edge_bundling.cpp

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/*************************************************************************
 * Copyright (c) 2011 AT&T Intellectual Property
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * https://www.eclipse.org/legal/epl-v10.html
 *
 * Contributors: Details at https://graphviz.org
 *************************************************************************/
 
#include <algorithm>
#include <common/types.h>
#include <common/globals.h>
#include <sparse/general.h>
#include <math.h>
#include <numeric>
#include <sparse/SparseMatrix.h>
#include <mingle/edge_bundling.h>
#include <time.h>
#include <sparse/clustering.h>
#include <mingle/ink.h>
#include <mingle/agglomerative_bundling.h>
#include <string.h>
#include <vector>
 
#define SMALL 1.e-10
 
static double norm(int n, const double *x) {
  return sqrt(std::inner_product(x, x + n, x, 0.0));
}
 
static double sqr_dist(int dim, const double *x, const double *y) {
  int i;
  double res = 0;
  for (i = 0; i < dim; i++) res += (x[i] - y[i])*(x[i] - y[i]);
  return res;
}
 
static double dist(int dim, const double *x, const double *y) {
  return sqrt(sqr_dist(dim,x,y));
}
 
static pedge pedge_new(int np, int dim, const double *x) {
  pedge e;
 
  e.npoints = np;
  e.dim = dim;
  e.len = np;
  e.x.assign(x, &x[dim * e.len]);
  e.edge_length = dist(dim, &x[0 * dim], &x[(np - 1) * dim]);
  e.wgt = 1;
  return e;
 
}
 
pedge pedge_wgt_new(int np, int dim, double *x, double wgt) {
  pedge e;
 
  e.npoints = np;
  e.dim = dim;
  e.len = np;
  e.x.assign(x, &x[dim * e.len]);
  e.edge_length = dist(dim, &x[0 * dim], &x[(np - 1) * dim]);
  e.wgt = wgt;
  e.wgts = std::vector<double>(np - 1, wgt);
  return e;
}
 
void pedge_delete(pedge &) { }
 
static double edge_compatibility(const pedge &e1, const pedge &e2) {
  /* two edges are u1->v1, u2->v2.
     return 1 if two edges are exactly the same, 0 if they are very different.
   */
  double dist1, dist2, len1, len2;
  const int dim = e1.dim;
  bool flipped = false;
 
  const double *u1 = e1.x.data();
  const double *v1 = e1.x.data() + e1.npoints * dim - dim;
  const double *u2 = e2.x.data();
  const double *v2 = e2.x.data() + e2.npoints * dim - dim;
  dist1 = sqr_dist(dim, u1, u2) + sqr_dist(dim, v1, v2);
  dist2 =  sqr_dist(dim, u1, v2) + sqr_dist(dim, v1, u2);
  if (dist1 > dist2){
    std::swap(u2, v2);
    dist1 = dist2;
    flipped = true;
  }
  len1 = dist(dim, u1, v1);
  len2 = dist(dim, u2, v2);
  dist1 = std::max(0.1, dist1 / (len1 + len2 + 0.0001 * dist1));
  if (flipped){
    return -1/dist1; 
  } else {
    return 1/dist1; 
  }
}
 
static double edge_compatibility_full(const pedge &e1, const pedge &e2) {
  /* two edges are u1->v1, u2->v2.
     return 1 if two edges are exactly the same, 0 if they are very different.
     This is based on Holten and van Wijk's paper
   */
  double dist1, dist2, len1, len2, len;
  double tmp, ca, cp, cs;
  int dim = e1.dim, i;
  bool flipped = false;
 
  const double *u1 = e1.x.data();
  const double *v1 = e1.x.data() + e1.npoints * dim - dim;
  const double *u2 = e2.x.data();
  const double *v2 = e2.x.data() + e2.npoints * dim - dim;
  dist1 = sqr_dist(dim, u1, u2) + sqr_dist(dim, v1, v2);
  dist2 =  sqr_dist(dim, u1, v2) + sqr_dist(dim, v1, u2);
  if (dist1 > dist2){
    std::swap(u2, v2);
    flipped = true;
  }
  len1 = std::max(dist(dim, u1, v1), SMALL);
  len2 = std::max(dist(dim, u2, v2), SMALL);
  len = 0.5*(len1+len2);
 
