diff --git a/.gitignore b/.gitignore
index 2ba7edec79a71c3affe1802207f82be2801d113a..f8dcb218fce7c4136c9aedd300cde151fa259618 100644
--- a/.gitignore
+++ b/.gitignore
@@ -22,3 +22,4 @@ cache/
.venv
.pixi
results*/
+environment.yaml
diff --git a/src/mednet/libs/classification/config/data/hivtb/datamodule.py b/src/mednet/libs/classification/config/data/hivtb/datamodule.py
index 190832504db85bd9e07b1f561a31e0d4841e3dad..5d8170b77d50d658b22f3716ed2890a2eb395545 100644
--- a/src/mednet/libs/classification/config/data/hivtb/datamodule.py
+++ b/src/mednet/libs/classification/config/data/hivtb/datamodule.py
@@ -10,11 +10,15 @@ import os
import pathlib
import PIL.Image
+from mednet.libs.classification.data.typing import (
+ ClassificationRawDataLoader as _ClassificationRawDataLoader,
+)
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.data.typing import RawDataLoader as _BaseRawDataLoader
+
from torchvision.transforms.functional import to_tensor
from ....utils.rc import load_rc
@@ -24,7 +28,7 @@ CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
database."""
-class RawDataLoader(_BaseRawDataLoader):
+class ClassificationRawDataLoader(_ClassificationRawDataLoader):
"""A specialized raw-data-loader for the HIV-TB dataset."""
datadir: pathlib.Path
@@ -123,7 +127,7 @@ class DataModule(CachingDataModule):
assert __package__ is not None
super().__init__(
database_split=make_split(__package__, split_filename),
- raw_data_loader=RawDataLoader(),
- database_name=__package__.rsplit(".", 1)[1],
+ raw_data_loader=_ClassificationRawDataLoader(),
+ database_name=__package__.rsplit(".", 1)[1],
split_name=pathlib.Path(split_filename).stem,
)
diff --git a/src/mednet/libs/classification/config/data/indian/datamodule.py b/src/mednet/libs/classification/config/data/indian/datamodule.py
index 6b4f9c77631e00f6a2cb1172b18147151112b0b9..63ff00c284201f797dc4eb51f5b1e7ef8c723f4f 100644
--- a/src/mednet/libs/classification/config/data/indian/datamodule.py
+++ b/src/mednet/libs/classification/config/data/indian/datamodule.py
@@ -11,8 +11,9 @@ import pathlib
from mednet.libs.common.data.datamodule import CachingDataModule
from mednet.libs.common.data.split import make_split
-from ....config.data.shenzhen.datamodule import RawDataLoader
-
+from mednet.libs.classification.data.typing import (
+ ClassificationRawDataLoader as _ClassificationRawDataLoader,
+)
CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
"""Key to search for in the configuration file for the root directory of this
database."""
