careamics 0.1.0rc7__py3-none-any.whl → 0.1.0rc8__py3-none-any.whl

careamics/prediction_utils/prediction_outputs.py

@@ -13,7 +13,9 @@ def convert_outputs(
     predictions: List[Any], tiled: bool
 ) -> Union[List[NDArray], NDArray]:
     """
-    Convert the outputs to the desired form.
+    Convert the Lightning trainer outputs to the desired form.
+
+    This method allows stitching back together tiled predictions.
 
     Parameters
     ----------
@@ -34,21 +36,10 @@ def convert_outputs(
     # this layout is to stop mypy complaining
     if tiled:
         predictions_comb = combine_batches(predictions, tiled)
-        # remove sample dimension (always 1) `stitch_predict` func expects no S dim
-        tiles = [pred[0] for pred in predictions_comb[0]]
-        tile_infos = predictions_comb[1]
-        predictions_output = stitch_prediction(tiles, tile_infos)
+        predictions_output = stitch_prediction(*predictions_comb)
     else:
         predictions_output = combine_batches(predictions, tiled)
 
-    # TODO: add this in? Returns output with same axes as input
-    # Won't work with tiling rn because stitch_prediction func removes S axis
-    # predictions = reshape(predictions, axes)
-    # At least make sure stitched prediction and non-tiled prediction have matching axes
-
-    # TODO: might want to remove this
-    if len(predictions_output) == 1:
-        return predictions_output[0]
     return predictions_output
 
 
@@ -94,7 +85,7 @@ def combine_batches(
     if tiled:
         return _combine_tiled_batches(predictions)
     else:
-        return _combine_untiled_batches(predictions)
+        return _combine_array_batches(predictions)
 
 
 def _combine_tiled_batches(
@@ -105,8 +96,11 @@ def _combine_tiled_batches(
 
     Parameters
     ----------
-    predictions : list
-        Predictions that are output from `Trainer.predict`.
+    predictions : list of (numpy.ndarray, list of TileInformation)
+        Predictions that are output from `Trainer.predict`. For tiled batches, this is
+        a list of tuples. The first element of the tuples is the prediction output of
+        tiles with dimension (B, C, (Z), Y, X), where B is batch size. The second
+        element of the tuples is a list of TileInformation objects of length B.
 
     Returns
     -------
@@ -117,49 +111,27 @@ 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_untiled_batches(
+    prediction_tiles: List[NDArray] = _combine_array_batches(
         [preds for preds, _ in predictions]
     )
     return prediction_tiles, tile_infos
 
 
-def _combine_untiled_batches(predictions: List[NDArray]) -> List[NDArray]:
+def _combine_array_batches(predictions: List[NDArray]) -> List[NDArray]:
     """
-    Combine batches from un-tiled output.
+    Combine batches of arrays.
 
     Parameters
     ----------
-        predictions : list
-            Predictions that are output from `Trainer.predict`.
+    predictions : list
+        Prediction arrays that are output from `Trainer.predict`. A list of arrays that
+        have dimensions (B, C, (Z), Y, X), where B is batch size.
 
     Returns
     -------
-        list of nunpy.ndarray
-            Combined batches.
+    list of numpy.ndarray
+        A list of arrays with dimensions (1, C, (Z), Y, X).
     """
     prediction_concat: NDArray = np.concatenate(predictions, axis=0)
     prediction_split = np.split(prediction_concat, prediction_concat.shape[0], axis=0)
     return prediction_split
-
-
-def reshape(predictions: List[NDArray], axes: str) -> List[NDArray]:
-    """
-    Reshape predictions to have dimensions of input.
-
-    Parameters
-    ----------
-    predictions : list
-        Predictions that are output from `Trainer.predict`.
-    axes : str
-        Axes SC(Z)YX.
-
-    Returns
-    -------
-    List[NDArray]
-        Reshaped predicitions.
-    """
-    if "C" not in axes:
-        predictions = [pred[:, 0] for pred in predictions]
-    if "S" not in axes:
-        predictions = [pred[0] for pred in predictions]
-    return predictions

careamics/prediction_utils/stitch_prediction.py

@@ -1,8 +1,10 @@
 """Prediction utility functions."""
 
