Diff of /pkg/Matrix/src/Csparse.c

Parent Directory | Revision Log | Patch

	pkg/src/Csparse.c revision 1657, Wed Nov 1 16:29:53 2006 UTC	pkg/Matrix/src/Csparse.c revision 2804, Thu Jun 28 13:45:01 2012 UTC
#	Line 1	Line 1
1	/* Sparse matrices in compressed column-oriented form */	/* Sparse matrices in compressed column-oriented form */
2
3	#include "Csparse.h"	#include "Csparse.h"
4		#include "Tsparse.h"
5	#include "chm_common.h"	#include "chm_common.h"
6
7	SEXP Csparse_validate(SEXP x)	/** "Cheap" C version of  Csparse_validate() - *not* sorting : */
8		Rboolean isValid_Csparse(SEXP x)
9	{	{
10	/* NB: we do *NOT* check a potential 'x' slot here, at all */	/* NB: we do *NOT* check a potential 'x' slot here, at all */
11	SEXP pslot = GET_SLOT(x, Matrix_pSym),	SEXP pslot = GET_SLOT(x, Matrix_pSym),
12	islot = GET_SLOT(x, Matrix_iSym);	islot = GET_SLOT(x, Matrix_iSym);
13	int j, k, ncol, nrow, sorted,	int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)), j,
14		nrow = dims[0],
15		ncol = dims[1],
16		*xp = INTEGER(pslot),
17		*xi = INTEGER(islot);
18
19		if (length(pslot) != dims[1] + 1)
20		return FALSE;
21		if (xp[0] != 0)
22		return FALSE;
23		if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
24		return FALSE;
25		for (j = 0; j < xp[ncol]; j++) {
26		if (xi[j] < 0 || xi[j] >= nrow)
27		return FALSE;
28		}
29		for (j = 0; j < ncol; j++) {
30		if (xp[j] > xp[j + 1])
31		return FALSE;
32		}
33		return TRUE;
34		}
35
36		SEXP Csparse_validate(SEXP x) {
37		return Csparse_validate_(x, FALSE);
38		}
39
40		SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
41		return Csparse_validate_(x, asLogical(maybe_modify));
42		}
43
44		SEXP Csparse_validate_(SEXP x, Rboolean maybe_modify)
45		{
46		/* NB: we do *NOT* check a potential 'x' slot here, at all */
47		SEXP pslot = GET_SLOT(x, Matrix_pSym),
48		islot = GET_SLOT(x, Matrix_iSym);
49		Rboolean sorted, strictly;
50		int j, k,
51	*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),	*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
52		nrow = dims[0],
53		ncol = dims[1],
54	*xp = INTEGER(pslot),	*xp = INTEGER(pslot),
55	*xi = INTEGER(islot);	*xi = INTEGER(islot);
56
	nrow = dims[0];
	ncol = dims[1];
57	if (length(pslot) != dims[1] + 1)	if (length(pslot) != dims[1] + 1)
58	return mkString(_("slot p must have length = ncol(.) + 1"));	return mkString(_("slot p must have length = ncol(.) + 1"));
59	if (xp[0] != 0)	if (xp[0] != 0)
60	return mkString(_("first element of slot p must be zero"));	return mkString(_("first element of slot p must be zero"));
61	if (length(islot) != xp[ncol])	if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
62	return	return
63	mkString(_("last element of slot p must match length of slots i and x"));	mkString(_("last element of slot p must match length of slots i and x"));
64	for (j = 0; j < length(islot); j++) {	for (j = 0; j < xp[ncol]; j++) {
65	if (xi[j] < 0 || xi[j] >= nrow)	if (xi[j] < 0 || xi[j] >= nrow)
66	return mkString(_("all row indices must be between 0 and nrow-1"));	return mkString(_("all row indices must be between 0 and nrow-1"));
67	}	}
68	sorted = TRUE;	sorted = TRUE; strictly = TRUE;
69	for (j = 0; j < ncol; j++) {	for (j = 0; j < ncol; j++) {
70	if (xp[j] > xp[j+1])	if (xp[j] > xp[j+1])
71	return mkString(_("slot p must be non-decreasing"));	return mkString(_("slot p must be non-decreasing"));
72	for (k = xp[j] + 1; k < xp[j + 1]; k++)	if(sorted) /* only act if >= 2 entries in column j : */
73	if (xi[k] < xi[k - 1]) sorted = FALSE;	for (k = xp[j] + 1; k < xp[j + 1]; k++) {
74		if (xi[k] < xi[k - 1])
75		sorted = FALSE;
76		else if (xi[k] == xi[k - 1])
77		strictly = FALSE;
78		}
79	}	}
80	if (!sorted) {	if (!sorted) {
81	cholmod_sparse *chx = as_cholmod_sparse(x);	if(maybe_modify) {
82	cholmod_sort(chx, &c);	CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
83	Free(chx);	R_CheckStack();
84		as_cholmod_sparse(chx, x, FALSE, TRUE);/*-> cholmod_l_sort() ! */
85		/* as chx = AS_CHM_SP__(x)  but  ^^^^ sorting x in_place !!! */
86
87		/* Now re-check that row indices are *strictly* increasing
88		* (and not just increasing) within each column : */
