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netcdf-c/ncdump/nccopy.c

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/*********************************************************************
* Copyright 2018, University Corporation for Atmospheric Research
* See netcdf/README file for copying and redistribution conditions.
* Thanks to Philippe Poilbarbe and Antonio S. Cofiño for
* compression additions.
* $Id: nccopy.c 400 2010-08-27 21:02:52Z russ $
*********************************************************************/
#include "config.h" /* for USE_NETCDF4 macro */
#include <stddef.h>
#include <stdlib.h>
#include <stdio.h>
#ifdef HAVE_GETOPT_H
#include <getopt.h>
#endif
#if defined(_WIN32) && !defined(__MINGW32__)
#include "XGetopt.h"
#endif
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#include <string.h>
#include "netcdf.h"
#include "netcdf_filter.h"
#include "netcdf_aux.h"
#include "nciter.h"
#include "utils.h"
#include "chunkspec.h"
#include "dimmap.h"
#include "nccomps.h"
#include "list.h"
#include "ncpathmgr.h"
#undef DEBUGFILTER
#undef DEBUGCHUNK
/* default bytes of memory we are willing to allocate for variable
* values during copy */
#define COPY_BUFFER_SIZE (5000000)
#define COPY_CHUNKCACHE_PREEMPTION (1.0F) /* for copying, can eject fully read chunks */
#define SAME_AS_INPUT (-1) /* default, if kind not specified */
#define CHUNK_THRESHOLD (8192) /* non-record variables with fewer bytes don't get chunked */
#ifndef USE_NETCDF4
#define NC_CLASSIC_MODEL 0x0100 /* Enforce classic model if netCDF-4 not available. */
#endif
/* Ascii characters requiring escaping as lead*/
#define ESCAPESD "0123456789"
#define ESCAPES " !\"#$%&'()*,:;<=>?[]\\^`{|}~"
#define DFALTUNLIMSIZE (4* 1<<20) /*4 megabytes */
#ifdef USE_NETCDF4
/* The unique id for a variable requires also the enclosing group id */
typedef struct VarID {
int grpid;
int varid;
} VarID;
#define MAX_FILTER_SPECS 64
#define MAX_FILTER_PARAMS 256
struct FilterOption {
char* fqn; /* Of variable */
int nofilter; /* 1=> do not apply any filters to this variable */
NC_H5_Filterspec pfs;
};
static List* filteroptions = NULL;
static int suppressfilters = 0; /* 1 => do not apply any output filters unless specified */
/* Forward declaration, because copy_type, copy_vlen_type call each other */
static int copy_type(int igrp, nc_type typeid, int ogrp);
static void freefilteroptlist(List* specs);
static void freefilterlist(size_t nfilters, NC_H5_Filterspec** filters);
#endif
/* table of formats for legal -k values */
static struct Kvalues {
char* name;
int kind;
} legalkinds[] = {
/* NetCDF-3 classic format (32-bit offsets) */
{"classic", NC_FORMAT_CLASSIC}, /* canonical format name */
{"nc3", NC_FORMAT_CLASSIC}, /* short format name */
{"1", NC_FORMAT_CLASSIC}, /* deprecated, use "-3" or "-k nc3" instead */
/* NetCDF-3 64-bit offset format */
{"64-bit offset", NC_FORMAT_64BIT_OFFSET}, /* canonical format name */
{"nc6", NC_FORMAT_64BIT_OFFSET}, /* short format name */
{"2", NC_FORMAT_64BIT_OFFSET}, /* deprecated, use "-6" or "-k nc6" instead */
{"64-bit-offset", NC_FORMAT_64BIT_OFFSET}, /* deprecated alias */
/* NetCDF-4 HDF5-based format */
{"netCDF-4", NC_FORMAT_NETCDF4}, /* canonical format name */
{"nc4", NC_FORMAT_NETCDF4}, /* short format name */
{"3", NC_FORMAT_NETCDF4}, /* deprecated, use "-4" or "-k nc4" instead */
{"netCDF4", NC_FORMAT_NETCDF4}, /* deprecated aliases */
{"hdf5", NC_FORMAT_NETCDF4},
{"enhanced", NC_FORMAT_NETCDF4},
/* NetCDF-4 HDF5-based format, restricted to classic data model */
{"netCDF-4 classic model", NC_FORMAT_NETCDF4_CLASSIC}, /* canonical format name */
{"nc7", NC_FORMAT_NETCDF4_CLASSIC}, /* short format name */
{"4", NC_FORMAT_NETCDF4_CLASSIC}, /* deprecated, use "-7" or -k nc7" */
{"netCDF-4-classic", NC_FORMAT_NETCDF4_CLASSIC}, /* deprecated aliases */
{"netCDF-4_classic", NC_FORMAT_NETCDF4_CLASSIC},
{"netCDF4_classic", NC_FORMAT_NETCDF4_CLASSIC},
{"hdf5-nc3", NC_FORMAT_NETCDF4_CLASSIC},
{"enhanced-nc3", NC_FORMAT_NETCDF4_CLASSIC},
/* The 64-bit data (CDF5) kind (5) */
{"5", NC_FORMAT_CDF5},
{"64-bit-data", NC_FORMAT_CDF5},
{"64-bit data", NC_FORMAT_CDF5},
{"nc5", NC_FORMAT_CDF5},
{"cdf5", NC_FORMAT_CDF5},
/* null terminate*/
{NULL,0}
};
/* Global variables for command-line requests */
char *progname; /* for error messages */
static int option_kind = SAME_AS_INPUT;
static int option_deflate_level = -1; /* default, compress output only if input compressed */
static int option_shuffle_vars = NC_NOSHUFFLE; /* default, no shuffling on compression */
static int option_fix_unlimdims = 0; /* default, preserve unlimited dimensions */
static List* option_chunkspecs = NULL; /* default, no chunk specification */
static size_t option_copy_buffer_size = COPY_BUFFER_SIZE;
static size_t option_chunk_cache_size = CHUNK_CACHE_SIZE; /* default from config.h */
static size_t option_chunk_cache_nelems = CHUNK_CACHE_NELEMS; /* default from config.h */
static int option_read_diskless = 0; /* default, don't read input into memory on open */
static int option_write_diskless = 0; /* default, don't write output to diskless file */
#ifdef USE_NETCDF4
static size_t option_min_chunk_bytes = CHUNK_THRESHOLD; /* default, don't chunk variable if prod of
* chunksizes of its dimensions is smaller
* than this */
#endif
static int option_nlgrps = 0; /* Number of groups specified with -g
* option on command line */
static char** option_lgrps = 0; /* list of group names specified with -g
* option on command line */
static idnode_t* option_grpids = 0; /* list of grpids matching list specified with -g option */
static bool_t option_grpstruct = false; /* if -g set, copy structure for non-selected groups */
static int option_nlvars = 0; /* Number of variables specified with -v * option on command line */
static char** option_lvars = 0; /* list of variable names specified with -v
* option on command line */
static bool_t option_varstruct = false; /* if -v set, copy structure for non-selected vars */
static int option_compute_chunkcaches = 0; /* default, don't try still flaky estimate of
* chunk cache for each variable */
/* get group id in output corresponding to group igrp in input,
* given parent group id (or root group id) parid in output. */
static int
get_grpid(int igrp, int parid, int *ogrpp) {
int stat = NC_NOERR;
int ogid = parid; /* like igrp but in output file */
#ifdef USE_NETCDF4
int inparid;
/* if not root group, get corresponding output groupid from group name */
stat = nc_inq_grp_parent(igrp, &inparid);
if(stat == NC_NOERR) { /* not root group */
char grpname[NC_MAX_NAME + 1];
NC_CHECK(nc_inq_grpname(igrp, grpname));
NC_CHECK(nc_inq_grp_ncid(parid, grpname, &ogid));
} else if(stat == NC_ENOGRP) { /* root group */
stat = NC_NOERR;
} else {
NC_CHECK(stat);
}
#endif /* USE_NETCDF4 */
*ogrpp = ogid;
return stat;
}
/* Return size in bytes of a variable value */
static size_t
val_size(int grpid, int varid) {
nc_type vartype;
size_t value_size;
NC_CHECK(nc_inq_vartype(grpid, varid, &vartype));
NC_CHECK(nc_inq_type(grpid, vartype, NULL, &value_size));
return value_size;
}
#ifdef USE_NETCDF4
/* Get parent id needed to define a new group from its full name in an
* open file identified by ncid. Assumes all intermediate groups are
* already defined. */
static int
nc_inq_parid(int ncid, const char *fullname, int *locidp) {
char *parent = strdup(fullname);
char *slash = "/"; /* groupname separator */
char *last_slash;
if(parent == NULL) {
return NC_ENOMEM; /* exits */
}
last_slash = strrchr(parent, '/');
if(last_slash == parent || last_slash == NULL) { /* parent is root */
free(parent);
parent = strdup(slash);
} else {
*last_slash = '\0'; /* truncate to get parent name */
}
NC_CHECK(nc_inq_grp_full_ncid(ncid, parent, locidp));
free(parent);
return NC_NOERR;
}
/* Compute the fully qualified name of a (grpid,varid) pair; caller must free */
static int
computeFQN(VarID vid, char** fqnp)
{
int stat = NC_NOERR;
size_t len;
char* fqn = NULL;
char vname[NC_MAX_NAME+1];
char escname[(2*NC_MAX_NAME)+1];
int first;
char *p, *q;
if((stat = nc_inq_grpname_full(vid.grpid,&len,NULL))) goto done;
fqn = (char*)malloc(len+1+(2*NC_MAX_NAME)+1);
if(fqn == NULL) {stat = NC_ENOMEM; goto done;}
if((stat=nc_inq_grpname_full(vid.grpid,&len,fqn))) goto done;
fqn[len] = '\0'; /* guarantee */
if((stat=nc_inq_varname(vid.grpid,vid.varid,vname))) goto done;
vname[NC_MAX_NAME] = '\0';
if(strlen(fqn) > 1) strcat(fqn,"/");
p = vname;
q = escname;
for(first=1;*p;first=0) {
if((first && strchr(ESCAPESD,*p) != NULL)
|| strchr(ESCAPES,*p) != NULL) *q++ = '\\';
*q++ = *p++;
}
*q++ = '\0'; /* guarantee */
strcat(fqn,escname);
done:
if(stat == NC_NOERR && fqnp != NULL) {*fqnp = fqn; fqn = NULL;}
return stat;
}
static int
parsevarlist(char* vars, List* vlist)
{
int stat = NC_NOERR;
char* q = NULL;
int nvars = 0;
/* Special case 1: empty set of vars */
if(vars == NULL || strlen(vars)==0) {stat = NC_EINVAL; goto done;}
/* Special case 2: "*" */
if(strcmp(vars,"*")==0) {
listpush(vlist,strdup("*"));
goto done;
}
/* Walk delimitng on '&' separators */
for(q=vars;*q;q++) {
if(*q == '\\') q++;
else if(*q == '&') {*q = '\0'; nvars++;}
/* else continue */
}
nvars++; /*for last var*/
/* Rewalk to capture the variables */
for(q=vars;nvars > 0; nvars--) {
listpush(vlist,strdup(q));
q += (strlen(q)+1); /* move to next */
}
done:
return stat;
}
static int
parsefilterspec(const char* optarg0, List* speclist)
{
int stat = NC_NOERR;
char* optarg = NULL;
char* p = NULL;
char* remainder = NULL;
List* vlist = NULL;
int isnone = 0;
size_t nfilters = 0;
NC_H5_Filterspec** filters = NULL;
if(optarg0 == NULL || strlen(optarg0) == 0 || speclist == NULL) return 0;
