cvapipe_analysis parameterization run ends up parameterization/representations empty #82
Description
Hi @vianamp I am also trying to just run the examples, I
- installed the
nature-paperversion, cvapipe_analysis loaddata run --testran without problemcvapipe_analysis computefeatures runran without problemscvapipe_analysis preprocessing runran without problemscvapipe_analysis shapemode runresults in segmentation fault:- I checked ant it seems to be from
generate_and_save_animated_2d_contours()inshapemode_tools.py - I tried to fix the warnings first and installed
ffmpegbut I guess this is not the problem
- I checked ant it seems to be from
Is it a known problem? segmentation fault is not so informative so I thought maybe the developers encountered this before.
My kindergarten debug:
def generate_and_save_animated_2d_contours(self):
swap = self.control.swapxy_on_zproj()
abs_path_avgshape = self.control.get_staging()/f"shapemode/avgshape"
for sm, meshes in tqdm(self.meshes.items(), total=len(self.meshes)):
projs = viz.MeshToolKit.get_2d_contours(meshes, swap)
print("This is printed only once"). # <---------------
for proj, contours in projs.items():
fname = f"{abs_path_avgshape}/{sm}_{proj}.gif"
viz.MeshToolKit.animate_contours(self.control, contours, save=fname)
print("This is also printed only once then `Segmentation fault (core dumped)`") # <----------------- Final logs
No LMNB1 cells found.
No NUP153 cells found.
No ATP2A2 cells found.
No RAB5A cells found.
No TOMM20 cells found.
No LAMP1 cells found.
No ST6GAL1 cells found.
No TUBA1B cells found.
No CETN2 cells found.
No GJA1 cells found.
No DSP cells found.
No CTNNB1 cells found.
No ACTB cells found.
No ACTN1 cells found.
No MYH10 cells found.
No PXN cells found.
your_path_to/local_staging_variance/shapemode/pca/feature_importance.txt
Generating 3D meshes. This might take some time...
0%| | 0/8 [00:00<?, ?it/s]This is printed only once
This is also printed only once then `Segmentation fault (core dumped)`
Segmentation fault (core dumped)Environment
I'm on a Linux node with enough resources, env:
conda list
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aics-dask-utils 0.2.4 pypi_0 pypi
aicscytoparam 0.1.6 pypi_0 pypi
aicsimageio 4.13.0 pypi_0 pypi
aicsshparam 0.1.7 pypi_0 pypi
aiohappyeyeballs 2.4.4 pypi_0 pypi
aiohttp 3.10.11 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
alsa-lib 1.2.13 hb9d3cd8_0 conda-forge
annotated-types 0.7.0 pypi_0 pypi
anyio 4.5.2 pypi_0 pypi
aom 3.9.1 hac33072_0 conda-forge
argon2-cffi 23.1.0 pypi_0 pypi
argon2-cffi-bindings 21.2.0 pypi_0 pypi
arrow 1.3.0 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
astropy 5.2.2 pypi_0 pypi
asttokens 3.0.0 pypi_0 pypi
async-lru 2.0.4 pypi_0 pypi
async-timeout 5.0.1 pypi_0 pypi
