//--------------------------------------------------------------------------
void Omu_IntODE::solve(int kk, double tstart, double tend,
const Omu_VariableVec &x, const Omu_VariableVec &u,
Omu_Program *sys, Omu_DependentVec &Ft,
Omu_StateVec &xt)
{
int i, j;
_sys = sys; // propagate to syseq()
_xt_ptr = &xt;
_Ft_ptr = &Ft;
v_zero(_y);
for (i = 0; i < _nd; i++) {
_u[i] = xt[i];
}
for (i = 0; i < _n; i++) {
_y[i] = xt[_nd + i]; // initial states
}
for (i = 0; i < _nu; i++) {
_u[_nd + i] = u[i];
}
v_zero(_dxt); // time derivatives passed to continuous
if (_sa) {
for (i = 0; i < _n; i++) {
for (j = 0; j < _nx; j++) {
_y[(1 + j) * _n + i] = xt.Sx[_nd + i][j];
}
for (j = 0; j < _nu; j++) {
_y[(1 + _nx + j) * _n + i] = xt.Su[_nd + i][j];
}
}
m_zero(_dxt.Sx);
m_zero(_dxt.Su);
}
_kk = kk; // propagate to syseq()
ode_solve(tstart, _y, _u, tend);
for (i = 0; i < _n; i++) {
xt[_nd + i] = _y[i];
}
if (_sa) {
for (i = 0; i < _n; i++) {
for (j = 0; j < _nx; j++) {
xt.Sx[_nd + i][j] = _y[(1 + j) * _n + i];
}
for (j = 0; j < _nu; j++) {
xt.Su[_nd + i][j] = _y[(1 + _nx + j) * _n + i];
}
}
}
}
/*******************************RK4***********************************
*********************************************************************/
void skew_mat(MAT *skew_mat, VEC *w)
{
if((skew_mat->m !=3) || (skew_mat->m !=4)){
m_resize(skew_mat,4,4);
m_zero(skew_mat);
}
if(skew_mat->m == 4){
skew_mat->me[0][1] = w->ve[2];
skew_mat->me[0][2] = (-1)*w->ve[1];
skew_mat->me[0][3] = w->ve[0];
skew_mat->me[1][0] = (-1)*w->ve[2];
skew_mat->me[1][2] = w->ve[0];
skew_mat->me[1][3] = w->ve[1];
skew_mat->me[2][0] = w->ve[1];
skew_mat->me[2][1] = (-1)*w->ve[0];
skew_mat->me[2][3] = w->ve[2];
skew_mat->me[3][0] = (-1)*w->ve[0];
skew_mat->me[3][1] = (-1)*w->ve[1];
skew_mat->me[3][2] = (-1)*w->ve[2];
}
else if(skew_mat->m == 3){// not needed
skew_mat->me[0][1] = w->ve[2];
skew_mat->me[0][2] = (-1)*w->ve[1];
skew_mat->me[1][2] = w->ve[0];
skew_mat->me[1][0] = (-1)*w->ve[2];
skew_mat->me[2][0] = w->ve[1];
skew_mat->me[2][1] = (-1)*w->ve[0];
}
}
void booz_sensors_model_mag_init( double time ) {
bsm.mag = v_get(AXIS_NB);
bsm.mag->ve[AXIS_X] = 0.;
bsm.mag->ve[AXIS_Y] = 0.;
bsm.mag->ve[AXIS_Z] = 0.;
// bsm.mag_resolution = BSM_MAG_RESOLUTION;
bsm.mag_imu_to_sensor = m_get(AXIS_NB, AXIS_NB);
VEC* tmp_eulers = v_get(AXIS_NB);
tmp_eulers->ve[EULER_PHI] = BSM_MAG_IMU_TO_SENSOR_PHI;
tmp_eulers->ve[EULER_THETA] = BSM_MAG_IMU_TO_SENSOR_THETA;
tmp_eulers->ve[EULER_PSI] = BSM_MAG_IMU_TO_SENSOR_PSI;
dcm_of_eulers (tmp_eulers, bsm.mag_imu_to_sensor );
bsm.mag_sensitivity = m_get(AXIS_NB, AXIS_NB);
m_zero(bsm.mag_sensitivity);
bsm.mag_sensitivity->me[AXIS_X][AXIS_X] = BSM_MAG_SENSITIVITY_XX;
bsm.mag_sensitivity->me[AXIS_Y][AXIS_Y] = BSM_MAG_SENSITIVITY_YY;
bsm.mag_sensitivity->me[AXIS_Z][AXIS_Z] = BSM_MAG_SENSITIVITY_ZZ;
bsm.mag_neutral = v_get(AXIS_NB);
bsm.mag_neutral->ve[AXIS_X] = BSM_MAG_NEUTRAL_X;
bsm.mag_neutral->ve[AXIS_Y] = BSM_MAG_NEUTRAL_Y;
bsm.mag_neutral->ve[AXIS_Z] = BSM_MAG_NEUTRAL_Z;
bsm.mag_noise_std_dev = v_get(AXIS_NB);
bsm.mag_noise_std_dev->ve[AXIS_X] = BSM_MAG_NOISE_STD_DEV_X;
bsm.mag_noise_std_dev->ve[AXIS_Y] = BSM_MAG_NOISE_STD_DEV_Y;
bsm.mag_noise_std_dev->ve[AXIS_Z] = BSM_MAG_NOISE_STD_DEV_Z;
bsm.mag_next_update = time;
bsm.mag_available = FALSE;
}
MAT *XVXt_mlt(MAT *X, MAT *V, MAT *out) {
/* for a symmetric matrix V, return X V X' */
static MAT *VXt = MNULL;
int i, j, k;
if (X==(MAT *)NULL || V==(MAT *)NULL )
error(E_NULL, "XtVX_mlt");
if (X->n != V->m)
error(E_SIZES, "XtVX_mlt");
if (V->m != V->n)
error(E_SQUARE, "XtVX_mlt");
out = m_resize(out, X->m, X->m);
VXt = m_resize(VXt, V->m, X->n);
m_zero(out);
VXt = mmtr_mlt(V, X, VXt);
for (i = 0; i < X->m; i++) {
for (j = i; j < X->m; j++)
for (k = 0; k < X->n; k++)
out->me[i][j] += X->me[i][k] * VXt->me[k][j];
for (j = 0; j <= i; j++) /* symmetry */
out->me[i][j] = out->me[j][i];
}
return out;
}
struct mbuf *
m_free(struct mbuf *m)
{
struct mbuf *n;
if (m == NULL)
return (NULL);
mtx_enter(&mbstatmtx);
mbstat.m_mtypes[m->m_type]--;
mtx_leave(&mbstatmtx);
n = m->m_next;
if (m->m_flags & M_ZEROIZE) {
m_zero(m);
/* propagate M_ZEROIZE to the next mbuf in the chain */
if (n)
n->m_flags |= M_ZEROIZE;
}
if (m->m_flags & M_PKTHDR)
m_tag_delete_chain(m);
if (m->m_flags & M_EXT)
m_extfree(m);
pool_put(&mbpool, m);
return (n);
}
void booz_sensors_model_accel_init(double time) {
bsm.accel = v_get(AXIS_NB);
bsm.accel->ve[AXIS_X] = 0.;
bsm.accel->ve[AXIS_Y] = 0.;
bsm.accel->ve[AXIS_Z] = 0.;
bsm.accel_resolution = BSM_ACCEL_RESOLUTION;
bsm.accel_sensitivity = m_get(AXIS_NB, AXIS_NB);
m_zero(bsm.accel_sensitivity);
bsm.accel_sensitivity->me[AXIS_X][AXIS_X] = BSM_ACCEL_SENSITIVITY_XX;
bsm.accel_sensitivity->me[AXIS_Y][AXIS_Y] = BSM_ACCEL_SENSITIVITY_YY;
bsm.accel_sensitivity->me[AXIS_Z][AXIS_Z] = BSM_ACCEL_SENSITIVITY_ZZ;
bsm.accel_neutral = v_get(AXIS_NB);
bsm.accel_neutral->ve[AXIS_X] = BSM_ACCEL_NEUTRAL_X;
bsm.accel_neutral->ve[AXIS_Y] = BSM_ACCEL_NEUTRAL_Y;
bsm.accel_neutral->ve[AXIS_Z] = BSM_ACCEL_NEUTRAL_Z;
bsm.accel_noise_std_dev = v_get(AXIS_NB);
bsm.accel_noise_std_dev->ve[AXIS_X] = BSM_ACCEL_NOISE_STD_DEV_X;
bsm.accel_noise_std_dev->ve[AXIS_Y] = BSM_ACCEL_NOISE_STD_DEV_Y;
bsm.accel_noise_std_dev->ve[AXIS_Z] = BSM_ACCEL_NOISE_STD_DEV_Z;
bsm.accel_bias = v_get(AXIS_NB);
bsm.accel_bias->ve[AXIS_P] = BSM_ACCEL_BIAS_X;
bsm.accel_bias->ve[AXIS_Q] = BSM_ACCEL_BIAS_Y;
bsm.accel_bias->ve[AXIS_R] = BSM_ACCEL_BIAS_Z;
bsm.accel_next_update = time;
bsm.accel_available = FALSE;
}
MAT *mtrm_mlt(const MAT *A, const MAT *B, MAT *OUT)
#endif
{
int i, k, limit;
/* Real *B_row, *OUT_row, multiplier; */
if ( ! A || ! B )
error(E_NULL,"mmtr_mlt");
if ( A == OUT || B == OUT )
error(E_INSITU,"mtrm_mlt");
if ( A->m != B->m )
error(E_SIZES,"mmtr_mlt");
if ( ! OUT || OUT->m != A->n || OUT->n != B->n )
OUT = m_resize(OUT,A->n,B->n);
limit = B->n;
m_zero(OUT);
for ( k = 0; k < A->m; k++ )
for ( i = 0; i < A->n; i++ )
{
if ( A->me[k][i] != 0.0 )
__mltadd__(OUT->me[i],B->me[k],A->me[k][i],(int)limit);
/**************************************************
multiplier = A->me[k][i];
OUT_row = OUT->me[i];
B_row = B->me[k];
for ( j = 0; j < limit; j++ )
*(OUT_row++) += multiplier*(*B_row++);
**************************************************/
}
return OUT;
}
MAT *band2mat(const BAND *bA, MAT *A)
#endif
{
int i,j,l,n,n1;
int lb, ub;
Real **bmat;
if ( !bA )
error(E_NULL,"band2mat");
if ( bA->mat == A )
error(E_INSITU,"band2mat");
ub = bA->ub;
lb = bA->lb;
n = bA->mat->n;
n1 = n-1;
bmat = bA->mat->me;
A = m_resize(A,n,n);
m_zero(A);
for (j=0; j < n; j++)
for (i=min(n1,j+lb),l=lb+j-i; i >= max(0,j-ub); i--,l++)
A->me[i][j] = bmat[l][j];
return A;
}
