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 3018, Sat Oct 11 17:52:10 2014 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	*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),	nrow = dims[0],
15		ncol = dims[1],
16	*xp = INTEGER(pslot),	*xp = INTEGER(pslot),
17	*xi = INTEGER(islot);	*xi = INTEGER(islot);
18
	nrow = dims[0];
	ncol = dims[1];
19	if (length(pslot) != dims[1] + 1)	if (length(pslot) != dims[1] + 1)
20	return mkString(_("slot p must have length = ncol(.) + 1"));	return FALSE;
21	if (xp[0] != 0)	if (xp[0] != 0)
22	return mkString(_("first element of slot p must be zero"));	return FALSE;
23	if (length(islot) != xp[ncol])	if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/
24	return	return FALSE;
25	mkString(_("last element of slot p must match length of slots i and x"));	for (j = 0; j < xp[ncol]; j++) {
	for (j = 0; j < length(islot); j++) {
26	if (xi[j] < 0 || xi[j] >= nrow)	if (xi[j] < 0 || xi[j] >= nrow)
27	return mkString(_("all row indices must be between 0 and nrow-1"));	return FALSE;
28	}	}
	sorted = TRUE;
29	for (j = 0; j < ncol; j++) {	for (j = 0; j < ncol; j++) {
30	if (xp[j] > xp[j+1])	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
41		#define _t_Csparse_validate
42		#include "t_Csparse_validate.c"
43
44		#define _t_Csparse_sort
45		#include "t_Csparse_validate.c"
46
47		// R: .validateCsparse(x, sort.if.needed = FALSE) :
48		SEXP Csparse_validate2(SEXP x, SEXP maybe_modify) {
49		return Csparse_validate_(x, asLogical(maybe_modify));
50		}
51
52		// R: Matrix:::.sortCsparse(x) :
53		SEXP Csparse_sort (SEXP x) {
54		int ok = Csparse_sort_2(x, TRUE); // modifying x directly
55		if(!ok) warning(_("Csparse_sort(x): x is not a valid (apart from sorting) CsparseMatrix"));
56		return x;
57		}
58
59		SEXP Rsparse_validate(SEXP x)
60		{
61		/* NB: we do *NOT* check a potential 'x' slot here, at all */
62		SEXP pslot = GET_SLOT(x, Matrix_pSym),
63		jslot = GET_SLOT(x, Matrix_jSym);
64		Rboolean sorted, strictly;
65		int i, k,
66		*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
67		nrow = dims[0],
68		ncol = dims[1],
69		*xp = INTEGER(pslot),
70		*xj = INTEGER(jslot);
71
72		if (length(pslot) != dims[0] + 1)
73		return mkString(_("slot p must have length = nrow(.) + 1"));
74		if (xp[0] != 0)
75		return mkString(_("first element of slot p must be zero"));
76		if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
77		return
78		mkString(_("last element of slot p must match length of slots j and x"));
79		for (i = 0; i < length(jslot); i++) {
80		if (xj[i] < 0 || xj[i] >= ncol)
81		return mkString(_("all column indices must be between 0 and ncol-1"));
82		}
83		sorted = TRUE; strictly = TRUE;
84		for (i = 0; i < nrow; i++) {
85		if (xp[i] > xp[i+1])
86	return mkString(_("slot p must be non-decreasing"));	return mkString(_("slot p must be non-decreasing"));
87	for (k = xp[j] + 1; k < xp[j + 1]; k++)	if(sorted)
88	if (xi[k] < xi[k - 1]) sorted = FALSE;	for (k = xp[i] + 1; k < xp[i + 1]; k++) {
89		if (xj[k] < xj[k - 1])
90		sorted = FALSE;
91		else if (xj[k] == xj[k - 1])
92		strictly = FALSE;
93	}	}
	if (!sorted) {
	cholmod_sparse *chx = as_cholmod_sparse(x);
	cholmod_sort(chx, &c);
	Free(chx);
94	}	}
95		if (!sorted)
96		/* cannot easily use cholmod_sort(.) ... -> "error out" :*/
97		return mkString(_("slot j is not increasing inside a column"));
98		else if(!strictly) /* sorted, but not strictly */
99		return mkString(_("slot j is not *strictly* increasing inside a column"));
100
101	return ScalarLogical(1);	return ScalarLogical(1);
102	}	}
103
104
105		/* Called from ../R/Csparse.R : */
106		/* Can only return [dln]geMatrix (no symm/triang);
107		* FIXME: replace by non-CHOLMOD code ! */
108	SEXP Csparse_to_dense(SEXP x)	SEXP Csparse_to_dense(SEXP x)
109	{	{
110	cholmod_sparse *chxs = as_cholmod_sparse(x);	CHM_SP chxs = AS_CHM_SP__(x);
111	cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);	/* This loses the symmetry property, since cholmod_dense has none,
112		* BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
113		* to numeric (CHOLMOD_REAL) ones : */
114		CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
115		int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
116		R_CheckStack();
117
118	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));
119	}	}
120
121		// FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
122	SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)	SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
123	{	{
124	cholmod_sparse *chxs = as_cholmod_sparse(x);	CHM_SP chxs = AS_CHM_SP__(x);
125	cholmod_sparse	CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
126	*chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);	int tr = asLogical(tri);
127	int uploT = 0; char *diag = "";	R_CheckStack();
128
129	Free(chxs);	return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
130	if (asLogical(tri)) {       /* triangular sparse matrices */	tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
