cellprofiler-library-nightly 5.0.0.dev324__tar.gz → 5.0.0.dev332__tar.gz

{cellprofiler_library_nightly-5.0.0.dev324 → cellprofiler_library_nightly-5.0.0.dev332}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev324
+Version: 5.0.0.dev332
 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.dev324 → cellprofiler_library_nightly-5.0.0.dev332}/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.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 = 'g3b394eae0'
+__commit_id__ = commit_id = 'g13c77e82d'

{cellprofiler_library_nightly-5.0.0.dev324 → cellprofiler_library_nightly-5.0.0.dev332}/cellprofiler_library/functions/image_processing.py

@@ -161,6 +161,40 @@ def morphology_erosion(image: ImageAny, structuring_element: StructuringElement)
     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_nightly-5.0.0.dev324 → cellprofiler_library_nightly-5.0.0.dev332}/cellprofiler_library/functions/object_processing.py

@@ -3,12 +3,12 @@ import centrosome.cpmorphology
 import numpy
 import scipy.ndimage
 import skimage.morphology
+import cellprofiler.utilities.morphology
 import mahotas
 import matplotlib.cm
 from numpy.typing import NDArray
 from typing import Optional, Literal, Tuple
-from cellprofiler_library.types import ObjectSegmentation, ImageAnyMask, ObjectLabel, ImageColor, ImageGrayscale, ImageBinary
-
+from cellprofiler_library.types import ImageAnyMask, ObjectLabel, ImageColor, ImageGrayscale, ImageBinary, ObjectSegmentation, StructuringElement
 
 def shrink_to_point(labels, fill):
     """
@@ -532,3 +532,100 @@ def image_mode_uint16(
     alpha[mask] = 1
     return pixel_data, alpha
 
+
+################################################################################
+# Morphological Operations Helpers
+################################################################################
+
+def morphological_gradient(x_data: ObjectSegmentation, structuring_element: StructuringElement) -> ObjectSegmentation:
+    is_strel_2d = structuring_element.ndim == 2
+
+    is_img_2d = x_data.ndim == 2
+
+    if is_strel_2d and not is_img_2d:
+        y_data = numpy.zeros_like(x_data)
+
+        for index, plane in enumerate(x_data):
+            y_data[index] = scipy.ndimage.morphological_gradient(
+                plane, footprint=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 = scipy.ndimage.morphological_gradient(x_data, footprint=structuring_element)
+
+    return y_data
+
+
+################################################################################
+# ErodeObjects
+################################################################################
+
+def erode_objects_with_structuring_element(
+    labels: ObjectSegmentation,
+    structuring_element: StructuringElement,
+    preserve_midpoints: bool = True,
+    relabel_objects: bool = False
+) -> ObjectSegmentation:
+    """Erode objects based on the structuring element provided.
+    
+    This function is similar to the "Shrink" function of ExpandOrShrinkObjects,
+    with two major distinctions:
+    1. ErodeObjects supports 3D objects
+    2. An object smaller than the structuring element will be removed entirely
+       unless preserve_midpoints is enabled.
+    
+    Args:
+        labels: Input labeled objects array
+        structuring_element: Structuring element for erosion operation
+        preserve_midpoints: If True, preserve central pixels to prevent object removal
+        relabel_objects: If True, assign new label numbers to resulting objects
+        
+    Returns:
+        Eroded objects array with same dimensions as input
+    """
+    
+    
+    # Calculate morphological gradient to identify object boundaries
+    contours = morphological_gradient(
+        labels, structuring_element
+    )
+    
+    # Erode by removing pixels at object boundaries (where contours != 0)
+    y_data = labels * (contours == 0)
+    
+    # Preserve midpoints if requested to prevent object removal
+    if preserve_midpoints:
+        missing_labels = numpy.setxor1d(labels, y_data)
+        
+        # Check if structuring element is disk with size 1 (special case optimization)
+        # Check based on the actual array properties since we're dealing with numpy array
+        is_simple_disk = (
+            structuring_element.ndim == 2 and 
+            structuring_element.shape == (3, 3) and
+            numpy.array_equal(structuring_element, skimage.morphology.disk(1))
+        )
+        
+        if is_simple_disk:
+            # For simple disk,1 case, restore missing pixels directly
+            y_data += labels * numpy.isin(labels, missing_labels)
+        else:
+            # For other structuring elements, find and preserve the most central pixels
+            for label in missing_labels:
+                binary = labels == label
+                # Find pixels furthest from the object's edge using distance transform
+                midpoint = scipy.ndimage.morphology.distance_transform_edt(binary)
+                # Preserve pixels at maximum distance (most central)
+                y_data[midpoint == numpy.max(midpoint)] = label
+    
+    # Relabel objects if requested
+    if relabel_objects:
+        y_data = skimage.morphology.label(y_data)
+    
+    return y_data
+