@@ -60,10 +61,11 @@ class DataModule(CachingDataModule):
"""
def __init__(self, split_filename: str):
- assert __package__
+ assert __package__ is not None
super().__init__(
database_split=make_split(__package__, split_filename),
- raw_data_loader=RawDataLoader(config_variable=CONFIGURATION_KEY_DATADIR),
- database_name=__package__.rsplit(".", 1)[1],
+ raw_data_loader=_ClassificationRawDataLoader(),
+ database_name=__package__.rsplit(".", 1)[1],
split_name=pathlib.Path(split_filename).stem,
)
+
diff --git a/src/mednet/libs/classification/config/data/montgomery/datamodule.py b/src/mednet/libs/classification/config/data/montgomery/datamodule.py
index ecdd12a8bc351e6c1ca4299a48a44444aaac3ec4..83753205a142a5c06548527dc224a75849718768 100644
--- a/src/mednet/libs/classification/config/data/montgomery/datamodule.py
+++ b/src/mednet/libs/classification/config/data/montgomery/datamodule.py
@@ -10,11 +10,15 @@ import os
import pathlib
import PIL.Image
+from mednet.libs.classification.data.typing import (
+ ClassificationRawDataLoader as _ClassificationRawDataLoader,
+)
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.data.typing import RawDataLoader as _BaseRawDataLoader
+
from torchvision.transforms.functional import to_tensor
from ....utils.rc import load_rc
@@ -136,7 +140,7 @@ class DataModule(CachingDataModule):
assert __package__ is not None
super().__init__(
database_split=make_split(__package__, split_filename),
- raw_data_loader=RawDataLoader(),
- database_name=__package__.rsplit(".", 1)[1],
+ raw_data_loader=_ClassificationRawDataLoader(),
+ database_name=__package__.rsplit(".", 1)[1],
split_name=pathlib.Path(split_filename).stem,
)
diff --git a/src/mednet/libs/classification/config/data/montgomery_shenzhen/datamodule.py b/src/mednet/libs/classification/config/data/montgomery_shenzhen/datamodule.py
index f3bf981423df05cf61b80fcd0382fa6fca05ad46..cce90f7a2a1fc48d7381653fcb09c04b8ec464ae 100644
--- a/src/mednet/libs/classification/config/data/montgomery_shenzhen/datamodule.py
+++ b/src/mednet/libs/classification/config/data/montgomery_shenzhen/datamodule.py
@@ -8,8 +8,10 @@ import pathlib
from mednet.libs.common.data.datamodule import ConcatDataModule
from mednet.libs.common.data.split import make_split
-from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
-from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
+from ..montgomery.datamodule import (
+ ClassificationRawDataLoader as MontgomeryLoader,
+)
+from ..shenzhen.datamodule import ClassificationRawDataLoader as ShenzhenLoader
class DataModule(ConcatDataModule):
diff --git a/src/mednet/libs/classification/config/data/montgomery_shenzhen_indian/datamodule.py b/src/mednet/libs/classification/config/data/montgomery_shenzhen_indian/datamodule.py
index 73b6d765be2a9e938f9d1675a2261fb263524ddc..b09fa338731907c6a5fcd0196eccff6d57013c2b 100644
--- a/src/mednet/libs/classification/config/data/montgomery_shenzhen_indian/datamodule.py
+++ b/src/mednet/libs/classification/config/data/montgomery_shenzhen_indian/datamodule.py
@@ -12,9 +12,11 @@ from mednet.libs.common.data.split import make_split
from ..indian.datamodule import CONFIGURATION_KEY_DATADIR as INDIAN_KEY_DATADIR
from ..indian.datamodule import DataModule as IndianDataModule
-from ..indian.datamodule import RawDataLoader as IndianLoader
-from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
-from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
+from ..indian.datamodule import ClassificationRawDataLoader as IndianLoader
+from ..montgomery.datamodule import (
+ ClassificationRawDataLoader as MontgomeryLoader,
+)
+from ..shenzhen.datamodule import ClassificationRawDataLoader as ShenzhenLoader
class DataModule(ConcatDataModule):
diff --git a/src/mednet/libs/classification/config/data/montgomery_shenzhen_indian_padchest/datamodule.py b/src/mednet/libs/classification/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
index 942326b2cde9e920bb764a812d8b0eea03cb3398..5daef8128be0293db3e45270593eb851337580a5 100644
--- a/src/mednet/libs/classification/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
