Nodes missing from .confmap

[HatmanStack]

Bug description

Nodes are not propagating from the anchor node as expected. They're greyed out and not present on the multi instance confmap.

Expected behaviour

All nodes with a single parent to be included in the confmap, predicted, and validated in the training loop.

Actual behaviour

Some nodes are included some are not. All are in a tree config.

Your personal set up

• OS:

Windows 10 pro 22h2

• Version(s):

SLEAP v1.3.3, python 3.7.12

• SLEAP installation method (listed here):
  • Conda from package
  • Conda from source
  • pip package
  • Apple Silicon Macs

Environment packages

(sleap) C:\Users\Crosby>conda list
# packages in environment at C:\Users\Crosby\miniconda3\envs\sleap:
#
# Name                    Version                   Build  Channel
absl-py                   1.0.0                    pypi_0    pypi
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               hdccc3a2_0    conda-forge
brotli                    1.0.9                hcfcfb64_9    conda-forge
brotli-bin                1.0.9                hcfcfb64_9    conda-forge
bzip2                     1.0.8                hcfcfb64_5    conda-forge
c-blosc2                  2.13.2               h183a6f4_0    conda-forge
ca-certificates           2024.2.2             h56e8100_0    conda-forge
cached-property           1.5.2                    pypi_0    pypi
cachetools                4.2.4                    pypi_0    pypi
cattrs                    1.1.1              pyhd8ed1ab_0    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
cfitsio                   4.0.0                hd67004f_0    conda-forge
charls                    2.3.4                h39d44d4_0    conda-forge
charset-normalizer        2.0.9                    pypi_0    pypi
cloudpickle               2.2.1              pyhd8ed1ab_0    conda-forge
cuda-nvcc                 11.3.58              hb8d16a4_0    nvidia
cudatoolkit               11.3.1              hf2f0253_13    conda-forge
cudnn                     8.2.1.32             h754d62a_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
cytoolz                   0.12.0           py37hcc03f2d_0    conda-forge
dask-core                 2022.2.0           pyhd8ed1ab_0    conda-forge
efficientnet              1.0.0                    pypi_0    pypi
flatbuffers               2.0                      pypi_0    pypi
fonttools                 4.38.0           py37h51bd9d9_0    conda-forge
freeglut                  3.2.2                h63175ca_2    conda-forge
freetype                  2.12.1               hdaf720e_2    conda-forge
fsspec                    2023.1.0           pyhd8ed1ab_0    conda-forge
gast                      0.4.0                    pypi_0    pypi
geos                      3.11.0               h39d44d4_0    conda-forge
giflib                    5.2.1                h64bf75a_3    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
grpcio                    1.43.0                   pypi_0    pypi
h5py                      3.1.0                    pypi_0    pypi
hdmf                      3.6.1                    pypi_0    pypi
icu                       69.1                 h0e60522_0    conda-forge
idna                      3.3                      pypi_0    pypi
image-classifiers         1.0.0                    pypi_0    pypi
imagecodecs               2021.11.20       py37hfea8715_2    conda-forge
imageio                   2.33.1             pyh8c1a49c_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
intel-openmp              2024.0.0         h57928b3_49841    conda-forge
jasper                    2.0.33               hc2e4405_1    conda-forge
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   hcfcfb64_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                  hcfcfb64_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
kiwisolver                1.4.4            py37h8c56517_0    conda-forge
krb5                      1.20.1               h6609f42_0    conda-forge
lcms2                     2.14                 h90d422f_0    conda-forge
lerc                      3.0                  h0e60522_0    conda-forge
libaec                    1.1.2                h63175ca_1    conda-forge
libblas                   3.9.0              21_win64_mkl    conda-forge
libbrotlicommon           1.0.9                hcfcfb64_9    conda-forge
libbrotlidec              1.0.9                hcfcfb64_9    conda-forge
libbrotlienc              1.0.9                hcfcfb64_9    conda-forge
libcblas                  3.9.0              21_win64_mkl    conda-forge
libclang                  12.0.0                   pypi_0    pypi
libcurl                   8.1.2                h68f0423_0    conda-forge
libdeflate                1.10                 h8ffe710_0    conda-forge
libhwloc                  2.9.3           default_haede6df_1009    conda-forge
libiconv                  1.17                 hcfcfb64_2    conda-forge
liblapack                 3.9.0              21_win64_mkl    conda-forge
liblapacke                3.9.0              21_win64_mkl    conda-forge
libopencv                 4.5.1            py37ha0199f4_0    conda-forge
libpng                    1.6.42               h19919ed_0    conda-forge
libprotobuf               3.21.8               h12be248_0    conda-forge
libsodium                 1.0.18               h8d14728_1    conda-forge
libsqlite                 3.45.1               hcfcfb64_0    conda-forge
libssh2                   1.10.0               h680486a_3    conda-forge
libtiff                   4.4.0                hc4061b1_0    conda-forge
libwebp-base              1.3.2                hcfcfb64_0    conda-forge
libxcb                    1.13              hcd874cb_1004    conda-forge
libxml2                   2.12.5               hc3477c8_0    conda-forge
libxslt                   1.1.39               h3df6e99_0    conda-forge
libzlib                   1.2.13               hcfcfb64_5    conda-forge
libzopfli                 1.0.3                h0e60522_0    conda-forge
locket                    1.0.0              pyhd8ed1ab_0    conda-forge
lz4-c                     1.9.3                h8ffe710_1    conda-forge
m2w64-gcc-libgfortran     5.3.0                         6    conda-forge
