careamics 0.1.0rc5__py3-none-any.whl → 0.1.0rc7__py3-none-any.whl

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Files changed (118) hide show
  1. careamics/callbacks/hyperparameters_callback.py +10 -3
  2. careamics/callbacks/progress_bar_callback.py +37 -4
  3. careamics/careamist.py +164 -231
  4. careamics/config/algorithm_model.py +5 -18
  5. careamics/config/architectures/architecture_model.py +7 -0
  6. careamics/config/architectures/custom_model.py +11 -4
  7. careamics/config/architectures/register_model.py +3 -1
  8. careamics/config/architectures/unet_model.py +2 -0
  9. careamics/config/architectures/vae_model.py +2 -0
  10. careamics/config/callback_model.py +3 -15
  11. careamics/config/configuration_example.py +4 -5
  12. careamics/config/configuration_factory.py +27 -41
  13. careamics/config/configuration_model.py +11 -11
  14. careamics/config/data_model.py +89 -63
  15. careamics/config/inference_model.py +28 -81
  16. careamics/config/optimizer_models.py +11 -11
  17. careamics/config/support/__init__.py +0 -2
  18. careamics/config/support/supported_activations.py +2 -0
  19. careamics/config/support/supported_algorithms.py +3 -1
  20. careamics/config/support/supported_architectures.py +2 -0
  21. careamics/config/support/supported_data.py +2 -0
  22. careamics/config/support/supported_loggers.py +2 -0
  23. careamics/config/support/supported_losses.py +2 -0
  24. careamics/config/support/supported_optimizers.py +2 -0
  25. careamics/config/support/supported_pixel_manipulations.py +3 -3
  26. careamics/config/support/supported_struct_axis.py +2 -0
  27. careamics/config/support/supported_transforms.py +4 -16
  28. careamics/config/tile_information.py +28 -58
  29. careamics/config/transformations/__init__.py +3 -2
  30. careamics/config/transformations/normalize_model.py +32 -4
  31. careamics/config/transformations/xy_flip_model.py +43 -0
  32. careamics/config/transformations/xy_random_rotate90_model.py +11 -3
  33. careamics/config/validators/validator_utils.py +1 -1
  34. careamics/conftest.py +12 -0
  35. careamics/dataset/__init__.py +12 -1
  36. careamics/dataset/dataset_utils/__init__.py +8 -1
  37. careamics/dataset/dataset_utils/dataset_utils.py +4 -4
  38. careamics/dataset/dataset_utils/file_utils.py +4 -3
  39. careamics/dataset/dataset_utils/iterate_over_files.py +83 -0
  40. careamics/dataset/dataset_utils/read_tiff.py +6 -11
  41. careamics/dataset/dataset_utils/read_utils.py +2 -0
  42. careamics/dataset/dataset_utils/read_zarr.py +11 -7
  43. careamics/dataset/dataset_utils/running_stats.py +186 -0
  44. careamics/dataset/in_memory_dataset.py +88 -154
  45. careamics/dataset/in_memory_pred_dataset.py +88 -0
  46. careamics/dataset/in_memory_tiled_pred_dataset.py +129 -0
  47. careamics/dataset/iterable_dataset.py +121 -191
  48. careamics/dataset/iterable_pred_dataset.py +121 -0
  49. careamics/dataset/iterable_tiled_pred_dataset.py +139 -0
  50. careamics/dataset/patching/patching.py +109 -39
  51. careamics/dataset/patching/random_patching.py +17 -6
  52. careamics/dataset/patching/sequential_patching.py +14 -8
  53. careamics/dataset/patching/validate_patch_dimension.py +7 -3
  54. careamics/dataset/tiling/__init__.py +10 -0
  55. careamics/dataset/tiling/collate_tiles.py +33 -0
  56. careamics/dataset/{patching → tiling}/tiled_patching.py +7 -5
