cellprofiler-library-nightly 5.0.0.dev669__tar.gz → 5.0.0.dev674__tar.gz

{cellprofiler_library_nightly-5.0.0.dev669/cellprofiler_library_nightly.egg-info → cellprofiler_library_nightly-5.0.0.dev674}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev669
+Version: 5.0.0.dev674
 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.dev669 → cellprofiler_library_nightly-5.0.0.dev674}/cellprofiler_library/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '5.0.0.dev669'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev669')
+__version__ = version = '5.0.0.dev674'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev674')
 
-__commit_id__ = commit_id = 'g51250caf3'
+__commit_id__ = commit_id = 'g70806405c'

{cellprofiler_library_nightly-5.0.0.dev669 → cellprofiler_library_nightly-5.0.0.dev674}/cellprofiler_library/functions/image_processing.py

@@ -24,6 +24,7 @@ from skimage.restoration import denoise_bilateral
 from centrosome.cpmorphology import get_line_pts, all_connected_components
 from scipy.ndimage import binary_erosion, binary_fill_holes
 from scipy.ndimage import mean as mean_of_labels
+from skimage.feature import peak_local_max
 from scipy.fftpack import fft2, ifft2
 from cellprofiler_library.types import (
     ImageGrayscale, ImageGrayscaleMask, 
@@ -3073,3 +3074,38 @@ def get_source_range(
         src_max = source_high
         
     return src_min, src_max
+
+################################################################################
+# FindMaxima
+################################################################################
+
+def find_maxima_in_data(
+        x_data: ImageAny, 
+        min_distance_value: int, 
+        label_maxima: bool, 
+        th_abs: Optional[float]=None
+    ) -> Union[ImageBinary, ObjectSegmentation]:
+    maxima_coords = peak_local_max(
+        x_data,
+        min_distance=min_distance_value,
+        threshold_abs=th_abs,
+    )
+    y_data = numpy.zeros(x_data.shape, dtype=bool)
+    y_data[tuple(maxima_coords.T)] = True
+
+    if label_maxima:
+        y_data = scipy.ndimage.label(y_data)[0]
+    return y_data
+
+def find_maxima_threshold(x_data: ImageAny) -> ImageAny:
+    """Identity function, just returns the input"""
+    return x_data
+
+def apply_target_mask(x_data: ImageAny, masking_image: Union[ImageAny,ObjectSegmentation]) -> ImageAny:
+    mask = masking_image.astype(bool)
+    x_data[~mask] = 0
+    return x_data
+
+
+
+

cellprofiler_library_nightly-5.0.0.dev674/cellprofiler_library/modules/_findmaxima.py

@@ -0,0 +1,31 @@
+import scipy.ndimage
+from typing import Optional, Annotated, Union
+from pydantic import validate_call, ConfigDict, Field
+from cellprofiler_library.types import ImageAny, ObjectSegmentation, ImageBinary
+from cellprofiler_library.opts.findmaxima import BackgroundExclusionMode
+from cellprofiler_library.functions.image_processing import find_maxima_in_data, find_maxima_threshold, apply_target_mask
+
+@validate_call(config=ConfigDict(arbitrary_types_allowed=True))
+def find_maxima(
+        x_data:              Annotated[ImageAny, Field(description="Input image to search for maxima")],
+        exclude_mode:        Annotated[BackgroundExclusionMode, Field(description="Method for excluding background")],
+        min_distance_value:  Annotated[int, Field(description="Minimum distance between maxima")], #Minimum distance between maxima
+        label_maxima:        Annotated[bool, Field(description="Individually label maxima?")],
+        min_intensity_value: Annotated[Optional[float], Field(description="Specify the minimum intensity of a peak")],
+        target_mask:         Annotated[Optional[Union[ImageAny,ObjectSegmentation]], Field(description="The image or objects to search within")], 
+    ) -> Union[ImageBinary, ObjectSegmentation]:
+    th_abs = min_intensity_value
+
+    if exclude_mode.value == BackgroundExclusionMode.THRESHOLD.value:
+        x_data = find_maxima_threshold(x_data)
+    elif exclude_mode.value == BackgroundExclusionMode.MASK.value:
+        assert target_mask is not None, "Mask image is required for mask mode"
+        x_data = apply_target_mask(x_data, target_mask)
+    elif exclude_mode.value == BackgroundExclusionMode.OBJECTS.value:
+        assert target_mask is not None, "Objects are required for within objects mode"
+        x_data = apply_target_mask(x_data, target_mask)
+    else:
+        raise NotImplementedError("Invalid background method choice")
+    
+    return find_maxima_in_data(x_data, min_distance_value, label_maxima, th_abs)
+

