forked from Unidata/netcdf-c
/
nccopy.c
2110 lines (1944 loc) · 65.8 KB
/
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>
#include <stdio.h>
#ifdef HAVE_GETOPT_H
#include <getopt.h>
#endif
#ifdef HAVE_UNISTD_H
#include <unistd.h>
#endif
#include <string.h>
#include "netcdf.h"
#include "nciter.h"
#include "utils.h"
#include "chunkspec.h"
#include "dimmap.h"
#include "nccomps.h"
#include "ncfilter.h"
#undef DEBUGFILTER
#ifdef _MSC_VER
#include "XGetopt.h"
#define snprintf _snprintf
int opterr;
int optind;
#endif
/* 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 " !\"#$%&'()*,:;<=>?[]\\^`{|}~"
#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 FilterSpec {
char* fqn;
int nofilter; /* 1=> do not apply any filters to this variable */
unsigned int filterid;
size_t nparams;
unsigned int* params;
};
static int nfilterspecs = 0; /* Number of defined filter specs */
static struct FilterSpec filterspecs[MAX_FILTER_SPECS];
static int suppressfilters = 0; /* 1 => do not apply any output filters unless specified */
#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_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 int 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;
return stat;
}
#if 0
static int
parseFQN(int ncid, const char* fqn0, VarID* idp)
{
int stat = NC_NOERR;
char* fqn;
VarID vid;
char* p;
char* q;
char* segment;
vid.grpid = ncid;
if(fqn0 == NULL || fqn0[1] != '/')
{stat = NC_EBADNAME; goto done;}
fqn = strdup(fqn0+1); /* skip leading '/'*/
p = fqn;
for(;;) {
int newgrp;
segment = p;
q = p;
while(*p != '\0' && *p != '/') {
if(*p == '\\') p++;
*q++ = *p++;
}
if(*p == '\0') break;
*p++ = '\0';
if((stat=nc_inq_grp_ncid(vid.grpid,segment,&newgrp))) goto done;
vid.grpid = newgrp;
}
/* Segment should point to the varname */
if((stat=nc_inq_varid(vid.grpid,segment,&vid.varid))) goto done;
done:
if(fqn) free(fqn);
if(stat == NC_NOERR && idp != NULL) *idp = vid;
return stat;
}
#endif
static int
parsefilterspec(const char* optarg0, struct FilterSpec* spec)
{
int stat = NC_NOERR;
char* optarg = NULL;
unsigned int* params = NULL;
size_t nparams;
unsigned int id;
char* p = NULL;
char* remainder = NULL;
if(optarg0 == NULL || strlen(optarg0) == 0 || spec == NULL) return 0;
memset(spec,0,sizeof(struct FilterSpec));
optarg = strdup(optarg0);
/* Collect the fqn, taking escapes into account */
p = optarg;
remainder = NULL;
for(;*p;p++) {
if(*p == '\\') p++;
else if(*p == ',') {*p = '\0'; remainder = p+1; break;}
else if(*p == '\0') {remainder = p; break;}
/* else continue */
}
if(strlen(optarg) == 0) {stat = NC_EINVAL; goto done;} /* fqn does not exist */
/* Make sure leading '/' is in place */
if(optarg[0]=='/')
spec->fqn = strdup(optarg);
else {
spec->fqn = (char*)malloc(1+strlen(optarg)+1);
strcpy(spec->fqn,"/");
strcat(spec->fqn,optarg);
}
/* Check for special cases */
if( (remainder == NULL) ||
(strncmp(remainder,"none",4) == 0)) {
spec->nofilter = 1;
goto done;
}
/* Collect the id+parameters */
if((stat = NC_parsefilterspec(remainder,&id,&nparams,¶ms)) == NC_NOERR) {
if(spec != NULL) {
spec->filterid = id;
spec->nparams = nparams;
spec->params = params;
}
}
done:
if(optarg) free(optarg);
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));
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(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++) {
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 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;
size_t *chunkp = (size_t *) emalloc(ndims * sizeof(size_t));
int *dimids = (int *) emalloc(ndims * sizeof(int));
int idim;
/* size of a chunk: product of dimension chunksizes and size of value */
size_t csprod = val_size(ogrp, o_varid);
int is_unlimited = 0;
NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, chunkp));
NC_CHECK(nc_inq_vardimid(igrp, varid, dimids));
for(idim = 0; idim < ndims; idim++) {
int idimid = dimids[idim];
int odimid = dimmap_odimid(idimid);
size_t chunksize = chunkspec_size(idimid);
if(chunksize > 0) { /* found in chunkspec */
chunkp[idim] = chunksize;
}
csprod *= chunkp[idim];
if(dimmap_ounlim(odimid))
is_unlimited = 1;
}
/* Explicitly set chunking, even if default */
/* If product of chunksizes is too small and no unlimited
* dimensions used, don't chunk. Also if chunking
* explicitly turned off with chunk spec, don't chunk. */
