careamics 0.1.0rc6__py3-none-any.whl → 0.1.0rc7__py3-none-any.whl

careamics/transforms/pixel_manipulation.py

@@ -13,7 +13,10 @@ from .struct_mask_parameters import StructMaskParameters
 
 
 def _apply_struct_mask(
-    patch: np.ndarray, coords: np.ndarray, struct_params: StructMaskParameters
+    patch: np.ndarray,
+    coords: np.ndarray,
+    struct_params: StructMaskParameters,
+    rng: Optional[np.random.Generator] = None,
 ) -> np.ndarray:
     """Apply structN2V masks to patch.
 
@@ -31,12 +34,17 @@ def _apply_struct_mask(
         Coordinates of the ROI(subpatch) centers.
     struct_params : StructMaskParameters
         Parameters for the structN2V mask (axis and span).
+    rng : np.random.Generator or None
+        Random number generator.
 
     Returns
     -------
     np.ndarray
         Patch with the structN2V mask applied.
     """
+    if rng is None:
+        rng = np.random.default_rng()
+
     # relative axis
     moving_axis = -1 - struct_params.axis
 
@@ -67,7 +75,7 @@ def _apply_struct_mask(
     mix = np.delete(mix, mix[:, moving_axis] > max_bound, axis=0)
 
     # replace neighbouring pixels with random values from flat dist
-    patch[tuple(mix.T)] = np.random.uniform(patch.min(), patch.max(), size=mix.shape[0])
+    patch[tuple(mix.T)] = rng.uniform(patch.min(), patch.max(), size=mix.shape[0])
 
     return patch
 
@@ -98,7 +106,9 @@ def _odd_jitter_func(step: float, rng: np.random.Generator) -> np.ndarray:
 
 
 def _get_stratified_coords(
-    mask_pixel_perc: float, shape: Tuple[int, ...]
+    mask_pixel_perc: float,
+    shape: Tuple[int, ...],
+    rng: Optional[np.random.Generator] = None,
 ) -> np.ndarray:
     """
     Generate coordinates of the pixels to mask.
@@ -113,6 +123,8 @@ def _get_stratified_coords(
         calculating the distance between masked pixels across each axis.
     shape : Tuple[int, ...]
         Shape of the input patch.
+    rng : np.random.Generator or None
+        Random number generator.
 
     Returns
     -------
@@ -124,7 +136,8 @@ def _get_stratified_coords(
             "Calculating coordinates is only possible for 2D and 3D patches"
         )
 
-    rng = np.random.default_rng()
+    if rng is None:
+        rng = np.random.default_rng()
 
     mask_pixel_distance = np.round((100 / mask_pixel_perc) ** (1 / len(shape))).astype(
         np.int32
@@ -228,6 +241,7 @@ def uniform_manipulate(
     subpatch_size: int = 11,
     remove_center: bool = True,
     struct_params: Optional[StructMaskParameters] = None,
+    rng: Optional[np.random.Generator] = None,
 ) -> Tuple[np.ndarray, np.ndarray]:
     """
     Manipulate pixels by replacing them with a neighbor values.
@@ -248,19 +262,23 @@ def uniform_manipulate(
         Size of the subpatch the new pixel value is sampled from, by default 11.
     remove_center : bool
         Whether to remove the center pixel from the subpatch, by default False.
-    struct_params : Optional[StructMaskParameters]
+    struct_params : StructMaskParameters or None
         Parameters for the structN2V mask (axis and span).
+    rng : np.random.Generator or None
+        Random number generator.
 
     Returns
     -------
     Tuple[np.ndarray]
         Tuple containing the manipulated patch and the corresponding mask.
     """
+    if rng is None:
+        rng = np.random.default_rng()
+
     # Get the coordinates of the pixels to be replaced
     transformed_patch = patch.copy()
 
-    subpatch_centers = _get_stratified_coords(mask_pixel_percentage, patch.shape)
-    rng = np.random.default_rng()
+    subpatch_centers = _get_stratified_coords(mask_pixel_percentage, patch.shape, rng)
 
     # Generate coordinate grid for subpatch
     roi_span_full = np.arange(
@@ -303,6 +321,7 @@ def median_manipulate(
     mask_pixel_percentage: float,
     subpatch_size: int = 11,
     struct_params: Optional[StructMaskParameters] = None,
+    rng: Optional[np.random.Generator] = None,
 ) -> Tuple[np.ndarray, np.ndarray]:
     """
     Manipulate pixels by replacing them with the median of their surrounding subpatch.
@@ -322,18 +341,23 @@ def median_manipulate(
         Approximate percentage of pixels to be masked.
     subpatch_size : int
         Size of the subpatch the new pixel value is sampled from, by default 11.
-    struct_params : Optional[StructMaskParameters]
+    struct_params : StructMaskParameters or None, optional
         Parameters for the structN2V mask (axis and span).
+    rng : np.random.Generator or None, optional
+        Random number generato, by default None.
 
