nco++/ncap2.cc File Reference

#include <assert.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/stat.h>
#include <time.h>
#include <unistd.h>
#include <string>
#include "nco_getopt.h"
#include <netcdf.h>
#include "nco_netcdf.h"
#include "ncap2.hh"
#include "libnco++.hh"
#include "libnco.h"

Include dependency graph for ncap2.cc:

Go to the source code of this file.

Defines
#define	MAIN_PROGRAM_FILE
#define	NCAP_SPT_NBR_MAX   100
Functions
int	main (int argc, char **argv)
Variables
size_t	ncap_ncl_dpt_crr = 0UL
size_t *	ncap_ln_nbr_crr
char **	ncap_fl_spt_glb = NULL

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Define Documentation

#define MAIN_PROGRAM_FILE

Definition at line 70 of file ncap2.cc.

#define NCAP_SPT_NBR_MAX   100

Referenced by main().

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Function Documentation

int main (  int  argc, char **  argv )

Definition at line 81 of file ncap2.cc. References acosf(), acoshf(), aed_overwrite, asinf(), asinhf(), atanf(), atanhf(), aed_sct::att_nm, ceilf(), copyright_prn(), cosf(), coshf(), dbg_lvl_get(), erfcf(), erff(), EXIT_FAILURE, EXIT_SUCCESS, expf(), fabsf(), False, FILE, NcapVarVector::find(), NcapVector< T >::find(), prs_sct::fl_in, prs_sct::fl_out, floorf(), gammaf(), getopt_long, nm_id_sct::id, prs_sct::in_id, int_CEWI, log10f(), logf(), lst_prs_2D(), aed_sct::mode, option::name, NC_FORMAT_64BIT, NC_FORMAT_CLASSIC, NC_FORMAT_NETCDF4, NC_GLOBAL, NC_MAX_ATTRS, NC_MAX_DIMS, NC_MAX_NAME, NC_NOERR, NC_NOFILL, NC_NOWRITE, ncap_att, NCAP_SPT_NBR_MAX, ncap_sym_init(), nco_aed_prc(), nco_att_cpy(), nco_att_lst_mk(), nco_bool, nco_close(), nco_cmd_ln_sng(), nco_cnv_ccm_ccsm_cf_inq(), nco_create_mode_prs(), nco_dmn_dfn(), nco_dmn_dpl(), nco_dmn_fll(), nco_dmn_lmt_mrg(), nco_dmn_lst(), nco_dmn_lst_ass_var(), nco_dmn_lst_free(), nco_dmn_xrf(), nco_enddef(), nco_exit(), nco_exit_gracefully(), nco_fl_lst_mk(), nco_fl_mk_lcl(), nco_fl_nm_prs(), nco_fl_out_cls(), nco_fl_out_open(), nco_fl_rm(), nco_free(), nco_hst_att_cat(), nco_inq(), nco_inq_varid_flg(), nco_lbr_vrs_prn(), nco_lmt_lst_free(), nco_lmt_prs(), nco_lst_srt_nm_id(), nco_malloc(), nco_nm_id_lst_free(), nco_open(), nco_pck_map_nil, nco_pck_plc_nil, nco_realloc(), nco_redef(), nco_set_fill(), nco_sng_lst_free(), nco_usg_prn(), nco_var_dfn(), nco_var_dpl(), nco_var_fll(), nco_var_lst_dvd(), nco_var_lst_free(), nco_var_lst_mk(), nco_var_lst_sub(), nco_var_val_cpy(), nco_xrf_dmn(), nco_xrf_var(), nearbyintf(), nm_id_sct::nm, no_argument, prs_sct::ntl_scn, NULL_CEWI, optarg, optind, prs_sct::out_id, parse_antlr(), prg_nm_get(), prg_prs(), NcapVector< T >::ptr(), prs_sct::ptr_dmn_in_vtr, prs_sct::ptr_dmn_out_vtr, prs_sct::ptr_sym_vtr, prs_sct::ptr_var_vtr, NcapVector< T >::push(), required_argument, rintf(), rnd_nbr(), rnd_nbrf(), roundf(), sinf(), sinhf(), NcapVarVector::size(), NcapVector< T >::size(), size_t_CEWI, sqrtf(), aed_sct::sz, tanf(), tanhf(), True, truncf(), aed_sct::type, aed_sct::val, aed_sct::var_nm, and yyin. { FILE *yyin; /* file handle used to check file existance */ int parse_antlr(prs_sct*,char*,char*); /* fxm TODO nco652 */ double rnd_nbr(double); 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 FILE_RETRIEVED_FROM_REMOTE_LOCATION; 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 HISTORY_APPEND=True; /* Option h */ nco_bool CNV_CCM_CCSM_CF; nco_bool PRN_FNC_TBL=False; /* Option f */ nco_bool PROCESS_ALL_VARS=True; /* Option v */ nco_bool REMOVE_REMOTE_FILES_AFTER_PROCESSING=True; /* Option R */ char **fl_lst_abb=NULL; /* Option n */ char **fl_lst_in; char **var_lst_in=NULL_CEWI; char *cmd_ln; 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 *fl_spt_usr=NULL; /* Option s */ char *lmt_arg[NC_MAX_DIMS]; char *opt_crr=NULL; /* [sng] String representation of current long-option name */ #define NCAP_SPT_NBR_MAX 100 char *spt_arg[NCAP_SPT_NBR_MAX]; /* fxm: Arbitrary size, should be dynamic */ char *spt_arg_cat=NULL; /* [sng] User-specified script */ char *time_bfr_srt; const char * const CVS_Id="$Id: ncap2.cc,v 1.7 2006/02/25 22:29:14 zender Exp $"; const char * const CVS_Revision="$Revision: 1.7 $"; const char * const opt_sht_lst="4ACcD:d:Ffhl:n:Oo:p:Rrs:S:vx-:"; /* [sng] Single letter command line options */ dmn_sct **dmn_in=NULL_CEWI; /* [lst] Dimensions in input file */ dmn_sct **dmn_out=NULL_CEWI; /* [lst] Dimensions written to output file */ dmn_sct *dmn_new; dmn_sct *dmn_item; // template lists NcapVector<sym_sct*> sym_vtr; NcapVector<dmn_sct*> dmn_in_vtr; NcapVector<dmn_sct*> dmn_out_vtr; // Holder for attributtes and vectors NcapVarVector var_vtr; extern char *optarg; extern int optind; /* Math float prototypes required by AIX, Solaris, but not by Linux, IRIX */ /* Basic math: acos, asin, atan, cos, exp, fabs, log, log10, sin, sqrt, tan */ /* GNU g++ barfs at these float declartions -- remove if g++ used */ #ifndef __GNUG__ extern float acosf(float); extern float asinf(float); extern float atanf(float); extern float cosf(float); extern float expf(float); extern float fabsf(float); /* 20040629: Only AIX may need this */ extern float logf(float); extern float log10f(float); extern float rnd_nbrf(float); extern float sinf(float); extern float sqrtf(float); extern float tanf(float); /* Advanced math: erf, erfc, gamma */ extern float erff(float); extern float erfcf(float); extern float gammaf(float); /* Hyperbolic trigonometric: acosh, asinh, atanh, cosh, sinh, tanh */ extern float acoshf(float); extern float asinhf(float); extern float atanhf(float); extern float coshf(float); extern float sinhf(float); extern float tanhf(float); /* Basic Rounding: ceil, floor */ extern float ceilf(float); extern float floorf(float); /* Advanced Rounding: nearbyint, rint, round, trunc */ extern float nearbyintf(float); extern float rintf(float); extern float roundf(float); extern float truncf(float); #endif int abb_arg_nbr=0; int fl_nbr=0; int fl_out_fmt=NC_FORMAT_CLASSIC; /* [enm] Output file format */ int fll_md_old; /* [enm] Old fill mode */ int idx; int in_id; int jdx; int lmt_nbr=0; /* Option d. NB: lmt_nbr gets incremented */ int nbr_dmn_ass=int_CEWI;/* Number of dimensions in temporary list */ int nbr_dmn_in=int_CEWI; /* Number of dimensions in dim_in */ int nbr_dmn_out=0; /* [nbr] Number of dimensions in list dmn_out */ int nbr_lst_a=0; /* size of xtr_lst_a */ int nbr_spt=0; /* Option s. NB: nbr_spt gets incremented */ int nbr_var_fix; /* nbr_var_fix gets incremented */ int nbr_var_fl;/* number of vars in a file */ int nbr_var_prc; /* nbr_var_prc gets incremented */ int nbr_xtr=0; /* nbr_xtr will not otherwise be set for -c with no -v */ int opt; int out_id; int rcd=NC_NOERR; /* [rcd] Return