careamics 0.0.3__py3-none-any.whl → 0.0.4.1__py3-none-any.whl

careamics/utils/metrics.py

@@ -4,88 +4,98 @@ Metrics submodule.
 This module contains various metrics and a metrics tracking class.
 """
 
-from typing import Optional, Union
+from typing import Callable, Optional, Union
 
 import numpy as np
 import torch
-from skimage.metrics import peak_signal_noise_ratio
+from skimage.metrics import peak_signal_noise_ratio, structural_similarity
+from torchmetrics.image import MultiScaleStructuralSimilarityIndexMeasure
 
+# TODO: does this add additional dependency?
 
-def psnr(gt: np.ndarray, pred: np.ndarray, range: float = 255.0) -> float:
+
+def psnr(gt: np.ndarray, pred: np.ndarray, data_range: float) -> float:
     """
     Peak Signal to Noise Ratio.
 
     This method calls skimage.metrics.peak_signal_noise_ratio. See:
     https://scikit-image.org/docs/dev/api/skimage.metrics.html.
 
+    NOTE: to avoid unwanted behaviors (e.g., data_range inferred from array dtype),
+    the data_range parameter is mandatory.
+
     Parameters
     ----------
-    gt : NumPy array
-        Ground truth image.
-    pred : NumPy array
-        Predicted image.
-    range : float, optional
-        The images pixel range, by default 255.0.
+    gt : np.ndarray
+        Ground truth array.
+    pred : np.ndarray
+        Predicted array.
+    data_range : float
+        The images pixel range.
 
     Returns
     -------
     float
         PSNR value.
     """
-    return peak_signal_noise_ratio(gt, pred, data_range=range)
+    return peak_signal_noise_ratio(gt, pred, data_range=data_range)
 
 
-def _zero_mean(x: np.ndarray) -> np.ndarray:
+def _zero_mean(x: Union[np.ndarray, torch.Tensor]) -> Union[np.ndarray, torch.Tensor]:
     """
     Zero the mean of an array.
 
     Parameters
     ----------
-    x : NumPy array
+    x : numpy.ndarray or torch.Tensor
         Input array.
 
     Returns
     -------
-    NumPy array
+    numpy.ndarray or torch.Tensor
         Zero-mean array.
     """
-    return x - np.mean(x)
+    return x - x.mean()
 
 
-def _fix_range(gt: np.ndarray, x: np.ndarray) -> np.ndarray:
+def _fix_range(
+    gt: Union[np.ndarray, torch.Tensor], x: Union[np.ndarray, torch.Tensor]
+) -> Union[np.ndarray, torch.Tensor]:
     """
     Adjust the range of an array based on a reference ground-truth array.
 
     Parameters
     ----------
-    gt : np.ndarray
-        Ground truth image.
-    x : np.ndarray
+    gt : Union[np.ndarray, torch.Tensor]
+        Ground truth array.
+    x : Union[np.ndarray, torch.Tensor]
         Input array.
 
     Returns
     -------
-    np.ndarray
+    Union[np.ndarray, torch.Tensor]
         Range-adjusted array.
     """
-    a = np.sum(gt * x) / (np.sum(x * x))
+    a = (gt * x).sum() / (x * x).sum()
     return x * a
 
 
-def _fix(gt: np.ndarray, x: np.ndarray) -> np.ndarray:
+def _fix(
+    gt: Union[np.ndarray, torch.Tensor], x: Union[np.ndarray, torch.Tensor]
+) -> Union[np.ndarray, torch.Tensor]:
     """
     Zero mean a groud truth array and adjust the range of the array.
 
     Parameters
     ----------
-    gt : np.ndarray
+    gt : Union[np.ndarray, torch.Tensor]
         Ground truth image.
-    x : np.ndarray
+    x : Union[np.ndarray, torch.Tensor]
         Input array.
 