  57. careamics/dataset/zarr_dataset.py +2 -0
  58. careamics/lightning_datamodule.py +46 -25
  59. careamics/lightning_module.py +19 -9
  60. careamics/lightning_prediction_datamodule.py +54 -84
  61. careamics/losses/__init__.py +2 -3
  62. careamics/losses/loss_factory.py +1 -1
  63. careamics/losses/losses.py +11 -7
  64. careamics/lvae_training/__init__.py +0 -0
  65. careamics/lvae_training/data_modules.py +1220 -0
  66. careamics/lvae_training/data_utils.py +618 -0
  67. careamics/lvae_training/eval_utils.py +905 -0
  68. careamics/lvae_training/get_config.py +84 -0
  69. careamics/lvae_training/lightning_module.py +701 -0
  70. careamics/lvae_training/metrics.py +214 -0
  71. careamics/lvae_training/train_lvae.py +339 -0
  72. careamics/lvae_training/train_utils.py +121 -0
  73. careamics/model_io/bioimage/model_description.py +40 -32
  74. careamics/model_io/bmz_io.py +3 -3
  75. careamics/model_io/model_io_utils.py +5 -2
  76. careamics/models/activation.py +2 -0
  77. careamics/models/layers.py +121 -25
  78. careamics/models/lvae/__init__.py +0 -0
  79. careamics/models/lvae/layers.py +1998 -0
  80. careamics/models/lvae/likelihoods.py +312 -0
  81. careamics/models/lvae/lvae.py +985 -0
  82. careamics/models/lvae/noise_models.py +409 -0
  83. careamics/models/lvae/utils.py +395 -0
  84. careamics/models/model_factory.py +1 -1
  85. careamics/models/unet.py +35 -14
  86. careamics/prediction_utils/__init__.py +12 -0
  87. careamics/prediction_utils/create_pred_datamodule.py +185 -0
  88. careamics/prediction_utils/prediction_outputs.py +165 -0
  89. careamics/prediction_utils/stitch_prediction.py +100 -0
  90. careamics/transforms/__init__.py +2 -2
  91. careamics/transforms/compose.py +33 -7
  92. careamics/transforms/n2v_manipulate.py +52 -14
  93. careamics/transforms/normalize.py +171 -48
  94. careamics/transforms/pixel_manipulation.py +35 -11
  95. careamics/transforms/struct_mask_parameters.py +3 -1
  96. careamics/transforms/transform.py +10 -19
  97. careamics/transforms/tta.py +43 -29
  98. careamics/transforms/xy_flip.py +123 -0
  99. careamics/transforms/xy_random_rotate90.py +38 -5
  100. careamics/utils/base_enum.py +28 -0
  101. careamics/utils/path_utils.py +2 -0
  102. careamics/utils/ram.py +4 -2
  103. careamics/utils/receptive_field.py +93 -87
  104. {careamics-0.1.0rc5.dist-info → careamics-0.1.0rc7.dist-info}/METADATA +8 -6
  105. careamics-0.1.0rc7.dist-info/RECORD +130 -0
  106. {careamics-0.1.0rc5.dist-info → careamics-0.1.0rc7.dist-info}/WHEEL +1 -1
  107. careamics/config/noise_models.py +0 -162
  108. careamics/config/support/supported_extraction_strategies.py +0 -25
  109. careamics/config/transformations/nd_flip_model.py +0 -27
  110. careamics/lightning_prediction_loop.py +0 -116
  111. careamics/losses/noise_model_factory.py +0 -40
  112. careamics/losses/noise_models.py +0 -524
  113. careamics/prediction/__init__.py +0 -7
  114. careamics/prediction/stitch_prediction.py +0 -74
  115. careamics/transforms/nd_flip.py +0 -67
  116. careamics/utils/running_stats.py +0 -43
  117. careamics-0.1.0rc5.dist-info/RECORD +0 -111
  118. {careamics-0.1.0rc5.dist-info → careamics-0.1.0rc7.dist-info}/licenses/LICENSE +0 -0
careamics/utils/running_stats.py DELETED
@@ -1,43 +0,0 @@
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- """Running stats submodule, used in the Zarr dataset."""
