void das_getHE(dasystem* das)
{
observations* obs = das->obs;
model* m = das->m;
ENSOBSTYPE* Hx = NULL;
int i, e;
das->s_mode = S_MODE_HE_f;
if (obs->nobs == 0)
return;
if (das->nmem <= 0)
das_getnmem(das);
enkf_printf(" ensemble size = %d\n", das->nmem);
assert(das->nmem > 0);
distribute_iterations(0, das->nmem - 1, nprocesses, rank, " ");
/*
* ensemble observation array to be filled
*/
assert(das->S == NULL);
das->S = alloc2d(das->nmem, obs->nobs, sizeof(ENSOBSTYPE));
if (das->mode == MODE_ENOI)
Hx = calloc(obs->nobs, sizeof(ENSOBSTYPE));
for (i = 0; i < obs->nobstypes; ++i) {
obstype* ot = &obs->obstypes[i];
float*** vvv = NULL;
float** vv = NULL;
H_fn H = NULL;
int mvid;
int ni, nj, nk;
int nobs;
int* obsids;
char fname[MAXSTRLEN];
enkf_printf(" %s ", ot->name);
fflush(stdout);
mvid = model_getvarid(m, obs->obstypes[i].varname);
if (mvid < 0)
enkf_quit("variable \"%s\" required for observation type \"%s\" is not defined", obs->obstypes[i].varname, ot->name);
if (ot->issurface) {
model_getvardims(m, mvid, &ni, &nj, NULL);
vv = alloc2d(nj, ni, sizeof(float));
} else {
model_getvardims(m, mvid, &ni, &nj, &nk);
vvv = alloc3d(nk, nj, ni, sizeof(float));
}
/*
* set H
*/
H = getH(ot->name, ot->hfunction);
if (ot->isasync) {
int t1 = get_tshift(ot->date_min, ot->async_tstep);
int t2 = get_tshift(ot->date_max, ot->async_tstep);
int t;
for (t = t1; t <= t2; ++t) {
enkf_printf("|");
obs_find_bytypeandtime(obs, i, t, &nobs, &obsids);
if (nobs == 0)
continue;
if (das->mode == MODE_ENKF || !enkf_fstatsonly) {
for (e = my_first_iteration; e <= my_last_iteration; ++e) {
int success = model_getmemberfname_async(m, das->ensdir, ot->varname, ot->name, e + 1, t, fname);
H(das, nobs, obsids, fname, e + 1, t, ot->varname, ot->varname2, (ot->issurface) ? (void*) vv : (void*) vvv, das->S[e]);
enkf_printf((success) ? "a" : "s");
fflush(stdout);
}
}
if (das->mode == MODE_ENOI) {
if (enkf_obstype == OBSTYPE_VALUE) {
int success = model_getbgfname_async(m, das->bgdir, ot->varname, ot->name, t, fname);
H(das, nobs, obsids, fname, -1, t, ot->varname, ot->varname2, (ot->issurface) ? (void*) vv : (void*) vvv, Hx);
enkf_printf((success) ? "A" : "S");
fflush(stdout);
} else if (enkf_obstype == OBSTYPE_INNOVATION) {
Hx[0] = 0;
enkf_printf("-");
fflush(stdout);
}
}
free(obsids);
}
} else {
obs_find_bytype(obs, i, &nobs, &obsids);
if (nobs == 0)
goto next;
if (das->mode == MODE_ENKF || !enkf_fstatsonly) {
for (e = my_first_iteration; e <= my_last_iteration; ++e) {
model_getmemberfname(m, das->ensdir, ot->varname, e + 1, fname);
H(das, nobs, obsids, fname, e + 1, MAXINT, ot->varname, ot->varname2, (ot->issurface) ? (void*) vv : (void*) vvv, das->S[e]);
enkf_printf(".");
fflush(stdout);
}
}
if (das->mode == MODE_ENOI) {
if (enkf_obstype == OBSTYPE_VALUE) {
model_getbgfname(m, das->bgdir, ot->varname, fname);
H(das, nobs, obsids, fname, -1, MAXINT, ot->varname, ot->varname2, (ot->issurface) ? (void*) vv : (void*) vvv, Hx);
enkf_printf("+");
fflush(stdout);
} else if (enkf_obstype == OBSTYPE_INNOVATION) {
Hx[0] = 0;
enkf_printf("-");
fflush(stdout);
}
}
free(obsids);
}
next:
if (ot->issurface)
free2d(vv);
else
free3d(vvv);
enkf_printf("\n");
} /* for i (over obstypes) */
#if defined(MPI)
if (das->mode == MODE_ENKF || !enkf_fstatsonly) {
#if !defined(HE_VIAFILE)
/*
* communicate HE via MPI
*/
int ierror, count;
/*
* Blocking communications can create a bottleneck in instances with
* large number of observations (e.g., 2e6 obs., 144 members, 48
* processes), but asynchronous send/receive seem to work well
*/
if (rank > 0) {
MPI_Request request;
/*
* send ensemble observations to master
*/
count = (my_last_iteration - my_first_iteration + 1) * obs->nobs;
ierror = MPI_Isend(das->S[my_first_iteration], count, MPIENSOBSTYPE, 0, rank, MPI_COMM_WORLD, &request);
assert(ierror == MPI_SUCCESS);
} else {
int r;
MPI_Request* requests = malloc((nprocesses - 1) * sizeof(MPI_Request));
/*
* collect ensemble observations from slaves
*/
for (r = 1; r < nprocesses; ++r) {
count = (last_iteration[r] - first_iteration[r] + 1) * obs->nobs;
ierror = MPI_Irecv(das->S[first_iteration[r]], count, MPIENSOBSTYPE, r, r, MPI_COMM_WORLD, &requests[r - 1]);
