CellProfiler-nightly 5.0.0.dev780__tar.gz → 5.0.0.dev784__tar.gz

{cellprofiler_nightly-5.0.0.dev780 → 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.dev780
+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.dev780 → cellprofiler_nightly-5.0.0.dev784}/CellProfiler_nightly.egg-info/SOURCES.txt

@@ -291,7 +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
@@ -329,7 +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
@@ -375,12 +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.dev780 → 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.dev780 → cellprofiler_nightly-5.0.0.dev784}/CellProfiler_nightly.egg-info/scm_file_list.json

@@ -282,7 +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",
@@ -320,7 +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",
@@ -370,12 +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.dev780 → 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.dev780 → cellprofiler_nightly-5.0.0.dev784}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: CellProfiler-nightly
-Version: 5.0.0.dev780
+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.dev780 → 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.dev780'
-__version_tuple__ = version_tuple = (5, 0, 0, 'dev780')
+__version__ = version = '5.0.0.dev784'
+__version_tuple__ = version_tuple = (5, 0, 0, 'dev784')
 
-__commit_id__ = commit_id = 'g47767c212'
+__commit_id__ = commit_id = 'g166605047'

{cellprofiler_nightly-5.0.0.dev780 → 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.dev780 → 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.dev780 → 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.dev780 → 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])))

{cellprofiler_nightly-5.0.0.dev780 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/gui/tools.py

@@ -3,7 +3,7 @@
 
 import io
 
-import centrosome.cpmorphology
+import centriole.cpmorphology
 import imageio
 import matplotlib
 import matplotlib.figure
@@ -55,4 +55,4 @@ def renumber_labels_for_display(labels):
     so a random numbering has more color-distance between labels than a
     straightforward one
     """
-    return centrosome.cpmorphology.distance_color_labels(labels)
+    return centriole.cpmorphology.distance_color_labels(labels)

{cellprofiler_nightly-5.0.0.dev780 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/modules/__init__.py

@@ -34,7 +34,6 @@ builtin_modules = {
     "flipandrotate": "FlipAndRotate",
     "gaussianfilter": "GaussianFilter",
     "graytocolor": "GrayToColor",
-    "identifydeadworms": "IdentifyDeadWorms",
     "identifyobjectsingrid": "IdentifyObjectsInGrid",
     "identifyobjectsmanually": "IdentifyObjectsManually",
     "identifyprimaryobjects": "IdentifyPrimaryObjects",
@@ -79,12 +78,10 @@ builtin_modules = {
     "shrinktoobjectcenters": "ShrinkToObjectCenters",
     "smooth": "Smooth",
     "splitormergeobjects": "SplitOrMergeObjects",
-    "straightenworms": "StraightenWorms",
     "matchtemplate": "MatchTemplate",
     "threshold": "Threshold",
     "trackobjects": "TrackObjects",
     "tile": "Tile",
     "unmixcolors": "UnmixColors",
-    "untangleworms": "UntangleWorms",
     "watershed": "Watershed",
 }

{cellprofiler_nightly-5.0.0.dev780 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/modules/crop.py

@@ -38,7 +38,7 @@ help for more information on saving cropping shapes.
 """
 
 import logging
-import centrosome.filter
+import centriole.filter
 import matplotlib.axes
 import matplotlib.cm
 import matplotlib.figure
@@ -527,7 +527,7 @@ objects:
         import wx
 
         """Show the cropping user interface"""
-        pixel_data = centrosome.filter.stretch(orig_image)
+        pixel_data = centriole.filter.stretch(orig_image)
         #
         # Create the UI - a dialog with a figure inside
         #

{cellprofiler_nightly-5.0.0.dev780 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/modules/definegrid.py

@@ -47,7 +47,7 @@ Measurements made by this module
 
 import logging
 
-import centrosome.cpmorphology
+import centriole.cpmorphology
 import numpy
 from cellprofiler_core.constants.measurement import COLTYPE_FLOAT
 from cellprofiler_core.constants.measurement import COLTYPE_INTEGER
@@ -628,7 +628,7 @@ first image.
         Returns a CPGridInfo object
         """
         objects = workspace.object_set.get_objects(self.object_name.value)
-        centroids = centrosome.cpmorphology.centers_of_labels(objects.segmented)
+        centroids = centriole.cpmorphology.centers_of_labels(objects.segmented)
         try:
             if centroids.shape[1] < 2:
                 #