m2w64-gcc-libs            5.3.0                         7    conda-forge
m2w64-gcc-libs-core       5.3.0                         7    conda-forge
m2w64-gmp                 6.1.0                         2    conda-forge
m2w64-libwinpthread-git   5.0.0.4634.697f757               2    conda-forge
markdown                  3.3.6                    pypi_0    pypi
markdown-it-py            2.2.0              pyhd8ed1ab_0    conda-forge
matplotlib-base           3.5.3            py37hbaab90a_2    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_0    conda-forge
mkl                       2024.0.0         h66d3029_49657    conda-forge
msys2-conda-epoch         20160418                      1    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ndx-pose                  0.1.1                    pypi_0    pypi
networkx                  2.6.3              pyhd8ed1ab_1    conda-forge
nixio                     1.5.3                    pypi_0    pypi
numpy                     1.19.5                   pypi_0    pypi
oauthlib                  3.1.1                    pypi_0    pypi
opencv                    4.5.1            py37h03978a9_0    conda-forge
opencv-python-headless    4.2.0.34                 pypi_0    pypi
openjpeg                  2.5.0                hc9384bd_1    conda-forge
openssl                   1.1.1w               hcfcfb64_0    conda-forge
opt-einsum                3.3.0                    pypi_0    pypi
packaging                 21.3                     pypi_0    pypi
pandas                    1.3.5            py37h9386db6_0    conda-forge
partd                     1.4.1              pyhd8ed1ab_0    conda-forge
patsy                     0.5.6              pyhd8ed1ab_0    conda-forge
pillow                    9.2.0            py37h42a8222_2    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10                   pypi_0    pypi
protobuf                  3.19.1                   pypi_0    pypi
psutil                    5.9.3            py37h51bd9d9_0    conda-forge
pthread-stubs             0.4               hcd874cb_1001    conda-forge
pthreads-win32            2.9.1                hfa6e2cd_3    conda-forge
py-opencv                 4.5.1            py37heaed05f_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           py37h760f651_8    conda-forge
python                    3.7.12          h7840368_100_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-rapidjson          1.9              py37h7f67f24_0    conda-forge
python_abi                3.7                     4_cp37m    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pywavelets                1.3.0            py37h3a130e4_1    conda-forge
pyyaml                    6.0              py37hcc03f2d_4    conda-forge
pyzmq                     24.0.1           py37h7347f05_0    conda-forge
qimage2ndarray            1.10.0                   pypi_0    pypi
qt                        5.12.9               h556501e_6    conda-forge
qtpy                      2.4.1              pyhd8ed1ab_0    conda-forge
requests                  2.26.0                   pypi_0    pypi
requests-oauthlib         1.3.0                    pypi_0    pypi
rich                      13.7.0             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           py37h3182a2c_1    conda-forge
scikit-learn              1.0              py37ha78be43_1    conda-forge
scikit-video              1.1.11             pyh24bf2e0_0    conda-forge
scipy                     1.7.3            py37hb6553fb_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           py37h03978a9_1    conda-forge
setuptools-scm            6.3.2                    pypi_0    pypi
shapely                   1.8.5            py37h475e9a0_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sleap                     1.3.3                    pypi_0    pypi
snappy                    1.1.10               hfb803bf_0    conda-forge
sqlite                    3.45.1               hcfcfb64_0    conda-forge
statsmodels               0.13.2           py37h3a130e4_0    conda-forge
tbb                       2021.11.0            h91493d7_1    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            0.12.0             pyhca92ed8_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               h5226925_1    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
tzdata                    2023.3                   pypi_0    pypi
tzlocal                   5.0.1                    pypi_0    pypi
ucrt                      10.0.22621.0         h57928b3_0    conda-forge
unicodedata2              14.0.0           py37hcc03f2d_1    conda-forge
urllib3                   1.26.7                   pypi_0    pypi
vc                        14.3                hcf57466_18    conda-forge
vc14_runtime              14.38.33130         h82b7239_18    conda-forge
vs2015_runtime            14.38.33130         hcb4865c_18    conda-forge
werkzeug                  2.0.2                    pypi_0    pypi
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
wrapt                     1.13.3                   pypi_0    pypi
xorg-libxau               1.0.11               hcd874cb_0    conda-forge
xorg-libxdmcp             1.1.3                hcd874cb_0    conda-forge
xz                        5.2.6                h8d14728_0    conda-forge
yaml                      0.2.5                h8ffe710_2    conda-forge
zeromq                    4.3.4                h0e60522_1    conda-forge
zfp                       0.5.5                h0e60522_8    conda-forge
zipp                      3.15.0                   pypi_0    pypi
zlib                      1.2.13               hcfcfb64_5    conda-forge
zlib-ng                   2.0.7                hcfcfb64_0    conda-forge
zstd                      1.5.5                h12be248_0    conda-forge

Logs

# paste relevant logs here, if any

Screenshots

multi_instance.json

How to reproduce

[talmo]

Hi @HatmanStack,

Apologies for the delay! This is actually working as intended.

SLEAP allows you to mark nodes as "not visible" which is denoted by the gray font and darkened background. They're treated as missing/occluded and will have no density in the confidence maps.

You can right click those nodes to mark them as visible and they'll show back up in the confidence maps.

Cheers,

Talmo