131	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,
132	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
133	}	}
134
135	SEXP Csparse_to_matrix(SEXP x)	// n.CMatrix --> [dli].CMatrix  (not going through CHM!)
136		SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
137		{
138		return nz2Csparse(x, asInteger(res_kind));
139		}
140		// n.CMatrix --> [dli].CMatrix  (not going through CHM!)
141		SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
142	{	{
143	cholmod_sparse *chxs = as_cholmod_sparse(x);	const char *cl_x = class_P(x);
144	cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);	if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
145		if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
146		int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
147		SEXP ans;
148		char *ncl = alloca(strlen(cl_x) + 1); /* not much memory required */
149		strcpy(ncl, cl_x);
150		double *dx_x; int *ix_x;
151		ncl[0] = (r_kind == x_double ? 'd' :
152		(r_kind == x_logical ? 'l' :
153		/* else (for now):  r_kind == x_integer : */ 'i'));
154		PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
155		// create a correct 'x' slot:
156		switch(r_kind) {
157		int i;
158		case x_double: // 'd'
159		dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
160		for (i=0; i < nnz; i++) dx_x[i] = 1.;
161		break;
162		case x_logical: // 'l'
163		ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
164		for (i=0; i < nnz; i++) ix_x[i] = TRUE;
165		break;
166		case x_integer: // 'i'
167		ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
168		for (i=0; i < nnz; i++) ix_x[i] = 1;
169		break;
170
171		default:
172		error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
173		r_kind);
174		}
175
176		// now copy all other slots :
177		slot_dup(ans, x, Matrix_iSym);
178		slot_dup(ans, x, Matrix_pSym);
179		slot_dup(ans, x, Matrix_DimSym);
180		slot_dup(ans, x, Matrix_DimNamesSym);
181		if(ncl[1] != 'g') { // symmetric or triangular ...
182		slot_dup_if_has(ans, x, Matrix_uploSym);
183		slot_dup_if_has(ans, x, Matrix_diagSym);
184		}
185		UNPROTECT(1);
186		return ans;
187		}
188
189	Free(chxs);	SEXP Csparse_to_matrix(SEXP x, SEXP chk)
190	return chm_dense_to_matrix(chxd, 1,	{
191	GET_SLOT(x, Matrix_DimNamesSym));	return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP2(x, asLogical(chk)), &c),
192		1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
193		}
194		SEXP Csparse_to_vector(SEXP x)
195		{
196		return chm_dense_to_vector(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c), 1);
197	}	}
198
199	SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)	SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
200	{	{
201	cholmod_sparse *chxs = as_cholmod_sparse(x);	CHM_SP chxs = AS_CHM_SP__(x);
202	cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);	CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
203	int uploT = 0;	int tr = asLogical(tri);
204	char *diag = "";	int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
205	int Rkind = (chxs->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	R_CheckStack();
206
207	Free(chxs);	return chm_triplet_to_SEXP(chxt, 1,
208	if (asLogical(tri)) {       /* triangular sparse matrices */	tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
209	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,
210	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
211	}	}
212
213	/* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */	/* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
214	SEXP Csparse_symmetric_to_general(SEXP x)	SEXP Csparse_symmetric_to_general(SEXP x)
215	{	{
216	cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;	CHM_SP chx = AS_CHM_SP__(x), chgx;
217	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
218		R_CheckStack();
219
220	if (!(chx->stype))	if (!(chx->stype))
221	error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));	error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
222	chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);	chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
223	/* xtype: pattern, "real", complex or .. */	/* xtype: pattern, "real", complex or .. */
	Free(chx);
224	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
225	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
226	}	}
227
228	SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)	SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
229	{	{
230	cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;	int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
231	int uploT = (*CHAR(asChar(uplo)) == 'U') ? -1 : 1;	if(n != adims[1]) {
232	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	error(_("Csparse_general_to_symmetric(): matrix is not square!"));
233		return R_NilValue; /* -Wall */
234		}
