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::= 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
<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]+
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";
}
}
}
|
HDF5 documents and links Introduction to HDF5 |
HDF5 User’s Guide HDF5 Reference Manual |