UnitMatchPy 2.31__tar.gz → 2.40__tar.gz

{UnitMatchPy-2.31/UnitMatchPy.egg-info → UnitMatchPy-2.40}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: UnitMatchPy
-Version: 2.31
+Version: 2.40
 Author: Enny van Beest, Celian Bimbard and Sam Dodgson
 Author-email: e.beest@ucl.ac.uk
 Requires-Python: >=3.7

{UnitMatchPy-2.31 → UnitMatchPy-2.40}/UnitMatchPy/Overlord.py

@@ -124,7 +124,6 @@ def extract_metric_scores(extracted_wave_properties, session_switch, within_sess
     thrs_opt = mf.get_threshold(total_score, within_session, euclid_dist, param, is_first_pass = False)
     param['n_expected_matches'] = np.sum( (total_score > thrs_opt).astype(int))
     prior_match = 1 - ( param['n_expected_matches'] / len(include_these_pairs))
-
     thrs_opt = np.quantile(total_score[include_these_pairs_idx.astype(bool)], prior_match)
     candidate_pairs = total_score > thrs_opt
 

{UnitMatchPy-2.31 → UnitMatchPy-2.40}/UnitMatchPy/metric_functions.py

@@ -506,7 +506,6 @@ def drift_correction_basic(candidate_pairs, session_switch, avg_centroid, avg_wa
 
     drift = np.nanmedian( np.nanmean( avg_centroid[:, best_pairs[idx,0].squeeze(),:], axis = 2) - np.nanmean( avg_centroid[:,best_pairs[idx,1].squeeze(),:], axis = 2), axis = 1)
 
-
     ##need to add the drift to the location
     avg_waveform_per_tp[0,session_switch[1]:,:,:] += drift[0]
     avg_waveform_per_tp[1,session_switch[1]:,:,:] += drift[1]
@@ -590,19 +589,27 @@ def apply_drift_correction_per_shank(pairs, sid, session_switch, avg_centroid, a
     drift_per_shank = np.zeros([n_shanks,3])
 
     for i in range(n_shanks):
-        max_dist += shank_dist
+        max_dist += shank_dist #beginning of loop shift maximum distance
 
         #get which shank each unit is on
         correct_shank_a = np.logical_and(centroid_a[1,:] < max_dist,  centroid_a[1,:] > min_dist)
         correct_shank_b = np.logical_and(centroid_b[1,:] < max_dist,  centroid_b[1,:] > min_dist)
 
+        if np.all(correct_shank_a == correct_shank_b) != True:
+            print(f'These pairs may be bad {np.argwhere(correct_shank_a != correct_shank_b)}')
+            #delete pairs which are on different shanks ##sam's fix
+                bad_idxs = np.argwhere(correct_shank_a != correct_shank_b)
+                correct_shank_a = np.delete(correct_shank_a, bad_idxs)
+                correct_shank_b = np.delete(correct_shank_b, bad_idxs)
+
+            
         drifts = centroid_a[:,correct_shank_a] - centroid_b[:,correct_shank_b]
-        drift = np.nanmedian(drifts, axis = 1)
+        drift =  np.nanmedian(drifts, axis = 1)
         drift_per_shank[i,:] = drift
 
         #need to get idx for each shank, to apply correct drift correction
 
-        shank_session_idx = session_switch[sid] + np.argwhere(shank_id == i) 
+        shank_session_idx = session_switch[sid] + np.argwhere( shank_id == i) 
 
         avg_waveform_per_tp[0,shank_session_idx,:,:] += drift[0]
         avg_waveform_per_tp[1,shank_session_idx,:,:] += drift[1]
@@ -699,10 +706,11 @@ def test_matches_per_shank(pairs, avg_centroid, sid, param):
             correct_shank_b = np.logical_and(centroid_b[1,:] < max_dist,  centroid_b[1,:] > min_dist)
 
             if np.all(correct_shank_a == correct_shank_b) != True:
-                #print(f'These pairs may be bad {np.argwhere(correct_shank_a != correct_shank_b)}')
+                print(f'These pairs may be bad {np.argwhere(correct_shank_a != correct_shank_b)}')
                 #delete pairs which are one different shanks
-                correct_shank_a = np.delete(correct_shank_a, np.argwhere(correct_shank_a != correct_shank_b))
-                correct_shank_b = np.delete(correct_shank_b, np.argwhere(correct_shank_a != correct_shank_b))
+                bad_idxs = np.argwhere(correct_shank_a != correct_shank_b)
+                correct_shank_a = np.delete(correct_shank_a, bad_idxs)
+                correct_shank_b = np.delete(correct_shank_b, bad_idxs)
                 
             shank_id_tmp[correct_shank_a] = i
 
@@ -770,10 +778,11 @@ def drift_n_sessions(candidate_pairs, session_switch, avg_centroid, avg_waveform
                 drifts = np.zeros( (n_sessions - 1, param['no_shanks'], 3))
                 drifts[did,:,:], avg_waveform_per_tp, avg_centroid = apply_drift_correction_per_shank(pairs, did, session_switch, avg_centroid, avg_waveform_per_tp, param)
                 print(f'Done drift correction per shank for session pair {did+1} and {did+2}')
-            else:
+            elif len(pairs)>0: #if there exist pairs across sessions:
                 drifts = np.zeros( (n_sessions - 1, 3))
                 drifts[did,:], avg_waveform_per_tp, avg_centroid = apply_drift_correction_basic(pairs, did, session_switch, avg_centroid, avg_waveform_per_tp)
-
+            elif len(pairs)==0:
+                print('No pairs across sessions to perform drift correction.')
     return drifts, avg_centroid, avg_waveform_per_tp
 
 

{UnitMatchPy-2.31 → UnitMatchPy-2.40/UnitMatchPy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: UnitMatchPy
-Version: 2.31
+Version: 2.40
 Author: Enny van Beest, Celian Bimbard and Sam Dodgson
 Author-email: e.beest@ucl.ac.uk
 Requires-Python: >=3.7

{UnitMatchPy-2.31 → UnitMatchPy-2.40}/setup.py

@@ -5,7 +5,7 @@ with open('README.md', 'r') as f:
 
 setup(
     name="UnitMatchPy",
-    version="2.31",
+    version="2.40",
     descriptin="Description of the package",
     author="Enny van Beest, Celian Bimbard and Sam Dodgson",
     author_email="e.beest@ucl.ac.uk",