     Returns
     -------
-    np.ndarray
+    Union[np.ndarray, torch.Tensor]
         Zero-mean and range-adjusted array.
     """
     gt_ = _zero_mean(gt)
@@ -186,3 +196,173 @@ class RunningPSNR:
             return None
         rmse = torch.sqrt(self.mse_sum / self.N)
         return 20 * torch.log10((self.max - self.min) / rmse)
+
+
+def _range_invariant_multiscale_ssim(
+    gt_: Union[np.ndarray, torch.Tensor], pred_: Union[np.ndarray, torch.Tensor]
+) -> float:
+    """Compute range invariant multiscale SSIM for a single channel.
+
+    The advantage of this metric in comparison to commonly used SSIM is that
+    it is invariant to scalar multiplications in the prediction.
+    # TODO: Add reference to the paper.
+
+    NOTE: images fed to this function should have channels dimension as the last one.
+
+    Parameters
+    ----------
+    gt_ : Union[np.ndarray, torch.Tensor]
+        Ground truth image with shape (N, H, W).
+    pred_ : Union[np.ndarray, torch.Tensor]
+        Predicted image with shape (N, H, W).
+
+    Returns
+    -------
+    float
+        Range invariant multiscale SSIM value.
+    """
+    shape = gt_.shape
+    gt_ = torch.Tensor(gt_.reshape((shape[0], -1)))
+    pred_ = torch.Tensor(pred_.reshape((shape[0], -1)))
+    gt_ = _zero_mean(gt_)
+    pred_ = _zero_mean(pred_)
+    pred_ = _fix(gt_, pred_)
+    pred_ = pred_.reshape(shape)
+    gt_ = gt_.reshape(shape)
+
+    ms_ssim = MultiScaleStructuralSimilarityIndexMeasure(
+        data_range=gt_.max() - gt_.min()
+    )
+    return ms_ssim(torch.Tensor(pred_[:, None]), torch.Tensor(gt_[:, None])).item()
+
+
+def multiscale_ssim(
+    gt_: Union[np.ndarray, torch.Tensor],
+    pred_: Union[np.ndarray, torch.Tensor],
+    range_invariant: bool = True,
+) -> list[Union[float, None]]:
+    """Compute channel-wise multiscale SSIM for each channel.
+
+    It allows to use either standard multiscale SSIM or its range-invariant version.
+
+    NOTE: images fed to this function should have channels dimension as the last one.
+    # TODO: do we want to allow this behavior? or we want the usual (N, C, H, W)?
+
+    Parameters
+    ----------
+    gt_ : Union[np.ndarray, torch.Tensor]
+        Ground truth image with shape (N, H, W, C).
+    pred_ : Union[np.ndarray, torch.Tensor]
+        Predicted image with shape (N, H, W, C).
+    range_invariant : bool
+        Whether to use standard or range invariant multiscale SSIM.
+
+    Returns
+    -------
+    list[float]
+        List of SSIM values for each channel.
+    """
+    ms_ssim_values = {}
+    for ch_idx in range(gt_.shape[-1]):
+        tar_tmp = gt_[..., ch_idx]
+        pred_tmp = pred_[..., ch_idx]
+        if range_invariant:
+            ms_ssim_values[ch_idx] = _range_invariant_multiscale_ssim(
+                gt_=tar_tmp, pred_=pred_tmp
+            )
+        else:
+            ms_ssim = MultiScaleStructuralSimilarityIndexMeasure(
+                data_range=tar_tmp.max() - tar_tmp.min()
+            )
+            ms_ssim_values[ch_idx] = ms_ssim(
+                torch.Tensor(pred_tmp[:, None]), torch.Tensor(tar_tmp[:, None])
+            ).item()
+
+    return [ms_ssim_values[i] for i in range(gt_.shape[-1])]  # type: ignore
+
+
+def _avg_psnr(target: np.ndarray, prediction: np.ndarray, psnr_fn: Callable) -> float:
+    """Compute the average PSNR over a batch of images.
+
+    Parameters
+    ----------
+    target : np.ndarray
+        Array of ground truth images, shape is (N, C, H, W).
+    prediction : np.ndarray
+        Array of predicted images, shape is (N, C, H, W).
+    psnr_fn : Callable
+        PSNR function to use.
+
+    Returns
+    -------
+    float
+        Average PSNR value over the batch.
+    """
+    return np.mean(
+        [
+            psnr_fn(target[i : i + 1], prediction[i : i + 1]).item()
+            for i in range(len(prediction))
+        ]
+    )
+
+
+def avg_range_inv_psnr(target: np.ndarray, prediction: np.ndarray) -> float:
+    """Compute the average range-invariant PSNR over a batch of images.
+
+    Parameters
+    ----------
+    target : np.ndarray
+        Array of ground truth images, shape is (N, C, H, W).
+    prediction : np.ndarray
+        Array of predicted images, shape is (N, C, H, W).
+
+    Returns
+    -------
+    float
+        Average range-invariant PSNR value over the batch.
+    """
+    return _avg_psnr(target, prediction, scale_invariant_psnr)
+
+
+def avg_psnr(target: np.ndarray, prediction: np.ndarray) -> float:
+    """Compute the average PSNR over a batch of images.
+
+    Parameters
+    ----------
+    target : np.ndarray
+        Array of ground truth images, shape is (N, C, H, W).
+    prediction : np.ndarray
+        Array of predicted images, shape is (N, C, H, W).
+
+    Returns
+    -------
+    float
+        Average PSNR value over the batch.
+    """
+    return _avg_psnr(target, prediction, psnr)
+
+
+def avg_ssim(
+    target: Union[np.ndarray, torch.Tensor], prediction: Union[np.ndarray, torch.Tensor]
+) -> tuple[float, float]:
+    """Compute the average Structural Similarity (SSIM) over a batch of images.
+
+    Parameters
+    ----------
+    target : np.ndarray
+        Array of ground truth images, shape is (N, C, H, W).
+    prediction : np.ndarray
+        Array of predicted images, shape is (N, C, H, W).
+
+    Returns
+    -------
+    tuple[float, float]
+        Mean and standard deviation of SSIM values over the batch.
+    """
+    ssim = [
+        structural_similarity(
+            target[i], prediction[i], data_range=(target[i].max() - target[i].min())
+        )
+        for i in range(len(target))
+    ]
+    return np.mean(ssim), np.std(ssim)

