void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
double dummy = 0, beta [2], *px ;
cholmod_sparse Amatrix, *A, *Lsparse ;
cholmod_factor *L ;
cholmod_common Common, *cm ;
Long n, minor ;
/* ---------------------------------------------------------------------- */
/* start CHOLMOD and set parameters */
/* ---------------------------------------------------------------------- */
cm = &Common ;
cholmod_l_start (cm) ;
sputil_config (SPUMONI, cm) ;
/* convert to packed LDL' when done */
cm->final_asis = FALSE ;
cm->final_super = FALSE ;
cm->final_ll = FALSE ;
cm->final_pack = TRUE ;
cm->final_monotonic = TRUE ;
/* since numerically zero entries are NOT dropped from the symbolic
* pattern, we DO need to drop entries that result from supernodal
* amalgamation. */
cm->final_resymbol = TRUE ;
cm->quick_return_if_not_posdef = (nargout < 2) ;
/* This will disable the supernodal LL', which will be slow. */
/* cm->supernodal = CHOLMOD_SIMPLICIAL ; */
/* ---------------------------------------------------------------------- */
/* get inputs */
/* ---------------------------------------------------------------------- */
if (nargin < 1 || nargin > 2 || nargout > 3)
{
mexErrMsgTxt ("usage: [L,p,q] = ldlchol (A,beta)") ;
}
n = mxGetM (pargin [0]) ;
if (!mxIsSparse (pargin [0]))
{
mexErrMsgTxt ("A must be sparse") ;
}
if (nargin == 1 && n != mxGetN (pargin [0]))
{
mexErrMsgTxt ("A must be square") ;
}
/* get sparse matrix A, use tril(A) */
A = sputil_get_sparse (pargin [0], &Amatrix, &dummy, -1) ;
if (nargin == 1)
{
A->stype = -1 ; /* use lower part of A */
beta [0] = 0 ;
beta [1] = 0 ;
}
else
{
A->stype = 0 ; /* use all of A, factorizing A*A' */
beta [0] = mxGetScalar (pargin [1]) ;
beta [1] = 0 ;
}
/* use natural ordering if no q output parameter */
if (nargout < 3)
{
cm->nmethods = 1 ;
cm->method [0].ordering = CHOLMOD_NATURAL ;
cm->postorder = FALSE ;
}
/* ---------------------------------------------------------------------- */
/* analyze and factorize */
/* ---------------------------------------------------------------------- */
L = cholmod_l_analyze (A, cm) ;
cholmod_l_factorize_p (A, beta, NULL, 0, L, cm) ;
if (nargout < 2 && cm->status != CHOLMOD_OK)
{
mexErrMsgTxt ("matrix is not positive definite") ;
}
/* ---------------------------------------------------------------------- */
/* convert L to a sparse matrix */
/* ---------------------------------------------------------------------- */
/* the conversion sets L->minor back to n, so get a copy of it first */
minor = L->minor ;
Lsparse = cholmod_l_factor_to_sparse (L, cm) ;
if (Lsparse->xtype == CHOLMOD_COMPLEX)
{
/* convert Lsparse from complex to zomplex */
cholmod_l_sparse_xtype (CHOLMOD_ZOMPLEX, Lsparse, cm) ;
}
/* ---------------------------------------------------------------------- */
/* return results to MATLAB */
/* ---------------------------------------------------------------------- */
/* return L as a sparse matrix (it may contain numerically zero entries) */
pargout [0] = sputil_put_sparse (&Lsparse, cm) ;
/* return minor (translate to MATLAB convention) */
if (nargout > 1)
{
pargout [1] = mxCreateDoubleMatrix (1, 1, mxREAL) ;
px = mxGetPr (pargout [1]) ;
px [0] = ((minor == n) ? 0 : (minor+1)) ;
}
/* return permutation */
if (nargout > 2)
{
pargout [2] = sputil_put_int (L->Perm, n, 1) ;
}
/* ---------------------------------------------------------------------- */
/* free workspace and the CHOLMOD L, except for what is copied to MATLAB */
/* ---------------------------------------------------------------------- */
cholmod_l_free_factor (&L, cm) ;
cholmod_l_finish (cm) ;
cholmod_l_print_common (" ", cm) ;
/*
if (cm->malloc_count != 3 + mxIsComplex (pargout[0])) mexErrMsgTxt ("!") ;
*/
}
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
double dummy = 0, *px ;
cholmod_sparse Amatrix, *A, *Lsparse, *R ;
cholmod_factor *L ;
cholmod_common Common, *cm ;
Long n, minor ;
/* ---------------------------------------------------------------------- */
/* start CHOLMOD and set parameters */
/* ---------------------------------------------------------------------- */
cm = &Common ;
cholmod_l_start (cm) ;
sputil_config (SPUMONI, cm) ;
/* convert to packed LL' when done */
cm->final_asis = FALSE ;
cm->final_super = FALSE ;
cm->final_ll = TRUE ;
cm->final_pack = TRUE ;
cm->final_monotonic = TRUE ;
/* no need to prune entries due to relaxed supernodal amalgamation, since
* zeros are dropped with sputil_drop_zeros instead */
cm->final_resymbol = FALSE ;
cm->quick_return_if_not_posdef = (nargout < 2) ;
/* ---------------------------------------------------------------------- */
/* get inputs */
/* ---------------------------------------------------------------------- */
if (nargin != 1 || nargout > 3)
{
mexErrMsgTxt ("usage: [R,p,q] = chol2 (A)") ;
}
n = mxGetN (pargin [0]) ;
if (!mxIsSparse (pargin [0]) || n != mxGetM (pargin [0]))
{
mexErrMsgTxt ("A must be square and sparse") ;
}
/* get input sparse matrix A. Use triu(A) only */
A = sputil_get_sparse (pargin [0], &Amatrix, &dummy, 1) ;
/* use natural ordering if no q output parameter */
if (nargout < 3)
{
cm->nmethods = 1 ;
cm->method [0].ordering = CHOLMOD_NATURAL ;
cm->postorder = FALSE ;
}
/* ---------------------------------------------------------------------- */
/* analyze and factorize */
/* ---------------------------------------------------------------------- */
L = cholmod_l_analyze (A, cm) ;
cholmod_l_factorize (A, L, cm) ;
if (nargout < 2 && cm->status != CHOLMOD_OK)
{
mexErrMsgTxt ("matrix is not positive definite") ;
}
/* ---------------------------------------------------------------------- */
/* convert L to a sparse matrix */
/* ---------------------------------------------------------------------- */
/* the conversion sets L->minor back to n, so get a copy of it first */
minor = L->minor ;
Lsparse = cholmod_l_factor_to_sparse (L, cm) ;
if (Lsparse->xtype == CHOLMOD_COMPLEX)
{
/* convert Lsparse from complex to zomplex */
cholmod_l_sparse_xtype (CHOLMOD_ZOMPLEX, Lsparse, cm) ;
}
if (minor < n)
{
/* remove columns minor to n-1 from Lsparse */
sputil_trim (Lsparse, minor, cm) ;
}
/* drop zeros from Lsparse */
sputil_drop_zeros (Lsparse) ;
/* Lsparse is lower triangular; conjugate transpose to get R */
R = cholmod_l_transpose (Lsparse, 2, cm) ;
cholmod_l_free_sparse (&Lsparse, cm) ;
/* ---------------------------------------------------------------------- */
/* return results to MATLAB */
/* ---------------------------------------------------------------------- */
/* return R */
pargout [0] = sputil_put_sparse (&R, cm) ;
/* return minor (translate to MATLAB convention) */
if (nargout > 1)
{
pargout [1] = mxCreateDoubleMatrix (1, 1, mxREAL) ;
px = mxGetPr (pargout [1]) ;
px [0] = ((minor == n) ? 0 : (minor+1)) ;
}
/* return permutation */
if (nargout > 2)
{
pargout [2] = sputil_put_int (L->Perm, n, 1) ;
}
/* ---------------------------------------------------------------------- */
/* free workspace and the CHOLMOD L, except for what is copied to MATLAB */
/* ---------------------------------------------------------------------- */
cholmod_l_free_factor (&L, cm) ;
cholmod_l_finish (cm) ;
cholmod_l_print_common (" ", cm) ;
/*
if (cm->malloc_count != (3 + mxIsComplex (pargout[0]))) mexErrMsgTxt ("!") ;
*/
}
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
int ki;
double dummy = 0 ;
double *Lx, *Lx2 ;
Int *Li, *Lp, *Li2, *Lp2, *Lnz2, *ColCount ;
cholmod_sparse Cmatrix, *R, *Lsparse ;
cholmod_factor *L ;
cholmod_common Common, *cm ;
Int j, k, s, update, n, lnz ;
char buf [LEN] ;
/* ---------------------------------------------------------------------- */
/* start CHOLMOD and set parameters */
/* ---------------------------------------------------------------------- */
cm = &Common ;
cholmod_l_start (cm) ;
sputil_config (SPUMONI, cm) ;
/* ---------------------------------------------------------------------- */
/* check inputs */
/* ---------------------------------------------------------------------- */
if (nargout > 1 || nargin < 3 || nargin > 4)
{
mexErrMsgTxt ("Usage: L = ldlrowupdate (k, L, R, '+')") ;
}
n = mxGetN (pargin [1]) ;
k = mxGetN (pargin [2]) ;
if (!mxIsSparse (pargin [1]) || !mxIsSparse (pargin [2])
|| n != mxGetM (pargin [1]) || n != mxGetM (pargin [2])
|| mxIsComplex (pargin [1]) || mxIsComplex (pargin [2]))
{
k = mxGetM (pargin [2]);
