mirror/netcdf-c
2
0
Fork 0
mirror of https://github.com/Unidata/netcdf-c.git synced 2024-12-27 08:49:16 +08:00
Code Issues Packages Projects Releases Wiki Activity
06ecd2412d
netcdf-c/libhdf5/hdf5var.c
Ed Hartnett d1198a3667 whitespace cleanup
2018-07-19 07:33:48 -06:00

1251 lines
39 KiB
C
Raw Blame History

/* Copyright 2003-2006, University Corporation for Atmospheric
* Research. See COPYRIGHT file for copying and redistribution
* conditions.*/
/**
* @file
* @internal This file handles the HDF5 variable functions.
*
* @author Ed Hartnett
*/
#include "config.h"
#include <hdf5internal.h>
#include <math.h>
/** @internal Default size for unlimited dim chunksize */
#define DEFAULT_1D_UNLIM_SIZE (4096)
/**
* @internal If the HDF5 dataset for this variable is open, then close
* it and reopen it, with the perhaps new settings for chunk caching.
*
* @param grp Pointer to the group info.
* @param var Pointer to the var info.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett
*/
int
nc4_reopen_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
{
hid_t access_pid;
if (var->hdf_datasetid)
{
if ((access_pid = H5Pcreate(H5P_DATASET_ACCESS)) < 0)
return NC_EHDFERR;
if (H5Pset_chunk_cache(access_pid, var->chunk_cache_nelems,
var->chunk_cache_size,
var->chunk_cache_preemption) < 0)
return NC_EHDFERR;
if (H5Dclose(var->hdf_datasetid) < 0)
return NC_EHDFERR;
if ((var->hdf_datasetid = H5Dopen2(grp->hdf_grpid, var->hdr.name,
access_pid)) < 0)
return NC_EHDFERR;
if (H5Pclose(access_pid) < 0)
return NC_EHDFERR;
}
return NC_NOERR;
}
/**
* @internal Check a set of chunksizes to see if they specify a chunk
* that is too big.
*
* @param grp Pointer to the group info.
* @param var Pointer to the var info.
* @param chunksizes Array of chunksizes to check.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_EBADCHUNK Bad chunksize.
*/
static int
check_chunksizes(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, const size_t *chunksizes)
{
double dprod;
size_t type_len;
int d;
int retval;
if ((retval = nc4_get_typelen_mem(grp->nc4_info, var->type_info->hdr.id, &type_len)))
return retval;
if (var->type_info->nc_type_class == NC_VLEN)
dprod = (double)sizeof(hvl_t);
else
dprod = (double)type_len;
for (d = 0; d < var->ndims; d++)
dprod *= (double)chunksizes[d];
if (dprod > (double) NC_MAX_UINT)
return NC_EBADCHUNK;
return NC_NOERR;
}
/**
* @internal Determine some default chunksizes for a variable.
*
* @param grp Pointer to the group info.
* @param var Pointer to the var info.
*
* @returns ::NC_NOERR for success
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @author Ed Hartnett
*/
static int
nc4_find_default_chunksizes2(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
{
int d;
size_t type_size;
float num_values = 1, num_unlim = 0;
int retval;
size_t suggested_size;
#ifdef LOGGING
double total_chunk_size;
#endif
if (var->type_info->nc_type_class == NC_STRING)
type_size = sizeof(char *);
else
type_size = var->type_info->size;
#ifdef LOGGING
/* Later this will become the total number of bytes in the default
* chunk. */
total_chunk_size = (double) type_size;
#endif
/* How many values in the variable (or one record, if there are
* unlimited dimensions). */
for (d = 0; d < var->ndims; d++)
{
assert(var->dim[d]);
if (! var->dim[d]->unlimited)
num_values *= (float)var->dim[d]->len;
else {
num_unlim++;
var->chunksizes[d] = 1; /* overwritten below, if all dims are unlimited */
}
}
/* Special case to avoid 1D vars with unlim dim taking huge amount
