add UnitSeries

src/pynwb/data/nwb.misc.yaml

@@ -257,3 +257,32 @@ groups:
     - null
     quantity: '?'
   default_name: Units
+- neurodata_type_def: UnitSeries
+  neurodata_type_inc: TimeSeries
+  doc: Unit spike times a stream of IDs of spiking units
+  attributes:
+  - name: help
+    dtype: text
+    doc: Value is 'Unit spike times a stream of IDs of spiking units'
+    value: Unit spike times a stream of IDs of spiking units
+  datasets:
+  - name: data
+    dtype: int
+    doc: the index of the spike unit in the DynamicTableRegion "units"
+    attributes:
+    - name: resolution
+      dtype: float
+      doc: Value is -1.0. Indices do not have resolution
+      value: -1.0
+    - name: unit
+      dtype: text
+      doc: Value is 'index'
+      value: index
+    dims:
+    - num_times
+    shape:
+    - null
+  links:
+   - name: units
+     doc: The units table that is being indexed
+     target_type: Units

src/pynwb/misc.py

@@ -327,3 +327,29 @@ def add_band(self, **kwargs):
             self.__check_column('band_stdev', 'the standard deviation of Gaussian filters in Hz')
 
         self.bands.add_row({k: v for k, v in kwargs.items() if v is not None})
+
+
+class UnitSeries(TimeSeries):
+
+    __nwbfields__ = ({'name': 'units', 'child': False, 'doc': 'link to Units table'},)
+
+    @docval({'name': 'name', 'type': str, 'doc': 'The name of this UnitSeries dataset'},
+            {'name': 'data', 'type': ('array_data', 'data', TimeSeries), 'shape': (None,),
+             'doc': 'Indices of Units table (0-indexed)'},
+            {'name': 'timestamps', 'type': ('array_data', 'data', TimeSeries), 'shape': (None,),
+             'doc': 'Timestamps for samples stored in data', 'default': None},
+            {'name': 'units', 'type': Units, 'doc': 'Units table', 'default': None},
+            {'name': 'description', 'type': str,
+             'doc': 'Description of this TimeSeries dataset', 'default': 'no description'},
+            {'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},
+            {'name': 'parent', 'type': NWBContainer,
+             'doc': 'The parent NWBContainer for this NWBContainer', 'default': None})
+    def __init__(self, **kwargs):
+        kwargs.update(conversion=np.nan, resolution=np.nan)
+
+        name, data, units = popargs('name', 'data', 'units', kwargs)
+        super(UnitSeries, self).__init__(name, data, **kwargs)
+        self.units = units

tests/unit/pynwb_tests/test_misc.py

@@ -3,7 +3,7 @@
 import numpy as np
 
 from pynwb.misc import AnnotationSeries, AbstractFeatureSeries, IntervalSeries, Units, \
-    DecompositionSeries
+    DecompositionSeries, UnitSeries
 from pynwb.file import TimeSeries, DynamicTable
 from pynwb.core import VectorData
 
@@ -150,5 +150,14 @@ def test_times_and_intervals(self):
         self.assertTrue(np.all(ut['obs_intervals'][1] == np.array([[2, 3], [4, 5]])))
 
 
+class UnitSeriesConstructor(unittest.TestCase):
+    def test_init(self):
+        units = Units()
+        us = UnitSeries('test_unit_series', np.array([0, 0, 1, 1], dtype=int),
+                        timestamps=[.1, .2, .3, .4], units=units, description='description')
+        self.assertTrue(all(us.data == np.array([0, 0, 1, 1], dtype=int)))
+        self.assertEqual(units, us.units)
+
+
 if __name__ == '__main__':
     unittest.main()