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

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	pkg/src/Csparse.c revision 1029, Wed Nov 9 15:26:22 2005 UTC	pkg/Matrix/src/Csparse.c revision 3055, Sat Mar 14 21:12:03 2015 UTC
#	Line 1	Line 1
1	/* Sparse matrices in compress column-oriented form */	/* Sparse matrices in compressed column-oriented form */
2
3	#include "Csparse.h"	#include "Csparse.h"
4	#ifdef USE_CHOLMOD	#include "Tsparse.h"
5	#include "chm_common.h"	#include "chm_common.h"
	#endif  /* USE_CHOLMOD */
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 */
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, ncol = length(pslot) - 1,	int *dims = INTEGER(GET_SLOT(x, Matrix_DimSym)), j,
14	*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),	nrow = dims[0],
15	nrow, *xp = INTEGER(pslot),	ncol = dims[1],
16		*xp = INTEGER(pslot),
17	*xi = INTEGER(islot);	*xi = INTEGER(islot);
18
19	nrow = dims[0];	if (length(pslot) != dims[1] + 1)
20	if (length(pslot) <= 0)	return FALSE;
	return mkString(_("slot p must have length > 0"));
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 mkString(_("last element of slot p must match length of slots i and x"));	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++) {	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		if(sorted)
88		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	}	}
	for (j = 0; j < length(islot); j++) {
	if (xi[j] < 0 || xi[j] >= nrow)
	return mkString(_("all row indices must be between 0 and nrow-1"));
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	SEXP Csparse_to_Tsparse(SEXP x)	/**
105		* From a CsparseMatrix, produce a dense one.
106		* Directly deals with symmetric, triangular and general.
107		* Called from ../R/Csparse.R's  C2dense()
108		*
109		* @param x a CsparseMatrix: currently all 9 of  "[dln][gst]CMatrix"
110		* @param symm_or_tri integer (NA, < 0, > 0, = 0) specifying the knowledge of the caller about x:
111		*      NA  : unknown => will be determined
112		*      = 0 : "generalMatrix" (not symm or tri);
113		*      < 0 : "triangularMatrix"
114		*      > 0 : "symmetricMatrix"
115		*
116		* @return a "denseMatrix"
117		*/
118		SEXP Csparse_to_dense(SEXP x, SEXP symm_or_tri)
119	{	{
120	#ifdef USE_CHOLMOD	Rboolean is_sym, is_tri;
121	cholmod_sparse *chxs = as_cholmod_sparse(x);	int is_sym_or_tri = asInteger(symm_or_tri),
122	cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);	ctype = 0; // <- default = "dgC"
123		static const char *valid[] = { MATRIX_VALID_Csparse, ""};
124		if(is_sym_or_tri == NA_INTEGER) { // find if  is(x, "symmetricMatrix") :
125		ctype = Matrix_check_class_etc(x, valid);
126		is_sym = (ctype % 3 == 1);
127		is_tri = (ctype % 3 == 2);
128		} else {
129		is_sym = is_sym_or_tri > 0;
130		is_tri = is_sym_or_tri < 0;
131		// => both are FALSE  iff  is_.. == 0
132		if(is_sym || is_tri)
133		ctype = Matrix_check_class_etc(x, valid);
134		}
135		CHM_SP chxs = AS_CHM_SP__(x);// -> chxs->stype = +- 1 <==> symmetric
136		R_CheckStack();
137		if(is_tri && *diag_P(x) == 'U') { // ==>  x := diagU2N(x), directly for chxs
138		CHM_SP eye = cholmod_speye(chxs->nrow, chxs->ncol, chxs->xtype, &c);
139		double one[] = {1, 0};
140		CHM_SP ans = cholmod_add(chxs, eye, one, one,
141		/* values: */ ((ctype / 3) != 2), // TRUE iff not "nMatrix"
142		TRUE, &c);
143		cholmod_free_sparse(&eye, &c);
144		chxs = cholmod_copy_sparse(ans, &c);
145		cholmod_free_sparse(&ans, &c);
146		}
147		/* The following loses the symmetry property, since cholmod_dense has none,
148		* BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
149		* to numeric (CHOLMOD_REAL) ones {and we "revert" via chm_dense_to_SEXP()}: */
150		CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
151		int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
152
153	free(chxs);	SEXP ans = chm_dense_to_SEXP(chxd, 1, Rkind,GET_SLOT(x, Matrix_DimNamesSym));
154	return chm_triplet_to_SEXP(chxt, 1);	// -> a [dln]geMatrix
155	#else	if(is_sym) { // ==> want  [dln]syMatrix
