git fetch -q --tags did not run successfully (related to add_ignore_timestamps_errors_to_interface)

[laurelrr]

I got an error while trying @weiglszonja's steps in #34 (comment) to create a new fresh environment:

conda create --name tyenwb39 python=3.9
conda activate tyenwb39
pip install -r src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_requirements.txt

gave this error:

(tyenwb39) lkeyes@node32:/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb$ pip install -r src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_requirements.txt
Obtaining neuroconv from git+https://github.com/catalystneuro/neuroconv@add_ignore_timestamps_errors_to_interface#egg=neuroconv (from -r src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_requirements.txt (line 1))
  Updating ./src/neuroconv clone (to revision add_ignore_timestamps_errors_to_interface)
  Running command git fetch -q --tags
  fatal: pack has 5 unresolved deltas
  fatal: index-pack failed
  error: subprocess-exited-with-error

  × git fetch -q --tags did not run successfully.
  │ exit code: 128
  ╰─> See above for output.

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× git fetch -q --tags did not run successfully.
│ exit code: 128
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

I attempted to pip uninstall neuroconv but it is not installed in this environment.

This is what is in my current neurotensin_valence_requirements.txt:

-e git+https://github.com/catalystneuro/neuroconv@add_ignore_timestamps_errors_to_interface#egg=neuroconv
neuroconv[openephys,plexon,video]
git+https://github.com/neuralensemble/python-neo@master
ndx_pose>=0.1.1
oiffile==2022.9.29
easydict>=1.10
openpyxl>=3.1.2

[weiglszonja]

@laurelrr I haven't seen this error before, looks like it installed neuroconv inside the project folder and now it's having troubles updating it. I you have a neuroconv folder at /snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb/src/neuroconv can you try deleting it first?
And then can you try to remove the -e flag in neurotensin_valence_requirements.txt, so the file should look like this:

git+https://github.com/catalystneuro/neuroconv@add_ignore_timestamps_errors_to_interface#egg=neuroconv
neuroconv[openephys,plexon,video]
git+https://github.com/neuralensemble/python-neo@master
ndx_pose>=0.1.1
oiffile==2022.9.29
easydict>=1.10
openpyxl>=3.1.2

and repeat

conda create --name tyenwbenv39 python=3.9
conda activate tyenwbenv39
pip install -r src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_requirements.txt
pip install -e .
python src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_convert_session.py

[laurelrr]

Thank you, I actually seemed to have two neuroconv folders installed for some reason. Anyway, I uninstalled both and applied your suggestions. It installed properly and I updated the neurotensin_valence_convert_session.py file to point to my example and ran python src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_convert_session.py

I received an error:

(tyenwbenv39) lkeyes@node32:/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb$ python src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_convert_session.py
Source data is valid!
Metadata is valid!
conversion_options is valid!
/home/lkeyes/anaconda3/envs/tyenwbenv39/lib/python3.9/site-packages/pynwb/file.py:471: UserWarning: Date is missing timezone information. Updating to local timezone.
  args_to_set['session_start_time'] = _add_missing_timezone(session_start_time)
/nadata/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb/src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_convert_session.py:203: UserWarning: There was an error during the conversion of /nadata/snlkt/data/hao/Neurotensin/NWB/nwbfiles/H41_Disc5_manual.nwb. The full traceback: The video file is not open!
  warn(f"There was an error during the conversion of {nwbfile_path}. The full traceback: {e}")

This is the error log text:

(tyenwbenv39) lkeyes@node32:/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb$ cat /snlkt/data/hao/Neurotensin/NWB/nwbfiles/H41_Disc5_manual_error_log.txt
Traceback (most recent call last):
  File "/nadata/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb/src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_convert_session.py", line 186, in session_to_nwb
    converter.run_conversion(
  File "/nadata/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb/src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valencenwbconverter.py", line 56, in run_conversion
    super().run_conversion(
  File "/home/lkeyes/anaconda3/envs/tyenwbenv39/lib/python3.9/site-packages/neuroconv/nwbconverter.py", line 160, in run_conversion
    self.add_to_nwbfile(nwbfile_out, metadata, conversion_options)
  File "/home/lkeyes/anaconda3/envs/tyenwbenv39/lib/python3.9/site-packages/neuroconv/nwbconverter.py", line 114, in add_to_nwbfile
    data_interface.add_to_nwbfile(
  File "/home/lkeyes/anaconda3/envs/tyenwbenv39/lib/python3.9/site-packages/neuroconv/datainterfaces/behavior/video/videodatainterface.py", line 337, in add_to_nwbfile
    rate = video.get_video_fps()
  File "/home/lkeyes/anaconda3/envs/tyenwbenv39/lib/python3.9/site-packages/neuroconv/datainterfaces/behavior/video/video_utils.py", line 61, in get_video_fps
    assert self.isOpened(), self._video_open_msg
AssertionError: The video file is not open!

