Revision f584db857045d794fb5a587b18f1ca3ed40b8679 authored by Douglas Bates on 15 January 2006, 00:00:00 UTC, committed by Gabor Csardi on 15 January 2006, 00:00:00 UTC
1 parent a2d2fd0
lgCMatrix.c
#include "lgCMatrix.h"
SEXP lgCMatrix_validate(SEXP x)
{
SEXP pslot = GET_SLOT(x, Matrix_pSym),
islot = GET_SLOT(x, Matrix_iSym);
int j,
ncol = length(pslot) - 1,
*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
nrow,
*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 slot i"));
for (j = 0; j < ncol; j++) {
if (xp[j] > xp[j+1])
return mkString(_("slot p must be non-decreasing"));
}
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"));
}
if (csc_unsorted_columns(ncol, xp, xi))
csc_sort_columns(ncol, xp, xi, (double *) NULL);
return ScalarLogical(1);
}
/* very parallel to csc_matrix() in ./dgeMatrix.c */
SEXP lcsc_to_matrix(SEXP x)
{
SEXP ans, pslot = GET_SLOT(x, Matrix_pSym);
int j, ncol = length(pslot) - 1,
nrow = INTEGER(GET_SLOT(x, Matrix_DimSym))[0],
*xp = INTEGER(pslot),
*xi = INTEGER(GET_SLOT(x, Matrix_iSym));
int *ax;
ax = LOGICAL(ans = PROTECT(allocMatrix(LGLSXP, nrow, ncol)));
for (j = 0; j < (nrow * ncol); j++) ax[j] = 0;
for (j = 0; j < ncol; j++) {
int ind;
for (ind = xp[j]; ind < xp[j+1]; ind++)
ax[j * nrow + xi[ind]] = 1;
}
UNPROTECT(1);
return ans;
}
/**
* C := op(A) %*% op(B) + beta ^ C for logical sparse column-oriented matrices
*
* @param tra nonzero if A is to be transposed
* @param trb nonzero if B is to be transposed
* @param m number of rows in C
* @param n number of columns in C
* @param k number of columns in A if tra == 0, otherwise number of
* rows in A
* @param ai vector of row indices of TRUE elements in A
* @param ap column pointers for A
* @param bi vector of row indices of TRUE elements in B
* @param bp column pointers for B
* @param beta if non-zero existing TRUE elements in C are retained
* @param ciP SEXP whose INTEGER part is the column indices of TRUE
* elements in C (not used if beta == 0).
* @param cp column pointers for C
*
* @return SEXP whose INTEGER part is the column indices of TRUE
* elements in the product. Note that the contents of cp may be modified.
*/
SEXP Matrix_lgClgCmm(int tra, int trb, int m, int n, int k,
const int ai[], const int ap[],
const int bi[], const int bp[],
int beta, SEXP CIP, int cp[])
{
int cnnz = cp[n], extra = 0;
int *ci, i, j, prot = 0; /* prot is the number of PROTECTs to UNPROTECT */
if (beta) {
ci = INTEGER(CIP);
} else { /* blank the C matrix */
for (j = 0; j <= n; j++) cp[j] = 0;
cnnz = 0;
ci = (int *) NULL;
}
if (tra) { /* replace ai and ap by els for transpose */
int nz = ap[m];
int *Ai = Calloc(nz, int),
*aj = expand_cmprPt(m, ap, Calloc(nz, int)),
*Ap = Calloc(k + 1, int);
triplet_to_col(m, k, nz, aj, ai, (double *) NULL,
Ap, Ai, (double *) NULL);
