mirror/netcdf-c
2
0
Fork 0
mirror of https://github.com/Unidata/netcdf-c.git synced 2025-01-30 16:10:44 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge branch 'ejh_hdf5_3' of https://github.com/NetCDF-World-Domination-Council/netcdf-c into misc-changes.wif

Browse Source
This commit is contained in:
Ward Fisher 2018-05-29 15:39:09 -06:00
commit 84fd054a29
7 changed files with 1064 additions and 977 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
include/nc4internal.h
View File

@ -104,6 +104,9 @@ typedef enum {NCNAT, NCVAR, NCDIM, NCATT, NCTYP, NCFLD, NCGRP} NC_SORT;
/** This is the name of the name HDF5 dimension scale attribute. */
#define HDF5_DIMSCALE_NAME_ATT_NAME "NAME"
/** This is the number of netCDF atomic types. */
#define NUM_ATOMIC_TYPES (NC_MAX_ATOMIC_TYPE + 1)
/* Boolean type, to make the code easier to read */
typedef enum {NC_FALSE = 0, NC_TRUE = 1} nc_bool_t;

2
libhdf5/CMakeLists.txt
View File

@ -7,7 +7,7 @@
# The source files for the HDF5 dispatch layer.
SET(libnchdf5_SOURCES nc4hdf.c nc4info.c hdf5file.c hdf5attr.c
hdf5dim.c hdf5grp.c)
hdf5dim.c hdf5grp.c hdf5type.c hdf5internal.c)
# Build the HDF4 dispatch layer as a library that will be included in
# the netCDF library.

2
libhdf5/Makefile.am
View File

@ -14,7 +14,7 @@ noinst_LTLIBRARIES = libnchdf5.la
# The source files.
libnchdf5_la_SOURCES = nc4hdf.c nc4info.c hdf5file.c hdf5attr.c \
hdf5dim.c hdf5grp.c
hdf5dim.c hdf5grp.c hdf5type.c hdf5internal.c
# Package this for cmake build.
EXTRA_DIST = CMakeLists.txt

510
libhdf5/hdf5internal.c Normal file
View File

@ -0,0 +1,510 @@
/* Copyright 2003-2018, University Corporation for Atmospheric
* Research. See the COPYRIGHT file for copying and redistribution
* conditions.
*/
/**
* @file @internal Internal netcdf-4 functions.
*
* This file contains functions internal to the netcdf4 library. None of
* the functions in this file are exposed in the exetnal API. These
* functions all relate to the manipulation of netcdf-4's in-memory
* buffer of metadata information, i.e. the linked list of NC
* structs.
*
* @author Ed Hartnett
*/
#include "config.h"
#include "nc4internal.h"
#include "nc.h" /* from libsrc */
#include "ncdispatch.h" /* from libdispatch */
#include "ncutf8.h"
#include "H5DSpublic.h"
#undef DEBUGH5
#ifdef DEBUGH5
/**
* @internal Provide a catchable error reporting function
*
* @param ignored Ignored.
*
* @return 0 for success.
*/
static herr_t
h5catch(void* ignored)
{
H5Eprint(NULL);
return 0;
}
#endif
/* These are the default chunk cache sizes for HDF5 files created or
* opened with netCDF-4. */
extern size_t nc4_chunk_cache_size;
extern size_t nc4_chunk_cache_nelems;
extern float nc4_chunk_cache_preemption;
#ifdef LOGGING
/* This is the severity level of messages which will be logged. Use
severity 0 for errors, 1 for important log messages, 2 for less
important, etc. */
extern int nc_log_level;
#endif /* LOGGING */
int nc4_hdf5_initialized = 0; /**< True if initialization has happened. */
/**
* @internal Provide a wrapper for H5Eset_auto
* @param func Pointer to func.
* @param client_data Client data.
*
* @return 0 for success
*/
static herr_t
set_auto(void* func, void *client_data)
{
#ifdef DEBUGH5
return H5Eset_auto2(H5E_DEFAULT,(H5E_auto2_t)h5catch,client_data);
#else
return H5Eset_auto2(H5E_DEFAULT,(H5E_auto2_t)func,client_data);
#endif
}
/**
* @internal Provide a function to do any necessary initialization of
* the HDF5 library.
*/
void
nc4_hdf5_initialize(void)
{
if (set_auto(NULL, NULL) < 0)
LOG((0, "Couldn't turn off HDF5 error messages!"));
LOG((1, "HDF5 error messages have been turned off."));
nc4_hdf5_initialized = 1;
}
/**
* @internal Given a varid, return the maximum length of a dimension
* using dimid.
*
* @param grp Pointer to group info struct.
* @param varid Variable ID.
* @param dimid Dimension ID.
* @param maxlen Pointer that gets the max length.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
find_var_dim_max_length(NC_GRP_INFO_T *grp, int varid, int dimid, size_t *maxlen)
{
hid_t datasetid = 0, spaceid = 0;
NC_VAR_INFO_T *var;
hsize_t *h5dimlen = NULL, *h5dimlenmax = NULL;
int d, dataset_ndims = 0;
int retval = NC_NOERR;
*maxlen = 0;
/* Find this var. */
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
if (!var) return NC_ENOTVAR;
assert(var->hdr.id == varid);
/* If the var hasn't been created yet, its size is 0. */
if (!var->created)
{
*maxlen = 0;
}
else
{
/* Get the number of records in the dataset. */
if ((retval = nc4_open_var_grp2(grp, var->hdr.id, &datasetid)))
BAIL(retval);
if ((spaceid = H5Dget_space(datasetid)) < 0)
BAIL(NC_EHDFERR);
/* If it's a scalar dataset, it has length one. */
if (H5Sget_simple_extent_type(spaceid) == H5S_SCALAR)
{
*maxlen = (var->dimids && var->dimids[0] == dimid) ? 1 : 0;
}
else
{
/* Check to make sure ndims is right, then get the len of each
dim in the space. */
if ((dataset_ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
BAIL(NC_EHDFERR);
if (dataset_ndims != var->ndims)
BAIL(NC_EHDFERR);
if (!(h5dimlen = malloc(dataset_ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
if (!(h5dimlenmax = malloc(dataset_ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid,
h5dimlen, h5dimlenmax)) < 0)
BAIL(NC_EHDFERR);
LOG((5, "find_var_dim_max_length: varid %d len %d max: %d",
varid, (int)h5dimlen[0], (int)h5dimlenmax[0]));
for (d=0; d<dataset_ndims; d++) {
if (var->dimids[d] == dimid) {
*maxlen = *maxlen > h5dimlen[d] ? *maxlen : h5dimlen[d];
}
}
}
}
exit:
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
if (h5dimlen) free(h5dimlen);
if (h5dimlenmax) free(h5dimlenmax);
return retval;
}
/**
* @internal Search for type with a given HDF type id.
*
* @param h5 File
* @param target_hdf_typeid HDF5 type ID to find.
*
* @return Pointer to type info struct, or NULL if not found.
* @author Ed Hartnett
*/
NC_TYPE_INFO_T *
nc4_rec_find_hdf_type(NC_HDF5_FILE_INFO_T* h5, hid_t target_hdf_typeid)
{
NC_TYPE_INFO_T *type;
htri_t equal;
int i;
assert(h5);
for(i=0;i<nclistlength(h5->alltypes);i++) {
type = (NC_TYPE_INFO_T*)nclistget(h5->alltypes,i);
if(type == NULL) continue;
/* Is this the type we are searching for? */
if ((equal = H5Tequal(type->native_hdf_typeid ? type->native_hdf_typeid : type->hdf_typeid, target_hdf_typeid)) < 0)
return NULL;
if (equal)
return type;
}
/* Can't find it. Fate, why do you mock me? */
return NULL;
}
/**
* @internal Find the actual length of a dim by checking the length of
* that dim in all variables that use it, in grp or children. **len
* must be initialized to zero before this function is called.