if ((csprod < option_min_chunk_bytes && !is_unlimited) || contig == 1
|| chunkspec_omit() == true) {
NC_CHECK(nc_def_var_chunking(ogrp, o_varid, NC_CONTIGUOUS, NULL));
} else {
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_in=0, deflate_in=0, deflate_level_in=0;
int shuffle_out=0, deflate_out=0, deflate_level_out=0;
if(option_deflate_level != 0) {
NC_CHECK(nc_inq_var_deflate(igrp, varid, &shuffle_in, &deflate_in, &deflate_level_in));
if(option_deflate_level == -1) { /* not specified, 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;
}
NC_CHECK(nc_def_var_deflate(ogrp, o_varid, shuffle_out, deflate_out, deflate_level_out));
}
}
{ /* 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;
}
/* 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 stat = NC_NOERR;
VarID vid = {igrp,varid};
VarID ovid = {ogrp,o_varid};
/* handle filter parameters, copying from input, overriding with command-line options */
struct FilterSpec inspec = {NULL,0,0,0,NULL},
ospec = {NULL,0,0,0,NULL},
actualspec = {NULL,0,0,0,NULL};
int i;
char* ofqn = NULL;
int format, oformat;
int inputdefined, outputdefined, unfiltered;
/* Get file format of the input and output */
if((stat=nc_inq_format(vid.grpid,&format))) goto done;
if((stat=nc_inq_format(ovid.grpid,&oformat))) goto done;
if(oformat != NC_FORMAT_NETCDF4 && oformat != NC_FORMAT_NETCDF4_CLASSIC)
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 */
memset(&inspec,0,sizeof(inspec));
memset(&ospec,0,sizeof(ospec));
memset(&actualspec,0,sizeof(actualspec));
/* Is there a filter on the output variable */
outputdefined = 0; /* default is no filter defined */
/* Only bother to look if output is netcdf-4 variant */
if(oformat == NC_FORMAT_NETCDF4 || oformat == NC_FORMAT_NETCDF4_CLASSIC) {
/* See if any output filter spec is defined for this output variable */
for(i=0;i<nfilterspecs;i++) {
if(strcmp(filterspecs[i].fqn,ofqn)==0) {
ospec = filterspecs[i];
outputdefined = 1;
break;
}
}
}
/* Is there a filter on the input variable */
inputdefined = 0; /* default is no filter defined */
/* Only bother to look if input is netcdf-4 variant */
if(format == NC_FORMAT_NETCDF4 || format == NC_FORMAT_NETCDF4_CLASSIC) {
stat=nc_inq_var_filter(vid.grpid,vid.varid,&inspec.filterid,&inspec.nparams,NULL);
if(stat && stat != NC_EFILTER)
goto done; /* true error */
if(stat == NC_NOERR) {/* input has a filter */
inspec.params = (unsigned int*)malloc(sizeof(unsigned int)*inspec.nparams);
if((stat=nc_inq_var_filter(vid.grpid,vid.varid,&inspec.filterid,&inspec.nparams,inspec.params)))
goto done;
inputdefined = 1;
}
}
/* Rules for choosing output filter are as follows:
global output input Actual Output
suppress filter filter filter
-----------------------------------------------
true undefined NA unfiltered
true 'none' NA unfiltered
true defined NA use output filter
false undefined defined use input filter
false 'none' NA unfiltered
false defined NA use output filter
*/
unfiltered = 0;
if(suppressfilters && !outputdefined) /* row 1 */
unfiltered = 1;
else if(suppressfilters && outputdefined && ospec.nofilter) /* row 2 */
unfiltered = 1;
else if(suppressfilters && outputdefined) /* row 3 */
actualspec = ospec;
else if(!suppressfilters && !outputdefined && inputdefined) /* row 4 */
actualspec = inspec;
else if(!suppressfilters && outputdefined && ospec.nofilter) /* row 5 */
unfiltered = 1;
else if(!suppressfilters && outputdefined) /* row 6 */
actualspec = ospec;
/* Apply actual filter spec if any */
if(!unfiltered) {
if((stat=nc_def_var_filter(ovid.grpid,ovid.varid,
actualspec.filterid,
actualspec.nparams,
actualspec.params)))
goto done;
}
done:
/* Cleanup */
if(ofqn != NULL) free(ofqn);
if(inspec.fqn) free(inspec.fqn);
if(inspec.params) free(inspec.params);
/* Note we do not clean actualspec because it is a copy of in|out spec */
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; /* whether vriable is unlimited */
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;
}
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 = chunkspec_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;
}
/* 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. */
#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 = 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
#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((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;