Merge branch 'dev' of https://github.com/stefanradev93/BayesFlow into dev

Author: stefanradev93

bayesflow/adapters/adapter.py

@@ -79,13 +79,15 @@ def get_config(self) -> dict:
 
         return serialize(config)
 
-    def forward(self, data: dict[str, any], **kwargs) -> dict[str, np.ndarray]:
+    def forward(self, data: dict[str, any], *, stage: str = "inference", **kwargs) -> dict[str, np.ndarray]:
         """Apply the transforms in the forward direction.
 
         Parameters
         ----------
         data : dict
             The data to be transformed.
+        stage : str, one of ["training", "validation", "inference"]
+            The stage the function is called in.
         **kwargs : dict
             Additional keyword arguments passed to each transform.
 
@@ -97,17 +99,19 @@ def forward(self, data: dict[str, any], **kwargs) -> dict[str, np.ndarray]:
         data = data.copy()
 
         for transform in self.transforms:
-            data = transform(data, **kwargs)
+            data = transform(data, stage=stage, **kwargs)
 
         return data
 
-    def inverse(self, data: dict[str, np.ndarray], **kwargs) -> dict[str, any]:
+    def inverse(self, data: dict[str, np.ndarray], *, stage: str = "inference", **kwargs) -> dict[str, any]:
         """Apply the transforms in the inverse direction.
 
         Parameters
         ----------
         data : dict
             The data to be transformed.
+        stage : str, one of ["training", "validation", "inference"]
+            The stage the function is called in.
         **kwargs : dict
             Additional keyword arguments passed to each transform.
 
@@ -119,11 +123,13 @@ def inverse(self, data: dict[str, np.ndarray], **kwargs) -> dict[str, any]:
         data = data.copy()
 
         for transform in reversed(self.transforms):
-            data = transform(data, inverse=True, **kwargs)
+            data = transform(data, stage=stage, inverse=True, **kwargs)
 
         return data
 
-    def __call__(self, data: Mapping[str, any], *, inverse: bool = False, **kwargs) -> dict[str, np.ndarray]:
+    def __call__(
+        self, data: Mapping[str, any], *, inverse: bool = False, stage="inference", **kwargs
+    ) -> dict[str, np.ndarray]:
         """Apply the transforms in the given direction.
 
         Parameters
@@ -132,6 +138,8 @@ def __call__(self, data: Mapping[str, any], *, inverse: bool = False, **kwargs)
             The data to be transformed.
         inverse : bool, optional
             If False, apply the forward transform, else apply the inverse transform (default False).
+        stage : str, one of ["training", "validation", "inference"]
+            The stage the function is called in.
         **kwargs
             Additional keyword arguments passed to each transform.
 
@@ -141,9 +149,9 @@ def __call__(self, data: Mapping[str, any], *, inverse: bool = False, **kwargs)
             The transformed data.
         """
         if inverse:
-            return self.inverse(data, **kwargs)
+            return self.inverse(data, stage=stage, **kwargs)
 
-        return self.forward(data, **kwargs)
+        return self.forward(data, stage=stage, **kwargs)
 
     def __repr__(self):
         result = ""

bayesflow/adapters/transforms/standardize.py

@@ -87,7 +87,7 @@ def get_config(self) -> dict:
         }
         return serialize(config)
 
-    def forward(self, data: np.ndarray, stage: str = "training", **kwargs) -> np.ndarray:
+    def forward(self, data: np.ndarray, stage: str = "inference", **kwargs) -> np.ndarray:
         if self.axis is None:
             self.axis = tuple(range(data.ndim - 1))
 

bayesflow/datasets/disk_dataset.py

@@ -31,6 +31,7 @@ def __init__(
         batch_size: int,
         load_fn: callable = None,
         adapter: Adapter | None,
+        stage: str = "training",
         **kwargs,
     ):
         super().__init__(**kwargs)
@@ -39,6 +40,7 @@ def __init__(
         self.load_fn = load_fn or pickle_load
         self.adapter = adapter
         self.files = list(map(str, self.root.glob(pattern)))
+        self.stage = stage
 
         self.shuffle()
 
@@ -55,7 +57,7 @@ def __getitem__(self, item) -> dict[str, np.ndarray]:
         batch = tree_stack(batch)
 
         if self.adapter is not None:
-            batch = self.adapter(batch)
+            batch = self.adapter(batch, stage=self.stage)
 
         return batch
 

bayesflow/datasets/offline_dataset.py

@@ -21,12 +21,15 @@ def __init__(
         batch_size: int,
         adapter: Adapter | None,
         num_samples: int = None,
+        *,
+        stage: str = "training",
         **kwargs,
     ):
         super().__init__(**kwargs)
         self.batch_size = batch_size
         self.data = data
         self.adapter = adapter
+        self.stage = stage
 
         if num_samples is None:
             self.num_samples = self._get_num_samples_from_data(data)
@@ -52,7 +55,7 @@ def __getitem__(self, item: int) -> dict[str, np.ndarray]:
         }
 
         if self.adapter is not None:
-            batch = self.adapter(batch)
+            batch = self.adapter(batch, stage=self.stage)
 
         return batch
 

bayesflow/datasets/online_dataset.py

@@ -16,6 +16,8 @@ def __init__(
         batch_size: int,
         num_batches: int,
         adapter: Adapter | None,
+        *,
+        stage: str = "training",
         **kwargs,
     ):
         super().__init__(**kwargs)
@@ -24,12 +26,13 @@ def __init__(
         self._num_batches = num_batches
         self.adapter = adapter
         self.simulator = simulator
+        self.stage = stage
 
     def __getitem__(self, item: int) -> dict[str, np.ndarray]:
         batch = self.simulator.sample((self.batch_size,))
 
         if self.adapter is not None:
-            batch = self.adapter(batch)
+            batch = self.adapter(batch, stage=self.stage)
 
         return batch
 

bayesflow/datasets/rounds_dataset.py

@@ -18,6 +18,8 @@ def __init__(
         num_batches: int,
         epochs_per_round: int,
         adapter: Adapter | None,
+        *,
+        stage: str = "training",
         **kwargs,
     ):
         super().__init__(**kwargs)
@@ -27,6 +29,7 @@ def __init__(
         self.batch_size = batch_size
         self.adapter = adapter
         self.epoch = 0
+        self.stage = stage
 
         if epochs_per_round == 1:
             logging.warning(
@@ -45,7 +48,7 @@ def __getitem__(self, item: int) -> dict[str, np.ndarray]:
         batch = self.batches[item]
 
         if self.adapter is not None:
-            batch = self.adapter(batch)
+            batch = self.adapter(batch, stage=self.stage)
 
         return batch
 

examples/Linear_Regression_Starter.ipynb

@@ -376,7 +376,7 @@
     "\n",
     "To ensure that the training data generated by the simulator can be used for deep learning, we have do a bunch of transformations via `adapter` objects. They provides multiple flexible functionalities, from standardization to renaming, and so on. \n",
     "\n",
-    "Below, we build our own `adapter` from scratch but later on, `BayesFlo` will also provide default adapters that will already automate most of the commonly required steps."
+    "Below, we build our own `adapter` from scratch but later on, `BayesFlow` will also provide default adapters that will already automate most of the commonly required steps."
    ]
   },
   {