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540 lines
15 KiB
C
540 lines
15 KiB
C
/* Copyright 2003-2006, University Corporation for Atmospheric
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* Research. See COPYRIGHT file for copying and redistribution
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* conditions.*/
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/**
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* @file
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* @internal This file is part of netcdf-4, a netCDF-like interface
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* for HDF5, or a HDF5 backend for netCDF, depending on your point of
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* view. This file handles the NetCDF-4 variable functions.
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*
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* @author Ed Hartnett, Dennis Heimbigner, Ward Fisher
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*/
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#include "config.h"
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#include <nc4internal.h>
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#include "nc4dispatch.h"
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#include "hdf5internal.h"
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#include <math.h>
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/**
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* @internal Set chunk cache size for a variable. This is the internal
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* function called by nc_set_var_chunk_cache().
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*
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* @param ncid File ID.
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* @param varid Variable ID.
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* @param size Size in bytes to set cache.
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* @param nelems Number of elements in cache.
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* @param preemption Controls cache swapping.
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*
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* @returns ::NC_NOERR No error.
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* @returns ::NC_EBADID Bad ncid.
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* @returns ::NC_ENOTVAR Invalid variable ID.
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* @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3 netcdf-4 file.
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* @returns ::NC_EINVAL Invalid input.
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* @returns ::NC_EHDFERR HDF5 error.
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* @author Ed Hartnett
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*/
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int
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NC4_set_var_chunk_cache(int ncid, int varid, size_t size, size_t nelems,
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float preemption)
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{
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NC *nc;
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NC_GRP_INFO_T *grp;
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NC_FILE_INFO_T *h5;
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NC_VAR_INFO_T *var;
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int retval;
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/* Check input for validity. */
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if (preemption < 0 || preemption > 1)
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return NC_EINVAL;
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/* Find info for this file and group, and set pointer to each. */
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if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
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return retval;
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assert(nc && grp && h5);
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/* Find the var. */
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var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
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if(!var)
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return NC_ENOTVAR;
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assert(var && var->hdr.id == varid);
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/* Set the values. */
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var->chunk_cache_size = size;
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var->chunk_cache_nelems = nelems;
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var->chunk_cache_preemption = preemption;
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if ((retval = nc4_reopen_dataset(grp, var)))
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return retval;
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return NC_NOERR;
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}
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/**
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* @internal A wrapper for NC4_set_var_chunk_cache(), we need this
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* version for fortran. Negative values leave settings as they are.
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*
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* @param ncid File ID.
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* @param varid Variable ID.
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* @param size Size in bytes to set cache.
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* @param nelems Number of elements in cache.
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* @param preemption Controls cache swapping.
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*
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* @returns ::NC_NOERR for success
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* @author Ed Hartnett
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*/
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int
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nc_set_var_chunk_cache_ints(int ncid, int varid, int size, int nelems,
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int preemption)
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{
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size_t real_size = H5D_CHUNK_CACHE_NBYTES_DEFAULT;
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size_t real_nelems = H5D_CHUNK_CACHE_NSLOTS_DEFAULT;
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float real_preemption = CHUNK_CACHE_PREEMPTION;
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if (size >= 0)
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real_size = ((size_t) size) * MEGABYTE;
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if (nelems >= 0)
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real_nelems = nelems;
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if (preemption >= 0)
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real_preemption = preemption / 100.;
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return NC4_set_var_chunk_cache(ncid, varid, real_size, real_nelems,
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real_preemption);
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}
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/**
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* @internal This is called by nc_get_var_chunk_cache(). Get chunk
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* cache size for a variable.
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*
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* @param ncid File ID.
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* @param varid Variable ID.
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* @param sizep Gets size in bytes of cache.
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* @param nelemsp Gets number of element slots in cache.
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* @param preemptionp Gets cache swapping setting.
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*
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* @returns ::NC_NOERR No error.
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* @returns ::NC_EBADID Bad ncid.
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* @returns ::NC_ENOTVAR Invalid variable ID.
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* @returns ::NC_ENOTNC4 Not a netCDF-4 file.