of space (DEFAULT_CHUNK_SIZE bytes). Instead we limit to about
4KB */
if (var->ndims == 1 && num_unlim == 1) {
if (DEFAULT_CHUNK_SIZE / type_size <= 0)
suggested_size = 1;
else if (DEFAULT_CHUNK_SIZE / type_size > DEFAULT_1D_UNLIM_SIZE)
suggested_size = DEFAULT_1D_UNLIM_SIZE;
else
suggested_size = DEFAULT_CHUNK_SIZE / type_size;
var->chunksizes[0] = suggested_size / type_size;
LOG((4, "%s: name %s dim %d DEFAULT_CHUNK_SIZE %d num_values %f type_size %d "
"chunksize %ld", __func__, var->hdr.name, d, DEFAULT_CHUNK_SIZE, num_values, type_size, var->chunksizes[0]));
}
if (var->ndims > 1 && var->ndims == num_unlim) { /* all dims unlimited */
suggested_size = pow((double)DEFAULT_CHUNK_SIZE/type_size, 1.0/(double)(var->ndims));
for (d = 0; d < var->ndims; d++)
{
var->chunksizes[d] = suggested_size ? suggested_size : 1;
LOG((4, "%s: name %s dim %d DEFAULT_CHUNK_SIZE %d num_values %f type_size %d "
"chunksize %ld", __func__, var->hdr.name, d, DEFAULT_CHUNK_SIZE, num_values, type_size, var->chunksizes[d]));
}
}
/* Pick a chunk length for each dimension, if one has not already
* been picked above. */
for (d = 0; d < var->ndims; d++)
if (!var->chunksizes[d])
{
suggested_size = (pow((double)DEFAULT_CHUNK_SIZE/(num_values * type_size),
1.0/(double)(var->ndims - num_unlim)) * var->dim[d]->len - .5);
if (suggested_size > var->dim[d]->len)
suggested_size = var->dim[d]->len;
var->chunksizes[d] = suggested_size ? suggested_size : 1;
LOG((4, "%s: name %s dim %d DEFAULT_CHUNK_SIZE %d num_values %f type_size %d "
"chunksize %ld", __func__, var->hdr.name, d, DEFAULT_CHUNK_SIZE, num_values, type_size, var->chunksizes[d]));
}
#ifdef LOGGING
/* Find total chunk size. */
for (d = 0; d < var->ndims; d++)
total_chunk_size *= (double) var->chunksizes[d];
LOG((4, "total_chunk_size %f", total_chunk_size));
#endif
/* But did this result in a chunk that is too big? */
retval = check_chunksizes(grp, var, var->chunksizes);
if (retval)
{
/* Other error? */
if (retval != NC_EBADCHUNK)
return retval;
/* Chunk is too big! Reduce each dimension by half and try again. */
for ( ; retval == NC_EBADCHUNK; retval = check_chunksizes(grp, var, var->chunksizes))
for (d = 0; d < var->ndims; d++)
var->chunksizes[d] = var->chunksizes[d]/2 ? var->chunksizes[d]/2 : 1;
}
/* Do we have any big data overhangs? They can be dangerous to
* babies, the elderly, or confused campers who have had too much
* beer. */
for (d = 0; d < var->ndims; d++)
{
size_t num_chunks;
size_t overhang;
assert(var->chunksizes[d] > 0);
num_chunks = (var->dim[d]->len + var->chunksizes[d] - 1) / var->chunksizes[d];
if(num_chunks > 0) {
overhang = (num_chunks * var->chunksizes[d]) - var->dim[d]->len;
var->chunksizes[d] -= overhang / num_chunks;
}
}
return NC_NOERR;
}
/**
* @internal This is called when a new netCDF-4 variable is defined
* with nc_def_var().
*
* @param ncid File ID.
* @param name Name.
* @param xtype Type.
* @param ndims Number of dims.
* @param dimidsp Array of dim IDs.
* @param varidp Gets the var ID.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
* netcdf-4 file.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EPERM File is read only.
* @returns ::NC_EMAXDIMS Classic model file exceeds ::NC_MAX_VAR_DIMS.
* @returns ::NC_ESTRICTNC3 Attempting to create netCDF-4 type var in
* classic model file
* @returns ::NC_EBADNAME Bad name.
* @returns ::NC_EBADTYPE Bad type.
* @returns ::NC_ENOMEM Out of memory.
* @returns ::NC_EHDFERR Error returned by HDF5 layer.
