careamics 0.1.0rc4__py3-none-any.whl → 0.1.0rc6__py3-none-any.whl

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Files changed (103) hide show
  1. careamics/callbacks/hyperparameters_callback.py +10 -3
  2. careamics/callbacks/progress_bar_callback.py +37 -4
  3. careamics/careamist.py +92 -55
  4. careamics/config/__init__.py +0 -1
  5. careamics/config/algorithm_model.py +5 -3
  6. careamics/config/architectures/architecture_model.py +7 -0
  7. careamics/config/architectures/custom_model.py +8 -1
  8. careamics/config/architectures/register_model.py +3 -1
  9. careamics/config/architectures/unet_model.py +3 -0
  10. careamics/config/architectures/vae_model.py +2 -0
  11. careamics/config/callback_model.py +4 -15
  12. careamics/config/configuration_example.py +4 -4
  13. careamics/config/configuration_factory.py +113 -55
  14. careamics/config/configuration_model.py +14 -16
  15. careamics/config/data_model.py +63 -165
  16. careamics/config/inference_model.py +9 -75
  17. careamics/config/optimizer_models.py +4 -4
  18. careamics/config/references/algorithm_descriptions.py +1 -0
  19. careamics/config/references/references.py +1 -0
  20. careamics/config/support/__init__.py +0 -2
  21. careamics/config/support/supported_activations.py +2 -0
  22. careamics/config/support/supported_algorithms.py +3 -1
  23. careamics/config/support/supported_architectures.py +2 -0
  24. careamics/config/support/supported_data.py +2 -0
  25. careamics/config/support/supported_loggers.py +2 -0
  26. careamics/config/support/supported_losses.py +2 -0
  27. careamics/config/support/supported_optimizers.py +2 -0
  28. careamics/config/support/supported_pixel_manipulations.py +3 -3
  29. careamics/config/support/supported_struct_axis.py +2 -0
  30. careamics/config/support/supported_transforms.py +4 -15
  31. careamics/config/tile_information.py +2 -0
  32. careamics/config/training_model.py +1 -0
  33. careamics/config/transformations/__init__.py +3 -2
  34. careamics/config/transformations/n2v_manipulate_model.py +1 -0
  35. careamics/config/transformations/normalize_model.py +1 -0
  36. careamics/config/transformations/transform_model.py +1 -0
  37. careamics/config/transformations/xy_flip_model.py +43 -0
  38. careamics/config/transformations/xy_random_rotate90_model.py +13 -7
  39. careamics/config/validators/validator_utils.py +1 -0
  40. careamics/conftest.py +13 -0
  41. careamics/dataset/dataset_utils/__init__.py +0 -1
  42. careamics/dataset/dataset_utils/dataset_utils.py +5 -4
  43. careamics/dataset/dataset_utils/file_utils.py +4 -3
  44. careamics/dataset/dataset_utils/read_tiff.py +6 -2
  45. careamics/dataset/dataset_utils/read_utils.py +2 -0
  46. careamics/dataset/dataset_utils/read_zarr.py +11 -7
  47. careamics/dataset/in_memory_dataset.py +84 -76
  48. careamics/dataset/iterable_dataset.py +166 -134
  49. careamics/dataset/patching/__init__.py +0 -7
  50. careamics/dataset/patching/patching.py +56 -14
  51. careamics/dataset/patching/random_patching.py +8 -2
  52. careamics/dataset/patching/sequential_patching.py +20 -14
  53. careamics/dataset/patching/tiled_patching.py +13 -7
  54. careamics/dataset/patching/validate_patch_dimension.py +2 -0
  55. careamics/dataset/zarr_dataset.py +2 -0
  56. careamics/lightning_datamodule.py +63 -41
  57. careamics/lightning_module.py +9 -3
  58. careamics/lightning_prediction_datamodule.py +15 -20
  59. careamics/lightning_prediction_loop.py +8 -6
  60. careamics/losses/__init__.py +1 -3
  61. careamics/losses/loss_factory.py +2 -1
  62. careamics/losses/losses.py +11 -7
  63. careamics/model_io/__init__.py +0 -1
  64. careamics/model_io/bioimage/_readme_factory.py +2 -1
  65. careamics/model_io/bioimage/bioimage_utils.py +1 -0
  66. careamics/model_io/bioimage/model_description.py +1 -0
  67. careamics/model_io/bmz_io.py +4 -3
  68. careamics/models/activation.py +2 -0
  69. careamics/models/layers.py +122 -25
  70. careamics/models/model_factory.py +2 -1
  71. careamics/models/unet.py +114 -19
  72. careamics/prediction/stitch_prediction.py +2 -5
  73. careamics/transforms/__init__.py +4 -25
  74. careamics/transforms/compose.py +124 -0
  75. careamics/transforms/n2v_manipulate.py +65 -34
  76. careamics/transforms/normalize.py +91 -28
  77. careamics/transforms/pixel_manipulation.py +7 -7
  78. careamics/transforms/struct_mask_parameters.py +3 -1
  79. careamics/transforms/transform.py +24 -0
  80. careamics/transforms/tta.py +2 -2
  81. careamics/transforms/xy_flip.py +123 -0
  82. careamics/transforms/xy_random_rotate90.py +66 -60
  83. careamics/utils/__init__.py +0 -1
  84. careamics/utils/base_enum.py +28 -0
  85. careamics/utils/context.py +1 -0
  86. careamics/utils/logging.py +1 -0
  87. careamics/utils/metrics.py +1 -0
  88. careamics/utils/path_utils.py +2 -0
  89. careamics/utils/ram.py +2 -0
  90. careamics/utils/receptive_field.py +93 -87
  91. careamics/utils/torch_utils.py +1 -0
  92. {careamics-0.1.0rc4.dist-info → careamics-0.1.0rc6.dist-info}/METADATA +17 -61
  93. careamics-0.1.0rc6.dist-info/RECORD +107 -0
  94. careamics/config/noise_models.py +0 -162
  95. careamics/config/support/supported_extraction_strategies.py +0 -24
  96. careamics/config/transformations/nd_flip_model.py +0 -32
  97. careamics/dataset/patching/patch_transform.py +0 -44
  98. careamics/losses/noise_model_factory.py +0 -40
  99. careamics/losses/noise_models.py +0 -524
  100. careamics/transforms/nd_flip.py +0 -93
  101. careamics-0.1.0rc4.dist-info/RECORD +0 -110
  102. {careamics-0.1.0rc4.dist-info → careamics-0.1.0rc6.dist-info}/WHEEL +0 -0
  103. {careamics-0.1.0rc4.dist-info → careamics-0.1.0rc6.dist-info}/licenses/LICENSE +0 -0
careamics-0.1.0rc4.dist-info/RECORD DELETED
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