assert(ierror == MPI_SUCCESS);
}
ierror = MPI_Waitall(nprocesses - 1, requests, MPI_STATUS_IGNORE);
assert(ierror == MPI_SUCCESS);
free(requests);
}
/*
* now send the full set of ensemble observations to slaves
*/
count = das->nmem * obs->nobs;
ierror = MPI_Bcast(das->S[0], count, MPIENSOBSTYPE, 0, MPI_COMM_WORLD);
assert(ierror == MPI_SUCCESS);
#else
/*
* communicate HE via file
*/
{
int ncid;
int varid;
size_t start[2], count[2];
if (rank == 0) {
int dimids[2];
ncw_create(FNAME_HE, NC_CLOBBER | NC_64BIT_OFFSET, &ncid);
ncw_def_dim(FNAME_HE, ncid, "m", das->nmem, &dimids[0]);
ncw_def_dim(FNAME_HE, ncid, "p", obs->nobs, &dimids[1]);
ncw_def_var(FNAME_HE, ncid, "HE", NC_FLOAT, 2, dimids, &varid);
ncw_close(FNAME_HE, ncid);
}
MPI_Barrier(MPI_COMM_WORLD);
ncw_open(FNAME_HE, NC_WRITE, &ncid);
ncw_inq_varid(FNAME_HE, ncid, "HE", &varid);
start[0] = my_first_iteration;
start[1] = 0;
count[0] = my_last_iteration - my_first_iteration + 1;
count[1] = obs->nobs;
ncw_put_vara_float(FNAME_HE, ncid, varid, start, count, das->S[my_first_iteration]);
ncw_close(FNAME_HE, ncid);
MPI_Barrier(MPI_COMM_WORLD);
ncw_open(FNAME_HE, NC_NOWRITE, &ncid);
ncw_inq_varid(FNAME_HE, ncid, "HE", &varid);
ncw_get_var_float(FNAME_HE, ncid, varid, das->S[0]);
ncw_close(FNAME_HE, ncid);
}
#endif
}
#endif
if (das->mode == MODE_ENOI) {
/*
* subtract ensemble mean; add background
*/
if (!enkf_fstatsonly) {
double* ensmean = calloc(obs->nobs, sizeof(double));
for (e = 0; e < das->nmem; ++e) {
ENSOBSTYPE* Se = das->S[e];
for (i = 0; i < obs->nobs; ++i)
ensmean[i] += Se[i];
}
for (i = 0; i < obs->nobs; ++i)
ensmean[i] /= (double) das->nmem;
for (e = 0; e < das->nmem; ++e) {
ENSOBSTYPE* Se = das->S[e];
for (i = 0; i < obs->nobs; ++i)
Se[i] += Hx[i] - ensmean[i];
}
free(ensmean);
} else {
for (e = 0; e < das->nmem; ++e) {
ENSOBSTYPE* Se = das->S[e];
for (i = 0; i < obs->nobs; ++i)
Se[i] = Hx[i];
}
}
}
if (das->mode == MODE_ENOI)
free(Hx);
}
void reader_xy_gridded_hfradar(char* fname, int fid, obsmeta* meta, grid* g, observations* obs)
{
int ksurf = grid_getsurflayerid(g);
int isperiodic_i = grid_isperiodic_i(g);
int** numlevels = grid_getnumlevels(g);
float** grid_angle = grid_getangle(g);
int grid_ni = 0, grid_nj = 0;
char* varname = NULL;
char* u_varname = NULL;
char* v_varname = NULL;
char* u_stdvarname = NULL;
char* v_stdvarname = NULL;
char* lonname = NULL;
char* latname = NULL;
char* gdopname = NULL;
char* npointsname_1 = NULL;
char* npointsname_2 = NULL;
char* stdname = NULL;
char* estdname = NULL;
char* timename = NULL;
char* qcflagname = NULL;
char* u_qcflagname = NULL;
char* v_qcflagname = NULL;
char* rotation_flag = NULL;
int ncid;
int ndim_var, ndim_xy;
size_t dimlen_var[3], dimlen_xy[2];
uint32_t qcflagvals = 0;
float varshift = 0.0;
float u_varshift = 0.0;
float v_varshift = 0.0;
double mindepth = 0.0;
char instrument[MAXSTRLEN];
int iscurv = -1;
int need_rotation = -1;
size_t ni = 0, nj = 0, n = 0, n_var = 0;
int varid_lon = -1, varid_lat = -1;
double* lon = NULL;
double* lat = NULL;
int varid_gdop = -1, varid_npoints_1 = -1, varid_npoints_2 = -1;
int varid_var = -1, varid_std = -1, varid_estd = -1, varid_qcflag = -1, varid_time = -1;
int varid_u = -1, varid_v =-1, varid_u_std = -1, varid_v_std = -1, varid_u_qcflag = -1, varid_v_qcflag = -1;
float* var = NULL;
float* u_var = NULL;
float* v_var = NULL;
float* u_std = NULL;
float* v_std = NULL;
float var_fill_value = NAN;
float var_add_offset = NAN, var_scale_factor = NAN;
float u_var_fill_value = NAN;
float u_var_add_offset = NAN, u_var_scale_factor = NAN;
float v_var_fill_value = NAN;
float v_var_add_offset = NAN, v_var_scale_factor = NAN;
float u_std_fill_value = NAN;
float u_std_add_offset = NAN, u_std_scale_factor = NAN;
float v_std_fill_value = NAN;
float v_std_add_offset = NAN, v_std_scale_factor = NAN;
double var_estd = NAN;
float* gdop = NULL;
short* npoints_1 = NULL;
short* npoints_2 = NULL;
float* std = NULL;
float std_add_offset = NAN, std_scale_factor = NAN;
float std_fill_value = NAN;
float* estd = NULL;
float estd_add_offset = NAN, estd_scale_factor = NAN;
float estd_fill_value = NAN;
int32_t* qcflag = NULL;
