careamics 0.0.14__py3-none-any.whl → 0.0.15__py3-none-any.whl

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Files changed (56) hide show
  1. careamics/careamist.py +49 -49
  2. careamics/cli/conf.py +6 -6
  3. careamics/cli/main.py +8 -8
  4. careamics/cli/utils.py +2 -4
  5. careamics/config/algorithms/vae_algorithm_model.py +4 -4
  6. careamics/config/callback_model.py +8 -8
  7. careamics/config/configuration_factories.py +49 -49
  8. careamics/config/data/data_model.py +7 -13
  9. careamics/config/data/ng_data_model.py +8 -14
  10. careamics/config/data/patching_strategies/_overlapping_patched_model.py +4 -5
  11. careamics/config/inference_model.py +6 -10
  12. careamics/config/likelihood_model.py +2 -2
  13. careamics/config/nm_model.py +5 -7
  14. careamics/config/training_model.py +4 -4
  15. careamics/config/transformations/normalize_model.py +3 -3
  16. careamics/config/transformations/xy_flip_model.py +2 -2
  17. careamics/config/transformations/xy_random_rotate90_model.py +2 -2
  18. careamics/config/validators/validator_utils.py +1 -2
  19. careamics/dataset/dataset_utils/iterate_over_files.py +3 -3
  20. careamics/dataset/in_memory_dataset.py +2 -2
  21. careamics/dataset/iterable_dataset.py +1 -2
  22. careamics/dataset/patching/random_patching.py +6 -6
  23. careamics/dataset/patching/sequential_patching.py +4 -4
  24. careamics/dataset/tiling/lvae_tiled_patching.py +2 -2
  25. careamics/dataset_ng/dataset.py +3 -3
  26. careamics/dataset_ng/factory.py +19 -19
  27. careamics/dataset_ng/patching_strategies/random_patching.py +2 -3
  28. careamics/dataset_ng/patching_strategies/sequential_patching.py +1 -2
  29. careamics/lightning/callbacks/prediction_writer_callback/prediction_writer_callback.py +5 -5
  30. careamics/lightning/callbacks/prediction_writer_callback/write_strategy.py +5 -5
  31. careamics/lightning/callbacks/prediction_writer_callback/write_strategy_factory.py +8 -8
  32. careamics/lightning/dataset_ng/data_module.py +43 -43
  33. careamics/lightning/lightning_module.py +12 -14
  34. careamics/lightning/predict_data_module.py +8 -8
  35. careamics/lightning/train_data_module.py +11 -11
  36. careamics/losses/lvae/losses.py +9 -9
  37. careamics/model_io/bioimage/model_description.py +12 -11
  38. careamics/model_io/bmz_io.py +4 -4
  39. careamics/models/layers.py +5 -5
  40. careamics/prediction_utils/lvae_prediction.py +5 -5
  41. careamics/transforms/compose.py +9 -9
  42. careamics/transforms/n2v_manipulate.py +3 -3
  43. careamics/transforms/n2v_manipulate_torch.py +4 -4
  44. careamics/transforms/normalize.py +4 -6
  45. careamics/transforms/pixel_manipulation.py +6 -8
  46. careamics/transforms/pixel_manipulation_torch.py +5 -7
  47. careamics/transforms/xy_flip.py +3 -5
  48. careamics/transforms/xy_random_rotate90.py +3 -5
  49. careamics/utils/logging.py +8 -8
  50. careamics/utils/metrics.py +2 -2
  51. careamics/utils/plotting.py +1 -3
  52. {careamics-0.0.14.dist-info → careamics-0.0.15.dist-info}/METADATA +2 -3
  53. {careamics-0.0.14.dist-info → careamics-0.0.15.dist-info}/RECORD +56 -56
  54. {careamics-0.0.14.dist-info → careamics-0.0.15.dist-info}/WHEEL +0 -0
  55. {careamics-0.0.14.dist-info → careamics-0.0.15.dist-info}/entry_points.txt +0 -0
  56. {careamics-0.0.14.dist-info → careamics-0.0.15.dist-info}/licenses/LICENSE +0 -0
@@ -1,6 +1,6 @@
1
1
  """A class chaining transforms together."""
2
2
 
3
- from typing import Optional, Union, cast
3
+ from typing import Union, cast
4
4
 
5
5
  from numpy.typing import NDArray
6
6
 
@@ -64,8 +64,8 @@ class Compose:
64
64
  ]
65
65
 
66
66
  def _chain_transforms(
67
- self, patch: NDArray, target: Optional[NDArray]
68
- ) -> tuple[Optional[NDArray], ...]:
67
+ self, patch: NDArray, target: NDArray | None
68
+ ) -> tuple[NDArray | None, ...]:
69
69
  """Chain transforms on the input data.
70
70
 