156	error("General conversion requires CHOLMOD");	const char cl1 = class_P(ans)[0];
157	return R_NilValue;          /* -Wall */	PROTECT(ans);
158	#endif  /* USE_CHOLMOD */	SEXP aa = PROTECT(NEW_OBJECT(MAKE_CLASS((cl1 == 'd') ? "dsyMatrix" :
159		((cl1 == 'l') ? "lsyMatrix" : "nsyMatrix"))));
160		// No need to duplicate() as slots of ans are freshly allocated and ans will not be used
161		SET_SLOT(aa, Matrix_xSym,       GET_SLOT(ans, Matrix_xSym));
162		SET_SLOT(aa, Matrix_DimSym,     GET_SLOT(ans, Matrix_DimSym));
163		SET_SLOT(aa, Matrix_DimNamesSym,GET_SLOT(ans, Matrix_DimNamesSym));
164		SET_SLOT(aa, Matrix_uploSym, mkString((chxs->stype > 0) ? "U" : "L"));
165		UNPROTECT(2);
166		return aa;
167		}
168		else if(is_tri) { // ==> want  [dln]trMatrix
169		const char cl1 = class_P(ans)[0];
170		PROTECT(ans);
171		SEXP aa = PROTECT(NEW_OBJECT(MAKE_CLASS((cl1 == 'd') ? "dtrMatrix" :
172		((cl1 == 'l') ? "ltrMatrix" : "ntrMatrix"))));
173		// No need to duplicate() as slots of ans are freshly allocated and ans will not be used
174		SET_SLOT(aa, Matrix_xSym,       GET_SLOT(ans, Matrix_xSym));
175		SET_SLOT(aa, Matrix_DimSym,     GET_SLOT(ans, Matrix_DimSym));
176		SET_SLOT(aa, Matrix_DimNamesSym,GET_SLOT(ans, Matrix_DimNamesSym));
177		slot_dup(aa, x, Matrix_uploSym);
178		/* already by NEW_OBJECT(..) above:
179		SET_SLOT(aa, Matrix_diagSym, mkString("N")); */
180		UNPROTECT(2);
181		return aa;
182		}
183		else
184		return ans;
185	}	}
186
187	SEXP Csparse_transpose(SEXP x)	// FIXME: do not go via CHM (should not be too hard, to just *drop* the x-slot, right?
188		SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
189	{	{
190	#ifdef USE_CHOLMOD	CHM_SP chxs = AS_CHM_SP__(x);
191	cholmod_sparse *chx = as_cholmod_sparse(x);	CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
192	cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);	int tr = asLogical(tri);
193		R_CheckStack();
194
195	free(chx);	return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
196	return chm_sparse_to_SEXP(chxt, 1);	tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
197	#else	0, tr ? diag_P(x) : "",
198	error("General conversion requires CHOLMOD");	GET_SLOT(x, Matrix_DimNamesSym));
199		}
200
201		// n.CMatrix --> [dli].CMatrix  (not going through CHM!)
202		SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
203		{
204		return nz2Csparse(x, asInteger(res_kind));
205		}
206
207		// n.CMatrix --> [dli].CMatrix  (not going through CHM!)
208		// NOTE: use chm_MOD_xtype(() to change type of  'cholmod_sparse' matrix
209		SEXP nz2Csparse(SEXP x, enum x_slot_kind r_kind)
210		{
211		const char *cl_x = class_P(x);
212		if(cl_x[0] != 'n') error(_("not a 'n.CMatrix'"));
213		if(cl_x[2] != 'C') error(_("not a CsparseMatrix"));
214		int nnz = LENGTH(GET_SLOT(x, Matrix_iSym));
215		SEXP ans;
216		char *ncl = alloca(strlen(cl_x) + 1); /* not much memory required */
217		strcpy(ncl, cl_x);
218		double *dx_x; int *ix_x;
219		ncl[0] = (r_kind == x_double ? 'd' :
220		(r_kind == x_logical ? 'l' :
221		/* else (for now):  r_kind == x_integer : */ 'i'));
222		PROTECT(ans = NEW_OBJECT(MAKE_CLASS(ncl)));
223		// create a correct 'x' slot:
224		switch(r_kind) {
225		int i;
226		case x_double: // 'd'
227		dx_x = REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz));
228		for (i=0; i < nnz; i++) dx_x[i] = 1.;
229		break;
230		case x_logical: // 'l'
231		ix_x = LOGICAL(ALLOC_SLOT(ans, Matrix_xSym, LGLSXP, nnz));
232		for (i=0; i < nnz; i++) ix_x[i] = TRUE;
233		break;
234		case x_integer: // 'i'
235		ix_x = INTEGER(ALLOC_SLOT(ans, Matrix_xSym, INTSXP, nnz));
236		for (i=0; i < nnz; i++) ix_x[i] = 1;
237		break;
238
239		default:
240		error(_("nz2Csparse(): invalid/non-implemented r_kind = %d"),
241		r_kind);
242		}
243
244		// now copy all other slots :
245		slot_dup(ans, x, Matrix_iSym);
246		slot_dup(ans, x, Matrix_pSym);
247		slot_dup(ans, x, Matrix_DimSym);
248		slot_dup(ans, x, Matrix_DimNamesSym);
249		if(ncl[1] != 'g') { // symmetric or triangular ...
250		slot_dup_if_has(ans, x, Matrix_uploSym);
251		slot_dup_if_has(ans, x, Matrix_diagSym);
252		}
253		UNPROTECT(1);
254		return ans;
255		}
256
257		SEXP Csparse_to_matrix(SEXP x, SEXP chk, SEXP symm)
258		{
259		int is_sym = asLogical(symm);
260		if(is_sym == NA_LOGICAL) { // find if  is(x, "symmetricMatrix") :
261		static const char *valid[] = { MATRIX_VALID_Csparse, ""};
262		int ctype = Matrix_check_class_etc(x, valid);
263		is_sym = (ctype % 3 == 1);
264		}
265		return chm_dense_to_matrix(
266		cholmod_sparse_to_dense(AS_CHM_SP2(x, asLogical(chk)), &c),
267		1 /*do_free*/,
268		(is_sym
269		? symmetric_DimNames(GET_SLOT(x, Matrix_DimNamesSym))
270		:                    GET_SLOT(x, Matrix_DimNamesSym)));
271		}
272
273		SEXP Csparse_to_vector(SEXP x)
274		{
275		return chm_dense_to_vector(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c), 1);
276		}
277
278		SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
279		{
280		CHM_SP chxs = AS_CHM_SP__(x);
281		CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
282		int tr = asLogical(tri);
283		int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
284		R_CheckStack();
285
286		return chm_triplet_to_SEXP(chxt, 1,
287		tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
288		Rkind, tr ? diag_P(x) : "",
289		GET_SLOT(x, Matrix_DimNamesSym));
290		}
291
292		SEXP Csparse_to_tCsparse(SEXP x, SEXP uplo, SEXP diag)
293		{
294		CHM_SP chxs = AS_CHM_SP__(x);
295		int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
296		R_CheckStack();
297		return chm_sparse_to_SEXP(chxs, /* dofree = */ 0,
298		/* uploT = */ (*CHAR(asChar(uplo)) == 'U')? 1: -1,
299		Rkind, /* diag = */ CHAR(STRING_ELT(diag, 0)),
300		GET_SLOT(x, Matrix_DimNamesSym));
301		}
302
303		SEXP Csparse_to_tTsparse(SEXP x, SEXP uplo, SEXP diag)
304		{
305		CHM_SP chxs = AS_CHM_SP__(x);
306		CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
307		int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
308		R_CheckStack();
309		return chm_triplet_to_SEXP(chxt, 1,
310		/* uploT = */ (*CHAR(asChar(uplo)) == 'U')? 1: -1,
311		Rkind, /* diag = */ CHAR(STRING_ELT(diag, 0)),
312		GET_SLOT(x, Matrix_DimNamesSym));
313		}
314
315
316		SEXP Csparse_symmetric_to_general(SEXP x)
317		{
318		CHM_SP chx = AS_CHM_SP__(x), chgx;
319		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
320		R_CheckStack();
321
322		if (!(chx->stype))
323		error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
324		chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
325		/* xtype: pattern, "real", complex or .. */
326		return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
327		symmetric_DimNames(GET_SLOT(x, Matrix_DimNamesSym)));
328		}
329
330		SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo, SEXP sym_dmns)
331		{
332		int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
333		if(n != adims[1]) {
334		error(_("Csparse_general_to_symmetric(): matrix is not square!"));
335	return R_NilValue;          /* -Wall */	return R_NilValue;          /* -Wall */
	#endif  /* USE_CHOLMOD */
336	}	}
337		CHM_SP chx = AS_CHM_SP__(x), chgx;
338		int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;
339		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
340		R_CheckStack();
341		chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
342
343		SEXP dns = GET_SLOT(x, Matrix_DimNamesSym);
344		if(asLogical(sym_dmns))
345		dns = symmetric_DimNames(dns);
346		else if((!isNull(VECTOR_ELT(dns, 0)) &&
347		!isNull(VECTOR_ELT(dns, 1))) ||
348		!isNull(getAttrib(dns, R_NamesSymbol))) {
349		/* symmetrize them if both are not NULL
350		* or names(dimnames(.)) is asymmetric : */
351		dns = PROTECT(duplicate(dns));
352		if(!equal_string_vectors(VECTOR_ELT(dns, 0),
353		VECTOR_ELT(dns, 1))) {
354		if(uploT == 1)
355		SET_VECTOR_ELT(dns, 0, VECTOR_ELT(dns,1));
356		else
357		SET_VECTOR_ELT(dns, 1, VECTOR_ELT(dns,0));
358		}
359		SEXP nms_dns = getAttrib(dns, R_NamesSymbol);
360		if(!isNull(nms_dns) &&  // names(dimnames(.)) :
361		!R_compute_identical(STRING_ELT(nms_dns, 0),
362		STRING_ELT(nms_dns, 1), 16)) {
363		if(uploT == 1)
364		SET_STRING_ELT(nms_dns, 0, STRING_ELT(nms_dns,1));
365		else
366		SET_STRING_ELT(nms_dns, 1, STRING_ELT(nms_dns,0));
367		setAttrib(dns, R_NamesSymbol, nms_dns);
368		}
369		UNPROTECT(1);
370		}
371		/* xtype: pattern, "real", complex or .. */
372		return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "", dns);
373		}
374
375		SEXP Csparse_transpose(SEXP x, SEXP tri)
376		{
377		/* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
378		*       since cholmod (& cs) lacks sparse 'int' matrices */
379		CHM_SP chx = AS_CHM_SP__(x);
380		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
381		CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
382		SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
383		int tr = asLogical(tri);
384		R_CheckStack();
385
386		tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
387		SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
388		SET_VECTOR_ELT(dn, 1, tmp);