Free(aj);
ai = Ai; ap = Ap;
}
if (trb) { /* replace bi and bp by els for transpose */
int nz = bp[k];
int *Bi = Calloc(nz, int),
*bj = expand_cmprPt(k, bp, Calloc(nz, int)),
*Bp = Calloc(n + 1, int);
triplet_to_col(k, n, nz, bj, bi, (double *) NULL,
Bp, Bi, (double *) NULL);
Free(bj);
bi = Bi; bp = Bp;
}
for (j = 0; j < n; j++) { /* col index for B and C */
int ii, ii2 = bp[j + 1];
for (ii = bp[j]; ii < ii2; ii++) { /* index into bi */
int jj = bi[ii]; /* row index of B; col index of A */
int i, i2 = ap[jj + 1]; /* index into ai */
for (i = ap[jj]; i < i2; i++)
if (check_csc_index(cp, ci, ai[i], j, -1) < 0) extra++;
}
}
if (extra) {
int ntot = cnnz + extra;
int *Cp = Calloc(n + 1, int),
*Ti = Calloc(ntot, int),
*rwInd = Calloc(m, int), /* indicator of TRUE in column j */
pos = 0;
Cp[0] = 0;
for (j = 0; j < n; j++) {
int ii, ii2 = bp[j + 1];
AZERO(rwInd, m); /* initialize column j of C */
for (i = cp[j]; i < cp[j+1]; i++) rwInd[ci[i]] = 1;
Cp[j + 1] = Cp[j];
for (ii = bp[j]; ii < ii2; ii++) { /* index into bi */
int jj = bi[ii]; /* row index of B; col index of A */
int i, i2 = ap[jj + 1]; /* index into ai */
for (i = ap[jj]; i < i2; i++) rwInd[ai[i]] = 1;
}
for (i = 0; i < m; i++)
if (rwInd[i]) {Cp[j + 1]++; Ti[pos++] = i;}
}
PROTECT(CIP = allocVector(INTSXP, Cp[n])); prot++;
Memcpy(INTEGER(CIP), Ti, Cp[n]);
Memcpy(cp, Cp, n + 1);
Free(Cp); Free(Ti); Free(rwInd);
}
if (tra) {Free(ai); Free(ap);}
if (trb) {Free(bi); Free(bp);}
UNPROTECT(prot);
return CIP;
}
SEXP lgCMatrix_lgCMatrix_mm(SEXP a, SEXP b)
{
SEXP ans = PROTECT(NEW_OBJECT(MAKE_CLASS("lgCMatrix")));
int *adims = INTEGER(GET_SLOT(a, Matrix_DimSym)),
*bdims = INTEGER(GET_SLOT(b, Matrix_DimSym)),
*cdims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
int k = adims[1], m = adims[0], n = bdims[1];
int *cp = INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, n + 1));
if (bdims[0] != k)
error(_("Matrices are not conformable for multiplication"));
cdims[0] = m; cdims[1] = n;
SET_SLOT(ans, Matrix_iSym,
Matrix_lgClgCmm(0, 0, m, n, k,
INTEGER(GET_SLOT(a, Matrix_iSym)),
INTEGER(GET_SLOT(a, Matrix_pSym)),
INTEGER(GET_SLOT(b, Matrix_iSym)),
INTEGER(GET_SLOT(b, Matrix_pSym)),
0, (SEXP) NULL, cp));
UNPROTECT(1);
return ans;
}
SEXP lgCMatrix_trans(SEXP x)
{
SEXP xi = GET_SLOT(x, Matrix_iSym);
SEXP ans = PROTECT(NEW_OBJECT(MAKE_CLASS("lgCMatrix")));
int *adims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2)),
*xdims = INTEGER(GET_SLOT(x, Matrix_DimSym)),
nz = length(xi);
int *xj = Calloc(nz, int);
SEXP adn = ALLOC_SLOT(ans, Matrix_DimNamesSym, VECSXP, 2),
xdn = GET_SLOT(x, Matrix_DimNamesSym);
adims[1] = xdims[0]; adims[0] = xdims[1];
SET_VECTOR_ELT(adn, 0, VECTOR_ELT(xdn, 1));
SET_VECTOR_ELT(adn, 1, VECTOR_ELT(xdn, 0));
triplet_to_col(adims[0], adims[1], nz,