235		CHM_SP chx = AS_CHM_SP__(x), chgx;
236		int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
237		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
238		R_CheckStack();
239	chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);	chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
240	/* xtype: pattern, "real", complex or .. */	/* xtype: pattern, "real", complex or .. */
	Free(chx);
241	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
242	GET_SLOT(x, Matrix_DimNamesSym));	GET_SLOT(x, Matrix_DimNamesSym));
243	}	}
244
245	SEXP Csparse_transpose(SEXP x, SEXP tri)	SEXP Csparse_transpose(SEXP x, SEXP tri)
246	{	{
247	cholmod_sparse *chx = as_cholmod_sparse(x);	/* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
248	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	*       since cholmod (& cs) lacks sparse 'int' matrices */
249	cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);	CHM_SP chx = AS_CHM_SP__(x);
250		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
251		CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
252	SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;	SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
253	int uploT = 0; char *diag = "";	int tr = asLogical(tri);
254		R_CheckStack();
255
	Free(chx);
256	tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */	tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
257	SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));	SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
258	SET_VECTOR_ELT(dn, 1, tmp);	SET_VECTOR_ELT(dn, 1, tmp);
259	UNPROTECT(1);	UNPROTECT(1);
260	if (asLogical(tri)) {       /* triangular sparse matrices */	return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
261	uploT = (*uplo_P(x) == 'U') ? -1 : 1;	tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
262	diag = diag_P(x);	Rkind, tr ? diag_P(x) : "", dn);
	}
	return chm_sparse_to_SEXP(chxt, 1, uploT, Rkind, diag, dn);
263	}	}
264
265	SEXP Csparse_Csparse_prod(SEXP a, SEXP b)	SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
266	{	{
267	cholmod_sparse *cha = as_cholmod_sparse(a),	CHM_SP
268	*chb = as_cholmod_sparse(b);	cha = AS_CHM_SP(a),
269	cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);	chb = AS_CHM_SP(b),
270	SEXP dn = allocVector(VECSXP, 2);	chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
271		/* values:= is_numeric (T/F) */ cha->xtype > 0,
272		/*out sorted:*/ 1, &c);
273		const char *cl_a = class_P(a), *cl_b = class_P(b);
274		char diag[] = {'\0', '\0'};
275		int uploT = 0;
276		SEXP dn = PROTECT(allocVector(VECSXP, 2));
277		R_CheckStack();
278
279	Free(cha); Free(chb);	#ifdef DEBUG_Matrix_verbose
280		Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
281		#endif
282
283		/* Preserve triangularity and even unit-triangularity if appropriate.
284		* Note that in that case, the multiplication itself should happen
285		* faster.  But there's no support for that in CHOLMOD */
286
287		/* UGLY hack -- rather should have (fast!) C-level version of
288		*       is(a, "triangularMatrix") etc */
289		if (cl_a[1] == 't' && cl_b[1] == 't')
290		/* FIXME: fails for "Cholesky","BunchKaufmann"..*/
291		if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
292		uploT = (*uplo_P(a) == 'U') ? 1 : -1;
293		if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
294		/* "remove the diagonal entries": */
295		chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
296		diag[0]= 'U';
297		}
298		else diag[0]= 'N';
299		}
300	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
301	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
302	SET_VECTOR_ELT(dn, 1,	SET_VECTOR_ELT(dn, 1,
303	duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));	duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
304	return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);	UNPROTECT(1);
305		return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
306	}	}
307
308	SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b)	SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
309	{	{
310	cholmod_sparse *cha = as_cholmod_sparse(a),	int tr = asLogical(trans);
311	*chb = as_cholmod_sparse(b);	CHM_SP
312	cholmod_sparse *chta = cholmod_transpose(cha, 1, &c);	cha = AS_CHM_SP(a),
313	cholmod_sparse *chc = cholmod_ssmult(chta, chb, 0, cha->xtype, 1, &c);	chb = AS_CHM_SP(b),
314	SEXP dn = allocVector(VECSXP, 2);	chTr, chc;
315		const char *cl_a = class_P(a), *cl_b = class_P(b);
316		char diag[] = {'\0', '\0'};
317		int uploT = 0;
318		SEXP dn = PROTECT(allocVector(VECSXP, 2));
319		R_CheckStack();
320
321	Free(cha); Free(chb); cholmod_free_sparse(&chta, &c);	chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
322		chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
323		/*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
324		cholmod_free_sparse(&chTr, &c);
325
326		/* Preserve triangularity and unit-triangularity if appropriate;
327		* see Csparse_Csparse_prod() for comments */
328		if (cl_a[1] == 't' && cl_b[1] == 't')
329		if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
330		uploT = (*uplo_P(b) == 'U') ? 1 : -1;
331		if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
332		chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
333		diag[0]= 'U';
334		}
335		else diag[0]= 'N';
336		}
337	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
338	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));	duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
339	SET_VECTOR_ELT(dn, 1,	SET_VECTOR_ELT(dn, 1,
340	duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));	duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
341	return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);	UNPROTECT(1);
342		return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
343	}	}
344
345	SEXP Csparse_dense_prod(SEXP a, SEXP b)	SEXP Csparse_dense_prod(SEXP a, SEXP b)
346	{	{
347	cholmod_sparse *cha = as_cholmod_sparse(a);	CHM_SP cha = AS_CHM_SP(a);
348	cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));	SEXP b_M = PROTECT(mMatrix_as_dgeMatrix2(b, // transpose_if_vector =
349	cholmod_dense *chc =	cha->ncol == 1));
350	cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);	CHM_DN chb = AS_CHM_DN(b_M);
351	double alpha[] = {1,0}, beta[] = {0,0};	CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
352		chb->xtype, &c);
353	cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);	SEXP dn = PROTECT(allocVector(VECSXP, 2));
354	Free(cha); Free(chb);	double one[] = {1,0}, zero[] = {0,0};
355	UNPROTECT(1);	int nprot = 2;
356	return chm_dense_to_SEXP(chc, 1, 0);	R_CheckStack();
357		/* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
358		if(cha->xtype == CHOLMOD_PATTERN) {
359		/* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
360		/*        " --> slightly inefficient coercion")); */
361
362		// This *fails* to produce a CHOLMOD_REAL ..
363		// CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
364		// --> use our Matrix-classes
365		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
366		cha = AS_CHM_SP(da);
367		}
368		cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
369		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
370		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
371		SET_VECTOR_ELT(dn, 1,
372		duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
373		UNPROTECT(nprot);
374		return chm_dense_to_SEXP(chc, 1, 0, dn);
375	}	}
376
377	SEXP Csparse_dense_crossprod(SEXP a, SEXP b)	SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
378	{	{
379	cholmod_sparse *cha = as_cholmod_sparse(a);	CHM_SP cha = AS_CHM_SP(a);
380	cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));	SEXP b_M = PROTECT(mMatrix_as_dgeMatrix2(b, // transpose_if_vector =
381	cholmod_dense *chc =	cha->nrow == 1));
382	cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);	CHM_DN chb = AS_CHM_DN(b_M);
383	double alpha[] = {1,0}, beta[] = {0,0};	CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
384		chb->xtype, &c);
385	cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);	SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
386	Free(cha); Free(chb);	double one[] = {1,0}, zero[] = {0,0};
387	UNPROTECT(1);	R_CheckStack();
388	return chm_dense_to_SEXP(chc, 1, 0);	// -- see Csparse_dense_prod() above :
389		if(cha->xtype == CHOLMOD_PATTERN) {
390		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
391		cha = AS_CHM_SP(da);
392		}
393		cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
394		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
395		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
396		SET_VECTOR_ELT(dn, 1,
397		duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
398		UNPROTECT(nprot);
399		return chm_dense_to_SEXP(chc, 1, 0, dn);
400	}	}
401
402		/* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
403		see Csparse_Csparse_crossprod above for  x'y and x y' */
404	SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)	SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
405	{	{
406	int trip = asLogical(triplet),	int trip = asLogical(triplet),
407	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
408	cholmod_triplet	#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
409	*cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;	CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
410	cholmod_sparse *chcp, *chxt,	#else /* workaround needed:*/
411	*chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)	SEXP xx = PROTECT(Tsparse_diagU2N(x));
412	: as_cholmod_sparse(x);	CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
413		#endif
414		CHM_SP chcp, chxt,
415		chx = (trip ?
