Open saugatkandel opened 4 months ago
Thanks for getting in touch :-) Will try to reproduce and fix it. Can you share the tomo+embedding+umap?
I just tried this with the example data from the tutorial, and I still get the same problem. This is with my following exactly the steps from the tutorial, starting from the installation.
Thanks! Did the installation recently and everything worked fine. Will try to reproduce it though.
23.05.2024 20:57:20 saugatkandel @.***>:
I just tried this with the example data from the tutorial, and I still get the same problem. This is with my following exactly the steps from the tutorial, starting from the installation.
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This is my conda environment requirements:
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
anyio 4.3.0 pyhd8ed1ab_0 conda-forge
archspec 0.2.3 pyhd8ed1ab_0 conda-forge
argon2-cffi 23.1.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py310h2372a71_4 conda-forge
arrow 1.3.0 pyhd8ed1ab_0 conda-forge
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-lru 2.0.4 pyhd8ed1ab_0 conda-forge
attrs 23.2.0 pyh71513ae_0 conda-forge
babel 2.14.0 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pyha770c72_0 conda-forge
bleach 6.1.0 pyhd8ed1ab_0 conda-forge
boltons 23.1.1 pyhd8ed1ab_0 conda-forge
brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.27.0 hd590300_0 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
cffi 1.16.0 py310h2fee648_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
comm 0.2.2 pyhd8ed1ab_0 conda-forge
conda 24.1.2 py310hff52083_0 conda-forge
conda-libmamba-solver 24.1.0 pyhd8ed1ab_0 conda-forge
conda-package-handling 2.2.0 pyh38be061_0 conda-forge
conda-package-streaming 0.9.0 pyhd8ed1ab_0 conda-forge
debugpy 1.8.1 py310hc6cd4ac_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge
distro 1.9.0 pyhd8ed1ab_0 conda-forge
entrypoints 0.4 pyhd8ed1ab_0 conda-forge
exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge
executing 2.0.1 pyhd8ed1ab_0 conda-forge
filelock 3.13.4 pypi_0 pypi
fmt 10.2.1 h00ab1b0_0 conda-forge
fqdn 1.5.1 pyhd8ed1ab_0 conda-forge
gdown 5.1.0 pypi_0 pypi
h11 0.14.0 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
httpcore 1.0.5 pyhd8ed1ab_0 conda-forge
httpx 0.27.0 pyhd8ed1ab_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
icu 73.2 h59595ed_0 conda-forge
idna 3.6 pyhd8ed1ab_0 conda-forge
importlib-metadata 7.1.0 pyha770c72_0 conda-forge
importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge
importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge
ipykernel 6.29.3 pyhd33586a_0 conda-forge
ipython 8.22.2 pyh707e725_0 conda-forge
isoduration 20.11.0 pyhd8ed1ab_0 conda-forge
jedi 0.19.1 pyhd8ed1ab_0 conda-forge
jinja2 3.1.3 pyhd8ed1ab_0 conda-forge
json5 0.9.24 pyhd8ed1ab_0 conda-forge
jsonpatch 1.33 pyhd8ed1ab_0 conda-forge
jsonpointer 2.4 py310hff52083_3 conda-forge
jsonschema 4.21.1 pyhd8ed1ab_0 conda-forge
jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge
jsonschema-with-format-nongpl 4.21.1 pyhd8ed1ab_0 conda-forge
jupyter-lsp 2.2.5 pyhd8ed1ab_0 conda-forge
jupyter_client 8.6.1 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 py310hff52083_0 conda-forge
jupyter_events 0.10.0 pyhd8ed1ab_0 conda-forge
jupyter_server 2.13.0 pyhd8ed1ab_0 conda-forge
jupyter_server_terminals 0.5.3 pyhd8ed1ab_0 conda-forge
jupyterlab 4.1.6 pyhd8ed1ab_0 conda-forge
jupyterlab_pygments 0.3.0 pyhd8ed1ab_1 conda-forge
jupyterlab_server 2.26.0 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
libarchive 3.7.2 h2aa1ff5_1 conda-forge
libcurl 8.6.0 hca28451_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h807b86a_5 conda-forge
libgomp 13.2.0 h807b86a_5 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libmamba 1.5.7 had39da4_0 conda-forge
libmambapy 1.5.7 py310h39ff949_0 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libsodium 1.0.18 h36c2ea0_1 conda-forge
libsolv 0.7.28 hfc55251_0 conda-forge
libsqlite 3.45.2 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.6 h232c23b_0 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 h516909a_1000 conda-forge
mamba 1.5.7 py310h51d5547_0 conda-forge
