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netcdf-c/include/nc4internal.h
Dennis Heimbigner 0cf1e2c49f re: Github issue netcdf-c 300 
Modified provenance code to allocate the minimal space
needed for _NCProperties attribute in file.  Basically
required using malloc in the provenance code and in ncdump.
Otherwise should cause no externally visible effects.
Also removed the ENABLE_FILEINFO from configure.ac since
the provenance code is no longer optional.
2016-08-08 09:24:19 -06:00

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/** \file
This header file contains the definitions of structs used to hold
netCDF file metadata in memory.
Copyright 2005-2011 University Corporation for Atmospheric
Research/Unidata.
*/
#ifndef _NC4INTERNAL_
#define _NC4INTERNAL_
#include "config.h"
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <stdarg.h>
#include <string.h>
#include <hdf5.h>
#include "ncdimscale.h"
#include "nc_logging.h"
#ifdef USE_PARALLEL
#include "netcdf_par.h"
#endif /* USE_PARALLEL */
#include "netcdf.h"
#include "netcdf_f.h"
/* Always needed */
#include "nc.h"
#ifdef USE_HDF4
#include <mfhdf.h>
#endif
#define FILE_ID_MASK (0xffff0000)
#define GRP_ID_MASK (0x0000ffff)
#define ID_SHIFT (16)
typedef enum {GET, PUT} NC_PG_T;
typedef enum {VAR, DIM, ATT} NC_OBJ_T;
#define NC_MAX_HDF5_NAME (NC_MAX_NAME + 10)
#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
#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)
/* These have to do with creating chuncked datasets in HDF5. */
#define NC_HDF5_UNLIMITED_DIMSIZE (0)
#define NC_HDF5_CHUNKSIZE_FACTOR (10)
#define NC_HDF5_MIN_CHUNK_SIZE (2)
#define NC_EMPTY_SCALE "NC_EMPTY_SCALE"
/* This is an attribute I had to add to handle multidimensional
* coordinate variables. */
#define COORDINATES "_Netcdf4Coordinates"
#define COORDINATES_LEN (NC_MAX_NAME * 5)
/* This is used when the user defines a non-coordinate variable with
* same name as a dimension. */
#define NON_COORD_PREPEND "_nc4_non_coord_"
/* An attribute in the HDF5 root group of this name means that the
* file must follow strict netCDF classic format rules. */
#define NC3_STRICT_ATT_NAME "_nc3_strict"
/* If this attribute is present on a dimscale variable, use the value
* as the netCDF dimid. */
#define NC_DIMID_ATT_NAME "_Netcdf4Dimid"
/* Boolean type, to make the code easier to read */
typedef enum {NC_FALSE = 0, NC_TRUE = 1} nc_bool_t;
/*Forward*/
struct NCFILEINFO;
/* Generic doubly-linked list node */
typedef struct NC_LIST_NODE
{
void *next;
void *prev;
} NC_LIST_NODE_T;
/* This is a struct to handle the dim metadata. */
typedef struct NC_DIM_INFO
{
NC_LIST_NODE_T l; /* Use generic doubly-linked list (must be first) */
char *name;
size_t len;
uint32_t hash;
int dimid;
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. */
hid_t hdf_dimscaleid;
HDF5_OBJID_T hdf5_objid;
struct NC_VAR_INFO *coord_var; /* The coord var, if it exists. */
} NC_DIM_INFO_T;
typedef struct NC_ATT_INFO
{
NC_LIST_NODE_T l; /* Use generic doubly-linked list (must be first) */
char *name;
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 */
hid_t native_hdf_typeid; /* Native HDF5 datatype for attribute's data */
int attnum;
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_LIST_NODE_T l; /* Use generic doubly-linked list (must be first) */
char *name;
char *hdf5_name; /* used if different from name */
int ndims;
int *dimids;
NC_DIM_INFO_T **dim;
int varid;
int natts;
uint32_t hash;
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;
hid_t hdf_datasetid;
NC_ATT_INFO_T *att;
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 */
HDF5_OBJID_T *dimscale_hdf5_objids;
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 */
nc_bool_t szip; /* True if var has szip filter applied */
int options_mask;
int pixels_per_block;
size_t chunk_cache_size, chunk_cache_nelems;
float chunk_cache_preemption;
#ifdef USE_HDF4
/* Stuff below is for hdf4 files. */
int sdsid;
int hdf4_data_type;
#endif /* USE_HDF4 */
/* Stuff below for diskless data files. */
void *diskless_data;
} NC_VAR_INFO_T;
typedef struct NC_FIELD_INFO
{
NC_LIST_NODE_T l; /* Use generic doubly-linked list (must be first) */
nc_type nc_typeid;
hid_t hdf_typeid;
hid_t native_hdf_typeid;
size_t offset;
char *name;
int fieldid; /* ID (index?) of field */
int ndims;
int *dim_size;
} NC_FIELD_INFO_T;
typedef struct NC_ENUM_MEMBER_INFO
{
NC_LIST_NODE_T l; /* Use generic doubly-linked list (must be first) */
char *name;
void *value;
} NC_ENUM_MEMBER_INFO_T;
typedef struct NC_TYPE_INFO
{
NC_LIST_NODE_T l; /* Use generic doubly-linked list (must be first) */
char *name;
nc_type nc_typeid; /* netCDF type ID, equivalent to a pre-defined type
* for atomic types, but a dynamically
* defined value for user-defined types (stored
* as named datatypes in the HDF5 file).
