Hierarchical Data Format (HDF) is a set of file formats (HDF4, HDF5) designed to store and organize large amounts of data. Originally developed at the U.S. National Center for Supercomputing Applications, it is supported by The HDF Group, a non-profit corporation whose mission is to ensure continued development of HDF5 technologies and the continued accessibility of data stored in HDF.
In keeping with this goal, the HDF libraries and associated tools are available under a liberal, BSD-like license for general use. HDF is supported by many commercial and non-commercial software platforms and programming languages. The freely available HDF distribution consists of the library, command-line utilities, test suite source, Java interface, and the Java-based HDF Viewer (HDFView).[2]
The current version, HDF5, differs significantly in design and API from the major legacy version HDF4.
The quest for a portable scientific data format, originally dubbed AEHOO (All Encompassing Hierarchical Object Oriented format) began in 1987 by the Graphics Foundations Task Force (GFTF) at the National Center for Supercomputing Applications (NCSA). NSF grants received in 1990 and 1992 were important to the project. Around this time NASA investigated 15 different file formats for use in the Earth Observing System (EOS) project. After a two-year review process, HDF was selected as the standard data and information system.[3]
HDF4
HDF4 is the older version of the format, although still actively supported by The HDF Group. It supports a proliferation of different data models, including multidimensional arrays, raster images, and tables. Each defines a specific aggregate data type and provides an API for reading, writing, and organizing the data and metadata. New data models can be added by the HDF developers or users.
HDF is self-describing, allowing an application to interpret the structure and contents of a file with no outside information. One HDF file can hold a mix of related objects which can be accessed as a group or as individual objects. Users can create their own grouping structures called "vgroups."
The HDF4 format has many limitations.[4][5] It lacks a clear object model, which makes continued support and improvement difficult. Supporting many different interface styles (images, tables, arrays) leads to a complex API. Support for metadata depends on which interface is in use; SD (Scientific Dataset) objects support arbitrary named attributes, while other types only support predefined metadata. Perhaps most importantly, the use of 32-bit signed integers for addressing limits HDF4 files to a maximum of 2 GB, which is unacceptable in many modern scientific applications.
HDF5
The HDF5 format is designed to address some of the limitations of the HDF4 library, and to address current and anticipated requirements of modern systems and applications. In 2002 it won an R&D 100 Award.[6]
HDF5 simplifies the file structure to include only two major types of object:
HDF Structure Example
Datasets, which are typed multidimensional arrays
Groups, which are container structures that can hold datasets and other groups
This results in a truly hierarchical, filesystem-like data format.[clarification needed][citation needed] In fact, resources in an HDF5 file can be accessed using the POSIX-like syntax /path/to/resource. Metadata is stored in the form of user-defined, named attributes attached to groups and datasets. More complex storage APIs representing images and tables can then be built up using datasets, groups and attributes.
In addition to these advances in the file format, HDF5 includes an improved type system, and dataspace objects which represent selections over dataset regions. The API is also object-oriented with respect to datasets, groups, attributes, types, dataspaces and property lists.
The latest version of NetCDF, version 4, is based on HDF5.
Because it uses B-trees to index table objects, HDF5 works well for time series data such as stock price series, network monitoring data, and 3D meteorological data. The bulk of the data goes into straightforward arrays (the table objects) that can be accessed much more quickly than the rows of an SQL database, but B-tree access is available for non-array data. The HDF5 data storage mechanism can be simpler and faster than an SQL star schema.[example needed]
Feedback
Criticism of HDF5 follows from its monolithic design and lengthy specification.
HDF5 does not enforce the use of UTF-8, so client applications may be expecting ASCII in most places.
Dataset data cannot be freed in a file without generating a file copy using an external tool (h5repack).[7]
Python supports HDF5 via h5py (both high- and low-level access to HDF5 abstractions) and via PyTables (a high-level interface with advanced indexing and database-like query capabilities). HDF4 is available via Python-HDF4 and/or PyHDF for both Python 2 and Python 3. The popular data manipulation package pandas can import from and export to HDF5 via PyTables.
