forked from Unidata/netcdf-c
/
nc4file.c
3306 lines (2870 loc) · 95.8 KB
/
nc4file.c
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/** \file
The netCDF-4 file functions.
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.
Copyright 2003, University Corporation for Atmospheric Research. See
COPYRIGHT file for copying and redistribution conditions.
*/
#include "config.h"
#include <errno.h> /* netcdf functions sometimes return system errors */
#include "nc.h"
#include "nc4internal.h"
#include "nc4dispatch.h"
/* must be after nc4internal.h */
#include <H5DSpublic.h>
#include <H5Fpublic.h>
#ifdef USE_HDF4
#include <mfhdf.h>
#endif
#ifdef USE_DISKLESS
#include <hdf5_hl.h>
#endif
/* When we have open objects at file close, should
we log them or print to stdout. Default is to log
*/
#define LOGOPEN 1
/* This is to track opened HDF5 objects to make sure they are
* closed. */
#ifdef EXTRA_TESTS
extern int num_plists;
extern int num_spaces;
#endif /* EXTRA_TESTS */
#define MIN_DEFLATE_LEVEL 0
#define MAX_DEFLATE_LEVEL 9
/* Define the illegal mode flags */
static const int ILLEGAL_OPEN_FLAGS = (NC_MMAP|NC_64BIT_OFFSET);
static const int ILLEGAL_CREATE_FLAGS = (NC_NOWRITE|NC_MMAP|NC_INMEMORY|NC_64BIT_OFFSET|NC_CDF5);
extern void reportopenobjects(int log, hid_t);
/*! Struct to track information about objects in a group, for nc4_rec_read_metadata()
\internal
*/
typedef struct NC4_rec_read_metadata_obj_info
{
hid_t oid; /* HDF5 object ID */
char oname[NC_MAX_NAME + 1]; /* Name of object */
H5G_stat_t statbuf; /* Information about the object */
struct NC4_rec_read_metadata_obj_info *next; /* Pointer to next node in list */
} NC4_rec_read_metadata_obj_info_t;
/*! User data struct for call to H5Literate() in nc4_rec_read_metadata()
\internal
Tracks the groups, named datatypes and datasets in the group, for later use.
*/
typedef struct NC4_rec_read_metadata_ud
{
NC4_rec_read_metadata_obj_info_t *grps_head, *grps_tail; /* Pointers to head & tail of list of groups */
NC_GRP_INFO_T *grp; /* Pointer to parent group */
} NC4_rec_read_metadata_ud_t;
/* Forward */
static int NC4_enddef(int ncid);
static int nc4_rec_read_metadata(NC_GRP_INFO_T *grp);
static int close_netcdf4_file(NC_HDF5_FILE_INFO_T *h5, int abort);
/* Define the names of attributes to ignore
* added by the HDF5 dimension scale; these
* attached to variables.
* They cannot be modified thru the netcdf-4 API.
*/
const char* NC_RESERVED_VARATT_LIST[] = {
NC_ATT_REFERENCE_LIST,
NC_ATT_CLASS,
NC_ATT_DIMENSION_LIST,
NC_ATT_NAME,
NC_ATT_COORDINATES,
NC_DIMID_ATT_NAME,
NULL
};
/* Define the names of attributes to ignore
* because they are "hidden" global attributes.
* They can be read, but not modified thru the netcdf-4 API.
