mirror of
https://github.com/HDFGroup/hdf5.git
synced 2024-12-21 07:51:46 +08:00
330b80a266
Fixed some conversion issues with Clang due to problematic undefined behavior when casting a negative floating-point value to an integer Fixed a bug in the library's software integer to floating-point conversion function where a user's conversion exception function returning H5T_CONV_UNHANDLED in the case of overflows would result in incorrect data after conversion Added configure checks for functions and macros related to _Float16 usage since some compilers expose the datatype but not the functions or macros Fixed a dt_arith test failure when H5_WANT_DCONV_EXCEPTION isn't defined Fixed a few warnings from not explicitly casting some _Float16 variables upwards
653 lines
18 KiB
Plaintext
653 lines
18 KiB
Plaintext
/** \page DDLBNF112 DDL in BNF for HDF5 1.12 through HDF5 1.14.3
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\todo Revise this & break it up!
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\section intro112 Introduction
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This document contains the data description language (DDL) for an HDF5 file. The
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description is in Backus-Naur Form (BNF).
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\section expo112 Explanation of Symbols
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This section contains a brief explanation of the symbols used in the DDL.
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\code{.unparsed}
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::= defined as
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<tname> a token with the name tname
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<a> | <b> one of <a> or <b>
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<a>opt zero or one occurrence of <a>
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<a>* zero or more occurrence of <a>
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<a>+ one or more occurrence of <a>
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[0-9] an element in the range between 0 and 9
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'[' the token within the quotes (used for special characters)
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TBD To Be Decided
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\endcode
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\section ddl112 The DDL
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\code{.unparsed}
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<file> ::= HDF5 <file_name> { <file_super_block>opt <root_group> }
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<file_name> ::= <identifier>
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<file_super_block> ::= SUPER_BLOCK {
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SUPERBLOCK_VERSION <int_value>
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FREELIST_VERSION <int_value>
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SYMBOLTABLE_VERSION <int_value>
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OBJECTHEADER_VERSION <int_value>
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OFFSET_SIZE <int_value>
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LENGTH_SIZE <int_value>
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BTREE_RANK <int_value>
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BTREE_LEAF <int_value>
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ISTORE_K <int_value>
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<super_block_filespace>
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USER_BLOCK {
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USERBLOCK_SIZE <int_value>
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}
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}
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<super_block_filespace> ::= FILE_SPACE_STRATEGY <super_block_strategy>
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FREE_SPACE_PERSIST <boolean_value>
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FREE_SPACE_SECTION_THRESHOLD <int_value>
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FILE_SPACE_PAGE_SIZE <int_value>
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<super_block_strategy> ::= H5F_FSPACE_STRATEGY_FSM_AGGR | H5F_FSPACE_STRATEGY_PAGE |
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H5F_FSPACE_STRATEGY_AGGR | H5F_FSPACE_STRATEGY_NONE |
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Unknown strategy
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<root_group> ::= GROUP "/" {
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<anon_named_datatype>*
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<object_id>opt
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<group_comment>opt
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<group_attribute>*
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<group_member>*
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}
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<datatype> ::= <atomic_type> | <compound_type> | <variable_length_type> | <array_type>
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<anon_named_datatype> ::= DATATYPE <anon_named_type_name> {
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<datatype>
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}
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<anon_named_type_name> ::= the assigned name for anonymous named type is
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in the form of #oid, where oid is the object id
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of the type
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<atomic_type> ::= <integer> | <float> | <time> | <string> |
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<bitfield> | <opaque> | <reference> | <enum>
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<boolean_value> ::= FALSE | TRUE
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<integer> ::= H5T_STD_I8BE | H5T_STD_I8LE |
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H5T_STD_I16BE | H5T_STD_I16LE |
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H5T_STD_I32BE | H5T_STD_I32LE |
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H5T_STD_I64BE | H5T_STD_I64LE |
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H5T_STD_U8BE | H5T_STD_U8LE |
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H5T_STD_U16BE | H5T_STD_U16LE |
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H5T_STD_U32BE | H5T_STD_U32LE |
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H5T_STD_U64BE | H5T_STD_U64LE |
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H5T_NATIVE_CHAR | H5T_NATIVE_UCHAR |
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H5T_NATIVE_SHORT | H5T_NATIVE_USHORT |
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H5T_NATIVE_INT | H5T_NATIVE_UINT |
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H5T_NATIVE_LONG | H5T_NATIVE_ULONG |
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H5T_NATIVE_LLONG | H5T_NATIVE_ULLONG
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<float> ::= H5T_IEEE_F32BE | H5T_IEEE_F32LE |
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H5T_IEEE_F64BE | H5T_IEEE_F64LE |
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H5T_NATIVE_FLOAT | H5T_NATIVE_DOUBLE |
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H5T_NATIVE_LDOUBLE
