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netcdf-c/include/nc4internal.h

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/* Copyright 2018-2018 University Corporation for Atmospheric
Research/Unidata. */
/**
* @file
* @internal This header file contains macros, types and prototypes
* used to build and manipulate the netCDF metadata model.
*
* @author Ed Hartnett, Dennis Heimbigner, Ward Fisher
*/
#ifndef _NC4INTERNAL_
#define _NC4INTERNAL_
#include "netcdf.h"
#include "config.h"
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include "ncdimscale.h"
#include "nc_logging.h"
#include "ncindex.h"
#include "nc_provenance.h"
#include "netcdf_f.h"
#include "netcdf_mem.h"
#include "netcdf_filter.h"
#ifdef USE_PARALLEL
#include "netcdf_par.h"
#endif /* USE_PARALLEL */
/* Always needed */
#include "nc.h"
/** The file ID is stored in the first two bytes of ncid. */
#define FILE_ID_MASK (0xffff0000)
/** The group ID is stored in the last two bytes of ncid. */
#define GRP_ID_MASK (0x0000ffff)
/** File and group IDs are each 16 bits of the ncid. */
#define ID_SHIFT (16)
/* typedef enum {GET, PUT} NC_PG_T; */
/** These are the different objects that can be in our hash-lists. */
typedef enum {NCNAT, NCVAR, NCDIM, NCATT, NCTYP, NCFLD, NCGRP} NC_SORT;
/** The netCDF V2 error code. */
#define NC_V2_ERR (-1)
/** The name of the root group. */
#define NC_GROUP_NAME "/"
/** One mega-byte. */
#define MEGABYTE 1048576
/** The HDF5 ID for the szip filter. */
#define HDF5_FILTER_SZIP 4
#define X_SCHAR_MIN (-128) /**< Minimum signed char value. */
#define X_SCHAR_MAX 127 /**< Maximum signed char value. */
#define X_UCHAR_MAX 255U /**< Maximum unsigned char value. */
#define X_SHORT_MIN (-32768) /**< Minimum short value. */
#define X_SHRT_MIN X_SHORT_MIN /**< This alias is compatible with limits.h. */
#define X_SHORT_MAX 32767 /**< Maximum short value. */
#define X_SHRT_MAX X_SHORT_MAX /**< This alias is compatible with limits.h. */
#define X_USHORT_MAX 65535U /**< Maximum unsigned short value. */
#define X_USHRT_MAX X_USHORT_MAX /**< This alias is compatible with limits.h. */
#define X_INT_MIN (-2147483647-1) /**< Minimum int value. */
#define X_INT_MAX 2147483647 /**< Maximum int value. */
#define X_LONG_MIN X_INT_MIN /**< Minimum long value. */
#define X_LONG_MAX X_INT_MAX /**< Maximum long value. */
#define X_UINT_MAX 4294967295U /**< Maximum unsigned int value. */
#define X_INT64_MIN (-9223372036854775807LL-1LL) /**< Minimum int64 value. */
#define X_INT64_MAX 9223372036854775807LL /**< Maximum int64 value. */
#define X_UINT64_MAX 18446744073709551615ULL /**< Maximum unsigned int64 value. */
#ifdef _WIN32 /* Windows, of course, has to be a *little* different. */
#define X_FLOAT_MAX 3.402823466e+38f
#else
#define X_FLOAT_MAX 3.40282347e+38f /**< Maximum float value. */
#endif /* _WIN32 */
#define X_FLOAT_MIN (-X_FLOAT_MAX) /**< Minimum float value. */
#define X_DOUBLE_MAX 1.7976931348623157e+308 /**< Maximum double value. */
#define X_DOUBLE_MIN (-X_DOUBLE_MAX) /**< Minimum double value. */
/** This is the number of netCDF atomic types. */
#define NUM_ATOMIC_TYPES (NC_MAX_ATOMIC_TYPE + 1)
/** Number of parameters needed for ZLIB filter. */
#define CD_NELEMS_ZLIB 1
/** Get a pointer to the NC_FILE_INFO_T from dispatchdata field. */
#define NC4_DATA(nc) ((NC_FILE_INFO_T *)(nc)->dispatchdata)
/** Set a pointer to the NC_FILE_INFO_T in the dispatchdata field. */
