dsa-helpers 1.1.3.dev0__tar.gz → 1.1.3.dev1__tar.gz

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  1. {dsa_helpers-1.1.3.dev0/dsa_helpers.egg-info → dsa_helpers-1.1.3.dev1}/PKG-INFO +1 -1
  2. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/__init__.py +1 -1
  3. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/girder_utils.py +10 -7
  4. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1/dsa_helpers.egg-info}/PKG-INFO +1 -1
  5. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/pyproject.toml +1 -1
  6. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/.gitignore +0 -0
  7. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/.readthedocs.yaml +0 -0
  8. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/LICENSE +0 -0
  9. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/README.md +0 -0
  10. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/app.py +0 -0
  11. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dev.py +0 -0
  12. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/docs/requirements.txt +0 -0
  13. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/docs/source/conf.py +0 -0
  14. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/docs/source/index.rst +0 -0
  15. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/cli_utils.py +0 -0
  16. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/dash/__init__.py +0 -0
  17. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/dash/dash_paperdragon_utils.py +0 -0
  18. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/dash/header.py +0 -0
  19. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/dash/header_callbacks.py +0 -0
  20. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/gpd_utils.py +0 -0
  21. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/image_utils.py +0 -0
  22. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/imread.py +0 -0
  23. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/imwrite.py +0 -0
  24. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/__init__.py +0 -0
  25. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/callbacks.py +0 -0
  26. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/datasets/SegFormerSegmentationDataset.py +0 -0
  27. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/datasets/__init__.py +0 -0
  28. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/datasets/utils.py +0 -0
  29. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/evaluate.py +0 -0
  30. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/metrics.py +0 -0
  31. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/object_detection/__init__.py +0 -0
  32. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/object_detection/get_pearce_roi_images.py +0 -0
  33. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/object_detection/tile_image.py +0 -0
  34. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/object_detection/utils.py +0 -0
  35. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/segformer_semantic_segmentation/__init__.py +0 -0
  36. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/segformer_semantic_segmentation/inference.py +0 -0
  37. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/transforms/__init__.py +0 -0
  38. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/ml/transforms/segformer_transforms.py +0 -0
  39. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/mongo_utils.py +0 -0
  40. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/tile_utils.py +0 -0
  41. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/tiling.py +0 -0
  42. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/utils.py +0 -0
  43. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers.egg-info/SOURCES.txt +0 -0
  44. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers.egg-info/dependency_links.txt +0 -0
  45. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers.egg-info/requires.txt +0 -0
  46. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers.egg-info/top_level.txt +0 -0
  47. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/setup.cfg +0 -0
  48. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/tests/app/Dockerfile +0 -0
  49. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/tests/app/app.py +0 -0
  50. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/tests/docker-compose.yaml +0 -0
  51. {dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/tests/test.ipynb +0 -0
{dsa_helpers-1.1.3.dev0/dsa_helpers.egg-info → dsa_helpers-1.1.3.dev1}/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: 1.1.3.dev0
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+ Version: 1.1.3.dev1
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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-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/__init__.py RENAMED
@@ -3,7 +3,7 @@ from .imread import imread
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  from .imwrite import imwrite
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  # Version of the dsa-helpers package
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- __version__ = "1.1.3.dev0"
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+ __version__ = "1.1.3.dev1"
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  # To avoid slow downs, do not allow from dsa_helpers import * to import anything.
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  __all__ = []
{dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/dsa_helpers/girder_utils.py RENAMED
@@ -779,6 +779,16 @@ def remove_overlapping_annotations(
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  if len(elements_to_process):
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  gdf = gpd.GeoDataFrame(elements_to_process)
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+ if max_coords is not None:
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+ # Create a bounding box polygon.
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+ bbox = box(0, 0, max_coords[0], max_coords[1])
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+
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+ # Clip the polygons to the bounding box.
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+ gdf = gdf.clip(bbox)
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+
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+ # This could have created multiple polygons, explode them.
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+ gdf = gdf.explode(index_parts=False).reset_index(drop=True)
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+
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  # Map by the groups.
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  group_map = {group: i for i, group in enumerate(group_order)}
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@@ -788,13 +798,6 @@ def remove_overlapping_annotations(
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  # Remove the overlapping polygons.
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  gdf = remove_gdf_overlaps(gdf, "order")
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- if max_coords is not None:
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- # Create a bounding box polygon.
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- bbox = box(0, 0, max_coords[0], max_coords[1])
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-
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- # Clip the polygons to the bounding box.
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- gdf = gdf.clip(bbox)
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-
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  # Convert the GeoDataFrame back to a list of dictionaries.
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  elements_to_process = gdf.to_dict(orient="records")
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{dsa_helpers-1.1.3.dev0 → dsa_helpers-1.1.3.dev1/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: 1.1.3.dev0
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+ Version: 1.1.3.dev1
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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-1.1.3.dev0 → dsa_helpers-1.1.3.dev1}/pyproject.toml RENAMED
@@ -36,7 +36,7 @@ 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 = "v1.1.3.dev0"
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+ version = "v1.1.3.dev1"
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  [project.urls]
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  Repository = "https://github.com/Gutman-Lab/dsa-python-utils"