optarg = strdup(optarg0);
/* Delimit the initial set of variables, taking escapes into account */
p = optarg;
remainder = NULL;
for(;;p++) {
if(*p == '\0') {remainder = p; break;}
else if(*p == ',') {*p = '\0'; remainder = p+1; break;}
else if(*p == '\\') p++;
/* else continue */
}
/* Parse the variable list */
if((vlist = listnew()) == NULL) {stat = NC_ENOMEM; goto done;}
if((stat=parsevarlist(optarg,vlist))) goto done;
if(strcasecmp(remainder,"none") != 0) {
/* Collect the id+parameters */
if((stat=ncaux_h5filterspec_parselist(remainder,NULL,&nfilters,&filters))) goto done;
} else {
isnone = 1;
if(nfilters == 0) {
/* Add a fake filter */
NC_H5_Filterspec* nilspec = (NC_H5_Filterspec*)calloc(1,sizeof(NC_H5_Filterspec));
if(nilspec == NULL) {stat = NC_ENOMEM; goto done;}
nfilters = 1;
filters = calloc(1,sizeof(NC_H5_Filterspec**));
if(filters == NULL) {free(nilspec); stat = NC_ENOMEM; goto done;}
filters[0] = nilspec; nilspec = NULL;
}
}
/* Construct a spec entry for each element in vlist */
for(size_t i=0;i<listlength(vlist);i++) {
int k;
size_t vlen;
struct FilterOption* filtopt = NULL;
const char* var = listget(vlist,i);
if(var == NULL || strlen(var) == 0) continue;
vlen = strlen(var);
for(k=0;k<nfilters;k++) {
NC_H5_Filterspec* nsf = filters[k];
if((filtopt = calloc(1,sizeof(struct FilterOption)))==NULL)
{stat = NC_ENOMEM; goto done;}
filtopt->fqn = malloc(vlen+1+1); /* make room for nul and possible prefix '/' */
if(filtopt->fqn == NULL) {stat = NC_ENOMEM; goto done;}
filtopt->fqn[0] = '\0'; /* for strlcat */
if(strcmp(var,"*") != 0 && var[0] != '/') strlcat(filtopt->fqn,"/",vlen+2);
strlcat(filtopt->fqn,var,vlen+2);
if(isnone) {
filtopt->nofilter = 1;
} else {
filtopt->pfs = *nsf;
if(nsf->nparams != 0) {
/* Duplicate the params */
filtopt->pfs.params = calloc(filtopt->pfs.nparams,sizeof(unsigned int));
if(filtopt->pfs.params == NULL) {stat = NC_ENOMEM; goto done;}
memcpy(filtopt->pfs.params,nsf->params,sizeof(unsigned int)*filtopt->pfs.nparams);
} else
filtopt->pfs.params = NULL;
}
listpush(filteroptions,filtopt);
filtopt = NULL;
}
}
done:
freefilterlist(nfilters,filters);
if(vlist) listfreeall(vlist);
if(optarg) free(optarg);
return stat;
}
/* Return 1 if variable has only active (ie not none) filters */
static int
varfiltersactive(const char* ofqn)
{
int hasnone = 0;
int hasactive = 0;
/* See which output filter options are defined for this output variable */
for(size_t i=0;i<listlength(filteroptions);i++) {
struct FilterOption* opt = listget(filteroptions,i);
if(strcmp(opt->fqn,"*")==0 || strcmp(opt->fqn,ofqn)==0)
{if(opt->nofilter) hasnone = 1;} else {hasactive = 1;}
}
return (hasactive && !hasnone ? 1 : 0);
}
/* Return 1 if variable has "none" filters */
static int
varfilterssuppress(const char* ofqn)
{
int hasnone = 0;
/* See which output filter options are defined for this output variable */
for(size_t i=0;i<listlength(filteroptions);i++) {
struct FilterOption* opt = listget(filteroptions,i);
if(strcmp(opt->fqn,"*")==0 || strcmp(opt->fqn,ofqn)==0)
{if(opt->nofilter) hasnone = 1;}
}
return hasnone || suppressfilters;
}
/* Return list of active filters */
static List*
filteroptsforvar(const char* ofqn)
{
List* list = listnew();
/* See which output filter options are defined for this output variable;
both active and none. */
for(size_t i=0;i<listlength(filteroptions);i++) {
struct FilterOption* opt = listget(filteroptions,i);
if(strcmp(opt->fqn,"*")==0 || strcmp(opt->fqn,ofqn)==0) {
if(!opt->nofilter) /* Add to the list */
listpush(list,opt);
}
}
return list;
}
/* Return size of chunk in bytes for a variable varid in a group igrp, or 0 if
* layout is contiguous|compact */
static int
inq_var_chunksize(int igrp, int varid, size_t* chunksizep) {
int stat = NC_NOERR;
int ndims;
size_t *chunksizes;
int dim;
int contig = NC_CONTIGUOUS;
nc_type vartype;
size_t value_size;
size_t prod;
NC_CHECK(nc_inq_vartype(igrp, varid, &vartype));
/* from type, get size in memory needed for each value */
NC_CHECK(nc_inq_type(igrp, vartype, NULL, &value_size));
prod = value_size;
NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
chunksizes = (size_t *) emalloc((size_t)(ndims + 1) * sizeof(size_t));
contig = NC_CHUNKED;
NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, NULL));
if(contig != NC_CHUNKED) {
*chunksizep = 0;
} else {
NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, chunksizes));
for(dim = 0; dim < ndims; dim++) {
prod *= chunksizes[dim];
}
*chunksizep = prod;
}
free(chunksizes);
return stat;
}
/* Return estimated number of elems required in chunk cache and
* estimated size of chunk cache adequate to efficiently copy input
* variable ivarid to output variable ovarid, which may have different
* chunk size and shape */
static int
inq_var_chunking_params(int igrp, int ivarid, int ogrp, int ovarid,
size_t* chunkcache_sizep,
size_t *chunkcache_nelemsp,
float * chunkcache_preemptionp)
{
int stat = NC_NOERR;
int ndims;
size_t *ichunksizes, *ochunksizes;
int icontig = NC_CONTIGUOUS, ocontig = NC_CONTIGUOUS;
nc_type vartype;
size_t value_size;
size_t prod, iprod, oprod;
size_t nelems;
*chunkcache_nelemsp = CHUNK_CACHE_NELEMS;
*chunkcache_sizep = CHUNK_CACHE_SIZE;
*chunkcache_preemptionp = COPY_CHUNKCACHE_PREEMPTION;
NC_CHECK(nc_inq_varndims(igrp, ivarid, &ndims));
icontig = (ocontig = NC_CHUNKED);
NC_CHECK(nc_inq_var_chunking(igrp, ivarid, &icontig, NULL));
NC_CHECK(nc_inq_var_chunking(ogrp, ovarid, &ocontig, NULL));
if(icontig != NC_CHUNKED && ocontig != NC_CHUNKED) { /* no chunking in input or output */
*chunkcache_nelemsp = 0;
*chunkcache_sizep = 0;
*chunkcache_preemptionp = 0;
return stat;
}
NC_CHECK(nc_inq_vartype(igrp, ivarid, &vartype));
NC_CHECK(nc_inq_type(igrp, vartype, NULL, &value_size));
iprod = value_size;
if(icontig == NC_CHUNKED && ocontig != NC_CHUNKED) { /* chunking only in input */
*chunkcache_nelemsp = 1; /* read one input chunk at a time */
*chunkcache_sizep = iprod;
*chunkcache_preemptionp = 1.0F;
return stat;
}
ichunksizes = (size_t *) emalloc((size_t)(ndims + 1) * sizeof(size_t));
if(icontig != NC_CHUNKED) { /* if input contiguous|compact, treat as if chunked on
* first dimension */
ichunksizes[0] = 1;
for(size_t dim = 1; dim < ndims; dim++) {
ichunksizes[dim] = dim;
}
} else {
NC_CHECK(nc_inq_var_chunking(igrp, ivarid, &icontig, ichunksizes));
}
/* now can pretend chunking in both input and output */
ochunksizes = (size_t *) emalloc((size_t)(ndims + 1) * sizeof(size_t));
NC_CHECK(nc_inq_var_chunking(ogrp, ovarid, &ocontig, ochunksizes));
nelems = 1;
oprod = value_size;
for(size_t dim = 0; dim < ndims; dim++) {
nelems += 1 + (ichunksizes[dim] - 1) / ochunksizes[dim];
iprod *= ichunksizes[dim];
oprod *= ochunksizes[dim];
}
prod = iprod + oprod * (nelems - 1);
*chunkcache_nelemsp = nelems;
*chunkcache_sizep = prod;
free(ichunksizes);
free(ochunksizes);
return stat;
}
/*
* copy a user-defined variable length type in the group igrp to the
* group ogrp
*/
static int
copy_vlen_type(int igrp, nc_type itype, int ogrp)
{
int stat = NC_NOERR;
nc_type ibasetype;
nc_type obasetype; /* base type in target group */
char name[NC_MAX_NAME];
size_t size;
char basename[NC_MAX_NAME];
size_t basesize;
nc_type vlen_type;
NC_CHECK(nc_inq_vlen(igrp, itype, name, &size, &ibasetype));
/* to get base type id in target group, use name of base type in
* source group */
NC_CHECK(nc_inq_type(igrp, ibasetype, basename, &basesize));
stat = nc_inq_typeid(ogrp, basename, &obasetype);
/* if no such type, create it now */
if(stat == NC_EBADTYPE) {
NC_CHECK(copy_type(igrp, ibasetype, ogrp));
stat = nc_inq_typeid(ogrp, basename, &obasetype);
}
NC_CHECK(stat);
/* Now we know base type exists in output and we know its type id */
NC_CHECK(nc_def_vlen(ogrp, name, obasetype, &vlen_type));
return stat;
}
/*
* copy a user-defined opaque type in the group igrp to the group ogrp
*/
static int
copy_opaque_type(int igrp, nc_type itype, int ogrp)
{
int stat = NC_NOERR;
nc_type otype;
char name[NC_MAX_NAME];
size_t size;
NC_CHECK(nc_inq_opaque(igrp, itype, name, &size));
NC_CHECK(nc_def_opaque(ogrp, size, name, &otype));
return stat;
}
/*
* copy a user-defined enum type in the group igrp to the group ogrp
*/
static int
copy_enum_type(int igrp, nc_type itype, int ogrp)
{
int stat = NC_NOERR;
nc_type otype;
nc_type basetype;
size_t basesize;
size_t nmembers;
char name[NC_MAX_NAME];
int i;
NC_CHECK(nc_inq_enum(igrp, itype, name, &basetype, &basesize, &nmembers));
NC_CHECK(nc_def_enum(ogrp, basetype, name, &otype));
for(i = 0; i < nmembers; i++) { /* insert enum members */
char ename[NC_MAX_NAME];
long long val; /* large enough to hold any integer type */
NC_CHECK(nc_inq_enum_member(igrp, itype, i, ename, &val));
NC_CHECK(nc_insert_enum(ogrp, otype, ename, &val));
}
return stat;
}
/*
* copy a user-defined compound type in the group igrp to the group ogrp
*/
static int
copy_compound_type(int igrp, nc_type itype, int ogrp)
{
int stat = NC_NOERR;
char name[NC_MAX_NAME];
size_t size;
size_t nfields;
nc_type otype;
int fid;
NC_CHECK(nc_inq_compound(igrp, itype, name, &size, &nfields));
NC_CHECK(nc_def_compound(ogrp, size, name, &otype));
for (fid = 0; fid < nfields; fid++) {
char fname[NC_MAX_NAME];
char ftypename[NC_MAX_NAME];
size_t foff;
nc_type iftype, oftype;
int fndims;
NC_CHECK(nc_inq_compound_field(igrp, itype, fid, fname, &foff, &iftype, &fndims, NULL));
/* type ids in source don't necessarily correspond to same
* typeids in destination, so look up destination typeid by using
* field type name */
NC_CHECK(nc_inq_type(igrp, iftype, ftypename, NULL));
NC_CHECK(nc_inq_typeid(ogrp, ftypename, &oftype));
if(fndims == 0) {
NC_CHECK(nc_insert_compound(ogrp, otype, fname, foff, oftype));
