alternativePlot.m

function cell_sig_merged_array = alternativePlot(ica_segments, cluster, cell_sig, subPlotCols, sortedIdx, data_r, frames, fileNamesGreen, clusterSize, sweepDelay, sweepInterval, numberOfSweeps, sweepDuration,frameSteps)
f = figure;
plot1 = subplot(1,2,1);
plot2 = subplot(1,2,2);


drawEverything(1, subPlotCols, 1, size(cell_sig,2));
for i=1:size(cluster, 2)
    cell_sig_merged{i} = cell_sig(sortedIdx,:);
    cell_sig_merged{i} = mean(cell_sig_merged{i}(cluster{i},:), 1);
end

%convert cell_sig_merged to array
cell_sig_merged_array = zeros(size(cell_sig_merged,2), size(cell_sig_merged{1},2));
for i = 1:size(cell_sig_merged,2)
    cell_sig_merged_array(i,:) = cell_sig_merged{i};
end
%% add slider
%slider for selection of signals
imageSlider = uicontrol('Parent',f,'Style','slider',...
    'value',0, 'min',0, 'max', ceil(size(cell_sig_merged,2)/clusterSize),...
    'SliderStep', [1 1]/(ceil(size(cell_sig_merged,2)/clusterSize)),'Callback', @redrawPlot,...
    'units','normalized','Position',[0.1 0.01 0.3 0.03]);
%slider for selection of x interval of right plot
plotSlider = uicontrol('Parent',f,'Style','slider',...
    'value',0, 'min',0, 'max', ceil(size(cell_sig_merged{1},2)/frameSteps),...
    'SliderStep', [1 1]/(ceil(size(cell_sig_merged{1},2)/frameSteps)),'Callback', @redrawPlot,...
    'units','normalized','Position',[0.6 0.01 0.3 0.03]);
imagetxt = uicontrol('units','normalized','Style','text',...
    'Position',[0.1 0.04 0.3 0.03],...
    'String','Showing All ROIs');
plottxt = uicontrol('units','normalized','Style','text',...
    'Position',[0.6 0.04 0.3 0.03],...
    'String','Showing All Frames');

    function redrawPlot(~,~)
        val1 = round(imageSlider.Value);
        val2 = round(plotSlider.Value);
        
        %determine intervals for each value
        if val1 == ceil(size(cell_sig_merged,2)/clusterSize)
            iStart = (val1 - 1) * clusterSize + 1;
            iEnd = subPlotCols;
        else
            iStart = (val1 - 1) * clusterSize + 1;
            iEnd = clusterSize * val1;
        end
        if val1 == 0
            iStart = 1;
            iEnd = subPlotCols;
        end
        
        if val2 ==  ceil(size(cell_sig_merged{1},2)/frameSteps)
            kStart = (val2 - 1) * frameSteps + 1;
            kEnd = size(cell_sig_merged{1},2);
        else
            kStart = (val2 - 1) * frameSteps + 1;
            kEnd = frameSteps * val2;
        end
        if val2 == 0
            kStart = 1;
            kEnd = size(cell_sig_merged{1},2);
        end
        imagetxt.String = ['Showing ROI ' num2str(iStart) ' to ' num2str(iEnd) ' of ' num2str(subPlotCols)];
        plottxt.String = ['Showing Frame ' num2str(kStart) ' to ' num2str(kEnd) ' of ' num2str(size(cell_sig_merged{1},2))];
        drawEverything(iStart, iEnd, kStart, kEnd);
    end

    function drawEverything(imageStart, imageEnd, plotStart, plotEnd)
        cm = colormap(jet);
        tempImage = zeros(size(ica_segments, 2), size(ica_segments, 3), 3);
        
        for i = imageStart:imageEnd
            rgb = cm(round(64/subPlotCols * (i-1)+1),:);
            for k = cluster{i}
                mask = squeeze(ica_segments(sortedIdx(k),:,:));
                %transform mask to only outlines
                mask = imfill(mask, 'holes');
                mask = bwboundaries(mask);
                mask = mask{:};
                %create image with drawn lines between points
                linemask = zeros(size(ica_segments, 2), size(ica_segments, 3));
                for l = 1:size(mask,1)
                    linemask(mask(l,1),mask(l,2)) = 1;
                end
                for rgbIdx = 1:3
                    tempImage(:,:,rgbIdx) = tempImage(:,:,rgbIdx) + rgb(rgbIdx)*linemask;
                end
            end
        end
        %set pixels 0 which are smaller than 0, seems to happen in rare cases..
        for i = 1:3
            tempImage(:,:,i) = (tempImage(:,:,i) > 0).*tempImage(:,:,i);
        end
        tempImage = uint16(tempImage*65535);
        
