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

Parent Directory | Revision Log | Patch

	pkg/src/Csparse.c revision 1029, Wed Nov 9 15:26:22 2005 UTC	pkg/Matrix/src/Csparse.c revision 2889, Thu Aug 8 21:06:22 2013 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		/* 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)
109	{	{
110	#ifdef USE_CHOLMOD	CHM_SP chxs = AS_CHM_SP__(x);
111	cholmod_sparse *chxs = as_cholmod_sparse(x);	/* This loses the symmetry property, since cholmod_dense has none,
112	cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);	* 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_triplet_to_SEXP(chxt, 1);
	#else
	error("General conversion requires CHOLMOD");
	return R_NilValue;          /* -Wall */
	#endif  /* USE_CHOLMOD */
119	}	}
120
121	SEXP Csparse_transpose(SEXP x)	// 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)
123	{	{
124	#ifdef USE_CHOLMOD	CHM_SP chxs = AS_CHM_SP__(x);
125	cholmod_sparse *chx = as_cholmod_sparse(x);	CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
126	cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);	int tr = asLogical(tri);
127		R_CheckStack();
128
129		return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
130		tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
131		0, tr ? diag_P(x) : "",
132		GET_SLOT(x, Matrix_DimNamesSym));
133		}
134
135	free(chx);	// n.CMatrix --> [dli].CMatrix  (not going through CHM!)
136	return chm_sparse_to_SEXP(chxt, 1);	SEXP nz_pattern_to_Csparse(SEXP x, SEXP res_kind)
137	#else	{
138	error("General conversion requires CHOLMOD");	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		const char *cl_x = class_P(x);
144		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		SEXP Csparse_to_matrix(SEXP x)
190		{
191		return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP__(x), &c),
192		1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
193		}
194
195		SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
196		{
197		CHM_SP chxs = AS_CHM_SP__(x);
198		CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
199		int tr = asLogical(tri);
200		int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
201		R_CheckStack();
202
203		return chm_triplet_to_SEXP(chxt, 1,
204		tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
205		Rkind, tr ? diag_P(x) : "",
206		GET_SLOT(x, Matrix_DimNamesSym));
207		}
208
209		/* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
210		SEXP Csparse_symmetric_to_general(SEXP x)
211		{
212		CHM_SP chx = AS_CHM_SP__(x), chgx;
213		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
214		R_CheckStack();
215
216		if (!(chx->stype))
217		error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
218		chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
219		/* xtype: pattern, "real", complex or .. */
220		return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
221		GET_SLOT(x, Matrix_DimNamesSym));
222		}
223
224		SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
225		{
226		int *adims = INTEGER(GET_SLOT(x, Matrix_DimSym)), n = adims[0];
227		if(n != adims[1]) {
228		error(_("Csparse_general_to_symmetric(): matrix is not square!"));
229	return R_NilValue;          /* -Wall */	return R_NilValue;          /* -Wall */
230	#endif  /* USE_CHOLMOD */	}
231		CHM_SP chx = AS_CHM_SP__(x), chgx;
232		int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;
233		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
234		R_CheckStack();
235		chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
236		/* xtype: pattern, "real", complex or .. */
237		return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
238		GET_SLOT(x, Matrix_DimNamesSym));
239	}	}
240
241		SEXP Csparse_transpose(SEXP x, SEXP tri)
242		{
243		/* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
244		*       since cholmod (& cs) lacks sparse 'int' matrices */
245		CHM_SP chx = AS_CHM_SP__(x);
246		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
247		CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
248		SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
249		int tr = asLogical(tri);
250		R_CheckStack();
251
252		tmp = VECTOR_ELT(dn, 0);    /* swap the dimnames */
253		SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
254		SET_VECTOR_ELT(dn, 1, tmp);
255		UNPROTECT(1);
256		return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
257		tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,
258		Rkind, tr ? diag_P(x) : "", dn);
259		}
260
261	SEXP Csparse_Csparse_prod(SEXP a, SEXP b)	SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
262	{	{
263	#ifdef USE_CHOLMOD	CHM_SP
264	cholmod_sparse *cha = as_cholmod_sparse(a), *chb = as_cholmod_sparse(b);	cha = AS_CHM_SP(a),
265	cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, (int) cha->xtype, 1, &c);	chb = AS_CHM_SP(b),
266		chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,
267		/* values:= is_numeric (T/F) */ cha->xtype > 0,
268		/*out sorted:*/ 1, &c);
269		const char *cl_a = class_P(a), *cl_b = class_P(b);
270		char diag[] = {'\0', '\0'};
271		int uploT = 0;
272		SEXP dn = PROTECT(allocVector(VECSXP, 2));
273		R_CheckStack();
274
275		#ifdef DEBUG_Matrix_verbose
276		Rprintf("DBG Csparse_C*_prod(%s, %s)\n", cl_a, cl_b);
277		#endif
278
279		/* Preserve triangularity and even unit-triangularity if appropriate.
