Merge pull request #538 from catalystneuro/abf_electrode_fixes

Abf electrode metadata fixes
catalystneuro · Aug 6, 2023 · 6dc72d6 · 6dc72d6
2 parents 7b978ca + ecf8489
commit 6dc72d6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,12 @@
 # (Upcoming)
 
+### Fixes
+
+* Propagated additional arguments, such as `cell_id`, from the `metadata["Icephys"]["Electrodes"]` dictionary used in `tools.neo.add_icephys_electrode`. [PR #538](https://github.com/catalystneuro/neuroconv/pull/538)
+* Fixed mismatch between expected `Electrodes` key in `tools.neo.add_icephys_electrode` and the metadata automatically generated by the `AbfInterface`. [PR #538](https://github.com/catalystneuro/neuroconv/pull/538)
+
+
+
 # v0.4.0
 
 ### Back-compatibility break

diff --git a/src/neuroconv/datainterfaces/icephys/baseicephysinterface.py b/src/neuroconv/datainterfaces/icephys/baseicephysinterface.py
@@ -59,7 +59,7 @@ def get_metadata(self) -> dict:
         metadata = super().get_metadata()
         metadata["Icephys"] = dict(
             Device=[dict(name="DeviceIcephys", description="no description")],
-            Electrode=[
+            Electrodes=[
                 dict(name=f"electrode-{i}", description="no description", device="DeviceIcephys")
                 for i in range(get_number_of_electrodes(self.readers_list[0]))
             ],

diff --git a/src/neuroconv/tools/neo/neo.py b/src/neuroconv/tools/neo/neo.py
@@ -1,6 +1,7 @@
 import distutils.version
 import uuid
 import warnings
+from copy import deepcopy
 from pathlib import Path
 from typing import Optional, Tuple
 
@@ -180,7 +181,7 @@ def add_icephys_electrode(neo_reader, nwbfile, metadata: dict = None):
     ]
 
     if "Electrodes" not in metadata["Icephys"] or len(metadata["Icephys"]["Electrodes"]) == 0:
-        metadata["Icephys"]["Electrodes"] = defaults
+        metadata["Icephys"]["Electrodes"] = deepcopy(defaults)
 
     assert all(
         [isinstance(x, dict) for x in metadata["Icephys"]["Electrodes"]]
@@ -189,15 +190,17 @@ def add_icephys_electrode(neo_reader, nwbfile, metadata: dict = None):
     # Create Icephys electrode from metadata
     for elec in metadata["Icephys"]["Electrodes"]:
         if elec.get("name", defaults[0]["name"]) not in nwbfile.icephys_electrodes:
-            device_name = elec.get("device_name", defaults[0]["device_name"])
+            device_name = elec.pop("device_name", None) or elec.pop("device", defaults[0]["device_name"])
+            # elec.pop("device_name", 0)
             if device_name not in nwbfile.devices:
                 new_device_metadata = dict(Ecephys=dict(Device=[dict(name=device_name)]))
                 add_device_from_metadata(nwbfile, modality="Icephys", metadata=new_device_metadata)
                 warnings.warn(
                     f"Device '{device_name}' not detected in "
                     "attempted link to icephys electrode! Automatically generating."
                 )
-            electrode_kwargs = dict(
+            electrode_kwargs = elec
+            electrode_kwargs.update(
                 name=elec.get("name", defaults[0]["name"]),
                 description=elec.get("description", defaults[0]["description"]),
                 device=nwbfile.devices[device_name],

diff --git a/src/neuroconv/utils/json_schema.py b/src/neuroconv/utils/json_schema.py
@@ -267,10 +267,10 @@ def get_schema_from_hdmf_class(hdmf_class):
 
 def get_metadata_schema_for_icephys():
     schema = get_base_schema(tag="Icephys")
-    schema["required"] = ["Device", "Electrode"]
+    schema["required"] = ["Device", "Electrodes"]
     schema["properties"] = dict(
         Device=dict(type="array", minItems=1, items={"$ref": "#/properties/Icephys/properties/definitions/Device"}),
-        Electrode=dict(
+        Electrodes=dict(
             type="array",
             minItems=1,
             items={"$ref": "#/properties/Icephys/properties/definitions/Electrode"},

diff --git a/tests/test_on_data/test_gin_icephys.py b/tests/test_on_data/test_gin_icephys.py
@@ -113,6 +113,9 @@ class TestConverter(NWBConverter):
                 )
         metadata = converter.get_metadata()
         metadata["NWBFile"].update(session_start_time=datetime.now().astimezone().strftime("%Y-%m-%dT%H:%M:%S"))
+
+        metadata["Icephys"]["Electrodes"][0].update(cell_id="ID001")
+
         converter.run_conversion(nwbfile_path=nwbfile_path, overwrite=True, metadata=metadata)
 
         with NWBHDF5IO(path=nwbfile_path, mode="r") as io:
@@ -123,6 +126,8 @@ class TestConverter(NWBConverter):
             self.check_set_aligned_starting_time()
             self.check_set_aligned_segment_starting_times()
 
+            assert nwbfile.ic_electrodes["electrode-0"].cell_id == "ID001"
+
 
 if __name__ == "__main__":
     unittest.main()