netcdf-c/ncdump/nccopy.c

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/*********************************************************************
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* Copyright 2010, University Corporation for Atmospheric Research
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* See netcdf/README file for copying and redistribution conditions.
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* Thanks to Philippe Poilbarbe and Antonio S. Cofiño for
* compression additions.
* $Id: nccopy.c 400 2010-08-27 21:02:52Z russ $
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*********************************************************************/
#include "config.h" /* for USE_NETCDF4 macro */
#include <stdlib.h>
#include <stdio.h>
#ifndef _WIN32
#include <unistd.h>
#endif
#include <string.h>
#include <netcdf.h>
#include "nciter.h"
/* default bytes of memory we are willing to allocate for variable
* values during copy */
#define COPY_BUFFER_SIZE (5000000)
#define SAME_AS_INPUT (-1) /* default, if kind not specified */
#define CHECK(stat,f) if(stat != NC_NOERR) {check(stat,#f,__FILE__,__LINE__);} else {}
#ifndef USE_NETCDF4
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#define NC_CLASSIC_MODEL 0x0100 /* Enforce classic model if netCDF-4 not available. */
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#endif
/* These are in unistd.h; for use with getopt() */
extern int optind;
extern int opterr;
extern char *optarg;
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/* Global variables for command-line requests */
static char *progname; /* for error messages */
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 */
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static void
check(int err, const char* fcn, const char* file, const int line)
{
fprintf(stderr,"%s\n",nc_strerror(err));
fprintf(stderr,"Location: function %s; file %s; line %d\n",
fcn,file,line);
fflush(stderr); fflush(stdout);
exit(1);
}
/* Check error return from malloc, and allow malloc(0) with subsequent free */
static void *
emalloc (size_t size)
{
void *p;
p = (void *) malloc (size==0 ? 1 : size); /* don't malloc(0) */
if (p == 0) {
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fprintf(stderr,"%s: out of memory\n", progname);
exit(1);
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}
return p;
}
/* 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; /* 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];
stat = nc_inq_grpname(igrp, grpname);
CHECK(stat, nc_inq_grpname);
stat = nc_inq_grp_ncid(parid, grpname, &ogid);
CHECK(stat, nc_inq_grp_ncid);
} else if(stat == NC_ENOGRP) { /* root group */
ogid = parid;
stat = NC_NOERR;
} else {
CHECK(stat, nc_inq_grp_parent);
}
#else
ogid = parid;
#endif /* USE_NETCDF4 */
*ogrpp = ogid;
return stat;
}
#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) {
int stat = NC_NOERR;
char *parent = strdup(fullname);
char *slash = "/"; /* groupname separator */
char *last_slash;
if(parent == NULL)
CHECK(NC_ENOMEM, strdup);
last_slash = strrchr(parent, '/');
if(last_slash == parent) { /* parent is root */
free(parent);
parent = strdup(slash);
} else {
*last_slash = '\0'; /* truncate to get parent name */
}
stat = nc_inq_grp_full_ncid(ncid, parent, locidp);
CHECK(stat, nc_inq_grp_full_ncid);
free(parent);
return stat;
}
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/* Return size of chunk in bytes for a variable varid in a group igrp, or 0 if
* layout is contiguous */
static int
inq_var_chunksize(int igrp, int varid, size_t* chunksizep) {
int stat = NC_NOERR;
int ndims;
size_t *chunksizes;
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int dim;
int contig = 1;
nc_type vartype;
size_t value_size;
size_t prod;
stat = nc_inq_vartype(igrp, varid, &vartype);
CHECK(stat, nc_inq_vartype);
/* from type, get size in memory needed for each value */
stat = nc_inq_type(igrp, vartype, NULL, &value_size);
CHECK(stat, nc_inq_type);
prod = value_size;
stat = nc_inq_varndims(igrp, varid, &ndims);
CHECK(stat, nc_inq_varndims);
chunksizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
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if(ndims > 0) {
