var_sct * /* O [sct] Output NCO variable structure representing value */
scl_ptr_mk_var /* [fnc] Convert void pointer to scalar of any type into NCO variable */
(const ptr_unn val_ptr_unn, /* I [unn] Scalar value to turn into netCDF variable */
const nc_type val_typ) /* I [enm] netCDF type of existing pointer/value */
{
/* Purpose: Convert void pointer to scalar of any type into NCO variable
Routine duplicates many functions of nco_var_fll()
Both functions should share as much initialization code as possible */
var_sct *var;
var=(var_sct *)nco_malloc(sizeof(var_sct));
/* Set defaults */
(void)var_dfl_set(var); /* [fnc] Set defaults for each member of variable structure */
/* Overwrite defaults with values appropriate for artificial variable */
var->nm=(char *)strdup("Internally_generated_variable");
var->nm_fll=NULL;
var->nbr_dim=0;
var->type=val_typ;
/* Allocate new space here so that variable can eventually be deleted
and associated memory free()'d */
/* free(val_ptr_unn.vp) is unpredictable since val_ptr_unn may point to constant data, e.g.,
a constant in scl_mk_var */
var->val.vp=(void *)nco_malloc(nco_typ_lng(var->type));
/* Copy value into variable structure */
(void)memcpy((void *)var->val.vp,val_ptr_unn.vp,nco_typ_lng(var->type));
return var;
} /* end scl_ptr_mk_var() */
double /* O [frc] Double precision representation of var->val.?p[0] */
ptr_unn_2_scl_dbl /* [fnc] Convert first element of NCO variable to a scalar double */
(const ptr_unn val, /* I [sct] Pointer union to convert to scalar double */
const nc_type type) /* I [enm] Type of values pointed to by pointer union */
{
/* Purpose: Return first element of NCO variable converted to a scalar double */
double scl_dbl; /* [sct] Double precision value of scale_factor */
ptr_unn ptr_unn_scl_dbl; /* [unn] Pointer union to double precision value of first element */
/* Variable must be in memory already */
if(val.vp == NULL) {
(void)fprintf(stdout,"%s: ERROR ptr_unn_2_scl_dbl() called with empty val.vp\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
} /* endif */
/* Valid memory address exists */
ptr_unn_scl_dbl.vp=(void *)nco_malloc(nco_typ_lng(NC_DOUBLE)); /* [unn] Pointer union to double precision value of first element */
(void)nco_val_cnf_typ(type,val,NC_DOUBLE,ptr_unn_scl_dbl);
scl_dbl=ptr_unn_scl_dbl.dp[0];
ptr_unn_scl_dbl.vp=nco_free(ptr_unn_scl_dbl.vp);
return scl_dbl;
} /* end ptr_unn_2_scl_dbl() */
nco_bool /* O [flg] File obeys CCM/CCSM/CF conventions */
nco_cnv_ccm_ccsm_cf_inq /* O [fnc] Check if file obeys CCM/CCSM/CF conventions */
(const int nc_id) /* I [id] netCDF file ID */
{
/* Purpose: Check if file adheres to CCM/CCSM/CF history tape format */
nco_bool CNV_CCM_CCSM_CF=False;
char *att_val;
char *cnv_sng=NULL_CEWI;
/* netCDF standard is uppercase Conventions, though some models user lowercase */
char cnv_sng_UC[]="Conventions"; /* Unidata standard string (uppercase) */
char cnv_sng_LC[]="conventions"; /* Unidata non-standard string (lowercase) */
int rcd; /* [rcd] Return code */
long att_sz;
nc_type att_typ;
/* Look for signature of a CCM/CCSM/CF-format file */
cnv_sng=cnv_sng_UC;
rcd=nco_inq_att_flg(nc_id,NC_GLOBAL,cnv_sng,&att_typ,&att_sz);
if(rcd != NC_NOERR){
/* Re-try with lowercase string because some models, e.g., CLM, user lowercase "conventions" */
cnv_sng=cnv_sng_LC;
rcd=nco_inq_att_flg(nc_id,NC_GLOBAL,cnv_sng,&att_typ,&att_sz);
} /* endif lowercase */
if(rcd == NC_NOERR && att_typ == NC_CHAR){
/* Add one for NUL byte */
att_val=(char *)nco_malloc(att_sz*nco_typ_lng(att_typ)+1L);
(void)nco_get_att(nc_id,NC_GLOBAL,cnv_sng,att_val,att_typ);
/* NUL-terminate convention attribute before using strcmp() */
att_val[att_sz]='\0';
/* CCM3, CCSM1 conventions */
if(strstr(att_val,"NCAR-CSM")) CNV_CCM_CCSM_CF=True; /* Backwards compatibility */
/* Climate-Forecast conventions */
if(strstr(att_val,"CF-1.")) CNV_CCM_CCSM_CF=True; /* NB: Not fully implemented TODO nco145 */
/* As of 20060514, CLM 3.0 uses CF1.0 not CF-1.0 (CAM gets it right) */
if(strstr(att_val,"CF1.")) CNV_CCM_CCSM_CF=True; /* NB: Not fully implemented TODO nco145 */
if(CNV_CCM_CCSM_CF && nco_dbg_lvl_get() >= nco_dbg_std){
(void)fprintf(stderr,"%s: CONVENTION File \"%s\" attribute is \"%s\"\n",nco_prg_nm_get(),cnv_sng,att_val);
if(cnv_sng == cnv_sng_LC) (void)fprintf(stderr,"%s: WARNING: This file uses a non-standard attribute (\"%s\") to indicate the netCDF convention. The correct attribute is \"%s\".\n",nco_prg_nm_get(),cnv_sng_LC,cnv_sng_UC);
/* Only warn in arithmetic operators where conventions change behavior */
if(nco_dbg_lvl_get() >= nco_dbg_fl && nco_dbg_lvl_get() != nco_dbg_dev && nco_is_rth_opr(nco_prg_id_get())) (void)fprintf(stderr,"%s: INFO NCO attempts to abide by many official and unofficial metadata conventions including ARM, CCM, CCSM, and CF. To adhere to these conventions, NCO implements variable-specific exceptions in certain operators, e.g., ncbo will not subtract variables named \"date\" or \"gw\", and many operators will always leave coordinate variables unchanged. The full list of exceptions is in the manual http://nco.sf.net/nco.html#CF\n",nco_prg_nm_get());
} /* endif dbg */
att_val=(char *)nco_free(att_val);
} /* endif */
return CNV_CCM_CCSM_CF;
} /* end nco_cnv_ccm_ccsm_cf_inq */
var_sct * /* O [sct] netCDF variable structure representing val */
scl_dbl_mk_var /* [fnc] Convert scalar double into netCDF variable */
(const double val) /* I [frc] Double precision value to turn into netCDF variable */
{
/* Purpose: Convert scalar double into netCDF variable
Routine duplicates most functions of nco_var_fll()
Both functions should share as much initialization code as possible */
var_sct *var;
var=(var_sct *)nco_malloc(sizeof(var_sct));
/* Set defaults */
(void)var_dfl_set(var); /* [fnc] Set defaults for each member of variable structure */
/* Overwrite defaults with values appropriate for artificial variable */
var->nm=(char *)strdup("Internally_generated_variable");
var->nm_fll=NULL;
var->nbr_dim=0;
var->type=NC_DOUBLE;
var->val.vp=(void *)nco_malloc(nco_typ_lng(var->type));
(void)memcpy((void *)var->val.vp,(const void *)(&val),nco_typ_lng(var->type));
return var;
} /* end scl_dbl_mk_var() */
size_t /* O [nbr] Number of elements successfully read */
nco_bnr_rd /* [fnc] Read unformatted binary data */
(FILE * const fp_bnr, /* I [fl] Unformatted binary input file handle */
const char * const var_nm, /* I [sng] Variable name */
const long var_sz, /* I [nbr] Variable size */
const nc_type var_typ, /* I [enm] Variable type */
void * const void_ptr) /* O [ptr] Data to read */
{
/* Purpose: Read unformatted binary data */
/* Testing:
ncks -O -D 73 ~/nco/data/in.nc ~/foo.nc */
long rd_nbr; /* [nbr] Number of elements successfully written */
/* Read unformatted data from binary input file */
rd_nbr=fread(void_ptr,(size_t)nco_typ_lng(var_typ),(size_t)var_sz,fp_bnr);
if(rd_nbr != var_sz){
(void)fprintf(stderr,"%s: ERROR only succeeded in reading %ld of %ld elements into variable %s\n",nco_prg_nm_get(),rd_nbr,var_sz,var_nm);
nco_exit(EXIT_FAILURE);
} /* end if */
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(stdout,"Binary read of %s (%s, %ld x %lu b)",var_nm,c_typ_nm(var_typ),var_sz,(unsigned long)nco_typ_lng(var_typ));
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fflush(stderr);
return rd_nbr; /* O [nbr] Number of elements successfully written */
} /* end nco_bnr_rd() */
size_t /* O [nbr] Number of elements successfully written */
nco_bnr_wrt /* [fnc] Write unformatted binary data */
(FILE * const fp_bnr, /* I [fl] Unformatted binary output file handle */
const char * const var_nm, /* I [sng] Variable name */
const long var_sz, /* I [nbr] Variable size */
const nc_type var_typ, /* I [enm] Variable type */
const void * const void_ptr) /* I [ptr] Data to write */
{
/* Purpose: Write unformatted binary data */
/* Testing:
ncks -O -D 3 -B -b foo.bnr ~/nco/data/in.nc ~/foo.nc */
long wrt_nbr; /* [nbr] Number of elements successfully written */
/* Write unformatted data to binary output file */
wrt_nbr=fwrite(void_ptr,(size_t)nco_typ_lng(var_typ),(size_t)var_sz,fp_bnr);
if(wrt_nbr != var_sz){
(void)fprintf(stderr,"%s: ERROR only succeeded in writing %ld of %ld elements of variable %s\n",nco_prg_nm_get(),wrt_nbr,var_sz,var_nm);
nco_exit(EXIT_FAILURE);
} /* end if */
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(stdout,"%s (%s, %ld x %lu b), ",var_nm,c_typ_nm(var_typ),var_sz,(unsigned long)nco_typ_lng(var_typ));
if(nco_dbg_lvl_get() >= nco_dbg_std) (void)fflush(stderr);
return wrt_nbr; /* O [nbr] Number of elements successfully written */
} /* end nco_bnr_wrt() */
int
main(int argc,char **argv)
{
nco_bool CNV_CCM_CCSM_CF;
nco_bool CPY_GLB_METADATA=True; /* Option M */
nco_bool EXCLUDE_INPUT_LIST=False; /* Option c */
nco_bool EXTRACT_ALL_COORDINATES=False; /* Option c */
nco_bool EXTRACT_ASSOCIATED_COORDINATES=True; /* Option C */
nco_bool FL_RTR_RMT_LCN;
nco_bool FL_LST_IN_APPEND=True; /* Option H */
nco_bool FL_LST_IN_FROM_STDIN=False; /* [flg] fl_lst_in comes from stdin */
nco_bool FORCE_APPEND=False; /* Option A */
nco_bool FORCE_OVERWRITE=False; /* Option O */
nco_bool FORTRAN_IDX_CNV=False; /* Option F */
nco_bool GROUP_AGGREGATE=False; /* Option G */
nco_bool GRP_VAR_UNN=False; /* [flg] Select union of specified groups and variables */
nco_bool HISTORY_APPEND=True; /* Option h */
nco_bool HAVE_LIMITS=False; /* [flg] Are there user limits? (-d) */
nco_bool MSA_USR_RDR=False; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
nco_bool RAM_CREATE=False; /* [flg] Create file in RAM */
nco_bool RAM_OPEN=False; /* [flg] Open (netCDF3-only) file(s) in RAM */
nco_bool RM_RMT_FL_PST_PRC=True; /* Option R */
nco_bool USE_MM3_WORKAROUND=False; /* [flg] Faster copy on Multi-record Multi-variable netCDF3 files */
nco_bool WRT_TMP_FL=True; /* [flg] Write output to temporary file */
nco_bool RECORD_AGGREGATE=True; /* Option G */
nco_bool flg_cln=True; /* [flg] Clean memory prior to exit */
char **fl_lst_abb=NULL; /* Option a */
char **fl_lst_in;
char **gaa_arg=NULL; /* [sng] Global attribute arguments */
char **grp_lst_in=NULL;
char **var_lst_in=NULL_CEWI;
char *aux_arg[NC_MAX_DIMS];
char *cmd_ln;
char *cnk_arg[NC_MAX_DIMS];
char *cnk_map_sng=NULL_CEWI; /* [sng] Chunking map */
char *cnk_plc_sng=NULL_CEWI; /* [sng] Chunking policy */
char *fl_in=NULL;
char *fl_out=NULL; /* Option o */
char *fl_out_tmp;
char *fl_pth=NULL; /* Option p */
char *fl_pth_lcl=NULL; /* Option l */
char *gpe_arg=NULL; /* [sng] GPE argument */
char *grp_out=NULL; /* [sng] Group name */
char *lmt_arg[NC_MAX_DIMS];
char *opt_crr=NULL; /* [sng] String representation of current long-option name */
char *optarg_lcl=NULL; /* [sng] Local copy of system optarg */
char *ppc_arg[NC_MAX_VARS]; /* [sng] PPC arguments */
char *rec_dmn_nm=NULL; /* [sng] New record dimension name */
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
/* NCO_GRP_OUT_SFX_LNG is number of consecutive numeric digits automatically generated as group name suffixes */
#define NCO_GRP_OUT_SFX_LNG 2
char grp_out_sfx[NCO_GRP_OUT_SFX_LNG+1L];
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
const char * const CVS_Id="$Id$";
const char * const CVS_Revision="$Revision$";
const char * const opt_sht_lst="3467ACcD:d:Fg:G:HhL:l:Mn:Oo:p:rRt:u:v:X:x-:";
cnk_sct cnk; /* [sct] Chunking structure */
#if defined(__cplusplus) || defined(PGI_CC)
ddra_info_sct ddra_info;
ddra_info.flg_ddra=False;
#else /* !__cplusplus */
ddra_info_sct ddra_info={.flg_ddra=False};
#endif /* !__cplusplus */
extern char *optarg;
extern int optind;
/* Using naked stdin/stdout/stderr in parallel region generates warning
Copy appropriate filehandle to variable scoped shared in parallel clause */
FILE * const fp_stderr=stderr; /* [fl] stderr filehandle CEWI */
FILE *fp_bnr=NULL; /* [fl] Unformatted binary output file handle */
gpe_sct *gpe=NULL; /* [sng] Group Path Editing (GPE) structure */
int *in_id_arr=NULL;
int abb_arg_nbr=0;
int aux_nbr=0; /* [nbr] Number of auxiliary coordinate hyperslabs specified */
int cnk_map=nco_cnk_map_nil; /* [enm] Chunking map */
int cnk_nbr=0; /* [nbr] Number of chunk sizes */
int cnk_plc=nco_cnk_plc_nil; /* [enm] Chunking policy */
int dfl_lvl=NCO_DFL_LVL_UNDEFINED; /* [enm] Deflate level */
int fl_idx;
int fl_nbr=0;
int fl_in_fmt; /* [enm] Input file format */
int fl_out_fmt=NCO_FORMAT_UNDEFINED; /* [enm] Output file format */
int fll_md_old; /* [enm] Old fill mode */
int gaa_nbr=0; /* [nbr] Number of global attributes to add */
int gpe_id; /* [id] Group ID of GPE path (diagnostic only) */
int grp_lst_in_nbr=0; /* [nbr] Number of groups explicitly specified by user */
int idx;
int in_id;
int lmt_nbr=0; /* Option d. NB: lmt_nbr gets incremented */
int lmt_nbr_rgn=0; /* Option d. Original limit number for GTT initialization */
int md_open; /* [enm] Mode flag for nc_open() call */
int nbr_dmn_fl;
int nbr_var_fix; /* nbr_var_fix gets incremented */
int nbr_var_fl;
int nbr_var_prc; /* nbr_var_prc gets incremented */
int xtr_nbr=0; /* xtr_nbr won't otherwise be set for -c with no -v */
int opt;
int out_id;
int ppc_nbr=0; /* [nbr] Number of PPC arguments */
int rcd=NC_NOERR; /* [rcd] Return code */
int thr_idx; /* [idx] Index of current thread */
int thr_nbr=int_CEWI; /* [nbr] Thread number Option t */
int var_idx;
int var_lst_in_nbr=0;
long idx_rec_out=0L; /* idx_rec_out gets incremented */
md5_sct *md5=NULL; /* [sct] MD5 configuration */
size_t bfr_sz_hnt=NC_SIZEHINT_DEFAULT; /* [B] Buffer size hint */
size_t cnk_min_byt=NCO_CNK_SZ_MIN_BYT_DFL; /* [B] Minimize size of variable to chunk */
size_t cnk_sz_byt=0UL; /* [B] Chunk size in bytes */
size_t cnk_sz_scl=0UL; /* [nbr] Chunk size scalar */
size_t grp_out_lng; /* [nbr] Length of original, canonicalized GPE specification filename component */
size_t hdr_pad=0UL; /* [B] Pad at end of header section */
var_sct **var=NULL;
var_sct **var_fix;
var_sct **var_fix_out;
var_sct **var_out=NULL;
var_sct **var_prc;
var_sct **var_prc_out;
trv_tbl_sct *trv_tbl=NULL; /* [lst] Traversal table */
nco_dmn_dne_t *flg_dne=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
#ifdef ENABLE_MPI
/* Declare all MPI-specific variables here */
MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
int prc_rnk; /* [idx] Process rank */
int prc_nbr=0; /* [nbr] Number of MPI processes */
#endif /* !ENABLE_MPI */
static struct option opt_lng[]={ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
{"cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"clean",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"mmr_cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"dirty",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"mmr_drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"gag",no_argument,0,0}, /* [flg] Group aggregation */
{"aggregate_group",no_argument,0,0}, /* [flg] Group aggregation */
{"hdf4",no_argument,0,0}, /* [flg] Treat file as HDF4 */
{"md5_dgs",no_argument,0,0}, /* [flg] Perform MD5 digests */
{"md5_digest",no_argument,0,0}, /* [flg] Perform MD5 digests */
{"mrd",no_argument,0,0}, /* [enm] Multiple Record Dimension convention */
{"multiple_record_dimension",no_argument,0,0}, /* [enm] Multiple Record Dimension convention */
{"msa_usr_rdr",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"msa_user_order",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"ram_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"create_ram",no_argument,0,0}, /* [flg] Create file in RAM */
{"open_ram",no_argument,0,0}, /* [flg] Open (netCDF3) file(s) in RAM */
{"diskless_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"wrt_tmp_fl",no_argument,0,0}, /* [flg] Write output to temporary file */
{"write_tmp_fl",no_argument,0,0}, /* [flg] Write output to temporary file */
{"no_tmp_fl",no_argument,0,0}, /* [flg] Do not write output to temporary file */
{"intersection",no_argument,0,0}, /* [flg] Select intersection of specified groups and variables */
{"nsx",no_argument,0,0}, /* [flg] Select intersection of specified groups and variables */
{"union",no_argument,0,0}, /* [flg] Select union of specified groups and variables */
{"unn",no_argument,0,0}, /* [flg] Select union of specified groups and variables */
{"version",no_argument,0,0},
{"vrs",no_argument,0,0},
/* Long options with argument, no short option counterpart */
{"bfr_sz_hnt",required_argument,0,0}, /* [B] Buffer size hint */
{"buffer_size_hint",required_argument,0,0}, /* [B] Buffer size hint */
{"cnk_byt",required_argument,0,0}, /* [B] Chunk size in bytes */
{"chunk_byte",required_argument,0,0}, /* [B] Chunk size in bytes */
{"cnk_dmn",required_argument,0,0}, /* [nbr] Chunk size */
