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2304 bates 1
			/* Sparse matrices in compressed column-oriented form */
1830 bates 2
#include "Csparse.h"
4972 maechler 3
#include "Tsparse.h"
1830 bates 4
#include "chm_common.h"
5
 
6
SEXP Csparse_validate(SEXP x)
7
{
3791 maechler 8
    /* NB: we do *NOT* check a potential 'x' slot here, at all */
1830 bates 9
    SEXP pslot = GET_SLOT(x, Matrix_pSym),
10
	islot = GET_SLOT(x, Matrix_iSym);
4456 maechler 11
    Rboolean sorted, strictly;
12
    int j, k,
1830 bates 13
	*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
3943 maechler 14
	nrow = dims[0],
15
	ncol = dims[1],
3931 maechler 16
	*xp = INTEGER(pslot),
1830 bates 17
	*xi = INTEGER(islot);
18
 
3931 maechler 19
    if (length(pslot) != dims[1] + 1)
20
	return mkString(_("slot p must have length = ncol(.) + 1"));
1830 bates 21
    if (xp[0] != 0)
22
	return mkString(_("first element of slot p must be zero"));
4456 maechler 23
    if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
3766 bates 24
	return
25
	    mkString(_("last element of slot p must match length of slots i and x"));
26
    for (j = 0; j < length(islot); j++) {
27
	if (xi[j] < 0 || xi[j] >= nrow)
28
	    return mkString(_("all row indices must be between 0 and nrow-1"));
29
    }
4456 maechler 30
    sorted = TRUE; strictly = TRUE;
1830 bates 31
    for (j = 0; j < ncol; j++) {
32
	if (xp[j] > xp[j+1])
33
	    return mkString(_("slot p must be non-decreasing"));
4456 maechler 34
	if(sorted)
35
	    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
	    }
1830 bates 41
    }
3931 maechler 42
    if (!sorted) {
4565 maechler 43
	CHM_SP chx = AS_CHM_SP(x);
44
	R_CheckStack();
45
 
3931 maechler 46
	cholmod_sort(chx, &c);
4456 maechler 47
	/* Now re-check that row indices are *strictly* increasing
48
	 * (and not just increasing) within each column : */
49
	for (j = 0; j < ncol; j++) {
50
	    for (k = xp[j] + 1; k < xp[j + 1]; k++)
51
		if (xi[k] == xi[k - 1])
52
		    return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));
53
	}
54
 
55
    } else if(!strictly) {  /* sorted, but not strictly */
56
	return mkString(_("slot i is not *strictly* increasing inside a column"));
3931 maechler 57
    }
1830 bates 58
    return ScalarLogical(1);
59
}
60
 
4573 maechler 61
SEXP Rsparse_validate(SEXP x)
62
{
63
    /* NB: we do *NOT* check a potential 'x' slot here, at all */
64
    SEXP pslot = GET_SLOT(x, Matrix_pSym),
65
	jslot = GET_SLOT(x, Matrix_jSym);
66
    Rboolean sorted, strictly;
67
    int i, k,
68
	*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
69
	nrow = dims[0],
70
	ncol = dims[1],
71
	*xp = INTEGER(pslot),
72
	*xj = INTEGER(jslot);
73
 
74
    if (length(pslot) != dims[0] + 1)
75
	return mkString(_("slot p must have length = nrow(.) + 1"));
76
    if (xp[0] != 0)
77
	return mkString(_("first element of slot p must be zero"));
78
    if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
79
	return
80
	    mkString(_("last element of slot p must match length of slots j and x"));
81
    for (i = 0; i < length(jslot); i++) {
82
	if (xj[i] < 0 || xj[i] >= ncol)
83
	    return mkString(_("all column indices must be between 0 and ncol-1"));
84
    }
85
    sorted = TRUE; strictly = TRUE;
86
    for (i = 0; i < nrow; i++) {
87
	if (xp[i] > xp[i+1])
88
	    return mkString(_("slot p must be non-decreasing"));
89
	if(sorted)
90
	    for (k = xp[i] + 1; k < xp[i + 1]; k++) {
91
		if (xj[k] < xj[k - 1])
92
		    sorted = FALSE;
93
		else if (xj[k] == xj[k - 1])
94
		    strictly = FALSE;
95
	    }
96
    }
97
    if (!sorted)
98
	/* cannot easily use cholmod_sort(.) ... -> "error out" :*/
99
	return mkString(_("slot j is not increasing inside a column"));
100
    else if(!strictly) /* sorted, but not strictly */
101
	return mkString(_("slot j is not *strictly* increasing inside a column"));
102
 
