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/* Sparse matrices in compressed column-oriented form */#include "Csparse.h"#include "Tsparse.h"#include "chm_common.h"SEXP Csparse_validate(SEXP x){/* NB: we do *NOT* check a potential 'x' slot here, at all */SEXP pslot = GET_SLOT(x, Matrix_pSym),islot = GET_SLOT(x, Matrix_iSym);Rboolean sorted, strictly;int j, k,*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),nrow = dims[0],ncol = dims[1],*xp = INTEGER(pslot),*xi = INTEGER(islot);if (length(pslot) != dims[1] + 1)return mkString(_("slot p must have length = ncol(.) + 1"));if (xp[0] != 0)return mkString(_("first element of slot p must be zero"));if (length(islot) < xp[ncol]) /* allow larger slots from over-allocation!*/returnmkString(_("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; strictly = TRUE;for (j = 0; j < ncol; j++) {if (xp[j] > xp[j+1])return mkString(_("slot p must be non-decreasing"));if(sorted)for (k = xp[j] + 1; k < xp[j + 1]; k++) {if (xi[k] < xi[k - 1])sorted = FALSE;else if (xi[k] == xi[k - 1])strictly = FALSE;}}if (!sorted) {CHM_SP chx = AS_CHM_SP(x);R_CheckStack();cholmod_sort(chx, &c);/* 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])return mkString(_("slot i is not *strictly* increasing inside a column (even after cholmod_sort)"));}} else if(!strictly) { /* sorted, but not strictly */return mkString(_("slot i is not *strictly* increasing inside a column"));}return ScalarLogical(1);}SEXP Rsparse_validate(SEXP x){/* NB: we do *NOT* check a potential 'x' slot here, at all */SEXP pslot = GET_SLOT(x, Matrix_pSym),jslot = GET_SLOT(x, Matrix_jSym);Rboolean sorted, strictly;int i, k,*dims = INTEGER(GET_SLOT(x, Matrix_DimSym)),nrow = dims[0],ncol = dims[1],*xp = INTEGER(pslot),*xj = INTEGER(jslot);if (length(pslot) != dims[0] + 1)return mkString(_("slot p must have length = nrow(.) + 1"));if (xp[0] != 0)return mkString(_("first element of slot p must be zero"));if (length(jslot) < xp[nrow]) /* allow larger slots from over-allocation!*/returnmkString(_("last element of slot p must match length of slots j and x"));for (i = 0; i < length(jslot); i++) {if (xj[i] < 0 || xj[i] >= ncol)return mkString(_("all column indices must be between 0 and ncol-1"));}sorted = TRUE; strictly = TRUE;for (i = 0; i < nrow; i++) {if (xp[i] > xp[i+1])return mkString(_("slot p must be non-decreasing"));if(sorted)for (k = xp[i] + 1; k < xp[i + 1]; k++) {if (xj[k] < xj[k - 1])sorted = FALSE;else if (xj[k] == xj[k - 1])strictly = FALSE;}}if (!sorted)/* cannot easily use cholmod_sort(.) ... -> "error out" :*/return mkString(_("slot j is not increasing inside a column"));else if(!strictly) /* sorted, but not strictly */return mkString(_("slot j is not *strictly* increasing inside a column"));return ScalarLogical(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){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 : */CHM_DN chxd = cholmod_sparse_to_dense(chxs, &c);int Rkind = (chxs->xtype == CHOLMOD_PATTERN)? -1 : Real_kind(x);R_CheckStack();return chm_dense_to_SEXP(chxd, 1, Rkind, GET_SLOT(x, Matrix_DimNamesSym));}SEXP Csparse_to_nz_pattern(SEXP x, SEXP tri){CHM_SP chxs = AS_CHM_SP(x);CHM_SP chxcp = cholmod_copy(chxs, chxs->stype, CHOLMOD_PATTERN, &c);int tr = asLogical(tri);R_CheckStack();return chm_sparse_to_SEXP(chxcp, 1/*do_free*/,tr ? ((*uplo_P(x) == 'U') ? 