89		for (j = 0; j < ncol; j++) {
90		for (k = xp[j] + 1; k < xp[j + 1]; k++)
91		if (xi[k] == xi[k - 1])
92		return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_l_sort)"));
93		}
94		} else { /* no modifying sorting : */
95		return mkString(_("row indices are not sorted within columns"));
96		}
97		} else if(!strictly) {  /* sorted, but not strictly */
98		return mkString(_("slot i is not *strictly* increasing inside a column"));
99	}	}
100	return ScalarLogical(1);	return ScalarLogical(1);
101	}	}
102
103		SEXP Rsparse_validate(SEXP x)
104		{
105		/* NB: we do *NOT* check a potential 'x' slot here, at all */
106		SEXP pslot = GET_SLOT(x, Matrix_pSym),
107		jslot = GET_SLOT(x, Matrix_jSym);
108		Rboolean sorted, strictly;
109		int i, k,
110		*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
111		nrow = dims[0],
112		ncol = dims[1],
113		*xp = INTEGER(pslot),
114		*xj = INTEGER(jslot);
115
116		if (length(pslot) != dims[0] + 1)
117		return mkString(_("slot p must have length = nrow(.) + 1"));
118		if (xp[0] != 0)
119		return mkString(_("first element of slot p must be zero"));
120		if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
121		return
122		mkString(_("last element of slot p must match length of slots j and x"));
123		for (i = 0; i < length(jslot); i++) {
124		if (xj[i] < 0 || xj[i] >= ncol)
125		return mkString(_("all column indices must be between 0 and ncol-1"));
126		}
127		sorted = TRUE; strictly = TRUE;
128		for (i = 0; i < nrow; i++) {
129		if (xp[i] > xp[i+1])
130		return mkString(_("slot p must be non-decreasing"));
131		if(sorted)
132		for (k = xp[i] + 1; k < xp[i + 1]; k++) {
133		if (xj[k] < xj[k - 1])
134		sorted = FALSE;
135		else if (xj[k] == xj[k - 1])
136		strictly = FALSE;
137		}
138		}
139		if (!sorted)
140		/* cannot easily use cholmod_sort(.) ... -> "error out" :*/
141		return mkString(_("slot j is not increasing inside a column"));
142		else if(!strictly) /* sorted, but not strictly */
143		return mkString(_("slot j is not *strictly* increasing inside a column"));
144
145		return ScalarLogical(1);
146		}
147
148
149		/* Called from ../R/Csparse.R : */
150		/* Can only return [dln]geMatrix (no symm/triang);
151		* FIXME: replace by non-CHOLMOD code ! */
152	SEXP Csparse_to_dense(SEXP x)	SEXP Csparse_to_dense(SEXP x)
153	{	{
154	cholmod_sparse *chxs = as_cholmod_sparse(x);	CHM_SP chxs = AS_CHM_SP__(x);
155	cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);	/* This loses the symmetry property, since cholmod_dense has none,
156		* BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
157		* to numeric (CHOLMOD_REAL) ones : */
158		CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
159		int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
160		R_CheckStack();
161
162	Free(chxs);	return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
	return chm_dense_to_SEXP(chxd, 1, Real_kind(x));
163	}	}
164
165		// FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
166	SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)	SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
167	{	{
168	cholmod_sparse *chxs = as_cholmod_sparse(x);	CHM_SP chxs = AS_CHM_SP__(x);
169	cholmod_sparse	CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
170	*chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);	int tr = asLogical(tri);
171	int uploT = 0; char *diag = "";	R_CheckStack();
172
173	Free(chxs);	return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
174	if (asLogical(tri)) {       /* triangular sparse matrices */	tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
175	uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?	0, tr ? diag_P(x) : "",
	-1 : 1;
	diag = CHAR(asChar(GET_SLOT(x, Matrix_diagSym)));
	}
	return chm_sparse_to_SEXP(chxcp, 1, uploT, 0, diag,
176	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
177	}	}
178
179	SEXP Csparse_to_matrix(SEXP x)	// n.CMatrix --> [dli].CMatrix  (not going through CHM!)
180		SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
181		{
182		return nz2Csparse(x, asInteger(res_kind));
183		}
184		// n.CMatrix --> [dli].CMatrix  (not going through CHM!)
