CellProfiler-nightly 5.0.0.dev324__py3-none-any.whl → 5.0.0.dev332__py3-none-any.whl

cellprofiler/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '5.0.0.dev324'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev324')
+__version__ = version = '5.0.0.dev332'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev332')
 
 __commit_id__ = commit_id = None

cellprofiler/modules/dilateimage.py

@@ -17,9 +17,8 @@ YES          YES          NO
 from cellprofiler_core.module import ImageProcessing
 from cellprofiler_core.setting import StructuringElement
 
-import cellprofiler.utilities.morphology
 from ._help import HELP_FOR_STREL
-
+from cellprofiler_library.modules._dilateimage import dilate_image
 
 class DilateImage(ImageProcessing):
     category = "Advanced"
@@ -46,6 +45,5 @@ class DilateImage(ImageProcessing):
         return __settings__ + [self.structuring_element]
 
     def run(self, workspace):
-        self.function = cellprofiler.utilities.morphology.dilation
-
+        self.function = dilate_image
         super(DilateImage, self).run(workspace)

cellprofiler/modules/erodeobjects.py

@@ -23,16 +23,12 @@ YES          YES          NO
 
 """
 
-import numpy
-import scipy.ndimage
-import skimage.measure
-import skimage.morphology
 from cellprofiler_core.module.image_segmentation import ObjectProcessing
 from cellprofiler_core.object import Objects
 from cellprofiler_core.setting import StructuringElement, Binary
 
-import cellprofiler.utilities.morphology
 from cellprofiler.modules._help import HELP_FOR_STREL
+from cellprofiler_library.modules._erodeobjects import erode_objects
 
 
 class ErodeObjects(ObjectProcessing):
@@ -94,24 +90,14 @@ label numbers.""",
         y_name = self.y_name.value
         objects = workspace.object_set
         x = objects.get_objects(x_name)
-        dimensions = x.dimensions
         x_data = x.segmented
 
-        contours = cellprofiler.utilities.morphology.morphological_gradient(x_data, self.structuring_element.value)
-        y_data = x_data * (contours == 0)
-
-        if self.preserve_midpoints.value:
-            missing_labels = numpy.setxor1d(x_data, y_data)
-            if self.structuring_element.value_text == "Disk,1":
-                y_data += x_data * numpy.isin(x_data, missing_labels)
-            else:
-                for label in missing_labels:
-                    binary = x_data == label
-                    midpoint = scipy.ndimage.morphology.distance_transform_edt(binary)
-                    y_data[midpoint == numpy.max(midpoint)] = label
-
-        if self.relabel_objects.value:
-            y_data = skimage.morphology.label(y_data)
+        y_data = erode_objects(
+            labels=x_data,
+            structuring_element=self.structuring_element.value,
+            preserve_midpoints=self.preserve_midpoints.value,
+            relabel_objects=self.relabel_objects.value
+        )
 
         y = Objects()
         y.segmented = y_data
@@ -122,4 +108,4 @@ label numbers.""",
         if self.show_window:
             workspace.display_data.x_data = x_data
             workspace.display_data.y_data = y_data
-            workspace.display_data.dimensions = dimensions
+            workspace.display_data.dimensions = x.dimensions

{cellprofiler_nightly-5.0.0.dev324.dist-info → cellprofiler_nightly-5.0.0.dev332.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev324
+Version: 5.0.0.dev332
 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.dev324.dist-info → cellprofiler_nightly-5.0.0.dev332.dist-info}/RECORD

