Annotation of /pkg/src/Csparse.c

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1 :	bates	1218	/* Sparse matrices in compressed column-oriented form */
2 :	bates	922	#include "Csparse.h"
3 :			#include "chm_common.h"
4 :
5 :			SEXP Csparse_validate(SEXP x)
6 :			{
7 :	bates	1555	cholmod_sparse *chx = as_cholmod_sparse(x);
8 :	bates	922	SEXP pslot = GET_SLOT(x, Matrix_pSym),
9 :			islot = GET_SLOT(x, Matrix_iSym);
10 :	bates	1555	int j, k, ncol = length(pslot) - 1,
11 :	bates	922	*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
12 :	bates	1555	nrow, sorted, *xp = INTEGER(pslot),
13 :	bates	922	*xi = INTEGER(islot);
14 :
15 :			nrow = dims[0];
16 :			if (length(pslot) <= 0)
17 :			return mkString(_("slot p must have length > 0"));
18 :			if (xp[0] != 0)
19 :			return mkString(_("first element of slot p must be zero"));
20 :			if (length(islot) != xp[ncol])
21 :	bates	1555	return
22 :			mkString(_("last element of slot p must match length of slots i and x"));
23 :			for (j = 0; j < length(islot); j++) {
24 :			if (xi[j] < 0 || xi[j] >= nrow)
25 :			return mkString(_("all row indices must be between 0 and nrow-1"));
26 :			}
27 :			sorted = TRUE;
28 :	bates	922	for (j = 0; j < ncol; j++) {
29 :			if (xp[j] > xp[j+1])
30 :			return mkString(_("slot p must be non-decreasing"));
31 :	bates	1555	for (k = xp[j] + 1; k < xp[j + 1]; k++)
32 :			if (xi[k] < xi[k - 1]) sorted = FALSE;
33 :	bates	922	}
34 :	bates	1555	if (!sorted) cholmod_sort(chx, &c);
35 :			Free(chx);
36 :	bates	922	return ScalarLogical(1);
37 :			}
38 :
39 :	bates	1059	SEXP Csparse_to_dense(SEXP x)
40 :			{
41 :			cholmod_sparse *chxs = as_cholmod_sparse(x);
42 :			cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);
43 :
44 :	bates	1141	Free(chxs);
45 :	maechler	1548	return chm_dense_to_SEXP(chxd, 1, Real_kind(x));
46 :	bates	1059	}
47 :
48 :	maechler	1548	SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
49 :	bates	1371	{
50 :			cholmod_sparse *chxs = as_cholmod_sparse(x);
51 :			cholmod_sparse
52 :			*chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
53 :			int uploT = 0; char *diag = "";
54 :
55 :			Free(chxs);
56 :			if (asLogical(tri)) { /* triangular sparse matrices */
57 :			uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?
58 :			-1 : 1;
59 :			diag = CHAR(asChar(GET_SLOT(x, Matrix_diagSym)));
60 :			}
61 :	maechler	1548	return chm_sparse_to_SEXP(chxcp, 1, uploT, 0, diag,
62 :			GET_SLOT(x, Matrix_DimNamesSym));
63 :	bates	1371	}
64 :
65 :	bates	1366	SEXP Csparse_to_matrix(SEXP x)
66 :	bates	922	{
67 :	maechler	925	cholmod_sparse *chxs = as_cholmod_sparse(x);
68 :	bates	1366	cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);
69 :
70 :			Free(chxs);
71 :			return chm_dense_to_matrix(chxd, 1,
72 :			GET_SLOT(x, Matrix_DimNamesSym));
73 :			}
74 :
75 :			SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
76 :			{
77 :			cholmod_sparse *chxs = as_cholmod_sparse(x);
78 :	bates	922	cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);
79 :	maechler	1548	int uploT = 0;
80 :			char *diag = "";
81 :			int Rkind = (chxs->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
82 :	bates	922
83 :	bates	1141	Free(chxs);
84 :	bates	1366	if (asLogical(tri)) { /* triangular sparse matrices */
85 :	bates	1419	uploT = (*uplo_P(x) == 'U') ? -1 : 1;
86 :			diag = diag_P(x);
87 :	bates	1366	}
88 :	maechler	1548	return chm_triplet_to_SEXP(chxt, 1, uploT, Rkind, diag,
89 :	bates	1371	GET_SLOT(x, Matrix_DimNamesSym));
90 :	bates	922	}
91 :
92 :	bates	1448	/* this used to be called sCMatrix_to_gCMatrix(..) [in ./dsCMatrix.c ]: */
93 :	bates	1371	SEXP Csparse_symmetric_to_general(SEXP x)
94 :			{
95 :			cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;
