careamics 0.0.4.2__py3-none-any.whl → 0.0.6__py3-none-any.whl

careamics/models/unet.py

@@ -4,7 +4,7 @@ UNet model.
 A UNet encoder, decoder and complete model.
 """
 
-from typing import Any, List, Tuple, Union
+from typing import Any, Union
 
 import torch
 import torch.nn as nn
@@ -104,7 +104,7 @@ class UnetEncoder(nn.Module):
             encoder_blocks.append(self.pooling)
         self.encoder_blocks = nn.ModuleList(encoder_blocks)
 
-    def forward(self, x: torch.Tensor) -> List[torch.Tensor]:
+    def forward(self, x: torch.Tensor) -> list[torch.Tensor]:
         """
         Forward pass.
 
@@ -115,7 +115,7 @@ class UnetEncoder(nn.Module):
 
         Returns
         -------
-        List[torch.Tensor]
+        list[torch.Tensor]
             Output of each encoder block (skip connections) and final output of the
             encoder.
         """
@@ -202,7 +202,7 @@ class UnetDecoder(nn.Module):
             groups=self.groups,
         )
 
-        decoder_blocks: List[nn.Module] = []
+        decoder_blocks: list[nn.Module] = []
         for n in range(depth):
             decoder_blocks.append(upsampling)
             in_channels = (num_channels_init * 2 ** (depth - n)) * groups
@@ -230,7 +230,7 @@ class UnetDecoder(nn.Module):
 
         Parameters
         ----------
-        *features :  List[torch.Tensor]
+        *features :  list[torch.Tensor]
             List containing the output of each encoder block(skip connections) and final
             output of the encoder.
 
@@ -240,7 +240,7 @@ class UnetDecoder(nn.Module):
             Output of the decoder.
         """
         x: torch.Tensor = features[0]
-        skip_connections: Tuple[torch.Tensor, ...] = features[-1:0:-1]
+        skip_connections: tuple[torch.Tensor, ...] = features[-1:0:-1]
 
         x = self.bottleneck(x)
 
@@ -289,10 +289,10 @@ class UnetDecoder(nn.Module):
         m = A.shape[1] // groups
         n = B.shape[1] // groups
 
-        A_groups: List[torch.Tensor] = [
+        A_groups: list[torch.Tensor] = [
             A[:, i * m : (i + 1) * m] for i in range(groups)
         ]
-        B_groups: List[torch.Tensor] = [
+        B_groups: list[torch.Tensor] = [
             B[:, i * n : (i + 1) * n] for i in range(groups)
         ]
 

careamics/prediction_utils/__init__.py

@@ -1,9 +1,9 @@
 """Package to house various prediction utilies."""
 
 __all__ = [
+    "convert_outputs",
     "stitch_prediction",
     "stitch_prediction_single",
-    "convert_outputs",
 ]
 
 from .prediction_outputs import convert_outputs

careamics/prediction_utils/prediction_outputs.py

@@ -1,6 +1,6 @@
 """Module containing functions to convert prediction outputs to desired form."""
 
-from typing import Any, List, Literal, Tuple, Union, overload
+from typing import Any, Literal, Union, overload
 
 import numpy as np
 from numpy.typing import NDArray
@@ -9,7 +9,7 @@ from ..config.tile_information import TileInformation
 from .stitch_prediction import stitch_prediction
 
 
-def convert_outputs(predictions: List[Any], tiled: bool) -> list[NDArray]:
+def convert_outputs(predictions: list[Any], tiled: bool) -> list[NDArray]:
     """
     Convert the Lightning trainer outputs to the desired form.
 
@@ -25,7 +25,7 @@ def convert_outputs(predictions: List[Any], tiled: bool) -> list[NDArray]:
     Returns
     -------
     list of numpy.ndarray or numpy.ndarray
-        List of arrays with the axes SC(Z)YX. If there is only 1 output it will not
+        list of arrays with the axes SC(Z)YX. If there is only 1 output it will not
         be in a list.
     """
     if len(predictions) == 0:
@@ -44,27 +44,27 @@ def convert_outputs(predictions: List[Any], tiled: bool) -> list[NDArray]:
 # for mypy
 @overload
 def combine_batches(  # numpydoc ignore=GL08
-    predictions: List[Any], tiled: Literal[True]
-) -> Tuple[List[NDArray], List[TileInformation]]: ...
+    predictions: list[Any], tiled: Literal[True]
+) -> tuple[list[NDArray], list[TileInformation]]: ...
 