{"chunk_dimension",required_argument,0,0}, /* [nbr] Chunk size */
{"cnk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"chunk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"cnk_min",required_argument,0,0}, /* [B] Minimize size of variable to chunk */
{"chunk_min",required_argument,0,0}, /* [B] Minimize size of variable to chunk */
{"cnk_plc",required_argument,0,0}, /* [nbr] Chunking policy */
{"chunk_policy",required_argument,0,0}, /* [nbr] Chunking policy */
{"cnk_scl",required_argument,0,0}, /* [nbr] Chunk size scalar */
{"chunk_scalar",required_argument,0,0}, /* [nbr] Chunk size scalar */
{"fl_fmt",required_argument,0,0},
{"file_format",required_argument,0,0},
{"gaa",required_argument,0,0}, /* [sng] Global attribute add */
{"glb_att_add",required_argument,0,0}, /* [sng] Global attribute add */
{"hdr_pad",required_argument,0,0},
{"header_pad",required_argument,0,0},
{"ppc",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
{"precision_preserving_compression",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
{"quantize",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
/* Long options with short counterparts */
{"3",no_argument,0,'3'},
{"4",no_argument,0,'4'},
{"64bit",no_argument,0,'4'},
{"netcdf4",no_argument,0,'4'},
{"append",no_argument,0,'A'},
{"coords",no_argument,0,'c'},
{"crd",no_argument,0,'c'},
{"no-coords",no_argument,0,'C'},
{"no-crd",no_argument,0,'C'},
{"debug",required_argument,0,'D'},
{"nco_dbg_lvl",required_argument,0,'D'},
{"dimension",required_argument,0,'d'},
{"dmn",required_argument,0,'d'},
{"fortran",no_argument,0,'F'},
{"ftn",no_argument,0,'F'},
{"gpe",required_argument,0,'G'}, /* [sng] Group Path Edit (GPE) */
{"group",required_argument,0,'g'},
{"grp",required_argument,0,'g'},
{"fl_lst_in",no_argument,0,'H'},
{"file_list",no_argument,0,'H'},
{"history",no_argument,0,'h'},
{"hst",no_argument,0,'h'},
{"dfl_lvl",required_argument,0,'L'}, /* [enm] Deflate level */
{"deflate",required_argument,0,'L'}, /* [enm] Deflate level */
{"local",required_argument,0,'l'},
{"lcl",required_argument,0,'l'},
{"no_glb_mtd",no_argument,0,'M'},
{"suppress_global_metadata",no_argument,0,'M'},
{"nintap",required_argument,0,'n'},
{"overwrite",no_argument,0,'O'},
{"ovr",no_argument,0,'O'},
{"output",required_argument,0,'o'},
{"fl_out",required_argument,0,'o'},
{"path",required_argument,0,'p'},
{"retain",no_argument,0,'R'},
{"rtn",no_argument,0,'R'},
{"revision",no_argument,0,'r'},
{"thr_nbr",required_argument,0,'t'},
{"threads",required_argument,0,'t'},
{"omp_num_threads",required_argument,0,'t'},
{"ulm_nm",required_argument,0,'u'},
{"rcd_nm",required_argument,0,'u'},
{"variable",required_argument,0,'v'},
{"auxiliary",required_argument,0,'X'},
{"exclude",no_argument,0,'x'},
{"xcl",no_argument,0,'x'},
{"help",no_argument,0,'?'},
{"hlp",no_argument,0,'?'},
{0,0,0,0}
}; /* end opt_lng */
int opt_idx=0; /* Index of current long option into opt_lng array */
/* Start timer and save command line */
ddra_info.tmr_flg=nco_tmr_srt;
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
ddra_info.tmr_flg=nco_tmr_mtd;
cmd_ln=nco_cmd_ln_sng(argc,argv);
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
#ifdef ENABLE_MPI
/* MPI Initialization */
if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
MPI_Init(&argc,&argv);
MPI_Comm_size(mpi_cmm,&prc_nbr);
MPI_Comm_rank(mpi_cmm,&prc_rnk);
#endif /* !ENABLE_MPI */
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
opt=getopt_long(argc,argv,opt_sht_lst,opt_lng,&opt_idx);
/* NB: access to opt_crr is only valid when long_opt is detected */
if(opt == EOF) break; /* Parse positional arguments once getopt_long() returns EOF */
opt_crr=(char *)strdup(opt_lng[opt_idx].name);
/* Process long options without short option counterparts */
if(opt == 0){
if(!strcmp(opt_crr,"bfr_sz_hnt") || !strcmp(opt_crr,"buffer_size_hint")){
bfr_sz_hnt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_byt") || !strcmp(opt_crr,"chunk_byte")){
cnk_sz_byt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk_byt */
if(!strcmp(opt_crr,"cnk_min") || !strcmp(opt_crr,"chunk_min")){
cnk_min_byt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk_min */
if(!strcmp(opt_crr,"cnk_dmn") || !strcmp(opt_crr,"chunk_dimension")){
/* Copy limit argument for later processing */
cnk_arg[cnk_nbr]=(char *)strdup(optarg);
cnk_nbr++;
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_scl") || !strcmp(opt_crr,"chunk_scalar")){
cnk_sz_scl=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_map") || !strcmp(opt_crr,"chunk_map")){
/* Chunking map */
cnk_map_sng=(char *)strdup(optarg);
cnk_map=nco_cnk_map_get(cnk_map_sng);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_plc") || !strcmp(opt_crr,"chunk_policy")){
/* Chunking policy */
cnk_plc_sng=(char *)strdup(optarg);
cnk_plc=nco_cnk_plc_get(cnk_plc_sng);
} /* endif cnk */
if(!strcmp(opt_crr,"cln") || !strcmp(opt_crr,"mmr_cln") || !strcmp(opt_crr,"clean")) flg_cln=True; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"drt") || !strcmp(opt_crr,"mmr_drt") || !strcmp(opt_crr,"dirty")) flg_cln=False; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"fl_fmt") || !strcmp(opt_crr,"file_format")) rcd=nco_create_mode_prs(optarg,&fl_out_fmt);
if(!strcmp(opt_crr,"gaa") || !strcmp(opt_crr,"glb_att_add")){
gaa_arg=(char **)nco_realloc(gaa_arg,(gaa_nbr+1)*sizeof(char *));
gaa_arg[gaa_nbr++]=(char *)strdup(optarg);
} /* endif gaa */
if(!strcmp(opt_crr,"gag") || !strcmp(opt_crr,"aggregate_group")) GROUP_AGGREGATE=True; /* [flg] Aggregate files into groups not records */
if(!strcmp(opt_crr,"hdf4")) nco_fmt_xtn=nco_fmt_xtn_hdf4; /* [enm] Treat file as HDF4 */
if(!strcmp(opt_crr,"hdr_pad") || !strcmp(opt_crr,"header_pad")){
hdr_pad=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif "hdr_pad" */
if(!strcmp(opt_crr,"md5_dgs") || !strcmp(opt_crr,"md5_digest")){
if(!md5) md5=nco_md5_ini();
md5->dgs=True;
if(nco_dbg_lvl >= nco_dbg_std) (void)fprintf(stderr,"%s: INFO Will perform MD5 digests of input and output hyperslabs\n",nco_prg_nm_get());
} /* endif "md5_dgs" */
if(!strcmp(opt_crr,"mrd") || !strcmp(opt_crr,"multiple_record_dimension")) nco_mrd_cnv=nco_mrd_allow; /* [enm] Multiple Record Dimension convention */
if(!strcmp(opt_crr,"msa_usr_rdr") || !strcmp(opt_crr,"msa_user_order")) MSA_USR_RDR=True; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
if(!strcmp(opt_crr,"ppc") || !strcmp(opt_crr,"precision_preserving_compression") || !strcmp(opt_crr,"quantize")){
ppc_arg[ppc_nbr]=(char *)strdup(optarg);
ppc_nbr++;
} /* endif "ppc" */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"create_ram") || !strcmp(opt_crr,"diskless_all")) RAM_CREATE=True; /* [flg] Open (netCDF3) file(s) in RAM */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"open_ram") || !strcmp(opt_crr,"diskless_all")) RAM_OPEN=True; /* [flg] Create file in RAM */
if(!strcmp(opt_crr,"unn") || !strcmp(opt_crr,"union")) GRP_VAR_UNN=True;
if(!strcmp(opt_crr,"nsx") || !strcmp(opt_crr,"intersection")) GRP_VAR_UNN=False;
if(!strcmp(opt_crr,"vrs") || !strcmp(opt_crr,"version")){
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
nco_exit(EXIT_SUCCESS);
} /* endif "vrs" */
if(!strcmp(opt_crr,"wrt_tmp_fl") || !strcmp(opt_crr,"write_tmp_fl")) WRT_TMP_FL=True;
if(!strcmp(opt_crr,"no_tmp_fl")) WRT_TMP_FL=False;
} /* opt != 0 */
/* Process short options */
switch(opt){
case 0: /* Long options have already been processed, return */
break;
case '3': /* Request netCDF3 output storage format */
fl_out_fmt=NC_FORMAT_CLASSIC;
break;
case '4': /* Catch-all to prescribe output storage format */
if(!strcmp(opt_crr,"64bit")) fl_out_fmt=NC_FORMAT_64BIT; else fl_out_fmt=NC_FORMAT_NETCDF4;
break;
case '6': /* Request netCDF3 64-bit offset output storage format */
fl_out_fmt=NC_FORMAT_64BIT;
break;
case '7': /* Request netCDF4-classic output storage format */
fl_out_fmt=NC_FORMAT_NETCDF4_CLASSIC;
break;
case 'A': /* Toggle FORCE_APPEND */
FORCE_APPEND=!FORCE_APPEND;
break;
case 'C': /* Extract all coordinates associated with extracted variables? */
EXTRACT_ASSOCIATED_COORDINATES=False;
break;
case 'c':
EXTRACT_ALL_COORDINATES=True;
break;
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
lmt_nbr++;
lmt_nbr_rgn=lmt_nbr;
HAVE_LIMITS=True;
break;
case 'F': /* Toggle index convention. Default is 0-based arrays (C-style). */
FORTRAN_IDX_CNV=!FORTRAN_IDX_CNV;
break;
case 'G': /* Apply Group Path Editing (GPE) to output group */
/* NB: GNU getopt() optional argument syntax is ugly (requires "=" sign) so avoid it
http://stackoverflow.com/questions/1052746/getopt-does-not-parse-optional-arguments-to-parameters */
gpe=nco_gpe_prs_arg(optarg);
grp_out=(char *)strdup(gpe->nm_cnn); /* [sng] Group name */
grp_out_lng=gpe->lng_cnn;
GROUP_AGGREGATE=True;
break;
case 'g': /* Copy group argument for later processing */
/* Replace commas with hashes when within braces (convert back later) */
optarg_lcl=(char *)strdup(optarg);
(void)nco_rx_comma2hash(optarg_lcl);
grp_lst_in=nco_lst_prs_2D(optarg_lcl,",",&grp_lst_in_nbr);
optarg_lcl=(char *)nco_free(optarg_lcl);
break;
case 'H': /* Toggle writing input file list attribute */
FL_LST_IN_APPEND=!FL_LST_IN_APPEND;
break;
case 'h': /* Toggle appending to history global attribute */
HISTORY_APPEND=!HISTORY_APPEND;
break;
case 'L': /* [enm] Deflate level. Default is 0. */
dfl_lvl=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
break;
case 'l': /* Local path prefix for files retrieved from remote file system */
fl_pth_lcl=(char *)strdup(optarg);
break;
case 'M': /* Toggle copying global metadata */
CPY_GLB_METADATA=!CPY_GLB_METADATA;
break;
case 'n': /* NINTAP-style abbreviation of files to process */
fl_lst_abb=nco_lst_prs_2D(optarg,",",&abb_arg_nbr);
if(abb_arg_nbr < 1 || abb_arg_nbr > 6){
(void)fprintf(stdout,"%s: ERROR Incorrect abbreviation for file list\n",nco_prg_nm);
(void)nco_usg_prn();
nco_exit(EXIT_FAILURE);
} /* end if */
break;
case 'O': /* Toggle FORCE_OVERWRITE */
FORCE_OVERWRITE=!FORCE_OVERWRITE;
break;
case 'o': /* Name of output file */
fl_out=(char *)strdup(optarg);
break;
case 'p': /* Common file path */
fl_pth=(char *)strdup(optarg);
break;
case 'R': /* Toggle removal of remotely-retrieved-files. Default is True. */
RM_RMT_FL_PST_PRC=!RM_RMT_FL_PST_PRC;
break;
case 'r': /* Print CVS program information and copyright notice */
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
(void)nco_lbr_vrs_prn();
(void)nco_cpy_prn();
(void)nco_cnf_prn();
nco_exit(EXIT_SUCCESS);
break;
case 't': /* Thread number */
thr_nbr=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
break;
case 'u': /* New record dimension name */
rec_dmn_nm=(char *)strdup(optarg);
break;
case 'v': /* Variables to extract/exclude */
/* Replace commas with hashes when within braces (convert back later) */
optarg_lcl=(char *)strdup(optarg);
(void)nco_rx_comma2hash(optarg_lcl);
var_lst_in=nco_lst_prs_2D(optarg_lcl,",",&var_lst_in_nbr);
optarg_lcl=(char *)nco_free(optarg_lcl);
xtr_nbr=var_lst_in_nbr;
break;
case 'X': /* Copy auxiliary coordinate argument for later processing */
aux_arg[aux_nbr]=(char *)strdup(optarg);
aux_nbr++;
MSA_USR_RDR=True; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
break;
case 'x': /* Exclude rather than extract variables specified with -v */
EXCLUDE_INPUT_LIST=True;
break;
case '?': /* Print proper usage */
(void)nco_usg_prn();
nco_exit(EXIT_SUCCESS);
break;
case '-': /* Long options are not allowed */
(void)fprintf(stderr,"%s: ERROR Long options are not available in this build. Use single letter options instead.\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
break;
default: /* Print proper usage */
(void)fprintf(stdout,"%s ERROR in command-line syntax/options. Please reformulate command accordingly.\n",nco_prg_nm_get());
(void)nco_usg_prn();
nco_exit(EXIT_FAILURE);
break;
} /* end switch */
if(opt_crr) opt_crr=(char *)nco_free(opt_crr);
} /* end while loop */
trv_tbl_init(&trv_tbl);
if(GROUP_AGGREGATE){
RECORD_AGGREGATE=!GROUP_AGGREGATE;
fl_out_fmt=NC_FORMAT_NETCDF4;
} /* !GROUP_AGGREGATE */
/* Process positional arguments and fill in filenames */
fl_lst_in=nco_fl_lst_mk(argv,argc,optind,&fl_nbr,&fl_out,&FL_LST_IN_FROM_STDIN);
/* Parse filename */
fl_in=nco_fl_nm_prs(fl_in,0,&fl_nbr,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
/* Make sure file is on local system and is readable or die trying */
fl_in=nco_fl_mk_lcl(fl_in,fl_pth_lcl,&FL_RTR_RMT_LCN);
if(RAM_OPEN) md_open=NC_NOWRITE|NC_DISKLESS; else md_open=NC_NOWRITE;
/* Open file using appropriate buffer size hints and verbosity */
rcd+=nco_fl_open(fl_in,md_open,&bfr_sz_hnt,&in_id);
(void)nco_inq_format(in_id,&fl_in_fmt);
if(RECORD_AGGREGATE){
/* Initialize thread information */
thr_nbr=nco_openmp_ini(thr_nbr);
in_id_arr=(int *)nco_malloc(thr_nbr*sizeof(int));
/* Construct GTT, Group Traversal Table (groups,variables,dimensions, limits) */
(void)nco_bld_trv_tbl(in_id,trv_pth,lmt_nbr,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,xtr_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl);
/* Were all user-specified dimensions found? */
(void)nco_chk_dmn(lmt_nbr,flg_dne);
/* Get number of variables, dimensions, and global attributes in file, file format */
(void)trv_tbl_inq((int *)NULL,(int *)NULL,(int *)NULL,&nbr_dmn_fl,(int *)NULL,(int *)NULL,(int *)NULL,(int *)NULL,&nbr_var_fl,trv_tbl);
/* Fill-in variable structure list for all extracted variables */
var=nco_fll_var_trv(in_id,&xtr_nbr,trv_tbl);
var_out=(var_sct **)nco_malloc(xtr_nbr*sizeof(var_sct *));
for(var_idx=0;var_idx<xtr_nbr;var_idx++) var_out[var_idx]=nco_var_dpl(var[var_idx]);
/* Is this a CCM/CCSM/CF-format history tape? */
CNV_CCM_CCSM_CF=nco_cnv_ccm_ccsm_cf_inq(in_id);
/* Divide variable lists into lists of fixed variables and variables to be processed */
(void)nco_var_lst_dvd(var,var_out,xtr_nbr,CNV_CCM_CCSM_CF,True,nco_pck_plc_nil,nco_pck_map_nil,(dmn_sct **)NULL,0,&var_fix,&var_fix_out,&nbr_var_fix,&var_prc,&var_prc_out,&nbr_var_prc,trv_tbl);
/* Store processed and fixed variables info into GTT */
(void)nco_var_prc_fix_trv(nbr_var_prc,var_prc,nbr_var_fix,var_fix,trv_tbl);
} /* !RECORD_AGGREGATE */
/* Make output and input files consanguinous */
if(fl_out_fmt == NCO_FORMAT_UNDEFINED) fl_out_fmt=fl_in_fmt;
/* Initialize, decode, and set PPC information */
if(ppc_nbr > 0) nco_ppc_ini(in_id,&dfl_lvl,fl_out_fmt,ppc_arg,ppc_nbr,trv_tbl);
/* Verify output file format supports requested actions */
(void)nco_fl_fmt_vet(fl_out_fmt,cnk_nbr,dfl_lvl);
/* Open output file */
fl_out_tmp=nco_fl_out_open(fl_out,FORCE_APPEND,FORCE_OVERWRITE,fl_out_fmt,&bfr_sz_hnt,RAM_CREATE,RAM_OPEN,WRT_TMP_FL,&out_id);
/* Initialize chunking from user-specified inputs */
if(fl_out_fmt == NC_FORMAT_NETCDF4 || fl_out_fmt == NC_FORMAT_NETCDF4_CLASSIC) rcd+=nco_cnk_ini(in_id,fl_out,cnk_arg,cnk_nbr,cnk_map,cnk_plc,cnk_min_byt,cnk_sz_byt,cnk_sz_scl,&cnk);
/* ncecat-specific operations */
if(RECORD_AGGREGATE){
if(!rec_dmn_nm) rec_dmn_nm=(char *)strdup("record");
/* Prepend record dimension to beginning of all vectors for processed variables */
for(idx=0;idx<nbr_var_prc;idx++){
var_prc_out[idx]->nbr_dim++;
var_prc_out[idx]->is_rec_var=True;
var_prc_out[idx]->sz_rec=var_prc_out[idx]->sz;
/* Allocate space to hold dimension IDs */
var_prc_out[idx]->dim=(dmn_sct **)nco_realloc(var_prc_out[idx]->dim,var_prc_out[idx]->nbr_dim*sizeof(dmn_sct *));
var_prc_out[idx]->dmn_id=(int *)nco_realloc(var_prc_out[idx]->dmn_id,var_prc_out[idx]->nbr_dim*sizeof(int));
var_prc_out[idx]->cnt=(long *)nco_realloc(var_prc_out[idx]->cnt,var_prc_out[idx]->nbr_dim*sizeof(long int));
var_prc_out[idx]->end=(long *)nco_realloc(var_prc_out[idx]->end,var_prc_out[idx]->nbr_dim*sizeof(long int));
var_prc_out[idx]->srd=(long *)nco_realloc(var_prc_out[idx]->srd,var_prc_out[idx]->nbr_dim*sizeof(long int));
var_prc_out[idx]->srt=(long *)nco_realloc(var_prc_out[idx]->srt,var_prc_out[idx]->nbr_dim*sizeof(long int));
/* Moves current array by one to make room for new record dimension info */
(void)memmove((void *)(var_prc_out[idx]->dim+1),(void *)(var_prc_out[idx]->dim),(var_prc_out[idx]->nbr_dim-1)*sizeof(dmn_sct *));
(void)memmove((void *)(var_prc_out[idx]->dmn_id+1),(void *)(var_prc_out[idx]->dmn_id),(var_prc_out[idx]->nbr_dim-1)*sizeof(int));
(void)memmove((void *)(var_prc_out[idx]->cnt+1L),(void *)(var_prc_out[idx]->cnt),(var_prc_out[idx]->nbr_dim-1)*sizeof(long int));
(void)memmove((void *)(var_prc_out[idx]->end+1L),(void *)(var_prc_out[idx]->end),(var_prc_out[idx]->nbr_dim-1)*sizeof(long int));
(void)memmove((void *)(var_prc_out[idx]->srd+1L),(void *)(var_prc_out[idx]->srd),(var_prc_out[idx]->nbr_dim-1)*sizeof(long int));