71
71
  Parameters
@@ -80,7 +80,7 @@ class Compose:
80
80
  tuple[np.ndarray, Optional[np.ndarray]]
81
81
  The output of the transformations.
82
82
  """
83
- params: Union[tuple[NDArray, Optional[NDArray]],] = (patch, target)
83
+ params: Union[tuple[NDArray, NDArray | None],] = (patch, target)
84
84
 
85
85
  for t in self.transforms:
86
86
  *params, _ = t(*params) # ignore additional_arrays dict
@@ -92,9 +92,9 @@ class Compose:
92
92
  def _chain_transforms_additional_arrays(
93
93
  self,
94
94
  patch: NDArray,
95
- target: Optional[NDArray],
95
+ target: NDArray | None,
96
96
  **additional_arrays: NDArray,
97
- ) -> tuple[NDArray, Optional[NDArray], dict[str, NDArray]]:
97
+ ) -> tuple[NDArray, NDArray | None, dict[str, NDArray]]:
98
98
  """Chain transforms on the input data, with additional arrays.
99
99
 
100
100
  Parameters
@@ -121,7 +121,7 @@ class Compose:
121
121
  return patch, target, additional_arrays
122
122
 
123
123
  def __call__(
124
- self, patch: NDArray, target: Optional[NDArray] = None
124
+ self, patch: NDArray, target: NDArray | None = None
125
125
  ) -> tuple[NDArray, ...]:
126
126
  """Apply the transforms to the input data.
127
127
 
@@ -143,9 +143,9 @@ class Compose:
143
143
  def transform_with_additional_arrays(
144
144
  self,
145
145
  patch: NDArray,
146
- target: Optional[NDArray] = None,
146
+ target: NDArray | None = None,
147
147
  **additional_arrays: NDArray,
148
- ) -> tuple[NDArray, Optional[NDArray], dict[str, NDArray]]:
148
+ ) -> tuple[NDArray, NDArray | None, dict[str, NDArray]]:
149
149
  """Apply the transforms to the input data, including additional arrays.
150
150
 
151
151
  Parameters
@@ -1,6 +1,6 @@
1
1
  """N2V manipulation transform."""
2
2
 
3
- from typing import Any, Literal, Optional
3
+ from typing import Any, Literal
4
4
 
5
5
  import numpy as np
6
6
  from numpy.typing import NDArray
@@ -61,7 +61,7 @@ class N2VManipulate(Transform):
61
61
  remove_center: bool = True,
62
62
  struct_mask_axis: Literal["horizontal", "vertical", "none"] = "none",
63
63
  struct_mask_span: int = 5,
64
- seed: Optional[int] = None,
64
+ seed: int | None = None,
65
65
  ):
66
66
  """Constructor.
67
67
 
@@ -88,7 +88,7 @@ class N2VManipulate(Transform):
88
88
  self.remove_center = remove_center # TODO is this ever used?
89
89
 
90
90
  if struct_mask_axis == SupportedStructAxis.NONE:
91
- self.struct_mask: Optional[StructMaskParameters] = None
91
+ self.struct_mask: StructMaskParameters | None = None
92
92
  else:
93
93
  self.struct_mask = StructMaskParameters(
94
94
  axis=0 if struct_mask_axis == SupportedStructAxis.HORIZONTAL else 1,
@@ -1,7 +1,7 @@
1
1
  """N2V manipulation transform for PyTorch."""
2
2
 
3
3
  import platform
4
- from typing import Any, Optional
4
+ from typing import Any
5
5
 
6
6
  import torch
7
7
 
@@ -49,8 +49,8 @@ class N2VManipulateTorch:
49
49
  def __init__(
50
50
  self,
51
51
  n2v_manipulate_config: N2VManipulateModel,
52
- seed: Optional[int] = None,
53
- device: Optional[str] = None,
52
+ seed: int | None = None,
53
+ device: str | None = None,
54
54
  ):
55
55
  """Constructor.
56
56
 
@@ -69,7 +69,7 @@ class N2VManipulateTorch:
69
69
  self.remove_center = n2v_manipulate_config.remove_center
70
70
 
71
71
  if n2v_manipulate_config.struct_mask_axis == SupportedStructAxis.NONE:
72
- self.struct_mask: Optional[StructMaskParameters] = None
72
+ self.struct_mask: StructMaskParameters | None = None
73
73
  else:
74
74
  self.struct_mask = StructMaskParameters(
75
75
  axis=(
@@ -1,7 +1,5 @@
1
1
  """Normalization and denormalization transforms for image patches."""
2
2
 
