/zmat

ZMat: A portable C-library and MATLAB/Octave toolbox for zlib/gzip/lzma/lz4/lz4hc data compression

Primary LanguageCGNU General Public License v3.0GPL-3.0

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ZMAT: A portable C-library and MATLAB/Octave toolbox for zlib/gzip/lzma/lz4/zstd/blosc2 data compression

  • Copyright (C) 2019-2023 Qianqian Fang <q.fang at neu.edu>
  • License: GNU General Public License version 3 (GPL v3), see License*.txt
  • Version: 0.9.9 (Foxy the Fantastic Mr. Fox - RC1)
  • URL: https://github.com/NeuroJSON/zmat
  • Acknowledgement: This project is part of the NeuroJSON project supported by US National Institute of Health (NIH) grant U24-NS124027

Table of Contents

Introduction

ZMat provides both an easy-to-use C-based data compression library - libzmat as well a portable mex function to enable zlib/gzip/lzma/lz4/zstd/blosc2 based data compression/decompression and base64 encoding/decoding support in MATLAB and GNU Octave. It is fast and compact, can process a large array within a fraction of a second.

Among all the supported compression methods, or codecs, lz4 is among the fastest for both compression/decompression; lzma is the slowest but offers the highest compression ratio; zlib/gzip have excellent balance between speed and compression time; zstd can be fast, although not as fast as lz4, at the low-compression levels, and can offer higher compression ratios than zlib/gzip, although not as high as lzma, at high compression levels. We understand there are many other existing general purpose data compression algorithms. We prioritize the support of these compression algorithms because they have widespread use.

Starting in v0.9.9, we added support to a high-performance meta-compressor, called blosc2 (https://blosc.org). The blosc2 compressor is not single compression method, but a container format that supports a diverse set of strategies to losslessly compress data, especially optimized for storing and retrieving N-D numerical data of uniform binary types. Users can choose between blosc2blosclz, blosc2lz4, blosc2lz4hc, blosc2zlib and blosc2zstd, to access these blosc2 codecs.

The libzmat library, including the static library (libzmat.a) and the dynamic library libzmat.so or libzmat.dll, provides a simple interface to conveniently compress or decompress a memory buffer:

int zmat_run(
      const size_t inputsize,     /* input buffer data length */
      unsigned char *inputstr,    /* input buffer */
      size_t *outputsize,         /* output buffer data length */
      unsigned char **outputbuf,  /* output buffer */
      const int zipid,            /* 0: zlib, 1: gzip, 2: base64, 3: lzma, 4: lzip, 5: lz4, 6: lz4hc
                                     7: zstd, 8: blosc2blosclz, 9: blosc2lz4, 10: blosc2lz4hc,
                                     11: blosc2zlib, 12: blosc2zstd */
      int *status,                /* return status for error handling */
      const int clevel            /* 1 to compress (default level); 0 to decompress, -1 to -9 (-22 for zstd): setting compression level */
    );

When blosc2 codes are used, users can set additional compression flags, including number of threads, byte-shuffling length, can be set via the flags.param interface in the following data structure, and pass on flags.iscompress as the last input to zmat_run.

union cflag {
    int iscompress;      /* combined flag used to pass on to zmat_run */
    struct settings {    /* unpacked flags */
        char clevel;     /* compression level */
        char nthread;    /* number of compression/decompression threads */
        char shuffle;    /* byte shuffle length */
        char typesize;   /* for ND-array, the byte-size for each array element */
    } param;
} flags = {0};

The zmat library is highly portable and can be directly embedded in the source code to provide maximal portability. In the test folder, we provided sample codes to call zmat_run/zmat_encode/zmat_decode for stream-level compression and decompression in C and Fortran90. The Fortran90 C-binding module can be found in the fortran90 folder.

The ZMat MATLAB function accepts 3 types of inputs: char-based strings, numerical arrays or vectors, or logical arrays/vectors. Any other input format will result in an error unless you typecast the input into int8/uint8 format. A multi-dimensional numerical array is accepted, and the original input's type/dimension info is stored in the 2nd output "info". If one calls zmat with both the encoded data (in byte vector) and the "info" structure, zmat will first decode the binary data and then restore the original input's type and size.

The pre-compiled mex binaries for MATLAB are stored inside the subfolder named private. Those precompiled for GNU Octave are stored in the subfolder named octave, with one operating system per subfolder. The PKG_ADD script should automatically select the correct mex file when one types addpath in Octave. These precompiled mex files are expected to run out-of-box across a wide-range of MATLAB (tested as old as R2008) and Octave (tested as old as v3.8).