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-
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- # from multiprocessing import Value
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- # from typing import Tuple
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-
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- # import numpy as np
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-
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-
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- # class RunningStats:
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- # """Calculates running mean and std."""
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-
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- # def __init__(self) -> None:
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- # self.reset()
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-
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- # def reset(self) -> None:
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- # """Reset the running stats."""
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- # self.avg_mean = Value("d", 0)
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- # self.avg_std = Value("d", 0)
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- # self.m2 = Value("d", 0)
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- # self.count = Value("i", 0)
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-
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- # def init(self, mean: float, std: float) -> None:
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- # """Initialize running stats."""
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- # with self.avg_mean.get_lock():
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- # self.avg_mean.value += mean
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- # with self.avg_std.get_lock():
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- # self.avg_std.value = std
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-
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- # def compute_std(self) -> Tuple[float, float]:
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- # """Compute std."""
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- # if self.count.value >= 2:
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- # self.avg_std.value = np.sqrt(self.m2.value / self.count.value)
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-
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- # def update(self, value: float) -> None:
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- # """Update running stats."""
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- # with self.count.get_lock():
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- # self.count.value += 1
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- # delta = value - self.avg_mean.value
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- # with self.avg_mean.get_lock():
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- # self.avg_mean.value += delta / self.count.value
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- # delta2 = value - self.avg_mean.value
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- # with self.m2.get_lock():
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- # self.m2.value += delta * delta2
careamics-0.1.0rc5.dist-info/RECORD DELETED
@@ -1,111 +0,0 @@
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- careamics/__init__.py,sha256=DkMGt4t9ua0gCgvZFEtb6eydvoxG976T0KUro8KnDNA,760
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- careamics/careamist.py,sha256=SI-ZQCzw3nAnsUONcaBDoX9CC5P_vfUU-y7LmUn448o,28755
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- careamics/conftest.py,sha256=mKIH8SQGO_MMynAQAtqjHkTIQ5KDtY_vKKfFB5F3vmU,659
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- careamics/lightning_datamodule.py,sha256=z88iqh_P5J1mWEHlL11JAs7FxWHgOP2TQJM_5zZvLV0,31661
