Add PyTorch dataloader

.pre-commit-config.yaml

@@ -33,3 +33,16 @@ repos:
     hooks:
       - id: prettier
         language_version: system
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.910
+    hooks:
+      - id: mypy
+        additional_dependencies: [
+            # Type stubs
+            types-setuptools,
+            types-pkg_resources,
+            # Dependencies that are typed
+            numpy,
+            xarray,
+          ]

conftest.py

@@ -1,3 +1,4 @@
+# type: ignore
 import pytest
 
 

dev-requirements.txt

@@ -1,3 +1,4 @@
 pytest
+torch
 coverage
 -r requirements.txt

doc/conf.py

@@ -12,6 +12,8 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
+# type: ignore
+
 import os
 import sys
 

setup.cfg

@@ -7,7 +7,7 @@ select = B,C,E,F,W,T4,B9
 
 [isort]
 known_first_party=xbatcher
-known_third_party=numpy,pkg_resources,pytest,setuptools,sphinx_autosummary_accessors,xarray
+known_third_party=numpy,pkg_resources,pytest,setuptools,sphinx_autosummary_accessors,torch,xarray
 multi_line_output=3
 include_trailing_comma=True
 force_grid_wrap=0

setup.py

@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+# type: ignore
 import os
 
 from setuptools import find_packages, setup

xbatcher/accessors.py

@@ -24,3 +24,21 @@ def generator(self, *args, **kwargs):
             Keyword arguments to pass to the `BatchGenerator` constructor.
         '''
         return BatchGenerator(self._obj, *args, **kwargs)
+
+
+@xr.register_dataarray_accessor('torch')
+class TorchAccessor:
+    def __init__(self, xarray_obj):
+        self._obj = xarray_obj
+
+    def to_tensor(self):
+        """Convert this DataArray to a torch.Tensor"""
+        import torch
+
+        return torch.tensor(self._obj.data)
+
+    def to_named_tensor(self):
+        """Convert this DataArray to a torch.Tensor with named dimensions"""
+        import torch
+
+        return torch.tensor(self._obj.data, names=self._obj.dims)

xbatcher/generators.py

@@ -2,6 +2,7 @@
 
 import itertools
 from collections import OrderedDict
+from typing import Any, Dict, Hashable, Iterator
 
 import xarray as xr
 
@@ -99,12 +100,12 @@ class BatchGenerator:
 
     def __init__(
         self,
-        ds,
-        input_dims,
-        input_overlap={},
-        batch_dims={},
-        concat_input_dims=False,
-        preload_batch=True,
+        ds: xr.Dataset,
+        input_dims: Dict[Hashable, int],
+        input_overlap: Dict[Hashable, int] = {},
+        batch_dims: Dict[Hashable, int] = {},
+        concat_input_dims: bool = False,
+        preload_batch: bool = True,
     ):
 
         self.ds = _as_xarray_dataset(ds)
@@ -115,7 +116,38 @@ def __init__(
         self.concat_input_dims = concat_input_dims
         self.preload_batch = preload_batch
 
-    def __iter__(self):
+        self._batches: Dict[
+            int, Any
+        ] = self._gen_batches()  # dict cache for batches
+        # in the future, we can make this a lru cache or similar thing (cachey?)
+
+    def __iter__(self) -> Iterator[xr.Dataset]:
+        for batch in self._batches.values():
+            yield batch
+
+    def __len__(self) -> int:
+        return len(self._batches)
+
+    def __getitem__(self, idx: int) -> xr.Dataset:
+
+        if not isinstance(idx, int):
+            raise NotImplementedError(
+                f'{type(self).__name__}.__getitem__ currently requires a single integer key'
+            )
+
+        if idx < 0:
+            idx = list(self._batches)[idx]
+
+        if idx in self._batches:
+            return self._batches[idx]
+        else:
+            raise IndexError('list index out of range')
+
+    def _gen_batches(self) -> dict:
+        # in the future, we will want to do the batch generation lazily
+        # going the eager route for now is allowing me to fill out the loader api
+        # but it is likely to perform poorly.
+        batches = []
         for ds_batch in self._iterate_batch_dims(self.ds):
             if self.preload_batch:
                 ds_batch.load()
@@ -130,15 +162,17 @@ def __iter__(self):
                 ]
                 dsc = xr.concat(all_dsets, dim='input_batch')
                 new_input_dims = [
-                    dim + new_dim_suffix for dim in self.input_dims
+                    str(dim) + new_dim_suffix for dim in self.input_dims
                 ]
-                yield _maybe_stack_batch_dims(dsc, new_input_dims)
+                batches.append(_maybe_stack_batch_dims(dsc, new_input_dims))
             else:
                 for ds_input in input_generator:
-                    yield _maybe_stack_batch_dims(
-                        ds_input, list(self.input_dims)
+                    batches.append(
+                        _maybe_stack_batch_dims(ds_input, list(self.input_dims))
                     )
 
+        return dict(zip(range(len(batches)), batches))
+
     def _iterate_batch_dims(self, ds):
         return _iterate_through_dataset(ds, self.batch_dims)
 

xbatcher/loaders/torch.py

@@ -0,0 +1,83 @@
+from typing import Any, Callable, Optional, Tuple
+
+import torch
+
+# Notes:
+# This module includes two PyTorch datasets.
+#  - The MapDataset provides an indexable interface
+#  - The IterableDataset provides a simple iterable interface
+# Both can be provided as arguments to the the Torch DataLoader
+# Assumptions made:
+#  - Each dataset takes pre-configured X/y xbatcher generators (may not always want two generators ina dataset)
+# TODOs:
+#  - sort out xarray -> numpy pattern. Currently there is a hardcoded variable name for x/y
+#  - need to test with additional dataset parameters (e.g. transforms)
+
+
+class MapDataset(torch.utils.data.Dataset):
+    def __init__(
+        self,
+        X_generator,
+        y_generator,
+        transform: Optional[Callable] = None,
+        target_transform: Optional[Callable] = None,
+    ) -> None:
+        '''
+        PyTorch Dataset adapter for Xbatcher
+
+        Parameters
+        ----------
+        X_generator : xbatcher.BatchGenerator
+        y_generator : xbatcher.BatchGenerator
+        transform : callable, optional
+            A function/transform that takes in an array and returns a transformed version.
+        target_transform : callable, optional
+            A function/transform that takes in the target and transforms it.
+        '''
+        self.X_generator = X_generator
+        self.y_generator = y_generator
+        self.transform = transform
+        self.target_transform = target_transform
+
+    def __len__(self) -> int:
+        return len(self.X_generator)
+
+    def __getitem__(self, idx) -> Tuple[Any, Any]:
+        if torch.is_tensor(idx):
+            idx = idx.tolist()
+            assert len(idx) == 1
+
+        # TODO: figure out the dataset -> array workflow
+        # currently hardcoding a variable name
+        X_batch = self.X_generator[idx]['x'].torch.to_tensor()
+        y_batch = self.y_generator[idx]['y'].torch.to_tensor()
+
+        if self.transform:
+            X_batch = self.transform(X_batch)
+
+        if self.target_transform:
+            y_batch = self.target_transform(y_batch)
+        return X_batch, y_batch
+
+
+class IterableDataset(torch.utils.data.IterableDataset):
+    def __init__(
+        self,
+        X_generator,
+        y_generator,
+    ) -> None:
+        '''
+        PyTorch Dataset adapter for Xbatcher
+
+        Parameters
+        ----------
+        X_generator : xbatcher.BatchGenerator
+        y_generator : xbatcher.BatchGenerator
+        '''
+
+        self.X_generator = X_generator
+        self.y_generator = y_generator
+
+    def __iter__(self):
+        for xb, yb in zip(self.X_generator, self.y_generator):
+            yield (xb['x'].torch.to_tensor(), yb['y'].torch.to_tensor())

xbatcher/tests/test_accessors.py

@@ -38,3 +38,25 @@ def test_batch_accessor_da(sample_ds_3d):
     assert isinstance(bg_acc, BatchGenerator)
     for batch_class, batch_acc in zip(bg_class, bg_acc):
         assert batch_class.equals(batch_acc)
+
+
+def test_torch_to_tensor(sample_ds_3d):
+    torch = pytest.importorskip('torch')
+
+    da = sample_ds_3d['foo']
+    t = da.torch.to_tensor()
+    assert isinstance(t, torch.Tensor)
+    assert t.names == (None, None, None)
+    assert t.shape == da.shape
+    np.testing.assert_array_equal(t, da.values)
+
+
+def test_torch_to_named_tensor(sample_ds_3d):
+    torch = pytest.importorskip('torch')
+
+    da = sample_ds_3d['foo']
+    t = da.torch.to_named_tensor()
+    assert isinstance(t, torch.Tensor)
+    assert t.names == da.dims
+    assert t.shape == da.shape
+    np.testing.assert_array_equal(t, da.values)

