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openPMD / openPMD-viewer

:snake: Python visualization tools for openPMD files
https://openpmd-viewer.readthedocs.io/
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openPMD_viewer will not plot #425

Open wode-melon1 opened 3 months ago

wode-melon1 commented 3 months ago

Hello all, I am an intern trying to work with openPMD_viewer. I'm having problems getting plotted data using the viewer. The matplotlib notebook and matplotlib widget commands run without error and the GUI pops up but nothing seems to plot. I will attach a picture of what the view looks like. My environment I'm running from seems to have the right packages (jupyterlab and notebook) and so it is a confusing issue. Any help is appreciated, thank you. M

Screenshot 2024-07-17 at 11 27 56 AM

OS: Ventura Version 13.2.1

Here are the packages I'm working with

packages in environment at /Users/wodes/miniconda3/envs/Wake_T:

#

Name Version Build Channel

alabaster 0.7.16 pypi_0 pypi anyio 4.4.0 pypi_0 pypi applaunchservices 0.3.0 pypi_0 pypi appnope 0.1.4 pypi_0 pypi aptools 0.2.5 pypi_0 pypi argon2-cffi 23.1.0 pypi_0 pypi argon2-cffi-bindings 21.2.0 pypi_0 pypi arrow 1.3.0 pypi_0 pypi astroid 3.2.3 pypi_0 pypi asttokens 2.4.1 pypi_0 pypi async-lru 2.0.4 pypi_0 pypi atomicwrites 1.4.1 pypi_0 pypi attrs 23.2.0 pypi_0 pypi autopep8 2.0.4 pypi_0 pypi babel 2.15.0 pypi_0 pypi beautifulsoup4 4.12.3 pypi_0 pypi binaryornot 0.4.4 pypi_0 pypi black 24.4.2 pypi_0 pypi bleach 6.1.0 pypi_0 pypi bzip2 1.0.8 h6c40b1e_6
c-ares 1.32.2 h51dda26_0 conda-forge ca-certificates 2024.7.4 h8857fd0_0 conda-forge cached-property 1.5.2 hd8ed1ab_1 conda-forge cached_property 1.5.2 pyha770c72_1 conda-forge certifi 2024.7.4 pypi_0 pypi cffi 1.16.0 pypi_0 pypi chardet 5.2.0 pypi_0 pypi charset-normalizer 3.3.2 pypi_0 pypi click 3.3 pypi_0 pypi cloudpickle 3.0.0 pypi_0 pypi comm 0.2.2 pypi_0 pypi contourpy 1.2.1 pypi_0 pypi cookiecutter 2.6.0 pypi_0 pypi cycler 0.12.1 pypi_0 pypi debugpy 1.8.2 pypi_0 pypi decorator 5.1.1 pypi_0 pypi defusedxml 0.7.1 pypi_0 pypi deprecated 1.2.14 pypi_0 pypi diff-match-patch 20230430 pypi_0 pypi dill 0.3.8 pypi_0 pypi docstring-to-markdown 0.15 pypi_0 pypi docutils 0.21.2 pypi_0 pypi executing 2.0.1 pypi_0 pypi expat 2.6.2 hcec6c5f_0
