first commit

Flowcytometer_Focusing_Jeevan2018/focusstack_1.m

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+function [Zval, Variance, currzpos] = focusstack_1(s,vid,z)
+    t1 = toc;currzpos=z;
+    snap = getsnapshot(vid);
+    imwrite(snap,strcat('images/withouthc/snap_at_start','.bmp'))
+    %fprintf(s,'L');
+    %       CRUDE AF. 
+    Z_travel_for_crude = 16000;  crude_step_count = 200;
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    crude_pulse_count = Z_travel_for_crude / crude_step_count;
+    crude_max_var=0;    crude_loc_max_var=0;
+    crude_start_loc = z-(Z_travel_for_crude/2);
+%    gotoZ(s,crude_start_loc,currzpos);pause(1) ;
+    fprintf(s,'M');pause(3)
+%     for i=1: crude_pulse_count/2
+%         fprintf(s,'T');pause(0.35)
+%     end
+    currzpos=crude_start_loc;
+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    % now keep going up and taking var
+    crude_curr_loc = crude_start_loc;
+    Variance = []; Zval = [];
+    for i=1: crude_pulse_count     
+        % variance
+        snap = getsnapshot(vid);
+        imwrite(snap,strcat('images/snap_at_',num2str(crude_curr_loc),'.bmp'))
+        crude_img = double(snap);     crude_curr_var=var(crude_img(:));
+        %display(strcat('Variance',num2str(crude_curr_var),'Iter:',num2str(i)))
+        %pause(0.5)
+        Variance = [Variance crude_curr_var];
+        Zval = [Zval crude_curr_loc];
+        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      ;
+        fprintf(s,'G');pause(0.1) 
+        %gotoZ(s,crude_curr_loc,currzpos); 
+        currzpos=crude_curr_loc;
+    end
+    disp(currzpos)
+    disp(crude_loc_max_var)
+    crude_pulse_count = round(abs(crude_loc_max_var - currzpos)/200);
+    for i=1: crude_pulse_count
+        if(currzpos>crude_loc_max_var)
+            fprintf(s,'T');pause(0.1)  
+            currzpos = currzpos - 200;
+        elseif(currzpos<crude_loc_max_var)
+            fprintf(s,'G');pause(0.1)  
+            currzpos = currzpos + 200;
+        end
+    end
+    pause(1)
+    snap = getsnapshot(vid);
+    imwrite(snap,strcat('images/withouthc/snap_at_end_crude','.bmp'))
+    t2 = toc;
+    disp(t2-t1)
+end