attr 2.5.1 h166bdaf_1 conda-forge
attrs 25.3.0 pypi_0 pypi
aws-requests-auth 0.4.3 pypi_0 pypi
babel 2.17.0 pypi_0 pypi
backcall 0.2.0 pypi_0 pypi
backports-zoneinfo 0.2.1 pypi_0 pypi
beautifulsoup4 4.13.3 pypi_0 pypi
bfio 2.4.7 pypi_0 pypi
bfiocpp 0.3.1 pypi_0 pypi
bleach 6.1.0 pypi_0 pypi
bokeh 3.1.1 pypi_0 pypi
boto3 1.37.23 pypi_0 pypi
botocore 1.37.23 pypi_0 pypi
bzip2 1.0.8 h4bc722e_7 conda-forge
ca-certificates 2025.1.31 hbcca054_0 conda-forge
cairo 1.18.4 h3394656_0 conda-forge
certifi 2025.1.31 pypi_0 pypi
cffi 1.17.1 pypi_0 pypi
charset-normalizer 3.4.1 pypi_0 pypi
click 8.1.8 pypi_0 pypi
cloudpickle 3.1.1 pypi_0 pypi
comm 0.2.2 pypi_0 pypi
contourpy 1.1.1 pypi_0 pypi
croniter 0.3.37 pypi_0 pypi
cvapipe-analysis 0.1.4 dev_0 <develop>
cycler 0.12.1 pypi_0 pypi
dask 2023.5.0 pypi_0 pypi
dask-jobqueue 0.8.5 pypi_0 pypi
datastep 0.1.9 pypi_0 pypi
dav1d 1.2.1 hd590300_0 conda-forge
dbus 1.13.6 h5008d03_3 conda-forge
debugpy 1.8.13 pypi_0 pypi
decorator 5.2.1 pypi_0 pypi
defusedxml 0.7.1 pypi_0 pypi
distributed 2023.5.0 pypi_0 pypi
docker 7.1.0 pypi_0 pypi
docutils 0.20.1 pypi_0 pypi
elementpath 4.8.0 pypi_0 pypi
exceptiongroup 1.2.2 pypi_0 pypi
executing 2.2.0 pypi_0 pypi
expat 2.6.4 h5888daf_0 conda-forge
fasteners 0.19 pypi_0 pypi
fastjsonschema 2.21.1 pypi_0 pypi
ffmpeg 1.4 pypi_0 pypi
fire 0.7.0 pypi_0 pypi
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 h77eed37_3 conda-forge
fontconfig 2.15.0 h7e30c49_1 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.56.0 pypi_0 pypi
fqdn 1.5.1 pypi_0 pypi
freetype 2.13.3 h48d6fc4_0 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
frozenlist 1.5.0 pypi_0 pypi
fsspec 2023.6.0 pypi_0 pypi
gdk-pixbuf 2.42.12 hb9ae30d_0 conda-forge
gettext 0.23.1 h5888daf_0 conda-forge
gettext-tools 0.23.1 h5888daf_0 conda-forge
gitdb 4.0.12 pypi_0 pypi
gitpython 3.1.44 pypi_0 pypi
gmp 6.3.0 hac33072_2 conda-forge
graphite2 1.3.13 h59595ed_1003 conda-forge
h11 0.14.0 pypi_0 pypi
harfbuzz 10.4.0 h76408a6_0 conda-forge
httpcore 1.0.7 pypi_0 pypi
httpx 0.28.1 pypi_0 pypi
icu 75.1 he02047a_0 conda-forge
idna 3.10 pypi_0 pypi
imagecodecs 2023.3.16 pypi_0 pypi
imageio 2.35.1 pypi_0 pypi
imgkit 1.0.2 pypi_0 pypi
importlib-metadata 8.5.0 pypi_0 pypi
importlib-resources 6.4.5 pypi_0 pypi
ipykernel 6.29.5 pypi_0 pypi
ipython 8.12.3 pypi_0 pypi
ipywidgets 8.1.5 pypi_0 pypi
isoduration 20.11.0 pypi_0 pypi
jack 1.9.22 h7c63dc7_2 conda-forge
jedi 0.19.2 pypi_0 pypi
jgo 1.0.6 pypi_0 pypi
jinja2 3.1.6 pypi_0 pypi
jmespath 1.0.1 pypi_0 pypi
joblib 1.4.2 pypi_0 pypi
jpype1 1.5.2 pypi_0 pypi
json5 0.10.0 pypi_0 pypi
jsonlines 1.2.0 pypi_0 pypi
jsonpointer 3.0.0 pypi_0 pypi
jsonschema 4.23.0 pypi_0 pypi
jsonschema-specifications 2023.12.1 pypi_0 pypi
jupyter-client 8.6.3 pypi_0 pypi
jupyter-core 5.7.2 pypi_0 pypi
