[Bug]: Stimulus API group not finding all objects
Closed this issue · 3 comments
What happened?
I'm guessing there was a missed test case when the ability to add tables to the stimulus was enabled? I successfully created such files but upon reading them back through PyNWB for demonstration purposes, the stimulus group in the file read back does not find anything besides the classic TimeSeries descendants
Also confirmed the HDF5 file contained the desired objects
Steps to Reproduce
import dandi
import h5py
import remfile
import warnings
def read_dandi_file(asset: RemoteAsset) -> pynwb.NWBFile:
"""Remotely load the NWB file from a DANDI asset object."""
# Harmless warnings from PyNWB
warnings.filterwarnings(action="ignore", message="No cached namespaces found in .*")
warnings.filterwarnings(action="ignore", message="Ignoring cached namespace .*")
s3_url = asset.get_content_url()
byte_stream = remfile.File(url=s3_url)
file = h5py.File(name=byte_stream)
io = pynwb.NWBHDF5IO(file=file, mode="r", load_namespaces=True)
nwbfile = io.read()
return nwbfile
def read_visual_coding_ophys_file(dandiset: RemoteDandiset, session_id: str) -> pynwb.NWBFile:
"""Load the NWB file from DANDI given only the unique session ID in the Visual Coding - Optical Physiology dataset."""
asset = next(asset for asset in dandiset.get_assets() if f"ses-{session_id}" in asset.path)
return read_dandi_file(asset=asset)
dandiset_id = "000728"
client = DandiAPIClient()
dandiset = client.get_dandiset(dandiset_id=dandiset_id)
session_id_with_drifting_gratings = "501940850"
nwbfile_with_drifting_gratings = read_visual_coding_ophys_file(dandiset=dandiset, session_id=session_id_with_drifting_gratings)
list(nwbfile_with_drifting_gratings.stimulus.keys())
> ['natural_movie_one_stimulus', 'natural_movie_three_stimulus']
# but...
list(nwbfile_with_drifting_gratings._AbstractContainer__read_io._HDF5IO__file["stimulus"]["presentation"].keys())
> ['drifting_gratings', 'natural_movie_one_stimulus', 'natural_movie_three_stimulus', 'spontaneous_stimulus']Traceback
No response
Operating System
Windows
Python Executable
Conda
Python Version
3.11
Package Versions
PyNWB==2.6.0
Code of Conduct
- I agree to follow this project's Code of Conduct
- Have you checked the Contributing document?
- Have you ensured this bug was not already reported?
Also, neurosift link from which it is also visible: https://neurosift.app/?p=/nwb&url=https://api.dandiarchive.org/api/assets/67612f94-76e9-4da6-b58e-6bbca60650c6/download/&dandisetId=000728&dandisetVersion=draft
Also worth mentioning the missing objects aren't even found in nwbfile_with_drifting_gratings.objects either