mirror of
https://github.com/Unidata/netcdf-c.git
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475 lines
22 KiB
C
475 lines
22 KiB
C
/* Copyright 2018-2018 University Corporation for Atmospheric
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Research/Unidata. */
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/**
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* @file
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* @internal This header file contains macros, types and prototypes
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* used to build and manipulate the netCDF metadata model.
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*
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* @author Ed Hartnett, Dennis Heimbigner, Ward Fisher
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*/
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#ifndef _NC4INTERNAL_
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#define _NC4INTERNAL_
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#include "netcdf.h"
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#include "config.h"
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#include <stdio.h>
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#include <stdlib.h>
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#include <ctype.h>
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#include <string.h>
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#include "nc_logging.h"
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#include "ncindex.h"
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#include "nc_provenance.h"
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#include "nchashmap.h"
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#include "netcdf_f.h"
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#include "netcdf_mem.h"
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#include "netcdf_filter.h"
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#ifdef USE_PARALLEL
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#include "netcdf_par.h"
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#endif /* USE_PARALLEL */
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/* Always needed */
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#include "nc.h"
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/** The file ID is stored in the first two bytes of ncid. */
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#define FILE_ID_MASK (0xffff0000)
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/** The group ID is stored in the last two bytes of ncid. */
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#define GRP_ID_MASK (0x0000ffff)
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/** File and group IDs are each 16 bits of the ncid. */
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#define ID_SHIFT (16)
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/* typedef enum {GET, PUT} NC_PG_T; */
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/** These are the different objects that can be in our hash-lists. */
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typedef enum {NCNAT, NCVAR, NCDIM, NCATT, NCTYP, NCFLD, NCGRP, NCFIL} NC_SORT;
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/** The netCDF V2 error code. */
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#define NC_V2_ERR (-1)
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/** The name of the root group. */
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#define NC_GROUP_NAME "/"
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/** One mega-byte. */
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#define MEGABYTE 1048576
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/** The HDF5 ID for the szip filter. */
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#define HDF5_FILTER_SZIP 4
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#define X_SCHAR_MIN (-128) /**< Minimum signed char value. */
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#define X_SCHAR_MAX 127 /**< Maximum signed char value. */
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#define X_UCHAR_MAX 255U /**< Maximum unsigned char value. */
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#define X_SHORT_MIN (-32768) /**< Minimum short value. */
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#define X_SHRT_MIN X_SHORT_MIN /**< This alias is compatible with limits.h. */
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#define X_SHORT_MAX 32767 /**< Maximum short value. */
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#define X_SHRT_MAX X_SHORT_MAX /**< This alias is compatible with limits.h. */
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#define X_USHORT_MAX 65535U /**< Maximum unsigned short value. */
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#define X_USHRT_MAX X_USHORT_MAX /**< This alias is compatible with limits.h. */
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#define X_INT_MIN (-2147483647-1) /**< Minimum int value. */
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#define X_INT_MAX 2147483647 /**< Maximum int value. */
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#define X_LONG_MIN X_INT_MIN /**< Minimum long value. */
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#define X_LONG_MAX X_INT_MAX /**< Maximum long value. */
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#define X_UINT_MAX 4294967295U /**< Maximum unsigned int value. */
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#define X_INT64_MIN (-9223372036854775807LL-1LL) /**< Minimum int64 value. */
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#define X_INT64_MAX 9223372036854775807LL /**< Maximum int64 value. */
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#define X_UINT64_MAX 18446744073709551615ULL /**< Maximum unsigned int64 value. */
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#ifdef _WIN32 /* Windows, of course, has to be a *little* different. */
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#define X_FLOAT_MAX 3.402823466e+38f
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#else
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#define X_FLOAT_MAX 3.40282347e+38f /**< Maximum float value. */
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#endif /* _WIN32 */
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#define X_FLOAT_MIN (-X_FLOAT_MAX) /**< Minimum float value. */
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#define X_DOUBLE_MAX 1.7976931348623157e+308 /**< Maximum double value. */
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#define X_DOUBLE_MIN (-X_DOUBLE_MAX) /**< Minimum double value. */
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/** This is the number of netCDF atomic types. */
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#define NUM_ATOMIC_TYPES (NC_MAX_ATOMIC_TYPE + 1)
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/** Number of parameters needed for ZLIB filter. */
