Feature - ArrayDataset (#872)

Co-authored-by: otaj <[email protected]>

pl_bolts/datamodules/__init__.py

@@ -9,7 +9,7 @@
 from pl_bolts.datamodules.imagenet_datamodule import ImagenetDataModule
 from pl_bolts.datamodules.kitti_datamodule import KittiDataModule
 from pl_bolts.datamodules.mnist_datamodule import MNISTDataModule
-from pl_bolts.datamodules.sklearn_datamodule import SklearnDataModule, SklearnDataset, TensorDataset
+from pl_bolts.datamodules.sklearn_datamodule import SklearnDataModule, SklearnDataset
 from pl_bolts.datamodules.sr_datamodule import TVTDataModule
 from pl_bolts.datamodules.ssl_imagenet_datamodule import SSLImagenetDataModule
 from pl_bolts.datamodules.stl10_datamodule import STL10DataModule
@@ -31,7 +31,6 @@
     "MNISTDataModule",
     "SklearnDataModule",
     "SklearnDataset",
-    "TensorDataset",
     "TVTDataModule",
     "SSLImagenetDataModule",
     "STL10DataModule",

pl_bolts/datamodules/sklearn_datamodule.py

@@ -2,9 +2,7 @@
 from typing import Any, Tuple
 
 import numpy as np
-import torch
 from pytorch_lightning import LightningDataModule
-from torch import Tensor
 from torch.utils.data import DataLoader, Dataset
 
 from pl_bolts.utils import _SKLEARN_AVAILABLE
@@ -65,50 +63,6 @@ def __getitem__(self, idx) -> Tuple[np.ndarray, np.ndarray]:
         return x, y
 
 
-@under_review()
-class TensorDataset(Dataset):
-    """Prepare PyTorch tensor dataset for data loaders.
-
-    Example:
-        >>> from pl_bolts.datamodules import TensorDataset
-        ...
-        >>> X = torch.rand(10, 3)
-        >>> y = torch.rand(10)
-        >>> dataset = TensorDataset(X, y)
-        >>> len(dataset)
-        10
-    """
-
-    def __init__(self, X: Tensor, y: Tensor, X_transform: Any = None, y_transform: Any = None) -> None:
-        """
-        Args:
-            X: PyTorch tensor
-            y: PyTorch tensor
-            X_transform: Any transform that works with PyTorch tensors
-            y_transform: Any transform that works with PyTorch tensors
-        """
-        super().__init__()
-        self.X = X
-        self.Y = y
-        self.X_transform = X_transform
-        self.y_transform = y_transform
-
-    def __len__(self) -> int:
-        return len(self.X)
-
-    def __getitem__(self, idx) -> Tuple[Tensor, Tensor]:
-        x = self.X[idx].float()
-        y = self.Y[idx]
-
-        if self.X_transform:
-            x = self.X_transform(x)
-
-        if self.y_transform:
-            y = self.y_transform(y)
-
-        return x, y
-
-
 @under_review()
 class SklearnDataModule(LightningDataModule):
     """Automatically generates the train, validation and test splits for a Numpy dataset. They are set up as
@@ -241,40 +195,3 @@ def test_dataloader(self) -> DataLoader:
             pin_memory=self.pin_memory,
         )
         return loader
-
-
-# TODO: this seems to be wrong, something missing here, another inherit class?
-# class TensorDataModule(SklearnDataModule):
-#     """
-#     Automatically generates the train, validation and test splits for a PyTorch tensor dataset. They are set up as
-#     dataloaders for convenience. Optionally, you can pass in your own validation and test splits.
-#
-#     Example:
-#
-#         >>> from pl_bolts.datamodules import TensorDataModule
-#         >>> import torch
-#         ...
-#         >>> # create dataset
-#         >>> X = torch.rand(100, 3)
-#         >>> y = torch.rand(100)
-#         >>> loaders = TensorDataModule(X, y)
-#         ...
-#         >>> # train set
-#         >>> train_loader = loaders.train_dataloader(batch_size=10)
-#         >>> len(train_loader.dataset)
-#         70
-#         >>> len(train_loader)
-#         7
-#         >>> # validation set
-#         >>> val_loader = loaders.val_dataloader(batch_size=10)
-#         >>> len(val_loader.dataset)
-#         20
-#         >>> len(val_loader)
-#         2
-#         >>> # test set
-#         >>> test_loader = loaders.test_dataloader(batch_size=10)
-#         >>> len(test_loader.dataset)
-#         10
-#         >>> len(test_loader)
-#         1
-#     """

pl_bolts/datasets/__init__.py

@@ -1,6 +1,7 @@
 import urllib
 
-from pl_bolts.datasets.base_dataset import LightDataset
+from pl_bolts.datasets.array_dataset import ArrayDataset
+from pl_bolts.datasets.base_dataset import DataModel, LightDataset
 from pl_bolts.datasets.cifar10_dataset import CIFAR10, TrialCIFAR10
 from pl_bolts.datasets.concat_dataset import ConcatDataset
 from pl_bolts.datasets.dummy_dataset import (
@@ -17,6 +18,8 @@
 from pl_bolts.datasets.ssl_amdim_datasets import CIFAR10Mixed, SSLDatasetMixin
 