j = mxGetM (pargin [1]);
printf("n=%d L=%d R=%d \n", n, j, k);
mexErrMsgTxt ("ldlrowupdate: R and/or L not sparse, complex, or wrong"
" dimensions") ;
}
/* ---------------------------------------------------------------------- */
/* determine if we're doing an update or downdate */
/* ---------------------------------------------------------------------- */
update = TRUE ;
if (nargin > 3 && mxIsChar (pargin [3]))
{
mxGetString (pargin [3], buf, LEN) ;
if (buf [0] == '-')
{
update = FALSE ;
}
else if (buf [0] != '+')
{
mexErrMsgTxt ("ldlrowupdate: update string must be '+' or '-'") ;
}
}
/* ---------------------------------------------------------------------- */
/* get ki: column integer of update */
/* ---------------------------------------------------------------------- */
ki = (int) *mxGetPr(pargin[0]);
ki = ki-1;
/* ---------------------------------------------------------------------- */
/* get R: sparse matrix of incoming/outgoing columns */
/* ---------------------------------------------------------------------- */
R = sputil_get_sparse (pargin [2], &Cmatrix, &dummy, 0) ;
/* ---------------------------------------------------------------------- */
/* construct a copy of the input sparse matrix L */
/* ---------------------------------------------------------------------- */
/* get the MATLAB L */
Lp = (Int *) mxGetJc (pargin [1]) ;
Li = (Int *) mxGetIr (pargin [1]) ;
Lx = mxGetPr (pargin [1]) ;
/* allocate the CHOLMOD symbolic L */
L = cholmod_l_allocate_factor (n, cm) ;
L->ordering = CHOLMOD_NATURAL ;
ColCount = L->ColCount ;
for (j = 0 ; j < n ; j++)
{
ColCount [j] = Lp [j+1] - Lp [j] ;
}
/* allocate space for a CHOLMOD LDL' packed factor */
cholmod_l_change_factor (CHOLMOD_REAL, FALSE, FALSE, TRUE, TRUE, L, cm) ;
/* copy MATLAB L into CHOLMOD L */
Lp2 = L->p ;
Li2 = L->i ;
Lx2 = L->x ;
Lnz2 = L->nz ;
lnz = L->nzmax ;
for (j = 0 ; j <= n ; j++)
{
Lp2 [j] = Lp [j] ;
}
for (j = 0 ; j < n ; j++)
{
Lnz2 [j] = Lp [j+1] - Lp [j] ;
}
for (s = 0 ; s < lnz ; s++)
{
Li2 [s] = Li [s] ;
}
for (s = 0 ; s < lnz ; s++)
{
Lx2 [s] = Lx [s] ;
}
/* ---------------------------------------------------------------------- */
/* update/downdate the LDL' factorization */
/* ---------------------------------------------------------------------- */
/* add row */
if (update){
if (!cholmod_l_rowadd (ki, R, L, cm))
{
mexErrMsgTxt ("rowadd failed\n") ;
}
}
/* delete row */
else {
if (!cholmod_l_rowdel (ki, NULL, L, cm))
{
mexErrMsgTxt ("rowdel failed\n") ;
}
}
/* ---------------------------------------------------------------------- */
/* copy the results back to MATLAB */
/* ---------------------------------------------------------------------- */
/* change L back to packed LDL' (it may have become unpacked if the
* sparsity pattern changed). This change takes O(n) time if the pattern
* of L wasn't updated. */
Lsparse = cholmod_l_factor_to_sparse (L, cm) ;
/* return L as a sparse matrix */
pargout [0] = sputil_put_sparse (&Lsparse, cm) ;
/* ---------------------------------------------------------------------- */
/* free workspace and the CHOLMOD L, except for what is copied to MATLAB */
/* ---------------------------------------------------------------------- */
cholmod_l_free_factor (&L, cm) ;
cholmod_l_finish (cm) ;
cholmod_l_print_common (" ", cm) ;
/*
if (cm->malloc_count != 3 + mxIsComplex (pargout[0])) mexErrMsgTxt ("!") ;
*/
}
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
double dummy = 0 ;
cholmod_sparse Amatrix, *A ;
cholmod_common Common, *cm ;
Long result, quick, option, xmatched, pmatched, nzoffdiag, nzdiag ;
/* ---------------------------------------------------------------------- */
/* start CHOLMOD and set parameters */
/* ---------------------------------------------------------------------- */
cm = &Common ;
cholmod_l_start (cm) ;
sputil_config (SPUMONI, cm) ;
/* ---------------------------------------------------------------------- */
/* get inputs */
/* ---------------------------------------------------------------------- */
if (nargin > 2 || nargin < 1 || nargout > 5)
{
mexErrMsgTxt ("usage: [s xmatch pmatch nzoff nzd] = spsym (A,quick)") ;
}
if (!mxIsSparse (pargin [0]))
{
mexErrMsgTxt ("A must be sparse and double") ;
}
/* get sparse matrix A */
A = sputil_get_sparse (pargin [0], &Amatrix, &dummy, 0) ;
/* get the "quick" parameter */
quick = (nargin > 1) ? (mxGetScalar (pargin [1]) != 0) : FALSE ;
if (nargout > 1)
{
option = 2 ;
}
else if (quick)
{
option = 0 ;
}
else
{
option = 1 ;
}
/* ---------------------------------------------------------------------- */
/* determine symmetry */
/* ---------------------------------------------------------------------- */
xmatched = 0 ;
pmatched = 0 ;
nzoffdiag = 0 ;
nzdiag = 0 ;
result = cholmod_l_symmetry (A, option, &xmatched, &pmatched, &nzoffdiag,
&nzdiag, cm) ;
/* ---------------------------------------------------------------------- */
/* return results to MATLAB */
/* ---------------------------------------------------------------------- */
pargout [0] = sputil_put_int (&result, 1, 0) ;
if (nargout > 1) pargout [1] = sputil_put_int (&xmatched, 1, 0) ;
if (nargout > 2) pargout [2] = sputil_put_int (&pmatched, 1, 0) ;
if (nargout > 3) pargout [3] = sputil_put_int (&nzoffdiag, 1, 0) ;
if (nargout > 4) pargout [4] = sputil_put_int (&nzdiag, 1, 0) ;
/* ---------------------------------------------------------------------- */
/* free workspace */
/* ---------------------------------------------------------------------- */
cholmod_l_finish (cm) ;
cholmod_l_print_common (" ", cm) ;
}
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
double dummy = 0, *Px, *Xsetx ;
Long *Lp, *Lnz, *Xp, *Xi, xnz, *Perm, *Lprev, *Lnext, *Xsetp ;
cholmod_sparse *Bset, Bmatrix, *Xset ;
cholmod_dense *Bdense, *X, *Y, *E ;
cholmod_factor *L ;
cholmod_common Common, *cm ;
Long k, j, n, head, tail, xsetlen ;
int sys, kind ;
/* ---------------------------------------------------------------------- */
/* start CHOLMOD and set parameters */
/* ---------------------------------------------------------------------- */
cm = &Common ;
cholmod_l_start (cm) ;
sputil_config (SPUMONI, cm) ;
/* ---------------------------------------------------------------------- */
/* check inputs */
/* ---------------------------------------------------------------------- */
if (nargin != 5 || nargout > 2)
{
mexErrMsgTxt ("usage: [x xset] = lsubsolve (L,kind,P,b,system)") ;
}
n = mxGetN (pargin [0]) ;
if (!mxIsSparse (pargin [0]) || n != mxGetM (pargin [0]))
{
mexErrMsgTxt ("lsubsolve: L must be sparse and square") ;
}
if (mxGetNumberOfElements (pargin [1]) != 1)
{
mexErrMsgTxt ("lsubsolve: kind must be a scalar") ;
}
if (mxIsSparse (pargin [2]) ||
!(mxIsEmpty (pargin [2]) || mxGetNumberOfElements (pargin [2]) == n))
{
mexErrMsgTxt ("lsubsolve: P must be size n, or empty") ;
}
if (mxGetM (pargin [3]) != n || mxGetN (pargin [3]) != 1)
{
mexErrMsgTxt ("lsubsolve: b wrong dimension") ;
}
if (!mxIsSparse (pargin [3]))
{
mexErrMsgTxt ("lxbpattern: b must be sparse") ;
}
if (mxGetNumberOfElements (pargin [4]) != 1)
{
mexErrMsgTxt ("lsubsolve: system must be a scalar") ;
}
/* ---------------------------------------------------------------------- */
/* get the inputs */
/* ---------------------------------------------------------------------- */
kind = (int) sputil_get_integer (pargin [1], FALSE, 0) ;
sys = (int) sputil_get_integer (pargin [4], FALSE, 0) ;
/* ---------------------------------------------------------------------- */
/* get the sparse b */
/* ---------------------------------------------------------------------- */
/* get sparse matrix B (unsymmetric) */
Bset = sputil_get_sparse (pargin [3], &Bmatrix, &dummy, 0) ;
Bdense = cholmod_l_sparse_to_dense (Bset, cm) ;
Bset->x = NULL ;
Bset->z = NULL ;
Bset->xtype = CHOLMOD_PATTERN ;
/* ---------------------------------------------------------------------- */
/* construct a shallow copy of the input sparse matrix L */
/* ---------------------------------------------------------------------- */
/* the construction of the CHOLMOD takes O(n) time and memory */
/* allocate the CHOLMOD symbolic L */
L = cholmod_l_allocate_factor (n, cm) ;
L->ordering = CHOLMOD_NATURAL ;
/* get the MATLAB L */
L->p = mxGetJc (pargin [0]) ;
L->i = mxGetIr (pargin [0]) ;
L->x = mxGetPr (pargin [0]) ;
L->z = mxGetPi (pargin [0]) ;
