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[matrix] Annotation of /pkg/Matrix/src/Csparse.c
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Annotation of /pkg/Matrix/src/Csparse.c

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Original Path: pkg/src/Csparse.c

1 : bates 1218 /* Sparse matrices in compressed column-oriented form */
2 : bates 922 #include "Csparse.h"
3 : maechler 2120 #include "Tsparse.h"
4 : bates 922 #include "chm_common.h"
5 :    
6 :     SEXP Csparse_validate(SEXP x)
7 :     {
8 : maechler 1575 /* NB: we do *NOT* check a potential 'x' slot here, at all */
9 : bates 922 SEXP pslot = GET_SLOT(x, Matrix_pSym),
10 :     islot = GET_SLOT(x, Matrix_iSym);
11 : maechler 1893 Rboolean sorted, strictly;
12 :     int j, k,
13 : bates 922 *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
14 : maechler 1660 nrow = dims[0],
15 :     ncol = dims[1],
16 : maechler 1654 *xp = INTEGER(pslot),
17 : bates 922 *xi = INTEGER(islot);
18 :    
19 : maechler 1654 if (length(pslot) != dims[1] + 1)
20 :     return mkString(_("slot p must have length = ncol(.) + 1"));
21 : bates 922 if (xp[0] != 0)
22 :     return mkString(_("first element of slot p must be zero"));
23 : maechler 1893 if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
24 : bates 1555 return
25 :     mkString(_("last element of slot p must match length of slots i and x"));
26 : mmaechler 2236 for (j = 0; j < xp[ncol]; j++) {
27 : bates 1555 if (xi[j] < 0 || xi[j] >= nrow)
28 :     return mkString(_("all row indices must be between 0 and nrow-1"));
29 :     }
30 : maechler 1893 sorted = TRUE; strictly = TRUE;
31 : bates 922 for (j = 0; j < ncol; j++) {
32 : mmaechler 2236 if (xp[j] > xp[j + 1])
33 : bates 922 return mkString(_("slot p must be non-decreasing"));
34 : mmaechler 2236 if(sorted) /* only act if >= 2 entries in column j : */
35 : maechler 1893 for (k = xp[j] + 1; k < xp[j + 1]; k++) {
36 :     if (xi[k] < xi[k - 1])
37 :     sorted = FALSE;
38 :     else if (xi[k] == xi[k - 1])
39 :     strictly = FALSE;
40 :     }
41 : bates 922 }
42 : maechler 1654 if (!sorted) {
43 : mmaechler 2235 CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
44 : maechler 1960 R_CheckStack();
45 : mmaechler 2235 as_cholmod_sparse(chx, x, FALSE, TRUE); /* includes cholmod_sort() ! */
46 :     /* as chx = AS_CHM_SP__(x) but ^^^^ sorting x in_place (no copying)*/
47 : maechler 1960
48 : maechler 1893 /* Now re-check that row indices are *strictly* increasing
49 :     * (and not just increasing) within each column : */
50 :     for (j = 0; j < ncol; j++) {
51 :     for (k = xp[j] + 1; k < xp[j + 1]; k++)
52 :     if (xi[k] == xi[k - 1])
53 :     return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));
54 :     }
55 :    
56 :     } else if(!strictly) { /* sorted, but not strictly */
57 :     return mkString(_("slot i is not *strictly* increasing inside a column"));
58 : maechler 1654 }
59 : bates 922 return ScalarLogical(1);
60 :     }
61 :    
62 : maechler 1968 SEXP Rsparse_validate(SEXP x)
63 :     {
64 :     /* NB: we do *NOT* check a potential 'x' slot here, at all */
65 :     SEXP pslot = GET_SLOT(x, Matrix_pSym),
66 :     jslot = GET_SLOT(x, Matrix_jSym);
67 :     Rboolean sorted, strictly;
68 :     int i, k,
69 :     *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