389		if(!isNull(tmp = getAttrib(dn, R_NamesSymbol))) { // swap names(dimnames(.)):
390		SEXP nms_dns = PROTECT(allocVector(VECSXP, 2));
391		SET_VECTOR_ELT(nms_dns, 1, STRING_ELT(tmp, 0));
392		SET_VECTOR_ELT(nms_dns, 0, STRING_ELT(tmp, 1));
393		setAttrib(dn, R_NamesSymbol, nms_dns);
394		UNPROTECT(1);
395		}
396		UNPROTECT(1);
397		return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
398		tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
399		Rkind, tr ? diag_P(x) : "", dn);
400		}
401
402	SEXP Csparse_Csparse_prod(SEXP a, SEXP b)	SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
403	{	{
404	#ifdef USE_CHOLMOD	CHM_SP
405	cholmod_sparse *cha = as_cholmod_sparse(a), *chb = as_cholmod_sparse(b);	cha = AS_CHM_SP(a),
406	cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, (int) cha->xtype, 1, &c);	chb = AS_CHM_SP(b),
407		chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
408		/* values:= is_numeric (T/F) */ cha->xtype > 0,
409		/*out sorted:*/ 1, &c);
410		const char *cl_a = class_P(a), *cl_b = class_P(b);
411		char diag[] = {'\0', '\0'};
412		int uploT = 0;
413		SEXP dn = PROTECT(allocVector(VECSXP, 2));
414		R_CheckStack();
415
416	free(cha); free(chb);	#ifdef DEBUG_Matrix_verbose
417	return chm_sparse_to_SEXP(chc, 1);	Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
418	#else	#endif
419	error("General multiplication requires CHOLMOD");
420	return R_NilValue;          /* -Wall */	/* Preserve triangularity and even unit-triangularity if appropriate.
421	#endif  /* USE_CHOLMOD */	* Note that in that case, the multiplication itself should happen
422		* faster.  But there's no support for that in CHOLMOD */
423
424		/* UGLY hack -- rather should have (fast!) C-level version of
425		*       is(a, "triangularMatrix") etc */
426		if (cl_a[1] == 't' && cl_b[1] == 't')
427		/* FIXME: fails for "Cholesky","BunchKaufmann"..*/
428		if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
429		uploT = (*uplo_P(a) == 'U') ? 1 : -1;
430		if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
431		/* "remove the diagonal entries": */
432		chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
433		diag[0]= 'U';
434		}
435		else diag[0]= 'N';
436		}
437		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
438		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
439		SET_VECTOR_ELT(dn, 1,
440		duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
441		UNPROTECT(1);
442		return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
443		}
444
445		SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
446		{
447		int tr = asLogical(trans);
448		CHM_SP
449		cha = AS_CHM_SP(a),
450		chb = AS_CHM_SP(b),
451		chTr, chc;
452		const char *cl_a = class_P(a), *cl_b = class_P(b);
453		char diag[] = {'\0', '\0'};
454		int uploT = 0;
455		SEXP dn = PROTECT(allocVector(VECSXP, 2));
456		R_CheckStack();
457
458		chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
459		chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
460		/*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
461		cholmod_free_sparse(&chTr, &c);
462
463		/* Preserve triangularity and unit-triangularity if appropriate;
464		* see Csparse_Csparse_prod() for comments */
465		if (cl_a[1] == 't' && cl_b[1] == 't')
466		if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
467		uploT = (*uplo_P(b) == 'U') ? 1 : -1;
468		if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
469		chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
470		diag[0]= 'U';
471		}
472		else diag[0]= 'N';
473		}
474		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
475		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
476		SET_VECTOR_ELT(dn, 1,
477		duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
478		UNPROTECT(1);
479		return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
480	}	}
481
482	SEXP Csparse_dense_prod(SEXP a, SEXP b)	SEXP Csparse_dense_prod(SEXP a, SEXP b)
483	{	{
484	#ifdef USE_CHOLMOD	CHM_SP cha = AS_CHM_SP(a);
485	cholmod_sparse *cha = as_cholmod_sparse(a);	SEXP b_M = PROTECT(mMatrix_as_dgeMatrix2(b, // transpose_if_vector =
486	cholmod_dense *chb = as_cholmod_dense(b);	cha->ncol == 1));
487	cholmod_dense *chc = cholmod_allocate_dense(cha->nrow, chb->ncol,	CHM_DN chb = AS_CHM_DN(b_M);
488	cha->nrow, chb->xtype, &c);	CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
489	double alpha = 1, beta = 0;	chb->xtype, &c);
490		SEXP dn = PROTECT(allocVector(VECSXP, 2));
491	cholmod_sdmult(cha, 0, &alpha, &beta, chb, chc, &c);	double one[] = {1,0}, zero[] = {0,0};
492	free(cha); free(chb);	int nprot = 2;
493	return chm_dense_to_SEXP(chc, 1);	R_CheckStack();
494	#else	/* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
495	error("General multiplication requires CHOLMOD");	if(cha->xtype == CHOLMOD_PATTERN) {
496	return R_NilValue;          /* -Wall */	/* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
497	#endif  /* USE_CHOLMOD */	/*        " --> slightly inefficient coercion")); */
498
499		// This *fails* to produce a CHOLMOD_REAL ..
