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0a7ff043a2
netcdf-c/libsrc4/nc4hdf.c
dmh 0a7ff043a2 re: Jira NCF-320 
Partially resolve by making
string variables and attributes use
UTF-8 encoding.
Normalization is not necessarily fixed,
however.
2015-08-20 15:53:48 -06:00

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/*
This file is part of netcdf-4, a netCDF-like interface for HDF5, or a
HDF5 backend for netCDF, depending on your point of view.
This file contains functions internal to the netcdf4 library. None of
the functions in this file are exposed in the exetnal API. These
functions handle the HDF interface.
Copyright 2003, University Corporation for Atmospheric
Research. See the COPYRIGHT file for copying and redistribution
conditions.
$Id: nc4hdf.c,v 1.273 2010/05/27 21:34:14 dmh Exp $
*/
#include "config.h"
#include "nc4internal.h"
#include "nc4dispatch.h"
#include <H5DSpublic.h>
#include <math.h>
#if 0 /*def USE_PNETCDF*/
#include <pnetcdf.h>
#endif
#define NC3_STRICT_ATT_NAME "_nc3_strict"
/* This is to track opened HDF5 objects to make sure they are
* closed. */
#ifdef EXTRA_TESTS
int num_plists;
int num_spaces;
#endif /* EXTRA_TESTS */
/* This function is needed to handle one special case: what if the
* user defines a dim, writes metadata, then goes back into define
* mode and adds a coordinate var for the already existing dim. In
* that case, I need to recreate the dim's dimension scale dataset,
* and then I need to go to every var in the file which uses that
* dimension, and attach the new dimension scale. */
int
rec_reattach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid)
{
NC_VAR_INFO_T *var;
NC_GRP_INFO_T *child_grp;
int d;
int retval;
assert(grp && grp->name && dimid >= 0 && dimscaleid >= 0);
LOG((3, "%s: grp->name %s", __func__, grp->name));
/* If there are any child groups, attach dimscale there, if needed. */
for (child_grp = grp->children; child_grp; child_grp = child_grp->l.next)
if ((retval = rec_reattach_scales(child_grp, dimid, dimscaleid)))
return retval;
/* Find any vars that use this dimension id. */
for (var = grp->var; var; var = var->l.next)
for (d = 0; d < var->ndims; d++)
if (var->dimids[d] == dimid && !var->dimscale)
{
LOG((2, "%s: attaching scale for dimid %d to var %s",
__func__, var->dimids[d], var->name));
if (var->created)
{
if (H5DSattach_scale(var->hdf_datasetid, dimscaleid, d) < 0)
return NC_EHDFERR;
var->dimscale_attached[d] = NC_TRUE;
}
}
return NC_NOERR;
}
/* This function is needed to handle one special case: what if the
* user defines a dim, writes metadata, then goes back into define
* mode and adds a coordinate var for the already existing dim. In
* that case, I need to recreate the dim's dimension scale dataset,
* and then I need to go to every var in the file which uses that
* dimension, and attach the new dimension scale. */
int
rec_detach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid)
{
NC_VAR_INFO_T *var;
NC_GRP_INFO_T *child_grp;
int d;
int retval;
assert(grp && grp->name && dimid >= 0 && dimscaleid >= 0);
LOG((3, "%s: grp->name %s", __func__, grp->name));
/* If there are any child groups, detach dimscale there, if needed. */
for (child_grp = grp->children; child_grp; child_grp = child_grp->l.next)
if ((retval = rec_detach_scales(child_grp, dimid, dimscaleid)))
return retval;
/* Find any vars that use this dimension id. */
for (var = grp->var; var; var = var->l.next)
for (d = 0; d < var->ndims; d++)
if (var->dimids[d] == dimid && !var->dimscale)
{
LOG((2, "%s: detaching scale for dimid %d to var %s",
__func__, var->dimids[d], var->name));
if (var->created)
if (var->dimscale_attached && var->dimscale_attached[d])
{
if (H5DSdetach_scale(var->hdf_datasetid, dimscaleid, d) < 0)
return NC_EHDFERR;
var->dimscale_attached[d] = NC_FALSE;
}
}
return NC_NOERR;
}
/* Open the dataset and leave it open. */
int
nc4_open_var_grp2(NC_GRP_INFO_T *grp, int varid, hid_t *dataset)
{
NC_VAR_INFO_T *var;
/* Find the requested varid. */
for (var = grp->var; var; var = var->l.next)
if (var->varid == varid)
break;
if (!var)
return NC_ENOTVAR;
/* Open this dataset if necessary. */
if (!var->hdf_datasetid)
if ((var->hdf_datasetid = H5Dopen2(grp->hdf_grpid, var->name,
H5P_DEFAULT)) < 0)
return NC_ENOTVAR;
*dataset = var->hdf_datasetid;
return NC_NOERR;
}
/* Get the default fill value for an atomic type. Memory for
* fill_value must already be allocated, or you are DOOMED!!!*/
int
nc4_get_default_fill_value(const NC_TYPE_INFO_T *type_info, void *fill_value)
{
switch (type_info->nc_typeid)
{
case NC_CHAR:
*(char *)fill_value = NC_FILL_CHAR;
break;
case NC_STRING:
*(char **)fill_value = strdup(NC_FILL_STRING);
break;
case NC_BYTE:
*(signed char *)fill_value = NC_FILL_BYTE;
break;
case NC_SHORT:
*(short *)fill_value = NC_FILL_SHORT;
break;
case NC_INT:
*(int *)fill_value = NC_FILL_INT;
break;
case NC_UBYTE:
*(unsigned char *)fill_value = NC_FILL_UBYTE;
break;
case NC_USHORT:
*(unsigned short *)fill_value = NC_FILL_USHORT;
break;
case NC_UINT:
*(unsigned int *)fill_value = NC_FILL_UINT;
break;
case NC_INT64:
*(long long *)fill_value = NC_FILL_INT64;
break;
case NC_UINT64:
*(unsigned long long *)fill_value = NC_FILL_UINT64;
break;
case NC_FLOAT:
*(float *)fill_value = NC_FILL_FLOAT;
break;
case NC_DOUBLE:
*(double *)fill_value = NC_FILL_DOUBLE;
break;
default:
return NC_EINVAL;
}
return NC_NOERR;
}
/* What fill value should be used for a variable? */
static int
get_fill_value(NC_HDF5_FILE_INFO_T *h5, NC_VAR_INFO_T *var, void **fillp)
{
size_t size;
int retval;
/* Find out how much space we need for this type's fill value. */
if (var->type_info->nc_type_class == NC_VLEN)
size = sizeof(nc_vlen_t);
else if (var->type_info->nc_type_class == NC_STRING)
size = sizeof(char *);
else
{
if ((retval = nc4_get_typelen_mem(h5, var->type_info->nc_typeid, 0, &size)))
return retval;
}
assert(size);
/* Allocate the space. */
if (!((*fillp) = calloc(1, size)))
return NC_ENOMEM;
/* If the user has set a fill_value for this var, use, otherwise
* find the default fill value. */
if (var->fill_value)
{
LOG((4, "Found a fill value for var %s", var->name));
if (var->type_info->nc_type_class == NC_VLEN)
{
nc_vlen_t *in_vlen = (nc_vlen_t *)(var->fill_value), *fv_vlen = (nc_vlen_t *)(*fillp);
fv_vlen->len = in_vlen->len;
if (!(fv_vlen->p = malloc(size * in_vlen->len)))
{
free(*fillp);
*fillp = NULL;
return NC_ENOMEM;
}
memcpy(fv_vlen->p, in_vlen->p, in_vlen->len * size);
}
else if (var->type_info->nc_type_class == NC_STRING)
{
if (*(char **)var->fill_value)
if (!(**(char ***)fillp = strdup(*(char **)var->fill_value)))
{
free(*fillp);
*fillp = NULL;
return NC_ENOMEM;
}
}
else
memcpy((*fillp), var->fill_value, size);
}
else
{
if (nc4_get_default_fill_value(var->type_info, *fillp))
{
/* Note: release memory, but don't return error on failure */
free(*fillp);
*fillp = NULL;
}
}
return NC_NOERR;
}
/* Given a netcdf type, return appropriate HDF typeid. */
/* (All hdf_typeid's returned from this routine must be H5Tclosed by the caller) */
int
nc4_get_hdf_typeid(NC_HDF5_FILE_INFO_T *h5, nc_type xtype,
hid_t *hdf_typeid, int endianness)
{
NC_TYPE_INFO_T *type;
hid_t typeid = 0;
int retval = NC_NOERR;
assert(hdf_typeid && h5);
*hdf_typeid = -1;
/* Determine an appropriate HDF5 datatype */
if (xtype == NC_NAT)
/* NAT = 'Not A Type' (c.f. NaN) */
return NC_EBADTYPE;
else if (xtype == NC_CHAR || xtype == NC_STRING)
{
/* NC_CHAR & NC_STRING types create a new HDF5 datatype */
if (xtype == NC_CHAR)
{
if ((typeid = H5Tcopy(H5T_C_S1)) < 0)
return NC_EHDFERR;
if (H5Tset_strpad(typeid, H5T_STR_NULLTERM) < 0)
BAIL(NC_EVARMETA);
if(H5Tset_cset(typeid, H5T_CSET_UTF8) < 0)
BAIL(NC_EVARMETA);
/* Take ownership of the newly created HDF5 datatype */
*hdf_typeid = typeid;
typeid = 0;
}
else
{
if ((typeid = H5Tcopy(H5T_C_S1)) < 0)
return NC_EHDFERR;
if (H5Tset_size(typeid, H5T_VARIABLE) < 0)
BAIL(NC_EVARMETA);
if(H5Tset_cset(typeid, H5T_CSET_UTF8) < 0)
BAIL(NC_EVARMETA);
/* Take ownership of the newly created HDF5 datatype */
*hdf_typeid = typeid;
typeid = 0;
}
}
else
{
/* All other types use an existing HDF5 datatype */
switch (xtype)
{
case NC_BYTE: /* signed 1 byte integer */
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_I8LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_I8BE;
else
typeid = H5T_NATIVE_SCHAR;
break;
case NC_SHORT: /* signed 2 byte integer */
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_I16LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_I16BE;
else
typeid = H5T_NATIVE_SHORT;
break;
case NC_INT:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_I32LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_I32BE;
else
typeid = H5T_NATIVE_INT;
break;
case NC_UBYTE:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_U8LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_U8BE;
else
typeid = H5T_NATIVE_UCHAR;
break;
case NC_USHORT:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_U16LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_U16BE;
else
typeid = H5T_NATIVE_USHORT;
break;
case NC_UINT:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_U32LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_U32BE;
else
typeid = H5T_NATIVE_UINT;
break;
case NC_INT64:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_I64LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_I64BE;
else
typeid = H5T_NATIVE_LLONG;
break;
case NC_UINT64:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_STD_U64LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_STD_U64BE;
else
typeid = H5T_NATIVE_ULLONG;
break;
case NC_FLOAT:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_IEEE_F32LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_IEEE_F32BE;
else
typeid = H5T_NATIVE_FLOAT;
break;
case NC_DOUBLE:
if (endianness == NC_ENDIAN_LITTLE)
typeid = H5T_IEEE_F64LE;
else if (endianness == NC_ENDIAN_BIG)
typeid = H5T_IEEE_F64BE;
else
typeid = H5T_NATIVE_DOUBLE;
break;
default:
/* Maybe this is a user defined type? */
if (nc4_find_type(h5, xtype, &type))
return NC_EBADTYPE;
if (!type)
return NC_EBADTYPE;
typeid = type->hdf_typeid;
break;
}
assert(typeid);
/* Copy the HDF5 datatype, so the function operates uniformly */
if ((*hdf_typeid = H5Tcopy(typeid)) < 0)
return NC_EHDFERR;
typeid = 0;
}
assert(*hdf_typeid != -1);
exit:
if (typeid > 0 && H5Tclose(typeid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/* Do some common check for nc4_put_vara and nc4_get_vara. These
* checks have to be done when both reading and writing data. */
static int
check_for_vara(nc_type *mem_nc_type, NC_VAR_INFO_T *var, NC_HDF5_FILE_INFO_T *h5)
{
int retval;
/* If mem_nc_type is NC_NAT, it means we want to use the file type
* as the mem type as well. */
assert(mem_nc_type);
if (*mem_nc_type == NC_NAT)
*mem_nc_type = var->type_info->nc_typeid;
assert(*mem_nc_type);
/* No NC_CHAR conversions, you pervert! */
if (var->type_info->nc_typeid != *mem_nc_type &&
(var->type_info->nc_typeid == NC_CHAR || *mem_nc_type == NC_CHAR))
return NC_ECHAR;
/* If we're in define mode, we can't read or write data. */
if (h5->flags & NC_INDEF)
{
if (h5->cmode & NC_CLASSIC_MODEL)
return NC_EINDEFINE;
if ((retval = nc4_enddef_netcdf4_file(h5)))
return retval;
}
return NC_NOERR;
}
#ifdef LOGGING
/* Print some debug info about dimensions to the log. */
static void
log_dim_info(NC_VAR_INFO_T *var, hsize_t *fdims, hsize_t *fmaxdims,
hsize_t *start, hsize_t *count)
{
int d2;
/* Print some debugging info... */
LOG((4, "%s: var name %s ndims %d", __func__, var->name, var->ndims));
LOG((4, "File space, and requested:"));
for (d2 = 0; d2 < var->ndims; d2++)
{
LOG((4, "fdims[%d]=%Ld fmaxdims[%d]=%Ld", d2, fdims[d2], d2,
fmaxdims[d2]));
LOG((4, "start[%d]=%Ld count[%d]=%Ld", d2, start[d2], d2, count[d2]));
}
}
#endif /* LOGGING */
#ifdef USE_PARALLEL
static int
set_par_access(NC_HDF5_FILE_INFO_T *h5, NC_VAR_INFO_T *var, hid_t xfer_plistid)
{
/* If netcdf is built with parallel I/O, then parallel access can
* be used, and, if this file was opened or created for parallel
* access, we need to set the transfer mode. */
if (h5->parallel)
{
H5FD_mpio_xfer_t hdf5_xfer_mode;
/* Decide on collective or independent. */
hdf5_xfer_mode = (var->parallel_access != NC_INDEPENDENT) ?
