Biosignal Tools Code
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Alois Schlögl
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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.
As a quick start, you can do:
wget https://sourceforge.net/projects/biosig/files/BioSig%20for%20C_C%2B%2B/src/biosig-2.6.1.src.tar.xz
tar xvf biosig-2.6.1.src.tar.xz
cd biosig-2.6.1
./configure && make -j
sudo make install
--- Required packages at build time ---
Debian (and derivatives)
apt-get install autoconf gawk libb64-dev tinyxml-dev libdcmtk-dev suitesparse-dev
MacOSX/homebrew
brew install biosig
Windows binaries: MSVC is not supported, some gnu compiler for windows (e.g. mingw, cygwin, wsl) is needed.
We are using this mingw-cross-compiler environment (MXE) on some linux host.
git clone https://github.com/schloegl/mxe
cd mxe
make biosig
--- Optional/Recommended packages at compile time ---
Debian (and derivatives)
apt-get install \
gawk \
libb64-dev tinyxml-dev libdcmtk-dev \
liboctave-dev octave \
python3-numpy \
python-setuptools python3-setuptools \
libpython3-dev \
R texlive-fonts-extra \
default-jdk
MacOSX/homebrew
brew install biosig
--- Recommended packages at runtime ---
apt-get install \
libb64 tinyxml libdcmtk{14..17} \
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
Compile Biosig from git (without installing):
WD=$HOME/src/biosig-code # working directory, adapt to your needs
git clone https://git.code.sf.net/p/biosig/code $WD
cd $WD
autoconf || autoreconf -fi
./configure
make
export PATH=$WD/biosig4c++:$PATH
export LD_LIBRARY_PATH=$WD/biosig4c++:$LD_LIBRARY_PATH
# make install # (optional) installs by default into /usr/local/
Installing Biosig from source is as simple as, and will install by default into
./configure && make -j && sudo make install
This should install libbiosig and als biosig command line tools like
save2gdf
biosig_fhir
physicalunits
biosig2gdf
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
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 || autoreconf -fi # needed only the first time after checkout
./configure
make
sudo make install
(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
biosig2gdf:
converts any file of a supported data format to GDF format
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.
sudo apt install libbiosig-dev # Debian, Ubuntu, etc.
brew install biosig # MacOSX with homebrew
pip install biosig
Debian/Ubuntu
sudo apt-get install python3-biosig
or
MYENV=$HOME/MyBiosigPythonEnv
python -m venv ${MYENV}
source ${MYENV}/bin/activate
cd biosig4c++/python && pip install .
or
python3 -m pip install https://sourceforge.net/projects/biosig/files/BioSig%20for%20Python/biosig-2.6.1.tar.gz
Use of the interface is shown in
pip install matplotlib
python biosig4c++/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) 2005-2024 Alois Schloegl <alois.schloegl@gmail.com>
This function is part of the BioSig repository at http://biosig.sf.net/
