cellprofiler-core-nightly 5.0.0.dev722__tar.gz → 5.0.0.dev728__tar.gz

{cellprofiler_core_nightly-5.0.0.dev722 → cellprofiler_core_nightly-5.0.0.dev728}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-core-nightly
-Version: 5.0.0.dev722
+Version: 5.0.0.dev728
 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.dev722 → cellprofiler_core_nightly-5.0.0.dev728}/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.dev722'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev722')
+__version__ = version = '5.0.0.dev728'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev728')
 
-__commit_id__ = commit_id = 'g4194718d7'
+__commit_id__ = commit_id = 'gf66c883bd'

cellprofiler_core_nightly-5.0.0.dev728/cellprofiler_core/constants/measurement.py

@@ -0,0 +1 @@
+from cellprofiler_library.opts.measurement import *

{cellprofiler_core_nightly-5.0.0.dev722 → cellprofiler_core_nightly-5.0.0.dev728}/cellprofiler_core/utilities/core/module/identify.py

@@ -11,6 +11,9 @@ 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_core.utilities.core.workspace import add_library_measurements_to_workspace_measurements
 
 
 def add_object_location_measurements(
@@ -25,44 +28,9 @@ def add_object_location_measurements(
                    takes the maximum value in the labels matrix which is
                    usually correct.
     """
-    if object_count is None:
-        object_count = numpy.max(labels)
-    #
-    # Get the centers of each object - center_of_mass <- list of two-tuples.
-    #
-    if object_count:
-        centers = scipy.ndimage.center_of_mass(
-            numpy.ones(labels.shape), labels, list(range(1, object_count + 1))
-        )
-        centers = numpy.array(centers)
-        centers = centers.reshape((object_count, len(labels.shape)))
-        if centers.shape[1] != 3:
-            location_center_y = centers[:, 0]
-            location_center_x = centers[:, 1]
-        else:
-            location_center_z = centers[:, 0]
-            location_center_y = centers[:, 1]
-            location_center_x = centers[:, 2]
-        number = numpy.arange(1, object_count + 1)
-    else:
-        location_center_z = numpy.zeros((0,), dtype=float)
-        location_center_y = numpy.zeros((0,), dtype=float)
-        location_center_x = numpy.zeros((0,), dtype=float)
-        number = numpy.zeros((0,), dtype=int)
-    measurements.add_measurement(
-        object_name, M_LOCATION_CENTER_X, location_center_x,
-    )
-    measurements.add_measurement(
-        object_name, M_LOCATION_CENTER_Y, location_center_y,
-    )
-    if len(labels.shape) > 2:
-        measurements.add_measurement(
-            object_name, M_LOCATION_CENTER_Z, location_center_z,
-        )
+    object_location_measurements = get_object_location_measurements(object_name, labels, object_count)
+    add_library_measurements_to_workspace_measurements(measurements, object_location_measurements)
 
-    measurements.add_measurement(
-        object_name, M_NUMBER_OBJECT_NUMBER, number,
-    )
 
 
 def add_object_location_measurements_ijv(
@@ -93,9 +61,8 @@ def add_object_location_measurements_ijv(
 
 def add_object_count_measurements(measurements, object_name, object_count):
     """Add the # of objects to the measurements"""
-    measurements.add_measurement(
-        "Image", FF_COUNT % object_name, numpy.array([object_count], dtype=float),
-    )
+    object_count_measurements = get_object_count_measurements(object_name, object_count)
+    add_library_measurements_to_workspace_measurements(measurements, object_count_measurements)
 
 
 def get_object_measurement_columns(object_name):

{cellprofiler_core_nightly-5.0.0.dev722 → cellprofiler_core_nightly-5.0.0.dev728}/cellprofiler_core/utilities/core/workspace.py

@@ -16,7 +16,7 @@ def is_workspace_file(path):
     finally:
         h5file.close()
 
-def add_library_measurements_to_workspace(library_measurements: LibraryMeasurements, workspace, module_num):
+def add_library_measurements_to_workspace_measurements(workspace_measurements, library_measurements: LibraryMeasurements, module_num=None):
     """Add the library measurements to the workspace
 
     library_measurements - the library measurements to be added
@@ -27,7 +27,7 @@ def add_library_measurements_to_workspace(library_measurements: LibraryMeasureme
     # Record the measurements
     #
     # assume isinstance(workspace, Workspace)
-    m = workspace.measurements
+    m = workspace_measurements
     # assume isinstance(m, Measurements)
     