#define NC4_DATA_SET(nc,data) ((nc)->dispatchdata = (void *)(data))
/* Reserved attribute flags: must be powers of 2. */
/** Hidden dimscale-related, per-variable attributes; immutable and
* unreadable thru API. */
#define DIMSCALEFLAG 1
/** Readonly global attributes; readable, but immutable thru the
* API. */
#define READONLYFLAG 2
/** Subset of readonly flags; readable by name only thru the API. */
#define NAMEONLYFLAG 4
/** Subset of readonly flags; Value is actually in file. */
#define MATERIALIZEDFLAG 8
/* Generic reserved Attributes */
#define NC_ATT_REFERENCE_LIST "REFERENCE_LIST" /**< HDF5 reference list attribute name. */
#define NC_ATT_CLASS "CLASS" /**< HDF5 class atttribute name. */
#define NC_ATT_DIMENSION_LIST "DIMENSION_LIST" /**< HDF5 dimension list attribute name. */
#define NC_ATT_NAME "NAME" /**< HDF5 name atttribute name. */
#define NC_ATT_COORDINATES COORDINATES /**< Coordinates atttribute name. */
#define NC_ATT_FORMAT "_Format" /**< Format atttribute name. */
/** Boolean type, to make the code easier to read. */
typedef enum {NC_FALSE = 0, NC_TRUE = 1} nc_bool_t;
/* Forward declarations. */
struct NC_GRP_INFO;
struct NC_TYPE_INFO;
struct NC_FIlterobject;
/**
* This struct provides indexed Access to Meta-data objects. See the
* document docs/indexing.dox for detailed information.
*
* Basically it provides a common header and use NCindex instances
* instead of linked lists.
*
* WARNING: ALL OBJECTS THAT CAN BE INSERTED INTO AN NCindex MUST HAVE
* AN INSTANCE of NC_OBJ AS THE FIRST FIELD.
*/
typedef struct NC_OBJ
{
NC_SORT sort; /**< Type of object. */
char* name; /**< Name, assumed to be null terminated. */
size_t id; /**< This objects ID. */
unsigned int hashkey; /**< The hash key, crc32(name). */
} NC_OBJ;
/**
* This struct holds information about reserved attributes. These
* attributes cannot be created or read by the user (through the
* netCDF API). */
typedef struct NC_reservedatt
{
const char *name; /**< Name of the reserved attribute. */
int flags; /**< Flags that control handling of reserved attribute. */
} NC_reservedatt;
/** This is a struct to handle the dimension metadata. */
typedef struct NC_DIM_INFO
{
NC_OBJ hdr; /**< The hdr contains the name and ID. */
struct NC_GRP_INFO *container; /**< Pointer to containing group. */
size_t len; /**< Length of this dimension. */
nc_bool_t unlimited; /**< True if the dimension is unlimited */
nc_bool_t extended; /**< True if the dimension needs to be extended. */
nc_bool_t too_long; /**< True if len is too big to fit in local size_t. */
void *format_dim_info; /**< Pointer to format-specific dim info. */
struct NC_VAR_INFO *coord_var; /**< The coord var, if it exists. */
} NC_DIM_INFO_T;
/** This is a struct to handle the attribute metadata. */
typedef struct NC_ATT_INFO
{
NC_OBJ hdr; /**< The hdr contains the name and ID. */
struct NC_OBJ *container; /**< Pointer to containing group|var. */
int len; /**< Length of attribute data. */
nc_bool_t dirty; /**< True if attribute modified. */
nc_bool_t created; /**< True if attribute already created. */
nc_type nc_typeid; /**< NetCDF type of attribute's data. */
void *format_att_info; /**< Pointer to format-specific att info. */
void *data; /**< The attribute data. */
nc_vlen_t *vldata; /**< VLEN data (only used for vlen types). */
char **stdata; /**< String data (only for string type). */
} NC_ATT_INFO_T;
/** This is a struct to handle the var metadata. */
