Add offline mosaic EXIF tagging (stitch --write-exif, tag_mosaic_exif CLI)

- spruce.exif: tag_mosaic_jpeg_for_scan_dir, resolve_machine_label_for_scan_dir; ProcessingSoftware for tile-stitched mosaics
- spruce.settings: load_config(require_credentials=False) for config without login
- scripts/tag_mosaic_exif.py and tests; stitch script --write-exif path

scripts/stitch_mosaic_from_tiles.py

@@ -26,6 +26,9 @@ if str(_REPO_ROOT) not in sys.path:
 
 from PIL import Image, ImageChops
 
+from spruce.exif import tag_mosaic_jpeg_for_scan_dir
+from spruce.settings import DEFAULT_CONFIG, load_config
+
 TILE_FILENAME_RE = re.compile(r"tile_r(\d+)_c(\d+)\.jpg$", re.IGNORECASE)
 
 
@@ -281,6 +284,20 @@ def main() -> None:
         default=95,
         help="JPEG quality for output (default: 95).",
     )
+    parser.add_argument(
+        "--write-exif",
+        action="store_true",
+        help=(
+            "After saving, write mosaic EXIF using metadata.json and config "
+            "(implies override if write_exif is false in config). JPEG output only."
+        ),
+    )
+    parser.add_argument(
+        "--config",
+        default=DEFAULT_CONFIG,
+        metavar="FILE",
+        help=f"YAML config for EXIF machine_metadata (default: {DEFAULT_CONFIG})",
+    )
     parser.add_argument(
         "--tile-gap",
         type=int,
@@ -339,6 +356,20 @@ def main() -> None:
         f"grid {nx}x{ny}, tile_gap={args.tile_gap})"
     )
 
+    if args.write_exif:
+        if out.suffix.lower() not in (".jpg", ".jpeg"):
+            raise SystemExit("--write-exif requires a .jpg or .jpeg output path.")
+        cfg_path = Path(args.config).expanduser()
+        if not cfg_path.is_file():
+            raise SystemExit(f"Config not found: {cfg_path}")
+        config = load_config(str(cfg_path), require_credentials=False)
+        try:
+            ok = tag_mosaic_jpeg_for_scan_dir(scan_dir, out, config, force=True)
+        except ValueError as exc:
+            raise SystemExit(str(exc)) from exc
+        if not ok:
+            raise SystemExit("EXIF tagging failed (see log).")
+
     if args.compare_mosaic:
         compare_mosaics(canvas, scan_dir / "mosaic.jpg", fit=args.fit)
 