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#define CD_NELEMS_ZLIB 1
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/** Get a pointer to the NC_FILE_INFO_T from dispatchdata field. */
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#define NC4_DATA(nc) ((NC_FILE_INFO_T *)(nc)->dispatchdata)
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/** Set a pointer to the NC_FILE_INFO_T in the dispatchdata field. */
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#define NC4_DATA_SET(nc,data) ((nc)->dispatchdata = (void *)(data))
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/* Reserved attribute flags: must be powers of 2. */
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/** Hidden attributes; immutable and unreadable thru API. */
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#define HIDDENATTRFLAG 1
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/** Readonly attributes; readable, but immutable thru the API. */
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#define READONLYFLAG 2
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/** Subset of readonly flags; readable by name only thru the API. */
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#define NAMEONLYFLAG 4
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/** Subset of readonly flags; Value is actually in file. */
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#define MATERIALIZEDFLAG 8
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/** Per-variable attribute, as opposed to global */
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#define VARFLAG 16
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/** Boolean type, to make the code easier to read. */
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typedef enum {NC_FALSE = 0, NC_TRUE = 1} nc_bool_t;
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/* Forward declarations. */
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struct NC_GRP_INFO;
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struct NC_TYPE_INFO;
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/**
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* This struct provides indexed Access to Meta-data objects. See the
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* document docs/indexing.dox for detailed information.
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*
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* Basically it provides a common header and use NCindex instances
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* instead of linked lists.
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*
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* WARNING: ALL OBJECTS THAT CAN BE INSERTED INTO AN NCindex MUST HAVE
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* AN INSTANCE of NC_OBJ AS THE FIRST FIELD.
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*/
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typedef struct NC_OBJ
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{
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NC_SORT sort; /**< Type of object. */
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char* name; /**< Name, assumed to be null terminated. */
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size_t id; /**< This objects ID. */
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} NC_OBJ;
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/**
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* This struct holds information about reserved attributes. These
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* attributes cannot be created or read by the user (through the
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* netCDF API). */
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typedef struct NC_reservedatt
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{
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const char *name; /**< Name of the reserved attribute. */
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int flags; /**< Flags that control handling of reserved attribute. */
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} NC_reservedatt;
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/** This is a struct to handle the dimension metadata. */
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typedef struct NC_DIM_INFO
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{
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NC_OBJ hdr; /**< The hdr contains the name and ID. */
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struct NC_GRP_INFO *container; /**< Pointer to containing group. */
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size_t len; /**< Length of this dimension. */
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nc_bool_t unlimited; /**< True if the dimension is unlimited */
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nc_bool_t extended; /**< True if the dimension needs to be extended. */
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nc_bool_t too_long; /**< True if len is too big to fit in local size_t. */
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void *format_dim_info; /**< Pointer to format-specific dim info. */
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struct NC_VAR_INFO *coord_var; /**< The coord var, if it exists. */
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} NC_DIM_INFO_T;
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/** This is a struct to handle the attribute metadata. */
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typedef struct NC_ATT_INFO
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{
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NC_OBJ hdr; /**< The hdr contains the name and ID. */
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struct NC_OBJ *container; /**< Pointer to containing group|var. */
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int len; /**< Length of attribute data. */
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nc_bool_t dirty; /**< True if attribute modified. */
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nc_bool_t created; /**< True if attribute already created. */
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nc_type nc_typeid; /**< NetCDF type of attribute's data. */
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void *format_att_info; /**< Pointer to format-specific att info. */
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void *data; /**< The attribute data. */
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nc_vlen_t *vldata; /**< VLEN data (only used for vlen types). */
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char **stdata; /**< String data (only for string type). */
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} NC_ATT_INFO_T;
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/** This is a struct to handle the var metadata. */
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typedef struct NC_VAR_INFO
