Merge pull request #1758 from AllenInstitute/rc/2.3.2

Issue #1755

Author: Matyasz

CHANGELOG.md

@@ -1,10 +1,15 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [2.3.2] = 2020-10-19
+
+### Bug Fixes
+- (Internal) Fixed a running\_processing bug for behavior ophys experiments when the input data would have one more encoder entry than timestamp. The behavior of the code now matches what the warning says.
+
 ## [2.3.1] = 2020-10-13
 
 ### Bug Fixes
-- (Internal) Fixed a write_nwb bug for behavior ophys experiments involving the BehaviorOphysJsonApi expecting a mesoscope-specific method.
+- (Internal) Fixed a write\_nwb bug for behavior ophys experiments involving the BehaviorOphysJsonApi expecting a mesoscope-specific method.
 
 ## [2.3.0] = 2020-10-09
 

allensdk/__init__.py

@@ -37,7 +37,7 @@
 
 
 
-__version__ = '2.3.1'
+__version__ = '2.3.2'
 
 
 try:

allensdk/brain_observatory/behavior/running_processing.py

@@ -55,7 +55,7 @@ def _shift(
         Iterable containing numeric data. If int, will be converted to
         float in returned object.
     periods: int (default=1)
-        The number of elements to shift. 
+        The number of elements to shift.
     fill_value: float (default=np.nan)
         The value to fill at the beginning of the shifted array
     Returns
@@ -364,7 +364,9 @@ def get_running_df(data, time: np.ndarray, lowpass: bool = True):
     if len(v_in) == len(time) + 1:
         warnings.warn(
             "Time array is 1 value shorter than encoder array. Last encoder "
-            "value removed\n", stacklevel=1)
+            "value removed\n", UserWarning, stacklevel=1)
+        v_in = v_in[:-1]
+        v_sig = v_sig[:-1]
 
     # dx = 'd_theta' = angular change
     # There are some issues with angular change in the raw data so we

allensdk/test/brain_observatory/behavior/test_running_processing.py

@@ -71,6 +71,43 @@ def test_get_running_df(running_data, timestamps, lowpass):
         assert np.count_nonzero(np.isnan(actual["speed"])) == 0
 
 
+@pytest.mark.parametrize(
+    "lowpass", [True, False]
+)
+def test_get_running_df_one_fewer_timestamp_check_warning(running_data,
+                                                          timestamps,
+                                                          lowpass):
+    with pytest.warns(
+        UserWarning,
+        match="Time array is 1 value shorter than encoder array.*"
+    ):
+        # Call with one fewer timestamp, check for a warning
+        _ = get_running_df(
+            data=running_data,
+            time=timestamps[:-1],
+            lowpass=lowpass
+        )
+
+
+@pytest.mark.parametrize(
+    "lowpass", [True, False]
+)
+def test_get_running_df_one_fewer_timestamp_check_truncation(running_data,
+                                                             timestamps,
+                                                             lowpass):
+    # Call with one fewer timestamp
+    output = get_running_df(
+        data=running_data,
+        time=timestamps[:-1],
+        lowpass=lowpass
+    )
+
+    # Check that the output is actually trimmed, and the values are the same
+    assert len(output) == len(timestamps) - 1
+    np.testing.assert_equal(output["v_sig"], running_data["items"]["behavior"]["encoders"][0]["vsig"][:-1])
+    np.testing.assert_equal(output["v_in"], running_data["items"]["behavior"]["encoders"][0]["vin"][:-1])
+
+
 @pytest.mark.parametrize(
     "arr, periods, fill, expected",
     [

doc_template/index.rst

@@ -91,12 +91,20 @@ The Allen SDK provides Python code for accessing experimental metadata along wit
 See the `mouse connectivity section <connectivity.html>`_ for more details.
 
 
+What's New - 2.3.2 (October 19, 2020)
+-----------------------------------------------------------------------
+As of the 2.3.2 release:
+
+- (Internal) Fixed a running_processing bug for behavior ophys experiments when the input data would have one more encoder entry than timestamp. The behavior of the code now matches what the warning says.
+
+
 What's New - 2.3.1 (October 13, 2020)
 -----------------------------------------------------------------------
 As of the 2.3.1 release:
 
 - (Internal) Fixed a write_nwb bug for behavior ophys experiments involving the BehaviorOphysJsonApi expecting a mesoscope-specific method.
 
+
 What's New - 2.3.0 (October 9, 2020)
 -----------------------------------------------------------------------
 As of the 2.3.0 release: