biosig-sf

Unofficial clone of http://biosig.sourceforge.net/ - 20220627

https://github.com/eegkit/biosig-sf

Repository

Unofficial clone of http://biosig.sourceforge.net/ - 20220627

README

Introduction:
=============

The aim of this repository is providing a software library for biomedical signal processing.
Biosig consists of the following parts:
(1) "Biosig for Octave and Matlab" and
(2) "Biosig for C/C++" provides libbiosig, and several command line tools
(3)  binding of libbiosig to the following programming languages:
      Python, Mathematica, Matlab/Octave, Java, and R.

== Installation ==

The build and installation is quite flexible, and will adapt to your configuration. If numpy/libpython-dev
is available, the biosig language binding for python will be installed. The same is try
for Octave, Matlab, Mathematica, R, and Java.

--- Recommended packages at compile time ---

   apt-get install \
	gawk \
	libb64-dev tinyxml-dev libdcmtk-dev \
	liboctave-dev octave \
	python-numpy python3-numpy \
	python-setuptools python3-setuptools \
	libpython-dev libpython3-dev \
	R texlive-fonts-extra \
	default-jdk

--- Recommended packages at runtime ---
   apt-get install \
	libb64 tinyxml libdcmtk14 \
	python-numpy python3-numpy \
	R default-jre \
	octave octave-tsa octave-nan octave-signal octave-statistics

--- msys2
    pacman -Su
    libiconv libiconv-dev unzip gcc autoconf make
    mingw-w64-x86_64-python-numpy
    mingw-w64-x86_64-python-setuptools

Installing Biosig from source is as simple as
   ./configure
   make
   sudo make install

This should install libbiosig and als biosig command line tools like

    save2gdf
    biosig_fhir
    physicalunits

Depending on your software configuration, also language bindings to
   Matlab, Octave, Python, Java, R, Mathematica
might be installed. If you have python/numpy/libpython-dev installed, also biosig for python will be installed.
If you have Octave/liboctave-dev installed, also mexbiosig will be installed in octave.

However there are some known (and probably also unknown) limitations. Known limitations are
- Java language binding does not compile on MacOSX
- Cross compilation for Windows does not work (except for Matlab and Mathematica language bindings)




BioSig4C++ provides several tools:

(1) = LIBRARIES =
(1a) "libbiosig" provides a library for accessing different dataformats.
The supported data formats are listed here:
   http://pub.ist.ac.at/~schloegl/biosig/TESTED
(1b) "libgdf" is a lightweight version of libbiosig, supporting only the GDF format.
it requires only GCC not G++ for linking, has potentially much less security loopholes (XML) and bugs,
and a much smaller memory footprint, which might be especially useful for embedded devices.
It's interface is the same than for libbiosig, namely biosig.h
(1c) "libphysicalunits" provides conversion tools for physical units from
ascii text to 16bit integers according to ISO/IEEE 11073-10101:2004 Table A.6.3: Vital signs units of measurements
text strings are cached for performance reasons, and can be used in a multi-threaded application.

* Installation of official source release (for users):
	download source release and run
        see above


* Installation from git repository (for developers, usually untested):
  Requirement: gawk
  ** Checkout code for the first time:

	git clone https://git.code.sf.net/p/biosig/code biosig-code
	cd biosig-code
	autoconf 	# needed only the first time after checkout
	./configure
	make
	sudo make install

  ** next time just update latest changes

	git pull
	autoreconf -fi  # usually this can be omitted
	./configure 	# usually this can be omitted
	make
	make install


For doing some advanced (special) configurations, you can modify these flags in Makefile.in

(2) = converter and tools =
contains several tools for data conversion,
	save2gdf: is a converter between different file formats, including but not limited to
		SCP-ECG(EN1064), HL7aECG (FDA-XML), GDF, EDF, BDF, CWFB and others
		save2gdf can be also used to upload or retrieve data
		from a bscs server, and to display the header information
		in ascii and in JSON format.
	biosig2fhir: is a tool than converts biosig data into a hl7/fhir binary template,
		the header information is encoded in JSON format, the data is converted
		into a base64-encoded GDF (OeNorm K2202:2015) formatted file.
	physicalunits:	is a tool to show the encoding of physical units according to ISO/IEEE 11073

These can can be build with:
   make tools


(3) language bindings and foreign function interfaces:
(3a) "mexSLOAD" is a MEX-interface for Octave and Matlab
and is linked statically to libbiosig. It can be build with
    make mex4o   # octave
    make mex4m   # matlab
for details see mex/README.

