Remove artefacts based of an envelope (#3715)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Alessio Buccino <alejoe9187@gmail.com>

Author: 3 people

src/spikeinterface/preprocessing/preprocessing_classes.py

@@ -50,6 +50,7 @@
 from .depth_order import DepthOrderRecording, depth_order
 from .astype import AstypeRecording, astype
 from .unsigned_to_signed import UnsignedToSignedRecording, unsigned_to_signed
+from .silence_artifacts import SilencedArtifactsRecording, silence_artifacts
 
 _all_preprocesser_dict = {
     # filter stuff
@@ -89,6 +90,7 @@
     DirectionalDerivativeRecording: directional_derivative,
     AstypeRecording: astype,
     UnsignedToSignedRecording: unsigned_to_signed,
+    SilencedArtifactsRecording: silence_artifacts,
 }
 # we control import in the preprocessing init by setting an __all__
 

src/spikeinterface/preprocessing/silence_artifacts.py

@@ -0,0 +1,224 @@
+from __future__ import annotations
+
+import numpy as np
+
+from spikeinterface.core.core_tools import define_function_handling_dict_from_class
+from spikeinterface.preprocessing.silence_periods import SilencedPeriodsRecording
+from spikeinterface.preprocessing.rectify import RectifyRecording
+from spikeinterface.preprocessing.common_reference import CommonReferenceRecording
+from spikeinterface.preprocessing.filter_gaussian import GaussianFilterRecording
+from spikeinterface.core.job_tools import split_job_kwargs, fix_job_kwargs
+from spikeinterface.core.recording_tools import get_noise_levels
+from spikeinterface.core.node_pipeline import PeakDetector, base_peak_dtype
+import numpy as np
+
+
+class DetectThresholdCrossing(PeakDetector):
+
+    name = "threshold_crossings"
+    preferred_mp_context = None
+
+    def __init__(
+        self,
+        recording,
+        detect_threshold=5,
+        noise_levels=None,
+        seed=None,
+        noise_levels_kwargs=dict(),
+    ):
+        PeakDetector.__init__(self, recording, return_output=True)
+        if noise_levels is None:
+            random_slices_kwargs = noise_levels_kwargs.pop("random_slices_kwargs", {}).copy()
+            random_slices_kwargs["seed"] = seed
+            noise_levels = get_noise_levels(recording, return_in_uV=False, random_slices_kwargs=random_slices_kwargs)
+        self.abs_thresholds = noise_levels * detect_threshold
+        self._dtype = np.dtype(base_peak_dtype + [("front", "bool")])
+
+    def get_trace_margin(self):
+        return 0
+
+    def get_dtype(self):
+        return self._dtype
+
+    def compute(self, traces, start_frame, end_frame, segment_index, max_margin):
+        z = np.median(traces / self.abs_thresholds, 1)
+        threshold_mask = np.diff((z > 1) != 0, axis=0)
+        indices = np.flatnonzero(threshold_mask)
+        threshold_crossings = np.zeros(indices.size, dtype=self._dtype)
+        threshold_crossings["sample_index"] = indices
+        threshold_crossings["front"][::2] = True
+        threshold_crossings["front"][1::2] = False
+        return (threshold_crossings,)
+
+
+def detect_period_artifacts_by_envelope(
+    recording,
+    detect_threshold=5,
+    min_duration_ms=50,
+    freq_max=20.0,
+    seed=None,
+    noise_levels=None,
+    **noise_levels_kwargs,
+):
+    """
+    Docstring for detect_period_artifacts. Function to detect putative artifact periods as threshold crossings of
+    a global envelope of the channels.
+
+    Parameters
+    ----------
+    recording : RecordingExtractor
+        The recording extractor to detect putative artifacts
+    detect_threshold : float, default: 5
+        The threshold to detect artifacts. The threshold is computed as `detect_threshold * noise_level`
+    freq_max : float, default: 20
+        The maximum frequency for the low pass filter used
+    min_duration_ms : float, default: 50
+        The minimum duration for a threshold crossing to be considered as an artefact.
+    noise_levels : array
+        Noise levels if already computed
+    seed : int | None, default: None
+        Random seed for `get_noise_levels`.
+        If none, `get_noise_levels` uses `seed=0`.
+    **noise_levels_kwargs : Keyword arguments for `spikeinterface.core.get_noise_levels()` function
+
+    """
+
+    envelope = RectifyRecording(recording)
+    envelope = GaussianFilterRecording(envelope, freq_min=None, freq_max=freq_max)
+    envelope = CommonReferenceRecording(envelope)
+
+    from spikeinterface.core.node_pipeline import (
+        run_node_pipeline,
+    )
+
+    _, job_kwargs = split_job_kwargs(noise_levels_kwargs)
+    job_kwargs = fix_job_kwargs(job_kwargs)
+
+    node0 = DetectThresholdCrossing(
+        recording, detect_threshold=detect_threshold, noise_levels=noise_levels, seed=seed, **noise_levels_kwargs
+    )
+
+    threshold_crossings = run_node_pipeline(
+        recording,
+        [node0],
+        job_kwargs,
+        job_name="detect threshold crossings",
