diff --git a/src/medbase/data/augmentations.py b/src/medbase/data/augmentations.py index fcf8887d06b23bdf7f4f187651e9041b43d5b38e..ff3f438e6f411d508a92643efdf1e0840b5a9391 100644 --- a/src/medbase/data/augmentations.py +++ b/src/medbase/data/augmentations.py @@ -22,7 +22,7 @@ import numpy.typing import torch from scipy.ndimage import gaussian_filter, map_coordinates -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet.medbase") def _elastic_deformation_on_image( diff --git a/src/medbase/data/datamodule.py b/src/medbase/data/datamodule.py index ff627d0397f753a40ff3ee811a3286f96cd457eb..1d6c14ebd084b583985bd3a2eb59791a4c2743dd 100644 --- a/src/medbase/data/datamodule.py +++ b/src/medbase/data/datamodule.py @@ -27,7 +27,7 @@ from .typing import ( TransformSequence, ) -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet.medbase") def _sample_size_bytes(s: Sample) -> int: diff --git a/src/medbase/data/split.py b/src/medbase/data/split.py index 0bcdf300850cff67c5e596245d3ba53b59f47d9c..3b412d9673d45535d314bca32b825e173a9d0cfe 100644 --- a/src/medbase/data/split.py +++ b/src/medbase/data/split.py @@ -14,7 +14,7 @@ import torch from medbase.data.typing import DatabaseSplit, RawDataLoader -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet.medbase") class JSONDatabaseSplit(DatabaseSplit): diff --git a/src/medbase/engine/callbacks.py b/src/medbase/engine/callbacks.py index 3d108a8d2c372478d7792de8d65a4b21e2ce3428..bd4755eb221b43f9405307e6d4b6a928315a77c8 100644 --- a/src/medbase/engine/callbacks.py +++ b/src/medbase/engine/callbacks.py @@ -13,7 +13,7 @@ import torch from ..utils.resources import ResourceMonitor, aggregate -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet.medbase") class LoggingCallback(lightning.pytorch.Callback): diff --git a/src/medbase/engine/device.py b/src/medbase/engine/device.py index 4375cbb3f03318d2507f0e33a7dac0ef2b626fef..851b053953ecc1b8f5c99e5fc4481aa8e91c4cce 100644 --- a/src/medbase/engine/device.py +++ b/src/medbase/engine/device.py @@ -9,7 +9,7 @@ import typing import torch import torch.backends -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet.medbase") SupportedPytorchDevice: typing.TypeAlias = typing.Literal[ diff --git a/src/medbase/engine/trainer.py b/src/medbase/engine/trainer.py index 5d3f2a0de703aa97faa055b2c269d1e3b816eba1..79b509fe51ec883eb3d64994eba64d029285578e 100644 --- a/src/medbase/engine/trainer.py +++ b/src/medbase/engine/trainer.py @@ -15,7 +15,7 @@ from ..utils.resources import ResourceMonitor from .callbacks import LoggingCallback from .device import DeviceManager -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet.medbase") def run( diff --git a/src/medbase/utils/checkpointer.py b/src/medbase/utils/checkpointer.py index 19450a13c81d45d7ce58a61e7c05deae48db6413..44e61da870201b1483a92d214e7e5bcb1dc7b8ec 100644 --- a/src/medbase/utils/checkpointer.py +++ b/src/medbase/utils/checkpointer.py @@ -7,7 +7,7 @@ import pathlib import re import typing -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet.medbase") CHECKPOINT_ALIASES = { diff --git a/src/medbase/utils/resources.py b/src/medbase/utils/resources.py index 5816771157435564113721bd44f6619ffc780ebb..645bf76a0c0429ba172025ca9ce304bb340129ae 100644 --- a/src/medbase/utils/resources.py +++ b/src/medbase/utils/resources.py @@ -20,7 +20,7 @@ import psutil from medbase.engine.device import SupportedPytorchDevice -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet") _nvidia_smi = shutil.which("nvidia-smi") """Location of the nvidia-smi program, if one exists.""" diff --git a/src/mednet/engine/evaluator.py b/src/mednet/engine/evaluator.py index acbf79b3fcdd9db808a6ee28e6ded77c42d887fb..598fb3b8f20759ec2e6d917acbb27661f9b93ce7 100644 --- a/src/mednet/engine/evaluator.py +++ b/src/mednet/engine/evaluator.py @@ -20,7 +20,7 @@ from matplotlib import pyplot as plt from ..models.typing import BinaryPrediction -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet") def eer_threshold(predictions: Iterable[BinaryPrediction]) -> float: diff --git a/src/mednet/engine/predictor.py b/src/mednet/engine/predictor.py index fce844a17151cd23e0271d34e162dd7b652c9a5b..5a5b3545a6a296c1901ac2245b57d72f61b744e3 100644 --- a/src/mednet/engine/predictor.py +++ b/src/mednet/engine/predictor.py @@ -6,7 +6,6 @@ import logging import lightning.pytorch import torch.utils.data - from medbase.engine.device import DeviceManager from ..models.typing import ( @@ -16,7 +15,7 @@ from ..models.typing import ( MultiClassPredictionSplit, ) -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet") def run( diff --git a/src/mednet/engine/saliency/completeness.py b/src/mednet/engine/saliency/completeness.py index 7c3cb3c624e1965508c243051c602080632acde0..84327ad4a81f544630c4f73d18f30842ebdfb714 100644 --- a/src/mednet/engine/saliency/completeness.py +++ b/src/mednet/engine/saliency/completeness.py @@ -11,18 +11,17 @@ import lightning.pytorch import numpy as np import torch import tqdm +from medbase.data.typing import Sample +from medbase.engine.device import DeviceManager from pytorch_grad_cam.metrics.road import ( ROADLeastRelevantFirstAverage, ROADMostRelevantFirstAverage, ) from pytorch_grad_cam.utils.model_targets import ClassifierOutputTarget -from medbase.data.typing import Sample -from medbase.engine.device import DeviceManager - from ...models.typing import SaliencyMapAlgorithm -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet") class SigmoidClassifierOutputTarget(torch.nn.Module): diff --git a/src/mednet/engine/saliency/generator.py b/src/mednet/engine/saliency/generator.py index f440eb086088686ef722b99323bdd62bae16f238..ddad6ce7129f0cd0dd3bfa7b44d64dfe8c7551f4 100644 --- a/src/mednet/engine/saliency/generator.py +++ b/src/mednet/engine/saliency/generator.py @@ -11,12 +11,11 @@ import numpy import torch import torch.nn import tqdm - from medbase.engine.device import DeviceManager from ...models.typing import SaliencyMapAlgorithm -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet") def _create_saliency_map_callable( diff --git a/src/mednet/engine/saliency/interpretability.py b/src/mednet/engine/saliency/interpretability.py index 54c72a4298b4dd8ad68a3c388d78b922da6595ae..621aa9d6138fc2fb6dcd2c85d2faf0eb8e502fb3 100644 --- a/src/mednet/engine/saliency/interpretability.py +++ b/src/mednet/engine/saliency/interpretability.py @@ -16,7 +16,7 @@ from tqdm import tqdm from ...config.data.tbx11k.datamodule import BoundingBox, BoundingBoxes -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet") SaliencyMap: typing.TypeAlias = ( typing.Sequence[typing.Sequence[float]] | numpy.typing.NDArray[numpy.double] diff --git a/src/mednet/engine/saliency/viewer.py b/src/mednet/engine/saliency/viewer.py index d969aa91ef6b959133a095d059a97dae69ffbf4f..588ba70ccf4584db6026de5cb88423321c2184f8 100644 --- a/src/mednet/engine/saliency/viewer.py +++ b/src/mednet/engine/saliency/viewer.py @@ -17,7 +17,7 @@ from tqdm import tqdm from ...config.data.tbx11k.datamodule import BoundingBox, BoundingBoxes -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet") def _overlay_saliency_map( diff --git