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lfp_electrode.py

LFPElectrodeGroup

Bases: SpyglassMixin, Manual

Source code in src/spyglass/lfp/lfp_electrode.py 
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@schema
class LFPElectrodeGroup(SpyglassMixin, dj.Manual):
    definition = """
     -> Session                             # the session for this LFP
     lfp_electrode_group_name: varchar(200) # name for this group of electrodes
     """

    class LFPElectrode(SpyglassMixin, dj.Part):
        definition = """
        -> LFPElectrodeGroup # the group of electrodes to be filtered
        -> Electrode        # the electrode to be filtered
        """

    @staticmethod
    def create_lfp_electrode_group(
        nwb_file_name: str, group_name: str, electrode_list: list[int]
    ):
        """Adds an LFPElectrodeGroup and the individual electrodes

        Parameters
        ----------
        nwb_file_name : str
            The name of the nwb file (e.g. the session)
        group_name : str
            The name of this group (< 200 char)
        electrode_list : list
            A list of the electrode ids to include in this group.
        """
        # remove the session and then recreate the session and Electrode list
        # check to see if the user allowed the deletion
        key = {
            "nwb_file_name": nwb_file_name,
            "lfp_electrode_group_name": group_name,
        }
        LFPElectrodeGroup().insert1(key, skip_duplicates=True)

        # TODO: do this in a better way
        all_electrodes = (Electrode() & {"nwb_file_name": nwb_file_name}).fetch(
            as_dict=True
        )
        primary_key = Electrode.primary_key
        if isinstance(electrode_list, ndarray):
            # convert to list if it is an numpy array
            electrode_list = list(electrode_list.astype(int).reshape(-1))
        for e in all_electrodes:
            # create a dictionary so we can insert the electrodes
            if e["electrode_id"] in electrode_list:
                lfpelectdict = {k: v for k, v in e.items() if k in primary_key}
                lfpelectdict["lfp_electrode_group_name"] = group_name
                LFPElectrodeGroup().LFPElectrode.insert1(
                    lfpelectdict, skip_duplicates=True
                )

create_lfp_electrode_group(nwb_file_name, group_name, electrode_list) staticmethod

Adds an LFPElectrodeGroup and the individual electrodes

Parameters:

Name Type Description Default
nwb_file_name str

The name of the nwb file (e.g. the session)

 required
group_name str

The name of this group (< 200 char)

 required
electrode_list list

A list of the electrode ids to include in this group.

 required
Source code in src/spyglass/lfp/lfp_electrode.py 
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@staticmethod
def create_lfp_electrode_group(
    nwb_file_name: str, group_name: str, electrode_list: list[int]
):
    """Adds an LFPElectrodeGroup and the individual electrodes

    Parameters
    ----------
    nwb_file_name : str
        The name of the nwb file (e.g. the session)
    group_name : str
        The name of this group (< 200 char)
    electrode_list : list
        A list of the electrode ids to include in this group.
    """
    # remove the session and then recreate the session and Electrode list
    # check to see if the user allowed the deletion
    key = {
        "nwb_file_name": nwb_file_name,
        "lfp_electrode_group_name": group_name,
    }
    LFPElectrodeGroup().insert1(key, skip_duplicates=True)

    # TODO: do this in a better way
    all_electrodes = (Electrode() & {"nwb_file_name": nwb_file_name}).fetch(
        as_dict=True
    )
    primary_key = Electrode.primary_key
    if isinstance(electrode_list, ndarray):
        # convert to list if it is an numpy array
        electrode_list = list(electrode_list.astype(int).reshape(-1))
    for e in all_electrodes:
        # create a dictionary so we can insert the electrodes
        if e["electrode_id"] in electrode_list:
            lfpelectdict = {k: v for k, v in e.items() if k in primary_key}
            lfpelectdict["lfp_electrode_group_name"] = group_name
            LFPElectrodeGroup().LFPElectrode.insert1(
                lfpelectdict, skip_duplicates=True
            )