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- careamics/lightning_module.py,sha256=DcZ2wja3Pyfd4XBISbXCOhqoFRzJRpBjhWUG2xYVnz4,10168
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- careamics/lightning_prediction_datamodule.py,sha256=vrNcTlmu0bKqDOn89DaQGxBm4tH2FP2rmVx7W1tRjyI,15517
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- careamics/lightning_prediction_loop.py,sha256=EcUSgM2BHkWhjR4zN0NNf2M8xQF_I3aQ9qAFk0slYYw,4483
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- careamics/py.typed,sha256=esB4cHc6c07uVkGtqf8at7ttEnprwRxwk8obY8Qumq4,187
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- careamics/callbacks/__init__.py,sha256=spxJlDByD-6QtMl9vcIty8Wb0tyHaSTKTItozHenI44,204
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- careamics/callbacks/hyperparameters_callback.py,sha256=CdOtxazXi6YXH3Fq4AahqBQ3Ai64YpAMkd8gFnAnkjc,1258
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- careamics/callbacks/progress_bar_callback.py,sha256=ojeat3wwaqq7uEAVZBren71CZtNiEch1FR7o8FiaEPg,1868
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- careamics/config/__init__.py,sha256=SP1oJKhK3VDN9ABwnpfR3H02qRprzymjRfNYeC7kHEo,1019
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- careamics/config/algorithm_model.py,sha256=7Y7-kr9Bc-cCOiavJ6vzahYTdlLZcLZo7FvKOPFZoWg,5732
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- careamics/config/callback_model.py,sha256=MAliEULQOTTAFJSXqqR9dlCQdJtknWjkCY3RkhknR2o,3226
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- careamics/config/configuration_example.py,sha256=g-y3HTsxz_q-UQ-11aLoprpbc6BjD1dD1gq7PsRgc0Q,2541
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- careamics/config/configuration_factory.py,sha256=SBJKjfxHwrxRfRxSfS7xHtWdet-kZbZnlZla-JZQT_I,21734
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- careamics/config/configuration_model.py,sha256=j7QryeMNQAsD_0byb81u99Oek2uyj3Syr0nUepFYTe8,18494
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- careamics/config/data_model.py,sha256=ueGsuAeH2OZs6Jt7SKDiH26OTU5A9iYcWVwcJ1KSN5s,12946
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- careamics/config/inference_model.py,sha256=sZzpsqQBwp8crsluTID3SdT1_gJ9p7gtkT5AsfUnpOs,7909
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- careamics/config/noise_models.py,sha256=1P6dXqqBhbVHT7EZ2hluO2aHKIywkAyl4BndrvtKRKU,4338
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- careamics/config/optimizer_models.py,sha256=Umu6O2qKv1o4ReWBuldAHmvF0u_DKS5eHCa7YdxvOaw,5266
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- careamics/config/tile_information.py,sha256=2bVLTvZfdjPOZVq7jYXVuAFLlPFmJ2DBiwtwm5n7K-U,2939
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- careamics/config/training_model.py,sha256=oghv91J7xIdI69wpNJGmLUAwgM9l3VhMsbsOo4USqkU,1559
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- careamics/config/architectures/__init__.py,sha256=CdnViydyTdQixus3uWHBIgbgxmu9t1_ADehqpjN_57U,444
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- careamics/config/architectures/architecture_model.py,sha256=EomNAhjuhu3uqEjzG6uvRclSQNVuGkcH_mt4R47yIHg,681
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- careamics/config/architectures/custom_model.py,sha256=2tMvr6XqFY8hY8Tfljba-kp1c61fDKaV4vylbg4AyUg,4473
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- careamics/config/architectures/register_model.py,sha256=sW6fvj54F6G1rg3fmXTwCAu_YcKs3xZTsdYnDGFRahY,2389
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- careamics/config/architectures/unet_model.py,sha256=frQp5nWPF0v9X4lR7Y7-KjbmBS1-FIpVVCKCBpIQ5VM,2864
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- careamics/config/architectures/vae_model.py,sha256=n1pvVmpelNqQXsXtxXPdmMBBkCLyMIlTQJbMqB-amCc,899
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- careamics/config/references/__init__.py,sha256=rZAQzmrciX5cNICcXaBH6sbE6N6L7_qYQUkasNy9y-c,763
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- careamics/config/references/algorithm_descriptions.py,sha256=wR3hIoeg5eiUEPbwTxMpQYLTKQyRl_5naSDbBZOZESU,3541