70 :     nrow = dims[0],
71 :     ncol = dims[1],
72 :     *xp = INTEGER(pslot),
73 :     *xj = INTEGER(jslot);
74 :    
75 :     if (length(pslot) != dims[0] + 1)
76 :     return mkString(_("slot p must have length = nrow(.) + 1"));
77 :     if (xp[0] != 0)
78 :     return mkString(_("first element of slot p must be zero"));
79 :     if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
80 :     return
81 :     mkString(_("last element of slot p must match length of slots j and x"));
82 :     for (i = 0; i < length(jslot); i++) {
83 :     if (xj[i] < 0 || xj[i] >= ncol)
84 :     return mkString(_("all column indices must be between 0 and ncol-1"));
85 :     }
86 :     sorted = TRUE; strictly = TRUE;
87 :     for (i = 0; i < nrow; i++) {
88 :     if (xp[i] > xp[i+1])
89 :     return mkString(_("slot p must be non-decreasing"));
90 :     if(sorted)
91 :     for (k = xp[i] + 1; k < xp[i + 1]; k++) {
92 :     if (xj[k] < xj[k - 1])
93 :     sorted = FALSE;
94 :     else if (xj[k] == xj[k - 1])
95 :     strictly = FALSE;
96 :     }
97 :     }
98 :     if (!sorted)
99 :     /* cannot easily use cholmod_sort(.) ... -> "error out" :*/
100 :     return mkString(_("slot j is not increasing inside a column"));
101 :     else if(!strictly) /* sorted, but not strictly */
102 :     return mkString(_("slot j is not *strictly* increasing inside a column"));
103 :    
104 :     return ScalarLogical(1);
105 :     }
106 :    
107 :    
108 : maechler 1751 /* Called from ../R/Csparse.R : */
109 :     /* Can only return [dln]geMatrix (no symm/triang);
110 :     * FIXME: replace by non-CHOLMOD code ! */
111 : bates 1059 SEXP Csparse_to_dense(SEXP x)
112 :     {
113 : mmaechler 2223 CHM_SP chxs = AS_CHM_SP__(x);
114 : maechler 1751 /* This loses the symmetry property, since cholmod_dense has none,
115 :     * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
116 :     * to numeric (CHOLMOD_REAL) ones : */
117 : maechler 1960 CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
118 : maechler 1751 int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
119 : maechler 1960 R_CheckStack();
120 : bates 1059
121 : maechler 1736 return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
122 : bates 1059 }
123 :    
124 : maechler 1548 SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
125 : bates 1371 {
126 : mmaechler 2223 CHM_SP chxs = AS_CHM_SP__(x);
127 : maechler 1960 CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
128 : bates 1867 int tr = asLogical(tri);
129 : maechler 1960 R_CheckStack();
130 : bates 1371
131 : maechler 1960 return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
132 : bates 1867 tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
133 :     0, tr ? diag_P(x) : "",
134 : maechler 1548 GET_SLOT(x, Matrix_DimNamesSym));
135 : bates 1371 }
136 :    
137 : bates 1366 SEXP Csparse_to_matrix(SEXP x)
138 : bates 922 {
139 : mmaechler 2223 return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
140 : maechler 1960 1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
141 : bates 1366 }
142 :    
143 :     SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
144 :     {
145 : mmaechler 2223 CHM_SP chxs = AS_CHM_SP__(x);
146 : maechler 1960 CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
147 : bates 1867 int tr = asLogical(tri);