280		* Note that in that case, the multiplication itself should happen
281		* faster.  But there's no support for that in CHOLMOD */
282
283		/* UGLY hack -- rather should have (fast!) C-level version of
284		*       is(a, "triangularMatrix") etc */
285		if (cl_a[1] == 't' && cl_b[1] == 't')
286		/* FIXME: fails for "Cholesky","BunchKaufmann"..*/
287		if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */
288		uploT = (*uplo_P(a) == 'U') ? 1 : -1;
289		if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
290		/* "remove the diagonal entries": */
291		chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
292		diag[0]= 'U';
293		}
294		else diag[0]= 'N';
295		}
296		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
297		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
298		SET_VECTOR_ELT(dn, 1,
299		duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
300		UNPROTECT(1);
301		return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
302		}
303
304	free(cha); free(chb);	SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
305	return chm_sparse_to_SEXP(chc, 1);	{
306	#else	int tr = asLogical(trans);
307	error("General multiplication requires CHOLMOD");	CHM_SP
308	return R_NilValue;          /* -Wall */	cha = AS_CHM_SP(a),
309	#endif  /* USE_CHOLMOD */	chb = AS_CHM_SP(b),
310		chTr, chc;
311		const char *cl_a = class_P(a), *cl_b = class_P(b);
312		char diag[] = {'\0', '\0'};
313		int uploT = 0;
314		SEXP dn = PROTECT(allocVector(VECSXP, 2));
315		R_CheckStack();
316
317		chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
318		chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
319		/*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);
320		cholmod_free_sparse(&chTr, &c);
321
322		/* Preserve triangularity and unit-triangularity if appropriate;
323		* see Csparse_Csparse_prod() for comments */
324		if (cl_a[1] == 't' && cl_b[1] == 't')
325		if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */
326		uploT = (*uplo_P(b) == 'U') ? 1 : -1;
327		if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */
328		chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);
329		diag[0]= 'U';
330		}
331		else diag[0]= 'N';
332		}
333		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
334		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
335		SET_VECTOR_ELT(dn, 1,
336		duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
337		UNPROTECT(1);
338		return chm_sparse_to_SEXP(chc, 1, uploT, /*Rkind*/0, diag, dn);
339	}	}
340
341	SEXP Csparse_dense_prod(SEXP a, SEXP b)	SEXP Csparse_dense_prod(SEXP a, SEXP b)
342	{	{
343	#ifdef USE_CHOLMOD	CHM_SP cha = AS_CHM_SP(a);
344	cholmod_sparse *cha = as_cholmod_sparse(a);	SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
345	cholmod_dense *chb = as_cholmod_dense(b);	CHM_DN chb = AS_CHM_DN(b_M);
346	cholmod_dense *chc = cholmod_allocate_dense(cha->nrow, chb->ncol,	CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
347	cha->nrow, chb->xtype, &c);	chb->xtype, &c);
348	double alpha = 1, beta = 0;	SEXP dn = PROTECT(allocVector(VECSXP, 2));
349		double one[] = {1,0}, zero[] = {0,0};
350	cholmod_sdmult(cha, 0, &alpha, &beta, chb, chc, &c);	int nprot = 2;
351	free(cha); free(chb);	R_CheckStack();
352	return chm_dense_to_SEXP(chc, 1);	/* Tim Davis, please FIXME:  currently (2010-11) *fails* when  a  is a pattern matrix:*/
353	#else	if(cha->xtype == CHOLMOD_PATTERN) {
354	error("General multiplication requires CHOLMOD");	/* warning(_("Csparse_dense_prod(): cholmod_sdmult() not yet implemented for pattern./ ngCMatrix" */
355	return R_NilValue;          /* -Wall */	/*        " --> slightly inefficient coercion")); */
356	#endif  /* USE_CHOLMOD */
357		// This *fails* to produce a CHOLMOD_REAL ..
