Add electrodes interface for Huszar

buzsaki_lab_to_nwb/huszar_hippocampus_dynamics/behaviorinterface.py

@@ -1,14 +1,12 @@
 from pathlib import Path
 
 import numpy as np
-from pynwb.file import NWBFile, TimeIntervals, TimeSeries
-from pynwb.behavior import SpatialSeries, Position
 from hdmf.backends.hdf5.h5_utils import H5DataIO
-
-from neuroconv.utils.json_schema import FolderPathType
 from neuroconv.basedatainterface import BaseDataInterface
 from neuroconv.tools.nwb_helpers import get_module
-
+from neuroconv.utils.json_schema import FolderPathType
+from pynwb.behavior import CompassDirection, Position, SpatialSeries
+from pynwb.file import NWBFile, TimeIntervals, TimeSeries
 from scipy.io import loadmat as loadmat_scipy
 from pymatreader import read_mat
 

buzsaki_lab_to_nwb/huszar_hippocampus_dynamics/convert_session.py

@@ -1,6 +1,6 @@
 """Primary script to run to convert an entire session of data using the NWBConverter."""
-from neuroconv.utils import load_dict_from_file, dict_deep_update
 
+from neuroconv.utils import load_dict_from_file, dict_deep_update
 from converter import HuzsarNWBConverter
 from pathlib import Path
 
@@ -23,19 +23,10 @@ def session_to_nwbfile(session_dir_path, output_dir_path, stub_test=False, write
     source_data = dict()
     conversion_options = dict()
 
-    # Add sorter
-    file_path = session_dir_path / f"{session_id}.spikes.cellinfo.mat"
-    source_data.update(Sorting=dict(file_path=str(file_path), sampling_frequency=30_000.0))
-
-    # Add behavior data
-    source_data.update(Behavior8Maze=dict(folder_path=str(session_dir_path)))
-    conversion_options.update(Behavior8Maze=dict(stub_test=stub_test))
-
-    source_data.update(BehaviorSleep=dict(folder_path=str(session_dir_path)))
-
     # Add Recordings
     file_path = session_dir_path / f"{session_id}.dat"
     xml_file_path = session_dir_path / f"{session_id}.xml"
+    raw_recording_file_available = file_path.is_file()
 
     if file_path.is_file():
         size_in_GB = file_path.stat().st_size / 1000
@@ -55,6 +46,8 @@ def session_to_nwbfile(session_dir_path, output_dir_path, stub_test=False, write
     # Add LFP
     file_path = session_dir_path / f"{session_id}.lfp"
     folder_path = session_dir_path
+    lfp_file_available = file_path.is_file()
+
     if file_path.is_file():
         size_in_GB = file_path.stat().st_size / 1000**3
 
@@ -64,12 +57,26 @@ def session_to_nwbfile(session_dir_path, output_dir_path, stub_test=False, write
 
             source_data.update(LFP=dict(file_path=str(file_path), xml_file_path=str(xml_file_path)))
             conversion_options.update(LFP=dict(stub_test=stub_test, write_electrical_series=write_electrical_series))
+
         else:
             print(f"Skipping LFP interface for {session_id} because the file {file_path} does not have any data.")
 
     else:
         print(f"Skipping LFP interface for {session_id} because the file {file_path} does not exist.")
 
+    write_ecephys_metadata = (not raw_recording_file_available) and (not lfp_file_available)
+
+    # Add sorter
+    file_path = session_dir_path / f"{session_id}.spikes.cellinfo.mat"
+    source_data.update(Sorting=dict(file_path=str(file_path), verbose=verbose))
+    conversion_options.update(Sorting=dict(write_ecephys_metadata=write_ecephys_metadata))
+
+    # Add behavior data
+    source_data.update(Behavior8Maze=dict(folder_path=str(session_dir_path)))
+    conversion_options.update(Behavior8Maze=dict(stub_test=stub_test))
+
+    source_data.update(BehaviorSleep=dict(folder_path=str(session_dir_path)))
+
     # Add epochs
     source_data.update(Epochs=dict(folder_path=str(session_dir_path)))
 
@@ -97,22 +104,22 @@ def session_to_nwbfile(session_dir_path, output_dir_path, stub_test=False, write
     metadata = dict_deep_update(metadata, editable_metadata)
 
     # Run conversion
-    converter.run_conversion(
+    nwbfile = converter.run_conversion(
         nwbfile_path=nwbfile_path,
         metadata=metadata,
         conversion_options=conversion_options,
         overwrite=True,
     )
 
