kaiko-eva 0.2.0__py3-none-any.whl → 0.2.1__py3-none-any.whl

eva/vision/data/datasets/segmentation/__init__.py

@@ -1,7 +1,7 @@
 """Segmentation datasets API."""
 
-from eva.vision.data.datasets.segmentation.base import ImageSegmentation
 from eva.vision.data.datasets.segmentation.bcss import BCSS
+from eva.vision.data.datasets.segmentation.btcv import BTCV
 from eva.vision.data.datasets.segmentation.consep import CoNSeP
 from eva.vision.data.datasets.segmentation.embeddings import EmbeddingsSegmentationDataset
 from eva.vision.data.datasets.segmentation.lits import LiTS
@@ -10,8 +10,8 @@ from eva.vision.data.datasets.segmentation.monusac import MoNuSAC
 from eva.vision.data.datasets.segmentation.total_segmentator_2d import TotalSegmentator2D
 
 __all__ = [
-    "ImageSegmentation",
     "BCSS",
+    "BTCV",
     "CoNSeP",
     "EmbeddingsSegmentationDataset",
     "LiTS",

eva/vision/data/datasets/segmentation/_utils.py

@@ -1,8 +1,12 @@
 from typing import Any, Tuple
 
 import numpy.typing as npt
+import torch
+from torchvision import tv_tensors
 
+from eva.vision.data import tv_tensors as eva_tv_tensors
 from eva.vision.data.datasets import wsi
+from eva.vision.utils import io
 
 
 def get_coords_at_index(
@@ -36,3 +40,46 @@ def extract_mask_patch(
     """
     (x, y), width, height = get_coords_at_index(dataset, index)
     return mask[y : y + height, x : x + width]
+
+
+def load_volume_tensor(file: str, orientation: str = "PLS") -> eva_tv_tensors.Volume:
+    """Load a volume from NIfTI file as :class:`eva.vision.data.tv_tensors.Volume`.
+
+    Args:
+        file: The path to the NIfTI file.
+        orientation: The orientation code to reorient the nifti image.
+
+    Returns:
+        Volume tensor representing of shape `[T, C, H, W]`.
+    """
+    nii = io.read_nifti(file, orientation=orientation)
+    array = io.nifti_to_array(nii)
+    array_reshaped_tchw = array[None, :, :, :].transpose(3, 0, 1, 2)
+
+    if nii.affine is None:
+        raise ValueError(f"Affine matrix is missing for {file}.")
+    affine = torch.tensor(nii.affine[:, [2, 0, 1, 3]], dtype=torch.float32)
+
+    return eva_tv_tensors.Volume(
+        array_reshaped_tchw, affine=affine, dtype=torch.float32
+    )  # type: ignore
+
+
+def load_mask_tensor(
+    file: str, volume_file: str | None = None, orientation: str = "PLS"
+) -> tv_tensors.Mask:
+    """Load a volume from NIfTI file as :class:`torchvision.tv_tensors.Mask`.
+
+    Args:
+        file: The path to the NIfTI file containing the mask.
+        volume_file: The path to the volume file used as orientation reference in case
+            the mask file is missing the pixdim array in the NIfTI header.
+        orientation: The orientation code to reorient the nifti image.
+
+    Returns:
+        Mask tensor of shape `[T, C, H, W]`.
+    """
+    nii = io.read_nifti(file, orientation="PLS", orientation_reference=volume_file)
+    array = io.nifti_to_array(nii)
+    array_reshaped_tchw = array[None, :, :, :].transpose(3, 0, 1, 2)
+    return tv_tensors.Mask(array_reshaped_tchw, dtype=torch.long)  # type: ignore

eva/vision/data/datasets/segmentation/bcss.py

@@ -12,13 +12,13 @@ from torchvision import tv_tensors
 from torchvision.transforms.v2 import functional
 from typing_extensions import override
 
-from eva.vision.data.datasets import _validators, wsi
-from eva.vision.data.datasets.segmentation import _utils, base
+from eva.vision.data.datasets import _validators, vision, wsi
+from eva.vision.data.datasets.segmentation import _utils
 from eva.vision.data.wsi.patching import samplers
 from eva.vision.utils import io
 
 
-class BCSS(wsi.MultiWsiDataset, base.ImageSegmentation):
+class BCSS(wsi.MultiWsiDataset, vision.VisionDataset[tv_tensors.Image, tv_tensors.Mask]):
     """Dataset class for BCSS semantic segmentation task.
 
