talmolab
Deleting instance causes segmentation fault
Bug description
Deleting instance causes segmentation fault on next action.
Expected behaviour
Added extra instance with Ctrl+I. Right clicked to hide all landmarks in the instance, which deleted the instance. Expected to continue digitising.
Actual behaviour
Slightly variable but may include:
Nothing appearing when adding instance to next frame.
Subsequent clicking causes segmentation fault and core dump.
Your personal set up
-
OS: Distributor ID: Ubuntu Description: Ubuntu 22.04.1 LTS Release: 22.04 Codename: jammy
-
Version(s):
SLEAP: 1.2.8 TensorFlow: 2.8.3 Numpy: 1.21.5 Python: 3.7.13 OS: Linux-5.15.0-48-generic-x86_64-with-debian-bookworm-sid
- SLEAP installation method (listed here):
- [ ] Conda from package
- [X] Conda from source
- [ ] pip package
- [ ] M1 Macs
Environment packages
# paste output of `pip freeze` or `conda list` here
packages in environment at /home/usr/anaconda3/envs/sleap:
Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
absl-py 1.2.0 pypi_0 pypi
alabaster 0.7.12 pypi_0 pypi
anyio 3.6.1 pypi_0 pypi
appdirs 1.4.4 pypi_0 pypi
argon2-cffi 21.3.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
astunparse 1.6.3 pypi_0 pypi
attrs 21.4.0 pypi_0 pypi
babel 2.10.3 pypi_0 pypi
backcall 0.2.0 pypi_0 pypi
backports-zoneinfo 0.2.1 pypi_0 pypi
beautifulsoup4 4.11.1 pypi_0 pypi
black 21.6b0 pypi_0 pypi
bleach 5.0.1 pypi_0 pypi
bzip2 1.0.8 h7b6447c_0
ca-certificates 2022.07.19 h06a4308_0
cached-property 1.5.2 py_0
cachetools 5.2.0 pypi_0 pypi
cattrs 1.1.1 pypi_0 pypi
certifi 2021.10.8 pypi_0 pypi
cffi 1.15.1 pypi_0 pypi
cfgv 3.3.1 pypi_0 pypi
charset-normalizer 2.1.1 pypi_0 pypi
click 8.0.4 pypi_0 pypi
colorama 0.4.5 pypi_0 pypi
commonmark 0.9.1 pypi_0 pypi
coverage 6.4.4 pypi_0 pypi
cryptography 38.0.1 pypi_0 pypi
cuda-nvcc 11.3.58 h2467b9f_0 nvidia
cudatoolkit 11.3.1 h2bc3f7f_2
cudnn 8.2.1 cuda11.3_0
cycler 0.11.0 pypi_0 pypi
dbus 1.13.18 hb2f20db_0
debugpy 1.6.3 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
defusedxml 0.7.1 pypi_0 pypi
deprecated 1.2.13 pypi_0 pypi
distlib 0.3.6 pypi_0 pypi
docutils 0.17.1 pypi_0 pypi
efficientnet 1.0.0 pypi_0 pypi
entrypoints 0.4 pypi_0 pypi
expat 2.4.4 h295c915_0
ffmpeg 4.2.2 h20bf706_0
filelock 3.8.0 pypi_0 pypi
flatbuffers 2.0.7 pypi_0 pypi
fontconfig 2.13.1 h6c09931_0
fonttools 4.37.3 pypi_0 pypi
freetype 2.11.0 h70c0345_0
gast 0.5.3 pypi_0 pypi
geos 3.8.0 he6710b0_0
gettext 0.21.0 hf68c758_0
giflib 5.2.1 h7b6447c_0
gitdb 4.0.9 pypi_0 pypi
gitpython 3.1.27 pypi_0 pypi
glib 2.68.2 h36276a3_0
gmp 6.2.1 h295c915_3
gnutls 3.6.15 he1e5248_0
google-auth 2.11.1 pypi_0 pypi
google-auth-oauthlib 0.4.6 pypi_0 pypi
