added numbers in plot

alternativePlot.asv

@@ -0,0 +1,94 @@
+function cell_sig_merged = alternativePlot(ica_segments, cluster, cell_sig, subPlotCols, sortedIdx, data_r)
+cm = colormap(hsv);
+tempImage = zeros(size(ica_segments, 2), size(ica_segments, 3), 3);
+
+for i = 1:subPlotCols
+    rgb = cm(round(64/subPlotCols * (i-1)+1),:);
+    for k = cluster{i}
+        for rgbIdx = 1:3
+            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
+
+            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
+%scale tempImage
+% maximum = max(tempImage(:));
+% minimum = min(tempImage(:));
+% tempImage = uint16(65535*(tempImage - minimum)/(maximum-minimum));
+tempImage = uint16(tempImage*65535);
+
+%make background white
+% blackMask = uint16(all((tempImage < 1),3));
+% for i = 1:3
+%     tempImage(:,:,i) = blackMask * 65535 + tempImage(:,:,i);
+% end
+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);
+%copy meanImage in every colorchannel
+for i = 1:3
+    tempImage(:,:,i) = tempImage(:,:,i) + meanImage;
+end
+
+subplot(1,2,1);
+imshow(tempImage);
+%draw number in each roi
+for drawNumberCt = 1:size(cluster{i})
+    number = cluster{i}(drawNumberCt);
+end
+subplot(1,2,2);
+hold on
+cell_sigPlot = cell_sig(sortedIdx,:);
+
+
+
+signal = zeros(size(cluster,2),size(cell_sig,2));
+for i = 1:size(cluster, 2)
+    cell_sig_merged{i} = mean(cell_sig_merged{i}(cluster{i},:), 1);
+    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))
+    %plot single components dotted
+    for clusterIdx = cluster{i}
+        cell_sigPlot(clusterIdx,:) = cell_sigPlot(clusterIdx,:) + maximum;
+        plot(cell_sigPlot(clusterIdx, :),':', 'Color', rgb);
+    end
+end
+xlim([0,size(signal,2)]);
+%maximum = max(cell_sigPlot(:));
+ylim auto;%([0, maximum]);
+end

alternativePlot.m

@@ -48,6 +48,20 @@
 
 subplot(1,2,1);
 imshow(tempImage);
+%draw number in each roi
+for i = 1:subPlotCols
+    for drawNumberCt = 1:size(cluster{i},2)
+        number = cluster{i}(drawNumberCt);
+        %get position to draw number in
+        mask = squeeze(ica_segments(number,:,:));
+        cog = centerofgravity(mask);
+        text(cog(2), cog(1), num2str(i), 'Color', 'white')
+
+    end
+end
+
+
+
 subplot(1,2,2);
 hold on
 cell_sigPlot = cell_sig(sortedIdx,:);
@@ -57,7 +71,7 @@
 signal = zeros(size(cluster,2),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);
+    cell_sig_merged{i} = mean(cell_sig_merged{i}(cluster{i},:), 1);
     for clusterIdx = cluster{i}
         %subtract minimum value
         minimum = min(cell_sigPlot(clusterIdx,:));