103
    return ScalarLogical(1);
104
}
105
 
106
 
4109 maechler 107
/* Called from ../R/Csparse.R : */
108
/* Can only return [dln]geMatrix (no symm/triang);
109
 * FIXME: replace by non-CHOLMOD code ! */
2022 bates 110
SEXP Csparse_to_dense(SEXP x)
111
{
4565 maechler 112
    CHM_SP chxs = AS_CHM_SP(x);
4109 maechler 113
    /* This loses the symmetry property, since cholmod_dense has none,
114
     * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
115
     * to numeric (CHOLMOD_REAL) ones : */
4565 maechler 116
    CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
4109 maechler 117
    int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
4565 maechler 118
    R_CheckStack();
2022 bates 119
 
4093 maechler 120
    return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
2022 bates 121
}
122
 
3755 maechler 123
SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
3406 bates 124
{
4565 maechler 125
    CHM_SP chxs = AS_CHM_SP(x);
126
    CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
4418 bates 127
    int tr = asLogical(tri);
4565 maechler 128
    R_CheckStack();
3406 bates 129
 
4565 maechler 130
    return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
4418 bates 131
			      tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
132
			      0, tr ? diag_P(x) : "",
3755 maechler 133
			      GET_SLOT(x, Matrix_DimNamesSym));
3406 bates 134
}
135
 
3401 bates 136
SEXP Csparse_to_matrix(SEXP x)
1830 bates 137
{
4565 maechler 138
    return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),
139
			       1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
3401 bates 140
}
141
 
142
SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
143
{
4565 maechler 144
    CHM_SP chxs = AS_CHM_SP(x);
145
    CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
4418 bates 146
    int tr = asLogical(tri);
4093 maechler 147
    int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
4565 maechler 148
    R_CheckStack();
1830 bates 149
 
4418 bates 150
    return chm_triplet_to_SEXP(chxt, 1,
151
			       tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
152
			       Rkind, tr ? diag_P(x) : "",
3406 bates 153
			       GET_SLOT(x, Matrix_DimNamesSym));
1830 bates 154
}
155
 
3502 bates 156
/* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
3406 bates 157
SEXP Csparse_symmetric_to_general(SEXP x)
158
{
4565 maechler 159
    CHM_SP chx = AS_CHM_SP(x), chgx;
4093 maechler 160
    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
4565 maechler 161
    R_CheckStack();
3406 bates 162
 
163
    if (!(chx->stype))
3755 maechler 164
	error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
3410 maechler 165
    chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
166
    /* xtype: pattern, "real", complex or .. */
3755 maechler 167
    return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
3406 bates 168
			      GET_SLOT(x, Matrix_DimNamesSym));
169
}
170
 
3876 maechler 171
SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
3835 maechler 172
{
4565 maechler 173
    CHM_SP chx = AS_CHM_SP(x), chgx;
4953 maechler 174
    int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
4093 maechler 175
    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
4565 maechler 176
    R_CheckStack();
3835 maechler 177
 
3876 maechler 178
    chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
3835 maechler 179
    /* xtype: pattern, "real", complex or .. */
180
    return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
181
			      GET_SLOT(x, Matrix_DimNamesSym));
182
}
183
 
