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HDF5
1.15.0.ac650fa
API Reference
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Figure 1: Relationships among the HDF5 root group, other groups, and objects
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Figure 2: HDF5 objects -- datasets, datatypes, or dataspaces
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The format of an HDF5 file on disk encompasses several key ideas of the HDF4 and AIO file formats as well as addressing some shortcomings therein. The new format is more self-describing than the HDF4 format and is more uniformly applied to data objects in the file.
An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs:
At the lowest level, as information is actually written to the disk, an HDF5 file is made up of the following objects:
This document describes the lower-level data objects; the higher-level objects and their properties are described in the HDF5 User Guide.
Three levels of information comprise the file format. Level 0 contains basic information for identifying and defining information about the file. Level 1 information contains the group information (stored as a B-tree) and is used as the index for all the objects in the file. Level 2 is the rest of the file and contains all of the data objects, with each object partitioned into header information, also known as meta information, and data.
The sizes of various fields in the following layout tables are
determined by looking at the number of columns the field spans
in the table. There are three exceptions: (1) The size may be
overridden by specifying a size in parentheses, (2) the size of
addresses is determined by the Size of Offsets field
in the super block, and (3) the size of size fields is determined
by the Size of Lengths field in the super block.
The super block may begin at certain predefined offsets within the HDF5 file, allowing a block of unspecified content for users to place additional information at the beginning (and end) of the HDF5 file without limiting the HDF5 library's ability to manage the objects within the file itself. This feature was designed to accommodate wrapping an HDF5 file in another file format or adding descriptive information to the file without requiring the modification of the actual file's information. The super block is located by searching for the HDF5 file signature at byte offset 0, byte offset 512 and at successive locations in the file, each a multiple of two of the previous location, i.e. 0, 512, 1024, 2048, etc.
The super block is composed of a file signature, followed by super block and group version numbers, information about the sizes of offset and length values used to describe items within the file, the size of each group page, and a group entry for the root object in the file.
byte | byte | byte | byte |
---|---|---|---|
HDF5 File Signature (8 bytes) |
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Version # of Super Block | Version # of Global Free-space Storage | Version # of Group | Reserved |
Version # of Shared Header Message Format | Size of Offsets | Size of Lengths | Reserved (zero) |
Group Leaf Node K | Group Internal Node K | ||
File Consistency Flags | |||
Base Address* | |||
Address of Global Free-space Heap* | |||
End of File Address* | |||
Driver Information Block Address* | |||
Root Group Address* |
(Items marked with an asterisk (*) in the above table
are of the size specified in "Size of Offsets.") |
Field Name | Description | |||||||||||||||||||||||||||
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File Signature | This field contains a constant value and can be used to
quickly identify a file as being an HDF5 file. The
constant value is designed to allow easy identification of
an HDF5 file and to allow certain types of data corruption
to be detected. The file signature of an HDF5 file always
contains the following values:
This signature both identifies the file as an HDF5 file and provides for immediate detection of common file-transfer problems. The first two bytes distinguish HDF5 files on systems that expect the first two bytes to identify the file type uniquely. The first byte is chosen as a non-ASCII value to reduce the probability that a text file may be misrecognized as an HDF5 file; also, it catches bad file transfers that clear bit 7. Bytes two through four name the format. The CR-LF sequence catches bad file transfers that alter newline sequences. The control-Z character stops file display under MS-DOS. The final line feed checks for the inverse of the CR-LF translation problem. (This is a direct descendent of the PNG file signature.) |
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Version Number of the Super Block | This value is used to determine the format of the information in the super block. When the format of the information in the super block is changed, the version number is incremented to the next integer and can be used to determine how the information in the super block is formatted. | |||||||||||||||||||||||||||
Version Number of the Global Free-space Heap | This value is used to determine the format of the information in the Global Free-space Heap. | |||||||||||||||||||||||||||
Version Number of the Group | This value is used to determine the format of the information in the Group. When the format of the information in the Group is changed, the version number is incremented to the next integer and can be used to determine how the information in the Group is formatted. | |||||||||||||||||||||||||||
Version Number of the Shared Header Message Format | This value is used to determine the format of the information in a shared object header message, which is stored in the global small-data heap. Since the format of the shared header messages differs from the private header messages, a version number is used to identify changes in the format. | |||||||||||||||||||||||||||
Size of Offsets | This value contains the number of bytes used to store addresses in the file. The values for the addresses of objects in the file are offsets relative to a base address, usually the address of the super block signature. This allows a wrapper to be added after the file is created without invalidating the internal offset locations. | |||||||||||||||||||||||||||
Size of Lengths | This value contains the number of bytes used to store the size of an object. | |||||||||||||||||||||||||||
Group Leaf Node K | Each leaf node of a group B-tree will have at least this many entries but not more than twice this many. If a group has a single leaf node then it may have fewer entries. | |||||||||||||||||||||||||||
Group Internal Node K | Each internal node of a group B-tree will have at least K pointers to other nodes but not more than 2K pointers. If the group has only one internal node then it might have fewer than K pointers. | |||||||||||||||||||||||||||
Bytes per B-tree Page | This value contains the number of bytes used for symbol
pairs per page of the B-trees used in the file. All
B-tree pages will have the same size per page.
