Lts ldy

extractFish.m

@@ -1,99 +1,95 @@
 function extractFish()
 
-[f,p] = uigetfile('*.avi');
-fName = [p,f];
-
-vobj = VideoReader(fName);
-for i = 1:200     % 200 frames
-frame = readFrame(vobj);
-grayImg = rgb2gray(frame);
-BW = imbinarize(grayImg,'adaptive','ForegroundPolarity','dark','Sensitivity',0.6);
-BW2=BW*(-1)+1;
-bwFish = bwareaopen(BW2,50000); 
-bwFish = removeLargeArea(bwFish,100000);
-bwFish=bwFish*(-1)+1;
-bwFish = bwareaopen(bwFish,10000);
-bwFish=bwFish*(-1)+1;
-s = regionprops( bwFish,'centroid');
-centroids = cat(1, s.Centroid);
-figure(1);
-imshow(bwFish,[]);
-hold on;
-scatter(centroids(:,1),centroids(:,2),20,'b','filled');
-pause(0.1);
+    [f,p] = uigetfile('*.avi');
+    fName = [p,f];
+    vobj = VideoReader(fName);
+    for i = 1:200     % 200 frames as a simple
+        frame = readFrame(vobj);
+        grayImg = rgb2gray(frame);
+        BW = imbinarize(grayImg,'adaptive','ForegroundPolarity','dark','Sensitivity',0.6);
+        BW = bwareaopen(BW,10000);  % Remove objects in image containing fewer than 10000 pixels which often appear in the fish brain
+        BW2 = BW*(-1)+1;
+        bwFish1 = bwareaopen(BW2,50000); % Remove objects in image containing fewer than 50000 pixels
+        bwFish2 = bwareaopen(bwFish1,80000);  % Remove the fish from image
+        bwFish = bwFish1 - bwFish2;     % get the fish from image
+        s = regionprops( bwFish,'centroid');
+        centroids = cat(1, s.Centroid);
+        figure(1);
+        imshow(bwFish,[]);
+        hold on;
+        scatter(centroids(:,1),centroids(:,2),20,'b','filled');
+        pause(0.1);
 
 %% scatter the tail of the two fishes     
-[B,~] = bwboundaries(bwFish,'noholes');
-
-L = bwlabel(bwFish);   %get the points of two fishes
-[fish_x, fish_y] = find(L==1);
-fish=[fish_x,fish_y]';           
-C=B{1,1};
-tail = find_tail(C,fish);
-scatter(tail(2,1),tail(1,1),20,'r','o')
-pause(0.1);
-disp(i);
-end     
+        [B,~] = bwboundaries(bwFish,'noholes');
+        L = bwlabel(bwFish);   %get the points of two fishes
+        [fish_x, fish_y] = find(L==1);
+        fish = [fish_x,fish_y]';           
+        C = B{1,1};
+        tail = find_tail(C,fish);
+        scatter(tail(2,1),tail(1,1),20,'r','o')
+        pause(0.1);
+        disp(i);
+   end     
 end     
 
