dcnum 0.20.4__tar.gz → 0.21.0__tar.gz

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  1. {dcnum-0.20.4 → dcnum-0.21.0}/CHANGELOG +4 -0
  2. {dcnum-0.20.4/src/dcnum.egg-info → dcnum-0.21.0}/PKG-INFO +1 -1
  3. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/_version.py +2 -2
  4. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/meta/ppid.py +1 -1
  5. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/segm/segmenter.py +1 -1
  6. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/segm/segmenter_gpu.py +0 -1
  7. {dcnum-0.20.4 → dcnum-0.21.0/src/dcnum.egg-info}/PKG-INFO +1 -1
  8. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_segm_base.py +6 -0
  9. {dcnum-0.20.4 → dcnum-0.21.0}/.github/workflows/check.yml +0 -0
  10. {dcnum-0.20.4 → dcnum-0.21.0}/.github/workflows/deploy_pypi.yml +0 -0
  11. {dcnum-0.20.4 → dcnum-0.21.0}/.gitignore +0 -0
  12. {dcnum-0.20.4 → dcnum-0.21.0}/.readthedocs.yml +0 -0
  13. {dcnum-0.20.4 → dcnum-0.21.0}/LICENSE +0 -0
  14. {dcnum-0.20.4 → dcnum-0.21.0}/README.rst +0 -0
  15. {dcnum-0.20.4 → dcnum-0.21.0}/docs/conf.py +0 -0
  16. {dcnum-0.20.4 → dcnum-0.21.0}/docs/extensions/github_changelog.py +0 -0
  17. {dcnum-0.20.4 → dcnum-0.21.0}/docs/index.rst +0 -0
  18. {dcnum-0.20.4 → dcnum-0.21.0}/docs/requirements.txt +0 -0
  19. {dcnum-0.20.4 → dcnum-0.21.0}/pyproject.toml +0 -0
  20. {dcnum-0.20.4 → dcnum-0.21.0}/setup.cfg +0 -0
  21. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/__init__.py +0 -0
  22. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/__init__.py +0 -0
  23. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/event_extractor_manager_thread.py +0 -0
  24. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_background/__init__.py +0 -0
  25. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_background/base.py +0 -0
  26. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_background/bg_copy.py +0 -0
  27. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_background/bg_roll_median.py +0 -0
  28. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_background/bg_sparse_median.py +0 -0
  29. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_brightness/__init__.py +0 -0
  30. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_brightness/bright_all.py +0 -0
  31. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_brightness/common.py +0 -0
  32. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_contour/__init__.py +0 -0
  33. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_contour/contour.py +0 -0
  34. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_contour/moments.py +0 -0
  35. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_contour/volume.py +0 -0
  36. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_texture/__init__.py +0 -0
  37. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_texture/common.py +0 -0
  38. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/feat_texture/tex_all.py +0 -0
  39. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/gate.py +0 -0
  40. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/feat/queue_event_extractor.py +0 -0
  41. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/logic/__init__.py +0 -0
  42. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/logic/ctrl.py +0 -0
  43. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/logic/job.py +0 -0
  44. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/logic/json_encoder.py +0 -0
  45. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/meta/__init__.py +0 -0
  46. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/meta/paths.py +0 -0
  47. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/read/__init__.py +0 -0
  48. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/read/cache.py +0 -0
  49. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/read/const.py +0 -0
  50. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/read/hdf5_data.py +0 -0
  51. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/read/mapped.py +0 -0
  52. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/segm/__init__.py +0 -0
  53. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/segm/segm_thresh.py +0 -0
  54. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/segm/segmenter_cpu.py +0 -0
  55. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/segm/segmenter_manager_thread.py +0 -0
  56. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/write/__init__.py +0 -0
  57. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/write/deque_writer_thread.py +0 -0
  58. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/write/queue_collector_thread.py +0 -0
  59. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/write/writer.py +0 -0
  60. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum.egg-info/SOURCES.txt +0 -0
  61. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum.egg-info/dependency_links.txt +0 -0
  62. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum.egg-info/requires.txt +0 -0
  63. {dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum.egg-info/top_level.txt +0 -0
  64. {dcnum-0.20.4 → dcnum-0.21.0}/tests/conftest.py +0 -0
  65. {dcnum-0.20.4 → dcnum-0.21.0}/tests/data/fmt-hdf5_cytoshot_extended-moments-features.zip +0 -0
  66. {dcnum-0.20.4 → dcnum-0.21.0}/tests/data/fmt-hdf5_cytoshot_full-features_2023.zip +0 -0
  67. {dcnum-0.20.4 → dcnum-0.21.0}/tests/data/fmt-hdf5_cytoshot_full-features_2024.zip +0 -0
  68. {dcnum-0.20.4 → dcnum-0.21.0}/tests/data/fmt-hdf5_cytoshot_full-features_legacy_allev_2023.zip +0 -0
  69. {dcnum-0.20.4 → dcnum-0.21.0}/tests/data/fmt-hdf5_shapein_empty.zip +0 -0
  70. {dcnum-0.20.4 → dcnum-0.21.0}/tests/data/fmt-hdf5_shapein_raw-with-variable-length-logs.zip +0 -0
  71. {dcnum-0.20.4 → dcnum-0.21.0}/tests/helper_methods.py +0 -0
  72. {dcnum-0.20.4 → dcnum-0.21.0}/tests/requirements.txt +0 -0
  73. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_feat_background_base.py +0 -0
  74. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_feat_background_bg_copy.py +0 -0
  75. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_feat_background_bg_roll_median.py +0 -0
  76. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_feat_background_bg_sparsemed.py +0 -0
  77. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_feat_brightness.py +0 -0
  78. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_feat_event_extractor_manager.py +0 -0
  79. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_feat_gate.py +0 -0
  80. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_feat_haralick.py +0 -0
  81. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_feat_moments_based.py +0 -0
  82. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_feat_moments_based_extended.py +0 -0
  83. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_feat_volume.py +0 -0
  84. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_init.py +0 -0
  85. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_logic_job.py +0 -0
  86. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_logic_join.py +0 -0
  87. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_logic_json.py +0 -0
