Support export of Fileset:ID

src/omero_zarr/cli.py

@@ -7,7 +7,7 @@
 
 from omero.cli import CLI, BaseControl, Parser, ProxyStringType
 from omero.gateway import BlitzGateway, BlitzObjectWrapper
-from omero.model import ImageI, PlateI
+from omero.model import FilesetI, ImageI, PlateI
 from zarr.hierarchy import open_group
 from zarr.storage import FSStore
 
@@ -20,6 +20,7 @@
 from .raw_pixels import (
     add_omero_metadata,
     add_toplevel_metadata,
+    fileset_to_zarr,
     image_to_zarr,
     plate_to_zarr,
 )
@@ -323,6 +324,9 @@ def export(self, args: argparse.Namespace) -> None:
         elif isinstance(args.object, PlateI):
             plate = self._lookup(self.gateway, "Plate", args.object.id)
             plate_to_zarr(plate, args)
+        elif isinstance(args.object, FilesetI):
+            fileset = self._lookup(self.gateway, "Fileset", args.object.id)
+            fileset_to_zarr(fileset, args)
 
     def _lookup(
         self, gateway: BlitzGateway, otype: str, oid: int

src/omero_zarr/raw_pixels.py

@@ -18,14 +18,74 @@
 
 from . import __version__
 from . import ngff_version as VERSION
-from .util import marshal_axes, marshal_transformations, open_store, print_status
+from .util import (
+    get_minimum_image_ome_xml,
+    marshal_axes,
+    marshal_transformations,
+    open_store,
+    print_status,
+)
 
 
-def image_to_zarr(image: omero.gateway.ImageWrapper, args: argparse.Namespace) -> None:
+def fileset_to_zarr(
+    fileset: omero.gateway.FilesetWrapper, args: argparse.Namespace
+) -> None:
+    """Exports a FileSet according to bioformats2raw.layout"""
+    images = list(fileset.copyImages())
+    images_to_zarr(images, args)
+
+
+def images_to_zarr(
+    images: List[omero.gateway.ImageWrapper],
+    args: argparse.Namespace,
+    target_dir: str = None,
+) -> None:
+    """Exports images in bioformats2raw.layout, each under path '0', '1' etc."""
+    if target_dir is None:
+        target_dir = args.output if args.output else "zarr_export"
+    dir_index = 1
+    dir_name = target_dir
+    while os.path.exists(dir_name):
+        dir_name = f"{target_dir}({dir_index})"
+        dir_index += 1
+    os.mkdir(dir_name)
+
+    # write bioformats2raw.layout
+    zattrs = os.path.join(dir_name, ".zattrs")
+    with open(zattrs, "w") as zfile:
+        zfile.write(
+            """{
+  "bioformats2raw.layout" : 3
+}"""
+        )
+    # write OME/METADATA.ome.xml
+    ome_dir = os.path.join(dir_name, "OME")
+    xml_path = os.path.join(ome_dir, "METADATA.ome.xml")
+    os.mkdir(ome_dir)
+    images = list(images)  # in case it's a generator
+    ome_xml = get_minimum_image_ome_xml(images)
+    with open(xml_path, "w") as xml_file:
+        xml_file.write(ome_xml)
+
+    # write images
+    for index, image in enumerate(images):
+        target = os.path.join(dir_name, str(index))
+        image_to_zarr(image, args, target)
+
+
+def image_to_zarr(
+    image: omero.gateway.ImageWrapper, args: argparse.Namespace, target: str = None
+) -> None:
+    """
+    Export an image to zarr
+    @param target: Optional path/to/image.zarr. Default is args.output/ID.zarr
+    """
     target_dir = args.output
     cache_dir = target_dir if args.cache_numpy else None
-
-    name = os.path.join(target_dir, "%s.zarr" % image.id)
+    if target is None:
+        name = os.path.join(target_dir, "%s.zarr" % image.id)
+    else:
+        name = target
     print(f"Exporting to {name} ({VERSION})")
     store = open_store(name)
     root = open_group(store)

src/omero_zarr/util.py

@@ -2,6 +2,16 @@
 from typing import Dict, List
 
 from omero.gateway import ImageWrapper
+from omero.model.enums import (
+    PixelsTypedouble,
+    PixelsTypefloat,
+    PixelsTypeint8,
+    PixelsTypeint16,
+    PixelsTypeint32,
+    PixelsTypeuint8,
+    PixelsTypeuint16,
+    PixelsTypeuint32,
+)
 from zarr.storage import FSStore
 
 
@@ -112,3 +122,55 @@ def marshal_transformations(
         zooms["y"] = zooms["y"] * multiscales_zoom
 
     return transformations
+
+
+def get_minimum_image_ome_xml(images: List[ImageWrapper]) -> str:
+    """Generates minimal OME.xml for"""
+
+    omero_pix_types = {
+        PixelsTypeint8: "int8",
+        PixelsTypeuint8: "uint8",
+        PixelsTypeint16: "int16",
+        PixelsTypeuint16: "uint16",
+        PixelsTypeint32: "int32",
+        PixelsTypeuint32: "uint32",
+        PixelsTypefloat: "float32",
+        PixelsTypedouble: "double",
+    }
+
+    images_xml = []
+    for image in images:
+        image_id = image.id
+        name = image.name
+        pixels_id = image.getPixelsId()
+        pixels_type = image.getPrimaryPixels().getPixelsType().getValue()
+        p_type = omero_pix_types[pixels_type]
+        size_x = image.getSizeX()
+        size_y = image.getSizeY()
+        size_z = image.getSizeZ()
+        size_c = image.getSizeC()
+        size_t = image.getSizeT()
+        images_xml.append(
+            f"""<Image ID="Image:{image_id}" Name="{name}">
+    <Pixels
+        ID="Pixels:{pixels_id}"
+        DimensionOrder="XYZCT"
+        Type="{p_type}"
+        SizeX="{size_x}"
+        SizeY="{size_y}"
+        SizeZ="{size_z}"
+        SizeC="{size_c}"
+        SizeT="{size_t}">
+        <MetadataOnly/>
+    </Pixels>
+  </Image>"""
+        )
+
+    img_xml = "\n".join(images_xml)
+    return f"""<?xml version="1.0" encoding="UTF-8"?>
+<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06"
+     xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+     xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06
+                         http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
+    {img_xml}
+</OME>"""