Deprecate EventWaveform class

docs/gallery/domain/ecephys.py

@@ -317,7 +317,7 @@
 # :py:class:`~pynwb.ecephys.ElectricalSeries` objects as :ref:`acquisition <basic_timeseries>` data, and use
 # the :py:class:`~pynwb.ecephys.EventDetection` class for identifying the spike events in your raw traces.
 # If you do not want to store the raw voltage traces and only the waveform 'snippets' surrounding spike events,
-# you should use :py:class:`~pynwb.ecephys.SpikeEventSeries` objects.
+# you should store the snippets with :py:class:`~pynwb.ecephys.SpikeEventSeries` objects.
 #
 # The results of spike sorting (or clustering) should be stored in the top-level :py:class:`~pynwb.misc.Units` table.
 # The :py:class:`~pynwb.misc.Units` table can contain simply the spike times of sorted units, or you can also include 

docs/gallery/general/plot_file.py

@@ -92,7 +92,6 @@
       :py:class:`~pynwb.behavior.EyeTracking`.
 
     * **Extracellular electrophysiology:** :py:class:`~pynwb.ecephys.EventDetection`,
-      :py:class:`~pynwb.ecephys.EventWaveform`,
       :py:class:`~pynwb.ecephys.FeatureExtraction`,
       :py:class:`~pynwb.ecephys.FilteredEphys`,
       :py:class:`~pynwb.ecephys.LFP`.
@@ -593,8 +592,7 @@
 
 ####################
 # .. [#] Some data interface objects have a default name. This default name is the type of the data interface. For
-#    example, the default name for :py:class:`~pynwb.ophys.ImageSegmentation` is "ImageSegmentation" and the default
-#    name for :py:class:`~pynwb.ecephys.EventWaveform` is "EventWaveform".
+#    example, the default name for :py:class:`~pynwb.ophys.ImageSegmentation` is "ImageSegmentation".
 #
 # .. [#] HDF5 is the primary backend supported by NWB.
 #

src/pynwb/ecephys.py

@@ -120,8 +120,7 @@ class SpikeEventSeries(ElectricalSeries):
     """
     Stores "snapshots" of spike events (i.e., threshold crossings) in data. This may also be raw data,
     as reported by ephys hardware. If so, the TimeSeries::description field should describing how
-    events were detected. All SpikeEventSeries should reside in a module (under EventWaveform
-    interface) even if the spikes were reported and stored by hardware. All events span the same
+    events were detected. All events span the same
     recording channels and store snapshots of equal duration. TimeSeries::data array structure:
     [num events] [num channels] [num samples] (or [num events] [num samples] for single
     electrode).
@@ -181,6 +180,7 @@ def __init__(self, **kwargs):
 @register_class('EventWaveform', CORE_NAMESPACE)
 class EventWaveform(MultiContainerInterface):
     """
+    DEPRECATED as of NWB 2.8.0 and PyNWB 3.0.0.
     Spike data for spike events detected in raw data
     stored in this NWBFile, or events detect at acquisition
     """
@@ -193,6 +193,13 @@ class EventWaveform(MultiContainerInterface):
         'create': 'create_spike_event_series'
     }
 
+    def __init__(self, **kwargs):
+        if not self._in_construct_mode:
+            raise ValueError(
+                "The EventWaveform neurodata type is deprecated. If you are interested in using it, "
+                "please create an issue on https://github.com/NeurodataWithoutBorders/nwb-schema/issues."
+            )
+
 
 @register_class('Clustering', CORE_NAMESPACE)
 class Clustering(NWBDataInterface):

tests/integration/hdf5/test_ecephys.py

@@ -9,7 +9,6 @@
     Clustering,
     ClusterWaveforms,
     SpikeEventSeries,
-    EventWaveform,
     EventDetection,
     FeatureExtraction,
 )
@@ -185,7 +184,7 @@ def roundtripExportContainer(self, cache_spec=False):
             return super().roundtripExportContainer(cache_spec)
 
 
-class EventWaveformConstructor(NWBH5IOFlexMixin, TestCase):
+class SpikeEventSeriesConstructor(NWBH5IOFlexMixin, TestCase):
 
     def getContainerType(self):
         return "SpikeEventSeries"
@@ -202,18 +201,16 @@ def addContainer(self):
                                     description='the first and third electrodes',
                                     table=table)
         ses = SpikeEventSeries(
-            name='test_sES',
+            name='SpikeEventSeries',
             data=((1, 1), (2, 2), (3, 3)),
             timestamps=[0., 1., 2.],
             electrodes=region
         )
 
-        ew = EventWaveform()
-        self.nwbfile.add_acquisition(ew)
-        ew.add_spike_event_series(ses)
+        self.nwbfile.add_acquisition(ses)
 
     def getContainer(self, nwbfile: NWBFile):
-        return nwbfile.acquisition['EventWaveform']
+        return nwbfile.acquisition['SpikeEventSeries']
 
 
 class ClusterWaveformsConstructor(AcquisitionH5IOMixin, TestCase):

tests/unit/test_ecephys.py

@@ -267,27 +267,9 @@ def test_init(self):
 
 class EventWaveformConstructor(TestCase):
 
-    def _create_table_and_region(self):
-        table = make_electrode_table()
-        region = DynamicTableRegion(
-            name='electrodes',
-            data=[0, 2],
-            description='the first and third electrodes',
-            table=table
-        )
-        return table, region
-
     def test_init(self):
-        table, region = self._create_table_and_region()
-        sES = SpikeEventSeries('test_sES', list(range(10)), list(range(10)), region)
-
-        pm = ProcessingModule(name='test_module', description='a test module')
-        ew = EventWaveform()
-        pm.add(table)
-        pm.add(ew)
-        ew.add_spike_event_series(sES)
-        self.assertEqual(ew.spike_event_series['test_sES'], sES)
-        self.assertEqual(ew['test_sES'], ew.spike_event_series['test_sES'])
+        with self.assertRaises(ValueError):
+            EventWaveform()
 
 
 class ClusteringConstructor(TestCase):