 
 # for mypy
 @overload
 def combine_batches(  # numpydoc ignore=GL08
-    predictions: List[Any], tiled: Literal[False]
-) -> List[NDArray]: ...
+    predictions: list[Any], tiled: Literal[False]
+) -> list[NDArray]: ...
 
 
 # for mypy
 @overload
 def combine_batches(  # numpydoc ignore=GL08
-    predictions: List[Any], tiled: Union[bool, Literal[True], Literal[False]]
-) -> Union[List[NDArray], Tuple[List[NDArray], List[TileInformation]]]: ...
+    predictions: list[Any], tiled: Union[bool, Literal[True], Literal[False]]
+) -> Union[list[NDArray], tuple[list[NDArray], list[TileInformation]]]: ...
 
 
 def combine_batches(
-    predictions: List[Any], tiled: bool
-) -> Union[List[NDArray], Tuple[List[NDArray], List[TileInformation]]]:
+    predictions: list[Any], tiled: bool
+) -> Union[list[NDArray], tuple[list[NDArray], list[TileInformation]]]:
     """
     If predictions are in batches, they will be combined.
 
@@ -87,8 +87,8 @@ def combine_batches(
 
 
 def _combine_tiled_batches(
-    predictions: List[Tuple[NDArray, List[TileInformation]]]
-) -> Tuple[List[NDArray], List[TileInformation]]:
+    predictions: list[tuple[NDArray, list[TileInformation]]]
+) -> tuple[list[NDArray], list[TileInformation]]:
     """
     Combine batches from tiled output.
 
@@ -109,13 +109,13 @@ def _combine_tiled_batches(
     tile_infos = [
         tile_info for _, tile_info_list in predictions for tile_info in tile_info_list
     ]
-    prediction_tiles: List[NDArray] = _combine_array_batches(
+    prediction_tiles: list[NDArray] = _combine_array_batches(
         [preds for preds, _ in predictions]
     )
     return prediction_tiles, tile_infos
 
 
-def _combine_array_batches(predictions: List[NDArray]) -> List[NDArray]:
+def _combine_array_batches(predictions: list[NDArray]) -> list[NDArray]:
     """
     Combine batches of arrays.
 

careamics/prediction_utils/stitch_prediction.py

@@ -1,7 +1,7 @@
 """Prediction utility functions."""
 
 import builtins
-from typing import List, Union
+from typing import Union
 
 import numpy as np
 from numpy.typing import NDArray
@@ -11,9 +11,9 @@ from careamics.config.tile_information import TileInformation
 
 # TODO: why not allow input and output of torch.tensor ?
 def stitch_prediction(
-    tiles: List[np.ndarray],
-    tile_infos: List[TileInformation],
-) -> List[np.ndarray]:
+    tiles: list[np.ndarray],
+    tile_infos: list[TileInformation],
+) -> list[np.ndarray]:
     """
     Stitch tiles back together to form a full image(s).
 
@@ -54,8 +54,8 @@ def stitch_prediction(
 
 
 def stitch_prediction_single(
-    tiles: List[NDArray],
-    tile_infos: List[TileInformation],
+    tiles: list[NDArray],
+    tile_infos: list[TileInformation],
 ) -> NDArray:
     """
     Stitch tiles back together to form a full image.

careamics/transforms/__init__.py

@@ -1,14 +1,14 @@
 """Transforms that are used to augment the data."""
 
 __all__ = [
-    "get_all_transforms",
+    "Compose",
+    "Denormalize",
+    "ImageRestorationTTA",
     "N2VManipulate",
+    "Normalize",
     "XYFlip",
     "XYRandomRotate90",
-    "ImageRestorationTTA",
-    "Denormalize",
-    "Normalize",
-    "Compose",
+    "get_all_transforms",
 ]
 
 

careamics/transforms/compose.py

@@ -1,10 +1,10 @@
 """A class chaining transforms together."""
 
-from typing import Dict, List, Optional, Tuple, Union, cast
+from typing import Optional, Union, cast
 
 from numpy.typing import NDArray
 
-from careamics.config.transformations import TransformModel
+from careamics.config.transformations import NORM_AND_SPATIAL_UNION
 
 from .n2v_manipulate import N2VManipulate
 from .normalize import Normalize
@@ -20,7 +20,7 @@ ALL_TRANSFORMS = {
 }
 
 
-def get_all_transforms() -> Dict[str, type]:
+def get_all_transforms() -> dict[str, type]:
     """Return all the transforms accepted by CAREamics.
 
     Returns
@@ -37,7 +37,7 @@ class Compose:
 
     Parameters
     ----------
-    transform_list : List[TransformModel]
+    transform_list : list[TransformModel]
         A list of dictionaries where each dictionary contains the name of a
         transform and its parameters.
 
