Add gRef-CW data

.gitattributes

@@ -1456,3 +1456,5 @@ AgroMind/CropHarvest/data/983-kenya-non-crop_2019-02-06_2020-02-01.tif filter=lf
 AgroMind/CropHarvest/data/986-kenya-non-crop_2019-02-06_2020-02-01.tif filter=lfs diff=lfs merge=lfs -text
 AgroMind/CropHarvest/data/996-germany_2018-02-06_2019-02-01.tif filter=lfs diff=lfs merge=lfs -text
 AgroMind/CropHarvest/data/999-tanzania-ceo.tif filter=lfs diff=lfs merge=lfs -text
+gRef-CW/data/grefs(unc).json filter=lfs diff=lfs merge=lfs -text
+gRef-CW/data/instances.json filter=lfs diff=lfs merge=lfs -text

gRef-CW/Weed-VG/checkpoints/stage_one.pth

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+size 918570101

gRef-CW/Weed-VG/checkpoints/stage_two.pth

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+version https://git-lfs.github.com/spec/v1
+oid sha256:8113bc775e77e379eb6c57bd82c5b7cc7adbc63b3c6344bd5101fba4494cd9e9
+size 997609381

gRef-CW/data/grefs(unc).json

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+oid sha256:3a07b9a27a2bd4406f7f9d68067dc0bc7f2775cde21e4795224892a1f45e01e3
+size 20740212

gRef-CW/data/instances.json

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+version https://git-lfs.github.com/spec/v1
+oid sha256:be4f0956f3c72e95ae0f13f9d72014815f52e09c7e4fc5a2a20ee8ced98348cc
+size 566170007