For 32-bit file offsets, 340 objects is the maximum per 4KB page; for 64-bit file offset, 254 objects will fit per 4KB page. In general, the equation is: <number of objects> =
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File Consistency Flags | This value contains flags to indicate information
about the consistency of the information contained
within the file. Currently, the following bit flags are
defined:
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Base Address | This is the absolute file address of the first byte of the HDF5 data within the file. The library currently constrains this value to be the absolute file address of the super block itself when creating new files; future versions of the library may provide greater flexibility. Unless otherwise noted, all other file addresses are relative to this base address. | |||||||||||||||||||||||||||
Address of Global Free-space Heap | Free-space management is not yet defined in the HDF5
file format and is not handled by the library.
Currently this field always contains the
undefined address 0xfff...ff .
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End of File Address | This is the relative file address of the first byte past the end of all HDF5 data. It is used to determine whether a file has been accidentally truncated and as an address where file data allocation can occur if the free list is not used. | |||||||||||||||||||||||||||
Driver Information Block Address | This is the relative file address of the file driver information block which contains driver-specific information needed to reopen the file. If there is no driver information block then this entry should be the undefined address (all bits set). | |||||||||||||||||||||||||||
Root Group Address | This is the address of the root group (described later in this document), which serves as the entry point into the group graph. |
The file driver information block is an optional region of the file which contains information needed by the file driver in order to reopen a file. The format of the file driver information block is:
byte | byte | byte | byte |
---|---|---|---|
Version | Reserved (zero) | ||
Driver Information Size (4 bytes) | |||
Driver Identification (8 bytes) |
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Driver Information |
Field Name | Description |
---|---|
Version | The version number of the driver information block. The file format documented here is version zero. |
Driver Information Size | The size in bytes of the Driver Information part of this structure. |
Driver Identification | This is an eight-byte ASCII string without null
termination which identifies the driver and version number
of the Driver Information block. The predefined drivers
supplied with the HDF5 library are identified by the
letters NCSA followed by the first four characters of
the driver name. If the Driver Information block is not
the original version then the last letter(s) of the
identification will be replaced by a version number in
ASCII.
For example, the various versions of the family driver
will be identified by NCSAfami , NCSAfam0 ,
NCSAfam1 , etc.
(NCSAfami is simply NCSAfamily truncated
to eight characters. Subsequent identifiers will be created by
substituting sequential numerical values for the final character,
starting with zero.)
Identification for user-defined drivers is arbitrary but should be unique. |
Driver Information | Driver information is stored in a format defined by the
file driver and encoded/decoded by the driver callbacks
invoked from the H5FD_sb_encode and
H5FD_sb_decode functions. |
B-link trees allow flexible storage for objects which tend to grow in ways that cause the object to be stored discontiguously. B-trees are described in various algorithms books including "Introduction to Algorithms" by Thomas H. Cormen, Charles E. Leiserson, and Ronald L. Rivest. The B-link tree, in which the sibling nodes at a particular level in the tree are stored in a doubly-linked list, is described in the "Efficient Locking for Concurrent Operations on B-trees" paper by Phillip Lehman and S. Bing Yao as published in the ACM Transactions on Database Systems, Vol. 6, No. 4, December 1981.
The B-link trees implemented by the file format contain one more key than the number of children. In other words, each child pointer out of a B-tree node has a left key and a right key. The pointers out of internal nodes point to sub-trees while the pointers out of leaf nodes point to symbol nodes and raw data chunks. Aside from that difference, internal nodes and leaf nodes are identical.
byte | byte | byte | byte |
---|---|---|---|
Node Signature | |||
Node Type | Node Level | Entries Used | |
Address of Left Sibling | |||
Address of Right Sibling | |||
Key 0 (variable size) | |||
Address of Child 0 | |||
Key 1 (variable size) | |||
Address of Child 1 | |||
... | |||
Key 2K (variable size) | |||
Address of Child 2K | |||
Key 2K+1 (variable size) |
Field Name | Description | ||||||||
---|---|---|---|---|---|---|---|---|---|
Node Signature | The ASCII character string TREE is
used to indicate the
beginning of a B-link tree node. This gives file
consistency checking utilities a better chance of
reconstructing a damaged file. |
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Node Type | Each B-link tree points to a particular type of data.
This field indicates the type of data as well as
implying the maximum degree K of the tree and
the size of each Key field.
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Node Level | The node level indicates the level at which this node appears in the tree (leaf nodes are at level zero). Not only does the level indicate whether child pointers point to sub-trees or to data, but it can also be used to help file consistency checking utilities reconstruct damaged trees. | ||||||||
Entries Used | This determines the number of children to which this node points. All nodes of a particular type of tree have the same maximum degree, but most nodes will point to less than that number of children. The valid child pointers and keys appear at the beginning of the node and the unused pointers and keys appear at the end of the node. The unused pointers and keys have undefined values. | ||||||||
Address of Left Sibling | This is the file address of the left sibling of the current node relative to the super block. If the current node is the left-most node at this level then this field is the undefined address (all bits set). | ||||||||
Address of Right Sibling | This is the file address of the right sibling of the current node relative to the super block. If the current node is the right-most node at this level then this field is the undefined address (all bits set). | ||||||||
Keys and Child Pointers | Each tree has 2K+1 keys with 2K child pointers interleaved between the keys. The number of keys and child pointers actually containing valid values is determined by the Entries Used field. If that field is N then the B-link tree contains N child pointers and N+1 keys. | ||||||||
Key | The format and size of the key values is determined by
the type of data to which this tree points. The keys are
ordered and are boundaries for the contents of the child
pointer; that is, the key values represented by child
N fall between Key N and Key
N+1. Whether the interval is open or closed on
each end is determined by the type of data to which the
tree points.
