ngio 0.5.0__py3-none-any.whl → 0.5.0a1__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 (54) hide show
  1. ngio/__init__.py +2 -5
  2. ngio/common/__init__.py +6 -11
  3. ngio/common/_masking_roi.py +54 -34
  4. ngio/common/_pyramid.py +87 -321
  5. ngio/common/_roi.py +330 -258
  6. ngio/experimental/iterators/_feature.py +3 -3
  7. ngio/experimental/iterators/_rois_utils.py +11 -10
  8. ngio/hcs/_plate.py +136 -192
  9. ngio/images/_abstract_image.py +35 -539
  10. ngio/images/_create.py +283 -0
  11. ngio/images/_create_synt_container.py +43 -40
  12. ngio/images/_image.py +251 -517
  13. ngio/images/_label.py +172 -249
  14. ngio/images/_masked_image.py +2 -2
  15. ngio/images/_ome_zarr_container.py +241 -644
  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 +8 -6
  21. ngio/io_pipes/_ops_slices_utils.py +5 -8
  22. ngio/ome_zarr_meta/__init__.py +18 -29
  23. ngio/ome_zarr_meta/_meta_handlers.py +708 -392
  24. ngio/ome_zarr_meta/ngio_specs/__init__.py +0 -4
  25. ngio/ome_zarr_meta/ngio_specs/_axes.py +51 -152
  26. ngio/ome_zarr_meta/ngio_specs/_dataset.py +22 -13
  27. ngio/ome_zarr_meta/ngio_specs/_ngio_hcs.py +91 -129
  28. ngio/ome_zarr_meta/ngio_specs/_ngio_image.py +68 -57
  29. ngio/ome_zarr_meta/v04/__init__.py +1 -5
  30. ngio/ome_zarr_meta/v04/{_v04_spec.py → _v04_spec_utils.py} +85 -54
  31. ngio/ome_zarr_meta/v05/__init__.py +1 -5
  32. ngio/ome_zarr_meta/v05/{_v05_spec.py → _v05_spec_utils.py} +87 -64
  33. ngio/resources/__init__.py +1 -1
  34. ngio/resources/resource_model.py +1 -1
  35. ngio/tables/_tables_container.py +27 -85
  36. ngio/tables/backends/_anndata.py +8 -58
  37. ngio/tables/backends/_anndata_utils.py +6 -1
  38. ngio/tables/backends/_csv.py +19 -3
  39. ngio/tables/backends/_json.py +13 -10
  40. ngio/tables/backends/_non_zarr_backends.py +196 -0
  41. ngio/tables/backends/_parquet.py +31 -3
  42. ngio/tables/v1/_roi_table.py +27 -44
  43. ngio/utils/__init__.py +12 -8
  44. ngio/utils/_datasets.py +0 -6
  45. ngio/utils/_logger.py +50 -0
  46. ngio/utils/_zarr_utils.py +250 -292
  47. {ngio-0.5.0.dist-info → ngio-0.5.0a1.dist-info}/METADATA +6 -13
  48. ngio-0.5.0a1.dist-info/RECORD +88 -0
  49. {ngio-0.5.0.dist-info → ngio-0.5.0a1.dist-info}/WHEEL +1 -1
  50. ngio/images/_create_utils.py +0 -406
  51. ngio/tables/backends/_py_arrow_backends.py +0 -222
  52. ngio/utils/_cache.py +0 -48
  53. ngio-0.5.0.dist-info/RECORD +0 -88
  54. {ngio-0.5.0.dist-info → ngio-0.5.0a1.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
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+ from ngio import Roi, RoiPixels
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  from ngio.images._abstract_image import AbstractImage
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@@ -48,17 +48,18 @@ 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 = Roi.from_values(
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+ roi = RoiPixels(
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  name=base_name,
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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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+ 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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  )
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- new_rois.append(roi.to_world(pixel_size=ref_image.pixel_size))
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+ new_rois.append(roi.to_roi(pixel_size=ref_image.pixel_size))
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  return rois_product(rois, new_rois)
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