careamics 0.0.14__py3-none-any.whl → 0.0.15__py3-none-any.whl
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- careamics/careamist.py +49 -49
- careamics/cli/conf.py +6 -6
- careamics/cli/main.py +8 -8
- careamics/cli/utils.py +2 -4
- careamics/config/algorithms/vae_algorithm_model.py +4 -4
- careamics/config/callback_model.py +8 -8
- careamics/config/configuration_factories.py +49 -49
- careamics/config/data/data_model.py +7 -13
- careamics/config/data/ng_data_model.py +8 -14
- careamics/config/data/patching_strategies/_overlapping_patched_model.py +4 -5
- careamics/config/inference_model.py +6 -10
- careamics/config/likelihood_model.py +2 -2
- careamics/config/nm_model.py +5 -7
- careamics/config/training_model.py +4 -4
- careamics/config/transformations/normalize_model.py +3 -3
- careamics/config/transformations/xy_flip_model.py +2 -2
- careamics/config/transformations/xy_random_rotate90_model.py +2 -2
- careamics/config/validators/validator_utils.py +1 -2
- careamics/dataset/dataset_utils/iterate_over_files.py +3 -3
- careamics/dataset/in_memory_dataset.py +2 -2
- careamics/dataset/iterable_dataset.py +1 -2
- careamics/dataset/patching/random_patching.py +6 -6
- careamics/dataset/patching/sequential_patching.py +4 -4
- careamics/dataset/tiling/lvae_tiled_patching.py +2 -2
- careamics/dataset_ng/dataset.py +3 -3
- careamics/dataset_ng/factory.py +19 -19
- careamics/dataset_ng/patching_strategies/random_patching.py +2 -3
- careamics/dataset_ng/patching_strategies/sequential_patching.py +1 -2
- careamics/lightning/callbacks/prediction_writer_callback/prediction_writer_callback.py +5 -5
- careamics/lightning/callbacks/prediction_writer_callback/write_strategy.py +5 -5
- careamics/lightning/callbacks/prediction_writer_callback/write_strategy_factory.py +8 -8
- careamics/lightning/dataset_ng/data_module.py +43 -43
- careamics/lightning/lightning_module.py +12 -14
- careamics/lightning/predict_data_module.py +8 -8
- careamics/lightning/train_data_module.py +11 -11
- careamics/losses/lvae/losses.py +9 -9
- careamics/model_io/bioimage/model_description.py +12 -11
- careamics/model_io/bmz_io.py +4 -4
- careamics/models/layers.py +5 -5
- careamics/prediction_utils/lvae_prediction.py +5 -5
- careamics/transforms/compose.py +9 -9
- careamics/transforms/n2v_manipulate.py +3 -3
- careamics/transforms/n2v_manipulate_torch.py +4 -4
- careamics/transforms/normalize.py +4 -6
- careamics/transforms/pixel_manipulation.py +6 -8
- careamics/transforms/pixel_manipulation_torch.py +5 -7
- careamics/transforms/xy_flip.py +3 -5
- careamics/transforms/xy_random_rotate90.py +3 -5
- careamics/utils/logging.py +8 -8
- careamics/utils/metrics.py +2 -2
- careamics/utils/plotting.py +1 -3
- {careamics-0.0.14.dist-info → careamics-0.0.15.dist-info}/METADATA +2 -3
- {careamics-0.0.14.dist-info → careamics-0.0.15.dist-info}/RECORD +56 -56
- {careamics-0.0.14.dist-info → careamics-0.0.15.dist-info}/WHEEL +0 -0
- {careamics-0.0.14.dist-info → careamics-0.0.15.dist-info}/entry_points.txt +0 -0
- {careamics-0.0.14.dist-info → careamics-0.0.15.dist-info}/licenses/LICENSE +0 -0
careamics/transforms/compose.py
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"""A class chaining transforms together."""
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from typing import
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from typing import Union, cast
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from numpy.typing import NDArray
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]
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def _chain_transforms(
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self, patch: NDArray, target: NDArray | None
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) -> tuple[NDArray | None, ...]:
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"""Chain transforms on the input data.
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Parameters
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tuple[np.ndarray, Optional[np.ndarray]]
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The output of the transformations.
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"""
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params: Union[tuple[NDArray,
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params: Union[tuple[NDArray, NDArray | None],] = (patch, target)
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for t in self.transforms:
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*params, _ = t(*params) # ignore additional_arrays dict
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def _chain_transforms_additional_arrays(
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self,
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patch: NDArray,
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target:
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target: NDArray | None,
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**additional_arrays: NDArray,
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) -> tuple[NDArray, NDArray | None, dict[str, NDArray]]:
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"""Chain transforms on the input data, with additional arrays.
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return patch, target, additional_arrays
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def __call__(
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self, patch: NDArray, target:
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self, patch: NDArray, target: NDArray | None = None
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) -> tuple[NDArray, ...]:
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"""Apply the transforms to the input data.