The format of the key depends on the node type. For nodes of node type 1, the key is formatted as follows:
For nodes of node type 0, the key is formatted as follows:
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Child Pointers | The tree node contains file addresses of subtrees or data depending on the node level. Nodes at Level 0 point to data addresses, either data chunk or group nodes. Nodes at non-zero levels point to other nodes of the same B-tree. |
Each B-tree node looks like this:
key[0] | child[0] | key[1] | child[1] | key[2] | ... | ... | key[N-1] | child[N-1] | key[N] |
The following question must next be answered: "Is the value described by key[i] contained in child[i-1] or in child[i]?" The answer depends on the type of tree. In trees for groups (node type 0) the object described by key[i] is the greatest object contained in child[i-1] while in chunk trees (node type 1) the chunk described by key[i] is the least chunk in child[i].
That means that key[0] for group trees is sometimes unused; it points to offset zero in the heap, which is always the empty string and compares as "less-than" any valid object name.
And key[N] for chunk trees is sometimes unused; it contains a chunk offset which compares as "greater-than" any other chunk offset and has a chunk byte size of zero to indicate that it is not actually allocated.
A group is an object internal to the file that allows arbitrary nesting of objects (including other groups). A group maps a set of names to a set of file address relative to the base address. Certain meta data for an object to which the group points can be duplicated in the group symbol table in addition to the object header.
An HDF5 object name space can be stored hierarchically by partitioning the name into components and storing each component in a group. The group entry for a non-ultimate component points to the group containing the next component. The group entry for the last component points to the object being named.
A group is a collection of group nodes pointed to by a B-link tree. Each group node contains entries for one or more symbols. If an attempt is made to add a symbol to an already full group node containing 2K entries, then the node is split and one node contains K symbols and the other contains K+1 symbols.
byte | byte | byte | byte |
---|---|---|---|
Node Signature | |||
Version Number | Reserved for Future Use | Number of Symbols | |
Group Entries |
Field Name | Description |
---|---|
Node Signature | The ASCII character string SNOD is
used to indicate the
beginning of a group node. This gives file
consistency checking utilities a better chance of
reconstructing a damaged file. |
Version Number | The version number for the group node. This document describes version 1. |
Number of Symbols | Although all group nodes have the same length, most contain fewer than the maximum possible number of symbol entries. This field indicates how many entries contain valid data. The valid entries are packed at the beginning of the group node while the remaining entries contain undefined values. |
Group Entries | Each symbol has an entry in the group node. The format of the entry is described below. |
Each group entry in a group node is designed to allow for very fast browsing of stored objects. Toward that design goal, the group entries include space for caching certain constant meta data from the object header.
byte | byte | byte | byte |
---|---|---|---|
Name Offset (<size> bytes) | |||
Object Header Address | |||
Cache Type | |||
Reserved | |||
Scratch-pad Space (16 bytes) |
Field Name | Description |
---|---|
Name Offset | This is the byte offset into the group local heap for the name of the object. The name is null terminated. |
Object Header Address | Every object has an object header which serves as a permanent location for the object's meta data. In addition to appearing in the object header, some meta data can be cached in the scratch-pad space. |
Cache Type | The cache type is determined from the object header.
It also determines the format for the scratch-pad space.
|
Reserved | These four bytes are present so that the scratch-pad space is aligned on an eight-byte boundary. They are always set to zero. |
Scratch-pad Space | This space is used for different purposes, depending on the value of the Cache Type field. Any meta-data about a dataset object represented in the scratch-pad space is duplicated in the object header for that dataset. This meta data can include the datatype and the size of the dataspace for a dataset whose datatype is atomic and whose dataspace is fixed and less than four dimensions. Furthermore, no data is cached in the group entry scratch-pad space if the object header for the group entry has a link count greater than one. |
The group entry scratch-pad space is formatted according to the value in the Cache Type field.
If the Cache Type field contains the value zero
(0
) then no information is
stored in the scratch-pad space.
