add cell_id to IntracellularElectrode (#1459)

* add cell_id to constructor and adjust tests accordingly * add cell_id to rountrip test for IntracellularElectrode * update submodule Co-authored-by: Ryan Ly <[email protected]>
NeurodataWithoutBorders · May 1, 2022 · 2973aeb · 2973aeb
1 parent c1e6fa1
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Showing 4 changed files with 25 additions and 15 deletions.
diff --git a/src/pynwb/icephys.py b/src/pynwb/icephys.py
@@ -30,7 +30,8 @@ class IntracellularElectrode(NWBContainer):
     '''
     '''
 
-    __nwbfields__ = ('slice',
+    __nwbfields__ = ('cell_id',
+                     'slice',
                      'seal',
                      'description',
                      'location',
@@ -51,11 +52,12 @@ class IntracellularElectrode(NWBContainer):
             {'name': 'resistance', 'type': str, 'doc': 'Electrode resistance COMMENT: unit: Ohm.', 'default': None},
             {'name': 'filtering', 'type': str, 'doc': 'Electrode specific filtering.', 'default': None},
             {'name': 'initial_access_resistance', 'type': str, 'doc': 'Initial access resistance.', 'default': None},
+            {'name': 'cell_id', 'type': str, 'doc': 'Unique ID of cell.', 'default': None}
             )
     def __init__(self, **kwargs):
-        slice, seal, description, location, resistance, filtering, initial_access_resistance, device = popargs(
+        slice, seal, description, location, resistance, filtering, initial_access_resistance, device, cell_id = popargs(
             'slice', 'seal', 'description', 'location', 'resistance',
-            'filtering', 'initial_access_resistance', 'device', kwargs)
+            'filtering', 'initial_access_resistance', 'device', 'cell_id', kwargs)
         call_docval_func(super().__init__, kwargs)
         self.slice = slice
         self.seal = seal
@@ -65,6 +67,7 @@ def __init__(self, **kwargs):
         self.filtering = filtering
         self.initial_access_resistance = initial_access_resistance
         self.device = device
+        self.cell_id = cell_id
 
 
 @register_class('PatchClampSeries', CORE_NAMESPACE)

diff --git a/src/pynwb/nwb-schema b/src/pynwb/nwb-schema
diff --git a/tests/integration/hdf5/test_icephys.py b/tests/integration/hdf5/test_icephys.py
@@ -14,15 +14,18 @@ class TestIntracellularElectrode(NWBH5IOMixin, TestCase):
     def setUpContainer(self):
         """ Return the test IntracellularElectrode to read/write """
         self.device = Device(name='device_name')
-        elec = IntracellularElectrode(name="elec0",
-                                      slice='tissue slice',
-                                      resistance='something measured in ohms',
-                                      seal='sealing method',
-                                      description='a fake electrode object',
-                                      location='Springfield Elementary School',
-                                      filtering='a meaningless free-form text field',
-                                      initial_access_resistance='I guess this changes',
-                                      device=self.device)
+        elec = IntracellularElectrode(
+            name="elec0",
+            slice='tissue slice',
+            resistance='something measured in ohms',
+            seal='sealing method',
+            description='a fake electrode object',
+            location='Springfield Elementary School',
+            filtering='a meaningless free-form text field',
+            initial_access_resistance='I guess this changes',
+            device=self.device,
+            cell_id="this_cell",
+        )
         return elec
 
     def addContainer(self, nwbfile):

diff --git a/tests/unit/test_icephys.py b/tests/unit/test_icephys.py
@@ -20,7 +20,9 @@ def GetElectrode():
         location='location',
         resistance='resistance',
         filtering='filtering',
-        initial_access_resistance='initial_access_resistance')
+        initial_access_resistance='initial_access_resistance',
+        cell_id='this_cell',
+    )
     return elec
 
 
@@ -118,7 +120,8 @@ def test_constructor(self):
                                       'location',
                                       'resistance',
                                       'filtering',
-                                      'initial_access_resistance')
+                                      'initial_access_resistance',
+                                      'this_cell')
         self.assertEqual(elec.name, 'test_iS')
         self.assertEqual(elec.device, device)
         self.assertEqual(elec.description, 'description')
@@ -128,6 +131,7 @@ def test_constructor(self):
         self.assertEqual(elec.resistance, 'resistance')
         self.assertEqual(elec.filtering, 'filtering')
         self.assertEqual(elec.initial_access_resistance, 'initial_access_resistance')
+        self.assertEqual(elec.cell_id, 'this_cell')
 
 
 class PatchClampSeriesConstructor(TestCase):
+10 −2		core/nwb.behavior.yaml
+2 −1		core/nwb.file.yaml
+4 −0		core/nwb.icephys.yaml
+1 −1		core/nwb.ophys.yaml
+5 −1		docs/Readme.md
+10 −10		docs/format/source/format_description.rst
+8 −0		docs/format/source/format_release_notes.rst
+2 −0		docs/format/source/index.rst
+0 −166		docs/general/Makefile
+0 −23		docs/general/Readme.md
+0 −202		docs/general/make.bat
+0 −13		docs/general/source/_static/theme_overrides.css
+0 −259		docs/general/source/conf.py
+0 −13		docs/general/source/index.rst
+4 −4		docs/storage/source/storage_hdf5.rst