(void)memmove((void *)(var_prc_out[idx]->srt+1L),(void *)(var_prc_out[idx]->srt),(var_prc_out[idx]->nbr_dim-1)*sizeof(long int));
/* Insert value for new record dimension */
var_prc_out[idx]->cnt[0]=1L;
var_prc_out[idx]->end[0]=-1L;
var_prc_out[idx]->srd[0]=-1L;
var_prc_out[idx]->srt[0]=-1L;
} /* end loop over idx */
/* Define dimensions, extracted groups, variables, and attributes in output file */
(void)nco_xtr_dfn(in_id,out_id,&cnk,dfl_lvl,gpe,md5,!FORCE_APPEND,True,False,nco_pck_plc_nil,rec_dmn_nm,trv_tbl);
/* Catenate time-stamped command line to "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln);
if(HISTORY_APPEND && FORCE_APPEND) (void)nco_prv_att_cat(fl_in,in_id,out_id);
if(gaa_nbr > 0) (void)nco_glb_att_add(out_id,gaa_arg,gaa_nbr);
if(HISTORY_APPEND) (void)nco_vrs_att_cat(out_id);
/* Add input file list global attribute */
if(FL_LST_IN_APPEND && HISTORY_APPEND && FL_LST_IN_FROM_STDIN) (void)nco_fl_lst_att_cat(out_id,fl_lst_in,fl_nbr);
if(thr_nbr > 0 && HISTORY_APPEND) (void)nco_thr_att_cat(out_id,thr_nbr);
/* Turn-off default filling behavior to enhance efficiency */
nco_set_fill(out_id,NC_NOFILL,&fll_md_old);
/* Take output file out of define mode */
if(hdr_pad == 0UL){
(void)nco_enddef(out_id);
}else{
(void)nco__enddef(out_id,hdr_pad);
if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(stderr,"%s: INFO Padding header with %lu extra bytes\n",nco_prg_nm_get(),(unsigned long)hdr_pad);
} /* hdr_pad */
/* Assign zero to start and unity to stride vectors in output variables */
(void)nco_var_srd_srt_set(var_out,xtr_nbr);
/* Copy variable data for non-processed variables */
(void)nco_cpy_fix_var_trv(in_id,out_id,gpe,trv_tbl);
/* Close first input netCDF file */
(void)nco_close(in_id);
/* Timestamp end of metadata setup and disk layout */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
ddra_info.tmr_flg=nco_tmr_rgl;
} /* !RECORD_AGGREGATE */
if(GROUP_AGGREGATE){
#ifndef ENABLE_NETCDF4
(void)fprintf(stderr,"%s: ERROR GAG requires netCDF4 capabilities. HINT: Rebuild NCO with netCDF4 enabled.\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
#endif /* ENABLE_NETCDF4 */
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"%s: INFO Group Aggregation (GAG) feature enabled\n",nco_prg_nm_get());
if(fl_out_fmt != NC_FORMAT_NETCDF4){
(void)fprintf(stderr,"%s: ERROR Group Aggregation requires netCDF4 output format but user explicitly requested format = %s\n",nco_prg_nm_get(),nco_fmt_sng(fl_out_fmt));
nco_exit(EXIT_FAILURE);
} /* endif err */
} /* !GROUP_AGGREGATE */
/* Loop over input files */
for(fl_idx=0;fl_idx<fl_nbr;fl_idx++){
/* Parse filename */
if(fl_idx) fl_in=nco_fl_nm_prs(fl_in,fl_idx,(int *)NULL,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"%s: INFO Input file %d is %s",nco_prg_nm_get(),fl_idx,fl_in);
/* Make sure file is on local system and is readable or die trying */
if(fl_idx) fl_in=nco_fl_mk_lcl(fl_in,fl_pth_lcl,&FL_RTR_RMT_LCN);
if(nco_dbg_lvl >= nco_dbg_fl && FL_RTR_RMT_LCN) (void)fprintf(stderr,", local file is %s",fl_in);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"\n");
if(GROUP_AGGREGATE){
size_t gpe_arg_lng; /* [nbr] Length of group specification */
if(grp_out){
/* Append enumerated counter to end of user-specified root group path */
sprintf(grp_out_sfx,"%02d",fl_idx);
gpe_arg_lng=grp_out_lng+NCO_GRP_OUT_SFX_LNG+gpe->lng_edt;
gpe_arg=(char *)nco_malloc((gpe_arg_lng+1L)*sizeof(char));
(void)strcpy(gpe_arg,grp_out);
(void)strcat(gpe_arg,grp_out_sfx);
if(gpe->edt) (void)strcat(gpe_arg,gpe->edt);
}else{
/* Use filename stub as group name */
char *stb_srt_psn; /* [sng] Starting position of "stub", i.e., last component of filename */
size_t fl_in_lng; /* [nbr] Length of filename */
size_t sfx_fst; /* [nbr] Offset of suffix from start of string */
size_t sfx_lng; /* [nbr] Suffix has this many characters */
/* Is there a .nc, .cdf, .nc3, or .nc4 suffix? or an .hdf, .HDF, .h5, .H5, or .he5 suffix? */
fl_in_lng=strlen(fl_in);
sfx_lng=3L;
sfx_fst=fl_in_lng-sfx_lng;
/* Sample data found in, e.g., ftp://ftp.unidata.ucar.edu/pub/netcdf/sample_data and http://hdfeos.org/zoo
Two versions of HDF-EOS exist: HDF-EOS2 for HDF4, and HDF-EOS5 for HDF5 */
if(strncmp(fl_in+sfx_fst,".nc",sfx_lng) && /* netCDF standard suffix */
strncmp(fl_in+sfx_fst,".H5",sfx_lng) && /* HDF5 suffix used by ICESat GLAS, e.g., GLAH05_633_2103_001_1107_3_01_0001.H5 */
strncmp(fl_in+sfx_fst,".h5",sfx_lng)){ /* HDF5 suffix used by BUV, ICESat GLAS, MABEL, MEaSUREs Ozone, SBUV, e.g., BUV-Nimbus04_L3zm_v01-00-2012m0203t144121.h5, GLAH13_633_2103_001_1317_0_01_0001.h5, mabel_l2_20130927t201800_008_1.h5, MSO3L3zm5_v01-02-2013m0907t142428.h5 */
sfx_lng=4L;
sfx_fst=fl_in_lng-sfx_lng;
if(strncmp(fl_in+sfx_fst,".cdf",sfx_lng) && /* netCDF old-fashioned suffix */
strncmp(fl_in+sfx_fst,".hdf",sfx_lng) && /* HDF-EOS2 (HDF4) suffix used by AIRS, AMSR-E, MODIS, MOPPITT, SeaWiFS, e.g., AIRS.2002.08.01.L3.RetStd_H031.v4.0.21.0.G06104133732.hdf, MSR_E_L2_Rain_V10_200905312326_A.hdf, MOD10CM.A2007001.005.2007108111758.hdf, MOP01-20121231-L1V3.34.10.hdf, S1999001.L3m_DAY_CDOM_cdom_index_9km.hdf */
strncmp(fl_in+sfx_fst,".HDF",sfx_lng) && /* HDF-EOS2 (HDF4) suffix used by TRMM, e.g., 3B43.070901.6A.HDF */
strncmp(fl_in+sfx_fst,".he5",sfx_lng) && /* HDF-EOS5 (HDF5) suffix used by HIRDLS, OMI Aerosols, e.g., HIRDLS-Aura_L3ZAD_v06-00-00-c02_2005d022-2008d077.he5, OMI-Aura_L2-OMAERUV_2013m1004t2338-o49057_v003-2013m1005t053932.he5 */
strncmp(fl_in+sfx_fst,".nc3",sfx_lng) && /* netCDF3 variant suffix */
strncmp(fl_in+sfx_fst,".nc4",sfx_lng)){ /* netCDF4 variant suffix */
(void)fprintf(stderr,"%s: WARNING GAG filename suffix is unusual---using whole filename as group name\n",nco_prg_nm_get());
sfx_lng=0;
} /* endif */
} /* endif */
stb_srt_psn=strrchr(fl_in,'/');
if(!stb_srt_psn) stb_srt_psn=fl_in; else stb_srt_psn++;
gpe_arg_lng=strlen(stb_srt_psn)-sfx_lng;
gpe_arg=(char *)nco_malloc((gpe_arg_lng+1L)*sizeof(char));
gpe_arg=strncpy(gpe_arg,stb_srt_psn,strlen(stb_srt_psn)-sfx_lng);
gpe_arg[gpe_arg_lng]='\0';
/* GPE arguments derived from filenames check for existence of path in output file */
rcd=nco_inq_grp_full_ncid_flg(out_id,gpe_arg,&gpe_id);
/* Existence implies current file may overwrite contents of previous file */
if(rcd == NC_NOERR) (void)fprintf(stderr,"%s: WARNING GAG path \"%s\" automatically derived from stub of filename %s conflicts with existing path in output file. Any input data with same absolute path names as contents of a previous input file will be overwritten. Is the same input file specified multiple times? Is this intentional?\nHINT: To distribute copies of a single input file into different groups, use GPE to generate distinct output group names, e.g., %s -G copy in.nc in.nc out.nc\n",nco_prg_nm_get(),gpe_arg,fl_in,nco_prg_nm_get()); else rcd=NC_NOERR;
} /* !grp_out */
/* Free old structure, if any, before re-use */
if(gpe) gpe=(gpe_sct *)nco_gpe_free(gpe);
gpe=nco_gpe_prs_arg(gpe_arg);
gpe_arg=(char *)nco_free(gpe_arg);
if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(stderr,"%s: INFO GAG current file has gpe->arg=%s\n",nco_prg_nm_get(),gpe->arg);
/* Open file using appropriate buffer size hints and verbosity */
if(fl_idx) rcd=nco_fl_open(fl_in,md_open,&bfr_sz_hnt,&in_id);
if(fl_idx == 0){
/* fxm: Copy global attributes of first file to root of output file to preserve history attribute */
/* Copy global attributes */
if(CPY_GLB_METADATA) (void)nco_att_cpy(in_id,out_id,NC_GLOBAL,NC_GLOBAL,(nco_bool)True);
/* Catenate time-stamped command line to "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln);
if(gaa_nbr > 0) (void)nco_glb_att_add(out_id,gaa_arg,gaa_nbr);
if(HISTORY_APPEND) (void)nco_vrs_att_cat(out_id);
/* Add input file list global attribute */
if(FL_LST_IN_APPEND && HISTORY_APPEND && FL_LST_IN_FROM_STDIN) (void)nco_fl_lst_att_cat(out_id,fl_lst_in,fl_nbr);
} /* endif first file */
trv_tbl_sct *trv_tbl_gpr=NULL; /* [lst] Traversal table for GROUP_AGGREGATE only */
/* Initialize traversal table */
trv_tbl_init(&trv_tbl_gpr);
/* Construct GTT, Group Traversal Table (groups,variables,dimensions, limits) */
(void)nco_bld_trv_tbl(in_id,trv_pth,lmt_nbr_rgn,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,xtr_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl_gpr);
/* Get number of variables, dimensions, and global attributes in file, file format */
(void)trv_tbl_inq((int *)NULL,(int *)NULL,(int *)NULL,&nbr_dmn_fl,(int *)NULL,(int *)NULL,(int *)NULL,(int *)NULL,&nbr_var_fl,trv_tbl_gpr);
(void)nco_inq_format(in_id,&fl_in_fmt);
/* We now have final list of variables to extract. Phew. */
/* Define extracted groups, variables, and attributes in output file */
(void)nco_xtr_dfn(in_id,out_id,&cnk,dfl_lvl,gpe,md5,CPY_GLB_METADATA,(nco_bool)True,(nco_bool)False,nco_pck_plc_nil,rec_dmn_nm,trv_tbl_gpr);
/* Turn-off default filling behavior to enhance efficiency */
nco_set_fill(out_id,NC_NOFILL,&fll_md_old);
/* Write extracted data to output file */
(void)nco_xtr_wrt(in_id,out_id,gpe,fp_bnr,md5,HAVE_LIMITS,trv_tbl_gpr);
/* Close input netCDF file */
(void)nco_close(in_id);
/* Free traversal table */
trv_tbl_free(trv_tbl_gpr);
} /* !GROUP_AGGREGATE */
if(RECORD_AGGREGATE){
/* Open file once per thread to improve caching */
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) rcd=nco_fl_open(fl_in,md_open,&bfr_sz_hnt,in_id_arr+thr_idx);
/* Perform various error-checks on input file */
if(False) (void)nco_fl_cmp_err_chk();
/* 20120309 Special case to improve copy speed on large blocksize filesystems (MM3s) */
USE_MM3_WORKAROUND=nco_use_mm3_workaround(in_id_arr[0],fl_out_fmt);
if(lmt_nbr > 0) USE_MM3_WORKAROUND=False;
if(!USE_MM3_WORKAROUND){
/* Copy all data variable-by-variable */
;
}else{
/* MM3 workaround algorithm */
/* ncecat-specific MM3 characteristics:
Only coordinates are "fixed" (non-processed) variables
All other variables are "processed"
These variables may be fixed or
record on input yet are all record on output
Makes sense to always use MM3? */
;
} /* endif MM3 workaround */
/* OpenMP with threading over variables, not files */
#ifdef _OPENMP
# pragma omp parallel for default(none) private(in_id) shared(nco_dbg_lvl,fl_nbr,idx_rec_out,in_id_arr,nbr_var_prc,out_id,var_prc,var_prc_out,nbr_dmn_fl,md5,trv_tbl)
#endif /* !_OPENMP */
/* Process all variables in current file */
for(idx=0;idx<nbr_var_prc;idx++){
int grp_id; /* [ID] Group ID (input) */
int grp_out_id; /* [ID] Group ID (output) */
int var_out_id; /* [ID] Variable ID (output) */
trv_sct *var_trv; /* [sct] Variable GTT object */
in_id=in_id_arr[omp_get_thread_num()];
if(nco_dbg_lvl >= nco_dbg_var) (void)fprintf(fp_stderr,"%s, ",var_prc[idx]->nm);
if(nco_dbg_lvl >= nco_dbg_var) (void)fflush(fp_stderr);
/* Obtain variable GTT object using full variable name */
var_trv=trv_tbl_var_nm_fll(var_prc[idx]->nm_fll,trv_tbl);
/* Variables may have different ID, missing_value, type, in each file */
(void)nco_inq_grp_full_ncid(in_id,var_trv->grp_nm_fll,&grp_id);
(void)nco_var_mtd_refresh(grp_id,var_prc[idx]);
/* Read */
(void)nco_msa_var_get_trv(in_id,var_prc[idx],trv_tbl);
/* Size of record dimension is 1 in output file */
var_prc_out[idx]->cnt[0]=1L;
var_prc_out[idx]->srt[0]=idx_rec_out;
/* Write variable into current record in output file */
/* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,var_trv->grp_nm_fll,&grp_out_id);
/* Get variable ID */
(void)nco_inq_varid(grp_out_id,var_trv->nm,&var_out_id);
/* Store the output variable ID */
var_prc_out[idx]->id=var_out_id;
if(var_trv->ppc != NC_MAX_INT){
if(var_trv->flg_nsd) (void)nco_ppc_bitmask(var_trv->ppc,var_prc[idx]->type,var_prc[idx]->sz,var_prc[idx]->has_mss_val,var_prc[idx]->mss_val,var_prc[idx]->val); else (void)nco_ppc_around(var_trv->ppc,var_prc[idx]->type,var_prc[idx]->sz,var_prc[idx]->has_mss_val,var_prc[idx]->mss_val,var_prc[idx]->val);
} /* endif ppc */
if(nco_is_xcp(var_trv->nm)) nco_xcp_prc(var_trv->nm,var_prc[idx]->type,var_prc[idx]->sz,(char *)var_prc[idx]->val.vp);
#ifdef _OPENMP
# pragma omp critical
#endif /* _OPENMP */
{ /* begin OpenMP critical */
if(var_prc[idx]->nbr_dim == 0){
(void)nco_put_var1(grp_out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc[idx]->val.vp,var_prc[idx]->type);
}else{ /* end if variable is scalar */
(void)nco_put_vara(grp_out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc_out[idx]->cnt,var_prc[idx]->val.vp,var_prc[idx]->type);
} /* end if variable is array */
/* Perform MD5 digest of input and output data if requested */
if(md5) (void)nco_md5_chk(md5,var_prc_out[idx]->nm,var_prc_out[idx]->sz*nco_typ_lng(var_prc[idx]->type),out_id,var_prc_out[idx]->srt,var_prc_out[idx]->cnt,var_prc[idx]->val.vp);
/* Free current input buffer */
var_prc[idx]->val.vp=nco_free(var_prc[idx]->val.vp);
} /* end OpenMP critical */
} /* end (OpenMP parallel for) loop over idx */
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"\n");
idx_rec_out++; /* [idx] Index of current record in output file (0 is first, ...) */
/* Close input netCDF file */
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) nco_close(in_id_arr[thr_idx]);
} /* !RECORD_AGGREGATE */
/* Remove local copy of file */
if(FL_RTR_RMT_LCN && RM_RMT_FL_PST_PRC) (void)nco_fl_rm(fl_in);
} /* end loop over fl_idx */
/* Close output file and move it from temporary to permanent location */
(void)nco_fl_out_cls(fl_out,fl_out_tmp,out_id);
/* Clean memory unless dirty memory allowed */
if(flg_cln){
/* NCO-generic clean-up */
/* Free individual strings/arrays */
if(cmd_ln) cmd_ln=(char *)nco_free(cmd_ln);
if(cnk_map_sng) cnk_map_sng=(char *)nco_free(cnk_map_sng);
if(cnk_plc_sng) cnk_plc_sng=(char *)nco_free(cnk_plc_sng);
if(grp_out) grp_out=(char *)nco_free(grp_out);
if(fl_in) fl_in=(char *)nco_free(fl_in);
if(fl_out) fl_out=(char *)nco_free(fl_out);
if(fl_out_tmp) fl_out_tmp=(char *)nco_free(fl_out_tmp);
if(fl_pth) fl_pth=(char *)nco_free(fl_pth);
if(fl_pth_lcl) fl_pth_lcl=(char *)nco_free(fl_pth_lcl);
if(in_id_arr) in_id_arr=(int *)nco_free(in_id_arr);
/* Free lists of strings */
if(fl_lst_in && !fl_lst_abb) fl_lst_in=nco_sng_lst_free(fl_lst_in,fl_nbr);
if(fl_lst_in && fl_lst_abb) fl_lst_in=nco_sng_lst_free(fl_lst_in,1);
if(fl_lst_abb) fl_lst_abb=nco_sng_lst_free(fl_lst_abb,abb_arg_nbr);
if(gaa_nbr > 0) gaa_arg=nco_sng_lst_free(gaa_arg,gaa_nbr);
if(var_lst_in_nbr > 0) var_lst_in=nco_sng_lst_free(var_lst_in,var_lst_in_nbr);
/* Free limits */
for(idx=0;idx<aux_nbr;idx++) aux_arg[idx]=(char *)nco_free(aux_arg[idx]);
for(idx=0;idx<lmt_nbr;idx++) lmt_arg[idx]=(char *)nco_free(lmt_arg[idx]);
for(idx=0;idx<ppc_nbr;idx++) ppc_arg[idx]=(char *)nco_free(ppc_arg[idx]);
/* Free chunking information */
for(idx=0;idx<cnk_nbr;idx++) cnk_arg[idx]=(char *)nco_free(cnk_arg[idx]);
if(cnk_nbr > 0) cnk.cnk_dmn=(cnk_dmn_sct **)nco_cnk_lst_free(cnk.cnk_dmn,cnk_nbr);
if(RECORD_AGGREGATE){
/* Free dimension lists */
/* ncecat-specific memory cleanup */
if(rec_dmn_nm) rec_dmn_nm=(char *)nco_free(rec_dmn_nm);
/* Free variable lists */
if(xtr_nbr > 0) var=nco_var_lst_free(var,xtr_nbr);
if(xtr_nbr > 0) var_out=nco_var_lst_free(var_out,xtr_nbr);
var_prc=(var_sct **)nco_free(var_prc);
var_prc_out=(var_sct **)nco_free(var_prc_out);
var_fix=(var_sct **)nco_free(var_fix);
var_fix_out=(var_sct **)nco_free(var_fix_out);
if(gpe) gpe=(gpe_sct *)nco_gpe_free(gpe);
if(md5) md5=(md5_sct *)nco_md5_free(md5);
/* Free traversal table */
trv_tbl_free(trv_tbl);
for(idx=0;idx<lmt_nbr;idx++) flg_dne[idx].dim_nm=(char *)nco_free(flg_dne[idx].dim_nm);
if(flg_dne) flg_dne=(nco_dmn_dne_t *)nco_free(flg_dne);
} /* RECORD_AGGREGATE */
} /* !flg_cln */
#ifdef ENABLE_MPI
MPI_Finalize();
#endif /* !ENABLE_MPI */
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
var_sct * /* O [sct] Pointer to conforming variable structure */
nco_var_cnf_dmn /* [fnc] Stretch second variable to match dimensions of first variable */
(const var_sct * const var, /* I [ptr] Pointer to variable structure to serve as template */
var_sct * const wgt, /* I [ptr] Pointer to variable structure to make conform to var */
var_sct *wgt_crr, /* I/O [ptr] Pointer to existing conforming variable structure, if any (destroyed when does not conform to var) */
const nco_bool MUST_CONFORM, /* I [flg] Must wgt and var conform? */
nco_bool *DO_CONFORM) /* O [flg] Do wgt and var conform? */
{
/* Threads: Routine is thread safe and calls no unsafe routines */
/* fxm: TODO 226. Is xrf in nco_var_cnf_dmn() really necessary? If not, remove it and make wgt arg const var_sct * const */
/* Purpose: Stretch second variable to match dimensions of first variable
Dimensions in var which are not in wgt will be present in wgt_out, with values
replicated from existing dimensions in wgt.