/* allocate and initialize the rest of L */
L->nz = cholmod_l_malloc (n, sizeof (Long), cm) ;
Lp = L->p ;
Lnz = L->nz ;
for (j = 0 ; j < n ; j++)
{
Lnz [j] = Lp [j+1] - Lp [j] ;
}
/* these pointers are not accessed in cholmod_solve2 */
L->prev = cholmod_l_malloc (n+2, sizeof (Long), cm) ;
L->next = cholmod_l_malloc (n+2, sizeof (Long), cm) ;
Lprev = L->prev ;
Lnext = L->next ;
head = n+1 ;
tail = n ;
Lnext [head] = 0 ;
Lprev [head] = -1 ;
Lnext [tail] = -1 ;
Lprev [tail] = n-1 ;
for (j = 0 ; j < n ; j++)
{
Lnext [j] = j+1 ;
Lprev [j] = j-1 ;
}
Lprev [0] = head ;
L->xtype = (mxIsComplex (pargin [0])) ? CHOLMOD_ZOMPLEX : CHOLMOD_REAL ;
L->nzmax = Lp [n] ;
/* get the permutation */
if (mxIsEmpty (pargin [2]))
{
L->Perm = NULL ;
Perm = NULL ;
}
else
{
L->ordering = CHOLMOD_GIVEN ;
L->Perm = cholmod_l_malloc (n, sizeof (Long), cm) ;
Perm = L->Perm ;
Px = mxGetPr (pargin [2]) ;
for (k = 0 ; k < n ; k++)
{
Perm [k] = ((Long) Px [k]) - 1 ;
}
}
/* set the kind, LL' or LDL' */
L->is_ll = (kind == 0) ;
/*
cholmod_l_print_factor (L, "L", cm) ;
*/
/* ---------------------------------------------------------------------- */
/* solve the system */
/* ---------------------------------------------------------------------- */
X = cholmod_l_zeros (n, 1, L->xtype, cm) ;
Xset = NULL ;
Y = NULL ;
E = NULL ;
cholmod_l_solve2 (sys, L, Bdense, Bset, &X, &Xset, &Y, &E, cm) ;
cholmod_l_free_dense (&Y, cm) ;
cholmod_l_free_dense (&E, cm) ;
/* ---------------------------------------------------------------------- */
/* return result */
/* ---------------------------------------------------------------------- */
pargout [0] = sputil_put_dense (&X, cm) ;
/* fill numerical values of Xset with one's */
Xsetp = Xset->p ;
xsetlen = Xsetp [1] ;
Xset->x = cholmod_l_malloc (xsetlen, sizeof (double), cm) ;
Xsetx = Xset->x ;
for (k = 0 ; k < xsetlen ; k++)
{
Xsetx [k] = 1 ;
}
Xset->xtype = CHOLMOD_REAL ;
pargout [1] = sputil_put_sparse (&Xset, cm) ;
/* ---------------------------------------------------------------------- */
/* free workspace and the CHOLMOD L, except for what is copied to MATLAB */
/* ---------------------------------------------------------------------- */
L->p = NULL ;
L->i = NULL ;
L->x = NULL ;
L->z = NULL ;
cholmod_l_free_factor (&L, cm) ;
cholmod_l_finish (cm) ;
cholmod_l_print_common (" ", cm) ;
}
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
double dummy = 0, beta [2], *px, *C, *Ct, *C2, *fil, *Zt, *zt, done=1.0, *zz, dzero=0.0;
cholmod_sparse Amatrix, *A, *Lsparse ;
cholmod_factor *L ;
cholmod_common Common, *cm ;
Int minor, *It2, *Jt2 ;
mwIndex l, k2, h, k, i, j, ik, *I, *J, *Jt, *It, *I2, *J2, lfi, *w, *w2, *r;
mwSize nnz, nnzlow, m, n;
int nz = 0;
mwSignedIndex one=1, lfi_si;
mxArray *Am, *Bm;
char *uplo="L", *trans="N";
/* ---------------------------------------------------------------------- */
/* Only one input. We have to find first the Cholesky factorization. */
/* start CHOLMOD and set parameters */
/* ---------------------------------------------------------------------- */
if (nargin == 1) {
cm = &Common ;
cholmod_l_start (cm) ;
sputil_config (SPUMONI, cm) ;
/* convert to packed LDL' when done */
cm->final_asis = FALSE ;
cm->final_super = FALSE ;
cm->final_ll = FALSE ;
cm->final_pack = TRUE ;
cm->final_monotonic = TRUE ;
/* since numerically zero entries are NOT dropped from the symbolic
* pattern, we DO need to drop entries that result from supernodal
* amalgamation. */
cm->final_resymbol = TRUE ;
cm->quick_return_if_not_posdef = (nargout < 2) ;
}
/* This will disable the supernodal LL', which will be slow. */
/* cm->supernodal = CHOLMOD_SIMPLICIAL ; */
/* ---------------------------------------------------------------------- */
/* get inputs */
/* ---------------------------------------------------------------------- */
if (nargin > 3)
{
mexErrMsgTxt ("usage: Z = sinv(A), or Z = sinv(LD, 1)") ;
}
n = mxGetM (pargin [0]) ;
m = mxGetM (pargin [0]) ;
if (!mxIsSparse (pargin [0]))
{
mexErrMsgTxt ("A must be sparse") ;
}
if (n != mxGetN (pargin [0]))
{
mexErrMsgTxt ("A must be square") ;
}
/* Only one input. We have to find first the Cholesky factorization. */
if (nargin == 1) {
/* get sparse matrix A, use tril(A) */
A = sputil_get_sparse (pargin [0], &Amatrix, &dummy, -1) ;
A->stype = -1 ; /* use lower part of A */
beta [0] = 0 ;
beta [1] = 0 ;
/* ---------------------------------------------------------------------- */
/* analyze and factorize */
/* ---------------------------------------------------------------------- */
L = cholmod_l_analyze (A, cm) ;
cholmod_l_factorize_p (A, beta, NULL, 0, L, cm) ;
if (cm->status != CHOLMOD_OK)
{
mexErrMsgTxt ("matrix is not positive definite") ;
}
/* ---------------------------------------------------------------------- */
/* convert L to a sparse matrix */
/* ---------------------------------------------------------------------- */
Lsparse = cholmod_l_factor_to_sparse (L, cm) ;
if (Lsparse->xtype == CHOLMOD_COMPLEX)
{
mexErrMsgTxt ("matrix is complex") ;
}
/* ---------------------------------------------------------------------- */
/* Set the sparse Cholesky factorization in Matlab format */
/* ---------------------------------------------------------------------- */
/*Am = sputil_put_sparse (&Lsparse, cm) ;
I = mxGetIr(Am);
J = mxGetJc(Am);
C = mxGetPr(Am);
nnz = mxGetNzmax(Am); */
It2 = Lsparse->i;
Jt2 = Lsparse->p;
Ct = Lsparse->x;
nnz = (mwSize) Lsparse->nzmax;
Am = mxCreateSparse(m, m, nnz, mxREAL) ;
I = mxGetIr(Am);
J = mxGetJc(Am);
C = mxGetPr(Am);
for (j = 0 ; j < n+1 ; j++) J[j] = (mwIndex) Jt2[j];
for ( i = 0 ; i < nnz ; i++) {
I[i] = (mwIndex) It2[i];
C[i] = Ct[i];
}
cholmod_l_free_sparse (&Lsparse, cm) ;
/*FILE *out1 = fopen( "output1.txt", "w" );
if( out1 != NULL )
fprintf( out1, "Hello %d\n", nnz );
fclose (out1);*/
} else {
/* The cholesky factorization is given as an input. */
/* We have to copy it into workspace */
It = mxGetIr(pargin [0]);
Jt = mxGetJc(pargin [0]);
Ct = mxGetPr(pargin [0]);
nnz = mxGetNzmax(pargin [0]);
Am = mxCreateSparse(m, m, nnz, mxREAL) ;
I = mxGetIr(Am);
J = mxGetJc(Am);
C = mxGetPr(Am);
for (j = 0 ; j < n+1 ; j++) J[j] = Jt[j];
for ( i = 0 ; i < nnz ; i++) {
I[i] = It[i];
C[i] = Ct[i];
}
}
/* Evaluate the sparse inverse */
C[nnz-1] = 1.0/C[J[m-1]]; /* set the last element of sparse inverse */
fil = mxCalloc((mwSize)1,sizeof(double));
zt = mxCalloc((mwSize)1,sizeof(double));
Zt = mxCalloc((mwSize)1,sizeof(double));
zz = mxCalloc((mwSize)1,sizeof(double));
for (j=m-2;j!=-1;j--){
lfi = J[j+1]-(J[j]+1);
/* if (lfi > 0) */
if ( J[j+1] > (J[j]+1) )
{
/* printf("lfi = %u \n ", lfi);
printf("lfi*double = %u \n", (mwSize)lfi*sizeof(double));
printf("lfi*lfi*double = %u \n", (mwSize)lfi*(mwSize)lfi*sizeof(double));
printf("\n \n");
*/
fil = mxRealloc(fil,(mwSize)lfi*sizeof(double));
for (i=0;i<lfi;i++) fil[i] = C[J[j]+i+1]; /* take the j'th lower triangular column of the Cholesky */
zt = mxRealloc(zt,(mwSize)lfi*sizeof(double)); /* memory for the sparse inverse elements to be evaluated */
Zt = mxRealloc(Zt,(mwSize)lfi*(mwSize)lfi*sizeof(double)); /* memory for the needed sparse inverse elements */
/* Set the lower triangular for Zt */
k2 = 0;
for (k=J[j]+1;k<J[j+1];k++){
ik = I[k];
h = k2;
for (l=J[ik];l<=J[ik+1];l++){
if (I[l] == I[ J[j]+h+1 ]){
Zt[h+lfi*k2] = C[l];
h++;
}
}
k2++;
}
/* evaluate zt = fil*Zt */
lfi_si = (mwSignedIndex) lfi;
dsymv(uplo, &lfi_si, &done, Zt, &lfi_si, fil, &one, &dzero, zt, &one);
/* Set the evaluated sparse inverse elements, zt, into C */
k=lfi-1;
for (i = J[j+1]-1; i!=J[j] ; i--){
C[i] = -zt[k];
k--;
}
/* evaluate the j'th diagonal of sparse inverse */
dgemv(trans, &one, &lfi_si, &done, fil, &one, zt, &one, &dzero, zz, &one);
C[J[j]] = 1.0/C[J[j]] + zz[0];
}
else
{
/* evaluate the j'th diagonal of sparse inverse */
C[J[j]] = 1.0/C[J[j]];
}
}
/* Free the temporary variables */
mxFree(fil);
mxFree(zt);
mxFree(Zt);
mxFree(zz);
/* ---------------------------------------------------------------------- */
/* Permute the elements according to r(q) = 1:n */
/* Done only if the Cholesky was evaluated here */
/* ---------------------------------------------------------------------- */
if (nargin == 1) {
Bm = mxCreateSparse(m, m, nnz, mxREAL) ;
It = mxGetIr(Bm);
Jt = mxGetJc(Bm);
Ct = mxGetPr(Bm); /* Ct = C(r,r) */
r = (mwIndex *) L->Perm; /* fill reducing ordering */