+++ b/src/mednet/libs/classification/config/data/montgomery_shenzhen_indian_padchest/datamodule.py
@@ -11,11 +11,13 @@ from mednet.libs.common.data.datamodule import ConcatDataModule
from mednet.libs.common.data.split import make_split
from ..indian.datamodule import CONFIGURATION_KEY_DATADIR as INDIAN_KEY_DATADIR
+from ..indian.datamodule import ClassificationRawDataLoader as IndianLoader
from ..indian.datamodule import DataModule as IndianDataModule
-from ..indian.datamodule import RawDataLoader as IndianLoader
-from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
-from ..padchest.datamodule import RawDataLoader as PadchestLoader
-from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
+from ..montgomery.datamodule import (
+ ClassificationRawDataLoader as MontgomeryLoader,
+)
+from ..padchest.datamodule import ClassificationRawDataLoader as PadchestLoader
+from ..shenzhen.datamodule import ClassificationRawDataLoader as ShenzhenLoader
class DataModule(ConcatDataModule):
diff --git a/src/mednet/libs/classification/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py b/src/mednet/libs/classification/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
index daf575f7abe5376659559ad168f72d2d31389368..532945277debb3558fae1a97c0a26d434690cea4 100644
--- a/src/mednet/libs/classification/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
+++ b/src/mednet/libs/classification/config/data/montgomery_shenzhen_indian_tbx11k/datamodule.py
@@ -12,10 +12,12 @@ from mednet.libs.common.data.split import make_split
from ..indian.datamodule import CONFIGURATION_KEY_DATADIR as INDIAN_KEY_DATADIR
from ..indian.datamodule import DataModule as IndianDataModule
-from ..indian.datamodule import RawDataLoader as IndianLoader
-from ..montgomery.datamodule import RawDataLoader as MontgomeryLoader
-from ..shenzhen.datamodule import RawDataLoader as ShenzhenLoader
-from ..tbx11k.datamodule import RawDataLoader as TBX11kLoader
+from ..indian.datamodule import ClassificationRawDataLoader as IndianLoader
+from ..montgomery.datamodule import (
+ ClassificationRawDataLoader as MontgomeryLoader,
+)
+from ..shenzhen.datamodule import ClassificationRawDataLoader as ShenzhenLoader
+from ..tbx11k.datamodule import ClassificationRawDataLoader as TBX11kLoader
class DataModule(ConcatDataModule):
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 10b02268f61c7105e7057e699f3580a4d80b89ff..900dcc9d0091a8571629bf283ee6c1829fa62286 100644
--- a/src/mednet/libs/classification/config/data/nih_cxr14/datamodule.py
+++ b/src/mednet/libs/classification/config/data/nih_cxr14/datamodule.py
@@ -10,10 +10,14 @@ import os
import pathlib
import PIL.Image
+from mednet.libs.classification.data.typing import (
+ ClassificationRawDataLoader as _ClassificationRawDataLoader,
+)
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.data.typing import RawDataLoader as _BaseRawDataLoader
+
from torchvision.transforms.functional import to_tensor
from ....utils.rc import load_rc
@@ -35,7 +39,7 @@ different folder structure, that was adapted to Idiap's requirements
"""
-class RawDataLoader(_BaseRawDataLoader):
+class ClassificationRawDataLoader(_ClassificationRawDataLoader):
"""A specialized raw-data-loader for the NIH CXR-14 dataset."""
datadir: pathlib.Path
@@ -172,7 +176,7 @@ class DataModule(CachingDataModule):
assert __package__ is not None
super().__init__(
database_split=make_split(__package__, split_filename),
- raw_data_loader=RawDataLoader(),
- database_name=__package__.rsplit(".", 1)[1],
+ raw_data_loader=_ClassificationRawDataLoader(),
+ database_name=__package__.rsplit(".", 1)[1],
split_name=pathlib.Path(split_filename).stem,
)
diff --git a/src/mednet/libs/classification/config/data/nih_cxr14_padchest/datamodule.py b/src/mednet/libs/classification/config/data/nih_cxr14_padchest/datamodule.py
index beeb3d9655cd434122d59fe36ee18eb63e7c12b8..d5a44ce64e5060f69083f95824a5995f63246e05 100644
--- a/src/mednet/libs/classification/config/data/nih_cxr14_padchest/datamodule.py
+++ b/src/mednet/libs/classification/config/data/nih_cxr14_padchest/datamodule.py
@@ -8,9 +8,8 @@ import pathlib
from mednet.libs.common.data.datamodule import ConcatDataModule