I do have a whitespace character in the movie filename original_video_file_path = "/nadata/snlkt/data/hao/Neurotensin/ephys/recordings/PVT-BLA_NT_KO_CeMproj batch3/videos/H41Disc5.mkv". Would this cause this issue?

[weiglszonja]

It could be the whitespace, can you try this in the single session conversion script? (easier to modify there) If it doesn't work, can you share this video with us and I'm going to take a closer look.

[laurelrr]

Here is the single session conversion script:

"""Primary script to run to convert an entire session for of data using the NWBConverter."""
import traceback
from importlib.metadata import version
from pathlib import Path
from typing import Optional, Dict
from warnings import warn

from dateutil import parser

from neuroconv.utils import (
    load_dict_from_file,
    dict_deep_update,
    FilePathType,
    FolderPathType,
)
from nwbinspector import inspect_nwbfile
from nwbinspector.inspector_tools import save_report, format_messages
from packaging.version import Version

from tye_lab_to_nwb.neurotensin_valence import NeurotensinValenceNWBConverter


def session_to_nwb(
    nwbfile_path: FilePathType,
    ecephys_recording_folder_path: Optional[FolderPathType] = None,
    subject_metadata: Optional[Dict[str, str]] = None,
    plexon_file_path: Optional[FilePathType] = None,
    events_file_path: Optional[FilePathType] = None,
    pose_estimation_file_path: Optional[FilePathType] = None,
    pose_estimation_config_file_path: Optional[FilePathType] = None,
    pose_estimation_sampling_rate: Optional[float] = None,
    session_start_time: Optional[str] = None,
    original_video_file_path: Optional[FilePathType] = None,
    labeled_video_file_path: Optional[FilePathType] = None,
    confocal_images_oif_file_path: Optional[FilePathType] = None,
    confocal_images_composite_tif_file_path: Optional[FilePathType] = None,
    stub_test: bool = False,
):
    """
    Converts a single session to NWB.

    Parameters
    ----------
    nwbfile_path : FilePathType
        The file path to the NWB file that will be created.
    ecephys_recording_folder_path: FolderPathType
         The path that points to the folder where the OpenEphys (.continuous) files are located.
    subject_metadata: dict, optional
        The optional metadata for the experimental subject.
    plexon_file_path: FilePathType, optional
        The path that points to the Plexon (.plx) file that contains the spike times.
    events_file_path: FilePathType, optional
        The path that points to the .mat file that contains the event onset and offset times.
    pose_estimation_file_path: FilePathType, optional
        The path that points to the .csv file that contains the DLC output.
    pose_estimation_config_file_path: FilePathType, optional
        The path that points to the .pickle file that contains the DLC configuration settings.
    original_video_file_path: FilePathType, optional
        The path that points to the original behavior movie that was used for pose estimation.
    labeled_video_file_path: FilePathType, optional
        The path that points to the labeled behavior movie.
    confocal_images_oif_file_path: FilePathType, optional
        The path that points to the Olympus Image File (.oif).
    confocal_images_composite_tif_file_path: FilePathType, optional
        The path that points to the TIF image that contains the confocal images aggregated over depth.
    stub_test: bool, optional
        For testing purposes, when stub_test=True only writes a subset of ecephys and plexon data.
        Default is to write the whole ecephys recording and plexon data to the file.
    """

    source_data = dict()
    conversion_options = dict()

