Merge pull request #3559 from chrishalcrow/hardcode-sync-sizes

Hard code `synchony_sizes`

doc/get_started/quickstart.rst

@@ -673,7 +673,7 @@ compute quality metrics (some quality metrics require certain extensions
                               'min_spikes': 0,
                               'window_size_s': 1},
      'snr': {'peak_mode': 'extremum', 'peak_sign': 'neg'},
-     'synchrony': {'synchrony_sizes': (2, 4, 8)}}
+     'synchrony': {}
 
 
 Since the recording is very short, let’s change some parameters to

doc/modules/qualitymetrics/synchrony.rst

@@ -12,7 +12,7 @@ trains. This way synchronous events can be found both in multi-unit and single-u
 Complexity is calculated by counting the number of spikes (i.e. non-empty bins) that occur at the same sample index,
 within and across spike trains.
 
-Synchrony metrics can be computed for different synchrony sizes (>1), defining the number of simultaneous spikes to count.
+Synchrony metrics are computed for 2, 4 and 8 synchronous spikes.
 
 
 
@@ -29,7 +29,7 @@ Example code
 
     import spikeinterface.qualitymetrics as sqm
     # Combine a sorting and recording into a sorting_analyzer
-    synchrony = sqm.compute_synchrony_metrics(sorting_analyzer=sorting_analyzer synchrony_sizes=(2, 4, 8))
+    synchrony = sqm.compute_synchrony_metrics(sorting_analyzer=sorting_analyzer)
     # synchrony is a tuple of dicts with the synchrony metrics for each unit
 
 

src/spikeinterface/qualitymetrics/__init__.py

@@ -6,4 +6,4 @@
     get_default_qm_params,
 )
 from .pca_metrics import get_quality_pca_metric_list
-from .misc_metrics import get_synchrony_counts
+from .misc_metrics import _get_synchrony_counts

src/spikeinterface/qualitymetrics/misc_metrics.py

@@ -520,18 +520,18 @@ def compute_sliding_rp_violations(
 )
 
 
-def get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids):
+def _get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids):
     """
     Compute synchrony counts, the number of simultaneous spikes with sizes `synchrony_sizes`.
 
     Parameters
     ----------
     spikes : np.array
         Structured numpy array with fields ("sample_index", "unit_index", "segment_index").
-    synchrony_sizes : numpy array
-        The synchrony sizes to compute. Should be pre-sorted.
     all_unit_ids : list or None, default: None
         List of unit ids to compute the synchrony metrics. Expecting all units.
+    synchrony_sizes : None or np.array, default: None
+        The synchrony sizes to compute. Should be pre-sorted.
 
     Returns
     -------
@@ -565,37 +565,38 @@ def get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids):
     return synchrony_counts
 
 
-def compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=(2, 4, 8), unit_ids=None):
+def compute_synchrony_metrics(sorting_analyzer, unit_ids=None, synchrony_sizes=None):
     """
     Compute synchrony metrics. Synchrony metrics represent the rate of occurrences of
-    "synchrony_size" spikes at the exact same sample index.
+    spikes at the exact same sample index, with synchrony sizes 2, 4 and 8.
 
     Parameters
     ----------
     sorting_analyzer : SortingAnalyzer
         A SortingAnalyzer object.
-    synchrony_sizes : list or tuple, default: (2, 4, 8)
-        The synchrony sizes to compute.
     unit_ids : list or None, default: None
         List of unit ids to compute the synchrony metrics. If None, all units are used.
+    synchrony_sizes: None, default: None
+        Deprecated argument. Please use private `_get_synchrony_counts` if you need finer control over number of synchronous spikes.
 
     Returns
     -------
     sync_spike_{X} : dict
         The synchrony metric for synchrony size X.
-        Returns are as many as synchrony_sizes.
 