* @returns ::NC_EINVAL Invalid input
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_def_var(int ncid, const char *name, nc_type xtype,
int ndims, const int *dimidsp, int *varidp)
{
NC_GRP_INFO_T *grp;
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim;
NC_FILE_INFO_T *h5;
NC_TYPE_INFO_T *type_info = NULL;
char norm_name[NC_MAX_NAME + 1];
int d;
int retval;
/* Find info for this file and group, and set pointer to each. */
if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
BAIL(retval);
assert(grp && h5);
/* If it's not in define mode, strict nc3 files error out,
* otherwise switch to define mode. This will also check that the
* file is writable. */
if (!(h5->flags & NC_INDEF))
{
if (h5->cmode & NC_CLASSIC_MODEL)
BAIL(NC_ENOTINDEFINE);
if ((retval = NC4_redef(ncid)))
BAIL(retval);
}
assert(!h5->no_write);
/* Check and normalize the name. */
if ((retval = nc4_check_name(name, norm_name)))
BAIL(retval);
/* Not a Type is, well, not a type.*/
if (xtype == NC_NAT)
BAIL(NC_EBADTYPE);
/* For classic files, only classic types are allowed. */
if (h5->cmode & NC_CLASSIC_MODEL && xtype > NC_DOUBLE)
BAIL(NC_ESTRICTNC3);
/* For classic files */
if (h5->cmode & NC_CLASSIC_MODEL && ndims > NC_MAX_VAR_DIMS)
BAIL(NC_EMAXDIMS);
/* cast needed for braindead systems with signed size_t */
if((unsigned long) ndims > X_INT_MAX) /* Backward compat */
BAIL(NC_EINVAL);
/* Check that this name is not in use as a var, grp, or type. */
if ((retval = nc4_check_dup_name(grp, norm_name)))
BAIL(retval);
/* For non-scalar vars, dim IDs must be provided. */
if (ndims && !dimidsp)
BAIL(NC_EINVAL);
/* Check all the dimids to make sure they exist. */
for (d = 0; d < ndims; d++)
if ((retval = nc4_find_dim(grp, dimidsp[d], &dim, NULL)))
BAIL(retval);
/* These degrubbing messages sure are handy! */
LOG((2, "%s: name %s type %d ndims %d", __func__, norm_name, xtype, ndims));
#ifdef LOGGING
{
int dd;
for (dd = 0; dd < ndims; dd++)
LOG((4, "dimid[%d] %d", dd, dimidsp[dd]));
}
#endif
/* If this is a user-defined type, there is a type_info struct with
* all the type information. For atomic types, fake up a type_info
* struct. */
if (xtype <= NC_STRING)
{
size_t len;
char name[NC_MAX_NAME+1];
char* atomname = nc4_atomic_name[xtype];
size_t namelen = strlen(atomname);
memcpy(name,atomname,namelen);
name[namelen] = '\0';
nc4_get_typelen_mem(h5,xtype,&len);
if((retval = nc4_type_new(grp,len,name,xtype,&type_info)))
BAIL(retval);
type_info->endianness = NC_ENDIAN_NATIVE;
if ((retval = nc4_get_hdf_typeid(h5, xtype, &type_info->hdf_typeid,
type_info->endianness)))
BAIL(retval);
if ((type_info->native_hdf_typeid = H5Tget_native_type(type_info->hdf_typeid,
H5T_DIR_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
if ((retval = nc4_get_typelen_mem(h5, type_info->hdr.id, &type_info->size)))
BAIL(retval);
/* Set the "class" of the type */
if (xtype == NC_CHAR)
type_info->nc_type_class = NC_CHAR;
else
{
H5T_class_t class;
if ((class = H5Tget_class(type_info->hdf_typeid)) < 0)
BAIL(NC_EHDFERR);
switch(class)
{
case H5T_STRING:
type_info->nc_type_class = NC_STRING;
break;
case H5T_INTEGER:
type_info->nc_type_class = NC_INT;
break;
case H5T_FLOAT:
type_info->nc_type_class = NC_FLOAT;
break;
default:
BAIL(NC_EBADTYPID);
}
}
}
/* If this is a user defined type, find it. */
else
{
if (nc4_find_type(grp->nc4_info, xtype, &type_info))
BAIL(NC_EBADTYPE);
}
/* Create a new var and fill in some HDF5 cache setting values. */
if ((retval = nc4_var_list_add(grp, norm_name, ndims, &var)))
BAIL(retval);
var->is_new_var = NC_TRUE;
/* Point to the type, and increment its ref. count */
var->type_info = type_info;
var->type_info->rc++;
type_info = NULL;
/* Set variables no_fill to match the database default
* unless the variable type is variable length (NC_STRING or NC_VLEN)
* or is user-defined type.