*/
const char* NC_RESERVED_ATT_LIST[] = {
NC_ATT_FORMAT,
NC3_STRICT_ATT_NAME,
#ifdef ENABLE_FILEINFO
NCPROPS,
ISNETCDF4ATT,
SUPERBLOCKATT,
#endif
NULL
};
#ifdef ENABLE_FILEINFO
/* Define the subset of the reserved list that is readable by name only */
const char* NC_RESERVED_SPECIAL_LIST[] = {
ISNETCDF4ATT,
SUPERBLOCKATT,
NCPROPS,
NULL
};
#endif
/* These are the default chunk cache sizes for HDF5 files created or
* opened with netCDF-4. */
size_t nc4_chunk_cache_size = CHUNK_CACHE_SIZE;
size_t nc4_chunk_cache_nelems = CHUNK_CACHE_NELEMS;
float nc4_chunk_cache_preemption = CHUNK_CACHE_PREEMPTION;
/* For performance, fill this array only the first time, and keep it
* in global memory for each further use. */
#define NUM_TYPES 12
static hid_t h5_native_type_constant_g[NUM_TYPES];
static const char nc_type_name_g[NUM_TYPES][NC_MAX_NAME + 1] = {"char", "byte", "short",
"int", "float", "double", "ubyte",
"ushort", "uint", "int64",
"uint64", "string"};
static const nc_type nc_type_constant_g[NUM_TYPES] = {NC_CHAR, NC_BYTE, NC_SHORT,
NC_INT, NC_FLOAT, NC_DOUBLE, NC_UBYTE,
NC_USHORT, NC_UINT, NC_INT64,
NC_UINT64, NC_STRING};
static const int nc_type_size_g[NUM_TYPES] = {sizeof(char), sizeof(char), sizeof(short),
sizeof(int), sizeof(float), sizeof(double), sizeof(unsigned char),
sizeof(unsigned short), sizeof(unsigned int), sizeof(long long),
sizeof(unsigned long long), sizeof(char *)};
/* Set chunk cache size. Only affects files opened/created *after* it
* is called. */
int
nc_set_chunk_cache(size_t size, size_t nelems, float preemption)
{
if (preemption < 0 || preemption > 1)
return NC_EINVAL;
nc4_chunk_cache_size = size;
nc4_chunk_cache_nelems = nelems;
nc4_chunk_cache_preemption = preemption;
return NC_NOERR;
}
/* Get chunk cache size. Only affects files opened/created *after* it
* is called. */
int
nc_get_chunk_cache(size_t *sizep, size_t *nelemsp, float *preemptionp)
{
if (sizep)
*sizep = nc4_chunk_cache_size;
if (nelemsp)
*nelemsp = nc4_chunk_cache_nelems;
if (preemptionp)
*preemptionp = nc4_chunk_cache_preemption;
return NC_NOERR;
}
/* Required for fortran to avoid size_t issues. */
int
nc_set_chunk_cache_ints(int size, int nelems, int preemption)
{
if (size <= 0 || nelems <= 0 || preemption < 0 || preemption > 100)
return NC_EINVAL;
nc4_chunk_cache_size = size;
nc4_chunk_cache_nelems = nelems;
nc4_chunk_cache_preemption = (float)preemption / 100;
return NC_NOERR;
}
int
nc_get_chunk_cache_ints(int *sizep, int *nelemsp, int *preemptionp)
{
if (sizep)
*sizep = (int)nc4_chunk_cache_size;
if (nelemsp)
*nelemsp = (int)nc4_chunk_cache_nelems;
if (preemptionp)
*preemptionp = (int)(nc4_chunk_cache_preemption * 100);
return NC_NOERR;
}
/* This will return the length of a netcdf data type in bytes. */
int
nc4typelen(nc_type type)
{
switch(type){
case NC_BYTE:
case NC_CHAR:
case NC_UBYTE:
return 1;
case NC_USHORT:
case NC_SHORT:
return 2;
case NC_FLOAT:
case NC_INT:
case NC_UINT:
return 4;
case NC_DOUBLE:
case NC_INT64:
case NC_UINT64:
return 8;
}
return -1;
}
/* Given a filename, check to see if it is a HDF5 file. */
#define MAGIC_NUMBER_LEN 4
#define NC_HDF5_FILE 1
#define NC_HDF4_FILE 2
static int
nc_check_for_hdf(const char *path, int flags, void* parameters, int *hdf_file)
{
char blob[MAGIC_NUMBER_LEN];
#ifdef USE_PARALLEL4
