Exemple #1
0
static void NN_chain_core(const t_index N, t_float * const D, t_members * const members, cluster_result & Z2) {
/*
    N: integer
    D: condensed distance matrix N*(N-1)/2
    Z2: output data structure

    This is the NN-chain algorithm, described on page 86 in the following book:

   Fionn Murtagh, Multidimensional Clustering Algorithms,
    Vienna, Würzburg: Physica-Verlag, 1985.

    This implementation does not give defined results when NaN or Inf values
    are present in the array D.
*/
  t_index i;

  auto_array_ptr<t_index> NN_chain(N);
  t_index NN_chain_tip = 0;

  t_index idx1, idx2;

  t_float size1, size2;
  doubly_linked_list AR(N);

  t_float min;

  for (t_index j=0; j<N-1; j++) {
    if (NN_chain_tip <= 3) {
      NN_chain[0] = idx1 = AR.start;
      NN_chain_tip = 1;

      idx2 = AR.succ[idx1];
      min = D_(idx1,idx2);
      for (i=AR.succ[idx2]; i<N; i=AR.succ[i]) {
        if (D_(idx1,i) < min) {
          min = D_(idx1,i);
          idx2 = i;
        }
      }
    }  // a: idx1   b: idx2
    else {
      NN_chain_tip -= 3;
      idx1 = NN_chain[NN_chain_tip-1];
      idx2 = NN_chain[NN_chain_tip];
      min = idx1<idx2 ? D_(idx1,idx2) : D_(idx2,idx1);
    }  // a: idx1   b: idx2

    do {
      NN_chain[NN_chain_tip] = idx2;

      for (i=AR.start; i<idx2; i=AR.succ[i]) {
        if (D_(i,idx2) < min) {
          min = D_(i,idx2);
          idx1 = i;
        }
      }
      for (i=AR.succ[idx2]; i<N; i=AR.succ[i]) {
        if (D_(idx2,i) < min) {
          min = D_(idx2,i);
          idx1 = i;
        }
      }

      idx2 = idx1;
      idx1 = NN_chain[NN_chain_tip++];

    } while (idx2 != NN_chain[NN_chain_tip-2]);

    Z2.append(idx1, idx2, min);

    if (idx1>idx2) {
      t_index tmp = idx1;
      idx1 = idx2;
      idx2 = tmp;
    }

    if (method==METHOD_METR_AVERAGE ||
        method==METHOD_METR_WARD) {
      size1 = static_cast<t_float>(members[idx1]);
      size2 = static_cast<t_float>(members[idx2]);
      members[idx2] += members[idx1];
    }

    // Remove the smaller index from the valid indices (AR).
    AR.remove(idx1);

    switch (method) {
    case METHOD_METR_SINGLE:
      /*
      Single linkage.

      Characteristic: new distances are never longer than the old distances.
      */
      // Update the distance matrix in the range [start, idx1).
      for (i=AR.start; i<idx1; i=AR.succ[i])
        f_single(&D_(i, idx2), D_(i, idx1) );
      // Update the distance matrix in the range (idx1, idx2).
      for (; i<idx2; i=AR.succ[i])
        f_single(&D_(i, idx2), D_(idx1, i) );
      // Update the distance matrix in the range (idx2, N).
      for (i=AR.succ[idx2]; i<N; i=AR.succ[i])
        f_single(&D_(idx2, i), D_(idx1, i) );
      break;

    case METHOD_METR_COMPLETE:
      /*
      Complete linkage.

      Characteristic: new distances are never shorter than the old distances.
      */
      // Update the distance matrix in the range [start, idx1).
      for (i=AR.start; i<idx1; i=AR.succ[i])
        f_complete(&D_(i, idx2), D_(i, idx1) );
      // Update the distance matrix in the range (idx1, idx2).
      for (; i<idx2; i=AR.succ[i])
        f_complete(&D_(i, idx2), D_(idx1, i) );
      // Update the distance matrix in the range (idx2, N).
      for (i=AR.succ[idx2]; i<N; i=AR.succ[i])
        f_complete(&D_(idx2, i), D_(idx1, i) );
      break;

    case METHOD_METR_AVERAGE: {
      /*
      Average linkage.

