ngio 0.2.0a2__py3-none-any.whl → 0.5.0b4__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 (106) hide show
  1. ngio/__init__.py +40 -12
  2. ngio/common/__init__.py +16 -32
  3. ngio/common/_dimensions.py +270 -48
  4. ngio/common/_masking_roi.py +153 -0
  5. ngio/common/_pyramid.py +267 -73
  6. ngio/common/_roi.py +290 -66
  7. ngio/common/_synt_images_utils.py +101 -0
  8. ngio/common/_zoom.py +54 -22
  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 +17 -58
  18. ngio/hcs/_plate.py +1354 -0
  19. ngio/images/__init__.py +30 -9
  20. ngio/images/_abstract_image.py +968 -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 +417 -0
  25. ngio/images/_masked_image.py +531 -0
  26. ngio/images/_ome_zarr_container.py +1235 -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 +39 -15
  40. ngio/ome_zarr_meta/_meta_handlers.py +490 -96
  41. ngio/ome_zarr_meta/ngio_specs/__init__.py +24 -10
  42. ngio/ome_zarr_meta/ngio_specs/_axes.py +268 -234
  43. ngio/ome_zarr_meta/ngio_specs/_channels.py +125 -41
  44. ngio/ome_zarr_meta/ngio_specs/_dataset.py +42 -87
  45. ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py +536 -2
  46. ngio/ome_zarr_meta/ngio_specs/_ngio_image.py +202 -198
  47. ngio/ome_zarr_meta/ngio_specs/_pixel_size.py +72 -34
  48. ngio/ome_zarr_meta/v04/__init__.py +21 -5
  49. ngio/ome_zarr_meta/v04/_custom_models.py +18 -0
  50. ngio/ome_zarr_meta/v04/{_v04_spec_utils.py → _v04_spec.py} +151 -90
  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 +20 -4
  60. ngio/tables/_abstract_table.py +270 -0
  61. ngio/tables/_tables_container.py +449 -0
  62. ngio/tables/backends/__init__.py +50 -1
  63. ngio/tables/backends/_abstract_backend.py +200 -31
  64. ngio/tables/backends/_anndata.py +139 -0
  65. ngio/tables/backends/_anndata_utils.py +10 -114
  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 +162 -38
  71. ngio/tables/backends/_utils.py +608 -0
  72. ngio/tables/v1/__init__.py +19 -4
  73. ngio/tables/v1/_condition_table.py +71 -0
  74. ngio/tables/v1/_feature_table.py +79 -115
  75. ngio/tables/v1/_generic_table.py +21 -90
  76. ngio/tables/v1/_roi_table.py +486 -137
  77. ngio/transforms/__init__.py +5 -0
  78. ngio/transforms/_zoom.py +19 -0
  79. ngio/utils/__init__.py +16 -14
  80. ngio/utils/_cache.py +48 -0
  81. ngio/utils/_datasets.py +121 -13
  82. ngio/utils/_fractal_fsspec_store.py +42 -0
  83. ngio/utils/_zarr_utils.py +374 -218
  84. ngio-0.5.0b4.dist-info/METADATA +147 -0
  85. ngio-0.5.0b4.dist-info/RECORD +88 -0
  86. {ngio-0.2.0a2.dist-info → ngio-0.5.0b4.dist-info}/WHEEL +1 -1
  87. ngio/common/_array_pipe.py +0 -160
  88. ngio/common/_axes_transforms.py +0 -63
  89. ngio/common/_common_types.py +0 -5
  90. ngio/common/_slicer.py +0 -97
  91. ngio/images/abstract_image.py +0 -240
  92. ngio/images/create.py +0 -251
  93. ngio/images/image.py +0 -389
  94. ngio/images/label.py +0 -236
  95. ngio/images/omezarr_container.py +0 -535
  96. ngio/ome_zarr_meta/_generic_handlers.py +0 -320
  97. ngio/ome_zarr_meta/v04/_meta_handlers.py +0 -54
  98. ngio/tables/_validators.py +0 -192
  99. ngio/tables/backends/_anndata_v1.py +0 -75
  100. ngio/tables/backends/_json_v1.py +0 -56
  101. ngio/tables/tables_container.py +0 -300
  102. ngio/tables/v1/_masking_roi_table.py +0 -175
  103. ngio/utils/_logger.py +0 -29
  104. ngio-0.2.0a2.dist-info/METADATA +0 -95
  105. ngio-0.2.0a2.dist-info/RECORD +0 -53
  106. {ngio-0.2.0a2.dist-info → ngio-0.5.0b4.dist-info}/licenses/LICENSE +0 -0
ngio/ome_zarr_meta/ngio_specs/__init__.py CHANGED
@@ -7,16 +7,15 @@ This models can be tr
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  """
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  from ngio.ome_zarr_meta.ngio_specs._axes import (
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- AxesExpand,
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- AxesMapper,
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+ AxesHandler,
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  AxesSetup,
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- AxesSqueeze,
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- AxesTransformation,
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- AxesTranspose,
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  Axis,
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  AxisType,
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+ DefaultSpaceUnit,
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+ DefaultTimeUnit,
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  SpaceUnits,
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  TimeUnits,
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+ build_canonical_axes_handler,
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  canonical_axes_order,
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  canonical_label_axes_order,
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  )
@@ -28,36 +27,51 @@ from ngio.ome_zarr_meta.ngio_specs._channels import (
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  default_channel_name,
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  )
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  from ngio.ome_zarr_meta.ngio_specs._dataset import Dataset
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+ from ngio.ome_zarr_meta.ngio_specs._ngio_hcs import (
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+ ImageInWellPath,
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+ NgioPlateMeta,
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+ NgioWellMeta,
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+ path_in_well_validation,
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+ )
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  from ngio.ome_zarr_meta.ngio_specs._ngio_image import (
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+ DefaultNgffVersion,
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  ImageLabelSource,
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+ NgffVersions,
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  NgioImageLabelMeta,
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  NgioImageMeta,
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  NgioLabelMeta,
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+ NgioLabelsGroupMeta,
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  )
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  from ngio.ome_zarr_meta.ngio_specs._pixel_size import PixelSize
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  __all__ = [
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- "AxesExpand",
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- "AxesMapper",
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+ "AxesHandler",
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  "AxesSetup",
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- "AxesSqueeze",
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- "AxesTransformation",
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- "AxesTranspose",
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  "Axis",
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  "AxisType",
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  "Channel",
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  "ChannelVisualisation",
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  "ChannelsMeta",
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  "Dataset",
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+ "DefaultNgffVersion",
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+ "DefaultSpaceUnit",
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+ "DefaultTimeUnit",
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+ "ImageInWellPath",
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  "ImageLabelSource",
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+ "NgffVersions",
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  "NgioColors",
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  "NgioImageLabelMeta",
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  "NgioImageMeta",
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  "NgioLabelMeta",
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+ "NgioLabelsGroupMeta",
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+ "NgioPlateMeta",
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+ "NgioWellMeta",
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  "PixelSize",
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  "SpaceUnits",
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  "TimeUnits",
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+ "build_canonical_axes_handler",
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  "canonical_axes_order",
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  "canonical_label_axes_order",
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  "default_channel_name",
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+ "path_in_well_validation",
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  ]