int model_z2fk(model* m, int vid, double fi, double fj, double z, double* fk)
{
void* grid = m->grids[m->vars[vid].gridid];
int isperiodic_x = grid_isperiodic_x(grid);
int** numlevels = grid_getnumlevels(grid);
int ni, nj;
int i1, i2, j1, j2, k2;
if (isnan(fi + fj)) {
*fk = NaN;
return STATUS_OUTSIDEGRID;
}
grid_z2fk(grid, fi, fj, z, fk);
if (isnan(*fk))
return STATUS_OUTSIDEGRID;
if (grid_getvtype(grid) == GRIDVTYPE_SIGMA)
return STATUS_OK;
/*
* a depth check for z-grid:
*/
model_getvardims(m, vid, &ni, &nj, NULL);
i1 = floor(fi);
i2 = ceil(fi);
if (i1 == -1)
i1 = (isperiodic_x) ? ni - 1 : i2;
if (i2 == ni)
i2 = (isperiodic_x) ? 0 : i1;
j1 = floor(fj);
j2 = ceil(fj);
if (j1 == -1)
j1 = j2;
if (j2 == nj)
j2 = j1;
k2 = floor(*fk);
if (numlevels[j1][i1] <= k2 && numlevels[j1][i2] <= k2 && numlevels[j2][i1] <= k2 && numlevels[j2][i2] <= k2) {
*fk = NaN;
return STATUS_LAND;
} else if (numlevels[j1][i1] <= k2 || numlevels[j1][i2] <= k2 || numlevels[j2][i1] <= k2 || numlevels[j2][i2] <= k2) {
float** depth = grid_getdepth(grid);
int ni, nj;
double v;
grid_getdims(grid, &ni, &nj, NULL);
v = interpolate2d(fi, fj, ni, nj, depth, numlevels, grid_isperiodic_x(grid));
if (z > v)
return STATUS_LAND;
}
return STATUS_OK;
}
void grid_print(grid* g, char offset[])
{
int nx, ny, nz;
enkf_printf("%sgrid info:\n", offset);
switch (g->htype) {
case GRIDHTYPE_LATLON:
enkf_printf("%s hor type = LATLON\n", offset);
enkf_printf("%s periodic by X = %s\n", offset, grid_isperiodic_x(g) ? "yes" : "no");
break;
#if !defined(NO_GRIDUTILS)
case GRIDHTYPE_CURVILINEAR:
enkf_printf("%s hor type = CURVILINEAR\n", offset);
if (g->maptype == GRIDMAP_TYPE_BINARY)
enkf_printf("%s map type = BINARY TREE\n", offset);
else if (g->maptype == GRIDMAP_TYPE_KDTREE)
enkf_printf("%s map type = KD-TREE\n", offset);
else
enkf_quit("unknown grid map type");
break;
#endif
default:
enkf_printf("%s h type = NONE\n", offset);
}
grid_getdims(g, &nx, &ny, &nz);
enkf_printf("%s dims = %d x %d x %d\n", offset, nx, ny, nz);
if (!isnan(g->lonbase))
enkf_printf("%s longitude range = [%.3f, %.3f]\n", offset, g->lonbase, g->lonbase + 360.0);
else
enkf_printf("%s longitude range = any\n", offset);
switch (g->vtype) {
case GRIDVTYPE_Z:
enkf_printf("%s vert type = Z\n", offset);
break;
case GRIDVTYPE_SIGMA:
enkf_printf("%s vert type = SIGMA\n", offset);
break;
default:
enkf_printf("%s vert type = NONE\n", offset);
}
if (g->sfactor != 1.0)
enkf_printf("%s SFACTOR = \"%.f\"\n", offset, g->sfactor);
}
int model_fk2z(model* m, int vid, int i, int j, double fk, double* z)
{
grid* g = m->grids[m->vars[vid].gridid];
float** depth;
int ni, nj;
grid_getdims(g, &ni, &nj, NULL);
if (i < 0 || j < 0 || i >= ni || j >= nj) {
*z = NaN;
return STATUS_OUTSIDEGRID;
}
grid_fk2z(g, i, j, fk, z);
depth = grid_getdepth(g);
if (*z > depth[j][i]) {
*z = NaN;
return STATUS_OUTSIDEGRID;
}
return STATUS_OK;
}
void grid_print(grid* g, char offset[])
{
int nx, ny, nz;
enkf_printf("%sgrid info:\n", offset);
switch (g->htype) {
case GRIDHTYPE_LATLON_REGULAR:
enkf_printf("%s hor type = LATLON_REGULAR\n", offset);
break;
case GRIDHTYPE_LATLON_IRREGULAR:
enkf_printf("%s hor type = LATLON_IRREGULAR\n", offset);
break;
#if !defined(NO_GRIDUTILS)
case GRIDHTYPE_CURVILINEAR:
enkf_printf("%s hor type = CURVILINEAR\n", offset);
break;
#endif
default:
enkf_printf("%s h type = NONE\n", offset);
}
enkf_printf("%s periodic by X = %s\n", offset, grid_isperiodic_x(g) ? "yes" : "no");
enkf_printf("%s periodic by Y = %s\n", offset, grid_isperiodic_y(g) ? "yes" : "no");
grid_getdims(g, &nx, &ny, &nz);
enkf_printf("%s dims = %d x %d x %d\n", offset, nx, ny, nz);
if (!isnan(g->lonbase))
enkf_printf("%s longitude range = [%.3f, %.3f]\n", offset, g->lonbase, g->lonbase + 360.0);
else
enkf_printf("%s longitude range = any\n", offset);
switch (g->vtype) {
case GRIDVTYPE_Z:
enkf_printf("%s vert type = Z\n", offset);
break;
case GRIDVTYPE_SIGMA:
enkf_printf("%s vert type = SIGMA\n", offset);
break;
default:
enkf_printf("%s vert type = NONE\n", offset);
}
}
void model_getvardims(model* m, int vid, int* ni, int* nj, int* nk)
{
grid_getdims(m->grids[m->vars[vid].gridid], ni, nj, nk);
}
/** Updates ensemble observations by applying X5
*/
static void update_HE(dasystem* das)
{
model* m = das->m;
int ngrid = model_getngrid(m);
int gid;
observations* obs = das->obs;
int e, o;
float* HEi_f;
float* HEi_a;
