Make get_data_in_units work with channel_conversion (#1806)

Co-authored-by: Ryan Ly <[email protected]>

CHANGELOG.md

@@ -8,6 +8,7 @@
 - Add `pynwb.get_nwbfile_version()`. @bendichter [#1703](https://github.com/NeurodataWithoutBorders/pynwb/pull/1703)
 - Updated timeseries data checks to warn instead of error when reading invalid files. @stephprince [#1793](https://github.com/NeurodataWithoutBorders/pynwb/pull/1793) and [#1809](https://github.com/NeurodataWithoutBorders/pynwb/pull/1809)
 - Expose the offset, conversion and channel conversion parameters in `mock_ElectricalSeries`. @h-mayorquin [#1796](https://github.com/NeurodataWithoutBorders/pynwb/pull/1796)
+- Enhance `get_data_in_units()` to work with objects that have a `channel_conversion` attribute like the `ElectricalSeries`  @h-mayorquin [#1806](https://github.com/NeurodataWithoutBorders/pynwb/pull/1806)
 
 ### Bug fixes
 - Fix bug where namespaces were loaded in "w-" mode. @h-mayorquin [#1795](https://github.com/NeurodataWithoutBorders/pynwb/pull/1795)

src/pynwb/base.py

@@ -298,7 +298,11 @@ def get_timestamps(self):
             return np.arange(len(self.data)) / self.rate + self.starting_time
 
     def get_data_in_units(self):
-        return np.asarray(self.data) * self.conversion + self.offset
+        if "channel_conversion" in self.fields:
+            scale_factor = self.conversion * self.channel_conversion[:, np.newaxis]
+        else:
+            scale_factor = self.conversion
+        return np.asarray(self.data) * scale_factor + self.offset
 
 
 @register_class('Image', CORE_NAMESPACE)

tests/unit/test_ecephys.py

@@ -18,6 +18,7 @@
 from pynwb.device import Device
 from pynwb.file import ElectrodeTable
 from pynwb.testing import TestCase
+from pynwb.testing.mock.ecephys import mock_ElectricalSeries
 
 from hdmf.common import DynamicTableRegion
 
@@ -115,6 +116,24 @@ def test_dimensions_warning(self):
                "but instead the first does. Data is oriented incorrectly and should be transposed."
                    ) in str(w[-1].message)
 
+    def test_get_data_in_units(self):
+
+        data = np.asarray([[1, 1, 1, 1, 1], [1, 1, 1, 1, 1]])
+        conversion = 1.0
+        offset = 3.0
+        channel_conversion = np.asarray([2.0, 2.0])
+        electrical_series = mock_ElectricalSeries(
+            data=data,
+            conversion=conversion,
+            offset=offset,
+            channel_conversion=channel_conversion,
+        )
+
+        data_in_units = electrical_series.get_data_in_units()
+        expected_data = data * conversion * channel_conversion[:, np.newaxis] + offset
+
+        np.testing.assert_almost_equal(data_in_units, expected_data)
+
 
 class SpikeEventSeriesConstructor(TestCase):