416		cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
417		AS_CHM_SP(x));
418	SEXP dn = PROTECT(allocVector(VECSXP, 2));	SEXP dn = PROTECT(allocVector(VECSXP, 2));
419		R_CheckStack();
420
421	if (!tr)	if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
	chxt = cholmod_transpose(chx, chx->xtype, &c);
422	chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);	chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
423	if(!chcp)	if(!chcp) {
424		UNPROTECT(1);
425	error(_("Csparse_crossprod(): error return from cholmod_aat()"));	error(_("Csparse_crossprod(): error return from cholmod_aat()"));
426		}
427	cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);	cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
428	chcp->stype = 1;	chcp->stype = 1;
429	if (trip) {	if (trip) cholmod_free_sparse(&chx, &c);
	cholmod_free_sparse(&chx, &c);
	Free(cht);
	} else {
	Free(chx);
	}
430	if (!tr) cholmod_free_sparse(&chxt, &c);	if (!tr) cholmod_free_sparse(&chxt, &c);
431	/* create dimnames */	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
	SET_VECTOR_ELT(dn, 0,
432	duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),	duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
433	(tr) ? 1 : 0)));	(tr) ? 0 : 1)));
434	SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));	SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
435		#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
436	UNPROTECT(1);	UNPROTECT(1);
437		#else
438		UNPROTECT(2);
439		#endif
440	return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);	return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
441	}	}
442
443		/* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
444		*  at least all "explicit" zeros */
445	SEXP Csparse_drop(SEXP x, SEXP tol)	SEXP Csparse_drop(SEXP x, SEXP tol)
446	{	{
447	cholmod_sparse *chx = as_cholmod_sparse(x),	const char *cl = class_P(x);
448	*ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);	/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
449		int tr = (cl[1] == 't');
450		CHM_SP chx = AS_CHM_SP__(x);
451		CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
452	double dtol = asReal(tol);	double dtol = asReal(tol);
453	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
454		R_CheckStack();
455
456	if(!cholmod_drop(dtol, ans, &c))	if(!cholmod_drop(dtol, ans, &c))
457	error(_("cholmod_drop() failed"));	error(_("cholmod_drop() failed"));
458	Free(chx);	return chm_sparse_to_SEXP(ans, 1,
459	/* FIXME: currently drops dimnames */	tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
460	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);	Rkind, tr ? diag_P(x) : "",
461		GET_SLOT(x, Matrix_DimNamesSym));
462	}	}
463
464	SEXP Csparse_horzcat(SEXP x, SEXP y)	SEXP Csparse_horzcat(SEXP x, SEXP y)
465	{	{
466	cholmod_sparse *chx = as_cholmod_sparse(x),	CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
467	*chy = as_cholmod_sparse(y), *ans;	int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
468	int Rkind = 0; /* only for "d" - FIXME */	Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
469		Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
470	ans = cholmod_horzcat(chx, chy, 1, &c);	R_CheckStack();
471	Free(chx); Free(chy);
472	/* FIXME: currently drops dimnames */	/* TODO: currently drops dimnames - and we fix at R level */
473	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);	return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
474		1, 0, Rkind, "", R_NilValue);
475	}	}
476
477	SEXP Csparse_vertcat(SEXP x, SEXP y)	SEXP Csparse_vertcat(SEXP x, SEXP y)
478	{	{
479	cholmod_sparse *chx = as_cholmod_sparse(x),	CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
480	*chy = as_cholmod_sparse(y), *ans;	int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
481	int Rkind = 0; /* only for "d" - FIXME */	Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
482		Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
483	ans = cholmod_vertcat(chx, chy, 1, &c);	R_CheckStack();
484	Free(chx); Free(chy);
485	/* FIXME: currently drops dimnames */	/* TODO: currently drops dimnames - and we fix at R level */
486	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);	return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
487		1, 0, Rkind, "", R_NilValue);
488	}	}
489
490	SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)	SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
491	{	{
492	cholmod_sparse *chx = as_cholmod_sparse(x), *ans;	CHM_SP chx = AS_CHM_SP__(x);
493	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
494		CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
495		R_CheckStack();
496
497	ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
498	Free(chx);	GET_SLOT(x, Matrix_DimNamesSym));
	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
499	}	}
500
501	SEXP Csparse_diagU2N(SEXP x)	SEXP Csparse_diagU2N(SEXP x)
502	{	{
503	cholmod_sparse *chx = as_cholmod_sparse(x);	const char *cl = class_P(x);
504	cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);	/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
505		if (cl[1] != 't' || *diag_P(x) != 'U') {
506		/* "trivially fast" when not triangular (<==> no 'diag' slot),
507		or not *unit* triangular */
508		return (x);
509		}
510		else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
511		CHM_SP chx = AS_CHM_SP__(x);
512		CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
513	double one[] = {1, 0};	double one[] = {1, 0};
514	cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);	CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
515	int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?	int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
516	-1 : 1;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
517
518	Free(chx); cholmod_free_sparse(&eye, &c);	R_CheckStack();
519		cholmod_free_sparse(&eye, &c);
520	return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",	return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
521	duplicate(GET_SLOT(x, Matrix_DimNamesSym)));	GET_SLOT(x, Matrix_DimNamesSym));
522	}	}
523		}
524
525		SEXP Csparse_diagN2U(SEXP x)
526		{
527		const char *cl = class_P(x);
528		/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
529		if (cl[1] != 't' || *diag_P(x) != 'N') {
530		/* "trivially fast" when not triangular (<==> no 'diag' slot),
531		or already *unit* triangular */
532		return (x);
