NWB export fails
Opened this issue · 3 comments
daskandalis commented
Bug description
Expected behaviour
Export nwb format.
Actual behaviour
NWB fails with message:
Your personal set up
- OS:
Distributor ID: Ubuntu
Description: Ubuntu 23.10
Release: 23.10
Codename: mantic
- Version(s):
- SLEAP installation method (listed here):
Environment packages
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 1.0.0 pypi_0 pypi
alsa-lib 1.2.3.2 h166bdaf_0 conda-forge
astunparse 1.6.3 pypi_0 pypi
attrs 21.4.0 pyhd8ed1ab_0 conda-forge
backports-zoneinfo 0.2.1 pypi_0 pypi
blosc 1.21.5 h0f2a231_0 conda-forge
brotli 1.0.9 h166bdaf_9 conda-forge
brotli-bin 1.0.9 h166bdaf_9 conda-forge
brunsli 0.1 h9c3ff4c_0 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.27.0 hd590300_0 conda-forge
c-blosc2 2.13.2 hb4ffafa_0 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 4.2.4 pypi_0 pypi
cairo 1.16.0 h6cf1ce9_1008 conda-forge
cattrs 1.1.1 pyhd8ed1ab_0 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cfitsio 4.0.0 h9a35b8e_0 conda-forge
charls 2.3.4 h9c3ff4c_0 conda-forge
charset-normalizer 2.0.9 pypi_0 pypi
cloudpickle 2.2.1 pyhd8ed1ab_0 conda-forge
cuda-nvcc 11.3.58 h2467b9f_0 nvidia
cudatoolkit 11.3.1 hb98b00a_13 conda-forge
cudnn 8.2.1.32 h86fa8c9_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cytoolz 0.12.0 py37h540881e_0 conda-forge
dask-core 2022.2.0 pyhd8ed1ab_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
efficientnet 1.0.0 pypi_0 pypi
expat 2.6.1 h59595ed_0 conda-forge
ffmpeg 4.3.2 h37c90e5_3 conda-forge
flatbuffers 2.0 pypi_0 pypi
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonttools 4.38.0 py37h540881e_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
fsspec 2023.1.0 pyhd8ed1ab_0 conda-forge
gast 0.4.0 pypi_0 pypi
geos 3.11.0 h27087fc_0 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
gmp 6.3.0 h59595ed_1 conda-forge
gnutls 3.6.13 h85f3911_1 conda-forge
google-auth 2.3.3 pypi_0 pypi
google-auth-oauthlib 0.4.6 pypi_0 pypi
google-pasta 0.2.0 pypi_0 pypi
graphite2 1.3.13 h58526e2_1001 conda-forge
grpcio 1.43.0 pypi_0 pypi
gst-plugins-base 1.18.5 hf529b03_3 conda-forge
gstreamer 1.18.5 h9f60fe5_3 conda-forge
h5py 3.1.0 nompi_py37h1e651dc_100 conda-forge
harfbuzz 2.9.1 h83ec7ef_1 conda-forge
hdf5 1.10.6 nompi_h6a2412b_1114 conda-forge
icu 68.2 h9c3ff4c_0 conda-forge
idna 3.3 pypi_0 pypi
image-classifiers 1.0.0 pypi_0 pypi
imagecodecs 2021.11.20 py37h119f88a_2 conda-forge
imageio 2.34.0 pyh4b66e23_0 conda-forge
imgaug 0.4.0 pyhd8ed1ab_1 conda-forge
imgstore 0.2.9 pypi_0 pypi
importlib-metadata 4.2.0 pypi_0 pypi
importlib-resources 5.12.0 pypi_0 pypi
jasper 1.900.1 h07fcdf6_1006 conda-forge
joblib 1.3.2 pyhd8ed1ab_0 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
jsmin 3.0.1 pyhd8ed1ab_0 conda-forge
jsonpickle 1.2 py_0 conda-forge
jsonschema 4.17.3 pypi_0 pypi
jxrlib 1.1 hd590300_3 conda-forge
keras 2.7.0 pypi_0 pypi
keras-applications 1.0.8 pypi_0 pypi
keras-preprocessing 1.1.2 pypi_0 pypi
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.4 py37h7cecad7_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lame 3.100 h166bdaf_1003 conda-forge
lcms2 2.14 h6ed2654_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libaec 1.1.2 h59595ed_1 conda-forge
libblas 3.9.0 20_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_9 conda-forge
