Example #1
0
double igraph_norm_rand(void) {
  
  double u1;

#define BIG 134217728 /* 2^27 */
  /* unif_rand() alone is not of high enough precision */
  u1 = RNG_UNIF(0,1);
  u1 = (int)(BIG*u1) + RNG_UNIF(0,1);
  return igraph_qnorm5(u1/BIG, 0.0, 1.0, 1, 0);
}
Example #2
0
int splicing_simulate_paired_reads(const splicing_gff_t *gff, int gene,
				   const splicing_vector_t *expression,
				   int noreads, int readLength,
				   const splicing_vector_t *fragmentProb,
				   int fragmentStart, double normalMean,
				   double normalVar, double numDevs,
				   splicing_vector_int_t *isoform,
				   splicing_vector_int_t *position,
				   splicing_strvector_t *cigar, 
				   splicing_vector_t *sampleprob) {
  
  size_t i, j, noiso, il, nogenes;
  splicing_vector_t *mysampleprob=sampleprob, vsampleprob;
  splicing_vector_t px, cpx;
  double sumpx, sumpsi=0.0;
  splicing_vector_int_t isolen;
  int goodiso=0;
  splicing_vector_int_t exstart, exend, exidx;
  splicing_vector_t *myfragmentProb=(splicing_vector_t*) fragmentProb,
    vfragmentProb;
  int fs, fl;

  SPLICING_CHECK(splicing_gff_nogenes(gff, &nogenes));
  if (gene < 0 || gene >= nogenes) {
    SPLICING_ERROR("Invalid gene id", SPLICING_EINVAL);
  }

  /* TODO: more error checks */

  if (!fragmentProb) { 
    myfragmentProb=&vfragmentProb;
    SPLICING_CHECK(splicing_vector_init(&vfragmentProb, 0));
    SPLICING_FINALLY(splicing_vector_destroy, &vfragmentProb);
    SPLICING_CHECK(splicing_normal_fragment(normalMean, normalVar, numDevs, 
					    readLength, myfragmentProb,
					    &fragmentStart));
    splicing_vector_scale(myfragmentProb, 
			  1.0/splicing_vector_sum(myfragmentProb));
  }

  il=splicing_vector_size(myfragmentProb);
  fs=fragmentStart;
  fl=fragmentStart+il-1;

  SPLICING_CHECK(splicing_gff_noiso_one(gff, gene, &noiso));
    
  if ( fabs(splicing_vector_sum(myfragmentProb) - 1.0) > 1e-10 ) {
    SPLICING_ERROR("Fragment length distribution does not sum up to 1", 
		   SPLICING_EINVAL);
  }

  SPLICING_CHECK(splicing_vector_int_init(&isolen, noiso));
  SPLICING_FINALLY(splicing_vector_int_destroy, &isolen);
  SPLICING_CHECK(splicing_gff_isolength_one(gff, gene, &isolen));
  
  SPLICING_CHECK(splicing_vector_copy(&px, myfragmentProb));
  SPLICING_FINALLY(splicing_vector_destroy, &px);
  SPLICING_CHECK(splicing_vector_init(&cpx, il));
  SPLICING_FINALLY(splicing_vector_destroy, &cpx);

  if (!sampleprob) {
    mysampleprob=&vsampleprob;
    SPLICING_CHECK(splicing_vector_init(mysampleprob, noiso));
    SPLICING_FINALLY(splicing_vector_destroy, mysampleprob);
  } else {
    SPLICING_CHECK(splicing_vector_resize(mysampleprob, noiso));
  }

  for (sumpx=VECTOR(px)[0], i=1; i<il; i++) {
    VECTOR(px)[i] += VECTOR(px)[i-1];
    sumpx += VECTOR(px)[i];
  }
  VECTOR(cpx)[0] = VECTOR(px)[0];
  for (i=1; i<il; i++) {
    VECTOR(cpx)[i] = VECTOR(cpx)[i-1] + VECTOR(px)[i];
  }

  for (i=0; i<noiso; i++) {
    int ilen=VECTOR(isolen)[i];
    int r1= ilen >= fl ? ilen - fl + 1 : 0;
    int r2= ilen >= fs ? (ilen >= fl ? fl - fs : ilen - fs + 1) : 0;
    /* int r3= fs - 1; */
    double sp=0.0;
    if (r1 > 0) { sp += r1; } 
    if (r2 > 0) { sp += VECTOR(cpx)[r2-1]; }
    VECTOR(*mysampleprob)[i] = sp * VECTOR(*expression)[i];
    if (VECTOR(*mysampleprob)[i] != 0) { goodiso += 1; }
    sumpsi += VECTOR(*mysampleprob)[i];
  }

  if (goodiso == 0) {
    SPLICING_ERROR("No isoform is possible", SPLICING_FAILURE);
  }

  for (i=1; i<noiso; i++) {
    VECTOR(*mysampleprob)[i] += VECTOR(*mysampleprob)[i-1];
  }

  SPLICING_CHECK(splicing_vector_int_resize(isoform, noreads*2));

  for (i=0; i<2*noreads; i+=2) {
    int w;
    double rand;
    if (noiso==1) {
      w=0;
    } else if (noiso==2) {
      rand = RNG_UNIF01() * sumpsi;
      w = (rand < VECTOR(*mysampleprob)[0]) ? 0 : 1;
    } else {
      rand = RNG_UNIF01() * sumpsi;
      for (w=0; rand > VECTOR(*mysampleprob)[w]; w++) ;
    }
    VECTOR(*isoform)[i]=VECTOR(*isoform)[i+1]=w;
  }

  if (!sampleprob) { 
    splicing_vector_destroy(mysampleprob);
    SPLICING_FINALLY_CLEAN(1);
  } else {
    for (i=noiso-1; i>0; i--) {
      VECTOR(*mysampleprob)[i] -= VECTOR(*mysampleprob)[i-1];
    }
  }

  /* We have the isoforms, now get the read positions. */
  
  SPLICING_CHECK(splicing_vector_int_resize(position, noreads*2));
  SPLICING_CHECK(splicing_vector_int_init(&exstart, 0));
  SPLICING_FINALLY(splicing_vector_int_destroy, &exstart);
  SPLICING_CHECK(splicing_vector_int_init(&exend, 0));
  SPLICING_FINALLY(splicing_vector_int_destroy, &exend);
  SPLICING_CHECK(splicing_vector_int_init(&exidx, 0));
  SPLICING_FINALLY(splicing_vector_int_destroy, &exidx);
  SPLICING_CHECK(splicing_gff_exon_start_end(gff, &exstart, &exend, &exidx,
					     gene));
  
  /* Positions in isoform coordinates first. 
     These are sampled based on the fragment length distribution. */

  for (i=0, j=0; i<noreads; i++) {
    int iso=VECTOR(*isoform)[2*i];
    int ilen=VECTOR(isolen)[iso];
    int r1= ilen >= fl ? ilen - fl + 1 : 0;
    int r2= ilen >= fs ? (ilen >= fl ? fl - fs : ilen - fs + 1) : 0;
    /* int r3= fs - 1; */
    int pos, fragment;
    double sp=0.0;
    if (r1 > 0) { sp += r1; } 
    if (r2 > 0) { sp += VECTOR(cpx)[r2-1]; }
    double rand=RNG_UNIF(0, sp);
    if (rand < r1) { 
      pos = ceil(rand);
    } else {
      int w;
      rand -= r1;
      for (w=0; VECTOR(cpx)[w] < rand; w++) ;
      pos = r1 + r2 - w;
    }

    if (pos <= r1) {
      rand=RNG_UNIF(0, 1.0);
    } else {
      rand=RNG_UNIF(0, VECTOR(px)[r1+r2-pos]);
    }
    for (fragment=0; VECTOR(px)[fragment] < rand; fragment++) ;
    fragment += fragmentStart;

    VECTOR(*position)[j++] = pos;
    VECTOR(*position)[j++] = pos+fragment-readLength;
    
  }

  /* Translate positions to genomic coordinates */

  /* TODO: some of this is already calculated */
  SPLICING_CHECK(splicing_iso_to_genomic(gff, gene, isoform, /*converter=*/ 0,
					 position));

