sequenzo 0.1.18__cp310-cp310-macosx_10_9_universal2.whl → 0.1.20__cp310-cp310-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/OrderingMethods/Amd.h

@@ -1,435 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2010 Gael Guennebaud <gael.guennebaud@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-/*
-NOTE: this routine has been adapted from the CSparse library:
-
-Copyright (c) 2006, Timothy A. Davis.
-http://www.suitesparse.com
-
-The author of CSparse, Timothy A. Davis., has executed a license with Google LLC
-to permit distribution of this code and derivative works as part of Eigen under
-the Mozilla Public License v. 2.0, as stated at the top of this file.
-*/
-
-#ifndef EIGEN_SPARSE_AMD_H
-#define EIGEN_SPARSE_AMD_H
-
-namespace Eigen { 
-
-namespace internal {
-  
-template<typename T> inline T amd_flip(const T& i) { return -i-2; }
-template<typename T> inline T amd_unflip(const T& i) { return i<0 ? amd_flip(i) : i; }
-template<typename T0, typename T1> inline bool amd_marked(const T0* w, const T1& j) { return w[j]<0; }
-template<typename T0, typename T1> inline void amd_mark(const T0* w, const T1& j) { return w[j] = amd_flip(w[j]); }
-
-/* clear w */
-template<typename StorageIndex>
-static StorageIndex cs_wclear (StorageIndex mark, StorageIndex lemax, StorageIndex *w, StorageIndex n)
-{
-  StorageIndex k;
-  if(mark < 2 || (mark + lemax < 0))
-  {
-    for(k = 0; k < n; k++)
-      if(w[k] != 0)
-        w[k] = 1;
-    mark = 2;
-  }
-  return (mark);     /* at this point, w[0..n-1] < mark holds */
-}
-
-/* depth-first search and postorder of a tree rooted at node j */
-template<typename StorageIndex>
-StorageIndex cs_tdfs(StorageIndex j, StorageIndex k, StorageIndex *head, const StorageIndex *next, StorageIndex *post, StorageIndex *stack)
-{
-  StorageIndex i, p, top = 0;
-  if(!head || !next || !post || !stack) return (-1);    /* check inputs */
-  stack[0] = j;                 /* place j on the stack */
-  while (top >= 0)                /* while (stack is not empty) */
-  {
-    p = stack[top];           /* p = top of stack */
-    i = head[p];              /* i = youngest child of p */
-    if(i == -1)
-    {
-      top--;                 /* p has no unordered children left */
-      post[k++] = p;        /* node p is the kth postordered node */
-    }
-    else
-    {
-      head[p] = next[i];   /* remove i from children of p */
-      stack[++top] = i;     /* start dfs on child node i */
-    }
-  }
-  return k;
-}
-
-
-/** \internal
-  * \ingroup OrderingMethods_Module 
-  * Approximate minimum degree ordering algorithm.
-  *
-  * \param[in] C the input selfadjoint matrix stored in compressed column major format.
-  * \param[out] perm the permutation P reducing the fill-in of the input matrix \a C
-  *
-  * Note that the input matrix \a C must be complete, that is both the upper and lower parts have to be stored, as well as the diagonal entries.
-  * On exit the values of C are destroyed */
-template<typename Scalar, typename StorageIndex>
-void minimum_degree_ordering(SparseMatrix<Scalar,ColMajor,StorageIndex>& C, PermutationMatrix<Dynamic,Dynamic,StorageIndex>& perm)
-{
-  using std::sqrt;
-  
-  StorageIndex d, dk, dext, lemax = 0, e, elenk, eln, i, j, k, k1,
-                k2, k3, jlast, ln, dense, nzmax, mindeg = 0, nvi, nvj, nvk, mark, wnvi,
-                ok, nel = 0, p, p1, p2, p3, p4, pj, pk, pk1, pk2, pn, q, t, h;
-  
-  StorageIndex n = StorageIndex(C.cols());
-  dense = std::max<StorageIndex> (16, StorageIndex(10 * sqrt(double(n))));   /* find dense threshold */
-  dense = (std::min)(n-2, dense);
-  
-  StorageIndex cnz = StorageIndex(C.nonZeros());
-  perm.resize(n+1);
-  t = cnz + cnz/5 + 2*n;                 /* add elbow room to C */
-  C.resizeNonZeros(t);
-  
-  // get workspace
-  ei_declare_aligned_stack_constructed_variable(StorageIndex,W,8*(n+1),0);
-  StorageIndex* len     = W;
-  StorageIndex* nv      = W +   (n+1);
-  StorageIndex* next    = W + 2*(n+1);
-  StorageIndex* head    = W + 3*(n+1);
-  StorageIndex* elen    = W + 4*(n+1);
-  StorageIndex* degree  = W + 5*(n+1);
-  StorageIndex* w       = W + 6*(n+1);
-  StorageIndex* hhead   = W + 7*(n+1);
-  StorageIndex* last    = perm.indices().data();                              /* use P as workspace for last */
-  
-  /* --- Initialize quotient graph ---------------------------------------- */
-  StorageIndex* Cp = C.outerIndexPtr();
-  StorageIndex* Ci = C.innerIndexPtr();
-  for(k = 0; k < n; k++)
-    len[k] = Cp[k+1] - Cp[k];
-  len[n] = 0;
-  nzmax = t;
-  
-  for(i = 0; i <= n; i++)
-  {
-    head[i]   = -1;                     // degree list i is empty
-    last[i]   = -1;
-    next[i]   = -1;
-    hhead[i]  = -1;                     // hash list i is empty 
-    nv[i]     = 1;                      // node i is just one node
-    w[i]      = 1;                      // node i is alive
-    elen[i]   = 0;                      // Ek of node i is empty
-    degree[i] = len[i];                 // degree of node i
-  }
-  mark = internal::cs_wclear<StorageIndex>(0, 0, w, n);         /* clear w */
-  
-  /* --- Initialize degree lists ------------------------------------------ */
-  for(i = 0; i < n; i++)
-  {
-    bool has_diag = false;
-    for(p = Cp[i]; p<Cp[i+1]; ++p)
-      if(Ci[p]==i)
-      {
-        has_diag = true;
-        break;
-      }
-   
-    d = degree[i];
-    if(d == 1 && has_diag)           /* node i is empty */
-    {
-      elen[i] = -2;                 /* element i is dead */
-      nel++;
-      Cp[i] = -1;                   /* i is a root of assembly tree */
-      w[i] = 0;
-    }
-    else if(d > dense || !has_diag)  /* node i is dense or has no structural diagonal element */
-    {
-      nv[i] = 0;                    /* absorb i into element n */
-      elen[i] = -1;                 /* node i is dead */
-      nel++;
-      Cp[i] = amd_flip (n);
-      nv[n]++;
-    }
-    else
-    {
-      if(head[d] != -1) last[head[d]] = i;
-      next[i] = head[d];           /* put node i in degree list d */
-      head[d] = i;
-    }
-  }
-  
-  elen[n] = -2;                         /* n is a dead element */
-  Cp[n] = -1;                           /* n is a root of assembly tree */
-  w[n] = 0;                             /* n is a dead element */
-  
-  while (nel < n)                         /* while (selecting pivots) do */
-  {
-    /* --- Select node of minimum approximate degree -------------------- */
-    for(k = -1; mindeg < n && (k = head[mindeg]) == -1; mindeg++) {}
-    if(next[k] != -1) last[next[k]] = -1;
-    head[mindeg] = next[k];          /* remove k from degree list */
-    elenk = elen[k];                  /* elenk = |Ek| */
-    nvk = nv[k];                      /* # of nodes k represents */
-    nel += nvk;                        /* nv[k] nodes of A eliminated */
-    
-    /* --- Garbage collection ------------------------------------------- */
-    if(elenk > 0 && cnz + mindeg >= nzmax)
-    {
-      for(j = 0; j < n; j++)
-      {
-        if((p = Cp[j]) >= 0)      /* j is a live node or element */
-        {
-          Cp[j] = Ci[p];          /* save first entry of object */
-          Ci[p] = amd_flip (j);    /* first entry is now amd_flip(j) */
-        }
-      }
-      for(q = 0, p = 0; p < cnz; ) /* scan all of memory */
-      {
-        if((j = amd_flip (Ci[p++])) >= 0)  /* found object j */
-        {
-          Ci[q] = Cp[j];       /* restore first entry of object */
-          Cp[j] = q++;          /* new pointer to object j */
-          for(k3 = 0; k3 < len[j]-1; k3++) Ci[q++] = Ci[p++];
-        }
-      }
-      cnz = q;                       /* Ci[cnz...nzmax-1] now free */
-    }
-    
-    /* --- Construct new element ---------------------------------------- */
-    dk = 0;
-    nv[k] = -nvk;                     /* flag k as in Lk */
-    p = Cp[k];
-    pk1 = (elenk == 0) ? p : cnz;      /* do in place if elen[k] == 0 */
-    pk2 = pk1;
-    for(k1 = 1; k1 <= elenk + 1; k1++)
-    {
-      if(k1 > elenk)
-      {
-        e = k;                     /* search the nodes in k */
-        pj = p;                    /* list of nodes starts at Ci[pj]*/
-        ln = len[k] - elenk;      /* length of list of nodes in k */
