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diff --git a/doc/html/Glossary.html b/doc/html/Glossary.html index 1a9d9c8..204d081 100644 --- a/doc/html/Glossary.html +++ b/doc/html/Glossary.html @@ -6,18 +6,19 @@ HDF5 Glossary <hr> <center> -<a href="RM_H5Front.html">HDF5 Reference Manual</a> -<a href="RM_H5.html">H5</a> -<a href="RM_H5A.html">H5A</a> -<a href="RM_H5D.html">H5D</a> -<a href="RM_H5E.html">H5E</a> -<a href="RM_H5F.html">H5F</a> -<a href="RM_H5G.html">H5G</a> -<a href="RM_H5P.html">H5P</a> -<a href="RM_H5S.html">H5S</a> -<a href="RM_H5T.html">H5T</a> -<a href="RM_H5Z.html">H5Z</a> -Glossary +<table border=0 width=98%> +<tr><td valign=top align=left> + <a href="index.html">Other HDF5 documents and links</a> <br> + <a href="H5.intro.html">Introduction to HDF5</a> +</td> +<td valign=top align=right> + +</td> +<td valign=top align=right> + <a href="H5.user.html">HDF5 User Guide</a> <br> + <a href="RM_H5Front.html">HDF5 Reference Manual</a> +</td></tr> +</table> </center> <hr> @@ -25,77 +26,512 @@ Glossary <h1>HDF5 Glossary</h1> </center> -<i>(<b>Under construction!</b> - This is the bare beginning of a Glossary to accompany the HDF5 - documentation; it is by no means complete.)</i> +<center> +<table width=90% border=0> +<tr><td valign=top align=left width=33%> +<dl> + <dt><a href="#Glossary-AtomicDType">atomic datatype</a> + <dt><a href="#Glossary-Attribute">attribute</a> +<!--<dt><a href="#Glossary-BasicDType">basic datatype</a>--> + <dt><a href="#Glossary-LayoutChunked">chunked layout</a> + <dt><a href="#Glossary-Chunking">chunking</a> +<!--<dt><a href="#Glossary-ComplexDType">complex datatype</a>--> + <dt><a href="#Glossary-CompoundDType">compound datatype</a> +<!--<dt>compound element--> + <dt><a href="#Glossary-LayoutContig">contiguous layout</a> +<!--<dt>conversion function--> + <dt><a href="#Glossary-Dataset">dataset</a> + <dt><a href="#Glossary-Dataspace">dataspace</a> +<!--<dl>--> +<!-- <dt>dimensions--> +<!-- <dt>selection--> +<!--</dl>--> + <dt><a href="#Glossary-Datatype">datatype</a> + <dl> + <dt><a href="#Glossary-AtomicDType">atomic</a> +<!-- <dt><a href="#Glossary-BasicDType">basic</a>--> +<!-- <dt><a href="#Glossary-ComplexDType">complex</a>--> + <dt><a href="#Glossary-CompoundDType">compound</a> +<!-- <dt>conversion function--> +<!-- <dt><a href="#Glossary-DiskIO">disk I/O</a>--> + <dt><a href="#Glossary-DTypeEnum">enumeration</a> + <dt><a href="#Glossary-DTypeNamed">named</a> + <dt><a href="#Glossary-DTypeOpaque">opaque</a> +<!-- <dt>transient--> + <dt><a href="#Glossary-DTypeVLen">variable-length</a> + </dl> +<!--<dt>DDL--> +<!--<dt>dimensions--> +<!--<dt><a href="#Glossary-DiskIO">disk I/O datatype</a>--> +<!--<dt>element--> + <dt><a href="#Glossary-DTypeEnum">enumeration datatype</a> + <dt><a href="#Glossary-File">file</a> + <dl> +<!-- <dt>compound element--> +<!-- <dt>element--> + <dt><a href="#Glossary-Group">group</a> + <dt><a href="#Glossary-Path">path</a> + <dt><a href="#Glossary-RootGroup">root group</a> + <dt><a href="#Glossary-SuperBlock">super block</a> + </dl> +</dl> +</td> +<td valign=top align=left width=34%> +<dl> + <dt><a href="#Glossary-FileAccessMode">file access mode</a> + <dt><a href="#Glossary-Group">group</a> + <dl> +<!-- <dt>element--> + <dt><a href="#Glossary-GroupMember">member</a> + <dt><a href="#Glossary-RootGroup">root group</a> + </dl> + <dt><a href="#Glossary-LinkHard">hard link</a> +<!--<dt>HDF5--> + <dt><a href="#Glossary-Hyperslab">hyperslab</a> + <dt><a href="#Glossary-Identifier">identifier</a> + <dt><a href="#Glossary-Link">link</a> + <dl> + <dt><a href="#Glossary-LinkHard">hard</a> + <dt><a href="#Glossary-LinkSoft">soft</a> +<!