stat = nc_inq_var_chunking(igrp, varid, &contig, NULL);
CHECK(stat, nc_inq_var_chunking);
}
if(contig == 1) {
*chunksizep = 0;
} else {
stat = nc_inq_var_chunking(igrp, varid, &contig, chunksizes);
CHECK(stat, nc_inq_var_chunking);
for(dim = 0; dim < ndims; dim++) {
prod *= chunksizes[dim];
}
*chunksizep = prod;
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}
free(chunksizes);
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return stat;
}
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/* Forward declaration, because copy_type, copy_vlen_type call each other */
static int copy_type(int igrp, nc_type typeid, int ogrp);
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/*
* 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;
stat = nc_inq_vlen(igrp, itype, name, &size, &ibasetype);
CHECK(stat, nc_inq_vlen);
/* to get base type id in target group, use name of base type in
* source group */
stat = nc_inq_type(igrp, ibasetype, basename, &basesize);
CHECK(stat, nc_inq_type);
stat = nc_inq_typeid(ogrp, basename, &obasetype);
/* if no such type, create it now */
if(stat == NC_EBADTYPE) {
copy_type(igrp, ibasetype, ogrp);
CHECK(stat, copy_type);
stat = nc_inq_typeid(ogrp, basename, &obasetype);
}
CHECK(stat, nc_inq_typeid);
/* Now we know base type exists in output and we know its type id */
stat = nc_def_vlen(ogrp, name, obasetype, &vlen_type);
CHECK(stat, nc_copy_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;
stat = nc_inq_opaque(igrp, itype, name, &size);
CHECK(stat, nc_inq_opaque_type);
stat = nc_def_opaque(ogrp, size, name, &otype);
CHECK(stat, copy_opaque_type);
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;
stat = nc_inq_enum(igrp, itype, name, &basetype, &basesize, &nmembers);
CHECK(stat, nc_inq_enum);
stat = nc_def_enum(ogrp, basetype, name, &otype);
CHECK(stat, nc_def_enum);
for(i = 0; i < nmembers; i++) { /* insert enum members */
char ename[NC_MAX_NAME];
long long val; /* large enough to hold any integer type */
stat = nc_inq_enum_member(igrp, itype, i, ename, &val);
CHECK(stat, nc_inq_enum_member);
stat = nc_insert_enum(ogrp, otype, ename, &val);
CHECK(stat, nc_insert_enum);
}
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;
stat = nc_inq_compound(igrp, itype, name, &size, &nfields);
CHECK(stat, nc_inq_compound);
stat = nc_def_compound(ogrp, size, name, &otype);
CHECK(stat, nc_def_compound);
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;
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stat = nc_inq_compound_field(igrp, itype, fid, fname, &foff, &iftype,
&fndims, NULL);
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CHECK(stat, nc_inq_compound_field);
/* type ids in source don't necessarily correspond to same
* typeids in destination, so look up destination typeid by using
* field type name */
stat = nc_inq_type(igrp, iftype, ftypename, NULL);
CHECK(stat, nc_inq_type);
stat = nc_inq_typeid(ogrp, ftypename, &oftype);
CHECK(stat, nc_inq_typeid);
if(fndims == 0) {
stat = nc_insert_compound(ogrp, otype, fname, foff, oftype);
CHECK(stat, nc_insert_compound);
} else { /* field is array type */
int *fdimsizes;
fdimsizes = (int *) emalloc((fndims + 1) * sizeof(int));
stat = nc_inq_compound_field(igrp, itype, fid, NULL, NULL, NULL,
NULL, fdimsizes);
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stat = nc_insert_array_compound(ogrp, otype, fname, foff,
oftype, fndims, fdimsizes);
CHECK(stat, nc_insert_array_compound);
free(fdimsizes);
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}
}
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;
stat = nc_inq_user_type(igrp, typeid, NULL, NULL, NULL, NULL, &type_class);
CHECK(stat, nc_inq_user_type);
switch(type_class) {
case NC_VLEN:
stat = copy_vlen_type(igrp, typeid, ogrp);
CHECK(stat, copy_vlen_type);
break;
case NC_OPAQUE:
stat = copy_opaque_type(igrp, typeid, ogrp);
CHECK(stat, copy_opaque_type);
break;
case NC_ENUM:
stat = copy_enum_type(igrp, typeid, ogrp);
CHECK(stat, copy_enum_type);
break;
case NC_COMPOUND:
stat = copy_compound_type(igrp, typeid, ogrp);
CHECK(stat, copy_compound_type);
break;
default:
stat = NC_EBADTYPE;
CHECK(stat, copy_type);
}