500		// CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
501		// --> use our Matrix-classes
502		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
503		cha = AS_CHM_SP(da);
504		}
505		cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
506		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
507		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
508		SET_VECTOR_ELT(dn, 1,
509		duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
510		UNPROTECT(nprot);
511		return chm_dense_to_SEXP(chc, 1, 0, dn);
512		}
513
514		SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
515		{
516		CHM_SP cha = AS_CHM_SP(a);
517		SEXP b_M = PROTECT(mMatrix_as_dgeMatrix2(b, // transpose_if_vector =
518		cha->nrow == 1));
519		CHM_DN chb = AS_CHM_DN(b_M);
520		CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
521		chb->xtype, &c);
522		SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
523		double one[] = {1,0}, zero[] = {0,0};
524		R_CheckStack();
525		// -- see Csparse_dense_prod() above :
526		if(cha->xtype == CHOLMOD_PATTERN) {
527		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
528		cha = AS_CHM_SP(da);
529		}
530		cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
531		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
532		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
533		SET_VECTOR_ELT(dn, 1,
534		duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
535		UNPROTECT(nprot);
536		return chm_dense_to_SEXP(chc, 1, 0, dn);
537	}	}
538
539		/* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
540		see Csparse_Csparse_crossprod above for  x'y and x y' */
541	SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)	SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
542	{	{
	#ifdef USE_CHOLMOD
543	int trip = asLogical(triplet),	int trip = asLogical(triplet),
544	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
545	cholmod_triplet	#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
546	*cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;	CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
547	cholmod_sparse *chcp, *chxt,	#else /* workaround needed:*/
548	*chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)	SEXP xx = PROTECT(Tsparse_diagU2N(x));
549	: as_cholmod_sparse(x);	CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
550		#endif
551		CHM_SP chcp, chxt,
552		chx = (trip ?
553		cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
554		AS_CHM_SP(x));
555		SEXP dn = PROTECT(allocVector(VECSXP, 2));
556		R_CheckStack();
557
558	if (!tr)	if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
	chxt = cholmod_transpose(chx, (int) chx->xtype, &c);
559	chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);	chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
560	if(!chcp)	if(!chcp) {
561	error("Csparse_crossprod(): error return from cholmod_aat()");	UNPROTECT(1);
562		error(_("Csparse_crossprod(): error return from cholmod_aat()"));
	if (trip) {
	cholmod_free_sparse(&chx, &c);
	free(cht);
	} else {
	free(chx);
563	}	}
564		cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
565		chcp->stype = 1;
566		if (trip) cholmod_free_sparse(&chx, &c);
567	if (!tr) cholmod_free_sparse(&chxt, &c);	if (!tr) cholmod_free_sparse(&chxt, &c);
568	return chm_sparse_to_SEXP(chcp, 1);	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
569		duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
570		(tr) ? 0 : 1)));
571		SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
572		#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
573		UNPROTECT(1);
574	#else	#else
575	error("General crossproduct requires CHOLMOD");	UNPROTECT(2);
576	return R_NilValue;          /* -Wall */	#endif
577	#endif  /* USE_CHOLMOD */	return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
578		}
579
580		/* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
581		*  at least all "explicit" zeros */
582		SEXP Csparse_drop(SEXP x, SEXP tol)
583		{
584		const char *cl = class_P(x);
585		/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
586		int tr = (cl[1] == 't');
587		CHM_SP chx = AS_CHM_SP__(x);
588		CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
589		double dtol = asReal(tol);
590		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
591		R_CheckStack();
592
593		if(!cholmod_drop(dtol, ans, &c))
594		error(_("cholmod_drop() failed"));
595		return chm_sparse_to_SEXP(ans, 1,
596		tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
597		Rkind, tr ? diag_P(x) : "",
598		GET_SLOT(x, Matrix_DimNamesSym));
599		}
600
601		SEXP Csparse_horzcat(SEXP x, SEXP y)
602		{
603		#define CSPARSE_CAT(_KIND_)                                             \
604		CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);                  \
605		R_CheckStack();                                                     \
606		int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : -3,     \
607		Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : -3, Rkind; \
608		if(Rk_x == -3 || Rk_y == -3) { /* at least one of them is patter"n" */ \
609		if(Rk_x == -3 && Rk_y == -3) { /* fine */                       \
610		} else { /* only one is a patter"n"                             \
611		* "Bug" in cholmod_horzcat()/vertcat(): returns patter"n" matrix if one of them is */ \
612		Rboolean ok;                                                \
613		if(Rk_x == -3) {                                            \
614		ok = chm_MOD_xtype(CHOLMOD_REAL, chx, &c); Rk_x = 0;    \
615		} else if(Rk_y == -3) {                                     \
616		ok = chm_MOD_xtype(CHOLMOD_REAL, chy, &c); Rk_y = 0;    \
617		} else                                                      \