w = mxCalloc(m,sizeof(mwIndex)); /* column counts of Am */
/* count entries in each column of Bm */
for (j=0; j<m; j++){
k = r ? r[j] : j ; /* column j of Bm is column k of Am */
for (l=J[j] ; l<J[j+1] ; l++){
i = I[l];
ik = r ? r[i] : i ; /* row i of Bm is row ik of Am */
w[ max(ik,k) ]++;
}
}
cumsum2(Jt, w, m);
for (j=0; j<m; j++){
k = r ? r[j] : j ; /* column j of Bm is column k of Am */
for (l=J[j] ; l<J[j+1] ; l++){
i= I[l];
ik = r ? r[i] : i ; /* row i of Bm is row ik of Am */
It [k2 = w[max(ik,k)]++ ] = min(ik,k);
Ct[k2] = C[l];
}
}
mxFree(w);
/* ---------------------------------------------------------------------- */
/* Transpose the permuted (upper triangular) matrix Bm into Am */
/* (this way we get sorted columns) */
/* ---------------------------------------------------------------------- */
w = mxCalloc(m,sizeof(mwIndex));
for (i=0 ; i<Jt[m] ; i++) w[It[i]]++; /* row counts of Bm */
cumsum2(J, w, m); /* row pointers */
for (j=0 ; j<m ; j++){
for (i=Jt[j] ; i<Jt[j+1] ; i++){
I[ l=w[ It[i] ]++ ] = j;
C[l] = Ct[i];
}
}
mxFree(w);
mxDestroyArray(Bm);
}
/* ---------------------------------------------------------------------- */
/* Fill the upper triangle of the sparse inverse */
/* ---------------------------------------------------------------------- */
w = mxCalloc(m,sizeof(mwIndex)); /* workspace */
w2 = mxCalloc(m,sizeof(mwIndex)); /* workspace */
for (k=0;k<J[m];k++) w[I[k]]++; /* row counts of the lower triangular */
for (k=0;k<m;k++) w2[k] = w[k] + J[k+1] - J[k] - 1; /* column counts of the sparse inverse */
nnz = (mwSize)2*nnz - m; /* The number of nonzeros in Z */
pargout[0] = mxCreateSparse(m,m,nnz,mxREAL); /* The sparse matrix */
It = mxGetIr(pargout[0]);
Jt = mxGetJc(pargout[0]);
Ct = mxGetPr(pargout[0]);
cumsum2(Jt, w2, m); /* column starting points */
for (j = 0 ; j < m ; j++){ /* fill the upper triangular */
for (k = J[j] ; k < J[j+1] ; k++){
It[l = w2[ I[k]]++] = j ; /* place C(i,j) as entry Ct(j,i) */
if (Ct) Ct[l] = C[k] ;
}
}
for (j = 0 ; j < m ; j++){ /* fill the lower triangular */
for (k = J[j]+1 ; k < J[j+1] ; k++){
It[l = w2[j]++] = I[k] ; /* place C(j,i) as entry Ct(j,i) */
if (Ct) Ct[l] = C[k] ;
}
}
mxFree(w2);
mxFree(w);
/* ---------------------------------------------------------------------- */
/* return to MATLAB */
/* ---------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
/* free workspace and the CHOLMOD L, except for what is copied to MATLAB */
/* ---------------------------------------------------------------------- */
if (nargin == 1) {
cholmod_l_free_factor (&L, cm) ;
cholmod_l_finish (cm) ;
cholmod_l_print_common (" ", cm) ;
}
mxDestroyArray(Am);
}
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
double dummy = 0, one [2] = {1,0}, zero [2] = {0,0} ;
cholmod_sparse *S, Smatrix ;
cholmod_dense *F, Fmatrix, *C ;
cholmod_common Common, *cm ;
Long srow, scol, frow, fcol, crow, transpose ;
/* ---------------------------------------------------------------------- */
/* start CHOLMOD and set parameters */
/* ---------------------------------------------------------------------- */
cm = &Common ;
cholmod_l_start (cm) ;
sputil_config (SPUMONI, cm) ;
/* ---------------------------------------------------------------------- */
/* check inputs */
/* ---------------------------------------------------------------------- */
if (nargout > 1 || nargin < 2 || nargin > 3)
{
mexErrMsgTxt ("Usage: C = sdmult (S,F,transpose)") ;
}
srow = mxGetM (pargin [0]) ;
scol = mxGetN (pargin [0]) ;
frow = mxGetM (pargin [1]) ;
fcol = mxGetN (pargin [1]) ;
transpose = !((nargin == 2) || (mxGetScalar (pargin [2]) == 0)) ;
if (frow != (transpose ? srow : scol))
{
mexErrMsgTxt ("invalid inner dimensions") ;
}
if (!mxIsSparse (pargin [0]) || mxIsSparse (pargin [1]))
{
mexErrMsgTxt ("sdmult (S,F): S must be sparse, F must be full") ;
}
/* ---------------------------------------------------------------------- */
/* get S and F */
/* ---------------------------------------------------------------------- */
S = sputil_get_sparse (pargin [0], &Smatrix, &dummy, 0) ;
F = sputil_get_dense (pargin [1], &Fmatrix, &dummy) ;
/* ---------------------------------------------------------------------- */
/* C = S*F or S'*F */
/* ---------------------------------------------------------------------- */
crow = transpose ? scol : srow ;
C = cholmod_l_allocate_dense (crow, fcol, crow, F->xtype, cm) ;
cholmod_l_sdmult (S, transpose, one, zero, F, C, cm) ;
pargout [0] = sputil_put_dense (&C, cm) ;
/* ---------------------------------------------------------------------- */
/* free workspace and the CHOLMOD L, except for what is copied to MATLAB */
/* ---------------------------------------------------------------------- */
cholmod_l_finish (cm) ;
cholmod_l_print_common (" ", cm) ;
/*
if (cm->malloc_count != (mxIsComplex (pargout [0]) + 1)) mexErrMsgTxt ("!");
*/
}
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
double dummy = 0 ;
double *Lx, *Lx2 ;
Long *Li, *Lp, *Li2, *Lp2, *Lnz2, *ColCount ;
cholmod_sparse Cmatrix, *C, *Lsparse ;
cholmod_factor *L ;
cholmod_common Common, *cm ;
Long j, k, s, rowadd, n, lnz, ok ;
/* ---------------------------------------------------------------------- */
/* start CHOLMOD and set parameters */
/* ---------------------------------------------------------------------- */
cm = &Common ;
cholmod_l_start (cm) ;
sputil_config (SPUMONI, cm) ;
/* ---------------------------------------------------------------------- */
/* check inputs */
/* ---------------------------------------------------------------------- */
if (nargout > 1 || nargin < 2 || nargin > 3)
{
mexErrMsgTxt ("Usage: LD = ldlrowmod (LD,k,C) or ldlrowmod (LD,k)") ;
}
n = mxGetN (pargin [0]) ;
k = (Long) mxGetScalar (pargin [1]) ;
k = k - 1 ; /* change from 1-based to 0-based */
if (!mxIsSparse (pargin [0])
|| n != mxGetM (pargin [0])
|| mxIsComplex (pargin [0]))
{
mexErrMsgTxt ("ldlrowmod: L must be real, square, and sparse") ;
}
/* ---------------------------------------------------------------------- */
/* determine if we're doing an rowadd or rowdel */
/* ---------------------------------------------------------------------- */
rowadd = (nargin > 2) ;
if (rowadd)
{
if (!mxIsSparse (pargin [2])
|| n != mxGetM (pargin [2])
|| 1 != mxGetN (pargin [2])
|| mxIsComplex (pargin [2]))
{
mexErrMsgTxt ("ldlrowmod: C must be a real sparse vector, "
"with the same number of rows as LD") ;
}
}
/* ---------------------------------------------------------------------- */
/* get C: sparse vector of incoming/outgoing column */
/* ---------------------------------------------------------------------- */
C = (rowadd) ? sputil_get_sparse (pargin [2], &Cmatrix, &dummy, 0) : NULL ;
/* ---------------------------------------------------------------------- */
/* construct a copy of the input sparse matrix L */
/* ---------------------------------------------------------------------- */
/* get the MATLAB L */
Lp = (Long *) mxGetJc (pargin [0]) ;
Li = (Long *) mxGetIr (pargin [0]) ;
Lx = mxGetPr (pargin [0]) ;
/* allocate the CHOLMOD symbolic L */
L = cholmod_l_allocate_factor (n, cm) ;
L->ordering = CHOLMOD_NATURAL ;
ColCount = L->ColCount ;
for (j = 0 ; j < n ; j++)
{
ColCount [j] = Lp [j+1] - Lp [j] ;
}
/* allocate space for a CHOLMOD LDL' packed factor */
cholmod_l_change_factor (CHOLMOD_REAL, FALSE, FALSE, TRUE, TRUE, L, cm) ;
/* copy MATLAB L into CHOLMOD L */
Lp2 = L->p ;
Li2 = L->i ;
Lx2 = L->x ;
Lnz2 = L->nz ;
lnz = L->nzmax ;
for (j = 0 ; j <= n ; j++)
{
Lp2 [j] = Lp [j] ;
}
for (j = 0 ; j < n ; j++)
{
Lnz2 [j] = Lp [j+1] - Lp [j] ;
}
for (s = 0 ; s < lnz ; s++)
{
Li2 [s] = Li [s] ;
}
for (s = 0 ; s < lnz ; s++)
{
Lx2 [s] = Lx [s] ;
}
/* ---------------------------------------------------------------------- */
/* rowadd/rowdel the LDL' factorization */
/* ---------------------------------------------------------------------- */
if (rowadd)
{
ok = cholmod_l_rowadd (k, C, L, cm) ;
}
else
{
ok = cholmod_l_rowdel (k, NULL, L, cm) ;
}
if (!ok) mexErrMsgTxt ("ldlrowmod failed\n") ;
/* ---------------------------------------------------------------------- */
/* copy the results back to MATLAB */
/* ---------------------------------------------------------------------- */
/* change L back to packed LDL' (it may have become unpacked if the
* sparsity pattern changed). This change takes O(n) time if the pattern