H5FD_MPIO_COLLECTIVE : H5FD_MPIO_INDEPENDENT;
/* Set the mode in the transfer property list. */
if (H5Pset_dxpl_mpio(xfer_plistid, hdf5_xfer_mode) < 0)
return NC_EPARINIT;
LOG((4, "%s: %d H5FD_MPIO_COLLECTIVE: %d H5FD_MPIO_INDEPENDENT: %d",
__func__, (int)hdf5_xfer_mode, H5FD_MPIO_COLLECTIVE, H5FD_MPIO_INDEPENDENT));
}
return NC_NOERR;
}
#endif
/* Write an array of data to a variable. When it comes right down to
* it, this is what netCDF-4 is all about, this is *the* function, the
* big enchilda, the grand poo-bah, the alpha dog, the head honcho,
* the big cheese, the mighty kahuna, the top bananna, the high
* muckity-muck, numero uno. Well, you get the idea. */
int
nc4_put_vara(NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, nc_type mem_nc_type, int is_long, void *data)
{
NC_GRP_INFO_T *grp;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim;
hid_t file_spaceid = 0, mem_spaceid = 0, xfer_plistid = 0;
hsize_t xtend_size[NC_MAX_VAR_DIMS] , count[NC_MAX_VAR_DIMS];
hsize_t fdims[NC_MAX_VAR_DIMS], fmaxdims[NC_MAX_VAR_DIMS];
hsize_t start[NC_MAX_VAR_DIMS];
char *name_to_use;
int need_to_extend = 0;
int retval = NC_NOERR, range_error = 0, i, d2;
void *bufr = NULL;
#ifndef HDF5_CONVERT
int need_to_convert = 0;
size_t len = 1;
#endif
#ifdef HDF5_CONVERT
hid_t mem_typeid = 0;
#endif
/* Find our metadata for this file, group, and var. */
assert(nc);
if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var)))
return retval;
h5 = NC4_DATA(nc);
assert(grp && h5 && var && var->name);
LOG((3, "%s: var->name %s mem_nc_type %d is_long %d",
__func__, var->name, mem_nc_type, is_long));
/* Check some stuff about the type and the file. If the file must
* be switched from define mode, it happens here. */
if ((retval = check_for_vara(&mem_nc_type, var, h5)))
return retval;
/* Convert from size_t and ptrdiff_t to hssize_t, and hsize_t. */
for (i = 0; i < var->ndims; i++)
{
start[i] = startp[i];
count[i] = countp[i];
}
/* Open this dataset if necessary, also checking for a weird case:
* a non-coordinate (and non-scalar) variable that has the same
* name as a dimension. */
if (var->hdf5_name && strlen(var->hdf5_name) >= strlen(NON_COORD_PREPEND) &&
strncmp(var->hdf5_name, NON_COORD_PREPEND, strlen(NON_COORD_PREPEND)) == 0 &&
var->ndims)
name_to_use = var->hdf5_name;
else
name_to_use = var->name;
if (!var->hdf_datasetid)
if ((var->hdf_datasetid = H5Dopen2(grp->hdf_grpid, name_to_use, H5P_DEFAULT)) < 0)
return NC_ENOTVAR;
/* Get file space of data. */
if ((file_spaceid = H5Dget_space(var->hdf_datasetid)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
/* Check to ensure the user selection is
* valid. H5Sget_simple_extent_dims gets the sizes of all the dims
* and put them in fdims. */
if (H5Sget_simple_extent_dims(file_spaceid, fdims, fmaxdims) < 0)
BAIL(NC_EHDFERR);
#ifdef LOGGING
log_dim_info(var, fdims, fmaxdims, start, count);
#endif
/* Check dimension bounds. Remember that unlimited dimnsions can
* put data beyond their current length. */
for (d2 = 0; d2 < var->ndims; d2++)
{
for (dim = grp->dim; dim; dim = dim->l.next)
{
if (dim->dimid == var->dimids[d2])
{
if (!dim->unlimited)
{
if (start[d2] >= (hssize_t)fdims[d2])
BAIL_QUIET(NC_EINVALCOORDS);
if (start[d2] + count[d2] > fdims[d2])
BAIL_QUIET(NC_EEDGE);
}
}
}
}
/* Now you would think that no one would be crazy enough to write
a scalar dataspace with one of the array function calls, but you
would be wrong. So let's check to see if the dataset is
scalar. If it is, we won't try to set up a hyperslab. */
if (H5Sget_simple_extent_type(file_spaceid) == H5S_SCALAR)
{
if ((mem_spaceid = H5Screate(H5S_SCALAR)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
}
else
{
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET, start, NULL,
count, NULL) < 0)
BAIL(NC_EHDFERR);
/* Create a space for the memory, just big enough to hold the slab
we want. */
if ((mem_spaceid = H5Screate_simple(var->ndims, count, NULL)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
}
#ifndef HDF5_CONVERT
/* Are we going to convert any data? (No converting of compound or
* opaque types.) */
if ((mem_nc_type != var->type_info->nc_typeid || (var->type_info->nc_typeid == NC_INT && is_long)) &&
mem_nc_type != NC_COMPOUND && mem_nc_type != NC_OPAQUE)
{
size_t file_type_size;
/* We must convert - allocate a buffer. */
need_to_convert++;
if (var->ndims)
for (d2=0; d2<var->ndims; d2++)
len *= countp[d2];
LOG((4, "converting data for var %s type=%d len=%d", var->name,
var->type_info->nc_typeid, len));
/* Later on, we will need to know the size of this type in the
* file. */
assert(var->type_info->size);
file_type_size = var->type_info->size;
/* If we're reading, we need bufr to have enough memory to store
* the data in the file. If we're writing, we need bufr to be
* big enough to hold all the data in the file's type. */
if(len > 0)
if (!(bufr = malloc(len * file_type_size)))
BAIL(NC_ENOMEM);
}
else
#endif /* ifndef HDF5_CONVERT */
bufr = data;
#ifdef HDF5_CONVERT
/* Get the HDF type of the data in memory. */
if ((retval = nc4_get_hdf_typeid(h5, mem_nc_type, &mem_typeid,
var->type_info->endianness)))
BAIL(retval);
#endif
/* Create the data transfer property list. */
if ((xfer_plistid = H5Pcreate(H5P_DATASET_XFER)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists++;
#endif
/* Apply the callback function which will detect range
* errors. Which one to call depends on the length of the
* destination buffer type. */
#ifdef HDF5_CONVERT
if (H5Pset_type_conv_cb(xfer_plistid, except_func, &range_error) < 0)
BAIL(NC_EHDFERR);
#endif
#ifdef USE_PARALLEL
/* Set up parallel I/O, if needed. */
if ((retval = set_par_access(h5, var, xfer_plistid)))
BAIL(retval);
#endif
/* Read/write this hyperslab into memory. */
/* Does the dataset have to be extended? If it's already
extended to the required size, it will do no harm to reextend
it to that size. */
if (var->ndims)
{
for (d2 = 0; d2 < var->ndims; d2++)
{
if ((retval = nc4_find_dim(grp, var->dimids[d2], &dim, NULL)))
BAIL(retval);
if (dim->unlimited)
{
if (start[d2] + count[d2] > fdims[d2])
{
xtend_size[d2] = start[d2] + count[d2];
need_to_extend++;
}
else
xtend_size[d2] = fdims[d2];
if (start[d2] + count[d2] > dim->len)
{
dim->len = start[d2] + count[d2];
dim->extended = NC_TRUE;
}
}
else
{
xtend_size[d2] = dim->len;
}
}
#ifdef USE_PARALLEL
/* Check if anyone wants to extend */
if (h5->parallel && NC_COLLECTIVE == var->parallel_access)
{
/* Form consensus opinion among all processes about whether to perform
* collective I/O
*/
if(MPI_SUCCESS != MPI_Allreduce(MPI_IN_PLACE, &need_to_extend, 1, MPI_INT, MPI_BOR, h5->comm))
BAIL(NC_EMPI);
}
#endif /* USE_PARALLEL */
/* If we need to extend it, we also need a new file_spaceid
to reflect the new size of the space. */
if (need_to_extend)
{
LOG((4, "extending dataset"));
#ifdef USE_PARALLEL
if (h5->parallel)
{
if(NC_COLLECTIVE != var->parallel_access)
BAIL(NC_ECANTEXTEND);
/* Reach consensus about dimension sizes to extend to */
/* (Note: Somewhat hackish, with the use of MPI_INTEGER, but MPI_MAX is
* correct with this usage, as long as it's not executed on
* heterogenous systems)
*/
if(MPI_SUCCESS != MPI_Allreduce(MPI_IN_PLACE, &xtend_size, (var->ndims * (sizeof(hsize_t) / sizeof(int))), MPI_UNSIGNED, MPI_MAX, h5->comm))
BAIL(NC_EMPI);
}
#endif /* USE_PARALLEL */
if (H5Dset_extent(var->hdf_datasetid, xtend_size) < 0)
BAIL(NC_EHDFERR);
if (file_spaceid > 0 && H5Sclose(file_spaceid) < 0)
BAIL2(NC_EHDFERR);
if ((file_spaceid = H5Dget_space(var->hdf_datasetid)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
start, NULL, count, NULL) < 0)
BAIL(NC_EHDFERR);
}
}
#ifndef HDF5_CONVERT
/* Do we need to convert the data? */
if (need_to_convert)
{
if ((retval = nc4_convert_type(data, bufr, mem_nc_type, var->type_info->nc_typeid,
len, &range_error, var->fill_value,
(h5->cmode & NC_CLASSIC_MODEL), is_long, 0)))
BAIL(retval);
}
#endif
/* Write the data. At last! */
LOG((4, "about to H5Dwrite datasetid 0x%x mem_spaceid 0x%x "
"file_spaceid 0x%x", var->hdf_datasetid, mem_spaceid, file_spaceid));
if (H5Dwrite(var->hdf_datasetid, var->type_info->hdf_typeid,
mem_spaceid, file_spaceid, xfer_plistid, bufr) < 0)
BAIL(NC_EHDFERR);
/* Remember that we have written to this var so that Fill Value
* can't be set for it. */
if (!var->written_to)
var->written_to = NC_TRUE;
/* For strict netcdf-3 rules, ignore erange errors between UBYTE
* and BYTE types. */
if ((h5->cmode & NC_CLASSIC_MODEL) &&
(var->type_info->nc_typeid == NC_UBYTE || var->type_info->nc_typeid == NC_BYTE) &&
(mem_nc_type == NC_UBYTE || mem_nc_type == NC_BYTE) &&
range_error)
range_error = 0;
exit:
#ifdef HDF5_CONVERT
if (mem_typeid > 0 && H5Tclose(mem_typeid) < 0)
BAIL2(NC_EHDFERR);
#endif
if (file_spaceid > 0 && H5Sclose(file_spaceid) < 0)
BAIL2(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces--;
#endif
if (mem_spaceid > 0 && H5Sclose(mem_spaceid) < 0)
BAIL2(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces--;
#endif
if (xfer_plistid && (H5Pclose(xfer_plistid) < 0))
BAIL2(NC_EPARINIT);
#ifdef EXTRA_TESTS
num_plists--;
#endif
#ifndef HDF5_CONVERT
if (need_to_convert && bufr) free(bufr);
#endif
/* If there was an error return it, otherwise return any potential
range error value. If none, return NC_NOERR as usual.*/
if (retval)
return retval;
if (range_error)
return NC_ERANGE;
return NC_NOERR;
}
int
nc4_get_vara(NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, nc_type mem_nc_type, int is_long, void *data)
{
NC_GRP_INFO_T *grp, *g;
NC_HDF5_FILE_INFO_T *h5;
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim;
hid_t file_spaceid = 0, mem_spaceid = 0;
hid_t xfer_plistid = 0;
size_t file_type_size;
hsize_t *xtend_size = NULL, count[NC_MAX_VAR_DIMS];
hsize_t fdims[NC_MAX_VAR_DIMS], fmaxdims[NC_MAX_VAR_DIMS];
hsize_t start[NC_MAX_VAR_DIMS];
char *name_to_use;
void *fillvalue = NULL;
int no_read = 0, provide_fill = 0;
int fill_value_size[NC_MAX_VAR_DIMS];
int scalar = 0, retval = NC_NOERR, range_error = 0, i, d2;
void *bufr = NULL;
#ifdef HDF5_CONVERT
hid_t mem_typeid = 0;
#endif
#ifndef HDF5_CONVERT
int need_to_convert = 0;
size_t len = 1;
#endif
/* Find our metadata for this file, group, and var. */
assert(nc);
if ((retval = nc4_find_g_var_nc(nc, ncid, varid, &grp, &var)))
return retval;
h5 = NC4_DATA(nc);
assert(grp && h5 && var && var->name);
LOG((3, "%s: var->name %s mem_nc_type %d is_long %d",
__func__, var->name, mem_nc_type, is_long));
/* Check some stuff about the type and the file. */
if ((retval = check_for_vara(&mem_nc_type, var, h5)))
return retval;
/* Convert from size_t and ptrdiff_t to hssize_t, and hsize_t. */
for (i = 0; i < var->ndims; i++)
{
start[i] = startp[i];
count[i] = countp[i];
}
/* Open this dataset if necessary, also checking for a weird case:
* a non-coordinate (and non-scalar) variable that has the same
* name as a dimension. */
if (var->hdf5_name && strlen(var->hdf5_name) >= strlen(NON_COORD_PREPEND) &&
strncmp(var->hdf5_name, NON_COORD_PREPEND, strlen(NON_COORD_PREPEND)) == 0 &&
var->ndims)
name_to_use = var->hdf5_name;
else
name_to_use = var->name;
if (!var->hdf_datasetid)
if ((var->hdf_datasetid = H5Dopen2(grp->hdf_grpid, name_to_use, H5P_DEFAULT)) < 0)
return NC_ENOTVAR;
/* Get file space of data. */
if ((file_spaceid = H5Dget_space(var->hdf_datasetid)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
/* Check to ensure the user selection is
* valid. H5Sget_simple_extent_dims gets the sizes of all the dims
