Merge pull request #2512 from AllenInstitute/rc/2.13.6

Rc/2.13.6

CHANGELOG.md

@@ -1,6 +1,10 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [2.13.6] = 2022-08-04
+- bugfix when accessing stimulus presentations table for vcn data
+- updates vbn notebooks
+- 
 ## [2.13.5] = 2022-07-27
 - Add support for visual behavior neuropixels data
 - 

allensdk/brain_observatory/ecephys/ecephys_session_api/ecephys_nwb_session_api.py

@@ -84,6 +84,11 @@ def get_stimulus_presentations(self):
         table = table.value
 
         if "color" in table.columns:
+            # .loc breaks on nan values so fill with empty string
+            # This is backwards compatible change for older nwb files
+            # Newer ones encode nan value here with empty string
+            table['color'] = table['color'].fillna('')
+
             # the color column actually contains two parameters. One is
             # coded as rgb triplets and the other as -1 or 1
             if "color_triplet" not in table.columns:

allensdk/test/brain_observatory/ecephys/test_write_nwb.py

@@ -151,7 +151,8 @@ def test_add_metadata(nwbfile, roundtripper, metadata, expected_metadata):
         'movie_specific_column': [np.nan, np.nan, np.nan, 1.0, np.nan],
         'start_time': [1., 2., 4., 5., 6.],
         'stimulus_name': ['gabors', 'gabors', 'random', 'movie', 'gabors'],
-        'stop_time': [2., 4., 5., 6., 8.]
+        'stop_time': [2., 4., 5., 6., 8.],
+        'color': [np.nan] + ['[1.0, 1.0, 1.0]'] * 4
     }, index=pd.Index(name='stimulus_presentations_id',
                       data=[0, 1, 2, 3, 4]))),
 ])
@@ -163,6 +164,9 @@ def test_add_stimulus_presentations(nwbfile, presentations, roundtripper):
     api = roundtripper(nwbfile, EcephysNwbSessionApi)
     obtained_stimulus_table = api.get_stimulus_presentations()
 
+    if 'color' in presentations.value:
+        presentations.value['color_triplet'] = [''] + ['[1.0, 1.0, 1.0]'] * 4
+        presentations.value['color'] = ''
     pd.testing.assert_frame_equal(
         presentations.value,
         obtained_stimulus_table,