Merge pull request #983 from t-b/icephys-fixes

Icephys fixes
NeurodataWithoutBorders · Jul 9, 2019 · 92a0463 · 92a0463
2 parents b346401 + a796dfd
commit 92a0463
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Showing 4 changed files with 17 additions and 16 deletions.
diff --git a/docs/gallery/domain/icephys.py b/docs/gallery/domain/icephys.py
@@ -84,8 +84,7 @@
     name='vcs', data=[0.1, 0.2, 0.3, 0.4, 0.5],
     unit='A', conversion=1e-12, resolution=np.nan, starting_time=123.6, rate=20e3,
     electrode=elec, gain=0.02, capacitance_slow=100e-12, resistance_comp_correction=70.0,
-    capacitance_fast=np.nan, resistance_comp_bandwidth=np.nan, resistance_comp_prediction=np.nan,
-    whole_cell_capacitance_comp=np.nan, whole_cell_series_resistance_comp=np.nan, sweep_number=15)
+    sweep_number=15)
 
 nwbfile.add_acquisition(vcs)
 

diff --git a/src/pynwb/data/nwb.icephys.yaml b/src/pynwb/data/nwb.icephys.yaml
@@ -138,7 +138,7 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      default_value: pecent
+      default_value: percent
       doc: "The base unit of measure used to store data. This should be in the SI\
         \ unit. COMMENT: This is the SI unit (when appropriate) of the stored data,\
         \ such as Volts. If the actual data is stored in millivolts, the field 'conversion'\
@@ -151,7 +151,7 @@ groups:
     attributes:
     - name: unit
       dtype: text
-      default_value: pecent
+      default_value: percent
       doc: "The base unit of measure used to store data. This should be in the SI\
         \ unit. COMMENT: This is the SI unit (when appropriate) of the stored data,\
         \ such as Volts. If the actual data is stored in millivolts, the field 'conversion'\

diff --git a/src/pynwb/icephys.py b/src/pynwb/icephys.py
@@ -146,9 +146,9 @@ class CurrentClampSeries(PatchClampSeries):
             {'name': 'gain', 'type': float, 'doc': 'Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)'},
             {'name': 'stimulus_description', 'type': str, 'doc': 'the stimulus name/protocol', 'default': "NA"},
 
-            {'name': 'bias_current', 'type': float, 'doc': 'Unit: Amp'},
-            {'name': 'bridge_balance', 'type': float, 'doc': 'Unit: Ohm'},
-            {'name': 'capacitance_compensation', 'type': float, 'doc': 'Unit: Farad'},
+            {'name': 'bias_current', 'type': float, 'doc': 'Unit: Amp', 'default': None},
+            {'name': 'bridge_balance', 'type': float, 'doc': 'Unit: Ohm', 'default': None},
+            {'name': 'capacitance_compensation', 'type': float, 'doc': 'Unit: Farad', 'default': None},
 
             {'name': 'resolution', 'type': float,
              'doc': 'The smallest meaningful difference (in specified unit) between values in data',
@@ -322,13 +322,13 @@ class VoltageClampSeries(PatchClampSeries):
              apply or record this data.'},
             {'name': 'gain', 'type': float, 'doc': 'Units: Volt/Amp (v-clamp) or Volt/Volt (c-clamp)'},
             {'name': 'stimulus_description', 'type': str, 'doc': 'the stimulus name/protocol', 'default': "NA"},
-            {'name': 'capacitance_fast', 'type': float, 'doc': 'Unit: Farad'},
-            {'name': 'capacitance_slow', 'type': float, 'doc': 'Unit: Farad'},
-            {'name': 'resistance_comp_bandwidth', 'type': float, 'doc': 'Unit: Hz'},
-            {'name': 'resistance_comp_correction', 'type': float, 'doc': 'Unit: %'},
-            {'name': 'resistance_comp_prediction', 'type': float, 'doc': 'Unit: %'},
-            {'name': 'whole_cell_capacitance_comp', 'type': float, 'doc': 'Unit: Farad'},
-            {'name': 'whole_cell_series_resistance_comp', 'type': float, 'doc': 'Unit: Ohm'},
+            {'name': 'capacitance_fast', 'type': float, 'doc': 'Unit: Farad', 'default': None},
+            {'name': 'capacitance_slow', 'type': float, 'doc': 'Unit: Farad', 'default': None},
+            {'name': 'resistance_comp_bandwidth', 'type': float, 'doc': 'Unit: Hz', 'default': None},
+            {'name': 'resistance_comp_correction', 'type': float, 'doc': 'Unit: %', 'default': None},
+            {'name': 'resistance_comp_prediction', 'type': float, 'doc': 'Unit: %', 'default': None},
+            {'name': 'whole_cell_capacitance_comp', 'type': float, 'doc': 'Unit: Farad', 'default': None},
+            {'name': 'whole_cell_series_resistance_comp', 'type': float, 'doc': 'Unit: Ohm', 'default': None},
             {'name': 'resolution', 'type': float,
              'doc': 'The smallest meaningful difference (in specified unit) between values in data',
              'default': _default_resolution},

diff --git a/tests/unit/test_icephys.py b/tests/unit/test_icephys.py
@@ -100,10 +100,11 @@ def test_init(self):
         electrode_name = GetElectrode()
 
         cCS = CurrentClampSeries('test_cCS', list(), 'unit',
-                                 electrode_name, 1.0, 2.0, 3.0, 4.0, timestamps=list())
+                                 electrode_name, 1.0, "stimset", 2.0, 3.0, 4.0, timestamps=list())
         self.assertEqual(cCS.name, 'test_cCS')
         self.assertEqual(cCS.unit, 'unit')
         self.assertEqual(cCS.electrode, electrode_name)
+        self.assertEqual(cCS.stimulus_description, "stimset")
         self.assertEqual(cCS.gain, 1.0)
         self.assertEqual(cCS.bias_current, 2.0)
         self.assertEqual(cCS.bridge_balance, 3.0)
@@ -145,10 +146,11 @@ def test_init(self):
         electrode_name = GetElectrode()
 
         vCS = VoltageClampSeries('test_vCS', list(), 'unit', electrode_name,
-                                 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, timestamps=list())
+                                 1.0, "stimset", 2.0, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, timestamps=list())
         self.assertEqual(vCS.name, 'test_vCS')
         self.assertEqual(vCS.unit, 'unit')
         self.assertEqual(vCS.electrode, electrode_name)
+        self.assertEqual(vCS.stimulus_description, "stimset")
         self.assertEqual(vCS.gain, 1.0)
         self.assertEqual(vCS.capacitance_fast, 2.0)
         self.assertEqual(vCS.capacitance_slow, 3.0)