CellProfiler-nightly 5.0.0.dev462__tar.gz → 5.0.0.dev466__tar.gz

{cellprofiler_nightly-5.0.0.dev462 → cellprofiler_nightly-5.0.0.dev466}/CellProfiler_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev462
+Version: 5.0.0.dev466
 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.dev462 → cellprofiler_nightly-5.0.0.dev466}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev462
+Version: 5.0.0.dev466
 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.dev462 → cellprofiler_nightly-5.0.0.dev466}/cellprofiler/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '5.0.0.dev462'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev462')
+__version__ = version = '5.0.0.dev466'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev466')
 
-__commit_id__ = commit_id = 'g8dcb1b2d8'
+__commit_id__ = commit_id = 'ge958a4dc2'

{cellprofiler_nightly-5.0.0.dev462 → cellprofiler_nightly-5.0.0.dev466}/cellprofiler/modules/graytocolor.py

@@ -25,6 +25,7 @@ See also **ColorToGray** and **InvertForPrinting**.
 """
 
 import numpy
+from typing import List
 from cellprofiler_core.image import Image
 from cellprofiler_core.module import Module
 from cellprofiler_core.setting import Color, Binary
@@ -35,6 +36,9 @@ from cellprofiler_core.setting.choice import Choice
 from cellprofiler_core.setting.do_something import DoSomething, RemoveSettingButton
 from cellprofiler_core.setting.subscriber import ImageSubscriber
 from cellprofiler_core.setting.text import ImageName, Float
+from cellprofiler_library.modules._graytocolor import gray_to_color
+from cellprofiler_library.types import Image2DGrayscale
+from cellprofiler_library.opts.graytocolor import Scheme
 
 OFF_RED_IMAGE_NAME = 0
 OFF_GREEN_IMAGE_NAME = 1
@@ -48,10 +52,6 @@ OFF_STACK_CHANNELS_V2 = 16
 OFF_STACK_CHANNEL_COUNT_V3 = 16
 OFF_STACK_CHANNEL_COUNT = 17
 
-SCHEME_RGB = "RGB"
-SCHEME_CMYK = "CMYK"
-SCHEME_STACK = "Stack"
-SCHEME_COMPOSITE = "Composite"
 LEAVE_THIS_BLACK = "Leave this black"
 
 DEFAULT_COLORS = [
@@ -75,32 +75,33 @@ class GrayToColor(Module):
     def create_settings(self):
         self.scheme_choice = Choice(
             "Select a color scheme",
-            [SCHEME_RGB, SCHEME_CMYK, SCHEME_STACK, SCHEME_COMPOSITE],
+            [Scheme.RGB, Scheme.CMYK, Scheme.STACK, Scheme.COMPOSITE],
             doc="""\
 This module can use one of two color schemes to combine images:
 
--  *%(SCHEME_RGB)s*: Each input image determines the intensity of one
+-  *{SCHEME_RGB}*: Each input image determines the intensity of one
    of the color channels: red, green, and blue.
--  *%(SCHEME_CMYK)s*: Three of the input images are combined to
+-  *{SCHEME_CMYK}*: Three of the input images are combined to
    determine the colors (cyan, magenta, and yellow) and a fourth is used
    only for brightness. The cyan image adds equally to the green and
    blue intensities. The magenta image adds equally to the red and blue
    intensities. The yellow image adds equally to the red and green
    intensities.
--  *%(SCHEME_STACK)s*: The channels are stacked in the order listed,
+-  *{SCHEME_STACK}*: The channels are stacked in the order listed,
    from top to bottom. An arbitrary number of channels is allowed.
 