     Source: https://github.com/PathologyDataScience/BCSS
@@ -71,7 +71,6 @@ class BCSS(wsi.MultiWsiDataset, base.ImageSegmentation):
             width: Width of the patches to be extracted, in pixels.
             height: Height of the patches to be extracted, in pixels.
             target_mpp: Target microns per pixel (mpp) for the patches.
-            backend: The backend to use for reading the whole-slide images.
             transforms: Transforms to apply to the extracted image & mask patches.
         """
         self._split = split
@@ -90,7 +89,7 @@ class BCSS(wsi.MultiWsiDataset, base.ImageSegmentation):
             overwrite_mpp=0.25,
             backend="pil",
         )
-        base.ImageSegmentation.__init__(self, transforms=transforms)
+        vision.VisionDataset.__init__(self, transforms=transforms)
 
     @property
     @override
@@ -129,15 +128,15 @@ class BCSS(wsi.MultiWsiDataset, base.ImageSegmentation):
 
     @override
     def __getitem__(self, index: int) -> Tuple[tv_tensors.Image, tv_tensors.Mask, Dict[str, Any]]:
-        return base.ImageSegmentation.__getitem__(self, index)
+        return vision.VisionDataset.__getitem__(self, index)
 
     @override
-    def load_image(self, index: int) -> tv_tensors.Image:
+    def load_data(self, index: int) -> tv_tensors.Image:
         image_array = wsi.MultiWsiDataset.__getitem__(self, index)
         return functional.to_image(image_array)
 
     @override
-    def load_mask(self, index: int) -> tv_tensors.Mask:
+    def load_target(self, index: int) -> tv_tensors.Mask:
         path = self._get_mask_path(index)
         mask = io.read_image_as_array(path)
         mask_patch = _utils.extract_mask_patch(mask, self, index)

