/** Replaces observation errors in the observation file with the modified
* values. The original values are stored as "std_orig".
*/
void das_addmodifiederrors(dasystem* das, char fname[])
{
int ncid;
int dimid_nobs[1];
size_t nobs;
int varid_std;
double* std;
int i;
if (rank != 0)
return;
ncw_open(fname, NC_WRITE, &ncid);
ncw_inq_dimid(fname, ncid, "nobs", dimid_nobs);
ncw_inq_dimlen(fname, ncid, dimid_nobs[0], &nobs);
ncw_redef(fname, ncid);
if (ncw_var_exists(ncid, "std_orig"))
enkf_quit("\"observations.nc\" has already been modified by `enkf_calc\'. To proceed please remove observations*.nc and rerun `enkf_prep\'.");
ncw_rename_var(fname, ncid, "std", "std_orig");
ncw_def_var(fname, ncid, "std", NC_FLOAT, 1, dimid_nobs, &varid_std);
ncw_enddef(fname, ncid);
std = malloc(nobs * sizeof(double));
for (i = 0; i < (int) nobs; ++i)
std[i] = das->obs->data[i].std;
ncw_put_var_double(fname, ncid, varid_std, std);
free(std);
ncw_close(fname, ncid);
}
/** Replaces observation errors in the observation file with the modified
* values. The original values are stored as "std_orig".
*/
void das_addmodifiederrors(dasystem* das, char fname[])
{
int ncid;
int dimid_nobs[1];
size_t nobs;
int varid_std;
double* std;
int i;
double da_julday = NaN;
if (rank != 0)
return;
ncw_open(fname, NC_WRITE, &ncid);
ncw_inq_dimid(ncid, "nobs", dimid_nobs);
ncw_inq_dimlen(ncid, dimid_nobs[0], &nobs);
ncw_get_att_double(ncid, NC_GLOBAL, "DA_JULDAY", &da_julday);
if (!enkf_noobsdatecheck && (isnan(da_julday) || fabs(das->obs->da_date - da_julday) > 1e-6))
enkf_quit("\"observations.nc\" from a different cycle");
if (ncw_var_exists(ncid, "std_orig")) {
enkf_printf(" nothing to do\n");
ncw_close(ncid);
return;
}
ncw_redef(ncid);
ncw_rename_var(ncid, "std", "std_orig");
ncw_def_var(ncid, "std", NC_FLOAT, 1, dimid_nobs, &varid_std);
ncw_enddef(ncid);
std = malloc(nobs * sizeof(double));
for (i = 0; i < (int) nobs; ++i)
std[i] = das->obs->data[i].std;
ncw_put_var_double(ncid, varid_std, std);
free(std);
ncw_close(ncid);
}
/** Adds forecast observations and forecast ensemble spread to the observation
* file.
*/
void das_addforecast(dasystem* das, char fname[])
{
int ncid;
int dimid_nobs[1];
size_t nobs;
int varid_Hx, varid_spread;
double* Hx;
int o;
if (das->obs->nobs == 0)
return;
if (rank != 0)
return;
assert(das->s_mode == S_MODE_HA_f);
ncw_open(fname, NC_WRITE, &ncid);
if (ncw_var_exists(ncid, "Hx_f")) {
enkf_printf(" Hx already added to \"%s\" (skipping)\n", fname);
goto finish;
}
ncw_inq_dimid(fname, ncid, "nobs", dimid_nobs);
ncw_inq_dimlen(fname, ncid, dimid_nobs[0], &nobs);
ncw_redef(fname, ncid);
ncw_def_var(fname, ncid, "Hx_f", NC_FLOAT, 1, dimid_nobs, &varid_Hx);
ncw_def_var(fname, ncid, "std_f", NC_FLOAT, 1, dimid_nobs, &varid_spread);
ncw_enddef(fname, ncid);
Hx = calloc(nobs, sizeof(double));
for (o = 0; o < (int) nobs; ++o)
Hx[o] = das->obs->data[o].value - das->s_f[o];
ncw_put_var_double(fname, ncid, varid_Hx, Hx);
ncw_put_var_double(fname, ncid, varid_spread, das->std_f);
free(Hx);
finish:
ncw_close(fname, ncid);
}
/** Add analysed observation estimates and ensemble spread to FNAME_SOBS.
*/
void das_addanalysis(dasystem* das, char fname[])
{
int ncid;
int dimid_nobs[1];
size_t nobs;
int varid_Hx, varid_spread;
observation* data = das->obs->data;
double* s;
int i;
if (rank != 0)
return;
assert(das->s_mode == S_MODE_HA_a);
ncw_open(fname, NC_WRITE, &ncid);
ncw_inq_dimid(fname, ncid, "nobs", dimid_nobs);
ncw_inq_dimlen(fname, ncid, dimid_nobs[0], &nobs);
ncw_redef(fname, ncid);
ncw_def_var(fname, ncid, "Hx_a", NC_FLOAT, 1, dimid_nobs, &varid_Hx);
ncw_def_var(fname, ncid, "std_a", NC_FLOAT, 1, dimid_nobs, &varid_spread);
ncw_enddef(fname, ncid);
ncw_put_var_double(fname, ncid, varid_spread, das->std_a);
s = malloc(nobs * sizeof(double));
/*
* the obs are still sorted by ij
*/
for (i = 0; i < (int) nobs; ++i)
s[data[i].id] = data[i].value;
for (i = 0; i < (int) nobs; ++i)
s[i] -= das->s_a[i];
ncw_put_var_double(fname, ncid, varid_Hx, s);
free(s);
ncw_close(fname, ncid);
}
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_windsat_standard(char* fname, int fid, obsmeta* meta, model* m, observations* obs)
{
int ncid;
int dimid_nobs;
size_t nobs_local;
int varid_lon, varid_lat, varid_sst, varid_error, varid_time;
double* lon;
double* lat;
double* sst;
double* error_std;
double* time;
int year, month, day;
char tunits[MAXSTRLEN];
size_t tunits_len;
double tunits_multiple, tunits_offset;
char* basename;
int mvid;
float** depth;
int ktop;
int i;
for (i = 0; i < meta->npars; ++i)
enkf_quit("unknown PARAMETER \"%s\"\n", meta->pars[i].name);
basename = strrchr(fname, '/');
if (basename == NULL)
basename = fname;
else
basename += 1;
ncw_open(fname, NC_NOWRITE, &ncid);
ncw_inq_dimid(ncid, "nobs", &dimid_nobs);
ncw_inq_dimlen(ncid, dimid_nobs, &nobs_local);
enkf_printf(" nobs = %u\n", (unsigned int) nobs_local);
if (nobs_local == 0) {
ncw_close(ncid);
return;
}
ncw_inq_varid(ncid, "lon", &varid_lon);
lon = malloc(nobs_local * sizeof(double));
ncw_get_var_double(ncid, varid_lon, lon);
