Merge pull request #3405 from yger/numba_similarity

Optimizations for template_similarity (numba and dependencies)

Author: samuelgarcia

src/spikeinterface/postprocessing/template_similarity.py

@@ -7,6 +7,13 @@
 from ..core.template_tools import get_dense_templates_array
 from ..core.sparsity import ChannelSparsity
 
+try:
+    import numba
+
+    HAVE_NUMBA = True
+except ImportError:
+    HAVE_NUMBA = False
+
 
 class ComputeTemplateSimilarity(AnalyzerExtension):
     """Compute similarity between templates with several methods.
@@ -147,54 +154,15 @@ def _get_data(self):
 compute_template_similarity = ComputeTemplateSimilarity.function_factory()
 
 
-def compute_similarity_with_templates_array(
-    templates_array, other_templates_array, method, support="union", num_shifts=0, sparsity=None, other_sparsity=None
-):
-    import sklearn.metrics.pairwise
+def _compute_similarity_matrix_numpy(templates_array, other_templates_array, num_shifts, mask, method):
 
-    if method == "cosine_similarity":
-        method = "cosine"
-
-    all_metrics = ["cosine", "l1", "l2"]
-
-    if method not in all_metrics:
-        raise ValueError(f"compute_template_similarity (method {method}) not exists")
-
-    assert (
-        templates_array.shape[1] == other_templates_array.shape[1]
-    ), "The number of samples in the templates should be the same for both arrays"
-    assert (
-        templates_array.shape[2] == other_templates_array.shape[2]
-    ), "The number of channels in the templates should be the same for both arrays"
     num_templates = templates_array.shape[0]
     num_samples = templates_array.shape[1]
-    num_channels = templates_array.shape[2]
     other_num_templates = other_templates_array.shape[0]
 
-    same_array = np.array_equal(templates_array, other_templates_array)
-
-    mask = None
-    if sparsity is not None and other_sparsity is not None:
-        if support == "intersection":
-            mask = np.logical_and(sparsity.mask[:, np.newaxis, :], other_sparsity.mask[np.newaxis, :, :])
-        elif support == "union":
-            mask = np.logical_and(sparsity.mask[:, np.newaxis, :], other_sparsity.mask[np.newaxis, :, :])
-            units_overlaps = np.sum(mask, axis=2) > 0
-            mask = np.logical_or(sparsity.mask[:, np.newaxis, :], other_sparsity.mask[np.newaxis, :, :])
-            mask[~units_overlaps] = False
-    if mask is not None:
-        units_overlaps = np.sum(mask, axis=2) > 0
-        overlapping_templates = {}
-        for i in range(num_templates):
-            overlapping_templates[i] = np.flatnonzero(units_overlaps[i])
-    else:
-        # here we make a dense mask and overlapping templates
-        overlapping_templates = {i: np.arange(other_num_templates) for i in range(num_templates)}
-        mask = np.ones((num_templates, other_num_templates, num_channels), dtype=bool)
-
-    assert num_shifts < num_samples, "max_lag is too large"
     num_shifts_both_sides = 2 * num_shifts + 1
     distances = np.ones((num_shifts_both_sides, num_templates, other_num_templates), dtype=np.float32)
+    same_array = np.array_equal(templates_array, other_templates_array)
 
     # We can use the fact that dist[i,j] at lag t is equal to dist[j,i] at time -t
     # So the matrix can be computed only for negative lags and be transposed
@@ -210,8 +178,9 @@ def compute_similarity_with_templates_array(
         tgt_sliced_templates = other_templates_array[:, num_shifts + shift : num_samples - num_shifts + shift]
         for i in range(num_templates):
             src_template = src_sliced_templates[i]
-            tgt_templates = tgt_sliced_templates[overlapping_templates[i]]
-            for gcount, j in enumerate(overlapping_templates[i]):
+            overlapping_templates = np.flatnonzero(np.sum(mask[i], 1))
+            tgt_templates = tgt_sliced_templates[overlapping_templates]
+            for gcount, j in enumerate(overlapping_templates):
                 # symmetric values are handled later
                 if same_array and j < i:
                     # no need exhaustive looping when same template
@@ -222,23 +191,156 @@ def compute_similarity_with_templates_array(
                 if method == "l1":
                     norm_i = np.sum(np.abs(src))
                     norm_j = np.sum(np.abs(tgt))
-                    distances[count, i, j] = sklearn.metrics.pairwise.pairwise_distances(src, tgt, metric="l1").item()
+                    distances[count, i, j] = np.sum(np.abs(src - tgt))
                     distances[count, i, j] /= norm_i + norm_j
                 elif method == "l2":
                     norm_i = np.linalg.norm(src, ord=2)
                     norm_j = np.linalg.norm(tgt, ord=2)
-                    distances[count, i, j] = sklearn.metrics.pairwise.pairwise_distances(src, tgt, metric="l2").item()
+                    distances[count, i, j] = np.linalg.norm(src - tgt, ord=2)
                     distances[count, i, j] /= norm_i + norm_j
-                else:
-                    distances[count, i, j] = sklearn.metrics.pairwise.pairwise_distances(
-                        src, tgt, metric="cosine"
-                    ).item()
+                elif method == "cosine":
+                    norm_i = np.linalg.norm(src, ord=2)
+                    norm_j = np.linalg.norm(tgt, ord=2)
+                    distances[count, i, j] = np.sum(src * tgt)
+                    distances[count, i, j] /= norm_i * norm_j
+                    distances[count, i, j] = 1 - distances[count, i, j]
 