    For example, you could create a 5-channel image by providing
    5 grayscale images. The first grayscale image you provide will fill
    the first channel, the second grayscale image you provide will fill
    the second channel, and so on.
--  *%(SCHEME_COMPOSITE)s*: A color is assigned to each grayscale image.
+-  *{SCHEME_COMPOSITE}*: A color is assigned to each grayscale image.
    Each grayscale image is converted to color by multiplying the
    intensity by the color and the resulting color images are added
    together. An arbitrary number of channels can be composited into a
    single color image.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_RGB": Scheme.RGB, "SCHEME_CMYK": Scheme.CMYK, "SCHEME_STACK": Scheme.STACK, "SCHEME_COMPOSITE": Scheme.COMPOSITE}
+            )
         )
 
         self.wants_rescale = Binary(
@@ -128,11 +129,12 @@ in clipping.""",
             can_be_blank=True,
             blank_text=LEAVE_THIS_BLACK,
             doc="""\
-*(Used only if "%(SCHEME_RGB)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_RGB}" is selected as the color scheme)*
 
 Select the input image to be displayed in red.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_RGB": Scheme.RGB}
+            )
         )
 
         self.green_image_name = ImageSubscriber(
@@ -140,11 +142,12 @@ Select the input image to be displayed in red.
             can_be_blank=True,
             blank_text=LEAVE_THIS_BLACK,
             doc="""\
-*(Used only if "%(SCHEME_RGB)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_RGB}" is selected as the color scheme)*
 
 Select the input image to be displayed in green.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_RGB": Scheme.RGB}
+            )
         )
 
         self.blue_image_name = ImageSubscriber(
@@ -152,11 +155,12 @@ Select the input image to be displayed in green.
             can_be_blank=True,
             blank_text=LEAVE_THIS_BLACK,
             doc="""\
-*(Used only if "%(SCHEME_RGB)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_RGB}" is selected as the color scheme)*
 
 Select the input image to be displayed in blue.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_RGB": Scheme.RGB}
+            )
         )
 
         self.rgb_image_name = ImageName(
@@ -170,14 +174,15 @@ Select the input image to be displayed in blue.
             value=1,
             minval=0,
             doc="""\
-*(Used only if "%(SCHEME_RGB)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_RGB}" is selected as the color scheme)*
 
 Enter the relative weight for the red image. If all relative weights are
 equal, all three colors contribute equally in the final image. To weight
 colors relative to each other, increase or decrease the relative
 weights.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_RGB": Scheme.RGB}
+            )
         )
 
         self.green_adjustment_factor = Float(
@@ -185,14 +190,15 @@ weights.
             value=1,
             minval=0,
             doc="""\
-*(Used only if "%(SCHEME_RGB)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_RGB}" is selected as the color scheme)*
 
 Enter the relative weight for the green image. If all relative weights
 are equal, all three colors contribute equally in the final image. To
 weight colors relative to each other, increase or decrease the relative
 weights.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_RGB": Scheme.RGB}
+            )
         )
 
         self.blue_adjustment_factor = Float(
@@ -200,14 +206,15 @@ weights.
             value=1,
             minval=0,
             doc="""\
-*(Used only if "%(SCHEME_RGB)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_RGB}" is selected as the color scheme)*
 
 Enter the relative weight for the blue image. If all relative weights
 are equal, all three colors contribute equally in the final image. To
 weight colors relative to each other, increase or decrease the relative
 weights.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_RGB": Scheme.RGB}
+            )
         )
         # # # # # # # # # # # # # #
         #
@@ -219,11 +226,12 @@ weights.
             can_be_blank=True,
             blank_text=LEAVE_THIS_BLACK,
             doc="""\
-*(Used only if "%(SCHEME_CMYK)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_CMYK}" is selected as the color scheme)*
 
 Select the input image to be displayed in cyan.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_CMYK": Scheme.CMYK}
+            )
         )
 
         self.magenta_image_name = ImageSubscriber(
@@ -231,11 +239,12 @@ Select the input image to be displayed in cyan.
             can_be_blank=True,
             blank_text=LEAVE_THIS_BLACK,
             doc="""\
-*(Used only if "%(SCHEME_CMYK)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_CMYK}" is selected as the color scheme)*
 
 Select the input image to be displayed in magenta.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_CMYK": Scheme.CMYK}
+            )
         )
 
         self.yellow_image_name = ImageSubscriber(
@@ -243,11 +252,12 @@ Select the input image to be displayed in magenta.
             can_be_blank=True,
             blank_text=LEAVE_THIS_BLACK,
             doc="""\
-*(Used only if "%(SCHEME_CMYK)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_CMYK}" is selected as the color scheme)*
 
