careamics 0.1.0rc5__py3-none-any.whl → 0.1.0rc6__py3-none-any.whl

careamics/transforms/xy_random_rotate90.py

@@ -1,3 +1,5 @@
+"""Patch transform applying XY random 90 degrees rotations."""
+
 from typing import Optional, Tuple
 
 import numpy as np
@@ -9,16 +11,40 @@ class XYRandomRotate90(Transform):
     """Applies random 90 degree rotations to the YX axis.
 
     This transform expects C(Z)YX dimensions.
+
+    Attributes
+    ----------
+    rng : np.random.Generator
+        Random number generator.
+    p : float
+        Probability of applying the transform.
+    seed : Optional[int]
+        Random seed.
+
+    Parameters
+    ----------
+    p : float
+        Probability of applying the transform, by default 0.5.
+    seed : Optional[int]
+        Random seed, by default None.
     """
 
-    def __init__(self, seed: Optional[int] = None):
+    def __init__(self, p: float = 0.5, seed: Optional[int] = None):
         """Constructor.
 
         Parameters
         ----------
-        seed : Optional[int], optional
-            Random seed, by default None
+        p : float
+            Probability of applying the transform, by default 0.5.
+        seed : Optional[int]
+            Random seed, by default None.
         """
+        if p < 0 or p > 1:
+            raise ValueError("Probability must be in [0, 1].")
+
+        # probability to apply the transform
+        self.p = p
+
         # numpy random generator
         self.rng = np.random.default_rng(seed=seed)
 
@@ -32,13 +58,16 @@ class XYRandomRotate90(Transform):
         patch : np.ndarray
             Patch, 2D or 3D, shape C(Z)YX.
         target : Optional[np.ndarray], optional
-            Target for the patch, by default None
+            Target for the patch, by default None.
 
         Returns
         -------
         Tuple[np.ndarray, Optional[np.ndarray]]
             Transformed patch and target.
         """
+        if self.rng.random() > self.p:
+            return patch, target
+
         # number of rotations
         n_rot = self.rng.integers(1, 4)
 
@@ -63,6 +92,10 @@ class XYRandomRotate90(Transform):
             Number of 90 degree rotations.
         axes : Tuple[int, int]
             Axes along which to rotate the patch.
+
+        Returns
+        -------
+        np.ndarray
+            Transformed patch.
         """
-        # TODO why ascontiguousarray?
         return np.ascontiguousarray(np.rot90(patch, k=n_rot, axes=axes))

careamics/utils/base_enum.py

@@ -1,9 +1,25 @@
+"""A base class for Enum that allows checking if a value is in the Enum."""
+
 from enum import Enum, EnumMeta
 from typing import Any
 
 
 class _ContainerEnum(EnumMeta):
+    """Metaclass for Enum with __contains__ method."""
+
     def __contains__(cls, item: Any) -> bool:
+        """Check if an item is in the Enum.
+
+        Parameters
+        ----------
+        item : Any
+            Item to check.
+
+        Returns
+        -------
+        bool
+            True if the item is in the Enum, False otherwise.
+        """
         try:
             cls(item)
         except ValueError:
@@ -12,6 +28,18 @@ class _ContainerEnum(EnumMeta):
 
     @classmethod
     def has_value(cls, value: Any) -> bool:
+        """Check if a value is in the Enum.
+
+        Parameters
+        ----------
+        value : Any
+            Value to check.
+
+        Returns
+        -------
+        bool
+            True if the value is in the Enum, False otherwise.
+        """
         return value in cls._value2member_map_
 
 

careamics/utils/path_utils.py

@@ -1,3 +1,5 @@
+"""Utility functions for paths."""
+
 from pathlib import Path
 from typing import Union
 

careamics/utils/ram.py

@@ -1,3 +1,5 @@
+"""Utility function to get RAM size."""
+
 import psutil
 
 

careamics/utils/receptive_field.py

@@ -1,102 +1,108 @@
 """Receptive field calculation for computing the tile overlap."""
 