libbrotlidec 1.0.9 h166bdaf_9 conda-forge
libbrotlienc 1.0.9 h166bdaf_9 conda-forge
libcblas 3.9.0 20_linux64_openblas conda-forge
libclang 12.0.0 pypi_0 pypi
libcurl 7.86.0 h7bff187_1 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.10 h9b69904_4 conda-forge
libexpat 2.6.1 h59595ed_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_5 conda-forge
libgfortran-ng 13.2.0 h69a702a_5 conda-forge
libgfortran5 13.2.0 ha4646dd_5 conda-forge
libglib 2.78.4 hf2295e7_4 conda-forge
libgomp 13.2.0 h807b86a_5 conda-forge
libiconv 1.17 hd590300_2 conda-forge
liblapack 3.9.0 20_linux64_openblas conda-forge
liblapacke 3.9.0 20_linux64_openblas conda-forge
libllvm11 11.1.0 he0ac6c6_5 conda-forge
libnghttp2 1.51.0 hdcd2b5c_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.4 h7f98852_1 conda-forge
libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge
libopencv 4.5.1 py37h90094e2_0 conda-forge
libopus 1.3.1 h7f98852_1 conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libpq 13.8 hd77ab85_0 conda-forge
libprotobuf 3.21.8 h6239696_0 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsqlite 3.45.1 h2797004_0 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
libtiff 4.4.0 h0fcbabc_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libwebp-base 1.3.2 hd590300_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.12 h72842e0_0 conda-forge
libxslt 1.1.33 h15afd5d_2 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
libzopfli 1.0.3 h9c3ff4c_0 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
markdown 3.3.6 pypi_0 pypi
markdown-it-py 2.2.0 pyhd8ed1ab_0 conda-forge
matplotlib-base 3.5.3 py37hf395dca_2 conda-forge
mdurl 0.1.2 pyhd8ed1ab_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
mysql-common 8.0.32 h14678bc_0 conda-forge
mysql-libs 8.0.32 h54cf53e_0 conda-forge
ncurses 6.4 h59595ed_2 conda-forge
ndx-pose 0.1.1 pypi_0 pypi
nettle 3.6 he412f7d_0 conda-forge
networkx 2.6.3 pyhd8ed1ab_1 conda-forge
nixio 1.5.3 pypi_0 pypi
nspr 4.35 h27087fc_0 conda-forge
nss 3.98 h1d7d5a4_0 conda-forge
numpy 1.19.5 pypi_0 pypi
oauthlib 3.1.1 pypi_0 pypi
opencv 4.5.1 py37h89c1867_0 conda-forge
opencv-python-headless 4.2.0.34 pypi_0 pypi
openh264 2.1.1 h780b84a_0 conda-forge
openjpeg 2.5.0 h7d73246_1 conda-forge
openssl 1.1.1w hd590300_0 conda-forge
opt-einsum 3.3.0 pypi_0 pypi
packaging 21.3 pypi_0 pypi
pandas 1.3.5 py37he8f5f7f_0 conda-forge
partd 1.4.1 pyhd8ed1ab_0 conda-forge
patsy 0.5.6 pyhd8ed1ab_0 conda-forge
pcre2 10.43 hcad00b1_0 conda-forge
pillow 9.2.0 py37h850a105_2 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pixman 0.43.2 h59595ed_0 conda-forge
pkgutil-resolve-name 1.3.10 pypi_0 pypi
protobuf 3.19.1 pypi_0 pypi
psutil 5.9.3 py37h540881e_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
py-opencv 4.5.1 py37h888b3d9_0 conda-forge
pyasn1 0.4.8 pypi_0 pypi
pyasn1-modules 0.2.8 pypi_0 pypi
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pykalman 0.9.5 py_1 conda-forge
pynwb 2.3.3 pypi_0 pypi
pyparsing 3.0.6 pypi_0 pypi
pyrsistent 0.19.3 pypi_0 pypi
pyside2 5.13.2 py37hfa98aef_7 conda-forge
python 3.7.12 hb7a2778_100_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-rapidjson 1.9 py37hd23a5d3_0 conda-forge
python_abi 3.7 4_cp37m conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pywavelets 1.3.0 py37hda87dfa_1 conda-forge
pyyaml 6.0 py37h540881e_4 conda-forge