     Returns
     -------
     Tuple[np.ndarray]
            Tuple containing the manipulated patch, the original patch and the mask.
     """
+    if rng is None:
+        rng = np.random.default_rng()
+
     transformed_patch = patch.copy()
 
     # Get the coordinates of the pixels to be replaced
-    subpatch_centers = _get_stratified_coords(mask_pixel_percentage, patch.shape)
+    subpatch_centers = _get_stratified_coords(mask_pixel_percentage, patch.shape, rng)
 
     # Generate coordinate grid for subpatch
     roi_span = np.array(

careamics/transforms/tta.py

@@ -1,11 +1,8 @@
 """Test-time augmentations."""
 
-from typing import List
-
 from torch import Tensor, flip, mean, rot90, stack
 
 
-# TODO add tests
 class ImageRestorationTTA:
     """
     Test-time augmentation for image restoration tasks.
@@ -13,62 +10,79 @@ class ImageRestorationTTA:
     The augmentation is performed using all 90 deg rotations and their flipped version,
     as well as the original image flipped.
 
-    Tensors should be of shape SC(Z)YX
+    Tensors should be of shape SC(Z)YX.
 
     This transformation is used in the LightningModule in order to perform test-time
-    agumentation.
+    augmentation.
     """
 
-    def __init__(self) -> None:
-        """Constructor."""
-        pass
-
-    def forward(self, x: Tensor) -> List[Tensor]:
+    def forward(self, input_tensor: Tensor) -> list[Tensor]:
         """
         Apply test-time augmentation to the input tensor.
 
         Parameters
         ----------
-        x : Tensor
+        input_tensor : Tensor
             Input tensor, shape SC(Z)YX.
 
         Returns
         -------
-        List[Tensor]
+        list of torch.Tensor
             List of augmented tensors.
         """
+        # axes: only applies to YX axes
+        axes = (-2, -1)
+
         augmented = [
-            x,
-            rot90(x, 1, dims=(-2, -1)),
-            rot90(x, 2, dims=(-2, -1)),
-            rot90(x, 3, dims=(-2, -1)),
+            # original
+            input_tensor,
+            # rotations
+            rot90(input_tensor, 1, dims=axes),
+            rot90(input_tensor, 2, dims=axes),
+            rot90(input_tensor, 3, dims=axes),
+            # original flipped
+            flip(input_tensor, dims=(axes[0],)),
+            flip(input_tensor, dims=(axes[1],)),
         ]
-        augmented_flip = augmented.copy()
-        for x_ in augmented:
-            augmented_flip.append(flip(x_, dims=(-3, -1)))
-        return augmented_flip
 
-    def backward(self, x: List[Tensor]) -> Tensor:
+        # rotated once, flipped
+        augmented.extend(
+            [
+                flip(augmented[1], dims=(axes[0],)),
+                flip(augmented[1], dims=(axes[1],)),
+            ]
+        )
+
+        return augmented
+
+    def backward(self, x: list[Tensor]) -> Tensor:
         """Undo the test-time augmentation.
 
         Parameters
         ----------
         x : Any
-            List of augmented tensors.
+            List of augmented tensors of shape SC(Z)YX.
 