*/
if (var->type_info->nc_type_class < NC_STRING)
var->no_fill = h5->fill_mode;
/* Assign dimensions to the variable */
/* At the same time, check to see if this is a coordinate
* variable. If so, it will have the same name as one of its
* dimensions. If it is a coordinate var, is it a coordinate var in
* the same group as the dim? */
/* Also, check whether we should use contiguous or chunked storage */
var->contiguous = NC_TRUE;
for (d = 0; d < ndims; d++)
{
NC_GRP_INFO_T *dim_grp;
/* Look up each dimension */
if ((retval = nc4_find_dim(grp, dimidsp[d], &dim, &dim_grp)))
BAIL(retval);
/* Check for dim index 0 having the same name, in the same group */
if (d == 0 && dim_grp == grp && strcmp(dim->hdr.name, norm_name) == 0)
{
var->dimscale = NC_TRUE;
dim->coord_var = var;
/* Use variable's dataset ID for the dimscale ID. So delete
* the HDF5 DIM_WITHOUT_VARIABLE dataset that was created for
* this dim. */
if (dim->hdf_dimscaleid)
{
/* Detach dimscale from any variables using it */
if ((retval = rec_detach_scales(grp, dimidsp[d], dim->hdf_dimscaleid)) < 0)
BAIL(retval);
/* Close the HDF5 DIM_WITHOUT_VARIABLE dataset. */
if (H5Dclose(dim->hdf_dimscaleid) < 0)
BAIL(NC_EHDFERR);
dim->hdf_dimscaleid = 0;
/* Now delete the DIM_WITHOUT_VARIABLE dataset (it will be
* recreated later, if necessary). */
if (H5Gunlink(grp->hdf_grpid, dim->hdr.name) < 0)
BAIL(NC_EDIMMETA);
}
}
/* Check for unlimited dimension and turn off contiguous storage. */
if (dim->unlimited)
var->contiguous = NC_FALSE;
/* Track dimensions for variable */
var->dimids[d] = dimidsp[d];
var->dim[d] = dim;
}
/* Determine default chunksizes for this variable. (Even for
* variables which may be contiguous.) */
LOG((4, "allocating array of %d size_t to hold chunksizes for var %s",
var->ndims, var->hdr.name));
if (var->ndims)
if (!(var->chunksizes = calloc(var->ndims, sizeof(size_t))))
BAIL(NC_ENOMEM);
if ((retval = nc4_find_default_chunksizes2(grp, var)))
BAIL(retval);
/* Is this a variable with a chunksize greater than the current
* cache size? */
if ((retval = nc4_adjust_var_cache(grp, var)))
BAIL(retval);
/* If the user names this variable the same as a dimension, but
* doesn't use that dimension first in its list of dimension ids,
* is not a coordinate variable. I need to change its HDF5 name,
* because the dimension will cause a HDF5 dataset to be created,
* and this var has the same name. */
dim = (NC_DIM_INFO_T*)ncindexlookup(grp->dim,norm_name);
if (dim && (!var->ndims || dimidsp[0] != dim->hdr.id))
{
/* Set a different hdf5 name for this variable to avoid name
* clash. */
if (strlen(norm_name) + strlen(NON_COORD_PREPEND) > NC_MAX_NAME)
BAIL(NC_EMAXNAME);
if (!(var->hdf5_name = malloc((strlen(NON_COORD_PREPEND) +
strlen(norm_name) + 1) * sizeof(char))))
BAIL(NC_ENOMEM);
sprintf(var->hdf5_name, "%s%s", NON_COORD_PREPEND, norm_name);
}
/* If this is a coordinate var, it is marked as a HDF5 dimension
* scale. (We found dim above.) Otherwise, allocate space to
* remember whether dimension scales have been attached to each
* dimension. */
if (!var->dimscale && ndims)
if (!(var->dimscale_attached = calloc(ndims, sizeof(nc_bool_t))))
BAIL(NC_ENOMEM);
/* Return the varid. */
if (varidp)
*varidp = var->hdr.id;
LOG((4, "new varid %d", var->hdr.id));
exit:
if (type_info)
if ((retval = nc4_type_free(type_info)))
BAIL2(retval);
return retval;
}
/**
* @internal This functions sets extra stuff about a netCDF-4 variable which
* must be set before the enddef but after the def_var.
*
* @note All pointer parameters may be NULL, in which case they are ignored.
* @param ncid File ID.
* @param varid Variable ID.
* @param shuffle Pointer to shuffle setting.
* @param deflate Pointer to deflate setting.
* @param deflate_level Pointer to deflate level.
* @param fletcher32 Pointer to fletcher32 setting.
* @param contiguous Pointer to contiguous setting.
* @param chunksizes Array of chunksizes.
* @param no_fill Pointer to no_fill setting.
* @param fill_value Pointer to fill value.
* @param endianness Pointer to endianness setting.
*
* @returns ::NC_NOERR for success
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
* netcdf-4 file.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EPERM File is read only.
* @returns ::NC_EINVAL Invalid input
* @returns ::NC_EBADCHUNK Bad chunksize.
