careamics 0.1.0rc6__py3-none-any.whl → 0.1.0rc8__py3-none-any.whl

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Files changed (91) hide show
  1. careamics/__init__.py +1 -14
  2. careamics/careamist.py +212 -294
  3. careamics/config/__init__.py +0 -3
  4. careamics/config/algorithm_model.py +8 -15
  5. careamics/config/architectures/architecture_model.py +1 -0
  6. careamics/config/architectures/custom_model.py +5 -3
  7. careamics/config/architectures/unet_model.py +19 -0
  8. careamics/config/architectures/vae_model.py +1 -0
  9. careamics/config/callback_model.py +76 -34
  10. careamics/config/configuration_factory.py +18 -98
  11. careamics/config/configuration_model.py +23 -18
  12. careamics/config/data_model.py +103 -54
  13. careamics/config/inference_model.py +41 -19
  14. careamics/config/optimizer_models.py +13 -7
  15. careamics/config/support/supported_data.py +29 -4
  16. careamics/config/support/supported_transforms.py +0 -1
  17. careamics/config/tile_information.py +36 -58
  18. careamics/config/training_model.py +5 -1
  19. careamics/config/transformations/normalize_model.py +32 -4
  20. careamics/config/validators/validator_utils.py +1 -1
  21. careamics/dataset/__init__.py +12 -1
  22. careamics/dataset/dataset_utils/__init__.py +8 -7
  23. careamics/dataset/dataset_utils/file_utils.py +2 -2
  24. careamics/dataset/dataset_utils/iterate_over_files.py +83 -0
  25. careamics/dataset/dataset_utils/running_stats.py +186 -0
  26. careamics/dataset/in_memory_dataset.py +84 -173
  27. careamics/dataset/in_memory_pred_dataset.py +88 -0
  28. careamics/dataset/in_memory_tiled_pred_dataset.py +129 -0
  29. careamics/dataset/iterable_dataset.py +97 -250
  30. careamics/dataset/iterable_pred_dataset.py +122 -0
  31. careamics/dataset/iterable_tiled_pred_dataset.py +140 -0
  32. careamics/dataset/patching/patching.py +97 -52
  33. careamics/dataset/patching/random_patching.py +9 -4
  34. careamics/dataset/patching/validate_patch_dimension.py +5 -3
  35. careamics/dataset/tiling/__init__.py +10 -0
  36. careamics/dataset/tiling/collate_tiles.py +33 -0
  37. careamics/dataset/{patching → tiling}/tiled_patching.py +4 -4
  38. careamics/file_io/__init__.py +7 -0
  39. careamics/file_io/read/__init__.py +11 -0
  40. careamics/file_io/read/get_func.py +56 -0
  41. careamics/{dataset/dataset_utils/read_tiff.py → file_io/read/tiff.py} +3 -10
  42. careamics/file_io/write/__init__.py +9 -0
  43. careamics/file_io/write/get_func.py +59 -0
  44. careamics/file_io/write/tiff.py +39 -0
  45. careamics/lightning/__init__.py +17 -0
  46. careamics/{lightning_module.py → lightning/lightning_module.py} +69 -92
  47. careamics/{lightning_prediction_datamodule.py → lightning/predict_data_module.py} +120 -178
  48. careamics/{lightning_datamodule.py → lightning/train_data_module.py} +135 -220
  49. careamics/lvae_training/__init__.py +0 -0
  50. careamics/lvae_training/data_modules.py +1220 -0
  51. careamics/lvae_training/data_utils.py +618 -0
  52. careamics/lvae_training/eval_utils.py +905 -0
  53. careamics/lvae_training/get_config.py +84 -0
  54. careamics/lvae_training/lightning_module.py +701 -0
  55. careamics/lvae_training/metrics.py +214 -0
  56. careamics/lvae_training/train_lvae.py +339 -0
  57. careamics/lvae_training/train_utils.py +121 -0
  58. careamics/model_io/bioimage/model_description.py +40 -32
  59. careamics/model_io/bmz_io.py +2 -2
  60. careamics/model_io/model_io_utils.py +6 -3
  61. careamics/models/lvae/__init__.py +0 -0
  62. careamics/models/lvae/layers.py +1998 -0
  63. careamics/models/lvae/likelihoods.py +312 -0
  64. careamics/models/lvae/lvae.py +985 -0
  65. careamics/models/lvae/noise_models.py +409 -0
  66. careamics/models/lvae/utils.py +395 -0
  67. careamics/prediction_utils/__init__.py +10 -0
  68. careamics/prediction_utils/prediction_outputs.py +137 -0
  69. careamics/prediction_utils/stitch_prediction.py +103 -0
  70. careamics/transforms/n2v_manipulate.py +3 -1
  71. careamics/transforms/normalize.py +139 -68
  72. careamics/transforms/pixel_manipulation.py +33 -9
  73. careamics/transforms/tta.py +43 -29
  74. careamics/utils/__init__.py +2 -0
  75. careamics/utils/autocorrelation.py +40 -0
  76. careamics/utils/ram.py +2 -2
  77. {careamics-0.1.0rc6.dist-info → careamics-0.1.0rc8.dist-info}/METADATA +7 -6
  78. careamics-0.1.0rc8.dist-info/RECORD +135 -0
  79. {careamics-0.1.0rc6.dist-info → careamics-0.1.0rc8.dist-info}/WHEEL +1 -1
  80. careamics/config/configuration_example.py +0 -89
  81. careamics/dataset/dataset_utils/read_utils.py +0 -27
  82. careamics/lightning_prediction_loop.py +0 -118
  83. careamics/prediction/__init__.py +0 -7
  84. careamics/prediction/stitch_prediction.py +0 -70
  85. careamics/utils/running_stats.py +0 -43
  86. careamics-0.1.0rc6.dist-info/RECORD +0 -107
  87. /careamics/{dataset/dataset_utils/read_zarr.py → file_io/read/zarr.py} +0 -0
  88. /careamics/{callbacks → lightning/callbacks}/__init__.py +0 -0
  89. /careamics/{callbacks → lightning/callbacks}/hyperparameters_callback.py +0 -0
  90. /careamics/{callbacks → lightning/callbacks}/progress_bar_callback.py +0 -0
  91. {careamics-0.1.0rc6.dist-info → careamics-0.1.0rc8.dist-info}/licenses/LICENSE +0 -0
careamics/__init__.py CHANGED
@@ -7,20 +7,7 @@ try:
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  except PackageNotFoundError:
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  __version__ = "uninstalled"
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- __all__ = [
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- "CAREamist",
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- "CAREamicsModuleWrapper",
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- "CAREamicsPredictData",
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- "CAREamicsTrainData",
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- "Configuration",
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- "load_configuration",
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- "save_configuration",
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- "TrainingDataWrapper",
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- "PredictDataWrapper",
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- ]
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+ __all__ = ["CAREamist", "Configuration", "load_configuration", "save_configuration"]
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  from .careamist import CAREamist
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  from .config import Configuration, load_configuration, save_configuration
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- from .lightning_datamodule import CAREamicsTrainData, TrainingDataWrapper
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- from .lightning_module import CAREamicsModuleWrapper
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- from .lightning_prediction_datamodule import CAREamicsPredictData, PredictDataWrapper