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{
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NC_OBJ hdr; /**< The hdr contains the name and ID. */
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char *alt_name; /**< Used if name in dispatcher must be different from hdr.name. */
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struct NC_GRP_INFO *container; /**< Pointer to containing group. */
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size_t ndims; /**< Number of dims. */
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int *dimids; /**< Dim IDs. */
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NC_DIM_INFO_T **dim; /**< Pointer to array of NC_DIM_INFO_T. */
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nc_bool_t is_new_var; /**< True if variable is newly created. */
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nc_bool_t was_coord_var; /**< True if variable was a coordinate var, but either the dim or var has been renamed. */
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nc_bool_t became_coord_var; /**< True if variable _became_ a coordinate var, because either the dim or var has been renamed. */
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nc_bool_t fill_val_changed; /**< True if variable's fill value changes after it has been created. */
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nc_bool_t attr_dirty; /**< True if variable's attributes are dirty and should be rewritten. */
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nc_bool_t created; /**< Variable has already been created (_not_ that it was just created). */
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nc_bool_t written_to; /**< True if variable has data written to it. */
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struct NC_TYPE_INFO *type_info; /**< Contains info about the variable type. */
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int atts_read; /**< If true, the atts have been read. */
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nc_bool_t meta_read; /**< True if this vars metadata has been completely read. */
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nc_bool_t coords_read; /**< True if this var has hidden coordinates att, and it has been read. */
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NCindex *att; /**< List of NC_ATT_INFO_T. */
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nc_bool_t no_fill; /**< True if no fill value is defined for var. */
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void *fill_value; /**< Pointer to fill value, or NULL. */
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size_t *chunksizes; /**< For chunked storage, an array (size ndims) of chunksizes. */
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int storage; /**< Storage of this var, compact, contiguous, or chunked. */
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int endianness; /**< What endianness for the var? */
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int parallel_access; /**< Type of parallel access for I/O on variable (collective or independent). */
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nc_bool_t shuffle; /**< True if var has shuffle filter applied. */
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nc_bool_t fletcher32; /**< True if var has fletcher32 filter applied. */
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size_t chunk_cache_size; /**< Size in bytes of the var chunk cache. */
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size_t chunk_cache_nelems; /**< Number of slots in var chunk cache. */
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float chunk_cache_preemption; /**< Chunk cache preemtion policy. */
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int quantize_mode; /**< Quantize mode. NC_NOQUANTIZE is 0, and means no quantization. */
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int nsd; /**< Number of significant digits if quantization is used, 0 if not. */
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void *format_var_info; /**< Pointer to any binary format info. */
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void* filters; /**< Record of the list of filters to be applied to var data; format dependent */
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} NC_VAR_INFO_T;
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/** This is a struct to handle the field metadata from a user-defined
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* type. */
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typedef struct NC_FIELD_INFO
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{
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NC_OBJ hdr; /**< The hdr contains the name and ID. */
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nc_type nc_typeid; /**< The type of this field. */
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size_t offset; /**< Offset in bytes of field. */
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int ndims; /**< Number of dims. */
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int *dim_size; /**< Dim sizes. */
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void *format_field_info; /**< Pointer to any binary format info for field. */
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} NC_FIELD_INFO_T;
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/** This is a struct to handle metadata for a user-defined enum
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* type. */
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typedef struct NC_ENUM_MEMBER_INFO
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{
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char *name; /**< Name of member. */
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void *value; /**< Value of member. */
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} NC_ENUM_MEMBER_INFO_T;
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/** This is a struct to handle metadata for a user-defined type. */
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typedef struct NC_TYPE_INFO
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{
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NC_OBJ hdr; /**< The hdr contains the name and ID. */
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struct NC_GRP_INFO *container; /**< Containing group */
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unsigned rc; /**< Ref. count of objects using this type */
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int endianness; /**< What endianness for the type? */
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size_t size; /**< Size of the type in memory, in bytes */
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nc_bool_t committed; /**< True when datatype is committed in the file */
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nc_type nc_type_class; /**< NC_VLEN, NC_COMPOUND, NC_OPAQUE, NC_ENUM, NC_INT, NC_FLOAT, or NC_STRING. */
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void *format_type_info; /**< HDF5-specific type info. */