careamics/utils/serializers.py

@@ -0,0 +1,60 @@
+"""A script for serializers in the careamics package."""
+
+import ast
+import json
+from typing import Union
+
+import numpy as np
+import torch
+
+
+def _array_to_json(arr: Union[np.ndarray, torch.Tensor]) -> str:
+    """Convert an array to a list and then to a JSON string.
+
+    Parameters
+    ----------
+    arr : Union[np.ndarray, torch.Tensor]
+        Array to be serialized.
+
+    Returns
+    -------
+    str
+        JSON string representing the array.
+    """
+    return json.dumps(arr.tolist())
+
+
+def _to_numpy(lst: Union[str, list]) -> np.ndarray:
+    """Deserialize a list or string representing a list into `np.ndarray`.
+
+    Parameters
+    ----------
+    lst : list
+        List or string representing a list with the array content to be deserialized.
+
+    Returns
+    -------
+    np.ndarray
+        The deserialized array.
+    """
+    if isinstance(lst, str):
+        lst = ast.literal_eval(lst)
+    return np.asarray(lst)
+
+
+def _to_torch(lst: Union[str, list]) -> torch.Tensor:
+    """Deserialize list or string representing a list into `torch.Tensor`.
+
+    Parameters
+    ----------
+    lst : Union[str, list]
+        List or string representing a list swith the array content to be deserialized.
+
+    Returns
+    -------
+    torch.Tensor
+        The deserialized tensor.
+    """
+    if isinstance(lst, str):
+        lst = ast.literal_eval(lst)
+    return torch.tensor(lst)

{careamics-0.0.3.dist-info → careamics-0.0.4.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: careamics
-Version: 0.0.3
+Version: 0.0.4.1
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
@@ -16,16 +16,17 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Typing :: Typed
 Requires-Python: >=3.9
-Requires-Dist: bioimageio-core>=0.6.0
+Requires-Dist: bioimageio-core>=0.6.9
 Requires-Dist: numpy<2.0.0
 Requires-Dist: psutil
-Requires-Dist: pydantic>=2.5
+Requires-Dist: pydantic<2.9,>=2.5
 Requires-Dist: pytorch-lightning>=2.2.0
 Requires-Dist: pyyaml
 Requires-Dist: scikit-image<=0.23.2
 Requires-Dist: tifffile
 Requires-Dist: torch>=2.0.0
 Requires-Dist: torchvision
+Requires-Dist: typer==0.12.3
 Requires-Dist: zarr<3.0.0
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == 'dev'