@@ -47,12 +47,12 @@ class Compose:
         A callable that applies the transforms to the input data.
     """
 
-    def __init__(self, transform_list: List[TransformModel]) -> None:
+    def __init__(self, transform_list: list[NORM_AND_SPATIAL_UNION]) -> None:
         """Instantiate a Compose object.
 
         Parameters
         ----------
-        transform_list : List[TransformModel]
+        transform_list : list[NORM_AND_SPATIAL_UNION]
             A list of dictionaries where each dictionary contains the name of a
             transform and its parameters.
         """
@@ -67,7 +67,7 @@ class Compose:
 
     def _chain_transforms(
         self, patch: NDArray, target: Optional[NDArray]
-    ) -> Tuple[Optional[NDArray], ...]:
+    ) -> tuple[Optional[NDArray], ...]:
         """Chain transforms on the input data.
 
         Parameters
@@ -79,7 +79,7 @@ class Compose:
 
         Returns
         -------
-        Tuple[np.ndarray, Optional[np.ndarray]]
+        tuple[np.ndarray, Optional[np.ndarray]]
             The output of the transformations.
         """
         params: Union[
@@ -103,7 +103,7 @@ class Compose:
         patch: NDArray,
         target: Optional[NDArray],
         **additional_arrays: NDArray,
-    ) -> Tuple[NDArray, Optional[NDArray], dict[str, NDArray]]:
+    ) -> tuple[NDArray, Optional[NDArray], dict[str, NDArray]]:
         """Chain transforms on the input data, with additional arrays.
 
         Parameters
@@ -118,7 +118,7 @@ class Compose:
 
         Returns
         -------
-        Tuple[np.ndarray, Optional[np.ndarray]]
+        tuple[np.ndarray, Optional[np.ndarray]]
             The output of the transformations.
         """
         params = {"patch": patch, "target": target, **additional_arrays}
@@ -131,7 +131,7 @@ class Compose:
 
     def __call__(
         self, patch: NDArray, target: Optional[NDArray] = None
-    ) -> Tuple[NDArray, ...]:
+    ) -> tuple[NDArray, ...]:
         """Apply the transforms to the input data.
 
         Parameters
@@ -143,11 +143,11 @@ class Compose:
 
         Returns
         -------
-        Tuple[np.ndarray, ...]
+        tuple[np.ndarray, ...]
             The output of the transformations.
         """
         # TODO: solve casting Compose.__call__ ouput
-        return cast(Tuple[NDArray, ...], self._chain_transforms(patch, target))
+        return cast(tuple[NDArray, ...], self._chain_transforms(patch, target))
 
     def transform_with_additional_arrays(
         self,

careamics/transforms/n2v_manipulate.py

@@ -1,6 +1,6 @@
 """N2V manipulation transform."""
 
-from typing import Any, Literal, Optional, Tuple
+from typing import Any, Literal, Optional
 
 import numpy as np
 from numpy.typing import NDArray
@@ -100,7 +100,7 @@ class N2VManipulate(Transform):
 
     def __call__(
         self, patch: NDArray, *args: Any, **kwargs: Any
-    ) -> Tuple[NDArray, NDArray, NDArray]:
+    ) -> tuple[NDArray, NDArray, NDArray]:
         """Apply the transform to the image.
 
         Parameters
@@ -114,7 +114,7 @@ class N2VManipulate(Transform):
 
         Returns
         -------
-        Tuple[np.ndarray, np.ndarray, np.ndarray]
+        tuple[np.ndarray, np.ndarray, np.ndarray]
             Masked patch, original patch, and mask.
         """
         masked = np.zeros_like(patch)

careamics/transforms/pixel_manipulation.py

@@ -5,7 +5,7 @@ Pixel manipulation is used in N2V and similar algorithm to replace the value of
 masked pixels.
 """
 
-from typing import Optional, Tuple
+from typing import Optional
 
 import numpy as np
 
@@ -107,7 +107,7 @@ def _odd_jitter_func(step: float, rng: np.random.Generator) -> np.ndarray:
 
 def _get_stratified_coords(
     mask_pixel_perc: float,
-    shape: Tuple[int, ...],
+    shape: tuple[int, ...],
     rng: Optional[np.random.Generator] = None,
 ) -> np.ndarray:
     """
@@ -121,7 +121,7 @@ def _get_stratified_coords(
     mask_pixel_perc : float
         Actual (quasi) percentage of masked pixels across the whole image. Used in
         calculating the distance between masked pixels across each axis.
-    shape : Tuple[int, ...]
+    shape : tuple[int, ...]
         Shape of the input patch.
     rng : np.random.Generator or None
         Random number generator.
@@ -242,7 +242,7 @@ def uniform_manipulate(
     remove_center: bool = True,
     struct_params: Optional[StructMaskParameters] = None,
     rng: Optional[np.random.Generator] = None,
-) -> Tuple[np.ndarray, np.ndarray]:
+) -> tuple[np.ndarray, np.ndarray]:
     """
     Manipulate pixels by replacing them with a neighbor values.
 