618		error(_("Impossible Rk_x/Rk_y in Csparse_%s(), please report"), _KIND_); \
619		if(!ok)                                                     \
620		error(_("chm_MOD_xtype() was not successful in Csparse_%s(), please report"), \
621		_KIND_);                                          \
622		}                                                               \
623		}                                                                   \
624		Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0
625
626		CSPARSE_CAT("horzcat");
627		// TODO: currently drops dimnames - and we fix at R level;
628
629		return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
630		1, 0, Rkind, "", R_NilValue);
631		}
632
633		SEXP Csparse_vertcat(SEXP x, SEXP y)
634		{
635		CSPARSE_CAT("vertcat");
636		// TODO: currently drops dimnames - and we fix at R level;
637
638		return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
639		1, 0, Rkind, "", R_NilValue);
640		}
641
642		SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
643		{
644		CHM_SP chx = AS_CHM_SP__(x);
645		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
646		CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
647		R_CheckStack();
648
649		return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
650		GET_SLOT(x, Matrix_DimNamesSym));
651		}
652
653		SEXP Csparse_diagU2N(SEXP x)
654		{
655		const char *cl = class_P(x);
656		/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
657		if (cl[1] != 't' || *diag_P(x) != 'U') {
658		/* "trivially fast" when not triangular (<==> no 'diag' slot),
659		or not *unit* triangular */
660		return (x);
661		}
662		else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
663		CHM_SP chx = AS_CHM_SP__(x);
664		CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
665		double one[] = {1, 0};
666		CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
667		int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
668		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
669
670		R_CheckStack();
671		cholmod_free_sparse(&eye, &c);
672		return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
673		GET_SLOT(x, Matrix_DimNamesSym));
674		}
675		}
676
677		SEXP Csparse_diagN2U(SEXP x)
678		{
679		const char *cl = class_P(x);
680		/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
681		if (cl[1] != 't' || *diag_P(x) != 'N') {
682		/* "trivially fast" when not triangular (<==> no 'diag' slot),
683		or already *unit* triangular */
684		return (x);
685		}
686		else { /* triangular with diag='N'): now drop the diagonal */
687		/* duplicate, since chx will be modified: */
688		SEXP xx = PROTECT(duplicate(x));
689		CHM_SP chx = AS_CHM_SP__(xx);
690		int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
691		Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
692		R_CheckStack();
693
694		chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
695
696		SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
697		uploT, Rkind, "U",
698		GET_SLOT(x, Matrix_DimNamesSym));
699		UNPROTECT(1);// only now !
700		return ans;
701		}
702		}
703
704		/**
705		* "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
706		* Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
707		* @param x CsparseMatrix
708		* @param i row     indices (0-origin), or NULL (R's)
709		* @param j columns indices (0-origin), or NULL
710		*
711		* @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
712		*/
713		SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
714		{
715		CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
716		int rsize = (isNull(i)) ? -1 : LENGTH(i),
717		csize = (isNull(j)) ? -1 : LENGTH(j);
718		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
719		R_CheckStack();
720
721		if (rsize >= 0 && !isInteger(i))
722		error(_("Index i must be NULL or integer"));
723		if (csize >= 0 && !isInteger(j))
724		error(_("Index j must be NULL or integer"));
725
726		#define CHM_SUB(_M_, _i_, _j_)                                  \
727		cholmod_submatrix(_M_,                                      \
728		(rsize < 0) ? NULL : INTEGER(_i_), rsize, \
729		(csize < 0) ? NULL : INTEGER(_j_), csize, \
730		TRUE, TRUE, &c)
731		CHM_SP ans;
732		if (!chx->stype) {/* non-symmetric Matrix */
733		ans = CHM_SUB(chx, i, j);
734		}
735		else {
736		/* for now, cholmod_submatrix() only accepts "generalMatrix" */
737		CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
738		ans = CHM_SUB(tmp, i, j);
739		cholmod_free_sparse(&tmp, &c);
740		}
741
742		// "FIXME": currently dropping dimnames, and adding them afterwards in R :
743		/* // dimnames: */
744		/* SEXP x_dns = GET_SLOT(x, Matrix_DimNamesSym), */
745		/*  dn = PROTECT(allocVector(VECSXP, 2)); */
746		return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", /* dimnames: */ R_NilValue);
747		}
748
749		#define _d_Csp_
750		#include "t_Csparse_subassign.c"
751
752		#define _l_Csp_
753		#include "t_Csparse_subassign.c"
754
755		#define _i_Csp_
756		#include "t_Csparse_subassign.c"
757
758		#define _n_Csp_
759		#include "t_Csparse_subassign.c"
760
761		#define _z_Csp_
762		#include "t_Csparse_subassign.c"
763
764
765
766		SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
767		{
768		FILE *f = fopen(CHAR(asChar(fname)), "w");
769
770		if (!f)
771		error(_("failure to open file \"%s\" for writing"),
772		CHAR(asChar(fname)));
773		if (!cholmod_write_sparse(f, AS_CHM_SP(x),
774		(CHM_SP)NULL, (char*) NULL, &c))
775		error(_("cholmod_write_sparse returned error code"));
776		fclose(f);
777		return R_NilValue;
778		}
779
780
781		/**
782		* Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
783		* cholmod_sparse factor (LDL = TRUE).