                 if same_array:
                     distances[count, j, i] = distances[count, i, j]
 
         if same_array and num_shifts != 0:
             distances[num_shifts_both_sides - count - 1] = distances[count].T
+    return distances
+
+
+if HAVE_NUMBA:
+
+    from math import sqrt
+
+    @numba.jit(nopython=True, parallel=True, fastmath=True, nogil=True)
+    def _compute_similarity_matrix_numba(templates_array, other_templates_array, num_shifts, mask, method):
+        num_templates = templates_array.shape[0]
+        num_samples = templates_array.shape[1]
+        other_num_templates = other_templates_array.shape[0]
+
+        num_shifts_both_sides = 2 * num_shifts + 1
+        distances = np.ones((num_shifts_both_sides, num_templates, other_num_templates), dtype=np.float32)
+        same_array = np.array_equal(templates_array, other_templates_array)
+
+        # We can use the fact that dist[i,j] at lag t is equal to dist[j,i] at time -t
+        # So the matrix can be computed only for negative lags and be transposed
+
+        if same_array:
+            # optimisation when array are the same because of symetry in shift
+            shift_loop = list(range(-num_shifts, 1))
+        else:
+            shift_loop = list(range(-num_shifts, num_shifts + 1))
+
+        if method == "l1":
+            metric = 0
+        elif method == "l2":
+            metric = 1
+        elif method == "cosine":
+            metric = 2
+
+        for count in range(len(shift_loop)):
+            shift = shift_loop[count]
+            src_sliced_templates = templates_array[:, num_shifts : num_samples - num_shifts]
+            tgt_sliced_templates = other_templates_array[:, num_shifts + shift : num_samples - num_shifts + shift]
+            for i in numba.prange(num_templates):
+                src_template = src_sliced_templates[i]
+                overlapping_templates = np.flatnonzero(np.sum(mask[i], 1))
+                tgt_templates = tgt_sliced_templates[overlapping_templates]
+                for gcount in range(len(overlapping_templates)):
+
+                    j = overlapping_templates[gcount]
+                    # symmetric values are handled later
+                    if same_array and j < i:
+                        # no need exhaustive looping when same template
+                        continue
+                    src = src_template[:, mask[i, j]].flatten()
+                    tgt = (tgt_templates[gcount][:, mask[i, j]]).flatten()
+
+                    norm_i = 0
+                    norm_j = 0
+                    distances[count, i, j] = 0
+
+                    for k in range(len(src)):
+                        if metric == 0:
+                            norm_i += abs(src[k])
+                            norm_j += abs(tgt[k])
+                            distances[count, i, j] += abs(src[k] - tgt[k])
+                        elif metric == 1:
+                            norm_i += src[k] ** 2
+                            norm_j += tgt[k] ** 2
+                            distances[count, i, j] += (src[k] - tgt[k]) ** 2
+                        elif metric == 2:
+                            distances[count, i, j] += src[k] * tgt[k]
+                            norm_i += src[k] ** 2
+                            norm_j += tgt[k] ** 2
+
+                    if metric == 0:
+                        distances[count, i, j] /= norm_i + norm_j
+                    elif metric == 1:
+                        norm_i = sqrt(norm_i)
+                        norm_j = sqrt(norm_j)
+                        distances[count, i, j] = sqrt(distances[count, i, j])
+                        distances[count, i, j] /= norm_i + norm_j
+                    elif metric == 2:
+                        norm_i = sqrt(norm_i)
+                        norm_j = sqrt(norm_j)
+                        distances[count, i, j] /= norm_i * norm_j
+                        distances[count, i, j] = 1 - distances[count, i, j]
+
+                    if same_array:
+                        distances[count, j, i] = distances[count, i, j]
+
+            if same_array and num_shifts != 0:
+                distances[num_shifts_both_sides - count - 1] = distances[count].T
+
+        return distances
+
+    _compute_similarity_matrix = _compute_similarity_matrix_numba
+else:
+    _compute_similarity_matrix = _compute_similarity_matrix_numpy
+
+
+def compute_similarity_with_templates_array(
+    templates_array, other_templates_array, method, support="union", num_shifts=0, sparsity=None, other_sparsity=None
+):
+
+    if method == "cosine_similarity":
+        method = "cosine"
+
+    all_metrics = ["cosine", "l1", "l2"]
+
+    if method not in all_metrics:
+        raise ValueError(f"compute_template_similarity (method {method}) not exists")
+
+    assert (
+        templates_array.shape[1] == other_templates_array.shape[1]
+    ), "The number of samples in the templates should be the same for both arrays"
+    assert (
+        templates_array.shape[2] == other_templates_array.shape[2]
+    ), "The number of channels in the templates should be the same for both arrays"
+    num_templates = templates_array.shape[0]
+    num_samples = templates_array.shape[1]
+    num_channels = templates_array.shape[2]
+    other_num_templates = other_templates_array.shape[0]
+
+    mask = np.ones((num_templates, other_num_templates, num_channels), dtype=bool)
+
+    if sparsity is not None and other_sparsity is not None:
+        if support == "intersection":
+            mask = np.logical_and(sparsity.mask[:, np.newaxis, :], other_sparsity.mask[np.newaxis, :, :])
+        elif support == "union":
+            mask = np.logical_and(sparsity.mask[:, np.newaxis, :], other_sparsity.mask[np.newaxis, :, :])
+            units_overlaps = np.sum(mask, axis=2) > 0
+            mask = np.logical_or(sparsity.mask[:, np.newaxis, :], other_sparsity.mask[np.newaxis, :, :])
+            mask[~units_overlaps] = False
+
+    assert num_shifts < num_samples, "max_lag is too large"
+    distances = _compute_similarity_matrix(templates_array, other_templates_array, num_shifts, mask, method)
 