int use_parallel = ((flags & NC_MPIIO) == NC_MPIIO);
NC_MPI_INFO* mpiinfo = (NC_MPI_INFO*)parameters;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
#endif
int inmemory = ((flags & NC_INMEMORY) == NC_INMEMORY);
#ifdef USE_DISKLESS
NC_MEM_INFO* meminfo = (NC_MEM_INFO*)parameters;
#endif
#ifdef USE_PARALLEL4
if(use_parallel) {
comm = mpiinfo->comm;
info = mpiinfo->info;
}
#endif
assert(hdf_file);
LOG((3, "%s: path %s", __func__, path));
/* HDF5 function handles possible user block at beginning of file */
if(!inmemory && H5Fis_hdf5(path))
{
*hdf_file = NC_HDF5_FILE;
} else {
/* Get the 4-byte blob from the beginning of the file. Don't use posix
* for parallel, use the MPI functions instead. */
#ifdef USE_PARALLEL4
if (!inmemory && use_parallel)
{
MPI_File fh;
MPI_Status status;
int retval;
if ((retval = MPI_File_open(comm, (char *)path, MPI_MODE_RDONLY,
info, &fh)) != MPI_SUCCESS)
return NC_EPARINIT;
if ((retval = MPI_File_read(fh, blob, MAGIC_NUMBER_LEN, MPI_CHAR,
&status)) != MPI_SUCCESS)
return NC_EPARINIT;
if ((retval = MPI_File_close(&fh)) != MPI_SUCCESS)
return NC_EPARINIT;
}
else
#endif /* USE_PARALLEL4 */
if(!inmemory) {
FILE *fp;
if (!(fp = fopen(path, "r")) ||
fread(blob, MAGIC_NUMBER_LEN, 1, fp) != 1) {
if(fp) fclose(fp);
return errno;
}
fclose(fp);
} else { /*inmemory*/
if(meminfo->size < MAGIC_NUMBER_LEN)
return NC_ENOTNC;
memcpy(blob,meminfo->memory,MAGIC_NUMBER_LEN);
}
/* Check for HDF4. */
if (memcmp(blob, "\016\003\023\001", 4)==0)
*hdf_file = NC_HDF4_FILE;
else if (memcmp(blob, "HDF", 3)==0)
*hdf_file = NC_HDF5_FILE;
else
*hdf_file = 0;
}
return NC_NOERR;
}
/* Create a HDF5/netcdf-4 file. */
static int
nc4_create_file(const char *path, int cmode, MPI_Comm comm, MPI_Info info,
NC *nc)
{
hid_t fcpl_id, fapl_id = -1;
unsigned flags;
FILE *fp;
int retval = NC_NOERR;
NC_HDF5_FILE_INFO_T* nc4_info = NULL;
#ifdef USE_PARALLEL4
int comm_duped = 0; /* Whether the MPI Communicator was duplicated */
int info_duped = 0; /* Whether the MPI Info object was duplicated */
#else /* !USE_PARALLEL4 */
int persist = 0; /* Should diskless try to persist its data into file?*/
#endif
assert(nc);
if(cmode & NC_DISKLESS)
flags = H5F_ACC_TRUNC;
else if(cmode & NC_NOCLOBBER)
flags = H5F_ACC_EXCL;
else
flags = H5F_ACC_TRUNC;
LOG((3, "%s: path %s mode 0x%x", __func__, path, cmode));
assert(nc && path);
/* If this file already exists, and NC_NOCLOBBER is specified,
return an error. */
if (cmode & NC_DISKLESS) {
#ifndef USE_PARALLEL4
if(cmode & NC_WRITE)
persist = 1;
#endif
} else if ((cmode & NC_NOCLOBBER) && (fp = fopen(path, "r"))) {
fclose(fp);
return NC_EEXIST;
}
/* Add necessary structs to hold netcdf-4 file data. */
if ((retval = nc4_nc4f_list_add(nc, path, (NC_WRITE | cmode))))
BAIL(retval);
nc4_info = NC4_DATA(nc);
assert(nc4_info && nc4_info->root_grp);
/* Need this access plist to control how HDF5 handles open objects
* on file close. (Setting H5F_CLOSE_SEMI will cause H5Fclose to
* fail if there are any open objects in the file. */
if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists++;
#endif
#ifdef EXTRA_TESTS
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI))
BAIL(NC_EHDFERR);
#else
if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_STRONG))
BAIL(NC_EHDFERR);
#endif /* EXTRA_TESTS */
