From 2a615e0e192b801097091cf13b47e174d7a8fad8 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 6 May 2024 17:25:56 +0000 Subject: [PATCH 1/2] ci(pre-commit.ci): autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/abravalheri/validate-pyproject: v0.14 → v0.16](https://github.com/abravalheri/validate-pyproject/compare/v0.14...v0.16) - [github.com/astral-sh/ruff-pre-commit: v0.0.292 → v0.4.3](https://github.com/astral-sh/ruff-pre-commit/compare/v0.0.292...v0.4.3) - [github.com/psf/black: 23.9.1 → 24.4.2](https://github.com/psf/black/compare/23.9.1...24.4.2) - [github.com/pre-commit/mirrors-mypy: v1.5.1 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.5.1...v1.10.0) - [github.com/numpy/numpydoc: v1.6.0 → v1.7.0](https://github.com/numpy/numpydoc/compare/v1.6.0...v1.7.0) - [github.com/nbQA-dev/nbQA: 1.7.0 → 1.8.5](https://github.com/nbQA-dev/nbQA/compare/1.7.0...1.8.5) - [github.com/kynan/nbstripout: 0.6.1 → 0.7.1](https://github.com/kynan/nbstripout/compare/0.6.1...0.7.1) --- .pre-commit-config.yaml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 220afd901..3c07cef36 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,23 +9,23 @@ ci: repos: - repo: https://github.com/abravalheri/validate-pyproject - rev: v0.14 + rev: v0.16 hooks: - id: validate-pyproject - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.0.292 + rev: v0.4.3 hooks: - id: ruff args: [--fix, --target-version, py38] - repo: https://github.com/psf/black - rev: 23.9.1 + rev: 24.4.2 hooks: - id: black - repo: https://github.com/pre-commit/mirrors-mypy - rev: v1.5.1 + rev: v1.10.0 hooks: - id: mypy files: "^src/" @@ -36,13 +36,13 @@ repos: # check docstrings - repo: https://github.com/numpy/numpydoc - rev: v1.6.0 + rev: v1.7.0 hooks: - id: numpydoc-validation # jupyter linting and formatting - repo: https://github.com/nbQA-dev/nbQA - rev: 1.7.0 + rev: 1.8.5 hooks: - id: nbqa-ruff args: [--fix] @@ -51,6 +51,6 @@ repos: # strip out jupyter notebooks - repo: https://github.com/kynan/nbstripout - rev: 0.6.1 + rev: 0.7.1 hooks: - id: nbstripout From 6fc377a12b5cbfef933c4167170746db5ec1ada8 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 6 May 2024 17:26:27 +0000 Subject: [PATCH 2/2] style(pre-commit.ci): auto fixes [...] --- src/careamics/careamist.py | 15 ++++------- src/careamics/config/__init__.py | 1 - src/careamics/config/callback_model.py | 1 + src/careamics/config/configuration_factory.py | 8 +++--- src/careamics/config/configuration_model.py | 1 + src/careamics/config/data_model.py | 1 + src/careamics/config/inference_model.py | 1 + .../references/algorithm_descriptions.py | 1 + src/careamics/config/references/references.py | 1 + .../supported_extraction_strategies.py | 1 + src/careamics/config/training_model.py | 1 + .../transformations/n2v_manipulate_model.py | 1 + .../config/transformations/nd_flip_model.py | 1 + .../config/transformations/normalize_model.py | 1 + .../config/transformations/transform_model.py | 1 + .../xy_random_rotate90_model.py | 1 + .../config/validators/validator_utils.py | 1 + src/careamics/conftest.py | 1 + .../dataset/dataset_utils/__init__.py | 1 - .../dataset/dataset_utils/dataset_utils.py | 1 + src/careamics/dataset/in_memory_dataset.py | 1 + src/careamics/dataset/patching/__init__.py | 1 - .../dataset/patching/patch_transform.py | 8 +++--- src/careamics/dataset/patching/patching.py | 1 + .../dataset/patching/tiled_patching.py | 16 +++++++----- src/careamics/lightning_datamodule.py | 25 ++++++++++--------- .../lightning_prediction_datamodule.py | 1 + src/careamics/losses/__init__.py | 1 - src/careamics/losses/loss_factory.py | 1 + src/careamics/model_io/__init__.py | 1 - .../model_io/bioimage/_readme_factory.py | 1 + .../model_io/bioimage/bioimage_utils.py | 1 + .../model_io/bioimage/model_description.py | 1 + src/careamics/model_io/bmz_io.py | 1 + src/careamics/models/layers.py | 1 + src/careamics/models/model_factory.py | 1 + src/careamics/models/unet.py | 7 +++--- src/careamics/prediction/stitch_prediction.py | 1 + .../transforms/pixel_manipulation.py | 1 + src/careamics/transforms/tta.py | 1 + src/careamics/utils/__init__.py | 1 - src/careamics/utils/context.py | 1 + src/careamics/utils/logging.py | 1 + src/careamics/utils/metrics.py | 1 + src/careamics/utils/torch_utils.py | 1 + 45 files changed, 75 insertions(+), 43 deletions(-) diff --git a/src/careamics/careamist.py b/src/careamics/careamist.py index 7968f638f..7a9c8dae1 100644 --- a/src/careamics/careamist.py +++ b/src/careamics/careamist.py @@ -73,8 +73,7 @@ def __init__( # numpydoc ignore=GL08 source: Union[Path, str], work_dir: Optional[str] = None, experiment_name: str = "CAREamics", - ) -> None: - ... + ) -> None: ... @overload def __init__( # numpydoc ignore=GL08 @@ -82,8 +81,7 @@ def __init__( # numpydoc ignore=GL08 source: Configuration, work_dir: Optional[str] = None, experiment_name: str = "CAREamics", - ) -> None: - ... + ) -> None: ... def __init__( self, @@ -478,8 +476,7 @@ def predict( # numpydoc ignore=GL08 source: CAREamicsPredictData, *, checkpoint: Optional[Literal["best", "last"]] = None, - ) -> Union[list, np.ndarray]: - ... + ) -> Union[list, np.ndarray]: ... @overload def predict( # numpydoc ignore=GL08 @@ -497,8 +494,7 @@ def predict( # numpydoc ignore=GL08 read_source_func: Optional[Callable] = None, extension_filter: str = "", checkpoint: Optional[Literal["best", "last"]] = None, - ) -> Union[list, np.ndarray]: - ... + ) -> Union[list, np.ndarray]: ... @overload def predict( # numpydoc ignore=GL08 @@ -514,8 +510,7 @@ def predict( # numpydoc ignore=GL08 tta_transforms: bool = True, dataloader_params: Optional[Dict] = None, checkpoint: Optional[Literal["best", "last"]] = None, - ) -> Union[list, np.ndarray]: - ... + ) -> Union[list, np.ndarray]: ... def predict( self, diff --git a/src/careamics/config/__init__.py b/src/careamics/config/__init__.py index 0b785e848..dd4a372d2 100644 --- a/src/careamics/config/__init__.py +++ b/src/careamics/config/__init__.py @@ -1,6 +1,5 @@ """Configuration module.""" - __all__ = [ "AlgorithmConfig", "DataConfig", diff --git a/src/careamics/config/callback_model.py b/src/careamics/config/callback_model.py index a4b522ce9..666e82533 100644 --- a/src/careamics/config/callback_model.py +++ b/src/careamics/config/callback_model.py @@ -1,4 +1,5 @@ """Checkpoint saving configuration.""" + from __future__ import annotations from datetime import timedelta diff --git a/src/careamics/config/configuration_factory.py b/src/careamics/config/configuration_factory.py index 2051b96f8..b26112a2e 100644 --- a/src/careamics/config/configuration_factory.py +++ b/src/careamics/config/configuration_factory.py @@ -493,9 +493,11 @@ def create_n2v_configuration( # n2v2 and structn2v nv2_transform = { "name": SupportedTransform.N2V_MANIPULATE.value, - "strategy": SupportedPixelManipulation.MEDIAN.value - if use_n2v2 - else SupportedPixelManipulation.UNIFORM.value, + "strategy": ( + SupportedPixelManipulation.MEDIAN.value + if use_n2v2 + else SupportedPixelManipulation.UNIFORM.value + ), "roi_size": roi_size, "masked_pixel_percentage": masked_pixel_percentage, "struct_mask_axis": struct_n2v_axis, diff --git a/src/careamics/config/configuration_model.py b/src/careamics/config/configuration_model.py index a3df16d10..ec02dd972 100644 --- a/src/careamics/config/configuration_model.py +++ b/src/careamics/config/configuration_model.py @@ -1,4 +1,5 @@ """Pydantic CAREamics configuration.""" + from __future__ import annotations import re diff --git a/src/careamics/config/data_model.py b/src/careamics/config/data_model.py index 18d6fef19..20900a93f 100644 --- a/src/careamics/config/data_model.py +++ b/src/careamics/config/data_model.py @@ -1,4 +1,5 @@ """Data configuration.""" + from __future__ import annotations from pprint import pformat diff --git a/src/careamics/config/inference_model.py b/src/careamics/config/inference_model.py index 22c72a892..faa71f017 100644 --- a/src/careamics/config/inference_model.py +++ b/src/careamics/config/inference_model.py @@ -1,4 +1,5 @@ """Pydantic model representing CAREamics prediction configuration.""" + from __future__ import annotations from typing import Any, List, Literal, Optional, Union diff --git a/src/careamics/config/references/algorithm_descriptions.py b/src/careamics/config/references/algorithm_descriptions.py index 97e4ba83f..e60c9164d 100644 --- a/src/careamics/config/references/algorithm_descriptions.py +++ b/src/careamics/config/references/algorithm_descriptions.py @@ -1,4 +1,5 @@ """Descriptions of the algorithms used in CAREmics.""" + from pydantic import BaseModel CUSTOM = "Custom" diff --git a/src/careamics/config/references/references.py b/src/careamics/config/references/references.py index 60c8413f9..1d13cfad4 100644 --- a/src/careamics/config/references/references.py +++ b/src/careamics/config/references/references.py @@ -1,4 +1,5 @@ """References for the CAREamics algorithms.""" + from bioimageio.spec.generic.v0_3 import CiteEntry N2VRef = CiteEntry( diff --git a/src/careamics/config/support/supported_extraction_strategies.py b/src/careamics/config/support/supported_extraction_strategies.py index d08c513f5..759f0156f 100644 --- a/src/careamics/config/support/supported_extraction_strategies.py +++ b/src/careamics/config/support/supported_extraction_strategies.py @@ -3,6 +3,7 @@ This module defines the various extraction strategies available in CAREamics. """ + from careamics.utils import BaseEnum diff --git a/src/careamics/config/training_model.py b/src/careamics/config/training_model.py index 530a3a5f1..58fe5c0c0 100644 --- a/src/careamics/config/training_model.py +++ b/src/careamics/config/training_model.py @@ -1,4 +1,5 @@ """Training configuration.""" + from __future__ import annotations from pprint import pformat diff --git a/src/careamics/config/transformations/n2v_manipulate_model.py b/src/careamics/config/transformations/n2v_manipulate_model.py index 3653bb0a2..aba176a29 100644 --- a/src/careamics/config/transformations/n2v_manipulate_model.py +++ b/src/careamics/config/transformations/n2v_manipulate_model.py @@ -1,4 +1,5 @@ """Pydantic model for the N2VManipulate transform.""" + from typing import Literal from pydantic import ConfigDict, Field, field_validator diff --git a/src/careamics/config/transformations/nd_flip_model.py b/src/careamics/config/transformations/nd_flip_model.py index 46ec8361d..677cd842e 100644 --- a/src/careamics/config/transformations/nd_flip_model.py +++ b/src/careamics/config/transformations/nd_flip_model.py @@ -1,4 +1,5 @@ """Pydantic model for the NDFlip