 Select the input image to be displayed in yellow.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_CMYK": Scheme.CMYK}
+            )
         )
 
         self.gray_image_name = ImageSubscriber(
@@ -255,11 +265,12 @@ Select the input image to be displayed in yellow.
             can_be_blank=True,
             blank_text=LEAVE_THIS_BLACK,
             doc="""\
-*(Used only if "%(SCHEME_CMYK)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_CMYK}" is selected as the color scheme)*
 
 Select the input image that will determine each pixel's brightness.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_CMYK": Scheme.CMYK}
+            )
         )
 
         self.cyan_adjustment_factor = Float(
@@ -267,14 +278,15 @@ Select the input image that will determine each pixel's brightness.
             value=1,
             minval=0,
             doc="""\
-*(Used only if "%(SCHEME_CMYK)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_CMYK}" is selected as the color scheme)*
 
 Enter the relative weight for the cyan image. If all relative weights
 are equal, all colors contribute equally in the final image. To weight
 colors relative to each other, increase or decrease the relative
 weights.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_CMYK": Scheme.CMYK}
+            )
         )
 
         self.magenta_adjustment_factor = Float(
@@ -282,14 +294,15 @@ weights.
             value=1,
             minval=0,
             doc="""\
-*(Used only if "%(SCHEME_CMYK)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_CMYK}" is selected as the color scheme)*
 
 Enter the relative weight for the magenta image. If all relative weights
 are equal, all colors contribute equally in the final image. To weight
 colors relative to each other, increase or decrease the relative
 weights.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_CMYK": Scheme.CMYK}
+            )
         )
 
         self.yellow_adjustment_factor = Float(
@@ -297,14 +310,15 @@ weights.
             value=1,
             minval=0,
             doc="""\
-*(Used only if "%(SCHEME_CMYK)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_CMYK}" is selected as the color scheme)*
 
 Enter the relative weight for the yellow image. If all relative weights
 are equal, all colors contribute equally in the final image. To weight
 colors relative to each other, increase or decrease the relative
 weights.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_CMYK": Scheme.CMYK}
+            )
         )
 
         self.gray_adjustment_factor = Float(
@@ -312,14 +326,15 @@ weights.
             value=1,
             minval=0,
             doc="""\
-*(Used only if "%(SCHEME_CMYK)s" is selected as the color scheme)*
+*(Used only if "{SCHEME_CMYK}" is selected as the color scheme)*
 
 Enter the relative weight for the brightness image. If all relative
 weights are equal, all colors contribute equally in the final image. To
 weight colors relative to each other, increase or decrease the relative
 weights.
-"""
-            % globals(),
+""".format(
+                **{"SCHEME_CMYK": Scheme.CMYK}
+            )
         )
 
         # # # # # # # # # # # # # #
@@ -349,11 +364,12 @@ weights.
                 "Image name",
                 "None",
                 doc="""\
-*(Used only if "%(SCHEME_STACK)s" or "%(SCHEME_COMPOSITE)s" is chosen)*
+*(Used only if "{SCHEME_STACK}" or "{SCHEME_COMPOSITE}" is chosen)*
 
 Select the input image to add to the stacked image.
-"""
-                % globals(),
+""".format(
+                **{"SCHEME_STACK": Scheme.STACK, "SCHEME_COMPOSITE": Scheme.COMPOSITE}
+            )
             ),
         )
         group.append(
@@ -362,11 +378,12 @@ Select the input image to add to the stacked image.
                 "Color",
                 default_color,
                 doc="""\
-*(Used only if "%(SCHEME_COMPOSITE)s" is chosen)*
+*(Used only if "{SCHEME_COMPOSITE}" is chosen)*
 
 The color to be assigned to the above image.
-"""
-                % globals(),
+""".format(
+                **{"SCHEME_COMPOSITE": Scheme.COMPOSITE}
+            )
             ),
         )
         group.append(
@@ -376,12 +393,13 @@ The color to be assigned to the above image.
                 1.0,
                 minval=0.5 / 255,
                 doc="""\
-*(Used only if "%(SCHEME_COMPOSITE)s" is chosen)*
+*(Used only if "{SCHEME_COMPOSITE}" is chosen)*
 
 The weighting of the above image relative to the others. The image’s
 pixel values are multiplied by this weight before assigning the color.
-"""
-                % globals(),
+""".format(
+                **{"SCHEME_COMPOSITE": Scheme.COMPOSITE}
+            )
             ),
         )
 
@@ -396,7 +414,7 @@ pixel values are multiplied by this weight before assigning the color.
 
