CellProfiler-nightly 5.0.0.dev306__tar.gz → 5.0.0.dev313__tar.gz

{cellprofiler_nightly-5.0.0.dev306 → cellprofiler_nightly-5.0.0.dev313}/CellProfiler_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev306
+Version: 5.0.0.dev313
 Summary: CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
 Author: Anne Carpenter, Thouis (Ray) Jones, Lee Kamentsky, Vebjorn Ljosa, David Logan, Mark Bray, Madison Swain-Bowden, Allen Goodman, Claire McQuinn, Alice Lucas, Callum Tromans-Coia
 Author-email: Beth Cimini <bcimini@broadinstitute.org>, David Stirling <dstirling@glencoesoftware.com>, Nodar Gogoberidze <ngogober@broadinstitute.org>

{cellprofiler_nightly-5.0.0.dev306 → cellprofiler_nightly-5.0.0.dev313}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev306
+Version: 5.0.0.dev313
 Summary: CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
 Author: Anne Carpenter, Thouis (Ray) Jones, Lee Kamentsky, Vebjorn Ljosa, David Logan, Mark Bray, Madison Swain-Bowden, Allen Goodman, Claire McQuinn, Alice Lucas, Callum Tromans-Coia
 Author-email: Beth Cimini <bcimini@broadinstitute.org>, David Stirling <dstirling@glencoesoftware.com>, Nodar Gogoberidze <ngogober@broadinstitute.org>

{cellprofiler_nightly-5.0.0.dev306 → cellprofiler_nightly-5.0.0.dev313}/cellprofiler/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '5.0.0.dev306'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev306')
+__version__ = version = '5.0.0.dev313'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev313')
 
-__commit_id__ = commit_id = 'g4a1da805d'
+__commit_id__ = commit_id = 'ge26d578fa'

{cellprofiler_nightly-5.0.0.dev306 → cellprofiler_nightly-5.0.0.dev313}/cellprofiler/modules/convertimagetoobjects.py

@@ -1,8 +1,7 @@
-import skimage
-import skimage.measure
 from cellprofiler_core.module.image_segmentation import ImageSegmentation
 from cellprofiler_core.setting import Binary
 from cellprofiler_core.setting.text import Integer
+from cellprofiler_library.modules._convertimagetoobjects import convert_image_to_objects
 
 HELP_BINARY_IMAGE = """\
 This module can also convert a grayscale image to binary before converting it to an object.
@@ -110,7 +109,12 @@ If set to 0, a full connectivity of the input dimension is used.
         return __settings__
 
     def run(self, workspace):
-        self.function = lambda data, cast_to_bool, preserve_label, background, connectivity: convert_to_objects(
+        def _validate_image(img):
+            if img.multichannel is not False:
+                raise TypeError("Input image should be grayscale")
+
+        self.validate_image = _validate_image
+        self.function = lambda data, cast_to_bool, preserve_label, background, connectivity: convert_image_to_objects(
             data, cast_to_bool, preserve_label, background, connectivity
         )
 
@@ -138,17 +142,3 @@ If set to 0, a full connectivity of the input dimension is used.
             x=1,
             y=0,
         )
-
-
-def convert_to_objects(data, cast_to_bool, preserve_label, background, connectivity):
-    # Compatibility with skimage
-    connectivity = None if connectivity == 0 else connectivity
-
-    caster = skimage.img_as_bool if cast_to_bool else skimage.img_as_uint
-    data = caster(data)
-
-    # If preservation is desired, just return the original labels
-    if preserve_label and not cast_to_bool:
-        return data
-
-    return skimage.measure.label(data, background=background, connectivity=connectivity)