#ifdef USE_PARALLEL4
/* If this is a parallel file create, set up the file creation
property list. */
if ((cmode & NC_MPIIO) || (cmode & NC_MPIPOSIX))
{
nc4_info->parallel = NC_TRUE;
if (cmode & NC_MPIIO) /* MPI/IO */
{
LOG((4, "creating parallel file with MPI/IO"));
if (H5Pset_fapl_mpio(fapl_id, comm, info) < 0)
BAIL(NC_EPARINIT);
}
#ifdef USE_PARALLEL_POSIX
else /* MPI/POSIX */
{
LOG((4, "creating parallel file with MPI/posix"));
if (H5Pset_fapl_mpiposix(fapl_id, comm, 0) < 0)
BAIL(NC_EPARINIT);
}
#else /* USE_PARALLEL_POSIX */
/* Should not happen! Code in NC4_create/NC4_open should alias the
* NC_MPIPOSIX flag to NC_MPIIO, if the MPI-POSIX VFD is not
* available in HDF5. -QAK
*/
else /* MPI/POSIX */
BAIL(NC_EPARINIT);
#endif /* USE_PARALLEL_POSIX */
/* Keep copies of the MPI Comm & Info objects */
if (MPI_SUCCESS != MPI_Comm_dup(comm, &nc4_info->comm))
BAIL(NC_EMPI);
comm_duped++;
if (MPI_INFO_NULL != info)
{
if (MPI_SUCCESS != MPI_Info_dup(info, &nc4_info->info))
BAIL(NC_EMPI);
info_duped++;
}
else
{
/* No dup, just copy it. */
nc4_info->info = info;
}
}
#else /* only set cache for non-parallel... */
if(cmode & NC_DISKLESS) {
if (H5Pset_fapl_core(fapl_id, 4096, persist))
BAIL(NC_EDISKLESS);
}
if (H5Pset_cache(fapl_id, 0, nc4_chunk_cache_nelems, nc4_chunk_cache_size,
nc4_chunk_cache_preemption) < 0)
BAIL(NC_EHDFERR);
LOG((4, "%s: set HDF raw chunk cache to size %d nelems %d preemption %f",
__func__, nc4_chunk_cache_size, nc4_chunk_cache_nelems, nc4_chunk_cache_preemption));
#endif /* USE_PARALLEL4 */
#ifdef HDF5_HAS_LIBVER_BOUNDS
if (H5Pset_libver_bounds(fapl_id, H5F_LIBVER_EARLIEST, H5F_LIBVER_LATEST) < 0)
BAIL(NC_EHDFERR);
#endif
/* Create the property list. */
if ((fcpl_id = H5Pcreate(H5P_FILE_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(fcpl_id,0)<0)
BAIL(NC_EHDFERR);
/* Set latest_format in access propertly list and
* H5P_CRT_ORDER_TRACKED in the creation property list. This turns
* on HDF5 creation ordering. */
if (H5Pset_link_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0)
BAIL(NC_EHDFERR);
if (H5Pset_attr_creation_order(fcpl_id, (H5P_CRT_ORDER_TRACKED |
H5P_CRT_ORDER_INDEXED)) < 0)
BAIL(NC_EHDFERR);
/* Create the file. */
if ((nc4_info->hdfid = H5Fcreate(path, flags, fcpl_id, fapl_id)) < 0)
/*Change the return error from NC_EFILEMETADATA to
System error EACCES because that is the more likely problem */
BAIL(EACCES);
/* Open the root group. */
if ((nc4_info->root_grp->hdf_grpid = H5Gopen2(nc4_info->hdfid, "/",
H5P_DEFAULT)) < 0)
BAIL(NC_EFILEMETA);
/* Release the property lists. */
if (H5Pclose(fapl_id) < 0 || H5Pclose(fcpl_id) < 0)
BAIL(NC_EHDFERR);
#ifdef EXTRA_TESTS
num_plists--;
num_plists--;
#endif
/* Define mode gets turned on automatically on create. */
nc4_info->flags |= NC_INDEF;
#ifdef ENABLE_FILEINFO
NC4_get_fileinfo(nc4_info,&globalpropinfo);
NC4_put_propattr(nc4_info);
#endif
return NC_NOERR;
exit: /*failure exit*/
#ifdef USE_PARALLEL4
if (comm_duped) MPI_Comm_free(&nc4_info->comm);
if (info_duped) MPI_Info_free(&nc4_info->info);
#endif
#ifdef EXTRA_TESTS
num_plists--;
#endif
if (fapl_id != H5P_DEFAULT) H5Pclose(fapl_id);
if(!nc4_info) return retval;
close_netcdf4_file(nc4_info,1); /* treat like abort */
return retval;
}
/** \ingroup netcdf4
Create a netCDF-4/HDF5 file.