@@ -269,8 +269,8 @@ def uniform_manipulate(
 
     Returns
     -------
-    Tuple[np.ndarray]
-        Tuple containing the manipulated patch and the corresponding mask.
+    tuple[np.ndarray]
+        tuple containing the manipulated patch and the corresponding mask.
     """
     if rng is None:
         rng = np.random.default_rng()
@@ -322,7 +322,7 @@ def median_manipulate(
     subpatch_size: int = 11,
     struct_params: Optional[StructMaskParameters] = None,
     rng: Optional[np.random.Generator] = None,
-) -> Tuple[np.ndarray, np.ndarray]:
+) -> tuple[np.ndarray, np.ndarray]:
     """
     Manipulate pixels by replacing them with the median of their surrounding subpatch.
 
@@ -348,8 +348,8 @@ def median_manipulate(
 
     Returns
     -------
-    Tuple[np.ndarray]
-           Tuple containing the manipulated patch, the original patch and the mask.
+    tuple[np.ndarray]
+           tuple containing the manipulated patch, the original patch and the mask.
     """
     if rng is None:
         rng = np.random.default_rng()

careamics/transforms/xy_random_rotate90.py

@@ -1,6 +1,6 @@
 """Patch transform applying XY random 90 degrees rotations."""
 
-from typing import Optional, Tuple
+from typing import Optional
 
 import numpy as np
 from numpy.typing import NDArray
@@ -69,7 +69,7 @@ class XYRandomRotate90(Transform):
 
         Returns
         -------
-        Tuple[np.ndarray, Optional[np.ndarray]]
+        tuple[np.ndarray, Optional[np.ndarray]]
             Transformed patch and target.
         """
         if self.rng.random() > self.p:
@@ -90,7 +90,7 @@ class XYRandomRotate90(Transform):
 
         return patch_transformed, target_transformed, additional_transformed
 
-    def _apply(self, patch: NDArray, n_rot: int, axes: Tuple[int, int]) -> NDArray:
+    def _apply(self, patch: NDArray, n_rot: int, axes: tuple[int, int]) -> NDArray:
         """Apply the transform to the image.
 
         Parameters
@@ -99,7 +99,7 @@ class XYRandomRotate90(Transform):
             Image or image patch, 2D or 3D, shape C(Z)YX.
         n_rot : int
             Number of 90 degree rotations.
-        axes : Tuple[int, int]
+        axes : tuple[int, int]
             Axes along which to rotate the patch.
 
         Returns

careamics/utils/__init__.py

@@ -1,13 +1,13 @@
 """Utils module."""
 
 __all__ = [
-    "cwd",
-    "get_ram_size",
-    "check_path_exists",
     "BaseEnum",
-    "get_logger",
-    "get_careamics_home",
     "autocorrelation",
+    "check_path_exists",
+    "cwd",
+    "get_careamics_home",
+    "get_logger",
+    "get_ram_size",
 ]
 
 

careamics/utils/context.py

@@ -5,9 +5,10 @@ A convenience function to change the working directory in order to save data.
 """
 
 import os
+from collections.abc import Iterator
 from contextlib import contextmanager
 from pathlib import Path
-from typing import Iterator, Union
+from typing import Union
 
 
 def get_careamics_home() -> Path:

careamics/utils/lightning_utils.py

@@ -0,0 +1,57 @@
+"""PyTorch lightning utilities."""
+
+from pathlib import Path
+from typing import Union
+
+
+def read_csv_logger(experiment_name: str, log_folder: Union[str, Path]) -> dict:
+    """Return the loss curves from the csv logs.
+
+    Parameters
+    ----------
+    experiment_name : str
+        Name of the experiment.
+    log_folder : Path or str
+        Path to the folder containing the csv logs.
+
+    Returns
+    -------
+    dict
+        Dictionary containing the loss curves, with keys "train_epoch", "val_epoch",
+        "train_loss" and "val_loss".
+    """
+    path = Path(log_folder) / experiment_name
+
+    # find the most recent of version_* folders
+    versions = [int(v.name.split("_")[-1]) for v in path.iterdir() if v.is_dir()]
+    version = max(versions)
+
+    path_log = path / f"version_{version}" / "metrics.csv"
+
+    epochs = []
+    train_losses_tmp = []
+    val_losses_tmp = []
+    with open(path_log) as f:
+        lines = f.readlines()
+
+        for single_line in lines[1:]:
+            epoch, _, train_loss, _, val_loss = single_line.strip().split(",")
+
+            epochs.append(epoch)
+            train_losses_tmp.append(train_loss)
+            val_losses_tmp.append(val_loss)
+
+    # train and val are not logged on the same row and can have different lengths
+    train_epoch = [
+        int(epochs[i]) for i in range(len(epochs)) if train_losses_tmp[i] != ""
+    ]
+    val_epoch = [int(epochs[i]) for i in range(len(epochs)) if val_losses_tmp[i] != ""]
+    train_losses = [float(loss) for loss in train_losses_tmp if loss != ""]
+    val_losses = [float(loss) for loss in val_losses_tmp if loss != ""]
+
+    return {
+        "train_epoch": train_epoch,
+        "val_epoch": val_epoch,
+        "train_loss": train_losses,
+        "val_loss": val_losses,
+    }

careamics/utils/logging.py

@@ -7,8 +7,9 @@ The methods are responsible for the in-console logger.
 import logging
 import sys
 import time
+from collections.abc import Generator
 from pathlib import Path
-from typing import Any, Dict, Generator, List, Optional, Union
+from typing import Any, Optional, Union
 
 LOGGERS: dict = {}
 
@@ -84,7 +85,7 @@ class ProgressBar:
         Zero-indexed current epoch, by default None.
     num_epochs : Optional[int], optional
         Total number of epochs, by default None.
-    stateful_metrics : Optional[List], optional
+    stateful_metrics : Optional[list], optional
         Iterable of string names of metrics that should *not* be averaged over time.
         Metrics in this list will be displayed as-is. All others will be averaged by
         the progress bar before display, by default None.
@@ -99,7 +100,7 @@ class ProgressBar:
         max_value: Optional[int] = None,
         epoch: Optional[int] = None,
         num_epochs: Optional[int] = None,
-        stateful_metrics: Optional[List] = None,
+        stateful_metrics: Optional[list] = None,
         always_stateful: bool = False,
         mode: str = "train",
     ) -> None:
@@ -114,7 +115,7 @@ class ProgressBar:
             Zero-indexed current epoch, by default None.
         num_epochs : Optional[int], optional
             Total number of epochs, by default None.
-        stateful_metrics : Optional[List], optional
+        stateful_metrics : Optional[list], optional
             Iterable of string names of metrics that should *not* be averaged over time.
             Metrics in this list will be displayed as-is. All others will be averaged by
             the progress bar before display, by default None.
@@ -145,8 +146,8 @@ class ProgressBar:
         self._seen_so_far = 0
         # We use a dict + list to avoid garbage collection
         # issues found in OrderedDict
-        self._values: Dict[Any, Any] = {}
-        self._values_order: List[Any] = []
+        self._values: dict[Any, Any] = {}
+        self._values_order: list[Any] = []
         self._start = time.time()
         self._last_update = 0.0
         self.spin = self.spinning_cursor() if self.max_value is None else None
@@ -158,7 +159,7 @@ class ProgressBar:
             self.message = "Denoising"
 
     def update(
-        self, current_step: int, batch_size: int = 1, values: Optional[List] = None
+        self, current_step: int, batch_size: int = 1, values: Optional[list] = None
     ) -> None:
         """
         Update the progress bar.
@@ -169,7 +170,7 @@ class ProgressBar:
             Index of the current step.
         batch_size : int, optional
             Batch size, by default 1.
-        values : Optional[List], optional
+        values : Optional[list], optional
             Updated metrics values, by default None.
         """
         values = values or []
@@ -263,7 +264,7 @@ class ProgressBar:
 
         self._last_update = now
 
-    def add(self, n: int, values: Optional[List] = None) -> None:
+    def add(self, n: int, values: Optional[list] = None) -> None:
         """
         Update the progress bar by n steps.
 
@@ -271,7 +272,7 @@ class ProgressBar:
         ----------
         n : int
             Number of steps to increase the progress bar with.
-        values : Optional[List], optional
+        values : Optional[list], optional
             Updated metrics values, by default None.
         """
         self.update(self._seen_so_far + n, 1, values=values)

careamics/utils/serializers.py

@@ -21,6 +21,8 @@ def _array_to_json(arr: Union[np.ndarray, torch.Tensor]) -> str:
     str
         JSON string representing the array.
     """
+    if isinstance(arr, str):
+        return arr
     return json.dumps(arr.tolist())