*
* @param grp Pointer to group info struct.
* @param dimid Dimension ID.
* @param len Pointer to pointer that gets length.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
nc4_find_dim_len(NC_GRP_INFO_T *grp, int dimid, size_t **len)
{
NC_GRP_INFO_T *g;
NC_VAR_INFO_T *var;
int retval;
int i;
assert(grp && len);
LOG((3, "nc4_find_dim_len: grp->name %s dimid %d", grp->hdr.name, dimid));
/* If there are any groups, call this function recursively on
* them. */
for(i=0;i<ncindexsize(grp->children);i++) {
g = (NC_GRP_INFO_T*)ncindexith(grp->children,i);
if(g == NULL) continue;
if ((retval = nc4_find_dim_len(g, dimid, len)))
return retval;
}
/* For all variables in this group, find the ones that use this
* dimension, and remember the max length. */
for (i=0; i < ncindexsize(grp->vars); i++)
{
size_t mylen;
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,i);
if (var == NULL) continue;
/* Find max length of dim in this variable... */
if ((retval = find_var_dim_max_length(grp, var->hdr.id, dimid, &mylen)))
return retval;
**len = **len > mylen ? **len : mylen;
}
return NC_NOERR;
}
/**
* @internal Break a coordinate variable to separate the dimension and
* the variable.
*
* This is called from nc_rename_dim() and nc_rename_var(). In some
* renames, the coord variable must stay, but it is no longer a coord
* variable. This function changes a coord var into an ordinary
* variable.
*
* @param grp Pointer to group info struct.
* @param coord_var Pointer to variable info struct.
* @param dim Pointer to dimension info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @author Quincey Koziol, Ed Hartnett
*/
int
nc4_break_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var, NC_DIM_INFO_T *dim)
{
int retval = NC_NOERR;
/* Sanity checks */
assert(grp && coord_var && dim && dim->coord_var == coord_var &&
coord_var->dim[0] == dim && coord_var->dimids[0] == dim->hdr.id &&
!dim->hdf_dimscaleid);
LOG((3, "%s dim %s was associated with var %s, but now has different name",
__func__, dim->hdr.name, coord_var->hdr.name));
/* If we're replacing an existing dimscale dataset, go to
* every var in the file and detach this dimension scale. */
if ((retval = rec_detach_scales(grp->nc4_info->root_grp,
dim->hdr.id, coord_var->hdf_datasetid)))
return retval;
/* Allow attached dimscales to be tracked on the [former]
* coordinate variable */
if (coord_var->ndims)
{
/* Coordinate variables shouldn't have dimscales attached. */
assert(!coord_var->dimscale_attached);
/* Allocate space for tracking them */
if (!(coord_var->dimscale_attached = calloc(coord_var->ndims,
sizeof(nc_bool_t))))
return NC_ENOMEM;
}
/* Remove the atts that go with being a coordinate var. */
/* if ((retval = remove_coord_atts(coord_var->hdf_datasetid))) */
/* return retval; */
/* Detach dimension from variable */
coord_var->dimscale = NC_FALSE;
dim->coord_var = NULL;
/* Set state transition indicators */
coord_var->was_coord_var = NC_TRUE;
coord_var->became_coord_var = NC_FALSE;
return NC_NOERR;
}
/**
* @internal Delete an existing dimscale-only dataset.
*
* A dimscale-only HDF5 dataset is created when a dim is defined
* without an accompanying coordinate variable.
*
* Sometimes, during renames, or late creation of variables, an
* existing, dimscale-only dataset must be removed. This means
* detaching all variables that use the dataset, then closing and
* unlinking it.
*
* @param grp The grp of the dimscale-only dataset to be deleted, or a
* higher group in the hierarchy (ex. root group).
* @param dimid id of the dimension
* @param dim Pointer to the dim with the dimscale-only dataset to be
* deleted.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett
*/
int
delete_existing_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T *dim)
{
int retval;
assert(grp && dim);
LOG((2, "%s: deleting dimscale dataset %s dimid %d", __func__, dim->hdr.name,
dimid));
/* Detach dimscale from any variables using it */
if ((retval = rec_detach_scales(grp, dimid, dim->hdf_dimscaleid)) < 0)
return retval;
/* Close the HDF5 dataset */
if (H5Dclose(dim->hdf_dimscaleid) < 0)
return NC_EHDFERR;
dim->hdf_dimscaleid = 0;
/* Now delete the dataset. */
if (H5Gunlink(grp->hdf_grpid, dim->hdr.name) < 0)
return NC_EHDFERR;
return NC_NOERR;
}
/**
* @internal Reform a coordinate variable from a dimension and a
* variable.
*
* @param grp Pointer to group info struct.
* @param var Pointer to variable info struct.
* @param dim Pointer to dimension info struct.
*
* @return ::NC_NOERR No error.
* @author Quincey Koziol
*/
int
nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
{
int need_to_reattach_scales = 0;
int retval = NC_NOERR;
assert(grp && var && dim);
LOG((3, "%s: dim->hdr.name %s var->hdr.name %s", __func__, dim->hdr.name, var->hdr.name));
/* Detach dimscales from the [new] coordinate variable */
if(var->dimscale_attached)
{
int dims_detached = 0;
int finished = 0;
int d;
/* Loop over all dimensions for variable */
for (d = 0; d < var->ndims && !finished; d++)
{
/* Is there a dimscale attached to this axis? */
if(var->dimscale_attached[d])
{
NC_GRP_INFO_T *g;
int k;
for (g = grp; g && !finished; g = g->parent)
{
NC_DIM_INFO_T *dim1;
for(k=0;k<ncindexsize(g->dim);k++)
{
if((dim1 = (NC_DIM_INFO_T*)ncindexith(g->dim,k)) == NULL) continue;
if (var->dimids[d] == dim1->hdr.id)
{
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;
/* dim_datasetid may be 0 in some cases when
* renames of dims and vars are happening. In
* this case, the scale has already been
* detached. */
if (dim_datasetid > 0)
{
LOG((3, "detaching scale from %s", var->hdr.name));
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++;
}
}
}
}
} /* next variable dimension */
/* Release & reset the array tracking attached dimscales */
free(var->dimscale_attached);
var->dimscale_attached = NULL;
need_to_reattach_scales++;
}
/* Use variable's dataset ID for the dimscale ID. */
if (dim->hdf_dimscaleid && grp != NULL)
{
LOG((3, "closing and unlinking dimscale dataset %s", dim->hdr.name));
if (H5Dclose(dim->hdf_dimscaleid) < 0)
BAIL(NC_EHDFERR);
dim->hdf_dimscaleid = 0;
/* Now delete the dimscale's dataset
(it will be recreated later, if necessary) */
if (H5Gunlink(grp->hdf_grpid, dim->hdr.name) < 0)
return NC_EDIMMETA;
}
/* Attach variable to dimension */
var->dimscale = NC_TRUE;
dim->coord_var = var;
/* Check if this variable used to be a coord. var */
if (need_to_reattach_scales || (var->was_coord_var && grp != NULL))
{
/* Reattach the scale everywhere it is used. */
/* (Recall that netCDF dimscales are always 1-D) */
if ((retval = rec_reattach_scales(grp->nc4_info->root_grp,
var->dimids[0], var->hdf_datasetid)))
return retval;
/* Set state transition indicator (cancels earlier transition) */
var->was_coord_var = NC_FALSE;
}
else
/* Set state transition indicator */
var->became_coord_var = NC_TRUE;
exit:
return retval;
}
#ifdef LOGGING
/**
* This is the same as nc_set_log_level(), but will also turn on HDF5
* internal logging, in addition to netCDF logging.
