mathjs-min 11.7.2

package/lib/esm/function/algebra/sparse/csAmd.js

@@ -0,0 +1,581 @@
+import { factory } from '../../../utils/factory.js';
+import { csFkeep } from './csFkeep.js';
+import { csFlip } from './csFlip.js';
+import { csTdfs } from './csTdfs.js';
+var name = 'csAmd';
+var dependencies = ['add', 'multiply', 'transpose'];
+export var createCsAmd = /* #__PURE__ */factory(name, dependencies, _ref => {
+  var {
+    add,
+    multiply,
+    transpose
+  } = _ref;
+  /**
+   * Approximate minimum degree ordering. The minimum degree algorithm is a widely used
+   * heuristic for finding a permutation P so that P*A*P' has fewer nonzeros in its factorization
+   * than A. It is a gready method that selects the sparsest pivot row and column during the course
+   * of a right looking sparse Cholesky factorization.
+   *
+   * Reference: http://faculty.cse.tamu.edu/davis/publications.html
+   *
+   * @param {Number} order    0: Natural, 1: Cholesky, 2: LU, 3: QR
+   * @param {Matrix} m        Sparse Matrix
+   */
+  return function csAmd(order, a) {
+    // check input parameters
+    if (!a || order <= 0 || order > 3) {
+      return null;
+    }
+    // a matrix arrays
+    var asize = a._size;
+    // rows and columns
+    var m = asize[0];
+    var n = asize[1];
+    // initialize vars
+    var lemax = 0;
+    // dense threshold
+    var dense = Math.max(16, 10 * Math.sqrt(n));
+    dense = Math.min(n - 2, dense);
+    // create target matrix C
+    var cm = _createTargetMatrix(order, a, m, n, dense);
+    // drop diagonal entries
+    csFkeep(cm, _diag, null);
+    // C matrix arrays
+    var cindex = cm._index;
+    var cptr = cm._ptr;
+
+    // number of nonzero elements in C
+    var cnz = cptr[n];
+
+    // allocate result (n+1)
+    var P = [];
+
+    // create workspace (8 * (n + 1))
+    var W = [];
+    var len = 0; // first n + 1 entries
+    var nv = n + 1; // next n + 1 entries
+    var next = 2 * (n + 1); // next n + 1 entries
+    var head = 3 * (n + 1); // next n + 1 entries
+    var elen = 4 * (n + 1); // next n + 1 entries
+    var degree = 5 * (n + 1); // next n + 1 entries
+    var w = 6 * (n + 1); // next n + 1 entries
+    var hhead = 7 * (n + 1); // last n + 1 entries
+
+    // use P as workspace for last
+    var last = P;
+
+    // initialize quotient graph
+    var mark = _initializeQuotientGraph(n, cptr, W, len, head, last, next, hhead, nv, w, elen, degree);
+
+    // initialize degree lists
+    var nel = _initializeDegreeLists(n, cptr, W, degree, elen, w, dense, nv, head, last, next);
+
+    // minimum degree node
+    var mindeg = 0;
+
+    // vars
+    var i, j, k, k1, k2, e, pj, ln, nvi, pk, eln, p1, p2, pn, h, d;
+
+    // while (selecting pivots) do
+    while (nel < n) {
+      // select node of minimum approximate degree. amd() is now ready to start eliminating the graph. It first
+      // finds a node k of minimum degree and removes it from its degree list. The variable nel keeps track of thow
+      // many nodes have been eliminated.
+      for (k = -1; mindeg < n && (k = W[head + mindeg]) === -1; mindeg++) {
+        ;
+      }
+      if (W[next + k] !== -1) {
+        last[W[next + k]] = -1;
+      }
+      // remove k from degree list
+      W[head + mindeg] = W[next + k];
+      // elenk = |Ek|
+      var elenk = W[elen + k];
+      // # of nodes k represents
+      var nvk = W[nv + k];
+      // W[nv + k] nodes of A eliminated
+      nel += nvk;
+
+      // Construct a new element. The new element Lk is constructed in place if |Ek| = 0. nv[i] is
+      // negated for all nodes i in Lk to flag them as members of this set. Each node i is removed from the
+      // degree lists. All elements e in Ek are absorved into element k.