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* @author Ed Hartnett
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*/
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int
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NC4_get_var_chunk_cache(int ncid, int varid, size_t *sizep,
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size_t *nelemsp, float *preemptionp)
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{
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NC *nc;
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NC_GRP_INFO_T *grp;
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NC_FILE_INFO_T *h5;
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NC_VAR_INFO_T *var;
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int retval;
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/* Find info for this file and group, and set pointer to each. */
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if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
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return retval;
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assert(nc && grp && h5);
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/* Find the var. */
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var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
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if(!var)
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return NC_ENOTVAR;
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assert(var && var->hdr.id == varid);
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/* Give the user what they want. */
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if (sizep)
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*sizep = var->chunk_cache_size;
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if (nelemsp)
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*nelemsp = var->chunk_cache_nelems;
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if (preemptionp)
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*preemptionp = var->chunk_cache_preemption;
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return NC_NOERR;
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}
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/**
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* @internal A wrapper for NC4_get_var_chunk_cache(), we need this
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* version for fortran.
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*
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* @param ncid File ID.
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* @param varid Variable ID.
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* @param sizep Gets size in bytes of cache.
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* @param nelemsp Gets number of element slots in cache.
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* @param preemptionp Gets cache swapping setting.
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*
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* @returns ::NC_NOERR No error.
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* @returns ::NC_EBADID Bad ncid.
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* @returns ::NC_ENOTVAR Invalid variable ID.
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* @returns ::NC_ENOTNC4 Not a netCDF-4 file.
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* @author Ed Hartnett
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*/
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int
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nc_get_var_chunk_cache_ints(int ncid, int varid, int *sizep,
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int *nelemsp, int *preemptionp)
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{
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size_t real_size, real_nelems;
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float real_preemption;
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int ret;
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if ((ret = NC4_get_var_chunk_cache(ncid, varid, &real_size,
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&real_nelems, &real_preemption)))
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return ret;
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if (sizep)
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*sizep = real_size / MEGABYTE;
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if (nelemsp)
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*nelemsp = (int)real_nelems;
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if(preemptionp)
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*preemptionp = (int)(real_preemption * 100);
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return NC_NOERR;
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}
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/**
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* @internal Get all the information about a variable. Pass NULL for
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* whatever you don't care about. This is the internal function called
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* by nc_inq_var(), nc_inq_var_deflate(), nc_inq_var_fletcher32(),
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* nc_inq_var_chunking(), nc_inq_var_chunking_ints(),
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* nc_inq_var_fill(), nc_inq_var_endian(), nc_inq_var_filter(), and
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* nc_inq_var_szip().
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*
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* @param ncid File ID.
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* @param varid Variable ID.
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* @param name Gets name.
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* @param xtypep Gets type.
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* @param ndimsp Gets number of dims.
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* @param dimidsp Gets array of dim IDs.
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* @param nattsp Gets number of attributes.
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* @param shufflep Gets shuffle setting.
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* @param deflatep Gets deflate setting.
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* @param deflate_levelp Gets deflate level.
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* @param fletcher32p Gets fletcher32 setting.
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* @param contiguousp Gets contiguous setting.
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* @param chunksizesp Gets chunksizes.
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* @param no_fill Gets fill mode.
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* @param fill_valuep Gets fill value.
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* @param endiannessp Gets one of ::NC_ENDIAN_BIG ::NC_ENDIAN_LITTLE
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* ::NC_ENDIAN_NATIVE
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* @param idp Pointer to memory to store filter id.
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* @param nparamsp Pointer to memory to store filter parameter count.
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* @param params Pointer to vector of unsigned integers into which
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* to store filter parameters.
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*
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* @returns ::NC_NOERR No error.
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* @returns ::NC_EBADID Bad ncid.
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* @returns ::NC_ENOTVAR Bad varid.
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* @returns ::NC_ENOMEM Out of memory.
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* @returns ::NC_EINVAL Invalid input.
