careamics 0.0.1__py3-none-any.whl → 0.0.3__py3-none-any.whl

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Files changed (155) hide show
  1. careamics/__init__.py +6 -1
  2. careamics/careamist.py +729 -0
  3. careamics/config/__init__.py +39 -0
  4. careamics/config/architectures/__init__.py +17 -0
  5. careamics/config/architectures/architecture_model.py +37 -0
  6. careamics/config/architectures/custom_model.py +162 -0
  7. careamics/config/architectures/lvae_model.py +174 -0
  8. careamics/config/architectures/register_model.py +103 -0
  9. careamics/config/architectures/unet_model.py +118 -0
  10. careamics/config/callback_model.py +123 -0
  11. careamics/config/configuration_factory.py +583 -0
  12. careamics/config/configuration_model.py +604 -0
  13. careamics/config/data_model.py +527 -0
  14. careamics/config/fcn_algorithm_model.py +147 -0
  15. careamics/config/inference_model.py +239 -0
  16. careamics/config/likelihood_model.py +43 -0
  17. careamics/config/nm_model.py +101 -0
  18. careamics/config/optimizer_models.py +187 -0
  19. careamics/config/references/__init__.py +45 -0
  20. careamics/config/references/algorithm_descriptions.py +132 -0
  21. careamics/config/references/references.py +39 -0
  22. careamics/config/support/__init__.py +31 -0
  23. careamics/config/support/supported_activations.py +27 -0
  24. careamics/config/support/supported_algorithms.py +33 -0
  25. careamics/config/support/supported_architectures.py +17 -0
  26. careamics/config/support/supported_data.py +109 -0
  27. careamics/config/support/supported_loggers.py +10 -0
  28. careamics/config/support/supported_losses.py +29 -0
  29. careamics/config/support/supported_optimizers.py +57 -0
  30. careamics/config/support/supported_pixel_manipulations.py +15 -0
  31. careamics/config/support/supported_struct_axis.py +21 -0
  32. careamics/config/support/supported_transforms.py +11 -0
  33. careamics/config/tile_information.py +65 -0
  34. careamics/config/training_model.py +72 -0
  35. careamics/config/transformations/__init__.py +15 -0
  36. careamics/config/transformations/n2v_manipulate_model.py +64 -0
  37. careamics/config/transformations/normalize_model.py +60 -0
  38. careamics/config/transformations/transform_model.py +45 -0
  39. careamics/config/transformations/xy_flip_model.py +43 -0
  40. careamics/config/transformations/xy_random_rotate90_model.py +35 -0
  41. careamics/config/vae_algorithm_model.py +171 -0
  42. careamics/config/validators/__init__.py +5 -0
  43. careamics/config/validators/validator_utils.py +101 -0
  44. careamics/conftest.py +39 -0
  45. careamics/dataset/__init__.py +17 -0
  46. careamics/dataset/dataset_utils/__init__.py +19 -0
  47. careamics/dataset/dataset_utils/dataset_utils.py +101 -0
  48. careamics/dataset/dataset_utils/file_utils.py +141 -0
  49. careamics/dataset/dataset_utils/iterate_over_files.py +83 -0
  50. careamics/dataset/dataset_utils/running_stats.py +186 -0
  51. careamics/dataset/in_memory_dataset.py +310 -0
  52. careamics/dataset/in_memory_pred_dataset.py +88 -0
  53. careamics/dataset/in_memory_tiled_pred_dataset.py +129 -0
  54. careamics/dataset/iterable_dataset.py +295 -0
  55. careamics/dataset/iterable_pred_dataset.py +122 -0
  56. careamics/dataset/iterable_tiled_pred_dataset.py +140 -0
  57. careamics/dataset/patching/__init__.py +1 -0
  58. careamics/dataset/patching/patching.py +299 -0
  59. careamics/dataset/patching/random_patching.py +201 -0
  60. careamics/dataset/patching/sequential_patching.py +212 -0
  61. careamics/dataset/patching/validate_patch_dimension.py +64 -0
  62. careamics/dataset/tiling/__init__.py +10 -0
  63. careamics/dataset/tiling/collate_tiles.py +33 -0
  64. careamics/dataset/tiling/lvae_tiled_patching.py +282 -0
  65. careamics/dataset/tiling/tiled_patching.py +164 -0
  66. careamics/dataset/zarr_dataset.py +151 -0
  67. careamics/file_io/__init__.py +15 -0
  68. careamics/file_io/read/__init__.py +12 -0
  69. careamics/file_io/read/get_func.py +56 -0
  70. careamics/file_io/read/tiff.py +58 -0
  71. careamics/file_io/read/zarr.py +60 -0
  72. careamics/file_io/write/__init__.py +15 -0
  73. careamics/file_io/write/get_func.py +63 -0
  74. careamics/file_io/write/tiff.py +40 -0
  75. careamics/lightning/__init__.py +18 -0
  76. careamics/lightning/callbacks/__init__.py +11 -0
  77. careamics/lightning/callbacks/hyperparameters_callback.py +49 -0
  78. careamics/lightning/callbacks/prediction_writer_callback/__init__.py +20 -0
  79. careamics/lightning/callbacks/prediction_writer_callback/file_path_utils.py +56 -0
  80. careamics/lightning/callbacks/prediction_writer_callback/prediction_writer_callback.py +233 -0
  81. careamics/lightning/callbacks/prediction_writer_callback/write_strategy.py +398 -0
  82. careamics/lightning/callbacks/prediction_writer_callback/write_strategy_factory.py +215 -0
