path: root/doxygen/dox/Glossary.dox

/** \page GLS Glossary

\section GLS_A A

<DL>
  <DT>Array datatype</DT>
  <DD>A family of HDF5 datatypes whose elements are arrays of a fixed rank (≤
  32) and fixed finite extent. All array elements must be of the same HDF5
  datatype.</DD>
</DL>

<DL>
  <DT>Array variable</DT>
  <DD><P>A variable that can store (logically) dense, rectilinear, multidimensional
      arrays of elements of a given HDF5 datatype.</P>
    <P>The combination of array rank (dimensionality) and extent is called an
    array variable's shape. This includes the degenerate array shapes of a
    singleton (scalar) and the empty array (null).</P>
    <P>The array element datatype is sometimes referred to as the array
    variable's type, which is not entirely accurate because the array variable's
    type is 'array of element type' rather than 'element type'.</P>
    <P>In HDF5, there are two kinds of array variables, attributes and datasets,
      and the distinction is functional (i.e., how they can be used) rather than
      conceptual. Attributes are commonly used for descriptive "light-weight"
      HDF5 object metadata while datasets are HDF5 objects used to store
      "heavy-weight" problem-sized data.</P>
  </DD>
</DL>

<DL>
  <DT>Attribute</DT>
  <DD><P>A named array variable that is associated with an HDF5 object, its
      owner or attributee, and used to represent application domain-specific
      metadata of the object. Intuitively, the set of an object's attributes can
      be thought of as its key-value pair collection. Attribute names (keys) can
      be arbitrary Unicode strings, but must be unique per object, i.e., an
      object can have at most one attribute with a given name.</P>
    <P>A scalar attribute is an attribute backed by a singleton array
    variable. A null attribute is attribute backed by an empty array
    variable.</P>
</DD>
</DL>

\section GLS_B B

<DL>
  <DT>Bitfield datatype</DT>
  <DD>A family of HDF5 datatypes whose elements are fixed-width bit fields.</DD>
</DL>

\section GLS_C C

<DL>
  <DT>Chunked layout</DT>
  <DD>
    <P>A dataset storage layout where the dataset elements are partitioned into
      fixed-size multidimensional chunks or tiles. Chunked layout is mandatory
      for datasets with one or more dimensions of indefinite (infinite) extent
      or where compression or other filters are applied to the dataset elements.</P>
    <P>Chunked layout may improve I/O performance for certain access patterns.</P>
</DD>
</DL>

<DL>
  <DT>Committed datatype</DT>
  <DD>An immutable kind of HDF5 object that is used to store an HDF5 datatype
  definition, which can be referenced by multiple array variables. When linked
  to an HDF5 group, a committed datatype can be located by an HDF5 path name,
  and is sometimes called a named datatype.</DD>
</DL>

<DL>
  <DT>Compact layout</DT>
  <DD></DD>
</DL>

<DL>
  <DT>Compound datatype</DT>
  <DD>
    <P>A family of HDF5 datatypes whose elements are records with named fields
    of other HDF5 datatypes. Currently, on ASCII field names are supported.</P>
    <P>Similar to a <CODE>struct</CODE> in C or a <CODE>COMMON</CODE> block in
    Fortran.</P>
</DD>
</DL>

<DL>
  <DT>Contiguous layout</DT>
  <DD>A dataset storage layout where the dataset elements are physically stored
  in an HDF5 file as a contiguous block of bytes.</DD>
</DL>

\section GLS_D D

<DL>
  <DT>Dataset</DT>
  <DD>
    <P>A kind of HDF5 object, a linked array variable. which can be located in
      an HDF5 file through a path name. Datasets are commonly used to store
      "heavy-weight" problem-sized data.</P>
    <P>The HDF5 library offers a lot of features aimed at optimized dataset
      access and storage, including compression and partial I/O.</P>
</DD>
</DL>

<DL>
  <DT>Dataspace</DT>
  <DD>The shape of an array variable. With the exception of degenerate cases
  (empty set, singleton), this is a rectilinear lattice or grid of a certain
  rank (dimensionality) and extent.</DD>
</DL>

