cellprofiler-library-nightly 5.0.0.dev306__py3-none-any.whl → 5.0.0.dev318__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.dev306'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev306')
+__version__ = version = '5.0.0.dev318'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev318')
 
 __commit_id__ = commit_id = None

cellprofiler_library/functions/image_processing.py

@@ -6,10 +6,9 @@ import centrosome.threshold
 import scipy
 import matplotlib
 from typing import Any, Optional, Tuple, Callable, Union, List
-from ..types import ImageGrayscale, ImageGrayscaleMask, Image2DColor, Image2DGrayscale
+from ..types import ImageGrayscale, ImageGrayscaleMask, Image2DColor, Image2DGrayscale, ImageAny, ObjectSegmentation, Image2D
 from ..opts import threshold as Threshold
 
-
 def rgb_to_greyscale(image):
     if image.shape[-1] == 4:
         output = skimage.color.rgba2rgb(image)
@@ -594,3 +593,44 @@ def split_rgb(input_image: Image2DColor) -> List[Image2DGrayscale]:
 def split_multichannel(input_image: Image2DColor) -> List[Image2DGrayscale]:
      return split_rgb(input_image)
 
+
+################################################################################
+# ConvertImageToObjects
+################################################################################
+
+def image_to_objects(
+        data:           ImageAny, 
+        cast_to_bool:   bool,
+        preserve_label: bool,
+        background:     int,
+        connectivity:   Union[int, None],
+        ) -> ObjectSegmentation:
+    # Compatibility with skimage
+    connectivity = None if connectivity == 0 else connectivity
+
+    caster = skimage.img_as_bool if cast_to_bool else skimage.img_as_uint
+    data = caster(data)
+
+    # If preservation is desired, just return the original labels
+    if preserve_label and not cast_to_bool:
+        return data
+
+    return skimage.measure.label(data, background=background, connectivity=connectivity)
+
+###########################################################################
+# CorrectIlluminationApply
+###########################################################################
+
+def apply_divide(image_pixels: Image2D, illum_function_pixel_data: Image2D) -> Image2D:
+    return image_pixels / illum_function_pixel_data
+
+def apply_subtract(image_pixels: Image2D, illum_function_pixel_data: Image2D) -> Image2D:
+    output_image = image_pixels - illum_function_pixel_data
+    output_image[output_image < 0] = 0
+    return output_image
+
+def clip_low(output_pixels: Image2D) -> Image2D:
+    return numpy.where(output_pixels < 0, 0, output_pixels)
+
+def clip_high(output_pixels: Image2D) -> Image2D:
+    return numpy.where(output_pixels > 1, 1, output_pixels)

cellprofiler_library/modules/_colortogray.py

@@ -1,7 +1,7 @@
 from pydantic import Field, validate_call, ConfigDict
 from typing import Annotated, List, Union, Optional
 
-from cellprofiler_library.opts.colortogray import ImageChannelType
+from ..opts.colortogray import ImageChannelType
 from ..types import Image2DColor, Image2DGrayscale
 from ..functions.image_processing import combine_colortogray, split_hsv, split_rgb, split_multichannel
 

cellprofiler_library/modules/_convertimagetoobjects.py

@@ -0,0 +1,14 @@
+from typing import Annotated, Optional, Union
+from pydantic import Field, validate_call, ConfigDict
+from cellprofiler_library.types import ImageGrayscale, ObjectLabelsDense, ImageBinary
+from cellprofiler_library.functions.image_processing import image_to_objects
+
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
+def convert_image_to_objects(
+        data:           Annotated[Union[ImageGrayscale, ImageBinary], Field(description="Image to be converted to Objects")],
+        cast_to_bool:   Annotated[bool, Field(description="Convert a grayscale image to binary before converting it to an object")],
+        preserve_label: Annotated[bool, Field(description="Preserve original labels of objects")],
+        background:     Annotated[int, Field(description="Pixel value of the background")],
+        connectivity:   Annotated[Optional[int], Field(description="Maximum number of orthogonal hops to consider a pixel/voxel as a neighbor")]
+        ) -> ObjectLabelsDense:
+    return image_to_objects(data, cast_to_bool, preserve_label, background, connectivity)

