cellprofiler-library-nightly 5.0.0.dev337__py3-none-any.whl → 5.0.0.dev343__py3-none-any.whl

cellprofiler_library/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '5.0.0.dev337'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev337')
+__version__ = version = '5.0.0.dev343'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev343')
 
 __commit_id__ = commit_id = None

cellprofiler_library/functions/object_processing.py

@@ -629,3 +629,50 @@ def erode_objects_with_structuring_element(
     
     return y_data
 
+################################################################################
+# DilateObjects
+################################################################################
+
+def dilate_objects_with_structuring_element(
+    labels: ObjectSegmentation,
+    structuring_element: StructuringElement
+) -> ObjectSegmentation:
+    """Dilate objects based on the structuring element provided.
+    
+    This function is similar to the "Expand" function of ExpandOrShrinkObjects,
+    with two major distinctions:
+    1. DilateObjects supports 3D objects, unlike ExpandOrShrinkObjects.
+    2. In ExpandOrShrinkObjects, two objects closer than the expansion distance
+       will expand until they meet and then stop there. In this module, the object with
+       the larger object number (the object that is lower in the image) will be expanded
+       on top of the object with the smaller object number.
+    
+    Args:
+        labels: Input labeled objects array
+        structuring_element: Structuring element for dilation operation
+        
+    Returns:
+        Dilated objects array with same dimensions as input
+    """
+    is_strel_2d = structuring_element.ndim == 2
+
+    is_img_2d = labels.ndim == 2
+
+    if is_strel_2d and not is_img_2d:
+        y_data = numpy.zeros_like(labels)
+
+        for index, plane in enumerate(labels):
+
+            y_data[index] = skimage.morphology.dilation(plane, structuring_element)
+
+        return y_data
+
+    if not is_strel_2d and is_img_2d:
+        raise NotImplementedError(
+            "A 3D structuring element cannot be applied to a 2D image."
+        )
+
+    y_data = skimage.morphology.dilation(labels, structuring_element)
+    
+    return y_data
+

cellprofiler_library/modules/_dilateobjects.py

@@ -0,0 +1,46 @@
+# coding=utf-8
+
+"""
+DilateObjects module for the CellProfiler library.
+
+This module contains the core algorithms for object dilation operations.
+"""
+
+from pydantic import validate_call, ConfigDict, Field
+from typing import Union, Tuple, Annotated
+from cellprofiler_library.types import StructuringElement, ObjectSegmentation
+from cellprofiler_library.functions.object_processing import dilate_objects_with_structuring_element
+from cellprofiler_library.functions.image_processing import get_structuring_element
+from cellprofiler_library.opts.structuring_elements import StructuringElementShape2D, StructuringElementShape3D
+
+StructuringElementSize = Annotated[int, Field(description="Size of structuring element", gt=0)]
+StructuringElementParameters = Tuple[Union[StructuringElementShape2D, StructuringElementShape3D], StructuringElementSize]
+
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
+def dilate_objects(
+    labels: Annotated[ObjectSegmentation, Field(description="Input object segmentations")],
+    structuring_element: Annotated[Union[StructuringElement, StructuringElementParameters], Field(description="Structuring element for dilation operation as either an NDArray or a tuple of (StructuringElement[N]D, size)")],
+) -> ObjectSegmentation:
+    """Dilate objects based on the structuring element provided.
+    
+    This function is similar to the "Expand" function of ExpandOrShrinkObjects,
+    with two major distinctions:
+    1. DilateObjects supports 3D objects, unlike ExpandOrShrinkObjects.
+    2. In ExpandOrShrinkObjects, two objects closer than the expansion distance
+       will expand until they meet and then stop there. In this module, the object with
+       the larger object number (the object that is lower in the image) will be expanded
+       on top of the object with the smaller object number.
+    
+    Args:
+        labels: Input labeled objects array
+        structuring_element: Structuring element for dilation operation
+        
+    Returns:
+        Dilated objects array with same dimensions as input
+    """
+    if isinstance(structuring_element, tuple):
+        structuring_element = get_structuring_element(structuring_element[0], structuring_element[1])
+    return dilate_objects_with_structuring_element(
+        labels=labels,
+        structuring_element=structuring_element
+    )