{careamics-0.0.3.dist-info → careamics-0.0.4.1.dist-info}/RECORD

@@ -1,24 +1,27 @@
 careamics/__init__.py,sha256=xBCerWN66hv3T7dRGiUYLflmbJtJt1HqbSg9JCWp8pY,391
-careamics/careamist.py,sha256=wZxIf5E2Sebbcsd1IbTi6-VrPkI71M-kI9-bFHGmh-M,27867
+careamics/careamist.py,sha256=eZttleBmhu649kkVj7spfBw7DLUuGjx58S2fTPem7g4,28351
 careamics/conftest.py,sha256=Od4WcaaP0UP-XUMrFr_oo4e6c2hi_RvNbuaRTopwlmI,911
 careamics/py.typed,sha256=esB4cHc6c07uVkGtqf8at7ttEnprwRxwk8obY8Qumq4,187
+careamics/cli/__init__.py,sha256=LbM9bVtU1dy-khmdiIDXwvKy2v8wPBCEUuWqV_8rosA,106
+careamics/cli/conf.py,sha256=1MRSzKcIL--IbYiNixW2aA58GC0ptQHWbBtp7b5eRwQ,13370
+careamics/cli/main.py,sha256=EAWBQoCxcNv-4t3h8_YLCXNjWWU08cOzFj5DYam5e6g,3441
 careamics/config/__init__.py,sha256=M_Y0sGIVr1lQF4IpDeVkWkspbUNlbdH-iDjapMSGOoc,1127
 careamics/config/callback_model.py,sha256=EeYHqpMIPQwyNxLRzzX32Uncl5mZuB1bJO76RHpNymg,4555
-careamics/config/configuration_factory.py,sha256=TcB15HD81P-e-A2w8EfCdJLoYw3537tQ6NAAwKrSU6g,18799
-careamics/config/configuration_model.py,sha256=efUHSlYonO_m6eUPQLRb4NlsTADCL5lGCrwXlOGIHFU,18893
-careamics/config/data_model.py,sha256=zcVx8wN8IW-hMLXZ2jB7AWSQ1C2gSt87UtkoEtsClJA,15776
-careamics/config/fcn_algorithm_model.py,sha256=rwABUX1XwMMenv5Ff4z-ZTneFIhW_qIjMAbb57RV150,5082
+careamics/config/configuration_factory.py,sha256=vHwRuYasELdZQv0KpX3fxPPUBbJfguBOOtPgqQJ3oks,30193
+careamics/config/configuration_model.py,sha256=pvANQOkWpA-bB60bzI40z_tTnk1zt1l8pfXg7KsDsRs,18843
+careamics/config/data_model.py,sha256=MOXnX6dmI-08b4H_43xOrnSlwdbCtO1UuI9YqOT8djA,15370
+careamics/config/fcn_algorithm_model.py,sha256=eBBjkoyavhvDJFTrjJDkNrWSP_-YaK0cy7qo0lCdBQ0,5105
 careamics/config/inference_model.py,sha256=UE_-ZmCX6LFCbDBOwyGnvuAboF_JNX2m2LcF0WiwgCI,6961
-careamics/config/likelihood_model.py,sha256=f8EmLi5MtOWXO_ZBrjSa27b7vThy579pY-cecstJQEw,1413
-careamics/config/nm_model.py,sha256=g1WR7uBtOcZuhfTWaO1Ma0-5Pu4YmRLchVj9eU1_GoY,3897
-careamics/config/optimizer_models.py,sha256=p6gDYtO-jFtL7zVX0-Id-rGJWkkyhbU3EBrWD_4TxZE,5726
+careamics/config/likelihood_model.py,sha256=CZtkaMqwGZLW5PWModv-tDDjjLxqGhhTkWpk27V3ERU,2274
+careamics/config/nm_model.py,sha256=lscJb31g3w2H_AY-PL2nL06KuknbaLAftZsVNYNDmxA,4742
+careamics/config/optimizer_models.py,sha256=OWpTydRBBR8wt_af1mZHNNwvL_RtnRFopAOdgjzLo30,5750
 careamics/config/tile_information.py,sha256=c-_xrVPOgcnjiEzQ-9A_GhNPamObkMANbeHaRP29R-4,2059
-careamics/config/training_model.py,sha256=9dfCcEcdPsGDW1Q0OIR_PmKjkWbZjeOmGIKuIyRd-0E,1875
-careamics/config/vae_algorithm_model.py,sha256=TkGyOPf_-vwfEFVRmst0q9Cnyz_Xa_U68Sy7VVKw4zE,6123
+careamics/config/training_model.py,sha256=67_ipo_-LxhT4-WqAs40Sg8PjU--my43Qn3BhjvlXxM,3212
+careamics/config/vae_algorithm_model.py,sha256=p4OSLCDokw2ADYKP6LvUy9eAHfapqKpcO5LE2RMkiT4,4678
 careamics/config/architectures/__init__.py,sha256=VyuBIopbqpR0KPq6cAeX3qPCrlbY8ZB_rGXwa2ApNvc,447
 careamics/config/architectures/architecture_model.py,sha256=qqPpmkNLwTBC3nwOmXpl33UAvpDFsAxFRBw9MIsQgws,921
 careamics/config/architectures/custom_model.py,sha256=-ROcKn_Ai7SZqzQLoEUc2BLAalgjyvoOnyDKUiY_cp0,4876
-careamics/config/architectures/lvae_model.py,sha256=JqcRYH6809GsiGb1Mta_rx-Uc9MmWjnS7IIeplg_UFk,4710
+careamics/config/architectures/lvae_model.py,sha256=erySFyLStHX-jUXPLYAEZ2q9bPhWzsMRdU6VFLZobpE,4585