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<time> ::= H5T_TIME: not yet implemented
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<string> ::= H5T_STRING {
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STRSIZE <strsize>;
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STRPAD <strpad>;
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CSET <cset>;
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CTYPE <ctype>;
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}
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<strsize> ::= <int_value>
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<strpad> ::= H5T_STR_NULLTERM | H5T_STR_NULLPAD | H5T_STR_SPACEPAD
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<cset> ::= H5T_CSET_ASCII | H5T_CSET_UTF8
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<ctype> ::= H5T_C_S1 | H5T_FORTRAN_S1
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<bitfield> ::= H5T_STD_B8BE | H5T_STD_B8LE |
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H5T_STD_B16BE | H5T_STD_B16LE |
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H5T_STD_B32BE | H5T_STD_B32LE |
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H5T_STD_B64BE | H5T_STD_B64LE
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<opaque> ::= H5T_OPAQUE {
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OPAQUE_TAG <identifier>;
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OPAQUE_SIZE <int_value>;opt
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}
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<reference> ::= H5T_REFERENCE { <ref_type> }
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<ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG | H5T_STD_REF | UNDEFINED
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<compound_type> ::= H5T_COMPOUND {
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<member_type_def>+
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}
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<member_type_def> ::= <datatype> <field_name>;
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<field_name> ::= <identifier>
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<variable_length_type> ::= H5T_VLEN { <datatype> }
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<array_type> ::= H5T_ARRAY { <dim_sizes> <datatype> }
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<dim_sizes> ::= '['<dimsize>']' | '['<dimsize>']'<dim_sizes>
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<dimsize> ::= <int_value>
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<attribute> ::= ATTRIBUTE <attr_name> {
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<dataset_type>
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<dataset_space>
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<data>opt
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}
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<attr_name> ::= <identifier>
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<dataset_type> ::= DATATYPE <path_name> | <datatype>
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<enum> ::= H5T_ENUM {
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<enum_base_type> <enum_def>+
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}
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<enum_base_type> ::= <integer>
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// Currently enums can only hold integer type data, but they may be expanded
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// in the future to hold any datatype
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<enum_def> ::= <enum_symbol> <enum_val>;
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<enum_symbol> ::= <identifier>
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<enum_val> ::= <int_value>
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<path_name> ::= <path_part>+
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<path_part> ::= /<identifier>
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<dataspace> ::= <scalar_space> | <simple_space> | <complex_space> | <null_space>
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<null_space> ::= NULL
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<scalar_space> ::= SCALAR
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<simple_space> ::= SIMPLE { <current_dims> / <max_dims> }
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<complex_space> ::= COMPLEX { <complex_space_definition> }
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<dataset_space> ::= DATASPACE <path_name> | <dataspace>
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<current_dims> ::= <dims>
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<max_dims> ::= '(' <max_dim_list> ')'
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<max_dim_list> ::= <max_dim> | <max_dim>, <max_dim_list>
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<max_dim> ::= <int_value> | H5S_UNLIMITED
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<data> ::= <subset> | <data_values>
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<data_values> ::= DATA {
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<scalar_space_data> | <simple_space_data>
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}
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<scalar_space_data> ::= <any_element>
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<any_element> ::= <atomic_element> | <compound_element> |
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<variable_length_element> | <array_element>
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<any_data_seq> ::= <any_element> | <any_element>, <any_data_seq>
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<atomic_element> :: = <integer_data> | <float_data> | <time_data> |
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<string_data> | <bitfield_data> | <opaque_data> |
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<enum_data> | <reference_data>
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<subset> ::= SUBSET {
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<start>;
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<stride>;
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<count>;
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<block>;
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DATA {
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<simple_space_data>
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}
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}
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<start> ::= START (<coor_list>)
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<stride> ::= STRIDE (<pos_list>)
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<count> ::= COUNT (<max_dim_list>)
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<block> ::= BLOCK (<max_dim_list>)
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<coor_list> ::= <coor_data>, <coor_list> | <coor_data>
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<coor_data> ::= <integer_data> | H5S_UNLIMITED
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<integer_data> ::= <int_value>
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<float_data> ::= a floating point number
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<time_data> ::= DATA{ not yet implemented.}
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<string_data> ::= a string
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// A string is enclosed in double quotes.
