Add support for OME-Zarr data

src/croissant_baker/handlers/ome_zarr_handler.py

@@ -0,0 +1,77 @@
+"""OME-Zarr handler for multiscale bioimaging data (Zarr v2)."""
+
+import json
+from pathlib import Path
+
+from croissant_baker.handlers.base_handler import FileTypeHandler
+
+
+class OMEZarrHandler(FileTypeHandler):
+    """
+    Handler for OME-Zarr stores (.zarr directories, Zarr v2 format).
+
+    OME-Zarr is a specification for storing multiscale bioimaging data
+    in Zarr format. This handler currently supports Zarr v2 only (OME-Zarr 0.4).
+    """
+
+    EXTENSIONS = (".zarr",)
+    FORMAT_NAME = "OME-Zarr"
+    FORMAT_DESCRIPTION = "OME-Zarr multiscale bioimaging data (Zarr v2, OME-Zarr 0.4)"
+
+    def can_handle(self, file_path: Path) -> bool:
+        """
+        Check if path is a .zarr directory with Zarr v2 format.
+
+        Zarr v2 is identified by presence of .zgroup or .zarray at root.
+        """
+        name = file_path.name.lower()
+        if not (name.endswith(".zarr") or name.endswith(".ome.zarr")):
+            return False
+
+        # For actual directories, check for Zarr v2 markers
+        if file_path.is_dir():
+            return (file_path / ".zgroup").exists() or (file_path / ".zarray").exists()
+
+        # For path-based detection (file doesn't exist yet), accept by extension
+        return True
+
+    def extract_metadata(self, file_path: Path, **kwargs) -> dict:
+        """Extract metadata from an OME-Zarr store."""
+        if not file_path.exists():
+            raise FileNotFoundError(f"OME-Zarr store not found: {file_path}")
+
+        zattrs_path = file_path / ".zattrs"
+        if not zattrs_path.exists():
+            raise ValueError(f"Missing .zattrs in OME-Zarr store: {file_path}")
+
+        with open(zattrs_path, "r", encoding="utf-8") as f:
+            zattrs = json.load(f)
+
+        props: dict = {}
+
+        # Extract multiscales metadata (OME-Zarr core)
+        multiscales = zattrs.get("multiscales", [])
+        if multiscales:
+            props["multiscales"] = multiscales
+            # Considering only a single multiscale; this is by far the most common case.
+            first_ms = multiscales[0]
+            props["ome_zarr_version"] = first_ms.get("version", "unknown")
+            props["axes"] = first_ms.get("axes", [])
+            props["num_scales"] = len(first_ms.get("datasets", []))
+
+        return {
+            "file_name": file_path.name,
+            # See https://github.com/zarr-developers/zarr-specs/issues/123 for the discussion
+            # "mime type / encoding format conventions #123" for Zarr
+            # There is not really an established convention.
+            # Data one lists application/x+zarr (https://cn.dataone.org/cn/v2/formats)
+            # vnd.zarr is also used by some.
+            "encoding_format": "application/x+zarr",
+            "ome_zarr_properties": props,
+        }
+
+    def build_croissant(
+        self, file_metas: list[dict], file_ids: list[str]
+    ) -> tuple[list, list]:
+        """Build Croissant FileSets and RecordSets for OME-Zarr stores."""
+        raise NotImplementedError("build_croissant not yet implemented")