If the Cache Type field contains the value one
(1
), then the scratch-pad space
contains cached meta data for another object header
in the following format:
byte | byte | byte | byte |
---|---|---|---|
Address of B-tree | |||
Address of Name Heap |
Field Name | Description |
---|---|
Address of B-tree | This is the file address for the root of the group's B-tree. |
Address of Name Heap | This is the file address for the group's local heap, in which are stored the symbol names. |
If the Cache Type field contains the value two
(2
), then the scratch-pad space
contains cached meta data for another symbolic link
in the following format:
byte | byte | byte | byte |
---|---|---|---|
Offset to Link Value |
Field Name | Description |
---|---|
Offset to Link Value | The value of a symbolic link (that is, the name of the thing to which it points) is stored in the local heap. This field is the 4-byte offset into the local heap for the start of the link value, which is null terminated. |
A heap is a collection of small heap objects. Objects can be inserted and removed from the heap at any time. The address of a heap does not change once the heap is created. References to objects are stored in the group table; the names of those objects are stored in the local heap.
byte | byte | byte | byte |
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Heap Signature | |||
Reserved (zero) | |||
Data Segment Size | |||
Offset to Head of Free-list (<size> bytes) | |||
Address of Data Segment |
Field Name | Description |
---|---|
Heap Signature | The ASCII character string HEAP
is used to indicate the
beginning of a heap. This gives file consistency
checking utilities a better chance of reconstructing a
damaged file. |
Data Segment Size | The total amount of disk memory allocated for the heap data. This may be larger than the amount of space required by the object stored in the heap. The extra unused space holds a linked list of free blocks. |
Offset to Head of Free-list | This is the offset within the heap data segment of the first free block (or all 0xff bytes if there is no free block). The free block contains <size> bytes that are the offset of the next free chunk (or all 0xff bytes if this is the last free chunk) followed by <size> bytes that store the size of this free chunk. |
Address of Data Segment | The data segment originally starts immediately after the heap header, but if the data segment must grow as a result of adding more objects, then the data segment may be relocated, in its entirety, to another part of the file. |
Objects within the heap should be aligned on an 8-byte boundary.
Each HDF5 file has a global heap which stores various types of information which is typically shared between datasets. The global heap was designed to satisfy these goals:
The implementation of the heap makes use of the memory management already available at the file level and combines that with a new top-level object called a collection to achieve Goal B. The global heap is the set of all collections. Each global heap object belongs to exactly one collection and each collection contains one or more global heap objects. For the purposes of disk I/O and caching, a collection is treated as an atomic object.
byte | byte | byte | byte |
---|---|---|---|
Magic Number | |||
Version | Reserved | ||
Collection Size | |||
Global Heap Object 1 (described below) |
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Global Heap Object 2 |
|||
... |
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Global Heap Object N |
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Global Heap Object 0 (free space) |
Field Name | Description |
---|---|
Magic Number | The magic number for global heap collections are the
four bytes G , C , O ,
and L . |
Version | Each collection has its own version number so that new collections can be added to old files. This document describes version zero of the collections. |
Collection Data Size | This is the size in bytes of the entire collection including this field. The default (and minimum) collection size is 4096 bytes which is a typical file system block size and which allows for 170 16-byte heap objects plus their overhead. |
Object 1 through N | The objects are stored in any order with no intervening unused space. |
Object 0 | Object 0 (zero), when present, represents the free space in the collection. Free space always appears at the end of the collection. If the free space is too small to store the header for Object 0 (described below) then the header is implied and the collection contains no free space. |
byte | byte | byte | byte |
---|---|---|---|
Object ID | Reference Count | ||
Reserved | |||
Object Data Size | |||
Object Data |
Field Name | Description |
---|---|
Object ID | Each object has a unique identification number within a
collection. The identification numbers are chosen so that
new objects have the smallest value possible with the
exception that the identifier 0 always refers to the
object which represents all free space within the
collection. |
Reference Count | All heap objects have a reference count field. An object which is referenced from some other part of the file will have a positive reference count. The reference count for Object 0 is always zero. |
Reserved | Zero padding to align next field on an 8-byte boundary. |
Object Size | This is the size of the fields above plus the object data stored for the object. The actual storage size is rounded up to a multiple of eight. |
Object Data | The object data is treated as a one-dimensional array of bytes to be interpreted by the caller. |
The Free-space Index is a collection of blocks of data, dispersed throughout the file, which are currently not used by any file objects.
The super block contains a pointer to root of the free-space description;
that pointer is currently (i.e., in HDF5 Release 1.2) required
to be the undefined address 0xfff...ff
.
The free-sapce index is not otherwise publicly defined at this time.
Data objects contain the real information in the file. These objects compose the scientific data and other information which are generally thought of as "data" by the end-user. All the other information in the file is provided as a framework for these data objects.
A data object is composed of header information and data information. The header information contains the information needed to interpret the data information for the data object as well as additional "meta-data" or pointers to additional "meta-data" used to describe or annotate each data object.
The header information of an object is designed to encompass all the information about an object which would be desired to be known, except for the data itself. This information includes the dimensionality, number-type, information about how the data is stored on disk (in external files, compressed, broken up in blocks, etc.), as well as other information used by the library to speed up access to the data objects or maintain a file's integrity. The header of each object is not necessarily located immediately prior to the object's data in the file and in fact may be located in any position in the file.
