cellprofiler-core-nightly 5.0.0.dev729__tar.gz → 5.0.0.dev737__tar.gz

{cellprofiler_core_nightly-5.0.0.dev729 → cellprofiler_core_nightly-5.0.0.dev737}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-core-nightly
-Version: 5.0.0.dev729
+Version: 5.0.0.dev737
 Summary: cellprofiler-core implements the bulk of CellProfiler's non-gui functionality
 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_core_nightly-5.0.0.dev729 → cellprofiler_core_nightly-5.0.0.dev737}/cellprofiler_core/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '5.0.0.dev729'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev729')
+__version__ = version = '5.0.0.dev737'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev737')
 
-__commit_id__ = commit_id = 'g9c74b2cb1'
+__commit_id__ = commit_id = 'gcb2ef7a2c'

{cellprofiler_core_nightly-5.0.0.dev729 → cellprofiler_core_nightly-5.0.0.dev737}/cellprofiler_core/measurement/_measurements.py

@@ -60,7 +60,7 @@ from ..utilities.hdf5_dict import HDF5Dict, NullLock
 from ..utilities.measurement import agg_ignore_feature
 from ..utilities.measurement import get_agg_measurement_name
 from ..utilities.measurement import make_temporary_file
-from cellprofiler_library.measurement_model import LibraryMeasurements, Relationship
+from cellprofiler_library.measurements.measurement_model import LibraryMeasurements, Relationship
 
 LOGGER = logging.getLogger(__name__)
 

{cellprofiler_core_nightly-5.0.0.dev729 → cellprofiler_core_nightly-5.0.0.dev737}/cellprofiler_core/module/image_segmentation/_image_segmentation.py

@@ -19,7 +19,7 @@ from ...constants.measurement import M_NUMBER_OBJECT_NUMBER
 from ...setting.subscriber import ImageSubscriber
 from ...setting.text import LabelName
 from cellprofiler_core.utilities.core.workspace import add_library_measurements_to_workspace_measurements
-from cellprofiler_library.functions.measurement import get_image_segmentation_measurements
+from cellprofiler_library.measurements.wrappers import wrap_image_segmentation_measurements
 
 class ImageSegmentation(Module):
     category = "Image Segmentation"
@@ -33,8 +33,7 @@ class ImageSegmentation(Module):
             object_name = self.y_name.value
 
         objects = workspace.object_set.get_objects(object_name)
-        # I have tested this when debugging relateobjects while working on the library/object_count _measurements branch and confirmed that it works.
-        lib_measurements = get_image_segmentation_measurements(
+        lib_measurements = wrap_image_segmentation_measurements(
             objects.segmented,
             objects.volumetric,
             objects.count,

{cellprofiler_core_nightly-5.0.0.dev729 → cellprofiler_core_nightly-5.0.0.dev737}/cellprofiler_core/module/image_segmentation/_object_processing.py

@@ -6,11 +6,10 @@ from ...constants.measurement import C_CHILDREN
 from ...constants.measurement import C_NUMBER
 from ...constants.measurement import C_PARENT
 from ...constants.measurement import FF_CHILDREN_COUNT
-from ...constants.measurement import FF_COUNT
 from ...constants.measurement import FF_PARENT
 from ...constants.measurement import FTR_OBJECT_NUMBER
 from ...object import Objects
-from cellprofiler_library.functions.measurement import get_object_processing_measurements
+from cellprofiler_library.measurements.wrappers import wrap_object_processing_measurements
 from cellprofiler_core.utilities.core.workspace import add_library_measurements_to_workspace_measurements
 
 class ObjectProcessing(ImageSegmentation):
@@ -26,7 +25,7 @@ class ObjectProcessing(ImageSegmentation):
             output_object_name = self.y_name.value
 
         #
-        # Output object name, labels, volumetric, count needed to run get_image_segmentation_measurements
+        # Output object name, labels, volumetric, count needed to run wrap_image_segmentation_measurements
         #
         output_objects = workspace.object_set.get_objects(output_object_name)
         output_objects_labels = output_objects.segmented
@@ -34,14 +33,14 @@ class ObjectProcessing(ImageSegmentation):
         output_objects_count = output_objects.count
 
         #
-        # Input object name, labels, ijv, and output object ijv needed to run relate_children inside get_object_processing_measurements, This is the parent object
+        # Input object name, labels, ijv, and output object ijv needed to run relate_children inside wrap_object_processing_measurements, This is the parent object
         #
         input_objects = workspace.object_set.get_objects(input_object_name)
         input_objects_labels = input_objects.segmented
         input_objects_ijv = input_objects.ijv
         output_objects_ijv = output_objects.ijv
 
-        lib_measurements = get_object_processing_measurements(
+        lib_measurements = wrap_object_processing_measurements(
             output_objects_labels, output_objects_volumetric, output_objects_count, 
             output_object_name, output_objects_ijv, 
             input_object_name, input_objects_labels, input_objects_ijv, 

{cellprofiler_core_nightly-5.0.0.dev729 → cellprofiler_core_nightly-5.0.0.dev737}/cellprofiler_core/utilities/core/module/identify.py

