Mercurial > octave
annotate libinterp/dldfcn/colamd.cc @ 23777:cda0614beaec
Replace static instances of OCTAVE_LOCAL_BUFFER with local variables.
* load-save.cc (check_gzip_magic): Replace OCTAVE_LOCAL_BUFFER magic with
"unsigned char magic[2]".
* regexp.cc (octregexp): Replace OCTAVE_LOCAL_BUFFER_INIT arg_used with
"int arg_used[7] {}". Aggregate initialization zero initializes ints.
* ccolamd.cc (Fccolamd, Fcsymand): Replace OCTAVE_LOCAL_BUFFER instances for
knobs and stats with 1) a local variable XXX_storage, and 2) a pointer to
the first element in XXX_storage. Also use static_assert to guarantee
at compile time that the size of the local variable storage is not too large.
* colamd.cc (Fcolamd, Fsymand): Replace OCTAVE_LOCAL_BUFFER instances for
knobs and stats with 1) a local variable XXX_storage, and 2) a pointer to
the first element in XXX_storage. Also use static_assert to guarantee
at compile time that the size of the local variable storage is not too large.
* Array.cc (hermitian): Remove comment about OCTAVE_LOCAL_BUFFER not being
appropriate.
author | Rik <rik@octave.org> |
---|---|
date | Thu, 20 Jul 2017 21:25:06 -0700 |
parents | b7747a2c88b2 |
children | 980f39c3ab90 |
rev | line source |
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5164 | 1 /* |
2 | |
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3 Copyright (C) 2004-2017 David Bateman |
11523 | 4 Copyright (C) 1998-2004 Andy Adler |
7016 | 5 |
6 This file is part of Octave. | |
5164 | 7 |
8 Octave is free software; you can redistribute it and/or modify it | |
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9 under the terms of the GNU General Public License as published by |
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10 the Free Software Foundation; either version 3 of the License, or |
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11 (at your option) any later version. |
5164 | 12 |
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13 Octave is distributed in the hope that it will be useful, but |
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14 WITHOUT ANY WARRANTY; without even the implied warranty of |
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15 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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16 GNU General Public License for more details. |
5164 | 17 |
18 You should have received a copy of the GNU General Public License | |
7016 | 19 along with Octave; see the file COPYING. If not, see |
20 <http://www.gnu.org/licenses/>. | |
5164 | 21 |
22 */ | |
23 | |
24 // This is the octave interface to colamd, which bore the copyright given | |
25 // in the help of the functions. | |
26 | |
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27 #if defined (HAVE_CONFIG_H) |
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28 # include "config.h" |
5164 | 29 #endif |
30 | |
31 #include <cstdlib> | |
32 | |
33 #include <string> | |
34 | |
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35 #include "CSparse.h" |
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36 #include "dNDArray.h" |
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37 #include "dSparse.h" |
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38 #include "oct-locbuf.h" |
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39 #include "oct-sparse.h" |
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40 |
5164 | 41 #include "defun-dld.h" |
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42 #include "error.h" |
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43 #include "errwarn.h" |
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44 #include "ovl.h" |
5164 | 45 #include "pager.h" |
46 | |
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47 // The symmetric column elimination tree code take from the Davis LDL code. |
5164 | 48 // Copyright given elsewhere in this file. |
7924 | 49 static void |
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50 symetree (const octave_idx_type *ridx, const octave_idx_type *cidx, |
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51 octave_idx_type *Parent, octave_idx_type *P, octave_idx_type n) |
5164 | 52 { |
5440 | 53 OCTAVE_LOCAL_BUFFER (octave_idx_type, Flag, n); |
54 OCTAVE_LOCAL_BUFFER (octave_idx_type, Pinv, (P ? n : 0)); | |
5164 | 55 if (P) |
56 // If P is present then compute Pinv, the inverse of P | |
5440 | 57 for (octave_idx_type k = 0 ; k < n ; k++) |
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58 Pinv[P[k]] = k; |
5164 | 59 |
5440 | 60 for (octave_idx_type k = 0 ; k < n ; k++) |
5164 | 61 { |
62 // L(k,:) pattern: all nodes reachable in etree from nz in A(0:k-1,k) | |
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63 Parent[k] = n ; // parent of k is not yet known |
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64 Flag[k] = k ; // mark node k as visited |
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65 octave_idx_type kk = (P ? P[k] // kth original, or permuted, column |
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66 : (k)); |
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67 octave_idx_type p2 = cidx[kk+1]; |
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68 for (octave_idx_type p = cidx[kk] ; p < p2 ; p++) |
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69 { |
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70 // A (i,k) is nonzero (original or permuted A) |
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71 octave_idx_type i = (Pinv) ? (Pinv[ridx[p]]) : (ridx[p]); |
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72 if (i < k) |
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73 { |
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74 // follow path from i to root of etree, stop at flagged node |
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75 for ( ; Flag[i] != k ; i = Parent[i]) |
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76 { |
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77 // find parent of i if not yet determined |
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78 if (Parent[i] == n) |
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79 Parent[i] = k; |
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80 Flag[i] = k ; // mark i as visited |
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81 } |
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82 } |
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83 } |
5164 | 84 } |
85 } | |
86 | |
87 // The elimination tree post-ordering code below is taken from SuperLU | |
7924 | 88 static inline octave_idx_type |
89 make_set (octave_idx_type i, octave_idx_type *pp) | |
5164 | 90 { |
91 pp[i] = i; | |
92 return i; | |
93 } | |
94 | |
7924 | 95 static inline octave_idx_type |
96 link (octave_idx_type s, octave_idx_type t, octave_idx_type *pp) | |
5164 | 97 { |
98 pp[s] = t; | |
99 return t; | |
100 } | |
101 | |
7924 | 102 static inline octave_idx_type |
103 find (octave_idx_type i, octave_idx_type *pp) | |
5164 | 104 { |
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105 octave_idx_type p = pp[i]; |
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106 octave_idx_type gp = pp[p]; |
7924 | 107 |
108 while (gp != p) | |
109 { | |
110 pp[i] = gp; | |
111 i = gp; | |
112 p = pp[i]; | |
113 gp = pp[p]; | |
114 } | |