byte | byte | byte | byte |
---|---|---|---|
Version # of Object Header | Reserved | Number of Header Messages | |
Object Reference Count | |||
Total Object Header Size |
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Header Message Type #1 | Size of Header Message Data #1 | ||
Flags | Reserved | ||
Header Message Data #1 |
|||
. . . |
|||
Header Message Type #n | Size of Header Message Data #n | ||
Flags | Reserved | ||
Header Message Data #n |
Field Name | Description |
---|---|
Version number of the object header | This value is used to determine the format of the information in the object header. When the format of the information in the object header is changed, the version number is incremented and can be used to determine how the information in the object header is formatted. |
Reserved | Always set to zero. |
Number of header messages | This value determines the number of messages listed in this object header. This provides a fast way for software to prepare storage for the messages in the header. |
Object Reference Count | This value specifies the number of references to this object within the current file. References to the data object from external files are not tracked. |
Total Object Header Size | This value specifies the total number of bytes of header message data following this length field for the current message as well as any continuation data located elsewhere in the file. |
Header Message Type | The header message type specifies the type of information included in the header message data following the type along with a small amount of other information. Bit 15 of the message type is set if the message is constant (constant messages cannot be changed since they may be cached in group entries throughout the file). The header message types for the pre-defined header messages will be included in further discussion below. |
Size of Header Message Data | This value specifies the number of bytes of header message data following the header message type and length information for the current message. The size includes padding bytes to make the message a multiple of eight bytes. |
Flags | This is a bit field with the following definition:
|
Header Message Data | The format and length of this field is determined by the header message type and size respectively. Some header message types do not require any data and this information can be eliminated by setting the length of the message to zero. The data is padded with enough zeros to make the size a multiple of eight. |
The header message types and the message data associated with them compose the critical "meta-data" about each object. Some header messages are required for each object while others are optional. Some optional header messages may also be repeated several times in the header itself, the requirements and number of times allowed in the header will be noted in each header message description below.
The following is a list of currently defined header messages:
The Simple Dataspace message describes the number of dimensions and size of each dimension that the data object has. This message is only used for datasets which have a simple, rectilinear grid layout; datasets requiring a more complex layout (irregularly structured or unstructured grids, etc.) must use the Complex Dataspace message for expressing the space the dataset inhabits. (Note: The Complex Dataspace functionality is not yet implemented (as of HDF5 Release 1.2). It is not described in this document.)
byte | byte | byte | byte |
---|---|---|---|
Version | Dimensionality | Flags | Reserved |
Reserved | |||
Dimension Size #1 (<size> bytes) | |||
. . . |
|||
Dimension Size #n (<size> bytes) | |||
Dimension Maximum #1 (<size> bytes) | |||
. . . |
|||
Dimension Maximum #n (<size> bytes) | |||
Permutation Index #1 | |||
. . . |
|||
Permutation Index #n |
Field Name | Description |
---|---|
Version | This value is used to determine the format of the Simple Dataspace Message. When the format of the information in the message is changed, the version number is incremented and can be used to determine how the information in the object header is formatted. |
Dimensionality | This value is the number of dimensions that the data object has. |
Flags | This field is used to store flags to indicate the presence of parts of this message. Bit 0 (the least significant bit) is used to indicate that maximum dimensions are present. Bit 1 is used to indicate that permutation indices are present for each dimension. |
Dimension Size #n (<size> bytes) | This value is the current size of the dimension of the data as stored in the file. The first dimension stored in the list of dimensions is the slowest changing dimension and the last dimension stored is the fastest changing dimension. |
Dimension Maximum #n (<size> bytes) | This value is the maximum size of the dimension of the data as stored in the file. This value may be the special value <UNLIMITED> (all bits set) which indicates that the data may expand along this dimension indefinitely. If these values are not stored, the maximum value of each dimension is assumed to be the same as the current size value. |
Permutation Index #n (4 bytes) | This value is the index permutation used to map each dimension from the canonical representation to an alternate axis for each dimension. If these values are not stored, the first dimension stored in the list of dimensions is the slowest changing dimension and the last dimension stored is the fastest changing dimension. |
The datatype message defines the datatype for each data point of a dataset. A datatype can describe an atomic type like a fixed- or floating-point type or a compound type like a C struct. A datatype does not, however, describe how data points are combined to produce a dataset. Datatypes are stored on disk as a datatype message, which is a list of datatype classes and their associated properties.
byte | byte | byte | byte |
---|---|---|---|
Type Class and Version | Class Bit Field | ||
Size in Bytes (4 bytes) | |||
Properties |
The Class Bit Field and Properties fields vary depending on the Type Class, which is the low-order four bits of the Type Class and Version field (the high-order four bits are the version, which should be set to the value one). The type class is one of 0 (fixed-point number), 1 (floating-point number), 2 (date and time), 3 (text string), 4 (bit field), 5 (opaque), 6 (compound), 7 (reference), 8 (enumeration), or 9 (variable-length). The Class Bit Field is zero and the size of the Properties field is zero except for the cases noted here.
