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Running on Zero
Running on Zero
| #!/usr/bin/env python3 | |
| """Bundle the annotated images for the app's validation section. | |
| python scripts/make_validation_set.py --data-dir /path/to/TIFs_and_CVAT_zips --out validation | |
| Every annotated image is written as a lossless PNG named after the image name | |
| recorded inside its CVAT export (so that cellquant.annotations.discover pairs them | |
| again) next to a copy of that export. Byte-identical duplicate TIFs collapse to one | |
| entry, exactly as in training. | |
| """ | |
| from __future__ import annotations | |
| import argparse | |
| import os | |
| import shutil | |
| import sys | |
| from PIL import Image | |
| sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__)))) | |
| from cellquant.annotations import discover, load_image # noqa: E402 | |
| from cellquant.labels import CELL_LABELS, NOSTRIL_LABELS # noqa: E402 | |
| def main(argv=None): | |
| ap = argparse.ArgumentParser() | |
| ap.add_argument("--data-dir", required=True) | |
| ap.add_argument("--out", default=os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), "validation")) | |
| a = ap.parse_args(argv) | |
| samples, _ = discover(a.data_dir, verbose=False) | |
| os.makedirs(a.out, exist_ok=True) | |
| for s in samples: | |
| img = load_image(s.image_path) | |
| stem = os.path.splitext(os.path.basename(s.annotation.image_name))[0].strip() | |
| png = os.path.join(a.out, stem + ".png") | |
| Image.fromarray(img).save(png, optimize=True) | |
| shutil.copyfile(s.annotation_path, os.path.join(a.out, os.path.basename(s.annotation_path))) | |
| n_nuc = sum(s.annotation.count(c) for c in CELL_LABELS) | |
| n_pun = sum(s.annotation.count(c) for c in NOSTRIL_LABELS) | |
| print(f"{s.key}: {os.path.basename(png)} ({os.path.getsize(png)/1e6:.1f} MB, {n_nuc} nuclei, {n_pun} puncta) + {os.path.basename(s.annotation_path)}") | |
| check, _ = discover(a.out, verbose=False) | |
| assert [c.key for c in check] == [s.key for s in samples], "re-discovery of the bundle failed" | |
| print(f"{len(check)} annotated images in {a.out}") | |
| if __name__ == "__main__": | |
| main() | |