eva/vision/data/datasets/segmentation/btcv.py

@@ -0,0 +1,236 @@
+"""BTCV dataset."""
+
+import glob
+import os
+import re
+from typing import Any, Callable, Dict, List, Literal, Tuple
+
+import huggingface_hub
+from torchvision import tv_tensors
+from torchvision.datasets import utils as data_utils
+from typing_extensions import override
+
+from eva.vision.data import tv_tensors as eva_tv_tensors
+from eva.vision.data.datasets import _utils as _data_utils
+from eva.vision.data.datasets.segmentation import _utils
+from eva.vision.data.datasets.vision import VisionDataset
+
+
+class BTCV(VisionDataset[eva_tv_tensors.Volume, tv_tensors.Mask]):
+    """Beyond the Cranial Vault (BTCV) Abdomen dataset.
+
+    The BTCV dataset comprises abdominal CT acquired at the Vanderbilt
+    University Medical Center from metastatic liver cancer patients or
+    post-operative ventral hernia patients. The dataset contains one
+    background class and thirteen organ classes.
+
+    More info:
+      - Multi-organ Abdominal CT Reference Standard Segmentations
+        https://zenodo.org/records/1169361
+      - Dataset Split
+        https://github.com/Luffy03/Large-Scale-Medical/blob/main/Downstream/monai/BTCV/dataset/dataset_0.json
+    """
+
+    _split_index_ranges = {
+        "train": [(0, 24)],
+        "val": [(24, 30)],
+        None: [(0, 30)],
+    }
+    """Sample indices for the dataset splits."""
+
+    def __init__(
+        self,
+        root: str,
+        split: Literal["train", "val"] | None = None,
+        download: bool = False,
+        transforms: Callable | None = None,
+    ) -> None:
+        """Initializes the dataset.
+
+        Args:
+            root: Path to the dataset root directory.
+            split: Dataset split to use ('train' or 'val').
+                If None, it uses the full dataset.
+            download: Whether to download the dataset.
+            transforms: A callable object for applying data transformations.
+                If None, no transformations are applied.
+        """
+        super().__init__(transforms=transforms)
+
+        self._root = root
+        self._split = split
+        self._download = download
+
+        self._samples: List[Tuple[str, str]]
+        self._indices: List[int]
+
+    @property
+    @override
+    def classes(self) -> List[str]:
+        return [
+            "background",
+            "spleen",
+            "right_kidney",
+            "left_kidney",
+            "gallbladder",
+            "esophagus",
+            "liver",
+            "stomach",
+            "aorta",
+            "inferior_vena_cava",
+            "portal_and_splenic_vein",
+            "pancreas",
+            "right_adrenal_gland",
+            "left_adrenal_gland",
+        ]
+
+    @property
+    @override
+    def class_to_idx(self) -> Dict[str, int]:
+        return {label: index for index, label in enumerate(self.classes)}
+
+    @override
+    def filename(self, index: int) -> str:
+        return os.path.basename(self._samples[self._indices[index]][0])
+
+    @override
+    def prepare_data(self) -> None:
+        if self._download:
+            self._download_dataset()
+
+    @override
+    def configure(self) -> None:
+        self._samples = self._find_samples()
+        self._indices = self._make_indices()
+
+    @override
+    def validate(self) -> None:
+        def _valid_sample(index: int) -> bool:
+            """Indicates if the sample files exist and are reachable."""
+            volume_file, segmentation_file = self._samples[self._indices[index]]
+            return os.path.isfile(volume_file) and os.path.isfile(segmentation_file)
+
+        if len(self._samples) < len(self._indices):
+            raise OSError(f"Dataset is missing {len(self._indices) - len(self._samples)} files.")
+
+        invalid_samples = [self._samples[i] for i in range(len(self)) if not _valid_sample(i)]
+        if invalid_samples:
+            raise OSError(
+                f"Dataset '{self.__class__.__qualname__}' contains missing or "
+                f"corrupted samples  ({len(invalid_samples)} in total). "
+                f"Examples of missing folders: {str(invalid_samples[:10])[:-1]}, ...]. "
+            )
+
+    @override
+    def __getitem__(
