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 2834, Mon Sep 3 10:30:03 2012 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),
12		islot = GET_SLOT(x, Matrix_iSym);
13		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),	SEXP pslot = GET_SLOT(x, Matrix_pSym),
48	islot = GET_SLOT(x, Matrix_iSym);	islot = GET_SLOT(x, Matrix_iSym);
49	int j, ncol = length(pslot) - 1,	Rboolean sorted, strictly;
50		int j, k,
51	*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),	*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
52	nrow, *xp = INTEGER(pslot),	nrow = dims[0],
53		ncol = dims[1],
54		*xp = INTEGER(pslot),
55	*xi = INTEGER(islot);	*xi = INTEGER(islot);
56
57	nrow = dims[0];	if (length(pslot) != dims[1] + 1)
58	if (length(pslot) <= 0)	return mkString(_("slot p must have length = ncol(.) + 1"));
	return mkString(_("slot p must have length > 0"));
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 mkString(_("last element of slot p must match length of slots i and x"));	return
63		mkString(_("last element of slot p must match length of slots i and x"));
64		for (j = 0; j < xp[ncol]; j++) {
65		if (xi[j] < 0 || xi[j] >= nrow)
66		return mkString(_("all row indices must be between 0 and nrow-1"));
67		}
68		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		if(sorted) /* only act if >= 2 entries in column j : */
73		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	for (j = 0; j < length(islot); j++) {	}
80	if (xi[j] < 0 || xi[j] >= nrow)	if (!sorted) {
81	return mkString(_("all row indices must be between 0 and nrow-1"));	if(maybe_modify) {
82		CHM_SP chx = (CHM_SP) alloca(sizeof(cholmod_sparse));
83		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 Csparse_to_Tsparse(SEXP x)	SEXP Rsparse_validate(SEXP x)
104	{	{
105	#ifdef USE_CHOLMOD	/* NB: we do *NOT* check a potential 'x' slot here, at all */
106	cholmod_sparse *chxs = as_cholmod_sparse(x);	SEXP pslot = GET_SLOT(x, Matrix_pSym),
107	cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);	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	free(chxs);	if (length(pslot) != dims[0] + 1)
117	return chm_triplet_to_SEXP(chxt, 1);	return mkString(_("slot p must have length = nrow(.) + 1"));
118	#else	if (xp[0] != 0)
119	error("General conversion requires CHOLMOD");	return mkString(_("first element of slot p must be zero"));
120	return R_NilValue;          /* -Wall */	if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/
121	#endif  /* USE_CHOLMOD */	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	SEXP Csparse_transpose(SEXP x)	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)
153	{	{
154	#ifdef USE_CHOLMOD	CHM_SP chxs = AS_CHM_SP__(x);
155	cholmod_sparse *chx = as_cholmod_sparse(x);	/* This loses the symmetry property, since cholmod_dense has none,
156	cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);	* 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(chx);	return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
163	return chm_sparse_to_SEXP(chxt, 1);	}
164	#else
165	error("General conversion requires CHOLMOD");	// 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)
167		{
168		CHM_SP chxs = AS_CHM_SP__(x);
169		CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
170		int tr = asLogical(tri);
171		R_CheckStack();
172
173		return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
174		tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
175		0, tr ? diag_P(x) : "",
176		GET_SLOT(x, Matrix_DimNamesSym));
177		}
178
179		// 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		const char *cl_x = class_P(x);
188		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		SEXP Csparse_to_matrix(SEXP x)
234		{
235		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)
240		{
241		CHM_SP chxs = AS_CHM_SP__(x);
242		CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
243		int tr = asLogical(tri);
244		int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
245		R_CheckStack();
246
247		return chm_triplet_to_SEXP(chxt, 1,
248		tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
249		Rkind, tr ? diag_P(x) : "",
250		GET_SLOT(x, Matrix_DimNamesSym));
251		}
252
253		/* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
254		SEXP Csparse_symmetric_to_general(SEXP x)
255		{
256		CHM_SP chx = AS_CHM_SP__(x), chgx;
257		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
258		R_CheckStack();
259
260		if (!(chx->stype))
261		error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
262		chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
263		/* xtype: pattern, "real", complex or .. */
264		return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
265		GET_SLOT(x, Matrix_DimNamesSym));
266		}
267
268		SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
269		{
270		int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
271		if(n != adims[1]) {
272		error(_("Csparse_general_to_symmetric(): matrix is not square!"));
273	return R_NilValue;          /* -Wall */	return R_NilValue;          /* -Wall */
274	#endif  /* USE_CHOLMOD */	}
275		CHM_SP chx = AS_CHM_SP__(x), chgx;
276		int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
277		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
278		R_CheckStack();
279		chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
280		/* xtype: pattern, "real", complex or .. */
281		return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
282		GET_SLOT(x, Matrix_DimNamesSym));
283	}	}
284
285		SEXP Csparse_transpose(SEXP x, SEXP tri)
286		{
287		/* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
288		*       since cholmod (& cs) lacks sparse 'int' matrices */
289		CHM_SP chx = AS_CHM_SP__(x);
290		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
291		CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
292		SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
293		int tr = asLogical(tri);
294		R_CheckStack();
295
296		tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
297		SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
298		SET_VECTOR_ELT(dn, 1, tmp);
299		UNPROTECT(1);
300		return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
301		tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
302		Rkind, tr ? diag_P(x) : "", dn);
303		}
304
305	SEXP Csparse_Csparse_prod(SEXP a, SEXP b)	SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
306	{	{
307	#ifdef USE_CHOLMOD	CHM_SP
308	cholmod_sparse *cha = as_cholmod_sparse(a), *chb = as_cholmod_sparse(b);	cha = AS_CHM_SP(a),
309	cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, (int) cha->xtype, 1, &c);	chb = AS_CHM_SP(b),
310		chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
311		/* values:= is_numeric (T/F) */ cha->xtype > 0,
312		/*out sorted:*/ 1, &c);
313		const char *cl_a = class_P(a), *cl_b = class_P(b);
314		char diag[] = {'\0', '\0'};
315		int uploT = 0;
316		SEXP dn = PROTECT(allocVector(VECSXP, 2));
317		R_CheckStack();
318
319		#ifdef DEBUG_Matrix_verbose
320		Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
321		#endif
322
323		/* Preserve triangularity and even unit-triangularity if appropriate.
324		* Note that in that case, the multiplication itself should happen
325		* faster.  But there's no support for that in CHOLMOD */
326
327		/* UGLY hack -- rather should have (fast!) C-level version of
328		*       is(a, "triangularMatrix") etc */
329		if (cl_a[1] == 't' && cl_b[1] == 't')
330		/* FIXME: fails for "Cholesky","BunchKaufmann"..*/
331		if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
332		uploT = (*uplo_P(a) == 'U') ? 1 : -1;
333		if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
334		/* "remove the diagonal entries": */
335		chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
336		diag[0]= 'U';
337		}
338		else diag[0]= 'N';
339		}
340		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
341		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
342		SET_VECTOR_ELT(dn, 1,
343		duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
344		UNPROTECT(1);
345		return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
346		}
347
348	free(cha); free(chb);	SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
349	return chm_sparse_to_SEXP(chc, 1);	{
350	#else	int tr = asLogical(trans);
351	error("General multiplication requires CHOLMOD");	CHM_SP
352	return R_NilValue;          /* -Wall */	cha = AS_CHM_SP(a),
353	#endif  /* USE_CHOLMOD */	chb = AS_CHM_SP(b),
354		chTr, chc;
355		const char *cl_a = class_P(a), *cl_b = class_P(b);
356		char diag[] = {'\0', '\0'};
357		int uploT = 0;
358		SEXP dn = PROTECT(allocVector(VECSXP, 2));
359		R_CheckStack();
360
361		chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
362		chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
363		/*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
364		cholmod_free_sparse(&chTr, &c);
365
366		/* Preserve triangularity and unit-triangularity if appropriate;
367		* see Csparse_Csparse_prod() for comments */
368		if (cl_a[1] == 't' && cl_b[1] == 't')
369		if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
370		uploT = (*uplo_P(b) == 'U') ? 1 : -1;
371		if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
372		chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
373		diag[0]= 'U';
374		}
375		else diag[0]= 'N';
376		}
377		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
378		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
379		SET_VECTOR_ELT(dn, 1,
380		duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
381		UNPROTECT(1);
382		return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
383	}	}
384
385	SEXP Csparse_dense_prod(SEXP a, SEXP b)	SEXP Csparse_dense_prod(SEXP a, SEXP b)
386	{	{
387	#ifdef USE_CHOLMOD	CHM_SP cha = AS_CHM_SP(a);
388	cholmod_sparse *cha = as_cholmod_sparse(a);	SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
389	cholmod_dense *chb = as_cholmod_dense(b);	CHM_DN chb = AS_CHM_DN(b_M);
390	cholmod_dense *chc = cholmod_allocate_dense(cha->nrow, chb->ncol,	CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
391	cha->nrow, chb->xtype, &c);	chb->xtype, &c);
392	double alpha = 1, beta = 0;	SEXP dn = PROTECT(allocVector(VECSXP, 2));
393		double one[] = {1,0}, zero[] = {0,0};
394	cholmod_sdmult(cha, 0, &alpha, &beta, chb, chc, &c);	int nprot = 2;
395	free(cha); free(chb);	R_CheckStack();
396	return chm_dense_to_SEXP(chc, 1);	/* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
397	#else	if(cha->xtype == CHOLMOD_PATTERN) {
398	error("General multiplication requires CHOLMOD");	/* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
399	return R_NilValue;          /* -Wall */	/*        " --> slightly inefficient coercion")); */
400	#endif  /* USE_CHOLMOD */
401		// This *fails* to produce a CHOLMOD_REAL ..
