sp_setting_defaults.m

function spParams = sp_setting_defaults(varargin)
% Establish basic parameter settings, then update for species
% specific defaults, and user preferences.
% Pulled into subroutine kf 10/4/2016

% get user input and set up file names
n = 1;
while n <= length(varargin)
    switch varargin{n}
        case 'sp'
            sp = varargin{n+1}; n=n+2;
        case 'srate'
            srate = varargin{n+1}; n=n+2;
        case 'analysis'
            analysis = varargin{n+1}; n=n+2;
        case 'spParamsUser'
            spParamsUser = varargin{n+1}; n=n+2;
        otherwise
            error('Bad optional argument: "%s"', varargin{n});
    end
end

% Set parameters according to sp
if (strcmp(sp,'Ko') || strcmp(sp,'k'))
    speName = 'Kogia'; specChar = 'K'; 
    tfSelect = 80000; 
    dtHi = 0.5;  
    fLow = 70;   
    threshRL = 116;
    iciRange = [40, 130];
    dbRange = [100, 150];
    frRange = [80, 160];
    frdbwRange = [0, 80];
    durRange = [30, 111];
    durstep = 3;
elseif (strcmp(sp,'Zc') || strcmp(sp,'z') || strcmp(sp,'Cuviers'))
    speName = 'Cuviers'; specChar = 'Z'; 
    tfSelect = 40200;
    dtHi = 1.0; 
    fLow = 10;  
    threshRL = 121; 
    threshRMS = 55;
    ltsaContrast = 150; ltsaBright = 50;
    iciRange = [40, 750];
    dbRange = [90, 170];
    frdbwRange = [0, 80];
    durRange = [30, 300];
    durstep = 2;
    minDur = 60;
    dfManual = 100;
elseif (strcmp(sp,'Me') || strcmp(sp,'m'))
    speName = 'Gervais'; specChar = 'M'; 
    tfSelect = 40200;
    dtHi = 1.0; 
    fLow = 25; 
    threshRL = 121;
    iciRange = [40, 750];
    dbRange = [90, 170];
    frdbwRange = [0, 80];
    durRange = [30, 300];
    durstep = 2;
elseif (strcmp(sp,'BWG') || strcmp(sp,'g'))
    speName = 'BWG'; specChar = 'G'; 
    tfSelect = 40200;
    dtHi = 1.0; 
    fLow = 25;   
    threshRL = 121; 
elseif (strcmp(sp,'Md') || strcmp(sp,'d'))
    speName = 'BW31'; specChar = 'D'; 
    tfSelect = 40200; 
    dtHi = 1.0; 
    fLow = 10;  
    threshRL = 121; 
    threshRMS = 55;
    ltsaContrast = 150; ltsaBright = 50;
    iciRange = [40, 750];
    dbRange = [90, 170];
    frdbwRange = [0, 80];
    durRange = [30, 300];
    durstep = 2;
    minDur = 60;
    dfManual = 100;
elseif strcmpi(sp,'De')
    speName = 'Delphin';  
    dtHi = 0.6; 
    fLow = 10;   
    threshRL = 118;
    rlLow = threshRL - 6.9; rlHi = 190;
elseif (strcmp(sp,'Po') || strcmp(sp,'p'))
    speName = 'Porpoise'; 
    dtHi = 0.5; 
    fLow = 25;  
    threshRL = 100;
    rlLow = threshRL - 5; rlHi = 190;
    ltsaContrast = 250; ltsaBright = 100; 
elseif strcmpi(sp,'MFA')
    speName = 'MFA';  
    tfSelect = 4000; 
    ltsaMax = .5; 
    threshRL = 80;
    dtHi = 2;
    fLow = 2;  
    rlLow = threshRL - 5; rlHi = 180;
    dfManual = 10;   
elseif strcmpi(sp,'whs')
    speName = 'whs';
    ltsaMax = .5;
    dtHi = 2; 
    fLow = 5;   
    rlLow = 0; rlHi = 20;
    dfManual = 10;   
    ltsaContrast = 310; ltsaBright = 100; 
    ltsaLims = [5,30];
elseif strcmpi(sp,'Dl') 
    speName = 'Beluga'; 
    tfSelect = 45000;
    dtHi = 0.5;
    fLow = 20;  
    threshRL = 110;
    rlLow = threshRL - 5; rlHi = 170;
    ltsaContrast = 200; ltsaBright = 70;
    iciRange = [20, 500];
    dbRange = [90, 170];
    durRange = [10, 300];
    durstep = 2;
elseif (strcmp(sp,'Mm') || strcmp(sp,'Narwhal'))
    speName = 'Narwhal';
    tfSelect = 48000;
    dtHi = 1; 
    fLow = 2;
    threshRL = 100; %threshHiFreq = 25;
    %threshRMS = 95; threshPP = 140;
    ltsaContrast = 240; ltsaBright = 35;
%     dfManual = 100;
    minBout = 75; %minDur = 30; 
    %slope = 1.05;
    iciRange = [40, 1000];
    durRange = [10, 300];
    frRange = [fLow fHi];
    rawFileDur = 300; % it is not HARP data
%     N = 512;
elseif (strcmp(sp,'PM') || strcmp(sp,'pm') || strcmp(sp,'Pm'))
    speName = 'Pm'; 
    dtHi = 2; 
    fLow = 5;
    threshRL = 125; threshHiFreq = 30;
    threshRMS = 95; threshPP = 140;
    ltsaContrast = 180; ltsaBright = 73;
    dfManual = 100;
    minBout = 75; minDur = 60; 
    slope = 1.05;
    iciRange = [300, 2000];
    frRange = [fLow fHi];
    N = 512;
else
    warning('Unknown Species Type!!!')
end

