[mednet] Use single rc file for both libs

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
 
 

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."""

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."""

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.

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."""

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."""

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."""

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."""

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()
 

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(

src/mednet/libs/classification/utils/rc.py → 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")

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."""

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."""

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."""

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."""

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."""

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."""

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."""

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."""

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."""