Allow to use bioformats2raw to export HCS data

setup.py

@@ -35,7 +35,7 @@ def get_long_description() -> str:
     author="The Open Microscopy Team",
     author_email="",
     python_requires=">=3",
-    install_requires=["omero-py>=5.6.0", "ome-zarr>=0.3.1.dev0"],
+    install_requires=["omero-py>=5.6.0", "ome-zarr>=0.3.0"],
     long_description=long_description,
     keywords=["OMERO.CLI", "plugin"],
     url="https://github.com/ome/omero-cli-zarr/",

src/omero_zarr/cli.py

@@ -6,7 +6,7 @@
 from typing import Any, Callable, List
 
 from omero.cli import CLI, BaseControl, Parser, ProxyStringType
-from omero.gateway import BlitzGateway, BlitzObjectWrapper
+from omero.gateway import BlitzGateway, BlitzObjectWrapper, ImageWrapper
 from omero.model import ImageI, PlateI
 from zarr.hierarchy import open_group
 from zarr.storage import FSStore
@@ -307,7 +307,11 @@ def export(self, args: argparse.Namespace) -> None:
                 image_to_zarr(image, args)
         elif isinstance(args.object, PlateI):
             plate = self._lookup(self.gateway, "Plate", args.object.id)
-            plate_to_zarr(plate, args)
+            if args.bf or args.bfpath:
+                self._bf_export(plate, args)
+                plate_to_zarr(plate, args, write_binary=False)
+            else:
+                plate_to_zarr(plate, args, write_binary=True)
 
     def _lookup(
         self, gateway: BlitzGateway, otype: str, oid: int
@@ -319,25 +323,35 @@ def _lookup(
             self.ctx.die(110, f"No such {otype}: {oid}")
         return obj
 
-    def _bf_export(self, image: BlitzObjectWrapper, args: argparse.Namespace) -> None:
+    def _bf_export(self, obj: BlitzObjectWrapper, args: argparse.Namespace) -> None:
+        def _get_first_image(obj: BlitzObjectWrapper) -> ImageWrapper:
+            if obj.OMERO_CLASS == "Plate":
+                for well in obj.listChildren():
+                    for ws in well.listChildren():
+                        return ws.getImage()
+            else:
+                return obj
+
         if args.bfpath:
             abs_path = Path(args.bfpath)
-        elif 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)
-        temp_target = (Path(args.output) or Path.cwd()) / f"{image.id}.tmp"
-        image_target = (Path(args.output) or Path.cwd()) / f"{image.id}.zarr"
+            first_image = _get_first_image(obj)
+            if first_image.getInplaceImport():
+                p = first_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 = first_image.getImportedImageFilePaths()["server_paths"][0]
+                abs_path = Path(desc._path._val) / Path(desc._name._val) / Path(p)
+        temp_target = (Path(args.output) or Path.cwd()) / f"{obj.id}.tmp"
+        zarr_target = (Path(args.output) or Path.cwd()) / f"{obj.id}.zarr"
 
         if temp_target.exists():
             self.ctx.die(111, f"{temp_target.resolve()} already exists")
-        if image_target.exists():
-            self.ctx.die(111, f"{image_target.resolve()} already exists")
+        if zarr_target.exists():
+            self.ctx.die(111, f"{zarr_target.resolve()} already exists")
 
         cmd: List[str] = [
             "bioformats2raw",
@@ -353,9 +367,10 @@ def _bf_export(self, image: BlitzObjectWrapper, args: argparse.Namespace) -> Non
             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")
+        if obj.OMERO_CLASS == "Image":
+            cmd.append(f"--series={obj.series}")
+            cmd.append("--no-root-group")
+            cmd.append("--no-ome-meta-export")
 
         self.ctx.dbg(" ".join(cmd))
         process = subprocess.Popen(
@@ -367,21 +382,26 @@ def _bf_export(self, image: BlitzObjectWrapper, args: argparse.Namespace) -> Non
         if stderr:
             self.ctx.err(stderr.decode("utf-8"))
         if process.returncode == 0:
-            image_source = temp_target / "0"
-            image_source.rename(image_target)
-            temp_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)
+            if obj.OMERO_CLASS == "Image":
+                image_source = temp_target / "0"
+                image_source.rename(zarr_target)
+                temp_target.rmdir()
+            else:
+                temp_target.rename(zarr_target)
+            self.ctx.out(f"{obj.OMERO_CLASS} exported to {zarr_target.resolve()}")
+
+        if obj.OMERO_CLASS == "Image":
+            # Add OMERO metadata
+            store = FSStore(
+                str(zarr_target.resolve()),
+                auto_mkdir=False,
+                normalize_keys=False,
+                mode="w",
+            )
+
+            root = open_group(store)
+            add_omero_metadata(root, obj)
+            add_toplevel_metadata(root)
 
 
 try:

src/omero_zarr/raw_pixels.py

@@ -210,7 +210,11 @@ def marshal_acquisition(acquisition: omero.gateway._PlateAcquisitionWrapper) ->
     return acq
 
 
-def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace) -> None:
+def plate_to_zarr(
+    plate: omero.gateway._PlateWrapper,
+    args: argparse.Namespace,
+    write_binary: Optional[bool] = True,
+) -> None:
     """
     Exports a plate to a zarr file using the hierarchy discussed here ('Option 3'):
     https://github.com/ome/omero-ms-zarr/issues/73#issuecomment-706770955
@@ -262,23 +266,26 @@ def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace)
                 row_group = root.require_group(row)
                 col_group = row_group.require_group(col)
                 field_group = col_group.require_group(field_name)
-                add_image(img, field_group, cache_dir=cache_dir)
+                if write_binary:
+                    add_image(img, field_group, cache_dir=cache_dir)
                 add_omero_metadata(field_group, img)
-                # Update Well metadata after each image
-                write_well_metadata(col_group, fields)
+                if write_binary:
+                    # Update Well metadata after each image
+                    write_well_metadata(col_group, fields)
                 max_fields = max(max_fields, field + 1)
             print_status(int(t0), int(time.time()), count, total)
 
-        # Update plate_metadata after each Well
-        write_plate_metadata(
-            root,
-            row_names,
-            col_names,
-            wells=list(well_paths),
-            field_count=max_fields,
-            acquisitions=plate_acq,
-            name=plate.name,
-        )
+        if write_binary:
+            # Update plate_metadata after each Well
+            write_plate_metadata(
+                root,
+                row_names,
+                col_names,
+                wells=list(well_paths),
+                field_count=max_fields,
+                acquisitions=plate_acq,
+                name=plate.name,
+            )
 
     add_toplevel_metadata(root)
     print("Finished.")
@@ -287,7 +294,7 @@ def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace)
 def add_omero_metadata(zarr_root: Group, image: omero.gateway.ImageWrapper) -> None:
 
     image_data = {
-        "id": 1,
+        "id": image.getId(),
         "channels": [channelMarshal(c) for c in image.getChannels()],
         "rdefs": {
             "model": (image.isGreyscaleRenderingModel() and "greyscale" or "color"),