Fix missing invalid time intervals (#1069)

* Refactor and clean up NWBFile IO mapper

* Map invalid times

* Map timestamps interval

* Add invalid times test

Author: rly

src/pynwb/io/base.py

@@ -27,8 +27,11 @@ def __init__(self, spec):
         self.map_spec('unit', data_spec.get_attribute('unit'))
         self.map_spec('resolution', data_spec.get_attribute('resolution'))
         self.map_spec('conversion', data_spec.get_attribute('conversion'))
+
         timestamps_spec = self.spec.get_dataset('timestamps')
         self.map_spec('timestamps_unit', timestamps_spec.get_attribute('unit'))
+        self.map_spec('interval', timestamps_spec.get_attribute('interval'))
+
         startingtime_spec = self.spec.get_dataset('starting_time')
         self.map_spec('starting_time_unit', startingtime_spec.get_attribute('unit'))
         self.map_spec('rate', startingtime_spec.get_attribute('rate'))

src/pynwb/io/file.py

@@ -13,35 +13,43 @@ def __init__(self, spec):
 
         acq_spec = self.spec.get_group('acquisition')
         self.unmap(acq_spec)
-        raw_ts_spec = acq_spec.get_neurodata_type('NWBDataInterface')
-        self.map_spec('acquisition', raw_ts_spec)
+        self.map_spec('acquisition', acq_spec.get_neurodata_type('NWBDataInterface'))
+
         self.map_spec('analysis', self.spec.get_group('analysis').get_neurodata_type('NWBContainer'))
 
+        # map constructor arg and property 'stimulus' -> stimulus__presentation
         stimulus_spec = self.spec.get_group('stimulus')
         self.unmap(stimulus_spec)
         self.map_spec('stimulus', stimulus_spec.get_group('presentation').get_neurodata_type('TimeSeries'))
         self.map_spec('stimulus_template', stimulus_spec.get_group('templates').get_neurodata_type('TimeSeries'))
 
         intervals_spec = self.spec.get_group('intervals')
+        self.map_spec('intervals', intervals_spec.get_neurodata_type('TimeIntervals'))
+
         epochs_spec = intervals_spec.get_group('epochs')
         self.map_spec('epochs', epochs_spec)
+
         trials_spec = intervals_spec.get_group('trials')
         self.map_spec('trials', trials_spec)
-        self.map_spec('intervals', intervals_spec.get_neurodata_type('TimeIntervals'))
+
+        invalid_times_spec = intervals_spec.get_group('invalid_times')
+        self.map_spec('invalid_times', invalid_times_spec)
 
         general_spec = self.spec.get_group('general')
+
         icephys_spec = general_spec.get_group('intracellular_ephys')
         self.map_spec('ic_electrodes', icephys_spec.get_neurodata_type('IntracellularElectrode'))
-        ecephys_spec = general_spec.get_group('extracellular_ephys')
         self.map_spec('sweep_table', icephys_spec.get_neurodata_type('SweepTable'))
+
+        ecephys_spec = general_spec.get_group('extracellular_ephys')
         self.map_spec('electrodes', ecephys_spec.get_group('electrodes'))
         self.map_spec('electrode_groups', ecephys_spec.get_neurodata_type('ElectrodeGroup'))
-        self.map_spec(
-            'ogen_sites',
-            general_spec.get_group('optogenetics').get_neurodata_type('OptogeneticStimulusSite'))
-        self.map_spec(
-            'imaging_planes',
-            general_spec.get_group('optophysiology').get_neurodata_type('ImagingPlane'))
+
+        self.map_spec('ogen_sites',
+                      general_spec.get_group('optogenetics').get_neurodata_type('OptogeneticStimulusSite'))
+
+        self.map_spec('imaging_planes',
+                      general_spec.get_group('optophysiology').get_neurodata_type('ImagingPlane'))
 
         general_datasets = ['data_collection',
                             'experiment_description',
@@ -62,17 +70,18 @@ def __init__(self, spec):
         for dataset_name in general_datasets:
             self.map_spec(dataset_name, general_spec.get_dataset(dataset_name))
 
-        proc_spec = self.spec.get_group('processing')
-        self.unmap(proc_spec)
-        self.map_spec('processing', proc_spec.get_neurodata_type('ProcessingModule'))
-        # self.unmap(general_spec.get_dataset('stimulus'))
+        # note: constructor arg and property 'stimulus' is already mapped above, so use a different name here
         self.map_spec('stimulus_notes', general_spec.get_dataset('stimulus'))
         self.map_spec('source_script_file_name', general_spec.get_dataset('source_script').get_attribute('file_name'))
 
         self.map_spec('subject', general_spec.get_group('subject'))
         self.map_spec('devices', general_spec.get_group('devices').get_neurodata_type('Device'))
         self.map_spec('lab_meta_data', general_spec.get_neurodata_type('LabMetaData'))
 
+        proc_spec = self.spec.get_group('processing')
+        self.unmap(proc_spec)
+        self.map_spec('processing', proc_spec.get_neurodata_type('ProcessingModule'))
+
         scratch_spec = self.spec.get_group('scratch')
         self.unmap(scratch_spec)
         self.map_spec('scratch_datas', scratch_spec.get_neurodata_type('ScratchData'))

tests/integration/ui_write/test_core.py

@@ -27,6 +27,26 @@ def getContainer(self, nwbfile):
         return nwbfile.trials
 
 
+class TestInvalidTimes(base.TestMapRoundTrip):
+
+    def setUpContainer(self):
+        # this will get ignored
+        return DynamicTable('trials', 'a placeholder table')
+
+    def addContainer(self, nwbfile):
+        nwbfile.add_invalid_times_column('foo', 'an int column')
+        nwbfile.add_invalid_times_column('bar', 'a float column')
+        nwbfile.add_invalid_times_column('baz', 'a string column')
+        nwbfile.add_invalid_times_column('qux', 'a boolean column')
+        nwbfile.add_invalid_time_interval(start_time=0., stop_time=1., foo=27, bar=28.0, baz="29", qux=True)
+        nwbfile.add_invalid_time_interval(start_time=2., stop_time=3., foo=37, bar=38.0, baz="39", qux=False)
+        # reset the thing
+        self.container = nwbfile.invalid_times
+
+    def getContainer(self, nwbfile):
+        return nwbfile.invalid_times
+
+
 class TestUnits(base.TestMapRoundTrip):
 
     def setUpContainer(self):