cellprofiler-library-nightly 5.0.0.dev321__py3-none-any.whl → 5.0.0.dev328__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.dev321'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev321')
+__version__ = version = '5.0.0.dev328'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev328')
 
 __commit_id__ = commit_id = None

cellprofiler_library/functions/image_processing.py

@@ -7,9 +7,10 @@ import scipy
 import matplotlib
 import math
 from typing import Any, Optional, Tuple, Callable, Union, List
-from cellprofiler_library.types import ImageGrayscale, ImageGrayscaleMask, Image2DColor, Image2DGrayscale, ImageAny, ObjectSegmentation, Image2D, Image2DMask
+from cellprofiler_library.types import ImageGrayscale, ImageGrayscaleMask, Image2DColor, Image2DGrayscale, ImageAny, ObjectSegmentation, Image2D, Image2DMask, StructuringElement
 from cellprofiler_library.opts import threshold as Threshold
 from cellprofiler_library.opts.crop import RemovalMethod
+from cellprofiler_library.opts.structuring_elements import StructuringElementShape2D, StructuringElementShape3D
 
 def rgb_to_greyscale(image):
     if image.shape[-1] == 4:
@@ -119,6 +120,81 @@ def morphological_skeleton_3d(image):
     return skimage.morphology.skeletonize_3d(image)
 
 
+################################################################################
+# Morphological Operations Helpers
+################################################################################
+
+def get_structuring_element(shape: Union[StructuringElementShape2D, StructuringElementShape3D], size: int) -> StructuringElement:
+    return getattr(skimage.morphology, shape.value.lower())(size)
+
+################################################################################
+# ErodeImage
+################################################################################
+
+def morphology_erosion(image: ImageAny, structuring_element: StructuringElement) -> ImageAny:
+    """Apply morphological erosion to an image.
+    
+    Args:
+        image: Input image (2D or 3D)
+        structuring_element: Structuring element for erosion
+        
+    Returns:
+        Eroded image with same dimensions as input
+    """
+    is_strel_2d = structuring_element.ndim == 2
+    is_img_2d = image.ndim == 2
+    
+    if is_strel_2d and not is_img_2d:
+        # Apply 2D structuring element to 3D image planewise
+        y_data = numpy.zeros_like(image)
+        for index, plane in enumerate(image):
+            y_data[index] = skimage.morphology.erosion(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."
+        )
+    
+    # Apply erosion directly for matching dimensions
+    y_data = skimage.morphology.erosion(image, structuring_element)
+    return y_data
+
+
+################################################################################
+# DilateImage
+################################################################################
+
+def morphology_dilation(image: ImageAny, structuring_element: StructuringElement) -> ImageAny:
+    """Apply morphological dilation to an image.
+    
+    Args:
+        image: Input image (2D or 3D)
+        structuring_element: Structuring element for dilation
+        
+    Returns:
+        Dilated image with same dimensions as input
+    """
+    is_strel_2d = structuring_element.ndim == 2
+    is_img_2d = image.ndim == 2
+    
+    if is_strel_2d and not is_img_2d:
+        # Apply 2D structuring element to 3D image planewise
+        y_data = numpy.zeros_like(image)
+        for index, plane in enumerate(image):
+            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."
+        )
+    
+    # Apply dilation directly for matching dimensions
+    y_data = skimage.morphology.dilation(image, structuring_element)
+    return y_data
+
+
 def median_filter(image, window_size, mode):
     return scipy.ndimage.median_filter(image, size=window_size, mode=mode)
 

cellprofiler_library/modules/_dilateimage.py

@@ -0,0 +1,37 @@
+# coding=utf-8
+
+"""
+DilateImage module for the CellProfiler library.
+
+This module contains the core algorithms for morphological dilation operations.
+"""
+
+from pydantic import validate_call, ConfigDict, Field
+from typing import Union, Tuple, Annotated
+from cellprofiler_library.types import ImageAny, StructuringElement
+from cellprofiler_library.functions.image_processing import morphology_dilation, 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_image(
+    image: Annotated[ImageAny, Field(description="Input image to perform dilation on")],
+    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)")]
+) -> ImageAny:
+    """Apply morphological dilation to an image.
+    
+    Args:
+        image: Input image (2D or 3D grayscale)
+        structuring_element: Structuring element for dilation operation as an NDArray or a tuple of (StructuringElement[N]D, size)
+        
+    Returns:
+        Dilated image with same dimensions and type as input
+        
+    Raises:
+        NotImplementedError: If trying to apply 3D structuring element to 2D image
+    """
+    if isinstance(structuring_element, tuple):
+        structuring_element = get_structuring_element(structuring_element[0], structuring_element[1])
+    return morphology_dilation(image, structuring_element)

