Microstim_FF-FB/SCRIPTS/FUNCTIONS/SUPPORT/preProcessV4MS.m

function V4MS = preProcessV4MS(V4MS,EffectWindow)


%     excitatoryWindow = [0 0.05];
%     supressionWindow = [0.25 2];

    excitatoryWindow = EffectWindow.exc;
    supressionWindow = EffectWindow.sup;


    nMaxs = 10;
    THRS = [];

    DIFFS = nan(3,length(V4MS.iCH), 19);
    for soa = 1:length(V4MS.META.SOAS)

        iTIME       = V4MS.TIME > (V4MS.META.SOAS(soa)) & V4MS.TIME < (V4MS.META.SOAS(soa)+0.025); 
        iTIMEplot   = V4MS.TIME > (V4MS.META.SOAS(soa)-0.01) & V4MS.TIME < (V4MS.META.SOAS(soa)+0.025+0.01); 
        plotDIFF    = squeeze(V4MS.ALLCHS(:,iTIMEplot,soa+1)-V4MS.ALLCHS(:,iTIMEplot,1));
        DIFFS(soa,:,:) = squeeze(V4MS.ALLCHS(:,iTIME,soa+1)-V4MS.ALLCHS(:,iTIME,1));
    end
    %%

    DIFF = squeeze(nanmean(DIFFS,1));
    MEANS = nan(1,size(DIFF,1));

    for ch = 1:size(DIFF,1)
        temp = sort(squeeze(DIFF(ch,:)));
        MEANS(ch) = nanmean(temp(end-(nMaxs-1):end));
    end

    temp = sort(MEANS);temp = temp(~isnan(temp));ind = round(0.75*length(temp));
    THRS = temp(ind);
    indS = MEANS < THRS;
    %%
    % Remove Channels below the threshold

    for chu = 1:size(V4MS.CHUNKS,2)    
        sign = V4MS.CHUNKS(chu).DATA;    
        for bl = 1:size(sign,1)        
            for ch = 1:size(sign,3)            
                diffs = nan(3,19);
                for soa = 1:length(V4MS.META.SOAS)   
                    iTIME       = V4MS.TIME > (V4MS.META.SOAS(soa)) & V4MS.TIME < (V4MS.META.SOAS(soa)+0.025); 
                    diffs(soa,:) = squeeze(sign(bl,iTIME,ch,soa+1)-sign(bl,iTIME,ch,1));
                end
    %             keyboard
                diff = sort(squeeze(nanmean(diffs,1))); %CHANGED 2015-07-06, before diff = sort(squeeze(nanmean(diffs,1)));
                MAX = nanmean(diff(end-(nMaxs-1):end));

                if MAX > THRS
                    sign(bl,:,ch,:) = nan;
                end            
            end        
        end
        V4MS.CHUNKS(chu).DATA = sign;
    end
    %%
    % Now procced to average for every chunk. Then take every electrode as a unit. 

    for chu = 1:size(V4MS.CHUNKS,2)    
        sign = V4MS.CHUNKS(chu).DATA;
        V4MS.CHUNKS(chu).AVE =  squeeze(nanmean(sign,1));
    end

    % Make a copy and check whther each electrode should or suoldn't be included.


    for chu = 1:size(V4MS.CHUNKS,2)

        V4MS.CHUNKS(chu).CLEAN.AVE = V4MS.CHUNKS(chu).AVE;
        V4MS.CHUNKS(chu).CLEAN.IND = nan(size(V4MS.CHUNKS(chu).MESBL,1),1);

        for ch = 1:size(V4MS.CHUNKS(chu).MESBL,1)
            tempSIGNIF = zeros(3,1);
            for soa = 1:3
                tempSIGNIF(soa) = ttest2(squeeze(V4MS.CHUNKS(chu).MESBL(ch,soa,:)),squeeze(V4MS.CHUNKS(chu).MESMS(ch,soa,:)));
            end

            if ~isnan(sum(tempSIGNIF)) && sum(tempSIGNIF)~= 0 && ~isnan(nanmean(nanmean(V4MS.CHUNKS(chu).AVE(:,ch,:))))
                V4MS.CHUNKS(chu).CLEAN.IND(ch) = 1;
            elseif isnan(sum(tempSIGNIF)) || isnan(nanmean(nanmean(V4MS.CHUNKS(chu).AVE(:,ch,:))))
                V4MS.CHUNKS(chu).CLEAN.IND(ch) = nan;
            else
                V4MS.CHUNKS(chu).CLEAN.IND(ch) = 0;
                V4MS.CHUNKS(chu).CLEAN.AVE(:,ch,:) = nan;
            end
        end

    end

    % Concatenate all elctrodes together

    V4MS.UNITS = [];
    V4MS.CLEAN.UNITS = [];
    V4MS.CLEAN.UNITSIND = [];
    V4MS.MONKEY         = [];
    V4MS.RFDATA         = [];
    V4MS.PERF           = [];
    V4MS.PERF_MONKEY = [];

    for chu = 1:size(V4MS.CHUNKS,2)

