CellProfiler-nightly 5.0.0.dev650__tar.gz → 5.0.0.dev669__tar.gz

{cellprofiler_nightly-5.0.0.dev650 → cellprofiler_nightly-5.0.0.dev669}/CellProfiler_nightly.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev650
+Version: 5.0.0.dev669
 Summary: CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
 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_nightly-5.0.0.dev650 → cellprofiler_nightly-5.0.0.dev669}/CellProfiler_nightly.egg-info/SOURCES.txt

@@ -7,6 +7,8 @@ CellProfiler_nightly.egg-info/SOURCES.txt
 CellProfiler_nightly.egg-info/dependency_links.txt
 CellProfiler_nightly.egg-info/entry_points.txt
 CellProfiler_nightly.egg-info/requires.txt
+CellProfiler_nightly.egg-info/scm_file_list.json
+CellProfiler_nightly.egg-info/scm_version.json
 CellProfiler_nightly.egg-info/top_level.txt
 cellprofiler/__init__.py
 cellprofiler/__main__.py

cellprofiler_nightly-5.0.0.dev669/CellProfiler_nightly.egg-info/scm_file_list.json

@@ -0,0 +1,384 @@
+{
+  "files": [
+    "LICENSE",
+    "README.md",
+    "cellprofiler/__init__.py",
+    "cellprofiler/__main__.py",
+    "cellprofiler/data/examples/ExampleFly/ExampleFly.cppipe",
+    "cellprofiler/data/examples/ExampleFly/images/01_POS002_D.TIF",
+    "cellprofiler/data/examples/ExampleFly/images/01_POS002_F.TIF",
+    "cellprofiler/data/examples/ExampleFly/images/01_POS002_R.TIF",
+    "cellprofiler/data/examples/ExampleFly/images/01_POS076_D.TIF",
+    "cellprofiler/data/examples/ExampleFly/images/01_POS076_F.TIF",
+    "cellprofiler/data/examples/ExampleFly/images/01_POS076_R.TIF",
+    "cellprofiler/data/examples/ExampleFly/images/01_POS218_D.TIF",
+    "cellprofiler/data/examples/ExampleFly/images/01_POS218_F.TIF",
+    "cellprofiler/data/examples/ExampleFly/images/01_POS218_R.TIF",
+    "cellprofiler/data/help/display_image_tools.rst",
+    "cellprofiler/data/help/display_interactive_navigation.rst",
+    "cellprofiler/data/help/display_menu_bar.rst",
+    "cellprofiler/data/help/legacy_matlab_image.rst",
+    "cellprofiler/data/help/navigation_edit_menu.rst",
+    "cellprofiler/data/help/navigation_file_menu.rst",
+    "cellprofiler/data/help/navigation_test_menu.rst",
+    "cellprofiler/data/help/navigation_window_menu.rst",
+    "cellprofiler/data/help/other_3d_identify.rst",
+    "cellprofiler/data/help/other_batch.rst",
+    "cellprofiler/data/help/other_logging.rst",
+    "cellprofiler/data/help/other_omero.rst",
+    "cellprofiler/data/help/other_plugins.rst",
+    "cellprofiler/data/help/other_shell.rst",
+    "cellprofiler/data/help/other_troubleshooting.rst",
+    "cellprofiler/data/help/other_widget_inspector.rst",
+    "cellprofiler/data/help/output_measurements.rst",
+    "cellprofiler/data/help/output_plateviewer.rst",
+    "cellprofiler/data/help/output_spreadsheets.rst",
+    "cellprofiler/data/help/pipelines_building.rst",
+    "cellprofiler/data/help/pipelines_running.rst",
+    "cellprofiler/data/help/projects_configure_images.rst",
+    "cellprofiler/data/help/projects_image_ordering.rst",
+    "cellprofiler/data/help/projects_image_sequences.rst",
+    "cellprofiler/data/help/projects_introduction.rst",
+    "cellprofiler/data/help/projects_selecting_images.rst",
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+    "cellprofiler/data/images/ColorToGray.png",
+    "cellprofiler/data/images/CorrectIlluminationApply.png",
+    "cellprofiler/data/images/CorrectIlluminationCalculate.png",
+    "cellprofiler/data/images/Crop.png",
+    "cellprofiler/data/images/ExpandOrShrinkObjects.png",
+    "cellprofiler/data/images/ExpandTree.png",
+    "cellprofiler/data/images/GrayToColor.png",
+    "cellprofiler/data/images/Groups_ExampleDisplayTable.png",
+    "cellprofiler/data/images/IMG_ANALYZED.png",
+    "cellprofiler/data/images/IMG_ANALYZE_16.png",
+    "cellprofiler/data/images/IMG_ANALYZE_24.png",
+    "cellprofiler/data/images/IMG_CLOSED_EYE.png",
+    "cellprofiler/data/images/IMG_DISABLED.png",
+    "cellprofiler/data/images/IMG_ERROR.png",
+    "cellprofiler/data/images/IMG_EYE.png",
+    "cellprofiler/data/images/IMG_GO.png",
+    "cellprofiler/data/images/IMG_GO_DIM.png",
+    "cellprofiler/data/images/IMG_IMAGE.png",
+    "cellprofiler/data/images/IMG_MEASURE.png",
+    "cellprofiler/data/images/IMG_OK.png",
+    "cellprofiler/data/images/IMG_PAUSE.png",
+    "cellprofiler/data/images/IMG_RUN.png",
+    "cellprofiler/data/images/IMG_SLIDER.png",
+    "cellprofiler/data/images/IMG_SLIDER_ACTIVE.png",
+    "cellprofiler/data/images/IMG_STOP.png",
+    "cellprofiler/data/images/IMG_TEST.png",
+    "cellprofiler/data/images/IMG_UNAVAILABLE.png",
+    "cellprofiler/data/images/IMG_UPDATE.png",
+    "cellprofiler/data/images/IMG_USE_INPUT.png",
+    "cellprofiler/data/images/IMG_USE_OUTPUT.png",
+    "cellprofiler/data/images/IMG_USE_SOURCE.png",
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+    "cellprofiler/data/images/IdentifyPrimaryObjects_ShapeDeclumping.png",
+    "cellprofiler/data/images/IdentifySecondaryObjects.png",
+    "cellprofiler/data/images/IdentifyTertiaryObjects.png",
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+    "cellprofiler/data/images/Images_UsingRules.png",
+    "cellprofiler/data/images/MeasureGranularity_example.png",
+    "cellprofiler/data/images/MeasureImageAreaOccupied.png",
+    "cellprofiler/data/images/MeasureObjectIntensityDistribution_Edges_Centers.png",
+    "cellprofiler/data/images/MeasureObjectIntensityDistribution_Magnitude_Phase.png",
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+    "cellprofiler/data/images/Measure_texture_3D_correspondences_1_highres.png",
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+    "cellprofiler/data/images/Measure_texture_3D_correspondences_2_highres.png",
+    "cellprofiler/data/images/Metadata_ExampleDisplayTable.png",
+    "cellprofiler/data/images/NamesAndTypes_ExampleDisplayTable.png",
+    "cellprofiler/data/images/Tile.png",
+    "cellprofiler/data/images/UnmixColors.png",
+    "cellprofiler/data/images/check.png",
+    "cellprofiler/data/images/color.png",
+    "cellprofiler/data/images/cp_panel_schematic.png",
+    "cellprofiler/data/images/dapi.png",
+    "cellprofiler/data/images/delete.png",
+    "cellprofiler/data/images/downarrow.png",
+    "cellprofiler/data/images/eye-close.png",
+    "cellprofiler/data/images/eye-open.png",
+    "cellprofiler/data/images/ffwd.png",
+    "cellprofiler/data/images/ffwddisabled.png",
+    "cellprofiler/data/images/filter.png",
+    "cellprofiler/data/images/folder_browse.png",
+    "cellprofiler/data/images/folder_create.png",
+    "cellprofiler/data/images/gear.png",
