity = 0;
+  int *ia = A->ia, *ja = A->ja;
+  real *a;
+  real *deg = grid->deg;
+  real *deg_new;
+  int i, j, jj, jc, jmax;
+  real inv_deg_total = 1./(grid->deg_total);
+  real *deg_inter, gain;
+  int *mask;
+  real maxgain;
+  real total_gain = 0;
+  modularity = grid->modularity;
+
+  deg_new = MALLOC(sizeof(real)*n);
+  deg_inter = MALLOC(sizeof(real)*n);
+  mask = MALLOC(sizeof(int)*n);
+  for (i = 0; i < n; i++) mask[i] = -1;
+
+  assert(n == A->n);
+  for (i = 0; i < n; i++) matching[i] = UNMATCHED;
+
+  /* gain in merging node i into cluster j is
+     deg(i,j)/deg_total - 2*deg(i)*deg(j)/deg_total^2
+  */
+  a = (real*) A->a;
+  for (i = 0; i < n; i++){
+    if (matching[i] != UNMATCHED) continue;
+    /* accumulate connections between i and clusters */
+    for (j = ia[i]; j < ia[i+1]; j++){
+      jj = ja[j];
+      if (jj == i) continue;
+      if ((jc=matching[jj]) != UNMATCHED){
+       if (mask[jc] != i) {
+         mask[jc] = i;
+         deg_inter[jc] = a[j];
+       } else {
+         deg_inter[jc] += a[j];
+       }
+      }
+    }
+
+    maxgain = 0;
+    jmax = -1;
+    for (j = ia[i]; j < ia[i+1]; j++){
+      jj = ja[j];
+      if (jj == i) continue;
+      if ((jc=matching[jj]) == UNMATCHED){
+       /* the first 2 is due to the fact that deg_iter gives edge weight from i to jj, but there are also edges from jj to i */
+       gain = (2*a[j] - 2*deg[i]*deg[jj]*inv_deg_total)*inv_deg_total;
+      } else {
+       if (deg_inter[jc] > 0){
+         /* the first 2 is due to the fact that deg_iter gives edge weight from i to jc, but there are also edges from jc to i */
+         gain = (2*deg_inter[jc] - 2*deg[i]*deg_new[jc]*inv_deg_total)*inv_deg_total;
+         //      printf("mod = %f deg_inter[jc] =%f, deg[i] = %f, deg_new[jc]=%f, gain = %f\n",modularity, deg_inter[jc],deg[i],deg_new[jc],gain);
+         deg_inter[jc] = -1; /* so that we do not redo the calulation when we hit another neighbor in cluster jc */
+       } else {
+         gain = -1;
+       }
+      }
+      if (j == ia[i] || gain > maxgain){
+       maxgain = gain;
+       jmax = jj;
+      }
+
+    }
+
+    /* now merge i and jmax */
+    if (maxgain > 0 || (nc >= 1 && nc > maxcluster)){
+      total_gain += maxgain;
+      jc = matching[jmax];
+      if (jc == UNMATCHED){
+       //     printf("maxgain=%f, merge %d, %d\n",maxgain, i, jmax);
+       matching[i] = matching[jmax] = nc;
+       deg_new[nc] = deg[i] + deg[jmax];
+       nc++;
+      } else {
+       //      printf("maxgain=%f, merge with existing cluster %d, %d\n",maxgain, i, jc);
+       deg_new[jc] += deg[i];
+       matching[i] = jc;
+      }
+    } else {
+      assert(maxgain <= 0);
+      matching[i] = nc;
+      deg_new[nc] = deg[i];
+      nc++;
+    }
+
+  }
+
+  if (Verbose) fprintf(stderr,"modularity = %f new modularity = %f level = %d, n = %d, nc = %d, gain = %g\n", modularity, modularity + total_gain, 
+                      level, n, nc, total_gain);
+
+  if (nc >= 1 && (total_gain > 0 || nc < n)){
+    /* now set up restriction and prolongation operator */
+    SparseMatrix P, R, R0, B, cA;
+    real one = 1.;
+    Multilevel_Modularity_Clustering cgrid;
+
+    R0 = SparseMatrix_new(nc, n, 1, MATRIX_TYPE_REAL, FORMAT_COORD);
+    for (i = 0; i < n; i++){
+      jj = matching[i];
+      SparseMatrix_coordinate_form_add_entries(R0, 1, &jj, &i, &one);
+    }
+    R = SparseMatrix_from_coordinate_format(R0);
+    SparseMatrix_delete(R0);
+    P = SparseMatrix_transpose(R);
+    B = SparseMatrix_multiply(R, A);
+    if (!B) goto RETURN;
+    cA = SparseMatrix_multiply(B, P); 
+    if (!cA) goto RETURN;
+    SparseMatrix_delete(B);
+    grid->P = P;
+    grid->R = R;
+    level++;
+    cgrid = Multilevel_Modularity_Clustering_init(cA, level); 
+    deg_new = REALLOC(deg_new, nc*sizeof(real));
+    cgrid->deg = deg_new;
+    cgrid->modularity = grid->modularity + total_gain;
+    cgrid->deg_total = grid->deg_total;
+    cgrid = Multilevel_Modularity_Clustering_establish(cgrid, maxcluster);
+    grid->next = cgrid;
+    cgrid->prev = grid;
+  } else {
+    /* no more improvement, stop and final clustering found */
+    for (i = 0; i < n; i++) matching[i] = i;
+    FREE(deg_new);
+  }
+
+ RETURN:
+  FREE(deg_inter);
+  FREE(mask);
+  return grid;
+}
+
+Multilevel_Modularity_Clustering Multilevel_Modularity_Clustering_new(SparseMatrix A0, int maxcluster){
+  /* maxcluster is used to specify the maximum number of cluster desired, e.g., maxcluster=10 means that a maximum of 10 clusters
+     is desired. this may not always be realized, and modularity may be low when this is specified. Default: maxcluster = 0 */
+  Multilevel_Modularity_Clustering grid;
+  SparseMatrix A = A0;
+
+  if (maxcluster <= 0) maxcluster = A->m;
+  if (!SparseMatrix_is_symmetric(A, FALSE) || A->type != MATRIX_TYPE_REAL){
+    A = SparseMatrix_get_real_adjacency_matrix_symmetrized(A);
+  }
+  grid = Multilevel_Modularity_Clustering_init(A, 0);
+
+  grid = Multilevel_Modularity_Clustering_establish(grid, maxcluster);
+
+  if (A != A0) grid->delete_top_level_A = TRUE;/* be sure to clean up later */
+  return grid;
+}
+
+
+static void hierachical_modularity_clustering(SparseMatrix A, int maxcluster,
+                                             int *nclusters, int **assignment, real *modularity, int *flag){
+  /* find a clustering of vertices by maximize modularity
+     A: symmetric square matrix n x n. If real value, value will be used as edges weights, otherwise edge weights are considered as 1.
+     maxcluster: used to specify the maximum number of cluster desired, e.g., maxcluster=10 means that a maximum of 10 clusters
+     .   is desired. this may not always be realized, and modularity may be low when this is specified. Default: maxcluster = 0 
+     nclusters: on output the number of clusters
+     assignment: dimension n. Node i is assigned to cluster "assignment[i]". 0 <= assignment < nclusters
+   */
+
+  Multilevel_Modularity_Clustering grid, cgrid;
+  int *matching, i;
+  SparseMatrix P;
+  real *u;
+  assert(A->m == A->n);
+
+  *modularity = 0.;
+
+  *flag = 0;
+
+  grid = Multilevel_Modularity_Clustering_new(A, maxcluster);
+
+  /* find coarsest */
+  cgrid = grid;
+  while (cgrid->next){
+    cgrid = cgrid->next;
+  }
+
+  /* project clustering up */
+  u =  MALLOC(sizeof(real)*cgrid->n);
+  for (i = 0; i < cgrid->n; i++) u[i] = (real) (cgrid->matching)[i];
+  *nclusters = cgrid->n;
+  *modularity = cgrid->modularity;
+
+  while (cgrid->prev){
+    real *v = NULL;
+    P = cgrid->prev->P;
+    SparseMatrix_multiply_vector(P, u, &v, FALSE);
+    FREE(u);
+    u = v;
+    cgrid = cgrid->prev;
+  }
+
+  if (*assignment){
+    matching = *assignment; 
+  } else {
+    matching = MALLOC(sizeof(int)*(grid->n));
+    *assignment = matching;
+  }
+  for (i = 0; i < grid->n; i++) (matching)[i] = (int) u[i];
+  FREE(u);
+
+  Multilevel_Modularity_Clustering_delete(grid);
+  
+}
+
+
+
+void modularity_clustering(SparseMatrix A, int inplace, int maxcluster, int use_value,
+                          int *nclusters, int **assignment, real *modularity, int *flag){
+  /* find a clustering of vertices by maximize modularity
+     A: symmetric square matrix n x n. If real value, value will be used as edges weights, otherwise edge weights are considered as 1.
+     inplace: whether A can e modified. If true, A will be modified by removing diagonal.
+     maxcluster: used to specify the maximum number of cluster desired, e.g., maxcluster=10 means that a maximum of 10 clusters
+     .   is desired. this may not always be realized, and modularity may be low when this is specified. Default: maxcluster = 0 
+     nclusters: on output the number of clusters
+     assignment: dimension n. Node i is assigned to cluster "assignment[i]". 0 <= assignment < nclusters
+   */
+  SparseMatrix B;
+
+  *flag = 0;
+  
+  assert(A->m == A->n);
+
+  B = SparseMatrix_symmetrize(A, FALSE);
+
+  if (!inplace && B == A) {
+    B = SparseMatrix_copy(A);
+  }
+
+  B = SparseMatrix_remove_diagonal(B);
+
+  if (B->type != MATRIX_TYPE_REAL || !use_value) B = SparseMatrix_set_entries_to_real_one(B);
+
+  hierachical_modularity_clustering(B, maxcluster, nclusters, assignment, modularity, flag);
+
+  if (B != A) SparseMatrix_delete(B);
+
+}

diff --git a/cmd/gvmap/clustering.h b/cmd/gvmap/clustering.h
new file mode 100644 (file)
index 0000000..26691e6
--- /dev/null
+++ b/cmd/gvmap/clustering.h
@@ -0,0 +1,52 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#ifndef CLUSTERING_H
+#define CLUSTERING_H
+
+typedef struct Multilevel_Modularity_Clustering_struct *Multilevel_Modularity_Clustering;
+
+struct Multilevel_Modularity_Clustering_struct {
+  int level;/* 0, 1, ... */
+  int n;
+  SparseMatrix A; /* n x n matrix */
+  SparseMatrix P; 
+  SparseMatrix R; 
+  Multilevel_Modularity_Clustering next;
+  Multilevel_Modularity_Clustering prev;
+  int delete_top_level_A;
+  int *matching; /* dimension n. matching[i] is the clustering assignment of node i */
+  real modularity;
+  real deg_total; /* total edge weights, including self-edges */
+  real *deg;/* dimension n. deg[i] equal to the sum of edge weights connected to vertex i. I.e., sum of  row i */
+};
+
+enum {CLUSTERING_MODULARITY = 0, CLUSTERING_MQ};
+
+/* find a clustering of vertices by maximize modularity
+   A: symmetric square matrix n x n. If real value, value will be used as edges weights, otherwise edge weights are considered as 1.
+   inplace: whether A can e modified. If true, A will be modified by removing diagonal.
+
+   maxcluster: used to specify the maximum number of cluster desired, e.g., maxcluster=10 means that a maximum of 10 clusters
+   .   is desired. this may not always be realized, and modularity may be low when this is specified. Default: maxcluster = 0 (no limit)
+
+   use_value: whether to use the entry value, or treat edge weights as 1.
+   nclusters: on output the number of clusters
+   assignment: dimension n. Node i is assigned to cluster "assignment[i]". 0 <= assignment < nclusters.
+   .   If *assignment = NULL on entry, it will be allocated. Otherwise used.
+   modularity: achieve modularity
+*/
+void modularity_clustering(SparseMatrix A, int inplace, int maxcluster, int use_value,
+                          int *nclusters, int **assignment, real *modularity, int *flag);
+
+#endif

diff --git a/cmd/gvmap/color_palette.h b/cmd/gvmap/color_palette.h
new file mode 100644 (file)
index 0000000..0ce6907
--- /dev/null
+++ b/cmd/gvmap/color_palette.h
@@ -0,0 +1,6215 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#ifndef COLOR_PALLETE_H
+#define COLOR_PALLETE
+
+enum {MAX_COLOR = 1001};
+float palette_pastel[1001][3]={{0.984313725490196, 0.7058823529411764, 0.6823529411764706}, 
+ {0.9831843137254901, 0.7062745098039215, 0.6831843137254903}, 
+ {0.9820549019607843, 0.7066666666666666, 0.6840156862745098}, 
+ {0.9809254901960783, 0.7070588235294117, 0.6848470588235295}, 
+ {0.9797960784313725, 0.7074509803921568, 0.685678431372549}, 
+ {0.9786666666666666, 0.7078431372549019, 0.6865098039215687}, 
+ {0.9775372549019608, 0.708235294117647, 0.6873411764705882}, 
+ {0.9764078431372548, 0.7086274509803921, 0.6881725490196079}, 
+ {0.975278431372549, 0.7090196078431372, 0.6890039215686274}, 
+ {0.9741490196078431, 0.7094117647058823, 0.6898352941176471}, 
+ {0.9730196078431372, 0.7098039215686274, 0.6906666666666667}, 
+ {0.9718901960784313, 0.7101960784313724, 0.6914980392156863}, 
+ {0.9707607843137255, 0.7105882352941176, 0.6923294117647059}, 
+ {0.9696313725490195, 0.7109803921568627, 0.6931607843137255}, 
+ {0.9685019607843137, 0.7113725490196078, 0.6939921568627451}, 
+ {0.9673725490196078, 0.7117647058823529, 0.6948235294117647}, 
+ {0.9662431372549019, 0.7121568627450979, 0.6956549019607843}, 
+ {0.965113725490196, 0.7125490196078431, 0.6964862745098039}, 
+ {0.9639843137254901, 0.7129411764705882, 0.6973176470588236}, 
+ {0.9628549019607843, 0.7133333333333333, 0.6981490196078431}, 
+ {0.9617254901960783, 0.7137254901960783, 0.6989803921568628}, 
+ {0.9605960784313725, 0.7141176470588235, 0.6998117647058824}, 
+ {0.9594666666666666, 0.7145098039215686, 0.700643137254902}, 
+ {0.9583372549019608, 0.7149019607843137, 0.7014745098039216}, 
+ {0.9572078431372548, 0.7152941176470587, 0.7023058823529412}, 
+ {0.956078431372549, 0.7156862745098038, 0.7031372549019608}, 
+ {0.9549490196078431, 0.716078431372549, 0.7039686274509804}, 
+ {0.9538196078431372, 0.7164705882352941, 0.7048}, 
+ {0.9526901960784313, 0.7168627450980392, 0.7056313725490196}, 
+ {0.9515607843137255, 0.7172549019607842, 0.7064627450980392}, 
+ {0.9504313725490195, 0.7176470588235293, 0.7072941176470589}, 
+ {0.9493019607843136, 0.7180392156862745, 0.7081254901960784}, 
+ {0.9481725490196078, 0.7184313725490196, 0.7089568627450981}, 
+ {0.9470431372549019, 0.7188235294117646, 0.7097882352941176}, 
+ {0.945913725490196, 0.7192156862745097, 0.7106196078431373}, 
+ {0.9447843137254901, 0.7196078431372549, 0.7114509803921569}, 
+ {0.9436549019607843, 0.72, 0.7122823529411765}, 
+ {0.9425254901960783, 0.720392156862745, 0.7131137254901961}, 
+ {0.9413960784313725, 0.7207843137254901, 0.7139450980392157}, 
+ {0.9402666666666666, 0.7211764705882352, 0.7147764705882353}, 
+ {0.9391372549019608, 0.7215686274509804, 0.7156078431372549}, 
+ {0.9380078431372548, 0.7219607843137255, 0.7164392156862746}, 
+ {0.936878431372549, 0.7223529411764705, 0.7172705882352941}, 
+ {0.9357490196078431, 0.7227450980392156, 0.7181019607843138}, 
+ {0.9346196078431372, 0.7231372549019608, 0.7189333333333333}, 
+ {0.9334901960784313, 0.7235294117647059, 0.719764705882353}, 
+ {0.9323607843137255, 0.7239215686274509, 0.7205960784313725}, 
+ {0.9312313725490196, 0.724313725490196, 0.7214274509803922}, 
+ {0.9301019607843136, 0.7247058823529411, 0.7222588235294117}, 
+ {0.9289725490196078, 0.7250980392156863, 0.7230901960784314}, 
+ {0.9278431372549019, 0.7254901960784313, 0.7239215686274509}, 
+ {0.926713725490196, 0.7258823529411764, 0.7247529411764706}, 
+ {0.9255843137254901, 0.7262745098039215, 0.7255843137254903}, 
+ {0.9244549019607843, 0.7266666666666666, 0.7264156862745098}, 
+ {0.9233254901960783, 0.7270588235294118, 0.7272470588235294}, 
+ {0.9221960784313725, 0.7274509803921568, 0.728078431372549}, 
+ {0.9210666666666666, 0.7278431372549019, 0.7289098039215687}, 
+ {0.9199372549019608, 0.728235294117647, 0.7297411764705882}, 
+ {0.9188078431372548, 0.7286274509803922, 0.7305725490196079}, 
+ {0.917678431372549, 0.7290196078431372, 0.7314039215686274}, 
+ {0.9165490196078431, 0.7294117647058823, 0.7322352941176471}, 
+ {0.9154196078431371, 0.7298039215686274, 0.7330666666666666}, 
+ {0.9142901960784313, 0.7301960784313725, 0.7338980392156863}, 
+ {0.9131607843137255, 0.7305882352941176, 0.7347294117647059}, 
+ {0.9120313725490196, 0.7309803921568627, 0.7355607843137255}, 
+ {0.9109019607843136, 0.7313725490196078, 0.7363921568627451}, 
+ {0.9097725490196078, 0.7317647058823529, 0.7372235294117647}, 
+ {0.9086431372549019, 0.7321568627450981, 0.7380549019607843}, 
+ {0.907513725490196, 0.7325490196078431, 0.7388862745098039}, 
+ {0.9063843137254901, 0.7329411764705882, 0.7397176470588236}, 
+ {0.9052549019607843, 0.7333333333333333, 0.7405490196078431}, 
+ {0.9041254901960784, 0.7337254901960784, 0.7413803921568628}, 
+ {0.9029960784313725, 0.7341176470588235, 0.7422117647058823}, 
+ {0.9018666666666666, 0.7345098039215686, 0.743043137254902}, 
+ {0.9007372549019608, 0.7349019607843137, 0.7438745098039216}, 
+ {0.8996078431372548, 0.7352941176470588, 0.7447058823529412}, 
+ {0.898478431372549, 0.7356862745098038, 0.7455372549019608}, 
+ {0.8973490196078431, 0.736078431372549, 0.7463686274509804}, 
+ {0.8962196078431373, 0.7364705882352941, 0.7472}, 
+ {0.8950901960784313, 0.7368627450980392, 0.7480313725490196}, 
+ {0.8939607843137254, 0.7372549019607842, 0.7488627450980392}, 
+ {0.8928313725490196, 0.7376470588235293, 0.7496941176470588}, 
+ {0.8917019607843136, 0.7380392156862745, 0.7505254901960784}, 
+ {0.8905725490196078, 0.7384313725490196, 0.751356862745098}, 
+ {0.8894431372549019, 0.7388235294117647, 0.7521882352941176}, 
+ {0.888313725490196, 0.7392156862745097, 0.7530196078431373}, 
+ {0.8871843137254901, 0.7396078431372549, 0.7538509803921569}, 
+ {0.8860549019607843, 0.74, 0.7546823529411765}, 
+ {0.8849254901960784, 0.7403921568627451, 0.755513725490196}, 
+ {0.8837960784313725, 0.7407843137254901, 0.7563450980392157}, 
+ {0.8826666666666666, 0.7411764705882352, 0.7571764705882353}, 
+ {0.8815372549019608, 0.7415686274509804, 0.7580078431372549}, 
+ {0.8804078431372548, 0.7419607843137255, 0.7588392156862745}, 
+ {0.879278431372549, 0.7423529411764705, 0.7596705882352941}, 
+ {0.8781490196078431, 0.7427450980392156, 0.7605019607843138}, 
+ {0.8770196078431372, 0.7431372549019608, 0.7613333333333333}, 
+ {0.8758901960784313, 0.7435294117647059, 0.762164705882353}, 
+ {0.8747607843137254, 0.743921568627451, 0.7629960784313725}, 
+ {0.8736313725490196, 0.744313725490196, 0.7638274509803922}, 
+ {0.8725019607843136, 0.7447058823529411, 0.7646588235294117}, 
+ {0.8713725490196078, 0.7450980392156863, 0.7654901960784314}, 
+ {0.8702431372549019, 0.7454901960784314, 0.7663215686274509}, 
+ {0.869113725490196, 0.7458823529411764, 0.7671529411764706}, 
+ {0.8679843137254901, 0.7462745098039215, 0.7679843137254903}, 
+ {0.8668549019607843, 0.7466666666666666, 0.7688156862745098}, 
+ {0.8657254901960784, 0.7470588235294118, 0.7696470588235294}, 
+ {0.8645960784313725, 0.7474509803921568, 0.770478431372549}, 
+ {0.8634666666666666, 0.7478431372549019, 0.7713098039215687}, 
+ {0.8623372549019608, 0.748235294117647, 0.7721411764705882}, 
+ {0.8612078431372548, 0.7486274509803922, 0.7729725490196078}, 
+ {0.8600784313725489, 0.7490196078431373, 0.7738039215686274}, 
+ {0.8589490196078431, 0.7494117647058823, 0.7746352941176471}, 
+ {0.8578196078431373, 0.7498039215686274, 0.7754666666666666}, 
+ {0.8566901960784313, 0.7501960784313725, 0.7762980392156863}, 
+ {0.8555607843137254, 0.7505882352941177, 0.7771294117647058}, 
+ {0.8544313725490196, 0.7509803921568627, 0.7779607843137255}, 
+ {0.8533019607843136, 0.7513725490196078, 0.778792156862745}, 
+ {0.8521725490196078, 0.7517647058823529, 0.7796235294117647}, 
+ {0.8510431372549019, 0.7521568627450981, 0.7804549019607843}, 
+ {0.8499137254901961, 0.7525490196078432, 0.7812862745098039}, 
+ {0.8487843137254901, 0.7529411764705882, 0.7821176470588235}, 
+ {0.8476549019607843, 0.7533333333333333, 0.7829490196078431}, 
+ {0.8465254901960784, 0.7537254901960784, 0.7837803921568627}, 
+ {0.8453960784313725, 0.7541176470588236, 0.7846117647058823}, 
+ {0.8442666666666666, 0.7545098039215686, 0.785443137254902}, 
+ {0.8431372549019607, 0.7549019607843137, 0.7862745098039216}, 
+ {0.8420078431372549, 0.7552941176470588, 0.7871058823529411}, 
+ {0.840878431372549, 0.7556862745098039, 0.7879372549019608}, 
+ {0.8397490196078431, 0.756078431372549, 0.7887686274509804}, 
+ {0.8386196078431372, 0.7564705882352941, 0.7896}, 
+ {0.8374901960784313, 0.7568627450980392, 0.7904313725490196}, 
+ {0.8363607843137254, 0.7572549019607843, 0.7912627450980392}, 
+ {0.8352313725490196, 0.7576470588235295, 0.7920941176470588}, 
+ {0.8341019607843136, 0.7580392156862745, 0.7929254901960784}, 
+ {0.8329725490196078, 0.7584313725490196, 0.793756862745098}, 
+ {0.8318431372549019, 0.7588235294117647, 0.7945882352941176}, 
+ {0.830713725490196, 0.7592156862745097, 0.7954196078431373}, 
+ {0.8295843137254901, 0.7596078431372549, 0.7962509803921568}, 
+ {0.8284549019607843, 0.76, 0.7970823529411765}, 
+ {0.8273254901960784, 0.7603921568627451, 0.797913725490196}, 
+ {0.8261960784313724, 0.7607843137254902, 0.7987450980392157}, 
+ {0.8250666666666666, 0.7611764705882353, 0.7995764705882353}, 
+ {0.8239372549019607, 0.7615686274509804, 0.8004078431372549}, 
+ {0.8228078431372549, 0.7619607843137255, 0.8012392156862745}, 
+ {0.8216784313725489, 0.7623529411764706, 0.8020705882352941}, 
+ {0.8205490196078431, 0.7627450980392156, 0.8029019607843138}, 
+ {0.8194196078431373, 0.7631372549019608, 0.8037333333333333}, 
+ {0.8182901960784313, 0.7635294117647059, 0.8045647058823528}, 
+ {0.8171607843137254, 0.763921568627451, 0.8053960784313725}, 
+ {0.8160313725490196, 0.764313725490196, 0.8062274509803922}, 
+ {0.8149019607843137, 0.7647058823529411, 0.8070588235294117}, 
+ {0.8137725490196078, 0.7650980392156863, 0.8078901960784314}, 
+ {0.8126431372549019, 0.7654901960784314, 0.8087215686274509}, 
+ {0.8115137254901961, 0.7658823529411765, 0.8095529411764706}, 
+ {0.8103843137254901, 0.7662745098039215, 0.8103843137254901}, 
+ {0.8092549019607842, 0.7666666666666666, 0.8112156862745098}, 
+ {0.8081254901960784, 0.7670588235294118, 0.8120470588235293}, 
+ {0.8069960784313726, 0.7674509803921569, 0.812878431372549}, 
+ {0.8058666666666666, 0.7678431372549019, 0.8137098039215687}, 
+ {0.8047372549019607, 0.768235294117647, 0.8145411764705882}, 
+ {0.8036078431372549, 0.7686274509803922, 0.8153725490196078}, 
+ {0.8024784313725489, 0.7690196078431373, 0.8162039215686274}, 
+ {0.8013490196078431, 0.7694117647058824, 0.8170352941176471}, 
+ {0.8002196078431372, 0.7698039215686274, 0.8178666666666666}, 
+ {0.7990901960784313, 0.7701960784313726, 0.8186980392156863}, 
+ {0.7979607843137254, 0.7705882352941177, 0.8195294117647058}, 
+ {0.7968313725490195, 0.7709803921568628, 0.8203607843137255}, 
+ {0.7957019607843137, 0.7713725490196078, 0.821192156862745}, 
+ {0.7945725490196078, 0.7717647058823529, 0.8220235294117647}, 
