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diff --git a/doxygen/dox/DDLBNF110.dox b/doxygen/dox/DDLBNF110.dox new file mode 100644 index 0000000..f7e4267 --- /dev/null +++ b/doxygen/dox/DDLBNF110.dox @@ -0,0 +1,650 @@ +/** \page DDLBNF110 DDL in BNF through HDF5 1.10 + +\todo Revise this & break it up! + +\section intro110 Introduction + +This document contains the data description language (DDL) for an HDF5 file. The +description is in Backus-Naur Form (BNF). + +\section expo110 Explanation of Symbols + +This section contains a brief explanation of the symbols used in the DDL. + +\code{.unparsed} +::= defined as + <tname> a token with the name tname + <a> | <b> one of <a> or <b> + <a>opt zero or one occurrence of <a> + <a>* zero or more occurrence of <a> + <a>+ one or more occurrence of <a> + [0-9] an element in the range between 0 and 9 + '[' the token within the quotes (used for special characters) + TBD To Be Decided +\endcode + +\section ddl110 The DDL + +\code{.unparsed} +<file> ::= HDF5 <file_name> { <file_super_block>opt <root_group> } + +<file_name> ::= <identifier> + +<file_super_block> ::= SUPER_BLOCK { + SUPERBLOCK_VERSION <int_value> + FREELIST_VERSION <int_value> + SYMBOLTABLE_VERSION <int_value> + OBJECTHEADER_VERSION <int_value> + OFFSET_SIZE <int_value> + LENGTH_SIZE <int_value> + BTREE_RANK <int_value> + BTREE_LEAF <int_value> + ISTORE_K <int_value> + <super_block_filespace> + USER_BLOCK { + USERBLOCK_SIZE <int_value> + } + } + +<super_block_filespace> ::= FILE_SPACE_STRATEGY <super_block_strategy> + FREE_SPACE_PERSIST <boolean_value> + FREE_SPACE_SECTION_THRESHOLD <int_value> + FILE_SPACE_PAGE_SIZE <int_value> + +<super_block_strategy> ::= H5F_FSPACE_STRATEGY_FSM_AGGR | H5F_FSPACE_STRATEGY_PAGE | + H5F_FSPACE_STRATEGY_AGGR | H5F_FSPACE_STRATEGY_NONE | + Unknown strategy + +<root_group> ::= GROUP "/" { + <anon_named_datatype>* + <object_id>opt + <group_comment>opt + <group_attribute>* + <group_member>* + } + +<datatype> ::= <atomic_type> | <compound_type> | <variable_length_type> | <array_type> + +<anon_named_datatype> ::= DATATYPE <anon_named_type_name> { + <datatype> + } + +<anon_named_type_name> ::= the assigned name for anonymous named type is + in the form of #oid, where oid is the object id + of the type + +<atomic_type> ::= <integer> | <float> | <time> | <string> | + <bitfield> | <opaque> | <reference> | <enum> + +<boolean_value> ::= FALSE | TRUE + +<integer> ::= H5T_STD_I8BE | H5T_STD_I8LE | + H5T_STD_I16BE | H5T_STD_I16LE | + H5T_STD_I32BE | H5T_STD_I32LE | + H5T_STD_I64BE | H5T_STD_I64LE | + H5T_STD_U8BE | H5T_STD_U8LE | + H5T_STD_U16BE | H5T_STD_U16LE | + H5T_STD_U32BE | H5T_STD_U32LE | + H5T_STD_U64BE | H5T_STD_U64LE | + H5T_NATIVE_CHAR | H5T_NATIVE_UCHAR | + H5T_NATIVE_SHORT | H5T_NATIVE_USHORT | + H5T_NATIVE_INT | H5T_NATIVE_UINT | + H5T_NATIVE_LONG | H5T_NATIVE_ULONG | + H5T_NATIVE_LLONG | H5T_NATIVE_ULLONG + +<float> ::= H5T_IEEE_F32BE | H5T_IEEE_F32LE | + H5T_IEEE_F64BE | H5T_IEEE_F64LE | + H5T_NATIVE_FLOAT | H5T_NATIVE_DOUBLE | + H5T_NATIVE_LDOUBLE + +<time> ::= H5T_TIME: not yet implemented + +<string> ::= H5T_STRING { + STRSIZE <strsize>; + STRPAD <strpad>; + CSET <cset>; + CTYPE <ctype>; + } + +<strsize> ::= <int_value> + +<strpad> ::= H5T_STR_NULLTERM | H5T_STR_NULLPAD | H5T_STR_SPACEPAD + +<cset> ::= H5T_CSET_ASCII | H5T_CSET_UTF8 + +<ctype> ::= H5T_C_S1 | H5T_FORTRAN_S1 + +<bitfield> ::= H5T_STD_B8BE | H5T_STD_B8LE | + H5T_STD_B16BE | H5T_STD_B16LE | + H5T_STD_B32BE | H5T_STD_B32LE | + H5T_STD_B64BE | H5T_STD_B64LE + +<opaque> ::= H5T_OPAQUE { + OPAQUE_TAG <identifier>; + OPAQUE_SIZE <int_value>;opt + } + +<reference> ::= H5T_REFERENCE { <ref_type> } + +<ref_type> ::= H5T_STD_REF_OBJECT | H5T_STD_REF_DSETREG | H5T_STD_REF | UNDEFINED + +<compound_type> ::= H5T_COMPOUND { + <member_type_def>+ + } + +<member_type_def> ::= <datatype> <field_name>; + +<field_name> ::= <identifier> + +<variable_length_type> ::= H5T_VLEN { <datatype> } + +<array_type> ::= H5T_ARRAY { <dim_sizes> <datatype> } + +<dim_sizes> ::= '['<dimsize>']' | '['<dimsize>']'<dim_sizes> + +<dimsize> ::= <int_value> + +<attribute> ::= ATTRIBUTE <attr_name> { + <dataset_type> + <dataset_space> + <data>opt + } + +<attr_name> ::= <identifier> + +<dataset_type> ::= DATATYPE <path_name> | <datatype> + +<enum> ::= H5T_ENUM { + <enum_base_type> <enum_def>+ + } + +<enum_base_type> ::= <integer> +// Currently enums can only hold integer type data, but they may be expanded +// in the future to hold any datatype + +<enum_def> ::= <enum_symbol> <enum_val>; + +<enum_symbol> ::= <identifier> + +<enum_val> ::= <int_value> + +<path_name> ::= <path_part>+ + +<path_part> ::= /<identifier> + +<dataspace> ::= <scalar_space> | <simple_space> | <complex_space> | <null_space> + +<null_space> ::= NULL + +<scalar_space> ::= SCALAR + +<simple_space> ::= SIMPLE { <current_dims> / <max_dims> } + +<complex_space> ::= COMPLEX { <complex_space_definition> } + +<dataset_space> ::= DATASPACE <path_name> | <dataspace> + +<current_dims> ::= <dims> + +<max_dims> ::= '(' <max_dim_list> ')' + +<max_dim_list> ::= <max_dim> | <max_dim>, <max_dim_list> + +<max_dim> ::= <int_value> | H5S_UNLIMITED + +<data> ::= <subset> | <data_values> + +<data_values> ::= DATA { + <scalar_space_data> | <simple_space_data> + } + +<scalar_space_data> ::= <any_element> + +<any_element> ::= <atomic_element> | <compound_element> | + <variable_length_element> | <array_element> + +<any_data_seq> ::= <any_element> | <any_element>, <any_data_seq> + +<atomic_element> :: = <integer_data> | <float_data> | <time_data> | + <string_data> | <bitfield_data> | <opaque_data> | + <enum_data> | <reference_data> + +<subset> ::= SUBSET { + <start>; + <stride>; + <count>; + <block>; + DATA { + <simple_space_data> + } + } + +<start> ::= START (<coor_list>) + +<stride> ::= STRIDE (<pos_list>) + +<count> ::= COUNT (<max_dim_list>) + +<block> ::= BLOCK (<max_dim_list>) + +<coor_list> ::= <coor_data>, <coor_list> | <coor_data> + +<coor_data> ::= <integer_data> | H5S_UNLIMITED + +<integer_data> ::= <int_value> + +<float_data> ::= a floating point number + +<time_data> ::= DATA{ not yet implemented.