catch cases where the track is outside the atlas region volume and remove these coordinates

Author: mayofaulkner

ibllib/pipes/ephys_alignment.py

@@ -35,6 +35,13 @@ def __init__(self, xyz_picks, chn_depths=None, track_prev=None,
         self.xyz_samples = histology.interpolate_along_track(self.xyz_track,
                                                              self.sampling_trk -
                                                              self.sampling_trk[0])
+        # ensure none of the track is outside the y or x lim of atlas
+        xlim = np.bitwise_and(self.xyz_samples[:, 0] > self.brain_atlas.bc.xlim[0],
+                              self.xyz_samples[:, 0] < self.brain_atlas.bc.xlim[1])
+        ylim = np.bitwise_and(self.xyz_samples[:, 1] < self.brain_atlas.bc.ylim[0],
+                              self.xyz_samples[:, 1] > self.brain_atlas.bc.ylim[1])
+        rem = np.bitwise_and(xlim, ylim)
+        self.xyz_samples = self.xyz_samples[rem]
 
         self.region, self.region_label, self.region_colour, self.region_id\
             = self.get_histology_regions(self.xyz_samples, self.sampling_trk, self.brain_atlas)