make PatchClampSeries gain optional to match the schema (NeurodataWit…

…houtBorders#1975) Co-authored-by: Ryan Ly <[email protected]>
h-mayorquin · Nov 8, 2024 · ad04661 · ad04661
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Showing 4 changed files with 47 additions and 17 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,7 +12,8 @@
 - Fixed bug in how `ElectrodeGroup.__init__` validates its `position` argument. @oruebel [#1770](https://github.com/NeurodataWithoutBorders/pynwb/pull/1770)
 - Changed `SpatialSeries.reference_frame` from required to optional as specified in the schema. @rly [#1986](https://github.com/NeurodataWithoutBorders/pynwb/pull/1986)
 
-### Enhancements and minor changes`
+### Enhancements and minor changes
+- Made gain an optional argument for PatchClampSeries to match the schema. @stephprince [#1975](https://github.com/NeurodataWithoutBorders/pynwb/pull/1975)
 - Added warning when writing files with `NWBHDF5IO` without the `.nwb` extension. @stephprince [#1978](https://github.com/NeurodataWithoutBorders/pynwb/pull/1978)
 
 ## PyNWB 2.8.2 (September 9, 2024)

diff --git a/src/pynwb/icephys.py b/src/pynwb/icephys.py
@@ -109,7 +109,8 @@ class PatchClampSeries(TimeSeries):
             'name': 'gain',
             'type': float,
             'doc': 'Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)',
-        },  # required
+            'default': None,
+        },
         {
             'name': 'stimulus_description',
             'type': str,
@@ -164,7 +165,7 @@ class CurrentClampSeries(PatchClampSeries):
                      'capacitance_compensation')
 
     @docval(*get_docval(PatchClampSeries.__init__, 'name', 'data', 'electrode'),  # required
-            {'name': 'gain', 'type': float, 'doc': 'Units - Volt/Volt'},
+            {'name': 'gain', 'type': float, 'doc': 'Units - Volt/Volt', 'default': None},
             *get_docval(PatchClampSeries.__init__, 'stimulus_description'),
             {'name': 'bias_current', 'type': float, 'doc': 'Unit - Amp', 'default': None},
             {'name': 'bridge_balance', 'type': float, 'doc': 'Unit - Ohm', 'default': None},
@@ -196,7 +197,7 @@ class IZeroClampSeries(CurrentClampSeries):
     __nwbfields__ = ()
 
     @docval(*get_docval(CurrentClampSeries.__init__, 'name', 'data', 'electrode'),  # required
-            {'name': 'gain', 'type': float, 'doc': 'Units: Volt/Volt'},  # required
+            {'name': 'gain', 'type': float, 'doc': 'Units: Volt/Volt', 'default': None},
             {'name': 'stimulus_description', 'type': str,
              'doc': ('The stimulus name/protocol. Setting this to a value other than "N/A" is deprecated as of '
                      'NWB 2.3.0.'),
@@ -238,16 +239,16 @@ class CurrentClampStimulusSeries(PatchClampSeries):
 
     __nwbfields__ = ()
 
-    @docval(*get_docval(PatchClampSeries.__init__, 'name', 'data', 'electrode', 'gain'),  # required
-            *get_docval(PatchClampSeries.__init__, 'stimulus_description', 'resolution', 'conversion', 'timestamps',
-                        'starting_time', 'rate', 'comments', 'description', 'control', 'control_description',
-                        'sweep_number', 'offset'),
+    @docval(*get_docval(PatchClampSeries.__init__, 'name', 'data', 'electrode'),  # required
+            *get_docval(PatchClampSeries.__init__, 'gain', 'stimulus_description', 'resolution', 'conversion', 
+                        'timestamps', 'starting_time', 'rate', 'comments', 'description', 'control', 
+                        'control_description', 'sweep_number', 'offset'),
             {'name': 'unit', 'type': str, 'doc': "The base unit of measurement (must be 'amperes')",
              'default': 'amperes'})
     def __init__(self, **kwargs):
-        name, data, unit, electrode, gain = popargs('name', 'data', 'unit', 'electrode', 'gain', kwargs)
+        name, data, unit, electrode = popargs('name', 'data', 'unit', 'electrode', kwargs)
         unit = ensure_unit(self, name, unit, 'amperes', '2.1.0')
-        super().__init__(name, data, unit, electrode, gain, **kwargs)
+        super().__init__(name, data, unit, electrode, **kwargs)
 
 
 @register_class('VoltageClampSeries', CORE_NAMESPACE)
@@ -267,7 +268,7 @@ class VoltageClampSeries(PatchClampSeries):
                      'whole_cell_series_resistance_comp')
 
     @docval(*get_docval(PatchClampSeries.__init__, 'name', 'data', 'electrode'),  # required
-            {'name': 'gain', 'type': float, 'doc': 'Units - Volt/Amp'},  # required
+            {'name': 'gain', 'type': float, 'doc': 'Units - Volt/Amp', 'default': None},
             *get_docval(PatchClampSeries.__init__, 'stimulus_description'),
             {'name': 'capacitance_fast', 'type': float, 'doc': 'Unit - Farad', 'default': None},
             {'name': 'capacitance_slow', 'type': float, 'doc': 'Unit - Farad', 'default': None},
@@ -307,16 +308,16 @@ class VoltageClampStimulusSeries(PatchClampSeries):
 
     __nwbfields__ = ()
 
-    @docval(*get_docval(PatchClampSeries.__init__, 'name', 'data', 'electrode', 'gain'),  # required
-            *get_docval(PatchClampSeries.__init__, 'stimulus_description', 'resolution', 'conversion', 'timestamps',
-                        'starting_time', 'rate', 'comments', 'description', 'control', 'control_description',
-                        'sweep_number', 'offset'),
+    @docval(*get_docval(PatchClampSeries.__init__, 'name', 'data', 'electrode'),  # required
+            *get_docval(PatchClampSeries.__init__, 'gain', 'stimulus_description', 'resolution', 'conversion', 
+                        'timestamps', 'starting_time', 'rate', 'comments', 'description', 'control',
+                        'control_description', 'sweep_number', 'offset'),
             {'name': 'unit', 'type': str, 'doc': "The base unit of measurement (must be 'volts')",
              'default': 'volts'})
     def __init__(self, **kwargs):
-        name, data, unit, electrode, gain = popargs('name', 'data', 'unit', 'electrode', 'gain', kwargs)
+        name, data, unit, electrode = popargs('name', 'data', 'unit', 'electrode', kwargs)
         unit = ensure_unit(self, name, unit, 'volts', '2.1.0')
-        super().__init__(name, data, unit, electrode, gain, **kwargs)
+        super().__init__(name, data, unit, electrode, **kwargs)
 
 
 @register_class('SweepTable', CORE_NAMESPACE)

diff --git a/tests/integration/hdf5/test_icephys.py b/tests/integration/hdf5/test_icephys.py
@@ -66,6 +66,27 @@ def addContainer(self, nwbfile):
         nwbfile.add_device(self.device)
         super().addContainer(nwbfile)
 
+class TestPatchClampSeriesMin(AcquisitionH5IOMixin, TestCase):
+    """ Test a PatchClampSeries with minimum required args to read/write """
+
+    def setUpElectrode(self):
+        """ Set up the test IntracellularElectrode """
+        self.device = Device(name='device_name')
+        self.elec = IntracellularElectrode(name="elec0", description='a fake electrode object',
+                                           device=self.device)
+
+    def setUpContainer(self):
+        self.setUpElectrode()
+        return PatchClampSeries(name="pcs", data=[1, 2, 3, 4, 5], unit='A',
+                                starting_time=123.6, rate=10e3, electrode=self.elec)
+
+    def addContainer(self, nwbfile):
+        """
+        Add the test PatchClampSeries as an acquisition and IntracellularElectrode and Device to the given NWBFile
+        """
+        nwbfile.add_icephys_electrode(self.elec)
+        nwbfile.add_device(self.device)
+        super().addContainer(nwbfile)
 
 class TestCurrentClampStimulusSeries(TestPatchClampSeries):
 

diff --git a/tests/unit/test_icephys.py b/tests/unit/test_icephys.py
@@ -154,6 +154,13 @@ def test_default(self):
         self.assertEqual(pCS.electrode, electrode_name)
         self.assertEqual(pCS.gain, 1.0)
 
+    def test_gain_optional(self):
+        electrode_name = GetElectrode()
+
+        pCS = PatchClampSeries('test_pCS', list(), 'unit',
+                               electrode_name, timestamps=list())
+        self.assertIsNone(pCS.gain)
+
     def test_sweepNumber_valid(self):
         electrode_name = GetElectrode()