static void test_mgcr(ITER *ip, int i, MAT *Q, MAT *R)
#endif
{
VEC vt, vt1;
static MAT *R1 = MNULL;
static VEC *r = VNULL, *r1 = VNULL;
VEC *rr;
int k, j;
Real sm;
/* check Q*Q^T = I */
vt.dim = vt.max_dim = ip->b->dim;
vt1.dim = vt1.max_dim = ip->b->dim;
Q = m_resize(Q, i + 1, ip->b->dim);
R1 = m_resize(R1, i + 1, i + 1);
r = v_resize(r, ip->b->dim);
r1 = v_resize(r1, ip->b->dim);
MEM_STAT_REG(R1, TYPE_MAT);
MEM_STAT_REG(r, TYPE_VEC);
MEM_STAT_REG(r1, TYPE_VEC);
m_zero(R1);
for (k = 1; k <= i; k++)
for (j = 1; j <= i; j++) {
vt.ve = Q->me[k];
vt1.ve = Q->me[j];
R1->me[k][j] = in_prod(&vt, &vt1);
}
for (j = 1; j <= i; j++)
R1->me[j][j] -= 1.0;
#ifndef MEX
if (m_norm_inf(R1) > MACHEPS * ip->b->dim)
printf(" ! (mgcr:) m_norm_inf(Q*Q^T) = %g\n", m_norm_inf(R1));
#endif
/* check (r_i,Ap_j) = 0 for j <= i */
ip->Ax(ip->A_par, ip->x, r);
v_sub(ip->b, r, r);
rr = r;
if (ip->Bx) {
ip->Bx(ip->B_par, r, r1);
rr = r1;
}
#ifndef MEX
printf(" ||r|| = %g\n", v_norm2(rr));
#endif
sm = 0.0;
for (j = 1; j <= i; j++) {
vt.ve = Q->me[j];
sm = max(sm, in_prod(&vt,rr));
}
#ifndef MEX
if (sm >= MACHEPS * ip->b->dim)
printf(" ! (mgcr:) max_j (r,Ap_j) = %g\n", sm);
#endif
}
BAND *bd_zero(BAND *A)
#endif
{
if ( ! A )
error(E_NULL,"bd_zero");
m_zero(A->mat);
return A;
}
/* mat_id -- set A to being closest to identity matrix as possible
-- i.e. A[i][j] == 1 if i == j and 0 otherwise */
MAT *m_ident(MAT *A)
{
int i, size;
if ( A == MNULL )
error(E_NULL,"m_ident");
m_zero(A);
size = min(A->m,A->n);
for ( i = 0; i < size; i++ )
A->me[i][i] = 1.0;
return A;
}
void m_invert(matrix m,matrix &dest)
{
int i,j;
float d;
d = m_det(m);
if (d == 0.0)
{
m_zero(dest);
return;
}
for (i = 0;i<=3;i++)
for (j = 0;j<=3;j++)
dest[i][j] = m_signedsubdet(m, i, j);
m_trans(dest);
m_mults(dest, 1/d, dest);
}
MAT *m_mlt(const MAT *A, const MAT *B, MAT *OUT)
#endif
{
unsigned int i, /* j, */ k, m, n, p;
Real **A_v, **B_v /*, *B_row, *OUT_row, sum, tmp */;
if ( A==(MAT *)NULL || B==(MAT *)NULL )
error(E_NULL,"m_mlt");
if ( A->n != B->m )
error(E_SIZES,"m_mlt");
if ( A == OUT || B == OUT )
error(E_INSITU,"m_mlt");
m = A->m; n = A->n; p = B->n;
A_v = A->me; B_v = B->me;
if ( OUT==(MAT *)NULL || OUT->m != A->m || OUT->n != B->n )
OUT = m_resize(OUT,A->m,B->n);
/****************************************************************
for ( i=0; i<m; i++ )
for ( j=0; j<p; j++ )
{
sum = 0.0;
for ( k=0; k<n; k++ )
sum += A_v[i][k]*B_v[k][j];
OUT->me[i][j] = sum;
}
****************************************************************/
m_zero(OUT);
for ( i=0; i<m; i++ )
for ( k=0; k<n; k++ )
{
if ( A_v[i][k] != 0.0 )
__mltadd__(OUT->me[i],B_v[k],A_v[i][k],(int)p);
/**************************************************
B_row = B_v[k]; OUT_row = OUT->me[i];
for ( j=0; j<p; j++ )
(*OUT_row++) += tmp*(*B_row++);
**************************************************/
}
return OUT;
}
MAT *XtdX_mlt(MAT *X, VEC *d, MAT *out) {
/* for a diagonal matrix in d, return X' d X */
int i, j, k;
if (X==(MAT *)NULL || d==(VEC *)NULL )
error(E_NULL, "XtVX_mlt");
if (X->m != d->dim)
error(E_SIZES, "XtVX_mlt");
out = m_resize(out, X->n, X->n);
m_zero(out);
for (i = 0; i < X->n; i++) {
for (j = i; j < X->n; j++)
for (k = 0; k < X->m; k++)
out->me[i][j] += X->me[k][i] * X->me[k][j] * d->ve[k];
for (j = 0; j <= i; j++) /* symmetry */
out->me[i][j] = out->me[j][i];
}
return out;
}
//--------------------------------------------------------------------------
void Omu_Integrator::setup_struct(int k,
const Omu_VariableVec &x,
const Omu_VariableVec &u,
const Omu_DependentVec &Ft)
{
// initialize Jacobians for high-level integrator interface
if (k >= _K) {
m_error(E_INTERN, "Omu_Integrator::setup_struct"
" that was called with wrong integrator setup");
}
int i;
Omu_DepVec &Fc = _Fcs[k];
init_dims(k, x, u, Ft);
Fc.size(_n, _n, 0, _n, 0, _nx+_nu);
m_move(Ft.Jx, _nd, _nd, _n, _n, Fc.Jx, 0, 0);
m_move(Ft.Jdx, _nd, _nd, _n, _n, Fc.Jdx, 0, 0);
m_zero(Fc.Jq); // zero Jq wrt. continuous states as Jx gets chained with Sx
m_move(Ft.Jx, _nd, 0, _n, _nd, Fc.Jq, 0, 0);
m_move(Ft.Ju, _nd, 0, _n, _nu, Fc.Jq, 0, _nx);
Fc.c_setup = true;
for (i = 0; i < _n; i++) {
int wrt = 0;
if (Ft.is_linear_element(_nd + i, Omu_Dependent::WRT_x))
wrt |= Omu_Dependent::WRT_x;
if (Ft.is_linear_element(_nd + i, Omu_Dependent::WRT_dx))
wrt |= Omu_Dependent::WRT_dx;
if ((_nd == 0 || Ft.is_linear_element(_nd + i, Omu_Dependent::WRT_x)) &&
Ft.is_linear_element(_nd + i, Omu_Dependent::WRT_u))
wrt |= Omu_Dependent::WRT_q;
Fc.set_linear_element(i, wrt);
}
Fc.analyze_struct();
Fc.c_setup = false;
}
// alternative implementation calling high-level _sys->continuous
//--------------------------------------------------------------------------
void Omu_IntODE::syseq_forward(double t, const VECP y, const VECP u,
VECP f)
{
#ifdef OMU_WITH_ADOLC
int i, j;
Omu_DependentVec &Ft = *_Ft_ptr;
//
// form a vector of independent variables
//
for (i = 0; i < _nd; i++) {
_x[i] = u[i];
}
for (i = 0; i < _n; i++) {
_x[_nd + i] = y[i];
_x[_nd + _n + i] = 0.0; // yprime[i]
}
for (i = 0; i < _nu; i++) {
_x[_nd + 2 * _n + i] = u[_nd + i];
}
//
// evaluate residual
//
// adoublev ax(_nd + _n);
static adoublev ax; ax.alloc(_nd + _n);
// adoublev adx(_nd + _n);
static adoublev adx; adx.alloc(_nd + _n);
// adoublev au(_nu);
static adoublev au; au.alloc(_nu);
// adoublev aF(_nd + _n);
static adoublev aF; aF.alloc(_nd + _n);
for (i = 0; i < _nd; i++)
adx[i] = 0.0;
for (i = _nd; i < _nxt; i++)
aF[i] = 0.0;
if (_sa)
trace_on(3); // tape 3
ax <<= _x->ve;
for (i = 0; i < _n; i++)
adx[_nd + i] <<= _x->ve[_nd + _n + i];
au <<= _x->ve + _nd + 2 * _n;
_sys->continuous(_kk, t, ax, au, adx, aF);
for (i = _nd; i < _nxt; i++) {
aF[i] >>= f[i - _nd];
f[i - _nd] /= -Ft.Jdx[i][i];
}
if (_sa) {
trace_off();
int nindep = _nd + 2 * _n + _nu;
int npar = _nx + _nu;
m_zero(_X2);
for (i = 0; i < _nd; i++) {
_X2[i][i] = 1.0;
}
for (i = 0; i < _n; i++) {
for (j = 0; j < npar; j++) {
_X2[_nd + i][j] = y[(1 + j) * _n + i];
_X2[_nd + _n + i][j] = 0.0; // yprime[(1 + j) * _n + i];
}
}
for (i = 0; i < _nu; i++) {
_X2[_nd + 2 * _n + i][_nd + _n + i] = 1.0;
}
forward(3, _n, nindep, npar, _x->ve, _X2->me, f->ve, _Y2->me);
for (i = _nd; i < _nxt; i++) {
f[i - _nd] /= -Ft.Jdx[i][i];
for (j = 0; j < npar; j++) {
f[(1 + j) * _n + i - _nd] = _Y2[i - _nd][j] / -Ft.Jdx[i][i];
}
}
}
_res_evals++;
if (_sa)
_sen_evals++;
#else
m_error(E_NULL, "Omu_IntODE::syseq_forward: was compiled without ADOL-C");
#endif
}
/* Routine to take the matrix given and calculate the log-
* determinant, by calling LU decomposition routine and
* then multiplying down diagonals. Returns the
* log-determinant calculated.*/
double * determinant(void){
int a,max,c;