ncw_inq_varid(ncid, "lat", &varid_lat);
lat = malloc(nobs_local * sizeof(double));
ncw_get_var_double(ncid, varid_lat, lat);
ncw_inq_varid(ncid, "sst", &varid_sst);
sst = malloc(nobs_local * sizeof(double));
ncw_get_var_double(ncid, varid_sst, sst);
ncw_inq_varid(ncid, "error", &varid_error);
error_std = malloc(nobs_local * sizeof(double));
ncw_get_var_double(ncid, varid_error, error_std);
ncw_inq_varid(ncid, "age", &varid_time);
time = malloc(nobs_local * sizeof(double));
ncw_get_var_double(ncid, varid_time, time);
ncw_inq_attlen(ncid, varid_time, "units", &tunits_len);
ncw_get_att_text(ncid, varid_time, "units", tunits);
basename[16] = 0;
if (!str2int(&basename[14], &day))
enkf_quit("WindSat reader: could not convert file name \"%s\" to date", fname);
basename[14] = 0;
if (!str2int(&basename[12], &month))
enkf_quit("WindSat reader: could not convert file name \"%s\" to date", fname);
basename[12] = 0;
if (!str2int(&basename[8], &year))
enkf_quit("WindSat reader: could not convert file name \"%s\" to date", fname);
snprintf(&tunits[tunits_len], MAXSTRLEN - tunits_len, " since %4d-%02d-%02d", year, month, day);
ncw_close(ncid);
tunits_convert(tunits, &tunits_multiple, &tunits_offset);
mvid = model_getvarid(m, obs->obstypes[obstype_getid(obs->nobstypes, obs->obstypes, meta->type, 1)].varnames[0], 1);
ktop = grid_gettoplayerid(model_getvargrid(m, mvid));
depth = model_getdepth(m, mvid, 0);
for (i = 0; i < (int) nobs_local; ++i)
if (time[i] != 0.0)
break;
if (i == (int) nobs_local)
for (i = 0; i < (int) nobs_local; ++i)
time[i] = 0.5;
for (i = 0; i < (int) nobs_local; ++i) {
observation* o;
obstype* ot;
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_ifabscent(obs->instruments, "WindSat", -1);
o->id = obs->nobs;
o->fid = fid;
o->batch = 0;
o->value = sst[i];
o->std = error_std[i];
o->lon = lon[i];
o->lat = lat[i];
o->depth = 0.0;
o->fk = (double) ktop;
o->status = model_xy2fij(m, mvid, 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->depth <= ot->zmin || o->depth >= ot->zmax))
o->status = STATUS_OUTSIDEOBSDOMAIN;
o->model_depth = (depth == NULL || isnan(o->fi + o->fj)) ? NaN : depth[(int) (o->fj + 0.5)][(int) (o->fi + 0.5)];
o->date = time[i] * tunits_multiple + tunits_offset;
o->aux = -1;
obs->nobs++;
}
free(lon);
free(lat);
free(sst);
free(error_std);
free(time);
}
/** For files of the form ??_yyyymmdd.nc. They are assumed to have "time"
* variable.
*/
void reader_rads_standard(char* fname, int fid, obsmeta* meta, model* m, observations* obs)
{
double mindepth = MINDEPTH_DEF;
char* addname = NULL;
int ncid;
int dimid_nobs;
size_t nobs_local;
int varid_lon, varid_lat, varid_pass, varid_sla, varid_time, varid_add;
double* lon;
double* lat;
int* pass;
double* sla;
double* time;
double error_std;
double* add = NULL;
size_t tunits_len;
char* tunits;
double tunits_multiple, tunits_offset;
char* basename;
char instname[3];
int mvid;
float** depth;
int i, ktop;
for (i = 0; i < meta->npars; ++i) {
if (strcasecmp(meta->pars[i].name, "MINDEPTH") == 0) {
if (!str2double(meta->pars[i].value, &mindepth))
enkf_quit("observation prm file: can not convert MINDEPTH = \"%s\" to double\n", meta->pars[i].value);
} else if (strcasecmp(meta->pars[i].name, "ADD") == 0) {
addname = meta->pars[i].value;
enkf_printf(" ADDING \"%s\"\n", addname);
} else
enkf_quit("unknown PARAMETER \"%s\"\n", meta->pars[i].name);
}
enkf_printf(" MINDEPTH = %.0f\n", mindepth);
ncw_open(fname, NC_NOWRITE, &ncid);
ncw_inq_dimid(ncid, "nobs", &dimid_nobs);
ncw_inq_dimlen(ncid, dimid_nobs, &nobs_local);
enkf_printf(" nobs = %u\n", (unsigned int) nobs_local);
if (nobs_local == 0) {
ncw_close(ncid);
return;
}
ncw_inq_varid(ncid, "lon", &varid_lon);
lon = malloc(nobs_local * sizeof(double));
ncw_get_var_double(ncid, varid_lon, lon);
ncw_inq_varid(ncid, "lat", &varid_lat);
lat = malloc(nobs_local * sizeof(double));
ncw_get_var_double(ncid, varid_lat, lat);
ncw_inq_varid(ncid, "pass", &varid_pass);
pass = malloc(nobs_local * sizeof(int));
ncw_get_var_int(ncid, varid_pass, pass);
ncw_inq_varid(ncid, "sla", &varid_sla);
sla = malloc(nobs_local * sizeof(double));
ncw_get_var_double(ncid, varid_sla, sla);
ncw_get_att_double(ncid, varid_sla, "error_std", &error_std);
enkf_printf(" error_std = %3g\n", error_std);
if (addname != NULL) {
ncw_inq_varid(ncid, addname, &varid_add);
add = malloc(nobs_local * sizeof(double));
ncw_get_var_double(ncid, varid_add, add);
}
ncw_inq_varid(ncid, "time", &varid_time);
time = malloc(nobs_local * sizeof(double));
ncw_get_var_double(ncid, varid_time, time);
ncw_inq_attlen(ncid, varid_time, "units", &tunits_len);
tunits = calloc(tunits_len + 1, 1);
ncw_get_att_text(ncid, varid_time, "units", tunits);
ncw_close(ncid);
tunits_convert(tunits, &tunits_multiple, &tunits_offset);
basename = strrchr(fname, '/');
if (basename == NULL)
basename = fname;
else
basename += 1;
strncpy(instname, basename, 2);
instname[2] = 0;
mvid = model_getvarid(m, obs->obstypes[obstype_getid(obs->nobstypes, obs->obstypes, meta->type, 1)].varnames[0], 1);
ktop = grid_gettoplayerid(model_getvargrid(m, mvid));