     References
     ----------
     Based on concepts described in [Grün]_
     This code was adapted from `Elephant - Electrophysiology Analysis Toolkit <https://github.com/NeuralEnsemble/elephant/blob/master/elephant/spike_train_synchrony.py#L245>`_
     """
-    assert min(synchrony_sizes) > 1, "Synchrony sizes must be greater than 1"
-    # Sort the synchrony times so we can slice numpy arrays, instead of using dicts
-    synchrony_sizes_np = np.array(synchrony_sizes, dtype=np.int16)
-    synchrony_sizes_np.sort()
 
-    res = namedtuple("synchrony_metrics", [f"sync_spike_{size}" for size in synchrony_sizes_np])
+    if synchrony_sizes is not None:
+        warning_message = "Custom `synchrony_sizes` is deprecated; the `synchrony_metrics` will be computed using `synchrony_sizes = [2,4,8]`"
+        warnings.warn(warning_message, DeprecationWarning, stacklevel=2)
+
+    synchrony_sizes = np.array([2, 4, 8])
+
+    res = namedtuple("synchrony_metrics", [f"sync_spike_{size}" for size in synchrony_sizes])
 
     sorting = sorting_analyzer.sorting
 
@@ -606,10 +607,10 @@ def compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=(2, 4, 8), unit_
 
     spikes = sorting.to_spike_vector()
     all_unit_ids = sorting.unit_ids
-    synchrony_counts = get_synchrony_counts(spikes, synchrony_sizes_np, all_unit_ids)
+    synchrony_counts = _get_synchrony_counts(spikes, synchrony_sizes, all_unit_ids)
 
     synchrony_metrics_dict = {}
-    for sync_idx, synchrony_size in enumerate(synchrony_sizes_np):
+    for sync_idx, synchrony_size in enumerate(synchrony_sizes):
         sync_id_metrics_dict = {}
         for i, unit_id in enumerate(all_unit_ids):
             if unit_id not in unit_ids:
@@ -623,7 +624,7 @@ def compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=(2, 4, 8), unit_
     return res(**synchrony_metrics_dict)
 
 
-_default_params["synchrony"] = dict(synchrony_sizes=(2, 4, 8))
+_default_params["synchrony"] = dict()
 
 
 def compute_firing_ranges(sorting_analyzer, bin_size_s=5, percentiles=(5, 95), unit_ids=None):

src/spikeinterface/qualitymetrics/tests/test_metrics_functions.py

@@ -39,7 +39,7 @@
     compute_firing_ranges,
     compute_amplitude_cv_metrics,
     compute_sd_ratio,
-    get_synchrony_counts,
+    _get_synchrony_counts,
     compute_quality_metrics,
 )
 
@@ -352,7 +352,7 @@ def test_synchrony_counts_no_sync():
     one_spike["sample_index"] = spike_times
     one_spike["unit_index"] = spike_units
 
-    sync_count = get_synchrony_counts(one_spike, np.array((2)), [0])
+    sync_count = _get_synchrony_counts(one_spike, np.array([2, 4, 8]), [0])
 
     assert np.all(sync_count[0] == np.array([0]))
 
@@ -372,7 +372,7 @@ def test_synchrony_counts_one_sync():
     two_spikes["sample_index"] = np.concatenate((spike_indices, added_spikes_indices))
     two_spikes["unit_index"] = np.concatenate((spike_labels, added_spikes_labels))
 
-    sync_count = get_synchrony_counts(two_spikes, np.array((2)), [0, 1])
+    sync_count = _get_synchrony_counts(two_spikes, np.array([2, 4, 8]), [0, 1])
 
     assert np.all(sync_count[0] == np.array([1, 1]))
 
@@ -392,7 +392,7 @@ def test_synchrony_counts_one_quad_sync():
     four_spikes["sample_index"] = np.concatenate((spike_indices, added_spikes_indices))
     four_spikes["unit_index"] = np.concatenate((spike_labels, added_spikes_labels))
 