3404 bates 184
SEXP Csparse_transpose(SEXP x, SEXP tri)
1830 bates 185
{
4500 maechler 186
    /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
187
     *       since cholmod (& cs) lacks sparse 'int' matrices */
4565 maechler 188
    CHM_SP chx = AS_CHM_SP(x);
4093 maechler 189
    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
4565 maechler 190
    CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
3401 bates 191
    SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
4418 bates 192
    int tr = asLogical(tri);
4565 maechler 193
    R_CheckStack();
3404 bates 194
 
3401 bates 195
    tmp = VECTOR_ELT(dn, 0);	/* swap the dimnames */
196
    SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
197
    SET_VECTOR_ELT(dn, 1, tmp);
198
    UNPROTECT(1);
4418 bates 199
    return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
200
			      tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
201
			      Rkind, tr ? diag_P(x) : "", dn);
1830 bates 202
}
203
 
204
SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
205
{
4972 maechler 206
    CHM_SP
207
	cha = AS_CHM_SP(Csparse_diagU2N(a)),
208
	chb = AS_CHM_SP(Csparse_diagU2N(b)),
4979 maechler 209
	chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
210
			     cha->xtype, /*out sorted:*/ 1, &c);
211
    const char *cl_a = class_P(a), *cl_b = class_P(b);
212
    char diag[] = {'\0', '\0'};
213
    int uploT = 0;
3401 bates 214
    SEXP dn = allocVector(VECSXP, 2);
4565 maechler 215
    R_CheckStack();
1830 bates 216
 
4979 maechler 217
    /* Preserve triangularity and even unit-triangularity if appropriate.
218
     * Note that in that case, the multiplication itself should happen
219
     * faster.  But there's no support for that in CHOLMOD */
220
 
221
    /* UGLY hack -- rather should have (fast!) C-level version of
222
     *       is(a, "triangularMatrix") etc */
223
    if (cl_a[1] == 't' && cl_b[1] == 't')
224
	/* FIXME: fails for "Cholesky","BunchKaufmann"..*/
225
	if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
226
	    uploT = (*uplo_P(a) == 'U') ? 1 : -1;
227
	    if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
228
		/* "remove the diagonal entries": */
229
		chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
230
		diag[0]= 'U';
231
	    }
232
	    else diag[0]= 'N';
233
	}
3401 bates 234
    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
235
		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
236
    SET_VECTOR_ELT(dn, 1,
237
		   duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
4979 maechler 238
    return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
1830 bates 239
}
240
 
3942 maechler 241
SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
3940 bates 242
{
3942 maechler 243
    int tr = asLogical(trans);
4972 maechler 244
    CHM_SP
245
	cha = AS_CHM_SP(Csparse_diagU2N(a)),
246
	chb = AS_CHM_SP(Csparse_diagU2N(b)),
247
	chTr, chc;
4979 maechler 248
    const char *cl_a = class_P(a), *cl_b = class_P(b);
249
    char diag[] = {'\0', '\0'};
250
    int uploT = 0;
3940 bates 251
    SEXP dn = allocVector(VECSXP, 2);
4565 maechler 252
    R_CheckStack();
3940 bates 253
 
4565 maechler 254
    chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
3942 maechler 255
    chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
4979 maechler 256
			 /*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
4565 maechler 257
    cholmod_free_sparse(&chTr, &c);
3942 maechler 258
 
4979 maechler 259
    /* Preserve triangularity and unit-triangularity if appropriate;
260
     * see Csparse_Csparse_prod() for comments */
261
    if (cl_a[1] == 't' && cl_b[1] == 't')
262
	if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
263
	    uploT = (*uplo_P(b) == 'U') ? 1 : -1;
264
	    if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
265
		chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
266
		diag[0]= 'U';
267
	    }
268
	    else diag[0]= 'N';
269
	}
270
 
3940 bates 271
    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
3942 maechler 272
		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
3940 bates 273
    SET_VECTOR_ELT(dn, 1,
3942 maechler 274
		   duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
4979 maechler 275
    return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
3940 bates 276
}
277
 
