cellprofiler-library-nightly 5.0.0.dev462__tar.gz → 5.0.0.dev466__tar.gz

{cellprofiler_library_nightly-5.0.0.dev462 → cellprofiler_library_nightly-5.0.0.dev466}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev462
+Version: 5.0.0.dev466
 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.dev462 → cellprofiler_library_nightly-5.0.0.dev466}/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.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_library_nightly-5.0.0.dev462 → cellprofiler_library_nightly-5.0.0.dev466}/cellprofiler_library/functions/image_processing.py

@@ -1854,3 +1854,88 @@ def imagemath_apply_unary_operation(
             "The operation %s has not been implemented" % opval
         )
     return output_pixel_data, output_mask
+
+
+###############################################################################
+# GrayToColor
+###############################################################################
+
+def gray_to_rgb(
+        pixel_data_arr: List[Optional[Image2DGrayscale]],
+        adjustment_factor_array: List[float],
+        intensities: List[Tuple[float, ...]]=[(1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0)],
+        wants_rescale: bool=True,
+        ) -> Image2DColor:
+    assert(len(pixel_data_arr) == len(adjustment_factor_array)), f"pixel_data_arr and adjustment_factor_array must be the same length. pixel_data_arr has {len(pixel_data_arr)} elements, adjustment_factor_array has {len(adjustment_factor_array)} elements."
+    assert(len(pixel_data_arr) == len(intensities)), f"pixel_data_arr and intensities must be the same length. pixel_data_arr has {len(pixel_data_arr)} elements, intensities has {len(intensities)} elements."
+
+    parent_image = None
+    rgb_pixel_data = None
+    for pixel_data, adjustment_factor, intensity_triplet in zip(pixel_data_arr, adjustment_factor_array, intensities):
+        if pixel_data is None:
+            continue
+        multiplier = numpy.array(intensity_triplet) * adjustment_factor
+        if wants_rescale:
+            pixel_data = pixel_data /numpy.max(pixel_data)
+        if parent_image is not None:
+            if parent_image.shape != pixel_data.shape:
+                raise ValueError(
+                    "The input images have different sizes (%s vs %s)"
+                    % (
+                        parent_image.shape, 
+                        pixel_data.shape,
+                    )
+                )
+            rgb_pixel_data += numpy.dstack([pixel_data] * 3) * multiplier
+        else:
+            parent_image = pixel_data
+            rgb_pixel_data = numpy.dstack([pixel_data] * 3) * multiplier
+    return rgb_pixel_data
+
+def gray_to_cmyk(*args, **kwargs):
+    # gray to cmyk has the same implementation as gray to rgb but with different intensities
+    return gray_to_rgb(*args, **kwargs)
+
+
+def gray_to_composite_color(
+        pixel_data_arr: List[Optional[Image2DGrayscale]],
+        color_array: List[Tuple[int, int, int]],
+        weight_array: List[float],
+        wants_rescale: bool,
+) -> Image2DColor:
+    source_channels = pixel_data_arr
+    parent_image = pixel_data_arr[0]
+    for idx, pd in enumerate(source_channels):
+        if pd is None:
+            continue
+        if pd.shape != source_channels[0].shape:
+            raise ValueError(
+                "The input images have different sizes (%s vs %s)"
+                % (
+                    source_channels[0].shape,
+                    pd.shape,
+                )
+            )
+
+    colors: List[NDArray[numpy.float32]] = []
+    pixel_data = parent_image
+    if wants_rescale:
+        pixel_data = pixel_data / numpy.max(pixel_data)
+    for color_tuple, weight in zip(color_array, weight_array):
+        color = (weight * numpy.array(color_tuple).astype(pixel_data.dtype) / 255)
+        colors += [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 wants_rescale:
+            image = image / numpy.max(image)
+        rgb_pixel_data = rgb_pixel_data + image[:, :, numpy.newaxis] * color
+
+    return rgb_pixel_data
+    
+
+def gray_to_stacked_color(
+    pixel_data_arr: List[Optional[Image2DGrayscale]]
+) -> Image2DColor:
+    source_channels = pixel_data_arr
+    rgb_pixel_data = numpy.dstack(source_channels)
+    return rgb_pixel_data

cellprofiler_library_nightly-5.0.0.dev466/cellprofiler_library/modules/_graytocolor.py

@@ -0,0 +1,58 @@
+import numpy
+from numpy.typing import NDArray
+from typing import List, Tuple, Optional
+from pydantic import validate_call, ConfigDict
+from cellprofiler_library.opts.graytocolor import Scheme
+from cellprofiler_library.types import Image2DGrayscale, Image2DColor
+from cellprofiler_library.functions.image_processing import gray_to_rgb, gray_to_cmyk, gray_to_composite_color, gray_to_stacked_color
+
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
+def gray_to_color(
+    pixel_data_arr: List[Optional[Image2DGrayscale]],
+    scheme: Scheme,
+    color_array: Optional[List[Tuple[int, int, int]]] = None,
+    weight_array: Optional[List[float]] = None,
+    adjustment_factor_array: Optional[List[float]] = None,
+    intensities: List[Tuple[float, ...]]=[(1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0)],
+    wants_rescale: bool=True,
+) -> Image2DColor:
+    rgb_pixel_data = None
+    if scheme == Scheme.RGB:
+        assert adjustment_factor_array is not None, "adjustment_factor_array must be provided for RGB mode"
+        assert intensities is not None, "intensities must be provided for RGB mode"
+        rgb_pixel_data = gray_to_rgb(
+            pixel_data_arr = pixel_data_arr,
+            adjustment_factor_array = adjustment_factor_array,
+            intensities = intensities,
+            wants_rescale = wants_rescale,
+        )
+    elif scheme == Scheme.CMYK:
+        assert adjustment_factor_array is not None, "adjustment_factor_array must be provided for CMYK mode"
+        assert intensities is not None, "intensities must be provided for CMYK mode"
+        rgb_pixel_data = gray_to_cmyk(
+            pixel_data_arr = pixel_data_arr,
+            adjustment_factor_array = adjustment_factor_array,
+            intensities = intensities,
+            wants_rescale = wants_rescale,
+        )
+    elif scheme == Scheme.COMPOSITE:
+        assert color_array is not None, "color_array must be provided for composite mode"
+        assert weight_array is not None, "weight_array must be provided for composite mode"
+        rgb_pixel_data = gray_to_composite_color(
+            pixel_data_arr = pixel_data_arr,
+            color_array = color_array,
+            weight_array = weight_array,
+            wants_rescale = wants_rescale,
+        )
+    elif scheme == Scheme.STACK:
+        assert pixel_data_arr is not None, "pixel_data_arr must be provided for stack mode"
+        rgb_pixel_data = gray_to_stacked_color(
+            pixel_data_arr = pixel_data_arr,
+        )
+    else:
+        raise ValueError(f"Unimplemented scheme: {scheme}")
+    if scheme.value != Scheme.STACK and wants_rescale:
+        # If we rescaled, clip values that went out of range after multiplication
+        rgb_pixel_data[rgb_pixel_data > 1] = 1
+    return rgb_pixel_data
+

cellprofiler_library_nightly-5.0.0.dev466/cellprofiler_library/opts/graytocolor.py

@@ -0,0 +1,20 @@
+from enum import Enum
+
+class Scheme(str, Enum):
+    RGB = "RGB"
+    CMYK = "CMYK"
+    STACK = "Stack"
+    COMPOSITE = "Composite"
+    LEAVE_THIS_BLACK = "Leave this black"
+
+DEFAULT_COLORS = [
+    "#%02x%02x%02x" % color
+    for color in (
+        (255, 0, 0),
+        (0, 255, 0),
+        (0, 0, 255),
+        (128, 128, 0),
+        (128, 0, 128),
+        (0, 128, 128),
+    )
+]

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev462
+Version: 5.0.0.dev466
 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.dev462 → cellprofiler_library_nightly-5.0.0.dev466}/cellprofiler_library_nightly.egg-info/SOURCES.txt

@@ -29,6 +29,7 @@ cellprofiler_library/modules/_erodeobjects.py
 cellprofiler_library/modules/_expandorshrinkobjects.py
 cellprofiler_library/modules/_fillobjects.py
 cellprofiler_library/modules/_gaussianfilter.py
+cellprofiler_library/modules/_graytocolor.py
 cellprofiler_library/modules/_identifyprimaryobjects.py
 cellprofiler_library/modules/_identifysecondaryobjects.py
 cellprofiler_library/modules/_identifytertiaryobjects.py
@@ -60,6 +61,7 @@ cellprofiler_library/opts/dilateobjects.py
 cellprofiler_library/opts/enhanceorsuppressfeatures.py
 cellprofiler_library/opts/erodeimage.py
 cellprofiler_library/opts/erodeobjects.py
+cellprofiler_library/opts/graytocolor.py
 cellprofiler_library/opts/identifyprimaryobjects.py
 cellprofiler_library/opts/identifysecondaryobjects.py
 cellprofiler_library/opts/identifytertiaryobjects.py