*
* @param new_level The new logging level.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
hdf5_set_log_level(int new_level)
{
if (!nc4_hdf5_initialized)
nc4_hdf5_initialize();
/* If the user wants to completely turn off logging, turn off HDF5
logging too. Now I truely can't think of what to do if this
fails, so just ignore the return code. */
if (new_level == NC_TURN_OFF_LOGGING)
{
set_auto(NULL, NULL);
LOG((1, "HDF5 error messages turned off!"));
}
/* Do we need to turn HDF5 logging back on? */
if (new_level > NC_TURN_OFF_LOGGING &&
nc_log_level <= NC_TURN_OFF_LOGGING)
{
if (set_auto((H5E_auto_t)&H5Eprint, stderr) < 0)
LOG((0, "H5Eset_auto failed!"));
LOG((1, "HDF5 error messages turned on."));
}
/* Now remember the new level. */
nc_set_log_level(new_level);
return NC_NOERR;
}
#endif /* LOGGING */

524
libhdf5/hdf5type.c Normal file
View File

@ -0,0 +1,524 @@
/* Copyright 2005-2018, University Corporation for Atmospheric
* Research. See the COPYRIGHT file for copying and redistribution
* conditions. */
/**
* @file @internal 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 handles the nc4 user-defined type functions
* (i.e. compound and opaque types).
*
* @author Ed Hartnett
*/
#include "nc4internal.h"
#include "nc4dispatch.h"
/**
* @internal Determine if two types are equal.
*
* @param ncid1 First file/group ID.
* @param typeid1 First type ID.
* @param ncid2 Second file/group ID.
* @param typeid2 Second type ID.
* @param equalp Pointer that will get 1 if the two types are equal.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EBADTYPE Type not found.
* @return ::NC_EINVAL Invalid type.
* @author Ed Hartnett
*/
extern int
NC4_inq_type_equal(int ncid1, nc_type typeid1, int ncid2,
nc_type typeid2, int *equalp)
{
NC_GRP_INFO_T *grpone, *grptwo;
NC_TYPE_INFO_T *type1, *type2;
int retval;
LOG((2, "nc_inq_type_equal: ncid1 0x%x typeid1 %d ncid2 0x%x typeid2 %d",
ncid1, typeid1, ncid2, typeid2));
/* Check input. */
if(equalp == NULL) return NC_NOERR;
if (typeid1 <= NC_NAT || typeid2 <= NC_NAT)
return NC_EINVAL;
/* If one is atomic, and the other user-defined, the types are not
* equal. */
if ((typeid1 <= NC_STRING && typeid2 > NC_STRING) ||
(typeid2 <= NC_STRING && typeid1 > NC_STRING))
{
if (equalp) *equalp = 0;
return NC_NOERR;
}
/* If both are atomic types, the answer is easy. */
if (typeid1 <= NUM_ATOMIC_TYPES)
{
if (equalp)
{
if (typeid1 == typeid2)
*equalp = 1;
else
*equalp = 0;
}
return NC_NOERR;
}
/* Not atomic types - so find type1 and type2 information. */
if ((retval = nc4_find_nc4_grp(ncid1, &grpone)))
return retval;
if (!(type1 = nc4_rec_find_nc_type(grpone->nc4_info,
typeid1)))
return NC_EBADTYPE;
if ((retval = nc4_find_nc4_grp(ncid2, &grptwo)))
return retval;
if (!(type2 = nc4_rec_find_nc_type(grptwo->nc4_info,
typeid2)))
return NC_EBADTYPE;
/* Are the two types equal? */
if (equalp)
{
if ((retval = H5Tequal(type1->native_hdf_typeid, type2->native_hdf_typeid)) < 0)
return NC_EHDFERR;
*equalp = 1 ? retval : 0;
}
return NC_NOERR;
}
/**
* @internal Get the id of a type from the name.
*
* @param ncid File and group ID.
* @param name Name of type.
* @param typeidp Pointer that will get the type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EINVAL Bad size.
* @return ::NC_ENOTNC4 User types in netCDF-4 files only.
* @return ::NC_EBADTYPE Type not found.
* @author Ed Hartnett
*/
extern int
NC4_inq_typeid(int ncid, const char *name, nc_type *typeidp)
{
NC_GRP_INFO_T *grp;
NC_GRP_INFO_T *grptwo;
NC_HDF5_FILE_INFO_T *h5;
NC_TYPE_INFO_T *type = NULL;
char *norm_name;
int i, retval;
/* Handle atomic types. */
for (i = 0; i < NUM_ATOMIC_TYPES; i++)
if (!strcmp(name, nc4_atomic_name[i]))
{
if (typeidp)
*typeidp = i;
return NC_NOERR;
}
/* Find info for this file and group, and set pointer to each. */
if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
return retval;
assert(h5 && grp);
/* If the first char is a /, this is a fully-qualified
* name. Otherwise, this had better be a local name (i.e. no / in
* the middle). */
if (name[0] != '/' && strstr(name, "/"))
return NC_EINVAL;
/* Normalize name. */
if (!(norm_name = (char*)malloc(strlen(name) + 1)))
return NC_ENOMEM;
if ((retval = nc4_normalize_name(name, norm_name))) {
free(norm_name);
return retval;
}
/* Is the type in this group? If not, search parents. */
for (grptwo = grp; grptwo; grptwo = grptwo->parent) {
type = (NC_TYPE_INFO_T*)ncindexlookup(grptwo->type,norm_name);
if(type)
{
if (typeidp)
*typeidp = type->hdr.id;
break;
}
}
/* Still didn't find type? Search file recursively, starting at the
* root group. */
if (!type)
if ((type = nc4_rec_find_named_type(grp->nc4_info->root_grp, norm_name)))
if (typeidp)
*typeidp = type->hdr.id;
free(norm_name);
/* OK, I give up already! */
if (!type)
return NC_EBADTYPE;
return NC_NOERR;
}
/**
* @internal This internal function adds a new user defined type to
* the metadata of a group of an open file.
*
* @param ncid File and group ID.
* @param size Size in bytes of new type.
* @param name Name of new type.
* @param base_typeid Base type ID.
* @param type_class NC_VLEN, NC_ENUM, or NC_STRING
* @param typeidp Pointer that gets new type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ENOTNC4 User types in netCDF-4 files only.
* @return ::NC_EINVAL Bad size.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
static int
add_user_type(int ncid, size_t size, const char *name, nc_type base_typeid,
nc_type type_class, nc_type *typeidp)
{
NC_HDF5_FILE_INFO_T *h5;
NC_GRP_INFO_T *grp;
NC_TYPE_INFO_T *type;
char norm_name[NC_MAX_NAME + 1];
int retval;
/* Check and normalize the name. */
if ((retval = nc4_check_name(name, norm_name)))
return retval;
LOG((2, "%s: ncid 0x%x size %d name %s base_typeid %d ",
__FUNCTION__, ncid, size, norm_name, base_typeid));
/* Find group metadata. */
if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
return retval;
assert(h5 && grp);
/* Turn on define mode if it is not on. */
if (!(h5->cmode & NC_INDEF))
if ((retval = NC4_redef(ncid)))
return retval;
/* No size is provided for vlens or enums, get it from the base type. */
if (type_class == NC_VLEN || type_class == NC_ENUM)
{
if ((retval = nc4_get_typelen_mem(grp->nc4_info, base_typeid, &size)))
return retval;
}
else if (size <= 0)
return NC_EINVAL;
/* Check that this name is not in use as a var, grp, or type. */
if ((retval = nc4_check_dup_name(grp, norm_name)))
return retval;
/* Add to our list of types. */
if ((retval = nc4_type_list_add(grp, size, norm_name, &type)))
return retval;
/* Remember info about this type. */
type->nc_type_class = type_class;
if (type_class == NC_VLEN)
type->u.v.base_nc_typeid = base_typeid;
else if (type_class == NC_ENUM) {
type->u.e.base_nc_typeid = base_typeid;
type->u.e.enum_member = nclistnew();
} else if (type_class == NC_COMPOUND)
type->u.c.field = nclistnew();
/* Return the typeid to the user. */
if (typeidp)
*typeidp = type->hdr.id;
return NC_NOERR;
}
/**
* @internal Create a compound type.
