implement syntax for alignment

src/ibl_to_nwb/_scripts/convert_brainwide_map_raw_only.py

@@ -1,5 +1,6 @@
 from pathlib import Path
 
+from brainbox.io.one import EphysSessionLoader, SpikeSortingLoader
 from neuroconv.datainterfaces import SpikeGLXRecordingInterface
 from one.api import ONE
 
@@ -26,24 +27,38 @@
     cache_dir=one_cache_folder_path,
 )
 
-# Specify the path to the SpikeGLX files on the server
+# Specify the path to the SpikeGLX files on the server but use ONE API for timestamps
 probe_1_source_folder_path = Path("D:/example_data/ephy_testing_data/spikeglx/Noise4Sam_g0")
 probe_2_source_folder_path = Path(
     "D:/example_data/ephy_testing_data/spikeglx/multi_trigger_multi_gate/SpikeGLX/5-19-2022-CI0/5-19-2022-CI0_g0/"
 )
 
-ap_1_file_path = probe_1_source_folder_path / "Noise4Sam_g0_imec0/Noise4Sam_g0_t0.imec0.ap.bin"
-ap_2_file_path = probe_2_source_folder_path / "5-19-2022-CI0_g0_imec0/5-19-2022-CI0_g0_t0.imec0.ap.bin"
 
-lf_1_file_path = probe_1_source_folder_path / "Noise4Sam_g0_imec0/Noise4Sam_g0_t0.imec0.lf.bin"
-lf_2_file_path = probe_2_source_folder_path / "5-19-2022-CI0_g0_imec0/5-19-2022-CI0_g0_t0.imec0.lf.bin"
+# Initialize interfaces one probe at a time and properly align raw timestamps
+ephys_session_loader = EphysSessionLoader(one=ibl_client, eid=session_id)
+
+probe_to_imec_map = {
+    "probe00": 0,
+    "probe01": 1,
+}
 
-# Initialize interfaces
 data_interfaces = list()
-data_interfaces.append(SpikeGLXRecordingInterface(file_path=ap_1_file_path))
-data_interfaces.append(SpikeGLXRecordingInterface(file_path=ap_2_file_path))
-data_interfaces.append(SpikeGLXRecordingInterface(file_path=lf_1_file_path))
-data_interfaces.append(SpikeGLXRecordingInterface(file_path=lf_2_file_path))
+for probe_name, pid in ephys_session_loader.probes.items():
+    spike_sorting_loader = SpikeSortingLoader(pid=pid, one=ibl_client)
+
+    probe_index = probe_to_imec_map[probe_name]
+    for band in ["ap", "lf"]:
+        file_path = probe_1_source_folder_path / f"Noise4Sam_g0_imec0/Noise4Sam_g0_t0.imec{probe_index}.{band}.bin"
+        interface = SpikeGLXRecordingInterface(file_path=file_path)
+
+        # This is the syntax for aligning the raw timestamps; I cannot test this without the actual data as stored
+        # on your end, so please work with Heberto if there are any problems after uncommenting
+
+        # band_info = spike_sorting_loader.raw_electrophysiology(band=band, stream=True)
+        # aligned_timestamps = spike_sorting_loader.samples2times(numpy.arange(0, band_info.ns), direction='forward')
+        # interface.set_aligned_timestamps(aligned_timestamps=aligned_timestamps)
+
+        data_interfaces.append(interface)
 
 # Raw video take some special handling
 metadata_retrieval = BrainwideMapConverter(one=ibl_client, session=session_id, data_interfaces=[], verbose=False)