cellprofiler-library-nightly 5.0.0.dev727__tar.gz → 5.0.0.dev729__tar.gz

{cellprofiler_library_nightly-5.0.0.dev727/cellprofiler_library_nightly.egg-info → cellprofiler_library_nightly-5.0.0.dev729}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev727
+Version: 5.0.0.dev729
 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.dev727 → cellprofiler_library_nightly-5.0.0.dev729}/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.dev727'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev727')
+__version__ = version = '5.0.0.dev729'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev729')
 
-__commit_id__ = commit_id = 'gbe847d907'
+__commit_id__ = commit_id = 'g9c74b2cb1'

{cellprofiler_library_nightly-5.0.0.dev727 → cellprofiler_library_nightly-5.0.0.dev729}/cellprofiler_library/functions/measurement.py

@@ -30,6 +30,7 @@ from cellprofiler_library.functions.segmentation import count_from_ijv
 from cellprofiler_library.functions.segmentation import areas_from_ijv
 from cellprofiler_library.functions.segmentation import cast_labels_to_label_set
 from cellprofiler_library.functions.segmentation import convert_label_set_to_ijv
+from cellprofiler_library.functions.segmentation import relate_children
 from cellprofiler_library.functions.image_processing import masked_erode, restore_scale, get_morphology_footprint
 from cellprofiler_library.functions.object_processing import size_similarly
 from cellprofiler_library.functions.segmentation import relate_labels
@@ -42,6 +43,7 @@ from cellprofiler_library.opts.measureobjectskeleton import VF_I, VF_J, VF_LABEL
 from cellprofiler_library.opts.measureobjectneighbors import DistanceMethod as NeighborsDistanceMethod
 from cellprofiler_library.opts.measureobjectneighbors import MeasurementScale as NeighborsMeasurementScale
 from cellprofiler_core.constants.measurement import (
+    FF_COUNT,
     FF_PARENT,
 )
 from cellprofiler_library.opts.relateobjects import TemplateMeasurementFormat
@@ -53,6 +55,7 @@ from cellprofiler_library.opts.measurement import (
     M_LOCATION_CENTER_Z,
     C_LOCATION,
     M_NUMBER_OBJECT_NUMBER,
+    FF_CHILDREN_COUNT,
 )
 
 ###############################################################################
@@ -4472,16 +4475,94 @@ def get_object_location_measurements(object_name, labels, object_count=None):
     )
     return measurements
 
-def get_object_count_measurements(*args, **kwargs):
-    # TODO: #5117 implement add_object_location_measurements from src/subpackages/core/cellprofiler_core/utilities/core/module/identify.py
-    pass
+def get_object_count_measurements(object_name, object_count):
+    """Add the # of objects to the measurements"""
+    lib_measurements = LibraryMeasurements()
+    lib_measurements.add_image_measurement(FF_COUNT % object_name, object_count)
+    return lib_measurements
+
+def get_object_processing_measurements(
+        object_labels,
+        object_volumetric,
+        object_count,
+        object_name,
+        object_ijv,
+        parent_object_name,  
+        parent_object_labels,
+        parent_object_ijv,
+    ):
+
+    lib_measurements = get_image_segmentation_measurements(
+        object_labels, object_volumetric, object_count, object_name
+    )
+    lib_measurements_relate = get_relate_object_measurements(
+        object_labels, object_volumetric, object_name, object_ijv, 
+        parent_object_name, parent_object_labels, parent_object_ijv, 
+    )
+    lib_measurements = lib_measurements.merge(lib_measurements_relate)
+
+    return lib_measurements
+
+def get_relate_object_measurements(
+        object_labels, object_volumetric, object_name, object_ijv,
+        parent_object_name, parent_object_labels, parent_object_ijv,
+    ):
+    lib_measurements = LibraryMeasurements()
+    children_per_parent, parents_of_children = relate_children(
+        parent_object_labels, 
+        object_labels, 
+        parent_object_ijv, 
+        object_ijv, 
+        volumetric=object_volumetric
+    )
+    lib_measurements.add_measurement(
+        parent_object_name,
+        FF_CHILDREN_COUNT % object_name,
+        children_per_parent,
+    )
+
+    lib_measurements.add_measurement(
+        object_name, FF_PARENT % parent_object_name, parents_of_children,
+    )
+    return lib_measurements
+
+def get_image_segmentation_measurements(
+        object_labels, 
+        objects_volumetric, 
+        objects_count, 
+        object_name
+    ):
+    lib_measurements = LibraryMeasurements()
+    centers = center_of_labels_mass(object_labels, validate=False)
+
+    if len(centers) == 0:
+        center_z, center_y, center_x = [], [], []
+    else:
+        if objects_volumetric:
+            center_z, center_y, center_x = centers.transpose()
+        else:
+            center_z = [0] * len(centers)
+
+            center_y, center_x = centers.transpose()
+
+    lib_measurements.add_measurement(
+        object_name, M_LOCATION_CENTER_X, center_x,
+    )
+
+    lib_measurements.add_measurement(
+        object_name, M_LOCATION_CENTER_Y, center_y,
+    )
 
-def get_object_processing_measurements(*args, **kwargs):
-    # TODO: #5117 implement add_measurements from src/subpackages/core/cellprofiler_core/module/image_segmentation/_object_processing.py
-    pass
+    lib_measurements.add_measurement(
+        object_name, M_LOCATION_CENTER_Z, center_z,
+    )
 
-def get_image_segmentation_measurements(*args, **kwargs):
-    # TODO: #5117 implement add_measurements from src/subpackages/core/cellprofiler_core/module/image_segmentation/_image_segmentation.py
-    pass
+    lib_measurements.add_measurement(
+        object_name, M_NUMBER_OBJECT_NUMBER, numpy.arange(1, objects_count + 1),
+    )
 
+    lib_measurements.add_image_measurement( 
+        FF_COUNT % object_name, numpy.array([objects_count], dtype=float),
+    )
+    return lib_measurements
 

{cellprofiler_library_nightly-5.0.0.dev727 → cellprofiler_library_nightly-5.0.0.dev729/cellprofiler_library_nightly.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev727
+Version: 5.0.0.dev729
 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.dev727 → cellprofiler_library_nightly-5.0.0.dev729}/cellprofiler_library_nightly.egg-info/scm_version.json

@@ -1,7 +1,7 @@
 {
   "tag": "5.0.0.dev0",
-  "distance": 727,
-  "node": "gbe847d907b81c90560885d9cd863bb9b0b343979",
+  "distance": 729,
+  "node": "g9c74b2cb10f732f964570cfe7184a0ca7587d352",
   "dirty": true,
   "branch": "main",
   "node_date": "2026-09-28"