By default, wgt's dimensions must be subset of var's dimensions (MUST_CONFORM=true)
Calling routine should set MUST_CONFORM=false if wgt and var need not conform
When wgt and var do not conform then then nco_var_cnf_dmn sets *DO_CONFORM=False and returns copy of var with all values set to 1.0
Calling procedure then decides what to do with unity output
MUST_CONFORM is True for ncbo: Variables of like name to be, e.g., differenced, must conform
MUST_CONFORM is False false for ncap, ncflint, ncwa: Some variables to be averaged may not conform to specified weight, e.g., lon will not conform to gw. This is fine and returned wgt_out may be discarded. */
/* There are many inelegant ways to accomplish this (without using C++): */
/* Perhaps most efficient method in general case is to expand weight array until
it is same size as variable array, and then multiply these arrays together
element-by-element in highly vectorized loop (possibly in Fortran or BLAS).
To enhance speed, (enlarged) weight-values array could be static, only re-made
when dimensions of incoming variables change. */
/* Another general method, though more expensive, is to use C to figure out the
multidimensional indices into the one dimensional hyperslab, a la ncks.
Knowing these indices, routine could loop over the one-dimensional array
element by element, choosing the appropriate index into the weight array from
those same multidimensional indices.
This method can also create a static weight-value array that is only destroyed
when an incoming variable changes dimensions from the previous variable. */
/* Another method, which is not completely general, but which may be good enough for
governement work, is to create Fortran subroutines which expect variables of
a given number of dimensions as input.
Creating these functions for up to five dimensions would satisfy most situations
C code would determine which branch to call based on number of dimensions
C++ or Fortran9x overloading could construct this interface more elegantly */
/* An (untested) simplification to some of these methods is to copy the 1-D array
value pointer of variable and cast it to an N-D array pointer
Then C could handle indexing
This method easily produce working, but non-general code
Implementation would require ugly branches or hard-to-understand recursive function calls */
/* Routine assumes weight will never have more dimensions than variable
(otherwise which hyperslab of weight to use would be ill-defined).
However, weight may (and often will) have fewer dimensions than variable */
nco_bool CONFORMABLE=False; /* [flg] wgt can be made to conform to var */
nco_bool USE_DUMMY_WGT=False; /* [flg] Fool NCO into thinking wgt conforms to var */
int idx; /* [idx] Counting index */
int idx_dmn; /* [idx] Dimension index */
int wgt_var_dmn_shr_nbr=0; /* [nbr] Number of dimensions wgt and var share */
var_sct *wgt_out=NULL;
/* Initialize flag to false. Overwrite by true after successful conformance */
*DO_CONFORM=False;
/* Does current weight (wgt_crr) conform to variable's dimensions? */
if(wgt_crr){
/* Test rank first because wgt_crr because of 19960218 bug (invalid dmn_id in old wgt_crr leads to match) */
if(var->nbr_dim == wgt_crr->nbr_dim){
/* Test whether all wgt and var dimensions match in sequence */
for(idx=0;idx<var->nbr_dim;idx++){
/* 20131002: nco_var_cnf_dmn() borken for groups as shown by dimension short-name strcmp() comparison here */
if(strcmp(wgt_crr->dim[idx]->nm,var->dim[idx]->nm)) break;
} /* end loop over dimensions */
if(idx == var->nbr_dim) *DO_CONFORM=True;
} /* end if ranks are equal */
/* 20060425: Weight re-use will not occur if wgt_crr is free()'d here
Some DDRA benchmarks need to know cost of broadcasting weights
To turn off weight re-use and cause broadcasting, execute "else" block below
by (temporarily) using
if(*DO_CONFORM && False){ ....instead of.... if(*DO_CONFORM){
in following condition */
if(*DO_CONFORM){
wgt_out=wgt_crr;
}else{
wgt_crr=nco_var_free(wgt_crr);
wgt_out=NULL;
} /* !*DO_CONFORM */
} /* wgt_crr == NULL */
/* Does original weight (wgt) conform to variable's dimensions? */
if(wgt_out == NULL){
if(var->nbr_dim > 0){
/* Test that all dimensions in wgt appear in var */
for(idx=0;idx<wgt->nbr_dim;idx++){
for(idx_dmn=0;idx_dmn<var->nbr_dim;idx_dmn++){
/* Compare names, not dimension IDs */
/* 20131002: nco_var_cnf_dmn() borken for groups as shown by dimension short-name strcmp() comparison here */
if(!strcmp(wgt->dim[idx]->nm,var->dim[idx_dmn]->nm)){
wgt_var_dmn_shr_nbr++; /* wgt and var share this dimension */
break;
} /* endif */
} /* end loop over var dimensions */
} /* end loop over wgt dimensions */
/* Decide whether wgt and var dimensions conform, are mutually exclusive, or are partially exclusive (an error) */
if(wgt_var_dmn_shr_nbr == wgt->nbr_dim){
/* wgt and var conform */
CONFORMABLE=True;
}else if(wgt_var_dmn_shr_nbr == 0){
/* Dimensions in wgt and var are mutually exclusive */
CONFORMABLE=False;
if(MUST_CONFORM){
(void)fprintf(stdout,"%s: ERROR %s and template %s share no dimensions\n",nco_prg_nm_get(),wgt->nm,var->nm);
nco_exit(EXIT_FAILURE);
}else{
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(stdout,"\n%s: DEBUG %s and template %s share no dimensions: Not broadcasting %s to %s\n",nco_prg_nm_get(),wgt->nm,var->nm,wgt->nm,var->nm);
USE_DUMMY_WGT=True;
} /* endif */
}else if(wgt->nbr_dim > var->nbr_dim){
/* wgt is larger rank than var---no possibility of conforming */
CONFORMABLE=False;
if(MUST_CONFORM){
(void)fprintf(stdout,"%s: ERROR %s is rank %d but template %s is rank %d: Impossible to broadcast\n",nco_prg_nm_get(),wgt->nm,wgt->nbr_dim,var->nm,var->nbr_dim);
nco_exit(EXIT_FAILURE);
}else{
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(stdout,"\n%s: DEBUG %s is rank %d but template %s is rank %d: Not broadcasting %s to %s\n",nco_prg_nm_get(),wgt->nm,wgt->nbr_dim,var->nm,var->nbr_dim,wgt->nm,var->nm);
USE_DUMMY_WGT=True;
} /* endif */
}else if(wgt_var_dmn_shr_nbr > 0 && wgt_var_dmn_shr_nbr < wgt->nbr_dim){
/* Some, but not all, of wgt dimensions are in var */
CONFORMABLE=False;
if(MUST_CONFORM){
(void)fprintf(stdout,"%s: ERROR %d dimensions of %s belong to template %s but %d dimensions do not\n",nco_prg_nm_get(),wgt_var_dmn_shr_nbr,wgt->nm,var->nm,wgt->nbr_dim-wgt_var_dmn_shr_nbr);
nco_exit(EXIT_FAILURE);
}else{
if(nco_dbg_lvl_get() >= nco_dbg_scl) (void)fprintf(stdout,"\n%s: DEBUG %d dimensions of %s belong to template %s but %d dimensions do not: Not broadcasting %s to %s\n",nco_prg_nm_get(),wgt_var_dmn_shr_nbr,wgt->nm,var->nm,wgt->nbr_dim-wgt_var_dmn_shr_nbr,wgt->nm,var->nm);
USE_DUMMY_WGT=True;
} /* endif */
} /* end if */
if(USE_DUMMY_WGT){
/* Variables do not truly conform, but this might be OK, depending on the application, so set DO_CONFORM flag to false and ... */
*DO_CONFORM=False;
/* ... return a dummy weight of 1.0, which allows program logic to pretend variable is weighted, but does not change answers */
wgt_out=nco_var_dpl(var);
(void)vec_set(wgt_out->type,wgt_out->sz,wgt_out->val,1.0);
} /* endif */
if(CONFORMABLE){
if(var->nbr_dim == wgt->nbr_dim){
/* var and wgt conform and are same rank */
/* Test whether all wgt and var dimensions match in sequence */
for(idx=0;idx<var->nbr_dim;idx++){
/* 20131002: nco_var_cnf_dmn() borken for groups as shown by dimension short-name strcmp() comparison here */
if(strcmp(wgt->dim[idx]->nm,var->dim[idx]->nm)) break;
/* if(wgt->dmn_id[idx] != var->dmn_id[idx]) break;*/
} /* end loop over dimensions */
/* If so, take shortcut and copy wgt to wgt_out */
if(idx == var->nbr_dim) *DO_CONFORM=True;
}else{
/* var and wgt conform but are not same rank, set flag to proceed to generic conform routine */
*DO_CONFORM=False;
} /* end else */
} /* endif CONFORMABLE */
}else{
/* var is scalar, if wgt is also then set flag to copy wgt to wgt_out else proceed to generic conform routine */
if(wgt->nbr_dim == 0) *DO_CONFORM=True; else *DO_CONFORM=False;
} /* end else */
if(CONFORMABLE && *DO_CONFORM){
wgt_out=nco_var_dpl(wgt);
(void)nco_xrf_var(wgt,wgt_out);
} /* end if */
} /* end if */
/* Set diagnostic DDRA information DDRA */
/* ddra_info->wgt_brd_flg=(wgt_out == NULL) ? True : False; *//* [flg] Broadcast weight for this variable */
if(wgt_out == NULL){
/* Expand original weight (wgt) to match size of current variable */
char * restrict wgt_cp;
char * restrict wgt_out_cp;
int idx_wgt_var[NC_MAX_DIMS];
int wgt_nbr_dim;
int var_nbr_dmn_m1;
long * restrict var_cnt;
long dmn_ss[NC_MAX_DIMS];
long dmn_var_map[NC_MAX_DIMS];
long dmn_wgt_map[NC_MAX_DIMS];
long var_lmn;
long wgt_lmn;
long var_sz;
size_t wgt_typ_sz;
/* Copy main attributes of variable into output weight */
wgt_out=nco_var_dpl(var);
(void)nco_xrf_var(wgt,wgt_out);
/* wgt_out variable was copied from template var
Modify key fields so its name and type are based on wgt, not var
wgt_out will then be hybrid between wgt and var
Remainder of routine fills wgt_out's var-dimensionality with wgt-values */
wgt_out->nm=(char *)nco_free(wgt_out->nm);
wgt_out->nm=(char *)strdup(wgt->nm);
wgt_out->id=wgt->id;
wgt_out->type=wgt->type;
wgt_out->val.vp=(void *)nco_free(wgt_out->val.vp);
wgt_out->val.vp=(void *)nco_malloc(wgt_out->sz*nco_typ_lng(wgt_out->type));
wgt_cp=(char *)wgt->val.vp;
wgt_out_cp=(char *)wgt_out->val.vp;
wgt_typ_sz=nco_typ_lng(wgt_out->type);
if(wgt_out->nbr_dim == 0){
/* Variable (and weight) are scalars, not arrays */
(void)memcpy(wgt_out_cp,wgt_cp,wgt_typ_sz);
}else if(wgt->nbr_dim == 0){
/* Lesser-ranked input variable is scalar
Expansion in this degenerate case needs no index juggling (reverse-mapping)
Code as special case to speed-up important applications of ncap
for synthetic file creation */
var_sz=var->sz;
for(var_lmn=0;var_lmn<var_sz;var_lmn++){
(void)memcpy(wgt_out_cp+var_lmn*wgt_typ_sz,wgt_cp,wgt_typ_sz);
} /* end loop over var_lmn */
}else{
/* Variable (and therefore wgt_out) are arrays, not scalars */
/* Create forward and reverse mappings from variable's dimensions to weight's dimensions:
dmn_var_map[i] is number of elements between one value of i_th
dimension of variable and next value of i_th dimension, i.e.,
number of elements in memory between indicial increments in i_th dimension.
This is computed as product of one (1) times size of all dimensions (if any) after i_th
dimension in variable.
dmn_wgt_map[i] contains analogous information, except for original weight variable
idx_wgt_var[i] contains index into variable's dimensions of i_th dimension of original weight
idx_var_wgt[i] contains index into original weight's dimensions of i_th dimension of variable
Since weight is a subset of variable, some elements of idx_var_wgt may be "empty", or unused
Since mapping arrays (dmn_var_map and dmn_wgt_map) are ultimately used for a
memcpy() operation, they could (read: should) be computed as byte offsets, not type offsets.
This is why netCDF generic hyperslab routines (ncvarputg(), ncvargetg())
request imap vector to specify offset (imap) vector in bytes. */
for(idx=0;idx<wgt->nbr_dim;idx++){
for(idx_dmn=0;idx_dmn<var->nbr_dim;idx_dmn++){
/* Compare names, not dimension IDs */
/* 20131002: nco_var_cnf_dmn() borken for groups as shown by dimension short-name strcmp() comparison here */
if(!strcmp(var->dim[idx_dmn]->nm,wgt->dim[idx]->nm)){
idx_wgt_var[idx]=idx_dmn;
break;
} /* end if */
/* Sanity check */
if(idx_dmn == var->nbr_dim-1){
(void)fprintf(stdout,"%s: ERROR wgt %s has dimension %s but var %s does not deep in nco_var_cnf_dmn()\n",nco_prg_nm_get(),wgt->nm,wgt->dim[idx]->nm,var->nm);
nco_exit(EXIT_FAILURE);
} /* end if err */
} /* end loop over variable dimensions */
} /* end loop over weight dimensions */
/* Figure out map for each dimension of variable */
for(idx=0;idx<var->nbr_dim;idx++) dmn_var_map[idx]=1L;
for(idx=0;idx<var->nbr_dim-1;idx++)
for(idx_dmn=idx+1;idx_dmn<var->nbr_dim;idx_dmn++)
dmn_var_map[idx]*=var->cnt[idx_dmn];
/* Figure out map for each dimension of weight */
for(idx=0;idx<wgt->nbr_dim;idx++) dmn_wgt_map[idx]=1L;
for(idx=0;idx<wgt->nbr_dim-1;idx++)
for(idx_dmn=idx+1;idx_dmn<wgt->nbr_dim;idx_dmn++)
dmn_wgt_map[idx]*=wgt->cnt[idx_dmn];
/* Define convenience variables to avoid repetitive indirect addressing */
wgt_nbr_dim=wgt->nbr_dim;
var_sz=var->sz;
var_cnt=var->cnt;
var_nbr_dmn_m1=var->nbr_dim-1;
/* var_lmn is offset into 1-D array corresponding to N-D indices dmn_ss */
for(var_lmn=0;var_lmn<var_sz;var_lmn++){
/* dmn_ss are corresponding indices (subscripts) into N-D array */
/* Operations: 1 modulo, 1 pointer offset, 1 user memory fetch
Repetitions: \lmnnbr
Total Counts: \rthnbr=2\lmnnbr, \mmrusrnbr=\lmnnbr
NB: LHS assumed compact and cached, counted RHS offsets and fetches only */
dmn_ss[var_nbr_dmn_m1]=var_lmn%var_cnt[var_nbr_dmn_m1];
for(idx=0;idx<var_nbr_dmn_m1;idx++){
/* Operations: 1 divide, 1 modulo, 2 pointer offset, 2 user memory fetch
Repetitions: \lmnnbr(\dmnnbr-1)
Counts: \rthnbr=4\lmnnbr(\dmnnbr-1), \mmrusrnbr=2\lmnnbr(\dmnnbr-1)
NB: LHS assumed compact and cached, counted RHS offsets and fetches only
NB: Neglected loop arithmetic/compare */
dmn_ss[idx]=(long int)(var_lmn/dmn_var_map[idx]);
dmn_ss[idx]%=var_cnt[idx];
} /* end loop over dimensions */
/* Map (shared) N-D array indices into 1-D index into original weight data */
wgt_lmn=0L;
/* Operations: 1 add, 1 multiply, 3 pointer offset, 3 user memory fetch
Repetitions: \lmnnbr\rnkwgt
Counts: \rthnbr=5\lmnnbr\rnkwgt, \mmrusrnbr=3\lmnnbr\rnkwgt */
for(idx=0;idx<wgt_nbr_dim;idx++) wgt_lmn+=dmn_ss[idx_wgt_var[idx]]*dmn_wgt_map[idx];
/* Operations: 2 add, 2 multiply, 0 pointer offset, 1 system memory copy
Repetitions: \lmnnbr
Counts: \rthnbr=4\lmnnbr, \mmrusrnbr=0, \mmrsysnbr=1 */
(void)memcpy(wgt_out_cp+var_lmn*wgt_typ_sz,wgt_cp+wgt_lmn*wgt_typ_sz,wgt_typ_sz);
} /* end loop over var_lmn */
} /* end if variable (and weight) are arrays, not scalars */
*DO_CONFORM=True;
} /* end if we had to stretch weight to fit variable */
int
main(int argc,char **argv)
{
aed_sct *aed_lst_add_fst=NULL_CEWI;
aed_sct *aed_lst_scl_fct=NULL_CEWI;
char **dmn_rdr_lst_in=NULL_CEWI; /* Option a */
char **fl_lst_abb=NULL; /* Option n */
char **fl_lst_in=NULL_CEWI;
char **gaa_arg=NULL; /* [sng] Global attribute arguments */
char **var_lst_in=NULL_CEWI;
char **grp_lst_in=NULL_CEWI;
char *aux_arg[NC_MAX_DIMS];
char *cmd_ln;
char *cnk_arg[NC_MAX_DIMS];
char *cnk_map_sng=NULL_CEWI; /* [sng] Chunking map */
char *cnk_plc_sng=NULL_CEWI; /* [sng] Chunking policy */
char *fl_in=NULL;
char *fl_out=NULL; /* Option o */
char *fl_out_tmp=NULL_CEWI;
char *fl_pth=NULL; /* Option p */
char *fl_pth_lcl=NULL; /* Option l */
char *lmt_arg[NC_MAX_DIMS];
char *nco_pck_plc_sng=NULL_CEWI; /* [sng] Packing policy Option P */
char *nco_pck_map_sng=NULL_CEWI; /* [sng] Packing map Option M */
char *opt_crr=NULL; /* [sng] String representation of current long-option name */
char *optarg_lcl; /* [sng] Local copy of system optarg */
char *ppc_arg[NC_MAX_VARS]; /* [sng] PPC arguments */
char *sng_cnv_rcd=NULL_CEWI; /* [sng] strtol()/strtoul() return code */
char add_fst_sng[]="add_offset"; /* [sng] Unidata standard string for add offset */
char scl_fct_sng[]="scale_factor"; /* [sng] Unidata standard string for scale factor */
char trv_pth[]="/"; /* [sng] Root path of traversal tree */
const char * const CVS_Id="$Id$";
const char * const CVS_Revision="$Revision$";
const char * const opt_sht_lst="3467Aa:CcD:d:Fg:G:hL:l:M:Oo:P:p:Rrt:v:UxZ-:";
cnk_sct cnk; /* [sct] Chunking structure */
#if defined(__cplusplus) || defined(PGI_CC)
ddra_info_sct ddra_info;
ddra_info.flg_ddra=False;
#else /* !__cplusplus */
ddra_info_sct ddra_info={.flg_ddra=False};
#endif /* !__cplusplus */
dmn_sct **dmn_rdr_trv=NULL; /* [sct] Dimension structures to be re-ordered (from global table) */
extern char *optarg;
extern int optind;
/* Using naked stdin/stdout/stderr in parallel region generates warning
Copy appropriate filehandle to variable scoped shared in parallel clause */
FILE * const fp_stderr=stderr; /* [fl] stderr filehandle CEWI */
FILE * const fp_stdout=stdout; /* [fl] stdout filehandle CEWI */
gpe_sct *gpe=NULL; /* [sng] Group Path Editing (GPE) structure */
int *in_id_arr;
int abb_arg_nbr=0;
int aux_nbr=0; /* [nbr] Number of auxiliary coordinate hyperslabs specified */
int cnk_map=nco_cnk_map_nil; /* [enm] Chunking map */
int cnk_nbr=0; /* [nbr] Number of chunk sizes */
int cnk_plc=nco_cnk_plc_nil; /* [enm] Chunking policy */
int dfl_lvl=NCO_DFL_LVL_UNDEFINED; /* [enm] Deflate level */
int dmn_rdr_nbr=0; /* [nbr] Number of dimension to re-order */
int dmn_rdr_nbr_trv=0; /* [nbr] Number of dimension to re-order (from global table) */
int dmn_rdr_nbr_in=0; /* [nbr] Original number of dimension to re-order */
int fl_idx=int_CEWI;
int fl_nbr=0;
int fl_in_fmt; /* [enm] Input file format */
int fl_out_fmt=NCO_FORMAT_UNDEFINED; /* [enm] Output file format */
int fll_md_old; /* [enm] Old fill mode */
int gaa_nbr=0; /* [nbr] Number of global attributes to add */
int idx=int_CEWI;
int idx_rdr=int_CEWI;
int in_id;
int lmt_nbr=0; /* Option d. NB: lmt_nbr gets incremented */
int md_open; /* [enm] Mode flag for nc_open() call */
int nbr_dmn_fl;
int nbr_var_fix; /* nbr_var_fix gets incremented */
int nbr_var_fl;
int nbr_var_prc; /* nbr_var_prc gets incremented */
int nco_pck_map=nco_pck_map_flt_sht; /* [enm] Packing map */
int nco_pck_plc=nco_pck_plc_nil; /* [enm] Packing policy */
int opt;
int out_id;
int ppc_nbr=0; /* [nbr] Number of PPC arguments */
int rcd=NC_NOERR; /* [rcd] Return code */
int thr_idx; /* [idx] Index of current thread */
int thr_nbr=int_CEWI; /* [nbr] Thread number Option t */
int xtr_nbr=0; /* xtr_nbr won't otherwise be set for -c with no -v */
int var_lst_in_nbr=0;
int grp_lst_in_nbr=0; /* [nbr] Number of groups explicitly specified by user */
md5_sct *md5=NULL; /* [sct] MD5 configuration */
nco_bool *dmn_rvr_rdr=NULL; /* [flg] Reverse dimensions */
nco_bool CNV_CCM_CCSM_CF;
nco_bool EXCLUDE_INPUT_LIST=False; /* Option c */
nco_bool EXTRACT_ALL_COORDINATES=False; /* Option c */
nco_bool EXTRACT_ASSOCIATED_COORDINATES=True; /* Option C */
nco_bool FL_RTR_RMT_LCN;
nco_bool FL_LST_IN_FROM_STDIN=False; /* [flg] fl_lst_in comes from stdin */
nco_bool FORCE_APPEND=False; /* Option A */
nco_bool FORCE_OVERWRITE=False; /* Option O */
nco_bool FORTRAN_IDX_CNV=False; /* Option F */
nco_bool GRP_VAR_UNN=False; /* [flg] Select union of specified groups and variables */
nco_bool HISTORY_APPEND=True; /* Option h */
nco_bool IS_REORDER=False; /* Re-order mode */
nco_bool MSA_USR_RDR=False; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order*/
nco_bool RAM_CREATE=False; /* [flg] Create file in RAM */
nco_bool RAM_OPEN=False; /* [flg] Open (netCDF3-only) file(s) in RAM */
nco_bool RM_RMT_FL_PST_PRC=True; /* Option R */
nco_bool WRT_TMP_FL=True; /* [flg] Write output to temporary file */
nco_bool flg_cln=True; /* [flg] Clean memory prior to exit */
nco_bool flg_dmn_prc_usr_spc=False; /* [flg] Processed dimensions specified on command line */
size_t bfr_sz_hnt=NC_SIZEHINT_DEFAULT; /* [B] Buffer size hint */
size_t cnk_min_byt=NCO_CNK_SZ_MIN_BYT_DFL; /* [B] Minimize size of variable to chunk */
size_t cnk_sz_byt=0UL; /* [B] Chunk size in bytes */
size_t cnk_sz_scl=0UL; /* [nbr] Chunk size scalar */
size_t hdr_pad=0UL; /* [B] Pad at end of header section */
var_sct **var;
var_sct **var_fix;
var_sct **var_fix_out;
var_sct **var_out;
var_sct **var_prc;
var_sct **var_prc_out;
trv_tbl_sct *trv_tbl=NULL; /* [lst] Traversal table */
nco_dmn_dne_t *flg_dne=NULL; /* [lst] Flag to check if input dimension -d "does not exist" */
#ifdef ENABLE_MPI
/* Declare all MPI-specific variables here */
MPI_Comm mpi_cmm=MPI_COMM_WORLD; /* [prc] Communicator */
int prc_rnk; /* [idx] Process rank */
int prc_nbr=0; /* [nbr] Number of MPI processes */
#endif /* !ENABLE_MPI */
static struct option opt_lng[]={ /* Structure ordered by short option key if possible */
/* Long options with no argument, no short option counterpart */
{"cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"clean",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"mmr_cln",no_argument,0,0}, /* [flg] Clean memory prior to exit */
{"drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"dirty",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"mmr_drt",no_argument,0,0}, /* [flg] Allow dirty memory on exit */
{"hdf4",no_argument,0,0}, /* [flg] Treat file as HDF4 */
{"hdf_upk",no_argument,0,0}, /* [flg] HDF unpack convention: unpacked=scale_factor*(packed-add_offset) */
{"hdf_unpack",no_argument,0,0}, /* [flg] HDF unpack convention: unpacked=scale_factor*(packed-add_offset) */
{"mrd",no_argument,0,0}, /* [enm] Multiple Record Dimension convention */
{"multiple_record_dimension",no_argument,0,0}, /* [enm] Multiple Record Dimension convention */
{"msa_usr_rdr",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"msa_user_order",no_argument,0,0}, /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
{"ram_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"create_ram",no_argument,0,0}, /* [flg] Create file in RAM */
{"open_ram",no_argument,0,0}, /* [flg] Open (netCDF3) file(s) in RAM */
{"diskless_all",no_argument,0,0}, /* [flg] Open (netCDF3) and create file(s) in RAM */
{"wrt_tmp_fl",no_argument,0,0}, /* [flg] Write output to temporary file */
{"write_tmp_fl",no_argument,0,0}, /* [flg] Write output to temporary file */
{"no_tmp_fl",no_argument,0,0}, /* [flg] Do not write output to temporary file */
{"intersection",no_argument,0,0}, /* [flg] Select intersection of specified groups and variables */
{"nsx",no_argument,0,0}, /* [flg] Select intersection of specified groups and variables */
{"union",no_argument,0,0}, /* [flg] Select union of specified groups and variables */
{"unn",no_argument,0,0}, /* [flg] Select union of specified groups and variables */
{"version",no_argument,0,0},
{"vrs",no_argument,0,0},
/* Long options with argument, no short option counterpart */
{"bfr_sz_hnt",required_argument,0,0}, /* [B] Buffer size hint */
{"buffer_size_hint",required_argument,0,0}, /* [B] Buffer size hint */
{"cnk_byt",required_argument,0,0}, /* [B] Chunk size in bytes */
{"chunk_byte",required_argument,0,0}, /* [B] Chunk size in bytes */
{"cnk_dmn",required_argument,0,0}, /* [nbr] Chunk size */
{"chunk_dimension",required_argument,0,0}, /* [nbr] Chunk size */
{"cnk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"chunk_map",required_argument,0,0}, /* [nbr] Chunking map */
{"cnk_min",required_argument,0,0}, /* [B] Minimize size of variable to chunk */
{"chunk_min",required_argument,0,0}, /* [B] Minimize size of variable to chunk */
{"cnk_plc",required_argument,0,0}, /* [nbr] Chunking policy */
{"chunk_policy",required_argument,0,0}, /* [nbr] Chunking policy */
{"cnk_scl",required_argument,0,0}, /* [nbr] Chunk size scalar */
{"chunk_scalar",required_argument,0,0}, /* [nbr] Chunk size scalar */
{"fl_fmt",required_argument,0,0},
{"file_format",required_argument,0,0},
{"gaa",required_argument,0,0}, /* [sng] Global attribute add */
{"glb_att_add",required_argument,0,0}, /* [sng] Global attribute add */
{"hdr_pad",required_argument,0,0},
{"header_pad",required_argument,0,0},
{"ppc",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
{"precision_preserving_compression",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
{"quantize",required_argument,0,0}, /* [nbr] Precision-preserving compression, i.e., number of total or decimal significant digits */
{"upk",required_argument,0,0}, /* [enm] Unpacking convention to utilize */
/* Long options with short counterparts */
{"3",no_argument,0,'3'},
{"4",no_argument,0,'4'},
{"64bit",no_argument,0,'4'},
{"netcdf4",no_argument,0,'4'},
{"append",no_argument,0,'A'},
{"arrange",required_argument,0,'a'},
{"permute",required_argument,0,'a'},
{"reorder",required_argument,0,'a'},
{"rdr",required_argument,0,'a'},
{"no-coords",no_argument,0,'C'},
{"no-crd",no_argument,0,'C'},
{"coords",no_argument,0,'c'},
{"crd",no_argument,0,'c'},
{"debug",required_argument,0,'D'},
{"nco_dbg_lvl",required_argument,0,'D'},
{"dimension",required_argument,0,'d'},
{"dmn",required_argument,0,'d'},
{"fortran",no_argument,0,'F'},
{"ftn",no_argument,0,'F'},
{"gpe",required_argument,0,'G'}, /* [sng] Group Path Edit (GPE) */
{"grp",required_argument,0,'g'},
{"group",required_argument,0,'g'},
{"history",no_argument,0,'h'},
{"hst",no_argument,0,'h'},
{"dfl_lvl",required_argument,0,'L'}, /* [enm] Deflate level */
{"deflate",required_argument,0,'L'}, /* [enm] Deflate level */
{"local",required_argument,0,'l'},
{"lcl",required_argument,0,'l'},
{"pack_map",required_argument,0,'M'},
{"pck_map",required_argument,0,'M'},
{"map",required_argument,0,'M'},
{"overwrite",no_argument,0,'O'},
{"ovr",no_argument,0,'O'},
{"output",required_argument,0,'o'},
{"fl_out",required_argument,0,'o'},
{"pack_policy",required_argument,0,'P'},
{"pck_plc",required_argument,0,'P'},
{"path",required_argument,0,'p'},
{"retain",no_argument,0,'R'},
{"rtn",no_argument,0,'R'},
{"revision",no_argument,0,'r'},
{"thr_nbr",required_argument,0,'t'},
{"threads",required_argument,0,'t'},
{"omp_num_threads",required_argument,0,'t'},
{"unpack",no_argument,0,'U'},
{"variable",required_argument,0,'v'},
{"auxiliary",required_argument,0,'X'},
{"exclude",no_argument,0,'x'},
{"xcl",no_argument,0,'x'},
{"help",no_argument,0,'?'},
{"hlp",no_argument,0,'?'},
{0,0,0,0}
}; /* end opt_lng */
int opt_idx=0; /* Index of current long option into opt_lng array */
/* Initialize traversal table */
trv_tbl_init(&trv_tbl);
/* Start timer and save command line */
ddra_info.tmr_flg=nco_tmr_srt;
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
ddra_info.tmr_flg=nco_tmr_mtd;
cmd_ln=nco_cmd_ln_sng(argc,argv);
/* Get program name and set program enum (e.g., nco_prg_id=ncra) */
nco_prg_nm=nco_prg_prs(argv[0],&nco_prg_id);
#ifdef ENABLE_MPI
/* MPI Initialization */
if(False) (void)fprintf(stdout,gettext("%s: WARNING Compiled with MPI\n"),nco_prg_nm);
MPI_Init(&argc,&argv);
MPI_Comm_size(mpi_cmm,&prc_nbr);
MPI_Comm_rank(mpi_cmm,&prc_rnk);
#endif /* !ENABLE_MPI */
/* Parse command line arguments */
while(1){
/* getopt_long_only() allows one dash to prefix long options */
opt=getopt_long(argc,argv,opt_sht_lst,opt_lng,&opt_idx);
/* NB: access to opt_crr is only valid when long_opt is detected */
if(opt == EOF) break; /* Parse positional arguments once getopt_long() returns EOF */
opt_crr=(char *)strdup(opt_lng[opt_idx].name);
/* Process long options without short option counterparts */
if(opt == 0){
if(!strcmp(opt_crr,"bfr_sz_hnt") || !strcmp(opt_crr,"buffer_size_hint")){
bfr_sz_hnt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_byt") || !strcmp(opt_crr,"chunk_byte")){
cnk_sz_byt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk_byt */
if(!strcmp(opt_crr,"cnk_min") || !strcmp(opt_crr,"chunk_min")){
cnk_min_byt=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk_min */
if(!strcmp(opt_crr,"cnk_dmn") || !strcmp(opt_crr,"chunk_dimension")){
/* Copy limit argument for later processing */
cnk_arg[cnk_nbr]=(char *)strdup(optarg);
cnk_nbr++;
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_scl") || !strcmp(opt_crr,"chunk_scalar")){
cnk_sz_scl=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_map") || !strcmp(opt_crr,"chunk_map")){
/* Chunking map */
cnk_map_sng=(char *)strdup(optarg);
cnk_map=nco_cnk_map_get(cnk_map_sng);
} /* endif cnk */
if(!strcmp(opt_crr,"cnk_plc") || !strcmp(opt_crr,"chunk_policy")){
/* Chunking policy */
cnk_plc_sng=(char *)strdup(optarg);
cnk_plc=nco_cnk_plc_get(cnk_plc_sng);
} /* endif cnk */
if(!strcmp(opt_crr,"cln") || !strcmp(opt_crr,"mmr_cln") || !strcmp(opt_crr,"clean")) flg_cln=True; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"drt") || !strcmp(opt_crr,"mmr_drt") || !strcmp(opt_crr,"dirty")) flg_cln=False; /* [flg] Clean memory prior to exit */
if(!strcmp(opt_crr,"fl_fmt") || !strcmp(opt_crr,"file_format")) rcd=nco_create_mode_prs(optarg,&fl_out_fmt);
if(!strcmp(opt_crr,"gaa") || !strcmp(opt_crr,"glb_att_add")){
gaa_arg=(char **)nco_realloc(gaa_arg,(gaa_nbr+1)*sizeof(char *));
gaa_arg[gaa_nbr++]=(char *)strdup(optarg);
} /* endif gaa */
if(!strcmp(opt_crr,"hdf4")) nco_fmt_xtn=nco_fmt_xtn_hdf4; /* [enm] Treat file as HDF4 */
if(!strcmp(opt_crr,"hdf_upk") || !strcmp(opt_crr,"hdf_unpack")) nco_upk_cnv=nco_upk_HDF_MOD10; /* [flg] HDF unpack convention: unpacked=scale_factor*(packed-add_offset) */
if(!strcmp(opt_crr,"hdr_pad") || !strcmp(opt_crr,"header_pad")){
hdr_pad=strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
} /* endif "hdr_pad" */
if(!strcmp(opt_crr,"ppc") || !strcmp(opt_crr,"precision_preserving_compression") || !strcmp(opt_crr,"quantize")){
ppc_arg[ppc_nbr]=(char *)strdup(optarg);
ppc_nbr++;
} /* endif "ppc" */
if(!strcmp(opt_crr,"mrd") || !strcmp(opt_crr,"multiple_record_dimension")) nco_mrd_cnv=nco_mrd_allow; /* [enm] Multiple Record Dimension convention */