\param path The file name of the new file.
\param cmode The creation mode flag.
\param initialsz Ignored by this function.
\param basepe Ignored by this function.
\param chunksizehintp Ignored by this function.
\param use_parallel 0 for sequential, non-zero for parallel I/O.
\param parameters pointer to struct holding extra data (e.g. for parallel I/O)
layer. Ignored if NULL.
\param dispatch Pointer to the dispatch table for this file.
\param nc_file Pointer to an instance of NC.
\return NC_INVAL Invalid input (check cmode).
*/
int
NC4_create(const char* path, int cmode, size_t initialsz, int basepe,
size_t *chunksizehintp, int use_parallel, void *parameters,
NC_Dispatch *dispatch, NC* nc_file)
{
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
int res;
NC* nc;
assert(nc_file && path);
LOG((1, "%s: path %s cmode 0x%x comm %d info %d",
__func__, path, cmode, comm, info));
#ifdef USE_PARALLEL4
if (parameters)
{
comm = ((NC_MPI_INFO *)parameters)->comm;
info = ((NC_MPI_INFO *)parameters)->info;
}
#endif /* USE_PARALLEL4 */
/* If this is our first file, turn off HDF5 error messages. */
if (!nc4_hdf5_initialized)
nc4_hdf5_initialize();
/* Check the cmode for validity. */
if((cmode & ILLEGAL_CREATE_FLAGS) != 0)
return NC_EINVAL;
/* Cannot have both */
if((cmode & (NC_MPIIO|NC_MPIPOSIX)) == (NC_MPIIO|NC_MPIPOSIX))
return NC_EINVAL;
/* Currently no parallel diskless io */
if((cmode & (NC_MPIIO | NC_MPIPOSIX)) && (cmode & NC_DISKLESS))
return NC_EINVAL;
#ifndef USE_PARALLEL_POSIX
/* If the HDF5 library has been compiled without the MPI-POSIX VFD, alias
* the NC_MPIPOSIX flag to NC_MPIIO. -QAK
*/
if(cmode & NC_MPIPOSIX)
{
cmode &= ~NC_MPIPOSIX;
cmode |= NC_MPIIO;
}
#endif /* USE_PARALLEL_POSIX */
cmode |= NC_NETCDF4;
/* Apply default create format. */
if (nc_get_default_format() == NC_FORMAT_CDF5)
cmode |= NC_CDF5;
else if (nc_get_default_format() == NC_FORMAT_64BIT_OFFSET)
cmode |= NC_64BIT_OFFSET;
else if (nc_get_default_format() == NC_FORMAT_NETCDF4_CLASSIC)
cmode |= NC_CLASSIC_MODEL;
LOG((2, "cmode after applying default format: 0x%x", cmode));
nc_file->int_ncid = nc_file->ext_ncid;
res = nc4_create_file(path, cmode, comm, info, nc_file);
return res;
}
/* This function is called by read_dataset when a dimension scale
* dataset is encountered. It reads in the dimension data (creating a
* new NC_DIM_INFO_T object), and also checks to see if this is a
* dimension without a variable - that is, a coordinate dimension
* which does not have any coordinate data. */
static int
read_scale(NC_GRP_INFO_T *grp, hid_t datasetid, const char *obj_name,
const H5G_stat_t *statbuf, hsize_t scale_size, hsize_t max_scale_size,
NC_DIM_INFO_T **dim)
{
NC_DIM_INFO_T *new_dim; /* Dimension added to group */
char dimscale_name_att[NC_MAX_NAME + 1] = ""; /* Dimscale name, for checking if dim without var */
htri_t attr_exists = -1; /* Flag indicating hidden attribute exists */
hid_t attid = -1; /* ID of hidden attribute (to store dim ID) */
int dimscale_created = 0; /* Remember if a dimension was created (for error recovery) */
int initial_grp_ndims = grp->ndims; /* Retain for error recovery */
short initial_next_dimid = grp->nc4_info->next_dimid;/* Retain for error recovery */
int retval;
/* Add a dimension for this scale. */
if ((retval = nc4_dim_list_add(&grp->dim, &new_dim)))
BAIL(retval);
dimscale_created++;
/* Does this dataset have a hidden attribute that tells us its
* dimid? If so, read it. */
if ((attr_exists = H5Aexists(datasetid, NC_DIMID_ATT_NAME)) < 0)
BAIL(NC_EHDFERR);
if (attr_exists)
