Fix compute matching v3 (#2182)

* some change to test * another change * another attempt * attempt merge * add condition * add auth * fix test and simpler implementation * small typo * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * avoid corner cose of doing the matching loop twice * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Remove n_jobs * Little docs cleanup * Remove internal n_jobs * Remove last internal n_jobs * Apply suggestions from code review * fix test * comment to test * docstring improvements * variable naming * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * new proposal for compute_matching * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: Heberto Mayorquin <[email protected]> Co-authored-by: Alessio Buccino <[email protected]>
SpikeInterface · Nov 9, 2023 · 3291976 · 3291976
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diff --git a/src/spikeinterface/comparison/comparisontools.py b/src/spikeinterface/comparison/comparisontools.py
@@ -124,103 +124,105 @@ def get_optimized_compute_matching_matrix():
 
     @numba.jit(nopython=True, nogil=True)
     def compute_matching_matrix(
-        frames_spike_train1,
-        frames_spike_train2,
+        spike_frames_train1,
+        spike_frames_train2,
         unit_indices1,
         unit_indices2,
-        num_units_sorting1,
-        num_units_sorting2,
+        num_units_train1,
+        num_units_train2,
         delta_frames,
     ):
         """
         Compute a matrix representing the matches between two spike trains.
 
         Given two spike trains, this function finds matching spikes based on a temporal proximity criterion
         defined by `delta_frames`. The resulting matrix indicates the number of matches between units
-        in `frames_spike_train1` and `frames_spike_train2`.
+        in `spike_frames_train1` and `spike_frames_train2`.
 
         Parameters
         ----------
-        frames_spike_train1 : ndarray
-            Array of frames for the first spike train. Should be ordered in ascending order.
-        frames_spike_train2 : ndarray
-            Array of frames for the second spike train. Should be ordered in ascending order.
+        spike_frames_train1 : ndarray
+            An array of integer frame numbers corresponding to spike times for the first train. Must be in ascending order.
+        spike_frames_train2 : ndarray
+            An array of integer frame numbers corresponding to spike times for the second train. Must be in ascending order.
         unit_indices1 : ndarray
-            Array indicating the unit indices corresponding to each spike in `frames_spike_train1`.
+            An array of integers where `unit_indices1[i]` gives the unit index associated with the spike at `spike_frames_train1[i]`.
         unit_indices2 : ndarray
-            Array indicating the unit indices corresponding to each spike in `frames_spike_train2`.
-        num_units_sorting1 : int
-            Total number of units in the first spike train.
-        num_units_sorting2 : int
-            Total number of units in the second spike train.
+            An array of integers where `unit_indices2[i]` gives the unit index associated with the spike at `spike_frames_train2[i]`.
+        num_units_train1 : int
+            The total count of unique units in the first spike train.
+        num_units_train2 : int
+            The total count of unique units in the second spike train.
         delta_frames : int
-            Maximum difference in frames between two spikes to consider them as a match.
+            The inclusive upper limit on the frame difference for which two spikes are considered matching. That is
+            if `abs(spike_frames_train1[i] - spike_frames_train2[j]) <= delta_frames` then the spikes at `spike_frames_train1[i]`
+            and `spike_frames_train2[j]` are considered matching.
 
         Returns
         -------
         matching_matrix : ndarray
-            A matrix of shape (num_units_sorting1, num_units_sorting2) where each entry [i, j] represents
-            the number of matching spikes between unit i of `frames_spike_train1` and unit j of `frames_spike_train2`.
+            A 2D numpy array of shape `(num_units_train1, num_units_train2)`. Each element `[i, j]` represents
+            the count of matching spike pairs between unit `i` from `spike_frames_train1` and unit `j` from `spike_frames_train2`.
+
 
         Notes
         -----
         This algorithm identifies matching spikes between two ordered spike trains.
         By iterating through each spike in the first train, it compares them against spikes in the second train,
         determining matches based on the two spikes frames being within `delta_frames` of each other.
 
