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Add skip channels to EDF interface #1110

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merged 2 commits into from
Oct 11, 2024
Merged

Add skip channels to EDF interface #1110

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b954bd3
add skip channels to EDF interface
h-mayorquin Oct 10, 2024
99fd8d6
changelog
h-mayorquin Oct 10, 2024
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32 changes: 29 additions & 3 deletions src/neuroconv/datainterfaces/ecephys/edf/edfdatainterface.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
from typing import Optional

from pydantic import FilePath

from ..baserecordingextractorinterface import BaseRecordingExtractorInterface
Expand All @@ -23,7 +25,22 @@ def get_source_schema(cls) -> dict:
source_schema["properties"]["file_path"]["description"] = "Path to the .edf file."
return source_schema

def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "ElectricalSeries"):
def _source_data_to_extractor_kwargs(self, source_data: dict) -> dict:

extractor_kwargs = source_data.copy()
extractor_kwargs.pop("channels_to_skip")
extractor_kwargs["all_annotations"] = True
extractor_kwargs["use_names_as_ids"] = True
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@bendichter
This is necessary to display meaningful names that the user can suppress with the newly added parameter. Otherwise, the channel ids are "1", "2", "3", etc.

This is technically a breaking change because we are changing the way we add the data to the NWBFile but I also consider this an improvement:

image


return extractor_kwargs

def __init__(
self,
file_path: FilePath,
verbose: bool = True,
es_key: str = "ElectricalSeries",
channels_to_skip: Optional[list] = None,
):
"""
Load and prepare data for EDF.
Currently, only continuous EDF+ files (EDF+C) and original EDF files (EDF) are supported
Expand All @@ -36,15 +53,24 @@ def __init__(self, file_path: FilePath, verbose: bool = True, es_key: str = "Ele
verbose : bool, default: True
Allows verbose.
es_key : str, default: "ElectricalSeries"
Key for the ElectricalSeries metadata
channels_to_skip : list, default: None
Channels to skip when adding the data to the nwbfile. These parameter can be used to skip non-neural
channels that are present in the EDF file.
"""
get_package(
package_name="pyedflib",
excluded_platforms_and_python_versions=dict(darwin=dict(arm=["3.8", "3.9"])),
excluded_platforms_and_python_versions=dict(darwin=dict(arm=["3.9"])),
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)

super().__init__(file_path=file_path, verbose=verbose, es_key=es_key)
super().__init__(file_path=file_path, verbose=verbose, es_key=es_key, channels_to_skip=channels_to_skip)
self.edf_header = self.recording_extractor.neo_reader.edf_header

# We remove the channels that are not neural
if channels_to_skip:
self.recording_extractor = self.recording_extractor.remove_channels(remove_channel_ids=channels_to_skip)

def extract_nwb_file_metadata(self) -> dict:
nwbfile_metadata = dict(
session_start_time=self.edf_header["startdate"],
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