148 : maechler 1736 int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
149 : maechler 1960 R_CheckStack();
150 : bates 922
151 : bates 1867 return chm_triplet_to_SEXP(chxt, 1,
152 :     tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
153 :     Rkind, tr ? diag_P(x) : "",
154 : bates 1371 GET_SLOT(x, Matrix_DimNamesSym));
155 : bates 922 }
156 :    
157 : bates 1448 /* this used to be called sCMatrix_to_gCMatrix(..) [in ./dsCMatrix.c ]: */
158 : bates 1371 SEXP Csparse_symmetric_to_general(SEXP x)
159 :     {
160 : mmaechler 2223 CHM_SP chx = AS_CHM_SP__(x), chgx;
161 : maechler 1736 int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
162 : maechler 1960 R_CheckStack();
163 : bates 1371
164 :     if (!(chx->stype))
165 : maechler 1548 error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
166 : maechler 1375 chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
167 :     /* xtype: pattern, "real", complex or .. */
168 : maechler 1548 return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
169 : bates 1371 GET_SLOT(x, Matrix_DimNamesSym));
170 :     }
171 :    
172 : maechler 1618 SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
173 : maechler 1598 {
174 : mmaechler 2223 CHM_SP chx = AS_CHM_SP__(x), chgx;
175 : maechler 2113 int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
176 : maechler 1736 int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
177 : maechler 1960 R_CheckStack();
178 : maechler 1598
179 : maechler 1618 chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
180 : maechler 1598 /* xtype: pattern, "real", complex or .. */
181 :     return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
182 :     GET_SLOT(x, Matrix_DimNamesSym));
183 :     }
184 :    
185 : bates 1369 SEXP Csparse_transpose(SEXP x, SEXP tri)
186 : bates 922 {
187 : maechler 1921 /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
188 :     * since cholmod (& cs) lacks sparse 'int' matrices */
189 : mmaechler 2223 CHM_SP chx = AS_CHM_SP__(x);
190 : maechler 1736 int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
191 : maechler 1960 CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
192 : bates 1366 SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
193 : bates 1867 int tr = asLogical(tri);
194 : maechler 1960 R_CheckStack();
195 : bates 1369
196 : bates 1366 tmp = VECTOR_ELT(dn, 0); /* swap the dimnames */
197 :     SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
198 :     SET_VECTOR_ELT(dn, 1, tmp);
199 :     UNPROTECT(1);
200 : bates 1867 return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
201 :     tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
202 :     Rkind, tr ? diag_P(x) : "", dn);
203 : bates 922 }
204 :    
205 :     SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
206 :     {
207 : maechler 2120 CHM_SP
208 : mmaechler 2223 cha = AS_CHM_SP(a),
209 :     chb = AS_CHM_SP(b),
210 : maechler 2125 chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
211 :     cha->xtype, /*out sorted:*/ 1, &c);
212 :     const char *cl_a = class_P(a), *cl_b = class_P(b);
213 :     char diag[] = {'\0', '\0'};
214 :     int uploT = 0;
215 : bates 1366 SEXP dn = allocVector(VECSXP, 2);
216 : maechler 1960 R_CheckStack();
217 : bates 922
218 : maechler 2125 /* Preserve triangularity and even unit-triangularity if appropriate.