533		}
534		else { /* triangular with diag='N'): now drop the diagonal */
535		/* duplicate, since chx will be modified: */
536		SEXP xx = PROTECT(duplicate(x));
537		CHM_SP chx = AS_CHM_SP__(xx);
538		int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
539		Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
540		R_CheckStack();
541
542		chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
543
544		SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
545		uploT, Rkind, "U",
546		GET_SLOT(x, Matrix_DimNamesSym));
547		UNPROTECT(1);// only now !
548		return ans;
549		}
550		}
551
552		/**
553		* "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
554		* Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
555		* @param x CsparseMatrix
556		* @param i row     indices (0-origin), or NULL (R's)
557		* @param j columns indices (0-origin), or NULL
558		*
559		* @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
560		*/
561	SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)	SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
562	{	{
563	cholmod_sparse *chx = as_cholmod_sparse(x);	CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
564	int rsize = (isNull(i)) ? -1 : LENGTH(i),	int rsize = (isNull(i)) ? -1 : LENGTH(i),
565	csize = (isNull(j)) ? -1 : LENGTH(j);	csize = (isNull(j)) ? -1 : LENGTH(j);
566	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
567		R_CheckStack();
568
569	if (rsize >= 0 && !isInteger(i))	if (rsize >= 0 && !isInteger(i))
570	error(_("Index i must be NULL or integer"));	error(_("Index i must be NULL or integer"));
571	if (csize >= 0 && !isInteger(j))	if (csize >= 0 && !isInteger(j))
572	error(_("Index j must be NULL or integer"));	error(_("Index j must be NULL or integer"));
573	return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
574	INTEGER(j), csize,	#define CHM_SUB(_M_, _i_, _j_)                                  \
575	TRUE, TRUE, &c),	cholmod_submatrix(_M_,                                      \
576	1, 0, Rkind, "", R_NilValue);	(rsize < 0) ? NULL : INTEGER(_i_), rsize, \
577		(csize < 0) ? NULL : INTEGER(_j_), csize, \
578		TRUE, TRUE, &c)
579		CHM_SP ans;
580		if (!chx->stype) {/* non-symmetric Matrix */
581		ans = CHM_SUB(chx, i, j);
582		}
583		else {
584		/* for now, cholmod_submatrix() only accepts "generalMatrix" */
585		CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
586		ans = CHM_SUB(tmp, i, j);
587		cholmod_free_sparse(&tmp, &c);
588		}
589
590		// "FIXME": currently dropping dimnames, and adding them afterwards in R :
591		/* // dimnames: */
592		/* SEXP x_dns = GET_SLOT(x, Matrix_DimNamesSym), */
593		/*  dn = PROTECT(allocVector(VECSXP, 2)); */
594		return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", /* dimnames: */ R_NilValue);
595		}
596
597		#define _d_Csp_
598		#include "t_Csparse_subassign.c"
599
600		#define _l_Csp_
601		#include "t_Csparse_subassign.c"
602
603		#define _i_Csp_
604		#include "t_Csparse_subassign.c"
605
606		#define _n_Csp_
607		#include "t_Csparse_subassign.c"
608
609		#define _z_Csp_
610		#include "t_Csparse_subassign.c"
611
612
613
614		SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
615		{
616		FILE *f = fopen(CHAR(asChar(fname)), "w");
617
618		if (!f)
619		error(_("failure to open file \"%s\" for writing"),
620		CHAR(asChar(fname)));
621		if (!cholmod_write_sparse(f, AS_CHM_SP(x),
622		(CHM_SP)NULL, (char*) NULL, &c))
623		error(_("cholmod_write_sparse returned error code"));
624		fclose(f);
625		return R_NilValue;
626		}
627
628
629		/**
630		* Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
631		* cholmod_sparse factor (LDL = TRUE).
632		*
633		* @param n  dimension of the matrix.
634		* @param x_p  'p' (column pointer) slot contents
635		* @param x_x  'x' (non-zero entries) slot contents
636		* @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
637		* @param resultKind a (SEXP) string indicating which kind of result is desired.