         Returns
         -------
         Any
             Original tensor.
         """
+        axes = (-2, -1)
+
         reverse = [
+            # original
             x[0],
-            rot90(x[1], -1, dims=(-2, -1)),
-            rot90(x[2], -2, dims=(-2, -1)),
-            rot90(x[3], -3, dims=(-2, -1)),
-            flip(x[4], dims=(-3, -1)),
-            rot90(flip(x[5], dims=(-3, -1)), -1, dims=(-2, -1)),
-            rot90(flip(x[6], dims=(-3, -1)), -2, dims=(-2, -1)),
-            rot90(flip(x[7], dims=(-3, -1)), -3, dims=(-2, -1)),
+            # rotated
+            rot90(x[1], -1, dims=axes),
+            rot90(x[2], -2, dims=axes),
+            rot90(x[3], -3, dims=axes),
+            # original flipped
+            flip(x[4], dims=(axes[0],)),
+            flip(x[5], dims=(axes[1],)),
+            # rotated once, flipped
+            rot90(flip(x[6], dims=(axes[0],)), -1, dims=axes),
+            rot90(flip(x[7], dims=(axes[1],)), -1, dims=axes),
         ]
+
         return mean(stack(reverse), dim=0)

careamics/utils/ram.py

@@ -5,11 +5,11 @@ import psutil
 
 def get_ram_size() -> int:
     """
-    Get RAM size in bytes.
+    Get RAM size in mbytes.
 
     Returns
     -------
     int
         RAM size in mbytes.
     """
-    return psutil.virtual_memory().total / 1024**2
+    return psutil.virtual_memory().available / 1024**2

{careamics-0.1.0rc6.dist-info → careamics-0.1.0rc7.dist-info}/METADATA

@@ -1,31 +1,32 @@
 Metadata-Version: 2.3
 Name: careamics
-Version: 0.1.0rc6
+Version: 0.1.0rc7
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics
-Author-email: Igor Zubarev <igor.zubarev@fht.org>, Joran Deschamps <joran.deschamps@fht.org>
+Author-email: Melisande Croft <melisande.croft@fht.org>, Joran Deschamps <joran.deschamps@fht.org>, Igor Zubarev <igor.zubarev@fht.org>
 License: BSD-3-Clause
 License-File: LICENSE
 Classifier: Development Status :: 3 - Alpha
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
-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-Python: >=3.9
 Requires-Dist: bioimageio-core>=0.6.0
+Requires-Dist: numpy<2.0.0
 Requires-Dist: psutil
 Requires-Dist: pydantic>=2.5
 Requires-Dist: pytorch-lightning>=2.2.0
 Requires-Dist: pyyaml
-Requires-Dist: scikit-image
+Requires-Dist: scikit-image<=0.23.2
 Requires-Dist: tifffile
 Requires-Dist: torch>=2.0.0
-Requires-Dist: zarr
+Requires-Dist: torchvision
+Requires-Dist: zarr<3.0.0
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == 'dev'
 Requires-Dist: pytest; extra == 'dev'