*
* @param ncid File and group ID.
* @param size Gets size in bytes of one element of type.
* @param name Name of the type.
* @param typeidp Gets the type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
int
NC4_def_compound(int ncid, size_t size, const char *name, nc_type *typeidp)
{
return add_user_type(ncid, size, name, 0, NC_COMPOUND, typeidp);
}
/**
* @internal Insert a named field into a compound type.
*
* @param ncid File and group ID.
* @param typeid1 Type ID.
* @param name Name of the type.
* @param offset Offset of field.
* @param field_typeid Field type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
int
NC4_insert_compound(int ncid, nc_type typeid1, const char *name, size_t offset,
nc_type field_typeid)
{
return nc_insert_array_compound(ncid, typeid1, name, offset,
field_typeid, 0, NULL);
}
/**
* @internal Insert a named array into a compound type.
*
* @param ncid File and group ID.
* @param typeid1 Type ID.
* @param name Name of the array field.
* @param offset Offset in bytes.
* @param field_typeid Type of field.
* @param ndims Number of dims for field.
* @param dim_sizesp Array of dim sizes.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
extern int
NC4_insert_array_compound(int ncid, int typeid1, const char *name,
size_t offset, nc_type field_typeid,
int ndims, const int *dim_sizesp)
{
NC_GRP_INFO_T *grp;
NC_TYPE_INFO_T *type;
char norm_name[NC_MAX_NAME + 1];
int retval;
LOG((2, "nc_insert_array_compound: ncid 0x%x, typeid %d name %s "
"offset %d field_typeid %d ndims %d", ncid, typeid1,
name, offset, field_typeid, ndims));
/* Check and normalize the name. */
if ((retval = nc4_check_name(name, norm_name)))
return retval;
/* Find file metadata. */
if ((retval = nc4_find_nc4_grp(ncid, &grp)))
return retval;
/* Find type metadata. */
if ((retval = nc4_find_type(grp->nc4_info, typeid1, &type)))
return retval;
/* Did the user give us a good compound type typeid? */
if (!type || type->nc_type_class != NC_COMPOUND)
return NC_EBADTYPE;
/* If this type has already been written to the file, you can't
* change it. */
if (type->committed)
return NC_ETYPDEFINED;
/* Insert new field into this type's list of fields. */
if ((retval = nc4_field_list_add(type, norm_name, offset, 0, 0, field_typeid,
ndims, dim_sizesp)))
return retval;
return NC_NOERR;
}
/* Opaque type. */
/**
* @internal Create an opaque type. Provide a size and a name.
*
* @param ncid File and group ID.
* @param datum_size Size in bytes of a datum.
* @param name Name of new vlen type.
* @param typeidp Pointer that gets new type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
int
NC4_def_opaque(int ncid, size_t datum_size, const char *name,
nc_type *typeidp)
{
return add_user_type(ncid, datum_size, name, 0, NC_OPAQUE, typeidp);
}
/**
* @internal Define a variable length type.
*
* @param ncid File and group ID.
* @param name Name of new vlen type.
* @param base_typeid Base type of vlen.
* @param typeidp Pointer that gets new type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
int
NC4_def_vlen(int ncid, const char *name, nc_type base_typeid,
nc_type *typeidp)
{
return add_user_type(ncid, 0, name, base_typeid, NC_VLEN, typeidp);
}
/**
* @internal Create an enum type. Provide a base type and a name. At
* the moment only ints are accepted as base types.
*
* @param ncid File and group ID.
* @param base_typeid Base type of vlen.
* @param name Name of new vlen type.
* @param typeidp Pointer that gets new type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
int
NC4_def_enum(int ncid, nc_type base_typeid, const char *name,
nc_type *typeidp)
{
return add_user_type(ncid, 0, name, base_typeid, NC_ENUM, typeidp);
}
/**
* @internal Insert a identifier value into an enum type. The value
* must fit within the size of the enum type, the identifier size must
* be <= NC_MAX_NAME.
*
* @param ncid File and group ID.
* @param typeid1 Type ID.
* @param identifier Name of this enum value.
* @param value Value of enum.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EBADTYPE Type not found.
* @return ::NC_ETYPDEFINED Type already defined.
* @author Ed Hartnett
*/
int
NC4_insert_enum(int ncid, nc_type typeid1, const char *identifier,
const void *value)
{
NC_GRP_INFO_T *grp;
NC_TYPE_INFO_T *type;
char norm_name[NC_MAX_NAME + 1];
int retval;
LOG((2, "nc_insert_enum: ncid 0x%x, typeid %d identifier %s value %d", ncid,
typeid1, identifier, value));
/* Check and normalize the name. */
if ((retval = nc4_check_name(identifier, norm_name)))
return retval;
/* Find file metadata. */
if ((retval = nc4_find_nc4_grp(ncid, &grp)))
return retval;
/* Find type metadata. */
if ((retval = nc4_find_type(grp->nc4_info, typeid1, &type)))
return retval;
/* Did the user give us a good enum typeid? */
if (!type || type->nc_type_class != NC_ENUM)
return NC_EBADTYPE;
/* If this type has already been written to the file, you can't
* change it. */
if (type->committed)
return NC_ETYPDEFINED;
/* Insert new field into this type's list of fields. */
if ((retval = nc4_enum_member_add(type, type->size,
norm_name, value)))
return retval;
return NC_NOERR;
}
/**
* @internal Insert one element into an already allocated vlen array
* element.
*
* @param ncid File and group ID.
* @param typeid1 Type ID.
* @param vlen_element The VLEN element to insert.
* @param len Length of element in bytes.
* @param data Element data.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
NC4_put_vlen_element(int ncid, int typeid1, void *vlen_element,
size_t len, const void *data)
{
nc_vlen_t *tmp = (nc_vlen_t*)vlen_element;
tmp->len = len;
tmp->p = (void *)data;
return NC_NOERR;
}
/**
* @internal Insert one element into an already allocated vlen array
* element.
*
* @param ncid File and group ID.
* @param typeid1 Type ID.
* @param vlen_element The VLEN element to insert.
* @param len Length of element in bytes.
* @param data Element data.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
NC4_get_vlen_element(int ncid, int typeid1, const void *vlen_element,
size_t *len, void *data)
{
const nc_vlen_t *tmp = (nc_vlen_t*)vlen_element;
int type_size = 4;
*len = tmp->len;
memcpy(data, tmp->p, tmp->len * type_size);
return NC_NOERR;
}

466
libsrc4/nc4internal.c
View File

@ -22,24 +22,6 @@
#include "ncutf8.h"
#include "H5DSpublic.h"
#undef DEBUGH5
#ifdef DEBUGH5
/**
* @internal Provide a catchable error reporting function
*
* @param ignored Ignored.
*
* @return 0 for success.
*/
static herr_t
h5catch(void* ignored)
{
H5Eprint(NULL);
return 0;
}
#endif
/* These are the default chunk cache sizes for HDF5 files created or
* opened with netCDF-4. */
extern size_t nc4_chunk_cache_size;
@ -54,38 +36,6 @@ int nc_log_level = NC_TURN_OFF_LOGGING;
#endif /* LOGGING */
int nc4_hdf5_initialized = 0; /**< True if initialization has happened. */
/**
* @internal Provide a wrapper for H5Eset_auto
* @param func Pointer to func.
* @param client_data Client data.
