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() */
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() */