Updated validator and EventManager to handle n/a onsets

hed/tools/remodeling/operations/factor_hed_tags_op.py

@@ -119,7 +119,7 @@ def do_op(self, dispatcher, df, name, sidecar=None):
                 raise ValueError("QueryNameAlreadyColumn",
                                  f"Query [{query_name}]: is already a column name of the data frame")
         df_list = [input_data.dataframe]
-        tag_man = HedTagManager(input_data, dispatcher.hed_schema, remove_types=self.remove_types)
+        tag_man = HedTagManager(EventManager(input_data, dispatcher.hed_schema), remove_types=self.remove_types)
         hed_objs = tag_man.get_hed_objs(include_context=self.expand_context, replace_defs=self.replace_defs)
         df_factors = query_service.search_hed_objs(hed_objs, self.query_handlers, query_names=self.query_names)
         if len(df_factors.columns) > 0:

hed/tools/remodeling/operations/factor_hed_type_op.py

@@ -73,7 +73,7 @@ def do_op(self, dispatcher, df, name, sidecar=None):
 
         input_data = TabularInput(df.copy().fillna('n/a'), sidecar=sidecar, name=name)
         df_list = [input_data.dataframe]
-        var_manager = HedTypeManager(input_data, dispatcher.hed_schema)
+        var_manager = HedTypeManager(EventManager(input_data, dispatcher.hed_schema))
         var_manager.add_type(self.type_tag.casefold())
 
         df_factors = var_manager.get_factor_vectors(

hed/tools/remodeling/operations/merge_consecutive_op.py

@@ -115,7 +115,7 @@ def do_op(self, dispatcher, df, name, sidecar=None):
 
         df_new = df.copy()
         code_mask = df_new[self.column_name] == self.event_code
-        if sum(code_mask.astype(int)) == 0:
+        if not code_mask.any():
             return df_new
         match_columns.append(self.column_name)
         match_df = df_new.loc[:, match_columns]

hed/tools/remodeling/operations/summarize_column_names_op.py

@@ -94,7 +94,7 @@ def __init__(self, sum_op):
         """ Constructor for column name summary manager.
 
         Parameters:
-            sum_op (BaseOp): Operation associated with this summary.
+            sum_op (SummarizeColumnNamesOp): Operation associated with this summary.
 
         """
         super().__init__(sum_op)

hed/tools/remodeling/operations/summarize_column_values_op.py

@@ -133,7 +133,7 @@ def __init__(self, sum_op):
         """ Constructor for column value summary manager.
 
         Parameters:
-            sum_op (BaseOp): Operation associated with this summary.
+            sum_op (SummarizeColumnValuesOp): Operation associated with this summary.
 
         """
         super().__init__(sum_op)

hed/tools/remodeling/operations/summarize_definitions_op.py

@@ -94,7 +94,7 @@ def __init__(self, sum_op, hed_schema, known_defs=None):
         """ Constructor for the summary of definitions.
 
         Parameters:
-            sum_op (BaseOp): Summary operation class for gathering definitions.
+            sum_op (SummarizeDefinitionsOp): Summary operation class for gathering definitions.
             hed_schema (HedSchema or HedSchemaGroup):  Schema used for the dataset.
             known_defs (str or list or DefinitionDict): Definitions already known to be used.
 

hed/tools/remodeling/operations/summarize_hed_tags_op.py

@@ -187,7 +187,7 @@ def __init__(self, parameters):
             }
             if self.word_cloud["use_mask"] and not self.word_cloud["mask_path"]:
                 self.word_cloud["mask_path"] = os.path.realpath(
-                    os.path.join(os.path.dirname(__file__),  '../../../resources/word_cloud_brain_mask.png'))
+                    os.path.join(os.path.dirname(__file__), '../../../resources/word_cloud_brain_mask.png'))
             if self.word_cloud["font_path"]:
                 self.word_cloud["font_path"] = os.path.realpath(self.word_cloud["font_path"])
 
@@ -224,11 +224,12 @@ def validate_input_data(parameters):
 
 class HedTagSummary(BaseSummary):
     """ Manager of the HED tag summaries. """
+
     def __init__(self, sum_op):
         """ Constructor for HED tag summary manager.
 
         Parameters:
-            sum_op (BaseOp): Operation associated with this summary.
+            sum_op (SummarizeHedTagsOp): Operation associated with this summary.
 
         """
 
@@ -249,7 +250,7 @@ def update_summary(self, new_info):
             new_info['name'], total_events=len(new_info['df']))
         input_data = TabularInput(
             new_info['df'], sidecar=new_info['sidecar'], name=new_info['name'])
-        tag_man = HedTagManager(input_data, new_info['schema'], remove_types=self.sum_op.remove_types)
+        tag_man = HedTagManager(EventManager(input_data, new_info['schema']), remove_types=self.sum_op.remove_types)
         hed_objs = tag_man.get_hed_objs(include_context=self.sum_op.include_context,
                                         replace_defs=self.sum_op.replace_defs)
         for hed in hed_objs:
@@ -392,8 +393,7 @@ def _get_dataset_string(result, indent=BaseSummary.DISPLAY_INDENT):
         """
         sum_list = [f"Dataset: Total events={result.get('Total events', 0)} "
                     f"Total files={len(result.get('Files', []))}"]
-        sum_list = sum_list + \
-            HedTagSummary._get_tag_list(result, indent=indent)
+        sum_list = sum_list + HedTagSummary._get_tag_list(result, indent=indent)
         return "\n".join(sum_list)
 
     @staticmethod
@@ -409,8 +409,7 @@ def _get_individual_string(result, indent=BaseSummary.DISPLAY_INDENT):
 
         """
         sum_list = [f"Total events={result.get('Total events', 0)}"]
-        sum_list = sum_list + \
-            HedTagSummary._get_tag_list(result, indent=indent)
+        sum_list = sum_list + HedTagSummary._get_tag_list(result, indent=indent)
         return "\n".join(sum_list)
 
     @staticmethod

hed/tools/remodeling/operations/summarize_hed_type_op.py

@@ -108,7 +108,7 @@ def __init__(self, sum_op):
         """ Constructor for HED type summary manager.
 
