1947 Enhance load decathlon datalist API

monai/data/decathlon_datalist.py

@@ -17,34 +17,43 @@
 
 
 @overload
-def _compute_path(base_dir: str, element: str) -> str:
+def _compute_path(base_dir: str, element: str, check_path: bool = False) -> str:
     ...
 
 
 @overload
-def _compute_path(base_dir: str, element: List[str]) -> List[str]:
+def _compute_path(base_dir: str, element: List[str], check_path: bool = False) -> List[str]:
     ...
 
 
-def _compute_path(base_dir, element):
+def _compute_path(base_dir, element, check_path=False):
     """
     Args:
         base_dir: the base directory of the dataset.
         element: file path(s) to append to directory.
+        check_path: if `True`, only compute when the result is an existing path.
 
     Raises:
         TypeError: When ``element`` contains a non ``str``.
         TypeError: When ``element`` type is not in ``Union[list, str]``.
 
     """
+
+    def _join_path(base_dir: str, item: str):
+        result = os.path.normpath(os.path.join(base_dir, item))
+        if check_path and not os.path.exists(result):
+            # if not an existing path, don't join with base dir
+            return item
+        return result
+
     if isinstance(element, str):
-        return os.path.normpath(os.path.join(base_dir, element))
+        return _join_path(base_dir, element)
     if isinstance(element, list):
         for e in element:
             if not isinstance(e, str):
-                raise TypeError(f"Every file path in element must be a str but got {type(element).__name__}.")
-        return [os.path.normpath(os.path.join(base_dir, e)) for e in element]
-    raise TypeError(f"element must be one of (str, list) but is {type(element).__name__}.")
+                return element
+        return [_join_path(base_dir, e) for e in element]
+    return element
 
 
 def _append_paths(base_dir: str, is_segmentation: bool, items: List[Dict]) -> List[Dict]:
@@ -63,9 +72,12 @@ def _append_paths(base_dir: str, is_segmentation: bool, items: List[Dict]) -> Li
             raise TypeError(f"Every item in items must be a dict but got {type(item).__name__}.")
         for k, v in item.items():
             if k == "image":
-                item[k] = _compute_path(base_dir, v)
+                item[k] = _compute_path(base_dir, v, check_path=False)
             elif is_segmentation and k == "label":
-                item[k] = _compute_path(base_dir, v)
+                item[k] = _compute_path(base_dir, v, check_path=False)
+            else:
+                # for other items, auto detect whether it's a valid path
+                item[k] = _compute_path(base_dir, v, check_path=True)
     return items
 
 

monai/transforms/utility/dictionary.py

@@ -656,10 +656,6 @@ def __init__(self, keys: KeysCollection, name: str, dim: int = 0, allow_missing_
             name: the name corresponding to the key to store the concatenated data.
             dim: on which dimension to concatenate the items, default is 0.
             allow_missing_keys: don't raise exception if key is missing.
-
-        Raises:
-            ValueError: When insufficient keys are given (``len(self.keys) < 2``).
-
         """
         super().__init__(keys, allow_missing_keys)
         self.name = name

tests/test_load_decathlon_datalist.py

@@ -96,6 +96,31 @@ def test_seg_no_labels(self):
             result = load_decathlon_datalist(file_path, True, "test", tempdir)
             self.assertEqual(result[0]["image"], os.path.join(tempdir, "spleen_15.nii.gz"))
 
+    def test_additional_items(self):
+        with tempfile.TemporaryDirectory() as tempdir:
+            with open(os.path.join(tempdir, "mask31.txt"), "w") as f:
+                f.write("spleen31 mask")
+
+            test_data = {
+                "name": "Spleen",
+                "description": "Spleen Segmentation",
+                "labels": {"0": "background", "1": "spleen"},
+                "training": [
+                    {"image": "spleen_19.nii.gz", "label": "spleen_19.nii.gz", "mask": "spleen mask"},
+                    {"image": "spleen_31.nii.gz", "label": "spleen_31.nii.gz", "mask": "mask31.txt"},
+                ],
+                "test": ["spleen_15.nii.gz", "spleen_23.nii.gz"],
+            }
+            json_str = json.dumps(test_data)
+            file_path = os.path.join(tempdir, "test_data.json")
+            with open(file_path, "w") as json_file:
+                json_file.write(json_str)
+            result = load_decathlon_datalist(file_path, True, "training", tempdir)
+            self.assertEqual(result[0]["image"], os.path.join(tempdir, "spleen_19.nii.gz"))
+            self.assertEqual(result[0]["label"], os.path.join(tempdir, "spleen_19.nii.gz"))
+            self.assertEqual(result[1]["mask"], os.path.join(tempdir, "mask31.txt"))
+            self.assertEqual(result[0]["mask"], "spleen mask")
+
 
 if __name__ == "__main__":
     unittest.main()