depth = model_getdepth(m, mvid, 1);
for (i = 0; i < (int) nobs_local; ++i) {
observation* o;
obstype* ot;
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_ifabscent(obs->instruments, instname, -1);
o->id = obs->nobs;
o->fid = fid;
o->batch = pass[i];
o->value = sla[i];
if (add != NULL)
o->value += add[i];
o->std = error_std;
o->lon = lon[i];
o->lat = lat[i];
o->depth = 0.0;
o->status = model_xy2fij(m, mvid, o->lon, o->lat, &o->fi, &o->fj);
if (!obs->allobs && o->status == STATUS_OUTSIDEGRID)
continue;
o->fk = (double) ktop;
o->model_depth = (isnan(o->fi + o->fj)) ? NaN : depth[(int) (o->fj + 0.5)][(int) (o->fi + 0.5)];
o->date = time[i] * tunits_multiple + tunits_offset;
if (o->status == STATUS_OK && o->model_depth < mindepth)
o->status = STATUS_SHALLOW;
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;
o->aux = -1;
obs->nobs++;
}
if (add != NULL)
free(add);
free(lon);
free(lat);
free(pass);
free(sla);
free(tunits);
free(time);
}
void reader_mmt_standard(char* fname, int fid, obsmeta* meta, model* m, observations* obs)
{
int ncid;
int dimid_nprof, dimid_nz;
size_t nprof, nz;
int varid_lon, varid_lat, varid_z, varid_type;
int varid_v = -1;
double* lon;
double* lat;
double** z;
double** v;
double missval;
double validmin = DBL_MAX;
double validmax = -DBL_MAX;
char* type;
char buf[MAXSTRLEN];
int len;
int year, month, day;
double tunits_multiple, tunits_offset;
int mvid;
int p, i;
for (i = 0; i < meta->npars; ++i)
enkf_quit("unknown PARAMETER \"%s\"\n", meta->pars[i].name);
if (meta->nstds == 0)
enkf_quit("ERROR_STD is necessary but not specified for product \"%s\"", meta->product);
ncw_open(fname, NC_NOWRITE, &ncid);
ncw_inq_dimid(fname, ncid, "N_PROF", &dimid_nprof);
ncw_inq_dimlen(fname, ncid, dimid_nprof, &nprof);
ncw_inq_dimid(fname, ncid, "N_LEVELS", &dimid_nz);
ncw_inq_dimlen(fname, ncid, dimid_nz, &nz);
enkf_printf(" # profiles = %u\n", (unsigned int) nprof);
if (nprof == 0) {
ncw_close(fname, ncid);
return;
}
enkf_printf(" # z levels = %u\n", (unsigned int) nz);
ncw_inq_varid(fname, ncid, "LONGITUDE", &varid_lon);
lon = malloc(nprof * sizeof(double));
ncw_get_var_double(fname, ncid, varid_lon, lon);
ncw_inq_varid(fname, ncid, "LATITUDE", &varid_lat);
lat = malloc(nprof * sizeof(double));
ncw_get_var_double(fname, ncid, varid_lat, lat);
ncw_inq_varid(fname, ncid, "PRES_BLUELINK", &varid_z);
z = alloc2d(nprof, nz, sizeof(double));
ncw_get_var_double(fname, ncid, varid_z, z[0]);
if (strncmp(meta->type, "TEM", 3) == 0) {
validmin = -2.0;
validmax = 40.0;
ncw_inq_varid(fname, ncid, "TEMP_BLUELINK", &varid_v);
} else if (strncmp(meta->type, "SAL", 3) == 0) {
validmin = 0;
validmax = 50.0;
ncw_inq_varid(fname, ncid, "PSAL_BLUELINK", &varid_v);
} else
enkf_quit("observation type \"%s\" not handled for MMT product", meta->type);
v = alloc2d(nprof, nz, sizeof(double));
ncw_get_var_double(fname, ncid, varid_v, v[0]);
ncw_get_att_double(fname, ncid, varid_v, "_FillValue", &missval);
ncw_inq_varid(fname, ncid, "WMO_INST_TYPE", &varid_type);
type = malloc(nprof * WMO_INSTSIZE);
ncw_get_var_text(fname, ncid, varid_type, type);
ncw_close(fname, ncid);
strcpy(buf, fname);
len = strlen(buf);
buf[len - 10] = 0; /* _mmt_qc.nc */
if (!str2int(&buf[len - 12], &day))
enkf_quit("MMT reader: could not convert file name \"%s\" to date", fname);
buf[len - 12] = 0;
if (!str2int(&buf[len - 14], &month))
enkf_quit("MMT reader: could not convert file name \"%s\" to date", fname);
buf[len - 14] = 0;
if (!str2int(&buf[len - 18], &year))
enkf_quit("MMT reader: could not convert file name \"%s\" to date", fname);
snprintf(buf, MAXSTRLEN, "days since %4d-%02d-%02d", year, month, day);
tunits_convert(buf, &tunits_multiple, &tunits_offset);
mvid = model_getvarid(m, obs->obstypes[obstype_getid(obs->nobstypes, obs->obstypes, meta->type)].varname, 1);
for (p = 0; p < (int) nprof; ++p) {
char inststr[MAXSTRLEN];
snprintf(inststr, MAXSTRLEN, "WMO%04u", type[p * WMO_INSTSIZE]);
for (i = 0; i < (int) nz; ++i) {
observation* o;
obstype* ot;
if (fabs(v[p][i] - missval) < EPS || v[p][i] < validmin || v[p][i] > validmax)
continue;
if (z[p][i] < 0.0)
continue;
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);
assert(o->type >= 0);
ot = &obs->obstypes[o->type];
o->instrument = st_add_ifabscent(obs->instruments, inststr, -1);
o->id = obs->nobs;
o->fid = fid;
o->batch = p;
o->value = v[p][i];
o->std = 0.0;
o->lon = lon[p];
o->lat = lat[p];
o->depth = z[p][i];
o->status = model_xy2fij(m, mvid, o->lon, o->lat, &o->fi, &o->fj);
if (!obs->allobs && o->status == STATUS_OUTSIDEGRID)
break;
if (o->status == STATUS_OK)
o->status = model_z2fk(m, mvid, o->fi, o->fj, o->depth, &o->fk);
else
o->fk = NaN;
if ((o->status == STATUS_OK) && (o->lon <= ot->xmin || o->lon >= ot->xmax || o->lat <= ot->ymin || o->lat >= ot->ymax || o->depth <= ot->zmin || o->depth >= ot->zmax))
o->status = STATUS_OUTSIDEOBSDOMAIN;
o->date = tunits_offset + 0.5;
o->aux = -1;
obs->nobs++;
}
}
free(lon);
free(lat);
free2d(v);
free2d(z);
free(type);
}
/** For files of the form ??_yyyymmdd.nc. They are assumed to have "time"
* variable.