<DL>
  <DT>Datatype</DT>
  <DD>
    <P>An HDF5 datatype consists of an abstract data type (a set of elements)
    and a bit-level representation of these elements in storage such as an HDF5
    file or memory.</P>
    <P>The HDF5 library comes with a large set of predefined datatypes and
    offers mechanisms for creating user-defined datatypes.</P>
    <P>The ten major families or classes of HDF5 datatypes are:</P>
    <UL>
      <LI>Integer datatypes</LI>
      <LI>Floating-point number datatypes</LI>
      <LI>String datatypes</LI>
      <LI>Bitfield datatypes</LI>
      <LI>Opaque datatypes</LI>
      <LI>Compound datatypes</LI>
      <LI>Reference datatypes</LI>
      <LI>Enumerated datatypes</LI>
      <LI>Variable-length sequence datatypes</LI>
      <LI>Array datatypes</LI>
    </UL>
</DD>
</DL>

\section GLS_E E

<DL>
  <DT>Enumeration datatype</DT>
  <DD>A family of HDF5 datatypes whose elements represent named integer values
  called members or enumerators. Currently, only ASCII names are supported.</DD>
</DL>

<DL>
  <DT>External layout</DT>
  <DD>A form of contiguous layout where a dataset's elements are physically
  stored in unformatted binary files outside the HDF5 file.</DD>
</DL>

<DL>
  <DT>External link</DT>
  <DD>An HDF5 link whose destination is specified as a pair of an HDF5 file name
and an HDF5 path name in that file.</DD>
</DL>

\section GLS_F F

<DL>
  <DT>Field</DT>
  <DD>See compound datatype.</DD>
</DL>

<DL>
  <DT>File</DT>
  <DD>
    <OL>
      <LI>A byte stream (in a storage context such as a file system or in
      memory) formatted according to the HDF5 File Format Specification.</LI>
      <LI>A (logical) container for HDF5 objects.</LI>
    </OL>
  </DD>
</DL>

<DL>
  <DT>File format</DT>
  <DD></DD>
</DL>

<DL>
  <DT>Fill value</DT>
  <DD></DD>
</DL>

<DL>
  <DT>Filter</DT>
  <DD></DD>
</DL>

\section GLS_G G

<DL>
  <DT>Group</DT>
  <DD>
    <P>A kind of HDF5 object that stores a collection of HDF5 links. Each HDF5
    file contains at least one group, it's root group.</P>
    <P>Among the destinations of an HDF5 group's links may be other HDF5 groups
    (including the group itself!). This ability is sometimes referred to as the
    closure property of groups. It is the basis for creating hierarchical or
    more general graph-like structures.</P>
</DD>
</DL>

\section GLS_H H

<DL>
  <DT>Hard link</DT>
  <DD>An HDF5 link whose destination is specified (internally) as the address of
  an HDF5 object in the same HDF5 file.</DD>
</DL>

<DL>
  <DT>Hierarchy</DT>
  <DD>See group.</DD>
</DL>

<DL>
  <DT>Hyperslab</DT>
  <DD>
    <P>A regular multidimensional pattern described by four vectors whose length
    equals the rank of the pattern.</P>
    <OL>
      <LI><CODE>start</CODE> - the offset where the first block of the hyperslab begins</LI>
      <LI><CODE>stride</CODE> - the offset between pattern blocks</LI>
      <LI><CODE>count</CODE> - the number of blocks</LI>
      <LI><CODE>block</CODE> - the extent of an individual pattern block</LI>
    </OL>
    <P>For example, the black squares on a (two-dimensional) chessboard with
      origin at <CODE>(0,0)</CODE> can be represented as the union of two
      hyperslabs representing the even <CODE>(0,2,4,6)</CODE> and
      odd <CODE>(1,3,5,7)</CODE> rows, respectively.</P>
    <IMG SRC="https://upload.wikimedia.org/wikipedia/commons/thumb/d/d7/Chessboard480.svg/176px-Chessboard480.svg.png"/>
    <P>The hyperslab parameters for the even rows are: <CODE>start (0,0)</CODE>,
      <CODE>stride (2,2)</CODE>, <CODE>count (4,4)</CODE>, <CODE>block
        (1,1)</CODE>. Likewise the parameters for the odd rows are: <CODE>start
        (1,1)</CODE>, <CODE>stride (2,2)</CODE>, <CODE>count
        (4,4)</CODE>, <CODE>block (1,1)</CODE>.</P>
</DD>
</DL>

\section GLS_I I

<DL>
  <DT>Identifier</DT>
  <DD>An opaque, transient handle used by the HDF5 library to manipulate
  in-memory representations of HDF5 items.</DD>
</DL>