358		// CHM_SP chd = cholmod_l_copy(cha, cha->stype, CHOLMOD_REAL, &c);
359		// --> use our Matrix-classes
360		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
361		cha = AS_CHM_SP(da);
362		}
363		cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
364		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
365		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
366		SET_VECTOR_ELT(dn, 1,
367		duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
368		UNPROTECT(nprot);
369		return chm_dense_to_SEXP(chc, 1, 0, dn);
370		}
371
372		SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
373		{
374		CHM_SP cha = AS_CHM_SP(a);
375		SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
376		CHM_DN chb = AS_CHM_DN(b_M);
377		CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
378		chb->xtype, &c);
379		SEXP dn = PROTECT(allocVector(VECSXP, 2)); int nprot = 2;
380		double one[] = {1,0}, zero[] = {0,0};
381		R_CheckStack();
382		// -- see Csparse_dense_prod() above :
383		if(cha->xtype == CHOLMOD_PATTERN) {
384		SEXP da = PROTECT(nz2Csparse(a, x_double)); nprot++;
385		cha = AS_CHM_SP(da);
386		}
387		cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
388		SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
389		duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
390		SET_VECTOR_ELT(dn, 1,
391		duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
392		UNPROTECT(nprot);
393		return chm_dense_to_SEXP(chc, 1, 0, dn);
394	}	}
395
396		/* Computes   x'x  or  x x' -- *also* for Tsparse (triplet = TRUE)
397		see Csparse_Csparse_crossprod above for  x'y and x y' */
398	SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)	SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
399	{	{
	#ifdef USE_CHOLMOD
400	int trip = asLogical(triplet),	int trip = asLogical(triplet),
401	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
402	cholmod_triplet	#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
403	*cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;	CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
404	cholmod_sparse *chcp, *chxt,	#else /* workaround needed:*/
405	*chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)	SEXP xx = PROTECT(Tsparse_diagU2N(x));
406	: as_cholmod_sparse(x);	CHM_TR cht = trip ? AS_CHM_TR__(xx) : (CHM_TR) NULL;
407		#endif
408		CHM_SP chcp, chxt,
409		chx = (trip ?
410		cholmod_triplet_to_sparse(cht, cht->nnz, &c) :
411		AS_CHM_SP(x));
412		SEXP dn = PROTECT(allocVector(VECSXP, 2));
413		R_CheckStack();
414
415	if (!tr)	if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
	chxt = cholmod_transpose(chx, (int) chx->xtype, &c);
416	chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);	chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
417	if(!chcp)	if(!chcp) {
418	error("Csparse_crossprod(): error return from cholmod_aat()");	UNPROTECT(1);
419		error(_("Csparse_crossprod(): error return from cholmod_aat()"));
	if (trip) {
	cholmod_free_sparse(&chx, &c);
	free(cht);
	} else {
	free(chx);
420	}	}
421		cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
422		chcp->stype = 1;
423		if (trip) cholmod_free_sparse(&chx, &c);
424	if (!tr) cholmod_free_sparse(&chxt, &c);	if (!tr) cholmod_free_sparse(&chxt, &c);
425	return chm_sparse_to_SEXP(chcp, 1);	SET_VECTOR_ELT(dn, 0,       /* establish dimnames */
426		duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
427		(tr) ? 0 : 1)));
428		SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
429		#ifdef AS_CHM_DIAGU2N_FIXED_FINALLY
430		UNPROTECT(1);
431	#else	#else
432	error("General crossproduct requires CHOLMOD");	UNPROTECT(2);
433	return R_NilValue;          /* -Wall */	#endif
434	#endif  /* USE_CHOLMOD */	return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
435		}
436
437		/* Csparse_drop(x, tol):  drop entries with absolute value < tol, i.e,
438		*  at least all "explicit" zeros */
439		SEXP Csparse_drop(SEXP x, SEXP tol)
440		{
441		const char *cl = class_P(x);
442		/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
443		int tr = (cl[1] == 't');
444		CHM_SP chx = AS_CHM_SP__(x);
445		CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
446		double dtol = asReal(tol);
447		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
448		R_CheckStack();
449
450		if(!cholmod_drop(dtol, ans, &c))
451		error(_("cholmod_drop() failed"));
452		return chm_sparse_to_SEXP(ans, 1,
453		tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
454		Rkind, tr ? diag_P(x) : "",
455		GET_SLOT(x, Matrix_DimNamesSym));
456		}
457
458		SEXP Csparse_horzcat(SEXP x, SEXP y)
459		{
460		CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
461		int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
462		Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
463		Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
464		R_CheckStack();
465
466		/* TODO: currently drops dimnames - and we fix at R level */
467		return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
468		1, 0, Rkind, "", R_NilValue);
469		}
470
471		SEXP Csparse_vertcat(SEXP x, SEXP y)
472		{
473		CHM_SP chx = AS_CHM_SP__(x), chy = AS_CHM_SP__(y);
474		int Rk_x = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0,
475		Rk_y = (chy->xtype != CHOLMOD_PATTERN) ? Real_kind(y) : 0,
476		Rkind = /* logical if both x and y are */ (Rk_x == 1 && Rk_y == 1) ? 1 : 0;
477		R_CheckStack();
478
479		/* TODO: currently drops dimnames - and we fix at R level */
480		return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
481		1, 0, Rkind, "", R_NilValue);
482		}
483
484		SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
485		{
486		CHM_SP chx = AS_CHM_SP__(x);
487		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
488		CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
489		R_CheckStack();
490
491		return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
492		GET_SLOT(x, Matrix_DimNamesSym));
493		}
494
495		SEXP Csparse_diagU2N(SEXP x)
496		{
497		const char *cl = class_P(x);
498		/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
499		if (cl[1] != 't' || *diag_P(x) != 'U') {
500		/* "trivially fast" when not triangular (<==> no 'diag' slot),
501		or not *unit* triangular */
502		return (x);
503		}
504		else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */
505		CHM_SP chx = AS_CHM_SP__(x);
506		CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
507		double one[] = {1, 0};
508		CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
509		int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
510		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
511
512		R_CheckStack();
513		cholmod_free_sparse(&eye, &c);
514		return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
515		GET_SLOT(x, Matrix_DimNamesSym));
516	}	}
517		}
518
519		SEXP Csparse_diagN2U(SEXP x)
520		{
521		const char *cl = class_P(x);
522		/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */
523		if (cl[1] != 't' || *diag_P(x) != 'N') {
524		/* "trivially fast" when not triangular (<==> no 'diag' slot),
525		or already *unit* triangular */
526		return (x);
527		}
528		else { /* triangular with diag='N'): now drop the diagonal */
529		/* duplicate, since chx will be modified: */
530		SEXP xx = PROTECT(duplicate(x));
531		CHM_SP chx = AS_CHM_SP__(xx);
532		int uploT = (*uplo_P(x) == 'U') ? 1 : -1,
533		Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
534		R_CheckStack();
535
536		chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);