+# TODO better docstring and function names
 # Adapted from: https://github.com/frgfm/torch-scan
 
-import math
-import warnings
-from typing import Tuple, Union
+# import math
+# import warnings
+# from typing import Tuple, Union
 
-from torch import Tensor, nn
-from torch.nn import Module
-from torch.nn.modules.batchnorm import _BatchNorm
-from torch.nn.modules.conv import _ConvNd, _ConvTransposeNd
-from torch.nn.modules.pooling import (
-    _AdaptiveAvgPoolNd,
-    _AdaptiveMaxPoolNd,
-    _AvgPoolNd,
-    _MaxPoolNd,
-)
+# from torch import Tensor, nn
+# from torch.nn import Module
+# from torch.nn.modules.batchnorm import _BatchNorm
+# from torch.nn.modules.conv import _ConvNd, _ConvTransposeNd
+# from torch.nn.modules.pooling import (
+#     _AdaptiveAvgPoolNd,
+#     _AdaptiveMaxPoolNd,
+#     _AvgPoolNd,
+#     _MaxPoolNd,
+# )
 
 
-def module_rf(module: Module, inp: Tensor, out: Tensor) -> Tuple[float, float, float]:
-    """Estimate the spatial receptive field of the module.
+# def module_rf(module: Module, inp: Tensor, out: Tensor) -> Tuple[float, float, float]:
+#     """Estimate the spatial receptive field of the module.
 
-    Args:
-        module (torch.nn.Module): PyTorch module
-        inp (torch.Tensor): input to the module
-        out (torch.Tensor): output of the module
-    Returns:
-        receptive field
-        effective stride
-        effective padding
-    """
-    if isinstance(
-        module,
-        (
-            nn.Identity,
-            nn.Flatten,
-            nn.ReLU,
-            nn.ELU,
-            nn.LeakyReLU,
-            nn.ReLU6,
-            nn.Tanh,
-            nn.Sigmoid,
-            _BatchNorm,
-            nn.Dropout,
-            nn.Linear,
-        ),
-    ):
-        return 1.0, 1.0, 0.0
-    elif isinstance(module, _ConvTransposeNd):
-        return rf_convtransposend(module, inp, out)
-    elif isinstance(module, (_ConvNd, _MaxPoolNd, _AvgPoolNd)):
-        return rf_aggregnd(module, inp, out)
-    elif isinstance(module, (_AdaptiveMaxPoolNd, _AdaptiveAvgPoolNd)):
-        return rf_adaptive_poolnd(module, inp, out)
-    else:
-        warnings.warn(
-            f"Module type not supported: {module.__class__.__name__}", stacklevel=1
-        )
-        return 1.0, 1.0, 0.0
+#     Parameters
+#     ----------
+#     module : Module
+#         Module to estimate the receptive field.
+#     inp : Tensor
+#         Input tensor.
+#     out : Tensor
+#         Output tensor.
 
+#     Returns
+#     -------
+#     Tuple[float, float, float]
+#         Receptive field, effective stride and padding.
+#     """
+#     if isinstance(
+#         module,
+#         (
+#             nn.Identity,
+#             nn.Flatten,
+#             nn.ReLU,
+#             nn.ELU,
+#             nn.LeakyReLU,
+#             nn.ReLU6,
+#             nn.Tanh,
+#             nn.Sigmoid,
+#             _BatchNorm,
+#             nn.Dropout,
+#             nn.Linear,
+#         ),
+#     ):
+#         return 1.0, 1.0, 0.0
+#     elif isinstance(module, _ConvTransposeNd):
+#         return rf_convtransposend(module, inp, out)
+#     elif isinstance(module, (_ConvNd, _MaxPoolNd, _AvgPoolNd)):
+#         return rf_aggregnd(module, inp, out)
+#     elif isinstance(module, (_AdaptiveMaxPoolNd, _AdaptiveAvgPoolNd)):
+#         return rf_adaptive_poolnd(module, inp, out)
+#     else:
+#         warnings.warn(
+#             f"Module type not supported: {module.__class__.__name__}", stacklevel=1
+#         )
+#         return 1.0, 1.0, 0.0
 
-def rf_convtransposend(
-    module: _ConvTransposeNd, _: Tensor, __: Tensor
-) -> Tuple[float, float, float]:
-    k = (
-        module.kernel_size[0]
-        if isinstance(module.kernel_size, tuple)
-        else module.kernel_size
-    )
-    s = module.stride[0] if isinstance(module.stride, tuple) else module.stride
-    return -k, 1.0 / s, 0.0
 
+# def rf_convtransposend(
+#     module: _ConvTransposeNd, _: Tensor, __: Tensor
+# ) -> Tuple[float, float, float]:
+#     k = (
+#         module.kernel_size[0]
+#         if isinstance(module.kernel_size, tuple)
+#         else module.kernel_size
+#     )
+#     s = module.stride[0] if isinstance(module.stride, tuple) else module.stride
+#     return -k, 1.0 / s, 0.0
 