-- <dt><a href="#Glossary-LinkSoftName">soft link name</a>--> +<!-- <dt>target--> + </dl> + <dt><a href="#Glossary-GroupMember">member</a> + <dt><a href="#Glossary-Name">name</a> + <dt><a href="#Glossary-DTypeNamed">named datatype</a> + <dt><a href="#Glossary-DTypeOpaque">opaque datatype</a> + <dt><a href="#Glossary-Path">path</a> +<!--<dt>parallel I/O--> + <dt><a href="#Glossary-PList">property list</a> + <dl> + <dt><a href="#Glossary-PListDataTransfer">data transfer</a> + <dt><a href="#Glossary-PListDSetAccess">dataset access</a> + <dt><a href="#Glossary-PListDSetCreate">dataset creation</a> + <dt><a href="#Glossary-PListFileAccess">file access</a> + <dt><a href="#Glossary-PListFileCreate">file creation</a> + </dl> +</dl> +</td> +<td valign=top align=left width=33%> +<dl> + <dt><a href="#Glossary-RootGroup">root group</a> + <dt><a href="#Glossary-Selection">selection</a> + <dl> + <dt><a href="#Glossary-Hyperslab">hyperslab</a> +<!-- <dt>point--> + </dl> + <dt><a href="#Glossary-Serialization">serialization</a> + <dt><a href="#Glossary-LinkSoft">soft link</a> +<!--<dt><a href="#Glossary-LinkSoftName">soft link name</a>--> + <dt><a href="#Glossary-StorageLayout">storage layout</a> + <dl> + <dt><a href="#Glossary-LayoutChunked">chunked</a> + <dt><a href="#Glossary-Chunking">chunking</a> + <dt><a href="#Glossary-LayoutContig">contiguous</a> + </dl> + <dt><a href="#Glossary-SuperBlock">super block</a> +<!--<dt>target--> +<!--<dt>threadsafe--> +<!--<dt>transient datatype--> + <dt><a href="#Glossary-DTypeVLen">variable-length datatype</a> +</dl> +</td></tr> +</table> +</center> -<ul> - <li><a href="#Glossary-Basic">basic data types</a> - <li><a href="#Glossary-Complex">complex data types</a> - <li>data types -<ul> - <li><a href="#Glossary-Basic">basic data types</a> - <li><a href="#Glossary-Complex">complex data types</a> - <li><a href="#Glossary-DiskIO">disk I/O data types</a> -</ul> - <li><a href="#Glossary-DiskIO">disk I/O data types</a> -</ul> +<hr> -<hr> +<DL> -<a name="Glossary-Basic">basic data types:</a> -<ul> - <li><em>(Some data types may change substantially en route to - Release 1.0.)</em> - <li>char - 8-bit character (only for ASCII information) - <li>int8 - 8-bit signed integer - <li>uint8 - 8-bit unsigned integer - <li>int16 - 16-bit signed integer - <li>uint16 - 16-bit unsigned integer - <li>int32 - 32-bit signed integer - <li>uint32 - 32-bit unsigned integer - <li>intn - "native" signed integer - <li>uintn - "native" unsigned integer - <li>int64 - 64-bit signed integer (new) - <li>uint64 - 64-bit unsigned integer (new) - <li>float32 - 32-bit IEEE float - <li>float64 - 64-bit IEEE float -</ul> +<dt><strong><a name="Glossary-AtomicDType">atomic datatype</a></strong> + <dd>A datatype which cannot be decomposed into smaller units at the + API level. +<P> -<a name="Glossary-Complex">Complex data types:</a> -<ul> - <li><em>(Some data types may change substantially en route to - Release 1.0.)</em> - <li>hid_t - 32-bit unsigned integer used as ID for memory objects - <li>hoid_t - 32-bit unsigned integer (currently) used as ID for disk-based - objects - <li>hbool_t - boolean to indicate true/false/error codes from functions - <li>herr_t - 32-bit integer to indicate succeed/fail codes from functions -</ul> +<DT><a name="Glossary-Attribute"><B>attribute</B></a> +<DD>A small dataset that can be used to describe the nature and/or + the intended usage of the object it is attached to. +<P> + +<!