add link spike_event_series to UnitSeries

src/pynwb/data/nwb.ecephys.yaml

@@ -98,6 +98,11 @@ groups:
     - num_times
     shape:
     - null
+  links:
+  - name: unit_series
+    doc: the UnitSeries that holds the unit ids for each waveform
+    quantity: '?'
+    target_type: UnitSeries
 - neurodata_type_def: ClusterWaveforms
   neurodata_type_inc: NWBDataInterface
   doc: 'DEPRECATED The mean waveform shape, including standard deviation, of the

src/pynwb/ecephys.py

@@ -8,7 +8,7 @@
 from .base import TimeSeries, _default_resolution, _default_conversion
 from .core import NWBContainer, NWBDataInterface, MultiContainerInterface, DynamicTableRegion
 from .device import Device
-from .misc import DecompositionSeries
+from .misc import DecompositionSeries, UnitSeries
 
 
 @register_class('ElectrodeGroup', CORE_NAMESPACE)
@@ -108,7 +108,9 @@ class SpikeEventSeries(ElectricalSeries):
     electrode).
     """
 
-    __nwbfields__ = ()
+    __nwbfields__ = ({'name': 'unit_series',
+                      'doc': 'the UnitSeries that holds the unit ids for each waveform',
+                      'child': False},)
 
     __help = "Snapshots of spike events from data."
 
@@ -119,6 +121,8 @@ class SpikeEventSeries(ElectricalSeries):
              'doc': 'Timestamps for samples stored in data'},
             {'name': 'electrodes', 'type': DynamicTableRegion,
              'doc': 'the table region corresponding to the electrodes from which this series was recorded'},
+            {'name': 'unit_series', 'type': UnitSeries, 'default': None,
+             'doc': 'UnitSeries that matches waveforms to spikes in Units table'},
             {'name': 'resolution', 'type': float,
              'doc': 'The smallest meaningful difference (in specified unit) between values in data',
              'default': _default_resolution},
@@ -135,7 +139,7 @@ class SpikeEventSeries(ElectricalSeries):
             {'name': 'parent', 'type': 'NWBContainer',
              'doc': 'The parent NWBContainer for this NWBContainer', 'default': None})
     def __init__(self, **kwargs):
-        name, data, electrodes = popargs('name', 'data', 'electrodes', kwargs)
+        name, data, electrodes, unit_series = popargs('name', 'data', 'electrodes', 'unit_series', kwargs)
         timestamps = getargs('timestamps', kwargs)
         if not (isinstance(data, TimeSeries) and isinstance(timestamps, TimeSeries)):
             if not (isinstance(data, DataChunkIterator) and isinstance(timestamps, DataChunkIterator)):
@@ -145,6 +149,7 @@ def __init__(self, **kwargs):
                 # TODO: add check when we have DataChunkIterators
                 pass
         super(SpikeEventSeries, self).__init__(name, data, electrodes, **kwargs)
+        self.unit_series = unit_series
 
 
 @register_class('EventDetection', CORE_NAMESPACE)

src/pynwb/form/build/map.py

@@ -540,12 +540,15 @@ def get_container_name(self, *args):
     def convert_dt_name(cls, **kwargs):
         '''Get the attribute name corresponding to a specification'''
         spec = getargs('spec', kwargs)
-        if spec.data_type_def is not None:
-            name = spec.data_type_def
-        elif spec.data_type_inc is not None:
-            name = spec.data_type_inc
+        if isinstance(spec, LinkSpec):
+            name = spec.target_type
         else:
-            raise ValueError('found spec without name or data_type')
+            if spec.data_type_def is not None:
+                name = spec.data_type_def
+            elif spec.data_type_inc is not None:
+                name = spec.data_type_inc
+            else:
+                raise ValueError('found spec without name or data_type')
         s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
         name = re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower()
         if name[-1] != 's' and spec.is_many():
@@ -1051,7 +1054,9 @@ def __get_subspec_values(self, builder, spec, manager):
             # now assign links to their respective specification
             for subspec in spec.links:
                 if subspec.name is not None:
-                    ret[subspec] = manager.construct(links[subspec.name].builder)
+                    sub_builder = links.get(subspec.name)
+                    if sub_builder is not None:
+                        ret[subspec] = manager.construct(sub_builder.builder)
                 else:
                     sub_builder = link_dt.get(subspec.target_type)
                     if sub_builder is not None:
@@ -1100,6 +1105,10 @@ def __get_sub_builders(self, sub_builders, subspecs, manager, ret):
                     ret[subspec] = manager.construct(sub_builder)
 
     def __flatten(self, sub_builder, subspec, manager):
+        """
+        Convert one-or-many to a single object or a list,
+        depending on the spec
+        """
         tmp = [manager.construct(b) for b in sub_builder]
         if len(tmp) == 1 and not subspec.is_many():
             tmp = tmp[0]

src/pynwb/form/spec/spec.py

@@ -945,9 +945,12 @@ def is_inherited_spec(self, **kwargs):
         if isinstance(spec, Spec):
             name = spec.name
             if name is None:
-                name = spec.data_type_def
-            if name is None:
-                name = spec.data_type_inc
+                if isinstance(spec, LinkSpec):
+                    name = spec.target_type
+                else:
+                    name = spec.data_type_def
+                    if name is None:
+                        name = spec.data_type_inc
             if name is None:
                 raise ValueError('received Spec with wildcard name but no data_type_inc or data_type_def')
             spec = name