char do_T = 'T';
float alpha = 1.0f;
float beta = 0.0f;
int inc = 1;
enkf_printf(" updating HE:\n");
assert(das->s_mode == S_MODE_HE_f);
HEi_f = malloc(das->nmem * sizeof(ENSOBSTYPE));
HEi_a = malloc(das->nmem * sizeof(ENSOBSTYPE));
/*
* the following code for interpolation of X5 essentially coincides with
* that in das_updatefields()
*/
for (gid = 0, o = 0; gid < ngrid && o < obs->nobs; ++gid) {
void* grid = model_getgridbyid(m, gid);
int periodic_i = grid_isperiodic_x(grid);
int periodic_j = grid_isperiodic_y(grid);
char fname_X5[MAXSTRLEN];
int ncid;
int varid;
int dimids[3];
size_t dimlens[3];
size_t start[3], count[3];
float** X5j = NULL;
float** X5jj = NULL;
float** X5jj1 = NULL;
float** X5jj2 = NULL;
int mni, mnj;
int* iiter;
int* jiter;
int i, j, ni, nj;
int jj, stepj, ii, stepi;
assert(obs->obstypes[obs->data[o].type].gridid == gid);
das_getfname_X5(das, grid, fname_X5);
ncw_open(fname_X5, NC_NOWRITE, &ncid);
ncw_inq_varid(fname_X5, ncid, "X5", &varid);
ncw_inq_vardimid(fname_X5, ncid, varid, dimids);
for (i = 0; i < 3; ++i)
ncw_inq_dimlen(fname_X5, ncid, dimids[i], &dimlens[i]);
ni = dimlens[1];
nj = dimlens[0];
assert((int) dimlens[2] == das->nmem * das->nmem);
jiter = malloc((nj + 1) * sizeof(int)); /* "+ 1" to handle periodic
* grids */
iiter = malloc((ni + 1) * sizeof(int));
for (j = 0, i = 0; j < nj; ++j, i += das->stride)
jiter[j] = i;
if (periodic_j)
jiter[nj] = jiter[nj - 1] + das->stride;
for (i = 0, j = 0; i < ni; ++i, j += das->stride)
iiter[i] = j;
if (periodic_i)
iiter[ni] = iiter[ni - 1] + das->stride;
grid_getdims(grid, &mni, &mnj, NULL);
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = ni;
count[2] = das->nmem * das->nmem;
X5j = alloc2d(mni, das->nmem * das->nmem, sizeof(float));
if (das->stride > 1) {
X5jj = alloc2d(ni, das->nmem * das->nmem, sizeof(float));
X5jj1 = alloc2d(ni, das->nmem * das->nmem, sizeof(float));
X5jj2 = alloc2d(ni, das->nmem * das->nmem, sizeof(float));
ncw_get_vara_float(fname_X5, ncid, varid, start, count, X5jj2[0]);
}
/*
* jj, ii are the indices of the subsampled grid; i, j are the indices
* of the model grid
*/
for (jj = 0, j = 0; jj < nj; ++jj) {
for (stepj = 0; stepj < das->stride && j < mnj; ++stepj, ++j) {
if (das->stride == 1) {
/*
* no interpolation necessary; simply read the ETMs for the
* j-th row from disk
*/
start[0] = j;
ncw_get_vara_float(fname_X5, ncid, varid, start, count, X5j[0]);
} else {
/*
* the following code interpolates the ETM back to the
* original grid, first by j, and then by i
*/
if (stepj == 0) {
memcpy(X5jj[0], X5jj2[0], ni * das->nmem * das->nmem * sizeof(float));
memcpy(X5jj1[0], X5jj2[0], ni * das->nmem * das->nmem * sizeof(float));
if (jj < nj - 1 || periodic_j) {
start[0] = (jj + 1) % nj;
ncw_get_vara_float(fname_X5, ncid, varid, start, count, X5jj2[0]);
}
} else {
float weight2 = (float) stepj / das->stride;
float weight1 = (float) 1.0 - weight2;
for (ii = 0; ii < ni; ++ii) {
float* X5jjii = X5jj[ii];
float* X5jj1ii = X5jj1[ii];
float* X5jj2ii = X5jj2[ii];
for (e = 0; e < das->nmem * das->nmem; ++e)
X5jjii[e] = X5jj1ii[e] * weight1 + X5jj2ii[e] * weight2;
}
}
for (ii = 0, i = 0; ii < ni; ++ii) {
for (stepi = 0; stepi < das->stride && i < mni; ++stepi, ++i) {
if (stepi == 0)
memcpy(X5j[i], X5jj[ii], das->nmem * das->nmem * sizeof(float));
else {
float weight2 = (float) stepi / das->stride;
float weight1 = (float) 1.0 - weight2;
float* X5jjii1 = X5jj[ii];
float* X5ji = X5j[i];
float* X5jjii2;
if (ii < ni - 1)
X5jjii2 = X5jj[ii + 1];
else
X5jjii2 = X5jj[(periodic_i) ? (ii + 1) % ni : ii];
for (e = 0; e < das->nmem * das->nmem; ++e)
X5ji[e] = X5jjii1[e] * weight1 + X5jjii2[e] * weight2;
}
}
}
} /* stride != 1 */
/*
* (at this stage X5j should contain the array of X5 matrices
* for the j-th row of the grid)
*/
if (o >= obs->nobs)
break;
if ((int) (obs->data[o].fj) > j)
continue;
for (; o < obs->nobs && (int) (obs->data[o].fj) == j; ++o) {
float inflation = model_getvarinflation(m, obs->obstypes[obs->data[o].type].vid);
/*
* HE(i, :) = HE(i, :) * X5
*/
i = (int) (obs->data[o].fi);
for (e = 0; e < das->nmem; ++e)
HEi_f[e] = das->S[e][o];
sgemv_(&do_T, &das->nmem, &das->nmem, &alpha, X5j[i], &das->nmem, HEi_f, &inc, &beta, HEi_a, &inc);
/*
* applying inflation:
*/
if (fabsf(inflation - 1.0f) > EPSF) {
float v_av = 0.0f;
for (e = 0; e < das->nmem; ++e)
v_av += HEi_a[e];
v_av /= (float) das->nmem;