cellprofiler_library/modules/_erodeimage.py

@@ -0,0 +1,36 @@
+# coding=utf-8
+
+"""
+ErodeImage module for the CellProfiler library.
+
+This module contains the core algorithms for morphological erosion operations.
+"""
+
+from pydantic import validate_call, ConfigDict, Field
+from typing import Union, Tuple, Annotated
+from cellprofiler_library.types import ImageAny, StructuringElement
+from cellprofiler_library.functions.image_processing import morphology_erosion, 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 erode_image( 
+    image: Annotated[ImageAny, Field(description="Input image to perform erosion on")],
+    structuring_element: Annotated[Union[StructuringElement, StructuringElementParameters], Field(description="Structuring element for erosion operation as either an NDArray or a tuple of (StructuringElement[N]D, size)")]
+) -> ImageAny:
+    """Apply morphological erosion to an image.
+    
+    Args:
+        image: Input image (2D or 3D grayscale)
+        structuring_element: Structuring element for erosion operation as an NDArray or a tuple of (StructuringElement[N]D, size)
+        
+    Returns:
+        Eroded image with same dimensions and type as input
+        
+    Raises:
+        NotImplementedError: If trying to apply 3D structuring element to 2D image
+    """
+    if isinstance(structuring_element, tuple):
+        structuring_element = get_structuring_element(structuring_element[0], structuring_element[1])
+    return morphology_erosion(image, structuring_element)

cellprofiler_library/opts/dilateimage.py

@@ -0,0 +1,15 @@
+# coding=utf-8
+
+"""
+Options and enums for DilateImage module
+"""
+
+# Note: DilateImage 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 DilateImage as it uses standard
+# StructuringElement configuration from cellprofiler_core. For structuring element shapes,
+# see cellprofiler_library.opts.structuring_elements
+

cellprofiler_library/opts/erodeimage.py

@@ -0,0 +1,14 @@
+# coding=utf-8
+
+"""
+Options and enums for ErodeImage module
+"""
+
+# Note: ErodeImage 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 ErodeImage as it uses standard
+# StructuringElement configuration from cellprofiler_core. For structuring element shapes,
+# see cellprofiler_library.opts.structuring_elements

cellprofiler_library/opts/structuring_elements.py

@@ -0,0 +1,12 @@
+from enum import Enum
+
+class StructuringElementShape2D(str, Enum):
+    DIAMOND = "Diamond"
+    DISK = "Disk"
+    SQUARE = "Square"
+    STAR = "Star"
+    
+class StructuringElementShape3D(str, Enum):
+    BALL = "Ball"
+    CUBE = "Cube"
+    OCTAHEDRON = "Octahedron"

cellprofiler_library/types.py

@@ -117,3 +117,5 @@ Image3D =               Union[Image3DColor, Image3DGrayscale, Image3DBinary]
 Image3DMask =           Union[Image3DColorMask, Image3DGrayscaleMask]
 
 ImageInt =              Union[Image2DInt, Image3DInt]
+
+StructuringElement =    NDArray[np.uint8]

{cellprofiler_library_nightly-5.0.0.dev321.dist-info → cellprofiler_library_nightly-5.0.0.dev328.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev321
+Version: 5.0.0.dev328
 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.dev321.dist-info → cellprofiler_library_nightly-5.0.0.dev328.dist-info}/RECORD