115 | |
116 return p; | |
5164 | 117 } |
118 | |
7924 | 119 static octave_idx_type |
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120 etdfs (octave_idx_type v, octave_idx_type *first_kid, |
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121 octave_idx_type *next_kid, octave_idx_type *post, |
7924 | 122 octave_idx_type postnum) |
5164 | 123 { |
7924 | 124 for (octave_idx_type w = first_kid[v]; w != -1; w = next_kid[w]) |
5164 | 125 postnum = etdfs (w, first_kid, next_kid, post, postnum); |
7924 | 126 |
5164 | 127 post[postnum++] = v; |
128 | |
129 return postnum; | |
130 } | |
131 | |
7924 | 132 static void |
133 tree_postorder (octave_idx_type n, octave_idx_type *parent, | |
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134 octave_idx_type *post) |
5164 | 135 { |
136 // Allocate storage for working arrays and results | |
5440 | 137 OCTAVE_LOCAL_BUFFER (octave_idx_type, first_kid, n+1); |
138 OCTAVE_LOCAL_BUFFER (octave_idx_type, next_kid, n+1); | |
5164 | 139 |
140 // Set up structure describing children | |
7924 | 141 for (octave_idx_type v = 0; v <= n; first_kid[v++] = -1) |
20946 | 142 ; // do nothing |
7924 | 143 |
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144 for (octave_idx_type v = n-1; v >= 0; v--) |
5164 | 145 { |
5440 | 146 octave_idx_type dad = parent[v]; |
5164 | 147 next_kid[v] = first_kid[dad]; |
148 first_kid[dad] = v; | |
149 } | |
150 | |
151 // Depth-first search from dummy root vertex #n | |
152 etdfs (n, first_kid, next_kid, post, 0); | |
153 } | |
154 | |
7924 | 155 static void |
156 coletree (const octave_idx_type *ridx, const octave_idx_type *colbeg, | |
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157 octave_idx_type *colend, octave_idx_type *parent, |
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158 octave_idx_type nr, octave_idx_type nc) |
5164 | 159 { |
5440 | 160 OCTAVE_LOCAL_BUFFER (octave_idx_type, root, nc); |
161 OCTAVE_LOCAL_BUFFER (octave_idx_type, pp, nc); | |
162 OCTAVE_LOCAL_BUFFER (octave_idx_type, firstcol, nr); | |
5164 | 163 |
164 // Compute firstcol[row] = first nonzero column in row | |
7924 | 165 for (octave_idx_type row = 0; row < nr; firstcol[row++] = nc) |
20946 | 166 ; // do nothing |
7924 | 167 |
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168 for (octave_idx_type col = 0; col < nc; col++) |
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169 for (octave_idx_type p = colbeg[col]; p < colend[col]; p++) |
5164 | 170 { |
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171 octave_idx_type row = ridx[p]; |
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172 if (firstcol[row] > col) |
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173 firstcol[row] = col; |
5164 | 174 } |
175 | |
176 // Compute etree by Liu's algorithm for symmetric matrices, | |
177 // except use (firstcol[r],c) in place of an edge (r,c) of A. | |
178 // Thus each row clique in A'*A is replaced by a star | |
179 // centered at its first vertex, which has the same fill. | |
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180 for (octave_idx_type col = 0; col < nc; col++) |
5164 | 181 { |
5440 | 182 octave_idx_type cset = make_set (col, pp); |
5164 | 183 root[cset] = col; |
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184 parent[col] = nc; |
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185 for (octave_idx_type p = colbeg[col]; p < colend[col]; p++) |
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186 { |
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187 octave_idx_type row = firstcol[ridx[p]]; |
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188 if (row >= col) |
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189 continue; |
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190 octave_idx_type rset = find (row, pp); |
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191 octave_idx_type rroot = root[rset]; |
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192 if (rroot != col) |
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193 { |
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194 parent[rroot] = col; |
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195 cset = link (cset, rset, pp); |
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196 root[cset] = col; |
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197 } |
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198 } |
5164 | 199 } |
200 } | |
201 | |
202 DEFUN_DLD (colamd, args, nargout, | |
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203 doc: /* -*- texinfo -*- |
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204 @deftypefn {} {@var{p} =} colamd (@var{S}) |
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205 @deftypefnx {} {@var{p} =} colamd (@var{S}, @var{knobs}) |
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206 @deftypefnx {} {[@var{p}, @var{stats}] =} colamd (@var{S}) |
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207 @deftypefnx {} {[@var{p}, @var{stats}] =} colamd (@var{S}, @var{knobs}) |
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208 |
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209 Compute the column approximate minimum degree permutation. |
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210 |
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211 @code{@var{p} = colamd (@var{S})} returns the column approximate minimum |
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212 degree permutation vector for the sparse matrix @var{S}. For a |
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213 non-symmetric matrix @var{S}, @code{@var{S}(:,@var{p})} tends to have |
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214 sparser LU@tie{}factors than @var{S}. The Cholesky@tie{}factorization of |
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215 @code{@var{S}(:,@var{p})' * @var{S}(:,@var{p})} also tends to be sparser |
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216 than that of @code{@var{S}' * @var{S}}. |
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217 |
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218 @var{knobs} is an optional one- to three-element input vector. If @var{S} |
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219 is m-by-n, then rows with more than @code{max(16,@var{knobs}(1)*sqrt(n))} |
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220 entries are ignored. Columns with more than |
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221 @code{max (16,@var{knobs}(2)*sqrt(min(m,n)))} entries are removed prior to |
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222 ordering, and ordered last in the output permutation @var{p}. Only |
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223 completely dense rows or columns are removed if @code{@var{knobs}(1)} and |
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224 @code{@var{knobs}(2)} are < 0, respectively. If @code{@var{knobs}(3)} is |
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225 nonzero, @var{stats} and @var{knobs} are printed. The default is |
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226 @code{@var{knobs} = [10 10 0]}. Note that @var{knobs} differs from earlier |
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227 versions of colamd. |
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228 |