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def transform_with_additional_arrays(
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self,
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patch: NDArray,
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target:
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target: NDArray | None = None,
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**additional_arrays: NDArray,
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) -> tuple[NDArray,
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) -> tuple[NDArray, NDArray | None, dict[str, NDArray]]:
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"""Apply the transforms to the input data, including additional arrays.
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"""N2V manipulation transform."""
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from typing import Any, Literal
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import numpy as np
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from numpy.typing import NDArray
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remove_center: bool = True,
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struct_mask_axis: Literal["horizontal", "vertical", "none"] = "none",
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struct_mask_span: int = 5,
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seed:
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seed: int | None = None,
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):
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"""Constructor.
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self.remove_center = remove_center # TODO is this ever used?
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if struct_mask_axis == SupportedStructAxis.NONE:
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self.struct_mask:
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self.struct_mask: StructMaskParameters | None = None
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else:
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self.struct_mask = StructMaskParameters(
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axis=0 if struct_mask_axis == SupportedStructAxis.HORIZONTAL else 1,
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"""N2V manipulation transform for PyTorch."""
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def __init__(
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n2v_manipulate_config: N2VManipulateModel,
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device:
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device: str | None = None,
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"""Constructor.
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self.remove_center = n2v_manipulate_config.remove_center
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self.struct_mask:
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self.struct_mask = StructMaskParameters(
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axis=(
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"""Normalization and denormalization transforms for image patches."""
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target_stds: list[float] | None = None,
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**additional_arrays: NDArray,
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careamics/transforms/xy_flip.py
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Metadata-Version: 2.4
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Name: careamics
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|
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@@ -1,38 +1,38 @@
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careamics/__init__.py,sha256=eHsl7oE8HTKmi7yLMj8Yyp0RbdtN3QDmQQb-4Sn9d8M,475
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careamics/careamist.py,sha256=
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careamics/careamist.py,sha256=DeOt9u_EvRtRkzQ9NzBoyMxSNb8vO1tFHVwopI_37TY,38172
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careamics/conftest.py,sha256=Od4WcaaP0UP-XUMrFr_oo4e6c2hi_RvNbuaRTopwlmI,911
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careamics/py.typed,sha256=esB4cHc6c07uVkGtqf8at7ttEnprwRxwk8obY8Qumq4,187
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careamics/cli/__init__.py,sha256=LbM9bVtU1dy-khmdiIDXwvKy2v8wPBCEUuWqV_8rosA,106
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careamics/cli/main.py,sha256=
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careamics/cli/conf.py,sha256=ePp0hxcP3vUQWr5m2bgsxNBw7sS6eMu8F6pGhV8TvAU,13049
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careamics/cli/main.py,sha256=21UcqLOP0tM7x25pslw0zRAfJMMEZEzG1xeJZI-QfN0,6533
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careamics/cli/utils.py,sha256=DJvHKpZB6LSSnABKxK6i15ITAyIdyaiAnSdpBPZhuuk,626
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careamics/config/__init__.py,sha256=K0N1GIqFCYhpPjalZG-Ygap6Ew_dDAC0uw5Npzhg9Lk,1524
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careamics/config/callback_model.py,sha256=
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careamics/config/callback_model.py,sha256=lxytx4rwqOI-UxW8eHTdfLE3K4eIlg907w4Xk9Nul7Y,4065
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careamics/config/configuration.py,sha256=gNBKxeHqAQLa8_btGuQ4-X4987cRPr5L6RI6hOv179Q,13345
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careamics/config/configuration_factories.py,sha256=
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careamics/config/configuration_factories.py,sha256=P_VWHOJEjW-s_yAOKul9TV41yufsQLzRyCPSKJrjUjc,45959
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careamics/config/configuration_io.py,sha256=P-bP1kzkXxJWOEFP02dEZFNmpuLAPJfJtYhX4bFeaKk,2324