{cellprofiler_nightly-5.0.0.dev780 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/modules/expandorshrinkobjects.py

@@ -58,7 +58,7 @@ Measurements made by this module
     **{"HELP_ON_SAVING_OBJECTS": _help.HELP_ON_SAVING_OBJECTS}
 )
 
-import centrosome.cpmorphology
+import centriole.cpmorphology
 import numpy
 import scipy.ndimage
 

{cellprofiler_nightly-5.0.0.dev780 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/modules/identifyobjectsingrid.py

@@ -65,7 +65,7 @@ See also **DefineGrid**.
 )
 
 import numpy
-from centrosome.cpmorphology import centers_of_labels
+from centriole.cpmorphology import centers_of_labels
 
 from cellprofiler_core.utilities.grid import Grid
 from cellprofiler_core.module import Module

{cellprofiler_nightly-5.0.0.dev780 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/modules/maskobjects.py

@@ -20,8 +20,8 @@ from cellprofiler_core.utilities.core.module.identify import (
     get_object_measurement_columns,
 )
 from cellprofiler_core.utilities.core.object import size_similarly
-from centrosome.cpmorphology import fixup_scipy_ndimage_result
-from centrosome.outline import outline
+from centriole.cpmorphology import fixup_scipy_ndimage_result
+from centriole.outline import outline
 
 from cellprofiler.modules import _help
 

{cellprofiler_nightly-5.0.0.dev780 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/modules/measureimagequality.py

@@ -1364,7 +1364,7 @@ to the foreground pixels or the background pixels.
         if variable_revision_number == 4:
             global_threshold_methods = [" ".join((x, "Global")) for x in THRESHOLD_METHODS]
             # Thresholding method name change: Strip off "Global" since
-            # centrosome.theshold.TM_GLOBAL_METHODS no longer used
+            # centriole.theshold.TM_GLOBAL_METHODS no longer used
             thresh_dict = dict(zip(global_threshold_methods, THRESHOLD_METHODS))
             # Naturally, this method assumes that the user didn't name their images "Otsu Global" or something similar
             setting_values = [

{cellprofiler_nightly-5.0.0.dev780 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/modules/plugins/measurementtemplate.py

@@ -4,8 +4,8 @@
 #
 #################################
 
-import centrosome.cpmorphology
-import centrosome.zernike
+import centriole.cpmorphology
+import centriole.zernike
 import numpy
 import scipy.ndimage
 
@@ -347,7 +347,7 @@ radial degree you enter here.
         # in those indexes. MEC returns the i and j coordinate of the center
         # and the radius of the circle and that defines the circle entirely.
         #
-        centers, radius = centrosome.cpmorphology.minimum_enclosing_circle(
+        centers, radius = centriole.cpmorphology.minimum_enclosing_circle(
             labels, indexes
         )
         #
@@ -401,7 +401,7 @@ radial degree you enter here.
         wants_negative - if True, return both positive and negative M, if false
                          return only positive
         """
-        zi = centrosome.zernike.get_zernike_indexes(self.radial_degree.value + 1)
+        zi = centriole.zernike.get_zernike_indexes(self.radial_degree.value + 1)
 
         if wants_negative:
             #
@@ -496,12 +496,12 @@ radial degree you enter here.
         # We use a mask of all of the non-zero labels so the calculation
         # runs a little faster.
         #
-        zernike_polynomial = centrosome.zernike.construct_zernike_polynomials(
+        zernike_polynomial = centriole.zernike.construct_zernike_polynomials(
             x, y, numpy.array([[n, m]]), labels > 0
         )
 
