diff --git a/doc/api.rst b/doc/api.rst index ac0884fb8bf5abc81e47512d2cc25cce6107f64e..793ad9e68cc1d69304b194fa95b6fc5241b4df62 100644 --- a/doc/api.rst +++ b/doc/api.rst @@ -164,7 +164,7 @@ Classification-specific utilities. .. autosummary:: :toctree: api/utils - mednet.libs.segmentation.utils.rc + mednet.libs.common.utils.rc Segmentation library @@ -234,7 +234,7 @@ Segmentation-specific utilities. mednet.libs.segmentation.utils.measure mednet.libs.segmentation.utils.plot - mednet.libs.segmentation.utils.rc + mednet.libs.common.utils.rc mednet.libs.segmentation.utils.table diff --git a/src/mednet/libs/classification/config/data/hivtb/datamodule.py b/src/mednet/libs/classification/config/data/hivtb/datamodule.py index 93627558cc62239c7341e412895c1d8931fb3910..cebf403692202adce19db45e65de68de4b9b707c 100644 --- a/src/mednet/libs/classification/config/data/hivtb/datamodule.py +++ b/src/mednet/libs/classification/config/data/hivtb/datamodule.py @@ -17,10 +17,9 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.image_utils import remove_black_borders from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample +from mednet.libs.common.utils.rc import load_rc from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/classification/config/data/montgomery/datamodule.py b/src/mednet/libs/classification/config/data/montgomery/datamodule.py index 8ccd7536981665214855016d98c482ef6dd90acc..4a61df7df30d507b4be259ce2e57d7ca91c37b03 100644 --- a/src/mednet/libs/classification/config/data/montgomery/datamodule.py +++ b/src/mednet/libs/classification/config/data/montgomery/datamodule.py @@ -17,10 +17,9 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.image_utils import remove_black_borders from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample +from mednet.libs.common.utils.rc import load_rc from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/classification/config/data/nih_cxr14/datamodule.py b/src/mednet/libs/classification/config/data/nih_cxr14/datamodule.py index b022d50a0e46edfdcf2572a18a736f558284d7ec..7712b4fe8aa864e6d27e033157552719b09bcdef 100644 --- a/src/mednet/libs/classification/config/data/nih_cxr14/datamodule.py +++ b/src/mednet/libs/classification/config/data/nih_cxr14/datamodule.py @@ -16,10 +16,9 @@ from mednet.libs.classification.data.typing import ( from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample +from mednet.libs.common.utils.rc import load_rc from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database. diff --git a/src/mednet/libs/classification/config/data/padchest/datamodule.py b/src/mednet/libs/classification/config/data/padchest/datamodule.py index 0c6dfba30d92ee353010ea2220220c96c19fb8e4..cc9bd7349a449f55cf9e134c4e8602b3645a90bb 100644 --- a/src/mednet/libs/classification/config/data/padchest/datamodule.py +++ b/src/mednet/libs/classification/config/data/padchest/datamodule.py @@ -18,10 +18,9 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.image_utils import remove_black_borders from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample +from mednet.libs.common.utils.rc import load_rc from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/classification/config/data/shenzhen/datamodule.py b/src/mednet/libs/classification/config/data/shenzhen/datamodule.py index b1b78c574b60f9b00fc48cd88d43746265cdc8b4..ba2ccc5ce2956fe376db7578cb413c0e52320fd4 100644 --- a/src/mednet/libs/classification/config/data/shenzhen/datamodule.py +++ b/src/mednet/libs/classification/config/data/shenzhen/datamodule.py @@ -17,10 +17,9 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.image_utils import remove_black_borders from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample +from mednet.libs.common.utils.rc import load_rc from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/classification/config/data/tbpoc/datamodule.py b/src/mednet/libs/classification/config/data/tbpoc/datamodule.py index 7c943b3e503c69bf1efb1f77be1468e2be910bf9..8f46b3beae6e6533bdb8354286737b7a87cf73fc 100644 --- a/src/mednet/libs/classification/config/data/tbpoc/datamodule.py +++ b/src/mednet/libs/classification/config/data/tbpoc/datamodule.py @@ -13,10 +13,9 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.image_utils import remove_black_borders from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample +from mednet.libs.common.utils.rc import load_rc from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/classification/config/data/tbx11k/datamodule.py b/src/mednet/libs/classification/config/data/tbx11k/datamodule.py index 47e97db8d085176e94c9d111ee17d63dece108dc..9cef49b1ea9960821b12674fad41e6fa650ffae2 100644 --- a/src/mednet/libs/classification/config/data/tbx11k/datamodule.py +++ b/src/mednet/libs/classification/config/data/tbx11k/datamodule.py @@ -16,11 +16,10 @@ from mednet.libs.classification.data.typing import ( from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample +from mednet.libs.common.utils.rc import load_rc from torch.utils.data._utils.collate import default_collate_fn_map from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/classification/scripts/database.py b/src/mednet/libs/classification/scripts/database.py index 038270d7e1c88a791d98f2d4dcf7a490827b27ba..974bf426ade241b4c02c2c224ebfa9e66c0e8101 100644 --- a/src/mednet/libs/classification/scripts/database.py +++ b/src/mednet/libs/classification/scripts/database.py @@ -29,8 +29,9 @@ def _get_raw_databases() -> dict[str, dict[str, str]]: import importlib import pkgutil + from mednet.libs.common.utils.rc import load_rc + from ..config import data - from ..utils.rc import load_rc user_configuration = load_rc() diff --git a/src/mednet/libs/classification/tests/conftest.py b/src/mednet/libs/classification/tests/conftest.py index 40e5f9d0bde84d4cdc24707a0563cc03e97d2722..97d423782a9b1e4c3bbafe05731ee5ad71eaff34 100644 --- a/src/mednet/libs/classification/tests/conftest.py +++ b/src/mednet/libs/classification/tests/conftest.py @@ -63,7 +63,7 @@ def pytest_runtest_setup(item): information. """ - from mednet.libs.classification.utils.rc import load_rc + from mednet.libs.common.utils.rc import load_rc rc = load_rc() @@ -85,7 +85,7 @@ def pytest_runtest_setup(item): def rc_variable_set(name): - from mednet.libs.classification.utils.rc import load_rc + from mednet.libs.common.utils.rc import load_rc rc = load_rc() pytest.mark.skipif( diff --git a/src/mednet/libs/classification/utils/rc.py b/src/mednet/libs/common/utils/rc.py similarity index 99% rename from src/mednet/libs/classification/utils/rc.py rename to src/mednet/libs/common/utils/rc.py index f1bdbc5d554d35d1e921bb7fef98fd5ef681576c..fcc1659d1f5304c44e0561a7e1e70c6bd905db7a 100644 --- a/src/mednet/libs/classification/utils/rc.py +++ b/src/mednet/libs/common/utils/rc.py @@ -12,5 +12,4 @@ def load_rc() -> UserDefaults: ------- The user defaults read from the user .toml configuration file. """ - return UserDefaults("mednet.toml") diff --git a/src/mednet/libs/segmentation/config/data/chasedb1/datamodule.py b/src/mednet/libs/segmentation/config/data/chasedb1/datamodule.py index 73c400be1a7ecb176eb2ed97ba6119d8d81135a3..3dc63ed535f319204235316f92db0f6e1a1c2436 100644 --- a/src/mednet/libs/segmentation/config/data/chasedb1/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/chasedb1/datamodule.py @@ -12,14 +12,13 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample from mednet.libs.common.models.transforms import crop_image_to_mask +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/cxr8/datamodule.py b/src/mednet/libs/segmentation/config/data/cxr8/datamodule.py index 5a5501f39f0044e07ce752dbd624fe719dc1d8fd..f1c0964839ed58508f629c229977593addc5411b 100644 --- a/src/mednet/libs/segmentation/config/data/cxr8/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/cxr8/datamodule.py @@ -12,14 +12,13 @@ import torch from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/drhagis/datamodule.py b/src/mednet/libs/segmentation/config/data/drhagis/datamodule.py index 519e635ffe43e0b64673c015ea4d210e1f6c5cd4..00052e7b15011baa98726e1b798e8affb752940b 100644 --- a/src/mednet/libs/segmentation/config/data/drhagis/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/drhagis/datamodule.py @@ -11,14 +11,13 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample from mednet.libs.common.models.transforms import crop_image_to_mask +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/drionsdb/datamodule.py b/src/mednet/libs/segmentation/config/data/drionsdb/datamodule.py index 554a44b99cf1c11c74517d98c9688dfe8b4bda72..f5b9085de92c4782bee1426aab021299669b1513 100644 --- a/src/mednet/libs/segmentation/config/data/drionsdb/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/drionsdb/datamodule.py @@ -13,14 +13,13 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample from mednet.libs.common.models.transforms import crop_image_to_mask +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/drishtigs1/datamodule.py b/src/mednet/libs/segmentation/config/data/drishtigs1/datamodule.py index f7c2fc7afbc0fc259c1be1cfa1ab40a80374c140..2a463df0d438c29a788caa4fe89b6e49e5649315 100644 --- a/src/mednet/libs/segmentation/config/data/drishtigs1/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/drishtigs1/datamodule.py @@ -12,14 +12,13 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample from mednet.libs.common.models.transforms import crop_image_to_mask +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/drive/datamodule.py b/src/mednet/libs/segmentation/config/data/drive/datamodule.py index 14aa36aeab721b7213adc5a4a552877d2ae4a0a7..06014c81efc338b24b3a30c06e614d5b36281f1c 100644 --- a/src/mednet/libs/segmentation/config/data/drive/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/drive/datamodule.py @@ -11,14 +11,13 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample from mednet.libs.common.models.transforms import crop_image_to_mask +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/hrf/datamodule.py b/src/mednet/libs/segmentation/config/data/hrf/datamodule.py index c918a2e894b0e4321f451bac6ac37ee0b9adb1bd..6227dd96e2e425fdc1d650e9a9587bd432f011e5 100644 --- a/src/mednet/libs/segmentation/config/data/hrf/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/hrf/datamodule.py @@ -11,14 +11,13 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample from mednet.libs.common.models.transforms import crop_image_to_mask +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/iostar/datamodule.py b/src/mednet/libs/segmentation/config/data/iostar/datamodule.py index 50df56780bdf891c26e47195e4e073d0ccb45fca..6c0e20fc19b6f30e37ae6cd41722fd079a831997 100644 --- a/src/mednet/libs/segmentation/config/data/iostar/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/iostar/datamodule.py @@ -11,14 +11,13 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample from mednet.libs.common.models.transforms import crop_image_to_mask +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/jsrt/datamodule.py b/src/mednet/libs/segmentation/config/data/jsrt/datamodule.py index 58f6a8ccd865031f6b505db656af2ce53b922863..fea4f9bd44a0919dc0e155dd469d5988ba791a6b 100644 --- a/src/mednet/libs/segmentation/config/data/jsrt/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/jsrt/datamodule.py @@ -13,14 +13,13 @@ import torch from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/montgomery/datamodule.py b/src/mednet/libs/segmentation/config/data/montgomery/datamodule.py index f24b9925a52ba7f38ffc0ce0e28180f9f9c9683c..4f2940fe5ab54621c586dc701994659b02b3c669 100644 --- a/src/mednet/libs/segmentation/config/data/montgomery/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/montgomery/datamodule.py @@ -13,14 +13,13 @@ import torch from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/refuge/datamodule.py b/src/mednet/libs/segmentation/config/data/refuge/datamodule.py index 1fa3e7d5c3c73b0a2d98524a3c3a4d60653b47bb..d36c5b96206142e48b9eb7fb72928dd9e1edf64c 100644 --- a/src/mednet/libs/segmentation/config/data/refuge/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/refuge/datamodule.py @@ -12,14 +12,13 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample from mednet.libs.common.models.transforms import crop_image_to_mask +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/rimoner3/datamodule.py b/src/mednet/libs/segmentation/config/data/rimoner3/datamodule.py index c5be56fe876e5510d50abd6bfd1e2ade4dfce2ba..f8055f575e434cbf609ecf34b43fdf28d2ee7c80 100644 --- a/src/mednet/libs/segmentation/config/data/rimoner3/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/rimoner3/datamodule.py @@ -11,14 +11,13 @@ import pkg_resources from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import crop, to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/shenzhen/datamodule.py b/src/mednet/libs/segmentation/config/data/shenzhen/datamodule.py index