expand_cmprPt(xdims[1], INTEGER(GET_SLOT(x, Matrix_pSym)), xj),
INTEGER(xi), (double *) NULL,
INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, adims[1] + 1)),
INTEGER(ALLOC_SLOT(ans, Matrix_iSym, INTSXP, nz)),
(double *) NULL);
Free(xj);
UNPROTECT(1);
return ans;
}
/**
* Replace C by AA' + beta*C or A'A + beta*C
*
* @param up Indicator of upper/lower triangle in the symmetric sparse matrix
* @param tra Transpose, in the sense of dsyrk. That is, tra TRUE indicates A'A
* @param n size of the product matrix
* @param k number of columns in A if tra is FALSE, otherwise the number of rows
* @param ai row indices for A
* @param ap column pointers for A
* @param beta TRUE if existing elements in C are to be preserved
* @param CIP SEXP whose INTEGER part is the row indices of C (not used if beta is FALSE)
* @param cp column pointers for C
*
* @return SEXP whose INTEGER part is the updated row indices of C
*/
SEXP Matrix_lgCsyrk(int up, int tra, int n, int k, const int ai[], const int ap[],
int beta, SEXP CIP, int cp[])
{
int extra = 0, i, ii, j, prot = 0;
int *ci, cnnz = cp[n];
if (beta) {
ci = INTEGER(CIP);
} else { /* blank the C matrix */
for (j = 0; j <= n; j++) cp[j] = 0;
cnnz = 0;
ci = (int *) NULL;
}
if (tra) { /* replace ai and ap by els for transpose */
int nz = ap[n];
int *Ai = Calloc(nz, int),
*aj = expand_cmprPt(n, ap, Calloc(nz, int)),
*Ap = Calloc(k + 1, int);
triplet_to_col(n, k, nz, aj, ai, (double *) NULL,
Ap, Ai, (double *) NULL);
Free(aj);
ai = Ai; ap = Ap;
}
for (j = 0; j < k; j++) {
int i2 = ap[j + 1];
for (i = ap[j]; i < i2; i++) {
int r1 = ai[i];
if (r1 < 0 || r1 >= n)
error(_("row %d not in row range [0,%d]"), r1, n - 1);
for (ii = i; ii < i2; ii++) {
int r2 = ai[ii];
if (r2 < 0 || r2 >= n)
error(_("row %d not in row range [0,%d]"), r2, n - 1);
if (check_csc_index(cp, ci, up?r1:r2, up?r2:r1, -1) < 0)
extra++;
}
}
}
if (extra) {
int ntot = cnnz + extra;
int *Ti = Memcpy(Calloc(ntot, int), ci, cnnz),
*Tj = expand_cmprPt(n, cp, Calloc(ntot, int)),
*Ci = Calloc(ntot, int),
pos = cnnz;
for (j = 0; j < k; j++) {
int i2 = ap[j + 1];
for (i = ap[j]; i < i2; i++) {
int r1 = ai[i];
for (ii = i; ii < i2; ii++) {
int r2 = ai[ii];
int row = up ? r1 : r2, col = up ? r2 : r1;
if (r2 < r1) error("[j,i,ii,r1,r2] = [%d,%d,%d,%d,%d]",
j,i,ii,r1,r2);
if (check_csc_index(cp, ci, row, col, -1) < 0) {
Ti[pos] = row;
Tj[pos] = col;
pos++;
}
}
}
}
triplet_to_col(n, n, pos, Ti, Tj, (double *) NULL,
cp, Ci, (double *) NULL);
PROTECT(CIP = allocVector(INTSXP, cp[n])); prot++;
Memcpy(INTEGER(CIP), Ci, cp[n]);
Free(Ti); Free(Tj); Free(Ci);
}
if (tra) {Free(ai); Free(ap);}
UNPROTECT(prot);
return CIP;
}
/**
* Create the cross-product or transpose cross-product of a logical
* sparse matrix in column-oriented compressed storage mode.
