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netcdf-c/ncdump/nccopy.c

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/*********************************************************************
* Copyright 2010, 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 <stdlib.h>
#ifdef HAVE_GETOPT_H
#include <getopt.h>
#endif
#ifndef _WIN32
#include <unistd.h>
#endif
#include <string.h>
#include <netcdf.h>
#include "nciter.h"
#include "chunkspec.h"
#include "utils.h"
#include "dimmap.h"
/* 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 (1024) /* 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
/* 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 char* option_chunkspec = 0; /* 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_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; /* 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 */
ogid = parid;
stat = NC_NOERR;
} else {
NC_CHECK(stat);
}
#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) {
NC_CHECK(NC_ENOMEM);
}
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 */
}
NC_CHECK(nc_inq_grp_full_ncid(ncid, parent, locidp));
free(parent);
return stat;
}
/* 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;
int dim;
int contig = 1;
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((ndims + 1) * sizeof(size_t));
if(ndims > 0) {
NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, NULL));
}
if(contig == 1) {
*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 dim;
int icontig = 1, ocontig = 1;
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));
if(ndims > 0) {
NC_CHECK(nc_inq_var_chunking(igrp, ivarid, &icontig, NULL));
NC_CHECK(nc_inq_var_chunking(ogrp, ovarid, &ocontig, NULL));
}
if(icontig == 1 && ocontig == 1) { /* 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 == 0 && ocontig == 1) { /* 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((ndims + 1) * sizeof(size_t));
if(icontig == 1) { /* if input contiguous, treat as if chunked on
* first dimension */
ichunksizes[0] = 1;
for(dim = 1; dim < ndims; dim++) {
ichunksizes[dim] = dim;
}
} else {
NC_CHECK(nc_inq_var_chunking(igrp, ivarid, &icontig, ichunksizes));
}
/* now can assume chunking in both input and output */
ochunksizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
NC_CHECK(nc_inq_var_chunking(ogrp, ovarid, &ocontig, ochunksizes));
nelems = 1;
oprod = value_size;
for(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;
}
/* Forward declaration, because copy_type, copy_vlen_type call each other */
static int copy_type(int igrp, nc_type typeid, int ogrp);
/*
* 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((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;
int 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));
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, oparid;
/* get full group name of input group */
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));
/* 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(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) * numgrps);
NC_CHECK(nc_inq_grps(igrp, &numgrps, grpids));
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 */
NC_CHECK(get_grpid(grpids[i], ogrp, &ogid));
NC_CHECK(copy_types(grpids[i], ogid));
}
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;
NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
if (ndims > 0) { /* no chunking for scalar variables */
int contig = 0;
NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, NULL));
if(contig == 1) {
NC_CHECK(nc_def_var_chunking(ogrp, o_varid, NC_CONTIGUOUS, NULL));
} else {
size_t *chunkp = (size_t *) emalloc(ndims * sizeof(size_t));
int *dimids = (int *) emalloc(ndims * sizeof(int));
int idim;
NC_CHECK(nc_inq_var_chunking(igrp, varid, NULL, chunkp));
NC_CHECK(nc_inq_vardimid(igrp, varid, dimids));
for(idim = 0; idim < ndims; idim++) {
int dimid = dimids[idim];
size_t chunksize = chunkspec_size(dimid);
if(chunkspec_size(dimid) > 0) { /* found in chunkspec */
chunkp[idim] = chunksize;
}
}
/* explicitly set chunking, even if default */
NC_CHECK(nc_def_var_chunking(ogrp, o_varid, NC_CHUNKED, chunkp));
free(dimids);
free(chunkp);
}
}
}
{ /* handle compression parameters, copying from input, overriding
* with command-line options */
int shuffle, deflate, deflate_level;
NC_CHECK(nc_inq_var_deflate(igrp, varid, &shuffle, &deflate, &deflate_level));
if(option_deflate_level >= 0) { /* change output compression, if requested */
deflate_level = option_deflate_level;