 %% function:get the point of tail
 function head = find_tail(B,fish)
-       c = minBoundingBox(B');
-       C = zeros(2,1);
-       C(1) = norm(c(:,1)-c(:,2));
-       C(2) = norm(c(:,1)-c(:,4));
-       min_norm_c=min(C);
-       if min_norm_c==C(1)
-           f1=c(:,1);  f2=c(:,2); f3=c(:,3);f4=c(:,4);
-       else     
-           f1=c(:,2);  f2=c(:,3); f3=c(:,4);f4=c(:,1);
-       end
-       f1_m = (f1+f2)./2;   f2_m=(f3+f4)./2;
-       f3_m = (f2+f3)./2;   f4_m=(f4+f1)./2;
-        [f_mid,D]=find_D(fish,f1_m,f2_m,f3_m,f4_m);
-        D_norm=sqrt(D(1,:).^2+D(2,:).^2);
-       min_D_norm=min(D_norm);
-       idx=find(D_norm==min_D_norm);
-       head=D(:,idx)+f_mid;
+    c = minBoundingBox(B');
+    C = zeros(2,1);
+    C(1) = norm(c(:,1) - c(:,2));
+    C(2) = norm(c(:,1) - c(:,4));
+    min_norm_c = min(C);
+    if min_norm_c == C(1)
+        f1 = c(:,1);  f2 = c(:,2);  f3 = c(:,3);  f4 = c(:,4);
+    else     
+        f1 = c(:,2);  f2 = c(:,3);  f3 = c(:,4);  f4 = c(:,1);
+    end
+    f1_m = (f1+f2)./2;   f2_m = (f3+f4)./2;
+    f3_m = (f2+f3)./2;   f4_m = (f4+f1)./2;
+    [f_mid,D] = find_D(fish,f1_m,f2_m,f3_m,f4_m);
+    D_norm = sqrt(D(1,:).^2+D(2,:).^2);
+    min_D_norm = min(D_norm);
+    idx = find(D_norm == min_D_norm);
+    head = D(:,idx) + f_mid;
 end
 
 %% get a matrix of distance and f_mid
-function  [f_mid,D]=find_D(fish,f1_m,f2_m,f3_m,f4_m)
-       k=(f3_m(1,1)- f4_m(1,1))./(f3_m(2,1)- f4_m(2,1));
-       b=f3_m(1,1)-k.*f3_m(2,1); 
-       if f3_m(2,1)== f4_m(2,1)
-           num1=length(find(fish(2,:)-f3_m(2,1)<0));
-           num2=length(find(fish(2,:)-f3_m(2,1)>0));
-           if num1>num2
-               if f1_m(2,1)>f2_m(2,1)
-                   f_mid=f1_m;    D=fish-f1_m;
-               else
-                    f_mid=f2_m;   D=fish-f2_m;
-               end
+function  [f_mid,D] = find_D(fish,f1_m,f2_m,f3_m,f4_m)
+    k = (f3_m(1,1) - f4_m(1,1))./(f3_m(2,1) - f4_m(2,1));
+    b = f3_m(1,1) - k.*f3_m(2,1); 
+    if f3_m(2,1) == f4_m(2,1)
+        num1 = length(find(fish(2,:) - f3_m(2,1)<0));
+        num2 = length(find(fish(2,:) - f3_m(2,1)>0));
+        if num1 > num2
+           if f1_m(2,1) > f2_m(2,1)
+                f_mid = f1_m;    D = fish - f1_m;
            else
-               if  f1_m(2,1)<f2_m(2,1)
-                    f_mid=f1_m;    D=fish-f1_m;
-               else
-                    f_mid=f2_m;     D=fish-f2_m;
-               end
+                f_mid = f2_m;   D = fish - f2_m;
            end
-
-       else
-       num1=length(find(k.*fish(2,:)+b-fish(1,:)<0));
-       num2=length(find(k.*fish(2,:)+b-fish(1,:)>0));
-         if num1>num2
+        else
+           if  f1_m(2,1) < f2_m(2,1)
+                f_mid = f1_m;    D = fish - f1_m;
+           else
+                f_mid = f2_m;    D = fish - f2_m;
+           end
+        end   
+    else
+        num1 = length(find(k.*fish(2,:)+b-fish(1,:)<0));
+        num2 = length(find(k.*fish(2,:)+b-fish(1,:)>0));
+        if num1 > num2
             if  f1_m(1,1) < f2_m(1,1)
-                  f_mid=f1_m;    D=fish-f1_m;
+                  f_mid = f1_m;    D = fish - f1_m;
             else
-                   f_mid=f2_m;   D=fish-f2_m;
+                  f_mid = f2_m;    D = fish - f2_m;
             end
-         else
+        else
            if  f1_m(1,1) > f2_m(1,1)
-                   f_mid=f1_m;   D=fish-f1_m;
+                   f_mid = f1_m;   D = fish - f1_m;
            else
                    f_mid=f1_m;   D=fish-f2_m;
            end
-         end
-       end
+        end
+    end
 
 end