/** 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_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);
}
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);
}
void reader_cars_standard(char* fname, int fid, obsmeta* meta, model* m, 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 mvid;
float** depth;
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);
mvid = model_getvarid(m, obs->obstypes[obstype_getid(obs->nobstypes, obs->obstypes, meta->type, 1)].varnames[0], 1);
depth = model_getdepth(m, mvid, 0);
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_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->model_depth = (depth == NULL || isnan(o->fi + o->fj)) ? NaN : depth[(int) (o->fj + 0.5)][(int) (o->fi + 0.5)];
o->date = tunits_offset + 0.5;
o->aux = -1;
obs->nobs++;
}
}
free(lon);
free(lat);
free(v);
free(z);
free(type);
}
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);
}
/** 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);
}
/** 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);
}