extern int branches;
double *det;
extern int mode;
extern int nodecount;
extern double **expect;
extern double **rootedexpect;
extern int individual;
extern int interesting_branches[];
extern int is_kappa;
double **matrix;
MAT * matrix2;
is_kappa=0;
if(ISMODE(HKY) && NOTMODE(NOKAPPA))
is_kappa=1;
matrix=expect;
max=branches;
if(ISMODE(ROOTED)){ /* If want rooted tree then create new*/
planttree(expect,rootedexpect); /* matrix*/
matrix=rootedexpect;
max=nodecount+2;
if(ISMODE(NODEASROOT))
max=nodecount+1;
}
if(ISMODE(MATRICES)){ /* If want intermediate matrices dumped*/
dump(matrix,max+is_kappa,"Full matrix");
}
if(ISMODE(INDIVIDUAL)){ /* We want information about some, but
* not all of the elements*/
if(NOTMODE(DETINDIV)){
det=calloc(individual+is_kappa,sizeof(double));
for(a=0;a<individual;a++)
det[a]=matrix[interesting_branches[a]][interesting_branches[a]];
if(is_kappa==1)
det[individual]=matrix[max][max];
is_kappa=0;
return det;
}
/* Case - we want the determinate of the sub-matrix formed
* by several parameters*/
/* Get memory for new matrix*/
matrix2 = m_get(individual+is_kappa,individual+is_kappa);
if(NULL==matrix2){
nomemory();
}
m_zero(matrix2);
/* Creates the sub-matrix from the original expected information
* matrix*/
for(a=0;a<individual;a++)
for(c=0;c<individual;c++)
matrix2->me[a][c]=matrix[interesting_branches[a]][interesting_branches[c]];
if(is_kappa==1){
matrix2->me[individual][individual]=matrix[max][max];
}
max=individual;
if(ISMODE(MATRICES))
dump(matrix2->me,max,"Sub-matrix to be calculated");
} else {
matrix2 = m_get(max,max);
if(NULL==matrix2){
nomemory();
}
m_zero(matrix2);
for ( a=0 ; a<max ; a++){
for ( c=0 ; c<max ; c++){
matrix2->me[a][c] = matrix[a][c];
}
}
}
/* Perform LU decomposition on whichever matrix we've been handed*/
det=calloc(1+is_kappa,sizeof(double));
matrix2=CHfactor(matrix2);
/* The determinant of the matrix is the product of
* the diagonal elements of the decomposed form*/
for(a=0;a<max;a++){
det[0] += 2.0 * log(matrix2->me[a][a]);
}
if(is_kappa==1){
det[1] = 2.0 * log(matrix2->me[max][max]);
}
M_FREE(matrix2);
return det;
}
long lsfn(
double *xd, double *yd, double *sy, /* data */
long nd, /* number of data points */
long nf, /* y = a_0 + a_1*x ... a_nf*x^nf */
double *coef, /* place to put co-efficients */
double *s_coef, /* and their sigmas */
double *chi, /* place to put reduced chi-squared */
double *diff /* place to put difference table */
)
{
long i, j, nt, unweighted;
double xp, *x_i, x0;
static MATRIX *X, *Y, *Yp, *C, *C_1, *Xt, *A, *Ca,
*XtC, *XtCX, *T, *Tt, *TC;
nt = nf + 1;
if (nd<nt) {
printf("error: insufficient data for requested order of fit\n");
printf("(%ld data points, %ld terms in fit)\n", nd, nt);
exit(1);
}
unweighted = 1;
if (sy)
for (i=1; i<nd; i++)
if (sy[i]!=sy[0]) {
unweighted = 0;
break;
}
/* allocate matrices */
m_alloc(&X, nd, nt);
m_alloc(&Y, nd, 1);
m_alloc(&Yp, nd, 1);
m_alloc(&Xt, nt, nd);
if (!unweighted) {
m_alloc(&C, nd, nd);
m_alloc(&C_1, nd, nd);
m_zero(C);
m_zero(C_1);
}
m_alloc(&A, nt, 1);
m_alloc(&Ca, nt, nt);
m_alloc(&XtC, nt, nd);
m_alloc(&XtCX, nt, nt);
m_alloc(&T, nt, nd);
m_alloc(&Tt, nd, nt);
m_alloc(&TC, nt, nd);
/* Compute X, Y, C, C_1. X[i][j] = (xd[i])^j. Y[i][0] = yd[i].
* C = delta(i,j)*sy[i]^2 (covariance matrix of yd)
* C_1 = INV(C)
*/
for (i=0; i<nd; i++) {
x_i = X->a[i];
x0 = xd[i];
xp = 1.0;
Y->a[i][0] = yd[i];
if (!unweighted) {
C->a[i][i] = sqr(sy[i]);
C_1->a[i][i] = 1/C->a[i][i];
}
for (j=0; j<nt; j++) {
x_i[j] = xp;
xp *= x0;
}
}
/* Compute A, the matrix of coefficients.
* Weighted least-squares solution is A = INV(Xt.INV(C).X).Xt.INV(C).y
* Unweighted solution is A = INV(Xt.X).Xt.y
*/
if (unweighted) {
/* eliminating 2 matrix operations makes this much faster than a weighted fit
* if there are many data points.
*/
if (!m_trans(Xt, X))
return(p_merror("transposing X"));
if (!m_mult(XtCX, Xt, X))
return(p_merror("multiplying Xt.X"));
if (!m_invert(XtCX, XtCX))
return(p_merror("inverting XtCX"));
if (!m_mult(T, XtCX, Xt))
return(p_merror("multiplying XtX.Xt"));
if (!m_mult(A, T, Y))
return(p_merror("multiplying T.Y"));
/* Compute covariance matrix of A, Ca = (T.Tt)*C[0][0] */
if (!m_trans(Tt, T))
return(p_merror("computing transpose of T"));
if (!m_mult(Ca, T, Tt))
return(p_merror("multiplying T.Tt"));
if (!m_scmul(Ca, Ca, sy?sqr(sy[0]):1))
return(p_merror("multiplying T.Tt by scalar"));
}
else {
if (!m_trans(Xt, X))
return(p_merror("transposing X"));
if (!m_mult(XtC, Xt, C_1))
return(p_merror("multiplying Xt.C_1"));
if (!m_mult(XtCX, XtC, X))
return(p_merror("multiplying XtC.X"));
if (!m_invert(XtCX, XtCX))
return(p_merror("inverting XtCX"));
if (!m_mult(T, XtCX, XtC))
return(p_merror("multiplying XtCX.XtC"));
if (!m_mult(A, T, Y))
return(p_merror("multiplying T.Y"));
/* Compute covariance matrix of A, Ca = T.C.Tt */
if (!m_mult(TC, T, C))
return(p_merror("multiplying T.C"));
if (!m_trans(Tt, T))
return(p_merror("computing transpose of T"));
if (!m_mult(Ca, TC, Tt))
return(p_merror("multiplying TC.Tt"));
}
for (i=0; i<nt; i++) {
coef[i] = A->a[i][0];
if (s_coef)
s_coef[i] = sqrt(Ca->a[i][i]);
}
/* Compute Yp = X.A, use to compute chi-squared */
if (chi) {
if (!m_mult(Yp, X, A))
return(p_merror("multiplying X.A"));
*chi = 0;
for (i=0; i<nd; i++) {
xp = (Yp->a[i][0] - yd[i]);
if (diff!=NULL)
diff[i] = xp;
xp /= sy?sy[i]:1;
*chi += xp*xp;
}
if (nd!=nt)
*chi /= (nd-nt);
}
m_free(&X);
m_free(&Y);
m_free(&Yp);
m_free(&Xt);
if (!unweighted) {
m_free(&C);
m_free(&C_1);
}
m_free(&A);
m_free(&Ca);
m_free(&XtC);
m_free(&XtCX);
m_free(&T);
m_free(&Tt);
m_free(&TC);
return(1);
}
void iter_lanczos(ITER *ip, VEC *a, VEC *b, Real *beta2, MAT *Q)
#endif
{
int j;
STATIC VEC *v = VNULL, *w = VNULL, *tmp = VNULL;
Real alpha, beta, c;
if ( ! ip )
error(E_NULL,"iter_lanczos");
if ( ! ip->Ax || ! ip->x || ! a || ! b )
error(E_NULL,"iter_lanczos");
if ( ip->k <= 0 )
error(E_BOUNDS,"iter_lanczos");
if ( Q && ( Q->n < ip->x->dim || Q->m < ip->k ) )
error(E_SIZES,"iter_lanczos");
a = v_resize(a,(unsigned int)ip->k);
b = v_resize(b,(unsigned int)(ip->k-1));
v = v_resize(v,ip->x->dim);
w = v_resize(w,ip->x->dim);
tmp = v_resize(tmp,ip->x->dim);
MEM_STAT_REG(v,TYPE_VEC);
MEM_STAT_REG(w,TYPE_VEC);
MEM_STAT_REG(tmp,TYPE_VEC);
beta = 1.0;
v_zero(a);
v_zero(b);
if (Q) m_zero(Q);
/* normalise x as w */
c = v_norm2(ip->x);
if (c <= MACHEPS) { /* ip->x == 0 */
*beta2 = 0.0;
return;
}
else
sv_mlt(1.0/c,ip->x,w);
(ip->Ax)(ip->A_par,w,v);
for ( j = 0; j < ip->k; j++ )
{
/* store w in Q if Q not NULL */
if ( Q ) set_row(Q,j,w);
alpha = in_prod(w,v);
a->ve[j] = alpha;
v_mltadd(v,w,-alpha,v);
beta = v_norm2(v);
if ( beta == 0.0 )
{
*beta2 = 0.0;