-from typing import List
+import builtins
+from typing import List, Union
 
 import numpy as np
+from numpy.typing import NDArray
 
 from careamics.config.tile_information import TileInformation
 
@@ -52,9 +54,9 @@ def stitch_prediction(
 
 
 def stitch_prediction_single(
-    tiles: List[np.ndarray],
+    tiles: List[NDArray],
     tile_infos: List[TileInformation],
-) -> np.ndarray:
+) -> NDArray:
     """
     Stitch tiles back together to form a full image.
 
@@ -72,29 +74,30 @@ def stitch_prediction_single(
     Returns
     -------
     numpy.ndarray
-        Full image.
+        Full image, with dimensions SC(Z)YX.
     """
     # retrieve whole array size
     input_shape = tile_infos[0].array_shape
     predicted_image = np.zeros(input_shape, dtype=np.float32)
 
+    # reshape
+    # TODO: can be more elegantly solved if TileInformation allows singleton dims
+    singleton_dims = tuple(np.where(np.array(tiles[0].shape) == 1)[0])
+    predicted_image = np.expand_dims(predicted_image, singleton_dims)
+
     for tile, tile_info in zip(tiles, tile_infos):
-        n_channels = tile.shape[0]
 
         # Compute coordinates for cropping predicted tile
-        slices = (slice(0, n_channels),) + tuple(
-            [slice(c[0], c[1]) for c in tile_info.overlap_crop_coords]
+        crop_slices: tuple[Union[builtins.ellipsis, slice], ...] = (
+            ...,
+            *[slice(c[0], c[1]) for c in tile_info.overlap_crop_coords],
         )
 
         # Crop predited tile according to overlap coordinates
-        cropped_tile = tile[slices]
+        cropped_tile = tile[crop_slices]
 
         # Insert cropped tile into predicted image using stitch coordinates
-        predicted_image[
-            (
-                ...,
-                *[slice(c[0], c[1]) for c in tile_info.stitch_coords],
-            )
-        ] = cropped_tile.astype(np.float32)
+        image_slices = (..., *[slice(c[0], c[1]) for c in tile_info.stitch_coords])
+        predicted_image[image_slices] = cropped_tile.astype(np.float32)
 
     return predicted_image

careamics/utils/__init__.py

@@ -7,9 +7,11 @@ __all__ = [
     "BaseEnum",
     "get_logger",
     "get_careamics_home",
+    "autocorrelation",
 ]
 
 
+from .autocorrelation import autocorrelation
 from .base_enum import BaseEnum
 from .context import cwd, get_careamics_home
 from .logging import get_logger

careamics/utils/autocorrelation.py

@@ -0,0 +1,40 @@
+"""Autocorrelation function."""
+
+import numpy as np
+from numpy.typing import NDArray
+
+
+def autocorrelation(image: NDArray) -> NDArray:
+    """Compute the autocorrelation of an image.
+
+    This method is used to explore spatial correlations in images,
+    in particular in the noise.
+
+    The autocorrelation is normalized to the zero-shift value, which is centered in
+    the resulting images.
+
+    Parameters
+    ----------
+    image : NDArray
+        Input image.
+
+    Returns
+    -------
+    numpy.ndarray
+        Autocorrelation of the input image.
+    """
+    # normalize image
+    image = (image - np.mean(image)) / np.std(image)
+
+    # compute autocorrelation in fourier space
+    image = np.fft.fftn(image)
+    image = np.abs(image) ** 2
+    image = np.fft.ifftn(image).real
+
+    # normalize to zero shift value
+    image = image / image.flat[0]
+
+    # shift zero frequency to center
+    image = np.fft.fftshift(image)
+
+    return image