3
- from typing import Optional
4
-
5
3
  import numpy as np
6
4
  from numpy.typing import NDArray
7
5
 
@@ -66,8 +64,8 @@ class Normalize(Transform):
66
64
  self,
67
65
  image_means: list[float],
68
66
  image_stds: list[float],
69
- target_means: Optional[list[float]] = None,
70
- target_stds: Optional[list[float]] = None,
67
+ target_means: list[float] | None = None,
68
+ target_stds: list[float] | None = None,
71
69
  ):
72
70
  """Constructor.
73
71
 
@@ -92,9 +90,9 @@ class Normalize(Transform):
92
90
  def __call__(
93
91
  self,
94
92
  patch: np.ndarray,
95
- target: Optional[NDArray] = None,
93
+ target: NDArray | None = None,
96
94
  **additional_arrays: NDArray,
97
- ) -> tuple[NDArray, Optional[NDArray], dict[str, NDArray]]:
95
+ ) -> tuple[NDArray, NDArray | None, dict[str, NDArray]]:
98
96
  """Apply the transform to the source patch and the target (optional).
99
97
 
100
98
  Parameters
@@ -5,8 +5,6 @@ Pixel manipulation is used in N2V and similar algorithm to replace the value of
5
5
  masked pixels.
6
6
  """
7
7
 
8
- from typing import Optional
9
-
10
8
  import numpy as np
11
9
 
12
10
  from .struct_mask_parameters import StructMaskParameters
@@ -16,7 +14,7 @@ def _apply_struct_mask(
16
14
  patch: np.ndarray,
17
15
  coords: np.ndarray,
18
16
  struct_params: StructMaskParameters,
19
- rng: Optional[np.random.Generator] = None,
17
+ rng: np.random.Generator | None = None,
20
18
  ) -> np.ndarray:
21
19
  """Apply structN2V masks to patch.
22
20
 
@@ -108,7 +106,7 @@ def _odd_jitter_func(step: float, rng: np.random.Generator) -> np.ndarray:
108
106
  def _get_stratified_coords(
109
107
  mask_pixel_perc: float,
110
108
  shape: tuple[int, ...],
111
- rng: Optional[np.random.Generator] = None,
109
+ rng: np.random.Generator | None = None,
112
110
  ) -> np.ndarray:
113
111
  """
114
112
  Generate coordinates of the pixels to mask.
@@ -241,8 +239,8 @@ def uniform_manipulate(
241
239
  mask_pixel_percentage: float,
242
240
  subpatch_size: int = 11,
243
241
  remove_center: bool = True,
244
- struct_params: Optional[StructMaskParameters] = None,
245
- rng: Optional[np.random.Generator] = None,
242
+ struct_params: StructMaskParameters | None = None,
243
+ rng: np.random.Generator | None = None,
246
244
  ) -> tuple[np.ndarray, np.ndarray]:
247
245
  """
248
246
  Manipulate pixels by replacing them with a neighbor values.
@@ -321,8 +319,8 @@ def median_manipulate(
321
319
  patch: np.ndarray,
322
320
  mask_pixel_percentage: float,
323
321
  subpatch_size: int = 11,
324
- struct_params: Optional[StructMaskParameters] = None,
325
- rng: Optional[np.random.Generator] = None,
322
+ struct_params: StructMaskParameters | None = None,
323
+ rng: np.random.Generator | None = None,
326
324
  ) -> tuple[np.ndarray, np.ndarray]:
327
325
  """
328
326
  Manipulate pixels by replacing them with the median of their surrounding subpatch.
@@ -1,7 +1,5 @@
1
1
  """N2V manipulation functions for PyTorch."""
2
2
 
3
- from typing import Optional
4
-
5
3
  import torch
6
4
 
7
5
  from .struct_mask_parameters import StructMaskParameters
@@ -11,7 +9,7 @@ def _apply_struct_mask_torch(
11
9
  patch: torch.Tensor,
12
10
  coords: torch.Tensor,
13
11
  struct_params: StructMaskParameters,
14
- rng: Optional[torch.Generator] = None,
12
+ rng: torch.Generator | None = None,
15
13
  ) -> torch.Tensor:
16
14
  """Apply structN2V masks to patch.
17
15
 