return;
}
if ( j < ip->k-1 )
b->ve[j] = beta;
v_copy(w,tmp);
sv_mlt(1/beta,v,w);
sv_mlt(-beta,tmp,v);
(ip->Ax)(ip->A_par,w,tmp);
v_add(v,tmp,v);
}
*beta2 = beta;
#ifdef THREADSAFE
V_FREE(v); V_FREE(w); V_FREE(tmp);
#endif
}
void Sy_m( VEC *x, VEC *Torq_ext, VEC *out)
{
static MAT *iI = {MNULL};
MAT *sk_om = {MNULL};
VEC *q, *w, *q_dot, *w_dot, *v_res1, *v_res2;
int i;
if ( x == VNULL || out == VNULL ){
error(E_NULL,"f");
}
if ( x->dim != 13 || out->dim != 13){
error(E_SIZES,"f");
}
q = v_get(4);
for (i=0; i<4; i++)
{
q->ve[i] = x->ve[i];
}
w = v_get(3);
for (i=4; i<7; i++)
{
w->ve[i-4] = x->ve[i];
}
v_res1 = v_get(3);
v_zero(v_res1);
v_res2 = v_get(3);
v_zero(v_res2);
q_dot = v_get(4);
v_zero(q_dot);
w_dot = v_get(3);
v_zero(w_dot);
if(iI == MNULL){
iI = m_get(3,3);
m_zero(iI);
}
sk_om = m_get(4,4);
skew_mat(sk_om, w);
mv_mlt(sk_om, q, q_dot);
sv_mlt(0.5, q_dot, q);
for (i=0; i<4; i++)
{
out->ve[i] = q->ve[i];
}
/*****wd********/
m_resize(sk_om, 3, 3);
mv_mlt(inertia, w, v_res1);
mv_mlt(sk_om, v_res1, v_res2);
v_sub(Torq_ext, v_res2, v_res1);
m_inverse(inertia,iI);
mv_mlt(iI, v_res1, w_dot);
for (i=4; i<7; i++)
{
out->ve[i] = w_dot->ve[i-4];
}
for (i=7; i<13; i++)
{
out->ve[i] = 0;
}
M_FREE(sk_om);
//M_FREE(iI);
V_FREE(q);
V_FREE(w);
V_FREE(q_dot);
V_FREE(w_dot);
V_FREE(v_res1);
V_FREE(v_res2);
}
void Ukf(VEC *omega, VEC *mag_vec, VEC *mag_vec_I, VEC *sun_vec, VEC *sun_vec_I, VEC *Torq_ext, double t, double h, int eclipse, VEC *state, VEC *st_error, VEC *residual, int *P_flag, double sim_time)
{
static VEC *omega_prev = VNULL, *mag_vec_prev = VNULL, *sun_vec_prev = VNULL, *q_s_c = VNULL, *x_prev = VNULL, *Torq_prev, *x_m_o;
static MAT *Q = {MNULL}, *R = {MNULL}, *Pprev = {MNULL};
static double alpha, kappa, lambda, sqrt_lambda, w_m_0, w_c_0, w_i, beta;
static int n_states, n_sig_pts, n_err_states, iter_num, initialize=0;
VEC *x = VNULL, *x_priori = VNULL, *x_err_priori = VNULL, *single_sig_pt = VNULL, *v_temp = VNULL, *q_err_quat = VNULL,
*err_vec = VNULL, *v_temp2 = VNULL, *x_ang_vel = VNULL, *meas = VNULL, *meas_priori = VNULL,
*v_temp3 = VNULL, *x_posteriori_err = VNULL, *x_b_m = VNULL, *x_b_g = VNULL;
MAT *sqrt_P = {MNULL}, *P = {MNULL}, *P_priori = {MNULL}, *sig_pt = {MNULL}, *sig_vec_mat = {MNULL},
*err_sig_pt_mat = {MNULL}, *result = {MNULL}, *result_larger = {MNULL}, *result1 = {MNULL}, *Meas_err_mat = {MNULL},
*P_zz = {MNULL}, *iP_vv = {MNULL}, *P_xz = {MNULL}, *K = {MNULL}, *result2 = {MNULL}, *result3 = {MNULL}, *C = {MNULL};
int update_mag_vec, update_sun_vec, update_omega, i, j;
double d_res;
if (inertia == MNULL)
{
inertia = m_get(3,3);
m_ident(inertia);
inertia->me[0][0] = 0.007;
inertia->me[1][1] = 0.014;
inertia->me[2][2] = 0.015;
}
if (initialize == 0){
iter_num = 1;
n_states = (7+6);
n_err_states = (6+6);
n_sig_pts = 2*n_err_states+1;
alpha = sqrt(3);
kappa = 3 - n_states;
lambda = alpha*alpha * (n_err_states+kappa) - n_err_states;
beta = -(1-(alpha*alpha));
w_m_0 = (lambda)/(n_err_states + lambda);
w_c_0 = (lambda/(n_err_states + lambda)) + (1 - (alpha*alpha) + beta);
w_i = 0.5/(n_err_states +lambda);
initialize = 1;
sqrt_lambda = (lambda+n_err_states);
if(q_s_c == VNULL)
{
q_s_c = v_get(4);
q_s_c->ve[0] = -0.020656;
q_s_c->ve[1] = 0.71468;
q_s_c->ve[2] = -0.007319;
q_s_c->ve[3] = 0.6991;
}
if(Torq_prev == VNULL)
{
Torq_prev = v_get(3);
v_zero(Torq_prev);
}
quat_normalize(q_s_c);
}
result = m_get(9,9);
m_zero(result);
result1 = m_get(n_err_states, n_err_states);
m_zero(result1);
if(x_m_o == VNULL)
{
x_m_o = v_get(n_states);
v_zero(x_m_o);
}
x = v_get(n_states);
v_zero(x);
x_err_priori = v_get(n_err_states);
v_zero(x_err_priori);
x_ang_vel = v_get(3);
v_zero(x_ang_vel);
sig_pt = m_get(n_states, n_err_states);
m_zero(sig_pt);
if (C == MNULL)
{
C = m_get(9, 12);
m_zero(C);
}
if (P_priori == MNULL)
{
P_priori = m_get(n_err_states, n_err_states);
m_zero(P_priori);
}
if (Q == MNULL)
{
Q = m_get(n_err_states, n_err_states);
m_ident(Q);
//
Q->me[0][0] = 0.0001;
Q->me[1][1] = 0.0001;
Q->me[2][2] = 0.0001;
Q->me[3][3] = 0.0001;
Q->me[4][4] = 0.0001;
Q->me[5][5] = 0.0001;
Q->me[6][6] = 0.000001;
Q->me[7][7] = 0.000001;
Q->me[8][8] = 0.000001;
Q->me[9][9] = 0.000001;
Q->me[10][10] = 0.000001;
Q->me[11][11] = 0.000001;
}
if( Pprev == MNULL)
{
Pprev = m_get(n_err_states, n_err_states);
m_ident(Pprev);
Pprev->me[0][0] = 1e-3;
Pprev->me[1][1] = 1e-3;
Pprev->me[2][2] = 1e-3;
Pprev->me[3][3] = 1e-3;
Pprev->me[4][4] = 1e-3;
Pprev->me[5][5] = 1e-3;
Pprev->me[6][6] = 1e-4;
Pprev->me[7][7] = 1e-4;
Pprev->me[8][8] = 1e-4;
Pprev->me[9][9] = 1e-3;
Pprev->me[10][10] = 1e-3;
Pprev->me[11][11] = 1e-3;
}
if (R == MNULL)
{
R = m_get(9,9);
m_ident(R);
R->me[0][0] = 0.034;
R->me[1][1] = 0.034;
R->me[2][2] = 0.034;
R->me[3][3] = 0.00027;
R->me[4][4] = 0.00027;
R->me[5][5] = 0.00027;
R->me[6][6] = 0.000012;
R->me[7][7] = 0.000012;
R->me[8][8] = 0.000012;
}
if(eclipse==0)
{
R->me[0][0] = 0.00034;
R->me[1][1] = 0.00034;
R->me[2][2] = 0.00034;
R->me[3][3] = 0.00027;
R->me[4][4] = 0.00027;
R->me[5][5] = 0.00027;
R->me[6][6] = 0.0000012;
R->me[7][7] = 0.0000012;
R->me[8][8] = 0.0000012;
Q->me[0][0] = 0.00001;
Q->me[1][1] = 0.00001;
Q->me[2][2] = 0.00001;
Q->me[3][3] = 0.0001;//0.000012;//0.0175;//1e-3;
Q->me[4][4] = 0.0001;//0.0175;//1e-3;
Q->me[5][5] = 0.0001;//0.0175;//1e-3;
Q->me[6][6] = 0.0000000001;//1e-6;
Q->me[7][7] = 0.0000000001;
Q->me[8][8] = 0.0000000001;
Q->me[9][9] = 0.0000000001;
Q->me[10][10] = 0.0000000001;
Q->me[11][11] = 0.0000000001;
}
else
{
R->me[0][0] = 0.34;
R->me[1][1] = 0.34;
R->me[2][2] = 0.34;
R->me[3][3] = 0.0027;
R->me[4][4] = 0.0027;
R->me[5][5] = 0.0027;
R->me[6][6] = 0.0000012;
R->me[7][7] = 0.0000012;
R->me[8][8] = 0.0000012;
Q->me[0][0] = 0.00001;
Q->me[1][1] = 0.00001;
Q->me[2][2] = 0.00001;
Q->me[3][3] = 0.0001;
Q->me[4][4] = 0.0001;
Q->me[5][5] = 0.0001;
Q->me[6][6] = 0.0000000001;
Q->me[7][7] = 0.0000000001;
Q->me[8][8] = 0.0000000001;
Q->me[9][9] = 0.0000000001;
Q->me[10][10] = 0.0000000001;
Q->me[11][11] = 0.0000000001;
}
if(omega_prev == VNULL)
{
omega_prev = v_get(3);
v_zero(omega_prev);
}
if(mag_vec_prev == VNULL)
{
mag_vec_prev = v_get(3);
v_zero(mag_vec_prev);
}
if(sun_vec_prev == VNULL)
{
sun_vec_prev = v_get(3);
v_zero(sun_vec_prev);
}
if (err_sig_pt_mat == MNULL)
{
err_sig_pt_mat = m_get(n_err_states, n_sig_pts);
m_zero(err_sig_pt_mat);
}
if(q_err_quat == VNULL)
{
q_err_quat = v_get(4);
// q_err_quat = v_resize(q_err_quat,4);
v_zero(q_err_quat);
}
if(err_vec == VNULL)
{
err_vec = v_get(3);
v_zero(err_vec);
}
v_temp = v_get(9);
v_resize(v_temp,3);
if(x_prev == VNULL)
{
x_prev = v_get(n_states);
v_zero(x_prev);
x_prev->ve[3] = 1;
quat_mul(x_prev,q_s_c,x_prev);
x_prev->ve[4] = 0.0;
