bioptimus-sdk 1.0.2__tar.gz

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Files changed (59) hide show
  1. bioptimus_sdk-1.0.2/LICENSE.md +11 -0
  2. bioptimus_sdk-1.0.2/PKG-INFO +68 -0
  3. bioptimus_sdk-1.0.2/README.md +14 -0
  4. bioptimus_sdk-1.0.2/bioptimus/LICENSE.md +11 -0
  5. bioptimus_sdk-1.0.2/bioptimus/README.md +14 -0
  6. bioptimus_sdk-1.0.2/bioptimus/__init__.py +0 -0
  7. bioptimus_sdk-1.0.2/bioptimus/data/cohort.py +1236 -0
  8. bioptimus_sdk-1.0.2/bioptimus/data/multi_model/multi_model_dataset.py +219 -0
  9. bioptimus_sdk-1.0.2/bioptimus/data/omics/bulkrna.py +172 -0
  10. bioptimus_sdk-1.0.2/bioptimus/data/tile_spec.py +108 -0
  11. bioptimus_sdk-1.0.2/bioptimus/data/wsi/__init__.py +17 -0
  12. bioptimus_sdk-1.0.2/bioptimus/data/wsi/torch_dataset.py +297 -0
  13. bioptimus_sdk-1.0.2/bioptimus/data/wsi/wsi_dataset.py +355 -0
  14. bioptimus_sdk-1.0.2/bioptimus/extraction/__init__.py +0 -0
  15. bioptimus_sdk-1.0.2/bioptimus/extraction/wsi/__init__.py +34 -0
  16. bioptimus_sdk-1.0.2/bioptimus/extraction/wsi/_wsi_extractor.py +84 -0
  17. bioptimus_sdk-1.0.2/bioptimus/extraction/wsi/megatile_extraction.py +650 -0
  18. bioptimus_sdk-1.0.2/bioptimus/extraction/wsi/tile_extraction.py +744 -0
  19. bioptimus_sdk-1.0.2/bioptimus/extraction/wsi/types.py +210 -0
  20. bioptimus_sdk-1.0.2/bioptimus/inference/__init__.py +32 -0
  21. bioptimus_sdk-1.0.2/bioptimus/inference/inference.py +1202 -0
  22. bioptimus_sdk-1.0.2/bioptimus/inference/schemas.py +107 -0
  23. bioptimus_sdk-1.0.2/bioptimus/inference/writers.py +481 -0
  24. bioptimus_sdk-1.0.2/bioptimus/io/__init__.py +0 -0
  25. bioptimus_sdk-1.0.2/bioptimus/io/omics/__init__.py +1 -0
  26. bioptimus_sdk-1.0.2/bioptimus/io/omics/_backends/__init__.py +0 -0
  27. bioptimus_sdk-1.0.2/bioptimus/io/omics/_backends/bulk.py +121 -0
  28. bioptimus_sdk-1.0.2/bioptimus/io/wsi/__init__.py +43 -0
  29. bioptimus_sdk-1.0.2/bioptimus/io/wsi/_backends/__init__.py +0 -0
  30. bioptimus_sdk-1.0.2/bioptimus/io/wsi/_backends/cucim.py +285 -0
  31. bioptimus_sdk-1.0.2/bioptimus/io/wsi/_backends/openslide.py +282 -0
  32. bioptimus_sdk-1.0.2/bioptimus/io/wsi/_backends/tifffile.py +85 -0
  33. bioptimus_sdk-1.0.2/bioptimus/io/wsi/_gc_guard.py +56 -0
  34. bioptimus_sdk-1.0.2/bioptimus/io/wsi/factory.py +193 -0
  35. bioptimus_sdk-1.0.2/bioptimus/io/wsi/interface.py +787 -0
  36. bioptimus_sdk-1.0.2/bioptimus/io/wsi/metadata.py +98 -0
  37. bioptimus_sdk-1.0.2/bioptimus/io/wsi/types.py +463 -0
  38. bioptimus_sdk-1.0.2/bioptimus/models/__init__.py +25 -0
  39. bioptimus_sdk-1.0.2/bioptimus/models/backbones/__init__.py +200 -0
  40. bioptimus_sdk-1.0.2/bioptimus/models/clients/__init__.py +49 -0
  41. bioptimus_sdk-1.0.2/bioptimus/models/clients/aws.py +180 -0
  42. bioptimus_sdk-1.0.2/bioptimus/models/clients/http.py +171 -0
  43. bioptimus_sdk-1.0.2/bioptimus/models/config_loader.py +223 -0
  44. bioptimus_sdk-1.0.2/bioptimus/models/configs/h1.yaml +32 -0
  45. bioptimus_sdk-1.0.2/bioptimus/models/configs/m-optimus.yaml +35 -0
  46. bioptimus_sdk-1.0.2/bioptimus/models/configs/tissue-seg.yaml +23 -0
  47. bioptimus_sdk-1.0.2/bioptimus/models/endpoint_model.py +158 -0
  48. bioptimus_sdk-1.0.2/bioptimus/models/types.py +151 -0
  49. bioptimus_sdk-1.0.2/bioptimus/preprocess/omics/__init__.py +23 -0
  50. bioptimus_sdk-1.0.2/bioptimus/preprocess/omics/base.py +80 -0
  51. bioptimus_sdk-1.0.2/bioptimus/preprocess/omics/factory.py +78 -0