google-pasta 0.2.0 pypi_0 pypi
greenlet 1.1.3 pypi_0 pypi
grpcio 1.49.1 pypi_0 pypi
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.18.4 h76c114f_2 conda-forge
h5py 3.1.0 nompi_py37h1e651dc_100 conda-forge
hdf5 1.10.6 h3ffc7dd_1
hdmf 3.4.5 pypi_0 pypi
icu 68.1 h2531618_0
identify 2.5.5 pypi_0 pypi
idna 3.4 pypi_0 pypi
image-classifiers 1.0.0 pypi_0 pypi
imageio 2.15.0 pypi_0 pypi
imagesize 1.4.1 pypi_0 pypi
imgaug 0.4.0 pypi_0 pypi
imgstore 0.2.9 pypi_0 pypi
importlib-metadata 4.12.0 pypi_0 pypi
importlib-resources 5.9.0 pypi_0 pypi
iniconfig 1.1.1 pypi_0 pypi
ipykernel 6.15.3 pypi_0 pypi
ipython 7.34.0 pypi_0 pypi
ipython-genutils 0.2.0 pypi_0 pypi
ipywidgets 7.7.2 pypi_0 pypi
jaraco-classes 3.2.2 pypi_0 pypi
jedi 0.17.2 pypi_0 pypi
jeepney 0.8.0 pypi_0 pypi
jinja2 3.1.2 pypi_0 pypi
joblib 1.2.0 pypi_0 pypi
jpeg 9e h7f8727e_0
jsmin 3.0.1 pypi_0 pypi
json5 0.9.10 pypi_0 pypi
jsonpickle 1.2 pypi_0 pypi
jsonschema 4.16.0 pypi_0 pypi
jupyter-cache 0.4.3 pypi_0 pypi
jupyter-client 7.3.5 pypi_0 pypi
jupyter-core 4.11.1 pypi_0 pypi
jupyter-server 1.13.5 pypi_0 pypi
jupyter-server-mathjax 0.2.6 pypi_0 pypi
jupyter-sphinx 0.3.2 pypi_0 pypi
jupyterlab 3.3.4 pypi_0 pypi
jupyterlab-pygments 0.2.2 pypi_0 pypi
jupyterlab-server 2.15.1 pypi_0 pypi
jupyterlab-widgets 1.1.1 pypi_0 pypi
keras 2.8.0 pypi_0 pypi
keras-applications 1.0.8 pypi_0 pypi
keras-preprocessing 1.1.2 pypi_0 pypi
keyring 23.9.3 pypi_0 pypi
kiwisolver 1.4.4 pypi_0 pypi
krb5 1.19.2 hac12032_0
lame 3.100 h7b6447c_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.38 h1181459_1
lerc 3.0 h295c915_0
libblas 3.9.0 15_linux64_openblas conda-forge
libcblas 3.9.0 15_linux64_openblas conda-forge
libclang 14.0.6 pypi_0 pypi
libdeflate 1.8 h7f8727e_5
libedit 3.1.20210910 h7f8727e_0
libevent 2.1.10 h9b69904_4 conda-forge
libffi 3.3 he6710b0_2
libgcc-ng 11.2.0 h1234567_1
libgfortran-ng 11.2.0 h00389a5_1
libgfortran5 11.2.0 h1234567_1
libglib 2.68.2 h3e27bee_0 conda-forge
libgomp 11.2.0 h1234567_1
libiconv 1.16 h7f8727e_2
libidn2 2.3.2 h7f8727e_0
liblapack 3.9.0 15_linux64_openblas conda-forge
libllvm11 11.1.0 h9e868ea_5
libopenblas 0.3.20 h043d6bf_1
libopus 1.3.1 h7b6447c_0
libpng 1.6.37 hbc83047_0
libpq 12.9 h16c4e8d_3
libstdcxx-ng 11.2.0 h1234567_1
libtasn1 4.16.0 h27cfd23_0
libtiff 4.4.0 hecacb30_0
libunistring 0.9.10 h27cfd23_0
libuuid 1.0.3 h7f8727e_2
libvpx 1.7.0 h439df22_0
libwebp 1.2.2 h55f646e_0
libwebp-base 1.2.2 h7f8727e_0
libxcb 1.15 h7f8727e_0
libxkbcommon 1.0.3 he3ba5ed_0 conda-forge
libxml2 2.9.12 h72842e0_0 conda-forge
libxslt 1.1.33 h15afd5d_2 conda-forge
linkify-it-py 2.0.0 pypi_0 pypi
livereload 2.6.3 pypi_0 pypi
lxml 4.9.1 pypi_0 pypi
lz4-c 1.9.3 h295c915_1