+ {0.7934431372549019, 0.7721568627450981, 0.8228549019607843}, 
+ {0.792313725490196, 0.7725490196078432, 0.8236862745098039}, 
+ {0.7911843137254901, 0.7729411764705882, 0.8245176470588236}, 
+ {0.7900549019607842, 0.7733333333333333, 0.8253490196078431}, 
+ {0.7889254901960784, 0.7737254901960784, 0.8261803921568627}, 
+ {0.7877960784313724, 0.7741176470588236, 0.8270117647058823}, 
+ {0.7866666666666666, 0.7745098039215687, 0.827843137254902}, 
+ {0.7855372549019608, 0.7749019607843137, 0.8286745098039215}, 
+ {0.7844078431372549, 0.7752941176470588, 0.8295058823529411}, 
+ {0.7832784313725489, 0.7756862745098039, 0.8303372549019608}, 
+ {0.7821490196078431, 0.7760784313725491, 0.8311686274509804}, 
+ {0.7810196078431372, 0.7764705882352941, 0.832}, 
+ {0.7798901960784314, 0.7768627450980392, 0.8328313725490195}, 
+ {0.7787607843137254, 0.7772549019607843, 0.8336627450980392}, 
+ {0.7776313725490196, 0.7776470588235294, 0.8344941176470588}, 
+ {0.7765019607843137, 0.7780392156862745, 0.8353254901960784}, 
+ {0.7753725490196077, 0.7784313725490196, 0.836156862745098}, 
+ {0.7742431372549019, 0.7788235294117647, 0.8369882352941176}, 
+ {0.7731137254901961, 0.7792156862745098, 0.8378196078431372}, 
+ {0.7719843137254901, 0.779607843137255, 0.8386509803921568}, 
+ {0.7708549019607842, 0.78, 0.8394823529411765}, 
+ {0.7697254901960784, 0.7803921568627451, 0.840313725490196}, 
+ {0.7685960784313725, 0.7807843137254902, 0.8411450980392157}, 
+ {0.7674666666666666, 0.7811764705882354, 0.8419764705882353}, 
+ {0.7663372549019607, 0.7815686274509804, 0.8428078431372549}, 
+ {0.7652078431372549, 0.7819607843137255, 0.8436392156862744}, 
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+{0.3686274509803922, 0.30980392156862746, 0.6352941176470588}};
+
+/*(Table[Blend[
+     Map[(RGBColor @@ # &), ({{255, 245, 240}, {254, 224, 210}, {252, 
+          187, 161}, {252, 146, 114}, {251, 106, 74}, {239, 59, 
+          44}, {203, 24, 29}, {165, 15, 21}, {103, 0, 13}}/255), {1}],
+         x/1000], {x, 0, 1000, 1.}] /. RGBColor -> List) >> /tmp/1*/
+
+float palette_sequential_singlehue_red[1001][3]={{1., 0.9607843137254902, 0.9411764705882353}, 
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+ {0.4078117647058824, 0.000941176470588237, 0.051482352941176465}, 
+ {0.4058666666666667, 0.0004705882352941185, 0.051231372549019605}, 
+                                            {0.403921568627451, 0., 0.050980392156862744}};
+
+/*(Table[Blend[
+            Map[(RGBColor @@ # &), ({{255, 245, 240}, {254, 224, 210}, {252, 
+                                                          187, 161}, {252, 146, 114}, {251, 106, 74}}/255), {1}], 
+            x/1000], {x, 0, 1000, 1.}] /. RGBColor -> List) >> /tmp/1
+*/
+float palette_sequential_singlehue_red_lighter[1001][3]={{1., 0.9607843137254902, 0.9411764705882353}, 
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+ {0.9846588235294117, 0.4294901960784314, 0.30400000000000005}, 
+ {0.9846431372549019, 0.42886274509803923, 0.30337254901960786}, 
+ {0.9846274509803921, 0.42823529411764705, 0.30274509803921573}, 
+ {0.9846117647058823, 0.4276078431372549, 0.3021176470588236}, 
+ {0.9845960784313725, 0.4269803921568628, 0.3014901960784314}, 
+ {0.9845803921568627, 0.4263529411764706, 0.30086274509803923}, 
+ {0.9845647058823529, 0.42572549019607847, 0.3002352941176471}, 
+ {0.9845490196078431, 0.42509803921568634, 0.29960784313725497}, 
+ {0.9845333333333333, 0.42447058823529416, 0.2989803921568628}, 
+ {0.9845176470588235, 0.42384313725490197, 0.2983529411764706}, 
+ {0.9845019607843136, 0.42321568627450984, 0.29772549019607847}, 
+ {0.9844862745098039, 0.4225882352941177, 0.29709803921568634}, 
+ {0.9844705882352941, 0.4219607843137255, 0.29647058823529415}, 
+ {0.9844549019607842, 0.42133333333333334, 0.29584313725490197}, 
+ {0.9844392156862745, 0.4207058823529412, 0.29521568627450984}, 
+ {0.9844235294117647, 0.4200784313725491, 0.2945882352941177}, 
+ {0.9844078431372548, 0.4194509803921569, 0.2939607843137255}, 
+ {0.9843921568627451, 0.4188235294117647, 0.29333333333333333}, 
+ {0.9843764705882352, 0.4181960784313726, 0.2927058823529412}, 
+ {0.9843607843137254, 0.41756862745098045, 0.2920784313725491}, 
+ {0.9843450980392157, 0.41694117647058826, 0.2914509803921569}, 
+ {0.9843294117647058, 0.4163137254901961, 0.2908235294117647}, 
+                                                    {0.984313725490196, 0.41568627450980394, 0.2901960784313726}};
+
+#endif

diff --git a/cmd/gvmap/colorutil.c b/cmd/gvmap/colorutil.c
new file mode 100644 (file)
index 0000000..4cf5d9a
--- /dev/null
+++ b/cmd/gvmap/colorutil.c
@@ -0,0 +1,95 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#include "general.h"
+#include "colorutil.h"
+
+static void r2hex(float r, char *h){
+  /* convert a number in [0,1] to 0 to 255 then to a hex */
+  static char hex[] = "0123456789abcdef";
+  int i = (int)(255*r+0.5);
+  int j = i%16;
+  int k = i/16;
+  h[0] = hex[k];
+  h[1] = hex[j];
+}
+
+void rgb2hex(float r, float g, float b, char *cstring){
+  cstring[0] = '#';
+  r2hex(r, &(cstring[1]));
+  r2hex(g, &(cstring[3]));
+  r2hex(b, &(cstring[5]));
+  //set to semitransparent for multiple sets vis
+  //cstring[7] = cstring[8] = '3';
+  //cstring[9]='\0';
+  cstring[7] = '\0';
+}
+
+real Hue2RGB(real v1, real v2, real H) {
+  if(H < 0.0) H += 1.0;
+  if(H > 1.0) H -= 1.0;
+  if((6.0*H) < 1.0) return (v1 + (v2 - v1) * 6.0 * H);
+  if((2.0*H) < 1.0) return v2;
+  if((3.0*H) < 2.0) return (v1 + (v2 - v1) * ((2.0/3.0) - H) * 6.0);
+  return v1;
+}
+
+char *hex[16]={"0","1","2","3","4","5","6","7","8","9","a","b","c","d","e","f"};
+
+char * hue2rgb(real hue, char *color){
+  real v1, v2, lightness = .5, saturation = 1;
+  int red, blue, green;
+
+  if(lightness < 0.5) 
+    v2 = lightness * (1.0 + saturation);
+  else
+    v2 = (lightness + saturation) - (saturation * lightness);
+
+  v1 = 2.0 * lightness - v2;
+
+  red =   (int)(255.0 * Hue2RGB(v1, v2, hue + (1.0/3.0)) + 0.5);
+  green = (int)(255.0 * Hue2RGB(v1, v2, hue) + 0.5);
+  blue =  (int)(255.0 * Hue2RGB(v1, v2, hue - (1.0/3.0)) + 0.5);
+  color[0] = '#';
+  sprintf(color+1,"%s",hex[red/16]);
+  sprintf(color+2,"%s",hex[red%16]);
+  sprintf(color+3,"%s",hex[green/16]);
+  sprintf(color+4,"%s",hex[green%16]);
+  sprintf(color+5,"%s",hex[blue/16]);
+  sprintf(color+6,"%s",hex[blue%16]);
+  color[7] = '\0';
+  return color;
+}
+
+
+void hue2rgb_real(real hue, real *color){
+  real v1, v2, lightness = .5, saturation = 1;
+  int red, blue, green;
+
+  if(lightness < 0.5) 
+    v2 = lightness * (1.0 + saturation);
+  else
+    v2 = (lightness + saturation) - (saturation * lightness);
+
+  v1 = 2.0 * lightness - v2;
+
+  red =   (int)(255.0 * Hue2RGB(v1, v2, hue + (1.0/3.0)) + 0.5);
+  green = (int)(255.0 * Hue2RGB(v1, v2, hue) + 0.5);
+  blue =  (int)(255.0 * Hue2RGB(v1, v2, hue - (1.0/3.0)) + 0.5);
+
+
+  color[0] = red/255.;
+  color[1] = green/255.;
+  color[2] = blue/255.;
+                 
+}

diff --git a/cmd/gvmap/colorutil.h b/cmd/gvmap/colorutil.h
new file mode 100644 (file)
index 0000000..e3a7daa
--- /dev/null
+++ b/cmd/gvmap/colorutil.h
@@ -0,0 +1,25 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#ifndef COLORUTIL_H
+#define COLORUTIL_H
+
+#include <color.h>
+
+extern int colorxlate(char *str, gvcolor_t * color, color_type_t target_type);
+
+void rgb2hex(float r, float g, float b, char *cstring);/* dimension of cstring must be >=7 */
+char* hue2rgb(real hue, char *color);
+void hue2rgb_real(real hue, real *color);
+
+#endif

diff --git a/cmd/gvmap/country_graph_coloring.c b/cmd/gvmap/country_graph_coloring.c
new file mode 100644 (file)
index 0000000..9aadeae
--- /dev/null
+++ b/cmd/gvmap/country_graph_coloring.c
@@ -0,0 +1,120 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#define STANDALONE
+#include "SparseMatrix.h"
+#include "country_graph_coloring.h"
+#include "power.h"
+
+static void get_local_12_norm(int n, int i, int *ia, int *ja, int *p, real *norm){
+  int j;
+  norm[0] = n; norm[1] = 0;
+  for (j = ia[i]; j < ia[i+1]; j++){
+    if (ja[j] == i) continue;
+    norm[0] = MIN(norm[0], ABS(p[i] - p[ja[j]]));
+    norm[1] += ABS(p[i] - p[ja[j]]);
+  }
+}
+static void get_12_norm(int n, int *ia, int *ja, int *p, real *norm){
+  int i, j;
+  norm[0] = n; norm[1] = 0;
+  for (i = 0; i < n; i++){
+    for (j = ia[i]; j < ia[i+1]; j++){
+      if (ja[j] == i) continue;
+      norm[0] = MIN(norm[0], ABS(p[i] - p[ja[j]]));
+      norm[1] += ABS(p[i] - p[ja[j]]);
+    }
+  }
+}
+
+void country_graph_coloring(int seed, SparseMatrix A, int **p, real *norm_1){
+  int n = A->m, i, j, jj;
+  SparseMatrix L, A2;
+  int *ia = A->ia, *ja = A->ja;
+  int a = -1.;
+  real nrow;
+  real *v = NULL;
+  real norm1[2], norm2[2], norm11[2], norm22[2], norm = n;
+  real pi, pj;
+  int improved = TRUE;
+
+
+  assert(A->m == A->n);
+  A2 = SparseMatrix_symmetrize(A, TRUE);
+  ia = A2->ia; ja = A2->ja;
+
+  /* Laplacian */
+  L = SparseMatrix_new(n, n, 1, MATRIX_TYPE_REAL, FORMAT_COORD);
+  for (i = 0; i < n; i++){
+    nrow = 0.;
+    for (j = ia[i]; j < ia[i+1]; j++){
+      jj = ja[j];
+      if (jj != i){
+       nrow ++;
+       L = SparseMatrix_coordinate_form_add_entries(L, 1, &i, &jj, &a);
+      }
+    }
+    L = SparseMatrix_coordinate_form_add_entries(L, 1, &i, &i, &nrow);
+  }
+  L = SparseMatrix_from_coordinate_format(L);
+
+  /* largest eigen vector */
+  {
+    int maxit = 100;
+    real tol = 0.00001;
+    power_method(L, seed, maxit, tol, &v);
+  }
+
+  vector_ordering(n, v, p, TRUE);
+
+  /* swapping */
+  while (improved){
+    improved = FALSE; norm = n;
+    for (i = 0; i < n; i++){
+      get_local_12_norm(n, i, ia, ja, *p, norm1);
+      for (j = 0; j < n; j++){
+       if (j == i) continue;
+       get_local_12_norm(n, j, ia, ja, *p, norm2);
+       norm = MIN(norm, norm2[0]);
+       pi = (*p)[i]; pj = (*p)[j];
+       (*p)[i] = pj;
+       (*p)[j] = pi;
+       get_local_12_norm(n, i, ia, ja, *p, norm11);
+       get_local_12_norm(n, j, ia, ja, *p, norm22);
+       if (MIN(norm11[0],norm22[0]) > MIN(norm1[0],norm2[0])){
+         //        ||
+         //(MIN(norm11[0],norm22[0]) == MIN(norm1[0],norm2[0]) && norm11[1]+norm22[1] > norm1[1]+norm2[1])) {
+         improved = TRUE;
+         norm1[0] = norm11[0];
+         norm1[1] = norm11[1];
+         continue;
+       }
+       (*p)[i] = pi;
+       (*p)[j] = pj;
+      }
+    }
+    if (Verbose) {
+      get_12_norm(n, ia, ja, *p, norm1);
+      fprintf(stderr, "norm = %f", norm);
+      fprintf(stderr, "norm1 = %f, norm2 = %f\n", norm1[0], norm1[1]);
+    }
+  }
+  get_12_norm(n, ia, ja, *p, norm1);
+
+  *norm_1 = norm1[0];
+  if (A2 != A) SparseMatrix_delete(A2);
+  SparseMatrix_delete(L);
+}
+
+
+

diff --git a/cmd/gvmap/country_graph_coloring.h b/cmd/gvmap/country_graph_coloring.h
new file mode 100644 (file)
index 0000000..9e90dfd
--- /dev/null
+++ b/cmd/gvmap/country_graph_coloring.h
@@ -0,0 +1,19 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#ifndef COUNTRY_GRAPH_CLUSTERING_H
+#define COUNTRY_GRAPH_CLUSTERING_H
+
+void country_graph_coloring(int seed, SparseMatrix A, int **p, real *norm_1);
+
+#endif

diff --git a/cmd/gvmap/gvmap.1 b/cmd/gvmap/gvmap.1
new file mode 100644 (file)
index 0000000..4c12770
--- /dev/null
+++ b/cmd/gvmap/gvmap.1
@@ -0,0 +1,32 @@
+.de TQ
+.  br
+.  ns
+.  TP \\$1
+..
+.TH GVMAP 1 "3 March 2011"
+.SH NAME
+gvmap \- geographical map create from graphs
+.SH SYNOPSIS
+.B gvmap
+[\fB\-ekov?\fP]
+[
+.I options
+]
+[
+.BI \-o
+.I outfile
+]
+[ 
+.I files
+]
+.SH DESCRIPTION
+.B gvmap
+takes as input a graph in DOT format with node position and size
+information, and produces a rendering of the graph as a geographic-style map.
+.SH AUTHOR
+Yifan Hu <yifanhu@research.att.com>
+.SH "SEE ALSO"
+.PP
+sfdp(1), neato(1), gvpr(1)
+.PP
+E. R. Gansner, Y. Hu, S. G. Kobourov, "GMap: Visualizing graphs and clusters as maps," Proc. Pacific Vis. 2010, pp. 201\(hy208.

diff --git a/cmd/gvmap/gvmap.c b/cmd/gvmap/gvmap.c
new file mode 100644 (file)
index 0000000..cda47aa
--- /dev/null
+++ b/cmd/gvmap/gvmap.c
@@ -0,0 +1,788 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#include <stdio.h>
+#include <stdlib.h>
+#define STANDALONE
+#include "general.h"
+#include "QuadTree.h"
+#include <time.h>
+#include "SparseMatrix.h"
+#include <getopt.h>
+#include "string.h"
+#include "make_map.h"
+#include "spring_electrical.h"
+#include "post_process.h"
+#include "overlap.h"
+#include "clustering.h"
+#include "ingraphs.h"
+#include "DotIO.h"
+#include "colorutil.h"
+
+int Verbose;
+enum {POINTS_ALL = 1, POINTS_LABEL, POINTS_RANDOM};
+enum {maxlen = 10000000};
+enum {MAX_GRPS = 10000};
+static char swork[maxlen];
+#if 0
+void *gmalloc(size_t nbytes)
+{
+    char *rv;
+    if (nbytes == 0)
+        return NULL;
+    rv = malloc(nbytes);
+    if (rv == NULL) {
+        fprintf(stderr, "out of memory\n");
+        abort();
+    }
+    return rv;
+}
+
+void *grealloc(void *ptr, size_t size)
+{
+    void *p = realloc(ptr, size);
+    if (p == NULL && size) {
+        fprintf(stderr, "out of memory\n");
+        abort();
+    }
+    return p;
+}
+
+#endif
+
+typedef struct {
+    char* cmd;
+    char **infiles; 
+    FILE* outfile;
+    int dim;
+    int rawData;
+    real shore_depth_tol;
+    int nrandom; 
+    int show_points; 
+    real bbox_margin[2]; 
+    int whatout;
+    int plotedges;
+    int color_scheme;
+    real line_width;
+    char *plot_label;
+    real *bg_color;
+    int improve_contiguity_n;
+    int nart;
+    int color_optimize;
+    int maxcluster;
+    int nedgep;
+    char *line_color;
+    int include_OK_points;
+    int highlight_cluster;
+    int seed;      /* seed used to calculate Fiedler vector */
+} params_t;
+
+int string_split(char *s, char sp, char ***ss0, int *ntokens0){
+  /* give a string s ending with a \0, split into an array of strings using separater sp, 
+     with \0 inserted. Return 0 if successful, 1 if length of string exceed buffer size */
+  int ntokens = 0, len = 0;
+
+  int i;
+  char **ss;
+  char *swork1 = swork;
+  if (strlen(s) > maxlen) {
+    swork1 = MALLOC(sizeof(char)*maxlen);
+  }
+
+  for (i = 0; i < strlen(s); i++){
+    if (s[i] == sp){
+      ntokens++;
+    } else if (s[i] == '\n' || s[i]== EOF){
+      ntokens++;
+      break;
+    }
+  }
+
+  ss = malloc(sizeof(char*)*(ntokens+1));
+  ntokens = 0;
+  for (i = 0; i < strlen(s); i++){
+    if (s[i] == sp){
+      swork1[len++] = '\0';
+      ss[ntokens] = malloc(sizeof(char)*(len+1));
+      strcpy(ss[ntokens], swork1);
+      len = 0;
+      ntokens++;
+      continue;
+    } else if (s[i] == '\n' || s[i] == EOF){
+      swork1[len++] = '\0';
+      ss[ntokens] = malloc(sizeof(char)*(len+1));
+      strcpy(ss[ntokens], swork1);
+      len = 0;
+      ntokens++;
+      break;
+    }
+    swork1[len++] = s[i];
+  }
+
+  *ntokens0 = ntokens;
+
+  *ss0 = ss;
+
+  if (swork1 != swork) FREE(swork1);
+  return 0;
+
+}
+
+static char* usestr =
+"    -a k - average number of artificial points added along the bounding box of the labels. (10)\n\
+    -b v - polygon line width, with v < 0 for no line. (0)\n\
+    -c v - polygon color scheme (1)\n\
+       0 : no polygons\n\
+       1 : pastel\n\
+       2 : blue to yellow\n\
+       3 : white to red\n\
+       4 : light grey to red\n\
+       5 : primary colors\n\
+       6 : sequential single hue red \n\
+       7 : sequential single hue lighter red \n\
+       8 : light grey\n\
+    -d s - seed used to calculate Fielder vector for optimal coloring\n\
+    -C k - generate at most k clusters. (0)\n\
+    -e   - show edges\n\
+    -g c - bounding box color. If not specified, bounding box is not drawn.\n\
+    -k   - increase randonesss of boundary\n\
+    -l s - specify label\n\
+    -m v - bounding box margin. If 0, auto assigned (0)\n\
+    -h k - number of artificial points added maintain bridge between endpoints (0)\n\
+    -o <file> - put output in <file> (stdout)\n\
+    -p k - show points. (0)\n\
+       0 : no points\n\
+       1 : all points\n\
+       2 : label points\n\
+       3 : random/artificial points\n\
+    -r v - number of points. If 0, auto assigned. (0)\n\
+    -s d - depth of the shore in points. If 0, auto assigned. (0)\n\
+    -t n - improve contiguity up to n times. (0)\n\
+    -O   - do NOT to optimize color differences\n\
+    -v   - verbose\n\
+    -z c - polygon line color (black)\n";
+
+/*
+    -q f - output format (3)\n\
+       0 : Mathematica\n\
+       1 : PostScript\n\
+       2 : country map\n\
+       3 : dot format\n\
+*/
+    /* e.g., 
+       1 [cluster=10, clustercolor="#ff0000"]
+       2 [cluster=10]
+       (and no ther nodes are in cluster10)
+
+       then since we can only use 1 color for the cluster 10, both 1 and 2 will be colored based on the color of node 2. However if you have
+
+       2 [cluster=10]
+       1 [cluster=10, clustercolor="#ff0000"]
+
+       then you get both colored red.
+       
+    */
+
+static void usage(char* cmd, int eval)
+{
+    fprintf(stderr, "Usage: %s <options> graphfile\n", cmd);
+    fputs (usestr, stderr);
+    exit(eval);
+}
+
+static FILE *openFile(char *name, char *mode, char* cmd)
+{
+    FILE *fp;
+    char *modestr;
+
+    fp = fopen(name, mode);
+    if (!fp) {
+       if (*mode == 'r')
+           modestr = "reading";
+       else
+           modestr = "writing";
+       fprintf(stderr, "%s: could not open file %s for %s\n",
+               cmd, name, modestr);
+       exit(-1);
+    }
+    return (fp);
+}
+
+#define HLPFX "ighlight="
+#define N_HLPFX (sizeof(HLPFX)-1)
+
+static void 
+init(int argc, char **argv, params_t* pm)
+{
+  char* cmd = argv[0];
+  unsigned int c;
+  real s;
+  int v, r;
+
+  pm->outfile = NULL;
+  pm->nrandom = -1;
+  pm->dim = 2;
+  pm->rawData = 0;
+  pm->shore_depth_tol = 0;
+  pm->highlight_cluster = 0;
+  pm->plotedges = 0;
+  pm->whatout = 0;
+  pm->show_points = 0;
+  pm->color_scheme = COLOR_SCHEME_PASTEL; 
+  pm->line_width = 0;
+  pm->plot_label = NULL;
+  pm->bg_color = NULL;
+  pm->improve_contiguity_n = 0;
+  pm->whatout = OUT_DOT;
+  pm->nart = 10;
+  pm->color_optimize = 1;
+  pm->maxcluster = 0;
+  pm->nedgep = 0;
+
+  pm->cmd = cmd;
+  pm->infiles = NULL;
+  pm->line_color = N_NEW(10,char);
+  strcpy(pm->line_color,"#000000");
+  pm->include_OK_points = FALSE;
+  pm->seed = 123;
+
+  /*  bbox_margin[0] =  bbox_margin[1] = -0.2;*/
+  pm->bbox_margin[0] =  pm->bbox_margin[1] = 0;
+
+  while ((c = getopt(argc, argv, ":efvOko:m:s:r:p:c:C:l:b:g:t:a:h:z:d:")) != -1) {
+    switch (c) {
+    case 'm':
+      if ((sscanf(optarg,"%lf",&s) > 0) && (s != 0)){
+           pm->bbox_margin[0] =  pm->bbox_margin[1] = s;
+      } else {
+        usage(cmd, 1);
+      }
+      break;
+#if 0
+    case 'q':
+      if ((sscanf(optarg,"%d",&r) > 0) && r >=0 && r <=OUT_PROCESSING){
+        pm->whatout = r;
+      } else {
+        usage(cmd,1);
+      }
+      break;
+#endif
+    case 's':
+      if ((sscanf(optarg,"%lf",&s) > 0)){
+        pm->shore_depth_tol = s;
+      } else {
+        usage(cmd,1);
+      }
+      break;
+    case 'h':
+      if ((sscanf(optarg,"%d",&v) > 0)){
+        pm->nedgep = MAX(0, v);
+      } else if (!strncmp(optarg, HLPFX, N_HLPFX) && (sscanf(optarg+N_HLPFX,"%d",&v) > 0)) {
+        pm->highlight_cluster = MAX(0, v);
+      } else {
+        usage(cmd,1);
+      }
+      break;
+     case 'f':
+        pm->rawData = 1;
+      break;
+     case 'r':
+      if ((sscanf(optarg,"%d",&r) > 0)){
+        pm->nrandom = r;
+      }
+      break;
+    case 't':
+      if ((sscanf(optarg,"%d",&r) > 0) && r > 0){
+        pm->improve_contiguity_n = r;
+      }
+      break;
+    case 'p':
+      pm->show_points = 1;
+      if ((sscanf(optarg,"%d",&r) > 0)){
+        pm->show_points = MIN(3, r);
+      }
+      break;
+    case 'k':
+      pm->include_OK_points = TRUE;
+      break;
+    case 'v':
+      Verbose = 1;
+      break;
+    case 'e':
+      pm->plotedges = 1;
+      break;
+    case 'o':
+         pm->outfile = openFile(optarg, "w", pm->cmd);
+      break;
+    case 'O':
+      pm->color_optimize = 0;
+      break;
+    case 'a':
+      if ((sscanf(optarg,"%d",&r) > 0) && r >= 0){
+           pm->nart = r;
+      } else {
+           usage(cmd,1);
+      }
+      break;
+    case 'c':
+      if ((sscanf(optarg,"%d",&r) > 0) && r >= COLOR_SCHEME_NONE && r <= COLOR_SCHEME_GREY){
+        pm->color_scheme = r;
+      } else {
+        usage(cmd,1);
+      }
+      break;
+    case 'd':
+      if (sscanf(optarg,"%d",&v) <= 0){
+        usage(cmd,1);
+      }
+      else
+        pm->seed = v;
+      break;
+    case 'C':
+      if (!((sscanf(optarg,"%d",&v) > 0) && v >= 0)){
+        usage(cmd,1);
+      }
+      else
+        pm->maxcluster = v;
+      break;
+    case 'g': {
+      gvcolor_t color;
+      if (colorxlate(optarg, &color, RGBA_DOUBLE) == COLOR_OK) {
+        if (!pm->bg_color) pm->bg_color = N_NEW(3,real);
+        pm->bg_color[0] = color.u.RGBA[0];
+        pm->bg_color[1] = color.u.RGBA[1];
+        pm->bg_color[2] = color.u.RGBA[2];
+      }
+      break;
+    }
+    case 'z': {
+      FREE (pm->line_color);
+      pm->line_color = strdup (optarg);
+      break;
+    }
+    case 'b':
+      if (sscanf(optarg,"%lf",&s) > 0) {
+        pm->line_width = s;
+      } else {
+        fprintf (stderr, "%s: unexpected argument \"%s\" for -b flag\n", cmd, optarg);
+      }
+      break;
+    case 'l':
+      if (pm->plot_label) free (pm->plot_label);
+      pm->plot_label = strdup (optarg);
+      break;
+    case '?':
+      if (optopt == '?')