Bits | Meaning |
---|---|
0 | Byte Order. If zero, byte order is little-endian; otherwise, byte order is big endian. |
1, 2 | Padding type. Bit 1 is the lo_pad type and bit 2 is the hi_pad type. If a datum has unused bits at either end, then the lo_pad or hi_pad bit is copied to those locations. |
3 | Signed. If this bit is set then the fixed-point number is in 2's complement form. |
4-23 | Reserved (zero). |
Byte | Byte | Byte | Byte |
---|---|---|---|
Bit Offset | Bit Precision |
Bits | Meaning |
---|---|
0 | Byte Order. If zero, byte order is little-endian; otherwise, byte order is big endian. |
1, 2, 3 | Padding type. Bit 1 is the low bits pad type, bit 2 is the high bits pad type, and bit 3 is the internal bits pad type. If a datum has unused bits at either or between the sign bit, exponent, or mantissa, then the value of bit 1, 2, or 3 is copied to those locations. |
4-5 | Normalization. The value can be 0 if there is no normalization, 1 if the most significant bit of the mantissa is always set (except for 0.0), and 2 if the most significant bit of the mantissa is not stored but is implied to be set. The value 3 is reserved and will not appear in this field. |
6-7 | Reserved (zero). |
8-15 | Sign. This is the bit position of the sign bit. |
16-23 | Reserved (zero). |
Byte | Byte | Byte | Byte |
---|---|---|---|
Bit Offset | Bit Precision | ||
Exponent Location | Exponent Size in Bits | Mantissa Location | Mantissa Size in Bits |
Exponent Bias |
Bits | Meaning |
---|---|
0-3 | Padding type. This four-bit value determines the
type of padding to use for the string. The values are:
|
4-7 | Character Set. The character set to use for encoding the string. The only character set supported is the 8-bit ASCII (zero) so no translations have been defined yet. |
8-23 | Reserved (zero). |
Bits | Meaning |
---|---|
0 | Byte Order. If zero, byte order is little-endian; otherwise, byte order is big endian. |
1, 2 | Padding type. Bit 1 is the lo_pad type and bit 2 is the hi_pad type. If a datum has unused bits at either end, then the lo_pad or hi_pad bit is copied to those locations. |
3-23 | Reserved (zero). |
Byte | Byte | Byte | Byte |
---|---|---|---|
Bit Offset | Bit Precision |
Bits | Meaning |
---|---|
0-23 | Reserved (zero). |
Byte | Byte | Byte | Byte |
---|---|---|---|
Null-terminated ASCII Tag (multiple of 8 bytes) |
Bits | Meaning |
---|---|
0-15 | Number of Members. This field contains the number of members defined for the compound datatype. The member definitions are listed in the Properties field of the data type message. |
15-23 | Reserved (zero). |
The Properties field of a compound datatype is a list of the member definitions of the compound datatype. The member definitions appear one after another with no intervening bytes. The member types are described with a recursive datatype message.
Byte | Byte | Byte | Byte |
---|---|---|---|
Name (null terminated, multiple of eight bytes) |
|||
Byte Offset of Member in Compound Instance | |||
Dimensionality | reserved | ||
Dimension Permutation | |||
Reserved | |||
Size of Dimension 0 (required) | |||
Size of Dimension 1 (required) | |||
Size of Dimension 2 (required) | |||
Size of Dimension 3 (required) | |||
Member Type Message |
Bits | Meaning |
---|---|
0-15 | Number of Members. The number of name/value pairs defined for the enumeration type. |
16-23 | Reserved (zero). |
Byte | Byte | Byte | Byte |
---|---|---|---|
Parent Type |
|||
Names |
|||
Values |
Parent Type: | Each enumeration type is based on some parent type, usually an integer. The information for that parent type is described recursively by this field. |
Names: | The name for each name/value pair. Each name is stored as a null terminated ASCII string in a multiple of eight bytes. The names are in no particular order. |
Values: | The list of values in the same order as the names. The values are packed (no inter-value padding) and the size of each value is determined by the parent type. |
Bits | Meaning |
---|---|
0-3 |
|
4-7 |
|
8-11 |
|
12-23 | Reserved (zero). |
Byte | Byte | Byte | Byte |
---|---|---|---|
Parent Type |
Parent Type: | Each variable-length type is based on some parent type. The information for that parent type is described recursively by this field. |
The fill value message stores a single data point value which is returned to the application when an uninitialized data point is read from the dataset. The fill value is interpreted with the same datatype as the dataset. If no fill value message is present then a fill value of all zero is assumed.
byte | byte | byte | byte |
---|---|---|---|
Size (4 bytes) | |||
Fill Value |
Field Name | Description |
---|---|
Size (4 bytes) | This is the size of the Fill Value field in bytes. |
Fill Value | The fill value. The bytes of the fill value are interpreted using the same datatype as for the dataset. |
This message indicates that the data for the data object is stored within the current HDF file by including the actual data as the header data for this message. The data is stored internally in the normal format, i.e. in one chunk, uncompressed, etc.
Note that one and only one of the Data Storage headers can be stored for each data object.
Format of Data: The message data is actually composed of dataset data, so the format will be determined by the dataset format.
Purpose and Description: The external object message indicates that the data for an object is stored outside the HDF5 file. The filename of the object is stored as a Universal Resource Location (URL) of the actual filename containing the data. An external file list record also contains the byte offset of the start of the data within the file and the amount of space reserved in the file for that data.
byte | byte | byte | byte |
---|---|---|---|
Version | Reserved | ||
Allocated Slots | Used Slots | ||
Heap Address |
|||
Slot Definitions... |
Field Name | Description |
---|---|
Version | This value is used to determine the format of the External File List Message. When the format of the information in the message is changed, the version number is incremented and can be used to determine how the information in the object header is formatted. |
Reserved | This field is reserved for future use. |
Allocated Slots | The total number of slots allocated in the message. Its value must be at least as large as the value contained in the Used Slots field. |
Used Slots | The number of initial slots which contain valid information. The remaining slots are zero filled. |
Heap Address | This is the address of a local name heap which contains the names for the external files. The name at offset zero in the heap is always the empty string. |
Slot Definitions | The slot definitions are stored in order according to the array addresses they represent. If more slots have been allocated than what has been used then the defined slots are all at the beginning of the list. |
byte | byte | byte | byte |
---|---|---|---|
Name Offset (<size> bytes) |
|||
File Offset (<size> bytes) |
|||
Size |
Field Name | Description |
---|---|
Name Offset (<size> bytes) | The byte offset within the local name heap for the name
of the file. File names are stored as a URL which has a
protocol name, a host name, a port number, and a file
name:
protocol:port//host/file .