638		*
639		* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
640		*/
641		SEXP diag_tC_ptr(int n, int *x_p, double *x_x, Rboolean is_U, int *perm,
642		/*                                ^^^^^^ FIXME[Generalize] to int / ... */
643		SEXP resultKind)
644		{
645		const char* res_ch = CHAR(STRING_ELT(resultKind,0));
646		enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log, min, max, range
647		} res_kind = ((!strcmp(res_ch, "trace")) ? trace :
648		((!strcmp(res_ch, "sumLog")) ? sum_log :
649		((!strcmp(res_ch, "prod")) ? prod :
650		((!strcmp(res_ch, "min")) ? min :
651		((!strcmp(res_ch, "max")) ? max :
652		((!strcmp(res_ch, "range")) ? range :
653		((!strcmp(res_ch, "diag")) ? diag :
654		((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
655		-1))))))));
656		int i, n_x, i_from;
657		SEXP ans = PROTECT(allocVector(REALSXP,
658		/*                                 ^^^^  FIXME[Generalize] */
659		(res_kind == diag ||
660		res_kind == diag_backpermuted) ? n :
661		(res_kind == range ? 2 : 1)));
662		double *v = REAL(ans);
663		/*  ^^^^^^      ^^^^  FIXME[Generalize] */
664
665		i_from = (is_U ? -1 : 0);
666
667		#define for_DIAG(v_ASSIGN)                                      \
668		for(i = 0; i < n; i++) {                                    \
669		/* looking at i-th column */                            \
670		n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
671		if( is_U) i_from += n_x;                                \
672		v_ASSIGN;                                               \
673		if(!is_U) i_from += n_x;                                \
674		}
675
676		/* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
677		*            for uplo = "U" (makes sense with a "dtCMatrix" !),
678		*            should use  x_x[i_from + (n_x - 1)] instead of x_x[i_from],
679		*            where n_x = (x_p[i+1] - x_p[i])
680		*/
681
682		switch(res_kind) {
683		case trace: // = sum
684		v[0] = 0.;
685		for_DIAG(v[0] += x_x[i_from]);
686		break;
687
688		case sum_log:
689		v[0] = 0.;
690		for_DIAG(v[0] += log(x_x[i_from]));
691		break;
692
693		case prod:
694		v[0] = 1.;
695		for_DIAG(v[0] *= x_x[i_from]);
696		break;
697
698		case min:
699		v[0] = R_PosInf;
700		for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from]);
701		break;
702
703		case max:
704		v[0] = R_NegInf;
705		for_DIAG(if(v[0] < x_x[i_from]) v[0] = x_x[i_from]);
706		break;
707
708		case range:
709		v[0] = R_PosInf;
710		v[1] = R_NegInf;
711		for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from];
712		if(v[1] < x_x[i_from]) v[1] = x_x[i_from]);
713		break;
714
715		case diag:
716		for_DIAG(v[i] = x_x[i_from]);
717		break;
718
719		case diag_backpermuted:
720		for_DIAG(v[i] = x_x[i_from]);
721
722		warning(_("%s = '%s' (back-permuted) is experimental"),
723		"resultKind", "diagBack");
724		/* now back_permute : */
725		for(i = 0; i < n; i++) {
726		double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
727		/*^^^^ FIXME[Generalize] */
728		}
729		break;
730
731		default: /* -1 from above */
732		error(_("diag_tC(): invalid 'resultKind'"));
733		/* Wall: */ ans = R_NilValue; v = REAL(ans);
734		}
735
736		UNPROTECT(1);
737		return ans;
738		}
739
740		/**
741		* Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
742		* cholmod_sparse factor (LDL = TRUE).
743		*
744		* @param obj -- now a cholmod_sparse factor or a dtCMatrix
745		* @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
746		* @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
747		* @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
748		*                   only used for "diagBack"
749		* @param resultKind a (SEXP) string indicating which kind of result is desired.
750		*
751		* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
752		*/
753		SEXP diag_tC(SEXP obj, SEXP resultKind)
754		{
755
756		SEXP
757		pslot = GET_SLOT(obj, Matrix_pSym),
758		xslot = GET_SLOT(obj, Matrix_xSym);
759		Rboolean is_U = (R_has_slot(obj, Matrix_uploSym) &&
760		*CHAR(asChar(GET_SLOT(obj, Matrix_uploSym))) == 'U');
761		int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
762		*x_p  = INTEGER(pslot), pp = -1, *perm;
763		double *x_x = REAL(xslot);
764		/*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
765
766		if(R_has_slot(obj, Matrix_permSym))
767		perm = INTEGER(GET_SLOT(obj, Matrix_permSym));
768		else perm = &pp;
769
770		return diag_tC_ptr(n, x_p, x_x, is_U, perm, resultKind);
771		}
772
773
774		/**
775		* Create a Csparse matrix object from indices and/or pointers.