  52. bioptimus_sdk-1.0.2/bioptimus/preprocess/omics/transforms.py +151 -0
  53. bioptimus_sdk-1.0.2/bioptimus/preprocess/wsi/__init__.py +20 -0
  54. bioptimus_sdk-1.0.2/bioptimus/preprocess/wsi/models/base.py +61 -0
  55. bioptimus_sdk-1.0.2/bioptimus/preprocess/wsi/models/bioptimus_mask.py +79 -0
  56. bioptimus_sdk-1.0.2/bioptimus/preprocess/wsi/provider/base.py +52 -0
  57. bioptimus_sdk-1.0.2/bioptimus/preprocess/wsi/provider/precomputed.py +200 -0
  58. bioptimus_sdk-1.0.2/bioptimus/preprocess/wsi/provider/tiled.py +308 -0
  59. bioptimus_sdk-1.0.2/pyproject.toml +89 -0
bioptimus_sdk-1.0.2/LICENSE.md ADDED
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+ # License
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+
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+ Copyright (c) Bioptimus. All rights reserved.
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+
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+ This software is provided under a proprietary license. Use of this software
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+ is subject to a separate written license agreement with Bioptimus. No rights
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+ are granted except as expressly set out in that agreement.
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+
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+ Any attempt to reverse engineer, decompile, or disassemble the models,
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+ binaries, or associated artifacts distributed with this software — whether in
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+ memory or on disk — is strictly prohibited.
bioptimus_sdk-1.0.2/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: bioptimus-sdk
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+ Version: 1.0.2
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+ Summary: Client-side SDK for Bioptimus foundation model inference.
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+ Project-URL: Homepage, https://www.bioptimus.com
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+ Project-URL: Documentation, https://www.bioptimus.com
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+ Author-email: Bioptimus <support@bioptimus.com>
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+ Maintainer-email: Bioptimus <support@bioptimus.com>
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+ License: # License
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+
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+ Copyright (c) Bioptimus. All rights reserved.
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+
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+ This software is provided under a proprietary license. Use of this software
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+ is subject to a separate written license agreement with Bioptimus. No rights
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+ are granted except as expressly set out in that agreement.
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+
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+ Any attempt to reverse engineer, decompile, or disassemble the models,
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+ binaries, or associated artifacts distributed with this software — whether in
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+ memory or on disk — is strictly prohibited.
