Added metadata to DictDataset

mlcolvar/data/dataset.py

@@ -16,7 +16,7 @@ class DictDataset(Dataset):
            'weights' : np.asarray([0.5,1.5,1.5,0.5]) }
     """
 
-    def __init__(self, dictionary: dict = None, feature_names=None, **kwargs):
+    def __init__(self, dictionary: dict=None, feature_names = None, metadata: dict = None, **kwargs):
         """Create a Dataset from a dictionary or from a list of kwargs.
 
         Parameters
@@ -32,7 +32,12 @@ def __init__(self, dictionary: dict = None, feature_names=None, **kwargs):
             raise TypeError(
                 f"DictDataset requires a dictionary , not {type(dictionary)}."
             )
-
+
+        if (metadata is not None) and (not isinstance(metadata, dict)):
+            raise TypeError(
+                f"DictDataset metadata requires a dictionary , not {type(metadata)}."
+            )
+
         # Add kwargs to dict
         if dictionary is None:
             dictionary = {}
@@ -43,7 +48,7 @@ def __init__(self, dictionary: dict = None, feature_names=None, **kwargs):
         # convert to torch.Tensors
         for key, val in dictionary.items():
             if not isinstance(val, torch.Tensor):
-                if key in ["data_list", "z_table", "cutoff"]:
+                if key =="data_list":
                     dictionary[key] = val
                 else:
                     dictionary[key] = torch.Tensor(val)
@@ -54,10 +59,13 @@ def __init__(self, dictionary: dict = None, feature_names=None, **kwargs):
         # save feature names
         self.feature_names = feature_names
 
+        # save metadata
+        self.metadata = metadata
+
         # check that all elements of dict have same length
-        it = iter(dictionary.items())
-        self.length = len(next(it)[1])
-        if not all([len(v)==self.length for l,v in it if l not in ["cutoff", "z_table"]]):
+        it = iter(dictionary.values())
+        self.length = len(next(it))
+        if not all([len(l)==self.length for l in it]):
             raise ValueError("not all arrays in dictionary have same length!")
 
     def __getitem__(self, index):
@@ -67,28 +75,16 @@ def __getitem__(self, index):
         else:
             slice_dict = {}
             for key, val in self._dictionary.items():
-                if key in ["z_table", "cutoff"]:
-                    slice_dict[key] = val
-                else:
-                    slice_dict[key] = val[index]
+                slice_dict[key] = val[index]
             return slice_dict
 
     def __setitem__(self, index, value):
         if isinstance(index, str):
             # check lengths
             if len(value) != len(self):
-                if index not in ["z_table", "cutoff"]:
-                    raise ValueError(
-                    f"length of value ({len(value)}) != length of dataset ({len(self)})."
-                    )
-                elif index=="z_table" and len(value) != len(self._dictionary[index]):
-                    raise ValueError(
-                    f"length of value ({len(value)}) != length of original dataset['{index}'] ({self._dictionary[index]})."
-                    )
-                elif index=="cutoff" and not isinstance(value, float):
-                    raise ValueError(
-                    f" 'cutoff' must be type float, found {type(value)} "
-                    )
+                raise ValueError(
+                f"length of value ({len(value)}) != length of dataset ({len(self)})."
+                )
             self._dictionary[index] = value
         else:
             raise NotImplementedError(
@@ -115,12 +111,14 @@ def get_stats(self):
     def __repr__(self) -> str:
         string = "DictDataset("
         for key, val in self._dictionary.items():
-            if key in ["data_list", "z_table"]:
+            if key=="data_list":
                 string += f' "{key}": {len(val)},'
             elif key in ["cutoff"]:
                 string += f' "{key}": {val},'
             else:
                 string += f' "{key}": {list(val.shape)},'
+        for key, val in self.metadata.items():
+            string += f' "{key}": {val},'
         string = string[:-1] + " )"
         return string
 

mlcolvar/data/graph/dataset.py

@@ -258,9 +258,9 @@ def create_dataset_from_configurations(
             data_list[i].cell = cell_list[i]
 
     # dataset = GraphDataSet(data_list, z_table.zs, cutoff)
-    dataset = DictDataset({'data_list' : data_list,
-                           'z_table' : z_table.zs,
-                           'cutoff' : cutoff})
+    dataset = DictDataset(dictionary={'data_list' : data_list},
+                          metadata={'z_table' : z_table.zs,
+                                    'cutoff' : cutoff})
 
     return dataset