+        self, index: int
+    ) -> tuple[eva_tv_tensors.Volume, tv_tensors.Mask, dict[str, Any]]:
+        volume = self.load_data(index)
+        mask = self.load_target(index)
+        metadata = self.load_metadata(index) or {}
+        volume_tensor, mask_tensor = self._apply_transforms(volume, mask)
+        return volume_tensor, mask_tensor, metadata
+
+    @override
+    def __len__(self) -> int:
+        return len(self._indices)
+
+    @override
+    def load_data(self, index: int) -> eva_tv_tensors.Volume:
+        """Loads the CT volume for a given sample.
+
+        Args:
+            index: The index of the desired sample.
+
+        Returns:
+            Tensor representing the CT volume of shape `[T, C, H, W]`.
+        """
+        ct_scan_file, _ = self._samples[self._indices[index]]
+        return _utils.load_volume_tensor(ct_scan_file)
+
+    @override
+    def load_target(self, index: int) -> tv_tensors.Mask:
+        """Loads the segmentation mask for a given sample.
+
+        Args:
+            index: The index of the desired sample.
+
+        Returns:
+            Tensor representing the segmentation mask of shape `[T, C, H, W]`.
+        """
+        ct_scan_file, mask_file = self._samples[self._indices[index]]
+        return _utils.load_mask_tensor(mask_file, ct_scan_file)
+
+    def _apply_transforms(
+        self, ct_scan: eva_tv_tensors.Volume, mask: tv_tensors.Mask
+    ) -> tuple[eva_tv_tensors.Volume, tv_tensors.Mask]:
+        """Applies transformations to the provided data.
+
+        Args:
+            ct_scan: The CT volume tensor.
+            mask: The segmentation mask tensor.
+
+        Returns:
+            A tuple containing the transformed CT and mask tensors.
+        """
+        return self._transforms(ct_scan, mask) if self._transforms else (ct_scan, mask)
+
+    def _find_samples(self) -> list[tuple[str, str]]:
+        """Retrieves the file paths for the CT volumes and segmentation.
+
+        Returns:
+            The a list of file path to the CT volumes and segmentation.
+        """
+
+        def filename_id(filename: str) -> int:
+            matches = re.match(r".*(?:\D|^)(\d+)", filename)
+            if matches is None:
+                raise ValueError(f"Filename '{filename}' is not valid.")
+
+            return int(matches.group(1))
+
+        subdir = os.path.join(self._root, "BTCV")
+        root = subdir if os.path.isdir(subdir) else self._root
+
+        volume_files_pattern = os.path.join(root, "imagesTr", "*.nii.gz")
+        volume_filenames = glob.glob(volume_files_pattern)
+        volume_ids = {filename_id(filename): filename for filename in volume_filenames}
+
+        segmentation_files_pattern = os.path.join(root, "labelsTr", "*.nii.gz")
+        segmentation_filenames = glob.glob(segmentation_files_pattern)
+        segmentation_ids = {filename_id(filename): filename for filename in segmentation_filenames}
+
+        return [
+            (volume_ids[file_id], segmentation_ids[file_id])
+            for file_id in sorted(volume_ids.keys() & segmentation_ids.keys())
+        ]
+
+    def _make_indices(self) -> list[int]:
+        """Builds the dataset indices for the specified split."""
+        index_ranges = self._split_index_ranges.get(self._split)
+        if index_ranges is None:
+            raise ValueError("Invalid data split. Use 'train', 'val' or `None`.")
+
+        return _data_utils.ranges_to_indices(index_ranges)
+
+    def _download_dataset(self) -> None:
+        hf_token = os.getenv("HF_TOKEN")
+        if not hf_token:
+            raise ValueError("Huggingface token required, please set the HF_TOKEN env variable.")
+
+        huggingface_hub.snapshot_download(
+            "Luffy503/VoCo_Downstream",
+            repo_type="dataset",
+            token=hf_token,
+            local_dir=self._root,
+            ignore_patterns=[".git*"],
+            allow_patterns=["BTCV.zip"],
+        )
+
+        zip_path = os.path.join(self._root, "BTCV.zip")
+        if not os.path.exists(zip_path):
+            raise FileNotFoundError(
+                f"BTCV.zip not found in {self._root}, something with the download went wrong."
+            )
+
+        data_utils.extract_archive(zip_path, self._root, remove_finished=True)