} else { /* field is array type */
int *fdimsizes;
fdimsizes = (int *) emalloc((size_t)(fndims + 1) * sizeof(int));
stat = nc_inq_compound_field(igrp, itype, fid, NULL, NULL, NULL,
NULL, fdimsizes);
NC_CHECK(nc_insert_array_compound(ogrp, otype, fname, foff, oftype, fndims, fdimsizes));
free(fdimsizes);
}
}
return stat;
}
/*
* copy a user-defined type in the group igrp to the group ogrp
*/
static int
copy_type(int igrp, nc_type typeid, int ogrp)
{
int stat = NC_NOERR;
nc_type type_class;
NC_CHECK(nc_inq_user_type(igrp, typeid, NULL, NULL, NULL, NULL, &type_class));
switch(type_class) {
case NC_VLEN:
NC_CHECK(copy_vlen_type(igrp, typeid, ogrp));
break;
case NC_OPAQUE:
NC_CHECK(copy_opaque_type(igrp, typeid, ogrp));
break;
case NC_ENUM:
NC_CHECK(copy_enum_type(igrp, typeid, ogrp));
break;
case NC_COMPOUND:
NC_CHECK(copy_compound_type(igrp, typeid, ogrp));
break;
default:
NC_CHECK(NC_EBADTYPE);
}
return stat;
}
/* Copy a group and all its subgroups, recursively, from iroot to
* oroot, the ncids of input file and output file. This just creates
* all the groups in the destination, but doesn't copy anything that's
* in the groups yet. */
static int
copy_groups(int iroot, int oroot)
{
int stat = NC_NOERR;
size_t numgrps;
int *grpids;
int i;
/* get total number of groups and their ids, including all descendants */
NC_CHECK(nc_inq_grps_full(iroot, &numgrps, NULL));
if(numgrps > 1) { /* there's always 1 root group */
grpids = emalloc(numgrps * sizeof(int));
NC_CHECK(nc_inq_grps_full(iroot, NULL, grpids));
/* create corresponding new groups in ogrp, except for root group */
for(i = 1; i < numgrps; i++) {
char *grpname_full;
char grpname[NC_MAX_NAME];
size_t len_name;
int ogid = 0, oparid = 0, iparid = 0;
/* get full group name of input group */
NC_CHECK(nc_inq_grpname(grpids[i], grpname));
if (option_grpstruct || group_wanted(grpids[i], option_nlgrps, option_grpids)) {
NC_CHECK(nc_inq_grpname_full(grpids[i], &len_name, NULL));
grpname_full = emalloc(len_name + 1);
NC_CHECK(nc_inq_grpname_full(grpids[i], &len_name, grpname_full));
/* Make sure, the parent group is also wanted (root group is always wanted) */
NC_CHECK(nc_inq_parid(iroot, grpname_full, &iparid));
if (!option_grpstruct && !group_wanted(iparid, option_nlgrps, option_grpids)
&& iparid != iroot) {
error("ERROR: trying to copy a group but not the parent: %s", grpname_full);
}
/* get id of parent group of corresponding group in output.
* Note that this exists, because nc_inq_groups returned
* grpids in preorder, so parents are always copied before
* their subgroups */
NC_CHECK(nc_inq_parid(oroot, grpname_full, &oparid));
NC_CHECK(nc_inq_grpname(grpids[i], grpname));
/* define corresponding group in output */
NC_CHECK(nc_def_grp(oparid, grpname, &ogid));
free(grpname_full);
}
}
free(grpids);
}
return stat;
}
/*
* Copy the user-defined types in this group (igrp) and all its
* subgroups, recursively, to corresponding group in output (ogrp)
*/
static int
copy_types(int igrp, int ogrp)
{
int stat = NC_NOERR;
int ntypes;
nc_type *types = NULL;
int numgrps;
int *grpids = NULL;
int i;
NC_CHECK(nc_inq_typeids(igrp, &ntypes, NULL));
if(ntypes > 0) {
types = (nc_type *) emalloc((size_t)ntypes * sizeof(nc_type));
NC_CHECK(nc_inq_typeids(igrp, &ntypes, types));
for (i = 0; i < ntypes; i++) {
NC_CHECK(copy_type(igrp, types[i], ogrp));
}
free(types);
}
/* Copy types from subgroups */
NC_CHECK(nc_inq_grps(igrp, &numgrps, NULL));
if(numgrps > 0) {
grpids = (int *)emalloc(sizeof(int) * (size_t)numgrps);
NC_CHECK(nc_inq_grps(igrp, &numgrps, grpids));
for(i = 0; i < numgrps; i++) {
if (option_grpstruct || group_wanted(grpids[i], option_nlgrps, option_grpids)) {
int ogid;
/* get groupid in output corresponding to grpids[i] in
* input, given parent group (or root group) ogrp in
* output */
NC_CHECK(get_grpid(grpids[i], ogrp, &ogid));
NC_CHECK(copy_types(grpids[i], ogid));
}
}
free(grpids);
}
return stat;
}
/* Copy netCDF-4 specific variable filter properties */
/* Watch out if input is netcdf-3 */
static int
copy_var_filter(int igrp, int varid, int ogrp, int o_varid, int inkind, int outkind)
{
int stat = NC_NOERR;
VarID vid = {igrp,varid};
VarID ovid = {ogrp,o_varid};
/* handle filter parameters, copying from input, overriding with command-line options */
List* ospecs = NULL;
List* inspecs = NULL;
List* actualspecs = NULL;
struct FilterOption inspec;
struct FilterOption* tmp = NULL;
char* ofqn = NULL;
int inputdefined, outputdefined, unfiltered;
int innc4 = (inkind == NC_FORMAT_NETCDF4 || inkind == NC_FORMAT_NETCDF4_CLASSIC);
int outnc4 = (outkind == NC_FORMAT_NETCDF4 || outkind == NC_FORMAT_NETCDF4_CLASSIC);
int suppressvarfilters = 0;
if(!outnc4)
goto done; /* Can only use filter when output is some netcdf4 variant */
/* Compute the output vid's FQN */
if((stat = computeFQN(ovid,&ofqn))) goto done;
/* Clear the in and out specs */
inspecs = listnew();
ospecs = NULL;
actualspecs = NULL;
if(varfilterssuppress(ofqn) || option_deflate_level == 0)
suppressvarfilters = 1;
/* Is there one or more filters on the output variable */
outputdefined = 0; /* default is no filter defined */
/* See if any output filter spec is defined for this output variable */
ospecs = filteroptsforvar(ofqn);
if(listlength(ospecs) > 0 && !suppressfilters && !suppressvarfilters)
outputdefined = 1;
/* Is there already a filter on the input variable */
inputdefined = 0; /* default is no filter defined */
/* Only bother to look if input is netcdf-4 variant */
if(innc4) {
size_t nfilters;
unsigned int* ids = NULL;
int k;
if((stat = nc_inq_var_filter_ids(vid.grpid,vid.varid,&nfilters,NULL)))
goto done;
if(nfilters > 0) ids = (unsigned int*)calloc(nfilters,sizeof(unsigned int));
if((stat = nc_inq_var_filter_ids(vid.grpid,vid.varid,&nfilters,ids)))
goto done;
memset(&inspec,0,sizeof(inspec));
for(k=0;k<nfilters;k++) {
inspec.pfs.filterid = ids[k];
stat=nc_inq_var_filter_info(vid.grpid,vid.varid,inspec.pfs.filterid,&inspec.pfs.nparams,NULL);
if(stat && stat != NC_ENOFILTER)
goto done; /* true error */
if(inspec.pfs.nparams > 0) {
inspec.pfs.params = (unsigned int*)calloc(sizeof(char*),inspec.pfs.nparams);
if((stat=nc_inq_var_filter_info(vid.grpid,vid.varid,inspec.pfs.filterid,NULL,inspec.pfs.params)))
goto done;
}
tmp = malloc(sizeof(struct FilterOption));
*tmp = inspec;
memset(&inspec,0,sizeof(inspec)); /*reset*/
listpush(inspecs,tmp);
inputdefined = 1;
}
nullfree(ids);
}
/* Rules for choosing output filter are as follows (Ugh!):
global output input Actual Output
suppress filter(s) filter(s) filter
-----------------------------------------------------------
1 true undefined NA unfiltered
2 true 'none' NA unfiltered
3 true defined NA use output filter(s)
4 false undefined defined use input filter(s)
5 false 'none' NA unfiltered
6 false defined NA use output filter(s)
7 false undefined undefined unfiltered
8 false defined defined use output filter(s)
*/
unfiltered = 0;
if(suppressfilters && !outputdefined) /* row 1 */
unfiltered = 1;
else if(suppressfilters || suppressvarfilters) /* row 2 */
unfiltered = 1;
else if(suppressfilters && outputdefined) /* row 3 */
actualspecs = ospecs;
else if(!suppressfilters && !outputdefined && inputdefined) /* row 4 */
actualspecs = inspecs;
else if(!suppressfilters && suppressvarfilters) /* row 5 */
unfiltered = 1;
else if(!suppressfilters && outputdefined) /* row 6*/
actualspecs = ospecs;
else if(!suppressfilters && !outputdefined && !inputdefined) /* row 7 */
unfiltered = 1;
else if(!suppressfilters && outputdefined && inputdefined) /* row 8 */
actualspecs = ospecs;
/* Apply actual filter spec if any */
if(!unfiltered) {
/* add all the actual filters */
for(size_t k=0;k<listlength(actualspecs);k++) {
struct FilterOption* actual = (struct FilterOption*)listget(actualspecs,k);
if((stat=nc_def_var_filter(ovid.grpid,ovid.varid,
actual->pfs.filterid,
actual->pfs.nparams,
actual->pfs.params)))
goto done;
}
}
done:
/* Cleanup */
if(ofqn != NULL) free(ofqn);
freefilteroptlist(inspecs); inspecs = NULL;
listfree(ospecs); ospecs = NULL; /* Contents are also in filterspecs */
/* Note we do not clean actualspec because it is a copy of in|out spec */
return stat;
}
/* Propagate chunking from input to output taking -c flags into account. */
/* Subsumes old set_var_chunked */
/* Must make sure we do not override the default chunking when input is classic */
static int
copy_chunking(int igrp, int i_varid, int ogrp, int o_varid, int ndims, int inkind, int outkind)
{
int stat = NC_NOERR;
int innc4 = (inkind == NC_FORMAT_NETCDF4 || inkind == NC_FORMAT_NETCDF4_CLASSIC);
int outnc4 = (outkind == NC_FORMAT_NETCDF4 || outkind == NC_FORMAT_NETCDF4_CLASSIC);
VarID ovid;
char* ofqn = NULL;
int icontig = NC_CONTIGUOUS;
int ocontig = NC_CONTIGUOUS;
size_t ichunkp[NC_MAX_VAR_DIMS];
size_t ochunkp[NC_MAX_VAR_DIMS];
size_t dimlens[NC_MAX_VAR_DIMS];
size_t perdimchunklen[NC_MAX_VAR_DIMS]; /* the values of relevant -c dim/n specifications */
size_t dfaltchunkp[NC_MAX_VAR_DIMS]; /* default chunking for ovarid */
int is_unlimited = 0;
/* First, check the file kinds */
if(!outnc4)
return stat; /* no chunking */
memset(ichunkp,0,sizeof(ichunkp));
memset(ochunkp,0,sizeof(ochunkp));
memset(dimlens,0,sizeof(dimlens));
memset(perdimchunklen,0,sizeof(perdimchunklen));
memset(dfaltchunkp,0,sizeof(dfaltchunkp));
/* Get the chunking, if any, on the current input variable */
if(innc4) {
NC_CHECK(nc_inq_var_chunking(igrp, i_varid, &icontig, ichunkp));
/* pretend that this is same as a -c option */
} else { /* !innc4 */
icontig = NC_CONTIGUOUS;
ichunkp[0] = 0;
}
/* If var specific chunking was specified for this output variable
then it overrides all else.
