cellprofiler-library-nightly 5.0.0.dev337__tar.gz → 5.0.0.dev343__tar.gz

{cellprofiler_library_nightly-5.0.0.dev337 → cellprofiler_library_nightly-5.0.0.dev343}/PKG-INFO

@@ -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 → cellprofiler_library_nightly-5.0.0.dev343}/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 = 'g6c4ae2cb6'
+__commit_id__ = commit_id = 'gc6a344488'

{cellprofiler_library_nightly-5.0.0.dev337 → cellprofiler_library_nightly-5.0.0.dev343}/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_nightly-5.0.0.dev343/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_nightly-5.0.0.dev343/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 → cellprofiler_library_nightly-5.0.0.dev343}/cellprofiler_library_nightly.egg-info/PKG-INFO

@@ -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 → cellprofiler_library_nightly-5.0.0.dev343}/cellprofiler_library_nightly.egg-info/SOURCES.txt

@@ -21,6 +21,7 @@ cellprofiler_library/modules/_convertobjectstoimage.py
 cellprofiler_library/modules/_correctilluminationapply.py
 cellprofiler_library/modules/_crop.py
 cellprofiler_library/modules/_dilateimage.py
+cellprofiler_library/modules/_dilateobjects.py
 cellprofiler_library/modules/_enhanceedges.py
 cellprofiler_library/modules/_enhanceorsuppressfeatures.py
 cellprofiler_library/modules/_erodeimage.py
@@ -46,6 +47,7 @@ cellprofiler_library/opts/convertobjectstoimage.py
 cellprofiler_library/opts/correctilluminationapply.py
 cellprofiler_library/opts/crop.py
 cellprofiler_library/opts/dilateimage.py
+cellprofiler_library/opts/dilateobjects.py
 cellprofiler_library/opts/enhanceorsuppressfeatures.py
 cellprofiler_library/opts/erodeimage.py
 cellprofiler_library/opts/erodeobjects.py