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229 @var{stats} is an optional 20-element output vector that provides data |
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230 about the ordering and the validity of the input matrix @var{S}. Ordering |
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231 statistics are in @code{@var{stats}(1:3)}. @code{@var{stats}(1)} and |
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232 @code{@var{stats}(2)} are the number of dense or empty rows and columns |
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233 ignored by @sc{colamd} and @code{@var{stats}(3)} is the number of garbage |
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234 collections performed on the internal data structure used by @sc{colamd} |
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235 (roughly of size @code{2.2 * nnz(@var{S}) + 4 * @var{m} + 7 * @var{n}} |
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236 integers). |
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237 |
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238 Octave built-in functions are intended to generate valid sparse matrices, |
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239 with no duplicate entries, with ascending row indices of the nonzeros |
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240 in each column, with a non-negative number of entries in each column (!) |
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241 and so on. If a matrix is invalid, then @sc{colamd} may or may not be able |
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242 to continue. If there are duplicate entries (a row index appears two or |
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243 more times in the same column) or if the row indices in a column are out |
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244 of order, then @sc{colamd} can correct these errors by ignoring the |
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245 duplicate entries and sorting each column of its internal copy of the |
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246 matrix @var{S} (the input matrix @var{S} is not repaired, however). If a |
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247 matrix is invalid in other ways then @sc{colamd} cannot continue, an error |
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248 message is printed, and no output arguments (@var{p} or @var{stats}) are |
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249 returned. |
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250 @sc{colamd} is thus a simple way to check a sparse matrix to see if it's |
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251 valid. |
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252 |
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253 @code{@var{stats}(4:7)} provide information if @sc{colamd} was able to |
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254 continue. The matrix is OK if @code{@var{stats}(4)} is zero, or 1 if |
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255 invalid. @code{@var{stats}(5)} is the rightmost column index that is |
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256 unsorted or contains duplicate entries, or zero if no such column exists. |
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257 @code{@var{stats}(6)} is the last seen duplicate or out-of-order row |
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258 index in the column index given by @code{@var{stats}(5)}, or zero if no |
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259 such row index exists. @code{@var{stats}(7)} is the number of duplicate |
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260 or out-of-order row indices. @code{@var{stats}(8:20)} is always zero in |
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261 the current version of @sc{colamd} (reserved for future use). |
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262 |
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263 The ordering is followed by a column elimination tree post-ordering. |
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264 |
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265 The authors of the code itself are @nospell{Stefan I. Larimore} and |
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266 @nospell{Timothy A. Davis @email{davis@@cise.ufl.edu}}, University of Florida. The algorithm was developed in collaboration with @nospell{John Gilbert}, |
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267 Xerox PARC, and @nospell{Esmond Ng}, Oak Ridge National Laboratory. (see |
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268 @url{http://www.cise.ufl.edu/research/sparse/colamd}) |
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269 @seealso{colperm, symamd, ccolamd} |
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270 @end deftypefn */) |
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272 #if defined (HAVE_COLAMD) |
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273 |
5164 | 274 int nargin = args.length (); |
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275 |
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276 if (nargin < 1 || nargin > 2) |
5823 | 277 print_usage (); |
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278 |
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279 octave_value_list retval (nargout == 2 ? 2 : 1); |
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280 int spumoni = 0; |
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281 |
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282 // Get knobs |
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283 static_assert (COLAMD_KNOBS <= 40, "colamd: # of COLAMD_KNOBS exceeded. Please report this to bugs.octave.org"); |
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284 double knob_storage[COLAMD_KNOBS]; |
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285 double *knobs = &knob_storage[0]; |
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286 COLAMD_NAME (_set_defaults) (knobs); |
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288 // Check for user-passed knobs |
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289 if (nargin == 2) |
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290 { |
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291 NDArray User_knobs = args(1).array_value (); |
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292 int nel_User_knobs = User_knobs.numel (); |
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293 |
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294 if (nel_User_knobs > 0) |
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295 knobs[COLAMD_DENSE_ROW] = User_knobs(0); |
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296 if (nel_User_knobs > 1) |
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297 knobs[COLAMD_DENSE_COL] = User_knobs(1); |
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298 if (nel_User_knobs > 2) |
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299 spumoni = static_cast<int> (User_knobs(2)); |
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301 // print knob settings if spumoni is set |
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302 if (spumoni) |