@@ -154,8 +152,8 @@ def uniform_manipulate_torch(
154
152
  mask_pixel_percentage: float,
155
153
  subpatch_size: int = 11,
156
154
  remove_center: bool = True,
157
- struct_params: Optional[StructMaskParameters] = None,
158
- rng: Optional[torch.Generator] = None,
155
+ struct_params: StructMaskParameters | None = None,
156
+ rng: torch.Generator | None = None,
159
157
  ) -> tuple[torch.Tensor, torch.Tensor]:
160
158
  """
161
159
  Manipulate pixels by replacing them with a neighbor values.
@@ -256,8 +254,8 @@ def median_manipulate_torch(
256
254
  batch: torch.Tensor,
257
255
  mask_pixel_percentage: float,
258
256
  subpatch_size: int = 11,
259
- struct_params: Optional[StructMaskParameters] = None,
260
- rng: Optional[torch.Generator] = None,
257
+ struct_params: StructMaskParameters | None = None,
258
+ rng: torch.Generator | None = None,
261
259
  ) -> tuple[torch.Tensor, torch.Tensor]:
262
260
  """
263
261
  Manipulate pixels by replacing them with the median of their surrounding subpatch.
@@ -1,7 +1,5 @@
1
1
  """XY flip transform."""
2
2
 
3
- from typing import Optional
4
-
5
3
  import numpy as np
6
4
  from numpy.typing import NDArray
7
5
 
@@ -43,7 +41,7 @@ class XYFlip(Transform):
43
41
  flip_x: bool = True,
44
42
  flip_y: bool = True,
45
43
  p: float = 0.5,
46
- seed: Optional[int] = None,
44
+ seed: int | None = None,
47
45
  ) -> None:
48
46
  """Constructor.
49
47
 
@@ -81,9 +79,9 @@ class XYFlip(Transform):
81
79
  def __call__(
82
80
  self,
83
81
  patch: NDArray,
84
- target: Optional[NDArray] = None,
82
+ target: NDArray | None = None,
85
83
  **additional_arrays: NDArray,
86
- ) -> tuple[NDArray, Optional[NDArray], dict[str, NDArray]]:
84
+ ) -> tuple[NDArray, NDArray | None, dict[str, NDArray]]:
87
85
  """Apply the transform to the source patch and the target (optional).
88
86
 
89
87
  Parameters
@@ -1,7 +1,5 @@
1
1
  """Patch transform applying XY random 90 degrees rotations."""
2
2
 
3
- from typing import Optional
4
-
5
3
  import numpy as np
6
4
  from numpy.typing import NDArray
7
5
 
@@ -30,7 +28,7 @@ class XYRandomRotate90(Transform):
30
28
  Random seed, by default None.
31
29
  """
32
30
 
33
- def __init__(self, p: float = 0.5, seed: Optional[int] = None):
31
+ def __init__(self, p: float = 0.5, seed: int | None = None):
34
32
  """Constructor.
35
33
 
36
34
  Parameters
@@ -52,9 +50,9 @@ class XYRandomRotate90(Transform):
52
50
  def __call__(
53
51
  self,
54
52
  patch: NDArray,
55
- target: Optional[NDArray] = None,
53
+ target: NDArray | None = None,
56
54
  **additional_arrays: NDArray,
57
- ) -> tuple[NDArray, Optional[NDArray], dict[str, NDArray]]:
55
+ ) -> tuple[NDArray, NDArray | None, dict[str, NDArray]]:
58
56
  """Apply the transform to the source patch and the target (optional).
59
57
 
60
58
  Parameters
@@ -9,7 +9,7 @@ import sys
9
9
  import time
10
10
  from collections.abc import Generator
11
11
  from pathlib import Path
12
- from typing import Any, Optional, Union
12
+ from typing import Any, Union
13
13
 
14
14
  LOGGERS: dict = {}
15
15
 
@@ -17,7 +17,7 @@ LOGGERS: dict = {}
17
17
  def get_logger(
18
18
  name: str,
19
19
  log_level: int = logging.INFO,
20
- log_path: Optional[Union[str, Path]] = None,
20
+ log_path: Union[str, Path] | None = None,
21
21
  ) -> logging.Logger:
22
22
  """
23
23
  Create a python logger instance with configured handlers.
@@ -97,10 +97,10 @@ class ProgressBar:
97
97
 
98
98
  def __init__(
99
99
  self,
100
- max_value: Optional[int] = None,
101
- epoch: Optional[int] = None,
102
- num_epochs: Optional[int] = None,
103
- stateful_metrics: Optional[list] = None,
100
+ max_value: int | None = None,
101
+ epoch: int | None = None,
102
+ num_epochs: int | None = None,
103
+ stateful_metrics: list | None = None,
104
104
  always_stateful: bool = False,
105
105
  mode: str = "train",
106
106
  ) -> None:
@@ -159,7 +159,7 @@ class ProgressBar:
159
159
  self.message = "Denoising"
160
160
 