402		// CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
403		// --> use our Matrix-classes
404		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
405		cha = AS_CHM_SP(da);
406		}
407		cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
408		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
409		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
410		SET_VECTOR_ELT(dn, 1,
411		duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
412		UNPROTECT(nprot);
413		return chm_dense_to_SEXP(chc, 1, 0, dn);
414		}
415
416		SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
417		{
418		CHM_SP cha = AS_CHM_SP(a);
419		SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
420		CHM_DN chb = AS_CHM_DN(b_M);
421		CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
422		chb->xtype, &c);
423		SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
424		double one[] = {1,0}, zero[] = {0,0};
425		R_CheckStack();
426		// -- see Csparse_dense_prod() above :
427		if(cha->xtype == CHOLMOD_PATTERN) {
428		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
429		cha = AS_CHM_SP(da);
430		}
431		cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
432		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
433		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
434		SET_VECTOR_ELT(dn, 1,
435		duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
436		UNPROTECT(nprot);
437		return chm_dense_to_SEXP(chc, 1, 0, dn);
438	}	}
439
440		/* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
441		see Csparse_Csparse_crossprod above for  x'y and x y' */
442	SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)	SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
443	{	{
	#ifdef USE_CHOLMOD
444	int trip = asLogical(triplet),	int trip = asLogical(triplet),
445	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
446	cholmod_triplet	#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
447	*cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;	CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
448	cholmod_sparse *chcp, *chxt,	#else /* workaround needed:*/
449	*chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)	SEXP xx = PROTECT(Tsparse_diagU2N(x));
450	: as_cholmod_sparse(x);	CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
451		#endif
452		CHM_SP chcp, chxt,
453		chx = (trip ?
454		cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
455		AS_CHM_SP(x));
456		SEXP dn = PROTECT(allocVector(VECSXP, 2));
457		R_CheckStack();
458
459	if (!tr)	if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
	chxt = cholmod_transpose(chx, (int) chx->xtype, &c);
460	chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);	chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
461	if(!chcp)	if(!chcp) {
462	error("Csparse_crossprod(): error return from cholmod_aat()");	UNPROTECT(1);
463		error(_("Csparse_crossprod(): error return from cholmod_aat()"));
	if (trip) {
	cholmod_free_sparse(&chx, &c);
	free(cht);
	} else {
	free(chx);
464	}	}
465		cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
466		chcp->stype = 1;
467		if (trip) cholmod_free_sparse(&chx, &c);
468	if (!tr) cholmod_free_sparse(&chxt, &c);	if (!tr) cholmod_free_sparse(&chxt, &c);
469	return chm_sparse_to_SEXP(chcp, 1);	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
470		duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
471		(tr) ? 0 : 1)));
472		SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
473		#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
474		UNPROTECT(1);
475	#else	#else
476	error("General crossproduct requires CHOLMOD");	UNPROTECT(2);
477	return R_NilValue;          /* -Wall */	#endif
478	#endif  /* USE_CHOLMOD */	return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
479		}
480
481		/* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
482		*  at least all "explicit" zeros */
483		SEXP Csparse_drop(SEXP x, SEXP tol)
484		{
485		const char *cl = class_P(x);
486		/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
487		int tr = (cl[1] == 't');
488		CHM_SP chx = AS_CHM_SP__(x);
489		CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
490		double dtol = asReal(tol);
491		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
492		R_CheckStack();
493
494		if(!cholmod_drop(dtol, ans, &c))
495		error(_("cholmod_drop() failed"));
496		return chm_sparse_to_SEXP(ans, 1,
497		tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
498		Rkind, tr ? diag_P(x) : "",
499		GET_SLOT(x, Matrix_DimNamesSym));
500		}
501
502		SEXP Csparse_horzcat(SEXP x, SEXP y)
503		{
504		CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
505		int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
506		Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
507		Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
508		R_CheckStack();
509
510		/* TODO: currently drops dimnames - and we fix at R level */
511		return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
512		1, 0, Rkind, "", R_NilValue);