} + +<string_data> ::= a string +// A string is enclosed in double quotes. +// If a string is displayed on more than one line, string concatenate +// operator '//'is used. + +<bitfield_data> ::= <hex_value> + +<opaque_data> ::= <hex_value>:<hex_value> | <hex_value> + +<enum_data> ::= <enum_symbol> + +<reference_data> ::= <object_ref_data> | <data_region_data> | <attribute_data> | NULL + +<object_ref_data> ::= <object_type> <object_num> + +<object_type> ::= DATASET | GROUP | DATATYPE + +<object_id> ::= OBJECTID { <object_num> } + +<object_num> ::= <int_value>:<int_value> | <int_value> + +<attribute_data> ::= ATTRIBUTE <attr_name> + +<data_region_data> ::= DATASET <dataset_name> { + <data_region_type>opt <data_region_data_list> + <dataset_type>opt <dataset_space>opt + <data>opt + } + +<data_region_type> ::= REGION_TYPE <data_region_data_type> + +<data_region_data_type> ::= POINT | BLOCK + +<data_region_data_list> ::= <data_region_data_info>, <data_region_data_list> | + <data_region_data_info> + +<data_region_data_info> ::= <region_info> | <point_info> + +<region_info> ::= (<lower_region_vals>)-(<upper_region_vals>) + +<lower_region_vals> ::= <lower_bound>, <lower_region_vals> | <lower_bound> + +<upper_region_vals> ::= <upper_bound>, <upper_region_vals> | <upper_bound> + +<lower_bound> ::= <int_value> + +<upper_bound> ::= <int_value> + +<point_info> ::= (<point_vals>) + +<point_vals> ::= <int_value> | <int_value>, <point_vals> + +<compound_element> ::= { <any_data_seq> } + +<atomic_simple_data> :: = <atomic_element>, <atomic_simple_data> | + <atomic_element> + +<simple_space_data> :: = <any_data_seq> + +<variable_length_element> ::= ( <any_data_seq> ) + +<array_element> ::= '[' <any_data_seq> ']' + +<named_datatype> ::= DATATYPE <type_name> { <datatype> } + +<type_name> ::= <identifier> + +<hardlink> ::= HARDLINK <path_name> + +<group> ::= GROUP <group_name> { <hardlink> | <group_info> } + +<group_comment> ::= COMMENT <string_data> + +<group_name> ::= <identifier> + +<group_info> ::= <object_id>opt <group_comment>opt <group_attribute>* + <group_member>* + +<group_attribute> ::= <attribute> + +<group_member> ::= <named_datatype> | <group> | <dataset> | + <softlink> | <external_link> + +<dataset> ::= DATASET <dataset_name> { <hardlink> | <dataset_info> } + +<dataset_info> ::= <dataset_type> + <dataset_space> + <dcpl_info>opt + <dataset_attribute>* <object_id>opt + <data>opt +// Tokens above can be in any order as long as <data> is +// after <dataset_type> and <dataset_space>. + +<dcpl_info> ::= <storagelayout> + <compression_filters> + <fillvalue> + <allocationtime> + +<dataset_name> ::= <identifier> + +<storagelayout> :: = STORAGE_LAYOUT { + <contiguous_layout> | <chunked_layout> | + <compact_layout> | <virtual_layout> + } + +<contiguous_layout> ::= CONTIGUOUS + <internal_layout> | <external_layout> + +<chunked_layout> ::= CHUNKED <dims> + <filter_ratio>opt + +<compact_layout> ::= COMPACT + <size> + +<internal_layout> ::= <size> + <offset> + +<external_layout> ::= EXTERNAL { + <external_file>+ + } + +<virtual_layout> ::= <vmaps>*opt + +<vmaps> ::= MAPPING <int_value> { + <virtual_map> + <source_map> + } + +<virtual_map> ::= VIRTUAL { + <vmaps_selection> + } + +<source_map> ::= SOURCE { + FILE <file_name> + DATASET <dataset_name> + <vmaps_selection> + } + +<vmaps_selection> ::= <regular_hyperslab> | <irregular_hyperslab> | + <select_points> | <select_none> | <select_all> + +<regular_hyperslab> ::= SELECTION REGULAR_HYPERSLAB { + <start> + <stride> + <count> + <block> + } + +<irregular_hyperslab> ::= SELECTION IRREGULAR_HYPERSLAB { + <region_info>+ + } + +<select_points> ::= SELECTION POINT { + (<coor_list>)+ + } + +<select_none> ::= SELECTION NONE + +<select_all> ::= SELECTION ALL + +<dims> ::= (<dims_values>) + +<dims_values> ::= <int_value> | <int_value>, <dims_values> + +<external_file> ::= FILENAME <file_name> <size> <offset> + +<offset> ::= OFFSET <int_value> + +<size> ::= SIZE <int_value> + +<filter_ratio> ::= <size> | <compressionratio> + +<compressionratio> :: = <size> (<float_data>:1 COMPRESSION) + +<compression_filters> :: = FILTERS { + <filter_type>+ | NONE + } + +<filter_type> :: = <filter_deflate> | <filter_shuffle> | + <filter_flecther> | <filter_szip> | + <filter_nbit> | <filter_scaleoffset> | + <filter_default> + +<filter_default> :: = <filter_user> { + FILTER_ID <int_value> + <filter_comment>opt + <filter_params>opt + } + +<filter_user> :: = USER_DEFINED_FILTER + +<filter_deflate> :: = COMPRESSION DEFLATE { LEVEL <int_value> } + +<filter_shuffle> :: = PREPROCESSING SHUFFLE + +<filter_flecther> :: = CHECKSUM FLETCHER32 + +<filter_szip> :: = COMPRESSION SZIP { + PIXELS_PER_BLOCK <int_value> + <filter_szip_mode>opt + <filter_szip_coding>opt + <filter_szip_order>opt + <filter_szip_header>opt + } + +<filter_szip_mode> :: = MODE HARDWARE | K13 + +<filter_szip_coding> :: = CODING ENTROPY | NEAREST NEIGHBOUR + +<filter_szip_order> :: = BYTE_ORDER LSB | MSB + +<filter_szip_header> :: = HEADER RAW + +<filter_nbit> :: = CHECKSUM NBIT + +<filter_scaleoffset> :: = COMPRESSION SCALEOFFSET { MIN BITS <int_value> } + +<filter_comment> :: = COMMENT <identifier> + +<filter_params> :: = PARAMS { <int_value>* } + +<fillvalue> ::= FILLVALUE { + FILL_TIME H5D_FILL_TIME_ALLOC | H5D_FILL_TIME_NEVER | H5D_FILL_TIME_IFSET + VALUE H5D_FILL_VALUE_UNDEFINED | H5D_FILL_VALUE_DEFAULT | <any_element> + } + +<allocationtime> ::= ALLOCATION_TIME { + H5D_ALLOC_TIME_EARLY | H5D_ALLOC_TIME_INCR | + H5D_ALLOC_TIME_LATE + } + +<dataset_attribute> ::= <attribute> + +<softlink> ::= SOFTLINK <softlink_name> { + LINKTARGET <target> + } + +<softlink_name> ::= <identifier> + +<target> ::= <identifier> + +<external_link> ::= EXTERNAL_LINK <external_link_name> { + TARGETFILE <targetfile> + TARGETPATH <targetpath> <targetobj>opt + } + +<external_link_name> ::= <identifier> + +<user_defined_link> ::= USERDEFINED_LINK <external_link_name> { + LINKCLASS <user_link_type> + } + +<user_link_type> ::= <int_value> + +<targetfile> ::= <file_name> + +<targetpath> ::= <identifier> + +<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 example110 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 + + */
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