  /* CIGAR strings */

  splicing_strvector_clear(cigar);
  SPLICING_CHECK(splicing_strvector_reserve(cigar, 2*noreads));
  for (j=0; j<2*noreads; j++) {
    char tmp[1000], *tmp2=tmp;
    int iso=VECTOR(*isoform)[j];
    size_t rs=VECTOR(*position)[j];
    int ex=0;
    int rl=readLength;
    for (ex=VECTOR(exidx)[iso]; VECTOR(exend)[ex] < rs; ex++) ;
    while (rs + rl - 1 > VECTOR(exend)[ex]) {
      tmp2 += snprintf(tmp2, sizeof(tmp)/sizeof(char)-(tmp2-tmp)-1, "%iM%iN",
		       (int) (VECTOR(exend)[ex]-rs+1), 
		       (int) (VECTOR(exstart)[ex+1]-VECTOR(exend)[ex]-1));
      if (tmp2 >= tmp + sizeof(tmp)/sizeof(char)) {
	SPLICING_ERROR("CIGAR string too long", SPLICING_EINVAL);
      }
      rl -= (VECTOR(exend)[ex] - rs + 1);
      rs = VECTOR(exstart)[ex+1];
      ex++;
    }
    tmp2 += snprintf(tmp2, sizeof(tmp)/sizeof(char)-(tmp2-tmp)-1, "%iM", rl);
    if (tmp2 >= tmp + sizeof(tmp)/sizeof(char)) {
      SPLICING_ERROR("CIGAR string too long", SPLICING_EINVAL);
    }
    SPLICING_CHECK(splicing_strvector_append(cigar, tmp));
  }

  splicing_vector_int_destroy(&exidx);
  splicing_vector_int_destroy(&exend);
  splicing_vector_int_destroy(&exstart);
  splicing_vector_destroy(&cpx);
  splicing_vector_destroy(&px);
  splicing_vector_int_destroy(&isolen);
  SPLICING_FINALLY_CLEAN(6);

  if (!fragmentProb) { 
    splicing_vector_destroy(myfragmentProb); 
    SPLICING_FINALLY_CLEAN(1);
  }

  return 0;
}
Example #3
0
int igraph_layout_gem(const igraph_t *graph, igraph_matrix_t *res,
		      igraph_bool_t use_seed, igraph_integer_t maxiter,
		      igraph_real_t temp_max, igraph_real_t temp_min,
		      igraph_real_t temp_init) {

  igraph_integer_t no_nodes = igraph_vcount(graph);
  igraph_vector_int_t perm;
  igraph_vector_float_t impulse_x, impulse_y, temp, skew_gauge;
  igraph_integer_t i;
  float temp_global;
  igraph_integer_t perm_pointer = 0;
  float barycenter_x = 0.0, barycenter_y = 0.0;
  igraph_vector_t phi;
  igraph_vector_t neis;
  const float elen_des2 = 128 * 128;
  const float gamma = 1/16.0;
  const float alpha_o = M_PI;
  const float alpha_r = M_PI / 3.0;
  const float sigma_o = 1.0 / 3.0;
  const float sigma_r = 1.0 / 2.0 / no_nodes;
  
  if (maxiter < 0) {
    IGRAPH_ERROR("Number of iterations must be non-negative in GEM layout",
		 IGRAPH_EINVAL);
  }
  if (use_seed && (igraph_matrix_nrow(res) != no_nodes ||
		   igraph_matrix_ncol(res) != 2)) {
    IGRAPH_ERROR("Invalid start position matrix size in GEM layout",
		 IGRAPH_EINVAL);
  }
  if (temp_max <= 0) {
    IGRAPH_ERROR("Maximum temperature should be positive in GEM layout",
		 IGRAPH_EINVAL);
  }
  if (temp_min <= 0) {
    IGRAPH_ERROR("Minimum temperature should be positive in GEM layout",
		 IGRAPH_EINVAL);
  }
  if (temp_init <= 0) {
    IGRAPH_ERROR("Initial temperature should be positive in GEM layout",
		 IGRAPH_EINVAL);
  }
  if (temp_max < temp_init || temp_init < temp_min) {
    IGRAPH_ERROR("Minimum <= Initial <= Maximum temperature is required "
		 "in GEM layout", IGRAPH_EINVAL);
  }

  if (no_nodes == 0) { return 0; }

  IGRAPH_CHECK(igraph_vector_float_init(&impulse_x, no_nodes));
  IGRAPH_FINALLY(igraph_vector_float_destroy, &impulse_x);
  IGRAPH_CHECK(igraph_vector_float_init(&impulse_y, no_nodes));
  IGRAPH_FINALLY(igraph_vector_float_destroy, &impulse_y);
  IGRAPH_CHECK(igraph_vector_float_init(&temp, no_nodes));
  IGRAPH_FINALLY(igraph_vector_float_destroy, &temp);
  IGRAPH_CHECK(igraph_vector_float_init(&skew_gauge, no_nodes));
  IGRAPH_FINALLY(igraph_vector_float_destroy, &skew_gauge);
  IGRAPH_CHECK(igraph_vector_int_init_seq(&perm, 0, no_nodes-1));
  IGRAPH_FINALLY(igraph_vector_int_destroy, &perm);
  IGRAPH_VECTOR_INIT_FINALLY(&phi, no_nodes);
  IGRAPH_VECTOR_INIT_FINALLY(&neis, 10);

  RNG_BEGIN();

  /* Initialization */
  igraph_degree(graph, &phi, igraph_vss_all(), IGRAPH_ALL, IGRAPH_LOOPS);
  if (!use_seed) {
    const igraph_real_t width_half=no_nodes*100, height_half=width_half;
    IGRAPH_CHECK(igraph_matrix_resize(res, no_nodes, 2));
    for (i=0; i<no_nodes; i++) {
      MATRIX(*res, i, 0) = RNG_UNIF(-width_half, width_half);
      MATRIX(*res, i, 1) = RNG_UNIF(-height_half, height_half);
      barycenter_x += MATRIX(*res, i, 0);
      barycenter_y += MATRIX(*res, i, 1);
      VECTOR(phi)[i] *= (VECTOR(phi)[i] / 2.0 + 1.0);
    }
  } else {
    for (i=0; i<no_nodes; i++) {
      barycenter_x += MATRIX(*res, i, 0);
      barycenter_y += MATRIX(*res, i, 1);
      VECTOR(phi)[i] *= (VECTOR(phi)[i] / 2.0 + 1.0);
    }
  }
  igraph_vector_float_fill(&temp, temp_init);
  temp_global = temp_init * no_nodes;
  
  while (temp_global > temp_min * no_nodes && maxiter > 0) {
    
    /* choose a vertex v to update */
    igraph_integer_t u, v, nlen, j;
    float px, py, pvx, pvy;
    if (!perm_pointer) { 
      igraph_vector_int_shuffle(&perm); 
      perm_pointer=no_nodes-1;
    }
    v=VECTOR(perm)[perm_pointer--];
    
    /* compute v's impulse */
    px = (barycenter_x/no_nodes - MATRIX(*res, v, 0)) * gamma * VECTOR(phi)[v];
    py = (barycenter_y/no_nodes - MATRIX(*res, v, 1)) * gamma * VECTOR(phi)[v];
    px += RNG_UNIF(-32.0, 32.0);
    py += RNG_UNIF(-32.0, 32.0);

    for (u = 0; u < no_nodes; u++) {
      float dx, dy, dist2;
      if (u == v) { continue; }
      dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0);
      dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1);
      dist2=dx * dx + dy * dy;
      if (dist2 != 0) {
	px += dx * elen_des2 / dist2;
	py += dy * elen_des2 / dist2;
      }
    }

    IGRAPH_CHECK(igraph_neighbors(graph, &neis, v, IGRAPH_ALL));
    nlen=igraph_vector_size(&neis);
    for (j = 0; j < nlen; j++) {
      igraph_integer_t u=VECTOR(neis)[j];
      float dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0);
      float dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1);
      float dist2= dx * dx + dy * dy;
      px -= dx * dist2 / (elen_des2 * VECTOR(phi)[v]);
      py -= dy * dist2 / (elen_des2 * VECTOR(phi)[v]);
    }