-        To avoid redundant comparisons the algorithm maintains a reference, `lower_search_limit_in_second_train`,
+        To avoid redundant comparisons the algorithm maintains a reference, `second_train_search_start `,
         which signifies the minimal index in the second spike train that might match the upcoming spike
-        in the first train. This means that the start of the search moves forward in the second train as the
-        matches between the two trains are found decreasing the number of comparisons needed.
+        in the first train.
+
+        The logic can be summarized as follows:
+        1. Iterate through each spike in the first train
+        2. For each spike, find the first match in the second train.
+        3. Save the index of the first match as the new `second_train_search_start `
+        3. For each match, find as many matches as possible from the first match onwards.
 
-        An important condition here is thatthe same spike is not matched twice. This is managed by keeping track
-        of the last matched frame for each unit pair in `previous_frame1_match` and `previous_frame2_match`
+        An important condition here is that the same spike is not matched twice. This is managed by keeping track
+        of the last matched frame for each unit pair in `last_match_frame1` and `last_match_frame2`
 
         For more details on the rationale behind this approach, refer to the documentation of this module and/or
-        the  metrics section in SpikeForest documentation.
+        the metrics section in SpikeForest documentation.
         """
 
-        matching_matrix = np.zeros((num_units_sorting1, num_units_sorting2), dtype=np.uint16)
+        matching_matrix = np.zeros((num_units_train1, num_units_train2), dtype=np.uint16)
 
         # Used to avoid the same spike matching twice
-        previous_frame1_match = -np.ones_like(matching_matrix, dtype=np.int64)
-        previous_frame2_match = -np.ones_like(matching_matrix, dtype=np.int64)
-
-        lower_search_limit_in_second_train = 0
-
-        for index1 in range(len(frames_spike_train1)):
-            # Keeps track of which frame in the second spike train should be used as a search start for matches
-            index2 = lower_search_limit_in_second_train
-            frame1 = frames_spike_train1[index1]
-
-            # Determine next_frame1 if current frame is not the last frame
-            not_in_the_last_loop = index1 < len(frames_spike_train1) - 1
-            if not_in_the_last_loop:
-                next_frame1 = frames_spike_train1[index1 + 1]
-
-            while index2 < len(frames_spike_train2):
-                frame2 = frames_spike_train2[index2]
-                not_a_match = abs(frame1 - frame2) > delta_frames
-                if not_a_match:
-                    # Go to the next frame in the first train
+        last_match_frame1 = -np.ones_like(matching_matrix, dtype=np.int64)
+        last_match_frame2 = -np.ones_like(matching_matrix, dtype=np.int64)
+
+        num_spike_frames_train1 = len(spike_frames_train1)
+        num_spike_frames_train2 = len(spike_frames_train2)
+
+        # Keeps track of which frame in the second spike train should be used as a search start for matches
+        second_train_search_start = 0
+        for index1 in range(num_spike_frames_train1):
+            frame1 = spike_frames_train1[index1]
+
+            for index2 in range(second_train_search_start, num_spike_frames_train2):
+                frame2 = spike_frames_train2[index2]
+                if frame2 < frame1 - delta_frames:
+                    # no match move the left limit for the next loop
+                    second_train_search_start += 1
+                    continue
+                elif frame2 > frame1 + delta_frames:
+                    # no match stop search in train2 and continue increment in train1
                     break
+                else:
+                    # match
+                    unit_index1, unit_index2 = unit_indices1[index1], unit_indices2[index2]
 
-                # Map the match to a matrix
-                row, column = unit_indices1[index1], unit_indices2[index2]
-
-                # The same spike cannot be matched twice see the notes in the docstring for more info on this constraint
-                if frame1 != previous_frame1_match[row, column] and frame2 != previous_frame2_match[row, column]:
-                    previous_frame1_match[row, column] = frame1
-                    previous_frame2_match[row, column] = frame2
-
-                    matching_matrix[row, column] += 1
-
-                index2 += 1
+                    if (
+                        frame1 != last_match_frame1[unit_index1, unit_index2]
+                        and frame2 != last_match_frame2[unit_index1, unit_index2]
+                    ):
+                        last_match_frame1[unit_index1, unit_index2] = frame1
+                        last_match_frame2[unit_index1, unit_index2] = frame2
 
-                # Advance the lower_search_limit_in_second_train if the next frame in the first train does not match
-                not_a_match_with_next = abs(next_frame1 - frame2) > delta_frames
-                if not_a_match_with_next:
-                    lower_search_limit_in_second_train = index2
+                        matching_matrix[unit_index1, unit_index2] += 1
 
         return matching_matrix
 
@@ -230,7 +232,7 @@ def compute_matching_matrix(
     return compute_matching_matrix
 
