Allow, but correct, non compliant user defined fields.

wtclarke · Mar 27, 2024 · d2004f8 · d2004f8
1 parent 62e0bab
commit d2004f8
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Showing 4 changed files with 27 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,9 @@
 This document contains the nifti_mrs_tools release history in reverse chronological order.
 
+1.1.2 (WIP)
+-----------------------------------
+- When reading files any user defined parameters without a description will print a warning to the user and generate an empty description key.
+
 1.1.1 (Wednesday 6th December 2023)
 -----------------------------------
 - Validator checks consistency of any `SpectraWidth` header extension value with the dwell time in `pixdim[4]`.

diff --git a/src/nifti_mrs/hdr_ext.py b/src/nifti_mrs/hdr_ext.py
@@ -90,7 +90,8 @@ def from_header_ext(cls, hdr_ext_dict):
             if key in standard_defined:
                 obj.set_standard_def(key, hdr_ext_dict[key])
             else:
-                if 'Value' in hdr_ext_dict[key]\
+                if isinstance(hdr_ext_dict[key], dict)\
+                        and 'Value' in hdr_ext_dict[key]\
                         and 'Description' in hdr_ext_dict[key]:
                     obj.set_user_def(
                         key,
@@ -103,7 +104,21 @@ def from_header_ext(cls, hdr_ext_dict):
                         hdr_ext_dict[key],
                         hdr_ext_dict[key]['Description'])
                 else:
-                    raise ValueError(f'User-defined key {key} must contain a "Description" field"')
+                    print(
+                        "This file's header extension is currently invalid. "
+                        f"Reason: User-defined key {key} does not contain a 'Description' field. "
+                        "Setting empty 'Description'.")
+                    if isinstance(hdr_ext_dict[key], dict)\
+                            and 'Value' in hdr_ext_dict[key]:
+                        obj.set_user_def(
+                            key,
+                            hdr_ext_dict[key]['Value'],
+                            '')
+                    else:
+                        obj.set_user_def(
+                            key,
+                            hdr_ext_dict[key],
+                            '')
 
         return obj
 

diff --git a/tests/test_hdr_ext.py b/tests/test_hdr_ext.py
@@ -130,6 +130,12 @@ def test_to_from_dict():
     assert hdr2._dim_info[1] == {"tag": "DIM_EDIT", "info": None, "hdr": None}
     assert 'RepetitionTime' in hdr2._standard_data
 
+    dict_rep['my_value3'] = 5.0
+    dict_rep['my_value4'] = {'foo': 5.0, }
+    hdr3 = Hdr_Ext.from_header_ext(dict_rep)
+    assert hdr3['my_value3'] == {'Value': 5.0, 'Description': ''}
+    assert hdr3['my_value4'] == {'foo': 5.0, 'Description': ''}
+
 
 def test_to_json():
     hdr = Hdr_Ext(100., '1H', dimensions=5)

diff --git a/tests/test_validator.py b/tests/test_validator.py
@@ -251,4 +251,3 @@ def test_spectralwidth():
     validator.validate_spectralwidth(
         json.dumps(test_dict),
         0.001)
-