if(!strcmp(opt_crr,"msa_usr_rdr") || !strcmp(opt_crr,"msa_user_order")) MSA_USR_RDR=True; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"create_ram") || !strcmp(opt_crr,"diskless_all")) RAM_CREATE=True; /* [flg] Open (netCDF3) file(s) in RAM */
if(!strcmp(opt_crr,"ram_all") || !strcmp(opt_crr,"open_ram") || !strcmp(opt_crr,"diskless_all")) RAM_OPEN=True; /* [flg] Create file in RAM */
if(!strcmp(opt_crr,"unn") || !strcmp(opt_crr,"union")) GRP_VAR_UNN=True;
if(!strcmp(opt_crr,"nsx") || !strcmp(opt_crr,"intersection")) GRP_VAR_UNN=False;
if(!strcmp(opt_crr,"upk")){ /* [enm] Unpacking convention to utilize */
nco_upk_cnv=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
} /* endif "hdr_pad" */
if(!strcmp(opt_crr,"vrs") || !strcmp(opt_crr,"version")){
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
nco_exit(EXIT_SUCCESS);
} /* endif "vrs" */
if(!strcmp(opt_crr,"wrt_tmp_fl") || !strcmp(opt_crr,"write_tmp_fl")) WRT_TMP_FL=True;
if(!strcmp(opt_crr,"no_tmp_fl")) WRT_TMP_FL=False;
} /* opt != 0 */
/* Process short options */
switch(opt){
case 0: /* Long options have already been processed, return */
break;
case '3': /* Request netCDF3 output storage format */
fl_out_fmt=NC_FORMAT_CLASSIC;
break;
case '4': /* Catch-all to prescribe output storage format */
if(!strcmp(opt_crr,"64bit")) fl_out_fmt=NC_FORMAT_64BIT; else fl_out_fmt=NC_FORMAT_NETCDF4;
break;
case '6': /* Request netCDF3 64-bit offset output storage format */
fl_out_fmt=NC_FORMAT_64BIT;
break;
case '7': /* Request netCDF4-classic output storage format */
fl_out_fmt=NC_FORMAT_NETCDF4_CLASSIC;
break;
case 'A': /* Toggle FORCE_APPEND */
FORCE_APPEND=!FORCE_APPEND;
break;
case 'a': /* Re-order dimensions */
flg_dmn_prc_usr_spc=True;
dmn_rdr_lst_in=nco_lst_prs_2D(optarg,",",&dmn_rdr_nbr_in);
dmn_rdr_nbr=dmn_rdr_nbr_in;
break;
case 'C': /* Extract all coordinates associated with extracted variables? */
EXTRACT_ASSOCIATED_COORDINATES=False;
break;
case 'c':
EXTRACT_ALL_COORDINATES=True;
break;
case 'D': /* Debugging level. Default is 0. */
nco_dbg_lvl=(unsigned short int)strtoul(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtoul",sng_cnv_rcd);
nc_set_log_level(nco_dbg_lvl);
break;
case 'd': /* Copy limit argument for later processing */
lmt_arg[lmt_nbr]=(char *)strdup(optarg);
lmt_nbr++;
break;
case 'F': /* Toggle index convention. Default is 0-based arrays (C-style). */
FORTRAN_IDX_CNV=!FORTRAN_IDX_CNV;
break;
case 'G': /* Apply Group Path Editing (GPE) to output group */
/* NB: GNU getopt() optional argument syntax is ugly (requires "=" sign) so avoid it
http://stackoverflow.com/questions/1052746/getopt-does-not-parse-optional-arguments-to-parameters */
gpe=nco_gpe_prs_arg(optarg);
fl_out_fmt=NC_FORMAT_NETCDF4;
break;
case 'g': /* Copy group argument for later processing */
/* Replace commas with hashes when within braces (convert back later) */
optarg_lcl=(char *)strdup(optarg);
(void)nco_rx_comma2hash(optarg_lcl);
grp_lst_in=nco_lst_prs_2D(optarg_lcl,",",&grp_lst_in_nbr);
optarg_lcl=(char *)nco_free(optarg_lcl);
break;
case 'h': /* Toggle appending to history global attribute */
HISTORY_APPEND=!HISTORY_APPEND;
break;
case 'L': /* [enm] Deflate level. Default is 0. */
dfl_lvl=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
break;
case 'l': /* Local path prefix for files retrieved from remote file system */
fl_pth_lcl=(char *)strdup(optarg);
break;
case 'M': /* Packing map */
nco_pck_map_sng=(char *)strdup(optarg);
nco_pck_map=nco_pck_map_get(nco_pck_map_sng);
break;
case 'O': /* Toggle FORCE_OVERWRITE */
FORCE_OVERWRITE=!FORCE_OVERWRITE;
break;
case 'o': /* Name of output file */
fl_out=(char *)strdup(optarg);
break;
case 'P': /* Packing policy */
nco_pck_plc_sng=(char *)strdup(optarg);
break;
case 'p': /* Common file path */
fl_pth=(char *)strdup(optarg);
break;
case 'R': /* Toggle removal of remotely-retrieved-files. Default is True. */
RM_RMT_FL_PST_PRC=!RM_RMT_FL_PST_PRC;
break;
case 'r': /* Print CVS program information and copyright notice */
(void)nco_vrs_prn(CVS_Id,CVS_Revision);
(void)nco_lbr_vrs_prn();
(void)nco_cpy_prn();
(void)nco_cnf_prn();
nco_exit(EXIT_SUCCESS);
break;
case 't': /* Thread number */
thr_nbr=(int)strtol(optarg,&sng_cnv_rcd,NCO_SNG_CNV_BASE10);
if(*sng_cnv_rcd) nco_sng_cnv_err(optarg,"strtol",sng_cnv_rcd);
break;
case 'U': /* Unpacking switch */
nco_pck_plc_sng=(char *)strdup("upk");
break;
case 'v': /* Variables to extract/exclude */
/* Replace commas with hashes when within braces (convert back later) */
optarg_lcl=(char *)strdup(optarg);
(void)nco_rx_comma2hash(optarg_lcl);
var_lst_in=nco_lst_prs_2D(optarg_lcl,",",&var_lst_in_nbr);
optarg_lcl=(char *)nco_free(optarg_lcl);
xtr_nbr=var_lst_in_nbr;
break;
case 'X': /* Copy auxiliary coordinate argument for later processing */
aux_arg[aux_nbr]=(char *)strdup(optarg);
aux_nbr++;
MSA_USR_RDR=True; /* [flg] Multi-Slab Algorithm returns hyperslabs in user-specified order */
break;
case 'x': /* Exclude rather than extract variables specified with -v */
EXCLUDE_INPUT_LIST=True;
break;
case '?': /* Print proper usage */
(void)nco_usg_prn();
nco_exit(EXIT_SUCCESS);
break;
case '-': /* Long options are not allowed */
(void)fprintf(stderr,"%s: ERROR Long options are not available in this build. Use single letter options instead.\n",nco_prg_nm_get());
nco_exit(EXIT_FAILURE);
break;
default: /* Print proper usage */
(void)fprintf(stdout,"%s ERROR in command-line syntax/options. Please reformulate command accordingly.\n",nco_prg_nm_get());
(void)nco_usg_prn();
nco_exit(EXIT_FAILURE);
break;
} /* end switch */
if(opt_crr) opt_crr=(char *)nco_free(opt_crr);
} /* end while loop */
/* Set re-order flag */
if(dmn_rdr_nbr > 0) IS_REORDER=True;
/* No re-order dimensions specified implies packing request */
if(dmn_rdr_nbr == 0){
if(nco_pck_plc == nco_pck_plc_nil) nco_pck_plc=nco_pck_plc_get(nco_pck_plc_sng);
if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(stderr,"%s: DEBUG Packing map is %s and packing policy is %s\n",nco_prg_nm_get(),nco_pck_map_sng_get(nco_pck_map),nco_pck_plc_sng_get(nco_pck_plc));
} /* dmn_rdr_nbr != 0 */
/* From this point forward, assume ncpdq operator packs or re-orders, not both */
if(dmn_rdr_nbr > 0 && nco_pck_plc != nco_pck_plc_nil){
(void)fprintf(fp_stdout,"%s: ERROR %s does not support simultaneous dimension re-ordering (-a switch) and packing (-P switch).\nHINT: Invoke %s twice, once to re-order (with -a), and once to pack (with -P).\n",nco_prg_nm,nco_prg_nm,nco_prg_nm);
nco_exit(EXIT_FAILURE);
} /* endif */
/* Process positional arguments and fill in filenames */
fl_lst_in=nco_fl_lst_mk(argv,argc,optind,&fl_nbr,&fl_out,&FL_LST_IN_FROM_STDIN);
/* Initialize thread information */
thr_nbr=nco_openmp_ini(thr_nbr);
in_id_arr=(int *)nco_malloc(thr_nbr*sizeof(int));
/* Parse filename */
fl_in=nco_fl_nm_prs(fl_in,0,&fl_nbr,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
/* Make sure file is on local system and is readable or die trying */
fl_in=nco_fl_mk_lcl(fl_in,fl_pth_lcl,&FL_RTR_RMT_LCN);
/* Open file using appropriate buffer size hints and verbosity */
if(RAM_OPEN) md_open=NC_NOWRITE|NC_DISKLESS; else md_open=NC_NOWRITE;
rcd+=nco_fl_open(fl_in,md_open,&bfr_sz_hnt,&in_id);
/* Get file format */
(void)nco_inq_format(in_id,&fl_in_fmt);
/* Construct GTT, Group Traversal Table (groups,variables,dimensions, limits) */
(void)nco_bld_trv_tbl(in_id,trv_pth,lmt_nbr,lmt_arg,aux_nbr,aux_arg,MSA_USR_RDR,FORTRAN_IDX_CNV,grp_lst_in,grp_lst_in_nbr,var_lst_in,xtr_nbr,EXTRACT_ALL_COORDINATES,GRP_VAR_UNN,False,EXCLUDE_INPUT_LIST,EXTRACT_ASSOCIATED_COORDINATES,nco_pck_plc_nil,&flg_dne,trv_tbl);
/* Were all user-specified dimensions found? */
(void)nco_chk_dmn(lmt_nbr,flg_dne);
/* Create reversed dimension list */
if(dmn_rdr_nbr_in > 0){
dmn_rvr_rdr=(nco_bool *)nco_malloc(dmn_rdr_nbr_in*sizeof(nco_bool));
/* Is dimension to be reversed? i.e., does string begin with minus-sign '-'? */
for(idx_rdr=0;idx_rdr<dmn_rdr_nbr_in;idx_rdr++){
if(dmn_rdr_lst_in[idx_rdr][0] == '-'){
dmn_rvr_rdr[idx_rdr]=True;
/* Strip-out '-': Copy string to new memory one past negative sign to avoid losing byte */
optarg_lcl=dmn_rdr_lst_in[idx_rdr];
dmn_rdr_lst_in[idx_rdr]=(char *)strdup(optarg_lcl+1L);
optarg_lcl=(char *)nco_free(optarg_lcl);
}else{
dmn_rvr_rdr[idx_rdr]=False;
} /* !'-' */
} /* !idx_rdr */
} /* !dmn_rdr_nbr_in */
/* Get number of variables, dimensions, and global attributes in file, file format */
(void)trv_tbl_inq((int *)NULL,(int *)NULL,(int *)NULL,&nbr_dmn_fl,(int *)NULL,(int *)NULL,(int *)NULL,(int *)NULL,&nbr_var_fl,trv_tbl);
/* Create list of dimensions to average(ncwa)/re-order(ncpdq) */
if(IS_REORDER) (void)nco_dmn_avg_mk(in_id,dmn_rdr_lst_in,dmn_rdr_nbr_in,flg_dmn_prc_usr_spc,False,trv_tbl,&dmn_rdr_trv,&dmn_rdr_nbr_trv);
/* Fill-in variable structure list for all extracted variables */
var=nco_fll_var_trv(in_id,&xtr_nbr,trv_tbl);
/* Duplicate to output array */
var_out=(var_sct **)nco_malloc(xtr_nbr*sizeof(var_sct *));
for(idx=0;idx<xtr_nbr;idx++){
var_out[idx]=nco_var_dpl(var[idx]);
(void)nco_xrf_var(var[idx],var_out[idx]);
(void)nco_xrf_dmn(var_out[idx]);
} /* end loop over variables */
/* Refresh var_out with dim_out data */
(void)nco_var_dmn_refresh(var_out,xtr_nbr);
/* Is this a CCM/CCSM/CF-format history tape? */
CNV_CCM_CCSM_CF=nco_cnv_ccm_ccsm_cf_inq(in_id);
/* Divide variable lists into lists of fixed variables and variables to be processed */
(void)nco_var_lst_dvd(var,var_out,xtr_nbr,CNV_CCM_CCSM_CF,True,nco_pck_map,nco_pck_plc,dmn_rdr_trv,dmn_rdr_nbr_trv,&var_fix,&var_fix_out,&nbr_var_fix,&var_prc,&var_prc_out,&nbr_var_prc,trv_tbl);
/* Store processed and fixed variables info into GTT */
(void)nco_var_prc_fix_trv(nbr_var_prc,var_prc,nbr_var_fix,var_fix,trv_tbl);
/* We now have final list of variables to extract. Phew. */
/* Make output and input files consanguinous */
if(fl_out_fmt == NCO_FORMAT_UNDEFINED) fl_out_fmt=fl_in_fmt;
/* Initialize, decode, and set PPC information */
if(ppc_nbr > 0) nco_ppc_ini(in_id,&dfl_lvl,fl_out_fmt,ppc_arg,ppc_nbr,trv_tbl);
/* Verify output file format supports requested actions */
(void)nco_fl_fmt_vet(fl_out_fmt,cnk_nbr,dfl_lvl);
/* Open output file */
fl_out_tmp=nco_fl_out_open(fl_out,&FORCE_APPEND,FORCE_OVERWRITE,fl_out_fmt,&bfr_sz_hnt,RAM_CREATE,RAM_OPEN,WRT_TMP_FL,&out_id);
/* Initialize chunking from user-specified inputs */
if(fl_out_fmt == NC_FORMAT_NETCDF4 || fl_out_fmt == NC_FORMAT_NETCDF4_CLASSIC) rcd+=nco_cnk_ini(in_id,fl_out,cnk_arg,cnk_nbr,cnk_map,cnk_plc,cnk_min_byt,cnk_sz_byt,cnk_sz_scl,&cnk);
if(IS_REORDER){
dmn_sct **dmn_rdr=NULL; /* [sct] Dimension structures to be re-ordered */
/* "dmn_rdr" is only used for input to function nco_var_dmn_rdr_mtd(), that compares dimensions by short name;
this is because the input list of -a are dimension short names; group support is obtained combining with -g option;
on input it contains a list of dimension short names (in "dmn_rdr"), that together with input array "dmn_rvr_rdr"
of flags that determine if dimension at index dmn_rvr_rdr[index] is to be reversed; use cases:
in_grp_8.nc contains the dimensions /g1/lat, /g1/lon, /g2/lat, /g2/lon
ncpdq -O -v lat,lon -a -lat,-lon -g g1,g2 ~/nco/data/in_grp_8.nc out1.nc
"dmn_rdr" contains names ["lat"], ["lon"], striped of '-' (minus) sign and dmn_rvr_rdr contains [True],[True ]
output is reversed /g1/lat, /g1/lon, /g2/lat, /g2/lon
ncpdq -O -v lat,lon -a lat,-lon -g g1,g2 ~/nco/data/in_grp_8.nc out1.nc
"dmn_rdr" contains names ["lat"], ["lon"], and dmn_rvr_rdr contains [False],[True ]
output is reversed /g1/lon, /g2/lon */
/* Form list of re-ordering dimensions from extracted input dimensions */
dmn_rdr=(dmn_sct **)nco_malloc(dmn_rdr_nbr*sizeof(dmn_sct *));
/* Initialize re-ordering dimensions; initialize only short name */
for(idx_rdr=0;idx_rdr<dmn_rdr_nbr_in;idx_rdr++){
dmn_rdr[idx_rdr]=(dmn_sct *)nco_malloc(sizeof(dmn_sct));
dmn_rdr[idx_rdr]->nm=(char *)strdup(dmn_rdr_lst_in[idx_rdr]);
dmn_rdr[idx_rdr]->nm_fll=NULL;
dmn_rdr[idx_rdr]->id=-1;
}
/* Determine and set new dimensionality in metadata of each re-ordered variable */
(void)nco_var_dmn_rdr_mtd_trv(trv_tbl,nbr_var_prc,var_prc,var_prc_out,nbr_var_fix,var_fix,dmn_rdr,dmn_rdr_nbr,dmn_rvr_rdr);
for(idx_rdr=0; idx_rdr<dmn_rdr_nbr_in; idx_rdr++){
dmn_rdr[idx_rdr]->nm=(char *)nco_free(dmn_rdr[idx_rdr]->nm);
dmn_rdr[idx_rdr]=(dmn_sct *)nco_free(dmn_rdr[idx_rdr]);
}
dmn_rdr=(dmn_sct **)nco_free(dmn_rdr);
} /* IS_REORDER */
/* Alter metadata for variables that will be packed */
if(nco_pck_plc != nco_pck_plc_nil){
if(nco_pck_plc != nco_pck_plc_upk){
/* Allocate attribute list container for maximum number of entries */
aed_lst_add_fst=(aed_sct *)nco_malloc(nbr_var_prc*sizeof(aed_sct));
aed_lst_scl_fct=(aed_sct *)nco_malloc(nbr_var_prc*sizeof(aed_sct));
} /* endif packing */
for(idx=0;idx<nbr_var_prc;idx++){
nco_pck_mtd(var_prc[idx],var_prc_out[idx],nco_pck_map,nco_pck_plc);
if(nco_pck_plc != nco_pck_plc_upk){
/* Use same copy of attribute name for all edits */
aed_lst_add_fst[idx].att_nm=add_fst_sng;
aed_lst_scl_fct[idx].att_nm=scl_fct_sng;
} /* endif packing */
} /* end loop over var_prc */
/* Transfer variable type to table. NB: Use processed variables set with new type. MUST be done before definition */
(void)nco_var_typ_trv(nbr_var_prc,var_prc_out,trv_tbl);
} /* nco_pck_plc == nco_pck_plc_nil */
/* Define dimensions, extracted groups, variables, and attributes in output file. NB: record name is NULL */
(void)nco_xtr_dfn(in_id,out_id,&cnk,dfl_lvl,gpe,md5,!FORCE_APPEND,True,False,nco_pck_plc,(char *)NULL,trv_tbl);
/* Catenate time-stamped command line to "history" global attribute */
if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln);
if(HISTORY_APPEND && FORCE_APPEND) (void)nco_prv_att_cat(fl_in,in_id,out_id);
if(gaa_nbr > 0) (void)nco_glb_att_add(out_id,gaa_arg,gaa_nbr);
if(HISTORY_APPEND) (void)nco_vrs_att_cat(out_id);
if(thr_nbr > 0 && HISTORY_APPEND) (void)nco_thr_att_cat(out_id,thr_nbr);
/* Turn-off default filling behavior to enhance efficiency */
nco_set_fill(out_id,NC_NOFILL,&fll_md_old);
/* Take output file out of define mode */
if(hdr_pad == 0UL){
(void)nco_enddef(out_id);
}else{
(void)nco__enddef(out_id,hdr_pad);
if(nco_dbg_lvl >= nco_dbg_scl) (void)fprintf(stderr,"%s: INFO Padding header with %lu extra bytes\n",nco_prg_nm_get(),(unsigned long)hdr_pad);
} /* hdr_pad */
/* Assign zero to start and unity to stride vectors in output variables */
(void)nco_var_srd_srt_set(var_out,xtr_nbr);
/* Copy variable data for non-processed variables */
(void)nco_cpy_fix_var_trv(in_id,out_id,gpe,trv_tbl);