+        usage(cmd, 0);
+      else {
+        fprintf(stderr, " option -%c unrecognized - ignored\n", optopt);
+        usage(cmd, 0);
+      }
+      break;
+    }
+  }
+
+  argv += optind;
+  argc -= optind;
+  if (argc)
+    pm->infiles = argv;
+  if (!pm->outfile)
+    pm->outfile = stdout;
+}
+
+static void add_return(char *s){
+  /* replace "\\n" by "\n" (return) */
+  int i, j, len =strlen(s);
+  for (i = 0; i < strlen(s); i++){
+    if (s[i] == '\\' && i < len - 1 && s[i+1] == 'n'){
+      s[i] = '\n';
+      for (j = i+1; j < len - 1; j++) s[j] = s[j+1];
+      s[len - 1] = '\0'; len--;
+    }
+  }
+}
+
+static int read_data(int n, int dim, int k, FILE *fp, real *x, real *width, int *grouping, char **labels, float *fsz,
+         float *rgb_r, float *rgb_g, float *rgb_b){
+  char **fields;
+  int nfields;
+  char buf[100000];
+  int i, nz = 0, len;
+  char s;
+
+  /* x|y|width|height|group|label|fontsize|rgbcolor|*/
+
+  for (i = 0; i < n; i++){
+    while ((s = buf[nz++] = fgetc(fp)) != '\n' && s != EOF);
+    buf[nz] = '\0';
+    if (nz < 1) break;
+
+    if (string_split(buf, '|', &fields, &nfields)) return 1;
+    assert(nfields >= k);
+
+    sscanf(fields[0], "%lf", &(x[i*dim]));
+    sscanf(fields[1], "%lf", &(x[i*dim+1]));
+    sscanf(fields[2], "%lf", &(width[i*dim]));
+    sscanf(fields[3], "%lf", &(width[i*dim+1]));
+    sscanf(fields[4], "%d", &(grouping[i]));
+    labels[i] = MALLOC(sizeof(char*)*(strlen(fields[5])+1));
+    strcpy(labels[i], fields[5]);
+    add_return(labels[i]);
+
+    sscanf(fields[6], "%f", &(fsz[i]));
+    /*fields[7] is of the form RGBColor[x, y, z]*/
+    len = strlen(fields[7]);
+    fields[7][len-1] = ',';
+    if (len < 10) {
+      fprintf(stderr,"line %d is funny, check you data! I am assign black color\n", i+2);
+      rgb_r[grouping[i]]=rgb_g[grouping[i]]=rgb_b[grouping[i]] = 0.;
+    } else {
+      strcpy(buf, fields[7]+9);
+      if (string_split(buf, ',', &fields, &nfields)) return 1;
+      
+      sscanf(fields[0], "%f", &(rgb_r[grouping[i]]));
+      sscanf(fields[1], "%f", &(rgb_g[grouping[i]]));
+      sscanf(fields[2], "%f", &(rgb_b[grouping[i]]));
+    }
+    if (s == EOF){
+      break;
+    }
+    nz = 0;
+  }
+
+  
+  return 0;
+}
+
+#if 0
+static void get_graph_node_attribute(Agraph_t* g, char *tag, char *format, size_t len, void *x_default_val, int *nn, void *x, int *flag){
+  /* read a node attribute. Example
+     {real x0[2];
+     real *x = NULL;
+
+     x0[0] = x0[1] = 0.;
+     get_graph_node_attribute(g, "pos", "%lf,%lf", sizeof(real)*2, x0, &n, &x, &flag)
+
+     or, do not supply x0 if you want error flagged when pos tag is not available:
+
+     get_graph_node_attribute(g, "pos", "%lf,%lf", sizeof(real)*2, NULL, &n, x, &flag);
+
+     assert(!flag);
+     FREE(x);
+     }
+  */
+  Agnode_t* n;
+  int nnodes;
+
+
+  *flag = 0;
+
+  if (!g) {
+    *flag = -1;
+    return;
+  }
+
+  nnodes = agnnodes (g);
+  *nn = nnodes;
+  for (n = agfstnode (g); n; n = agnxtnode (g, n)) {
+    if (agget(n, tag)){
+      if (strcmp(format,"%s") == 0){
+       strcpy(x, agget(n, tag));
+      } else {
+       sscanf(agget(n, tag), format, x);
+      }
+
+    } else if (x_default_val){
+      memcpy(x, x_default_val, len);
+    } else {
+      *flag = -1;
+      return;
+    }
+    x += len;
+  }
+
+}
+#endif
+
+static void 
+makeMap (SparseMatrix graph, int n, real* x, real* width, int* grouping, 
+  char** labels, float* fsz, float* rgb_r, float* rgb_g, float* rgb_b, params_t* pm, Agraph_t* g )
+{
+  int dim = pm->dim;
+  int i, flag = 0;
+  SparseMatrix poly_lines, polys, poly_point_map;
+  real edge_bridge_tol = 0.;
+  int npolys, nverts, *polys_groups, exclude_random;
+  real *x_poly, *xcombined;
+  enum {max_string_length = 1000};
+  enum {MAX_GRPS = 10000};
+  SparseMatrix country_graph;
+  int improve_contiguity_n = pm->improve_contiguity_n;
+#ifdef TIME
+  clock_t  cpu;
+#endif
+  int nr0, nart0;
+  int nart, nrandom;
+
+  exclude_random = TRUE;
+#if 0
+  if (argc >= 2) {
+    fp = fopen(argv[1],"r");
+    graph = SparseMatrix_import_matrix_market(fp, FORMAT_CSR);
+  }
+
+  if (whatout == OUT_M){
+    printf("Show[{");
+  }
+#endif
+
+
+#ifdef TIME
+  cpu = clock();
+#endif
+  nr0 = nrandom = pm->nrandom; nart0 = nart = pm->nart;
+  make_map_from_rectangle_groups(exclude_random, pm->include_OK_points,
+                                n, dim, x, width, grouping, graph, pm->bbox_margin, &nrandom, &nart, pm->nedgep, 
+                                pm->shore_depth_tol, edge_bridge_tol, &xcombined, &nverts, &x_poly, &npolys, &poly_lines, 
+                                &polys, &polys_groups, &poly_point_map, &country_graph, pm->highlight_cluster, &flag);
+
+  /* compute a good color permutation */
+  if (pm->color_optimize && country_graph && rgb_r && rgb_g && rgb_b) 
+    map_optimal_coloring(pm->seed, country_graph, rgb_r,  rgb_g, rgb_b);
+
+#ifdef TIME
+  fprintf(stderr, "map making time = %f\n",((real) (clock() - cpu)) / CLOCKS_PER_SEC);
+#endif
+
+
+  /* now we check to see if all points in the same group are also in the same polygon, if not, the map is not very
+     contiguous so we move point positions to improve contiguity */
+  if (graph && improve_contiguity_n) {
+    for (i = 0; i < improve_contiguity_n; i++){
+      improve_contiguity(n, dim, grouping, poly_point_map, x, graph, width);
+      nart = nart0;
+      nrandom = nr0;
+      make_map_from_rectangle_groups(exclude_random, pm->include_OK_points,
+                                    n, dim, x, width, grouping, graph, pm->bbox_margin, &nrandom, &nart, pm->nedgep, 
+                                    pm->shore_depth_tol, edge_bridge_tol, &xcombined, &nverts, &x_poly, &npolys, &poly_lines, 
+                                    &polys, &polys_groups, &poly_point_map, &country_graph, pm->highlight_cluster, &flag);
+    }
+    assert(!flag);    
+    {
+      SparseMatrix D;
+      D = SparseMatrix_get_real_adjacency_matrix_symmetrized(graph);
+      remove_overlap(dim, D, x, width, 1000, 5000.,
+                    ELSCHEME_NONE, 0, NULL, NULL, &flag);
+      
+      nart = nart0;
+      nrandom = nr0;
+      make_map_from_rectangle_groups(exclude_random, pm->include_OK_points,
+                                    n, dim, x, width, grouping, graph, pm->bbox_margin, &nrandom, &nart, pm->nedgep, 
+                                    pm->shore_depth_tol, edge_bridge_tol, &xcombined, &nverts, &x_poly, &npolys, &poly_lines, 
+                                    &polys, &polys_groups, &poly_point_map, &country_graph, pm->highlight_cluster, &flag);
+    }
+    assert(!flag);
+    
+  }
+
+#if 0
+  if (whatout == OUT_DOT){
+#endif
+    Dot_SetClusterColor(g, rgb_r,  rgb_g,  rgb_b, grouping);
+    plot_dot_map(g, n, dim, x, polys, poly_lines, pm->line_width, pm->line_color, x_poly, polys_groups, labels, width, fsz, rgb_r, rgb_g, rgb_b, pm->plot_label, pm->bg_color, (pm->plotedges?graph:NULL), pm->outfile);
+#if 0
+    }
+    goto RETURN;
+  }
+
+  if (whatout == OUT_PROCESSING){
+    if (plotedges){
+      plot_processing_map(g, n, dim, x, polys, poly_lines, line_width, nverts, x_poly, polys_groups, labels, width, fsz, rgb_r, rgb_g, rgb_b, plot_label, bg_color, graph);
+    } else {
+      plot_processing_map(g, n, dim, x, polys, poly_lines, line_width, nverts, x_poly, polys_groups, labels, width, fsz, rgb_r, rgb_g, rgb_b, plot_label, bg_color, NULL);
+    }
+
+    goto RETURN;
+  }
+
+  if (whatout == OUT_PS){
+    if (plotedges){
+      plot_ps_map(n, dim, x, polys, poly_lines, line_width, x_poly, polys_groups, labels, width, fsz, rgb_r, rgb_g, rgb_b, plot_label, bg_color, graph);
+    } else {
+      plot_ps_map(n, dim, x, polys, poly_lines, line_width, x_poly, polys_groups, labels, width, fsz, rgb_r, rgb_g, rgb_b, plot_label, bg_color, NULL);
+    }
+
+    goto RETURN;
+  }
+
+
+  if (whatout == OUT_M_COUNTRY_GRAPH){
+    SparseMatrix_print("(*country graph=*)",country_graph);
+    goto RETURN;
+    
+  }
+
+  
+  /*plot_polys(FALSE, polys, x_poly, polys_groups, rgb_r, rgb_g, rgb_b);*/
+  if (whatout == OUT_M){
+    plot_polys(FALSE, polys, x_poly, polys_groups, NULL, NULL, NULL);
+    printf(",");
+
+    plot_polys(TRUE, poly_lines, x_poly, polys_groups, NULL, NULL, NULL);
+ 
+    if (show_points){
+      if (show_points == POINTS_ALL){
+       printf(",");
+       plot_points(n + nart + nrandom - 4, dim, xcombined);
+      } else if (show_points == POINTS_LABEL){
+       printf(",");
+       plot_points(n + nart - 4, dim, xcombined);
+      } else if (show_points == POINTS_RANDOM){
+       printf(",");
+       plot_points(MAX(1,nrandom - 4), dim, xcombined+dim*(n+nart));
+      } else {
+       assert(0);
+      }
+    }
+    if (plotedges){
+      printf(",");
+      plot_edges(n, dim, x, graph);
+    }
+    
+    if (labels){
+      printf(",");
+      plot_labels(n, dim, xcombined, labels);
+    }
+    
+    printf("}]\n");
+  }
+
+ RETURN:
+#endif
+  SparseMatrix_delete(polys);
+  SparseMatrix_delete(poly_lines);
+  SparseMatrix_delete(poly_point_map);
+  FREE(xcombined);
+  FREE(x_poly);
+  FREE(polys_groups);
+}
+
+static void doRawData (FILE* fp, params_t* pm)
+{
+  real* x;
+  real* width;
+  int dim = pm->dim;
+  char** labels = NULL;
+  int* grouping;
+  float* rgb_r;
+  float* rgb_g;
+  float* rgb_b;
+  float* fsz;
+  int ierr, n, nentries;
+
+  ierr = fscanf(fp, "%d\t%d\n",&n, &nentries);
+  if (nentries == 8) {
+    /* x|y|width|height|group|label|fontsize|rgbcolor|*/
+    labels = MALLOC(sizeof(char*)*n);
+  }
+  x = N_NEW(dim*n, real);
+  width = N_NEW(dim*n, real);
+  grouping = N_NEW(n,int);
+  rgb_r = N_NEW(MAX_GRPS,float);
+  rgb_g = N_NEW(MAX_GRPS,float);
+  rgb_b = N_NEW(MAX_GRPS,float);
+  fsz = N_NEW(n,float);
+    
+  read_data(n, dim, nentries, fp, x, width, grouping, labels, fsz, rgb_r, rgb_g, rgb_b);
+
+  makeMap (NULL, n, x, width, grouping, labels, fsz, rgb_r, rgb_g, rgb_b, pm, NULL);
+
+  free (x);
+  free (width);
+  free (grouping);
+  free (rgb_r);
+  free (rgb_g);
+  free (rgb_b);
+  free (fsz);
+  if (labels) free (labels);
+      
+}
+
+static void mapFromRaw (params_t* pm)
+{
+  char* fname;
+  FILE* fp;
+    
+  if (pm->infiles[0] == NULL)
+    doRawData (stdin, pm);
+  else {
+    int i = 0;
+    while ((fname = pm->infiles[i])) { 
+      fp = fopen(fname, "r");
+      if (!fp) {
+        fprintf (stderr, "%s: could not open %s for reading\n", pm->cmd, fname);
+      }
+      else {
+        doRawData (fp, pm);
+        fclose(fp);
+      }
+      i++;
+    }
+  }
+}
+
+static void mapFromGraph (Agraph_t* g, params_t* pm)
+{
+  int n;
+  real* width = NULL;
+  real* x;
+  char** labels = NULL;
+  int* grouping;
+  float* rgb_r;
+  float* rgb_g;
+  float* rgb_b;
+  float* fsz;
+
+  initDotIO(g);
+  SparseMatrix graph = Import_coord_clusters_from_dot(g, pm->maxcluster, pm->dim, &n, &width, NULL, &x, &grouping, 
+                                          &rgb_r,  &rgb_g,  &rgb_b,  &fsz, &labels, pm->color_scheme, CLUSTERING_MODULARITY);
+  makeMap (graph, n, x, width, grouping, labels, fsz, rgb_r, rgb_g, rgb_b, pm, g);
+}
+
+static Agraph_t *gread(FILE * fp)
+{
+    return agread(fp, (Agdisc_t *) 0);
+}
+
+int main(int argc, char *argv[])
+{
+  params_t pm;
+  Agraph_t* g;
+  Agraph_t* prevg = NULL;
+  ingraph_state ig;
+
+  init(argc, argv, &pm);
+
+  if (pm.rawData) 
+    mapFromRaw (&pm);
+  else {
+    newIngraph (&ig, pm.infiles, gread);
+    while ((g = nextGraph (&ig)) != 0) {
+      if (prevg) agclose (prevg);
+      mapFromGraph (g, &pm);
+      prevg = g;
+    }
+  }
+
+  return 0; 
+}

diff --git a/cmd/gvmap/make_map.c b/cmd/gvmap/make_map.c
new file mode 100644 (file)
index 0000000..bc21805
--- /dev/null
+++ b/cmd/gvmap/make_map.c
@@ -0,0 +1,2329 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#define STANDALONE
+#include "SparseMatrix.h"
+#include "general.h"
+#include "QuadTree.h"
+#include "string.h"
+/* #include "types.h" */
+#include <cgraph.h>
+#include "make_map.h"
+/* #include "ps.h" */
+#include "stress_model.h"
+#include "country_graph_coloring.h"
+#include "colorutil.h"
+#include "delaunay.h"
+
+#ifdef SINGLE
+#define REAL float
+#else /* not SINGLE */
+#define REAL double
+#endif /* not SINGLE */
+/* #include "triangle.h" */
+
+void map_optimal_coloring(int seed, SparseMatrix A, float *rgb_r,  float *rgb_g, float *rgb_b){
+  int *p = NULL;
+  float *u = NULL;
+  int n = A->m;
+  int i;
+  real norm1;
+
+  country_graph_coloring(seed, A, &p, &norm1);
+
+  rgb_r++; rgb_b++; rgb_g++;/* seems necessary, but need to better think about cases when clusters are not contigous */
+  vector_float_take(n, rgb_r, n, p, &u);
+  for (i = 0; i < n; i++) rgb_r[i] = u[i];
+  vector_float_take(n, rgb_g, n, p, &u);
+  for (i = 0; i < n; i++) rgb_g[i] = u[i];
+  vector_float_take(n, rgb_b, n, p, &u);
+  for (i = 0; i < n; i++) rgb_b[i] = u[i];
+  FREE(u);
+
+}
+
+static int get_poly_id(int ip, SparseMatrix point_poly_map){
+  return point_poly_map->ja[point_poly_map->ia[ip]];
+}
+ 
+void improve_contiguity(int n, int dim, int *grouping, SparseMatrix poly_point_map, real *x, SparseMatrix graph, real *label_sizes){
+ /* 
+     grouping: which group each of the vertex belongs to
+     poly_point_map: a matrix of dimension npolys x (n + nrandom), poly_point_map[i,j] != 0 if polygon i contains the point j.
+     .  If j < n, it is the original point, otherwise it is artificial point (forming the rectangle around a label) or random points.
+  */
+  int i, j, *ia, *ja, *ib, *jb, u, v;
+  real *a;
+  SparseMatrix point_poly_map, D;
+  real dist;
+  int nbad = 0, flag;
+  int maxit = 10;
+  real tol = 0.001;
+
+  D = SparseMatrix_get_real_adjacency_matrix_symmetrized(graph);
+
+  assert(graph->m == n);
+  ia = D->ia; ja = D->ja;
+  a = (real*) D->a;
+
+  /* point_poly_map: each row i has only 1 entry at column j, which says that point i is in polygon j */
+  point_poly_map = SparseMatrix_transpose(poly_point_map);
+
+  ib = point_poly_map->ia;
+  jb = point_poly_map->ja;
+
+
+  for (i = 0; i < n; i++){
+    u = i;
+    for (j = ia[i]; j < ia[i+1]; j++){
+      v = ja[j];
+      dist = distance_cropped(x, dim, u, v);
+      /*
+       if ((grouping[u] != grouping[v]) || (get_poly_id(u, point_poly_map) == get_poly_id(v, point_poly_map))){
+       a[j] = 1.1*dist;
+       } else {
+       nbad++;
+       a[j] = 0.9*dist;
+       }
+      */
+      if (grouping[u] != grouping[v]){
+       a[j] = 1.1*dist;
+      }        else if (get_poly_id(u, point_poly_map) == get_poly_id(v, point_poly_map)){
+       a[j] = dist;
+      } else {
+       nbad++;
+       a[j] = 0.9*dist;
+      }
+
+    }
+  }
+
+  if (Verbose || 1) fprintf(stderr,"ratio (edges among discontigous regions vs total edges)=%f\n",((real) nbad)/ia[n]);
+  stress_model(dim, D, &x, maxit, tol, &flag);
+
+  assert(!flag);
+
+  SparseMatrix_delete(D);
+  SparseMatrix_delete(point_poly_map);
+}
+
+/*
+struct color_card{
+  int ncolor;
+  real *rgb;
+};
+
+color_card color_card_new(int ncolor, real *rgb){
+  color_card c;
+
+  c->ncolor = ncolor;
+  c->rgb = MALLOC(sizeof(real)*ncolor);
+  for (i = 0; i < ncolor*3; i++){
+    c->rgb[i] = rgb[i];
+  }
+  return c;
+}
+
+void color_card_delete(color_card c){
+  FREE(c->rgb);
+}
+
+color_card_blend(color_card c, real x){
+  real c1[3], c2[3];
+  int ista, isto;
+  if (x > 1) x = 1;
+  if (x < 0) x = 0;
+  ista = x*(ncolor-1);
+  
+}
+
+*/
+
+struct Triangle {
+  int vertices[3];/* 3 points */
+  real center[2]; /* center of the triangle */
+};
+
+static void normal(real v[], real normal[]){
+  if (v[0] == 0){
+    normal[0] = 1; normal[1] = 0;
+  } else {
+    normal[0] = -v[1];
+    normal[1] = v[0];
+  }
+  return;
+}
+
+
+
+static void triangle_center(real x[], real y[], real z[], real c[]){
+  /* find the "center" c, which is the intersection of the 3 vectors that are normal to each
+     of the edges respectively, and which passes through the center of the edges respectively
+     center[{x_, y_, z_}] := Module[
+     {xy = 0.5*(x + y), yz = 0.5*(y + z), zx = 0.5*(z + x), nxy, nyz, 
+     beta, cen},
+     nxy = normal[y - x];
+     nyz = normal[y - z];
+     beta = (y-x).(xy - yz)/(nyz.(y-x));
+     cen = yz + beta*nyz;
+     Graphics[{Line[{x, y, z, x}], Red, Point[cen], Line[{cen, xy}], 
+     Line[{cen, yz}], Green, Line[{cen, zx}]}]
+     
+     ]
+ */
+  real xy[2], yz[2], nxy[2], nyz[2], ymx[2], ymz[2], beta, bot;
+  int i;
+
+  for (i = 0; i < 2; i++) ymx[i] = y[i] - x[i];
+  for (i = 0; i < 2; i++) ymz[i] = y[i] - z[i];
+  for (i = 0; i < 2; i++) xy[i] = 0.5*(x[i] + y[i]);
+  for (i = 0; i < 2; i++) yz[i] = 0.5*(y[i] + z[i]);
+
+
+  normal(ymx, nxy);
+  normal(ymz, nyz);
+  bot = nyz[0]*(x[0]-y[0])+nyz[1]*(x[1]-y[1]);
+  if (bot == 0){/* xy and yz are parallel */
+    c[0] = xy[0]; c[1] = xy[1];
+    return;
+  }
+  beta = ((x[0] - y[0])*(xy[0] - yz[0])+(x[1] - y[1])*(xy[1] - yz[1]))/bot;
+  c[0] = yz[0] + beta*nyz[0];
+  c[1] = yz[1] + beta*nyz[1];
+  return;
+
+}
+
+static SparseMatrix matrix_add_entry(SparseMatrix A, int i, int j, int val){
+  int i1 = i, j1 = j;
+  if (i < j) {
+    i1 = j; j1 = i;
+  }
+  A = SparseMatrix_coordinate_form_add_entries(A, 1, &j1, &i1, &val);
+  return SparseMatrix_coordinate_form_add_entries(A, 1, &i1, &j1, &val);
+}
+
+
+
+void plot_polys(int use_line, SparseMatrix polys, real *x_poly, int *polys_groups, float *r, float *g, float *b){
+  int i, j, *ia = polys->ia, *ja = polys->ja, *a = (int*) polys->a, npolys = polys->m, nverts = polys->n, ipoly = -1, max_grp,
+    min_grp;
+
+
+  min_grp = max_grp = polys_groups[0];
+  for (i = 0; i < npolys; i++) {
+    max_grp = MAX(polys_groups[i], max_grp);
+    min_grp = MIN(polys_groups[i], min_grp);
+  }
+  if (max_grp == min_grp) max_grp++;
+  if (Verbose) fprintf(stderr,"npolys = %d\n",npolys);
+  printf("Graphics[{");
+  for (i = 0; i < npolys; i++){
+    for (j = ia[i]; j < ia[i+1]; j++){
+      assert(ja[j] < nverts && ja[j] >= 0);
+      if (a[j] != ipoly){/* the first poly, or a hole */
+       ipoly = a[j];
+       if (ipoly != a[0]) printf("}],");
+       if (use_line){
+         printf("Black,");
+         printf("Line[{");
+       } else {
+         /*printf("Hue[%f],",0.6*(polys_groups[i]/(real) (max_grp-min_grp)));*/
+         if (r && g && b){
+           printf("RGBColor[%f,%f,%f],",r[polys_groups[i]], g[polys_groups[i]], b[polys_groups[i]]);
+         } else {
+           printf("Hue[%f],",((polys_groups[i]-min_grp)/(real) (max_grp-min_grp)));
+         }
+         printf("Polygon[{");
+       }
+
+      } else {
+       if (j > ia[i]) printf(",");
+      }
+      printf("{%f,%f}",x_poly[2*ja[j]],x_poly[2*ja[j]+1]);
+    }
+  }
+  printf("}]}]");
+}
+
+#if 0
+void ps_one_poly(psfile_t *f, int use_line, int border, int fill, int close, int is_river, int np, float *xp, float *yp){
+  if (use_line){
+    if (is_river){
+      /*river*/
+    } else {
+    }
+    ps_polygon(f, np, xp, yp, border, fill, close);
+  } else {
+    ps_polygon(f, np, xp, yp, border, fill, close);
+  }
+}
+
+void plot_ps_polygons(psfile_t *f, int use_line, SparseMatrix polys, real *x_poly, int *polys_groups){
+  int i, j, *ia = polys->ia, *ja = polys->ja, *a = (int*) polys->a, npolys = polys->m, nverts = polys->n, ipoly,first;
+  int np = 0, maxlen = 0;
+  float *xp, *yp;
+  int border = 0, fill = -1, close = 1;
+  int is_river;
+
+  for (i = 0; i < npolys; i++) maxlen = MAX(maxlen, ia[i+1]-ia[i]);
+
+  xp = MALLOC(sizeof(float)*maxlen);
+  yp = MALLOC(sizeof(float)*maxlen);
+
+  if (Verbose) fprintf(stderr,"npolys = %d\n",npolys);
+  first = ABS(a[0]); ipoly = first + 1;
+  for (i = 0; i < npolys; i++){
+    np = 0;
+    for (j = ia[i]; j < ia[i+1]; j++){
+      assert(ja[j] < nverts && ja[j] >= 0);
+      if (ABS(a[j]) != ipoly){/* the first poly, or a hole */
+       ipoly = ABS(a[j]);
+       is_river = (a[j] < 0);
+       ps_one_poly(f, use_line, border, fill, close, is_river, np, xp, yp);
+       np = 0;/* start a new polygon */
+
+      } 
+      xp[np] = x_poly[2*ja[j]]; yp[np++] = x_poly[2*ja[j]+1];
+    }
+    if (use_line) {
+      ps_one_poly(f, use_line, border, fill, close, is_river, np, xp, yp);
+    } else {
+      ps_one_poly(f, use_line, polys_groups[i], polys_groups[i], close, is_river, np, xp, yp);
+    }
+  }
+  FREE(xp);
+  FREE(yp);
+
+}
+
+static void plot_line(real *x, real *y){
+  printf("Line[{{%f,%f},{%f,%f}}]", x[0], x[1], y[0], y[1]);
+}
+static void plot_voronoi(int n, SparseMatrix A, struct Triangle *T){ 
+  int *val, i, j, nline = 0;
+  val = (int*) A->a;
+  
+  printf("Graphics[{");
+  for (i = 0; i < n; i++){
+    for (j = A->ia[i]; j < A->ia[i+1]; j++){
+      if (j < A->ia[n] - A->ia[0] - 1 && A->ja[j] == A->ja[j+1]){
+       if (nline > 0) printf(",");
+       nline++;
+       plot_line((T)[val[j]].center, (T)[val[j+1]].center);
+       j++;
+      }
+    }
+  }
+  printf("}]");
+}
+
+
+void plot_ps_labels(psfile_t *f, int n, int dim, real *x, char **labels, real *width, float *fsz){
+
+  int i;
+
+  for (i = 0; i < n; i++){
+    if (fsz){
+      ps_font(f, NULL, 3*fsz[i]); /* name can be NULL if the current font name is to be used */
+    } else {
+      ps_font(f, NULL, -7); /* name can be NULL if the current font name is to be used */
+    }
+    ps_textc(f, x[i*dim], x[i*dim+1], labels[i], 0);
+  }
+
+}
+
+static void plot_ps_edges(psfile_t *f, SparseMatrix A, int dim, real *x){
+  int i, *ia, *ja, n, j;
+  float xx[2], yy[2];
+  n = A->m;
+  ia = A->ia;
+  ja = A->ja;
+  for (i = 0; i < n; i++){
+    for (j = ia[i]; j < ia[i+1]; j++){
+      if (ja[j] == i) continue;
+      xx[0] = x[i*dim];
+      xx[1] = x[ja[j]*dim];
+      yy[0] = x[i*dim+1];
+      yy[1] = x[ja[j]*dim+1];
+      ps_polygon(f, 2, xx, yy, TRUE, -1, FALSE);
+    }
+  }
+}
+static void plot_triangles(int n, SparseMatrix A, int dim, real *x){
+  int i, j, ii, jj;
+  printf("Graphics[{Green");
+  for (i = 0; i < n; i++) {
+    for (j = A->ia[i]; j < A->ia[i+1]; j++){
+      ii = i;
+      jj = A->ja[j];
+      if (j < A->ia[n] - A->ia[0] - 1 && A->ja[j] == A->ja[j+1]) j++;
+      printf(",Line[{{%f,%f},{%f,%f}}]", x[ii*dim], x[ii*dim+1], x[jj*dim], x[jj*dim+1]);
+    }
+  }
+  printf("}]");
+}
+
+static void poly_bbox(SparseMatrix polys, real *x_poly, real *bbox){
+  /* get the bounding box of a polygon. 