If you do not want to compile zmat yourself, you can download the precompiled package by either clicking on the "Download ZIP" button on the above URL, or use the below git command:

git clone https://github.com/NeuroJSON/zmat.git

Installation

The installation of ZMat is no different from any other simple MATLAB toolboxes. You only need to download/unzip the package to a folder, and add the folder's path (that contains zmat.m and the "private" folder) to MATLAB's path list by using the following command:

addpath('/path/to/zmat');

For Octave, one needs to copy the zipmat.mat file inside the "octave", from the subfolder matching the OS into the "private" subfolder.

If you want to add this path permanently, you need to type "pathtool", browse to the zmat root folder and add to the list, then click "Save". Then, run "rehash" in MATLAB, and type "which zmat", if you see an output, that means ZMat is installed for MATLAB/Octave.

If you use MATLAB in a shared environment such as a Linux server, the best way to add path is to type

mkdir ~/matlab/
nano ~/matlab/startup.m

and type addpath('/path/to/zmat') in this file, save and quit the editor. MATLAB will execute this file every time it starts. For Octave, the file you need to edit is ~/.octaverc , where "~" is your home directory.

Installing ZMat on Linux Distributions

One can directly install zmat on Fedora Linux 29 or later via the below shell command

sudo dnf install octave-zmat

Similarly, the below command installs the libzmat library for developing software using this library:

sudo dnf install zmat zmat-devel zmat-static

The above command installs the dynamic library, C/Fortran90 header files and static library, respectively

Similarly, if one uses Debian (11) or Ubuntu 21.04 or newer, the command to install zmat toolbox for Octave (and optionally for MATLAB) is

sudo apt-get install octave-zmat matlab-zmat

and that for installing the development environment is

sudo apt-get install libzmat1 libzmat1-dev

A Ubuntu (16.04/18.04) user can use the same commands as Debian to install these packages but one must first run

sudo add-apt-repository ppa:fangq/ppa
sudo apt-get update

to enable the relevant PPA (personal package achieve) first.

Using ZMat in MATLAB

ZMat provides a single mex function, zipmat.mex* -- for both compressing/encoding or decompresing/decoding data streams. The help info of the function is shown below

zmat.m

output=zmat(input)
   or
[output, info]=zmat(input, iscompress, method)
[output, info]=zmat(input, iscompress, method, options ...)
output=zmat(input, info)

A portable data compression/decompression toolbox for MATLAB/GNU Octave

author: Qianqian Fang <q.fang at neu.edu>
initial version created on 04/30/2019

input:
     input: a char, non-complex numeric or logical vector or array
     iscompress: (optional) if iscompress is 1, zmat compresses/encodes the input,
            if 0, it decompresses/decodes the input. Default value is 1.

            if iscompress is set to a negative integer, (-iscompress) specifies
            the compression level. For zlib/gzip, default level is 6 (1-9); for
            lzma/lzip, default level is 5 (1-9); for lz4hc, default level is 8 (1-16).
            the default compression level is used if iscompress is set to 1.

            zmat removes the trailing newline when iscompress=2 and method='base64'
            all newlines are kept when iscompress=3 and method='base64'

            if one defines iscompress as the info struct (2nd output of zmat), zmat
            will perform a decoding/decompression operation and recover the original
            input using the info stored in the info structure.
     method: (optional) compression method, currently, zmat supports the below methods
            'zlib': zlib/zip based data compression (default)
            'gzip': gzip formatted data compression
            'lzip': lzip formatted data compression
            'lzma': lzma formatted data compression
            'lz4':  lz4 formatted data compression
            'lz4hc':lz4hc (LZ4 with high-compression ratio) formatted data compression
            'zstd':  zstd formatted data compression
            'blosc2blosclz':  blosc2 meta-compressor with blosclz compression
            'blosc2lz4':  blosc2 meta-compressor with lz4 compression
            'blosc2lz4hc':  blosc2 meta-compressor with lz4hc compression
            'blosc2zlib':  blosc2 meta-compressor with zlib/zip compression
            'blosc2zstd':  blosc2 meta-compressor with zstd compression
            'base64': encode or decode use base64 format
    options: a series of ('name', value) pairs, supported options include
            'nthread': followed by an integer specifying number of threads for blosc2 meta-compressors
            'typesize': followed by an integer specifying the number of bytes per data element (used for shuffle)
            'shuffle': shuffle methods in blosc2 meta-compressor, 0 disable, 1, byte-shuffle

output:
     output: a uint8 row vector, storing the compressed or decompressed data;
            empty when an error is encountered
     info: (optional) a struct storing additional info regarding the input data, may have
           'type': the class of the input array
           'size': the dimensions of the input array
           'byte': the number of bytes per element in the input array
           'method': a copy of the 3rd input indicating the encoding method
           'status': the zlib/lzma/lz4 compression/decompression function return value,
                   including potential error codes; see documentation of the respective
                   libraries for details
           'level': a copy of the iscompress flag; if non-zero, specifying compression
                   level, see above

example:

  [ss, info]=zmat(eye(5))
  orig=zmat(ss,0)
  orig=zmat(ss,info)
  ss=char(zmat('zmat test',1,'base64'))
  orig=char(zmat(ss,0,'base64'))

-- this function is part of the zmat toolbox (https://github.com/NeuroJSON/zmat)

examples

Under the "example" folder, you can find a demo script showing the basic utilities of ZMat. Running the "demo_zmat_basic.m" script, you can see how to compress/decompress a simple array, as well as apply base64 encoding/decoding to strings.