         #
-        # For historical reasons, centrosome didn't multiply by the per/zernike
+        # For historical reasons, centriole didn't multiply by the per/zernike
         # normalizing factor: 2*n + 2 / E / pi where E is 2 if m is zero and 1
         # if m is one. We do it here to aid with the reconstruction
         #
@@ -659,7 +659,7 @@ radial degree you enter here.
         zernike_indexes = numpy.array(list(feature_dictionary.keys()))
         zernike_features = numpy.array(list(feature_dictionary.values()))
 
-        z = centrosome.zernike.construct_zernike_polynomials(
+        z = centriole.zernike.construct_zernike_polynomials(
             j, i, numpy.abs(zernike_indexes), mask=mask
         )
         zn = (

{cellprofiler_nightly-5.0.0.dev780 → cellprofiler_nightly-5.0.0.dev784}/cellprofiler/modules/threshold.py

@@ -16,7 +16,7 @@ YES          YES          YES
 ============ ============ ===============
 """
 
-import centrosome.threshold
+import centriole.threshold
 import numpy
 from cellprofiler_core.constants.measurement import (
     FF_WEIGHTED_VARIANCE,
@@ -951,13 +951,13 @@ staining.
 
         mask = image.mask
 
-        wv = centrosome.threshold.weighted_variance(data, mask, binary_image)
+        wv = centriole.threshold.weighted_variance(data, mask, binary_image)
 
         measurements.add_measurement(
             "Image", FF_WEIGHTED_VARIANCE % objname, numpy.array([wv], dtype=float),
         )
 
-        entropies = centrosome.threshold.sum_of_entropies(data, mask, binary_image)
+        entropies = centriole.threshold.sum_of_entropies(data, mask, binary_image)
 
         measurements.add_measurement(
             "Image",
@@ -1035,18 +1035,18 @@ staining.
                 setting_values[2] = ThresholdOpts.Scope.GLOBAL
 
             if setting_values[2] == ThresholdOpts.Scope.ADAPTIVE and setting_values[3] in [
-                centrosome.threshold.TM_MCT,
-                centrosome.threshold.TM_ROBUST_BACKGROUND,
+                centriole.threshold.TM_MCT,
+                centriole.threshold.TM_ROBUST_BACKGROUND,
             ]:
                 setting_values[2] = ThresholdOpts.Scope.GLOBAL
 
-            if setting_values[3] == centrosome.threshold.TM_MCT:
+            if setting_values[3] == centriole.threshold.TM_MCT:
                 setting_values[3] = ThresholdOpts.Method.MINIMUM_CROSS_ENTROPY
 
             if setting_values[2] == ThresholdOpts.Scope.ADAPTIVE:
                 setting_values += [setting_values[3]]
             else:
-                setting_values += [centrosome.threshold.TM_OTSU]
+                setting_values += [centriole.threshold.TM_OTSU]
             variable_revision_number = 10
         used_log_otsu = False
         if variable_revision_number == 10:
@@ -1092,23 +1092,23 @@ staining.
 
             if setting_values[1] == "Automatic":
                 setting_values[1] = ThresholdOpts.Scope.GLOBAL
-                setting_values[2] = centrosome.threshold.TM_MCT
+                setting_values[2] = centriole.threshold.TM_MCT
                 setting_values[3] = "Manual"
                 setting_values[4] = "1.3488"
                 setting_values[5] = "1"
                 setting_values[6] = "(0.0, 1.0)"
 
             removed_threshold_methods = [
-                centrosome.threshold.TM_KAPUR,
-                centrosome.threshold.TM_MOG,
-                centrosome.threshold.TM_RIDLER_CALVARD,
+                centriole.threshold.TM_KAPUR,
+                centriole.threshold.TM_MOG,
+                centriole.threshold.TM_RIDLER_CALVARD,
             ]
 
             if setting_values[2] in removed_threshold_methods:
                 setting_values[2] = "None"
 
-            if setting_values[2] == centrosome.threshold.TM_BACKGROUND:
-                setting_values[2] = centrosome.threshold.TM_ROBUST_BACKGROUND
+            if setting_values[2] == centriole.threshold.TM_BACKGROUND:
+                setting_values[2] = centriole.threshold.TM_ROBUST_BACKGROUND
                 setting_values[17] = "Custom"
                 setting_values[18] = "0.02"
                 setting_values[19] = "0.02"