* and put them in fdims. */
if (H5Sget_simple_extent_dims(file_spaceid, fdims, fmaxdims) < 0)
BAIL(NC_EHDFERR);
#ifdef LOGGING
log_dim_info(var, fdims, fmaxdims, start, count);
#endif
/* Check dimension bounds. Remember that unlimited dimensions can
* put data beyond their current length. */
for (d2 = 0; d2 < var->ndims; d2++)
for (g = grp; g; g = g->parent)
for (dim = g->dim; dim; dim = dim->l.next)
if (dim->dimid == var->dimids[d2])
{
if (dim->unlimited)
{
size_t ulen;
/* We can't go beyond the largest current extent of
the unlimited dim. */
if ((retval = NC4_inq_dim(ncid, dim->dimid, NULL, &ulen)))
BAIL(retval);
/* Check for out of bound requests. */
if (start[d2] >= (hssize_t)ulen && count[d2])
BAIL_QUIET(NC_EINVALCOORDS);
if (start[d2] + count[d2] > ulen)
BAIL_QUIET(NC_EEDGE);
/* Things get a little tricky here. If we're getting
a GET request beyond the end of this var's
current length in an unlimited dimension, we'll
later need to return the fill value for the
variable. */
if (start[d2] >= (hssize_t)fdims[d2])
fill_value_size[d2] = count[d2];
else if (start[d2] + count[d2] > fdims[d2])
fill_value_size[d2] = count[d2] - (fdims[d2] - start[d2]);
else
fill_value_size[d2] = 0;
count[d2] -= fill_value_size[d2];
if (fill_value_size[d2])
provide_fill++;
}
else
{
/* Check for out of bound requests. */
if (start[d2] >= (hssize_t)fdims[d2])
BAIL_QUIET(NC_EINVALCOORDS);
if (start[d2] + count[d2] > fdims[d2])
BAIL_QUIET(NC_EEDGE);
/* Set the fill value boundary */
fill_value_size[d2] = count[d2];
}
}
/* A little quirk: if any of the count values are zero, don't
* read. */
for (d2 = 0; d2 < var->ndims; d2++)
if (count[d2] == 0)
no_read++;
/* Later on, we will need to know the size of this type in the
* file. */
assert(var->type_info->size);
file_type_size = var->type_info->size;
if (!no_read)
{
/* Now you would think that no one would be crazy enough to write
a scalar dataspace with one of the array function calls, but you
would be wrong. So let's check to see if the dataset is
scalar. If it is, we won't try to set up a hyperslab. */
if (H5Sget_simple_extent_type(file_spaceid) == H5S_SCALAR)
{
if ((mem_spaceid = H5Screate(H5S_SCALAR)) < 0)
BAIL(NC_EHDFERR);
scalar++;
#ifdef EXTRA_TESTS
num_spaces++;
#endif
}
else
{
if (H5Sselect_hyperslab(file_spaceid, H5S_SELECT_SET,
start, NULL, count, NULL) < 0)
BAIL(NC_EHDFERR);
/* Create a space for the memory, just big enough to hold the slab
we want. */
if ((mem_spaceid = H5Screate_simple(var->ndims, count, NULL)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
}
/* Fix bug when reading HDF5 files with variable of type
* fixed-length string. We need to make it look like a
* variable-length string, because that's all netCDF-4 data
* model supports, lacking anonymous dimensions. So
* variable-length strings are in allocated memory that user has
* to free, which we allocate here. */
if(var->type_info->nc_type_class == NC_STRING &&
H5Tget_size(var->type_info->hdf_typeid) > 1 &&
!H5Tis_variable_str(var->type_info->hdf_typeid)) {
hsize_t fstring_len;
if ((fstring_len = H5Tget_size(var->type_info->hdf_typeid)) == 0)
BAIL(NC_EHDFERR);
if (!(*(char **)data = malloc(1 + fstring_len)))
BAIL(NC_ENOMEM);
bufr = *(char **)data;
}
#ifndef HDF5_CONVERT
/* Are we going to convert any data? (No converting of compound or
* opaque types.) */
if ((mem_nc_type != var->type_info->nc_typeid || (var->type_info->nc_typeid == NC_INT && is_long)) &&
mem_nc_type != NC_COMPOUND && mem_nc_type != NC_OPAQUE)
{
/* We must convert - allocate a buffer. */
need_to_convert++;
if (var->ndims)
for (d2 = 0; d2 < var->ndims; d2++)
len *= countp[d2];
LOG((4, "converting data for var %s type=%d len=%d", var->name,
var->type_info->nc_typeid, len));
/* If we're reading, we need bufr to have enough memory to store
* the data in the file. If we're writing, we need bufr to be
* big enough to hold all the data in the file's type. */
if(len > 0)
if (!(bufr = malloc(len * file_type_size)))
BAIL(NC_ENOMEM);
}
else
#endif /* ifndef HDF5_CONVERT */
if(!bufr)
bufr = data;
/* Get the HDF type of the data in memory. */
#ifdef HDF5_CONVERT
if ((retval = nc4_get_hdf_typeid(h5, mem_nc_type, &mem_typeid,
var->type_info->endianness)))
BAIL(retval);
#endif
/* Create the data transfer property list. */
if ((xfer_plistid = H5Pcreate(H5P_DATASET_XFER)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists++;
#endif
#ifdef HDF5_CONVERT
/* Apply the callback function which will detect range
* errors. Which one to call depends on the length of the
* destination buffer type. */
if (H5Pset_type_conv_cb(xfer_plistid, except_func, &range_error) < 0)
BAIL(NC_EHDFERR);
#endif
#ifdef USE_PARALLEL
/* Set up parallel I/O, if needed. */
if ((retval = set_par_access(h5, var, xfer_plistid)))
BAIL(retval);
#endif
/* Read this hyperslab into memory. */
LOG((5, "About to H5Dread some data..."));
if (H5Dread(var->hdf_datasetid, var->type_info->native_hdf_typeid,
mem_spaceid, file_spaceid, xfer_plistid, bufr) < 0)
BAIL(NC_EHDFERR);
#ifndef HDF5_CONVERT
/* Eventually the block below will go away. Right now it's
needed to support conversions between int/float, and range
checking converted data in the netcdf way. These features are
being added to HDF5 at the HDF5 World Hall of Coding right
now, by a staff of thousands of programming gnomes. */
if (need_to_convert)
{
if ((retval = nc4_convert_type(bufr, data, var->type_info->nc_typeid, mem_nc_type,
len, &range_error, var->fill_value,
(h5->cmode & NC_CLASSIC_MODEL), 0, is_long)))
BAIL(retval);
/* For strict netcdf-3 rules, ignore erange errors between UBYTE
* and BYTE types. */
if ((h5->cmode & NC_CLASSIC_MODEL) &&
(var->type_info->nc_typeid == NC_UBYTE || var->type_info->nc_typeid == NC_BYTE) &&
(mem_nc_type == NC_UBYTE || mem_nc_type == NC_BYTE) &&
range_error)
range_error = 0;
}
#endif
/* For strict netcdf-3 rules, ignore erange errors between UBYTE
* and BYTE types. */
if ((h5->cmode & NC_CLASSIC_MODEL) &&
(var->type_info->nc_typeid == NC_UBYTE || var->type_info->nc_typeid == NC_BYTE) &&
(mem_nc_type == NC_UBYTE || mem_nc_type == NC_BYTE) &&
range_error)
range_error = 0;
} /* endif ! no_read */
/* Now we need to fake up any further data that was asked for,
using the fill values instead. First skip past the data we
just read, if any. */
if (!scalar && provide_fill)
{
void *filldata;
size_t real_data_size = 0;
size_t fill_len;
/* Skip past the real data we've already read. */
if (!no_read)
for (real_data_size = file_type_size, d2 = 0; d2 < var->ndims; d2++)
real_data_size *= (count[d2] - start[d2]);
/* Get the fill value from the HDF5 variable. Memory will be
* allocated. */
if (get_fill_value(h5, var, &fillvalue) < 0)
BAIL(NC_EHDFERR);
/* How many fill values do we need? */
for (fill_len = 1, d2 = 0; d2 < var->ndims; d2++)
fill_len *= (fill_value_size[d2] ? fill_value_size[d2] : 1);
/* Copy the fill value into the rest of the data buffer. */
filldata = (char *)data + real_data_size;
for (i = 0; i < fill_len; i++)
{
if (var->type_info->nc_type_class == NC_STRING)
{
if (*(char **)fillvalue)
{
if (!(*(char **)filldata = strdup(*(char **)fillvalue)))
BAIL(NC_ENOMEM);
}
else
*(char **)filldata = NULL;
}
else
memcpy(filldata, fillvalue, file_type_size);
filldata = (char *)filldata + file_type_size;
}
}
exit:
#ifdef HDF5_CONVERT
if (mem_typeid > 0 && H5Tclose(mem_typeid) < 0)
BAIL2(NC_EHDFERR);
#endif
if (file_spaceid > 0)
{
if (H5Sclose(file_spaceid) < 0)
BAIL2(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces--;
#endif
}
if (mem_spaceid > 0)
{
if (H5Sclose(mem_spaceid) < 0)
BAIL2(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces--;
#endif
}
if (xfer_plistid > 0)
{
if (H5Pclose(xfer_plistid) < 0)
BAIL2(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists--;
#endif
}
#ifndef HDF5_CONVERT
if (need_to_convert && bufr != NULL)
free(bufr);
#endif
if (xtend_size)
free(xtend_size);
if (fillvalue)
{
if (var->type_info->nc_type_class == NC_VLEN)
nc_free_vlen((nc_vlen_t *)fillvalue);
else if (var->type_info->nc_type_class == NC_STRING && *(char **)fillvalue)
free(*(char **)fillvalue);
free(fillvalue);
}
/* If there was an error return it, otherwise return any potential
range error value. If none, return NC_NOERR as usual.*/
if (retval)
return retval;
if (range_error)
return NC_ERANGE;
return NC_NOERR;
}
/* Read or write an attribute. */
static int
put_att_grpa(NC_GRP_INFO_T *grp, int varid, NC_ATT_INFO_T *att)
{
hid_t datasetid = 0, locid;
hid_t attid = 0, spaceid = 0, file_typeid = 0;
hsize_t dims[1]; /* netcdf attributes always 1-D. */
htri_t attr_exists;
int retval = NC_NOERR;
void *data;
int phoney_data = 99;
assert(att->name);
LOG((3, "%s: varid %d att->attnum %d att->name %s att->nc_typeid %d att->len %d",
__func__, varid, att->attnum, att->name,
att->nc_typeid, att->len));
/* If the file is read-only, return an error. */
if (grp->nc4_info->no_write)
BAIL(NC_EPERM);
/* Get the hid to attach the attribute to, or read it from. */
if (varid == NC_GLOBAL)
locid = grp->hdf_grpid;
else
{
if ((retval = nc4_open_var_grp2(grp, varid, &datasetid)))
BAIL(retval);
locid = datasetid;
}
/* Delete the att if it exists already. */
if ((attr_exists = H5Aexists(locid, att->name)) < 0)
BAIL(NC_EHDFERR);
if (attr_exists)
{
if (H5Adelete(locid, att->name) < 0)
BAIL(NC_EHDFERR);
}
/* Get the length ready, and find the HDF type we'll be
* writing. */
dims[0] = att->len;
if ((retval = nc4_get_hdf_typeid(grp->nc4_info, att->nc_typeid,
&file_typeid, 0)))
BAIL(retval);
/* Even if the length is zero, HDF5 won't let me write with a
* NULL pointer. So if the length of the att is zero, point to
* some phoney data (which won't be written anyway.)*/
if (!dims[0])
data = &phoney_data;
else if (att->data)
data = att->data;
else if (att->stdata)
data = att->stdata;
else
data = att->vldata;
/* NC_CHAR types require some extra work. The space ID is set to
* scalar, and the type is told how long the string is. If it's
* really zero length, set the size to 1. (The fact that it's
* really zero will be marked by the NULL dataspace, but HDF5
* doesn't allow me to set the size of the type to zero.)*/
if (att->nc_typeid == NC_CHAR)
{
size_t string_size = dims[0];
if (!string_size)
{
string_size = 1;
if ((spaceid = H5Screate(H5S_NULL)) < 0)
BAIL(NC_EATTMETA);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
}
else
{
if ((spaceid = H5Screate(H5S_SCALAR)) < 0)
BAIL(NC_EATTMETA);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
}
if (H5Tset_size(file_typeid, string_size) < 0)
BAIL(NC_EATTMETA);
if (H5Tset_strpad(file_typeid, H5T_STR_NULLTERM) < 0)
BAIL(NC_EATTMETA);
}
else
{
if (!att->len)
{
if ((spaceid = H5Screate(H5S_NULL)) < 0)
BAIL(NC_EATTMETA);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
}
else
{
if ((spaceid = H5Screate_simple(1, dims, NULL)) < 0)
BAIL(NC_EATTMETA);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
}
}
if ((attid = H5Acreate(locid, att->name, file_typeid, spaceid,
H5P_DEFAULT)) < 0)
BAIL(NC_EATTMETA);
/* Write the values, (even if length is zero). */
if (H5Awrite(attid, file_typeid, data) < 0)
BAIL(NC_EATTMETA);
exit:
if (file_typeid && H5Tclose(file_typeid))
BAIL2(NC_EHDFERR);
if (attid > 0 && H5Aclose(attid) < 0)
BAIL2(NC_EHDFERR);
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces--;
#endif
return retval;
}
/* Write all the dirty atts in an attlist. */
static int
write_attlist(NC_ATT_INFO_T *attlist, int varid, NC_GRP_INFO_T *grp)
{
NC_ATT_INFO_T *att;
int retval;
for (att = attlist; att; att = att->l.next)