* of L wasn't updated. */
Lsparse = cholmod_l_factor_to_sparse (L, cm) ;
/* return L as a sparse matrix */
pargout [0] = sputil_put_sparse (&Lsparse, cm) ;
/* ---------------------------------------------------------------------- */
/* free workspace and the CHOLMOD L, except for what is copied to MATLAB */
/* ---------------------------------------------------------------------- */
cholmod_l_free_factor (&L, cm) ;
cholmod_l_finish (cm) ;
cholmod_l_print_common (" ", cm) ;
/*
if (cm->malloc_count != 3 + mxIsComplex (pargout[0])) mexErrMsgTxt ("!") ;
*/
}
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
double dummy = 0 ;
cholmod_sparse Amatrix, Zmatrix, *A, *Z ;
cholmod_dense Xmatrix, *X ;
cholmod_common Common, *cm ;
Int arg_z, arg_comments, sym ;
char filename [MAXLEN], comments [MAXLEN] ;
/* ---------------------------------------------------------------------- */
/* start CHOLMOD and set parameters */
/* ---------------------------------------------------------------------- */
cm = &Common ;
cholmod_l_start (cm) ;
sputil_config (SPUMONI, cm) ;
/* ---------------------------------------------------------------------- */
/* check inputs */
/* ---------------------------------------------------------------------- */
if (nargin < 2 || nargin > 4 || nargout > 1)
{
mexErrMsgTxt ("Usage: mwrite (filename, A, Z, comments_filename)") ;
}
/* ---------------------------------------------------------------------- */
/* get the output filename */
/* ---------------------------------------------------------------------- */
if (!mxIsChar (pargin [0]))
{
mexErrMsgTxt ("first parameter must be a filename") ;
}
mxGetString (pargin [0], filename, MAXLEN) ;
/* ---------------------------------------------------------------------- */
/* get the A matrix (sparse or dense) */
/* ---------------------------------------------------------------------- */
if (mxIsSparse (pargin [1]))
{
A = sputil_get_sparse (pargin [1], &Amatrix, &dummy, 0) ;
X = NULL ;
}
else
{
X = sputil_get_dense (pargin [1], &Xmatrix, &dummy) ;
A = NULL ;
}
/* ---------------------------------------------------------------------- */
/* determine if the Z matrix and comments_file are present */
/* ---------------------------------------------------------------------- */
if (nargin == 3)
{
if (mxIsChar (pargin [2]))
{
/* mwrite (file, A, comments) */
arg_z = -1 ;
arg_comments = 2 ;
}
else
{
/* mwrite (file, A, Z). Ignore Z if A is full */
arg_z = (A == NULL) ? -1 : 2 ;
arg_comments = -1 ;
}
}
else if (nargin == 4)
{
/* mwrite (file, A, Z, comments). Ignore Z is A is full */
arg_z = (A == NULL) ? -1 : 2 ;
arg_comments = 3 ;
}
else
{
arg_z = -1 ;
arg_comments = -1 ;
}
/* ---------------------------------------------------------------------- */
/* get the Z matrix */
/* ---------------------------------------------------------------------- */
if (arg_z == -1 ||
mxGetM (pargin [arg_z]) == 0 || mxGetN (pargin [arg_z]) == 0)
{
/* A is dense, Z is not present, or Z is empty. Ignore Z. */
Z = NULL ;
}
else
{
/* A is sparse and Z is present and not empty */
if (!mxIsSparse (pargin [arg_z]))
{
mexErrMsgTxt ("Z must be sparse") ;
}
Z = sputil_get_sparse (pargin [arg_z], &Zmatrix, &dummy, 0) ;
}
/* ---------------------------------------------------------------------- */
/* get the comments filename */
/* ---------------------------------------------------------------------- */
comments [0] = '\0' ;
if (arg_comments != -1)
{
if (!mxIsChar (pargin [arg_comments]))
{
mexErrMsgTxt ("comments filename must be a string") ;
}
mxGetString (pargin [arg_comments], comments, MAXLEN) ;
}
/* ---------------------------------------------------------------------- */
/* write the matrix to the file */
/* ---------------------------------------------------------------------- */
sputil_file = fopen (filename, "w") ;
if (sputil_file == NULL)
{
mexErrMsgTxt ("error opening file") ;
}
if (A != NULL)
{
sym = cholmod_l_write_sparse (sputil_file, A, Z, comments, cm) ;
}
else
{
sym = cholmod_l_write_dense (sputil_file, X, comments, cm) ;
}
fclose (sputil_file) ;
sputil_file = NULL ;
if (sym < 0)
{
mexErrMsgTxt ("mwrite failed") ;
}
/* ---------------------------------------------------------------------- */
/* free workspace and return symmetry */
/* ---------------------------------------------------------------------- */
pargout [0] = sputil_put_int (&sym, 1, 0) ;
cholmod_l_finish (cm) ;
cholmod_l_print_common (" ", cm) ;
}
void mexFunction(
int nlhs, /* number of expected outputs */
mxArray *plhs[], /* array of pointers to output arguments */
int nrhs, /* number of inputs */
const mxArray *prhs[] /* array of pointers to input arguments */
)
{
size_t k,k1;
const mxArray *arg;
mxArray *HDR;
HDRTYPE *hdr;
CHANNEL_TYPE* cp;
size_t count;
time_t T0;
char *FileName=NULL;
int status;
int CHAN = 0;
int TARGETSEGMENT = 1;
double *ChanList=NULL;
int NS = -1;
char FlagOverflowDetection = 1, FlagUCAL = 0;
int argSweepSel = -1;
#ifdef CHOLMOD_H
cholmod_sparse RR,*rr=NULL;
double dummy;
#endif
// ToDO: output single data
// mxClassId FlagMXclass=mxDOUBLE_CLASS;
if (nrhs<1) {
#ifdef mexSOPEN
mexPrintf(" Usage of mexSOPEN:\n");
mexPrintf("\tHDR = mexSOPEN(f)\n");
mexPrintf(" Input:\n\tf\tfilename\n");
mexPrintf(" Output:\n\tHDR\theader structure\n\n");
#else
mexPrintf(" Usage of mexSLOAD:\n");
mexPrintf("\t[s,HDR]=mexSLOAD(f)\n");
mexPrintf("\t[s,HDR]=mexSLOAD(f,chan)\n\t\tchan must be sorted in ascending order\n");
mexPrintf("\t[s,HDR]=mexSLOAD(f,ReRef)\n\t\treref is a (sparse) matrix for rerefencing\n");
mexPrintf("\t[s,HDR]=mexSLOAD(f,chan,'...')\n");
mexPrintf("\t[s,HDR]=mexSLOAD(f,chan,'OVERFLOWDETECTION:ON')\n");
mexPrintf("\t[s,HDR]=mexSLOAD(f,chan,'OVERFLOWDETECTION:OFF')\n");
mexPrintf("\t[s,HDR]=mexSLOAD(f,chan,'UCAL:ON')\n");
mexPrintf("\t[s,HDR]=mexSLOAD(f,chan,'UCAL:OFF')\n");
mexPrintf("\t[s,HDR]=mexSLOAD(f,chan,'OUTPUT:SINGLE')\n");
mexPrintf("\t[s,HDR]=mexSLOAD(f,chan,'TARGETSEGMENT:<N>')\n");
mexPrintf("\t[s,HDR]=mexSLOAD(f,chan,'SWEEP',[NE, NG, NS])\n");
mexPrintf(" Input:\n\tf\tfilename\n");
mexPrintf("\tchan\tlist of selected channels; 0=all channels [default]\n");
mexPrintf("\tUCAL\tON: do not calibrate data; default=OFF\n");
// mexPrintf("\tOUTPUT\tSINGLE: single precision; default='double'\n");
mexPrintf("\tOVERFLOWDETECTION\tdefault = ON\n\t\tON: values outside dynamic range are not-a-number (NaN)\n");
mexPrintf("\tTARGETSEGMENT:<N>\n\t\tselect segment <N> in multisegment files (like Nihon-Khoden), default=1\n\t\tIt has no effect for other data formats.\n");
mexPrintf("\t[NE, NG, NS] are the number of the experiment, the series and the sweep, resp. for sweep selection in HEKA/PatchMaster files. (0 indicates all)\n");
mexPrintf("\t\t examples: [1,2,3] the 3rd sweep from the 2nd series of experiment 1; [1,3,0] selects all sweeps from experiment=1, series=3. \n\n");
mexPrintf(" Output:\n\ts\tsignal data, each column is one channel\n");
mexPrintf("\tHDR\theader structure\n\n");
#endif
return;
}
/*
improve checks for input arguments
*/
/* process input arguments */
for (k = 0; k < nrhs; k++) {
arg = prhs[k];
if (mxIsEmpty(arg) && (k>0)) {
#ifdef DEBUG
mexPrintf("arg[%i] Empty\n",k);
#endif
}
else if ((k==0) && mxIsCell(arg) && mxGetNumberOfElements(arg)==1 && mxGetCell(arg,0) && mxIsChar(mxGetCell(arg,0))) {
FileName = mxArrayToString(mxGetCell(arg,0));
#ifdef DEBUG
mexPrintf("arg[%i] IsCell\n",k);
#endif
}
else if ((k==0) && mxIsStruct(arg)) {
FileName = mxArrayToString(mxGetField(prhs[k],0,"FileName"));
#ifdef DEBUG
mexPrintf("arg[%i] IsStruct\n",k);
#endif
}
#ifdef CHOLMOD_H
else if ((k==1) && mxIsSparse(arg)) {
rr = sputil_get_sparse(arg,&RR,&dummy,0);
}
#endif
else if ((k==1) && mxIsNumeric(arg)) {
#ifdef DEBUG
mexPrintf("arg[%i] IsNumeric\n",k);
#endif
ChanList = (double*)mxGetData(prhs[k]);
NS = mxGetNumberOfElements(prhs[k]);
}
else if (mxIsChar(arg)) {
#ifdef DEBUG
mexPrintf("arg[%i]=%s \n",k,mxArrayToString(prhs[k]));
#endif
if (k==0)
FileName = mxArrayToString(prhs[k]);
else if (!strcmp(mxArrayToString(prhs[k]), "CNT32"))
; // obsolete - supported for backwards compatibility
else if (!strcmp(mxArrayToString(prhs[k]), "OVERFLOWDETECTION:ON"))
FlagOverflowDetection = 1;
else if (!strcmp(mxArrayToString(prhs[k]), "OVERFLOWDETECTION:OFF"))
FlagOverflowDetection = 0;
else if (!strcmp(mxArrayToString(prhs[k]), "UCAL:ON"))
FlagUCAL = 1;