code */ int var_id; int sym_tbl_nbr; /* [nbr] Size of symbol table */ lmt_sct **lmt=NULL_CEWI; nm_id_sct *dmn_lst=NULL; nm_id_sct *xtr_lst=NULL; /* Non-processed variables to copy to OUTPUT */ nm_id_sct *xtr_lst_a=NULL; /* Initialize to ALL variables in OUTPUT file */ size_t sng_lng; size_t spt_arg_lng=size_t_CEWI; time_t time_crr_time_t; 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; aed_sct att_item; //Used to convert atts in vector to normal form size_t att_char_posn; char att_sng[3*NC_MAX_NAME]; prs_sct prs_arg; /* [sct] Global information required in parser routines */ static struct option opt_lng[]= { /* Structure ordered by short option key if possible */ /* Long options with no argument, no short option counterpart */ /* Long options with argument, no short option counterpart */ {"fl_fmt",required_argument,0,0}, {"file_format",required_argument,0,0}, /* Long options with short counterparts */ {"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'}, {"dbg_lvl",required_argument,0,'D'}, {"dimension",required_argument,0,'d'}, {"dmn",required_argument,0,'d'}, {"fnc_tbl",no_argument,0,'f'}, {"prn_fnc_tbl",no_argument,0,'f'}, {"ftn",no_argument,0,'F'}, {"history",no_argument,0,'h'}, {"hst",no_argument,0,'h'}, {"local",required_argument,0,'l'}, {"lcl",required_argument,0,'l'}, {"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'}, {"file",required_argument,0,'S'}, {"script-file",required_argument,0,'S'}, {"fl_spt",required_argument,0,'S'}, {"spt",required_argument,0,'s'}, {"script",required_argument,0,'s'}, {"units",no_argument,0,'u'}, {"variable",no_argument,0,'v'}, {"version",no_argument,0,'r'}, {"vrs",no_argument,0,'r'}, {"exclude",no_argument,0,'x'}, {"xcl",no_argument,0,'x'}, {"help",no_argument,0,'?'}, {0,0,0,0} }; /* end opt_lng */ int opt_idx=0; /* Index of current long option into opt_lng array */ /* Start clock and save command line */ cmd_ln=nco_cmd_ln_sng(argc,argv); time_crr_time_t=time((time_t *)NULL); time_bfr_srt=ctime(&time_crr_time_t); time_bfr_srt=time_bfr_srt; /* Avoid compiler warning until variable is used for something */ /* Get program name and set program enum (e.g., prg=ncra) */ prg_nm=prg_prs(argv[0],&prg); /* 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,"fl_fmt") || !strcmp(opt_crr,"file_format")) rcd=nco_create_mode_prs(optarg,&fl_out_fmt); } /* opt != 0 */ /* Process short options */ switch(opt){ case 0: /* Long options have already been processed, return */ break; case '4': /* [flg] 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 '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. */ dbg_lvl=(unsigned short)strtol(optarg,(char **)NULL,10); break; case 'd': /* Copy 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 'f': /* Print function table */ PRN_FNC_TBL=True; break; case 'h': /* Toggle appending to history global attribute */ HISTORY_APPEND=!HISTORY_APPEND; break; case 'l': /* Local path prefix for files retrieved from remote file system */ fl_pth_lcl=(char *)strdup(optarg); break; case 'n': /* NINTAP-style abbreviation of files to process */ /* Currently not used in ncap but should be to allow processing multiple input files by same script */ (void)fprintf(stderr,"%s: ERROR %s does not currently implement -n option\n",prg_nm_get(),prg_nm_get()); fl_lst_abb=lst_prs_2D(optarg,",",&abb_arg_nbr); if(abb_arg_nbr < 1 || abb_arg_nbr > 3){ (void)fprintf(stderr,"%s: ERROR Incorrect abbreviation for file list\n",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. */ REMOVE_REMOTE_FILES_AFTER_PROCESSING=!REMOVE_REMOTE_FILES_AFTER_PROCESSING; break; case 'r': /* Print CVS program information and copyright notice */ (void)copyright_prn(CVS_Id,CVS_Revision); (void)nco_lbr_vrs_prn(); nco_exit(EXIT_SUCCESS); break; case 's': /* Copy command script for later processing */ spt_arg[nbr_spt++]=(char *)strdup(optarg); if(nbr_spt == NCAP_SPT_NBR_MAX-1) (void)fprintf(stderr,"%s: WARNING No more than %d script arguments allowed. TODO #24\n",prg_nm_get(),NCAP_SPT_NBR_MAX); break; case 'S': /* Read command script from file rather than from command line */ fl_spt_usr=(char *)strdup(optarg); break; case 'v': /* Variables to extract/exclude */ PROCESS_ALL_VARS=False; nbr_xtr=0; break; case 'x': /* Exclude rather than extract variables specified with -v */ EXCLUDE_INPUT_LIST=True; if(EXCLUDE_INPUT_LIST) (void)fprintf(stderr,"%s: ERROR %s does not currently implement -x option\n",prg_nm_get(),prg_nm_get()); nco_exit(EXIT_FAILURE); 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",prg_nm_get()); nco_exit(EXIT_FAILURE); break; default: /* Print proper usage */ (void)nco_usg_prn(); nco_exit(EXIT_FAILURE); break; } /* end switch */ if(opt_crr != NULL) opt_crr=(char *)nco_free(opt_crr); } /* end while loop */ /* Append ";\n" to command-script arguments, then concatenate them */ for(idx=0;idx<nbr_spt;idx++){ sng_lng=strlen(spt_arg[idx]); if(idx == 0){ spt_arg_cat=(char *)nco_malloc(sng_lng+3); strcpy(spt_arg_cat,spt_arg[idx]); strcat(spt_arg_cat,";\n"); spt_arg_lng=sng_lng+3; }else{ spt_arg_lng+=sng_lng+2; spt_arg_cat=(char *)nco_realloc(spt_arg_cat,spt_arg_lng); strcat(spt_arg_cat,spt_arg[idx]); strcat(spt_arg_cat,";\n"); } /* end else */ } /* end if */ /* Create function table */ sym_tbl_nbr= /* fxm: Make this dynamic */ +12 /* Basic math: acos, asin, atan, cos, exp, fabs, log, log10, rnd_nbr, sin, sqrt, tan */ +1 /* Basic math synonyms: ln */ +6 /* Hyperbolic trigonometric: acosh, asinh, atanh, cosh, sinh, tanh */ +2 /* Basic Rounding: ceil, floor */ +4 /* Advanced Rounding: nearbyint, rint, round, trunc */ +3 /* Advanced math: erf, erfc, gamma */ ; /* Basic math: acos, asin, atan, cos, exp, log, log10, rnd_nbr, sin, sqrt, tan */ sym_vtr.push(ncap_sym_init("acos",acos,acosf)); sym_vtr.push(ncap_sym_init("asin",asin,asinf)); sym_vtr.push(ncap_sym_init("atan",atan,atanf)); sym_vtr.push(ncap_sym_init("cos",cos,cosf)); sym_vtr.push(ncap_sym_init("exp",exp,expf)); sym_vtr.push(ncap_sym_init("fabs",fabs,fabsf)); sym_vtr.push(ncap_sym_init("log",log,logf)); sym_vtr.push(ncap_sym_init("log10",log10,log10f)); //sym_vtr.push(ncap_sym_init("rnd_nbr",rnd_nbr,rnd_nbrf)); sym_vtr.push(ncap_sym_init("sin",sin,sinf)); sym_vtr.push(ncap_sym_init("sqrt",sqrt,sqrtf)); sym_vtr.push(ncap_sym_init("tan",tan,tanf)); /* Basic math synonyms: ln */ sym_vtr.push(ncap_sym_init("ln",log,logf)); /* ln() is synonym for log() */ /* Basic Rounding: ceil, fl<oor */ sym_vtr.push(ncap_sym_init("ceil",ceil,ceilf)); /* Round up to nearest integer */ sym_vtr.push(ncap_sym_init("floor",floor,floorf)); /* Round down to nearest integer */ /* fxm: Change whole function symbol table section to autotools format #if HAVE_ERF ... */ /* Advanced math: erf, erfc, gamma LINUX*, MACOSX*, and SUN* provide these functions with C89 20020122 and 20020422: AIX, CRAY, SGI*, WIN32 do not define erff(), erfcf(), gammaf() with C89 20050610: C99 mandates support for erf(), erfc(), tgamma() Eventually users without C99 will forego ncap */ #if defined(LINUX) || defined(LINUXAMD64) || defined(MACOSX) sym_vtr.push(ncap_sym_init("erf",erf,erff)); sym_vtr.push(ncap_sym_init("erfc",erfc,erfcf)); sym_vtr.push(ncap_sym_init("gamma",tgamma,tgammaf)); #endif /* !LINUX */ /* Hyperbolic trigonometric: acosh, asinh, atanh, cosh, sinh, tanh 20020703: AIX, SGI*, WIN32 do not define acoshf, asinhf, atanhf 20050610: C99 mandates support for acosh(), asinh(), atanh(), cosh(), sinh(), tanh() Eventually users without C99 will forego ncap */ #if defined(LINUX) || defined(LINUXAMD64) sym_vtr.push(ncap_sym_init("acosh",acosh,acoshf)); sym_vtr.push(ncap_sym_init("asinh",asinh,asinhf)); sym_vtr.push(ncap_sym_init("atanh",atanh,atanhf)); sym_vtr.push(ncap_sym_init("cosh",cosh,coshf)); sym_vtr.push(ncap_sym_init("sinh",sinh,sinhf)); sym_vtr.push(ncap_sym_init("tanh",tanh,tanhf)); #endif /* !LINUX */ /* 20020703: AIX, MACOSX, SGI*, WIN32 do not define rintf Only LINUX* supplies all of these and I do not care about them enough to activate them on LINUX* but not on MACOSX* and SUN* */ /* Advanced Rounding: nearbyint, rint, round, trunc */ /* Advanced Rounding: nearbyint, round, trunc */ /* sym_vtr.push(ncap_sym_init("nearbyint",nearbyint,nearbyintf)); *//* Round to integer value in floating point format using current rounding direction, do not raise inexact exceptions */ /* sym_vtr.push(ncap_sym_init("round",round,roundf)); *//* Round to nearest integer away from zero */ /* sym_vtr.push(ncap_sym_init("trunc",trunc,truncf)); *//* Round to nearest integer not larger in absolute value */ /* sym_vtr.push(ncap_sym_init("rint",rint,rintf)); *//* Round to integer value in floating point format using current rounding direction, raise inexact exceptions */ if(PRN_FNC_TBL){ /* ncap TODO #43: alphabetize this list */ (void)fprintf(stdout,"Maths functions available in %s:\n",prg_nm_get()); (void)fprintf(stdout,"Name\tFloat\tDouble\n"); for(idx=0;idx<sym_vtr.size();idx++) (void)fprintf(stdout,"%s\t%c\t%c\n",sym_vtr[idx]->nm, (sym_vtr[idx]->fnc_flt ? 'y' : 'n'),(sym_vtr[idx]->fnc_dbl ? 'y' : 'n')); nco_exit(EXIT_SUCCESS); } /* end if PRN_FNC_TBL */ /* 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); /* Make uniform list of user-specified dimension limits */ if(lmt_nbr > 0) lmt=nco_lmt_prs(lmt_nbr,lmt_arg); /* 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,&FILE_RETRIEVED_FROM_REMOTE_LOCATION); /* Open file for reading */ rcd=nco_open(fl_in,NC_NOWRITE,&in_id); /* Form list of all dimensions in file */ dmn_lst=nco_dmn_lst(in_id,&nbr_dmn_in); //dmn_in=(dmn_sct **)nco_malloc(nbr_dmn_in*sizeof(dmn_sct *)); for(idx=0;idx<nbr_dmn_in;idx++) dmn_in_vtr.push(nco_dmn_fll(in_id,dmn_lst[idx].id,dmn_lst[idx].nm)); dmn_in=dmn_in_vtr.ptr(0); /* Merge hyperslab limit information into dimension structures */ if(lmt_nbr > 0) (void)nco_dmn_lmt_mrg(dmn_in,nbr_dmn_in,lmt,lmt_nbr); /* Open output file */ fl_out_tmp=nco_fl_out_open(fl_out,FORCE_APPEND,FORCE_OVERWRITE,fl_out_fmt,&out_id); /* Copy global attributes */ (void)nco_att_cpy(in_id,out_id,NC_GLOBAL,NC_GLOBAL,True); /* Catenate