Batched inference CEBRA & padding at the Solver level

cebra/data/base.py

@@ -193,6 +193,7 @@ def load_batch(self, index: BatchIndex) -> Batch:
         """
         raise NotImplementedError()
 
+    @abc.abstractmethod
     def configure_for(self, model: "cebra.models.Model"):
         """Configure the dataset offset for the provided model.
 
@@ -202,7 +203,7 @@ def configure_for(self, model: "cebra.models.Model"):
         Args:
             model: The model to configure the dataset for.
         """
-        self.offset = model.get_offset()
+        raise NotImplementedError
 
 
 @dataclasses.dataclass
@@ -227,6 +228,8 @@ class Loader(abc.ABC, cebra.io.HasDevice):
         doc="""A dataset instance specifying a ``__getitem__`` function.""",
     )
 
+    time_offset: int = dataclasses.field(default=10)
+
     num_steps: int = dataclasses.field(
         default=None,
         doc=

cebra/data/multi_session.py

@@ -28,7 +28,7 @@
 import torch
 
 import cebra.data as cebra_data
-import cebra.distributions as cebra_distr
+import cebra.distributions
 from cebra.data.datatypes import Batch
 from cebra.data.datatypes import BatchIndex
 
@@ -104,10 +104,17 @@ def load_batch(self, index: BatchIndex) -> List[Batch]:
             ) for session_id, session in enumerate(self.iter_sessions())
         ]
 
-    def configure_for(self, model):
-        self.offset = model.get_offset()
-        for session in self.iter_sessions():
-            session.configure_for(model)
+    def configure_for(self, model: "cebra.models.Model"):
+        """Configure the dataset offset for the provided model.
+
+        Call this function before indexing the dataset. This sets the
+        `offset` attribute of the dataset.
+
+        Args:
+            model: The model to configure the dataset for.
+        """
+        for i, session in enumerate(self.iter_sessions()):
+            session.configure_for(model[i])
 
 
 @dataclasses.dataclass
@@ -119,12 +126,10 @@ class MultiSessionLoader(cebra_data.Loader):
     dimension, it is better to use a :py:class:`cebra.data.single_session.MixedDataLoader`.
     """
 
-    time_offset: int = dataclasses.field(default=10)
-
     def __post_init__(self):
         super().__post_init__()
-        self.sampler = cebra_distr.MultisessionSampler(self.dataset,
-                                                       self.time_offset)
+        self.sampler = cebra.distributions.MultisessionSampler(
+            self.dataset, self.time_offset)
 
     def get_indices(self, num_samples: int) -> List[BatchIndex]:
         ref_idx = self.sampler.sample_prior(self.batch_size)
@@ -149,7 +154,6 @@ class ContinuousMultiSessionDataLoader(MultiSessionLoader):
     """Contrastive learning conditioned on a continuous behavior variable."""
 
     conditional: str = "time_delta"
-    time_offset: int = dataclasses.field(default=10)
 
     @property
     def index(self):
@@ -163,7 +167,8 @@ class DiscreteMultiSessionDataLoader(MultiSessionLoader):
     # Overwrite sampler with the discrete implementation
     # Generalize MultisessionSampler to avoid doing this?
     def __post_init__(self):
-        self.sampler = cebra_distr.DiscreteMultisessionSampler(self.dataset)
+        self.sampler = cebra.distributions.DiscreteMultisessionSampler(
+            self.dataset)
 
     @property
     def index(self):

cebra/data/single_session.py

@@ -69,6 +69,17 @@ def load_batch(self, index: BatchIndex) -> Batch:
             reference=self[index.reference],
         )
 
+    def configure_for(self, model: "cebra.models.Model"):
+        """Configure the dataset offset for the provided model.
+
+        Call this function before indexing the dataset. This sets the
+        `offset` attribute of the dataset.
+
+        Args:
+            model: The model to configure the dataset for.
+        """
+        self.offset = model.get_offset()
+
 
 @dataclasses.dataclass
 class DiscreteDataLoader(cebra_data.Loader):
@@ -189,7 +200,6 @@ class ContinuousDataLoader(cebra_data.Loader):
     and become equivalent to time contrastive learning.
     """,
     )
-    time_offset: int = dataclasses.field(default=10)
     delta: float = dataclasses.field(default=0.1)
 
     def __post_init__(self):
@@ -271,7 +281,6 @@ class MixedDataLoader(cebra_data.Loader):
     """
 
     conditional: str = dataclasses.field(default="time_delta")
-    time_offset: int = dataclasses.field(default=10)
 
     @property
     def dindex(self):
@@ -334,7 +343,6 @@ class HybridDataLoader(cebra_data.Loader):
     """
 
     conditional: str = dataclasses.field(default="time_delta")
-    time_offset: int = dataclasses.field(default=10)
     delta: float = dataclasses.field(default=0.1)
 
     @property

cebra/integrations/sklearn/cebra.py

@@ -778,8 +778,6 @@ def _configure_for_all(
                             "receptive fields/offsets larger than 1 via the sklearn API. "
                             "Please use a different model, or revert to the pytorch "
                             "API for training.")
-
-                d.configure_for(model[n])
         else:
             if not isinstance(model, cebra.models.ConvolutionalModelMixin):
                 if len(model.get_offset()) > 1:
@@ -789,37 +787,11 @@ def _configure_for_all(
                         "Please use a different model, or revert to the pytorch "
                         "API for training.")
 