-      }
-      else
-      {
-        e = Ci[p++];              /* search the nodes in e */
-        pj = Cp[e];
-        ln = len[e];              /* length of list of nodes in e */
-      }
-      for(k2 = 1; k2 <= ln; k2++)
-      {
-        i = Ci[pj++];
-        if((nvi = nv[i]) <= 0) continue; /* node i dead, or seen */
-        dk += nvi;                 /* degree[Lk] += size of node i */
-        nv[i] = -nvi;             /* negate nv[i] to denote i in Lk*/
-        Ci[pk2++] = i;            /* place i in Lk */
-        if(next[i] != -1) last[next[i]] = last[i];
-        if(last[i] != -1)         /* remove i from degree list */
-        {
-          next[last[i]] = next[i];
-        }
-        else
-        {
-          head[degree[i]] = next[i];
-        }
-      }
-      if(e != k)
-      {
-        Cp[e] = amd_flip (k);      /* absorb e into k */
-        w[e] = 0;                 /* e is now a dead element */
-      }
-    }
-    if(elenk != 0) cnz = pk2;         /* Ci[cnz...nzmax] is free */
-    degree[k] = dk;                   /* external degree of k - |Lk\i| */
-    Cp[k] = pk1;                      /* element k is in Ci[pk1..pk2-1] */
-    len[k] = pk2 - pk1;
-    elen[k] = -2;                     /* k is now an element */
-    
-    /* --- Find set differences ----------------------------------------- */
-    mark = internal::cs_wclear<StorageIndex>(mark, lemax, w, n);  /* clear w if necessary */
-    for(pk = pk1; pk < pk2; pk++)    /* scan 1: find |Le\Lk| */
-    {
-      i = Ci[pk];
-      if((eln = elen[i]) <= 0) continue;/* skip if elen[i] empty */
-      nvi = -nv[i];                      /* nv[i] was negated */
-      wnvi = mark - nvi;
-      for(p = Cp[i]; p <= Cp[i] + eln - 1; p++)  /* scan Ei */
-      {
-        e = Ci[p];
-        if(w[e] >= mark)
-        {
-          w[e] -= nvi;          /* decrement |Le\Lk| */
-        }
-        else if(w[e] != 0)        /* ensure e is a live element */
-        {
-          w[e] = degree[e] + wnvi; /* 1st time e seen in scan 1 */
-        }
-      }
-    }
-    
-    /* --- Degree update ------------------------------------------------ */
-    for(pk = pk1; pk < pk2; pk++)    /* scan2: degree update */
-    {
-      i = Ci[pk];                   /* consider node i in Lk */
-      p1 = Cp[i];
-      p2 = p1 + elen[i] - 1;
-      pn = p1;
-      for(h = 0, d = 0, p = p1; p <= p2; p++)    /* scan Ei */
-      {
-        e = Ci[p];
-        if(w[e] != 0)             /* e is an unabsorbed element */
-        {
-          dext = w[e] - mark;   /* dext = |Le\Lk| */
-          if(dext > 0)
-          {
-            d += dext;         /* sum up the set differences */
-            Ci[pn++] = e;     /* keep e in Ei */
-            h += e;            /* compute the hash of node i */
-          }
-          else
-          {
-            Cp[e] = amd_flip (k);  /* aggressive absorb. e->k */
-            w[e] = 0;             /* e is a dead element */
-          }
-        }
-      }
-      elen[i] = pn - p1 + 1;        /* elen[i] = |Ei| */
-      p3 = pn;
-      p4 = p1 + len[i];
-      for(p = p2 + 1; p < p4; p++) /* prune edges in Ai */
-      {
-        j = Ci[p];
-        if((nvj = nv[j]) <= 0) continue; /* node j dead or in Lk */
-        d += nvj;                  /* degree(i) += |j| */
-        Ci[pn++] = j;             /* place j in node list of i */
-        h += j;                    /* compute hash for node i */
-      }
-      if(d == 0)                     /* check for mass elimination */
-      {
-        Cp[i] = amd_flip (k);      /* absorb i into k */
-        nvi = -nv[i];
-        dk -= nvi;                 /* |Lk| -= |i| */
-        nvk += nvi;                /* |k| += nv[i] */
-        nel += nvi;
-        nv[i] = 0;
-        elen[i] = -1;             /* node i is dead */
-      }
-      else
-      {
-        degree[i] = std::min<StorageIndex> (degree[i], d);   /* update degree(i) */
-        Ci[pn] = Ci[p3];         /* move first node to end */
-        Ci[p3] = Ci[p1];         /* move 1st el. to end of Ei */
-        Ci[p1] = k;               /* add k as 1st element in of Ei */
-        len[i] = pn - p1 + 1;     /* new len of adj. list of node i */
-        h %= n;                    /* finalize hash of i */
-        next[i] = hhead[h];      /* place i in hash bucket */
-        hhead[h] = i;
-        last[i] = h;      /* save hash of i in last[i] */
-      }
-    }                                   /* scan2 is done */
-    degree[k] = dk;                   /* finalize |Lk| */
-    lemax = std::max<StorageIndex>(lemax, dk);
-    mark = internal::cs_wclear<StorageIndex>(mark+lemax, lemax, w, n);    /* clear w */
-    
-    /* --- Supernode detection ------------------------------------------ */
-    for(pk = pk1; pk < pk2; pk++)
-    {
-      i = Ci[pk];
-      if(nv[i] >= 0) continue;         /* skip if i is dead */
-      h = last[i];                      /* scan hash bucket of node i */
-      i = hhead[h];
-      hhead[h] = -1;                    /* hash bucket will be empty */
-      for(; i != -1 && next[i] != -1; i = next[i], mark++)
-      {
-        ln = len[i];
-        eln = elen[i];
-        for(p = Cp[i]+1; p <= Cp[i] + ln-1; p++) w[Ci[p]] = mark;
-        jlast = i;
-        for(j = next[i]; j != -1; ) /* compare i with all j */
-        {
-          ok = (len[j] == ln) && (elen[j] == eln);
-          for(p = Cp[j] + 1; ok && p <= Cp[j] + ln - 1; p++)
-          {
-            if(w[Ci[p]] != mark) ok = 0;    /* compare i and j*/
-          }
-          if(ok)                     /* i and j are identical */
-          {
-            Cp[j] = amd_flip (i);  /* absorb j into i */
-            nv[i] += nv[j];
-            nv[j] = 0;
-            elen[j] = -1;         /* node j is dead */
-            j = next[j];          /* delete j from hash bucket */
-            next[jlast] = j;
-          }
-          else
-          {
-            jlast = j;             /* j and i are different */
-            j = next[j];
-          }
-        }
-      }
-    }
-    
-    /* --- Finalize new element------------------------------------------ */
-    for(p = pk1, pk = pk1; pk < pk2; pk++)   /* finalize Lk */
-    {
-      i = Ci[pk];
-      if((nvi = -nv[i]) <= 0) continue;/* skip if i is dead */
-      nv[i] = nvi;                      /* restore nv[i] */
-      d = degree[i] + dk - nvi;         /* compute external degree(i) */
-      d = std::min<StorageIndex> (d, n - nel - nvi);
-      if(head[d] != -1) last[head[d]] = i;
-      next[i] = head[d];               /* put i back in degree list */
-      last[i] = -1;
-      head[d] = i;
-      mindeg = std::min<StorageIndex> (mindeg, d);       /* find new minimum degree */
-      degree[i] = d;
-      Ci[p++] = i;                      /* place i in Lk */
-    }
-    nv[k] = nvk;                      /* # nodes absorbed into k */
-    if((len[k] = p-pk1) == 0)         /* length of adj list of element k*/
-    {
-      Cp[k] = -1;                   /* k is a root of the tree */
-      w[k] = 0;                     /* k is now a dead element */
-    }
-    if(elenk != 0) cnz = p;           /* free unused space in Lk */
-  }
-  
-  /* --- Postordering ----------------------------------------------------- */
-  for(i = 0; i < n; i++) Cp[i] = amd_flip (Cp[i]);/* fix assembly tree */
-  for(j = 0; j <= n; j++) head[j] = -1;
-  for(j = n; j >= 0; j--)              /* place unordered nodes in lists */
-  {
-    if(nv[j] > 0) continue;          /* skip if j is an element */
-    next[j] = head[Cp[j]];          /* place j in list of its parent */
-    head[Cp[j]] = j;
-  }
-  for(e = n; e >= 0; e--)              /* place elements in lists */
-  {
-    if(nv[e] <= 0) continue;         /* skip unless e is an element */
-    if(Cp[e] != -1)
-    {
-      next[e] = head[Cp[e]];      /* place e in list of its parent */
-      head[Cp[e]] = e;
-    }
-  }
-  for(k = 0, i = 0; i <= n; i++)       /* postorder the assembly tree */
-  {
-    if(Cp[i] == -1) k = internal::cs_tdfs<StorageIndex>(i, k, head, next, perm.indices().data(), w);
-  }
-  
-  perm.indices().conservativeResize(n);
-}
-
-} // namespace internal
-
-} // end namespace Eigen
-
-#endif // EIGEN_SPARSE_AMD_H