96 :	maechler	1548	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
97 :	bates	1371
98 :			if (!(chx->stype))
99 :	maechler	1548	error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
100 :	maechler	1375	chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
101 :			/* xtype: pattern, "real", complex or .. */
102 :	bates	1371	Free(chx);
103 :	maechler	1548	return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
104 :	bates	1371	GET_SLOT(x, Matrix_DimNamesSym));
105 :			}
106 :
107 :	bates	1369	SEXP Csparse_transpose(SEXP x, SEXP tri)
108 :	bates	922	{
109 :			cholmod_sparse *chx = as_cholmod_sparse(x);
110 :	maechler	1568	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
111 :	bates	922	cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);
112 :	bates	1366	SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
113 :	bates	1369	int uploT = 0; char *diag = "";
114 :
115 :	bates	1141	Free(chx);
116 :	bates	1366	tmp = VECTOR_ELT(dn, 0); /* swap the dimnames */
117 :			SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
118 :			SET_VECTOR_ELT(dn, 1, tmp);
119 :			UNPROTECT(1);
120 :	bates	1369	if (asLogical(tri)) { /* triangular sparse matrices */
121 :	bates	1419	uploT = (*uplo_P(x) == 'U') ? -1 : 1;
122 :			diag = diag_P(x);
123 :	bates	1369	}
124 :	maechler	1548	return chm_sparse_to_SEXP(chxt, 1, uploT, Rkind, diag, dn);
125 :	bates	922	}
126 :
127 :			SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
128 :			{
129 :	bates	1059	cholmod_sparse *cha = as_cholmod_sparse(a),
130 :			*chb = as_cholmod_sparse(b);
131 :			cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);
132 :	bates	1366	SEXP dn = allocVector(VECSXP, 2);
133 :	bates	922
134 :	bates	1141	Free(cha); Free(chb);
135 :	bates	1366	SET_VECTOR_ELT(dn, 0, /* establish dimnames */
136 :			duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
137 :			SET_VECTOR_ELT(dn, 1,
138 :			duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
139 :	maechler	1548	return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);
140 :	bates	922	}
141 :
142 :			SEXP Csparse_dense_prod(SEXP a, SEXP b)
143 :			{
144 :			cholmod_sparse *cha = as_cholmod_sparse(a);
145 :	bates	1461	cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));
146 :	maechler	1548	cholmod_dense *chc =
147 :	bates	1448	cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);
148 :			double alpha[] = {1,0}, beta[] = {0,0};
149 :	bates	922
150 :	bates	1448	cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);
151 :	bates	1141	Free(cha); Free(chb);
152 :	bates	1461	UNPROTECT(1);
153 :	maechler	1548	return chm_dense_to_SEXP(chc, 1, 0);
154 :	bates	922	}
155 :	maechler	925
156 :	bates	1067	SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
157 :			{
158 :			cholmod_sparse *cha = as_cholmod_sparse(a);
159 :	bates	1461	cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));
160 :	bates	1448	cholmod_dense *chc =
161 :			cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);
162 :			double alpha[] = {1,0}, beta[] = {0,0};
163 :	bates	1067
164 :	bates	1448	cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);
165 :	bates	1067	Free(cha); Free(chb);
166 :	bates	1461	UNPROTECT(1);
167 :	maechler	1548	return chm_dense_to_SEXP(chc, 1, 0);
168 :	bates	1067	}
169 :
170 :	bates	928	SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
171 :	bates	922	{
172 :	maechler	957	int trip = asLogical(triplet),
173 :			tr = asLogical(trans); /* gets reversed because _aat is tcrossprod */
174 :	bates	928	cholmod_triplet
175 :			*cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;
176 :			cholmod_sparse *chcp, *chxt,
177 :			*chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)
178 :			: as_cholmod_sparse(x);
179 :	bates	1366	SEXP dn = PROTECT(allocVector(VECSXP, 2));