eva/vision/data/datasets/segmentation/consep.py

@@ -11,13 +11,13 @@ from torchvision import tv_tensors
 from torchvision.transforms.v2 import functional
 from typing_extensions import override
 
-from eva.vision.data.datasets import _validators, wsi
-from eva.vision.data.datasets.segmentation import _utils, base
+from eva.vision.data.datasets import _validators, vision, wsi
+from eva.vision.data.datasets.segmentation import _utils
 from eva.vision.data.wsi.patching import samplers
 from eva.vision.utils import io
 
 
-class CoNSeP(wsi.MultiWsiDataset, base.ImageSegmentation):
+class CoNSeP(wsi.MultiWsiDataset, vision.VisionDataset[tv_tensors.Image, tv_tensors.Mask]):
     """Dataset class for CoNSeP semantic segmentation task.
 
     As in [1], we combine classes 3 (healthy epithelial) & 4 (dysplastic/malignant epithelial)
@@ -55,7 +55,6 @@ class CoNSeP(wsi.MultiWsiDataset, base.ImageSegmentation):
             width: Width of the patches to be extracted, in pixels.
             height: Height of the patches to be extracted, in pixels.
             target_mpp: Target microns per pixel (mpp) for the patches.
-            backend: The backend to use for reading the whole-slide images.
             transforms: Transforms to apply to the extracted image & mask patches.
         """
         self._split = split
@@ -112,15 +111,15 @@ class CoNSeP(wsi.MultiWsiDataset, base.ImageSegmentation):
 
     @override
     def __getitem__(self, index: int) -> Tuple[tv_tensors.Image, tv_tensors.Mask, Dict[str, Any]]:
-        return base.ImageSegmentation.__getitem__(self, index)
+        return vision.VisionDataset.__getitem__(self, index)
 
     @override
-    def load_image(self, index: int) -> tv_tensors.Image:
+    def load_data(self, index: int) -> tv_tensors.Image:
         image_array = wsi.MultiWsiDataset.__getitem__(self, index)
         return functional.to_image(image_array)
 
     @override
-    def load_mask(self, index: int) -> tv_tensors.Mask:
+    def load_target(self, index: int) -> tv_tensors.Mask:
         path = self._get_mask_path(index)
         mask = np.array(io.read_mat(path)["type_map"])
         mask_patch = _utils.extract_mask_patch(mask, self, index)

eva/vision/data/datasets/segmentation/lits.py

@@ -13,12 +13,11 @@ from typing_extensions import override
 
 from eva.core import utils
 from eva.core.data import splitting
-from eva.vision.data.datasets import _validators
-from eva.vision.data.datasets.segmentation import base
+from eva.vision.data.datasets import _validators, vision
 from eva.vision.utils import io
 
 
-class LiTS(base.ImageSegmentation):
+class LiTS(vision.VisionDataset[tv_tensors.Image, tv_tensors.Mask]):
     """LiTS - Liver Tumor Segmentation Challenge.
 
     Webpage: https://competitions.codalab.org/competitions/17094
@@ -110,21 +109,23 @@ class LiTS(base.ImageSegmentation):
         )
 
     @override
-    def load_image(self, index: int) -> tv_tensors.Image:
+    def load_data(self, index: int) -> tv_tensors.Image:
         sample_index, slice_index = self._indices[index]
         volume_path = self._volume_files[sample_index]
-        image_array = io.read_nifti(volume_path, slice_index)
+        image_nii = io.read_nifti(volume_path, slice_index)
+        image_array = io.nifti_to_array(image_nii)
         if self._fix_orientation:
             image_array = self._orientation(image_array, sample_index)
         return tv_tensors.Image(image_array.transpose(2, 0, 1))
 
     @override
-    def load_mask(self, index: int) -> tv_tensors.Mask:
+    def load_target(self, index: int) -> tv_tensors.Mask:
         sample_index, slice_index = self._indices[index]
         segmentation_path = self._segmentation_file(sample_index)
-        semantic_labels = io.read_nifti(segmentation_path, slice_index)
+        mask_nii = io.read_nifti(segmentation_path, slice_index)
+        mask_array = io.nifti_to_array(mask_nii)
         if self._fix_orientation:
-            semantic_labels = self._orientation(semantic_labels, sample_index)
+            semantic_labels = self._orientation(mask_array, sample_index)
         return tv_tensors.Mask(semantic_labels.squeeze(), dtype=torch.int64)  # type: ignore[reportCallIssue]
 
     def _orientation(self, array: npt.NDArray, sample_index: int) -> npt.NDArray:

eva/vision/data/datasets/segmentation/lits_balanced.py

@@ -64,7 +64,8 @@ class LiTSBalanced(lits.LiTS):
             if sample_idx not in split_indices:
                 continue
 
-            segmentation = io.read_nifti(self._segmentation_file(sample_idx))
+            segmentation_nii = io.read_nifti(self._segmentation_file(sample_idx))
+            segmentation = io.nifti_to_array(segmentation_nii)
             tumor_filter = segmentation == 2
             tumor_slice_filter = tumor_filter.sum(axis=(0, 1)) > 0
 

eva/vision/data/datasets/segmentation/monusac.py

@@ -16,12 +16,11 @@ from torchvision.datasets import utils
 from typing_extensions import override
 
 from eva.core.utils.progress_bar import tqdm
-from eva.vision.data.datasets import _validators, structs
-from eva.vision.data.datasets.segmentation import base
+from eva.vision.data.datasets import _validators, structs, vision
 from eva.vision.utils import io
 
 
-class MoNuSAC(base.ImageSegmentation):
+class MoNuSAC(vision.VisionDataset[tv_tensors.Image, tv_tensors.Mask]):
     """MoNuSAC2020: A Multi-organ Nuclei Segmentation and Classification Challenge.
 
