Ejemplo n.º 1
0
/** 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);
}
Ejemplo n.º 2
0
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);
}
Ejemplo n.º 3
0
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);
}
Ejemplo n.º 4
0
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);
}
Ejemplo n.º 5
0
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);
}
Ejemplo n.º 6
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);
}
Ejemplo n.º 7
0
Archivo: grid.c Proyecto: sakov/enkf-c
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;
}
Ejemplo n.º 8
0
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;
}
Ejemplo n.º 9
0
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);
}
Ejemplo n.º 10
0
/** 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);
}
Ejemplo n.º 11
0
/** 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);
}