allocateShake: restore size kilt kernels, aiareaOpen speed

matlab/+Segment/aiAreaOpen.m

@@ -16,4 +16,12 @@ if ~is3D(bw)
 end
 ee=HIP.MakeEllipsoidMask(maskRadius);
 bwSeeds=imerode(bw,ee);
-bw=imreconstruct(bwSeeds,bw);   
+% bw=imreconstruct(bwSeeds,bw); 
+% faster by 2x compared to imreconstruct...
+idx=find(bwSeeds);
+cc=bwconncomp(bw);
+L=labelmatrix(cc);
+idxIntersect=cellfun(@(x) intersect(x,idx),cc.PixelIdxList,'UniformOutput',false);
+idxDelete=cellfun(@isempty,idxIntersect);
+bw(vertcat(cc.PixelIdxList{idxDelete}))=0;
+

matlab/+Segment/allocateShake.m

 function [L,num,bwBoundary]=allocateShake(bw,bw2,min_radius_pixels,segParams)
 
+bwBoundary=assignShake(bw,bw2,true);
+bwReduce=Segment.aiAreaOpen(bwBoundary,min_radius_pixels);
+% any components that were not big enough?
+if find(bwBoundary & ~bwReduce,1,'first')
+    % "re-absorb" components too small to exist on their own
+    % allow disconnected components in case whole CC was removed
+    bwBoundary=assignShake(bwReduce,bw2,false);
+    bwBoundary=Segment.aiAreaOpen(bwBoundary,min_radius_pixels);
+end
+% now, the boundary has been resent, label that and done
+[L,num]=bwlabeln(bwBoundary);
+return
+
+function bwBoundary=assignShake(bw,bw2,bNoDisconnected)
 d=bwdist(bw);
 L=watershed(d);
 L(~bw2)=0;
 bwBoundary=logical(L); % cell image with boundaries set to 0
 % don't allow disconnected components
+if bNoDisconnected
     [LX,nx]=bwlabeln(bwBoundary);
     idx=unique(LX(bw));
     % the boundary image, remove the connected components not from bw (e.g.
     % bw2 only)
     bwBoundary=bwBoundary&ismember(LX,idx);
-bwBoundary=Segment.aiAreaOpen(bwBoundary,min_radius_pixels);
+end
+
+
+
 
-% now, the boundary has been resent, label that and done
-[L,num]=bwlabeln(bwBoundary);
-return

matlab/+Segment/getParams.m

@@ -24,6 +24,13 @@ for i=1:length(names)
         segParams=setfield(segParams,names{i},fv);
     end
 end
+% convert to row vectors for easier readability
+if isfield(segParams,'minimumRadius_um')
+    segParams.minimumRadius_um=segParams.minimumRadius_um(:)';
+end
+if isfield(segParams,'NLM')
+    segParams.NLM=segParams.NLM(:)';
+end