*/
/* Note, using goto done instead of nested if-then-else */
/* First check on output contiguous'ness */
/* Note: the chunkspecs are defined in terms of input variable+grp ids.
The grp may differ if !innc4 && outnc4 */
if(varchunkspec_omit(igrp,i_varid))
ocontig = NC_CONTIGUOUS;
else if(varchunkspec_exists(igrp,i_varid))
ocontig = varchunkspec_kind(igrp,i_varid);
else
ocontig = icontig;
/* Figure out the chunking even if we do not decide to do so*/
if(varchunkspec_exists(igrp,i_varid)
&& varchunkspec_kind(igrp,i_varid) == NC_CHUNKED)
memcpy(ochunkp,varchunkspec_chunksizes(igrp,i_varid),(size_t)ndims*sizeof(size_t));
/* If any kind of output filter was specified, then not contiguous */
ovid.grpid = ogrp;
ovid.varid = o_varid;
if((stat=computeFQN(ovid,&ofqn))) goto done;
if(!varfilterssuppress(ofqn) && (option_deflate_level > 0 || varfiltersactive(ofqn)))
ocontig = NC_CHUNKED;
/* See about dim-specific chunking; does not override specific variable chunk spec*/
{
int idim;
/* size of a chunk: product of dimension chunksizes and size of value */
size_t csprod;
size_t typesize;
int dimids[NC_MAX_VAR_DIMS];
/* See if dim-specific chunking was suppressed */
if(dimchunkspec_omit()) { /* no chunking at all on output, except as overridden by e.g. compression */
ocontig = NC_CONTIGUOUS;
goto next2;
}
/* Setup for possible output chunking */
typesize = val_size(igrp, i_varid);
csprod = typesize;
memset(&dimids,0,sizeof(dimids));
/* Prepare to iterate over the dimids of this input variable */
NC_CHECK(nc_inq_vardimid(igrp, i_varid, dimids));
/* Capture dimension lengths for all dimensions of variable */
/* Also, capture per-dimension -c specs even if we decide to not chunk */
for(idim = 0; idim < ndims; idim++) {
int idimid = dimids[idim];
int odimid = dimmap_odimid(idimid);
/* Get input dimension length */
NC_CHECK(nc_inq_dimlen(igrp, idimid, &dimlens[idim]));
/* Check for unlimited */
if(dimmap_ounlim(odimid)) {
is_unlimited = 1;
ocontig = NC_CHUNKED; /* force chunking */
}
if(dimchunkspec_exists(idimid)) {
/* If the -c set a chunk size for this dimension, capture it */
perdimchunklen[idim] = dimchunkspec_size(idimid); /* Save it */
ocontig = NC_CHUNKED; /* force chunking */
}
/* Default for unlimited is max(4 megabytes, current dim size) */
if(is_unlimited) {
size_t mb4dimsize = DFALTUNLIMSIZE / typesize;
if(dimlens[idim] > mb4dimsize)
dimlens[idim] = mb4dimsize;
}
}
/* Get the current default chunking on the output variable */
/* Unfortunately, there is no way to get this info except by
forcing chunking */
if(ocontig == NC_CHUNKED) {
/* this may fail if chunking is not possible, in which case ignore */
int ret = nc_def_var_chunking(ogrp, o_varid, NC_CHUNKED, dfaltchunkp);
if(ret == NC_NOERR) {
int storage;
NC_CHECK(nc_inq_var_chunking(ogrp, o_varid, &storage, dfaltchunkp));
if(storage != NC_CHUNKED) return NC_EINTERNAL;
}
}
/* compute the final ochunksizes: precedence is output, per-dim-spec, input, defaults, dimlen */
for(idim = 0; idim < ndims; idim++) {
if(ochunkp[idim] == 0) { /* use -c dim/n if specified */
if(perdimchunklen[idim] != 0)
ochunkp[idim] = perdimchunklen[idim];
}
if(ochunkp[idim] == 0) { /* use input chunk size */
if(ichunkp[idim] != 0)
ochunkp[idim] = ichunkp[idim];
}
if(ochunkp[idim] == 0) { /* use chunk defaults */
if(dfaltchunkp[idim] != 0)
ochunkp[idim] = dfaltchunkp[idim];
}
if(ochunkp[idim] == 0) { /* last resort: use full dimension size */
if(dimlens[idim] != 0)
ochunkp[idim] = dimlens[idim];
}
if(ochunkp[idim] == 0) {stat = NC_EINTERNAL; goto done;}
/* compute on-going dimension product */
csprod *= ochunkp[idim];
}
/* if total chunksize is too small (and dim is not unlimited) => do not chunk */
if(csprod < option_min_chunk_bytes && !is_unlimited)
ocontig = NC_CONTIGUOUS; /* Force contiguous */
}
next2:
/* Apply the chunking, if any */
switch (ocontig) {
case NC_CHUNKED:
NC_CHECK(nc_def_var_chunking(ogrp, o_varid, NC_CHUNKED, ochunkp));
break;
case NC_CONTIGUOUS:
case NC_COMPACT:
NC_CHECK(nc_def_var_chunking(ogrp, o_varid, ocontig, NULL));
break;
default: stat = NC_EINVAL; goto done;
}
#ifdef USE_NETCDF4
#ifdef DEBUGFILTER
{ int d;
size_t chunksizes[NC_MAX_VAR_DIMS];
char name[NC_MAX_NAME];
if(ocontig == NC_CONTIGUOUS) {
fprintf(stderr,"contig]\n");
} else if(ocontig == NC_COMPACT) {
fprintf(stderr,"compact]\n");
} else {
for(d=0;d<ndims;d++) {
totalsize *= ochunkp[d];
if(d > 0) fprintf(stderr,",");
fprintf(stderr,"%lu",(unsigned long)ochunkp[d]);
}
fprintf(stderr,"]=%llu\n",totalsize);
}
fflush(stderr);
}
#endif /*DEBUGFILTER*/
#endif /*USE_NETCDF4*/
done:
if(ofqn) free(ofqn);
return stat;
}
/* Copy all netCDF-4 specific variable properties such as chunking,
* endianness, deflation, checksumming, fill, etc. */
static int
copy_var_specials(int igrp, int varid, int ogrp, int o_varid, int inkind, int outkind)
{
int stat = NC_NOERR;
int innc4 = (inkind == NC_FORMAT_NETCDF4 || inkind == NC_FORMAT_NETCDF4_CLASSIC);
int outnc4 = (outkind == NC_FORMAT_NETCDF4 || outkind == NC_FORMAT_NETCDF4_CLASSIC);
int deflated = 0; /* true iff deflation is applied */
int ndims;
char* ofqn = NULL;
int nofilters = 0;
VarID ovid = {ogrp,o_varid};
if(!outnc4)
return stat; /* Ignore non-netcdf4 files */
{ /* handle chunking parameters */
NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
if (ndims > 0) { /* no chunking for scalar variables */
NC_CHECK(copy_chunking(igrp, varid, ogrp, o_varid, ndims, inkind, outkind));
}
}
if((stat=computeFQN(ovid,&ofqn))) goto done;
nofilters = varfilterssuppress(ofqn);
if(ndims > 0 && !nofilters)
{ /* handle compression parameters, copying from input, overriding
* with command-line options */
int shuffle_in=0, deflate_in=0, deflate_level_in=0;
int shuffle_out=0, deflate_out=0, deflate_level_out=0;
if(innc4) { /* See if the input variable has deflation applied */
NC_CHECK(nc_inq_var_deflate(igrp, varid, &shuffle_in, &deflate_in, &deflate_level_in));
}
if(option_deflate_level == -1) {
/* not specified by -d flag, copy input compression and shuffling */
shuffle_out = shuffle_in;
deflate_out = deflate_in;
deflate_level_out = deflate_level_in;
} else if(option_deflate_level > 0) { /* change to specified compression, shuffling */
shuffle_out = option_shuffle_vars;
deflate_out=1;
deflate_level_out = option_deflate_level;
} else if(option_deflate_level == 0) { /* special case; force off */
shuffle_out = 0;
deflate_out = 0;
deflate_level_out = 0;
}
/* Apply output deflation (unless suppressed) */
if(outnc4) {
/* Note that if we invoke this function and even if shuffle and deflate flags are 0,
then default chunking will be turned on; so do a special check for that. */
if(shuffle_out != 0 || deflate_out != 0)
NC_CHECK(nc_def_var_deflate(ogrp, o_varid, shuffle_out, deflate_out, deflate_level_out));
deflated = deflate_out;
}
}
if(!nofilters && innc4 && outnc4 && ndims > 0)
{ /* handle checksum parameters */
int fletcher32 = 0;
NC_CHECK(nc_inq_var_fletcher32(igrp, varid, &fletcher32));
if(fletcher32 != 0) {
NC_CHECK(nc_def_var_fletcher32(ogrp, o_varid, fletcher32));
}
}
if(innc4 && outnc4)
{ /* handle endianness */
int endianness = 0;
NC_CHECK(nc_inq_var_endian(igrp, varid, &endianness));
if(endianness != NC_ENDIAN_NATIVE) { /* native is the default */
NC_CHECK(nc_def_var_endian(ogrp, o_varid, endianness));
}
}
if(!nofilters && !deflated && ndims > 0) {
/* handle other general filters */
NC_CHECK(copy_var_filter(igrp, varid, ogrp, o_varid, inkind, outkind));
}
done:
if(ofqn) free(ofqn);
return stat;
}
#if 0
Subsumed into copy_chunking.