    # Add Recording
    if ecephys_recording_folder_path:
        recording_source_data = dict(folder_path=str(ecephys_recording_folder_path), stream_name="Signals CH")
        if Version(version("neo")) > Version("0.12.0"):
            recording_source_data.update(ignore_timestamps_errors=True)

        source_data.update(dict(Recording=recording_source_data))
        conversion_options.update(dict(Recording=dict(stub_test=stub_test)))

    # Add Sorting (optional)
    if plexon_file_path:
        source_data.update(dict(Sorting=dict(file_path=str(plexon_file_path))))
        conversion_options.update(dict(Sorting=dict(stub_test=stub_test)))

    # Add Behavior (optional)
    # Add events
    if events_file_path:
        event_names_mapping = {
            0: "reward_stimulus_presentation",
            1: "phototagging",
            2: "shock_stimulus_presentation",
            3: "reward_delivery",
            4: "shock_relay",
            5: "port_entry",
            6: "neutral_stimulus_presentation",
        }
        read_kwargs = dict(event_names_mapping=event_names_mapping)
        events_source_data = dict(file_path=str(events_file_path), read_kwargs=read_kwargs)
        source_data.update(dict(Events=events_source_data))

        events_column_mappings = dict(onset="start_time", offset="stop_time")
        events_conversion_options = dict(column_name_mapping=events_column_mappings)
        conversion_options.update(
            dict(
                Events=events_conversion_options,
            )
        )

    # Add pose estimation (optional)
    pose_estimation_source_data = dict()
    pose_estimation_conversion_options = dict()
    if pose_estimation_file_path:
        pose_estimation_source_data.update(file_path=str(pose_estimation_file_path))
        if pose_estimation_config_file_path:
            pose_estimation_source_data.update(config_file_path=str(pose_estimation_config_file_path))
        elif pose_estimation_sampling_rate is not None:
            pose_estimation_conversion_options.update(rate=float(pose_estimation_sampling_rate))

        source_data.update(dict(PoseEstimation=pose_estimation_source_data))

    if original_video_file_path:
        pose_estimation_conversion_options.update(original_video_file_path=original_video_file_path)
        source_data.update(
            dict(
                OriginalVideo=dict(file_paths=[str(original_video_file_path)]),
            )
        )
    if labeled_video_file_path:
        pose_estimation_conversion_options.update(labeled_video_file_path=labeled_video_file_path)

    if pose_estimation_source_data:
        # The edges between the nodes (e.g. labeled body parts) defined as array of pairs of indices.
        edges = [(0, 1), (0, 2), (2, 3), (1, 3), (5, 6), (5, 7), (5, 8), (5, 9)]
        pose_estimation_conversion_options.update(edges=edges)
        conversion_options.update(dict(PoseEstimation=pose_estimation_conversion_options))

    # Add confocal images
    images_source_data = dict()
    if confocal_images_oif_file_path:
        images_source_data.update(file_path=str(confocal_images_oif_file_path))
        if confocal_images_composite_tif_file_path:
            images_source_data.update(composite_tif_file_path=str(confocal_images_composite_tif_file_path))

        source_data.update(dict(Images=images_source_data))

    converter = NeurotensinValenceNWBConverter(source_data=source_data)

    # Add datetime to conversion
    metadata = converter.get_metadata()

    # Update default metadata with the editable in the corresponding yaml file
    editable_metadata_path = Path(__file__).parent / "metadata" / "general_metadata.yaml"
    editable_metadata = load_dict_from_file(editable_metadata_path)
    metadata = dict_deep_update(metadata, editable_metadata)

    if subject_metadata:
        metadata = dict_deep_update(metadata, dict(Subject=subject_metadata))

    if "session_id" not in metadata["NWBFile"]:
        if ecephys_recording_folder_path:
            ecephys_recording_folder_path = Path(ecephys_recording_folder_path)
            ecephys_folder_name = ecephys_recording_folder_path.name
            session_id = ecephys_folder_name.replace(" ", "").replace("_", "-")
        elif pose_estimation_file_path:
            session_id = Path(pose_estimation_file_path).name.replace(" ", "").replace("_", "-")
        else:
            session_id = Path(nwbfile_path).stem.replace(" ", "").replace("_", "-")

        metadata["NWBFile"].update(session_id=session_id)

    if "session_start_time" not in metadata["NWBFile"]:
        if session_start_time is None:
            raise ValueError(
                "When ecephys recording is not specified the start time of the session must be provided."
                "Specify session_start_time in YYYY-MM-DDTHH:MM:SS format (e.g. 2023-08-21T15:30:00)."
            )
        session_start_time_dt = parser.parse(session_start_time)
        metadata["NWBFile"].update(session_start_time=session_start_time_dt)

    nwbfile_path = Path(nwbfile_path)
    try:
        # Run conversion
        converter.run_conversion(
            nwbfile_path=str(nwbfile_path), metadata=metadata, conversion_options=conversion_options
        )

