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

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev722
+Version: 5.0.0.dev728
 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.dev722 → cellprofiler_library_nightly-5.0.0.dev728}/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.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_library_nightly-5.0.0.dev722 → cellprofiler_library_nightly-5.0.0.dev728}/cellprofiler_library/functions/measurement.py

@@ -42,11 +42,19 @@ 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
 from cellprofiler_library.measurement_model import LibraryMeasurements
 from cellprofiler_library.functions.segmentation import center_of_labels_mass
+from cellprofiler_library.opts.measurement import (
+    M_LOCATION_CENTER_X,
+    M_LOCATION_CENTER_Y,
+    M_LOCATION_CENTER_Z,
+    C_LOCATION,
+    M_NUMBER_OBJECT_NUMBER,
+)
 
 ###############################################################################
 # MeasureImageOverlap
@@ -4422,13 +4430,54 @@ def find_parents_of(
 
     return parents_of
 
-def get_object_location_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_location_measurements(object_name, labels, object_count=None):
+    measurements = LibraryMeasurements()
+    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_z = None
+            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,
+        )
 
-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
+    measurements.add_measurement(
+        object_name, M_NUMBER_OBJECT_NUMBER, number,
+    )
+    return measurements
+
+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(*args, **kwargs):
     # TODO: #5117 implement add_measurements from src/subpackages/core/cellprofiler_core/module/image_segmentation/_object_processing.py

cellprofiler_library_nightly-5.0.0.dev728/cellprofiler_library/opts/measurement.py

@@ -0,0 +1,116 @@
+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)
+]

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

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cellprofiler-library-nightly
-Version: 5.0.0.dev722
+Version: 5.0.0.dev728
 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.dev722 → cellprofiler_library_nightly-5.0.0.dev728}/cellprofiler_library_nightly.egg-info/SOURCES.txt

@@ -104,6 +104,7 @@ cellprofiler_library/opts/measureimageintensity.py
 cellprofiler_library/opts/measureimageoverlap.py
 cellprofiler_library/opts/measureimagequality.py
 cellprofiler_library/opts/measureimageskeleton.py
+cellprofiler_library/opts/measurement.py
 cellprofiler_library/opts/measureobjectintensity.py
 cellprofiler_library/opts/measureobjectintensitydistribution.py
 cellprofiler_library/opts/measureobjectneighbors.py

{cellprofiler_library_nightly-5.0.0.dev722 → cellprofiler_library_nightly-5.0.0.dev728}/cellprofiler_library_nightly.egg-info/scm_file_list.json

@@ -101,6 +101,7 @@
     "cellprofiler_library/opts/measureimageoverlap.py",
     "cellprofiler_library/opts/measureimagequality.py",
     "cellprofiler_library/opts/measureimageskeleton.py",
+    "cellprofiler_library/opts/measurement.py",
     "cellprofiler_library/opts/measureobjectintensity.py",
     "cellprofiler_library/opts/measureobjectintensitydistribution.py",
     "cellprofiler_library/opts/measureobjectneighbors.py",

{cellprofiler_library_nightly-5.0.0.dev722 → cellprofiler_library_nightly-5.0.0.dev728}/cellprofiler_library_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"