careamics 0.1.0rc2__py3-none-any.whl → 0.1.0rc4__py3-none-any.whl

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Files changed (134) hide show
  1. careamics/__init__.py +16 -4
  2. careamics/callbacks/__init__.py +6 -0
  3. careamics/callbacks/hyperparameters_callback.py +42 -0
  4. careamics/callbacks/progress_bar_callback.py +57 -0
  5. careamics/careamist.py +761 -0
  6. careamics/config/__init__.py +31 -3
  7. careamics/config/algorithm_model.py +167 -0
  8. careamics/config/architectures/__init__.py +17 -0
  9. careamics/config/architectures/architecture_model.py +29 -0
  10. careamics/config/architectures/custom_model.py +150 -0
  11. careamics/config/architectures/register_model.py +101 -0
  12. careamics/config/architectures/unet_model.py +96 -0
  13. careamics/config/architectures/vae_model.py +39 -0
  14. careamics/config/callback_model.py +92 -0
  15. careamics/config/configuration_example.py +89 -0
  16. careamics/config/configuration_factory.py +597 -0
  17. careamics/config/configuration_model.py +597 -0
  18. careamics/config/data_model.py +555 -0
  19. careamics/config/inference_model.py +283 -0
  20. careamics/config/noise_models.py +162 -0
  21. careamics/config/optimizer_models.py +181 -0
  22. careamics/config/references/__init__.py +45 -0
  23. careamics/config/references/algorithm_descriptions.py +131 -0
  24. careamics/config/references/references.py +38 -0
  25. careamics/config/support/__init__.py +33 -0
  26. careamics/config/support/supported_activations.py +24 -0
  27. careamics/config/support/supported_algorithms.py +18 -0
  28. careamics/config/support/supported_architectures.py +18 -0
  29. careamics/config/support/supported_data.py +82 -0
  30. careamics/{dataset/extraction_strategy.py → config/support/supported_extraction_strategies.py} +5 -2
  31. careamics/config/support/supported_loggers.py +8 -0
  32. careamics/config/support/supported_losses.py +25 -0
  33. careamics/config/support/supported_optimizers.py +55 -0
  34. careamics/config/support/supported_pixel_manipulations.py +15 -0
  35. careamics/config/support/supported_struct_axis.py +19 -0
  36. careamics/config/support/supported_transforms.py +23 -0
  37. careamics/config/tile_information.py +104 -0
  38. careamics/config/training_model.py +65 -0
  39. careamics/config/transformations/__init__.py +14 -0
  40. careamics/config/transformations/n2v_manipulate_model.py +63 -0
  41. careamics/config/transformations/nd_flip_model.py +32 -0
  42. careamics/config/transformations/normalize_model.py +31 -0
  43. careamics/config/transformations/transform_model.py +44 -0
  44. careamics/config/transformations/xy_random_rotate90_model.py +29 -0
  45. careamics/config/validators/__init__.py +5 -0
  46. careamics/config/validators/validator_utils.py +100 -0
  47. careamics/conftest.py +26 -0
  48. careamics/dataset/__init__.py +5 -0
  49. careamics/dataset/dataset_utils/__init__.py +19 -0
  50. careamics/dataset/dataset_utils/dataset_utils.py +100 -0
  51. careamics/dataset/dataset_utils/file_utils.py +140 -0
  52. careamics/dataset/dataset_utils/read_tiff.py +61 -0
  53. careamics/dataset/dataset_utils/read_utils.py +25 -0
  54. careamics/dataset/dataset_utils/read_zarr.py +56 -0
  55. careamics/dataset/in_memory_dataset.py +323 -134
  56. careamics/dataset/iterable_dataset.py +416 -0
  57. careamics/dataset/patching/__init__.py +8 -0
  58. careamics/dataset/patching/patch_transform.py +44 -0
  59. careamics/dataset/patching/patching.py +212 -0
  60. careamics/dataset/patching/random_patching.py +190 -0
  61. careamics/dataset/patching/sequential_patching.py +206 -0
  62. careamics/dataset/patching/tiled_patching.py +158 -0
  63. careamics/dataset/patching/validate_patch_dimension.py +60 -0
  64. careamics/dataset/zarr_dataset.py +149 -0
