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https://github.com/Unidata/netcdf-c.git
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1770 lines
56 KiB
C
1770 lines
56 KiB
C
/*********************************************************************
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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
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* compression additions.
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* $Id: nccopy.c 400 2010-08-27 21:02:52Z russ $
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*********************************************************************/
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#include "config.h" /* for USE_NETCDF4 macro */
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#include <stdlib.h>
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#ifdef HAVE_GETOPT_H
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#include <getopt.h>
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#endif
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#ifdef HAVE_UNISTD_H
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#include <unistd.h>
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#endif
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#include <string.h>
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#include <netcdf.h>
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#include "nciter.h"
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#include "utils.h"
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#include "chunkspec.h"
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#include "dimmap.h"
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#include "nccomps.h"
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#ifdef _MSC_VER
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#include "XGetopt.h"
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#define snprintf _snprintf
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int opterr;
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int optind;
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#endif
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/* default bytes of memory we are willing to allocate for variable
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* values during copy */
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#define COPY_BUFFER_SIZE (5000000)
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#define COPY_CHUNKCACHE_PREEMPTION (1.0f) /* for copying, can eject fully read chunks */
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#define SAME_AS_INPUT (-1) /* default, if kind not specified */
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#define CHUNK_THRESHOLD (8192) /* non-record variables with fewer bytes don't get chunked */
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#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
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/* Global variables for command-line requests */
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char *progname; /* for error messages */
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static int option_kind = SAME_AS_INPUT;
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static int option_deflate_level = -1; /* default, compress output only if input compressed */
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static int option_shuffle_vars = NC_NOSHUFFLE; /* default, no shuffling on compression */
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static int option_fix_unlimdims = 0; /* default, preserve unlimited dimensions */
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static char* option_chunkspec = 0; /* default, no chunk specification */
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static size_t option_copy_buffer_size = COPY_BUFFER_SIZE;
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static size_t option_chunk_cache_size = CHUNK_CACHE_SIZE; /* default from config.h */
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static size_t option_chunk_cache_nelems = CHUNK_CACHE_NELEMS; /* default from config.h */
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static int option_read_diskless = 0; /* default, don't read input into memory on open */
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static int option_write_diskless = 0; /* default, don't write output to diskless file */
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static int option_min_chunk_bytes = CHUNK_THRESHOLD; /* default, don't chunk variable if prod of
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* chunksizes of its dimensions is smaller
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* than this */
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static int option_nlgrps = 0; /* Number of groups specified with -g
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* option on command line */
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static char** option_lgrps = 0; /* list of group names specified with -g
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* option on command line */
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static idnode_t* option_grpids = 0; /* list of grpids matching list specified with -g option */
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static bool_t option_grpstruct = false; /* if -g set, copy structure for non-selected groups */
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static int option_nlvars = 0; /* Number of variables specified with -v * option on command line */
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static char** option_lvars = 0; /* list of variable names specified with -v
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* option on command line */
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static bool_t option_varstruct = false; /* if -v set, copy structure for non-selected vars */
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static int option_compute_chunkcaches = 0; /* default, don't try still flaky estimate of
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* chunk cache for each variable */
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/* get group id in output corresponding to group igrp in input,
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* given parent group id (or root group id) parid in output. */
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static int
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get_grpid(int igrp, int parid, int *ogrpp) {
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int stat = NC_NOERR;
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int ogid = parid; /* like igrp but in output file */
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#ifdef USE_NETCDF4
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int inparid;
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/* if not root group, get corresponding output groupid from group name */
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stat = nc_inq_grp_parent(igrp, &inparid);
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if(stat == NC_NOERR) { /* not root group */
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char grpname[NC_MAX_NAME + 1];
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NC_CHECK(nc_inq_grpname(igrp, grpname));
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NC_CHECK(nc_inq_grp_ncid(parid, grpname, &ogid));
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} else if(stat == NC_ENOGRP) { /* root group */
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stat = NC_NOERR;
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} else {
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NC_CHECK(stat);
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}
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#endif /* USE_NETCDF4 */
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*ogrpp = ogid;
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return stat;
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}
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/* Return size in bytes of a variable value */
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static size_t
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val_size(int grpid, int varid) {
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nc_type vartype;
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size_t value_size;
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NC_CHECK(nc_inq_vartype(grpid, varid, &vartype));
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NC_CHECK(nc_inq_type(grpid, vartype, NULL, &value_size));
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return value_size;
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}
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#ifdef USE_NETCDF4
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/* Get parent id needed to define a new group from its full name in an
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* open file identified by ncid. Assumes all intermediate groups are
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* already defined. */
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static int
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nc_inq_parid(int ncid, const char *fullname, int *locidp) {
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char *parent = strdup(fullname);
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char *slash = "/"; /* groupname separator */
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char *last_slash;
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if(parent == NULL) {
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return NC_ENOMEM; /* exits */
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}
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last_slash = strrchr(parent, '/');
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if(last_slash == parent || last_slash == NULL) { /* parent is root */
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free(parent);
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parent = strdup(slash);
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} else {
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*last_slash = '\0'; /* truncate to get parent name */
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}
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NC_CHECK(nc_inq_grp_full_ncid(ncid, parent, locidp));
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free(parent);
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return NC_NOERR;
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}
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/* Return size of chunk in bytes for a variable varid in a group igrp, or 0 if
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* layout is contiguous */
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static int
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inq_var_chunksize(int igrp, int varid, size_t* chunksizep) {
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int stat = NC_NOERR;
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int ndims;
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size_t *chunksizes;
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int dim;
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int contig = 1;
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nc_type vartype;
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size_t value_size;
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size_t prod;
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NC_CHECK(nc_inq_vartype(igrp, varid, &vartype));
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/* from type, get size in memory needed for each value */
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NC_CHECK(nc_inq_type(igrp, vartype, NULL, &value_size));
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prod = value_size;
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NC_CHECK(nc_inq_varndims(igrp, varid, &ndims));
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chunksizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