784		*
785		* @param n  dimension of the matrix.
786		* @param x_p  'p' (column pointer) slot contents
787		* @param x_x  'x' (non-zero entries) slot contents
788		* @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
789		* @param resultKind a (SEXP) string indicating which kind of result is desired.
790		*
791		* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
792		*/
793		SEXP diag_tC_ptr(int n, int *x_p, double *x_x, Rboolean is_U, int *perm,
794		/*                                ^^^^^^ FIXME[Generalize] to int / ... */
795		SEXP resultKind)
796		{
797		const char* res_ch = CHAR(STRING_ELT(resultKind,0));
798		enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log, min, max, range
799		} res_kind = ((!strcmp(res_ch, "trace")) ? trace :
800		((!strcmp(res_ch, "sumLog")) ? sum_log :
801		((!strcmp(res_ch, "prod")) ? prod :
802		((!strcmp(res_ch, "min")) ? min :
803		((!strcmp(res_ch, "max")) ? max :
804		((!strcmp(res_ch, "range")) ? range :
805		((!strcmp(res_ch, "diag")) ? diag :
806		((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
807		-1))))))));
808		int i, n_x, i_from;
809		SEXP ans = PROTECT(allocVector(REALSXP,
810		/*                                 ^^^^  FIXME[Generalize] */
811		(res_kind == diag ||
812		res_kind == diag_backpermuted) ? n :
813		(res_kind == range ? 2 : 1)));
814		double *v = REAL(ans);
815		/*  ^^^^^^      ^^^^  FIXME[Generalize] */
816
817		i_from = (is_U ? -1 : 0);
818
819		#define for_DIAG(v_ASSIGN)                                      \
820		for(i = 0; i < n; i++) {                                    \
821		/* looking at i-th column */                            \
822		n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
823		if( is_U) i_from += n_x;                                \
824		v_ASSIGN;                                               \
825		if(!is_U) i_from += n_x;                                \
826		}
827
828		/* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
829		*            for uplo = "U" (makes sense with a "dtCMatrix" !),
830		*            should use  x_x[i_from + (n_x - 1)] instead of x_x[i_from],
831		*            where n_x = (x_p[i+1] - x_p[i])
832		*/
833
834		switch(res_kind) {
835		case trace: // = sum
836		v[0] = 0.;
837		for_DIAG(v[0] += x_x[i_from]);
838		break;
839
840		case sum_log:
841		v[0] = 0.;
842		for_DIAG(v[0] += log(x_x[i_from]));
843		break;
844
845		case prod:
846		v[0] = 1.;
847		for_DIAG(v[0] *= x_x[i_from]);
848		break;
849
850		case min:
851		v[0] = R_PosInf;
852		for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from]);
853		break;
854
855		case max:
856		v[0] = R_NegInf;
857		for_DIAG(if(v[0] < x_x[i_from]) v[0] = x_x[i_from]);
858		break;
859
860		case range:
861		v[0] = R_PosInf;
862		v[1] = R_NegInf;
863		for_DIAG(if(v[0] > x_x[i_from]) v[0] = x_x[i_from];
864		if(v[1] < x_x[i_from]) v[1] = x_x[i_from]);
865		break;
866
867		case diag:
868		for_DIAG(v[i] = x_x[i_from]);
869		break;
870
871		case diag_backpermuted:
872		for_DIAG(v[i] = x_x[i_from]);
873
874		warning(_("%s = '%s' (back-permuted) is experimental"),
875		"resultKind", "diagBack");
876		/* now back_permute : */
877		for(i = 0; i < n; i++) {
878		double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
879		/*^^^^ FIXME[Generalize] */
880		}
881		break;
882
883		default: /* -1 from above */
884		error(_("diag_tC(): invalid 'resultKind'"));
885		/* Wall: */ ans = R_NilValue; v = REAL(ans);
886		}
887
888		UNPROTECT(1);
889		return ans;
890	}	}
891
892		/**
893		* Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
894		* cholmod_sparse factor (LDL = TRUE).
895		*
896		* @param obj -- now a cholmod_sparse factor or a dtCMatrix
897		* @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
898		* @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
899		* @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
900		*                   only used for "diagBack"
901		* @param resultKind a (SEXP) string indicating which kind of result is desired.
902		*
903		* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
904		*/
905		SEXP diag_tC(SEXP obj, SEXP resultKind)
906		{
907
908		SEXP
909		pslot = GET_SLOT(obj, Matrix_pSym),
910		xslot = GET_SLOT(obj, Matrix_xSym);
911		Rboolean is_U = (R_has_slot(obj, Matrix_uploSym) &&
912		*CHAR(asChar(GET_SLOT(obj, Matrix_uploSym))) == 'U');
913		int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
914		*x_p  = INTEGER(pslot), pp = -1, *perm;
915		double *x_x = REAL(xslot);
916		/*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
917
918		if(R_has_slot(obj, Matrix_permSym))
919		perm = INTEGER(GET_SLOT(obj, Matrix_permSym));
920		else perm = &pp;
921
922		return diag_tC_ptr(n, x_p, x_x, is_U, perm, resultKind);
923		}
924
925
926		/**
927		* Create a Csparse matrix object from indices and/or pointers.
