sleap
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Published
20 hours ago •
talmolab
talmolab
Possibility to save training visualization images
Bug description
There is apparently no working way to save the images shown during the training of models. I have tried manually editing the training_config.json fields save_visualizations and delete_viz_images to True and False, respectively, before training, but after training is completed both appear as True....and of course the viz folder is gone.
Expected behaviour
Both training and validation images used during training are saved to defined folder.
Actual behaviour
Images are displayed during training but not saved.
Your personal set up
- OS: Linux-5.4.0-131-generic-x86_64-with-debian-bullseye-sid (Linux Mint 20.2)
- Version(s): SLEAP: 1.2.8 TensorFlow: 2.6.3 Numpy: 1.19.5 Python: 3.7.12
- SLEAP installation method (listed here):
- [X] Conda from package
- [ ] Conda from source
- [ ] pip package
- [ ] M1 Macs
Environment packages
# packages in environment at /home/auesro/mambaforge/envs/Sleap:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 0.15.0 pypi_0 pypi
aom 3.3.0 h27087fc_1 conda-forge
astunparse 1.6.3 pypi_0 pypi
attrs 21.2.0 pypi_0 pypi
backports-zoneinfo 0.2.1 pypi_0 pypi
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2022.9.24 ha878542_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
cattrs 1.1.1 pypi_0 pypi
certifi 2021.10.8 pypi_0 pypi
charset-normalizer 2.0.12 pypi_0 pypi
clang 5.0 pypi_0 pypi
colorama 0.4.5 pypi_0 pypi
commonmark 0.9.1 pypi_0 pypi
cuda-nvcc 11.3.58 h2467b9f_0 nvidia
cudatoolkit 11.3.1 ha36c431_9 nvidia
cudnn 8.2.1.32 h86fa8c9_0 conda-forge
cycler 0.11.0 pypi_0 pypi
efficientnet 1.0.0 pypi_0 pypi
ffmpeg 5.0.1 h594f047_1 conda-forge
flatbuffers 1.12 pypi_0 pypi
fonttools 4.37.1 pypi_0 pypi
freetype 2.10.4 h0708190_1 conda-forge
gast 0.4.0 pypi_0 pypi
geos 3.9.1 h9c3ff4c_2 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
gnutls 3.6.13 h85f3911_1 conda-forge
google-auth 1.35.0 pypi_0 pypi
google-auth-oauthlib 0.4.6 pypi_0 pypi
google-pasta 0.2.0 pypi_0 pypi
grpcio 1.44.0 pypi_0 pypi
h5py 3.1.0 nompi_py37h1e651dc_100 conda-forge
hdf5 1.10.6 nompi_h3c11f04_101 conda-forge
hdmf 3.4.2 pypi_0 pypi
icu 70.1 h27087fc_0 conda-forge
idna 3.3 pypi_0 pypi
image-classifiers 1.0.0 pypi_0 pypi
imageio 2.15.0 pypi_0 pypi
imgaug 0.4.0 pypi_0 pypi
imgstore 0.2.9 pypi_0 pypi
importlib-metadata 4.11.1 pypi_0 pypi
importlib-resources 5.9.0 pypi_0 pypi
jbig 2.1 h7f98852_2003 conda-forge
joblib 1.1.0 pypi_0 pypi
jpeg 9e h166bdaf_1 conda-forge
jsmin 3.0.1 pypi_0 pypi
jsonpickle 1.2 pypi_0 pypi
jsonschema 4.16.0 pypi_0 pypi
keras 2.6.0 pypi_0 pypi
keras-applications 1.0.8 pypi_0 pypi
keras-preprocessing 1.1.2 pypi_0 pypi
kiwisolver 1.4.4 pypi_0 pypi
lame 3.100 h7f98852_1001 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 8_openblas conda-forge
libcblas 3.9.0 8_openblas conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libdrm 2.4.109 h7f98852_0 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgfortran-ng 7.5.0 h14aa051_20 conda-forge
libgfortran4 7.5.0 h14aa051_20 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 8_openblas conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.12 pthreads_hb3c22a3_1 conda-forge
