stuck at the 'interactive_rectangle_clip'

[Li-ZhiD]

Hi,
I followed the tutorial section ”Three dims models reconstruction“, but my spateo ENV stopped at the following step for long time without messages, and ENV died when I restarted the kernel:

subtype_tpc = st.tdr.interactive_rectangle_clip(model=subtype_rpc, key="tissue", invert=True)[0]

Anyone can help me? Thanks!

[Li-ZhiD]

Here is my conda env.

Package                      Version
---------------------------- ----------
absl-py                      2.1.0
access                       1.1.9
addict                       2.4.0
adjustText                   1.3.0
affine                       2.4.0
aiohappyeyeballs             2.4.3
aiohttp                      3.10.10
aiosignal                    1.3.1
alphashape                   1.3.1
anndata                      0.10.9
appdirs                      1.4.4
array_api_compat             1.9.1
asttokens                    2.4.1
astunparse                   1.6.3
async-timeout                4.0.3
attrs                        24.2.0
backcall                     0.2.0
beautifulsoup4               4.12.3
bleach                       6.2.0
blinker                      1.9.0
blosc2                       2.5.1
branca                       0.8.0
certifi                      2024.8.30
cfgv                         3.4.0
charset-normalizer           3.4.0
click                        8.1.7
click-log                    0.4.0
click-plugins                1.1.1
cligj                        0.7.2
colorcet                     3.1.0
comm                         0.2.2
ConfigArgParse               1.7
contourpy                    1.3.0
csbdeep                      0.8.1
cvxopt                       1.3.2
cycler                       0.12.1
dash                         2.18.2
dash-core-components         2.0.0
dash-html-components         2.0.0
dash-table                   5.0.0
debugpy                      1.8.8
decorator                    4.4.2
defusedxml                   0.7.1
deprecation                  2.1.0
descartes                    1.1.0
distlib                      0.3.9
dunamai                      1.22.0
dynamo-release               1.4.1
esda                         2.5.1
et_xmlfile                   2.0.0
exceptiongroup               1.2.2
executing                    2.1.0
fastjsonschema               2.20.0
filelock                     3.16.1
fiona                        1.10.1
Flask                        3.0.3
flatbuffers                  24.3.25
folium                       0.18.0
fonttools                    4.54.1
frozenlist                   1.5.0
fsspec                       2024.10.0
gast                         0.6.0
geopandas                    1.0.1
get-annotations              0.1.2
get_version                  3.5.5
giddy                        2.3.5
google-pasta                 0.2.0
gpytorch                     1.13
grpcio                       1.67.1
h5py                         3.12.1
hnswlib                      0.8.0
identify                     2.6.2
idna                         3.10
igraph                       0.11.8
imageio                      2.19.3
imageio-ffmpeg               0.4.7
importlib_metadata           8.5.0
importlib_resources          6.4.5
inequality                   1.0.0
ipykernel                    6.29.5
ipython                      8.12.0
ipywidgets                   8.1.5
itsdangerous                 2.2.0
jaxtyping                    0.2.19
jedi                         0.19.2
Jinja2                       3.1.4
joblib                       1.4.2
jsonschema                   4.23.0
jsonschema-specifications    2024.10.1
jupyter_client               8.6.3
jupyter_core                 5.7.2
jupyterlab_pygments          0.3.0
jupyterlab_widgets           3.0.13
keras                        3.6.0
kiwisolver                   1.4.7
kneed                        0.8.5
kornia                       0.7.4
kornia_rs                    0.1.7
lazy_loader                  0.4
legacy-api-wrap              1.4
leidenalg                    0.10.2
libclang                     18.1.1
libpysal                     4.8.1
linear-operator              0.5.3
llvmlite                     0.43.0
loompy                       3.0.7
mapclassify                  2.8.1
Markdown                     3.7
markdown-it-py               3.0.0
MarkupSafe                   3.0.2
matplotlib                   3.9.2
matplotlib-inline            0.1.7
mdurl                        0.1.2
meshio                       4.4.6
mgwr                         2.2.1
mistune                      3.0.2
ml-dtypes                    0.4.1
momepy                       0.6.0
more-itertools               10.5.0
moviepy                      1.0.3
mpmath                       1.3.0
msgpack                      1.1.0
multidict                    6.1.0
namex                        0.0.8
natsort                      8.4.0
nbclient                     0.10.0
nbconvert                    7.16.4
nbformat                     5.10.4
ndindex                      1.9.2
nest_asyncio                 1.6.0
networkx                     3.2.1
nodeenv                      1.9.1
numba                        0.60.0
numdifftools                 0.9.41
numexpr                      2.10.1
numpy                        1.26.4
numpy-groupies               0.11.2
nvidia-cublas-cu12           12.4.5.8
nvidia-cuda-cupti-cu12       12.4.127