{
if ((attid = H5Aopen_name(datasetid, NC_DIMID_ATT_NAME)) < 0)
BAIL(NC_EHDFERR);
if (H5Aread(attid, H5T_NATIVE_INT, &new_dim->dimid) < 0)
BAIL(NC_EHDFERR);
/* Check if scale's dimid should impact the group's next dimid */
if (new_dim->dimid >= grp->nc4_info->next_dimid)
grp->nc4_info->next_dimid = new_dim->dimid + 1;
}
else
{
/* Assign dimid */
new_dim->dimid = grp->nc4_info->next_dimid++;
}
/* Increment number of dimensions. */
grp->ndims++;
if (!(new_dim->name = strdup(obj_name)))
BAIL(NC_ENOMEM);
if (SIZEOF_SIZE_T < 8 && scale_size > NC_MAX_UINT)
{
new_dim->len = NC_MAX_UINT;
new_dim->too_long = NC_TRUE;
}
else
new_dim->len = scale_size;
new_dim->hdf5_objid.fileno[0] = statbuf->fileno[0];
new_dim->hdf5_objid.fileno[1] = statbuf->fileno[1];
new_dim->hdf5_objid.objno[0] = statbuf->objno[0];
new_dim->hdf5_objid.objno[1] = statbuf->objno[1];
new_dim->hash = hash_fast(obj_name, strlen(obj_name));
/* If the dimscale has an unlimited dimension, then this dimension
* is unlimited. */
if (max_scale_size == H5S_UNLIMITED)
new_dim->unlimited = NC_TRUE;
/* If the scale name is set to DIM_WITHOUT_VARIABLE, then this is a
* dimension, but not a variable. (If get_scale_name returns an
* error, just move on, there's no NAME.) */
if (H5DSget_scale_name(datasetid, dimscale_name_att, NC_MAX_NAME) >= 0)
{
if (!strncmp(dimscale_name_att, DIM_WITHOUT_VARIABLE,
strlen(DIM_WITHOUT_VARIABLE)))
{
if (new_dim->unlimited)
{
size_t len = 0, *lenp = &len;
if ((retval = nc4_find_dim_len(grp, new_dim->dimid, &lenp)))
BAIL(retval);
new_dim->len = *lenp;
}
/* Hold open the dataset, since the dimension doesn't have a coordinate variable */
new_dim->hdf_dimscaleid = datasetid;
H5Iinc_ref(new_dim->hdf_dimscaleid); /* Increment number of objects using ID */
}
}
/* Set the dimension created */
*dim = new_dim;
exit:
/* Close the hidden attribute, if it was opened (error, or no error) */
if (attid > 0 && H5Aclose(attid) < 0)
BAIL2(NC_EHDFERR);
/* On error, undo any dimscale creation */
if (retval < 0 && dimscale_created)
{
/* Delete the dimension */
if ((retval = nc4_dim_list_del(&grp->dim, new_dim)))
BAIL2(retval);
/* Reset the group's information */
grp->ndims = initial_grp_ndims;
grp->nc4_info->next_dimid = initial_next_dimid;
}
return retval;
}
/* This function reads the hacked in coordinates attribute I use for
* multi-dimensional coordinates. */
static int
read_coord_dimids(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var)
{
hid_t coord_att_typeid = -1, coord_attid = -1, spaceid = -1;
hssize_t npoints;
int ret = 0;
int d;
/* There is a hidden attribute telling us the ids of the
* dimensions that apply to this multi-dimensional coordinate
* variable. Read it. */
if ((coord_attid = H5Aopen_name(var->hdf_datasetid, COORDINATES)) < 0) ret++;
if (!ret && (coord_att_typeid = H5Aget_type(coord_attid)) < 0) ret++;
/* How many dimensions are there? */
if (!ret && (spaceid = H5Aget_space(coord_attid)) < 0) ret++;
#ifdef EXTRA_TESTS
num_spaces++;
#endif
if (!ret && (npoints = H5Sget_simple_extent_npoints(spaceid)) < 0) ret++;
/* Check that the number of points is the same as the number of dimensions
* for the variable */
if (!ret && npoints != var->ndims) ret++;
if (!ret && H5Aread(coord_attid, coord_att_typeid, var->dimids) < 0) ret++;
LOG((4, "dimscale %s is multidimensional and has coords", var->name));
/* Update var->dim field based on the var->dimids */
for (d = 0; d < var->ndims; d++) {
/* Ok if does not find a dim at this time, but if found set it */
nc4_find_dim(grp, var->dimids[d], &var->dim[d], NULL);
