Merge branch 'main' into change_default_in_generate_recording

doc/modules/qualitymetrics/references.rst

@@ -11,6 +11,8 @@ References
 
 .. [Hruschka] Hruschka, E.R., de Castro, L.N., Campello R.J.G.B. "Evolutionary algorithms for clustering gene-expression data." Fourth IEEE International Conference on Data Mining (ICDM'04) 2004, pp 403-406.
 
+.. [Gruen] Sonja Grün, Moshe Abeles, and Markus Diesmann. Impact of higher-order correlations on coincidence distributions of massively parallel data. In International School on Neural Networks, Initiated by IIASS and EMFCSC, volume 5286, 96–114. Springer, 2007.
+
 .. [IBL] International Brain Laboratory. “Spike sorting pipeline for the International Brain Laboratory”. 4 May 2022.
 
 .. [Jackson] Jadin Jackson, Neil Schmitzer-Torbert, K.D. Harris, and A.D. Redish. Quantitative assessment of extracellular multichannel recording quality using measures of cluster separation. Soc Neurosci Abstr, 518, 01 2005.

doc/modules/qualitymetrics/synchrony.rst

@@ -0,0 +1,49 @@
+Synchrony Metrics (:code:`synchrony`)
+=====================================
+
+Calculation
+-----------
+This function is providing a metric for the presence of synchronous spiking events across multiple spike trains.
+
+The complexity is used to characterize synchronous events within the same spike train and across different spike
+trains. This way synchronous events can be found both in multi-unit and single-unit spike trains.
+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.
+
+
+
+Expectation and use
+-------------------
+
+A larger value indicates a higher synchrony of the respective spike train with the other spike trains.
+Larger values, especially for larger sizes, indicate a higher probability of noisy spikes in spike trains.
+
+Example code
+------------
+
+.. code-block:: python
+
+    import spikeinterface.qualitymetrics as qm
+    # Make recording, sorting and wvf_extractor object for your data.
+    synchrony = qm.compute_synchrony_metrics(wvf_extractor, synchrony_sizes=(2, 4, 8))
+    # synchrony is a tuple of dicts with the synchrony metrics for each unit
+
+
+Links to original implementations
+---------------------------------
+
+The SpikeInterface implementation is a partial port of the low-level complexity functions from `Elephant - Electrophysiology Analysis Toolkit <https://github.com/NeuralEnsemble/elephant/blob/master/elephant/spike_train_synchrony.py#L245>`_
+
+References
+----------
+
+.. automodule:: spikeinterface.toolkit.qualitymetrics.misc_metrics
+
+    .. autofunction:: compute_synchrony_metrics
+
+Literature
+----------
+
+Based on concepts described in Gruen_

src/spikeinterface/core/__init__.py

@@ -28,6 +28,7 @@
 from .generate import (
     generate_recording,
     generate_sorting,
+    add_synchrony_to_sorting,
     create_sorting_npz,
     generate_snippets,
     synthesize_random_firings,

src/spikeinterface/core/generate.py

@@ -125,6 +125,31 @@ def generate_sorting(
     refractory_period_ms=3.0,  # in ms
     seed=None,
 ):
+    """
+    Generates sorting object with random firings.
+
+    Parameters
+    ----------
+    num_units : int, default: 5
+        Number of units
+    sampling_frequency : float, default: 30000.0
+        The sampling frequency
+    durations : list, default: [10.325, 3.5]
+        Duration of each segment in s
+    firing_rates : float, default: 3.0
+        The firing rate of each unit (in Hz).
+    empty_units : list, default: None
+        List of units that will have no spikes. (used for testing mainly).
+    refractory_period_ms : float, default: 3.0
+        The refractory period in ms
+    seed : int, default: None
+        The random seed
+
+    Returns
+    -------
+    sorting : NumpySorting
+        The sorting object
+    """
     seed = _ensure_seed(seed)
     num_segments = len(durations)
     unit_ids = np.arange(num_units)
@@ -157,6 +182,59 @@ def generate_sorting(
     return sorting
 