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- careamics/config/references/references.py,sha256=AXx08FJQxHb7SYOluCr_eQn_mbOris5dXqhKrCnhBTE,1573
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- careamics/config/support/__init__.py,sha256=XMnPEPHVy63DDxAfczIFqFjuYrtDRrbzA5b0Ff1qmyU,1149
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- careamics/config/support/supported_activations.py,sha256=-KaTxdm8IJ9c6xkCVMw3SWjbw6wmvV-1WuoeSbyCdH4,476
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- careamics/config/support/supported_algorithms.py,sha256=wc3pTYhgoZ0W_O6jcJY0ZsVErYMSTmi24ptw3ezAuUw,316
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- careamics/config/support/supported_architectures.py,sha256=EDrh8eghqxWcwjXVhhJpfymV6dsmyaUxk2E397VXXbA,495
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- careamics/config/support/supported_data.py,sha256=AvdoWVLLpX5jzozJGUqeo5EJVkb6Z_OcQbaS8AkyHSg,2048
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- careamics/config/support/supported_extraction_strategies.py,sha256=aMh6pTcEpvtSN1-gls9DN58SEzHEkHJxxI_tGMh8_X0,579
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- careamics/config/support/supported_loggers.py,sha256=slbpUZSMdRMCKNAQfnCxh7n1Sql2NFoH79cIoiuavcU,159
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- careamics/config/support/supported_losses.py,sha256=fu0SPPhubMVq3zXJk8G8Av9ojWNw62EKm7WnUmapuRs,502
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- careamics/config/support/supported_optimizers.py,sha256=Y_Ns3DijRU9xUoY54AMm0VEeIx0ntS_4UkpyBKaSSl4,1337
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- careamics/config/support/supported_pixel_manipulations.py,sha256=0lZfCwL9bwPK5E8qzi7l9UGOq41U2fCH9KpxnDEpznc,360
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- careamics/config/support/supported_struct_axis.py,sha256=VzyKEVwNARtF9HviAmsHqAjyenHCRFR5UObks6s6R9Y,378
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- careamics/config/support/supported_transforms.py,sha256=7lF2ZdWC7Fa7ExemQ6JzM9s9RXM0_tsGWilmmq-MoMw,889
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- careamics/config/transformations/__init__.py,sha256=FnLBxNyJ0cTPf8e1dhtkhks5vu_z8Wi48aBjvAPDErk,357
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- careamics/config/transformations/n2v_manipulate_model.py,sha256=UTyfpm1mmMvYg_HoMzXilZhJGx_muiV-lLQ4UThCFJ0,1854
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- careamics/config/transformations/nd_flip_model.py,sha256=ooQdHZdHQdeAuOJolTArw2hpSIF_NSxc9bqAItsjWy4,586
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- careamics/config/transformations/normalize_model.py,sha256=fua-JAcfNdTuikERreaR_0mz9ExsYSDJ7mUgIDl-U0M,804
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- careamics/config/transformations/transform_model.py,sha256=i7KAtSv4nah2H7uyJFKqg7RdKF68OHIPMNNvDo0HxGY,1000
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- careamics/config/transformations/xy_random_rotate90_model.py,sha256=G9WsuZ02OnpiBeYEPGhEryRiuEvITwVYrohYfEuhhYE,636
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- careamics/config/validators/__init__.py,sha256=iv0nVI0W7j9DxFPwh0DjRCzM9P8oLQn4Gwi5rfuFrrI,180
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- careamics/config/validators/validator_utils.py,sha256=H11pttfXFdnlUw9FFIgPWy3sxO1ks38dtmYAS6Kl9-c,2624
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- careamics/dataset/__init__.py,sha256=cUcqy1Nxa5WhDQim6948r3i1kGQ-HijUqAACyyM7cuU,174
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- careamics/dataset/in_memory_dataset.py,sha256=1LmI0aeRalacBkdI1tcoQPWJhi7p9iqUILSa8QaYWZc,10900
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- careamics/dataset/iterable_dataset.py,sha256=KDm66o_AFVY2e6eCnydvT16zAeP5hqUHPQ49EQX4VuI,12333
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- careamics/dataset/zarr_dataset.py,sha256=cpouzhaWUOkqAjjliJhrtfqVvZEMaq1d9V3LDoEvJQA,5644