  /* angle compatibility */
  ca = 0;
  for (i = 0; i < dim; i++) 
    ca += (v1[i]-u1[i])*(v2[i]-u2[i]);
  ca = fabs(ca/(len1*len2));
  assert(ca > -0.001);
 
  /* scale compatibility */
  cs = 2 / (std::max(len1, len2) / len + len / std::min(len1, len2));
  assert(cs > -0.001 && cs < 1.001);
 
  /* position compatibility */
  cp = 0;
  for (i = 0; i < dim; i++) {
    tmp = .5*(v1[i]+u1[i])-.5*(v2[i]+u2[i]);
    cp += tmp*tmp;
  }
  cp = sqrt(cp);
  cp = len/(len + cp);
  assert(cp > -0.001 && cp < 1.001);
 
  /* visibility compatibility */
 
  dist1 = cp*ca*cs;
  if (flipped){
    return -dist1; 
  } else {
    return dist1; 
  }
}
 
static void fprint_rgb(FILE* fp, int r, int g, int b, int alpha){
  fprintf(fp, "#%02x%02x%02x%02x", r, g, b, alpha);
}
 
void pedge_export_gv(FILE *fp, int ne, const std::vector<pedge> &edges) {
  double maxwgt = 0;
 
  fprintf(fp,"strict graph{\n");
  /* points */
  for (int i = 0; i < ne; i++){
    const pedge &edge = edges[i];
    const std::vector<double> &x = edge.x;
    const int dim = edge.dim;
    const int sta = 0;
    const int sto = edge.npoints - 1;
 
    fprintf(fp, "%d [pos=\"", i);
    for (int k = 0; k < dim; k++) {
      if (k != 0)  fprintf(fp, ",");
      fprintf(fp, "%f", x[sta*dim+k]);
    }
    fprintf(fp, "\"];\n");
 
    fprintf(fp, "%d [pos=\"", i + ne);
    for (int k = 0; k < dim; k++) {
      if (k != 0)  fprintf(fp, ",");
      fprintf(fp, "%f", x[sto*dim+k]);
    }
    fprintf(fp, "\"];\n");
 
  }
 
  /* figure out max number of bundled original edges in a pedge */
  for (int i = 0; i < ne; i++){
    const pedge &edge = edges[i];
    if (!edge.wgts.empty()) {
      for (int j = 0; j < edge.npoints - 1; j++) {
        maxwgt = std::max(maxwgt, edge.wgts[j]);
      }
    }
  }
 
  /* spline and colors */
  for (int i = 0; i < ne; i++){
    fprintf(fp,"%d -- %d [pos=\"", i, i + ne);
    const pedge &edge = edges[i];
    const std::vector<double> &x = edge.x;
    const int dim = edge.dim;
    /* splines */
    for (int j = 0; j < edge.npoints; j++) {
      if (j != 0) {
        int mm = 3;
        fprintf(fp," ");
        /* there are ninterval+1 points, add 3*ninterval+2 points, get rid of internal ninternal-1 points,
          make into 3*ninterval+4 points so that gviz spline rendering can work */
        const double *tt;
        const double tt1[] = {0.15, 0.5, 0.85};
        const double tt2[] = {0.15, 0.4, 0.6, 0.85};
        if (j == 1 || j == edge.npoints - 1) {
          // every interval gets 3 points inserted except the first and last one
          tt = tt2;
          mm = 4;
        } else {
          tt = tt1;
        }
        for (int kk = 1; kk <= mm; kk++){
          const double t = tt[kk - 1];
          for (int k = 0; k < dim; k++) {
            if (k != 0) fprintf(fp,",");
            fprintf(fp, "%f", x[(j - 1) * dim + k] * (1 - t) + x[j * dim + k] * t);
          }
          fprintf(fp," ");
        }
      }
      if (j == 0 || j == edge.npoints - 1){
        for (int k = 0; k < dim; k++) {
          if (k != 0) fprintf(fp,",");
          fprintf(fp, "%f", x[j*dim+k]);
        }
      }
    }
    /* colors based on how much bundling */
    if (!edge.wgts.empty()) {
      fprintf(fp, "\", wgts=\"");
      for (int j = 0; j < edge.npoints - 1; j++){
        if (j != 0) fprintf(fp,",");
        fprintf(fp, "%f", edge.wgts[j]);
      }
 