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if(ndims > 0) {
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NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, NULL));
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}
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if(contig == 1) {
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*chunksizep = 0;
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} else {
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NC_CHECK(nc_inq_var_chunking(igrp, varid, &contig, chunksizes));
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for(dim = 0; dim < ndims; dim++) {
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prod *= chunksizes[dim];
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}
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*chunksizep = prod;
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}
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free(chunksizes);
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return stat;
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}
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/* Return estimated number of elems required in chunk cache and
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* estimated size of chunk cache adequate to efficiently copy input
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* variable ivarid to output variable ovarid, which may have different
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* chunk size and shape */
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static int
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inq_var_chunking_params(int igrp, int ivarid, int ogrp, int ovarid,
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size_t* chunkcache_sizep,
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size_t *chunkcache_nelemsp,
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float * chunkcache_preemptionp)
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{
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int stat = NC_NOERR;
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int ndims;
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size_t *ichunksizes, *ochunksizes;
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int dim;
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int icontig = 1, ocontig = 1;
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nc_type vartype;
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size_t value_size;
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size_t prod, iprod, oprod;
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size_t nelems;
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*chunkcache_nelemsp = CHUNK_CACHE_NELEMS;
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*chunkcache_sizep = CHUNK_CACHE_SIZE;
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*chunkcache_preemptionp = COPY_CHUNKCACHE_PREEMPTION;
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NC_CHECK(nc_inq_varndims(igrp, ivarid, &ndims));
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if(ndims > 0) {
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NC_CHECK(nc_inq_var_chunking(igrp, ivarid, &icontig, NULL));
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NC_CHECK(nc_inq_var_chunking(ogrp, ovarid, &ocontig, NULL));
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}
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if(icontig == 1 && ocontig == 1) { /* no chunking in input or output */
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*chunkcache_nelemsp = 0;
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*chunkcache_sizep = 0;
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*chunkcache_preemptionp = 0;
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return stat;
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}
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NC_CHECK(nc_inq_vartype(igrp, ivarid, &vartype));
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NC_CHECK(nc_inq_type(igrp, vartype, NULL, &value_size));
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iprod = value_size;
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if(icontig == 0 && ocontig == 1) { /* chunking only in input */
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*chunkcache_nelemsp = 1; /* read one input chunk at a time */
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*chunkcache_sizep = iprod;
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*chunkcache_preemptionp = 1.0f;
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return stat;
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}
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ichunksizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
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if(icontig == 1) { /* if input contiguous, treat as if chunked on
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* first dimension */
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ichunksizes[0] = 1;
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for(dim = 1; dim < ndims; dim++) {
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ichunksizes[dim] = dim;
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}
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} else {
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NC_CHECK(nc_inq_var_chunking(igrp, ivarid, &icontig, ichunksizes));
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}
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/* now can assume chunking in both input and output */
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ochunksizes = (size_t *) emalloc((ndims + 1) * sizeof(size_t));
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NC_CHECK(nc_inq_var_chunking(ogrp, ovarid, &ocontig, ochunksizes));
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nelems = 1;
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oprod = value_size;
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for(dim = 0; dim < ndims; dim++) {
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nelems += 1 + (ichunksizes[dim] - 1) / ochunksizes[dim];
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iprod *= ichunksizes[dim];
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oprod *= ochunksizes[dim];
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}
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prod = iprod + oprod * (nelems - 1);
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*chunkcache_nelemsp = nelems;
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*chunkcache_sizep = prod;
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free(ichunksizes);
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free(ochunksizes);
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return stat;
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}
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/* Forward declaration, because copy_type, copy_vlen_type call each other */
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static int copy_type(int igrp, nc_type typeid, int ogrp);
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/*
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* copy a user-defined variable length type in the group igrp to the
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* group ogrp
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*/
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static int
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copy_vlen_type(int igrp, nc_type itype, int ogrp)
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{
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int stat = NC_NOERR;
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nc_type ibasetype;
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nc_type obasetype; /* base type in target group */
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char name[NC_MAX_NAME];
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size_t size;
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char basename[NC_MAX_NAME];
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size_t basesize;
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nc_type vlen_type;
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NC_CHECK(nc_inq_vlen(igrp, itype, name, &size, &ibasetype));
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/* to get base type id in target group, use name of base type in
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* source group */
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NC_CHECK(nc_inq_type(igrp, ibasetype, basename, &basesize));
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stat = nc_inq_typeid(ogrp, basename, &obasetype);
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/* if no such type, create it now */
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if(stat == NC_EBADTYPE) {
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NC_CHECK(copy_type(igrp, ibasetype, ogrp));
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stat = nc_inq_typeid(ogrp, basename, &obasetype);
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}
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NC_CHECK(stat);
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/* Now we know base type exists in output and we know its type id */
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NC_CHECK(nc_def_vlen(ogrp, name, obasetype, &vlen_type));
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return stat;
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}
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/*
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* copy a user-defined opaque type in the group igrp to the group ogrp
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*/
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static int
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copy_opaque_type(int igrp, nc_type itype, int ogrp)
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{
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int stat = NC_NOERR;
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nc_type otype;
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char name[NC_MAX_NAME];
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size_t size;
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NC_CHECK(nc_inq_opaque(igrp, itype, name, &size));
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NC_CHECK(nc_def_opaque(ogrp, size, name, &otype));
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return stat;
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}
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/*
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* copy a user-defined enum type in the group igrp to the group ogrp
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*/
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static int
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copy_enum_type(int igrp, nc_type itype, int ogrp)
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{
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int stat = NC_NOERR;
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nc_type otype;
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nc_type basetype;
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size_t basesize;
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size_t nmembers;
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char name[NC_MAX_NAME];
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int i;
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NC_CHECK(nc_inq_enum(igrp, itype, name, &basetype, &basesize, &nmembers));
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NC_CHECK(nc_def_enum(ogrp, basetype, name, &otype));
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for(i = 0; i < nmembers; i++) { /* insert enum members */
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char ename[NC_MAX_NAME];
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long long val; /* large enough to hold any integer type */
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NC_CHECK(nc_inq_enum_member(igrp, itype, i, ename, &val));