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303 { |
5164 | 304 |
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305 octave_stdout << "\ncolamd version " << COLAMD_MAIN_VERSION |
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306 << "." << COLAMD_SUB_VERSION |
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307 << ", " << COLAMD_DATE << ":\n"; |
5440 | 308 |
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309 if (knobs[COLAMD_DENSE_ROW] >= 0) |
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310 octave_stdout << "knobs(1): " << User_knobs (0) |
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311 << ", rows with > max (16," |
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312 << knobs[COLAMD_DENSE_ROW] << "*sqrt (size(A,2)))" |
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313 << " entries removed\n"; |
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314 else |
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315 octave_stdout << "knobs(1): " << User_knobs (0) |
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316 << ", only completely dense rows removed\n"; |
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318 if (knobs[COLAMD_DENSE_COL] >= 0) |
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319 octave_stdout << "knobs(2): " << User_knobs (1) |
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320 << ", cols with > max (16," |
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321 << knobs[COLAMD_DENSE_COL] << "*sqrt (size(A)))" |
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322 << " entries removed\n"; |
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323 else |
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324 octave_stdout << "knobs(2): " << User_knobs (1) |
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325 << ", only completely dense columns removed\n"; |
5164 | 326 |
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327 octave_stdout << "knobs(3): " << User_knobs (2) |
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328 << ", statistics and knobs printed\n"; |
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329 |
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330 } |
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331 } |
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332 |
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333 octave_idx_type n_row, n_col, nnz; |
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334 octave_idx_type *ridx, *cidx; |
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335 SparseComplexMatrix scm; |
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336 SparseMatrix sm; |
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337 |
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338 if (args(0).issparse ()) |
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339 { |
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340 if (args(0).iscomplex ()) |
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341 { |
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342 scm = args(0).sparse_complex_matrix_value (); |
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343 n_row = scm.rows (); |
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344 n_col = scm.cols (); |
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345 nnz = scm.nnz (); |
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346 ridx = scm.xridx (); |
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347 cidx = scm.xcidx (); |
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348 } |
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350 { |
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351 sm = args(0).sparse_matrix_value (); |
5164 | 352 |
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353 n_row = sm.rows (); |
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354 n_col = sm.cols (); |
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355 nnz = sm.nnz (); |
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356 ridx = sm.xridx (); |
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357 cidx = sm.xcidx (); |
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358 } |
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359 } |
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360 else |
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361 { |
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362 if (args(0).iscomplex ()) |
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363 sm = SparseMatrix (real (args(0).complex_matrix_value ())); |
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364 else |
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365 sm = SparseMatrix (args(0).matrix_value ()); |
5164 | 366 |
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367 n_row = sm.rows (); |
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368 n_col = sm.cols (); |
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369 nnz = sm.nnz (); |
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370 ridx = sm.xridx (); |
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371 cidx = sm.xcidx (); |
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372 } |
5164 | 373 |
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374 // Allocate workspace for colamd |
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375 OCTAVE_LOCAL_BUFFER (octave::suitesparse_integer, p, n_col+1); |
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376 for (octave_idx_type i = 0; i < n_col+1; i++) |
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377 p[i] = cidx[i]; |
5164 | 378 |
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379 octave_idx_type Alen = COLAMD_NAME (_recommended) (nnz, n_row, n_col); |
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380 OCTAVE_LOCAL_BUFFER (octave::suitesparse_integer, A, Alen); |
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381 for (octave_idx_type i = 0; i < nnz; i++) |
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382 A[i] = ridx[i]; |
5164 | 383 |
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384 // Order the columns (destroys A) |
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385 static_assert (COLAMD_STATS <= 40, "colamd: # of COLAMD_STATS exceeded. Please report this to bugs.octave.org"); |
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386 octave::suitesparse_integer stats_storage[COLAMD_STATS]; |
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387 octave::suitesparse_integer *stats = &stats_storage[0]; |
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388 if (! COLAMD_NAME () (n_row, n_col, Alen, A, p, knobs, stats)) |
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389 { |
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390 COLAMD_NAME (_report)(stats); |
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391 |
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392 error ("colamd: internal error!"); |
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393 } |
5164 | 394 |
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395 // column elimination tree post-ordering (reuse variables) |
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396 OCTAVE_LOCAL_BUFFER (octave_idx_type, colbeg, n_col + 1); |
