CellProfiler-nightly 5.0.0.dev306__py3-none-any.whl → 5.0.0.dev318__py3-none-any.whl

cellprofiler/_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/modules/convertimagetoobjects.py

@@ -1,8 +1,7 @@
-import skimage
-import skimage.measure
 from cellprofiler_core.module.image_segmentation import ImageSegmentation
 from cellprofiler_core.setting import Binary
 from cellprofiler_core.setting.text import Integer
+from cellprofiler_library.modules._convertimagetoobjects import convert_image_to_objects
 
 HELP_BINARY_IMAGE = """\
 This module can also convert a grayscale image to binary before converting it to an object.
@@ -110,7 +109,12 @@ If set to 0, a full connectivity of the input dimension is used.
         return __settings__
 
     def run(self, workspace):
-        self.function = lambda data, cast_to_bool, preserve_label, background, connectivity: convert_to_objects(
+        def _validate_image(img):
+            if img.multichannel is not False:
+                raise TypeError("Input image should be grayscale")
+
+        self.validate_image = _validate_image
+        self.function = lambda data, cast_to_bool, preserve_label, background, connectivity: convert_image_to_objects(
             data, cast_to_bool, preserve_label, background, connectivity
         )
 
@@ -138,17 +142,3 @@ If set to 0, a full connectivity of the input dimension is used.
             x=1,
             y=0,
         )
-
-
-def convert_to_objects(data, cast_to_bool, preserve_label, background, connectivity):
-    # 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)

cellprofiler/modules/correctilluminationapply.py

@@ -25,7 +25,6 @@ See also
 
 See also **CorrectIlluminationCalculate**.
 """
-
 import numpy
 from cellprofiler_core.image import Image
 from cellprofiler_core.module import Module
@@ -37,9 +36,8 @@ from cellprofiler_core.setting.do_something import DoSomething
 from cellprofiler_core.setting.do_something import RemoveSettingButton
 from cellprofiler_core.setting.subscriber import ImageSubscriber
 from cellprofiler_core.setting.text import ImageName
-
-DOS_DIVIDE = "Divide"
-DOS_SUBTRACT = "Subtract"
+from cellprofiler_library.opts.correctilluminationapply import Method
+from cellprofiler_library.modules._correctilluminationapply import correct_illumination_apply
 
 ######################################
 #
@@ -58,7 +56,6 @@ RE_MATCH = "Match maximums"
 
 SETTINGS_PER_IMAGE = 4
 
-
 class CorrectIlluminationApply(Module):
     category = "Image Processing"
     variable_revision_number = 5
@@ -116,22 +113,22 @@ a future version of CellProfiler. You can export .mat format images as
 
         divide_or_subtract = Choice(
             "Select how the illumination function is applied",
-            [DOS_DIVIDE, DOS_SUBTRACT],
-            doc="""\
+            [Method.DIVIDE.value, Method.SUBTRACT.value],
+            doc=f"""\
 This choice depends on how the illumination function was calculated and
 on your physical model of the way illumination variation affects the
 background of images relative to the objects in images; it is also
 somewhat empirical.
 
