wfdbloadlib.m

function [varargout]=wfdbloadlib(varargin)
%
% [isloaded,config]=wfdbloadlib(debugLevel,networkWaitTime)
%
% Loads the WDFDB libarary if it has not been loaded already into the
% MATLAB classpath. And optionally prints configuration environment and debug information
% regarding the settings used by the classes in the JAR file.
%
% Inputs:
%
% debugLevel
%       (Optional) 1x1 integer between 0 and 5 represeting the level of debug information to output from
%       Java class when output configuration information. Level 0 (no debug information),
%       level =5 is maximum level of information output by the class (logger set to finest). Default is level 0.
%
% networkWaitTime
%       (Optional) 1x1 integer representing the longest time in
%       milliseconds  for which the JVM should wait for a data stream from
%       PhysioNet (default is =1000  , ie one second). If you need to change this time to a
%       longer value across the entire toolbox, it is better modify to default value in the source
%       code below and restart MATLAB.
%
%
% Written by Ikaro Silva, 2013
%         Last Modified: April 7, 2015
% Since 0.0.1
%
%

%endOfHelp
mlock
persistent isloaded wfdb_path wfdb_native_path config

%%%%% SYSTEM WIDE CONFIGURATION PARAMETERS %%%%%%%
%%% Change these values for system wide configuration of the WFDB binaries

%If you are using your own custom version of the WFDB binaries, set this to true
%NOTE: this parameter is completely ignored if the 'WFDB_COMMAND_PATH' parameter
%described above is set (i.e.: the library will used the WFDB commands located
% according to the path in 'WFDB_COMMAND_PATH'). 
%You will need to restart MATLAB/Octave if to sync the changes.
%The default is to used commands shipped with the toolbox, this location can be obtained by running the command:
%[~,config]=wfdbloadlib; config.WFDB_NATIVE_BIN
WFDB_CUSTOMLIB=0;

%WFDB_PATH: If empty, will use the default given config.WFDB_PATH
%this is where the toolbox searches  for data files (*.dat, *.hea etc).
%When unistalling the toolbox, you may wish to clear this directory to save space.
%See http://www.physionet.org/physiotools/wag/setwfd-1.htm for more details.
WFDB_PATH=[];

%WFDBCAL: If empty, will use the default giveng confing.WFDBCAL
%The WFDB library require calibration data in order to convert between sample values
%(expressed in analog-to-digital converter units, or adus) and physical units.
%See http://www.physionet.org/physiotools/wag/wfdbca-5.htm for more details.
WFDBCAL=[];

%CACHE: If CACHE==1, the toolbox will attemp to download data from 
%CACHE_SOURCE to CACHE_DEST if the record is not found no the standard 
%WFDB PATH. Change CACHE_DEST path to a PhysioNet mirror, if you wish to
%use a server closer to your geographical location. It is safe to delete files on
%CACHE_SOURCE, as they can be re-downloaded if need me.

CACHE=1; %Default is to use the cache system
CACHE_SOURCE=[]; %If empty, defaults to last element of WFDB_PATH
CACHE_DEST=[]; %If empty, defaults to WFDB_JAVA_HOME/../database


%debugLevel: Ouput JVM information while running commands
debugLevel=0;

%networkWaitTime: Setting maximum waiting period for fetching data from
%PhysioNet servers (default location: http://physionet.org/physiobank).
networkWaitTime=1000;

%%%% END OF SYSTEM WIDE CONFIGURATION PARAMETERS

inputs={'debugLevel','networkWaitTime'};
for n=1:nargin
    if(~isempty(varargin{n}))
        eval([inputs{n} '=varargin{n};'])
    end
end


inOctave=is_octave;
fsep=filesep;
if(ispc && inOctave)
	fsep=['\\']; %Need to escape '\' for regexp in Octave and Windows
end
if(isempty(isloaded))
    jar_path=which('wfdbloadlib');
    cut=strfind(jar_path,'wfdbloadlib.m');
    wfdb_path=jar_path(1:cut-1);
    
    if(~inOctave)
        ml_jar_version=version('-java');
    else
        %In Octave
        ml_jar_version=javaMethod('getProperty','java.lang.System','java.version');
        ml_jar_version=['Java ' ml_jar_version];
    end
    %Check if path has not been added yet
    wfdb_path=[wfdb_path 'wfdb-app-JVM7-0-10-0.jar'];
    javaaddpath(wfdb_path)
    isloaded=1;
    