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NC_CHECK(nc_insert_enum(ogrp, otype, ename, &val));
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}
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return stat;
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}
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/*
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* copy a user-defined compound type in the group igrp to the group ogrp
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*/
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static int
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copy_compound_type(int igrp, nc_type itype, int ogrp)
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{
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int stat = NC_NOERR;
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char name[NC_MAX_NAME];
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size_t size;
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size_t nfields;
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nc_type otype;
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int fid;
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NC_CHECK(nc_inq_compound(igrp, itype, name, &size, &nfields));
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NC_CHECK(nc_def_compound(ogrp, size, name, &otype));
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for (fid = 0; fid < nfields; fid++) {
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char fname[NC_MAX_NAME];
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char ftypename[NC_MAX_NAME];
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size_t foff;
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nc_type iftype, oftype;
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int fndims;
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NC_CHECK(nc_inq_compound_field(igrp, itype, fid, fname, &foff, &iftype, &fndims, NULL));
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/* type ids in source don't necessarily correspond to same
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* typeids in destination, so look up destination typeid by using
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* field type name */
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NC_CHECK(nc_inq_type(igrp, iftype, ftypename, NULL));
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NC_CHECK(nc_inq_typeid(ogrp, ftypename, &oftype));
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if(fndims == 0) {
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NC_CHECK(nc_insert_compound(ogrp, otype, fname, foff, oftype));
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} else { /* field is array type */
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int *fdimsizes;
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fdimsizes = (int *) emalloc((fndims + 1) * sizeof(int));
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stat = nc_inq_compound_field(igrp, itype, fid, NULL, NULL, NULL,
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NULL, fdimsizes);
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NC_CHECK(nc_insert_array_compound(ogrp, otype, fname, foff, oftype, fndims, fdimsizes));
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free(fdimsizes);
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}
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}
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return stat;
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}
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/*
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* copy a user-defined type in the group igrp to the group ogrp
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*/
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static int
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copy_type(int igrp, nc_type typeid, int ogrp)
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{
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int stat = NC_NOERR;
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nc_type type_class;
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NC_CHECK(nc_inq_user_type(igrp, typeid, NULL, NULL, NULL, NULL, &type_class));
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switch(type_class) {
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case NC_VLEN:
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NC_CHECK(copy_vlen_type(igrp, typeid, ogrp));
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break;
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case NC_OPAQUE:
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NC_CHECK(copy_opaque_type(igrp, typeid, ogrp));
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break;
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case NC_ENUM:
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NC_CHECK(copy_enum_type(igrp, typeid, ogrp));
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break;
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case NC_COMPOUND:
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NC_CHECK(copy_compound_type(igrp, typeid, ogrp));
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break;
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default:
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NC_CHECK(NC_EBADTYPE);
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}
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return stat;
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}
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/* Copy a group and all its subgroups, recursively, from iroot to
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* oroot, the ncids of input file and output file. This just creates
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* all the groups in the destination, but doesn't copy anything that's
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* in the groups yet. */
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static int
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copy_groups(int iroot, int oroot)
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{
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int stat = NC_NOERR;
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int numgrps;
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int *grpids;
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int i;
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/* get total number of groups and their ids, including all descendants */
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NC_CHECK(nc_inq_grps_full(iroot, &numgrps, NULL));
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if(numgrps > 1) { /* there's always 1 root group */
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grpids = emalloc(numgrps * sizeof(int));
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NC_CHECK(nc_inq_grps_full(iroot, NULL, grpids));
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/* create corresponding new groups in ogrp, except for root group */
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for(i = 1; i < numgrps; i++) {
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char *grpname_full;
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char grpname[NC_MAX_NAME];
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size_t len_name;
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int ogid = 0, oparid = 0, iparid = 0;
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/* get full group name of input group */
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NC_CHECK(nc_inq_grpname(grpids[i], grpname));
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if (option_grpstruct || group_wanted(grpids[i], option_nlgrps, option_grpids)) {
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NC_CHECK(nc_inq_grpname_full(grpids[i], &len_name, NULL));
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grpname_full = emalloc(len_name + 1);
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NC_CHECK(nc_inq_grpname_full(grpids[i], &len_name, grpname_full));
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/* Make sure, the parent group is also wanted (root group is always wanted) */
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NC_CHECK(nc_inq_parid(iroot, grpname_full, &iparid));
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if (!option_grpstruct && !group_wanted(iparid, option_nlgrps, option_grpids)
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&& iparid != iroot) {
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error("ERROR: trying to copy a group but not the parent: %s", grpname_full);
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}
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/* get id of parent group of corresponding group in output.
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* Note that this exists, because nc_inq_groups returned
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* grpids in preorder, so parents are always copied before
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* their subgroups */
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NC_CHECK(nc_inq_parid(oroot, grpname_full, &oparid));
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NC_CHECK(nc_inq_grpname(grpids[i], grpname));
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/* define corresponding group in output */
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NC_CHECK(nc_def_grp(oparid, grpname, &ogid));
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free(grpname_full);
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}
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}
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free(grpids);
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}
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return stat;
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}
|
|
|
|
/*
|
|
* 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;
|
|
}
|
|
|
|
/* 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;
|
|
int o_is_unlim;
|
|
int idimid, odimid;
|
|
#ifdef USE_NETCDF4
|
|
int uld;
|
|
#endif
|
|
|
|
i_is_unlim = 0;
|
|
#ifdef USE_NETCDF4
|
|
idimid = dimids[dgrp];
|
|
for (uld = 0; uld < nunlims; uld++) {
|
|
if(idimid == unlimids[uld]) {
|
|
i_is_unlim = 1;
|
|
break;
|
|
}
|
|
}
|
|
#else
|
|
idimid = dgrp;
|
|
if(unlimid != -1 && (idimid == unlimid)) {
|
|
i_is_unlim = 1;
|
|
}
|
|
#endif /* USE_NETCDF4 */
|
|
|
|
stat = nc_inq_dim(igrp, idimid, name, &length);
|
|
if (stat == NC_EDIMSIZE && sizeof(size_t) < 8) {
|
|
error("dimension \"%s\" requires 64-bit platform", name);
|
|
}
|
|
NC_CHECK(stat);
|
|
o_is_unlim = i_is_unlim;
|
|
if(i_is_unlim && !option_fix_unlimdims) {
|
|
NC_CHECK(nc_def_dim(ogrp, name, NC_UNLIMITED, &odimid));
|
|
} else {
|
|
NC_CHECK(nc_def_dim(ogrp, name, length, &odimid));
|
|
o_is_unlim = 0;
|
|
}
|
|
/* Store (idimid, odimid) mapping for later use, also whether unlimited */
|
|
dimmap_store(idimid, odimid, i_is_unlim, o_is_unlim);
|
|
}
|
|
#ifdef USE_NETCDF4
|
|
free(dimids);
|
|
free(unlimids);
|
|
#endif /* USE_NETCDF4 */
|
|
return stat;
|
|
}
|
|
|
|
/* Copy the attributes for variable ivar in group igrp to variable
|
|
* ovar in group ogrp. Global (group) attributes are specified by
|
|
* using the varid NC_GLOBAL */
|
|
static int
|
|
copy_atts(int igrp, int ivar, int ogrp, int ovar)
|
|
{
|
|
int natts;
|
|
int iatt;
|
|
int stat = NC_NOERR;
|
|
|
|
NC_CHECK(nc_inq_varnatts(igrp, ivar, &natts));
|
|
|
|
for(iatt = 0; iatt < natts; iatt++) {
|
|
char name[NC_MAX_NAME];
|
|
NC_CHECK(nc_inq_attname(igrp, ivar, iatt, name));
|
|
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));
|
|
} else {
|
|
/* 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;
|
|
|
|
int iv; /* variable number */
|
|
idnode_t* vlist = 0; /* list for vars specified with -v option */
|
|
|
|
/*
|
|
* If any vars were specified with -v option, get list of
|
|
* associated variable ids relative to this group. Assume vars
|
|
* specified with syntax like "grp1/grp2/varname" or
|
|
* "/grp1/grp2/varname" if they are in groups.