*
* @return 0 for success
*/
static herr_t
set_auto(void* func, void *client_data)
{
#ifdef DEBUGH5
return H5Eset_auto2(H5E_DEFAULT,(H5E_auto2_t)h5catch,client_data);
#else
return H5Eset_auto2(H5E_DEFAULT,(H5E_auto2_t)func,client_data);
#endif
}
/**
* @internal Provide a function to do any necessary initialization of
* the HDF5 library.
*/
void
nc4_hdf5_initialize(void)
{
if (set_auto(NULL, NULL) < 0)
LOG((0, "Couldn't turn off HDF5 error messages!"));
LOG((1, "HDF5 error messages have been turned off."));
nc4_hdf5_initialized = 1;
}
/**
* @internal Check and normalize and name.
*
@ -139,85 +89,6 @@ nc4_check_name(const char *name, char *norm_name)
return NC_NOERR;
}
/**
* @internal Given a varid, return the maximum length of a dimension
* using dimid.
*
* @param grp Pointer to group info struct.
* @param varid Variable ID.
* @param dimid Dimension ID.
* @param maxlen Pointer that gets the max length.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
static int
find_var_dim_max_length(NC_GRP_INFO_T *grp, int varid, int dimid, size_t *maxlen)
{
hid_t datasetid = 0, spaceid = 0;
NC_VAR_INFO_T *var;
hsize_t *h5dimlen = NULL, *h5dimlenmax = NULL;
int d, dataset_ndims = 0;
int retval = NC_NOERR;
*maxlen = 0;
/* Find this var. */
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,varid);
if (!var) return NC_ENOTVAR;
assert(var->hdr.id == varid);
/* If the var hasn't been created yet, its size is 0. */
if (!var->created)
{
*maxlen = 0;
}
else
{
/* Get the number of records in the dataset. */
if ((retval = nc4_open_var_grp2(grp, var->hdr.id, &datasetid)))
BAIL(retval);
if ((spaceid = H5Dget_space(datasetid)) < 0)
BAIL(NC_EHDFERR);
/* If it's a scalar dataset, it has length one. */
if (H5Sget_simple_extent_type(spaceid) == H5S_SCALAR)
{
*maxlen = (var->dimids && var->dimids[0] == dimid) ? 1 : 0;
}
else
{
/* Check to make sure ndims is right, then get the len of each
dim in the space. */
if ((dataset_ndims = H5Sget_simple_extent_ndims(spaceid)) < 0)
BAIL(NC_EHDFERR);
if (dataset_ndims != var->ndims)
BAIL(NC_EHDFERR);
if (!(h5dimlen = malloc(dataset_ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
if (!(h5dimlenmax = malloc(dataset_ndims * sizeof(hsize_t))))
BAIL(NC_ENOMEM);
if ((dataset_ndims = H5Sget_simple_extent_dims(spaceid,
h5dimlen, h5dimlenmax)) < 0)
BAIL(NC_EHDFERR);
LOG((5, "find_var_dim_max_length: varid %d len %d max: %d",
varid, (int)h5dimlen[0], (int)h5dimlenmax[0]));
for (d=0; d<dataset_ndims; d++) {
if (var->dimids[d] == dimid) {
*maxlen = *maxlen > h5dimlen[d] ? *maxlen : h5dimlen[d];
}
}
}
}
exit:
if (spaceid > 0 && H5Sclose(spaceid) < 0)
BAIL2(NC_EHDFERR);
if (h5dimlen) free(h5dimlen);
if (h5dimlenmax) free(h5dimlenmax);
return retval;
}
/**
* @internal Given an NC pointer, add the necessary stuff for a
* netcdf-4 file.
@ -487,37 +358,6 @@ nc4_find_var(NC_GRP_INFO_T *grp, const char *name, NC_VAR_INFO_T **var)
return NC_NOERR;
}
/**
* @internal Search for type with a given HDF type id.
*
* @param h5 File
* @param target_hdf_typeid HDF5 type ID to find.
*
* @return Pointer to type info struct, or NULL if not found.
* @author Ed Hartnett
*/
NC_TYPE_INFO_T *
nc4_rec_find_hdf_type(NC_HDF5_FILE_INFO_T* h5, hid_t target_hdf_typeid)
{
NC_TYPE_INFO_T *type;
htri_t equal;
int i;
assert(h5);
for(i=0;i<nclistlength(h5->alltypes);i++) {
type = (NC_TYPE_INFO_T*)nclistget(h5->alltypes,i);
if(type == NULL) continue;
/* Is this the type we are searching for? */
if ((equal = H5Tequal(type->native_hdf_typeid ? type->native_hdf_typeid : type->hdf_typeid, target_hdf_typeid)) < 0)
return NULL;
if (equal)
return type;
}
/* Can't find it. Fate, why do you mock me? */
return NULL;
}
/**
* @internal Locate netCDF type by name.
*
@ -599,56 +439,6 @@ nc4_find_type(const NC_HDF5_FILE_INFO_T *h5, nc_type typeid, NC_TYPE_INFO_T **ty
return NC_NOERR;
}
/**
* @internal Find the actual length of a dim by checking the length of
* that dim in all variables that use it, in grp or children. **len
* must be initialized to zero before this function is called.
*
* @param grp Pointer to group info struct.
* @param dimid Dimension ID.
* @param len Pointer to pointer that gets length.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
nc4_find_dim_len(NC_GRP_INFO_T *grp, int dimid, size_t **len)
{
NC_GRP_INFO_T *g;
NC_VAR_INFO_T *var;
int retval;
int i;
assert(grp && len);
LOG((3, "nc4_find_dim_len: grp->name %s dimid %d", grp->hdr.name, dimid));
/* If there are any groups, call this function recursively on
* them. */
for(i=0;i<ncindexsize(grp->children);i++) {
g = (NC_GRP_INFO_T*)ncindexith(grp->children,i);
if(g == NULL) continue;
if ((retval = nc4_find_dim_len(g, dimid, len)))
return retval;
}
/* For all variables in this group, find the ones that use this
* dimension, and remember the max length. */
for (i=0; i < ncindexsize(grp->vars); i++)
{
size_t mylen;
var = (NC_VAR_INFO_T*)ncindexith(grp->vars,i);
if (var == NULL) continue;
/* Find max length of dim in this variable... */
if ((retval = find_var_dim_max_length(grp, var->hdr.id, dimid, &mylen)))
return retval;
**len = **len > mylen ? **len : mylen;
}
return NC_NOERR;
}
/**
* @internal Given a group, find an att. If name is provided, use that,
* otherwise use the attnum.
@ -1757,230 +1547,6 @@ nc4_att_free(NC_ATT_INFO_T *att)
return NC_NOERR;
}
/**
* @internal Break a coordinate variable to separate the dimension and
* the variable.
*
* This is called from nc_rename_dim() and nc_rename_var(). In some
* renames, the coord variable must stay, but it is no longer a coord
* variable. This function changes a coord var into an ordinary
* variable.
*
* @param grp Pointer to group info struct.
* @param coord_var Pointer to variable info struct.
