Create hmrR_CrossCorrelation.m

% SYNTAX:

% [cc, ml, cc_thresh] = hmrR_CrossCorrelation(data, cc_thresh, plot_on)

%

% UI NAME:

% hmrR_CrossCorrelation

%

% DESCRIPTION:

% This script calculates cross correlation across all channel pairs.

%

%

% INPUTS:

% data - this is the concentration data with dimensions #time points x [HbO/HbR/HbT] x #channels

% cc_thresh - cross correlation theshold, sets any correlation below cc_thresh to 0 in plots (display purpose only)

% plot_on - (1) displays cross correlation for HbO and HbR for each run; (0) no display

%

% OUTPUTS:

% cc -  cross correlation matrix

% ml -  measurement list

% cc_thresh - cross correlation theshold, sets any correlation below cc_thresh to 0 in plots (display purpose only)

%

% USAGE OPTIONS:

% hmrR_CrossCorrelation_conc: [cc, ml, cc_thresh] = hmrR_CrossCorrelation(dc, cc_thresh, plot_on)

%

% PARAMETERS:

% cc_thresh: 0.4

% plot_on: 0

%

% PREREQUISITES:

% Delta_OD_to_Conc: dc = hmrR_OD2Conc( dod, ppf )

function [cc, ml, cc_thresh] = hmrR_CrossCorrelation(data, cc_thresh, plot_on)

for iBlk=1:length(data)

    y      = data(iBlk).GetDataTimeSeries('reshape');

    ml     = data(iBlk).GetMeasListSrcDetPairs();

end

% HbO

dc = squeeze(y(:,1,:));

dc = (dc-ones(length(dc),1)*mean(dc,1))./(ones(length(dc),1)*std(dc,[],1));

cc(:,:,1) = dc'*dc / length(dc);

% HbR

dc = squeeze(y(:,2,:));

dc = (dc-ones(length(dc),1)*mean(dc,1))./(ones(length(dc),1)*std(dc,[],1));

cc(:,:,2) = dc'*dc / length(dc);

%% plot

if plot_on == 1

    nch = length(ml);

    tlabel = '';

    for ii = 1:length(ml)

        tlabel = sprintf( '%s,''%c%d''',tlabel,char(64+ml(ii,1)), ml(ii,2) );

    end

    tlabel(1) = [];

    % HbO

    figure;

    cc0 = cc(:,:,1);

    cc0(find(abs(cc(:,:,1))<cc_thresh))=0;

    imagesc(cc0,[-1 1])

    colorbar

    set(gca,'xtick',[1:nch])

    set(gca,'xticklabel',eval(sprintf('{%s}', tlabel)) )

    set(gca,'ytick',[1:nch])

    set(gca,'yticklabel',eval(sprintf('{%s}', tlabel)) )

    title( 'HbO Cross-Correlation')

    % HbR

    figure;

    cc0 = cc(:,:,2);

    cc0(find(abs(cc(:,:,2))<cc_thresh))=0;

    imagesc(cc0,[-1 1])

    colorbar

    set(gca,'xtick',[1:nch])

    set(gca,'xticklabel',eval(sprintf('{%s}', tlabel)) )

    set(gca,'ytick',[1:nch])

    set(gca,'yticklabel',eval(sprintf('{%s}', tlabel)) )

    title( 'HbR Cross-Correlation')

end

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