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careamics/config/inference_model.py,sha256=
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careamics/config/likelihood_model.py,sha256=
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careamics/config/inference_model.py,sha256=OiNLR4srvbaNcsvA5_Zwc3tqr7yQAXXeSxm5aAEpySM,6978
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careamics/config/likelihood_model.py,sha256=mxyhEHC6wS02t5lqFE3l-8N1DpzrTqEiQSswEy3DJgs,2246
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careamics/config/loss_model.py,sha256=yYcUBS90Qyon1MxeaHiVP3dJHPJFC0GUvWKGcAb3IHk,2036
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careamics/config/nm_model.py,sha256=
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careamics/config/nm_model.py,sha256=M_YE2fiYgJT1pGF7JpzhDvgTnd8CP6DxZXIjxG9q5Qg,4722
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careamics/config/optimizer_models.py,sha256=9qxcLjtDp5LjYX52u21Rom4F3_GZUV2GJimrK3un574,5717
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careamics/config/tile_information.py,sha256=c-_xrVPOgcnjiEzQ-9A_GhNPamObkMANbeHaRP29R-4,2059
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careamics/config/training_model.py,sha256=
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careamics/config/training_model.py,sha256=6XvXMIT2H8vxyGfb9L4cSRqpmlurBPeyWYS6RYhDZaA,3095
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careamics/config/algorithms/__init__.py,sha256=on5D6zBO9Lu-Tf5To8xpF6owIFqdN7RSmZdpyXDOaNw,404
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careamics/config/algorithms/care_algorithm_model.py,sha256=ncf89BC2aFPFSquJ65-Y7NpwVbvgPE0BKH6Up1OHa1s,3238
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careamics/config/algorithms/n2n_algorithm_model.py,sha256=OZbRis9jhRKWNK1-Z_aw2tfJRuGdlJiYEYlH4Hr1FRs,3066
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careamics/config/algorithms/n2v_algorithm_model.py,sha256=IkHsTj-IkWq--mlWjBHfH18CGK_3p2uaC3Zz2tfieaA,9469
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careamics/config/algorithms/unet_algorithm_model.py,sha256=OaBFVlhsb9YhF3f2x1ImazvfnZ4_DPWvYWihRwurkeg,2587
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careamics/config/algorithms/vae_algorithm_model.py,sha256=JFHWtoLEKt0PthJYiDq3TfBl7fJudODUvtCyTeFZvvg,4661
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careamics/config/architectures/__init__.py,sha256=lYUz56R7LDqVQWQDLkLgJL8VtOyxc_ege1r4bXGEBqA,220
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careamics/config/architectures/architecture_model.py,sha256=gXn4gdLrQP3bmTQxIhzkEHYlodPaIp6LI-kwZl23W-Y,911
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careamics/config/architectures/lvae_model.py,sha256=lwOiJYNUqPrZFl9SpPLYon77EiRbe2eI7pmpx45rO78,7606
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careamics/config/architectures/unet_model.py,sha256=Aqc_KPf2VKMhNrYwOdmr_ez3iIQz8ZRtsA6t5FFT354,3686
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careamics/config/data/__init__.py,sha256=YS04_USNswKL7kpSn_6BeTvhobAiUVst46_SlCztCxs,171
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careamics/config/data/data_model.py,sha256=4zqLKfH1dhOl7CDHvIANrfSbJnUhnkfrCvAJF5F7MdQ,13374
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careamics/config/data/ng_data_model.py,sha256=0RSUvSMoIVcQY4a1drCMHMcOBp15xHchtnEk-nUiTvU,12244
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careamics/config/data/patching_strategies/__init__.py,sha256=6ZUors-WzBBQCwMyaSojYJzdXeleFRBlrFls1r-Otdo,394
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careamics/config/data/patching_strategies/_overlapping_patched_model.py,sha256=
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careamics/config/data/patching_strategies/_overlapping_patched_model.py,sha256=ysGd8QNNdNzLD6NITmvyjVETG6ohhEFLgWPCS_CYSxE,3030
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careamics/config/data/patching_strategies/_patched_model.py,sha256=wmhM1Qt5qDuMCs76ab7dPoNTjy_lLVIL8TD5AzaIoak,1429
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careamics/config/data/patching_strategies/random_patching_model.py,sha256=HZfPLkkhwYNQ11O-ahmoaE1bTw7rXg2mIIqsBNkY4WE,533
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careamics/config/data/patching_strategies/sequential_patching_model.py,sha256=sS1h-sHUGvlh41b4kc_3B858ZCPDMJlPb6roAhDL63Y,865
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@@ -52,39 +52,39 @@ careamics/config/support/supported_struct_axis.py,sha256=alZMA5Y-BpDymLPUEd1zqVY
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careamics/config/support/supported_transforms.py,sha256=ylTiS8fUFKFwfn85gh7kKF4Trb9Q4ENPKm-XDWCe-SY,311
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careamics/config/transformations/__init__.py,sha256=6THr9oNI06umw_cchXW9sCeBLpFIcJfGC4hdq3WvUsI,577
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careamics/config/transformations/n2v_manipulate_model.py,sha256=IJ_MeNbVzwnmvLhBjAVZPj5fxPzUXYGYYRe5PHcWIzQ,2428
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careamics/config/transformations/normalize_model.py,sha256=
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careamics/config/transformations/normalize_model.py,sha256=_gQmUTlrPlMx5fptoZbB0Ov7PdJQoeDAw81XMCtQRr4,1920
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careamics/config/transformations/transform_model.py,sha256=6UVbXnxm-LLZOQQ-ZBwWwgmS_99DiBuERLfMxrta3-8,990
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careamics/config/transformations/transform_unions.py,sha256=lOwwX2LZPhfb0GR8B1jtJeuoDa9jIbOmh_W0rlebS1g,784
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careamics/config/transformations/xy_random_rotate90_model.py,sha256=Z0vhD9Hal_rpwWHlOA53ADDcUrrApESzZBa50HD7gRc,881
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