one instantiation removed in IblSortingInterface, but requires hack i…

…n neuroconv

src/ibl_to_nwb/_scripts/convert_brainwide_map_processed_only_local_testing.py

@@ -48,8 +48,6 @@
 data_interfaces = list()
 
 # These interfaces should always be present in source data
-# data_interfaces.append(IblSortingInterface(session=eid, cache_folder=one_cache_folder_path / "sorting", revision=revision))
-
 data_interfaces.append(IblSortingInterface(one=one, session=eid, revision=revision))
 data_interfaces.append(BrainwideMapTrialsInterface(one=one, session=eid, revision=revision))
 data_interfaces.append(WheelInterface(one=one, session=eid, revision=revision))
@@ -88,11 +86,6 @@
     metadata=metadata,
     overwrite=True,
 )
-# automatic_dandi_upload(
-#     dandiset_id="000409",
-#     nwb_folder_path=nwbfile_path.parent,
-#     cleanup=cleanup,
-# )
 
 # if cleanup:
 #     rmtree(cache_folder)

src/ibl_to_nwb/_scripts/convert_brainwide_map_raw_only.py

@@ -32,6 +32,8 @@
 data_interfaces = []
 
 # spikeglx_source_folder_path = Path("D:/example_data/ephy_testing_data/spikeglx/Noise4Sam_g0")
+session_folder = ibl_client.eid2path(session_id)
+spikeglx_source_folder_path = session_folder / "raw_ephys_data"
 spikeglx_subconverter = IblSpikeGlxConverter(folder_path=spikeglx_source_folder_path, one=ibl_client)
 data_interfaces.append(spikeglx_subconverter)
 

src/ibl_to_nwb/converters/_ibl_spikeglx_converter.py

@@ -10,7 +10,7 @@ class IblSpikeGlxConverter(SpikeGLXConverterPipe):
     def __init__(self, folder_path: DirectoryPath, one: ONE, eid: str) -> None:
         super().__init__(folder_path=folder_path)
         self.one = one
-        self.eid = eid  # probably should better name this session_id ?
+        self.eid = eid
 
     def temporally_align_data_interfaces(self) -> None:
         """Align the raw data timestamps to the other data streams using the ONE API."""
@@ -22,21 +22,14 @@ def temporally_align_data_interfaces(self) -> None:
         }
 
         ephys_session_loader = EphysSessionLoader(one=self.one, eid=self.eid)
-        probes = ephys_session_loader.probes
         for probe_name, pid in ephys_session_loader.probes.items():
             spike_sorting_loader = SpikeSortingLoader(pid=pid, one=self.one)
 
             probe_index = probe_to_imec_map[probe_name]
             for band in ["ap", "lf"]:
                 recording_interface = self.data_interface_objects[f"imec{probe_index}.{band}"]
-                # recording_interface = next(
-                #     interface
-                #     for interface in self.data_interface_objects
-                #     if f"imec{probe_index}.{band}" in interface.source_data["file_path"]
-                # )
-
-                band_info = spike_sorting_loader.raw_electrophysiology(band=band, stream=True)
-                aligned_timestamps = spike_sorting_loader.samples2times(np.arange(0, band_info.ns), direction="forward")
+                sl = spike_sorting_loader.raw_electrophysiology(band=band, stream=True)
+                aligned_timestamps = spike_sorting_loader.samples2times(np.arange(0, sl.ns), direction="forward")
                 recording_interface.set_aligned_timestamps(aligned_timestamps=aligned_timestamps)
         pass
 

src/ibl_to_nwb/datainterfaces/_brainwide_map_trials.py

@@ -1,13 +1,13 @@
 from pathlib import Path
 from typing import Optional
 
+from brainbox.io.one import SessionLoader
 from hdmf.common import VectorData
 from neuroconv.basedatainterface import BaseDataInterface
 from neuroconv.utils import load_dict_from_file
 from one.api import ONE
 from pynwb import NWBFile
 from pynwb.epoch import TimeIntervals
-from brainbox.io.one import SessionLoader
 