185		SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
186	{	{
187	cholmod_sparse *chxs = as_cholmod_sparse(x);	const char *cl_x = class_P(x);
188	cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);	if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
189		if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
190		int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
191		SEXP ans;
192		char *ncl = alloca(strlen(cl_x) + 1); /* not much memory required */
193		strcpy(ncl, cl_x);
194		double *dx_x; int *ix_x;
195		ncl[0] = (r_kind == x_double ? 'd' :
196		(r_kind == x_logical ? 'l' :
197		/* else (for now):  r_kind == x_integer : */ 'i'));
198		PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
199		// create a correct 'x' slot:
200		switch(r_kind) {
201		int i;
202		case x_double: // 'd'
203		dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
204		for (i=0; i < nnz; i++) dx_x[i] = 1.;
205		break;
206		case x_logical: // 'l'
207		ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
208		for (i=0; i < nnz; i++) ix_x[i] = TRUE;
209		break;
210		case x_integer: // 'i'
211		ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
212		for (i=0; i < nnz; i++) ix_x[i] = 1;
213		break;
214
215		default:
216		error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
217		r_kind);
218		}
219
220		// now copy all other slots :
221		slot_dup(ans, x, Matrix_iSym);
222		slot_dup(ans, x, Matrix_pSym);
223		slot_dup(ans, x, Matrix_DimSym);
224		slot_dup(ans, x, Matrix_DimNamesSym);
225		if(ncl[1] != 'g') { // symmetric or triangular ...
226		slot_dup_if_has(ans, x, Matrix_uploSym);
227		slot_dup_if_has(ans, x, Matrix_diagSym);
228		}
229		UNPROTECT(1);
230		return ans;
231		}
232
233	Free(chxs);	SEXP Csparse_to_matrix(SEXP x)
234	return chm_dense_to_matrix(chxd, 1,	{
235	GET_SLOT(x, Matrix_DimNamesSym));	return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
236		1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
237	}	}
238
239	SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)	SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
240	{	{
241	cholmod_sparse *chxs = as_cholmod_sparse(x);	CHM_SP chxs = AS_CHM_SP__(x);
242	cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);	CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
243	int uploT = 0;	int tr = asLogical(tri);
244	char *diag = "";	int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
245	int Rkind = (chxs->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	R_CheckStack();
246
247	Free(chxs);	return chm_triplet_to_SEXP(chxt, 1,
248	if (asLogical(tri)) {       /* triangular sparse matrices */	tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
249	uploT = (*uplo_P(x) == 'U') ? -1 : 1;	Rkind, tr ? diag_P(x) : "",
	diag = diag_P(x);
	}
	return chm_triplet_to_SEXP(chxt, 1, uploT, Rkind, diag,
250	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
251	}	}
252
253	/* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */	/* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
254	SEXP Csparse_symmetric_to_general(SEXP x)	SEXP Csparse_symmetric_to_general(SEXP x)
255	{	{
256	cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;	CHM_SP chx = AS_CHM_SP__(x), chgx;
257	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
258		R_CheckStack();
259
260	if (!(chx->stype))	if (!(chx->stype))
261	error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));	error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
262	chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);	chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
263	/* xtype: pattern, "real", complex or .. */	/* xtype: pattern, "real", complex or .. */
	Free(chx);
264	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
265	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
266	}	}
267
268	SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)	SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
269	{	{
270	cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;	CHM_SP chx = AS_CHM_SP__(x), chgx;
271	int uploT = (*CHAR(asChar(uplo)) == 'U') ? -1 : 1;	int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
272	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
273		R_CheckStack();
274
275	chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);	chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
276	/* xtype: pattern, "real", complex or .. */	/* xtype: pattern, "real", complex or .. */
	Free(chx);
277	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
278	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
279	}	}
280
281	SEXP Csparse_transpose(SEXP x, SEXP tri)	SEXP Csparse_transpose(SEXP x, SEXP tri)
282	{	{
283	cholmod_sparse *chx = as_cholmod_sparse(x);	/* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
284	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	*       since cholmod (& cs) lacks sparse 'int' matrices */
285	cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);	CHM_SP chx = AS_CHM_SP__(x);
286		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
287		CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
288	SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;	SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
289	int uploT = 0; char *diag = "";	int tr = asLogical(tri);
290		R_CheckStack();
291
	Free(chx);
292	tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */	tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
293	SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));	SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
294	SET_VECTOR_ELT(dn, 1, tmp);	SET_VECTOR_ELT(dn, 1, tmp);
295	UNPROTECT(1);	UNPROTECT(1);
296	if (asLogical(tri)) {       /* triangular sparse matrices */	return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
297	uploT = (*uplo_P(x) == 'U') ? -1 : 1;	tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
298	diag = diag_P(x);	Rkind, tr ? diag_P(x) : "", dn);
	}
	return chm_sparse_to_SEXP(chxt, 1, uploT, Rkind, diag, dn);
299	}	}
300
301	SEXP Csparse_Csparse_prod(SEXP a, SEXP b)	SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
302	{	{
303	cholmod_sparse *cha = as_cholmod_sparse(a),	CHM_SP
304	*chb = as_cholmod_sparse(b);	cha = AS_CHM_SP(a),
305	cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);	chb = AS_CHM_SP(b),
306	SEXP dn = allocVector(VECSXP, 2);	chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
307		/* values:= is_numeric (T/F) */ cha->xtype > 0,
308		/*out sorted:*/ 1, &c);
309		const char *cl_a = class_P(a), *cl_b = class_P(b);
310		char diag[] = {'\0', '\0'};
311		int uploT = 0;
312		SEXP dn = PROTECT(allocVector(VECSXP, 2));
313		R_CheckStack();
314
315	Free(cha); Free(chb);	#ifdef DEBUG_Matrix_verbose
316		Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
317		#endif
318
319		/* Preserve triangularity and even unit-triangularity if appropriate.