-- +<dt><strong><a name="Glossary-Basic">basic datatypes</a></strong> + <ul> + <li>char - 8-bit character (only for ASCII information) + <li>int8 - 8-bit signed integer + <li>uint8 - 8-bit unsigned integer + <li>int16 - 16-bit signed integer + <li>uint16 - 16-bit unsigned integer + <li>int32 - 32-bit signed integer + <li>uint32 - 32-bit unsigned integer + <li>intn - "native" signed integer + <li>uintn - "native" unsigned integer + <li>int64 - 64-bit signed integer (new) + <li>uint64 - 64-bit unsigned integer (new) + <li>float32 - 32-bit IEEE float + <li>float64 - 64-bit IEEE float + </ul> +<P> +--> -<a name="Glossary-DiskIO">disk I/O data types:</a> +<dt><strong><a name="Glossary-LayoutChunked">chunked layout</a></strong> +<dd>The storage layout of a chunked dataset. +<P> + +<dt><strong><a name="Glossary-Chunking">chunking</a></strong> +<dd>A storage layout where a dataset is partitioned into fixed-size + multi-dimensional chunks. Chunking tends to improve performance + and facilitates dataset extensibility. +<P> + +<dt><strong><a name="Glossary-CompoundDType">compound datatype</a></strong> +<dd>A collection of one or more atomic types or small arrays of such types. + Similar to a struct in C or a common block in Fortran. +<P> + +<!-- +<dt><strong><a name="Glossary-ComplexDType">complex datatype</a></strong> +<dd>A collection of one or more atomic types or small arrays of such types. + <ul> + <li>hid_t - 32-bit unsigned integer used as ID for memory objects + <li>hoid_t - 32-bit unsigned integer (currently) used as ID for + disk-based objects + <li>hbool_t - boolean to indicate true/false/error codes from functions + <li>herr_t - 32-bit integer to indicate succeed/fail codes from + functions + </ul> +<P> +--> + +<dt><strong><a name="Glossary-LayoutContig">contiguous layout</a></strong> +<dd>The storage layout of a dataset that is not chunked, so that the entire + data portion of the dataset is stored in a single contiguous block. +<P> + +<DT><B><a name="Glossary-PListDataTransfer">data transfer property list</B></a> +<DD>The data transfer property list is used to control various aspects + of the I/O, such as caching hints or collective I/O information. +<P> + +<DT><B><a name="Glossary-Dataset">dataset</B></a> +<DD>A multi-dimensional array of data elements, together with + supporting metadata. +<P> + +<DT><B><a name="Glossary-PListDSetAccess">dataset access property list</B></a> +<DD>A property list containing information on how a dataset is to be accessed. +<P> + +<DT><B><a name="Glossary-PListDSetCreate">dataset creation property list</B></a> +<DD>A property list containing information on how + raw data is organized on disk and how the raw data is compressed. +<!-- + The dataset API partitions these terms by layout, compression, + and external storage: + <UL> + <B> Layout:</B> + <UL> + <LI>H5D_COMPACT: Data is small and can be stored in object header (not + implemented yet). This eliminates disk seek/read requests. + <LI>H5D_CONTIGUOUS: (<B>default</B>) The data is large, non-extendible, + non-compressible, non-sparse, and can be stored externally. + <LI>H5D_CHUNKED: The data is large and can be extended in any dimension. + It is partitioned into chunks so each chunk is the same logical size. + </UL> + <B>Compression:</B> (gzip compression)<BR> + <B>External Storage Properties:</B> The data must be contiguous to be + stored externally. It allows you to store + the data in one or more non-HDF5 files. + </UL> +--> +<P> + +<DT><B><a name="Glossary-Dataspace">dataspace</B></a> +<DD>An object that describes the dimensionality of the data array. + A dataspace is either a regular N-dimensional array of data points, + called a simple dataspace, or a more general collection of data points + organized in another manner, called a complex dataspace. +<P> + +<DT><B><a name="Glossary-Datatype">datatype</B></a> +<DD>An object that describes the storage format of the individual data + points of a data set. + There are two categories of datatypes: atomic and compound datatypes. + An atomic type is a type which cannot be decomposed into smaller + units at the API level. A compound datatype is a collection of one or + more atomic types or small arrays of such types. +<P> + +<!