cellprofiler_library/modules/_correctilluminationapply.py

@@ -0,0 +1,40 @@
+from typing import Annotated, Optional
+from pydantic import Field, validate_call, ConfigDict
+from cellprofiler_library.opts.correctilluminationapply import Method
+from ..types import Image2D
+from ..functions.image_processing import apply_divide, apply_subtract, clip_low, clip_high
+
+
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
+def correct_illumination_apply(
+        image_pixels:               Annotated[Image2D, Field(description="Pixel data of image to apply the illumination function to")],
+        illum_function_pixel_data:  Annotated[Image2D, Field(description="Pixel data of illumination function")],
+        method_divide_or_subtract:  Annotated[Method, Field(description="Method to apply the illumination function")],
+        truncate_low:               Annotated[Optional[bool], Field(description="Set output image values less than 0 equal to 0?")],
+        truncate_high:              Annotated[Optional[bool], Field(description="Set output image values greater than 1 equal to 1?")],
+        ) -> Annotated[Image2D, Field(description="Pixel data of image with illumination function applied")]:
+    """
+    Perform illumination according to the parameters of one image setting group
+    """
+    assert image_pixels.shape[:2] == illum_function_pixel_data.shape[:2], "Input image shape and illumination function shape must be equal"
+    #
+    # Either divide or subtract the illumination image from the original
+    #
+    if method_divide_or_subtract == Method.DIVIDE:
+        output_pixels = apply_divide(image_pixels, illum_function_pixel_data)
+    elif method_divide_or_subtract == Method.SUBTRACT:
+        output_pixels = apply_subtract(image_pixels, illum_function_pixel_data)
+    else:
+        raise ValueError(
+            "Unhandled option for divide or subtract: %s"
+            % method_divide_or_subtract.value
+        )
+    #
+    # Optionally, clip high and low values
+    #
+    if truncate_low:
+        output_pixels = clip_low(output_pixels)
+    if truncate_high:
+        output_pixels = clip_high(output_pixels)
+
+    return output_pixels

cellprofiler_library/opts/convertimagetoobjects.py

@@ -0,0 +1,3 @@
+'''
+The convertimagetoobjects module does not have any options.
+'''

cellprofiler_library/opts/correctilluminationapply.py

@@ -0,0 +1,5 @@
+from enum import Enum
+
+class Method(str, Enum):
+    DIVIDE = "Divide"
+    SUBTRACT = "Subtract"

{cellprofiler_library_nightly-5.0.0.dev306.dist-info → cellprofiler_library_nightly-5.0.0.dev318.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev306
+Version: 5.0.0.dev318
 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.dev306.dist-info → cellprofiler_library_nightly-5.0.0.dev318.dist-info}/RECORD