scripts/tag_mosaic_exif.py

@@ -0,0 +1,112 @@
+#!/usr/bin/env python3
+"""
+Write mosaic EXIF into a JPEG using metadata.json and config machine_metadata.
+
+Usage:
+  python scripts/tag_mosaic_exif.py /path/to/scan_dir
+  python scripts/tag_mosaic_exif.py /path/to/scan_dir --jpeg mosaic.jpg --machine "BW1-6 [AMR-19]"
+"""
+
+from __future__ import annotations
+
+import argparse
+import logging
+import sys
+from pathlib import Path
+
+_REPO_ROOT = Path(__file__).resolve().parent.parent
+if str(_REPO_ROOT) not in sys.path:
+    sys.path.insert(0, str(_REPO_ROOT))
+
+from spruce.exif import tag_mosaic_jpeg_for_scan_dir
+from spruce.settings import DEFAULT_CONFIG, load_config
+
+log = logging.getLogger(__name__)
+
+
+def main() -> None:
+    logging.basicConfig(
+        level=logging.INFO,
+        format="%(asctime)s  %(levelname)-8s  %(message)s",
+        datefmt="%H:%M:%S",
+    )
+    parser = argparse.ArgumentParser(
+        description=(
+            "Insert RootView-style mosaic EXIF (piexif, no re-encode) using "
+            "scan_dir/metadata.json and machine_metadata from config."
+        )
+    )
+    parser.add_argument(
+        "scan_dir",
+        type=Path,
+        help="Directory containing metadata.json (…/<machine>/<date>/<scan_id>/)",
+    )
+    parser.add_argument(
+        "--jpeg",
+        type=Path,
+        default=None,
+        help="JPEG to tag (default: <scan_dir>/mosaic_reconstructed.jpg)",
+    )
+    parser.add_argument(
+        "--config",
+        default=DEFAULT_CONFIG,
+        metavar="FILE",
+        help=f"YAML config (default: {DEFAULT_CONFIG})",
+    )
+    parser.add_argument(
+        "--machine",
+        metavar="LABEL",
+        default=None,
+        help='RootView machine label, e.g. "BW1-6 [AMR-19]" (skip archive slug inference)',
+    )
+    parser.add_argument(
+        "--force",
+        action="store_true",
+        help="Tag even when write_exif is false in config",
+    )
+    parser.add_argument(
+        "--processing-software",
+        default=None,
+        metavar="STR",
+        help="Override ProcessingSoftware EXIF string",
+    )
+    args = parser.parse_args()
+
+    scan_dir = args.scan_dir.expanduser().resolve()
+    if not scan_dir.is_dir():
+        sys.exit(f"Not a directory: {scan_dir}")
+
+    jpeg = args.jpeg
+    if jpeg is None:
+        jpeg = scan_dir / "mosaic_reconstructed.jpg"
+    else:
+        jpeg = jpeg.expanduser().resolve()
+
+    if not jpeg.is_file():
+        sys.exit(f"JPEG not found: {jpeg}")
+
+    cfg_path = Path(args.config).expanduser()
+    if not cfg_path.is_file():
+        sys.exit(f"Config not found: {cfg_path}")
+
+    config = load_config(str(cfg_path), require_credentials=False)
+
+    try:
+        ok = tag_mosaic_jpeg_for_scan_dir(
+            scan_dir,
+            jpeg,
+            config,
+            machine_label=args.machine,
+            processing_software=args.processing_software,
+            force=args.force,
+        )
+    except ValueError as exc:
+        sys.exit(str(exc))
+
+    if not ok:
+        sys.exit("EXIF tagging was skipped or failed (see log).")
+    log.info("EXIF written: %s", jpeg)
+
+
+if __name__ == "__main__":
+    main()

spruce/exif.py

@@ -2,18 +2,24 @@
 Write EXIF metadata into downloaded mosaic JPEGs (piexif, no re-encode).
 """
 
+import json
 import logging
 import re
 from pathlib import Path
 from typing import Any
 
 import piexif
+
+from spruce.paths import machine_dir_name
 from piexif import ExifIFD, GPSIFD, ImageIFD
 
 log = logging.getLogger(__name__)
 
 USER_COMMENT_ASCII = b"ASCII\x00\x00\x00"
 
+# ProcessingSoftware for mosaics stitched from tiles (distinct from server download path).
+DEFAULT_PROCESSING_SOFTWARE_MOSAIC_FROM_TILES = "spruce-scraper/1.0 mosaic_from_tiles"
+
 