{careamics-0.1.0rc6.dist-info → careamics-0.1.0rc7.dist-info}/RECORD

@@ -1,28 +1,27 @@
 careamics/__init__.py,sha256=DkMGt4t9ua0gCgvZFEtb6eydvoxG976T0KUro8KnDNA,760
-careamics/careamist.py,sha256=vn-XiawERTTIKZqcfTg8leoVoLdBmHWIe9tkGrgkEGY,29719
+careamics/careamist.py,sha256=BtCJWXD4zlKAo05acHj-k-r7wdBcH9eHMQQ6x0wERjo,25911
 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/lightning_datamodule.py,sha256=NoMJIaJU0BizBNTSC-dzR1mWED1urHMXdH6hIFi-QfE,32536
+careamics/lightning_module.py,sha256=T1G_QmBAMHfZyynD6nywT9F6bFdjDDdXqJQnjqiODek,10483
+careamics/lightning_prediction_datamodule.py,sha256=cZuiwImD-e4Fuy493PWfwhR0fWm_uqor8itjgsQCWos,14595
 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/algorithm_model.py,sha256=Lu7eYyLql5bEeTDLnJ4ms-kqSQ-EufNbt9SNa91K_Ec,5109
 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/configuration_example.py,sha256=fhV02Y3wm9anwWFx4Yi5y-OoP31wEYBJYggbyGONQuk,2486
+careamics/config/configuration_factory.py,sha256=viTuBK8bUD266OG9w7B9XZDXlH39D-FaxMq6mai3k6E,21323
+careamics/config/configuration_model.py,sha256=mmHNnWDK7BklCwd3JV6EcHU57EJ6JKBK0mK11G6Cvxo,18472
+careamics/config/data_model.py,sha256=JANDySUFo2iU74RYPhHgjQjfzn1x2mUZlFJFLiW42TA,14257
+careamics/config/inference_model.py,sha256=3n3jy922lTD9NhnSNA876Rmrr2MavFk2pmOE967itLQ,6447
+careamics/config/optimizer_models.py,sha256=-XVzi7CsxfcThTUjlyn4btJa6oHbFOf-q3h9qLM9t0k,5346
+careamics/config/tile_information.py,sha256=TAqfAthPSnIqerq72qP4KlTXPqci9XE9pCVN7J3bMJ4,2246
 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/custom_model.py,sha256=K2RXK2YINm3SCzTxhxzUzFbFV-FYvWQVEDQ-i5bOIoQ,4592
 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
@@ -39,56 +38,81 @@ careamics/config/support/supported_losses.py,sha256=TPsMCuDdgb64TRyDwonnwHb1R-rk
 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/support/supported_transforms.py,sha256=4uob-bnZ5aqpN5aEI67-aa7bsmVCrKxEknzf2BAZ3W4,283
 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/normalize_model.py,sha256=1Rkk6IkF-7ytGU6HSzP-TpOi4RRWiQJ6fOd8zammXcg,1936
 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/config/validators/validator_utils.py,sha256=aNFzpBVbef3BZIt6MiNMVc2kW6MJDWqQgdYkFM8Gjig,2621
+careamics/dataset/__init__.py,sha256=NQSWdpQu6BhqGGHUYuOt1hXJrGUN1LPNCP1A8duMY84,547
+careamics/dataset/in_memory_dataset.py,sha256=DfFpSdsYM4aNw6FWn_yDHA6seQDSozGyt-Q57pDpJDA,9457
+careamics/dataset/in_memory_pred_dataset.py,sha256=VvwW5D8TjgO_kR8eZinP-9qepSiI6ZsUN7FZ0Rvc8Bs,2161
+careamics/dataset/in_memory_tiled_pred_dataset.py,sha256=DANmlnlV1ysXKdwGvmJoOYKcjlgoMhnSGSDRpeK79ZA,3552
+careamics/dataset/iterable_dataset.py,sha256=uEmiO8n2qirJv5XkMU5lKmPMBL7rw06GRQQL6BQpfus,9694
+careamics/dataset/iterable_pred_dataset.py,sha256=AtsNRKOEkfDG8y3wa0bi5ImEqEaU2E5LM_iXcuK4Ehw,3706
+careamics/dataset/iterable_tiled_pred_dataset.py,sha256=Q0OkAtYWlsClRSNdl74sPIvbq5rLGZvORzywOJ_YrUw,4499
 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/__init__.py,sha256=DuPIjndTs0VhZsUIk2IcSk6H9N0d0ARyA5U3v3Qz-hw,666
 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/file_utils.py,sha256=s7RmmnHa7ojl4kauXfuj7hn0dAx0HB1d2ES7sUSS7IQ,4062
+careamics/dataset/dataset_utils/iterate_over_files.py,sha256=ACiltjAH2aKR0UOEvWPuuxv68NWEd2aDMFE07caxhWo,2859
+careamics/dataset/dataset_utils/read_tiff.py,sha256=emzQgodEaBsLB0ULH4lUUbsDd9PylR8DQ3rb7g0l2b8,1336
 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/dataset_utils/running_stats.py,sha256=0uOLaXpNwmY4lIElsHg4Ezf1YRbHy9An8GHXGYOaYmg,5565
 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/patching.py,sha256=XoJMfOwYItNQNJOJmRN9swtFiFu0G2L6qvUhP7jhYes,8432
