HenriquesLab / HenriquesLab/VLab4Mic
random_seed not propagated to randomise_axial_position (dormant reproducibility gap)
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- Python
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Description
Follow-up from the random-seed propagation work in #134.
What
CoordinatesField.randomise_axial_position() (src/vlab4mic/generate/coordinates_field.py) builds its RNG as np.random.default_rng(seed=random_seed), but its only caller, _gen_abs_from_rel_positions() (line ~501), invokes it with no argument:
if self.axial_offset is not None:
self.randomise_axial_position() # random_seed defaults to None
So when axial offsets are in use, the axial z-placement draws from a fresh non-deterministic Generator and ignores the seed (a default_rng(None) does not read the global np.random.seed set in experiments.py). All other stochastic inputs (positions via the global seed, orientations and rotations via the threaded random_seed) are reproducible after #134.
Impact: dormant. randomise_axial_position only runs when self.axial_offset is not None. No current article-figure script sets axial_offset (the NPC scripts use axial_precision / axial_resolution_nm, which are unrelated PSF params), so the manuscript figures are unaffected and reproducible. This only bites a user who explicitly configures axial_offset.
Suggested fix
_gen_abs_from_rel_positions() is a no-arg helper called from many places, so threading the seed through the call site is awkward. Cleaner: persist the seed on the field instance (e.g. set self.random_seed in set_molecules_params / create_minimal_field) and have randomise_axial_position default to self.random_seed. Then drop the now-redundant random_seed params that are accepted but unused in the global-np.random position helpers (generate_random_positions), or wire them similarly, for a consistent seeding story.
Priority: low (latent; does not affect current figures).
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start in src/vlab4mic/generate/coordinates_field.py, reading CoordinatesField.randomise_axial_position() and its call from _gen_abs_from_rel_positions() around line 501. Trace how set_molecules_params or create_minimal_field handles the seed, then verify that configurations using axial_offset produce repeatable axial placement with the same seed without breaking the existing position and orientation behavior.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- numpy, python
- Domain
- backend
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 55/100