Implement a temporary dataset class (#10)

pyproject.toml

@@ -15,6 +15,7 @@ dependencies = [
     "torch",
     "rascaline-torch @ git+https://github.com/luthaf/rascaline#subdirectory=python/rascaline-torch",
     "metatensor-core",
+    "metatensor-operations",
     "metatensor-torch"
 ]
 

src/metatensor_models/utils/data/__init__.py

@@ -0,0 +1,2 @@
+from .dataset import Dataset, collate_fn  # noqa: F401
+from .readers import read_structures, read_targets  # noqa: F401

src/metatensor_models/utils/data/dataset.py

@@ -0,0 +1,76 @@
+from typing import Dict, List
+
+import metatensor.torch
+import rascaline.torch
+import torch
+from metatensor.torch import Labels, TensorMap
+
+
+class Dataset(torch.utils.data.Dataset):
+    def __init__(
+        self, structures: List[rascaline.torch.System], targets: Dict[str, TensorMap]
+    ):
+        """Creates a dataset from a list of `rascaline.torch.System`s and
+        a list of dictionaries of `TensorMap`s."""
+
+        for tensor_map in targets.values():
+            n_structures = (
+                torch.max(tensor_map.block(0).samples["structure"]).item() + 1
+            )
+            if n_structures != len(structures):
+                raise ValueError(
+                    f"Number of structures in input ({len(structures)}) and "
+                    f"output ({n_structures}) must be the same"
+                )
+
+        self.structures = structures
+        self.targets = targets
+
+    def __len__(self):
+        """
+        Return the total number of samples in the dataset.
+        """
+        return len(self.structures)
+
+    def __getitem__(self, index):
+        """
+        Generates one sample of data.
+        Args:
+            index: The index of the item in the dataset.
+        Returns:
+            A tuple containing the structure and targets for the given index.
+        """
+        structure = self.structures[index]
+
+        structure_index_samples = Labels(
+            names=["structure"],
+            values=torch.tensor([[index]]),  # must be a 2D-array
+        )
+
+        targets = {}
+        for name, tensor_map in self.targets.items():
+            targets[name] = metatensor.torch.slice(
+                tensor_map, "samples", structure_index_samples
+            )
+
+        return structure, targets
+
+
+def collate_fn(batch):
+    """
+    Creates a batch from a list of samples.
+    Args:
+        batch: A list of samples, where each sample is a tuple containing a
+            structure and targets.
+    Returns:
+        A tuple containing the structures and targets for the batch.
+    """
+
+    structures = [sample[0] for sample in batch]
+    targets = {}
+    for name in batch[0][1].keys():
+        targets[name] = metatensor.torch.join(
+            [sample[1][name] for sample in batch], "samples"
+        )
+
+    return structures, targets

src/metatensor_models/readers/__init__.py → src/metatensor_models/utils/data/readers/__init__.py

@@ -9,10 +9,10 @@
 from .structures import STRUCTURE_READERS
 from .targets import TARGET_READERS
 
-from rascaline.torch.system import Systems
+from rascaline.torch.system import System
 
 
-def read_structures(filename: str, fileformat: Optional[str] = None) -> List[Systems]:
+def read_structures(filename: str, fileformat: Optional[str] = None) -> List[System]:
     """Reads a structure information from file."""
 
     if fileformat is None:

src/metatensor_models/readers/structures/ase.py → src/metatensor_models/utils/data/readers/structures/ase.py

@@ -2,10 +2,10 @@
 
 import ase.io
 from rascaline.systems import AseSystem
-from rascaline.torch.system import Systems, systems_to_torch
+from rascaline.torch.system import System, systems_to_torch
 
 
-def read_ase(filename: str) -> List[Systems]:
+def read_ase(filename: str) -> List[System]:
     systems = [AseSystem(atoms) for atoms in ase.io.read(filename, ":")]
 
     return systems_to_torch(systems)

tests/data.py

@@ -0,0 +1,19 @@
+import os
+import torch
+
+from metatensor_models.utils.data import Dataset, collate_fn, read_structures, read_targets
+
+
+def test_dataset():
+    """Tests the readers and the dataset class."""
+
+    dataset_path = os.path.join(os.path.dirname(__file__), "data/qm9_reduced_100.xyz")
+
+    structures = read_structures(dataset_path)
+    targets = read_targets(dataset_path, "U0")
+
+    dataset = Dataset(structures, targets)
+    dataloader = torch.utils.data.DataLoader(dataset, batch_size=10, collate_fn=collate_fn)
+
+    for batch in dataloader:
+        assert batch[1]["U0"].block().values.shape == (10, 1)