219 :     * Note that in that case, the multiplication itself should happen
220 :     * faster. But there's no support for that in CHOLMOD */
221 :    
222 :     /* UGLY hack -- rather should have (fast!) C-level version of
223 :     * is(a, "triangularMatrix") etc */
224 :     if (cl_a[1] == 't' && cl_b[1] == 't')
225 :     /* FIXME: fails for "Cholesky","BunchKaufmann"..*/
226 :     if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
227 :     uploT = (*uplo_P(a) == 'U') ? 1 : -1;
228 :     if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
229 :     /* "remove the diagonal entries": */
230 :     chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
231 :     diag[0]= 'U';
232 :     }
233 :     else diag[0]= 'N';
234 :     }
235 : bates 1366 SET_VECTOR_ELT(dn, 0, /* establish dimnames */
236 :     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
237 :     SET_VECTOR_ELT(dn, 1,
238 :     duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
239 : maechler 2125 return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
240 : bates 922 }
241 :    
242 : maechler 1659 SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
243 : bates 1657 {
244 : maechler 1659 int tr = asLogical(trans);
245 : maechler 2120 CHM_SP
246 : mmaechler 2223 cha = AS_CHM_SP(a),
247 :     chb = AS_CHM_SP(b),
248 : maechler 2120 chTr, chc;
249 : maechler 2125 const char *cl_a = class_P(a), *cl_b = class_P(b);
250 :     char diag[] = {'\0', '\0'};
251 :     int uploT = 0;
252 : bates 1657 SEXP dn = allocVector(VECSXP, 2);
253 : maechler 1960 R_CheckStack();
254 : bates 1657
255 : maechler 1960 chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
256 : maechler 1659 chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
257 : maechler 2125 /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
258 : maechler 1960 cholmod_free_sparse(&chTr, &c);
259 : maechler 1659
260 : maechler 2125 /* Preserve triangularity and unit-triangularity if appropriate;
261 :     * see Csparse_Csparse_prod() for comments */
262 :     if (cl_a[1] == 't' && cl_b[1] == 't')
263 :     if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
264 :     uploT = (*uplo_P(b) == 'U') ? 1 : -1;
265 :     if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
266 :     chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
267 :     diag[0]= 'U';
268 :     }
269 :     else diag[0]= 'N';
270 :     }
271 :    
272 : bates 1657 SET_VECTOR_ELT(dn, 0, /* establish dimnames */
273 : maechler 1659 duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
274 : bates 1657 SET_VECTOR_ELT(dn, 1,
275 : maechler 1659 duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
276 : maechler 2125 return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
277 : bates 1657 }
278 :    
279 : bates 922 SEXP Csparse_dense_prod(SEXP a, SEXP b)
280 :     {
281 : mmaechler 2223 CHM_SP cha = AS_CHM_SP(a);
282 : maechler 1660 SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
283 : maechler 1960 CHM_DN chb = AS_CHM_DN(b_M);
284 :     CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
285 :     chb->xtype, &c);
286 :     SEXP dn = PROTECT(allocVector(VECSXP, 2));
287 :     double one[] = {1,0}, zero[] = {0,0};
288 :     R_CheckStack();
289 : bates 922
290 : maechler 1960 cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
291 : maechler 1660 SET_VECTOR_ELT(dn, 0, /* establish dimnames */
292 :     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
293 :     SET_VECTOR_ELT(dn, 1,
294 :     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
295 : maechler 1960 UNPROTECT(2);
296 : maechler 1660 return chm_dense_to_SEXP(chc, 1, 0, dn);
297 : bates 922 }
298 : maechler 925
299 : bates 1067 SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
300 :     {
301 : mmaechler 2223 CHM_SP cha = AS_CHM_SP(a);
302 : maechler 1660 SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
303 : maechler 1960 CHM_DN chb = AS_CHM_DN(b_M);
304 :     CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
305 :     chb->xtype, &c);
306 :     SEXP dn = PROTECT(allocVector(VECSXP, 2));
307 :     double one[] = {1,0}, zero[] = {0,0};
308 :     R_CheckStack();
309 : bates 1067
310 : maechler 1960 cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
311 : maechler 1660 SET_VECTOR_ELT(dn, 0, /* establish dimnames */
312 :     duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
313 :     SET_VECTOR_ELT(dn, 1,
314 :     duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
315 : maechler 1960 UNPROTECT(2);
316 : maechler 1660 return chm_dense_to_SEXP(chc, 1, 0, dn);
317 : bates 1067 }
318 :    
319 : maechler 2125 /* Computes x'x or x x' -- *also* for Tsparse (triplet = TRUE)
320 :     see Csparse_Csparse_crossprod above for x'y and x y' */
321 : bates 928 SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
322 : bates 922 {
323 : maechler 957 int trip = asLogical(triplet),
324 :     tr = asLogical(trans); /* gets reversed because _aat is tcrossprod */
325 : mmaechler 2223 CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
326 : maechler 1960 CHM_SP chcp, chxt,
327 : maechler 2120 chx = (trip ?
