The R Project SVN – R-packages – Diff – /branches/Matrix-APIchange/src/Csparse.c

 		else if (xi[k] == xi[k - 1])
 		    strictly = FALSE;
+	    }
+    }
     if (!sorted) {
-	cholmod_sparse *chx = as_cholmod_sparse(x);
+	CHM_SP chx = AS_CHM_SP(x);
 	cholmod_sort(chx, &c);
-	Free(chx);
 	/* Now re-check that row indices are *strictly* increasing
 	 * (and not just increasing) within each column : */
 	for (j = 0; j < ncol; j++) {
 	    for (k = xp[j] + 1; k < xp[j + 1]; k++)
 		if (xi[k] == xi[k - 1])
 /* Called from ../R/Csparse.R : */
 /* Can only return [dln]geMatrix (no symm/triang);
  * FIXME: replace by non-CHOLMOD code ! */
 SEXP Csparse_to_dense(SEXP x)
+{
-    cholmod_sparse *chxs = as_cholmod_sparse(x);
+    CHM_SP chxs = AS_CHM_SP(x);
     /* This loses the symmetry property, since cholmod_dense has none,
      * BUT, much worse (FIXME!), it also transforms CHOLMOD_PATTERN ("n") matrices
      * to numeric (CHOLMOD_REAL) ones : */
-    cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);
+    CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);
     int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);
-    Free(chxs);
     return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));
+}
 SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
+{
-    cholmod_sparse *chxs = as_cholmod_sparse(x);
+    CHM_SP chxs = AS_CHM_SP(x);
-    cholmod_sparse
-	*chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
+    CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
     int tr = asLogical(tri);
-    Free(chxs);
-    return chm_sparse_to_SEXP(chxcp, 1,
+    return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,
 			      tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
 , tr ? diag_P(x) : "",
 			      GET_SLOT(x, Matrix_DimNamesSym));
+}
 SEXP Csparse_to_matrix(SEXP x)
+{
-    cholmod_sparse *chxs = as_cholmod_sparse(x);
-    cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);
+    return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),
-    Free(chxs);
-    return chm_dense_to_matrix(chxd, 1,
-			       GET_SLOT(x, Matrix_DimNamesSym));
+/*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));
+}
 SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
+{
-    cholmod_sparse *chxs = as_cholmod_sparse(x);
+    CHM_SP chxs = AS_CHM_SP(x);
-    cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);
+    CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);
     int tr = asLogical(tri);
     int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
-    Free(chxs);
     return chm_triplet_to_SEXP(chxt, 1,
 			       tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,
 			       Rkind, tr ? diag_P(x) : "",
 			       GET_SLOT(x, Matrix_DimNamesSym));
+}
 /* this used to be called  sCMatrix_to_gCMatrix(..)   [in ./dsCMatrix.c ]: */
 SEXP Csparse_symmetric_to_general(SEXP x)
+{
-    cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;
+    CHM_SP chx = AS_CHM_SP(x), chgx;
     int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
     if (!(chx->stype))
 	error(_("Nonsymmetric matrix in Csparse_symmetric_to_general"));
     chgx = cholmod_copy(chx, /* stype: */ 0, chx->xtype, &c);
     /* xtype: pattern, "real", complex or .. */
-    Free(chx);
     return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
 			      GET_SLOT(x, Matrix_DimNamesSym));
+}
 SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo)
+{
-    cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;
+    CHM_SP chx = AS_CHM_SP(x), chgx;
     int uploT = (*CHAR(asChar(uplo)) == 'U') ? 1 : -1;
     int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
     chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);
     /* xtype: pattern, "real", complex or .. */
-    Free(chx);
     return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
 			      GET_SLOT(x, Matrix_DimNamesSym));
+}
 SEXP Csparse_transpose(SEXP x, SEXP tri)
+{
     /* TODO: lgCMatrix & igC* currently go via double prec. cholmod -
      *       since cholmod (& cs) lacks sparse 'int' matrices */
-    cholmod_sparse *chx = as_cholmod_sparse(x);
+    CHM_SP chx = AS_CHM_SP(x);
     int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
-    cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);
+    CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);
     SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
     int tr = asLogical(tri);
-    Free(chx);
     tmp = VECTOR_ELT(dn, 0);	/* swap the dimnames */
     SET_VECTOR_ELT(dn, 0, VECTOR_ELT(dn, 1));