1 : -1) : 0,0, tr ? diag_P(x) : "",GET_SLOT(x, Matrix_DimNamesSym));}SEXP Csparse_to_matrix(SEXP x){return chm_dense_to_matrix(cholmod_sparse_to_dense(AS_CHM_SP(x), &c),1 /*do_free*/, GET_SLOT(x, Matrix_DimNamesSym));}SEXP Csparse_to_Tsparse(SEXP x, SEXP tri){CHM_SP chxs = AS_CHM_SP(x);CHM_TR chxt = cholmod_sparse_to_triplet(chxs, &c);int tr = asLogical(tri);int Rkind = (chxs->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;R_CheckStack();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){CHM_SP chx = AS_CHM_SP(x), chgx;int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;R_CheckStack();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 .. */return chm_sparse_to_SEXP(chgx, 1, 0, Rkind, "",GET_SLOT(x, Matrix_DimNamesSym));}SEXP Csparse_general_to_symmetric(SEXP x, SEXP uplo){CHM_SP chx = AS_CHM_SP(x), chgx;int uploT = (*CHAR(STRING_ELT(uplo,0)) == 'U') ? 1 : -1;int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;R_CheckStack();chgx = cholmod_copy(chx, /* stype: */ uploT, chx->xtype, &c);/* xtype: pattern, "real", complex or .. */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 */CHM_SP chx = AS_CHM_SP(x);int Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;CHM_SP chxt = cholmod_transpose(chx, chx->xtype, &c);SEXP dn = PROTECT(duplicate(GET_SLOT(x, Matrix_DimNamesSym))), tmp;int tr = asLogical(tri);R_CheckStack();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 */tr ? ((*uplo_P(x) == 'U') ? -1 : 1) : 0,Rkind, tr ? diag_P(x) : "", dn);}SEXP Csparse_Csparse_prod(SEXP a, SEXP b){CHM_SPcha = AS_CHM_SP(Csparse_diagU2N(a)),chb = AS_CHM_SP(Csparse_diagU2N(b)),chc = cholmod_ssmult(cha, chb, /*out_stype:*/ 0,cha->xtype, /*out sorted:*/ 1, &c);const char *cl_a = class_P(a), *cl_b = class_P(b);char diag[] = {'\0', '\0'};int uploT = 0;SEXP dn = allocVector(VECSXP, 2);R_CheckStack();/* Preserve triangularity and even unit-triangularity if appropriate.* Note that in that case, the multiplication itself should happen* faster. But there's no support for that in CHOLMOD *//* UGLY hack -- rather should have (fast!) C-level version of* is(a, "triangularMatrix") etc */if (cl_a[1] == 't' && cl_b[1] == 't')/* FIXME: fails for "Cholesky","BunchKaufmann"..*/if(*uplo_P(a) == *uplo_P(b)) { /* both upper, or both lower tri. */uploT = (*uplo_P(a) == 'U') ? 1 : -1;if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. *//* "remove the diagonal entries": */chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);diag[0]= 'U';}else diag[0]= 'N';}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, uploT, /*Rkind*/0, diag, dn);}SEXP Csparse_Csparse_crossprod(SEXP a, SEXP b, SEXP trans){int tr = asLogical(trans);CHM_SPcha = AS_CHM_SP(Csparse_diagU2N(a)),chb = AS_CHM_SP(Csparse_diagU2N(b)),chTr, chc;const char *cl_a = class_P(a), *cl_b = class_P(b);char diag[] = {'\0', '\0'};int uploT = 0;SEXP dn = allocVector(VECSXP, 2);R_CheckStack();chTr = cholmod_transpose((tr) ? chb : cha, chb->xtype, &c);chc = cholmod_ssmult((tr) ? cha : chTr, (tr) ? chTr : chb,/*out_stype:*/ 0, cha->xtype, /*out sorted:*/ 1, &c);cholmod_free_sparse(&chTr, &c);/* Preserve triangularity and unit-triangularity if appropriate;* see Csparse_Csparse_prod() for comments */if (cl_a[1] == 't' && cl_b[1] == 't')if(*uplo_P(a) != *uplo_P(b)) { /* one 'U', the other 'L' */uploT = (*uplo_P(b) == 'U') ? 