angles

vbSPT_to_SpotOn.m

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Convert the output of vbSPT synthetic to input for Spot-On
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+clear
+clear all
+% Select the xml result file generated by icy
+[fn pt] = uigetfile(('*.mat'), 'Choose a File');
+load(fn)
+
+time_int = 0.050;
+min_length = 1; %min trajectory length minus 1
+%% set number of trajectories 
+traj_no = 10000;
+ct=1;
+for k = 1 : traj_no
+    l = size(finalTraj{k},1);
+    V = [];
+   
+    %create required struct
+    for i = 1:l
+        
+        %take slice
+        if finalTraj{k}(i,3)>= -100 && finalTraj{k}(i,3)<= 100
+           V(i) = i;
+        end
+    end
+        
+        V(V==0) = [];
+   
+        
+        %if M(i) = 2 then particle has reappeared in frame i+1 after
+        %disappearing for 1 or more frames
+        M = zeros(length(V)-1:1);
+        for j = 2 : length(V)
+            if V(j) - V(j-1) == 1
+               M(j-1) = 1;
+            else
+               M(j-1) = 2;
+            end
+        end
+        
+        %chop trajectories
+        chop = [1, find(M == 2)];
+           
+            %in case there are no blinks
+            if length(chop) == 1 && length(V)> 1
+               trackedPar(ct).xy = [finalTraj{k}(V,1)/1000, finalTraj{k}(V,2)/1000];
+               trackedPar(ct).Frame = transpose(V);
+               trackedPar(ct).TimeStamp = trackedPar(ct).Frame * time_int;  
+               ct = ct+1;
+            elseif length(chop)>1 && length(V)> 1
+                %in case there are blinks
+                %add trajectories before the first 2
+                if  chop(2) > min_length
+                    trackedPar(ct).xy = [finalTraj{k}(V(1:chop(2)),1)/1000, finalTraj{k}(V(1:chop(2)),2)/1000];
+                    trackedPar(ct).Frame = transpose(V(1:chop(2)));
+                    trackedPar(ct).TimeStamp = trackedPar(ct).Frame * time_int;
+                    ct = ct+1;
+                else
+                end
+            
+                if length(chop) > 2
+                %add trajectories between 2s
+                for m =3:length(chop)
+                    if (chop(m)-chop(m-1)) > min_length
+                        trackedPar(ct).xy = [finalTraj{k}(V(chop(m-1)+1:chop(m)),1)/1000, finalTraj{k}(V(chop(m-1)+1:chop(m)),2)/1000];
+                        trackedPar(ct).Frame = transpose(V(chop(m-1)+1:chop(m)));
+                        trackedPar(ct).TimeStamp = trackedPar(ct).Frame * time_int;
+                        ct = ct+1;
+                    else
+                    end
+                end
+                end
+            
+                %add remaining trajectory after the last 2
+            if length(V) - chop(end) > min_length
+                trackedPar(ct).xy = [finalTraj{k}(V(chop(end)+1:end),1)/1000, finalTraj{k}(V(chop(end)+1:end),2)/1000];
+                trackedPar(ct).Frame = transpose(V(chop(end)+1:end));
+                trackedPar(ct).TimeStamp = trackedPar(ct).Frame * time_int;
+                ct = ct+1; 
+            end
+            end
+               
+end
+    
+  
+            
+ %       if length(V) >= 3
+ %           trackedPar(k).xy = [finalTraj{k}(V,1), finalTraj{k}(V,2)];
+ %           trackedPar(k).Frame = transpose(V);
+  %          trackedPar(k).TimeStamp = trackedPar(k).Frame * time_int; 
+ %       else
+ %       end
+  
+
+
+trackedPar = trackedPar(~cellfun(@isempty,{trackedPar.xy}));
+save(strcat('spot-On_',strtok(fn, '.'), '.mat'))