Update to move files to make straighten worms work

.gitignore

@@ -1,6 +1,6 @@
 data/*
 *.jpg
 *.png
-scripts/testing/
 !data/placeholder.md
 .DS_Store
+App/

scripts/testing/Lightsaver_batch_align_worms.m

@@ -53,11 +53,11 @@
 
 [~,final_save_name,~] = fileparts(img_dir_path);
 
-output_path = fullfile(erase(erase(curr_path,'multiple_samples'),'scripts'),'exported_images');
+output_path = fullfile(erase(erase(curr_path,'testing'),'scripts'),'exported_images');
 mkdir(output_path);
 
 if isempty(output_name)
-    output_name = final_save_name;
+    output_name = [final_save_name ' -- aligned_worms'];
 end
 
 [~,message,~] = fileattrib(fullfile(img_dir_path,'*'));

scripts/testing/bresenham.m

@@ -0,0 +1,59 @@
+function [x y]=bresenham(x1,y1,x2,y2)
+
+%Matlab optmized version of Bresenham line algorithm. No loops.
+%Format:
+%               [x y]=bham(x1,y1,x2,y2)
+%
+%Input:
+%               (x1,y1): Start position
+%               (x2,y2): End position
+%
+%Output:
+%               x y: the line coordinates from (x1,y1) to (x2,y2)
+%
+%Usage example:
+%               [x y]=bham(1,1, 10,-5);
+%               plot(x,y,'or');
+x1=round(x1); x2=round(x2);
+y1=round(y1); y2=round(y2);
+dx=abs(x2-x1);
+dy=abs(y2-y1);
+steep=abs(dy)>abs(dx);
+if steep 
+    t=dx;
+    dx=dy;
+    dy=t; 
+end
+
+%The main algorithm goes here.
+if dy==0 
+    q=zeros(dx+1,1);
+else
+    q=[0;diff(mod([floor(dx/2):-dy:-dy*dx+floor(dx/2)]',dx))>=0];
+end
+
+%and ends here.
+
+if steep
+    if y1<=y2 
+        y=[y1:y2]'; 
+    else 
+        y=[y1:-1:y2]'; 
+    end
+    if x1<=x2 
+        x=x1+cumsum(q);
+    else 
+        x=x1-cumsum(q); 
+    end
+else
+    if x1<=x2 
+        x=[x1:x2]'; 
+    else 
+        x=[x1:-1:x2]'; 
+    end
+    if y1<=y2 
+        y=y1+cumsum(q);
+    else 
+        y=y1-cumsum(q); 
+    end
+end

scripts/testing/find_adjacent_pixel.m

@@ -0,0 +1,22 @@
+function [outx,outy] = find_adjacent_pixel(bw,x,y)
+try
+    idy = y-1:y+1;
+    idx = x-1:x+1;
+    nhood = bw(idx,idy);
+
+    x_hood = [-1,-1,-1;0,0,0;1,1,1];
+    y_hood = [-1,0,1;-1,0,1;-1,0,1];
+
+    [subx,suby] = find(nhood==1);
+
+    x_add = x_hood(subx,suby);
+    y_add = y_hood(subx,suby);
+
+    outx = x + x_add;
+    outy = y + y_add;
+catch
+    outx = [];
+    outy = [];
+end
+
+end