320		* Note that in that case, the multiplication itself should happen
321		* faster.  But there's no support for that in CHOLMOD */
322
323		/* UGLY hack -- rather should have (fast!) C-level version of
324		*       is(a, "triangularMatrix") etc */
325		if (cl_a[1] == 't' && cl_b[1] == 't')
326		/* FIXME: fails for "Cholesky","BunchKaufmann"..*/
327		if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
328		uploT = (*uplo_P(a) == 'U') ? 1 : -1;
329		if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
330		/* "remove the diagonal entries": */
331		chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
332		diag[0]= 'U';
333		}
334		else diag[0]= 'N';
335		}
336	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
337	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
338	SET_VECTOR_ELT(dn, 1,	SET_VECTOR_ELT(dn, 1,
339	duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));	duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
340	return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);	UNPROTECT(1);
341		return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
342	}	}
343
344	SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b)	SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
345	{	{
346	cholmod_sparse *cha = as_cholmod_sparse(a),	int tr = asLogical(trans);
347	*chb = as_cholmod_sparse(b);	CHM_SP
348	cholmod_sparse *chta = cholmod_transpose(cha, 1, &c);	cha = AS_CHM_SP(a),
349	cholmod_sparse *chc = cholmod_ssmult(chta, chb, 0, cha->xtype, 1, &c);	chb = AS_CHM_SP(b),
350	SEXP dn = allocVector(VECSXP, 2);	chTr, chc;
351		const char *cl_a = class_P(a), *cl_b = class_P(b);
352		char diag[] = {'\0', '\0'};
353		int uploT = 0;
354		SEXP dn = PROTECT(allocVector(VECSXP, 2));
355		R_CheckStack();
356
357	Free(cha); Free(chb); cholmod_free_sparse(&chta, &c);	chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
358		chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
359		/*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
360		cholmod_free_sparse(&chTr, &c);
361
362		/* Preserve triangularity and unit-triangularity if appropriate;
363		* see Csparse_Csparse_prod() for comments */
364		if (cl_a[1] == 't' && cl_b[1] == 't')
365		if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
366		uploT = (*uplo_P(b) == 'U') ? 1 : -1;
367		if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
368		chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
369		diag[0]= 'U';
370		}
371		else diag[0]= 'N';
372		}
373	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
374	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
375	SET_VECTOR_ELT(dn, 1,	SET_VECTOR_ELT(dn, 1,
376	duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));	duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
377	return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);	UNPROTECT(1);
378		return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
379	}	}
380
381	SEXP Csparse_dense_prod(SEXP a, SEXP b)	SEXP Csparse_dense_prod(SEXP a, SEXP b)
382	{	{
383	cholmod_sparse *cha = as_cholmod_sparse(a);	CHM_SP cha = AS_CHM_SP(a);
384	cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));	SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
385	cholmod_dense *chc =	CHM_DN chb = AS_CHM_DN(b_M);
386	cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);	CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
387	double alpha[] = {1,0}, beta[] = {0,0};	chb->xtype, &c);
388		SEXP dn = PROTECT(allocVector(VECSXP, 2));
389	cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);	double one[] = {1,0}, zero[] = {0,0};
390	Free(cha); Free(chb);	int nprot = 2;
391	UNPROTECT(1);	R_CheckStack();
392	return chm_dense_to_SEXP(chc, 1, 0);	/* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
393		if(cha->xtype == CHOLMOD_PATTERN) {
394		/* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
395		/*        " --> slightly inefficient coercion")); */
396
397		// This *fails* to produce a CHOLMOD_REAL ..