*
* @param x Pointer to a lgCMatrix
* @param trans logical indicator of transpose, in the sense of dsyrk.
* That is, trans == TRUE is used for crossprod.
* @param C
*
* @return An lsCMatrix of the form if(trans) X'X else XX'
*/
SEXP lgCMatrix_crossprod(SEXP x, SEXP trans, SEXP C)
{
int tra = asLogical(trans);
int *adims, *xdims = INTEGER(GET_SLOT(x, Matrix_DimSym));
int k = xdims[tra ? 0 : 1], n = xdims[tra ? 1 : 0];
if (C == R_NilValue) {
SEXP ans = PROTECT(NEW_OBJECT(MAKE_CLASS("lsCMatrix")));
adims = INTEGER(ALLOC_SLOT(ans, Matrix_DimSym, INTSXP, 2));
adims[0] = adims[1] = n;
SET_SLOT(ans, Matrix_uploSym, mkString("U"));
SET_SLOT(ans, Matrix_iSym,
Matrix_lgCsyrk(1, tra, n, k,
INTEGER(GET_SLOT(x, Matrix_iSym)),
INTEGER(GET_SLOT(x, Matrix_pSym)),
0, R_NilValue,
INTEGER(ALLOC_SLOT(ans, Matrix_pSym, INTSXP, n + 1))));
UNPROTECT(1);
return ans;
}
adims = INTEGER(GET_SLOT(C, Matrix_DimSym));
if (adims[0] != n || adims[1] != n)
error(_("Dimensions of x and y are not compatible for crossprod"));
SET_SLOT(C, Matrix_iSym,
Matrix_lgCsyrk(uplo_P(C)[0] == 'U',
tra, n, k,
INTEGER(GET_SLOT(x, Matrix_iSym)),
INTEGER(GET_SLOT(x, Matrix_pSym)),
1, GET_SLOT(C, Matrix_iSym),
INTEGER(GET_SLOT(C, Matrix_pSym))));
return C;
}
/**
* Special-purpose function that returns a permutation of the columns
* of a lgTMatrix for which nrow(x) > ncol(x). The ordering puts
* columns with fewer entries on the left. Once a column has been
* moved to the left the rows in where that column is TRUE are removed
* from the counts.
*
* @param x Pointer to an lgTMatrix object
*
* @return 0-based permutation vector for the columns of x
*/
SEXP lgCMatrix_picky_column(SEXP x)
{
int *xdims = INTEGER(GET_SLOT(x, Matrix_DimSym));
int *xi = INTEGER(GET_SLOT(x, Matrix_iSym)),
*xp = INTEGER(GET_SLOT(x, Matrix_pSym)),
m = xdims[0], n = xdims[1];
SEXP ans = PROTECT(allocVector(INTSXP, n));
int *actr = Calloc(m, int),
*actc = Calloc(n, int),
cj, i, j, mincount, minloc = -1, pos;
for (i = 0; i < m; i++) actr[i] = 1;
mincount = m + 1;
for (j = 0; j < n; j++) {
cj = xp[j + 1] - xp[j];
actc[j] = 1;
if (cj < mincount) {
mincount = cj;
minloc = j;
}
}
pos = 0;
while (pos < n) {
INTEGER(ans)[pos++] = minloc;
actc[minloc] = 0;
for (i = xp[minloc]; i < xp[minloc + 1]; i++) actr[xi[i]] = 0;
mincount = m + 1;
for (j = 0; j < n; j++) {
if (actc[j]) {
cj = 0;
for (i = xp[j]; i < xp[j + 1]; i++) {
if (actr[xi[i]]) cj++;
if (cj < mincount) {
mincount = cj;
minloc = j;
}
}
}
}
}
Free(actr); Free(actc);
UNPROTECT(1);
return ans;
}
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