537
538		SEXP ans = chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,
539		uploT, Rkind, "U",
540		GET_SLOT(x, Matrix_DimNamesSym));
541		UNPROTECT(1);// only now !
542		return ans;
543		}
544		}
545
546		/**
547		* "Indexing" aka subsetting : Compute  x[i,j], also for vectors i and j
548		* Working via CHOLMOD_submatrix, see ./CHOLMOD/MatrixOps/cholmod_submatrix.c
549		* @param x CsparseMatrix
550		* @param i row     indices (0-origin), or NULL (R's)
551		* @param j columns indices (0-origin), or NULL
552		*
553		* @return x[i,j]  still CsparseMatrix --- currently, this loses dimnames
554		*/
555		SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
556		{
557		CHM_SP chx = AS_CHM_SP(x); /* << does diagU2N() when needed */
558		int rsize = (isNull(i)) ? -1 : LENGTH(i),
559		csize = (isNull(j)) ? -1 : LENGTH(j);
560		int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
561		R_CheckStack();
562
563		if (rsize >= 0 && !isInteger(i))
564		error(_("Index i must be NULL or integer"));
565		if (csize >= 0 && !isInteger(j))
566		error(_("Index j must be NULL or integer"));
567
568		if (!chx->stype) {/* non-symmetric Matrix */
569		return chm_sparse_to_SEXP(cholmod_submatrix(chx,
570		(rsize < 0) ? NULL : INTEGER(i), rsize,
571		(csize < 0) ? NULL : INTEGER(j), csize,
572		TRUE, TRUE, &c),
573		1, 0, Rkind, "",
574		/* FIXME: drops dimnames */ R_NilValue);
575		}
576		/* for now, cholmod_submatrix() only accepts "generalMatrix" */
577		CHM_SP tmp = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
578		CHM_SP ans = cholmod_submatrix(tmp,
579		(rsize < 0) ? NULL : INTEGER(i), rsize,
580		(csize < 0) ? NULL : INTEGER(j), csize,
581		TRUE, TRUE, &c);
582		cholmod_free_sparse(&tmp, &c);
583		return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
584		}
585
586		#define _d_Csp_
587		#include "t_Csparse_subassign.c"
588
589		#define _l_Csp_
590		#include "t_Csparse_subassign.c"
591
592		#define _i_Csp_
593		#include "t_Csparse_subassign.c"
594
595		#define _n_Csp_
596		#include "t_Csparse_subassign.c"
597
598		#define _z_Csp_
599		#include "t_Csparse_subassign.c"
600
601
602
603		SEXP Csparse_MatrixMarket(SEXP x, SEXP fname)
604		{
605		FILE *f = fopen(CHAR(asChar(fname)), "w");
606
607		if (!f)
608		error(_("failure to open file \"%s\" for writing"),
609		CHAR(asChar(fname)));
610		if (!cholmod_write_sparse(f, AS_CHM_SP(x),
611		(CHM_SP)NULL, (char*) NULL, &c))
612		error(_("cholmod_write_sparse returned error code"));
613		fclose(f);
614		return R_NilValue;
615		}
616
617
618		/**
619		* Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
620		* cholmod_sparse factor (LDL = TRUE).
621		*
622		* @param n  dimension of the matrix.
623		* @param x_p  'p' (column pointer) slot contents
624		* @param x_x  'x' (non-zero entries) slot contents
625		* @param perm 'perm' (= permutation vector) slot contents; only used for "diagBack"
626		* @param resultKind a (SEXP) string indicating which kind of result is desired.
627		*
628		* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
629		*/
630		SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)
631		/*                                ^^^^^^ FIXME[Generalize] to int / ... */
632		{
633		const char* res_ch = CHAR(STRING_ELT(resultKind,0));
634		enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log
635		} res_kind = ((!strcmp(res_ch, "trace")) ? trace :
636		((!strcmp(res_ch, "sumLog")) ? sum_log :
637		((!strcmp(res_ch, "prod")) ? prod :
638		((!strcmp(res_ch, "diag")) ? diag :
639		((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :
640		-1)))));
641		int i, n_x, i_from = 0;
642		SEXP ans = PROTECT(allocVector(REALSXP,
