first commit

Flowcytometer_Focusing_Jeevan2018/focusstack_3.m

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+function [Zval, Variance] = focusstack_3(s,vid,z)
+    t1 = toc;currzpos=z;
+    %       fINECRUDE AF. 
+    Z_travel_for_crude = 1000;  crude_step_count = 50;
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    crude_pulse_count = Z_travel_for_crude / crude_step_count;
+    crude_max_var=0;   
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    %        go to starting Z loc (we've hit limit switch via arduino already so its z=0)
+    crude_start_loc = z - (Z_travel_for_crude/2);
+    gotoZ(s,crude_start_loc,currzpos); currzpos=crude_start_loc;
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    % now keep going up and taking var
+    crude_curr_loc = crude_start_loc;
+
+    for i=1: crude_pulse_count     
+        % variance
+        crude_img = double(getsnapshot(vid));     crude_curr_var=var(crude_img(:));
+
+        if (crude_curr_var > crude_max_var) 
+            crude_max_var = crude_curr_var;
+            crude_loc_max_var = crude_curr_loc;
+        end 
+        % update loc 
+        crude_curr_loc = crude_curr_loc + crude_step_count      ;
+        gotoZ(s,crude_curr_loc,currzpos); currzpos=crude_curr_loc;
+    end
+    gotoZ(s,crude_loc_max_var,currzpos);currzpos=crude_loc_max_var;
+    
+    % The fine AF begins here
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    Ztotaltravel = 100;     final_go_backpulses = 0 ;
+    currZ = crude_loc_max_var;
+
+    % first go above
+    start_above_loc = currZ - (Ztotaltravel/2);
+    gotoZ(s,start_above_loc,currzpos);currzpos=start_above_loc;
+    % now build the var array
+    localAF_loc_array = zeros(1,Ztotaltravel);   localAF_var_array = zeros(1,Ztotaltravel);
+    localAF_curr_loc = start_above_loc;
+    for q=1:(Ztotaltravel/5)
+        % location
+        localAF_loc_array(q) = localAF_curr_loc;
+        % variance
+        localAF_img = double(getsnapshot(vid)); localAF_var_array(q)=var(localAF_img(:));
+
+        % move and update loc    
+        localAF_curr_loc = localAF_curr_loc + 5;    gotoZ(s,localAF_curr_loc,currzpos); 
+        currzpos=localAF_curr_loc;
+    end  
+
+    % Finally go to the max var location
+    index_of_max_var =  localAF_var_array == max(localAF_var_array);
+    loc_of_max_var = localAF_loc_array(index_of_max_var) - final_go_backpulses  ;    
+    gotoZ(s,loc_of_max_var,currzpos);currzpos=loc_of_max_var;
+    Zval = loc_of_max_var;
+    Variance = max(localAF_var_array);
+    t2 = toc;
+    disp(t2-t1)
+end