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).
Follow-up from the random-seed propagation work in #134.
What
CoordinatesField.randomise_axial_position()(src/vlab4mic/generate/coordinates_field.py) builds its RNG asnp.random.default_rng(seed=random_seed), but its only caller,_gen_abs_from_rel_positions()(line ~501), invokes it with no argument: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 globalnp.random.seedset in experiments.py). All other stochastic inputs (positions via the global seed, orientations and rotations via the threadedrandom_seed) are reproducible after #134.Impact: dormant.
randomise_axial_positiononly runs whenself.axial_offset is not None. No current article-figure script setsaxial_offset(the NPC scripts useaxial_precision/axial_resolution_nm, which are unrelated PSF params), so the manuscript figures are unaffected and reproducible. This only bites a user who explicitly configuresaxial_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. setself.random_seedinset_molecules_params/create_minimal_field) and haverandomise_axial_positiondefault toself.random_seed. Then drop the now-redundantrandom_seedparams that are accepted but unused in the global-np.randomposition helpers (generate_random_positions), or wire them similarly, for a consistent seeding story.Priority: low (latent; does not affect current figures).