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netcdf-c/include/nc4internal.h
Dennis Heimbigner 5ca78309cc The effect of this change is to make the struct NC structure 
contain as little file-type specific info as possible.  It
modifies especially libsrc so that all of the netcdf-3 data
that used to be in struct NC is now kept in a separate chunk
of data pointed to by the struct NC. This makes all of
current protocols consistent: netcdf-3, netcdf-4, and dap.
2012-09-06 19:44:03 +00:00

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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>
#else
#define MPI_Info int
#define MPI_Comm int
#include <netcdf.h>
#endif /* USE_PARALLEL */
#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"
/* This is a struct to handle the dim metadata. */
typedef struct NC_DIM_INFO
{
char *name;
size_t len;
int dimid;
int unlimited;
int extended;
struct NC_DIM_INFO *next;
struct NC_DIM_INFO *prev;
hid_t hdf_dimscaleid;
char *old_name; /* only used to rename dim */
int dirty;
unsigned char coord_var_in_grp;
struct NC_VAR_INFO *coord_var; /* The coord var, if it exists. */
int too_long; /* True if len it too big to fit in local size_t. */
} NC_DIM_INFO_T;
typedef struct NC_ATT_INFO
{
int len;
char *name;
struct NC_ATT_INFO *next;
struct NC_ATT_INFO *prev;
int dirty;
int created;
nc_type xtype;
hid_t native_typeid;
int attnum;
void *data;
nc_vlen_t *vldata; /* only used for vlen */
char **stdata; /* only for string type. */
int class;
} NC_ATT_INFO_T;
/* This is a struct to handle the var metadata. */
typedef struct NC_VAR_INFO
{
char *name;
char *hdf5_name; /* used if different from name */
int ndims;
int *dimids;
NC_DIM_INFO_T **dim;
int varid;
int natts;
struct NC_VAR_INFO *next;
struct NC_VAR_INFO *prev;
int dirty;
int created;
int written_to;
int *dimscale_attached;
struct NC_TYPE_INFO *type_info;
nc_type xtype;
hid_t hdf_datasetid;
NC_ATT_INFO_T *att;
int no_fill;
void *fill_value;
size_t *chunksizes;
int contiguous;
int parallel_access;
int dimscale;
HDF5_OBJID_T *dimscale_hdf5_objids;
int deflate;
int deflate_level;
int shuffle;
int fletcher32;
int options_mask;
int pixels_per_block;
size_t chunk_cache_size, chunk_cache_nelems;
float chunk_cache_preemption;
/* Stuff below is for hdf4 files. */
int sdsid;
int hdf4_data_type;
/* Stuff below for diskless data files. */
void *diskless_data;
} NC_VAR_INFO_T;
typedef struct NC_FIELD_INFO
{
struct NC_FIELD_INFO *next;
struct NC_FIELD_INFO *prev;
nc_type nctype;
hid_t hdf_typeid;
hid_t native_typeid;
size_t offset;
char *name;
int fieldid;
int ndims;
int *dim_size;
} NC_FIELD_INFO_T;
typedef struct NC_ENUM_MEMBER_INFO
{
struct NC_ENUM_MEMBER_INFO *next;
struct NC_ENUM_MEMBER_INFO *prev;
char *name;
void *value;
} NC_ENUM_MEMBER_INFO_T;
typedef struct NC_TYPE_INFO
{
struct NC_TYPE_INFO *next;
struct NC_TYPE_INFO *prev;
nc_type nc_typeid;
hid_t hdf_typeid;
hid_t native_typeid;
size_t size;
int committed; /* What the pig is, but the hen isn't, at breakfast. */
char *name;
int class; /* NC_VLEN, NC_COMPOUND, NC_OPAQUE, or NC_ENUM */
int num_enum_members;
NC_ENUM_MEMBER_INFO_T *enum_member;
NC_FIELD_INFO_T *field; /* Used for compound types. */
int num_fields;
nc_type base_nc_type; /* for VLEN and ENUM only */
hid_t base_hdf_typeid; /* for VLEN only */
int close_hdf_typeid; /* True when hdf_typeid must be H5Tclosed. */
int endianness;
} NC_TYPE_INFO_T;
/* This holds information for one group. Groups reproduce with
* parthenogenesis. */
typedef struct NC_GRP_INFO
