Add support for plates

Author: dominikl

src/omero_zarr/cli.py

@@ -44,7 +44,6 @@
 from .extinfo import (
     get_images,
     set_external_info,
-    get_path,
 )
 
 HELP = """Export data in zarr format.
@@ -348,17 +347,14 @@ def export(self, args: argparse.Namespace) -> None:
 
     @gateway_required
     def extinfo(self, args: argparse.Namespace) -> None:
-        for img in get_images(self.gateway, args.object):
-            path = get_path(self.gateway, img.getId())
+        for img, well, idx in get_images(self.gateway, args.object):
             img = img._obj
-            if path.endswith("OME/METADATA.ome.xml"):
-                path = path.replace("OME/METADATA.ome.xml", "0")
-                path = f"/{path}"
-                img = set_external_info(img, path)
+            try:
+                img = set_external_info(self.gateway, img, well, idx)
                 img = self.gateway.getUpdateService().saveAndReturnObject(img)
-                self.ctx.out(f"Set path to '{path}' for image {img.id._val}")
-            else:
-                self.ctx.out(f"'{path}' for image {img.id._val} doesn't seem to be an ome.zarr, skipping.")
+                self.ctx.out(f"Set path to '{img.details.externalInfo.lsid._val}' for image {img.id._val}")
+            except Exception as e:
+                self.ctx.err(f"Failed to set external info for image {img.id._val}: {e}")
 
 
     def _lookup(

src/omero_zarr/extinfo.py

@@ -8,9 +8,27 @@
 from omero.model import Screen
 from omero.model import Dataset
 from omero.model import Project
+import re
 
 
-def get_path(conn: BlitzGateway, image_id: int) -> str:
+# Regex to match well positions (eg. A1)
+WELL_POS_RE = re.compile(r"(?P<row>\D+)(?P<col>\d+)")
+
+
+def _get_path(conn: BlitzGateway, image_id: int) -> str:
+    """
+    Retrieve the (first) original file path for a given OMERO image.
+
+    Args:
+        conn (BlitzGateway): Active OMERO gateway connection
+        image_id (int): ID of the OMERO image
+
+    Returns:
+        str: path of the image file
+
+    Raises:
+        Exception: If the query fails or the path cannot be retrieved
+    """
     params = ParametersI()
     params.addId(image_id)
     query = """
@@ -25,24 +43,49 @@ def get_path(conn: BlitzGateway, image_id: int) -> str:
     return res
 
 
-def set_external_info(img: ImageI, path: str) -> ImageI:
-    info = ExternalInfoI()
-    info.entityType = rstring("com.glencoesoftware.ngff:multiscales")
-    info.entityId = rlong(3)
-    info.lsid = rstring(path)
-    img.details.externalInfo = info
-    return img
+def _lookup(conn: BlitzGateway, type: str, oid: int) -> BlitzObjectWrapper:
+    """
+    Look up an OMERO object by its type and ID.
 
+    Args:
+        conn (BlitzGateway): Active OMERO gateway connection
+        type (str): Type of OMERO object (e.g., "Screen", "Plate", "Image")
+        oid (int): Object ID to look up
 
-def _lookup(conn: BlitzGateway, type: str, oid: int) -> BlitzObjectWrapper:
+    Returns:
+        BlitzObjectWrapper: Wrapped OMERO object
+
+    Raises:
+        ValueError: If the object doesn't exist
+    """
     conn.SERVICE_OPTS.setOmeroGroup("-1")
     obj = conn.getObject(type, oid)
     if not obj:
         raise ValueError(f"No such {type}: {oid}")
     return obj
 
 
-def get_images(conn: BlitzGateway, object):
+def get_images(conn: BlitzGateway, object) -> tuple[BlitzObjectWrapper, str | None, int | None]:
+    """
+    Generator that yields images from any OMERO container object.
+
+    Recursively traverses OMERO container hierarchies (Screen/Plate/Project/Dataset)
+    to find all contained images.
+
+    Args:
+        conn (BlitzGateway): Active OMERO gateway connection
+        object: OMERO container object (Screen, Plate, Project, Dataset, Image)
+              or a list of such objects
+
+    Yields:
+        tuple: Contains:
+            - BlitzObjectWrapper: Image object
+            - str | None: Well position (eg. A1) if from plate, None otherwise
+            - int | None: Well sample index if from plate, None otherwise
+
+    Raises:
+        ValueError: If given an unsupported object type
+    """
     if isinstance(object, list):
         for x in object:
             yield from get_images(conn, x)
@@ -55,17 +98,73 @@ def get_images(conn: BlitzGateway, object):
         for well in plt.listChildren():
             for idx in range(0, well.countWellSample()):
                 img = well.getImage(idx)
-                yield img
+                yield img, well.getWellPos(), idx
     elif isinstance(object, Project):
         prj = _lookup(conn, "Project", object.id)
         for ds in prj.listChildren():
             yield from get_images(conn, ds._obj)
     elif isinstance(object, Dataset):
         ds = _lookup(conn, "Dataset", object.id)
         for img in ds.listChildren():
-            yield img
+            yield img, None, None
     elif isinstance(object, Image):
         img = _lookup(conn, "Image", object.id)
-        yield img
+        yield img, None, None
     else:
         raise ValueError(f"Unsupported type: {object.__class__.__name__}")
+
+
+def set_external_info(conn: BlitzGateway, img: ImageI, well: str, idx: int) -> ImageI:
+    """
+    Set external info for an image to enable omero zarr pixel buffer handling.
+    
+    This function configures an image for use with the omero-zarr-pixel-buffer by:
+    1. Retrieving the original file path
+    2. Converting it to point to the 5d multiscale image directory
+    3. Setting up the external info with the path and metadata
+    
+    For plate-based images (with wells), the path structure follows:
+    /<base_path>/<row>/<column>/<field index>
+    
+    For regular images:
+    /<base_path>/0
+    
+    Args:
+        conn (BlitzGateway): Active OMERO gateway connection
+        img (ImageI): OMERO image object to modify
+        well (str): Well position (e.g., 'A1', 'B2') for plate-based images, or None
+        idx (int): Well sample / field index for plate-based images, or None
+        
+    Returns:
+        ImageI: Modified image object with updated external info
+        
+    Raises:
+        ValueError: If the image path is not an OME-Zarr format or if well position is invalid
+        
+    Note:
+        The external info is configured with entity type 'com.glencoesoftware.ngff:multiscales'
+        and entity ID 3, which are required by the omero-zarr-pixel-buffer.
+    """
+    path = _get_path(conn, img.id)
+    if path.endswith("OME/METADATA.ome.xml"):
+        if well:
+            match = WELL_POS_RE.match(well)
+            if match:
+                col = match.group("col")
+                row = match.group("row")
+                path = path.replace("OME/METADATA.ome.xml", f"{row}")
+                path = f"/{path}/{col}/{idx}"
+            else:
+                raise ValueError(f"Couldn't parse well position: {well}")
+        else:
+            path = path.replace("OME/METADATA.ome.xml", "0")
+            path = f"/{path}"
+    else:
+        raise ValueError(f"Doesn't seem to be an ome.zarr: {path}")
+
+    info = ExternalInfoI()
+    info.entityType = rstring("com.glencoesoftware.ngff:multiscales")
+    info.entityId = rlong(3)
+    info.lsid = rstring(path)
+    img.details.externalInfo = info
+    return img