FpgaTrials supports alignment of Bpod datasets not part of trials object

ibllib/__init__.py

@@ -2,7 +2,7 @@
 import logging
 import warnings
 
-__version__ = '2.32.0'
+__version__ = '2.32.1'
 warnings.filterwarnings('always', category=DeprecationWarning, module='ibllib')
 
 # if this becomes a full-blown library we should let the logging configuration to the discretion of the dev

ibllib/io/extractors/ephys_fpga.py

@@ -46,6 +46,7 @@
 import spikeglx
 import ibldsp.utils
 import one.alf.io as alfio
+from one.alf.files import filename_parts
 from iblutil.util import Bunch
 from iblutil.spacer import Spacer
 
@@ -816,6 +817,34 @@ def _extract(self, sync=None, chmap=None, sync_collection='raw_ephys_data',
         assert self.var_names == tuple(out.keys())
         return out
 
+    def _is_trials_object_attribute(self, var_name, variable_length_vars=None):
+        """
+        Check if variable name is expected to have the same length as trials.intervals.
+
+        Parameters
+        ----------
+        var_name : str
+            The variable name to check.
+        variable_length_vars : list
+            Set of variable names that are not expected to have the same length as trials.intervals.
+            This list may be passed by superclasses.
+
+        Returns
+        -------
+        bool
+            True if variable is a trials dataset.
+
+        Examples
+        --------
+        >>> assert self._is_trials_object_attribute('stimOnTrigger_times') is True
+        >>> assert self._is_trials_object_attribute('wheel_position') is False
+        """
+        save_name = self.save_names[self.var_names.index(var_name)] if var_name in self.var_names else None
+        if save_name:
+            return filename_parts(save_name)[1] == 'trials'
+        else:
+            return var_name not in (variable_length_vars or [])
+
     def build_trials(self, sync, chmap, display=False, **kwargs):
         """
         Extract task related event times from the sync.
@@ -914,7 +943,10 @@ def build_trials(self, sync, chmap, display=False, **kwargs):
         # Add the Bpod trial events, converting the timestamp fields to FPGA time.
         # NB: The trial intervals are by default a Bpod rsync field.
         out.update({k: self.bpod_trials[k][ibpod] for k in self.bpod_fields})
-        out.update({k: self.bpod2fpga(self.bpod_trials[k][ibpod]) for k in self.bpod_rsync_fields})
+        for k in self.bpod_rsync_fields:
+            # Some personal projects may extract non-trials object datasets that may not have 1 event per trial
+            idx = ibpod if self._is_trials_object_attribute(k) else np.arange(len(self.bpod_trials[k]), dtype=int)
+            out[k] = self.bpod2fpga(self.bpod_trials[k][idx])
         out.update({k: fpga_trials[k][ifpga] for k in fpga_trials.keys()})
 
         if display:  # pragma: no cover

ibllib/tests/extractors/test_ephys_fpga.py

@@ -524,6 +524,23 @@ def test_time_fields(self):
         fields = ephys_fpga.FpgaTrials._time_fields(expected + ('position', 'timebase', 'fooBaz'))
         self.assertCountEqual(expected, fields)
 
+    def test_is_trials_object_attribute(self):
+        """Test for FpgaTrials._is_trials_object_attribute method."""
+        extractor = ephys_fpga.FpgaTrials('subject/2020-01-01/001')
+        # Should assume this is a trials attribute if no save name defined
+        self.assertTrue(extractor._is_trials_object_attribute('stimOnTrigger_times'))
+        # Save name not trials attribute
+        self.assertFalse(extractor._is_trials_object_attribute('wheel_position'))
+        # Save name is trials attribute
+        self.assertTrue(extractor._is_trials_object_attribute('table'))
+        # Check with toy variables
+        extractor.var_names += ('foo_bar',)
+        extractor.save_names += (None,)
+        self.assertTrue(extractor._is_trials_object_attribute('foo_bar'))
+        self.assertFalse(extractor._is_trials_object_attribute('foo_bar', variable_length_vars='foo_bar'))
+        extractor.save_names = extractor.save_names[:-1] + ('_ibl_foo.bar_times.csv',)
+        self.assertFalse(extractor._is_trials_object_attribute('foo_bar'))
+
 
 if __name__ == '__main__':
     unittest.main(exit=False, verbosity=2)

release_notes.md

@@ -1,16 +1,19 @@
 ## Release Notes 2.32
 
 ## features
-- SDSC patcher automatically support revisons
+- SDSC patcher automatically support revisions
 
-## others
+## other
 - Add extra key to alignment qc with manual resolution for channel upload
-- 
+
+#### 2.32.1
+- FpgaTrials supports alignment of Bpod datasets not part of trials object
+
 ## Release Notes 2.31
 
 ### features
-- training status uses new extractor map
-- refactor neurodsp to ibldsp
+- Training status uses new extractor map
+- Refactor neurodsp to ibldsp
 - ITI qc check for iblrig v8
 - Support habituationChoiceWorld extraction in iblrig v8.15.0