jupyter-events 0.10.0 pypi_0 pypi
jupyter-lsp 2.2.5 pypi_0 pypi
jupyter-server 2.14.2 pypi_0 pypi
jupyter-server-terminals 0.5.3 pypi_0 pypi
jupyterlab 4.3.6 pypi_0 pypi
jupyterlab-pygments 0.3.0 pypi_0 pypi
jupyterlab-server 2.27.3 pypi_0 pypi
jupyterlab-widgets 3.0.13 pypi_0 pypi
kiwisolver 1.4.7 pypi_0 pypi
lame 3.100 h166bdaf_1003 conda-forge
lazy-loader 0.4 pypi_0 pypi
ld_impl_linux-64 2.43 h712a8e2_4 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
level-zero 1.21.6 h84d6215_0 conda-forge
libabseil 20250127.1 cxx17_hbbce691_0 conda-forge
libasprintf 0.23.1 h8e693c7_0 conda-forge
libasprintf-devel 0.23.1 h8e693c7_0 conda-forge
libass 0.17.3 hba53ac1_1 conda-forge
libcap 2.75 h39aace5_0 conda-forge
libdb 6.2.32 h9c3ff4c_0 conda-forge
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libdrm 2.4.124 hb9d3cd8_0 conda-forge
libegl 1.7.0 ha4b6fd6_2 conda-forge
libexpat 2.6.4 h5888daf_0 conda-forge
libffi 3.4.6 h2dba641_0 conda-forge
libflac 1.4.3 h59595ed_0 conda-forge
libgcc 14.2.0 h767d61c_2 conda-forge
libgcc-ng 14.2.0 h69a702a_2 conda-forge
libgcrypt-lib 1.11.0 hb9d3cd8_2 conda-forge
libgettextpo 0.23.1 h5888daf_0 conda-forge
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libgl 1.7.0 ha4b6fd6_2 conda-forge
libglib 2.84.0 h2ff4ddf_0 conda-forge
libglvnd 1.7.0 ha4b6fd6_2 conda-forge
libglx 1.7.0 ha4b6fd6_2 conda-forge
libgomp 14.2.0 h767d61c_2 conda-forge
libgpg-error 1.51 hbd13f7d_1 conda-forge
libhwloc 2.11.2 default_h0d58e46_1001 conda-forge
libiconv 1.18 h4ce23a2_1 conda-forge
libjpeg-turbo 3.0.0 hd590300_1 conda-forge
liblzma 5.6.4 hb9d3cd8_0 conda-forge
liblzma-devel 5.6.4 hb9d3cd8_0 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libogg 1.3.5 h4ab18f5_0 conda-forge
libopenvino 2025.0.0 hdc3f47d_3 conda-forge
libopenvino-auto-batch-plugin 2025.0.0 h4d9b6c2_3 conda-forge
libopenvino-auto-plugin 2025.0.0 h4d9b6c2_3 conda-forge
libopenvino-hetero-plugin 2025.0.0 h981d57b_3 conda-forge
libopenvino-intel-cpu-plugin 2025.0.0 hdc3f47d_3 conda-forge
libopenvino-intel-gpu-plugin 2025.0.0 hdc3f47d_3 conda-forge
libopenvino-intel-npu-plugin 2025.0.0 hdc3f47d_3 conda-forge
libopenvino-ir-frontend 2025.0.0 h981d57b_3 conda-forge
libopenvino-onnx-frontend 2025.0.0 h0e684df_3 conda-forge
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libopenvino-pytorch-frontend 2025.0.0 h5888daf_3 conda-forge
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libsndfile 1.2.2 hc60ed4a_1 conda-forge
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libstdcxx 14.2.0 h8f9b012_2 conda-forge
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libsystemd0 257.4 h4e0b6ca_1 conda-forge
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libunwind 1.6.2 h9c3ff4c_0 conda-forge
liburing 2.9 h84d6215_0 conda-forge