      double len_total0 = 0;
      fprintf(fp, "\", color=\"");
      for (int j = 0; j < edge.npoints - 1; j++){
        double len = 0;
        int k;
        for (k = 0; k < dim; k++){
          len += (edge.x[dim * j + k] - edge.x[dim * (j + 1) + k]) * (edge.x[dim * j + k] - edge.x[dim * (j + 1) + k]);
        }
        len = sqrt(len/k);
        len_total0 += len;
      }
      for (int j = 0; j < edge.npoints - 1; j++) {
        double len = 0;
        int k;
        for (k = 0; k < dim; k++){
          len += (edge.x[dim * j + k] - edge.x[dim * (j + 1) + k]) * (edge.x[dim * j + k] - edge.x[dim * (j + 1) + k]);
        }
        len = sqrt(len/k);
        const double t = edge.wgts[j] / maxwgt;
        // interpolate between red (t = 1) to blue (t = 0)
        const int r = 255 * t;
        const int g = 0;
        const int b = 255 * (1 - t);
        if (j != 0) fprintf(fp,":");
        fprint_rgb(fp, r, g, b, 85);
        if (j < edge.npoints - 2) fprintf(fp, ";%f", len / len_total0);
      }
 
    }
    fprintf(fp, "\"];\n");
    
  }
  fprintf(fp,"}\n");
}
 
#ifdef DEBUG
static void pedge_print(char *comments, const pedge &e) {
  int i, j, dim;
  dim = e.dim;
  fprintf(stderr,"%s", comments);
  for (i = 0; i < e.npoints; i++){
    if (i > 0) fprintf(stderr,",");
    fprintf(stderr,"{");
    for (j = 0; j < dim; j++){
      if (j > 0) fprintf(stderr,",");
      fprintf(stderr, "%f", e.x[dim * i + j]);
    }
    fprintf(stderr,"}");
  }
  fprintf(stderr,"\n");
}
#endif
 
void pedge_wgts_realloc(pedge &e, int n) {
  int i;
  if (n <= e.npoints)
    return;
  e.x.resize(e.dim * n, 0);
  if (e.wgts.empty()) {
    e.wgts.resize(n - 1);
    for (i = 0; i < e.npoints; i++)
      e.wgts[i] = e.wgt;
  } else {
    e.wgts.resize(n - 1);
  }
  e.len = n;
}
 
void pedge_double(pedge &e) {
  /* double the number of points (more precisely, add a point between two points in the polyline */
  int npoints = e.npoints, len = e.len, i, dim = e.dim;
  int j, ii, ii2, np;
 
  assert(npoints >= 2);
  if (npoints*2-1 > len){
    len = 3*npoints;
    e.x.resize(dim * len, 0);
  }
  std::vector<double> &x = e.x;
 
  for (i = npoints - 1; i >= 0; i--){
    ii = 2*i;
    for (j = 0; j < dim; j++){
      x[dim*ii + j] = x[dim*i + j];
    }
  }
 
