injecting a sequence of stimuli on the same cell in isolation

[anilbey]

Module that enables injecting a stimulus with a sequence of amplitude values.

Changes

• add analysis/inject_sequence.py to inject multiple stim to the same cell in isolation
• core.py:: rename attribute 'all' to 'sections'
• have a class TemplateParams to represent all template related values

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 98.44560% with 3 lines in your changes are missing coverage. Please review.

Project coverage is 91.16%. Comparing base (8bfa9b5) to head (94d6766).

Files	Patch %	Lines
bluecellulab/cell/core.py	94.11%	2 Missing :warning:
bluecellulab/analysis/inject_sequence.py	98.24%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #151 +/- ## ========================================== + Coverage 90.86% 91.16% +0.30% ========================================== Files 89 93 +4 Lines 5320 5480 +160 ========================================== + Hits 4834 4996 +162 + Misses 486 484 -2 ```

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[stefanoantonel]

When I try to pass section parameter to apply_multiple_step_stimuli function

https://github.com/BlueBrain/BlueCelluLab/blob/sequence-stim/bluecellulab/analysis/inject_sequence.py#L78

I get an error cannot pickle 'nrn.Section' object

Using the simple

cell = create_ball_stick()

[stefanoantonel]

Also this is more like a question...

If I iterate over the responses

    for stimulus, recording in responses.items():
        print(len(recording.time))

the length is not the same for all of them. 🤔 I was trying to create a matrix to send to the UI and I need all the vectors (voltage) to be the same length.

Is this difference of the len a bug or something intentional?

[anilbey]

When I try to pass section parameter to apply_multiple_step_stimuli function

Good. Thanks for reporting this. Yes, NEURON objects are not pickleable. There are solutions to overcome it. I will try to see which one suits this usage the best.

[anilbey]

the length is not the same for all of them. 🤔

Yes, it is because the NEURON simulator is using a performance trick (called variable time step) to report the result upon seeing changes in the response. It can be disabled. Shall I disable it here since you need to put the data in a matrix?

[stefanoantonel]

Yes, it is because the NEURON simulator is using a performance trick (called variable time step) to report the result upon seeing changes in the response. It can be disabled. Shall I disable it here since you need to put the data in a matrix?

I don't think it is necessary for now., there are a lot of changes that I need to make on the UI part. If there is any issue, I'll let. you know

[stefanoantonel]

Amazing job Anil!

Thanks a lot

Let's merge :)