}
/* Set my HDF5 IDs free! */
if (spaceid >= 0 && H5Sclose(spaceid) < 0) ret++;
#ifdef EXTRA_TESTS
num_spaces--;
#endif
if (coord_att_typeid >= 0 && H5Tclose(coord_att_typeid) < 0) ret++;
if (coord_attid >= 0 && H5Aclose(coord_attid) < 0) ret++;
return ret ? NC_EATTMETA : NC_NOERR;
}
/* This function is called when reading a file's metadata for each
* dimension scale attached to a variable.*/
static herr_t
dimscale_visitor(hid_t did, unsigned dim, hid_t dsid,
void *dimscale_hdf5_objids)
{
H5G_stat_t statbuf;
/* Get more info on the dimscale object.*/
if (H5Gget_objinfo(dsid, ".", 1, &statbuf) < 0)
return -1;
/* Pass this information back to caller. */
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno[0] = statbuf.fileno[0];
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).fileno[1] = statbuf.fileno[1];
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno[0] = statbuf.objno[0];
(*(HDF5_OBJID_T *)dimscale_hdf5_objids).objno[1] = statbuf.objno[1];
return 0;
}
/* Given an HDF5 type, set a pointer to netcdf type. */
static int
get_netcdf_type(NC_HDF5_FILE_INFO_T *h5, hid_t native_typeid,
nc_type *xtype)
{
NC_TYPE_INFO_T *type;
H5T_class_t class;
htri_t is_str, equal = 0;
assert(h5 && xtype);
if ((class = H5Tget_class(native_typeid)) < 0)
return NC_EHDFERR;
/* H5Tequal doesn't work with H5T_C_S1 for some reason. But
* H5Tget_class will return H5T_STRING if this is a string. */
if (class == H5T_STRING)
{
if ((is_str = H5Tis_variable_str(native_typeid)) < 0)
return NC_EHDFERR;
if (is_str)
*xtype = NC_STRING;
else
*xtype = NC_CHAR;
return NC_NOERR;
}
else if (class == H5T_INTEGER || class == H5T_FLOAT)
{
/* For integers and floats, we don't have to worry about
* endianness if we compare native types. */
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_SCHAR)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_BYTE;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_SHORT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_SHORT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_INT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_INT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_FLOAT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_FLOAT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_DOUBLE)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_DOUBLE;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_UCHAR)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_UBYTE;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_USHORT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_USHORT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_UINT)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_UINT;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_LLONG)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_INT64;
return NC_NOERR;
}
if ((equal = H5Tequal(native_typeid, H5T_NATIVE_ULLONG)) < 0)
return NC_EHDFERR;
if (equal)
{
*xtype = NC_UINT64;
return NC_NOERR;
}
}
/* Maybe we already know about this type. */
if (!equal)
if((type = nc4_rec_find_hdf_type(h5->root_grp, native_typeid)))
{
*xtype = type->nc_typeid;
return NC_NOERR;
}
*xtype = NC_NAT;
return NC_EBADTYPID;
}
/* Given an HDF5 type, set a pointer to netcdf type_info struct,
* either an existing one (for user-defined types) or a newly created
* one. */
static int
get_type_info2(NC_HDF5_FILE_INFO_T *h5, hid_t datasetid,
NC_TYPE_INFO_T **type_info)
{
htri_t is_str, equal = 0;
H5T_class_t class;
hid_t native_typeid, hdf_typeid;
H5T_order_t order;
int t;