Please run these examples and understand how ZMat works before you use it to process your data.

Under the "c" and "f90" folders, sample C/Fortran90 units calling the compression/decompression APIs provided by zmat are also provided. You may run "make" in each of the folders to build the binary and execute the output program.

unit tests

Under the "test" folder, you can run "run_zmat_test.m" script to run unit tests on the key features provided by zmat.

Compile ZMat

To recompile ZMat, you first need to check out ZMat source code, along with the needed submodules from the Github repository using the below command

git clone https://github.com/NeuroJSON/zmat.git zmat

Next, you need to make sure your system has gcc, g++, mex and mkoctfile (if compiling for Octave is needed). If not, please install gcc, MATLAB and GNU Octave and add the paths to these utilities to the system PATH environment variable.

To compile zmat, you may choose one of the three methods:

  1. Method 1: please open MATLAB or Octave, and run the below commands
cd zmat/src
compilezmat

The above script utilizes the MinGW-w64 MATLAB Compiler plugin.

To install the MinGW-w64 compiler plugin for MATLAB, please follow the below steps

pacman -Syu
pacman -S base-devel gcc git zlib-devel

Then, start MATLAB, and in the command window, run

setenv('MW_MINGW64_LOC','C:\msys64\usr');
  • After installation of MATLAB MinGW support, you must type mex -setup C in MATLAB and select "MinGW64 Compiler (C)".
  • Once you select the MingW C compiler, you should run mex -setup C++ again in MATLAB and select "MinGW64 Compiler (C++)" to compile C++.
  1. Method 2: Compile with cmake (3.3 or later)

Please open a terminal, and run the below shall commands

cd zmat/src
rm -rf build
mkdir build && cd build
cmake ../
make clean
make

if MATLAB was not installed in a standard path, you may change cmake ../ to

cmake Matlab_ROOT_DIR=/path/to/matlab/root ../

by default, this will first compile libzmat.a and then create the .mex file that is statically linked with libzmat.a. If one prefers to create a dynamic library libzmat.so and then a dynamically linked .mex file, this can be done by

cmake Matlab_ROOT_DIR=/path/to/matlab/root -DSTATIC_LIB=off ../
  1. Method 3: please open a terminal, and run the below shall commands
cd zmat/src
make clean
make mex

to create the mex file for MATLAB, and run make clean oct to compile the mex file for Octave.

The compilex mex files are named as zipmat.mex* under the zmat root folder. One may move those into the private folder to overwrite the existing files, or leave them in the root folder. MATLAB/Octave will use these files when zmat is called.

Contribution and feedback

ZMat is an open-source project. This means you can not only use it and modify it as you wish, but also you can contribute your changes back to ZMat so that everyone else can enjoy the improvement. For anyone who want to contribute, please download ZMat source code from its source code repositories by using the following command:

git clone https://github.com/NeuroJSON/zmat.git zmat

or browsing the github site at

https://github.com/NeuroJSON/zmat

You can make changes to the files as needed. Once you are satisfied with your changes, and ready to share it with others, please submit your changes as a "pull request" on github. The project maintainer, Dr. Qianqian Fang will review the changes and choose to accept the patch.

We appreciate any suggestions and feedbacks from you. Please use the NeuroJSON forum to report any questions you may have regarding ZMat:

NeuroJSON forum

(Subscription to the mailing list is needed in order to post messages).

Acknowledgement

ZMat is linked against 4 open-source data compression libraries

  1. ZLib library: https://www.zlib.net/
  • Copyright (C) 1995-2017 Jean-loup Gailly and Mark Adler
  • License: Zlib license
  1. Eazylzma: https://github.com/lloyd/easylzma
  • Author: Lloyd Hilaiel (lloyd)
  • License: public domain
  1. Original LZMA library:
  • Author: Igor Pavlov
  • License: public domain
  1. LZ4 library: https://lz4.github.io/lz4/
  1. C-blosc2: https://blosc.org/
  1. ZStd: https://facebook.github.io/zstd/
  1. miniz: https://github.com/richgel999/miniz