+careamics/dataset/patching/random_patching.py,sha256=61sLxA4eJN5TIWBVIDZdJahS_CkclpM7Kc_VdPj91dU,6486
 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/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/tiled_patching.py,sha256=Zhhc0TwXVy4P_tZxS3B5tQZK6SRhGiQwnzVr-1BC4ww,5952
 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/lvae_training/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+careamics/lvae_training/data_modules.py,sha256=A5Uoo4qtPdX99QSi-Zl22LzO0I1DszJbQuXMGUXGQEE,46665
+careamics/lvae_training/data_utils.py,sha256=tRk0k0TkBLPocqlUlkwQN_dm5jzw5z74YNs2DsCuy9Y,21670
+careamics/lvae_training/eval_utils.py,sha256=_AlXNXk4uGS2AGsF4PHJZpJoWBgq32kvQLEh7awOIvc,32405
+careamics/lvae_training/get_config.py,sha256=-CWVxlPo71_huUSmXnmYvOmgvcvrZiv0wIpXnR32l6E,3054
+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=Eu--3-RHSfhQVsJ-CTDXhUeoM1fzf_H9IGtBaNPOsHI,11044
+careamics/lvae_training/train_utils.py,sha256=e-d4QsF-li8MmAPkAmB1daHpkuU16nBTnQFZYqpTjn4,3567
 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/bmz_io.py,sha256=Gc6uN0aO_kEDzQnJTSTNDS7PiYC684FfDNI0X9rZm8g,7031
+careamics/model_io/model_io_utils.py,sha256=Pxm_9uYRBDOMa8dC4ENk-Vre9CXsTIORGvMwn8mLzXY,2347
 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/model_io/bioimage/model_description.py,sha256=3jw4wkJDefLEW-2BbEfAml3AwyteZszL-v8JYpJRcOo,9635
 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/models/lvae/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+careamics/models/lvae/layers.py,sha256=wFuQgmtJtB7YNuNi2dVoOEWq1ndR6ku4iGvC2u0TJlM,84991
+careamics/models/lvae/likelihoods.py,sha256=FRFTh34FaBLGxn9OXFzqFyHhhJMSKYhgqxwG65VbGh8,10489
+careamics/models/lvae/lvae.py,sha256=5RlK4-h55dGz9UMCh8JCbLsaaIQ5S2IKGeI9d4nD5dA,40167
+careamics/models/lvae/noise_models.py,sha256=yotY5gkPAowbI7esOmHlzBWcSsZlH2G3U7uYIWghGwY,15703
+careamics/models/lvae/utils.py,sha256=muy4nLHmnB3BPAI0tQbJK_vVtBZOLBvhrJigHIOx5V4,11542
+careamics/prediction_utils/__init__.py,sha256=0rtfNXeH5RvJ9ieeCbBV9i9eyLXxo_IMpqVH1-H2N8E,359
+careamics/prediction_utils/create_pred_datamodule.py,sha256=rv_Q0v4Es-NE1IU_nUkJYUsYo3Gh3whvOj43WlTw2hc,5846
+careamics/prediction_utils/prediction_outputs.py,sha256=1BHJF_dpw3QwH8uF_uE1u4tVui01mm899O2VcGvWYvM,4730
+careamics/prediction_utils/stitch_prediction.py,sha256=VRJc51KHg_3gWTCNdvQpHfrGaNqDHd9hHhnvqxg2cjE,3081
 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/n2v_manipulate.py,sha256=Gty7Jtu-RiFb1EnlrOi652qAOGKU5ZHvidRvykWqJxg,5438
+careamics/transforms/normalize.py,sha256=dfGWCGPyNwyEqg5wUCAA8cGdT1MvNkpKUEpw8Cw8DfA,7274
+careamics/transforms/pixel_manipulation.py,sha256=lNA19Vlo_3GHzRnT_4AFuv6eWQaxbie2PTYGalCY4YQ,13346
 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/tta.py,sha256=78S7Df9rLHmEVSQSI1qDcRrRJGauyG3oaIrXkckCkmw,2335
 careamics/transforms/xy_flip.py,sha256=Q1kKTa2kE3W1P3dlpT4GAVSSHM3TebnrvIyWh75Fnko,3443
 careamics/transforms/xy_random_rotate90.py,sha256=zWdBROLLjgxTMSQEQesJr17j84BmZhKWCMVVONHU8mw,2781
 careamics/utils/__init__.py,sha256=tO1X5QTfnthepuW0uYagz5fWehtLtwK2gPmkUeqhdOw,334
@@ -97,11 +121,10 @@ careamics/utils/context.py,sha256=Ljf70OR1FcYpsVpxb5Sr2fzmPVIZgDS1uZob_3BcELg,14
 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/ram.py,sha256=tksyn8dVX_iJXmrDZDGub32hFZWIaNxnMheO5G1p43I,244
 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-0.1.0rc7.dist-info/METADATA,sha256=ZIJHL8fCiF2MDXpkvtegSSA889deeY9USh0emDYJncM,3525
+careamics-0.1.0rc7.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+careamics-0.1.0rc7.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
+careamics-0.1.0rc7.dist-info/RECORD,,

{careamics-0.1.0rc6.dist-info → careamics-0.1.0rc7.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.24.2
+Generator: hatchling 1.25.0
 Root-Is-Purelib: true
 Tag: py3-none-any

careamics/lightning_prediction_loop.py

@@ -1,118 +0,0 @@
-"""Lithning prediction loop allowing tiling."""
-
-from typing import Optional
-
-import pytorch_lightning as L
-from pytorch_lightning.loops.fetchers import _DataLoaderIterDataFetcher
-from pytorch_lightning.loops.utilities import _no_grad_context
-from pytorch_lightning.trainer import call
-from pytorch_lightning.utilities.types import _PREDICT_OUTPUT
-
-from careamics.prediction import stitch_prediction
-
-
-class CAREamicsPredictionLoop(L.loops._PredictionLoop):
-    """
-    CAREamics prediction loop.
-
-    This class extends the PyTorch Lightning `_PredictionLoop` class to include
-    the stitching of the tiles into a single prediction result.
-    """
-
-    def _on_predict_epoch_end(self) -> Optional[_PREDICT_OUTPUT]:
-        """Call `on_predict_epoch_end` hook.
-
-        Adapted from the parent method.
-
-        Returns
-        -------
-        Optional[_PREDICT_OUTPUT]
-            Prediction output.
-        """
-        trainer = self.trainer
-        call._call_callback_hooks(trainer, "on_predict_epoch_end")
-        call._call_lightning_module_hook(trainer, "on_predict_epoch_end")
-
-        if self.return_predictions:
-            ########################################################
-            ################ CAREamics specific code ###############
-            if len(self.predicted_array) == 1:
-                # TODO does this make sense to here? (force numpy array)
-                return self.predicted_array[0].numpy()
-            else:
-                # TODO revisit logic
-                return [element.numpy() for element in self.predicted_array]
-            ########################################################
-        return None
-
-    @_no_grad_context
-    def run(self) -> Optional[_PREDICT_OUTPUT]:
-        """Run the prediction loop.
-
-        Adapted from the parent method in order to stitch the predictions.
-
-        Returns
-        -------
-        Optional[_PREDICT_OUTPUT]
-            Prediction output.
-        """
-        self.setup_data()
-        if self.skip:
-            return None
-        self.reset()
-        self.on_run_start()
-        data_fetcher = self._data_fetcher
-        assert data_fetcher is not None
-
-        self.predicted_array = []
-        self.tiles = []
-        self.stitching_data = []
-
-        while True:
-            try:
-                if isinstance(data_fetcher, _DataLoaderIterDataFetcher):
-                    dataloader_iter = next(data_fetcher)
-                    # hook's batch_idx and dataloader_idx arguments correctness cannot
-                    # be guaranteed in this setting
-                    batch = data_fetcher._batch
-                    batch_idx = data_fetcher._batch_idx
-                    dataloader_idx = data_fetcher._dataloader_idx
-                else:
-                    dataloader_iter = None
-                    batch, batch_idx, dataloader_idx = next(data_fetcher)
-                self.batch_progress.is_last_batch = data_fetcher.done
-
-                # run step hooks
-                self._predict_step(batch, batch_idx, dataloader_idx, dataloader_iter)
-
-                ########################################################
-                ################ CAREamics specific code ###############
-                # TODO: next line is not compatible with muSplit
-                is_tiled = len(self.predictions[batch_idx]) == 2
-                if is_tiled:
-                    # extract the last tile flag and the coordinates (crop and stitch)
-                    last_tile, *stitch_data = self.predictions[batch_idx][1]
-
-                    # append the tile and the coordinates to the lists
-                    self.tiles.append(self.predictions[batch_idx][0])
-                    self.stitching_data.append(stitch_data)
-
-                    # if last tile, stitch the tiles and add array to the prediction
-                    if any(last_tile):
-                        predicted_batches = stitch_prediction(
-                            self.tiles, self.stitching_data
-                        )
-                        self.predicted_array.append(predicted_batches)
-                        self.tiles.clear()
-                        self.stitching_data.clear()
-                else:
-                    # simply add the prediction to the list
-                    self.predicted_array.append(self.predictions[batch_idx])
-                ########################################################
-            except StopIteration:
-                break
-            finally:
-                self._restarting = False
-        return self.on_run_end()
-
-    # TODO predictions aren't stacked, list returned

careamics/prediction/__init__.py

@@ -1,7 +0,0 @@
-"""Prediction functions."""
-
-__all__ = [
-    "stitch_prediction",
-]
-
-from .stitch_prediction import stitch_prediction