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// If a string is displayed on more than one line, string concatenate
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// operator '//'is used.
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<bitfield_data> ::= <hex_value>
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<opaque_data> ::= <hex_value>:<hex_value> | <hex_value>
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<enum_data> ::= <enum_symbol>
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<reference_data> ::= <object_ref_data> | <data_region_data> | <attribute_data> | NULL
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<object_ref_data> ::= <object_type> <object_ref>
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<object_type> ::= ATTRIBUTE | DATASET | GROUP | DATATYPE
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<object_ref> ::= <object_id>
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<object_id> ::= <path_name> | OBJECTID { <object_num> }
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<object_num> ::= <int_value>:<int_value> | <int_value>
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<attribute_data> ::= ATTRIBUTE <attr_name>opt
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<data>opt
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<data_region_data> ::= DATASET <dataset_name> {
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<data_region_type>opt <data_region_data_list>
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<dataset_type>opt <dataset_space>opt
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<data>opt
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}
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<data_region_type> ::= REGION_TYPE <data_region_data_type>
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<data_region_data_type> ::= POINT | BLOCK
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<data_region_data_list> ::= <data_region_data_info>, <data_region_data_list> |
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<data_region_data_info>
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<data_region_data_info> ::= <region_info> | <point_info>
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<region_info> ::= (<lower_region_vals>)-(<upper_region_vals>)
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<lower_region_vals> ::= <lower_bound>, <lower_region_vals> | <lower_bound>
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<upper_region_vals> ::= <upper_bound>, <upper_region_vals> | <upper_bound>
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<lower_bound> ::= <int_value>
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<upper_bound> ::= <int_value>
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<point_info> ::= (<point_vals>)
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<point_vals> ::= <int_value> | <int_value>, <point_vals>
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<compound_element> ::= { <any_data_seq> }
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<atomic_simple_data> :: = <atomic_element>, <atomic_simple_data> |
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<atomic_element>
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<simple_space_data> :: = <any_data_seq>
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<variable_length_element> ::= ( <any_data_seq> )
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<array_element> ::= '[' <any_data_seq> ']'
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<named_datatype> ::= DATATYPE <type_name> { <datatype> }
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<type_name> ::= <identifier>
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<hardlink> ::= HARDLINK <path_name>
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<group> ::= GROUP <group_name> { <hardlink> | <group_info> }
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<group_comment> ::= COMMENT <string_data>
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<group_name> ::= <identifier>
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<group_info> ::= <object_id>opt <group_comment>opt <group_attribute>*
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<group_member>*
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<group_attribute> ::= <attribute>
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<group_member> ::= <named_datatype> | <group> | <dataset> |
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<softlink> | <external_link>
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<dataset> ::= DATASET <dataset_name> { <hardlink> | <dataset_info> }
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<dataset_info> ::= <dataset_type>
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<dataset_space>
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<dcpl_info>opt
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<dataset_attribute>* <object_id>opt
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<data>opt
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// Tokens above can be in any order as long as <data> is
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// after <dataset_type> and <dataset_space>.
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<dcpl_info> ::= <storagelayout>
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<compression_filters>
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<fillvalue>
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<allocationtime>
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<dataset_name> ::= <identifier>
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<storagelayout> :: = STORAGE_LAYOUT {
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<contiguous_layout> | <chunked_layout> |
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<compact_layout> | <virtual_layout>
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}
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<contiguous_layout> ::= CONTIGUOUS
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<internal_layout> | <external_layout>
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<chunked_layout> ::= CHUNKED <dims>
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<filter_ratio>opt
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<compact_layout> ::= COMPACT
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<size>
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<internal_layout> ::= <size>
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<offset>
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<external_layout> ::= EXTERNAL {
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<external_file>+
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}
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<virtual_layout> ::= <vmaps>*opt
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<vmaps> ::= MAPPING <int_value> {
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<virtual_map>
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<source_map>
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}
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<virtual_map> ::= VIRTUAL {
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<vmaps_selection>
