#include "chm_common.h"
#include "Mutils.h"

Include dependency graph for chm_common.c:

Defines
#define	_AS_cholmod_dense_1
#define	_AS_cholmod_dense_2
#define	_i(I) ( (int*) chx->i)[I]
#define	_p(I) ( (int*) chx->p)[I]
#define	_x(I) ((double*) chx->x)[I]
Functions
CHM_DN	as_cholmod_dense (CHM_DN ans, SEXP x)
	Populate ans with the pointers from x and modify its scalar elements accordingly.
CHM_FR	as_cholmod_factor (CHM_FR ans, SEXP x)
	Populate ans with the pointers from x and modify its scalar elements accordingly.
CHM_SP	as_cholmod_sparse (CHM_SP ans, SEXP x, Rboolean check_Udiag, Rboolean sort_in_place)
	Populate ans with the pointers from x and modify its scalar elements accordingly.
CHM_TR	as_cholmod_triplet (CHM_TR ans, SEXP x, Rboolean check_Udiag)
	Populate ans with the pointers from x and modify its scalar elements accordingly.
CHM_DN	as_cholmod_x_dense (cholmod_dense *ans, SEXP x)
Rboolean	check_sorted_chm (CHM_SP A)
static void	chm2Ralloc (CHM_SP dest, CHM_SP src)
	Copy cholmod_sparse, to an R_alloc()ed version of it.
SEXP	chm_dense_to_matrix (CHM_DN a, int dofree, SEXP dn)
	Copy the contents of a to a matrix object and, optionally, free a or free both a and its pointer to its contents.
SEXP	chm_dense_to_SEXP (CHM_DN a, int dofree, int Rkind, SEXP dn)
	Copy the contents of a to an appropriate denseMatrix object and, optionally, free a or free both a and its pointer to its contents.
void	chm_diagN2U (CHM_SP chx, int uploT, Rboolean do_realloc)
	Drop the (unit) diagonal entries from a cholmod_sparse matrix.
SEXP	chm_factor_to_SEXP (CHM_FR f, int dofree)
	Copy the contents of f to an appropriate CHMfactor object and, optionally, free f or free both f and its pointer to its contents.
void	CHM_restore_common ()
SEXP	CHM_set_common_env (SEXP rho)
SEXP	chm_sparse_to_SEXP (CHM_SP a, int dofree, int uploT, int Rkind, const char *diag, SEXP dn)
	Copy the contents of a to an appropriate CsparseMatrix object and, optionally, free a or free both a and its the pointers to its contents.
void	CHM_store_common ()
SEXP	chm_triplet_to_SEXP (CHM_TR a, int dofree, int uploT, int Rkind, const char *diag, SEXP dn)
	Copy the contents of a to an appropriate TsparseMatrix object and, optionally, free a or free both a and its the pointers to its contents.
SEXP	CHMfactor_validate (SEXP obj)
SEXP	CHMsimpl_validate (SEXP obj)
SEXP	CHMsuper_validate (SEXP obj)
static void	chTr2Ralloc (CHM_TR dest, CHM_TR src)
	Copy cholmod_triplet to an R_alloc()ed version of it.
Rboolean	isValid_Csparse (SEXP x)
	"Cheap" C version of Csparse_validate() - not sorting :
CHM_DN	numeric_as_chm_dense (CHM_DN ans, double *v, int nr, int nc)
void	R_cholmod_error (int status, const char file, int line, const char message)
static int	R_cholmod_printf (const char *fmt,...)
int	R_cholmod_start (CHM_CM c)
	Initialize the CHOLMOD library and replace the print and error functions by R-specific versions.
static void *	RallocedREAL (SEXP x)
static int	stype (int ctype, SEXP x)
static void *	xpt (int ctype, SEXP x)
static int	xtype (int ctype)
Variables
cholmod_common	c
SEXP	chm_common_env
cholmod_common	cl
static SEXP	dboundSym
static SEXP	final_asisSym
static SEXP	final_llSym
static SEXP	final_monotonicSym
static SEXP	final_packSym
static SEXP	final_resymbolSym
static SEXP	final_superSym
static SEXP	grow0Sym
static SEXP	grow1Sym
static SEXP	grow2Sym
static SEXP	m0_ordSym
static SEXP	maxrankSym
static SEXP	nmethodsSym
static SEXP	postorderSym
static SEXP	prefer_upperSym
static SEXP	prefer_zomplexSym
static SEXP	quick_return_if_not_posdefSym
static SEXP	supernodal_switchSym
static SEXP	supernodalSym