/* Set output variable o_varid (in group ogrp) to use chunking
* specified on command line, only called for classic format input and
* netCDF-4 format output, so no existing chunk lengths to override. */
static int
set_var_chunked(int ogrp, int o_varid)
{
int stat = NC_NOERR;
int ndims;
int odim;
size_t chunk_threshold = CHUNK_THRESHOLD;
if(dimchunkspec_ndims() == 0) /* no chunking specified on command line */
return stat;
NC_CHECK(nc_inq_varndims(ogrp, o_varid, &ndims));
if (ndims > 0) { /* no chunking for scalar variables */
int chunked = 0;
int *dimids = (int *) emalloc(ndims * sizeof(int));
size_t varsize;
nc_type vartype;
size_t value_size;
int is_unlimited = 0;
NC_CHECK(nc_inq_vardimid (ogrp, o_varid, dimids));
NC_CHECK(nc_inq_vartype(ogrp, o_varid, &vartype));
/* from type, get size in memory needed for each value */
NC_CHECK(nc_inq_type(ogrp, vartype, NULL, &value_size));
varsize = value_size;
/* Determine if this variable should be chunked. A variable
* should be chunked if any of its dims are in command-line
* chunk spec. It will also be chunked if any of its
* dims are unlimited. */
for(odim = 0; odim < ndims; odim++) {
int odimid = dimids[odim];
int idimid = dimmap_idimid(odimid); /* corresponding dimid in input file */
if(dimmap_ounlim(odimid))
is_unlimited = 1; /* whether vriable is unlimited */
if(idimid != -1) {
size_t chunksize = dimchunkspec_size(idimid); /* from chunkspec */
size_t dimlen;
NC_CHECK(nc_inq_dimlen(ogrp, odimid, &dimlen));
if( (chunksize > 0) || dimmap_ounlim(odimid)) {
chunked = 1;
}
if(dimlen > 0) { /* dimlen for unlimited dims is still 0 before copying data */
varsize *= dimlen;
}
}
}
/* Don't chunk small variables that don't use an unlimited
* dimension. */
if(varsize < chunk_threshold && !is_unlimited)
chunked = 0;
if(chunked) {
/* Allocate chunksizes and set defaults to dimsize for any
* dimensions not mentioned in chunkspec, except use 1 for unlimited dims. */
size_t *chunkp = (size_t *) emalloc(ndims * sizeof(size_t));
for(odim = 0; odim < ndims; odim++) {
int odimid = dimids[odim];
int idimid = dimmap_idimid(odimid);
size_t chunksize = dimchunkspec_size(idimid);
if(chunksize > 0) {
chunkp[odim] = chunksize;
} else {
if(dimmap_ounlim(odimid)){
chunkp[odim] = 1;
} else {
NC_CHECK(nc_inq_dimlen(ogrp, odimid, &chunkp[odim]));
}
}
}
NC_CHECK(nc_def_var_chunking(ogrp, o_varid, NC_CHUNKED, chunkp));
free(chunkp);
}
free(dimids);
}
return stat;
}
#endif
#if 0
/* Set variable to compression specified on command line */
static int
set_var_compressed(int ogrp, int o_varid)
{
int stat = NC_NOERR;
if (option_deflate_level > 0) {
int deflate = 1;
NC_CHECK(nc_def_var_deflate(ogrp, o_varid, option_shuffle_vars, deflate, option_deflate_level));
}
return stat;
}
#endif
/* Release the variable chunk cache allocated for variable varid in
* group grp. This is not necessary, but will save some memory when
* processing one variable at a time. */
#ifdef UNUSED
static int
free_var_chunk_cache(int grp, int varid)
{
int stat = NC_NOERR;
size_t chunk_cache_size = 1;
size_t cache_nelems = 1;
float cache_preemp = 0;
int kind;
NC_CHECK(nc_inq_format(grp, &kind));
if(kind == NC_FORMAT_NETCDF4 || kind == NC_FORMAT_NETCDF4_CLASSIC) {
int contig = NC_CONTIGUOUS
NC_CHECK(nc_inq_var_chunking(grp, varid, &contig, NULL));
if(contig == NC_CHUNKED) { /* chunked */
NC_CHECK(nc_set_var_chunk_cache(grp, varid, chunk_cache_size, cache_nelems, cache_preemp));
}
}
return stat;
}
#endif
#endif /* USE_NETCDF4 */
/* Copy dimensions from group igrp to group ogrp, also associate input
* dimids with output dimids (they need not match, because the input
* dimensions may have been defined in a different order than we define
* the output dimensions here. */
static int
copy_dims(int igrp, int ogrp)
{
int stat = NC_NOERR;
int ndims;
int dgrp;
#ifdef USE_NETCDF4
int nunlims;
int *dimids;
int *unlimids;
#else
int unlimid;
#endif /* USE_NETCDF4 */
NC_CHECK(nc_inq_ndims(igrp, &ndims));
#ifdef USE_NETCDF4
/* In netCDF-4 files, dimids may not be sequential because they
* may be defined in various groups, and we are only looking at one
* group at a time. */
/* Find the dimension ids in this group, don't include parents. */
dimids = (int *) emalloc((size_t)(ndims + 1) * sizeof(int));
NC_CHECK(nc_inq_dimids(igrp, NULL, dimids, 0));
/* Find the number of unlimited dimensions and get their IDs */
NC_CHECK(nc_inq_unlimdims(igrp, &nunlims, NULL));
unlimids = (int *) emalloc((size_t)(nunlims + 1) * sizeof(int));
NC_CHECK(nc_inq_unlimdims(igrp, NULL, unlimids));
#else
NC_CHECK(nc_inq_unlimdim(igrp, &unlimid));
#endif /* USE_NETCDF4 */
/* Copy each dimension to output, including unlimited dimension(s) */
for (dgrp = 0; dgrp < ndims; dgrp++) {
char name[NC_MAX_NAME];
size_t length;
int i_is_unlim;
int o_is_unlim;
int idimid, odimid;
#ifdef USE_NETCDF4
int uld;
#endif
i_is_unlim = 0;
#ifdef USE_NETCDF4
idimid = dimids[dgrp];
for (uld = 0; uld < nunlims; uld++) {
if(idimid == unlimids[uld]) {
i_is_unlim = 1;
break;
}
}
#else
idimid = dgrp;
if(unlimid != -1 && (idimid == unlimid)) {
i_is_unlim = 1;
}
#endif /* USE_NETCDF4 */
stat = nc_inq_dim(igrp, idimid, name, &length);
if (stat == NC_EDIMSIZE && sizeof(size_t) < 8) {
error("dimension \"%s\" requires 64-bit platform", name);
}
NC_CHECK(stat);
o_is_unlim = i_is_unlim;
if(i_is_unlim && !option_fix_unlimdims) {
NC_CHECK(nc_def_dim(ogrp, name, NC_UNLIMITED, &odimid));
} else {
NC_CHECK(nc_def_dim(ogrp, name, length, &odimid));
o_is_unlim = 0;
}
/* Store (idimid, odimid) mapping for later use, also whether unlimited */
dimmap_store(idimid, odimid, i_is_unlim, o_is_unlim);
}
#ifdef USE_NETCDF4
free(dimids);
free(unlimids);
#endif /* USE_NETCDF4 */
return stat;
}
/* Copy the attributes for variable ivar in group igrp to variable
* ovar in group ogrp. Global (group) attributes are specified by
* using the varid NC_GLOBAL */
static int
copy_atts(int igrp, int ivar, int ogrp, int ovar)
{
int natts;
int iatt;
int stat = NC_NOERR;
NC_CHECK(nc_inq_varnatts(igrp, ivar, &natts));
for(iatt = 0; iatt < natts; iatt++) {
char name[NC_MAX_NAME];
NC_CHECK(nc_inq_attname(igrp, ivar, iatt, name));
if(!strcmp(name,"_NCProperties"))
return stat;
NC_CHECK(nc_copy_att(igrp, ivar, name, ogrp, ovar));
}
return stat;
}
/* copy the schema for a single variable in group igrp to group ogrp */
static int
copy_var(int igrp, int varid, int ogrp)
{
int stat = NC_NOERR;
int ndims;
int *idimids; /* ids of dims for input variable */
int *odimids; /* ids of dims for output variable */
char name[NC_MAX_NAME];
nc_type typeid, o_typeid;
int natts;
int i;
int o_varid;
NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
idimids = (int *) emalloc((size_t)(ndims + 1) * sizeof(int));
NC_CHECK(nc_inq_var(igrp, varid, name, &typeid, NULL, idimids, &natts));
o_typeid = typeid;
#ifdef USE_NETCDF4
if (typeid > NC_STRING) { /* user-defined type */
/* type ids in source don't necessarily correspond to same
* typeids in destination, so look up destination typeid by
* using type name */
char type_name[NC_MAX_NAME];
NC_CHECK(nc_inq_type(igrp, typeid, type_name, NULL));
NC_CHECK(nc_inq_typeid(ogrp, type_name, &o_typeid));
}
#endif /* USE_NETCDF4 */
/* get the corresponding dimids in the output file */
odimids = (int *) emalloc((size_t)(ndims + 1) * sizeof(int));
for(i = 0; i < ndims; i++) {
odimids[i] = dimmap_odimid(idimids[i]);
if(odimids[i] == -1) {
error("Oops, no dimension in output associated with input dimid %d", idimids[i]);
}
}
/* define the output variable */
NC_CHECK(nc_def_var(ogrp, name, o_typeid, ndims, odimids, &o_varid));
/* attach the variable attributes to the output variable */
NC_CHECK(copy_atts(igrp, varid, ogrp, o_varid));
#ifdef USE_NETCDF4
{
int inkind;
int outkind;
NC_CHECK(nc_inq_format(igrp, &inkind));
NC_CHECK(nc_inq_format(ogrp, &outkind));
/* Copy all variable properties such as
* chunking, endianness, deflation, checksumming, fill, etc.
* Ok to call if outkind is netcdf-3
*/
NC_CHECK(copy_var_specials(igrp, varid, ogrp, o_varid, inkind, outkind));
}
#endif /* USE_NETCDF4 */
free(idimids);
free(odimids);
return stat;
}
/* copy the schema for all the variables in group igrp to group ogrp */
static int
copy_vars(int igrp, int ogrp)
{
int stat = NC_NOERR;
int nvars;
int varid;
int iv; /* variable number */
idnode_t* vlist = 0; /* list for vars specified with -v option */
/*
* If any vars were specified with -v option, get list of
* associated variable ids relative to this group. Assume vars
* specified with syntax like "grp1/grp2/varname" or
* "/grp1/grp2/varname" if they are in groups.
*/
vlist = newidlist(); /* list for vars specified with -v option */
for (iv=0; iv < option_nlvars; iv++) {
if(nc_inq_gvarid(igrp, option_lvars[iv], &varid) == NC_NOERR)
idadd(vlist, varid);
}
NC_CHECK(nc_inq_nvars(igrp, &nvars));
for (varid = 0; varid < nvars; varid++) {
if (!option_varstruct && option_nlvars > 0 && ! idmember(vlist, varid))
continue;
NC_CHECK(copy_var(igrp, varid, ogrp));
}
freeidlist(vlist);
return stat;
}
#if DEBUGCHUNK
static void
report(int rank, size_t* start, size_t* count, void* buf)
{
int i;
size_t prod = 1;
for(i=0;i<rank;i++) prod *= count[i];
fprintf(stderr,"start=");
for(i=0;i<rank;i++)
fprintf(stderr,"%s%ld",(i==0?"(":" "),(long)start[i]);
fprintf(stderr,")");
fprintf(stderr," count=");
for(i=0;i<rank;i++)
fprintf(stderr,"%s%ld",(i==0?"(":" "),(long)count[i]);
fprintf(stderr,")");
fprintf(stderr," data=");
for(i=0;i<prod;i++)
fprintf(stderr,"%s%d",(i==0?"(":" "),((int*)buf)[i]);
fprintf(stderr,"\n");
fflush(stderr);
}
#endif
/* Copy the schema in a group and all its subgroups, recursively, from
* group igrp in input to parent group ogrp in destination. Use
* dimmap array to map input dimids to output dimids. */
static int
copy_schema(int igrp, int ogrp)
{
int stat = NC_NOERR;
int ogid; /* like igrp but in output file */
/* get groupid in output corresponding to group igrp in input,
* given parent group (or root group) ogrp in output */
NC_CHECK(get_grpid(igrp, ogrp, &ogid));
NC_CHECK(copy_dims(igrp, ogid));
NC_CHECK(copy_atts(igrp, NC_GLOBAL, ogid, NC_GLOBAL));
NC_CHECK(copy_vars(igrp, ogid));
#ifdef USE_NETCDF4
{
int numgrps;
int *grpids;
int i;
/* Copy schema from subgroups */
stat = nc_inq_grps(igrp, &numgrps, NULL);
grpids = (int *)emalloc((size_t)(numgrps + 1) * sizeof(int));
NC_CHECK(nc_inq_grps(igrp, &numgrps, grpids));
for(i = 0; i < numgrps; i++) {
if (option_grpstruct || group_wanted(grpids[i], option_nlgrps, option_grpids)) {
NC_CHECK(copy_schema(grpids[i], ogid));
}
}
free(grpids);
}
#endif /* USE_NETCDF4 */
return stat;
}
/* Return number of values for a variable varid in a group igrp */
static int
inq_nvals(int igrp, int varid, size_t *nvalsp) {
int stat = NC_NOERR;
int ndims;
int *dimids;
int dim;
size_t nvals = 1;
NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
dimids = (int *) emalloc((size_t)(ndims + 1) * sizeof(int));
NC_CHECK(nc_inq_vardimid (igrp, varid, dimids));
for(dim = 0; dim < ndims; dim++) {
size_t len;
NC_CHECK(nc_inq_dimlen(igrp, dimids[dim], &len));
nvals *= len;
}
if(nvalsp)
*nvalsp = nvals;
free(dimids);
return stat;
}
/* Copy data from variable varid in group igrp to corresponding group
* ogrp. */
static int
copy_var_data(int igrp, int varid, int ogrp)
{
int stat = NC_NOERR;
nc_type vartype;
size_t nvalues; /* number of values for this variable */
size_t ntoget; /* number of values to access this iteration */
size_t value_size; /* size of a single value of this variable */
static void *buf = 0; /* buffer for the variable values */
char varname[NC_MAX_NAME];
int ovarid;
size_t *start;
size_t *count;
nciter_t *iterp; /* opaque structure for iteration status */
int do_realloc = 0;
#ifdef USE_NETCDF4
int okind;
size_t chunksize;
#endif
NC_CHECK(inq_nvals(igrp, varid, &nvalues));
if(nvalues == 0)
return stat;
/* get corresponding output variable */
NC_CHECK(nc_inq_varname(igrp, varid, varname));
NC_CHECK(nc_inq_varid(ogrp, varname, &ovarid));
NC_CHECK(nc_inq_vartype(igrp, varid, &vartype));
value_size = val_size(igrp, varid);
if(value_size > option_copy_buffer_size) {
option_copy_buffer_size = value_size;
do_realloc = 1;
}
#ifdef USE_NETCDF4
NC_CHECK(nc_inq_format(ogrp, &okind));
if(okind == NC_FORMAT_NETCDF4 || okind == NC_FORMAT_NETCDF4_CLASSIC) {
/* if this variable chunked, set variable chunk cache size */
int contig = NC_CONTIGUOUS;
NC_CHECK(nc_inq_var_chunking(ogrp, ovarid, &contig, NULL));
if(contig == NC_CHUNKED) { /* chunked */
if(option_compute_chunkcaches) {
/* Try to estimate variable-specific chunk cache,
* depending on specific size and shape of this
* variable's chunks. This doesn't work yet. */
size_t chunkcache_size, chunkcache_nelems;
float chunkcache_preemption;
NC_CHECK(inq_var_chunking_params(igrp, varid, ogrp, ovarid,
&chunkcache_size,
&chunkcache_nelems,
&chunkcache_preemption));
NC_CHECK(nc_set_var_chunk_cache(ogrp, ovarid,
chunkcache_size,
chunkcache_nelems,
chunkcache_preemption));
} else {
/* by default, use same chunk cache for all chunked variables */
NC_CHECK(nc_set_var_chunk_cache(ogrp, ovarid,
option_chunk_cache_size,
option_chunk_cache_nelems,
COPY_CHUNKCACHE_PREEMPTION));
}
}
}
/* For chunked variables, option_copy_buffer_size must also be at least as large as
* size of a chunk in input, otherwise resize it. */
{
NC_CHECK(inq_var_chunksize(igrp, varid, &chunksize));
if(chunksize > option_copy_buffer_size) {
option_copy_buffer_size = chunksize;
do_realloc = 1;
}
}
#endif /* USE_NETCDF4 */
if(buf && do_realloc) {
free(buf);
buf = 0;
}
if(buf == 0) { /* first time or needs to grow */
buf = emalloc(option_copy_buffer_size);
memset((void*)buf,0,option_copy_buffer_size);
}
/* initialize variable iteration */
NC_CHECK(nc_get_iter(igrp, varid, option_copy_buffer_size, &iterp));
start = (size_t *) emalloc((size_t)(iterp->rank + 1) * sizeof(size_t));
count = (size_t *) emalloc((size_t)(iterp->rank + 1) * sizeof(size_t));
/* nc_next_iter() initializes start and count on first call,
* changes start and count to iterate through whole variable on
* subsequent calls. */
while((ntoget = nc_next_iter(iterp, start, count)) > 0) {
NC_CHECK(nc_get_vara(igrp, varid, start, count, buf));
#ifdef DEBUGCHUNK
report(iterp->rank,start,count,buf);
#endif
NC_CHECK(nc_put_vara(ogrp, ovarid, start, count, buf));
#ifdef USE_NETCDF4
/* we have to explicitly free values for strings and vlens */
if(vartype == NC_STRING) {
NC_CHECK(nc_free_string(ntoget, (char **)buf));
} else if(vartype > NC_STRING) { /* user-defined type */
nc_type vclass;
NC_CHECK(nc_inq_user_type(igrp, vartype, NULL, NULL, NULL, NULL, &vclass));
if(vclass == NC_VLEN) {
NC_CHECK(nc_free_vlens(ntoget, (nc_vlen_t *)buf));
}
}
#endif /* USE_NETCDF4 */
} /* end main iteration loop */
#ifdef USE_NETCDF4
/* We're all done with this input and output variable, so if
* either variable is chunked, free up its variable chunk cache */
/* NC_CHECK(free_var_chunk_cache(igrp, varid)); */
/* NC_CHECK(free_var_chunk_cache(ogrp, ovarid)); */
#endif /* USE_NETCDF4 */
free(start);
free(count);
NC_CHECK(nc_free_iter(iterp));
return stat;
}
/* Copy data from variables in group igrp to variables in
* corresponding group with parent ogrp, and all subgroups
* recursively */
static int
copy_data(int igrp, int ogrp)
{
int stat = NC_NOERR;
int ogid;
int nvars;
int varid;
#ifdef USE_NETCDF4
int numgrps;
int *grpids;
int i;
#endif
int iv; /* variable number */
idnode_t* vlist = NULL; /* list for vars specified with -v option */
/*
* If any vars were specified with -v option, get list of
* associated variable ids relative to this group. Assume vars
* specified with syntax like "grp1/grp2/varname" or
* "/grp1/grp2/varname" if they are in groups.