    %Check if there are any empty space on the path directory, and 
    %issue a warning if there is
    warnMe=strfind(wfdb_path,' ');
    if(~isempty(warnMe))
       warning('Your WFDB Toolbox installation  path contain white spaces!! This may cause issues with the WFDB Toolbox!') 
       warning(['The installation path is set to: ' wfdb_path])
    end
end

%set configuration
if(isempty(config))
        config.MATLAB_VERSION=version;
        config.inOctave=inOctave;
        if(inOctave)
            javaWfdbExec=javaObject('org.physionet.wfdb.Wfdbexec','wfdb-config',WFDB_CUSTOMLIB);
            javaWfdbExec.setLogLevel(debugLevel);
            config.WFDB_VERSION=char(javaMethod('execToStringList',javaWfdbExec,{'--version'}));
        else
            javaWfdbExec=org.physionet.wfdb.Wfdbexec('wfdb-config',WFDB_CUSTOMLIB);
            javaWfdbExec.setLogLevel(debugLevel);
            config.WFDB_VERSION=char(javaWfdbExec.execToStringList('--version'));
        end
        env=regexp(char(javaWfdbExec.getEnvironment),',','split');
        for e=1:length(env)
            tmpstr=regexp(env{e},'=','split');
            varname=strrep(tmpstr{1},'[','');
            varname=strrep(varname,' ','');
            varname=strrep(varname,']','');
            eval(['config.' varname '=''' tmpstr{2} ''';'])
        end
        config.MATLAB_PATH=strrep(which('wfdbloadlib'),'wfdbloadlib.m','');
        wver=regexp(wfdb_path,fsep,'split');
        config.WFDB_JAVA_VERSION=wver{end};
        config.DEBUG_LEVEL=debugLevel;
        config.NETWORK_WAIT_TIME=networkWaitTime;
        config.MATLAB_ARCH=computer('arch');
        %Remove empty spaces from arch name
        del=strfind(config.osName,' ');
        config.osName(del)=[];
        
        %Define WFDB Environment variables
        if(isempty(WFDB_PATH))
            tmpCache=[config.MATLAB_PATH '..' filesep 'database' filesep];
            WFDB_PATH=['. ' tmpCache ' http://physionet.org/physiobank/database/'];
        end
        if(isempty(WFDBCAL))
            WFDBCAL=[config.WFDB_JAVA_HOME fsep 'database' fsep 'wfdbcal'];
        end
        config.WFDB_PATH=WFDB_PATH;
        config.WFDBCAL=WFDBCAL;
        config.WFDB_CUSTOMLIB=WFDB_CUSTOMLIB;
            warnMe=strfind(wfdb_path,' ');
    if(~isempty(warnMe))
       warning('Your WFDB Toolbox installation  path contain white spaces!! This may cause issues with the WFDB Toolbox!') 
    end
    
    %Set CACHE configurations
    if(isempty(CACHE_SOURCE) && CACHE)
        ind=strfind(config.WFDB_PATH,'http');
        if(~isempty(ind))
            CACHE_SOURCE=config.WFDB_PATH(ind:end);
        else
            warning(['Could not set CACHE, CACHE_SOURCE invalid'])
            CACHE=0;   
        end
    end
    config.CACHE_SOURCE=CACHE_SOURCE;
    
    if(isempty(CACHE_DEST) && CACHE)
        CACHE_DEST=[config.MATLAB_PATH '..' filesep 'database' filesep];
        if(~isdir(CACHE_DEST))
            mkdir(CACHE_DEST);
        end
        if(~isdir(CACHE_DEST))
            warning(['Could not set CACHE, CACHE_DEST directory does not exist: ' CACHE_DEST])
            CACHE=0;   
        end
    end
    config.CACHE_DEST=CACHE_DEST;   
    config.CACHE=CACHE; 
    
    %Set enviroment variables used by WFBD
    setenv('WFDB',config.WFDB_PATH);
    setenv('WFDBCAL',config.WFDBCAL);
end


outputs={'isloaded','config'};
for n=1:nargout
    eval(['varargout{n}=' outputs{n} ';'])
end


%% subfunction that checks if we are in octave
function r = is_octave ()
    r = exist ('OCTAVE_VERSION', 'builtin')>0;