  65. careamics/lightning_datamodule.py +743 -0
  66. careamics/lightning_module.py +292 -0
  67. careamics/lightning_prediction_datamodule.py +396 -0
  68. careamics/lightning_prediction_loop.py +116 -0
  69. careamics/losses/__init__.py +4 -1
  70. careamics/losses/loss_factory.py +24 -14
  71. careamics/losses/losses.py +65 -5
  72. careamics/losses/noise_model_factory.py +40 -0
  73. careamics/losses/noise_models.py +524 -0
  74. careamics/model_io/__init__.py +8 -0
  75. careamics/model_io/bioimage/__init__.py +11 -0
  76. careamics/model_io/bioimage/_readme_factory.py +120 -0
  77. careamics/model_io/bioimage/bioimage_utils.py +48 -0
  78. careamics/model_io/bioimage/model_description.py +318 -0
  79. careamics/model_io/bmz_io.py +231 -0
  80. careamics/model_io/model_io_utils.py +80 -0
  81. careamics/models/__init__.py +4 -1
  82. careamics/models/activation.py +35 -0
  83. careamics/models/layers.py +244 -0
  84. careamics/models/model_factory.py +21 -221
  85. careamics/models/unet.py +46 -20
  86. careamics/prediction/__init__.py +1 -3
  87. careamics/prediction/stitch_prediction.py +73 -0
  88. careamics/transforms/__init__.py +41 -0
  89. careamics/transforms/n2v_manipulate.py +113 -0
  90. careamics/transforms/nd_flip.py +93 -0
  91. careamics/transforms/normalize.py +109 -0
  92. careamics/transforms/pixel_manipulation.py +383 -0
  93. careamics/transforms/struct_mask_parameters.py +18 -0
  94. careamics/transforms/tta.py +74 -0
  95. careamics/transforms/xy_random_rotate90.py +95 -0
  96. careamics/utils/__init__.py +10 -12
  97. careamics/utils/base_enum.py +32 -0
  98. careamics/utils/context.py +22 -2
  99. careamics/utils/metrics.py +0 -46
  100. careamics/utils/path_utils.py +24 -0
  101. careamics/utils/ram.py +13 -0
  102. careamics/utils/receptive_field.py +102 -0
  103. careamics/utils/running_stats.py +43 -0
  104. careamics/utils/torch_utils.py +112 -75
  105. careamics-0.1.0rc4.dist-info/METADATA +122 -0
  106. careamics-0.1.0rc4.dist-info/RECORD +110 -0
  107. {careamics-0.1.0rc2.dist-info → careamics-0.1.0rc4.dist-info}/WHEEL +1 -1
  108. careamics/bioimage/__init__.py +0 -15
  109. careamics/bioimage/docs/Noise2Void.md +0 -5
  110. careamics/bioimage/docs/__init__.py +0 -1
  111. careamics/bioimage/io.py +0 -182
  112. careamics/bioimage/rdf.py +0 -105
  113. careamics/config/algorithm.py +0 -231
  114. careamics/config/config.py +0 -297
  115. careamics/config/config_filter.py +0 -44
  116. careamics/config/data.py +0 -194
  117. careamics/config/torch_optim.py +0 -118
  118. careamics/config/training.py +0 -534
  119. careamics/dataset/dataset_utils.py +0 -111
  120. careamics/dataset/patching.py +0 -492
  121. careamics/dataset/prepare_dataset.py +0 -175
  122. careamics/dataset/tiff_dataset.py +0 -212
  123. careamics/engine.py +0 -1014
  124. careamics/manipulation/__init__.py +0 -4
  125. careamics/manipulation/pixel_manipulation.py +0 -158
  126. careamics/prediction/prediction_utils.py +0 -106
  127. careamics/utils/ascii_logo.txt +0 -9
  128. careamics/utils/augment.py +0 -65
  129. careamics/utils/normalization.py +0 -55
  130. careamics/utils/validators.py +0 -170
  131. careamics/utils/wandb.py +0 -121
  132. careamics-0.1.0rc2.dist-info/METADATA +0 -81
  133. careamics-0.1.0rc2.dist-info/RECORD +0 -47
  134. {careamics-0.1.0rc2.dist-info → careamics-0.1.0rc4.dist-info}/licenses/LICENSE +0 -0
careamics-0.1.0rc2.dist-info/METADATA DELETED
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- Metadata-Version: 2.1
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- Name: careamics
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- Version: 0.1.0rc2
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- Summary: Toolbox for running N2V and friends.