|
|
*/
|
|
vlist = newidlist(); /* list for vars specified with -v option */
|
|
for (iv=0; iv < option_nlvars; iv++) {
|
|
if(nc_inq_gvarid(igrp, option_lvars[iv], &varid) == NC_NOERR)
|
|
idadd(vlist, varid);
|
|
}
|
|
|
|
NC_CHECK(nc_inq_nvars(igrp, &nvars));
|
|
for (varid = 0; varid < nvars; varid++) {
|
|
if (!option_varstruct && option_nlvars > 0 && ! idmember(vlist, varid))
|
|
continue;
|
|
NC_CHECK(copy_var(igrp, varid, ogrp));
|
|
}
|
|
freeidlist(vlist);
|
|
return stat;
|
|
}
|
|
|
|
/* Copy the schema in a group and all its subgroups, recursively, from
|
|
* group igrp in input to parent group ogrp in destination. Use
|
|
* dimmap array to map input dimids to output dimids. */
|
|
static int
|
|
copy_schema(int igrp, int ogrp)
|
|
{
|
|
int stat = NC_NOERR;
|
|
int ogid; /* like igrp but in output file */
|
|
|
|
/* get groupid in output corresponding to group igrp in input,
|
|
* given parent group (or root group) ogrp in output */
|
|
NC_CHECK(get_grpid(igrp, ogrp, &ogid));
|
|
|
|
NC_CHECK(copy_dims(igrp, ogid));
|
|
NC_CHECK(copy_atts(igrp, NC_GLOBAL, ogid, NC_GLOBAL));
|
|
NC_CHECK(copy_vars(igrp, ogid));
|
|
#ifdef USE_NETCDF4
|
|
{
|
|
int numgrps;
|
|
int *grpids;
|
|
int i;
|
|
/* Copy schema from subgroups */
|
|
stat = nc_inq_grps(igrp, &numgrps, NULL);
|
|
grpids = (int *)emalloc((numgrps + 1) * sizeof(int));
|
|
NC_CHECK(nc_inq_grps(igrp, &numgrps, grpids));
|
|
|
|
for(i = 0; i < numgrps; i++) {
|
|
if (option_grpstruct || group_wanted(grpids[i], option_nlgrps, option_grpids)) {
|
|
NC_CHECK(copy_schema(grpids[i], ogid));
|
|
}
|
|
}
|
|
free(grpids);
|
|
}
|
|
#endif /* USE_NETCDF4 */
|
|
return stat;
|
|
}
|
|
|
|
/* Return number of values for a variable varid in a group igrp */
|
|
static int
|
|
inq_nvals(int igrp, int varid, 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;
|
|
#ifdef USE_NETCDF4
|
|
int okind;
|
|
size_t chunksize;
|
|
#endif
|
|
|
|
NC_CHECK(inq_nvals(igrp, varid, &nvalues));
|
|
if(nvalues == 0)
|
|
return stat;
|
|
/* get corresponding output variable */
|
|
NC_CHECK(nc_inq_varname(igrp, varid, varname));
|
|
NC_CHECK(nc_inq_varid(ogrp, varname, &ovarid));
|
|
NC_CHECK(nc_inq_vartype(igrp, varid, &vartype));
|
|
value_size = val_size(igrp, varid);
|
|
if(value_size > option_copy_buffer_size) {
|
|
option_copy_buffer_size = value_size;
|
|
do_realloc = 1;
|
|
}
|
|
#ifdef USE_NETCDF4
|
|
NC_CHECK(nc_inq_format(ogrp, &okind));
|
|
if(okind == NC_FORMAT_NETCDF4 || okind == NC_FORMAT_NETCDF4_CLASSIC) {
|
|
/* if this variable chunked, set variable chunk cache size */
|
|
int contig = 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 nvars;
|
|
int varid;
|
|
#ifdef USE_NETCDF4
|
|
int numgrps;
|
|
int *grpids;
|
|
int i;
|
|
#endif
|
|
|
|
int iv; /* variable number */
|
|
idnode_t* vlist = NULL; /* list for vars specified with -v option */
|
|
|
|
/*
|
|
* If any vars were specified with -v option, get list of
|
|
* associated variable ids relative to this group. Assume vars
|
|
* specified with syntax like "grp1/grp2/varname" or
|
|
* "/grp1/grp2/varname" if they are in groups.
|
|
*/
|
|
vlist = newidlist(); /* list for vars specified with -v option */
|
|
for (iv=0; iv < option_nlvars; iv++) {
|
|
if(nc_inq_gvarid(igrp, option_lvars[iv], &varid) == NC_NOERR)
|
|
idadd(vlist, varid);
|
|
}
|
|
|
|
/* get groupid in output corresponding to group igrp in input,
|
|
* given parent group (or root group) ogrp in output */
|
|
NC_CHECK(get_grpid(igrp, ogrp, &ogid));
|
|
|
|
/* Copy data from this group */
|
|
NC_CHECK(nc_inq_nvars(igrp, &nvars));
|
|
|
|
for (varid = 0; varid < nvars; varid++) {
|
|
if (option_nlvars > 0 && ! idmember(vlist, varid))
|
|
continue;
|
|
if (!group_wanted(igrp, option_nlgrps, option_grpids))
|
|
continue;
|
|
NC_CHECK(copy_var_data(igrp, varid, ogid));
|
|
}
|
|
#ifdef USE_NETCDF4
|
|
/* Copy data from subgroups */
|
|
stat = nc_inq_grps(igrp, &numgrps, NULL);
|
|
grpids = (int *)emalloc((numgrps + 1) * sizeof(int));
|
|
NC_CHECK(nc_inq_grps(igrp, &numgrps, grpids));
|
|
|
|
for(i = 0; i < numgrps; i++) {
|
|
if (!option_grpstruct && !group_wanted(grpids[i], option_nlgrps, option_grpids))
|
|
continue;
|
|
NC_CHECK(copy_data(grpids[i], ogid));
|
|
}
|
|
free(grpids);
|
|
#endif /* USE_NETCDF4 */
|
|
freeidlist(vlist);
|
|
return stat;
|
|
}
|
|
|
|
/* Count total number of dimensions in ncid and all its descendant subgroups */
|
|
int
|
|
count_dims(int ncid) {
|
|
int numgrps;
|
|
int ndims;
|
|
NC_CHECK(nc_inq_ndims(ncid, &ndims));
|
|
#ifdef USE_NETCDF4
|
|
NC_CHECK(nc_inq_grps(ncid, &numgrps, NULL));
|
|
if(numgrps > 0) {
|
|
int igrp;
|
|
int *grpids = emalloc(numgrps * sizeof(int));
|
|
NC_CHECK(nc_inq_grps(ncid, &numgrps, grpids));
|
|
for(igrp = 0; igrp < numgrps; igrp++) {
|
|
ndims += count_dims(grpids[igrp]);
|
|
}
|
|
free(grpids);
|
|
}
|
|
#endif /* USE_NETCDF4 */
|
|
return ndims;
|
|
}
|
|
|
|
/* Test if special case: netCDF-3 file with more than one record
|
|
* variable. Performance can be very slow for this case when the disk
|
|
* block size is large, there are many record variables, and a
|
|
* record's worth of data for some variables is smaller than the disk
|
|
* block size. In this case, copying the record variables a variable
|
|
* at a time causes much rereading of record data, so instead we want
|
|
* to copy data a record at a time. */
|
|
static int
