skip video if missing

src/datta_lab_to_nwb/markowitz_gillis_nature_2023/basevideointerface.py

@@ -1,17 +1,17 @@
 """Base class for converting raw video data."""
-from pynwb import NWBFile
-from datetime import datetime
-from pytz import timezone
-import h5py
+from pathlib import Path
+
 import numpy as np
 import pandas as pd
+from pynwb import NWBFile
 from neuroconv.datainterfaces import VideoInterface
+
 from .basedattainterface import BaseDattaInterface
 from .utils import convert_timestamps_to_seconds
 
 
 class BaseVideoInterface(BaseDattaInterface):
-    """Base video interface for markowitz_gillis_nature_2023 conversion"""
+    """Base video interface for markowitz_gillis_nature_2023 conversion."""
 
     def __init__(
         self,
@@ -51,6 +51,9 @@ def align_timestamps(self, metadata: dict) -> np.ndarray:
     def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict) -> None:
         timestamps = self.align_timestamps(metadata=metadata)
 
+        if not Path(self.source_data["data_path"]).exists():
+            return
+
         video_interface = VideoInterface(file_paths=[self.source_data["data_path"]], verbose=True)
         video_interface.set_aligned_timestamps(aligned_timestamps=[timestamps])
         video_interface.add_to_nwbfile(

src/datta_lab_to_nwb/markowitz_gillis_nature_2023/convert_dataset.py

@@ -101,7 +101,7 @@ def dataset_to_nwb(
         folder
         for folder in raw_dir_path.iterdir()
         if folder.is_dir() and folder.name not in skip_experiments and folder.name.startswith("_")
-    ][11:]
+    ]
     for experimental_folder in tqdm(
         iterable=experimental_folders, position=0, desc="Converting experiments...", leave=False
     ):
@@ -157,7 +157,7 @@ def dataset_to_nwb(
 
 
 if __name__ == "__main__":
-    number_of_jobs = 2
+    number_of_jobs = 1
 
     processed_path = Path("E:/Datta/dopamine-reinforces-spontaneous-behavior")
     raw_dir_path = Path("E:/Datta")

src/datta_lab_to_nwb/markowitz_gillis_nature_2023/convert_session.py

@@ -53,9 +53,7 @@ def session_to_nwb(
     session_id = f"{experiment_type}-{session_uuid}"
 
     nwbfile_path = output_dir_path / f"{session_id}.nwb"
-    if (
-        nwbfile_path.parent.parent / "initial_nwbfiles" / nwbfile_path.name
-    ).exists() or nwbfile_path.exists():  # temporary
+    if nwbfile_path.exists():
         return
 
     photometry_path = processed_path / "dlight_raw_data/dlight_photometry_processed_full.parquet"