    /* update v's position and temperature */
    if (px != 0 || py != 0) {
      float plen = sqrtf(px * px + py * py);
      px *= VECTOR(temp)[v] / plen;
      py *= VECTOR(temp)[v] / plen;
      MATRIX(*res, v, 0) += px;
      MATRIX(*res, v, 1) += py;
      barycenter_x += px;
      barycenter_y += py;
    }
    
    pvx=VECTOR(impulse_x)[v]; pvy=VECTOR(impulse_y)[v];
    if (pvx != 0 || pvy != 0) {
      float beta = atan2f(pvy - py, pvx - px);
      float sin_beta = sinf(beta);
      float sign_sin_beta = (sin_beta > 0) ? 1 : ((sin_beta < 0) ? -1 : 0);
      float cos_beta = cosf(beta);
      float abs_cos_beta = fabsf(cos_beta);
      float old_temp=VECTOR(temp)[v];
      if (sin(beta) >= sin(M_PI_2 + alpha_r / 2.0)) {
	VECTOR(skew_gauge)[v] += sigma_r * sign_sin_beta;
      }
      if (abs_cos_beta >= cosf(alpha_o / 2.0)) {
	VECTOR(temp)[v] *= sigma_o * cos_beta;
      }
      VECTOR(temp)[v] *= (1 - fabsf(VECTOR(skew_gauge)[v]));
      if (VECTOR(temp)[v] > temp_max) { VECTOR(temp)[v] = temp_max; }
      VECTOR(impulse_x)[v] = px;
      VECTOR(impulse_y)[v] = py;
      temp_global += VECTOR(temp)[v] - old_temp;
    }

    maxiter--;

  } /* while temp && iter */
  

  RNG_END();
    
  igraph_vector_destroy(&neis);
  igraph_vector_destroy(&phi);
  igraph_vector_int_destroy(&perm);
  igraph_vector_float_destroy(&skew_gauge);
  igraph_vector_float_destroy(&temp);
  igraph_vector_float_destroy(&impulse_y);
  igraph_vector_float_destroy(&impulse_x);
  IGRAPH_FINALLY_CLEAN(7);
  
  return 0;
}
Example #4
0
int igraph_layout_fruchterman_reingold_3d(const igraph_t *graph, 
					  igraph_matrix_t *res,
					  igraph_bool_t use_seed,
					  igraph_integer_t niter,
					  igraph_real_t start_temp,
					  const igraph_vector_t *weight, 
					  const igraph_vector_t *minx,
					  const igraph_vector_t *maxx,
					  const igraph_vector_t *miny,
					  const igraph_vector_t *maxy,
					  const igraph_vector_t *minz,
					  const igraph_vector_t *maxz) {

  igraph_integer_t no_nodes=igraph_vcount(graph);
  igraph_integer_t no_edges=igraph_ecount(graph);
  igraph_integer_t i;
  igraph_vector_float_t dispx, dispy, dispz;
  igraph_real_t temp=start_temp;
  igraph_real_t difftemp=start_temp / niter;
  float width=sqrtf(no_nodes), height=width, depth=width;
  igraph_bool_t conn=1;
  float C;

  if (niter < 0) {
    IGRAPH_ERROR("Number of iterations must be non-negative in "
		 "Fruchterman-Reingold layout", IGRAPH_EINVAL);
  }

  if (use_seed && (igraph_matrix_nrow(res) != no_nodes ||
		   igraph_matrix_ncol(res) != 3)) {
    IGRAPH_ERROR("Invalid start position matrix size in "
		 "Fruchterman-Reingold layout", IGRAPH_EINVAL);
  }

  if (weight && igraph_vector_size(weight) != igraph_ecount(graph)) {
    IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL);
  }

  if (minx && igraph_vector_size(minx) != no_nodes) {
    IGRAPH_ERROR("Invalid minx vector length", IGRAPH_EINVAL);
  }
  if (maxx && igraph_vector_size(maxx) != no_nodes) {
    IGRAPH_ERROR("Invalid maxx vector length", IGRAPH_EINVAL);
  }
  if (minx && maxx && !igraph_vector_all_le(minx, maxx)) {
    IGRAPH_ERROR("minx must not be greater than maxx", IGRAPH_EINVAL);
  }
  if (miny && igraph_vector_size(miny) != no_nodes) {
    IGRAPH_ERROR("Invalid miny vector length", IGRAPH_EINVAL);
  }
  if (maxy && igraph_vector_size(maxy) != no_nodes) {
    IGRAPH_ERROR("Invalid maxy vector length", IGRAPH_EINVAL);
  }
  if (miny && maxy && !igraph_vector_all_le(miny, maxy)) {
    IGRAPH_ERROR("miny must not be greater than maxy", IGRAPH_EINVAL);
  }
  if (minz && igraph_vector_size(minz) != no_nodes) {
    IGRAPH_ERROR("Invalid minz vector length", IGRAPH_EINVAL);
  }
  if (maxz && igraph_vector_size(maxz) != no_nodes) {
    IGRAPH_ERROR("Invalid maxz vector length", IGRAPH_EINVAL);
  }
  if (minz && maxz && !igraph_vector_all_le(minz, maxz)) {
    IGRAPH_ERROR("minz must not be greater than maxz", IGRAPH_EINVAL);
  }

  igraph_is_connected(graph, &conn, IGRAPH_WEAK);
  if (!conn) { C = no_nodes * sqrtf(no_nodes); }

  RNG_BEGIN();

  if (!use_seed) {
    IGRAPH_CHECK(igraph_matrix_resize(res, no_nodes, 3));
    for (i=0; i<no_nodes; i++) {
      igraph_real_t x1=minx ? VECTOR(*minx)[i] : -width/2;
      igraph_real_t x2=maxx ? VECTOR(*maxx)[i] :  width/2;
      igraph_real_t y1=miny ? VECTOR(*miny)[i] : -height/2;
      igraph_real_t y2=maxy ? VECTOR(*maxy)[i] :  height/2;
      igraph_real_t z1=minz ? VECTOR(*minz)[i] : -depth/2;
      igraph_real_t z2=maxz ? VECTOR(*maxz)[i] :  depth/2;
      MATRIX(*res, i, 0) = RNG_UNIF(x1, x2);
      MATRIX(*res, i, 1) = RNG_UNIF(y1, y2);
      MATRIX(*res, i, 2) = RNG_UNIF(z1, z2);
    }
  }

  IGRAPH_CHECK(igraph_vector_float_init(&dispx, no_nodes));
  IGRAPH_FINALLY(igraph_vector_float_destroy, &dispx);
  IGRAPH_CHECK(igraph_vector_float_init(&dispy, no_nodes));
  IGRAPH_FINALLY(igraph_vector_float_destroy, &dispy);
  IGRAPH_CHECK(igraph_vector_float_init(&dispz, no_nodes));
  IGRAPH_FINALLY(igraph_vector_float_destroy, &dispz);

  for (i=0; i<niter; i++) {
    igraph_integer_t v, u, e;
    
    /* calculate repulsive forces, we have a special version
       for unconnected graphs */
    igraph_vector_float_null(&dispx);
    igraph_vector_float_null(&dispy);
    igraph_vector_float_null(&dispz);
    if (conn) {
      for (v=0; v<no_nodes; v++) {
	for (u=v+1; u<no_nodes; u++) {
	  float dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0);
	  float dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1);
	  float dz=MATRIX(*res, v, 2) - MATRIX(*res, u, 2);
	  float dlen=dx * dx + dy * dy + dz * dz;

          if (dlen == 0) {
            dx = RNG_UNIF01() * 1e-9;
            dy = RNG_UNIF01() * 1e-9;
            dz = RNG_UNIF01() * 1e-9;
            dlen = dx * dx + dy * dy + dz * dz;
          }

	  VECTOR(dispx)[v] += dx/dlen;
	  VECTOR(dispy)[v] += dy/dlen;
	  VECTOR(dispz)[v] += dz/dlen;
	  VECTOR(dispx)[u] -= dx/dlen;
	  VECTOR(dispy)[u] -= dy/dlen;
	  VECTOR(dispz)[u] -= dz/dlen;
	}
      }
    } else {
      for (v=0; v<no_nodes; v++) {
	for (u=v+1; u<no_nodes; u++) {
	  float dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0);
	  float dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1);
	  float dz=MATRIX(*res, v, 2) - MATRIX(*res, u, 2);
	  float dlen, rdlen;

	  dlen=dx * dx + dy * dy + dz * dz;
          if (dlen == 0) {
            dx = RNG_UNIF01() * 1e-9;
            dy = RNG_UNIF01() * 1e-9;
            dz = RNG_UNIF01() * 1e-9;
            dlen = dx * dx + dy * dy + dz * dz;
          }

	  rdlen=sqrt(dlen);

	  VECTOR(dispx)[v] += dx * (C-dlen * rdlen) / (dlen*C);
	  VECTOR(dispy)[v] += dy * (C-dlen * rdlen) / (dlen*C);
	  VECTOR(dispy)[v] += dz * (C-dlen * rdlen) / (dlen*C);
	  VECTOR(dispx)[u] -= dx * (C-dlen * rdlen) / (dlen*C);
	  VECTOR(dispy)[u] -= dy * (C-dlen * rdlen) / (dlen*C);
	  VECTOR(dispz)[u] -= dz * (C-dlen * rdlen) / (dlen*C);
	}
      }
    }

    /* calculate attractive forces */
    for (e=0; e<no_edges; e++) {
      /* each edges is an ordered pair of vertices v and u */
      igraph_integer_t v=IGRAPH_FROM(graph, e);
      igraph_integer_t u=IGRAPH_TO(graph, e);
      igraph_real_t dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0);
      igraph_real_t dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1);
      igraph_real_t dz=MATRIX(*res, v, 2) - MATRIX(*res, u, 2);
      igraph_real_t w=weight ? VECTOR(*weight)[e] : 1.0;
      igraph_real_t dlen=sqrt(dx * dx + dy * dy + dz * dz) * w;
      VECTOR(dispx)[v] -= (dx * dlen);
      VECTOR(dispy)[v] -= (dy * dlen);
      VECTOR(dispz)[v] -= (dz * dlen);
      VECTOR(dispx)[u] += (dx * dlen);
      VECTOR(dispy)[u] += (dy * dlen);
      VECTOR(dispz)[u] += (dz * dlen);
    }
    
    /* limit max displacement to temperature t and prevent from
       displacement outside frame */
    for (v=0; v<no_nodes; v++) {
      igraph_real_t dx=VECTOR(dispx)[v] + RNG_UNIF01() * 1e-9;
      igraph_real_t dy=VECTOR(dispy)[v] + RNG_UNIF01() * 1e-9;
      igraph_real_t dz=VECTOR(dispz)[v] + RNG_UNIF01() * 1e-9;
      igraph_real_t displen=sqrt(dx * dx + dy * dy + dz * dz);
      igraph_real_t mx=fabs(dx) < temp ? dx : temp;
      igraph_real_t my=fabs(dy) < temp ? dy : temp;
      igraph_real_t mz=fabs(dz) < temp ? dz : temp;
      if (displen > 0) {
        MATRIX(*res, v, 0) += (dx / displen) * mx;
        MATRIX(*res, v, 1) += (dy / displen) * my;
        MATRIX(*res, v, 2) += (dz / displen) * mz;
      }
      if (minx && MATRIX(*res, v, 0) < VECTOR(*minx)[v]) { 
	MATRIX(*res, v, 0) = VECTOR(*minx)[v]; 
      }
      if (maxx && MATRIX(*res, v, 0) > VECTOR(*maxx)[v]) {
	MATRIX(*res, v, 0) = VECTOR(*maxx)[v];
      }
      if (miny && MATRIX(*res, v, 1) < VECTOR(*miny)[v]) {
	MATRIX(*res, v, 1) = VECTOR(*miny)[v];
      }
      if (maxy && MATRIX(*res, v, 1) > VECTOR(*maxy)[v]) {
	MATRIX(*res, v, 1) = VECTOR(*maxy)[v];
      }
      if (minz && MATRIX(*res, v, 2) < VECTOR(*minz)[v]) {
	MATRIX(*res, v, 2) = VECTOR(*minz)[v];
      }
      if (maxz && MATRIX(*res, v, 2) > VECTOR(*maxz)[v]) {
	MATRIX(*res, v, 2) = VECTOR(*maxz)[v];
      }
    }

    temp -= difftemp;
  }

  RNG_END();

  igraph_vector_float_destroy(&dispx);
  igraph_vector_float_destroy(&dispy);
  igraph_vector_float_destroy(&dispz);
  IGRAPH_FINALLY_CLEAN(3);
  
  return 0;
}
Example #5
0
int igraph_layout_i_fr(const igraph_t *graph,
		       igraph_matrix_t *res,
		       igraph_bool_t use_seed,
		       igraph_integer_t niter,
		       igraph_real_t start_temp,
		       const igraph_vector_t *weight,
		       const igraph_vector_t *minx,
		       const igraph_vector_t *maxx,
		       const igraph_vector_t *miny,
		       const igraph_vector_t *maxy) {

  igraph_integer_t no_nodes=igraph_vcount(graph);
  igraph_integer_t no_edges=igraph_ecount(graph);
  igraph_integer_t i;
  igraph_vector_float_t dispx, dispy;
  igraph_real_t temp=start_temp;
  igraph_real_t difftemp=start_temp / niter;
  float width=sqrtf(no_nodes), height=width;
  igraph_bool_t conn=1;
  float C;

  igraph_is_connected(graph, &conn, IGRAPH_WEAK);
  if (!conn) { C = no_nodes * sqrtf(no_nodes); }

  RNG_BEGIN();

  if (!use_seed) {
    IGRAPH_CHECK(igraph_matrix_resize(res, no_nodes, 2));
    for (i=0; i<no_nodes; i++) {
      igraph_real_t x1=minx ? VECTOR(*minx)[i] : -width/2;
      igraph_real_t x2=maxx ? VECTOR(*maxx)[i] :  width/2;
      igraph_real_t y1=miny ? VECTOR(*miny)[i] : -height/2;
      igraph_real_t y2=maxy ? VECTOR(*maxy)[i] :  height/2;
      if (!igraph_finite(x1)) { x1 = -sqrt(no_nodes)/2; }
      if (!igraph_finite(x2)) { x2 =  sqrt(no_nodes)/2; }
      if (!igraph_finite(y1)) { y1 = -sqrt(no_nodes)/2; }
      if (!igraph_finite(y2)) { y2 =  sqrt(no_nodes)/2; }
      MATRIX(*res, i, 0) = RNG_UNIF(x1, x2);
      MATRIX(*res, i, 1) = RNG_UNIF(y1, y2);
    }
  }

  IGRAPH_CHECK(igraph_vector_float_init(&dispx, no_nodes));
  IGRAPH_FINALLY(igraph_vector_float_destroy, &dispx);
  IGRAPH_CHECK(igraph_vector_float_init(&dispy, no_nodes));
  IGRAPH_FINALLY(igraph_vector_float_destroy, &dispy);

  for (i=0; i<niter; i++) {
    igraph_integer_t v, u, e;

    /* calculate repulsive forces, we have a special version
       for unconnected graphs */
    igraph_vector_float_null(&dispx);
    igraph_vector_float_null(&dispy);
    if (conn) {
      for (v=0; v<no_nodes; v++) {
	for (u=v+1; u<no_nodes; u++) {
	  float dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0);
	  float dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1);
	  float dlen=dx * dx + dy * dy;

          if (dlen == 0) {
            dx = RNG_UNIF01() * 1e-9;
            dy = RNG_UNIF01() * 1e-9;
            dlen = dx * dx + dy * dy;
          }

	  VECTOR(dispx)[v] += dx/dlen;
	  VECTOR(dispy)[v] += dy/dlen;
	  VECTOR(dispx)[u] -= dx/dlen;
	  VECTOR(dispy)[u] -= dy/dlen;
	}
      }
    } else {
      for (v=0; v<no_nodes; v++) {
	for (u=v+1; u<no_nodes; u++) {
	  float dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0);
	  float dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1);
	  float dlen, rdlen;

	  dlen=dx * dx + dy * dy;
          if (dlen == 0) {
            dx = RNG_UNIF(0, 1e-6);
            dy = RNG_UNIF(0, 1e-6);
            dlen = dx * dx + dy * dy;
          }

	  rdlen=sqrt(dlen);

	  VECTOR(dispx)[v] += dx * (C-dlen * rdlen) / (dlen*C);
	  VECTOR(dispy)[v] += dy * (C-dlen * rdlen) / (dlen*C);
	  VECTOR(dispx)[u] -= dx * (C-dlen * rdlen) / (dlen*C);
	  VECTOR(dispy)[u] -= dy * (C-dlen * rdlen) / (dlen*C);
	}
      }
    }

    /* calculate attractive forces */
    for (e=0; e<no_edges; e++) {
      /* each edges is an ordered pair of vertices v and u */
      igraph_integer_t v=IGRAPH_FROM(graph, e);
      igraph_integer_t u=IGRAPH_TO(graph, e);
      igraph_real_t dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0);
      igraph_real_t dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1);
      igraph_real_t w=weight ? VECTOR(*weight)[e] : 1.0;
      igraph_real_t dlen=sqrt(dx * dx + dy * dy) * w;
      VECTOR(dispx)[v] -= (dx * dlen);
      VECTOR(dispy)[v] -= (dy * dlen);
      VECTOR(dispx)[u] += (dx * dlen);
      VECTOR(dispy)[u] += (dy * dlen);
    }

