add --allow_overlaps arg to cli

README.rst

@@ -59,10 +59,10 @@ To export images via bioformats2raw we use the ```--bf``` flag::
     $ omero zarr --output /home/user/zarr_files export 1 --bf
     Image exported to /home/user/zarr_files/2chZT.lsm
 
-Masks
-^^^^^
+Masks and Polygons
+^^^^^^^^^^^^^^^^^^
 
-To export Masks for an Image or Plate::
+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
     $ omero zarr masks Image:1
@@ -78,12 +78,16 @@ To export Masks for an Image or Plate::
     # e.g. Export to 1.zarr/labels/A
     $ omero zarr masks Image:1 --label-name=A
 
-The default behaviour is to export all masks on the Image to a single 5D
-"labeled" zarr array, with a different value for each mask Shape.
-An exception will be thrown if any of the masks overlap.
+    # Allow overlapping masks or polygons (overlap will be maximum value of the dtype)
+    $ omero zarr polygons Image:1 --overlaps=dtype_max
 
-To handle overlapping masks, split masks into non-overlapping zarr groups
-using a "label-map" which is a csv file of that specifies the name of
+The default behaviour is to export all masks or polygons on the Image to a single 5D
+"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.
+
+An alternative to handle overlapping masks is to split masks into non-overlapping zarr
+groups using a "label-map" which is a csv file that specifies the name of
 the zarr group for each ROI on the Image. Columns are ID, NAME, ROI_ID.
 
 For example, to create a group from the `textValue` of each Shape,

src/omero_zarr/cli.py

@@ -11,7 +11,12 @@
 from zarr.hierarchy import open_group
 from zarr.storage import FSStore
 
-from .masks import MASK_DTYPE_SIZE, image_shapes_to_zarr, plate_shapes_to_zarr
+from .masks import (
+    MASK_DTYPE_SIZE,
+    MaskSaver,
+    image_shapes_to_zarr,
+    plate_shapes_to_zarr,
+)
 from .raw_pixels import (
     add_omero_metadata,
     add_toplevel_metadata,
@@ -272,6 +277,16 @@ def _configure(self, parser: Parser) -> None:
             subcommand.add_argument(
                 "--output", type=str, default="", help="The output directory"
             )
+        for subcommand in (polygons, masks):
+            subcommand.add_argument(
+                "--overlaps",
+                type=str,
+                default=MaskSaver.OVERLAPS[0],
+                choices=MaskSaver.OVERLAPS,
+                help="To allow overlapping shapes, use 'dtype_max':"
+                " All overlapping regions will be set to the"
+                " max value for the dtype",
+            )
 
     @gateway_required
     def masks(self, args: argparse.Namespace) -> None:

src/omero_zarr/masks.py

@@ -62,7 +62,13 @@ def plate_shapes_to_zarr(
 
     dtype = MASK_DTYPE_SIZE[int(args.label_bits)]
     saver = MaskSaver(
-        plate, None, dtype, args.label_path, args.style, args.source_image
+        plate,
+        None,
+        dtype,
+        args.label_path,
+        args.style,
+        args.source_image,
+        args.overlaps,
     )
 
     count = 0
@@ -154,7 +160,13 @@ def image_shapes_to_zarr(
 
     if masks:
         saver = MaskSaver(
-            None, image, dtype, args.label_path, args.style, args.source_image
+            None,
+            image,
+            dtype,
+            args.label_path,
+            args.style,
+            args.source_image,
+            args.overlaps,
         )
 
         if args.style == "split":
@@ -178,6 +190,8 @@ class MaskSaver:
     masks to zarr groups/arrays.
     """
 
+    OVERLAPS = ["error", "dtype_max"]
+
     def __init__(
         self,
         plate: Optional[omero.gateway.PlateWrapper],
@@ -186,13 +200,15 @@ def __init__(
         path: str = "labels",
         style: str = "labeled",
         source: str = "..",
+        overlaps: str = "error",
     ) -> None:
         self.dtype = dtype
         self.path = path
         self.style = style
         self.source_image = source
         self.plate = plate
         self.plate_path = Optional[str]
+        self.overlaps = overlaps
         if image:
             self.image = image
             self.size_t = image.getSizeT()
@@ -302,7 +318,6 @@ def save(self, masks: List[omero.model.Shape], name: str) -> None:
             masks,
             mask_shape,
             ignored_dimensions,
-            check_overlaps=True,
         )
 
         axes = marshal_axes(self.image)
@@ -433,7 +448,7 @@ def masks_to_labels(
         masks: List[omero.model.Mask],
         mask_shape: Tuple[int, ...],
         ignored_dimensions: Set[str] = None,
-        check_overlaps: bool = True,
+        check_overlaps: bool = None,
     ) -> Tuple[np.ndarray, Dict[int, str], Dict[int, Dict]]:
         """
         :param masks [MaskI]: Iterable container of OMERO masks
@@ -464,6 +479,11 @@ def masks_to_labels(
         sorted_roi_ids = list(set(roi_ids))
         sorted_roi_ids.sort()
 
+        if check_overlaps is None:
+            # If overlaps isn't 'dtype_max', an exception is thrown
+            # if any overlaps exist
+            check_overlaps = self.overlaps != "dtype_max"
+
         # label values are 1...n
         max_value = len(sorted_roi_ids)
         # find most suitable dtype...
@@ -512,22 +532,27 @@ def masks_to_labels(
                         for i_z in self._get_indices(
                             ignored_dimensions, "Z", z, size_z
                         ):
-                            if check_overlaps and np.any(
-                                np.logical_and(
-                                    labels[
-                                        i_t, i_c, i_z, y : (y + h), x : (x + w)
-                                    ].astype(np.bool),
-                                    binim_yx,
-                                )
-                            ):
-                                raise Exception(
-                                    f"Mask {shape.roi.id.val} overlaps "
-                                    "with existing labels"
-                                )
+                            overlap = np.logical_and(
+                                labels[i_t, i_c, i_z, y : (y + h), x : (x + w)].astype(
+                                    np.bool
+                                ),
+                                binim_yx,
+                            )
                             # ADD to the array, so zeros in our binarray don't
                             # wipe out previous shapes
                             labels[i_t, i_c, i_z, y : (y + h), x : (x + w)] += (
                                 binim_yx * shape_value
                             )
 
+                            if np.any(overlap):
+                                if check_overlaps:
+                                    raise Exception(
+                                        f"Shape {shape.roi.id.val} overlaps "
+                                        "with existing labels"
+                                    )
+                                else:
+                                    # set overlapping region to max(dtype)
+                                    labels[i_t, i_c, i_z, y : (y + h), x : (x + w)][
+                                        overlap
+                                    ] = np.iinfo(labels_dtype).max
         return labels, fillColors, properties