         Parameters:
-            sum_op (BaseOp): Operation associated with this summary.
+            sum_op (SummarizeHedTypeOp): Operation associated with this summary.
 
         """
         super().__init__(sum_op)

hed/tools/remodeling/operations/summarize_hed_validation_op.py

@@ -106,7 +106,7 @@ def __init__(self, sum_op):
         """ Constructor for validation issue manager.
 
         Parameters:
-            sum_op (BaseOp): Operation associated with this summary.
+            sum_op (SummarizeHedValidationOp): Operation associated with this summary.
 
         """
         super().__init__(sum_op)
@@ -153,8 +153,7 @@ def update_summary(self, new_info):
 
         sidecar = new_info.get('sidecar', None)
         if sidecar and not isinstance(sidecar, Sidecar):
-            sidecar = Sidecar(
-                files=new_info['sidecar'], name=os.path.basename(sidecar))
+            sidecar = Sidecar(files=new_info['sidecar'], name=os.path.basename(sidecar))
         results = self._get_sidecar_results(
             sidecar, new_info, self.sum_op.check_for_warnings)
         if not results['sidecar_had_issues']:

tests/tools/analysis/test_event_manager.py

@@ -33,6 +33,11 @@ def setUpClass(cls):
                     "whatever": "Black",
                     "whatelse": "Purple"
                 }
+            },
+            "defs": {
+                "HED": {
+                    "defs1": "(Definition/Con1, (Condition-variable/Cond-one)), (Definition/Con2, (Condition-variable/Cond-one))"
+                }
             }
         }
 
@@ -61,7 +66,7 @@ def test_constructor(self):
                     self.assertEqual(event.end_index, len(manager1.input_data.dataframe))
 
     def test_no_onset_constructor(self):
-        #
+        # No onsets --- has an event manager
         tsv = {
             "event_code": ["show", "respond", "show", "respond", "whatever", "show", "whatelse", "respond"],
             "HED": ["Age/100", "n/a", "n/a", "n/a", "Green", "n/a", "Female", "n/a"],
@@ -79,6 +84,43 @@ def test_no_onset_constructor(self):
         self.assertIsNone(eman2.onsets)
         self.assertEqual(str(eman2.hed_strings[0]), "Age/100,Sensory-event,Visual-presentation")
         self.assertFalse(str(eman2.hed_strings[2]))
+        self.assertIsNone(eman2.base)
+        self.assertIsNone(eman2.context)
+
+    def test_bad_onset_constructor(self):
+        tsv = {
+            "onset": [0.0, 1.2, 1.2, 3.0, 5, 3.5, 4, 6],
+            "duration": [0.5, "n/a", "n/a", "n/a", "n/a", "n/a", "n/a", "n/a"],
+            "event_code": ["show", "respond", "show", "respond", "whatever", "show", "whatelse", "respond"],
+            "HED": ["Age/100", "n/a", "n/a", "n/a", "Green", "n/a", "Female", "n/a"],
+        }
+
+        tab = TabularInput(pd.DataFrame(tsv), sidecar=self.sidecar2)
+        with self.assertRaises(HedFileError):
+            EventManager(tab, self.schema)
+
+        tsv = {
+            "onset": [0.0, 1.2, 1.2, 3.0, "n/a", 3.5, "n/a", 6],
+            "duration": [0.5, "n/a", "n/a", "n/a", "n/a", "n/a", "n/a", "n/a"],
+            "event_code": ["show", "respond", "show", "respond", "whatever", "show", "whatelse", "respond"],
+            "HED": ["Age/100", "n/a", "n/a", "n/a", "Green", "n/a", "Female", "n/a"],
+        }
+        tab = TabularInput(pd.DataFrame(tsv), sidecar=self.sidecar2)
+        with self.assertRaises(HedFileError):
+            EventManager(tab, self.schema)
+
+    def test_unfold_no_onset(self):
+        tsv = {
+            "event_code": ["show", "respond", "show", "respond", "whatever", "show", "whatelse", "respond"],
+            "HED": ["Age/100,Condition-variable/Temp", "Def/Con1", "Def/Con2", "n/a", "Green", "n/a", "Female", "n/a"],
+        }
+        tab = TabularInput(pd.DataFrame(tsv), sidecar=self.sidecar2)
+        defs = self.sidecar2.get_def_dict(self.schema)
+        manager1 = EventManager(tab, self.schema)
+        hed1, base1, context1 = manager1.unfold_context()
+        hed2, base2, context2 = manager1.unfold_context(remove_types=["Condition-variable"])
+        self.assertEqual(hed1[1], "Def/Con1,Press")
+        self.assertEqual(hed2[1], "Press")
 
     def test_unfold_context_no_remove(self):
         manager1 = EventManager(self.input_data, self.schema)
@@ -87,6 +129,8 @@ def test_unfold_context_no_remove(self):
             self.assertIsInstance(hed[index], str)
             self.assertIsInstance(base[index], str)
 
+
+
     def test_unfold_context_remove(self):
         manager1 = EventManager(self.input_data, self.schema)
         hed, base, context = manager1.unfold_context(remove_types=['Condition-variable', 'Task'])