     SET_VECTOR_ELT(dn, 1, tmp);
     UNPROTECT(1);
     return chm_sparse_to_SEXP(chxt, 1, /* SWAP 'uplo' for triangular */
 			      Rkind, tr ? diag_P(x) : "", dn);
+}
 SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
+{
-    cholmod_sparse
-	*cha = as_cholmod_sparse(a),
-	*chb = as_cholmod_sparse(b);
+    CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b);
-    cholmod_sparse *chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);
+    CHM_SP chc = cholmod_ssmult(cha, chb, 0, cha->xtype, 1, &c);
     SEXP dn = allocVector(VECSXP, 2);
-    Free(cha); Free(chb);
     SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
 		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
     SET_VECTOR_ELT(dn, 1,
 		   duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), 1)));
     return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);
+}
 SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans)
+{
     int tr = asLogical(trans);
-    cholmod_sparse
-	*cha = as_cholmod_sparse(a),
-	*chb = as_cholmod_sparse(b);
-    cholmod_sparse *chTr, *chc;
+    CHM_SP cha = AS_CHM_SP(a), chb = AS_CHM_SP(b), chTr, chc;
     SEXP dn = allocVector(VECSXP, 2);
-/*     cholmod_sparse *chTr = cholmod_transpose(cha, 1, &c); */
-/*     cholmod_sparse *chc = cholmod_ssmult(chTr, chb, 0, cha->xtype, 1, &c); */
-    if (tr)
-	chTr = cholmod_transpose(chb, chb->xtype, &c);
+    chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);
-    else
-	chTr = cholmod_transpose(cha, cha->xtype, &c);
     chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,
 , cha->xtype, 1, &c);
-    Free(cha); Free(chb); cholmod_free_sparse(&chTr, &c);
+    cholmod_free_sparse(&chTr, &c);
     SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
 		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), (tr) ? 0 : 1)));
     SET_VECTOR_ELT(dn, 1,
 		   duplicate(VECTOR_ELT(GET_SLOT(b, Matrix_DimNamesSym), (tr) ? 0 : 1)));
     return chm_sparse_to_SEXP(chc, 1, 0, 0, "", dn);
+}
 SEXP Csparse_dense_prod(SEXP a, SEXP b)
+{
-    cholmod_sparse *cha = as_cholmod_sparse(a);
+    CHM_SP cha = AS_CHM_SP(a);
     SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
-    cholmod_dense *chb = as_cholmod_dense(b_M);
+    CHM_DN chb = AS_CHM_DN(b_M);
-    cholmod_dense *chc =
-	cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);
+    CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,
+					chb->xtype, &c);
-    SEXP dn = allocVector(VECSXP, 2);
+    SEXP dn = PROTECT(allocVector(VECSXP, 2));
-    double alpha[] = {1,0}, beta[] = {0,0};
+    double one[] = {1,0}, zero[] = {0,0};
-    cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);
+    cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);
-    Free(cha); Free(chb);
-    UNPROTECT(1);
     SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
 		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 0)));
     SET_VECTOR_ELT(dn, 1,
 		   duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
+    UNPROTECT(2);
     return chm_dense_to_SEXP(chc, 1, 0, dn);
+}
 SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
+{
-    cholmod_sparse *cha = as_cholmod_sparse(a);
+    CHM_SP cha = AS_CHM_SP(a);
     SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));
-    cholmod_dense *chb = as_cholmod_dense(b_M);
+    CHM_DN chb = AS_CHM_DN(b_M);
-    cholmod_dense *chc =
-	cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);
+    CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,
+					chb->xtype, &c);
-    SEXP dn = allocVector(VECSXP, 2);
+    SEXP dn = PROTECT(allocVector(VECSXP, 2));
-    double alpha[] = {1,0}, beta[] = {0,0};
+    double one[] = {1,0}, zero[] = {0,0};
-    cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);
+    cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);
-    Free(cha); Free(chb);
-    UNPROTECT(1);
     SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
 		   duplicate(VECTOR_ELT(GET_SLOT(a, Matrix_DimNamesSym), 1)));
     SET_VECTOR_ELT(dn, 1,
 		   duplicate(VECTOR_ELT(GET_SLOT(b_M, Matrix_DimNamesSym), 1)));
+    UNPROTECT(2);
     return chm_dense_to_SEXP(chc, 1, 0, dn);
+}
 /* Computes   x'x  or  x x'  -- see Csparse_Csparse_crossprod above for  x'y and x y' */
 SEXP Csparse_crossprod(SEXP x, SEXP trans, SEXP triplet)
+{
     int trip = asLogical(triplet),
 	tr   = asLogical(trans); /* gets reversed because _aat is tcrossprod */
-    cholmod_triplet
-	*cht = trip ? as_cholmod_triplet(x) : (cholmod_triplet*) NULL;