-- +<DT><B>DDL</B> +<DD>A detailed description of the HDF5 format and objects, written in a + Data Description Language using Backus-Naur Form. +<P> +--> + +<!-- +<dt><strong><a name="Glossary-DiskIO">disk I/O datatypes</a></strong> <ul> - <li><em>(Some data types may change substantially en route to - Release 1.0.)</em> <li>hoff_t - (64-bit?) offset on disk in bytes <li>hlen_t - (64-bit?) length on disk in bytes </ul> +<P> +--> + +<dt><strong><a name="Glossary-DTypeEnum">enumeration datatype</a></strong> +<dd>A one-to-one mapping between a set of symbols and a set of + integer values, and an order is imposed on the symbols by their + integer values. The symbols are passed between the application + and library as character strings and all the values for a + particular enumeration datatype are of the same integer type, + which is not necessarily a native type. +<P> + +<DT><B><a name="Glossary-File">file</B></a> +<DD>A container for storing grouped collections of + multi-dimensional arrays containing scientific data. +<P> + +<DT><B><a name="Glossary-FileAccessMode">file access mode</B></a> +<DD>Determines whether an existing file will be overwritten, + opened for read-only access, or opened for read/write access. + All newly created files are opened for both reading and + writing. +<!-- + Possible values are: + <PRE> + H5F_ACC_RDWR: Allow read and write access to file. + H5F_ACC_RDONLY: Allow read-only access to file. + H5F_ACC_TRUNC: Truncate file, if it already exists, erasing all data + previously stored in the file. + H5F_ACC_EXCL: Fail if file already exists. + H5F_ACC_DEBUG: Print debug information. + H5P_DEFAULT: Apply default file access and creation properties. + </PRE> +--> +<P> + +<DT><B><a name="Glossary-PListFileAccess">file access property list</B></a> +<DD>File access property lists are used to control different methods + of performing I/O on files: +<!-- + <UL> + <B>Unbuffered I/O:</B> Local permanent files can be accessed with the + functions described in Section 2 of the Posix manual, namely open(), + lseek(), read(), write(), and close(). <BR> + <B>Buffered I/O:</B> Local permanent files can be accessed with the + functions declared in the stdio.h header file, namely fopen(), + fseek(), fread(), fwrite(), and fclose().<BR> + <B>Memory I/O:</B> Local temporary files can be created and accessed + directly from memory without ever creating permanent storage. + The library uses malloc() and free() to create storage space for the + file<BR> + <B>Parallel Files using MPI I/O:</B> This driver allows parallel access + to a file through the MPI I/O library. The parameters which can be + modified are the MPI communicator, the info object, and the access mode. + The communicator and info object are saved and then passed to + MPI_File_open() during file creation or open. The access_mode + controls the kind of parallel access the application intends.<BR> + <B>Data Alignment:</B> Sometimes file access is faster if certain things + are aligned on file blocks. This can be controlled by setting alignment + properties of a file access property list with the H5Pset_alignment() + function. + </UL> +--> +<P> + +<DT><B><a name="Glossary-PListFileCreate">file creation property list</B></a> +<DD>The property list used to control file metadata. +<!