513	}	}
514
515		SEXP Csparse_vertcat(SEXP x, SEXP y)
516		{
517		CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
518		int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
519		Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
520		Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
521		R_CheckStack();
522
523		/* TODO: currently drops dimnames - and we fix at R level */
524		return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
525		1, 0, Rkind, "", R_NilValue);
526		}
527
528		SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
529		{
530		CHM_SP chx = AS_CHM_SP__(x);
531		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
532		CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
533		R_CheckStack();
534
535		return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
536		GET_SLOT(x, Matrix_DimNamesSym));
537		}
538
539		SEXP Csparse_diagU2N(SEXP x)
540		{
541		const char *cl = class_P(x);
542		/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
543		if (cl[1] != 't' || *diag_P(x) != 'U') {
544		/* "trivially fast" when not triangular (<==> no 'diag' slot),
545		or not *unit* triangular */
546		return (x);
547		}
548		else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
549		CHM_SP chx = AS_CHM_SP__(x);
550		CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
551		double one[] = {1, 0};
552		CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
553		int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
554		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
555
556		R_CheckStack();
557		cholmod_free_sparse(&eye, &c);
558		return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
559		GET_SLOT(x, Matrix_DimNamesSym));
560		}
561		}
562
563		SEXP Csparse_diagN2U(SEXP x)
564		{
565		const char *cl = class_P(x);
566		/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
567		if (cl[1] != 't' || *diag_P(x) != 'N') {
568		/* "trivially fast" when not triangular (<==> no 'diag' slot),
569		or already *unit* triangular */
570		return (x);
571		}
572		else { /* triangular with diag='N'): now drop the diagonal */
573		/* duplicate, since chx will be modified: */
574		SEXP xx = PROTECT(duplicate(x));
575		CHM_SP chx = AS_CHM_SP__(xx);
576		int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
577		Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
578		R_CheckStack();
579
580		chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
581
582		SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
583		uploT, Rkind, "U",
584		GET_SLOT(x, Matrix_DimNamesSym));
585		UNPROTECT(1);// only now !
586		return ans;
587		}
588		}
589
590		/**
591		* "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
592		* Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
593		* @param x CsparseMatrix
594		* @param i row     indices (0-origin), or NULL (R's)
595		* @param j columns indices (0-origin), or NULL
596		*
597		* @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
598		*/
599		SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
600		{
601		CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
602		int rsize = (isNull(i)) ? -1 : LENGTH(i),
603		csize = (isNull(j)) ? -1 : LENGTH(j);
604		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
605		R_CheckStack();
606
607		if (rsize >= 0 && !isInteger(i))
608		error(_("Index i must be NULL or integer"));
609		if (csize >= 0 && !isInteger(j))
610		error(_("Index j must be NULL or integer"));
611
612		if (!chx->stype) {/* non-symmetric Matrix */
613		return chm_sparse_to_SEXP(cholmod_submatrix(chx,
614		(rsize < 0) ? NULL : INTEGER(i), rsize,
615		(csize < 0) ? NULL : INTEGER(j), csize,
616		TRUE, TRUE, &c),
617		1, 0, Rkind, "",
618		/* FIXME: drops dimnames */ R_NilValue);
619		}
620		/* for now, cholmod_submatrix() only accepts "generalMatrix" */
621		CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
622		CHM_SP ans = cholmod_submatrix(tmp,
623		(rsize < 0) ? NULL : INTEGER(i), rsize,
624		(csize < 0) ? NULL : INTEGER(j), csize,
625		TRUE, TRUE, &c);
626		cholmod_free_sparse(&tmp, &c);
627		return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
628		}
629
630		#define _d_Csp_
631		#include "t_Csparse_subassign.c"
632
633		#define _l_Csp_
634		#include "t_Csparse_subassign.c"
635
636		#define _i_Csp_
637		#include "t_Csparse_subassign.c"
638
639		#define _n_Csp_
640		#include "t_Csparse_subassign.c"
641
642		#define _z_Csp_
643		#include "t_Csparse_subassign.c"
644
645
646
647		SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
648		{
649		FILE *f = fopen(CHAR(asChar(fname)), "w");
650
651		if (!f)
652		error(_("failure to open file \"%s\" for writing"),
653		CHAR(asChar(fname)));
654		if (!cholmod_write_sparse(f, AS_CHM_SP(x),
655		(CHM_SP)NULL, (char*) NULL, &c))
656		error(_("cholmod_write_sparse returned error code"));
657		fclose(f);
658		return R_NilValue;
659		}
660
661
662		/**
663		* Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
664		* cholmod_sparse factor (LDL = TRUE).