      Shorter and longer distances can occur.
      */
      // Update the distance matrix in the range [start, idx1).
      t_float s = size1/(size1+size2);
      t_float t = size2/(size1+size2);
      for (i=AR.start; i<idx1; i=AR.succ[i])
        f_average(&D_(i, idx2), D_(i, idx1), s, t );
      // Update the distance matrix in the range (idx1, idx2).
      for (; i<idx2; i=AR.succ[i])
        f_average(&D_(i, idx2), D_(idx1, i), s, t );
      // Update the distance matrix in the range (idx2, N).
      for (i=AR.succ[idx2]; i<N; i=AR.succ[i])
        f_average(&D_(idx2, i), D_(idx1, i), s, t );
      break;
    }

    case METHOD_METR_WEIGHTED:
      /*
      Weighted linkage.

      Shorter and longer distances can occur.
      */
      // Update the distance matrix in the range [start, idx1).
      for (i=AR.start; i<idx1; i=AR.succ[i])
        f_weighted(&D_(i, idx2), D_(i, idx1) );
      // Update the distance matrix in the range (idx1, idx2).
      for (; i<idx2; i=AR.succ[i])
        f_weighted(&D_(i, idx2), D_(idx1, i) );
      // Update the distance matrix in the range (idx2, N).
      for (i=AR.succ[idx2]; i<N; i=AR.succ[i])
        f_weighted(&D_(idx2, i), D_(idx1, i) );
      break;

    case METHOD_METR_WARD:
      /*
      Ward linkage.

      Shorter and longer distances can occur, not smaller than min(d1,d2)
      but maybe bigger than max(d1,d2).
      */
      // Update the distance matrix in the range [start, idx1).
      //t_float v = static_cast<t_float>(members[i]);
      for (i=AR.start; i<idx1; i=AR.succ[i])
        f_ward(&D_(i, idx2), D_(i, idx1), min,
               size1, size2, static_cast<t_float>(members[i]) );
      // Update the distance matrix in the range (idx1, idx2).
      for (; i<idx2; i=AR.succ[i])
        f_ward(&D_(i, idx2), D_(idx1, i), min,
               size1, size2, static_cast<t_float>(members[i]) );
      // Update the distance matrix in the range (idx2, N).
      for (i=AR.succ[idx2]; i<N; i=AR.succ[i])
        f_ward(&D_(idx2, i), D_(idx1, i), min,
               size1, size2, static_cast<t_float>(members[i]) );
      break;
    }
  }
}
Exemple #2
0
static void NN_chain_core(const t_index N, t_float * const D, t_members * const members, cluster_result & Z2) {
/*
    N: integer
    D: condensed distance matrix N*(N-1)/2
    Z2: output data structure

    This is the NN-chain algorithm, described on page 86 in the following book:

    Fionn Murtagh, Multidimensional Clustering Algorithms,
    Vienna, Würzburg: Physica-Verlag, 1985.
*/
  t_index i;

  auto_array_ptr<t_index> NN_chain(N);
  t_index NN_chain_tip = 0;

  t_index idx1, idx2;

  t_float size1, size2;
  doubly_linked_list active_nodes(N);

  t_float min;

  for (t_float const * DD=D; DD!=D+(static_cast<std::ptrdiff_t>(N)*(N-1)>>1);
       ++DD) {
#if HAVE_DIAGNOSTIC
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Wfloat-equal"
#endif
    if (fc_isnan(*DD)) {
      throw(nan_error());
    }
#if HAVE_DIAGNOSTIC
#pragma GCC diagnostic pop
#endif
  }

  #ifdef FE_INVALID
  if (feclearexcept(FE_INVALID)) throw fenv_error();
  #endif

  for (t_index j=0; j<N-1; ++j) {
    if (NN_chain_tip <= 3) {
      NN_chain[0] = idx1 = active_nodes.start;
      NN_chain_tip = 1;

      idx2 = active_nodes.succ[idx1];
      min = D_(idx1,idx2);
      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i]) {
        if (D_(idx1,i) < min) {
          min = D_(idx1,i);
          idx2 = i;
        }
      }
    }  // a: idx1   b: idx2
    else {
      NN_chain_tip -= 3;
      idx1 = NN_chain[NN_chain_tip-1];
      idx2 = NN_chain[NN_chain_tip];
      min = idx1<idx2 ? D_(idx1,idx2) : D_(idx2,idx1);
    }  // a: idx1   b: idx2

    do {
      NN_chain[NN_chain_tip] = idx2;

      for (i=active_nodes.start; i<idx2; i=active_nodes.succ[i]) {
        if (D_(i,idx2) < min) {
          min = D_(i,idx2);
          idx1 = i;
        }
      }
      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i]) {
        if (D_(idx2,i) < min) {
          min = D_(idx2,i);
          idx1 = i;
        }
      }

      idx2 = idx1;
      idx1 = NN_chain[NN_chain_tip++];

    } while (idx2 != NN_chain[NN_chain_tip-2]);

    Z2.append(idx1, idx2, min);

    if (idx1>idx2) {
      t_index tmp = idx1;
      idx1 = idx2;
      idx2 = tmp;
    }

    if (method==METHOD_METR_AVERAGE ||
        method==METHOD_METR_WARD) {
      size1 = static_cast<t_float>(members[idx1]);
      size2 = static_cast<t_float>(members[idx2]);
      members[idx2] += members[idx1];
    }

    // Remove the smaller index from the valid indices (active_nodes).
    active_nodes.remove(idx1);

    switch (method) {
    case METHOD_METR_SINGLE:
      /*
      Single linkage.