-def rf_aggregnd(
-    module: Union[_ConvNd, _MaxPoolNd, _AvgPoolNd], _: Tensor, __: Tensor
-) -> Tuple[float, float, float]:
-    k = (
-        module.kernel_size[0]
-        if isinstance(module.kernel_size, tuple)
-        else module.kernel_size
-    )
-    if hasattr(module, "dilation"):
-        d = (
-            module.dilation[0]
-            if isinstance(module.dilation, tuple)
-            else module.dilation
-        )
-        k = d * (k - 1) + 1
-    s = module.stride[0] if isinstance(module.stride, tuple) else module.stride
-    p = module.padding[0] if isinstance(module.padding, tuple) else module.padding
-    return k, s, p  # type: ignore[return-value]
 
+# def rf_aggregnd(
+#     module: Union[_ConvNd, _MaxPoolNd, _AvgPoolNd], _: Tensor, __: Tensor
+# ) -> Tuple[float, float, float]:
+#     k = (
+#         module.kernel_size[0]
+#         if isinstance(module.kernel_size, tuple)
+#         else module.kernel_size
+#     )
+#     if hasattr(module, "dilation"):
+#         d = (
+#             module.dilation[0]
+#             if isinstance(module.dilation, tuple)
+#             else module.dilation
+#         )
+#         k = d * (k - 1) + 1
+#     s = module.stride[0] if isinstance(module.stride, tuple) else module.stride
+#     p = module.padding[0] if isinstance(module.padding, tuple) else module.padding
+#     return k, s, p  # type: ignore[return-value]
 
-def rf_adaptive_poolnd(
-    _: Union[_AdaptiveMaxPoolNd, _AdaptiveAvgPoolNd], inp: Tensor, out: Tensor
-) -> Tuple[int, int, float]:
-    stride = math.ceil(inp.shape[-1] / out.shape[-1])
-    kernel_size = stride
-    padding = (inp.shape[-1] - kernel_size * stride) / 2
 
-    return kernel_size, stride, padding
+# def rf_adaptive_poolnd(
+#     _: Union[_AdaptiveMaxPoolNd, _AdaptiveAvgPoolNd], inp: Tensor, out: Tensor
+# ) -> Tuple[int, int, float]:
+#     stride = math.ceil(inp.shape[-1] / out.shape[-1])
+#     kernel_size = stride
+#     padding = (inp.shape[-1] - kernel_size * stride) / 2
+
+#     return kernel_size, stride, padding

{careamics-0.1.0rc5.dist-info → careamics-0.1.0rc6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: careamics
-Version: 0.1.0rc5
+Version: 0.1.0rc6
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -14,6 +14,7 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Typing :: Typed
 Requires-Python: >=3.8
 Requires-Dist: bioimageio-core>=0.6.0