+      var dk = 0;
+      // flag k as in Lk
+      W[nv + k] = -nvk;
+      var p = cptr[k];
+      // do in place if W[elen + k] === 0
+      var pk1 = elenk === 0 ? p : cnz;
+      var pk2 = pk1;
+      for (k1 = 1; k1 <= elenk + 1; k1++) {
+        if (k1 > elenk) {
+          // search the nodes in k
+          e = k;
+          // list of nodes starts at cindex[pj]
+          pj = p;
+          // length of list of nodes in k
+          ln = W[len + k] - elenk;
+        } else {
+          // search the nodes in e
+          e = cindex[p++];
+          pj = cptr[e];
+          // length of list of nodes in e
+          ln = W[len + e];
+        }
+        for (k2 = 1; k2 <= ln; k2++) {
+          i = cindex[pj++];
+          // check  node i dead, or seen
+          if ((nvi = W[nv + i]) <= 0) {
+            continue;
+          }
+          // W[degree + Lk] += size of node i
+          dk += nvi;
+          // negate W[nv + i] to denote i in Lk
+          W[nv + i] = -nvi;
+          // place i in Lk
+          cindex[pk2++] = i;
+          if (W[next + i] !== -1) {
+            last[W[next + i]] = last[i];
+          }
+          // check we need to remove i from degree list
+          if (last[i] !== -1) {
+            W[next + last[i]] = W[next + i];
+          } else {
+            W[head + W[degree + i]] = W[next + i];
+          }
+        }
+        if (e !== k) {
+          // absorb e into k
+          cptr[e] = csFlip(k);
+          // e is now a dead element
+          W[w + e] = 0;
+        }
+      }
+      // cindex[cnz...nzmax] is free
+      if (elenk !== 0) {
+        cnz = pk2;
+      }
+      // external degree of k - |Lk\i|
+      W[degree + k] = dk;
+      // element k is in cindex[pk1..pk2-1]
+      cptr[k] = pk1;
+      W[len + k] = pk2 - pk1;
+      // k is now an element
+      W[elen + k] = -2;
+
+      // Find set differences. The scan1 function now computes the set differences |Le \ Lk| for all elements e. At the start of the
+      // scan, no entry in the w array is greater than or equal to mark.
+
+      // clear w if necessary
+      mark = _wclear(mark, lemax, W, w, n);
+      // scan 1: find |Le\Lk|
+      for (pk = pk1; pk < pk2; pk++) {
+        i = cindex[pk];
+        // check if W[elen + i] empty, skip it
+        if ((eln = W[elen + i]) <= 0) {
+          continue;
+        }
+        // W[nv + i] was negated
+        nvi = -W[nv + i];
+        var wnvi = mark - nvi;
+        // scan Ei
+        for (p = cptr[i], p1 = cptr[i] + eln - 1; p <= p1; p++) {
+          e = cindex[p];
+          if (W[w + e] >= mark) {
+            // decrement |Le\Lk|
+            W[w + e] -= nvi;
+          } else if (W[w + e] !== 0) {
+            // ensure e is a live element, 1st time e seen in scan 1
+            W[w + e] = W[degree + e] + wnvi;
+          }
+        }
+      }
+
+      // degree update
+      // The second pass computes the approximate degree di, prunes the sets Ei and Ai, and computes a hash
+      // function h(i) for all nodes in Lk.
