Add Example_RunFuncOffline

function PlotData(t, y, hbType, channels)

% Plot always to 

hf = 5; 

try

    close(hf);

catch

end

% y = y*1e6;

figure(hf);

axes;

p = get(gcf, 'position');

set(gcf, 'position', [p(1), p(2), p(3)*1.3, p(4)]);

hold on;

for iHb = 1:length(hbType)

    for iCh = 1:length(channels)

        plot(t, y(:, hbType(iHb), channels(iCh)));

    end

end

xlim([min(t), max(t)]);

hold off;

function [y, t] = Raw_to_DeltaConc_Example(filename, hbType, channels)

%

%    Example 1:   Plot channel 1 delta HbO concentration, derived from

%                 acquisition file test.snirf

%

%       cd '<root folder>\Homer3\UnitTests\Example_RunFuncOffline'

%       Raw_to_DeltaConc_Example('./test.snirf');

%    

%    Example 2:   Plot channels 1 and 2 delta HbR concentration, derived 

%                 from acquisition file test.snirf

%

%       cd '<root folder>\Homer3\UnitTests\Example_RunFuncOffline'

%       Raw_to_DeltaConc_Example('./test.snirf', 2, [1,2]);

%    

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Parse args 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Arg 1

[pname, fname] = fileparts(filename);

% Arg 2:  Hb type - {1 -> HbO,  2 -> HbR,  3 -> HbT}

if ~exist('hbType','var') || isempty(hbType)

    hbType   = 1;

end

% Arg 3: 

if ~exist('channels','var') || isempty(channels)

    channels = 1;

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Load acquisition file 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

acquired = SnirfClass([pname, '/', fname, '.snirf']);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Call sequence of user functions to get from acquired data 

% to delta concentration 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

dod = hmrR_Intensity2OD(acquired.data); 

dod = hmrR_BandpassFilt(dod, 0.01, 0.50);

dc  = hmrR_OD2Conc_new(dod, acquired.probe, [1,1]);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Extract plot data from output of last function 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

t = dc.time;

y = dc.GetDataTimeSeries('reshape');

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Plot data

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

PlotData(t, y, hbType, channels);

function [y, t] = Raw_to_HRF_Example(filename, hbType, channels)

%

%    Example 1:   Plot channel 1 HbO HRF, derived from acquisition 

%                 file test.snirf

%

%       cd '<root folder>\Homer3\UnitTests\Example_RunFuncOffline'

%       Raw_to_HRF_Example('./test.snirf');

%    

%    Example 2:   Plot channels 1 and 2 HbT HRF, derived from acquisition file test.snirf

%                 

%       cd '<root folder>\Homer3\UnitTests\Example_RunFuncOffline'

%       Raw_to_HRF_Example('./test.snirf', 3, [1,2]);

%    

%    Example 3:   Plot channel 2 HbO and HbR HRF, derived from acquisition

%                 file test.snirf

%

%       cd '<root folder>\Homer3\UnitTests\Example_RunFuncOffline'

%       Raw_to_HRF_Example('./test.snirf', [1,2], 2);

%    

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Parse args 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Arg 1

[pname, fname] = fileparts(filename);

if isempty(pname)

    pname = pwd;

end

% Arg 2:  Hb type - {1 -> HbO,  2 -> HbR,  3 -> HbT}

if ~exist('hbType','var') || isempty(hbType)

    hbType   = 1;

end

% Arg 3: 

if ~exist('channels','var') || isempty(channels)

    channels = 1;

end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Load acquisition file 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Acquired data (See SNIRF spec for list of acquired data parameters) 

acquired = SnirfClass([pname, '/', fname, '.snirf']);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% String together user functions to get from acquired data 

% to HRF

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

dod   = hmrR_Intensity2OD(acquired.data); 

dod   = hmrR_BandpassFilt(dod, 0.01, 0.50);

dc    = hmrR_OD2Conc_new(dod, acquired.probe, [1,1]);

dcAvg = hmrR_BlockAvg (dc, acquired.stim, [-2,20]);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Extract plot data from output of last function 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

t = dcAvg.time;

y = dcAvg.GetDataTimeSeries('reshape');

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Plot data

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

PlotData(t, y, hbType, channels);