Support chained protocols in BehaviourPlots task

ibllib/io/extractors/base.py

@@ -161,6 +161,9 @@ def extract(self, bpod_trials=None, settings=None, **kwargs):
             self.settings = {"IBLRIG_VERSION": "100.0.0"}
         elif self.settings.get("IBLRIG_VERSION", "") == "":
             self.settings["IBLRIG_VERSION"] = "100.0.0"
+        # Get all detected TTLs. These are stored for QC purposes
+        self.frame2ttl, self.audio = raw.load_bpod_fronts(self.session_path, data=self.bpod_trials)
+
         return super(BaseBpodTrialsExtractor, self).extract(**kwargs)
 
     @property

ibllib/io/raw_data_loaders.py

@@ -926,6 +926,23 @@ def patch_settings(session_path, collection='raw_behavior_data',
     -------
     dict
         The modified settings.
+
+    Examples
+    --------
+    File is in /data/subject/2020-01-01/002/raw_behavior_data. Patch the file then move to new location.
+    >>> patch_settings('/data/subject/2020-01-01/002', number='001')
+    >>> shutil.move('/data/subject/2020-01-01/002/raw_behavior_data/', '/data/subject/2020-01-01/001/raw_behavior_data/')
+
+    File is moved into new collection within the same session, then patched.
+    >>> shutil.move('./subject/2020-01-01/002/raw_task_data_00/', './subject/2020-01-01/002/raw_task_data_01/')
+    >>> patch_settings('/data/subject/2020-01-01/002', collection='raw_task_data_01', new_collection='raw_task_data_01')
+
+    Update subject, date and number.
+    >>> new_session_path = Path('/data/foobar/2024-02-24/002')
+    >>> old_session_path = Path('/data/baz/2024-02-23/001')
+    >>> patch_settings(old_session_path, collection='raw_task_data_00',
+    ...     subject=new_session_path.parts[-3], date=new_session_path.parts[-2], number=new_session_path.parts[-1])
+    >>> shutil.move(old_session_path, new_session_path)
     """
     settings = load_settings(session_path, collection)
     if not settings:

ibllib/pipes/behavior_tasks.py

@@ -311,6 +311,8 @@ def _run(self, update=True, save=True):
 
     def extract_behaviour(self, **kwargs):
         self.extractor = get_bpod_extractor(self.session_path, task_collection=self.collection)
+        _logger.info('Bpod trials extractor: %s.%s',
+                     self.extractor.__module__, self.extractor.__class__.__name__)
         self.extractor.default_path = self.output_collection
         return self.extractor.extract(task_collection=self.collection, **kwargs)
 
@@ -453,12 +455,11 @@ def run_qc(self, trials_data=None, update=False, plot_qc=False, QC=None):
         if plot_qc:
             _logger.info('Creating Trials QC plots')
             try:
-                # TODO needs to be adapted for chained protocols
                 session_id = self.one.path2eid(self.session_path)
-                plot_task = BehaviourPlots(session_id, self.session_path, one=self.one)
+                plot_task = BehaviourPlots(
+                    session_id, self.session_path, one=self.one, task_collection=self.output_collection)
                 _ = plot_task.run()
                 self.plot_tasks.append(plot_task)
-
             except Exception:
                 _logger.error('Could not create Trials QC Plot')
                 _logger.error(traceback.format_exc())

ibllib/plots/figures.py

@@ -71,35 +71,58 @@ def remove_axis_outline(ax):
 
 
 class BehaviourPlots(ReportSnapshot):
-    """
-    Behavioural plots
-    """
-
-    signature = {
-        'input_files': [
-            ('*trials.table.pqt', 'alf', True),
-        ],
-        'output_files': [
-            ('psychometric_curve.png', 'snapshot/behaviour', True),
-            ('chronometric_curve.png', 'snapshot/behaviour', True),
-            ('reaction_time_with_trials.png', 'snapshot/behaviour', True)
-        ]
-    }
+    """Behavioural plots."""
+
+    @property
+    def signature(self):
+        signature = {
+            'input_files': [
+                ('*trials.table.pqt', self.trials_collection, True),
+            ],
+            'output_files': [
+                ('psychometric_curve.png', 'snapshot/behaviour', True),
+                ('chronometric_curve.png', 'snapshot/behaviour', True),
+                ('reaction_time_with_trials.png', 'snapshot/behaviour', True)
+            ]
+        }
+        return signature
 
     def __init__(self, eid, session_path=None, one=None, **kwargs):
+        """
+        Generate and upload behaviour plots.
+
+        Parameters
+        ----------
+        eid : str, uuid.UUID
+            An experiment UUID.
+        session_path : pathlib.Path
+            A session path.
+        one : one.api.One
+            An instance of ONE for registration to Alyx.
+        trials_collection : str
+            The location of the trials data (default: 'alf').
+        kwargs
+            Arguments for ReportSnapshot constructor.
+        """
         self.one = one
         self.eid = eid
         self.session_path = session_path or self.one.eid2path(self.eid)
+        self.trials_collection = kwargs.pop('trials_collection', 'alf')
         super(BehaviourPlots, self).__init__(self.session_path, self.eid, one=self.one,
                                              **kwargs)
-        self.output_directory = self.session_path.joinpath('snapshot', 'behaviour')
+        # Output directory should mirror trials collection, sans 'alf' part
+        self.output_directory = self.session_path.joinpath(
+            'snapshot', 'behaviour', self.trials_collection.removeprefix('alf').strip('/'))
         self.output_directory.mkdir(exist_ok=True, parents=True)
 
     def _run(self):
 
         output_files = []
-        trials = alfio.load_object(self.session_path.joinpath('alf'), 'trials')
-        title = '_'.join(list(self.session_path.parts[-3:]))
+        trials = alfio.load_object(self.session_path.joinpath(self.trials_collection), 'trials')
+        if self.one:
+            title = self.one.path2ref(self.session_path, as_dict=False)
+        else:
+            title = '_'.join(list(self.session_path.parts[-3:]))
 
         fig, ax = training.plot_psychometric(trials, title=title, figsize=(8, 6))
         set_axis_label_size(ax)
@@ -127,9 +150,7 @@ def _run(self):
 
 # TODO put into histology and alignment pipeline
 class HistologySlices(ReportSnapshotProbe):
-    """
-    Plots coronal and sagittal slice showing electrode locations
-    """
+    """Plots coronal and sagittal slice showing electrode locations."""
 
     def _run(self):
 

release_notes.md

@@ -8,6 +8,7 @@
 
 #### 2.32.1
 - FpgaTrials supports alignment of Bpod datasets not part of trials object
+- Support chained protocols in BehaviourPlots task
 
 ## Release Notes 2.31