+    CHM_TR cht = trip ? AS_CHM_TR(x) : (CHM_TR) NULL;
-    cholmod_sparse *chcp, *chxt,
+    CHM_SP chcp, chxt,
-	*chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)
+	chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c) : AS_CHM_SP(x);
-	: as_cholmod_sparse(x);
     SEXP dn = PROTECT(allocVector(VECSXP, 2));
-    if (!tr)
-	chxt = cholmod_transpose(chx, chx->xtype, &c);
+    if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);
     chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);
-    if(!chcp)
-	error(_("Csparse_crossprod(): error return from cholmod_aat()"));
+    if(!chcp) error(_("Csparse_crossprod(): error return from cholmod_aat()"));
     cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
     chcp->stype = 1;
-    if (trip) {
-	cholmod_free_sparse(&chx, &c);
+    if (trip) cholmod_free_sparse(&chx, &c);
-	Free(cht);
-    } else {
-	Free(chx);
-    }
     if (!tr) cholmod_free_sparse(&chxt, &c);
-				/* create dimnames */
-    SET_VECTOR_ELT(dn, 0,
+    SET_VECTOR_ELT(dn, 0,	/* establish dimnames */
 		   duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
 					(tr) ? 0 : 1)));
     SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
     UNPROTECT(1);
     return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
+}
 SEXP Csparse_drop(SEXP x, SEXP tol)
+{
-    cholmod_sparse *chx = as_cholmod_sparse(x),
+    CHM_SP chx = AS_CHM_SP(x);
-	*ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
+    CHM_SP ans = cholmod_copy(chx, chx->stype, chx->xtype, &c);
     double dtol = asReal(tol);
     int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
     if(!cholmod_drop(dtol, ans, &c))
 	error(_("cholmod_drop() failed"));
-    Free(chx);
     return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
 			      GET_SLOT(x, Matrix_DimNamesSym));
+}
 SEXP Csparse_horzcat(SEXP x, SEXP y)
+{
-    cholmod_sparse *chx = as_cholmod_sparse(x),
+    CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);
-	*chy = as_cholmod_sparse(y), *ans;
     int Rkind = 0; /* only for "d" - FIXME */
-    ans = cholmod_horzcat(chx, chy, 1, &c);
-    Free(chx); Free(chy);
     /* FIXME: currently drops dimnames */
-    return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
+    return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),
+, 0, Rkind, "", R_NilValue);
+}
 SEXP Csparse_vertcat(SEXP x, SEXP y)
+{
-    cholmod_sparse *chx = as_cholmod_sparse(x),
+    CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);
-	*chy = as_cholmod_sparse(y), *ans;
     int Rkind = 0; /* only for "d" - FIXME */
-    ans = cholmod_vertcat(chx, chy, 1, &c);
-    Free(chx); Free(chy);
     /* FIXME: currently drops dimnames */
-    return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
+    return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),
+, 0, Rkind, "", R_NilValue);
+}
 SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
+{
-    cholmod_sparse *chx = as_cholmod_sparse(x), *ans;
+    CHM_SP chx = AS_CHM_SP(x);
     int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
+    CHM_SP ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
-    ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
-    Free(chx);
     return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",
 			      GET_SLOT(x, Matrix_DimNamesSym));
+}
 SEXP Csparse_diagU2N(SEXP x)
+{
     if (*diag_P(x) != 'U') {/* "trivially fast" when there's no 'diag' slot at all */
 	return (x);
+    }
     else {
-	cholmod_sparse *chx = as_cholmod_sparse(x);
+	CHM_SP chx = AS_CHM_SP(x);
-	cholmod_sparse *eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
+	CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);
 	double one[] = {1, 0};
-	cholmod_sparse *ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
+	CHM_SP ans = cholmod_add(chx, eye, one, one, TRUE, TRUE, &c);
 	int uploT = (*uplo_P(x) == 'U') ? 1 : -1;
 	int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
-	Free(chx); cholmod_free_sparse(&eye, &c);
+	cholmod_free_sparse(&eye, &c);
 	return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
 				  GET_SLOT(x, Matrix_DimNamesSym));
+    }
+}
 SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
+{
-    cholmod_sparse *chx = as_cholmod_sparse(x);
+    CHM_SP chx = AS_CHM_SP(x);
     int rsize = (isNull(i)) ? -1 : LENGTH(i),
 	csize = (isNull(j)) ? -1 : LENGTH(j);
     int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;
     if (rsize >= 0 && !isInteger(i))

The R Project SVN R-packages

(root)/branches/Matrix-APIchange/src/Csparse.c – Rev 4529 → 4530