angles

icy_to_SpotOn_conversion.m

+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Convert the output of icy to input for Spot-On
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Select the xml result file generated by icy
+[fn pt]= uigetfile(('*.xml'), 'Choose a File')
+% read as an Excel file
+A = xlsread(fullfile(pt,fn)); % select the xml file
+%% set pixel size - if icy results are in pixels. Otherwise px = 1
+px = 0.11;
+time_int = 0.050;
+
+%% create tracks
+id = unique(A(:,5));
+ct = 1;
+
+for k = 1 : length(id)-1
+    ii = find(A(:,5)==id(k));
+    B = A(ii,:);
+    
+   % B(B(:, 9)== 2, :)= [];
+    
+    chop = [1, transpose(find(B(:, 9)== 2))];
+    
+    if length(chop) == 1
+               trackedPar(ct).xy = [B(:,10) * px, B(:,11) * px];
+               trackedPar(ct).Frame = B(:,8);
+               trackedPar(ct).TimeStamp = B(:,8) * time_int;  
+               ct = ct+1;
+    else
+    
+    
+        if chop(2) > 2
+            trackedPar(ct).xy = [B(1:chop(2)-1,10)* px, B(1:chop(2)-1,11)* px];
+            trackedPar(ct).Frame = B(1:chop(2)-1,8);
+            trackedPar(ct).TimeStamp = B(1:chop(2)-1,8) * 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)) > 3
+                    trackedPar(ct).xy = [B((chop(m-1)+1:chop(m)-1),10)*px, B((chop(m-1)+1:chop(m)-1),11)*px];
+                    trackedPar(ct).Frame = B((chop(m-1)+1:chop(m)-1),8);
+                    trackedPar(ct).TimeStamp = B((chop(m-1)+1:chop(m)-1),8) * time_int;
+                    ct = ct+1;
+                else
+                end
+            end
+        end
+    end
+end
+
+save(strcat('spot-on1_',strtok(fn, '.'), '.mat'))
+