reworked thresholdImages

matlab/+Segment/thresholdImages.m

@@ -12,7 +12,6 @@ else
 end
 
 if is3D(im)
-    
     nsz=2*floor(size(im)/16)+1;
     T=adaptthresh(imLog,0.5,'NeighborhoodSize',nsz,'statistic','gaussian');
     bwLog=imbinarize(imLog,T);
@@ -32,6 +31,19 @@ bwLog=imbinarize(imLog,T);
 bwLog=bwareaopen(bwLog,4*min_area_pixels);
 
 if segParams.isPhase
+    [bw,bwLog]=phaseThreshold(im,bwLog,min_radius_pixels,segParams,...
+        sensitivity,medianMask);
+    return;
+else
+    % use 2x the default nhood size
+    T=adaptthresh(im,sensitivity,'NeighborhoodSize',4*floor(size(im)/16)+1,'statistic','gaussian');
+    bw=imbinarize(im,T);
+end
+bw=bwareaopen(bw,min_area_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));
 if segParams.isPhase>0
@@ -46,6 +58,11 @@ if segParams.isPhase
 bw=imclose(bw,se2);
 bw=imfill(bw,'holes');
 if true==segParams.wellRadius
+    [bw,bwLog]=thesholdMask(medianMask,bw,bwLog,se,se2);
+end
+
+
+function [bw,bwLog]=thesholdMask(medianMask,bw,bwLog,se,se2)
 bwMask=imbinarize(medianMask,adaptthresh(medianMask,'statistic','gaussian'));
 bw=bw&~bwMask;
 bwh=imfill(bw,'holes');
@@ -61,15 +78,7 @@ if segParams.isPhase
 bw=imopen(bw,se);
 bwLog=bwLog&~bwMask;
 bwLog=imclose(bwLog,se2);
-    end
-    bw=imfill(bw,'holes');
-else
-    % use 2x the default nhood size
-    T=adaptthresh(im,sensitivity,'NeighborhoodSize',4*floor(size(im)/16)+1,'statistic','gaussian');
-    bw=imbinarize(im,T);
-end
-bw=bwareaopen(bw,min_area_pixels);
-4;
+