dsa-helpers 1.0.4.dev0__tar.gz → 1.0.4.dev2__tar.gz

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Files changed (48) hide show
  1. {dsa_helpers-1.0.4.dev0/dsa_helpers.egg-info → dsa_helpers-1.0.4.dev2}/PKG-INFO +1 -1
  2. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/image_utils.py +8 -7
  3. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2/dsa_helpers.egg-info}/PKG-INFO +1 -1
  4. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/pyproject.toml +1 -1
  5. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/.gitignore +0 -0
  6. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/.readthedocs.yaml +0 -0
  7. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/LICENSE +0 -0
  8. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/README.md +0 -0
  9. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/app.py +0 -0
  10. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/docs/requirements.txt +0 -0
  11. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/docs/source/conf.py +0 -0
  12. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/docs/source/index.rst +0 -0
  13. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/__init__.py +0 -0
  14. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/dash/__init__.py +0 -0
  15. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/dash/dash_paperdragon_utils.py +0 -0
  16. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/dash/header.py +0 -0
  17. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/dash/header_callbacks.py +0 -0
  18. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/girder_utils.py +0 -0
  19. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/imread.py +0 -0
  20. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/imwrite.py +0 -0
  21. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/__init__.py +0 -0
  22. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/callbacks.py +0 -0
  23. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/datasets/SegFormerSegmentationDataset.py +0 -0
  24. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/datasets/__init__.py +0 -0
  25. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/datasets/utils.py +0 -0
  26. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/evaluate.py +0 -0
  27. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/metrics.py +0 -0
  28. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/object_detection/__init__.py +0 -0
  29. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/object_detection/get_pearce_roi_images.py +0 -0
  30. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/object_detection/tile_image.py +0 -0
  31. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/object_detection/utils.py +0 -0
  32. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/segformer_semantic_segmentation/__init__.py +0 -0
  33. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/segformer_semantic_segmentation/inference.py +0 -0
  34. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/transforms/__init__.py +0 -0
  35. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/ml/transforms/segformer_transforms.py +0 -0
  36. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/mongo_utils.py +0 -0
  37. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/tile_utils.py +0 -0
  38. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/tiling.py +0 -0
  39. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/utils.py +0 -0
  40. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers.egg-info/SOURCES.txt +0 -0
  41. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers.egg-info/dependency_links.txt +0 -0
  42. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers.egg-info/requires.txt +0 -0
  43. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers.egg-info/top_level.txt +0 -0
  44. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/setup.cfg +0 -0
  45. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/tests/app/Dockerfile +0 -0
  46. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/tests/app/app.py +0 -0
  47. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/tests/docker-compose.yaml +0 -0
  48. {dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/tests/test.ipynb +0 -0
{dsa_helpers-1.0.4.dev0/dsa_helpers.egg-info → dsa_helpers-1.0.4.dev2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: dsa_helpers
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- Version: 1.0.4.dev0
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+ Version: 1.0.4.dev2
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  Summary: Utility functions for working with the DSA girder client.
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  Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
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  Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
{dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/dsa_helpers/image_utils.py RENAMED
@@ -20,7 +20,7 @@ from shapely.affinity import translate
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  from shapely.geometry import Polygon
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- def label_mask_to_geojson(
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+ def label_mask_to_polygons(
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  mask: str | np.ndarray,
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  x_offset: int = 0,
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  y_offset: int = 0,
@@ -89,13 +89,14 @@ def label_mask_to_geojson(
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  # Convert to shapely polygon objects.
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  for data in polygons_dict.values():
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- polygon = Polygon(data["polygon"], holes=data["holes"])
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+ if "polygon" in data:
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+ polygon = Polygon(data["polygon"], holes=data["holes"])
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- # Shift the polygon by the offset.
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- polygon = translate(polygon, xoff=x_offset, yoff=y_offset)
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+ # Shift the polygon by the offset.
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+ polygon = translate(polygon, xoff=x_offset, yoff=y_offset)
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- # Include the polygon if it's greater than the minimum area.
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- if polygon.area >= min_area:
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- polygons.append([polygon, int(label)])
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+ # Include the polygon if it's greater than the minimum area.
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+ if polygon.area >= min_area:
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+ polygons.append([polygon, int(label)])
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  return polygons
{dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2/dsa_helpers.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: dsa_helpers
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- Version: 1.0.4.dev0
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+ Version: 1.0.4.dev2
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  Summary: Utility functions for working with the DSA girder client.
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  Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
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  Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
{dsa_helpers-1.0.4.dev0 → dsa_helpers-1.0.4.dev2}/pyproject.toml RENAMED
@@ -35,7 +35,7 @@ classifiers = [
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  "License :: OSI Approved :: MIT License",
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  ]
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  keywords = ["dsa", "girder", "girder_client"]
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- version = "v1.0.4.dev0"
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+ version = "v1.0.4.dev2"
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  [project.urls]
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  Repository = "https://github.com/Gutman-Lab/dsa-python-utils"