Csparse.c
/* Sparse matrices in compressed column-oriented form */
#include "Csparse.h"
#include "chm_common.h"
SEXP Csparse_validate(SEXP x)
{
/* NB: we do *NOT* check a potential 'x' slot here, at all */
cholmod_sparse *chx = as_cholmod_sparse(x);
SEXP pslot = GET_SLOT(x, Matrix_pSym),
islot = GET_SLOT(x, Matrix_iSym);
int j, k, ncol = length(pslot) - 1,
*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
nrow, sorted, *xp = INTEGER(pslot),
*xi = INTEGER(islot);
nrow = dims[0];
if (length(pslot) <= 0)
return mkString(_("slot p must have length > 0"));
if (xp[0] != 0)
return mkString(_("first element of slot p must be zero"));
if (length(islot) != xp[ncol])
return
mkString(_("last element of slot p must match length of slots i and x"));
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"));
}
sorted = TRUE;
for (j = 0; j < ncol; j++) {
if (xp[j] > xp[j+1])
return mkString(_("slot p must be non-decreasing"));
for (k = xp[j] + 1; k < xp[j + 1]; k++)
if (xi[k] < xi[k - 1]) sorted = FALSE;
}
if (!sorted) cholmod_sort(chx, &c);
Free(chx);
return ScalarLogical(1);
}
SEXP Csparse_to_dense(SEXP x)
{
cholmod_sparse *chxs = as_cholmod_sparse(x);
cholmod_dense *chxd = cholmod_sparse_to_dense(chxs, &c);
Free(chxs);
return chm_dense_to_SEXP(chxd, 1, Real_kind(x));
}
SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri)
{
cholmod_sparse *chxs = as_cholmod_sparse(x);
cholmod_sparse
*chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);
int uploT = 0; char *diag = "";
Free(chxs);
if (asLogical(tri)) { /* triangular sparse matrices */
uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?
-1 : 1;
diag = CHAR(asChar(GET_SLOT(x, Matrix_diagSym)));
}
return chm_sparse_to_SEXP(chxcp, 1, uploT, 0, diag,
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);
Free(chxs);
return chm_dense_to_matrix(chxd, 1,
GET_SLOT(x, Matrix_DimNamesSym));
}
SEXP Csparse_to_Tsparse(SEXP x, SEXP tri)
{
cholmod_sparse *chxs = as_cholmod_sparse(x);
cholmod_triplet *chxt = cholmod_sparse_to_triplet(chxs, &c);
int uploT = 0;
char *diag = "";
int Rkind = (chxs->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
Free(chxs);
if (asLogical(tri)) { /* triangular sparse matrices */
uploT = (*uplo_P(x) == 'U') ? -1 : 1;
diag = diag_P(x);
}
return chm_triplet_to_SEXP(chxt, 1, uploT, Rkind, diag,
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;
int Rkind = (chx->xtype == CHOLMOD_REAL) ? 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));
}
#ifdef _not_yet_FIXME_
/* MM: This would seem useful; e.g. lsC* can hardly be coerced to ! */
SEXP Csparse_general_to_symmetric(SEXP x,
int stype)/*-1 : "L", +1 : "U" */
{
cholmod_sparse *chx = as_cholmod_sparse(x), *chgx;
int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
chgx = cholmod_copy(chx, /* stype: */ stype, chx->xtype, &c);
/* xtype: pattern, "real", complex or .. */
Free(chx);
return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",
GET_SLOT(x, Matrix_DimNamesSym));
}
#endif
SEXP Csparse_transpose(SEXP x, SEXP tri)
{
cholmod_sparse *chx = as_cholmod_sparse(x);
int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
cholmod_sparse *chxt = cholmod_transpose(chx, (int) chx->xtype, &c);
SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;
int uploT = 0; char *diag = "";
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);