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. */
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static int
copy_groups(int iroot, int oroot)
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{
int stat = NC_NOERR;
int numgrps;
int *grpids, ogrpid;
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int i;
/* get total number of groups and their ids, including all descendants */
stat = nc_inq_grps_full(iroot, &numgrps, NULL);
CHECK(stat, nc_inq_grps_full);
grpids = emalloc(numgrps * sizeof(int));
stat = nc_inq_grps_full(iroot, NULL, grpids);
CHECK(stat, nc_inq_grps_full);
/* 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, oparid;
/* get full group name of input group */
stat = nc_inq_grpname_full(grpids[i], &len_name, NULL);
CHECK(stat, nc_inq_grpname);
grpname_full = emalloc(len_name + 1);
stat = nc_inq_grpname_full(grpids[i], &len_name, grpname_full);
CHECK(stat, nc_inq_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 */
stat = nc_inq_parid(oroot, grpname_full, &oparid);
CHECK(stat, get_oparid);
stat = nc_inq_grpname(grpids[i], grpname);
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CHECK(stat, nc_inq_grpname);
/* define corresponding group in output */
stat = nc_def_grp(oparid, grpname, &ogid);
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CHECK(stat, nc_def_grp);
free(grpname_full);
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}
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;
stat = nc_inq_typeids(igrp, &ntypes, NULL);
CHECK(stat, nc_inq_typeids);
if(ntypes > 0) {
types = (nc_type *) emalloc(ntypes * sizeof(nc_type));
stat = nc_inq_typeids(igrp, &ntypes, types);
CHECK(stat, nc_inq_typeids);
for (i = 0; i < ntypes; i++) {
stat = copy_type(igrp, types[i], ogrp);
CHECK(stat, copy_type);
}
free(types);
}
/* Copy types from subgroups */
stat = nc_inq_grps(igrp, &numgrps, NULL);
CHECK(stat, nc_inq_grps);
if(numgrps > 0) {
grpids = (int *)emalloc(sizeof(int) * numgrps);
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stat = nc_inq_grps(igrp, &numgrps, grpids);
CHECK(stat, nc_inq_grps);
for(i = 0; i < numgrps; i++) {
int ogid;
/* get groupid in output corresponding to grpids[i] in
* input, given parent group (or root group) ogrp in
* output */
stat = get_grpid(grpids[i], ogrp, &ogid);
CHECK(stat, get_grpid);
stat = copy_types(grpids[i], ogid);
CHECK(stat, copy_types);
}
free(grpids);
}
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 stat = NC_NOERR;
{ /* handle chunking parameters */
int ndims;
stat = nc_inq_varndims(igrp, varid, &ndims);
CHECK(stat, nc_inq_varndims);
if (ndims > 0) { /* no chunking for scalar variables */
int contig = 0;
stat = nc_inq_var_chunking(igrp, varid, &contig, NULL);
CHECK(stat, nc_inq_var_chunking);
if(contig == 1) {
stat = nc_def_var_chunking(ogrp, o_varid, NC_CONTIGUOUS, NULL);
CHECK(stat, nc_def_var_chunking);
} else {
size_t *chunkp = (size_t *) emalloc(ndims * sizeof(size_t));
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stat = nc_inq_var_chunking(igrp, varid, NULL, chunkp);
CHECK(stat, nc_inq_var_chunking);
/* explicitly set chunking, even if default */
stat = nc_def_var_chunking(ogrp, o_varid, NC_CHUNKED, chunkp);
CHECK(stat, nc_def_var_chunking);
free(chunkp);
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}
}
}
{ /* handle compression parameters */
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int shuffle, deflate, deflate_level;
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stat = nc_inq_var_deflate(igrp, varid,
&shuffle, &deflate, &deflate_level);
CHECK(stat, nc_inq_var_deflate);
if(option_deflate_level >= 0) { /* change output compression, if requested */
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deflate = (option_deflate_level > 0);
deflate_level = option_deflate_level;
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}
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if(deflate != 0 || shuffle != 0) {
stat = nc_def_var_deflate(ogrp, o_varid,
shuffle, deflate, deflate_level);
CHECK(stat, nc_def_var_deflate);
}
}
{ /* handle checksum parameters */
int fletcher32 = 0;
stat = nc_inq_var_fletcher32(igrp, varid, &fletcher32);
CHECK(stat, nc_inq_var_fletcher32);
if(fletcher32 != 0) {