 careamics/config/architectures/register_model.py,sha256=lHH0aUPmXtI3Bq_76zkhg07_Yb_nOJZkZJLCC_G-rZM,2434
 careamics/config/architectures/unet_model.py,sha256=8F2KosNkrXUP2bxlm-D1mowS9x3GOjyXjsEo1Kf-05k,3497
 careamics/config/references/__init__.py,sha256=rZAQzmrciX5cNICcXaBH6sbE6N6L7_qYQUkasNy9y-c,763
@@ -31,14 +34,15 @@ careamics/config/support/supported_architectures.py,sha256=f93cRyeBOu5rYzvYrvWPV
 careamics/config/support/supported_data.py,sha256=T_mDiWLFMVji_EpjBABUObAJcnv-XBnqp9XUZP37Tdk,2902
 careamics/config/support/supported_loggers.py,sha256=ubSOkGoYabGbm_jmyc1R3eFcvcP-sHmuyiBi_d3_wLg,197
 careamics/config/support/supported_losses.py,sha256=2x5sZuxRbWJzodoL35I1mMYUUDMzk8UFiFdbyPwbJ4E,583
-careamics/config/support/supported_optimizers.py,sha256=xxbJsyohJTlHeUz2I4eRwcE3BeACs-6PH8cpX6w2wX8,1394
+careamics/config/support/supported_optimizers.py,sha256=_2XmwzYENB6xpTedyWHUdWuGcDzdlfEAJjzm_qI3yRM,1392
 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=4uob-bnZ5aqpN5aEI67-aa7bsmVCrKxEknzf2BAZ3W4,283
-careamics/config/transformations/__init__.py,sha256=oqwBAL2XXbPRZZ5iOzNqalX6SyJ1M-S0lkfbDGZOzyE,378
+careamics/config/support/supported_transforms.py,sha256=ODvmoTywvJWG_5-SJJZu-X1FNtKGhkNWQc-t26IFZWI,311
+careamics/config/transformations/__init__.py,sha256=lW9DcsCfemnlcmECyw5Id28nIuwg1YPKWhGgdfzcv5s,493
 careamics/config/transformations/n2v_manipulate_model.py,sha256=Mdxc4J3vxe_dM2CIhmTwwGOIirQvrQXLoa2vRsTzoYI,1855
 careamics/config/transformations/normalize_model.py,sha256=1Rkk6IkF-7ytGU6HSzP-TpOi4RRWiQJ6fOd8zammXcg,1936
 careamics/config/transformations/transform_model.py,sha256=i7KAtSv4nah2H7uyJFKqg7RdKF68OHIPMNNvDo0HxGY,1000
+careamics/config/transformations/transform_union.py,sha256=3PnzsWlD2ymIgRPrUDZzPT9vMOVLVDtUcEorZTYx_-I,574
 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
@@ -63,7 +67,7 @@ careamics/dataset/patching/sequential_patching.py,sha256=_l3Q2uYIhjMJMaxDdSbHC9_
 careamics/dataset/patching/validate_patch_dimension.py,sha256=sQQ0-4b4uu60MNKkoWv95KxQ80J7Ku0CEk0-kAXlKeI,2134
 careamics/dataset/tiling/__init__.py,sha256=XynyAz85hVfkLtrG0lrMr_aBQm_YEwfu5uFcXMGHlOA,190
 careamics/dataset/tiling/collate_tiles.py,sha256=OrPZ-n-V3uGOc_7CcPnyEJqdbEVDlTfJfWmZnyBZ-HA,978
-careamics/dataset/tiling/lvae_tiled_patching.py,sha256=MIdwy_tNOlkErHbiykHJNLTdDEc3sdjKX5DnMvgDILo,10157
+careamics/dataset/tiling/lvae_tiled_patching.py,sha256=AOS_1m1q74YhfLgWeUx1xkRNvgw1dq6Vi7yJhmMR-A0,12992
 careamics/dataset/tiling/tiled_patching.py,sha256=ouxUWvttzmTY310CuiR25IGNVWgksVQAXoN4IXSi_G0,5942
 careamics/file_io/__init__.py,sha256=vdIx5JV3JwoyOeWnY_0tY6aekwPFy_8hBqe0Yj-aOH8,334
 careamics/file_io/read/__init__.py,sha256=I2Ios3fOoe_7f1nYT88qt2hcl0107aJCvA8yPfdpVIA,259
@@ -74,9 +78,9 @@ careamics/file_io/write/__init__.py,sha256=syy-e55OKPqa2Fn7G6szJrAmmJ4JUJyr4Y4ZS
 careamics/file_io/write/get_func.py,sha256=hyGHe1RX-lfa9QFAnwRCz_gS0NRiRnXEtg4Bdeh2Esc,1627
 careamics/file_io/write/tiff.py,sha256=tBGIgl-I1sMyBivgx-dOTBykXBODkgwPH8MT3_4KAE8,1050
 careamics/lightning/__init__.py,sha256=iS9dYpYrkjyeZfodcohc25rBTPzxj9l50iTb5Jv0j0o,588
-careamics/lightning/lightning_module.py,sha256=daUVIJei8bICfmZvshFBz0-6gS4m4MA2Xx9vVTbj0xI,21522
+careamics/lightning/lightning_module.py,sha256=afQVpEqVeug_hyy28yljPGajtTLLSOZbQB4UkgJQDT8,21846