If the protocol is omitted then "file:" is assumed. If
the port number is omitted then a default port for that
protocol is used. If both the protocol and the port
number are omitted then the colon can also be omitted. If
the double slash and host name are omitted then
"localhost" is assumed. The file name is the only
mandatory part, and if the leading slash is missing then
it is relative to the application's current working
directory (the use of relative names is not
recommended). |
File Offset (<size> bytes) | This is the byte offset to the start of the data in the specified file. For files that contain data for a single dataset this will usually be zero. |
Size | This is the total number of bytes reserved in the specified file for raw data storage. For a file that contains exactly one complete dataset which is not extendable, the size will usually be the exact size of the dataset. However, by making the size larger one allows HDF5 to extend the dataset. The size can be set to a value larger than the entire file since HDF5 will read zeros past the end of the file without failing. |
Purpose and Description: Data layout describes how the elements of a multi-dimensional array are arranged in the linear address space of the file. Two types of data layout are supported:
byte | byte | byte | byte |
---|---|---|---|
Version | Dimensionality | Layout Class | Reserved |
Reserved | |||
Address |
|||
Dimension 0 (4-bytes) | |||
Dimension 1 (4-bytes) | |||
... |
Field Name | Description |
---|---|
Version | A version number for the layout message. This documentation describes version one. |
Dimensionality | An array has a fixed dimensionality. This field specifies the number of dimension size fields later in the message. |
Layout Class | The layout class specifies how the other fields of the layout message are to be interpreted. A value of one indicates contiguous storage while a value of two indicates chunked storage. Other values will be defined in the future. |
Address | For contiguous storage, this is the address of the first byte of storage. For chunked storage this is the address of the B-tree that is used to look up the addresses of the chunks. |
Dimensions | For contiguous storage the dimensions define the entire size of the array while for chunked storage they define the size of a single chunk. |
Purpose and Description: This message describes the filter pipeline which should be applied to the data stream by providing filter identification numbers, flags, a name, an client data.
byte | byte | byte | byte |
---|---|---|---|
Version | Number of Filters | Reserved | |
Reserved | |||
Filter List |
Field Name | Description |
---|---|
Version | The version number for this message. This document describes version one. |
Number of Filters | The total number of filters described by this message. The maximum possible number of filters in a message is 32. |
Filter List | A description of each filter. A filter description appears in the next table. |
byte | byte | byte | byte |
---|---|---|---|
Filter Identification | Name Length | ||
Flags | Client Data Number of Values | ||
Name |
|||
Client Data |
|||
Padding |
Field Name | Description |
---|---|
Filter Identification | This is a unique (except in the case of testing) identifier for the filter. Values from zero through 255 are reserved for filters defined by the NCSA HDF5 library. Values 256 through 511 have been set aside for use when developing/testing new filters. The remaining values are allocated to specific filters by contacting the HDF5 Development Team. |
Name Length | Each filter has an optional null-terminated ASCII name and this field holds the length of the name including the null termination padded with nulls to be a multiple of eight. If the filter has no name then a value of zero is stored in this field. |
Flags | The flags indicate certain properties for a filter. The
bit values defined so far are:
|
Client Data Number of Values | Each filter can store a few integer values to control how the filter operates. The number of entries in the Client Data array is stored in this field. |
Name | If the Name Length field is non-zero then it will contain the size of this field, a multiple of eight. This field contains a null-terminated, ASCII character string to serve as a comment/name for the filter. |
Client Data | This is an array of four-byte integers which will be passed to the filter function. The Client Data Number of Values determines the number of elements in the array. |
Padding | Four bytes of zeros are added to the message at this point if the Client Data Number of Values field contains an odd number. |
Purpose and Description: The Attribute message is used to list objects in the HDF file which are used as attributes, or "meta-data" about the current object. An attribute is a small dataset; it has a name, a datatype, a data space, and raw data. Since attributes are stored in the object header they must be relatively small (<64kb) and can be associated with any type of object which has an object header (groups, datasets, named types and spaces, etc.).
byte | byte | byte | byte |
---|---|---|---|
Version | Reserved | Name Size | |
Type Size | Space Size | ||
Name |
|||
Type |
|||
Space |
|||
Data |
Field Name | Description |
---|---|
Version | Version number for the message. This document describes version 1 of attribute messages. |
Reserved | This field is reserved for later use and is set to zero. |
Name Size | The length of the attribute name in bytes including the null terminator. Note that the Name field below may contain additional padding not represented by this field. |
Type Size | The length of the datatype description in the Type field below. Note that the Type field may contain additional padding not represented by this field. |
Space Size | The length of the dataspace description in the Space field below. Note that the Space field may contain additional padding not represented by this field. |
Name | The null-terminated attribute name. This field is padded with additional null characters to make it a multiple of eight bytes. |
Type | The datatype description follows the same format as described for the datatype object header message. This field is padded with additional zero bytes to make it a multiple of eight bytes. |
Space | The dataspace description follows the same format as described for the dataspace object header message. This field is padded with additional zero bytes to make it a multiple of eight bytes. |
Data | The raw data for the attribute. The size is determined from the datatype and dataspace descriptions. This field is not padded with additional zero bytes. |
Type: 0x000D
Length: varies
Status: Optional, may not be repeated.
