dsa-helpers 1.1.17.dev0__tar.gz → 1.1.18.dev0__tar.gz

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  1. {dsa_helpers-1.1.17.dev0/dsa_helpers.egg-info → dsa_helpers-1.1.18.dev0}/PKG-INFO +7 -2
  2. dsa_helpers-1.1.18.dev0/docker/Dockerfile +14 -0
  3. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/__init__.py +1 -1
  4. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0/dsa_helpers.egg-info}/PKG-INFO +7 -2
  5. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers.egg-info/requires.txt +9 -1
  6. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/pyproject.toml +7 -2
  7. dsa_helpers-1.1.17.dev0/docker/Dockerfile +0 -6
  8. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/.gitignore +0 -0
  9. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/.readthedocs.yaml +0 -0
  10. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/LICENSE +0 -0
  11. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/README.md +0 -0
  12. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/app.py +0 -0
  13. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dev.py +0 -0
  14. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/docker/README.md +0 -0
  15. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/docs/requirements.txt +0 -0
  16. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/docs/source/conf.py +0 -0
  17. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/docs/source/index.rst +0 -0
  18. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/cli_utils.py +0 -0
  19. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/dash/__init__.py +0 -0
  20. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/dash/dash_paperdragon_utils.py +0 -0
  21. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/dash/header.py +0 -0
  22. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/dash/header_callbacks.py +0 -0
  23. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/girder_utils.py +0 -0
  24. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/gpd_utils.py +0 -0
  25. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/image_utils.py +0 -0
  26. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/imread.py +0 -0
  27. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/imwrite.py +0 -0
  28. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/__init__.py +0 -0
  29. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/callbacks.py +0 -0
  30. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/datasets/SegFormerSegmentationDataset.py +0 -0
  31. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/datasets/__init__.py +0 -0
  32. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/datasets/utils.py +0 -0
  33. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/evaluate.py +0 -0
  34. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/metrics.py +0 -0
  35. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/object_detection/__init__.py +0 -0
  36. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/object_detection/get_pearce_roi_images.py +0 -0
  37. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/object_detection/tile_image.py +0 -0
  38. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/object_detection/utils.py +0 -0
  39. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/segformer_semantic_segmentation/__init__.py +0 -0
  40. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/segformer_semantic_segmentation/datasets.py +0 -0
  41. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/segformer_semantic_segmentation/evaluate.py +0 -0
  42. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/segformer_semantic_segmentation/inference.py +0 -0
  43. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/segformer_semantic_segmentation/train.py +0 -0
  44. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/segformer_semantic_segmentation/transforms.py +0 -0
  45. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/segformer_semantic_segmentation/utils.py +0 -0
  46. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/transforms/__init__.py +0 -0
  47. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/ml/transforms/segformer_transforms.py +0 -0
  48. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/mongo_utils.py +0 -0
  49. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/tile_utils.py +0 -0
  50. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/tiling.py +0 -0
  51. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers/utils.py +0 -0
  52. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers.egg-info/SOURCES.txt +0 -0
  53. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers.egg-info/dependency_links.txt +0 -0
  54. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers.egg-info/top_level.txt +0 -0
  55. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/requirements.txt +0 -0
  56. {dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/setup.cfg +0 -0
{dsa_helpers-1.1.17.dev0/dsa_helpers.egg-info → dsa_helpers-1.1.18.dev0}/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: 1.1.17.dev0
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+ Version: 1.1.18.dev0
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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>
@@ -15,7 +15,6 @@ Requires-Dist: matplotlib
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  Requires-Dist: girder-client
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  Requires-Dist: numpy
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  Requires-Dist: setuptools
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- Requires-Dist: opencv-python
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  Requires-Dist: pandas
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  Requires-Dist: pymongo
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  Requires-Dist: pillow
@@ -30,6 +29,12 @@ Requires-Dist: large-image
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  Requires-Dist: rasterio
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  Requires-Dist: colorama
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  Requires-Dist: albumentations
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+ Provides-Extra: opencv
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+ Requires-Dist: opencv-python; extra == "opencv"
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+ Provides-Extra: opencv-headless
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+ Requires-Dist: opencv-python-headless; extra == "opencv-headless"
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+ Provides-Extra: all
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+ Requires-Dist: opencv-python; extra == "all"
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  Dynamic: license-file
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  # Digital Slide Archive (DSA) Helpers
dsa_helpers-1.1.18.dev0/docker/Dockerfile ADDED
@@ -0,0 +1,14 @@
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+ FROM pytorch/pytorch:2.8.0-cuda12.9-cudnn9-runtime
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+
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+ RUN pip install --no-cache-dir dsa-helpers
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+ RUN pip install --no-cache-dir large-image[all] --find-links https://girder.github.io/large_image_wheels
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+ RUN python -m pip install --no-cache-dir histomicstk --find-links https://girder.github.io/large_image_wheels
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+
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+ # Dependencies for OpenCV.
