Add Benchmark 7 of Aubry et al. (2022) as a Scenario2 variant

[charlesbmi]

Introduction

NDK's simulation scenarios are based on Jean-Francois Aubry, et al. (2022). Specifically, Scenario 1 corresponds to Benchmark 4 in the paper, and Scenario 2 corresponds to Benchmark 8 in the paper.

NDK's 3-D simulations run much faster on a GPU, but at standard resolutions, Scenario 2 (i.e., benchmark 8) is too large to fit on a single GPU's memory. Aubry, et al. (2022) also mention a related Benchmark 7, which is the same set up as benchmark 8 but simulated over a sub-volume of the skull/brain. Benchmark 7 uses the same volume size as Benchmark 4 and thus fits in a GPU.

Benchmark 7 would thus be useful as an easier-to-run alternative to Benchmark 8.

Changes

• Add Scenario2_2D_Benchmark7 as a subclass of Scenario2_2D
• Add Scenario2_3D_Benchmark7 as a subclass of Scenario2_3D
• Check in the skull mask for Benchmark 7
• Load in the appropriate skull mask file (Benchmark 8 vs 7) for the given scenario type.

Design decisions:

• Made the new scenarios as subclasses of the existing Scenario2
  • Alternative considered: use extent variable to subslice the existing Scenario. Con: resulting code was less straightforward
  • Alternative considered: create entirely new Scenario class. Con: more places to update/maintain code if refactoring in the future

Testing

• Can initialize Scenario2_3D_Benchmark7 in your code

• Can adapt plot_scenarios.py (did not check in this change) to include Scenario2_3D_Benchmark7 and see results:

• New scenarios added to test_builtin.py

[codecov-commenter]

Codecov Report

All modified lines are covered by tests :white_check_mark:

Files	Coverage Δ
src/neurotechdevkit/scenarios/built_in/__init__.py	100.00% <100.00%> (ø)
.../neurotechdevkit/scenarios/built_in/_scenario_2.py	98.88% <100.00%> (+0.38%)	:arrow_up:

:loudspeaker: Thoughts on this report? Let us know!.

[charlesbmi]

Per discussion with Diogo: let's rename these scenarios to something meaningful, e.g. something like "FullSkull" or "3-layer model"

Made a ticket for this here: https://github.com/agencyenterprise/neurotechdevkit/issues/156

I will fix that in a different PR.

[charlesbmi]

Slack-approval on this one from Diogo - merging.