ngio 0.5.0b6__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (88) hide show
  1. ngio/__init__.py +69 -0
  2. ngio/common/__init__.py +28 -0
  3. ngio/common/_dimensions.py +335 -0
  4. ngio/common/_masking_roi.py +153 -0
  5. ngio/common/_pyramid.py +408 -0
  6. ngio/common/_roi.py +315 -0
  7. ngio/common/_synt_images_utils.py +101 -0
  8. ngio/common/_zoom.py +188 -0
  9. ngio/experimental/__init__.py +5 -0
  10. ngio/experimental/iterators/__init__.py +15 -0
  11. ngio/experimental/iterators/_abstract_iterator.py +390 -0
  12. ngio/experimental/iterators/_feature.py +189 -0
  13. ngio/experimental/iterators/_image_processing.py +130 -0
  14. ngio/experimental/iterators/_mappers.py +48 -0
  15. ngio/experimental/iterators/_rois_utils.py +126 -0
  16. ngio/experimental/iterators/_segmentation.py +235 -0
  17. ngio/hcs/__init__.py +19 -0
  18. ngio/hcs/_plate.py +1354 -0
  19. ngio/images/__init__.py +44 -0
  20. ngio/images/_abstract_image.py +967 -0
  21. ngio/images/_create_synt_container.py +132 -0
  22. ngio/images/_create_utils.py +423 -0
  23. ngio/images/_image.py +926 -0
  24. ngio/images/_label.py +411 -0
  25. ngio/images/_masked_image.py +531 -0
  26. ngio/images/_ome_zarr_container.py +1237 -0
  27. ngio/images/_table_ops.py +471 -0
  28. ngio/io_pipes/__init__.py +75 -0
  29. ngio/io_pipes/_io_pipes.py +361 -0
  30. ngio/io_pipes/_io_pipes_masked.py +488 -0
  31. ngio/io_pipes/_io_pipes_roi.py +146 -0
  32. ngio/io_pipes/_io_pipes_types.py +56 -0
  33. ngio/io_pipes/_match_shape.py +377 -0
  34. ngio/io_pipes/_ops_axes.py +344 -0
  35. ngio/io_pipes/_ops_slices.py +411 -0
  36. ngio/io_pipes/_ops_slices_utils.py +199 -0
  37. ngio/io_pipes/_ops_transforms.py +104 -0
  38. ngio/io_pipes/_zoom_transform.py +180 -0
  39. ngio/ome_zarr_meta/__init__.py +65 -0
  40. ngio/ome_zarr_meta/_meta_handlers.py +536 -0
  41. ngio/ome_zarr_meta/ngio_specs/__init__.py +77 -0
  42. ngio/ome_zarr_meta/ngio_specs/_axes.py +515 -0
  43. ngio/ome_zarr_meta/ngio_specs/_channels.py +462 -0
  44. ngio/ome_zarr_meta/ngio_specs/_dataset.py +89 -0
  45. ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py +539 -0
  46. ngio/ome_zarr_meta/ngio_specs/_ngio_image.py +438 -0
  47. ngio/ome_zarr_meta/ngio_specs/_pixel_size.py +122 -0
  48. ngio/ome_zarr_meta/v04/__init__.py +27 -0
  49. ngio/ome_zarr_meta/v04/_custom_models.py +18 -0
  50. ngio/ome_zarr_meta/v04/_v04_spec.py +473 -0
  51. ngio/ome_zarr_meta/v05/__init__.py +27 -0
  52. ngio/ome_zarr_meta/v05/_custom_models.py +18 -0
  53. ngio/ome_zarr_meta/v05/_v05_spec.py +511 -0
  54. ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/mask.png +0 -0
  55. ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/nuclei.png +0 -0
  56. ngio/resources/20200812-CardiomyocyteDifferentiation14-Cycle1_B03/raw.jpg +0 -0
  57. ngio/resources/__init__.py +55 -0
  58. ngio/resources/resource_model.py +36 -0
  59. ngio/tables/__init__.py +43 -0
  60. ngio/tables/_abstract_table.py +270 -0
  61. ngio/tables/_tables_container.py +449 -0
  62. ngio/tables/backends/__init__.py +57 -0
  63. ngio/tables/backends/_abstract_backend.py +240 -0
  64. ngio/tables/backends/_anndata.py +139 -0
  65. ngio/tables/backends/_anndata_utils.py +90 -0
  66. ngio/tables/backends/_csv.py +19 -0
  67. ngio/tables/backends/_json.py +92 -0
  68. ngio/tables/backends/_parquet.py +19 -0
  69. ngio/tables/backends/_py_arrow_backends.py +222 -0
  70. ngio/tables/backends/_table_backends.py +226 -0
  71. ngio/tables/backends/_utils.py +608 -0
  72. ngio/tables/v1/__init__.py +23 -0
  73. ngio/tables/v1/_condition_table.py +71 -0
  74. ngio/tables/v1/_feature_table.py +125 -0
  75. ngio/tables/v1/_generic_table.py +49 -0
  76. ngio/tables/v1/_roi_table.py +575 -0
  77. ngio/transforms/__init__.py +5 -0
  78. ngio/transforms/_zoom.py +19 -0
  79. ngio/utils/__init__.py +45 -0
  80. ngio/utils/_cache.py +48 -0
  81. ngio/utils/_datasets.py +165 -0
  82. ngio/utils/_errors.py +37 -0
  83. ngio/utils/_fractal_fsspec_store.py +42 -0
  84. ngio/utils/_zarr_utils.py +534 -0
  85. ngio-0.5.0b6.dist-info/METADATA +148 -0
  86. ngio-0.5.0b6.dist-info/RECORD +88 -0
  87. ngio-0.5.0b6.dist-info/WHEEL +4 -0
  88. ngio-0.5.0b6.dist-info/licenses/LICENSE +28 -0
ngio/images/__init__.py ADDED
@@ -0,0 +1,44 @@
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+ """OME-Zarr object models."""
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+
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+ from ngio.images._create_synt_container import create_synthetic_ome_zarr
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+ from ngio.images._image import ChannelSelectionModel, Image, ImagesContainer
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+ from ngio.images._label import Label, LabelsContainer
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+ from ngio.images._ome_zarr_container import (
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+ OmeZarrContainer,
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+ create_empty_ome_zarr,
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+ create_ome_zarr_from_array,
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+ open_image,
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+ open_label,
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+ open_ome_zarr_container,
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+ )
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+ from ngio.images._table_ops import (
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+ concatenate_image_tables,
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+ concatenate_image_tables_as,
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+ concatenate_image_tables_as_async,
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+ concatenate_image_tables_async,
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+ conctatenate_tables,
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+ list_image_tables,
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+ list_image_tables_async,
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+ )
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+
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+ __all__ = [
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+ "ChannelSelectionModel",
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+ "Image",
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+ "ImagesContainer",
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+ "Label",
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+ "LabelsContainer",
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+ "OmeZarrContainer",
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+ "concatenate_image_tables",
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+ "concatenate_image_tables_as",
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+ "concatenate_image_tables_as_async",
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+ "concatenate_image_tables_async",
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+ "conctatenate_tables",
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+ "create_empty_ome_zarr",
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+ "create_ome_zarr_from_array",
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+ "create_synthetic_ome_zarr",
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+ "list_image_tables",
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+ "list_image_tables_async",
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+ "open_image",
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+ "open_label",
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+ "open_ome_zarr_container",
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+ ]