angles

slice_synthetic_data.m

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Take 200nm slice of vbSPT synthetic data
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Select the mat result file generated by simulation
+[fn pt] = uigetfile(('*.mat'), 'Choose a File');
+load(fn)
+
+min_length = 3;%minimum length minus 1
+%% set number of trajectories 
+traj_no = 10000;
+
+for k = 1 : traj_no
+    l = size(finalTraj{k},1);
+   
+    for i = 1:l
+        
+        %take slice
+        if finalTraj{k}(i,3)>= -100 && finalTraj{k}(i,3)<= 100
+           finalTraj{k}(i,5) = 1;
+        %if not in our z range then it is a blink
+        else finalTraj{k}(i,5) = 2;
+        end 
+    end
+    
+end
+%% 
+ct = 1;
+for k = 1:traj_no
+    chop = [1; find(finalTraj{k}(:,5)==2)];
+    if length(chop) == 1
+        chtrack{ct} =  finalTraj{k}(:,1:5); 
+        ct = ct+1;
+    else
+        if chop(2) > min_length + 1
+           chtrack{ct} =  finalTraj{k}(1:chop(2)-1,1:5); 
+           ct = ct+1;
+        end
+        for m =3:length(chop)
+            if (chop(m)-chop(m-1)) > min_length+1
+                chtrack{ct} = finalTraj{k}((chop(m-1)+1:chop(m)-1), 1:5);
+                ct = ct+1;
+            end
+        end
+        if l - chop(end) > min_length
+             chtrack{ct} = finalTraj{k}((chop(end)+1:end), 1:5);
+             ct = ct+1;
+        end
+         
+    end
+end
+
+        
+chtrack = chtrack(~cellfun('isempty',chtrack));
+save(fullfile(pt, strcat('chtrack_',strtok(fn, '.'), '.mat')), 'chtrack');
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