 careamics/lightning/predict_data_module.py,sha256=JNwujK6QwObSx6P25ghpGl2f2gGT3KVgYMTlonZzH20,12745
-careamics/lightning/train_data_module.py,sha256=rwhui0Oh2EyBMQsXADOrI-IXPTG_YePpM0KcDw15H8s,27895
+careamics/lightning/train_data_module.py,sha256=x532RUaB6lN8ojUevE0Kgv-MYCVRwkaLZaq-M6wnA6E,27896
 careamics/lightning/callbacks/__init__.py,sha256=neTWqF6EbBRVf0FqtBkPHeGIR3j1yTk0OASraEVN0Pg,312
 careamics/lightning/callbacks/hyperparameters_callback.py,sha256=u45knOZHwoVHz6yYfrnERQuozT_SfZ1OrKP0QjeU4EM,1495
 careamics/lightning/callbacks/progress_bar_callback.py,sha256=8HvNSWZldixd6pjz0dLDo0apIbzTovv5smKmZ6tZQ8U,2444
@@ -86,31 +90,36 @@ careamics/lightning/callbacks/prediction_writer_callback/prediction_writer_callb
 careamics/lightning/callbacks/prediction_writer_callback/write_strategy.py,sha256=aqc6DDewD4n3tbLfqS4y-FfNKV9zy3-CZ0K2Mu16Mms,12567
 careamics/lightning/callbacks/prediction_writer_callback/write_strategy_factory.py,sha256=F1IpbNNgkv5eK8Xpqp7wqv2lsqEdP1wMRlBL7RBn93U,7114
 careamics/losses/__init__.py,sha256=4s73OlMCGJdNCVfOteJPyaPwflgIiu_fj3zpKLx7j6o,351
-careamics/losses/loss_factory.py,sha256=L68kC1Q13Yacr1PJ9IL6dhGjAsZSfhpfKeaptwLUpgE,4379
+careamics/losses/loss_factory.py,sha256=MlhcU5KI9sXWuYUBBmIZtXj4TLi7r6hgiqZQQ3jg5_E,4378
 careamics/losses/fcn/__init__.py,sha256=kf92MKFGHr6upiztZVgWwtGPf734DZyub92Rn8uEq8o,18
 careamics/losses/fcn/losses.py,sha256=NdOz29hzJ7D26p13q-g0NWoYwNauIWrP2xWww6YPbB8,2360
 careamics/losses/lvae/__init__.py,sha256=0FNtMLHrOMfagtWkaBdz1NTjyf2y0QLgysxJv5jq5uw,19
 careamics/losses/lvae/loss_utils.py,sha256=QxzA2N1TglR4H0X0uyTWWytDagE1lA9IB_TK1lms3ao,2720
-careamics/losses/lvae/losses.py,sha256=CotmiPlBBxWZwZ4reLG4SZBUKGu_jRfPukA4u1sn5Xw,16100
+careamics/losses/lvae/losses.py,sha256=lLwfuxGPqgkKj25jCONx0Mkx6iBrHSFavgCSazmyRUo,16076
 careamics/lvae_training/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-careamics/lvae_training/eval_utils.py,sha256=_AlXNXk4uGS2AGsF4PHJZpJoWBgq32kvQLEh7awOIvc,32405
-careamics/lvae_training/get_config.py,sha256=1PeqVo0iMDeKfGftUEypEBKGed9iepxgQmLkZQrWpyg,3062
+careamics/lvae_training/eval_utils.py,sha256=_YxERlXdvITFkCa3P6jkzMDGkUaKn95KrAofmwomG9o,34486
+careamics/lvae_training/get_config.py,sha256=dwVfaQS7nzjQss0E1gGLUpQpjPcOWwLgIhbu3Z0I1rg,3068
 careamics/lvae_training/lightning_module.py,sha256=ryr7iHqCMzCl5esi6_gEcnKFDQkMrw0EXK9Zfgv1Nek,27186
 careamics/lvae_training/metrics.py,sha256=KTDAKhe3vh-YxzGibjtkIG2nnUyujbnwqX4xGwaRXwE,6718
-careamics/lvae_training/train_lvae.py,sha256=uuLhBSbekLClg-I5hp7XTTlQhXO_j8hliIlpRvzKOI0,11074
+careamics/lvae_training/train_lvae.py,sha256=lJEBlBGdISVkZBcEnPNRYgJ7VbapYzZHRaFOrZ0xYGE,11080
 careamics/lvae_training/train_utils.py,sha256=e-d4QsF-li8MmAPkAmB1daHpkuU16nBTnQFZYqpTjn4,3567
-careamics/lvae_training/dataset/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-careamics/lvae_training/dataset/data_utils.py,sha256=LNKpPEnk97oELj1F9Yo8fO4zXGrJXBRkENYL50kAB8M,27117
-careamics/lvae_training/dataset/lc_dataset.py,sha256=EvCM2YeiXeSn5GXvqTvZPRriYzKf5Hz3JVmy5a6w44k,10460
-careamics/lvae_training/dataset/lc_dataset_config.py,sha256=vgsjNZaotH0MqrauIUZcwPQd9Fpfj4ZVASnhTTB2OKE,398
-careamics/lvae_training/dataset/vae_data_config.py,sha256=EzGrjqGNGrlBbYWEoIwgdoL7MNguLGVKn89yp1WIfv8,5981
