IntracellularRecordingsTable: infer electrode (#1598)

* IntracellularRecordingsTable: allow electrode to be inferred by response or stimulus and add tests * Update CHANGELOG.md Co-authored-by: Oliver Ruebel <[email protected]>
NeurodataWithoutBorders · Dec 12, 2022 · f4bd3bc · f4bd3bc
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,8 @@
 
 ### Enhancements and minor changes
 - `Subject.age` can be input as a `timedelta`. @bendichter [#1590](https://github.com/NeurodataWithoutBorders/pynwb/pull/1590)
+- `IntracellularRecordingsTable.add_recording`: the `electrode` arg is now optional, and is automatically populated from the stimulus or response.
+  [#1597](https://github.com/NeurodataWithoutBorders/pynwb/pull/1597)
 - Add module `pynwb.testing.mock.icephys` and corresponding tests. @bendichter
   [1595](https://github.com/NeurodataWithoutBorders/pynwb/pull/1595)
 - Remove redundant object mapper code. @rly [#1600](https://github.com/NeurodataWithoutBorders/pynwb/pull/1600)

diff --git a/src/pynwb/icephys.py b/src/pynwb/icephys.py
@@ -506,26 +506,33 @@ def __init__(self, **kwargs):
 
         super().__init__(**kwargs)
 
-    @docval({'name': 'electrode', 'type': IntracellularElectrode, 'doc': 'The intracellular electrode used'},
-            {'name': 'stimulus_start_index', 'type': int, 'doc': 'Start index of the stimulus', 'default': None},
-            {'name': 'stimulus_index_count', 'type': int, 'doc': 'Stop index of the stimulus', 'default': None},
-            {'name': 'stimulus', 'type': TimeSeries,
-             'doc': 'The TimeSeries (usually a PatchClampSeries) with the stimulus',
-             'default': None},
-            {'name': 'response_start_index', 'type': int, 'doc': 'Start index of the response', 'default': None},
-            {'name': 'response_index_count', 'type': int, 'doc': 'Stop index of the response', 'default': None},
-            {'name': 'response', 'type': TimeSeries,
-             'doc': 'The TimeSeries (usually a PatchClampSeries) with the response',
-             'default': None},
-            {'name': 'electrode_metadata', 'type': dict,
-             'doc': 'Additional electrode metadata to be stored in the electrodes table', 'default': None},
-            {'name': 'stimulus_metadata', 'type': dict,
-             'doc': 'Additional stimulus metadata to be stored in the stimuli table', 'default': None},
-            {'name': 'response_metadata', 'type': dict,
-             'doc': 'Additional resposnse metadata to be stored in the responses table', 'default': None},
-            returns='Integer index of the row that was added to this table',
-            rtype=int,
-            allow_extra=True)
+    @docval(
+        {
+            "name": "electrode",
+            "type": IntracellularElectrode,
+            "doc": "The intracellular electrode used",
+            "default": None,
+        },
+        {'name': 'stimulus_start_index', 'type': int, 'doc': 'Start index of the stimulus', 'default': None},
+        {'name': 'stimulus_index_count', 'type': int, 'doc': 'Stop index of the stimulus', 'default': None},
+        {'name': 'stimulus', 'type': TimeSeries,
+         'doc': 'The TimeSeries (usually a PatchClampSeries) with the stimulus',
+         'default': None},
+        {'name': 'response_start_index', 'type': int, 'doc': 'Start index of the response', 'default': None},
+        {'name': 'response_index_count', 'type': int, 'doc': 'Stop index of the response', 'default': None},
+        {'name': 'response', 'type': TimeSeries,
+         'doc': 'The TimeSeries (usually a PatchClampSeries) with the response',
+         'default': None},
+        {'name': 'electrode_metadata', 'type': dict,
+         'doc': 'Additional electrode metadata to be stored in the electrodes table', 'default': None},
+        {'name': 'stimulus_metadata', 'type': dict,
+         'doc': 'Additional stimulus metadata to be stored in the stimuli table', 'default': None},
+        {'name': 'response_metadata', 'type': dict,
+         'doc': 'Additional resposnse metadata to be stored in the responses table', 'default': None},
+        returns='Integer index of the row that was added to this table',
+        rtype=int,
+        allow_extra=True,
+    )
     def add_recording(self, **kwargs):
         """
         Add a single recording to the IntracellularRecordingsTable table.
@@ -546,6 +553,14 @@ def add_recording(self, **kwargs):
                                                                        'response',
                                                                        kwargs)
         electrode = popargs('electrode', kwargs)
+
+        # if electrode is not provided, take from stimulus or response object
+        if electrode is None:
+            if stimulus:
+                electrode = stimulus.electrode
+            elif response:
+                electrode = response.electrode
+
         # Confirm that we have at least a valid stimulus or response
         if stimulus is None and response is None:
             raise ValueError("stimulus and response cannot both be None.")
@@ -580,8 +595,10 @@ def add_recording(self, **kwargs):
             #     warnings.warn("sweep_number are usually expected to be the same for PatchClampSeries type "
             #                   "stimulus and response pairs in an intracellular recording.")
             if response.electrode != stimulus.electrode:
-                raise ValueError("electrodes are usually expected to be the same for PatchClampSeries type "
-                                 "stimulus and response pairs in an intracellular recording.")
+                raise ValueError(
+                    "electrodes are usually expected to be the same for PatchClampSeries type stimulus and response "
+                    "pairs in an intracellular recording."
+                )
 
         # Compile the electrodes table data
         electrodes = copy(popargs('electrode_metadata', kwargs))

diff --git a/tests/unit/test_icephys.py b/tests/unit/test_icephys.py
@@ -1,7 +1,15 @@
 import numpy as np
 
-from pynwb.icephys import (PatchClampSeries, CurrentClampSeries, IZeroClampSeries, CurrentClampStimulusSeries,
-                           VoltageClampSeries, VoltageClampStimulusSeries, IntracellularElectrode, SweepTable)
+from pynwb.icephys import (
+    PatchClampSeries,
+    CurrentClampSeries,
+    IZeroClampSeries,
+    CurrentClampStimulusSeries,
+    VoltageClampSeries,
+    VoltageClampStimulusSeries,
+    IntracellularElectrode,
+    SweepTable,
+)
 from pynwb.device import Device
 from pynwb.testing import TestCase
 from pynwb.file import NWBFile  # Needed to test icephys functionality defined on NWBFile

diff --git a/tests/unit/test_icephys_metadata_tables.py b/tests/unit/test_icephys_metadata_tables.py
@@ -16,9 +16,20 @@
 
 from pynwb.testing import TestCase, remove_test_file, create_icephys_stimulus_and_response
 from pynwb.file import NWBFile
-from pynwb.icephys import (VoltageClampStimulusSeries, VoltageClampSeries, CurrentClampStimulusSeries,
-                           IZeroClampSeries, IntracellularRecordingsTable, SimultaneousRecordingsTable,
-                           SequentialRecordingsTable, RepetitionsTable, ExperimentalConditionsTable)
+from pynwb.icephys import (
+    VoltageClampStimulusSeries,
+    VoltageClampSeries,
+    CurrentClampStimulusSeries,
+    IZeroClampSeries,
+    SimultaneousRecordingsTable,
+    SequentialRecordingsTable,
+    RepetitionsTable,
+    ExperimentalConditionsTable,
+    IntracellularElectrode,
+    CurrentClampSeries,
+    IntracellularRecordingsTable
+)
+from pynwb.device import Device
 from pynwb.base import TimeSeriesReferenceVectorData
 from pynwb import NWBHDF5IO
 from hdmf.utils import docval, popargs
@@ -629,6 +640,54 @@ def test_write_with_stimulus_template(self):
         with NWBHDF5IO(self.path, 'w') as io:
             io.write(local_nwbfile)
 
+    def test_no_electrode(self):
+        device = Device(name='device_name')
+        elec = IntracellularElectrode(
+            name='test_iS',
+            device=device,
+            description='description',
+            slice='slice',
+            seal='seal',
+            location='location',
+            resistance='resistance',
+            filtering='filtering',
+            initial_access_resistance='initial_access_resistance',
+            cell_id='this_cell',
+        )
+
+        cCSS = CurrentClampStimulusSeries(
+            name="test_cCSS",
+            data=np.ones((30,)),
+            electrode=elec,
+            gain=1.0,
+            rate=100_000.,
+        )
+
+        cCS = CurrentClampSeries(
+            name="test_cCS",
+            data=np.ones((30,)),
+            electrode=elec,
+            gain=1.0,
+            rate=100_000.,
+        )
+
+        # test retrieve electrode from stimulus (when both stimulus and response are given)
+        itr = IntracellularRecordingsTable()
+        itr.add_recording(stimulus=cCSS, response=cCS)
+        self.assertEqual(itr["electrodes"].values[0], elec)
+        del itr
+
+        # test retrieve electrode from stimulus (when only stimulus is given)
+        itr = IntracellularRecordingsTable()
+        itr.add_recording(stimulus=cCSS, response=None)
+        self.assertEqual(itr["electrodes"].values[0], elec)
+        del itr
+
+        # test retrieve electrode from response (when only response is given)
+        itr = IntracellularRecordingsTable()
+        itr.add_recording(stimulus=None, response=cCS)
+        self.assertEqual(itr["electrodes"].values[0], elec)
+
 
 class SimultaneousRecordingsTableTests(ICEphysMetaTestBase):
     """