     distances = np.min(distances, axis=0)
     similarity = 1 - distances

src/spikeinterface/postprocessing/tests/test_correlograms.py

@@ -93,7 +93,6 @@ def test_equal_results_correlograms(window_and_bin_ms):
     )
 
     assert np.array_equal(result_numpy, result_numba)
-    assert np.array_equal(result_numpy, result_numba)
 
 
 @pytest.mark.parametrize("method", ["numpy", param("numba", marks=SKIP_NUMBA)])

src/spikeinterface/postprocessing/tests/test_template_similarity.py

@@ -7,7 +7,23 @@
 )
 
 from spikeinterface.postprocessing import check_equal_template_with_distribution_overlap, ComputeTemplateSimilarity
-from spikeinterface.postprocessing.template_similarity import compute_similarity_with_templates_array
+from spikeinterface.postprocessing.template_similarity import (
+    compute_similarity_with_templates_array,
+    _compute_similarity_matrix_numpy,
+)
+
+try:
+    import numba
+
+    HAVE_NUMBA = True
+    from spikeinterface.postprocessing.template_similarity import _compute_similarity_matrix_numba
+except ModuleNotFoundError as err:
+    HAVE_NUMBA = False
+
+import pytest
+from pytest import param
+
+SKIP_NUMBA = pytest.mark.skipif(not HAVE_NUMBA, reason="Numba not available")
 
 
 class TestSimilarityExtension(AnalyzerExtensionCommonTestSuite):
@@ -72,6 +88,35 @@ def test_compute_similarity_with_templates_array(params):
     print(similarity.shape)
 
 
+pytest.mark.skipif(not HAVE_NUMBA, reason="Numba not available")
+
+
+@pytest.mark.parametrize(
+    "params",
+    [
+        dict(method="cosine", num_shifts=8),
+        dict(method="l1", num_shifts=0),
+        dict(method="l2", num_shifts=0),
+        dict(method="cosine", num_shifts=0),
+    ],
+)
+def test_equal_results_numba(params):
+    """
+    Test that the 2 methods have same results with some varied time bins
+    that are not tested in other tests.
+    """
+
+    rng = np.random.default_rng(seed=2205)
+    templates_array = rng.random(size=(4, 20, 5), dtype=np.float32)
+    other_templates_array = rng.random(size=(2, 20, 5), dtype=np.float32)
+    mask = np.ones((4, 2, 5), dtype=bool)
+
+    result_numpy = _compute_similarity_matrix_numba(templates_array, other_templates_array, mask=mask, **params)
+    result_numba = _compute_similarity_matrix_numpy(templates_array, other_templates_array, mask=mask, **params)
+
+    assert np.allclose(result_numpy, result_numba, 1e-3)
+
+
 if __name__ == "__main__":
     from spikeinterface.postprocessing.tests.common_extension_tests import get_dataset
     from spikeinterface.core import estimate_sparsity