libpciaccess 0.16 h516909a_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_16 conda-forge
libtiff 4.3.0 h542a066_3 conda-forge
libva 2.14.0 h7f98852_0 conda-forge
libvpx 1.11.0 h9c3ff4c_3 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.9.13 h22db469_0 conda-forge
libzlib 1.2.11 h166bdaf_1014 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
markdown 3.3.6 pypi_0 pypi
matplotlib 3.5.3 pypi_0 pypi
ncurses 6.3 h27087fc_1 conda-forge
ndx-pose 0.1.1 pypi_0 pypi
nettle 3.6 he412f7d_0 conda-forge
networkx 2.6.3 pypi_0 pypi
numpy 1.19.5 py37h3e96413_3 conda-forge
oauthlib 3.2.0 pypi_0 pypi
olefile 0.46 pyh9f0ad1d_1 conda-forge
opencv-python 4.5.5.62 pypi_0 pypi
opencv-python-headless 4.5.5.62 pypi_0 pypi
openh264 2.1.1 h780b84a_0 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openssl 3.0.5 h166bdaf_2 conda-forge
opt-einsum 3.3.0 pypi_0 pypi
packaging 21.3 pyhd8ed1ab_0 conda-forge
pandas 1.3.5 py37he8f5f7f_0 conda-forge
pillow 8.4.0 py37h0f21c89_0 conda-forge
pip 22.3 pyhd8ed1ab_0 conda-forge
pkgutil-resolve-name 1.3.10 pypi_0 pypi
protobuf 3.19.4 pypi_0 pypi
psutil 5.9.2 pypi_0 pypi
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyasn1 0.4.8 pypi_0 pypi
pyasn1-modules 0.2.8 pypi_0 pypi
pygments 2.13.0 pypi_0 pypi
pykalman 0.9.5 pypi_0 pypi
pynwb 2.1.0 pypi_0 pypi
pyparsing 3.0.6 pypi_0 pypi
pyrsistent 0.18.1 pypi_0 pypi
pyside2 5.14.1 pypi_0 pypi
python 3.7.12 hf930737_100_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-rapidjson 1.8 pypi_0 pypi
python_abi 3.7 2_cp37m conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
pytz-deprecation-shim 0.1.0.post0 pypi_0 pypi
pywavelets 1.3.0 pypi_0 pypi
pyzmq 23.2.1 pypi_0 pypi
qimage2ndarray 1.9.0 pypi_0 pypi
qtpy 2.2.1 pyhd8ed1ab_0 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
requests 2.27.1 pypi_0 pypi
requests-oauthlib 1.3.1 pypi_0 pypi
rich 10.16.1 pypi_0 pypi
ruamel-yaml 0.17.21 pypi_0 pypi
ruamel-yaml-clib 0.2.6 pypi_0 pypi
scikit-image 0.19.3 pypi_0 pypi
scikit-learn 1.0.2 pypi_0 pypi
scikit-video 1.1.11 pypi_0 pypi
scipy 1.5.3 py37h8911b10_0 conda-forge
seaborn 0.12.0 pypi_0 pypi
segmentation-models 1.0.1 pypi_0 pypi
setuptools 59.8.0 py37h89c1867_1 conda-forge
setuptools-scm 6.4.2 pypi_0 pypi
shapely 1.7.1 py37h48c49eb_5 conda-forge
shiboken2 5.14.1 pypi_0 pypi
six 1.15.0 pyh9f0ad1d_0 conda-forge
sleap 1.2.8 pypi_0 pypi
sqlite 3.38.2 h4ff8645_0 conda-forge
svt-av1 0.9.1 h27087fc_0 conda-forge
tensorboard 2.6.0 pypi_0 pypi
tensorboard-data-server 0.6.1 pypi_0 pypi
tensorboard-plugin-wit 1.8.1 pypi_0 pypi
tensorflow 2.6.3 pypi_0 pypi
tensorflow-estimator 2.6.0 pypi_0 pypi
termcolor 1.1.0 pypi_0 pypi
threadpoolctl 3.1.0 pypi_0 pypi
tifffile 2021.11.2 pypi_0 pypi
tk 8.6.12 h27826a3_0 conda-forge
tomli 2.0.1 pypi_0 pypi
typing-extensions 3.10.0.2 pypi_0 pypi
tzdata 2022.2 pypi_0 pypi
tzlocal 4.2 pypi_0 pypi
urllib3 1.26.8 pypi_0 pypi
werkzeug 2.0.3 pypi_0 pypi
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
wrapt 1.12.1 pypi_0 pypi
x264 1!161.3030 h7f98852_1 conda-forge
x265 3.5 h924138e_3 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zipp 3.7.0 pypi_0 pypi
zlib 1.2.11 h166bdaf_1014 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge
