make patchclampseries gain optional

NeurodataWithoutBorders · Oct 24, 2024 · 2fff4f9 · 2fff4f9
1 parent e938202
commit 2fff4f9
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Showing 2 changed files with 24 additions and 16 deletions.
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/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()