 def _fmt_exif_datetime(scan_time: str) -> str:
     """`YYYY-MM-DD HH:MM:SS` -> `YYYY:MM:DD HH:MM:SS` for EXIF; empty on failure."""
@@ -252,3 +258,92 @@ def write_mosaic_exif(
         log.warning("EXIF write failed for %s: %s", jpeg_path, exc)
         return False
     return True
+
+
+def resolve_machine_label_for_scan_dir(
+    scan_dir: Path,
+    config: dict[str, Any],
+    machine_label: str | None,
+) -> str:
+    """
+    Return the RootView machine label for EXIF.
+
+    If ``machine_label`` is set, it is returned stripped. Otherwise the parent
+    of ``scan_dir`` is walked (archive slug under ``machine_dir_name``) and
+    matched uniquely against keys in ``config['machine_metadata']``.
+    """
+    if machine_label is not None and str(machine_label).strip() != "":
+        return str(machine_label).strip()
+    slug = scan_dir.parent.parent.name
+    meta = config.get("machine_metadata") or {}
+    matches = [lbl for lbl in meta if machine_dir_name({"label": lbl}) == slug]
+    if len(matches) == 1:
+        return matches[0]
+    if not matches:
+        raise ValueError(
+            f"Could not map archive folder {slug!r} to a machine label. "
+            f"Add it under machine_metadata in config or pass machine_label explicitly."
+        )
+    raise ValueError(
+        f"Ambiguous archive folder {slug!r}: multiple machine_metadata keys "
+        f"match ({matches!r}). Pass machine_label explicitly."
+    )
+
+
+def tag_mosaic_jpeg_for_scan_dir(
+    scan_dir: Path,
+    jpeg_path: Path,
+    config: dict[str, Any],
+    *,
+    machine_label: str | None = None,
+    processing_software: str | None = None,
+    force: bool = False,
+) -> bool:
+    """
+    Write the same mosaic EXIF as the scraper, using ``metadata.json`` in
+    ``scan_dir`` and optional ``machine_metadata`` from ``config``.
+
+    Returns False if tagging was skipped (e.g. ``write_exif`` disabled and not
+    ``force``). Raises ``ValueError`` for invalid paths or JPEG suffix.
+
+    ``force=True`` tags even when ``config['write_exif']`` is false (e.g. stitch
+    script ``--write-exif``).
+    """
+    scan_dir = scan_dir.resolve()
+    jpeg_path = jpeg_path.resolve()
+    suffix = jpeg_path.suffix.lower()
+    if suffix not in (".jpg", ".jpeg"):
+        raise ValueError(
+            f"EXIF tagging only supports JPEG files; got suffix {jpeg_path.suffix!r}: {jpeg_path}"
+        )
+
+    if not force and not config.get("write_exif", True):
+        log.warning(
+            "Skipping EXIF: write_exif is false in config (use force=True to override)."
+        )
+        return False
+
+    meta_path = scan_dir / "metadata.json"
+    if not meta_path.is_file():
+        raise ValueError(f"Missing metadata.json: {meta_path}")
+    with meta_path.open(encoding="utf-8") as fh:
+        scan_meta: dict[str, Any] = json.load(fh)
+    scan_id = int(scan_meta["scan_id"])
+    if scan_dir.name != str(scan_id):
+        raise ValueError(
+            f"scan_dir must be the scan id folder (got name {scan_dir.name!r}, "
+            f"metadata scan_id={scan_id}). Expected …/<date>/{scan_id}/"
+        )
+
+    label = resolve_machine_label_for_scan_dir(scan_dir, config, machine_label)
+    machine: dict[str, Any] = {"label": label, "version": ""}
+    mmeta = (config.get("machine_metadata") or {}).get(label)
+    proc = processing_software or DEFAULT_PROCESSING_SOFTWARE_MOSAIC_FROM_TILES
+    return write_mosaic_exif(
+        jpeg_path,
+        scan_meta,
+        machine,
+        scan_id,
+        mmeta,
+        processing_software=proc,
+    )

spruce/settings.py

@@ -99,13 +99,20 @@ def _clamp_workers(n: int) -> int:
 # ---------------------------------------------------------------------------
 
 
-def load_config(path: str) -> dict:
-    """Load and validate config.yaml. Exits on missing required fields."""
+def load_config(path: str, *, require_credentials: bool = True) -> dict:
+    """Load and validate config.yaml. Exits on missing required fields.
+
+    With ``require_credentials=False`` (e.g. offline EXIF tagging), username and
+    password are not required; only fields needed for tagging are defaulted.
+    """
     with open(path) as fh:
         cfg = yaml.safe_load(fh)
-    missing = [k for k in ("username", "password") if not cfg.get(k)]
-    if missing:
-        sys.exit(f"Config {path} is missing required fields: {missing}")
+    if cfg is None:
+        cfg = {}
+    if require_credentials:
+        missing = [k for k in ("username", "password") if not cfg.get(k)]
+        if missing:
+            sys.exit(f"Config {path} is missing required fields: {missing}")
     cfg.setdefault("base_url", "http://205.149.147.131:8010/")
     cfg.setdefault("image_base_url", "http://205.149.147.131:8011/")
     cfg.setdefault("output_dir", "archives")