@@ -11,8 +11,8 @@ from cellprofiler_core.constants.measurement import (
     IMAGE,
     M_LOCATION_CENTER_Z,
 )
-from cellprofiler_library.functions.measurement import get_object_location_measurements
-from cellprofiler_library.functions.measurement import get_object_count_measurements
+from cellprofiler_library.measurements.wrappers import wrap_object_location_measurements
+from cellprofiler_library.measurements.wrappers import wrap_object_count_measurements
 from cellprofiler_core.utilities.core.workspace import add_library_measurements_to_workspace_measurements
 
 
@@ -28,7 +28,7 @@ def add_object_location_measurements(
                    takes the maximum value in the labels matrix which is
                    usually correct.
     """
-    object_location_measurements = get_object_location_measurements(object_name, labels, object_count)
+    object_location_measurements = wrap_object_location_measurements(object_name, labels, object_count)
     add_library_measurements_to_workspace_measurements(measurements, object_location_measurements)
 
 
@@ -61,7 +61,7 @@ def add_object_location_measurements_ijv(
 
 def add_object_count_measurements(measurements, object_name, object_count):
     """Add the # of objects to the measurements"""
-    object_count_measurements = get_object_count_measurements(object_name, object_count)
+    object_count_measurements = wrap_object_count_measurements(object_name, object_count)
     add_library_measurements_to_workspace_measurements(measurements, object_count_measurements)
 
 

{cellprofiler_core_nightly-5.0.0.dev729 → cellprofiler_core_nightly-5.0.0.dev737}/cellprofiler_core/utilities/core/workspace.py

@@ -2,8 +2,10 @@ import h5py
 
 from ..hdf5_dict import HDF5FileList
 from ..hdf5_dict import HDF5Dict
-from cellprofiler_library.measurement_model import LibraryMeasurements, R_FIRST_OBJECT_NUMBER, R_SECOND_OBJECT_NUMBER
-import numpy as np
+from cellprofiler_library.measurements.measurement_model import LibraryMeasurements, R_FIRST_OBJECT_NUMBER, R_SECOND_OBJECT_NUMBER
+import numpy
+
+
 def is_workspace_file(path):
     """Return True if the file along the given path is a workspace file"""
     if not h5py.is_hdf5(path):
@@ -17,10 +19,10 @@ def is_workspace_file(path):
         h5file.close()
 
 def add_library_measurements_to_workspace_measurements(workspace_measurements, library_measurements: LibraryMeasurements, module_num=None):
-    """Add the library measurements to the workspace
+    """Add the library measurements to the workspace measurements
 
+    workspace_measurements - the Measurements instance to add to
     library_measurements - the library measurements to be added
-    workspace - the workspace to which the measurements will be added
     module_num - the module number of the module that generated the library measurements
     """
     #
@@ -39,15 +41,20 @@ def add_library_measurements_to_workspace_measurements(workspace_measurements, l
         for feature_name, data in features.items():
             m.add_measurement(object_name, feature_name, data)
 
-    for relationship in library_measurements.get_relationship_groups():
-        assert module_num is not None, "Module number must be provided to add relate measurements"
+    relationship_groups = library_measurements.get_relationship_groups()
+    if relationship_groups and module_num is None:
+        raise ValueError(
+            "module_num must be provided to add_library_measurements_to_workspace_measurements "
+            "when library_measurements contains relationships"
+        )
+    for relationship in relationship_groups:
         data = library_measurements.get_relationships(
             relationship.relationship,
             relationship.object_name1,
             relationship.object_name2
         )
         n_records = len(data)
-        img_nums = np.ones(n_records, int) * m.image_set_number
+        img_nums = numpy.ones(n_records, int) * m.image_set_number
 
         m.add_relate_measurement(
             module_num,
@@ -57,5 +64,5 @@ def add_library_measurements_to_workspace_measurements(workspace_measurements, l
             img_nums,
             data[R_FIRST_OBJECT_NUMBER],
             img_nums,
-            data[R_SECOND_OBJECT_NUMBER], 
+            data[R_SECOND_OBJECT_NUMBER],
         )

{cellprofiler_core_nightly-5.0.0.dev729 → cellprofiler_core_nightly-5.0.0.dev737}/cellprofiler_core_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-core-nightly
-Version: 5.0.0.dev729
+Version: 5.0.0.dev737
 Summary: cellprofiler-core implements the bulk of CellProfiler's non-gui functionality
 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_core_nightly-5.0.0.dev729 → cellprofiler_core_nightly-5.0.0.dev737}/cellprofiler_core_nightly.egg-info/scm_version.json

@@ -1,7 +1,7 @@
 {
   "tag": "5.0.0.dev0",
-  "distance": 729,
-  "node": "g9c74b2cb10f732f964570cfe7184a0ca7587d352",
+  "distance": 737,
+  "node": "gcb2ef7a2c2bff190d85bff9aaae1b000385e32fb",
   "dirty": true,
   "branch": "main",
   "node_date": "2026-09-28"