careamics-0.1.0rc6.dist-info/RECORD

@@ -0,0 +1,107 @@
+careamics/__init__.py,sha256=DkMGt4t9ua0gCgvZFEtb6eydvoxG976T0KUro8KnDNA,760
+careamics/careamist.py,sha256=vn-XiawERTTIKZqcfTg8leoVoLdBmHWIe9tkGrgkEGY,29719
+careamics/conftest.py,sha256=Od4WcaaP0UP-XUMrFr_oo4e6c2hi_RvNbuaRTopwlmI,911
+careamics/lightning_datamodule.py,sha256=TBKTpVfOvgsQg_8gwU68Au-aw_OXfUSsah7snXef43Y,32685
+careamics/lightning_module.py,sha256=MSUxZfkhM1-D5AEZrkuNazOBbZCgbxCuuGtgYjhLEHU,10313
+careamics/lightning_prediction_datamodule.py,sha256=4aTyMSbHiy1ebp6WSfDMDoYCJJU4qf4T5ShAjRNn_yM,15057
+careamics/lightning_prediction_loop.py,sha256=qDfRVXPiCVyRz-P3l9tmlCfMT8mx9waKNfNrIMrjt3w,4599
+careamics/py.typed,sha256=esB4cHc6c07uVkGtqf8at7ttEnprwRxwk8obY8Qumq4,187
+careamics/callbacks/__init__.py,sha256=spxJlDByD-6QtMl9vcIty8Wb0tyHaSTKTItozHenI44,204
+careamics/callbacks/hyperparameters_callback.py,sha256=ODJpwwdgc1-Py8yEUpXLar8_IOAcfR7lF3--6LfSiGc,1496
+careamics/callbacks/progress_bar_callback.py,sha256=8HvNSWZldixd6pjz0dLDo0apIbzTovv5smKmZ6tZQ8U,2444
+careamics/config/__init__.py,sha256=SP1oJKhK3VDN9ABwnpfR3H02qRprzymjRfNYeC7kHEo,1019
+careamics/config/algorithm_model.py,sha256=2y4SWagzIyZH_WWYeZWLF-4SGcBk-g04QwKdSzmYTiM,5771
+careamics/config/callback_model.py,sha256=CcamVhgRsVdskCe_9EtyWi1YbrNX5vKEplc97AYz1h8,3118
+careamics/config/configuration_example.py,sha256=vxXYGB05cOqQwGGBuPN4kQ3uQJxRwzyFq5Tflk5HNvc,2575
+careamics/config/configuration_factory.py,sha256=cnv6Qod5Wx1J0h951wgbayMO1KVUWxK0OmAIvscPzm8,21286
+careamics/config/configuration_model.py,sha256=j7QryeMNQAsD_0byb81u99Oek2uyj3Syr0nUepFYTe8,18494
+careamics/config/data_model.py,sha256=58cS8a1Tk4ZXMf8z4QA7NtJKi_EwlfGTsB0e59q9hhE,12741
+careamics/config/inference_model.py,sha256=gbLV4B_7VRAc0QCa8r2EYk-YOdGuGswJIQGDFkj7XUM,5936
+careamics/config/optimizer_models.py,sha256=eWCyH9rMTUl82ubqrHFHssQwVyTYNh9lRpVQGv96ppM,5336
+careamics/config/tile_information.py,sha256=-k9hcJrL-QBp9n0Nf5qufEMcudnNNe8pWY37NtlWLxs,3009
+careamics/config/training_model.py,sha256=oghv91J7xIdI69wpNJGmLUAwgM9l3VhMsbsOo4USqkU,1559
+careamics/config/architectures/__init__.py,sha256=CdnViydyTdQixus3uWHBIgbgxmu9t1_ADehqpjN_57U,444
+careamics/config/architectures/architecture_model.py,sha256=545hlbOZU9EJNGTcSpy7eXpfzCtvIm28dDJGMo36AfQ,886
+careamics/config/architectures/custom_model.py,sha256=MxsFK4cvwjt59_-ZWeIFrlExQ9PpR5X0s9SqxN_B4YQ,4598
+careamics/config/architectures/register_model.py,sha256=lHH0aUPmXtI3Bq_76zkhg07_Yb_nOJZkZJLCC_G-rZM,2434
+careamics/config/architectures/unet_model.py,sha256=sQjfqTjh1kTNi369U3_94jroU6LyLlflaIe8FwdHQvo,2892