398		// CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
399		// --> use our Matrix-classes
400		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
401		cha = AS_CHM_SP(da);
402		}
403		cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
404		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
405		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
406		SET_VECTOR_ELT(dn, 1,
407		duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
408		UNPROTECT(nprot);
409		return chm_dense_to_SEXP(chc, 1, 0, dn);
410	}	}
411
412	SEXP Csparse_dense_crossprod(SEXP a, SEXP b)	SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
413	{	{
414	cholmod_sparse *cha = as_cholmod_sparse(a);	CHM_SP cha = AS_CHM_SP(a);
415	cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));	SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
416	cholmod_dense *chc =	CHM_DN chb = AS_CHM_DN(b_M);
417	cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);	CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
418	double alpha[] = {1,0}, beta[] = {0,0};	chb->xtype, &c);
419		SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
420	cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);	double one[] = {1,0}, zero[] = {0,0};
421	Free(cha); Free(chb);	R_CheckStack();
422	UNPROTECT(1);	// -- see Csparse_dense_prod() above :
423	return chm_dense_to_SEXP(chc, 1, 0);	if(cha->xtype == CHOLMOD_PATTERN) {
424		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
425		cha = AS_CHM_SP(da);
426		}
427		cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
428		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
429		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
430		SET_VECTOR_ELT(dn, 1,
431		duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
432		UNPROTECT(nprot);
433		return chm_dense_to_SEXP(chc, 1, 0, dn);
434	}	}
435
436		/* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
437		see Csparse_Csparse_crossprod above for  x'y and x y' */
438	SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)	SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
439	{	{
440	int trip = asLogical(triplet),	int trip = asLogical(triplet),
441	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
442	cholmod_triplet	#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
443	*cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;	CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
444	cholmod_sparse *chcp, *chxt,	#else /* workaround needed:*/
445	*chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)	SEXP xx = PROTECT(Tsparse_diagU2N(x));
446	: as_cholmod_sparse(x);	CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
447		#endif
448		CHM_SP chcp, chxt,
449		chx = (trip ?
450		cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
451		AS_CHM_SP(x));
452	SEXP dn = PROTECT(allocVector(VECSXP, 2));	SEXP dn = PROTECT(allocVector(VECSXP, 2));
453		R_CheckStack();
454
455	if (!tr)	if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
	chxt = cholmod_transpose(chx, chx->xtype, &c);
456	chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);	chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
457	if(!chcp)	if(!chcp) {
458		UNPROTECT(1);
459	error(_("Csparse_crossprod(): error return from cholmod_aat()"));	error(_("Csparse_crossprod(): error return from cholmod_aat()"));
460		}
461	cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);	cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
462	chcp->stype = 1;	chcp->stype = 1;
463	if (trip) {	if (trip) cholmod_free_sparse(&chx, &c);
	cholmod_free_sparse(&chx, &c);
	Free(cht);
	} else {
	Free(chx);
	}
464	if (!tr) cholmod_free_sparse(&chxt, &c);	if (!tr) cholmod_free_sparse(&chxt, &c);
465	/* create dimnames */	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
	SET_VECTOR_ELT(dn, 0,
466	duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),	duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
467	(tr) ? 1 : 0)));	(tr) ? 0 : 1)));
468	SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));	SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
469		#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
470	UNPROTECT(1);	UNPROTECT(1);
471		#else
472		UNPROTECT(2);
473		#endif
474	return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);	return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
475	}	}
476
477		/* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
478		*  at least all "explicit" zeros */
479	SEXP Csparse_drop(SEXP x, SEXP tol)	SEXP Csparse_drop(SEXP x, SEXP tol)
480	{	{
481	cholmod_sparse *chx = as_cholmod_sparse(x),	const char *cl = class_P(x);
482	*ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);	/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
483		int tr = (cl[1] == 't');
484		CHM_SP chx = AS_CHM_SP__(x);
485		CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
486	double dtol = asReal(tol);	double dtol = asReal(tol);
487	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
488		R_CheckStack();
489
490	if(!cholmod_drop(dtol, ans, &c))	if(!cholmod_drop(dtol, ans, &c))
491	error(_("cholmod_drop() failed"));	error(_("cholmod_drop() failed"));
492	Free(chx);	return chm_sparse_to_SEXP(ans, 1,
493	/* FIXME: currently drops dimnames */	tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
494	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);	Rkind, tr ? diag_P(x) : "",