*/
void reader_rads_standard(char* fname, int fid, obsmeta* meta, model* m, observations* obs)
{
int ncid;
int dimid_nobs;
size_t nobs_local;
int varid_lon, varid_lat, varid_pass, varid_sla, varid_time;
double* lon;
double* lat;
int* pass;
double* sla;
double* time;
double error_std;
size_t tunits_len;
char* tunits;
double tunits_multiple, tunits_offset;
char* basename;
char instname[3];
int mvid;
float** depth;
int i;
ncw_open(fname, NC_NOWRITE, &ncid);
ncw_inq_dimid(fname, ncid, "nobs", &dimid_nobs);
ncw_inq_dimlen(fname, ncid, dimid_nobs, &nobs_local);
enkf_printf(" nobs = %u\n", (unsigned int) nobs_local);
if (nobs_local == 0) {
ncw_close(fname, ncid);
return;
}
ncw_inq_varid(fname, ncid, "lon", &varid_lon);
lon = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_lon, lon);
ncw_inq_varid(fname, ncid, "lat", &varid_lat);
lat = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_lat, lat);
ncw_inq_varid(fname, ncid, "pass", &varid_pass);
pass = malloc(nobs_local * sizeof(int));
ncw_get_var_int(fname, ncid, varid_pass, pass);
ncw_inq_varid(fname, ncid, "sla", &varid_sla);
sla = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_sla, sla);
ncw_get_att_double(fname, ncid, varid_sla, "error_std", &error_std);
enkf_printf(" error_std = %3g\n", error_std);
ncw_inq_varid(fname, ncid, "time", &varid_time);
time = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_time, time);
ncw_inq_attlen(fname, ncid, varid_time, "units", &tunits_len);
tunits = calloc(tunits_len + 1, 1);
ncw_get_att_text(fname, ncid, varid_time, "units", tunits);
ncw_close(fname, ncid);
tunits_convert(tunits, &tunits_multiple, &tunits_offset);
basename = strrchr(fname, '/');
if (basename == NULL)
basename = fname;
else
basename += 1;
strncpy(instname, basename, 2);
instname[2] = 0;
mvid = model_getvarid(m, obs->obstypes[obstype_getid(obs->nobstypes, obs->obstypes, meta->type)].varname, 1);
depth = model_getdepth(m, mvid);
for (i = 0; i < (int) nobs_local; ++i) {
observation* o;
obstype* ot;
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);
assert(o->type >= 0);
ot = &obs->obstypes[o->type];
o->instrument = st_add_ifabscent(obs->instruments, instname, -1);
o->id = obs->nobs;
o->fid = fid;
o->batch = pass[i];
o->value = sla[i];
o->std = error_std;
o->lon = lon[i];
o->lat = lat[i];
o->depth = 0.0;
o->status = model_xy2fij(m, mvid, o->lon, o->lat, &o->fi, &o->fj);
if (!obs->allobs && o->status == STATUS_OUTSIDEGRID)
continue;
o->fk = 0.0;
o->date = time[i] * tunits_multiple + tunits_offset;
if (o->status == STATUS_OK && depth[(int) floor(o->fj + 0.5)][(int) floor(o->fi + 0.5)] < MINDEPTH)
o->status = STATUS_SHALLOW;
if ((o->status == STATUS_OK) && (o->lon <= ot->xmin || o->lon >= ot->xmax || o->lat <= ot->ymin || o->lat >= ot->ymax || o->depth <= ot->zmin || o->depth >= ot->zmax))
o->status = STATUS_OUTSIDEOBSDOMAIN;
o->aux = -1;
obs->nobs++;
}
free(lon);
free(lat);
free(pass);
free(sla);
free(tunits);
free(time);
}
int main(int argc, char** argv)
{
int ndims = 0;
char** dims = NULL;
int nsrc = 0;
char** src = NULL;
char* dst = NULL;
int i;
int** dimids = NULL;
int nvars = 0;
int* varids = NULL;
size_t* size = NULL;
int nvars0;
if (argc == 1) {
usage();
description();
exit(0);
}
i = 1;
while (i < argc) {
if (argv[i][0] != '-') {
usage();
exit(1);
}
if (argv[i][1] == 'd') {
i++;
while (i < argc && argv[i][0] != '-') {
if (ndims % INC == 0)
dims = realloc(dims, (ndims + INC) * sizeof(char*));
dims[ndims] = argv[i];
ndims++;
i++;
}
} else if (argv[i][1] == 'i') {
i++;
while (i < argc && argv[i][0] != '-') {
if (nsrc % INC == 0)
src = realloc(src, (nsrc + INC) * sizeof(char*));
src[nsrc] = strdup(argv[i]);
nsrc++;
i++;
}
} else if (argv[i][1] == 'o') {
i++;
if (i < argc && argv[i][0] != '-') {
dst = argv[i];
i++;
}
} else if (argv[i][1] == 'v') {
verbose = 1;
i++;
} else {
usage();
exit(1);
}
}
if (argc == 2 && verbose) {
printf(" ncw version %s\n", ncw_version);
exit(1);
}
if (ndims == 0 || nsrc < 1 || dst == NULL) {
usage();
exit(1);
}
printf_v(" src:\n");
for (i = 0; i < nsrc; ++i)
printf_v(" \"%s\"\n", src[i]);
printf_v(" dst = \"%s\"\n", dst);
printf_v(" merged dimensions:\n");
for (i = 0; i < ndims; ++i)
printf_v(" %s\n", dims[i]);
dimids = alloc2d(nsrc, ndims, sizeof(int));
for (i = 0; i < nsrc; ++i) {
int ncid, j;
ncw_open(src[i], NC_NOWRITE, &ncid);
for (j = 0; j < ndims; ++j)
ncw_inq_dimid(ncid, dims[j], &dimids[i][j]);
ncw_close(ncid);
}
{
int ncid;
ncw_open(src[0], NC_NOWRITE, &ncid);
ncw_inq_nvars(ncid, &nvars0);
varids = malloc(nvars0 * sizeof(int));
printf_v(" merged variables:\n");
for (i = 0; i < nvars0; ++i) {
int dimids_now[NC_MAX_VAR_DIMS];
char varname[NC_MAX_NAME] = "";
int j;
ncw_inq_vardimid(ncid, i, dimids_now);
for (j = 0; j < ndims; ++j) {
if (dimids_now[0] == dimids[0][j]) {
varids[nvars] = i;
nvars++;
ncw_inq_varname(ncid, i, varname);
printf_v(" %s\n", varname);
break;
}
}
}
ncw_close(ncid);
}
printf_v(" creating dst:");
{
int ncid_dst, ncid0;
int ndims0;
ncw_create(dst, NC_CLOBBER | NC_64BIT_OFFSET, &ncid_dst);
ncw_open(src[0], NC_NOWRITE, &ncid0);
ncw_inq_ndims(ncid0, &ndims0);
for (i = 0; i < ndims0; ++i) {
char dimname[NC_MAX_NAME];
size_t dimlen;
int dimid;
int j;
ncw_inq_dim(ncid0, i, dimname, &dimlen);
for (j = 0; j < ndims; ++j) {
if (i == dimids[0][j]) {
int ncid_now, dimid_now;
size_t dimlen_now;
int s;
for (s = 1; s < nsrc; ++s) {
ncw_open(src[s], NC_NOWRITE, &ncid_now);
ncw_inq_dimid(ncid_now, dimname, &dimid_now);
ncw_inq_dimlen(ncid_now, dimid_now, &dimlen_now);
ncw_close(ncid_now);
dimlen += dimlen_now;
}
break;
}
}
ncw_def_dim(ncid_dst, dimname, dimlen, &dimid);
}
for (i = 0; i < nvars0; ++i) {
nc_type type;
int nvardims;
char varname[NC_MAX_NAME];
int dimids0[NC_MAX_DIMS], dimids_dst[NC_MAX_DIMS];
int natts;
int varid_dst;
int j;
ncw_inq_var(ncid0, i, varname, &type, &nvardims, dimids0, &natts);
