NWB export fails

[daskandalis]

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):
  • Conda from package
  • Conda from source
  • pip package
  • Apple Silicon Macs

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]

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]

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]

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:

• Notes from discussion regarding training input rly/ndx-pose#8
• Initial implementation of a PoseTraining Group rly/ndx-pose#9
• Update PoseTraining types rly/ndx-pose#21
• Enhance training dataset format support rly/ndx-pose#24
• Adding support for more .nwb training data to SLEAP sleap-io#104