+     bbox[0]: xmin
+     bbox[1]: xmax
+     bbox[2]: ymin 
+     bbox[3]: ymax
+  */
+  int i, j, *ia = polys->ia, *ja = polys->ja;
+  int npolys = polys->m;
+
+  bbox[0] = bbox[1] = x_poly[2*ja[ia[0]]];
+  bbox[2] = bbox[3] = x_poly[2*ja[ia[0]] + 1];
+  
+  for (i = 0; i < npolys; i++){
+    for (j = ia[i]; j < ia[i+1]; j++){
+      bbox[0] = MIN(bbox[0], x_poly[2*ja[j]]); 
+      bbox[1] = MAX(bbox[1], x_poly[2*ja[j]]); 
+      bbox[2] = MIN(bbox[2], x_poly[2*ja[j]+1]);
+      bbox[3] = MAX(bbox[3], x_poly[2*ja[j]+1]);
+    }
+  }
+}
+
+void plot_ps_map(int n, int dim, real *x, SparseMatrix polys, SparseMatrix poly_lines, real line_width, real *x_poly, int *polys_groups, char **labels, real *width,
+                float *fsz, float *r, float *g, float *b, char *plot_label, real *bg_color, SparseMatrix A){
+ 
+  psfile_t *f;
+  int i;
+  real xmin[2], xmax[2], w = 7, h = 10;
+  real asp;
+  real bbox[4];
+  float pad = 20, label_fsz = 10;
+  int MAX_GRP;
+  int IBG;/*back ground color number */
+  int plot_polyQ = TRUE;
+
+  if (!r || !g || !b) plot_polyQ = FALSE;
+
+  xmin[0] = xmax[0] = x[0];
+  xmin[1] = xmax[1] = x[1];
+
+  for (i = 0; i < n; i++){
+    xmin[0] = MIN(xmin[0], x[i*dim] - width[i*dim]);
+    xmax[0] = MAX(xmax[0], x[i*dim] + width[i*dim]);
+    xmin[1] = MIN(xmin[1], x[i*dim + 1] - width[i*dim+1]);
+    xmax[1] = MAX(xmax[1], x[i*dim + 1] + width[i*dim+1]);
+  }
+
+  if (polys){
+    poly_bbox(polys, x_poly, bbox);
+    xmin[0] = MIN(xmin[0], bbox[0]);
+    xmax[0] = MAX(xmax[0], bbox[1]);
+    xmin[1] = MIN(xmin[1], bbox[2]);
+    xmax[1] = MAX(xmax[1], bbox[3]);
+  }
+
+  if (poly_lines){
+    poly_bbox(poly_lines, x_poly, bbox);
+    xmin[0] = MIN(xmin[0], bbox[0]);
+    xmax[0] = MAX(xmax[0], bbox[1]);
+    xmin[1] = MIN(xmin[1], bbox[2]);
+    xmax[1] = MAX(xmax[1], bbox[3]);
+  }
+
+  pad = .08*MIN(xmax[0] - xmin[0], xmax[1] - xmin[1]);
+  label_fsz = pad/3;
+
+  xmin[0] -= pad;
+  xmax[0] += pad;
+  xmin[1] -= pad;
+  xmax[1] += pad;
+
+
+ if ((xmax[1] - xmin[1]) < 0.001*(xmax[0] - xmin[0])){
+    asp = 0.001;
+  } else {
+    asp = (xmax[1] - xmin[1])/(xmax[0] - xmin[0]);
+  }
+  if (w*asp > h){
+    w = h/asp;
+  } else {
+    h = w*asp;
+  }
+  fprintf(stderr, "asp = %f, w = %f, h = %f\n",asp,w,h);
+
+  /*  f = ps_create_autoscale("test.ps", "title", 7, 7, 0);*/
+  f = ps_create_autoscale(NULL, "title", w, h, 0);
+  /*f = ps_create_epsf(NULL, "title", xmin[0], xmin[1], xmax[0] - xmin[0], xmax[1] - xmin[1]);*/
+
+  ps_line_width(f, 0.00001); // line width 1 point
+
+  ps_font(f, NULL, 10); /* name can be NULL if the current font name is to be used */
+
+  MAX_GRP = polys_groups[0];
+
+  for (i = 0; i < polys->m; i++){
+    if (r && g && b) ps_define_color_rgb(f, polys_groups[i], r[polys_groups[i]], g[polys_groups[i]], b[polys_groups[i]]);
+    MAX_GRP = MAX(MAX_GRP, polys_groups[i]);
+    assert(polys_groups[i] < PS_MAX_COLORS && polys_groups[i] >= 0);
+  }
+
+  /* set bg color */
+  IBG = MAX_GRP + 1;
+  assert(MAX_GRP + 1 < PS_MAX_COLORS);
+  if (bg_color) ps_define_color_rgb(f, IBG, bg_color[0], bg_color[1], bg_color[2]);
+
+  ps_color_model(f, PS_COLOR_MODEL_PALETTE);
+  if (bg_color) ps_rect(f, (float) xmin[0], (float) xmin[1], xmax[0] - xmin[0], xmax[1] - xmin[1], -1, IBG);
+
+
+  /* labels */
+  ps_color_model(f, PS_COLOR_MODEL_RGB);
+  ps_font(f, NULL, label_fsz); /* name can be NULL if the current font name is to be used */
+  ps_textc(f, (float)(.5*(xmin[0] + xmax[0])), (float) xmin[1] + pad, plot_label, 0);
+  
+  ps_color_model(f, PS_COLOR_MODEL_PALETTE);
+
+  /*polygons */
+  if (plot_polyQ) plot_ps_polygons(f, FALSE, polys, x_poly, polys_groups);
+  
+  ps_color_model(f, PS_COLOR_MODEL_RGB);
+  /* polylines*/
+  if (line_width >= 0){
+    ps_line_width(f, (float) line_width);
+    plot_ps_polygons(f, TRUE, poly_lines, x_poly, polys_groups);
+  }
+
+  /* edges*/
+  if (A) plot_ps_edges(f, A, dim, x);
+  
+  if (labels) plot_ps_labels(f, n, dim, x, labels, width, fsz);
+  
+  ps_done(f);
+  
+  
+}
+ 
+#endif
+
+
+static void plot_dot_edges(FILE *f, SparseMatrix A, int dim, real *x){
+  int i, *ia, *ja, j;
+
+  
+  int n = A->m;
+  ia = A->ia;
+  ja = A->ja;
+  for (i = 0; i < n; i++){
+    for (j = ia[i]; j < ia[i+1]; j++){
+      if (ja[j] == i) continue;
+      fprintf(f,"%d -- %d;\n",i,ja[j]);
+    }
+  }
+}
+#if 0
+static void plot_processing_edges(FILE *f, SparseMatrix A, int dim, real *x){
+  int i, *ia, *ja, j;
+
+  //fprintf(f,"stroke(.5);\n");
+  fprintf(f, "beginLines\n");
+  fprintf(f, "color(125,125,125)\n");
+  int n = A->m;
+  ia = A->ia;
+  ja = A->ja;
+  for (i = 0; i < n; i++){
+    for (j = ia[i]; j < ia[i+1]; j++){
+      if (ja[j] == i) continue;
+      //fprintf(f,"line(%f, %f, %f, %f);\n", x[i*dim], x[i*dim+1], x[ja[j]*dim], x[ja[j]*dim+1]);
+      fprintf(f,"%f %f %f %f\n", x[i*dim], x[i*dim+1], x[ja[j]*dim], x[ja[j]*dim+1]);
+    }
+  }
+  fprintf(f,"endLines\n");
+}
+#endif
+
+void plot_dot_labels(FILE *f, int n, int dim, real *x, char **labels, real *width, float *fsz){
+  int i;
+
+  for (i = 0; i < n; i++){
+    if (fsz){
+      fprintf(f, "%d [label=\"%s\", pos=\"%lf,%lf\", fontsize=%f];\n",i, labels[i], x[i*dim], x[i*dim+1], fsz[i]); 
+    } else {
+      fprintf(f, "%d [label=\"%s\", pos=\"%lf,%lf\"];\n",i, labels[i], x[i*dim], x[i*dim+1]); 
+    }
+  }
+
+}
+
+#if 0
+void plot_processing_labels(FILE *f, int n, int dim, real *x, char **labels, real *width, float *fsz){
+  int i;
+  //  fprintf(f, "PFont myFont; myFont = createFont(\"FFScala\",8); fill(0,0,0);\n");
+  for (i = 0; i < n; i++){
+    if (fsz){
+      //   fprintf(f, "textFont(myFont, %f); text(\"%s\", %f, %f);\n", fsz[i], labels[i], x[i*dim], x[i*dim+1]);
+      fprintf(f, "beginText\nfontSize(%f)\ntext(\"%s\")\nposition(%f, %f)\nendText\n", fsz[i], labels[i], x[i*dim], x[i*dim+1]);
+    } else {
+      fprintf(f, "beginText\ntext(\"%s\")\nposition(%f, %f)\nendText\n", labels[i], x[i*dim], x[i*dim+1]);
+    }
+  }
+
+}
+#endif
+
+static void dot_polygon(char **sbuff, int *len, int *len_max, int np, float *xp, float *yp, real line_width,  
+                       int fill, int close, char *cstring){
+  int i;
+  int ret = 0;
+  char buf[10000];
+  char swidth[10000];
+  int len_swidth;
+
+  if (np > 0){
+    /* figure out the size needed */
+    if (fill >= 0){/* poly*/
+      ret += sprintf(buf, " c %d -%s C %d -%s P %d ",(int) strlen(cstring), cstring, (int) strlen(cstring), cstring, np);
+    } else {/* line*/
+      assert(line_width >= 0);
+      if (line_width > 0){
+       sprintf(swidth,"%f",line_width);
+       len_swidth = strlen(swidth);
+       sprintf(swidth,"S %d -setlinewidth(%f)",len_swidth+14, line_width);
+       ret += sprintf(buf, " c %d -%s %s L %d ",(int) strlen(cstring), cstring, swidth, np);
+      } else {
+       ret += sprintf(buf, " c %d -%s L %d ",(int) strlen(cstring), cstring, np);
+      }
+    }
+    for (i = 0; i < np; i++){
+      ret += sprintf(buf, " %f %f",xp[i], yp[i]);
+    }
+
+    if (*len + ret > *len_max - 1){
+      *len_max = *len_max + MAX(100, 0.2*(*len_max)) + ret;
+      *sbuff = REALLOC(*sbuff, *len_max);
+    }
+
+    /* do the actual string */
+    if (fill >= 0){
+      ret = sprintf(&((*sbuff)[*len]), " c %d -%s C %d -%s P %d ",(int) strlen(cstring), cstring, (int) strlen(cstring), cstring, np);
+    } else {
+      if (line_width > 0){
+        sprintf(swidth,"%f",line_width);
+        len_swidth = strlen(swidth);
+        sprintf(swidth,"S %d -setlinewidth(%f)",len_swidth+14, line_width);
+       ret = sprintf(&((*sbuff)[*len]), " c %d -%s %s L %d ",(int) strlen(cstring), cstring, swidth, np);
+      } else {
+       ret = sprintf(&((*sbuff)[*len]), " c %d -%s L %d ",(int) strlen(cstring), cstring, np);
+      }
+    }
+    (*len) += ret;
+    for (i = 0; i < np; i++){
+      assert(*len < *len_max);
+      ret = sprintf(&((*sbuff)[*len]), " %f %f",xp[i], yp[i]);
+      (*len) += ret;
+    }
+
+
+  }
+}
+static void processing_polygon(FILE *f, int np, float *xp, float *yp, real line_width, int fill, int close, 
+                              float rr, float gg, float bb){
+  int i;
+
+  if (np > 0){
+    if (fill >= 0){
+      // fprintf(f, "beginShape();\n noStroke(); fill(%f, %f, %f);\n", 255*rr, 255*gg, 255*bb);
+      fprintf(f, "beginPolygons\ncolor(%f, %f, %f)\n", 255*rr, 255*gg, 255*bb);
+    } else {
+      //fprintf(f, "beginShape();\n");
+      fprintf(f, "beginPolylines\n");
+      if (line_width > 0){
+       fprintf(f, "strokeWeight(%f);\n", line_width);
+      }
+    }
+    for (i = 0; i < np; i++){
+      //fprintf(f, "vertex(%f, %f);\n",xp[i], yp[i]);
+      fprintf(f, "%f %f\n",xp[i], yp[i]);
+    }
+    //fprintf(f, "endShape(CLOSE);\n");
+    if (fill >= 0){
+      fprintf(f, "endPolygons\n");
+    } else {
+      fprintf(f, "endPolylines\n");
+    }
+
+  }
+}
+
+void dot_one_poly(char **sbuff, int *len, int *len_max, int use_line, real line_width, int fill, int close, int is_river, int np, float *xp, float *yp, char *cstring){
+  if (use_line){
+    if (is_river){
+      /*river*/
+    } else {
+    }
+    dot_polygon(sbuff, len, len_max, np, xp, yp, line_width, fill, close, cstring);
+  } else {
+    dot_polygon(sbuff, len, len_max, np, xp, yp, line_width, fill, close, cstring);
+  }
+}
+
+void processing_one_poly(FILE *f, int use_line, real line_width, int fill, int close, int is_river, int np, float *xp, float *yp, 
+                     float rr, float gg, float bb){
+  if (use_line){
+    if (is_river){
+      /*river*/
+    } else {
+    }
+    processing_polygon(f, np, xp, yp, line_width, fill, close, rr, gg, bb);
+  } else {
+    processing_polygon(f, np, xp, yp, line_width, fill, close, rr, gg, bb);
+  }
+}
+
+
+void plot_dot_polygons(char **sbuff, int *len, int *len_max, real line_width, char *line_color, SparseMatrix polys, real *x_poly, int *polys_groups, float *r, float *g, float *b){
+  int i, j, *ia = polys->ia, *ja = polys->ja, *a = (int*) polys->a, npolys = polys->m, nverts = polys->n, ipoly,first;
+  int np = 0, maxlen = 0;
+  float *xp, *yp;
+  int fill = -1, close = 1;
+  int is_river = FALSE;
+  char cstring[] = "#00000011";
+  int use_line = (line_width >= 0);
+  
+  for (i = 0; i < npolys; i++) maxlen = MAX(maxlen, ia[i+1]-ia[i]);
+
+  xp = MALLOC(sizeof(float)*maxlen);
+  yp = MALLOC(sizeof(float)*maxlen);
+
+  if (Verbose) fprintf(stderr,"npolys = %d\n",npolys);
+  first = ABS(a[0]); ipoly = first + 1;
+  for (i = 0; i < npolys; i++){
+    np = 0;
+    for (j = ia[i]; j < ia[i+1]; j++){
+      assert(ja[j] < nverts && ja[j] >= 0);
+      if (ABS(a[j]) != ipoly){/* the first poly, or a hole */
+       ipoly = ABS(a[j]);
+       is_river = (a[j] < 0);
+       if (r && g && b) {
+         rgb2hex(r[polys_groups[i]], g[polys_groups[i]], b[polys_groups[i]], cstring);
+       }
+       dot_one_poly(sbuff, len, len_max, use_line, line_width, fill, close, is_river, np, xp, yp, cstring);
+       np = 0;/* start a new polygon */
+      } 
+      xp[np] = x_poly[2*ja[j]]; yp[np++] = x_poly[2*ja[j]+1];
+    }
+    if (use_line) {
+      dot_one_poly(sbuff, len, len_max, use_line, line_width, fill, close, is_river, np, xp, yp, line_color);
+    } else {
+      /* why set fill to polys_groups[i]?*/
+      //dot_one_poly(sbuff, len, len_max, use_line, polys_groups[i], polys_groups[i], close, is_river, np, xp, yp, cstring);
+      dot_one_poly(sbuff, len, len_max, use_line, -1, 1, close, is_river, np, xp, yp, cstring);
+    }
+  }
+  FREE(xp);
+  FREE(yp);
+
+}
+
+void plot_processing_polygons(FILE *f, real line_width, SparseMatrix polys, real *x_poly, int *polys_groups, float *r, float *g, float *b){
+  int i, j, *ia = polys->ia, *ja = polys->ja, *a = (int*) polys->a, npolys = polys->m, nverts = polys->n, ipoly,first;
+  int np = 0, maxlen = 0;
+  float *xp, *yp;
+  int fill = -1, close = 1;
+  int is_river = FALSE;
+  int use_line = (line_width >= 0);
+  float rr = 0, gg = 0, bb = 0;
+
+  for (i = 0; i < npolys; i++) maxlen = MAX(maxlen, ia[i+1]-ia[i]);
+
+  xp = MALLOC(sizeof(float)*maxlen);
+  yp = MALLOC(sizeof(float)*maxlen);
+
+  if (Verbose) fprintf(stderr,"npolys = %d\n",npolys);
+  first = ABS(a[0]); ipoly = first + 1;
+  for (i = 0; i < npolys; i++){
+    np = 0;
+    for (j = ia[i]; j < ia[i+1]; j++){
+      assert(ja[j] < nverts && ja[j] >= 0);
+      if (ABS(a[j]) != ipoly){/* the first poly, or a hole */
+       ipoly = ABS(a[j]);
+       is_river = (a[j] < 0);
+       if (r && g && b) {
+         rr = r[polys_groups[i]]; gg = g[polys_groups[i]]; bb = b[polys_groups[i]];
+       }
+         processing_one_poly(f, use_line, line_width, fill, close, is_river, np, xp, yp, rr, gg, bb);
+       np = 0;/* start a new polygon */
+      } 
+      xp[np] = x_poly[2*ja[j]]; yp[np++] = x_poly[2*ja[j]+1];
+    }
+    if (use_line) {
+      processing_one_poly(f, use_line, line_width, fill, close, is_river, np, xp, yp, rr, gg, bb);
+    } else {
+      /* why set fill to polys_groups[i]?*/
+      processing_one_poly(f,  use_line, -1, 1, close, is_river, np, xp, yp, rr, gg, bb);
+    }
+  }
+  FREE(xp);
+  FREE(yp);
+
+}
+
+
+void plot_dot_map(Agraph_t* gr, int n, int dim, real *x, SparseMatrix polys, SparseMatrix poly_lines, real line_width, char *line_color, real *x_poly, int *polys_groups, char **labels, real *width,
+                float *fsz, float *r, float *g, float *b, char *plot_label, real *bg_color, SparseMatrix A, FILE* f){
+  /* if graph object exist, we just modify some attributes, otherwise we dump the whole graph */
+  int plot_polyQ = TRUE;
+  char *sbuff;
+  int len = 0, len_max = 1000;
+
+  sbuff = N_NEW(len_max,char);
+
+  if (!r || !g || !b) plot_polyQ = FALSE;
+
+  if (!gr) {
+    fprintf(f, "graph map {\n node [margin = 0 width=0.0001 height=0.00001 shape=plaintext];\n graph [outputorder=edgesfirst, bgcolor=\"#dae2ff\"]\n edge [color=\"#55555515\",fontname=\"Helvetica-Bold\"]\n");
+  } else {
+    agattr(gr, AGNODE, "margin", "0"); 
+    agattr(gr, AGNODE, "width", "0.0001"); 
+    agattr(gr, AGNODE, "height", "0.0001"); 
+    agattr(gr, AGNODE, "shape", "plaintext"); 
+    agattr(gr, AGNODE, "margin", "0"); 
+    agattr(gr, AGNODE, "fontname", "Helvetica-Bold"); 
+    agattr(gr, AGRAPH, "outputorder", "edgesfirst");
+    agattr(gr, AGRAPH, "bgcolor", "#dae2ff");
+    if (!A) agattr(gr, AGEDGE, "style","invis");/* do not plot edges */
+    //    agedgeattr(gr, "color", "#55555515"); 
+  }
+
+  /*polygons */
+  if (plot_polyQ) {
+    if (!gr) fprintf(f,"_draw_ = \"");
+    plot_dot_polygons(&sbuff, &len, &len_max, -1., NULL, polys, x_poly, polys_groups, r, g, b);
+  }
+
+  /* polylines: line width is set here */
+  if (line_width >= 0){
+    plot_dot_polygons(&sbuff, &len, &len_max, line_width, line_color, poly_lines, x_poly, polys_groups, NULL, NULL, NULL);
+  }
+  if (!gr) {
+    fprintf(f,"%s",sbuff);
+    fprintf(f,"\"\n");/* close polygons/lines */
+  } else {
+    agattr(gr, AGRAPH, "_draw_", sbuff);
+    agwrite(gr, f);
+  }
+
+  /* nodes */
+  if (!gr && labels) plot_dot_labels(f, n, dim, x, labels, width, fsz);
+  /* edges */
+  if (!gr && A) plot_dot_edges(f, A, dim, x);
+
+  /* background color + plot label?*/
+
+  if (!gr) fprintf(f, "}\n");
+  
+ 
+}
+
+#if 0
+static void get_polygon_bbox(SparseMatrix polys, real *x_poly, real *bbox_x, real *bbox_y){
+  /* find bounding box. bbox_x is the xmin and xmax, bbox_y is ymin and ymax */
+  int i, j, *ia = polys->ia, *ja = polys->ja, *a = (int*) polys->a, npolys = polys->m, nverts = polys->n, ipoly,first;
+  int NEW = TRUE;
+
+  first = ABS(a[0]); ipoly = first + 1;
+  for (i = 0; i < npolys; i++){
+    for (j = ia[i]; j < ia[i+1]; j++){
+      assert(ja[j] < nverts && ja[j] >= 0);
+      if (NEW){
+       bbox_x[0] = bbox_x[1] =  x_poly[2*ja[j]];
+       bbox_y[0] = bbox_y[1] =  x_poly[2*ja[j]+1];
+       NEW = FALSE;
+      } else {
+       bbox_x[0] = MIN(bbox_x[0], x_poly[2*ja[j]]);
+       bbox_x[1] = MAX(bbox_x[1], x_poly[2*ja[j]]);
+       bbox_y[0] = MIN(bbox_y[0], x_poly[2*ja[j]+1]);
+       bbox_y[1] = MAX(bbox_y[1], x_poly[2*ja[j]+1]);
+      }
+    }
+  }
+}
+#endif
+
+#if 0
+void plot_processing_map(Agraph_t* gr, int n, int dim, real *x, SparseMatrix polys, SparseMatrix poly_lines, real line_width, int nverts, real *x_poly, int *polys_groups, char **labels, real *width,
+                float *fsz, float *r, float *g, float *b, char *plot_label, real *bg_color, SparseMatrix A){
+  /* if graph object exist, we just modify some attributes, otherwise we dump the whole graph */
+  int plot_polyQ = TRUE;
+  FILE *f = stdout;
+  real xmin[2], xwidth[2], scaling=1, bbox_x[2], bbox_y[2];
+  int i;
+
+  /* shift to make all coordinates position */
+  get_polygon_bbox(polys, x_poly, bbox_x, bbox_y);
+  xmin[0] = bbox_x[0]; xmin[1] = bbox_y[0]; 
+  xwidth[0] = (bbox_x[1] - bbox_x[0])*scaling;
+  xwidth[1] = (bbox_y[1] - bbox_y[0])*scaling;
+  for (i = 0; i < n; i++) {
+    xmin[0] = MIN(xmin[0], x[i*dim]);
+    xmin[1] = MIN(xmin[1], x[i*dim+1]);
+  }
+
+  fprintf(stderr,"xmin={%f, %f}\n", xmin[0], xmin[1]);
+
+  for (i = 0; i < n; i++) {
+    x[i*dim] = (x[i*dim] - xmin[0])*scaling;
+    x[i*dim+1] = (x[i*dim+1] - xmin[1])*scaling;
+    xwidth[0] = MAX(xwidth[0], x[i*dim]);
+    xwidth[1] = MAX(xwidth[1], x[i*dim+1]);
+  }
+  for (i = 0; i < nverts; i++) {
+    x_poly[i*dim] = (x_poly[i*dim] - xmin[0])*scaling;
+    x_poly[i*dim+1] = (x_poly[i*dim+1] - xmin[1])*scaling;
+  }
+  /*
+  fprintf(f,"//This file is for processing language. Syntax:\n//\n");
+  fprintf(f,"//beginPolygons\n//[color(r,g,b)]\n//x y\n...\n//endPolygons\n//\n");
+  fprintf(f,"//beginPolylines\n//[color(r,g,b)]\n//...\n//endPolylines\n\n");
+  fprintf(f,"//beginLines\n//[color(r,g,b)]\n//x1 y1 x2 y2\n//...\n endLines\n//\n");
+  fprintf(f,"//beginText\n//[fontSize(x)]\n//text(\"foo\")\n//position(x,y)\n\\endText\n//\n");
+  fprintf(f,"//\n");
+
+  fprintf(f, "size(%d, %d);\n", (int)(xwidth[0]+1), (int) (xwidth[1]+1));
+  */
+
+  if (!r || !g || !b) plot_polyQ = FALSE;
+
+  if (!gr) {
+    fprintf(f, "background(234, 242, 255)");
+  }
+
+  /*polygons */
+  if (plot_polyQ) {
+    plot_processing_polygons(f, -1., polys, x_poly, polys_groups, r, g, b);
+  }
+
+  /* polylines: line width is set here */
+  if (line_width >= 0){
+    plot_processing_polygons(f, line_width, poly_lines, x_poly, polys_groups, NULL, NULL, NULL);
+  }
+
+  /* edges */
+  if (A) plot_processing_edges(f, A, dim, x);
+
+  /* nodes */
+  if (labels) plot_processing_labels(f, n, dim, x, labels, width, fsz);
+
+ 
+}
+#endif
+
+static void get_tri(int n, int dim, real *x, int *nt, struct Triangle **T, SparseMatrix *E, int *flag) {
+   /* always contains a self edge and is symmetric.