+careamics/config/architectures/vae_model.py,sha256=Z0satmte4udManh_bxtl93ZmQlmo6JFE1NQIuZkTsQk,926
+careamics/config/references/__init__.py,sha256=rZAQzmrciX5cNICcXaBH6sbE6N6L7_qYQUkasNy9y-c,763
+careamics/config/references/algorithm_descriptions.py,sha256=wR3hIoeg5eiUEPbwTxMpQYLTKQyRl_5naSDbBZOZESU,3541
+careamics/config/references/references.py,sha256=AXx08FJQxHb7SYOluCr_eQn_mbOris5dXqhKrCnhBTE,1573
+careamics/config/support/__init__.py,sha256=pKqk76kyBraiSC1SQos-cyiQwsfOLLkLuWj6Hw60LZ4,1041
+careamics/config/support/supported_activations.py,sha256=O27_dGDgw2P-DslKJsXGVAyS2NUQM6Ta4jeo2uTQlW0,519
+careamics/config/support/supported_algorithms.py,sha256=GCkauFDlmb2hJwFSdoIpGmpLjPeYFHOGy2NweKdw8T4,358
+careamics/config/support/supported_architectures.py,sha256=LLD6hyje9Q0BcvA7p2E8WW_cY5yEgMI_NAP4HBi27UU,540
+careamics/config/support/supported_data.py,sha256=C0VcP1DkZqJ4MPn6UZcCZX8ZfVNdz0ZJk6y89fiim2I,2084
+careamics/config/support/supported_loggers.py,sha256=ubSOkGoYabGbm_jmyc1R3eFcvcP-sHmuyiBi_d3_wLg,197
+careamics/config/support/supported_losses.py,sha256=TPsMCuDdgb64TRyDwonnwHb1R-rkn3OzhtHimyVtrOY,540
+careamics/config/support/supported_optimizers.py,sha256=xxbJsyohJTlHeUz2I4eRwcE3BeACs-6PH8cpX6w2wX8,1394
+careamics/config/support/supported_pixel_manipulations.py,sha256=rFiktUlvoFU7s1NAKEMqsXOzLw5eaw9GtCKUznvq6xc,432
+careamics/config/support/supported_struct_axis.py,sha256=alZMA5Y-BpDymLPUEd1zqVY0xMkgl9Rv1d4ujED6sco,424
+careamics/config/support/supported_transforms.py,sha256=ylTiS8fUFKFwfn85gh7kKF4Trb9Q4ENPKm-XDWCe-SY,311
+careamics/config/transformations/__init__.py,sha256=oqwBAL2XXbPRZZ5iOzNqalX6SyJ1M-S0lkfbDGZOzyE,378
+careamics/config/transformations/n2v_manipulate_model.py,sha256=UTyfpm1mmMvYg_HoMzXilZhJGx_muiV-lLQ4UThCFJ0,1854
+careamics/config/transformations/normalize_model.py,sha256=fua-JAcfNdTuikERreaR_0mz9ExsYSDJ7mUgIDl-U0M,804
+careamics/config/transformations/transform_model.py,sha256=i7KAtSv4nah2H7uyJFKqg7RdKF68OHIPMNNvDo0HxGY,1000
+careamics/config/transformations/xy_flip_model.py,sha256=zU-uZ1b1zNZWckbho3onN-B7BHKhN7jbgbNZyRQhv2s,1025
+careamics/config/transformations/xy_random_rotate90_model.py,sha256=6sYKmtCLvz0SV1qZgBSHUTH-CUjwvHnohq1HyPntbyE,894
+careamics/config/validators/__init__.py,sha256=iv0nVI0W7j9DxFPwh0DjRCzM9P8oLQn4Gwi5rfuFrrI,180
+careamics/config/validators/validator_utils.py,sha256=H11pttfXFdnlUw9FFIgPWy3sxO1ks38dtmYAS6Kl9-c,2624
+careamics/dataset/__init__.py,sha256=cUcqy1Nxa5WhDQim6948r3i1kGQ-HijUqAACyyM7cuU,174
