ngio 0.1.5__py3-none-any.whl → 0.2.0__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 (87) hide show
  1. ngio/__init__.py +33 -5
  2. ngio/common/__init__.py +54 -0
  3. ngio/common/_array_pipe.py +265 -0
  4. ngio/common/_axes_transforms.py +64 -0
  5. ngio/common/_common_types.py +5 -0
  6. ngio/common/_dimensions.py +120 -0
  7. ngio/common/_masking_roi.py +158 -0
  8. ngio/common/_pyramid.py +228 -0
  9. ngio/common/_roi.py +165 -0
  10. ngio/common/_slicer.py +96 -0
  11. ngio/{pipes/_zoom_utils.py → common/_zoom.py} +51 -83
  12. ngio/hcs/__init__.py +5 -0
  13. ngio/hcs/plate.py +448 -0
  14. ngio/images/__init__.py +23 -0
  15. ngio/images/abstract_image.py +349 -0
  16. ngio/images/create.py +270 -0
  17. ngio/images/image.py +453 -0
  18. ngio/images/label.py +285 -0
  19. ngio/images/masked_image.py +273 -0
  20. ngio/images/ome_zarr_container.py +738 -0
  21. ngio/ome_zarr_meta/__init__.py +47 -0
  22. ngio/ome_zarr_meta/_meta_handlers.py +791 -0
  23. ngio/ome_zarr_meta/ngio_specs/__init__.py +71 -0
  24. ngio/ome_zarr_meta/ngio_specs/_axes.py +481 -0
  25. ngio/ome_zarr_meta/ngio_specs/_channels.py +389 -0
  26. ngio/ome_zarr_meta/ngio_specs/_dataset.py +134 -0
  27. ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py +377 -0
  28. ngio/ome_zarr_meta/ngio_specs/_ngio_image.py +489 -0
  29. ngio/ome_zarr_meta/ngio_specs/_pixel_size.py +116 -0
  30. ngio/ome_zarr_meta/v04/__init__.py +23 -0
  31. ngio/ome_zarr_meta/v04/_v04_spec_utils.py +485 -0
  32. ngio/tables/__init__.py +24 -6
  33. ngio/tables/_validators.py +190 -0
  34. ngio/tables/backends/__init__.py +8 -0
  35. ngio/tables/backends/_abstract_backend.py +71 -0
  36. ngio/tables/backends/_anndata_utils.py +198 -0
  37. ngio/tables/backends/_anndata_v1.py +76 -0
  38. ngio/tables/backends/_json_v1.py +56 -0
  39. ngio/tables/backends/_table_backends.py +102 -0
  40. ngio/tables/tables_container.py +310 -0
  41. ngio/tables/v1/__init__.py +5 -5
  42. ngio/tables/v1/_feature_table.py +182 -0
  43. ngio/tables/v1/_generic_table.py +160 -179
  44. ngio/tables/v1/_roi_table.py +366 -0
  45. ngio/utils/__init__.py +26 -10
  46. ngio/utils/_datasets.py +53 -0
  47. ngio/utils/_errors.py +10 -4
  48. ngio/utils/_fractal_fsspec_store.py +13 -0
  49. ngio/utils/_logger.py +3 -1
  50. ngio/utils/_zarr_utils.py +401 -0
  51. {ngio-0.1.5.dist-info → ngio-0.2.0.dist-info}/METADATA +31 -43
  52. ngio-0.2.0.dist-info/RECORD +54 -0
  53. ngio/core/__init__.py +0 -7
  54. ngio/core/dimensions.py +0 -122
  55. ngio/core/image_handler.py +0 -228
  56. ngio/core/image_like_handler.py +0 -549
  57. ngio/core/label_handler.py +0 -410
  58. ngio/core/ngff_image.py +0 -387
  59. ngio/core/roi.py +0 -92
  60. ngio/core/utils.py +0 -287
  61. ngio/io/__init__.py +0 -19
  62. ngio/io/_zarr.py +0 -88
  63. ngio/io/_zarr_array_utils.py +0 -0
  64. ngio/io/_zarr_group_utils.py +0 -61
  65. ngio/iterators/__init__.py +0 -1
  66. ngio/ngff_meta/__init__.py +0 -27
  67. ngio/ngff_meta/fractal_image_meta.py +0 -1267
  68. ngio/ngff_meta/meta_handler.py +0 -92
  69. ngio/ngff_meta/utils.py +0 -235
  70. ngio/ngff_meta/v04/__init__.py +0 -6
  71. ngio/ngff_meta/v04/specs.py +0 -158
  72. ngio/ngff_meta/v04/zarr_utils.py +0 -376
  73. ngio/pipes/__init__.py +0 -7
  74. ngio/pipes/_slicer_transforms.py +0 -176
  75. ngio/pipes/_transforms.py +0 -33
  76. ngio/pipes/data_pipe.py +0 -52
  77. ngio/tables/_ad_reader.py +0 -80
  78. ngio/tables/_utils.py +0 -301
  79. ngio/tables/tables_group.py +0 -252
  80. ngio/tables/v1/feature_tables.py +0 -182
  81. ngio/tables/v1/masking_roi_tables.py +0 -243
  82. ngio/tables/v1/roi_tables.py +0 -285
  83. ngio/utils/_common_types.py +0 -5
  84. ngio/utils/_pydantic_utils.py +0 -52
  85. ngio-0.1.5.dist-info/RECORD +0 -44
  86. {ngio-0.1.5.dist-info → ngio-0.2.0.dist-info}/WHEEL +0 -0
  87. {ngio-0.1.5.dist-info → ngio-0.2.0.dist-info}/licenses/LICENSE +0 -0
ngio/ome_zarr_meta/__init__.py ADDED
@@ -0,0 +1,47 @@
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+ """Utilities for reading and writing OME-Zarr metadata."""
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+
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+ from ngio.ome_zarr_meta._meta_handlers import (
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+ ImageMetaHandler,
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+ LabelMetaHandler,
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+ find_image_meta_handler,
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+ find_label_meta_handler,
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+ find_plate_meta_handler,
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+ find_well_meta_handler,
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+ get_image_meta_handler,
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+ get_label_meta_handler,
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+ get_plate_meta_handler,
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+ get_well_meta_handler,
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+ )
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+ from ngio.ome_zarr_meta.ngio_specs import (
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+ AxesMapper,
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+ Dataset,
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+ ImageInWellPath,
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+ NgioImageMeta,
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+ NgioLabelMeta,
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+ NgioPlateMeta,
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+ NgioWellMeta,
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+ PixelSize,
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+ )
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+
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+ __all__ = [
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+ "AxesMapper",
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+ "Dataset",
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+ "ImageInWellPath",
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+ "ImageMetaHandler",
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+ "ImageMetaHandler",
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+ "LabelMetaHandler",
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+ "LabelMetaHandler",
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+ "NgioImageMeta",
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+ "NgioLabelMeta",
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+ "NgioPlateMeta",
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+ "NgioWellMeta",
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+ "PixelSize",
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+ "find_image_meta_handler",
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+ "find_label_meta_handler",
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+ "find_plate_meta_handler",
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+ "find_well_meta_handler",
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+ "get_image_meta_handler",
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+ "get_label_meta_handler",
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+ "get_plate_meta_handler",
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+ "get_well_meta_handler",
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+ ]