scripts/make_example.py

"""Bake a degraded microscopy image (+ clean ground-truth sidecar) into APP_TMP_DIR.

  example.tif         — the DEGRADED input (blurred + Poisson/Gaussian noise)
  .example_clean.npy  — the CLEAN ground truth (leading dot so the validator's
                        input-picker can't grab it instead of the TIFF)

Run at build time via `python -m scripts.make_example`.
"""
from __future__ import annotations

import numpy as np
import tifffile

from core.io import APP_TMP_DIR, register_protected
from core.synth import clean_image, degrade


def main() -> int:
    clean = clean_image(256, 256, seed=0)
    deg = degrade(clean, psf_sigma=2.0, peak=40.0, read_sigma=0.03, seed=1)

    out = APP_TMP_DIR / "example.tif"
    tifffile.imwrite(out, (deg * 65535).astype(np.uint16))
    register_protected(out)
    np.save(APP_TMP_DIR / ".example_clean.npy", clean.astype(np.float32))
    register_protected(APP_TMP_DIR / ".example_clean.npy")
    print(f"[make_example] wrote {out} (degraded) + .example_clean.npy (GT)")
    return 0


if __name__ == "__main__":
    raise SystemExit(main())