cellprofiler-library-nightly 5.0.0.dev413__tar.gz → 5.0.0.dev454__tar.gz

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  1. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/PKG-INFO +1 -1
  2. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/_version.py +3 -3
  3. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/functions/image_processing.py +1 -1
  4. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/functions/object_processing.py +541 -26
  5. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/__init__.py +3 -0
  6. cellprofiler_library_nightly-5.0.0.dev454/cellprofiler_library/modules/_identifyprimaryobjects.py +223 -0
  7. cellprofiler_library_nightly-5.0.0.dev454/cellprofiler_library/modules/_identifysecondaryobjects.py +264 -0
  8. cellprofiler_library_nightly-5.0.0.dev454/cellprofiler_library/modules/_identifytertiaryobjects.py +66 -0
  9. cellprofiler_library_nightly-5.0.0.dev454/cellprofiler_library/modules/_shrinktoobjectcenters.py +10 -0
  10. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_threshold.py +1 -2
  11. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/dilateimage.py +0 -2
  12. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/dilateobjects.py +0 -2
  13. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/erodeimage.py +0 -2
  14. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/erodeobjects.py +0 -3
  15. cellprofiler_library_nightly-5.0.0.dev454/cellprofiler_library/opts/identifyprimaryobjects.py +22 -0
  16. cellprofiler_library_nightly-5.0.0.dev454/cellprofiler_library/opts/identifysecondaryobjects.py +8 -0
  17. cellprofiler_library_nightly-5.0.0.dev454/cellprofiler_library/opts/identifytertiaryobjects.py +5 -0
  18. cellprofiler_library_nightly-5.0.0.dev454/cellprofiler_library/opts/shrinktoobjectcenters.py +6 -0
  19. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library_nightly.egg-info/PKG-INFO +1 -1
  20. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library_nightly.egg-info/SOURCES.txt +8 -0
  21. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/LICENSE +0 -0
  22. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/README.md +0 -0
  23. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/__init__.py +0 -0
  24. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/functions/__init__.py +0 -0
  25. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/functions/file_processing.py +0 -0
  26. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/functions/measurement.py +0 -0
  27. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/functions/segmentation.py +0 -0
  28. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_closing.py +0 -0
  29. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_colortogray.py +0 -0
  30. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_combineobjects.py +0 -0
  31. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_convertimagetoobjects.py +0 -0
  32. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_convertobjectstoimage.py +0 -0
  33. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_correctilluminationapply.py +0 -0
  34. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_crop.py +0 -0
  35. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_dilateimage.py +0 -0
  36. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_dilateobjects.py +0 -0
  37. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_enhanceedges.py +0 -0
  38. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_enhanceorsuppressfeatures.py +0 -0
  39. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_erodeimage.py +0 -0
  40. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_erodeobjects.py +0 -0
  41. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_expandorshrinkobjects.py +0 -0
  42. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_fillobjects.py +0 -0
  43. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_gaussianfilter.py +0 -0
  44. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_measureimageoverlap.py +0 -0
  45. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_measureobjectsizeshape.py +0 -0
  46. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_medialaxis.py +0 -0
  47. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_medianfilter.py +0 -0
  48. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_morph.py +0 -0
  49. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_morphologicalskeleton.py +0 -0
  50. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_opening.py +0 -0
  51. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_overlayobjects.py +0 -0
  52. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_overlayoutlines.py +0 -0
  53. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_reducenoise.py +0 -0
  54. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_removeholes.py +0 -0
  55. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_resize.py +0 -0
  56. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_savecroppedobjects.py +0 -0
  57. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/modules/_watershed.py +0 -0
  58. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/__init__.py +0 -0
  59. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/colortogray.py +0 -0
  60. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/convertimagetoobjects.py +0 -0
  61. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/convertobjectstoimage.py +0 -0
  62. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/correctilluminationapply.py +0 -0
  63. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/crop.py +0 -0
  64. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/enhanceorsuppressfeatures.py +0 -0
  65. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/measureimageoverlap.py +0 -0
  66. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/morph.py +0 -0
  67. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/objectsizeshapefeatures.py +0 -0
  68. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/overlayoutlines.py +0 -0
  69. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/removeholes.py +0 -0
  70. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/resize.py +0 -0
  71. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/structuring_elements.py +0 -0
  72. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/opts/threshold.py +0 -0
  73. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/py.typed +0 -0
  74. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/types.py +0 -0
  75. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library_nightly.egg-info/dependency_links.txt +0 -0
  76. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library_nightly.egg-info/requires.txt +0 -0
  77. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library_nightly.egg-info/top_level.txt +0 -0
  78. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/environment.yml +0 -0
  79. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/pyproject.toml +0 -0
  80. {cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/setup.cfg +0 -0
{cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: cellprofiler-library-nightly
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- Version: 5.0.0.dev413
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+ Version: 5.0.0.dev454
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  Summary: cellprofiler-library implements CellProfiler's image processing and mathematical code, and is usable as a standalone library
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  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
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  Author-email: Beth Cimini <bcimini@broadinstitute.org>, David Stirling <dstirling@glencoesoftware.com>, Nodar Gogoberidze <ngogober@broadinstitute.org>
{cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/_version.py RENAMED
@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
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  commit_id: COMMIT_ID
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  __commit_id__: COMMIT_ID
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- __version__ = version = '5.0.0.dev413'
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- __version_tuple__ = version_tuple = (5, 0, 0, 'dev413')
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+ __version__ = version = '5.0.0.dev454'
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+ __version_tuple__ = version_tuple = (5, 0, 0, 'dev454')
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- __commit_id__ = commit_id = 'gd6becfb42'
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+ __commit_id__ = commit_id = 'g957fa6e04'
{cellprofiler_library_nightly-5.0.0.dev413 → cellprofiler_library_nightly-5.0.0.dev454}/cellprofiler_library/functions/image_processing.py RENAMED
@@ -382,7 +382,7 @@ def get_threshold_robust_background(
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  upper_outlier_fraction: float = 0.05,
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  averaging_method: Threshold.AveragingMethod = Threshold.AveragingMethod.MEAN,
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  variance_method: Threshold.VarianceMethod = Threshold.VarianceMethod.STANDARD_DEVIATION,
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- number_of_deviations: int = 2,
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+ number_of_deviations: float = 2.0,
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  ) -> float:
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  """Calculate threshold based on mean & standard deviation.
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  The threshold is calculated by trimming the top and bottom 5% of