a/src/mednet/models/alexnet.py b/src/mednet/models/alexnet.py index 22c415471b50adf4c684130d8b692679189181f7..5c686de328355a01c1d9caebef227cfaf9518542 100644 --- a/src/mednet/models/alexnet.py +++ b/src/mednet/models/alexnet.py @@ -11,13 +11,12 @@ import torch.optim.optimizer import torch.utils.data import torchvision.models as models import torchvision.transforms - from medbase.data.typing import TransformSequence from .model import Model from .separate import separate from .transforms import RGB, SquareCenterPad -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet") class Alexnet(Model): diff --git a/src/mednet/models/densenet.py b/src/mednet/models/densenet.py index 3feb2adebff2611ac6848088fb3df32c81e8d7d2..e9433b994b5373f997ea9f880519e115bf75db94 100644 --- a/src/mednet/models/densenet.py +++ b/src/mednet/models/densenet.py @@ -11,13 +11,12 @@ import torch.optim.optimizer import torch.utils.data import torchvision.models as models import torchvision.transforms - from medbase.data.typing import TransformSequence from .model import Model from .separate import separate from .transforms import RGB, SquareCenterPad -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet") class Densenet(Model): diff --git a/src/mednet/models/loss_weights.py b/src/mednet/models/loss_weights.py index 382a7ae5123c44fdd91a4eebe2c9d93d7c17e805..2264a44da1c9ebacf3a3eef193a23b62706fc3e2 100644 --- a/src/mednet/models/loss_weights.py +++ b/src/mednet/models/loss_weights.py @@ -8,10 +8,9 @@ from collections import Counter import torch import torch.utils.data - from medbase.data.typing import DataLoader -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet") def compute_binary_weights(targets): diff --git a/src/mednet/models/pasa.py b/src/mednet/models/pasa.py index 0e1d24f15973e374539a8eff7e370ff6f2aa602a..f6e83d83f0aa85fc7fd37dd8ce2551a823001e4a 100644 --- a/src/mednet/models/pasa.py +++ b/src/mednet/models/pasa.py @@ -11,13 +11,12 @@ import torch.nn.functional as F # noqa: N812 import torch.optim.optimizer import torch.utils.data import torchvision.transforms - from medbase.data.typing import TransformSequence from .model import Model from .separate import separate from .transforms import Grayscale, SquareCenterPad -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet") class Pasa(Model): diff --git a/src/mednet/scripts/train.py b/src/mednet/scripts/train.py index df8b1fec1c9e9b150d6932b489fdd39ada63377c..2fd63221fda89033cb87d46dea16e89a302f6d98 100644 --- a/src/mednet/scripts/train.py +++ b/src/mednet/scripts/train.py @@ -12,7 +12,8 @@ from clapper.logging import setup from .click import ConfigCommand -logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s") +# logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s") +logger = setup("mednet", format="%(levelname)s: %(message)s") def reusable_options(f): @@ -271,7 +272,6 @@ def train( import torch from lightning.pytorch import seed_everything - from medbase.engine.device import DeviceManager from medbase.engine.trainer import run from medbase.utils.checkpointer import get_checkpoint_to_resume_training diff --git a/src/mednet/scripts/utils.py b/src/mednet/scripts/utils.py index 4c894bd708c0db4a4ce464dcd243b90c0a774b3f..164f46b4831fd6b82e42d8507441d65ea7805614 100644 --- a/src/mednet/scripts/utils.py +++ b/src/mednet/scripts/utils.py @@ -14,7 +14,7 @@ import lightning.pytorch.callbacks import torch.nn from medbase.engine.device import SupportedPytorchDevice -logger = logging.getLogger(__name__) +logger = logging.getLogger("mednet") def model_summary(