{
if (att->dirty)
{
LOG((4, "%s: writing att %s to varid %d", __func__, att->name, varid));
if ((retval = put_att_grpa(grp, varid, att)))
return retval;
att->dirty = NC_FALSE;
att->created = NC_TRUE;
}
}
return NC_NOERR;
}
/* This function is a bit of a hack. Turns out that HDF5 dimension
* scales cannot themselves have scales attached. This leaves
* multidimensional coordinate variables hosed. So this function
* writes a special attribute for such a variable, which has the ids
* of all the dimensions for that coordinate variable. This sucks,
* really. But that's the way the cookie crumbles. Better luck next
* time. This function also contains a new way of dealing with HDF5
* error handling, abandoning the BAIL macros for a more organic and
* natural approach, made with whole grains, and locally-grown
* vegetables. */
static int
write_coord_dimids(NC_VAR_INFO_T *var)
{
hsize_t coords_len[1];
hid_t c_spaceid = -1, c_attid = -1;
int ret = 0;
/* Write our attribute. */
coords_len[0] = var->ndims;
if ((c_spaceid = H5Screate_simple(1, coords_len, coords_len)) < 0) ret++;
#ifdef EXTRA_TESTS
num_spaces++;
#endif
if (!ret && (c_attid = H5Acreate(var->hdf_datasetid, COORDINATES, H5T_NATIVE_INT,
c_spaceid, H5P_DEFAULT)) < 0) ret++;
if (!ret && H5Awrite(c_attid, H5T_NATIVE_INT, var->dimids) < 0) ret++;
/* Close up shop. */
if (c_spaceid > 0 && H5Sclose(c_spaceid) < 0) ret++;
#ifdef EXTRA_TESTS
num_spaces--;
#endif
if (c_attid > 0 && H5Aclose(c_attid) < 0) ret++;
return ret ? NC_EHDFERR : 0;
}
/* Write a special attribute for the netCDF-4 dimension ID. */
static int
write_netcdf4_dimid(hid_t datasetid, int dimid)
{
hid_t dimid_spaceid, dimid_attid;
htri_t attr_exists;
/* Create the space. */
if ((dimid_spaceid = H5Screate(H5S_SCALAR)) < 0)
return NC_EHDFERR;
#ifdef EXTRA_TESTS
num_spaces++;
#endif
/* Does the attribute already exist? If so, don't try to create it. */
if ((attr_exists = H5Aexists(datasetid, NC_DIMID_ATT_NAME)) < 0)
return NC_EHDFERR;
if (attr_exists)
dimid_attid = H5Aopen_by_name(datasetid, ".", NC_DIMID_ATT_NAME,
H5P_DEFAULT, H5P_DEFAULT);
else
/* Create the attribute if needed. */
dimid_attid = H5Acreate(datasetid, NC_DIMID_ATT_NAME,
H5T_NATIVE_INT, dimid_spaceid, H5P_DEFAULT);
if (dimid_attid < 0)
return NC_EHDFERR;
/* Write it. */
LOG((4, "%s: writing secret dimid %d", __func__, dimid));
if (H5Awrite(dimid_attid, H5T_NATIVE_INT, &dimid) < 0)
return NC_EHDFERR;
/* Close stuff*/
if (H5Sclose(dimid_spaceid) < 0)
return NC_EHDFERR;
#ifdef EXTRA_TESTS
num_spaces--;
#endif
if (H5Aclose(dimid_attid) < 0)
return NC_EHDFERR;
return NC_NOERR;
}
/* This function creates the HDF5 dataset for a variable. */
static int
var_create_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, nc_bool_t write_dimid)
{
NC_GRP_INFO_T *g;
hid_t plistid = 0, access_plistid = 0, typeid = 0, spaceid = 0;
hsize_t chunksize[H5S_MAX_RANK], dimsize[H5S_MAX_RANK], maxdimsize[H5S_MAX_RANK];
int d;
void *fillp = NULL;
NC_DIM_INFO_T *dim = NULL;
int dims_found = 0;
char *name_to_use;
int retval = NC_NOERR;
LOG((3, "%s:: name %s", __func__, var->name));
/* Scalar or not, we need a creation property list. */
if ((plistid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists++;
#endif
if ((access_plistid = H5Pcreate(H5P_DATASET_ACCESS)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists++;
#endif
/* RJ: this suppose to be FALSE that is defined in H5 private.h as 0 */
if (H5Pset_obj_track_times(plistid,0)<0)
BAIL(NC_EHDFERR);
/* Find the HDF5 type of the dataset. */
if ((retval = nc4_get_hdf_typeid(grp->nc4_info, var->type_info->nc_typeid, &typeid,
var->type_info->endianness)))
BAIL(retval);
/* Figure out what fill value to set, if any. */
if (var->no_fill)
{
/* Required to truly turn HDF5 fill values off */
if (H5Pset_fill_time(plistid, H5D_FILL_TIME_NEVER) < 0)
BAIL(NC_EHDFERR);
}
else
{
if ((retval = get_fill_value(grp->nc4_info, var, &fillp)))
BAIL(retval);
/* If there is a fill value, set it. */
if (fillp)
{
if (var->type_info->nc_type_class == NC_STRING)
{
if (H5Pset_fill_value(plistid, typeid, fillp) < 0)
BAIL(NC_EHDFERR);
}
else
{
/* The fill value set in HDF5 must always be presented as
* a native type, even if the endianness for this dataset
* is non-native. HDF5 will translate the fill value to
* the target endiannesss. */
hid_t fill_typeid = 0;
if ((retval = nc4_get_hdf_typeid(grp->nc4_info, var->type_info->nc_typeid, &fill_typeid,
NC_ENDIAN_NATIVE)))
BAIL(retval);
if (H5Pset_fill_value(plistid, fill_typeid, fillp) < 0)
{
if (H5Tclose(fill_typeid) < 0)
BAIL(NC_EHDFERR);
BAIL(NC_EHDFERR);
}
if (H5Tclose(fill_typeid) < 0)
BAIL(NC_EHDFERR);
}
}
}
/* If the user wants to shuffle the data, set that up now. */
if (var->shuffle)
if (H5Pset_shuffle(plistid) < 0)
BAIL(NC_EHDFERR);
/* If the user wants to deflate the data, set that up now. */
if (var->deflate)
if (H5Pset_deflate(plistid, var->deflate_level) < 0)
BAIL(NC_EHDFERR);
/* Szip? NO! We don't want anyone to produce szipped netCDF files! */
/* #ifdef USE_SZIP */
/* if (var->options_mask) */
/* if (H5Pset_szip(plistid, var->options_mask, var->bits_per_pixel) < 0) */
/* BAIL(NC_EHDFERR); */
/* #endif */
/* If the user wants to fletcher error correcton, set that up now. */
if (var->fletcher32)
if (H5Pset_fletcher32(plistid) < 0)
BAIL(NC_EHDFERR);
/* If ndims non-zero, get info for all dimensions. We look up the
dimids and get the len of each dimension. We need this to create
the space for the dataset. In netCDF a dimension length of zero
means an unlimited dimension. */
if (var->ndims)
{
int unlimdim = 0;
/* Check to see if any unlimited dimensions are used in this var. */
for (d = 0; d < var->ndims; d++) {
for (g = grp; g; g = g->parent)
for (dim = g->dim; dim; dim = dim->l.next)
if (dim->dimid == var->dimids[d])
if (dim->unlimited)
unlimdim++;
}
/* If there are no unlimited dims, and no filters, and the user
* has not specified chunksizes, use contiguous variable for
* better performance. */
if(!var->shuffle && !var->deflate && !var->options_mask &&
!var->fletcher32 && (var->chunksizes == NULL || !var->chunksizes[0])) {
#ifdef USE_HDF4
NC_HDF5_FILE_INFO_T *h5 = grp->nc4_info;
if(h5->hdf4 || !unlimdim)
#else
if(!unlimdim)
#endif
var->contiguous = NC_TRUE;
}
/* Gather current & maximum dimension sizes, along with chunk sizes */
for (d = 0; d < var->ndims; d++)
{
for (g = grp; g && (dims_found < var->ndims); g = g->parent)
{
for (dim = g->dim; dim; dim = dim->l.next)
{
if (dim->dimid == var->dimids[d])
{
dimsize[d] = dim->unlimited ? NC_HDF5_UNLIMITED_DIMSIZE : dim->len;
maxdimsize[d] = dim->unlimited ? H5S_UNLIMITED : (hsize_t)dim->len;
if (!var->contiguous) {
if (var->chunksizes[d])
chunksize[d] = var->chunksizes[d];
else
{
size_t type_size;
if (var->type_info->nc_type_class == NC_STRING)
type_size = sizeof(char *);
else
type_size = var->type_info->size;
/* Unlimited dim always gets chunksize of 1. */
if (dim->unlimited)
chunksize[d] = 1;
else
chunksize[d] = pow((double)DEFAULT_CHUNK_SIZE/type_size,
1/(double)(var->ndims - unlimdim));
/* If the chunksize is greater than the dim
* length, make it the dim length. */
if (!dim->unlimited && chunksize[d] > dim->len)
chunksize[d] = dim->len;
/* Remember the computed chunksize */
var->chunksizes[d] = chunksize[d];
}
}
dims_found++;
break;
}
}
}
}
if (var->contiguous)
{
if (H5Pset_layout(plistid, H5D_CONTIGUOUS) < 0)
BAIL(NC_EHDFERR);
}
else
{
if (H5Pset_chunk(plistid, var->ndims, chunksize) < 0)
BAIL(NC_EHDFERR);
}
/* Create the dataspace. */
if ((spaceid = H5Screate_simple(var->ndims, dimsize, maxdimsize)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
}
else
{
if ((spaceid = H5Screate(H5S_SCALAR)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
}
/* Turn on creation order tracking. */
if (H5Pset_attr_creation_order(plistid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0)
BAIL(NC_EHDFERR);
/* Set per-var chunk cache, for chunked datasets. */
if (!var->contiguous && var->chunk_cache_size)
if (H5Pset_chunk_cache(access_plistid, var->chunk_cache_nelems,
var->chunk_cache_size, var->chunk_cache_preemption) < 0)
BAIL(NC_EHDFERR);
/* At long last, create the dataset. */
name_to_use = var->hdf5_name ? var->hdf5_name : var->name;
LOG((4, "%s: about to H5Dcreate2 dataset %s of type 0x%x", __func__,
name_to_use, typeid));
if ((var->hdf_datasetid = H5Dcreate2(grp->hdf_grpid, name_to_use, typeid,
spaceid, H5P_DEFAULT, plistid, access_plistid)) < 0)
BAIL(NC_EHDFERR);
var->created = NC_TRUE;
var->is_new_var = NC_FALSE;
/* If this is a dimscale, mark it as such in the HDF5 file. Also
* find the dimension info and store the dataset id of the dimscale
* dataset. */
if (var->dimscale)
{
if (H5DSset_scale(var->hdf_datasetid, var->name) < 0)
BAIL(NC_EHDFERR);
/* If this is a multidimensional coordinate variable, write a
* coordinates attribute. */
if (var->ndims > 1)
if ((retval = write_coord_dimids(var)))
BAIL(retval);
/* If desired, write the netCDF dimid. */
if (write_dimid)
if ((retval = write_netcdf4_dimid(var->hdf_datasetid, var->dimids[0])))
BAIL(retval);
}
/* Write attributes for this var. */
if ((retval = write_attlist(var->att, var->varid, grp)))
BAIL(retval);
var->attr_dirty = NC_FALSE;
exit:
if (typeid > 0 && H5Tclose(typeid) < 0)
BAIL2(NC_EHDFERR);
if (plistid > 0 && H5Pclose(plistid) < 0)
BAIL2(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists--;
#endif
if (access_plistid > 0 && H5Pclose(access_plistid) < 0)
BAIL2(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists--;
#endif
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces--;
#endif
if (fillp)
{
if (var->type_info->nc_type_class == NC_VLEN)
nc_free_vlen((nc_vlen_t *)fillp);
else if (var->type_info->nc_type_class == NC_STRING && *(char **)fillp)
free(*(char **)fillp);
free(fillp);
}
return retval;
}
/* Adjust the chunk cache of a var for better performance. */
int
nc4_adjust_var_cache(NC_GRP_INFO_T *grp, NC_VAR_INFO_T * var)
{
size_t chunk_size_bytes = 1;
int d;
int retval;
/* Nothing to be done. */
if (var->contiguous)
return NC_NOERR;
#ifdef USE_PARALLEL
return NC_NOERR;
#endif
/* How many bytes in the chunk? */
for (d = 0; d < var->ndims; d++)
chunk_size_bytes *= var->chunksizes[d];
if (var->type_info->size)
chunk_size_bytes *= var->type_info->size;
else
chunk_size_bytes *= sizeof(char *);
/* If the chunk cache is too small, and the user has not changed
* the default value of the chunk cache size, then increase the
* size of the cache. */
if (var->chunk_cache_size == CHUNK_CACHE_SIZE)
if (chunk_size_bytes > var->chunk_cache_size)
{
var->chunk_cache_size = chunk_size_bytes * DEFAULT_CHUNKS_IN_CACHE;
if (var->chunk_cache_size > MAX_DEFAULT_CACHE_SIZE)
var->chunk_cache_size = MAX_DEFAULT_CACHE_SIZE;
if ((retval = nc4_reopen_dataset(grp, var)))
return retval;
}
return NC_NOERR;
}
/* Create a HDF5 defined type from a NC_TYPE_INFO_T struct, and commit
* it to the file. */
static int
commit_type(NC_GRP_INFO_T *grp, NC_TYPE_INFO_T *type)
{
int retval;
assert(grp && type);
/* Did we already record this type? */
if (type->committed)
return NC_NOERR;
/* Is this a compound type? */
if (type->nc_type_class == NC_COMPOUND)
{
NC_FIELD_INFO_T *field;
hid_t hdf_base_typeid, hdf_typeid;
if ((type->hdf_typeid = H5Tcreate(H5T_COMPOUND, type->size)) < 0)
return NC_EHDFERR;
LOG((4, "creating compound type %s hdf_typeid 0x%x", type->name,
type->hdf_typeid));
for (field = type->u.c.field; field; field = field->l.next)
{
if ((retval = nc4_get_hdf_typeid(grp->nc4_info, field->nc_typeid,
&hdf_base_typeid, type->endianness)))
return retval;
/* If this is an array, create a special array type. */
if (field->ndims)
{
int d;
hsize_t dims[NC_MAX_VAR_DIMS];
for (d = 0; d < field->ndims; d++)
dims[d] = field->dim_size[d];
if ((hdf_typeid = H5Tarray_create(hdf_base_typeid, field->ndims,
dims, NULL)) < 0)
{
if (H5Tclose(hdf_base_typeid) < 0)
return NC_EHDFERR;
return NC_EHDFERR;
}
if (H5Tclose(hdf_base_typeid) < 0)
return NC_EHDFERR;
}
else
hdf_typeid = hdf_base_typeid;
LOG((4, "inserting field %s offset %d hdf_typeid 0x%x", field->name,
field->offset, hdf_typeid));
if (H5Tinsert(type->hdf_typeid, field->name, field->offset,
hdf_typeid) < 0)
return NC_EHDFERR;
if (H5Tclose(hdf_typeid) < 0)
return NC_EHDFERR;
}
}
else if (type->nc_type_class == NC_VLEN)
{
/* Find the HDF typeid of the base type of this vlen. */
if ((retval = nc4_get_hdf_typeid(grp->nc4_info, type->u.v.base_nc_typeid,
&type->u.v.base_hdf_typeid, type->endianness)))
return retval;
/* Create a vlen type. */
if ((type->hdf_typeid = H5Tvlen_create(type->u.v.base_hdf_typeid)) < 0)
return NC_EHDFERR;
}
else if (type->nc_type_class == NC_OPAQUE)
{
/* Create the opaque type. */
if ((type->hdf_typeid = H5Tcreate(H5T_OPAQUE, type->size)) < 0)
return NC_EHDFERR;
}
else if (type->nc_type_class == NC_ENUM)
{
NC_ENUM_MEMBER_INFO_T *enum_m;
if (!type->u.e.enum_member)
return NC_EINVAL;
/* Find the HDF typeid of the base type of this enum. */
if ((retval = nc4_get_hdf_typeid(grp->nc4_info, type->u.e.base_nc_typeid,
&type->u.e.base_hdf_typeid, type->endianness)))
return retval;
/* Create an enum type. */
if ((type->hdf_typeid = H5Tenum_create(type->u.e.base_hdf_typeid)) < 0)
return NC_EHDFERR;
/* Add all the members to the HDF5 type. */
for (enum_m = type->u.e.enum_member; enum_m; enum_m = enum_m->l.next)
if (H5Tenum_insert(type->hdf_typeid, enum_m->name, enum_m->value) < 0)
return NC_EHDFERR;
}
else
{
LOG((0, "Unknown class: %d", type->nc_type_class));
return NC_EBADTYPE;
}
/* Commit the type. */
if (H5Tcommit(grp->hdf_grpid, type->name, type->hdf_typeid) < 0)
return NC_EHDFERR;
type->committed = NC_TRUE;
LOG((4, "just committed type %s, HDF typeid: 0x%x", type->name,
type->hdf_typeid));
/* Later we will always use the native typeid. In this case, it is
* a copy of the same type pointed to by hdf_typeid, but it's
* easier to maintain a copy. */
if ((type->native_hdf_typeid = H5Tget_native_type(type->hdf_typeid,
H5T_DIR_DEFAULT)) < 0)
return NC_EHDFERR;
return NC_NOERR;
}
/* Write an attribute, with value 1, to indicate that strict NC3 rules
* apply to this file. */
static int
write_nc3_strict_att(hid_t hdf_grpid)
{
hid_t attid = 0, spaceid = 0;
int one = 1, num, a;
char att_name[NC_MAX_NAME + 1];
int retval = NC_NOERR;
/* If the attribute already exists, call that a success and return
* NC_NOERR. */
if ((num = H5Aget_num_attrs(hdf_grpid)) < 0)
return NC_EHDFERR;
for (a = 0; a < num; a++)
{
if ((attid = H5Aopen_idx(hdf_grpid, (unsigned int)a)) < 0)
BAIL(NC_EHDFERR);
if (H5Aget_name(attid, NC_MAX_HDF5_NAME, att_name) < 0)
BAIL(NC_EHDFERR);
if (!strcmp(att_name, NC3_STRICT_ATT_NAME))
{
if (H5Aclose(attid) < 0)
return NC_EFILEMETA;
return NC_NOERR;
}
}
/* Create the attribute to mark this as a file that needs to obey
* strict netcdf-3 rules. */
if ((spaceid = H5Screate(H5S_SCALAR)) < 0)
BAIL(NC_EFILEMETA);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
if ((attid = H5Acreate(hdf_grpid, NC3_STRICT_ATT_NAME,
H5T_NATIVE_INT, spaceid, H5P_DEFAULT)) < 0)
BAIL(NC_EFILEMETA);
if (H5Awrite(attid, H5T_NATIVE_INT, &one) < 0)
BAIL(NC_EFILEMETA);
exit:
if (spaceid && (H5Sclose(spaceid) < 0))
BAIL2(NC_EFILEMETA);
#ifdef EXTRA_TESTS
num_spaces--;
#endif
if (attid && (H5Aclose(attid) < 0))
BAIL2(NC_EFILEMETA);
return retval;
}
static int
create_group(NC_GRP_INFO_T *grp)
{
hid_t gcpl_id = 0;
int retval = NC_NOERR;;
assert(grp);
/* If this is not the root group, create it in the HDF5 file. */
if (grp->parent)
{
/* Create group, with link_creation_order set in the group
* creation property list. */
if ((gcpl_id = H5Pcreate(H5P_GROUP_CREATE)) < 0)
return NC_EHDFERR;
#ifdef EXTRA_TESTS
num_plists++;
#endif
/* RJ: this suppose to be FALSE that is defined in H5 private.h as 0 */
if (H5Pset_obj_track_times(gcpl_id,0)<0)
BAIL(NC_EHDFERR);
if (H5Pset_link_creation_order(gcpl_id, H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEXED) < 0)
BAIL(NC_EHDFERR);
if (H5Pset_attr_creation_order(gcpl_id, H5P_CRT_ORDER_TRACKED|H5P_CRT_ORDER_INDEXED) < 0)
BAIL(NC_EHDFERR);
if ((grp->hdf_grpid = H5Gcreate2(grp->parent->hdf_grpid, grp->name,
H5P_DEFAULT, gcpl_id, H5P_DEFAULT)) < 0)
BAIL(NC_EHDFERR);
if (H5Pclose(gcpl_id) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists--;
#endif
}
else
{
/* Since this is the root group, we have to open it. */
if ((grp->hdf_grpid = H5Gopen2(grp->nc4_info->hdfid, "/", H5P_DEFAULT)) < 0)
BAIL(NC_EFILEMETA);
}
return NC_NOERR;
exit:
if (gcpl_id > 0 && H5Pclose(gcpl_id) < 0)
BAIL2(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists--;
#endif
if (grp->hdf_grpid > 0 && H5Gclose(grp->hdf_grpid) < 0)
BAIL2(NC_EHDFERR);
return retval;
}
/* After all the datasets of the file have been read, it's time to
* sort the wheat from the chaff. Which of the datasets are netCDF
* dimensions, and which are coordinate variables, and which are
* non-coordinate variables. */
static int
attach_dimscales(NC_GRP_INFO_T *grp)
{
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim1;
NC_GRP_INFO_T *g;
int d;
int retval = NC_NOERR;
/* Attach dimension scales. */
for (var = grp->var; var; var = var->l.next)
{
/* Scales themselves do not attach. But I really wish they
* would. */
if (var->dimscale)
{
/* If this is a multidimensional coordinate variable, it will
* have a special coords attribute (read earlier) with a list
* of the dimensions for this variable. */
}
else /* not a dimscale... */
{
/* Find the scale for each dimension and attach it. */
for (d = 0; d < var->ndims; d++)
{
/* Is there a dimscale for this dimension? */
if (var->dimscale_attached)
{
if (!var->dimscale_attached[d])
{
for (g = grp; g && !var->dimscale_attached[d]; g = g->parent)
for (dim1 = g->dim; dim1; dim1 = dim1->l.next)
if (var->dimids[d] == dim1->dimid)
{
hid_t dim_datasetid; /* Dataset ID for dimension */
LOG((2, "%s: attaching scale for dimid %d to var %s",
__func__, var->dimids[d], var->name));
/* Find dataset ID for dimension */
if (dim1->coord_var)
dim_datasetid = dim1->coord_var->hdf_datasetid;
else
dim_datasetid = dim1->hdf_dimscaleid;
assert(dim_datasetid > 0);
if (H5DSattach_scale(var->hdf_datasetid, dim_datasetid, d) < 0)
BAIL(NC_EHDFERR);
var->dimscale_attached[d] = NC_TRUE;
break;
}
}
/* If we didn't find a dimscale to attach, that's a problem! */
if (!var->dimscale_attached[d])
{
LOG((0, "no dimscale found!"));
return NC_EDIMSCALE;
}
}
else
{
/* Create a phoney dimension! */
}
}
} /* next d */
}
exit:
return retval;
}
static int
var_exists(hid_t grpid, char *name, nc_bool_t *exists)
{
htri_t link_exists;
/* Reset the boolean */
*exists = NC_FALSE;
/* Check if the object name exists in the group */
if ((link_exists = H5Lexists(grpid, name, H5P_DEFAULT)) < 0)
return NC_EHDFERR;
if (link_exists)
{
H5G_stat_t statbuf;
/* Get info about the object */
if (H5Gget_objinfo(grpid, name, 1, &statbuf) < 0)
return NC_EHDFERR;
if (H5G_DATASET == statbuf.type)
*exists = NC_TRUE;
}
return NC_NOERR;
}
/* This function writes a variable. The principle difficulty comes
* from the possibility that this is a coordinate variable, and was
* already written to the file as a dimension-only dimscale. If this
* occurs, then it must be deleted and recreated. */
static int
write_var(NC_VAR_INFO_T *var, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
{
nc_bool_t replace_existing_var = NC_FALSE;
int retval;
LOG((4, "%s: writing var %s", __func__, var->name));
/* If the variable has already been created & the fill value changed,
* indicate that the existing variable should be replaced. */
if (var->created && var->fill_val_changed)
{
replace_existing_var = NC_TRUE;
var->fill_val_changed = NC_FALSE;
}
/* Is this a coordinate var that has already been created in
* the HDF5 file as a dimscale dataset? Check for dims with the
* same name in this group. If there is one, check to see if
* this object exists in the HDF group. */
if (var->became_coord_var)
{
NC_DIM_INFO_T *d1;
for (d1 = grp->dim; d1; d1 = d1->l.next)
if (!strcmp(d1->name, var->name))
{
nc_bool_t exists;
if ((retval = var_exists(grp->hdf_grpid, var->name, &exists)))
return retval;
if (exists)
{
/* Indicate that the variable already exists, and should be replaced */
replace_existing_var = NC_TRUE;
break;
}
}
}
/* Check dims if the variable will be replaced, so that the dimensions
* will be de-attached and re-attached correctly. */
/* (Note: There's a temptation to merge this loop over the dimensions with
* the prior loop over dimensions, but that blurs the line over the
* purpose of them, so they are currently separate. If performance
* becomes an issue here, it would be possible to merge them. -QAK)
*/
if (replace_existing_var)
{
NC_DIM_INFO_T *d1;
for (d1 = grp->dim; d1; d1 = d1->l.next)
if (!strcmp(d1->name, var->name))
{
nc_bool_t exists;
if ((retval = var_exists(grp->hdf_grpid, var->name, &exists)))
return retval;
if (exists)
{
hid_t dim_datasetid; /* Dataset ID for dimension */
/* Find dataset ID for dimension */
if (d1->coord_var)
dim_datasetid = d1->coord_var->hdf_datasetid;
else
dim_datasetid = d1->hdf_dimscaleid;
assert(dim_datasetid > 0);
/* If we're replacing an existing dimscale dataset, go to
* every var in the file and detach this dimension scale,
* because we have to delete it. */
if ((retval = rec_detach_scales(grp->nc4_info->root_grp,
var->dimids[0], dim_datasetid)))
return retval;
break;
}
}
}
/* If this is not a dimension scale, do this stuff. */
if (var->was_coord_var && var->dimscale_attached)
{
/* If the variable already exists in the file, Remove any dimension scale
* attributes from it, if they exist. */
/* (The HDF5 Dimension Scale API should really have an API routine
* for making a dataset not a scale. -QAK) */
if (var->created)
{
htri_t attr_exists;
/* (We could do a better job here and verify that the attributes are
* really dimension scale 'CLASS' & 'NAME' attributes, but that would be
* poking about in the HDF5 DimScale internal data) */
if ((attr_exists = H5Aexists(var->hdf_datasetid, "CLASS")) < 0)
BAIL(NC_EHDFERR);
if (attr_exists)
{
if (H5Adelete(var->hdf_datasetid, "CLASS") < 0)
BAIL(NC_EHDFERR);
}
if ((attr_exists = H5Aexists(var->hdf_datasetid, "NAME")) < 0)
BAIL(NC_EHDFERR);
if (attr_exists)
{
if (H5Adelete(var->hdf_datasetid, "NAME") < 0)
BAIL(NC_EHDFERR);
}
}
if (var->dimscale_attached)
{
int dims_detached = 0;
nc_bool_t finished = NC_FALSE;
int d;
/* If this is a regular var, detach all its dim scales. */
for (d = 0; d < var->ndims; d++)
if (var->dimscale_attached[d])
{
NC_GRP_INFO_T *g;
for (g = grp; g && !finished; g = g->parent)
{
NC_DIM_INFO_T *dim1;
for (dim1 = g->dim; dim1; dim1 = dim1->l.next)
if (var->dimids[d] == dim1->dimid)
{
hid_t dim_datasetid; /* Dataset ID for dimension */
/* Find dataset ID for dimension */
if (dim1->coord_var)
dim_datasetid = dim1->coord_var->hdf_datasetid;
else
dim_datasetid = dim1->hdf_dimscaleid;
assert(dim_datasetid > 0);
if (H5DSdetach_scale(var->hdf_datasetid, dim_datasetid, d) < 0)
BAIL(NC_EHDFERR);
var->dimscale_attached[d] = NC_FALSE;
