draft complete

src/pynwb/ecephys.py

@@ -43,17 +43,17 @@ class ElectrodesTable(DynamicTable):
 
     __columns__ = (
         {'name': 'location', 'description': 'TODO', 'required': True},
-        {'name': 'group', 'description': 'TODO', 'required': True})
-
-    @docval({'name': 'group_name', 'type': VectorData, 'doc':'TODO', 'default': None},
-            {'name': 'x', 'type': float, 'doc':'TODO', 'default': None},
-            {'name': 'y', 'type': float, 'doc':'TODO', 'default': None},
-            {'name': 'z', 'type': float, 'doc':'TODO', 'default': None},
-            {'name': 'imp', 'type': float, 'doc':'TODO', 'default': None},
-            {'name': 'filtering', 'type': str, 'doc':'TODO', 'default': None},
-            {'name': 'rel_x', 'type': float, 'doc':'TODO', 'default': None},
-            {'name': 'rel_y', 'type': float, 'doc':'TODO', 'default': None},
-            {'name': 'rel_z', 'type': float, 'doc':'TODO', 'default': None},
+        {'name': 'group', 'description': 'TODO', 'required': True},
+        {'name': 'group_name', 'description': 'TODO', 'required': False })
+
+    @docval({'name': 'x', 'type': VectorData, 'doc':'TODO', 'default': None},
+            {'name': 'y', 'type': VectorData, 'doc':'TODO', 'default': None},
+            {'name': 'z', 'type': VectorData, 'doc':'TODO', 'default': None},
+            {'name': 'imp', 'type': VectorData, 'doc':'TODO', 'default': None},
+            {'name': 'filtering', 'type': VectorData, 'doc':'TODO', 'default': None},
+            {'name': 'rel_x', 'type': VectorData, 'doc':'TODO', 'default': None},
+            {'name': 'rel_y', 'type': VectorData, 'doc':'TODO', 'default': None},
+            {'name': 'rel_z', 'type': VectorData, 'doc':'TODO', 'default': None},
             {'name': 'reference', 'type': VectorData, 'doc':'TODO', 'default': None},
             *get_docval(DynamicTable.__init__, 'id', 'columns', 'colnames'))
     def __init__(self, **kwargs):
@@ -62,7 +62,6 @@ def __init__(self, **kwargs):
 
         # optional fields
         keys_to_set = (
-            'group_name',
             'x',
             'y',
             'z',
@@ -78,6 +77,14 @@ def __init__(self, **kwargs):
 
         super().__init__(**kwargs)
 
+    def copy(self):
+        """
+        Return a copy of this DynamicTable.
+        This is useful for linking.
+        """
+        kwargs = dict(id=self.id, columns=self.columns, colnames=self.colnames)
+        return self.__class__(**kwargs)
+
 
 @register_class('ElectricalSeries', CORE_NAMESPACE)
 class ElectricalSeries(TimeSeries):

src/pynwb/io/file.py

@@ -182,15 +182,15 @@ def scratch(self, builder, manager):
 
     @ObjectMapper.constructor_arg('electrodes')
     def electrodes(self, builder, manager):
-        electrodes_builder = builder['general']['extracellular_ephys']['electrodes']
-
+        try:
+            electrodes_builder = builder['general']['extracellular_ephys']['electrodes']
+        except KeyError:
+            electrodes_builder = None
         if (electrodes_builder is not None and electrodes_builder.attributes['neurodata_type'] != 'ElectrodesTable'):
             electrodes_builder.attributes['neurodata_type'] = 'ElectrodesTable'
             electrodes_builder.attributes['namespace'] = 'core'
 
             new_container =  manager.construct(electrodes_builder, True)
-            # mapper = manager.get_map(electrodes_builder)
-            breakpoint()
             return new_container
         else:
             return None

src/pynwb/testing/mock/ecephys.py

@@ -35,10 +35,10 @@ def mock_ElectrodeGroup(
     return electrode_group
 
 
-def mock_ElectrodeTable(
+def mock_ElectrodesTable(
         n_rows: int = 5, group: Optional[ElectrodeGroup] = None, nwbfile: Optional[NWBFile] = None
 ) -> DynamicTable:
-    electrodes_table = ElectrodeTable()
+    electrodes_table = ElectrodesTable()
     group = group if group is not None else mock_ElectrodeGroup(nwbfile=nwbfile)
     for i in range(n_rows):
         electrodes_table.add_row(
@@ -57,7 +57,7 @@ def mock_electrodes(
         n_electrodes: int = 5, table: Optional[DynamicTable] = None, nwbfile: Optional[NWBFile] = None
 ) -> DynamicTableRegion:
 
-    table = table or mock_ElectrodeTable(n_rows=5, nwbfile=nwbfile)
+    table = table or mock_ElectrodesTable(n_rows=5, nwbfile=nwbfile)
     return DynamicTableRegion(
         name="electrodes",
         data=list(range(n_electrodes)),
@@ -80,7 +80,7 @@ def mock_ElectricalSeries(
     conversion: float = 1.0,
     offset: float = 0.,
 ) -> ElectricalSeries:
-    
+
     # Set a default rate if timestamps are not provided
     rate = 30_000.0 if (timestamps is None and rate is None) else rate
 

tests/integration/hdf5/test_nwbfile.py

@@ -508,6 +508,7 @@ def getContainer(self, nwbfile):
 
     def test_roundtrip(self):
         super().test_roundtrip()
+
         # When comparing the pandas dataframes for the row we drop the 'group' column since the
         # ElectrodeGroup object after reading will naturally have a different address
         pd.testing.assert_frame_equal(self.read_container[0].drop('group', axis=1),

tests/unit/test_ecephys.py

@@ -24,7 +24,7 @@
 
 
 def make_electrode_table():
-    table = ElectrodeTable()
+    table = ElectrodesTable()
     dev1 = Device('dev1')
     group = ElectrodeGroup('tetrode1', 'tetrode description', 'tetrode location', dev1)
     table.add_row(location='CA1', group=group, group_name='tetrode1')

tests/unit/test_file.py

@@ -245,7 +245,7 @@ def test_add_acquisition_invalid_name(self):
             self.nwbfile.get_acquisition("TEST_TS")
 
     def test_set_electrode_table(self):
-        table = ElectrodeTable()
+        table = ElectrodesTable()
         dev1 = self.nwbfile.create_device('dev1')
         group = self.nwbfile.create_electrode_group('tetrode1', 'tetrode description', 'tetrode location', dev1)
 

tests/unit/test_mock.py

@@ -32,7 +32,7 @@
 
 from pynwb.testing.mock.ecephys import (
     mock_ElectrodeGroup,
-    mock_ElectrodeTable,
+    mock_ElectrodesTable,
     mock_ElectricalSeries,
     mock_SpikeEventSeries,
     mock_Units,
@@ -70,7 +70,7 @@
     mock_CompassDirection,
     mock_SpatialSeries,
     mock_ElectrodeGroup,
-    mock_ElectrodeTable,
+    mock_ElectrodesTable,
     mock_ElectricalSeries,
     mock_SpikeEventSeries,
     mock_Subject,
@@ -121,4 +121,3 @@ def test_name_generator():
 
     assert name_generator("TimeSeries") == "TimeSeries"
     assert name_generator("TimeSeries") == "TimeSeries2"
-