Incorporated mlActMan and Auto to tCCAGLM function

% SYNTAX:

% [Aaux, rcMap] = hmrR_tCCA(data, aux, probe, runIdx, subjIdx, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

% [Aaux, rcMap] = hmrR_tCCA(data, aux, probe, runIdx, subjIdx, mlActMan, mlActAuto, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_on, runIdxResting, tResting)

%

% UI NAME:

% hmrR_tCCA

% probe - SNIRF probe type containing source/detector geometry data (See SNIRF Spec for more details)

% runIdx - the index of the run in a multi-run session

% subjIdx - the index of the subject in a group 

% mlActMan: Cell array of vectors, one for each time base in data, specifying 

%        active/inactive channels with 1 meaning active, 0 meaning inactive

% mlActAuto: Cell array of vectors, one for each time base in data, specifying 

%        active/inactive channels with 1 meaning active, 0 meaning inactive

% flagtCCA - turns the function on / off

% tCCAparams - These are the parameters for tCCA function

%            1 - 1 timelag [s]

%          if you do not want to regress the short separation measurements.

%          Follows the static estimate procedure described in Gagnon et al (2011).

%          NeuroImage, 56(3), 1362?1371.

% ss_ch_inx - short separation channel index, starts from one ends with the

% total number of short separation channels

% ss_ch_on - Include short separation channels in tCCA, on (1) off (0)

% NOTE Please include hmrR_prune_channel function to remove noisy short

% separation channels

% runIdxResting - resting state run index

% tResting - start/stop time [s] to use from resting data for tCCA training

%

%           Only relevant when flagICRegressors = 1.

%

% USAGE OPTIONS:

% hmrR_tCCA_Concentration_Data: [Aaux, rcMap] = hmrR_tCCA(dc, aux, probe, iRun, iSubj, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

% hmrR_tCCA_OD_Data: [Aaux, rcMap] = hmrR_tCCA(dod, aux, probe, iRun, iSubj, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

% hmrR_tCCA_Concentration_Data: [Aaux, rcMap] = hmrR_tCCA(dc, aux, probe, iRun, iSubj, mlActMan, mlActAuto, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_on, runIdxResting, tResting)

% hmrR_tCCA_OD_Data: [Aaux, rcMap] = hmrR_tCCA(dod, aux, probe, iRun, iSubj, mlActMan, mlActAuto, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_on, runIdxResting, tResting)

%

%

% PARAMETERS:

% tCCAparams: [3 0.08 0.3]

% tCCAaux_inx: [1 1 1 1 0 0 0 0]

% rhoSD_ssThresh: 15.0

% ss_ch_inx: [1 2 3 4 5]

% ss_ch_on: 1

% runIdxResting: 1

% tResting: [30 210]

%

function [Aaux, rcMap] = hmrR_tCCA(data, aux, probe, runIdx, subjIdx, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

function [Aaux, rcMap] = hmrR_tCCA(data, aux, probe, runIdx, subjIdx, mlActMan, mlActAuto, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_on, runIdxResting, tResting)

%% COMMENTS/THOUGHTS/QUESTIONS ALEX

% 2) Output canonical correlation coefficients as quality metric?

% checksum for tCCA filter file

chksm = int16(7*flagICRegressors + sum(11*tCCAparams(:)) + sum(13*tCCAaux_inx(:)) + 17*rhoSD_ssThresh + 19*runIdxResting + sum(23*tResting(:)));

% initialize active channel list

if isempty(mlActMan)

    mlActMan = cell(length(data),1);

end

if isempty(mlActAuto)

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

end

if flagtCCA

    SrcPos  = probe.GetSrcPos();

        t        = data(iBlk).GetTime();

        ml       = data(iBlk).GetMeasListSrcDetPairs();

        fq = 1/(t(2)-t(1));

% get  a list of active channels

        if isempty(mlActMan{iBlk})

            mlActMan{iBlk} = ones(size(ml,1)*2,1);

        end

        if isempty(mlActAuto{iBlk})

            mlActAuto{iBlk} = ones(size(ml,1)*2,1);

        end

        MeasListAct = mlActMan{iBlk} & mlActAuto{iBlk};

        %% find the list of short and long distance channels

        lst = 1:size(ml,1);

        rhoSD = zeros(length(lst),1);

            rhoSD(iML) = sum((SrcPos(ml(lst(iML),1),:) - DetPos(ml(lst(iML),2),:)).^2).^0.5;

            posM(iML,:) = (SrcPos(ml(lst(iML),1),:) + DetPos(ml(lst(iML),2),:)) / 2;

        end

        lstSS = lst(find(rhoSD<=rhoSD_ssThresh)); %#ok<*FNDSB>

        lstLS = lst(find(rhoSD>rhoSD_ssThresh));

        lstSS = lst(find(rhoSD<=rhoSD_ssThresh &  MeasListAct(lst)==1)); %#ok<*FNDSB>

        lstLS = lst(find(rhoSD>rhoSD_ssThresh & MeasListAct(lst)==1));

        if length(lstSS) == 0

           errordlg('No short separation channels fall within rhoSD_ssThresh!');

        end

        if ss_ch_inx ~= 0

            lstSS = lstSS(ss_ch_inx);

        end

        %% get long and short separation data

        if strncmp(datatype{1}, 'Hb', 2)

            end

        end

        % AUX signals + add ss signal if it exists

        if ~isempty(d_short) & exist('AUX')

        if ~isempty(d_short) & exist('AUX') & ss_ch_on == 1

            AUX = [AUX, d_short]; % this should be of the current run

        elseif ss_ch_inx ~= 0

        elseif ss_ch_on ~= 0

            AUX = d_short;

        else

            msg = 'No auxiliary or short separation measurement to regress out.';