-- + The parameters that can be modified are: + <UL> + <B>User-Block Size:</B> The "user-block" is a fixed length block + of data located at the beginning of the file which is ignored + by the HDF5 library and may be used to store any data information + found to be useful to applications. + <BR> + <B>Offset and Length Sizes:</B> The number of bytes used to store the + offset and length of objects in the HDF5 file can be controlled + with this parameter. + <BR> + <b>Symbol Table Parameters:</b> The size of symbol table B-trees can + be controlled by setting the 1/2 rank and 1/2 node size + parameters of the B-tree. + <BR> + <B>Indexed Storage Parameters:</B> The size of indexed storage + B-trees can be controlled by setting the 1/2 rank and 1/2 node + size parameters of the B-tree. + </UL> +--> +<P> + +<DT><B><a name="Glossary-Group">group</B></a> +<DD>A structure containing zero or more HDF5 objects, + together with supporting metadata. + The two primary HDF5 objects are datasets and groups. +<P> + +<dt><strong><a name="Glossary-LinkHard">hard link</a></strong> +<dd>A direct association between a name and the object where both exist + in a single HDF5 address space. +<P> + +<!-- +<DT><B>HDF5</B> +<DD>HDF5 is an abbreviation for Hierarchical Data Format Version 5. + This file format is intended to make it easy to write and read + scientific data + <P> + <UL> + <LI>by including the information needed to understand the data + within the file + <P> + <LI>by providing a library of C, FORTRAN, and other language + programs that reduce the work required to provide efficient + writing and reading - even with parallel IO + </UL> +<P> +--> + +<DT><B><a name="Glossary-Hyperslab">hyperslab</B></a> +<DD>A portion of a dataset. A hyperslab selection can be a + logically contiguous collection of points in a dataspace or + a regular pattern of points or blocks in a dataspace. +<P> + +<dt><strong><a name="Glossary-Identifier">identifier</a></strong> +<dd>A unique entity provided by the HDF5 library and used to access + an HDF5 object, such as a file, goup, dataset, datatype, etc. +<P> + +<dt><strong><a name="Glossary-Link">link</a></strong> +<dd>An association between a name and the object in an HDF5 file group. +<P> + +<dt><strong><a name="Glossary-GroupMember">member</a></strong> +<dd>A group or dataset that is in another dataset, <i>dataset A</i>, + is a member of <i>dataset A</i>. +<P> + +<DT><B><a name="Glossary-Name">name</B></a> +<DD>A slash-separated list of components that uniquely identifies an + element of an HDF5 file. A name begins that begins with a slash + is an absolute name which is accessed beginning with the root group + of the file; all other names are relative names and the associated + objects are accessed beginning with the current or specified group. +<P> + +<dt><strong><a name="Glossary-DTypeNamed">named datatype</a></strong> +<dd>A datatype that is named and stored in a file. Naming is permanent; + a datatype cannot be changed after being named. +<P> + +<dt><strong><a name="Glossary-DTypeOpaque">opaque datatype</a></strong> +<dd>A mechanism for describing data which cannot be otherwise described + by HDF5. The only properties associated with opaque types are a + size in bytes and an ASCII tag. +<P> + +<!