+    return nwbfile
+
 
 if __name__ == "__main__":
     # Parameters for conversion
     stub_test = True  # Converts a only a stub of the data for quick iteration and testing
     verbose = True
     output_dir_path = Path.home() / "conversion_nwb"
-    # session_dir_path = Path("/Volumes/neurodata/buzaki/HuszarR/optotagCA1/e13/e13_16f1/e13_16f1_210302")
-    # session_dir_path = Path("/Volumes/neurodata/buzaki/HuszarR/optotagCA1/e13/e13_26m1/e13_26m1_211019/e13_26m1_211019")
-    # session_dir_path = Path("/home/heberto/buzaki/e13_16f1_210302/")
-    session_dir_path = Path("/shared/catalystneuro/HuszarR/optotagCA1/e13/e13_26m1/e13_26m1_211019")
-
-    session_to_nwbfile(session_dir_path, output_dir_path, stub_test=stub_test, verbose=verbose)
+    project_root = Path("/shared/catalystneuro/HuszarR/optotagCA1")
+    session_dir_path = project_root / "e13" / "e13_26m1" / "e13_26m1_211119"
+    assert session_dir_path.is_dir()
+    nwbfile = session_to_nwbfile(session_dir_path, output_dir_path, stub_test=stub_test, verbose=verbose)

buzsaki_lab_to_nwb/huszar_hippocampus_dynamics/converter.py

@@ -1,15 +1,13 @@
-from pathlib import Path
 from datetime import datetime
+from pathlib import Path
 from zoneinfo import ZoneInfo
 
 import numpy as np
-from scipy.io import loadmat as loadmat_scipy
-
 from neuroconv import NWBConverter
+from scipy.io import loadmat as loadmat_scipy
 
 from neuroconv.datainterfaces import NeuroScopeLFPInterface, NeuroScopeRecordingInterface
 
-# from laserpulsesinterface import ValeroLaserPulsesInterface
 from ripplesinterface import (
     HuszarProcessingRipplesEventsInterface,
 )
@@ -24,8 +22,7 @@
 from epochsinterface import HuszarEpochsInterface
 from trialsinterface import HuszarTrialsInterface
 
-
-from sortinginterface import CellExplorerSortingInterface
+from neuroconv.datainterfaces import CellExplorerSortingInterface
 
 
 class HuzsarNWBConverter(NWBConverter):
@@ -49,24 +46,6 @@ def __init__(self, source_data: dict, verbose: bool = True):
         self.session_folder_path = Path(self.data_interface_objects["Behavior8Maze"].source_data["folder_path"])
         self.session_id = self.session_folder_path.stem
 
-        # Add electrode locations (modeled after yutavcnwbconverter)
-        electrode_chan_map_file_path = self.session_folder_path / "chanMap.mat"
-        chan_map = loadmat_scipy(electrode_chan_map_file_path)
-        xcoords = [x[0] for x in chan_map["xcoords"]]
-        ycoords = [y[0] for y in chan_map["ycoords"]]
-        kcoords = [y[0] for y in chan_map["kcoords"]]
-
-        for channel_id in chan_map["chanMap0ind"]:
-            if self.data_interface_objects.get("LFP"):
-                self.data_interface_objects["LFP"].recording_extractor.set_channel_locations(
-                    locations=[xcoords[channel_id], ycoords[channel_id], kcoords[channel_id]], channel_ids=channel_id
-                )
-
-            if self.data_interface_objects.get("Recording"):
-                self.data_interface_objects["Recording"].recording_extractor.set_channel_locations(
-                    locations=[xcoords[channel_id], ycoords[channel_id], kcoords[channel_id]], channel_ids=channel_id
-                )
-
     def get_metadata(self):
         metadata = super().get_metadata()
         session_file = self.session_folder_path / f"{self.session_id}.session.mat"

buzsaki_lab_to_nwb/huszar_hippocampus_dynamics/requirements.txt

@@ -2,4 +2,5 @@ hdf5storage>=0.1.18
 neuroconv @ git+https://github.com/catalystneuro/neuroconv.git@main
 pymatreader==0.0.31
 ndx-events==0.2.0
-spikeinterface==0.97.1
+spikeinterface==0.97.1
+lxml==4.9.2

buzsaki_lab_to_nwb/huszar_hippocampus_dynamics/trialsinterface.py

@@ -11,15 +11,16 @@
 
 def access_behavior_property_safe(property, parent, behavior_mat):
     trial_info = behavior_mat["behavior"]["trials"]
-    nest_depth = len(trial_info["position_trcat"])
 
+    position_trcat = trial_info["position_trcat"]
     value = parent[property]
-    if nest_depth > 1:
+
+    if isinstance(position_trcat, list) and len(position_trcat) > 1:  # Check nest depth
         value = [num for sublist in value for num in sublist]  # Flatten the list if large depth
 
     assert len(value) == len(
         trial_info["recordings"]
-    )  # Save access properties should have the same length as the number of recordings
+    )  # Safe access properties should have the same length as the number of recordings
 
     return value