transform.""" + from typing import Literal from pydantic import ConfigDict, Field diff --git a/src/careamics/config/transformations/normalize_model.py b/src/careamics/config/transformations/normalize_model.py index 1c82a56bd..132b7bc9c 100644 --- a/src/careamics/config/transformations/normalize_model.py +++ b/src/careamics/config/transformations/normalize_model.py @@ -1,4 +1,5 @@ """Pydantic model for the Normalize transform.""" + from typing import Literal from pydantic import ConfigDict, Field diff --git a/src/careamics/config/transformations/transform_model.py b/src/careamics/config/transformations/transform_model.py index ffbc6022d..a8dcc23e9 100644 --- a/src/careamics/config/transformations/transform_model.py +++ b/src/careamics/config/transformations/transform_model.py @@ -1,4 +1,5 @@ """Parent model for the transforms.""" + from typing import Any, Dict from pydantic import BaseModel, ConfigDict diff --git a/src/careamics/config/transformations/xy_random_rotate90_model.py b/src/careamics/config/transformations/xy_random_rotate90_model.py index c5fa44f1b..381bf52e1 100644 --- a/src/careamics/config/transformations/xy_random_rotate90_model.py +++ b/src/careamics/config/transformations/xy_random_rotate90_model.py @@ -1,4 +1,5 @@ """Pydantic model for the XYRandomRotate90 transform.""" + from typing import Literal from pydantic import ConfigDict, Field diff --git a/src/careamics/config/validators/validator_utils.py b/src/careamics/config/validators/validator_utils.py index 6743d249a..da5eb0ae7 100644 --- a/src/careamics/config/validators/validator_utils.py +++ b/src/careamics/config/validators/validator_utils.py @@ -3,6 +3,7 @@ These functions are used to validate dimensions and axes of inputs. """ + from typing import List, Optional, Tuple, Union _AXES = "STCZYX" diff --git a/src/careamics/conftest.py b/src/careamics/conftest.py index e0a1fae6c..a192658ca 100644 --- a/src/careamics/conftest.py +++ b/src/careamics/conftest.py @@ -2,6 +2,7 @@ See https://sybil.readthedocs.io/en/latest/use.html#pytest """ + from pathlib import Path import pytest diff --git a/src/careamics/dataset/dataset_utils/__init__.py b/src/careamics/dataset/dataset_utils/__init__.py index 01517da8f..242405769 100644 --- a/src/careamics/dataset/dataset_utils/__init__.py +++ b/src/careamics/dataset/dataset_utils/__init__.py @@ -1,6 +1,5 @@ """Files and arrays utils used in the datasets.""" - __all__ = [ "reshape_array", "get_files_size", diff --git a/src/careamics/dataset/dataset_utils/dataset_utils.py b/src/careamics/dataset/dataset_utils/dataset_utils.py index ace44bc9e..4ce652752 100644 --- a/src/careamics/dataset/dataset_utils/dataset_utils.py +++ b/src/careamics/dataset/dataset_utils/dataset_utils.py @@ -1,4 +1,5 @@ """Convenience methods for datasets.""" + from typing import List, Tuple import numpy as np diff --git a/src/careamics/dataset/in_memory_dataset.py b/src/careamics/dataset/in_memory_dataset.py index b72882619..ab586f055 100644 --- a/src/careamics/dataset/in_memory_dataset.py +++ b/src/careamics/dataset/in_memory_dataset.py @@ -1,4 +1,5 @@ """In-memory dataset module.""" + from __future__ import annotations import copy diff --git a/src/careamics/dataset/patching/__init__.py b/src/careamics/dataset/patching/__init__.py index c9f5f219e..9ed6f095d 100644 --- a/src/careamics/dataset/patching/__init__.py +++ b/src/careamics/dataset/patching/__init__.py @@ -1,6 +1,5 @@ """Patching and tiling functions.""" - __all__ = [ "get_patch_transform", ] diff --git a/src/careamics/dataset/patching/patch_transform.py