|
|
nc3_special_case(int ncid, int kind) {
|
|
if (kind == NC_FORMAT_CLASSIC || kind == NC_FORMAT_64BIT_OFFSET
|
|
|| kind == NC_FORMAT_CDF5) {
|
|
int recdimid = 0;
|
|
NC_CHECK(nc_inq_unlimdim(ncid, &recdimid));
|
|
if (recdimid != -1) { /* we have a record dimension */
|
|
int nvars;
|
|
int varid;
|
|
NC_CHECK(nc_inq_nvars(ncid, &nvars));
|
|
for (varid = 0; varid < nvars; varid++) {
|
|
int *dimids = 0;
|
|
int ndims;
|
|
NC_CHECK( nc_inq_varndims(ncid, varid, &ndims) );
|
|
if (ndims > 0) {
|
|
int dimids0;
|
|
dimids = (int *) emalloc((ndims + 1) * sizeof(int));
|
|
NC_CHECK( nc_inq_vardimid(ncid, varid, dimids) );
|
|
dimids0 = dimids[0];
|
|
free(dimids);
|
|
if(dimids0 == recdimid) {
|
|
return 1; /* found a record variable */
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
return 0;
|
|
}
|
|
|
|
/* Classify variables in ncid as either fixed-size variables (with no
|
|
* unlimited dimension) or as record variables (with an unlimited
|
|
* dimension) */
|
|
static int
|
|
classify_vars(
|
|
int ncid, /* netCDF ID */
|
|
size_t *nf, /* for returning number of fixed-size variables */
|
|
int **fvars, /* the array of fixed_size variable IDS, caller should free */
|
|
size_t *nr, /* for returning number of record variables */
|
|
int **rvars) /* the array of record variable IDs, caller should free */
|
|
{
|
|
int varid;
|
|
int varindex = 0;
|
|
int nvars;
|
|
NC_CHECK(nc_inq_nvars(ncid, &nvars));
|
|
*nf = 0;
|
|
*fvars = (int *) emalloc(nvars * sizeof(int));
|
|
*nr = 0;
|
|
*rvars = (int *) emalloc(nvars * sizeof(int));
|
|
|
|
if(option_nlvars > 0) {
|
|
for (varindex = 0; varindex < option_nlvars; varindex++) {
|
|
nc_inq_varid(ncid,option_lvars[varindex],&varid);
|
|
|
|
if (isrecvar(ncid, varid)) {
|
|
(*rvars)[*nr] = varid;
|
|
(*nr)++;
|
|
} else {
|
|
(*fvars)[*nf] = varid;
|
|
(*nf)++;
|
|
}
|
|
}
|
|
} else {
|
|
for (varid = 0; varid < nvars; varid++) {
|
|
if (isrecvar(ncid, varid)) {
|
|
(*rvars)[*nr] = varid;
|
|
(*nr)++;
|
|
} else {
|
|
(*fvars)[*nf] = varid;
|
|
(*nf)++;
|
|
}
|
|
}
|
|
}
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/* Only called for classic format or 64-bit offset format files, to speed up special case */
|
|
static int
|
|
copy_fixed_size_data(int igrp, int ogrp, size_t nfixed_vars, int *fixed_varids) {
|
|
size_t ivar;
|
|
/* for each fixed-size variable, copy data */
|
|
for (ivar = 0; ivar < nfixed_vars; ivar++) {
|
|
int varid = fixed_varids[ivar];
|
|
NC_CHECK(copy_var_data(igrp, varid, ogrp));
|
|
}
|
|
if (fixed_varids)
|
|
free(fixed_varids);
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/* copy a record's worth of data for a variable from input to output */
|
|
static int
|
|
copy_rec_var_data(int ncid, /* input */
|
|
int ogrp, /* output */
|
|
int irec, /* record number */
|
|
int varid, /* input variable id */
|
|
int ovarid, /* output variable id */
|
|
size_t *start, /* start indices for record data */
|
|
size_t *count, /* edge lengths for record data */
|
|
void *buf /* buffer large enough to hold data */
|
|
)
|
|
{
|
|
NC_CHECK(nc_get_vara(ncid, varid, start, count, buf));
|
|
NC_CHECK(nc_put_vara(ogrp, ovarid, start, count, buf));
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/* Only called for classic format or 64-bit offset format files, to speed up special case */
|
|
static int
|
|
copy_record_data(int ncid, int ogrp, size_t nrec_vars, int *rec_varids) {
|
|
int unlimid;
|
|
size_t nrecs = 0; /* how many records? */
|
|
size_t irec;
|
|
size_t ivar;
|
|
void **buf; /* space for reading in data for each variable */
|
|
int *rec_ovarids; /* corresponding varids in output */
|
|
size_t **start;
|
|
size_t **count;
|
|
NC_CHECK(nc_inq_unlimdim(ncid, &unlimid));
|
|
NC_CHECK(nc_inq_dimlen(ncid, unlimid, &nrecs));
|
|
buf = (void **) emalloc(nrec_vars * sizeof(void *));
|
|
rec_ovarids = (int *) emalloc(nrec_vars * sizeof(int));
|
|
start = (size_t **) emalloc(nrec_vars * sizeof(size_t*));
|
|
count = (size_t **) emalloc(nrec_vars * sizeof(size_t*));
|
|
/* get space to hold one record's worth of data for each record variable */
|
|
for (ivar = 0; ivar < nrec_vars; ivar++) {
|
|
int varid;
|
|
int ndims;
|
|
int *dimids;
|
|
size_t value_size;
|
|
int dimid;
|
|
int ii;
|
|
size_t nvals;
|
|
char varname[NC_MAX_NAME];
|
|
varid = rec_varids[ivar];
|
|
NC_CHECK(nc_inq_varndims(ncid, varid, &ndims));
|
|
dimids = (int *) emalloc((1 + ndims) * sizeof(int));
|
|
start[ivar] = (size_t *) emalloc(ndims * sizeof(size_t));
|
|
count[ivar] = (size_t *) emalloc(ndims * sizeof(size_t));
|
|
NC_CHECK(nc_inq_vardimid (ncid, varid, dimids));
|
|
value_size = val_size(ncid, varid);
|
|
nvals = 1;
|
|
for(ii = 1; ii < ndims; ii++) { /* for rec size, don't include first record dimension */
|
|
size_t dimlen;
|
|
dimid = dimids[ii];
|
|
NC_CHECK(nc_inq_dimlen(ncid, dimid, &dimlen));
|
|
nvals *= dimlen;
|
|
start[ivar][ii] = 0;
|
|
count[ivar][ii] = dimlen;
|
|
}
|
|
start[ivar][0] = 0;
|
|
count[ivar][0] = 1; /* 1 record */
|
|
buf[ivar] = (void *) emalloc(nvals * value_size);
|
|
NC_CHECK(nc_inq_varname(ncid, varid, varname));
|
|
NC_CHECK(nc_inq_varid(ogrp, varname, &rec_ovarids[ivar]));
|
|
if(dimids)
|
|
free(dimids);
|
|
}
|
|
|
|
/* for each record, copy all variable data */
|
|
for(irec = 0; irec < nrecs; irec++) {
|
|
for (ivar = 0; ivar < nrec_vars; ivar++) {
|
|
int varid, ovarid;
|
|
varid = rec_varids[ivar];
|
|
ovarid = rec_ovarids[ivar];
|
|
start[ivar][0] = irec;
|
|
NC_CHECK(copy_rec_var_data(ncid, ogrp, irec, varid, ovarid,
|
|
start[ivar], count[ivar], buf[ivar]));
|
|
}
|
|
}
|
|
for (ivar = 0; ivar < nrec_vars; ivar++) {
|
|
if(start[ivar])
|
|
free(start[ivar]);
|
|
if(count[ivar])
|
|
free(count[ivar]);
|
|
}
|
|
if(start)
|
|
free(start);
|
|
if(count)
|
|
free(count);
|
|
for (ivar = 0; ivar < nrec_vars; ivar++) {
|
|
if(buf[ivar]) {
|
|
free(buf[ivar]);
|
|
}
|
|
}
|
|
if (rec_varids)
|
|
free(rec_varids);
|
|
if(buf)
|
|
free(buf);
|
|
if(rec_ovarids)
|
|
free(rec_ovarids);
|
|
return NC_NOERR;
|
|
}
|
|
|
|
/* copy infile to outfile using netCDF API
|
|
*/
|
|
static int
|
|
copy(char* infile, char* outfile)
|
|
{
|
|
int stat = NC_NOERR;
|
|
int igrp, ogrp;
|
|
int inkind, outkind;
|
|
int open_mode = NC_NOWRITE;
|
|
int create_mode = NC_CLOBBER;
|
|
size_t ndims;
|
|
|
|
if(option_read_diskless) {
|
|
open_mode |= NC_DISKLESS;
|
|
}
|
|
|
|
NC_CHECK(nc_open(infile, open_mode, &igrp));
|
|
|
|
NC_CHECK(nc_inq_format(igrp, &inkind));
|
|
|
|
/* option_kind specifies which netCDF format for output, one of
|
|
*
|
|
* SAME_AS_INPUT, NC_FORMAT_CLASSIC, NC_FORMAT_64BIT,
|
|
* NC_FORMAT_NETCDF4, NC_FORMAT_NETCDF4_CLASSIC
|
|
*
|
|
* However, if compression or shuffling was specified and kind was SAME_AS_INPUT,
|
|
* option_kind is changed to NC_FORMAT_NETCDF4_CLASSIC, if input format is
|
|
* NC_FORMAT_CLASSIC or NC_FORMAT_64BIT .
|
|
*/
|
|
outkind = option_kind;
|
|
if (option_kind == SAME_AS_INPUT) { /* default, kind not specified */
|
|
outkind = inkind;
|
|
/* Deduce output kind if netCDF-4 features requested */
|
|
if (inkind == NC_FORMAT_CLASSIC || inkind == NC_FORMAT_64BIT_OFFSET
|
|
|| inkind == NC_FORMAT_CDF5) {
|
|
if (option_deflate_level > 0 ||
|
|
option_shuffle_vars == NC_SHUFFLE ||
|
|
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 */
|
|
|
|
/* Check if any vars in -v don't exist */
|
|
if(missing_vars(igrp, option_nlvars, option_lvars))
|
|
exit(EXIT_FAILURE);
|
|
|
|
if(option_nlgrps > 0) {
|
|
if(inkind != NC_FORMAT_NETCDF4) {
|
|
error("Group list (-g ...) only permitted for netCDF-4 file");
|
|
exit(EXIT_FAILURE);
|
|
}
|
|
/* Check if any grps in -g don't exist */
|
|
if(grp_matches(igrp, option_nlgrps, option_lgrps, option_grpids) == 0)
|
|
exit(EXIT_FAILURE);
|
|
}
|
|
|
|
if(option_write_diskless)
|
|
create_mode |= NC_WRITE | NC_DISKLESS; /* NC_WRITE persists diskless file on close */
|
|
switch(outkind) {
|
|
case NC_FORMAT_CLASSIC:
|
|
/* nothing to do */
|
|
break;
|
|
case NC_FORMAT_64BIT_OFFSET:
|
|
create_mode |= NC_64BIT_OFFSET;
|
|
break;
|
|
case NC_FORMAT_CDF5:
|
|
#ifdef USE_CDF5
|
|
create_mode |= NC_64BIT_DATA;
|
|
break;
|
|
#else
|
|
error("netCDF library built without CDF5 support, can't create CDF5 files");
|
|
break;
|
|
#endif
|
|
#ifdef USE_NETCDF4
|
|
case NC_FORMAT_NETCDF4:
|
|
create_mode |= NC_NETCDF4;
|
|
break;
|
|
case NC_FORMAT_NETCDF4_CLASSIC:
|
|
create_mode |= NC_NETCDF4 | NC_CLASSIC_MODEL;
|
|
break;
|
|
#else
|
|
case NC_FORMAT_NETCDF4:
|
|
case NC_FORMAT_NETCDF4_CLASSIC:
|
|
error("netCDF library built with --disable-netcdf4, can't create netCDF-4 files");
|
|
break;
|
|
#endif /* USE_NETCDF4 */
|
|
default:
|
|
error("bad value for option specifying desired output format, see usage\n");
|
|
break;
|
|
}
|
|
NC_CHECK(nc_create(outfile, create_mode, &ogrp));
|
|
NC_CHECK(nc_set_fill(ogrp, NC_NOFILL, NULL));
|
|
|
|
#ifdef USE_NETCDF4
|
|
/* Because types in one group may depend on types in a different
|
|
* group, need to create all groups before defining types */
|
|
if(inkind == NC_FORMAT_NETCDF4) {
|
|
NC_CHECK(copy_groups(igrp, ogrp));
|
|
NC_CHECK(copy_types(igrp, ogrp));
|
|
}
|
|
#endif /* USE_NETCDF4 */
|
|
|
|
ndims = count_dims(igrp);
|
|
NC_CHECK(dimmap_init(ndims));
|
|
NC_CHECK(copy_schema(igrp, ogrp));
|
|
NC_CHECK(nc_enddef(ogrp));
|
|
|
|
/* For performance, special case netCDF-3 input or output file with record
|
|
* variables, to copy a record-at-a-time instead of a
|
|
* variable-at-a-time. */
|
|
/* TODO: check that these special cases work with -v option */
|
|
if(nc3_special_case(igrp, inkind)) {
|
|
size_t nfixed_vars, nrec_vars;
|
|
int *fixed_varids;
|
|
int *rec_varids;
|
|
NC_CHECK(classify_vars(igrp, &nfixed_vars, &fixed_varids, &nrec_vars, &rec_varids));
|
|
NC_CHECK(copy_fixed_size_data(igrp, ogrp, nfixed_vars, fixed_varids));
|
|
NC_CHECK(copy_record_data(igrp, ogrp, nrec_vars, rec_varids));
|
|
} else if (nc3_special_case(ogrp, outkind)) {
|
|
size_t nfixed_vars, nrec_vars;
|
|
int *fixed_varids;
|
|
int *rec_varids;
|
|
/* classifies output vars, but returns input varids */
|
|
NC_CHECK(classify_vars(ogrp, &nfixed_vars, &fixed_varids, &nrec_vars, &rec_varids));
|
|
NC_CHECK(copy_fixed_size_data(igrp, ogrp, nfixed_vars, fixed_varids));
|
|
NC_CHECK(copy_record_data(igrp, ogrp, nrec_vars, rec_varids));
|
|
} else {
|
|
NC_CHECK(copy_data(igrp, ogrp)); /* recursive, to handle nested groups */
|
|
}
|
|
|
|
NC_CHECK(nc_close(igrp));
|
|
NC_CHECK(nc_close(ogrp));
|
|
return stat;
|
|
}
|
|
|
|
/*
|
|
* For non-negative numeric string with multiplier suffix K, M, G, T,
|
|
* or P (or lower-case equivalent), return corresponding value
|
|
* incorporating multiplier 1000, 1000000, 1.0d9, ... 1.0d15, or -1.0
|
|
* for error.