for (e = 0; e < das->nmem; ++e)
HEi_a[e] = (HEi_a[e] - v_av) * inflation + v_av;
}
for (e = 0; e < das->nmem; ++e)
das->S[e][o] = HEi_a[e];
}
} /* for stepj */
} /* for jj */
ncw_close(fname_X5, ncid);
free(iiter);
free(jiter);
free2d(X5j);
if (das->stride > 1) {
free2d(X5jj);
free2d(X5jj1);
free2d(X5jj2);
}
} /* for gid */
free(HEi_a);
free(HEi_f);
das->s_mode = S_MODE_HE_a;
} /* update_HE() */
static void update_Hx(dasystem* das)
{
model* m = das->m;
int ngrid = model_getngrid(m);
int gid;
observations* obs = das->obs;
int e, o;
enkf_printf(" updating Hx:\n");
assert(das->s_mode == S_MODE_HE_f);
/*
* the following code for interpolation of X5 essentially coincides with
* that in das_updatefields()
*/
for (gid = 0, o = 0; gid < ngrid && o < obs->nobs; ++gid) {
void* grid = model_getgridbyid(m, gid);
int periodic_i = grid_isperiodic_x(grid);
int periodic_j = grid_isperiodic_y(grid);
char fname_w[MAXSTRLEN];
int ncid;
int varid;
int dimids[3];
size_t dimlens[3];
size_t start[3], count[3];
float** wj = NULL;
float** wjj = NULL;
float** wjj1 = NULL;
float** wjj2 = NULL;
int mni, mnj;
int* iiter;
int* jiter;
int i, j, ni, nj;
int jj, stepj, ii, stepi;
assert(obs->obstypes[obs->data[o].type].gridid == gid);
das_getfname_w(das, grid, fname_w);
ncw_open(fname_w, NC_NOWRITE, &ncid);
ncw_inq_varid(fname_w, ncid, "w", &varid);
ncw_inq_vardimid(fname_w, ncid, varid, dimids);
for (i = 0; i < 3; ++i)
ncw_inq_dimlen(fname_w, ncid, dimids[i], &dimlens[i]);
ni = dimlens[1];
nj = dimlens[0];
assert((int) dimlens[2] == das->nmem);
jiter = malloc((nj + 1) * sizeof(int)); /* "+ 1" to handle periodic
* grids */
iiter = malloc((ni + 1) * sizeof(int));
for (j = 0, i = 0; j < nj; ++j, i += das->stride)
jiter[j] = i;
if (periodic_j)
jiter[nj] = jiter[nj - 1] + das->stride;
for (i = 0, j = 0; i < ni; ++i, j += das->stride)
iiter[i] = j;
if (periodic_i)
iiter[ni] = iiter[ni - 1] + das->stride;
grid_getdims(grid, &mni, &mnj, NULL);
start[0] = 0;
start[1] = 0;
start[2] = 0;
count[0] = 1;
count[1] = ni;
count[2] = das->nmem;
wj = alloc2d(mni, das->nmem, sizeof(float));
if (das->stride > 1) {
wjj = alloc2d(ni, das->nmem, sizeof(float));
wjj1 = alloc2d(ni, das->nmem, sizeof(float));
wjj2 = alloc2d(ni, das->nmem, sizeof(float));
ncw_get_vara_float(fname_w, ncid, varid, start, count, wjj2[0]);
}
/*
* jj, ii are the indices of the subsampled grid; i, j are the indices
* of the model grid
*/
for (jj = 0, j = 0; jj < nj; ++jj) {
for (stepj = 0; stepj < das->stride && j < mnj; ++stepj, ++j) {
if (das->stride == 1) {
/*
* no interpolation necessary; simply read the ETMs for the
* j-th row from disk
*/
start[0] = j;
ncw_get_vara_float(fname_w, ncid, varid, start, count, wj[0]);
} else {
/*
* the following code interpolates the ETM back to the
* original grid, first by j, and then by i
*/
if (stepj == 0) {
memcpy(wjj[0], wjj2[0], ni * das->nmem * sizeof(float));
memcpy(wjj1[0], wjj2[0], ni * das->nmem * sizeof(float));
if (jj < nj - 1 || periodic_j) {
start[0] = (jj + 1) % nj;
ncw_get_vara_float(fname_w, ncid, varid, start, count, wjj2[0]);
}
} else {
float weight2 = (float) stepj / das->stride;
float weight1 = (float) 1.0 - weight2;
for (ii = 0; ii < ni; ++ii) {
float* wjjii = wjj[ii];
float* wjj1ii = wjj1[ii];
float* wjj2ii = wjj2[ii];
for (e = 0; e < das->nmem; ++e)
wjjii[e] = wjj1ii[e] * weight1 + wjj2ii[e] * weight2;
}
}
for (ii = 0, i = 0; ii < ni; ++ii) {
for (stepi = 0; stepi < das->stride && i < mni; ++stepi, ++i) {
if (stepi == 0)
memcpy(wj[i], wjj[ii], das->nmem * sizeof(float));
else {
float weight2 = (float) stepi / das->stride;
float weight1 = (float) 1.0 - weight2;
float* wjjii1 = wjj[ii];
float* wji = wj[i];
float* wjjii2;
if (ii < ni - 1)
wjjii2 = wjj[ii + 1];
else
wjjii2 = wjj[(periodic_i) ? (ii + 1) % ni : ii];
for (e = 0; e < das->nmem; ++e)
wji[e] = wjjii1[e] * weight1 + wjjii2[e] * weight2;
}
}
}
} /* stride != 1 */
/*
* (at this stage wj should contain the array of b vectors for
* the j-th row of the grid)
*/
if (o >= obs->nobs)
break;
if ((int) (obs->data[o].fj) > j)
continue;
for (; o < obs->nobs && (int) (obs->data[o].fj) == j; ++o) {
double dHx = 0.0;
double Hx = 0.0;
for (e = 0; e < das->nmem; ++e)
Hx += das->S[e][o];
Hx /= (double) das->nmem;
i = (int) (obs->data[o].fi);
/*
* HE(i, :) += HA(i, :) * b * 1'
*/
for (e = 0; e < das->nmem; ++e)
dHx += (das->S[e][o] - Hx) * wj[i][e];