int32_t* u_qcflag = NULL;
int32_t* v_qcflag = NULL;
int have_time = 1;
int singletime = -1;
float* time = NULL;
float time_add_offset = NAN, time_scale_factor = NAN;
float time_fill_value = NAN;
char tunits[MAXSTRLEN];
double tunits_multiple = NAN, tunits_offset = NAN;
int i, nobs_read;
strcpy(instrument, meta->product);
for (i = 0; i < meta->npars; ++i) {
if (strcasecmp(meta->pars[i].name, "VARNAME") == 0)
varname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "ROTATION") == 0)
rotation_flag = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "U_VARNAME") == 0)
u_varname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "V_VARNAME") == 0)
v_varname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "U_STD") == 0)
u_stdvarname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "V_STD") == 0)
v_stdvarname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "TIMENAME") == 0)
timename = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "GDOPNAME") == 0)
gdopname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "NPOINTSNAME_1") == 0)
npointsname_1 = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "NPOINTSNAME_2") == 0)
npointsname_2 = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "LONNAME") == 0)
lonname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "LATNAME") == 0)
latname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "STDNAME") == 0)
stdname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "ESTDNAME") == 0)
estdname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "QCFLAGNAME") == 0)
qcflagname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "U_QCFLAGNAME") == 0)
u_qcflagname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "V_QCFLAGNAME") == 0)
v_qcflagname = meta->pars[i].value;
else if (strcasecmp(meta->pars[i].name, "QCFLAGVALS") == 0) {
char* pline = meta->pars[i].value;
int linelen = sizeof(pline);
char lineval[linelen];
char* line = strcpy(lineval,pline);
char seps[] = " ,";
char* token;
int val;
qcflagvals = 0;
while ((token = strtok(line, seps)) != NULL) {
if (!str2int(token, &val))
enkf_quit("%s: could not convert QCFLAGVALS entry \"%s\" to integer", meta->prmfname, token);
if (val < 0 || val > 31)
enkf_quit("%s: QCFLAGVALS entry = %d (supposed to be in [0,31] interval", meta->prmfname, val);
qcflagvals |= 1 << val;
line = NULL;
}
if (qcflagvals == 0)
enkf_quit("%s: no valid flag entries found after QCFLAGVALS\n", meta->prmfname);
} else if (strcasecmp(meta->pars[i].name, "VARSHIFT") == 0) {
if (!str2float(meta->pars[i].value, &varshift))
enkf_quit("%s: can not convert VARSHIFT = \"%s\" to float\n", meta->prmfname, meta->pars[i].value);
enkf_printf(" VARSHIFT = %s\n", meta->pars[i].value);
} else if (strcasecmp(meta->pars[i].name, "U_VARSHIFT") == 0) {
if (!str2float(meta->pars[i].value, &u_varshift))
enkf_quit("%s: can not convert U_VARSHIFT = \"%s\" to float\n", meta->prmfname, meta->pars[i].value);
enkf_printf(" U_VARSHIFT = %s\n", meta->pars[i].value);
} else if (strcasecmp(meta->pars[i].name, "V_VARSHIFT") == 0) {
if (!str2float(meta->pars[i].value, &v_varshift))
enkf_quit("%s: can not convert V_VARSHIFT = \"%s\" to float\n", meta->prmfname, meta->pars[i].value);
enkf_printf(" V_VARSHIFT = %s\n", meta->pars[i].value);
} else if (strcasecmp(meta->pars[i].name, "MINDEPTH") == 0) {
if (!str2double(meta->pars[i].value, &mindepth))
enkf_quit("%s: can not convert MINDEPTH = \"%s\" to double\n", meta->prmfname, meta->pars[i].value);
enkf_printf(" MINDEPTH = %f\n", mindepth);
} else if (strcasecmp(meta->pars[i].name, "INSTRUMENT") == 0) {
strncpy(instrument, meta->pars[i].value, MAXSTRLEN);
} else
enkf_quit("unknown PARAMETER \"%s\"\n", meta->pars[i].name);
}
if (varname == NULL)
enkf_quit("reader_xy_gridded(): %s variable name not specified", fname);
if (rotation_flag != NULL) {
int bool_rotation_flag, valid_rotation_flag;
bool_rotation_flag = atoi(rotation_flag);
valid_rotation_flag = (bool_rotation_flag == 0 || bool_rotation_flag == 1);
if (valid_rotation_flag) {
need_rotation = bool_rotation_flag == 1;
grid_getdims(g, &grid_ni, &grid_nj, NULL);
if (need_rotation == 1 && grid_angle == NULL)