776		*
777		* @param cls name of actual class of object to create
778		* @param i optional integer vector of length nnz of row indices
779		* @param j optional integer vector of length nnz of column indices
780		* @param p optional integer vector of length np of row or column pointers
781		* @param np length of integer vector p.  Must be zero if p == (int*)NULL
782		* @param x optional vector of values
783		* @param nnz length of vectors i, j and/or x, whichever is to be used
784		* @param dims optional integer vector of length 2 to be used as
785		*     dimensions.  If dims == (int*)NULL then the maximum row and column
786		*     index are used as the dimensions.
787		* @param dimnames optional list of length 2 to be used as dimnames
788		* @param index1 indicator of 1-based indices
789		*
790		* @return an SEXP of class cls inheriting from CsparseMatrix.
791		*/
792		SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
793		void* x, int nnz, int* dims, SEXP dimnames,
794		int index1)
795		{
796		SEXP ans;
797		int *ij = (int*)NULL, *tri, *trj,
798		mi, mj, mp, nrow = -1, ncol = -1;
799		int xtype = -1;             /* -Wall */
800		CHM_TR T;
801		CHM_SP A;
802
803		if (np < 0 || nnz < 0)
804		error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
805		np, nnz);
806		if (1 != ((mi = (i == (int*)NULL)) +
807		(mj = (j == (int*)NULL)) +
808		(mp = (p == (int*)NULL))))
809		error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
810		if (mp) {
811		if (np) error(_("np = %d, must be zero when p is NULL"), np);
812		} else {
813		if (np) {               /* Expand p to form i or j */
814		if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
815		for (int ii = 0; ii < np; ii++)
816		if (p[ii] > p[ii + 1])
817		error(_("p must be non-decreasing"));
818		if (p[np] != nnz)
819		error("p[np] = %d != nnz = %d", p[np], nnz);
820		ij = Calloc(nnz, int);
821		if (mi) {
822		i = ij;
823		nrow = np;
824		} else {
825		j = ij;
826		ncol = np;
827		}
828		/* Expand p to 0-based indices */
829		for (int ii = 0; ii < np; ii++)
830		for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
831		} else {
832		if (nnz)
833		error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
834		nnz);
835		}
836		}
837		/* calculate nrow and ncol */
838		if (nrow < 0) {
839		for (int ii = 0; ii < nnz; ii++) {
840		int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
841		if (i1 < 1) error(_("invalid row index at position %d"), ii);
842		if (i1 > nrow) nrow = i1;
843		}
844		}
845		if (ncol < 0) {
846		for (int jj = 0; jj < nnz; jj++) {
847		int j1 = j[jj] + (index1 ? 0 : 1);
848		if (j1 < 1) error(_("invalid column index at position %d"), jj);
849		if (j1 > ncol) ncol = j1;
850		}
851		}
852		if (dims != (int*)NULL) {
853		if (dims[0] > nrow) nrow = dims[0];
854		if (dims[1] > ncol) ncol = dims[1];
855		}
856		/* check the class name */
857		if (strlen(cls) != 8)
858		error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
859		if (!strcmp(cls + 2, "CMatrix"))
860		error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
861		switch(cls[0]) {
862		case 'd':
863		case 'l':
864		xtype = CHOLMOD_REAL;
865		break;
866		case 'n':
867		xtype = CHOLMOD_PATTERN;
868		break;
869		default:
870		error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
871		}
872		if (cls[1] != 'g')
873		error(_("Only 'g'eneral sparse matrix types allowed"));
874		/* allocate and populate the triplet */
875		T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
876		xtype, &c);
877		T->x = x;
878		tri = (int*)T->i;
879		trj = (int*)T->j;
880		for (int ii = 0; ii < nnz; ii++) {
881		tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
882		trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
883		}
884		/* create the cholmod_sparse structure */
885		A = cholmod_triplet_to_sparse(T, nnz, &c);
886		cholmod_free_triplet(&T, &c);
887		/* copy the information to the SEXP */
888		ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
889		/* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
890		/* allocate and copy common slots */
891		nnz = cholmod_nnz(A, &c);
892		dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
893		dims[0] = A->nrow; dims[1] = A->ncol;
894		Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
895		Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
896		switch(cls[1]) {
897		case 'd':
898		Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
899		break;
900		case 'l':
901		error(_("code not yet written for cls = \"lgCMatrix\""));
902		}
903		/* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
904		cholmod_free_sparse(&A, &c);
905		UNPROTECT(1);
906		return ans;
907	}	}

---

Colored Diff Long Colored Diff Unidiff Context Diff Side by Side

Legend: Removed from v.1657   changed lines   Added in v.3018

---

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