(3b) "python" is an interface to python and dynamically linked to libbiosig.
Requirement: python, python-dev, python-numpy
for Debian/Ubuntu:
	sudo apt-get install python  python-dev  python-numpy  python-setuptools
	sudo apt-get install python3 python3-dev python3-numpy python3-setuptools
It can be build with any of the following commands:
	make python
	make -C biosig4c++/python build
	make -C biosig4c++/python release
For installation, you can than do either
	cd biosig4c++/python && python setup.py install
	cd biosig4c++/python && python3 setup.py install
or
	python  -m pip install python/dist/Biosig-2.1.1.tar.gz
	python3 -m pip install python/dist/Biosig-2.1.1.tar.gz
Use of the interface is shown in ./python/demo2.py


(3c) mathematica
is linked dynamically to libbiosig and can be build with:
	make mma
see also biosig4c++/mma/README, and biosig4c++/mma/biosig, biosig4c++/mma/hdrinfo.nb, biosig4c++/mma/mySLOAD.nb for more details.

(3z) other language interfaces
Basic interfaces for R and Java are also available. For other languages
(including PHP, Perl and TCL) are considered, but these still need to be implemented and tested.


(5) Biosig tools for Matlab and Octave
The easiest approach is to change into the directory
    cd biosig4matlab
and run "install" from within Matlab or Octave. This will set the path to the subdirectories.


(6) Precompiled binaries for Win32 and Win64
   biosig4c++/win##/save2gdf.exe  binary converter
   biosig4c++/win##/libbiosig.{lib,dll}  static and dynamic library (requires zlib and libws2_32)
   biosig4c++/mma/biosig.exe     Mathematica binding through Mathlink interface
   biosig4c++/mex/mexSLOAD.mexw32   Mex-file for Win32/Matlab


The internal data structure resemble the header structure similar to
  https://sourceforge.net/p/biosig/code/ci/master/tree/biosig4matlab/doc/header.txt
and is defined in
  https://sourceforge.net/p/biosig/code/ci/master/tree/biosig4c++/biosig-dev.h
(see HDRTYPE and CHANNEL_TYPE)

Encoding of Event/Markers/Annotations is available here:
  http://pub.ist.ac.at/~schloegl/matlab/eeg/EventCodes.html

The latest list of supported data formats is available here:
  http://pub.ist.ac.at/~schloegl/biosig/TESTED


File(s):
-------------
    README 	this file
    biosig.h	definition of external biosig interface
    biosig-dev.h definition of internal functions
    biosig.c	SOPEN, SREAD, SWRITE, SEOF, SCLOSE functions
    save2gdf.c	converter between various file formats.
    physicalunit.c         en-/decodes physical units according to ISO/DIS 11073-10101:2003
    mexSLOAD.cpp is a MEX-File for loading data in Octave and Matab.
    t210/*	reading SCP,FAMOS file format
    t220/*      writing SCP file format
    t230/*      support of HL7aECG file format
    t240/*	Support for CNSystems' File Exchange Format (CNS-FEF), note this is different to CENTS14271 in t241/
    t241/*.asn1	ASN.1 specification of ISO11073-xxxxx and CENTS-14271 (FEF),
    test0/*	scripts and functions for testing
    Makefile	script for compiling and testing under GNU/Linux
    Makefile.win32	script for compiling and testing on win32 using mingw
    mex/*       Octave/Matlab binding through MEX-interface
    mma/*	MathLink interface to mathematica
    win32/*	library and executables for Windows
    python/*.py show example and demo
    src/*.c	applications: flowmon reads data from serial port, ttl2trig reads data from audio card


More information is available at http://biosig.sf.net/

If you have any questions you can also contact the mailinglist
https://lists.sourceforge.net/lists/listinfo/biosig-general


    Copyright (C) 2005-2020 Alois Schloegl 
    This function is part of the BioSig repository at http://biosig.sf.net/

Owner

Citation (CITATION)

# You may cite any of these: 

A Schlögl
BioSig-An application of Octave
arXiv preprint cs/0603001, 2006

A. Schlögl, C. Brunner, R. Scherer, A. Glatz;
BioSig - an open source software library for BCI research.
(Eds.) G. Dornhege, J.R. Millan, T. Hinterberger, D.J. McFarland, K.-R. Müller;
Towards Brain-Computer Interfacing, MIT Press, 2007, p.347-358. 

Schlögl A., Brunner C.
BioSig: A Free and Open Source Software Library for BCI Research,
Computer, vol. 41, no. 10, pp. 44-50, October, 2008.

C. Vidaurre, T.H. Sander, A. Schlögl
BioSig: The Free and Open Source Software Library for Biomedical Signal Processing.
Computational intelligence and neuroscience (2011) Volume 2011 (2011), Article ID 935364, 12 pages




	

GitHub Events