643		/*                                 ^^^^  FIXME[Generalize] */
644		(res_kind == diag ||
645		res_kind == diag_backpermuted) ? n : 1));
646		double *v = REAL(ans);
647		/*  ^^^^^^      ^^^^  FIXME[Generalize] */
648
649		#define for_DIAG(v_ASSIGN)                                      \
650		for(i = 0; i < n; i++, i_from += n_x) {                     \
651		/* looking at i-th column */                            \
652		n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \
653		v_ASSIGN;                                               \
654		}
655
656		/* NOTA BENE: we assume  -- uplo = "L" i.e. lower triangular matrix
657		*            for uplo = "U" (makes sense with a "dtCMatrix" !),
658		*            should use  x_x[i_from + (nx - 1)] instead of x_x[i_from],
659		*            where nx = (x_p[i+1] - x_p[i])
660		*/
661
662		switch(res_kind) {
663		case trace:
664		v[0] = 0.;
665		for_DIAG(v[0] += x_x[i_from]);
666		break;
667
668		case sum_log:
669		v[0] = 0.;
670		for_DIAG(v[0] += log(x_x[i_from]));
671		break;
672
673		case prod:
674		v[0] = 1.;
675		for_DIAG(v[0] *= x_x[i_from]);
676		break;
677
678		case diag:
679		for_DIAG(v[i] = x_x[i_from]);
680		break;
681
682		case diag_backpermuted:
683		for_DIAG(v[i] = x_x[i_from]);
684
685		warning(_("%s = '%s' (back-permuted) is experimental"),
686		"resultKind", "diagBack");
687		/* now back_permute : */
688		for(i = 0; i < n; i++) {
689		double tmp = v[i]; v[i] = v[perm[i]]; v[perm[i]] = tmp;
690		/*^^^^ FIXME[Generalize] */
691		}
692		break;
693
694		default: /* -1 from above */
695		error(_("diag_tC(): invalid 'resultKind'"));
696		/* Wall: */ ans = R_NilValue; v = REAL(ans);
697		}
698
699		UNPROTECT(1);
700		return ans;
701		}
702
703		/**
704		* Extract the diagonal entries from *triangular* Csparse matrix  __or__ a
705		* cholmod_sparse factor (LDL = TRUE).
706		*
707		* @param pslot  'p' (column pointer)   slot of Csparse matrix/factor
708		* @param xslot  'x' (non-zero entries) slot of Csparse matrix/factor
709		* @param perm_slot  'perm' (= permutation vector) slot of corresponding CHMfactor;
710		*                   only used for "diagBack"
711		* @param resultKind a (SEXP) string indicating which kind of result is desired.
712		*
713		* @return  a SEXP, either a (double) number or a length n-vector of diagonal entries
714		*/
715		SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind)
716		{
717		int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */
718		*x_p  = INTEGER(pslot),
719		*perm = INTEGER(perm_slot);
720		double *x_x = REAL(xslot);
721		/*  ^^^^^^        ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/
722
723		return diag_tC_ptr(n, x_p, x_x, perm, resultKind);
724		}
725
726		/**
727		* Create a Csparse matrix object from indices and/or pointers.
728		*
729		* @param cls name of actual class of object to create
730		* @param i optional integer vector of length nnz of row indices
731		* @param j optional integer vector of length nnz of column indices
732		* @param p optional integer vector of length np of row or column pointers
733		* @param np length of integer vector p.  Must be zero if p == (int*)NULL
734		* @param x optional vector of values
735		* @param nnz length of vectors i, j and/or x, whichever is to be used
736		* @param dims optional integer vector of length 2 to be used as
737		*     dimensions.  If dims == (int*)NULL then the maximum row and column
738		*     index are used as the dimensions.
739		* @param dimnames optional list of length 2 to be used as dimnames
740		* @param index1 indicator of 1-based indices
741		*
742		* @return an SEXP of class cls inheriting from CsparseMatrix.