+
+      // scan2: degree update
+      for (pk = pk1; pk < pk2; pk++) {
+        // consider node i in Lk
+        i = cindex[pk];
+        p1 = cptr[i];
+        p2 = p1 + W[elen + i] - 1;
+        pn = p1;
+        // scan Ei
+        for (h = 0, d = 0, p = p1; p <= p2; p++) {
+          e = cindex[p];
+          // check e is an unabsorbed element
+          if (W[w + e] !== 0) {
+            // dext = |Le\Lk|
+            var dext = W[w + e] - mark;
+            if (dext > 0) {
+              // sum up the set differences
+              d += dext;
+              // keep e in Ei
+              cindex[pn++] = e;
+              // compute the hash of node i
+              h += e;
+            } else {
+              // aggressive absorb. e->k
+              cptr[e] = csFlip(k);
+              // e is a dead element
+              W[w + e] = 0;
+            }
+          }
+        }
+        // W[elen + i] = |Ei|
+        W[elen + i] = pn - p1 + 1;
+        var p3 = pn;
+        var p4 = p1 + W[len + i];
+        // prune edges in Ai
+        for (p = p2 + 1; p < p4; p++) {
+          j = cindex[p];
+          // check node j dead or in Lk
+          var nvj = W[nv + j];
+          if (nvj <= 0) {
+            continue;
+          }
+          // degree(i) += |j|
+          d += nvj;
+          // place j in node list of i
+          cindex[pn++] = j;
+          // compute hash for node i
+          h += j;
+        }
+        // check for mass elimination
+        if (d === 0) {
+          // absorb i into k
+          cptr[i] = csFlip(k);
+          nvi = -W[nv + i];
+          // |Lk| -= |i|
+          dk -= nvi;
+          // |k| += W[nv + i]
+          nvk += nvi;
+          nel += nvi;
+          W[nv + i] = 0;
+          // node i is dead
+          W[elen + i] = -1;
+        } else {
+          // update degree(i)
+          W[degree + i] = Math.min(W[degree + i], d);
+          // move first node to end
+          cindex[pn] = cindex[p3];
+          // move 1st el. to end of Ei
+          cindex[p3] = cindex[p1];
+          // add k as 1st element in of Ei
+          cindex[p1] = k;
+          // new len of adj. list of node i
+          W[len + i] = pn - p1 + 1;
+          // finalize hash of i
+          h = (h < 0 ? -h : h) % n;
+          // place i in hash bucket
+          W[next + i] = W[hhead + h];
+          W[hhead + h] = i;
+          // save hash of i in last[i]
+          last[i] = h;
+        }
+      }
+      // finalize |Lk|
+      W[degree + k] = dk;
+      lemax = Math.max(lemax, dk);
+      // clear w
+      mark = _wclear(mark + lemax, lemax, W, w, n);
+
+      // Supernode detection. Supernode detection relies on the hash function h(i) computed for each node i.
+      // If two nodes have identical adjacency lists, their hash functions wil be identical.
+      for (pk = pk1; pk < pk2; pk++) {
+        i = cindex[pk];
+        // check i is dead, skip it
+        if (W[nv + i] >= 0) {
+          continue;
+        }
+        // scan hash bucket of node i
+        h = last[i];
+        i = W[hhead + h];
+        // hash bucket will be empty
+        W[hhead + h] = -1;
+        for (; i !== -1 && W[next + i] !== -1; i = W[next + i], mark++) {
+          ln = W[len + i];
+          eln = W[elen + i];
+          for (p = cptr[i] + 1; p <= cptr[i] + ln - 1; p++) {
+            W[w + cindex[p]] = mark;
+          }
+          var jlast = i;
+          // compare i with all j
+          for (j = W[next + i]; j !== -1;) {
+            var ok = W[len + j] === ln && W[elen + j] === eln;
+            for (p = cptr[j] + 1; ok && p <= cptr[j] + ln - 1; p++) {
+              // compare i and j
+              if (W[w + cindex[p]] !== mark) {
+                ok = 0;
+              }
+            }
+            // check i and j are identical
+            if (ok) {
+              // absorb j into i
+              cptr[j] = csFlip(i);
+              W[nv + i] += W[nv + j];
+              W[nv + j] = 0;
+              // node j is dead
+              W[elen + j] = -1;
+              // delete j from hash bucket
+              j = W[next + j];
+              W[next + jlast] = j;
+            } else {
+              // j and i are different
+              jlast = j;
+              j = W[next + j];
+            }
+          }
+        }
+      }
+
+      // Finalize new element. The elimination of node k is nearly complete. All nodes i in Lk are scanned one last time.
+      // Node i is removed from Lk if it is dead. The flagged status of nv[i] is cleared.