typedef struct NC_VAR_INFO
{
NC_OBJ hdr; /**< The hdr contains the name and ID. */
char *hdf5_name; /**< Used if name in HDF5 must be different from name. */
struct NC_GRP_INFO *container; /**< Pointer to containing group. */
size_t ndims; /**< Number of dims. */
int *dimids; /**< Dim IDs. */
NC_DIM_INFO_T **dim; /**< Pointer to array of NC_DIM_INFO_T. */
nc_bool_t is_new_var; /**< True if variable is newly created. */
nc_bool_t was_coord_var; /**< True if variable was a coordinate var, but either the dim or var has been renamed. */
nc_bool_t became_coord_var; /**< True if variable _became_ a coordinate var, because either the dim or var has been renamed. */
nc_bool_t fill_val_changed; /**< True if variable's fill value changes after it has been created. */
nc_bool_t attr_dirty; /**< True if variable's attributes are dirty and should be rewritten. */
nc_bool_t created; /**< Variable has already been created (_not_ that it was just created). */
nc_bool_t written_to; /**< True if variable has data written to it. */
struct NC_TYPE_INFO *type_info; /**< Contains info about the variable type. */
int atts_read; /**< If true, the atts have been read. */
nc_bool_t meta_read; /**< True if this vars metadata has been completely read. */
nc_bool_t coords_read; /**< True if this var has hidden coordinates att, and it has been read. */
NCindex *att; /**< List of NC_ATT_INFO_T. */
nc_bool_t no_fill; /**< True if no fill value is defined for var. */
void *fill_value; /**< Pointer to fill value, or NULL. */
size_t *chunksizes; /**< For chunked storage, an array (size ndims) of chunksizes. */
int storage; /**< Storage of this var, compact, contiguous, or chunked. */
int parallel_access; /**< Type of parallel access for I/O on variable (collective or independent). */
nc_bool_t dimscale; /**< True if var is a dimscale. */
nc_bool_t *dimscale_attached; /**< Array of flags that are true if dimscale is attached for that dim index. */
nc_bool_t shuffle; /**< True if var has shuffle filter applied. */
nc_bool_t fletcher32; /**< True if var has fletcher32 filter applied. */
size_t chunk_cache_size; /**< Size in bytes of the var chunk chache. */
size_t chunk_cache_nelems; /**< Number of slots in var chunk cache. */
float chunk_cache_preemption; /**< Chunk cache preemtion policy. */
void *format_var_info; /**< Pointer to any binary format info. */
NClist* filters; /**< List of filters to be applied to var data. */
} NC_VAR_INFO_T;
/** This is a struct to handle the field metadata from a user-defined
* type. */
typedef struct NC_FIELD_INFO
{
NC_OBJ hdr; /**< The hdr contains the name and ID. */
nc_type nc_typeid; /**< The type of this field. */
size_t offset; /**< Offset in bytes of field. */
int ndims; /**< Number of dims. */
int *dim_size; /**< Dim sizes. */
void *format_field_info; /**< Pointer to any binary format info for field. */
} NC_FIELD_INFO_T;
/** This is a struct to handle metadata for a user-defined enum
* type. */
typedef struct NC_ENUM_MEMBER_INFO
{
char *name; /**< Name of member. */
void *value; /**< Value of member. */
} NC_ENUM_MEMBER_INFO_T;
/** This is a struct to handle metadata for a user-defined type. */
typedef struct NC_TYPE_INFO
{
NC_OBJ hdr; /**< The hdr contains the name and ID. */
struct NC_GRP_INFO *container; /**< Containing group */
unsigned rc; /**< Ref. count of objects using this type */
int endianness; /**< What endianness for the type? */
size_t size; /**< Size of the type in memory, in bytes */
