hmrR_OD2Conc_3 and adding 2 wavelength spec to hmrR_OD2Conc docs

% OD_to_Conc

%

% DESCRIPTION:

% Convert OD to concentrations

% Convert OD to concentrations. For use with 2-wavelength data only: use

% hmrR_OD2Conc_3 or hmrR_OD2Conc_multi for 3 or more wavelengths.

%

% INPUTS:

% dod: SNIRF.data container with the Change in OD tim course 

% probe: SNIRF.probe container with the source/detector geometry

% ppf: Partial path length factors for each wavelength. If there are 2 wavelengths 

%      of data, then this is a vector of 2 elements.  Typical value is ~6 for each 

% ppf: Partial path length factors for each wavelength. This is a vector of 

%      of 2 elements, one for each wavelength.  Typical value is ~6 for each 

%      wavelength if the absorption change is uniform over the volume of tissue measured. 

%      To approximate the partial volume effect of a small localized absorption change 

%      within an adult human head, this value could be as small as 0.1. It is recommended 

%      to use default values of 1 1 which will result in concentration units of 

%      molar ppf such that the user can then divide by an estimated ppf at any future 

%      point to estimate what the molar concentration change would be.%

%      within an adult human head, this value could be as small as 0.1. Convention is 

%      becoming to set ppf=1 and to not divide by the source-detector separation such that 

%      the resultant "concentration" is in units of Molar mm (or Molar cm if those are the 

%      spatial units). This is becoming wide spread in the literature but there is no 

%      fixed citation. Use a value of 1 to choose this option.

%

% OUTPUTS:

% dc: SNIRF.data container with the concentration data 

% SYNTAX:

% dc = hmrR_OD2Conc_new( dod, probe, ppf )

%

% UI NAME:

% OD_to_Conc

%

% DESCRIPTION:

% Convert OD to concentrations. For use with 3-wavelength data only.

%

% INPUTS:

% dod: SNIRF.data container with the Change in OD tim course 

% probe: SNIRF.probe container with the source/detector geometry

% ppf: Partial path length factors for each wavelength. This is a vector of  

%      3 elements, one for each wavelength.  Typical value is ~6 for each 

%      wavelength if the absorption change is uniform over the volume of tissue measured. 

%      To approximate the partial volume effect of a small localized absorption change 

%      within an adult human head, this value could be as small as 0.1. Convention is 

%      becoming to set ppf=1 and to not divide by the source-detector separation such that 

%      the resultant "concentration" is in units of Molar mm (or Molar cm if those are the 

%      spatial units). This is becoming wide spread in the literature but there is no 

%      fixed citation. Use a value of 1 to choose this option.

%

% OUTPUTS:

% dc: SNIRF.data container with the concentration data 

%

% USAGE OPTIONS:

% Delta_OD_to_Conc: dc = hmrR_OD2Conc_new( dod, probe, ppf )

%

% PARAMETERS:

% ppf: [1.0, 1.0, 1.0]

%

function dc = hmrR_OD2Conc_new( dod, probe, ppf )

dc = DataClass().empty();

for ii=1:length(dod)

    dc(ii) = DataClass();

    Lambda = probe.GetWls();

    SrcPos = probe.GetSrcPos();

    DetPos = probe.GetDetPos();

    nWav   = length(Lambda);

    ml     = dod(ii).GetMeasList();

    y      = dod(ii).GetDataTimeSeries();

    if length(ppf)~=nWav

        errordlg('The length of PPF must match the number of wavelengths in SD.Lambda');

        dc = zeros(size(y,1),3,length(find(ml(:,4)==1)));

        return

    end

    if ~isempty(find(ppf==1))

        ppf = ones(size(ppf));

    end

    nTpts = size(y,1);

    e = GetExtinctions(Lambda);

    e = e(:,1:2) / 10; % convert from /cm to /mm

    einv = inv( e'*e )*e';

    lst = find( ml(:,4)==1 );

    y2 = zeros(nTpts, 3*length(lst));

    for idx=1:length(lst)

        k = 3*(idx-1)+1;

        idx1 = lst(idx);

        idx2 = find( ml(:,4)>1 & ml(:,1)==ml(idx1,1) & ml(:,2)==ml(idx1,2) );

        rho = norm(SrcPos(ml(idx1,1),:)-DetPos(ml(idx1,2),:));

        if ppf(1)~=1

            y2(:,k:k+1) = ( einv * (y(:,[idx1 idx2'])./(ones(nTpts,1)*rho*ppf))' )';

        else

            y2(:,k:k+1) = ( einv * (y(:,[idx1 idx2'])./(ones(nTpts,nWav)))' )';

        end

        y2(:,k+2) = y2(:,k) + y2(:,k+1);

        dc(ii).AddChannelHbO(ml(idx1,1), ml(idx1,2));

        dc(ii).AddChannelHbR(ml(idx1,1), ml(idx1,2));

        dc(ii).AddChannelHbT(ml(idx1,1), ml(idx1,2));

    end   

    dc(ii).SetDataTimeSeries(y2);

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

end

% OD_to_Conc

%

% DESCRIPTION:

% Convert OD to concentrations

% Convert OD to concentrations. For use with 2-wavelength data only: use

% hmrR_OD2Conc_3 or hmrR_OD2Conc_multi for 3 or more wavelengths.

%

% INPUTS:

% dod: SNIRF.data container with the Change in OD tim course 

% probe: SNIRF.probe container with the source/detector geometry

% ppf: Partial path length factors for each wavelength. If there are 2 wavelengths 

%      of data, then this is a vector of 2 elements.  Typical value is ~6 for each 

% ppf: Partial path length factors for each wavelength. This is a vector of 

%      of 2 elements, one for each wavelength.  Typical value is ~6 for each 

%      wavelength if the absorption change is uniform over the volume of tissue measured. 

%      To approximate the partial volume effect of a small localized absorption change 

%      within an adult human head, this value could be as small as 0.1. Convention is