* @author Ed Hartnett
*/
static int
nc_def_var_extra(int ncid, int varid, int *shuffle, int *deflate,
int *deflate_level, int *fletcher32, int *contiguous,
const size_t *chunksizes, int *no_fill,
const void *fill_value, int *endianness)
{
NC *nc;
NC_GRP_INFO_T *grp;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
int d;
int retval;
/* All or none of these will be provided. */
assert((deflate && deflate_level && shuffle) ||
(!deflate && !deflate_level && !shuffle));
LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
/* 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;
assert(nc && grp && h5);
/* Trying to write to a read-only file? No way, Jose! */
if (h5->no_write)
return NC_EPERM;
/* Find the var. */
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
if(!var)
return NC_ENOTVAR;
assert(var && var->hdr.id == varid);
/* Can't turn on parallel and deflate/fletcher32/szip/shuffle. */
if (nc->mode & (NC_MPIIO | NC_MPIPOSIX)) {
if (deflate || fletcher32 || shuffle)
return NC_EINVAL;
}
/* If the HDF5 dataset has already been created, then it is too
* late to set all the extra stuff. */
if (var->created)
return NC_ELATEDEF;
/* Check compression options. */
if (deflate && !deflate_level)
return NC_EINVAL;
/* Valid deflate level? */
if (deflate)
{
if (*deflate)
if (*deflate_level < NC_MIN_DEFLATE_LEVEL ||
*deflate_level > NC_MAX_DEFLATE_LEVEL)
return NC_EINVAL;
/* For scalars, just ignore attempt to deflate. */
if (!var->ndims)
return NC_NOERR;
/* Well, if we couldn't find any errors, I guess we have to take
* the users settings. Darn! */
var->contiguous = NC_FALSE;
var->deflate = *deflate;
if (*deflate)
var->deflate_level = *deflate_level;
LOG((3, "%s: *deflate_level %d", __func__, *deflate_level));
}
/* Shuffle filter? */
if (shuffle)
{
var->shuffle = *shuffle;
var->contiguous = NC_FALSE;
}
/* Fletcher32 checksum error protection? */
if (fletcher32)
{
var->fletcher32 = *fletcher32;
var->contiguous = NC_FALSE;
}
/* Does the user want a contiguous dataset? Not so fast! Make sure
* that there are no unlimited dimensions, and no filters in use
* for this data. */
if (contiguous && *contiguous)
{
if (var->deflate || var->fletcher32 || var->shuffle)
return NC_EINVAL;
for (d = 0; d < var->ndims; d++)
if (var->dim[d]->unlimited)
return NC_EINVAL;
var->contiguous = NC_TRUE;
}
/* Chunksizes anyone? */
if (contiguous && *contiguous == NC_CHUNKED)
{
var->contiguous = NC_FALSE;
/* If the user provided chunksizes, check that they are not too
* big, and that their total size of chunk is less than 4 GB. */
if (chunksizes)
{
if ((retval = check_chunksizes(grp, var, chunksizes)))
return retval;
/* Ensure chunksize is smaller than dimension size */
for (d = 0; d < var->ndims; d++)
if(!var->dim[d]->unlimited && var->dim[d]->len > 0 && chunksizes[d] > var->dim[d]->len)
return NC_EBADCHUNK;
/* Set the chunksizes for this variable. */
for (d = 0; d < var->ndims; d++)
var->chunksizes[d] = chunksizes[d];
}
}
/* Is this a variable with a chunksize greater than the current
* cache size? */
if (!var->contiguous && (deflate || contiguous))
{
/* Determine default chunksizes for this variable (do nothing
* for scalar vars). */
if (var->chunksizes && !var->chunksizes[0])
if ((retval = nc4_find_default_chunksizes2(grp, var)))
return retval;
/* Adjust the cache. */
if ((retval = nc4_adjust_var_cache(grp, var)))
return retval;
}
/* Are we setting a fill modes? */
if (no_fill)
{
if (*no_fill)
{
/* NC_STRING types may not turn off fill mode. It's disallowed
* by HDF5 and will cause a HDF5 error later. */
if (*no_fill)
if (var->type_info->hdr.id == NC_STRING)
return NC_EINVAL;
/* Set the no-fill mode. */
var->no_fill = NC_TRUE;
}
else
var->no_fill = NC_FALSE;
}
/* Are we setting a fill value? */
if (fill_value && !var->no_fill)
{
/* Copy the fill_value. */
LOG((4, "Copying fill value into metadata for variable %s",
var->hdr.name));
/* If there's a _FillValue attribute, delete it. */
retval = NC4_del_att(ncid, varid, _FillValue);
if (retval && retval != NC_ENOTATT)
return retval;
/* Create a _FillValue attribute. */
if ((retval = nc_put_att(ncid, varid, _FillValue, var->type_info->hdr.id, 1, fill_value)))
return retval;
}
/* Is the user setting the endianness? */
if (endianness)
var->type_info->endianness = *endianness;
return NC_NOERR;
}
/**
* @internal Set compression settings on a variable. This is called by
* nc_def_var_deflate().
*
* @param ncid File ID.
* @param varid Variable ID.
* @param shuffle True to turn on the shuffle filter.
* @param deflate True to turn on deflation.
* @param deflate_level A number between 0 (no compression) and 9
* (maximum compression).
