careamics 0.1.0rc6__py3-none-any.whl → 0.1.0rc8__py3-none-any.whl

careamics-0.1.0rc8.dist-info/RECORD

@@ -0,0 +1,135 @@
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+careamics-0.1.0rc8.dist-info/licenses/LICENSE,sha256=6zdNW-k_xHRKYWUf9tDI_ZplUciFHyj0g16DYuZ2udw,1509
+careamics-0.1.0rc8.dist-info/RECORD,,

{careamics-0.1.0rc6.dist-info → careamics-0.1.0rc8.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/config/configuration_example.py

@@ -1,89 +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.NORMALIZE.value,
-            },
-            {
-                "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.")

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

careamics/prediction/stitch_prediction.py

@@ -1,70 +0,0 @@
-"""Prediction utility functions."""
-
-from typing import List
-
-import numpy as np
-import torch
-
-
-def stitch_prediction(
-    tiles: List[torch.Tensor],
-    stitching_data: List[List[torch.Tensor]],
-) -> torch.Tensor:
-    """
-    Stitch tiles back together to form a full image.
-
-    Parameters
-    ----------
-    tiles : List[torch.Tensor]
-        Cropped tiles and their respective stitching coordinates.
-    stitching_data : List
-        List of information and coordinates obtained from
-        `dataset.tiled_patching.extract_tiles`.
-
-    Returns
-    -------
-    np.ndarray
-        Full image.
-    """
-    # retrieve whole array size, there is two cases to consider:
-    # 1. the tiles are stored in a list
-    # 2. the tiles are stored in a list with batches along the first dim
-    if tiles[0].shape[0] > 1:
-        input_shape = np.array(
-            [el.numpy() for el in stitching_data[0][0][0]], dtype=int
-        ).squeeze()
-    else:
-        input_shape = np.array(
-            [el.numpy() for el in stitching_data[0][0]], dtype=int
-        ).squeeze()
-
-    # TODO should use torch.zeros instead of np.zeros
-    predicted_image = torch.Tensor(np.zeros(input_shape, dtype=np.float32))
-
-    for tile_batch, (_, overlap_crop_coords_batch, stitch_coords_batch) in zip(
-        tiles, stitching_data
-    ):
-        for batch_idx in range(tile_batch.shape[0]):
-            # Compute coordinates for cropping predicted tile
-            slices = tuple(
-                [
-                    slice(c[0][batch_idx], c[1][batch_idx])
-                    for c in overlap_crop_coords_batch
-                ]
-            )
-
-            # Crop predited tile according to overlap coordinates
-            cropped_tile = tile_batch[batch_idx].squeeze()[slices]
-
-            # Insert cropped tile into predicted image using stitch coordinates
-            predicted_image[
-                (
-                    ...,
-                    *[
-                        slice(c[0][batch_idx], c[1][batch_idx])
-                        for c in stitch_coords_batch
-                    ],
-                )
-            ] = cropped_tile.to(torch.float32)
-
-    return predicted_image

careamics/utils/running_stats.py

@@ -1,43 +0,0 @@
-"""Running stats submodule, used in the Zarr dataset."""
-
-# from multiprocessing import Value
-# from typing import Tuple
-
-# import numpy as np
-
-
-# class RunningStats:
-#     """Calculates running mean and std."""
-
-#     def __init__(self) -> None:
-#         self.reset()
-
-#     def reset(self) -> None:
-#         """Reset the running stats."""
-#         self.avg_mean = Value("d", 0)
-#         self.avg_std = Value("d", 0)
-#         self.m2 = Value("d", 0)
-#         self.count = Value("i", 0)
-
-#     def init(self, mean: float, std: float) -> None:
-#         """Initialize running stats."""
-#         with self.avg_mean.get_lock():
-#             self.avg_mean.value += mean
-#         with self.avg_std.get_lock():
-#             self.avg_std.value = std
-
-#     def compute_std(self) -> Tuple[float, float]:
-#         """Compute std."""
-#         if self.count.value >= 2:
-#             self.avg_std.value = np.sqrt(self.m2.value / self.count.value)
-
-#     def update(self, value: float) -> None:
-#         """Update running stats."""
-#         with self.count.get_lock():
-#             self.count.value += 1
-#         delta = value - self.avg_mean.value
-#         with self.avg_mean.get_lock():
-#             self.avg_mean.value += delta / self.count.value
-#         delta2 = value - self.avg_mean.value
-#         with self.m2.get_lock():
-#             self.m2.value += delta * delta2

careamics-0.1.0rc6.dist-info/RECORD

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