*/
unsigned rc; /* Ref. count of objects using this type */
hid_t hdf_typeid; /* HDF5 type ID, in the file */
hid_t native_hdf_typeid; /* HDF5 type ID, in memory */
int endianness; /* What endianness for the type? */
/* (Set for integer types as well as "complex"
* types, like compound/enum/vlen, used for the
* endianness of the fields and/or base 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, or NC_ENUM
* NOTE: NC_INT is used for all integer types,
* NC_FLOAT is used for all floating-point
* types, and NC_STRING is also used for
* fixed- and variable-length strings.
* (NC_CHAR is used for characters though)
*
* This is somewhat redundant with the
* nc_type field, but allows the code to
* have a single location to look at for
* the "kind" of a type.
*/
/* Information for each type or class */
union {
struct {
int num_members;
NC_ENUM_MEMBER_INFO_T *enum_member;
nc_type base_nc_typeid;
hid_t base_hdf_typeid;
} e; /* Enum */
struct {
int num_fields;
NC_FIELD_INFO_T *field;
} c; /* Compound */
struct {
nc_type base_nc_typeid;
hid_t base_hdf_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_LIST_NODE_T l; /* Use generic doubly-linked list (must be first) */
char *name;
hid_t hdf_grpid;
int nc_grpid;
struct NC_HDF5_FILE_INFO *nc4_info;
struct NC_GRP_INFO *parent;
struct NC_GRP_INFO *children;
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim;
NC_ATT_INFO_T *att;
NC_TYPE_INFO_T *type;
int nvars;
int ndims;
int natts;
} 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_HDF5_FILE_INFO
{
NC* controller;
hid_t hdfid;
#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;
int nvars;
int ndims;
int natts;
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;
short next_nc_grpid;
NC_TYPE_INFO_T *type;
int next_typeid;
int next_dimid;
#ifdef USE_HDF4
nc_bool_t hdf4; /* True for HDF4 file */
int sdid;
#endif /* USE_HDF4 */
struct NCFILEINFO* fileinfo;
} NC_HDF5_FILE_INFO_T;
/* Defined in lookup3.c */
extern uint32_t hash_fast(const void *key, size_t length);
/* These functions convert between netcdf and HDF5 types. */
int nc4_get_typelen_mem(NC_HDF5_FILE_INFO_T *h5, nc_type xtype,
int is_long, 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, int src_long,
int dest_long);
/* These functions do HDF5 things. */
int rec_detach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
int rec_reattach_scales(NC_GRP_INFO_T *grp, int dimid, hid_t dimscaleid);
int nc4_open_var_grp2(NC_GRP_INFO_T *grp, int varid, hid_t *dataset);
int nc4_put_vara(NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, nc_type xtype, int is_long, void *op);
int nc4_get_vara(NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, nc_type xtype, int is_long, void *op);
int nc4_rec_match_dimscales(NC_GRP_INFO_T *grp);
int nc4_rec_detect_need_to_preserve_dimids(NC_GRP_INFO_T *grp, nc_bool_t *bad_coord_orderp);
int nc4_rec_write_metadata(NC_GRP_INFO_T *grp, nc_bool_t bad_coord_order);
int nc4_rec_write_groups_types(NC_GRP_INFO_T *grp);
int nc4_enddef_netcdf4_file(NC_HDF5_FILE_INFO_T *h5);
int nc4_reopen_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var);
int nc4_adjust_var_cache(NC_GRP_INFO_T *grp, NC_VAR_INFO_T * var);
/* The following functions manipulate the in-memory linked list of
metadata, without using HDF calls. */
int nc4_find_nc_grp_h5(int ncid, NC **nc, NC_GRP_INFO_T **grp,
NC_HDF5_FILE_INFO_T **h5);
int nc4_find_grp_h5(int ncid, NC_GRP_INFO_T **grp, NC_HDF5_FILE_INFO_T **h5);
int nc4_find_nc4_grp(int ncid, NC_GRP_INFO_T **grp);
NC_GRP_INFO_T *nc4_find_nc_grp(int ncid);
NC_GRP_INFO_T *nc4_rec_find_grp(NC_GRP_INFO_T *start_grp, int target_nc_grpid);
NC *nc4_find_nc_file(int ncid, NC_HDF5_FILE_INFO_T**);
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_HDF5_FILE_INFO_T *h5, int typeid1, NC_TYPE_INFO_T **type);
NC_TYPE_INFO_T *nc4_rec_find_nc_type(const NC_GRP_INFO_T *start_grp, nc_type target_nc_typeid);