1 : -1;if(*diag_P(a) == 'U' && *diag_P(b) == 'U') { /* return UNIT-triag. */chm_diagN2U(chc, uploT, /* do_realloc */ FALSE);diag[0]= 'U';}else diag[0]= 'N';}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, uploT, /*Rkind*/0, diag, dn);}SEXP Csparse_dense_prod(SEXP a, SEXP b){CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));CHM_DN chb = AS_CHM_DN(b_M);CHM_DN chc = cholmod_allocate_dense(cha->nrow, chb->ncol, cha->nrow,chb->xtype, &c);SEXP dn = PROTECT(allocVector(VECSXP, 2));double one[] = {1,0}, zero[] = {0,0};R_CheckStack();cholmod_sdmult(cha, 0, one, zero, chb, chc, &c);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){CHM_SP cha = AS_CHM_SP(Csparse_diagU2N(a));SEXP b_M = PROTECT(mMatrix_as_dgeMatrix(b));CHM_DN chb = AS_CHM_DN(b_M);CHM_DN chc = cholmod_allocate_dense(cha->ncol, chb->ncol, cha->ncol,chb->xtype, &c);SEXP dn = PROTECT(allocVector(VECSXP, 2));double one[] = {1,0}, zero[] = {0,0};R_CheckStack();cholmod_sdmult(cha, 1, one, zero, chb, chc, &c);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' -- *also* for Tsparse (triplet = TRUE)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 */CHM_TR cht = trip ? AS_CHM_TR(Tsparse_diagU2N(x)) : (CHM_TR) NULL;CHM_SP chcp, chxt,chx = (trip ?cholmod_triplet_to_sparse(cht, cht->nnz, &c) :AS_CHM_SP(Csparse_diagU2N(x)));SEXP dn = PROTECT(allocVector(VECSXP, 2));R_CheckStack();if (!tr) chxt = cholmod_transpose(chx, chx->xtype, &c);chcp = cholmod_aat((!tr) ? chxt : chx, (int *) NULL, 0, chx->xtype, &c);if(!chcp) {UNPROTECT(1);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 (!tr) cholmod_free_sparse(&chxt, &c);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){CHM_SP chx = AS_CHM_SP(x);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;R_CheckStack();if(!cholmod_drop(dtol, ans, &c))error(_("cholmod_drop() failed"));return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",GET_SLOT(x, Matrix_DimNamesSym));}SEXP Csparse_horzcat(SEXP x, SEXP y){CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);int Rkind = 0; /* only for "d" - FIXME */R_CheckStack();/* FIXME: currently drops dimnames */return chm_sparse_to_SEXP(cholmod_horzcat(chx, chy, 1, &c),1, 0, Rkind, "", R_NilValue);}SEXP Csparse_vertcat(SEXP x, SEXP y){CHM_SP chx = AS_CHM_SP(x), chy = AS_CHM_SP(y);int Rkind = 0; /* only for "d" - FIXME */R_CheckStack();/* FIXME: currently drops dimnames */return chm_sparse_to_SEXP(cholmod_vertcat(chx, chy, 1, &c),1, 0, Rkind, "", R_NilValue);}SEXP Csparse_band(SEXP x, SEXP k1, SEXP k2){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);R_CheckStack();return chm_sparse_to_SEXP(ans, 1, 0, Rkind, "",GET_SLOT(x, Matrix_DimNamesSym));}SEXP Csparse_diagU2N(SEXP x){const char *cl = class_P(x);/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */if (cl[1] != 't' || *diag_P(x) != 'U') {/* "trivially fast" when not triangular (<==> no 'diag' slot),or not *unit* triangular */return (x);}else { /* unit triangular (diag='U'): "fill the diagonal" & diag:= "N" */CHM_SP chx = AS_CHM_SP(x);CHM_SP eye = cholmod_speye(chx->nrow, chx->ncol, chx->xtype, &c);double one[] = {1, 0};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;R_CheckStack();cholmod_free_sparse(&eye, &c);return chm_sparse_to_SEXP(ans, 1, uploT, Rkind, "N",GET_SLOT(x, Matrix_DimNamesSym));}}SEXP Csparse_diagN2U(SEXP x){const char *cl = class_P(x);/* dtCMatrix, etc; [1] = the second character =?= 't' for triangular */if (cl[1] != 't' || *diag_P(x) != 'N') {/* "trivially fast" when not triangular (<==> no 'diag' slot),or already *unit* triangular */return (x);}else { /* triangular with diag='N'): now drop the diagonal *//* duplicate, since chx will be modified: */CHM_SP chx = AS_CHM_SP(duplicate(x));int uploT = (*uplo_P(x) == 'U') ? 