SSF equiprobable quantization

matlab/+SSF/getClipLimits.m

@@ -13,6 +13,7 @@ if ~exist('tClip','var')
 end
 p = ljsStartParallel(); 
 kymoPixels = {};
+clipLimits = {};
 parfor ff=1:length(flist)
     kp = {};
     for c = 1:length(targetChannelNumbers)
@@ -25,22 +26,27 @@ parfor ff=1:length(flist)
             im_ff(im_ff>0)=0;
             im_ff = abs(im_ff);
         end
-        kp{c} = im_ff(find(im_ff));
-        kymoPixels{ff} = kp;
-    end
-end 
-kymoPixels = vertcat(kymoPixels{:});
+        px = im_ff(find(im_ff));
+        kymoPixels{ff} = px;
 
-clipLimits = [];
-for c = 1:size(kymoPixels,2)
-    % anything other than [0,1] gets set to the corresponding percentile
-    idx = find(clipRange);
-    if ~isempty(idx)
-        px = kymoPixels{:,c};
-        clipLimits(c,idx) = [prctile(px,clipRange(idx))];
+%         clipLimits{ff} = [mean(px)-std(px),mean(px)+std(px)]; %prctile(kp{c},[0.5,99.5]);
+        clipLimits{ff} = prctile(px,100.*[1/255:1/255:1-1/255]);
     end    
-    clipLimits(c,find(clipRange==0)) = 0;
 end 
 
+% kymoPixels = vertcat(kymoPixels{:});
+% clipLimits = prctile(kymoPixels,100.*[1/255:1/255:1-1/255]);
 
-4;
\ No newline at end of file
+% clipLimits = []; 
+% for c = 1:size(kymoPixels,2)
+%     % anything other than [0,1] gets set to the corresponding percentile
+%     idx = find(clipRange);
+%     if ~isempty(idx)
+%         px = kymoPixels{:,c};
+%         clipLimits(c,idx) = [mean(px)-std(px),mean(px)+std(px)]; %[prctile(px,clipRange(idx))];
+%     end   
+%     clipLimits(c,find(clipRange==0)) = 0;
+% end
+% 
+% 
+%  4;
\ No newline at end of file

matlab/+SSF/quantize8.m

@@ -5,11 +5,15 @@ im = im_in;
 if isa(im,'uint8')
     return
 end
-for c = 1:size(im,4)
-    im(:,:,:,c) = max(im(:,:,:,c),clipLimits(c,1));
-    im(:,:,:,c) = min(im(:,:,:,c),clipLimits(c,2));
-    im(:,:,:,c) = (im(:,:,:,c) - clipLimits(c,1)) ./ (clipLimits(c,2) - clipLimits(c,1));
-end
-im = im2uint8(im);
+
+im = uint8(imquantize(im,clipLimits));
+% 
+% for c = 1:size(im,4)
+%     im(:,:,:,c) = max(im(:,:,:,c),clipLimits(c,1));
+%     im(:,:,:,c) = min(im(:,:,:,c),clipLimits(c,2));
+%     im(:,:,:,c) = (im(:,:,:,c) - clipLimits(c,1)) ./ (clipLimits(c,2) - clipLimits(c,1));
+% end
+% im = im2uint8(im);
+
 im = max(im,1);
 im(0 == im_in) = 0;
\ No newline at end of file