\section GLS_L L

<DL>
  <DT>Library</DT>
  <DD></DD>
</DL>

<DL>
  <DT>Link</DT>
  <DD>
    <P>A named, uni-directional association between a source and a
    destination. In HDF5, the source is always the HDF5 group that hosts the
    link in its link collection.</P>
    <P>There are several ways to specify a link's destination:</P>
    <UL>
      <LI>The address of an HDF5 object in the same HDF5 file; so-called hard
      link.</LI>
      <LI>A path name in the same or a different file; so-called soft or
      external link.</LI>
      <LI>User-defined</LI>
    </UL>
    <P>A link name can be any Unicode string that does not contain slashes
      (<CODE>"/"</CODE>) or consists of a single dot character
      (<CODE>"."</CODE>). A link name must be unique in a group's link
      collection.</P>
  </DD>
</DL>

\section GLS_M M

<DL>
  <DT>Metadata</DT>
  <DD>Data that in a given context has a descriptive or documentation function
  for other data. Typically, the metadata is small compared to the data it
  describes.</DD>
</DL>

<DL>
  <DT>Member</DT>
  <DD>
    <P>A link destination is sometimes referred to as a member of the link's
    source (group). This way of speaking invites confusion: A destination (e.g.,
    object) can be the destination of multiple links in the same (!) or
    different groups. It would then be a "member" of a given group with
    multiplicity greater than one and be a member of multiple groups.</P>
    <P> It is the link that is a member of the group's link collection and not
    the link destination.</P>
  </DD>
</DL>

\section GLS_N N

<DL>
  <DT>Name</DT>
  <DD>
    <P>A Unicode string that depending on the item it names might be subject to
    certain character restrictions, such as ASCII-encoded only. In HDF5, the
    user might encounter the following names:</P>
    <UL>
      <LI>A link name</LI>
      <LI>A path name</LI>
      <LI>An attribute name</LI>
      <LI>A field name (compound datatypes)</LI>
      <LI>A constant name (enumeration datatypes)</LI>
      <LI>A tag name (opaque datatypes)</LI>
      <LI>A file name</LI>
    </UL>
  </DD>
</DL>


<DL>
  <DT>Named datatype</DT>
  <DD>See committed datatype.</DD>
</DL>

<DL>
  <DT>Null dataspace</DT>
  <DD>A shape which represents the empty set. Array variables with this shape
  cannot store any values.</DD>
</DL>

\section GLS_O O

<DL>
  <DT>Object</DT>
  <DD>An HDF5 group, dataset or named datatype; an HDF5 item that can be linked
  to zero or more groups and decorated with zero or more HDF5 attributes.</DD>
</DL>

<DL>
  <DT>Object reference</DT>
  <DD>
    <OL>
      <LI>A datatype for representing references to objects in a file.</LI>
      <LI>A value of the object reference datatype.</LI>
    </OL>
  </DD>
</DL>

<DL>
  <DT>Opaque datatype</DT>
  <DD>A family of HDF5 datatypes whose elements are byte sequences of a given
  fixed length. An opaque datatype can be tagged with a sequence of up to 256
  ASCII characters, e.g., MIME code.</DD>
</DL>

\section GLS_P P

<DL>
  <DT>Path name</DT>
  <DD>A Unicode string that is the concatenation of link names separated by
    slashes (<CODE>'/'</CODE>). In HDF5, path names are used to locate and refer
    to HDF5 objects.</DD>
</DL>

<DL>
  <DT>Plugin</DT>
  <DD>An HDF5 library feature or capability that can be added dynamically at
    application run time rather than library compilation time. Plugins are
    usually implemented as shared libraries, and their discovery and loading
    behavior can be controlled programmatically or through environment
    variables.
  </DD>
</DL>

<DL>
  <DT>Point selection</DT>
  <DD>A dataspace selection that consists of a set of points (coordinates) in
  the same dataspace.</DD>
</DL>

<DL>
  <DT>Property list</DT>
  <DD>
    <P>An HDF5 API construct, a means of customizing the behavior of the HDF5
    library when creating, accessing or modifying HDF5 items.</P>
    <P>While the default property settings are sufficient in many cases, certain
    HDF5 features, such as compression, can be reasonably controlled only by the
    user who has to provide the desired settings via property lists.</P>
</DD>
</DL>

\section GLS_R R

<DL>
  <DT>Rank</DT>
  <DD>The number of dimensions of a non-null dataspace.</DD>
</DL>

<DL>
  <DT>Reference</DT>
  <DD>
    <OL>
      <LI>An HDF5 object reference</LI>
      <LI>An HDF5 dataset region reference</LI>
    </OL>
  </DD>
</DL>