x_prev->ve[5] = 0.0;
x_prev->ve[6] = 0.0;
x_prev->ve[7] = 0.0;
x_prev->ve[8] = 0.0;
x_prev->ve[9] = 0.0;
x_prev->ve[10] = 0.0;
x_prev->ve[11] = 0.0;
x_prev->ve[12] = 0.0;
}
sqrt_P = m_get(n_err_states, n_err_states);
m_zero(sqrt_P);
//result = m_resize(result, n_err_states, n_err_states);
result_larger = m_get(n_err_states, n_err_states);
int n, m;
for(n = 0; n < result->n; n++)
{
for(m = 0; m < result->m; m++)
{
result_larger->me[m][n] = result->me[m][n];
}
}
//v_resize(v_temp, n_err_states);
V_FREE(v_temp);
v_temp = v_get(n_err_states);
symmeig(Pprev, result_larger, v_temp);
i = 0;
for (j=0;j<n_err_states;j++){
if(v_temp->ve[j]>=0);
else{
i = 1;
}
}
m_copy(Pprev, result1);
sm_mlt(sqrt_lambda, result1, result_larger);
catchall(CHfactor(result_larger), printerr(sim_time));
for(i=0; i<n_err_states; i++){
for(j=i+1; j<n_err_states; j++){
result_larger->me[i][j] = 0;
}
}
expandstate(result_larger, x_prev, sig_pt);
sig_vec_mat = m_get(n_states, n_sig_pts);
m_zero(sig_vec_mat);
for(j = 0; j<(n_err_states+1); j++)
{
for(i = 0; i<n_states; i++)
{
if(j==0)
{
sig_vec_mat->me[i][j] = x_prev->ve[i];
}
else if(j>0)
{
sig_vec_mat->me[i][j] = sig_pt->me[i][j-1];
}
}
}
sm_mlt(-1,result_larger,result_larger);
expandstate(result_larger, x_prev, sig_pt);
for(j = (n_err_states+1); j<n_sig_pts; j++)
{
for(i = 0; i<n_states; i++)
{
sig_vec_mat->me[i][j] = sig_pt->me[i][j-(n_err_states+1)];
}
}
single_sig_pt = v_get(n_states);
quat_rot_vec(q_s_c, Torq_ext);
for(j=0; j<(n_sig_pts); j++)
{
//v_temp = v_resize(v_temp,n_states);
V_FREE(v_temp);
v_temp = v_get(n_states);
get_col(sig_vec_mat, j, single_sig_pt);
v_copy(single_sig_pt, v_temp);
rk4(t, v_temp, h, Torq_prev);
set_col(sig_vec_mat, j, v_temp);
}
v_copy(Torq_ext, Torq_prev);
x_priori = v_get(n_states);
v_zero(x_priori);
v_resize(v_temp,n_states);
v_zero(v_temp);
for(j=0; j<n_sig_pts; j++)
{
get_col( sig_vec_mat, j, v_temp);
if(j == 0)
{
v_mltadd(x_priori, v_temp, w_m_0, x_priori);
}
else
{
v_mltadd(x_priori, v_temp, w_i, x_priori);
}
}
v_copy(x_priori, v_temp);
v_resize(v_temp,4);
quat_normalize(v_temp);//zaroori hai ye
for(i=0; i<4; i++)
{
x_priori->ve[i] = v_temp->ve[i];
}
v_resize(v_temp, n_states);
v_copy(x_priori, v_temp);
v_resize(v_temp, 4);
quat_inv(v_temp, v_temp);
for(i=0; i<3; i++)
{
x_ang_vel->ve[i] = x_priori->ve[i+4];
}
x_b_m = v_get(3);
v_zero(x_b_m);
x_b_g = v_get(3);
v_zero(x_b_g);
/////////////////////////check it!!!!!!!! checked... doesnt change much the estimate
for(i=0; i<3; i++)
{
x_b_m->ve[i] = x_priori->ve[i+7];
x_b_g->ve[i] = x_priori->ve[i+10];
}
v_temp2 = v_get(n_states);
v_zero(v_temp2);
for(j=0; j<n_sig_pts; j++)
{
v_resize(v_temp2, n_states);
get_col( sig_vec_mat, j, v_temp2);
for(i=0; i<3; i++)
{
err_vec->ve[i] = v_temp2->ve[i+4];
}
v_resize(v_temp2, 4);
quat_mul(v_temp2, v_temp, q_err_quat);
v_resize(q_err_quat, n_err_states);
v_sub(err_vec, x_ang_vel, err_vec);
for(i=3; i<6; i++)
{
q_err_quat->ve[i] = err_vec->ve[i-3];
}
for(i=0; i<3; i++)
{
err_vec->ve[i] = v_temp2->ve[i+7];
}
v_sub(err_vec, x_b_m, err_vec);
for(i=6; i<9; i++)
{
q_err_quat->ve[i] = err_vec->ve[i-6];
}
for(i=0; i<3; i++)
{
err_vec->ve[i] = v_temp2->ve[i+10];
}
v_sub(err_vec, x_b_g, err_vec);
for(i=9; i<12; i++)
{
q_err_quat->ve[i] = err_vec->ve[i-9];
}
set_col(err_sig_pt_mat, j, q_err_quat);
if(j==0){
v_mltadd(x_err_priori, q_err_quat, w_m_0, x_err_priori);
}
else{
v_mltadd(x_err_priori, q_err_quat, w_i, x_err_priori);
}
}
v_resize(v_temp,n_err_states);
for (j=0;j<13;j++)
{
get_col(err_sig_pt_mat, j, v_temp);
v_sub(v_temp, x_err_priori, v_temp);
get_dyad(v_temp, v_temp, result_larger);
if(j==0){
sm_mlt(w_c_0, result_larger, result_larger);
}
else{
sm_mlt(w_i, result_larger, result_larger);
}
m_add(P_priori, result_larger, P_priori);
}
symmeig(P_priori, result_larger, v_temp);
i = 0;
for (j=0;j<n_err_states;j++){
if(v_temp->ve[j]>=0);
else{
i = 1;
}
}
m_add(P_priori, Q, P_priori);
v_resize(v_temp,3);
meas = v_get(9);
if (!(is_vec_equal(sun_vec, sun_vec_prev)) /*&& (eclipse==0)*/ ){
update_sun_vec =1;
v_copy(sun_vec, sun_vec_prev);
v_copy(sun_vec, v_temp);
normalize_vec(v_temp);
quat_rot_vec(q_s_c, v_temp);
normalize_vec(v_temp);
for(i = 0; i<3;i++){
meas->ve[i] = v_temp->ve[i];
}
}
else{
update_sun_vec =0;
for(i = 0; i<3;i++){
meas->ve[i] = 0;
}
}
if (!(is_vec_equal(mag_vec, mag_vec_prev)) ){
update_mag_vec =1;
v_copy(mag_vec, mag_vec_prev);
v_copy(mag_vec, v_temp);
normalize_vec(v_temp);
quat_rot_vec(q_s_c, v_temp);
normalize_vec(v_temp);
for(i=3; i<6; i++){
meas->ve[i] = v_temp->ve[i-3];
}
}
else{
update_mag_vec =0;
for(i=3; i<6; i++){
meas->ve[i] = 0;//mag_vec_prev->ve[i-3];
}
}
if (!(is_vec_equal(omega, omega_prev) ) ){
update_omega =1;
v_copy(omega, omega_prev);
v_copy(omega, v_temp);
quat_rot_vec(q_s_c, v_temp);
for(i=6; i<9; i++){
meas->ve[i] = v_temp->ve[i-6];
}
}
else{
update_omega =0;
for(i=6; i<9; i++){
meas->ve[i] = 0;
}
}
v_resize(v_temp, 9);
v_resize(v_temp2, n_states);
v_temp3 = v_get(3);
Meas_err_mat = m_get(9, n_sig_pts);
m_zero(Meas_err_mat);
meas_priori = v_get(9);
v_zero(meas_priori);
for(j=0; j<n_sig_pts; j++)
{
get_col( sig_vec_mat, j, v_temp2);
if(update_omega){
for(i=6;i<9;i++){
v_temp->ve[i] = v_temp2->ve[i-2] + x_b_g->ve[i-6];
}
}
else{
for(i=6;i<9;i++){
v_temp->ve[i] = 0;
}
}
v_resize(v_temp2, 4);
if(update_sun_vec){
for(i=0;i<3;i++){
v_temp3->ve[i] = sun_vec_I->ve[i];
}
quat_rot_vec(v_temp2, v_temp3);
normalize_vec(v_temp3);
for(i=0;i<3;i++){
v_temp->ve[i] = v_temp3->ve[i];
}
}
else{
for(i=0;i<3;i++){
v_temp->ve[i] = 0;
}
}
if(update_mag_vec){
for(i=0;i<3;i++){
v_temp3->ve[i] = mag_vec_I->ve[i];
}
normalize_vec(v_temp3);
for(i=0;i<3;i++){
v_temp3->ve[i] = v_temp3->ve[i] + x_b_m->ve[i];
}
quat_rot_vec(v_temp2, v_temp3);
normalize_vec(v_temp3);
for(i=3;i<6;i++){
v_temp->ve[i] = v_temp3->ve[i-3];
}
}
else{
for(i=3;i<6;i++){
v_temp->ve[i] = 0;
}
}
set_col(Meas_err_mat, j, v_temp);
if(j==0){
v_mltadd(meas_priori, v_temp, w_m_0, meas_priori);
}
else{
v_mltadd(meas_priori, v_temp, w_i, meas_priori);
}
}
v_resize(v_temp, 9);
m_resize(result_larger, 9, 9);
m_zero(result_larger);
P_zz = m_get(9, 9);
m_zero(P_zz);
iP_vv = m_get(9, 9);
m_zero(iP_vv);
P_xz = m_get(n_err_states, 9);
m_zero(P_xz);
v_resize(v_temp2, n_err_states);
result1 = m_resize(result1,n_err_states,9);
for (j=0; j<n_sig_pts; j++)
{
get_col( Meas_err_mat, j, v_temp);
get_col( err_sig_pt_mat, j, v_temp2);
v_sub(v_temp, meas_priori, v_temp);
get_dyad(v_temp, v_temp, result_larger);
get_dyad(v_temp2, v_temp, result1);
if(j==0){
sm_mlt(w_c_0, result_larger, result_larger);
sm_mlt(w_c_0, result1, result1);
}
else{
sm_mlt(w_i, result_larger, result_larger);
sm_mlt(w_i, result1, result1);
}
m_add(P_zz, result_larger, P_zz);