{careamics-0.1.0rc7.dist-info → careamics-0.1.0rc8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: careamics
-Version: 0.1.0rc7
+Version: 0.1.0rc8
 Summary: Toolbox for running N2V and friends.
 Project-URL: homepage, https://careamics.github.io/
 Project-URL: repository, https://github.com/CAREamics/careamics

{careamics-0.1.0rc7.dist-info → careamics-0.1.0rc8.dist-info}/RECORD

@@ -1,30 +1,23 @@
-careamics/__init__.py,sha256=DkMGt4t9ua0gCgvZFEtb6eydvoxG976T0KUro8KnDNA,760
-careamics/careamist.py,sha256=BtCJWXD4zlKAo05acHj-k-r7wdBcH9eHMQQ6x0wERjo,25911
+careamics/__init__.py,sha256=xBCerWN66hv3T7dRGiUYLflmbJtJt1HqbSg9JCWp8pY,391
+careamics/careamist.py,sha256=Sk6tY8J4dErVHS3HgwCnR0in78Hh0shPB2CH3Woh-_I,26593
 careamics/conftest.py,sha256=Od4WcaaP0UP-XUMrFr_oo4e6c2hi_RvNbuaRTopwlmI,911
-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=Lu7eYyLql5bEeTDLnJ4ms-kqSQ-EufNbt9SNa91K_Ec,5109
-careamics/config/callback_model.py,sha256=CcamVhgRsVdskCe_9EtyWi1YbrNX5vKEplc97AYz1h8,3118
-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/__init__.py,sha256=qaR98bVRFnEHYGG5EgGBIa9P9AtMRmKzpXuc1exdteo,913
+careamics/config/algorithm_model.py,sha256=-Nx4E6M2EyBDozSTkXeYaj9b0KcIli0Gy6DE3P1WVfE,5443
+careamics/config/callback_model.py,sha256=EeYHqpMIPQwyNxLRzzX32Uncl5mZuB1bJO76RHpNymg,4555
+careamics/config/configuration_factory.py,sha256=Ckkv4ber2WSaa-BaoDNuyvpVMd02Q-9T27yziXJ-1Ak,18538
+careamics/config/configuration_model.py,sha256=4LbAt3zUtx05mfTRrXBqD57iQn2s0Y93f81M8Gce4zo,18698
+careamics/config/data_model.py,sha256=dpRthXU8lINT3laJygqka-fmUDT7U34QUHZYBX95oY8,15070
+careamics/config/inference_model.py,sha256=UE_-ZmCX6LFCbDBOwyGnvuAboF_JNX2m2LcF0WiwgCI,6961
+careamics/config/optimizer_models.py,sha256=p6gDYtO-jFtL7zVX0-Id-rGJWkkyhbU3EBrWD_4TxZE,5726
+careamics/config/tile_information.py,sha256=t82zG54BBwXCwy-IEdALNx7pghEDyvXcf_nBiOhGSTw,2598
+careamics/config/training_model.py,sha256=9I9xn1V7yIMC-1GSAxxeevDc4qQENAtCFnJVMd8haqA,1769
 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=K2RXK2YINm3SCzTxhxzUzFbFV-FYvWQVEDQ-i5bOIoQ,4592
+careamics/config/architectures/architecture_model.py,sha256=4WvQQJGz5DLFjOUryZx0fqPuEMlF2RhtlV5XudJTIbc,922
+careamics/config/architectures/custom_model.py,sha256=IRaequRi5BXMPL14gLr1B_27_XWPeWxQwgHF9_EJMaU,4664
 careamics/config/architectures/register_model.py,sha256=lHH0aUPmXtI3Bq_76zkhg07_Yb_nOJZkZJLCC_G-rZM,2434
-careamics/config/architectures/unet_model.py,sha256=sQjfqTjh1kTNi369U3_94jroU6LyLlflaIe8FwdHQvo,2892
-careamics/config/architectures/vae_model.py,sha256=Z0satmte4udManh_bxtl93ZmQlmo6JFE1NQIuZkTsQk,926
+careamics/config/architectures/unet_model.py,sha256=8F2KosNkrXUP2bxlm-D1mowS9x3GOjyXjsEo1Kf-05k,3497
+careamics/config/architectures/vae_model.py,sha256=iLPwjI4B_Ivv_qQNUJc4-Gwm4z8UA3P5BsKQucRFEMI,962