928		*
929		* @param cls name of actual class of object to create
930		* @param i optional integer vector of length nnz of row indices
931		* @param j optional integer vector of length nnz of column indices
932		* @param p optional integer vector of length np of row or column pointers
933		* @param np length of integer vector p.  Must be zero if p == (int*)NULL
934		* @param x optional vector of values
935		* @param nnz length of vectors i, j and/or x, whichever is to be used
936		* @param dims optional integer vector of length 2 to be used as
937		*     dimensions.  If dims == (int*)NULL then the maximum row and column
938		*     index are used as the dimensions.
939		* @param dimnames optional list of length 2 to be used as dimnames
940		* @param index1 indicator of 1-based indices
941		*
942		* @return an SEXP of class cls inheriting from CsparseMatrix.
943		*/
944		SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
945		void* x, int nnz, int* dims, SEXP dimnames,
946		int index1)
947		{
948		SEXP ans;
949		int *ij = (int*)NULL, *tri, *trj,
950		mi, mj, mp, nrow = -1, ncol = -1;
951		int xtype = -1;             /* -Wall */
952		CHM_TR T;
953		CHM_SP A;
954
955		if (np < 0 || nnz < 0)
956		error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
957		np, nnz);
958		if (1 != ((mi = (i == (int*)NULL)) +
959		(mj = (j == (int*)NULL)) +
960		(mp = (p == (int*)NULL))))
961		error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
962		if (mp) {
963		if (np) error(_("np = %d, must be zero when p is NULL"), np);
964		} else {
965		if (np) {               /* Expand p to form i or j */
966		if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
967		for (int ii = 0; ii < np; ii++)
968		if (p[ii] > p[ii + 1])
969		error(_("p must be non-decreasing"));
970		if (p[np] != nnz)
971		error("p[np] = %d != nnz = %d", p[np], nnz);
972		ij = Calloc(nnz, int);
973		if (mi) {
974		i = ij;
975		nrow = np;
976		} else {
977		j = ij;
978		ncol = np;
979		}
980		/* Expand p to 0-based indices */
981		for (int ii = 0; ii < np; ii++)
982		for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
983		} else {
984		if (nnz)
985		error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
986		nnz);
987		}
988		}
989		/* calculate nrow and ncol */
990		if (nrow < 0) {
991		for (int ii = 0; ii < nnz; ii++) {
992		int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
993		if (i1 < 1) error(_("invalid row index at position %d"), ii);
994		if (i1 > nrow) nrow = i1;
995		}
996		}
997		if (ncol < 0) {
998		for (int jj = 0; jj < nnz; jj++) {
999		int j1 = j[jj] + (index1 ? 0 : 1);
1000		if (j1 < 1) error(_("invalid column index at position %d"), jj);
1001		if (j1 > ncol) ncol = j1;
1002		}
1003		}
1004		if (dims != (int*)NULL) {
1005		if (dims[0] > nrow) nrow = dims[0];
1006		if (dims[1] > ncol) ncol = dims[1];
1007		}
1008		/* check the class name */
1009		if (strlen(cls) != 8)
1010		error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
1011		if (!strcmp(cls + 2, "CMatrix"))
1012		error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
1013		switch(cls[0]) {
1014		case 'd':
1015		case 'l':
1016		xtype = CHOLMOD_REAL;
1017		break;
1018		case 'n':
1019		xtype = CHOLMOD_PATTERN;
1020		break;
1021		default:
1022		error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
1023		}
1024		if (cls[1] != 'g')
1025		error(_("Only 'g'eneral sparse matrix types allowed"));
1026		/* allocate and populate the triplet */
1027		T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
1028		xtype, &c);
1029		T->x = x;
1030		tri = (int*)T->i;
1031		trj = (int*)T->j;
1032		for (int ii = 0; ii < nnz; ii++) {
1033		tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
1034		trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
1035		}
1036		/* create the cholmod_sparse structure */
1037		A = cholmod_triplet_to_sparse(T, nnz, &c);
1038		cholmod_free_triplet(&T, &c);
1039		/* copy the information to the SEXP */
1040		ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
1041		// FIXME: This has been copied from chm_sparse_to_SEXP in  chm_common.c
1042		/* allocate and copy common slots */
1043		nnz = cholmod_nnz(A, &c);
1044		dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
1045		dims[0] = A->nrow; dims[1] = A->ncol;
1046		Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
1047		Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
1048		switch(cls[1]) {
1049		case 'd':
1050		Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
1051		break;
1052		case 'l':
1053		error(_("code not yet written for cls = \"lgCMatrix\""));
1054		}
1055		/* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
1056		cholmod_free_sparse(&A, &c);
1057		UNPROTECT(1);
1058		return ans;
1059		}

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