pyzmq 24.0.1 py37h0c0c2a8_0 conda-forge
qimage2ndarray 1.10.0 pypi_0 pypi
qt 5.12.9 hda022c4_4 conda-forge
qtpy 2.4.1 pyhd8ed1ab_0 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.26.0 pypi_0 pypi
requests-oauthlib 1.3.0 pypi_0 pypi
rich 13.7.1 pyhd8ed1ab_0 conda-forge
ruamel-yaml 0.17.32 pypi_0 pypi
ruamel-yaml-clib 0.2.7 pypi_0 pypi
scikit-image 0.19.3 py37hfb7772e_1 conda-forge
scikit-learn 1.0 py37hf0f1638_1 conda-forge
scikit-video 1.1.11 pyh24bf2e0_0 conda-forge
scipy 1.7.3 py37hf2a6cf1_0 conda-forge
seaborn 0.12.2 hd8ed1ab_0 conda-forge
seaborn-base 0.12.2 pyhd8ed1ab_0 conda-forge
segmentation-models 1.0.1 pypi_0 pypi
setuptools 59.8.0 py37h89c1867_1 conda-forge
setuptools-scm 6.3.2 pypi_0 pypi
shapely 1.8.5 py37ha4e3bd1_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sleap 1.3.3 pypi_0 pypi
snappy 1.1.10 h9fff704_0 conda-forge
sqlite 3.45.1 h2c6b66d_0 conda-forge
statsmodels 0.13.2 py37hda87dfa_0 conda-forge
tensorboard 2.7.0 pypi_0 pypi
tensorboard-data-server 0.6.1 pypi_0 pypi
tensorboard-plugin-wit 1.8.0 pypi_0 pypi
tensorflow 2.7.0 pypi_0 pypi
tensorflow-estimator 2.7.0 pypi_0 pypi
tensorflow-hub 0.13.0 pyh56297ac_0 conda-forge
tensorflow-io-gcs-filesystem 0.23.1 pypi_0 pypi
termcolor 1.1.0 pypi_0 pypi
threadpoolctl 3.1.0 pyh8a188c0_0 conda-forge
tifffile 2021.11.2 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.0.0 pypi_0 pypi
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
typing-extensions 4.0.1 pypi_0 pypi
typing_extensions 4.7.1 pyha770c72_0 conda-forge
tzlocal 5.0.1 pypi_0 pypi
unicodedata2 14.0.0 py37h540881e_1 conda-forge
urllib3 1.26.7 pypi_0 pypi
werkzeug 2.0.2 pypi_0 pypi
wheel 0.42.0 pyhd8ed1ab_0 conda-forge
wrapt 1.13.3 pypi_0 pypi
x264 1!161.3030 h7f98852_1 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.1.1 hd590300_0 conda-forge
xorg-libsm 1.2.4 h7391055_0 conda-forge
xorg-libx11 1.8.4 h0b41bf4_0 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zeromq 4.3.5 h59595ed_1 conda-forge
zfp 0.5.5 h9c3ff4c_8 conda-forge
zipp 3.15.0 pypi_0 pypi
zlib 1.2.13 hd590300_5 conda-forge
zlib-ng 2.0.7 h0b41bf4_0 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
Logs
Could not find the file specified: /home/user/<save directory>/<save filename>.slp.nwb
Screenshots
How to reproduce
File > Export NWB... > save with defaults
talmo commented
Hi @daskandalis,
This should definitely work, so I suspect there's something funky going on here. Do you mind sharing the SLP file so we can troubleshoot?
Thanks!
Talmo
daskandalis commented
This does not work on any sleap project I have created, and should be testable on e.g. the slp file uploaded in this discussion.
talmo commented
Hi @daskandalis,
I tried looking up the project from #1893 but it seems to have been deleted after we did the troubleshooting. I'm guessing it was a training package though given the context.
Currently we can't export training data to NWB as it hasn't supported saving arbitrary frames, as it was originally designed to store tracked predictions/inference outputs.
We've worked with the NWB team to add support for the equivalent of SLEAP Labels and training packages, but we're not quite done.
We're hoping to fully support this through sleap-io soon and within core SLEAP by the end of the year 🤞.
Let us know if you have any questions!
Cheers,
Talmo
Relevant references: