CellProfiler-nightly 5.0.0.dev745__tar.gz → 5.0.0.dev784__tar.gz

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/CellProfiler_nightly.egg-info/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev745
+Version: 5.0.0.dev784
 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>
 Maintainer-email: Beth Cimini <bcimini@broadinstitute.org>, Nodar Gogoberidze <ngogober@broadinstitute.org>
 License: The BSD 3-Clause License
         
-        Copyright © 2003 - 2021 Broad Institute, Inc. All rights reserved.
+        Copyright © 2003 - 2026 Broad Institute, Inc. All rights reserved.
         
         Redistribution and use in source and binary forms, with or without
         modification, are permitted provided that the following conditions are met:
@@ -68,8 +68,8 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: cellprofiler-library-nightly>=5.dev
 Requires-Dist: cellprofiler-core-nightly>=5.dev
+Requires-Dist: centriole-nightly>=5.dev
 Requires-Dist: boto3>=1.28.41
-Requires-Dist: centrosome>=1.3.0
 Requires-Dist: docutils==0.15.2
 Requires-Dist: h5py>=3.7.0
 Requires-Dist: imageio>=2.31.3

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/CellProfiler_nightly.egg-info/SOURCES.txt

@@ -265,6 +265,8 @@ cellprofiler/gui/module_view/_module_view.py
 cellprofiler/gui/module_view/_setting_edited_event.py
 cellprofiler/gui/module_view/_table_controller.py
 cellprofiler/gui/module_view/_validation_request_controller.py
+cellprofiler/gui/plugins_dialog/__init__.py
+cellprofiler/gui/plugins_dialog/_plugins_dialog.py
 cellprofiler/gui/preferences_dialog/__init__.py
 cellprofiler/gui/preferences_dialog/_integer_preference.py
 cellprofiler/gui/preferences_dialog/_preferences_dialog.py
@@ -289,7 +291,6 @@ cellprofiler/gui/workspace_view/_workspace_view_measurement_row.py
 cellprofiler/gui/workspace_view/_workspace_view_objects_row.py
 cellprofiler/gui/workspace_view/_workspace_view_row.py
 cellprofiler/icons/__init__.py
-cellprofiler/modules/UntangleWorms.xsd
 cellprofiler/modules/__init__.py
 cellprofiler/modules/_help.py
 cellprofiler/modules/calculatemath.py
@@ -327,7 +328,6 @@ cellprofiler/modules/flagimage.py
 cellprofiler/modules/flipandrotate.py
 cellprofiler/modules/gaussianfilter.py
 cellprofiler/modules/graytocolor.py
-cellprofiler/modules/identifydeadworms.py
 cellprofiler/modules/identifyobjectsingrid.py
 cellprofiler/modules/identifyobjectsmanually.py
 cellprofiler/modules/identifyprimaryobjects.py
@@ -373,12 +373,10 @@ 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/modules/plugins/__init__.py
 cellprofiler/modules/plugins/imagetemplate.py

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/CellProfiler_nightly.egg-info/requires.txt

@@ -1,7 +1,7 @@
 cellprofiler-library-nightly>=5.dev
 cellprofiler-core-nightly>=5.dev
+centriole-nightly>=5.dev
 boto3>=1.28.41
-centrosome>=1.3.0
 docutils==0.15.2
 h5py>=3.7.0
 imageio>=2.31.3

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/CellProfiler_nightly.egg-info/scm_file_list.json

