Add SONATA support for spatially_uniform_e_field stimulus#82
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darshanmandge wants to merge 16 commits into
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Add SONATA support for spatially_uniform_e_field stimulus#82darshanmandge wants to merge 16 commits into
darshanmandge wants to merge 16 commits into
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darshanmandge
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Apr 13, 2026
darshanmandge
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- Solves Add SONATA support for spatially_uniform_e_field stimulus module #80.
- Merged main into uniform_e_field_stimulus branch - Re-applied SpatiallyUniformEField stimulus pattern and class - Re-applied ElectrodeSource integration in circuit_simulation.py - Re-applied compute_segment_coordinates() to Cell class - Ported axon/myelin interpolation methods from neurodamus - Updated _add_extracellular_stimulus to use coordinate interpolation - Added unit tests for coordinate helpers (interp_axon_positions, interp_myelin_positions) - All pytest tests pass
- Import Callable from typing instead of using builtins.callable - Add proper type annotation for func_loc2glob parameter - Change return type to Optional[np.ndarray] for get_segment_position - Add type annotation for cell_targets dict in circuit_simulation.py - Remove unused variable post_sec_id (ruff F841)
- Add spatially_uniform_e_field to test_pattern_from_sonata_valid test - Fix docformatter issue in circuit_simulation.py (wrap docstring) - All 68 stimulus tests pass - All 58 cell core tests pass
- Add tests for ElectrodeSource.__iadd__() edge cases (delay, non-overlapping, concatenation) - Add test for cleanup() method - Add tests for Pattern.from_blueconfig() method - Add tests for SINUSOIDAL and SECLAMP patterns in from_sonata() - Coverage increased from 93% to 94%
Previously _add_extracellular_stimulus only iterated over the soma segments from the resolved targets list (seg_list), causing the e-field displacement to be ~zero and producing no visible effect. Neurodamus iterates over all sections/segments of each target cell. This fix replaces the seg_list loop with iteration over all sections and segments of each cell, matching the neurodamus implementation. Verified: voltage difference with vs without e-field increased from ~0 mV to >48 mV.
- Add Cell.set_local_to_global_matrix() and local_to_global_coord_mapping() with quaternion->rotation matrix construction (no scipy dependency). - Rename compute_segment_coordinates -> compute_segment_local_coordinates; add compute_segment_global_coordinates that applies the cell transform. - Switch _add_extracellular_stimulus to iterate the resolved seg_list (honoring compartment_set or node_set->all sections per neurodamus target_point_list semantics). - Set soma displacement to zero in _add_extracellular_stimulus. - Pass a local-to-global closure to get_segment_position for axon/myelin sections that lack 3D points. - Populate the cell transform during instantiate_gids using a new SonataCircuitAccess.get_cell_position_rotation helper. - Make Cell.delete robust against partially-initialized cells. - Add unit tests for cell coordinate helpers, integration tests for the e-field stimulus glue, and additional ElectrodeSource coverage.
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