xbatcher/tests/test_generators.py

@@ -18,6 +18,28 @@ def sample_ds_1d():
     return ds
 
 
+@pytest.mark.parametrize('bsize', [5, 6])
+def test_batcher_lenth(sample_ds_1d, bsize):
+    bg = BatchGenerator(sample_ds_1d, input_dims={'x': bsize})
+    assert len(bg) == sample_ds_1d.dims['x'] // bsize
+
+
+def test_batcher_getitem(sample_ds_1d):
+    bg = BatchGenerator(sample_ds_1d, input_dims={'x': 10})
+
+    # first batch
+    assert bg[0].dims['x'] == 10
+    # last batch
+    assert bg[-1].dims['x'] == 10
+    # raises IndexError for out of range index
+    with pytest.raises(IndexError, match=r'list index out of range'):
+        bg[9999999]
+
+    # raises NotImplementedError for iterable index
+    with pytest.raises(NotImplementedError):
+        bg[[1, 2, 3]]
+
+
 # TODO: decide how to handle bsizes like 15 that don't evenly divide the dimension
 # Should we enforce that each batch size always has to be the same
 @pytest.mark.parametrize('bsize', [5, 10])

xbatcher/tests/test_torch_loaders.py

@@ -0,0 +1,78 @@
+import numpy as np
+import pytest
+import xarray as xr
+
+torch = pytest.importorskip('torch')
+
+from xbatcher import BatchGenerator
+from xbatcher.loaders.torch import IterableDataset, MapDataset
+
+
+@pytest.fixture(scope='module')
+def ds_xy():
+    n_samples = 100
+    n_features = 5
+    ds = xr.Dataset(
+        {
+            'x': (
+                ['sample', 'feature'],
+                np.random.random((n_samples, n_features)),
+            ),
+            'y': (['sample'], np.random.random(n_samples)),
+        },
+    )
+    return ds
+
+
+def test_map_dataset(ds_xy):
+
+    x = ds_xy['x']
+    y = ds_xy['y']
+
+    x_gen = BatchGenerator(x, {'sample': 10})
+    y_gen = BatchGenerator(y, {'sample': 10})
+
+    dataset = MapDataset(x_gen, y_gen)
+
+    # test __getitem__
+    x_batch, y_batch = dataset[0]
+    assert len(x_batch) == len(y_batch)
+    assert isinstance(x_batch, torch.Tensor)
+
+    # test __len__
+    assert len(dataset) == len(x_gen)
+
+    # test integration with torch DataLoader
+    loader = torch.utils.data.DataLoader(dataset)
+
+    for x_batch, y_batch in loader:
+        assert len(x_batch) == len(y_batch)
+        assert isinstance(x_batch, torch.Tensor)
+
+    # TODO: why does pytorch add an extra dimension (length 1) to x_batch
+    assert x_gen[-1]['x'].shape == x_batch.shape[1:]
+    # TODO: also need to revisit the variable extraction bits here
+    assert np.array_equal(x_gen[-1]['x'], x_batch[0, :, :])
+
+
+def test_iterable_dataset(ds_xy):
+
+    x = ds_xy['x']
+    y = ds_xy['y']
+
+    x_gen = BatchGenerator(x, {'sample': 10})
+    y_gen = BatchGenerator(y, {'sample': 10})
+
+    dataset = IterableDataset(x_gen, y_gen)
+
+    # test integration with torch DataLoader
+    loader = torch.utils.data.DataLoader(dataset)
+
+    for x_batch, y_batch in loader:
+        assert len(x_batch) == len(y_batch)
+        assert isinstance(x_batch, torch.Tensor)
+
+    # TODO: why does pytorch add an extra dimension (length 1) to x_batch
+    assert x_gen[-1]['x'].shape == x_batch.shape[1:]
+    # TODO: also need to revisit the variable extraction bits here
+    assert np.array_equal(x_gen[-1]['x'], x_batch[0, :, :])