From 252156bb93b71ca967dba3b90da126177287fc21 Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Fri, 26 Apr 2024 10:17:53 +0200
Subject: [PATCH] [dataloader] Create specialized RawDataLoaders per task
---
.gitignore | 1 +
.../config/data/hivtb/datamodule.py | 12 ++++--
.../config/data/indian/datamodule.py | 12 +++---
.../config/data/montgomery/datamodule.py | 10 +++--
.../data/montgomery_shenzhen/datamodule.py | 6 ++-
.../montgomery_shenzhen_indian/datamodule.py | 8 ++--
.../datamodule.py | 10 +++--
.../datamodule.py | 10 +++--
.../config/data/nih_cxr14/datamodule.py | 12 ++++--
.../data/nih_cxr14_padchest/datamodule.py | 5 +--
.../config/data/padchest/datamodule.py | 12 ++++--
.../config/data/shenzhen/datamodule.py | 12 ++++--
.../config/data/tbpoc/datamodule.py | 12 ++++--
.../config/data/tbx11k/datamodule.py | 8 ++--
.../libs/classification/data/__init__.py | 0
src/mednet/libs/classification/data/typing.py | 41 +++++++++++++++++++
src/mednet/libs/common/data/typing.py | 20 ---------
.../config/data/drive/datamodule.py | 8 ++--
src/mednet/libs/segmentation/data/typing.py | 21 ++++++++++
19 files changed, 150 insertions(+), 70 deletions(-)
create mode 100644 src/mednet/libs/classification/data/__init__.py
create mode 100644 src/mednet/libs/classification/data/typing.py
create mode 100644 src/mednet/libs/segmentation/data/typing.py
diff --git a/.gitignore b/.gitignore
index 2ba7edec..f8dcb218 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 19083250..5d8170b7 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 6b4f9c77..63ff00c2 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 ecdd12a8..83753205 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 f3bf9814..cce90f7a 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 73b6d765..b09fa338 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 942326b2..5daef812 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 daf575f7..53294527 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 10b02268..900dcc9d 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 beeb3d96..d5a44ce6 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 8ea0eb7c..0fed49ab 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 f68851b6..7ab4d171 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 122f6686..2ba9f688 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 b633d8e9..fb860307 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 00000000..e69de29b
diff --git a/src/mednet/libs/classification/data/typing.py b/src/mednet/libs/classification/data/typing.py
new file mode 100644
index 00000000..8cd21405
--- /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 93bbfc97..48cce9e7 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 b61941a5..2ef7d1cb 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 00000000..e1d95cdb
--- /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")
--
GitLab