enkf_quit("reader_xy_gridded_hfradar(): %s cannot rotate vectors without ANGLE parameter defined within grid prm file",fname);
enkf_printf("\t#Rotation of vectors enabled\n");
}
else
enkf_quit("reader_xy_gridded_hfradar(): %s invalid ROTATION parameter. Need to be a boolean digit");
}
ncw_open(fname, NC_NOWRITE, &ncid);
ncw_inq_varid(ncid, varname, &varid_var);
ncw_inq_vardims(ncid, varid_var, 3, &ndim_var, dimlen_var);
if (ndim_var == 3) {
int dimid[3];
size_t nr;
ncw_inq_vardimid(ncid, varid_var, dimid);
ncw_inq_dimlen(ncid, dimid[0], &nr);
if (nr != 1)
enkf_quit("reader_xy_gridded(): %d records (currently only one is allowed)", nr);
n_var = dimlen_var[1] * dimlen_var[2];
} else if (ndim_var == 2) {
if (nc_hasunlimdim(ncid))
enkf_quit("reader_xy_gridded(): %s: %s: not enough spatial dimensions (must be 2)", fname, varname);
n_var = dimlen_var[0] * dimlen_var[1];
} else if (ndim_var != 2)
enkf_quit("reader_xy_gridded(): %s: # dimensions = %d (must be 2 or 3 with only one record)", fname, ndim_var);
if (lonname != NULL)
ncw_inq_varid(ncid, lonname, &varid_lon);
else if (ncw_var_exists(ncid, "lon"))
ncw_inq_varid(ncid, "lon", &varid_lon);
else if (ncw_var_exists(ncid, "longitude"))
ncw_inq_varid(ncid, "longitude", &varid_lon);
else if (ncw_var_exists(ncid, "LONGITUDE"))
ncw_inq_varid(ncid, "LONGITUDE", &varid_lon);
else
enkf_quit("reader_xy_gridded(): %s: could not find longitude variable", fname);
ncw_inq_vardims(ncid, varid_lon, 2, &ndim_xy, dimlen_xy);
if (ndim_xy == 1) {
iscurv = 0;
ni = dimlen_xy[0];
} else if (ndim_xy == 2) {
iscurv = 1;
ni = dimlen_xy[1];
nj = dimlen_xy[0];
} else
enkf_quit("reader_xy_gridded(): %s: coordinate variable \"%s\" has neither 1 or 2 dimensions", fname, lonname);
if (latname != NULL)
ncw_inq_varid(ncid, latname, &varid_lat);
else if (ncw_var_exists(ncid, "lat"))
ncw_inq_varid(ncid, "lat", &varid_lat);
else if (ncw_var_exists(ncid, "latitude"))
ncw_inq_varid(ncid, "latitude", &varid_lat);
else if (ncw_var_exists(ncid, "LATITUDE"))
ncw_inq_varid(ncid, "LATITUDE", &varid_lat);
else
enkf_quit("reader_xy_gridded(): %s: could not find latitude variable", fname);
if (iscurv == 0) {
ncw_check_varndims(ncid, varid_lat, 1);
ncw_inq_vardims(ncid, varid_lat, 1, NULL, &nj);
} else
ncw_check_vardims(ncid, varid_lat, 2, dimlen_xy);
enkf_printf(" (ni, nj) = (%u, %u)\n", ni, nj);
n = ni * nj;
if (n != n_var)
enkf_quit("reader_xy_gridded(): %s: dimensions of variable \"%s\" do not match coordinate dimensions", fname, varname);
if (dimlen_var[ndim_var - 1] != ni)
enkf_quit("reader_xy_gridded(): %s: %s: longitude must be the inner coordinate", fname, varname);
if (iscurv == 0) {
lon = malloc(ni * sizeof(double));
lat = malloc(nj * sizeof(double));
} else {
lon = malloc(n * sizeof(double));
lat = malloc(n * sizeof(double));
}
ncw_get_var_double(ncid, varid_lon, lon);
ncw_get_var_double(ncid, varid_lat, lat);
var = malloc(n * sizeof(float));
ncw_get_var_float(ncid, varid_var, var);
if (ncw_att_exists(ncid, varid_var, "add_offset")) {
ncw_get_att_float(ncid, varid_var, "add_offset", &var_add_offset);
ncw_get_att_float(ncid, varid_var, "scale_factor", &var_scale_factor);
}
if (ncw_att_exists(ncid, varid_var, "_FillValue"))
ncw_get_att_float(ncid, varid_var, "_FillValue", &var_fill_value);
if (gdopname != NULL)
ncw_inq_varid(ncid, gdopname, &varid_gdop);
else if (ncw_var_exists(ncid, "GDOP"))
ncw_inq_varid(ncid, "GDOP", &varid_gdop);
if (varid_gdop >= 0) {
gdop = malloc(n * sizeof(float));
ncw_get_var_float(ncid, varid_gdop, gdop);
float gdop_fill_value, gdop_add_offset, gdop_scale_factor;
if (ncw_att_exists(ncid, varid_gdop, "_FillValue"))
ncw_get_att_float(ncid, varid_gdop, "_FillValue", &gdop_fill_value);
if (ncw_att_exists(ncid, varid_gdop, "add_offset")) {
ncw_get_att_float(ncid, varid_gdop, "add_offset", &gdop_add_offset);
ncw_get_att_float(ncid, varid_gdop, "scale_factor", &gdop_scale_factor);
}
}
if (npointsname_1 != NULL)
ncw_inq_varid(ncid, npointsname_1, &varid_npoints_1);
else if (ncw_var_exists(ncid, "NOBS1"))
ncw_inq_varid(ncid, "NOBS1", &varid_npoints_1);
if (varid_npoints_1 >= 0) {
npoints_1 = malloc(n * sizeof(short));
ncw_get_var_short(ncid, varid_npoints_1, npoints_1);