|
|
*/
|
|
static double
|
|
double_with_suffix(char *str) {
|
|
double dval;
|
|
char *suffix = 0;
|
|
errno = 0;
|
|
dval = strtod(str, &suffix);
|
|
if(dval < 0 || errno != 0)
|
|
return -1.0;
|
|
if(*suffix) {
|
|
switch (*suffix) {
|
|
case 'k': case 'K':
|
|
dval *= 1000;
|
|
break;
|
|
case 'm': case 'M':
|
|
dval *= 1000000;
|
|
break;
|
|
case 'g': case 'G':
|
|
dval *= 1000000000;
|
|
break;
|
|
case 't': case 'T':
|
|
dval *= 1.0e12;
|
|
break;
|
|
case 'p': case 'P':
|
|
dval *= 1.0e15;
|
|
break;
|
|
default:
|
|
dval = -1.0; /* error, suffix multiplier must be K, M, G, or T */
|
|
}
|
|
}
|
|
return dval;
|
|
}
|
|
|
|
static void
|
|
usage(void)
|
|
{
|
|
#define USAGE "\
|
|
[-k kind] specify kind of netCDF format for output file, default same as input\n\
|
|
kind strings: 'classic', '64-bit offset', 'cdf5',\n\
|
|
'netCDF-4', 'netCDF-4 classic model'\n\
|
|
[-3] netCDF classic output (same as -k 'classic')\n\
|
|
[-6] 64-bit-offset output (same as -k '64-bit offset')\n\
|
|
[-4] netCDF-4 output (same as -k 'netCDF-4')\n\
|
|
[-7] netCDF-4-classic output (same as -k 'netCDF-4 classic model')\n\
|
|
[-5] CDF5 output (same as -k 'cdf5)\n\
|
|
[-d n] set output deflation compression level, default same as input (0=none 9=max)\n\
|
|
[-s] add shuffle option to deflation compression\n\
|
|
[-c chunkspec] specify chunking for dimensions, e.g. \"dim1/N1,dim2/N2,...\"\n\
|
|
[-u] convert unlimited dimensions to fixed-size dimensions in output copy\n\
|
|
[-w] write whole output file from diskless netCDF on close\n\
|
|
[-v var1,...] include data for only listed variables, but definitions for all variables\n\
|
|
[-V var1,...] include definitions and data for only listed variables\n\
|
|
[-g grp1,...] include data for only variables in listed groups, but all definitions\n\
|
|
[-G grp1,...] include definitions and data only for variables in listed groups\n\
|
|
[-m n] set size in bytes of copy buffer, default is 5000000 bytes\n\
|
|
[-h n] set size in bytes of chunk_cache for chunked variables\n\
|
|
[-e n] set number of elements that chunk_cache can hold\n\
|
|
[-r] read whole input file into diskless file on open (classic or 64-bit offset or cdf5 formats only)\n\
|
|
infile name of netCDF input file\n\
|
|
outfile name for netCDF output file\n"
|
|
|
|
/* Don't document this flaky option until it works better */
|
|
/* [-x] use experimental computed estimates for variable-specific chunk caches\n\ */
|
|
|
|
error("%s [-k kind] [-[3|4|6|7]] [-d n] [-s] [-c chunkspec] [-u] [-w] [-[v|V] varlist] [-[g|G] grplist] [-m n] [-h n] [-e n] [-r] infile outfile\n%s\nnetCDF library version %s",
|
|
progname, USAGE, nc_inq_libvers());
|
|
}
|
|
|
|
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[] = {
|
|
/* NetCDF-3 classic format (32-bit offsets) */
|
|
{"classic", NC_FORMAT_CLASSIC}, /* canonical format name */
|
|
{"nc3", NC_FORMAT_CLASSIC}, /* short format name */
|
|
{"1", NC_FORMAT_CLASSIC}, /* deprecated, use "-3" or "-k nc3" instead */
|
|
|
|
/* NetCDF-3 64-bit offset format */
|
|
{"64-bit offset", NC_FORMAT_64BIT_OFFSET}, /* canonical format name */
|
|
{"nc6", NC_FORMAT_64BIT_OFFSET}, /* short format name */
|
|
{"2", NC_FORMAT_64BIT_OFFSET}, /* deprecated, use "-6" or "-k nc6" instead */
|
|
{"64-bit-offset", NC_FORMAT_64BIT_OFFSET}, /* deprecated alias */
|
|
|
|
/* NetCDF-4 HDF5-based format */
|
|
{"netCDF-4", NC_FORMAT_NETCDF4}, /* canonical format name */
|
|
{"nc4", NC_FORMAT_NETCDF4}, /* short format name */
|
|
{"3", NC_FORMAT_NETCDF4}, /* deprecated, use "-4" or "-k nc4" instead */
|
|
{"netCDF4", NC_FORMAT_NETCDF4}, /* deprecated aliases */
|
|
{"hdf5", NC_FORMAT_NETCDF4},
|
|
{"enhanced", NC_FORMAT_NETCDF4},
|
|
|
|
/* NetCDF-4 HDF5-based format, restricted to classic data model */
|
|
{"netCDF-4 classic model", NC_FORMAT_NETCDF4_CLASSIC}, /* canonical format name */
|
|
{"nc7", NC_FORMAT_NETCDF4_CLASSIC}, /* short format name */
|
|
{"4", NC_FORMAT_NETCDF4_CLASSIC}, /* deprecated, use "-7" or -k nc7" */
|
|
{"netCDF-4-classic", NC_FORMAT_NETCDF4_CLASSIC}, /* deprecated aliases */
|
|
{"netCDF-4_classic", NC_FORMAT_NETCDF4_CLASSIC},
|
|
{"netCDF4_classic", NC_FORMAT_NETCDF4_CLASSIC},
|
|
{"hdf5-nc3", NC_FORMAT_NETCDF4_CLASSIC},
|
|
{"enhanced-nc3", NC_FORMAT_NETCDF4_CLASSIC},
|
|
|
|
/* The 64-bit data (CDF5) kind (5) */
|
|
{"5", NC_FORMAT_CDF5},
|
|
{"64-bit-data", NC_FORMAT_CDF5},
|
|
{"64-bit data", NC_FORMAT_CDF5},