nc_bool_t committed; /**< True when datatype is committed in the file */
nc_type nc_type_class; /**< NC_VLEN, NC_COMPOUND, NC_OPAQUE, NC_ENUM, NC_INT, NC_FLOAT, or NC_STRING. */
void *format_type_info; /**< HDF5-specific type info. */
/** Information for each type or class */
union {
struct {
NClist* enum_member; /**< <! NClist<NC_ENUM_MEMBER_INFO_T*> */
nc_type base_nc_typeid; /**< Typeid of the base type. */
} e; /**< Enum */
struct Fields {
NClist* field; /**< <! NClist<NC_FIELD_INFO_T*> */
} c; /**< Compound */
struct {
nc_type base_nc_typeid; /**< Typeid of the base type. */
} v; /**< Variable-length. */
} u; /**< Union of structs, for each type/class. */
} NC_TYPE_INFO_T;
/** This holds information for one group. Groups reproduce with
* parthenogenesis. */
typedef struct NC_GRP_INFO
{
NC_OBJ hdr; /**< The hdr contains the name and ID. */
void *format_grp_info; /**< Pointer to binary format info for group. */
struct NC_FILE_INFO *nc4_info; /**< Pointer containing NC_FILE_INFO_T. */
struct NC_GRP_INFO *parent; /**< Pointer tp parent group. */
int atts_read; /**< True if atts have been read for this group. */
NCindex* children; /**< NCindex<struct NC_GRP_INFO*> */
NCindex* dim; /**< NCindex<NC_DIM_INFO_T> * */
NCindex* att; /**< NCindex<NC_ATT_INFO_T> * */
NCindex* type; /**< NCindex<NC_TYPE_INFO_T> * */
/* Note that this is the list of vars with position == varid */
NCindex* vars; /**< NCindex<NC_VAR_INFO_T> * */
} NC_GRP_INFO_T;
/* These constants apply to the cmode parameter in the
* HDF5_FILE_INFO_T defined below. */
#define NC_CREAT 2 /**< in create phase, cleared by ncendef */
#define NC_INDEF 8 /**< in define mode, cleared by ncendef */
#define NC_NSYNC 0x10 /**< synchronise numrecs on change */
#define NC_HSYNC 0x20 /**< synchronise whole header on change */
#define NC_NDIRTY 0x40 /**< numrecs has changed */
#define NC_HDIRTY 0x80 /**< header info has changed */
/** This is the metadata we need to keep track of for each
* netcdf-4/HDF5 file. */
typedef struct NC_FILE_INFO
{
NC *controller; /**< Pointer to containing NC. */
#ifdef USE_PARALLEL4
MPI_Comm comm; /**< Copy of MPI Communicator used to open the file. */
MPI_Info info; /**< Copy of MPI Information Object used to open the file. */
#endif
int flags; /**< Flags used to open the file. */
int cmode; /**< Create mode used to create the file. */
nc_bool_t parallel; /**< True if file is open for parallel access */
nc_bool_t redef; /**< True if redefining an existing file */
int fill_mode; /**< Fill mode for vars - Unused internally currently */
nc_bool_t no_write; /**< true if nc_open has mode NC_NOWRITE. */
NC_GRP_INFO_T *root_grp; /**< Pointer to root group. */
short next_nc_grpid; /**< Next available group ID. */
int next_typeid; /**< Next available type ID. */
int next_dimid; /**< Next available dim ID. */
/* Provide convenience vectors indexed by the object id. This
allows for direct conversion of e.g. an nc_type to the
corresponding NC_TYPE_INFO_T object. */
NClist *alldims; /**< List of all dims. */
NClist *alltypes; /**< List of all types. */
NClist *allgroups; /**< List of all groups, including root group. */
void *format_file_info; /**< Pointer to binary format info for file. */
NC4_Provenance provenance; /**< File provenence info. */
struct NC4_Memio
{
NC_memio memio; /**< What we sent to image_init and what comes back. */
int locked; /**< Do not copy and do not free. */