+    )
+
+    order = np.lexsort((threshold_crossings["sample_index"], threshold_crossings["segment_index"]))
+    threshold_crossings = threshold_crossings[order]
+
+    periods = []
+    fs = recording.sampling_frequency
+    max_duration_samples = int(min_duration_ms * fs / 1000)
+    num_seg = recording.get_num_segments()
+
+    for seg_index in range(num_seg):
+        sub_periods = []
+        mask = threshold_crossings["segment_index"] == seg_index
+        sub_thr = threshold_crossings[mask]
+        if len(sub_thr) > 0:
+            local_thr = np.zeros(1, dtype=np.dtype(base_peak_dtype + [("front", "bool")]))
+            if not sub_thr["front"][0]:
+                local_thr["sample_index"] = 0
+                local_thr["front"] = True
+                sub_thr = np.hstack((local_thr, sub_thr))
+            if sub_thr["front"][-1]:
+                local_thr["sample_index"] = recording.get_num_samples(seg_index)
+                local_thr["front"] = False
+                sub_thr = np.hstack((sub_thr, local_thr))
+
+            indices = np.flatnonzero(np.diff(sub_thr["front"]))
+            for i, j in zip(indices[:-1], indices[1:]):
+                if sub_thr["front"][i]:
+                    start = sub_thr["sample_index"][i]
+                    end = sub_thr["sample_index"][j]
+                    if end - start > max_duration_samples:
+                        sub_periods.append((start, end))
+
+        periods.append(sub_periods)
+
+    return periods, envelope
+
+
+class SilencedArtifactsRecording(SilencedPeriodsRecording):
+    """
+    Silence user-defined periods from recording extractor traces. The code will construct
+    an enveloppe of the recording (as a low pass filtered version of the traces) and detect
+    threshold crossings to identify the periods to silence. The periods are then silenced either
+    on a per channel basis or across all channels by replacing the values by zeros or by
+    adding gaussian noise with the same variance as the one in the recordings
+
+    Parameters
+    ----------
+    recording : RecordingExtractor
+        The recording extractor to silence putative artifacts
+    detect_threshold : float, default: 5
+        The threshold to detect artifacts. The threshold is computed as `detect_threshold * noise_level`
+    freq_max : float, default: 20
+        The maximum frequency for the low pass filter used
+    min_duration_ms : float, default: 50
+        The minimum duration for a threshold crossing to be considered as an artefact.
+    noise_levels : array
+        Noise levels if already computed
+    seed : int | None, default: None
+        Random seed for `get_noise_levels` and `NoiseGeneratorRecording`.
+        If none, `get_noise_levels` uses `seed=0` and `NoiseGeneratorRecording` generates a random seed using `numpy.random.default_rng`.
+    mode : "zeros" | "noise", default: "zeros"
+        Determines what periods are replaced by. Can be one of the following:
+
+        - "zeros": Artifacts are replaced by zeros.
+
+        - "noise": The periods are filled with a gaussion noise that has the
+                   same variance that the one in the recordings, on a per channel
+                   basis
+    **noise_levels_kwargs : Keyword arguments for `spikeinterface.core.get_noise_levels()` function
+
+    Returns
+    -------
+    silenced_recording : SilencedArtifactsRecording
+        The recording extractor after silencing detected artifacts
+    """
+
+    _precomputable_kwarg_names = ["list_periods"]
+
+    def __init__(
+        self,
+        recording,
+        detect_threshold=5,
+        verbose=False,
+        freq_max=20.0,
+        min_duration_ms=50,
+        mode="zeros",
+        noise_levels=None,
+        seed=None,
+        list_periods=None,
+        **noise_levels_kwargs,
+    ):
+
+        if list_periods is None:
+            list_periods, _ = detect_period_artifacts_by_envelope(
+                recording,
+                detect_threshold=detect_threshold,
+                min_duration_ms=min_duration_ms,
+                freq_max=freq_max,
+                seed=seed,
+                noise_levels=noise_levels,
+                **noise_levels_kwargs,
+            )
+
+            if verbose:
+                for i, periods in enumerate(list_periods):
+                    total_time = np.sum([end - start for start, end in periods])
+                    percentage = 100 * total_time / recording.get_num_samples(i)
+                    print(f"{percentage}% of segment {i} has been flagged as artifactual")
+
+        SilencedPeriodsRecording.__init__(
+            self, recording, list_periods, mode=mode, noise_levels=noise_levels, seed=seed, **noise_levels_kwargs
+        )
+
+
+# function for API
+silence_artifacts = define_function_handling_dict_from_class(
+    source_class=SilencedArtifactsRecording, name="silence_artifacts"
+)