+    "cellprofiler/data/images/gfp.png",
+    "cellprofiler/data/images/icon_copyrights.txt",
+    "cellprofiler/data/images/illumination_function.png",
+    "cellprofiler/data/images/image_to_object_dataflow.png",
+    "cellprofiler/data/images/image_to_object_dataflow.psd",
+    "cellprofiler/data/images/mask.png",
+    "cellprofiler/data/images/microscope-color_16.png",
+    "cellprofiler/data/images/microscope-icon_16.png",
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+    "cellprofiler/gui/_welcome_frame.py",
+    "cellprofiler/gui/_workspace_model.py",
+    "cellprofiler/gui/addmoduleframe.py",
+    "cellprofiler/gui/app.py",
+    "cellprofiler/gui/artist.py",
+    "cellprofiler/gui/checkupdate.py",
+    "cellprofiler/gui/constants/__init__.py",
+    "cellprofiler/gui/constants/figure.py",
+    "cellprofiler/gui/constants/module_view.py",
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+    "cellprofiler/gui/constants/preferences_view.py",
+    "cellprofiler/gui/constants/workspace_view.py",
+    "cellprofiler/gui/cpframe.py",
+    "cellprofiler/gui/dialog.py",
+    "cellprofiler/gui/editobjectsdlg.py",
+    "cellprofiler/gui/errordialog.py",
+    "cellprofiler/gui/figure/__init__.py",
+    "cellprofiler/gui/figure/_figure.py",
+    "cellprofiler/gui/figure/_navigation_toolbar.py",
+    "cellprofiler/gui/figure/_outline_artist.py",
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+    "cellprofiler/gui/help/__init__.py",
+    "cellprofiler/gui/help/content.py",
+    "cellprofiler/gui/help/menu.py",
+    "cellprofiler/gui/help/search.py",
+    "cellprofiler/gui/html/__init__.py",
+    "cellprofiler/gui/html/configure_images_help.html",
+    "cellprofiler/gui/html/exporting_results_help.html",
+    "cellprofiler/gui/html/getting_started.html",
+    "cellprofiler/gui/html/htmlwindow.py",
+    "cellprofiler/gui/html/identify_features_help.html",
+    "cellprofiler/gui/html/in_app_help.html",
+    "cellprofiler/gui/html/making_measurements_help.html",
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+    "cellprofiler/gui/html/welcome.html",
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+    "cellprofiler/gui/menu.py",
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+    "cellprofiler/modules/measuretexture.py",
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+    "cellprofiler/modules/morphologicalskeleton.py",
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+    "cellprofiler/modules/overlayoutlines.py",
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+    "cellprofiler/modules/runimagejmacro.py",
+    "cellprofiler/modules/savecroppedobjects.py",
+    "cellprofiler/modules/saveimages.py",
+    "cellprofiler/modules/shrinktoobjectcenters.py",
+    "cellprofiler/modules/smooth.py",
+    "cellprofiler/modules/splitormergeobjects.py",
+    "cellprofiler/modules/straightenworms.py",
+    "cellprofiler/modules/threshold.py",
+    "cellprofiler/modules/tile.py",
+    "cellprofiler/modules/trackobjects.py",
+    "cellprofiler/modules/unmixcolors.py",
+    "cellprofiler/modules/untangleworms.py",
+    "cellprofiler/modules/watershed.py",
+    "cellprofiler/utilities/__init__.py",
+    "cellprofiler/utilities/morphology.py",
+    "cellprofiler/utilities/rules.py",
+    "environment.yml",
+    "pyproject.toml"
+  ]
+}

