cellprofiler-library-nightly 5.0.0.dev475__tar.gz → 5.0.0.dev478__tar.gz

{cellprofiler_library_nightly-5.0.0.dev475 → cellprofiler_library_nightly-5.0.0.dev478}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev475
+Version: 5.0.0.dev478
 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.dev475 → cellprofiler_library_nightly-5.0.0.dev478}/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.dev475'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev475')
+__version__ = version = '5.0.0.dev478'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev478')
 
-__commit_id__ = commit_id = 'gc4686c345'
+__commit_id__ = commit_id = 'g030288a08'

{cellprofiler_library_nightly-5.0.0.dev475 → cellprofiler_library_nightly-5.0.0.dev478}/cellprofiler_library/functions/image_processing.py

@@ -17,6 +17,7 @@ import matplotlib
 import math
 from typing import Any, Optional, Tuple, Callable, Union, List, cast, Dict, TypeVar
 from numpy.typing import NDArray
+from skimage.restoration import denoise_bilateral
 from cellprofiler_library.types import ImageGrayscale, ImageGrayscaleMask, Image2DColor, Image2DGrayscale, Image2DGrayscaleMask, ImageAny, ImageAnyMask, ObjectSegmentation, Image2D, Image2DMask, StructuringElement, ObjectLabelSet, ImageColor, ImageBinaryMask
 from cellprofiler_library.opts import threshold as Threshold
 from cellprofiler_library.opts.enhanceorsuppressfeatures import SpeckleAccuracy, NeuriteMethod
@@ -27,6 +28,7 @@ from cellprofiler_library.opts.resize import ResizingMethod, DimensionMethod, In
 from cellprofiler_library.opts.imagemath import Operator
 from cellprofiler_library.opts.flipandrotate import RotationCoordinateAlignmnet
 from cellprofiler_library.opts.enhanceedges import EdgeDirection
+
 invert = cast(Callable[[ImageAny], ImageAny], _invert)
 isscalar = cast(Callable[[Optional[ImageAny]], bool], _isscalar)
 
@@ -2068,3 +2070,44 @@ def rotate_image_coordinates(pixel_data: Image2D, mask: Image2DMask, rotate_poin
             "Unknown axis: %s" % rotate_coordinate_alignment.value
         )
     return angle
+
+
+###############################################################################
+# Smoothing
+###############################################################################
+
+def smoothing_gaussian(pixel_data: Image2D, mask: Optional[Image2DMask], sigma: float) -> Image2D:
+    def fn(image: Image2D) -> Image2D:
+            return scipy.ndimage.gaussian_filter(
+                image, sigma, mode="constant", cval=0
+            )
+    return centrosome.smooth.smooth_with_function_and_mask(pixel_data, fn, mask)
+     
+
+def smoothing_median(pixel_data: Image2D, mask: Optional[Image2DMask], obj_size: float) -> Image2D:
+    return centrosome.filter.median_filter(pixel_data, mask, obj_size / 2 + 1)
+
+
+def smoothing_keeping_edges(pixel_data: Image2D, multichannel: bool, sigma_range: float, sigma: float) -> Image2D:
+    assert sigma_range is not None, "sigma_range must be provided for smooth_keeping_edges"
+    return denoise_bilateral(
+        image=pixel_data.astype(float),
+        channel_axis=2 if multichannel else None,
+        sigma_color=sigma_range,
+        sigma_spatial=sigma,
+    )
+
+
+def smoothing_fit_polynomial(pixel_data: Image2D, mask: Optional[Image2DMask], clip: bool) -> Image2D:
+    return centrosome.smooth.fit_polynomial(pixel_data, mask, clip)
+
+
+def smoothing_circular_average(pixel_data: Image2D, mask: Optional[Image2DMask], obj_size: float) -> Image2D:
+    return centrosome.filter.circular_average_filter(pixel_data, obj_size / 2 + 1, mask)
+
+def smoothing_smooth_to_average(pixel_data: Image2D, mask: Optional[Image2DMask]) -> Image2D:
+    if mask is not None:
+        mean = numpy.mean(pixel_data[mask])
+    else:
+        mean = numpy.mean(pixel_data)
+    return numpy.ones(pixel_data.shape, pixel_data.dtype) * mean

cellprofiler_library_nightly-5.0.0.dev478/cellprofiler_library/modules/_smooth.py

@@ -0,0 +1,44 @@
+import numpy
+from typing import Annotated, Optional
+from pydantic import Field, validate_call, ConfigDict
+
+from cellprofiler_library.functions.image_processing import smoothing_gaussian, smoothing_median, smoothing_keeping_edges, smoothing_fit_polynomial, smoothing_circular_average, smoothing_smooth_to_average
+from cellprofiler_library.opts.smooth import SmoothingMethod
+from cellprofiler_library.types import Image2D, Image2DMask
+
+
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
+def smooth(
+        pixel_data:         Annotated[Image2D, Field(description="Pixel data of image to be smoothed")],
+        mask:               Annotated[Optional[Image2DMask], Field(description="Mask of the pixel data")],
+        multichannel:       Annotated[bool, Field(description="Set to true if image is multichannel")],
+        object_size:        Annotated[Optional[float], Field(description="Object size")],
+        smoothing_method:   Annotated[SmoothingMethod, Field(description="Smoothing method")],
+        sigma_range:        Annotated[Optional[float], Field(description="Sigma range")],
+        clip:               Annotated[Optional[bool], Field(description="Clip intensities to 0 and 1")] = True,
+) -> Image2D:
+    if object_size is not None:
+        obj_size = float(object_size)
+    else:
+        obj_size = float(min(30, max(1, numpy.mean(pixel_data.shape) / 40)))
+    sigma = obj_size / 2.35
+
+    if smoothing_method == SmoothingMethod.GAUSSIAN_FILTER:
+        output_pixels = smoothing_gaussian(pixel_data, mask, sigma)
+    elif smoothing_method == SmoothingMethod.MEDIAN_FILTER:
+        output_pixels = smoothing_median(pixel_data, mask, obj_size)
+    elif smoothing_method == SmoothingMethod.SMOOTH_KEEPING_EDGES:
+        assert sigma_range is not None, "sigma_range must be provided for smooth_keeping_edges"
+        output_pixels = smoothing_keeping_edges(pixel_data, multichannel, sigma_range, sigma)
+    elif smoothing_method == SmoothingMethod.FIT_POLYNOMIAL:
+        assert clip is not None, "clip must be provided for fit_polynomial"
+        output_pixels = smoothing_fit_polynomial(pixel_data, mask, clip)
+    elif smoothing_method == SmoothingMethod.CIRCULAR_AVERAGE_FILTER:
+        output_pixels = smoothing_circular_average(pixel_data, mask, obj_size)
+    elif smoothing_method == SmoothingMethod.SM_TO_AVERAGE:
+        output_pixels = smoothing_smooth_to_average(pixel_data, mask)
+    else:
+        raise ValueError(
+            "Unsupported smoothing method: %s" % smoothing_method
+        )
+    return output_pixels

cellprofiler_library_nightly-5.0.0.dev478/cellprofiler_library/opts/smooth.py

@@ -0,0 +1,9 @@
+from enum import Enum
+
+class SmoothingMethod(str, Enum):
+    FIT_POLYNOMIAL = "Fit Polynomial"
+    MEDIAN_FILTER = "Median Filter"
+    GAUSSIAN_FILTER = "Gaussian Filter"
+    SMOOTH_KEEPING_EDGES = "Smooth Keeping Edges"
+    CIRCULAR_AVERAGE_FILTER = "Circular Average Filter"
+    SM_TO_AVERAGE = "Smooth to Average"

{cellprofiler_library_nightly-5.0.0.dev475 → cellprofiler_library_nightly-5.0.0.dev478}/cellprofiler_library_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev475
+Version: 5.0.0.dev478
 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.dev475 → cellprofiler_library_nightly-5.0.0.dev478}/cellprofiler_library_nightly.egg-info/SOURCES.txt

@@ -49,6 +49,7 @@ cellprofiler_library/modules/_removeholes.py
 cellprofiler_library/modules/_resize.py
 cellprofiler_library/modules/_savecroppedobjects.py
 cellprofiler_library/modules/_shrinktoobjectcenters.py
+cellprofiler_library/modules/_smooth.py
 cellprofiler_library/modules/_threshold.py
 cellprofiler_library/modules/_watershed.py
 cellprofiler_library/opts/__init__.py
@@ -76,6 +77,7 @@ cellprofiler_library/opts/overlayoutlines.py
 cellprofiler_library/opts/removeholes.py
 cellprofiler_library/opts/resize.py
 cellprofiler_library/opts/shrinktoobjectcenters.py
+cellprofiler_library/opts/smooth.py
 cellprofiler_library/opts/structuring_elements.py
 cellprofiler_library/opts/threshold.py
 cellprofiler_library_nightly.egg-info/PKG-INFO