*/
vlist = newidlist(); /* list for vars specified with -v option */
for (iv=0; iv < option_nlvars; iv++) {
if(nc_inq_gvarid(igrp, option_lvars[iv], &varid) == NC_NOERR)
idadd(vlist, varid);
}
/* get groupid in output corresponding to group igrp in input,
* given parent group (or root group) ogrp in output */
NC_CHECK(get_grpid(igrp, ogrp, &ogid));
/* Copy data from this group */
NC_CHECK(nc_inq_nvars(igrp, &nvars));
for (varid = 0; varid < nvars; varid++) {
if (option_nlvars > 0 && ! idmember(vlist, varid))
continue;
if (!group_wanted(igrp, option_nlgrps, option_grpids))
continue;
NC_CHECK(copy_var_data(igrp, varid, ogid));
}
#ifdef USE_NETCDF4
/* Copy data from subgroups */
stat = nc_inq_grps(igrp, &numgrps, NULL);
grpids = (int *)emalloc((size_t)(numgrps + 1) * sizeof(int));
NC_CHECK(nc_inq_grps(igrp, &numgrps, grpids));
for(i = 0; i < numgrps; i++) {
if (!option_grpstruct && !group_wanted(grpids[i], option_nlgrps, option_grpids))
continue;
NC_CHECK(copy_data(grpids[i], ogid));
}
free(grpids);
#endif /* USE_NETCDF4 */
freeidlist(vlist);
return stat;
}
/* Count total number of dimensions in ncid and all its descendant subgroups */
int
count_dims(int ncid) {
#ifdef USE_NETCDF4
int numgrps;
#endif
int ndims;
NC_CHECK(nc_inq_ndims(ncid, &ndims));
#ifdef USE_NETCDF4
NC_CHECK(nc_inq_grps(ncid, &numgrps, NULL));
if(numgrps > 0) {
int igrp;
int *grpids = emalloc((size_t)numgrps * sizeof(int));
NC_CHECK(nc_inq_grps(ncid, &numgrps, grpids));
for(igrp = 0; igrp < numgrps; igrp++) {
ndims += count_dims(grpids[igrp]);
}
free(grpids);
}
#endif /* USE_NETCDF4 */
return ndims;
}
/* Test if special case: netCDF-3 file with more than one record
* variable. Performance can be very slow for this case when the disk
* block size is large, there are many record variables, and a
* record's worth of data for some variables is smaller than the disk
* block size. In this case, copying the record variables a variable
* at a time causes much rereading of record data, so instead we want
* to copy data a record at a time. */
static int
nc3_special_case(int ncid, int kind) {
if (kind == NC_FORMAT_CLASSIC || kind == NC_FORMAT_64BIT_OFFSET
|| kind == NC_FORMAT_CDF5) {
int recdimid = 0;
NC_CHECK(nc_inq_unlimdim(ncid, &recdimid));
if (recdimid != -1) { /* we have a record dimension */
int nvars;
int varid;
NC_CHECK(nc_inq_nvars(ncid, &nvars));
for (varid = 0; varid < nvars; varid++) {
int *dimids = 0;
int ndims;
NC_CHECK( nc_inq_varndims(ncid, varid, &ndims) );
if (ndims > 0) {
int dimids0;
dimids = (int *) emalloc((size_t)(ndims + 1) * sizeof(int));
NC_CHECK( nc_inq_vardimid(ncid, varid, dimids) );
dimids0 = dimids[0];
free(dimids);
if(dimids0 == recdimid) {
return 1; /* found a record variable */
}
}
}
}
}
return 0;
}
/* Classify variables in ncid as either fixed-size variables (with no
* unlimited dimension) or as record variables (with an unlimited
* dimension) */
static int
classify_vars(
int ncid, /* netCDF ID */
size_t *nf, /* for returning number of fixed-size variables */
int **fvars, /* the array of fixed_size variable IDS, caller should free */
size_t *nr, /* for returning number of record variables */
int **rvars) /* the array of record variable IDs, caller should free */
{
int varid;
int varindex = 0;
int nvars;
NC_CHECK(nc_inq_nvars(ncid, &nvars));
*nf = 0;
*fvars = (int *) emalloc((size_t)nvars * sizeof(int));
*nr = 0;
*rvars = (int *) emalloc((size_t)nvars * sizeof(int));
if(option_nlvars > 0) {
for (varindex = 0; varindex < option_nlvars; varindex++) {
nc_inq_varid(ncid,option_lvars[varindex],&varid);
if (isrecvar(ncid, varid)) {
(*rvars)[*nr] = varid;
(*nr)++;
} else {
(*fvars)[*nf] = varid;
(*nf)++;
}
}
} else {
for (varid = 0; varid < nvars; varid++) {
if (isrecvar(ncid, varid)) {
(*rvars)[*nr] = varid;
(*nr)++;
} else {
(*fvars)[*nf] = varid;
(*nf)++;
}
}
}
return NC_NOERR;
}
/* Only called for classic format or 64-bit offset format files, to speed up special case */
static int
copy_fixed_size_data(int igrp, int ogrp, size_t nfixed_vars, int *fixed_varids) {
size_t ivar;
/* for each fixed-size variable, copy data */
for (ivar = 0; ivar < nfixed_vars; ivar++) {
int varid = fixed_varids[ivar];
NC_CHECK(copy_var_data(igrp, varid, ogrp));
}
if (fixed_varids)
free(fixed_varids);
return NC_NOERR;
}
/* copy a record's worth of data for a variable from input to output */
static int
copy_rec_var_data(int ncid, /* input */
int ogrp, /* output */
int varid, /* input variable id */
int ovarid, /* output variable id */
size_t *start, /* start indices for record data */
size_t *count, /* edge lengths for record data */
void *buf /* buffer large enough to hold data */
)
{
NC_CHECK(nc_get_vara(ncid, varid, start, count, buf));
NC_CHECK(nc_put_vara(ogrp, ovarid, start, count, buf));
return NC_NOERR;
}
/* Only called for classic format or 64-bit offset format files, to speed up special case */
static int
copy_record_data(int ncid, int ogrp, size_t nrec_vars, int *rec_varids) {
int unlimid;
size_t nrecs = 0; /* how many records? */
size_t irec;
size_t ivar;
void **buf; /* space for reading in data for each variable */
int *rec_ovarids; /* corresponding varids in output */
size_t **start;
size_t **count;
NC_CHECK(nc_inq_unlimdim(ncid, &unlimid));
NC_CHECK(nc_inq_dimlen(ncid, unlimid, &nrecs));
buf = (void **) emalloc(nrec_vars * sizeof(void *));
rec_ovarids = (int *) emalloc(nrec_vars * sizeof(int));
start = (size_t **) emalloc(nrec_vars * sizeof(size_t*));
count = (size_t **) emalloc(nrec_vars * sizeof(size_t*));
/* get space to hold one record's worth of data for each record variable */
for (ivar = 0; ivar < nrec_vars; ivar++) {
int varid;
int ndims;
int *dimids;
size_t value_size;
int dimid;
int ii;
size_t nvals;
char varname[NC_MAX_NAME];
varid = rec_varids[ivar];
NC_CHECK(nc_inq_varndims(ncid, varid, &ndims));
dimids = (int *) emalloc((size_t)(1 + ndims) * sizeof(int));
start[ivar] = (size_t *) emalloc((size_t)ndims * sizeof(size_t));
count[ivar] = (size_t *) emalloc((size_t)ndims * sizeof(size_t));
NC_CHECK(nc_inq_vardimid (ncid, varid, dimids));
value_size = val_size(ncid, varid);
nvals = 1;
for(ii = 1; ii < ndims; ii++) { /* for rec size, don't include first record dimension */
size_t dimlen;
dimid = dimids[ii];
NC_CHECK(nc_inq_dimlen(ncid, dimid, &dimlen));
nvals *= dimlen;
start[ivar][ii] = 0;
count[ivar][ii] = dimlen;
}
start[ivar][0] = 0;
count[ivar][0] = 1; /* 1 record */
buf[ivar] = (void *) emalloc(nvals * value_size);
NC_CHECK(nc_inq_varname(ncid, varid, varname));
NC_CHECK(nc_inq_varid(ogrp, varname, &rec_ovarids[ivar]));
if(dimids)
free(dimids);
}
/* for each record, copy all variable data */
for(irec = 0; irec < nrecs; irec++) {
for (ivar = 0; ivar < nrec_vars; ivar++) {
int varid, ovarid;
varid = rec_varids[ivar];
ovarid = rec_ovarids[ivar];
start[ivar][0] = irec;
NC_CHECK(copy_rec_var_data(ncid, ogrp, varid, ovarid,
start[ivar], count[ivar], buf[ivar]));
}
}
for (ivar = 0; ivar < nrec_vars; ivar++) {
if(start[ivar])
free(start[ivar]);
if(count[ivar])
free(count[ivar]);
}
if(start)
free(start);
if(count)
free(count);
for (ivar = 0; ivar < nrec_vars; ivar++) {
if(buf[ivar]) {
free(buf[ivar]);
}
}
if (rec_varids)
free(rec_varids);
if(buf)
free(buf);
if(rec_ovarids)
free(rec_ovarids);
return NC_NOERR;
}
/* copy infile to outfile using netCDF API
*/
static int
copy(char* infile, char* outfile)
{
int stat = NC_NOERR;
int igrp, ogrp;
int inkind, outkind;
int open_mode = NC_NOWRITE;
int create_mode = NC_CLOBBER;
size_t ndims;
if(option_read_diskless) {
open_mode |= NC_DISKLESS;
}
NC_CHECK(nc_open(infile, open_mode, &igrp));
NC_CHECK(nc_inq_format(igrp, &inkind));
/* option_kind specifies which netCDF format for output, one of
*
* SAME_AS_INPUT, NC_FORMAT_CLASSIC, NC_FORMAT_64BIT,
* NC_FORMAT_NETCDF4, NC_FORMAT_NETCDF4_CLASSIC
*
* However, if compression or shuffling was specified and kind was SAME_AS_INPUT,
* option_kind is changed to NC_FORMAT_NETCDF4_CLASSIC, if input format is
* NC_FORMAT_CLASSIC or NC_FORMAT_64BIT .
*/
outkind = option_kind;
if (option_kind == SAME_AS_INPUT) { /* default, kind not specified */
outkind = inkind;
/* Deduce output kind if netCDF-4 features requested */
if (inkind == NC_FORMAT_CLASSIC || inkind == NC_FORMAT_64BIT_OFFSET
|| inkind == NC_FORMAT_CDF5) {
if (option_deflate_level > 0 ||
option_shuffle_vars == NC_SHUFFLE ||
listlength(option_chunkspecs) > 0)
{
outkind = NC_FORMAT_NETCDF4_CLASSIC;
}
}
}
#ifdef USE_NETCDF4
if(listlength(option_chunkspecs) > 0) {
/* Now that input is open, can parse option_chunkspecs into binary
* structure. */
for(size_t i=0;i<listlength(option_chunkspecs);i++) {
char* spec = (char*)listget(option_chunkspecs,i);
NC_CHECK(chunkspec_parse(igrp, spec));
}
}
#endif /* USE_NETCDF4 */
/* Check if any vars in -v don't exist */
if(missing_vars(igrp, option_nlvars, option_lvars))
goto fail;
if(option_nlgrps > 0) {
if(inkind != NC_FORMAT_NETCDF4) {
error("Group list (-g ...) only permitted for netCDF-4 file");
goto fail;
}
/* Check if any grps in -g don't exist */
if(grp_matches(igrp, option_nlgrps, option_lgrps, option_grpids) == 0)
goto fail;
}
if(option_write_diskless)
create_mode |= NC_PERSIST | NC_DISKLESS; /* NC_WRITE persists diskless file on close */
switch(outkind) {
case NC_FORMAT_CLASSIC:
/* nothing to do */
break;
case NC_FORMAT_64BIT_OFFSET:
create_mode |= NC_64BIT_OFFSET;
break;
case NC_FORMAT_CDF5:
#ifdef ENABLE_CDF5
create_mode |= NC_64BIT_DATA;
break;
#else
error("netCDF library built without CDF5 support, can't create CDF5 files");
break;
#endif
#ifdef USE_NETCDF4
case NC_FORMAT_NETCDF4:
create_mode |= NC_NETCDF4;
break;
case NC_FORMAT_NETCDF4_CLASSIC:
create_mode |= NC_NETCDF4 | NC_CLASSIC_MODEL;
break;
#else
case NC_FORMAT_NETCDF4:
case NC_FORMAT_NETCDF4_CLASSIC:
error("netCDF library built with --disable-netcdf4, can't create netCDF-4 files");
break;
#endif /* USE_NETCDF4 */
default:
error("bad value for option specifying desired output format, see usage\n");
break;
}
NC_CHECK(nc_create(outfile, create_mode, &ogrp));
NC_CHECK(nc_set_fill(ogrp, NC_NOFILL, NULL));
#ifdef USE_NETCDF4
/* Because types in one group may depend on types in a different
* group, need to create all groups before defining types */
if(inkind == NC_FORMAT_NETCDF4) {
NC_CHECK(copy_groups(igrp, ogrp));
NC_CHECK(copy_types(igrp, ogrp));
}
#endif /* USE_NETCDF4 */
ndims = (size_t)count_dims(igrp);
NC_CHECK(dimmap_init(ndims));
NC_CHECK(copy_schema(igrp, ogrp));
NC_CHECK(nc_enddef(ogrp));
/* For performance, special case netCDF-3 input or output file with record
* variables, to copy a record-at-a-time instead of a
* variable-at-a-time. */
/* TODO: check that these special cases work with -v option */
if(nc3_special_case(igrp, inkind)) {
size_t nfixed_vars, nrec_vars;
int *fixed_varids;
int *rec_varids;
NC_CHECK(classify_vars(igrp, &nfixed_vars, &fixed_varids, &nrec_vars, &rec_varids));
NC_CHECK(copy_fixed_size_data(igrp, ogrp, nfixed_vars, fixed_varids));
NC_CHECK(copy_record_data(igrp, ogrp, nrec_vars, rec_varids));
} else if (nc3_special_case(ogrp, outkind)) {
size_t nfixed_vars, nrec_vars;
int *fixed_varids;
int *rec_varids;
/* classifies output vars, but returns input varids */
NC_CHECK(classify_vars(ogrp, &nfixed_vars, &fixed_varids, &nrec_vars, &rec_varids));
NC_CHECK(copy_fixed_size_data(igrp, ogrp, nfixed_vars, fixed_varids));
NC_CHECK(copy_record_data(igrp, ogrp, nrec_vars, rec_varids));
} else {
NC_CHECK(copy_data(igrp, ogrp)); /* recursive, to handle nested groups */
}
NC_CHECK(nc_close(igrp));
NC_CHECK(nc_close(ogrp));
return stat;
fail:
nc_finalize();
exit(EXIT_FAILURE);
}
/*
* For non-negative numeric string with multiplier suffix K, M, G, T,
* or P (or lower-case equivalent), return corresponding value
* incorporating multiplier 1000, 1000000, 1.0d9, ... 1.0d15, or -1.0
* for error.