if (asLogical(tri)) { /* triangular sparse matrices */
uploT = (*uplo_P(x) == 'U') ? -1 : 1;
diag = diag_P(x);
}
return chm_sparse_to_SEXP(chxt, 1, uploT, Rkind, diag, dn);
}
SEXP Csparse_Csparse_prod(SEXP a, SEXP b)
{
cholmod_sparse *cha = as_cholmod_sparse(a),
*chb = as_cholmod_sparse(b);
cholmod_sparse *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_dense_prod(SEXP a, SEXP b)
{
cholmod_sparse *cha = as_cholmod_sparse(a);
cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));
cholmod_dense *chc =
cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow, chb->xtype, &c);
double alpha[] = {1,0}, beta[] = {0,0};
cholmod_sdmult(cha, 0, alpha, beta, chb, chc, &c);
Free(cha); Free(chb);
UNPROTECT(1);
return chm_dense_to_SEXP(chc, 1, 0);
}
SEXP Csparse_dense_crossprod(SEXP a, SEXP b)
{
cholmod_sparse *cha = as_cholmod_sparse(a);
cholmod_dense *chb = as_cholmod_dense(PROTECT(mMatrix_as_dgeMatrix(b)));
cholmod_dense *chc =
cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol, chb->xtype, &c);
double alpha[] = {1,0}, beta[] = {0,0};
cholmod_sdmult(cha, 1, alpha, beta, chb, chc, &c);
Free(cha); Free(chb);
UNPROTECT(1);
return chm_dense_to_SEXP(chc, 1, 0);
}
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;
cholmod_sparse *chcp, *chxt,
*chx = trip ? cholmod_triplet_to_sparse(cht, cht->nnz, &c)
: as_cholmod_sparse(x);
SEXP dn = PROTECT(allocVector(VECSXP, 2));
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()");
cholmod_band_inplace(0, chcp->ncol, chcp->xtype, chcp, &c);
chcp->stype = 1;
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,
duplicate(VECTOR_ELT(GET_SLOT(x, Matrix_DimNamesSym),
(tr) ? 1 : 0)));
SET_VECTOR_ELT(dn, 1, duplicate(VECTOR_ELT(dn, 0)));
UNPROTECT(1);
return chm_sparse_to_SEXP(chcp, 1, 0, 0, "", dn);
}
SEXP Csparse_horzcat(SEXP x, SEXP y)
{
cholmod_sparse *chx = as_cholmod_sparse(x),
*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);
}
SEXP Csparse_vertcat(SEXP x, SEXP y)
{
cholmod_sparse *chx = as_cholmod_sparse(x),
*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);
}
SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2)
{
cholmod_sparse *chx = as_cholmod_sparse(x), *ans;
int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
ans = cholmod_band(chx, asInteger(k1), asInteger(k2), chx->xtype, &c);
Free(chx);
return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "", R_NilValue);
}
SEXP Csparse_diagU2N(SEXP x)
{
cholmod_sparse *chx = as_cholmod_sparse(x);
cholmod_sparse *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);
int uploT = (strcmp(CHAR(asChar(GET_SLOT(x, Matrix_uploSym))), "U")) ?
-1 : 1;
int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
Free(chx); cholmod_free_sparse(&eye, &c);
return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",
duplicate(GET_SLOT(x, Matrix_DimNamesSym)));
}
SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j)
{
cholmod_sparse *chx = as_cholmod_sparse(x);
int rsize = (isNull(i)) ? -1 : LENGTH(i),
csize = (isNull(j)) ? -1 : LENGTH(j);
int Rkind = (chx->xtype == CHOLMOD_REAL) ? Real_kind(x) : 0;
if (rsize >= 0 && !isInteger(i))
error(_("Index i must be NULL or integer"));
if (csize >= 0 && !isInteger(j))
error(_("Index j must be NULL or integer"));
return chm_sparse_to_SEXP(cholmod_submatrix(chx, INTEGER(i), rsize,
INTEGER(j), csize,
TRUE, TRUE, &c),
1, 0, Rkind, "", R_NilValue);
}