180 :	bates	922
181 :	bates	923	if (!tr)
182 :	bates	1353	chxt = cholmod_transpose(chx, chx->xtype, &c);
183 :	bates	928	chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
184 :	maechler	957	if(!chcp)
185 :			error("Csparse_crossprod(): error return from cholmod_aat()");
186 :	bates	1360	cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
187 :			chcp->stype = 1;
188 :	bates	930	if (trip) {
189 :			cholmod_free_sparse(&chx, &c);
190 :	bates	1141	Free(cht);
191 :	bates	930	} else {
192 :	bates	1141	Free(chx);
193 :	bates	930	}
194 :	bates	923	if (!tr) cholmod_free_sparse(&chxt, &c);
195 :	bates	1366	/* create dimnames */
196 :			SET_VECTOR_ELT(dn, 0,
197 :			duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
198 :			(tr) ? 1 : 0)));
199 :			SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
200 :			UNPROTECT(1);
201 :	maechler	1548	return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
202 :	bates	922	}
203 :	bates	923
204 :	bates	1218	SEXP Csparse_horzcat(SEXP x, SEXP y)
205 :			{
206 :			cholmod_sparse *chx = as_cholmod_sparse(x),
207 :			*chy = as_cholmod_sparse(y), *ans;
208 :	maechler	1548	int Rkind = 0; /* only for "d" - FIXME */
209 :	maechler	1375
210 :	bates	1218	ans = cholmod_horzcat(chx, chy, 1, &c);
211 :			Free(chx); Free(chy);
212 :	bates	1366	/* FIXME: currently drops dimnames */
213 :	maechler	1548	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
214 :	bates	1218	}
215 :
216 :			SEXP Csparse_vertcat(SEXP x, SEXP y)
217 :			{
218 :			cholmod_sparse *chx = as_cholmod_sparse(x),
219 :			*chy = as_cholmod_sparse(y), *ans;
220 :	maechler	1548	int Rkind = 0; /* only for "d" - FIXME */
221 :	maechler	1375
222 :	bates	1218	ans = cholmod_vertcat(chx, chy, 1, &c);
223 :			Free(chx); Free(chy);
224 :	bates	1366	/* FIXME: currently drops dimnames */
225 :	maechler	1548	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
226 :	bates	1218	}
227 :	bates	1265
228 :			SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
229 :			{
230 :			cholmod_sparse *chx = as_cholmod_sparse(x), *ans;
231 :	maechler	1548	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
232 :	bates	1265
233 :			ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
234 :			Free(chx);
235 :	maechler	1548	return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
236 :	bates	1265	}
237 :	bates	1366
238 :			SEXP Csparse_diagU2N(SEXP x)
239 :			{
240 :			cholmod_sparse *chx = as_cholmod_sparse(x);
241 :			cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
242 :			double one[] = {1, 0};
243 :			cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
244 :			int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?
245 :			-1 : 1;
246 :	maechler	1548	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
247 :	bates	1366
248 :			Free(chx); cholmod_free_sparse(&eye, &c);
249 :	maechler	1548	return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
250 :	bates	1366	duplicate(GET_SLOT(x, Matrix_DimNamesSym)));
251 :			}
252 :
253 :			SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
254 :			{
255 :			cholmod_sparse *chx = as_cholmod_sparse(x);
256 :			int rsize = (isNull(i)) ? -1 : LENGTH(i),
257 :			csize = (isNull(j)) ? -1 : LENGTH(j);
258 :	maechler	1548	int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
259 :	bates	1366
260 :			if (rsize >= 0 && !isInteger(i))
261 :			error(_("Index i must be NULL or integer"));
262 :			if (csize >= 0 && !isInteger(j))
263 :			error(_("Index j must be NULL or integer"));
264 :			return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
265 :	maechler	1375	INTEGER(j), csize,
266 :	bates	1366	TRUE, TRUE, &c),
267 :	maechler	1548	1, 0, Rkind, "", R_NilValue);
268 :	bates	1366	}

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