/** \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 #include #include #include #include #include #include #include #include #ifdef USE_PARALLEL #include #else #define MPI_Info int #define MPI_Comm int #include #endif /* USE_PARALLEL */ #include /* Always needed */ #include "nc.h" #ifdef USE_HDF4 #include #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_ */