@@ -251,6 +251,8 @@
     "cellprofiler/gui/pipelinecontroller.py",
     "cellprofiler/gui/pipelinelistview.py",
     "cellprofiler/gui/plateviewer.py",
+    "cellprofiler/gui/plugins_dialog/__init__.py",
+    "cellprofiler/gui/plugins_dialog/_plugins_dialog.py",
     "cellprofiler/gui/plugins_menu.py",
     "cellprofiler/gui/preferences_dialog/__init__.py",
     "cellprofiler/gui/preferences_dialog/_integer_preference.py",
@@ -280,7 +282,6 @@
     "cellprofiler/icons/__init__.py",
     "cellprofiler/knime_bridge.py",
     "cellprofiler/misc.py",
-    "cellprofiler/modules/UntangleWorms.xsd",
     "cellprofiler/modules/__init__.py",
     "cellprofiler/modules/_help.py",
     "cellprofiler/modules/calculatemath.py",
@@ -318,7 +319,6 @@
     "cellprofiler/modules/flipandrotate.py",
     "cellprofiler/modules/gaussianfilter.py",
     "cellprofiler/modules/graytocolor.py",
-    "cellprofiler/modules/identifydeadworms.py",
     "cellprofiler/modules/identifyobjectsingrid.py",
     "cellprofiler/modules/identifyobjectsmanually.py",
     "cellprofiler/modules/identifyprimaryobjects.py",
@@ -368,12 +368,10 @@
     "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_nightly-5.0.0.dev784/CellProfiler_nightly.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "5.0.0.dev0",
+  "distance": 784,
+  "node": "g166605047",
+  "dirty": true,
+  "branch": "main",
+  "node_date": "2026-10-20"
+}

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/LICENSE

@@ -1,6 +1,6 @@
 The BSD 3-Clause License
 
-Copyright © 2003 - 2021 Broad Institute, Inc. All rights reserved.
+Copyright © 2003 - 2026 Broad Institute, Inc. All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev745
+Version: 5.0.0.dev784
 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>
 Maintainer-email: Beth Cimini <bcimini@broadinstitute.org>, Nodar Gogoberidze <ngogober@broadinstitute.org>
 License: The BSD 3-Clause License
         
-        Copyright © 2003 - 2021 Broad Institute, Inc. All rights reserved.
+        Copyright © 2003 - 2026 Broad Institute, Inc. All rights reserved.
         
         Redistribution and use in source and binary forms, with or without
         modification, are permitted provided that the following conditions are met:
@@ -68,8 +68,8 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: cellprofiler-library-nightly>=5.dev
 Requires-Dist: cellprofiler-core-nightly>=5.dev
+Requires-Dist: centriole-nightly>=5.dev
 Requires-Dist: boto3>=1.28.41
-Requires-Dist: centrosome>=1.3.0
 Requires-Dist: docutils==0.15.2
 Requires-Dist: h5py>=3.7.0
 Requires-Dist: imageio>=2.31.3

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '5.0.0.dev745'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev745')
+__version__ = version = '5.0.0.dev784'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev784')
 
-__commit_id__ = commit_id = 'gc1d642698'
+__commit_id__ = commit_id = 'g166605047'

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/gui/addmoduleframe.py

@@ -8,6 +8,7 @@ from cellprofiler_core.utilities.core.modules import (
     instantiate_module,
     get_module_class,
 )
+from cellprofiler_core.utilities.core.plugins import get_module_display_name
 
 import cellprofiler.gui
 import cellprofiler.gui.cpframe
@@ -166,11 +167,12 @@ class AddModuleFrame(wx.Frame):
                     if isinstance(module.category, str)
                     else list(module.category)
                 ) + ["All"]
+                display_name = get_module_display_name(module)
                 for category in categories:
                     if category not in self.__module_files:
                         self.__module_files.insert(-2, category)
                         self.__module_dict[category] = {}
-                    self.__module_dict[category][module.module_name] = loader
+                    self.__module_dict[category][display_name] = loader
             except Exception as e:
                 import traceback
                 import logging

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/gui/app.py

@@ -6,6 +6,7 @@ import sys
 import sentry_sdk
 import wx
 import wx.lib.inspection
+from cellprofiler_core.preferences import APP_NAME
 from cellprofiler_core.preferences import get_telemetry_prompt
 from cellprofiler_core.preferences import get_telemetry
 from cellprofiler_core.preferences import set_telemetry
@@ -70,9 +71,19 @@ class App(wx.App):
 
         # wx.lib.inspection.InspectionTool().Show()
 
-        self.SetAppName("CellProfiler{0:s}".format(cellprofiler_version))
-
-        self.frame = CPFrame(None, -1, "CellProfiler")
+        # WARN: APP_NAME also names the user data directory
+        # (cellprofiler_core.preferences.get_user_data_directory), where the
+        # official plugins live, and the user config directory
+        # (cellprofiler_core.preferences.get_user_config_directory), where the
+        # config file lives.
+        # Be careful changing this, as it will change the config file location,
+        # and where official plugins live.
+        self.SetAppName(APP_NAME)
+        self.SetAppDisplayName("{0:s} {1:s}".format(APP_NAME, cellprofiler_version))
+        # useful for Linux - e.g. window manager's "class hint"
+        self.SetClassName(APP_NAME)
+
+        self.frame = CPFrame(None, -1, APP_NAME)
 
         self.frame.start(self.workspace_path, self.pipeline_path)
 