*/
static double
double_with_suffix(char *str) {
double dval;
char *suffix = 0;
errno = 0;
dval = strtod(str, &suffix);
if(dval < 0 || errno != 0)
return -1.0;
if(*suffix) {
switch (*suffix) {
case 'k': case 'K':
dval *= 1000;
break;
case 'm': case 'M':
dval *= 1000000;
break;
case 'g': case 'G':
dval *= 1000000000;
break;
case 't': case 'T':
dval *= 1.0e12;
break;
case 'p': case 'P':
dval *= 1.0e15;
break;
default:
dval = -1.0; /* error, suffix multiplier must be K, M, G, or T */
}
}
return dval;
}
static void
usage(void)
{
#define USAGE "\
[-k kind] specify kind of netCDF format for output file, default same as input\n\
kind strings: 'classic', '64-bit offset', 'cdf5',\n\
'netCDF-4', 'netCDF-4 classic model'\n\
[-3] netCDF classic output (same as -k 'classic')\n\
[-6] 64-bit-offset output (same as -k '64-bit offset')\n\
[-4] netCDF-4 output (same as -k 'netCDF-4')\n\
[-7] netCDF-4-classic output (same as -k 'netCDF-4 classic model')\n\
[-5] CDF5 output (same as -k 'cdf5)\n\
[-d n] set output deflation compression level, default same as input (0=none 9=max)\n\
[-s] add shuffle option to deflation compression\n\
[-c chunkspec] specify chunking for variable and dimensions, e.g. \"var:N1,N2,...\" or \"dim1/N1,dim2/N2,...\"\n\
[-u] convert unlimited dimensions to fixed-size dimensions in output copy\n\
[-w] write whole output file from diskless netCDF on close\n\
[-v var1,...] include data for only listed variables, but definitions for all variables\n\
[-V var1,...] include definitions and data for only listed variables\n\
[-g grp1,...] include data for only variables in listed groups, but all definitions\n\
[-G grp1,...] include definitions and data only for variables in listed groups\n\
[-m n] set size in bytes of copy buffer, default is 5000000 bytes\n\
[-h n] set size in bytes of chunk_cache for chunked variables\n\
[-e n] set number of elements that chunk_cache can hold\n\
[-r] read whole input file into diskless file on open (classic or 64-bit offset or cdf5 formats only)\n\
[-F filterspec] specify a compression algorithm to apply to an output variable (may be repeated).\n\
[-Ln] set log level to n (>= 0); ignored if logging isn't enabled.\n\
[-Mn] set minimum chunk size to n bytes (n >= 0)\n\
infile name of netCDF input file\n\
outfile name for netCDF output file\n"
/* Don't document this flaky option until it works better */
/* [-x] use experimental computed estimates for variable-specific chunk caches\n\ */
error("%s [-k kind] [-[3|4|6|7]] [-d n] [-s] [-c chunkspec] [-u] [-w] [-[v|V] varlist] [-[g|G] grplist] [-m n] [-h n] [-e n] [-r] [-F filterspec] [-Ln] [-Mn] infile outfile\n%s\nnetCDF library version %s",
progname, USAGE, nc_inq_libvers());
}
int
main(int argc, char**argv)
{
int exitcode = EXIT_SUCCESS;
char* inputfile = NULL;
char* outputfile = NULL;
int c;
chunkspecinit();
option_chunkspecs = listnew();
progname = argv[0];
if (argc <= 1)
{
usage();
}
opterr = 1;
while ((c = getopt(argc, argv, "k:3467d:sum:c:h:e:rwxg:G:v:V:F:L:M:")) != -1) {
switch(c) {
case 'k': /* for specifying variant of netCDF format to be generated
Format names:
"classic" or "nc3"
"64-bit offset" or "nc6"
"netCDF-4" or "nc4"
"netCDF-4 classic model" or "nc7"
"64-bit-data" | "64-bit data" | "cdf5" | "nc5"
Format version numbers (deprecated):
1 (=> classic)
2 (=> 64-bit offset)
3 (=> netCDF-4)
4 (=> netCDF-4 classic model)
5 (=> classic 64 bit data, CDF-5)
*/
{
struct Kvalues* kvalue;
char *kind_name = (char *) emalloc(strlen(optarg)+1);
(void)strcpy(kind_name, optarg);
for(kvalue=legalkinds;kvalue->name;kvalue++) {
if(strcmp(kind_name,kvalue->name) == 0) {
option_kind = kvalue->kind;
break;
}
}
if(kvalue->name == NULL) {
error("invalid output format: %s", kind_name);
}
nullfree(kind_name);
}
break;
case '3': /* output format is classic (netCDF-3) */
option_kind = NC_FORMAT_CLASSIC;
break;
case '5': /* output format is cdf5 */
option_kind = NC_FORMAT_CDF5;
break;
case '6': /* output format is 64-bit-offset (netCDF-3 version 2) */
option_kind = NC_FORMAT_64BIT_OFFSET;
break;
case '4': /* output format is netCDF-4 (variant of HDF5) */
option_kind = NC_FORMAT_NETCDF4;
break;
case '7': /* output format is netCDF-4 (restricted to classic model)*/
option_kind = NC_FORMAT_NETCDF4_CLASSIC;
break;
case 'd': /* non-default compression level specified */
option_deflate_level = (int)strtol(optarg, NULL, 10);
if(option_deflate_level < 0 || option_deflate_level > 9) {
error("invalid deflation level: %d", option_deflate_level);
}
break;
case 's': /* shuffling, may improve compression */
option_shuffle_vars = NC_SHUFFLE;
break;
case 'u': /* convert unlimited dimensions to fixed size */
option_fix_unlimdims = 1;
break;
case 'm': /* non-default size of data copy buffer */
{
double dval = double_with_suffix(optarg); /* "K" for kilobytes. "M" for megabytes, ... */
if(dval < 0)
error("Suffix used for '-m' option value must be K, M, G, T, or P");
option_copy_buffer_size = (size_t)dval;
break;
}
case 'h': /* non-default size of chunk cache */
{
double dval = double_with_suffix(optarg); /* "K" for kilobytes. "M" for megabytes, ... */
if(dval < 0)
error("Suffix used for '-h' option value must be K, M, G, T, or P");
option_chunk_cache_size = (size_t)dval;
break;
}
case 'e': /* number of elements chunk cache can hold */
{
double dval = double_with_suffix(optarg); /* "K" for kilobytes. "M" for megabytes, ... */
if(dval < 0 )
error("Suffix used for '-e' option value must be K, M, G, T, or P");
option_chunk_cache_nelems = (size_t)dval;
break;
}
case 'r':
option_read_diskless = 1; /* read into memory on open */
break;
case 'w':
option_write_diskless = 1; /* write to memory, persist on close */
break;
case 'x': /* use experimental variable-specific chunk caches */
option_compute_chunkcaches = 1;
break;
case 'c': /* optional chunking spec for each dimension in list */
/* save chunkspec string for parsing later, once we know input ncid */
listpush(option_chunkspecs,strdup(optarg));
break;
case 'g': /* group names */
/* make list of names of groups specified */
make_lgrps (optarg, &option_nlgrps, &option_lgrps, &option_grpids);
option_grpstruct = true;
break;
case 'G': /* group names */
/* make list of names of groups specified */
make_lgrps (optarg, &option_nlgrps, &option_lgrps, &option_grpids);
option_grpstruct = false;
break;
case 'v': /* variable names */
/* make list of names of variables specified */
make_lvars (optarg, &option_nlvars, &option_lvars);
option_varstruct = true;
break;
case 'V': /* variable names */
/* make list of names of variables specified */
make_lvars (optarg, &option_nlvars, &option_lvars);
option_varstruct = false;
break;
case 'L': /* Set logging, if logging support was compiled in. */
#ifdef LOGGING
{
int level = atoi(optarg);
if(level >= 0)
nc_set_log_level(level);
}
#else
error("-L specified, but logging support not enabled");
#endif
break;
case 'F': /* optional filter spec for a specified variable */
#ifdef USE_NETCDF4
/* If the arg is "none" or "*,none" then suppress all filters
on output unless explicit */
if(strcmp(optarg,"none")==0
|| strcasecmp(optarg,"*,none")==0) {
suppressfilters = 1;
} else {
if(filteroptions == NULL)
filteroptions = listnew();
NC_CHECK(parsefilterspec(optarg,filteroptions));
/* Force output to be netcdf-4 */
option_kind = NC_FORMAT_NETCDF4;
}
#else
error("-F requires netcdf-4");
#endif
break;
case 'M': /* set min chunk size */
#ifdef USE_NETCDF4
if(optarg == NULL)
option_min_chunk_bytes = 0;
else
option_min_chunk_bytes = (size_t)atol(optarg);
break;
#else
error("-M requires netcdf-4");
#endif
default:
usage();
}
}
argc -= optind;
argv += optind;
if (argc != 2) {
error("one input file and one output file required");
}
/* Canonicalize the input and output files names */
inputfile = NC_shellUnescape(argv[0]); /* Remove shell added escapes */
outputfile = NC_shellUnescape(argv[1]);
if(strcmp(inputfile, outputfile) == 0) {
error("output would overwrite input");
}
#ifdef USE_NETCDF4
#ifdef DEBUGFILTER
{ int i,j;
for(i=0;i<listlength(filterspecs);i++) {
struct FilterSpec *spec = listget(filterspecs,i);
fprintf(stderr,"filterspecs[%d]={fqn=|%s| filterid=%u nparams=%ld params=",
i,spec->fqn,spec->filterid,(unsigned long)spec->nparams);
for(j=0;j<spec->nparams;j++) {
if(j>0) fprintf(stderr,",");
fprintf(stderr,"%u",spec->params[j]);
}
fprintf(stderr,"}\n");
fflush(stderr);
}
}
#endif /*DEBUGFILTER*/
#endif /*USE_NETCDF4*/
if(copy(inputfile, outputfile) != NC_NOERR)
exitcode = EXIT_FAILURE;
nullfree(inputfile);
nullfree(outputfile);
#ifdef USE_NETCDF4
/* Clean up */
freefilteroptlist(filteroptions);
filteroptions = NULL;
#endif /*USE_NETCDF4*/
nc_finalize();
exit(exitcode);
}
#ifdef USE_NETCDF4
static void
freefilteroptlist(List* specs)
{
for(size_t i=0;i<listlength(specs);i++) {
struct FilterOption* spec = (struct FilterOption*)listget(specs,i);
if(spec->fqn) free(spec->fqn);
nullfree(spec->pfs.params);
free(spec);
}
listfree(specs);
}
static void
freefilterlist(size_t nfilters, NC_H5_Filterspec** filters)
{
int i;
if(filters != NULL) {
for(i=0;i<nfilters;i++)
ncaux_h5filterspec_free(filters[i]);
nullfree(filters);
}
}
#endif
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