from mednet.libs.common.data.split import make_split
-from ..nih_cxr14.datamodule import RawDataLoader as CXR14Loader
-from ..padchest.datamodule import RawDataLoader as PadchestLoader
-
+from ..nih_cxr14.datamodule import ClassificationRawDataLoader as CXR14Loader
+from ..padchest.datamodule import ClassificationRawDataLoader as PadchestLoader
class DataModule(ConcatDataModule):
"""Aggregated dataset composed of NIH CXR14 relabeld and PadChest
diff --git a/src/mednet/libs/classification/config/data/padchest/datamodule.py b/src/mednet/libs/classification/config/data/padchest/datamodule.py
index 8ea0eb7c0262c0dac7a713828d6c0ec749589131..0fed49ab85d409ed6ae4b248de849cb31851a3eb 100644
--- a/src/mednet/libs/classification/config/data/padchest/datamodule.py
+++ b/src/mednet/libs/classification/config/data/padchest/datamodule.py
@@ -11,11 +11,15 @@ import pathlib
import numpy
import PIL.Image
+from mednet.libs.classification.data.typing import (
+ ClassificationRawDataLoader as _ClassificationRawDataLoader,
+)
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.data.typing import RawDataLoader as _BaseRawDataLoader
+
from torchvision.transforms.functional import to_tensor
from ....utils.rc import load_rc
@@ -25,7 +29,7 @@ CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
database."""
-class RawDataLoader(_BaseRawDataLoader):
+class ClassificationRawDataLoader(_ClassificationRawDataLoader):
"""A specialized raw-data-loader for the PadChest dataset."""
datadir: pathlib.Path
@@ -325,7 +329,7 @@ class DataModule(CachingDataModule):
assert __package__ is not None
super().__init__(
database_split=make_split(__package__, split_filename),
- raw_data_loader=RawDataLoader(),
- database_name=__package__.rsplit(".", 1)[1],
+ raw_data_loader=_ClassificationRawDataLoader(),
+ database_name=__package__.rsplit(".", 1)[1],
split_name=pathlib.Path(split_filename).stem,
)
diff --git a/src/mednet/libs/classification/config/data/shenzhen/datamodule.py b/src/mednet/libs/classification/config/data/shenzhen/datamodule.py
index f68851b6bb53ddc9fbff044c3eee87db24f23003..7ab4d171825e4894c4d25eb0dfe35c72ba7229a9 100644
--- a/src/mednet/libs/classification/config/data/shenzhen/datamodule.py
+++ b/src/mednet/libs/classification/config/data/shenzhen/datamodule.py
@@ -10,11 +10,15 @@ import os
import pathlib
import PIL.Image
+from mednet.libs.classification.data.typing import (
+ ClassificationRawDataLoader as _ClassificationRawDataLoader,
+)
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.data.typing import RawDataLoader as _BaseRawDataLoader
+
from torchvision.transforms.functional import to_tensor
from ....utils.rc import load_rc
@@ -24,7 +28,7 @@ CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
database."""
-class RawDataLoader(_BaseRawDataLoader):
+class ClassificationRawDataLoader(_ClassificationRawDataLoader):
"""A specialized raw-data-loader for the Shenzhen dataset.
Parameters
@@ -135,7 +139,7 @@ class DataModule(CachingDataModule):
assert __package__ is not None
super().__init__(
database_split=make_split(__package__, split_filename),
- raw_data_loader=RawDataLoader(),
- database_name=__package__.rsplit(".", 1)[1],
+ raw_data_loader=_ClassificationRawDataLoader(),
+ database_name=__package__.rsplit(".", 1)[1],
split_name=pathlib.Path(split_filename).stem,
)
diff --git a/src/mednet/libs/classification/config/data/tbpoc/datamodule.py b/src/mednet/libs/classification/config/data/tbpoc/datamodule.py
index 122f6686b4831cfb74e35320a7d23e5ee64192e6..2ba9f688a1abc5a3fc38a45ae92d4d6f7f2d38be 100644
--- a/src/mednet/libs/classification/config/data/tbpoc/datamodule.py
+++ b/src/mednet/libs/classification/config/data/tbpoc/datamodule.py
@@ -6,11 +6,15 @@ import os
import pathlib
import PIL.Image
+from mednet.libs.classification.data.typing import (
+ ClassificationRawDataLoader as _ClassificationRawDataLoader,
+)
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.data.typing import RawDataLoader as _BaseRawDataLoader
+
from torchvision.transforms.functional import to_tensor
from ....utils.rc import load_rc
@@ -20,7 +24,7 @@ CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
database."""