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/** Information for each type or class */
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union {
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struct {
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NClist* enum_member; /**< <! NClist<NC_ENUM_MEMBER_INFO_T*> */
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nc_type base_nc_typeid; /**< Typeid of the base type. */
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} e; /**< Enum */
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struct Fields {
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NClist* field; /**< <! NClist<NC_FIELD_INFO_T*> */
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} c; /**< Compound */
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struct {
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nc_type base_nc_typeid; /**< Typeid of the base type. */
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} v; /**< Variable-length. */
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} u; /**< Union of structs, for each type/class. */
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} NC_TYPE_INFO_T;
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/** This holds information for one group. Groups reproduce with
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* parthenogenesis. */
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typedef struct NC_GRP_INFO
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{
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NC_OBJ hdr; /**< The hdr contains the name and ID. */
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void *format_grp_info; /**< Pointer to binary format info for group. */
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struct NC_FILE_INFO *nc4_info; /**< Pointer containing NC_FILE_INFO_T. */
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struct NC_GRP_INFO *parent; /**< Pointer tp parent group. */
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int atts_read; /**< True if atts have been read for this group. */
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NCindex* children; /**< NCindex<struct NC_GRP_INFO*> */
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NCindex* dim; /**< NCindex<NC_DIM_INFO_T> * */
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NCindex* att; /**< NCindex<NC_ATT_INFO_T> * */
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NCindex* type; /**< NCindex<NC_TYPE_INFO_T> * */
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/* Note that this is the list of vars with position == varid */
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NCindex* vars; /**< NCindex<NC_VAR_INFO_T> * */
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} NC_GRP_INFO_T;
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/* These constants apply to the cmode parameter in the
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* HDF5_FILE_INFO_T defined below. */
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/* Make sure they do not conflict with defined flags in netcdf.h */
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#define NC_CREAT 0x10002 /**< in create phase, cleared by ncendef */
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#define NC_INDEF 0x10008 /**< in define mode, cleared by ncendef */
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#define NC_NSYNC 0x10010 /**< synchronise numrecs on change */
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#define NC_HSYNC 0x10020 /**< synchronise whole header on change */
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#define NC_NDIRTY 0x10040 /**< numrecs has changed */
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#define NC_HDIRTY 0x10080 /**< header info has changed */
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/** This is the metadata we need to keep track of for each
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* netcdf-4/HDF5 file. */
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typedef struct NC_FILE_INFO
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{
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NC_OBJ hdr;
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NC *controller; /**< Pointer to containing NC. */
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#ifdef USE_PARALLEL4
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MPI_Comm comm; /**< Copy of MPI Communicator used to open the file. */
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MPI_Info info; /**< Copy of MPI Information Object used to open the file. */
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#endif
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int flags; /**< Flags used to open the file. */
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int cmode; /**< Create mode used to create the file. */
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nc_bool_t parallel; /**< True if file is open for parallel access */
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nc_bool_t redef; /**< True if redefining an existing file */
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nc_bool_t no_attr_create_order; /**< True if the creation order tracking of attributes is disabled (netcdf-4 only) */
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nc_bool_t no_dimscale_attach; /**< True if attaching dimscales to variables is disabled (netcdf-4 only) */
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int fill_mode; /**< Fill mode for vars - Unused internally currently */
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nc_bool_t no_write; /**< true if nc_open has mode NC_NOWRITE. */
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NC_GRP_INFO_T *root_grp; /**< Pointer to root group. */
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short next_nc_grpid; /**< Next available group ID. */
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int next_typeid; /**< Next available type ID. */
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int next_dimid; /**< Next available dim ID. */
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/* Provide convenience vectors indexed by the object id. This
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allows for direct conversion of e.g. an nc_type to the
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corresponding NC_TYPE_INFO_T object. */
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NClist *alldims; /**< List of all dims. */
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NClist *alltypes; /**< List of all types. */
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NClist *allgroups; /**< List of all groups, including root group. */
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void *format_file_info; /**< Pointer to binary format info for file. */
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NC4_Provenance provenance; /**< File provenence info. */
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struct NC4_Memio
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{
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NC_memio memio; /**< What we sent to image_init and what comes back. */
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int locked; /**< Do not copy and do not free. */
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int persist; /**< Should file be persisted out on close? */
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int inmemory; /**< NC_INMEMORY flag was set. */
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int diskless; /**< NC_DISKLESS flag was set => inmemory. */
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int created; /**< 1 => create, 0 => open. */
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unsigned int imageflags; /**< for H5LTopen_file_image. */
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size_t initialsize; /**< Initial size. */
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void *udata; /**< Extra memory allocated in NC4_image_init. */
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} mem;
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} NC_FILE_INFO_T;
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/** Variable Length Datatype struct in memory. Must be identical to
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* HDF5 hvl_t. (This is only used for VL sequences, not VL strings,
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* which are stored in char *'s) */
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typedef struct
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{
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size_t len; /**< Length of VL data (in base type units) */
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void *p; /**< Pointer to VL data */
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} nc_hvl_t;
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/* Misc functions */
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extern int NC4_inq_atomic_type(nc_type typeid1, char *name, size_t *size);
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extern int NC4_lookup_atomic_type(const char *name, nc_type* idp, size_t *sizep);
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/* These functions convert between netcdf and HDF5 types. */
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extern int nc4_get_typelen_mem(NC_FILE_INFO_T *h5, nc_type xtype, size_t *len);
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extern int nc4_convert_type(const void *src, void *dest, const nc_type src_type,
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const nc_type dest_type, const size_t len, int *range_error,
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const void *fill_value, int strict_nc3, int quantize_mode,
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int nsd);
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/* These functions do HDF5 things. */
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extern int nc4_reopen_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var);
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extern int nc4_read_atts(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var);
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/* Find items in the in-memory lists of metadata. */
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extern int nc4_find_nc_grp_h5(int ncid, NC **nc, NC_GRP_INFO_T **grp,
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NC_FILE_INFO_T **h5);
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extern int nc4_find_grp_h5(int ncid, NC_GRP_INFO_T **grp, NC_FILE_INFO_T **h5);
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extern int nc4_find_nc4_grp(int ncid, NC_GRP_INFO_T **grp);
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extern int nc4_find_dim(NC_GRP_INFO_T *grp, int dimid, NC_DIM_INFO_T **dim,
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NC_GRP_INFO_T **dim_grp);
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extern int nc4_find_var(NC_GRP_INFO_T *grp, const char *name, NC_VAR_INFO_T **var);
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extern int nc4_find_dim_len(NC_GRP_INFO_T *grp, int dimid, size_t **len);
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extern int nc4_find_type(const NC_FILE_INFO_T *h5, int typeid1, NC_TYPE_INFO_T **type);
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extern NC_TYPE_INFO_T *nc4_rec_find_named_type(NC_GRP_INFO_T *start_grp, char *name);
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extern NC_TYPE_INFO_T *nc4_rec_find_equal_type(NC_GRP_INFO_T *start_grp, int ncid1,
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NC_TYPE_INFO_T *type);
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extern int nc4_find_nc_att(int ncid, int varid, const char *name, int attnum,
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NC_ATT_INFO_T **att);
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extern int nc4_find_grp_h5_var(int ncid, int varid, NC_FILE_INFO_T **h5,
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NC_GRP_INFO_T **grp, NC_VAR_INFO_T **var);
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extern int nc4_find_grp_att(NC_GRP_INFO_T *grp, int varid, const char *name,
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int attnum, NC_ATT_INFO_T **att);
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extern int nc4_get_typeclass(const NC_FILE_INFO_T *h5, nc_type xtype,
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int *type_class);
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/* Free various types */
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extern int nc4_type_free(NC_TYPE_INFO_T *type);
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/* These list functions add and delete vars, atts. */
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extern int nc4_nc4f_list_add(NC *nc, const char *path, int mode);
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extern int nc4_nc4f_list_del(NC_FILE_INFO_T *h5);
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extern int nc4_file_list_add(int ncid, const char *path, int mode,
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void **dispatchdata);
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extern int nc4_file_list_get(int ncid, char **path, int *mode,
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void **dispatchdata);
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extern int nc4_file_list_del(int ncid);
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extern int nc4_file_change_ncid(int ncid, unsigned short new_ncid_index);
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extern int nc4_var_list_add(NC_GRP_INFO_T* grp, const char* name, int ndims,
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NC_VAR_INFO_T **var);
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extern int nc4_var_list_add2(NC_GRP_INFO_T* grp, const char* name,