m_add(P_xz, result1, P_xz);
}
symmeig(P_zz, result_larger, v_temp);
i = 0;
for (j=0; j<9; j++){
if(v_temp->ve[j]>=0);
else{
i = 1;
}
}
m_add(P_zz, R, P_zz);
m_inverse(P_zz, iP_vv);
K = m_get(n_err_states, 9);
m_zero(K);
m_mlt(P_xz, iP_vv, K);
if(x_posteriori_err == VNULL)
{
x_posteriori_err = v_get(n_err_states);
v_zero(x_posteriori_err);
}
v_resize(v_temp,9);
v_sub(meas, meas_priori, v_temp);
v_copy(v_temp, residual);
mv_mlt(K, v_temp, x_posteriori_err);
v_resize(v_temp2,3);
for(i=0;i<3;i++){
v_temp2->ve[i] = x_posteriori_err->ve[i];
}
for(i=4; i<n_states; i++){
x_prev->ve[i] = (x_posteriori_err->ve[i-1] + x_priori->ve[i]);
}
d_res = v_norm2(v_temp2);
v_resize(v_temp2,4);
if(d_res<=1 /*&& d_res!=0*/){
v_temp2->ve[0] = v_temp2->ve[0];
v_temp2->ve[1] = v_temp2->ve[1];
v_temp2->ve[2] = v_temp2->ve[2];
v_temp2->ve[3] = sqrt(1-d_res);
}
else//baad main daala hai
{
v_temp2->ve[0] = (v_temp2->ve[0])/(sqrt(1+d_res));
v_temp2->ve[1] = (v_temp2->ve[1])/(sqrt(1+d_res));
v_temp2->ve[2] = (v_temp2->ve[2])/(sqrt(1+d_res));
v_temp2->ve[3] = 1/sqrt(1 + d_res);
}
v_resize(x_posteriori_err, n_states);
for(i=(n_states-1); i>3; i--){
x_posteriori_err->ve[i] = x_posteriori_err->ve[i-1];
}
for(i=0; i<4; i++){
x_posteriori_err->ve[i] = v_temp2->ve[i];
}
quat_mul(v_temp2, x_priori, v_temp2);
for(i=0;i<4;i++){
x_prev->ve[i] = v_temp2->ve[i];
}
m_resize(result_larger, n_err_states, 9);
m_mlt(K, P_zz, result_larger);
result2 = m_get(9, n_err_states);
m_transp(K,result2);
m_resize(result1, n_err_states, n_err_states);
m_mlt(result_larger, result2, result1);
v_resize(v_temp, n_err_states);
m_sub(P_priori, result1, Pprev);
symmeig(Pprev, result1 , v_temp);
i = 0;
for (j=0;j<n_err_states;j++){
if(v_temp->ve[j]>=0);
else{
i = 1;
}
}
v_copy(x_prev, v_temp);
v_resize(v_temp,4);
v_copy(x_prev, v_temp2);
v_resize(v_temp2,4);
v_copy(x_prev, x_m_o);
//v_resize(x_m_o, 4);
v_resize(v_temp,3);
quat_inv(q_s_c, v_temp2);
v_copy( x_prev, state);
quat_mul(state, v_temp2, state);
for(i=0; i<3; i++){
v_temp->ve[i] = state->ve[i+4];
}
quat_rot_vec(v_temp2, v_temp);
for(i=0; i<3; i++){
state->ve[i+4] = v_temp->ve[i];
}
v_copy( x_posteriori_err, st_error);
iter_num++;
V_FREE(x);
V_FREE(x_priori);
V_FREE(x_err_priori);
V_FREE(single_sig_pt);
V_FREE(v_temp);
V_FREE(q_err_quat);
V_FREE(err_vec);
V_FREE(v_temp2);
V_FREE(x_ang_vel);
V_FREE(meas);
V_FREE(meas_priori);
V_FREE(v_temp3);
V_FREE(x_posteriori_err);
V_FREE(x_b_m);
V_FREE(x_b_g);
M_FREE(sqrt_P);
M_FREE(P);
M_FREE(P_priori);
M_FREE(sig_pt);
M_FREE(sig_vec_mat);
M_FREE(err_sig_pt_mat);
M_FREE(result);
M_FREE(result_larger);
M_FREE(result1);
M_FREE(Meas_err_mat);
M_FREE(P_zz);
M_FREE(iP_vv);
M_FREE(P_xz);
M_FREE(K);
M_FREE(result2);
M_FREE(result3);
}
static int reml(VEC *Y, MAT *X, MAT **Vk, int n_k, int max_iter,
double fit_limit, VEC *teta) {
volatile int n_iter = 0;
int i;
volatile double rel_step = DBL_MAX;
VEC *rhs = VNULL;
VEC *dteta = VNULL;
MAT *Vw = MNULL, *Tr_m = MNULL, *VinvIminAw = MNULL;
Vw = m_resize(Vw, X->m, X->m);
VinvIminAw = m_resize(VinvIminAw, X->m, X->m);
rhs = v_resize(rhs, n_k);
Tr_m = m_resize(Tr_m, n_k, n_k);
dteta = v_resize(dteta, n_k);
while (n_iter < max_iter && rel_step > fit_limit) {
print_progress(n_iter, max_iter);
n_iter++;
dteta = v_copy(teta, dteta);
/* fill Vw, calc VinvIminAw, rhs; */
for (i = 0, m_zero(Vw); i < n_k; i++)
ms_mltadd(Vw, Vk[i], teta->ve[i], Vw); /* Vw = Sum_i teta[i]*V[i] */
VinvIminAw = calc_VinvIminAw(Vw, X, VinvIminAw, n_iter == 1);
calc_rhs_Tr_m(n_k, Vk, VinvIminAw, Y, rhs, Tr_m);
/* Tr_m * teta = Rhs; symmetric, solve for teta: */
LDLfactor(Tr_m);
LDLsolve(Tr_m, rhs, teta);
if (DEBUG_VGMFIT) {
printlog("teta_%d [", n_iter);
for (i = 0; i < teta->dim; i++)
printlog(" %g", teta->ve[i]);
printlog("] -(log.likelyhood): %g\n",
calc_ll(Vw, X, Y, n_k));
}
v_sub(teta, dteta, dteta); /* dteta = teta_prev - teta_curr */
if (v_norm2(teta) == 0.0)
rel_step = 0.0;
else
rel_step = v_norm2(dteta) / v_norm2(teta);
} /* while (n_iter < gl_iter && rel_step > fit_limit) */
print_progress(max_iter, max_iter);
if (n_iter == gl_iter)
pr_warning("No convergence after %d iterations", n_iter);
if (DEBUG_VGMFIT) { /* calculate and report covariance matrix */
/* first, update to current est */
for (i = 0, m_zero(Vw); i < n_k; i++)
ms_mltadd(Vw, Vk[i], teta->ve[i], Vw); /* Vw = Sum_i teta[i]*V[i] */
VinvIminAw = calc_VinvIminAw(Vw, X, VinvIminAw, 0);
calc_rhs_Tr_m(n_k, Vk, VinvIminAw, Y, rhs, Tr_m);
m_inverse(Tr_m, Tr_m);
sm_mlt(2.0, Tr_m, Tr_m); /* Var(YAY)=2tr(AVAV) */
printlog("Lower bound of parameter covariance matrix:\n");
m_logoutput(Tr_m);
printlog("# Negative log-likelyhood: %g\n", calc_ll(Vw, X, Y, n_k));
}
m_free(Vw);
m_free(VinvIminAw);
m_free(Tr_m);
v_free(rhs);
v_free(dteta);
return (n_iter < max_iter && rel_step < fit_limit); /* converged? */
}
/*
* n_vars is the number of variables to be considered,
* d is the data array of variables d[0],...,d[n_vars-1],
* pred determines which estimate is required: BLUE, BLUP, or BLP
*/
void gls(DATA **d /* pointer to DATA array */,
int n_vars, /* length of DATA array (to consider) */
enum GLS_WHAT pred, /* what type of prediction is requested */
DPOINT *where, /* prediction location */
double *est /* output: array that holds the predicted values and variances */)
{
GLM *glm = NULL; /* to be copied to/from d */
static MAT *X0 = MNULL, *C0 = MNULL, *MSPE = MNULL, *CinvC0 = MNULL,
*Tmp1 = MNULL, *Tmp2 = MNULL, *Tmp3 = MNULL, *R = MNULL;
static VEC *blup = VNULL, *tmpa = VNULL, *tmpb = VNULL;
PERM *piv = PNULL;
volatile unsigned int i, rows_C;
unsigned int j, k, l = 0, row, col, start_i, start_j, start_X, global,
one_nbh_empty;
VARIOGRAM *v = NULL;
static enum GLS_WHAT last_pred = GLS_INIT; /* the initial value */
double c_value, *X_ori;
int info;
if (d == NULL) { /* clean up */
if (X0 != MNULL) M_FREE(X0);
if (C0 != MNULL) M_FREE(C0);
if (MSPE != MNULL) M_FREE(MSPE);
if (CinvC0 != MNULL) M_FREE(CinvC0);
if (Tmp1 != MNULL) M_FREE(Tmp1);
if (Tmp2 != MNULL) M_FREE(Tmp2);
if (Tmp3 != MNULL) M_FREE(Tmp3);
if (R != MNULL) M_FREE(R);
if (blup != VNULL) V_FREE(blup);
if (tmpa != VNULL) V_FREE(tmpa);
if (tmpb != VNULL) V_FREE(tmpb);
last_pred = GLS_INIT;
return;
}
if (DEBUG_COV) {
printlog("we're at %s X: %g Y: %g Z: %g\n",
IS_BLOCK(where) ? "block" : "point",
where->x, where->y, where->z);
}
if (pred != UPDATE) /* it right away: */
last_pred = pred;
assert(last_pred != GLS_INIT);
if (d[0]->glm == NULL) { /* allocate and initialize: */
glm = new_glm();
d[0]->glm = (void *) glm;
} else
glm = (GLM *) d[0]->glm;
glm->mu0 = v_resize(glm->mu0, n_vars);
MSPE = m_resize(MSPE, n_vars, n_vars);
if (pred == GLS_BLP || UPDATE_BLP) {