495		GET_SLOT(x, Matrix_DimNamesSym));
496	}	}
497
498	SEXP Csparse_horzcat(SEXP x, SEXP y)	SEXP Csparse_horzcat(SEXP x, SEXP y)
499	{	{
500	cholmod_sparse *chx = as_cholmod_sparse(x),	CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
501	*chy = as_cholmod_sparse(y), *ans;	int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
502	int Rkind = 0; /* only for "d" - FIXME */	Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
503		Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
504	ans = cholmod_horzcat(chx, chy, 1, &c);	R_CheckStack();
505	Free(chx); Free(chy);
506	/* FIXME: currently drops dimnames */	/* TODO: currently drops dimnames - and we fix at R level */
507	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);	return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
508		1, 0, Rkind, "", R_NilValue);
509	}	}
510
511	SEXP Csparse_vertcat(SEXP x, SEXP y)	SEXP Csparse_vertcat(SEXP x, SEXP y)
512	{	{
513	cholmod_sparse *chx = as_cholmod_sparse(x),	CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
514	*chy = as_cholmod_sparse(y), *ans;	int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
515	int Rkind = 0; /* only for "d" - FIXME */	Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
516		Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
517	ans = cholmod_vertcat(chx, chy, 1, &c);	R_CheckStack();
518	Free(chx); Free(chy);
519	/* FIXME: currently drops dimnames */	/* TODO: currently drops dimnames - and we fix at R level */
520	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);	return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
521		1, 0, Rkind, "", R_NilValue);
522	}	}
523
524	SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)	SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
525	{	{
526	cholmod_sparse *chx = as_cholmod_sparse(x), *ans;	CHM_SP chx = AS_CHM_SP__(x);
527	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
528		CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
529		R_CheckStack();
530
531	ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
532	Free(chx);	GET_SLOT(x, Matrix_DimNamesSym));
	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
533	}	}
534
535	SEXP Csparse_diagU2N(SEXP x)	SEXP Csparse_diagU2N(SEXP x)
536	{	{
537	cholmod_sparse *chx = as_cholmod_sparse(x);	const char *cl = class_P(x);
538	cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);	/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
539		if (cl[1] != 't' || *diag_P(x) != 'U') {
540		/* "trivially fast" when not triangular (<==> no 'diag' slot),
541		or not *unit* triangular */
542		return (x);
543		}
544		else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
545		CHM_SP chx = AS_CHM_SP__(x);
546		CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
547	double one[] = {1, 0};	double one[] = {1, 0};
548	cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);	CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
549	int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?	int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
550	-1 : 1;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
551
552	Free(chx); cholmod_free_sparse(&eye, &c);	R_CheckStack();
553		cholmod_free_sparse(&eye, &c);
554	return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",	return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
555	duplicate(GET_SLOT(x, Matrix_DimNamesSym)));	GET_SLOT(x, Matrix_DimNamesSym));
556		}
557		}
558
559		SEXP Csparse_diagN2U(SEXP x)
560		{
561		const char *cl = class_P(x);
562		/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
563		if (cl[1] != 't' || *diag_P(x) != 'N') {
564		/* "trivially fast" when not triangular (<==> no 'diag' slot),
565		or already *unit* triangular */
566		return (x);
567		}
568		else { /* triangular with diag='N'): now drop the diagonal */
569		/* duplicate, since chx will be modified: */
570		SEXP xx = PROTECT(duplicate(x));
571		CHM_SP chx = AS_CHM_SP__(xx);
572		int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
573		Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
574		R_CheckStack();
575
576		chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
577
578		UNPROTECT(1);
579		return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
580		uploT, Rkind, "U",
581		GET_SLOT(x, Matrix_DimNamesSym));
582		}
583	}	}
584
585		/**
586		* "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
587		* Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
588		* @param x CsparseMatrix
589		* @param i row     indices (0-origin), or NULL (R's)
590		* @param j columns indices (0-origin), or NULL
591		*
592		* @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
593		*/
594	SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)	SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
595	{	{
596	cholmod_sparse *chx = as_cholmod_sparse(x);	CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
597	int rsize = (isNull(i)) ? -1 : LENGTH(i),	int rsize = (isNull(i)) ? -1 : LENGTH(i),
598	csize = (isNull(j)) ? -1 : LENGTH(j);	csize = (isNull(j)) ? -1 : LENGTH(j);
599	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
600		R_CheckStack();
601
602	if (rsize >= 0 && !isInteger(i))	if (rsize >= 0 && !isInteger(i))
603	error(_("Index i must be NULL or integer"));	error(_("Index i must be NULL or integer"));
604	if (csize >= 0 && !isInteger(j))	if (csize >= 0 && !isInteger(j))