 
+def add_synchrony_to_sorting(sorting, sync_event_ratio=0.3, seed=None):
+    """
+    Generates sorting object with added synchronous events from an existing sorting objects.
+
+    Parameters
+    ----------
+    sorting : BaseSorting
+        The sorting object
+    sync_event_ratio : float
+        The ratio of added synchronous spikes with respect to the total number of spikes.
+        E.g., 0.5 means that the final sorting will have 1.5 times number of spikes, and all the extra
+        spikes are synchronous (same sample_index), but on different units (not duplicates).
+    seed : int, default: None
+        The random seed
+
+
+    Returns
+    -------
+    sorting : NumpySorting
+        The sorting object
+
+    """
+    rng = np.random.default_rng(seed)
+    spikes = sorting.to_spike_vector()
+    unit_ids = sorting.unit_ids
+
+    # add syncrhonous events
+    num_sync = int(len(spikes) * sync_event_ratio)
+    spikes_duplicated = rng.choice(spikes, size=num_sync, replace=True)
+    # change unit_index
+    new_unit_indices = np.zeros(len(spikes_duplicated))
+    # make sure labels are all unique, keep unit_indices used for each spike
+    units_used_for_spike = {}
+    for i, spike in enumerate(spikes_duplicated):
+        sample_index = spike["sample_index"]
+        if sample_index not in units_used_for_spike:
+            units_used_for_spike[sample_index] = np.array([spike["unit_index"]])
+        units_not_used = unit_ids[~np.in1d(unit_ids, units_used_for_spike[sample_index])]
+
+        if len(units_not_used) == 0:
+            continue
+        new_unit_indices[i] = rng.choice(units_not_used)
+        units_used_for_spike[sample_index] = np.append(units_used_for_spike[sample_index], new_unit_indices[i])
+    spikes_duplicated["unit_index"] = new_unit_indices
+    spikes_all = np.concatenate((spikes, spikes_duplicated))
+    sort_idxs = np.lexsort([spikes_all["sample_index"], spikes_all["segment_index"]])
+    spikes_all = spikes_all[sort_idxs]
+
+    sorting = NumpySorting(spikes=spikes_all, sampling_frequency=sorting.sampling_frequency, unit_ids=unit_ids)
+
+    return sorting
+
+
 def create_sorting_npz(num_seg, file_path):
     # create a NPZ sorting file
     d = {}

src/spikeinterface/postprocessing/tests/test_align_sorting.py

@@ -6,7 +6,7 @@
 
 import numpy as np
 
-from spikeinterface import WaveformExtractor, load_extractor, extract_waveforms, NumpySorting
+from spikeinterface import NumpySorting
 from spikeinterface.core import generate_sorting
 
 from spikeinterface.postprocessing import align_sorting
@@ -17,8 +17,8 @@
     cache_folder = Path("cache_folder") / "postprocessing"
 
 
-def test_compute_unit_center_of_mass():
-    sorting = generate_sorting(durations=[10.0])
+def test_align_sorting():
+    sorting = generate_sorting(durations=[10.0], seed=0)
     print(sorting)
 
     unit_ids = sorting.unit_ids
@@ -43,4 +43,4 @@ def test_compute_unit_center_of_mass():
 
 
 if __name__ == "__main__":
-    test_compute_unit_center_of_mass()
+    test_align_sorting()

src/spikeinterface/postprocessing/tests/test_correlograms.py

@@ -38,7 +38,7 @@ def test_compute_correlograms(self):
 
 
 def test_make_bins():
-    sorting = generate_sorting(num_units=5, sampling_frequency=30000.0, durations=[10.325, 3.5])
+    sorting = generate_sorting(num_units=5, sampling_frequency=30000.0, durations=[10.325, 3.5], seed=0)
 
     window_ms = 43.57
     bin_ms = 1.6421
@@ -82,14 +82,14 @@ def test_equal_results_correlograms():
     if HAVE_NUMBA:
         methods.append("numba")
 
-    sorting = generate_sorting(num_units=5, sampling_frequency=30000.0, durations=[10.325, 3.5])
+    sorting = generate_sorting(num_units=5, sampling_frequency=30000.0, durations=[10.325, 3.5], seed=0)
 
     _test_correlograms(sorting, window_ms=60.0, bin_ms=2.0, methods=methods)
     _test_correlograms(sorting, window_ms=43.57, bin_ms=1.6421, methods=methods)
 
 
 def test_flat_cross_correlogram():
-    sorting = generate_sorting(num_units=2, sampling_frequency=10000.0, durations=[100000.0])
+    sorting = generate_sorting(num_units=2, sampling_frequency=10000.0, durations=[100000.0], seed=0)
 
     methods = ["numpy"]
     if HAVE_NUMBA:

src/spikeinterface/preprocessing/normalize_scale.py

@@ -293,7 +293,7 @@ def __init__(
             means = means[None, :]
             stds = np.std(random_data, axis=0)
             stds = stds[None, :]
-            gain = 1 / stds
+            gain = 1.0 / stds
             offset = -means / stds
 
         if int_scale is not None:

src/spikeinterface/preprocessing/tests/test_normalize_scale.py

@@ -78,13 +78,18 @@ def test_zscore():
     assert np.all(np.abs(np.mean(tr, axis=0)) < 0.01)
     assert np.all(np.abs(np.std(tr, axis=0) - 1) < 0.01)
 