 careamics/config/references/__init__.py,sha256=rZAQzmrciX5cNICcXaBH6sbE6N6L7_qYQUkasNy9y-c,763
 careamics/config/references/algorithm_descriptions.py,sha256=wR3hIoeg5eiUEPbwTxMpQYLTKQyRl_5naSDbBZOZESU,3541
 careamics/config/references/references.py,sha256=AXx08FJQxHb7SYOluCr_eQn_mbOris5dXqhKrCnhBTE,1573
@@ -32,7 +25,7 @@ careamics/config/support/__init__.py,sha256=pKqk76kyBraiSC1SQos-cyiQwsfOLLkLuWj6
 careamics/config/support/supported_activations.py,sha256=O27_dGDgw2P-DslKJsXGVAyS2NUQM6Ta4jeo2uTQlW0,519
 careamics/config/support/supported_algorithms.py,sha256=GCkauFDlmb2hJwFSdoIpGmpLjPeYFHOGy2NweKdw8T4,358
 careamics/config/support/supported_architectures.py,sha256=LLD6hyje9Q0BcvA7p2E8WW_cY5yEgMI_NAP4HBi27UU,540
-careamics/config/support/supported_data.py,sha256=C0VcP1DkZqJ4MPn6UZcCZX8ZfVNdz0ZJk6y89fiim2I,2084
+careamics/config/support/supported_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=TPsMCuDdgb64TRyDwonnwHb1R-rkn3OzhtHimyVtrOY,540
 careamics/config/support/supported_optimizers.py,sha256=xxbJsyohJTlHeUz2I4eRwcE3BeACs-6PH8cpX6w2wX8,1394
@@ -48,29 +41,41 @@ careamics/config/transformations/xy_random_rotate90_model.py,sha256=6sYKmtCLvz0S
 careamics/config/validators/__init__.py,sha256=iv0nVI0W7j9DxFPwh0DjRCzM9P8oLQn4Gwi5rfuFrrI,180
 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_dataset.py,sha256=7YRpbKg6nqrECDhaA88HNlstyTObQxTN9jPcNlE_aWE,9906
 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/iterable_dataset.py,sha256=vHwkzoQs-CvbGHcGtvYMF52dO6zLau89A13xDOWSGUU,9770
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 careamics/dataset/zarr_dataset.py,sha256=lojnK5bhiF1vyjuPtWXBrZ9sy5fT_rBvZJbbbnE-H_I,5665
-careamics/dataset/dataset_utils/__init__.py,sha256=DuPIjndTs0VhZsUIk2IcSk6H9N0d0ARyA5U3v3Qz-hw,666
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 careamics/dataset/dataset_utils/dataset_utils.py,sha256=zYNglet5lYKxIhTeOGG2K24oujC-m5zyYlwJcQcleVA,2662
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-careamics/dataset/dataset_utils/read_zarr.py,sha256=2jzREAnJDQSv0qmsL-v00BxmiZ_sp0ijq667LZSQ_hY,1685
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 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=XoJMfOwYItNQNJOJmRN9swtFiFu0G2L6qvUhP7jhYes,8432
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 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/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
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+careamics/file_io/read/zarr.py,sha256=2jzREAnJDQSv0qmsL-v00BxmiZ_sp0ijq667LZSQ_hY,1685
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+careamics/file_io/write/tiff.py,sha256=YU0TarBCG3w1f_HMZ_Hy7ifVdadgp9CuUD1l5_IY6zg,997
+careamics/lightning/__init__.py,sha256=IAhfuveylgTdwIqynRqmGNOGrBlNmsXNgK3TuPDqU-o,572
