add meta transform (#411)

Co-authored-by: Benjamin Morris <[email protected]>

cyto_dl/image/transforms/add_meta.py

@@ -0,0 +1,35 @@
+from typing import Sequence
+
+from monai.data import MetaTensor
+from monai.transforms import Transform
+
+
+class AddMeta(Transform):
+    """Transform to update image key metadata with new keys."""
+
+    def __init__(self, image_key: str, meta_keys: Sequence[str], delete: bool = False):
+        """
+        Parameters
+        ----------
+        image_key: str
+            Key in batch dictionary for image data. Must be a MetaTensor
+        meta_keys: Sequence[str]
+            List of keys to add to image metadata
+        delete: bool
+            If True, delete the original meta_keys from the image metadata after they have been added as metadata
+        """
+        self.image_key = image_key
+        self.meta_keys = meta_keys
+        self.delete = delete
+
+    def __call__(self, data):
+        if not isinstance(data[self.image_key], MetaTensor):
+            raise ValueError(
+                f"Image key {self.image_key} must be a MetaTensor, got {type(data[self.image_key])}"
+            )
+        new_meta = {k: data[k] for k in self.meta_keys}
+        if self.delete:
+            for k in self.meta_keys:
+                del data[k]
+        data[self.image_key].meta.update(new_meta)
+        return data