}
if(deflate != 0 || shuffle != 0) {
NC_CHECK(nc_def_var_deflate(ogrp, o_varid, shuffle, deflate_level > 0, deflate_level));
}
}
{ /* 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));
}
}
{ /* 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));
}
}
return stat;
}
/* 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(chunkspec_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;
if(idimid != -1) {
size_t chunksize = chunkspec_size(idimid); /* from chunkspec */
size_t dimlen;
NC_CHECK(nc_inq_dimlen(ogrp, odimid, &dimlen));
if( (chunksize > 0) || dimmap_ounlim(odimid)) {
chunked = 1;
}
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. */
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 = chunkspec_size(idimid);
if(chunksize > 0) {
chunkp[odim] = chunksize;
} 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;
}
/* 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;
}
/* 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. */
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 = 1;
NC_CHECK(nc_inq_var_chunking(grp, varid, &contig, NULL));
if(contig == 0) { /* chunked */
NC_CHECK(nc_set_var_chunk_cache(grp, varid, chunk_cache_size, cache_nelems, cache_preemp));
}
}
return stat;
}
#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 nunlims;
int dgrp;
#ifdef USE_NETCDF4
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((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((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 uld;
int idimid, odimid;
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));
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((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((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));
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. */
NC_CHECK(copy_var_specials(igrp, varid, ogrp, o_varid));
}
/* Set chunking if specified in command line option */
NC_CHECK(set_var_chunked(ogrp, o_varid));
/* Set compression if specified in command line option */
NC_CHECK(set_var_compressed(ogrp, o_varid));
}
}
#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;
NC_CHECK(nc_inq_nvars(igrp, &nvars));
for (varid = 0; varid < nvars; varid++) {
NC_CHECK(copy_var(igrp, varid, ogrp));
}
return stat;
}
/* 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 */
int i;
/* 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;
/* Copy schema from subgroups */
stat = nc_inq_grps(igrp, &numgrps, NULL);
grpids = (int *)emalloc((numgrps + 1) * sizeof(int));
NC_CHECK(nc_inq_grps(igrp, &numgrps, grpids));
for(i = 0; i < numgrps; i++) {
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, long long *nvalsp) {
int stat = NC_NOERR;
int ndims;
int *dimids;
int dim;
long long nvals = 1;
NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
dimids = (int *) emalloc((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;
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 */
int do_realloc = 0;
size_t chunksize;
int okind;
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));
/* from type, get size in memory needed for each value */
NC_CHECK(nc_inq_type(igrp, vartype, NULL, &value_size));
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 = 1;
NC_CHECK(nc_inq_var_chunking(ogrp, ovarid, &contig, NULL));
if(contig == 0) { /* 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((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) {
NC_CHECK(nc_get_vara(igrp, varid, start, count, buf));
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 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 */
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++) {
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((numgrps + 1) * sizeof(int));
NC_CHECK(nc_inq_grps(igrp, &numgrps, grpids));
for(i = 0; i < numgrps; i++) {
NC_CHECK(copy_data(grpids[i], ogid));
}
free(grpids);
#endif /* USE_NETCDF4 */
return stat;
}
/* Count total number of dimensions in ncid and all its subgroups */
int
count_dims(ncid) {
int numgrps;
int *grpids;
int igrp;
int ndims=0;
/* get total number of groups and their ids, including all descendants */
NC_CHECK(nc_inq_grps_full(ncid, &numgrps, NULL));
grpids = emalloc(numgrps * sizeof(int));
NC_CHECK(nc_inq_grps_full(ncid, NULL, grpids));
for(igrp = 0; igrp < numgrps; igrp++) {
int ndims_local;
nc_inq_ndims(grpids[igrp], &ndims_local);
ndims += ndims_local;
}
free(grpids);
return ndims;
}
/* 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.