if (dims_detached++ == var->ndims)
finished = NC_TRUE;
}
}
}
}
}
/* Delete the HDF5 dataset that is to be replaced. */
if (replace_existing_var)
{
/* Free the HDF5 dataset id. */
if (var->hdf_datasetid && H5Dclose(var->hdf_datasetid) < 0)
BAIL(NC_EHDFERR);
var->hdf_datasetid = 0;
/* Now delete the variable. */
if (H5Gunlink(grp->hdf_grpid, var->name) < 0)
return NC_EDIMMETA;
}
/* Create the dataset. */
if (var->is_new_var || replace_existing_var)
{
if ((retval = var_create_dataset(grp, var, write_dimid)))
return retval;
}
else
{
if (write_dimid && var->ndims)
if ((retval = write_netcdf4_dimid(var->hdf_datasetid, var->dimids[0])))
BAIL(retval);
}
if (replace_existing_var)
{
/* If this is a dimension scale, reattach the scale everywhere it
* is used. (Recall that netCDF dimscales are always 1-D). */
if(var->dimscale)
{
if ((retval = rec_reattach_scales(grp->nc4_info->root_grp,
var->dimids[0], var->hdf_datasetid)))
return retval;
}
/* If it's not a dimension scale, clear the dimscale attached flags,
* so the dimensions are re-attached. */
else
{
if (var->dimscale_attached)
memset(var->dimscale_attached, 0, sizeof(nc_bool_t) * var->ndims);
}
}
/* Clear coord. var state transition flags */
var->was_coord_var = NC_FALSE;
var->became_coord_var = NC_FALSE;
/* Now check the attributes for this var. */
if (var->attr_dirty)
{
/* Write attributes for this var. */
if ((retval = write_attlist(var->att, var->varid, grp)))
BAIL(retval);
var->attr_dirty = NC_FALSE;
}
return NC_NOERR;
exit:
return retval;
}
static int
write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, nc_bool_t write_dimid)
{
int retval;
/* If there's no dimscale dataset for this dim, create one,
* and mark that it should be hidden from netCDF as a
* variable. (That is, it should appear as a dimension
* without an associated variable.) */
if (0 == dim->hdf_dimscaleid)
{
hid_t spaceid, create_propid;
hsize_t dims[1], max_dims[1], chunk_dims[1] = {1};
char dimscale_wo_var[NC_MAX_NAME];
LOG((4, "%s: creating dim %s", __func__, dim->name));
/* Sanity check */
assert(NULL == dim->coord_var);
/* Create a property list. If this dimension scale is
* unlimited (i.e. it's an unlimited dimension), then set
* up chunking, with a chunksize of 1. */
if ((create_propid = H5Pcreate(H5P_DATASET_CREATE)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists++;
#endif
/* RJ: this suppose to be FALSE that is defined in H5 private.h as 0 */
if (H5Pset_obj_track_times(create_propid,0)<0)
BAIL(NC_EHDFERR);
dims[0] = dim->len;
max_dims[0] = dim->len;
if (dim->unlimited)
{
max_dims[0] = H5S_UNLIMITED;
if (H5Pset_chunk(create_propid, 1, chunk_dims) < 0)
BAIL(NC_EHDFERR);
}
/* Set up space. */
if ((spaceid = H5Screate_simple(1, dims, max_dims)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces++;
#endif
if (H5Pset_attr_creation_order(create_propid, H5P_CRT_ORDER_TRACKED|
H5P_CRT_ORDER_INDEXED) < 0)
BAIL(NC_EHDFERR);
/* Create the dataset that will be the dimension scale. */
LOG((4, "%s: about to H5Dcreate1 a dimscale dataset %s", __func__, dim->name));
if ((dim->hdf_dimscaleid = H5Dcreate1(grp->hdf_grpid, dim->name, H5T_IEEE_F32BE,
spaceid, create_propid)) < 0)
BAIL(NC_EHDFERR);
/* Close the spaceid and create_propid. */
if (H5Sclose(spaceid) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_spaces--;
#endif
if (H5Pclose(create_propid) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists--;
#endif
/* Indicate that this is a scale. Also indicate that not
* be shown to the user as a variable. It is hidden. It is
* a DIM WITHOUT A VARIABLE! */
sprintf(dimscale_wo_var, "%s%10d", DIM_WITHOUT_VARIABLE, (int)dim->len);
if (H5DSset_scale(dim->hdf_dimscaleid, dimscale_wo_var) < 0)
BAIL(NC_EHDFERR);
}
/* Did we extend an unlimited dimension? */
if (dim->extended)
{
NC_VAR_INFO_T *v1;
assert(dim->unlimited);
/* If this is a dimension without a variable, then update
* the secret length information at the end of the NAME
* attribute. */
for (v1 = grp->var; v1; v1 = v1->l.next)
if (!strcmp(v1->name, dim->name))
break;
if (v1)
{
hsize_t *new_size = NULL;
NC_GRP_INFO_T *g;
NC_DIM_INFO_T *dim1;
int d1;
/* Extend the dimension scale dataset to reflect the new
* length of the dimension. */
if (!(new_size = malloc(v1->ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
for (d1 = 0; d1 < v1->ndims; d1++)
{
if (v1->dimids[d1] == dim->dimid)
new_size[d1] = dim->len;
else
{
int break_it = 0;
for (g = grp; g && !break_it; g = g->parent)
for (dim1 = g->dim; dim1; dim1 = dim1->l.next)
if (dim1->dimid == v1->dimids[d1])
{
new_size[d1] = dim1->len;
break_it++;
break;
}
}
}
if (H5Dset_extent(v1->hdf_datasetid, new_size) < 0) {
free(new_size);
BAIL(NC_EHDFERR);
}
free(new_size);
}
}
/* If desired, write the secret dimid. This will be used instead of
* the dimid that the dimension would otherwise receive based on
* creation order. This can be necessary when dims and their
* coordinate variables were created in different order. */
if (write_dimid && dim->hdf_dimscaleid)
if ((retval = write_netcdf4_dimid(dim->hdf_dimscaleid, dim->dimid)))
BAIL(retval);
return NC_NOERR;
exit:
return retval;
}
/* Recursively determine if there is a mismatch between order of
* coordinate creation and associated dimensions in this group or any
* subgroups, to find out if we have to handle that situation. Also
* check if there are any multidimensional coordinate variables
* defined, which require the same treatment to fix a potential bug
* when such variables occur in subgroups. */
int
nc4_rec_detect_need_to_preserve_dimids(NC_GRP_INFO_T *grp, nc_bool_t *bad_coord_orderp)
{
NC_VAR_INFO_T *var;
NC_GRP_INFO_T *child_grp;
int last_dimid = -1;
int retval;
/* Iterate over variables in this group */
for (var = grp->var; var; var = var->l.next)
{
/* Only matters for dimension scale variables, with non-scalar dimensionality */
if (var->dimscale && var->ndims)
{
/* If the user writes coord vars in a different order then he
* defined their dimensions, then, when the file is reopened, the
* order of the dimids will change to match the order of the coord
* vars. Detect if this is about to happen. */
if (var->dimids[0] < last_dimid)
{
LOG((5, "%s: %s is out of order coord var", __func__, var->name));
*bad_coord_orderp = NC_TRUE;
return NC_NOERR;
}
last_dimid = var->dimids[0];
/* If there are multidimensional coordinate variables defined, then
* it's also necessary to preserve dimension IDs when the file is
* reopened ... */
if (var->ndims > 1)
{
LOG((5, "%s: %s is multidimensional coord var", __func__, var->name));
*bad_coord_orderp = NC_TRUE;
return NC_NOERR;
}
/* Did the user define a dimension, end define mode, reenter define
* mode, and then define a coordinate variable for that dimension?
* If so, dimensions will be out of order. */
if (var->is_new_var || var->became_coord_var)
{
LOG((5, "%s: coord var defined after enddef/redef", __func__));
*bad_coord_orderp = NC_TRUE;
return NC_NOERR;
}
}
}
/* If there are any child groups, check them also for this condition. */
for (child_grp = grp->children; child_grp; child_grp = child_grp->l.next)
if ((retval = nc4_rec_detect_need_to_preserve_dimids(child_grp, bad_coord_orderp)))
return retval;
return NC_NOERR;
}
/* Recursively write all the metadata in a group. Groups and types
* have all already been written. Propagate bad cooordinate order to
* subgroups, if detected. */
int
nc4_rec_write_metadata(NC_GRP_INFO_T *grp, nc_bool_t bad_coord_order)
{
NC_DIM_INFO_T *dim;
NC_VAR_INFO_T *var;
NC_GRP_INFO_T *child_grp;
int coord_varid = -1;
int retval;
assert(grp && grp->name && grp->hdf_grpid);
LOG((3, "%s: grp->name %s, bad_coord_order %d", __func__, grp->name, bad_coord_order));
/* Write global attributes for this group. */
if ((retval = write_attlist(grp->att, NC_GLOBAL, grp)))
return retval;
/* Set the pointers to the beginning of the list of dims & vars in this
* group. */
dim = grp->dim;
var = grp->var;
/* Because of HDF5 ordering the dims and vars have to be stored in
* this way to ensure that the dims and coordinate vars come out in
* the correct order. */
while (dim || var)
{
nc_bool_t found_coord, wrote_coord;
/* Write non-coord dims in order, stopping at the first one that
* has an associated coord var. */
for (found_coord = NC_FALSE; dim && !found_coord; dim = dim->l.next)
{
if (!dim->coord_var)
{
if ((retval = write_dim(dim, grp, bad_coord_order)))
return retval;
}
else
{
coord_varid = dim->coord_var->varid;
found_coord = NC_TRUE;
}
}
/* Write each var. When we get to the coord var we are waiting
* for (if any), then we break after writing it. */
for (wrote_coord = NC_FALSE; var && !wrote_coord; var = var->l.next)
{
if ((retval = write_var(var, grp, bad_coord_order)))
return retval;
if (found_coord && var->varid == coord_varid)
wrote_coord = NC_TRUE;
}
} /* end while */
if ((retval = attach_dimscales(grp)))
return retval;
/* If there are any child groups, write their metadata. */
for (child_grp = grp->children; child_grp; child_grp = child_grp->l.next)
if ((retval = nc4_rec_write_metadata(child_grp, bad_coord_order)))
return retval;
return NC_NOERR;
}
/* Recursively write all groups and types. */
int
nc4_rec_write_groups_types(NC_GRP_INFO_T *grp)
{
NC_GRP_INFO_T *child_grp;
NC_TYPE_INFO_T *type;
int retval;
assert(grp && grp->name);
LOG((3, "%s: grp->name %s", __func__, grp->name));
/* Create the group in the HDF5 file if it doesn't exist. */
if (!grp->hdf_grpid)
if ((retval = create_group(grp)))
return retval;
/* If this is the root group of a file with strict NC3 rules, write
* an attribute. But don't leave the attribute open. */
if (!grp->parent && (grp->nc4_info->cmode & NC_CLASSIC_MODEL))
if ((retval = write_nc3_strict_att(grp->hdf_grpid)))
return retval;
/* If there are any user-defined types, write them now. */
for (type = grp->type; type; type = type->l.next)
if ((retval = commit_type(grp, type)))
return retval;
/* If there are any child groups, write their groups and types. */
for (child_grp = grp->children; child_grp; child_grp = child_grp->l.next)
if ((retval = nc4_rec_write_groups_types(child_grp)))
return retval;
return NC_NOERR;
}
/*! Copy data from one buffer to another, performing appropriate data conversion.
This function will copy data from one buffer to another, in
accordance with the types. Range errors will be noted, and the fill
value used (or the default fill value if none is supplied) for
values that overflow the type.
I should be able to take this out when HDF5 does the right thing
with data type conversion.
Ed Hartnett, 11/15/3
*/
int
nc4_convert_type(const void *src, void *dest,
const nc_type src_type, const nc_type dest_type,
const size_t len, int *range_error,
const void *fill_value, int strict_nc3, int src_long,
int dest_long)
{
char *cp, *cp1;
float *fp, *fp1;
double *dp, *dp1;
int *ip, *ip1;
signed long *lp, *lp1;
short *sp, *sp1;
signed char *bp, *bp1;
unsigned char *ubp, *ubp1;
unsigned short *usp, *usp1;
unsigned int *uip, *uip1;
long long *lip, *lip1;
unsigned long long *ulip, *ulip1;
size_t count = 0;
*range_error = 0;
LOG((3, "%s: len %d src_type %d dest_type %d src_long %d dest_long %d",
__func__, len, src_type, dest_type, src_long, dest_long));
/* OK, this is ugly. If you can think of anything better, I'm open
to suggestions!
Note that we don't use a default fill value for type
NC_BYTE. This is because Lord Voldemort cast a nofilleramous spell
at Harry Potter, but it bounced off his scar and hit the netcdf-4
code.