328 :     cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
329 : mmaechler 2223 AS_CHM_SP(x));
330 : bates 1366 SEXP dn = PROTECT(allocVector(VECSXP, 2));
331 : maechler 1960 R_CheckStack();
332 : bates 922
333 : maechler 1960 if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
334 : bates 928 chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
335 : maechler 2120 if(!chcp) {
336 :     UNPROTECT(1);
337 :     error(_("Csparse_crossprod(): error return from cholmod_aat()"));
338 :     }
339 : bates 1360 cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
340 :     chcp->stype = 1;
341 : maechler 1960 if (trip) cholmod_free_sparse(&chx, &c);
342 : bates 923 if (!tr) cholmod_free_sparse(&chxt, &c);
343 : maechler 1960 SET_VECTOR_ELT(dn, 0, /* establish dimnames */
344 : bates 1366 duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
345 : maechler 1660 (tr) ? 0 : 1)));
346 : bates 1366 SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
347 :     UNPROTECT(1);
348 : maechler 1548 return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
349 : bates 922 }
350 : bates 923
351 : maechler 1618 SEXP Csparse_drop(SEXP x, SEXP tol)
352 :     {
353 : mmaechler 2175 const char *cl = class_P(x);
354 :     /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
355 :     int tr = (cl[1] == 't');
356 : mmaechler 2223 CHM_SP chx = AS_CHM_SP__(x);
357 : maechler 1960 CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
358 : maechler 1618 double dtol = asReal(tol);
359 : maechler 1736 int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
360 : maechler 1960 R_CheckStack();
361 : maechler 1618
362 :     if(!cholmod_drop(dtol, ans, &c))
363 :     error(_("cholmod_drop() failed"));
364 : mmaechler 2175 return chm_sparse_to_SEXP(ans, 1,
365 :     tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
366 :     Rkind, tr ? diag_P(x) : "",
367 : maechler 1736 GET_SLOT(x, Matrix_DimNamesSym));
368 : maechler 1618 }
369 :    
370 : bates 1218 SEXP Csparse_horzcat(SEXP x, SEXP y)
371 :     {
372 : mmaechler 2223 CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
373 : maechler 1548 int Rkind = 0; /* only for "d" - FIXME */
374 : maechler 1960 R_CheckStack();
375 : maechler 1375
376 : bates 1366 /* FIXME: currently drops dimnames */
377 : maechler 1960 return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
378 :     1, 0, Rkind, "", R_NilValue);
379 : bates 1218 }
380 :    
381 :     SEXP Csparse_vertcat(SEXP x, SEXP y)
382 :     {
383 : mmaechler 2223 CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
384 : maechler 1548 int Rkind = 0; /* only for "d" - FIXME */
385 : maechler 1960 R_CheckStack();
386 : maechler 1375
387 : bates 1366 /* FIXME: currently drops dimnames */
388 : maechler 1960 return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
389 :     1, 0, Rkind, "", R_NilValue);
390 : bates 1218 }
391 : bates 1265
392 :     SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
393 :     {
394 : mmaechler 2223 CHM_SP chx = AS_CHM_SP__(x);
395 : maechler 1736 int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
396 : maechler 1960 CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
397 :     R_CheckStack();
398 : bates 1265
399 : maechler 1736 return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
400 :     GET_SLOT(x, Matrix_DimNamesSym));
401 : bates 1265 }
402 : bates 1366
403 :     SEXP Csparse_diagU2N(SEXP x)
404 :     {
405 : maechler 2120 const char *cl = class_P(x);
406 :     /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
407 :     if (cl[1] != 't' || *diag_P(x) != 'U') {
408 : maechler 2125 /* "trivially fast" when not triangular (<==> no 'diag' slot),