@@ -1,6 +1,6 @@
 cellprofiler/__init__.py,sha256=AL2XeOBhIeYkBRyDd0QRgJan7j0DKjT1GD-RdzKvMUY,46
 cellprofiler/__main__.py,sha256=uy78oz5c6NBGRwDZkZ2Gl4HfhbJZQH6K1n54Qfl2OFc,38075
-cellprofiler/_version.py,sha256=X_dsIS438JBC3vSFB9YEnaGPIPrvCqTB7mibbwXlkv0,721
+cellprofiler/_version.py,sha256=NfpldqGmqBug3AODFm5JWZ6AHxP27dqT2kCCX1xJJuI,721
 cellprofiler/knime_bridge.py,sha256=T6Op-KO79oULx92nGXRQ6lHsEcTutx1Uep1L4ZOKJgc,27767
 cellprofiler/misc.py,sha256=yqv873lP_mquxxkKcLgE_ZU4Hrc1trtuQ-NXLK2qQVc,553
 cellprofiler/data/examples/ExampleFly/ExampleFly.cppipe,sha256=JGZK9IZuYlOHOI4hi6a3DK36IahY69cfeLEd7eJ_rO0,15409
@@ -292,7 +292,7 @@ cellprofiler/modules/correctilluminationcalculate.py,sha256=wJMCy3W9zK-xPI8PUvh2
 cellprofiler/modules/createbatchfiles.py,sha256=a8R5PpbaQYqF8OIvWBuC0uh-yhjzBaU4Uni4m3MRLok,19512
 cellprofiler/modules/crop.py,sha256=gnAHZNjPCNr-RLc7xQjZYViRpmKCTfJjuZ8MwHRiT1Y,34177
 cellprofiler/modules/definegrid.py,sha256=tjYcrzHu6TV7rkh1l2T0pNqcjBLwCfz9BCqTPWhQr_A,47160
-cellprofiler/modules/dilateimage.py,sha256=xcdsDdgvuplD69pcyJTOmVTxXFlwDWRNxapoQZHTiVc,1382
+cellprofiler/modules/dilateimage.py,sha256=b9VAqHtvynAKog-Zy7X8qapqqSaJzWuUQMiiNVtzrxY,1376
 cellprofiler/modules/dilateobjects.py,sha256=lnipjKkd6A3hhY3G1ttU9ZlhsTZp3oVU-QnU7_ayWbE,1828
 cellprofiler/modules/displaydataonimage.py,sha256=8WWaEniPbt9Z8zP_vzPyCHXjf9TMkPFyd3v3Agypcr4,22720
 cellprofiler/modules/displaydensityplot.py,sha256=a2te0z0t76y_rN0FFWmk8eFpZYR-t0r1ohAl9mx5BIg,7531
@@ -303,7 +303,7 @@ cellprofiler/modules/editobjectsmanually.py,sha256=fkTFMTlrTfIiHNhhPzYsfFvZBSBDE
 cellprofiler/modules/enhanceedges.py,sha256=bivBs2OMNYvNnJ7tYrs9yheJP9JGIkgJDQfB2u837HE,11398
 cellprofiler/modules/enhanceorsuppressfeatures.py,sha256=vc_LLANt2gEsntqog9JwbzCVaaBQEM3ayvvY7CSJCF0,24062
 cellprofiler/modules/erodeimage.py,sha256=GGO6EjgA_6A0pjrsATxcfs1a_QmZ1rS5Lec7Kkb21hw,1402
-cellprofiler/modules/erodeobjects.py,sha256=cDQR8y7XqSt-ssp1nAQp3wXdQk5OE1uT7GrhTgjfdlI,4381
+cellprofiler/modules/erodeobjects.py,sha256=vajQ5ikn0i6hw8PkqAGcuIjJCDdzHYv0AtP_A5TV_-U,3792
 cellprofiler/modules/expandorshrinkobjects.py,sha256=fiFf4q2BplR4u6Cym-jdlOOdOKc6oZVtEkZE-O-Ansg,13911
 cellprofiler/modules/exporttodatabase.py,sha256=Tb5Hf329m96zUNaxPStQoTkr_MV62HGNBetZL_Y1iyk,217927
 cellprofiler/modules/exporttospreadsheet.py,sha256=ikY_XNGI7SZ-DyIIWcf5FCWzPqx1VZLOOJCsCk3zyTs,67607
@@ -374,9 +374,9 @@ cellprofiler/modules/plugins/segmentationtemplatewithdependencies.py,sha256=Sh76
 cellprofiler/utilities/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellprofiler/utilities/morphology.py,sha256=8-81TrP8AmE3ETXIvQUKFD1vmKNBy2lfbc1QnM1eGIM,2685
 cellprofiler/utilities/rules.py,sha256=NoIHwFTA37zGvIP7vcB-aYeys0MDYVYxspfhLJe00OU,8790
-cellprofiler_nightly-5.0.0.dev324.dist-info/licenses/LICENSE,sha256=QLWaBS7kAioYx7PmJNXAMJaY8NODcFAag60YlUWuyz0,2276
-cellprofiler_nightly-5.0.0.dev324.dist-info/METADATA,sha256=rcJmOQxLnbrpJc0xxW9H88YMgZrJgDMvTA-W-YDrcPE,6063
-cellprofiler_nightly-5.0.0.dev324.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-cellprofiler_nightly-5.0.0.dev324.dist-info/entry_points.txt,sha256=MNDCjguFW3dKiS5Pcdu1NfWo4I0HHI3DekJLUJ4AKkY,60
-cellprofiler_nightly-5.0.0.dev324.dist-info/top_level.txt,sha256=bK7AacDeSj9qAmW8MGlO5wA79hDj6-ACt_mENUNKSIk,13
-cellprofiler_nightly-5.0.0.dev324.dist-info/RECORD,,
+cellprofiler_nightly-5.0.0.dev332.dist-info/licenses/LICENSE,sha256=QLWaBS7kAioYx7PmJNXAMJaY8NODcFAag60YlUWuyz0,2276
+cellprofiler_nightly-5.0.0.dev332.dist-info/METADATA,sha256=mbvouhW6H7MSYdw1LEqTVdjFYxUnrnvaxYf7Z0HQRV0,6063
+cellprofiler_nightly-5.0.0.dev332.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+cellprofiler_nightly-5.0.0.dev332.dist-info/entry_points.txt,sha256=MNDCjguFW3dKiS5Pcdu1NfWo4I0HHI3DekJLUJ4AKkY,60
+cellprofiler_nightly-5.0.0.dev332.dist-info/top_level.txt,sha256=bK7AacDeSj9qAmW8MGlO5wA79hDj6-ACt_mENUNKSIk,13
+cellprofiler_nightly-5.0.0.dev332.dist-info/RECORD,,