-- +<DT><B>parallel I/O HDF5</B> +<DD>The parallel I/O version of HDF5 supports parallel file access using + MPI (Message Passing Interface). +<P> +--> + +<dt><strong><a name="Glossary-Path">path</a></strong> +<dd>The slash-separated list of components that forms the name + uniquely identifying an element of an HDF5 file. +<P> + +<dt><strong><a name="Glossary-PList">property list</a></strong> +<dd>A collection of name/value pairs that can be passed to other + HDF5 functions to control features that are typically unimportant + or whose default values are usually used. +<P> + +<dt><strong><a name="Glossary-RootGroup">root group</a></strong> +<dd>The group that is the entry point to the group graph in an HDF5 file. + Every HDF5 file has exactly one root group. +<P> + +<dt><strong><a name="Glossary-Selection">selection</a></strong> +<dd>A subset of a dataset or a dataspace, up to the entire dataset or + dataspace. +<P> + +<dt><strong><a name="Glossary-Serialization">serialization</a></strong> +<dd>The flattening of an <em>N</em>-dimensional data object into a + 1-dimensional object so that, for example, the data object can be + transmitted over the network as a 1-dimensional bitstream. +<P> + +<dt><strong><a name="Glossary-LinkSoft">soft link</a></strong> +<dd>An indirect association between a name and an object in an + HDF5 file group. +<P> + +<dt><strong><a name="Glossary-StorageLayout">storage layout</a></strong> +<dd>The manner in which a dataset is stored, either contiguous or + chunked, in the HDF5 file. +<P> + +<DT><B><a name="Glossary-SuperBlock">super block</B></a> +<DD>A block of data containing the information required to portably access + HDF5 files on multiple platforms, followed by information about the groups + and datasets in the file. + The super block contains information about the size of offsets, + lengths of objects, the number of entries in group tables, + and additional version information for the file. +<P> + +<!-- +<DT><B>threadsafe</B> +<DD>A "thread-safe" version of HDF-5 (TSHDF5) is one that can be called + from any thread of a multi-threaded program. Any calls to HDF + can be made in any order, and each individual HDF call will perform + correctly. A calling program does not have to explicitly lock the HDF + library in order to do I/O. Applications programmers may assume that + the TSHDF5 guarantees the following: + <UL> + <LI>the HDF-5 library does not create or destroy threads. + <LI>the HDF-5 library uses modest amounts of per-thread + private memory. + <LI>the HDF-5 library only locks/unlocks it's own locks (no locks + are passed in or returned from HDF), and the internal locking + is guaranteed to be deadlock free. + </UL> + <P> + These properties mean that the TSHDF5 library will not interfere + with an application's use of threads. A TSHDF5 library is the same + library as regular HDF-5 library, with additional code to synchronize + access to the HDF-5 library's internal data structures. +<P> +--> + +<dt><strong><a name="Glossary-DTypeVLen">variable-length datatype</a></strong> +<dd>A sequence of an existing datatype (atomic, variable-length (VL), + or compound) which are not fixed in length from one dataset location + to another. +<P> + +</DL> <hr> <center> -<a href="RM_H5Front.html">HDF5 Reference Manual</a> -<a href="RM_H5.html">H5</a> -<a href="RM_H5A.html">H5A</a> -<a href="RM_H5D.html">H5D</a> -<a href="RM_H5E.html">H5E</a> -<a href="RM_H5F.html">H5F</a> -<a href="RM_H5G.html">H5G</a> -<a href="RM_H5P.html">H5P</a> -<a href="RM_H5S.html">H5S</a> -<a href="RM_H5T.html">H5T</a> -<a href="RM_H5Z.html">H5Z</a> -Glossary +<table border=0 width=98%> +<tr><td valign=top align=left> + <a href="index.html">Other HDF5 documents and links</a> <br> + <a href="H5.intro.html">Introduction to HDF5</a> +</td> +<td valign=top align=right> + +</td> +<td valign=top align=right> + <a href="H5.user.html">HDF5 User Guide</a> <br> + <a href="RM_H5Front.html">HDF5 Reference Manual</a> +</td></tr> +</table> </center> <hr> @@ -103,7 +539,7 @@ Glossary <a href="mailto:hdfhelp@ncsa.uiuc.edu">HDF Help Desk</a> <br> -Last modified: 14 July 1998 +Last modified: 18 October 1999 </body> </html> |