int persist; /**< Should file be persisted out on close? */
int inmemory; /**< NC_INMEMORY flag was set. */
int diskless; /**< NC_DISKLESS flag was set => inmemory. */
int created; /**< 1 => create, 0 => open. */
unsigned int imageflags; /**< for H5LTopen_file_image. */
size_t initialsize; /**< Initial size. */
void *udata; /**< Extra memory allocated in NC4_image_init. */
} mem;
} NC_FILE_INFO_T;
/** Variable Length Datatype struct in memory. Must be identical to
* HDF5 hvl_t. (This is only used for VL sequences, not VL strings,
* which are stored in char *'s) */
typedef struct
{
size_t len; /**< Length of VL data (in base type units) */
void *p; /**< Pointer to VL data */
} nc_hvl_t;
/** The names of the atomic data types. */
extern const char *nc4_atomic_name[NC_MAX_ATOMIC_TYPE + 1];
/* These functions convert between netcdf and HDF5 types. */
int nc4_get_typelen_mem(NC_FILE_INFO_T *h5, nc_type xtype, size_t *len);
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);
/* These functions do HDF5 things. */
int nc4_reopen_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var);
int nc4_read_atts(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var);
/* Find items in the in-memory lists of metadata. */
int nc4_find_nc_grp_h5(int ncid, NC **nc, NC_GRP_INFO_T **grp,
NC_FILE_INFO_T **h5);
int nc4_find_grp_h5(int ncid, NC_GRP_INFO_T **grp, NC_FILE_INFO_T **h5);
int nc4_find_nc4_grp(int ncid, NC_GRP_INFO_T **grp);
int nc4_find_dim(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T **dim,
NC_GRP_INFO_T **dim_grp);
int nc4_find_var(NC_GRP_INFO_T *grp, const char *name, NC_VAR_INFO_T **var);
int nc4_find_dim_len(NC_GRP_INFO_T *grp, int dimid, size_t **len);
int nc4_find_type(const NC_FILE_INFO_T *h5, int typeid1, NC_TYPE_INFO_T **type);
NC_TYPE_INFO_T *nc4_rec_find_named_type(NC_GRP_INFO_T *start_grp, char *name);
NC_TYPE_INFO_T *nc4_rec_find_equal_type(NC_GRP_INFO_T *start_grp, int ncid1,
NC_TYPE_INFO_T *type);
int nc4_find_nc_att(int ncid, int varid, const char *name, int attnum,
NC_ATT_INFO_T **att);
int nc4_find_grp_h5_var(int ncid, int varid, NC_FILE_INFO_T **h5,
NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var);
int nc4_find_grp_att(NC_GRP_INFO_T *grp, int varid, const char *name,
int attnum, NC_ATT_INFO_T **att);
int nc4_get_typeclass(const NC_FILE_INFO_T *h5, nc_type xtype,
int *type_class);
/* Free various types */
int nc4_type_free(NC_TYPE_INFO_T *type);
/* These list functions add and delete vars, atts. */
int nc4_nc4f_list_add(NC *nc, const char *path, int mode);
int nc4_nc4f_list_del(NC_FILE_INFO_T *h5);
int nc4_file_list_add(int ncid, const char *path, int mode,
void **dispatchdata);
int nc4_file_list_get(int ncid, char **path, int *mode,
void **dispatchdata);
int nc4_file_list_del(int ncid);
int nc4_file_change_ncid(int ncid, unsigned short new_ncid_index);
int nc4_var_list_add(NC_GRP_INFO_T* grp, const char* name, int ndims,
NC_VAR_INFO_T **var);
int nc4_var_list_add2(NC_GRP_INFO_T* grp, const char* name,
NC_VAR_INFO_T **var);
int nc4_var_set_ndims(NC_VAR_INFO_T *var, int ndims);
int nc4_var_list_del(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var);
int nc4_dim_list_add(NC_GRP_INFO_T *grp, const char *name, size_t len,
int assignedid, NC_DIM_INFO_T **dim);
int nc4_dim_list_del(NC_GRP_INFO_T *grp, NC_DIM_INFO_T *dim);
int nc4_type_new(size_t size, const char *name, int assignedid,
NC_TYPE_INFO_T **type);
