Diagnostic code which does not effect main Homer3 operation (so version number stays the same):

        if strcmp(obj.config.InclArchivedFunctions, 'Yes')

            userfuncdir{end+1} = fullpath([userfuncdir{1}, 'Archive/']); %#ok<*AGROW>

        end

    elseif strcmp(dirs(ii).name, 'Sim')

        obj.config = struct('InclArchivedFunctions','');

        obj.config.InclArchivedFunctions = cfg.GetValue('Include Archived User Functions');        

        if strcmp(obj.config.InclArchivedFunctions, 'Yes')

            userfuncdir{end+1} = fullpath([userfuncdir{1}, 'Sim/']); %#ok<*AGROW>

        end

    else

        userfuncdir{end+1} = filesepStandard(fullpath([userfuncdir{1}, dirs(ii).name]));

    end

% SYNTAX:

% dod = hmrR_Intensity2OD_sim( intensity )

%

% UI NAME:

% Intensity_to_Delta_OD

%

% DESCRIPTION:

% Converts intensity data to optical density

%

% INPUT:

% intensity - SNIRF data type where the d matrix is intensity

%

% OUTPUT:

% dod - SNIRF data type where the d matrix is change in optical density

%

% USAGE OPTIONS:

% Intensity_to_Delta_OD: dod = hmrR_Intensity2OD_sim(data)

%

function dod = hmrR_Intensity2OD_sim( intensity )

% convert to dod

dod = DataClass().empty();

for ii=1:length(intensity)

    dod(ii) = DataClass();

    d = intensity(ii).GetDataTimeSeries();

    dod(ii).SetTime(intensity(ii).GetTime());

    dod(ii).SetDataTimeSeries(d);

    dod(ii).SetMl(intensity(ii).GetMl());

    dod(ii).SetDataTypeDod();

end

% SYNTAX:

% function data_dc = hmrR_MotionCorrectCbsi_sim(data_dc, mlActAuto, turnon)

%

% UI NAME:

% Cbsi_Motion_Correction

%

% DESCRIPTION:

% Perform a correlation-based signal improvement of the concentration

% changes in order to correct for motion artifacts.

% The algorithm follows the procedure described by

% Cui et al.,NeuroImage, 49(4), 3039-46 (2010).

%

% INPUTS:

% data_dc:   Concentration changes (it works with HbO and HbR)

% mlActAuto: 

% turnon:    Skip this function if turnon=1. Otherwise execute function.

%            Default is to execute function if this does not exist.

%

%

% OUTPUTS:

% data_dc:  dc after correlation-based signal improvement correction, same

%           size as dc (Channels that are not in the active ml remain unchanged)

%

% USAGE OPTIONS:

% Cbsi_Motion_Correction: dc = hmrR_MotionCorrectCbsi_sim(dc, mlActAuto, turnon)

%

% PARAMETERS:

% turnon: 1

%

% PREREQUISITES:

% Delta_OD_to_Conc: dc = hmrR_OD2Conc( dod, probe, ppf )

%

% LOG:

% created 10-17-2012, S. Brigadoi

%

function data_dc = hmrR_MotionCorrectCbsi_sim(data_dc, mlActAuto, turnon)

% Added turn on/off option

if ~exist('turnon','var')

    turnon = 1;

end

if turnon==0

    return;

end

for iBlk = 1:length(data_dc)

    dc0 = data_dc(iBlk).GetDataTimeSeries();

    ml0 = data_dc(iBlk).GetMeasurementList();

    [dc, ~, ~, order] = data_dc(iBlk).GetDataTimeSeries('reshape');

    ml = data_dc(iBlk).GetMeasurementList('matrix','reshape');

    dcCbsi = dc;

    dcCbsi(:,order) = dcCbsi(:,:);

    data_dc(iBlk).SetDataTimeSeries(dcCbsi);

end

% SYNTAX:

% data_d = hmrR_MotionCorrectSplineSG_sim(data_d, mlActAuto, p, FrameSize_sec, turnon)

%

% UI NAME:

% SplineSG_Motion_Correction

%

% DESCRIPTION:

% The function first identifies the baseline shifts and spikes in the signal. The baseline shifts are corrected using

% a spline interpolation method. The remaining spikes are corrected by Savitzky-Golay filtering, which is a digital smoothing filter

% that substitutes each value of the signal series with a new value obtained by applying a cubic fitting to a subset of adjacent data points.

% The length of the subset is defined by the parameter FrameSize_sec.

% The method is described in the following paper.

% Citation: Jahani et al., Neurophotonics, 2018; doi: 10.1117/1.NPh.5.1.015003. 

% 

% INPUTS:

% data_d:        SNIRF object containing time course data

% mlActAuto:

% p:             Parameter p used in the spline interpolation. The value

%                recommended in the literature is 0.99. Use -1 if you want to skip this

%                motion correction.

% FrameSize_sec: The step lenght in seconds that a least-squares minimization will be applied using a cubic Savitzky-Golay filter.  

% turnon:        Optional argument to enable/disable this function in a processing stream chain

%

% OUTPUTS:

% data_d:        SNIRF object containing time course data after spline interpolation correction

%

% USAGE OPTIONS:

% SplineSG_Motion_Correction: dod = hmrR_MotionCorrectSplineSG_sim(dod, mlActAuto, p, FrameSize_sec, turnon)

%

% PARAMETERS:

% p: 0.99

% FrameSize_sec: 10

% turnon: 1

%

% 

% PREREQUISITES:

% Intensity_to_Delta_OD: dod = hmrR_Intensity2OD( intensity )

%

% LOG:

% Sahar Jahani, October 2017

function data_d = hmrR_MotionCorrectSplineSG_sim(data_d, mlActAuto, p, FrameSize_sec, turnon)

if ~exist('turnon','var')

   turnon = 1;

end

if turnon==0

    return;

end

if isempty(mlActAuto)

    mlActAuto = cell(length(data_d),1);

end

for iBlk = 1:length(data_d)

    dod = data_d(iBlk).GetDataTimeSeries();               

    data_d(iBlk).SetDataTimeSeries(dod);

end