b/src/careamics/dataset/patching/patch_transform.py index 15cde203b..1177f5279 100644 --- a/src/careamics/dataset/patching/patch_transform.py +++ b/src/careamics/dataset/patching/patch_transform.py @@ -38,7 +38,9 @@ def get_patch_transform( return Aug.Compose( transforms, # apply image aug to "target" - additional_targets={"target": "image"} - if (with_target and normalize_mask) # TODO check this - else {}, + additional_targets=( + {"target": "image"} + if (with_target and normalize_mask) # TODO check this + else {} + ), ) diff --git a/src/careamics/dataset/patching/patching.py b/src/careamics/dataset/patching/patching.py index def9ce25e..49e3d3f75 100644 --- a/src/careamics/dataset/patching/patching.py +++ b/src/careamics/dataset/patching/patching.py @@ -3,6 +3,7 @@ These functions are used to tile images into patches or tiles. """ + from pathlib import Path from typing import Callable, List, Tuple, Union diff --git a/src/careamics/dataset/patching/tiled_patching.py b/src/careamics/dataset/patching/tiled_patching.py index bd618daeb..04489fb86 100644 --- a/src/careamics/dataset/patching/tiled_patching.py +++ b/src/careamics/dataset/patching/tiled_patching.py @@ -43,9 +43,11 @@ def _compute_crop_and_stitch_coords_1d( stitch_coords.append( ( i + overlap // 2 if i > 0 else 0, - i + tile_size - overlap // 2 - if crop_coords[-1][1] < axis_size - else axis_size, + ( + i + tile_size - overlap // 2 + if crop_coords[-1][1] < axis_size + else axis_size + ), ) ) @@ -53,9 +55,11 @@ def _compute_crop_and_stitch_coords_1d( overlap_crop_coords.append( ( overlap // 2 if i > 0 else 0, - tile_size - overlap // 2 - if crop_coords[-1][1] < axis_size - else tile_size, + ( + tile_size - overlap // 2 + if crop_coords[-1][1] < axis_size + else tile_size + ), ) ) diff --git a/src/careamics/lightning_datamodule.py b/src/careamics/lightning_datamodule.py index ca4fedad3..3a0d666c7 100644 --- a/src/careamics/lightning_datamodule.py +++ b/src/careamics/lightning_datamodule.py @@ -1,4 +1,5 @@ """Training and validation Lightning data modules.""" + from pathlib import Path from typing import Any, Callable, Dict, List, Literal, Optional, Union @@ -341,9 +342,9 @@ def setup(self, *args: Any, **kwargs: Any) -> None: self.train_dataset = InMemoryDataset( data_config=self.data_config, inputs=self.train_files, - data_target=self.train_target_files - if self.train_data_target - else None, + data_target=( + self.train_target_files if self.train_data_target else None + ), read_source_func=self.read_source_func, ) @@ -352,9 +353,9 @@ def setup(self, *args: Any, **kwargs: Any) -> None: self.val_dataset = InMemoryDataset( data_config=self.data_config, inputs=self.val_files, - data_target=self.val_target_files - if self.val_data_target - else None, + data_target=( + self.val_target_files if self.val_data_target else None + ), read_source_func=self.read_source_func, ) else: @@ -370,9 +371,9 @@ def setup(self, *args: Any, **kwargs: Any) -> None: self.train_dataset = PathIterableDataset( data_config=self.data_config, src_files=self.train_files, - target_files=self.train_target_files - if self.train_data_target - else None, + target_files=( + self.train_target_files if self.train_data_target else None + ), read_source_func=self.read_source_func, ) @@ -382,9 +383,9 @@ def setup(self, *args: Any, **kwargs: Any) -> None: self.val_dataset = PathIterableDataset( data_config=self.data_config, src_files=self.val_files, - target_files=self.val_target_files - if self.val_data_target - else