markupsafe 2.1.5 py310h2372a71_0 conda-forge
matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge
menuinst 2.0.2 py310hff52083_0 conda-forge
mistune 3.0.2 pyhd8ed1ab_0 conda-forge
nbclient 0.10.0 pyhd8ed1ab_0 conda-forge
nbconvert-core 7.16.3 pyhd8ed1ab_1 conda-forge
nbformat 5.10.4 pyhd8ed1ab_0 conda-forge
ncurses 6.4.20240210 h59595ed_0 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
notebook-shim 0.2.4 pyhd8ed1ab_0 conda-forge
openssl 3.2.1 hd590300_1 conda-forge
overrides 7.7.0 pyhd8ed1ab_0 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge
parso 0.8.4 pyhd8ed1ab_0 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge
platformdirs 4.2.0 pyhd8ed1ab_0 conda-forge
pluggy 1.4.0 pyhd8ed1ab_0 conda-forge
prometheus_client 0.20.0 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.42 pyha770c72_0 conda-forge
psutil 5.9.8 py310h2372a71_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.6 py310h2372a71_0 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pygments 2.17.2 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.14 hd12c33a_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-fastjsonschema 2.19.1 pyhd8ed1ab_0 conda-forge
python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge
python_abi 3.10 4_cp310 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.1 py310h2372a71_1 conda-forge
pyzmq 25.1.2 py310h795f18f_0 conda-forge
readline 8.2 h8228510_1 conda-forge
referencing 0.34.0 pyhd8ed1ab_0 conda-forge
reproc 14.2.4.post0 hd590300_1 conda-forge
reproc-cpp 14.2.4.post0 h59595ed_1 conda-forge
requests 2.31.0 pyhd8ed1ab_0 conda-forge
rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge
rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge
rpds-py 0.18.0 py310hcb5633a_0 conda-forge
ruamel.yaml 0.18.6 py310h2372a71_0 conda-forge
ruamel.yaml.clib 0.2.8 py310h2372a71_0 conda-forge
send2trash 1.8.3 pyh0d859eb_0 conda-forge
setuptools 69.2.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sniffio 1.3.1 pyhd8ed1ab_0 conda-forge
soupsieve 2.5 pyhd8ed1ab_1 conda-forge
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
terminado 0.18.1 pyh0d859eb_0 conda-forge
tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.0.1 pyhd8ed1ab_0 conda-forge
tornado 6.4 py310h2372a71_0 conda-forge
tqdm 4.66.2 pyhd8ed1ab_0 conda-forge
traitlets 5.14.2 pyhd8ed1ab_0 conda-forge
truststore 0.8.0 pyhd8ed1ab_0 conda-forge
types-python-dateutil 2.9.0.20240316 pyhd8ed1ab_0 conda-forge
typing-extensions 4.11.0 hd8ed1ab_0 conda-forge
typing_extensions 4.11.0 pyha770c72_0 conda-forge
typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
uri-template 1.3.0 pyhd8ed1ab_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
webcolors 1.13 pyhd8ed1ab_0 conda-forge
webencodings 0.5.1 pyhd8ed1ab_2 conda-forge
websocket-client 1.7.0 pyhd8ed1ab_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yaml-cpp 0.8.0 h59595ed_0 conda-forge
zeromq 4.3.5 h59595ed_1 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zstandard 0.22.0 py310h1275a96_0 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
The linux version is:
Linux 4.18.0-513.18.1.el8_9.x86_64 x86_64
LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
Distributor ID: Rocky
Description: Rocky Linux release 8.9 (Green Obsidian)
Release: 8.9
Codename: GreenObsidian
Hey! The environment you posted has no napari installed. Is it maybe your base environment? Anyway, I just released a couple of fixes for the installation.
Can you run the following commands and try again?
mamba env remove -n napari-tomotwin
mamba env create -n napari-tomotwin -f https://raw.githubusercontent.com/MPI-Dortmund/napari-tomotwin/main/conda_env.yml
conda activate napari-tomotwin
pip install napari-tomotwin
I am following the tutorial steps, and have napari-tomotwin installed using the following command:
mamba env create -n napari-tomotwin -f https://raw.githubusercontent.com/MPI-Dortmund/napari-tomotwin/main/conda_env.yml
I can load the UMAP data into napari. At this point, my napari window looks like:
Now, when I click on the tomogram, I immediately get the error message:
Do you have any suggestions on how to resolve this?