X_ori = where->X;
for (i = 0; i < n_vars; i++) { /* mu(0) */
glm->mu0->ve[i] = calc_mu(d[i], where);
blup = v_copy(glm->mu0, v_resize(blup, glm->mu0->dim));
where->X += d[i]->n_X; /* shift to next x0 entry */
}
where->X = X_ori; /* ... and set back */
for (i = 0; i < n_vars; i++) { /* Cij(0,0): */
for (j = 0; j <= i; j++) {
v = get_vgm(LTI(d[i]->id,d[j]->id));
ME(MSPE, i, j) = ME(MSPE, j, i) = COVARIANCE0(v, where, where, d[j]->pp_norm2);
}
}
fill_est(NULL, blup, MSPE, n_vars, est); /* in case of empty neighbourhood */
}
/* xxx */
/*
logprint_variogram(v, 1);
*/
/*
* selection dependent problem dimensions:
*/
for (i = rows_C = 0, one_nbh_empty = 0; i < n_vars; i++) {
rows_C += d[i]->n_sel;
if (d[i]->n_sel == 0)
one_nbh_empty = 1;
}
if (rows_C == 0 /* all selection lists empty */
|| one_nbh_empty == 1) { /* one selection list empty */
if (pred == GLS_BLP || UPDATE_BLP)
debug_result(blup, MSPE, pred);
return;
}
for (i = 0, global = 1; i < n_vars && global; i++)
global = (d[i]->sel == d[i]->list
&& d[i]->n_list == d[i]->n_original
&& d[i]->n_list == d[i]->n_sel);
/*
* global things: enter whenever (a) first time, (b) local selections or
* (c) the size of the problem grew since the last call (e.g. simulation)
*/
if (glm->C == NULL || !global || rows_C > glm->C->m) {
/*
* fill y:
*/
glm->y = get_y(d, glm->y, n_vars);
if (pred != UPDATE) {
glm->C = m_resize(glm->C, rows_C, rows_C);
if (gl_choleski == 0) /* use LDL' decomposition, allocate piv: */
piv = px_resize(piv, rows_C);
m_zero(glm->C);
glm->X = get_X(d, glm->X, n_vars);
M_DEBUG(glm->X, "X");
glm->CinvX = m_resize(glm->CinvX, rows_C, glm->X->n);
glm->XCinvX = m_resize(glm->XCinvX, glm->X->n, glm->X->n);
glm->beta = v_resize(glm->beta, glm->X->n);
for (i = start_X = start_i = 0; i < n_vars; i++) { /* row var */
/* fill C, mu: */
for (j = start_j = 0; j <= i; j++) { /* col var */
v = get_vgm(LTI(d[i]->id,d[j]->id));
for (k = 0; k < d[i]->n_sel; k++) { /* rows */
row = start_i + k;
for (l = 0, col = start_j; col <= row && l < d[j]->n_sel; l++, col++) {
if (pred == GLS_BLUP)
c_value = GCV(v, d[i]->sel[k], d[j]->sel[l]);
else
c_value = COVARIANCE(v, d[i]->sel[k], d[j]->sel[l]);
/* on the diagonal, if necessary, add measurement error variance */
if (d[i]->colnvariance && i == j && k == l)
c_value += d[i]->sel[k]->variance;
ME(glm->C, col, row) = c_value; /* fill upper */
if (col != row)
ME(glm->C, row, col) = c_value; /* fill all */
} /* for l */
} /* for k */
start_j += d[j]->n_sel;
} /* for j */
start_i += d[i]->n_sel;
if (d[i]->n_sel > 0)
start_X += d[i]->n_X - d[i]->n_merge;
} /* for i */
/*
if (d[0]->colnvmu)
glm->C = convert_vmuC(glm->C, d[0]);
*/
if (d[0]->variance_fn) {
glm->mu = get_mu(glm->mu, glm->y, d, n_vars);
convert_C(glm->C, glm->mu, d[0]->variance_fn);
}
if (DEBUG_COV && pred == GLS_BLUP)
printlog("[using generalized covariances: max_val - semivariance()]");
M_DEBUG(glm->C, "Covariances (x_i, x_j) matrix C (upper triangle)");
/*
* factorize C:
*/
CHfactor(glm->C, piv, &info);
if (info != 0) { /* singular: */
pr_warning("Covariance matrix singular at location [%g,%g,%g]: skipping...",
where->x, where->y, where->z);
m_free(glm->C);
glm->C = MNULL; /* assure re-entrance if global */
P_FREE(piv);
return;
}
if (piv == NULL)
M_DEBUG(glm->C, "glm->C, Choleski decomposed:")
else
M_DEBUG(glm->C, "glm->C, LDL' decomposed:")
} /* if (pred != UPDATE) */
MAT *iter_arnoldi_iref(ITER *ip, Real *h_rem, MAT *Q, MAT *H)
#endif
{
STATIC VEC *u=VNULL, *r=VNULL, *s=VNULL, *tmp=VNULL;
VEC v; /* auxiliary vector */
int i,j;
Real h_val, c;
if (ip == INULL)
error(E_NULL,"iter_arnoldi_iref");
if ( ! ip->Ax || ! Q || ! ip->x )
error(E_NULL,"iter_arnoldi_iref");
if ( ip->k <= 0 )
error(E_BOUNDS,"iter_arnoldi_iref");
if ( Q->n != ip->x->dim || Q->m != ip->k )
error(E_SIZES,"iter_arnoldi_iref");
m_zero(Q);
H = m_resize(H,ip->k,ip->k);
m_zero(H);
u = v_resize(u,ip->x->dim);
r = v_resize(r,ip->k);
s = v_resize(s,ip->k);
tmp = v_resize(tmp,ip->x->dim);
MEM_STAT_REG(u,TYPE_VEC);
MEM_STAT_REG(r,TYPE_VEC);
MEM_STAT_REG(s,TYPE_VEC);
MEM_STAT_REG(tmp,TYPE_VEC);
v.dim = v.max_dim = ip->x->dim;
c = v_norm2(ip->x);
if ( c <= 0.0)
return H;
else {
v.ve = Q->me[0];
sv_mlt(1.0/c,ip->x,&v);
}
v_zero(r);
v_zero(s);
for ( i = 0; i < ip->k; i++ )
{
v.ve = Q->me[i];
u = (ip->Ax)(ip->A_par,&v,u);
for (j = 0; j <= i; j++) {
v.ve = Q->me[j];
/* modified Gram-Schmidt */
r->ve[j] = in_prod(&v,u);
v_mltadd(u,&v,-r->ve[j],u);
}
h_val = v_norm2(u);
/* if u == 0 then we have an exact subspace */
if ( h_val <= 0.0 )
{
*h_rem = h_val;
return H;
}
/* iterative refinement -- ensures near orthogonality */
do {
v_zero(tmp);
for (j = 0; j <= i; j++) {
v.ve = Q->me[j];
s->ve[j] = in_prod(&v,u);
v_mltadd(tmp,&v,s->ve[j],tmp);
}
v_sub(u,tmp,u);
v_add(r,s,r);
} while ( v_norm2(s) > 0.1*(h_val = v_norm2(u)) );
/* now that u is nearly orthogonal to Q, update H */
set_col(H,i,r);
/* check once again if h_val is zero */
if ( h_val <= 0.0 )
{
*h_rem = h_val;
return H;
}
if ( i == ip->k-1 )
{
*h_rem = h_val;
continue;
}
/* H->me[i+1][i] = h_val; */
m_set_val(H,i+1,i,h_val);
v.ve = Q->me[i+1];
sv_mlt(1.0/h_val,u,&v);
}
#ifdef THREADSAFE
V_FREE(u);
V_FREE(r);
V_FREE(s);
V_FREE(tmp);
#endif
return H;
}
MAT *iter_arnoldi(ITER *ip, Real *h_rem, MAT *Q, MAT *H)
#endif
{
STATIC VEC *u=VNULL, *r=VNULL;
VEC v; /* auxiliary vector */
int i,j;
Real h_val, c;
if (ip == INULL)
error(E_NULL,"iter_arnoldi");
if ( ! ip->Ax || ! Q || ! ip->x )
error(E_NULL,"iter_arnoldi");
if ( ip->k <= 0 )
error(E_BOUNDS,"iter_arnoldi");
if ( Q->n != ip->x->dim || Q->m != ip->k )
error(E_SIZES,"iter_arnoldi");
m_zero(Q);
H = m_resize(H,ip->k,ip->k);
m_zero(H);
u = v_resize(u,ip->x->dim);
r = v_resize(r,ip->k);
MEM_STAT_REG(u,TYPE_VEC);
MEM_STAT_REG(r,TYPE_VEC);
v.dim = v.max_dim = ip->x->dim;
c = v_norm2(ip->x);
if ( c <= 0.0)
return H;
else {
v.ve = Q->me[0];
sv_mlt(1.0/c,ip->x,&v);
}
v_zero(r);
for ( i = 0; i < ip->k; i++ )
{
v.ve = Q->me[i];
u = (ip->Ax)(ip->A_par,&v,u);
for (j = 0; j <= i; j++) {
v.ve = Q->me[j];
/* modified Gram-Schmidt */
r->ve[j] = in_prod(&v,u);
v_mltadd(u,&v,-r->ve[j],u);
}
h_val = v_norm2(u);
/* if u == 0 then we have an exact subspace */
if ( h_val <= 0.0 )
{
*h_rem = h_val;
return H;
}
set_col(H,i,r);
if ( i == ip->k-1 )
{
*h_rem = h_val;
continue;
}
/* H->me[i+1][i] = h_val; */
m_set_val(H,i+1,i,h_val);
v.ve = Q->me[i+1];
sv_mlt(1.0/h_val,u,&v);
}
#ifdef THREADSAFE
V_FREE(u);
V_FREE(r);
#endif
return H;
}
/*
* n_vars is the number of variables to be considered,
* d is the data array of variables d[0],...,d[n_vars-1],
* pred determines which estimate is required: BLUE, BLUP, or BLP
*/
void gls(DATA **d /* pointer to DATA array */,
