Label imported objects sequentially (#81)

Author: David Stirling

cellprofiler_core/modules/namesandtypes.py

@@ -6,6 +6,7 @@
 
 import javabridge
 import numpy
+import skimage.morphology
 
 from ..constants.image import C_FRAME
 from ..constants.image import C_HEIGHT
@@ -2150,6 +2151,7 @@ def add_objects(self, workspace, name, stack):
         image = provider.provide_image(workspace.image_set)
         o = Objects()
         shape = image.pixel_data.shape
+        image.set_image(skimage.morphology.label(image.pixel_data), convert=False)
         if shape[2] == 1:
             o.segmented = image.pixel_data[:, :, 0]
             add_object_location_measurements(

tests/modules/test_namesandtypes.py

@@ -10,6 +10,7 @@
 import numpy
 import pytest
 import six
+import skimage.morphology
 import zlib
 
 import cellprofiler_core.constants.image
@@ -1911,6 +1912,8 @@ def test_load_objects():
         ["ExampleSBSImages"], "Channel2-01-A-01.tif"
     )
     target = bioformats.load_image(path, rescale=False)
+    target = skimage.morphology.label(target)
+
     with open(path, "rb") as fd:
         md5 = hashlib.md5(fd.read()).hexdigest()
     workspace = run_workspace(
@@ -2038,6 +2041,7 @@ def test_load_single_object():
         ["ExampleSBSImages"], "Channel2-01-A-01.tif"
     )
     target = bioformats.load_image(lsi_path, rescale=False)
+    target = skimage.morphology.label(target)
     with open(lsi_path, "rb") as fd:
         md5 = hashlib.md5(fd.read()).hexdigest()
     workspace = run_workspace(