Change epoch tags to property (#1935)

* make epoch_tags a property * remove epoch tags from fields dict * remove epoch_tags from print assertion * add test for single string tags * add test for no epochs table * update CHANGELOG.md
NeurodataWithoutBorders · Jul 18, 2024 · fcd7008 · fcd7008
1 parent a9f6332
commit fcd7008
Show file tree

Hide file tree

Showing 4 changed files with 17 additions and 11 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@
 
 ### Bug fixes
 - Fixed `can_read` method to return False if no nwbfile version can be found @stephprince [#1934](https://github.com/NeurodataWithoutBorders/pynwb/pull/1934)
+- Changed `epoch_tags` to be a NWBFile property instead of constructor argument. @stephprince [#1935](https://github.com/NeurodataWithoutBorders/pynwb/pull/1935)
 
 ## PyNWB 2.8.1 (July 3, 2024)
 

diff --git a/src/pynwb/file.py b/src/pynwb/file.py
@@ -273,7 +273,6 @@ class NWBFile(MultiContainerInterface, HERDManager):
                      {'name': 'subject', 'child': True, 'required_name': 'subject'},
                      {'name': 'sweep_table', 'child': True, 'required_name': 'sweep_table'},
                      {'name': 'invalid_times', 'child': True, 'required_name': 'invalid_times'},
-                     'epoch_tags',
                      # icephys_filtering is temporary. /intracellular_ephys/filtering dataset will be deprecated
                      {'name': 'icephys_filtering', 'settable': False},
                      {'name': 'intracellular_recordings', 'child': True,
@@ -362,8 +361,6 @@ class NWBFile(MultiContainerInterface, HERDManager):
              'doc': 'Stimulus template TimeSeries objects belonging to this NWBFile', 'default': None},
             {'name': 'epochs', 'type': TimeIntervals,
              'doc': 'Epoch objects belonging to this NWBFile', 'default': None},
-            {'name': 'epoch_tags', 'type': (tuple, list, set),
-             'doc': 'A sorted list of tags used across all epochs', 'default': set()},
             {'name': 'trials', 'type': TimeIntervals,
              'doc': 'A table containing trial data', 'default': None},
             {'name': 'invalid_times', 'type': TimeIntervals,
@@ -426,7 +423,6 @@ def __init__(self, **kwargs):
             'stimulus_template',
             'keywords',
             'processing',
-            'epoch_tags',
             'electrodes',
             'electrode_groups',
             'devices',
@@ -555,6 +551,10 @@ def modules(self):
         warn("NWBFile.modules has been replaced by NWBFile.processing.", DeprecationWarning)
         return self.processing
 
+    @property
+    def epoch_tags(self):
+        return set(self.epochs.tags[:]) if self.epochs is not None else set()
+
     @property
     def ec_electrode_groups(self):
         warn("NWBFile.ec_electrode_groups has been replaced by NWBFile.electrode_groups.", DeprecationWarning)
@@ -616,7 +616,6 @@ def add_epoch_column(self, **kwargs):
         See :py:meth:`~hdmf.common.table.DynamicTable.add_column` for more details
         """
         self.__check_epochs()
-        self.epoch_tags.update(kwargs.pop('tags', list()))
         self.epochs.add_column(**kwargs)
 
     def add_epoch_metadata_column(self, *args, **kwargs):
@@ -638,8 +637,6 @@ def add_epoch(self, **kwargs):
         enclosure versus sleeping between explorations)
         """
         self.__check_epochs()
-        if kwargs['tags'] is not None:
-            self.epoch_tags.update(kwargs['tags'])
         self.epochs.add_interval(**kwargs)
 
     def __check_electrodes(self):

diff --git a/tests/unit/test_core.py b/tests/unit/test_core.py
@@ -135,10 +135,6 @@ def test_print_file(self):
     name1 <class 'pynwb\.base\.TimeSeries'>,
     name2 <class 'pynwb\.base\.TimeSeries'>
   }
-  epoch_tags: {
-    tag1,
-    tag2
-  }
   epochs: epochs <class 'pynwb.epoch.TimeIntervals'>
   file_create_date: \[datetime.datetime\(.*\)\]
   identifier: identifier

diff --git a/tests/unit/test_file.py b/tests/unit/test_file.py
@@ -142,6 +142,18 @@ def test_epoch_tags(self):
         tags = self.nwbfile.epoch_tags
         self.assertEqual(set(expected_tags), set(tags))
 
+    def test_epoch_tags_single_string(self):
+        tags1 = 't1'
+        tags2 = 't2'
+        expected_tags = set([tags1, tags2])
+        self.nwbfile.add_epoch(0.0, 1.0, tags=tags1)
+        self.nwbfile.add_epoch(1.0, 2.0, tags=tags2)
+        tags = self.nwbfile.epoch_tags
+        self.assertEqual(expected_tags, tags)
+
+    def test_epoch_tags_no_table(self):
+        self.assertEqual(set(), self.nwbfile.epoch_tags)
+
     def test_add_acquisition(self):
         self.nwbfile.add_acquisition(TimeSeries('test_ts', [0, 1, 2, 3, 4, 5],
                                                 'grams', timestamps=[0.0, 0.1, 0.2, 0.3, 0.4, 0.5]))