+      for (p = pk1, pk = pk1; pk < pk2; pk++) {
+        i = cindex[pk];
+        // check  i is dead, skip it
+        if ((nvi = -W[nv + i]) <= 0) {
+          continue;
+        }
+        // restore W[nv + i]
+        W[nv + i] = nvi;
+        // compute external degree(i)
+        d = W[degree + i] + dk - nvi;
+        d = Math.min(d, n - nel - nvi);
+        if (W[head + d] !== -1) {
+          last[W[head + d]] = i;
+        }
+        // put i back in degree list
+        W[next + i] = W[head + d];
+        last[i] = -1;
+        W[head + d] = i;
+        // find new minimum degree
+        mindeg = Math.min(mindeg, d);
+        W[degree + i] = d;
+        // place i in Lk
+        cindex[p++] = i;
+      }
+      // # nodes absorbed into k
+      W[nv + k] = nvk;
+      // length of adj list of element k
+      if ((W[len + k] = p - pk1) === 0) {
+        // k is a root of the tree
+        cptr[k] = -1;
+        // k is now a dead element
+        W[w + k] = 0;
+      }
+      if (elenk !== 0) {
+        // free unused space in Lk
+        cnz = p;
+      }
+    }
+
+    // Postordering. The elimination is complete, but no permutation has been computed. All that is left
+    // of the graph is the assembly tree (ptr) and a set of dead nodes and elements (i is a dead node if
+    // nv[i] is zero and a dead element if nv[i] > 0). It is from this information only that the final permutation
+    // is computed. The tree is restored by unflipping all of ptr.
+
+    // fix assembly tree
+    for (i = 0; i < n; i++) {
+      cptr[i] = csFlip(cptr[i]);
+    }
+    for (j = 0; j <= n; j++) {
+      W[head + j] = -1;
+    }
+    // place unordered nodes in lists
+    for (j = n; j >= 0; j--) {
+      // skip if j is an element
+      if (W[nv + j] > 0) {
+        continue;
+      }
+      // place j in list of its parent
+      W[next + j] = W[head + cptr[j]];
+      W[head + cptr[j]] = j;
+    }
+    // place elements in lists
+    for (e = n; e >= 0; e--) {
+      // skip unless e is an element
+      if (W[nv + e] <= 0) {
+        continue;
+      }
+      if (cptr[e] !== -1) {
+        // place e in list of its parent
+        W[next + e] = W[head + cptr[e]];
+        W[head + cptr[e]] = e;
+      }
+    }
+    // postorder the assembly tree
+    for (k = 0, i = 0; i <= n; i++) {
+      if (cptr[i] === -1) {
+        k = csTdfs(i, k, W, head, next, P, w);
+      }
+    }
+    // remove last item in array
+    P.splice(P.length - 1, 1);
+    // return P
+    return P;
+  };
+
+  /**
+   * Creates the matrix that will be used by the approximate minimum degree ordering algorithm. The function accepts the matrix M as input and returns a permutation
+   * vector P. The amd algorithm operates on a symmetrix matrix, so one of three symmetric matrices is formed.
+   *
+   * Order: 0
+   *   A natural ordering P=null matrix is returned.
+   *
+   * Order: 1
+   *   Matrix must be square. This is appropriate for a Cholesky or LU factorization.
+   *   P = M + M'
+   *
+   * Order: 2
+   *   Dense columns from M' are dropped, M recreated from M'. This is appropriatefor LU factorization of unsymmetric matrices.
+   *   P = M' * M
+   *
+   * Order: 3
+   *   This is best used for QR factorization or LU factorization is matrix M has no dense rows. A dense row is a row with more than 10*sqr(columns) entries.