fastjsonschema 2.20.0 pypi_0 pypi fbpic 0.26.0 pypi_0 pypi flake8 7.0.0 pypi_0 pypi fonttools 4.53.1 pypi_0 pypi fqdn 1.5.1 pypi_0 pypi h11 0.14.0 pypi_0 pypi h5py 3.11.0 nompi_py312hfc94b03_102 conda-forge hdf5 1.14.3 nompi_h687a608_105 conda-forge httpcore 1.0.5 pypi_0 pypi httpx 0.27.0 pypi_0 pypi icu 75.1 h120a0e1_0 conda-forge idna 3.7 pypi_0 pypi imagesize 1.4.1 pypi_0 pypi importlib-metadata 8.0.0 pypi_0 pypi inflection 0.5.1 pypi_0 pypi intervaltree 3.1.0 pypi_0 pypi ipykernel 6.29.5 pypi_0 pypi ipympl 0.9.4 pypi_0 pypi ipython 8.26.0 pypi_0 pypi ipython-genutils 0.2.0 pypi_0 pypi ipywidgets 8.1.3 pypi_0 pypi isoduration 20.11.0 pypi_0 pypi isort 5.13.2 pypi_0 pypi jaraco-classes 3.4.0 pypi_0 pypi jaraco-context 5.3.0 pypi_0 pypi jaraco-functools 4.0.1 pypi_0 pypi jedi 0.19.1 pypi_0 pypi jellyfish 1.0.4 pypi_0 pypi jinja2 3.1.4 pypi_0 pypi json5 0.9.25 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 8.6.2 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 4.2.3 pypi_0 pypi jupyterlab-pygments 0.3.0 pypi_0 pypi jupyterlab-server 2.27.3 pypi_0 pypi jupyterlab-widgets 3.0.11 pypi_0 pypi keyring 25.2.1 pypi_0 pypi kiwisolver 1.4.5 pypi_0 pypi krb5 1.21.3 h37d8d59_0 conda-forge libaec 1.1.3 h73e2aa4_0 conda-forge libblas 3.9.0 22_osx64_openblas conda-forge libcblas 3.9.0 22_osx64_openblas conda-forge libcurl 8.8.0 hf9fcc65_1 conda-forge libcxx 18.1.8 hef8daea_0 conda-forge libedit 3.1.20191231 h0678c8f_2 conda-forge libev 4.33 h10d778d_2 conda-forge libexpat 2.6.2 h73e2aa4_0 conda-forge libffi 3.4.4 hecd8cb5_1
libgfortran 5.0.0 13_2_0_h97931a8_3 conda-forge libgfortran5 13.2.0 h2873a65_3 conda-forge libhwloc 2.11.1 default_h456cccd_1000 conda-forge libiconv 1.17 hd75f5a5_2 conda-forge liblapack 3.9.0 22_osx64_openblas conda-forge libllvm14 14.0.6 hc8e404f_4 conda-forge libnghttp2 1.58.0 h64cf6d3_1 conda-forge libopenblas 0.3.27 openmp_h8869122_1 conda-forge libsqlite 3.45.2 h92b6c6a_0 conda-forge libssh2 1.11.0 hd019ec5_0 conda-forge libxml2 2.12.7 heaf3512_4 conda-forge libzlib 1.3.1 h87427d6_1 conda-forge llvm-openmp 18.1.8 h15ab845_0 conda-forge llvmlite 0.43.0 py312hdeb90da_0 conda-forge markdown-it-py 3.0.0 pypi_0 pypi markupsafe 2.1.5 pypi_0 pypi matplotlib 3.9.1 pypi_0 pypi matplotlib-inline 0.1.7 pypi_0 pypi mccabe 0.7.0 pypi_0 pypi mdurl 0.1.2 pypi_0 pypi mistune 3.0.2 pypi_0 pypi mkl 2023.2.0 h54c2260_50500 conda-forge more-itertools 10.3.0 pypi_0 pypi mpi 1.0 mpich conda-forge mpi4py 3.1.6 py312h908beef_1 conda-forge mpich 4.2.2 hd5a4e64_100 conda-forge mypy-extensions 1.0.0 pypi_0 pypi nbclient 0.10.0 pypi_0 pypi nbconvert 7.16.4 pypi_0 pypi nbformat 5.10.4 pypi_0 pypi ncurses 6.4 hcec6c5f_0
nest-asyncio 1.6.0 pypi_0 pypi notebook 7.2.1 pypi_0 pypi notebook-shim 0.2.4 pypi_0 pypi numba 0.60.0 py312hc3b515d_0 conda-forge numpy 1.26.4 pypi_0 pypi numpydoc 1.7.0 pypi_0 pypi openpmd-api 0.15.2 pypi_0 pypi openpmd-viewer 1.10.0 pypi_0 pypi openssl 3.3.1 h87427d6_1 conda-forge overrides 7.7.0 pypi_0 pypi packaging 24.1 pypi_0 pypi pandocfilters 1.5.1 pypi_0 pypi parso 0.8.4 pypi_0 pypi pathspec 0.12.1 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 24.0 py312hecd8cb5_0