tests/test_mosaic_exif_tag.py

@@ -0,0 +1,164 @@
+"""Tests for offline mosaic EXIF tagging (tag_mosaic_jpeg_for_scan_dir, resolver)."""
+
+from __future__ import annotations
+
+import json
+import logging
+import os
+import shutil
+import subprocess
+import sys
+from pathlib import Path
+
+import piexif
+import pytest
+from piexif import ImageIFD
+
+from spruce.exif import (
+    DEFAULT_PROCESSING_SOFTWARE_MOSAIC_FROM_TILES,
+    resolve_machine_label_for_scan_dir,
+    tag_mosaic_jpeg_for_scan_dir,
+)
+from spruce.paths import machine_dir_name
+
+FIXTURES = Path(__file__).parent / "fixtures"
+BLANK_JPEG = FIXTURES / "blank.jpg"
+ROOT = Path(__file__).resolve().parents[1]
+TAG_SCRIPT = ROOT / "scripts" / "tag_mosaic_exif.py"
+
+
+def _scan_tree(tmp_path: Path, *, machine_label: str, scan_id: int) -> Path:
+    slug = machine_dir_name({"label": machine_label})
+    scan_dir = tmp_path / "archives" / slug / "2024-01-01" / str(scan_id)
+    scan_dir.mkdir(parents=True)
+    meta = {
+        "scan_id": scan_id,
+        "name": "Test scan",
+        "scan_time": "2024-06-28 11:00:00",
+        "user": "Tester",
+        "nx": 2,
+        "ny": 2,
+        "dx": 1.0,
+        "dy": 1.0,
+        "end_x": 10.0,
+        "end_y": 10.0,
+    }
+    (scan_dir / "metadata.json").write_text(json.dumps(meta), encoding="utf-8")
+    return scan_dir
+
+
+def test_resolve_machine_label_from_slug_unique(tmp_path: Path) -> None:
+    label = "BW1-7 [AMR-18]"
+    scan_dir = _scan_tree(tmp_path, machine_label=label, scan_id=42)
+    cfg = {"machine_metadata": {label: {"plot_number": 7}}}
+    assert resolve_machine_label_for_scan_dir(scan_dir, cfg, None) == label
+
+
+def test_resolve_machine_label_explicit_overrides_slug(tmp_path: Path) -> None:
+    scan_dir = _scan_tree(tmp_path, machine_label="BW1-7 [AMR-18]", scan_id=1)
+    cfg = {"machine_metadata": {"Other [X]": {}}}
+    assert (
+        resolve_machine_label_for_scan_dir(scan_dir, cfg, "Custom [Label]")
+        == "Custom [Label]"
+    )
+
+
+def test_resolve_machine_label_no_match_raises(tmp_path: Path) -> None:
+    scan_dir = _scan_tree(tmp_path, machine_label="BW1-7 [AMR-18]", scan_id=1)
+    cfg = {"machine_metadata": {}}
+    with pytest.raises(ValueError, match="Could not map"):
+        resolve_machine_label_for_scan_dir(scan_dir, cfg, None)
+
+
+def test_tag_mosaic_jpeg_for_scan_dir_writes_exif(tmp_path: Path) -> None:
+    label = "BW1-7 [AMR-18]"
+    scan_dir = _scan_tree(tmp_path, machine_label=label, scan_id=99)
+    jpeg = tmp_path / "out.jpg"
+    shutil.copy(BLANK_JPEG, jpeg)
+    cfg = {"write_exif": True, "machine_metadata": {label: {}}}
+    assert tag_mosaic_jpeg_for_scan_dir(scan_dir, jpeg, cfg, force=True)
+    exif = piexif.load(str(jpeg))
+    assert (
+        exif["0th"][ImageIFD.ProcessingSoftware]
+        == DEFAULT_PROCESSING_SOFTWARE_MOSAIC_FROM_TILES.encode("ascii")
+    )
+    assert b"SPRUCE scan 99" in exif["Exif"][piexif.ExifIFD.UserComment]
+
+
+def test_tag_mosaic_skipped_when_write_exif_false_without_force(
+    tmp_path: Path, caplog: pytest.LogCaptureFixture
+) -> None:
+    label = "BW1-7 [AMR-18]"
+    scan_dir = _scan_tree(tmp_path, machine_label=label, scan_id=1)
+    jpeg = tmp_path / "out.jpg"
+    shutil.copy(BLANK_JPEG, jpeg)
+    cfg = {"write_exif": False, "machine_metadata": {label: {}}}