*/
static int
copy(char* infile, char* outfile)
{
int stat = NC_NOERR;
int igrp, ogrp;
int inkind, outkind;
size_t ndims;
NC_CHECK(nc_open(infile,NC_NOWRITE,&igrp));
NC_CHECK(nc_inq_format(igrp, &inkind));
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) {
if (option_deflate_level > 0 ||
option_shuffle_vars == NC_SHUFFLE ||
option_chunkspec)
{
outkind = NC_FORMAT_NETCDF4_CLASSIC;
}
}
}
#ifdef USE_NETCDF4
if(option_chunkspec) {
/* Now that input is open, can parse option_chunkspec into binary
* structure. */
NC_CHECK(chunkspec_parse(igrp, option_chunkspec));
}
#endif /* USE_NETCDF4 */
switch(outkind) {
case NC_FORMAT_CLASSIC:
NC_CHECK(nc_create(outfile,NC_CLOBBER,&ogrp));
break;
case NC_FORMAT_64BIT:
NC_CHECK(nc_create(outfile,NC_CLOBBER|NC_64BIT_OFFSET,&ogrp));
break;
#ifdef USE_NETCDF4
case NC_FORMAT_NETCDF4:
NC_CHECK(nc_create(outfile,NC_CLOBBER|NC_NETCDF4,&ogrp));
break;
case NC_FORMAT_NETCDF4_CLASSIC:
NC_CHECK(nc_create(outfile,NC_CLOBBER|NC_NETCDF4|NC_CLASSIC_MODEL,&ogrp));
break;
#else
case NC_FORMAT_NETCDF4:
case NC_FORMAT_NETCDF4_CLASSIC:
error("built without ability to create netCDF-4 files");
break;
#endif /* USE_NETCDF4 */
default:
error("bad value (%d) for -k option\n", option_kind);
break;
}
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 = count_dims(igrp);
NC_CHECK(dimmap_init(ndims));
NC_CHECK(copy_schema(igrp, ogrp));
NC_CHECK(nc_enddef(ogrp));
NC_CHECK(copy_data(igrp, ogrp));
NC_CHECK(nc_close(igrp));
NC_CHECK(nc_close(ogrp));
return stat;
}
static void
usage(void)
{
#define USAGE "\
[-k n] specify 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\
[-d n] set 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 dimensions, e.g. \"dim1/N1,dim2/N2,...\"\n\
[-u] convert unlimited dimensions to fixed-size dimensions in output copy\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\
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 n] [-d n] [-s] [-c chunkspec] [-u] [-m n] [-h n] [-e n] infile outfile\n%s",
progname, USAGE);
}
int
main(int argc, char**argv)
{
char* inputfile = NULL;
char* outputfile = NULL;
int c;
/* 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();
}
while ((c = getopt(argc, argv, "k:d:sum:c:h:e:x")) != -1) {
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) {
option_kind = kvalue->kind;
break;
}
}
if(kvalue->name == NULL) {
error("invalid format: %s", kind_name);
}
}
break;
case 'd': /* non-default compression level specified */
option_deflate_level = 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;
char *suffix = 0; /* "K" for kilobytes. "M" for megabytes, ... */
dval = strtod(optarg, &suffix);
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;
default:
error("If suffix used for '-m' option value, it must be K, M, G, or T: %c",
*suffix);
}
}
option_copy_buffer_size = dval;
break;
}
case 'h': /* non-default size of chunk cache */
{
double dval;
char *suffix = 0; /* "K" for kilobytes, "M" for megabytes, ... */
dval = strtod(optarg, &suffix);
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;
default:
error("If suffix used for '-h' option value, it must be K, M, G, or T: %c",
*suffix);
}
}
option_chunk_cache_size = dval;
break;
}
case 'e': /* number of elements chunk cache can hold */
option_chunk_cache_nelems = strtol(optarg, NULL, 10);
if(option_chunk_cache_nelems <= 0) {
error("invalid value for number of chunk cache elements: %d", option_chunk_cache_nelems);
}
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 */
option_chunkspec = strdup(optarg);
break;
}
default:
usage();
}
}
argc -= optind;
argv += optind;
if (argc != 2) {
error("one input file and one output file required");
}
inputfile = argv[0];
outputfile = argv[1];
if(strcmp(inputfile, outputfile) == 0) {
error("output would overwrite input");
}
if(copy(inputfile, outputfile) != NC_NOERR)
exit(1);
return 0;
}
END_OF_MAIN();
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