Add support for ElectricalSeries.filtering dataset

src/pynwb/base.py

@@ -92,7 +92,8 @@ class TimeSeries(NWBDataInterface):
                      "rate",
                      "starting_time_unit",
                      "control",
-                     "control_description")
+                     "control_description",
+                     "continuity")
 
     __time_unit = "seconds"
 
@@ -118,18 +119,28 @@ class TimeSeries(NWBDataInterface):
             {'name': 'control', 'type': Iterable, 'doc': 'Numerical labels that apply to each element in data',
              'default': None},
             {'name': 'control_description', 'type': Iterable, 'doc': 'Description of each control value',
-             'default': None})
+             'default': None},
+            {'name': 'continuity', 'type': str, 'default': None, 'enum': ["continuous", "instantaneous", "step"],
+             'doc': 'Optionally describe the continuity of the data. Can be "continuous", "instantaneous", or'
+                    '"step". For example, a voltage trace would be "continuous", because samples are recorded from a '
+                    'continuous process. An array of lick times would be "instantaneous", because the data represents '
+                    'distinct moments in time. Times of image presentations would be  "step" because the picture '
+                    'remains the same until the next time-point. This field is optional, but is useful in providing '
+                    'information about the underlying data. It may inform the way this data is interpreted, the way it '
+                    'is visualized, and what analysis methods are applicable.'})
     def __init__(self, **kwargs):
         """Create a TimeSeries object
         """
+
         call_docval_func(super(TimeSeries, self).__init__, kwargs)
         keys = ("resolution",
                 "comments",
                 "description",
                 "conversion",
                 "unit",
                 "control",
-                "control_description")
+                "control_description",
+                "continuity")
         for key in keys:
             val = kwargs.get(key)
             if val is not None:

src/pynwb/ecephys.py

@@ -49,7 +49,8 @@ class ElectricalSeries(TimeSeries):
 
     __nwbfields__ = ({'name': 'electrodes', 'required_name': 'electrodes',
                       'doc': 'the electrodes that generated this electrical series', 'child': True},
-                     'channel_conversion')
+                     'channel_conversion',
+                     'filtering')
 
     @docval(*get_docval(TimeSeries.__init__, 'name'),  # required
             {'name': 'data', 'type': ('array_data', 'data', TimeSeries),  # required
@@ -65,13 +66,21 @@ class ElectricalSeries(TimeSeries):
              "to support the storage of electrical recordings as native values generated by data acquisition systems. "
              "If this dataset is not present, then there is no channel-specific conversion factor, i.e. it is 1 for all"
              " channels.", 'default': None},
+            {'name': 'filtering', 'type': str, 'doc':
+             "Filtering applied to all channels of the data. For example, if this ElectricalSeries represents "
+             "high-pass-filtered data (also known as AP Band), then this value could be 'High-pass 4-pole Bessel "
+             "filter at 500 Hz'. If this ElectricalSeries represents low-pass-filtered LFP data and the type of "
+             "filter is unknown, then this value could be 'Low-pass filter at 300 Hz'. If a non-standard filter "
+             "type is used, provide as much detail about the filter properties as possible.", 'default': None},
             *get_docval(TimeSeries.__init__, 'resolution', 'conversion', 'timestamps', 'starting_time', 'rate',
                         'comments', 'description', 'control', 'control_description'))
     def __init__(self, **kwargs):
-        name, electrodes, data, channel_conversion = popargs('name', 'electrodes', 'data', 'channel_conversion', kwargs)
+        name, electrodes, data, channel_conversion, filtering = popargs('name', 'electrodes', 'data',
+                                                                        'channel_conversion', 'filtering', kwargs)
         super(ElectricalSeries, self).__init__(name, data, 'volts', **kwargs)
         self.electrodes = electrodes
         self.channel_conversion = channel_conversion
+        self.filtering = filtering
 
 
 @register_class('SpikeEventSeries', CORE_NAMESPACE)

src/pynwb/io/base.py

@@ -29,6 +29,7 @@ def __init__(self, spec):
         self.map_spec('unit', data_spec.get_attribute('unit'))
         self.map_spec('resolution', data_spec.get_attribute('resolution'))
         self.map_spec('conversion', data_spec.get_attribute('conversion'))
+        self.map_spec('continuity', data_spec.get_attribute('continuity'))
 
         timestamps_spec = self.spec.get_dataset('timestamps')
         self.map_spec('timestamps_unit', timestamps_spec.get_attribute('unit'))

tests/integration/hdf5/test_base.py

@@ -15,7 +15,8 @@ def setUpContainer(self):
             data=list(range(1000)),
             unit='SIunit',
             timestamps=np.arange(1000.),
-            resolution=0.1
+            resolution=0.1,
+            continuity='continuous',
         )
 
 

tests/integration/hdf5/test_ecephys.py

@@ -52,11 +52,16 @@ def setUpContainer(self):
                                     table=self.table)
         data = list(zip(range(10), range(10, 20)))
         timestamps = list(map(lambda x: x/10., range(10)))
-        es = ElectricalSeries(name='test_eS',
-                              data=data,
-                              electrodes=region,
-                              channel_conversion=[4., .4],
-                              timestamps=timestamps)
+        channel_conversion = [1., 2., 3., 4.]
+        filtering = 'Low-pass filter at 300 Hz'
+        es = ElectricalSeries(
+            name='test_eS',
+            data=data,
+            electrodes=region,
+            channel_conversion=channel_conversion,
+            filtering=filtering,
+            timestamps=timestamps
+        )
         return es
 
     def addContainer(self, nwbfile):

tests/unit/test_base.py

@@ -124,6 +124,18 @@ def test_timestamps_timeseries(self):
                          'grams', timestamps=ts1)
         self.assertEqual(ts2.timestamps, [0.0, 0.1, 0.2, 0.3, 0.4, 0.5])
 
+    def test_good_continuity_timeseries(self):
+        ts1 = TimeSeries('test_ts1', [0, 1, 2, 3, 4, 5],
+                         'grams', timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5],
+                         continuity='continuous')
+        self.assertEqual(ts1.continuity, 'continuous')
+
+    def test_bad_continuity_timeseries(self):
+        with self.assertRaises(ValueError):
+            TimeSeries('test_ts1', [0, 1, 2, 3, 4, 5],
+                       'grams', timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5],
+                       continuity='wrong')
+
     def test_nodata(self):
         ts1 = TimeSeries('test_ts1', starting_time=0.0, rate=0.1)
         with self.assertWarns(UserWarning):

tests/unit/test_ecephys.py

@@ -29,12 +29,24 @@ class ElectricalSeriesConstructor(TestCase):
     def test_init(self):
         data = list(range(10))
         ts = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]
+        channel_conversion = [2., 6.3]
+        filtering = 'Low-pass filter at 300 Hz'
         table = make_electrode_table()
         region = DynamicTableRegion('electrodes', [0, 2], 'the first and third electrodes', table)
-        eS = ElectricalSeries('test_eS', data, region, channel_conversion=[2., 6.3], timestamps=ts)
+        eS = ElectricalSeries(
+            name='test_eS',
+            data=data,
+            electrodes=region,
+            channel_conversion=channel_conversion,
+            filtering=filtering,
+            timestamps=ts
+        )
         self.assertEqual(eS.name, 'test_eS')
         self.assertEqual(eS.data, data)
+        self.assertEqual(eS.electrodes, region)
         self.assertEqual(eS.timestamps, ts)
+        self.assertEqual(eS.channel_conversion, [2., 6.3])
+        self.assertEqual(eS.filtering, filtering)
 
     def test_link(self):
         table = make_electrode_table()