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/gui/artist.py

@@ -2,8 +2,8 @@
 """artist.py - Specialized matplotlib artists for CellProfiler
 """
 
-import centrosome.cpmorphology
-import centrosome.outline
+import centriole.cpmorphology
+import centriole.outline
 import matplotlib
 import matplotlib.artist
 import matplotlib.cm
@@ -259,9 +259,9 @@ class OutlinesMixin(ColorMixin):
         if self._outlines is None:
             for i, labels in enumerate(self.labels):
                 if i == 0:
-                    self._outlines = centrosome.outline.outline(labels) != 0
+                    self._outlines = centriole.outline.outline(labels) != 0
                 else:
-                    self._outlines |= centrosome.outline.outline(labels) != 0
+                    self._outlines |= centriole.outline.outline(labels) != 0
             if self.line_width is not None and self.line_width > 1:
                 hw = float(self.line_width) / 2
                 d = scipy.ndimage.distance_transform_edt(~self._outlines)
@@ -1296,7 +1296,7 @@ class CPOutlineArtist(matplotlib.collections.LineCollection):
             else:
                 my_range = numpy.arange(1, len(unique))
             idx.shape = l.shape
-            pts, offs, counts = centrosome.cpmorphology.get_outline_pts(idx, my_range)
+            pts, offs, counts = centriole.cpmorphology.get_outline_pts(idx, my_range)
             pts = pts + 0.5  # Target the centers of the pixels.
             pts = pts[:, ::-1]  # matplotlib x, y reversed from i,j
             for off, count in zip(offs, counts):

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/gui/cpframe.py

@@ -40,6 +40,7 @@ from .pipelinecontroller import PipelineController
 from .pipelinelistview import PipelineListView
 from .preferences_dialog._preferences_dialog import PreferencesDialog
 from .readers_dialog._readers_dialog import ReadersDialog
+from .plugins_dialog._plugins_dialog import PluginsDialog
 from .preferences_view import PreferencesView
 from .utilities.module_view import stop_validation_queue_thread
 
@@ -119,6 +120,7 @@ ID_FIND_USAGES = wx.NewId()
 
 ID_OPTIONS_PREFERENCES = wx.ID_PREFERENCES
 ID_OPTIONS_READERS = wx.NewId()
+ID_FILE_PLUGINS = wx.NewId()
 ID_CHECK_NEW_VERSION = wx.NewId()
 
 ID_DEBUG_TOGGLE = wx.NewId()
@@ -212,6 +214,7 @@ class CPFrame(wx.Frame):
         #
         #  right_win
         #    Notes window
+        #    plugin_warning_panel (conditional)
         #    path_module_imageset_panel
         #        path_list_sash
         #            group_box
@@ -227,6 +230,13 @@ class CPFrame(wx.Frame):
         self.__notes_panel = wx.Panel(self.__right_win)
         self.__right_win.GetSizer().Add(self.__notes_panel, 0, wx.EXPAND | wx.ALL)
         self.__right_win.GetSizer().AddSpacer(4)
+        self.__plugin_warning_panel = wx.Panel(
+            self.__right_win, name="plugin_warning_panel"
+        )
+        self.__right_win.GetSizer().Add(
+            self.__plugin_warning_panel, 0, wx.EXPAND | wx.LEFT | wx.RIGHT
+        )
+        self.__right_win.GetSizer().AddSpacer(4)
         self.__path_module_imageset_panel = wx.Panel(self.__right_win, name="path_module_imageset_panel")
         self.__right_win.GetSizer().Add(
             self.__path_module_imageset_panel, 1, wx.EXPAND | wx.ALL
@@ -450,6 +460,18 @@ class CPFrame(wx.Frame):
         right_sizer = self.__right_win.GetSizer()
         assert isinstance(right_sizer, wx.Sizer)
         right_sizer.Show(self.__notes_panel, show)
+        # whether plugin_warning_panel itself should be shown is
+        # per-module (most modules don't get a warning at all) and is
+        # governed entirely by ModuleView.set_selection()/clear_selection(),
+        # which runs independently of this method and may well have
+        # already run *before* this call (e.g. __on_pipeline_loaded()
+        # selects the first module, then calls show_module_ui(True)) - so
+        # only ever force it off here (nothing selected => definitely no
+        # warning either), never force it on, or this would clobber
+        # whatever ModuleView correctly decided for the actual selected
+        # module with a blank, unstyled panel.
+        if not show:
+            right_sizer.Show(self.__plugin_warning_panel, False)
         right_sizer.Show(self.__path_module_imageset_panel, show)
         self.__right_win.Layout()
         if show:
@@ -557,7 +579,7 @@ class CPFrame(wx.Frame):
         wx.GetApp().ExitMainLoop()
 
