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lfp_artifact.py

LFPArtifactDetectionParameters

Bases: SpyglassMixin, Manual

Source code in src/spyglass/lfp/v1/lfp_artifact.py 
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@schema
class LFPArtifactDetectionParameters(SpyglassMixin, dj.Manual):
    definition = """
    # Parameters for detecting LFP artifact times within a LFP group.
    artifact_params_name: varchar(200)
    ---
    artifact_params: blob  # dictionary of parameters
    """

    def insert_default(self):
        """Insert the default artifact parameters."""
        diff_params = [
            "default_difference",
            {
                "artifact_detection_algorithm": "difference",
                "artifact_detection_algorithm_params": {
                    "amplitude_thresh_1st": 500,  # must be None or >= 0
                    "proportion_above_thresh_1st": 0.1,
                    "amplitude_thresh_2nd": 1000,  # must be None or >= 0
                    "proportion_above_thresh_2nd": 0.05,
                    "removal_window_ms": 10.0,  # in milliseconds
                    "local_window_ms": 40.0,  # in milliseconds
                },
            },
        ]

        diff_ref_params = [
            "default_difference_ref",
            {
                "artifact_detection_algorithm": "difference",
                "artifact_detection_algorithm_params": {
                    "amplitude_thresh_1st": 500,  # must be None or >= 0
                    "proportion_above_thresh_1st": 0.1,
                    "amplitude_thresh_2nd": 1000,  # must be None or >= 0
                    "proportion_above_thresh_2nd": 0.05,
                    "removal_window_ms": 10.0,  # in milliseconds
                    "local_window_ms": 40.0,  # in milliseconds
                },
                "referencing": {
                    "ref_on": 1,
                    "reference_list": [0, 0, 0, 0, 0],
                    "electrode_list": [0, 0],
                },
            },
        ]

        no_params = [
            "none",
            {
                "artifact_detection_algorithm": "difference",
                "artifact_detection_algorithm_params": {
                    "amplitude_thresh_1st": None,  # must be None or >= 0
                    "proportion_above_thresh_1st": None,
                    "amplitude_thresh_2nd": None,  # must be None or >= 0
                    "proportion_above_thresh_2nd": None,
                    "removal_window_ms": None,  # in milliseconds
                    "local_window_ms": None,  # in milliseconds
                },
            },
        ]

        mad_params = [
            "default_mad",
            {
                "artifact_detection_algorithm": "mad",
                "artifact_detection_algorithm_params": {
                    # akin to z-score std dev if the distribution is normal
                    "mad_thresh": 6.0,
                    "proportion_above_thresh": 0.1,
                    "removal_window_ms": 10.0,  # in milliseconds
                },
            },
        ]

        self.insert(
            [diff_params, diff_ref_params, no_params, mad_params],
            skip_duplicates=True,
        )

insert_default()

Insert the default artifact parameters.

Source code in src/spyglass/lfp/v1/lfp_artifact.py 
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def insert_default(self):
    """Insert the default artifact parameters."""
    diff_params = [
        "default_difference",
        {
            "artifact_detection_algorithm": "difference",
            "artifact_detection_algorithm_params": {
                "amplitude_thresh_1st": 500,  # must be None or >= 0
                "proportion_above_thresh_1st": 0.1,
                "amplitude_thresh_2nd": 1000,  # must be None or >= 0
                "proportion_above_thresh_2nd": 0.05,
                "removal_window_ms": 10.0,  # in milliseconds
                "local_window_ms": 40.0,  # in milliseconds
            },
        },
    ]

    diff_ref_params = [
        "default_difference_ref",
        {
            "artifact_detection_algorithm": "difference",
            "artifact_detection_algorithm_params": {
                "amplitude_thresh_1st": 500,  # must be None or >= 0
                "proportion_above_thresh_1st": 0.1,
                "amplitude_thresh_2nd": 1000,  # must be None or >= 0
                "proportion_above_thresh_2nd": 0.05,
                "removal_window_ms": 10.0,  # in milliseconds
                "local_window_ms": 40.0,  # in milliseconds
            },
            "referencing": {
                "ref_on": 1,
                "reference_list": [0, 0, 0, 0, 0],
                "electrode_list": [0, 0],
            },
        },
    ]

    no_params = [
        "none",
        {
            "artifact_detection_algorithm": "difference",
            "artifact_detection_algorithm_params": {
                "amplitude_thresh_1st": None,  # must be None or >= 0
                "proportion_above_thresh_1st": None,
                "amplitude_thresh_2nd": None,  # must be None or >= 0
                "proportion_above_thresh_2nd": None,
                "removal_window_ms": None,  # in milliseconds
                "local_window_ms": None,  # in milliseconds
            },
        },
    ]

    mad_params = [
        "default_mad",
        {
            "artifact_detection_algorithm": "mad",
            "artifact_detection_algorithm_params": {
                # akin to z-score std dev if the distribution is normal
                "mad_thresh": 6.0,
                "proportion_above_thresh": 0.1,
                "removal_window_ms": 10.0,  # in milliseconds
            },
        },
    ]

    self.insert(
        [diff_params, diff_ref_params, no_params, mad_params],
        skip_duplicates=True,
    )