NC_TYPE_INFO_T *nc4_rec_find_hdf_type(NC_GRP_INFO_T *start_grp, hid_t target_hdf_typeid);
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_g_var_nc(NC *nc, int ncid, int varid,
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_hdf_typeid(NC_HDF5_FILE_INFO_T *h5, nc_type xtype,
hid_t *hdf_typeid, int endianness);
int nc4_get_typeclass(const NC_HDF5_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_var_list_add(NC_VAR_INFO_T **list, NC_VAR_INFO_T **var);
int nc4_var_list_del(NC_VAR_INFO_T **list, NC_VAR_INFO_T *var);
int nc4_dim_list_add(NC_DIM_INFO_T **list, NC_DIM_INFO_T **dim);
int nc4_dim_list_del(NC_DIM_INFO_T **list, NC_DIM_INFO_T *dim);
int nc4_att_list_add(NC_ATT_INFO_T **list, NC_ATT_INFO_T **att);
int nc4_type_list_add(NC_GRP_INFO_T *grp, size_t size, const char *name,
NC_TYPE_INFO_T **type);
int nc4_field_list_add(NC_FIELD_INFO_T **list, int fieldid, const char *name,
size_t offset, hid_t field_hdf_typeid, hid_t native_typeid,
nc_type xtype, int ndims, const int *dim_sizesp);
void nc4_file_list_del(NC *nc);
int nc4_att_list_del(NC_ATT_INFO_T **list, NC_ATT_INFO_T *att);
int nc4_grp_list_add(NC_GRP_INFO_T **list, int new_nc_grpid, NC_GRP_INFO_T *parent_grp,
NC *nc, char *name, NC_GRP_INFO_T **grp);
int nc4_rec_grp_del(NC_GRP_INFO_T **list, NC_GRP_INFO_T *grp);
int nc4_enum_member_add(NC_ENUM_MEMBER_INFO_T **list, size_t size,
const char *name, const void *value);
/* Break & reform coordinate variables */
int nc4_break_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var, NC_DIM_INFO_T *dim);
int nc4_reform_coord_var(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *coord_var, NC_DIM_INFO_T *dim);
/* 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);
/* HDF5 initialization */
extern int nc4_hdf5_initialized;
extern void nc4_hdf5_initialize(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 *nc);
#endif
/* Define accessors for the dispatchdata */
#define NC4_DATA(nc) ((NC_HDF5_FILE_INFO_T*)(nc)->dispatchdata)
#define NC4_DATA_SET(nc,data) ((nc)->dispatchdata = (void*)(data))
/* Reserved Attributes */
extern const char* NC_RESERVED_VARATT_LIST[];
extern const char* NC_RESERVED_ATT_LIST[];
extern const char* NC_RESERVED_SPECIAL_LIST[];
#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"
/**************************************************/
/**
For netcdf4 files, capture state information about the following:
1. Global: netcdf library version
2. Global: hdf5 library version
3. Per file: superblock version
4. Per File: was it created by netcdf-4?
5. Per file: _NCProperties attribute
*/
#define NCPROPS "_NCProperties"
#define NCPROPS_VERSION (1)
#define NCPROPSSEP '|'
/* Currently used properties */
#define NCPVERSION "version" /* Of the properties format */
#define NCPHDF5LIBVERSION "hdf5libversion"
#define NCPNCLIBVERSION "netcdflibversion"
/* Other hidden attributes */
#define ISNETCDF4ATT "_IsNetcdf4"
#define SUPERBLOCKATT "_SuperblockVersion"
struct NCFILEINFO {
int superblockversion;
/* Following is filled from NCPROPS attribute or from global version */
struct NCPROPINFO {
int version; /* 0 => not defined */
char hdf5ver[NC_MAX_NAME+1];
char netcdfver[NC_MAX_NAME+1];
} propattr;
};
extern struct NCPROPINFO globalpropinfo;
extern int NC4_fileinfo_init(void); /*libsrc4/ncinfo.c*/
extern int NC4_get_fileinfo(struct NC_HDF5_FILE_INFO* info, struct NCPROPINFO*); /*libsrc4/ncinfo.c*/
extern int NC4_put_propattr(struct NC_HDF5_FILE_INFO* info); /*libsrc4/ncinfo.c*/
extern int NC4_buildpropinfo(struct NCPROPINFO* info,char** propdatap);
extern int NC4_hdf5get_libversion(unsigned*,unsigned*,unsigned*);/*libsrc4/nc4hdf.c*/
extern int NC4_hdf5get_superblock(struct NC_HDF5_FILE_INFO*, int*);/*libsrc4/nc4hdf.c*/
extern int NC4_isnetcdf4(struct NC_HDF5_FILE_INFO*); /*libsrc4/nc4hdf.c*/
#endif /* _NETCDF4_ */
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