--  *%(DOS_SUBTRACT)s:* Use this option if the background signal is
+-  *{Method.SUBTRACT.value}:* Use this option if the background signal is
    significant relative to the real signal coming from the cells. If you
    created the illumination correction function using
    *Background*, then you will want to choose
-   *%(DOS_SUBTRACT)s* here.
--  *%(DOS_DIVIDE)s:* Choose this option if the signal to background
+   *{Method.SUBTRACT.value}* here.
+-  *{Method.DIVIDE.value}:* Choose this option if the signal to background
    ratio is high (the cells are stained very strongly). If you created
    the illumination correction function using *Regular*, then
-   you will want to choose *%(DOS_DIVIDE)s* here.
+   you will want to choose *{Method.DIVIDE.value}* here.
 """
             % globals(),
         )
@@ -248,6 +245,9 @@ somewhat empirical.
         orig_image = workspace.image_set.get_image(image_name)
         illum_function = workspace.image_set.get_image(illum_correct_name)
         illum_function_pixel_data = illum_function.pixel_data
+        #
+        # Validate the illumination function
+        #
         if orig_image.pixel_data.ndim == 2:
             illum_function = workspace.image_set.get_image(
                 illum_correct_name, must_be_grayscale=True
@@ -257,7 +257,6 @@ somewhat empirical.
                 illum_function_pixel_data = illum_function_pixel_data[
                     :, :, numpy.newaxis
                 ]
-        # Throw an error if image and illum data are incompatible
         if orig_image.pixel_data.shape[:2] != illum_function_pixel_data.shape[:2]:
             raise ValueError(
                 "This module requires that the image and illumination function have equal dimensions.\n"
@@ -271,27 +270,16 @@ somewhat empirical.
                 )
             )
         #
-        # Either divide or subtract the illumination image from the original
+        # Apply the illumination function
         #
-        if image.divide_or_subtract == DOS_DIVIDE:
-            output_pixels = orig_image.pixel_data / illum_function_pixel_data
-        elif image.divide_or_subtract == DOS_SUBTRACT:
-            output_pixels = orig_image.pixel_data - illum_function_pixel_data
-            output_pixels[output_pixels < 0] = 0
-        else:
-            raise ValueError(
-                "Unhandled option for divide or subtract: %s"
-                % image.divide_or_subtract.value
-            )
-        
-        #
-        # Optionally, clip high and low values
-        #
-        if self.truncate_low.value:
-            output_pixels = numpy.where(output_pixels < 0, 0, output_pixels)
-        if self.truncate_high.value:
-            output_pixels = numpy.where(output_pixels > 1, 1, output_pixels)
-        
+        output_pixels = correct_illumination_apply(
+            orig_image.pixel_data,
+            illum_function_pixel_data,
+            image.divide_or_subtract.value,
+            truncate_low=self.truncate_low.value,
+            truncate_high=self.truncate_high.value,
+        )
+
         #
         # Save the output image in the image set and have it inherit
         # mask & cropping from the original image.

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev306
+Version: 5.0.0.dev318
 Summary: CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
 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_nightly-5.0.0.dev306.dist-info → cellprofiler_nightly-5.0.0.dev318.dist-info}/RECORD

@@ -1,6 +1,6 @@
 cellprofiler/__init__.py,sha256=AL2XeOBhIeYkBRyDd0QRgJan7j0DKjT1GD-RdzKvMUY,46
 cellprofiler/__main__.py,sha256=uy78oz5c6NBGRwDZkZ2Gl4HfhbJZQH6K1n54Qfl2OFc,38075
-cellprofiler/_version.py,sha256=G7VoognR8cVzAPvjy716XjRcsJUGbmEf3x2OzMxn-4o,721
+cellprofiler/_version.py,sha256=VKwI68zHVxr7qKLpGyfYE5ws8C3HO1sHftyVZcFWLQk,721
 cellprofiler/knime_bridge.py,sha256=T6Op-KO79oULx92nGXRQ6lHsEcTutx1Uep1L4ZOKJgc,27767
 cellprofiler/misc.py,sha256=yqv873lP_mquxxkKcLgE_ZU4Hrc1trtuQ-NXLK2qQVc,553
 cellprofiler/data/examples/ExampleFly/ExampleFly.cppipe,sha256=JGZK9IZuYlOHOI4hi6a3DK36IahY69cfeLEd7eJ_rO0,15409
@@ -285,9 +285,9 @@ cellprofiler/modules/classifyobjects.py,sha256=wlQ5IqVEhCChFTtFY2GadUL1pAMB78DUS
 cellprofiler/modules/closing.py,sha256=62ug-EgtRYqJn6e0_jF1z8JE2EZqJu8H2Uc57JAiDSA,1879
 cellprofiler/modules/colortogray.py,sha256=RlFGmNxai_7vqtxprIceb0XILfdpm89c-DVBpuX2Cv4,24129
 cellprofiler/modules/combineobjects.py,sha256=N5cFbqAsGM11VuXdAlfr6L0AbnK0fxqB_Vb04C7ltOg,11043
-cellprofiler/modules/convertimagetoobjects.py,sha256=2uXlDgGGpixC1GhsGVW3GvJXB5xQwuDYjwjN3CMcKfQ,4953
+cellprofiler/modules/convertimagetoobjects.py,sha256=qgPb6xNuvELt_GOdkyHsaH2tdSDKtZGVMpNtVcV28sI,4700
 cellprofiler/modules/convertobjectstoimage.py,sha256=zvn2nlnF3-i6g16F0um1yNT-Y03e2j5AIueZtKbfkoc,7113
-cellprofiler/modules/correctilluminationapply.py,sha256=ijqdJHt1keYFvssff46O36BWyGP6uOhtekXBPi79vH8,16247
+cellprofiler/modules/correctilluminationapply.py,sha256=eEcXliF2xNkT36Bo7xkNNh7l2YGbSqkqpss4O7RbwaM,15862
 cellprofiler/modules/correctilluminationcalculate.py,sha256=wJMCy3W9zK-xPI8PUvh25MLtE_JSI3QuVVzdLjuTwD4,54200
 cellprofiler/modules/createbatchfiles.py,sha256=a8R5PpbaQYqF8OIvWBuC0uh-yhjzBaU4Uni4m3MRLok,19512
 cellprofiler/modules/crop.py,sha256=Lg1cQCIzO7o8wcwEgRlsccdt8mgiiugowcNEe44vT0k,36039
@@ -374,9 +374,9 @@ cellprofiler/modules/plugins/segmentationtemplatewithdependencies.py,sha256=Sh76
 cellprofiler/utilities/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cellprofiler/utilities/morphology.py,sha256=8-81TrP8AmE3ETXIvQUKFD1vmKNBy2lfbc1QnM1eGIM,2685
 cellprofiler/utilities/rules.py,sha256=NoIHwFTA37zGvIP7vcB-aYeys0MDYVYxspfhLJe00OU,8790
-cellprofiler_nightly-5.0.0.dev306.dist-info/licenses/LICENSE,sha256=QLWaBS7kAioYx7PmJNXAMJaY8NODcFAag60YlUWuyz0,2276
-cellprofiler_nightly-5.0.0.dev306.dist-info/METADATA,sha256=oBF7FN7-iCY7cJF-9KdIGiIGr4fwSZwntFi2gtC4CEA,6063
-cellprofiler_nightly-5.0.0.dev306.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-cellprofiler_nightly-5.0.0.dev306.dist-info/entry_points.txt,sha256=MNDCjguFW3dKiS5Pcdu1NfWo4I0HHI3DekJLUJ4AKkY,60
-cellprofiler_nightly-5.0.0.dev306.dist-info/top_level.txt,sha256=bK7AacDeSj9qAmW8MGlO5wA79hDj6-ACt_mENUNKSIk,13
-cellprofiler_nightly-5.0.0.dev306.dist-info/RECORD,,
+cellprofiler_nightly-5.0.0.dev318.dist-info/licenses/LICENSE,sha256=QLWaBS7kAioYx7PmJNXAMJaY8NODcFAag60YlUWuyz0,2276
+cellprofiler_nightly-5.0.0.dev318.dist-info/METADATA,sha256=x_cH5kn90YFPhDW1njHHwH4IHwMxcUKR5bfXgxSIKvQ,6063
+cellprofiler_nightly-5.0.0.dev318.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+cellprofiler_nightly-5.0.0.dev318.dist-info/entry_points.txt,sha256=MNDCjguFW3dKiS5Pcdu1NfWo4I0HHI3DekJLUJ4AKkY,60
+cellprofiler_nightly-5.0.0.dev318.dist-info/top_level.txt,sha256=bK7AacDeSj9qAmW8MGlO5wA79hDj6-ACt_mENUNKSIk,13
+cellprofiler_nightly-5.0.0.dev318.dist-info/RECORD,,