libusb 1.0.28 hb9d3cd8_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libva 2.22.0 h4f16b4b_2 conda-forge
libvorbis 1.3.7 h9c3ff4c_0 conda-forge
libvpx 1.14.1 hac33072_0 conda-forge
libwebp-base 1.5.0 h851e524_0 conda-forge
libxcb 1.17.0 h8a09558_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxkbcommon 1.8.1 hc4a0caf_0 conda-forge
libxml2 2.13.7 h8d12d68_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
locket 1.0.0 pypi_0 pypi
lxml 4.9.4 pypi_0 pypi
lz4-c 1.10.0 h5888daf_1 conda-forge
markupsafe 2.1.5 pypi_0 pypi
marshmallow 3.22.0 pypi_0 pypi
marshmallow-oneofschema 3.1.1 pypi_0 pypi
matplotlib 3.7.5 pypi_0 pypi
matplotlib-inline 0.1.7 pypi_0 pypi
mistune 3.1.3 pypi_0 pypi
mpg123 1.32.9 hc50e24c_0 conda-forge
msgpack 1.1.0 pypi_0 pypi
multidict 6.1.0 pypi_0 pypi
mypy-extensions 1.0.0 pypi_0 pypi
natsort 8.4.0 pypi_0 pypi
nbclient 0.10.1 pypi_0 pypi
nbconvert 7.16.6 pypi_0 pypi
nbformat 5.10.4 pypi_0 pypi
ncurses 6.5 h2d0b736_3 conda-forge
nest-asyncio 1.6.0 pypi_0 pypi
networkx 3.1 pypi_0 pypi
notebook-shim 0.2.4 pypi_0 pypi
numcodecs 0.12.1 pypi_0 pypi
numpy 1.23.0 pypi_0 pypi
ocl-icd 2.3.2 hb9d3cd8_2 conda-forge
ome-types 0.5.3 pypi_0 pypi
ome-zarr 0.9.0 pypi_0 pypi
opencl-headers 2024.10.24 h5888daf_0 conda-forge
openh264 2.6.0 hc22cd8d_0 conda-forge
openssl 3.4.1 h7b32b05_0 conda-forge
overrides 7.7.0 pypi_0 pypi
packaging 24.2 pypi_0 pypi
pandas 1.5.3 pypi_0 pypi
pandocfilters 1.5.1 pypi_0 pypi
pango 1.56.3 h861ebed_0 conda-forge
parso 0.8.4 pypi_0 pypi
partd 1.4.1 pypi_0 pypi
pcre2 10.44 hba22ea6_2 conda-forge
pendulum 3.0.0 pypi_0 pypi
pexpect 4.9.0 pypi_0 pypi
pickleshare 0.7.5 pypi_0 pypi
pillow 10.4.0 pypi_0 pypi
pip 24.3.1 pyh8b19718_0 conda-forge
pixman 0.44.2 h29eaf8c_0 conda-forge
pkgutil-resolve-name 1.3.10 pypi_0 pypi
platformdirs 4.3.6 pypi_0 pypi
pooch 1.8.2 pypi_0 pypi
prefect 0.14.15 pypi_0 pypi
prometheus-client 0.21.1 pypi_0 pypi
prompt-toolkit 3.0.50 pypi_0 pypi
propcache 0.2.0 pypi_0 pypi
psutil 7.0.0 pypi_0 pypi
pthread-stubs 0.4 hb9d3cd8_1002 conda-forge
ptyprocess 0.7.0 pypi_0 pypi
pugixml 1.15 h3f63f65_0 conda-forge
pulseaudio-client 17.0 hac146a9_1 conda-forge
pure-eval 0.2.3 pypi_0 pypi
pyarrow 17.0.0 pypi_0 pypi
pycparser 2.22 pypi_0 pypi
pydantic 2.10.6 pypi_0 pypi
pydantic-compat 0.1.2 pypi_0 pypi
pydantic-core 2.27.2 pypi_0 pypi
pyerfa 2.0.0.3 pypi_0 pypi
pygments 2.19.1 pypi_0 pypi
pyparsing 3.1.4 pypi_0 pypi
pyshtools 4.10 pypi_0 pypi
python 3.8.20 h4a871b0_2_cpython conda-forge
python-box 7.2.0 pypi_0 pypi
python-dateutil 2.9.0.post0 pypi_0 pypi
python-json-logger 3.3.0 pypi_0 pypi
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pytz 2025.2 pypi_0 pypi
pywavelets 1.4.1 pypi_0 pypi
pyyaml 6.0.2 pypi_0 pypi
pyzmq 26.3.0 pypi_0 pypi
quilt3 5.4.0 pypi_0 pypi
readline 8.2 h8c095d6_2 conda-forge