Define Documentation

#define _AS_cholmod_dense_1

Value:

static const char *valid[] = { MATRIX_VALID_dense, ""};         \
    int dims[2], ctype = Matrix_check_class_etc(x, valid), nprot = 0;   \
                                                                        \
    if (ctype < 0) {            /* not a classed matrix */              \
        if (isMatrix(x)) Memcpy(dims, INTEGER(getAttrib(x, R_DimSymbol)), 2); \
        else {dims[0] = LENGTH(x); dims[1] = 1;}                        \
        if (isInteger(x)) {                                             \
            x = PROTECT(coerceVector(x, REALSXP));                      \
            nprot++;                                                    \
        }                                                               \
        ctype = (isReal(x) ? 0 :                                        \
                 (isLogical(x) ? 2 : /* logical -> default to "l", not "n" */ \
                  (isComplex(x) ? 6 : -1)));                            \
    } else Memcpy(dims, INTEGER(GET_SLOT(x, Matrix_DimSym)), 2);        \
    if (ctype < 0) error(_("invalid class of object to as_cholmod_dense")); \
    memset(ans, 0, sizeof(cholmod_dense)); /* zero the struct */        \
                                                                        \
    ans->dtype = CHOLMOD_DOUBLE; /* characteristics of the system */    \
    ans->x = ans->z = (void *) NULL;                                    \
                                /* dimensions and nzmax */              \
    ans->d = ans->nrow = dims[0];                                       \
    ans->ncol = dims[1];                                                \
    ans->nzmax = dims[0] * dims[1];                                     \
                                /* set the xtype and any elements */    \
    switch(ctype / 2) {                                                 \
    case 0: /* "d" */                                                   \
        ans->xtype = CHOLMOD_REAL;                                      \
        ans->x = (void *) REAL((ctype % 2) ? GET_SLOT(x, Matrix_xSym) : x); \
        break

Referenced by as_cholmod_dense(), and as_cholmod_x_dense().

#define _AS_cholmod_dense_2

Value:

case 3: /* "z" */                                                       \
        ans->xtype = CHOLMOD_COMPLEX;                                   \
        ans->x = (void *) COMPLEX((ctype % 2) ? GET_SLOT(x, Matrix_xSym) : x); \
        break;                                                          \
    }                                                                   \
    UNPROTECT(nprot);                                                   \
    return ans

Referenced by as_cholmod_dense(), and as_cholmod_x_dense().

#define _i ( I ) ( (int*) chx->i)[I]

Referenced by chm_diagN2U().

#define _p ( I ) ( (int*) chx->p)[I]

Referenced by chm_diagN2U().

#define _x ( I ) ((double*) chx->x)[I]

Referenced by chm_diagN2U().

Function Documentation

CHM_DN as_cholmod_dense	(	CHM_DN	ans,
		SEXP	x
	)

Populate ans with the pointers from x and modify its scalar elements accordingly.

Note that later changes to the contents of ans will change the contents of the SEXP.

In most cases this function is called through the macro AS_CHM_DN. It is unusual to call it directly.

Parameters:

ans	a CHM_DN pointer.
x	pointer to an object that inherits from (denseMatrix ^ generalMatrix)

Returns:: ans containing pointers to the slots of x.

Definition at line 593 of file chm_common.c.

References _AS_cholmod_dense_1, _AS_cholmod_dense_2, Matrix_xSym, and RallocedREAL().

Referenced by R_init_Matrix().

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CHM_FR as_cholmod_factor	(	CHM_FR	ans,
		SEXP	x
	)

Populate ans with the pointers from x and modify its scalar elements accordingly.

Note that later changes to the contents of ans will change the contents of the SEXP.

In most cases this function is called through the macro AS_CHM_FR. It is unusual to call it directly.

Parameters:

ans	an CHM_FR object
x	pointer to an object that inherits from CHMfactor

Returns:: ans containing pointers to the slots of x.

Definition at line 865 of file chm_common.c.

References _, c, Matrix_check_class_etc(), Matrix_iSym, Matrix_permSym, Matrix_pSym, MATRIX_VALID_CHMfactor, and Matrix_xSym.

Referenced by R_init_Matrix().

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CHM_SP as_cholmod_sparse	(	CHM_SP	ans,
		SEXP	x,
		Rboolean	check_Udiag,
		Rboolean	sort_in_place
	)

Populate ans with the pointers from x and modify its scalar elements accordingly.

Note that later changes to the contents of ans will change the contents of the SEXP.

In most cases this function is called through the macros AS_CHM_SP() or AS_CHM_SP__(). It is unusual to call it directly.

Parameters:

ans	a CHM_SP pointer
x	pointer to an object that inherits from CsparseMatrix
check_Udiag	boolean - should a check for (and consequent expansion of) a unit diagonal be performed.
sort_in_place	boolean - if the i and x slots are to be sorted should they be sorted in place? If the i and x slots are pointers to an input SEXP they should not be modified.