+careamics/lightning/lightning_module.py,sha256=ml0aGFP6MlSRtGkcoWcmX9DAlMSqJ8rW16HObBWK9MI,8881
+careamics/lightning/predict_data_module.py,sha256=rgHhS5fKoa5wscWyvmPP_FHHdVnDnLbF4sG7y_C7ZOM,12747
+careamics/lightning/train_data_module.py,sha256=72G19J26fg_kkNtCO2M9pcjq9sVkchL7MvZ8wrjS1So,27891
+careamics/lightning/callbacks/__init__.py,sha256=spxJlDByD-6QtMl9vcIty8Wb0tyHaSTKTItozHenI44,204
+careamics/lightning/callbacks/hyperparameters_callback.py,sha256=ODJpwwdgc1-Py8yEUpXLar8_IOAcfR7lF3--6LfSiGc,1496
+careamics/lightning/callbacks/progress_bar_callback.py,sha256=8HvNSWZldixd6pjz0dLDo0apIbzTovv5smKmZ6tZQ8U,2444
 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
@@ -84,8 +89,8 @@ careamics/lvae_training/metrics.py,sha256=KTDAKhe3vh-YxzGibjtkIG2nnUyujbnwqX4xGw
 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=Gc6uN0aO_kEDzQnJTSTNDS7PiYC684FfDNI0X9rZm8g,7031
-careamics/model_io/model_io_utils.py,sha256=Pxm_9uYRBDOMa8dC4ENk-Vre9CXsTIORGvMwn8mLzXY,2347
+careamics/model_io/bmz_io.py,sha256=53PvOMTZ3ZkSgFg-OtGopuf_vJ51xs6nfv1v0tufd7g,7041
+careamics/model_io/model_io_utils.py,sha256=EebZL3t6oIHY0kuTKacmAEriTQ4B77KuAQ84UHG7XW4,2357
 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
@@ -101,10 +106,9 @@ careamics/models/lvae/likelihoods.py,sha256=FRFTh34FaBLGxn9OXFzqFyHhhJMSKYhgqxwG
 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/prediction_utils/__init__.py,sha256=uYKzirlF-unFL9GbDPxFnYgOwSjGAtik9fonU7DfuEY,270
+careamics/prediction_utils/prediction_outputs.py,sha256=cHbt45txofkMBWMUpJmdwOgHgG2By1gwnR6ZQv4n5qU,4104
+careamics/prediction_utils/stitch_prediction.py,sha256=XSu2aSEbX1oXaXxhkXMnmhy2gKE8W28CmzH_bNc1Cm8,3369
 careamics/transforms/__init__.py,sha256=VIHIsC8sMAh1TCm67ifB816Zp-LRo6rAONPuT2Qs3bs,483
 careamics/transforms/compose.py,sha256=mTkhoxvgvsBqNoz9RWpJ_tqsDl1CDp0-UARTjUuBRf4,3477
 careamics/transforms/n2v_manipulate.py,sha256=Gty7Jtu-RiFb1EnlrOi652qAOGKU5ZHvidRvykWqJxg,5438
@@ -115,7 +119,8 @@ careamics/transforms/transform.py,sha256=cEqc4ci8na70i-HIGYC7udRfVa8D_8OjdRVrr3t
 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
+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
@@ -124,7 +129,7 @@ careamics/utils/path_utils.py,sha256=8AugiG5DOmzgSnTCJI8vypXaPE0XhnR-9pzeiFUZ-0I
 careamics/utils/ram.py,sha256=tksyn8dVX_iJXmrDZDGub32hFZWIaNxnMheO5G1p43I,244
 careamics/utils/receptive_field.py,sha256=Y2h4c8S6glX3qcx5KHDmO17Kkuyey9voxfoXyqcAfiM,3296
 careamics/utils/torch_utils.py,sha256=g1zxdlM7_BA7mMLcCzmrxZX4LmH__KXlJibC95muVaA,3014
-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-0.1.0rc8.dist-info/METADATA,sha256=7hTsctBI62YC9wmgYwUaByOXUJzKrlHLV8iMpnTNY00,3525
+careamics-0.1.0rc8.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+careamics-0.1.0rc8.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
+careamics-0.1.0rc8.dist-info/RECORD,,