stat = nc_def_var_fletcher32(ogrp, o_varid, fletcher32);
CHECK(stat, nc_def_var_fletcher32);
}
}
{ /* handle endianness */
int endianness = 0;
stat = nc_inq_var_endian(igrp, varid, &endianness);
CHECK(stat, nc_inq_var_endian);
if(endianness != NC_ENDIAN_NATIVE) { /* native is the default */
stat = nc_def_var_endian(ogrp, o_varid, endianness);
CHECK(stat, nc_def_var_endian);
}
}
return stat;
}
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/* set variable to compression specified on command line */
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static int
set_var_compressed(int ogrp, int o_varid)
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{
int stat = NC_NOERR;
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if (option_deflate_level >= 0) {
int deflate = 1;
stat = nc_def_var_deflate(ogrp, o_varid, option_shuffle_vars,
deflate, option_deflate_level);
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CHECK(stat, nc_def_var_deflate);
}
return stat;
}
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/* Release the variable chunk cache allocated for variable varid in
* group igrp with it. This is not necessary, but will save some
* memory if processing one variable at a time. */
static int
free_var_chunk_cache(int igrp, int varid)
{
int stat = NC_NOERR;
size_t chunk_cache_size = 1;
size_t cache_nelems = 1;
float cache_preemp = 0;
int inkind, outkind;
stat = nc_inq_format(igrp, &inkind);
CHECK(stat,nc_inq_format);
if(inkind == NC_FORMAT_NETCDF4 || inkind == NC_FORMAT_NETCDF4_CLASSIC) {
int contig = 1;
stat = nc_inq_var_chunking(igrp, varid, &contig, NULL);
CHECK(stat, nc_inq_var_chunking);
if(contig == 0) { /* chunked */
stat = nc_set_var_chunk_cache(igrp, varid, chunk_cache_size,
cache_nelems, cache_preemp);
CHECK(stat, nc_set_var_chunk_cache);
}
}
return stat;
}
#endif /* USE_NETCDF4 */
/* Copy dimensions from group igrp to group ogrp */
static int
copy_dims(int igrp, int ogrp)
{
int stat = NC_NOERR;
int ndims;
int nunlims;
int dgrp;
#ifdef USE_NETCDF4
int *dimids;
int *unlimids;
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#else
int unlimid;
#endif /* USE_NETCDF4 */
stat = nc_inq_ndims(igrp, &ndims);
CHECK(stat, nc_inq_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((ndims + 1) * sizeof(int));
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stat = nc_inq_dimids(igrp, NULL, dimids, 0);
CHECK(stat, nc_inq_dimids);
/* Find the number of unlimited dimensions and get their IDs */
stat = nc_inq_unlimdims(igrp, &nunlims, NULL);
CHECK(stat, nc_inq_unlimdims);
unlimids = (int *) emalloc((nunlims + 1) * sizeof(int));
stat = nc_inq_unlimdims(igrp, NULL, unlimids);
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CHECK(stat, nc_inq_unlimdims);
#else
stat = nc_inq_unlimdim(igrp, &unlimid);
CHECK(stat, nc_inq_unlimdim);
#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 is_unlim;
int uld;
int dimid;
is_unlim = 0;
#ifdef USE_NETCDF4
dimid = dimids[dgrp];
for (uld = 0; uld < nunlims; uld++) {
if(dimid == unlimids[uld]) {
is_unlim = 1;
break;
}
}
#else
dimid = dgrp;
if(unlimid != -1 && (dimid == unlimid)) {
is_unlim = 1;
}
#endif /* USE_NETCDF4 */
stat = nc_inq_dim(igrp, dimid, name, &length);
if (stat == NC_EDIMSIZE && sizeof(size_t) < 8) {
fprintf(stderr, "dimension \"%s\" requires 64-bit platform\n",
name);
}
CHECK(stat, nc_inq_dim);
if(is_unlim && !option_fix_unlimdims) {
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stat = nc_def_dim(ogrp, name, NC_UNLIMITED, NULL);
} else {
stat = nc_def_dim(ogrp, name, length, NULL);
}
CHECK(stat, nc_def_dim);
}
#ifdef USE_NETCDF4
free(dimids);
free(unlimids);
#endif /* USE_NETCDF4 */
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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;
stat = nc_inq_varnatts(igrp, ivar, &natts);
CHECK(stat, nc_inq_varnatts);
for(iatt = 0; iatt < natts; iatt++) {
char name[NC_MAX_NAME];
stat = nc_inq_attname(igrp, ivar, iatt, name);
CHECK(stat, nc_inq_attname);
stat = nc_copy_att(igrp, ivar, name, ogrp, ovar);
CHECK(stat, nc_copy_att);
}
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 */
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char name[NC_MAX_NAME];