* @param dim Pointer to dimension info struct.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @author Quincey Koziol, Ed Hartnett
*/
int
nc4_break_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var, NC_DIM_INFO_T *dim)
{
int retval = NC_NOERR;
/* Sanity checks */
assert(grp && coord_var && dim && dim->coord_var == coord_var &&
coord_var->dim[0] == dim && coord_var->dimids[0] == dim->hdr.id &&
!dim->hdf_dimscaleid);
LOG((3, "%s dim %s was associated with var %s, but now has different name",
__func__, dim->hdr.name, coord_var->hdr.name));
/* If we're replacing an existing dimscale dataset, go to
* every var in the file and detach this dimension scale. */
if ((retval = rec_detach_scales(grp->nc4_info->root_grp,
dim->hdr.id, coord_var->hdf_datasetid)))
return retval;
/* Allow attached dimscales to be tracked on the [former]
* coordinate variable */
if (coord_var->ndims)
{
/* Coordinate variables shouldn't have dimscales attached. */
assert(!coord_var->dimscale_attached);
/* Allocate space for tracking them */
if (!(coord_var->dimscale_attached = calloc(coord_var->ndims,
sizeof(nc_bool_t))))
return NC_ENOMEM;
}
/* Remove the atts that go with being a coordinate var. */
/* if ((retval = remove_coord_atts(coord_var->hdf_datasetid))) */
/* return retval; */
/* Detach dimension from variable */
coord_var->dimscale = NC_FALSE;
dim->coord_var = NULL;
/* Set state transition indicators */
coord_var->was_coord_var = NC_TRUE;
coord_var->became_coord_var = NC_FALSE;
return NC_NOERR;
}
/**
* @internal Delete an existing dimscale-only dataset.
*
* A dimscale-only HDF5 dataset is created when a dim is defined
* without an accompanying coordinate variable.
*
* Sometimes, during renames, or late creation of variables, an
* existing, dimscale-only dataset must be removed. This means
* detaching all variables that use the dataset, then closing and
* unlinking it.
*
* @param grp The grp of the dimscale-only dataset to be deleted, or a
* higher group in the hierarchy (ex. root group).
* @param dimid id of the dimension
* @param dim Pointer to the dim with the dimscale-only dataset to be
* deleted.
*
* @return ::NC_NOERR No error.
* @return ::NC_EHDFERR HDF5 error.
* @author Ed Hartnett
*/
int
delete_existing_dimscale_dataset(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T *dim)
{
int retval;
assert(grp && dim);
LOG((2, "%s: deleting dimscale dataset %s dimid %d", __func__, dim->hdr.name,
dimid));
/* Detach dimscale from any variables using it */
if ((retval = rec_detach_scales(grp, dimid, dim->hdf_dimscaleid)) < 0)
return retval;
/* Close the HDF5 dataset */
if (H5Dclose(dim->hdf_dimscaleid) < 0)
return NC_EHDFERR;
dim->hdf_dimscaleid = 0;
/* Now delete the dataset. */
if (H5Gunlink(grp->hdf_grpid, dim->hdr.name) < 0)
return NC_EHDFERR;
return NC_NOERR;
}
/**
* @internal Reform a coordinate variable from a dimension and a
* variable.
*
* @param grp Pointer to group info struct.
* @param var Pointer to variable info struct.
* @param dim Pointer to dimension info struct.
*
* @return ::NC_NOERR No error.
* @author Quincey Koziol
*/
int
nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, NC_DIM_INFO_T *dim)
{
int need_to_reattach_scales = 0;
int retval = NC_NOERR;
assert(grp && var && dim);
LOG((3, "%s: dim->hdr.name %s var->hdr.name %s", __func__, dim->hdr.name, var->hdr.name));
/* Detach dimscales from the [new] coordinate variable */
if(var->dimscale_attached)
{
int dims_detached = 0;
int finished = 0;
int d;
/* Loop over all dimensions for variable */
for (d = 0; d < var->ndims && !finished; d++)
{
/* Is there a dimscale attached to this axis? */
if(var->dimscale_attached[d])
{
NC_GRP_INFO_T *g;
int k;
for (g = grp; g && !finished; g = g->parent)
{
NC_DIM_INFO_T *dim1;
for(k=0;k<ncindexsize(g->dim);k++)
{
if((dim1 = (NC_DIM_INFO_T*)ncindexith(g->dim,k)) == NULL) continue;
if (var->dimids[d] == dim1->hdr.id)
{
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;
/* dim_datasetid may be 0 in some cases when
* renames of dims and vars are happening. In
* this case, the scale has already been
* detached. */
if (dim_datasetid > 0)
{
LOG((3, "detaching scale from %s", var->hdr.name));
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++;
}
}
}
}
} /* next variable dimension */
/* Release & reset the array tracking attached dimscales */
free(var->dimscale_attached);
var->dimscale_attached = NULL;
need_to_reattach_scales++;
}
/* Use variable's dataset ID for the dimscale ID. */
if (dim->hdf_dimscaleid && grp != NULL)
{
LOG((3, "closing and unlinking dimscale dataset %s", dim->hdr.name));
if (H5Dclose(dim->hdf_dimscaleid) < 0)
BAIL(NC_EHDFERR);
dim->hdf_dimscaleid = 0;
/* Now delete the dimscale's dataset
(it will be recreated later, if necessary) */
if (H5Gunlink(grp->hdf_grpid, dim->hdr.name) < 0)
return NC_EDIMMETA;
}
/* Attach variable to dimension */
var->dimscale = NC_TRUE;
dim->coord_var = var;
/* Check if this variable used to be a coord. var */
if (need_to_reattach_scales || (var->was_coord_var && grp != NULL))
{
/* Reattach the scale everywhere it is used. */
/* (Recall that netCDF dimscales are always 1-D) */
if ((retval = rec_reattach_scales(grp->nc4_info->root_grp,
var->dimids[0], var->hdf_datasetid)))
return retval;
/* Set state transition indicator (cancels earlier transition) */
var->was_coord_var = NC_FALSE;
}
else
/* Set state transition indicator */
var->became_coord_var = NC_TRUE;
exit:
return retval;
}
/**
* @internal Normalize a UTF8 name. Put the result in norm_name, which
* can be NC_MAX_NAME + 1 in size. This function makes sure the free()
@ -2030,23 +1596,23 @@ nc_set_log_level(int new_level)
if(!nc4_hdf5_initialized)
nc4_hdf5_initialize();
/* If the user wants to completely turn off logging, turn off HDF5
logging too. Now I truly can't think of what to do if this
fails, so just ignore the return code. */
if (new_level == NC_TURN_OFF_LOGGING)
{
set_auto(NULL,NULL);
LOG((1, "HDF5 error messages turned off!"));
}
/* /\* If the user wants to completely turn off logging, turn off HDF5 */
/* logging too. Now I truly can't think of what to do if this */
/* fails, so just ignore the return code. *\/ */
/* if (new_level == NC_TURN_OFF_LOGGING) */
/* { */
/* set_auto(NULL,NULL); */
/* LOG((1, "HDF5 error messages turned off!")); */
/* } */
/* Do we need to turn HDF5 logging back on? */
if (new_level > NC_TURN_OFF_LOGGING &&
nc_log_level <= NC_TURN_OFF_LOGGING)
{
if (set_auto((H5E_auto_t)&H5Eprint, stderr) < 0)
LOG((0, "H5Eset_auto failed!"));
LOG((1, "HDF5 error messages turned on."));
}
/* /\* Do we need to turn HDF5 logging back on? *\/ */
/* if (new_level > NC_TURN_OFF_LOGGING && */
/* nc_log_level <= NC_TURN_OFF_LOGGING) */
/* { */
/* if (set_auto((H5E_auto_t)&H5Eprint, stderr) < 0) */
/* LOG((0, "H5Eset_auto failed!")); */
/* LOG((1, "HDF5 error messages turned on.")); */
/* } */
/* Now remember the new level. */
nc_log_level = new_level;

534
libsrc4/nc4type.c
View File

@ -1,29 +1,24 @@
/* Copyright 2005, University Corporation for Atmospheric Research. See
* the COPYRIGHT file for copying and redistribution conditions. */
/**
* @file
*
* @internal 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.
* @file @internal 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 handles the nc4 user-defined type functions
* (i.e. compound and opaque types).
*
* Copyright 2005, University Corporation for Atmospheric Research. See
* the COPYRIGHT file for copying and redistribution conditions.
