Universal reader output base classes

iohub/dataset_base.py

@@ -0,0 +1,88 @@
+from abc import ABC, abstractmethod
+from types import TracebackType
+from typing import Generator, Optional, Type, Union
+
+import numpy as np
+from numpy.typing import ArrayLike
+
+
+class BaseFOV(ABC):
+    # NOTE: not using the `data` method from ngff Position
+
+    @property
+    @abstractmethod
+    def channels(self) -> list[str]:
+        raise NotImplementedError
+
+    def channel_index(self, key: str) -> int:
+        """Return index of given channel."""
+        return self.channels.index(key)
+
+    @property
+    @abstractmethod
+    def shape(self) -> tuple[int, int, int, int, int]:
+        # NOTE: suggestion, fix dimension to 5?
+        # We could me more restrictive than ome-zarr
+        raise NotImplementedError
+
+    @abstractmethod
+    def __getitem__(
+        self,
+        key: Union[int, slice, tuple[Union[int, slice], ...]],
+    ) -> ArrayLike:
+        """
+        Returned object must support the ``__array__`` interface,
+        so that ``np.asarray(...)`` will work.
+        """
+        raise NotImplementedError
+
+    @property
+    @abstractmethod
+    def ndim(self) -> int:
+        raise NotImplementedError
+
+    @property
+    @abstractmethod
+    def dtype(self) -> np.dtype:
+        raise NotImplementedError
+
+    @property
+    def zyx_scale(self) -> tuple[float, float, float]:
+        """Helper function for FOV spatial scale."""
+        raise NotImplementedError
+
+
+class BaseFOVCollection(ABC):
+    @abstractmethod
+    def __enter__(self) -> "BaseFOVCollection":
+        """Open the underlying file and return self."""
+        raise NotImplementedError
+
+    @abstractmethod
+    def __exit__(
+        self,
+        exc_type: Optional[Type[BaseException]],
+        exc_val: Optional[BaseException],
+        exc_tb: Optional[TracebackType],
+    ) -> bool:
+        """Close the files."""
+        raise NotImplementedError
+
+    @abstractmethod
+    def __contains__(self, position_key: str) -> bool:
+        """Check if a position is present in the collection."""
+        raise NotImplementedError
+
+    @abstractmethod
+    def __len__(self) -> int:
+        raise NotImplementedError
+
+    @abstractmethod
+    def __getitem__(self, position_key: str) -> BaseFOV:
+        """FOV key position to FOV object."""
+        raise NotImplementedError
+
+    @abstractmethod
+    def __iter__(self) -> Generator[tuple[str, BaseFOV], None, None]:
+        """Iterates over pairs of keys and FOVs."""
+        raise NotImplementedError