 
 class BrainwideMapTrialsInterface(BaseDataInterface):

src/ibl_to_nwb/datainterfaces/_ibl_sorting_extractor.py

@@ -5,12 +5,12 @@
 
 import numpy as np
 import pandas as pd
-from pydantic import DirectoryPath
-from spikeinterface import BaseSorting, BaseSortingSegment
-from one.api import ONE
 from brainbox.io.one import SpikeSortingLoader
 from iblatlas.atlas import AllenAtlas
 from iblatlas.regions import BrainRegions
+from one.api import ONE
+from pydantic import DirectoryPath
+from spikeinterface import BaseSorting, BaseSortingSegment
 
 
 class IblSortingExtractor(BaseSorting):
@@ -27,12 +27,6 @@ def __init__(
         session: str,
         revision: Optional[str] = None,
     ):
-        # one = ONE(
-        #     base_url="https://openalyx.internationalbrainlab.org",
-        #     password="international",
-        #     silent=True,
-        #     cache_dir=cache_folder,
-        # )
         if revision is None:  # latest
             revision = one.list_revisions(session)[-1]
 

src/ibl_to_nwb/datainterfaces/_ibl_sorting_interface.py

@@ -7,24 +7,21 @@
     BaseSortingExtractorInterface,
 )
 from neuroconv.utils import load_dict_from_file
-from pydantic import DirectoryPath
+from one.api import ONE
 
 from ._ibl_sorting_extractor import IblSortingExtractor
-from one.api import ONE
+
 
 class IblSortingInterface(BaseSortingExtractorInterface):
     Extractor = IblSortingExtractor
 
     def __init__(
         self,
-        one: ONE,
         session: str,
-        # cache_folder: Optional[DirectoryPath] = None,
+        one: ONE,
         revision: Optional[str] = None,
-        # verbose: bool = False,
     ):
-        # super().__init__(verbose, session=session, cache_folder=cache_folder, revision=revision)
-        super().__init__(one=one, session=session, revision=revision)
+        super().__init__(session=session, one=one, revision=revision)
 
     def get_metadata(self) -> dict:
         metadata = super().get_metadata()
@@ -40,4 +37,3 @@ def get_metadata(self) -> dict:
                 )
 
         return metadata
-

src/ibl_to_nwb/datainterfaces/_lick_times.py

@@ -6,7 +6,7 @@
 from one.api import ONE
 from pynwb import NWBFile
 from pynwb.file import DynamicTable
-from brainbox.io.one import SessionLoader
+
 
 class LickInterface(BaseDataInterface):
     def __init__(self, one: ONE, session: str, revision: Optional[str] = None):

src/ibl_to_nwb/datainterfaces/_pupil_tracking.py

@@ -4,13 +4,14 @@
 from typing import Optional
 
 import numpy as np
+from brainbox.io.one import SessionLoader
 from neuroconv.basedatainterface import BaseDataInterface
 from neuroconv.tools.nwb_helpers import get_module
 from neuroconv.utils import load_dict_from_file
 from one.api import ONE
 from pynwb import TimeSeries
 from pynwb.behavior import PupilTracking
-from brainbox.io.one import SessionLoader
+
 
 class PupilTrackingInterface(BaseDataInterface):
     def __init__(self, one: ONE, session: str, camera_name: str, revision: Optional[str] = None):

src/ibl_to_nwb/datainterfaces/_wheel_movement.py

@@ -2,14 +2,15 @@
 from typing import Optional
 
 from brainbox.behavior import wheel as wheel_methods
+from brainbox.io.one import SessionLoader
 from neuroconv.basedatainterface import BaseDataInterface
 from neuroconv.tools.nwb_helpers import get_module
 from neuroconv.utils import load_dict_from_file
 from one.api import ONE
 from pynwb import TimeSeries
 from pynwb.behavior import CompassDirection, SpatialSeries
 from pynwb.epoch import TimeIntervals
-from brainbox.io.one import SessionLoader
+
 
 class WheelInterface(BaseDataInterface):
     def __init__(self, one: ONE, session: str, revision: Optional[str] = None):