+careamics/dataset/in_memory_dataset.py,sha256=WcVfE7sdqac07dzmb4Wz2yML6t-0PmQaIfmvyv6uQQE,12567
+careamics/dataset/iterable_dataset.py,sha256=aJKL3F6SesOy-WTRXarYDJjGh7RlxqmYDrYAv09J4I0,15070
+careamics/dataset/zarr_dataset.py,sha256=lojnK5bhiF1vyjuPtWXBrZ9sy5fT_rBvZJbbbnE-H_I,5665
+careamics/dataset/dataset_utils/__init__.py,sha256=5U_kavgh_QEvTiDuM-O4hsqmDOKh6_y6iDvZPE8Jtsc,446
+careamics/dataset/dataset_utils/dataset_utils.py,sha256=zYNglet5lYKxIhTeOGG2K24oujC-m5zyYlwJcQcleVA,2662
+careamics/dataset/dataset_utils/file_utils.py,sha256=hOCDYlVcoBCFR3B9Eh5nTYSiTW0wskAecUfykB1Mj_I,4047
+careamics/dataset/dataset_utils/read_tiff.py,sha256=nbSAU11Tv-jViFHRAtrG8pGH09CG3IIdF2WF6duAxxQ,1729
+careamics/dataset/dataset_utils/read_utils.py,sha256=0nsfzHq3zr9kjm2qZZrMRKI5LC5MiRSH35xPBCYyBrQ,579
+careamics/dataset/dataset_utils/read_zarr.py,sha256=2jzREAnJDQSv0qmsL-v00BxmiZ_sp0ijq667LZSQ_hY,1685
+careamics/dataset/patching/__init__.py,sha256=7-s12oUAZNlMOwSkxSwbD7vojQINWYFzn_4qIJ87WBg,37
+careamics/dataset/patching/patching.py,sha256=vS7wQ1JdSNsFlqJi41Y_NupFIez2BXOO86r0UY1gDJA,7535
+careamics/dataset/patching/random_patching.py,sha256=B1POeDApLyvcRRBpg0loLsOoUGWVkMojEzt4xD_WiaQ,6281
+careamics/dataset/patching/sequential_patching.py,sha256=_l3Q2uYIhjMJMaxDdSbHC9_2kRF9eLz-Xs3r9i7j3Nc,5903
+careamics/dataset/patching/tiled_patching.py,sha256=_IUl5zcBM-BMcRfQajDOQ7RIXmqympM3O75jRHqRi0M,5888
+careamics/dataset/patching/validate_patch_dimension.py,sha256=Y7SWajYWtU7pdZpAI3t_H3Mxw5GMjd9hPpdRygORwK8,2036
+careamics/losses/__init__.py,sha256=kVEwfZ2xXfd8x0n-VHGKm6qvzbto5pIIJYP_jN-bCtw,89
+careamics/losses/loss_factory.py,sha256=vaMlxH5oescWTKlK1adWwbeD9tW4Ti-p7qKmc1iHCi0,1005
+careamics/losses/losses.py,sha256=DKwHZ9ifVe6wMd3tBOiswLC-saU1bj1RCcXGOkREmKU,2328
+careamics/model_io/__init__.py,sha256=HITzjiuZQwo-rQ2_Ma3bz9l7PDANv1_S489E-tffV9s,155
+careamics/model_io/bmz_io.py,sha256=MGZklRek3WI8VqV0gt63hL-APDsMkYbDGdqkih_iWAY,7031
+careamics/model_io/model_io_utils.py,sha256=x5u1HszZgRfvuku4eKQhmInyxRaEzkgNqAhGSyLS6e4,2116
+careamics/model_io/bioimage/__init__.py,sha256=r94nu8WDAvj0Fbu4C-iJXdOhfSQXeZBvN3UKsLG0RNI,298
+careamics/model_io/bioimage/_readme_factory.py,sha256=LZAuEiWNBTPaD8KrLPMq16yJuOPKDZiGQuTMHKLvoT4,3514
+careamics/model_io/bioimage/bioimage_utils.py,sha256=nlW0J1daYyLbL6yVN3QSn3HhA2joMjIG-thK64lpVTY,1085
+careamics/model_io/bioimage/model_description.py,sha256=wXGJBzGGSwEds-V0G4mgPvoi4dDXNn_7Tp6iPCsAeTY,9208
+careamics/models/__init__.py,sha256=Wty5hwQb_As33pQOZqY5j-DpDOdh5ArBH4BhQDSuXTQ,133
+careamics/models/activation.py,sha256=xdqz4-yKV7oElG_dDrYuibS8HOiYvKdV_r9FwWPvaDE,977