nc_type typeid, o_typeid;
int natts;
int i;
int o_varid;
stat = nc_inq_varndims(igrp, varid, &ndims);
CHECK(stat, nc_inq_varndims);
idimids = (int *) emalloc((ndims + 1) * sizeof(int));
stat = nc_inq_var(igrp, varid, name, &typeid, NULL, idimids, &natts);
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CHECK(stat, nc_inq_var);
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];
stat = nc_inq_type(igrp, typeid, type_name, NULL);
CHECK(stat, nc_inq_type);
stat = nc_inq_typeid(ogrp, type_name, &o_typeid);
CHECK(stat, nc_inq_typeid);
}
#endif /* USE_NETCDF4 */
/* get the corresponding dimids in the output file */
odimids = (int *) emalloc((ndims + 1) * sizeof(int));
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for(i = 0; i < ndims; i++) {
char dimname[NC_MAX_NAME];
stat = nc_inq_dimname(igrp, idimids[i], dimname);
CHECK(stat, nc_inq_dimname);
stat = nc_inq_dimid(ogrp, dimname, &odimids[i]);
CHECK(stat, nc_inq_dimid);
}
/* define the output variable */
stat = nc_def_var(ogrp, name, o_typeid, ndims, odimids, &o_varid);
CHECK(stat, nc_def_var);
/* attach the variable attributes to the output variable */
stat = copy_atts(igrp, varid, ogrp, o_varid);
CHECK(stat, copy_atts);
#ifdef USE_NETCDF4
{
int inkind;
int outkind;
stat = nc_inq_format(igrp, &inkind);
CHECK(stat,nc_inq_format);
stat = nc_inq_format(ogrp, &outkind);
CHECK(stat,nc_inq_format);
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if(outkind == NC_FORMAT_NETCDF4 || outkind == NC_FORMAT_NETCDF4_CLASSIC) {
if((inkind == NC_FORMAT_NETCDF4 || inkind == NC_FORMAT_NETCDF4_CLASSIC)) {
/* Copy all netCDF-4 specific variable properties such as
* chunking, endianness, deflation, checksumming, fill, etc. */
stat = copy_var_specials(igrp, varid, ogrp, o_varid);
CHECK(stat, copy_var_specials);
}
else { /* classic or 64-bit offset input file */
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/* Set compression if specified on command line option */
stat = set_var_compressed(ogrp, o_varid);
CHECK(stat, set_var_compressed);
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}
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}
}
#endif /* USE_NETCDF4 */
free(idimids);
free(odimids);
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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;
stat = nc_inq_nvars(igrp, &nvars);
CHECK(stat, nc_inq_nvars);
for (varid = 0; varid < nvars; varid++) {
stat = copy_var(igrp, varid, ogrp);
CHECK(stat, copy_var);
}
return stat;
}
/* Copy the schema in a group and all its subgroups, recursively, from
* group igrp in input to parent group ogrp in destination. */
static int
copy_schema(int igrp, int ogrp)
{
int stat = NC_NOERR;
int ogid; /* like igrp but in output file */
int i;
/* get groupid in output corresponding to group igrp in input,
* given parent group (or root group) ogrp in output */
stat = get_grpid(igrp, ogrp, &ogid);
CHECK(stat, get_grpid);
stat = copy_dims(igrp, ogid);
CHECK(stat, copy_dims);
stat = copy_atts(igrp, NC_GLOBAL, ogid, NC_GLOBAL);
CHECK(stat, copy_atts);
stat = copy_vars(igrp, ogid);
CHECK(stat, copy_vars);
#ifdef USE_NETCDF4
{
int numgrps;
int *grpids;
/* Copy schema from subgroups */
stat = nc_inq_grps(igrp, &numgrps, NULL);
grpids = (int *)emalloc((numgrps + 1) * sizeof(int));
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stat = nc_inq_grps(igrp, &numgrps, grpids);
CHECK(stat, nc_inq_grps);
for(i = 0; i < numgrps; i++) {
stat = copy_schema(grpids[i], ogid);
CHECK(stat, copy_schema);
}
free(grpids);
}
#endif /* USE_NETCDF4 */
return stat;
}
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/* Return number of values for a variable varid in a group igrp */
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static int
inq_nvals(int igrp, int varid, long long *nvalsp) {
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int stat = NC_NOERR;
int ndims;
int *dimids;
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int dim;
long long nvals = 1;
stat = nc_inq_varndims(igrp, varid, &ndims);
CHECK(stat, nc_inq_varndims);
dimids = (int *) emalloc((ndims + 1) * sizeof(int));
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stat = nc_inq_vardimid (igrp, varid, dimids);
