Merge branch 'master' of https://git-bioimage.coe.drexel.edu/opensource/ljsctc

src/evalRC.m

 
 % eval all the datasets in the release folder
-ROOT='/f/leverjs/ctc2020rc'
+ROOT='/g/leverjs/ctc2021a/3d'
 flist=dir(fullfile(ROOT,'**/*training*.LEVER'));
 results=[];
 for ff=1:length(flist)
@@ -18,4 +18,4 @@ for ff=1:length(flist)
     res.Properties.VariableNames{2}='strDB';
     results=[results;res]
 end
-writetable(results,'/f/leverjs/ctc2020rc/results.txt')
\ No newline at end of file
+writetable(results,'/g/leverjs/ctc2021a/3d/results.txt')
\ No newline at end of file

src/huh7Helper.m

-root = 'F:\leverjs\ctc\huh7\refined';
-gtPath = '\\BIOIMAGE20\G\gRaw\ctc2020';
+root = '/g/leverjs/ctc2021a/huh7/refined/diModified';
+gtPath = '/g/gRaw/ctc2020';
 flist = dir(fullfile(root,'*.LEVER'));
 results = [];
 
 for ff = 1:length(flist)
    strDB = fullfile(flist(ff).folder,flist(ff).name);
-   Dilation.huh7Refine(strDB);
+   huh7Refine(strDB);
 end
 
 flist = dir(fullfile(root,'*training*.LEVER'));

src/huh7Refine.m

@@ -12,7 +12,6 @@ for i = 1:CONSTANTS.imageData.NumberOfFrames
     im = DenoiseCache.readImages(i,CONSTANTS,segParams,[]);
     
     di = dilationThreshold(im);
-    
     imx=mat2gray(0*im);
    
     for j=1:length(cx)
@@ -20,6 +19,8 @@ for i = 1:CONSTANTS.imageData.NumberOfFrames
         imx(dx(2),dx(1)) = j;
     end
 
+    di = logical(imreconstruct(imx,mat2gray(di)));
+    
     [~,idxd]=bwdist(imx);
     rp = regionprops((imx(idxd).*di),im, 'PixelList');
 
@@ -28,15 +29,32 @@ for i = 1:CONSTANTS.imageData.NumberOfFrames
         if isempty(rp(j).PixelList)
             continue
         end
-        cx(j).pts = rp(j).PixelList;
         
-        idxPixels = sub2ind(imSize,cx(j).pts(:,2),cx(j).pts(:,1));
-        [r,c] = ind2sub(imSize,idxPixels);
+        idxPixels = sub2ind(imSize,rp(j).PixelList(:,2),rp(j).PixelList(:,1));
         
         bw = logical(zeros(imSize));
         bw(idxPixels) = 1;
-        bounds = bwboundaries(bw);
         
+        % keep only the connected components with the centroid
+        bw2 = logical(0*bw);
+        centroid = round(cx(j).centroid);
+        
+        % todo - make sure 1 <= centroid<imSize
+        bw2(centroid(2),centroid(1)) = 1;
+        bw2 = imreconstruct(bw2,bw);
+        
+        idxPixels = find(bw2);
+        [r,c] = find(bw2);
+        bounds = bwboundaries(bw2);
+        
+        % use r,c idxPixels to build new cell struct
+        
+        if isempty(bounds)
+            continue
+        end
+        
+        cx(j).pts = [c,r];
+        cx(j).idxPixels = idxPixels;
         cx(j).surface = [bounds{1}(:,2),bounds{1}(:,1)];  
         cx(j).centroid = [mean([c,r]) 0];