    /* limit max displacement to temperature t and prevent from
       displacement outside frame */
    for (v=0; v<no_nodes; v++) {
      igraph_real_t dx=VECTOR(dispx)[v] + RNG_UNIF01() * 1e-9;
      igraph_real_t dy=VECTOR(dispy)[v] + RNG_UNIF01() * 1e-9;
      igraph_real_t displen=sqrt(dx * dx + dy * dy);
      igraph_real_t mx=fabs(dx) < temp ? dx : temp;
      igraph_real_t my=fabs(dy) < temp ? dy : temp;
      if (displen > 0) {
        MATRIX(*res, v, 0) += (dx / displen) * mx;
        MATRIX(*res, v, 1) += (dy / displen) * my;
      }
      if (minx && MATRIX(*res, v, 0) < VECTOR(*minx)[v]) {
	MATRIX(*res, v, 0) = VECTOR(*minx)[v];
      }
      if (maxx && MATRIX(*res, v, 0) > VECTOR(*maxx)[v]) {
	MATRIX(*res, v, 0) = VECTOR(*maxx)[v];
      }
      if (miny && MATRIX(*res, v, 1) < VECTOR(*miny)[v]) {
	MATRIX(*res, v, 1) = VECTOR(*miny)[v];
      }
      if (maxy && MATRIX(*res, v, 1) > VECTOR(*maxy)[v]) {
	MATRIX(*res, v, 1) = VECTOR(*maxy)[v];
      }
    }

    temp -= difftemp;
  }

  RNG_END();

  igraph_vector_float_destroy(&dispx);
  igraph_vector_float_destroy(&dispy);
  IGRAPH_FINALLY_CLEAN(2);
  
  return 0;
}
Example #6
0
int igraph_layout_i_grid_fr(const igraph_t *graph,
            igraph_matrix_t *res, igraph_bool_t use_seed,
	    igraph_integer_t niter, igraph_real_t start_temp,
	    const igraph_vector_t *weight, const igraph_vector_t *minx,
	    const igraph_vector_t *maxx, const igraph_vector_t *miny,
	    const igraph_vector_t *maxy) {

  igraph_integer_t no_nodes=igraph_vcount(graph);
  igraph_integer_t no_edges=igraph_ecount(graph);
  float width=sqrtf(no_nodes), height=width;
  igraph_2dgrid_t grid;
  igraph_vector_float_t dispx, dispy;
  igraph_real_t temp=start_temp;
  igraph_real_t difftemp=start_temp / niter;
  igraph_2dgrid_iterator_t vidit;
  igraph_integer_t i;
  const float cellsize=2.0;

  RNG_BEGIN();

  if (!use_seed) {
    IGRAPH_CHECK(igraph_matrix_resize(res, no_nodes, 2));
    for (i=0; i<no_nodes; i++) {
      igraph_real_t x1=minx ? VECTOR(*minx)[i] : -width/2;
      igraph_real_t x2=maxx ? VECTOR(*maxx)[i] :  width/2;
      igraph_real_t y1=miny ? VECTOR(*miny)[i] : -height/2;
      igraph_real_t y2=maxy ? VECTOR(*maxy)[i] :  height/2;
      if (!igraph_finite(x1)) { x1 = -sqrt(no_nodes)/2; }
      if (!igraph_finite(x2)) { x2 =  sqrt(no_nodes)/2; }
      if (!igraph_finite(y1)) { y1 = -sqrt(no_nodes)/2; }
      if (!igraph_finite(y2)) { y2 =  sqrt(no_nodes)/2; }
      MATRIX(*res, i, 0) = RNG_UNIF(x1, x2);
      MATRIX(*res, i, 1) = RNG_UNIF(y1, y2);
    }
  }

  /* make grid */
  IGRAPH_CHECK(igraph_2dgrid_init(&grid, res, -width/2, width/2, cellsize,
				  -height/2, height/2, cellsize));
  IGRAPH_FINALLY(igraph_2dgrid_destroy, &grid);

  /* place vertices on grid */
  for (i=0; i<no_nodes; i++) {
    igraph_2dgrid_add2(&grid, i);
  }

  IGRAPH_CHECK(igraph_vector_float_init(&dispx, no_nodes));
  IGRAPH_FINALLY(igraph_vector_float_destroy, &dispx);
  IGRAPH_CHECK(igraph_vector_float_init(&dispy, no_nodes));
  IGRAPH_FINALLY(igraph_vector_float_destroy, &dispy);

  for (i=0; i<niter; i++) {
    igraph_integer_t v, u, e;

    igraph_vector_float_null(&dispx);
    igraph_vector_float_null(&dispy);

    /* repulsion */
    igraph_2dgrid_reset(&grid, &vidit);
    while ( (v=igraph_2dgrid_next(&grid, &vidit)-1) != -1) {
      while ( (u=igraph_2dgrid_next_nei(&grid, &vidit)-1) != -1) {
	float dx=MATRIX(*res, v, 0)-MATRIX(*res, u, 0);
	float dy=MATRIX(*res, v, 1)-MATRIX(*res, u, 1);
	float dlen=dx * dx + dy * dy;
	if (dlen < cellsize * cellsize) {
	  VECTOR(dispx)[v] += dx/dlen;
	  VECTOR(dispy)[v] += dy/dlen;
	  VECTOR(dispx)[u] -= dx/dlen;
	  VECTOR(dispy)[u] -= dy/dlen;
	}
      }
    }

    /* attraction */
    for (e=0; e<no_edges; e++) {
      igraph_integer_t v=IGRAPH_FROM(graph, e);
      igraph_integer_t u=IGRAPH_TO(graph, e);
      igraph_real_t dx=MATRIX(*res, v, 0) - MATRIX(*res, u, 0);
      igraph_real_t dy=MATRIX(*res, v, 1) - MATRIX(*res, u, 1);
      igraph_real_t w=weight ? VECTOR(*weight)[e] : 1.0;
      igraph_real_t dlen=sqrt(dx * dx + dy * dy) * w;
      VECTOR(dispx)[v] -= (dx * dlen);
      VECTOR(dispy)[v] -= (dy * dlen);
      VECTOR(dispx)[u] += (dx * dlen);
      VECTOR(dispy)[u] += (dy * dlen);
    }

    /* update */
    for (v=0; v<no_nodes; v++) {
      igraph_real_t dx=VECTOR(dispx)[v] + RNG_UNIF01() * 1e-9;
      igraph_real_t dy=VECTOR(dispy)[v] + RNG_UNIF01() * 1e-9;
      igraph_real_t displen=sqrt(dx * dx + dy * dy);
      igraph_real_t mx=fabs(dx) < temp ? dx : temp;
      igraph_real_t my=fabs(dy) < temp ? dy : temp;
      if (displen > 0) {
        MATRIX(*res, v, 0) += (dx / displen) * mx;
        MATRIX(*res, v, 1) += (dy / displen) * my;
      }
      if (minx && MATRIX(*res, v, 0) < VECTOR(*minx)[v]) {
	MATRIX(*res, v, 0) = VECTOR(*minx)[v];
      }
      if (maxx && MATRIX(*res, v, 0) > VECTOR(*maxx)[v]) {
	MATRIX(*res, v, 0) = VECTOR(*maxx)[v];
      }
      if (miny && MATRIX(*res, v, 1) < VECTOR(*miny)[v]) {
	MATRIX(*res, v, 1) = VECTOR(*miny)[v];
      }
      if (maxy && MATRIX(*res, v, 1) > VECTOR(*maxy)[v]) {
	MATRIX(*res, v, 1) = VECTOR(*maxy)[v];
      }
    }

    temp -= difftemp;
  }

  igraph_vector_float_destroy(&dispx);
  igraph_vector_float_destroy(&dispy);
  igraph_2dgrid_destroy(&grid);
  IGRAPH_FINALLY_CLEAN(3);
  return 0;
}
Example #7
0
int igraph_layout_kamada_kawai(const igraph_t *graph, igraph_matrix_t *res,
	       igraph_bool_t use_seed, igraph_integer_t maxiter,
	       igraph_real_t epsilon, igraph_real_t kkconst, 
	       const igraph_vector_t *weights,
	       const igraph_vector_t *minx, const igraph_vector_t *maxx,
	       const igraph_vector_t *miny, const igraph_vector_t *maxy) {
  
  igraph_integer_t no_nodes=igraph_vcount(graph);
  igraph_integer_t no_edges=igraph_ecount(graph);
  igraph_real_t L, L0=sqrt(no_nodes);  
  igraph_matrix_t dij, lij, kij;
  igraph_real_t max_dij;
  igraph_vector_t D1, D2;
  igraph_integer_t i, j, m;

  if (maxiter < 0) {
    IGRAPH_ERROR("Number of iterations must be non-negatice in "
		 "Kamada-Kawai layout", IGRAPH_EINVAL);
  }
  if (kkconst <= 0) {
    IGRAPH_ERROR("`K' constant must be positive in Kamada-Kawai layout",
		 IGRAPH_EINVAL);
  }

  if (use_seed && (igraph_matrix_nrow(res) != no_nodes ||
		   igraph_matrix_ncol(res) != 2)) {
    IGRAPH_ERROR("Invalid start position matrix size in "
		 "Kamada-Kawai layout", IGRAPH_EINVAL);
  }
  if (weights && igraph_vector_size(weights) != no_edges) {
    IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL);
  }

  if (minx && igraph_vector_size(minx) != no_nodes) {
    IGRAPH_ERROR("Invalid minx vector length", IGRAPH_EINVAL);
  }
  if (maxx && igraph_vector_size(maxx) != no_nodes) {
    IGRAPH_ERROR("Invalid maxx vector length", IGRAPH_EINVAL);
  }
  if (minx && maxx && !igraph_vector_all_le(minx, maxx)) {
    IGRAPH_ERROR("minx must not be greater than maxx", IGRAPH_EINVAL);
  }
  if (miny && igraph_vector_size(miny) != no_nodes) {
    IGRAPH_ERROR("Invalid miny vector length", IGRAPH_EINVAL);
  }
  if (maxy && igraph_vector_size(maxy) != no_nodes) {
    IGRAPH_ERROR("Invalid maxy vector length", IGRAPH_EINVAL);
  }
  if (miny && maxy && !igraph_vector_all_le(miny, maxy)) {
    IGRAPH_ERROR("miny must not be greater than maxy", IGRAPH_EINVAL);
  }

  if (!use_seed) {
    if (minx || maxx || miny || maxy) {
      const igraph_real_t width=sqrt(no_nodes), height=width;
      IGRAPH_CHECK(igraph_matrix_resize(res, no_nodes, 2));
      RNG_BEGIN();
      for (i=0; i<no_nodes; i++) {
	igraph_real_t x1=minx ? VECTOR(*minx)[i] : -width/2;
	igraph_real_t x2=maxx ? VECTOR(*maxx)[i] :  width/2;
	igraph_real_t y1=miny ? VECTOR(*miny)[i] : -height/2;
	igraph_real_t y2=maxy ? VECTOR(*maxy)[i] :  height/2;
	if (!igraph_finite(x1)) { x1 = -width/2; }
	if (!igraph_finite(x2)) { x2 =  width/2; }
	if (!igraph_finite(y1)) { y1 = -height/2; }
	if (!igraph_finite(y2)) { y2 =  height/2; }
	MATRIX(*res, i, 0) = RNG_UNIF(x1, x2);
	MATRIX(*res, i, 1) = RNG_UNIF(y1, y2);
      }
      RNG_END();
    } else {
      igraph_layout_circle(graph, res, /* order= */ igraph_vss_all());
    }
  }

  if (no_nodes <= 1) { return 0; }

  IGRAPH_MATRIX_INIT_FINALLY(&dij, no_nodes, no_nodes);
  IGRAPH_MATRIX_INIT_FINALLY(&kij, no_nodes, no_nodes);
  IGRAPH_MATRIX_INIT_FINALLY(&lij, no_nodes, no_nodes);
  IGRAPH_CHECK(igraph_shortest_paths_dijkstra(graph, &dij, igraph_vss_all(),
					      igraph_vss_all(), weights,
					      IGRAPH_ALL));
  
  max_dij = 0.0;
  for (i=0; i<no_nodes; i++) {
    for (j=i+1; j<no_nodes; j++) {
      if (!igraph_finite(MATRIX(dij, i, j))) { continue; }
      if (MATRIX(dij, i, j) > max_dij) { max_dij = MATRIX(dij, i, j); }
    }
  }
  for (i=0; i<no_nodes; i++) {
    for (j=0; j<no_nodes; j++) {
      if (MATRIX(dij, i, j) > max_dij) { MATRIX(dij, i, j) = max_dij; }
    }
  }

  L = L0 / max_dij;
  for (i=0; i<no_nodes; i++) {
    for (j=0; j<no_nodes; j++) {      
      igraph_real_t tmp=MATRIX(dij, i, j) * MATRIX(dij, i, j);
      if (i==j) { continue; }
      MATRIX(kij, i, j) = kkconst / tmp;
      MATRIX(lij, i, j) = L * MATRIX(dij, i, j);
    }
  }

  /* Initialize delta */
  IGRAPH_VECTOR_INIT_FINALLY(&D1, no_nodes);
  IGRAPH_VECTOR_INIT_FINALLY(&D2, no_nodes);
  for (m=0; m<no_nodes; m++) {
    igraph_real_t myD1=0.0, myD2=0.0;
    for (i=0; i<no_nodes; i++) { 
      if (i==m) { continue; }
      igraph_real_t dx=MATRIX(*res, m, 0) - MATRIX(*res, i, 0);
      igraph_real_t dy=MATRIX(*res, m, 1) - MATRIX(*res, i, 1);
      igraph_real_t mi_dist=sqrt(dx * dx + dy * dy);
      myD1 += MATRIX(kij, m, i) * (dx - MATRIX(lij, m, i) * dx / mi_dist);
      myD2 += MATRIX(kij, m, i) * (dy - MATRIX(lij, m, i) * dy / mi_dist);
    }
    VECTOR(D1)[m] = myD1;
    VECTOR(D2)[m] = myD2;
  }

  for (j=0; j<maxiter; j++) {
    
    igraph_real_t myD1=0.0, myD2=0.0, A=0.0, B=0.0, C=0.0;
    igraph_real_t max_delta, delta_x, delta_y;
    igraph_real_t old_x, old_y, new_x, new_y;

    /* Select maximal delta */
    m=0; max_delta=-1;
    for (i=0; i<no_nodes; i++) {
      igraph_real_t delta=(VECTOR(D1)[i] * VECTOR(D1)[i] + 
			   VECTOR(D2)[i] * VECTOR(D2)[i]);
      if (delta > max_delta) { 
	m=i; max_delta=delta;
      }
    }
    if (max_delta < epsilon) { break; }
    old_x=MATRIX(*res, m, 0);
    old_y=MATRIX(*res, m, 1);
    
    /* Calculate D1 and D2, A, B, C */
    for (i=0; i<no_nodes; i++) {
      if (i==m) { continue; }
      igraph_real_t dx=old_x - MATRIX(*res, i, 0);
      igraph_real_t dy=old_y - MATRIX(*res, i, 1);
      igraph_real_t dist=sqrt(dx * dx + dy * dy);
      igraph_real_t den=dist * (dx * dx + dy * dy);
      A += MATRIX(kij, m, i) * (1 - MATRIX(lij, m, i) * dy * dy / den);
      B += MATRIX(kij, m, i) * MATRIX(lij, m, i) * dx * dy / den;
      C += MATRIX(kij, m, i) * (1 - MATRIX(lij, m, i) * dx * dx / den);
    }
    myD1 = VECTOR(D1)[m];
    myD2 = VECTOR(D2)[m];

    /* Need to solve some linear equations */
    delta_y = (B * myD1 - myD2 * A) / (C * A - B * B);
    delta_x = - (myD1 + B * delta_y) / A;
    
    new_x = old_x + delta_x;
    new_y = old_y + delta_y;

    /* Limits, if given */
    if (minx && new_x < VECTOR(*minx)[m]) { new_x = VECTOR(*minx)[m]; }
    if (maxx && new_x > VECTOR(*maxx)[m]) { new_x = VECTOR(*maxx)[m]; }
    if (miny && new_y < VECTOR(*miny)[m]) { new_y = VECTOR(*miny)[m]; }
    if (maxy && new_y > VECTOR(*maxy)[m]) { new_y = VECTOR(*maxy)[m]; }

