workflow correction to BG image

example/workflow.py

@@ -624,12 +624,22 @@ def calculate_BG_image(dirname, extension):
 
             # segmenting the image if there are more than 1 frames
             if N_img is None or N_img>1:
+
+                if type(remove_BG)==str:
+                    print('\n','using given background image')
+                    BG = imread(remove_BG)*1.0
+                elif remove_BG==True:
+                    print('\n','calculating background image')
+                    BG = calculate_BG_image(dirname, ext)
+                else:
+                    BG=False
+
                 loopSegment = loop_segmentation(dirname, 
                                                 particle_size=p_size,
                                                 extension=ext,
                                                 image_start=image_start,
                                                 N_img=N_img,
-                                                remove_ststic_BG=remove_BG,
+                                                remove_ststic_BG=BG,
                                                 sigma=sigma, 
                                                 median=median,
                                                 threshold=threshold, 

myptv/tracking_mod.py

@@ -983,16 +983,24 @@ def build_trajectories_from_frame(self, frame_num, backwards=False,
         
         If backwards=True then the tracking is backwards in time.
         '''
+
+        # ensure there are particles to track in this frame number
+        if frame_num not in list(self.particles.keys()):
+            return None
+
         # a list to hold trajectories and trajectory particle identifiers
         trajs = []
 
         # a list to hold the trajectory noise levels
         NSRs = []
 
         # 0) if above 20% of particles in the frame were used, clear them
-        uf = len(self.used_particles[frame_num])/len(self.particles[frame_num])
-        if uf > 0.2:
-            self.clear_used_particles()
+        if frame_num in list(self.used_particles.keys()):
+            Nused = len(self.used_particles[frame_num])
+            Nf = len(self.particles[frame_num])
+            uf = Nused / Nf
+            if uf > 0.2:
+                self.clear_used_particles()
 
         # 1) building trajectories from particles in the given frame number
         if backwards==False: 
@@ -1380,14 +1388,17 @@ def smooth_trajectory(traj, Ns):
 
 
 # Tests:
-
-fname = '/home/ron/Desktop/Research/jetArrayTank/20240821/Rec2/particles'
-max_dt = 3 
-Ns = 11
-NSR_th = 0.25
-tmf = tracker_multiframe(fname, max_dt, Ns, d_max=0.5, dv_max=0.5, NSR_th=NSR_th)    
-
-tmf.track_frames(f0=None, fe=None, frame_skips=5)
+if __name__ == "__main__":
+    fname = '/home/ron/Desktop/Research/jetArrayTank/20241020_puffs/Rec18/particles'
+    max_dt = 3 
+    Ns = 11
+    NSR_th = 0.25
+    tmf = tracker_multiframe(fname, max_dt, Ns, d_max=0.5, dv_max=0.5, NSR_th=NSR_th)
+
+    f0 = 134
+    fe = None
+    frame_skips = 5
+    tmf.track_frames(f0=f0, fe=fe, frame_skips=frame_skips)