{
int nc_grpid;
struct NC_GRP_INFO *parent;
struct NC_GRP_INFO *children;
struct NC_GRP_INFO *next; /* points to siblings */
struct NC_GRP_INFO *prev; /* points to siblings */
NC_VAR_INFO_T *var;
NC_DIM_INFO_T *dim;
NC_ATT_INFO_T *att;
int nvars;
int ndims;
int natts;
struct NC_HDF5_FILE_INFO *nc4_info;
char *name;
hid_t hdf_grpid;
NC_TYPE_INFO_T *type;
} 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;
int flags;
int cmode;
int nvars;
int ndims;
int natts;
int parallel; /* true if file is open for parallel access */
int redef;
int fill_mode;
int 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;
int ignore_creationorder;
int hdf4;
int sdid;
#ifdef USE_PNETCDF
/* pnetcdf_file will be true if the file is created/opened with the
* parallel-netcdf library. pnetcdf_access_mode keeps track of
* whether independpent or collective mode is
* desired. pnetcdf_ndims keeps track of how many dims each var
* has, which I need to know to convert start, count, and stride
* arrays from size_t to MPI_Offset. (I can't use an inq function
* to find out the number of dims, because these are collective in
* pnetcdf.) */
int pnetcdf_file;
int pnetcdf_access_mode;
int pnetcdf_ndims[NC_MAX_VARS];
#endif /* USE_PNETCDF */
} NC_HDF5_FILE_INFO_T;
/* These functions only use the netcdf API calls, so they will work on
both new format and old format files. */
/*int copy_dataset(int ncid_in, int ncid_out);*/
/* These functions convert beteen 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 nc4_open_var_grp2(NC_GRP_INFO_T *grp, int varid, hid_t *dataset);
int pg_var(NC_PG_T pg, NC *nc, int ncid, int varid, nc_type xtype, int is_long, void *ip);
int nc4_pg_var1(NC_PG_T pg, NC *nc, int ncid, int varid, const size_t *indexp,
nc_type xtype, int is_long, void *ip);
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_pg_varm(NC_PG_T pg, NC *nc, int ncid, int varid, const size_t *startp,
const size_t *countp, const ptrdiff_t *stridep,
const ptrdiff_t *imapp, nc_type xtype, int is_long, void *op);
int nc4_rec_match_dimscales(NC_GRP_INFO_T *grp);
int nc4_rec_write_metadata(NC_GRP_INFO_T *grp);
int nc4_rec_write_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_dim_len(NC_GRP_INFO_T *grp, int dimid, size_t **len);
int nc4_find_type(NC_HDF5_FILE_INFO_T *h5, int typeid, NC_TYPE_INFO_T **type);
NC_TYPE_INFO_T *nc4_rec_find_nc_type(NC_GRP_INFO_T *start_grp, hid_t 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 var_info_nc(NC_PG_T pg, hid_t dataset, NC_VAR_INFO_T *var_info);*/
/* 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_dim_list_add(NC_DIM_INFO_T **list);
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);
int nc4_type_list_add(NC_TYPE_INFO_T **list, NC_TYPE_INFO_T **new_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);
int NC_check_name(const char *name);
/* Check and normalize names. */
int nc4_check_name(const char *name, char *norm_name);
int nc4_normalize_name(const char *name, char *norm_name);
/* Check for name collisions. */
int nc4_check_dup_name(NC_GRP_INFO_T *grp, char *norm_name);
/* Insert and read one element into an already allocated vlen array
* element (this is for F77). */
/*int nc_put_vlen_element(int ncid, int typeid, void *vlen_element, size_t len, const void *data);
int nc_get_vlen_element(int ncid, int typeid, const void *vlen_element, size_t *len, void *data);*/
/* 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))
#endif /* _NETCDF4_ */
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