Biosignal Tools Code
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schloegl
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/