for (e = 0; e < das->nmem; ++e)
das->S[e][o] += dHx;
}
} /* for stepj */
} /* for jj */
ncw_close(fname_w, ncid);
free(iiter);
free(jiter);
free2d(wj);
if (das->stride > 1) {
free2d(wjj);
free2d(wjj1);
free2d(wjj2);
}
} /* for gid */
das->s_mode = S_MODE_HE_a;
} /* update_Hx() */
void reader_xy_gridded_hfradar(char* fname, int fid, obsmeta* meta, grid* g, observations* obs)
{
int ksurf = grid_getsurflayerid(g);
int isperiodic_i = grid_isperiodic_i(g);
int** numlevels = grid_getnumlevels(g);
float** grid_angle = grid_getangle(g);
int grid_ni = 0, grid_nj = 0;
char* varname = NULL;
char* u_varname = NULL;
char* v_varname = NULL;
char* u_stdvarname = NULL;
char* v_stdvarname = NULL;
char* lonname = NULL;
char* latname = NULL;
char* gdopname = NULL;
char* npointsname_1 = NULL;
char* npointsname_2 = NULL;
char* stdname = NULL;
char* estdname = NULL;
char* timename = NULL;
char* qcflagname = NULL;
char* u_qcflagname = NULL;
char* v_qcflagname = NULL;
char* rotation_flag = NULL;
int ncid;
int ndim_var, ndim_xy;
size_t dimlen_var[3], dimlen_xy[2];
uint32_t qcflagvals = 0;
float varshift = 0.0;
float u_varshift = 0.0;
float v_varshift = 0.0;
double mindepth = 0.0;
char instrument[MAXSTRLEN];
int iscurv = -1;
int need_rotation = -1;
size_t ni = 0, nj = 0, n = 0, n_var = 0;
int varid_lon = -1, varid_lat = -1;
double* lon = NULL;
double* lat = NULL;
int varid_gdop = -1, varid_npoints_1 = -1, varid_npoints_2 = -1;
int varid_var = -1, varid_std = -1, varid_estd = -1, varid_qcflag = -1, varid_time = -1;
int varid_u = -1, varid_v =-1, varid_u_std = -1, varid_v_std = -1, varid_u_qcflag = -1, varid_v_qcflag = -1;
float* var = NULL;
float* u_var = NULL;
float* v_var = NULL;
float* u_std = NULL;
float* v_std = NULL;
float var_fill_value = NAN;
float var_add_offset = NAN, var_scale_factor = NAN;
float u_var_fill_value = NAN;
float u_var_add_offset = NAN, u_var_scale_factor = NAN;
float v_var_fill_value = NAN;
float v_var_add_offset = NAN, v_var_scale_factor = NAN;
float u_std_fill_value = NAN;
float u_std_add_offset = NAN, u_std_scale_factor = NAN;
float v_std_fill_value = NAN;
float v_std_add_offset = NAN, v_std_scale_factor = NAN;
double var_estd = NAN;
float* gdop = NULL;
short* npoints_1 = NULL;
short* npoints_2 = NULL;
float* std = NULL;
float std_add_offset = NAN, std_scale_factor = NAN;
float std_fill_value = NAN;
float* estd = NULL;
float estd_add_offset = NAN, estd_scale_factor = NAN;
float estd_fill_value = NAN;
int32_t* qcflag = NULL;
int32_t* u_qcflag = NULL;
int32_t* v_qcflag = NULL;
int have_time = 1;
int singletime = -1;
float* time = NULL;
float time_add_offset = NAN, time_scale_factor = NAN;
float time_fill_value = NAN;
char tunits[MAXSTRLEN];
double tunits_multiple = NAN, tunits_offset = NAN;
int i, nobs_read;
strcpy(instrument, meta->product);
for (i = 0; i < meta->npars; ++i) {
if (strcasecmp(meta->pars[i].name, "VARNAME") == 0)
varname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "ROTATION") == 0)
rotation_flag = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "U_VARNAME") == 0)
u_varname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "V_VARNAME") == 0)
v_varname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "U_STD") == 0)
u_stdvarname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "V_STD") == 0)
v_stdvarname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "TIMENAME") == 0)
timename = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "GDOPNAME") == 0)
gdopname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "NPOINTSNAME_1") == 0)
npointsname_1 = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "NPOINTSNAME_2") == 0)
npointsname_2 = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "LONNAME") == 0)
lonname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "LATNAME") == 0)
latname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "STDNAME") == 0)
stdname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "ESTDNAME") == 0)
estdname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "QCFLAGNAME") == 0)
qcflagname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "U_QCFLAGNAME") == 0)
u_qcflagname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "V_QCFLAGNAME") == 0)
v_qcflagname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "QCFLAGVALS") == 0) {
char* pline = meta->pars[i].value;
int linelen = sizeof(pline);