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Hierarchical Data Format HDF is a set of file formats HDF4 HDF5 designed to store and organize large amounts of data Originally developed at the U S National Center for Supercomputing Applications it is supported by The HDF Group a non profit corporation whose mission is to ensure continued development of HDF5 technologies and the continued accessibility of data stored in HDF Hierarchical Data FormatFilename extension hdf h4 hdf4 he2 h5 hdf5 he5Internet media typeapplication x hdf application x hdf5Magic number 211HDF r n 032 nDeveloped byThe HDF GroupLatest release5 1 12 2 1 April 19 2022 9 months ago 2022 04 19 Type of formatScientific data formatOpen format YesWebsitewww wbr hdfgroup wbr orgIn keeping with this goal the HDF libraries and associated tools are available under a liberal BSD like license for general use HDF is supported by many commercial and non commercial software platforms and programming languages The freely available HDF distribution consists of the library command line utilities test suite source Java interface and the Java based HDF Viewer HDFView 2 The current version HDF5 differs significantly in design and API from the major legacy version HDF4 Contents 1 Early history 2 HDF4 3 HDF5 3 1 Feedback 4 Interfaces 4 1 Officially supported APIs 4 2 Third party bindings 5 Tools 6 See also 7 References 8 External linksEarly history EditThe quest for a portable scientific data format originally dubbed AEHOO All Encompassing Hierarchical Object Oriented format began in 1987 by the Graphics Foundations Task Force GFTF at the National Center for Supercomputing Applications NCSA NSF grants received in 1990 and 1992 were important to the project Around this time NASA investigated 15 different file formats for use in the Earth Observing System EOS project After a two year review process HDF was selected as the standard data and information system 3 HDF4 EditHDF4 is the older version of the format although still actively supported by The HDF Group It supports a proliferation of different data models including multidimensional arrays raster images and tables Each defines a specific aggregate data type and provides an API for reading writing and organizing the data and metadata New data models can be added by the HDF developers or users HDF is self describing allowing an application to interpret the structure and contents of a file with no outside information One HDF file can hold a mix of related objects which can be accessed as a group or as individual objects Users can create their own grouping structures called vgroups The HDF4 format has many limitations 4 5 It lacks a clear object model which makes continued support and improvement difficult Supporting many different interface styles images tables arrays leads to a complex API Support for metadata depends on which interface is in use SD Scientific Dataset objects support arbitrary named attributes while other types only support predefined metadata Perhaps most importantly the use of 32 bit signed integers for addressing limits HDF4 files to a maximum of 2 GB which is unacceptable in many modern scientific applications HDF5 EditThe HDF5 format is designed to address some of the limitations of the HDF4 library and to address current and anticipated requirements of modern systems and applications In 2002 it won an R amp D 100 Award 6 HDF5 simplifies the file structure to include only two major types of object HDF Structure Example Datasets which are typed multidimensional arrays Groups which are container structures that can hold datasets and other groupsThis results in a truly hierarchical filesystem like data format clarification needed citation needed In fact resources in an HDF5 file can be accessed using the POSIX like syntax path to resource Metadata is stored in the form of user defined named attributes attached to groups and datasets More complex storage APIs representing images and tables can then be built up using datasets groups and attributes In addition to these advances in the file format HDF5 includes an improved type system and dataspace objects which represent selections over dataset regions The API is also object oriented with respect to datasets groups attributes types dataspaces and property lists The latest version of NetCDF version 4 is based on HDF5 