updated threshold and segreduce for phase

matlab/+Segment/segReduce.m

@@ -51,6 +51,8 @@ function bwReduce=phaseReduce(bw,bwLog,min_radius_pixels)
 bwLogHoles=bwLog;
 bwLogHoles=imfill(bwLogHoles,'holes')&~bwLogHoles;
 bwReduce=bw&bwLogHoles;
+bwReduce=imfill(bwReduce,'holes');
+bwReduce=Segment.aiAreaOpen(bwReduce,min_radius_pixels);
 [L,num]=bwlabeln(bw);
 for n=1:num
     idx=find(L==n);

matlab/+Segment/thresholdImages.m

@@ -21,17 +21,14 @@ if sensitivity>1 && round(sensitivity)==sensitivity
     return;
 end
 
-if segParams.isPhase
-    [bw,bwLog]=phaseThreshold(im,bwLog,min_radius_pixels,segParams,...
-        sensitivity,medianMask);
-    return;
-end
-
 nsz=4*floor(size(im)/16)+1;
 T=adaptthresh(imLog,0.5,'NeighborhoodSize',nsz,'statistic','gaussian');
 bwLog=imbinarize(imLog,T);
-bwLog=Segment.aiAreaOpen(bwLog,2*min_radius_pixels);
 
+if segParams.isPhase
+    [bw,bwLog]=phaseThreshold(im,bwLog,min_radius_pixels,segParams,...
+        sensitivity,medianMask);
+else
     if is3D(im)
         % lower density (generally?) use smaller radius
         nsz=2*floor(size(im)/16)+1;
@@ -40,13 +37,17 @@ else
     end
     T=adaptthresh(im,sensitivity,'NeighborhoodSize',nsz,'statistic','gaussian');
     bw=imbinarize(im,T);
+   
+end
+bwLog=Segment.aiAreaOpen(bwLog,2*min_radius_pixels);
 bw=Segment.aiAreaOpen(bw,min_radius_pixels);
 4;
 
 function [bw,bwLog]=phaseThreshold(im,bwLog,min_radius_pixels,segParams,...
     sensitivity,medianMask)
 se=strel('disk',1);
-se2=strel('disk',ceil(min_radius_pixels/2));
+rClose=max(1,ceil(min_radius_pixels/2));
+se2=strel('disk',rClose);
 if segParams.isPhase>0
     T=adaptthresh(im,sensitivity,'foregroundpolarity','dark','statistic','gaussian');
 else
@@ -56,15 +57,24 @@ bw=imbinarize(im,T);
 if segParams.isPhase>0
     bw=imcomplement(bw);
 end
-bw=imclose(bw,se2);
-bw=imfill(bw,'holes');
+
 if true==segParams.wellRadius
-    [bw,bwLog]=thesholdMask(medianMask,bw,bwLog,se,se2);
+    [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=imfill(bw,'holes');
+
+
+function [bw,bwLog]=thresholdMask(medianMask,bw,bwLog,se,se2)
 
+imf=stdfilt(medianMask,true(5));
+bwMask=imbinarize(imf);
+bwMask=imclose(bwMask,true(10));
+bwMask=imopen(bwMask,true(5));
 
-function [bw,bwLog]=thesholdMask(medianMask,bw,bwLog,se,se2)
-bwMask=imbinarize(medianMask,adaptthresh(medianMask,'statistic','gaussian'));
 bw=bw&~bwMask;
 bwh=imfill(bw,'holes');
 nrep=0;
@@ -78,7 +88,6 @@ end
 bw=imfill(bw,'holes');
 bw=imopen(bw,se);
 bwLog=bwLog&~bwMask;
-bwLog=imclose(bwLog,se2);