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397 OCTAVE_LOCAL_BUFFER (octave_idx_type, colend, n_col + 1); |
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398 OCTAVE_LOCAL_BUFFER (octave_idx_type, etree, n_col + 1); |
5164 | 399 |
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400 for (octave_idx_type i = 0; i < n_col; i++) |
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401 { |
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402 colbeg[i] = cidx[p[i]]; |
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403 colend[i] = cidx[p[i]+1]; |
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404 } |
5164 | 405 |
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406 coletree (ridx, colbeg, colend, etree, n_row, n_col); |
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407 |
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408 // Calculate the tree post-ordering |
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409 tree_postorder (n_col, etree, colbeg); |
5164 | 410 |
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411 // return the permutation vector |
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412 NDArray out_perm (dim_vector (1, n_col)); |
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413 for (octave_idx_type i = 0; i < n_col; i++) |
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414 out_perm(i) = p[colbeg[i]] + 1; |
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415 |
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416 retval(0) = out_perm; |
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417 |
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418 // print stats if spumoni > 0 |
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419 if (spumoni > 0) |
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420 COLAMD_NAME (_report)(stats); |
5164 | 421 |
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422 // Return the stats vector |
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423 if (nargout == 2) |
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424 { |
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425 NDArray out_stats (dim_vector (1, COLAMD_STATS)); |
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426 for (octave_idx_type i = 0 ; i < COLAMD_STATS ; i++) |
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427 out_stats(i) = stats[i]; |
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428 retval(1) = out_stats; |
5164 | 429 |
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430 // fix stats (5) and (6), for 1-based information on |
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431 // jumbled matrix. note that this correction doesn't |
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432 // occur if symamd returns FALSE |
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433 out_stats(COLAMD_INFO1)++; |
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434 out_stats(COLAMD_INFO2)++; |
5164 | 435 } |
436 | |
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437 return retval; |
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438 |
5451 | 439 #else |
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440 |
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441 octave_unused_parameter (args); |
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442 octave_unused_parameter (nargout); |
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443 |
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444 err_disabled_feature ("colamd", "COLAMD"); |
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445 |
5451 | 446 #endif |
5164 | 447 } |
448 | |
449 DEFUN_DLD (symamd, args, nargout, | |
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450 doc: /* -*- texinfo -*- |
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451 @deftypefn {} {@var{p} =} symamd (@var{S}) |
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452 @deftypefnx {} {@var{p} =} symamd (@var{S}, @var{knobs}) |
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453 @deftypefnx {} {[@var{p}, @var{stats}] =} symamd (@var{S}) |
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454 @deftypefnx {} {[@var{p}, @var{stats}] =} symamd (@var{S}, @var{knobs}) |
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455 |
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456 For a symmetric positive definite matrix @var{S}, returns the permutation |
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457 vector p such that @code{@var{S}(@var{p}, @var{p})} tends to have a |
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458 sparser Cholesky@tie{}factor than @var{S}. |
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459 |
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460 Sometimes @code{symamd} works well for symmetric indefinite matrices too. |
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461 The matrix @var{S} is assumed to be symmetric; only the strictly lower |
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462 triangular part is referenced. @var{S} must be square. |
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463 |
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464 @var{knobs} is an optional one- to two-element input vector. If @var{S} is |
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465 n-by-n, then rows and columns with more than |
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466 @code{max (16,@var{knobs}(1)*sqrt(n))} entries are removed prior to |
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467 ordering, and ordered last in the output permutation @var{p}. No |
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468 rows/columns are removed if @code{@var{knobs}(1) < 0}. If |
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469 @code{@var{knobs} (2)} is nonzero, @code{stats} and @var{knobs} are |
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470 printed. The default is @code{@var{knobs} = [10 0]}. Note that |
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471 @var{knobs} differs from earlier versions of @code{symamd}. |
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472 |
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473 @var{stats} is an optional 20-element output vector that provides data |
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474 about the ordering and the validity of the input matrix @var{S}. Ordering |
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475 statistics are in @code{@var{stats}(1:3)}. |
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476 @code{@var{stats}(1) = @var{stats}(2)} is the number of dense or empty rows |
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477 and columns ignored by SYMAMD and @code{@var{stats}(3)} is the number of |
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478 garbage collections performed on the internal data structure used by SYMAMD |
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479 (roughly of size @code{8.4 * nnz (tril (@var{S}, -1)) + 9 * @var{n}} |
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480 integers). |
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481 |
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482 Octave built-in functions are intended to generate valid sparse matrices, |
