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netcdf-c/include/nc4internal.h
edwardhartnett 83c6cd58a7 more changes in support of user-defined formats
2019-08-03 17:19:13 -06:00

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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 "config.h"
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <stdarg.h>
#include <string.h>
#include "ncdimscale.h"
#include "nc_logging.h"
#include "ncindex.h"
#include "nc_provenance.h"
#ifdef USE_PARALLEL
#include "netcdf_par.h"
#endif /* USE_PARALLEL */
#include "netcdf.h"
#include "netcdf_f.h"
#include "netcdf_mem.h"
/* Always needed */
#include "nc.h"
#define FILE_ID_MASK (0xffff0000)
#define GRP_ID_MASK (0x0000ffff)
#define ID_SHIFT (16)
typedef enum {GET, PUT} NC_PG_T;
typedef enum {NCNAT, NCVAR, NCDIM, NCATT, NCTYP, NCFLD, NCGRP} NC_SORT;
#define NC_V2_ERR (-1)
/* The name of the root group. */
#define NC_GROUP_NAME "/"
#define MEGABYTE 1048576
/*
* limits of the external representation
*/
#define X_SCHAR_MIN (-128)
#define X_SCHAR_MAX 127
#define X_UCHAR_MAX 255U
#define X_SHORT_MIN (-32768)
#define X_SHRT_MIN X_SHORT_MIN /* alias compatible with limits.h */
#define X_SHORT_MAX 32767
#define X_SHRT_MAX X_SHORT_MAX /* alias compatible with limits.h */
#define X_USHORT_MAX 65535U
#define X_USHRT_MAX X_USHORT_MAX /* alias compatible with limits.h */
#define X_INT_MIN (-2147483647-1)
#define X_INT_MAX 2147483647
#define X_LONG_MIN X_INT_MIN
#define X_LONG_MAX X_INT_MAX
#define X_UINT_MAX 4294967295U
#define X_INT64_MIN (-9223372036854775807LL-1LL)
#define X_INT64_MAX 9223372036854775807LL
#define X_UINT64_MAX 18446744073709551615ULL
#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
#endif /* WIN32 */
#define X_FLOAT_MIN (-X_FLOAT_MAX)
#define X_DOUBLE_MAX 1.7976931348623157e+308
#define X_DOUBLE_MIN (-X_DOUBLE_MAX)
/** 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
/* Boolean type, to make the code easier to read */
typedef enum {NC_FALSE = 0, NC_TRUE = 1} nc_bool_t;
/*Forward*/
struct NC_GRP_INFO;
struct NC_TYPE_INFO;
/*
Indexed Access to Meta-data objects:
See the document docs/indexing.dox for detailed information.
Basically provide 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;
char* name; /* assumed to be null terminated */
size_t id;
unsigned int hashkey; /* crc32(name) */
} NC_OBJ;
/* This is a struct to handle the dim metadata. */
typedef struct NC_DIM_INFO
{
NC_OBJ hdr;
struct NC_GRP_INFO *container; /* containing group */
size_t len;
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;
typedef struct NC_ATT_INFO
{
NC_OBJ hdr;
struct NC_OBJ *container; /* containing group|var */
int len;
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;
void *data;
nc_vlen_t *vldata; /* only used for vlen */
char **stdata; /* 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;
char *hdf5_name; /* used if different from name */
struct NC_GRP_INFO *container; /* containing group */
size_t ndims;
int *dimids;
NC_DIM_INFO_T **dim;
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;
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; /* NCindex<NC_ATT_INFO_T*> */
nc_bool_t no_fill; /* True if no fill value is defined for var */
void *fill_value;
size_t *chunksizes;
nc_bool_t contiguous; /* True if variable is stored contiguously in HDF5 file */
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 deflate; /* True if var has deflate filter applied */
int deflate_level;
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, chunk_cache_nelems;
float chunk_cache_preemption;
void *format_var_info; /* Pointer to any binary format info. */
/* Stuff for arbitrary filters */
unsigned int filterid;
size_t nparams;
unsigned int *params;
} NC_VAR_INFO_T;
typedef struct NC_FIELD_INFO
{
NC_OBJ hdr;
nc_type nc_typeid;
size_t offset;
int ndims;
int *dim_size;
void *format_field_info; /* Pointer to any binary format info for field. */
} NC_FIELD_INFO_T;
typedef struct NC_ENUM_MEMBER_INFO
{
char *name;
void *value;
} NC_ENUM_MEMBER_INFO_T;
typedef struct NC_TYPE_INFO
{
NC_OBJ hdr; /* NetCDF type 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;
} e; /* Enum */
struct Fields {
NClist* field; /* <! NClist<NC_FIELD_INFO_T*> */
} c; /* Compound */
struct {
nc_type base_nc_typeid;
} 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;
void *format_grp_info;
struct NC_FILE_INFO *nc4_info;
struct NC_GRP_INFO *parent;
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;
#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;
int cmode;
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;
/* Track indices to assign to grps, types, and dims */
short next_nc_grpid;
int next_typeid;
int next_dimid;
/* 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;
NClist* alltypes;
NClist* allgroups; /* including root group */
void *format_file_info;
NC4_Provenance provenance;
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;
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;
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_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
/* Define accessors for the dispatchdata */
#define NC4_DATA(nc) ((NC_FILE_INFO_T*)(nc)->dispatchdata)
#define NC4_DATA_SET(nc,data) ((nc)->dispatchdata = (void*)(data))
/* Reserved Attributes Info */
typedef struct NC_reservedatt {
const char* name;
int flags;
} NC_reservedatt;
/* 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
/* Binary searcher for reserved attributes */
extern const NC_reservedatt* NC_findreserved(const char* name);
/* Generic reserved Attributes */
#define NC_ATT_REFERENCE_LIST "REFERENCE_LIST"
#define NC_ATT_CLASS "CLASS"
#define NC_ATT_DIMENSION_LIST "DIMENSION_LIST"
#define NC_ATT_NAME "NAME"
#define NC_ATT_COORDINATES COORDINATES /*defined above*/
#define NC_ATT_FORMAT "_Format"
#endif /* _NC4INTERNAL_ */
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