409 :     or not *unit* triangular */
410 : maechler 1708 return (x);
411 :     }
412 : maechler 2125 else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
413 : mmaechler 2223 CHM_SP chx = AS_CHM_SP__(x);
414 : maechler 1960 CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
415 : maechler 1708 double one[] = {1, 0};
416 : maechler 1960 CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
417 : maechler 1710 int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
418 : maechler 1736 int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
419 : bates 1366
420 : maechler 1960 R_CheckStack();
421 :     cholmod_free_sparse(&eye, &c);
422 : maechler 1708 return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
423 : maechler 1736 GET_SLOT(x, Matrix_DimNamesSym));
424 : maechler 1708 }
425 : bates 1366 }
426 :    
427 : maechler 2125 SEXP Csparse_diagN2U(SEXP x)
428 :     {
429 :     const char *cl = class_P(x);
430 :     /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
431 :     if (cl[1] != 't' || *diag_P(x) != 'N') {
432 :     /* "trivially fast" when not triangular (<==> no 'diag' slot),
433 :     or already *unit* triangular */
434 :     return (x);
435 :     }
436 :     else { /* triangular with diag='N'): now drop the diagonal */
437 :     /* duplicate, since chx will be modified: */
438 : mmaechler 2223 CHM_SP chx = AS_CHM_SP__(duplicate(x));
439 : maechler 2125 int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
440 :     Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
441 :     R_CheckStack();
442 :    
443 :     chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
444 :    
445 :     return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
446 :     uploT, Rkind, "U",
447 :     GET_SLOT(x, Matrix_DimNamesSym));
448 :     }
449 :     }
450 :    
451 : bates 1366 SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
452 :     {
453 : mmaechler 2223 CHM_SP chx = AS_CHM_SP__(x);
454 : bates 1366 int rsize = (isNull(i)) ? -1 : LENGTH(i),
455 :     csize = (isNull(j)) ? -1 : LENGTH(j);
456 : maechler 1736 int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
457 : maechler 1960 R_CheckStack();
458 : bates 1366
459 :     if (rsize >= 0 && !isInteger(i))
460 :     error(_("Index i must be NULL or integer"));
461 :     if (csize >= 0 && !isInteger(j))
462 :     error(_("Index j must be NULL or integer"));
463 : maechler 1736
464 : bates 1366 return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
465 : maechler 1375 INTEGER(j), csize,
466 : bates 1366 TRUE, TRUE, &c),
467 : maechler 1736 1, 0, Rkind, "",
468 :     /* FIXME: drops dimnames */ R_NilValue);
469 : bates 1366 }
470 : bates 2049
471 :     SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
472 :     {
473 :     FILE *f = fopen(CHAR(asChar(fname)), "w");
474 :    
475 :     if (!f)
476 :     error(_("failure to open file \"%s\" for writing"),
477 :     CHAR(asChar(fname)));
478 : mmaechler 2223 if (!cholmod_write_sparse(f, AS_CHM_SP(x),
479 : maechler 2120 (CHM_SP)NULL, (char*) NULL, &c))
480 : bates 2049 error(_("cholmod_write_sparse returned error code"));
481 :     fclose(f);
482 :     return R_NilValue;
483 :     }
484 : maechler 2137
485 :    
486 :     /**
487 :     * Extract the diagonal entries from *triangular* Csparse matrix __or__ a
488 :     * cholmod_sparse factor (LDL = TRUE).
489 :     *
490 :     * @param n dimension of the matrix.
491 :     * @param x_p 'p' (column pointer) slot contents
492 :     * @param x_x 'x' (non-zero entries) slot contents
493 : mmaechler 2175 * @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
494 : maechler 2137 * @param resultKind a (SEXP) string indicating which kind of result is desired.