 __all__ = [
+    "ArrayDataset",
+    "DataModel",
     "LightDataset",
     "CIFAR10",
     "TrialCIFAR10",

pl_bolts/datasets/array_dataset.py

@@ -0,0 +1,52 @@
+from typing import Tuple, Union
+
+from pytorch_lightning.utilities import exceptions
+from torch.utils.data import Dataset
+
+from pl_bolts.datasets.base_dataset import DataModel, TArrays
+
+
+class ArrayDataset(Dataset):
+    """Dataset wrapping tensors, lists, numpy arrays.
+
+    Any number of ARRAYS can be inputted into the dataset. The ARRAYS are transformed on each `__getitem__`. When
+        transforming, please refrain from chaning the hape of ARRAYS in the first demension.
+
+    Attributes:
+        data_models: Sequence of data models.
+
+    Raises:
+        MisconfigurationException: if there is a shape mismatch between arrays in the first dimension.
+
+    Example:
+        >>> from pl_bolts.datasets import ArrayDataset, DataModel
+        >>> from pl_bolts.datasets.utils import to_tensor
+
+        >>> features = DataModel(data=[[1, 0, -1, 2], [1, 0, -2, -1], [2, 5, 0, 3]], transform=to_tensor)
+        >>> target = DataModel(data=[1, 0, 0], transform=to_tensor)
+
+        >>> ds = ArrayDataset(features, target)
+        >>> len(ds)
+        3
+    """
+
+    def __init__(self, *data_models: DataModel) -> None:
+        """Initialises class and checks if arrays are the same shape in the first dimension."""
+        self.data_models = data_models
+
+        if not self._equal_size():
+            raise exceptions.MisconfigurationException("Shape mismatch between arrays in the first dimension")
+
+    def __len__(self) -> int:
+        return len(self.data_models[0].data)
+
+    def __getitem__(self, idx: int) -> Tuple[Union[TArrays, float], ...]:
+        return tuple(data_model.process(data_model.data[idx]) for data_model in self.data_models)
+
+    def _equal_size(self) -> bool:
+        """Checks the size of the data_models are equal in the first dimension.
+
+        Returns:
+            bool: True if size of data_models are equal in the first dimension. False, if not.
+        """
+        return len({len(data_model.data) for data_model in self.data_models}) == 1

pl_bolts/datasets/base_dataset.py

@@ -2,13 +2,15 @@
 import os
 import urllib.request
 from abc import ABC
-from typing import Sequence, Tuple
+from dataclasses import dataclass
+from typing import Callable, Optional, Sequence, Tuple, Union
 from urllib.error import HTTPError
 
 from torch import Tensor
 from torch.utils.data import Dataset
 
 from pl_bolts.utils.stability import under_review
+from pl_bolts.utils.types import TArrays
 
 
 @under_review()
@@ -58,3 +60,31 @@ def _download_from_url(self, base_url: str, data_folder: str, file_name: str):
             urllib.request.urlretrieve(url, fpath)
         except HTTPError as err:
             raise RuntimeError(f"Failed download from {url}") from err
+
+
+@dataclass
+class DataModel:
+    """Data model dataclass.
+
+    Ties together data and callable transforms.
+
+    Attributes:
+        data: Sequence of indexables.
+        transform: Callable to transform data. The transform is called on a subset of data.
+    """
+
+    data: TArrays
+    transform: Optional[Callable[[TArrays], TArrays]] = None
+
+    def process(self, subset: Union[TArrays, float]) -> Union[TArrays, float]:
+        """Transforms a subset of data.
+
+        Args:
+            subset: Sequence of indexables.
+
+        Returns:
+            data: Transformed data if transform is not None.
+        """
+        if self.transform is not None:
+            subset = self.transform(subset)
+        return subset

pl_bolts/datasets/utils.py

@@ -1,9 +1,11 @@
+import torch
 from torch.utils.data.dataset import random_split
 
 from pl_bolts.datasets.sr_celeba_dataset import SRCelebA
 from pl_bolts.datasets.sr_mnist_dataset import SRMNIST
 from pl_bolts.datasets.sr_stl10_dataset import SRSTL10
 from pl_bolts.utils.stability import under_review
+from pl_bolts.utils.types import TArrays
 