     Webpage: https://monusac-2020.grand-challenge.org/
@@ -112,13 +111,13 @@ class MoNuSAC(base.ImageSegmentation):
         )
 
     @override
-    def load_image(self, index: int) -> tv_tensors.Image:
+    def load_data(self, index: int) -> tv_tensors.Image:
         image_path = self._image_files[index]
         image_rgb_array = io.read_image(image_path)
         return tv_tensors.Image(image_rgb_array.transpose(2, 0, 1))
 
     @override
-    def load_mask(self, index: int) -> tv_tensors.Mask:
+    def load_target(self, index: int) -> tv_tensors.Mask:
         semantic_labels = (
             self._load_semantic_mask_file(index)
             if self._export_masks

eva/vision/data/datasets/segmentation/total_segmentator_2d.py

@@ -17,12 +17,12 @@ from typing_extensions import override
 
 from eva.core.utils import io as core_io
 from eva.core.utils import multiprocessing
-from eva.vision.data.datasets import _validators, structs
-from eva.vision.data.datasets.segmentation import _total_segmentator, base
+from eva.vision.data.datasets import _validators, structs, vision
+from eva.vision.data.datasets.segmentation import _total_segmentator
 from eva.vision.utils import io
 
 
-class TotalSegmentator2D(base.ImageSegmentation):
+class TotalSegmentator2D(vision.VisionDataset[tv_tensors.Image, tv_tensors.Mask]):
     """TotalSegmentator 2D segmentation dataset."""
 
     _expected_dataset_lengths: Dict[str, int] = {
@@ -206,19 +206,20 @@ class TotalSegmentator2D(base.ImageSegmentation):
         return len(self._indices)
 
     @override
-    def load_image(self, index: int) -> tv_tensors.Image:
+    def load_data(self, index: int) -> tv_tensors.Image:
         sample_index, slice_index = self._indices[index]
         image_path = self._get_image_path(sample_index)
-        image_array = io.read_nifti(image_path, slice_index)
+        image_nii = io.read_nifti(image_path, slice_index)
+        image_array = io.nifti_to_array(image_nii)
         image_array = self._fix_orientation(image_array)
         return tv_tensors.Image(image_array.copy().transpose(2, 0, 1))
 
     @override
-    def load_mask(self, index: int) -> tv_tensors.Mask:
+    def load_target(self, index: int) -> tv_tensors.Mask:
         if self._optimize_mask_loading:
             mask = self._load_semantic_label_mask(index)
         else:
-            mask = self._load_mask(index)
+            mask = self._load_target(index)
         mask = self._fix_orientation(mask)
         return tv_tensors.Mask(mask.copy().squeeze(), dtype=torch.int64)  # type: ignore
 
@@ -227,14 +228,15 @@ class TotalSegmentator2D(base.ImageSegmentation):
         _, slice_index = self._indices[index]
         return {"slice_index": slice_index}
 
-    def _load_mask(self, index: int) -> npt.NDArray[Any]:
+    def _load_target(self, index: int) -> npt.NDArray[Any]:
         sample_index, slice_index = self._indices[index]
         return self._load_masks_as_semantic_label(sample_index, slice_index)
 
     def _load_semantic_label_mask(self, index: int) -> npt.NDArray[Any]:
         """Loads the segmentation mask from a semantic label NifTi file."""
         sample_index, slice_index = self._indices[index]
-        return io.read_nifti(self._get_optimized_masks_file(sample_index), slice_index)
+        nii = io.read_nifti(self._get_optimized_masks_file(sample_index), slice_index)
+        return io.nifti_to_array(nii)
 
