[FIX] Add function to prep data for JSON serialization (#859)

* Adds attempt at fix

* Addres @handwerkerd review

* Trailing whitespace fix

tedana/io.py

@@ -8,6 +8,7 @@
 import logging
 import os
 import os.path as op
+from copy import deepcopy
 from string import Formatter
 
 import nibabel as nib
@@ -198,7 +199,8 @@ def save_file(self, data, description, **kwargs):
         if description.endswith("img"):
             self.save_img(data, name)
         elif description.endswith("json"):
-            self.save_json(data, name)
+            prepped = prep_data_for_json(data)
+            self.save_json(prepped, name)
         elif description.endswith("tsv"):
             self.save_tsv(data, name)
 
@@ -680,3 +682,45 @@ def split_ts(data, mmix, mask, comptable):
     resid = data - hikts
 
     return hikts, resid
+
+
+def prep_data_for_json(d) -> dict:
+    """Attempts to create a JSON serializable dictionary from a data dictionary
+
+    Parameters
+    ----------
+    d: dict
+        A dictionary that will be converted into something JSON serializable
+
+    Raises
+    ------
+    ValueError if it cannot force the dictionary to be serializable
+    TypeError if you do not supply a dict
+
+    Returns
+    -------
+    An attempt at JSON serializable data
+
+    Notes
+    -----
+    Use this to make something serializable when writing JSON to disk.
+    To speed things up since there are a small number of conversions, this
+    function does not check for serializability, but does use conversion
+    rules for cases encountered where things were not serializable.
+    Add more conversion rules to this function in cases where a
+    tedana-generated object does not serialize to JSON.
+    """
+    if not isinstance(d, dict):
+        raise TypeError(f"Dictionary required to force serialization; got type {type(d)} instead.")
+    # The input dictionary may want to retain types, so we copy
+    d = deepcopy(d)
+    for k, v in d.items():
+        if isinstance(v, dict):
+            # One of the values in the dict is the problem, need to recurse
+            v = prep_data_for_json(v)
+        elif isinstance(v, np.ndarray):
+            v = v.tolist()
+        # NOTE: add more special cases for type conversions above this
+        # comment line as an elif block
+        d[k] = v
+    return d

tedana/tests/test_io.py

@@ -189,3 +189,32 @@ def test_smoke_load_data():
 
 
 # TODO: "BREAK" AND UNIT TESTS
+
+
+def test_prep_data_for_json():
+    """
+    Tests for prep_data_for_json
+    """
+    # Should reject non-dict entities since that is required for saver
+    with pytest.raises(TypeError):
+        me.prep_data_for_json(1)
+
+    # Should not modify something with no special types
+    d = {"mustang": "vroom"}
+    new_d = me.prep_data_for_json(d)
+    assert new_d == d
+
+    # Should coerce an ndarray into a list
+    d = {"number": np.ndarray(1)}
+    new_d = me.prep_data_for_json(d)
+    assert isinstance(new_d["number"], list)
+
+    # Should work for nested dict
+    d = {
+        "dictionary": {
+            "serializable": "cat",
+            "array": np.ndarray([1, 2, 3]),
+        }
+    }
+    new_d = me.prep_data_for_json(d)
+    assert isinstance(new_d["dictionary"]["array"], list)