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483 with no duplicate entries, with ascending row indices of the nonzeros |
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484 in each column, with a non-negative number of entries in each column (!) |
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485 and so on. If a matrix is invalid, then SYMAMD may or may not be able |
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486 to continue. If there are duplicate entries (a row index appears two or |
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487 more times in the same column) or if the row indices in a column are out |
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488 of order, then SYMAMD can correct these errors by ignoring the duplicate |
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489 entries and sorting each column of its internal copy of the matrix S (the |
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490 input matrix S is not repaired, however). If a matrix is invalid in |
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491 other ways then SYMAMD cannot continue, an error message is printed, and |
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492 no output arguments (@var{p} or @var{stats}) are returned. SYMAMD is |
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493 thus a simple way to check a sparse matrix to see if it's valid. |
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494 |
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495 @code{@var{stats}(4:7)} provide information if SYMAMD was able to |
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496 continue. The matrix is OK if @code{@var{stats} (4)} is zero, or 1 |
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497 if invalid. @code{@var{stats}(5)} is the rightmost column index that |
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498 is unsorted or contains duplicate entries, or zero if no such column |
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499 exists. @code{@var{stats}(6)} is the last seen duplicate or out-of-order |
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500 row index in the column index given by @code{@var{stats}(5)}, or zero |
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501 if no such row index exists. @code{@var{stats}(7)} is the number of |
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502 duplicate or out-of-order row indices. @code{@var{stats}(8:20)} is |
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503 always zero in the current version of SYMAMD (reserved for future use). |
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504 |
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505 The ordering is followed by a column elimination tree post-ordering. |
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506 |
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507 The authors of the code itself are @nospell{Stefan I. Larimore} and |
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508 @nospell{Timothy A. Davis @email{davis@@cise.ufl.edu}}, University of Florida. The algorithm was developed in collaboration with @nospell{John Gilbert}, |
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509 Xerox PARC, and @nospell{Esmond Ng}, Oak Ridge National Laboratory. (see |
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510 @url{http://www.cise.ufl.edu/research/sparse/colamd}) |
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511 @seealso{colperm, colamd} |
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512 @end deftypefn */) |
5164 | 513 { |
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514 #if defined (HAVE_COLAMD) |
5451 | 515 |
5164 | 516 int nargin = args.length (); |
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517 |
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518 if (nargin < 1 || nargin > 2) |
5823 | 519 print_usage (); |
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520 |
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521 octave_value_list retval (nargin == 2 ? 2 : 1); |
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522 int spumoni = 0; |
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523 |
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524 // Get knobs |
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525 static_assert (COLAMD_KNOBS <= 40, "symamd: # of COLAMD_KNOBS exceeded. Please report this to bugs.octave.org"); |
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526 double knob_storage[COLAMD_KNOBS]; |
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527 double *knobs = &knob_storage[0]; |
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528 COLAMD_NAME (_set_defaults) (knobs); |
5164 | 529 |
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530 // Check for user-passed knobs |
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531 if (nargin == 2) |
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532 { |
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533 NDArray User_knobs = args(1).array_value (); |
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534 int nel_User_knobs = User_knobs.numel (); |
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535 |
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536 if (nel_User_knobs > 0) |
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537 knobs[COLAMD_DENSE_ROW] = User_knobs(COLAMD_DENSE_ROW); |
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538 if (nel_User_knobs > 1) |
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539 spumoni = static_cast<int> (User_knobs (1)); |
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540 } |
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541 |
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542 // print knob settings if spumoni is set |
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543 if (spumoni > 0) |
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544 octave_stdout << "symamd: dense row/col fraction: " |
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545 << knobs[COLAMD_DENSE_ROW] << std::endl; |
5164 | 546 |
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547 octave_idx_type n_row, n_col; |
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548 octave_idx_type *ridx, *cidx; |
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549 SparseMatrix sm; |
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550 SparseComplexMatrix scm; |
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551 |
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552 if (args(0).issparse ()) |
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553 { |
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554 if (args(0).iscomplex ()) |
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555 { |
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556 scm = args(0).sparse_complex_matrix_value (); |
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557 n_row = scm.rows (); |
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558 n_col = scm.cols (); |
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559 ridx = scm.xridx (); |
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560 cidx = scm.xcidx (); |
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561 } |
5164 | 562 else |