    /* Update delta, only with/for the affected node */
    VECTOR(D1)[m] = VECTOR(D2)[m] = 0.0;
    for (i=0; i<no_nodes; i++) {
      if (i==m) { continue; }
      igraph_real_t old_dx=old_x - MATRIX(*res, i, 0);
      igraph_real_t old_dy=old_y - MATRIX(*res, i, 1);
      igraph_real_t old_mi_dist=sqrt(old_dx * old_dx + old_dy * old_dy);
      igraph_real_t new_dx=new_x - MATRIX(*res, i, 0);
      igraph_real_t new_dy=new_y - MATRIX(*res, i, 1);
      igraph_real_t new_mi_dist=sqrt(new_dx * new_dx + new_dy * new_dy);

      VECTOR(D1)[i] -= MATRIX(kij, m, i) * 
	(-old_dx + MATRIX(lij, m, i) * old_dx / old_mi_dist);
      VECTOR(D2)[i] -= MATRIX(kij, m, i) *
	(-old_dy + MATRIX(lij, m, i) * old_dy / old_mi_dist);
      VECTOR(D1)[i] += MATRIX(kij, m, i) *
	(-new_dx + MATRIX(lij, m, i) * new_dx / new_mi_dist);
      VECTOR(D2)[i] += MATRIX(kij, m, i) *
	(-new_dy + MATRIX(lij, m, i) * new_dy / new_mi_dist);

      VECTOR(D1)[m] += MATRIX(kij, m, i) *
	(new_dx - MATRIX(lij, m, i) * new_dx / new_mi_dist);
      VECTOR(D2)[m] += MATRIX(kij, m, i) *
	(new_dy - MATRIX(lij, m, i) * new_dy / new_mi_dist);
    }
      
    /* Update coordinates*/
    MATRIX(*res, m, 0) = new_x;
    MATRIX(*res, m, 1) = new_y;
  }

  igraph_vector_destroy(&D2);
  igraph_vector_destroy(&D1);
  igraph_matrix_destroy(&lij);
  igraph_matrix_destroy(&kij);
  igraph_matrix_destroy(&dij);
  IGRAPH_FINALLY_CLEAN(5);

  return 0;
}
Example #8
0
int igraph_layout_kamada_kawai_3d(const igraph_t *graph, igraph_matrix_t *res,
	       igraph_bool_t use_seed, igraph_integer_t maxiter,
	       igraph_real_t epsilon, igraph_real_t kkconst, 
	       const igraph_vector_t *weights,
	       const igraph_vector_t *minx, const igraph_vector_t *maxx,
	       const igraph_vector_t *miny, const igraph_vector_t *maxy,
	       const igraph_vector_t *minz, const igraph_vector_t *maxz) {
  
  igraph_integer_t no_nodes=igraph_vcount(graph);
  igraph_integer_t no_edges=igraph_ecount(graph);
  igraph_real_t L, L0=sqrt(no_nodes);  
  igraph_matrix_t dij, lij, kij;
  igraph_real_t max_dij;
  igraph_vector_t D1, D2, D3;
  igraph_integer_t i, j, m;

  if (maxiter < 0) {
    IGRAPH_ERROR("Number of iterations must be non-negatice in "
		 "Kamada-Kawai layout", IGRAPH_EINVAL);
  }
  if (kkconst <= 0) {
    IGRAPH_ERROR("`K' constant must be positive in Kamada-Kawai layout",
		 IGRAPH_EINVAL);
  }

  if (use_seed && (igraph_matrix_nrow(res) != no_nodes ||
		   igraph_matrix_ncol(res) != 3)) {
    IGRAPH_ERROR("Invalid start position matrix size in "
		 "3d Kamada-Kawai layout", IGRAPH_EINVAL);
  }
  if (weights && igraph_vector_size(weights) != no_edges) {
    IGRAPH_ERROR("Invalid weight vector length", IGRAPH_EINVAL);
  }

  if (minx && igraph_vector_size(minx) != no_nodes) {
    IGRAPH_ERROR("Invalid minx vector length", IGRAPH_EINVAL);
  }
  if (maxx && igraph_vector_size(maxx) != no_nodes) {
    IGRAPH_ERROR("Invalid maxx vector length", IGRAPH_EINVAL);
  }
  if (minx && maxx && !igraph_vector_all_le(minx, maxx)) {
    IGRAPH_ERROR("minx must not be greater than maxx", IGRAPH_EINVAL);
  }
  if (miny && igraph_vector_size(miny) != no_nodes) {
    IGRAPH_ERROR("Invalid miny vector length", IGRAPH_EINVAL);
  }
  if (maxy && igraph_vector_size(maxy) != no_nodes) {
    IGRAPH_ERROR("Invalid maxy vector length", IGRAPH_EINVAL);
  }
  if (miny && maxy && !igraph_vector_all_le(miny, maxy)) {
    IGRAPH_ERROR("miny must not be greater than maxy", IGRAPH_EINVAL);
  }
  if (minz && igraph_vector_size(minz) != no_nodes) {
    IGRAPH_ERROR("Invalid minz vector length", IGRAPH_EINVAL);
  }
  if (maxz && igraph_vector_size(maxz) != no_nodes) {
    IGRAPH_ERROR("Invalid maxz vector length", IGRAPH_EINVAL);
  }
  if (minz && maxz && !igraph_vector_all_le(minz, maxz)) {
    IGRAPH_ERROR("minz must not be greater than maxz", IGRAPH_EINVAL);
  }

  if (!use_seed) {
    if (minx || maxx || miny || maxy || minz || maxz) {
      const igraph_real_t width=sqrt(no_nodes), height=width, depth=width;
      IGRAPH_CHECK(igraph_matrix_resize(res, no_nodes, 3));
      RNG_BEGIN();
      for (i=0; i<no_nodes; i++) {
	igraph_real_t x1=minx ? VECTOR(*minx)[i] : -width/2;
	igraph_real_t x2=maxx ? VECTOR(*maxx)[i] :  width/2;
	igraph_real_t y1=miny ? VECTOR(*miny)[i] : -height/2;
	igraph_real_t y2=maxy ? VECTOR(*maxy)[i] :  height/2;
	igraph_real_t z1=minz ? VECTOR(*minz)[i] : -depth/2;
	igraph_real_t z2=maxz ? VECTOR(*maxz)[i] :  depth/2;
	if (!igraph_finite(x1)) { x1 = -width/2; }
	if (!igraph_finite(x2)) { x2 =  width/2; }
	if (!igraph_finite(y1)) { y1 = -height/2; }
	if (!igraph_finite(y2)) { y2 =  height/2; }
	if (!igraph_finite(z1)) { z1 = -depth/2; }
	if (!igraph_finite(z2)) { z2 =  depth/2; }
	MATRIX(*res, i, 0) = RNG_UNIF(x1, x2);
	MATRIX(*res, i, 1) = RNG_UNIF(y1, y2);
	MATRIX(*res, i, 2) = RNG_UNIF(z1, z2);
      }
      RNG_END();
    } else {
      igraph_layout_sphere(graph, res);
    }
  }

  if (no_nodes <= 1) { return 0; }

  IGRAPH_MATRIX_INIT_FINALLY(&dij, no_nodes, no_nodes);
  IGRAPH_MATRIX_INIT_FINALLY(&kij, no_nodes, no_nodes);
  IGRAPH_MATRIX_INIT_FINALLY(&lij, no_nodes, no_nodes);
  IGRAPH_CHECK(igraph_shortest_paths_dijkstra(graph, &dij, igraph_vss_all(),
					      igraph_vss_all(), weights,
					      IGRAPH_ALL));
  
  max_dij = 0.0;
  for (i=0; i<no_nodes; i++) {
    for (j=i+1; j<no_nodes; j++) {
      if (!igraph_finite(MATRIX(dij, i, j))) { continue; }
      if (MATRIX(dij, i, j) > max_dij) { max_dij = MATRIX(dij, i, j); }
    }
  }
  for (i=0; i<no_nodes; i++) {
    for (j=0; j<no_nodes; j++) {
      if (MATRIX(dij, i, j) > max_dij) { MATRIX(dij, i, j) = max_dij; }
    }
  }

  L = L0 / max_dij;
  for (i=0; i<no_nodes; i++) {
    for (j=0; j<no_nodes; j++) {      
      igraph_real_t tmp=MATRIX(dij, i, j) * MATRIX(dij, i, j);
      if (i==j) { continue; }
      MATRIX(kij, i, j) = kkconst / tmp;
      MATRIX(lij, i, j) = L * MATRIX(dij, i, j);
    }
  }