int nc4_type_list_add(NC_GRP_INFO_T *grp, size_t size, const char *name,
NC_TYPE_INFO_T **type);
int nc4_type_list_del(NC_GRP_INFO_T *grp, NC_TYPE_INFO_T *type);
int nc4_type_free(NC_TYPE_INFO_T *type);
int nc4_field_list_add(NC_TYPE_INFO_T* parent, const char *name,
size_t offset, nc_type xtype, int ndims,
const int *dim_sizesp);
int nc4_att_list_add(NCindex *list, const char *name, NC_ATT_INFO_T **att);
int nc4_att_list_del(NCindex *list, NC_ATT_INFO_T *att);
int nc4_grp_list_add(NC_FILE_INFO_T *h5, NC_GRP_INFO_T *parent, char *name,
NC_GRP_INFO_T **grp);
int nc4_build_root_grp(NC_FILE_INFO_T *h5);
int nc4_rec_grp_del(NC_GRP_INFO_T *grp);
int nc4_enum_member_add(NC_TYPE_INFO_T *type, size_t size, const char *name,
const void *value);
/* Check and normalize names. */
int NC_check_name(const char *name);
int nc4_check_name(const char *name, char *norm_name);
int nc4_normalize_name(const char *name, char *norm_name);
int nc4_check_dup_name(NC_GRP_INFO_T *grp, char *norm_name);
/* Find default fill value. */
int nc4_get_default_fill_value(const NC_TYPE_INFO_T *type_info, void *fill_value);
/* Get an att given pointers to file, group, and perhaps ver info. */
int nc4_get_att_ptrs(NC_FILE_INFO_T *h5, NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var,
const char *name, nc_type *xtype, nc_type mem_type,
size_t *lenp, int *attnum, void *data);
/* Close the file. */
int nc4_close_netcdf4_file(NC_FILE_INFO_T *h5, int abort, NC_memio *memio);
/* HDF5 initialization/finalization */
extern int nc4_hdf5_initialized;
extern void nc4_hdf5_initialize(void);
extern void nc4_hdf5_finalize(void);
/* This is only included if --enable-logging is used for configure; it
prints info about the metadata to stderr. */
#ifdef LOGGING
int log_metadata_nc(NC_FILE_INFO_T *h5);
#endif
/* Binary searcher for reserved attributes */
extern const NC_reservedatt *NC_findreserved(const char *name);
/**************************************************/
/* Internal filter related structures */
/* Internal filter actions */
#define NCFILTER_DEF 1
#define NCFILTER_REMOVE 2
#define NCFILTER_INQ 3
#define NCFILTER_FILTERIDS 4
#define NCFILTER_INFO 5
#define NCFILTER_FREESPEC 6
#define NCFILTER_CLIENT_REG 10
#define NCFILTER_CLIENT_UNREG 11
#define NCFILTER_CLIENT_INQ 12
typedef enum NC_FILTER_SORT {
NC_FILTER_SORT_SPEC=((int)1),
NC_FILTER_SORT_IDS=((int)2),
NC_FILTER_SORT_CLIENT=((int)3),
} NC_FILTER_SORT;
/* Provide structs to pass args to filter_actions function for HDF5*/
typedef struct NC_FILTER_SPEC_HDF5 {
int active; /**< true iff HDF5 library was told to activate filter */
unsigned int filterid; /**< ID for arbitrary filter. */
size_t nparams; /**< nparams for arbitrary filter. */
unsigned int* params; /**< Params for arbitrary filter. */
} NC_FILTER_SPEC_HDF5;
typedef struct NC_FILTERIDS_HDF5 {
size_t nfilters; /**< number of filters */
unsigned int* filterids; /**< Filter ids. */
} NC_FILTERIDS_HDF5;
typedef struct NC_FILTER_CLIENT_HDF5 {
unsigned int id;
/* The filter info for hdf5 */
/* Avoid needing hdf.h by using void* */
void* info;
} NC_FILTER_CLIENT_HDF5;
typedef struct NC_FILTER_OBJ_HDF5 {
NC_Filterobject hdr; /* So we can cast it */
NC_FILTER_SORT sort; /* discriminate union */
union {
NC_FILTER_SPEC_HDF5 spec;
NC_FILTERIDS_HDF5 ids;
NC_FILTER_CLIENT_HDF5 client;
} u;
} NC_FILTER_OBJ_HDF5;
extern void NC4_freefilterspec(NC_FILTER_SPEC_HDF5* f);
#endif /* _NC4INTERNAL_ */
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