Returns:: ans containing pointers to the slots of x, *unless* check_Udiag and x is unitriangular.

Definition at line 217 of file chm_common.c.

References _, c, check_sorted_chm(), chm2Ralloc(), diag_P, isValid_Csparse(), Matrix_check_class_etc(), Matrix_DimSym, Matrix_iSym, Matrix_pSym, stype(), xpt(), and xtype().

Referenced by Csparse_validate_(), and R_init_Matrix().

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CHM_TR as_cholmod_triplet	(	CHM_TR	ans,
		SEXP	x,
		Rboolean	check_Udiag
	)

Populate ans with the pointers from x and modify its scalar elements accordingly.

Note that later changes to the contents of ans will change the contents of the SEXP.

In most cases this function is called through the macros AS_CHM_TR() or AS_CHM_TR__(). It is unusual to call it directly.

Parameters:

ans	a CHM_TR pointer
x	pointer to an object that inherits from TsparseMatrix
check_Udiag	boolean - should a check for (and consequent expansion of) a unit diagonal be performed.

Returns:: ans containing pointers to the slots of x, *unless* check_Udiag and x is unitriangular.

Definition at line 410 of file chm_common.c.

References _, c, chTr2Ralloc(), diag_P, Matrix_check_class_etc(), Matrix_DimSym, Matrix_iSym, Matrix_jSym, MATRIX_VALID_Tsparse, stype(), xpt(), and xtype().

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CHM_DN as_cholmod_x_dense	(	cholmod_dense *	ans,
		SEXP	x
	)

Definition at line 652 of file chm_common.c.

References _AS_cholmod_dense_1, _AS_cholmod_dense_2, Matrix_xSym, and RallocedREAL().

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Rboolean check_sorted_chm ( CHM_SP A )

Definition at line 141 of file chm_common.c.

Referenced by as_cholmod_sparse().

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static void chm2Ralloc	(	CHM_SP	dest,
		CHM_SP	src
	)		`[static]`

Copy cholmod_sparse, to an R_alloc()ed version of it.

Definition at line 158 of file chm_common.c.

References c.

Referenced by as_cholmod_sparse().

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SEXP chm_dense_to_matrix	(	CHM_DN	a,
		int	dofree,
		SEXP	dn
	)

Copy the contents of a to a matrix object and, optionally, free a or free both a and its pointer to its contents.

Parameters:

a	cholmod_dense structure to be converted
dofree	0 - don't free a; > 0 cholmod_free a; < 0 Free a
dn	either R_NilValue or an SEXP suitable for the Dimnames slot.

Returns:: SEXP containing a copy of a as a matrix object

Definition at line 809 of file chm_common.c.

References _, and c.

Referenced by Csparse_to_matrix().

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SEXP chm_dense_to_SEXP	(	CHM_DN	a,
		int	dofree,
		int	Rkind,
		SEXP	dn
	)

Copy the contents of a to an appropriate denseMatrix object and, optionally, free a or free both a and its pointer to its contents.

Parameters:

a	matrix to be converted
dofree	0 - don't free a; > 0 cholmod_free a; < 0 Free a
Rkind	type of R matrix to be generated (special to this function)
dn	-- dimnames [list(.,.) or NULL]

Returns:: SEXP containing a copy of a

Definition at line 736 of file chm_common.c.

References _, ALLOC_SLOT(), c, cl, Matrix_DimNamesSym, Matrix_DimSym, and Matrix_xSym.

Referenced by CHMfactor_solve(), Csparse_dense_crossprod(), Csparse_dense_prod(), Csparse_to_dense(), and dsCMatrix_matrix_solve().

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void chm_diagN2U	(	CHM_SP	chx,
		int	uploT,
		Rboolean	do_realloc
	)

Drop the (unit) diagonal entries from a cholmod_sparse matrix.

Parameters:

chx	cholmod_sparse matrix. Note that the matrix "slots" are modified _in place_
uploT	integer code (= +/- 1) indicating if chx is upper (+1) or lower (-1) triangular
do_realloc	Rboolean indicating, if a cholmod_sprealloc() should finalize the procedure; not needed, e.g. when the result is converted to a SEXP immediately afterwards.

Definition at line 1019 of file chm_common.c.

References _, _i, _p, _x, and c.

Referenced by Csparse_Csparse_crossprod(), Csparse_Csparse_prod(), and Csparse_diagN2U().

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SEXP chm_factor_to_SEXP	(	CHM_FR	f,
		int	dofree
	)

Copy the contents of f to an appropriate CHMfactor object and, optionally, free f or free both f and its pointer to its contents.

Parameters:

f	cholmod_factor object to be converted
dofree	0 - don't free a; > 0 cholmod_free a; < 0 Free a

Returns:: SEXP containing a copy of a

Definition at line 940 of file chm_common.c.