time-stamped command line to "history" global attribute */ if(HISTORY_APPEND) (void)nco_hst_att_cat(out_id,cmd_ln); (void)nco_enddef(out_id); /* Set arguments for script execution */ prs_arg.fl_in=fl_in; /* [sng] Input data file */ prs_arg.in_id=in_id; /* [id] Input data file ID */ prs_arg.fl_out=fl_out; /* [sng] Output data file */ prs_arg.out_id=out_id; /* [id] Output data file ID */ prs_arg.ptr_dmn_in_vtr=&dmn_in_vtr; prs_arg.ptr_dmn_out_vtr=&dmn_out_vtr; prs_arg.ptr_sym_vtr=&sym_vtr; prs_arg.ptr_var_vtr=&var_vtr; prs_arg.ntl_scn=False; //[flg] Initial scan of script */ if(fl_spt_usr == NULL){ /* No script file specified, look for command-line scripts */ if(nbr_spt == 0){ (void)fprintf(stderr,"%s: ERROR no script file or command line scripts specified\n",prg_nm_get()); (void)fprintf(stderr,"%s: HINT Use, e.g., -s \"foo=bar\"\n",prg_nm_get()); nco_exit(EXIT_FAILURE); } /* end if */ /* Print all command-line scripts */ if(dbg_lvl_get() > 0){ for(idx=0;idx<nbr_spt;idx++) (void)fprintf(stderr,"spt_arg[%d] = %s\n",idx,spt_arg[idx]); } /* endif debug */ /* Parse command line scripts */ fl_spt_usr=(char *)strdup("Command-line script"); }else{ /* ...endif command-line scripts, begin script file... */ /* Open script file for reading */ if((yyin=fopen(fl_spt_usr,"r")) == NULL){ (void)fprintf(stderr,"%s: ERROR Unable to open script file %s\n",prg_nm_get(),fl_spt_usr); nco_exit(EXIT_FAILURE); } /* end if */ fclose(yyin); } /* end else script file */ /* Invoke ANTLR parser */ rcd=parse_antlr(&prs_arg,fl_spt_usr,spt_arg_cat); /* Tidy up */ fl_spt_usr=(char*)nco_free(fl_spt_usr); /* Get number of variables in output file */ rcd=nco_inq(out_id,(int *)NULL,&nbr_var_fl,(int *)NULL,(int*)NULL); /* Make list of all new variables in output_file */ xtr_lst_a=nco_var_lst_mk(out_id,nbr_var_fl,var_lst_in,False,&nbr_lst_a); if(PROCESS_ALL_VARS){ /* Get number of variables in input file */ rcd=nco_inq(in_id,(int *)NULL,&nbr_var_fl,(int *)NULL,(int *)NULL); /* Form initial list of all variables in input file */ xtr_lst=nco_var_lst_mk(in_id,nbr_var_fl,var_lst_in,False,&nbr_xtr); }else{ /* Make list of variables of new attributes whose parent variable is only in input file */ xtr_lst=nco_att_lst_mk(in_id,out_id,var_vtr,&nbr_xtr); } /* endif */ /* Find dimensions associated with xtr_lst */ /* Write to O only new dims Add apropriate coordinate variables to extraction list options -c -process all cordinates i.e., add coordinates to var list Also add their dims options --none -process associated co-ords loop though dim_out and append to var list options -C no co-ordinates Do nothing */ /* Subtract list A again */ /* Finally extract variables on list */ /* Subtract list A */ if(nbr_lst_a > 0) xtr_lst=nco_var_lst_sub(xtr_lst,&nbr_xtr,xtr_lst_a,nbr_lst_a); /* Put file in define mode to allow metadata writing */ (void)nco_redef(out_id); /* Free current list of all dimensions in input file */ dmn_lst=nco_nm_id_lst_free(dmn_lst,nbr_dmn_in); /* Make list of dimensions of variables in xtr_lst */ if(nbr_xtr > 0) dmn_lst=nco_dmn_lst_ass_var(in_id,xtr_lst,nbr_xtr,&nbr_dmn_ass); /* Find and add any new dimensions to output */ for(idx=0;idx<nbr_dmn_ass;idx++){ dmn_item=dmn_out_vtr.find(dmn_lst[idx].nm); if(dmn_item != NULL) continue; dmn_item=dmn_in_vtr.find(dmn_lst[idx].nm); if(dmn_item == NULL) continue; dmn_new=nco_dmn_dpl(dmn_item); (void)nco_dmn_dfn(fl_out,out_id,&dmn_new,1); (void)nco_dmn_xrf(dmn_new,dmn_item); (void)dmn_out_vtr.push(dmn_new); } /* end loop over idx */ /* Free current list of all dimensions in input file */ dmn_lst=nco_nm_id_lst_free(dmn_lst,nbr_dmn_ass); /* Dimensions for manually specified extracted variables are now defined in output file Add coordinate variables to extraction list If EXTRACT_ALL_COORDINATES then write associated dimension to output */ if(EXTRACT_ASSOCIATED_COORDINATES){ for(idx=0;idx<dmn_in_vtr.size();idx++){ if(!dmn_in_vtr[idx]->is_crd_dmn) continue; if(EXTRACT_ALL_COORDINATES && !dmn_in_vtr[idx]->xrf){ /* Add dimensions to output list dmn_out */ dmn_item=dmn_in_vtr[idx]; dmn_new=nco_dmn_dpl(dmn_item); (void)nco_dmn_xrf(dmn_new,dmn_item); /* Write dimension to output */ (void)nco_dmn_dfn(fl_out,out_id,&dmn_new,1); (void)dmn_out_vtr.push(dmn_new); } /* end if */ /* Add coordinate variable to extraction list, dimension has already been output */ if(dmn_in_vtr[idx]->xrf){ for(jdx=0;jdx<nbr_xtr;jdx++) if(!strcmp(xtr_lst[jdx].nm,dmn_in_vtr[idx]->nm)) break; if(jdx != nbr_xtr) continue; /* If coordinate is not on list then add it to extraction list */ xtr_lst=(nm_id_sct *)nco_realloc(xtr_lst,(nbr_xtr+1)*sizeof(nm_id_sct)); xtr_lst[nbr_xtr].nm=(char *)strdup(dmn_in_vtr[idx]->nm); xtr_lst[nbr_xtr++].id=dmn_in_vtr[idx]->cid; } /* endif */ } /* end loop over idx */ } /* end if */ /* Subtract list A again (it may contain re-defined coordinates) */ if(nbr_xtr > 0) xtr_lst=nco_var_lst_sub(xtr_lst,&nbr_xtr,xtr_lst_a,nbr_lst_a); /* Sort extraction list for faster I/O */ if(nbr_xtr > 1) xtr_lst=nco_lst_srt_nm_id(xtr_lst,nbr_xtr,False); /* Is this an CCM/CCSM/CF-format history tape? */ CNV_CCM_CCSM_CF=nco_cnv_ccm_ccsm_cf_inq(in_id); /* Write "fixed" variables */ var=(var_sct **)nco_malloc(nbr_xtr*sizeof(var_sct *)); var_out=(var_sct **)nco_malloc(nbr_xtr*sizeof(var_sct *)); for(idx=0;idx<nbr_xtr;idx++){ var[idx]=nco_var_fll(in_id,xtr_lst[idx].id,xtr_lst[idx].nm,dmn_in_vtr.ptr(0),dmn_in_vtr.size()); 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 idx */ /* NB: ncap is not well-suited for nco_var_lst_dvd() */ /* Divide variable lists into lists of fixed variables and variables to be processed */ (void)nco_var_lst_dvd(var,var_out,nbr_xtr,CNV_CCM_CCSM_CF,nco_pck_plc_nil,nco_pck_map_nil,(dmn_sct **)NULL,(int)0,&var_fix,&var_fix_out,&nbr_var_fix,&var_prc,&var_prc_out,&nbr_var_prc); /* csz: Why not call this with var_fix? */ /* Define non-processed vars */ (void)nco_var_dfn(in_id,fl_out,out_id,var_out,nbr_xtr,(dmn_sct **)NULL,(int)0,nco_pck_plc_nil,nco_pck_map_nil); /* Write out new attributes possibly overwriting old ones */ for(idx=0;idx<var_vtr.size();idx++){ // Check if attrribute if( var_vtr[idx]->type != ncap_att) continue; att_char_posn=var_vtr[idx]->s_va_nm.find("@"); if(att_char_posn == std::string::npos) continue; (void)strcpy(att_sng,var_vtr[idx]->s_va_nm.c_str()); att_sng[att_char_posn]='\0'; att_item.att_nm=(att_sng+att_char_posn+1); att_item.var_nm=att_sng; att_item.sz=var_vtr[idx]->var->sz; att_item.type=var_vtr[idx]->var->type; att_item.val=var_vtr[idx]->var->val; att_item.mode=aed_overwrite; if(!strcmp(att_item.var_nm,"global")) var_id=NC_GLOBAL; else { rcd=nco_inq_varid_flg(out_id,att_item.var_nm,&var_id); if(rcd != NC_NOERR) continue; } // Check size; if(att_item.sz > NC_MAX_ATTRS ){ (void)fprintf(stdout,"%s: Attribute %s size %ld excceeds maximium %d\n",prg_nm_get(),att_item.att_nm,att_item.sz, NC_MAX_ATTRS ); continue; } /* NB: These attributes should probably be written prior to last data mode */ (void)nco_aed_prc(out_id,var_id,att_item); // delete NcapVar delete var_vtr[idx]; }/* end for */ /* Turn off default filling behavior to enhance efficiency */ rcd=nco_set_fill(out_id,NC_NOFILL,&fll_md_old); /* Take output file out of define mode */ (void)nco_enddef(out_id); /* Copy non-processed vars */ (void)nco_var_val_cpy(in_id,out_id,var_fix,nbr_var_fix); /* Close input netCDF file */ rcd=nco_close(in_id); /* Remove local copy of file */ if(FILE_RETRIEVED_FROM_REMOTE_LOCATION && REMOVE_REMOTE_FILES_AFTER_PROCESSING) (void)nco_fl_rm(fl_in); /* Close output file and move it from temporary to permanent location */ (void)nco_fl_out_cls(fl_out,fl_out_tmp,out_id); /* ncap-unique memory */ /* fxm: ncap-specific memory freeing instructions go here */ /* for(idx=0;idx<sym_tbl_nbr;idx++){ sym_tbl[idx]->nm=(char*)nco_free(sym_tbl[idx]->nm); sym_tbl[idx]=(sym_sct*)nco_free(sym_tbl[idx]); } sym_tbl=(sym_sct **)nco_free(sym_tbl); */ if(fl_spt_usr != NULL) fl_spt_usr=(char *)nco_free(fl_spt_usr); /* Free extraction lists */ xtr_lst=nco_nm_id_lst_free(xtr_lst,nbr_xtr); xtr_lst_a=nco_nm_id_lst_free(xtr_lst_a,nbr_lst_a); /* Free command line algebraic arguments, if any */ for(idx=0;idx<nbr_spt;idx++) spt_arg[idx]=(char *)nco_free(spt_arg[idx]); if(spt_arg_cat != NULL) spt_arg_cat=(char *)nco_free(spt_arg_cat); /* NCO-generic clean-up */ /* Free individual strings/arrays */ if(cmd_ln != NULL) cmd_ln=(char *)nco_free(cmd_ln); if(fl_in != NULL) fl_in=(char*)nco_free(fl_in); if(fl_out != NULL) fl_out=(char *)nco_free(fl_out); if(fl_out_tmp != NULL) fl_out_tmp=(char *)nco_free(fl_out_tmp); if(fl_pth != NULL) fl_pth=(char *)nco_free(fl_pth); if(fl_pth_lcl != NULL) fl_pth_lcl=(char *)nco_free(fl_pth_lcl); /* Free lists of strings */ if(fl_lst_in != NULL && fl_lst_abb == NULL) fl_lst_in=nco_sng_lst_free(fl_lst_in,fl_nbr); if(fl_lst_in != NULL && fl_lst_abb != NULL) fl_lst_in=nco_sng_lst_free(fl_lst_in,1); if(fl_lst_abb != NULL) fl_lst_abb=nco_sng_lst_free(fl_lst_abb,abb_arg_nbr); /* Free limits */ for(idx=0;idx<lmt_nbr;idx++) lmt_arg[idx]=(char *)nco_free(lmt_arg[idx]); if(lmt_nbr > 0) lmt=nco_lmt_lst_free(lmt,lmt_nbr); /* Free dimension lists */ if(nbr_dmn_in > 0) dmn_in=nco_dmn_lst_free(dmn_in,nbr_dmn_in); if(nbr_dmn_out > 0) dmn_out=nco_dmn_lst_free(dmn_out,nbr_dmn_out); /* Free variable lists */ if(nbr_xtr > 0) var=nco_var_lst_free(var,nbr_xtr); if(nbr_xtr > 0) var_out=nco_var_lst_free(var_out,nbr_xtr); 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); nco_exit_gracefully(); return EXIT_SUCCESS; } /* end main() */

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Variable Documentation

char** ncap_fl_spt_glb = NULL

Definition at line 78 of file ncap2.cc. Referenced by glb_init_free(), and main().

size_t* ncap_ln_nbr_crr

Definition at line 77 of file ncap2.cc. Referenced by glb_init_free(), and main().

size_t ncap_ncl_dpt_crr = 0UL

Definition at line 76 of file ncap2.cc. Referenced by glb_init_free(), and main().

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