}
if (npointsname_2 != NULL)
ncw_inq_varid(ncid, npointsname_2, &varid_npoints_2);
else if (ncw_var_exists(ncid, "NOBS2"))
ncw_inq_varid(ncid, "NOBS2", &varid_npoints_2);
if (varid_npoints_2 >= 0) {
npoints_2 = malloc(n * sizeof(short));
ncw_get_var_short(ncid, varid_npoints_2, npoints_2);
}
if (need_rotation == 1) {
if (u_varname != NULL )
ncw_inq_varid(ncid, u_varname, &varid_u);
else if (ncw_var_exists(ncid, "UCUR")) {
ncw_inq_varid(ncid, "UCUR", &varid_u);
u_varname = "UCUR";
}
if (varid_u >= 0) {
u_var = malloc(n * sizeof(float));
ncw_get_var_float(ncid,varid_u,u_var);
if (ncw_att_exists(ncid,varid_u, "_FillValue"))
ncw_get_att_float(ncid, varid_u, "_FillValue", &u_var_fill_value);
if (ncw_att_exists(ncid,varid_u,"add_offset")) {
ncw_get_att_float(ncid, varid_u, "add_offset", &u_var_add_offset);
ncw_get_att_float(ncid, varid_u, "scale_factor", &u_var_scale_factor);
}
}
else
enkf_quit("reader_xy_gridded(): %s: Variable %s not found.",fname, u_varname);
if (v_varname != NULL)
ncw_inq_varid(ncid, v_varname, &varid_v);
else if (ncw_var_exists(ncid, "VCUR")) {
ncw_inq_varid(ncid, "VCUR", &varid_v);
v_varname = "VCUR";
}
if (varid_v >= 0) {
v_var = malloc(n * sizeof(float));
ncw_get_var_float(ncid,varid_v,v_var);
if (ncw_att_exists(ncid,varid_v, "_FillValue"))
ncw_get_att_float(ncid,varid_v, "_FillValue", &v_var_fill_value);
if (ncw_att_exists(ncid,varid_v,"add_offset")) {
ncw_get_att_float(ncid, varid_v, "add_offset", &v_var_add_offset);
ncw_get_att_float(ncid, varid_v, "scale_factor", &v_var_scale_factor);
}
}
else
enkf_quit("reader_xy_gridded(): %s: Variable %s not found.",fname, v_varname);
}
if (stdname != NULL)
ncw_inq_varid(ncid, stdname, &varid_std);
else if (ncw_var_exists(ncid, "std"))
ncw_inq_varid(ncid, "std", &varid_std);
if (varid_std >= 0) {
std = malloc(n * sizeof(float));
ncw_get_var_float(ncid, varid_std, std);
if (ncw_att_exists(ncid, varid_std, "_FillValue"))
ncw_get_att_float(ncid, varid_std, "_FillValue", &std_fill_value);
if (ncw_att_exists(ncid, varid_std, "add_offset")) {
ncw_get_att_float(ncid, varid_std, "add_offset", &std_add_offset);
ncw_get_att_float(ncid, varid_std, "scale_factor", &std_scale_factor);
}
}
if (estdname != NULL)
ncw_inq_varid(ncid, estdname, &varid_estd);
else if (ncw_var_exists(ncid, "error_std"))
ncw_inq_varid(ncid, "error_std", &varid_estd);
if (varid_estd >= 0) {
estd = malloc(n * sizeof(float));
ncw_get_var_float(ncid, varid_estd, estd);
if (ncw_att_exists(ncid, varid_estd, "_FillValue"))
ncw_get_att_float(ncid, varid_estd, "_FillValue", &estd_fill_value);
if (ncw_att_exists(ncid, varid_estd, "add_offset")) {
ncw_get_att_float(ncid, varid_estd, "add_offset", &estd_add_offset);
ncw_get_att_float(ncid, varid_estd, "scale_factor", &estd_scale_factor);
}
}
if (std == NULL && estd == NULL)
if (ncw_att_exists(ncid, varid_var, "error_std")) {
ncw_check_attlen(ncid, varid_var, "error_std", 1);
ncw_get_att_double(ncid, varid_var, "error_std", &var_estd);
}
if (u_stdvarname != NULL)
ncw_inq_varid(ncid, u_stdvarname, &varid_u_std);
else if (ncw_var_exists(ncid, "UCUR_sd"))
ncw_inq_varid(ncid, "UCUR_sd", &varid_u_std);
if (varid_u_std >= 0) {
u_std = malloc(n * sizeof(float));
ncw_get_var_float(ncid, varid_u_std, u_std);
if (ncw_att_exists(ncid, varid_u_std, "_FillValue"))
ncw_get_att_float(ncid, varid_u_std, "_FillValue", &u_std_fill_value);
if (ncw_att_exists(ncid, varid_u_std, "add_offset")) {
ncw_get_att_float(ncid, varid_u_std, "add_offset", &u_std_add_offset);
ncw_get_att_float(ncid, varid_u_std, "scale_factor", &u_std_scale_factor);
}
}
if (v_stdvarname != NULL)
ncw_inq_varid(ncid, v_stdvarname, &varid_v_std);
else if (ncw_var_exists(ncid, "vcur_sd"))
ncw_inq_varid(ncid, "vcur_sd", &varid_v_std);
if (varid_v_std >= 0) {
v_std = malloc(n * sizeof(float));
ncw_get_var_float(ncid, varid_v_std, v_std);
if (ncw_att_exists(ncid, varid_v_std, "_FillValue"))
ncw_get_att_float(ncid, varid_v_std, "_FillValue", &v_std_fill_value);
if (ncw_att_exists(ncid, varid_v_std, "add_offset")) {
ncw_get_att_float(ncid, varid_v_std, "add_offset", &v_std_add_offset);
ncw_get_att_float(ncid, varid_v_std, "scale_factor", &v_std_scale_factor);
