Ticket/2594/dev

[mikejhuang]

This PR address three issues

1. _build_stimulus_presentations method has pandas operations that trigger errors.
   • stimulus_presentations.replace triggering error with pandas 1.1.5
     • Error reported in ticket on pandas repo, fixed on Nov 20 2021 This coincides to the pandas 1.4 release
   • stimulus_presentations.fillna triggering an error when replacing pd.NA values with a string in a boolean type column (opacity).
     • solution: first convert all "boolean" type columns to the "object" type.
2. stimulus_presentations['spatial_frequency'] contains numeric values of mixed str and float types, along with str(list)
   • Unique values from spatial_frequency column - current ['0.08', '[0.0, 0.0]', '0.04', 0.08, 0.04, 0.32, 0.02, 0.16]
   • Unique values from spatial_frequency column - 2020 pre-release: ['0.02' '0.04' '0.08' '0.16' '0.32' '[0.0, 0.0]']
   • Test in static_gratings expects float vals for spatial_frequency (sfvals)
   • Stimulus table fixture expects string values
     • However, no tests fail when eval all numeric/list strings in the stimulus_presentation tables.
3. Replace instance of local_index to probe_channel_number as reported in ticket #2573

[mikejhuang]

One other issue is making sure that the data that is currently released and accessed via the ecephys_session objects can still be loaded from it's NWBs.

Does the ephys_session notebook do this? It currently runs through the notebook.

[morriscb]

Does the ephys_session notebook do this? It currently runs through the notebook.

You'll have to check. As I said during sprint planning, you're about the first of the current Pika's to look at this code. My guess is yes, but it wouldn't hurt to double check.

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[mikejhuang]

You'll have to check. As I said during sprint planning, you're about the first of the current Pika's to look at this code. My guess is yes, but it wouldn't hurt to double check.

I believe it does do it. I committed the re-ran notebook. You can see the comparison here: 2020 pre-release run current PR re-run

The table values are now either floating point or tuples instead of string. Cell 17 is a good overview in the differences.

The re-run is oddly cut off at cell 36 in this preview. It isn't cut off when I view it locally. Seems like it's something to do with the animation.jhtml.

[ZeroAda]

just to follow up the first issue: _build_stimulus_presentations method has pandas operations that trigger errors. I change the lines # stimulus_presentations.replace("", nonapplicable, inplace=True) in ecephys_session.pyto the following:

bool_columns = stimulus_presentations.select_dtypes(include=['bool']).columns stimulus_presentations[bool_columns] = stimulus_presentations[bool_columns].astype('object') stimulus_presentations[bool_columns] = stimulus_presentations[bool_columns].fillna(nonapplicable)

and it works