markdown 3.4.1 pypi_0 pypi
markdown-it-py 1.1.0 pypi_0 pypi
markupsafe 2.1.1 pypi_0 pypi
matplotlib 3.5.3 pypi_0 pypi
matplotlib-inline 0.1.6 pypi_0 pypi
mdit-py-plugins 0.2.8 pypi_0 pypi
mistune 0.8.4 pypi_0 pypi
more-itertools 8.14.0 pypi_0 pypi
mypy-extensions 0.4.3 pypi_0 pypi
mysql-common 8.0.25 ha770c72_2 conda-forge
mysql-libs 8.0.25 hfa10184_2 conda-forge
myst-nb 0.13.2 pypi_0 pypi
myst-parser 0.15.2 pypi_0 pypi
nbclassic 0.4.3 pypi_0 pypi
nbclient 0.5.13 pypi_0 pypi
nbconvert 6.5.3 pypi_0 pypi
nbdime 3.1.1 pypi_0 pypi
nbformat 5.1.3 pypi_0 pypi
ncurses 6.3 h5eee18b_3
ndx-pose 0.1.1 pypi_0 pypi
nest-asyncio 1.5.5 pypi_0 pypi
nettle 3.7.3 hbbd107a_1
networkx 2.6.3 pypi_0 pypi
nodeenv 1.7.0 pypi_0 pypi
notebook 6.4.12 pypi_0 pypi
notebook-shim 0.1.0 pypi_0 pypi
nspr 4.33 h295c915_0
nss 3.74 h0370c37_0
numpy 1.21.5 py37h976b520_1 conda-forge
oauthlib 3.2.1 pypi_0 pypi
olefile 0.46 py37_0
opencv-python 4.5.5.64 pypi_0 pypi
openh264 2.1.1 h4ff587b_0
openssl 1.1.1q h7f8727e_0
opt-einsum 3.3.0 pypi_0 pypi
packaging 21.3 pyhd3eb1b0_0
pandas 1.3.5 py37he8f5f7f_0 conda-forge
pandocfilters 1.5.0 pypi_0 pypi
parso 0.7.1 pypi_0 pypi
pathspec 0.10.1 pypi_0 pypi
pcre 8.45 h295c915_0
pexpect 4.8.0 pypi_0 pypi
pickleshare 0.7.5 pypi_0 pypi
pillow 8.4.0 py37h5aabda8_0
pip 22.2.2 pyhd8ed1ab_0 conda-forge
pkginfo 1.8.3 pypi_0 pypi
pkgutil-resolve-name 1.3.10 pypi_0 pypi
platformdirs 2.5.2 pypi_0 pypi
pluggy 1.0.0 pypi_0 pypi
pre-commit 2.20.0 pypi_0 pypi
prometheus-client 0.14.1 pypi_0 pypi
prompt-toolkit 3.0.31 pypi_0 pypi
protobuf 3.19.5 pypi_0 pypi
psutil 5.9.2 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
py 1.11.0 pypi_0 pypi
pyasn1 0.4.8 pypi_0 pypi
pyasn1-modules 0.2.8 pypi_0 pypi
pycparser 2.21 pypi_0 pypi
pydata-sphinx-theme 0.8.1 pypi_0 pypi
pygithub 1.55 pypi_0 pypi
pygments 2.13.0 pypi_0 pypi
pyjwt 2.5.0 pypi_0 pypi
pykalman 0.9.5 pypi_0 pypi
pynacl 1.5.0 pypi_0 pypi
pynwb 2.1.0 pypi_0 pypi
pyparsing 3.0.9 py37h06a4308_0
pyrsistent 0.18.1 pypi_0 pypi
pyside2 5.13.2 py37hfa98aef_7 conda-forge
pytest 7.1.3 pypi_0 pypi
pytest-cov 3.0.0 pypi_0 pypi
pytest-qt 4.1.0 pypi_0 pypi
pytest-xvfb 2.0.0 pypi_0 pypi
python 3.7.13 h12debd9_0
python-dateutil 2.8.2 pyhd3eb1b0_0
python-rapidjson 1.8 pypi_0 pypi
python_abi 3.7 2_cp37m conda-forge
pytz 2022.1 py37h06a4308_0
pytz-deprecation-shim 0.1.0.post0 pypi_0 pypi
pyvirtualdisplay 3.0 pypi_0 pypi
pywavelets 1.3.0 pypi_0 pypi
pyyaml 6.0 pypi_0 pypi
pyzmq 24.0.1 pypi_0 pypi
qimage2ndarray 1.9.0 pypi_0 pypi
qt 5.12.9 h9d6b050_2 conda-forge
qtpy 2.2.0 py37h06a4308_0
readline 8.1.2 h7f8727e_1
readme-renderer 37.2 pypi_0 pypi
regex 2022.9.13 pypi_0 pypi
requests 2.28.1 pypi_0 pypi
requests-oauthlib 1.3.1 pypi_0 pypi
requests-toolbelt 0.9.1 pypi_0 pypi
rfc3986 2.0.0 pypi_0 pypi
rich 10.16.1 pypi_0 pypi
rsa 4.9 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 1.7.3 py37hf2a6cf1_0 conda-forge
seaborn 0.12.0 pypi_0 pypi
secretstorage 3.3.3 pypi_0 pypi
segmentation-models 1.0.1 pypi_0 pypi
send2trash 1.8.0 pypi_0 pypi
setuptools 58.0.4 py37h06a4308_0
shapely 1.7.1 py37h1728cc4_0
six 1.16.0 pyhd3eb1b0_1
sleap 1.2.8 dev_0
tensorboard 2.8.0 pypi_0 pypi
tensorboard-data-server 0.6.1 pypi_0 pypi
tensorboard-plugin-wit 1.8.1 pypi_0 pypi
tensorflow 2.8.3 pypi_0 pypi
tensorflow-estimator 2.8.0 pypi_0 pypi
tensorflow-io-gcs-filesystem 0.27.0 pypi_0 pypi
termcolor 2.0.1 pypi_0 pypi
terminado 0.15.0 pypi_0 pypi
threadpoolctl 3.1.0 pypi_0 pypi
tifffile 2021.11.2 pypi_0 pypi
tinycss2 1.1.1 pypi_0 pypi
tk 8.6.12 h1ccaba5_0
toml 0.10.2 pypi_0 pypi
tomli 2.0.1 pypi_0 pypi
tornado 6.2 pypi_0 pypi
tqdm 4.64.1 pypi_0 pypi
traitlets 5.4.0 pypi_0 pypi
twine 3.3.0 pypi_0 pypi
typed-ast 1.5.4 pypi_0 pypi
typing-extensions 4.3.0 pypi_0 pypi
tzdata 2022.2 pypi_0 pypi
tzlocal 4.2 pypi_0 pypi
uc-micro-py 1.0.1 pypi_0 pypi
urllib3 1.26.12 pypi_0 pypi
virtualenv 20.16.5 pypi_0 pypi
wcwidth 0.2.5 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.4.1 pypi_0 pypi
werkzeug 2.2.2 pypi_0 pypi
wheel 0.37.1 pyhd3eb1b0_0
widgetsnbextension 3.6.1 pypi_0 pypi
wrapt 1.14.1 pypi_0 pypi
x264 1!157.20191217 h7b6447c_0
xz 5.2.5 h7f8727e_1
zipp 3.8.1 pypi_0 pypi
zlib 1.2.12 h5eee18b_3
zstd 1.5.2 ha4553b6_0
Logs
Saving config: /home/usr/.sleap/1.2.8/preferences.yaml
2022-09-26 09:31:27.657784: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:936] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2022-09-26 09:31:27.686165: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:936] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
2022-09-26 09:31:27.686360: I tensorflow/stream_executor/cuda/cuda_gpu_executor.cc:936] successful NUMA node read from SysFS had negative value (-1), but there must be at least one NUMA node, so returning NUMA node zero
Software versions:
SLEAP: 1.2.8
TensorFlow: 2.8.3
Numpy: 1.21.5
Python: 3.7.13
OS: Linux-5.15.0-48-generic-x86_64-with-debian-bookworm-sid
Happy SLEAPing! :)
Segmentation fault (core dumped)
Screenshots
How to reproduce
- Create new project
- Add video
- Create skeleton (e.g. two landmarks)
- Add instance
- Add instance
- Right click landmarks until instance disappears
- Next action will usually cause a segmentation fault (e.g. adding instance, generating suggested frames)
First-Pass Analysis
The segmentation/program crashing bug seems to be caused by the hidden user-labeled instances. This issue is also mentioned in #971.