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563 { |
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564 sm = args(0).sparse_matrix_value (); |
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565 n_row = sm.rows (); |
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566 n_col = sm.cols (); |
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567 ridx = sm.xridx (); |
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568 cidx = sm.xcidx (); |
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569 } |
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570 } |
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571 else |
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572 { |
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573 if (args(0).iscomplex ()) |
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574 sm = SparseMatrix (real (args(0).complex_matrix_value ())); |
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575 else |
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576 sm = SparseMatrix (args(0).matrix_value ()); |
5164 | 577 |
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578 n_row = sm.rows (); |
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579 n_col = sm.cols (); |
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580 ridx = sm.xridx (); |
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581 cidx = sm.xcidx (); |
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582 } |
5164 | 583 |
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584 if (n_row != n_col) |
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585 err_square_matrix_required ("symamd", "S"); |
5164 | 586 |
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587 // Allocate workspace for symamd |
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588 OCTAVE_LOCAL_BUFFER (octave_idx_type, perm, n_col+1); |
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589 static_assert (COLAMD_STATS <= 40, "symamd: # of COLAMD_STATS exceeded. Please report this to bugs.octave.org"); |
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590 octave::suitesparse_integer stats_storage[COLAMD_STATS]; |
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591 octave::suitesparse_integer *stats = &stats_storage[0]; |
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592 if (! SYMAMD_NAME () (n_col, octave::to_suitesparse_intptr (ridx), |
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593 octave::to_suitesparse_intptr (cidx), |
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594 octave::to_suitesparse_intptr (perm), |
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595 knobs, stats, &calloc, &free)) |
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596 { |
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597 SYMAMD_NAME (_report)(stats); |
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598 |
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599 error ("symamd: internal error!"); |
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600 } |
5164 | 601 |
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602 // column elimination tree post-ordering |
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603 OCTAVE_LOCAL_BUFFER (octave_idx_type, etree, n_col + 1); |
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604 symetree (ridx, cidx, etree, perm, n_col); |
5164 | 605 |
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606 // Calculate the tree post-ordering |
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607 OCTAVE_LOCAL_BUFFER (octave_idx_type, post, n_col + 1); |
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608 tree_postorder (n_col, etree, post); |
5164 | 609 |
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610 // return the permutation vector |
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611 NDArray out_perm (dim_vector (1, n_col)); |
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612 for (octave_idx_type i = 0; i < n_col; i++) |
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613 out_perm(i) = perm[post[i]] + 1; |
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614 |
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615 retval(0) = out_perm; |
5164 | 616 |
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617 // print stats if spumoni > 0 |
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618 if (spumoni > 0) |
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619 SYMAMD_NAME (_report)(stats); |
5164 | 620 |
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621 // Return the stats vector |
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622 if (nargout == 2) |
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623 { |
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624 NDArray out_stats (dim_vector (1, COLAMD_STATS)); |
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625 for (octave_idx_type i = 0 ; i < COLAMD_STATS ; i++) |
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626 out_stats(i) = stats[i]; |
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627 retval(1) = out_stats; |
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628 |
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629 // fix stats (5) and (6), for 1-based information on |
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630 // jumbled matrix. note that this correction doesn't |
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631 // occur if symamd returns FALSE |
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632 out_stats(COLAMD_INFO1)++; |
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633 out_stats(COLAMD_INFO2)++; |
5164 | 634 } |
635 | |
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636 return retval; |
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637 |
5451 | 638 #else |
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639 |
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640 octave_unused_parameter (args); |
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641 octave_unused_parameter (nargout); |
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642 |
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643 err_disabled_feature ("symamd", "COLAMD"); |
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644 |
5451 | 645 #endif |
5164 | 646 } |
647 | |
648 DEFUN_DLD (etree, args, nargout, | |
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649 doc: /* -*- texinfo -*- |
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650 @deftypefn {} {@var{p} =} etree (@var{S}) |
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651 @deftypefnx {} {@var{p} =} etree (@var{S}, @var{typ}) |
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652 @deftypefnx {} {[@var{p}, @var{q}] =} etree (@var{S}, @var{typ}) |
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653 |
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654 Return the elimination tree for the matrix @var{S}. |
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655 |
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656 By default @var{S} is assumed to be symmetric and the symmetric elimination |
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657 tree is returned. The argument @var{typ} controls whether a symmetric or |
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658 column elimination tree is returned. Valid values of @var{typ} are |
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659 @qcode{"sym"} or @qcode{"col"}, for symmetric or column elimination tree |
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660 respectively. |
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661 |
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662 Called with a second argument, @code{etree} also returns the postorder |
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663 permutations on the tree. |
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664 @end deftypefn */) |
5164 | 665 { |
666 int nargin = args.length (); | |
667 | |
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668 if (nargin < 1 || nargin > 2) |
5823 | 669 print_usage (); |
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670 |
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671 octave_value_list retval (nargout == 2 ? 2 : 1); |
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672 |
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673 octave_idx_type n_row = 0; |
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674 octave_idx_type n_col = 0; |
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675 octave_idx_type *ridx = nullptr; |
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676 octave_idx_type *cidx = nullptr; |
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677 |
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678 if (args(0).issparse ()) |
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679 error ("etree: S must be a sparse matrix"); |
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680 |
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681 if (args(0).iscomplex ()) |
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682 { |
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683 SparseComplexMatrix scm = args(0).sparse_complex_matrix_value (); |
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684 |
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685 n_row = scm.rows (); |
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686 n_col = scm.cols (); |
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687 ridx = scm.xridx (); |
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688 cidx = scm.xcidx (); |
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689 } |
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690 else |
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691 { |
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692 SparseMatrix sm = args(0).sparse_matrix_value (); |
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693 |
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694 n_row = sm.rows (); |
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695 n_col = sm.cols (); |
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696 ridx = sm.xridx (); |
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697 cidx = sm.xcidx (); |
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698 } |
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699 |
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700 bool is_sym = true; |
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701 |
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702 if (nargin == 2) |
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703 { |
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704 std::string str = args(1).xstring_value ("etree: TYP must be a string"); |
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705 if (str.find ("C") == 0 || str.find ("c") == 0) |
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706 is_sym = false; |
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707 } |
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708 |
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709 // column elimination tree post-ordering (reuse variables) |
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710 OCTAVE_LOCAL_BUFFER (octave_idx_type, etree, n_col + 1); |
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711 |
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712 if (is_sym) |
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713 { |
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714 if (n_row != n_col) |
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715 error ("etree: S is marked as symmetric, but is not square"); |
5164 | 716 |
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717 symetree (ridx, cidx, etree, 0, n_col); |
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718 } |
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719 else |
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720 { |
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721 OCTAVE_LOCAL_BUFFER (octave_idx_type, colbeg, n_col); |
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722 OCTAVE_LOCAL_BUFFER (octave_idx_type, colend, n_col); |
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723 |
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724 for (octave_idx_type i = 0; i < n_col; i++) |
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725 { |
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726 colbeg[i] = cidx[i]; |
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727 colend[i] = cidx[i+1]; |
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728 } |
7924 | 729 |
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730 coletree (ridx, colbeg, colend, etree, n_row, n_col); |
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731 } |
7924 | 732 |
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733 NDArray tree (dim_vector (1, n_col)); |
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734 for (octave_idx_type i = 0; i < n_col; i++) |
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735 // We flag a root with n_col while Matlab does it with zero |
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736 // Convert for matlab compatiable output |
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737 if (etree[i] == n_col) |
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738 tree(i) = 0; |
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739 else |
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740 tree(i) = etree[i] + 1; |
5164 | 741 |
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742 retval(0) = tree; |
5164 | 743 |
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744 if (nargout == 2) |
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745 { |
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746 // Calculate the tree post-ordering |
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747 OCTAVE_LOCAL_BUFFER (octave_idx_type, post, n_col + 1); |
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748 tree_postorder (n_col, etree, post); |
5164 | 749 |
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750 NDArray postorder (dim_vector (1, n_col)); |
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751 for (octave_idx_type i = 0; i < n_col; i++) |
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752 postorder(i) = post[i] + 1; |
5164 | 753 |
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754 retval(1) = postorder; |
5164 | 755 } |
756 | |
757 return retval; | |
758 } |