src/spikeinterface/preprocessing/silence_periods.py

@@ -56,12 +56,10 @@ def __init__(
     ):
         available_modes = ("zeros", "noise")
         num_seg = recording.get_num_segments()
-
         if num_seg == 1:
             if isinstance(list_periods, (list, np.ndarray)) and np.array(list_periods).ndim == 2:
-                # when unique segment accept list instead of of list of list/arrays
+                # when unique segment accept list instead of list of list/arrays
                 list_periods = [list_periods]
-
         # some checks
         assert mode in available_modes, f"mode {mode} is not an available mode: {available_modes}"
 
@@ -80,10 +78,12 @@ def __init__(
 
         if mode in ["noise"]:
             if noise_levels is None:
-                noise_levels_kwargs = noise_levels_kwargs.copy()
-                noise_levels_kwargs["return_in_uV"] = False
-                noise_levels_kwargs["seed"] = seed
-                noise_levels = get_noise_levels(recording, **noise_levels_kwargs)
+                random_slices_kwargs = noise_levels_kwargs.pop("random_slices_kwargs", {}).copy()
+                random_slices_kwargs["seed"] = seed
+                noise_levels = get_noise_levels(
+                    recording, return_in_uV=False, random_slices_kwargs=random_slices_kwargs
+                )
+
             noise_generator = NoiseGeneratorRecording(
                 num_channels=recording.get_num_channels(),
                 sampling_frequency=recording.sampling_frequency,
@@ -121,8 +121,7 @@ def __init__(self, parent_recording_segment, periods, mode, noise_generator, seg
     def get_traces(self, start_frame, end_frame, channel_indices):
         traces = self.parent_recording_segment.get_traces(start_frame, end_frame, channel_indices)
         traces = traces.copy()
-
-        if len(self.periods) > 0:
+        if self.periods.size > 0:
             new_interval = np.array([start_frame, end_frame])
             lower_index = np.searchsorted(self.periods[:, 1], new_interval[0])
             upper_index = np.searchsorted(self.periods[:, 0], new_interval[1])

src/spikeinterface/preprocessing/tests/test_silence_artifacts.py

@@ -0,0 +1,16 @@
+import pytest
+
+import numpy as np
+
+from spikeinterface.core import generate_recording
+from spikeinterface.preprocessing import silence_artifacts
+
+
+def test_silence_artifacts():
+    # one segment only
+    rec = generate_recording(durations=[10.0, 10])
+    new_rec = silence_artifacts(rec, detect_threshold=5, freq_max=5.0, min_duration_ms=50)
+
+
+if __name__ == "__main__":
+    test_silence_artifacts()