        # Run inspection for nwbfile
        results = list(inspect_nwbfile(nwbfile_path=nwbfile_path))
        report_path = nwbfile_path.parent / f"{nwbfile_path.stem}_inspector_result.txt"
        save_report(
            report_file_path=report_path,
            formatted_messages=format_messages(
                results,
                levels=["importance", "file_path"],
            ),
        )
    except Exception as e:
        with open(f"{nwbfile_path.parent}/{nwbfile_path.stem}_error_log.txt", "w") as f:
            f.write(traceback.format_exc())
        warn(f"There was an error during the conversion of {nwbfile_path}. The full traceback: {e}")


if __name__ == "__main__":
    # Parameters for conversion
    # The path that points to the folder where the OpenEphys (.continuous) files are located.
    ecephys_folder_path = Path("/nadata/snlkt/data/hao/Neurotensin/ephys/recordings/forLaurel/H41_2020-04-29_16-55-26_Disc5_9")

    # The path that points to the Plexon file (optional)
    # plexon_file_path = None
    plexon_file_path = Path("/nadata/snlkt/data/hao/Neurotensin/ephys/recordings/forLaurel/H41_2020-04-29_16-55-26_Disc5_9/0041_20200430_9.plx")

    # Parameters for events data (optional)
    # The file path that points to the events.mat file
    # events_mat_file_path = None
    events_mat_file_path = Path(
        "/nadata/snlkt/data/hao/Neurotensin/ephys/recordings/forLaurel/H41_2020-04-29_16-55-26_Disc5_9/0041_20200430_9_events.mat"
    )

    # Parameters for pose estimation data (optional)
    # The file path that points to the DLC output (.CSV file)
    # pose_estimation_file_path = None
    pose_estimation_file_path = (
        "/nadata/snlkt/data/hao/Neurotensin/DLC/DLCresults/41_Disc5DLC_resnet50_Hao_MedPC_ephysFeb9shuffle1_800000.csv"
    )
    # The file path that points to the DLC configuration file (.pickle file), optional
    # pose_estimation_config_file_path = None
    pose_estimation_config_file_path = (
        "/nadata/snlkt/data/hao/Neurotensin/DLC/DLCresults/H41Disc5DLC_resnet50_Hao_MedPC_ephysFeb9shuffle1_800000includingmetadata.pickle"
    )
    # If the pickle file is not available the sampling rate in units of Hz for the behavior data must be provided.
    pose_estimation_sampling_rate = None

    # For sessions where only the pose estimation data is available the start time of the session must be provided.
    # The session_start_time in YYYY-MM-DDTHH:MM:SS format (e.g. 2023-08-21T15:30:00).
    session_start_time = None

    # The file path that points to the behavior movie file, optional
    # original_video_file_path = None
    original_video_file_path = r"/nadata/snlkt/data/hao/Neurotensin/ephys/recordings/PVT-BLA_NT_KO_CeMproj batch3/videos/H41Disc5.mkv"
    # The file path that points to the labeled behavior movie file, optional
    # labeled_video_file_path = None
    labeled_video_file_path = "/nadata/snlkt/data/hao/Neurotensin/DLC/DLCresults/H41Disc5DLC_resnet50_Hao_MedPC_ephysFeb9shuffle1_800000_labeled.mp4"

    # Parameters for histology images (optional)
    # The file path to the Olympus Image File (.oif)
    confocal_images_oif_file_path = "/nadata/snlkt/data/hao/Neurotensin/Imaging/H21-H42/H41PVT_40x.oif"
    # The file path to the aggregated confocal images in TIF format.
    # confocal_images_composite_tif_file_path = None
    confocal_images_composite_tif_file_path = r"/snlkt/data/hao/Neurotensin/CellProfiler/NT CRISPR/channel merged/H41_MAX_Composite.tif"