assert(h5 && type_info);
/* Because these N5T_NATIVE_* constants are actually function calls
* (!) in H5Tpublic.h, I can't initialize this array in the usual
* way, because at least some C compilers (like Irix) complain
* about calling functions when defining constants. So I have to do
* it like this. Note that there's no native types for char or
* string. Those are handled later. */
if (!h5_native_type_constant_g[1])
{
h5_native_type_constant_g[1] = H5T_NATIVE_SCHAR;
h5_native_type_constant_g[2] = H5T_NATIVE_SHORT;
h5_native_type_constant_g[3] = H5T_NATIVE_INT;
h5_native_type_constant_g[4] = H5T_NATIVE_FLOAT;
h5_native_type_constant_g[5] = H5T_NATIVE_DOUBLE;
h5_native_type_constant_g[6] = H5T_NATIVE_UCHAR;
h5_native_type_constant_g[7] = H5T_NATIVE_USHORT;
h5_native_type_constant_g[8] = H5T_NATIVE_UINT;
h5_native_type_constant_g[9] = H5T_NATIVE_LLONG;
h5_native_type_constant_g[10] = H5T_NATIVE_ULLONG;
}
/* Get the HDF5 typeid - we'll need it later. */
if ((hdf_typeid = H5Dget_type(datasetid)) < 0)
return NC_EHDFERR;
/* Get the native typeid. Will be equivalent to hdf_typeid when
* creating but not necessarily when reading, a variable. */
if ((native_typeid = H5Tget_native_type(hdf_typeid, H5T_DIR_DEFAULT)) < 0)
return NC_EHDFERR;
/* Is this type an integer, string, compound, or what? */
if ((class = H5Tget_class(native_typeid)) < 0)
return NC_EHDFERR;
/* Is this an atomic type? */
if (class == H5T_STRING || class == H5T_INTEGER || class == H5T_FLOAT)
{
/* Allocate a phony NC_TYPE_INFO_T struct to hold type info. */
if (!(*type_info = calloc(1, sizeof(NC_TYPE_INFO_T))))
return NC_ENOMEM;
/* H5Tequal doesn't work with H5T_C_S1 for some reason. But
* H5Tget_class will return H5T_STRING if this is a string. */
if (class == H5T_STRING)
{
if ((is_str = H5Tis_variable_str(native_typeid)) < 0)
return NC_EHDFERR;
/* Make sure fixed-len strings will work like variable-len strings */
if (is_str || H5Tget_size(hdf_typeid) > 1)
{
/* Set a class for the type */
t = NUM_TYPES - 1;
(*type_info)->nc_type_class = NC_STRING;
}
else
{
/* Set a class for the type */
t = 0;
(*type_info)->nc_type_class = NC_CHAR;
}
}
else if (class == H5T_INTEGER || class == H5T_FLOAT)
{
for (t = 1; t < NUM_TYPES - 1; t++)
{
if ((equal = H5Tequal(native_typeid, h5_native_type_constant_g[t])) < 0)
return NC_EHDFERR;
if (equal)
break;
}
/* Find out about endianness.
* As of HDF 1.8.6, this works with all data types
* Not just H5T_INTEGER.
*
* See https://www.hdfgroup.org/HDF5/doc/RM/RM_H5T.html#Datatype-GetOrder
*/
if((order = H5Tget_order(hdf_typeid)) < 0)
return NC_EHDFERR;
if(order == H5T_ORDER_LE)
(*type_info)->endianness = NC_ENDIAN_LITTLE;
else if(order == H5T_ORDER_BE)
(*type_info)->endianness = NC_ENDIAN_BIG;
else
return NC_EBADTYPE;
if(class == H5T_INTEGER)
(*type_info)->nc_type_class = NC_INT;
else
(*type_info)->nc_type_class = NC_FLOAT;
}
(*type_info)->nc_typeid = nc_type_constant_g[t];
(*type_info)->size = nc_type_size_g[t];
if (!((*type_info)->name = strdup(nc_type_name_g[t])))
return NC_ENOMEM;
(*type_info)->hdf_typeid = hdf_typeid;
(*type_info)->native_hdf_typeid = native_typeid;
return NC_NOERR;
}
else
{
NC_TYPE_INFO_T *type;
/* This is a user-defined type. */
if((type = nc4_rec_find_hdf_type(h5->root_grp, native_typeid)))
*type_info = type;
/* The type entry in the array of user-defined types already has
* an open data typeid (and native typeid), so close the ones we
* opened above. */
if (H5Tclose(native_typeid) < 0)
return NC_EHDFERR;
if (H5Tclose(hdf_typeid) < 0)
return NC_EHDFERR;
if (type)