        %calculate mean image
        meanImage = mean(data_r,3);
        maximum = max(meanImage(:));
        minimum = min(meanImage(:));
        meanImage = (meanImage - minimum)/(maximum-minimum);
        meanImage = uint16(imadjust(meanImage, [0, 1], [0, 1], 0.4)*65535);
        
        %set meanImage zero in every pixel which is not equal 0 in tempImage
        meanImage = meanImage.*uint16(tempImage(:,:,1) == 0);
        meanImage = meanImage.*uint16(tempImage(:,:,2) == 0);
        meanImage = meanImage.*uint16(tempImage(:,:,3) == 0);
        
        %copy meanImage in every colorchannel
        for i = 1:3
            tempImage(:,:,i) = tempImage(:,:,i) + meanImage;
        end
        
        axes(plot1);
        cla reset
        imshow(tempImage);
        
        %draw number in each roi
        for i = imageStart:imageEnd
            for drawNumberCt = cluster{i}
                number = sortedIdx(drawNumberCt);        %get position to draw number in
                mask = squeeze(ica_segments(number,:,:));
                cog = centerofgravity(mask);
                text(cog(2), cog(1), num2str(i), 'Color', 'white', 'FontSize', 15)
                
            end
        end
        
        
        
        axes(plot2);
        cla reset
        
        hold on
        cell_sigPlot = cell_sig(sortedIdx,:);
        
        
        
        signal = zeros(size(cluster,2),size(cell_sig,2));
        for i = imageStart:imageEnd
            
            for clusterIdx = cluster{i}
                %subtract minimum value
                minimum = min(cell_sigPlot(clusterIdx,:));
                cell_sigPlot(clusterIdx,:) = cell_sigPlot(clusterIdx,:) - minimum;
                %norm cell signals
                integral = median(cell_sigPlot(clusterIdx,:));
                cell_sigPlot(clusterIdx,:)=cell_sigPlot(clusterIdx,:)/abs(integral);
            end
            %mean value of all cluster signals
            signal(i,:) = mean(cell_sigPlot(cluster{i},:), 1);
            %add maximum position from signal from before
            if i ~= 1
                %maximum = max(signal(i-1,:));
                maximum = max(max(cell_sigPlot(cluster{i-1},:)));
            else
                maximum = 0;
            end
            signal(i,:) = signal(i,:) + maximum;
            rgb = cm(round(64/subPlotCols * (i-1)+1),:);
            plot(signal(i,:), 'Color', rgb);
            %text(size(signal,2), maximum, num2str(i))
            
            text(plotEnd, maximum, num2str(i))
            %plot single components dotted
            for clusterIdx = cluster{i}
                cell_sigPlot(clusterIdx,:) = cell_sigPlot(clusterIdx,:) + maximum;
                plot(cell_sigPlot(clusterIdx, :),':', 'Color', rgb);
            end
        end
        xlim([plotStart,plotEnd]);
        %maximum = max(cell_sigPlot(:));
        ylim auto;%([0, maximum]);
        %draw vertical lines
        %ending of trials:
        for i = 1:(size(frames,2)-1)
            vline(frames(i), 'black', fileNamesGreen(i).name);
            for s=1:numberOfSweeps
                %draw begin of sweep
                vline(frames(i)+sweepDelay+s*sweepInterval, 'b');
                %draw end of sweep
                vline(frames(i)+sweepDelay+s*sweepInterval+sweepDuration, 'r');
            end
        end
        xlabel('Frames');
        ylabel('Intensity + Arbitrary Offset');
    end
end