cellprofiler-library-nightly 5.0.0.dev544__tar.gz → 5.0.0.dev548__tar.gz

{cellprofiler_library_nightly-5.0.0.dev544/cellprofiler_library_nightly.egg-info → cellprofiler_library_nightly-5.0.0.dev548}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev544
+Version: 5.0.0.dev548
 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.dev544 → cellprofiler_library_nightly-5.0.0.dev548}/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.dev544'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev544')
+__version__ = version = '5.0.0.dev548'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev548')
 
-__commit_id__ = commit_id = 'g3d03e7dab'
+__commit_id__ = commit_id = 'g206f9390a'

{cellprofiler_library_nightly-5.0.0.dev544 → cellprofiler_library_nightly-5.0.0.dev548}/cellprofiler_library/functions/measurement.py

@@ -2198,3 +2198,58 @@ def compute_earth_movers_distance_objects(
         extra_mass_penalty=extra_mass_penalty,
     )
     return emd
+
+
+###############################################################################
+# Measure Image Skeleton
+###############################################################################
+
+
+def neighbors(image: ImageBinary):
+    """
+
+    Counts the neighbor pixels for each pixel of an image:
+
+            x = [
+                [0, 1, 0],
+                [1, 1, 1],
+                [0, 1, 0]
+            ]
+
+            _neighbors(x)
+
+            [
+                [0, 3, 0],
+                [3, 4, 3],
+                [0, 3, 0]
+            ]
+
+    :type image: numpy.ndarray
+
+    :param image: A two-or-three dimensional image
+
+    :return: neighbor pixels for each pixel of an image
+
+    """
+    padding = numpy.pad(image, 1, "constant")
+    mask = padding > 0
+
+    padding = padding.astype(float)
+
+    if image.ndim == 2:
+        response = 3 ** 2 * scipy.ndimage.uniform_filter(padding) - 1
+        labels = (response * mask)[1:-1, 1:-1]
+
+        return labels.astype(numpy.uint16)
+    elif image.ndim == 3:
+        response = 3 ** 3 * scipy.ndimage.uniform_filter(padding) - 1
+        labels = (response * mask)[1:-1, 1:-1, 1:-1]
+
+        return labels.astype(numpy.uint16)
+    else:
+        raise ValueError("Only 2D and 3D images are supported")
+
+def branches(image: ImageBinary):
+    return neighbors(image) > 2
+def endpoints(image: ImageBinary):
+    return neighbors(image) == 1

cellprofiler_library_nightly-5.0.0.dev548/cellprofiler_library/modules/_measureimageskeleton.py

@@ -0,0 +1,60 @@
+import numpy
+from numpy.typing import NDArray
+import skimage.segmentation
+from typing import Annotated, Tuple, Union, List, Any
+from pydantic import Field, validate_call, ConfigDict, BaseModel
+from cellprofiler_library.types import ImageGrayscale
+from cellprofiler_library.opts.measureimageskeleton import TemplateMeasurementFormat
+from cellprofiler_library.functions.measurement import branches, endpoints
+from cellprofiler_library.measurement_model import LibraryMeasurements
+
+
+ImageSkeletonStatistics = List[Tuple[int, int]]
+
+class ImageSkeletonDisplayData(BaseModel):
+    model_config = ConfigDict(
+        arbitrary_types_allowed=True, 
+        populate_by_name=True
+    )
+
+    statistics: ImageSkeletonStatistics
+    nodes: NDArray[Any]
+
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
+def measure_image_skeleton(
+        im_pixel_data: Annotated[ImageGrayscale, Field(description="Input image")],
+        im_name: Annotated[str, Field(description="Input image name")]="Image1",
+        return_visualization_data: Annotated[bool, Field(description="Return data for display")] = False,
+    ) -> Union[LibraryMeasurements, Tuple[LibraryMeasurements, ImageSkeletonDisplayData]]:
+    pixels = im_pixel_data > 0
+    branch_nodes = branches(pixels)
+    endpoint_nodes = endpoints(pixels)
+    num_branches = numpy.count_nonzero(branch_nodes)
+    num_endpoints = numpy.count_nonzero(endpoint_nodes)
+    
+    measurements = LibraryMeasurements()
+
+    measurements.add_image_measurement(
+        TemplateMeasurementFormat.BRANCHES % im_name,
+        num_branches
+    )
+    measurements.add_image_measurement(
+        TemplateMeasurementFormat.ENDPOINTS % im_name,
+        num_endpoints
+    )
+    
+    if return_visualization_data:
+        a = numpy.copy(branch_nodes).astype(numpy.uint16)
+        b = numpy.copy(endpoint_nodes).astype(numpy.uint16)
+
+        a[a == 1] = 1
+        b[b == 1] = 2
+
+        nodes: NDArray[Any] = skimage.segmentation.join_segmentations(a, b)
+
+        return measurements, ImageSkeletonDisplayData(
+            statistics=[(num_branches, num_endpoints)],
+            nodes=nodes
+        )
+    
+    return measurements

cellprofiler_library_nightly-5.0.0.dev548/cellprofiler_library/opts/measureimageskeleton.py

@@ -0,0 +1,3 @@
+class TemplateMeasurementFormat(str):
+    BRANCHES = "Skeleton_Branches_%s"
+    ENDPOINTS = "Skeleton_Endpoints_%s"

{cellprofiler_library_nightly-5.0.0.dev544 → cellprofiler_library_nightly-5.0.0.dev548/cellprofiler_library_nightly.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev544
+Version: 5.0.0.dev548
 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.dev544 → cellprofiler_library_nightly-5.0.0.dev548}/cellprofiler_library_nightly.egg-info/SOURCES.txt

@@ -41,6 +41,7 @@ cellprofiler_library/modules/_measuregranularity.py
 cellprofiler_library/modules/_measureimageareaoccupied.py
 cellprofiler_library/modules/_measureimageintensity.py
 cellprofiler_library/modules/_measureimageoverlap.py
+cellprofiler_library/modules/_measureimageskeleton.py
 cellprofiler_library/modules/_measureobjectintensity.py
 cellprofiler_library/modules/_measureobjectoverlap.py
 cellprofiler_library/modules/_measureobjectsizeshape.py
@@ -82,6 +83,7 @@ cellprofiler_library/opts/measuregranularity.py
 cellprofiler_library/opts/measureimageareaoccupied.py
 cellprofiler_library/opts/measureimageintensity.py
 cellprofiler_library/opts/measureimageoverlap.py
+cellprofiler_library/opts/measureimageskeleton.py
 cellprofiler_library/opts/measureobjectintensity.py
 cellprofiler_library/opts/measureobjectoverlap.py
 cellprofiler_library/opts/morph.py