cellprofiler_library/opts/dilateobjects.py

@@ -0,0 +1,15 @@
+# coding=utf-8
+
+"""
+Options and enums for DilateObjects module
+"""
+
+# Note: DilateObjects is a simple morphological operation module that doesn't require
+# complex enums. The main configuration is handled through the StructuringElement
+# setting which is managed by the core framework. This file is created for 
+# consistency with the refactoring pattern but may be minimal.
+
+# Currently no custom enums needed for DilateObjects as it uses standard
+# StructuringElement configuration from cellprofiler_core. For structuring element shapes,
+# see cellprofiler_library.opts.structuring_elements
+

{cellprofiler_library_nightly-5.0.0.dev337.dist-info → cellprofiler_library_nightly-5.0.0.dev343.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev337
+Version: 5.0.0.dev343
 Summary: cellprofiler-library implements CellProfiler's image processing and mathematical code, and is usable as a standalone library
 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_library_nightly-5.0.0.dev337.dist-info → cellprofiler_library_nightly-5.0.0.dev343.dist-info}/RECORD

@@ -1,12 +1,12 @@
 cellprofiler_library/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellprofiler_library/_version.py,sha256=uqhbZqMaLWPM_eN5M1IR2mS3YSSFhvbkhyhU3mlT590,721
+cellprofiler_library/_version.py,sha256=hHfirX4ltVJs32-gRsCUTurfTDi5DV9l3kEHu8iRv4A,721
 cellprofiler_library/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellprofiler_library/types.py,sha256=cU38AwLLsMiI3XCwfrmWmDNpGWgLfpCpsuwnijaT8vU,8559
 cellprofiler_library/functions/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellprofiler_library/functions/file_processing.py,sha256=jumpdgxReyV5xzF4YXZWhkei9CQ9GtWD-VUCuFh-FZM,5168
 cellprofiler_library/functions/image_processing.py,sha256=d9T0Ro2BaOS9Y9CrNgqUlOjUHTJVLnxOG696IWeLQeg,43556
 cellprofiler_library/functions/measurement.py,sha256=8pXcEb1fLgwOEDiTJho1_O-fFGTtIp-Qn1lStjQBjbo,29221
-cellprofiler_library/functions/object_processing.py,sha256=5yHR_toKMH0KfWPAtEESQfK9JOdaD3L7WZskjGyoZ2o,23209
+cellprofiler_library/functions/object_processing.py,sha256=5dPl8PWRSJbPLWjxV0kCRZDKLCg0tJCTmRnRd1CXys4,24897
 cellprofiler_library/functions/segmentation.py,sha256=LNE22ByY0X7GepQaHqLdxkzlmIXjD3EglAYJjtT2dGo,25257
 cellprofiler_library/modules/__init__.py,sha256=Z4Wy42OTD9ujAON4g1oyLJ0oA6K7h3XQiV66JzHGkOw,789
 cellprofiler_library/modules/_closing.py,sha256=aIqIE0IcT2OcrOmTSWjFzu4iIQKk2yDC9qPHARqRIkc,204
@@ -17,6 +17,7 @@ cellprofiler_library/modules/_convertobjectstoimage.py,sha256=PMYjH_prBKma4LNgUx
 cellprofiler_library/modules/_correctilluminationapply.py,sha256=8bZC3AnQv3vpUrNSnLvcc_s0E-P63XbrfwMv7OZNjt4,2084
 cellprofiler_library/modules/_crop.py,sha256=0T0sQsK7o5dHVXMZ4OqvAJkskkyez1MXcnPlU5yqsV4,2422
 cellprofiler_library/modules/_dilateimage.py,sha256=9mdB3Ft7muCkArTcEebs-Dz7_Ptg3YZsdL1qkr9K_0o,1812
