nm_id_sct * /* O [sct] Extraction list */
nco_cnv_cf_crd_add /* [fnc] Add coordinates defined by CF convention */
(const int nc_id, /* I netCDF file ID */
nm_id_sct *xtr_lst, /* I/O current extraction list (destroyed) */
int * const xtr_nbr) /* I/O number of variables in current extraction list */
{
/* Purpose: Detect coordinates specified by CF convention and add them to extraction list
http://www.cgd.ucar.edu/cms/eaton/cf-metadata/CF-1.0.html#grid_ex2 */
const char dlm_sng[]=" "; /* [sng] Delimiter string */
const char fnc_nm[]="nco_cnv_cf_crd_add()"; /* [sng] Function name */
char **crd_lst; /* [sng] 1D array of list elements */
char *att_val;
char att_nm[NC_MAX_NAME];
int crd_id;
int idx_att;
int idx_crd;
int idx_var;
int idx_var2;
int nbr_att;
int nbr_crd; /* [nbr] Number of coordinates specified in "coordinates" attribute */
int rcd=NC_NOERR; /* [rcd] Return code */
int var_id;
long att_sz;
nc_type att_typ;
/* ...for each variable in extraction list... */
for(idx_var=0;idx_var<*xtr_nbr;idx_var++){
/* Eschew indirection */
var_id=xtr_lst[idx_var].id;
/* Find number of attributes */
(void)nco_inq_varnatts(nc_id,var_id,&nbr_att);
for(idx_att=0;idx_att<nbr_att;idx_att++){
(void)nco_inq_attname(nc_id,var_id,idx_att,att_nm);
/* Is attribute part of CF convention? */
if(!strcmp(att_nm,"coordinates")){
/* Yes, get list of specified attributes */
(void)nco_inq_att(nc_id,var_id,att_nm,&att_typ,&att_sz);
if(att_typ != NC_CHAR){
(void)fprintf(stderr,"%s: WARNING the \"%s\" attribute for variable %s is type %s, not %s. This violates the CF convention for specifying additional attributes. Therefore %s will skip this attribute.\n",nco_prg_nm_get(),att_nm,xtr_lst[idx_var].nm,nco_typ_sng(att_typ),nco_typ_sng(NC_CHAR),fnc_nm);
return xtr_lst;
} /* end if */
att_val=(char *)nco_malloc((att_sz+1L)*sizeof(char));
if(att_sz > 0) (void)nco_get_att(nc_id,var_id,att_nm,(void *)att_val,NC_CHAR);
/* NUL-terminate attribute */
att_val[att_sz]='\0';
/* Split list into separate coordinate names */
/* using nco_lst_prs_sgl_2D() and not nco_lst_prs_2D */
/* see TODO 944 */
crd_lst=nco_lst_prs_sgl_2D(att_val,dlm_sng,&nbr_crd);
/* ...for each coordinate in "coordinates" attribute... */
for(idx_crd=0;idx_crd<nbr_crd;idx_crd++){
/* Verify "coordinate" exists in input file */
rcd=nco_inq_varid_flg(nc_id,crd_lst[idx_crd],&crd_id);
/* NB: Do not check that dimension by this name exists
CF files often use "coordinates" convention to identify
two-dimensional (or greater) variables which serve as coordinates.
In other words, we want to allow N-D variables to work as coordinates
for the purpose of adding them to the extraction list only. */
if(rcd == NC_NOERR){
/* idx_var2 labels inner loop over variables */
/* Is "coordinate" already on extraction list? */
for(idx_var2=0;idx_var2<*xtr_nbr;idx_var2++){
if(crd_id == xtr_lst[idx_var2].id) break;
} /* end loop over idx_var2 */
if(idx_var2 == *xtr_nbr){
/* Add coordinate to list */
xtr_lst=(nm_id_sct *)nco_realloc((void *)xtr_lst,(*xtr_nbr+1)*sizeof(nm_id_sct));
xtr_lst[*xtr_nbr].nm=(char *)strdup(crd_lst[idx_crd]);
xtr_lst[*xtr_nbr].id=crd_id;
(*xtr_nbr)++; /* NB: Changes size of current loop! */
/* Continue to next coordinate in loop */
continue;
} /* end if coordinate was not already in list */
} /* end if named coordinate exists in input file */
} /* end loop over idx_crd */
/* Free allocated memory */
att_val=(char *)nco_free(att_val);
crd_lst=nco_sng_lst_free(crd_lst,nbr_crd);
} /* !coordinates */
} /* end loop over attributes */
} /* end loop over idx_var */
return xtr_lst;
} /* end nco_cnv_cf_crd_add() */
void
nco_att_cpy /* [fnc] Copy attributes from input netCDF file to output netCDF file */
(const int in_id, /* I [id] netCDF input-file ID */
const int out_id, /* I [id] netCDF output-file ID */
const int var_in_id, /* I [id] netCDF input-variable ID */
const int var_out_id, /* I [id] netCDF output-variable ID */
