From de199659765ea3dbfbf959f90e20eee35c5d5dd1 Mon Sep 17 00:00:00 2001
From: Dominik Lindner <d.lindner@dundee.ac.uk>
Date: Wed, 10 Jun 2020 19:50:20 +0100
Subject: [PATCH] Add method to create masks grouped by label id

---
 src/omero_rois/library.py | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/src/omero_rois/library.py b/src/omero_rois/library.py
index 55a7a6c..f6cac60 100644
--- a/src/omero_rois/library.py
+++ b/src/omero_rois/library.py
@@ -134,3 +134,37 @@ def masks_from_label_image(
                                       raise_on_no_mask)
         masks.append(mask)
     return masks
+
+
+def masks_from_3d_label_image(
+      planes, rgba=None, c=None, t=None, text=None,
+      raise_on_no_mask=True):
+    """
+    Create mask shapes from a 3d label image (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 c: Optional C-index for the mask
+    :param t: Optional T-index for the mask
+    :param text: Optional text for the mask
+    :param raise_on_no_mask: If True (default) throw an exception if no mask
+           found, otherwise return an empty Mask
+    :return: A dictionary of OMERO masks with the labels as keys
+           ({} if no labels found)
+
+    """
+    maxlabel = 1
+    for plane in planes:
+        pmax = plane.max()
+        if pmax > maxlabel:
+            maxlabel = pmax
+
+    masks = {}
+    for label in range(1, maxlabel + 1):
+        label_masks = []
+        for z, plane in enumerate(planes):
+            mask = mask_from_binary_image(plane == label, rgba, z, c, t, text,
+                                          raise_on_no_mask)
+            label_masks.append(mask)
+        masks[label] = label_masks
+    return masks