1830 bates 278
SEXP Csparse_dense_prod(SEXP a, SEXP b)
279
{
4972 maechler 280
    CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));
3943 maechler 281
    SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
4565 maechler 282
    CHM_DN chb = AS_CHM_DN(b_M);
283
    CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
284
					chb->xtype, &c);
285
    SEXP dn = PROTECT(allocVector(VECSXP, 2));
286
    double one[] = {1,0}, zero[] = {0,0};
287
    R_CheckStack();
1830 bates 288
 
4565 maechler 289
    cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
3943 maechler 290
    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
291
		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
292
    SET_VECTOR_ELT(dn, 1,
293
		   duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
4565 maechler 294
    UNPROTECT(2);
3943 maechler 295
    return chm_dense_to_SEXP(chc, 1, 0, dn);
1830 bates 296
}
1833 maechler 297
 
2030 bates 298
SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
299
{
4972 maechler 300
    CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));
3943 maechler 301
    SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
4565 maechler 302
    CHM_DN chb = AS_CHM_DN(b_M);
303
    CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
304
					chb->xtype, &c);
305
    SEXP dn = PROTECT(allocVector(VECSXP, 2));
306
    double one[] = {1,0}, zero[] = {0,0};
307
    R_CheckStack();
2030 bates 308
 
4565 maechler 309
    cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
3943 maechler 310
    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
311
		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
312
    SET_VECTOR_ELT(dn, 1,
313
		   duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
4565 maechler 314
    UNPROTECT(2);
3943 maechler 315
    return chm_dense_to_SEXP(chc, 1, 0, dn);
2030 bates 316
}
317
 
4979 maechler 318
/* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
319
   see Csparse_Csparse_crossprod above for  x'y and x y' */
1836 bates 320
SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
1830 bates 321
{
1870 maechler 322
    int trip = asLogical(triplet),
323
	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
4972 maechler 324
    CHM_TR cht = trip ? AS_CHM_TR(Tsparse_diagU2N(x)) : (CHM_TR) NULL;
4565 maechler 325
    CHM_SP chcp, chxt,
4972 maechler 326
	chx = (trip ?
327
	       cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
328
	       AS_CHM_SP(Csparse_diagU2N(x)));
3401 bates 329
    SEXP dn = PROTECT(allocVector(VECSXP, 2));
4565 maechler 330
    R_CheckStack();
1830 bates 331
 
4565 maechler 332
    if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
1836 bates 333
    chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
4972 maechler 334
    if(!chcp) {
335
	UNPROTECT(1);
336
	error(_("Csparse_crossprod(): error return from cholmod_aat()"));
337
    }
3388 bates 338
    cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
339
    chcp->stype = 1;
4565 maechler 340
    if (trip) cholmod_free_sparse(&chx, &c);
1831 bates 341
    if (!tr) cholmod_free_sparse(&chxt, &c);
4565 maechler 342
    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
3401 bates 343
		   duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
3943 maechler 344
					(tr) ? 0 : 1)));
3401 bates 345
    SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
346
    UNPROTECT(1);
3755 maechler 347
    return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
1830 bates 348
}
1831 bates 349
 
3876 maechler 350
SEXP Csparse_drop(SEXP x, SEXP tol)
351
{
4565 maechler 352
    CHM_SP chx = AS_CHM_SP(x);
353
    CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
3876 maechler 354
    double dtol = asReal(tol);
4093 maechler 355
    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
4565 maechler 356
    R_CheckStack();
3876 maechler 357
 
358
    if(!cholmod_drop(dtol, ans, &c))
359
	error(_("cholmod_drop() failed"));
4093 maechler 360
    return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
361
			      GET_SLOT(x, Matrix_DimNamesSym));
3876 maechler 362
}
363
 
2304 bates 364
SEXP Csparse_horzcat(SEXP x, SEXP y)
365
{
4565 maechler 366
    CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);
3755 maechler 367
    int Rkind = 0; /* only for "d" - FIXME */
4565 maechler 368
    R_CheckStack();
3410 maechler 369
 
3401 bates 370
    /* FIXME: currently drops dimnames */
4565 maechler 371
    return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
372
			      1, 0, Rkind, "", R_NilValue);
2304 bates 373
}
374
 