-careamics/lvae_training/dataset/vae_dataset.py,sha256=wYT0s0LuECDQCXCrN91p2vUyo-tzagIFJyRD8FPTXa0,39947
+careamics/lvae_training/dataset/__init__.py,sha256=dvdHHaRA9ZfOt_uOnXkYyra2_b0Wsxs8qmrze6zxJAE,377
+careamics/lvae_training/dataset/config.py,sha256=SeCHjyxwqP2Oa9oE1rQxThBs6I4PxY40zXhRp7oPE08,4294
+careamics/lvae_training/dataset/lc_dataset.py,sha256=xErygllUu6Q-PfPZ24sHf5_NP7YGHD2NVyzmDZgDd2U,10697
+careamics/lvae_training/dataset/multich_dataset.py,sha256=iNkCv9ohahhp8A0c5m6auVrvubbAGbyRBC_VxCNyeYM,41707
+careamics/lvae_training/dataset/multifile_dataset.py,sha256=bbEyAZ8_ODDANXsJWn7tTr59VovEnbjGSSUI_PlwrQM,10246
+careamics/lvae_training/dataset/types.py,sha256=ww89Fj9w85CVGxPkLhuWiBV7ZXaVeCb0lanZSJ__PvQ,821
+careamics/lvae_training/dataset/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+careamics/lvae_training/dataset/utils/data_utils.py,sha256=8PvRPqSbYHPCl87cycZHxXIFOT_EoBV-8XCt3ZLh36s,3125
+careamics/lvae_training/dataset/utils/empty_patch_fetcher.py,sha256=OFjeqhZ6vFULJsF5tnoByhEhE8aLHujFToU_yyqMCP4,2266
+careamics/lvae_training/dataset/utils/index_manager.py,sha256=mmj1p-Ez5Qeiu99WdsFq8aCr6WaVUgn_bQ2INqNpuI4,9978
+careamics/lvae_training/dataset/utils/index_switcher.py,sha256=ZoMi8LsaIkm8MFqIFaxN4oQGyzCcwOlCom8SYNus15E,6716
 careamics/model_io/__init__.py,sha256=HITzjiuZQwo-rQ2_Ma3bz9l7PDANv1_S489E-tffV9s,155
-careamics/model_io/bmz_io.py,sha256=YugFDqEHXqGnXrOkEBp_6utWUkTxJSNXUce7B5iCKOo,7575
+careamics/model_io/bmz_io.py,sha256=tt21GHO2UD_jV7fGSnKhMSNK6iRRyCON5w9SPcxqW3I,7646
 careamics/model_io/model_io_utils.py,sha256=Dc_0YmcUfS3HuEVgN7KFfbDH8SGywT_eUCIJDVpEUHc,2755
 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=Md6y0-85q772A_G_lyhR8WKk17QTl1-0fqsEh5tAGyk,1157
+careamics/model_io/bioimage/bioimage_utils.py,sha256=YVr75SDfafOiuYGonPbcsO-xVS0wI1WkmWQQZx6DXYQ,1246
 careamics/model_io/bioimage/model_description.py,sha256=au8NtLwYVtjRI0BW2hEAlDen5ZGt25KAcy7_ZnAoQO4,9640
 careamics/models/__init__.py,sha256=Xui2BLJd1I2r_E3Sj24fJALFTi2FGtfNscUWj_0c9Hk,93
 careamics/models/activation.py,sha256=nu3sDgd7Lsyw8rvmUwxNN-7SM09cEMfxZ9DRDzdSKns,1049
@@ -119,9 +128,9 @@ careamics/models/model_factory.py,sha256=hqhV8sDq1JBLKt_7Vrw4wJSugKmBt2FIWyO7ePn
 careamics/models/unet.py,sha256=3pXpiCIw7WUaDV0Jmczkxi99C5-Zu3NpQpWxgRkeGL8,14321
 careamics/models/lvae/__init__.py,sha256=6dT6uqgT__V08EjoTGxXguTbTkySZmByS9J2Bj6WWLM,53
 careamics/models/lvae/layers.py,sha256=zRHlIHaFp4nMZwTKdzhKNKGPdarefaITTqNWO8YrkMM,85022
-careamics/models/lvae/likelihoods.py,sha256=aMzmofJCzrRPGKNhIxO_mZQGoSuXxeu3OKt-BKTWfdo,11625
-careamics/models/lvae/lvae.py,sha256=MVj8rMFMuY896H0UYR4f85qcmdI5sU01fmilGbazBP8,36391
-careamics/models/lvae/noise_models.py,sha256=ITapvSDjqfO91uZxrDDfnrbKpgS0yAk_Yo2ESoZDvb0,19707
+careamics/models/lvae/likelihoods.py,sha256=yTlIjhMpGPNJrdgbsvTLEKmtfjboiG_DsUcyBaqDgDs,11940
+careamics/models/lvae/lvae.py,sha256=YCC_te_s-l-GV0iwuYSv8OYb2PJmc-39p6Jop5kp4Zc,36335
+careamics/models/lvae/noise_models.py,sha256=RxIv_QdmBR2cMzGlhNZWY23ZAAeRc3C3-8MHYk2Rh6A,19709
 careamics/models/lvae/utils.py,sha256=4b6VKB8brg3yjv2mMb6I2KnT6HxnD5ZrfGcxGYKauHQ,11542
 careamics/prediction_utils/__init__.py,sha256=uYKzirlF-unFL9GbDPxFnYgOwSjGAtik9fonU7DfuEY,270
 careamics/prediction_utils/lvae_prediction.py,sha256=ZwPFCSeUGsULIMoMQWRYKHfLFaDm7UKyGaUMVfSUqfs,6210