     def _load_masks_as_semantic_label(
         self, sample_index: int, slice_index: int | None = None
@@ -248,7 +250,7 @@ class TotalSegmentator2D(base.ImageSegmentation):
         masks_dir = self._get_masks_dir(sample_index)
         classes = self._class_mappings.keys() if self._class_mappings else self.classes[1:]
         mask_paths = [os.path.join(masks_dir, f"{label}.nii.gz") for label in classes]
-        binary_masks = [io.read_nifti(path, slice_index) for path in mask_paths]
+        binary_masks = [io.nifti_to_array(io.read_nifti(path, slice_index)) for path in mask_paths]
 
         if self._class_mappings:
             mapped_binary_masks = [np.zeros_like(binary_masks[0], dtype=np.bool_)] * len(

eva/vision/data/datasets/vision.py

@@ -1,17 +1,92 @@
 """Vision Dataset base class."""
 
 import abc
-from typing import Generic, TypeVar
+from typing import Any, Callable, Dict, Generic, List, Tuple, TypeVar
 
 from eva.core.data.datasets import base
 
-DataSample = TypeVar("DataSample")
-"""The data sample type."""
+InputType = TypeVar("InputType")
+"""The input data type."""
 
+TargetType = TypeVar("TargetType")
+"""The target data type."""
 
-class VisionDataset(base.MapDataset, abc.ABC, Generic[DataSample]):
+
+class VisionDataset(
+    base.MapDataset[Tuple[InputType, TargetType, Dict[str, Any]]],
+    abc.ABC,
+    Generic[InputType, TargetType],
+):
     """Base dataset class for vision tasks."""
 
+    def __init__(
+        self,
+        transforms: Callable | None = None,
+    ) -> None:
+        """Initializes the dataset.
+
+        Args:
+            transforms: A function/transform which returns a transformed
+                version of the raw data samples.
+        """
+        super().__init__()
+
+        self._transforms = transforms
+
+    @property
+    def classes(self) -> List[str] | None:
+        """Returns the list with names of the dataset names."""
+
+    @property
+    def class_to_idx(self) -> Dict[str, int] | None:
+        """Returns a mapping of the class name to its target index."""
+
+    def __getitem__(self, index: int) -> Tuple[InputType, TargetType, Dict[str, Any]]:
+        """Returns the `index`'th data sample.
+
+        Args:
+            index: The index of the data sample to load.
+
+        Returns:
+            A tuple with the image, the target and the metadata.
+        """
+        image = self.load_data(index)
+        target = self.load_target(index)
+        image, target = self._apply_transforms(image, target)
+        return image, target, self.load_metadata(index) or {}
+
+    def load_metadata(self, index: int) -> Dict[str, Any] | None:
+        """Returns the dataset metadata.
+
+        Args:
+            index: The index of the data sample to return the metadata of.
+
+        Returns:
+            The sample metadata.
+        """
+
+    @abc.abstractmethod
+    def load_data(self, index: int) -> InputType:
+        """Returns the `index`'th data sample.
+
+        Args:
+            index: The index of the data sample to load.
+
+        Returns:
+            The sample data.
+        """
+
+    @abc.abstractmethod
+    def load_target(self, index: int) -> TargetType:
+        """Returns the `index`'th target sample.
+
+        Args:
+            index: The index of the data sample to load.
+
+        Returns:
+            The sample target.
+        """
+
     @abc.abstractmethod
     def filename(self, index: int) -> str:
         """Returns the filename of the `index`'th data sample.
@@ -24,3 +99,19 @@ class VisionDataset(base.MapDataset, abc.ABC, Generic[DataSample]):
         Returns:
             The filename of the `index`'th data sample.
         """
+
+    def _apply_transforms(
+        self, image: InputType, target: TargetType
+    ) -> Tuple[InputType, TargetType]:
+        """Applies the transforms to the provided data and returns them.
+
+        Args:
+            image: The desired image.
+            target: The target of the image.
+
+        Returns:
+            A tuple with the image and the target transformed.
+        """
+        if self._transforms is not None:
+            image, target = self._transforms(image, target)
+        return image, target