References _, ALLOC_SLOT(), c, chm_factor_ok(), Matrix_iSym, Matrix_pSym, Matrix_xSym, and xtype().

Referenced by CHMfactor_update(), destructive_CHM_update(), dgCMatrix_cholsol(), dsCMatrix_Cholesky(), internal_chm_factor(), and R_init_Matrix().

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void CHM_restore_common ( )

Definition at line 41 of file chm_common.c.

References c, chm_common_env, dboundSym, final_asisSym, final_llSym, final_monotonicSym, final_packSym, final_resymbolSym, final_superSym, grow0Sym, grow1Sym, grow2Sym, m0_ordSym, maxrankSym, nmethodsSym, postorderSym, prefer_upperSym, prefer_zomplexSym, quick_return_if_not_posdefSym, supernodal_switchSym, and supernodalSym.

Referenced by internal_chm_factor(), and R_cholmod_error().

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SEXP CHM_set_common_env ( SEXP rho )

Definition at line 65 of file chm_common.c.

References _, chm_common_env, CHM_store_common(), dboundSym, final_asisSym, final_llSym, final_monotonicSym, final_packSym, final_resymbolSym, final_superSym, grow0Sym, grow1Sym, grow2Sym, m0_ordSym, maxrankSym, nmethodsSym, postorderSym, prefer_upperSym, prefer_zomplexSym, quick_return_if_not_posdefSym, supernodal_switchSym, and supernodalSym.

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SEXP chm_sparse_to_SEXP	(	CHM_SP	a,
		int	dofree,
		int	uploT,
		int	Rkind,
		const char *	diag,
		SEXP	dn
	)

Copy the contents of a to an appropriate CsparseMatrix object and, optionally, free a or free both a and its the pointers to its contents.

Parameters:

a	(cholmod_sparse) matrix to be converted
dofree	0 - don't free a; > 0 cholmod_free a; < 0 Free a
uploT	0 - not triangular; > 0 upper triangular; < 0 lower
Rkind	- vector type to store for a->xtype == CHOLMOD_REAL, 0 - REAL; 1 - LOGICAL
diag	character string suitable for the diag slot of a triangular matrix (not accessed if uploT == 0).
dn	either R_NilValue or an SEXP suitable for the Dimnames slot.

Returns:: SEXP containing a copy of a

Definition at line 311 of file chm_common.c.

References _, ALLOC_SLOT(), c, cl, Matrix_diagSym, Matrix_DimNamesSym, Matrix_DimSym, Matrix_iSym, Matrix_pSym, Matrix_uploSym, and Matrix_xSym.

Referenced by CHMfactor_spsolve(), CHMfactor_to_sparse(), Csparse_band(), Csparse_crossprod(), Csparse_Csparse_crossprod(), Csparse_Csparse_prod(), Csparse_diagN2U(), Csparse_diagU2N(), Csparse_drop(), Csparse_general_to_symmetric(), Csparse_horzcat(), Csparse_submatrix(), Csparse_symmetric_to_general(), Csparse_to_nz_pattern(), Csparse_transpose(), Csparse_vertcat(), dense_to_Csparse(), dsCMatrix_chol(), dsCMatrix_Csparse_solve(), R_init_Matrix(), Tsparse_to_Csparse(), and Tsparse_to_tCsparse().

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void CHM_store_common ( )

Definition at line 16 of file chm_common.c.

References c, chm_common_env, dboundSym, final_asisSym, final_llSym, final_monotonicSym, final_packSym, final_resymbolSym, final_superSym, grow0Sym, grow1Sym, grow2Sym, m0_ordSym, maxrankSym, nmethodsSym, postorderSym, prefer_upperSym, prefer_zomplexSym, quick_return_if_not_posdefSym, supernodal_switchSym, and supernodalSym.

Referenced by CHM_set_common_env(), and internal_chm_factor().

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SEXP chm_triplet_to_SEXP	(	CHM_TR	a,
		int	dofree,
		int	uploT,
		int	Rkind,
		const char *	diag,
		SEXP	dn
	)

Copy the contents of a to an appropriate TsparseMatrix object and, optionally, free a or free both a and its the pointers to its contents.

Parameters:

a	matrix to be converted
dofree	0 - don't free a; > 0 cholmod_free a; < 0 Free a
uploT	0 - not triangular; > 0 upper triangular; < 0 lower
Rkind	- vector type to store for a->xtype == CHOLMOD_REAL, 0 - REAL; 1 - LOGICAL
diag	character string suitable for the diag slot of a triangular matrix (not accessed if uploT == 0).
dn	either R_NilValue or an SEXP suitable for the Dimnames slot.