375
SEXP Csparse_vertcat(SEXP x, SEXP y)
376
{
4565 maechler 377
    CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);
3755 maechler 378
    int Rkind = 0; /* only for "d" - FIXME */
4565 maechler 379
    R_CheckStack();
3410 maechler 380
 
3401 bates 381
    /* FIXME: currently drops dimnames */
4565 maechler 382
    return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
383
			      1, 0, Rkind, "", R_NilValue);
2304 bates 384
}
3134 bates 385
 
386
SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
387
{
4565 maechler 388
    CHM_SP chx = AS_CHM_SP(x);
4093 maechler 389
    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
4565 maechler 390
    CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
391
    R_CheckStack();
3134 bates 392
 
4093 maechler 393
    return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
394
			      GET_SLOT(x, Matrix_DimNamesSym));
3134 bates 395
}
3401 bates 396
 
397
SEXP Csparse_diagU2N(SEXP x)
398
{
4972 maechler 399
    const char *cl = class_P(x);
400
    /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
401
    if (cl[1] != 't' || *diag_P(x) != 'U') {
4979 maechler 402
	/* "trivially fast" when not triangular (<==> no 'diag' slot),
403
	   or not *unit* triangular */
4052 maechler 404
	return (x);
405
    }
4979 maechler 406
    else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
4565 maechler 407
	CHM_SP chx = AS_CHM_SP(x);
408
	CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
4052 maechler 409
	double one[] = {1, 0};
4565 maechler 410
	CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
4055 maechler 411
	int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
4093 maechler 412
	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
3401 bates 413
 
4565 maechler 414
	R_CheckStack();
415
	cholmod_free_sparse(&eye, &c);
4052 maechler 416
	return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
4093 maechler 417
				  GET_SLOT(x, Matrix_DimNamesSym));
4052 maechler 418
    }
3401 bates 419
}
420
 
4979 maechler 421
SEXP Csparse_diagN2U(SEXP x)
422
{
423
    const char *cl = class_P(x);
424
    /* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
425
    if (cl[1] != 't' || *diag_P(x) != 'N') {
426
	/* "trivially fast" when not triangular (<==> no 'diag' slot),
427
	   or already *unit* triangular */
428
	return (x);
429
    }
430
    else { /* triangular with diag='N'): now drop the diagonal */
431
	/* duplicate, since chx will be modified: */
432
	CHM_SP chx = AS_CHM_SP(duplicate(x));
433
	int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
434
	    Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
435
	R_CheckStack();
436
 
437
	chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
438
 
439
	return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
440
				  uploT, Rkind, "U",
441
				  GET_SLOT(x, Matrix_DimNamesSym));
442
    }
443
}
444
 
3401 bates 445
SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
446
{
4565 maechler 447
    CHM_SP chx = AS_CHM_SP(x);
3401 bates 448
    int rsize = (isNull(i)) ? -1 : LENGTH(i),
449
	csize = (isNull(j)) ? -1 : LENGTH(j);
4093 maechler 450
    int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
4565 maechler 451
    R_CheckStack();
3401 bates 452
 
453
    if (rsize >= 0 && !isInteger(i))
454
	error(_("Index i must be NULL or integer"));
455
    if (csize >= 0 && !isInteger(j))
456
	error(_("Index j must be NULL or integer"));
4093 maechler 457
 
3401 bates 458
    return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
3410 maechler 459
						INTEGER(j), csize,
3401 bates 460
						TRUE, TRUE, &c),
4093 maechler 461
			      1, 0, Rkind, "",
462
			      /* FIXME: drops dimnames */ R_NilValue);
3401 bates 463
}
4734 bates 464
 
