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openbraininstitute / neurodamus / 21910816959
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DEFAULT BRANCH: main
Ran 11 Feb 2026 03:22PM UTC
Jobs 4
Files 49
Run time 1min
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11 Feb 2026 03:16PM UTC coverage: 90.83% (+0.3%) from 90.566%
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Implement extracellular stimulus: module "spatially_uniform_e_field" (#425)

## Context
Implements the extracellular stimulus of pattern
spatially_uniform_e_field. It allows the summation of multiple `fields`
in the same stimulus block, as well as the combination of multiple
spatially_uniform_e_field stimulus blocks. For each spatially_uniform_e_field stimulus:
- Rotate/translate all segments' local positions to obtain the global coordinates
- For the new axon and myelin sections, interpolate their local positions along local soma y-axis, then rotate/translate them into global coordinates
- Compute extracellular potentials by (seg_global_pos - vec_soma_global_pos) .dot (Ex,Ey,Ez)

## Scope
1. New class `SpatiallyUniformEField` in `stimulus_manger.py`
2. New class `ElectrodeSource` in `stimuli.py`
3. Function `get_all_segment_points` in `metype.py` to compute the
global coordinates of all the segment points

## Testing
1. new unit test in `test_metype.py` for `get_all_segment_points`
2. fix `test_get_section_id` in `test_metype.py` which should assert the
section ids of the test cell.
3. new unit tests for the new electric field stimulus
- unit/test_single_extracellular_stimulus.py (single stimulus block)
- unit/test_multiple_extracellular_stimulus.py (multiple stimulus
blocks)
- unit-mpi/test_extracellular_stimulus.py (mpi test)
- scientific/test_extracellular_stimulation (for reporting)
4. And the rotation to the current ring test big-cell nodes file, to
enable the computation of segments' global coordinates. Should have no
impact on the other unit tests.

## Review
* [x] PR description is complete
* [x] Coding style (imports, function length, New functions, classes or
files) are good
* [x] Unit/Scientific test added
* [ ] Updated Readme, in-code, developer documentation

## Docs


https://github.com/openbraininstitute/sonata-extension/blob/master/source/sonata_simulation.rst

---------

Co-authored-by: Alessandro Cattabiani <cattabiani@users.noreply.github.com>

246 of 255 new or added lines in 6 files covered. (96.47%)

7538 of 8299 relevant lines covered (90.83%)

2.29 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
3
86.49
1.94% neurodamus/metype.py
6
95.17
-0.25% neurodamus/stimulus_manager.py
Subprojects
ID Flag name Job ID Ran Files Coverage
1 baseline 21910816959.1 11 Feb 2026 03:22PM UTC 49
25.7
GitHub Action Run
2 unit 21910816959.2 11 Feb 2026 03:22PM UTC 49
88.38
GitHub Action Run
3 unit-ngv-mpi 21910816959.3 11 Feb 2026 03:22PM UTC 49
54.62
GitHub Action Run
4 unit-mpi 21910816959.4 11 Feb 2026 03:22PM UTC 49
60.79
GitHub Action Run
Source Files on build 21910816959
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