     @property
     def color_scheme_settings(self):
-        if self.scheme_choice == SCHEME_RGB:
+        if self.scheme_choice == Scheme.RGB:
             return [
                 ColorSchemeSettings(
                     self.red_image_name, self.red_adjustment_factor, 1, 0, 0
@@ -408,7 +426,7 @@ pixel values are multiplied by this weight before assigning the color.
                     self.blue_image_name, self.blue_adjustment_factor, 0, 0, 1
                 ),
             ]
-        elif self.scheme_choice == SCHEME_CMYK:
+        elif self.scheme_choice == Scheme.CMYK:
             return [
                 ColorSchemeSettings(
                     self.cyan_image_name, self.cyan_adjustment_factor, 0, 0.5, 0.5
@@ -475,15 +493,15 @@ pixel values are multiplied by this weight before assigning the color.
             for color_scheme_setting in self.color_scheme_settings
         ]
         result += [self.rgb_image_name]
-        if self.scheme_choice != SCHEME_STACK:
+        if self.scheme_choice != Scheme.STACK:
             result += [self.wants_rescale]
         for color_scheme_setting in self.color_scheme_settings:
             if not color_scheme_setting.image_name.is_blank:
                 result.append(color_scheme_setting.adjustment_factor)
-        if self.scheme_choice in (SCHEME_STACK, SCHEME_COMPOSITE):
+        if self.scheme_choice in (Scheme.STACK, Scheme.COMPOSITE):
             for sc_group in self.stack_channels:
                 result.append(sc_group.image_name)
-                if self.scheme_choice == SCHEME_COMPOSITE:
+                if self.scheme_choice == Scheme.COMPOSITE:
                     result.append(sc_group.color)
                     result.append(sc_group.weight)
                 if hasattr(sc_group, "remover"):
@@ -496,7 +514,7 @@ pixel values are multiplied by this weight before assigning the color.
 
         We need at least one image name to be filled in
         """
-        if self.scheme_choice not in (SCHEME_STACK, SCHEME_COMPOSITE):
+        if self.scheme_choice not in (Scheme.STACK, Scheme.COMPOSITE):
             if all(
                 [
                     color_scheme_setting.image_name.is_blank
@@ -510,87 +528,102 @@ pixel values are multiplied by this weight before assigning the color.
 
