From 396426371ab638d24e252fa57019e5bc6338ed1e Mon Sep 17 00:00:00 2001 From: "deepsource-autofix[bot]" <62050782+deepsource-autofix[bot]@users.noreply.github.com> Date: Fri, 29 Mar 2024 12:32:34 +0000 Subject: [PATCH] style: format code with isort and Yapf This commit fixes the style issues introduced in 3dcd9b0 according to the output from isort and Yapf. Details: None --- hsf/augmentation.py | 4 ++-- hsf/factory.py | 11 ++++++----- hsf/multispectrality.py | 3 +-- hsf/roiloc_wrapper.py | 3 ++- hsf/segment.py | 7 +++---- tests/test_hsf.py | 11 ++++++----- 6 files changed, 20 insertions(+), 19 deletions(-) diff --git a/hsf/augmentation.py b/hsf/augmentation.py index 7c8a693..21a9fab 100644 --- a/hsf/augmentation.py +++ b/hsf/augmentation.py @@ -27,9 +27,9 @@ def get_augmentation_pipeline(augmentation_cfg: DictConfig) -> tio.Compose: flip = tio.RandomFlip(**augmentation_cfg.flip) resample = tio.OneOf({ tio.RandomAffine(**augmentation_cfg.affine): - augmentation_cfg.affine_probability, + augmentation_cfg.affine_probability, tio.RandomElasticDeformation(**augmentation_cfg.elastic): - augmentation_cfg.elastic_probability + augmentation_cfg.elastic_probability }) return tio.Compose((flip, resample)) diff --git a/hsf/factory.py b/hsf/factory.py index 737436f..05918dd 100644 --- a/hsf/factory.py +++ b/hsf/factory.py @@ -28,7 +28,6 @@ log = logging.getLogger(__name__) - def get_lr_hippocampi(mri: PosixPath, cfg: DictConfig) -> tuple: """ Get left and right hippocampi from a given MRI. @@ -63,8 +62,8 @@ def get_lr_hippocampi(mri: PosixPath, cfg: DictConfig) -> tuple: original_mri_path=mri) -def predict(mri: PosixPath, second_mri: Optional[PosixPath], engines: Generator, - cfg: DictConfig) -> tuple: +def predict(mri: PosixPath, second_mri: Optional[PosixPath], + engines: Generator, cfg: DictConfig) -> tuple: """ Predict the hippocampal segmentation for a given MRI. @@ -156,7 +155,8 @@ def filter_mris(mris: List[PosixPath], overwrite: bool) -> List[PosixPath]: def _get_segmentations(mri: PosixPath) -> List[PosixPath]: extensions = "".join(mri.suffixes) stem = mri.name.replace(extensions, "") - segmentations = list(mri.parent.glob(f"{stem}*_hippocampus_seg.nii.gz")) + segmentations = list( + mri.parent.glob(f"{stem}*_hippocampus_seg.nii.gz")) if len(segmentations) > 2: log.warning( @@ -229,7 +229,8 @@ def main(cfg: DictConfig) -> None: else: additional_hippocampi = [None, None] - for j, hippocampus in enumerate(zip(hippocampi, additional_hippocampi)): + for j, hippocampus in enumerate(zip(hippocampi, + additional_hippocampi)): engines = get_inference_engines( cfg.segmentation.models_path, engine_name=cfg.hardware.engine, diff --git a/hsf/multispectrality.py b/hsf/multispectrality.py index 7bfe95f..f1db0b5 100644 --- a/hsf/multispectrality.py +++ b/hsf/multispectrality.py @@ -78,8 +78,7 @@ def register(mri: PosixPath, transformlist=transformation["fwdtransforms"]) extensions = "".join(second_contrast.suffixes) - fname = second_contrast.name.replace(extensions, - "") + "_registered.nii.gz" + fname = second_contrast.name.replace(extensions, "") + "_registered.nii.gz" output_dir = mri.parent / cfg.files.output_dir output_dir.mkdir(parents=True, exist_ok=True) diff --git a/hsf/roiloc_wrapper.py b/hsf/roiloc_wrapper.py index 38a3613..98f3623 100644 --- a/hsf/roiloc_wrapper.py +++ b/hsf/roiloc_wrapper.py @@ -50,7 +50,8 @@ def get_mri(mri: PosixPath, mask_pattern: Optional[str] = None) -> tuple: else: mask = None log.warning( - "Couldn't find brain extraction mask for the provided pattern.") + "Couldn't find brain extraction mask for the provided pattern." + ) else: mask = None diff --git a/hsf/segment.py b/hsf/segment.py index ed0e200..a28610d 100644 --- a/hsf/segment.py +++ b/hsf/segment.py @@ -67,14 +67,13 @@ def to_ca_mode(logits: torch.Tensor, ca_mode: str = "1/2/3") -> torch.Tensor: _pre = logits[:, :2, :, :, :] _in = logits[:, 2:3, :, :, :] + logits[:, - 3:4, :, :, :] + logits[:, - 4:5, :, :, :] + 3:4, :, :, :] + logits[:, 4: + 5, :, :, :] _post = logits[:, 5:, :, :, :] return torch.cat([_pre, _in, _post], dim=1) raise ValueError( - f"Unknown `ca_mode` ({ca_mode}). `ca_mode` must be 1/2/3, 1/23 or 123" - ) + f"Unknown `ca_mode` ({ca_mode}). `ca_mode` must be 1/2/3, 1/23 or 123") def predict(mris: list, diff --git a/tests/test_hsf.py b/tests/test_hsf.py index c9713d8..89264d4 100644 --- a/tests/test_hsf.py +++ b/tests/test_hsf.py @@ -62,7 +62,8 @@ def config(models_path): "gpu_mem_limit": 2147483648 } ], "CPUExecutionProvider"], - "batch_size": 1 + "batch_size": + 1 } }, "roiloc": { @@ -102,9 +103,8 @@ def config(models_path): "models": { "model.onnx": { "url": - "https://zenodo.org/record/6457484/files/arunet_3.0.0_single.onnx?download=1", - "xxh3_64": - "71edec9011f7f304" + "https://zenodo.org/record/6457484/files/arunet_3.0.0_single.onnx?download=1", + "xxh3_64": "71edec9011f7f304" } }, "segmentation": { @@ -220,7 +220,8 @@ def test_multispectrality(models_path): } }) - mri = hsf.roiloc_wrapper.load_from_config(models_path, "sub0_tse.nii.gz")[0] + mri = hsf.roiloc_wrapper.load_from_config(models_path, + "sub0_tse.nii.gz")[0] second_contrast = hsf.multispectrality.get_second_contrast( mri, "sub0_tse.nii.gz")