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- Project-URL: homepage, https://careamics.github.io/
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- Project-URL: repository, https://github.com/CAREamics/careamics
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- Author-email: Igor Zubarev <igor.zubarev@fht.org>, Joran Deschamps <joran.deschamps@fht.org>, Vera Galinova <vera.galinova@fht.org>, Mehdi Seifi <mehdi.seifi@fht.org>
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- License: BSD-3-Clause
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- License-File: LICENSE
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- Classifier: Development Status :: 3 - Alpha
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- Classifier: License :: OSI Approved :: BSD License
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- Classifier: Programming Language :: Python :: 3
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- Classifier: Programming Language :: Python :: 3.8
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- Classifier: Programming Language :: Python :: 3.9
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- Classifier: Programming Language :: Python :: 3.10
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- Classifier: Programming Language :: Python :: 3.11
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- Classifier: Programming Language :: Python :: 3.12
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- Classifier: Typing :: Typed
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- Requires-Python: >=3.8
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- Requires-Dist: bioimageio-core
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- Requires-Dist: pydantic>=2.0
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- Requires-Dist: pyyaml
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- Requires-Dist: scikit-image
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- Requires-Dist: tifffile
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- Requires-Dist: torch
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- Requires-Dist: torchvision
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- Requires-Dist: zarr
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- Provides-Extra: all
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- Requires-Dist: careamics-portfolio; extra == 'all'
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- Requires-Dist: ipython; extra == 'all'
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- Requires-Dist: itkwidgets; extra == 'all'
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- Requires-Dist: jupyter; extra == 'all'
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- Requires-Dist: pre-commit; extra == 'all'
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- Requires-Dist: pytest; extra == 'all'
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- Requires-Dist: pytest-cov; extra == 'all'
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- Requires-Dist: torchsummary; extra == 'all'
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- Requires-Dist: wandb; extra == 'all'
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- Provides-Extra: dev
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- Requires-Dist: pre-commit; extra == 'dev'
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- Requires-Dist: pytest; extra == 'dev'
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- Requires-Dist: pytest-cov; extra == 'dev'
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- Provides-Extra: notebooks
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- Requires-Dist: careamics-portfolio; extra == 'notebooks'
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- Requires-Dist: ipython; extra == 'notebooks'
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- Requires-Dist: itkwidgets; extra == 'notebooks'
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- Requires-Dist: jupyter; extra == 'notebooks'
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- Requires-Dist: torchsummary; extra == 'notebooks'
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- Requires-Dist: wandb; extra == 'notebooks'
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- Provides-Extra: test
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- Requires-Dist: pytest; extra == 'test'
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- Requires-Dist: pytest-cov; extra == 'test'
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- Requires-Dist: wandb; extra == 'test'
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- Description-Content-Type: text/markdown
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-
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- <p align="center">
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- <a href="https://careamics.github.io/">
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- <img src="https://raw.githubusercontent.com/CAREamics/.github/main/profile/images/banner_careamics.png">
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- </a>
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- </p>
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-
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- # CAREamics
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-
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- [![License](https://img.shields.io/pypi/l/careamics.svg?color=green)](https://github.com/CAREamics/careamics/blob/main/LICENSE)
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- [![PyPI](https://img.shields.io/pypi/v/careamics.svg?color=green)](https://pypi.org/project/careamics)
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- [![Python Version](https://img.shields.io/pypi/pyversions/careamics.svg?color=green)](https://python.org)
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- [![CI](https://github.com/CAREamics/careamics/actions/workflows/ci.yml/badge.svg)](https://github.com/CAREamics/careamics/actions/workflows/ci.yml)
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- [![codecov](https://codecov.io/gh/CAREamics/careamics/branch/main/graph/badge.svg)](https://codecov.io/gh/CAREamics/careamics)
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-
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- ## Installation
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-
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- ``` bash
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- pip install careamics
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- ```
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- For more details on the options please follow the installation [guide](https://careamics.github.io/installation/).
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-
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- <!--
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- ## Contributing
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-
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- ## Citing us
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-
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- -->
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