thresholdImages fixes

hole fill on aiAreaOpen for LoG, phase threshold morphology and hole fill

matlab/+Segment/thresholdImages.m

@@ -39,8 +39,8 @@ else
     bw=imbinarize(im,T);
    
 end
-bwLog=Segment.aiAreaOpen(bwLog,2*min_radius_pixels);
-bw=Segment.aiAreaOpen(bw,min_radius_pixels,true);
+bwLog=Segment.aiAreaOpen(bwLog,2*min_radius_pixels,true);
+bw=Segment.aiAreaOpen(bw,min_radius_pixels);
 4;
 
 function [bw,bwLog]=phaseThreshold(im,bwLog,min_radius_pixels,segParams,...
@@ -62,11 +62,14 @@ if true==segParams.wellRadius
     [bw,bwLog]=thresholdMask(medianMask,bw,bwLog,se,se2);
 end
 % fill in holes
-bwh=imclose(bw,se2);
-bwh=imfill(bwh,'holes')&~bwh;
-bw=bw|bwh;
+bw=imclose(bw,se2);
+bw=imopen(bw,se);
 bw=imfill(bw,'holes');
 
+bwLog=imclose(bwLog,se2);
+4;
+
+
 
 function [bw,bwLog]=thresholdMask(medianMask,bw,bwLog,se,se2)