    # The file path where the NWB file will be created.
    nwbfile_path = Path("/nadata/snlkt/data/hao/Neurotensin/NWB/nwbfiles/H41_Disc5_manual.nwb")

    # For faster conversion, stub_test=True would only write a subset of ecephys and plexon data.
    # When running a full conversion, use stub_test=False.
    stub_test = False

    # subject metadata (optional)
    subject_metadata = dict(sex="M",age="P60D",genotype="Wild type",strain="C57BL/6J")

    session_to_nwb(
        nwbfile_path=nwbfile_path,
        ecephys_recording_folder_path=ecephys_folder_path,
        subject_metadata=subject_metadata,
        plexon_file_path=plexon_file_path,
        events_file_path=events_mat_file_path,
        pose_estimation_file_path=pose_estimation_file_path,
        pose_estimation_config_file_path=pose_estimation_config_file_path,
        pose_estimation_sampling_rate=pose_estimation_sampling_rate,
        session_start_time=session_start_time,
        original_video_file_path=original_video_file_path,
        labeled_video_file_path=labeled_video_file_path,
        confocal_images_oif_file_path=confocal_images_oif_file_path,
        confocal_images_composite_tif_file_path=confocal_images_composite_tif_file_path,
        stub_test=stub_test,
    )

I have the same error:

(tyenwbenv39) lkeyes@node32:~/Projects/GIT/tye-lab-to-nwb$ python src/tye_lab_to_nwb/neurotensin_valence/neurote                                                                                  nsin_valence_convert_session.py
Source data is valid!
Metadata is valid!
conversion_options is valid!
/home/lkeyes/anaconda3/envs/tyenwbenv39/lib/python3.9/site-packages/pynwb/file.py:471: UserWarning: Date is missing timezone information. Updating to local timezone.
  args_to_set['session_start_time'] = _add_missing_timezone(session_start_time)
/nadata/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb/src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_convert_session.py:203: UserWarning: There was an error during the conversion of /nadata/snlkt/data/hao/Neurotensin/NWB/nwbfiles/H41_Disc5_manual.nwb. The full traceback: The video file is not open!
  warn(f"There was an error during the conversion of {nwbfile_path}. The full traceback: {e}")

I will upload the video via Globus shortly.

[laurelrr]

Also, this is the log output:

(tyenwbenv39) lkeyes@node32:~/Projects/GIT/tye-lab-to-nwb$ cat /snlkt/data/hao/Neurotensin/NWB/nwbfiles/H41_Disc5_manual_error_log.txt
Traceback (most recent call last):
  File "/nadata/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb/src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valence_convert_session.py", line 186, in session_to_nwb
    converter.run_conversion(
  File "/nadata/snlkt/home/lkeyes/Projects/GIT/tye-lab-to-nwb/src/tye_lab_to_nwb/neurotensin_valence/neurotensin_valencenwbconverter.py", line 56, in run_conversion
    super().run_conversion(
  File "/home/lkeyes/anaconda3/envs/tyenwbenv39/lib/python3.9/site-packages/neuroconv/nwbconverter.py", line 160, in run_conversion
    self.add_to_nwbfile(nwbfile_out, metadata, conversion_options)
  File "/home/lkeyes/anaconda3/envs/tyenwbenv39/lib/python3.9/site-packages/neuroconv/nwbconverter.py", line 114, in add_to_nwbfile
    data_interface.add_to_nwbfile(
  File "/home/lkeyes/anaconda3/envs/tyenwbenv39/lib/python3.9/site-packages/neuroconv/datainterfaces/behavior/video/videodatainterface.py", line 337, in add_to_nwbfile
    rate = video.get_video_fps()
  File "/home/lkeyes/anaconda3/envs/tyenwbenv39/lib/python3.9/site-packages/neuroconv/datainterfaces/behavior/video/video_utils.py", line 61, in get_video_fps
    assert self.isOpened(), self._video_open_msg
AssertionError: The video file is not open!

[laurelrr]

Ah! This was my mistake. I had the wrong file extension listed. (We have a mixture of .mkv and .asf videos across subjects.)
It is running now.