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* @author Ed Hartnett, Dennis Heimbigner
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*/
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int
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NC4_inq_var_all(int ncid, int varid, char *name, nc_type *xtypep,
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int *ndimsp, int *dimidsp, int *nattsp,
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int *shufflep, int *deflatep, int *deflate_levelp,
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int *fletcher32p, int *contiguousp, size_t *chunksizesp,
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int *no_fill, void *fill_valuep, int *endiannessp,
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unsigned int* idp, size_t* nparamsp, unsigned int* params
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)
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{
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NC *nc;
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NC_GRP_INFO_T *grp;
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NC_FILE_INFO_T *h5;
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NC_VAR_INFO_T *var;
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int d;
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int retval;
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LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
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/* Find info for this file and group, and set pointer to each. */
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if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
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return retval;
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assert(nc);
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assert(grp && h5);
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/* Walk through the list of vars, and return the info about the one
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with a matching varid. If the varid is -1, find the global
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atts and call it a day. */
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if (varid == NC_GLOBAL)
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{
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if (nattsp)
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{
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/* Do we need to read the atts? */
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if (grp->atts_not_read)
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if ((retval = nc4_read_grp_atts2(grp)))
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return retval;
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*nattsp = ncindexcount(grp->att);
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}
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return NC_NOERR;
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}
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/* Find the var. */
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var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
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if(!var)
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return NC_ENOTVAR;
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assert(var && var->hdr.id == varid);
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/* Copy the data to the user's data buffers. */
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if (name)
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strcpy(name, var->hdr.name);
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if (xtypep)
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*xtypep = var->type_info->hdr.id;
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if (ndimsp)
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*ndimsp = var->ndims;
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if (dimidsp)
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for (d = 0; d < var->ndims; d++)
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dimidsp[d] = var->dimids[d];
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if (nattsp)
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{
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if (var->atts_not_read)
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if ((retval = nc4_read_var_atts(grp, var)))
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return retval;
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*nattsp = ncindexcount(var->att);
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}
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/* Chunking stuff. */
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if (!var->contiguous && chunksizesp)
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for (d = 0; d < var->ndims; d++)
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{
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chunksizesp[d] = var->chunksizes[d];
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LOG((4, "chunksizesp[%d]=%d", d, chunksizesp[d]));
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}
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if (contiguousp)
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*contiguousp = var->contiguous ? NC_CONTIGUOUS : NC_CHUNKED;
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/* Filter stuff. */
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if (deflatep)
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*deflatep = (int)var->deflate;
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if (deflate_levelp)
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*deflate_levelp = var->deflate_level;
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if (shufflep)
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*shufflep = (int)var->shuffle;
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if (fletcher32p)
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*fletcher32p = (int)var->fletcher32;
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if (idp)
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*idp = var->filterid;
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if (nparamsp)
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*nparamsp = (var->params == NULL ? 0 : var->nparams);
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if (params && var->params != NULL)
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memcpy(params,var->params,var->nparams*sizeof(unsigned int));
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/* Fill value stuff. */
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if (no_fill)
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*no_fill = (int)var->no_fill;
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/* Don't do a thing with fill_valuep if no_fill mode is set for
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* this var, or if fill_valuep is NULL. */
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if (!var->no_fill && fill_valuep)
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{
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/* Do we have a fill value for this var? */
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if (var->fill_value)
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{
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if (var->type_info->nc_type_class == NC_STRING)
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{
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assert(*(char **)var->fill_value);
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/* This will allocate memeory and copy the string. */
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if (!(*(char **)fill_valuep = strdup(*(char **)var->fill_value)))
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{
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free(*(char **)fill_valuep);
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return NC_ENOMEM;
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}
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}
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else
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{
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assert(var->type_info->size);
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memcpy(fill_valuep, var->fill_value, var->type_info->size);
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}
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}
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else
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{
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if (var->type_info->nc_type_class == NC_STRING)
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{
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if (!(*(char **)fill_valuep = calloc(1, sizeof(char *))))
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return NC_ENOMEM;
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if ((retval = nc4_get_default_fill_value(var->type_info, (char **)fill_valuep)))
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{
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free(*(char **)fill_valuep);
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return retval;
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}
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}
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else
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{
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if ((retval = nc4_get_default_fill_value(var->type_info, fill_valuep)))
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return retval;
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}
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}
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}
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/* Does the user want the endianness of this variable? */
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if (endiannessp)
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*endiannessp = var->type_info->endianness;
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return NC_NOERR;
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}
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/**
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* @internal Inquire about chunking settings for a var. This is used
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* by the fortran API.
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*
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* @param ncid File ID.
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* @param varid Variable ID.
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* @param contiguousp Gets contiguous setting.
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* @param chunksizesp Gets chunksizes.
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*
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* @returns ::NC_NOERR No error.
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* @returns ::NC_EBADID Bad ncid.
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* @returns ::NC_ENOTVAR Invalid variable ID.
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* @returns ::NC_EINVAL Invalid input
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* @returns ::NC_ENOMEM Out of memory.