CHECK(stat, nc_inq_vardimid);
for(dim = 0; dim < ndims; dim++) {
size_t len;
stat = nc_inq_dimlen(igrp, dimids[dim], &len);
CHECK(stat, nc_inq_dimlen);
nvals *= len;
}
if(nvalsp)
*nvalsp = nvals;
free(dimids);
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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, size_t copybuf_size) {
int stat = NC_NOERR;
nc_type vartype;
long long 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 */
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int do_realloc = 0;
size_t chunksize;
stat = inq_nvals(igrp, varid, &nvalues);
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CHECK(stat, inq_nvals);
if(nvalues == 0)
return stat;
/* get corresponding output variable */
stat = nc_inq_varname(igrp, varid, varname);
CHECK(stat, nc_inq_varname);
stat = nc_inq_varid(ogrp, varname, &ovarid);
CHECK(stat, nc_inq_varid);
stat = nc_inq_vartype(igrp, varid, &vartype);
CHECK(stat, nc_inq_vartype);
/* from type, get size in memory needed for each value */
stat = nc_inq_type(igrp, vartype, NULL, &value_size);
CHECK(stat, nc_inq_type);
if(value_size > copybuf_size) {
copybuf_size = value_size;
do_realloc = 1;
}
#ifdef USE_NETCDF4
/* For chunked variables, copy_buf must also be at least as large as
* size of a chunk in input */
{
stat = inq_var_chunksize(igrp, varid, &chunksize);
CHECK(stat, inq_var_chunksize);
if(chunksize > copybuf_size) {
copybuf_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(copybuf_size);
memset((void*)buf,0,copybuf_size);
}
/* initialize variable iteration */
stat = nc_get_iter(igrp, varid, copybuf_size, &iterp);
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CHECK(stat, nc_get_iter);
start = (size_t *) emalloc((iterp->rank + 1) * sizeof(size_t));
count = (size_t *) emalloc((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) {
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stat = nc_get_vara(igrp, varid, start, count, buf);
CHECK(stat, nc_get_vara);
stat = nc_put_vara(ogrp, ovarid, start, count, buf);
CHECK(stat, nc_put_vara);
#ifdef USE_NETCDF4
/* we have to explicitly free values for strings and vlens */
if(vartype == NC_STRING) {
stat = nc_free_string(ntoget, (char **)buf);
CHECK(stat, nc_free_string);
} else if(vartype > NC_STRING) { /* user-defined type */
nc_type vclass;
stat = nc_inq_user_type(igrp, vartype, NULL, NULL, NULL,
NULL, &vclass);
CHECK(stat, nc_inq_user_type);
if(vclass == NC_VLEN) {
stat = nc_free_vlens(ntoget, (nc_vlen_t *)buf);
CHECK(stat, nc_free_vlens);
}
}
/* We're all done with this input and output variable, so if
* either variable is chunked, we might as well free up its
* variable chunk cache */
stat = free_var_chunk_cache(igrp, varid);
CHECK(stat, free_var_chunk_cache);
stat = free_var_chunk_cache(ogrp, ovarid);
CHECK(stat, free_var_chunk_cache);
#endif /* USE_NETCDF4 */
} /* end main iteration loop */
free(start);
free(count);
stat = nc_free_iter(iterp);
CHECK(stat, nc_free_iter);
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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, size_t copybuf_size)
{
int stat = NC_NOERR;
int ogid;
int numgrps;
int *grpids;
int i;
int nvars;
int varid;
/* get groupid in output corresponding to group igrp in input,
* given parent group (or root group) ogrp in output */
stat = get_grpid(igrp, ogrp, &ogid);
CHECK(stat, get_grpid);
/* Copy data from this group */
stat = nc_inq_nvars(igrp, &nvars);
CHECK(stat, nc_inq_nvars);
for (varid = 0; varid < nvars; varid++) {
stat = copy_var_data(igrp, varid, ogid, copybuf_size);
CHECK(stat, copy_var_data);
}
#ifdef USE_NETCDF4
/* Copy data from subgroups */
stat = nc_inq_grps(igrp, &numgrps, NULL);
grpids = (int *)emalloc((numgrps + 1) * sizeof(int));
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stat = nc_inq_grps(igrp, &numgrps, grpids);
CHECK(stat, nc_inq_grps);
for(i = 0; i < numgrps; i++) {
stat = copy_data(grpids[i], ogid, copybuf_size);
CHECK(stat, copy_data);
}
free(grpids);
#endif /* USE_NETCDF4 */
return stat;
}
/* copy infile to outfile using netCDF API, kind specifies which
* netCDF format for output: -1 -> same as input, 1 -> classic, 2 ->
* 64-bit offset, 3 -> netCDF-4, 4 -> netCDF-4 classic model.