*
* @author Ed Hartnett
*/
#include "nc4internal.h"
#include "nc4dispatch.h"
#define NUM_ATOMIC_TYPES (NC_MAX_ATOMIC_TYPE+1) /**< Number of netCDF atomic types. */
/** @internal Names of atomic types. */
char* nc4_atomic_name[NUM_ATOMIC_TYPES] = {"none", "byte", "char",
"short", "int", "float",
"double", "ubyte",
"ushort", "uint",
"int64", "uint64", "string"};
"short", "int", "float",
"double", "ubyte",
"ushort", "uint",
"int64", "uint64", "string"};
/* The sizes of types may vary from platform to platform, but within
* netCDF files, type sizes are fixed. */
@ -36,161 +31,6 @@ char* nc4_atomic_name[NUM_ATOMIC_TYPES] = {"none", "byte", "char",
#define NC_DOUBLE_LEN 8 /**< @internal Size of double. */
#define NC_INT64_LEN 8 /**< @internal Size of int64. */
/**
* @internal Determine if two types are equal.
*
* @param ncid1 First file/group ID.
* @param typeid1 First type ID.
* @param ncid2 Second file/group ID.
* @param typeid2 Second type ID.
* @param equalp Pointer that will get 1 if the two types are equal.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EBADTYPE Type not found.
* @return ::NC_EINVAL Invalid type.
* @author Ed Hartnett
*/
extern int
NC4_inq_type_equal(int ncid1, nc_type typeid1, int ncid2,
nc_type typeid2, int *equalp)
{
NC_GRP_INFO_T *grpone, *grptwo;
NC_TYPE_INFO_T *type1, *type2;
int retval;
LOG((2, "nc_inq_type_equal: ncid1 0x%x typeid1 %d ncid2 0x%x typeid2 %d",
ncid1, typeid1, ncid2, typeid2));
/* Check input. */
if(equalp == NULL) return NC_NOERR;
if (typeid1 <= NC_NAT || typeid2 <= NC_NAT)
return NC_EINVAL;
/* If one is atomic, and the other user-defined, the types are not
* equal. */
if ((typeid1 <= NC_STRING && typeid2 > NC_STRING) ||
(typeid2 <= NC_STRING && typeid1 > NC_STRING))
{
if (equalp) *equalp = 0;
return NC_NOERR;
}
/* If both are atomic types, the answer is easy. */
if (typeid1 <= NUM_ATOMIC_TYPES)
{
if (equalp)
{
if (typeid1 == typeid2)
*equalp = 1;
else
*equalp = 0;
}
return NC_NOERR;
}
/* Not atomic types - so find type1 and type2 information. */
if ((retval = nc4_find_nc4_grp(ncid1, &grpone)))
return retval;
if (!(type1 = nc4_rec_find_nc_type(grpone->nc4_info,
typeid1)))
return NC_EBADTYPE;
if ((retval = nc4_find_nc4_grp(ncid2, &grptwo)))
return retval;
if (!(type2 = nc4_rec_find_nc_type(grptwo->nc4_info,
typeid2)))
return NC_EBADTYPE;
/* Are the two types equal? */
if (equalp)
{
if ((retval = H5Tequal(type1->native_hdf_typeid, type2->native_hdf_typeid)) < 0)
return NC_EHDFERR;
*equalp = 1 ? retval : 0;
}
return NC_NOERR;
}
/**
* @internal Get the id of a type from the name.
*
* @param ncid File and group ID.
* @param name Name of type.
* @param typeidp Pointer that will get the type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_ENOMEM Out of memory.
* @return ::NC_EINVAL Bad size.
* @return ::NC_ENOTNC4 User types in netCDF-4 files only.
* @return ::NC_EBADTYPE Type not found.
* @author Ed Hartnett
*/
extern int
NC4_inq_typeid(int ncid, const char *name, nc_type *typeidp)
{
NC_GRP_INFO_T *grp;
NC_GRP_INFO_T *grptwo;
NC_HDF5_FILE_INFO_T *h5;
NC_TYPE_INFO_T *type = NULL;
char *norm_name;
int i, retval;
/* Handle atomic types. */
for (i = 0; i < NUM_ATOMIC_TYPES; i++)
if (!strcmp(name, nc4_atomic_name[i]))
{
if (typeidp)
*typeidp = i;
return NC_NOERR;
}
/* Find info for this file and group, and set pointer to each. */
if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
return retval;
assert(h5 && grp);
/* If the first char is a /, this is a fully-qualified
* name. Otherwise, this had better be a local name (i.e. no / in
* the middle). */
if (name[0] != '/' && strstr(name, "/"))
return NC_EINVAL;
/* Normalize name. */
if (!(norm_name = (char*)malloc(strlen(name) + 1)))
return NC_ENOMEM;
if ((retval = nc4_normalize_name(name, norm_name))) {
free(norm_name);
return retval;
}
/* Is the type in this group? If not, search parents. */
for (grptwo = grp; grptwo; grptwo = grptwo->parent) {
type = (NC_TYPE_INFO_T*)ncindexlookup(grptwo->type,norm_name);
if(type)
{
if (typeidp)
*typeidp = type->hdr.id;
break;
}
}
/* Still didn't find type? Search file recursively, starting at the
* root group. */
if (!type)
if ((type = nc4_rec_find_named_type(grp->nc4_info->root_grp, norm_name)))
if (typeidp)
*typeidp = type->hdr.id;
free(norm_name);
/* OK, I give up already! */
if (!type)
return NC_EBADTYPE;
return NC_NOERR;
}
/**
* @internal Find all user-defined types for a location. This finds
* all user-defined types in a group.
@ -239,86 +79,6 @@ NC4_inq_typeids(int ncid, int *ntypes, int *typeids)
return NC_NOERR;
}
/**
* @internal This internal function adds a new user defined type to
* the metadata of a group of an open file.
*
* @param ncid File and group ID.
* @param size Size in bytes of new type.
* @param name Name of new type.
* @param base_typeid Base type ID.
* @param type_class NC_VLEN, NC_ENUM, or NC_STRING
* @param typeidp Pointer that gets new type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_ENOTNC4 User types in netCDF-4 files only.
* @return ::NC_EINVAL Bad size.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
static int
add_user_type(int ncid, size_t size, const char *name, nc_type base_typeid,
nc_type type_class, nc_type *typeidp)
{
NC_HDF5_FILE_INFO_T *h5;
NC_GRP_INFO_T *grp;
NC_TYPE_INFO_T *type;
char norm_name[NC_MAX_NAME + 1];
int retval;
/* Check and normalize the name. */
if ((retval = nc4_check_name(name, norm_name)))
return retval;
LOG((2, "%s: ncid 0x%x size %d name %s base_typeid %d ",
__FUNCTION__, ncid, size, norm_name, base_typeid));
/* Find group metadata. */
if ((retval = nc4_find_grp_h5(ncid, &grp, &h5)))
return retval;
assert(h5 && grp);
/* Turn on define mode if it is not on. */
if (!(h5->cmode & NC_INDEF))
if ((retval = NC4_redef(ncid)))
return retval;
/* No size is provided for vlens or enums, get it from the base type. */
if (type_class == NC_VLEN || type_class == NC_ENUM)
{
if ((retval = nc4_get_typelen_mem(grp->nc4_info, base_typeid, &size)))
return retval;
}
else if (size <= 0)
return NC_EINVAL;
/* Check that this name is not in use as a var, grp, or type. */
if ((retval = nc4_check_dup_name(grp, norm_name)))
return retval;
/* Add to our list of types. */
if ((retval = nc4_type_list_add(grp, size, norm_name, &type)))
return retval;
/* Remember info about this type. */
type->nc_type_class = type_class;
if (type_class == NC_VLEN)
type->u.v.base_nc_typeid = base_typeid;
else if (type_class == NC_ENUM) {
type->u.e.base_nc_typeid = base_typeid;
type->u.e.enum_member = nclistnew();
} else if (type_class == NC_COMPOUND)
type->u.c.field = nclistnew();
/* Return the typeid to the user. */
if (typeidp)
*typeidp = type->hdr.id;
return NC_NOERR;
}
/**
* @internal Get the name and size of a type. For strings, 1 is
* returned. For VLEN the base type len is returned.