Because it uses B trees to index table objects HDF5 works well for time series data such as stock price series network monitoring data and 3D meteorological data The bulk of the data goes into straightforward arrays the table objects that can be accessed much more quickly than the rows of an SQL database but B tree access is available for non array data The HDF5 data storage mechanism can be simpler and faster than an SQL star schema example needed Feedback Edit Criticism of HDF5 follows from its monolithic design and lengthy specification HDF5 does not enforce the use of UTF 8 so client applications may be expecting ASCII in most places Dataset data cannot be freed in a file without generating a file copy using an external tool h5repack 7 Interfaces EditOfficially supported APIs Edit C C CLI Net Fortran Fortran 90 HDF5 Lite H5LT a light weight interface for C HDF5 Image H5IM a C interface for images or rasters HDF5 Table H5TB a C interface for tables HDF5 Packet Table H5PT interfaces for C and C to handle packet data accessed at high speeds HDF5 Dimension Scale H5DS allows dimension scales to be added to HDF5 JavaThird party bindings Edit CGNS uses HDF5 as main storage Common Lisp library hdf5 cffi D offers bindings to the C API with a high level h5py style D wrapper under development Dymola introduced support for HDF5 export using an implementation called SDF Scientific Data Format with release Dymola 2016 FD01 Erlang Elixir and LFE may use the bindings for BEAM languages GNU Data Language Go gonum s hdf5 package HDFql enables users to manage HDF5 files through a high level language similar to SQL in C C Java Python C Fortran and R Huygens Software uses HDF5 as primary storage format since version 3 5 IDL IGOR Pro offers full support of HDF5 files JHDF5 8 an alternative Java binding that takes a different approach from the official HDF5 Java binding which some users find simpler jHDF A pure Java implementation providing read only access to HDF5 files JSON through hdf5 json Julia provides HDF5 support through the HDF5 package LabVIEW can gain HDF support through third party libraries such as h5labview and lvhdf5 Lua through the lua hdf5 library MATLAB Scilab or Octave use HDF5 as primary storage format in recent releases Mathematica 9 offers immediate analysis of HDF and HDF5 data Perl 10 Python supports HDF5 via h5py both high and low level access to HDF5 abstractions and via PyTables a high level interface with advanced indexing and database like query capabilities HDF4 is available via Python HDF4 and or PyHDF for both Python 2 and Python 3 The popular data manipulation package pandas can import from and export to HDF5 via PyTables R offers support in the rhdf5 and hdf5r packages Rust can gain HDF support through third party libraries like hdf5 Tools EditApache Spark HDF5 Connector HDF5 Connector for Apache Spark Apache Drill HDF5 Plugin HDF5 Plugin for Apache Drill enables SQL Queries over HDF5 Files HDF Product Designer Interoperable HDF5 data product creation GUI tool HDF Explorer A data visualization program that reads the HDF HDF5 and netCDF data file formats HDFView A browser and editor for HDF files ViTables A browser and editor for HDF5 and PyTables files written in Python Panoply A netCDF HDF and GRIB Data ViewerSee also EditCommon Data Format CDF FITS a data format used in astronomy GRIB GRIdded Binary a data format used in meteorology HDF Explorer NetCDF The Netcdf Java library reads HDF5 HDF4 HDF EOS and other formats using pure Java Protocol Buffers Google s data interchange formatReferences Edit HDF5 version 1 12 2 released on 2022 04 19 Retrieved 27 Apr 2022 Java based HDF Viewer HDFView History of HDF Group Retrieved 15 July 2014 How is HDF5 different from HDF4 Archived 2009 03 30 at the Wayback Machine Are there limitations to HDF4 files Archived from the original on 2016 04 19 Retrieved 2009 03 29 R amp D 100 Awards Archives Archived 2011 01 04 at the Wayback Machine Rossant Cyrille Moving away from HDF5 cyrille rossant net Retrieved 21 April 2016 JHDF5 library HDF Import and Export Mathematica documentation PDL IO HDF5External links EditOfficial website What is HDF5 HDF EOS Tools and Information Center Open Navigation Surface Retrieved from https en wikipedia org w index php title Hierarchical Data Format amp oldid 1102498915, wikipedia, wiki, book, books, library,