     def run(self, workspace):
         parent_image = None
-        parent_image_name = None
         imgset = workspace.image_set
         rgb_pixel_data = None
         input_image_names = []
         channel_names = []
-        channelstack =  self.scheme_choice == SCHEME_STACK
-        if self.scheme_choice not in (SCHEME_STACK, SCHEME_COMPOSITE):
-            for color_scheme_setting in self.color_scheme_settings:
-                if color_scheme_setting.image_name.is_blank:
-                    channel_names.append("Blank")
-                    continue
-                image_name = color_scheme_setting.image_name.value
-                input_image_names.append(image_name)
-                channel_names.append(image_name)
-                image = imgset.get_image(image_name, must_be_grayscale=True)
-                multiplier = (
-                    color_scheme_setting.intensities
-                    * color_scheme_setting.adjustment_factor.value
-                )
-                pixel_data = image.pixel_data
-                if self.wants_rescale.value:
-                    pixel_data = pixel_data / numpy.max(pixel_data)
-                if parent_image is not None:
-                    if parent_image.pixel_data.shape != pixel_data.shape:
-                        raise ValueError(
-                            "The %s image and %s image have different sizes (%s vs %s)"
-                            % (
-                                parent_image_name,
-                                color_scheme_setting.image_name.value,
-                                parent_image.pixel_data.shape,
-                                image.pixel_data.shape,
-                            )
-                        )
-                    rgb_pixel_data += numpy.dstack([pixel_data] * 3) * multiplier
-                else:
-                    parent_image = image
-                    parent_image_name = color_scheme_setting.image_name.value
-                    rgb_pixel_data = numpy.dstack([pixel_data] * 3) * multiplier
+        channelstack =  self.scheme_choice == Scheme.STACK
+        if self.scheme_choice.value not in (Scheme.STACK, Scheme.COMPOSITE):
+            if self.scheme_choice.value == Scheme.RGB:
+                image_arr: List[Image2DGrayscale] = [
+                    None if self.red_image_name.value == LEAVE_THIS_BLACK else imgset.get_image(self.red_image_name.value, must_be_grayscale=True).pixel_data,
+                    None if self.green_image_name.value == LEAVE_THIS_BLACK else imgset.get_image(self.green_image_name.value, must_be_grayscale=True).pixel_data,
+                    None if self.blue_image_name.value == LEAVE_THIS_BLACK else imgset.get_image(self.blue_image_name.value, must_be_grayscale=True).pixel_data,
+                ]
+                adjustment_factor_array = [
+                    self.red_adjustment_factor.value,
+                    self.green_adjustment_factor.value,
+                    self.blue_adjustment_factor.value,
+                ]
+                intensities = [
+                    (1.0, 0.0, 0.0),
+                    (0.0, 1.0, 0.0),
+                    (0.0, 0.0, 1.0),
+                ]
+                rgb_pixel_data = gray_to_color(
+                    pixel_data_arr = image_arr, 
+                    scheme = self.scheme_choice.value,
+                    adjustment_factor_array = adjustment_factor_array, 
+                    intensities = intensities, 
+                    wants_rescale = self.wants_rescale.value
+                    )
+                # First non-blank image is considered to be the parent image
+                non_blank_image_names = [i for i in [self.red_image_name.value, self.green_image_name.value, self.blue_image_name.value] if i != LEAVE_THIS_BLACK]
+                assert len(non_blank_image_names) != 0, "At least one of the images must not be blank"
+                parent_image = imgset.get_image(non_blank_image_names[0], must_be_grayscale=True)
+            elif self.scheme_choice.value == Scheme.CMYK:
+                image_arr: List[Image2DGrayscale] = [
+                    None if self.cyan_image_name.value == LEAVE_THIS_BLACK else imgset.get_image(self.cyan_image_name.value, must_be_grayscale=True).pixel_data,
+                    None if self.magenta_image_name.value == LEAVE_THIS_BLACK else imgset.get_image(self.magenta_image_name.value, must_be_grayscale=True).pixel_data,
+                    None if self.yellow_image_name.value == LEAVE_THIS_BLACK else imgset.get_image(self.yellow_image_name.value, must_be_grayscale=True).pixel_data,
+                    None if self.gray_image_name.value == LEAVE_THIS_BLACK else imgset.get_image(self.gray_image_name.value, must_be_grayscale=True).pixel_data,
+                ]
+                adjustment_factor_array = [
+                    self.cyan_adjustment_factor.value,
+                    self.magenta_adjustment_factor.value,
+                    self.yellow_adjustment_factor.value,
+                    self.gray_adjustment_factor.value,
+                ]
+                intensities = [
+                    (0, 0.5, 0.5),
+                    (0.5, 0, 0.5),
+                    (0.5, 0.5, 0),
+                    (1.0/3.0, 1.0/3.0, 1.0/3.0),
