Photometry integration

ibllib/pipes/dynamic_pipeline.py

@@ -588,11 +588,35 @@ def make_pipeline(session_path, **pkwargs):
             **kwargs, **mscope_kwargs, parents=[tasks['MesoscopePreprocess']])
 
     if 'neurophotometrics' in devices:
-        # {'collection': 'raw_photometry_data', 'datetime': '2024-09-18T16:43:55.207000',
-        #   'fibers': {'G0': {'location': 'NBM'}, 'G1': {'location': 'SI'}}, 'sync_channel': 1}
-        photometry_kwargs = devices['neurophotometrics']
-        tasks['FibrePhotometrySync'] = type('FibrePhotometrySync', (
-            ptasks.FibrePhotometrySync,), {})(**kwargs, **photometry_kwargs)
+        # note: devices['neurophotometrics'] is the acquisition_description
+        sync_mode = devices['neurophotometrics'].get('sync_mode', 'bpod')  # default to bpod for downward compatibility
+
+        # passive photometry
+        task_protocols = acquisition_description['tasks']
+        assert len(task_protocols) == 1, 'chained protocols are not yet supported for photometry extraction'
+        protocol = task_protocols[0]
+        if 'passive' in protocol:
+            assert sync_mode == 'daqami', 'passive protocol syncing only supported for DAQ based syncing'
+            tasks['FibrePhotometryPassiveChoiceWorld'] = type(
+                'FibrePhotometryPassiveChoiceWorld', (ptasks.FibrePhotometryPassiveChoiceWorld,), {}
+            )(
+                **kwargs,
+            )
+
+        match sync_mode:
+            case 'bpod':
+                # for synchronization with the BNC inputs of the neurophotometrics receiving the sync pulses
+                # from the individual bpods
+                tasks['FibrePhotometryBpodSync'] = type('FibrePhotometryBpodSync', (ptasks.FibrePhotometryBpodSync,), {})(
+                    **kwargs,
+                )
+            case 'daqami':
+                # for synchronization with the DAQami receiving the sync pulses from the individual bpods
+                # as well as the frame clock from the FP3002
+                if 'passive' not in protocol:  # excluding passive session
+                    tasks['FibrePhotometryDAQSync'] = type('FibrePhotometryDAQSync', (ptasks.FibrePhotometryDAQSync,), {})(
+                        **kwargs,
+                    )
 
     p = mtasks.Pipeline(session_path=session_path, **pkwargs)
     p.tasks = tasks