}
}
if (qcflagname != NULL) {
ncw_inq_varid(ncid, qcflagname, &varid_qcflag);
qcflag = malloc(n * sizeof(int32_t));
ncw_get_var_int(ncid, varid_qcflag, qcflag);
}
if (u_qcflagname != NULL)
ncw_inq_varid(ncid, u_qcflagname, &varid_u_qcflag);
else if (ncw_var_exists(ncid, "UCUR_quality_control"))
ncw_inq_varid(ncid, "UCUR_quality_control", &varid_u_qcflag);
if (varid_u_qcflag >= 0) {
u_qcflag = malloc(n * sizeof(int32_t));
ncw_get_var_int(ncid, varid_u_qcflag, u_qcflag);
}
if (v_qcflagname != NULL)
ncw_inq_varid(ncid, v_qcflagname, &varid_v_qcflag);
else if (ncw_var_exists(ncid, "VCUR_quality_control"))
ncw_inq_varid(ncid, "VCUR_quality_control", &varid_v_qcflag);
if (varid_v_qcflag >= 0) {
v_qcflag = malloc(n * sizeof(int32_t));
ncw_get_var_int(ncid, varid_v_qcflag, v_qcflag);
}
if (timename != NULL)
ncw_inq_varid(ncid, timename, &varid_time);
else if (ncw_var_exists(ncid, "time"))
ncw_inq_varid(ncid, "time", &varid_time);
else if (ncw_var_exists(ncid, "TIME"))
ncw_inq_varid(ncid, "TIME", &varid_time);
else {
enkf_printf(" reader_xy_gridded(): %s: no TIME variable\n", fname);
have_time = 0;
}
if (have_time) {
int timendims;
int timedimids[NC_MAX_DIMS];
size_t timelen = 1;
ncw_inq_varndims(ncid, varid_time, &timendims);
ncw_inq_vardimid(ncid, varid_time, timedimids);
for (i = 0; i < timendims; ++i) {
size_t dimlen;
ncw_inq_dimlen(ncid, timedimids[i], &dimlen);
timelen *= dimlen;
}
if (timelen == 1) {
singletime = 1;
time = malloc(sizeof(float));
} else {
singletime = 0;
assert(timelen == n);
time = malloc(n * sizeof(float));
}
ncw_get_var_float(ncid, varid_time, time);
if (ncw_att_exists(ncid, varid_time, "_FillValue"))
ncw_get_att_float(ncid, varid_time, "_FillValue", &time_fill_value);
if (ncw_att_exists(ncid, varid_time, "add_offset")) {
ncw_get_att_float(ncid, varid_time, "add_offset", &time_add_offset);
ncw_get_att_float(ncid, varid_time, "scale_factor", &time_scale_factor);
}
ncw_get_att_text(ncid, varid_time, "units", tunits);
tunits_convert(tunits, &tunits_multiple, &tunits_offset);
}
ncw_close(ncid);
nobs_read = 0;
for (i = 0; i < (int) n; ++i) {
observation* o;
obstype* ot;
int invalid_gdop, invalid_npoints1, invalid_npoints2, invalid_var, invalid_std, invalid_estd, invalid_u_var, invalid_v_var, invalid_time;
invalid_gdop = (gdop != NULL && (gdop[i] > 180.0 || gdop[i] < 0.0));
invalid_npoints1 = (npoints_1 != NULL && (npoints_1[i] == 0 || npoints_1[i]< 0));
invalid_npoints2 = (npoints_2 != NULL && (npoints_2[i] == 0 || npoints_2[i] < 0));
invalid_var = var[i] == var_fill_value || isnan(var[i]);
invalid_std = (std != NULL && (std[i] == std_fill_value || isnan(std[i])));
invalid_estd = (estd != NULL && (estd[i] == estd_fill_value || isnan(estd[i])));
invalid_u_var = (u_var != NULL && (u_var[i] == u_var_fill_value || isnan(u_var[i])));
invalid_v_var = (v_var != NULL && (v_var[i] == v_var_fill_value || isnan(v_var[i])));
invalid_time = (have_time && !singletime && (time[i] == time_fill_value || isnan(time[i])));
if (invalid_gdop || invalid_npoints1 || invalid_npoints2 || invalid_var || invalid_std || invalid_estd || invalid_u_var || invalid_v_var || invalid_time)
continue;
if (qcflag != NULL) {
/* general qcflags has precedence in discarding obs*/
if ( (qcflagvals != (qcflagvals | 1<<qcflag[i])) || (u_qcflag != NULL && (qcflagvals != (qcflagvals | 1<<u_qcflag[i]))) || (v_qcflag != NULL && (qcflagvals != (qcflagvals | 1<<v_qcflag[i]))) )
continue;
}
/* [u,v]_qcflags has precedence in values. */
if (u_qcflagname != NULL && v_qcflagname != NULL) {
if ( (u_qcflag != NULL && (qcflagvals != (qcflagvals | 1<<u_qcflag[i]))) || (v_qcflag != NULL && (qcflagvals != (qcflagvals | 1<<v_qcflag[i]))) )
continue;
} else if (u_qcflagname != NULL) {
if (u_qcflag != NULL && (qcflagvals != (qcflagvals | 1<<u_qcflag[i])))
continue;
} else if (v_qcflagname != NULL) {
if (v_qcflag != NULL && (qcflagvals != (qcflagvals | 1<<v_qcflag[i])))
continue;
}
nobs_read++;
obs_checkalloc(obs);
o = &obs->data[obs->nobs];
o->product = st_findindexbystring(obs->products, meta->product);
assert(o->product >= 0);
o->type = obstype_getid(obs->nobstypes, obs->obstypes, meta->type, 1);