cellprofiler_library_nightly-5.0.0.dev332/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_nightly-5.0.0.dev332/cellprofiler_library/modules/_erodeobjects.py

@@ -0,0 +1,50 @@
+# coding=utf-8
+
+"""
+ErodeObjects module for the CellProfiler library.
+
+This module contains the core algorithms for object erosion 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 erode_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 erode_objects(
+    labels: Annotated[ObjectSegmentation, Field(description="Input object segmentations")],
+    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)")],
+    preserve_midpoints: Annotated[bool, Field(description="If set to True, the central pixels for each object will not be eroded. This ensures that objects are not lost.")] = False,
+    relabel_objects: Annotated[bool, Field(description="Selecting True will assign new label numbers to resulting objects")] = False
+) -> ObjectSegmentation:
+    """Erode objects based on the structuring element provided.
+    
+    This function is similar to the "Shrink" function of ExpandOrShrinkObjects,
+    with two major distinctions:
+    1. ErodeObjects supports 3D objects, unlike ExpandOrShrinkObjects.
+    2. An object smaller than the structuring element will be removed entirely
+       unless preserve_midpoints is enabled.
+    
+    Args:
+        labels: Input labeled objects array
+        structuring_element: Structuring element for erosion operation
+        preserve_midpoints: If set to True, the central pixels for each object will not be eroded. This ensures that objects are not lost.
+        relabel_objects: If set to True, the resulting objects will be relabeled with new label numbers
+        
+    Returns:
+        Eroded objects array with same dimensions as input
+    """
+    if isinstance(structuring_element, tuple):
+        structuring_element = get_structuring_element(structuring_element[0], structuring_element[1])
+    return erode_objects_with_structuring_element(
+        labels=labels,
+        structuring_element=structuring_element,
+        preserve_midpoints=preserve_midpoints,
+        relabel_objects=relabel_objects
+    )

cellprofiler_library_nightly-5.0.0.dev332/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_nightly-5.0.0.dev332/cellprofiler_library/opts/erodeobjects.py

@@ -0,0 +1,15 @@
+# coding=utf-8
+
+"""
+Options and enums for ErodeObjects module
+"""
+
+# Note: ErodeObjects 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 ErodeObjects 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.dev324 → cellprofiler_library_nightly-5.0.0.dev332}/cellprofiler_library_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev324
+Version: 5.0.0.dev332
 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.dev324 → cellprofiler_library_nightly-5.0.0.dev332}/cellprofiler_library_nightly.egg-info/SOURCES.txt

@@ -20,8 +20,10 @@ cellprofiler_library/modules/_convertimagetoobjects.py
 cellprofiler_library/modules/_convertobjectstoimage.py
 cellprofiler_library/modules/_correctilluminationapply.py
 cellprofiler_library/modules/_crop.py
+cellprofiler_library/modules/_dilateimage.py
 cellprofiler_library/modules/_enhanceedges.py
 cellprofiler_library/modules/_erodeimage.py
+cellprofiler_library/modules/_erodeobjects.py
 cellprofiler_library/modules/_expandorshrinkobjects.py
 cellprofiler_library/modules/_fillobjects.py
 cellprofiler_library/modules/_gaussianfilter.py
@@ -42,7 +44,9 @@ cellprofiler_library/opts/convertimagetoobjects.py
 cellprofiler_library/opts/convertobjectstoimage.py
 cellprofiler_library/opts/correctilluminationapply.py
 cellprofiler_library/opts/crop.py
+cellprofiler_library/opts/dilateimage.py
 cellprofiler_library/opts/erodeimage.py
+cellprofiler_library/opts/erodeobjects.py
 cellprofiler_library/opts/measureimageoverlap.py
 cellprofiler_library/opts/objectsizeshapefeatures.py
 cellprofiler_library/opts/structuring_elements.py