-class RawDataLoader(_BaseRawDataLoader):
+class ClassificationRawDataLoader(_ClassificationRawDataLoader):
"""A specialized raw-data-loader for the Shenzen dataset."""
datadir: pathlib.Path
@@ -121,7 +125,7 @@ class DataModule(CachingDataModule):
assert __package__ is not None
super().__init__(
database_split=make_split(__package__, split_filename),
- raw_data_loader=RawDataLoader(),
- database_name=__package__.rsplit(".", 1)[1],
+ raw_data_loader=_ClassificationRawDataLoader(),
+ database_name=__package__.rsplit(".", 1)[1],
split_name=pathlib.Path(split_filename).stem,
)
diff --git a/src/mednet/libs/classification/config/data/tbx11k/datamodule.py b/src/mednet/libs/classification/config/data/tbx11k/datamodule.py
index b633d8e9e4d87fdf6c9113f16c2703e3bcf71b1b..fb86030754971e0dc6551009d161a4965f029bac 100644
--- a/src/mednet/libs/classification/config/data/tbx11k/datamodule.py
+++ b/src/mednet/libs/classification/config/data/tbx11k/datamodule.py
@@ -10,10 +10,12 @@ import typing
import PIL.Image
import typing_extensions
+from mednet.libs.classification.data.typing import (
+ ClassificationRawDataLoader as _ClassificationRawDataLoader,
+)
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.data.typing import RawDataLoader as _BaseRawDataLoader
from torch.utils.data._utils.collate import default_collate_fn_map
from torchvision.transforms.functional import to_tensor
@@ -167,7 +169,7 @@ finding locations, as described above.
"""
-class RawDataLoader(_BaseRawDataLoader):
+class ClassificationRawDataLoader(_ClassificationRawDataLoader):
"""A specialized raw-data-loader for the TBX11k dataset.
Parameters
@@ -377,7 +379,7 @@ class DataModule(CachingDataModule):
assert __package__ is not None
super().__init__(
database_split=make_split(__package__, split_filename),
- raw_data_loader=RawDataLoader(ignore_bboxes=ignore_bboxes),
+ raw_data_loader=ClassificationRawDataLoader(ignore_bboxes=ignore_bboxes),
database_name=__package__.rsplit(".", 1)[1],
split_name=pathlib.Path(split_filename).stem,
)
diff --git a/src/mednet/libs/classification/data/__init__.py b/src/mednet/libs/classification/data/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/src/mednet/libs/classification/data/typing.py b/src/mednet/libs/classification/data/typing.py
new file mode 100644
index 0000000000000000000000000000000000000000..8cd214053c02cc975bfc1d48c4f5418bd8c28bf5
--- /dev/null
+++ b/src/mednet/libs/classification/data/typing.py
@@ -0,0 +1,41 @@
+import typing
+
+from mednet.libs.common.data.typing import RawDataLoader, Sample
+
+
+class ClassificationRawDataLoader(RawDataLoader):
+ """A loader object can load samples and labels from storage for classification tasks."""
+
+ def __init__(self):
+ super().__init__()
+
+ def sample(self, _: typing.Any) -> Sample:
+ """Load whole samples from media.
+
+ Parameters
+ ----------
+ _
+ Information about the sample to load. Implementation dependent.
+ """
+
+ raise NotImplementedError("You must implement the `sample()` method")
+
+ def label(self, k: typing.Any) -> int | list[int]:
+ """Load only sample label from media.
+
+ If you do not override this implementation, then, by default,
+ this method will call :py:meth:`sample` to load the whole sample
+ and extract the label.