  for (i = 0; i < npoints - 1; i++){
    ii = 2*i;/* left and right interpolant of a new point */
    ii2 = 2*(i+1);
    for (j = 0; j < dim; j++){
      x[dim*(2*i + 1) + j] = 0.5*(x[dim*ii + j] + x[dim*ii2 + j]);
    }
  }
  e.len = len;
  np = e.npoints = 2 * e.npoints - 1;
  e.edge_length = dist(dim, &x.data()[0 * dim], &x.data()[(np - 1) * dim]);
}
 
static void edge_tension_force(std::vector<double> &force, const pedge &e) {
  const std::vector<double> &x = e.x;
  const int dim = e.dim;
  const int np = e.npoints;
  int i, left, right, j;
  double s;
 
  /* tension force = ((np-1)*||2x-xleft-xright||)/||e||, so the force is nominal and unitless
  */
  s =  (np - 1) / std::max(SMALL, e.edge_length);
  for (i = 1; i <= np - 2; i++){
    left = i - 1;
    right = i + 1;
    for (j = 0; j < dim; j++) force[i*dim + j] += s*(x[left*dim + j] - x[i*dim + j]);
    for (j = 0; j < dim; j++) force[i*dim + j] += s*(x[right*dim + j] - x[i*dim + j]);
  }
}
 
static void edge_attraction_force(double similarity, const pedge &e1,
                                  const pedge &e2, std::vector<double> &force) {
  /* attractive force from x2 applied to x1 */
  const std::vector<double> &x1 = e1.x, &x2 = e2.x;
  const int dim = e1.dim;
  const int np = e1.npoints;
  const double edge_length = e1.edge_length;
 
  assert(e1.npoints == e2.npoints);
 
  /* attractive force = 1/d where d = D/||e1|| is the relative distance, D is the distance between e1 and e2.
   so the force is nominal and unitless
  */
  if (similarity > 0){
    const double s = similarity * edge_length;
    for (int i = 1; i <= np - 2; i++){
      double dist = sqr_dist(dim, &x1.data()[i * dim], &x2.data()[i * dim]);
      if (dist < SMALL) dist = SMALL;
      const double ss = s / (dist + 0.1 * edge_length * sqrt(dist));
      for (int j = 0; j < dim; j++) force[i*dim + j] += ss*(x2[i*dim + j] - x1[i*dim + j]);
    }
  } else {/* clip e2 */
    const double s = -similarity * edge_length;
    for (int i = 1; i <= np - 2; i++){
      double dist = sqr_dist(dim, &x1.data()[i * dim], &x2.data()[(np - 1 - i) * dim]);
      if (dist < SMALL) dist = SMALL;
      const double ss = s / (dist + 0.1 * edge_length * sqrt(dist));
      for (int j = 0; j < dim; j++) force[i*dim + j] += ss*(x2[(np - 1 - i)*dim + j] - x1[i*dim + j]);
    }
  }
 
}
 
static void force_directed_edge_bundling(SparseMatrix A,
                                         std::vector<pedge> &edges, int maxit,
                                         double step0, double K) {
  int i, j, ne = A->n, k;
  int *ia = A->ia, *ja = A->ja, iter = 0;
  double *a = (double*) A->a;
  const int np = edges[0].npoints, dim = edges[0].dim;
  double step = step0;
  double fnorm_a, fnorm_t, edge_length, start;
  
  if (Verbose > 1)
    fprintf(stderr, "total interaction pairs = %d out of %d, avg neighbors per edge = %f\n",A->nz, A->m*A->m, A->nz/(double) A->m);
 
  std::vector<double> force_t(dim * np);
  std::vector<double> force_a(dim * np);
  while (step > 0.001 && iter < maxit){
    start = clock();
    iter++;
    for (i = 0; i < ne; i++){
      for (j = 0; j < dim*np; j++) {
        force_t[j] = 0.;
        force_a[j] = 0.;
      }
      pedge &e1 = edges[i];
      std::vector<double> &x = e1.x;
      edge_tension_force(force_t, e1);
      for (j = ia[i]; j < ia[i+1]; j++){
        const pedge &e2 = edges[ja[j]];
        edge_attraction_force(a[j], e1, e2, force_a);
      }
      fnorm_t = std::max(SMALL, norm(dim * (np - 2), &force_t.data()[dim]));
      fnorm_a = std::max(SMALL, norm(dim * (np - 2), &force_a.data()[dim]));
      edge_length = e1.edge_length;
 