cellprofiler_nightly-5.0.0.dev669/CellProfiler_nightly.egg-info/scm_version.json

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

{cellprofiler_nightly-5.0.0.dev650 → cellprofiler_nightly-5.0.0.dev669}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev650
+Version: 5.0.0.dev669
 Summary: CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
 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_nightly-5.0.0.dev669/cellprofiler/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+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')
+
+__commit_id__ = commit_id = 'g51250caf3'

{cellprofiler_nightly-5.0.0.dev650 → cellprofiler_nightly-5.0.0.dev669}/cellprofiler/modules/classifyobjects.py

@@ -101,10 +101,20 @@ import os
 import numpy
 
 from cellprofiler.modules import _help
-from cellprofiler.utilities.rules import Rules
-from cellprofiler_core.constants.measurement import COLTYPE_FLOAT, M_LOCATION_CENTER_X, M_LOCATION_CENTER_Y, \
-    COLTYPE_VARCHAR, C_COUNT, C_CHILDREN, C_LOCATION, C_NUMBER, C_PARENT, FTR_OBJECT_NUMBER, FTR_CENTER_X, FTR_CENTER_Y, \
+from cellprofiler.utilities.rules import Rules, Rule
+from cellprofiler_core.constants.measurement import (
+    COLTYPE_FLOAT,
+    COLTYPE_VARCHAR,
+    C_COUNT,
+    C_CHILDREN,
+    C_LOCATION,
+    C_NUMBER,
+    C_PARENT,
+    FTR_OBJECT_NUMBER,
+    FTR_CENTER_X,
+    FTR_CENTER_Y,
     FTR_CENTER_Z
+)
 from cellprofiler_core.constants.measurement import COLTYPE_INTEGER
 from cellprofiler_core.constants.measurement import IMAGE
 from cellprofiler_core.image import Image
@@ -147,6 +157,7 @@ M_CATEGORY = "Classify"
 F_PCT_PER_BIN = "PctObjectsPerBin"
 F_NUM_PER_BIN = "NumObjectsPerBin"
 
+S_RULES = "Rules"
 
 class ClassifyObjects(Module):
     category = "Object Processing"
@@ -1263,12 +1274,12 @@ Select a name for the object set generated by your classifier.
         src_objects = workspace.get_objects(self.object_name.value)
         classifier = self.get_classifier()
         class_labels = self.get_bin_labels()
-        if self.get_classifier_type() == 'Rules':
+        if self.get_classifier_type() == S_RULES:
             class_id_dict = dict((j, i) for i, j in enumerate(class_labels, 1))
         else:
             class_id_dict = dict(zip(class_labels, classifier.classes_))
         if src_objects.count >=1:
-            if self.get_classifier_type() == 'Rules':
+            if self.get_classifier_type() == S_RULES:
                 # Working with CPA rules.
                 probabilities = classifier.score(workspace.measurements)
                 if len(probabilities) > 0:
@@ -1284,7 +1295,7 @@ Select a name for the object set generated by your classifier.
                     [
                         workspace.measurements[
                             object_name, 
-                            self.rules.Rule.return_fuzzy_measurement_name(
+                            Rule.return_fuzzy_measurement_name(
                                 workspace.measurements.get_measurement_columns(),
                                 object_name,
                                 feature_name,
@@ -1469,7 +1480,7 @@ Select a name for the object set generated by your classifier.
                         rules.load(d[path_][0])
                         d[path_] = (rules,
                                     d[path_][1],
-                                    "Rules",
+                                    S_RULES,
                                     [f"{rule.object_name}_{rule.feature}" for rule in rules.rules])
                 else:
                     # Probably a rules list
@@ -1478,7 +1489,7 @@ Select a name for the object set generated by your classifier.
                     # Construct a classifier-like object
                     d[path_] = (rules,
                                 rules.get_classes(),
-                                "Rules",
+                                S_RULES,
                                 [f"{rule.object_name}_{rule.feature}" for rule in rules.rules])
         return d[path_]
 
@@ -1524,7 +1535,7 @@ Select a name for the object set generated by your classifier.
         elif self.contrast_choice == BY_MODEL:
             features = self.get_classifier_features()
             for feature in features:
-                fuzzy_feature = self.rules.Rule.return_fuzzy_measurement_name(
+                fuzzy_feature = Rule.return_fuzzy_measurement_name(
                     pipeline.get_measurement_columns(),
                     feature[:feature.index('_')],
                     feature[feature.index('_'):],
@@ -1747,10 +1758,6 @@ measurement is not available at this stage of the pipeline. Consider adding modu
                         result += [self.object_name.value]
         return result
 
-    def get_dictionary_for_worker(self):
-        # Sklearn models can't be serialized, so workers will need to read them from disk.
-        return {}
-
     def split_feature_names(self, features, available_objects):
         # Attempts to split measurement names into object and feature pairs. Tests against a list of available objects.
         features_list = []