else if (!strcmp(mxArrayToString(prhs[k]), "UCAL:OFF"))
FlagUCAL = 0;
// else if (!strcmp(mxArrayToString(prhs[k]),"OUTPUT:SINGLE"))
// FlagMXclass = mxSINGLE_CLASS;
else if (!strncmp(mxArrayToString(prhs[k]),"TARGETSEGMENT:",14))
TARGETSEGMENT = atoi(mxArrayToString(prhs[k])+14);
else if (!strcasecmp(mxArrayToString(prhs[k]), "SWEEP") && (prhs[k+1] != NULL) && mxIsNumeric(prhs[k+1]))
argSweepSel = ++k;
}
else {
#ifndef mexSOPEN
mexPrintf("mexSLOAD: argument #%i is invalid.",k+1);
mexErrMsgTxt("mexSLOAD failes because of unknown parameter\n");
#else
mexPrintf("mexSOPEN: argument #%i is invalid.",k+1);
mexErrMsgTxt("mexSOPEN fails because of unknown parameter\n");
#endif
}
}
if (VERBOSE_LEVEL>7)
mexPrintf("110: input arguments checked\n");
hdr = constructHDR(0,0);
#ifdef __LIBBIOSIG2_H__
unsigned flags = (!!FlagOverflowDetection)*BIOSIG_FLAG_OVERFLOWDETECTION + (!!FlagUCAL)*BIOSIG_FLAG_UCAL;
#ifdef CHOLMOD_H
flags += (rr!=NULL)*BIOSIG_FLAG_ROW_BASED_CHANNELS;
#else
biosig_reset_flag(hdr, BIOSIG_FLAG_ROW_BASED_CHANNELS);
#endif
biosig_set_flag(hdr, flags);
biosig_set_targetsegment(hdr, TARGETSEGMENT);
// sweep selection for Heka format
if (argSweepSel>0) {
double *SZ = (double*) mxGetData(prhs[argSweepSel]);
k = 0;
while (k < mxGetNumberOfElements(prhs[argSweepSel]) && k < 5) {
biosig_set_segment_selection(hdr, k+1, (uint32_t)SZ[k]);
k++;
}
}
#else //__LIBBIOSIG2_H__
hdr->FLAG.OVERFLOWDETECTION = FlagOverflowDetection;
hdr->FLAG.UCAL = FlagUCAL;
#ifdef CHOLMOD_H
hdr->FLAG.ROW_BASED_CHANNELS = (rr!=NULL);
#else
hdr->FLAG.ROW_BASED_CHANNELS = 0;
#endif
hdr->FLAG.TARGETSEGMENT = TARGETSEGMENT;
// sweep selection for Heka format
if (argSweepSel>0) {
double *SZ = (double*) mxGetData(prhs[argSweepSel]);
k = 0;
while (k < mxGetNumberOfElements(prhs[argSweepSel]) && k < 5) {
hdr->AS.SegSel[k] = (uint32_t)SZ[k];
k++;
}
}
#endif // __LIBBIOSIG2_H__ : TODO: below, nothing is converted to level-2 interface, yet
if (VERBOSE_LEVEL>7)
mexPrintf("120: going to sopen\n");
hdr = sopen(FileName, "r", hdr);
/*
#ifdef WITH_PDP
if (hdr->AS.B4C_ERRNUM) {
hdr->AS.B4C_ERRNUM = 0;
sopen_pdp_read(hdr);
}
#endif
*/
if (VERBOSE_LEVEL>7)
mexPrintf("121: sopen done\n");
if ((status=serror2(hdr))) {
const char* fields[]={"TYPE","VERSION","FileName","FLAG","ErrNum","ErrMsg"};
HDR = mxCreateStructMatrix(1, 1, 6, fields);
#ifdef __LIBBIOSIG2_H__
mxSetField(HDR,0,"FileName",mxCreateString(biosig_get_filename(hdr)));
const char *FileTypeString = GetFileTypeString(biosig_get_filetype(hdr));
mxSetField(HDR,0,"VERSION",mxCreateDoubleScalar(biosig_get_version(hdr)));
#else
mxSetField(HDR,0,"FileName",mxCreateString(hdr->FileName));
const char *FileTypeString = GetFileTypeString(hdr->TYPE);
mxSetField(HDR,0,"VERSION",mxCreateDoubleScalar(hdr->VERSION));
#endif
mxArray *errnum = mxCreateNumericMatrix(1,1,mxUINT8_CLASS,mxREAL);
*(uint8_t*)mxGetData(errnum) = (uint8_t)status;
mxSetField(HDR,0,"ErrNum",errnum);
#ifdef HAVE_OCTAVE
// handle bug in octave: mxCreateString(NULL) causes segmentation fault
// Octave 3.2.3 causes a seg-fault in mxCreateString(NULL)
if (FileTypeString) FileTypeString="\0";
#endif
mxSetField(HDR,0,"TYPE",mxCreateString(FileTypeString));
char *msg = (char*)malloc(72+23+strlen(FileName)); // 72: max length of constant text, 23: max length of GetFileTypeString()
if (msg == NULL)
mxSetField(HDR,0,"ErrMsg",mxCreateString("Error mexSLOAD: Cannot open file\n"));
else {
if (status==B4C_CANNOT_OPEN_FILE)
sprintf(msg,"Error mexSLOAD: file %s not found.\n",FileName); /* Flawfinder: ignore *** sufficient memory is allocated above */
else if (status==B4C_FORMAT_UNKNOWN)
sprintf(msg,"Error mexSLOAD: Cannot open file %s - format %s not known.\n",FileName,FileTypeString); /* Flawfinder: ignore *** sufficient memory is allocated above */
else if (status==B4C_FORMAT_UNSUPPORTED)
sprintf(msg,"Error mexSLOAD: Cannot open file %s - format %s not supported [%s].\n", FileName, FileTypeString, hdr->AS.B4C_ERRMSG); /* Flawfinder: ignore *** sufficient memory is allocated above */
else
sprintf(msg,"Error %i mexSLOAD: Cannot open file %s - format %s not supported [%s].\n", status, FileName, FileTypeString, hdr->AS.B4C_ERRMSG); /* Flawfinder: ignore *** sufficient memory is allocated above */
mxSetField(HDR,0,"ErrMsg",mxCreateString(msg));
free(msg);
}
if (VERBOSE_LEVEL>7)
mexPrintf("737: abort mexSLOAD - sopen failed\n");
destructHDR(hdr);
if (VERBOSE_LEVEL>7)
mexPrintf("757: abort mexSLOAD - sopen failed\n");
#ifdef mexSOPEN
plhs[0] = HDR;
#else
plhs[0] = mxCreateDoubleMatrix(0,0, mxREAL);
plhs[1] = HDR;
#endif
if (VERBOSE_LEVEL>7)
mexPrintf("777: abort mexSLOAD - sopen failed\n");
return;
}
#ifdef CHOLMOD_H
RerefCHANNEL(hdr,rr,2);
#endif
if (hdr->FLAG.OVERFLOWDETECTION != FlagOverflowDetection)
mexPrintf("Warning mexSLOAD: Overflowdetection not supported in file %s\n",hdr->FileName);
if (hdr->FLAG.UCAL != FlagUCAL)
mexPrintf("Warning mexSLOAD: Flag UCAL is %i instead of %i (%s)\n",hdr->FLAG.UCAL,FlagUCAL,hdr->FileName);
if (VERBOSE_LEVEL>7)
fprintf(stderr,"[112] SOPEN-R finished NS=%i %i\n",hdr->NS,NS);
// convert2to4_eventtable(hdr);
#ifdef CHOLMOD_H
if (hdr->Calib != NULL) {
NS = hdr->Calib->ncol;
}
else
#endif
if ((NS<0) || ((NS==1) && (ChanList[0] == 0.0))) { // all channels
for (k=0, NS=0; k<hdr->NS; ++k) {
if (hdr->CHANNEL[k].OnOff) NS++;
}
}
else {
for (k=0; k<hdr->NS; ++k)
hdr->CHANNEL[k].OnOff = 0; // reset
for (k=0; k<NS; ++k) {
int ch = (int)ChanList[k];
if ((ch < 1) || (ch > hdr->NS))
mexPrintf("Invalid channel number CHAN(%i) = %i!\n",k+1,ch);
else
hdr->CHANNEL[ch-1].OnOff = 1; // set
}
}
if (VERBOSE_LEVEL>7)
fprintf(stderr,"[113] NS=%i %i\n",hdr->NS,NS);
#ifndef mexSOPEN
if (hdr->FLAG.ROW_BASED_CHANNELS)
plhs[0] = mxCreateDoubleMatrix(NS, hdr->NRec*hdr->SPR, mxREAL);
else
plhs[0] = mxCreateDoubleMatrix(hdr->NRec*hdr->SPR, NS, mxREAL);
count = sread(mxGetPr(plhs[0]), 0, hdr->NRec, hdr);
hdr->NRec = count;
#endif
sclose(hdr);
#ifdef CHOLMOD_H
if (hdr->Calib && hdr->rerefCHANNEL) {
hdr->NS = hdr->Calib->ncol;
free(hdr->CHANNEL);
hdr->CHANNEL = hdr->rerefCHANNEL;
hdr->rerefCHANNEL = NULL;
hdr->Calib = NULL;
}
#endif
if ((status=serror2(hdr))) return;
if (VERBOSE_LEVEL>7)
fprintf(stderr,"\n[129] SREAD/SCLOSE on %s successful [%i,%i] [%i,%i] %i.\n",hdr->FileName,(int)hdr->data.size[0],(int)hdr->data.size[1],(int)hdr->NRec,(int)count,(int)NS);
// hdr2ascii(hdr,stderr,4);
#ifndef mexSOPEN
if (nlhs>1) {
#endif
char* mexFileName = (char*)mxMalloc(strlen(hdr->FileName)+1);
mxArray *tmp, *tmp2, *Patient, *Manufacturer, *ID, *EVENT, *Filter, *Flag, *FileType;
uint16_t numfields;
const char *fnames[] = {"TYPE","VERSION","FileName","T0","tzmin","FILE","Patient",\
"HeadLen","NS","SPR","NRec","SampleRate", "FLAG", \
"EVENT","Label","LeadIdCode","PhysDimCode","PhysDim","Filter",\
"PhysMax","PhysMin","DigMax","DigMin","Transducer","Cal","Off","GDFTYP","TOffset",\
"LowPass","HighPass","Notch","ELEC","Impedance","fZ","AS","Dur","REC","Manufacturer",NULL};
for (numfields=0; fnames[numfields++] != NULL; );
HDR = mxCreateStructMatrix(1, 1, --numfields, fnames);
mxSetField(HDR,0,"TYPE",mxCreateString(GetFileTypeString(hdr->TYPE)));
mxSetField(HDR,0,"HeadLen",mxCreateDoubleScalar(hdr->HeadLen));
mxSetField(HDR,0,"VERSION",mxCreateDoubleScalar(hdr->VERSION));
mxSetField(HDR,0,"NS",mxCreateDoubleScalar(NS));
mxSetField(HDR,0,"SPR",mxCreateDoubleScalar(hdr->SPR));
mxSetField(HDR,0,"NRec",mxCreateDoubleScalar(hdr->NRec));
mxSetField(HDR,0,"SampleRate",mxCreateDoubleScalar(hdr->SampleRate));
mxSetField(HDR,0,"Dur",mxCreateDoubleScalar(hdr->SPR/hdr->SampleRate));
mxSetField(HDR,0,"FileName",mxCreateString(hdr->FileName));
mxSetField(HDR,0,"T0",mxCreateDoubleScalar(ldexp(hdr->T0,-32)));
mxSetField(HDR,0,"tzmin",mxCreateDoubleScalar(hdr->tzmin));
/* Channel information */
#ifdef CHOLMOD_H
/*
if (hdr->Calib == NULL) { // is refering to &RR, do not destroy
mxArray *Calib = mxCreateDoubleMatrix(hdr->Calib->nrow, hdr->Calib->ncol, mxREAL);
}
*/
#endif
mxArray *LeadIdCode = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *PhysDimCode = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *GDFTYP = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *PhysMax = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *PhysMin = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *DigMax = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *DigMin = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *Cal = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *Off = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *Toffset = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *ELEC_POS = mxCreateDoubleMatrix(NS,3, mxREAL);