 
 @under_review()
@@ -39,3 +41,17 @@ def prepare_sr_datasets(dataset: str, scale_factor: int, data_dir: str):
         dataset_test = dataset_cls(scale_factor, root=data_dir, split="test", download=True)
 
     return (dataset_train, dataset_val, dataset_test)
+
+
+def to_tensor(arrays: TArrays) -> torch.Tensor:
+    """Takes a sequence of type `TArrays` and returns a tensor.
+
+    This function serves as a use case for the ArrayDataset.
+
+    Args:
+        arrays: Sequence of type `TArrays`
+
+    Returns:
+        Tensor of the integers
+    """
+    return torch.tensor(arrays)

pl_bolts/utils/types.py

@@ -0,0 +1,6 @@
+from typing import Sequence, Union
+
+import numpy as np
+import torch
+
+TArrays = Union[torch.Tensor, np.ndarray, Sequence[float], Sequence["TArrays"]]  # type: ignore

tests/datasets/test_array_dataset.py

@@ -0,0 +1,52 @@
+import numpy as np
+import pytest
+import torch
+from pytorch_lightning.utilities import exceptions
+
+from pl_bolts.datasets import ArrayDataset, DataModel
+from pl_bolts.datasets.utils import to_tensor
+
+
+class TestArrayDataset:
+    @pytest.fixture
+    def array_dataset(self):
+        features_1 = DataModel(data=[[1, 0, -1, 2], [1, 0, -2, -1], [2, 5, 0, 3], [-7, 1, 2, 2]], transform=to_tensor)
+        target_1 = DataModel(data=[1, 0, 0, 1], transform=to_tensor)
+
+        features_2 = DataModel(data=np.array([[2, 1, -5, 1], [1, 0, -2, -1], [2, 5, 0, 3], [-7, 1, 2, 2]]))
+        target_2 = DataModel(data=[1, 0, 1, 1])
+        return ArrayDataset(features_1, target_1, features_2, target_2)
+
+    def test_len(self, array_dataset):
+        assert len(array_dataset) == 4
+
+    def test_getitem_with_transforms(self, array_dataset):
+        assert len(array_dataset[0]) == 4
+        assert len(array_dataset[1]) == 4
+        assert len(array_dataset[2]) == 4
+        assert len(array_dataset[3]) == 4
+        torch.testing.assert_close(array_dataset[0][0], torch.tensor([1, 0, -1, 2]))
+        torch.testing.assert_close(array_dataset[0][1], torch.tensor(1))
+        np.testing.assert_array_equal(array_dataset[0][2], np.array([2, 1, -5, 1]))
+        assert array_dataset[0][3] == 1
+        torch.testing.assert_close(array_dataset[1][0], torch.tensor([1, 0, -2, -1]))
+        torch.testing.assert_close(array_dataset[1][1], torch.tensor(0))
+        np.testing.assert_array_equal(array_dataset[1][2], np.array([1, 0, -2, -1]))
+        assert array_dataset[1][3] == 0
+        torch.testing.assert_close(array_dataset[2][0], torch.tensor([2, 5, 0, 3]))
+        torch.testing.assert_close(array_dataset[2][1], torch.tensor(0))
+        np.testing.assert_array_equal(array_dataset[2][2], np.array([2, 5, 0, 3]))
+        assert array_dataset[2][3] == 1
+        torch.testing.assert_close(array_dataset[3][0], torch.tensor([-7, 1, 2, 2]))
+        torch.testing.assert_close(array_dataset[3][1], torch.tensor(1))
+        np.testing.assert_array_equal(array_dataset[3][2], np.array([-7, 1, 2, 2]))
+        assert array_dataset[3][3] == 1
+
+    def test__equal_size_true(self, array_dataset):
+        assert array_dataset._equal_size() is True
+
+    def test__equal_size_false(self):
+        features = DataModel(data=[[1, 0, 1]])
+        target = DataModel([1, 0, 1])
+        with pytest.raises(exceptions.MisconfigurationException):
+            ArrayDataset(features, target)

tests/datasets/test_base_dataset.py

@@ -0,0 +1,22 @@
+import numpy as np
+import pytest
+import torch
+
+from pl_bolts.datasets.base_dataset import DataModel
+from pl_bolts.datasets.utils import to_tensor
+
+
+class TestDataModel:
+    @pytest.fixture
+    def data(self):
+        return np.array([[1, 0, 0, 1], [0, 1, 1, 0]])
+
+    def test_process_transform_is_none(self, data):
+        dm = DataModel(data=data)
+        np.testing.assert_array_equal(dm.process(data[0]), data[0])
+        np.testing.assert_array_equal(dm.process(data[1]), data[1])
+
+    def test_process_transform_is_not_none(self, data):
+        dm = DataModel(data=data, transform=to_tensor)
+        torch.testing.assert_close(dm.process(data[0]), torch.tensor([1, 0, 0, 1]))
+        torch.testing.assert_close(dm.process(data[1]), torch.tensor([0, 1, 1, 0]))

tests/datasets/test_utils.py

@@ -0,0 +1,18 @@
+import numpy as np
+import torch.testing
+
+from pl_bolts.datasets.utils import to_tensor
+
+
+class TestToTensor:
+    def test_to_tensor_list(self):
+        _list = [1, 2, 3]
+        torch.testing.assert_close(to_tensor(_list), torch.tensor(_list))
+
+    def test_to_tensor_array(self):
+        _array = np.array([1, 2, 3])
+        torch.testing.assert_close(to_tensor(_array), torch.tensor(_array))
+
+    def test_to_tensor_sequence_(self):
+        _sequence = [[1.0, 2.0, 3.0]]
+        torch.testing.assert_close(to_tensor(_sequence), torch.tensor(_sequence))