@ -381,109 +141,6 @@ NC4_inq_type(int ncid, nc_type typeid1, char *name, size_t *size)
return NC_NOERR;
}
/**
* @internal Create a compound type.
*
* @param ncid File and group ID.
* @param size Gets size in bytes of one element of type.
* @param name Name of the type.
* @param typeidp Gets the type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
int
NC4_def_compound(int ncid, size_t size, const char *name, nc_type *typeidp)
{
return add_user_type(ncid, size, name, 0, NC_COMPOUND, typeidp);
}
/**
* @internal Insert a named field into a compound type.
*
* @param ncid File and group ID.
* @param typeid1 Type ID.
* @param name Name of the type.
* @param offset Offset of field.
* @param field_typeid Field type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
int
NC4_insert_compound(int ncid, nc_type typeid1, const char *name, size_t offset,
nc_type field_typeid)
{
return nc_insert_array_compound(ncid, typeid1, name, offset,
field_typeid, 0, NULL);
}
/**
* @internal Insert a named array into a compound type.
*
* @param ncid File and group ID.
* @param typeid1 Type ID.
* @param name Name of the array field.
* @param offset Offset in bytes.
* @param field_typeid Type of field.
* @param ndims Number of dims for field.
* @param dim_sizesp Array of dim sizes.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
extern int
NC4_insert_array_compound(int ncid, int typeid1, const char *name,
size_t offset, nc_type field_typeid,
int ndims, const int *dim_sizesp)
{
NC_GRP_INFO_T *grp;
NC_TYPE_INFO_T *type;
char norm_name[NC_MAX_NAME + 1];
int retval;
LOG((2, "nc_insert_array_compound: ncid 0x%x, typeid %d name %s "
"offset %d field_typeid %d ndims %d", ncid, typeid1,
name, offset, field_typeid, ndims));
/* Check and normalize the name. */
if ((retval = nc4_check_name(name, norm_name)))
return retval;
/* Find file metadata. */
if ((retval = nc4_find_nc4_grp(ncid, &grp)))
return retval;
/* Find type metadata. */
if ((retval = nc4_find_type(grp->nc4_info, typeid1, &type)))
return retval;
/* Did the user give us a good compound type typeid? */
if (!type || type->nc_type_class != NC_COMPOUND)
return NC_EBADTYPE;
/* If this type has already been written to the file, you can't
* change it. */
if (type->committed)
return NC_ETYPDEFINED;
/* Insert new field into this type's list of fields. */
if ((retval = nc4_field_list_add(type, norm_name, offset, 0, 0, field_typeid,
ndims, dim_sizesp)))
return retval;
return NC_NOERR;
}
/**
* @internal Find info about any user defined type.
*
@ -705,74 +362,6 @@ NC4_inq_compound_fieldindex(int ncid, nc_type typeid1, const char *name, int *fi
return NC_NOERR;
}
/* Opaque type. */
/**
* @internal Create an opaque type. Provide a size and a name.
*
* @param ncid File and group ID.
* @param datum_size Size in bytes of a datum.
* @param name Name of new vlen type.
* @param typeidp Pointer that gets new type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
int
NC4_def_opaque(int ncid, size_t datum_size, const char *name,
nc_type *typeidp)
{
return add_user_type(ncid, datum_size, name, 0, NC_OPAQUE, typeidp);
}
/**
* @internal Define a variable length type.
*
* @param ncid File and group ID.
* @param name Name of new vlen type.
* @param base_typeid Base type of vlen.
* @param typeidp Pointer that gets new type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
int
NC4_def_vlen(int ncid, const char *name, nc_type base_typeid,
nc_type *typeidp)
{
return add_user_type(ncid, 0, name, base_typeid, NC_VLEN, typeidp);
}
/**
* @internal Create an enum type. Provide a base type and a name. At
* the moment only ints are accepted as base types.
*
* @param ncid File and group ID.
* @param base_typeid Base type of vlen.
* @param name Name of new vlen type.
* @param typeidp Pointer that gets new type ID.
*
* @return ::NC_NOERR No error.
* @return ::NC_EMAXNAME Name is too long.
* @return ::NC_EBADNAME Name breaks netCDF name rules.
* @author Ed Hartnett
*/
int
NC4_def_enum(int ncid, nc_type base_typeid, const char *name,
nc_type *typeidp)
{
return add_user_type(ncid, 0, name, base_typeid, NC_ENUM, typeidp);
}
/**
* @internal Get enum name from enum value. Name size will be <=
* NC_MAX_NAME.
@ -915,108 +504,3 @@ NC4_inq_enum_member(int ncid, nc_type typeid1, int idx, char *identifier,
return NC_NOERR;
}
/**
* @internal Insert a identifier value into an enum type. The value
* must fit within the size of the enum type, the identifier size must
* be <= NC_MAX_NAME.
*
* @param ncid File and group ID.
* @param typeid1 Type ID.
* @param identifier Name of this enum value.
* @param value Value of enum.
*
* @return ::NC_NOERR No error.
* @return ::NC_EBADID Bad ncid.
* @return ::NC_EBADTYPE Type not found.
* @return ::NC_ETYPDEFINED Type already defined.
* @author Ed Hartnett
*/
int
NC4_insert_enum(int ncid, nc_type typeid1, const char *identifier,
const void *value)
{
NC_GRP_INFO_T *grp;
NC_TYPE_INFO_T *type;
char norm_name[NC_MAX_NAME + 1];
int retval;
LOG((2, "nc_insert_enum: ncid 0x%x, typeid %d identifier %s value %d", ncid,
typeid1, identifier, value));
/* Check and normalize the name. */
if ((retval = nc4_check_name(identifier, norm_name)))
return retval;
/* Find file metadata. */
if ((retval = nc4_find_nc4_grp(ncid, &grp)))
return retval;
/* Find type metadata. */
if ((retval = nc4_find_type(grp->nc4_info, typeid1, &type)))
return retval;
/* Did the user give us a good enum typeid? */
if (!type || type->nc_type_class != NC_ENUM)
return NC_EBADTYPE;
/* If this type has already been written to the file, you can't
* change it. */
if (type->committed)
return NC_ETYPDEFINED;
/* Insert new field into this type's list of fields. */
if ((retval = nc4_enum_member_add(type, type->size,
norm_name, value)))
return retval;
return NC_NOERR;
}
/**
* @internal Insert one element into an already allocated vlen array
* element.
*
* @param ncid File and group ID.
* @param typeid1 Type ID.
* @param vlen_element The VLEN element to insert.
* @param len Length of element in bytes.
* @param data Element data.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
NC4_put_vlen_element(int ncid, int typeid1, void *vlen_element,
size_t len, const void *data)
{
nc_vlen_t *tmp = (nc_vlen_t*)vlen_element;
tmp->len = len;
tmp->p = (void *)data;
return NC_NOERR;
}
/**
* @internal Insert one element into an already allocated vlen array
* element.
*
* @param ncid File and group ID.
* @param typeid1 Type ID.
* @param vlen_element The VLEN element to insert.
* @param len Length of element in bytes.
* @param data Element data.
*
* @return ::NC_NOERR No error.
* @author Ed Hartnett
*/
int
NC4_get_vlen_element(int ncid, int typeid1, const void *vlen_element,
size_t *len, void *data)
{
const nc_vlen_t *tmp = (nc_vlen_t*)vlen_element;
int type_size = 4;
*len = tmp->len;
memcpy(data, tmp->p, tmp->len * type_size);
return NC_NOERR;
}