1 : -1,Rkind = (chx->xtype != CHOLMOD_PATTERN) ? Real_kind(x) : 0;R_CheckStack();chm_diagN2U(chx, uploT, /* do_realloc */ FALSE);return chm_sparse_to_SEXP(chx, /*dofree*/ 0/* or 1 ?? */,uploT, Rkind, "U",GET_SLOT(x, Matrix_DimNamesSym));}}SEXP Csparse_submatrix(SEXP x, SEXP i, SEXP j){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;R_CheckStack();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, "",/* FIXME: drops dimnames */ R_NilValue);}SEXP Csparse_MatrixMarket(SEXP x, SEXP fname){FILE *f = fopen(CHAR(asChar(fname)), "w");if (!f)error(_("failure to open file \"%s\" for writing"),CHAR(asChar(fname)));if (!cholmod_write_sparse(f, AS_CHM_SP(Csparse_diagU2N(x)),(CHM_SP)NULL, (char*) NULL, &c))error(_("cholmod_write_sparse returned error code"));fclose(f);return R_NilValue;}/*** Extract the diagonal entries from *triangular* Csparse matrix __or__ a* cholmod_sparse factor (LDL = TRUE).** @param n dimension of the matrix.* @param x_p 'p' (column pointer) slot contents* @param x_x 'x' (non-zero entries) slot contents* @param perm 'perm' (= permutation vector) slot contents* @param resultKind a (SEXP) string indicating which kind of result is desired.** @return a SEXP, either a (double) number or a length n-vector of diagonal entries*/SEXP diag_tC_ptr(int n, int *x_p, double *x_x, int *perm, SEXP resultKind)/* ^^^^^^ FIXME[Generalize] to int / ... */{const char* res_ch = CHAR(STRING_ELT(resultKind,0));enum diag_kind { diag, diag_backpermuted, trace, prod, sum_log} res_kind = ((!strcmp(res_ch, "trace")) ? trace :((!strcmp(res_ch, "sumLog")) ? sum_log :((!strcmp(res_ch, "prod")) ? prod :((!strcmp(res_ch, "diag")) ? diag :((!strcmp(res_ch, "diagBack")) ? diag_backpermuted :-1)))));int i, n_x, i_from = 0;SEXP ans = PROTECT(allocVector(REALSXP,/* ^^^^ FIXME[Generalize] */(res_kind == diag ||res_kind == diag_backpermuted) ? n : 1));double *v = REAL(ans);/* ^^^^^^ ^^^^ FIXME[Generalize] */#define for_DIAG(v_ASSIGN) \for(i = 0; i < n; i++, i_from += n_x) { \/* looking at i-th column */ \n_x = x_p[i+1] - x_p[i];/* #{entries} in this column */ \v_ASSIGN; \}/* NOTA BENE: we assume -- uplo = "L" i.e. lower triangular matrix* for uplo = "U" (makes sense with a "dtCMatrix" !),* should use x_x[i_from + (nx - 1)] instead of x_x[i_from],* where nx = (x_p[i+1] - x_p[i])*/switch(res_kind) {case trace:v[0] = 0.;for_DIAG(v[0] += x_x[i_from]);break;case sum_log:v[0] = 0.;for_DIAG(v[0] += log(x_x[i_from]));break;case prod:v[0] = 1.;for_DIAG(v[0] *= x_x[i_from]);break;case diag:for_DIAG(v[i] = x_x[i_from]);break;case diag_backpermuted:for_DIAG(v[i] = x_x[i_from]);/* now back_permute : */error(_("resultKind = 'diagBack' (back-permuted) is not yet implemented"));break;default: /* -1 from above */error("diag_tC(): invalid 'resultKind'");/* Wall: */ ans = R_NilValue; v = REAL(ans);}UNPROTECT(1);return ans;}/*** Extract the diagonal entries from *triangular* Csparse matrix __or__ a* cholmod_sparse factor (LDL = TRUE).** @param pslot 'p' (column pointer) slot of Csparse matrix/factor* @param xslot 'x' (non-zero entries) slot of Csparse matrix/factor* @param perm_slot 'perm' (= permutation vector) slot of corresponding CHMfactor* @param resultKind a (SEXP) string indicating which kind of result is desired.** @return a SEXP, either a (double) number or a length n-vector of diagonal entries*/SEXP diag_tC(SEXP pslot, SEXP xslot, SEXP perm_slot, SEXP resultKind){int n = length(pslot) - 1, /* n = ncol(.) = nrow(.) */*x_p = INTEGER(pslot),*perm = INTEGER(perm_slot);double *x_x = REAL(xslot);/* ^^^^^^ ^^^^ FIXME[Generalize] to INTEGER(.) / LOGICAL(.) / ... xslot !*/return diag_tC_ptr(n, x_p, x_x, perm, resultKind);}