merge master -Dorg -Ssuccess-only: PR 147 (Name option)

Author: snoopycrimecop

README.rst

@@ -12,16 +12,15 @@ from OMERO as zarr files, according to the spec at
 https://github.com/ome/omero-ms-zarr/blob/master/spec.md
 as well as Masks associated with Images.
 
-Images are 5D arrays of shape `(t, c, z, y, x)`.
+Images are nD arrays of shape, up to `(t, c, z, y, x)`.
 Plates are a hierarchy of `plate/row/column/field(image)`.
 Masks are 2D bitmasks which can exist on muliplte planes of an Image.
 In `ome-zarr` sets of Masks are collected together into "labels".
 
 It supports export using 2 alternative methods:
 
 - By default the OMERO API is used to load planes as numpy arrays
-  and the zarr file is created from this data. NB: currently, large
-  tiled images are not supported by this method.
+  and the zarr file is created from this data.
 
 - Alternatively, if you can read directly from the OMERO binary
   repository and have installed https://github.com/glencoesoftware/bioformats2raw
@@ -37,16 +36,19 @@ Images and Plates
 To export Images or Plates via the OMERO API::
 
 
-    # Image will be saved in current directory as 1.zarr
+    # Image will be saved in current directory as 1.ome.zarr
     $ omero zarr export Image:1
 
-    # Plate will be saved in current directory as 2.zarr
+    # Plate will be saved in current directory as 2.ome.zarr
     $ omero zarr export Plate:2
 
+    # Use the Image or Plate 'name' to save e.g. my_image.ome.zarr
+    $ omero zarr --name_by name export Image:1
+
     # Specify an output directory
     $ omero zarr --output /home/user/zarr_files export Image:1
 
-    # By default, a tile size of 1024 is used. Specify values with
+    # By default, a tile (chunk) size of 1024 is used. Specify values with
     $ omero zarr export Image:1 --tile_width 256 --tile_height 256
 
 
@@ -66,24 +68,28 @@ 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...
     $ omero zarr masks Image:1
 
-    # Labels saved under each image. e.g 2.zarr/A/1/0/labels/0
-    # Plate should already be exported
+    # ...or specify path with --source-image
+    $ omero zarr masks Image:1 --source-image my_image.ome.zarr
+
+    # 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.

src/omero_zarr/cli.py

@@ -278,6 +278,15 @@ def _configure(self, parser: Parser) -> None:
             default=None,
             help="Maximum number of workers (only for use with bioformats2raw)",
         )
+        export.add_argument(
+            "--name_by",
+            default="id",
+            choices=["id", "name"],
+            help=(
+                "How to name the Image or Plate zarr. Default 'id' is [ID].ome.zarr. "
+                "'name' is [NAME].ome.zarr"
+            ),
+        )
         export.add_argument(
             "object",
             type=ProxyStringType("Image"),

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

src/omero_zarr/raw_pixels.py

@@ -41,12 +41,29 @@
 from .util import marshal_axes, marshal_transformations, open_store, print_status
 
 
-def image_to_zarr(image: omero.gateway.ImageWrapper, args: argparse.Namespace) -> None:
+def sanitize_name(zarr_name: str) -> str:
+    # Avoids re.compile errors when writing Zarr data with the named root
+    # https://github.com/ome/omero-cli-zarr/pull/147#issuecomment-1669075660
+    return zarr_name.replace("[", "(").replace("]", ")")
+
+
+def get_zarr_name(
+    obj: omero.gateway.BlitzObjectWrapper, args: argparse.Namespace
+) -> str:
     target_dir = args.output
+    name_by = args.name_by
+    if name_by == "name":
+        obj_name = sanitize_name(obj.name)
+        name = os.path.join(target_dir, "%s.ome.zarr" % obj_name)
+    else:
+        name = os.path.join(target_dir, "%s.ome.zarr" % obj.id)
+    return name
+
+
+def image_to_zarr(image: omero.gateway.ImageWrapper, args: argparse.Namespace) -> None:
     tile_width = args.tile_width
     tile_height = args.tile_height
-
-    name = os.path.join(target_dir, "%s.zarr" % image.id)
+    name = get_zarr_name(image, args)
     print(f"Exporting to {name} ({VERSION})")
     store = open_store(name)
     root = open_group(store)
@@ -243,9 +260,8 @@ def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace)
     n_cols = gs["columns"]
     n_fields = plate.getNumberOfFields()
     total = n_rows * n_cols * (n_fields[1] - n_fields[0] + 1)
+    name = get_zarr_name(plate, args)
 
-    target_dir = args.output
-    name = os.path.join(target_dir, "%s.zarr" % plate.id)
     store = open_store(name)
     print(f"Exporting to {name} ({VERSION})")
     root = open_group(store)
@@ -296,6 +312,8 @@ def plate_to_zarr(plate: omero.gateway._PlateWrapper, args: argparse.Namespace)
             print_status(int(t0), int(time.time()), count, total)
 
         # Update plate_metadata after each Well
+        if len(well_paths) == 0:
+            continue
         write_plate_metadata(
             root,
             row_names,

src/omero_zarr/util.py

@@ -32,7 +32,7 @@ def print_status(t0: int, t: int, count: int, total: int) -> None:
     """
     percent_done = float(count) * 100 / total
     dt = t - t0
-    if dt > 0:
+    if dt > 0 and count > 0:
         rate = float(count) / (t - t0)
         eta_f = float(total - count) / rate
         eta = time.strftime("%H:%M:%S", time.gmtime(eta_f))