<DL>
  <DT>Reference datatype</DT>
  <DD>
    <OL>
      <LI>An HDF5 datatype whose elements represent references to HDF5
      objects.</LI>
      <LI>An HDF5 datatype whose elements represent references to regions of an
      HDF5 dataset.</LI>
    </OL>
  </DD>
</DL>

<DL>
  <DT>Region reference</DT>
  <DD>See dataset region reference.</DD>
</DL>

<DL>
  <DT>Root group</DT>
  <DD>
    <P>An HDF5 group that is present in all HDF5 files and that acts as the
    entry or base point for all other data stored in an HDF5 file.</P>
    <P>The root group is "the mother of all objects" in an HDF5 file in the
    sense that all objects (and their attributes) can be discovered,
    beginning at the root group, by combinations of the following
    operations:</P>
    <UL>
      <LI>Link traversal</LI>
      <LI>De-referencing of object references</LI>
    </UL>
    <P>This discovery is portable and robust with respect to file-internal
    storage reorganization.</P>
</DD>
</DL>

\section GLS_S S

<DL>
  <DT>Scalar dataspace</DT>
  <DD>A kind of HDF5 dataspace that has the shape of a singleton, i.e., a set
  containing a single element. Array variables with this shape store exactly one
  element.</DD>
</DL>

<DL>
  <DT>Selection</DT>
  <DD>
    <OL>
      <LI>A subset of points of an HDF5 dataspace. The subset might be a point
        selection or a combination (union, intersection, etc.) of hyperslabs.</LI>
      <LI>A subset of dataset elements associated with a dataspace selection as
      described under 1.</LI>
    </OL>
  </DD>
</DL>

<DL>
  <DT>Serialization</DT>
  <DD>
    <OL>
      <LI>The flattening of an N-dimensional array into a 1-dimensional
        array.</LI>
      <LI>The encoding of a complex data item as a linear byte stream.</LI>
    </OL>
  </DD>
</DL>

<DL>
  <DT>Soft link</DT>
  <DD>A kind of HDF5 link in which the link destination is specified as an HDF5
  path name. The path name may or may not refer to an actual object.</DD>
</DL>

<DL>
  <DT>Storage layout</DT>
  <DD>The storage arrangement for dataset elements, links in a group's link
  collection, or attributes in an object's attribute collection.</DD>
</DL>

<DL>
  <DT>String datatype</DT>
  <DD></DD>
</DL>

<DL>
  <DT>Super block</DT>
  <DD>An HDF5 file format primitive; a block of data which contains information
  required to access HDF5 files in a portable manner on multiple platforms. The
  super block contains information such as version numbers, the size of offsets
  and lengths, and the location of the root group.</DD>
</DL>

<DL>
  <DT>SWMR</DT>
  <DD>Single Writer Multiple Reader, a file access mode in which a single
  process is permitted to write data to an HDF5 file while other processes are
  permitted to read data from the same file without the need of inter-process
  communication or synchronization.</DD>
</DL>

<DL>
  <DT>Symbolic link</DT>
  <DD>An external link or a soft link.</DD>
</DL>

\section GLS_U U

<DL>
  <DT>User block</DT>
  <DD>An HDF5 file format primitive that allows one to set aside a fixed-size
  (at least 512 bytes or any power of 2 thereafter) contiguous range of bytes at
  the beginning of an HDF5 file for application purposes which will be
  skipped/ignored by the HDF5 library.</DD>
</DL>

<DL>
  <DT>UTF-8</DT>
  <DD>
    <P>A variable-length (1-4 bytes per code point) encoding of the Unicode set
    of code points. This is the encoding supported by HDF5 to represent Unicode
    strings.</P>
    <P>The ASCII encoding is a proper subset of UTF-8.</P>
</DD>
</DL>

\section GLS_V V

<DL>
  <DT>Variable-length (sequence) datatype</DT>
  <DD>A family of HDF5 datatypes whose elements are variable-length sequences of
  a given datatype.</DD>
</DL>

<DL>
  <DT>Virtual Dataset (VDS)</DT>
  <DD>An HDF5 dataset with virtual storage layout. A dataset whose elements are
  partially or entirely stored physically in other datasets.</DD>
</DL>

<DL>
  <DT>Virtual File Driver (VFD)</DT>
  <DD></DD>
</DL>


<DL>
  <DT>Virtual layout</DT>
  <DD></DD>
</DL>


<DL>
  <DT>Virtual Object Layer (VOL)</DT>
  <DD></DD>
</DL>

*/