Merge pull request #604 from VisLab/develop

Minor updates to remodeling formats

hed/tools/remodeling/cli/run_remodel.py

@@ -148,11 +148,12 @@ def main(arg_list=None):
     args, operations = parse_arguments(arg_list)
     if not os.path.isdir(args.data_dir):
         raise HedFileError("DataDirectoryDoesNotExist", f"The root data directory {args.data_dir} does not exist", "")
-    backup_man = BackupManager(args.data_dir)
-    if not backup_man.get_backup(args.backup_name):
-        raise HedFileError("BackupDoesNotExist", f"Backup {args.backup_name} does not exist. "
-                           f"Please run_remodel_backup first", "")
-    backup_man.restore_backup(args.backup_name, args.task_names, verbose=args.verbose)
+    if args.backup_name:
+        backup_man = BackupManager(args.data_dir)
+        if not backup_man.get_backup(args.backup_name):
+            raise HedFileError("BackupDoesNotExist", f"Backup {args.backup_name} does not exist. "
+                               f"Please run_remodel_backup first", "")
+        backup_man.restore_backup(args.backup_name, args.task_names, verbose=args.verbose)
     dispatch = Dispatcher(operations, data_root=args.data_dir, backup_name=args.backup_name,
                           hed_versions=args.hed_versions)
     if args.use_bids:

hed/tools/remodeling/operations/summarize_column_names_op.py

@@ -97,7 +97,7 @@ def _get_result_string(self, name, result, indent=BaseContext.DISPLAY_INDENT):
         if name == "Dataset":
             return self._get_dataset_string(result, indent)
         columns = result["Columns"][0]
-        return f"{indent}{indent}{name}: {str(columns['Column names'])}"
+        return f"{indent}{str(columns['Column names'])}"
 
     @staticmethod
     def _get_dataset_string(result, indent=BaseContext.DISPLAY_INDENT):

hed/tools/remodeling/operations/summarize_column_values_op.py

@@ -122,7 +122,7 @@ def _get_dataset_string(result, indent=BaseContext.DISPLAY_INDENT):
 
     @staticmethod
     def _get_individual_string(name, result, indent=BaseContext.DISPLAY_INDENT):
-        sum_list = [f"{name}: {result.get('Total events', 0)} events"]
+        sum_list = [f"Total events={result.get('Total events', 0)}"]
         cat_cols = result.get("Categorical columns", {})
         if cat_cols:
             sum_list.append(ColumnValueSummaryContext._get_categorical_string(cat_cols, offset=indent, indent=indent))

hed/tools/remodeling/operations/summarize_hed_tags_op.py

@@ -116,15 +116,6 @@ def _get_result_string(self, name, result, indent=BaseContext.DISPLAY_INDENT):
         if name == 'Dataset':
             return self._get_dataset_string(result, indent=indent)
         return self._get_individual_string(name, result, indent=indent)
-        # sum_list = [f"\n{name}\n{indent}Main tags[events,files]:"]
-        # for category, tags in result['Main tags'].items():
-        #     sum_list.append(f"{indent}{indent}{category}:")
-        #     if tags:
-        #         sum_list.append(f"{indent}{indent}{indent}{' '.join(self._tag_details(tags))}")
-        # if result['Other tags']:
-        #     sum_list.append(f"\tOther tags[events,files]:")
-        #     sum_list.append(f"{indent}{indent}{' '.join(self._tag_details(result['Other tags']))}")
-        # return "\n".join(sum_list)
 
     def _merge_all(self):
         all_counts = HedTagCounts('Dataset')
@@ -137,14 +128,14 @@ def _merge_all(self):
 
     @staticmethod
     def _get_dataset_string(result, indent=BaseContext.DISPLAY_INDENT):
-        sum_list = [f"Dataset: {len(result.get('files', []))} files with a total of "
-                    f"{result.get('total_events', 0)} events"]
+        sum_list = [f"Dataset: Total events={result.get('total_events', 0)} "
+                    f"Total files={len(result.get('files', []))}"]
         sum_list = sum_list + HedTagSummaryContext._get_tag_list(result, indent=indent)
         return "\n".join(sum_list)
 
     @staticmethod
     def _get_individual_string(name, result, indent=BaseContext.DISPLAY_INDENT):
-        sum_list = [f"{name}: {result.get('total_events', 0)} events"]
+        sum_list = [f"Total events={result.get('total_events', 0)}"]
         sum_list = sum_list + HedTagSummaryContext._get_tag_list(result, indent=indent)
         return "\n".join(sum_list)
 

hed/tools/remodeling/operations/summarize_hed_type_op.py

@@ -124,11 +124,11 @@ def _get_result_string(self, name, result, indent=BaseContext.DISPLAY_INDENT):
     @staticmethod
     def _get_dataset_string(result, indent=BaseContext.DISPLAY_INDENT):
         details = result.get('details', {})
-        sum_list = [f"Dataset: {len(details)} {result['type_tag']} types in {len(result.get('files', []))} files" 
-                    f" with a total of {result.get('total_events', 0)}"]
+        sum_list = [f"Dataset: Type={result['type_tag']} Type values={len(details)} "
+                    f"Total events={result.get('total_events', 0)} Total files={len(result.get('files', []))}"]
 
         for key, item in details.items():
-            str1 = f"{item['events']} events out of {item['total_events']} total events in {len(item['files'])} files"
+            str1 = f"{item['events']} event(s) out of {item['total_events']} total events in {len(item['files'])} file(s)"
             if item['level_counts']:
                 str1 = f"{len(item['level_counts'])} levels in " + str1
             if item['direct_references']:
@@ -142,8 +142,10 @@ def _get_dataset_string(result, indent=BaseContext.DISPLAY_INDENT):
 
     @staticmethod
     def _get_individual_string(name, result, indent=BaseContext.DISPLAY_INDENT):
-        sum_list = [f"{indent}{name}: Type={result['type_tag']} Total events={result.get('total_events', 0)} "]
         details = result.get('details', {})
+        sum_list = [f"Type={result['type_tag']} Type values={len(details)} "
+                    f"Total events={result.get('total_events', 0)}"]
+
         for key, item in details.items():
             sum_list.append(f"{indent*2}{key}: {item['levels']} levels in {item['events']} events")
             str1 = ""

hed/tools/remodeling/operations/summarize_hed_validation_op.py

@@ -110,7 +110,8 @@ def update_context(self, new_context):
         sidecar = new_context.get('sidecar', None)
         filtered_issues = []
         if sidecar:
-            sidecar = Sidecar(files=new_context['sidecar'], name=os.path.basename(sidecar))
+            if not isinstance(sidecar, Sidecar):
+                sidecar = Sidecar(files=new_context['sidecar'], name=os.path.basename(sidecar))
             results["sidecar_issues"][sidecar.name] = []
             sidecar_issues = sidecar.validate_entries(validator, check_for_warnings=self.check_for_warnings)
             filtered_issues = ErrorHandler.filter_issues_by_severity(sidecar_issues, ErrorSeverity.ERROR)