for (j = 0; j < nvardims; ++j) {
char dimname[NC_MAX_NAME];
size_t dimlen;
ncw_inq_dim(ncid0, dimids0[j], dimname, &dimlen);
ncw_inq_dimid(ncid_dst, dimname, &dimids_dst[j]);
}
ncw_def_var(ncid_dst, varname, type, nvardims, dimids_dst, &varid_dst);
ncw_copy_atts(ncid0, i, ncid_dst, varid_dst);
}
ncw_close(ncid_dst);
ncw_close(ncid0);
}
printf_v("\n");
printf_v(" copying data:");
size = malloc(nsrc * sizeof(size_t));
{
int ncid_dst;
ncw_open(dst, NC_WRITE, &ncid_dst);
for (i = 0; i < nvars0; ++i) {
int j;
for (j = 0; j < nvars; ++j)
if (varids[j] == i)
break;
if (j == nvars) {
int ncid0;
ncw_open(src[0], NC_NOWRITE, &ncid0);
ncw_copy_vardata(ncid0, i, ncid_dst);
ncw_close(ncid0);
} else {
int ncid;
char varname[NC_MAX_NAME];
int s;
size_t size_total = 0;
size_t nbytes;
void* data = NULL;
void* data_now;
nc_type type;
int varid_dst;
ncw_open(src[0], NC_NOWRITE, &ncid);
ncw_inq_varname(ncid, i, varname);
ncw_close(ncid);
size_total = 0;
for (s = 0; s < nsrc; ++s) {
int ncid;
int varid;
int ndims;
int dimids[NC_MAX_DIMS];
size_t dimlens[NC_MAX_DIMS];
ncw_open(src[s], NC_NOWRITE, &ncid);
ncw_inq_varid(ncid, varname, &varid);
ncw_inq_var(ncid, varid, NULL, &type, &ndims, dimids, NULL);
for (j = 0; j < ndims; ++j)
ncw_inq_dimlen(ncid, dimids[j], &dimlens[j]);
ncw_close(ncid);
size[s] = 1;
for (j = 0; j < ndims; ++j)
size[s] *= dimlens[j];
size_total += size[s];
}
nbytes = size_total * ncw_sizeof(type);
if (nbytes > 4294967296)
quit("sizeof(%s) = %zu exceeds 4GB", varname, nbytes);
data = malloc(nbytes);
if (data == NULL)
quit("malloc(): could not allocate memory for variable \"%s\" (size = %zu)", varname, size_total * ncw_sizeof(type));
data_now = data;
for (s = 0; s < nsrc; ++s) {
int ncid;
int varid;
ncw_open(src[s], NC_NOWRITE, &ncid);
ncw_inq_varid(ncid, varname, &varid);
ncw_get_var(ncid, varid, data_now);
ncw_close(ncid);
data_now = &((char*) data_now)[size[s] * ncw_sizeof(type)];
}
ncw_inq_varid(ncid_dst, varname, &varid_dst);
ncw_put_var(ncid_dst, varid_dst, data);
free(data);
}
printf_v(".");
}
ncw_close(ncid_dst);
}
printf_v("\n");
/*
* clean up
*/
free(size);
free(varids);
free(dimids);
for (i = 0; i < nsrc; ++i)
free(src[i]);
free(src);
return 0;
}
void reader_cars_standard(char* fname, int fid, obsmeta* meta, grid* g, observations* obs)
{
int ncid;
int dimid_nprof, dimid_nz = -1;
size_t nprof, nz;
int varid_lon, varid_lat, varid_z, varid_type;
int varid_v = -1;
double* lon;
double* lat;
double** z;
double** v;
double missval, validmin, validmax;
int* type;
char buf[MAXSTRLEN];
int len;
int year, month, day;
double tunits_multiple, tunits_offset;
int p, i;
for (i = 0; i < meta->npars; ++i)
enkf_quit("unknown PARAMETER \"%s\"\n", meta->pars[i].name);
if (meta->nstds == 0)
enkf_quit("ERROR_STD is necessary but not specified for product \"%s\"", meta->product);
ncw_open(fname, NC_NOWRITE, &ncid);
ncw_inq_dimid(ncid, "nobs", &dimid_nprof);
ncw_inq_dimlen(ncid, dimid_nprof, &nprof);
enkf_printf(" # profiles = %u\n", (unsigned int) nprof);
if (nprof == 0) {
ncw_close(ncid);
return;
}
if (ncw_dim_exists(ncid, "zt"))
ncw_inq_dimid(ncid, "zt", &dimid_nz);
else if (ncw_dim_exists(ncid, "ztd"))
ncw_inq_dimid(ncid, "ztd", &dimid_nz);
else
enkf_quit("reader_cars_standard(): neither dimension \"zt\" ot \"ztd\" exist");
ncw_inq_dimlen(ncid, dimid_nz, &nz);
enkf_printf(" # z levels = %u\n", (unsigned int) nz);
ncw_inq_varid(ncid, "lon", &varid_lon);
lon = malloc(nprof * sizeof(double));
ncw_get_var_double(ncid, varid_lon, lon);
ncw_inq_varid(ncid, "lat", &varid_lat);
lat = malloc(nprof * sizeof(double));
ncw_get_var_double(ncid, varid_lat, lat);
ncw_inq_varid(ncid, "zt", &varid_z);
z = alloc2d(nprof, nz, sizeof(double));
ncw_get_var_double(ncid, varid_z, z[0]);
if (strncmp(meta->type, "TEM", 3) == 0)
ncw_inq_varid(ncid, "temp", &varid_v);
else if (strncmp(meta->type, "SAL", 3) == 0)
ncw_inq_varid(ncid, "salt", &varid_v);
else
enkf_quit("observation type \"%s\" not handled for CARS product", meta->type);
v = alloc2d(nprof, nz, sizeof(double));
ncw_get_var_double(ncid, varid_v, v[0]);
ncw_get_att_double(ncid, varid_v, "missing_value", &missval);
ncw_get_att_double(ncid, varid_v, "valid_min", &validmin);
ncw_get_att_double(ncid, varid_v, "valid_max", &validmax);
ncw_inq_varid(ncid, "type", &varid_type);
type = malloc(nprof * sizeof(int));
ncw_get_var_int(ncid, varid_type, type);
ncw_close(ncid);
strcpy(buf, fname);
len = strlen(buf);
buf[len - 3] = 0; /* .nc */
if (!str2int(&buf[len - 5], &day))
enkf_quit("CARS reader: could not convert file name \"%s\" to date", fname);
buf[len - 17] = 0;
if (!str2int(&buf[len - 19], &month))
enkf_quit("CARS reader: could not convert file name \"%s\" to date", fname);
buf[len - 21] = 0;
if (!str2int(&buf[len - 25], &year))
enkf_quit("CARS reader: could not convert file name \"%s\" to date", fname);
snprintf(buf, MAXSTRLEN, "days since %4d-%02d-%02d", year, month, day);
tunits_convert(buf, &tunits_multiple, &tunits_offset);
for (p = 0; p < (int) nprof; ++p) {
char inststr[MAXSTRLEN];
if (type[p] == 11)
strcpy(inststr, "ARGO");
else if (type[p] == 12)
strcpy(inststr, "TAO");
else if (type[p] == 61)
strcpy(inststr, "PIRATA");
else if (type[p] == 7 || type[p] == 9 || type[p] == 13 || type[p] == 35 || type[p] == 41)
strcpy(inststr, "CTD");
else if (type[p] == 8 || type[p] == 17)
strcpy(inststr, "XBT");
else
snprintf(inststr, MAXSTRLEN, "CARS%02u", type[p]);
for (i = 0; i < (int) nz; ++i) {
observation* o;
obstype* ot;
if (fabs(v[p][i] - missval) < EPS || v[p][i] < validmin || v[p][i] > validmax)
continue;
if (z[p][i] < 0.0)
continue;
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, inststr, -1);
o->id = obs->nobs;
o->fid = fid;
o->batch = p;
o->value = v[p][i];
o->std = 0.0;
o->lon = lon[p];
o->lat = lat[p];
o->depth = z[p][i];
o->status = grid_xy2fij(g, o->lon, o->lat, &o->fi, &o->fj);
if (!obs->allobs && o->status == STATUS_OUTSIDEGRID)
break;
if (o->status == STATUS_OK)
o->status = grid_z2fk(g, o->fi, o->fj, o->depth, &o->fk);
else
o->fk = NAN;
if ((o->status == STATUS_OK) && (o->lon <= ot->xmin || o->lon >= ot->xmax || o->lat <= ot->ymin || o->lat >= ot->ymax || o->depth <= ot->zmin || o->depth >= ot->zmax))
o->status = STATUS_OUTSIDEOBSDOMAIN;
o->model_depth = NAN; /* set in obs_add() */
o->date = tunits_offset + 0.5;
o->aux = -1;
obs->nobs++;
}
}
free(lon);
free(lat);
free(v);
free(z);
free(type);
}
void reader_jplmur_gridded(char* fname, int fid, obsmeta* meta, grid* g, observations* obs)
{
int ksurf = grid_getsurflayerid(g);
char* varname = "analysed_sst";
char* lonname = "lon";
char* latname = "lat";
char* npointsname = NULL;
char* stdname = "analysis_error";
char* estdname = NULL;
char* timename = "time";
int ncid;
int ndim_var, ndim_xy;
size_t dimlen_var[3], dimlen_xy[2];
float varshift = -273.15;
double mindepth = 0.0;
char instrument[MAXSTRLEN];
int iscurv = -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_var = -1, varid_npoints = -1, varid_std = -1, varid_estd = -1, varid_time = -1;
float* var = NULL;
float var_fill_value = NAN;
float var_add_offset = NAN, var_scale_factor = NAN;
double var_estd = NAN;
short* npoints = 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;
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, "TIMENAME") == 0)
timename = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "NPOINTSNAME") == 0)
npointsname = 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, "VARSHIFT") == 0) {
if (!str2float(meta->pars[i].value, &varshift))
enkf_quit("observation prm file: can not convert VARSHIFT = \"%s\" to float\n", meta->pars[i].value);
enkf_printf(" 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("observation prm file: can not convert MINDEPTH = \"%s\" to double\n", 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);
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
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
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 (npointsname != NULL)
ncw_inq_varid(ncid, npointsname, &varid_npoints);
else if (ncw_var_exists(ncid, "npoints"))
ncw_inq_varid(ncid, "npoints", &varid_npoints);
if (varid_npoints >= 0) {
npoints = malloc(n * sizeof(short));
ncw_get_var_short(ncid, varid_npoints, npoints);
}
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 (timename != NULL)
ncw_inq_varid(ncid, timename, &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;
if ((npoints != NULL && npoints[i] == 0) || var[i] == var_fill_value || isnan(var[i]) || (std != NULL && (std[i] == std_fill_value || isnan(std[i]))) || (estd != NULL && (estd[i] == estd_fill_value || isnan(estd[i]))) || (have_time && !singletime && (time[i] == time_fill_value || isnan(time[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;
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 (!isnan(var_estd)) {
o->std = var_estd;
}
else {
if (!isnan(std_add_offset))
o->std = (double) (std[i] * std_scale_factor + std_add_offset);
else
o->std = (double) std[i];
if (!isnan(estd_add_offset)) {
double std2 = (double) (estd[i] * estd_scale_factor + estd_add_offset);
o->std = (o->std > std2) ? o->std : std2;
}
}
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->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;
o->model_depth = NAN; /* set in obs_add() */
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);
}
grid* grid_create(void* p, int id)
{
gridprm* prm = (gridprm*) p;
grid* g = calloc(1, sizeof(grid));
char* fname = prm->fname;
int ncid;
int dimid_x, dimid_y, dimid_z;
int varid_x, varid_y, varid_z;
int ndims_x, ndims_y, ndims_z;
size_t nx, ny, nz;
int varid_depth, varid_numlevels;
g->name = strdup(prm->name);
g->id = id;
g->vtype = gridprm_getvtype(prm);
g->sfactor = prm->sfactor;
#if !defined(NO_GRIDUTILS)
#if !defined(GRIDMAP_TYPE_DEF)
#error("GRIDMAP_TYPE_DEF not defined; please update gridutils-c");
#endif
if (prm->maptype == 'b' || prm->maptype == 'B')
g->maptype = GRIDMAP_TYPE_BINARY;
else if (prm->maptype == 'k' || prm->maptype == 'K')
g->maptype = GRIDMAP_TYPE_KDTREE;
else
enkf_quit("unknown grid map type \"%c\"", prm->maptype);
#endif
ncw_open(fname, NC_NOWRITE, &ncid);
ncw_inq_dimid(ncid, prm->xdimname, &dimid_x);
ncw_inq_dimid(ncid, prm->ydimname, &dimid_y);
ncw_inq_dimid(ncid, prm->zdimname, &dimid_z);
ncw_inq_dimlen(ncid, dimid_x, &nx);
ncw_inq_dimlen(ncid, dimid_y, &ny);
ncw_inq_dimlen(ncid, dimid_z, &nz);
ncw_inq_varid(ncid, prm->xvarname, &varid_x);
ncw_inq_varid(ncid, prm->yvarname, &varid_y);
ncw_inq_varid(ncid, prm->zvarname, &varid_z);
ncw_inq_varndims(ncid, varid_x, &ndims_x);
ncw_inq_varndims(ncid, varid_y, &ndims_y);
ncw_inq_varndims(ncid, varid_z, &ndims_z);
if (ndims_x == 1 && ndims_y == 1) {
double* x;
double* y;
double* z;
x = malloc(nx * sizeof(double));
y = malloc(ny * sizeof(double));
z = malloc(nz * sizeof(double));
ncw_get_var_double(ncid, varid_x, x);
ncw_get_var_double(ncid, varid_y, y);
ncw_get_var_double(ncid, varid_z, z);
grid_setcoords(g, GRIDHTYPE_LATLON, NT_NONE, nx, ny, nz, x, y, z);
}
#if !defined(NO_GRIDUTILS)
else if (ndims_x == 2 && ndims_y == 2) {
double** x;
double** y;
double* z;
x = gu_alloc2d(ny, nx, sizeof(double));
y = gu_alloc2d(ny, nx, sizeof(double));
z = malloc(nz * sizeof(double));
ncw_get_var_double(ncid, varid_x, x[0]);
ncw_get_var_double(ncid, varid_y, y[0]);
ncw_get_var_double(ncid, varid_z, z);
grid_setcoords(g, GRIDHTYPE_CURVILINEAR, NT_COR, nx, ny, nz, x, y, z);
}
#endif
else
enkf_quit("%s: could not determine the grid type", fname);
if (prm->depthvarname != NULL) {
float** depth = alloc2d(ny, nx, sizeof(float));
ncw_inq_varid(ncid, prm->depthvarname, &varid_depth);
ncw_get_var_float(ncid, varid_depth, depth[0]);
g->depth = depth;
}
if (prm->levelvarname != NULL) {
g->numlevels = alloc2d(ny, nx, sizeof(int));
ncw_inq_varid(ncid, prm->levelvarname, &varid_numlevels);
ncw_get_var_int(ncid, varid_numlevels, g->numlevels[0]);
if (g->vtype == GRIDVTYPE_SIGMA) {
int i, j;
for (j = 0; j < ny; ++j)
for (i = 0; i < nx; ++i)
g->numlevels[j][i] *= nz;
}
}
ncw_close(ncid);
if (g->numlevels == NULL) {
g->numlevels = alloc2d(ny, nx, sizeof(int));
if (g->vtype == GRIDVTYPE_SIGMA) {
int i, j;
for (j = 0; j < ny; ++j)
for (i = 0; i < nx; ++i)
if (g->depth == NULL || g->depth[j][i] > 0.0)
g->numlevels[j][i] = nz;
} else {
int i, j;
assert(g->depth != NULL);
for (j = 0; j < ny; ++j) {
for (i = 0; i < nx; ++i) {
double depth = g->depth[j][i];
double fk = NaN;
if (depth > 0.0) {
z2fk(g, j, i, depth, &fk);
g->numlevels[j][i] = ceil(fk + 0.5);
}
}
}
}
}
gridprm_print(prm, " ");
grid_print(g, " ");
return g;
}
grid* grid_create(void* p, int id)
{
gridprm* prm = (gridprm*) p;
grid* g = calloc(1, sizeof(grid));
char* fname = prm->fname;
int ncid;
int dimid_x, dimid_y, dimid_z;
int varid_x, varid_y, varid_z;
int ndims_x, ndims_y, ndims_z;
size_t nx, ny, nz;
int varid_depth, varid_numlevels;
g->name = strdup(prm->name);
g->id = id;
g->vtype = gridprm_getvtype(prm);
ncw_open(fname, NC_NOWRITE, &ncid);
ncw_inq_dimid(fname, ncid, prm->xdimname, &dimid_x);
ncw_inq_dimid(fname, ncid, prm->ydimname, &dimid_y);
ncw_inq_dimid(fname, ncid, prm->zdimname, &dimid_z);
ncw_inq_dimlen(fname, ncid, dimid_x, &nx);
ncw_inq_dimlen(fname, ncid, dimid_y, &ny);
ncw_inq_dimlen(fname, ncid, dimid_z, &nz);
ncw_inq_varid(fname, ncid, prm->xvarname, &varid_x);
ncw_inq_varid(fname, ncid, prm->yvarname, &varid_y);
ncw_inq_varid(fname, ncid, prm->zvarname, &varid_z);
ncw_inq_varndims(fname, ncid, varid_x, &ndims_x);
ncw_inq_varndims(fname, ncid, varid_y, &ndims_y);
ncw_inq_varndims(fname, ncid, varid_z, &ndims_z);
if (ndims_x == 1 && ndims_y == 1) {
double* x;
double* y;
double* z;
int i;
double dx, dy;
int periodic_x;
x = malloc(nx * sizeof(double));
y = malloc(ny * sizeof(double));
z = malloc(nz * sizeof(double));
ncw_get_var_double(fname, ncid, varid_x, x);
ncw_get_var_double(fname, ncid, varid_y, y);
ncw_get_var_double(fname, ncid, varid_z, z);
periodic_x = fabs(fmod(2.0 * x[nx - 1] - x[nx - 2], 360.0) - x[0]) < EPS_LON;
dx = (x[nx - 1] - x[0]) / (double) (nx - 1);
for (i = 1; i < (int) nx; ++i)
if (fabs(x[i] - x[i - 1] - dx) / fabs(dx) > EPS_LON)
break;
if (i != (int) nx)
grid_setcoords(g, GRIDHTYPE_LATLON_IRREGULAR, NT_NONE, periodic_x, 0, nx, ny, nz, x, y, z);
else {
dy = (y[ny - 1] - y[0]) / (double) (ny - 1);
for (i = 1; i < (int) ny; ++i)
if (fabs(y[i] - y[i - 1] - dy) / fabs(dy) > EPS_LON)
break;
if (i != (int) ny)
grid_setcoords(g, GRIDHTYPE_LATLON_IRREGULAR, NT_NONE, periodic_x, 0, nx, ny, nz, x, y, z);
else
grid_setcoords(g, GRIDHTYPE_LATLON_REGULAR, NT_NONE, periodic_x, 0, nx, ny, nz, x, y, z);
}
}
#if !defined(NO_GRIDUTILS)
else if (ndims_x == 2 && ndims_y == 2) {
double** x;
double** y;
double* z;
x = alloc2d(ny, nx, sizeof(double));
y = alloc2d(ny, nx, sizeof(double));
z = malloc(nz * sizeof(double));
ncw_get_var_double(fname, ncid, varid_x, x[0]);
ncw_get_var_double(fname, ncid, varid_y, y[0]);
ncw_get_var_double(fname, ncid, varid_z, z);
grid_setcoords(g, GRIDHTYPE_CURVILINEAR, NT_COR, 0, 0, nx, ny, nz, x, y, z);
}
#endif
else
enkf_quit("%s: could not determine the grid type", fname);
if (prm->depthvarname != NULL) {
float** depth = alloc2d(ny, nx, sizeof(float));
ncw_inq_varid(fname, ncid, prm->depthvarname, &varid_depth);
ncw_get_var_float(fname, ncid, varid_depth, depth[0]);
g->depth = depth;
}
if (prm->levelvarname != NULL) {
g->numlevels = alloc2d(ny, nx, sizeof(int));
ncw_inq_varid(fname, ncid, prm->levelvarname, &varid_numlevels);
ncw_get_var_int(fname, ncid, varid_numlevels, g->numlevels[0]);
if (g->vtype == GRIDVTYPE_SIGMA) {
int i, j;
for (j = 0; j < ny; ++j)
for (i = 0; i < nx; ++i)
g->numlevels[j][i] *= nz;
}
}
ncw_close(fname, ncid);
if (g->numlevels == NULL && g->depth != NULL) {
g->numlevels = alloc2d(ny, nx, sizeof(int));
if (g->vtype == GRIDVTYPE_SIGMA) {
int i, j;
for (j = 0; j < ny; ++j)
for (i = 0; i < nx; ++i)
if (g->depth[j][i] > 0.0)
g->numlevels[j][i] = nz;
} else {
int i, j;
for (j = 0; j < ny; ++j) {
for (i = 0; i < nx; ++i) {
double depth = g->depth[j][i];
double fk = NaN;
if (depth > 0.0) {
z2fk(g, j, i, depth, &fk);
g->numlevels[j][i] = ceil(fk + 0.5);
}
}
}
}
}
gridprm_print(prm, " ");
grid_print(g, " ");
return g;
}
void reader_navo_standard(char* fname, int fid, obsmeta* meta, model* m, observations* obs)
{
int addbias = ADDBIAS_DEF;
int ncid;
int dimid_nobs;
size_t nobs_local;
int varid_lon, varid_lat, varid_sst, varid_sstb, varid_error, varid_time;
double* lon = NULL;
double* lat = NULL;
double* sst = NULL;
double* sstb = NULL;
double* error_std = NULL;
double* time = NULL;
int year, month, day;
char tunits[MAXSTRLEN];
size_t tunits_len;
double tunits_multiple, tunits_offset;
char* basename;
int model_vid;
int k, i;
for (i = 0; i < meta->npars; ++i) {
if (strcasecmp(meta->pars[i].name, "ADDBIAS") == 0)
addbias = (istrue(meta->pars[i].value)) ? 1 : 0;
else
enkf_quit("unknown PARAMETER \"%s\"\n", meta->pars[i].name);
}
enkf_printf(" ADDBIAS = %s\n", (addbias) ? "YES" : "NO");
basename = strrchr(fname, '/');
if (basename == NULL)
basename = fname;
else
basename += 1;
ncw_open(fname, NC_NOWRITE, &ncid);
ncw_inq_dimid(fname, ncid, (ncw_dim_exists(ncid, "nobs")) ? "nobs" : "length", &dimid_nobs);
ncw_inq_dimlen(fname, ncid, dimid_nobs, &nobs_local);
enkf_printf(" nobs = %u\n", (unsigned int) nobs_local);
if (nobs_local == 0) {
ncw_close(fname, ncid);
return;
}
ncw_inq_varid(fname, ncid, "lon", &varid_lon);
lon = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_lon, lon);
ncw_inq_varid(fname, ncid, "lat", &varid_lat);
lat = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_lat, lat);
ncw_inq_varid(fname, ncid, "sst", &varid_sst);
sst = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_sst, sst);
if (addbias) {
ncw_inq_varid(fname, ncid, "SST_bias", &varid_sstb);
sstb = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_sstb, sstb);
}
ncw_inq_varid(fname, ncid, "error", &varid_error);
error_std = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_error, error_std);
ncw_inq_varid(fname, ncid, "GMT_time", &varid_time);
time = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_time, time);
ncw_inq_attlen(fname, ncid, varid_time, "units", &tunits_len);
ncw_get_att_text(fname, ncid, varid_time, "units", tunits);
basename[13] = 0;
if (!str2int(&basename[11], &day))
enkf_quit("NAVO reader: could not convert file name \"%s\" to date", fname);
basename[11] = 0;
if (!str2int(&basename[9], &month))
enkf_quit("NAVO reader: could not convert file name \"%s\" to date", fname);
basename[9] = 0;
if (!str2int(&basename[5], &year))
enkf_quit("NAVO reader: could not convert file name \"%s\" to date", fname);
snprintf(&tunits[tunits_len], MAXSTRLEN - tunits_len, " since %4d-%02d-%02d", year, month, day);
ncw_close(fname, ncid);
tunits_convert(tunits, &tunits_multiple, &tunits_offset);
model_vid = model_getvarid(m, obs->obstypes[obstype_getid(obs->nobstypes, obs->obstypes, meta->type)].varname, 1);
k = grid_gettoplayerid(model_getvargrid(m, model_vid));
for (i = 0; i < (int) nobs_local; ++i) {
observation* o;
obstype* ot;
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);
assert(o->type >= 0);
ot = &obs->obstypes[o->type];
o->instrument = st_add_ifabscent(obs->instruments, "AVHRR", -1);
o->id = obs->nobs;
o->fid = fid;
o->batch = 0;
o->value = (addbias) ? sst[i] + sstb[i] : sst[i];
o->std = error_std[i];
o->lon = lon[i];
o->lat = lat[i];
o->depth = 0.0;
o->status = model_xy2fij(m, model_vid, 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->depth <= ot->zmin || o->depth >= ot->zmax))
o->status = STATUS_OUTSIDEOBSDOMAIN;
o->fk = (double) k;
o->date = time[i] * tunits_multiple + tunits_offset;
o->aux = -1;
obs->nobs++;
}
free(lon);
free(lat);
free(sst);
if (addbias)
free(sstb);
free(error_std);
free(time);
}
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);
}
/** 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() */
/** For files of the form y<yyyy>/m<mm>/??_d<dd>.nc with no "time" variable.
*/
void reader_rads_standard2(char* fname, int fid, obsmeta* meta, model* m, observations* obs)
{
int ncid;
int dimid_nobs;
size_t nobs_local;
int varid_lon, varid_lat, varid_pass, varid_sla, varid_flag;
double* lon;
double* lat;
int* pass;
double* sla;
int* flag;
double error_std;
char buf[MAXSTRLEN];
int len;
int year, month, day;
double tunits_multiple, tunits_offset;
char* basename;
char instname[3];
int mvid;
float** depth;
int i;
ncw_open(fname, NC_NOWRITE, &ncid);
ncw_inq_dimid(fname, ncid, "nobs", &dimid_nobs);
ncw_inq_dimlen(fname, ncid, dimid_nobs, &nobs_local);
enkf_printf(" nobs = %u\n", (unsigned int) nobs_local);
if (nobs_local == 0)
return;
ncw_inq_varid(fname, ncid, "lon", &varid_lon);
lon = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_lon, lon);
ncw_inq_varid(fname, ncid, "lat", &varid_lat);
lat = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_lat, lat);
ncw_inq_varid(fname, ncid, "pass", &varid_pass);
pass = malloc(nobs_local * sizeof(int));
ncw_get_var_int(fname, ncid, varid_pass, pass);
ncw_inq_varid(fname, ncid, "sla", &varid_sla);
sla = malloc(nobs_local * sizeof(double));
ncw_get_var_double(fname, ncid, varid_sla, sla);
ncw_get_att_double(fname, ncid, varid_sla, "error_std", &error_std);
enkf_printf(" error_std = %3g\n", error_std);
ncw_inq_varid(fname, ncid, "local_flag", &varid_flag);
flag = malloc(nobs_local * sizeof(int));
ncw_get_var_int(fname, ncid, varid_flag, flag);
ncw_close(fname, ncid);
strcpy(buf, fname);
len = strlen(buf);
buf[len - 3] = 0; /* .nc */
if (!str2int(&buf[len - 5], &day))
enkf_quit("RADS reader: could not convert file name \"%s\" to date", fname);
buf[len - 10] = 0;
if (!str2int(&buf[len - 12], &month))
enkf_quit("RADS reader: could not convert file name \"%s\" to date", fname);
buf[len - 14] = 0;
if (!str2int(&buf[len - 18], &year))
enkf_quit("RADS reader: could not convert file name \"%s\" to date", fname);
snprintf(buf, MAXSTRLEN, "days since %4d-%02d-%02d", year, month, day);
tunits_convert(buf, &tunits_multiple, &tunits_offset);
basename = strrchr(fname, '/');
if (basename == NULL)
basename = fname;
else
basename += 1;
strncpy(instname, basename, 2);
instname[2] = 0;
mvid = model_getvarid(m, obs->obstypes[obstype_getid(obs->nobstypes, obs->obstypes, meta->type)].varname, 1);
depth = model_getdepth(m, mvid);
for (i = 0; i < (int) nobs_local; ++i) {
observation* o;
obstype* ot;
if (flag[i] != 0)
continue;
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);
assert(o->type >= 0);
ot = &obs->obstypes[o->type];
o->instrument = st_add_ifabscent(obs->instruments, instname, -1);
o->id = obs->nobs;
o->fid = fid;
o->batch = pass[i];
o->value = sla[i];
o->std = error_std;
o->lon = lon[i];
o->lat = lat[i];
o->depth = 0.0;
o->status = model_xy2fij(m, mvid, o->lon, o->lat, &o->fi, &o->fj);
if (!obs->allobs && o->status == STATUS_OUTSIDEGRID)
continue;
o->fk = 0.0;
o->date = tunits_offset + 0.5;
if (o->status == STATUS_OK && depth[(int) floor(o->fj + 0.5)][(int) floor(o->fi + 0.5)] < MINDEPTH)
o->status = STATUS_SHALLOW;
if ((o->status == STATUS_OK) && (o->lon <= ot->xmin || o->lon >= ot->xmax || o->lat <= ot->ymin || o->lat >= ot->ymax || o->depth <= ot->zmin || o->depth >= ot->zmax))
o->status = STATUS_OUTSIDEOBSDOMAIN;
o->aux = -1;
obs->nobs++;
}
free(lon);
free(lat);
free(pass);
free(sla);
free(flag);
}