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+ License-File: LICENSE.md
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+ Keywords: bioptimus,foundation-models,histology,inference,pathology,sdk,whole-slide-image
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+ Classifier: Development Status :: 5 - Production/Stable
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+ Classifier: Intended Audience :: Healthcare Industry
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+ Classifier: Intended Audience :: Science/Research
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+ Classifier: License :: Other/Proprietary License
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+ Classifier: Operating System :: POSIX :: Linux
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
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+ Classifier: Topic :: Scientific/Engineering :: Image Processing
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+ Classifier: Typing :: Typed
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+ Requires-Python: >=3.12
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+ Requires-Dist: aiohttp>=3.9.0
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+ Requires-Dist: boto3>=1.35.0
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+ Requires-Dist: h5py>=3.10.0
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+ Requires-Dist: numcodecs<0.16.0,>=0.12.0
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+ Requires-Dist: numpy>=2.0.2
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+ Requires-Dist: opencv-python>=4.11.0
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+ Requires-Dist: openslide-bin>=4.0.0.8
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+ Requires-Dist: openslide-python>=1.4.2
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+ Requires-Dist: pandas>=2.3.1
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+ Requires-Dist: pillow>=11.3.0
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+ Requires-Dist: pydantic>=2.13.1
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+ Requires-Dist: pyyaml>=6.0.3
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+ Requires-Dist: requests>=2.32.5
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+ Requires-Dist: tiffslide>=2.5.1
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+ Requires-Dist: tqdm>=4.67.1
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+ Requires-Dist: zarr<3.0.0,>=2.18.2
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+ Provides-Extra: cucim
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+ Requires-Dist: cucim-cu12>=25.6.0; extra == 'cucim'
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+ Provides-Extra: torch
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+ Requires-Dist: torch>=2.9.0; extra == 'torch'
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+ Description-Content-Type: text/markdown
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+
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+ # Bioptimus SDK
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+
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+ The Bioptimus SDK is the official client library for accessing Bioptimus
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+ foundation models. This is an early release.
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+
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+ The SDK acts primarily as a client to the Bioptimus inference web service and
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+ provides convenience functionality for whole-slide image inference workflows
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+ built around it.
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+
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+ Usage examples and detailed documentation are distributed through separate
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+ official channels.
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+
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+ Please refer to [LICENSE.md](LICENSE.md) for the terms governing use of this
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+ software.
bioptimus_sdk-1.0.2/README.md ADDED
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+ # Bioptimus SDK
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+
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+ The Bioptimus SDK is the official client library for accessing Bioptimus
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+ foundation models. This is an early release.
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+
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+ The SDK acts primarily as a client to the Bioptimus inference web service and
7
+ provides convenience functionality for whole-slide image inference workflows
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+ built around it.
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+
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+ Usage examples and detailed documentation are distributed through separate
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+ official channels.
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+
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+ Please refer to [LICENSE.md](LICENSE.md) for the terms governing use of this
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+ software.
bioptimus_sdk-1.0.2/bioptimus/LICENSE.md ADDED
@@ -0,0 +1,11 @@
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+ # License
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+
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+ Copyright (c) Bioptimus. All rights reserved.
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+
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+ This software is provided under a proprietary license. Use of this software
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+ is subject to a separate written license agreement with Bioptimus. No rights
7
+ are granted except as expressly set out in that agreement.
8
+
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+ Any attempt to reverse engineer, decompile, or disassemble the models,
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+ binaries, or associated artifacts distributed with this software — whether in
11
+ memory or on disk — is strictly prohibited.
bioptimus_sdk-1.0.2/bioptimus/README.md ADDED
@@ -0,0 +1,14 @@
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+ # Bioptimus SDK
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+
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+ The Bioptimus SDK is the official client library for accessing Bioptimus
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+ foundation models. This is an early release.
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+
6
+ The SDK acts primarily as a client to the Bioptimus inference web service and
7
+ provides convenience functionality for whole-slide image inference workflows
8
+ built around it.
9
+
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+ Usage examples and detailed documentation are distributed through separate
11
+ official channels.
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+
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+ Please refer to [LICENSE.md](LICENSE.md) for the terms governing use of this
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+ software.
bioptimus_sdk-1.0.2/bioptimus/__init__.py ADDED
File without changes