+   *   P = M' * M
+   */
+  function _createTargetMatrix(order, a, m, n, dense) {
+    // compute A'
+    var at = transpose(a);
+
+    // check order = 1, matrix must be square
+    if (order === 1 && n === m) {
+      // C = A + A'
+      return add(a, at);
+    }
+
+    // check order = 2, drop dense columns from M'
+    if (order === 2) {
+      // transpose arrays
+      var tindex = at._index;
+      var tptr = at._ptr;
+      // new column index
+      var p2 = 0;
+      // loop A' columns (rows)
+      for (var j = 0; j < m; j++) {
+        // column j of AT starts here
+        var p = tptr[j];
+        // new column j starts here
+        tptr[j] = p2;
+        // skip dense col j
+        if (tptr[j + 1] - p > dense) {
+          continue;
+        }
+        // map rows in column j of A
+        for (var p1 = tptr[j + 1]; p < p1; p++) {
+          tindex[p2++] = tindex[p];
+        }
+      }
+      // finalize AT
+      tptr[m] = p2;
+      // recreate A from new transpose matrix
+      a = transpose(at);
+      // use A' * A
+      return multiply(at, a);
+    }
+
+    // use A' * A, square or rectangular matrix
+    return multiply(at, a);
+  }
+
+  /**
+   * Initialize quotient graph. There are four kind of nodes and elements that must be represented:
+   *
+   *  - A live node is a node i (or a supernode) that has not been selected as a pivot nad has not been merged into another supernode.
+   *  - A dead node i is one that has been removed from the graph, having been absorved into r = flip(ptr[i]).
+   *  - A live element e is one that is in the graph, having been formed when node e was selected as the pivot.
+   *  - A dead element e is one that has benn absorved into a subsequent element s = flip(ptr[e]).
+   */
+  function _initializeQuotientGraph(n, cptr, W, len, head, last, next, hhead, nv, w, elen, degree) {
+    // Initialize quotient graph
+    for (var k = 0; k < n; k++) {
+      W[len + k] = cptr[k + 1] - cptr[k];
+    }
+    W[len + n] = 0;
+    // initialize workspace
+    for (var i = 0; i <= n; i++) {
+      // degree list i is empty
+      W[head + i] = -1;
+      last[i] = -1;
+      W[next + i] = -1;
+      // hash list i is empty
+      W[hhead + i] = -1;
+      // node i is just one node
+      W[nv + i] = 1;
+      // node i is alive
+      W[w + i] = 1;
+      // Ek of node i is empty
+      W[elen + i] = 0;
+      // degree of node i
+      W[degree + i] = W[len + i];
+    }
+    // clear w
+    var mark = _wclear(0, 0, W, w, n);
+    // n is a dead element
+    W[elen + n] = -2;
+    // n is a root of assembly tree
+    cptr[n] = -1;
+    // n is a dead element
+    W[w + n] = 0;
+    // return mark
+    return mark;
+  }
+
+  /**
+   * Initialize degree lists. Each node is placed in its degree lists. Nodes of zero degree are eliminated immediately. Nodes with
+   * degree >= dense are alsol eliminated and merged into a placeholder node n, a dead element. Thes nodes will appera last in the
+   * output permutation p.
+   */
+  function _initializeDegreeLists(n, cptr, W, degree, elen, w, dense, nv, head, last, next) {
+    // result
+    var nel = 0;
+    // loop columns
+    for (var i = 0; i < n; i++) {
+      // degree @ i
+      var d = W[degree + i];
+      // check node i is empty
+      if (d === 0) {
+        // element i is dead
+        W[elen + i] = -2;
+        nel++;
+        // i is a root of assembly tree
+        cptr[i] = -1;
+        W[w + i] = 0;
+      } else if (d > dense) {
+        // absorb i into element n
+        W[nv + i] = 0;
+        // node i is dead
+        W[elen + i] = -1;
+        nel++;
+        cptr[i] = csFlip(n);
+        W[nv + n]++;
+      } else {
+        var h = W[head + d];
+        if (h !== -1) {
+          last[h] = i;
+        }
+        // put node i in degree list d
+        W[next + i] = W[head + d];
+        W[head + d] = i;
+      }
+    }
+    return nel;
+  }
+  function _wclear(mark, lemax, W, w, n) {
+    if (mark < 2 || mark + lemax < 0) {
+      for (var k = 0; k < n; k++) {
+        if (W[w + k] !== 0) {
+          W[w + k] = 1;
+        }
+      }
+      mark = 2;
+    }
+    // at this point, W [0..n-1] < mark holds
+    return mark;
+  }
+  function _diag(i, j) {
+    return i !== j;
+  }
+});