Map Units waveform metadata to waveforms

src/pynwb/io/core.py

@@ -42,9 +42,9 @@ def get_attr_value(self, **kwargs):
         ''' Get the value of the attribute corresponding to this spec from the given container '''
         spec, container, manager = getargs('spec', 'container', 'manager', kwargs)
 
-        # handle custom mapping of container Units.waveform_rate -> spec Units.waveform_mean.sampling_rate
+        # handle custom mapping of Units waveform metadata onto waveform-bearing columns
         if isinstance(container.parent, Units):
-            if container.name == 'waveform_mean' or container.name == 'waveform_sd':
+            if container.name in ('waveform_mean', 'waveform_sd', 'waveforms'):
                 if spec.name == 'sampling_rate':
                     return container.parent.waveform_rate
                 if spec.name == 'unit':

src/pynwb/io/misc.py

@@ -22,19 +22,17 @@ def waveform_unit_carg(self, builder, manager):
         return self._get_waveform_stat(builder, 'unit')
 
     def _get_waveform_stat(self, builder, attribute):
-        if 'waveform_mean' not in builder and 'waveform_sd' not in builder:
+        waveform_columns = ('waveform_mean', 'waveform_sd', 'waveforms')
+        stats = [builder[column].attributes.get(attribute) for column in waveform_columns if column in builder]
+        if not stats:
             return None
-        mean_stat = None
-        sd_stat = None
-        if 'waveform_mean' in builder:
-            mean_stat = builder['waveform_mean'].attributes.get(attribute)
-        if 'waveform_sd' in builder:
-            sd_stat = builder['waveform_sd'].attributes.get(attribute)
-        if mean_stat is not None and sd_stat is not None:
-            if mean_stat != sd_stat:
-                # throw warning
-                pass
-        return mean_stat
+        populated_stats = [stat for stat in stats if stat is not None]
+        if len(set(populated_stats)) > 1:
+            # throw warning
+            pass
+        if populated_stats:
+            return populated_stats[0]
+        return None
 
     @DynamicTableMap.object_attr("electrodes")
     def electrodes_column(self, container, manager):

tests/integration/hdf5/test_misc.py

@@ -1,3 +1,4 @@
+import h5py
 import numpy as np
 
 from hdmf.common import VectorData, DynamicTableRegion
@@ -70,6 +71,58 @@ def test_get_obs_intervals(self):
         np.testing.assert_array_equal(ut['obs_intervals'][:], [[[0., 1.], [2., 3.]], [[2., 5.], [6., 7.]]])
 
 
+class TestUnitsWaveformsOnlyIO(AcquisitionH5IOMixin, TestCase):
+    """Test roundtripping waveform metadata when only waveforms are present."""
+
+    def setUpContainer(self):
+        ut = Units(name='UnitsWaveformsOnlyTest', description='a simple table for testing Units waveforms')
+        ut.add_unit(
+            spike_times=[0., 1., 2.],
+            waveforms=[
+                [
+                    [1, 2, 3],
+                    [1, 2, 3],
+                    [1, 2, 3]
+                ], [
+                    [1, 2, 3],
+                    [1, 2, 3],
+                    [1, 2, 3]
+                ]
+            ]
+        )
+        ut.add_unit(
+            spike_times=[3., 4., 5.],
+            waveforms=np.array([
+                [
+                    [1, 2, 3],
+                    [1, 2, 3],
+                    [1, 2, 3]
+                ], [
+                    [1, 2, 3],
+                    [1, 2, 3],
+                    [1, 2, 3]
+                ]
+            ])
+        )
+        ut.waveform_rate = 40000.
+        return ut
+
+    def test_waveform_metadata_roundtrip(self):
+        ut = self.roundtripContainer()
+        self.assertEqual(ut.waveform_rate, 40000.)
+        self.assertEqual(ut.waveform_unit, 'volts')
+
+    def test_waveforms_attributes_written(self):
+        self.roundtripContainer()
+        with h5py.File(self.filename, 'r') as infile:
+            waveforms = infile['acquisition'][self.container.name]['waveforms']
+            self.assertEqual(waveforms.attrs['sampling_rate'], 40000.)
+            unit = waveforms.attrs['unit']
+            if isinstance(unit, bytes):
+                unit = unit.decode('utf-8')
+            self.assertEqual(unit, 'volts')
+
+
 class TestUnitsFileIO(NWBH5IOMixin, TestCase):
 
     def setUpContainer(self):