 
-def make_match_count_matrix(sorting1, sorting2, delta_frames, n_jobs=None):
+def make_match_count_matrix(sorting1, sorting2, delta_frames):
     num_units_sorting1 = sorting1.get_num_units()
     num_units_sorting2 = sorting2.get_num_units()
     matching_matrix = np.zeros((num_units_sorting1, num_units_sorting2), dtype=np.uint16)
@@ -275,7 +277,7 @@ def make_match_count_matrix(sorting1, sorting2, delta_frames, n_jobs=None):
     return match_event_counts_df
 
 
-def make_agreement_scores(sorting1, sorting2, delta_frames, n_jobs=1):
+def make_agreement_scores(sorting1, sorting2, delta_frames):
     """
     Make the agreement matrix.
     No threshold (min_score) is applied at this step.
@@ -291,8 +293,6 @@ def make_agreement_scores(sorting1, sorting2, delta_frames, n_jobs=1):
         The second sorting extractor
     delta_frames: int
         Number of frames to consider spikes coincident
-    n_jobs: int
-        Number of jobs to run in parallel
 
     Returns
     -------
@@ -309,7 +309,7 @@ def make_agreement_scores(sorting1, sorting2, delta_frames, n_jobs=1):
     event_counts1 = pd.Series(ev_counts1, index=unit1_ids)
     event_counts2 = pd.Series(ev_counts2, index=unit2_ids)
 
-    match_event_count = make_match_count_matrix(sorting1, sorting2, delta_frames, n_jobs=n_jobs)
+    match_event_count = make_match_count_matrix(sorting1, sorting2, delta_frames)
 
     agreement_scores = make_agreement_scores_from_count(match_event_count, event_counts1, event_counts2)
 

diff --git a/src/spikeinterface/comparison/paircomparisons.py b/src/spikeinterface/comparison/paircomparisons.py
@@ -84,9 +84,7 @@ def _do_agreement(self):
         self.event_counts2 = do_count_event(self.sorting2)
 
         # matrix of  event match count for each pair
-        self.match_event_count = make_match_count_matrix(
-            self.sorting1, self.sorting2, self.delta_frames, n_jobs=self.n_jobs
-        )
+        self.match_event_count = make_match_count_matrix(self.sorting1, self.sorting2, self.delta_frames)
 
         # agreement matrix score for each pair
         self.agreement_scores = make_agreement_scores_from_count(

diff --git a/src/spikeinterface/comparison/tests/test_comparisontools.py b/src/spikeinterface/comparison/tests/test_comparisontools.py
@@ -135,6 +135,23 @@ def test_make_match_count_matrix_repeated_matching_but_no_double_counting():
     assert_array_equal(result.to_numpy(), expected_result)
 
 
+def test_make_match_count_matrix_test_proper_search_in_the_second_train():
+    "Search exhaustively in the second train, but only within the delta_frames window, do not terminate search early"
+    frames_spike_train1 = [500, 600, 800]
+    frames_spike_train2 = [0, 100, 200, 300, 500, 800]
+    unit_indices1 = [0, 0, 0]
+    unit_indices2 = [0, 0, 0, 0, 0, 0]
+    delta_frames = 20
+
+    sorting1, sorting2 = make_sorting(frames_spike_train1, unit_indices1, frames_spike_train2, unit_indices2)
+
+    result = make_match_count_matrix(sorting1, sorting2, delta_frames=delta_frames)
+
+    expected_result = np.array([[2]])
+
+    assert_array_equal(result.to_numpy(), expected_result)
+
+
 def test_make_agreement_scores():
     delta_frames = 10
 
@@ -150,15 +167,15 @@ def test_make_agreement_scores():
         [0, 0, 5],
     )
 
-    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames, n_jobs=1)
+    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames)
     print(agreement_scores)
 
     ok = np.array([[2 / 3, 0], [0, 1.0]], dtype="float64")
 
     assert_array_equal(agreement_scores.values, ok)
 