  88. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_logic_pipeline.py +0 -0
  89. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_meta_paths.py +0 -0
  90. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_meta_ppid_base.py +0 -0
  91. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_meta_ppid_bg.py +0 -0
  92. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_meta_ppid_data.py +0 -0
  93. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_meta_ppid_feat.py +0 -0
  94. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_meta_ppid_gate.py +0 -0
  95. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_meta_ppid_segm.py +0 -0
  96. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_read_basin.py +0 -0
  97. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_read_concat_hdf5.py +0 -0
  98. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_read_hdf5.py +0 -0
  99. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_read_hdf5_basins.py +0 -0
  100. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_read_hdf5_index_mapping.py +0 -0
  101. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_segm_no_mask_proc.py +0 -0
  102. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_segm_thresh.py +0 -0
  103. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_write_deque_writer_thread.py +0 -0
  104. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_write_queue_collector_thread.py +0 -0
  105. {dcnum-0.20.4 → dcnum-0.21.0}/tests/test_write_writer.py +0 -0
{dcnum-0.20.4 → dcnum-0.21.0}/CHANGELOG RENAMED
@@ -1,3 +1,7 @@
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+ 0.21.0
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+ - fix: GPUSegmenter did not perform mask postprocessing
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+ - ref: enable mask postprocessing by default for all segmenters
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+ - ref: increment DCNUM_PPID_GENERATION to 9
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  0.20.4
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  - fix: slot_chunks were not performed in increasing order, making it
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  impossible for writer to continue writing and consequent OOM
{dcnum-0.20.4/src/dcnum.egg-info → dcnum-0.21.0}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: dcnum
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- Version: 0.20.4
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+ Version: 0.21.0
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  Summary: numerics toolbox for imaging deformability cytometry
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  Author: Maximilian Schlögel, Paul Müller
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  Maintainer-email: Paul Müller <dev@craban.de>
{dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/_version.py RENAMED
@@ -12,5 +12,5 @@ __version__: str
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  __version_tuple__: VERSION_TUPLE
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  version_tuple: VERSION_TUPLE
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- __version__ = version = '0.20.4'
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- __version_tuple__ = version_tuple = (0, 20, 4)
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+ __version__ = version = '0.21.0'
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+ __version_tuple__ = version_tuple = (0, 21, 0)
{dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/meta/ppid.py RENAMED
@@ -10,7 +10,7 @@ import warnings
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  #: Increment this string if there are breaking changes that make
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  #: previous pipelines unreproducible.
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- DCNUM_PPID_GENERATION = "8"
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+ DCNUM_PPID_GENERATION = "9"
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  class ClassWithPPIDCapabilities(Protocol):
{dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/segm/segmenter.py RENAMED
@@ -19,7 +19,7 @@ class Segmenter(abc.ABC):
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  #: Whether to enable mask post-processing. If disabled, you should
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  #: make sure that your mask is properly defined and cleaned or you
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  #: have to call `process_mask` in your `segment_approach` implementation.
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- mask_postprocessing = False
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+ mask_postprocessing = True
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  #: Default keyword arguments for mask post-processing. See `process_mask`
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  #: for available options.
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  mask_default_kwargs = {}
{dcnum-0.20.4 → dcnum-0.21.0}/src/dcnum/segm/segmenter_gpu.py RENAMED
@@ -10,7 +10,6 @@ from .segmenter import Segmenter
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  class GPUSegmenter(Segmenter, abc.ABC):
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  hardware_processor = "gpu"
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- mask_postprocessing = False
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  def __init__(self,
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  *,
{dcnum-0.20.4 → dcnum-0.21.0/src/dcnum.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: dcnum
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- Version: 0.20.4
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+ Version: 0.21.0
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  Summary: numerics toolbox for imaging deformability cytometry
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  Author: Maximilian Schlögel, Paul Müller
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  Maintainer-email: Paul Müller <dev@craban.de>
{dcnum-0.20.4 → dcnum-0.21.0}/tests/test_segm_base.py RENAMED
@@ -37,6 +37,12 @@ class MockImageData:
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  return chunk
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+ def test_segmenter_properties():
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+ assert segm.CPUSegmenter.mask_postprocessing # sanity check
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+ assert segm.GPUSegmenter.mask_postprocessing # fixed in 0.21.0
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+ assert segm.Segmenter.mask_postprocessing # new default in 0.21.0
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+
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+
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  def test_segmenter_labeled_mask():
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  mask = np.array([
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  [0, 0, 0, 0, 0, 0, 0, 0],
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