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* @author Ed Hartnett
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*/
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int
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nc_inq_var_chunking_ints(int ncid, int varid, int *contiguousp, int *chunksizesp)
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{
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NC *nc;
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NC_GRP_INFO_T *grp;
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NC_VAR_INFO_T *var;
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NC_FILE_INFO_T *h5;
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size_t *cs = NULL;
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int i, retval;
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/* Find this ncid's file info. */
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if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
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return retval;
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assert(nc);
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/* Find var cause I need the number of dims. */
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if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var)))
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return retval;
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/* Allocate space for the size_t copy of the chunksizes array. */
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if (var->ndims)
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if (!(cs = malloc(var->ndims * sizeof(size_t))))
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return NC_ENOMEM;
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retval = NC4_inq_var_all(ncid, varid, NULL, NULL, NULL, NULL, NULL,
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NULL, NULL, NULL, NULL, contiguousp, cs, NULL,
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NULL, NULL, NULL, NULL, NULL);
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/* Copy from size_t array. */
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if (chunksizesp && var->contiguous == NC_CHUNKED)
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for (i = 0; i < var->ndims; i++)
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{
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chunksizesp[i] = (int)cs[i];
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if (cs[i] > NC_MAX_INT)
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retval = NC_ERANGE;
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}
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if (var->ndims)
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free(cs);
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return retval;
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}
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/**
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* @internal Find the ID of a variable, from the name. This function
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* is called by nc_inq_varid().
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*
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* @param ncid File ID.
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* @param name Name of the variable.
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* @param varidp Gets variable ID.
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* @returns ::NC_NOERR No error.
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* @returns ::NC_EBADID Bad ncid.
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* @returns ::NC_ENOTVAR Bad variable ID.
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*/
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int
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NC4_inq_varid(int ncid, const char *name, int *varidp)
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{
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NC *nc;
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NC_GRP_INFO_T *grp;
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NC_VAR_INFO_T *var;
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char norm_name[NC_MAX_NAME + 1];
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int retval;
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if (!name)
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return NC_EINVAL;
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if (!varidp)
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return NC_NOERR;
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LOG((2, "%s: ncid 0x%x name %s", __func__, ncid, name));
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/* Find info for this file and group, and set pointer to each. */
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if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, NULL)))
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return retval;
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/* Normalize name. */
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if ((retval = nc4_normalize_name(name, norm_name)))
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return retval;
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/* Find var of this name. */
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var = (NC_VAR_INFO_T*)ncindexlookup(grp->vars,norm_name);
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if(var)
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{
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*varidp = var->hdr.id;
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return NC_NOERR;
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}
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return NC_ENOTVAR;
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}
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/**
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* @internal
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*
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* This function will change the parallel access of a variable from
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* independent to collective.
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*
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* @param ncid File ID.
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* @param varid Variable ID.
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* @param par_access NC_COLLECTIVE or NC_INDEPENDENT.
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*
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|
* @returns ::NC_NOERR No error.
|
|
* @returns ::NC_EBADID Invalid ncid passed.
|
|
* @returns ::NC_ENOTVAR Invalid varid passed.
|
|
* @returns ::NC_ENOPAR LFile was not opened with nc_open_par/nc_create_var.
|
|
* @returns ::NC_EINVAL Invalid par_access specified.
|
|
* @returns ::NC_NOERR for success
|
|
* @author Ed Hartnett, Dennis Heimbigner
|
|
*/
|
|
int
|
|
NC4_var_par_access(int ncid, int varid, int par_access)
|
|
{
|
|
#ifndef USE_PARALLEL4
|
|
return NC_ENOPAR;
|
|
#else
|
|
NC *nc;
|
|
NC_GRP_INFO_T *grp;
|
|
NC_FILE_INFO_T *h5;
|
|
NC_VAR_INFO_T *var;
|
|
int retval;
|
|
|
|
LOG((1, "%s: ncid 0x%x varid %d par_access %d", __func__, ncid,
|
|
varid, par_access));
|
|
|
|
if (par_access != NC_INDEPENDENT && par_access != NC_COLLECTIVE)
|
|
return NC_EINVAL;
|
|
|
|
/* Find info for this file and group, and set pointer to each. */
|
|
if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
|
|
return retval;
|
|
|
|
/* This function only for files opened with nc_open_par or nc_create_par. */
|
|
if (!h5->parallel)
|
|
return NC_ENOPAR;
|
|
|
|
/* Find the var, and set its preference. */
|
|
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
|
|
if (!var) return NC_ENOTVAR;
|
|
assert(var->hdr.id == varid);
|
|
|
|
if (par_access)
|
|
var->parallel_access = NC_COLLECTIVE;
|
|
else
|
|
var->parallel_access = NC_INDEPENDENT;
|
|
return NC_NOERR;
|
|
#endif /* USE_PARALLEL4 */
|
|
}
|