     # test if symetric
-    agreement_scores2 = make_agreement_scores(sorting2, sorting1, delta_frames, n_jobs=1)
+    agreement_scores2 = make_agreement_scores(sorting2, sorting1, delta_frames)
     assert_array_equal(agreement_scores, agreement_scores2.T)
 
 
@@ -178,7 +195,7 @@ def test_make_possible_match():
         [0, 0, 5],
     )
 
-    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames, n_jobs=1)
+    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames)
 
     possible_match_12, possible_match_21 = make_possible_match(agreement_scores, min_accuracy)
 
@@ -207,7 +224,7 @@ def test_make_best_match():
         [0, 0, 5],
     )
 
-    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames, n_jobs=1)
+    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames)
 
     best_match_12, best_match_21 = make_best_match(agreement_scores, min_accuracy)
 
@@ -236,7 +253,7 @@ def test_make_hungarian_match():
         [0, 0, 5],
     )
 
-    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames, n_jobs=1)
+    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames)
 
     hungarian_match_12, hungarian_match_21 = make_hungarian_match(agreement_scores, min_accuracy)
 
@@ -344,8 +361,8 @@ def test_do_confusion_matrix():
 
     event_counts1 = do_count_event(sorting1)
     event_counts2 = do_count_event(sorting2)
-    match_event_count = make_match_count_matrix(sorting1, sorting2, delta_frames, n_jobs=1)
-    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames, n_jobs=1)
+    match_event_count = make_match_count_matrix(sorting1, sorting2, delta_frames)
+    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames)
     hungarian_match_12, hungarian_match_21 = make_hungarian_match(agreement_scores, min_accuracy)
 
     confusion = do_confusion_matrix(event_counts1, event_counts2, hungarian_match_12, match_event_count)
@@ -363,8 +380,8 @@ def test_do_confusion_matrix():
 
     event_counts1 = do_count_event(sorting1)
     event_counts2 = do_count_event(sorting2)
-    match_event_count = make_match_count_matrix(sorting1, sorting2, delta_frames, n_jobs=1)
-    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames, n_jobs=1)
+    match_event_count = make_match_count_matrix(sorting1, sorting2, delta_frames)
+    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames)
     hungarian_match_12, hungarian_match_21 = make_hungarian_match(agreement_scores, min_accuracy)
 
     confusion = do_confusion_matrix(event_counts1, event_counts2, hungarian_match_12, match_event_count)
@@ -391,8 +408,8 @@ def test_do_count_score_and_perf():
 
     event_counts1 = do_count_event(sorting1)
     event_counts2 = do_count_event(sorting2)
-    match_event_count = make_match_count_matrix(sorting1, sorting2, delta_frames, n_jobs=1)
-    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames, n_jobs=1)
+    match_event_count = make_match_count_matrix(sorting1, sorting2, delta_frames)
+    agreement_scores = make_agreement_scores(sorting1, sorting2, delta_frames)
     hungarian_match_12, hungarian_match_21 = make_hungarian_match(agreement_scores, min_accuracy)
 
     count_score = do_count_score(event_counts1, event_counts2, hungarian_match_12, match_event_count)
@@ -415,13 +432,20 @@ def test_do_count_score_and_perf():
 
 if __name__ == "__main__":
     test_make_match_count_matrix()
-    test_make_agreement_scores()
-
-    test_make_possible_match()
-    test_make_best_match()
-    test_make_hungarian_match()
-
-    test_do_score_labels()
-    test_compare_spike_trains()
-    test_do_confusion_matrix()
-    test_do_count_score_and_perf()
+    test_make_match_count_matrix_sorting_with_itself_simple()
+    test_make_match_count_matrix_sorting_with_itself_longer()
+    test_make_match_count_matrix_with_mismatched_sortings()
+    test_make_match_count_matrix_no_double_matching()
+    test_make_match_count_matrix_repeated_matching_but_no_double_counting()
+    test_make_match_count_matrix_test_proper_search_in_the_second_train()
+
+    # test_make_agreement_scores()
+
+    # test_make_possible_match()
+    # test_make_best_match()
+    # test_make_hungarian_match()
+
+    # test_do_score_labels()
+    # test_compare_spike_trains()
+    # test_do_confusion_matrix()
+    # test_do_count_score_and_perf()