+careamics/models/layers.py,sha256=oWzpq8OdHFEJqPWC9X8IRPNe0XqAnesSqwoT6V3t1Mw,13712
+careamics/models/model_factory.py,sha256=5YRwRRUemxb-pTRL3VWn8N61tCGyhrurqPgcFaNETb0,1360
+careamics/models/unet.py,sha256=3pXpiCIw7WUaDV0Jmczkxi99C5-Zu3NpQpWxgRkeGL8,14321
+careamics/prediction/__init__.py,sha256=-Bfc7UqPSqpGx0NGvHMkE-bHOkZYMn7EaxQ9tO6A3uU,118
+careamics/prediction/stitch_prediction.py,sha256=lC9qdcR4BTNezCxoTeombg6k8mmTmN45TZSbEHg13Mk,2163
+careamics/transforms/__init__.py,sha256=VIHIsC8sMAh1TCm67ifB816Zp-LRo6rAONPuT2Qs3bs,483
+careamics/transforms/compose.py,sha256=mTkhoxvgvsBqNoz9RWpJ_tqsDl1CDp0-UARTjUuBRf4,3477
+careamics/transforms/n2v_manipulate.py,sha256=6O0RmL6zgBvZgbga6yyu1FwrxPlWXuviDoHzyxQQXfY,5404
+careamics/transforms/normalize.py,sha256=Ts1gOuzWYPmjAlMf4OgN3y6bHVgvBaq91GdkKGWpTy4,4237
+careamics/transforms/pixel_manipulation.py,sha256=qjTfgk86VkwVVu69E0sXQEfASi170IlzxorpAPmYOe0,12657
+careamics/transforms/struct_mask_parameters.py,sha256=jE29Li9sx3olaRnqYfJsSlKi2t0WQzJmCm9aCbIQEsA,421
+careamics/transforms/transform.py,sha256=cEqc4ci8na70i-HIGYC7udRfVa8D_8OjdRVrr3txLvQ,464
+careamics/transforms/tta.py,sha256=6H0E0yxmZT_TEslenOIXqlEM-l_0oCtIk59gAGP0byM,1960
+careamics/transforms/xy_flip.py,sha256=Q1kKTa2kE3W1P3dlpT4GAVSSHM3TebnrvIyWh75Fnko,3443
+careamics/transforms/xy_random_rotate90.py,sha256=zWdBROLLjgxTMSQEQesJr17j84BmZhKWCMVVONHU8mw,2781
+careamics/utils/__init__.py,sha256=tO1X5QTfnthepuW0uYagz5fWehtLtwK2gPmkUeqhdOw,334
+careamics/utils/base_enum.py,sha256=bz1D8mDx5V5hdnJ3WAzJXWHJTbgwAky5FprUt9F5cMA,1387
+careamics/utils/context.py,sha256=Ljf70OR1FcYpsVpxb5Sr2fzmPVIZgDS1uZob_3BcELg,1409
+careamics/utils/logging.py,sha256=coIscjkDYpqcsGnsONuYOdIYd6_gHxdnYIZ-e9Y2Ybg,10322
+careamics/utils/metrics.py,sha256=9YQe5Aj2Pv2h9jnRFeRbDQ_3qXAW0QHpucSqiUtwDcA,2382
+careamics/utils/path_utils.py,sha256=8AugiG5DOmzgSnTCJI8vypXaPE0XhnR-9pzeiFUZ-0I,554
+careamics/utils/ram.py,sha256=mhZVA_DsIlXMvABSxot4eBBxbvWx7JzfijC_cVBtF1s,239
+careamics/utils/receptive_field.py,sha256=Y2h4c8S6glX3qcx5KHDmO17Kkuyey9voxfoXyqcAfiM,3296
+careamics/utils/running_stats.py,sha256=GIPMPuH9EOUKD_cYBkJFPggXRKnQEiOXx68Pq9UCCVI,1384
+careamics/utils/torch_utils.py,sha256=g1zxdlM7_BA7mMLcCzmrxZX4LmH__KXlJibC95muVaA,3014
+careamics-0.1.0rc6.dist-info/METADATA,sha256=o_1ZDxRYCTLnSruXdXEHT8Y3qNiBW-fShITOyT_wO3E,3464
+careamics-0.1.0rc6.dist-info/WHEEL,sha256=zEMcRr9Kr03x1ozGwg5v9NQBKn3kndp6LSoSlVg-jhU,87
+careamics-0.1.0rc6.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
+careamics-0.1.0rc6.dist-info/RECORD,,