*/
switch (src_type)
{
case NC_CHAR:
switch (dest_type)
{
case NC_CHAR:
for (cp = (char *)src, cp1 = dest; count < len; count++)
*cp1++ = *cp++;
break;
default:
LOG((0, "%s: Uknown destination type.", __func__));
}
break;
case NC_BYTE:
switch (dest_type)
{
case NC_BYTE:
for (bp = (signed char *)src, bp1 = dest; count < len; count++)
*bp1++ = *bp++;
break;
case NC_UBYTE:
for (bp = (signed char *)src, ubp = dest; count < len; count++)
{
if (*bp < 0)
(*range_error)++;
*ubp++ = *bp++;
}
break;
case NC_SHORT:
for (bp = (signed char *)src, sp = dest; count < len; count++)
*sp++ = *bp++;
break;
case NC_USHORT:
for (bp = (signed char *)src, usp = dest; count < len; count++)
{
if (*bp < 0)
(*range_error)++;
*usp++ = *bp++;
}
break;
case NC_INT:
if (dest_long)
{
for (bp = (signed char *)src, lp = dest; count < len; count++)
*lp++ = *bp++;
break;
}
else
{
for (bp = (signed char *)src, ip = dest; count < len; count++)
*ip++ = *bp++;
break;
}
case NC_UINT:
for (bp = (signed char *)src, uip = dest; count < len; count++)
{
if (*bp < 0)
(*range_error)++;
*uip++ = *bp++;
}
break;
case NC_INT64:
for (bp = (signed char *)src, lip = dest; count < len; count++)
*lip++ = *bp++;
break;
case NC_UINT64:
for (bp = (signed char *)src, ulip = dest; count < len; count++)
{
if (*bp < 0)
(*range_error)++;
*ulip++ = *bp++;
}
break;
case NC_FLOAT:
for (bp = (signed char *)src, fp = dest; count < len; count++)
*fp++ = *bp++;
break;
case NC_DOUBLE:
for (bp = (signed char *)src, dp = dest; count < len; count++)
*dp++ = *bp++;
break;
default:
LOG((0, "%s: unexpected dest type. src_type %d, dest_type %d",
__func__, src_type, dest_type));
return NC_EBADTYPE;
}
break;
case NC_UBYTE:
switch (dest_type)
{
case NC_BYTE:
for (ubp = (unsigned char *)src, bp = dest; count < len; count++)
{
if (!strict_nc3 && *ubp > X_SCHAR_MAX)
(*range_error)++;
*bp++ = *ubp++;
}
break;
case NC_SHORT:
for (ubp = (unsigned char *)src, sp = dest; count < len; count++)
*sp++ = *ubp++;
break;
case NC_UBYTE:
for (ubp = (unsigned char *)src, ubp1 = dest; count < len; count++)
*ubp1++ = *ubp++;
break;
case NC_USHORT:
for (ubp = (unsigned char *)src, usp = dest; count < len; count++)
*usp++ = *ubp++;
break;
case NC_INT:
if (dest_long)
{
for (ubp = (unsigned char *)src, lp = dest; count < len; count++)
*lp++ = *ubp++;
break;
}
else
{
for (ubp = (unsigned char *)src, ip = dest; count < len; count++)
*ip++ = *ubp++;
break;
}
case NC_UINT:
for (ubp = (unsigned char *)src, uip = dest; count < len; count++)
*uip++ = *ubp++;
break;
case NC_INT64:
for (ubp = (unsigned char *)src, lip = dest; count < len; count++)
*lip++ = *ubp++;
break;
case NC_UINT64:
for (ubp = (unsigned char *)src, ulip = dest; count < len; count++)
*ulip++ = *ubp++;
break;
case NC_FLOAT:
for (ubp = (unsigned char *)src, fp = dest; count < len; count++)
*fp++ = *ubp++;
break;
case NC_DOUBLE:
for (ubp = (unsigned char *)src, dp = dest; count < len; count++)
*dp++ = *ubp++;
break;
default:
LOG((0, "%s: unexpected dest type. src_type %d, dest_type %d",
__func__, src_type, dest_type));
return NC_EBADTYPE;
}
break;
case NC_SHORT:
switch (dest_type)
{
case NC_UBYTE:
for (sp = (short *)src, ubp = dest; count < len; count++)
{
if (*sp > X_UCHAR_MAX || *sp < 0)
(*range_error)++;
*ubp++ = *sp++;
}
break;
case NC_BYTE:
for (sp = (short *)src, bp = dest; count < len; count++)
{
if (*sp > X_SCHAR_MAX || *sp < X_SCHAR_MIN)
(*range_error)++;
*bp++ = *sp++;
}
break;
case NC_SHORT:
for (sp = (short *)src, sp1 = dest; count < len; count++)
*sp1++ = *sp++;
break;
case NC_USHORT:
for (sp = (short *)src, usp = dest; count < len; count++)
{
if (*sp < 0)
(*range_error)++;
*usp++ = *sp++;
}
break;
case NC_INT:
if (dest_long)
for (sp = (short *)src, lp = dest; count < len; count++)
*lp++ = *sp++;
else
for (sp = (short *)src, ip = dest; count < len; count++)
*ip++ = *sp++;
break;
case NC_UINT:
for (sp = (short *)src, uip = dest; count < len; count++)
{
if (*sp < 0)
(*range_error)++;
*uip++ = *sp++;
}
break;
case NC_INT64:
for (sp = (short *)src, lip = dest; count < len; count++)
*lip++ = *sp++;
break;
case NC_UINT64:
for (sp = (short *)src, ulip = dest; count < len; count++)
{
if (*sp < 0)
(*range_error)++;
*ulip++ = *sp++;
}
break;
case NC_FLOAT:
for (sp = (short *)src, fp = dest; count < len; count++)
*fp++ = *sp++;
break;
case NC_DOUBLE:
for (sp = (short *)src, dp = dest; count < len; count++)
*dp++ = *sp++;
break;
default:
LOG((0, "%s: unexpected dest type. src_type %d, dest_type %d",
__func__, src_type, dest_type));
return NC_EBADTYPE;
}
break;
case NC_USHORT:
switch (dest_type)
{
case NC_UBYTE:
for (usp = (unsigned short *)src, ubp = dest; count < len; count++)
{
if (*usp > X_UCHAR_MAX)
(*range_error)++;
*ubp++ = *usp++;
}
break;
case NC_BYTE:
for (usp = (unsigned short *)src, bp = dest; count < len; count++)
{
if (*usp > X_SCHAR_MAX)
(*range_error)++;
*bp++ = *usp++;
}
break;
case NC_SHORT:
for (usp = (unsigned short *)src, sp = dest; count < len; count++)
{
if (*usp > X_SHORT_MAX)
(*range_error)++;
*sp++ = *usp++;
}
break;
case NC_USHORT:
for (usp = (unsigned short *)src, usp1 = dest; count < len; count++)
*usp1++ = *usp++;
break;
case NC_INT:
if (dest_long)
for (usp = (unsigned short *)src, lp = dest; count < len; count++)
*lp++ = *usp++;
else
for (usp = (unsigned short *)src, ip = dest; count < len; count++)
*ip++ = *usp++;
break;
case NC_UINT:
for (usp = (unsigned short *)src, uip = dest; count < len; count++)
*uip++ = *usp++;
break;
case NC_INT64:
for (usp = (unsigned short *)src, lip = dest; count < len; count++)
*lip++ = *usp++;
break;
case NC_UINT64:
for (usp = (unsigned short *)src, ulip = dest; count < len; count++)
*ulip++ = *usp++;
break;
case NC_FLOAT:
for (usp = (unsigned short *)src, fp = dest; count < len; count++)
*fp++ = *usp++;
break;
case NC_DOUBLE:
for (usp = (unsigned short *)src, dp = dest; count < len; count++)
*dp++ = *usp++;
break;
default:
LOG((0, "%s: unexpected dest type. src_type %d, dest_type %d",
__func__, src_type, dest_type));
return NC_EBADTYPE;
}
break;
case NC_INT:
if (src_long)
{
switch (dest_type)
{
case NC_UBYTE:
for (lp = (long *)src, ubp = dest; count < len; count++)
{
if (*lp > X_UCHAR_MAX || *lp < 0)
(*range_error)++;
*ubp++ = *lp++;
}
break;
case NC_BYTE:
for (lp = (long *)src, bp = dest; count < len; count++)
{
if (*lp > X_SCHAR_MAX || *lp < X_SCHAR_MIN)
(*range_error)++;
*bp++ = *lp++;
}
break;
case NC_SHORT:
for (lp = (long *)src, sp = dest; count < len; count++)
{
if (*lp > X_SHORT_MAX || *lp < X_SHORT_MIN)
(*range_error)++;
*sp++ = *lp++;
}
break;
case NC_USHORT:
for (lp = (long *)src, usp = dest; count < len; count++)
{
if (*lp > X_USHORT_MAX || *lp < 0)
(*range_error)++;
*usp++ = *lp++;
}
break;
case NC_INT: /* src is long */
if (dest_long)
{
for (lp = (long *)src, lp1 = dest; count < len; count++)
{
if (*lp > X_LONG_MAX || *lp < X_LONG_MIN)
(*range_error)++;
*lp1++ = *lp++;
}
}
else /* dest is int */
{
for (lp = (long *)src, ip = dest; count < len; count++)
{
if (*lp > X_INT_MAX || *lp < X_INT_MIN)
(*range_error)++;
*ip++ = *lp++;
}
}
break;
case NC_UINT:
for (lp = (long *)src, uip = dest; count < len; count++)
{
if (*lp > X_UINT_MAX || *lp < 0)
(*range_error)++;
*uip++ = *lp++;
}
break;
case NC_INT64:
for (lp = (long *)src, lip = dest; count < len; count++)
*lip++ = *lp++;
break;
case NC_UINT64:
for (lp = (long *)src, ulip = dest; count < len; count++)
{
if (*lp < 0)
(*range_error)++;
*ulip++ = *lp++;
}
break;
case NC_FLOAT:
for (lp = (long *)src, fp = dest; count < len; count++)
*fp++ = *lp++;
break;
case NC_DOUBLE:
for (lp = (long *)src, dp = dest; count < len; count++)
*dp++ = *lp++;
break;
default:
LOG((0, "%s: unexpected dest type. src_type %d, dest_type %d",
__func__, src_type, dest_type));
return NC_EBADTYPE;
}
}
else
{
switch (dest_type)
{
case NC_UBYTE:
for (ip = (int *)src, ubp = dest; count < len; count++)
{
if (*ip > X_UCHAR_MAX || *ip < 0)
(*range_error)++;
*ubp++ = *ip++;
}
break;
case NC_BYTE:
for (ip = (int *)src, bp = dest; count < len; count++)
{
if (*ip > X_SCHAR_MAX || *ip < X_SCHAR_MIN)
(*range_error)++;
*bp++ = *ip++;
}
break;
case NC_SHORT:
for (ip = (int *)src, sp = dest; count < len; count++)
{
if (*ip > X_SHORT_MAX || *ip < X_SHORT_MIN)
(*range_error)++;
*sp++ = *ip++;
}
break;
case NC_USHORT:
for (ip = (int *)src, usp = dest; count < len; count++)
{
if (*ip > X_USHORT_MAX || *ip < 0)
(*range_error)++;
*usp++ = *ip++;
}
break;
case NC_INT: /* src is int */
if (dest_long)
{
for (ip = (int *)src, lp1 = dest; count < len; count++)
{
if (*ip > X_LONG_MAX || *ip < X_LONG_MIN)
(*range_error)++;
*lp1++ = *ip++;
}
}
else /* dest is int */
{
for (ip = (int *)src, ip1 = dest; count < len; count++)
{
if (*ip > X_INT_MAX || *ip < X_INT_MIN)
(*range_error)++;
*ip1++ = *ip++;
}
}
break;
case NC_UINT:
for (ip = (int *)src, uip = dest; count < len; count++)
{
if (*ip > X_UINT_MAX || *ip < 0)
(*range_error)++;
*uip++ = *ip++;
}
break;
case NC_INT64:
for (ip = (int *)src, lip = dest; count < len; count++)
*lip++ = *ip++;
break;
case NC_UINT64:
for (ip = (int *)src, ulip = dest; count < len; count++)
{
if (*ip < 0)
(*range_error)++;
*ulip++ = *ip++;
}
break;
case NC_FLOAT:
for (ip = (int *)src, fp = dest; count < len; count++)
*fp++ = *ip++;
break;
case NC_DOUBLE:
for (ip = (int *)src, dp = dest; count < len; count++)
*dp++ = *ip++;
break;
default:
LOG((0, "%s: unexpected dest type. src_type %d, dest_type %d",
__func__, src_type, dest_type));
return NC_EBADTYPE;
}
}
break;
case NC_UINT:
switch (dest_type)
{
case NC_UBYTE:
for (uip = (unsigned int *)src, ubp = dest; count < len; count++)
{
if (*uip > X_UCHAR_MAX)
(*range_error)++;
*ubp++ = *uip++;
}
break;
case NC_BYTE:
for (uip = (unsigned int *)src, bp = dest; count < len; count++)
{
if (*uip > X_SCHAR_MAX)
(*range_error)++;
*bp++ = *uip++;
}
break;
case NC_SHORT:
for (uip = (unsigned int *)src, sp = dest; count < len; count++)
{
if (*uip > X_SHORT_MAX)
(*range_error)++;
*sp++ = *uip++;
}
break;
case NC_USHORT:
for (uip = (unsigned int *)src, usp = dest; count < len; count++)
{
if (*uip > X_USHORT_MAX)
(*range_error)++;
*usp++ = *uip++;
}
break;
case NC_INT:
if (dest_long)
for (uip = (unsigned int *)src, lp = dest; count < len; count++)
{
if (*uip > X_LONG_MAX)
(*range_error)++;
*lp++ = *uip++;
}
else
for (uip = (unsigned int *)src, ip = dest; count < len; count++)
{
if (*uip > X_INT_MAX)
(*range_error)++;
*ip++ = *uip++;
}
break;
case NC_UINT:
for (uip = (unsigned int *)src, uip1 = dest; count < len; count++)
{
if (*uip > X_UINT_MAX)
(*range_error)++;
*uip1++ = *uip++;
}
break;
case NC_INT64:
for (uip = (unsigned int *)src, lip = dest; count < len; count++)
*lip++ = *uip++;
break;
case NC_UINT64:
for (uip = (unsigned int *)src, ulip = dest; count < len; count++)
*ulip++ = *uip++;
break;
case NC_FLOAT:
for (uip = (unsigned int *)src, fp = dest; count < len; count++)
*fp++ = *uip++;
break;
case NC_DOUBLE:
for (uip = (unsigned int *)src, dp = dest; count < len; count++)
*dp++ = *uip++;
break;
default:
LOG((0, "%s: unexpected dest type. src_type %d, dest_type %d",
__func__, src_type, dest_type));
return NC_EBADTYPE;
}
break;
case NC_INT64:
switch (dest_type)
{
case NC_UBYTE:
for (lip = (long long *)src, ubp = dest; count < len; count++)
{
if (*lip > X_UCHAR_MAX || *lip < 0)
(*range_error)++;
*ubp++ = *lip++;
}
break;
case NC_BYTE:
for (lip = (long long *)src, bp = dest; count < len; count++)
{
if (*lip > X_SCHAR_MAX || *lip < X_SCHAR_MIN)
(*range_error)++;
*bp++ = *lip++;
}
break;
case NC_SHORT:
for (lip = (long long *)src, sp = dest; count < len; count++)
{
if (*lip > X_SHORT_MAX || *lip < X_SHORT_MIN)
(*range_error)++;
*sp++ = *lip++;
}
break;
case NC_USHORT:
for (lip = (long long *)src, usp = dest; count < len; count++)
{
if (*lip > X_USHORT_MAX || *lip < 0)
(*range_error)++;
*usp++ = *lip++;
}
break;
case NC_UINT:
for (lip = (long long *)src, uip = dest; count < len; count++)
{
if (*lip > X_UINT_MAX || *lip < 0)
(*range_error)++;
*uip++ = *lip++;
}
break;
case NC_INT:
if (dest_long)
for (lip = (long long *)src, lp = dest; count < len; count++)
{
if (*lip > X_LONG_MAX || *lip < X_LONG_MIN)
(*range_error)++;
*lp++ = *lip++;
}
else
for (lip = (long long *)src, ip = dest; count < len; count++)
{
if (*lip > X_INT_MAX || *lip < X_INT_MIN)
(*range_error)++;
*ip++ = *lip++;
}
break;
case NC_INT64:
for (lip = (long long *)src, lip1 = dest; count < len; count++)
*lip1++ = *lip++;
break;
case NC_UINT64:
for (lip = (long long *)src, ulip = dest; count < len; count++)
{
if (*lip < 0)
(*range_error)++;
*ulip++ = *lip++;
}
break;
case NC_FLOAT:
for (lip = (long long *)src, fp = dest; count < len; count++)
*fp++ = *lip++;
break;
case NC_DOUBLE:
for (lip = (long long *)src, dp = dest; count < len; count++)
*dp++ = *lip++;
break;
default:
LOG((0, "%s: unexpected dest type. src_type %d, dest_type %d",
__func__, src_type, dest_type));
return NC_EBADTYPE;
}
break;
case NC_UINT64:
switch (dest_type)
{
case NC_UBYTE:
for (ulip = (unsigned long long *)src, ubp = dest; count < len; count++)
{
if (*ulip > X_UCHAR_MAX)
(*range_error)++;
*ubp++ = *ulip++;
}
break;
case NC_BYTE:
for (ulip = (unsigned long long *)src, bp = dest; count < len; count++)
{
if (*ulip > X_SCHAR_MAX)
(*range_error)++;
*bp++ = *ulip++;
}
break;
case NC_SHORT:
for (ulip = (unsigned long long *)src, sp = dest; count < len; count++)
{
if (*ulip > X_SHORT_MAX)
(*range_error)++;
*sp++ = *ulip++;
}
break;
case NC_USHORT:
for (ulip = (unsigned long long *)src, usp = dest; count < len; count++)
{
if (*ulip > X_USHORT_MAX)
(*range_error)++;
*usp++ = *ulip++;
}
break;
case NC_UINT:
for (ulip = (unsigned long long *)src, uip = dest; count < len; count++)
{
if (*ulip > X_UINT_MAX)
(*range_error)++;
*uip++ = *ulip++;
}
break;
case NC_INT:
if (dest_long)
for (ulip = (unsigned long long *)src, lp = dest; count < len; count++)
{
if (*ulip > X_LONG_MAX)
(*range_error)++;
*lp++ = *ulip++;
}
else
for (ulip = (unsigned long long *)src, ip = dest; count < len; count++)
{
if (*ulip > X_INT_MAX)
(*range_error)++;
*ip++ = *ulip++;
}
break;
case NC_INT64:
for (ulip = (unsigned long long *)src, lip = dest; count < len; count++)
{
if (*ulip > X_INT64_MAX)
(*range_error)++;
*lip++ = *ulip++;
}
break;
case NC_UINT64:
for (ulip = (unsigned long long *)src, ulip1 = dest; count < len; count++)
*ulip1++ = *ulip++;
break;
case NC_FLOAT:
for (ulip = (unsigned long long *)src, fp = dest; count < len; count++)
*fp++ = *ulip++;
break;
case NC_DOUBLE:
for (ulip = (unsigned long long *)src, dp = dest; count < len; count++)
*dp++ = *ulip++;
break;
default:
LOG((0, "%s: unexpected dest type. src_type %d, dest_type %d",
__func__, src_type, dest_type));
return NC_EBADTYPE;
}
break;
case NC_FLOAT:
switch (dest_type)
{
case NC_UBYTE:
for (fp = (float *)src, ubp = dest; count < len; count++)
{
if (*fp > X_UCHAR_MAX || *fp < 0)
(*range_error)++;
*ubp++ = *fp++;
}
break;
case NC_BYTE:
for (fp = (float *)src, bp = dest; count < len; count++)
{
if (*fp > (double)X_SCHAR_MAX || *fp < (double)X_SCHAR_MIN)
(*range_error)++;
*bp++ = *fp++;
}
break;
case NC_SHORT:
for (fp = (float *)src, sp = dest; count < len; count++)
{
if (*fp > (double)X_SHORT_MAX || *fp < (double)X_SHORT_MIN)
(*range_error)++;
*sp++ = *fp++;
}
break;
case NC_USHORT:
for (fp = (float *)src, usp = dest; count < len; count++)
{
if (*fp > X_USHORT_MAX || *fp < 0)
(*range_error)++;
*usp++ = *fp++;
}
break;
case NC_UINT:
for (fp = (float *)src, uip = dest; count < len; count++)
{
if (*fp > X_UINT_MAX || *fp < 0)
(*range_error)++;
*uip++ = *fp++;
}
break;
case NC_INT:
if (dest_long)
for (fp = (float *)src, lp = dest; count < len; count++)
{
if (*fp > (double)X_LONG_MAX || *fp < (double)X_LONG_MIN)
(*range_error)++;
*lp++ = *fp++;
}
else
for (fp = (float *)src, ip = dest; count < len; count++)
{
if (*fp > (double)X_INT_MAX || *fp < (double)X_INT_MIN)
(*range_error)++;
*ip++ = *fp++;
}
break;
case NC_INT64:
for (fp = (float *)src, lip = dest; count < len; count++)
{
if (*fp > X_INT64_MAX || *fp <X_INT64_MIN)
(*range_error)++;
*lip++ = *fp++;
}
break;
case NC_UINT64:
for (fp = (float *)src, lip = dest; count < len; count++)
{
if (*fp > X_UINT64_MAX || *fp < 0)
(*range_error)++;
*lip++ = *fp++;
}
break;
case NC_FLOAT:
for (fp = (float *)src, fp1 = dest; count < len; count++)
{
/* if (*fp > X_FLOAT_MAX || *fp < X_FLOAT_MIN)
(*range_error)++;*/
*fp1++ = *fp++;
}
break;
case NC_DOUBLE:
for (fp = (float *)src, dp = dest; count < len; count++)
*dp++ = *fp++;
break;
default:
LOG((0, "%s: unexpected dest type. src_type %d, dest_type %d",
__func__, src_type, dest_type));
return NC_EBADTYPE;
}
break;
case NC_DOUBLE:
switch (dest_type)
{
case NC_UBYTE:
for (dp = (double *)src, ubp = dest; count < len; count++)
{
if (*dp > X_UCHAR_MAX || *dp < 0)
(*range_error)++;
*ubp++ = *dp++;
}
break;
case NC_BYTE:
for (dp = (double *)src, bp = dest; count < len; count++)
{
if (*dp > X_SCHAR_MAX || *dp < X_SCHAR_MIN)
(*range_error)++;
*bp++ = *dp++;
}
break;
case NC_SHORT:
for (dp = (double *)src, sp = dest; count < len; count++)
{
if (*dp > X_SHORT_MAX || *dp < X_SHORT_MIN)
(*range_error)++;
*sp++ = *dp++;
}
break;
case NC_USHORT:
for (dp = (double *)src, usp = dest; count < len; count++)
{
if (*dp > X_USHORT_MAX || *dp < 0)
(*range_error)++;
*usp++ = *dp++;
}
break;
case NC_UINT:
for (dp = (double *)src, uip = dest; count < len; count++)
{
if (*dp > X_UINT_MAX || *dp < 0)
(*range_error)++;
*uip++ = *dp++;
}
break;
case NC_INT:
if (dest_long)
for (dp = (double *)src, lp = dest; count < len; count++)
{
if (*dp > X_LONG_MAX || *dp < X_LONG_MIN)
(*range_error)++;
*lp++ = *dp++;
}
else
for (dp = (double *)src, ip = dest; count < len; count++)
{
if (*dp > X_INT_MAX || *dp < X_INT_MIN)
(*range_error)++;
*ip++ = *dp++;
}
break;
case NC_INT64:
for (dp = (double *)src, lip = dest; count < len; count++)
{
if (*dp > X_INT64_MAX || *dp < X_INT64_MIN)
(*range_error)++;
*lip++ = *dp++;
}
break;
case NC_UINT64:
for (dp = (double *)src, lip = dest; count < len; count++)
{
if (*dp > X_UINT64_MAX || *dp < 0)
(*range_error)++;
*lip++ = *dp++;
}
break;
case NC_FLOAT:
for (dp = (double *)src, fp = dest; count < len; count++)
{
if (*dp > X_FLOAT_MAX || *dp < X_FLOAT_MIN)
(*range_error)++;
*fp++ = *dp++;
}
break;
case NC_DOUBLE:
for (dp = (double *)src, dp1 = dest; count < len; count++)
{
/* if (*dp > X_DOUBLE_MAX || *dp < X_DOUBLE_MIN) */
/* (*range_error)++; */
*dp1++ = *dp++;
}
break;
default:
LOG((0, "%s: unexpected dest type. src_type %d, dest_type %d",
__func__, src_type, dest_type));
return NC_EBADTYPE;
}
break;
default:
LOG((0, "%s: unexpected src type. src_type %d, dest_type %d",
__func__, src_type, dest_type));
return NC_EBADTYPE;
}
return NC_NOERR;
}
/* In our first pass through the data, we may have encountered
* variables before encountering their dimscales, so go through the
* vars in this file and make sure we've got a dimid for each. */
int
nc4_rec_match_dimscales(NC_GRP_INFO_T *grp)
{
NC_GRP_INFO_T *g;
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim;
int retval = NC_NOERR;
assert(grp && grp->name);
LOG((4, "%s: grp->name %s", __func__, grp->name));
/* Perform var dimscale match for child groups. */
for (g = grp->children; g; g = g->l.next)
if ((retval = nc4_rec_match_dimscales(g)))
return retval;
/* Check all the vars in this group. If they have dimscale info,
* try and find a dimension for them. */
for (var = grp->var; var; var = var->l.next)
{
/* Skip dimension scale variables */
if (!var->dimscale)
{
int d;
/* Are there dimscales for this variable? */
if (var->dimscale_hdf5_objids)
{
for (d = 0; d < var->ndims; d++)
{
nc_bool_t finished = NC_FALSE;
LOG((5, "%s: var %s has dimscale info...", __func__, var->name));
/* Look at all the dims in this group to see if they
* match. */
for (g = grp; g && !finished; g = g->parent)
{
for (dim = g->dim; dim; dim = dim->l.next)
{
if (var->dimscale_hdf5_objids[d].fileno[0] == dim->hdf5_objid.fileno[0] &&
var->dimscale_hdf5_objids[d].objno[0] == dim->hdf5_objid.objno[0] &&
var->dimscale_hdf5_objids[d].fileno[1] == dim->hdf5_objid.fileno[1] &&
var->dimscale_hdf5_objids[d].objno[1] == dim->hdf5_objid.objno[1])
{
LOG((4, "%s: for dimension %d, found dim %s",
__func__, d, dim->name));
var->dimids[d] = dim->dimid;
finished = NC_TRUE;
break;
}
} /* next dim */
} /* next grp */
LOG((5, "%s: dimid for this dimscale is %d", __func__, var->type_info->nc_typeid));
} /* next var->dim */
}
/* No dimscales for this var! Invent phony dimensions. */
else
{
hid_t spaceid = 0;
hsize_t *h5dimlen = NULL, *h5dimlenmax = NULL;
int dataset_ndims;
/* Find the space information for this dimension. */
if ((spaceid = H5Dget_space(var->hdf_datasetid)) < 0)
return NC_EHDFERR;
#ifdef EXTRA_TESTS
num_spaces++;
#endif
/* Get the len of each dim in the space. */
if (var->ndims)
{
if (!(h5dimlen = malloc(var->ndims * sizeof(hsize_t))))
return NC_ENOMEM;
if (!(h5dimlenmax = malloc(var->ndims * sizeof(hsize_t))))
{
free(h5dimlen);
return NC_ENOMEM;
}
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid, h5dimlen,
h5dimlenmax)) < 0) {
free(h5dimlenmax);
free(h5dimlen);
return NC_EHDFERR;
}
if (dataset_ndims != var->ndims) {
free(h5dimlenmax);
free(h5dimlen);
return NC_EHDFERR;
}
}
else
{
/* Make sure it's scalar. */
if (H5Sget_simple_extent_type(spaceid) != H5S_SCALAR)
return NC_EHDFERR;
}
/* Release the space object. */
if (H5Sclose(spaceid) < 0) {
free(h5dimlen);
free(h5dimlenmax);
return NC_EHDFERR;
}
#ifdef EXTRA_TESTS
num_spaces--;
#endif
/* Create a phony dimension for each dimension in the
* dataset, unless there already is one the correct
* size. */
for (d = 0; d < var->ndims; d++)
{
/* Is there already a phony dimension of the correct size? */
for (dim = grp->dim; dim; dim = dim->l.next)
if ((dim->len == h5dimlen[d]) &&
((h5dimlenmax[d] == H5S_UNLIMITED && dim->unlimited) ||
(h5dimlenmax[d] != H5S_UNLIMITED && !dim->unlimited)))
break;
/* Didn't find a phony dim? Then create one. */
if (!dim)
{
char phony_dim_name[NC_MAX_NAME + 1];
LOG((3, "%s: creating phony dim for var %s", __func__, var->name));
if ((retval = nc4_dim_list_add(&grp->dim, &dim))) {
free(h5dimlenmax);
free(h5dimlen);
return retval;
}
grp->ndims++;
dim->dimid = grp->nc4_info->next_dimid++;
sprintf(phony_dim_name, "phony_dim_%d", dim->dimid);
if (!(dim->name = strdup(phony_dim_name))) {
free(h5dimlenmax);
free(h5dimlen);
return NC_ENOMEM;
}
dim->len = h5dimlen[d];
if (h5dimlenmax[d] == H5S_UNLIMITED)
dim->unlimited = NC_TRUE;
}
/* The variable must remember the dimid. */
var->dimids[d] = dim->dimid;
} /* next dim */
/* Free the memory we malloced. */
free(h5dimlen);
free(h5dimlenmax);
}
}
}
return retval;
}
/* Get the length, in bytes, of one element of a type in memory. */
int
nc4_get_typelen_mem(NC_HDF5_FILE_INFO_T *h5, nc_type xtype, int is_long,
size_t *len)
{
NC_TYPE_INFO_T *type;
int retval;
LOG((4, "%s xtype: %d", __func__, xtype));
assert(len);
/* If this is an atomic type, the answer is easy. */
switch (xtype)
{
case NC_BYTE:
case NC_CHAR:
case NC_UBYTE:
*len = sizeof(char);
return NC_NOERR;
case NC_SHORT:
case NC_USHORT:
*len = sizeof(short);
return NC_NOERR;
case NC_INT:
case NC_UINT:
if (is_long)
*len = sizeof(long);
else
*len = sizeof(int);
return NC_NOERR;
case NC_FLOAT:
*len = sizeof(float);
return NC_NOERR;
case NC_DOUBLE:
*len = sizeof(double);
return NC_NOERR;
case NC_INT64:
case NC_UINT64:
*len = sizeof(long long);
return NC_NOERR;
case NC_STRING:
*len = sizeof(char *);
return NC_NOERR;
}
/* See if var is compound type. */
if ((retval = nc4_find_type(h5, xtype, &type)))
return retval;
if (!type)
return NC_EBADTYPE;
*len = type->size;
LOG((5, "type->size ", type->size));
return NC_NOERR;
}
/* Get the class of a type */
int
nc4_get_typeclass(const NC_HDF5_FILE_INFO_T *h5, nc_type xtype, int *type_class)
{
int retval = NC_NOERR;
LOG((4, "%s xtype: %d", __func__, xtype));
assert(type_class);
/* If this is an atomic type, the answer is easy. */
if (xtype <= NC_STRING)
{
switch (xtype)
{
case NC_BYTE:
case NC_UBYTE:
case NC_SHORT:
case NC_USHORT:
case NC_INT:
case NC_UINT:
case NC_INT64:
case NC_UINT64:
/* NC_INT is class used for all integral types */
*type_class = NC_INT;
break;
case NC_FLOAT:
case NC_DOUBLE:
/* NC_FLOAT is class used for all floating-point types */
*type_class = NC_FLOAT;
break;
case NC_CHAR:
*type_class = NC_CHAR;
break;
case NC_STRING:
*type_class = NC_STRING;
break;
default:
BAIL(NC_EBADTYPE);
}
}
else
{
NC_TYPE_INFO_T *type;
/* See if it's a used-defined type */
if ((retval = nc4_find_type(h5, xtype, &type)))
BAIL(retval);
if (!type)
BAIL(NC_EBADTYPE);
*type_class = type->nc_type_class;
}
exit:
return retval;
}
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