* However, if compression or shuffling was specified and kind was -1,
* kind is changed to format 4 that supports compression for input of
* type 1 or 2.
*/
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static int
copy(char* infile, char* outfile, int kind, size_t copybuf_size)
{
int stat = NC_NOERR;
int igrp, ogrp;
int inkind, outkind;
stat = nc_open(infile,NC_NOWRITE,&igrp);
CHECK(stat,nc_open);
stat = nc_inq_format(igrp, &inkind);
CHECK(stat,nc_inq_format);
if (kind == SAME_AS_INPUT) { /* default, kind not specified */
outkind = inkind;
/* allow kind to be deduced in this case, instead of returning error */
if ((inkind == NC_FORMAT_CLASSIC || inkind == NC_FORMAT_64BIT) &&
(option_deflate_level > 0 || option_shuffle_vars == NC_SHUFFLE) ) {
kind = NC_FORMAT_NETCDF4_CLASSIC;
outkind = kind;
}
} else {
outkind = kind;
}
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switch(outkind) {
case NC_FORMAT_CLASSIC:
stat = nc_create(outfile,NC_CLOBBER,&ogrp);
break;
case NC_FORMAT_64BIT:
stat = nc_create(outfile,NC_CLOBBER|NC_64BIT_OFFSET,&ogrp);
break;
#ifdef USE_NETCDF4
case NC_FORMAT_NETCDF4:
stat = nc_create(outfile,NC_CLOBBER|NC_NETCDF4,&ogrp);
break;
case NC_FORMAT_NETCDF4_CLASSIC:
stat = nc_create(outfile,NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL,&ogrp);
break;
#else
case NC_FORMAT_NETCDF4:
case NC_FORMAT_NETCDF4_CLASSIC:
fprintf(stderr,
"%s built without ability to create netCDF-4 files\n",
progname);
exit(1);
#endif /* USE_NETCDF4 */
default:
fprintf(stderr,"%s: bad value (%d) for -k option\n", progname, kind);
exit(1);
}
CHECK(stat,nc_create);
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stat = nc_set_fill(ogrp, NC_NOFILL, NULL); /* will just copy fill values, if any */
CHECK(stat,nc_set_fill);
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#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) {
stat = copy_groups(igrp, ogrp);
CHECK(stat,copy_groups);
stat = copy_types(igrp, ogrp);
CHECK(stat,copy_types);
}
#endif /* USE_NETCDF4 */
stat = copy_schema(igrp, ogrp);
CHECK(stat,copy_schema);
stat = nc_enddef(ogrp);
CHECK(stat, nc_enddef);
stat = copy_data(igrp, ogrp, copybuf_size);
CHECK(stat,copy_data);
stat = nc_close(igrp);
CHECK(stat,nc_close);
stat = nc_close(ogrp);
CHECK(stat,nc_close);
return stat;
}
static void
usage(void)
{
#define USAGE "\
[-k n] kind of netCDF format for output file, default same as input\n\
1 classic, 2 64-bit offset, 3 netCDF-4, 4 netCDF-4 classic model\n\
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[-d n] deflation compression level, default same as input (0=none 9=max)\n\
[-s] adds shuffle option to deflation compression\n\
[-u] converts unlimited dimensions to fixed-size dimensions in output copy\n\
[-m n] size in bytes of copy buffer, default is 5000000 bytes\n\
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infile name of netCDF input file\n\
outfile name for netCDF output file\n"
(void) fprintf(stderr,
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"%s [-k n] [-d n] [-s] [-u] [-m n] infile outfile\n%s",
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progname,
USAGE);
}
int
main(int argc, char**argv)
{
char* inputfile = NULL;
char* outputfile = NULL;
int kind = SAME_AS_INPUT; /* default, output same format as input */