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+ RUN apt-get update && apt-get install ffmpeg libsm6 libxext6 -y
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+
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+ RUN mkdir /app
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+ RUN chmod 777 /app
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+
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+ RUN mkdir /data
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+ RUN chmod 777 /data
{dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/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__ = "1.1.17dev0"
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+ __version__ = "1.1.18dev0"
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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-1.1.17.dev0 → dsa_helpers-1.1.18.dev0/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: 1.1.17.dev0
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+ Version: 1.1.18.dev0
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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>
@@ -15,7 +15,6 @@ Requires-Dist: matplotlib
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  Requires-Dist: girder-client
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  Requires-Dist: numpy
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  Requires-Dist: setuptools
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- Requires-Dist: opencv-python
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  Requires-Dist: pandas
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  Requires-Dist: pymongo
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  Requires-Dist: pillow
@@ -30,6 +29,12 @@ Requires-Dist: large-image
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  Requires-Dist: rasterio
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  Requires-Dist: colorama
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  Requires-Dist: albumentations
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+ Provides-Extra: opencv
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+ Requires-Dist: opencv-python; extra == "opencv"
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+ Provides-Extra: opencv-headless
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+ Requires-Dist: opencv-python-headless; extra == "opencv-headless"
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+ Provides-Extra: all
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+ Requires-Dist: opencv-python; extra == "all"
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  Dynamic: license-file
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  # Digital Slide Archive (DSA) Helpers
{dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/dsa_helpers.egg-info/requires.txt RENAMED
@@ -2,7 +2,6 @@ matplotlib
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  girder-client
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  numpy
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  setuptools
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- opencv-python
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  pandas
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  pymongo
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  pillow
@@ -17,3 +16,12 @@ large-image
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  rasterio
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  colorama
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  albumentations
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+
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+ [all]
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+ opencv-python
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+
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+ [opencv]
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+ opencv-python
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+
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+ [opencv-headless]
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+ opencv-python-headless
{dsa_helpers-1.1.17.dev0 → dsa_helpers-1.1.18.dev0}/pyproject.toml RENAMED
@@ -10,7 +10,6 @@ dependencies = [
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  'girder-client',
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  'numpy',
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  'setuptools',
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- 'opencv-python',
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  'pandas',
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  'pymongo',
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  'pillow',
@@ -26,6 +25,7 @@ dependencies = [
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  "colorama",
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  "albumentations"
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  ]
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+
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  name = "dsa_helpers"
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  authors = [
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  {name = "Juan C. Vizcarra", email = "jvizcar@emory.edu"},
@@ -41,7 +41,12 @@ 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 = "v1.1.17dev0"
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+ version = "v1.1.18dev0"
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+
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+ [project.optional-dependencies]
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+ opencv = ["opencv-python"]
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+ opencv-headless = ["opencv-python-headless"]
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+ all = ["opencv-python"] # Default to full opencv if user installs [all]
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  [project.urls]
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  Repository = "https://github.com/Gutman-Lab/dsa-python-utils"
dsa_helpers-1.1.17.dev0/docker/Dockerfile DELETED
@@ -1,6 +0,0 @@
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- FROM pytorch/pytorch:2.7.0-cuda11.8-cudnn9-runtime
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-
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- # Dependencies for OpenCV.
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- RUN apt-get update && apt-get install ffmpeg libsm6 libxext6 -y
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- RUN pip install --no-cache-dir dsa-helpers
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- RUN pip install large-image[all] --find-links https://girder.github.io/large_image_wheels