     def __set_properties(self):
-        self.SetTitle("CellProfiler %s" % cellprofiler_version)
+        self.SetTitle(wx.GetApp().GetAppDisplayName())
         self.SetSize((1024, 600))
 
     def enable_edit_commands(self, ids):
@@ -686,6 +708,11 @@ class CPFrame(wx.Frame):
             "&Preferences...",
             "Set global application preferences",
         )
+        self.__menu_file.Append(
+            ID_FILE_PLUGINS,
+            "&Plugins...",
+            "Manage CellProfiler plugins",
+        )
 
         self.recent_files = wx.Menu()
         self.recent_pipeline_files = wx.Menu()
@@ -915,6 +942,7 @@ class CPFrame(wx.Frame):
         self.Bind(wx.EVT_MENU, self.__on_readers, id=ID_OPTIONS_READERS)
         
         self.Bind(wx.EVT_MENU, self.__on_preferences, id=ID_OPTIONS_PREFERENCES)
+        self.Bind(wx.EVT_MENU, self.__on_plugins, id=ID_FILE_PLUGINS)
         self.Bind(wx.EVT_MENU, self.__on_close_all, id=ID_WINDOW_CLOSE_ALL)
         self.Bind(wx.EVT_MENU, self.__debug_pdb, id=ID_DEBUG_PDB)
         self.Bind(wx.EVT_MENU, self.__on_debug_help, id=ID_DEBUG_HELP)
@@ -1071,6 +1099,11 @@ class CPFrame(wx.Frame):
         dlg = PreferencesDialog()
         dlg.Show()
 
+    @staticmethod
+    def __on_plugins(event):
+        dlg = PluginsDialog()
+        dlg.Show()
+
     def __on_close_all(self, event):
         close_all(self)
 
@@ -1300,6 +1333,7 @@ class CPFrame(wx.Frame):
             self.__workspace,
             frame=self,
             notes_panel=self.__notes_panel,
+            plugin_warning_panel=self.__plugin_warning_panel,
         )
         self.__pipeline_controller.attach_to_module_view(self.__module_view)
         self.__pipeline_list_view.attach_to_module_view(self.__module_view)

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/gui/dialog.py

@@ -10,10 +10,10 @@ class AboutDialogInfo(wx.adv.AboutDialogInfo):
         super(AboutDialogInfo, self).__init__()
 
         self.SetCopyright(
-            "Copyright © 2003 - 2021 Broad Institute, Inc.\nAll rights reserved."
+            "Copyright © 2003 - 2026 Broad Institute, Inc.\nAll rights reserved."
         )
 
-        self.SetName("CellProfiler")
+        self.SetName(wx.GetApp().GetAppName())
         self.SetVersion(cellprofiler_version)
         self.SetIcon(get_cp_icon(100))
 

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/gui/editobjectsdlg.py

@@ -6,8 +6,8 @@
 import logging
 import sys
 
-import centrosome.cpmorphology
-import centrosome.index
+import centriole.cpmorphology
+import centriole.index
 import matplotlib
 import matplotlib.backend_bases
 import matplotlib.backends.backend_wxagg
@@ -577,7 +577,7 @@ class EditObjectsDialog(wx.Dialog):
         self.lj = numpy.zeros(0, int)
         self.ll = numpy.zeros(0, int)
         for label_and_touching in self.labels:
-            colored_labels = centrosome.cpmorphology.color_labels(label_and_touching)
+            colored_labels = centriole.cpmorphology.color_labels(label_and_touching)
             for color in range(1, numpy.max(colored_labels) + 1):
                 label = numpy.zeros(label_and_touching.shape, label_and_touching.dtype)
                 label[colored_labels == color] = label_and_touching[
@@ -595,7 +595,7 @@ class EditObjectsDialog(wx.Dialog):
                 l, ct = scipy.ndimage.label(
                     label != 0, structure=numpy.ones((3, 3), bool)
                 )
-                coords, offsets, counts = centrosome.cpmorphology.get_outline_pts(
+                coords, offsets, counts = centriole.cpmorphology.get_outline_pts(
                     l, numpy.arange(1, ct + 1)
                 )
                 oi, oj = coords.transpose()
@@ -614,7 +614,7 @@ class EditObjectsDialog(wx.Dialog):
                 if len(ledge) > 0:
                     l[l == ledge[0]] = 0
 
-                coords, offsets, counts = centrosome.cpmorphology.get_outline_pts(
+                coords, offsets, counts = centriole.cpmorphology.get_outline_pts(
                     l, numpy.arange(1, ct + 1)
                 )
                 if coords.shape[0] > 0:
@@ -810,7 +810,7 @@ class EditObjectsDialog(wx.Dialog):
                         lmap = numpy.zeros(len(k), int)
                         lmap[k] = numpy.arange(numpy.sum(k))
                         counts = numpy.bincount(lmap[self.ol[mask]])
-                        indexer = centrosome.index.Indexes((counts,))
+                        indexer = centriole.index.Indexes((counts,))
                         e = 1 + 3 * (counts[indexer.rev_idx] >= 16)
                         dash_mask = (indexer.idx[0] & (2 ** e - 1)) >= 2 ** (e - 1)
                         color[self.oi[mask], self.oj[mask]] = (
@@ -1243,7 +1243,7 @@ class EditObjectsDialog(wx.Dialog):
             l0 = xydata[:-1, :]
             l1 = xydata[1:, :]
             neww_pt = numpy.ones(l0.shape) * new_pt[numpy.newaxis, :]
-            d = centrosome.cpmorphology.distance2_to_line(neww_pt, l0, l1)
+            d = centriole.cpmorphology.distance2_to_line(neww_pt, l0, l1)
             different_sign = numpy.sign(neww_pt - l0) != numpy.sign(neww_pt - l1)
             on_segment = (d < eps) & different_sign[:, 0] & different_sign[:, 1]
 
@@ -1368,7 +1368,7 @@ class EditObjectsDialog(wx.Dialog):
         for n in all_labels:
             self.remove_label(n)
 
-        mask = centrosome.cpmorphology.convex_hull_image(mask)
+        mask = centriole.cpmorphology.convex_hull_image(mask)
         self.replace_label(mask, object_number)
         self.init_labels()
         self.make_control_points(object_number)
@@ -1400,7 +1400,7 @@ class EditObjectsDialog(wx.Dialog):
             # In either case, don't add.
             #
             proj = numpy.sum(v * (pt - l0), 1)
-            d2 = centrosome.cpmorphology.distance2_to_line(pt, l0, l1)
+            d2 = centriole.cpmorphology.distance2_to_line(pt, l0, l1)
             d2[proj <= 0] = numpy.inf
             d2[proj >= llen] = numpy.inf
             best = numpy.argmin(d2)
@@ -1666,7 +1666,7 @@ class EditObjectsDialog(wx.Dialog):
                         and attrs[self.K_LABEL] == old_object_number
                     ):
                         hx, hy = artist.get_data()
-                        hmask = hmask | centrosome.cpmorphology.polygon_lines_to_mask(
+                        hmask = hmask | centriole.cpmorphology.polygon_lines_to_mask(
                             hy[:-1], hx[:-1], hy[1:], hx[1:], self.shape
                         )
                 temp = numpy.ones(self.to_keep.shape[0] + 1, bool)
@@ -1847,7 +1847,7 @@ class EditObjectsDialog(wx.Dialog):
             xydata = numpy.vstack((xydata, numpy.array([[event.xdata, event.ydata]])))
         xydata = numpy.vstack((xydata, numpy.array([[xydata[0, 0], xydata[0, 1]]])))
 