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}
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<source_map> ::= SOURCE {
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FILE <file_name>
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DATASET <dataset_name>
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<vmaps_selection>
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}
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<vmaps_selection> ::= <regular_hyperslab> | <irregular_hyperslab> |
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<select_points> | <select_none> | <select_all>
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<regular_hyperslab> ::= SELECTION REGULAR_HYPERSLAB {
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<start>
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<stride>
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<count>
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<block>
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}
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<irregular_hyperslab> ::= SELECTION IRREGULAR_HYPERSLAB {
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<region_info>+
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}
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<select_points> ::= SELECTION POINT {
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(<coor_list>)+
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}
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<select_none> ::= SELECTION NONE
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<select_all> ::= SELECTION ALL
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<dims> ::= (<dims_values>)
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<dims_values> ::= <int_value> | <int_value>, <dims_values>
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<external_file> ::= FILENAME <file_name> <size> <offset>
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<offset> ::= OFFSET <int_value>
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<size> ::= SIZE <int_value>
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<filter_ratio> ::= <size> | <compressionratio>
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<compressionratio> :: = <size> (<float_data>:1 COMPRESSION)
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<compression_filters> :: = FILTERS {
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<filter_type>+ | NONE
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}
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<filter_type> :: = <filter_deflate> | <filter_shuffle> |
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<filter_flecther> | <filter_szip> |
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<filter_nbit> | <filter_scaleoffset> |
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<filter_default>
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<filter_default> :: = <filter_user> {
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FILTER_ID <int_value>
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<filter_comment>opt
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<filter_params>opt
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}
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<filter_user> :: = USER_DEFINED_FILTER
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<filter_deflate> :: = COMPRESSION DEFLATE { LEVEL <int_value> }
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<filter_shuffle> :: = PREPROCESSING SHUFFLE
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<filter_flecther> :: = CHECKSUM FLETCHER32
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<filter_szip> :: = COMPRESSION SZIP {
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PIXELS_PER_BLOCK <int_value>
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<filter_szip_mode>opt
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<filter_szip_coding>opt
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<filter_szip_order>opt
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<filter_szip_header>opt
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}
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<filter_szip_mode> :: = MODE HARDWARE | K13
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<filter_szip_coding> :: = CODING ENTROPY | NEAREST NEIGHBOUR
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<filter_szip_order> :: = BYTE_ORDER LSB | MSB
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<filter_szip_header> :: = HEADER RAW
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<filter_nbit> :: = CHECKSUM NBIT
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<filter_scaleoffset> :: = COMPRESSION SCALEOFFSET { MIN BITS <int_value> }
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<filter_comment> :: = COMMENT <identifier>
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<filter_params> :: = PARAMS { <int_value>* }
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<fillvalue> ::= FILLVALUE {
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FILL_TIME H5D_FILL_TIME_ALLOC | H5D_FILL_TIME_NEVER | H5D_FILL_TIME_IFSET
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VALUE H5D_FILL_VALUE_UNDEFINED | H5D_FILL_VALUE_DEFAULT | <any_element>
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}
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<allocationtime> ::= ALLOCATION_TIME {
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H5D_ALLOC_TIME_EARLY | H5D_ALLOC_TIME_INCR |
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H5D_ALLOC_TIME_LATE
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}
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<dataset_attribute> ::= <attribute>
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<softlink> ::= SOFTLINK <softlink_name> {
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LINKTARGET <target>
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}
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<softlink_name> ::= <identifier>
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<target> ::= <identifier>
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<external_link> ::= EXTERNAL_LINK <external_link_name> {
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TARGETFILE <targetfile>
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TARGETPATH <targetpath> <targetobj>opt
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}
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<external_link_name> ::= <identifier>
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<user_defined_link> ::= USERDEFINED_LINK <external_link_name> {
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LINKCLASS <user_link_type>
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}
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<user_link_type> ::= <int_value>
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<targetfile> ::= <file_name>
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<targetpath> ::= <identifier>
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<targetobj> ::= <named_datatype> | <group> | <dataset>
|
|
|
|
<identifier> ::= "a string"
|
|
// character '/' should be used with care.