@@ -1,18 +1,20 @@
 cellprofiler_library/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cellprofiler_library/_version.py,sha256=G7VoognR8cVzAPvjy716XjRcsJUGbmEf3x2OzMxn-4o,721
+cellprofiler_library/_version.py,sha256=VKwI68zHVxr7qKLpGyfYE5ws8C3HO1sHftyVZcFWLQk,721
 cellprofiler_library/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellprofiler_library/types.py,sha256=5cCxXOO_TE-uSF4ZB6sDG3eTZ1VWDSXUFifg0N4JYs8,8516
 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=nE7frZyHBSYA5wX5div8VtjYf_IkIOjUKKmRLS-b3Uk,23161
+cellprofiler_library/functions/image_processing.py,sha256=3mGdRhWaVUqCxIh1hjde6Ffnq_wJfJAWxZZU3MNfQkM,24780
 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
 cellprofiler_library/modules/__init__.py,sha256=Z4Wy42OTD9ujAON4g1oyLJ0oA6K7h3XQiV66JzHGkOw,789
 cellprofiler_library/modules/_closing.py,sha256=aIqIE0IcT2OcrOmTSWjFzu4iIQKk2yDC9qPHARqRIkc,204
-cellprofiler_library/modules/_colortogray.py,sha256=_56iPZR-gmKPhAQTYAVQjwC_F6tS5esa9X5o81-5P_I,1852
+cellprofiler_library/modules/_colortogray.py,sha256=UtiBgh7AXduRBMkHsv2L0u7FayOCfaB58qFGNVIGskM,1833
 cellprofiler_library/modules/_combineobjects.py,sha256=dZz0RXjvVukem3e46wPfQWOQCOfMLHaq0KoFzjKVQqs,830
+cellprofiler_library/modules/_convertimagetoobjects.py,sha256=_X2YWEHK4hFaP13LEBD-vIwwUUhgJEJLcTkhyMe4JBA,1075
 cellprofiler_library/modules/_convertobjectstoimage.py,sha256=PMYjH_prBKma4LNgUxmA5GzF7fQ6ko09XszKatTulB4,2274
+cellprofiler_library/modules/_correctilluminationapply.py,sha256=8bZC3AnQv3vpUrNSnLvcc_s0E-P63XbrfwMv7OZNjt4,2084
 cellprofiler_library/modules/_enhanceedges.py,sha256=PaXZck8fPcxRf-IXCstu-OWmsvM_rDDPMMQ3cZFfVZc,2951
 cellprofiler_library/modules/_expandorshrinkobjects.py,sha256=A1oeW_O8C5NLJr-xU1R9pSulDau8XUeWaKiilpr-85g,856
 cellprofiler_library/modules/_fillobjects.py,sha256=1zvlZNJhG8kEzAnVyiSLGPNE338EB5wopD2eK0BVWrc,469
@@ -30,12 +32,14 @@ cellprofiler_library/modules/_threshold.py,sha256=Z2mFd1xBtoctyF5jnkuwuNyBfjSkRt
 cellprofiler_library/modules/_watershed.py,sha256=T-xmYE8_21wpFCH5HbCTAHu5k5A9-5BL3ToUSpODxPY,1824
 cellprofiler_library/opts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellprofiler_library/opts/colortogray.py,sha256=ptAanLQW9iMgQHgC7xvYlbIbshBd5d7uE48t2F0Z5e8,344
+cellprofiler_library/opts/convertimagetoobjects.py,sha256=9e3VOdpjd4084ATZyFtSQg_VpxbyXrYVFmEFJkrHakg,67
 cellprofiler_library/opts/convertobjectstoimage.py,sha256=U3jeVtKYFgfxbO7NYndanAyZFoEvbyScOq4T8cpjfX8,188
+cellprofiler_library/opts/correctilluminationapply.py,sha256=IkAqjMjaRdsoY2aXw5_dLI1iRYqCwvcNwCWEpWNZrN4,96
 cellprofiler_library/opts/measureimageoverlap.py,sha256=uopQCJTX1Uk-NNDAISsdYEOuOtiEBYOyCwu57ZT7X84,134
 cellprofiler_library/opts/objectsizeshapefeatures.py,sha256=3GIntOH3qXs7F16Tpjmtg7opHYAmmOjEdEwW6q3ht_Y,6306
 cellprofiler_library/opts/threshold.py,sha256=yg_i5to22Nd9hTakaRxo9UIQZRYWFpavJimjl5JONx4,938
-cellprofiler_library_nightly-5.0.0.dev306.dist-info/licenses/LICENSE,sha256=QLWaBS7kAioYx7PmJNXAMJaY8NODcFAag60YlUWuyz0,2276
-cellprofiler_library_nightly-5.0.0.dev306.dist-info/METADATA,sha256=zxH7-gWJTKsSPBNW1D1eheNIyVNjcnexF4kPwCwMe5M,5534
-cellprofiler_library_nightly-5.0.0.dev306.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-cellprofiler_library_nightly-5.0.0.dev306.dist-info/top_level.txt,sha256=LXq0ApDeDD4gotb6YFTySzdyScvHfS_pqoTg1QsNLBs,21
-cellprofiler_library_nightly-5.0.0.dev306.dist-info/RECORD,,
+cellprofiler_library_nightly-5.0.0.dev318.dist-info/licenses/LICENSE,sha256=QLWaBS7kAioYx7PmJNXAMJaY8NODcFAag60YlUWuyz0,2276
+cellprofiler_library_nightly-5.0.0.dev318.dist-info/METADATA,sha256=knZAToPornredt8suy093xlyBp6eTYhKl4A_wEElejs,5534
+cellprofiler_library_nightly-5.0.0.dev318.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+cellprofiler_library_nightly-5.0.0.dev318.dist-info/top_level.txt,sha256=LXq0ApDeDD4gotb6YFTySzdyScvHfS_pqoTg1QsNLBs,21
+cellprofiler_library_nightly-5.0.0.dev318.dist-info/RECORD,,