%% create struct to return parameters
switch analysis
    case {'detEdit','mkLTSA'} 
        spParams.specchar = specChar;
        spParams.speName = speName;
        spParams.tfSelect = tfSelect;
        spParams.dtHi = dtHi;
        spParams.fLow = fLow;
        spParams.fHi = fHi;
        spParams.threshRL = threshRL;
        spParams.threshRMS = threshRMS;
        spParams.threshPP = threshPP;
        spParams.threshHiFreq = threshHiFreq;
        spParams.ltsaContrast = ltsaContrast;
        spParams.ltsaBright = ltsaBright;
        spParams.ltsaLims = ltsaLims;
        spParams.ltsaMax = ltsaMax;
        spParams.rlLow = rlLow;
        spParams.rlHi = rlHi;
        spParams.dfManual = dfManual;
        spParams.dfManual = dfManual;
        spParams.p1Low = p1Low;
        spParams.p1Hi = p1Hi;
        spParams.minBout = minBout;
        spParams.minDur = minDur;
        spParams.slope = slope;
        spParams.binDur = binDur;
        spParams.rawFileDur = rawFileDur;
        
        % apply default if user has not specified a value
        if exist('spParamsUser','var')
            for fn = fieldnames(spParamsUser)'
                spParams.(fn{1}) = spParamsUser.(fn{1});
            end
        end
    case {'modDet'} 
        spParams.tfSelect = tfSelect;
        spParams.threshRL = threshRL;
        spParams.dbRange = dbRange;
        spParams.iciRange = iciRange;
        spParams.frRange = frRange;
        spParams.frdbwRange = frdbwRange;
        spParams.durRange = durRange;
        spParams.durstep = durstep;
        spParams.N = N;
        spParams.gth = gth;
        spParams.minBout = minBout;
        spParams.p1Hi = p1Hi;
    case {'SumPPICIBin'}
        spParams.iciRange = iciRange;
        spParams.speName = speName;
        spParams.threshRL = threshRL;
        spParams.gth = gth;
        spParams.p1Hi = p1Hi;
        spParams.binDur = binDur;
    otherwise
        sprintf(['No analysis specified. Please add one of these options:\n',...
        'detEdit, mkLTSA or modDet'])
end