     # Record Image Measurements
@@ -40,6 +40,7 @@ def add_library_measurements_to_workspace(library_measurements: LibraryMeasureme
             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"
         data = library_measurements.get_relationships(
             relationship.relationship,
             relationship.object_name1,

{cellprofiler_core_nightly-5.0.0.dev722 → cellprofiler_core_nightly-5.0.0.dev728}/cellprofiler_core_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-core-nightly
-Version: 5.0.0.dev722
+Version: 5.0.0.dev728
 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.dev722 → cellprofiler_core_nightly-5.0.0.dev728}/cellprofiler_core_nightly.egg-info/scm_version.json

@@ -1,7 +1,7 @@
 {
   "tag": "5.0.0.dev0",
-  "distance": 722,
-  "node": "g4194718d72d5faaec1ec85e916af8c7bd7723915",
+  "distance": 728,
+  "node": "gf66c883bd90c65d71095cd85bea58cc7c6b092e1",
   "dirty": true,
   "branch": "main",
   "node_date": "2026-09-28"

cellprofiler_core_nightly-5.0.0.dev722/cellprofiler_core/constants/measurement.py

@@ -1,116 +0,0 @@
-AGG_MEAN = "Mean"
-AGG_STD_DEV = "StDev"
-AGG_MEDIAN = "Median"
-AGG_NAMES = [AGG_MEAN, AGG_MEDIAN, AGG_STD_DEV]
-IMAGE = "Image"
-EXPERIMENT = "Experiment"
-RELATIONSHIP = "Relationship"
-DB_TEMP = "ExportToDb"
-NEIGHBORS = "Neighbors"
-OBJECT = "Object"
-disallowed_object_names = [IMAGE, EXPERIMENT, RELATIONSHIP]
-COLTYPE_INTEGER = "integer"
-COLTYPE_FLOAT = "float"
-COLTYPE_BLOB = "blob"
-COLTYPE_MEDIUMBLOB = "mediumblob"
-COLTYPE_LONGBLOB = "longblob"
-COLTYPE_VARCHAR_FORMAT = "varchar(%d)"
-COLTYPE_VARCHAR = "varchar"
-PATH_NAME_LENGTH = 256
-FILE_NAME_LENGTH = 128
-COLTYPE_VARCHAR_FILE_NAME = COLTYPE_VARCHAR_FORMAT % FILE_NAME_LENGTH
-COLTYPE_VARCHAR_PATH_NAME = COLTYPE_VARCHAR_FORMAT % PATH_NAME_LENGTH
-MCA_AVAILABLE_EACH_CYCLE = "AvailableEachCycle"
-MCA_AVAILABLE_POST_GROUP = "AvailablePostGroup"
-MCA_AVAILABLE_POST_RUN = "AvailablePostRun"
-C_METADATA = "Metadata"
-FTR_SITE = "Site"
-FTR_WELL = "Well"
-FTR_ROW = "Row"
-FTR_COLUMN = "Column"
-FTR_PLATE = "Plate"
-ROW_KEYS = ("wellrow", "well_row", "row")
-COL_KEYS = ("wellcol", "well_col", "wellcolumn", "well_column", "column", "col")
-MEASUREMENTS_GROUP_NAME = "Measurements"
-IMAGE_NUMBER = "ImageNumber"
-OBJECT_NUMBER = "ObjectNumber"
-GROUP_NUMBER = "Group_Number"  # 1-based group index
-GROUP_INDEX = "Group_Index"  # 1-based index within group
-GROUP_LENGTH = "Group_Length"
-R_FIRST_IMAGE_NUMBER = IMAGE_NUMBER + "_" + "First"
-R_FIRST_OBJECT_NUMBER = OBJECT_NUMBER + "_" + "First"
-R_SECOND_IMAGE_NUMBER = IMAGE_NUMBER + "_" + "Second"
-R_SECOND_OBJECT_NUMBER = OBJECT_NUMBER + "_" + "Second"