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EINVAL Invalid input
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_def_var_deflate(int ncid, int varid, int shuffle, int deflate,
int deflate_level)
{
return nc_def_var_extra(ncid, varid, &shuffle, &deflate,
&deflate_level, NULL, NULL, NULL, NULL, NULL, NULL);
}
/**
* @internal Set checksum on a variable. This is called by
* nc_def_var_fletcher32().
*
* @param ncid File ID.
* @param varid Variable ID.
* @param fletcher32 Pointer to fletcher32 setting.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EINVAL Invalid input
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_def_var_fletcher32(int ncid, int varid, int fletcher32)
{
return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, &fletcher32,
NULL, NULL, NULL, NULL, NULL);
}
/**
* @internal Define chunking stuff for a var. This is called by
* nc_def_var_chunking(). Chunking is required in any dataset with one
* or more unlimited dimensions in HDF5, or any dataset using a
* filter.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param contiguous Pointer to contiguous setting.
* @param chunksizesp Array of chunksizes.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EINVAL Invalid input
* @returns ::NC_EBADCHUNK Bad chunksize.
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_def_var_chunking(int ncid, int varid, int contiguous, const size_t *chunksizesp)
{
return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL,
&contiguous, chunksizesp, NULL, NULL, NULL);
}
/**
* @internal Define chunking stuff for a var. This is called by
* the fortran API.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param contiguous Pointer to contiguous setting.
* @param chunksizesp Array of chunksizes.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EINVAL Invalid input
* @returns ::NC_EBADCHUNK Bad chunksize.
* @author Ed Hartnett
*/
int
nc_def_var_chunking_ints(int ncid, int varid, int contiguous, int *chunksizesp)
{
NC *nc;
NC_GRP_INFO_T *grp;
NC_VAR_INFO_T *var;
NC_FILE_INFO_T *h5;
size_t *cs = NULL;
int i, retval;
/* Find this ncid's file info. */
if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
return retval;
assert(nc);
/* Find var cause I need the number of dims. */
if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var)))
return retval;
/* Allocate space for the size_t copy of the chunksizes array. */
if (var->ndims)
if (!(cs = malloc(var->ndims * sizeof(size_t))))
return NC_ENOMEM;
/* Copy to size_t array. */
for (i = 0; i < var->ndims; i++)
cs[i] = chunksizesp[i];
retval = nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL,
&contiguous, cs, NULL, NULL, NULL);
if (var->ndims)
free(cs);
return retval;
}
/**
* @internal This functions sets fill value and no_fill mode for a
* netCDF-4 variable. It is called by nc_def_var_fill().
*
* @note All pointer parameters may be NULL, in which case they are ignored.
* @param ncid File ID.
* @param varid Variable ID.
* @param no_fill No_fill setting.
* @param fill_value Pointer to fill value.
*
* @returns ::NC_NOERR for success
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
* netcdf-4 file.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EPERM File is read only.
* @returns ::NC_EINVAL Invalid input
* @author Ed Hartnett
*/
int
NC4_def_var_fill(int ncid, int varid, int no_fill, const void *fill_value)
{
return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, NULL,
NULL, &no_fill, fill_value, NULL);
}
/**
* @internal This functions sets endianness for a netCDF-4
* variable. Called by nc_def_var_endian().
*
* @note All pointer parameters may be NULL, in which case they are ignored.
* @param ncid File ID.
* @param varid Variable ID.
* @param endianness Endianness setting.
*
* @returns ::NC_NOERR for success
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ESTRICTNC3 Attempting netcdf-4 operation on strict nc3
* netcdf-4 file.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_ENOTINDEFINE Not in define mode.
* @returns ::NC_EPERM File is read only.
* @returns ::NC_EINVAL Invalid input
* @author Ed Hartnett
*/
int
NC4_def_var_endian(int ncid, int varid, int endianness)
{
return nc_def_var_extra(ncid, varid, NULL, NULL, NULL, NULL, NULL,
NULL, NULL, NULL, &endianness);
}
/**
* @internal Define filter settings. Called by nc_def_var_filter().
*
* @param ncid File ID.
* @param varid Variable ID.
* @param id Filter ID
* @param nparams Number of parameters for filter.
* @param parms Filter parameters.
*
* @returns ::NC_NOERR for success
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_ENOTNC4 Attempting netcdf-4 operation on file that is
* not netCDF-4/HDF5.
* @returns ::NC_ELATEDEF Too late to change settings for this variable.
* @returns ::NC_EFILTER Filter error.