/*
mxArray *ELEC_Orient = mxCreateDoubleMatrix(NS,3, mxREAL);
mxArray *ELEC_Area = mxCreateDoubleMatrix(NS,1, mxREAL);
*/
mxArray *LowPass = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *HighPass = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *Notch = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *Impedance = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *fZ = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *SPR = mxCreateDoubleMatrix(1,NS, mxREAL);
mxArray *Label = mxCreateCellMatrix(NS,1);
mxArray *Transducer = mxCreateCellMatrix(NS,1);
mxArray *PhysDim1 = mxCreateCellMatrix(NS,1);
for (k=0,k1=0; k1<NS; ++k)
if (hdr->CHANNEL[k].OnOff) {
*(mxGetPr(LeadIdCode)+k1) = (double)hdr->CHANNEL[k].LeadIdCode;
*(mxGetPr(PhysDimCode)+k1) = (double)hdr->CHANNEL[k].PhysDimCode;
*(mxGetPr(GDFTYP)+k1) = (double)hdr->CHANNEL[k].GDFTYP;
*(mxGetPr(PhysMax)+k1) = (double)hdr->CHANNEL[k].PhysMax;
*(mxGetPr(PhysMin)+k1) = (double)hdr->CHANNEL[k].PhysMin;
*(mxGetPr(DigMax)+k1) = (double)hdr->CHANNEL[k].DigMax;
*(mxGetPr(DigMin)+k1) = (double)hdr->CHANNEL[k].DigMin;
*(mxGetPr(Toffset)+k1) = (double)hdr->CHANNEL[k].TOffset;
*(mxGetPr(Cal)+k1) = (double)hdr->CHANNEL[k].Cal;
*(mxGetPr(Off)+k1) = (double)hdr->CHANNEL[k].Off;
*(mxGetPr(SPR)+k1) = (double)hdr->CHANNEL[k].SPR;
*(mxGetPr(LowPass)+k1) = (double)hdr->CHANNEL[k].LowPass;
*(mxGetPr(HighPass)+k1) = (double)hdr->CHANNEL[k].HighPass;
*(mxGetPr(Notch)+k1) = (double)hdr->CHANNEL[k].Notch;
*(mxGetPr(Impedance)+k1) = (double)hdr->CHANNEL[k].Impedance;
*(mxGetPr(fZ)+k1) = (double)hdr->CHANNEL[k].fZ;
*(mxGetPr(ELEC_POS)+k1) = (double)hdr->CHANNEL[k].XYZ[0];
*(mxGetPr(ELEC_POS)+k1+NS) = (double)hdr->CHANNEL[k].XYZ[1];
*(mxGetPr(ELEC_POS)+k1+NS*2) = (double)hdr->CHANNEL[k].XYZ[2];
/*
*(mxGetPr(ELEC_Orient)+k1) = (double)hdr->CHANNEL[k].Orientation[0];
*(mxGetPr(ELEC_Orient)+k1+NS) = (double)hdr->CHANNEL[k].Orientation[1];
*(mxGetPr(ELEC_Orient)+k1+NS*2) = (double)hdr->CHANNEL[k].Orientation[2];
*(mxGetPr(ELEC_Area)+k1) = (double)hdr->CHANNEL[k].Area;
*/
mxSetCell(Label,k1,mxCreateString(hdr->CHANNEL[k].Label));
mxSetCell(Transducer,k1,mxCreateString(hdr->CHANNEL[k].Transducer));
mxSetCell(PhysDim1,k1,mxCreateString(PhysDim3(hdr->CHANNEL[k].PhysDimCode)));
k1++;
}
mxSetField(HDR,0,"LeadIdCode",LeadIdCode);
mxSetField(HDR,0,"PhysDimCode",PhysDimCode);
mxSetField(HDR,0,"GDFTYP",GDFTYP);
mxSetField(HDR,0,"PhysMax",PhysMax);
mxSetField(HDR,0,"PhysMin",PhysMin);
mxSetField(HDR,0,"DigMax",DigMax);
mxSetField(HDR,0,"DigMin",DigMin);
mxSetField(HDR,0,"TOffset",Toffset);
mxSetField(HDR,0,"Cal",Cal);
mxSetField(HDR,0,"Off",Off);
mxSetField(HDR,0,"Impedance",Impedance);
mxSetField(HDR,0,"fZ",fZ);
mxSetField(HDR,0,"Off",Off);
mxSetField(HDR,0,"PhysDim",PhysDim1);
mxSetField(HDR,0,"Transducer",Transducer);
mxSetField(HDR,0,"Label",Label);
const char* field[] = {"XYZ","Orientation","Area","GND","REF",NULL};
for (numfields=0; field[numfields++] != 0; );
tmp = mxCreateStructMatrix(1, 1, --numfields, field);
mxSetField(tmp,0,"XYZ",ELEC_POS);
/*
mxSetField(tmp,0,"Orientation",ELEC_Orient);
mxSetField(tmp,0,"Area",ELEC_Area);
*/
mxSetField(HDR,0,"ELEC",tmp);
const char* field2[] = {"SPR",NULL};
for (numfields=0; field2[numfields++] != 0; );
tmp2 = mxCreateStructMatrix(1, 1, --numfields, field2);
mxSetField(tmp2,0,"SPR",SPR);
if (hdr->AS.bci2000!=NULL) {
mxAddField(tmp2, "BCI2000");
mxSetField(tmp2,0,"BCI2000",mxCreateString(hdr->AS.bci2000));
}
if (hdr->TYPE==Sigma) {
mxAddField(tmp2, "H1");
mxSetField(tmp2,0,"H1",mxCreateString((char*)hdr->AS.Header));
}
mxSetField(HDR,0,"AS",tmp2);
/* FLAG */
const char* field3[] = {"UCAL","OVERFLOWDETECTION","ROW_BASED_CHANNELS",NULL};
for (numfields=0; field3[numfields++] != 0; );
Flag = mxCreateStructMatrix(1, 1, --numfields, field3);
#ifdef MX_API_VER
//#if 1
// Matlab, Octave 3.6.1
mxSetField(Flag,0,"UCAL",mxCreateLogicalScalar(hdr->FLAG.UCAL));
mxSetField(Flag,0,"OVERFLOWDETECTION",mxCreateLogicalScalar(hdr->FLAG.OVERFLOWDETECTION));
mxSetField(Flag,0,"ROW_BASED_CHANNELS",mxCreateLogicalScalar(hdr->FLAG.ROW_BASED_CHANNELS));
#else
// mxCreateLogicalScalar are not included in Octave 3.0
mxSetField(Flag,0,"UCAL",mxCreateDoubleScalar(hdr->FLAG.UCAL));
mxSetField(Flag,0,"OVERFLOWDETECTION",mxCreateDoubleScalar(hdr->FLAG.OVERFLOWDETECTION));
mxSetField(Flag,0,"ROW_BASED_CHANNELS",mxCreateDoubleScalar(hdr->FLAG.ROW_BASED_CHANNELS));
#endif
mxSetField(HDR,0,"FLAG",Flag);
/* Filter */
const char *filter_fields[] = {"HighPass","LowPass","Notch",NULL};
for (numfields=0; filter_fields[numfields++] != 0; );
Filter = mxCreateStructMatrix(1, 1, --numfields, filter_fields);
mxSetField(Filter,0,"LowPass",LowPass);
mxSetField(Filter,0,"HighPass",HighPass);
mxSetField(Filter,0,"Notch",Notch);
mxSetField(HDR,0,"Filter",Filter);
/* annotation, marker, event table */
const char *event_fields[] = {"SampleRate","TYP","POS","DUR","CHN","Desc",NULL};
if (hdr->EVENT.DUR == NULL)
EVENT = mxCreateStructMatrix(1, 1, 3, event_fields);
else {
EVENT = mxCreateStructMatrix(1, 1, 5, event_fields);
mxArray *DUR = mxCreateDoubleMatrix(hdr->EVENT.N,1, mxREAL);
mxArray *CHN = mxCreateDoubleMatrix(hdr->EVENT.N,1, mxREAL);
for (k=0; k<hdr->EVENT.N; ++k) {
*(mxGetPr(DUR)+k) = (double)hdr->EVENT.DUR[k];
*(mxGetPr(CHN)+k) = (double)hdr->EVENT.CHN[k]; // channels use a 1-based index, 0 indicates all channels
}
mxSetField(EVENT,0,"DUR",DUR);
mxSetField(EVENT,0,"CHN",CHN);
}
if (hdr->EVENT.CodeDesc != NULL) {
mxAddField(EVENT, "CodeDesc");
mxArray *CodeDesc = mxCreateCellMatrix(hdr->EVENT.LenCodeDesc-1,1);
for (k=1; k < hdr->EVENT.LenCodeDesc; ++k) {
mxSetCell(CodeDesc,k-1,mxCreateString(hdr->EVENT.CodeDesc[k]));
}
mxSetField(EVENT,0,"CodeDesc",CodeDesc);
}
mxArray *TYP = mxCreateDoubleMatrix(hdr->EVENT.N,1, mxREAL);
mxArray *POS = mxCreateDoubleMatrix(hdr->EVENT.N,1, mxREAL);
for (k=0; k<hdr->EVENT.N; ++k) {
*(mxGetPr(TYP)+k) = (double)hdr->EVENT.TYP[k];
*(mxGetPr(POS)+k) = (double)hdr->EVENT.POS[k]+1; // conversion from 0-based to 1-based indexing
}
mxSetField(EVENT,0,"TYP",TYP);
mxSetField(EVENT,0,"POS",POS);
#if (BIOSIG_VERSION >= 10500)
if (hdr->EVENT.TimeStamp) {
mxArray *TimeStamp = mxCreateDoubleMatrix(hdr->EVENT.N,1, mxREAL);
for (k=0; k<hdr->EVENT.N; ++k) {
*(mxGetPr(TimeStamp)+k) = ldexp(hdr->EVENT.TimeStamp[k],-32);
}
mxAddField(EVENT, "TimeStamp");
mxSetField(EVENT,0,"TimeStamp",TimeStamp);
}
#endif
mxSetField(EVENT,0,"SampleRate",mxCreateDoubleScalar(hdr->EVENT.SampleRate));
mxSetField(HDR,0,"EVENT",EVENT);
/* Record identification */
const char *ID_fields[] = {"Recording","Technician","Hospital","Equipment","IPaddr",NULL};
for (numfields=0; ID_fields[numfields++] != 0; );
ID = mxCreateStructMatrix(1, 1, --numfields, ID_fields);
mxSetField(ID,0,"Recording",mxCreateString(hdr->ID.Recording));
mxSetField(ID,0,"Technician",mxCreateString(hdr->ID.Technician));
mxSetField(ID,0,"Hospital",mxCreateString(hdr->ID.Hospital));
mxSetField(ID,0,"Equipment",mxCreateString((char*)&hdr->ID.Equipment));
int len = 4;
uint8_t IPv6=0;
for (k=4; k<16; k++) IPv6 |= hdr->IPaddr[k];
if (IPv6) len=16;
mxArray *IPaddr = mxCreateNumericMatrix(1,len,mxUINT8_CLASS,mxREAL);
memcpy(mxGetData(IPaddr),hdr->IPaddr,len);
mxSetField(ID,0,"IPaddr",IPaddr);
mxSetField(HDR,0,"REC",ID);
/* Patient Information */
const char *patient_fields[] = {"Sex","Handedness","Id","Name","Weight","Height","Birthday",NULL};
for (numfields=0; patient_fields[numfields++] != 0; );
Patient = mxCreateStructMatrix(1, 1, --numfields, patient_fields);
const char *strarray[1];
#ifdef __LIBBIOSIG2_H__
strarray[0] = biosig_get_patient_name(hdr);
if (strarray[0]) {
mxSetField(Patient,0,"Name",mxCreateCharMatrixFromStrings(1,strarray));
}
strarray[0] = biosig_get_patient_id(hdr);
if (strarray[0]) {
mxSetField(Patient,0,"Id",mxCreateCharMatrixFromStrings(1,strarray));
}
#else
strarray[0] = hdr->Patient.Name;
if (strarray[0]) {
mxSetField(Patient,0,"Name",mxCreateCharMatrixFromStrings(1,strarray));
}
strarray[0] = hdr->Patient.Id;
if (strarray[0]) {
mxSetField(Patient,0,"Id",mxCreateCharMatrixFromStrings(1,strarray));
}
#endif
mxSetField(Patient,0,"Handedness",mxCreateDoubleScalar(hdr->Patient.Handedness));
mxSetField(Patient,0,"Sex",mxCreateDoubleScalar(hdr->Patient.Sex));
mxSetField(Patient,0,"Weight",mxCreateDoubleScalar((double)hdr->Patient.Weight));
mxSetField(Patient,0,"Height",mxCreateDoubleScalar((double)hdr->Patient.Height));
mxSetField(Patient,0,"Birthday",mxCreateDoubleScalar(ldexp(hdr->Patient.Birthday,-32)));
double d;
if (hdr->Patient.Weight==0) d = NAN; // not-a-number
else if (hdr->Patient.Weight==255) d = INFINITY; // Overflow
else d = (double)hdr->Patient.Weight;
mxSetField(Patient,0,"Weight",mxCreateDoubleScalar(d));
if (hdr->Patient.Height==0) d = NAN; // not-a-number
else if (hdr->Patient.Height==255) d = INFINITY; // Overflow
else d = (double)hdr->Patient.Height;
mxSetField(Patient,0,"Height",mxCreateDoubleScalar(d));
/* Manufacturer Information */
const char *manufacturer_fields[] = {"Name","Model","Version","SerialNumber",NULL};
for (numfields=0; manufacturer_fields[numfields++] != 0; );
Manufacturer = mxCreateStructMatrix(1, 1, --numfields, manufacturer_fields);
#ifdef __LIBBIOSIG2_H__
strarray[0] = biosig_get_manufacturer_name(hdr);
if (strarray[0]) {
mxSetField(Manufacturer,0,"Name",mxCreateCharMatrixFromStrings(1,strarray));
}
strarray[0] = biosig_get_manufacturer_model(hdr);
if (strarray[0]) {
biosig_get_manufacturer_model(hdr);
mxSetField(Manufacturer,0,"Model",mxCreateCharMatrixFromStrings(1,strarray));
}
strarray[0] = biosig_get_manufacturer_version(hdr);
if (strarray[0]) {
biosig_get_manufacturer_version(hdr);
mxSetField(Manufacturer,0,"Version",mxCreateCharMatrixFromStrings(1,strarray));
}
strarray[0] = biosig_get_manufacturer_serial_number(hdr);
if (strarray[0]) {
mxSetField(Manufacturer,0,"SerialNumber",mxCreateCharMatrixFromStrings(1,strarray));
}
#else
strarray[0] = hdr->ID.Manufacturer.Name;
if (strarray[0]) {
mxSetField(Manufacturer,0,"Name",mxCreateCharMatrixFromStrings(1,strarray));
}
strarray[0] = hdr->ID.Manufacturer.Model;
if (strarray[0]) {
mxSetField(Manufacturer,0,"Model",mxCreateCharMatrixFromStrings(1,strarray));
}
strarray[0] = hdr->ID.Manufacturer.Version;
if (strarray[0]) {
mxSetField(Manufacturer,0,"Version",mxCreateCharMatrixFromStrings(1,strarray));
}
strarray[0] = hdr->ID.Manufacturer.SerialNumber;
if (strarray[0]) {
mxSetField(Manufacturer,0,"SerialNumber",mxCreateCharMatrixFromStrings(1,strarray));
}
#endif
mxSetField(HDR,0,"Manufacturer",Manufacturer);
if (VERBOSE_LEVEL>7)
fprintf(stdout,"[148] going for SCLOSE\n");
mxSetField(HDR,0,"Patient",Patient);
#ifndef mexSOPEN
plhs[1] = HDR;
}
#else
plhs[0] = HDR;
#endif
if (VERBOSE_LEVEL>7) fprintf(stdout,"[151] going for SCLOSE\n");
#ifdef CHOLMOD_H
hdr->Calib = NULL; // is refering to &RR, do not destroy
#endif
if (VERBOSE_LEVEL>7) fprintf(stdout,"[156] SCLOSE finished\n");
destructHDR(hdr);
hdr = NULL;
if (VERBOSE_LEVEL>7) fprintf(stdout,"[157] SCLOSE finished\n");
};
void mexFunction
(
int nargout,
mxArray *pargout [ ],
int nargin,
const mxArray *pargin [ ]
)
{
double dummy = 0, rcond, *p ;
cholmod_sparse Amatrix, Bspmatrix, *A, *Bs, *Xs ;
cholmod_dense Bmatrix, *X, *B ;
cholmod_factor *L ;
cholmod_common Common, *cm ;
Int n, B_is_sparse, ordering, k, *Perm ;
/* ---------------------------------------------------------------------- */
/* start CHOLMOD and set parameters */
/* ---------------------------------------------------------------------- */
cm = &Common ;
cholmod_l_start (cm) ;
sputil_config (SPUMONI, cm) ;
/* There is no supernodal LDL'. If cm->final_ll = FALSE (the default), then
* this mexFunction will use a simplicial LDL' when flops/lnz < 40, and a
* supernodal LL' otherwise. This may give suprising results to the MATLAB
* user, so always perform an LL' factorization by setting cm->final_ll
* to TRUE. */
cm->final_ll = TRUE ;
cm->quick_return_if_not_posdef = TRUE ;
/* ---------------------------------------------------------------------- */
/* get inputs */
/* ---------------------------------------------------------------------- */
if (nargout > 2 || nargin < 2 || nargin > 3)
{
mexErrMsgTxt ("usage: [x,rcond] = cholmod2 (A,b,ordering)") ;
}
n = mxGetM (pargin [0]) ;
if (!mxIsSparse (pargin [0]) || (n != mxGetN (pargin [0])))
{
mexErrMsgTxt ("A must be square and sparse") ;
}
if (n != mxGetM (pargin [1]))
{
mexErrMsgTxt ("# of rows of A and B must match") ;
}
/* get sparse matrix A. Use triu(A) only. */
A = sputil_get_sparse (pargin [0], &Amatrix, &dummy, 1) ;
/* get sparse or dense matrix B */
B = NULL ;
Bs = NULL ;
B_is_sparse = mxIsSparse (pargin [1]) ;
if (B_is_sparse)
{
/* get sparse matrix B (unsymmetric) */
Bs = sputil_get_sparse (pargin [1], &Bspmatrix, &dummy, 0) ;
}
else
{
/* get dense matrix B */
B = sputil_get_dense (pargin [1], &Bmatrix, &dummy) ;
}
/* get the ordering option */
if (nargin < 3)
{
/* use default ordering */
ordering = -1 ;
}
else
{
/* use a non-default option */
ordering = mxGetScalar (pargin [2]) ;
}
p = NULL ;
Perm = NULL ;
if (ordering == 0)
{
/* natural ordering */
cm->nmethods = 1 ;
cm->method [0].ordering = CHOLMOD_NATURAL ;
cm->postorder = FALSE ;
}
else if (ordering == -1)
{
/* default strategy ... nothing to change */
}
else if (ordering == -2)
{
/* default strategy, but with NESDIS in place of METIS */
cm->default_nesdis = TRUE ;
}
else if (ordering == -3)
{
/* use AMD only */
cm->nmethods = 1 ;
cm->method [0].ordering = CHOLMOD_AMD ;
cm->postorder = TRUE ;
}
else if (ordering == -4)
{
/* use METIS only */
cm->nmethods = 1 ;
cm->method [0].ordering = CHOLMOD_METIS ;
cm->postorder = TRUE ;
}
else if (ordering == -5)
{
/* use NESDIS only */
cm->nmethods = 1 ;
cm->method [0].ordering = CHOLMOD_NESDIS ;
cm->postorder = TRUE ;
}
else if (ordering == -6)
{
/* natural ordering, but with etree postordering */
cm->nmethods = 1 ;
cm->method [0].ordering = CHOLMOD_NATURAL ;
cm->postorder = TRUE ;
}
else if (ordering == -7)
{
/* always try both AMD and METIS, and pick the best */
cm->nmethods = 2 ;
cm->method [0].ordering = CHOLMOD_AMD ;
cm->method [1].ordering = CHOLMOD_METIS ;
cm->postorder = TRUE ;
}
else if (ordering >= 1)
{
/* assume the 3rd argument is a user-provided permutation of 1:n */
if (mxGetNumberOfElements (pargin [2]) != n)
{
mexErrMsgTxt ("invalid input permutation") ;
}
/* copy from double to integer, and convert to 0-based */
p = mxGetPr (pargin [2]) ;
Perm = cholmod_l_malloc (n, sizeof (Int), cm) ;
for (k = 0 ; k < n ; k++)
{
Perm [k] = p [k] - 1 ;
}
/* check the permutation */
if (!cholmod_l_check_perm (Perm, n, n, cm))
{
mexErrMsgTxt ("invalid input permutation") ;
}
/* use only the given permutation */
cm->nmethods = 1 ;
cm->method [0].ordering = CHOLMOD_GIVEN ;
cm->postorder = FALSE ;
}
else
{
mexErrMsgTxt ("invalid ordering option") ;
}
/* ---------------------------------------------------------------------- */
/* analyze and factorize */
/* ---------------------------------------------------------------------- */
L = cholmod_l_analyze_p (A, Perm, NULL, 0, cm) ;
cholmod_l_free (n, sizeof (Int), Perm, cm) ;
cholmod_l_factorize (A, L, cm) ;
rcond = cholmod_l_rcond (L, cm) ;
if (rcond == 0)
{
mexWarnMsgTxt ("Matrix is indefinite or singular to working precision");
}
else if (rcond < DBL_EPSILON)
{
mexWarnMsgTxt ("Matrix is close to singular or badly scaled.") ;
mexPrintf (" Results may be inaccurate. RCOND = %g.\n", rcond) ;
}
/* ---------------------------------------------------------------------- */
/* solve and return solution to MATLAB */
/* ---------------------------------------------------------------------- */
if (B_is_sparse)
{
/* solve AX=B with sparse X and B; return sparse X to MATLAB */
Xs = cholmod_l_spsolve (CHOLMOD_A, L, Bs, cm) ;
pargout [0] = sputil_put_sparse (&Xs, cm) ;
}
else
{
/* solve AX=B with dense X and B; return dense X to MATLAB */
X = cholmod_l_solve (CHOLMOD_A, L, B, cm) ;
pargout [0] = sputil_put_dense (&X, cm) ;
}
/* return statistics, if requested */
if (nargout > 1)
{
pargout [1] = mxCreateDoubleMatrix (1, 5, mxREAL) ;
p = mxGetPr (pargout [1]) ;
p [0] = rcond ;
p [1] = L->ordering ;
p [2] = cm->lnz ;
p [3] = cm->fl ;
p [4] = cm->memory_usage / 1048576. ;
}
cholmod_l_free_factor (&L, cm) ;
cholmod_l_finish (cm) ;
cholmod_l_print_common (" ", cm) ;
/*
if (cm->malloc_count !=
(mxIsComplex (pargout [0]) + (mxIsSparse (pargout[0]) ? 3:1)))
mexErrMsgTxt ("memory leak!") ;
*/
}