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## set up env via bash: | |
conda create -n stream_nwb -c conda-forge -y python=3.7 hdf5=1.12.0 jupyter pip | |
conda activate stream_nwb | |
pip install nwbwidgets | |
pip install git+https://github.com/NeurodataWithoutBorders/pynwb | |
pip install git+https://github.com/hdmf-dev/hdmf | |
git clone https://github.com/satra/h5py.git | |
cd h5py | |
HDF5_DIR=~/Users/bendichter/opt/anaconda3/envs/stream_nwb/ pip install --force-reinstall --no-binary=h5py . | |
## test out streaming | |
from pynwb import NWBHDF5IO | |
from nwbwidgets import nwb2widget | |
import requests | |
def get_s3_url(url): | |
s3_url = requests.request(url=url, method='head').url | |
return s3_url[:s3_url.index('?')] | |
path = "https://dandiarchive.s3.amazonaws.com/girder-assetstore/58/07/58074d0a5a4a4086afebb4d29912c419" | |
io = NWBHDF5IO(get_s3_url(url), mode='r', load_namespaces=True, driver='ros3') | |
nwb = io.read() | |
nwb2widget(nwb) |
we managed to make it work on a Binder deployment, if anyone is interested: https://github.com/catalystneuro/binder-nwb-stream
you may want to file an issue on conda-forge for hdf5-feedstock, if it is not being compiled on windows with ROS3 VFD support.
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I can reproduce the problem on my windows machine, with both conda-forge installation and manual installation of hdf5.
Seems to be a problem specific to windows. I found this, it might help (search for Windows): https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0-RELEASE.txt