605	error(_("Index j must be NULL or integer"));	error(_("Index j must be NULL or integer"));
606	return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
607	INTEGER(j), csize,	if (!chx->stype) {/* non-symmetric Matrix */
608		return chm_sparse_to_SEXP(cholmod_submatrix(chx,
609		(rsize < 0) ? NULL : INTEGER(i), rsize,
610		(csize < 0) ? NULL : INTEGER(j), csize,
611	TRUE, TRUE, &c),	TRUE, TRUE, &c),
612	1, 0, Rkind, "", R_NilValue);	1, 0, Rkind, "",
613		/* FIXME: drops dimnames */ R_NilValue);
614		}
615		/* for now, cholmod_submatrix() only accepts "generalMatrix" */
616		CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
617		CHM_SP ans = cholmod_submatrix(tmp,
618		(rsize < 0) ? NULL : INTEGER(i), rsize,
619		(csize < 0) ? NULL : INTEGER(j), csize,
620		TRUE, TRUE, &c);
621		cholmod_free_sparse(&tmp, &c);
622		return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
623		}
624
625		#define _d_Csp_
626		#include "t_Csparse_subassign.c"
627
628		#define _l_Csp_
629		#include "t_Csparse_subassign.c"
630
631		#define _i_Csp_
632		#include "t_Csparse_subassign.c"
633
634		#define _n_Csp_
635		#include "t_Csparse_subassign.c"
636
637		#define _z_Csp_
638		#include "t_Csparse_subassign.c"
639
640
641
642		SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
643		{
644		FILE *f = fopen(CHAR(asChar(fname)), "w");
645
646		if (!f)
647		error(_("failure to open file \"%s\" for writing"),
648		CHAR(asChar(fname)));
649		if (!cholmod_write_sparse(f, AS_CHM_SP(x),
650		(CHM_SP)NULL, (char*) NULL, &c))
651		error(_("cholmod_write_sparse returned error code"));
652		fclose(f);
653		return R_NilValue;
654		}
655
656
657		/**
658		* Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
659		* cholmod_sparse factor (LDL = TRUE).
660		*
661		* @param n  dimension of the matrix.
662		* @param x_p  'p' (column pointer) slot contents
663		* @param x_x  'x' (non-zero entries) slot contents
664		* @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
665		* @param resultKind a (SEXP) string indicating which kind of result is desired.
666		*
667		* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
668		*/
669		SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
670		/*                                ^^^^^^ FIXME[Generalize] to int / ... */
671		{
672		const char* res_ch = CHAR(STRING_ELT(resultKind,0));
673		enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
674		} res_kind = ((!strcmp(res_ch, "trace")) ? trace :
675		((!strcmp(res_ch, "sumLog")) ? sum_log :
676		((!strcmp(res_ch, "prod")) ? prod :
677		((!strcmp(res_ch, "diag")) ? diag :
678		((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
679		-1)))));
680		int i, n_x, i_from = 0;
681		SEXP ans = PROTECT(allocVector(REALSXP,
682		/*                                 ^^^^  FIXME[Generalize] */
683		(res_kind == diag ||
684		res_kind == diag_backpermuted) ? n : 1));
685		double *v = REAL(ans);
686		/*  ^^^^^^      ^^^^  FIXME[Generalize] */
687
688		#define for_DIAG(v_ASSIGN)                                      \
689		for(i = 0; i < n; i++, i_from += n_x) {                     \
690		/* looking at i-th column */                            \
691		n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
692		v_ASSIGN;                                               \
693		}
694
695		/* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
696		*            for uplo = "U" (makes sense with a "dtCMatrix" !),
697		*            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
698		*            where nx = (x_p[i+1] - x_p[i])
699		*/
700
701		switch(res_kind) {
702		case trace:
703		v[0] = 0.;
704		for_DIAG(v[0] += x_x[i_from]);
705		break;
706
707		case sum_log:
708		v[0] = 0.;
709		for_DIAG(v[0] += log(x_x[i_from]));
710		break;
711
712		case prod:
713		v[0] = 1.;
714		for_DIAG(v[0] *= x_x[i_from]);
715		break;
716
717		case diag:
718		for_DIAG(v[i] = x_x[i_from]);
719		break;
720
721		case diag_backpermuted:
722		for_DIAG(v[i] = x_x[i_from]);
723
724		warning(_("%s = '%s' (back-permuted) is experimental"),
725		"resultKind", "diagBack");
726		/* now back_permute : */
727		for(i = 0; i < n; i++) {
728		double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
729		/*^^^^ FIXME[Generalize] */
730		}
731		break;
732
733		default: /* -1 from above */
734		error(_("diag_tC(): invalid 'resultKind'"));
735		/* Wall: */ ans = R_NilValue; v = REAL(ans);
736		}
737
738		UNPROTECT(1);
739		return ans;
740		}
741
742		/**
743		* Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
744		* cholmod_sparse factor (LDL = TRUE).
745		*
746		* @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
747		* @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
748		* @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
749		*                   only used for "diagBack"
750		* @param resultKind a (SEXP) string indicating which kind of result is desired.
751		*
752		* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
753		*/
754		SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
755		{
756		int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
757		*x_p  = INTEGER(pslot),
758		*perm = INTEGER(perm_slot);
759		double *x_x = REAL(xslot);
760		/*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
761
762		return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
763		}
764
765		/**
766		* Create a Csparse matrix object from indices and/or pointers.