+                ]
+
+                rgb_pixel_data = gray_to_color(
+                    pixel_data_arr = image_arr, 
+                    scheme=self.scheme_choice.value,
+                    adjustment_factor_array = adjustment_factor_array, 
+                    intensities = intensities, 
+                    wants_rescale = self.wants_rescale.value
+                    )
+
+                non_blank_image_names = [i for i in [self.cyan_image_name, self.magenta_image_name, self.yellow_image_name, self.gray_image_name] if i != LEAVE_THIS_BLACK]
+                assert len(non_blank_image_names) != 0, "At least one of the images must not be blank"
+                # First non-blank image is considered to be the parent image
+                parent_image = imgset.get_image(non_blank_image_names[0], must_be_grayscale=True)
+            else:
+                raise ValueError(f"Unimplemented scheme: {self.scheme_choice}")
         else:
             input_image_names = [sc.image_name.value for sc in self.stack_channels]
             channel_names = input_image_names
-            source_channels = [
+            source_channels: List[Image2DGrayscale] = [
                 imgset.get_image(name, must_be_grayscale=True).pixel_data
                 for name in input_image_names
             ]
             parent_image = imgset.get_image(input_image_names[0])
-            for idx, pd in enumerate(source_channels):
-                if pd.shape != source_channels[0].shape:
-                    raise ValueError(
-                        "The %s image and %s image have different sizes (%s vs %s)"
-                        % (
-                            self.stack_channels[0].image_name.value,
-                            self.stack_channels[idx].image_name.value,
-                            source_channels[0].shape,
-                            pd.pixel_data.shape,
-                        )
-                    )
-            if self.scheme_choice == SCHEME_STACK:
-                rgb_pixel_data = numpy.dstack(source_channels)
-            else:
-                colors = []
-                pixel_data = parent_image.pixel_data
-                if self.wants_rescale.value:
-                    pixel_data = pixel_data / numpy.max(pixel_data)
+            if self.scheme_choice.value == Scheme.STACK:
+                rgb_pixel_data = gray_to_color(
+                    pixel_data_arr=source_channels,
+                    scheme=self.scheme_choice.value,
+                )
+            elif self.scheme_choice.value == Scheme.COMPOSITE:
+                color_array = []
+                weight_array = []
                 for sc in self.stack_channels:
-                    color_tuple = sc.color.to_rgb()
-                    color = (
-                        sc.weight.value
-                        * numpy.array(color_tuple).astype(pixel_data.dtype)
-                        / 255
-                    )
-                    colors.append(color[numpy.newaxis, numpy.newaxis, :])
-                rgb_pixel_data = pixel_data[:, :, numpy.newaxis] * colors[0]
-                for image, color in zip(source_channels[1:], colors[1:]):
-                    if self.wants_rescale.value:
-                        image = image / numpy.max(image)
-                    rgb_pixel_data = rgb_pixel_data + image[:, :, numpy.newaxis] * color
-
-        if self.scheme_choice != SCHEME_STACK and self.wants_rescale.value:
-            # If we rescaled, clip values that went out of range after multiplication
-            rgb_pixel_data[rgb_pixel_data > 1] = 1
+                    color_array += [sc.color.to_rgb()]
+                    weight_array += [sc.weight.value]
+                rgb_pixel_data = gray_to_color(
+                    pixel_data_arr = source_channels,
+                    scheme=self.scheme_choice.value,
+                    color_array = color_array,
+                    weight_array = weight_array,
+                    wants_rescale =self.wants_rescale.value,
+                
+            )
+            else:
+                raise ValueError(f"Unimplemented scheme: {self.scheme_choice}")
 
         ##############
         # Save image #
@@ -615,11 +648,11 @@ pixel values are multiplied by this weight before assigning the color.
         images = workspace.display_data.images
         nsubplots = len(input_image_names)
 
-        if self.scheme_choice == SCHEME_CMYK:
+        if self.scheme_choice == Scheme.CMYK:
             subplots = (3, 2)
             subplot_indices = ((0, 0), (0, 1), (1, 0), (1, 1), (2, 0))
             color_subplot = (2, 1)
-        elif self.scheme_choice == SCHEME_RGB:
+        elif self.scheme_choice == Scheme.RGB:
             subplots = (2, 2)
             subplot_indices = ((0, 0), (0, 1), (1, 0))
             color_subplot = (1, 1)
@@ -656,7 +689,7 @@ pixel values are multiplied by this weight before assigning the color.
             #
             # Was RGB-only. Convert values to CYMK-style
             #
-            setting_values = [SCHEME_CMYK] + setting_values + ["None"] * 4 + [1] * 4
+            setting_values = [Scheme.CMYK.value] + setting_values + ["None"] * 4 + [1] * 4
             variable_revision_number = 2
         if variable_revision_number == 2:
             #