495 :     *
496 :     * @return a SEXP, either a (double) number or a length n-vector of diagonal entries
497 :     */
498 :     SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
499 :     /* ^^^^^^ FIXME[Generalize] to int / ... */
500 :     {
501 :     const char* res_ch = CHAR(STRING_ELT(resultKind,0));
502 :     enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
503 :     } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
504 :     ((!strcmp(res_ch, "sumLog")) ? sum_log :
505 :     ((!strcmp(res_ch, "prod")) ? prod :
506 :     ((!strcmp(res_ch, "diag")) ? diag :
507 :     ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
508 :     -1)))));
509 :     int i, n_x, i_from = 0;
510 :     SEXP ans = PROTECT(allocVector(REALSXP,
511 :     /* ^^^^ FIXME[Generalize] */
512 :     (res_kind == diag ||
513 :     res_kind == diag_backpermuted) ? n : 1));
514 :     double *v = REAL(ans);
515 :     /* ^^^^^^ ^^^^ FIXME[Generalize] */
516 :    
517 :     #define for_DIAG(v_ASSIGN) \
518 :     for(i = 0; i < n; i++, i_from += n_x) { \
519 :     /* looking at i-th column */ \
520 :     n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
521 :     v_ASSIGN; \
522 :     }
523 :    
524 :     /* NOTA BENE: we assume -- uplo = "L" i.e. lower triangular matrix
525 :     * for uplo = "U" (makes sense with a "dtCMatrix" !),
526 :     * should use x_x[i_from + (nx - 1)] instead of x_x[i_from],
527 :     * where nx = (x_p[i+1] - x_p[i])
528 :     */
529 :    
530 :     switch(res_kind) {
531 :     case trace:
532 :     v[0] = 0.;
533 :     for_DIAG(v[0] += x_x[i_from]);
534 :     break;
535 :    
536 :     case sum_log:
537 :     v[0] = 0.;
538 :     for_DIAG(v[0] += log(x_x[i_from]));
539 :     break;
540 :    
541 :     case prod:
542 :     v[0] = 1.;
543 :     for_DIAG(v[0] *= x_x[i_from]);
544 :     break;
545 :    
546 :     case diag:
547 :     for_DIAG(v[i] = x_x[i_from]);
548 :     break;
549 :    
550 :     case diag_backpermuted:
551 :     for_DIAG(v[i] = x_x[i_from]);
552 :    
553 : mmaechler 2175 warning(_("resultKind = 'diagBack' (back-permuted) is experimental"));
554 : maechler 2144 /* now back_permute : */
555 :     for(i = 0; i < n; i++) {
556 :     double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
557 :     /*^^^^ FIXME[Generalize] */
558 :     }
559 : maechler 2137 break;
560 :    
561 :     default: /* -1 from above */
562 :     error("diag_tC(): invalid 'resultKind'");
563 :     /* Wall: */ ans = R_NilValue; v = REAL(ans);
564 :     }
565 :    
566 :     UNPROTECT(1);
567 :     return ans;
568 :     }
569 :    
570 :     /**
571 :     * Extract the diagonal entries from *triangular* Csparse matrix __or__ a
572 :     * cholmod_sparse factor (LDL = TRUE).
573 :     *
574 :     * @param pslot 'p' (column pointer) slot of Csparse matrix/factor
575 :     * @param xslot 'x' (non-zero entries) slot of Csparse matrix/factor
576 : mmaechler 2175 * @param perm_slot 'perm' (= permutation vector) slot of corresponding CHMfactor;
577 :     * only used for "diagBack"
578 : maechler 2137 * @param resultKind a (SEXP) string indicating which kind of result is desired.
579 :     *
580 :     * @return a SEXP, either a (double) number or a length n-vector of diagonal entries
581 :     */
582 :     SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
583 :     {
584 :     int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
585 :     *x_p = INTEGER(pslot),
586 :     *perm = INTEGER(perm_slot);
587 :     double *x_x = REAL(xslot);
588 :     /* ^^^^^^ ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
589 :    
590 :     return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
591 :     }

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