Introduction:
=============
The aim of this repository is providing a software library for biomedical signal processing.
Biosig consists of two main parts:
(1) "Biosig for Octave and Matlab" and
(2) "Biosig for C/C++" which contains also a number of bindings to other programming languages
== 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 \
liboctave-dev \
python-numpy python3-numpy \
libpython-dev libpython3-dev \
R openjdk-11-jdk
--- Recommended packages at runtime ---
apt-get install \
libb64 tinyxml \
python-numpy python3-numpy \
R openjdk-11-jre \
octave octave-tsa octave-nan
Installing biosig 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 -fim # 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-wheels
sudo apt-get install python3 python3-dev python3-numpy python3-wheels
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-1.9.2.tar.gz
python3 -m pip install python/dist/Biosig-1.9.2.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 Java, 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 <alois.schloegl@gmail.com>
This function is part of the BioSig repository at http://biosig.sf.net/
Biosignal Tools Files
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