* @returns ::NC_EINVAL Invalid input
* @author Dennis Heimbigner
*/
int
NC4_def_var_filter(int ncid, int varid, unsigned int id, size_t nparams,
const unsigned int* parms)
{
int retval = NC_NOERR;
NC *nc;
NC_GRP_INFO_T *grp;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
LOG((2, "%s: ncid 0x%x varid %d", __func__, ncid, varid));
/* 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;
assert(nc && grp && h5);
/* Find the var. */
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
if(!var)
return NC_ENOTVAR;
assert(var->hdr.id == varid);
/* Can't turn on parallel and filters */
if (nc->mode & (NC_MPIIO | NC_MPIPOSIX)) {
return NC_EINVAL;
}
/* If the HDF5 dataset has already been created, then it is too
* late to set all the extra stuff. */
if (var->created)
return NC_ELATEDEF;
#ifdef HAVE_H5Z_SZIP
if(id == H5Z_FILTER_SZIP) {
if(nparams != 2)
return NC_EFILTER; /* incorrect no. of parameters */
}
#else /*!HAVE_H5Z_SZIP*/
if(id == H5Z_FILTER_SZIP)
return NC_EFILTER; /* Not allowed */
#endif
#if 0
{
unsigned int fcfg = 0;
herr_t herr = H5Zget_filter_info(id,&fcfg);
if(herr < 0)
return NC_EFILTER;
if((H5Z_FILTER_CONFIG_ENCODE_ENABLED & fcfg) == 0
|| (H5Z_FILTER_CONFIG_DECODE_ENABLED & fcfg) == 0)
return NC_EFILTER;
}
#endif /*0*/
var->filterid = id;
var->nparams = nparams;
var->params = NULL;
if(parms != NULL) {
var->params = (unsigned int*)calloc(nparams,sizeof(unsigned int));
if(var->params == NULL) return NC_ENOMEM;
memcpy(var->params,parms,sizeof(unsigned int)*var->nparams);
}
return NC_NOERR;
}
/**
* @internal Rename a var to "bubba," for example. This is called by
* nc_rename_var() for netCDF-4 files.
*
* @param ncid File ID.
* @param varid Variable ID
* @param name New name of the variable.
*
* @returns ::NC_NOERR No error.
* @returns ::NC_EBADID Bad ncid.
* @returns ::NC_ENOTVAR Invalid variable ID.
* @returns ::NC_EBADNAME Bad name.
* @returns ::NC_EMAXNAME Name is too long.
* @returns ::NC_ENAMEINUSE Name in use.
* @returns ::NC_ENOMEM Out of memory.
* @author Ed Hartnett
*/
int
NC4_rename_var(int ncid, int varid, const char *name)
{
NC *nc;
NC_GRP_INFO_T *grp;
NC_FILE_INFO_T *h5;
NC_VAR_INFO_T *var, *tmpvar;
int retval = NC_NOERR;
if (!name)
return NC_EINVAL;
LOG((2, "%s: ncid 0x%x varid %d name %s", __func__, ncid, varid,
name));
/* 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;
assert(h5 && grp && h5);
/* Is the new name too long? */
if (strlen(name) > NC_MAX_NAME)
return NC_EMAXNAME;
/* Trying to write to a read-only file? No way, Jose! */
if (h5->no_write)
return NC_EPERM;
/* Check name validity, if strict nc3 rules are in effect for this
* file. */
if ((retval = NC_check_name(name)))
return retval;
/* Get the variable wrt varid */
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
if (!var)
return NC_ENOTVAR;
/* Check if new name is in use; note that renaming to same name is still an error
according to the nc_test/test_write.c code. Why?*/
tmpvar = (NC_VAR_INFO_T*)ncindexlookup(grp->vars,name);
if(tmpvar != NULL)
return NC_ENAMEINUSE;
/* If we're not in define mode, new name must be of equal or
less size, if strict nc3 rules are in effect for this . */
if (!(h5->flags & NC_INDEF) && strlen(name) > strlen(var->hdr.name) &&
(h5->cmode & NC_CLASSIC_MODEL))
return NC_ENOTINDEFINE;
/* Change the HDF5 file, if this var has already been created
there. Should we check here to ensure there is not already a
dimscale dataset of name name??? */
if (var->created)
{
/* Is there an existing dimscale-only dataset of this name? If
* so, it must be deleted. */
if (var->ndims && var->dim[0]->hdf_dimscaleid)
{
if ((retval = delete_existing_dimscale_dataset(grp, var->dim[0]->hdr.id, var->dim[0])))
return retval;
}
LOG((3, "Moving dataset %s to %s", var->hdr.name, name));
if (H5Gmove(grp->hdf_grpid, var->hdr.name, name) < 0)
BAIL(NC_EHDFERR);
}
/* Now change the name in our metadata. */
free(var->hdr.name);
if (!(var->hdr.name = strdup(name)))
return NC_ENOMEM;
LOG((3, "var is now %s", var->hdr.name));
var->hdr.hashkey = NC_hashmapkey(var->hdr.name,strlen(var->hdr.name)); /* Fix hash key */
if(!ncindexrebuild(grp->vars))
return NC_EINTERNAL;
/* Check if this was a coordinate variable previously, but names are different now */
if (var->dimscale && strcmp(var->hdr.name, var->dim[0]->hdr.name))
{
/* Break up the coordinate variable */
if ((retval = nc4_break_coord_var(grp, var, var->dim[0])))
return retval;
}
/* Check if this should become a coordinate variable */
if (!var->dimscale)
{
/* Only variables with >0 dimensions can become coordinate variables */
if (var->ndims)
{
NC_GRP_INFO_T *dim_grp;
NC_DIM_INFO_T *dim;
/* Check to see if this is became a coordinate variable. If so, it
* will have the same name as dimension index 0. If it is a
* coordinate var, is it a coordinate var in the same group as the dim?
*/
if ((retval = nc4_find_dim(grp, var->dimids[0], &dim, &dim_grp)))
return retval;
if (!strcmp(dim->hdr.name, name) && dim_grp == grp)
{
/* Reform the coordinate variable */
if ((retval = nc4_reform_coord_var(grp, var, dim)))
return retval;
var->became_coord_var = NC_TRUE;
}
}
}
exit:
return retval;
}
/**
* @internal Write an array of data to a variable. This is called by
* nc_put_vara() and other nc_put_vara_* functions, for netCDF-4
* files.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param startp Array of start indices.
* @param countp Array of counts.
* @param op pointer that gets the data.
* @param memtype The type of these data in memory.
*
* @returns ::NC_NOERR for success
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_put_vara(int ncid, int varid, const size_t *startp,
const size_t *countp, const void *op, int memtype)
{
NC *nc;
if (!(nc = nc4_find_nc_file(ncid, NULL)))
return NC_EBADID;
return nc4_put_vars(nc, ncid, varid, startp, countp, NULL, memtype,
(void *)op);
}
/**
* Read an array of values. This is called by nc_get_vara() for
* netCDF-4 files, as well as all the other nc_get_vara_*
* functions.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param startp Array of start indices.
* @param countp Array of counts.
* @param ip pointer that gets the data.
* @param memtype The type of these data after it is read into memory.
* @returns ::NC_NOERR for success
* @author Ed Hartnett, Dennis Heimbigner
*/
int
NC4_get_vara(int ncid, int varid, const size_t *startp,
const size_t *countp, void *ip, int memtype)
{
NC *nc;
NC_FILE_INFO_T* h5;
LOG((2, "%s: ncid 0x%x varid %d memtype %d", __func__, ncid, varid,
memtype));
if (!(nc = nc4_find_nc_file(ncid, &h5)))
return NC_EBADID;
/* Get the data. */
return nc4_get_vars(nc, ncid, varid, startp, countp, NULL, memtype,
(void *)ip);
}
/**
* @internal Write an array of data to a variable. This is called by
* nc_put_vars() and other nc_put_vars_* functions, for netCDF-4
* files.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param startp Array of start indices.
* @param countp Array of counts.
* @param stridep Array of strides.
* @param op pointer that gets the data.
* @param memtype The type of these data in memory.
*
* @returns ::NC_NOERR for success
* @author Dennis Heimbigner
*/
int
NC4_put_vars(int ncid, int varid, const size_t *startp,
const size_t *countp, const ptrdiff_t* stridep,
const void *op, int memtype)
{
NC *nc;
if (!(nc = nc4_find_nc_file(ncid, NULL)))
return NC_EBADID;
return nc4_put_vars(nc, ncid, varid, startp, countp, stridep, memtype,
(void *)op);
}
/**
* Read an array of values. This is called by nc_get_vars() for
* netCDF-4 files, as well as all the other nc_get_vars_*
* functions.
*
* @param ncid File ID.
* @param varid Variable ID.
* @param startp Array of start indices.
* @param countp Array of counts.
* @param stridep Array of strides.
* @param ip pointer that gets the data.
* @param memtype The type of these data after it is read into memory.
* @returns ::NC_NOERR for success
* @author Dennis Heimbigner
*/
int
NC4_get_vars(int ncid, int varid, const size_t *startp,
const size_t *countp, const ptrdiff_t *stridep,
void *ip, int memtype)
{
NC *nc;
NC_FILE_INFO_T *h5;
LOG((2, "%s: ncid 0x%x varid %d memtype %d", __func__, ncid, varid,
memtype));
if (!(nc = nc4_find_nc_file(ncid, &h5)))
return NC_EBADID;
/* Get the data. */
return nc4_get_vars(nc, ncid, varid, startp, countp, stridep, memtype,
(void *)ip);
}
Reference in New Issue View Git Blame Copy Permalink