|
|
{"nc5", NC_FORMAT_CDF5},
|
|
{"cdf5", NC_FORMAT_CDF5},
|
|
|
|
/* null terminate*/
|
|
{NULL,0}
|
|
};
|
|
|
|
opterr = 1;
|
|
progname = argv[0];
|
|
|
|
if (argc <= 1)
|
|
{
|
|
usage();
|
|
}
|
|
|
|
while ((c = getopt(argc, argv, "k:3467d:sum:c:h:e:rwxg:G:v:V:")) != -1) {
|
|
switch(c) {
|
|
case 'k': /* for specifying variant of netCDF format to be generated
|
|
Format names:
|
|
"classic" or "nc3"
|
|
"64-bit offset" or "nc6"
|
|
"netCDF-4" or "nc4"
|
|
"netCDF-4 classic model" or "nc7"
|
|
"64-bit-data" | "64-bit data" | "cdf5" | "nc5"
|
|
Format version numbers (deprecated):
|
|
1 (=> classic)
|
|
2 (=> 64-bit offset)
|
|
3 (=> netCDF-4)
|
|
4 (=> netCDF-4 classic model)
|
|
5 (=> classic 64 bit data, CDF-5)
|
|
*/
|
|
{
|
|
struct Kvalues* kvalue;
|
|
char *kind_name = (char *) emalloc(strlen(optarg)+1);
|
|
(void)strcpy(kind_name, optarg);
|
|
for(kvalue=legalkinds;kvalue->name;kvalue++) {
|
|
if(strcmp(kind_name,kvalue->name) == 0) {
|
|
option_kind = kvalue->kind;
|
|
break;
|
|
}
|
|
}
|
|
if(kvalue->name == NULL) {
|
|
error("invalid output format: %s", kind_name);
|
|
}
|
|
}
|
|
break;
|
|
case '3': /* output format is classic (netCDF-3) */
|
|
option_kind = NC_FORMAT_CLASSIC;
|
|
break;
|
|
case '5': /* output format is cdf5 */
|
|
option_kind = NC_FORMAT_CDF5;
|
|
break;
|
|
case '6': /* output format is 64-bit-offset (netCDF-3 version 2) */
|
|
option_kind = NC_FORMAT_64BIT_OFFSET;
|
|
break;
|
|
case '4': /* output format is netCDF-4 (variant of HDF5) */
|
|
option_kind = NC_FORMAT_NETCDF4;
|
|
break;
|
|
case '7': /* output format is netCDF-4 (restricted to classic model)*/
|
|
option_kind = NC_FORMAT_NETCDF4_CLASSIC;
|
|
break;
|
|
case 'd': /* non-default compression level specified */
|
|
option_deflate_level = strtol(optarg, NULL, 10);
|
|
if(option_deflate_level < 0 || option_deflate_level > 9) {
|
|
error("invalid deflation level: %d", option_deflate_level);
|
|
}
|
|
break;
|
|
case 's': /* shuffling, may improve compression */
|
|
option_shuffle_vars = NC_SHUFFLE;
|
|
break;
|
|
case 'u': /* convert unlimited dimensions to fixed size */
|
|
option_fix_unlimdims = 1;
|
|
break;
|
|
case 'm': /* non-default size of data copy buffer */
|
|
{
|
|
double dval = double_with_suffix(optarg); /* "K" for kilobytes. "M" for megabytes, ... */
|
|
if(dval < 0)
|
|
error("Suffix used for '-m' option value must be K, M, G, T, or P");
|
|
option_copy_buffer_size = dval;
|
|
break;
|
|
}
|
|
case 'h': /* non-default size of chunk cache */
|
|
{
|
|
double dval = double_with_suffix(optarg); /* "K" for kilobytes. "M" for megabytes, ... */
|
|
if(dval < 0)
|
|
error("Suffix used for '-h' option value must be K, M, G, T, or P");
|
|
option_chunk_cache_size = dval;
|
|
break;
|
|
}
|
|
case 'e': /* number of elements chunk cache can hold */
|
|
{
|
|
double dval = double_with_suffix(optarg); /* "K" for kilobytes. "M" for megabytes, ... */
|
|
if(dval < 0 )
|
|
error("Suffix used for '-e' option value must be K, M, G, T, or P");
|
|
option_chunk_cache_nelems = (long)dval;
|
|
break;
|
|
}
|
|
case 'r':
|
|
option_read_diskless = 1; /* read into memory on open */
|
|
break;
|
|
case 'w':
|
|
option_write_diskless = 1; /* write to memory, persist on close */
|
|
break;
|
|
case 'x': /* use experimental variable-specific chunk caches */
|
|
option_compute_chunkcaches = 1;
|
|
break;
|
|
case 'c': /* optional chunking spec for each dimension in list */
|
|
/* save chunkspec string for parsing later, once we know input ncid */
|
|
option_chunkspec = strdup(optarg);
|
|
break;
|
|
case 'g': /* group names */
|
|
/* make list of names of groups specified */
|
|
make_lgrps (optarg, &option_nlgrps, &option_lgrps, &option_grpids);
|
|
option_grpstruct = true;
|
|
break;
|
|
case 'G': /* group names */
|
|
/* make list of names of groups specified */
|
|
make_lgrps (optarg, &option_nlgrps, &option_lgrps, &option_grpids);
|
|
option_grpstruct = false;
|
|
break;
|
|
case 'v': /* variable names */
|
|
/* make list of names of variables specified */
|
|
make_lvars (optarg, &option_nlvars, &option_lvars);
|
|
option_varstruct = true;
|
|
break;
|
|
case 'V': /* variable names */
|
|
/* make list of names of variables specified */
|
|
make_lvars (optarg, &option_nlvars, &option_lvars);
|
|
option_varstruct = false;
|
|
break;
|
|
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(EXIT_FAILURE);
|
|
exit(EXIT_SUCCESS);
|
|
}
|
|
END_OF_MAIN()
|