/* Close first input netCDF file */
nco_close(in_id);
/* Loop over input files (not currently used, fl_nbr == 1) */
for(fl_idx=0;fl_idx<fl_nbr;fl_idx++){
/* Parse filename */
if(fl_idx != 0) fl_in=nco_fl_nm_prs(fl_in,fl_idx,&fl_nbr,fl_lst_in,abb_arg_nbr,fl_lst_abb,fl_pth);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"%s: INFO Input file %d is %s",nco_prg_nm_get(),fl_idx,fl_in);
/* Make sure file is on local system and is readable or die trying */
if(fl_idx != 0) fl_in=nco_fl_mk_lcl(fl_in,fl_pth_lcl,&FL_RTR_RMT_LCN);
if(nco_dbg_lvl >= nco_dbg_fl && FL_RTR_RMT_LCN) (void)fprintf(stderr,", local file is %s",fl_in);
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(stderr,"\n");
/* Open file once per thread to improve caching */
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) rcd+=nco_fl_open(fl_in,md_open,&bfr_sz_hnt,in_id_arr+thr_idx);
/* Timestamp end of metadata setup and disk layout */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
ddra_info.tmr_flg=nco_tmr_rgl;
#ifdef _OPENMP
#pragma omp parallel for default(none) private(idx,in_id) shared(aed_lst_add_fst,aed_lst_scl_fct,nco_dbg_lvl,dmn_rdr_nbr,gpe,in_id_arr,nbr_var_prc,nco_pck_map,nco_pck_plc,out_id,nco_prg_nm,rcd,var_prc,var_prc_out,nbr_dmn_fl,trv_tbl,IS_REORDER,fl_out_fmt)
#endif /* !_OPENMP */
/* Process all variables in current file */
for(idx=0;idx<nbr_var_prc;idx++){
char *grp_out_fll=NULL; /* [sng] Group name */
int grp_out_id; /* [ID] Group ID (output) */
int var_out_id; /* [ID] Variable ID (output) */
trv_sct *var_trv; /* [sct] Variable GTT object */
in_id=in_id_arr[omp_get_thread_num()];
var_prc[idx]->nc_id=in_id;
if(nco_dbg_lvl >= nco_dbg_var) rcd+=nco_var_prc_crr_prn(idx,var_prc[idx]->nm);
if(nco_dbg_lvl >= nco_dbg_var) (void)fflush(fp_stderr);
/* Obtain variable GTT object using full variable name */
var_trv=trv_tbl_var_nm_fll(var_prc[idx]->nm_fll,trv_tbl);
/* Retrieve variable from disk into memory */
(void)nco_msa_var_get_trv(in_id,var_prc[idx],trv_tbl);
/* If re-ordering */
if(IS_REORDER){
if((var_prc_out[idx]->val.vp=(void *)nco_malloc_flg(var_prc_out[idx]->sz*nco_typ_lng(var_prc_out[idx]->type))) == NULL){
(void)fprintf(fp_stdout,"%s: ERROR Unable to malloc() %ld*%lu bytes for value buffer for variable %s in main()\n",nco_prg_nm_get(),var_prc_out[idx]->sz,(unsigned long)nco_typ_lng(var_prc_out[idx]->type),var_prc_out[idx]->nm);
nco_exit(EXIT_FAILURE);
} /* endif err */
/* Change dimensionionality of values */
(void)nco_var_dmn_rdr_val_trv(var_prc[idx],var_prc_out[idx],trv_tbl);
/* Re-ordering required two value buffers, time to free() input buffer */
var_prc[idx]->val.vp=nco_free(var_prc[idx]->val.vp);
} /* IS_REORDER */
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
/* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
if(grp_out_fll) grp_out_fll=(char *)nco_free(grp_out_fll);
/* Get variable ID */
(void)nco_inq_varid(grp_out_id,var_trv->nm,&var_out_id);
/* Store the output variable ID */
var_prc_out[idx]->id=var_out_id;
if(nco_pck_plc != nco_pck_plc_nil){
/* Copy input variable buffer to processed variable buffer */
/* fxm: this is dangerous and leads to double free()'ing variable buffer */
var_prc_out[idx]->val=var_prc[idx]->val;
/* (Un-)Pack variable according to packing specification */
nco_pck_val(var_prc[idx],var_prc_out[idx],nco_pck_map,nco_pck_plc,aed_lst_add_fst+idx,aed_lst_scl_fct+idx);
} /* endif nco_pck_plc != nco_pck_plc_nil */
if(var_trv->ppc != NC_MAX_INT){
if(var_trv->flg_nsd) (void)nco_ppc_bitmask(var_trv->ppc, var_prc_out[idx]->type, var_prc_out[idx]->sz, var_prc_out[idx]->has_mss_val, var_prc_out[idx]->mss_val, var_prc_out[idx]->val); else (void)nco_ppc_around(var_trv->ppc, var_prc_out[idx]->type, var_prc_out[idx]->sz, var_prc_out[idx]->has_mss_val, var_prc_out[idx]->mss_val, var_prc_out[idx]->val);
} /* endif ppc */
if(nco_is_xcp(var_trv->nm)) nco_xcp_prc(var_trv->nm,var_prc_out[idx]->type,var_prc_out[idx]->sz,(char *)var_prc_out[idx]->val.vp);
#ifdef _OPENMP
#pragma omp critical
#endif /* _OPENMP */
{ /* begin OpenMP critical */
/* Copy variable to output file then free value buffer */
if(var_prc_out[idx]->nbr_dim == 0){
(void)nco_put_var1(grp_out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc_out[idx]->val.vp,var_prc_out[idx]->type);
}else{ /* end if variable is scalar */
(void)nco_put_vara(grp_out_id,var_prc_out[idx]->id,var_prc_out[idx]->srt,var_prc_out[idx]->cnt,var_prc_out[idx]->val.vp,var_prc_out[idx]->type);
} /* end if variable is array */
} /* end OpenMP critical */
/* Free current output buffer */
var_prc_out[idx]->val.vp=nco_free(var_prc_out[idx]->val.vp);
} /* end (OpenMP parallel for) loop over idx */
if(nco_dbg_lvl >= nco_dbg_fl) (void)fprintf(fp_stderr,"\n");
/* Write/overwrite packing attributes for newly packed and re-packed variables
Logic here should nearly mimic logic in nco_var_dfn() */
if(nco_pck_plc != nco_pck_plc_nil && nco_pck_plc != nco_pck_plc_upk){
/* ...put file in define mode to allow metadata writing... */
(void)nco_redef(out_id);
/* ...loop through all variables that may have been packed... */
for(idx=0;idx<nbr_var_prc;idx++){
char *grp_out_fll=NULL; /* [sng] Group name */
int grp_out_id; /* [ID] Group ID (output) */
int var_out_id; /* [ID] Variable ID (output) */
trv_sct *var_trv; /* [sct] Variable GTT object */
/* Obtain variable GTT object using full variable name */
var_trv=trv_tbl_var_nm_fll(var_prc[idx]->nm_fll,trv_tbl);
/* Edit group name for output */
if(gpe) grp_out_fll=nco_gpe_evl(gpe,var_trv->grp_nm_fll); else grp_out_fll=(char *)strdup(var_trv->grp_nm_fll);
/* Obtain output group ID */
(void)nco_inq_grp_full_ncid(out_id,grp_out_fll,&grp_out_id);
/* Memory management after current extracted group */
if(grp_out_fll) grp_out_fll=(char *)nco_free(grp_out_fll);
/* Get variable ID */
(void)nco_inq_varid(grp_out_id,var_trv->nm,&var_out_id);
/* nco_var_dfn() pre-defined dummy packing attributes in output file only for "packable" input variables */
if(nco_pck_plc_typ_get(nco_pck_map,var_prc[idx]->typ_upk,(nc_type *)NULL)){
/* Verify input variable was newly packed by this operator
Writing pre-existing (non-re-packed) attributes here would fail because
nco_pck_dsk_inq() never fills in var->scl_fct.vp and var->add_fst.vp
Logic is same as in nco_var_dfn() (except var_prc[] instead of var[])
If operator newly packed this particular variable... */
if(
/* ...either because operator newly packs all variables... */
(nco_pck_plc == nco_pck_plc_all_new_att) ||
/* ...or because operator newly packs un-packed variables like this one... */
(nco_pck_plc == nco_pck_plc_all_xst_att && !var_prc[idx]->pck_ram) ||
/* ...or because operator re-packs packed variables like this one... */
(nco_pck_plc == nco_pck_plc_xst_new_att && var_prc[idx]->pck_ram)
){
/* Replace dummy packing attributes with final values, or delete them */
if(nco_dbg_lvl >= nco_dbg_io) (void)fprintf(stderr,"%s: main() replacing dummy packing attribute values for variable %s\n",nco_prg_nm,var_prc[idx]->nm);
(void)nco_aed_prc(grp_out_id,aed_lst_add_fst[idx].id,aed_lst_add_fst[idx]);
(void)nco_aed_prc(grp_out_id,aed_lst_scl_fct[idx].id,aed_lst_scl_fct[idx]);
} /* endif variable is newly packed by this operator */
} /* !nco_pck_plc_alw */
} /* end loop over var_prc */
/* Take output file out of define mode */
if(hdr_pad == 0UL) (void)nco_enddef(out_id); else (void)nco__enddef(out_id,hdr_pad);
} /* nco_pck_plc == nco_pck_plc_nil || nco_pck_plc == nco_pck_plc_upk */
/* Close input netCDF file */
for(thr_idx=0;thr_idx<thr_nbr;thr_idx++) nco_close(in_id_arr[thr_idx]);
/* Remove local copy of file */
if(FL_RTR_RMT_LCN && RM_RMT_FL_PST_PRC) (void)nco_fl_rm(fl_in);
} /* end loop over fl_idx */
/* Close output file and move it from temporary to permanent location */
(void)nco_fl_out_cls(fl_out,fl_out_tmp,out_id);
/* Clean memory unless dirty memory allowed */
if(flg_cln){
/* ncpdq-specific memory cleanup */
if(dmn_rdr_nbr > 0){
if(dmn_rdr_nbr_in > 0) dmn_rdr_lst_in=nco_sng_lst_free(dmn_rdr_lst_in,dmn_rdr_nbr_in);
dmn_rvr_rdr=(nco_bool *)nco_free(dmn_rvr_rdr);
/* Free dimension list pointers */
for(idx_rdr=0; idx_rdr<dmn_rdr_nbr_trv; idx_rdr++){
dmn_rdr_trv[idx_rdr]->nm=(char *)nco_free(dmn_rdr_trv[idx_rdr]->nm);
dmn_rdr_trv[idx_rdr]->nm_fll=(char *)nco_free(dmn_rdr_trv[idx_rdr]->nm_fll);
dmn_rdr_trv[idx_rdr]=(dmn_sct *)nco_free(dmn_rdr_trv[idx_rdr]);
}
dmn_rdr_trv=(dmn_sct **)nco_free(dmn_rdr_trv);
/* Dimension structures in dmn_rdr are owned by dmn and dmn_out, free'd later */
} /* endif dmn_rdr_nbr > 0 */
if(nco_pck_plc != nco_pck_plc_nil){
if(nco_pck_plc_sng) nco_pck_plc_sng=(char *)nco_free(nco_pck_plc_sng);
if(nco_pck_map_sng) nco_pck_map_sng=(char *)nco_free(nco_pck_map_sng);
if(nco_pck_plc != nco_pck_plc_upk){
/* No need for loop over var_prc variables to free attribute values
Variable structures and attribute edit lists share same attribute values
Free them only once, and do it in nco_var_free() */
aed_lst_add_fst=(aed_sct *)nco_free(aed_lst_add_fst);
aed_lst_scl_fct=(aed_sct *)nco_free(aed_lst_scl_fct);
} /* nco_pck_plc == nco_pck_plc_upk */
} /* nco_pck_plc == nco_pck_plc_nil */
/* NCO-generic clean-up */
/* Free individual strings/arrays */
if(cmd_ln) cmd_ln=(char *)nco_free(cmd_ln);
if(cnk_map_sng) cnk_map_sng=(char *)nco_free(cnk_map_sng);
if(cnk_plc_sng) cnk_plc_sng=(char *)nco_free(cnk_plc_sng);
if(fl_in) fl_in=(char *)nco_free(fl_in);
if(fl_out) fl_out=(char *)nco_free(fl_out);
if(fl_out_tmp) fl_out_tmp=(char *)nco_free(fl_out_tmp);
if(fl_pth) fl_pth=(char *)nco_free(fl_pth);
if(fl_pth_lcl) fl_pth_lcl=(char *)nco_free(fl_pth_lcl);
if(in_id_arr) in_id_arr=(int *)nco_free(in_id_arr);
/* Free lists of strings */
if(fl_lst_in && fl_lst_abb == NULL) fl_lst_in=nco_sng_lst_free(fl_lst_in,fl_nbr);
if(fl_lst_in && fl_lst_abb) fl_lst_in=nco_sng_lst_free(fl_lst_in,1);
if(fl_lst_abb) fl_lst_abb=nco_sng_lst_free(fl_lst_abb,abb_arg_nbr);
if(gaa_nbr > 0) gaa_arg=nco_sng_lst_free(gaa_arg,gaa_nbr);
if(var_lst_in_nbr > 0) var_lst_in=nco_sng_lst_free(var_lst_in,var_lst_in_nbr);
/* Free limits */
for(idx=0;idx<aux_nbr;idx++) aux_arg[idx]=(char *)nco_free(aux_arg[idx]);
for(idx=0;idx<lmt_nbr;idx++) lmt_arg[idx]=(char *)nco_free(lmt_arg[idx]);
for(idx=0;idx<ppc_nbr;idx++) ppc_arg[idx]=(char *)nco_free(ppc_arg[idx]);
/* Free chunking information */
for(idx=0;idx<cnk_nbr;idx++) cnk_arg[idx]=(char *)nco_free(cnk_arg[idx]);
if(cnk_nbr > 0) cnk.cnk_dmn=(cnk_dmn_sct **)nco_cnk_lst_free(cnk.cnk_dmn,cnk_nbr);
if(xtr_nbr > 0) var=nco_var_lst_free(var,xtr_nbr);
if(xtr_nbr > 0) var_out=nco_var_lst_free(var_out,xtr_nbr);
var_prc=(var_sct **)nco_free(var_prc);
var_prc_out=(var_sct **)nco_free(var_prc_out);
var_fix=(var_sct **)nco_free(var_fix);
var_fix_out=(var_sct **)nco_free(var_fix_out);
trv_tbl_free(trv_tbl);
for(idx=0;idx<lmt_nbr;idx++) flg_dne[idx].dim_nm=(char *)nco_free(flg_dne[idx].dim_nm);
if(flg_dne) flg_dne=(nco_dmn_dne_t *)nco_free(flg_dne);
if(gpe) gpe=(gpe_sct *)nco_gpe_free(gpe);
} /* !flg_cln */
#ifdef ENABLE_MPI
MPI_Finalize();
#endif /* !ENABLE_MPI */
/* End timer */
ddra_info.tmr_flg=nco_tmr_end; /* [enm] Timer flag */
rcd+=nco_ddra((char *)NULL,(char *)NULL,&ddra_info);
if(rcd != NC_NOERR) nco_err_exit(rcd,"main");
nco_exit_gracefully();
return EXIT_SUCCESS;
} /* end main() */
aed_sct * /* O [sct] List of attribute edit structures */
nco_prs_aed_lst /* [fnc] Parse user-specified attribute edits into structure list */
(const int nbr_aed, /* I [nbr] Number of attributes in list */
X_CST_PTR_CST_PTR_Y(char,aed_arg)) /* I/O [sng] List of user-specified attribute edits (delimiters are changed to NULL on output */
{
/* Purpose: Parse name, type, size, and value elements of comma-separated list of attribute edit information
Routine merely evaluates syntax of input expressions
Routine does not validate attributes or variables against those present in input netCDF file */
/* Options are:
-a att_nm,var_nm,mode,att_typ,att_val (modifies attribute att_nm for the single variable var_nm)
-a att_nm,,mode,att_typ,att_val (modifies attribute att_nm for every variable in file)
If option -a is given with var_nm = NULL, then var_nm is expanded into every variable name in file
Thus attribute editing operation is performed on every variable in file.
mode,att_nm,att_typ,att_val (modifies global attribute att_nm for file)
This option may be combined with modes -a, -c, -d, or -o to specify
appending to, changing, deleting, or overwriting, any existing global attribute named att_nm
One mode must be set for each edited attribute: append (a), create (c), delete (d), modify (m), or overwrite (o).
-a: Attribute append mode
Append value att_val to current var_nm attribute att_nm value att_val, if any.
If var_nm does not have an attribute att_nm, there is not effect.
-c: Attribute create mode
Create variable var_nm attribute att_nm with att_val if att_nm does not yet exist.
If var_nm already has an attribute att_nm, there is not effect.
-d: Attribute delete mode
Delete current var_nm attribute att_nm.
If var_nm does not have an attribute att_nm, there is not effect.
-m: Attribute modify mode
Change value of current var_nm attribute att_nm to value att_val.
If var_nm does not have an attribute att_nm, there is not effect.
-o: Attribute overwrite mode
Write attribute att_nm with value att_val to variable var_nm, overwriting existing attribute att_nm, if any.
This is default mode.
*/
char **arg_lst;
const char * const dlm_sng=",";
const long idx_att_val_arg=4L; /* Number of required delimiters preceding attribute values in -a argument list */
aed_sct *aed_lst;
int idx;
int arg_nbr;
aed_lst=(aed_sct *)nco_malloc(nbr_aed*sizeof(aed_sct));
for(idx=0;idx<nbr_aed;idx++){
/* Process attribute edit specifications as normal text list */
arg_lst=nco_lst_prs_2D(aed_arg[idx],dlm_sng,&arg_nbr);
/* Check syntax */
if(
arg_nbr < 5 || /* Need more info */
/* arg_lst[0] == NULL || */ /* att_nm not specified */
arg_lst[2] == NULL || /* mode not specified */
(*(arg_lst[2]) != 'd' && (arg_lst[3] == NULL || (arg_lst[idx_att_val_arg] == NULL && *(arg_lst[3]) != 'c'))) || /* att_typ and att_val must be specified when mode is not delete, except that att_val = "" is valid for character type */
False){
(void)fprintf(stdout,"%s: ERROR in attribute edit specification %s\n",prg_nm_get(),aed_arg[idx]);
nco_exit(EXIT_FAILURE);
} /* end if */
/* Initialize structure */
/* aed strings not explicitly set by user remain NULL,
i.e., specifying default setting appears as if nothing was set.