      Characteristic: new distances are never longer than the old distances.
      */
      // Update the distance matrix in the range [start, idx1).
      for (i=active_nodes.start; i<idx1; i=active_nodes.succ[i])
        f_single(&D_(i, idx2), D_(i, idx1) );
      // Update the distance matrix in the range (idx1, idx2).
      for (; i<idx2; i=active_nodes.succ[i])
        f_single(&D_(i, idx2), D_(idx1, i) );
      // Update the distance matrix in the range (idx2, N).
      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i])
        f_single(&D_(idx2, i), D_(idx1, i) );
      break;

    case METHOD_METR_COMPLETE:
      /*
      Complete linkage.

      Characteristic: new distances are never shorter than the old distances.
      */
      // Update the distance matrix in the range [start, idx1).
      for (i=active_nodes.start; i<idx1; i=active_nodes.succ[i])
        f_complete(&D_(i, idx2), D_(i, idx1) );
      // Update the distance matrix in the range (idx1, idx2).
      for (; i<idx2; i=active_nodes.succ[i])
        f_complete(&D_(i, idx2), D_(idx1, i) );
      // Update the distance matrix in the range (idx2, N).
      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i])
        f_complete(&D_(idx2, i), D_(idx1, i) );
      break;

    case METHOD_METR_AVERAGE: {
      /*
      Average linkage.

      Shorter and longer distances can occur.
      */
      // Update the distance matrix in the range [start, idx1).
      t_float s = size1/(size1+size2);
      t_float t = size2/(size1+size2);
      for (i=active_nodes.start; i<idx1; i=active_nodes.succ[i])
        f_average(&D_(i, idx2), D_(i, idx1), s, t );
      // Update the distance matrix in the range (idx1, idx2).
      for (; i<idx2; i=active_nodes.succ[i])
        f_average(&D_(i, idx2), D_(idx1, i), s, t );
      // Update the distance matrix in the range (idx2, N).
      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i])
        f_average(&D_(idx2, i), D_(idx1, i), s, t );
      break;
    }

    case METHOD_METR_WEIGHTED:
      /*
      Weighted linkage.

      Shorter and longer distances can occur.
      */
      // Update the distance matrix in the range [start, idx1).
      for (i=active_nodes.start; i<idx1; i=active_nodes.succ[i])
        f_weighted(&D_(i, idx2), D_(i, idx1) );
      // Update the distance matrix in the range (idx1, idx2).
      for (; i<idx2; i=active_nodes.succ[i])
        f_weighted(&D_(i, idx2), D_(idx1, i) );
      // Update the distance matrix in the range (idx2, N).
      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i])
        f_weighted(&D_(idx2, i), D_(idx1, i) );
      break;

    case METHOD_METR_WARD:
      /*
      Ward linkage.

      Shorter and longer distances can occur, not smaller than min(d1,d2)
      but maybe bigger than max(d1,d2).
      */
      // Update the distance matrix in the range [start, idx1).
      //t_float v = static_cast<t_float>(members[i]);
      for (i=active_nodes.start; i<idx1; i=active_nodes.succ[i])
        f_ward(&D_(i, idx2), D_(i, idx1), min,
               size1, size2, static_cast<t_float>(members[i]) );
      // Update the distance matrix in the range (idx1, idx2).
      for (; i<idx2; i=active_nodes.succ[i])
        f_ward(&D_(i, idx2), D_(idx1, i), min,
               size1, size2, static_cast<t_float>(members[i]) );
      // Update the distance matrix in the range (idx2, N).
      for (i=active_nodes.succ[idx2]; i<N; i=active_nodes.succ[i])
        f_ward(&D_(idx2, i), D_(idx1, i), min,
               size1, size2, static_cast<t_float>(members[i]) );
      break;

    default:
      throw std::runtime_error(std::string("Invalid method."));
    }
  }
  #ifdef FE_INVALID
  if (fetestexcept(FE_INVALID)) throw fenv_error();
  #endif
}