const nco_bool PCK_ATT_CPY) /* I [flg] Copy attributes "scale_factor", "add_offset" */
{
/* Purpose: Copy attributes from input netCDF file to output netCDF file
If var_in_id == NC_GLOBAL, then copy global attributes
Otherwise copy only indicated variable's attributes
When PCK_ATT_CPY is false, copy all attributes except "scale_factor", "add_offset" */
char att_nm[NC_MAX_NAME];
char var_nm[NC_MAX_NAME];
int idx;
int nbr_att;
int rcd; /* [enm] Return code */
if(var_in_id == NC_GLOBAL){
(void)nco_inq_natts(in_id,&nbr_att);
}else{
(void)nco_inq_varnatts(in_id,var_in_id,&nbr_att);
} /* end else */
/* Jump back to here if current attribute is treated specially */
for(idx=0;idx<nbr_att;idx++){
(void)nco_inq_attname(in_id,var_in_id,idx,att_nm);
/* Look for same attribute in output variable in output file */
rcd=nco_inq_att_flg(out_id,var_out_id,att_nm,(nc_type *)NULL,(long *)NULL);
/* If instructed not to copy packing attributes... */
if(!PCK_ATT_CPY)
/* ...and attribute is "scale_factor" or "add_offset" ... */
if(!strcmp(att_nm,"scale_factor") || !strcmp(att_nm,"add_offset"))
/* ...then skip remainder of loop, thereby skipping attribute copy... */
continue;
/* Inform user when copy will overwrite an existing attribute */
if(dbg_lvl_get() >= nco_dbg_std){
if(rcd == NC_NOERR){
if(var_out_id == NC_GLOBAL){
(void)fprintf(stderr,"%s: INFO Overwriting global attribute %s\n",prg_nm_get(),att_nm);
}else{
(void)nco_inq_varname(out_id,var_out_id,var_nm);
(void)fprintf(stderr,"%s: INFO Overwriting attribute %s for output variable %s\n",prg_nm_get(),att_nm,var_nm);
} /* end else */
} /* end if */
} /* end if dbg */
if(strcmp(att_nm,nco_mss_val_sng_get())){
/* Copy all attributes except _FillValue with fast library routine */
(void)nco_copy_att(in_id,var_in_id,att_nm,out_id,var_out_id);
}else{
/* Convert "_FillValue" attribute to unpacked type then copy
Impose NCO convention that _FillValue is same type as variable,
whether variable is packed or not */
aed_sct aed;
long att_sz;
size_t att_lng_in;
nc_type att_typ_in;
nc_type att_typ_out;
ptr_unn mss_tmp;
(void)nco_inq_att(in_id,var_in_id,att_nm,&att_typ_in,&att_sz);
if(att_sz != 1L){
(void)fprintf(stderr,"%s: ERROR input \"%s\" attribute has %li elements, but nco_att_cpy() only works for size of 1\n",prg_nm_get(),att_nm,att_sz);
nco_exit(EXIT_FAILURE);
} /* end if */
/* Convert "_FillValue" to unpacked type before copying */
aed.att_nm=att_nm; /* Name of attribute */
if(var_out_id == NC_GLOBAL){
aed.var_nm=NULL;
}else{
(void)nco_inq_varname(out_id,var_out_id,var_nm);
aed.var_nm=var_nm; /* Name of variable, or NULL for global attribute */
} /* end if */
aed.id=out_id; /* Variable ID or NC_GLOBAL ( = -1) for global attribute */
aed.sz=att_sz; /* Number of elements in attribute */
/* Do not convert global attributes or PCK_ATT_CPY */
if(PCK_ATT_CPY || var_out_id==NC_GLOBAL) att_typ_out=att_typ_in; else (void)nco_inq_vartype(out_id,var_out_id,&att_typ_out);
if(att_typ_out==att_typ_in){
aed.type=att_typ_out; /* Type of attribute */
aed.val.vp=(void *)nco_malloc(nco_typ_lng(aed.type)); /* Pointer to attribute value */
(void)nco_get_att(in_id,var_in_id,att_nm,aed.val.vp,att_typ_out);
}else{ /* att_typ_out!=att_typ_in */
/* Convert type */
aed.type=att_typ_out; /* Type of attribute */
aed.val.vp=(void *)nco_malloc(nco_typ_lng(aed.type)); /* Pointer to attribute value */
att_lng_in=att_sz*nco_typ_lng(att_typ_in);
mss_tmp.vp=(void *)nco_malloc(att_lng_in);
(void)nco_get_att(in_id,var_in_id,att_nm,mss_tmp.vp,att_typ_in);
(void)nco_val_cnf_typ(att_typ_in,mss_tmp,att_typ_out,aed.val);
mss_tmp.vp=nco_free(mss_tmp.vp);
} /* att_typ_out!=att_typ_in */
/* Overwrite mode causes problems with netCDF4 and "_FillValue"
Use create mode instead */
aed.mode=aed_create;
(void)nco_aed_prc(out_id,var_out_id,aed);
/* Release temporary memory */
aed.val.vp=nco_free(aed.val.vp);
} /* endif copying _FillValue */
} /* end loop over attributes */
} /* end nco_att_cpy() */
