ngio 0.4.8__py3-none-any.whl → 0.5.0__py3-none-any.whl

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Files changed (56) hide show
  1. ngio/__init__.py +5 -2
  2. ngio/common/__init__.py +11 -6
  3. ngio/common/_masking_roi.py +34 -54
  4. ngio/common/_pyramid.py +322 -75
  5. ngio/common/_roi.py +258 -330
  6. ngio/experimental/iterators/_feature.py +3 -3
  7. ngio/experimental/iterators/_rois_utils.py +10 -11
  8. ngio/hcs/_plate.py +192 -136
  9. ngio/images/_abstract_image.py +539 -35
  10. ngio/images/_create_synt_container.py +45 -47
  11. ngio/images/_create_utils.py +406 -0
  12. ngio/images/_image.py +524 -248
  13. ngio/images/_label.py +257 -180
  14. ngio/images/_masked_image.py +2 -2
  15. ngio/images/_ome_zarr_container.py +658 -255
  16. ngio/io_pipes/_io_pipes.py +9 -9
  17. ngio/io_pipes/_io_pipes_masked.py +7 -7
  18. ngio/io_pipes/_io_pipes_roi.py +6 -6
  19. ngio/io_pipes/_io_pipes_types.py +3 -3
  20. ngio/io_pipes/_match_shape.py +6 -8
  21. ngio/io_pipes/_ops_slices_utils.py +8 -5
  22. ngio/ome_zarr_meta/__init__.py +29 -18
  23. ngio/ome_zarr_meta/_meta_handlers.py +402 -689
  24. ngio/ome_zarr_meta/ngio_specs/__init__.py +4 -0
  25. ngio/ome_zarr_meta/ngio_specs/_axes.py +152 -51
  26. ngio/ome_zarr_meta/ngio_specs/_dataset.py +13 -22
  27. ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py +129 -91
  28. ngio/ome_zarr_meta/ngio_specs/_ngio_image.py +69 -69
  29. ngio/ome_zarr_meta/v04/__init__.py +5 -1
  30. ngio/ome_zarr_meta/v04/{_v04_spec_utils.py → _v04_spec.py} +55 -86
  31. ngio/ome_zarr_meta/v05/__init__.py +27 -0
  32. ngio/ome_zarr_meta/v05/_custom_models.py +18 -0
  33. ngio/ome_zarr_meta/v05/_v05_spec.py +495 -0
  34. ngio/resources/__init__.py +1 -1
  35. ngio/resources/resource_model.py +1 -1
  36. ngio/tables/_tables_container.py +82 -24
  37. ngio/tables/backends/_abstract_backend.py +7 -0
  38. ngio/tables/backends/_anndata.py +60 -7
  39. ngio/tables/backends/_anndata_utils.py +2 -4
  40. ngio/tables/backends/_csv.py +3 -19
  41. ngio/tables/backends/_json.py +10 -13
  42. ngio/tables/backends/_parquet.py +3 -31
  43. ngio/tables/backends/_py_arrow_backends.py +222 -0
  44. ngio/tables/backends/_utils.py +1 -1
  45. ngio/tables/v1/_roi_table.py +41 -24
  46. ngio/utils/__init__.py +8 -12
  47. ngio/utils/_cache.py +48 -0
  48. ngio/utils/_zarr_utils.py +354 -236
  49. {ngio-0.4.8.dist-info → ngio-0.5.0.dist-info}/METADATA +12 -5
  50. ngio-0.5.0.dist-info/RECORD +88 -0
  51. ngio/images/_create.py +0 -276
  52. ngio/tables/backends/_non_zarr_backends.py +0 -196
  53. ngio/utils/_logger.py +0 -50
  54. ngio-0.4.8.dist-info/RECORD +0 -85
  55. {ngio-0.4.8.dist-info → ngio-0.5.0.dist-info}/WHEEL +0 -0
  56. {ngio-0.4.8.dist-info → ngio-0.5.0.dist-info}/licenses/LICENSE +0 -0
ngio/experimental/iterators/_rois_utils.py CHANGED
@@ -1,4 +1,4 @@
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- from ngio import Roi, RoiPixels
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+ from ngio import Roi
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  from ngio.images._abstract_image import AbstractImage
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3
 
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@@ -48,18 +48,17 @@ def grid(
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  for z in range(0, z_dim, stride_z):
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  for y in range(0, y_dim, stride_y):
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  for x in range(0, x_dim, stride_x):
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- roi = RoiPixels(
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+ roi = Roi.from_values(
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  name=base_name,
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- x=x,
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- y=y,
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- z=z,
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- t=t,
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- x_length=size_x,
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- y_length=size_y,
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- z_length=size_z,
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- t_length=size_t,
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+ slices={
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+ "x": (x, size_x),
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+ "y": (y, size_y),
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+ "z": (z, size_z),
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+ "t": (t, size_t),
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+ },
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+ space="pixel",
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  )
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- new_rois.append(roi.to_roi(pixel_size=ref_image.pixel_size))
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+ new_rois.append(roi.to_world(pixel_size=ref_image.pixel_size))
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  return rois_product(rois, new_rois)
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