+
+ Parameters
+ ----------
+ k
+ The sample to load. This is implementation-dependent.
+
+ Returns
+ -------
+ int | list[int]
+ The label corresponding to the specified sample.
+ """
+
+ return self.sample(k)[1]["label"]
diff --git a/src/mednet/libs/common/data/typing.py b/src/mednet/libs/common/data/typing.py
index 93bbfc970b50549ae03a125ef89b785e62a161d0..48cce9e780dd1be756d5f7b85947feda2b7dc0be 100644
--- a/src/mednet/libs/common/data/typing.py
+++ b/src/mednet/libs/common/data/typing.py
@@ -35,26 +35,6 @@ class RawDataLoader:
raise NotImplementedError("You must implement the `sample()` method")
- def label(self, k: typing.Any) -> int | list[int]:
- """Load only sample label from media.
-
- If you do not override this implementation, then, by default,
- this method will call :py:meth:`sample` to load the whole sample
- and extract the label.
-
- Parameters
- ----------
- k
- The sample to load. This is implementation-dependent.
-
- Returns
- -------
- int | list[int]
- The label corresponding to the specified sample.
- """
-
- return self.sample(k)[1]["label"]
-
Transform: typing.TypeAlias = typing.Callable[[torch.Tensor], torch.Tensor]
"""A callable that transforms tensors into (other) tensors.
diff --git a/src/mednet/libs/segmentation/config/data/drive/datamodule.py b/src/mednet/libs/segmentation/config/data/drive/datamodule.py
index b61941a59797ed80baf01f580cd6f92e50da5829..2ef7d1cbd97dd0361ad7d00221b016c3e4d77ab1 100644
--- a/src/mednet/libs/segmentation/config/data/drive/datamodule.py
+++ b/src/mednet/libs/segmentation/config/data/drive/datamodule.py
@@ -11,7 +11,9 @@ import PIL.Image
from mednet.libs.common.data.datamodule import CachingDataModule
from mednet.libs.common.data.split import JSONDatabaseSplit
from mednet.libs.common.data.typing import DatabaseSplit, Sample
-from mednet.libs.common.data.typing import RawDataLoader as _BaseRawDataLoader
+from mednet.libs.segmentation.data.typing import (
+ SegmentationRawDataLoader as _SegmentationRawDataLoader,
+)
from torchvision import tv_tensors
from torchvision.transforms.functional import to_tensor
@@ -22,7 +24,7 @@ CONFIGURATION_KEY_DATADIR = "datadir." + (__name__.rsplit(".", 2)[-2])
database."""
-class RawDataLoader(_BaseRawDataLoader):
+class SegmentationRawDataLoader(_SegmentationRawDataLoader):
"""A specialized raw-data-loader for the Montgomery dataset."""
datadir: str
@@ -116,5 +118,5 @@ class DataModule(CachingDataModule):
def __init__(self, split_filename: str):
super().__init__(
database_split=make_split(split_filename),
- raw_data_loader=RawDataLoader(),
+ raw_data_loader=SegmentationRawDataLoader(),
)
diff --git a/src/mednet/libs/segmentation/data/typing.py b/src/mednet/libs/segmentation/data/typing.py
new file mode 100644
index 0000000000000000000000000000000000000000..e1d95cdbb276c58bd8e21467948c44a6343e00e2
--- /dev/null
+++ b/src/mednet/libs/segmentation/data/typing.py
@@ -0,0 +1,21 @@
+import typing
+
+from mednet.libs.common.data.typing import RawDataLoader, Sample
+
+
+class SegmentationRawDataLoader(RawDataLoader):
+ """A loader object can load samples and labels from storage for classification tasks."""
+
+ def __init__(self):
+ super().__init__()
+
+ def sample(self, _: typing.Any) -> Sample:
+ """Load whole samples from media.
+
+ Parameters
+ ----------
+ _
+ Information about the sample to load. Implementation dependent.
+ """
+
+ raise NotImplementedError("You must implement the `sample()` method")