nvidia-cuda-nvrtc-cu12       12.4.127
nvidia-cuda-runtime-cu12     12.4.127
nvidia-cudnn-cu12            9.1.0.70
nvidia-cufft-cu12            11.2.1.3
nvidia-curand-cu12           10.3.5.147
nvidia-cusolver-cu12         11.6.1.9
nvidia-cusparse-cu12         12.3.1.170
nvidia-nccl-cu12             2.21.5
nvidia-nvjitlink-cu12        12.4.127
nvidia-nvtx-cu12             12.4.127
open3d                       0.18.0
opencv-python                4.10.0.84
openpyxl                     3.1.5
opt_einsum                   3.4.0
optree                       0.13.0
packaging                    24.1
pandana                      0.7
pandas                       2.2.3
pandocfilters                1.5.1
parso                        0.8.4
paste-bio                    1.4.0
patsy                        0.5.6
pexpect                      4.9.0
pickleshare                  0.7.5
pillow                       10.4.0
pip                          24.3.1
platformdirs                 4.3.6
plotly                       5.24.1
pointpats                    2.4.0
pooch                        1.8.2
POT                          0.9.5
pre_commit                   4.0.1
proglog                      0.1.10
prompt_toolkit               3.0.48
propcache                    0.2.0
protobuf                     5.28.3
psutil                       6.1.0
ptyprocess                   0.7.0
PuLP                         2.9.0
pure_eval                    0.2.3
py-cpuinfo                   9.0.0
pyacvd                       0.3.1
Pygments                     2.18.0
pykdtree                     1.3.13
PyMCubes                     0.1.6
pymeshfix                    0.17.0
pynndescent                  0.5.13
pyogrio                      0.10.0
pyparsing                    3.2.0
pyproj                       3.6.1
pyquaternion                 0.9.9
pyro-api                     0.1.2
pyro-ppl                     1.9.1
pysal                        24.1
python-dateutil              2.9.0
python-dotenv                1.0.1
python-igraph                0.11.8
pytz                         2024.2
pyvista                      0.40.4
PyWavelets                   1.6.0
PyYAML                       6.0.2
pyzmq                        26.2.0
quantecon                    0.7.2
rasterio                     1.4.2
rasterstats                  0.20.0
referencing                  0.35.1
requests                     2.32.3
retrying                     1.3.4
rich                         13.9.4
rpds-py                      0.21.0
Rtree                        1.3.0
scanpy                       1.10.3
scikit-image                 0.18.0
scikit-learn                 1.4.2
scipy                        1.13.1
scooby                       0.10.0
seaborn                      0.13.2
segregation                  2.5.1
session-info                 1.0.0
setuptools                   75.3.0
shapely                      2.0.6
simplejson                   3.19.3
six                          1.16.0
soupsieve                    2.6
spaghetti                    1.7.4
spateo-release               1.1.0
spglm                        1.1.0
spint                        1.0.7
splot                        1.1.7
spopt                        0.5.0
spreg                        1.8
spvcm                        0.3.0
stack-data                   0.6.2
statsmodels                  0.14.4
stdlib-list                  0.11.0
sympy                        1.13.1
tables                       3.9.2
tenacity                     9.0.0
tensorboard                  2.18.0
tensorboard-data-server      0.7.2
tensorflow                   2.18.0
tensorflow-io-gcs-filesystem 0.37.1
termcolor                    2.5.0
texttable                    1.7.0
threadpoolctl                3.5.0
tifffile                     2024.8.30
tinycss2                     1.4.0
tobler                       0.12.0
torch                        2.5.1
tornado                      6.4.1
tqdm                         4.67.0
traitlets                    5.14.3
trame                        3.7.0
trame-client                 3.4.0
trame-server                 3.2.3
transforms3d                 0.3.1
trimesh                      4.5.2
triton                       3.1.0
typeguard                    4.4.1
typing_extensions            4.12.2
tzdata                       2024.2
umap-learn                   0.5.7
urllib3                      2.2.3
virtualenv                   20.27.1
vtk                          9.3.1
wcwidth                      0.2.13
webcolors                    24.11.1
webencodings                 0.5.1
Werkzeug                     3.0.6
wheel                        0.45.0
widgetsnbextension           4.0.13
wrapt                        1.16.0
wslink                       2.2.1
xyzservices                  2024.9.0
yarl                         1.17.1
zipp                         3.21.0

[YifanLu2000]

Hi @Li-ZhiD, are you running this on your local computer or on a server? Currently, st.tdr.interactive_rectangle_clip can only be run on a local computer.

[Li-ZhiD]

It doesn't work on my server's Desktop command line or jupyter.

[YifanLu2000]

Hi @Li-ZhiD, since Spateo internally uses PyVista, I’m unable to provide more specific suggestions. Generally, we recommend performing interactive operations, such as st.tdr.interactive_rectangle_clip, on a local Windows or Mac machine. Please refer to issue #278 for further guidance.