char lineval[linelen];
char* line = strcpy(lineval,pline);
char seps[] = " ,";
char* token;
int val;
qcflagvals = 0;
while ((token = strtok(line, seps)) != NULL) {
if (!str2int(token, &val))
enkf_quit("%s: could not convert QCFLAGVALS entry \"%s\" to integer", meta->prmfname, token);
if (val < 0 || val > 31)
enkf_quit("%s: QCFLAGVALS entry = %d (supposed to be in [0,31] interval", meta->prmfname, val);
qcflagvals |= 1 << val;
line = NULL;
}
if (qcflagvals == 0)
enkf_quit("%s: no valid flag entries found after QCFLAGVALS\n", meta->prmfname);
} else if (strcasecmp(meta->pars[i].name, "VARSHIFT") == 0) {
if (!str2float(meta->pars[i].value, &varshift))
enkf_quit("%s: can not convert VARSHIFT = \"%s\" to float\n", meta->prmfname, meta->pars[i].value);
enkf_printf(" VARSHIFT = %s\n", meta->pars[i].value);
} else if (strcasecmp(meta->pars[i].name, "U_VARSHIFT") == 0) {
if (!str2float(meta->pars[i].value, &u_varshift))
enkf_quit("%s: can not convert U_VARSHIFT = \"%s\" to float\n", meta->prmfname, meta->pars[i].value);
enkf_printf(" U_VARSHIFT = %s\n", meta->pars[i].value);
} else if (strcasecmp(meta->pars[i].name, "V_VARSHIFT") == 0) {
if (!str2float(meta->pars[i].value, &v_varshift))
enkf_quit("%s: can not convert V_VARSHIFT = \"%s\" to float\n", meta->prmfname, meta->pars[i].value);
enkf_printf(" V_VARSHIFT = %s\n", meta->pars[i].value);
} else if (strcasecmp(meta->pars[i].name, "MINDEPTH") == 0) {
if (!str2double(meta->pars[i].value, &mindepth))
enkf_quit("%s: can not convert MINDEPTH = \"%s\" to double\n", meta->prmfname, meta->pars[i].value);
enkf_printf(" MINDEPTH = %f\n", mindepth);
} else if (strcasecmp(meta->pars[i].name, "INSTRUMENT") == 0) {
strncpy(instrument, meta->pars[i].value, MAXSTRLEN);
} else
enkf_quit("unknown PARAMETER \"%s\"\n", meta->pars[i].name);
}
if (varname == NULL)
enkf_quit("reader_xy_gridded(): %s variable name not specified", fname);
if (rotation_flag != NULL) {
int bool_rotation_flag, valid_rotation_flag;
bool_rotation_flag = atoi(rotation_flag);
valid_rotation_flag = (bool_rotation_flag == 0 || bool_rotation_flag == 1);
if (valid_rotation_flag) {
need_rotation = bool_rotation_flag == 1;
grid_getdims(g, &grid_ni, &grid_nj, NULL);
if (need_rotation == 1 && grid_angle == NULL)
enkf_quit("reader_xy_gridded_hfradar(): %s cannot rotate vectors without ANGLE parameter defined within grid prm file",fname);
enkf_printf("\t#Rotation of vectors enabled\n");
}
else
enkf_quit("reader_xy_gridded_hfradar(): %s invalid ROTATION parameter. Need to be a boolean digit");
}
ncw_open(fname, NC_NOWRITE, &ncid);
ncw_inq_varid(ncid, varname, &varid_var);
ncw_inq_vardims(ncid, varid_var, 3, &ndim_var, dimlen_var);
if (ndim_var == 3) {
int dimid[3];
size_t nr;
ncw_inq_vardimid(ncid, varid_var, dimid);
ncw_inq_dimlen(ncid, dimid[0], &nr);
if (nr != 1)
enkf_quit("reader_xy_gridded(): %d records (currently only one is allowed)", nr);
n_var = dimlen_var[1] * dimlen_var[2];
} else if (ndim_var == 2) {
if (nc_hasunlimdim(ncid))
enkf_quit("reader_xy_gridded(): %s: %s: not enough spatial dimensions (must be 2)", fname, varname);
n_var = dimlen_var[0] * dimlen_var[1];
} else if (ndim_var != 2)
enkf_quit("reader_xy_gridded(): %s: # dimensions = %d (must be 2 or 3 with only one record)", fname, ndim_var);
if (lonname != NULL)
ncw_inq_varid(ncid, lonname, &varid_lon);
else if (ncw_var_exists(ncid, "lon"))
ncw_inq_varid(ncid, "lon", &varid_lon);
else if (ncw_var_exists(ncid, "longitude"))
ncw_inq_varid(ncid, "longitude", &varid_lon);
else if (ncw_var_exists(ncid, "LONGITUDE"))
ncw_inq_varid(ncid, "LONGITUDE", &varid_lon);
else
enkf_quit("reader_xy_gridded(): %s: could not find longitude variable", fname);
ncw_inq_vardims(ncid, varid_lon, 2, &ndim_xy, dimlen_xy);
if (ndim_xy == 1) {
iscurv = 0;
ni = dimlen_xy[0];
} else if (ndim_xy == 2) {
iscurv = 1;
ni = dimlen_xy[1];
nj = dimlen_xy[0];
} else
enkf_quit("reader_xy_gridded(): %s: coordinate variable \"%s\" has neither 1 or 2 dimensions", fname, lonname);
if (latname != NULL)
ncw_inq_varid(ncid, latname, &varid_lat);
else if (ncw_var_exists(ncid, "lat"))
ncw_inq_varid(ncid, "lat", &varid_lat);
else if (ncw_var_exists(ncid, "latitude"))
ncw_inq_varid(ncid, "latitude", &varid_lat);
else if (ncw_var_exists(ncid, "LATITUDE"))
ncw_inq_varid(ncid, "LATITUDE", &varid_lat);
else
enkf_quit("reader_xy_gridded(): %s: could not find latitude variable", fname);