161
161
  def update(
162
- self, current_step: int, batch_size: int = 1, values: Optional[list] = None
162
+ self, current_step: int, batch_size: int = 1, values: list | None = None
163
163
  ) -> None:
164
164
  """
165
165
  Update the progress bar.
@@ -264,7 +264,7 @@ class ProgressBar:
264
264
 
265
265
  self._last_update = now
266
266
 
267
- def add(self, n: int, values: Optional[list] = None) -> None:
267
+ def add(self, n: int, values: list | None = None) -> None:
268
268
  """
269
269
  Update the progress bar by n steps.
270
270
 
@@ -5,7 +5,7 @@ This module contains various metrics and a metrics tracking class.
5
5
  """
6
6
 
7
7
  from collections.abc import Callable
8
- from typing import Optional, Union
8
+ from typing import Union
9
9
 
10
10
  import numpy as np
11
11
  import torch
@@ -210,7 +210,7 @@ class RunningPSNR:
210
210
  self.mse_sum += torch.nansum(elementwise_mse)
211
211
  self.N += len(elementwise_mse) - torch.sum(torch.isnan(elementwise_mse))
212
212
 
213
- def get(self) -> Optional[torch.Tensor]:
213
+ def get(self) -> torch.Tensor | None:
214
214
  """Get the actual PSNR value given the running statistics.
215
215
 