        V4MS.UNITS          = cat(2,V4MS.UNITS,V4MS.CHUNKS(chu).AVE);
        V4MS.CLEAN.UNITS    = cat(2,V4MS.CLEAN.UNITS,V4MS.CHUNKS(chu).CLEAN.AVE);
        V4MS.CLEAN.UNITSIND = [V4MS.CLEAN.UNITSIND; V4MS.CHUNKS(chu).CLEAN.IND];
        V4MS.MONKEY         = cat(2,V4MS.MONKEY,V4MS.CHUNKS(chu).INFO.MONKEY);
        V4MS.RFDATA         =  cat(1,V4MS.RFDATA,V4MS.CHUNKS(chu).INFO.RFDATA);
        if nansum(V4MS.CHUNKS(chu).CLEAN.IND)
            V4MS.PERF         =  cat(1,V4MS.PERF,V4MS.CHUNKS(chu).PERF); 
            V4MS.PERF_MONKEY=   [V4MS.PERF_MONKEY ones(1,size(V4MS.CHUNKS(chu).PERF,1))*(strcmp(V4MS.CHUNKS(chu).INFO.MONKEY{1},'C')+1)];
        end
    end

    for m = 1:length(V4MS.MONKEY)
        if isempty(V4MS.MONKEY{m})
            V4MS.MONKEY{m} = 'B';
        end
    end

    V4MS.CLEAN.UNITSIND(isnan(V4MS.CLEAN.UNITSIND)) = 0;

    %%
    % compute average accross channels

    V4MS.AVE = squeeze(nanmean(V4MS.UNITS,2));

    V4MS.AVE_NON_SIG = squeeze(nanmean(V4MS.UNITS(:,~V4MS.CLEAN.UNITSIND,:),2));

    % compute average accross channels with an effect

    V4MS.CLEAN.AVE = squeeze(nanmean(V4MS.CLEAN.UNITS,2));

    % Effect for all channels

    EFFECT = nan(3,size(V4MS.UNITS,2));
    S = 10;
    BINS = 40;
    for soa = 1:3
        for ch = 1:size(V4MS.UNITS,2);

            iT = V4MS.TIME > (V4MS.META.SOAS(soa)+supressionWindow(1)) & V4MS.TIME < (V4MS.META.SOAS(soa)+supressionWindow(2));        
            EFFECT(soa,ch) = nanmean(1*squeeze(V4MS.UNITS(iT,ch,soa+1) - V4MS.UNITS(iT,ch,1)));

        end

    end

    V4MS.EFFECT = EFFECT;

    % Effect for significative channels

    EFFECT = nan(3,size(V4MS.CLEAN.UNITS,2));
    S = 10;
    BINS = 40;
    for soa = 1:3
        for ch = 1:size(V4MS.CLEAN.UNITS,2);        
            iT = V4MS.TIME > (V4MS.META.SOAS(soa)+supressionWindow(1)) & V4MS.TIME < (V4MS.META.SOAS(soa)+supressionWindow(2));       
            EFFECT(soa,ch) = nanmean(1*squeeze(V4MS.CLEAN.UNITS(iT,ch,soa+1) - V4MS.CLEAN.UNITS(iT,ch,1)));        
        end
    end

    V4MS.CLEAN.EFFECT = EFFECT;
    
    
    % Excitatory Effect for all channels

    EXCIT_EFFECT = nan(3,size(V4MS.UNITS,2));
    S = 10;
    BINS = 40;
    for soa = 1:3
        for ch = 1:size(V4MS.UNITS,2);

            iT = V4MS.TIME > (V4MS.META.SOAS(soa)+excitatoryWindow(1)) & V4MS.TIME < (V4MS.META.SOAS(soa)+excitatoryWindow(2));        
            EXCIT_EFFECT(soa,ch) = nanmean(1*squeeze(V4MS.UNITS(iT,ch,soa+1) - V4MS.UNITS(iT,ch,1)));

        end

    end

    V4MS.EXCIT_EFFECT = EXCIT_EFFECT;

    % Effect for significative channels

    EXCIT_EFFECT = nan(3,size(V4MS.CLEAN.UNITS,2));
    S = 10;
    BINS = 40;
    for soa = 1:3
        for ch = 1:size(V4MS.CLEAN.UNITS,2);        
            iT = V4MS.TIME > (V4MS.META.SOAS(soa)+excitatoryWindow(1)) & V4MS.TIME < (V4MS.META.SOAS(soa)+excitatoryWindow(2));       
            EXCIT_EFFECT(soa,ch) = nanmean(1*squeeze(V4MS.CLEAN.UNITS(iT,ch,soa+1) - V4MS.CLEAN.UNITS(iT,ch,1)));        
        end
    end

    V4MS.CLEAN.EXCIT_EFFECT = EXCIT_EFFECT;

end