  /* Initialize delta */
  IGRAPH_VECTOR_INIT_FINALLY(&D1, no_nodes);
  IGRAPH_VECTOR_INIT_FINALLY(&D2, no_nodes);
  IGRAPH_VECTOR_INIT_FINALLY(&D3, no_nodes);
  for (m=0; m<no_nodes; m++) {
    igraph_real_t myD1=0.0, myD2=0.0, myD3=0.0;
    for (i=0; i<no_nodes; i++) { 
      if (i==m) { continue; }
      igraph_real_t dx=MATRIX(*res, m, 0) - MATRIX(*res, i, 0);
      igraph_real_t dy=MATRIX(*res, m, 1) - MATRIX(*res, i, 1);
      igraph_real_t dz=MATRIX(*res, m, 2) - MATRIX(*res, i, 2);
      igraph_real_t mi_dist=sqrt(dx * dx + dy * dy + dz * dz);
      myD1 += MATRIX(kij, m, i) * (dx - MATRIX(lij, m, i) * dx / mi_dist);
      myD2 += MATRIX(kij, m, i) * (dy - MATRIX(lij, m, i) * dy / mi_dist);
      myD3 += MATRIX(kij, m, i) * (dz - MATRIX(lij, m, i) * dz / mi_dist);
    }
    VECTOR(D1)[m] = myD1;
    VECTOR(D2)[m] = myD2;
    VECTOR(D3)[m] = myD3;
  }

  for (j=0; j<maxiter; j++) {
    
    igraph_real_t Ax=0.0, Ay=0.0, Az=0.0;
    igraph_real_t Axx=0.0, Axy=0.0, Axz=0.0, Ayy=0.0, Ayz=0.0, Azz=0.0;
    igraph_real_t max_delta, delta_x, delta_y, delta_z;
    igraph_real_t old_x, old_y, old_z, new_x, new_y, new_z;
    igraph_real_t detnum;

    /* Select maximal delta */
    m=0; max_delta=-1;
    for (i=0; i<no_nodes; i++) {
      igraph_real_t delta=(VECTOR(D1)[i] * VECTOR(D1)[i] + 
			   VECTOR(D2)[i] * VECTOR(D2)[i] +
			   VECTOR(D3)[i] * VECTOR(D3)[i]);
      if (delta > max_delta) { 
	m=i; max_delta=delta;
      }
    }
    if (max_delta < epsilon) { break; }
    old_x=MATRIX(*res, m, 0);
    old_y=MATRIX(*res, m, 1);
    old_z=MATRIX(*res, m, 2);
    
    /* Calculate D1, D2 and D3, and other coefficients */
    for (i=0; i<no_nodes; i++) {
      if (i==m) { continue; }
      igraph_real_t dx=old_x - MATRIX(*res, i, 0);
      igraph_real_t dy=old_y - MATRIX(*res, i, 1);
      igraph_real_t dz=old_z - MATRIX(*res, i, 2);
      igraph_real_t dist=sqrt(dx * dx + dy * dy + dz *dz);
      igraph_real_t den=dist * (dx * dx + dy * dy + dz * dz);
      igraph_real_t k_mi=MATRIX(kij, m, i);
      igraph_real_t l_mi=MATRIX(lij, m, i);
      Axx += k_mi * (1 - l_mi * (dy*dy + dz*dz) / den);
      Ayy += k_mi * (1 - l_mi * (dx*dx + dz*dz) / den);
      Azz += k_mi * (1 - l_mi * (dx*dx + dy*dy) / den);
      Axy += k_mi * l_mi * dx * dy / den;
      Axz += k_mi * l_mi * dx * dz / den;
      Ayz += k_mi * l_mi * dy * dz / den;
    }
    Ax = -VECTOR(D1)[m];
    Ay = -VECTOR(D2)[m];
    Az = -VECTOR(D3)[m];

    /* Need to solve some linear equations, we just use Cramer's rule */
#define DET(a,b,c,d,e,f,g,h,i) ((a*e*i+b*f*g+c*d*h)-(c*e*g+b*d*i+a*f*h))
    
    detnum  = DET(Axx,Axy,Axz, Axy,Ayy,Ayz, Axz,Ayz,Azz);
    delta_x = DET(Ax ,Ay ,Az , Axy,Ayy,Ayz, Axz,Ayz,Azz) / detnum;
    delta_y = DET(Axx,Axy,Axz, Ax ,Ay ,Az , Axz,Ayz,Azz) / detnum;
    delta_z = DET(Axx,Axy,Axz, Axy,Ayy,Ayz, Ax ,Ay ,Az ) / detnum;
    
    new_x = old_x + delta_x;
    new_y = old_y + delta_y;
    new_z = old_z + delta_z;

    /* Limits, if given */
    if (minx && new_x < VECTOR(*minx)[m]) { new_x = VECTOR(*minx)[m]; }
    if (maxx && new_x > VECTOR(*maxx)[m]) { new_x = VECTOR(*maxx)[m]; }
    if (miny && new_y < VECTOR(*miny)[m]) { new_y = VECTOR(*miny)[m]; }
    if (maxy && new_y > VECTOR(*maxy)[m]) { new_y = VECTOR(*maxy)[m]; }
    if (minz && new_z < VECTOR(*minz)[m]) { new_z = VECTOR(*minz)[m]; }
    if (maxz && new_z > VECTOR(*maxz)[m]) { new_z = VECTOR(*maxz)[m]; }

    /* Update delta, only with/for the affected node */
    VECTOR(D1)[m] = VECTOR(D2)[m] = VECTOR(D3)[m] = 0.0;
    for (i=0; i<no_nodes; i++) {
      if (i==m) { continue; }
      igraph_real_t old_dx=old_x - MATRIX(*res, i, 0);
      igraph_real_t old_dy=old_y - MATRIX(*res, i, 1);
      igraph_real_t old_dz=old_z - MATRIX(*res, i, 2);
      igraph_real_t old_mi_dist=sqrt(old_dx * old_dx + old_dy * old_dy + 
				     old_dz * old_dz);
      igraph_real_t new_dx=new_x - MATRIX(*res, i, 0);
      igraph_real_t new_dy=new_y - MATRIX(*res, i, 1);
      igraph_real_t new_dz=new_z - MATRIX(*res, i, 2);
      igraph_real_t new_mi_dist=sqrt(new_dx * new_dx + new_dy * new_dy +
				     new_dz * new_dz);

      VECTOR(D1)[i] -= MATRIX(kij, m, i) * 
	(-old_dx + MATRIX(lij, m, i) * old_dx / old_mi_dist);
      VECTOR(D2)[i] -= MATRIX(kij, m, i) *
	(-old_dy + MATRIX(lij, m, i) * old_dy / old_mi_dist);
      VECTOR(D3)[i] -= MATRIX(kij, m, i) *
	(-old_dz + MATRIX(lij, m, i) * old_dz / old_mi_dist);

      VECTOR(D1)[i] += MATRIX(kij, m, i) *
	(-new_dx + MATRIX(lij, m, i) * new_dx / new_mi_dist);
      VECTOR(D2)[i] += MATRIX(kij, m, i) *
	(-new_dy + MATRIX(lij, m, i) * new_dy / new_mi_dist);
      VECTOR(D3)[i] += MATRIX(kij, m, i) *
	(-new_dz + MATRIX(lij, m, i) * new_dz / new_mi_dist);

      VECTOR(D1)[m] += MATRIX(kij, m, i) *
	(new_dx - MATRIX(lij, m, i) * new_dx / new_mi_dist);
      VECTOR(D2)[m] += MATRIX(kij, m, i) *
	(new_dy - MATRIX(lij, m, i) * new_dy / new_mi_dist);
      VECTOR(D3)[m] += MATRIX(kij, m, i) *
	(new_dz - MATRIX(lij, m, i) * new_dz / new_mi_dist);
    }
      
    /* Update coordinates*/
    MATRIX(*res, m, 0) = new_x;
    MATRIX(*res, m, 1) = new_y;
    MATRIX(*res, m, 2) = new_z;
  }

  igraph_vector_destroy(&D3);
  igraph_vector_destroy(&D2);
  igraph_vector_destroy(&D1);
  igraph_matrix_destroy(&lij);
  igraph_matrix_destroy(&kij);
  igraph_matrix_destroy(&dij);
  IGRAPH_FINALLY_CLEAN(6);

  return 0;
}