From 52cd6aa0ea46c0d143739767da4951ade17c3b74 Mon Sep 17 00:00:00 2001
From: Heberto Mayorquin <h.mayorquin@gmail.com>
Date: Fri, 11 Oct 2024 08:54:53 -0600
Subject: [PATCH] Add skip channels to EDF interface (#1110)

---
 CHANGELOG.md                                  |  1 +
 .../ecephys/edf/edfdatainterface.py           | 32 +++++++++++++++++--
 2 files changed, 30 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9c7bc13be..d748d79e6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@
 ## Features
 * Using in-house `GenericDataChunkIterator` [PR #1068](https://github.com/catalystneuro/neuroconv/pull/1068)
 * Data interfaces now perform source (argument inputs) validation with the json schema  [PR #1020](https://github.com/catalystneuro/neuroconv/pull/1020)
+* Added `channels_to_skip` to `EDFRecordingInterface` so the user can skip non-neural channels [PR #1110](https://github.com/catalystneuro/neuroconv/pull/1110)
 
 ## Improvements
 * Remove dev test from PR  [PR #1092](https://github.com/catalystneuro/neuroconv/pull/1092)
diff --git a/src/neuroconv/datainterfaces/ecephys/edf/edfdatainterface.py b/src/neuroconv/datainterfaces/ecephys/edf/edfdatainterface.py
index 119e9f8d2..ef169f66f 100644
--- a/src/neuroconv/datainterfaces/ecephys/edf/edfdatainterface.py
+++ b/src/neuroconv/datainterfaces/ecephys/edf/edfdatainterface.py
@@ -1,3 +1,5 @@
+from typing import Optional
+
 from pydantic import FilePath
 
 from ..baserecordingextractorinterface import BaseRecordingExtractorInterface
@@ -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
+
+        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
@@ -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"])),
         )
 
-        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"],