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- careamics/dataset/dataset_utils/__init__.py,sha256=5U_kavgh_QEvTiDuM-O4hsqmDOKh6_y6iDvZPE8Jtsc,446
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- careamics/dataset/dataset_utils/dataset_utils.py,sha256=luTUsKx11gYsbWY10NgmcrRLC6tbh8BTd0FnWpdfTqA,2667
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- careamics/dataset/dataset_utils/file_utils.py,sha256=VHK7__34keJfkYWfyrOApalFA0wyINLK7CB79T_Sqm4,4030
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- careamics/dataset/dataset_utils/read_tiff.py,sha256=KcO5pZXaXEGXlJoCLnFriAHmHACCPI5kRWZK-oovfBo,1648
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- careamics/dataset/dataset_utils/read_utils.py,sha256=hwb2pFr-ueusVf8hoTtDsD71V5HDVU-6eQ14cpPp6d4,547
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- careamics/dataset/dataset_utils/read_zarr.py,sha256=B75gaOsLctkonYqwouCDWBu-AVwy697mJbEXDC0ft3I,1635
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- careamics/dataset/patching/__init__.py,sha256=7-s12oUAZNlMOwSkxSwbD7vojQINWYFzn_4qIJ87WBg,37
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- careamics/dataset/patching/patching.py,sha256=CcVgg9pBYFK6rU3ZxBG9ZSxbaZASoR8ATqQT0HeN8vI,6259
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- careamics/dataset/patching/random_patching.py,sha256=93R5a56O4k6CxrWvRpTwkFDnw37tpDTaajcPAQbc4Nw,6025
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- careamics/dataset/patching/sequential_patching.py,sha256=2p52u0y8h_mOomMfCuM4icVk7TqdRbjixOtaKUHnQbs,5651
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- careamics/dataset/patching/tiled_patching.py,sha256=zypmytFXEMo5V-LTjA4qGyNJGd7tV7aUgLXSUvo90U8,5814
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- careamics/dataset/patching/validate_patch_dimension.py,sha256=cHiD2XNX44eArlRR7ZK7_4Mihv3DzjncthgN-nXqR4s,2001
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- careamics/losses/__init__.py,sha256=Os1S7QHHd0o3SI1GMHD9eNRmXblXK3I8e80WU6eamCU,215
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- careamics/losses/loss_factory.py,sha256=Fj_TiOupo694AC5FABfBF69RXJNySy4Dd88Zq62Dgj4,992
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- careamics/losses/losses.py,sha256=a-8NLw0R86r2XxcHh97D7Mnhtbn0c5VFjZLPfttKCCM,2304
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- careamics/losses/noise_model_factory.py,sha256=zbRxlU3hTLJR9fM-PkeTthQ8idrwJD7-AelvXxaoHEQ,988
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- careamics/losses/noise_models.py,sha256=fRr4_mxP_jirC-UkQDVF09RcwqvZJES9JVCc8tccCFc,17801
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- careamics/model_io/__init__.py,sha256=HITzjiuZQwo-rQ2_Ma3bz9l7PDANv1_S489E-tffV9s,155
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- careamics/model_io/bmz_io.py,sha256=4zcIGopVmDUwkJPmpdnceyRIJQ3PbJjMZ0tTL6OZrFM,6967
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- careamics/model_io/model_io_utils.py,sha256=x5u1HszZgRfvuku4eKQhmInyxRaEzkgNqAhGSyLS6e4,2116
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- careamics/model_io/bioimage/__init__.py,sha256=r94nu8WDAvj0Fbu4C-iJXdOhfSQXeZBvN3UKsLG0RNI,298
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- careamics/model_io/bioimage/_readme_factory.py,sha256=LZAuEiWNBTPaD8KrLPMq16yJuOPKDZiGQuTMHKLvoT4,3514
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- careamics/model_io/bioimage/bioimage_utils.py,sha256=nlW0J1daYyLbL6yVN3QSn3HhA2joMjIG-thK64lpVTY,1085
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- careamics/model_io/bioimage/model_description.py,sha256=wXGJBzGGSwEds-V0G4mgPvoi4dDXNn_7Tp6iPCsAeTY,9208
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- careamics/models/__init__.py,sha256=Wty5hwQb_As33pQOZqY5j-DpDOdh5ArBH4BhQDSuXTQ,133
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- careamics/models/activation.py,sha256=21g0isrf_SpY4MUQoxbcsc1hAP5luSmWgtzGOvXKzTw,936
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