-    sync_count = get_synchrony_counts(four_spikes, np.array((2, 4)), [0, 1, 2, 3])
+    sync_count = _get_synchrony_counts(four_spikes, np.array([2, 4, 8]), [0, 1, 2, 3])
 
     assert np.all(sync_count[0] == np.array([1, 1, 1, 1]))
     assert np.all(sync_count[1] == np.array([1, 1, 1, 1]))
@@ -409,7 +409,7 @@ def test_synchrony_counts_not_all_units():
     three_spikes["sample_index"] = np.concatenate((spike_indices, added_spikes_indices))
     three_spikes["unit_index"] = np.concatenate((spike_labels, added_spikes_labels))
 
-    sync_count = get_synchrony_counts(three_spikes, np.array((2)), [0, 1, 2])
+    sync_count = _get_synchrony_counts(three_spikes, np.array([2, 4, 8]), [0, 1, 2])
 
     assert np.all(sync_count[0] == np.array([0, 1, 1]))
 
@@ -610,9 +610,9 @@ def test_calculate_rp_violations(sorting_analyzer_violations):
 def test_synchrony_metrics(sorting_analyzer_simple):
     sorting_analyzer = sorting_analyzer_simple
     sorting = sorting_analyzer.sorting
-    synchrony_sizes = (2, 3, 4)
-    synchrony_metrics = compute_synchrony_metrics(sorting_analyzer, synchrony_sizes=synchrony_sizes)
-    print(synchrony_metrics)
+    synchrony_metrics = compute_synchrony_metrics(sorting_analyzer)
+
+    synchrony_sizes = np.array([2, 4, 8])
 
     # check returns
     for size in synchrony_sizes:
@@ -625,10 +625,8 @@ def test_synchrony_metrics(sorting_analyzer_simple):
         sorting_sync = add_synchrony_to_sorting(sorting, sync_event_ratio=sync_level)
         sorting_analyzer_sync = create_sorting_analyzer(sorting_sync, sorting_analyzer.recording, format="memory")
 
-        previous_synchrony_metrics = compute_synchrony_metrics(
-            previous_sorting_analyzer, synchrony_sizes=synchrony_sizes
-        )
-        current_synchrony_metrics = compute_synchrony_metrics(sorting_analyzer_sync, synchrony_sizes=synchrony_sizes)
+        previous_synchrony_metrics = compute_synchrony_metrics(previous_sorting_analyzer)
+        current_synchrony_metrics = compute_synchrony_metrics(sorting_analyzer_sync)
         print(current_synchrony_metrics)
         # check that all values increased
         for i, col in enumerate(previous_synchrony_metrics._fields):
@@ -647,22 +645,17 @@ def test_synchrony_metrics_unit_id_subset(sorting_analyzer_simple):
 
     unit_ids_subset = [3, 7]
 
-    synchrony_sizes = (2,)
-    (synchrony_metrics,) = compute_synchrony_metrics(
-        sorting_analyzer_simple, synchrony_sizes=synchrony_sizes, unit_ids=unit_ids_subset
-    )
+    synchrony_metrics = compute_synchrony_metrics(sorting_analyzer_simple, unit_ids=unit_ids_subset)
 
-    assert list(synchrony_metrics.keys()) == [3, 7]
+    assert list(synchrony_metrics.sync_spike_2.keys()) == [3, 7]
+    assert list(synchrony_metrics.sync_spike_4.keys()) == [3, 7]
+    assert list(synchrony_metrics.sync_spike_8.keys()) == [3, 7]
 
 
 def test_synchrony_metrics_no_unit_ids(sorting_analyzer_simple):
 
-    # all_unit_ids = sorting_analyzer_simple.sorting.unit_ids
-
-    synchrony_sizes = (2,)
-    (synchrony_metrics,) = compute_synchrony_metrics(sorting_analyzer_simple, synchrony_sizes=synchrony_sizes)
-
-    assert np.all(list(synchrony_metrics.keys()) == sorting_analyzer_simple.unit_ids)
+    synchrony_metrics = compute_synchrony_metrics(sorting_analyzer_simple)
+    assert np.all(list(synchrony_metrics.sync_spike_2.keys()) == sorting_analyzer_simple.unit_ids)
 
 
 @pytest.mark.sortingcomponents