Update ecephys.py

[bendichter]

Motivation

The ecephys tutorial currently generates data of shape (50, 4), but there are 12 electrodes so this fails inspection, generating two critical InspectorMessage objects:

from nwbinspector import inspect_nwb
list(inspect_nwb("ecephys_tutorial.nwb"))

[InspectorMessage(
     message='The second dimension of data does not match the length of electrodes. Your data may be transposed.',
     importance=<Importance.CRITICAL: 2>,
     severity=<Severity.LOW: 1>,
     check_function_name='check_electrical_series_dims',
     object_type='ElectricalSeries',
     object_name='ElectricalSeries',
     location='/processing/ecephys/LFP/ElectricalSeries',
     file_path='/Users/bendichter/dev/sandbox/ecephys_tutorial.nwb'
 ),
 InspectorMessage(
     message='The second dimension of data does not match the length of electrodes. Your data may be transposed.',
     importance=<Importance.CRITICAL: 2>,
     severity=<Severity.LOW: 1>,
     check_function_name='check_electrical_series_dims',
     object_type='ElectricalSeries',
     object_name='ElectricalSeries',
     location='/acquisition/ElectricalSeries',
     file_path='/Users/bendichter/dev/sandbox/ecephys_tutorial.nwb'
 ), ...

The shape needs to be changed to (50, 12), which resolves both of these messages.

Checklist

• Did you update CHANGELOG.md with your changes?
• Have you checked our Contributing document?
• Have you ensured the PR clearly describes the problem and the solution?
• Is your contribution compliant with our coding style? This can be checked running flake8 from the source directory.
• Have you checked to ensure that there aren't other open Pull Requests for the same change?
• Have you included the relevant issue number using "Fix #XXX" notation where XXX is the issue number? By including "Fix #XXX" you allow GitHub to close issue #XXX when the PR is merged.

[codecov]

Codecov Report

Merging #1581 (bd7c379) into dev (d50e372) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##              dev    #1581   +/-   ##
=======================================
  Coverage   91.34%   91.34%           
=======================================
  Files          25       25           
  Lines        2507     2507           
  Branches      471      471           
=======================================
  Hits         2290     2290           
  Misses        137      137           
  Partials       80       80           

Flag	Coverage Δ
integration	70.56% <ø> (ø)
unit	84.44% <ø> (ø)

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[CodyCBakerPhD]

(i) do we have a tutorial that shows how to use a DynamicTableRegion to subselect from a larger electrodes table (if you have multiple probes and want to split the ElectricalSeries for some reason)

(ii) does the inspector correctly assess the shape from those subselected DynamicTableRegions?

[oruebel]

(ii) does the inspector correctly assess the shape from those subselected DynamicTableRegions?

Since these are 1D arrays in the case of electrodes, the shape is just the length of the dataset so as long as ElectricSeries.electrodes.shape[0] == ElectricalSeries.data.shape[0] the check should be correct independent of the size of the ElectrodesTable. If you also want to check that the indices are valid you would need to chck that np.min(ElectricSeries.electrodes[:]) >=0 and np.max(ElectricSeries.electrodes[:]) < len(ElectricSeries.electrodes.table). The latter check is not quite correct, because you want to load the indices not the actual electrodes so [:] is not correct.

(i) do we have a tutorial that shows how to use a DynamicTableRegion to subselect from a larger electrodes table (if you have multiple probes and want to split the ElectricalSeries for some reason)

Not sure, but that would be good to add to the ECEphys tutorial if it is missing.