cellprofiler_library_nightly-5.0.0.dev674/cellprofiler_library/opts/findmaxima.py

@@ -0,0 +1,7 @@
+from enum import Enum
+
+class BackgroundExclusionMode(str, Enum):
+    """Background exclusion method"""
+    THRESHOLD = "Threshold"
+    MASK = "Mask"
+    OBJECTS = "Within Objects"

{cellprofiler_library_nightly-5.0.0.dev669 → cellprofiler_library_nightly-5.0.0.dev674/cellprofiler_library_nightly.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev669
+Version: 5.0.0.dev674
 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.dev669 → cellprofiler_library_nightly-5.0.0.dev674}/cellprofiler_library_nightly.egg-info/SOURCES.txt

@@ -31,6 +31,7 @@ cellprofiler_library/modules/_erodeobjects.py
 cellprofiler_library/modules/_expandorshrinkobjects.py
 cellprofiler_library/modules/_fillobjects.py
 cellprofiler_library/modules/_filterobjects.py
+cellprofiler_library/modules/_findmaxima.py
 cellprofiler_library/modules/_flipandrotate.py
 cellprofiler_library/modules/_gaussianfilter.py
 cellprofiler_library/modules/_graytocolor.py
@@ -83,6 +84,7 @@ cellprofiler_library/opts/enhanceorsuppressfeatures.py
 cellprofiler_library/opts/erodeimage.py
 cellprofiler_library/opts/erodeobjects.py
 cellprofiler_library/opts/filterobjects.py
+cellprofiler_library/opts/findmaxima.py
 cellprofiler_library/opts/flipandrotate.py
 cellprofiler_library/opts/graytocolor.py
 cellprofiler_library/opts/identifydeadworms.py

{cellprofiler_library_nightly-5.0.0.dev669 → cellprofiler_library_nightly-5.0.0.dev674}/cellprofiler_library_nightly.egg-info/scm_file_list.json

@@ -28,6 +28,7 @@
     "cellprofiler_library/modules/_expandorshrinkobjects.py",
     "cellprofiler_library/modules/_fillobjects.py",
     "cellprofiler_library/modules/_filterobjects.py",
+    "cellprofiler_library/modules/_findmaxima.py",
     "cellprofiler_library/modules/_flipandrotate.py",
     "cellprofiler_library/modules/_gaussianfilter.py",
     "cellprofiler_library/modules/_graytocolor.py",
@@ -80,6 +81,7 @@
     "cellprofiler_library/opts/erodeimage.py",
     "cellprofiler_library/opts/erodeobjects.py",
     "cellprofiler_library/opts/filterobjects.py",
+    "cellprofiler_library/opts/findmaxima.py",
     "cellprofiler_library/opts/flipandrotate.py",
     "cellprofiler_library/opts/graytocolor.py",
     "cellprofiler_library/opts/identifydeadworms.py",

cellprofiler_library_nightly-5.0.0.dev674/cellprofiler_library_nightly.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "5.0.0.dev0",
+  "distance": 674,
+  "node": "g70806405c22aad5d5e470413232c1491aac2661d",
+  "dirty": true,
+  "branch": "main",
+  "node_date": "2026-08-24"
+}

cellprofiler_library_nightly-5.0.0.dev669/cellprofiler_library_nightly.egg-info/scm_version.json

@@ -1,8 +0,0 @@
-{
-  "tag": "5.0.0.dev0",
-  "distance": 669,
-  "node": "g51250caf343cdf434f15b90b277ba794c7510c79",
-  "dirty": true,
-  "branch": "main",
-  "node_date": "2026-08-21"
-}