665		*
666		* @param n  dimension of the matrix.
667		* @param x_p  'p' (column pointer) slot contents
668		* @param x_x  'x' (non-zero entries) slot contents
669		* @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
670		* @param resultKind a (SEXP) string indicating which kind of result is desired.
671		*
672		* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
673		*/
674		SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
675		/*                                ^^^^^^ FIXME[Generalize] to int / ... */
676		{
677		const char* res_ch = CHAR(STRING_ELT(resultKind,0));
678		enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
679		} res_kind = ((!strcmp(res_ch, "trace")) ? trace :
680		((!strcmp(res_ch, "sumLog")) ? sum_log :
681		((!strcmp(res_ch, "prod")) ? prod :
682		((!strcmp(res_ch, "diag")) ? diag :
683		((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
684		-1)))));
685		int i, n_x, i_from = 0;
686		SEXP ans = PROTECT(allocVector(REALSXP,
687		/*                                 ^^^^  FIXME[Generalize] */
688		(res_kind == diag ||
689		res_kind == diag_backpermuted) ? n : 1));
690		double *v = REAL(ans);
691		/*  ^^^^^^      ^^^^  FIXME[Generalize] */
692
693		#define for_DIAG(v_ASSIGN)                                      \
694		for(i = 0; i < n; i++, i_from += n_x) {                     \
695		/* looking at i-th column */                            \
696		n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
697		v_ASSIGN;                                               \
698		}
699
700		/* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
701		*            for uplo = "U" (makes sense with a "dtCMatrix" !),
702		*            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
703		*            where nx = (x_p[i+1] - x_p[i])
704		*/
705
706		switch(res_kind) {
707		case trace:
708		v[0] = 0.;
709		for_DIAG(v[0] += x_x[i_from]);
710		break;
711
712		case sum_log:
713		v[0] = 0.;
714		for_DIAG(v[0] += log(x_x[i_from]));
715		break;
716
717		case prod:
718		v[0] = 1.;
719		for_DIAG(v[0] *= x_x[i_from]);
720		break;
721
722		case diag:
723		for_DIAG(v[i] = x_x[i_from]);
724		break;
725
726		case diag_backpermuted:
727		for_DIAG(v[i] = x_x[i_from]);
728
729		warning(_("%s = '%s' (back-permuted) is experimental"),
730		"resultKind", "diagBack");
731		/* now back_permute : */
732		for(i = 0; i < n; i++) {
733		double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
734		/*^^^^ FIXME[Generalize] */
735		}
736		break;
737
738		default: /* -1 from above */
739		error(_("diag_tC(): invalid 'resultKind'"));
740		/* Wall: */ ans = R_NilValue; v = REAL(ans);
741		}
742
743		UNPROTECT(1);
744		return ans;
745		}
746
747		/**
748		* Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
749		* cholmod_sparse factor (LDL = TRUE).
750		*
751		* @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
752		* @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
753		* @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
754		*                   only used for "diagBack"
755		* @param resultKind a (SEXP) string indicating which kind of result is desired.
756		*
757		* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
758		*/
759		SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
760		{
761		int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
762		*x_p  = INTEGER(pslot),
763		*perm = INTEGER(perm_slot);
764		double *x_x = REAL(xslot);
765		/*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
766
767		return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
768		}
769
770		/**
771		* Create a Csparse matrix object from indices and/or pointers.