if (iscurv == 0) {
ncw_check_varndims(ncid, varid_lat, 1);
ncw_inq_vardims(ncid, varid_lat, 1, NULL, &nj);
} else
ncw_check_vardims(ncid, varid_lat, 2, dimlen_xy);
enkf_printf(" (ni, nj) = (%u, %u)\n", ni, nj);
n = ni * nj;
if (n != n_var)
enkf_quit("reader_xy_gridded(): %s: dimensions of variable \"%s\" do not match coordinate dimensions", fname, varname);
if (dimlen_var[ndim_var - 1] != ni)
enkf_quit("reader_xy_gridded(): %s: %s: longitude must be the inner coordinate", fname, varname);
if (iscurv == 0) {
lon = malloc(ni * sizeof(double));
lat = malloc(nj * sizeof(double));
} else {
lon = malloc(n * sizeof(double));
lat = malloc(n * sizeof(double));
}
ncw_get_var_double(ncid, varid_lon, lon);
ncw_get_var_double(ncid, varid_lat, lat);
var = malloc(n * sizeof(float));
ncw_get_var_float(ncid, varid_var, var);
if (ncw_att_exists(ncid, varid_var, "add_offset")) {
ncw_get_att_float(ncid, varid_var, "add_offset", &var_add_offset);
ncw_get_att_float(ncid, varid_var, "scale_factor", &var_scale_factor);
}
if (ncw_att_exists(ncid, varid_var, "_FillValue"))
ncw_get_att_float(ncid, varid_var, "_FillValue", &var_fill_value);
if (gdopname != NULL)
ncw_inq_varid(ncid, gdopname, &varid_gdop);
else if (ncw_var_exists(ncid, "GDOP"))
ncw_inq_varid(ncid, "GDOP", &varid_gdop);
if (varid_gdop >= 0) {
gdop = malloc(n * sizeof(float));
ncw_get_var_float(ncid, varid_gdop, gdop);
float gdop_fill_value, gdop_add_offset, gdop_scale_factor;
if (ncw_att_exists(ncid, varid_gdop, "_FillValue"))
ncw_get_att_float(ncid, varid_gdop, "_FillValue", &gdop_fill_value);
if (ncw_att_exists(ncid, varid_gdop, "add_offset")) {
ncw_get_att_float(ncid, varid_gdop, "add_offset", &gdop_add_offset);
ncw_get_att_float(ncid, varid_gdop, "scale_factor", &gdop_scale_factor);
}
}
if (npointsname_1 != NULL)
ncw_inq_varid(ncid, npointsname_1, &varid_npoints_1);
else if (ncw_var_exists(ncid, "NOBS1"))
ncw_inq_varid(ncid, "NOBS1", &varid_npoints_1);
if (varid_npoints_1 >= 0) {
npoints_1 = malloc(n * sizeof(short));
ncw_get_var_short(ncid, varid_npoints_1, npoints_1);
}
if (npointsname_2 != NULL)
ncw_inq_varid(ncid, npointsname_2, &varid_npoints_2);
else if (ncw_var_exists(ncid, "NOBS2"))
ncw_inq_varid(ncid, "NOBS2", &varid_npoints_2);
if (varid_npoints_2 >= 0) {
npoints_2 = malloc(n * sizeof(short));
ncw_get_var_short(ncid, varid_npoints_2, npoints_2);
}
if (need_rotation == 1) {
if (u_varname != NULL )
ncw_inq_varid(ncid, u_varname, &varid_u);
else if (ncw_var_exists(ncid, "UCUR")) {
ncw_inq_varid(ncid, "UCUR", &varid_u);
u_varname = "UCUR";
}
if (varid_u >= 0) {
u_var = malloc(n * sizeof(float));
ncw_get_var_float(ncid,varid_u,u_var);
if (ncw_att_exists(ncid,varid_u, "_FillValue"))
ncw_get_att_float(ncid, varid_u, "_FillValue", &u_var_fill_value);
if (ncw_att_exists(ncid,varid_u,"add_offset")) {
ncw_get_att_float(ncid, varid_u, "add_offset", &u_var_add_offset);
ncw_get_att_float(ncid, varid_u, "scale_factor", &u_var_scale_factor);
}
}
else
enkf_quit("reader_xy_gridded(): %s: Variable %s not found.",fname, u_varname);
if (v_varname != NULL)
ncw_inq_varid(ncid, v_varname, &varid_v);
else if (ncw_var_exists(ncid, "VCUR")) {
ncw_inq_varid(ncid, "VCUR", &varid_v);
v_varname = "VCUR";
}
if (varid_v >= 0) {
v_var = malloc(n * sizeof(float));
ncw_get_var_float(ncid,varid_v,v_var);
if (ncw_att_exists(ncid,varid_v, "_FillValue"))
ncw_get_att_float(ncid,varid_v, "_FillValue", &v_var_fill_value);
if (ncw_att_exists(ncid,varid_v,"add_offset")) {
ncw_get_att_float(ncid, varid_v, "add_offset", &v_var_add_offset);
ncw_get_att_float(ncid, varid_v, "scale_factor", &v_var_scale_factor);
}
}
else
enkf_quit("reader_xy_gridded(): %s: Variable %s not found.",fname, v_varname);
}
if (stdname != NULL)
ncw_inq_varid(ncid, stdname, &varid_std);
else if (ncw_var_exists(ncid, "std"))
ncw_inq_varid(ncid, "std", &varid_std);
if (varid_std >= 0) {
std = malloc(n * sizeof(float));
ncw_get_var_float(ncid, varid_std, std);
if (ncw_att_exists(ncid, varid_std, "_FillValue"))
ncw_get_att_float(ncid, varid_std, "_FillValue", &std_fill_value);
if (ncw_att_exists(ncid, varid_std, "add_offset")) {
ncw_get_att_float(ncid, varid_std, "add_offset", &std_add_offset);
ncw_get_att_float(ncid, varid_std, "scale_factor", &std_scale_factor);
}
}
if (estdname != NULL)
ncw_inq_varid(ncid, estdname, &varid_estd);
else if (ncw_var_exists(ncid, "error_std"))