bbb44b3e94687eb296f43d551b3d5507525b1fd9..ade62cd9bb937239252b3c555477f3b1e49602e0 100644 --- a/src/mednet/libs/segmentation/config/data/shenzhen/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/shenzhen/datamodule.py @@ -12,14 +12,13 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample from mednet.libs.common.models.transforms import crop_image_to_mask +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/config/data/stare/datamodule.py b/src/mednet/libs/segmentation/config/data/stare/datamodule.py index 9bf18d18827707c1d8ad868c815028802326970a..14a352ab41ffc1d4c58bb16d240caac94c673805 100644 --- a/src/mednet/libs/segmentation/config/data/stare/datamodule.py +++ b/src/mednet/libs/segmentation/config/data/stare/datamodule.py @@ -12,14 +12,13 @@ from mednet.libs.common.data.datamodule import CachingDataModule from mednet.libs.common.data.split import make_split from mednet.libs.common.data.typing import Sample from mednet.libs.common.models.transforms import crop_image_to_mask +from mednet.libs.common.utils.rc import load_rc from mednet.libs.segmentation.data.typing import ( SegmentationRawDataLoader as _SegmentationRawDataLoader, ) from torchvision import tv_tensors from torchvision.transforms.functional import to_tensor -from ....utils.rc import load_rc - CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2]) """Key to search for in the configuration file for the root directory of this database.""" diff --git a/src/mednet/libs/segmentation/scripts/database.py b/src/mednet/libs/segmentation/scripts/database.py index a58bea038150f4fdfa3fd6df569069a4742c2f6c..1610c16c8b2c958b9d3dae903e5c554d5289e048 100644 --- a/src/mednet/libs/segmentation/scripts/database.py +++ b/src/mednet/libs/segmentation/scripts/database.py @@ -29,8 +29,9 @@ def _get_raw_databases() -> dict[str, dict[str, str]]: import importlib import pkgutil + from mednet.libs.common.utils.rc import load_rc + from ..config import data - from ..utils.rc import load_rc user_configuration = load_rc() diff --git a/src/mednet/libs/segmentation/tests/conftest.py b/src/mednet/libs/segmentation/tests/conftest.py index 5f8efecc9ba6cd913b9de9d92453d7ced866e0de..ce7e932ffc97775ac2cddd80fc50fd6cb8dde757 100644 --- a/src/mednet/libs/segmentation/tests/conftest.py +++ b/src/mednet/libs/segmentation/tests/conftest.py @@ -63,7 +63,7 @@ def pytest_runtest_setup(item): information. """ - from mednet.libs.segmentation.utils.rc import load_rc + from mednet.libs.common.utils.rc import load_rc rc = load_rc() @@ -85,7 +85,7 @@ def pytest_runtest_setup(item): def rc_variable_set(name): - from mednet.libs.segmentation.utils.rc import load_rc + from mednet.libs.common.utils.rc import load_rc rc = load_rc() pytest.mark.skipif( diff --git a/src/mednet/libs/segmentation/utils/rc.py b/src/mednet/libs/segmentation/utils/rc.py deleted file mode 100644 index d7b3c48d83a9882f28d9392a36058e35b6405df9..0000000000000000000000000000000000000000 --- a/src/mednet/libs/segmentation/utils/rc.py +++ /dev/null @@ -1,15 +0,0 @@ -# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch> -# -# SPDX-License-Identifier: GPL-3.0-or-later - -from clapper.rc import UserDefaults - - -def load_rc() -> UserDefaults: - """Return global configuration variables. - - Returns - ------- - The user defaults read from the user .toml configuration file. - """ - return UserDefaults("deepdraw.toml") diff --git a/src/mednet/scripts/info.py b/src/mednet/scripts/info.py index 5d4d35084b37ed8318cce946e2e9b9dbb35b7d12..6334b266ab38e1e8521ec3c7510a983173914fec 100644 --- a/src/mednet/scripts/info.py +++ b/src/mednet/scripts/info.py @@ -73,16 +73,16 @@ def info( from mednet.libs.classification.scripts.database import ( _get_raw_databases as _get_raw_databases_classification, ) - from mednet.libs.classification.utils.rc import ( + from mednet.libs.common.scripts.utils import execution_metadata + from mednet.libs.common.utils.rc import ( load_rc as load_rc_classification, ) - from mednet.libs.common.scripts.utils import execution_metadata + from mednet.libs.common.utils.rc import ( + load_rc as load_rc_segmentation, + ) from mednet.libs.segmentation.scripts.database import ( _get_raw_databases as _get_raw_databases_segmentation, ) - from mednet.libs.segmentation.utils.rc import ( - load_rc as load_rc_segmentation, - ) m = execution_metadata()