From 3ca2c58fca5c6a4fb90a26d5a0e51df041890033 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 23 Aug 2023 12:41:57 +0100
Subject: [PATCH] Update README and masks.py to use ID.ome.zarr

---
 README.rst              | 13 +++++++------
 src/omero_zarr/masks.py |  4 ++--
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/README.rst b/README.rst
index 8972c62..50c66b8 100644
--- a/README.rst
+++ b/README.rst
@@ -68,24 +68,25 @@ Masks and Polygons
 
 To export Masks or Polygons for an Image or Plate, use the `masks` or `polygons` command::
 
-    # Saved under 1.zarr/labels/0 - 1.zarr/ must already exist
+    # Saved under 1.ome.zarr/labels/0
+    # 1.ome.zarr/ should already exist or specify path with --source-image
     $ omero zarr masks Image:1
 
-    # Labels saved under each image. e.g 2.zarr/A/1/0/labels/0
-    # Plate should already be exported
+    # Labels saved under each image. e.g 2.ome.zarr/A/1/0/labels/0
+    # 2.ome.zarr should already be exported or specify path with --source-image
     $ omero zarr masks Plate:2
 
-    # Saved under zarr_files/1.zarr/labels/0
+    # Saved under zarr_files/1.ome.zarr/labels/0
     $ omero zarr --output /home/user/zarr_files masks Image:1
 
     # Specify the label-name. (default is '0')
-    # e.g. Export to 1.zarr/labels/A
+    # e.g. Export to 1.ome.zarr/labels/A
     $ omero zarr masks Image:1 --label-name=A
 
     # Allow overlapping masks or polygons (overlap will be maximum value of the dtype)
     $ omero zarr polygons Image:1 --overlaps=dtype_max
 
-The default behaviour is to export all masks or polygons on the Image to a single 5D
+The default behaviour is to export all masks or polygons on the Image to a single nD
 "labeled" zarr array, with a different value for each Shape.
 An exception will be thrown if any of the masks overlap, unless the `--overlaps`
 option is used as above.
diff --git a/src/omero_zarr/masks.py b/src/omero_zarr/masks.py
index d54a07d..bf8e668 100644
--- a/src/omero_zarr/masks.py
+++ b/src/omero_zarr/masks.py
@@ -289,9 +289,9 @@ def save(self, masks: List[omero.model.Shape], name: str) -> None:
                 ignored_dimensions.add(d)
 
         if self.plate:
-            filename = f"{self.plate.id}.zarr"
+            filename = f"{self.plate.id}.ome.zarr"
         else:
-            filename = f"{self.image.id}.zarr"
+            filename = f"{self.image.id}.ome.zarr"
 
         # Verify that we are linking this mask to a real ome-zarr
         source_image = self.source_image