ncw_inq_varid(ncid, "error_std", &varid_estd);
if (varid_estd >= 0) {
estd = malloc(n * sizeof(float));
ncw_get_var_float(ncid, varid_estd, estd);
if (ncw_att_exists(ncid, varid_estd, "_FillValue"))
ncw_get_att_float(ncid, varid_estd, "_FillValue", &estd_fill_value);
if (ncw_att_exists(ncid, varid_estd, "add_offset")) {
ncw_get_att_float(ncid, varid_estd, "add_offset", &estd_add_offset);
ncw_get_att_float(ncid, varid_estd, "scale_factor", &estd_scale_factor);
}
}
if (std == NULL && estd == NULL)
if (ncw_att_exists(ncid, varid_var, "error_std")) {
ncw_check_attlen(ncid, varid_var, "error_std", 1);
ncw_get_att_double(ncid, varid_var, "error_std", &var_estd);
}
if (u_stdvarname != NULL)
ncw_inq_varid(ncid, u_stdvarname, &varid_u_std);
else if (ncw_var_exists(ncid, "UCUR_sd"))
ncw_inq_varid(ncid, "UCUR_sd", &varid_u_std);
if (varid_u_std >= 0) {
u_std = malloc(n * sizeof(float));
ncw_get_var_float(ncid, varid_u_std, u_std);
if (ncw_att_exists(ncid, varid_u_std, "_FillValue"))
ncw_get_att_float(ncid, varid_u_std, "_FillValue", &u_std_fill_value);
if (ncw_att_exists(ncid, varid_u_std, "add_offset")) {
ncw_get_att_float(ncid, varid_u_std, "add_offset", &u_std_add_offset);
ncw_get_att_float(ncid, varid_u_std, "scale_factor", &u_std_scale_factor);
}
}
if (v_stdvarname != NULL)
ncw_inq_varid(ncid, v_stdvarname, &varid_v_std);
else if (ncw_var_exists(ncid, "vcur_sd"))
ncw_inq_varid(ncid, "vcur_sd", &varid_v_std);
if (varid_v_std >= 0) {
v_std = malloc(n * sizeof(float));
ncw_get_var_float(ncid, varid_v_std, v_std);
if (ncw_att_exists(ncid, varid_v_std, "_FillValue"))
ncw_get_att_float(ncid, varid_v_std, "_FillValue", &v_std_fill_value);
if (ncw_att_exists(ncid, varid_v_std, "add_offset")) {
ncw_get_att_float(ncid, varid_v_std, "add_offset", &v_std_add_offset);
ncw_get_att_float(ncid, varid_v_std, "scale_factor", &v_std_scale_factor);
}
}
if (qcflagname != NULL) {
ncw_inq_varid(ncid, qcflagname, &varid_qcflag);
qcflag = malloc(n * sizeof(int32_t));
ncw_get_var_int(ncid, varid_qcflag, qcflag);
}
if (u_qcflagname != NULL)
ncw_inq_varid(ncid, u_qcflagname, &varid_u_qcflag);
else if (ncw_var_exists(ncid, "UCUR_quality_control"))
ncw_inq_varid(ncid, "UCUR_quality_control", &varid_u_qcflag);
if (varid_u_qcflag >= 0) {
u_qcflag = malloc(n * sizeof(int32_t));
ncw_get_var_int(ncid, varid_u_qcflag, u_qcflag);
}
if (v_qcflagname != NULL)
ncw_inq_varid(ncid, v_qcflagname, &varid_v_qcflag);
else if (ncw_var_exists(ncid, "VCUR_quality_control"))
ncw_inq_varid(ncid, "VCUR_quality_control", &varid_v_qcflag);
if (varid_v_qcflag >= 0) {
v_qcflag = malloc(n * sizeof(int32_t));
ncw_get_var_int(ncid, varid_v_qcflag, v_qcflag);
}
if (timename != NULL)
ncw_inq_varid(ncid, timename, &varid_time);
else if (ncw_var_exists(ncid, "time"))
ncw_inq_varid(ncid, "time", &varid_time);
else if (ncw_var_exists(ncid, "TIME"))
ncw_inq_varid(ncid, "TIME", &varid_time);
else {
enkf_printf(" reader_xy_gridded(): %s: no TIME variable\n", fname);
have_time = 0;
}
if (have_time) {
int timendims;
int timedimids[NC_MAX_DIMS];
size_t timelen = 1;
ncw_inq_varndims(ncid, varid_time, &timendims);
ncw_inq_vardimid(ncid, varid_time, timedimids);
for (i = 0; i < timendims; ++i) {
size_t dimlen;
ncw_inq_dimlen(ncid, timedimids[i], &dimlen);
timelen *= dimlen;
}
if (timelen == 1) {
singletime = 1;
time = malloc(sizeof(float));
} else {
singletime = 0;
assert(timelen == n);
time = malloc(n * sizeof(float));
}
ncw_get_var_float(ncid, varid_time, time);
if (ncw_att_exists(ncid, varid_time, "_FillValue"))
ncw_get_att_float(ncid, varid_time, "_FillValue", &time_fill_value);
if (ncw_att_exists(ncid, varid_time, "add_offset")) {
ncw_get_att_float(ncid, varid_time, "add_offset", &time_add_offset);
ncw_get_att_float(ncid, varid_time, "scale_factor", &time_scale_factor);
}
ncw_get_att_text(ncid, varid_time, "units", tunits);
tunits_convert(tunits, &tunits_multiple, &tunits_offset);
}
ncw_close(ncid);
nobs_read = 0;
for (i = 0; i < (int) n; ++i) {
observation* o;
obstype* ot;
int invalid_gdop, invalid_npoints1, invalid_npoints2, invalid_var, invalid_std, invalid_estd, invalid_u_var, invalid_v_var, invalid_time;
invalid_gdop = (gdop != NULL && (gdop[i] > 180.0 || gdop[i] < 0.0));
invalid_npoints1 = (npoints_1 != NULL && (npoints_1[i] == 0 || npoints_1[i]< 0));
invalid_npoints2 = (npoints_2 != NULL && (npoints_2[i] == 0 || npoints_2[i] < 0));
