Add method to create masks grouped by label id

src/omero_rois/library.py

@@ -18,6 +18,7 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 
 import numpy as np
+from collections import defaultdict
 from omero.gateway import ColorHolder
 from omero.model import MaskI
 from omero.rtypes import (
@@ -134,3 +135,35 @@ def masks_from_label_image(
                                       raise_on_no_mask)
         masks.append(mask)
     return masks
+
+
+def masks_from_3d_label_image(
+      planes, rgba=None, z=None, c=None, z_stack=True, t=None, text=None):
+    """
+    Create mask shapes from a 3d label image, either z stack or timepoints,
+    grouped by label ID (background=0)
+
+    :param list of numpy.array planes: list of 2D label arrays in z order
+    :param rgba int-4-tuple: Optional (red, green, blue, alpha) colour
+    :param z: Optional Z-index for the mask
+    :param c: Optional C-index for the mask
+    :param t: Optional T-index for the mask
+    :param z_stack: Flag if the planes represent a z stack, timepoints
+                    otherwise (default: True)
+    :param text: Optional text for the mask
+    :return: A dictionary of OMERO masks with the labels as keys
+           ({} if no labels found)
+
+    """
+    masks = defaultdict(list)
+    for i, plane in enumerate(planes):
+        if z_stack:
+            plane_masks = masks_from_label_image(plane, rgba, i, c, t,
+                                                 text, False)
+        else:
+            plane_masks = masks_from_label_image(plane, rgba, z, c, i,
+                                                 text, False)
+        for label, mask in enumerate(plane_masks):
+            if mask.getBytes().any():
+                masks[label].append(mask)
+    return masks