gRef-CW/scripts/build_dataset.py

@@ -0,0 +1,195 @@
+#!/usr/bin/env python3
+"""
+build_dataset.py — reconstruct the gRef-CW image set locally.
+
+gRef-CW ships only the ANNOTATIONS (``grefs(unc).json`` and ``instances.json``).
+The underlying images are part of the CropAndWeed dataset (AIT) and, under its
+non-commercial licence, **may not be redistributed**. This script therefore
+obtains the images from the official CropAndWeed source and arranges them to
+match the gRef-CW annotations.
+
+Pipeline
+--------
+  1. (``--auto``) clone the official CropAndWeed repo and run its downloader
+     (``python cnw/setup.py``), or point at an existing CropAndWeed checkout
+     with ``--cnw-images``.
+  2. index the downloaded CropAndWeed images by file name / stem.
+  3. for every image referenced by ``instances.json``, link (or copy) it into
+     ``<data-dir>/images/``.
+  4. verify that every referenced image is present; report anything missing.
+
+Usage
+-----
+  # Fully automatic: clone CropAndWeed, download images, then build.
+  python scripts/build_dataset.py --data-dir data --auto
+
+  # If you already have CropAndWeed images on disk:
+  python scripts/build_dataset.py --data-dir data \
+      --cnw-images /path/to/cropandweed-dataset/data/images
+
+  # Copy instead of symlink (e.g. across filesystems):
+  python scripts/build_dataset.py --data-dir data --cnw-images <dir> --copy
+
+Notes
+-----
+* CropAndWeed image files are named ``ave_<session>_<id>`` / ``vwg_<session>_<id>``
+  (see the CropAndWeed README). Matching is done on the file name, falling back
+  to the stem (name without extension), so it is tolerant of ``.jpg``/``.png``.
+* Stdlib only — no third-party dependencies.
+* Licence details: see ``DATASHEET.md`` and ``LICENSE``.
+"""
+
+from __future__ import annotations
+
+import argparse
+import json
+import os
+import shutil
+import subprocess
+import sys
+from pathlib import Path
+
+CNW_REPO = "https://github.com/cropandweed/cropandweed-dataset.git"
+IMAGE_EXTS = (".jpg", ".jpeg", ".png", ".tif", ".tiff", ".bmp")
+
+
+def log(msg: str) -> None:
+    print(f"[build_dataset] {msg}", flush=True)
+
+
+def referenced_file_names(instances_json: Path) -> list[str]:
+    """Return the list of image file names referenced by instances.json (COCO-style)."""
+    with instances_json.open(encoding="utf-8") as f:
+        data = json.load(f)
+    images = data.get("images")
+    if not images:
+        sys.exit(f"ERROR: no 'images' array found in {instances_json}. "
+                 "Confirm this is a COCO-style instances file.")
+    names = []
+    for img in images:
+        name = img.get("file_name") or img.get("filename") or img.get("name")
+        if not name:
+            sys.exit(f"ERROR: an entry in {instances_json} has no file_name field: {img!r}")
+        names.append(name)
+    return names
+
+
+def index_images(images_dir: Path) -> dict[str, Path]:
+    """Map both full file name and stem -> path for every image under images_dir."""
+    if not images_dir.is_dir():
+        sys.exit(f"ERROR: CropAndWeed images directory not found: {images_dir}")
+    index: dict[str, Path] = {}
+    count = 0
+    for path in images_dir.rglob("*"):
+        if path.is_file() and path.suffix.lower() in IMAGE_EXTS:
+            index.setdefault(path.name, path)
+            index.setdefault(path.stem, path)
+            count += 1
+    log(f"indexed {count} image files under {images_dir}")
+    if count == 0:
+        sys.exit("ERROR: no image files found. Did the CropAndWeed download succeed? "
+                 "Pass the correct --cnw-images directory.")
+    return index
+
+
+def resolve(name: str, index: dict[str, Path]) -> Path | None:
+    """Find a CropAndWeed image for a referenced gRef-CW file name."""
+    if name in index:
+        return index[name]
+    stem = Path(name).stem
+    return index.get(stem)
+
+
+def auto_download(workdir: Path) -> Path:
+    """Clone CropAndWeed and run its downloader. Returns the images directory."""
+    repo_dir = workdir / "cropandweed-dataset"
+    if not repo_dir.exists():
+        log(f"cloning CropAndWeed into {repo_dir} ...")
+        subprocess.run(["git", "clone", "--depth", "1", CNW_REPO, str(repo_dir)], check=True)
+    else:
+        log(f"reusing existing CropAndWeed checkout at {repo_dir}")
+
+    setup = repo_dir / "cnw" / "setup.py"
+    if not setup.exists():
+        sys.exit(f"ERROR: expected CropAndWeed downloader at {setup} but it is missing. "
+                 "Check the CropAndWeed repo layout and use --cnw-images instead.")
+    log("running CropAndWeed downloader (python cnw/setup.py) — this fetches the images ...")
+    subprocess.run([sys.executable, "cnw/setup.py"], cwd=str(repo_dir), check=True)
+
+    # CropAndWeed extracts images under data/images by convention; fall back to a search.
+    candidate = repo_dir / "data" / "images"
+    if candidate.is_dir() and any(candidate.rglob("*")):
+        return candidate
+    for sub in repo_dir.rglob("images"):
+        if sub.is_dir() and any(p.suffix.lower() in IMAGE_EXTS for p in sub.rglob("*") if p.is_file()):
+            return sub
+    sys.exit("ERROR: CropAndWeed download finished but no images directory was found. "
+             "Locate it manually and re-run with --cnw-images.")
+
+
+def link_or_copy(src: Path, dst: Path, copy: bool) -> None:
+    if dst.exists() or dst.is_symlink():
+        dst.unlink()
+    if copy:
+        shutil.copy2(src, dst)
+    else:
+        try:
+            os.symlink(os.path.relpath(src, dst.parent), dst)
+        except OSError:
+            shutil.copy2(src, dst)  # symlinks unsupported (e.g. some Windows setups)
+
+
+def main() -> int:
+    ap = argparse.ArgumentParser(description="Reconstruct the gRef-CW image set from CropAndWeed.")
+    ap.add_argument("--data-dir", type=Path, default=Path("data"),
+                    help="gRef-CW data dir containing instances.json; images written to <data-dir>/images.")
+    ap.add_argument("--instances-json", type=Path, default=None,
+                    help="Path to instances.json (default: <data-dir>/instances.json).")
+    src = ap.add_mutually_exclusive_group(required=True)
+    src.add_argument("--auto", action="store_true",
+                     help="Clone CropAndWeed and run its official downloader automatically.")
+    src.add_argument("--cnw-images", type=Path,
+                     help="Path to an existing CropAndWeed images directory.")
+    ap.add_argument("--workdir", type=Path, default=Path(".cropandweed_cache"),
+                    help="Where to clone CropAndWeed when using --auto.")
+    ap.add_argument("--copy", action="store_true",
+                    help="Copy image files instead of symlinking.")
+    args = ap.parse_args()
+
+    instances_json = args.instances_json or (args.data_dir / "instances.json")
+    if not instances_json.exists():
+        sys.exit(f"ERROR: {instances_json} not found. Download the gRef-CW annotations first "
+                 "(see README 'Data and Weights').")
+
+    out_dir = args.data_dir / "images"
+    out_dir.mkdir(parents=True, exist_ok=True)
+
+    cnw_images = auto_download(args.workdir) if args.auto else args.cnw_images
+    log(f"CropAndWeed images: {cnw_images}")
+
+    index = index_images(cnw_images)
+    names = referenced_file_names(instances_json)
+    log(f"{len(names)} images referenced by {instances_json.name}")
+
+    matched, missing = 0, []
+    for name in names:
+        src_path = resolve(name, index)
+        if src_path is None:
+            missing.append(name)
+            continue
+        link_or_copy(src_path, out_dir / Path(name).name, args.copy)
+        matched += 1
+
+    log(f"linked/copied {matched}/{len(names)} images into {out_dir}")
+    if missing:
+        log(f"WARNING: {len(missing)} referenced images were NOT found in CropAndWeed. "
+            f"First few: {missing[:10]}")
+        log("This usually means the CropAndWeed download is incomplete or the file-name "
+            "convention differs — verify the source and re-run.")
+        return 1
+    log("Done — every referenced image was found. Dataset is ready.")
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())