invalid_var = var[i] == var_fill_value || isnan(var[i]);
invalid_std = (std != NULL && (std[i] == std_fill_value || isnan(std[i])));
invalid_estd = (estd != NULL && (estd[i] == estd_fill_value || isnan(estd[i])));
invalid_u_var = (u_var != NULL && (u_var[i] == u_var_fill_value || isnan(u_var[i])));
invalid_v_var = (v_var != NULL && (v_var[i] == v_var_fill_value || isnan(v_var[i])));
invalid_time = (have_time && !singletime && (time[i] == time_fill_value || isnan(time[i])));
if (invalid_gdop || invalid_npoints1 || invalid_npoints2 || invalid_var || invalid_std || invalid_estd || invalid_u_var || invalid_v_var || invalid_time)
continue;
if (qcflag != NULL) {
/* general qcflags has precedence in discarding obs*/
if ( (qcflagvals != (qcflagvals | 1<<qcflag[i])) || (u_qcflag != NULL && (qcflagvals != (qcflagvals | 1<<u_qcflag[i]))) || (v_qcflag != NULL && (qcflagvals != (qcflagvals | 1<<v_qcflag[i]))) )
continue;
}
/* [u,v]_qcflags has precedence in values. */
if (u_qcflagname != NULL && v_qcflagname != NULL) {
if ( (u_qcflag != NULL && (qcflagvals != (qcflagvals | 1<<u_qcflag[i]))) || (v_qcflag != NULL && (qcflagvals != (qcflagvals | 1<<v_qcflag[i]))) )
continue;
} else if (u_qcflagname != NULL) {
if (u_qcflag != NULL && (qcflagvals != (qcflagvals | 1<<u_qcflag[i])))
continue;
} else if (v_qcflagname != NULL) {
if (v_qcflag != NULL && (qcflagvals != (qcflagvals | 1<<v_qcflag[i])))
continue;
}
nobs_read++;
obs_checkalloc(obs);
o = &obs->data[obs->nobs];
o->product = st_findindexbystring(obs->products, meta->product);
assert(o->product >= 0);
o->type = obstype_getid(obs->nobstypes, obs->obstypes, meta->type, 1);
ot = &obs->obstypes[o->type];
o->instrument = st_add_ifabsent(obs->instruments, instrument, -1);
o->id = obs->nobs;
o->fid = fid;
o->batch = 0;
/* Shifted the reading order for HF-Radar to obtain indexes */
if (iscurv == 0) {
o->lon = lon[i % ni];
o->lat = lat[i / ni];
} else {
o->lon = lon[i];
o->lat = lat[i];
}
o->depth = 0.0;
o->fk = (double) ksurf;
o->model_depth = NAN; /* set in obs_add() */
o->status = grid_xy2fij(g, o->lon, o->lat, &o->fi, &o->fj);
if (!obs->allobs && o->status == STATUS_OUTSIDEGRID)
continue;
if ((o->status == STATUS_OK) && (o->lon <= ot->xmin || o->lon >= ot->xmax || o->lat <= ot->ymin || o->lat >= ot->ymax))
o->status = STATUS_OUTSIDEOBSDOMAIN;
if (need_rotation == 1) {
double zonal, meridional, oangle;
if (!isnan(u_var_add_offset))
zonal = u_var[i] * u_var_scale_factor + u_var_add_offset + varshift + u_varshift;
else
zonal = u_var[i];
if (!isnan(v_var_add_offset))
meridional = v_var[i] * v_var_scale_factor + v_var_add_offset + varshift + u_varshift;
else
meridional = v_var[i];
oangle = interpolate2d(o->fi, o-> fj, grid_ni, grid_nj, grid_angle, numlevels, isperiodic_i);
if (strcmp(varname,u_varname) == 0)
o->value = zonal*cos(oangle) - meridional*sin(oangle);
if (strcmp(varname,v_varname) == 0)
o->value = zonal*sin(oangle) + meridional*cos(oangle);
}
else {
if (!isnan(var_add_offset))
o->value = (double) (var[i] * var_scale_factor + var_add_offset + varshift);
else
o->value = (double) (var[i] + varshift);
}
if (estd == NULL && std == NULL){
if (!isnan(var_estd))
o->std = var_estd;
}
else {
if (std == NULL)
o->std = 0.0;
else {
if (!isnan(std_add_offset))
o->std = (double) (std[i] * std_scale_factor + std_add_offset);
else
o->std = (double) std[i];
}
if (estd != NULL) {
if (!isnan(estd_add_offset)) {
double std2 = (double) (estd[i] * estd_scale_factor + estd_add_offset);
o->std = (o->std > std2) ? o->std : std2;
} else
o->std = (o->std > estd[i]) ? o->std : estd[i];
}
}
if (have_time) {
float t = (singletime) ? time[0] : time[i];
if (!isnan(time_add_offset))
o->date = (double) (t * time_scale_factor + time_add_offset) * tunits_multiple + tunits_offset;
else
o->date = (double) t* tunits_multiple + tunits_offset;
} else
o->date = NAN;
o->aux = -1;
obs->nobs++;
}
enkf_printf(" nobs = %d\n", nobs_read);
free(lon);
free(lat);
free(var);
if (gdop != NULL)
free(gdop);
if (npoints_1 != NULL)
free(npoints_1);
if (npoints_2 != NULL)
free(npoints_2);
if (u_var != NULL)
free(u_var);
if (v_var != NULL)
free(v_var);
if (std != NULL)
free(std);
if (estd != NULL)
free(estd);
if (u_std != NULL)
free(u_std);
if (v_std != NULL)
free(v_std);
if (qcflag != NULL)
free(qcflag);
if (u_qcflag != NULL)
free(u_qcflag);
if (v_qcflag != NULL)
free(v_qcflag);
if (time != NULL)
free(time);
}