  83. careamics/lightning/callbacks/progress_bar_callback.py +90 -0
  84. careamics/lightning/lightning_module.py +632 -0
  85. careamics/lightning/predict_data_module.py +333 -0
  86. careamics/lightning/train_data_module.py +680 -0
  87. careamics/losses/__init__.py +15 -0
  88. careamics/losses/fcn/__init__.py +1 -0
  89. careamics/losses/fcn/losses.py +98 -0
  90. careamics/losses/loss_factory.py +155 -0
  91. careamics/losses/lvae/__init__.py +1 -0
  92. careamics/losses/lvae/loss_utils.py +83 -0
  93. careamics/losses/lvae/losses.py +445 -0
  94. careamics/lvae_training/__init__.py +0 -0
  95. careamics/lvae_training/dataset/__init__.py +0 -0
  96. careamics/lvae_training/dataset/data_utils.py +701 -0
  97. careamics/lvae_training/dataset/lc_dataset.py +259 -0
  98. careamics/lvae_training/dataset/lc_dataset_config.py +13 -0
  99. careamics/lvae_training/dataset/vae_data_config.py +179 -0
  100. careamics/lvae_training/dataset/vae_dataset.py +1054 -0
  101. careamics/lvae_training/eval_utils.py +905 -0
  102. careamics/lvae_training/get_config.py +84 -0
  103. careamics/lvae_training/lightning_module.py +701 -0
  104. careamics/lvae_training/metrics.py +214 -0
  105. careamics/lvae_training/train_lvae.py +342 -0
  106. careamics/lvae_training/train_utils.py +121 -0
  107. careamics/model_io/__init__.py +7 -0
  108. careamics/model_io/bioimage/__init__.py +11 -0
  109. careamics/model_io/bioimage/_readme_factory.py +121 -0
  110. careamics/model_io/bioimage/bioimage_utils.py +52 -0
  111. careamics/model_io/bioimage/model_description.py +327 -0
  112. careamics/model_io/bmz_io.py +246 -0
  113. careamics/model_io/model_io_utils.py +95 -0
  114. careamics/models/__init__.py +5 -0
  115. careamics/models/activation.py +39 -0
  116. careamics/models/layers.py +493 -0
  117. careamics/models/lvae/__init__.py +3 -0
  118. careamics/models/lvae/layers.py +1998 -0
  119. careamics/models/lvae/likelihoods.py +364 -0
  120. careamics/models/lvae/lvae.py +901 -0
  121. careamics/models/lvae/noise_models.py +541 -0
  122. careamics/models/lvae/utils.py +395 -0
  123. careamics/models/model_factory.py +67 -0
  124. careamics/models/unet.py +443 -0
  125. careamics/prediction_utils/__init__.py +10 -0
  126. careamics/prediction_utils/lvae_prediction.py +158 -0
  127. careamics/prediction_utils/lvae_tiling_manager.py +362 -0
  128. careamics/prediction_utils/prediction_outputs.py +135 -0
  129. careamics/prediction_utils/stitch_prediction.py +112 -0
  130. careamics/transforms/__init__.py +20 -0
  131. careamics/transforms/compose.py +107 -0
  132. careamics/transforms/n2v_manipulate.py +146 -0
  133. careamics/transforms/normalize.py +243 -0
  134. careamics/transforms/pixel_manipulation.py +407 -0
  135. careamics/transforms/struct_mask_parameters.py +20 -0
  136. careamics/transforms/transform.py +24 -0
  137. careamics/transforms/tta.py +88 -0
  138. careamics/transforms/xy_flip.py +123 -0
  139. careamics/transforms/xy_random_rotate90.py +101 -0
  140. careamics/utils/__init__.py +19 -0
  141. careamics/utils/autocorrelation.py +40 -0
  142. careamics/utils/base_enum.py +60 -0
  143. careamics/utils/context.py +66 -0
  144. careamics/utils/logging.py +322 -0
  145. careamics/utils/metrics.py +188 -0
  146. careamics/utils/path_utils.py +26 -0
  147. careamics/utils/ram.py +15 -0
  148. careamics/utils/receptive_field.py +108 -0
  149. careamics/utils/torch_utils.py +127 -0
  150. careamics-0.0.3.dist-info/METADATA +78 -0
  151. careamics-0.0.3.dist-info/RECORD +154 -0
  152. {careamics-0.0.1.dist-info → careamics-0.0.3.dist-info}/WHEEL +1 -1
  153. {careamics-0.0.1.dist-info → careamics-0.0.3.dist-info}/licenses/LICENSE +1 -1
  154. careamics-0.0.1.dist-info/METADATA +0 -46
  155. careamics-0.0.1.dist-info/RECORD +0 -6
careamics/__init__.py CHANGED
@@ -1,4 +1,4 @@
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- """CAREamics"""
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+ """Main CAREamics module."""
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  from importlib.metadata import PackageNotFoundError, version
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@@ -6,3 +6,8 @@ try:
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  __version__ = version("careamics")
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  except PackageNotFoundError:
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  __version__ = "uninstalled"
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+
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+ __all__ = ["CAREamist", "Configuration", "load_configuration", "save_configuration"]
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+
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+ from .careamist import CAREamist
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+ from .config import Configuration, load_configuration, save_configuration