|
|
|
|
<pos_list> ::= <pos_int>, <pos_list> | <pos_int>
|
|
|
|
<int_value> ::= 0 | <pos_int>
|
|
|
|
<pos_int> ::= [1-9][0-9]*
|
|
|
|
<hex_value> ::= 0x[0-F][0-F]+ | [0-F][0-F]+
|
|
\endcode
|
|
|
|
\section example112 An Example of an HDF5 File in DDL
|
|
|
|
\code{.unparsed}
|
|
HDF5 "example.h5" {
|
|
GROUP "/" {
|
|
ATTRIBUTE "attr1" {
|
|
DATATYPE H5T_STRING {
|
|
STRSIZE 17;
|
|
STRPAD H5T_STR_NULLTERM;
|
|
CSET H5T_CSET_ASCII;
|
|
CTYPE H5T_C_S1;
|
|
}
|
|
DATASPACE SCALAR
|
|
DATA {
|
|
"string attribute"
|
|
}
|
|
}
|
|
DATASET "dset1" {
|
|
DATATYPE H5T_STD_I32BE
|
|
DATASPACE SIMPLE { ( 10, 10 ) / ( 10, 10 ) }
|
|
DATA {
|
|
0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
|
|
0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
|
|
0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
|
|
0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
|
|
0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
|
|
0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
|
|
0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
|
|
0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
|
|
0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
|
|
0, 1, 2, 3, 4, 5, 6, 7, 8, 9
|
|
}
|
|
}
|
|
DATASET "dset2" {
|
|
DATATYPE H5T_COMPOUND {
|
|
H5T_STD_I32BE "a";
|
|
H5T_IEEE_F32BE "b";
|
|
H5T_IEEE_F64BE "c";
|
|
}
|
|
DATASPACE SIMPLE { ( 5 ) / ( 5 ) }
|
|
DATA {
|
|
{
|
|
1,
|
|
0.1,
|
|
0.01
|
|
},
|
|
{
|
|
2,
|
|
0.2,
|
|
0.02
|
|
},
|
|
{
|
|
3,
|
|
0.3,
|
|
0.03
|
|
},
|
|
{
|
|
4,
|
|
0.4,
|
|
0.04
|
|
},
|
|
{
|
|
5,
|
|
0.5,
|
|
0.05
|
|
}
|
|
}
|
|
}
|
|
GROUP "group1" {
|
|
COMMENT "This is a comment for group1";
|
|
DATASET "dset3" {
|
|
DATATYPE "/type1"
|
|
DATASPACE SIMPLE { ( 5 ) / ( 5 ) }
|
|
DATA {
|
|
{
|
|
[ 0, 1, 2, 3 ],
|
|
[ 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
|
|
0.2, 0.2, 0.2, 0.2, 0.2, 0.2,
|
|
0.3, 0.3, 0.3, 0.3, 0.3, 0.3,
|
|
0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
|
|
0.5, 0.5, 0.5, 0.5, 0.5, 0.5 ]
|
|
},
|
|
{
|
|
[ 0, 1, 2, 3 ],
|
|
[ 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
|
|
0.2, 0.2, 0.2, 0.2, 0.2, 0.2,
|
|
0.3, 0.3, 0.3, 0.3, 0.3, 0.3,
|
|
0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
|
|
0.5, 0.5, 0.5, 0.5, 0.5, 0.5 ]
|
|
},
|
|
{
|
|
[ 0, 1, 2, 3 ],
|
|
[ 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
|
|
0.2, 0.2, 0.2, 0.2, 0.2, 0.2,
|
|
0.3, 0.3, 0.3, 0.3, 0.3, 0.3,
|
|
0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
|
|
0.5, 0.5, 0.5, 0.5, 0.5, 0.5 ]
|
|
},
|
|
{
|
|
[ 0, 1, 2, 3 ],
|
|
[ 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
|
|
0.2, 0.2, 0.2, 0.2, 0.2, 0.2,
|
|
0.3, 0.3, 0.3, 0.3, 0.3, 0.3,
|
|
0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
|
|
0.5, 0.5, 0.5, 0.5, 0.5, 0.5 ]
|
|
},
|
|
{
|
|
[ 0, 1, 2, 3 ],
|
|
[ 0.1, 0.1, 0.1, 0.1, 0.1, 0.1,
|
|
0.2, 0.2, 0.2, 0.2, 0.2, 0.2,
|
|
0.3, 0.3, 0.3, 0.3, 0.3, 0.3,
|
|
0.4, 0.4, 0.4, 0.4, 0.4, 0.4,
|
|
0.5, 0.5, 0.5, 0.5, 0.5, 0.5 ]
|
|
}
|
|
}
|
|
}
|
|
}
|
|
DATASET "dset3" {
|
|
DATATYPE H5T_VLEN { H5T_STD_I32LE }
|
|
DATASPACE SIMPLE { ( 4 ) / ( 4 ) }
|
|
DATA {
|
|
(0), (10, 11), (20, 21, 22), (30, 31, 32, 33)
|
|
}
|
|
}
|
|
GROUP "group2" {
|
|
HARDLINK "/group1"
|
|
}
|
|
SOFTLINK "slink1" {
|
|
LINKTARGET "somevalue"
|
|
}
|
|
DATATYPE "type1" H5T_COMPOUND {
|
|
H5T_ARRAY { [4] H5T_STD_I32BE } "a";
|
|
H5T_ARRAY { [5][6] H5T_IEEE_F32BE } "b";
|
|
}
|
|
}
|
|
}
|
|
\endcode
|
|
|
|
*/ |