The HDF Group


Got HDF5?

Visualization of an HDF5 file
Curious to see what’s inside? Try this
(This free tool will show you the contents of an HDF5 file in your browser, without any data leaving your computer! For more info, check out H5Web.)

Registered Filter Plugins

Please be sure to see HDF5 Filter Plugins, a convenience software that packages together many of the commonly used filters that users have created and registered.

Information on Registered Filter Plugins

Members of the HDF5 user community can create and register Third-Party (compression or other) filters for use with HDF5. See Example Code to Enable BZIP2 Compression in HDF5 for how to create a filter.

To register a filter please contact The HDF Helpdesk with the following information:

Here is the current policy regarding filter identifier assignment:

Please contact the maintainer of a filter for help with the filter/compression support in HDF5.

List of Filters Registered with The HDF Group

Filter Identifier Name Short Description
305 LZO LZO lossless compression used by PyTables
307 BZIP2 BZIP2 lossless compression used by PyTables
32000 LZF LZF lossless compression used by H5Py project
32001 BLOSC Blosc lossless compression used by PyTables
32002 MAFISC Modified LZMA compression filter, MAFISC (Multidimensional Adaptive Filtering Improved Scientific data Compression)
32003 Snappy Snappy lossless compression
32004 LZ4 LZ4 fast lossless compression algorithm
32005 APAX Samplify’s APAX Numerical Encoding Technology
32006 CBF All imgCIF/CBF compressions and decompressions, including Canonical, Packed, Packed Version 2, Byte Offset and Nibble Offset
32007 JPEG-XR Enables images to be compressed/decompressed with JPEG-XR compression
32008 bitshuffle Extreme version of shuffle filter that shuffles data at bit level instead of byte level
32009 SPDP SPDP fast lossless compression algorithm for single- and double-precision floating-point data
32010 LPC-Rice LPC-Rice multi-threaded lossless compression
32011 CCSDS-123 ESA CCSDS-123 multi-threaded compression filter
32012 JPEG-LS CharLS JPEG-LS multi-threaded compression filter
32013 zfp Rate, accuracy or precision bounded compression for floating-point arrays
32014 fpzip Fast and Efficient Lossy or Lossless Compressor for Floating-Point Data
32015 Zstandard Real-time compression algorithm with wide range of compression / speed trade-off and fast decoder
32016 B³D GPU based image compression method developed for light-microscopy applications
32017 SZ An error-bounded lossy compressor for scientific floating-point data
32018 FCIDECOMP EUMETSAT CharLS compression filter for use with netCDF
32019 JPEG Jpeg compression filter
32020 VBZ Compression filter for raw dna signal data used by Oxford Nanopore
32021 FAPEC Versatile and efficient data compressor supporting many kinds of data and using an outlier-resilient entropy coder
32022 BitGroom The BitGroom quantization algorithm
32023 Granular BitRound (GBR) The GBG quantization algorithm is a significant improvement to the BitGroom filter
32024 SZ3 A modular error-bounded lossy compression framework for scientific datasets
32025 Delta-Rice Lossless compression algorithm optimized for digitized analog signals based on delta encoding and rice coding
32026 BLOSC The recent new-generation version of the Blosc compression library
32027 FLAC FLAC audio compression filter in HDF5

Example Code to enable BZIP2 Compression in HDF5

Please be aware that compression filters require that the library not use H5_MEMORY_ALLOC_SANITY_CHECK. Building in debug mode automatically enables this feature in earlier releases, which causes memory allocation and free problems in filter applications. Future versions of HDF5 will not enable this feature.

The bz_example.tar.gz file contains an example of implementing the BZIP2 filter to enable BZIP2 compression in HDF5. (This example is based on PyTables code that uses BZIP2 compression.). Download and uncompress this file as follows:

  gzip -cd bz_example.tar.gz | tar xvf -

To compile the example, you will need to install the HDF5 library and use the h5cc compile script found in the bin/ directory of the HDF5 installation.

For information on h5cc, see Compiling Your HDF5 Application.

Please note that tools like h5dump that display information in an HDF5 file will not be able to display data that is compressed with BZIP2 compression, since BZIP2 is not implemented in HDF5.

However, as of HDF5-1.8.11, a new HDF5 feature will enable the h5dump tool to determine that the data is compressed with an external compression filter such as BZIP2, and will automatically load the appropriate library and display the uncompressed data.

The bz_example example code can be used for modifying the HDF5 source to “include” BZIP2 as one of the “internal” filters. For information on how to do this, see how ZLIB (the deflate filter) is implemented in the HDF5 source code. Specifically look at these files:

H5Z.c, H5Zdeflate.c and H5Pocpl.c