743		*/
744		SEXP create_Csparse(char* cls, int* i, int* j, int* p, int np,
745		void* x, int nnz, int* dims, SEXP dimnames,
746		int index1)
747		{
748		SEXP ans;
749		int *ij = (int*)NULL, *tri, *trj,
750		mi, mj, mp, nrow = -1, ncol = -1;
751		int xtype = -1;             /* -Wall */
752		CHM_TR T;
753		CHM_SP A;
754
755		if (np < 0 || nnz < 0)
756		error(_("negative vector lengths not allowed: np = %d, nnz = %d"),
757		np, nnz);
758		if (1 != ((mi = (i == (int*)NULL)) +
759		(mj = (j == (int*)NULL)) +
760		(mp = (p == (int*)NULL))))
761		error(_("exactly 1 of 'i', 'j' or 'p' must be NULL"));
762		if (mp) {
763		if (np) error(_("np = %d, must be zero when p is NULL"), np);
764		} else {
765		if (np) {               /* Expand p to form i or j */
766		if (!(p[0])) error(_("p[0] = %d, should be zero"), p[0]);
767		for (int ii = 0; ii < np; ii++)
768		if (p[ii] > p[ii + 1])
769		error(_("p must be non-decreasing"));
770		if (p[np] != nnz)
771		error("p[np] = %d != nnz = %d", p[np], nnz);
772		ij = Calloc(nnz, int);
773		if (mi) {
774		i = ij;
775		nrow = np;
776		} else {
777		j = ij;
778		ncol = np;
779		}
780		/* Expand p to 0-based indices */
781		for (int ii = 0; ii < np; ii++)
782		for (int jj = p[ii]; jj < p[ii + 1]; jj++) ij[jj] = ii;
783		} else {
784		if (nnz)
785		error(_("Inconsistent dimensions: np = 0 and nnz = %d"),
786		nnz);
787		}
788		}
789		/* calculate nrow and ncol */
790		if (nrow < 0) {
791		for (int ii = 0; ii < nnz; ii++) {
792		int i1 = i[ii] + (index1 ? 0 : 1); /* 1-based index */
793		if (i1 < 1) error(_("invalid row index at position %d"), ii);
794		if (i1 > nrow) nrow = i1;
795		}
796		}
797		if (ncol < 0) {
798		for (int jj = 0; jj < nnz; jj++) {
799		int j1 = j[jj] + (index1 ? 0 : 1);
800		if (j1 < 1) error(_("invalid column index at position %d"), jj);
801		if (j1 > ncol) ncol = j1;
802		}
803		}
804		if (dims != (int*)NULL) {
805		if (dims[0] > nrow) nrow = dims[0];
806		if (dims[1] > ncol) ncol = dims[1];
807		}
808		/* check the class name */
809		if (strlen(cls) != 8)
810		error(_("strlen of cls argument = %d, should be 8"), strlen(cls));
811		if (!strcmp(cls + 2, "CMatrix"))
812		error(_("cls = \"%s\" does not end in \"CMatrix\""), cls);
813		switch(cls[0]) {
814		case 'd':
815		case 'l':
816		xtype = CHOLMOD_REAL;
817		break;
818		case 'n':
819		xtype = CHOLMOD_PATTERN;
820		break;
821		default:
822		error(_("cls = \"%s\" must begin with 'd', 'l' or 'n'"), cls);
823		}
824		if (cls[1] != 'g')
825		error(_("Only 'g'eneral sparse matrix types allowed"));
826		/* allocate and populate the triplet */
827		T = cholmod_allocate_triplet((size_t)nrow, (size_t)ncol, (size_t)nnz, 0,
828		xtype, &c);
829		T->x = x;
830		tri = (int*)T->i;
831		trj = (int*)T->j;
832		for (int ii = 0; ii < nnz; ii++) {
833		tri[ii] = i[ii] - ((!mi && index1) ? 1 : 0);
834		trj[ii] = j[ii] - ((!mj && index1) ? 1 : 0);
835		}
836		/* create the cholmod_sparse structure */
837		A = cholmod_triplet_to_sparse(T, nnz, &c);
838		cholmod_free_triplet(&T, &c);
839		/* copy the information to the SEXP */
840		ans = PROTECT(NEW_OBJECT(MAKE_CLASS(cls)));
841		/* FIXME: This has been copied from chm_sparse_to_SEXP in chm_common.c */
842		/* allocate and copy common slots */
843		nnz = cholmod_nnz(A, &c);
844		dims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
845		dims[0] = A->nrow; dims[1] = A->ncol;
846		Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, A->ncol + 1)), (int*)A->p, A->ncol + 1);
847		Memcpy(INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nnz)), (int*)A->i, nnz);
848		switch(cls[1]) {
849		case 'd':
850		Memcpy(REAL(ALLOC_SLOT(ans, Matrix_xSym, REALSXP, nnz)), (double*)A->x, nnz);
851		break;
852		case 'l':
853		error(_("code not yet written for cls = \"lgCMatrix\""));
854		}
855		/* FIXME: dimnames are *NOT* put there yet (if non-NULL) */
856		cholmod_free_sparse(&A, &c);
857		UNPROTECT(1);
858		return ans;
859		}

---

Colored Diff Long Colored Diff Unidiff Context Diff Side by Side

Legend: Removed from v.1029   changed lines   Added in v.2889

---

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