int n_vars, /* length of DATA array (to consider) */
enum GLS_WHAT pred, /* what type of prediction is requested */
DPOINT *where, /* prediction location */
double *est /* output: array that holds the predicted values and variances */)
{
GLM *glm = NULL; /* to be copied to/from d */
static MAT *X0 = MNULL, *C0 = MNULL, *MSPE = MNULL, *CinvC0 = MNULL,
*Tmp1 = MNULL, *Tmp2 = MNULL, *Tmp3, *R = MNULL;
static VEC *blup = VNULL, *tmpa = VNULL, *tmpb = VNULL;
volatile unsigned int i, rows_C;
unsigned int j, k, l = 0, row, col, start_i, start_j, start_X, global;
VARIOGRAM *v = NULL;
static enum GLS_WHAT last_pred = GLS_INIT; /* the initial value */
double c_value, *X_ori;
if (d == NULL) { /* clean up */
if (X0 != MNULL) M_FREE(X0);
if (C0 != MNULL) M_FREE(C0);
if (MSPE != MNULL) M_FREE(MSPE);
if (CinvC0 != MNULL) M_FREE(CinvC0);
if (Tmp1 != MNULL) M_FREE(Tmp1);
if (Tmp2 != MNULL) M_FREE(Tmp2);
if (Tmp3 != MNULL) M_FREE(Tmp3);
if (R != MNULL) M_FREE(R);
if (blup != VNULL) V_FREE(blup);
if (tmpa != VNULL) V_FREE(tmpa);
if (tmpb != VNULL) V_FREE(tmpb);
last_pred = GLS_INIT;
return;
}
#ifndef HAVE_SPARSE
if (gl_sparse) {
pr_warning("sparse matrices not supported: compile with --with-sparse");
gl_sparse = 0;
}
#endif
if (DEBUG_COV) {
printlog("we're at %s X: %g Y: %g Z: %g\n",
IS_BLOCK(where) ? "block" : "point",
where->x, where->y, where->z);
}
if (pred != UPDATE) /* it right away: */
last_pred = pred;
assert(last_pred != GLS_INIT);
if (d[0]->glm == NULL) { /* allocate and initialize: */
glm = new_glm();
d[0]->glm = (void *) glm;
} else
glm = (GLM *) d[0]->glm;
glm->mu0 = v_resize(glm->mu0, n_vars);
MSPE = m_resize(MSPE, n_vars, n_vars);
if (pred == GLS_BLP || UPDATE_BLP) {
X_ori = where->X;
for (i = 0; i < n_vars; i++) { /* mu(0) */
glm->mu0->ve[i] = calc_mu(d[i], where);
blup = v_copy(glm->mu0, v_resize(blup, glm->mu0->dim));
where->X += d[i]->n_X; /* shift to next x0 entry */
}
where->X = X_ori; /* ... and set back */
for (i = 0; i < n_vars; i++) { /* Cij(0,0): */
for (j = 0; j <= i; j++) {
v = get_vgm(LTI(d[i]->id,d[j]->id));
MSPE->me[i][j] = MSPE->me[j][i] = COVARIANCE0(v, where, where, d[j]->pp_norm2);
}
}
fill_est(NULL, blup, MSPE, n_vars, est); /* in case of empty neighbourhood */
}
/* xxx */
/*
logprint_variogram(v, 1);
*/
/*
* selection dependent problem dimensions:
*/
for (i = rows_C = 0; i < n_vars; i++)
rows_C += d[i]->n_sel;
if (rows_C == 0) { /* empty selection list(s) */
if (pred == GLS_BLP || UPDATE_BLP)
debug_result(blup, MSPE, pred);
return;
}
for (i = 0, global = 1; i < n_vars && global; i++)
global = (d[i]->sel == d[i]->list && d[i]->n_list == d[i]->n_original);
/*
* global things: enter whenever (a) first time, (b) local selections or
* (c) the size of the problem grew since the last call (e.g. simulation)
*/
if ((glm->C == NULL && glm->spC == NULL) || !global || rows_C > glm->C->m) {
/*
* fill y:
*/
glm->y = get_y(d, glm->y, n_vars);
if (pred != UPDATE) {
if (! gl_sparse) {
glm->C = m_resize(glm->C, rows_C, rows_C);
m_zero(glm->C);
}
#ifdef HAVE_SPARSE
else {
if (glm->C == NULL) {
glm->spC = sp_get(rows_C, rows_C, gl_sparse);
/* d->spLLT = spLLT = sp_get(rows_C, rows_C, gl_sparse); */
} else {
glm->spC = sp_resize(glm->spC, rows_C, rows_C);
/* d->spLLT = spLLT = sp_resize(spLLT, rows_C, rows_C); */
}
sp_zero(glm->spC);
}
#endif
glm->X = get_X(d, glm->X, n_vars);
M_DEBUG(glm->X, "X");
glm->CinvX = m_resize(glm->CinvX, rows_C, glm->X->n);
glm->XCinvX = m_resize(glm->XCinvX, glm->X->n, glm->X->n);
glm->beta = v_resize(glm->beta, glm->X->n);
for (i = start_X = start_i = 0; i < n_vars; i++) { /* row var */
/* fill C, mu: */
for (j = start_j = 0; j <= i; j++) { /* col var */
v = get_vgm(LTI(d[i]->id,d[j]->id));
for (k = 0; k < d[i]->n_sel; k++) { /* rows */
row = start_i + k;
for (l = 0, col = start_j; col <= row && l < d[j]->n_sel; l++, col++) {
if (pred == GLS_BLUP)
c_value = GCV(v, d[i]->sel[k], d[j]->sel[l]);
else
c_value = COVARIANCE(v, d[i]->sel[k], d[j]->sel[l]);
/* on the diagonal, if necessary, add measurement error variance */
if (d[i]->colnvariance && i == j && k == l)
c_value += d[i]->sel[k]->variance;
if (! gl_sparse)
glm->C->me[row][col] = c_value;
#ifdef HAVE_SPARSE
else {
if (c_value != 0.0)
sp_set_val(glm->spC, row, col, c_value);
}
#endif
} /* for l */
} /* for k */
start_j += d[j]->n_sel;
} /* for j */
start_i += d[i]->n_sel;
if (d[i]->n_sel > 0)
start_X += d[i]->n_X - d[i]->n_merge;
} /* for i */
/*
if (d[0]->colnvmu)
glm->C = convert_vmuC(glm->C, d[0]);
*/
if (d[0]->variance_fn) {
glm->mu = get_mu(glm->mu, glm->y, d, n_vars);
convert_C(glm->C, glm->mu, d[0]->variance_fn);
}
if (DEBUG_COV && pred == GLS_BLUP)
printlog("[using generalized covariances: max_val - semivariance()]");
if (! gl_sparse) {
M_DEBUG(glm->C, "Covariances (x_i, x_j) matrix C (lower triangle only)");
}
#ifdef HAVE_SPARSE
else {
SM_DEBUG(glm->spC, "Covariances (x_i, x_j) sparse matrix C (lower triangle only)")
}
#endif
/* check for singular C: */
if (! gl_sparse && gl_cn_max > 0.0) {
for (i = 0; i < rows_C; i++) /* row */
for (j = i+1; j < rows_C; j++) /* col > row */
glm->C->me[i][j] = glm->C->me[j][i]; /* fill symmetric */
if (is_singular(glm->C, gl_cn_max)) {
pr_warning("Covariance matrix (nearly) singular at location [%g,%g,%g]: skipping...",
where->x, where->y, where->z);
m_free(glm->C); glm->C = MNULL; /* assure re-entrance if global */
return;
}
}
/*
* factorize C:
*/
if (! gl_sparse)
LDLfactor(glm->C);
#ifdef HAVE_SPARSE
else {
sp_compact(glm->spC, 0.0);
spCHfactor(glm->spC);
}
#endif
} /* if (pred != UPDATE) */
if (pred != GLS_BLP && !UPDATE_BLP) { /* C-1 X and X'C-1 X, beta */
/*
* calculate CinvX:
*/
tmpa = v_resize(tmpa, rows_C);
for (i = 0; i < glm->X->n; i++) {
tmpa = get_col(glm->X, i, tmpa);
if (! gl_sparse)
tmpb = LDLsolve(glm->C, tmpa, tmpb);
#ifdef HAVE_SPARSE
else
tmpb = spCHsolve(glm->spC, tmpa, tmpb);
#endif
set_col(glm->CinvX, i, tmpb);
}
/*
* calculate X'C-1 X:
*/
glm->XCinvX = mtrm_mlt(glm->X, glm->CinvX, glm->XCinvX); /* X'C-1 X */
M_DEBUG(glm->XCinvX, "X'C-1 X");
if (gl_cn_max > 0.0 && is_singular(glm->XCinvX, gl_cn_max)) {
pr_warning("X'C-1 X matrix (nearly) singular at location [%g,%g,%g]: skipping...",
where->x, where->y, where->z);
m_free(glm->C); glm->C = MNULL; /* assure re-entrance if global */
return;
}
m_inverse(glm->XCinvX, glm->XCinvX);
/*
* calculate beta:
*/
tmpa = vm_mlt(glm->CinvX, glm->y, tmpa); /* X'C-1 y */
glm->beta = vm_mlt(glm->XCinvX, tmpa, glm->beta); /* (X'C-1 X)-1 X'C-1 y */
V_DEBUG(glm->beta, "beta");
M_DEBUG(glm->XCinvX, "Cov(beta), (X'C-1 X)-1");
M_DEBUG(R = get_corr_mat(glm->XCinvX, R), "Corr(beta)");
} /* if pred != GLS_BLP */
} /* if redo the heavy part */