216
216
  Returns
@@ -1,7 +1,5 @@
1
1
  """Plotting utilities."""
2
2
 
3
- from typing import Optional
4
-
5
3
  import matplotlib.pyplot as plt
6
4
  import numpy as np
7
5
  import torch
@@ -14,7 +12,7 @@ def plot_noise_model_probability_distribution(
14
12
  noise_model: GaussianMixtureNoiseModel,
15
13
  signalBinIndex: int,
16
14
  histogram: NDArray,
17
- channel: Optional[str] = None,
15
+ channel: str | None = None,
18
16
  number_of_bins: int = 100,
19
17
  ) -> None:
20
18
  """Plot probability distribution P(x|s) for a certain ground truth signal.
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: careamics
3
- Version: 0.0.14
3
+ Version: 0.0.15
4
4
  Summary: Toolbox for running N2V and friends.
5
5
  Project-URL: homepage, https://careamics.github.io/
6
6
  Project-URL: repository, https://github.com/CAREamics/careamics
@@ -15,7 +15,7 @@ Classifier: Programming Language :: Python :: 3.11
15
15
  Classifier: Programming Language :: Python :: 3.12
16
16
  Classifier: Typing :: Typed
17
17
  Requires-Python: >=3.10
18
- Requires-Dist: bioimageio-core==0.7
18
+ Requires-Dist: bioimageio-core==0.9.0
19
19
  Requires-Dist: matplotlib<=3.10.3
20
20
  Requires-Dist: numpy<2.0.0
21
21
  Requires-Dist: pillow<=11.2.1
@@ -28,7 +28,6 @@ Requires-Dist: tifffile<=2025.5.10
28
28
  Requires-Dist: torch<=2.7.1,>=2.0
29
29
  Requires-Dist: torchvision<=0.22.1
30
30
  Requires-Dist: typer<=0.16.0,>=0.12.3
31
- Requires-Dist: xarray<2025.3.0
32
31
  Requires-Dist: zarr<3.0.0
33
32
  Provides-Extra: czi
34
33
  Requires-Dist: pylibczirw<6.0.0,>=4.1.2; extra == 'czi'
@@ -1,38 +1,38 @@
1
1
  careamics/__init__.py,sha256=eHsl7oE8HTKmi7yLMj8Yyp0RbdtN3QDmQQb-4Sn9d8M,475
2
- careamics/careamist.py,sha256=GhT6Ue3HZGnc0-TIJkR8izgTc3ip3DPO-f0GPJtAthk,38326
2
+ careamics/careamist.py,sha256=DeOt9u_EvRtRkzQ9NzBoyMxSNb8vO1tFHVwopI_37TY,38172
3
3
  careamics/conftest.py,sha256=Od4WcaaP0UP-XUMrFr_oo4e6c2hi_RvNbuaRTopwlmI,911
4
4
  careamics/py.typed,sha256=esB4cHc6c07uVkGtqf8at7ttEnprwRxwk8obY8Qumq4,187
5
5
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- careamics/cli/conf.py,sha256=oixGRZNylW-NTM_rkDtQkSRw8KUYwtmUC_hK5BEeLnA,13074
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- careamics/cli/main.py,sha256=S4B3c1ZN-OQK0l2_W42CaW0KmF_Pe_y4pKgn_UOuyDg,6564
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- careamics/cli/utils.py,sha256=ESeKm86je_6dzJNNEMI6LHYkHEMff0OMvzP5bnxotYk,661
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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/callback_model.py,sha256=YRXE-qgnTrI-KInYQK4UwxC55ttY6eg_eb1wvrGhCDU,4096
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+ careamics/config/callback_model.py,sha256=lxytx4rwqOI-UxW8eHTdfLE3K4eIlg907w4Xk9Nul7Y,4065
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- careamics/config/configuration_factories.py,sha256=lg3tG4LYzMsanoiD_c2jX2hY50fXIk1d6ALsRTny1uM,46113
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+ careamics/config/configuration_factories.py,sha256=P_VWHOJEjW-s_yAOKul9TV41yufsQLzRyCPSKJrjUjc,45959
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- careamics/config/inference_model.py,sha256=NEgRN-VZulMKNwY42fecnK0shLh75xVnrY-odMJpwHA,7034
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- careamics/config/likelihood_model.py,sha256=VorUtc0_-xIWNxwVrd1kBba-003ICdVMtxpcDCxH4Io,2259
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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/nm_model.py,sha256=5dAhDBLa4WPfKaNEK6ATNsSUwtlH8u8gYweEA4gZP6g,4758
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+ careamics/config/nm_model.py,sha256=M_YE2fiYgJT1pGF7JpzhDvgTnd8CP6DxZXIjxG9q5Qg,4722
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- careamics/config/training_model.py,sha256=VfK2bk_1FHaamKZw5S8UDPVxasyUqz1rY1ahcaxYZ7s,3114
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+ careamics/config/training_model.py,sha256=6XvXMIT2H8vxyGfb9L4cSRqpmlurBPeyWYS6RYhDZaA,3095
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- careamics/config/algorithms/vae_algorithm_model.py,sha256=1ZrShUGHA7zbjSiCQwhUSv7l7Hr7MbpcLOw8ucM27p8,4680
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+ careamics/config/algorithms/vae_algorithm_model.py,sha256=JFHWtoLEKt0PthJYiDq3TfBl7fJudODUvtCyTeFZvvg,4661
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- careamics/config/data/data_model.py,sha256=d_7_bDdLCzl0HgykpObbBYM1-NLBycJ5iOXN1JYS2SI,13444
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- careamics/config/data/ng_data_model.py,sha256=DKmNY84KQLwFsLem3RZJBJYq54FdSfQYlI3NnXhIsTQ,12317
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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/_overlapping_patched_model.py,sha256=Qyz4qlFzhZ6e-1aPlV89heKINIaoHfVIBO3dCTyBbOE,3073
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+ careamics/config/data/patching_strategies/_overlapping_patched_model.py,sha256=ysGd8QNNdNzLD6NITmvyjVETG6ohhEFLgWPCS_CYSxE,3030
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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/normalize_model.py,sha256=1Rkk6IkF-7ytGU6HSzP-TpOi4RRWiQJ6fOd8zammXcg,1936
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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/xy_flip_model.py,sha256=zU-uZ1b1zNZWckbho3onN-B7BHKhN7jbgbNZyRQhv2s,1025
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- careamics/config/transformations/xy_random_rotate90_model.py,sha256=6sYKmtCLvz0SV1qZgBSHUTH-CUjwvHnohq1HyPntbyE,894
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+ careamics/config/transformations/xy_flip_model.py,sha256=2k4tiUZK3GVn9hEjFlWi0ypz-k5C2XKKO6elU7HlKmI,1012
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+ careamics/config/transformations/xy_random_rotate90_model.py,sha256=Z0vhD9Hal_rpwWHlOA53ADDcUrrApESzZBa50HD7gRc,881
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- careamics/config/validators/validator_utils.py,sha256=7wBQzf4YcxiL0h9yOEaFM4RoeOtLPEBp4W7ZVabfqBA,2609
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+ careamics/config/validators/validator_utils.py,sha256=NUmH_NheVwbx3rQi_pKTjMqX-_k89UIAlKBc7RlQLls,2578
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- careamics/dataset/in_memory_dataset.py,sha256=INiamRPZGKf0yWIyLds1ZQlBiK4A86XVijOJ65BSH1A,9692
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+ careamics/dataset/in_memory_dataset.py,sha256=Grt9w4QuhJrTbcHmEJeifmTm06-U09M-6FGyaFw_UXU,9679
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  careamics/dataset/in_memory_tiled_pred_dataset.py,sha256=fKg3_Mmx0hXlOjuWU6lhTVRsm02D21J-IOYmTIm4UsE,3561
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- careamics/dataset/iterable_dataset.py,sha256=ZBiQh96TgThcOB0flRGZmh0arFn30fX3shAafvetq3s,9783
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+ careamics/dataset/iterable_dataset.py,sha256=xDt2985m-K1P5G2EaNHOHg54-fjRI6MfZTdNB4NdSJI,9752
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- careamics/dataset/dataset_utils/iterate_over_files.py,sha256=xQJZQhusFiI3oPJmSsL8fFBVVRA3WS8R1TcAXW-xfdE,2898
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+ careamics/dataset/dataset_utils/iterate_over_files.py,sha256=mVY1PAnLQn-xr8PDfXspiPrsv0k6o8ypor6_1MB59_k,2882
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- careamics/dataset/patching/random_patching.py,sha256=gm1jxye9yvHbdijLzCtDSzRU_9j110GRLMnJaUwLAHQ,6487
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- careamics/dataset/patching/sequential_patching.py,sha256=4F5E1Ta0M5kFXGwI2-QXRxeOx0CyUwbFaB5awkMCN_Q,5890
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+ careamics/dataset/patching/random_patching.py,sha256=8ZrC5CygBLnA4e1yXJg4XT3RnsIeN9PMzuTRkO_wPo8,6462
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+ careamics/dataset/patching/sequential_patching.py,sha256=Dg5C57hO7BqnKP2sJh2xylupzmuV2lvTs4vYe5KTH-Q,5871
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- careamics/dataset/tiling/lvae_tiled_patching.py,sha256=rGcUOOL0nC5zv22RLn_WiLV9cxrqCwZc-btJ6zrtAy8,13223
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+ careamics/dataset/tiling/lvae_tiled_patching.py,sha256=2oOXnVsZ_L2jtA02Jw7bLfkugZ2ZO8lF105cjxGADoY,13210
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- careamics/dataset_ng/dataset.py,sha256=ZrFnB4Xj3mWDYQyP2yMoazRnKs8wrkJYL28pHsOC8Yc,8826
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- careamics/dataset_ng/factory.py,sha256=lPh61FIkvXdqW5nH68d5Jvn4vg8wxB7bNmTCvea1_2Q,14787
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+ careamics/dataset_ng/dataset.py,sha256=2R7jMUJFBECI-MBROg4QhGM3vJ8EEIpwOMDoBYEQhN8,8810
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+ careamics/dataset_ng/factory.py,sha256=bjzolF1k9iTj6cY75licyGYielZZvpp3xJwLbw8t5uU,14723
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  careamics/dataset_ng/demos/care_U2OS_demo.ipynb,sha256=fxuiJ0g65Ts7jFUxHgCGbf30Xoz8kIB4dfh9qfpW1D8,9501
@@ -105,8 +105,8 @@ careamics/dataset_ng/patch_extractor/image_stack/in_memory_image_stack.py,sha256
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  careamics/dataset_ng/patch_extractor/image_stack/zarr_image_stack.py,sha256=hmNOl6-FMUNQS65YMSa4eAz3Rp_2es98p1_UY6S8B50,6590
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  careamics/dataset_ng/patching_strategies/patching_strategy_protocol.py,sha256=ukw5G9hIOPEJz-DEFDMuJsGYou7wUeRjALNU8qdgn9g,3475
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- careamics/dataset_ng/patching_strategies/random_patching.py,sha256=Q7CnM-ah3wnv2B0Eo2RSzeHWMhfbqfGcwZxNDzRKW2U,13524
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- careamics/dataset_ng/patching_strategies/sequential_patching.py,sha256=T65DszwUmCvLBZXbMmTYYWFn702tuECkPKJ_x8ps00A,2491
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+ careamics/dataset_ng/patching_strategies/random_patching.py,sha256=0qEhUgANJAuhnVYeCiCaiW1gwLWOGAIIFcvriW0_byM,13490
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+ careamics/dataset_ng/patching_strategies/sequential_patching.py,sha256=Qsqqf8D_2SxSRgrhYMpD0VgmAqHX-jiw-wRvDfwTYHA,2460
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  careamics/file_io/__init__.py,sha256=vgMI77X820VOWywAEW5W20FXfmbqBzx4V63D3V3_HhI,334
@@ -118,19 +118,19 @@ careamics/file_io/write/__init__.py,sha256=CUt33cRjG9hm18L9a7XqaUKWQ_3xiuQ9ztz4A
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  careamics/file_io/write/get_func.py,sha256=hyGHe1RX-lfa9QFAnwRCz_gS0NRiRnXEtg4Bdeh2Esc,1627
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  careamics/lightning/__init__.py,sha256=ATCVAGnX08Ik4TxbIv0-cXb52UinR42JgvZh_GIMSpc,588
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- careamics/lightning/lightning_module.py,sha256=C7BylX4uMok7q_ioAsptrWpFt-INIxaLjLFOjz0usSw,24384
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- careamics/lightning/predict_data_module.py,sha256=Ve_ADYLo67yoFlY-04xofkt8KvbJXKIkviF_9bZ3fVc,12772
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- careamics/lightning/train_data_module.py,sha256=A4nVrL5tXQTCeeXlGD_oGlAMPEWryykVKElnSmDhmjQ,26581
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+ careamics/lightning/lightning_module.py,sha256=EgRIWOHxZ9FZyS2lGaRSGaVecT8revXjd4mE59se7T0,24311
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+ careamics/lightning/predict_data_module.py,sha256=yahMMPbEIX0AXNgA2PKIABm9cYEXlyhl0SKc1GCDEZU,12741
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+ careamics/lightning/train_data_module.py,sha256=028si-InvNHbr78ne1sEudhwKz-ReZGNIoOtr9hUlvc,26541
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- careamics/lightning/callbacks/prediction_writer_callback/prediction_writer_callback.py,sha256=8HHUSKcG7G0FSCVPnpGQHLfpara5mnKAwsiiyWp2wzo,8210
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- careamics/lightning/callbacks/prediction_writer_callback/write_strategy.py,sha256=lxsLjLskRpYnzdyWCdOICUJxF9YzuUi1RH0LJnOCVgo,12594
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- careamics/lightning/callbacks/prediction_writer_callback/write_strategy_factory.py,sha256=F1IpbNNgkv5eK8Xpqp7wqv2lsqEdP1wMRlBL7RBn93U,7114
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+ careamics/lightning/callbacks/prediction_writer_callback/prediction_writer_callback.py,sha256=aWj6TbNmRNSxAL32GjrVQ1TNtK0Jr7t2od33nSgGjW4,8188
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+ careamics/lightning/callbacks/prediction_writer_callback/write_strategy.py,sha256=BulDaQdXoLYoU39sfKrtdnHjY_TIQ8qOvfDjkSWi13s,12572
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+ careamics/lightning/callbacks/prediction_writer_callback/write_strategy_factory.py,sha256=WLPWuZbLZ1pJWwAssqK9ObLZsljMhu-lxN0xe7_yCKc,7083
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- careamics/lightning/dataset_ng/data_module.py,sha256=acRjHcJSUEb9Unmc6n_BvyBOwMEnCaHr8wl0UH52wQU,26365
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+ careamics/lightning/dataset_ng/data_module.py,sha256=PyU7igSn22vnrPJLyVn2UYo9szS3NXayRZY5wqo8iu8,26229
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+ careamics/transforms/n2v_manipulate.py,sha256=pAwGEZW_SFwbbVQGwpfWl6SVIa7slvfSSfve6sIHq_w,5670
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+ careamics/transforms/normalize.py,sha256=Do4oo56rojDzG6gWzWIHYW74OMaReAwwn2_EbtiLEnY,8273
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+ careamics/utils/logging.py,sha256=lSjoXbOTnOjzz70E9NtNVbnPBROn_72s1i9wxwnecOE,10306
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+ careamics/utils/plotting.py,sha256=muoN3y5JonZOg_kHSCOa06bJt6PH6a0O8gBFw502i9g,2486
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- careamics-0.0.14.dist-info/METADATA,sha256=jI7wBOg2luJpEUpkYEnLjkpApJPRhJdCSr4QNwzSE2w,3940
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- careamics-0.0.14.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
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- careamics-0.0.14.dist-info/RECORD,,
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+ careamics-0.0.15.dist-info/METADATA,sha256=1lpIRjfRtM_XPs7eZP-JnV9rYZtRer2XrqK1rykEE84,3911
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+ careamics-0.0.15.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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+ careamics-0.0.15.dist-info/entry_points.txt,sha256=2fSNVXJWDJgFLATVj7MkjFNvpl53amG8tUzC3jf7G1s,53
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+ careamics-0.0.15.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
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+ careamics-0.0.15.dist-info/RECORD,,