int c;
size_t copybuf_size = COPY_BUFFER_SIZE; /* default */
/* table of formats for legal -k values */
struct Kvalues {
char* name;
int kind;
} legalkinds[] = {
{"1", NC_FORMAT_CLASSIC},
{"classic", NC_FORMAT_CLASSIC},
/* The 64-bit offset kind (2) */
{"2", NC_FORMAT_64BIT},
{"64-bit-offset", NC_FORMAT_64BIT},
{"64-bit offset", NC_FORMAT_64BIT},
/* NetCDF-4 HDF5 format */
{"3", NC_FORMAT_NETCDF4},
{"hdf5", NC_FORMAT_NETCDF4},
{"netCDF-4", NC_FORMAT_NETCDF4},
{"netCDF4", NC_FORMAT_NETCDF4},
{"enhanced", NC_FORMAT_NETCDF4},
/* NetCDF-4 HDF5 format, but using only nc3 data model */
{"4", NC_FORMAT_NETCDF4_CLASSIC},
{"hdf5-nc3", NC_FORMAT_NETCDF4_CLASSIC},
{"netCDF-4 classic model", NC_FORMAT_NETCDF4_CLASSIC},
{"netCDF4_classic", NC_FORMAT_NETCDF4_CLASSIC},
{"enhanced-nc3", NC_FORMAT_NETCDF4_CLASSIC},
/* null terminate*/
{NULL,0}
};
opterr = 1;
progname = argv[0];
if (argc <= 1)
{
usage();
return 1;
}
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while ((c = getopt(argc, argv, "k:d:sum:")) != EOF) {
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switch(c) {
case 'k': /* for specifying variant of netCDF format to be generated
Possible values are:
1 (=> classic 32 bit)
2 (=> classic 64 bit offsets)
3 (=> netCDF-4/HDF5)
4 (=> classic, but stored in netCDF-4/HDF5 format)
Also allow string versions of above
"classic"
"64-bit-offset"
"64-bit offset"
"enhanced" | "hdf5" | "netCDF-4"
"enhanced-nc3" | "hdf5-nc3" | "netCDF-4 classic model"
*/
{
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) {
kind = kvalue->kind;
break;
}
}
if(kvalue->name == NULL) {
fprintf(stderr, "invalid format: %s\n", kind_name);
return 1;
}
}
break;
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case 'd': /* non-default compression level specified */
option_deflate_level = strtol(optarg, NULL, 10);
if(option_deflate_level < 0 || option_deflate_level > 9) {
fprintf(stderr, "invalid deflation level: %d\n",
option_deflate_level);
return 1;
}
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break;
case 's': /* shuffling, may improve compression */
option_shuffle_vars = NC_SHUFFLE;
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break;
case 'u': /* convert unlimited dimensions to fixed size */
option_fix_unlimdims = 1;
break;
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case 'm': /* non-default size of data copy buffer */
{
char *suffix = 0; /* "k" for kilobytes or "m" for megabytes */
copybuf_size = strtoll(optarg, &suffix, 10);
switch (suffix[0]) {
case 'k':
case 'K':
copybuf_size *= 1000;
break;
case 'm':
case 'M':
copybuf_size *= 1000000;
break;
case 'g':
case 'G':
copybuf_size *= 1000000000;
break;
default:
fprintf(stderr,"Suffix for '-m' option value not k, m, or g: %c",
suffix[0]);
exit(1);
}
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break;
}
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default:
usage();
exit(1);
break;
}
}
argc -= optind;
argv += optind;
if (argc != 2) {
fprintf(stderr,"one input file and one output file required\n");
exit(1);
}
inputfile = argv[0];
outputfile = argv[1];
if(strcmp(inputfile, outputfile) == 0) {
fprintf(stderr,"output would overwrite input\n");
exit(1);
}
if(copy(inputfile, outputfile, kind, copybuf_size) != NC_NOERR)
exit(1);
return 0;
}