767		*
768		* @param cls name of actual class of object to create
769		* @param i optional integer vector of length nnz of row indices
770		* @param j optional integer vector of length nnz of column indices
771		* @param p optional integer vector of length np of row or column pointers
772		* @param np length of integer vector p.  Must be zero if p == (int*)NULL
773		* @param x optional vector of values
774		* @param nnz length of vectors i, j and/or x, whichever is to be used
775		* @param dims optional integer vector of length 2 to be used as
776		*     dimensions.  If dims == (int*)NULL then the maximum row and column
777		*     index are used as the dimensions.
778		* @param dimnames optional list of length 2 to be used as dimnames
779		* @param index1 indicator of 1-based indices
780		*
781		* @return an SEXP of class cls inheriting from CsparseMatrix.
782		*/
783		SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
784		void* x, int nnz, int* dims, SEXP dimnames,
785		int index1)
786		{
787		SEXP ans;
788		int *ij = (int*)NULL, *tri, *trj,
789		mi, mj, mp, nrow = -1, ncol = -1;
790		int xtype = -1;             /* -Wall */
791		CHM_TR T;
792		CHM_SP A;
793
794		if (np < 0 || nnz < 0)
795		error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
796		np, nnz);
797		if (1 != ((mi = (i == (int*)NULL)) +
798		(mj = (j == (int*)NULL)) +
799		(mp = (p == (int*)NULL))))
800		error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
801		if (mp) {
802		if (np) error(_("np = %d, must be zero when p is NULL"), np);
803		} else {
804		if (np) {               /* Expand p to form i or j */
805		if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
806		for (int ii = 0; ii < np; ii++)
807		if (p[ii] > p[ii + 1])
808		error(_("p must be non-decreasing"));
809		if (p[np] != nnz)
810		error("p[np] = %d != nnz = %d", p[np], nnz);
811		ij = Calloc(nnz, int);
812		if (mi) {
813		i = ij;
814		nrow = np;
815		} else {
816		j = ij;
817		ncol = np;
818		}
819		/* Expand p to 0-based indices */
820		for (int ii = 0; ii < np; ii++)
821		for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
822		} else {
823		if (nnz)
824		error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
825		nnz);
826		}
827		}
828		/* calculate nrow and ncol */
829		if (nrow < 0) {
830		for (int ii = 0; ii < nnz; ii++) {
831		int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
832		if (i1 < 1) error(_("invalid row index at position %d"), ii);
833		if (i1 > nrow) nrow = i1;
834		}
835		}
836		if (ncol < 0) {
837		for (int jj = 0; jj < nnz; jj++) {
838		int j1 = j[jj] + (index1 ? 0 : 1);
839		if (j1 < 1) error(_("invalid column index at position %d"), jj);
840		if (j1 > ncol) ncol = j1;
841		}
842		}
843		if (dims != (int*)NULL) {
844		if (dims[0] > nrow) nrow = dims[0];
845		if (dims[1] > ncol) ncol = dims[1];
846		}
847		/* check the class name */
848		if (strlen(cls) != 8)
849		error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
850		if (!strcmp(cls + 2, "CMatrix"))
851		error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
852		switch(cls[0]) {
853		case 'd':
854		case 'l':
855		xtype = CHOLMOD_REAL;
856		break;
857		case 'n':
858		xtype = CHOLMOD_PATTERN;
859		break;
860		default:
861		error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
862		}
863		if (cls[1] != 'g')
864		error(_("Only 'g'eneral sparse matrix types allowed"));
865		/* allocate and populate the triplet */
866		T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
867		xtype, &c);
868		T->x = x;
869		tri = (int*)T->i;
870		trj = (int*)T->j;
871		for (int ii = 0; ii < nnz; ii++) {
872		tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
873		trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
874		}
875		/* create the cholmod_sparse structure */
876		A = cholmod_triplet_to_sparse(T, nnz, &c);
877		cholmod_free_triplet(&T, &c);
878		/* copy the information to the SEXP */
879		ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
880		/* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
881		/* allocate and copy common slots */
882		nnz = cholmod_nnz(A, &c);
883		dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
884		dims[0] = A->nrow; dims[1] = A->ncol;
885		Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
886		Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
887		switch(cls[1]) {
888		case 'd':
889		Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
890		break;
891		case 'l':
892		error(_("code not yet written for cls = \"lgCMatrix\""));
893		}
894		/* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
895		cholmod_free_sparse(&A, &c);
896		UNPROTECT(1);
897		return ans;
898	}	}

---

Colored Diff Long Colored Diff Unidiff Context Diff Side by Side

Legend: Removed from v.1657   changed lines   Added in v.2804

---

R-Forge@R-project.org	ViewVC Help
Powered by ViewVC 1.0.0