465
SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
466
{
467
    FILE *f = fopen(CHAR(asChar(fname)), "w");
468
 
469
    if (!f)
470
	error(_("failure to open file \"%s\" for writing"),
471
	      CHAR(asChar(fname)));
4972 maechler 472
    if (!cholmod_write_sparse(f, AS_CHM_SP(Csparse_diagU2N(x)),
473
			      (CHM_SP)NULL, (char*) NULL, &c))
4734 bates 474
	error(_("cholmod_write_sparse returned error code"));
475
    fclose(f);
476
    return R_NilValue;
477
}
4994 maechler 478
 
479
 
480
/**
481
 * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
482
 * cholmod_sparse factor (LDL = TRUE).
483
 *
484
 * @param n  dimension of the matrix.
485
 * @param x_p  'p' (column pointer) slot contents
486
 * @param x_x  'x' (non-zero entries) slot contents
487
 * @param perm 'perm' (= permutation vector) slot contents
488
 * @param resultKind a (SEXP) string indicating which kind of result is desired.
489
 *
490
 * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
491
 */
492
SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
493
/*                                ^^^^^^ FIXME[Generalize] to int / ... */
494
{
495
    const char* res_ch = CHAR(STRING_ELT(resultKind,0));
496
    enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
497
    } res_kind = ((!strcmp(res_ch, "trace")) ? trace :
498
		  ((!strcmp(res_ch, "sumLog")) ? sum_log :
499
		   ((!strcmp(res_ch, "prod")) ? prod :
500
		    ((!strcmp(res_ch, "diag")) ? diag :
501
		     ((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
502
		      -1)))));
503
    int i, n_x, i_from = 0;
504
    SEXP ans = PROTECT(allocVector(REALSXP,
505
/*                                 ^^^^  FIXME[Generalize] */
506
				   (res_kind == diag ||
507
				    res_kind == diag_backpermuted) ? n : 1));
508
    double *v = REAL(ans);
509
/*  ^^^^^^      ^^^^  FIXME[Generalize] */
510
 
511
#define for_DIAG(v_ASSIGN)						\
512
    for(i = 0; i < n; i++, i_from += n_x) {				\
513
	/* looking at i-th column */					\
514
	n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */	\
515
	v_ASSIGN;							\
516
    }
517
 
518
    /* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
519
     *            for uplo = "U" (makes sense with a "dtCMatrix" !),
520
     *            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
521
     *            where nx = (x_p[i+1] - x_p[i])
522
     */
523
 
524
    switch(res_kind) {
525
    case trace:
526
	v[0] = 0.;
527
	for_DIAG(v[0] += x_x[i_from]);
528
	break;
529
 
530
    case sum_log:
531
	v[0] = 0.;
532
	for_DIAG(v[0] += log(x_x[i_from]));
533
	break;
534
 
535
    case prod:
536
	v[0] = 1.;
537
	for_DIAG(v[0] *= x_x[i_from]);
538
	break;
539
 
540
    case diag:
541
	for_DIAG(v[i] = x_x[i_from]);
542
	break;
543
 
544
    case diag_backpermuted:
545
	for_DIAG(v[i] = x_x[i_from]);
546
 
547
	error(_("resultKind = 'diagBack' (back-permuted) is not yet implemented"));
5003 maechler 548
	/* now back_permute : */
549
	for(i = 0; i < n; i++) {
550
	    double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
551
	    /*^^^^ FIXME[Generalize] */
552
	}
4994 maechler 553
	break;
554
 
555
    default: /* -1 from above */
556
	error("diag_tC(): invalid 'resultKind'");
557
	/* Wall: */ ans = R_NilValue; v = REAL(ans);
558
    }
559
 
560
    UNPROTECT(1);
561
    return ans;
562
}
563
 
564
/**
565
 * Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
566
 * cholmod_sparse factor (LDL = TRUE).
567
 *
568
 * @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
569
 * @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
570
 * @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor
571
 * @param resultKind a (SEXP) string indicating which kind of result is desired.
572
 *
573
 * @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
574
 */
575
SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
576
{
577
    int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
578
	*x_p  = INTEGER(pslot),
579
	*perm = INTEGER(perm_slot);
580
    double *x_x = REAL(xslot);
581
/*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
582
 
583
    return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
584
}