-            dataset.configure_for(model)
+        dataset.configure_for(model)
 
     def _select_model(self, X: Union[npt.NDArray, torch.Tensor],
                       session_id: int):
-        # Choose the model and get its corresponding offset
-        if self.num_sessions is not None:  # multisession implementation
-            if session_id is None:
-                raise RuntimeError(
-                    "No session_id provided: multisession model requires a session_id to choose the model corresponding to your data shape."
-                )
-            if session_id >= self.num_sessions or session_id < 0:
-                raise RuntimeError(
-                    f"Invalid session_id {session_id}: session_id for the current multisession model must be between 0 and {self.num_sessions-1}."
-                )
-            if self.n_features_[session_id] != X.shape[1]:
-                raise ValueError(
-                    f"Invalid input shape: model for session {session_id} requires an input of shape"
-                    f"(n_samples, {self.n_features_[session_id]}), got (n_samples, {X.shape[1]})."
-                )
-
-            model = self.model_[session_id]
-            model.to(self.device_)
-        else:  # single session
-            if session_id is not None and session_id > 0:
-                raise RuntimeError(
-                    f"Invalid session_id {session_id}: single session models only takes an optional null session_id."
-                )
-            model = self.model_
-
-        offset = model.get_offset()
-        return model, offset
+        return self.solver_._select_model(X, session_id=session_id)
 
     def _check_labels_types(self, y: tuple, session_id: Optional[int] = None):
         """Check that the input labels are compatible with the labels used to fit the model.
@@ -1201,9 +1173,60 @@ def fit(
 
     def transform(self,
                   X: Union[npt.NDArray, torch.Tensor],
+                  batch_size: Optional[int] = None,
                   session_id: Optional[int] = None) -> npt.NDArray:
         """Transform an input sequence and return the embedding.
 
+        Args:
+            X: A numpy array or torch tensor of size ``time x dimension``.
+            batch_size:
+            session_id: The session ID, an :py:class:`int` between 0 and :py:attr:`num_sessions` for
+                multisession, set to ``None`` for single session.
+
+        Returns:
+            A :py:func:`numpy.array` of size ``time x output_dimension``.
+
+        Example:
+
+            >>> import cebra
+            >>> import numpy as np
+            >>> dataset =  np.random.uniform(0, 1, (1000, 30))
+            >>> cebra_model = cebra.CEBRA(max_iterations=10)
+            >>> cebra_model.fit(dataset)
+            CEBRA(max_iterations=10)
+            >>> embedding = cebra_model.transform(dataset)
+
+        """
+        sklearn_utils_validation.check_is_fitted(self, "n_features_")
+        self.solver_._check_is_session_id_valid(session_id=session_id)
+
+        if torch.is_tensor(X):
+            X = X.detach().cpu()
+
+        X = sklearn_utils.check_input_array(X, min_samples=len(self.offset_))
+
+        if isinstance(X, np.ndarray):
+            X = torch.from_numpy(X)
+
+        if batch_size is not None and batch_size < 1:
+            raise ValueError(
+                f"Batch size should be at least 1, got {batch_size}")
+
+        with torch.no_grad():
+            output = self.solver_.transform(
+                inputs=X,
+                pad_before_transform=self.pad_before_transform,
+                session_id=session_id,
+                batch_size=batch_size)
+
+        return output.detach().cpu().numpy()
+
+    # Deprecated, kept for testing.
+    def transform_deprecated(self,
+                             X: Union[npt.NDArray, torch.Tensor],
+                             session_id: Optional[int] = None) -> npt.NDArray:
+        """Transform an input sequence and return the embedding.
+
         Args:
             X: A numpy array or torch tensor of size ``time x dimension``.
             session_id: The session ID, an :py:class:`int` between 0 and :py:attr:`num_sessions` for
@@ -1453,6 +1476,11 @@ def load(cls,
         else:
             cebra_ = _check_type_checkpoint(checkpoint)
 
+        n_features = cebra_.n_features_
+        cebra_.solver_.n_features = ([
+            session_n_features for session_n_features in n_features
+        ] if isinstance(n_features, list) else n_features)
+
         return cebra_
 
     def to(self, device: Union[str, torch.device]):

cebra/integrations/sklearn/metrics.py

@@ -83,7 +83,8 @@ def infonce_loss(
             f"got {len(y[0])} sessions.")
 
     model, _ = cebra_model._select_model(
-        X, session_id)  # check session_id validity and corresponding model
+        X, session_id=session_id
+    )  # check session_id validity and corresponding model
     cebra_model._check_labels_types(y, session_id=session_id)
 
     dataset, is_multisession = cebra_model._prepare_data(X, y)  # single session

cebra/integrations/sklearn/utils.py

@@ -78,7 +78,8 @@ def check_input_array(X: npt.NDArray, *, min_samples: int) -> npt.NDArray:
         X,
         accept_sparse=False,
         accept_large_sparse=False,
-        dtype=("float16", "float32", "float64"),
+        # NOTE: remove float16 because F.pad does not allow float16.
+        dtype=("float32", "float64"),
         order=None,
         copy=False,
         force_all_finite=True,