-C_FILE_NAME = "FileName"
-C_PATH_NAME = "PathName"
-C_URL = "URL"
-C_INDEX = "Index"
-C_SERIES = "Series"
-C_SERIES_NAME = "SeriesName"
-C_FRAME = "Frame"
-C_FRAMES = "Frames"
-C_CHANNEL = "Channel"
-C_C = "C"
-C_Z = "Z"
-C_T = "T"
-C_TILE = "TileXYWH"
-C_CHANNEL_NAME = "ChannelName"
-C_COLOR_FORMAT = "ColorFormat"
-C_MONOCHROME = "monochrome"
-C_RGB = "RGB"
-
-C_OBJECTS_FILE_NAME = "ObjectsFileName"
-C_OBJECTS_PATH_NAME = "ObjectsPathName"
-C_OBJECTS_URL = "ObjectsURL"
-C_OBJECTS_SERIES = "ObjectsSeries"
-C_OBJECTS_SERIES_NAME = "ObjectsSeriesName"
-C_OBJECTS_FRAME = "ObjectsFrame"
-C_OBJECTS_CHANNEL = "ObjectsChannel"
-C_OBJECTS_Z = "ObjectsZPlane"
-C_OBJECTS_T = "ObjectsTimepoint"
-C_CHANNEL_TYPE = "ChannelType"
-C_FILE_LOCATION = "FileLocation"
-M_METADATA_TAGS = "_".join((C_METADATA, "Tags"))
-M_GROUPING_TAGS = "_".join((C_METADATA, "GroupingTags"))
-RESERVED_METADATA_KEYS = (C_URL, C_SERIES, C_SERIES_NAME, C_FRAME, C_FILE_LOCATION,
-                          C_COLOR_FORMAT, C_CHANNEL_NAME, C_CHANNEL, C_C, C_Z, C_T, C_TILE)
-M_PATH_MAPPINGS = "Path_Mappings"
-K_CASE_SENSITIVE = "CaseSensitive"
-K_PATH_MAPPINGS = "PathMappings"
-K_LOCAL_SEPARATOR = "LocalSeparator"
-K_URL2PATHNAME_PACKAGE_NAME = "Url2PathnamePackageName"
-F_BATCH_DATA = "Batch_data.mat"
-F_BATCH_DATA_H5 = "Batch_data.h5"
-C_LOCATION = "Location"
-C_NUMBER = "Number"
-C_COUNT = "Count"
-C_THRESHOLD = "Threshold"
-C_PARENT = "Parent"
-R_PARENT = "Parent"
-C_CHILDREN = "Children"
-R_CHILD = "Child"
-FTR_CENTER_X = "Center_X"
-M_LOCATION_CENTER_X = "%s_%s" % (C_LOCATION, FTR_CENTER_X)
-FTR_CENTER_Y = "Center_Y"
-M_LOCATION_CENTER_Y = "%s_%s" % (C_LOCATION, FTR_CENTER_Y)
-FTR_CENTER_Z = "Center_Z"
-M_LOCATION_CENTER_Z = "%s_%s" % (C_LOCATION, FTR_CENTER_Z)
-FTR_OBJECT_NUMBER = "Object_Number"
-M_NUMBER_OBJECT_NUMBER = "%s_%s" % (C_NUMBER, FTR_OBJECT_NUMBER)
-FF_COUNT = "%s_%%s" % C_COUNT
-FTR_FINAL_THRESHOLD = "FinalThreshold"
-FF_FINAL_THRESHOLD = "%s_%s_%%s" % (C_THRESHOLD, FTR_FINAL_THRESHOLD)
-FTR_ORIG_THRESHOLD = "OrigThreshold"
-FF_ORIG_THRESHOLD = "%s_%s_%%s" % (C_THRESHOLD, FTR_ORIG_THRESHOLD)
-FTR_GUIDE_THRESHOLD = "GuideThreshold"
-FF_GUIDE_THRESHOLD = "%s_%s_%%s" % (C_THRESHOLD, FTR_GUIDE_THRESHOLD)
-FTR_WEIGHTED_VARIANCE = "WeightedVariance"
-FF_WEIGHTED_VARIANCE = "%s_%s_%%s" % (C_THRESHOLD, FTR_WEIGHTED_VARIANCE)
-FTR_SUM_OF_ENTROPIES = "SumOfEntropies"
-FF_SUM_OF_ENTROPIES = "%s_%s_%%s" % (C_THRESHOLD, FTR_SUM_OF_ENTROPIES)
-FF_CHILDREN_COUNT = "%s_%%s_Count" % C_CHILDREN
-FF_PARENT = "%s_%%s" % C_PARENT
-M_SITE, M_WELL, M_ROW, M_COLUMN, M_PLATE = [
-    "_".join((C_METADATA, x))
-    for x in (FTR_SITE, FTR_WELL, FTR_ROW, FTR_COLUMN, FTR_PLATE)
-]