cell boundary efficiency - use adaptthresh

matlab/+Ensemble/setCellBoundaryEfficiency.m

@@ -25,7 +25,12 @@ if sensitivity>1
     T=lm(end);
 else
     T=adaptthresh(im,sensitivity,'NeighborhoodSize',4*floor(size(im)/16)+1,'statistic','gaussian');
-    T=imdilate(T,se);
+%     T=imdilate(T,se);
+end
+bw=logical(0*im);
+for i=1:length(Cells)
+    idx=sub2ind(size(im),Cells(i).pts(:,2),Cells(i).pts(:,1));
+    bw(idx)=1;
 end
 for i=1:length(Cells)
     if is3D(im)
@@ -41,11 +46,13 @@ for i=1:length(Cells)
     imBGmu=median(imBG(idx));
     if sensitivity>1
         minFG=T;
+        imBGeff=1-imBGmu/minFG; %
     else
-        minFG=max(T(idx));
+        imBGeff=1-median(imBG(idx)-T(idx));
     end
-    imBGeff=1-imBGmu/minFG; % 
-    imBGeff=min(imBGeff,1);
+    % clamp??? ac 10 14 2020 ??? ACK
+    %     imBGeff=min(imBGeff,1);
+    %     imBGeff=max(imBGeff,0);
 
     % how dark on average the surface neighborhood is (1 is good)
     Cells(i).ensemble.boundaryEfficiency=imBGeff;