772		*
773		* @param cls name of actual class of object to create
774		* @param i optional integer vector of length nnz of row indices
775		* @param j optional integer vector of length nnz of column indices
776		* @param p optional integer vector of length np of row or column pointers
777		* @param np length of integer vector p.  Must be zero if p == (int*)NULL
778		* @param x optional vector of values
779		* @param nnz length of vectors i, j and/or x, whichever is to be used
780		* @param dims optional integer vector of length 2 to be used as
781		*     dimensions.  If dims == (int*)NULL then the maximum row and column
782		*     index are used as the dimensions.
783		* @param dimnames optional list of length 2 to be used as dimnames
784		* @param index1 indicator of 1-based indices
785		*
786		* @return an SEXP of class cls inheriting from CsparseMatrix.
787		*/
788		SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
789		void* x, int nnz, int* dims, SEXP dimnames,
790		int index1)
791		{
792		SEXP ans;
793		int *ij = (int*)NULL, *tri, *trj,
794		mi, mj, mp, nrow = -1, ncol = -1;
795		int xtype = -1;             /* -Wall */
796		CHM_TR T;
797		CHM_SP A;
798
799		if (np < 0 || nnz < 0)
800		error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
801		np, nnz);
802		if (1 != ((mi = (i == (int*)NULL)) +
803		(mj = (j == (int*)NULL)) +
804		(mp = (p == (int*)NULL))))
805		error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
806		if (mp) {
807		if (np) error(_("np = %d, must be zero when p is NULL"), np);
808		} else {
809		if (np) {               /* Expand p to form i or j */
810		if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
811		for (int ii = 0; ii < np; ii++)
812		if (p[ii] > p[ii + 1])
813		error(_("p must be non-decreasing"));
814		if (p[np] != nnz)
815		error("p[np] = %d != nnz = %d", p[np], nnz);
816		ij = Calloc(nnz, int);
817		if (mi) {
818		i = ij;
819		nrow = np;
820		} else {
821		j = ij;
822		ncol = np;
823		}
824		/* Expand p to 0-based indices */
825		for (int ii = 0; ii < np; ii++)
826		for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
827		} else {
828		if (nnz)
829		error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
830		nnz);
831		}
832		}
833		/* calculate nrow and ncol */
834		if (nrow < 0) {
835		for (int ii = 0; ii < nnz; ii++) {
836		int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
837		if (i1 < 1) error(_("invalid row index at position %d"), ii);
838		if (i1 > nrow) nrow = i1;
839		}
840		}
841		if (ncol < 0) {
842		for (int jj = 0; jj < nnz; jj++) {
843		int j1 = j[jj] + (index1 ? 0 : 1);
844		if (j1 < 1) error(_("invalid column index at position %d"), jj);
845		if (j1 > ncol) ncol = j1;
846		}
847		}
848		if (dims != (int*)NULL) {
849		if (dims[0] > nrow) nrow = dims[0];
850		if (dims[1] > ncol) ncol = dims[1];
851		}
852		/* check the class name */
853		if (strlen(cls) != 8)
854		error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
855		if (!strcmp(cls + 2, "CMatrix"))
856		error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
857		switch(cls[0]) {
858		case 'd':
859		case 'l':
860		xtype = CHOLMOD_REAL;
861		break;
862		case 'n':
863		xtype = CHOLMOD_PATTERN;
864		break;
865		default:
866		error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
867		}
868		if (cls[1] != 'g')
869		error(_("Only 'g'eneral sparse matrix types allowed"));
870		/* allocate and populate the triplet */
871		T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
872		xtype, &c);
873		T->x = x;
874		tri = (int*)T->i;
875		trj = (int*)T->j;
876		for (int ii = 0; ii < nnz; ii++) {
877		tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
878		trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
879		}
880		/* create the cholmod_sparse structure */
881		A = cholmod_triplet_to_sparse(T, nnz, &c);
882		cholmod_free_triplet(&T, &c);
883		/* copy the information to the SEXP */
884		ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
885		/* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
886		/* allocate and copy common slots */
887		nnz = cholmod_nnz(A, &c);
888		dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
889		dims[0] = A->nrow; dims[1] = A->ncol;
890		Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
891		Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
892		switch(cls[1]) {
893		case 'd':
894		Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
895		break;
896		case 'l':
897		error(_("code not yet written for cls = \"lgCMatrix\""));
898		}
899		/* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
900		cholmod_free_sparse(&A, &c);
901		UNPROTECT(1);
902		return ans;
903		}

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Legend: Removed from v.1029   changed lines   Added in v.2834

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