+cellprofiler_library/modules/_dilateobjects.py,sha256=lq5uY8uogp1CcVPVOXSLUfpxcw0ZRUFk8P8PwoksfW0,2338
 cellprofiler_library/modules/_enhanceedges.py,sha256=PaXZck8fPcxRf-IXCstu-OWmsvM_rDDPMMQ3cZFfVZc,2951
 cellprofiler_library/modules/_enhanceorsuppressfeatures.py,sha256=UkcJ2qM32hmnB_68yyjKmdaus78OXcpWi7E5OwRz9R8,3469
 cellprofiler_library/modules/_erodeimage.py,sha256=nFHn4hdpjXJaPvnpSyfPAxWgd7UXi0fUUgPqEl26CCY,1802
@@ -42,6 +43,7 @@ cellprofiler_library/opts/convertobjectstoimage.py,sha256=U3jeVtKYFgfxbO7NYndanA
 cellprofiler_library/opts/correctilluminationapply.py,sha256=IkAqjMjaRdsoY2aXw5_dLI1iRYqCwvcNwCWEpWNZrN4,96
 cellprofiler_library/opts/crop.py,sha256=GaArWq3WZd_Ykunj1SSbFOYkqDQ6TXy2MDKxG4fA6ZE,879
 cellprofiler_library/opts/dilateimage.py,sha256=KsRf7gTKzFcTcylfIBrwue9csKBtJZdbVPFT5P_OjOM,588
+cellprofiler_library/opts/dilateobjects.py,sha256=gQXrxyTtHYcVvAB5PrNlwBVNB6hsZ95Lcv4KQljZT1w,594
 cellprofiler_library/opts/enhanceorsuppressfeatures.py,sha256=8Ej5TFUX-EKTbUcV3AidcIaomwh_A9A5lNJVRu76pc4,449
 cellprofiler_library/opts/erodeimage.py,sha256=T3LCqu83rTqTDlc_7ebuPBKnr-FKomRHA8WD0uA9Y1g,584
 cellprofiler_library/opts/erodeobjects.py,sha256=jOooDWqy01qdh17nAF0nbluU1lPToO2ZZqqsAzj2iNg,591
@@ -49,8 +51,8 @@ cellprofiler_library/opts/measureimageoverlap.py,sha256=uopQCJTX1Uk-NNDAISsdYEOu
 cellprofiler_library/opts/objectsizeshapefeatures.py,sha256=3GIntOH3qXs7F16Tpjmtg7opHYAmmOjEdEwW6q3ht_Y,6306
 cellprofiler_library/opts/structuring_elements.py,sha256=Q4pBdCgDmjPx05t61Zqi40Iof8Nj3UR5k-F7brImLZY,263
 cellprofiler_library/opts/threshold.py,sha256=yg_i5to22Nd9hTakaRxo9UIQZRYWFpavJimjl5JONx4,938
-cellprofiler_library_nightly-5.0.0.dev337.dist-info/licenses/LICENSE,sha256=QLWaBS7kAioYx7PmJNXAMJaY8NODcFAag60YlUWuyz0,2276
-cellprofiler_library_nightly-5.0.0.dev337.dist-info/METADATA,sha256=lIKBVisf5Nx_AsUb84QM6RnhSzuUngvrS0wGzFRy4-w,5534
-cellprofiler_library_nightly-5.0.0.dev337.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-cellprofiler_library_nightly-5.0.0.dev337.dist-info/top_level.txt,sha256=LXq0ApDeDD4gotb6YFTySzdyScvHfS_pqoTg1QsNLBs,21
-cellprofiler_library_nightly-5.0.0.dev337.dist-info/RECORD,,
+cellprofiler_library_nightly-5.0.0.dev343.dist-info/licenses/LICENSE,sha256=QLWaBS7kAioYx7PmJNXAMJaY8NODcFAag60YlUWuyz0,2276
+cellprofiler_library_nightly-5.0.0.dev343.dist-info/METADATA,sha256=1ntqPcoI25QFWfqFcfG743HLq0n5_awtWK23WFMruLU,5534
+cellprofiler_library_nightly-5.0.0.dev343.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+cellprofiler_library_nightly-5.0.0.dev343.dist-info/top_level.txt,sha256=LXq0ApDeDD4gotb6YFTySzdyScvHfS_pqoTg1QsNLBs,21
+cellprofiler_library_nightly-5.0.0.dev343.dist-info/RECORD,,

{cellprofiler_library_nightly-5.0.0.dev337.dist-info → cellprofiler_library_nightly-5.0.0.dev343.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any