@@ -1,10 +1,10 @@
 cellprofiler_library/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellprofiler_library/_version.py,sha256=mYUqqa6M-iE4MBhf8kLEwQQ_kh9UFT5QdUWnnrI5Hl0,721
+cellprofiler_library/_version.py,sha256=PsxcwOzzb9oolouEbYbSgdrb1UXw3VQZXFhGnok7G2U,721
 cellprofiler_library/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellprofiler_library/types.py,sha256=5cCxXOO_TE-uSF4ZB6sDG3eTZ1VWDSXUFifg0N4JYs8,8516
+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=s13691o7-peaL-mVOA4J50ZynqXioSjfJ7vfTjfdm5M,33152
+cellprofiler_library/functions/image_processing.py,sha256=AqOq2Sf6YykX7wv2o4i94QehaCkUpamNLigqSMtWJ4g,36077
 cellprofiler_library/functions/measurement.py,sha256=8pXcEb1fLgwOEDiTJho1_O-fFGTtIp-Qn1lStjQBjbo,29221
 cellprofiler_library/functions/object_processing.py,sha256=3cKNq5ewBf_HWz6rdX3XR4WUbd6SklbHZ_H40xt9ODM,19443
 cellprofiler_library/functions/segmentation.py,sha256=LNE22ByY0X7GepQaHqLdxkzlmIXjD3EglAYJjtT2dGo,25257
@@ -16,7 +16,9 @@ cellprofiler_library/modules/_convertimagetoobjects.py,sha256=_X2YWEHK4hFaP13LEB
 cellprofiler_library/modules/_convertobjectstoimage.py,sha256=PMYjH_prBKma4LNgUxmA5GzF7fQ6ko09XszKatTulB4,2274
 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/_enhanceedges.py,sha256=PaXZck8fPcxRf-IXCstu-OWmsvM_rDDPMMQ3cZFfVZc,2951
+cellprofiler_library/modules/_erodeimage.py,sha256=nFHn4hdpjXJaPvnpSyfPAxWgd7UXi0fUUgPqEl26CCY,1802
 cellprofiler_library/modules/_expandorshrinkobjects.py,sha256=A1oeW_O8C5NLJr-xU1R9pSulDau8XUeWaKiilpr-85g,856
 cellprofiler_library/modules/_fillobjects.py,sha256=1zvlZNJhG8kEzAnVyiSLGPNE338EB5wopD2eK0BVWrc,469
 cellprofiler_library/modules/_gaussianfilter.py,sha256=zVt562oviuoyy6l85Tgg_rjyQdOFCEnYLuykHYnYni8,174
@@ -37,11 +39,14 @@ cellprofiler_library/opts/convertimagetoobjects.py,sha256=9e3VOdpjd4084ATZyFtSQg
 cellprofiler_library/opts/convertobjectstoimage.py,sha256=U3jeVtKYFgfxbO7NYndanAyZFoEvbyScOq4T8cpjfX8,188
 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/erodeimage.py,sha256=T3LCqu83rTqTDlc_7ebuPBKnr-FKomRHA8WD0uA9Y1g,584
 cellprofiler_library/opts/measureimageoverlap.py,sha256=uopQCJTX1Uk-NNDAISsdYEOuOtiEBYOyCwu57ZT7X84,134
 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.dev321.dist-info/licenses/LICENSE,sha256=QLWaBS7kAioYx7PmJNXAMJaY8NODcFAag60YlUWuyz0,2276
-cellprofiler_library_nightly-5.0.0.dev321.dist-info/METADATA,sha256=Ib4P-ixq4tVByZcQfLqOeJ6ZbhOfoYEsXV4C0Z2qAa8,5534
-cellprofiler_library_nightly-5.0.0.dev321.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-cellprofiler_library_nightly-5.0.0.dev321.dist-info/top_level.txt,sha256=LXq0ApDeDD4gotb6YFTySzdyScvHfS_pqoTg1QsNLBs,21
-cellprofiler_library_nightly-5.0.0.dev321.dist-info/RECORD,,
+cellprofiler_library_nightly-5.0.0.dev328.dist-info/licenses/LICENSE,sha256=QLWaBS7kAioYx7PmJNXAMJaY8NODcFAag60YlUWuyz0,2276
+cellprofiler_library_nightly-5.0.0.dev328.dist-info/METADATA,sha256=13FKaSOrSkR-hnmCuPWJ6v2wW5AbcscIqxuN586eV2A,5534
+cellprofiler_library_nightly-5.0.0.dev328.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+cellprofiler_library_nightly-5.0.0.dev328.dist-info/top_level.txt,sha256=LXq0ApDeDD4gotb6YFTySzdyScvHfS_pqoTg1QsNLBs,21
+cellprofiler_library_nightly-5.0.0.dev328.dist-info/RECORD,,