Segmentation Fault
This seems to be caused because we do not add user-labeled instances to the scene in cases where all nodes are hidden. When I change the conditional in https://github.com/talmolab/sleap/blob/develop/sleap/gui/widgets/video.py#L449-L466 such that user-labeled instances are always added to the scene:
if instance.instance.n_visible_points > 0 or not isinstance(instance.instance, PredictedInstance):
self.view.scene.addItem(instance)
# connect signal so we can adjust QtNodeLabel positions after zoom
self.view.updatedViewer.connect(instance.updatePoints)
then the program no longer crashes.
To replicate issue. However, my terminal gives no error message and just exits out of the program:
(sleap_v128) λ sleap-label
Saving config: C:\Users\Liezl/.sleap/1.2.8/preferences.yaml
Restoring GUI state...
Software versions:
SLEAP: 1.2.8
TensorFlow: 2.8.3
Numpy: 1.21.5
Python: 3.7.13
OS: Windows-10-10.0.19041-SP0
Happy SLEAPing! :)
Steps to replicate (same as described by @daskandalis)
- New Project
- Add video
- Create 2 node skeleton, no edges
- Add 2 instances on first frame
- Right click all nodes on a single instance until instance disappears
- Do action (either right click to add a new instance [default, random, average], or generate suggestions [sample] - either lead to issue)
Hidden User-Labeled Instances
User-labeled instances with all nodes set as invisible should still be visible. We currently set instances with all NaNs to be hidden from view. This was originally implemented to hide predicted instances which had all low-scoring nodes (these low-scoring nodes are also denoted by NaNs).
Proposal
We can add an extra conditional that ensures user-labeled instances are always added while PredictedInstances are still subject to a minimum visible node limit.
Relevant Code
https://github.com/talmolab/sleap/blob/develop/sleap/gui/widgets/video.py#L449-L466
I replicated this issue in Windows 11 Anaconda Prompt (anaconda3) with the same steps as above:
(sleap) C:\Users\daska\Desktop\PROJECTS\sleap\sleap>sleap-label
Saving config: C:\Users\daska/.sleap/1.2.8/preferences.yaml
2022-09-26 20:23:35.137862: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'nvcuda.dll'; dlerror: nvcuda.dll not found
2022-09-26 20:23:35.138357: W tensorflow/stream_executor/cuda/cuda_driver.cc:269] failed call to cuInit: UNKNOWN ERROR (303)
2022-09-26 20:23:35.141271: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:169] retrieving CUDA diagnostic information for host: TOKAMAK-IX
2022-09-26 20:23:35.141412: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:176] hostname: TOKAMAK-IX
Software versions:
SLEAP: 1.2.8
TensorFlow: 2.8.3
Numpy: 1.21.5
Python: 3.7.13
OS: Windows-10-10.0.22000-SP0
Happy SLEAPing! :)
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\daska\anaconda3\envs\sleap\lib\multiprocessing\spawn.py", line 105, in spawn_main
exitcode = _main(fd)
File "C:\Users\daska\anaconda3\envs\sleap\lib\multiprocessing\spawn.py", line 113, in _main
preparation_data = reduction.pickle.load(from_parent)
EOFError: Ran out of input