None, + target_files=( + self.val_target_files if self.val_data_target else None + ), read_source_func=self.read_source_func, ) elif len(self.train_files) <= self.val_minimum_split: diff --git a/src/careamics/lightning_prediction_datamodule.py b/src/careamics/lightning_prediction_datamodule.py index 81ed637f8..670f45740 100644 --- a/src/careamics/lightning_prediction_datamodule.py +++ b/src/careamics/lightning_prediction_datamodule.py @@ -1,4 +1,5 @@ """Prediction Lightning data modules.""" + from pathlib import Path from typing import Any, Callable, List, Literal, Optional, Tuple, Union diff --git a/src/careamics/losses/__init__.py b/src/careamics/losses/__init__.py index e984229fb..07a8972e0 100644 --- a/src/careamics/losses/__init__.py +++ b/src/careamics/losses/__init__.py @@ -1,6 +1,5 @@ """Losses module.""" - from .loss_factory import loss_factory # from .noise_model_factory import noise_model_factory as noise_model_factory diff --git a/src/careamics/losses/loss_factory.py b/src/careamics/losses/loss_factory.py index 054f09c58..80fe66e7e 100644 --- a/src/careamics/losses/loss_factory.py +++ b/src/careamics/losses/loss_factory.py @@ -3,6 +3,7 @@ This module contains a factory function for creating loss functions. """ + from typing import Callable, Union from ..config.support import SupportedLoss diff --git a/src/careamics/model_io/__init__.py b/src/careamics/model_io/__init__.py index 0e99771f4..68c9e41b8 100644 --- a/src/careamics/model_io/__init__.py +++ b/src/careamics/model_io/__init__.py @@ -1,6 +1,5 @@ """Model I/O utilities.""" - __all__ = ["load_pretrained", "export_to_bmz"] diff --git a/src/careamics/model_io/bioimage/_readme_factory.py b/src/careamics/model_io/bioimage/_readme_factory.py index e823f3781..00542148f 100644 --- a/src/careamics/model_io/bioimage/_readme_factory.py +++ b/src/careamics/model_io/bioimage/_readme_factory.py @@ -1,4 +1,5 @@ """Functions used to create a README.md file for BMZ export.""" + from pathlib import Path from typing import Optional diff --git a/src/careamics/model_io/bioimage/bioimage_utils.py b/src/careamics/model_io/bioimage/bioimage_utils.py index 1ce28bfcd..3377299eb 100644 --- a/src/careamics/model_io/bioimage/bioimage_utils.py +++ b/src/careamics/model_io/bioimage/bioimage_utils.py @@ -1,4 +1,5 @@ """Bioimage.io utils.""" + from pathlib import Path from typing import Union diff --git a/src/careamics/model_io/bioimage/model_description.py b/src/careamics/model_io/bioimage/model_description.py index aee00efc0..59f1f1db6 100644 --- a/src/careamics/model_io/bioimage/model_description.py +++ b/src/careamics/model_io/bioimage/model_description.py @@ -1,4 +1,5 @@ """Module use to build BMZ model description.""" + from pathlib import Path from typing import List, Optional, Tuple, Union diff --git a/src/careamics/model_io/bmz_io.py b/src/careamics/model_io/bmz_io.py index e32f2476b..1785584fc 100644 --- a/src/careamics/model_io/bmz_io.py +++ b/src/careamics/model_io/bmz_io.py @@ -1,4 +1,5 @@ """Function to export to the BioImage Model Zoo format.""" + import tempfile from pathlib import Path from typing import List, Optional, Tuple, Union diff --git a/src/careamics/models/layers.py b/src/careamics/models/layers.py index fe46e3ed4..0fa846835 100644 --- a/src/careamics/models/layers.py +++ b/src/careamics/models/layers.py @@ -3,6 +3,7 @@ This submodule contains layers used in the CAREamics models. """ + from typing import List, Optional, Tuple, Union import torch diff --git a/src/careamics/models/model_factory.py