bioformats2raw export: unify Zarr layout and add OMERO metadata

.pre-commit-config.yaml

@@ -10,6 +10,7 @@ repos:
     rev: 5.9.3
     hooks:
       - id: isort
+        args: ["--profile", "black"]
 
   - repo: https://github.com/psf/black
     rev: 21.7b0

src/omero_zarr/cli.py

@@ -8,9 +8,16 @@
 from omero.cli import CLI, BaseControl, Parser, ProxyStringType
 from omero.gateway import BlitzGateway, BlitzObjectWrapper
 from omero.model import ImageI, PlateI
+from zarr.hierarchy import open_group
+from zarr.storage import FSStore
 
 from .masks import MASK_DTYPE_SIZE, image_shapes_to_zarr, plate_shapes_to_zarr
-from .raw_pixels import image_to_zarr, plate_to_zarr
+from .raw_pixels import (
+    add_omero_metadata,
+    add_toplevel_metadata,
+    image_to_zarr,
+    plate_to_zarr,
+)
 
 HELP = """Export data in zarr format.
 
@@ -237,19 +244,8 @@ def polygons(self, args: argparse.Namespace) -> None:
     def export(self, args: argparse.Namespace) -> None:
         if isinstance(args.object, ImageI):
             image = self._lookup(self.gateway, "Image", args.object.id)
-            inplace = image.getInplaceImport()
-
             if args.bf:
-                if self.client is None:
-                    raise Exception("This cannot happen")  # mypy is confused
-                prx, desc = self.client.getManagedRepository(description=True)
-                repo_path = Path(desc._path._val) / Path(desc._name._val)
-                if inplace:
-                    for p in image.getImportedImageFilePaths()["client_paths"]:
-                        self._bf_export(Path("/") / Path(p), args)
-                else:
-                    for p in image.getImportedImageFilePaths()["server_paths"]:
-                        self._bf_export(repo_path / p, args)
+                self._bf_export(image, args)
             else:
                 image_to_zarr(image, args)
         elif isinstance(args.object, PlateI):
@@ -266,8 +262,23 @@ def _lookup(
             self.ctx.die(110, f"No such {otype}: {oid}")
         return obj
 
-    def _bf_export(self, abs_path: Path, args: argparse.Namespace) -> None:
+    def _bf_export(self, image: BlitzObjectWrapper, args: argparse.Namespace) -> None:
+        if image.getInplaceImport():
+            p = image.getImportedImageFilePaths()["client_paths"][0]
+            abs_path = Path("/") / Path(p)
+        else:
+            if self.client is None:
+                raise Exception("This cannot happen")  # mypy is confused
+            prx, desc = self.client.getManagedRepository(description=True)
+            p = image.getImportedImageFilePaths()["server_paths"][0]
+            abs_path = Path(desc._path._val) / Path(desc._name._val) / Path(p)
         target = (Path(args.output) or Path.cwd()) / Path(abs_path).name
+        image_target = (Path(args.output) or Path.cwd()) / f"{image.id}.zarr"
+
+        if target.exists():
+            self.ctx.die(111, f"{target.resolve()} already exists")
+        if image_target.exists():
+            self.ctx.die(111, f"{image_target.resolve()} already exists")
 
         cmd: List[str] = [
             "bioformats2raw",
@@ -283,6 +294,9 @@ def _bf_export(self, abs_path: Path, args: argparse.Namespace) -> None:
             cmd.append(f"--resolutions={args.resolutions}")
         if args.max_workers:
             cmd.append(f"--max_workers={args.max_workers}")
+        cmd.append(f"--series={image.series}")
+        cmd.append("--no-root-group")
+        cmd.append("--no-ome-meta-export")
 
         self.ctx.dbg(" ".join(cmd))
         process = subprocess.Popen(
@@ -294,7 +308,21 @@ def _bf_export(self, abs_path: Path, args: argparse.Namespace) -> None:
         if stderr:
             self.ctx.err(stderr.decode("utf-8"))
         if process.returncode == 0:
-            self.ctx.out(f"Image exported to {target.resolve()}")
+            image_source = target / "0"
+            image_source.rename(image_target)
+            target.rmdir()
+            self.ctx.out(f"Image exported to {image_target.resolve()}")
+
+        # Add OMERO metadata
+        store = FSStore(
+            str(image_target.resolve()),
+            auto_mkdir=False,
+            normalize_keys=False,
+            mode="w",
+        )
+        root = open_group(store)
+        add_omero_metadata(root, image)
+        add_toplevel_metadata(root)
 
 
 try:

src/omero_zarr/raw_pixels.py

@@ -39,7 +39,8 @@ def image_to_zarr(image: omero.gateway.ImageWrapper, args: argparse.Namespace) -
     store = _open_store(name)
     root = open_group(store)
     n_levels, axes = add_image(image, root, cache_dir=cache_dir)
-    add_group_metadata(root, image, axes, n_levels)
+    add_multiscales_metadata(root, axes, n_levels)
+    add_omero_metadata(root, image)
     add_toplevel_metadata(root)
     print("Finished.")
 
@@ -268,7 +269,8 @@ def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace)
                 col_group = row_group.require_group(col)
                 field_group = col_group.require_group(field_name)
                 n_levels, axes = add_image(img, field_group, cache_dir=cache_dir)
-                add_group_metadata(field_group, img, axes, n_levels)
+                add_multiscales_metadata(field_group, axes, n_levels)
+                add_omero_metadata(field_group, img)
                 # Update Well metadata after each image
                 col_group.attrs["well"] = {"images": fields, "version": VERSION}
                 max_fields = max(max_fields, field + 1)
@@ -283,26 +285,12 @@ def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace)
     print("Finished.")
 
 
-def add_group_metadata(
+def add_multiscales_metadata(
     zarr_root: Group,
-    image: Optional[omero.gateway.ImageWrapper],
     axes: List[str],
     resolutions: int = 1,
 ) -> None:
 
-    if image:
-        image_data = {
-            "id": 1,
-            "channels": [channelMarshal(c) for c in image.getChannels()],
-            "rdefs": {
-                "model": (image.isGreyscaleRenderingModel() and "greyscale" or "color"),
-                "defaultZ": image._re.getDefaultZ(),
-                "defaultT": image._re.getDefaultT(),
-            },
-            "version": VERSION,
-        }
-        zarr_root.attrs["omero"] = image_data
-        image._closeRE()
     multiscales = [
         {
             "version": "0.3",
@@ -313,6 +301,22 @@ def add_group_metadata(
     zarr_root.attrs["multiscales"] = multiscales
 
 
+def add_omero_metadata(zarr_root: Group, image: omero.gateway.ImageWrapper) -> None:
+
+    image_data = {
+        "id": 1,
+        "channels": [channelMarshal(c) for c in image.getChannels()],
+        "rdefs": {
+            "model": (image.isGreyscaleRenderingModel() and "greyscale" or "color"),
+            "defaultZ": image._re.getDefaultZ(),
+            "defaultT": image._re.getDefaultT(),
+        },
+        "version": VERSION,
+    }
+    zarr_root.attrs["omero"] = image_data
+    image._closeRE()
+
+
 def add_toplevel_metadata(zarr_root: Group) -> None:
 
     zarr_root.attrs["_creator"] = {"name": "omero-zarr", "version": __version__}