-        mask = centrosome.cpmorphology.polygon_lines_to_mask(
+        mask = centriole.cpmorphology.polygon_lines_to_mask(
             xydata[:-1, 1], xydata[:-1, 0], xydata[1:, 1], xydata[1:, 0], self.shape
         )
         if not self.allow_overlap:
@@ -2084,7 +2084,7 @@ class EditObjectsDialog(wx.Dialog):
             sub_object_numbers = [
                 n for n in range(1, count + 1) if polarity or n != border_object
             ]
-            coords, offsets, counts = centrosome.cpmorphology.get_outline_pts(
+            coords, offsets, counts = centriole.cpmorphology.get_outline_pts(
                 labels, sub_object_numbers
             )
             coords -= 1  # account for mask padding
@@ -2109,7 +2109,7 @@ class EditObjectsDialog(wx.Dialog):
                         idx0 = idx1 - 1
                         ca = chain[accepted]
                         aidx = numpy.argwhere(accepted).flatten()
-                        a = centrosome.cpmorphology.triangle_areas(
+                        a = centriole.cpmorphology.triangle_areas(
                             ca[idx0], ca[idx1], chain[:-1]
                         )
                         idxmax = numpy.argmax(a)
@@ -2156,7 +2156,7 @@ class EditObjectsDialog(wx.Dialog):
             mask = numpy.zeros(self.shape, bool)
             for artist in my_artists:
                 j, i = artist.get_data()
-                m1 = centrosome.cpmorphology.polygon_lines_to_mask(
+                m1 = centriole.cpmorphology.polygon_lines_to_mask(
                     i[:-1], j[:-1], i[1:], j[1:], self.shape
                 )
                 mask[m1] = ~mask[m1]

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/gui/errordialog.py

@@ -445,7 +445,7 @@ def display_error_message(parent, message, title, buttons=None, size=(300, 200))
         sizer.Add(
             wx.StaticBitmap(dlg, bitmap=icon),
             0,
-            wx.ALIGN_CENTER_HORIZONTAL | wx.ALIGN_TOP | wx.ALL,
+            wx.ALIGN_TOP | wx.ALL,
             10,
         )
         sizer.AddSpacer(10)

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/gui/figure/_figure.py

@@ -5,8 +5,8 @@ import sys
 import textwrap
 import uuid
 
-import centrosome.cpmorphology
-import centrosome.outline
+import centriole.cpmorphology
+import centriole.outline
 import matplotlib
 import matplotlib.axes
 import matplotlib.backend_bases
@@ -2142,7 +2142,7 @@ class Figure(wx.Frame):
             for labels in cplabel[CPLD_LABELS]:
                 if cplabel[CPLD_MODE] == CPLDM_OUTLINES:
                     oc = numpy.array(cplabel[CPLD_OUTLINE_COLOR], float)[:3] / 255
-                    lm = centrosome.outline.outline(labels) != 0
+                    lm = centriole.outline.outline(labels) != 0
                     lo = lm.astype(float)
                     lw = float(cplabel[CPLD_LINE_WIDTH])
                     if lw > 1:

{cellprofiler_nightly-5.0.0.dev745 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/gui/figure/_outline_artist.py

@@ -1,4 +1,4 @@
-import centrosome.cpmorphology
+import centriole.cpmorphology
 import matplotlib
 import matplotlib.collections
 import numpy
@@ -40,7 +40,7 @@ class OutlineArtist(matplotlib.collections.LineCollection):
             else:
                 my_range = numpy.arange(1, len(unique))
             idx.shape = l.shape
-            pts, offs, counts = centrosome.cpmorphology.get_outline_pts(idx, my_range)
+            pts, offs, counts = centriole.cpmorphology.get_outline_pts(idx, my_range)
             pts = pts[:, ::-1]  # matplotlib x, y reversed from i,j
             for off, count in zip(offs, counts):
                 lines.append(numpy.vstack((pts[off : off + count], pts[off : off + 1])))