+     input:
+     n: number of points
+     dim: dimension, only first2D used
+     x: point j is stored x[j*dim]--x[j*dim+dim-1]
+     output: 
+     nt: number of triangles
+     T: triangles
+     E: a matrix of size nxn, if two points i > j are connected by an taiangulation edge, and is neighboring two triangles 
+     .  t1 and t2, then A[i,j] is both t1 and t2
+   */
+  int i, j, i0, i1, i2, ntri;
+  SparseMatrix A, B;
+
+  int* trilist = get_triangles(x, n, &ntri);
+  *flag = 0;
+
+
+  *T = N_NEW(ntri,struct Triangle);
+
+  A = SparseMatrix_new(n, n, 1, MATRIX_TYPE_INTEGER, FORMAT_COORD);
+  for (i = 0; i < ntri; i++) {
+    for (j = 0; j < 3; j++) {
+      ((*T)[i]).vertices[j] = trilist[i * 3 + j];
+    }
+    i0 = (*T)[i].vertices[0]; i1 = (*T)[i].vertices[1]; i2 = (*T)[i].vertices[2];
+
+    triangle_center(&x[i0*dim], &x[i1*dim], &x[i2*dim], (*T)[i].center);
+    A = matrix_add_entry(A, i0, i1, i);
+    A = matrix_add_entry(A, i1, i2, i);
+    A = matrix_add_entry(A, i2, i0, i);
+  }
+
+  B = SparseMatrix_from_coordinate_format_not_compacted(A, SUM_REPEATED_NONE);
+  SparseMatrix_delete(A);
+  B = SparseMatrix_sort(B);
+  *E = B;
+
+  *nt = ntri;
+
+  FREE(trilist);
+
+  return;
+}
+
+
+
+void plot_labels(int n, int dim, real *x, char **labels){
+  int i, j;
+
+  printf("Graphics[{");
+
+  for (i = 0; i < n; i++){
+    printf("Text[\"%s\",{",labels[i]);
+    for (j = 0; j < 2; j++) {
+      printf("%f",x[i*dim+j]);
+      if (j == 0) printf(",");
+    }
+    printf("}]");
+    if (i < n - 1) printf(",\n");
+  }
+  printf("}]");
+
+
+}
+void plot_points(int n, int dim, real *x){
+  int i, j;
+
+  printf("Graphics[{Point[{");
+  for (i = 0; i < n; i++){
+    printf("{");
+    for (j = 0; j < 2; j++) {
+      printf("%f",x[i*dim+j]);
+      if (j == 0) printf(",");
+    }
+    printf("}");
+    if (i < n - 1) printf(",");
+  }
+  printf("}]");
+
+  /*
+  printf(",");
+  for (i = 0; i < n; i++){
+    printf("Text[%d,{",i);
+    for (j = 0; j < 2; j++) {
+      printf("%f",x[i*dim+j]);
+      if (j == 0) printf(",");
+    }
+    printf("}]");
+    if (i < n - 1) printf(",");
+  }
+  */
+  printf("}]");
+
+}
+
+void plot_edges(int n, int dim, real *x, SparseMatrix A){
+  int i, j, k;
+  int *ia, *ja;
+
+  if (!A) {
+    printf("Graphics[{}]");
+    return;
+  }
+  ia = A->ia; ja = A->ja;
+
+  printf("Graphics[(* edges of the graph*){");
+  for (i = 0; i < n; i++){
+    for (j = ia[i]; j < ia[i+1]; j++){
+      if (i > 0 && j == ia[i]) printf(",");;
+      printf("Line[{{");
+      for (k = 0; k < 2; k++) {
+       printf("%f",x[i*dim+k]);
+       if (k == 0) printf(",");
+      }
+      printf("},{");
+      for (k = 0; k < 2; k++) {
+       printf("%f",x[ja[j]*dim+k]);
+       if (k == 0) printf(",");
+      }
+      printf("}}]");
+      if (j < ia[i+1] - 1) printf(",");
+    }
+  }
+  printf("}(* end of edges of the graph*)]");
+
+}
+static SparseMatrix get_country_graph(int n, SparseMatrix A, int *groups, SparseMatrix *poly_point_map, int GRP_RANDOM, int GRP_BBOX){
+  /* form a graph each vertex is a group (a country), and a vertex is connected to another if the two countryes shares borders.
+   since the group ID may not be contigous (e.g., only groups 2,3,5, -1), we will return NULL if one of the group has non-positive ID! */
+  int *ia, *ja;
+  int one = 1, jj, i, j, ig1, ig2;
+  SparseMatrix B, BB;
+  int min_grp, max_grp;
+  
+  min_grp = max_grp = groups[0];
+  for (i = 0; i < n; i++) {
+    max_grp = MAX(groups[i], max_grp);
+    min_grp = MIN(groups[i], min_grp);
+  }
+  if (min_grp <= 0) return NULL;
+  B = SparseMatrix_new(max_grp, max_grp, 1, MATRIX_TYPE_INTEGER, FORMAT_COORD);
+  ia = A->ia;
+  ja = A->ja;
+  for (i = 0; i < n; i++){
+    ig1 = groups[i]-1;/* add a diagonal entry */
+    SparseMatrix_coordinate_form_add_entries(B, 1, &ig1, &ig1, &one);
+    for (j = ia[i]; j < ia[i+1]; j++){
+      jj = ja[j];
+      if (i != jj && groups[i] != groups[jj] && groups[jj] != GRP_RANDOM && groups[jj] != GRP_BBOX){
+       ig1 = groups[i]-1; ig2 = groups[jj]-1;
+       SparseMatrix_coordinate_form_add_entries(B, 1, &ig1, &ig2, &one);
+      }
+    }
+  }
+  BB = SparseMatrix_from_coordinate_format(B);
+  SparseMatrix_delete(B);
+  return BB;
+}
+
+static void conn_comp(int n, SparseMatrix A, int *groups, SparseMatrix *poly_point_map){
+  /* form a graph where only vertices that are connected as well as in the same group are connected */
+  int *ia, *ja;
+  int one = 1, jj, i, j;
+  SparseMatrix B, BB;
+  int ncomps, *comps = NULL, *comps_ptr = NULL;
+
+  B = SparseMatrix_new(n, n, 1, MATRIX_TYPE_INTEGER, FORMAT_COORD);
+  ia = A->ia;
+  ja = A->ja;
+  for (i = 0; i < n; i++){
+    for (j = ia[i]; j < ia[i+1]; j++){
+      jj = ja[j];
+      if (i != jj && groups[i] == groups[jj]){
+       SparseMatrix_coordinate_form_add_entries(B, 1, &i, &jj, &one);
+      }
+    }
+  }
+  BB = SparseMatrix_from_coordinate_format(B);
+
+  SparseMatrix_weakly_connected_components(BB, &ncomps, &comps, &comps_ptr);
+  SparseMatrix_delete(B);
+  SparseMatrix_delete(BB);
+  *poly_point_map = SparseMatrix_new(ncomps, n, n, MATRIX_TYPE_PATTERN, FORMAT_CSR);
+  FREE((*poly_point_map)->ia);
+  FREE((*poly_point_map)->ja);
+  (*poly_point_map)->ia = comps_ptr;
+  (*poly_point_map)->ja = comps;
+  (*poly_point_map)->nz = n;
+
+}
+
+
+static void get_poly_lines(int exclude_random, int nt, SparseMatrix graph, SparseMatrix E, int ncomps, int *comps_ptr, int *comps, 
+                          int *groups, int *mask, SparseMatrix *poly_lines, int **polys_groups,
+                          int GRP_RANDOM, int GRP_BBOX){
+  /*============================================================
+
+    polygon outlines 
+
+    ============================================================*/
+  int i, *tlist, nz, ipoly, ipoly2, nnt, ii, jj, t1, t2, t, cur, next, nn, j, nlink, sta;
+  int *elist, edim = 3;/* a list tell which vertex a particular vertex is linked with during poly construction.
+               since the surface is a cycle, each can only link with 2 others, the 3rd position is used to record how many links
+             */
+  int *ie = E->ia, *je = E->ja, *e = (int*) E->a, n = E->m;
+  int *ia = NULL, *ja = NULL;
+  SparseMatrix A;
+  int *gmask = NULL;
+
+
+  graph = NULL;/* we disable checking whether a polyline cross an edge for now due to issues with labels */
+  if (graph) {
+    assert(graph->m == n);
+    gmask = malloc(sizeof(int)*n);
+    for (i = 0; i < n; i++) gmask[i] = -1;
+    ia = graph->ia; ja = graph->ja;
+    edim = 5;/* we also store info about whether an edge of a polygon correspondes to a real edge or not. */
+  }
+
+  for (i = 0; i < nt; i++) mask[i] = -1;
+  /* loop over every point in each connected component */
+  elist = MALLOC(sizeof(int)*(nt)*edim);
+  tlist = MALLOC(sizeof(int)*nt*2);
+  *poly_lines = SparseMatrix_new(ncomps, nt, 1, MATRIX_TYPE_INTEGER, FORMAT_COORD);
+  *polys_groups = MALLOC(sizeof(int)*(ncomps));
+
+  for (i = 0; i < nt; i++) elist[i*edim + 2] = 0;
+  nz = ie[E->m] - ie[0];
+
+  ipoly = 1;
+
+  for (i = 0; i < ncomps; i++){
+    /*fprintf(stderr, "comp %d has %d members\n",i, comps_ptr[i+1]-comps_ptr[i]);*/
+    nnt = 0;
+    for (j = comps_ptr[i]; j < comps_ptr[i+1]; j++){
+      ii = comps[j];
+
+      if (graph){
+       for (jj = ia[ii]; jj < ia[ii+1]; jj++) gmask[ja[jj]] = ii;
+      }
+
+      (*polys_groups)[i] = groups[ii];/* assign the grouping of each poly */
+
+      /* skip the country formed by random points */
+      if (exclude_random && (groups[ii] == GRP_RANDOM || groups[ii] == GRP_BBOX)) continue;
+
+      /* always skip bounding box */
+      if (groups[ii] == GRP_BBOX) continue;
+
+      /*fprintf(stderr, "member %d is in group %d, it is\n",ii, groups[ii]);*/
+      for (jj = ie[ii]; jj < ie[ii+1]; jj++){
+       /*
+       fprintf(stderr, "connected with %d in group %d\n",je[jj], groups[je[jj]]);
+       fprintf(stderr, "jj=%d nz = %d je[jj]=%d je[jj+1]=%d\n",jj,nz, je[jj],je[jj+1]);
+       */
+       if (groups[je[jj]] != groups[ii] && jj < nz - 1  && je[jj] == je[jj+1]){/* an triangle edge neighboring 2 triangles and two ends not in the same groups */
+         t1 = e[jj];
+         t2 = e[jj+1];
+
+         nlink = elist[t1*edim + 2]%2;
+         elist[t1*edim + nlink] = t2;/* t1->t2*/
+         if (graph){
+           if (gmask[je[jj]] == ii){/* a real edge */
+             elist[t1*edim+nlink+3] = POLY_LINE_REAL_EDGE;
+           } else {
+             fprintf(stderr,"not real!!!\n");
+             elist[t1*edim+nlink+3] = POLY_LINE_NOT_REAL_EDGE;
+           }
+         }
+         elist[t1*edim + 2]++;
+
+         nlink = elist[t2*edim + 2]%2;
+         elist[t2*edim + nlink] = t1;/* t1->t2*/
+         elist[t2*edim + 2]++;
+         if (graph){
+           if (gmask[je[jj]] == ii){/* a real edge */
+             elist[t2*edim+nlink+3] = POLY_LINE_REAL_EDGE;
+           } else {
+             fprintf(stderr,"not real!!!\n");
+             elist[t2*edim+nlink+3] = POLY_LINE_NOT_REAL_EDGE;
+           }
+         }
+
+         tlist[nnt++] = t1; tlist[nnt++] = t2;
+         jj++;
+       }
+      }
+    }/* done poly edges for this component i */
+
+
+    /* debugging*/
+#ifdef DEBUG
+    /*
+    for (j = 0; j < nnt; j++) {
+      if (elist[tlist[j]*edim + 2]%2 != 0){
+       printf("wrong: elist[%d*edim+2] = %d\n",j,elist[tlist[j]*edim + 2]%);
+       assert(0);
+      }
+    }
+    */
+#endif
+
+    /* form one or more (if there is a hole) polygon outlines for this component  */
+    for (j = 0; j < nnt; j++){
+      t = tlist[j];
+      if (mask[t] != i){
+       cur = sta = t; mask[cur] = i;
+       next = neighbor(t, 1, edim, elist);
+       nlink = 1;
+       if (graph && neighbor(cur, 3, edim, elist) == POLY_LINE_NOT_REAL_EDGE){
+         ipoly2 = - ipoly;
+       } else {
+         ipoly2 = ipoly;
+       }
+       SparseMatrix_coordinate_form_add_entries(*poly_lines, 1, &i, &cur, &ipoly2);
+       while (next != sta){
+         mask[next] = i;
+         
+         if (graph && neighbor(cur, nlink + 3, edim, elist) == POLY_LINE_NOT_REAL_EDGE){
+           ipoly2 = -ipoly;
+         } else {
+           ipoly2 = ipoly;
+         }
+         SparseMatrix_coordinate_form_add_entries(*poly_lines, 1, &i, &next, &ipoly2);
+
+         nn = neighbor(next, 0, edim, elist);
+         nlink = 0;
+         if (nn == cur) {
+           nlink = 1;
+           nn = neighbor(next, 1, edim, elist);
+         }
+         assert(nn != cur);
+
+         cur = next;
+         next = nn;
+       }
+
+       if (graph && neighbor(cur, nlink + 3, edim, elist) == POLY_LINE_NOT_REAL_EDGE){
+         ipoly2 = -ipoly;
+       } else {
+         ipoly2 = ipoly;
+       }
+       SparseMatrix_coordinate_form_add_entries(*poly_lines, 1, &i, &sta, &ipoly2);/* complete a cycle by adding starting point */
+
+       ipoly++;
+      }
+
+    }/* found poly_lines for this comp */
+  }
+
+  A = SparseMatrix_from_coordinate_format_not_compacted(*poly_lines, SUM_REPEATED_NONE);
+  SparseMatrix_delete(*poly_lines);
+  *poly_lines = A;
+
+  FREE(tlist);
+  FREE(elist);
+}
+
+static void plot_cycle(int head, int *cycle, int *edge_table, real *x){
+  int cur, next;
+  real x1, x2, y1, y2;
+
+  printf("Graphics[{");
+  cur = head;
+  while ((next = cycle_next(cur)) != head){
+    x1 = x[2*edge_head(cur)];
+    y1 = x[2*edge_head(cur)+1];
+    x2 = x[2*edge_tail(cur)];
+    y2 = x[2*edge_tail(cur)+1];
+    printf("{Black,Arrow[{{%f,%f},{%f,%f}}],Green,Text[%d, {%f,%f}],Text[%d, {%f,%f}]},",x1,y1,x2,y2,edge_head(cur),x1,y1,edge_tail(cur),x2,y2);
+    cur = next;
+  }
+  x1 = x[2*edge_head(cur)];
+  y1 = x[2*edge_head(cur)+1];
+  x2 = x[2*edge_tail(cur)];
+  y2 = x[2*edge_tail(cur)+1];
+  printf("{Black,Arrow[{{%f,%f},{%f,%f}}],Green,Text[%d, {%f,%f}],Text[%d, {%f,%f}]}}]",x1,y1,x2,y2,edge_head(cur),x1,y1,edge_tail(cur),x2,y2);
+
+
+}
+
+static void cycle_print(int head, int *cycle, int *edge_table){
+  int cur, next;
+
+  cur = head;
+  fprintf(stderr, "cycle (edges): {");
+  while ((next = cycle_next(cur)) != head){
+    fprintf(stderr, "%d,",cur);
+    cur = next;
+  }
+  fprintf(stderr, "%d}\n",cur);
+
+  cur = head;
+  fprintf(stderr, "cycle (vertices): ");
+  while ((next = cycle_next(cur)) != head){
+    fprintf(stderr, "%d--",edge_head(cur));
+    cur = next;
+  }
+  fprintf(stderr, "%d--%d\n",edge_head(cur),edge_tail(cur));
+
+
+
+
+
+
+}
+
+static int same_edge(int ecur, int elast, int *edge_table){
+  return ((edge_head(ecur) == edge_head(elast) && edge_tail(ecur) == edge_tail(elast))
+         || (edge_head(ecur) == edge_tail(elast) && edge_tail(ecur) == edge_head(elast)));
+}
+
+static void get_polygon_solids(int exclude_random, int nt, SparseMatrix E, int ncomps, int *comps_ptr, int *comps, 
+                              int *groups, int *mask, real *x_poly, SparseMatrix *polys, int **polys_groups,
+                              int GRP_RANDOM, int GRP_BBOX){
+  /*============================================================
+
+    polygon slids that will be colored
+
+    ============================================================*/
+  int *edge_table;/* a table of edges of the triangle graph. If two vertex u and v are connected and are adjencent to two triangles
+                    t1 and t2, then from u there are two edges to v, one denoted as t1->t2, and the other t2->t1. They are
+                    numbered as e1 and e2. edge_table[e1]={t1,t2} and edge_table[e2]={t2,t1}
+                 */
+  SparseMatrix half_edges;/* a graph of triangle edges. If two vertex u and v are connected and are adjencent to two triangles
+                    t1 and t2, then from u there are two edges to v, one denoted as t1->t2, and the other t2->t1. They are
+                    numbered as e1 and e2. Likewise from v to u there are also two edges e1 and e2.
+                 */
+
+  int n = E->m, *ie = E->ia, *je = E->ja, *e = (int*) E->a, ne, i, j, t1, t2, jj, ii;
+  int *cycle, cycle_head = 0;/* a list of edges that form a cycle that describe the polygon. cycle[e][0] gives the prev edge in the cycle from e,
+              cycle[e][1] gives the next edge
+            */
+  int *edge_cycle_map, NOT_ON_CYCLE = -1;/* map an edge e to its position on cycle, unless it does not exist (NOT_ON_CYCLE) */
+  int *emask;/* whether an edge is seens this iter */
+  enum {NO_DUPLICATE = -1};
+  int *elist, edim = 3;/* a list tell which edge a particular vertex is linked with when a voro cell has been visited,
+               since the surface is a cycle, each vertex can only link with 2 edges, the 3rd position is used to record how many links
+             */
+
+  int k, duplicate, ee = 0, ecur, enext, eprev, cur, next, nn, nlink, head, elast = 0, etail, tail, ehead, efirst; 
+
+  int DEBUG_CYCLE = 0;
+  SparseMatrix B;
+
+  ne = E->nz;
+  edge_table = MALLOC(sizeof(int)*ne*2);  
+
+  for (i = 0; i < n; i++) mask[i] = -1;
+
+  half_edges = SparseMatrix_new(n, n, 1, MATRIX_TYPE_INTEGER, FORMAT_COORD);
+
+  ne = 0;
+  for (i = 0; i < n; i++){
+    for (j = ie[i]; j < ie[i+1]; j++){
+      if (j < ie[n] - ie[0] - 1 && i > je[j] && je[j] == je[j+1]){/* an triangle edge neighboring 2 triangles. Since E is symmetric, we only do one edge of E*/
+       t1 = e[j];
+       t2 = e[j+1];
+       jj = je[j];       
+       assert(jj < n);
+       edge_table[ne*2] = t1;/*t1->t2*/
+       edge_table[ne*2+1] = t2;
+       half_edges = SparseMatrix_coordinate_form_add_entries(half_edges, 1, &i, &jj, &ne);
+       half_edges = SparseMatrix_coordinate_form_add_entries(half_edges, 1, &jj, &i, &ne);
+       ne++;
+
+       edge_table[ne*2] = t2;/*t2->t1*/
+       edge_table[ne*2+1] = t1;
+       half_edges = SparseMatrix_coordinate_form_add_entries(half_edges, 1, &i, &jj, &ne);
+       half_edges = SparseMatrix_coordinate_form_add_entries(half_edges, 1, &jj, &i, &ne);     
+
+
+       ne++;
+       j++;
+      }
+    }
+  }
+  assert(E->nz >= ne);
+
+  cycle = MALLOC(sizeof(int)*ne*2);
+  B = SparseMatrix_from_coordinate_format_not_compacted(half_edges, SUM_REPEATED_NONE);
+  SparseMatrix_delete(half_edges);half_edges = B;
+
+  edge_cycle_map = MALLOC(sizeof(int)*ne);
+  emask = MALLOC(sizeof(int)*ne);
+  for (i = 0; i < ne; i++) edge_cycle_map[i] = NOT_ON_CYCLE;
+  for (i = 0; i < ne; i++) emask[i] = -1;
+
+  ie = half_edges->ia;
+  je = half_edges->ja;
+  e = (int*) half_edges->a;
+  elist = MALLOC(sizeof(int)*(nt)*3);
+  for (i = 0; i < nt; i++) elist[i*edim + 2] = 0;
+
+  *polys = SparseMatrix_new(ncomps, nt, 1, MATRIX_TYPE_INTEGER, FORMAT_COORD);
+
+  for (i = 0; i < ncomps; i++){
+    if (DEBUG_CYCLE) fprintf(stderr, "\n ============  comp %d has %d members\n",i, comps_ptr[i+1]-comps_ptr[i]);
+    for (k = comps_ptr[i]; k < comps_ptr[i+1]; k++){
+      ii = comps[k];
+      mask[ii] = i;
+      duplicate = NO_DUPLICATE;
+      if (DEBUG_CYCLE) fprintf(stderr,"member = %d has %d neighbors\n",ii, ie[ii+1]-ie[ii]);
+      for (j = ie[ii]; j < ie[ii+1]; j++){
+       jj = je[j];
+       ee = e[j];
+       t1 = edge_head(ee);
+       if (DEBUG_CYCLE) fprintf(stderr," linked with %d using half-edge %d, {head,tail} of the edge = {%d, %d}\n",jj, ee, t1, edge_tail(ee));
+       nlink = elist[t1*edim + 2]%2;
+       elist[t1*edim + nlink] = ee;/* t1->t2*/
+       elist[t1*edim + 2]++;
+
+       if (edge_cycle_map[ee] != NOT_ON_CYCLE) duplicate = ee;
+       emask[ee] = ii;
+      }
+
+      if (duplicate == NO_DUPLICATE){
+       /* this must be the first time the cycle is being established, a new voro cell*/
+       ecur = ee;
+       cycle_head = ecur;
+       cycle_next(ecur) = ecur;
+       cycle_prev(ecur) = ecur;
+       edge_cycle_map[ecur] = 1;
+       head = cur = edge_head(ecur);
+       next = edge_tail(ecur);
+       if (DEBUG_CYCLE) fprintf(stderr, "NEW CYCLE\n starting with edge %d, {head,tail}={%d,%d}\n", ee, head, next);
+       while (next != head){
+         enext = neighbor(next, 0, edim, elist);/* two voro edges linked with triangle "next" */
+         if ((edge_head(enext) == cur && edge_tail(enext) == next)
+             || (edge_head(enext) == next && edge_tail(enext) == cur)){/* same edge */
+           enext = neighbor(next, 1, edim, elist);
+         };
+         if (DEBUG_CYCLE) fprintf(stderr, "cur edge = %d, next edge %d, {head,tail}={%d,%d},\n",ecur, enext, edge_head(enext), edge_tail(enext));
+         nn = edge_head(enext);
+         if (nn == next) nn = edge_tail(enext);
+         cycle_next(enext) = cycle_next(ecur);
+         cycle_prev(enext) = ecur;
+         cycle_next(ecur) = enext;
+         cycle_prev(ee) = enext;
+         edge_cycle_map[enext] = 1;
+
+         ecur = enext;
+         cur = next;
+         next = nn;
+       } 
+       if (DEBUG_CYCLE) cycle_print(ee, cycle,edge_table);
+      } else {
+       /* we found a duplicate edge, remove that, and all contiguous neighbors that overlap with the current voro
+        */
+       ecur = ee = duplicate;
+       while (emask[ecur] == ii){
+         /* contigous overlapping edges, Cycling is not possible
+            since the cycle can not complete surround the new voro cell and yet
+            do not contain any other edges
+         */
+         ecur = cycle_next(ecur);
+       }
+       if (DEBUG_CYCLE) fprintf(stderr," duplicating edge = %d, starting from the a non-duplicating edge %d, search backwards\n",ee, ecur);
+
+       ecur = cycle_prev(ecur);
+       efirst = ecur;
+       while (emask[ecur] == ii){
+         if (DEBUG_CYCLE) fprintf(stderr," remove edge %d (%d--%d)\n",ecur, edge_head(ecur), edge_tail(ecur));
+         /* short this duplicating edge */
+         edge_cycle_map[ecur] = NOT_ON_CYCLE;
+         enext = cycle_next(ecur);
+         eprev = cycle_prev(ecur);
+         cycle_next(ecur) = ecur;/* isolate this edge */
+         cycle_prev(ecur) = ecur;
+         cycle_next(eprev) = enext;/* short */
+         cycle_prev(enext) = eprev;
+         elast = ecur;/* record the last removed edge */
+         ecur = eprev;
+       }
+
+       if (DEBUG_CYCLE) {
+         fprintf(stderr, "remaining (broken) cycle = ");
+         cycle_print(cycle_next(ecur), cycle,edge_table);
+       }
+
+       /* we now have a broken cycle of head = edge_tail(ecur) and tail = edge_head(cycle_next(ecur)) */
+       ehead = ecur; etail = cycle_next(ecur);
+       cycle_head = ehead;
+       head = edge_tail(ehead); 
+       tail = edge_head(etail);
+
+       /* pick an edge ev from head in the voro that is a removed edge: since the removed edges form a path starting from
+          efirst, and at elast (head of elast is head), usually we just need to check that ev is not the same as elast,
+          but in the case of a voro filling in a hole, we also need to check that ev is not efirst,
+          since in this case every edge of the voro cell is removed
+        */
+       ecur = neighbor(head, 0, edim, elist);
+       if (same_edge(ecur, elast, edge_table)){
+         ecur = neighbor(head, 1, edim, elist);
+       };
+
+       if (DEBUG_CYCLE) fprintf(stderr, "forwarding now from edge %d = {%d, %d}, try to reach vtx %d, first edge from voro = %d\n",
+                                ehead, edge_head(ehead), edge_tail(ehead), tail, ecur);
+
+       /* now go along voro edges till we reach the tail of the broken cycle*/
+       cycle_next(ehead) = ecur;
+       cycle_prev(ecur) = ehead;
+       cycle_prev(etail) = ecur;
+       cycle_next(ecur) = etail;
+       if (same_edge(ecur, efirst, edge_table)){
+         if (DEBUG_CYCLE) fprintf(stderr, "this voro cell fill in a hole completely!!!!\n");
+       } else {
+       
+         edge_cycle_map[ecur] = 1;
+         head = cur = edge_head(ecur);
+         next = edge_tail(ecur);
+         if (DEBUG_CYCLE) fprintf(stderr, "starting with edge %d, {head,tail}={%d,%d}\n", ecur, head, next);
+         while (next != tail){
+           enext = neighbor(next, 0, edim, elist);/* two voro edges linked with triangle "next" */
+           if ((edge_head(enext) == cur && edge_tail(enext) == next)
+               || (edge_head(enext) == next && edge_tail(enext) == cur)){/* same edge */
+             enext = neighbor(next, 1, edim, elist);
+           };
+           if (DEBUG_CYCLE) fprintf(stderr, "cur edge = %d, next edge %d, {head,tail}={%d,%d},\n",ecur, enext, edge_head(enext), edge_tail(enext));
+
+
+           nn = edge_head(enext);
+           if (nn == next) nn = edge_tail(enext);
+           cycle_next(enext) = cycle_next(ecur);
+           cycle_prev(enext) = ecur;
+           cycle_next(ecur) = enext;
+           cycle_prev(etail) = enext;
+           edge_cycle_map[enext] = 1;
+           
+           ecur = enext;
+           cur = next;
+           next = nn;
+         }
+       }
+       if (DEBUG_CYCLE && 0) {
+         cycle_print(etail, cycle,edge_table);
+         plot_cycle(etail, cycle,edge_table, x_poly);
+         printf(",");
+       }
+
+      }
+      
+    }
+    /* done this component, load to sparse matrix, unset edge_map*/
+    ecur = cycle_head;
+    while ((enext = cycle_next(ecur)) != cycle_head){
+      edge_cycle_map[ecur] = NOT_ON_CYCLE;
+      head = edge_head(ecur);
+      SparseMatrix_coordinate_form_add_entries(*polys, 1, &i, &head, &i);
+      ecur = enext;
+    }
+    edge_cycle_map[ecur] = NOT_ON_CYCLE;
+    head = edge_head(ecur); tail = edge_tail(ecur);
+    SparseMatrix_coordinate_form_add_entries(*polys, 1, &i, &head, &i);
+    SparseMatrix_coordinate_form_add_entries(*polys, 1, &i, &tail, &i);
+
+
+    /* unset edge_map */
+  }
+
+
+
+  B = SparseMatrix_from_coordinate_format_not_compacted(*polys, SUM_REPEATED_NONE);
+  SparseMatrix_delete(*polys);
+  *polys = B;
+  
+  SparseMatrix_delete(half_edges);
+  FREE(cycle);
+  FREE(edge_cycle_map);
+  FREE(elist);
+  FREE(emask);
+  FREE(edge_table);
+
+}
+static void get_polygons(int exclude_random, int n, int nrandom, int dim, SparseMatrix graph, real *xcombined, int *grouping, 
+                        int nt, struct Triangle *Tp, SparseMatrix E, int *nverts, real **x_poly, 
+                        int *npolys, SparseMatrix *poly_lines, SparseMatrix *polys, int **polys_groups, SparseMatrix *poly_point_map, SparseMatrix *country_graph,
+                        int *flag){
+  int i, j;
+  int *mask;
+  int *groups;
+  int maxgrp;
+  int *comps = NULL, *comps_ptr = NULL, ncomps;
+  int GRP_RANDOM, GRP_BBOX;
+  SparseMatrix B;
+
+  *flag = 0;
+
+  assert(dim == 2);
+  *nverts = nt;
+ 
+  groups = MALLOC(sizeof(int)*(n + nrandom));
+  maxgrp = grouping[0];
+  for (i = 0; i < n; i++) {
+    maxgrp = MAX(maxgrp, grouping[i]);
+    groups[i] = grouping[i];
+  }
+
+  GRP_RANDOM = maxgrp + 1; GRP_BBOX = maxgrp + 2;
+  for (i = n; i < n + nrandom - 4; i++) {/* all random points in the same group */
+    groups[i] = GRP_RANDOM;
+  }
+  for (i = n + nrandom - 4; i < n + nrandom; i++) {/* last 4 pts of the expanded bonding box in the same group */
+    groups[i] = GRP_BBOX;
+  }
+  
+  /* finding connected componts: vertices that are connected in the triangle graph, as well as in the same group */
+  mask = MALLOC(sizeof(int)*MAX(n + nrandom, 2*nt));
+  conn_comp(n + nrandom, E, groups, poly_point_map);
+
+  ncomps = (*poly_point_map)->m;
+  comps = (*poly_point_map)->ja;
+  comps_ptr = (*poly_point_map)->ia;
+
+  if (exclude_random){
+    /* connected components are such that  the random points and the bounding box 4 points forms the last
+     remaining components */
+    for (i = ncomps - 1; i >= 0; i--) {
+      if ((groups[comps[comps_ptr[i]]] != GRP_RANDOM) &&
+         (groups[comps[comps_ptr[i]]] != GRP_BBOX)) break;
+    }
+    ncomps = i + 1;
+    if (Verbose) fprintf(stderr," ncomps = %d\n",ncomps);
+  } else {/* alwasy exclud bounding box */
+    for (i = ncomps - 1; i >= 0; i--) {
+      if (groups[comps[comps_ptr[i]]] != GRP_BBOX) break;
+    }
+    ncomps = i + 1;
+    if (Verbose) fprintf(stderr," ncomops = %d\n",ncomps);
+  }
+  *npolys = ncomps;
+
+  *x_poly = MALLOC(sizeof(real)*dim*nt);
+  for (i = 0; i < nt; i++){
+    for (j = 0; j < dim; j++){
+      (*x_poly)[i*dim+j] = (Tp[i]).center[j];
+    }
+  }
+  
+
+  /*============================================================
+
+    polygon outlines 
+
+    ============================================================*/
+  get_poly_lines(exclude_random, nt, graph, E, ncomps, comps_ptr, comps, groups, mask, poly_lines, polys_groups, GRP_RANDOM, GRP_BBOX);
+
+  /*============================================================
+
+    polygon solids
+
+    ============================================================*/
+  get_polygon_solids(exclude_random, nt, E, ncomps, comps_ptr, comps, groups, mask, *x_poly, polys, polys_groups, GRP_RANDOM, GRP_BBOX);
+
+  B = get_country_graph(n, E, groups, poly_point_map, GRP_RANDOM, GRP_BBOX);
+  *country_graph = B;
+
+  FREE(groups);
+  FREE(mask);
+
+}
+
+
+int make_map_internal(int exclude_random, int include_OK_points,
+                     int n, int dim, real *x0, int *grouping0, SparseMatrix graph, real bounding_box_margin[], int *nrandom, int nedgep, 
+                     real shore_depth_tol, real edge_bridge_tol, real **xcombined, int *nverts, real **x_poly, 
+                     int *npolys, SparseMatrix *poly_lines, SparseMatrix *polys, int **polys_groups, SparseMatrix *poly_point_map,
+                     SparseMatrix *country_graph, int highlight_cluster, int *flag){
+
+
+  real xmax[2], xmin[2], area, *x = x0;
+  int i, j;
+  QuadTree qt;
+  int dim2 = 2, nn = 0;
+  int max_qtree_level = 10;
+  real ymin[2], min;
+  int imin, nz, nzok = 0, nzok0 = 0, nt;
+  real *xran, point[2];
+  struct Triangle *Tp;
+  SparseMatrix E;
+  real boxsize[2];
+  int INCLUDE_OK_POINTS = include_OK_points;/* OK points are random points inserted and found to be within shore_depth_tol of real/artificial points,
+                             including them instead of throwing away increase realism of boundary */
+  int *grouping = grouping0;
+
+  int HIGHLIGHT_SET = highlight_cluster;
+
+  *flag = 0;
+  for (j = 0; j < dim2; j++) {
+    xmax[j] = x[j];
+    xmin[j] = x[j];
+  }
+
+  for (i = 0; i < n; i++){
+    for (j = 0; j < dim2; j++) {
+      xmax[j] = MAX(xmax[j], x[i*dim+j]);
+      xmin[j] = MIN(xmin[j], x[i*dim+j]);
+    }
+  }
+  boxsize[0] = (xmax[0] - xmin[0]);
+  boxsize[1] = (xmax[1] - xmin[1]);
+  area = boxsize[0]*boxsize[1];
+
+  if (*nrandom == 0) {
+    *nrandom = n;
+  } else if (*nrandom < 0){
+    *nrandom = -(*nrandom)*n;
+  } else if (*nrandom < 4) {/* by default we add 4 point on 4 corners anyway */
+    *nrandom = 0;
+  } else {
+    *nrandom -= 4;
+  }
+  if (Verbose) fprintf(stderr,"nrandom=%d\n",*nrandom);
+
+  if (Verbose) fprintf(stderr,"nrandom=%d\n",*nrandom);
+
+  if (shore_depth_tol < 0) shore_depth_tol = sqrt(area/(real) n); /* set to average distance for random distribution */
+
+
+  /* add artificial points along each edge to avoid as much as possible 
+     two connected components be separated due to small shore depth */
+  {
+    int nz;
+    real *y;
+    int k, t, np=nedgep;
+    if (graph && np){
+      fprintf(stderr,"add art np = %d\n",np);
+      nz = graph->nz;
+      y = MALLOC(sizeof(real)*(dim*n + dim*nz*np));
+      for (i = 0; i < n*dim; i++) y[i] = x[i];
+      grouping = MALLOC(sizeof(int)*(n + nz*np));
+      for (i = 0; i < n; i++) grouping[i] = grouping0[i];
+      nz = n;
+      for (i = 0; i < graph->m; i++){
+
+       for (j = graph->ia[i]; j < graph->ia[i+1]; j++){
+         if (!HIGHLIGHT_SET || (grouping[i] == grouping[graph->ja[j]] && grouping[i] == HIGHLIGHT_SET)){
+           for (t = 0; t < np; t++){
+             for (k = 0; k < dim; k++){
+               y[nz*dim+k] = t/((real) np)*x[i*dim+k] + (1-t/((real) np))*x[(graph->ja[j])*dim + k];
+             }
+             assert(n + (nz-n)*np + t < n + nz*np && n + (nz-n)*np + t >= 0);
+             if (t/((real) np) > 0.5){
+               grouping[nz] = grouping[i];
+             } else {
+               grouping[nz] = grouping[graph->ja[j]];
+             }
+             nz++;
+           }
+         }
+       }
+      }
+      fprintf(stderr, "after adding edge points, n:%d->%d\n",n, nz);
+      n = nz;
+      x = y;
+      qt = QuadTree_new_from_point_list(dim, nz, max_qtree_level, y, NULL);
+    } else {
+      qt = QuadTree_new_from_point_list(dim, n, max_qtree_level, x, NULL);
+    }
+  }
+  graph = NULL;
+
+  fprintf(stderr,"margin=%f\n",bounding_box_margin[0]);
+
+  /* generate random points for lake/sea effect */
+  if (*nrandom != 0){
+    for (i = 0; i < dim2; i++) {
+      if (bounding_box_margin[i] > 0){
+       xmin[i] -= bounding_box_margin[i];
+       xmax[i] += bounding_box_margin[i];
+      } else if (bounding_box_margin[i] == 0) {/* auto bounding box */
+       xmin[i] -= MAX(boxsize[i]*0.2, 2.*shore_depth_tol);
+       xmax[i] += MAX(boxsize[i]*0.2, 2*shore_depth_tol);
+      } else {
+       xmin[i] -= boxsize[i]*(-bounding_box_margin[i]);
+       xmax[i] += boxsize[i]*(-bounding_box_margin[i]);
+      }
+    }
+    if (*nrandom < 0) {
+      real n1, n2, area2;
+      area2 = (xmax[1] - xmin[1])*(xmax[0] - xmin[0]);
+      n1 = (int) area2/(shore_depth_tol*shore_depth_tol);
+      n2 = n*((int) area2/area);
+      *nrandom = MAX(n1, n2);
+    }
+    srand(123);
+    xran = MALLOC(sizeof(real)*(*nrandom + 4)*dim2);
+    nz = 0;
+    if (INCLUDE_OK_POINTS){
+      int *grouping2;
+      nzok0 = nzok = *nrandom - 1;/* points that are within tolerance of real or artificial points */
+      grouping2 = MALLOC(sizeof(int)*(n + *nrandom));
+      MEMCPY(grouping2, grouping, sizeof(int)*n);
+      grouping = grouping2;
+    }
+    nn = n;
+
+    for (i = 0; i < *nrandom; i++){
+
+      for (j = 0; j < dim2; j++){
+       point[j] = xmin[j] + (xmax[j] - xmin[j])*drand(0);
+      }
+      
+      QuadTree_get_nearest(qt, point, ymin, &imin, &min, flag);
+      assert(!(*flag));
+
+      if (min > shore_depth_tol){/* point not too close, accepted */
+       for (j = 0; j < dim2; j++){
+         xran[nz*dim2+j] = point[j];
+       }
+       nz++;
+      } else if (INCLUDE_OK_POINTS && min > shore_depth_tol/10){/* avoid duplicate points */
+       for (j = 0; j < dim2; j++){
+         xran[nzok*dim2+j] = point[j];
+       }
+       grouping[nn++] = grouping[imin];
+       nzok--;
+
+      }
+
+    }
+    *nrandom = nz;
+    if (Verbose) fprintf( stderr, "nn nrandom=%d\n",*nrandom);
+  } else {
+    xran = MALLOC(sizeof(real)*4*dim2);
+  }
+
+
+
+  /* add 4 corners even if nrandom = 0. The corners should be further away from the other points to avoid skinny triangles */
+  for (i = 0; i < dim2; i++) xmin[i] -= 0.2*(xmax[i]-xmin[i]);
+  for (i = 0; i < dim2; i++) xmax[i] += 0.2*(xmax[i]-xmin[i]);
+  i = *nrandom;
+  for (j = 0; j < dim2; j++) xran[i*dim2+j] = xmin[j];
+  i++;
+  for (j = 0; j < dim2; j++) xran[i*dim2+j] = xmax[j];
+  i++;
+  xran[i*dim2] = xmin[0]; xran[i*dim2+1] = xmax[1];
+  i++;
+  xran[i*dim2] = xmax[0]; xran[i*dim2+1] = xmin[1];
+  *nrandom += 4;
+
+
+  if (INCLUDE_OK_POINTS){
+    *xcombined = MALLOC(sizeof(real)*(nn+*nrandom)*dim2);
+  } else {
+    *xcombined = MALLOC(sizeof(real)*(n+*nrandom)*dim2);
+  }
+  for (i = 0; i < n; i++) {
+    for (j = 0; j < dim2; j++) (*xcombined)[i*dim2+j] = x[i*dim+j];
+  }
+  for (i = 0; i < *nrandom; i++) {
+    for (j = 0; j < dim2; j++) (*xcombined)[(i + nn)*dim2+j] = xran[i*dim+j];
+  }
+
+  if (INCLUDE_OK_POINTS){
+    for (i = 0; i < nn - n; i++) {
+      for (j = 0; j < dim2; j++) (*xcombined)[(i + n)*dim2+j] = xran[(nzok0 - i)*dim+j];
+    }
+    n = nn;
+  }
+
+
+  {
+    int nz, nh = 0;/* the set to highlight */
+    real *xtemp;
+    if (HIGHLIGHT_SET){
+      fprintf(stderr," hightlight cluster %d, n = %d\n",HIGHLIGHT_SET, n);
+      xtemp = MALLOC(sizeof(real)*n*dim);
+      /* shift set to the beginning */
+      nz = 0;
+      for (i = 0; i < n; i++){
+       if (grouping[i] == HIGHLIGHT_SET){
+         nh++;
+         for (j = 0; j < dim; j++){
+           xtemp[nz++] = x[i*dim+j];
+         }
+       }
+      }
+      for (i = 0; i < n; i++){
+       if (grouping[i] != HIGHLIGHT_SET){
+         for (j = 0; j < dim; j++){
+           xtemp[nz++] = x[i*dim+j];
+         }
+       }
+      }
+      assert(nz == n*dim);
+      for (i = 0; i < nh; i++){
+       grouping[i] = 1;
+      }
+      for (i = nh; i < n; i++){
+       grouping[i] = 2;
+      }
+      MEMCPY(*xcombined, xtemp, n*dim*sizeof(real));
+      *nrandom = *nrandom + n - nh;/* count everything except cluster HIGHLIGHT_SET as random */
+      n = nh;
+      fprintf(stderr,"nh = %d\n",nh);
+      FREE(xtemp);
+    }
+  }
+
+  get_tri(n + *nrandom, dim2, *xcombined, &nt, &Tp, &E, flag);
+  get_polygons(exclude_random, n, *nrandom, dim2, graph, *xcombined, grouping, nt, Tp, E, nverts, x_poly, npolys, poly_lines, polys, polys_groups, 
+              poly_point_map, country_graph, flag);
+  /*
+  {
+    plot_voronoi(n + *nrandom, E, Tp);
+    printf("(*voronoi*),");
+    
+  }
+*/
+
+
+
+
+  SparseMatrix_delete(E);
+  FREE(Tp);
+  FREE(xran);
+  if (grouping != grouping0) FREE(grouping);
+  if (x != x0) FREE(x);
+  return 0;
+}
+
+
+int make_map_from_point_groups(int exclude_random, int include_OK_points,
+                              int n, int dim, real *x, int *grouping, SparseMatrix graph, real bounding_box_margin[], int *nrandom,
+                              real shore_depth_tol, real edge_bridge_tol, real **xcombined, int *nverts, real **x_poly, 
+                              int *npolys, SparseMatrix *poly_lines, SparseMatrix *polys, int **polys_groups, SparseMatrix *poly_point_map,
+                              SparseMatrix *country_graph, int *flag){
+
+  /* create a list of polygons from a list of points in 2D. Points belong to groups. Points in the same group that are also close 
+     gemetrically will be in the same polygon describing the outline of the group.
+
+     input: 
+     exclude_random:
+     include_OK_points: OK points are random points inserted and found to be within shore_depth_tol of real/artificial points,
+     .                  including them instead of throwing away increase realism of boundary 
+     n: number of points
+     dim: dimension of the points. If dim > 2, only the first 2D is used.
+     x: coordinates
+     grouping: which group each of the vertex belongs to
+     graph: the link structure between points. If graph == NULL, this is not used. otherwise
+     .      it is assumed that matrix is symmetric and the graph is undirected
+     bounding_box_margin: margins used to form the bounding box. Dimension 2.
+     .      if negative, it is taken as relative. i.e., -0.5 means a margin of 0.5*box_size
+     nrandom (inout): number of random points to insert in the bounding box to figure out lakes and seas.
+     .        If nrandom = 0, no points are inserted, if nrandom < 0, the number is decided automatically.
+     .        On exit, it is the actual number of random points used. The last 4 "random" points is always the
+     .        
+     shore_depth_tol: nrandom random points are inserted in the bounding box of the points,
+     .      such random points are then weeded out if it is within distance of shore_depth_tol from 
+     .      real points. If < 0, auto assigned
+     edge_bridge_tol: insert points on edges to give an bridge effect.These points will be evenly spaced
+     .       along each edge, and be less than a distance of edge_bridge_tol from each other and from the two ends of the edge.
+     .       If < 0, -edge_bridge_tol is the average number of points inserted per half edge
+     output:
+     xcombined: combined points which contains n + ncombined number of points, dimension 2x(n+nrandom)
+     npolys: number of polygons generated to reprsent the real points, the edge insertion points, and the sea/lake points.
+     nverts: number of vertices in the Voronoi diagram
+     x_poly: the 2D coordinates of these polygons
+     poly_lines: the sparse matrix representation of the polygon indices, as well as their identity. The matrix is of size
+     .       npolygons x nverts. The i-th polygon is formed by linking vertices with index in the i-th row of the sparse matrix.
+     .       Each row is of the form {{i,j1,m},...{i,jk,m},{i,j1,m},{i,l1,m+1},...}, where j1--j2--jk--j1 form one loop,
+     .       and l1 -- l2 -- ... form another. Each row can have more than 1 loop only when the connected region the polylines represent
+     .       has at least 1 holes.
+     polys: the sparse matrix representation of the polygon indices, as well as their identity. The matrix is of size
+     .       npolygons x nverts. The i-th polygon is formed by linking vertices with index in the i-th row of the sparse matrix.
+     .       Unlike poly_lines, here each row represent an one stroke drawing of the SOLID polygon, vertices
+     .       along this path may repeat
+     polys_groups: the group (color) each polygon belongs to, this include all groups of the real points,
+     .       plus the random point group and the bounding box group
+     poly_point_map: a matrix of dimension npolys x (n + nrandom), poly_point_map[i,j] != 0 if polygon i contains the point j.
+     .  If j < n, it is the original point, otherwise it is 
+     country_graph: shows which country is a neighbor of which country.
+     .     if country i and country j are neighbor, then the {i,j} entry is the total number of vertices that
+     .     belongs to i and j, and share an edge of the triangulation. In addition, {i,i} and {j,j} have values equal 
+     .     to the number of vertices in each of the countries. If the input "grouping" has negative or zero value, then
+     .     country_graph = NULL. 
+     
+  */
+  int res;
+  int nedgep = 0;
+  int highlight_cluster = FALSE;
+  /* get poly outlines */
+  res = make_map_internal(exclude_random, include_OK_points, n, dim, x, grouping, graph, bounding_box_margin, nrandom, nedgep,
+                 shore_depth_tol, edge_bridge_tol, xcombined, nverts, x_poly, 
+                         npolys, poly_lines, polys, polys_groups, poly_point_map, country_graph, highlight_cluster, flag);
+
+  printf("Show[{");
+
+  plot_points(n + *nrandom, dim, *xcombined);
+
+
+  printf(",");
+  plot_polys(TRUE, *poly_lines, *x_poly, *polys_groups, NULL, NULL, NULL);
+
+  printf("}]\n");
+
+  return res;
+}
+
+static void add_point(int *n, int igrp, real **x, int *nmax, real point[], int **groups){
+
+  if (*n >= *nmax){
+    *nmax = MAX((int) 0.2*(*n), 20) + *n;
+    *x = REALLOC(*x, sizeof(real)*2*(*nmax));
+    *groups = REALLOC(*groups, sizeof(int)*(*nmax));
+  }
+
+  (*x)[(*n)*2] = point[0];
+  (*x)[(*n)*2+1] = point[1];
+  (*groups)[*n] = igrp;
+  (*n)++;
+
+}
+
+static void get_boundingbox(int n, int dim, real *x, real *width, real *bbox){
+  int i;
+  bbox[0] = bbox[1] = x[0];
+  bbox[2] = bbox[3] = x[1];
+  
+  for (i = 0; i < n; i++){
+    bbox[0] = MIN(bbox[0], x[i*dim] - width[i*dim]);
+    bbox[1] = MAX(bbox[1], x[i*dim] + width[i*dim]);
+    bbox[2] = MIN(bbox[2], x[i*dim + 1] - width[i*dim+1]);
+    bbox[3] = MAX(bbox[3], x[i*dim + 1] + width[i*dim+1]);
+  }
+}
+
+
+int make_map_from_rectangle_groups(int exclude_random, int include_OK_points,
+                                  int n, int dim, real *x, real *sizes, 
+                                  int *grouping, SparseMatrix graph0, real bounding_box_margin[], int *nrandom, int *nart, int nedgep, 
+                                  real shore_depth_tol, real edge_bridge_tol,
+                                  real **xcombined, int *nverts, real **x_poly, 
+                                  int *npolys, SparseMatrix *poly_lines, SparseMatrix *polys, int **polys_groups, SparseMatrix *poly_point_map, 
+                                  SparseMatrix *country_graph, int highlight_cluster, int *flag){
+
+  /* create a list of polygons from a list of rectangles in 2D. rectangles belong to groups. rectangles in the same group that are also close 
+     gemetrically will be in the same polygon describing the outline of the group. The main difference for this function and
+     make_map_from_point_groups is that in this function, the input are points with width/heights, and we try not to place
+     "lakes" inside these rectangles. The is achieved approximately by adding artificial points along the perimeter of the rectangles,
+     as well as near the center.
+
+     input:
+     include_OK_points: OK points are random points inserted and found to be within shore_depth_tol of real/artificial points,
+     .                  including them instead of throwing away increase realism of boundary 
+     n: number of points
+     dim: dimension of the points. If dim > 2, only the first 2D is used.
+     x: coordinates
+     sizes: width and height
+     grouping: which group each of the vertex belongs to
+     graph: the link structure between points. If graph == NULL, this is not used. otherwise
+     .      it is assumed that matrix is symmetric and the graph is undirected
+     bounding_box_margin: margins used to form the bounding box. Dimension 2.
+     .      if negative, it is taken as relative. i.e., -0.5 means a margin of 0.5*box_size
+     nrandom (inout): number of random points to insert in the bounding box to figure out lakes and seas.
+     .        If nrandom = 0, no points are inserted, if nrandom < 0, the number is decided automatically.
+     .        On exit, it is the actual number of random points used. The last 4 "random" points is always the
+     .        
+     nart: on entry, number of artificla points to be added along rach side of a rectangle enclosing the labels
+     . On exit, actual number of artificial points added.
+     nedgep: number of artificial points are adding along edges to establish as much as possible a bright between nodes 
+     .       connected by the edge, and avoid islands that are connected. k = 0 mean no points.
+     shore_depth_tol: nrandom random points are inserted in the bounding box of the points,
+     .      such random points are then weeded out if it is within distance of shore_depth_tol from 
+     .      real points. If < 0, auto assigned
+     edge_bridge_tol: insert points on edges to give an bridge effect.These points will be evenly spaced
+     .       along each edge, and be less than a distance of edge_bridge_tol from each other and from the two ends of the edge.
+     .       If < 0, -edge_bridge_tol is the average number of points inserted per half edge
+
+     output:
+     xcombined: combined points which contains n + ncombined number of points, dimension 2x(n+nrandom)
+     npolys: number of polygons generated to reprsent the real points, the edge insertion points, and the sea/lake points.
+     nverts: number of vertices in the Voronoi diagram
+     x_poly: the 2D coordinates of these polygons, dimension nverts*2
+     poly_lines: the sparse matrix representation of the polygon indices, as well as their identity. The matrix is of size
+     .       npolygons x nverts. The i-th polygon is formed by linking vertices with index in the i-th row of the sparse matrix.
+     .       Each row is of the form {{i,j1,m},...{i,jk,m},{i,j1,m},{i,l1,m+1},...}, where j1--j2--jk--j1 form one loop,
+     .       and l1 -- l2 -- ... form another. Each row can have more than 1 loop only when the connected region the polylines represent
+     .       has at least 1 holes.
+     polys: the sparse matrix representation of the polygon indices, as well as their identity. The matrix is of size
+     .       npolygons x nverts. The i-th polygon is formed by linking vertices with index in the i-th row of the sparse matrix.
+     .       Unlike poly_lines, here each row represent an one stroke drawing of the SOLID polygon, vertices
+     .       along this path may repeat
+     polys_groups: the group (color) each polygon belongs to, this include all groups of the real points,
+     .       plus the random point group and the bounding box group
+     poly_point_map: a matrix of dimension npolys x (n + nrandom), poly_point_map[i,j] != 0 if polygon i contains the point j.
+     .  If j < n, it is the original point, otherwise it is artificial point (forming the rectangle around a label) or random points.
+    country_graph: shows which country is a neighbor of which country.
+     .     if country i and country j are neighbor, then the {i,j} entry is the total number of vertices that
+     .     belongs to i and j, and share an edge of the triangulation. In addition, {i,i} and {j,j} have values equal 
+     .     to the number of vertices in each of the countries. If the input "grouping" has negative or zero value, then
+     .     country_graph = NULL. 
+
+     
+  */
+
+  real *X;
+  int N, nmax, i, j, k, igrp;
+  int *groups, K = *nart;/* average number of points added per side of rectangle */
+
+  real avgsize[2],  avgsz, h[2], p1, p0;
+  real point[2];
+  int nadded[2];
+  int res;
+  real delta[2];
+  SparseMatrix graph = graph0;
+  real bbox[4];
+
+  *nart = 0;
+  if (Verbose){
+    int maxgp = grouping[0];
+    int mingp = grouping[0];
+    for (i = 0; i < n; i++) {
+      maxgp = MAX(maxgp, grouping[i]);
+      mingp = MIN(mingp, grouping[i]);
+    }
+    fprintf(stderr, "max grouping - min grouping + 1 = %d\n",maxgp - mingp + 1); 
+  }
+
+  if (!sizes){
+    return make_map_internal(exclude_random, include_OK_points, n, dim, x, grouping, graph, bounding_box_margin, nrandom, nedgep, 
+                           shore_depth_tol, edge_bridge_tol, xcombined, nverts, x_poly, 
+                            npolys, poly_lines, polys, polys_groups, poly_point_map, country_graph, highlight_cluster, flag);
+  } else {
+
+    /* add artificial node due to node sizes */
+    avgsize[0] = 0;
+    avgsize[1] = 0;
+    for (i = 0; i < n; i++){
+      for (j = 0; j < 2; j++) {
+       avgsize[j] += sizes[i*dim+j];
+      }
+    }
+    for (i = 0; i < 2; i++) avgsize[i] /= n;
+    avgsz = 0.5*(avgsize[0] + avgsize[1]);
+    if (Verbose) fprintf(stderr, "avgsize = {%f, %f}\n",avgsize[0], avgsize[1]);
+
+    nmax = 2*n;
+    X = MALLOC(sizeof(real)*dim*(n+nmax));
+    groups = MALLOC(sizeof(int)*(n+nmax));
+    for (i = 0; i < n; i++) {
+      groups[i] = grouping[i];
+      for (j = 0; j < 2; j++){
+       X[i*2+j] = x[i*dim+j];
+      }
+    }
+    N = n;
+
+    if (shore_depth_tol < 0) {
+      shore_depth_tol = -(shore_depth_tol)*avgsz;
+    } else if (shore_depth_tol == 0){
+      get_boundingbox(n, dim, x, sizes, bbox);
+      shore_depth_tol = MIN(bbox[1] - bbox[0], bbox[3] - bbox[2])*0.05;
+    } else {
+      /*
+      get_boundingbox(n, dim, x, sizes, bbox);
+      shore_depth_tol = MIN(bbox[1] - bbox[0], bbox[3] - bbox[2])*shore_depth_tol;
+      */
+
+    }
+
+    /* add artificial points in an anti-clockwise fashion */
+
+    if (K > 0){
+      delta[0] = .5*avgsize[0]/K; delta[1] = .5*avgsize[1]/K;/* small pertubation to make boundary between labels looks more fractal */
+    } else {
+      delta[0] = delta[1] = 0.;
+    }
+    for (i = 0; i < n; i++){
+      igrp = grouping[i];
+      for (j = 0; j < 2; j++) {
+       if (avgsz == 0){
+         nadded[j] = 0;
+       } else {
+         nadded[j] = (int) K*sizes[i*dim+j]/avgsz;
+       }
+      }
+
+      /*top: left to right */
+      if (nadded[0] > 0){
+       h[0] = sizes[i*dim]/nadded[0];
+       point[0] = x[i*dim] - sizes[i*dim]/2;
+       p1 = point[1] = x[i*dim+1] + sizes[i*dim + 1]/2;
+       add_point(&N, igrp, &X, &nmax, point, &groups);
+       for (k = 0; k < nadded[0] - 1; k++){
+         point[0] += h[0];
+         point[1] = p1 + (0.5-drand(0))*delta[1];
+         add_point(&N, igrp, &X, &nmax, point, &groups);
+       }
+       
+       /* bot: right to left */
+       point[0] = x[i*dim] + sizes[i*dim]/2;
+       p1 = point[1] = x[i*dim+1] - sizes[i*dim + 1]/2;
+       add_point(&N, igrp, &X, &nmax, point, &groups);
+       for (k = 0; k < nadded[0] - 1; k++){
+         point[0] -= h[0];
+         point[1] = p1 + (0.5-drand(0))*delta[1];
+         add_point(&N, igrp, &X, &nmax, point, &groups);
+       }
+      }
+
+      if (nadded[1] > 0){      
+       /* left: bot to top */
+       h[1] = sizes[i*dim + 1]/nadded[1];
+       p0 = point[0] = x[i*dim] - sizes[i*dim]/2;
+       point[1] = x[i*dim+1] - sizes[i*dim + 1]/2;
+       add_point(&N, igrp, &X, &nmax, point, &groups);
+       for (k = 0; k < nadded[1] - 1; k++){
+         point[0] = p0 + (0.5-drand(0))*delta[0];
+         point[1] += h[1];
+         add_point(&N, igrp, &X, &nmax, point, &groups);
+       }
+       
+       /* right: top to bot */
+       p0 = point[0] = x[i*dim] + sizes[i*dim]/2;
+       point[1] = x[i*dim+1] + sizes[i*dim + 1]/2;
+       add_point(&N, igrp, &X, &nmax, point, &groups);
+       for (k = 0; k < nadded[1] - 1; k++){
+         point[0] = p0 + (0.5-drand(0))*delta[0];
+         point[1] -= h[1];
+         add_point(&N, igrp, &X, &nmax, point, &groups);
+       }       
+      }
+      *nart = N - n;
+
+    }/* done adding artificial points due to node size*/
+
+
+    /* add artificial node due to edges */
+    if (graph && edge_bridge_tol != 0){
+      int *ia = graph->ia, *ja = graph->ja, nz = 0, jj;
+      int KB;
+
+      graph = SparseMatrix_symmetrize(graph, TRUE);
+      ia = graph->ia; ja = graph->ja;
+      real dist, avgdist = 0.;
+      for (i = 0; i < n; i++){
+       for (j = ia[i]; j < ia[i+1]; j++){
+         jj = ja[j];
+         if (jj <= i) continue;
+         dist = distance(x, dim, i, jj);
+         avgdist += dist;
+         nz++;
+       }
+      }
+      avgdist /= nz;
+      if (edge_bridge_tol < 0){
+       KB = (int) (-edge_bridge_tol);
+      } else {
+       KB = (int) (avgdist/edge_bridge_tol);
+      }
+
+      assert(avgdist > 0);
+      for (i = 0; i < n; i++){
+       for (j = ia[i]; j < ia[i+1]; j++){
+         jj = ja[j];
+         if (jj <= i) continue;
+         dist = distance(x, dim, i, jj);
+         nadded[0] = (int) 2*KB*dist/avgdist;
+
+         /* half the line segment near i */
+         h[0] = 0.5*(x[jj*dim] - x[i*dim])/nadded[0];
+         h[1] = 0.5*(x[jj*dim+1] - x[i*dim+1])/nadded[0];
+         point[0] = x[i*dim];
+         point[1] = x[i*dim+1];
+         for (k = 0; k < nadded[0] - 1; k++){
+           point[0] += h[0];
+           point[1] += h[1];
+           add_point(&N, grouping[i], &X, &nmax, point, &groups);
+         }     
+
+         /* half the line segment near jj */
+         h[0] = 0.5*(x[i*dim] - x[jj*dim])/nadded[0];
+         h[1] = 0.5*(x[i*dim+1] - x[jj*dim+1])/nadded[0];
+         point[0] = x[jj*dim];
+         point[1] = x[jj*dim+1];
+         for (k = 0; k < nadded[0] - 1; k++){
+           point[0] += h[0];
+           point[1] += h[1];
+           add_point(&N, grouping[jj], &X, &nmax, point, &groups);
+         }     
+       }
+
+      }/* done adding artifial points for edges */
+    }
+
+    res = make_map_internal(exclude_random, include_OK_points, N, dim, X, groups, graph, bounding_box_margin, nrandom, nedgep, 
+                           shore_depth_tol, edge_bridge_tol, xcombined, nverts, x_poly, 
+                           npolys, poly_lines, polys, polys_groups, poly_point_map, country_graph, highlight_cluster, flag);
+    if (graph != graph0) SparseMatrix_delete(graph);
+    FREE(groups); 
+    FREE(X);
+  }
+
+  return res;
+
+}

diff --git a/cmd/gvmap/make_map.h b/cmd/gvmap/make_map.h
new file mode 100644 (file)
index 0000000..180d7ef
--- /dev/null
+++ b/cmd/gvmap/make_map.h
@@ -0,0 +1,60 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#ifndef MAKE_MAP_H
+#define MAKE_MAP_H
+
+#include <SparseMatrix.h>
+#include <cgraph.h>
+
+int make_map_from_rectangle_groups(int exclude_random, int include_OK_points, int n, int dim, real *x, real *sizes, 
+                                  int *grouping, SparseMatrix graph, real bounding_box_margin[], int *nrandom,int *nart, int nedgep, 
+                                  real shore_depth_tol, real edge_bridge_tol, real **xcombined, int *nverts, real **x_poly, 
+                                  int *npolys, SparseMatrix *poly_lines, SparseMatrix *polys, int **polys_groups, SparseMatrix *poly_point_map, 
+                                  SparseMatrix *country_graph, int highlight_cluster, int *flag);
+
+int make_map_from_point_groups(int exclude_random, int include_OK_points, int n, int dim, real *x, int *grouping, SparseMatrix graph, real bounding_box_margin[], int *nrandom,
+                              real shore_depth_tol, real edge_bridge_tol, real **xcombined, int *nverts, real **x_poly, 
+                              int *npolys, SparseMatrix *poly_lines, SparseMatrix *polys, int **polys_groups, SparseMatrix *poly_point_map, 
+                              SparseMatrix *country_graph, int *flag);
+
+
+void improve_contiguity(int n, int dim, int *grouping, SparseMatrix poly_point_map, real *x, SparseMatrix graph, real *label_sizes);
+
+
+#if 0
+void plot_polys(int use_line, SparseMatrix polys, real *x_poly, int *polys_groups, float *r, float *g, float *b);
+void plot_points(int n, int dim, real *x);
+void plot_edges(int n, int dim, real *x, SparseMatrix A);
+void plot_labels(int n, int dim, real *x, char **labels);
+void plot_ps_map(int n, int dim, real *x, SparseMatrix polys, SparseMatrix poly_lines, real line_width, real *x_poly, int *polys_groups, char **labels, real *width,
+                float *fsz, float *r, float *g, float *b, char *plot_label, real *bg_color, SparseMatrix A);
+#endif
+
+void plot_dot_map(Agraph_t* gr, int n, int dim, real *x, SparseMatrix polys, SparseMatrix poly_lines, real line_width, char *line_color, real *x_poly, int *polys_groups, char **labels, real *width, float *fsz, float *r, float *g, float *b, char *plot_label, real *bg_color, SparseMatrix A, FILE*);
+
+#if 0
+void plot_processing_map(Agraph_t* gr, int n, int dim, real *x, SparseMatrix polys, SparseMatrix poly_lines, real line_width, int nverts, real *x_poly, int *polys_groups, char **labels, real *width, float *fsz, float *r, float *g, float *b, char *plot_label, real *bg_color, SparseMatrix A);
+#endif
+
+void map_optimal_coloring(int seed, SparseMatrix A, float *rgb_r,  float *rgb_g, float *rgb_b);
+
+enum {POLY_LINE_REAL_EDGE, POLY_LINE_NOT_REAL_EDGE};
+enum {OUT_PS = 1, OUT_M = 0, OUT_M_COUNTRY_GRAPH = 2, OUT_DOT = 3, OUT_PROCESSING = 4};
+#define neighbor(t, i, edim, elist) elist[(edim)*(t)+i]
+#define edge_head(e) edge_table[2*(e)]
+#define edge_tail(e) edge_table[2*(e)+1]
+#define cycle_prev(e) cycle[2*(e)]
+#define cycle_next(e) cycle[2*(e)+1]
+
+#endif

diff --git a/cmd/gvmap/mq.c b/cmd/gvmap/mq.c
new file mode 100644 (file)
index 0000000..e5e2140
--- /dev/null
+++ b/cmd/gvmap/mq.c
@@ -0,0 +1,618 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+/* Modularity Quality definitation:
+
+   We assume undirected graph. Directed graph should be converted by summing edge weights.
+
+   Given a partition P of V into k clusters.
+
+   Let E(i,j) be the set of edges between cluster i and j.
+   Let |E(i,j)| be the sum of edge weights of edges in E(i,j).
+
+   Let E(i,i) be the set of edges within cluster i, but excluding self-edges.
+   Let |E(i,i)| be the sum of edge weights of edges in E(i,i).
+
+   Let V(i) be the sets of vertices in i
+
+   The intra-cluster edges concentration for a cluster i is 
+   (the denominator could be |V(i)|*(|V(i)-1)/2 strictly speaking as we exclude self-edges):
+
+     |E(i,i)|
+   -----------
+   (|V(i)|^2/2)
+
+   The inter-cluster edges concentration between cluster i and j is
+
+     |E(i,j)|
+   ------------
+   |V(i)|*|V(j)|
+
+   So the cluster index is defined as the average intra cluster edge concentration, minus
+   the inter-cluster edge concentration:
+
+   .                               |E(i,i)|                                        |E(i,j)|
+   MQ(P) = (1/k) * \sum_{i=1...k} ------------ - (1/(k*(k-1)/2)) * \sum_{i<j} ------------------- = mq_in/k - mq_out/(k*(k-1)/2)
+   .                              (|V(i)|^2/2)                                   |V(i)|*|V(j)|
+
+   or
+
+   .                                 |E(i,i)|                                     |E(i,j)|
+   MQ(P)/2 = (1/k) * \sum_{i=1...k} ------------ - (1/(k*(k-1))) * \sum_{i<j} ------------------ = mq_in/k - mq_out/(k*(k-1))
+   .                                |V(i)|^2                                   |V(i)|*|V(j)|
+
+   Notice that if we assume the graph is unweights (edge weights = 1), then 0<= MQ <= 1.
+   For weighted graph, MQ may not be within 0 to 1. We could normalized it, but 
+   for comparing clustering quality of the same graph but different partitioning, this 
+   unnormalized quantity is not a problem.
+
+*/
+
+#define STANDALONE
+#include "general.h"
+#include "SparseMatrix.h"
+#include "mq.h"
+#include "LinkedList.h"
+
+static real get_mq(SparseMatrix A, int *assignment, int *ncluster0, real *mq_in0, real *mq_out0, real **dout0){
+  /* given a symmetric matrix representation of a graph and an assignment of nodes into clusters, calculate the modularity quality.
+   assignment: assignmenet[i] gives the cluster assignment of node i. 0 <= assignment[i] < ncluster.