@@ -129,26 +138,28 @@ careamics/prediction_utils/lvae_tiling_manager.py,sha256=SI-JaJvLrKWBSHdm-FjcqWd
 careamics/prediction_utils/prediction_outputs.py,sha256=p3Nbw9wRLU_M5uixPbzj_DmfxcSL7Y8rAQ_aTx70KQI,4082
 careamics/prediction_utils/stitch_prediction.py,sha256=HlfkJDirzbmil6Db-kFzlmhUREmGEZ2Ag8g-URbdIb0,3899
 careamics/transforms/__init__.py,sha256=VIHIsC8sMAh1TCm67ifB816Zp-LRo6rAONPuT2Qs3bs,483
-careamics/transforms/compose.py,sha256=dUHH-_ryZtnHuDZrbypf9B1oFsQv0_nYwS2ZbpGiaXw,2959
-careamics/transforms/n2v_manipulate.py,sha256=Gty7Jtu-RiFb1EnlrOi652qAOGKU5ZHvidRvykWqJxg,5438
-careamics/transforms/normalize.py,sha256=dfGWCGPyNwyEqg5wUCAA8cGdT1MvNkpKUEpw8Cw8DfA,7274
+careamics/transforms/compose.py,sha256=EOEsga7oGNZZW8zerOz7TgirbLpGyaLf1WEnTXlRjoo,5677
+careamics/transforms/n2v_manipulate.py,sha256=op-BT3LJaHgHULuqRRqTI6e45FtvvUZ0y-Smzbrh2WU,5693
+careamics/transforms/normalize.py,sha256=fxs813ydCWrIzrxFzkbk1gW8OGSr0esQSrNUFSJuGL0,7715
 careamics/transforms/pixel_manipulation.py,sha256=sMR3A1GrgL5AactzZYzvvtz7L13sA34ckVEoNTBmDqM,13362
 careamics/transforms/struct_mask_parameters.py,sha256=jE29Li9sx3olaRnqYfJsSlKi2t0WQzJmCm9aCbIQEsA,421
 careamics/transforms/transform.py,sha256=cEqc4ci8na70i-HIGYC7udRfVa8D_8OjdRVrr3txLvQ,464
 careamics/transforms/tta.py,sha256=78S7Df9rLHmEVSQSI1qDcRrRJGauyG3oaIrXkckCkmw,2335
-careamics/transforms/xy_flip.py,sha256=Q1kKTa2kE3W1P3dlpT4GAVSSHM3TebnrvIyWh75Fnko,3443
-careamics/transforms/xy_random_rotate90.py,sha256=zWdBROLLjgxTMSQEQesJr17j84BmZhKWCMVVONHU8mw,2781
+careamics/transforms/xy_flip.py,sha256=64BDo8bmAEwO1TNhbIYcUJPzzVmY5ZyNaSNmmGLkn0U,3842
+careamics/transforms/xy_random_rotate90.py,sha256=0SsCTPGlpt-VCJvmr55KRULp3dwFMBN8fTDboJcEbWg,3192
 careamics/utils/__init__.py,sha256=rG_dnqX7rdyNTFWlDkIdNtDwwMQBpg_ym14ZFeYrWfs,402
 careamics/utils/autocorrelation.py,sha256=M_WYzrEOQngc5iSXWar4S3-EOnK6DfYHPC2vVMeu_Bs,945
 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=qx4QhOW9ACOgCjTUpYv631RrZ5YsdR0QQA1BY0YoRM8,4532
+careamics/utils/metrics.py,sha256=yAoCvrZ1kQx-kT9xdTBYz-oh0I52ef6uBnw8qgzpwn8,10318
 careamics/utils/path_utils.py,sha256=8AugiG5DOmzgSnTCJI8vypXaPE0XhnR-9pzeiFUZ-0I,554
 careamics/utils/ram.py,sha256=tksyn8dVX_iJXmrDZDGub32hFZWIaNxnMheO5G1p43I,244
 careamics/utils/receptive_field.py,sha256=Y2h4c8S6glX3qcx5KHDmO17Kkuyey9voxfoXyqcAfiM,3296
+careamics/utils/serializers.py,sha256=tovAjYoYjM26FbwjKuMD4xiyiISgqROs7aiCPa_rbVs,1379
 careamics/utils/torch_utils.py,sha256=g1zxdlM7_BA7mMLcCzmrxZX4LmH__KXlJibC95muVaA,3014
-careamics-0.0.3.dist-info/METADATA,sha256=MjZrNQfB-fS45U5SMjx2S6jOaFIbKPYSOBI30ZtqPmw,3626
-careamics-0.0.3.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
-careamics-0.0.3.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
-careamics-0.0.3.dist-info/RECORD,,
+careamics-0.0.4.1.dist-info/METADATA,sha256=YemNt_kHIk852-I426HXUdc-gMN-18xR9Vs4WaP8NZ0,3662
+careamics-0.0.4.1.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+careamics-0.0.4.1.dist-info/entry_points.txt,sha256=2fSNVXJWDJgFLATVj7MkjFNvpl53amG8tUzC3jf7G1s,53
+careamics-0.0.4.1.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
+careamics-0.0.4.1.dist-info/RECORD,,

careamics-0.0.4.1.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+careamics = careamics.cli.main:run