perf: 🎨 Remove use of numpy random number generator.

src/cellmap_data/dataset.py

@@ -69,7 +69,7 @@ def __init__(
         is_train: bool = False,
         axis_order: str = "zyx",
         context: Optional[tensorstore.Context] = None,  # type: ignore
-        rng: Optional[np.random.Generator] = None,
+        rng: Optional[torch.Generator] = None,
         force_has_data: bool = False,
     ):
         """Initializes the CellMapDataset class.
@@ -101,7 +101,7 @@ def __init__(
             target_value_transforms (Optional[Callable | Sequence[Callable] | dict[str, Callable]], optional): A function to convert the ground truth data to target arrays. Defaults to None. Example is to convert the ground truth data to a signed distance transform. May be a single function, a list of functions, or a dictionary of functions for each class. In the case of a list of functions, it is assumed that the functions correspond to each class in the classes list in order.
             is_train (bool, optional): Whether the dataset is for training. Defaults to False.
             context (Optional[tensorstore.Context], optional): The context for the image data. Defaults to None.
-            rng (Optional[np.random.Generator], optional): A random number generator. Defaults to None.
+            rng (Optional[torch.Generator], optional): A random number generator. Defaults to None.
             force_has_data (bool, optional): Whether to force the dataset to report that it has data. Defaults to False.
         """
         self.raw_path = raw_path
@@ -116,7 +116,7 @@ def __init__(
         self.is_train = is_train
         self.axis_order = axis_order
         self.context = context
-        self._rng = rng
+        self.rng = rng
         self.force_has_data = force_has_data
         self._bounding_box = None
         self._bounding_box_shape = None
@@ -217,8 +217,6 @@ def __getitem__(self, idx):
                     spatial_transforms
                 )
                 array = self.target_sources[array_name][label][center]
-                # if array.shape[0] != 1:
-                #     array = array[None, ...]
                 class_arrays.append(array)
             outputs[array_name] = torch.stack(class_arrays)
         return outputs
@@ -402,10 +400,7 @@ def to(self, device):
 
     def generate_spatial_transforms(self) -> Optional[dict[str, Any]]:
         """Generates spatial transforms for the dataset."""
-        # TODO: use torch random number generator so accerlerators can synchronize across workers
-        if self._rng is None:
-            self._rng = np.random.default_rng()
-        rng = self._rng
+        # *TODO: use torch random number generator so accerlerators can synchronize across workers
 
         if not self.is_train or self.spatial_transforms is None:
             return None
@@ -416,20 +411,27 @@ def generate_spatial_transforms(self) -> Optional[dict[str, Any]]:
                 # output: {"mirror": ["x", "y"]}
                 spatial_transforms[transform] = []
                 for axis, prob in params["axes"].items():
-                    if rng.random() < prob:
+                    if torch.rand(1, generator=self.rng).item() < prob:
                         spatial_transforms[transform].append(axis)
             elif transform == "transpose":
                 # only reorder axes specified in params
                 # input: "transpose": {"axes": ["x", "z"]}
-                # output: {"transpose": {"x": 2, "y": 1, "z": 0}}
+                # params["axes"] = ["x", "z"]
+                # axes = {"x": 0, "y": 1, "z": 2}
                 axes = {axis: i for i, axis in enumerate(self.axis_order)}
-                shuffled_axes = rng.permutation(
-                    [axes[a] for a in params["axes"]]
-                )  # shuffle indices
+                # shuffled_axes = [0, 2]
+                shuffled_axes = [axes[a] for a in params["axes"]]
+                # shuffled_axes = [2, 0]
+                shuffled_axes = shuffled_axes[
+                    torch.randperm(len(shuffled_axes), generator=self.rng)
+                ]  # shuffle indices
+                # shuffled_axes = {"x": 2, "z": 0}
                 shuffled_axes = {
                     axis: shuffled_axes[i] for i, axis in enumerate(params["axes"])
                 }  # reassign axes
+                # axes = {"x": 2, "y": 1, "z": 0}
                 axes.update(shuffled_axes)
+                # output: {"transpose": {"x": 2, "y": 1, "z": 0}}
                 spatial_transforms[transform] = axes
             else:
                 raise ValueError(f"Unknown spatial transform: {transform}")

src/cellmap_data/multidataset.py

@@ -41,7 +41,11 @@ def __repr__(self) -> str:
 
     @property
     def class_counts(self):
-        if not hasattr(self, "_class_counts"):
+        if (
+            not hasattr(self, "_class_counts")
+            or self._class_counts is None
+            or len(self._class_counts) == 0
+        ):
             class_counts = {}
             for c in self.classes:
                 class_counts[c] = {}