+   ncluster: number of clusters
+   mq_in: the part of MQ to do with intra-cluster edges, before divide by 1/k
+   mq_out: the part of MQ to do with inter-cluster edges, before divide by 1/(k*(k-1))
+   mq = 2*(mq_in/k - mq_out/(k*(k-1)));
+  */
+  int ncluster = 0;
+  int n = A->m;
+  int test_pattern_symmetry_only = FALSE;
+  int *counts, *ia = A->ia, *ja = A->ja, k, i, j, jj;
+  real mq_in = 0, mq_out = 0, *a = NULL, Vi, Vj;
+  int c;
+  real *dout;
+
+
+  assert(SparseMatrix_is_symmetric(A, test_pattern_symmetry_only));
+  assert(A->n == n);
+  if (A->type == MATRIX_TYPE_REAL) a = (real*) A->a;
+
+  counts = MALLOC(sizeof(int)*n);
+
+  for (i = 0; i < n; i++) counts[i] = 0;
+
+  for (i = 0; i < n; i++){
+    assert(assignment[i] >= 0 && assignment[i] < n);
+    if (counts[assignment[i]] == 0) ncluster++;
+    counts[assignment[i]]++;
+  }
+  k = ncluster;
+  assert(ncluster <= n);
+
+  for (i = 0; i < n; i++){
+    assert(assignment[i] < ncluster);
+    c = assignment[i];
+    Vi = counts[c];
+    for (j = ia[i] ; j < ia[i+1]; j++){
+      /* ASSUME UNDIRECTED */
+      jj = ja[j];
+      if (jj >= i) continue;
+      assert(assignment[jj] < ncluster);
+      Vj = counts[assignment[jj]];
+      if (assignment[jj] == c){
+       if (a) {
+         mq_in += a[j]/(Vi*Vi);
+       } else {
+         mq_in += 1./(Vi*Vi);
+       }
+      } else {
+       if (a) {
+         mq_out += a[j]/(Vi*Vj);
+       } else {
+         mq_out += 1./(Vi*Vj);
+       }
+      }
+      
+    }
+  }
+
+  /* calculate scaled out degree */
+  dout = MALLOC(sizeof(real)*n);
+  for (i = 0; i < n; i++){
+    dout[i] = 0;
+    for (j = ia[i]; j < ia[i+1]; j++){
+      jj = ja[j];
+      if (jj == i) continue;
+      if (a){
+       dout[i] += a[j]/(real) counts[assignment[jj]];
+      } else {
+       dout[i] += 1./(real) counts[assignment[jj]];
+      }
+    }
+  }
+
+  *ncluster0 = k;
+  *mq_in0 = mq_in;
+  *mq_out0 = mq_out;
+  *dout0 = dout;
+  FREE(counts);
+
+  if (k > 1){
+    return 2*(mq_in/k - mq_out/(k*(k-1)));
+  } else {
+    return 2*mq_in;
+  }
+}
+
+Multilevel_MQ_Clustering Multilevel_MQ_Clustering_init(SparseMatrix A, int level){
+  Multilevel_MQ_Clustering grid;
+  int n = A->n, i;
+  int *matching;
+
+  assert(A->type == MATRIX_TYPE_REAL);
+  assert(SparseMatrix_is_symmetric(A, FALSE));
+
+  if (!A) return NULL;
+  assert(A->m == n);
+  grid = MALLOC(sizeof(struct Multilevel_MQ_Clustering_struct));
+  grid->level = level;
+  grid->n = n;
+  grid->A = A;
+  grid->P = NULL;
+  grid->R = NULL;
+  grid->next = NULL;
+  grid->prev = NULL;
+  grid->delete_top_level_A = FALSE;
+  matching = grid->matching = MALLOC(sizeof(real)*(n));
+  grid->deg_intra = NULL;
+  grid->dout = NULL;
+  grid->wgt = NULL;
+
+  if (level == 0){
+    real mq = 0, mq_in, mq_out;
+    int n = A->n, ncluster;
+    real *deg_intra, *wgt, *dout;
+
+    grid->deg_intra = MALLOC(sizeof(real)*(n));
+    deg_intra = grid->deg_intra;
+
+    grid->wgt = MALLOC(sizeof(real)*n);
+    wgt = grid->wgt;
+
+    for (i = 0; i < n; i++){
+      deg_intra[i] = 0;
+      wgt[i] = 1.;
+    }
+    for (i = 0; i < n; i++) matching[i] = i;
+    mq = get_mq(A, matching, &ncluster, &mq_in, &mq_out, &dout);
+    fprintf(stderr,"ncluster = %d, mq = %f\n", ncluster, mq);
+    grid->mq = mq;
+    grid->mq_in = mq_in;
+    grid->mq_out = mq_out;
+    grid->dout = dout;
+    grid->ncluster = ncluster;
+
+  }
+
+
+  return grid;
+} 
+
+void Multilevel_MQ_Clustering_delete(Multilevel_MQ_Clustering grid){
+  if (!grid) return;
+  if (grid->A){
+    if (grid->level == 0) {
+      if (grid->delete_top_level_A) SparseMatrix_delete(grid->A);
+    } else {
+      SparseMatrix_delete(grid->A);
+    }
+  }
+  SparseMatrix_delete(grid->P);
+  SparseMatrix_delete(grid->R);
+  FREE(grid->matching);
+  FREE(grid->deg_intra);
+  FREE(grid->dout);
+  FREE(grid->wgt);
+  Multilevel_MQ_Clustering_delete(grid->next);
+  FREE(grid);
+}
+
+Multilevel_MQ_Clustering Multilevel_MQ_Clustering_establish(Multilevel_MQ_Clustering grid, int maxcluster){
+  int *matching = grid->matching;
+  SparseMatrix A = grid->A;
+  int n = grid->n, level = grid->level, nc = 0, nclusters = n;
+  real mq = 0, mq_in = 0, mq_out = 0, mq_new, mq_in_new, mq_out_new, mq_max = 0, mq_in_max = 0, mq_out_max = 0;
+  int *ia = A->ia, *ja = A->ja;
+  real *a, amax = 0;
+  real *deg_intra = grid->deg_intra, *wgt = grid->wgt;
+  real *deg_intra_new, *wgt_new = NULL;
+  int i, j, k, jj, jc, jmax;
+  real *deg_inter, gain = 0, *dout = grid->dout, *dout_new, deg_in_i, deg_in_j, wgt_i, wgt_j, a_ij, dout_i, dout_j, dout_max = 0, wgt_jmax = 0;
+  int *mask;
+  real maxgain = 0;
+  real total_gain = 0;
+  SingleLinkedList *neighbors = NULL, lst;
+
+
+  neighbors = MALLOC(sizeof(SingleLinkedList)*n);
+  for (i = 0; i < n; i++) neighbors[i] = NULL;
+
+  mq = grid->mq;
+  mq_in = grid->mq_in;
+  mq_out = grid->mq_out;
+
+  deg_intra_new = MALLOC(sizeof(real)*n);
+  wgt_new = MALLOC(sizeof(real)*n);
+  deg_inter = MALLOC(sizeof(real)*n);
+  mask = MALLOC(sizeof(int)*n);
+  dout_new = MALLOC(sizeof(real)*n);
+  for (i = 0; i < n; i++) mask[i] = -1;
+
+  assert(n == A->n);
+  for (i = 0; i < n; i++) matching[i] = UNMATCHED;
+
+  /* gain in merging node A into cluster B is
+     mq_in_new = mq_in - |E(A,A)|/(V(A))^2 - |E(B,B)|/(V(B))^2 + (|E(A,A)|+|E(B,B)|+|E(A,B)|)/(|V(A)|+|V(B)|)^2
+     .         = mq_in - deg_intra(A)/|A|^2 - deg_intra(B)/|B|^2 + (deg_intra(A)+deg_intra(B)+a(A,B))/(|A|+|B|)^2
+
+     mq_out_new = mq_out - |E(A,B)|/(|V(A)|*V(B)|)-\sum_{C and A connected, C!=B} |E(A,C)|/(|V(A)|*|V(C)|)-\sum_{C and B connected,C!=B} |E(B,C)|/(|V(B)|*|V(C)|)
+     .                  + \sum_{C connected to A or B, C!=A, C!=B} (|E(A,C)|+|E(B,C)|)/(|V(C)|*(|V(A)|+|V(B)|)
+     .          = mq_out + a(A,B)/(|A|*|B|)-\sum_{C and A connected} a(A,C)/(|A|*|C|)-\sum_{C and B connected} a(B,C)/(|B|*|C|)
+     .                  + \sum_{C connected to A or B, C!=A, C!=B} (a(A,C)+a(B,C))/(|C|*(|A|+|B|))
+     Denote:
+     dout(i) = \sum_{j -- i} a(i,j)/|j|
+     then
+
+     mq_out_new = mq_out - |E(A,B)|/(|V(A)|*V(B)|)-\sum_{C and A connected, C!=B} |E(A,C)|/(|V(A)|*|V(C)|)-\sum_{C and B connected,C!=B} |E(B,C)|/(|V(B)|*|V(C)|)
+     .                  + \sum_{C connected to A or B, C!=A, C!=B} (|E(A,C)|+|E(B,C)|)/(|V(C)|*(|V(A)|+|V(B)|)
+     .          = mq_out + a(A,B)/(|A|*|B|)-dout(A)/|A| - dout(B)/|B|
+     .                  + (dout(A)+dout(B))/(|A|+|B|) - (a(A,B)/|A|+a(A,B)/|B|)/(|A|+|B|)
+     .          = mq_out -dout(A)/|A| - dout(B)/|B| + (dout(A)+dout(B))/(|A|+|B|)
+     after merging A and B into cluster AB,
+     dout(AB) = dout(A) + dout(B);
+     dout(C) := dout(C) - a(A,C)/|A| - a(B,C)/|B| + a(A,C)/(|A|+|B|) + a(B, C)/(|A|+|B|) 
+
+     mq_new = mq_in_new/(k-1) - mq_out_new/((k-1)*(k-2))
+     gain = mq_new - mq
+  */
+  a = (real*) A->a;
+  for (i = 0; i < n; i++){
+    if (matching[i] != UNMATCHED) continue;
+    /* accumulate connections between i and clusters */
+    for (j = ia[i]; j < ia[i+1]; j++){
+      jj = ja[j];
+      if (jj == i) continue;
+      if ((jc=matching[jj]) != UNMATCHED){
+       if (mask[jc] != i) {
+         mask[jc] = i;
+         deg_inter[jc] = a[j];
+       } else {
+         deg_inter[jc] += a[j];
+       }
+      }
+    }
+    deg_in_i = deg_intra[i];
+    wgt_i = wgt[i];
+    dout_i = dout[i];
+
+    maxgain = 0; 
+    jmax = -1;
+    for (j = ia[i]; j < ia[i+1]; j++){
+      jj = ja[j];
+      if (jj == i) continue;
+      jc = matching[jj];
+      if (jc == UNMATCHED){
+       a_ij = a[j];
+       wgt_j = wgt[jj];
+       deg_in_j = deg_intra[jj];
+       dout_j = dout[jj];
+      } else if (deg_inter[jc] < 0){
+       continue;
+      } else {
+       a_ij = deg_inter[jc];
+       wgt_j = wgt_new[jc];
+       deg_inter[jc] = -1; /* so that we do not redo the calulation when we hit another neighbor in cluster jc */
+       deg_in_j = deg_intra_new[jc];
+       dout_j = dout_new[jc];
+      }
+
+      mq_in_new = mq_in - deg_in_i/pow(wgt_i, 2) - deg_in_j/pow(wgt_j,2) 
+       + (deg_in_i + deg_in_j + a_ij)/pow(wgt_i + wgt_j,2);
+
+      mq_out_new = mq_out - dout_i/wgt_i - dout_j/wgt_j + (dout_i + dout_j)/(wgt_i + wgt_j);
+
+      if (nclusters > 2){
+       mq_new =  2*(mq_in_new/(nclusters - 1) - mq_out_new/((nclusters - 1)*(nclusters - 2)));
+      } else {
+       mq_new =  2*mq_in_new/(nclusters - 1);
+      }
+
+#ifdef DEBUG
+      {int ncluster;
+       double mq2, mq_in2, mq_out2, *dout2;
+       int *matching2, nc2 = nc;
+       matching2 = MALLOC(sizeof(int)*A->m);
+       matching2 = MEMCPY(matching2, matching, sizeof(real)*A->m);
+       if (jc != UNMATCHED) {
+         matching2[i] = jc;
+       } else {
+         matching2[i] = nc2;
+         matching2[jj] = nc2;
+         nc2++;
+       }
+       for (k = 0; k < n; k++) if (matching2[k] == UNMATCHED) matching2[k] =nc2++;
+       mq2 = get_mq(A, matching2, &ncluster, &mq_in2, &mq_out2, &dout2);
+       fprintf(stderr," {dout_i, dout_j}={%f,%f}, {predicted, calculated}: mq = {%f, %f}, mq_in ={%f,%f}, mq_out = {%f,%f}\n",dout_i, dout_j, mq_new, mq2, mq_in_new, mq_in2, mq_out_new, mq_out2);
+
+       mq_new = mq2;
+       
+      }
+#endif
+
+      gain = mq_new - mq;
+      if (Verbose) fprintf(stderr,"gain in merging node %d with node %d = %f-%f = %f\n", i, jj, mq, mq_new, gain);
+      if (j == ia[i] || gain > maxgain){
+       maxgain = gain;
+       jmax = jj;
+       amax = a_ij;
+       dout_max = dout_j;
+       wgt_jmax = wgt_j;
+       mq_max = mq_new;
+       mq_in_max = mq_in_new;
+       mq_out_max = mq_out_new;
+      }
+
+    }
+
+    /* now merge i and jmax */
+    if (maxgain > 0 || (nc >= 1 && nc > maxcluster)){
+      total_gain += maxgain;
+      jc = matching[jmax];
+      if (jc == UNMATCHED){
+       fprintf(stderr, "maxgain=%f, merge %d, %d\n",maxgain, i, jmax);
+       neighbors[nc] = SingleLinkedList_new_int(jmax);
+       neighbors[nc] = SingleLinkedList_prepend_int(neighbors[nc], i);
+       dout_new[nc] = dout_i + dout_max;
+       matching[i] = matching[jmax] = nc;
+       wgt_new[nc] = wgt[i] + wgt[jmax];
+       deg_intra_new[nc] = deg_intra[i] + deg_intra[jmax] + amax;
+       nc++;
+      } else { 
+       fprintf(stderr,"maxgain=%f, merge with existing cluster %d, %d\n",maxgain, i, jc);
+       neighbors[jc] = SingleLinkedList_prepend_int(neighbors[jc], i);
+       dout_new[jc] = dout_i + dout_max;
+       wgt_new[jc] += wgt[i];
+       matching[i] = jc;
+       deg_intra_new[jc] += deg_intra[i] + amax;
+      }
+      mq = mq_max;
+      mq_in = mq_in_max;
+      mq_out = mq_out_max;
+      nclusters--;
+    } else {
+      fprintf(stderr,"gain: %f -- no gain, skip merging node %d\n", maxgain, i);
+      assert(maxgain <= 0);
+      neighbors[nc] = SingleLinkedList_new_int(i);
+      matching[i] = nc;
+      deg_intra_new[nc] = deg_intra[i];
+      wgt_new[nc] = wgt[i];
+      nc++;
+    }
+
+
+    /* update scaled outdegree of neighbors of i and its merged node/cluster jmax */
+    jc = matching[i];
+    lst = neighbors[jc];
+    do {
+      mask[*((int*) SingleLinkedList_get_data(lst))] = n+i;
+      lst = SingleLinkedList_get_next(lst);
+    } while (lst);
+
+    lst = neighbors[jc];
+
+    do {
+      k = *((int*) SingleLinkedList_get_data(lst));
+      for (j = ia[k]; j < ia[k+1]; j++){
+       jj = ja[j]; 
+       if (mask[jj] == n+i) continue;/* link to within cluster */
+       if ((jc = matching[jj]) == UNMATCHED){
+         if (k == i){
+           dout[jj] += -a[j]/wgt_i + a[j]/(wgt_i + wgt_jmax);
+         } else {
+           dout[jj] += -a[j]/wgt_jmax + a[j]/(wgt_i + wgt_jmax);
+         }
+       } else {
+         if (k == i){
+           dout_new[jc] += -a[j]/wgt_i + a[j]/(wgt_i + wgt_jmax);
+         } else {
+           dout_new[jc] += -a[j]/wgt_jmax + a[j]/(wgt_i + wgt_jmax);
+         }
+       }
+      }
+      lst = SingleLinkedList_get_next(lst);
+    } while (lst);
+
+  }
+
+  fprintf(stderr,"verbose=%d\n",Verbose);
+  if (Verbose) fprintf(stderr,"mq = %f new mq = %f level = %d, n = %d, nc = %d, gain = %g, mq_in = %f, mq_out = %f\n", mq, mq + total_gain, 
+                      level, n, nc, total_gain, mq_in, mq_out);
+  
+#ifdef DEBUG
+  {int ncluster;
+
+  mq = get_mq(A, matching, &ncluster, &mq_in, &mq_out, &dout);
+  fprintf(stderr," mq = %f\n",mq);
+
+  }
+#endif
+
+  if (nc >= 1 && (total_gain > 0 || nc < n)){
+    /* now set up restriction and prolongation operator */
+    SparseMatrix P, R, R0, B, cA;
+    real one = 1.;
+    Multilevel_MQ_Clustering cgrid;
+
+    R0 = SparseMatrix_new(nc, n, 1, MATRIX_TYPE_REAL, FORMAT_COORD);
+    for (i = 0; i < n; i++){
+      jj = matching[i];
+      SparseMatrix_coordinate_form_add_entries(R0, 1, &jj, &i, &one);
+    }
+    R = SparseMatrix_from_coordinate_format(R0);
+    SparseMatrix_delete(R0);
+    P = SparseMatrix_transpose(R);
+    B = SparseMatrix_multiply(R, A);
+    if (!B) goto RETURN;
+    cA = SparseMatrix_multiply(B, P); 
+    if (!cA) goto RETURN;
+    SparseMatrix_delete(B);
+    grid->P = P;
+    grid->R = R;
+    level++;
+    cgrid = Multilevel_MQ_Clustering_init(cA, level); 
+    deg_intra_new = REALLOC(deg_intra_new, nc*sizeof(real));
+    wgt_new = REALLOC(wgt_new, nc*sizeof(real));
+    cgrid->deg_intra = deg_intra_new;
+    cgrid->mq = grid->mq + total_gain;
+    cgrid->wgt = wgt_new;
+    dout_new =  REALLOC(dout_new, nc*sizeof(real));
+    cgrid->dout = dout_new;
+
+    cgrid = Multilevel_MQ_Clustering_establish(cgrid, maxcluster);
+
+    grid->next = cgrid;
+    cgrid->prev = grid;
+  } else {
+    /* no more improvement, stop and final clustering found */
+    for (i = 0; i < n; i++) matching[i] = i;
+
+    FREE(deg_intra_new);
+    FREE(wgt_new);
+    FREE(dout_new);
+  }
+
+ RETURN:
+  for (i = 0; i < n; i++) SingleLinkedList_delete(neighbors[i], free);
+  FREE(neighbors);
+
+  FREE(deg_inter);
+  FREE(mask);
+  return grid;
+}
+
+Multilevel_MQ_Clustering Multilevel_MQ_Clustering_new(SparseMatrix A0, int maxcluster){
+  /* maxcluster is used to specify the maximum number of cluster desired, e.g., maxcluster=10 means that a maximum of 10 clusters
+     is desired. this may not always be realized, and mq may be low when this is specified. Default: maxcluster = 0 */
+  Multilevel_MQ_Clustering grid;
+  SparseMatrix A = A0;
+
+  if (maxcluster <= 0) maxcluster = A->m;
+  if (!SparseMatrix_is_symmetric(A, FALSE) || A->type != MATRIX_TYPE_REAL){
+    A = SparseMatrix_get_real_adjacency_matrix_symmetrized(A);
+  }
+  grid = Multilevel_MQ_Clustering_init(A, 0);
+
+  grid = Multilevel_MQ_Clustering_establish(grid, maxcluster);
+
+  if (A != A0) grid->delete_top_level_A = TRUE;/* be sure to clean up later */
+  return grid;
+}
+
+
+static void hierachical_mq_clustering(SparseMatrix A, int maxcluster,
+                                             int *nclusters, int **assignment, real *mq, int *flag){
+  /* find a clustering of vertices by maximize mq
+     A: symmetric square matrix n x n. If real value, value will be used as edges weights, otherwise edge weights are considered as 1.
+     maxcluster: used to specify the maximum number of cluster desired, e.g., maxcluster=10 means that a maximum of 10 clusters
+     .   is desired. this may not always be realized, and mq may be low when this is specified. Default: maxcluster = 0 
+     nclusters: on output the number of clusters
+     assignment: dimension n. Node i is assigned to cluster "assignment[i]". 0 <= assignment < nclusters
+   */
+
+  Multilevel_MQ_Clustering grid, cgrid;
+  int *matching, i;
+  SparseMatrix P;
+  real *u;
+  assert(A->m == A->n);
+
+  *mq = 0.;
+
+  *flag = 0;
+
+  grid = Multilevel_MQ_Clustering_new(A, maxcluster);
+
+  /* find coarsest */
+  cgrid = grid;
+  while (cgrid->next){
+    cgrid = cgrid->next;
+  }
+
+  /* project clustering up */
+  u =  MALLOC(sizeof(real)*cgrid->n);
+  for (i = 0; i < cgrid->n; i++) u[i] = (real) (cgrid->matching)[i];
+  *nclusters = cgrid->n;
+  *mq = cgrid->mq;
+
+  while (cgrid->prev){
+    real *v = NULL;
+    P = cgrid->prev->P;
+    SparseMatrix_multiply_vector(P, u, &v, FALSE);
+    FREE(u);
+    u = v;
+    cgrid = cgrid->prev;
+  }
+
+  if (*assignment){
+    matching = *assignment; 
+  } else {
+    matching = MALLOC(sizeof(int)*(grid->n));
+    *assignment = matching;
+  }
+  for (i = 0; i < grid->n; i++) (matching)[i] = (int) u[i];
+  FREE(u);
+
+  Multilevel_MQ_Clustering_delete(grid);
+  
+}
+
+
+
+void mq_clustering(SparseMatrix A, int inplace, int maxcluster, int use_value,
+                          int *nclusters, int **assignment, real *mq, int *flag){
+  /* find a clustering of vertices by maximize mq
+     A: symmetric square matrix n x n. If real value, value will be used as edges weights, otherwise edge weights are considered as 1.
+     inplace: whether A can e modified. If true, A will be modified by removing diagonal.
+     maxcluster: used to specify the maximum number of cluster desired, e.g., maxcluster=10 means that a maximum of 10 clusters
+     .   is desired. this may not always be realized, and mq may be low when this is specified. Default: maxcluster = 0 
+     nclusters: on output the number of clusters
+     assignment: dimension n. Node i is assigned to cluster "assignment[i]". 0 <= assignment < nclusters
+   */
+  SparseMatrix B;
+
+  *flag = 0;
+  
+  assert(A->m == A->n);
+
+  B = SparseMatrix_symmetrize(A, FALSE);
+
+  if (!inplace && B == A) {
+    B = SparseMatrix_copy(A);
+  }
+
+  B = SparseMatrix_remove_diagonal(B);
+
+  if (B->type != MATRIX_TYPE_REAL || !use_value) B = SparseMatrix_set_entries_to_real_one(B);
+
+  hierachical_mq_clustering(B, maxcluster, nclusters, assignment, mq, flag);
+
+  if (B != A) SparseMatrix_delete(B);
+
+}

diff --git a/cmd/gvmap/mq.h b/cmd/gvmap/mq.h
new file mode 100644 (file)
index 0000000..b2cfcdf
--- /dev/null
+++ b/cmd/gvmap/mq.h
@@ -0,0 +1,63 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#ifndef MG_H
+#define MG_H
+
+typedef struct Multilevel_MQ_Clustering_struct *Multilevel_MQ_Clustering;
+
+struct Multilevel_MQ_Clustering_struct {
+  int level;/* 0, 1, ... */
+  int n;
+  SparseMatrix A; /* n x n matrix */
+  SparseMatrix P; 
+  SparseMatrix R; 
+  Multilevel_MQ_Clustering next;
+  Multilevel_MQ_Clustering prev;
+  int delete_top_level_A;
+  int *matching; /* dimension n. matching[i] is the clustering assignment of node i */
+
+  /*
+
+   .                                 |E(i,i)|                                     |E(i,j)|
+   MQ/2 = (1/k) * \sum_{i=1...k} ------------ - (1/(k*(k-1))) * \sum_{i<j} -------------------  
+   .                                |V(i)|^2                                   |V(i)|*|V(j)|
+   .   = mq_in/k - mq_out/(k*(k-1))
+  */
+
+  real mq;
+  real mq_in, mq_out;/* mqs(A) = deg_in(A)/|A|^2 - deg_out(A)/|A|/(|V|-|A|) */
+  int ncluster; /* number of clusters */
+
+  real *deg_intra;/* dimension n. deg[i] equal to the sum of edge weights within cluster i */
+  real *dout;/* dimension n, dout[i] = \sum_{j -- i} a(i,j)/|j| is the scaled sum of outdegree */
+  real *wgt; /* total vertex weight each coarse grid vertex represent */
+};
+
+/* find a clustering of vertices by maximize modularity quality
+   A: symmetric square matrix n x n. If real value, value will be used as edges weights, otherwise edge weights are considered as 1.
+   inplace: whether A can e modified. If true, A will be modified by removing diagonal.
+
+   maxcluster: used to specify the maximum number of cluster desired, e.g., maxcluster=10 means that a maximum of 10 clusters
+   .   is desired. this may not always be realized, and modularity quality may be low when this is specified. Default: maxcluster = 0 (no limit)
+
+   use_value: whether to use the entry value, or treat edge weights as 1.
+   nclusters: on output the number of clusters
+   assignment: dimension n. Node i is assigned to cluster "assignment[i]". 0 <= assignment < nclusters.
+   .   If *assignment = NULL on entry, it will be allocated. Otherwise used.
+   mq: achieve modularity
+*/
+void mq_clustering(SparseMatrix A, int inplace, int maxcluster, int use_value,
+                          int *nclusters, int **assignment, real *mq, int *flag);
+
+#endif

diff --git a/cmd/gvmap/power.c b/cmd/gvmap/power.c
new file mode 100644 (file)
index 0000000..897bf03
--- /dev/null
+++ b/cmd/gvmap/power.c
@@ -0,0 +1,101 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#include "SparseMatrix.h"
+/* #include "matrix_market.h" */
+void power_method(SparseMatrix A, int random_seed, int maxit, real tol, real **eigv){
+  /* find the largest eigenvector of a matrix A. Result in eigv. if eigv == NULL; memory will be allocated.
+     maxium of maxit iterations will be done, and tol is the convergence criterion
+
+     This converges only if the largest eigenvector/value is real and the next largest eigenvalue separate from teh largest one
+
+   */
+  int n;
+  real *v, *u;
+  int iter = 0;
+  real res, unorm;
+  int i;
+  assert(A->m == A->n);
+  assert(A->type = MATRIX_TYPE_REAL || A->type == MATRIX_TYPE_INTEGER);
+
+  n = A->m;
+  if (!(*eigv)) *eigv = MALLOC(sizeof(real)*n);
+  u = MALLOC(sizeof(real)*n);
+
+  srand(random_seed);
+
+  for (i = 0; i < n; i++) (*eigv)[i] = drand();
+
+  res = vector_product(n, *eigv, *eigv);
+  if (res > 0) res =  1/res;
+  for (i = 0; i < n; i++) (*eigv)[i] = (*eigv)[i]*res;
+  
+  v = *eigv;
+  
+  do {
+    SparseMatrix_multiply_vector(A, v, &u, FALSE);
+
+    unorm = vector_product(n, u, u);/* ||u||^2 */
+    unorm = sqrt(unorm);
+    if (unorm > 0) unorm = 1/unorm;
+    res = 0.;
+    for (i = 0; i < n; i++) {
+      u[i] = u[i]*unorm;
+      res = res + (u[i] - v[i])*(u[i] - v[i]);
+      v[i] = u[i];
+    }
+   
+    /* 
+    printf("=== %d === %f\n",iter,res);
+    printf("{");
+    {int j;
+      for (j = 0; j < MIN(10,n); j++){
+      if (j == n-1){
+       printf("%f",v[j]);
+      } else {
+       printf("%f,",v[j]);
+      }
+    }
+    printf("\n");
+    }
+    */
+
+  } while (res/n > tol*tol && iter++ < maxit);
+  
+  
+}
+
+/*
+main(){
+  real *v = NULL;
+  int i;
+  int n;
+
+  SparseMatrix A;
+
+  A = SparseMatrix_import_matrix_market(stdin, FORMAT_CSR);
+  n = A->m;
+  
+  power_method(A, 123, 100, 0.00001, &v);
+
+  printf("{");
+  for (i = 0; i < n; i++){
+    if (i == n-1){
+      printf("%f",v[i]);
+    } else {
+      printf("%f,",v[i]);
+    }
+  }
+  printf("}\n");
+}
+*/

diff --git a/cmd/gvmap/power.h b/cmd/gvmap/power.h
new file mode 100644 (file)
index 0000000..1854928
--- /dev/null
+++ b/cmd/gvmap/power.h
@@ -0,0 +1,19 @@
+/* $Id$Revision: */
+/* vim:set shiftwidth=4 ts=8: */
+
+/*************************************************************************
+ * 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
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors: See CVS logs. Details at http://www.graphviz.org/
+ *************************************************************************/
+
+#ifndef POWER_H
+#define POWER_H
+
+void power_method(SparseMatrix A, int random_seed, int maxit, real tol, real **eigv);
+
+#endif