+    with caplog.at_level(logging.WARNING):
+        ok = tag_mosaic_jpeg_for_scan_dir(scan_dir, jpeg, cfg, force=False)
+    assert not ok
+    assert "Skipping EXIF" in caplog.text
+
+
+def test_tag_mosaic_scan_dir_name_mismatch_raises(tmp_path: Path) -> None:
+    label = "BW1-7 [AMR-18]"
+    scan_dir = _scan_tree(tmp_path, machine_label=label, scan_id=100)
+    bad = scan_dir.parent / "wrong_name"
+    shutil.move(str(scan_dir), str(bad))
+    jpeg = tmp_path / "out.jpg"
+    shutil.copy(BLANK_JPEG, jpeg)
+    cfg = {"machine_metadata": {label: {}}}
+    with pytest.raises(ValueError, match="scan_dir must be the scan id folder"):
+        tag_mosaic_jpeg_for_scan_dir(bad, jpeg, cfg, force=True)
+
+
+def test_tag_mosaic_non_jpeg_raises(tmp_path: Path) -> None:
+    label = "BW1-7 [AMR-18]"
+    scan_dir = _scan_tree(tmp_path, machine_label=label, scan_id=1)
+    png = tmp_path / "out.png"
+    png.write_bytes(b"not really png")
+    cfg = {"machine_metadata": {label: {}}}
+    with pytest.raises(ValueError, match="only supports JPEG"):
+        tag_mosaic_jpeg_for_scan_dir(scan_dir, png, cfg, force=True)
+
+
+def test_tag_mosaic_second_run_replaces_exif(tmp_path: Path) -> None:
+    label = "BW1-7 [AMR-18]"
+    scan_dir = _scan_tree(tmp_path, machine_label=label, scan_id=5)
+    jpeg = tmp_path / "out.jpg"
+    shutil.copy(BLANK_JPEG, jpeg)
+    cfg = {"machine_metadata": {label: {}}}
+    assert tag_mosaic_jpeg_for_scan_dir(scan_dir, jpeg, cfg, force=True)
+    assert tag_mosaic_jpeg_for_scan_dir(
+        scan_dir, jpeg, cfg, force=True, processing_software="custom/2.0"
+    )
+    exif = piexif.load(str(jpeg))
+    assert exif["0th"][ImageIFD.ProcessingSoftware] == b"custom/2.0"
+
+
+def test_tag_mosaic_exif_script_cli(tmp_path: Path) -> None:
+    label = "BW1-6 [AMR-19]"
+    scan_dir = _scan_tree(tmp_path, machine_label=label, scan_id=156875)
+    jpeg = scan_dir / "mosaic_reconstructed.jpg"
+    shutil.copy(BLANK_JPEG, jpeg)
+    cfg = tmp_path / "mini.yaml"
+    cfg.write_text(
+        f"write_exif: true\nmachine_metadata:\n  {label!r}: {{}}\n",
+        encoding="utf-8",
+    )
+    env = {**os.environ, "PYTHONPATH": str(ROOT)}
+    r = subprocess.run(
+        [
+            sys.executable,
+            str(TAG_SCRIPT),
+            str(scan_dir),
+            "--config",
+            str(cfg),
+        ],
+        cwd=str(ROOT),
+        capture_output=True,
+        text=True,
+        env=env,
+    )
+    assert r.returncode == 0, r.stderr + r.stdout
+    exif = piexif.load(str(jpeg))
+    assert b"SPRUCE scan 156875" in exif["Exif"][piexif.ExifIFD.UserComment]

tests/test_settings.py

@@ -95,6 +95,16 @@ def test_load_config_missing_password_exits(tmp_path):
         load_config(str(path))
 
 
+def test_load_config_optional_credentials(tmp_path):
+    path = tmp_path / "config.yaml"
+    path.write_text(
+        yaml.dump({"machine_metadata": {"A [B]": {"plot_number": 2}}})
+    )
+    cfg = load_config(str(path), require_credentials=False)
+    assert cfg["machine_metadata"]["A [B]"]["plot_number"] == 2
+    assert cfg["write_exif"] is True
+
+
 # ---------------------------------------------------------------------------
 # CSV schemas (failure columns)
 # ---------------------------------------------------------------------------