      for (j = 1; j <= np - 2; j++){
        for (k = 0; k < dim; k++) {
          x[j * dim + k] += step * edge_length
                          * (force_t[j * dim + k] + K * force_a[j * dim+k])
                          / hypot(fnorm_t, K * fnorm_a);
        }
      }
      
    }
    step = step*0.9;
  if (Verbose > 1)
    fprintf(stderr, "iter ==== %d cpu = %f npoints = %d\n", iter, (double)(clock() - start) / CLOCKS_PER_SEC, np - 2);
  }
}
 
static void modularity_ink_bundling(int dim, int ne, SparseMatrix B,
                                    std::vector<pedge> &edges,
                                    double angle_param, double angle) {
  int *assignment = NULL, nclusters;
  double modularity;
  int *clusterp, *clusters;
  SparseMatrix D, C;
  point_t meet1, meet2;
  double ink0, ink1;
  int i, j, jj;
 
  SparseMatrix BB;
 
  /* B may contain negative entries */
  BB = SparseMatrix_copy(B);
  BB = SparseMatrix_apply_fun(BB, fabs);
  modularity_clustering(BB, true, 0, &nclusters, &assignment, &modularity);
  SparseMatrix_delete(BB);
 
  if (Verbose > 1) fprintf(stderr, "there are %d clusters, modularity = %f\n",nclusters, modularity);
  
  C = SparseMatrix_new(1, 1, 1, MATRIX_TYPE_PATTERN, FORMAT_COORD);
  
  for (i = 0; i < ne; i++){
    jj = assignment[i];
    SparseMatrix_coordinate_form_add_entry(C, jj, i, NULL);
  }
  
  D = SparseMatrix_from_coordinate_format(C);
  SparseMatrix_delete(C);
  clusterp = D->ia;
  clusters = D->ja;
  for (i = 0; i < nclusters; i++) {
    ink1 = ink(edges, clusterp[i + 1] - clusterp[i], &clusters[clusterp[i]],
               &ink0, &meet1, &meet2, angle_param, angle);
    if (Verbose > 1)
      fprintf(stderr,"nedges = %d ink0 = %f, ink1 = %f\n",clusterp[i+1] - clusterp[i], ink0, ink1);
    if (ink1 < ink0){
      for (j = clusterp[i]; j < clusterp[i+1]; j++){
        /* make this edge 5 points, insert two meeting points at 1 and 2, make 3 the last point */
        pedge_double(edges[clusters[j]]);
        pedge_double(edges[clusters[j]]);
        pedge &e = edges[clusters[j]];
        e.x[1 * dim] = meet1.x;
        e.x[1 * dim + 1] = meet1.y;
        e.x[2 * dim] = meet2.x;
        e.x[2 * dim + 1] = meet2.y;
        e.x[3 * dim] = e.x[4 * dim];
        e.x[3 * dim + 1] = e.x[4 * dim + 1];
        e.npoints = 4;
      }
    }
  }
  SparseMatrix_delete(D);
}
 
static SparseMatrix check_compatibility(SparseMatrix A, int ne,
                                        const std::vector<pedge> &edges,
                                        int compatibility_method, double tol) {
  /* go through the links and make sure edges are compatible */
  SparseMatrix B, C;
  int *ia, *ja, i, j, jj;
  double start;
  double dist;
 
  B = SparseMatrix_new(1, 1, 1, MATRIX_TYPE_REAL, FORMAT_COORD);
  ia = A->ia; ja = A->ja;
  start = clock();
  for (i = 0; i < ne; i++){
    for (j = ia[i]; j < ia[i+1]; j++){
      jj = ja[j];
      if (i == jj) continue;
      if (compatibility_method == COMPATIBILITY_DIST){
        dist = edge_compatibility_full(edges[i], edges[jj]);
      } else if (compatibility_method == COMPATIBILITY_FULL){
        dist = edge_compatibility(edges[i], edges[jj]);
      } 
 
      if (fabs(dist) > tol){
        B = SparseMatrix_coordinate_form_add_entry(B, i, jj, &dist);
        B = SparseMatrix_coordinate_form_add_entry(B, jj, i, &dist);
      }
    }
  }
  C = SparseMatrix_from_coordinate_format(B);
  SparseMatrix_delete(B);
  B = C;
  if (Verbose > 1)
    fprintf(stderr, "edge compatibilitu time = %f\n",((double) (clock() - start))/CLOCKS_PER_SEC);
  return B;
}
 
std::vector<pedge> edge_bundling(SparseMatrix A0, int dim,
                                 const std::vector<double> &x, int maxit_outer,
                                 double K, int method, int nneighbor,
                                 int compatibility_method, int max_recursion,
                                 double angle_param, double angle) {
  /* bundle edges.
     A: edge graph
     x: edge i is at {p,q}, 
     .  where p = x[2*dim*i : 2*dim*i+dim-1]
     .    and q = x[2*dim*i+dim : 2*dim*i+2*dim-1]
     maxit_outer: max outer iteration for force directed bundling. Every outer iter subdivide each edge segment into 2.
     K: nominal edge length in force directed bundling
     method: which method to use.
     nneighbor: number of neighbors to be used in forming nearest neighbor graph. Used only in agglomerative method
     compatibility_method: which method to use to calculate compatibility. Used only in force directed.
     max_recursion: used only in agglomerative method. Specify how many level of recursion to do to bundle bundled edges again
 
  */
  int ne = A0->m;
  SparseMatrix A = A0, B = NULL;
  int i;
  double tol = 0.001;
  int k;
  double step0 = 0.1, start = 0.0;
  int maxit = 10;
 
  assert(A->n == ne);
  std::vector<pedge> edges;
  edges.reserve(ne);
 
  for (i = 0; i < ne; i++){
    edges.emplace_back(pedge_new(2, dim, &x.data()[dim * 2 * i]));
  }
 
  A = SparseMatrix_symmetrize(A0, true);
 
 
 
  if (Verbose) start = clock();
  if (method == METHOD_INK){
 
    /* go through the links and make sure edges are compatible */
    B = check_compatibility(A, ne, edges, compatibility_method, tol);
 
    modularity_ink_bundling(dim, ne, B, edges, angle_param, angle);
 
  } else if (method == METHOD_INK_AGGLOMERATE){
    /* plan: merge a node with its neighbors if doing so improve. Form coarsening graph, repeat until no more ink saving */
    agglomerative_ink_bundling(dim, A, edges, nneighbor, max_recursion,
                               angle_param, angle);
  } else if (method == METHOD_FD){/* FD method */
    
    /* go through the links and make sure edges are compatible */
    B = check_compatibility(A, ne, edges, compatibility_method, tol);
 
 
    for (k = 0; k < maxit_outer; k++){
      for (i = 0; i < ne; i++){
        pedge_double(edges[i]);
      }
      step0 /= 2;
      force_directed_edge_bundling(B, edges, maxit, step0, K);
    }
    
  } else if (method == METHOD_NONE){
    ;
  } else {
    assert(0);
  }
  if (Verbose)
    fprintf(stderr, "total edge bundling cpu = %f\n", (double)(clock() - start) / CLOCKS_PER_SEC);
  if (B != A) SparseMatrix_delete(B);
  if (A != A0) SparseMatrix_delete(A);
 
  return edges;
}