b/src/careamics/models/model_factory.py index 5b93622b3..40a2f9013 100644 --- a/src/careamics/models/model_factory.py +++ b/src/careamics/models/model_factory.py @@ -3,6 +3,7 @@ Model creation factory functions. """ + from typing import Union import torch diff --git a/src/careamics/models/unet.py b/src/careamics/models/unet.py index 79edd699a..34c026e3d 100644 --- a/src/careamics/models/unet.py +++ b/src/careamics/models/unet.py @@ -3,6 +3,7 @@ A UNet encoder, decoder and complete model. """ + from typing import Any, List, Union import torch @@ -188,9 +189,9 @@ def __init__( decoder_blocks.append( Conv_Block( conv_dim, - in_channels=in_channels + in_channels // 2 - if n > 0 - else in_channels, + in_channels=( + in_channels + in_channels // 2 if n > 0 else in_channels + ), out_channels=out_channels, intermediate_channel_multiplier=2, dropout_perc=dropout, diff --git a/src/careamics/prediction/stitch_prediction.py b/src/careamics/prediction/stitch_prediction.py index 5e0ee7e11..b849f3b55 100644 --- a/src/careamics/prediction/stitch_prediction.py +++ b/src/careamics/prediction/stitch_prediction.py @@ -3,6 +3,7 @@ These functions are used during prediction. """ + from typing import List import numpy as np diff --git a/src/careamics/transforms/pixel_manipulation.py b/src/careamics/transforms/pixel_manipulation.py index 03e40e89f..45a0dc82a 100644 --- a/src/careamics/transforms/pixel_manipulation.py +++ b/src/careamics/transforms/pixel_manipulation.py @@ -4,6 +4,7 @@ Pixel manipulation is used in N2V and similar algorithm to replace the value of masked pixels. """ + from typing import Optional, Tuple, Union import numpy as np diff --git a/src/careamics/transforms/tta.py b/src/careamics/transforms/tta.py index 39e65950e..d72c60848 100644 --- a/src/careamics/transforms/tta.py +++ b/src/careamics/transforms/tta.py @@ -1,4 +1,5 @@ """Test-time augmentations.""" + from typing import List import numpy as np diff --git a/src/careamics/utils/__init__.py b/src/careamics/utils/__init__.py index 3207fe2b2..13423c05f 100644 --- a/src/careamics/utils/__init__.py +++ b/src/careamics/utils/__init__.py @@ -1,6 +1,5 @@ """Utils module.""" - __all__ = [ "cwd", "get_ram_size", diff --git a/src/careamics/utils/context.py b/src/careamics/utils/context.py index d39626c89..41ad445a9 100644 --- a/src/careamics/utils/context.py +++ b/src/careamics/utils/context.py @@ -3,6 +3,7 @@ A convenience function to change the working directory in order to save data. """ + import os from contextlib import contextmanager from pathlib import Path diff --git a/src/careamics/utils/logging.py b/src/careamics/utils/logging.py index 6d772ceee..eee7a97da 100644 --- a/src/careamics/utils/logging.py +++ b/src/careamics/utils/logging.py @@ -3,6 +3,7 @@ The methods are responsible for the in-console logger. """ + import logging import sys import time diff --git a/src/careamics/utils/metrics.py b/src/careamics/utils/metrics.py index 23283c3a4..2389316d4 100644 --- a/src/careamics/utils/metrics.py +++ b/src/careamics/utils/metrics.py @@ -3,6 +3,7 @@ This module contains various metrics and a metrics tracking class. """ + from typing import Union import numpy as np diff --git a/src/careamics/utils/torch_utils.py b/src/careamics/utils/torch_utils.py index 1cc0fb014..f13306a6c 100644 --- a/src/careamics/utils/torch_utils.py +++ b/src/careamics/utils/torch_utils.py @@ -3,6 +3,7 @@ These functions are used to control certain aspects and behaviours of PyTorch. """ + import inspect from typing import Dict, Union