ot = &obs->obstypes[o->type];
o->instrument = st_add_ifabsent(obs->instruments, instrument, -1);
o->id = obs->nobs;
o->fid = fid;
o->batch = 0;
/* Shifted the reading order for HF-Radar to obtain indexes */
if (iscurv == 0) {
o->lon = lon[i % ni];
o->lat = lat[i / ni];
} else {
o->lon = lon[i];
o->lat = lat[i];
}
o->depth = 0.0;
o->fk = (double) ksurf;
o->model_depth = NAN; /* set in obs_add() */
o->status = grid_xy2fij(g, o->lon, o->lat, &o->fi, &o->fj);
if (!obs->allobs && o->status == STATUS_OUTSIDEGRID)
continue;
if ((o->status == STATUS_OK) && (o->lon <= ot->xmin || o->lon >= ot->xmax || o->lat <= ot->ymin || o->lat >= ot->ymax))
o->status = STATUS_OUTSIDEOBSDOMAIN;
if (need_rotation == 1) {
double zonal, meridional, oangle;
if (!isnan(u_var_add_offset))
zonal = u_var[i] * u_var_scale_factor + u_var_add_offset + varshift + u_varshift;
else
zonal = u_var[i];
if (!isnan(v_var_add_offset))
meridional = v_var[i] * v_var_scale_factor + v_var_add_offset + varshift + u_varshift;
else
meridional = v_var[i];
oangle = interpolate2d(o->fi, o-> fj, grid_ni, grid_nj, grid_angle, numlevels, isperiodic_i);
if (strcmp(varname,u_varname) == 0)
o->value = zonal*cos(oangle) - meridional*sin(oangle);
if (strcmp(varname,v_varname) == 0)
o->value = zonal*sin(oangle) + meridional*cos(oangle);
}
else {
if (!isnan(var_add_offset))
o->value = (double) (var[i] * var_scale_factor + var_add_offset + varshift);
else
o->value = (double) (var[i] + varshift);
}
if (estd == NULL && std == NULL){
if (!isnan(var_estd))
o->std = var_estd;
}
else {
if (std == NULL)
o->std = 0.0;
else {
if (!isnan(std_add_offset))
o->std = (double) (std[i] * std_scale_factor + std_add_offset);
else
o->std = (double) std[i];
}
if (estd != NULL) {
if (!isnan(estd_add_offset)) {
double std2 = (double) (estd[i] * estd_scale_factor + estd_add_offset);
o->std = (o->std > std2) ? o->std : std2;
} else
o->std = (o->std > estd[i]) ? o->std : estd[i];
}
}
if (have_time) {
float t = (singletime) ? time[0] : time[i];
if (!isnan(time_add_offset))
o->date = (double) (t * time_scale_factor + time_add_offset) * tunits_multiple + tunits_offset;
else
o->date = (double) t* tunits_multiple + tunits_offset;
} else
o->date = NAN;
o->aux = -1;
obs->nobs++;
}
enkf_printf(" nobs = %d\n", nobs_read);
free(lon);
free(lat);
free(var);
if (gdop != NULL)
free(gdop);
if (npoints_1 != NULL)
free(npoints_1);
if (npoints_2 != NULL)
free(npoints_2);
if (u_var != NULL)
free(u_var);
if (v_var != NULL)
free(v_var);
if (std != NULL)
free(std);
if (estd != NULL)
free(estd);
if (u_std != NULL)
free(u_std);
if (v_std != NULL)
free(v_std);
if (qcflag != NULL)
free(qcflag);
if (u_qcflag != NULL)
free(u_qcflag);
if (v_qcflag != NULL)
free(v_qcflag);
if (time != NULL)
free(time);
}
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;
}
void das_getHE(dasystem* das)
{
observations* obs = das->obs;
model* m = das->m;
ENSOBSTYPE* Hx = NULL;
int i, e;
das->s_mode = S_MODE_HE_f;
if (obs->nobs == 0)
return;
if (das->nmem <= 0)
das_setnmem(das);
enkf_printf(" ensemble size = %d\n", das->nmem);
assert(das->nmem > 0);
distribute_iterations(0, das->nmem - 1, nprocesses, rank, " ");
/*
* ensemble observation array to be filled
*/
assert(das->S == NULL);
das->S = alloc2d(das->nmem, obs->nobs, sizeof(ENSOBSTYPE));
if (das->mode == MODE_ENOI)
Hx = calloc(obs->nobs, sizeof(ENSOBSTYPE));
for (i = 0; i < obs->nobstypes; ++i) {
obstype* ot = &obs->obstypes[i];
float*** vvv = NULL;
float** vv = NULL;
H_fn H = NULL;
int mvid;
int ni, nj, nk;
int nobs;
int* obsids;
char fname[MAXSTRLEN];
enkf_printf(" %s ", ot->name);
fflush(stdout);
mvid = model_getvarid(m, obs->obstypes[i].varnames[0], 1);
if (ot->issurface) {
model_getvardims(m, mvid, &ni, &nj, NULL);
vv = alloc2d(nj, ni, sizeof(float));
} else {
model_getvardims(m, mvid, &ni, &nj, &nk);
vvv = alloc3d(nk, nj, ni, sizeof(float));
}
/*
* set H
*/
H = getH(ot->name, ot->hfunction);
if (ot->isasync) {
int t1 = get_tshift(ot->date_min, ot->async_tstep);
int t2 = get_tshift(ot->date_max, ot->async_tstep);
int t;
for (t = t1; t <= t2; ++t) {
enkf_printf("|");
obs_find_bytypeandtime(obs, i, t, &nobs, &obsids);
if (nobs == 0)
continue;
/*