Purpose and Description: The object name or comment is
designed to be a short description of an object. An object name
is a sequence of non-zero (\0
) ASCII characters with no other
formatting included by the library.
byte | byte | byte | byte |
---|---|---|---|
Name |
Field Name | Description |
---|---|
Name | A null terminated ASCII character string. |
Type: 0x000E
Length: fixed
Status: Optional, may not be repeated.
Purpose and Description: The object modification date and time is a timestamp which indicates (using ISO-8601 date and time format) the last modification of an object. The time is updated when any object header message changes according to the system clock where the change was posted.
byte | byte | byte | byte |
---|---|---|---|
Year | |||
Month | Day of Month | ||
Hour | Minute | ||
Second | Reserved |
Field Name | Description |
---|---|
Year | The four-digit year as an ASCII string. For example,
1998 . All fields of this message should be interpreted
as coordinated universal time (UTC) |
Month | The month number as a two digit ASCII string where
January is 01 and December is 12 . |
Day of Month | The day number within the month as a two digit ASCII
string. The first day of the month is 01 . |
Hour | The hour of the day as a two digit ASCII string where
midnight is 00 and 11:00pm is 23 . |
Minute | The minute of the hour as a two digit ASCII string where
the first minute of the hour is 00 and
the last is 59 . |
Second | The second of the minute as a two digit ASCII string
where the first second of the minute is 00
and the last is 59 . |
Reserved | This field is reserved and should always be zero. |
A constant message can be shared among several object headers by writing that message in the global heap and having the object headers all point to it. The pointing is accomplished with a Shared Object message which is understood directly by the object header layer of the library. It is also possible to have a message of one object header point to a message in some other object header, but care must be exercised to prevent cycles.
If a message is shared, then the message appears in the global
heap and its message ID appears in the Header Message Type
field of the object header. Also, the Flags field in the object
header for that message will have bit two set (the
H5O_FLAG_SHARED
bit). The message body in the
object header will be that of a Shared Object message defined
here and not that of the pointed-to message.
byte | byte | byte | byte |
---|---|---|---|
Version | Flags | Reserved | |
Reserved | |||
Pointer |
Field Name | Description |
---|---|
Version | The version number for the message. This document describes version one of shared messages. |
Flags | The Shared Message message points to a message which is
shared among multiple object headers. The Flags field
describes the type of sharing:
|
Pointer | This field points to the actual message. The format of the pointer depends on the value of the Flags field. If the actual message is in the global heap then the pointer is the file address of the global heap collection that holds the message, and a four-byte index into that collection. Otherwise the pointer is a group entry that points to some other object header. |
The object header continuation is formatted as follows (assuming a 4-byte length & offset are being used in the current file):
byte | byte | byte | byte |
---|---|---|---|
Header Continuation Offset | |||
Header Continuation Length |
The group message is formatted as follows:
byte | byte | byte | byte |
---|---|---|---|
B-tree Address | |||
Heap Address |
In order to share header messages between several dataset objects, object
header messages may be placed into the global heap. Since these
messages require additional information beyond the basic object header message
information, the format of the shared message is detailed below.
byte | byte | byte | byte |
---|---|---|---|
Reference Count of Shared Header Message | |||
Shared Object Header Message |
The data for an object is stored separately from the header information in the file and may not actually be located in the HDF5 file itself if the header indicates that the data is stored externally. The information for each record in the object is stored according to the dimensionality of the object (indicated in the dimensionality header message). Multi-dimensional data is stored in C order [same as current scheme], i.e. the "last" dimension changes fastest.
Data whose elements are composed of simple number-types are stored in native-endian IEEE format, unless they are specifically defined as being stored in a different machine format with the architecture-type information from the number-type header message. This means that each architecture will need to [potentially] byte-swap data values into the internal representation for that particular machine.
Data with a "variable" sized number-type is stored in a data heap internal to the HDF5 file. Global heap identifiers are stored in the data object storage.
Data whose elements are composed of pointer number-types are stored in several different ways depending on the particular pointer type involved. Simple pointers are just stored as the dataset offset of the object being pointed to with the size of the pointer being the same number of bytes as offsets in the file. Partial-object pointers are stored as a heap-ID which points to the following information within the file-heap: an offset of the object pointed to, number-type information (same format as header message), dimensionality information (same format as header message), sub-set start and end information (i.e. a coordinate location for each), and field start and end names (i.e. a [pointer to the] string indicating the first field included and a [pointer to the] string name for the last field).
Data of a compound datatype is stored as a contiguous stream of the items in the structure, with each item formatted according to its datatype.