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NC_VAR_INFO_T **var);
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extern int nc4_var_set_ndims(NC_VAR_INFO_T *var, int ndims);
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extern int nc4_var_list_del(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var);
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extern int nc4_dim_list_add(NC_GRP_INFO_T *grp, const char *name, size_t len,
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int assignedid, NC_DIM_INFO_T **dim);
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extern int nc4_dim_list_del(NC_GRP_INFO_T *grp, NC_DIM_INFO_T *dim);
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extern int nc4_type_new(size_t size, const char *name, int assignedid,
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NC_TYPE_INFO_T **type);
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extern int nc4_type_list_add(NC_GRP_INFO_T *grp, size_t size, const char *name,
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NC_TYPE_INFO_T **type);
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extern int nc4_type_list_del(NC_GRP_INFO_T *grp, NC_TYPE_INFO_T *type);
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extern int nc4_type_free(NC_TYPE_INFO_T *type);
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extern int nc4_field_list_add(NC_TYPE_INFO_T* parent, const char *name,
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size_t offset, nc_type xtype, int ndims,
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const int *dim_sizesp);
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extern int nc4_att_list_add(NCindex *list, const char *name, NC_ATT_INFO_T **att);
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extern int nc4_att_list_del(NCindex *list, NC_ATT_INFO_T *att);
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extern int nc4_grp_list_add(NC_FILE_INFO_T *h5, NC_GRP_INFO_T *parent, char *name,
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NC_GRP_INFO_T **grp);
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extern int nc4_build_root_grp(NC_FILE_INFO_T *h5);
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extern int nc4_rec_grp_del(NC_GRP_INFO_T *grp);
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extern int nc4_enum_member_add(NC_TYPE_INFO_T *type, size_t size, const char *name,
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const void *value);
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extern int nc4_att_free(NC_ATT_INFO_T *att);
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/* Check and normalize names. */
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extern int NC_check_name(const char *name);
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extern int nc4_check_name(const char *name, char *norm_name);
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extern int nc4_normalize_name(const char *name, char *norm_name);
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extern int nc4_check_dup_name(NC_GRP_INFO_T *grp, char *norm_name);
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/* Get the fill value for a var. */
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extern int nc4_get_fill_value(NC_FILE_INFO_T *h5, NC_VAR_INFO_T *var, void **fillp);
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/* Find default fill value. */
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extern int nc4_get_default_fill_value(nc_type typecode, void *fill_value);
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/* Get an att given pointers to file, group, and perhaps ver info. */
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extern int nc4_get_att_ptrs(NC_FILE_INFO_T *h5, NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var,
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const char *name, nc_type *xtype, nc_type mem_type,
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size_t *lenp, int *attnum, void *data);
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/* Close the file. */
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extern int nc4_close_netcdf4_file(NC_FILE_INFO_T *h5, int abort, NC_memio *memio);
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/* Compute default chunksizes */
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extern int nc4_find_default_chunksizes2(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var);
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extern int nc4_check_chunksizes(NC_GRP_INFO_T* grp, NC_VAR_INFO_T* var, const size_t* chunksizes);
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/* HDF5 initialization/finalization */
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extern int nc4_hdf5_initialized;
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extern void nc4_hdf5_initialize(void);
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extern void nc4_hdf5_finalize(void);
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/* This is only included if --enable-logging is used for configure; it
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prints info about the metadata to stderr. */
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#ifdef LOGGING
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extern int log_metadata_nc(NC_FILE_INFO_T *h5);
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#endif
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/** @internal Names of atomic types. */
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extern const char* nc4_atomic_name[NUM_ATOMIC_TYPES];
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/* Binary searcher for reserved attributes */
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extern const NC_reservedatt* NC_findreserved(const char* name);
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/* Generic reserved Attributes */
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#define NC_ATT_REFERENCE_LIST "REFERENCE_LIST"
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#define NC_ATT_CLASS "CLASS"
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#define NC_ATT_DIMENSION_LIST "DIMENSION_LIST"
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#define NC_ATT_NAME "NAME"
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#define NC_ATT_COORDINATES "_Netcdf4Coordinates" /*see hdf5internal.h:COORDINATES*/
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#define NC_ATT_FORMAT "_Format"
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#define NC_ATT_DIMID_NAME "_Netcdf4Dimid"
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#define NC_ATT_NC3_STRICT_NAME "_nc3_strict"
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#define NC_XARRAY_DIMS "_ARRAY_DIMENSIONS"
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#define NC_ATT_CODECS "_Codecs"
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#define NC_NCZARR_ATTR "_NCZARR_ATTR"
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#endif /* _NC4INTERNAL_ */
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