Merge branch 'hed-standard:develop' into develop

Author: IanCa

hed/models/string_util.py

@@ -1,6 +1,27 @@
 from hed.models.hed_string import HedString
 
 
+def gather_descriptions(hed_string):
+    """Removes any description tags from the string and concatenates them
+
+    Parameters:
+        hed_string(HedString): To be modified
+
+    Returns: tuple
+        description(str): The concatenated values of all description tags.
+ 
+    Side-effect:
+         The input HedString has its Definition tags removed.
+
+    """
+    desc_tags = hed_string.find_tags("description", recursive=True, include_groups=0)
+    desc_string = " ".join([tag.extension if tag.extension.endswith(".") else tag.extension + "." for tag in desc_tags])
+
+    hed_string.remove(desc_tags)
+
+    return desc_string
+
+
 def split_base_tags(hed_string, base_tags, remove_group=False):
     """ Splits a HedString object into two separate HedString objects based on the presence of base tags.
 

hed/tools/analysis/annotation_util.py

@@ -165,6 +165,7 @@ def merge_hed_dict(sidecar_dict, hed_dict):
         hed_dict(dict):       Dictionary derived from a dataframe representation of HED in sidecar.
 
     """
+
     for key, value_dict in hed_dict.items():
         if key not in sidecar_dict:
             sidecar_dict[key] = value_dict

tests/data/bids_tests/eeg_ds003645s_hed/task-FacePerception_events.json

@@ -60,8 +60,7 @@
     }
   },
   "trial": {
-    "Description": "Indicates which trial this event belongs to.",
-    "HED": "Experimental-trial/#"
+    "Description": "Indicates which trial this event belongs to."
   },
   "rep_lag": {
     "Description": "How face images before this one was the image was previously presented.",

tests/data/bids_tests/eeg_ds003645s_hed_inheritance/task-FacePerception_events.json

@@ -43,8 +43,7 @@
     }
   },
   "trial": {
-    "Description": "Indicates which trial this event belongs to.",
-    "HED": "Experimental-trial/#"
+    "Description": "Indicates which trial this event belongs to."
   },
   "stim_file": {
     "Description": "Path of the stimulus file in the stimuli directory.",

tests/data/bids_tests/eeg_ds003645s_hed_library/task-FacePerception_events.json

@@ -60,8 +60,7 @@
     }
   },
   "trial": {
-    "Description": "Indicates which trial this event belongs to.",
-    "HED": "Experimental-trial/#, test:Informational-property, sc:Discontinuous-background-activity"
+    "Description": "Indicates which trial this event belongs to."
   },
   "rep_lag": {
     "Description": "How face images before this one was the image was previously presented.",

tests/data/bids_tests/eeg_ds003645s_hed_remodel.zip

@@ -65,12 +65,11 @@ def test_str_list_to_hed(self):
 
         hed_obj2 = manager.str_list_to_hed([hed[1], base[1], '(Event-context, (' + context[1] + '))'])
         self.assertIsInstance(hed_obj2, HedString)
-        self.assertEqual(10, len(hed_obj2.children))
+        self.assertEqual(9, len(hed_obj2.children))
         hed3, base3, context3 = manager.unfold_context(remove_types=['Condition-variable', 'Task'])
-
         hed_obj3 = manager.str_list_to_hed([hed3[1], base3[1], '(Event-context, (' + context3[1] + '))'])
         self.assertIsInstance(hed_obj3, HedString)
-        self.assertEqual(6, len(hed_obj3.children))
+        self.assertEqual(5, len(hed_obj3.children))
 
     def test_get_type_defs(self):
         manager1 = EventManager(self.input_data, self.schema)

tests/tools/analysis/test_event_manager.py

@@ -48,7 +48,7 @@ def test_constructor(self):
             counts.update_event_counts(HedString(self.input_df.iloc[k]['HED_assembled'], self.hed_schema),
                                        file_name='Base_name')
         self.assertIsInstance(counts.tag_dict, dict)
-        self.assertEqual(len(counts.tag_dict), 15)
+        self.assertEqual(14, len(counts.tag_dict))
 
     def test_merge_tag_dicts(self):
         counts1 = HedTagCounts('Base_name1', 50)
@@ -61,10 +61,10 @@ def test_merge_tag_dicts(self):
         counts3 = HedTagCounts("All", 0)
         counts3.merge_tag_dicts(counts1.tag_dict)
         counts3.merge_tag_dicts(counts2.tag_dict)
-        self.assertEqual(len(counts1.tag_dict), 15)
-        self.assertEqual(len(counts2.tag_dict), 15)
-        self.assertEqual(len(counts3.tag_dict), 15)
-        self.assertEqual(counts3.tag_dict['experiment-structure'].events, 2)
+        self.assertEqual(14, len(counts1.tag_dict))
+        self.assertEqual(14, len(counts2.tag_dict))
+        self.assertEqual(14, len(counts3.tag_dict))
+        self.assertEqual(2, counts3.tag_dict['experiment-structure'].events)
 
     def test_hed_tag_count(self):
         name = 'Base_name1'
@@ -82,10 +82,10 @@ def test_organize_tags(self):
         for hed in hed_strings:
             counts.update_event_counts(hed, 'run-1')
         self.assertIsInstance(counts.tag_dict, dict)
-        self.assertEqual(len(counts.tag_dict), 47)
+        self.assertEqual(46, len(counts.tag_dict))
         org_tags, leftovers = counts.organize_tags(self.tag_template)
-        self.assertEqual(len(org_tags), 19)
-        self.assertEqual(len(leftovers), 22)
+        self.assertEqual(19, len(org_tags))
+        self.assertEqual(21, len(leftovers))
 
 
 if __name__ == '__main__':