Hopefully, in routines that follow, the branch followed by an aed for which
all default settings were specified (e.g.,"-a foo,,,,") will yield same result
as branch for which all defaults were set. */
aed_lst[idx].att_nm=NULL;
aed_lst[idx].var_nm=NULL;
aed_lst[idx].val.vp=NULL;
aed_lst[idx].type=NC_CHAR;
aed_lst[idx].mode=aed_overwrite;
aed_lst[idx].sz=-1L;
aed_lst[idx].id=-1;
/* Fill in structure */
if(arg_lst[0]) aed_lst[idx].att_nm=strdup(arg_lst[0]);
if(arg_lst[1]) aed_lst[idx].var_nm=strdup(arg_lst[1]);
/* fxm: Change these switches to string comparisons someday */
/* Set mode of current aed structure */
/* Convert single letter code to mode enum */
/* if(!strcmp("append",arg_lst[2])){aed_lst[idx].mode=aed_append;
}else if(!strcmp("create",arg_lst[2])){aed_lst[idx].mode=aed_create;
}else if(!strcmp("delete",arg_lst[2])){aed_lst[idx].mode=aed_delete;
}else if(!strcmp("modify",arg_lst[2])){aed_lst[idx].mode=aed_modify;
}else if(!strcmp("overwrite",arg_lst[2])){aed_lst[idx].mode=aed_overwrite;} */
switch(*(arg_lst[2])){
case 'a': aed_lst[idx].mode=aed_append; break;
case 'c': aed_lst[idx].mode=aed_create; break;
case 'd': aed_lst[idx].mode=aed_delete; break;
case 'm': aed_lst[idx].mode=aed_modify; break;
case 'o': aed_lst[idx].mode=aed_overwrite; break;
default:
(void)fprintf(stderr,"%s: ERROR `%s' is not a supported mode\n",prg_nm_get(),arg_lst[2]);
(void)fprintf(stderr,"%s: HINT: Valid modes are `a' = append, `c' = create,`d' = delete, `m' = modify, and `o' = overwrite",prg_nm_get());
nco_exit(EXIT_FAILURE);
break;
} /* end switch */
/* Attribute type and value do not matter if we are deleting it */
if(aed_lst[idx].mode != aed_delete){
/* Set type of current aed structure */
/* Convert single letter code to type enum */
switch(*(arg_lst[3])){
case 'f': aed_lst[idx].type=(nc_type)NC_FLOAT; break;
case 'd': aed_lst[idx].type=(nc_type)NC_DOUBLE; break;
case 'l':
case 'i': aed_lst[idx].type=(nc_type)NC_INT; break;
case 's': aed_lst[idx].type=(nc_type)NC_SHORT; break;
case 'c': aed_lst[idx].type=(nc_type)NC_CHAR; break;
case 'b': aed_lst[idx].type=(nc_type)NC_BYTE; break;
default:
if(!strcasecmp(arg_lst[3],"ub")) aed_lst[idx].type=(nc_type)NC_UBYTE;
else if(!strcasecmp(arg_lst[3],"us")) aed_lst[idx].type=(nc_type)NC_USHORT;
else if(!strcasecmp(arg_lst[3],"u") || !strcasecmp(arg_lst[3],"ui") || !strcasecmp(arg_lst[3],"ul")) aed_lst[idx].type=(nc_type)NC_UINT;
else if(!strcasecmp(arg_lst[3],"ll") || !strcasecmp(arg_lst[3],"int64")) aed_lst[idx].type=(nc_type)NC_INT64;
else if(!strcasecmp(arg_lst[3],"ull") || !strcasecmp(arg_lst[3],"uint64")) aed_lst[idx].type=(nc_type)NC_UINT64;
else if(!strcasecmp(arg_lst[3],"sng")) aed_lst[idx].type=(nc_type)NC_STRING;
else{
(void)fprintf(stderr,"%s: ERROR `%s' is not a supported netCDF data type\n",prg_nm_get(),arg_lst[3]);
(void)fprintf(stderr,"%s: HINT: Valid data types are `c' = char, `f' = float, `d' = double,`s' = short, 'l' = `i' = integer, `b' = byte",prg_nm_get());
nco_exit(EXIT_FAILURE);} /* end if error */
break;
} /* end switch */
/* Re-assemble string list values which inadvertently contain delimiters */
if(aed_lst[idx].type == NC_CHAR && arg_nbr > idx_att_val_arg+1){
/* Number of elements which must be concatenated into single string value */
long lmn_nbr;
lmn_nbr=arg_nbr-idx_att_val_arg;
if(dbg_lvl_get() >= nco_dbg_var) (void)fprintf(stdout,"%s: WARNING NC_CHAR (string) attribute is embedded with %li literal element delimiters (\"%s\"), re-assembling...\n",prg_nm_get(),lmn_nbr-1L,dlm_sng);
/* Rewrite list, splicing in original delimiter string */
/* fxm: TODO nco527 ncatted memory may be lost here */
arg_lst[idx_att_val_arg]=sng_lst_cat(arg_lst+idx_att_val_arg,lmn_nbr,dlm_sng);
/* Keep bookkeeping straight, just in case */
arg_nbr=idx_att_val_arg+1L;
lmn_nbr=1L;
} /* endif arg_nbr > idx_att_val_arg+1 */
/* Replace any C language '\X' escape codes with ASCII bytes */
if(aed_lst[idx].type == NC_CHAR) (void)sng_ascii_trn(arg_lst[idx_att_val_arg]);
/* Set size of current aed structure */
if(aed_lst[idx].type == NC_CHAR){
/* 20100409 Remove extra space formerly allocated for NUL-terminator
This caused each append to insert a NUL at end of NC_CHAR attributes
Multiple appends would then result in attributes pockmarked with NULs
Solves TODO nco985
Not yet sure there are no ill side-effects though... */
aed_lst[idx].sz=(arg_lst[idx_att_val_arg] == NULL) ? 0L : strlen(arg_lst[idx_att_val_arg]);
}else{
/* Number of elements of numeric types is determined by number of delimiters */
aed_lst[idx].sz=arg_nbr-idx_att_val_arg;
} /* end else */
/* Set value of current aed structure */
if(aed_lst[idx].type == NC_CHAR){
aed_lst[idx].val.cp=(nco_char *)strdup(arg_lst[idx_att_val_arg]);
}else{
double *val_arg_dbl=NULL_CEWI;
long long *val_arg_lng_lng=NULL_CEWI;
unsigned long long *val_arg_ulng_lng=NULL_CEWI;
long lmn;
aed_lst[idx].val.vp=(void *)nco_malloc(aed_lst[idx].sz*nco_typ_lng(aed_lst[idx].type));
/* Use type-appropriate conversion */
switch(aed_lst[idx].type){
case NC_FLOAT:
case NC_DOUBLE:
val_arg_dbl=(double *)nco_malloc(aed_lst[idx].sz*sizeof(double));
for(lmn=0L;lmn<aed_lst[idx].sz;lmn++){val_arg_dbl[lmn]=strtod(arg_lst[idx_att_val_arg+lmn],(char **)NULL);} break;
case NC_BYTE:
case NC_INT:
case NC_SHORT:
case NC_INT64:
val_arg_lng_lng=(long long *)nco_malloc(aed_lst[idx].sz*sizeof(long long));
for(lmn=0L;lmn<aed_lst[idx].sz;lmn++){val_arg_lng_lng[lmn]=strtoll(arg_lst[idx_att_val_arg+lmn],(char **)NULL,10);} break;
case NC_CHAR:
case NC_UBYTE:
case NC_USHORT:
case NC_UINT:
case NC_UINT64:
val_arg_ulng_lng=(unsigned long long *)nco_malloc(aed_lst[idx].sz*sizeof(unsigned long long));
for(lmn=0L;lmn<aed_lst[idx].sz;lmn++){val_arg_ulng_lng[lmn]=strtoull(arg_lst[idx_att_val_arg+lmn],(char **)NULL,10);} break;
case NC_STRING: break;
default: nco_dfl_case_nc_type_err(); break;
} /* end switch */
/* Copy and typecast entire array of values, using implicit coercion rules of C */
/* 20011001: Use explicit coercion rules to quiet C++ compiler warnings */
switch(aed_lst[idx].type){
case NC_FLOAT: for(lmn=0L;lmn<aed_lst[idx].sz;lmn++) {aed_lst[idx].val.fp[lmn]=(float)val_arg_dbl[lmn];} break;
case NC_DOUBLE: for(lmn=0L;lmn<aed_lst[idx].sz;lmn++) {aed_lst[idx].val.dp[lmn]=(double)val_arg_dbl[lmn];} break;
case NC_INT: for(lmn=0L;lmn<aed_lst[idx].sz;lmn++) {aed_lst[idx].val.ip[lmn]=(nco_int)val_arg_lng_lng[lmn];} break;
case NC_SHORT: for(lmn=0L;lmn<aed_lst[idx].sz;lmn++) {aed_lst[idx].val.sp[lmn]=(nco_short)val_arg_lng_lng[lmn];} break;
case NC_CHAR: for(lmn=0L;lmn<aed_lst[idx].sz;lmn++) {aed_lst[idx].val.cp[lmn]=(nco_char)val_arg_ulng_lng[lmn];} break;
case NC_BYTE: for(lmn=0L;lmn<aed_lst[idx].sz;lmn++) {aed_lst[idx].val.bp[lmn]=(nco_byte)val_arg_lng_lng[lmn];} break;
case NC_UBYTE: for(lmn=0L;lmn<aed_lst[idx].sz;lmn++) {aed_lst[idx].val.ubp[lmn]=(nco_ubyte)val_arg_ulng_lng[lmn];} break;
case NC_USHORT: for(lmn=0L;lmn<aed_lst[idx].sz;lmn++) {aed_lst[idx].val.usp[lmn]=(nco_ushort)val_arg_ulng_lng[lmn];} break;
case NC_UINT: for(lmn=0L;lmn<aed_lst[idx].sz;lmn++) {aed_lst[idx].val.uip[lmn]=(nco_uint)val_arg_ulng_lng[lmn];} break;
case NC_INT64: for(lmn=0L;lmn<aed_lst[idx].sz;lmn++) {aed_lst[idx].val.i64p[lmn]=(nco_int64)val_arg_lng_lng[lmn];} break;
case NC_UINT64: for(lmn=0L;lmn<aed_lst[idx].sz;lmn++) {aed_lst[idx].val.ui64p[lmn]=(nco_uint64)val_arg_ulng_lng[lmn];} break;
case NC_STRING: break;
default: nco_dfl_case_nc_type_err(); break;
} /* end switch */
/* Free array used to hold input values */
if(val_arg_dbl) val_arg_dbl=(double *)nco_free(val_arg_dbl);
if(val_arg_lng_lng) val_arg_lng_lng=(long long *)nco_free(val_arg_lng_lng);
if(val_arg_ulng_lng) val_arg_ulng_lng=(unsigned long long *)nco_free(val_arg_ulng_lng);
} /* end else */
/* Un-typecast pointer to values after access */
(void)cast_nctype_void(aed_lst[idx].type,&aed_lst[idx].val);
} /* end if mode is not delete */
arg_lst=nco_sng_lst_free(arg_lst,arg_nbr);
} /* end loop over aed */
if(dbg_lvl_get() >= nco_dbg_io){
for(idx=0;idx<nbr_aed;idx++){
(void)fprintf(stderr,"aed_lst[%d].att_nm = %s\n",idx,aed_lst[idx].att_nm);
(void)fprintf(stderr,"aed_lst[%d].var_nm = %s\n",idx,aed_lst[idx].var_nm == NULL ? "NULL" : aed_lst[idx].var_nm);
(void)fprintf(stderr,"aed_lst[%d].id = %i\n",idx,aed_lst[idx].id);
(void)fprintf(stderr,"aed_lst[%d].sz = %li\n",idx,aed_lst[idx].sz);
(void)fprintf(stderr,"aed_lst[%d].type = %s\n",idx,nco_typ_sng(aed_lst[idx].type));
/* (void)fprintf(stderr,"aed_lst[%d].val = %s\n",idx,aed_lst[idx].val);*/
(void)fprintf(stderr,"aed_lst[%d].mode = %i\n",idx,aed_lst[idx].mode);
} /* end loop over idx */
} /* end debug */
return aed_lst;
} /* end nco_prs_aed_lst() */
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() */
void
nco_aed_prc /* [fnc] Process single attribute edit for single variable */
(const int nc_id, /* I [id] Input netCDF file ID */
const int var_id, /* I [id] ID of variable on which to perform attribute editing */
const aed_sct aed) /* I [sct] Structure containing information necessary to edit */
{
/* Purpose: Process single attribute edit for single variable */
/* If var_id == NC_GLOBAL ( = -1) then global attribute will be edited */
#ifdef NCO_NETCDF4_AND_FILLVALUE
char att_nm_tmp[]="eulaVlliF_"; /* String of same length as "_FillValue" for name hack with netCDF4 */
nco_bool flg_netCDF4=False; /* [flg] File format is netCDF4 */
#endif /* !NCO_NETCDF4_AND_FILLVALUE */
char att_nm[NC_MAX_NAME];
char var_nm[NC_MAX_NAME];
/* NB: netCDF2 specifies att_sz is type int, netCDF3 and netCDF4 use size_t */
int nbr_att; /* [nbr] Number of attributes */
int rcd=NC_NOERR; /* [rcd] Return code */
long att_sz;
nc_type att_typ;
void *att_val_new=NULL;
if(var_id == NC_GLOBAL){
/* Get number of global attributes in file */
(void)nco_inq(nc_id,(int *)NULL,(int *)NULL,&nbr_att,(int *)NULL);
(void)strcpy(var_nm,"Global");
}else{
/* Get name and number of attributes for variable */
(void)nco_inq_var(nc_id,var_id,var_nm,(nc_type *)NULL,(int *)NULL,(int *)NULL,&nbr_att);
} /* end else */
/* Query attribute metadata when attribute name was specified */
if(aed.att_nm) rcd=nco_inq_att_flg(nc_id,var_id,aed.att_nm,&att_typ,&att_sz);
/* Before changing metadata, change missing values to new missing value if warranted
This capability is add-on feature not implemented too cleanly or efficiently
If every variable has "_FillValue" attribute and "_FillValue" is changed
globally, then algorithm goes into and out of define mode for each variable,
rather than collecting all information in first pass and replacing all data in second pass.
This is because ncatted was originally designed to change only metadata and so was
architected differently from other NCO operators. */
if(
aed.att_nm /* Linux strcmp() dumps core if attribute name is blank */
&& strcmp(aed.att_nm,nco_mss_val_sng_get()) == 0 /* Current attribute is "_FillValue" */
&& var_id != NC_GLOBAL /* Current attribute is not global */
&& (aed.mode == aed_modify || aed.mode == aed_overwrite) /* Modifying or overwriting existing value */
&& rcd == NC_NOERR /* Only when existing _FillValue attribute is modified */
&& att_sz == 1L /* Old _FillValue attribute must be of size 1 */
&& aed.sz == 1L /* New _FillValue attribute must be of size 1 */
){
int *dmn_id;
long *dmn_sz;
long *dmn_srt;
long idx;
long var_sz=long_CEWI;
ptr_unn mss_val_crr;
ptr_unn mss_val_new;
ptr_unn var_val;
var_sct *var=NULL_CEWI;
if(dbg_lvl_get() >= nco_dbg_std) (void)fprintf(stdout,"%s: INFO Replacing missing value data in variable %s\n",prg_nm_get(),var_nm);
/* Take file out of define mode */
(void)nco_enddef(nc_id);
/* Initialize (partially) variable structure */
var=(var_sct *)nco_malloc(sizeof(var_sct));
var->nc_id=nc_id;
var->id=var_id;
var->sz=1L;
/* Get type of variable and number of dimensions */
(void)nco_inq_var(nc_id,var_id,(char *)NULL,&var->type,&var->nbr_dim,(int *)NULL,(int *)NULL);
dmn_id=(int *)nco_malloc(var->nbr_dim*sizeof(int));
dmn_sz=(long *)nco_malloc(var->nbr_dim*sizeof(long));
dmn_srt=(long *)nco_malloc(var->nbr_dim*sizeof(long));
(void)nco_inq_vardimid(nc_id,var_id,dmn_id);
/* Get dimension sizes and construct variable size */
for(idx=0;idx<var->nbr_dim;idx++){
(void)nco_inq_dimlen(nc_id,dmn_id[idx],dmn_sz+idx);
var->sz*=dmn_sz[idx];
dmn_srt[idx]=0L;
} /* end loop over dim */
var->dmn_id=dmn_id;
var->cnt=dmn_sz;
var->srt=dmn_srt;
/* Place nco_var_get() code inline since var struct is not truly complete */
if((var->val.vp=(void *)nco_malloc_flg(var->sz*nco_typ_lng(var->type))) == NULL){
(void)fprintf(stdout,"%s: ERROR Unable to malloc() %ld*%lu bytes in nco_aed_prc()\n",prg_nm_get(),var->sz,(unsigned long)nco_typ_lng(var->type));
nco_exit(EXIT_FAILURE);
} /* end if */
if(var->sz > 1L){
(void)nco_get_vara(nc_id,var_id,var->srt,var->cnt,var->val.vp,var->type);
}else{
(void)nco_get_var1(nc_id,var_id,var->srt,var->val.vp,var->type);
} /* end else */
/* Get current missing value attribute */
var->mss_val.vp=NULL;
var->has_mss_val=nco_mss_val_get(nc_id,var);
/* Sanity check */
if(var->has_mss_val == False){
(void)fprintf(stdout,"%s: ERROR variable %s does not have \"%s\" attribute in nco_aed_prc()\n",prg_nm_get(),var_nm,nco_mss_val_sng_get());
nco_exit(EXIT_FAILURE);
} /* end if */
/* Shortcuts to avoid indirection */
var_val=var->val;
var_sz=var->sz;
/* Get new and old missing values in same type as variable */
mss_val_crr.vp=(void *)nco_malloc(att_sz*nco_typ_lng(var->type));
mss_val_new.vp=(void *)nco_malloc(aed.sz*nco_typ_lng(var->type));
(void)nco_val_cnf_typ(var->type,var->mss_val,var->type,mss_val_crr);
(void)nco_val_cnf_typ(aed.type,aed.val,var->type,mss_val_new);
/* Typecast pointer to values before access */
(void)cast_void_nctype(var->type,&var_val);
(void)cast_void_nctype(var->type,&mss_val_crr);
(void)cast_void_nctype(var->type,&mss_val_new);
switch(var->type){
case NC_FLOAT: for(idx=0L;idx<var_sz;idx++) {if(var_val.fp[idx] == *mss_val_crr.fp) var_val.fp[idx]=*mss_val_new.fp;} break;
case NC_DOUBLE: for(idx=0L;idx<var_sz;idx++) {if(var_val.dp[idx] == *mss_val_crr.dp) var_val.dp[idx]=*mss_val_new.dp;} break;
case NC_INT: for(idx=0L;idx<var_sz;idx++) {if(var_val.ip[idx] == *mss_val_crr.ip) var_val.ip[idx]=*mss_val_new.ip;} break;
case NC_SHORT: for(idx=0L;idx<var_sz;idx++) {if(var_val.sp[idx] == *mss_val_crr.sp) var_val.sp[idx]=*mss_val_new.sp;} break;
case NC_CHAR: for(idx=0L;idx<var_sz;idx++) {if(var_val.cp[idx] == *mss_val_crr.cp) var_val.cp[idx]=*mss_val_new.cp;} break;
case NC_BYTE: for(idx=0L;idx<var_sz;idx++) {if(var_val.bp[idx] == *mss_val_crr.bp) var_val.bp[idx]=*mss_val_new.bp;} break;
case NC_UBYTE: for(idx=0L;idx<var_sz;idx++) {if(var_val.ubp[idx] == *mss_val_crr.ubp) var_val.ubp[idx]=*mss_val_new.ubp;} break;
case NC_USHORT: for(idx=0L;idx<var_sz;idx++) {if(var_val.usp[idx] == *mss_val_crr.usp) var_val.usp[idx]=*mss_val_new.usp;} break;
case NC_UINT: for(idx=0L;idx<var_sz;idx++) {if(var_val.uip[idx] == *mss_val_crr.uip) var_val.uip[idx]=*mss_val_new.uip;} break;
case NC_INT64: for(idx=0L;idx<var_sz;idx++) {if(var_val.i64p[idx] == *mss_val_crr.i64p) var_val.i64p[idx]=*mss_val_new.i64p;} break;
case NC_UINT64: for(idx=0L;idx<var_sz;idx++) {if(var_val.ui64p[idx] == *mss_val_crr.ui64p) var_val.ui64p[idx]=*mss_val_new.ui64p;} break;
case NC_STRING: for(idx=0L;idx<var_sz;idx++) {if(var_val.sngp[idx] == *mss_val_crr.sngp) var_val.sngp[idx]=*mss_val_new.sngp;} break;
default: nco_dfl_case_nc_type_err(); break;
} /* end switch */
/* Un-typecast the pointer to values after access */
(void)cast_nctype_void(var->type,&var_val);
(void)cast_nctype_void(var->type,&mss_val_crr);
(void)cast_nctype_void(var->type,&mss_val_new);
/* Write to disk */
if(var->nbr_dim == 0){
(void)nco_put_var1(nc_id,var_id,var->srt,var->val.vp,var->type);
}else{ /* end if variable is scalar */
(void)nco_put_vara(nc_id,var_id,var->srt,var->cnt,var->val.vp,var->type);
} /* end else */
/* Free memory */
mss_val_crr.vp=nco_free(mss_val_crr.vp);
mss_val_new.vp=nco_free(mss_val_new.vp);
var->mss_val.vp=nco_free(var->mss_val.vp);
var->val.vp=nco_free(var->val.vp);
var->dmn_id=(int *)nco_free(var->dmn_id);
var->srt=(long *)nco_free(var->srt);
var->cnt=(long *)nco_free(var->cnt);
/* 20050704 try and use nco_free() to avoid valgrind error message */
var=(var_sct *)nco_free(var);
/* Put file back in define mode */
(void)nco_redef(nc_id);
} /* end if replacing missing value data */
/* Change metadata (as written, this must be done after _FillValue data is replaced) */
#ifdef NCO_NETCDF4_AND_FILLVALUE
/* Bold hack which gets around problem of modifying netCDF4 "_FillValue" attributes
netCDF4 does not allow this by default, though netCDF3 does
Change attribute name to att_nm_tmp, modify value, then restore name */
/* Check if file is netCDF3 classic with netCDF4 library
If so, do not kludge. NB: create global variable for output file format? */
{ /* scope for fl_fmt temporary */
int fl_fmt;
(void)nco_inq_format(nc_id,&fl_fmt);
flg_netCDF4=(fl_fmt==NC_FORMAT_NETCDF4 || fl_fmt==NC_FORMAT_NETCDF4_CLASSIC);
} /* end scope */
if(flg_netCDF4 && !strcmp(aed.att_nm,nco_mss_val_sng_get()) && aed.mode != aed_delete){
if(aed.mode != aed_create) (void)nco_rename_att(nc_id,var_id,aed.att_nm,att_nm_tmp);
strcpy(aed.att_nm,att_nm_tmp);
} /* endif libnetCDF may have netCDF4 restrictions */
#endif /* !NCO_NETCDF4_AND_FILLVALUE */
switch(aed.mode){
case aed_append:
if(rcd == NC_NOERR){
/* Append to existing attribute value */
if(aed.type != att_typ){
(void)fprintf(stdout,"%s: ERROR %s attribute %s is of type %s not %s, unable to append\n",prg_nm_get(),var_nm,aed.att_nm,nco_typ_sng(att_typ),nco_typ_sng(aed.type));
nco_exit(EXIT_FAILURE);
} /* end if */
att_val_new=(void *)nco_malloc((att_sz+aed.sz)*nco_typ_lng(aed.type));
(void)nco_get_att(nc_id,var_id,aed.att_nm,(void *)att_val_new,aed.type);
/* NB: Following assumes sizeof(char) = 1 byte */
(void)memcpy((void *)((char *)att_val_new+att_sz*nco_typ_lng(aed.type)),
(void *)aed.val.vp,
aed.sz*nco_typ_lng(aed.type));
(void)nco_put_att(nc_id,var_id,aed.att_nm,aed.type,att_sz+aed.sz,att_val_new);
att_val_new=nco_free(att_val_new);
}else{
/* Create new attribute */
(void)nco_put_att(nc_id,var_id,aed.att_nm,aed.type,aed.sz,aed.val.vp);
} /* end else */
break;
case aed_create:
if(rcd != NC_NOERR) (void)nco_put_att(nc_id,var_id,aed.att_nm,aed.type,aed.sz,aed.val.vp);
break;
case aed_delete:
/* Delete specified attribute if attribute name was specified... */
if(aed.att_nm){
/* ...and if attribute is known to exist from previous inquire call... */
if(rcd == NC_NOERR) (void)nco_del_att(nc_id,var_id,aed.att_nm);
}else{
/* ...else delete all attributes for this variable... */
while(nbr_att){
(void)nco_inq_attname(nc_id,var_id,nbr_att-1,att_nm);
(void)nco_del_att(nc_id,var_id,att_nm);
nbr_att--;
} /* end while */
} /* end else */
break;
case aed_modify:
if(rcd == NC_NOERR) (void)nco_put_att(nc_id,var_id,aed.att_nm,aed.type,aed.sz,aed.val.vp);
break;
case aed_overwrite:
(void)nco_put_att(nc_id,var_id,aed.att_nm,aed.type,aed.sz,aed.val.vp);
break;
default:
break;
} /* end switch */
#ifdef NCO_NETCDF4_AND_FILLVALUE
if(flg_netCDF4 && !strcmp(aed.att_nm,att_nm_tmp) && aed.mode != aed_delete){
(void)nco_rename_att(nc_id,var_id,att_nm_tmp,nco_mss_val_sng_get());
/* Restore original name (space already allocated) */
strcpy(aed.att_nm,nco_mss_val_sng_get());
} /* !flg_netCDF4 */
#endif /* !NCO_NETCDF4_AND_FILLVALUE */
} /* end nco_aed_prc() */