referencing 0.35.1 pypi_0 pypi
requests 2.32.3 pypi_0 pypi
requests-futures 1.0.0 pypi_0 pypi
resource-backed-dask-array 0.1.0 pypi_0 pypi
rfc3339-validator 0.1.4 pypi_0 pypi
rfc3986-validator 0.1.1 pypi_0 pypi
rpds-py 0.20.1 pypi_0 pypi
s3fs 0.4.2 pypi_0 pypi
s3transfer 0.11.4 pypi_0 pypi
scikit-image 0.21.0 pypi_0 pypi
scikit-learn 1.3.2 pypi_0 pypi
scipy 1.10.1 pypi_0 pypi
scyjava 1.10.2 pypi_0 pypi
sdl2 2.32.50 h9b8e6db_1 conda-forge
sdl3 3.2.8 h3083f51_0 conda-forge
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setuptools 75.3.0 pyhd8ed1ab_0 conda-forge
six 1.17.0 pypi_0 pypi
smmap 5.0.2 pypi_0 pypi
snappy 1.2.1 h8bd8927_1 conda-forge
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stack-data 0.6.3 pypi_0 pypi
svt-av1 3.0.1 h5888daf_0 conda-forge
tabulate 0.9.0 pypi_0 pypi
tbb 2022.0.0 hceb3a55_0 conda-forge
tblib 3.0.0 pypi_0 pypi
tenacity 9.0.0 pypi_0 pypi
termcolor 2.4.0 pypi_0 pypi
terminado 0.18.1 pypi_0 pypi
text-unidecode 1.3 pypi_0 pypi
threadpoolctl 3.5.0 pypi_0 pypi
tifffile 2023.2.28 pypi_0 pypi
time-machine 2.15.0 pypi_0 pypi
tinycss2 1.2.1 pypi_0 pypi
tk 8.6.13 noxft_h4845f30_101 conda-forge
toml 0.10.2 pypi_0 pypi
tomli 2.2.1 pypi_0 pypi
toolz 1.0.0 pypi_0 pypi
tornado 6.4.2 pypi_0 pypi
tqdm 4.67.1 pypi_0 pypi
traitlets 5.14.3 pypi_0 pypi
types-python-dateutil 2.9.0.20241206 pypi_0 pypi
typing-extensions 4.13.0 pypi_0 pypi
tzdata 2025.2 pypi_0 pypi
uri-template 1.3.0 pypi_0 pypi
urllib3 1.26.20 pypi_0 pypi
vtk 9.0.1 pypi_0 pypi
wayland 1.23.1 h3e06ad9_0 conda-forge
wayland-protocols 1.42 hd8ed1ab_0 conda-forge
wcwidth 0.2.13 pypi_0 pypi
webcolors 24.8.0 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
websocket-client 1.8.0 pypi_0 pypi
wheel 0.45.1 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.13 pypi_0 pypi
wrapt 1.17.2 pypi_0 pypi
x264 1!164.3095 h166bdaf_2 conda-forge
x265 3.5 h924138e_3 conda-forge
xarray 2023.1.0 pypi_0 pypi
xkeyboard-config 2.43 hb9d3cd8_0 conda-forge
xmlschema 3.4.5 pypi_0 pypi
xorg-libice 1.1.2 hb9d3cd8_0 conda-forge
xorg-libsm 1.2.6 he73a12e_0 conda-forge
xorg-libx11 1.8.12 h4f16b4b_0 conda-forge
xorg-libxau 1.0.12 hb9d3cd8_0 conda-forge
xorg-libxcursor 1.2.3 hb9d3cd8_0 conda-forge
xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge
xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge
xorg-libxfixes 6.0.1 hb9d3cd8_0 conda-forge
xorg-libxrender 0.9.12 hb9d3cd8_0 conda-forge
xorg-libxscrnsaver 1.2.4 hb9d3cd8_0 conda-forge
xsdata 24.3.1 pypi_0 pypi
xvfbwrapper 0.2.9 pypi_0 pypi
xyzservices 2025.1.0 pypi_0 pypi
xz 5.6.4 hbcc6ac9_0 conda-forge
xz-gpl-tools 5.6.4 hbcc6ac9_0 conda-forge
xz-tools 5.6.4 hb9d3cd8_0 conda-forge
yarl 1.15.2 pypi_0 pypi
zarr 2.15.0 pypi_0 pypi
zict 3.0.0 pypi_0 pypi
zipp 3.20.2 pypi_0 pypi
zstd 1.5.7 hb8e6e7a_2 conda-forge