careamics/config/configuration_example.py

@@ -1,86 +0,0 @@
-"""Example of configurations."""
-
-from .algorithm_model import AlgorithmConfig
-from .architectures import UNetModel
-from .configuration_model import Configuration
-from .data_model import DataConfig
-from .optimizer_models import LrSchedulerModel, OptimizerModel
-from .support import (
-    SupportedActivation,
-    SupportedAlgorithm,
-    SupportedArchitecture,
-    SupportedData,
-    SupportedLogger,
-    SupportedLoss,
-    SupportedOptimizer,
-    SupportedPixelManipulation,
-    SupportedScheduler,
-    SupportedTransform,
-)
-from .training_model import TrainingConfig
-
-
-def full_configuration_example() -> Configuration:
-    """Return a dictionnary representing a full configuration example.
-
-    Returns
-    -------
-    Configuration
-        Full configuration example.
-    """
-    experiment_name = "Full example"
-    algorithm_model = AlgorithmConfig(
-        algorithm=SupportedAlgorithm.N2V.value,
-        loss=SupportedLoss.N2V.value,
-        model=UNetModel(
-            architecture=SupportedArchitecture.UNET.value,
-            in_channels=1,
-            num_classes=1,
-            depth=2,
-            num_channels_init=32,
-            final_activation=SupportedActivation.NONE.value,
-            n2v2=True,
-        ),
-        optimizer=OptimizerModel(
-            name=SupportedOptimizer.ADAM.value, parameters={"lr": 0.0001}
-        ),
-        lr_scheduler=LrSchedulerModel(
-            name=SupportedScheduler.REDUCE_LR_ON_PLATEAU.value,
-        ),
-    )
-    data_model = DataConfig(
-        data_type=SupportedData.ARRAY.value,
-        patch_size=(256, 256),
-        batch_size=8,
-        axes="YX",
-        transforms=[
-            {
-                "name": SupportedTransform.XY_FLIP.value,
-            },
-            {
-                "name": SupportedTransform.XY_RANDOM_ROTATE90.value,
-            },
-            {
-                "name": SupportedTransform.N2V_MANIPULATE.value,
-                "roi_size": 11,
-                "masked_pixel_percentage": 0.2,
-                "strategy": SupportedPixelManipulation.MEDIAN.value,
-            },
-        ],
-        mean=0.485,
-        std=0.229,
-        dataloader_params={
-            "num_workers": 4,
-        },
-    )
-    training_model = TrainingConfig(
-        num_epochs=30,
-        logger=SupportedLogger.WANDB.value,
-    )
-
-    return Configuration(
-        experiment_name=experiment_name,
-        algorithm_config=algorithm_model,
-        data_config=data_model,
-        training_config=training_model,
-    )

careamics/dataset/dataset_utils/read_utils.py

@@ -1,27 +0,0 @@
-"""Read function utilities."""
-
-from typing import Callable, Union
-
-from careamics.config.support import SupportedData
-
-from .read_tiff import read_tiff
-
-
-def get_read_func(data_type: Union[SupportedData, str]) -> Callable:
-    """
-    Get the read function for the data type.
-
-    Parameters
-    ----------
-    data_type : SupportedData
-        Data type.
-
-    Returns
-    -------
-    Callable
-        Read function.
-    """
-    if data_type == SupportedData.TIFF:
-        return read_tiff
-    else:
-        raise NotImplementedError(f"Data type {data_type} is not supported.")