* for EnOI it is essential sometimes (e.g. in some bias
* correction cases) that the background is interpolated first
*/
if (das->mode == MODE_ENOI) {
if (enkf_obstype == OBSTYPE_VALUE) {
int success = model_getbgfname_async(m, das->bgdir, ot->varnames[0], ot->name, t, fname);
H(das, nobs, obsids, fname, -1, t, (ot->issurface) ? (void*) vv : (void*) vvv, Hx);
enkf_printf((success) ? "A" : "S");
fflush(stdout);
} else if (enkf_obstype == OBSTYPE_INNOVATION) {
Hx[0] = 0;
enkf_printf("-");
fflush(stdout);
}
}
if (das->mode == MODE_ENKF || !enkf_fstatsonly) {
for (e = my_first_iteration; e <= my_last_iteration; ++e) {
int success = model_getmemberfname_async(m, das->ensdir, ot->varnames[0], ot->name, e + 1, t, fname);
H(das, nobs, obsids, fname, e + 1, t, (ot->issurface) ? (void*) vv : (void*) vvv, das->S[e]);
enkf_printf((success) ? "a" : "s");
fflush(stdout);
}
}
free(obsids);
}
} else {
obs_find_bytype(obs, i, &nobs, &obsids);
if (nobs == 0)
goto next;
/*
* for EnOI it is essential sometimes (e.g. in some bias correction
* cases) that the background is interpolated first
*/
if (das->mode == MODE_ENOI) {
if (enkf_obstype == OBSTYPE_VALUE) {
model_getbgfname(m, das->bgdir, ot->varnames[0], fname);
H(das, nobs, obsids, fname, -1, INT_MAX, (ot->issurface) ? (void*) vv : (void*) vvv, Hx);
enkf_printf("+");
fflush(stdout);
} else if (enkf_obstype == OBSTYPE_INNOVATION) {
Hx[0] = 0;
enkf_printf("-");
fflush(stdout);
}
}
if (das->mode == MODE_ENKF || !enkf_fstatsonly) {
for (e = my_first_iteration; e <= my_last_iteration; ++e) {
model_getmemberfname(m, das->ensdir, ot->varnames[0], e + 1, fname);
H(das, nobs, obsids, fname, e + 1, INT_MAX, (ot->issurface) ? (void*) vv : (void*) vvv, das->S[e]);
enkf_printf(".");
fflush(stdout);
}
}
free(obsids);
}
next:
if (ot->issurface)
free(vv);
else
free(vvv);
enkf_printf("\n");
} /* for i (over obstypes) */
#if defined(MPI)
if (das->mode == MODE_ENKF || !enkf_fstatsonly) {
#if !defined(HE_VIAFILE)
/*
* communicate HE via MPI
*/
int ierror, sendcount, *recvcounts, *displs;
recvcounts = malloc(nprocesses * sizeof(int));
displs = malloc(nprocesses * sizeof(int));
sendcount = my_number_of_iterations * obs->nobs;
for (i = 0; i < nprocesses; ++i) {
recvcounts[i] = number_of_iterations[i] * obs->nobs;
displs[i] = first_iteration[i] * obs->nobs;
}
ierror = MPI_Allgatherv(das->S[my_first_iteration], sendcount, MPIENSOBSTYPE, das->S[0], recvcounts, displs, MPIENSOBSTYPE, MPI_COMM_WORLD);
assert(ierror == MPI_SUCCESS);
free(recvcounts);
free(displs);
#else
/*
* communicate HE via file
*/
{
int ncid;
int varid;
size_t start[2], count[2];
if (rank == 0) {
int dimids[2];
ncw_create(FNAME_HE, NC_CLOBBER | NETCDF_FORMAT, &ncid);
ncw_def_dim(FNAME_HE, ncid, "m", das->nmem, &dimids[0]);
ncw_def_dim(FNAME_HE, ncid, "p", obs->nobs, &dimids[1]);
ncw_def_var(FNAME_HE, ncid, "HE", NC_FLOAT, 2, dimids, &varid);
ncw_close(FNAME_HE, ncid);
}
MPI_Barrier(MPI_COMM_WORLD);
ncw_open(FNAME_HE, NC_WRITE, &ncid);
ncw_inq_varid(FNAME_HE, ncid, "HE", &varid);
start[0] = my_first_iteration;
start[1] = 0;
count[0] = my_last_iteration - my_first_iteration + 1;
count[1] = obs->nobs;
ncw_put_vara_float(FNAME_HE, ncid, varid, start, count, das->S[my_first_iteration]);
ncw_close(FNAME_HE, ncid);
MPI_Barrier(MPI_COMM_WORLD);
ncw_open(FNAME_HE, NC_NOWRITE, &ncid);
ncw_inq_varid(FNAME_HE, ncid, "HE", &varid);
ncw_get_var_float(FNAME_HE, ncid, varid, das->S[0]);
ncw_close(FNAME_HE, ncid);
}
#endif
}
#endif
if (das->mode == MODE_ENOI) {
/*
* subtract ensemble mean; add background
*/
if (!enkf_fstatsonly) {
double* ensmean = calloc(obs->nobs, sizeof(double));
for (e = 0; e < das->nmem; ++e) {
ENSOBSTYPE* Se = das->S[e];
for (i = 0; i < obs->nobs; ++i)
ensmean[i] += Se[i];
}
for (i = 0; i < obs->nobs; ++i)
ensmean[i] /= (double) das->nmem;
for (e = 0; e < das->nmem; ++e) {
ENSOBSTYPE* Se = das->S[e];
for (i = 0; i < obs->nobs; ++i)
Se[i] += Hx[i] - ensmean[i];
}
free(ensmean);
} else {
for (e = 0; e < das->nmem; ++e) {
ENSOBSTYPE* Se = das->S[e];
for (i = 0; i < obs->nobs; ++i)
Se[i] = Hx[i];
}
}
}
if (das->mode == MODE_ENOI)
free(Hx);
}
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;
}