careamics/config/noise_models.py

@@ -1,162 +0,0 @@
-from __future__ import annotations
-
-from enum import Enum
-from typing import Dict, Union
-
-from pydantic import BaseModel, ConfigDict, Field, field_validator
-
-
-class NoiseModelType(str, Enum):
-    """
-    Available noise models.
-
-    Currently supported noise models:
-
-        - hist: Histogram noise model.
-        - gmm: Gaussian mixture model noise model.F
-    """
-
-    NONE = "none"
-    HIST = "hist"
-    GMM = "gmm"
-
-    # TODO add validator decorator
-    @classmethod
-    def validate_noise_model_type(
-        cls, noise_model: Union[str, NoiseModel], parameters: dict
-    ) -> None:
-        """_summary_.
-
-        Parameters
-        ----------
-        noise_model : Union[str, NoiseModel]
-            _description_
-        parameters : dict
-            _description_
-
-        Returns
-        -------
-        BaseModel
-            _description_
-        """
-        if noise_model == NoiseModelType.HIST.value:
-            HistogramNoiseModel(**parameters)
-            return HistogramNoiseModel().model_dump() if not parameters else parameters
-
-        elif noise_model == NoiseModelType.GMM.value:
-            GaussianMixtureNoiseModel(**parameters)
-            return (
-                GaussianMixtureNoiseModel().model_dump()
-                if not parameters
-                else parameters
-            )
-
-
-class NoiseModel(BaseModel):
-    """_summary_.
-
-    Parameters
-    ----------
-    BaseModel : _type_
-        _description_
-
-    Returns
-    -------
-    _type_
-        _description_
-
-    Raises
-    ------
-    ValueError
-        _description_
-    """
-
-    model_config = ConfigDict(
-        use_enum_values=True,
-        protected_namespaces=(),  # allows to use model_* as a field name
-        validate_assignment=True,
-    )
-
-    model_type: NoiseModelType
-    parameters: Dict = Field(default_factory=dict, validate_default=True)
-
-    @field_validator("parameters")
-    @classmethod
-    def validate_parameters(cls, data, values) -> Dict:
-        """_summary_.
-
-        Parameters
-        ----------
-        parameters : Dict
-            _description_
-
-        Returns
-        -------
-        Dict
-            _description_
-        """
-        if values.data["model_type"] not in [NoiseModelType.GMM, NoiseModelType.HIST]:
-            raise ValueError(
-                f"Incorrect noise model {values.data['model_type']}."
-                f"Please refer to the documentation"  # TODO add link to documentation
-            )
-
-        parameters = NoiseModelType.validate_noise_model_type(
-            values.data["model_type"], data
-        )
-        return parameters
-
-
-class HistogramNoiseModel(BaseModel):
-    """
-    Histogram noise model.
-
-    Attributes
-    ----------
-    min_value : float
-        Minimum value in the input.
-    max_value : float
-        Maximum value in the input.
-    bins : int
-        Number of bins of the histogram.
-    """
-
-    min_value: float = Field(default=350.0, ge=0.0, le=65535.0)
-    max_value: float = Field(default=6500.0, ge=0.0, le=65535.0)
-    bins: int = Field(default=256, ge=1)
-
-
-class GaussianMixtureNoiseModel(BaseModel):
-    """
-    Gaussian mixture model noise model.
-
-    Attributes
-    ----------
-    min_signal : float
-    Minimum signal intensity expected in the image.
-    max_signal : float
-    Maximum signal intensity expected in the image.
-    weight : array
-    A [3*n_gaussian, n_coeff] sized array containing the values of the weights
-    describing the noise model.
-    Each gaussian contributes three parameters (mean, standard deviation and weight),
-    hence the number of rows in `weight` are 3*n_gaussian.
-    If `weight = None`, the weight array is initialized using the `min_signal` and
-    `max_signal` parameters.
-    n_gaussian: int
-    Number of gaussians.
-    n_coeff: int
-    Number of coefficients to describe the functional relationship between gaussian
-    parameters and the signal.
-    2 implies a linear relationship, 3 implies a quadratic relationship and so on.
-    device: device
-    GPU device.
-    min_sigma: int
-    """
-
-    num_components: int = Field(default=3, ge=1)
-    min_value: float = Field(default=350.0, ge=0.0, le=65535.0)
-    max_value: float = Field(default=6500.0, ge=0.0, le=65535.0)
-    n_gaussian: int = Field(default=3, ge=1)
-    n_coeff: int = Field(default=2, ge=1)
-    min_sigma: int = Field(default=50, ge=1)

careamics/config/support/supported_extraction_strategies.py

@@ -1,25 +0,0 @@
-"""
-Extraction strategy module.
-
-This module defines the various extraction strategies available in CAREamics.
-"""
-
-from careamics.utils import BaseEnum
-
-
-class SupportedExtractionStrategy(str, BaseEnum):
-    """
-    Available extraction strategies.
-
-    Currently supported:
-        - random: random extraction.
-        # TODO
-        - sequential: grid extraction, can miss edge values.
-        - tiled: tiled extraction, covers the whole image.
-    """
-
-    RANDOM = "random"
-    RANDOM_ZARR = "random_zarr"
-    SEQUENTIAL = "sequential"
-    TILED = "tiled"
-    NONE = "none"

careamics/config/transformations/nd_flip_model.py

@@ -1,27 +0,0 @@
-"""Pydantic model for the NDFlip transform."""
-
-from typing import Literal, Optional
-
-from pydantic import ConfigDict
-
-from .transform_model import TransformModel
-
-
-class NDFlipModel(TransformModel):
-    """
-    Pydantic model used to represent NDFlip transformation.
-
-    Attributes
-    ----------
-    name : Literal["NDFlip"]
-        Name of the transformation.
-    seed : Optional[int]
-        Seed for the random number generator.
-    """
-
-    model_config = ConfigDict(
-        validate_assignment=True,
-    )
-
-    name: Literal["NDFlip"] = "NDFlip"
-    seed: Optional[int] = None