+
+def test_zscore_int():
+    seed = 1
+    rec = generate_recording(seed=seed, mode="legacy")
     rec_int = scale(rec, dtype="int16", gain=100)
     with pytest.raises(AssertionError):
-        rec4 = zscore(rec_int, dtype=None)
-    rec4 = zscore(rec_int, dtype="int16", int_scale=256, mode="mean+std", seed=seed)
-    tr = rec4.get_traces(segment_index=0)
-    trace_mean = np.mean(tr, axis=0)
-    trace_std = np.std(tr, axis=0)
+        zscore(rec_int, dtype=None)
+
+    zscore_recording = zscore(rec_int, dtype="int16", int_scale=256, mode="mean+std", seed=seed)
+    traces = zscore_recording.get_traces(segment_index=0)
+    trace_mean = np.mean(traces, axis=0)
+    trace_std = np.std(traces, axis=0)
     assert np.all(np.abs(trace_mean) < 1)
     assert np.all(np.abs(trace_std - 256) < 1)
 

src/spikeinterface/qualitymetrics/misc_metrics.py

@@ -499,6 +499,73 @@ def compute_sliding_rp_violations(
 )
 
 
+def compute_synchrony_metrics(waveform_extractor, synchrony_sizes=(2, 4, 8), **kwargs):
+    """
+    Compute synchrony metrics. Synchrony metrics represent the rate of occurrences of
+    "synchrony_size" spikes at the exact same sample index.
+
+    Parameters
+    ----------
+    waveform_extractor : WaveformExtractor
+        The waveform extractor object.
+    synchrony_sizes : list or tuple, default: (2, 4, 8)
+        The synchrony sizes to compute.
+
+    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 [Gruen]_
+    This code was adapted from `Elephant - Electrophysiology Analysis Toolkit <https://github.com/NeuralEnsemble/elephant/blob/master/elephant/spike_train_synchrony.py#L245>`_
+    """
+    assert np.all(s > 1 for s in synchrony_sizes), "Synchrony sizes must be greater than 1"
+    spike_counts = waveform_extractor.sorting.count_num_spikes_per_unit()
+    sorting = waveform_extractor.sorting
+    spikes = sorting.to_spike_vector(concatenated=False)
+
+    # Pre-allocate synchrony counts
+    synchrony_counts = {}
+    for synchrony_size in synchrony_sizes:
+        synchrony_counts[synchrony_size] = np.zeros(len(waveform_extractor.unit_ids), dtype=np.int64)
+
+    for segment_index in range(sorting.get_num_segments()):
+        spikes_in_segment = spikes[segment_index]
+
+        # we compute just by counting the occurrence of each sample_index
+        unique_spike_index, complexity = np.unique(spikes_in_segment["sample_index"], return_counts=True)
+
+        # add counts for this segment
+        for unit_index in np.arange(len(sorting.unit_ids)):
+            spikes_per_unit = spikes_in_segment[spikes_in_segment["unit_index"] == unit_index]
+            # some segments/units might have no spikes
+            if len(spikes_per_unit) == 0:
+                continue
+            spike_complexity = complexity[np.in1d(unique_spike_index, spikes_per_unit["sample_index"])]
+            for synchrony_size in synchrony_sizes:
+                synchrony_counts[synchrony_size][unit_index] += np.count_nonzero(spike_complexity >= synchrony_size)
+
+    # add counts for this segment
+    synchrony_metrics_dict = {
+        f"sync_spike_{synchrony_size}": {
+            unit_id: synchrony_counts[synchrony_size][unit_index] / spike_counts[unit_id]
+            for unit_index, unit_id in enumerate(sorting.unit_ids)
+        }
+        for synchrony_size in synchrony_sizes
+    }
+
+    # Convert dict to named tuple
+    synchrony_metrics_tuple = namedtuple("synchrony_metrics", synchrony_metrics_dict.keys())
+    synchrony_metrics = synchrony_metrics_tuple(**synchrony_metrics_dict)
+    return synchrony_metrics
+
+
+_default_params["synchrony_metrics"] = dict(synchrony_sizes=(0, 2, 4))
+
+
 def compute_amplitude_cutoffs(
     waveform_extractor,
     peak_sign="neg",

src/spikeinterface/qualitymetrics/quality_metric_list.py

@@ -11,6 +11,7 @@
     compute_amplitude_cutoffs,
     compute_amplitude_medians,
     compute_drift_metrics,
+    compute_synchrony_metrics,
 )
 
 from .pca_metrics import (
@@ -39,5 +40,6 @@
     "sliding_rp_violation": compute_sliding_rp_violations,
     "amplitude_cutoff": compute_amplitude_cutoffs,
     "amplitude_median": compute_amplitude_medians,
+    "synchrony": compute_synchrony_metrics,
     "drift": compute_drift_metrics,
 }