perftune segReduce use bwconncomp

matlab/+Read/findImageFolder.m

@@ -39,6 +39,7 @@ end
 
 override=fscanf(fid,'%s');
 fclose(fid);
+override=strrep(override,'\','\\');
 override=jsondecode(override);
 leverFile=fullfile(override.ROOT,[CONSTANTS.imageData.DatasetName '.h5']);
 if exist(leverFile,'file')

matlab/+Segment/segReduce.m

@@ -19,24 +19,19 @@ nIter=100; %10*max(min_radius_pixels);
 for nDilate=1:nIter
     bwKernels=bwOut&~bwLog;
     bwKernels=bwareaopen(bwKernels,minKernelArea);    
-%     if isempty(find(bwKernels, 1))
-%         break;
-%     end 
-%     
     L=bwlabeln(bwKernels);
-    workingL=bwlabeln(bwOut);
+    CC=bwconncomp(bwOut);
+    workingL=double(labelmatrix(CC));
     % 3 things can happen: (0) CC s (1) CC disappears (2) CC splits
-    idxWL=find(workingL);
+    idxWL=vertcat(CC.PixelIdxList{:});
     map=unique([workingL(idxWL),L(idxWL)],'rows');
     map(map(:,2)==0,:)=[];    
-%     h=histogram(map(:,1),[0.5:max(map(:,1))+0.5]);
-%     mapCounts=h.Values;
     mapCounts=hist(map(:,1),[1:max(map(:,1))])';
     idxChange=find(mapCounts>1);
     for i=1:length(idxChange)
         % copy over new objects to bwOut
         idxMap=find(map(:,1)==idxChange(i),1,'first');
-        idx=find(workingL==map(idxMap,1));
+        idx=CC.PixelIdxList{map(idxMap,1)};
         bwOut(idx)=logical(L(idx));
     end
     
@@ -47,14 +42,9 @@ for nDilate=1:nIter
     bwLog=imdilate(bwLog,se);
     
 end
-
-
-
 4;
+
 function bwReduce=phaseReduce(bw,bwLog,min_radius_pixels)
-% min_radius_pixels=min_radius_pixels(1);
-% se=strel('disk',ceil(min_radius_pixels/2));
-% bwLogHoles=imclose(bwLog,se);
 bwLogHoles=bwLog;
 bwLogHoles=imfill(bwLogHoles,'holes')&~bwLogHoles;
 bwReduce=bw&bwLogHoles;