platformdirs 4.2.2 pypi_0 pypi pluggy 1.5.0 pypi_0 pypi prometheus-client 0.20.0 pypi_0 pypi prompt-toolkit 3.0.47 pypi_0 pypi psutil 6.0.0 pypi_0 pypi ptyprocess 0.7.0 pypi_0 pypi pure-eval 0.2.2 pypi_0 pypi pycodestyle 2.11.1 pypi_0 pypi pycparser 2.22 pypi_0 pypi pydocstyle 6.3.0 pypi_0 pypi pyflakes 3.2.0 pypi_0 pypi pygments 2.18.0 pypi_0 pypi pylint 3.2.5 pypi_0 pypi pylint-venv 3.0.3 pypi_0 pypi pyls-spyder 0.4.0 pypi_0 pypi pyobjc-core 10.3.1 pypi_0 pypi pyobjc-framework-cocoa 10.3.1 pypi_0 pypi pyobjc-framework-coreservices 10.3.1 pypi_0 pypi pyobjc-framework-fsevents 10.3.1 pypi_0 pypi pyparsing 3.1.2 pypi_0 pypi pyqt5 5.15.10 pypi_0 pypi pyqt5-qt5 5.15.14 pypi_0 pypi pyqt5-sip 12.15.0 pypi_0 pypi pyqtwebengine 5.15.6 pypi_0 pypi pyqtwebengine-qt5 5.15.14 pypi_0 pypi python 3.12.2 h9f0c242_0_cpython conda-forge python-dateutil 2.9.0.post0 pypi_0 pypi python-json-logger 2.0.7 pypi_0 pypi python-lsp-black 2.0.0 pypi_0 pypi python-lsp-jsonrpc 1.1.2 pypi_0 pypi python-lsp-server 1.11.0 pypi_0 pypi python-slugify 8.0.4 pypi_0 pypi python_abi 3.12 4_cp312 conda-forge pytoolconfig 1.3.1 pypi_0 pypi pyyaml 6.0.1 pypi_0 pypi pyzmq 26.0.3 pypi_0 pypi qdarkstyle 3.2.3 pypi_0 pypi qstylizer 0.2.3 pypi_0 pypi qtawesome 1.3.1 pypi_0 pypi qtconsole 5.5.2 pypi_0 pypi qtpy 2.4.1 pypi_0 pypi readline 8.2 hca72f7f_0
referencing 0.35.1 pypi_0 pypi requests 2.32.3 pypi_0 pypi rfc3339-validator 0.1.4 pypi_0 pypi rfc3986-validator 0.1.1 pypi_0 pypi rich 13.7.1 pypi_0 pypi rope 1.13.0 pypi_0 pypi rpds-py 0.19.0 pypi_0 pypi rtree 1.3.0 pypi_0 pypi scipy 1.14.0 py312hb9702fa_1 conda-forge send2trash 1.8.3 pypi_0 pypi setuptools 69.5.1 py312hecd8cb5_0
six 1.16.0 pypi_0 pypi sniffio 1.3.1 pypi_0 pypi snowballstemmer 2.2.0 pypi_0 pypi sortedcontainers 2.4.0 pypi_0 pypi soupsieve 2.5 pypi_0 pypi sphinx 7.4.4 pypi_0 pypi sphinxcontrib-applehelp 1.0.8 pypi_0 pypi sphinxcontrib-devhelp 1.0.6 pypi_0 pypi sphinxcontrib-htmlhelp 2.0.5 pypi_0 pypi sphinxcontrib-jsmath 1.0.1 pypi_0 pypi sphinxcontrib-qthelp 1.0.7 pypi_0 pypi sphinxcontrib-serializinghtml 1.1.10 pypi_0 pypi spyder 5.5.5 pypi_0 pypi spyder-kernels 2.5.2 pypi_0 pypi sqlite 3.45.2 h7461747_0 conda-forge stack-data 0.6.3 pypi_0 pypi sublime 0.1.0 pypi_0 pypi tabulate 0.9.0 pypi_0 pypi tbb 2021.12.0 h3c5361c_3 conda-forge terminado 0.18.1 pypi_0 pypi text-unidecode 1.3 pypi_0 pypi textdistance 4.6.3 pypi_0 pypi three-merge 0.1.1 pypi_0 pypi tinycss2 1.3.0 pypi_0 pypi tk 8.6.13 h1abcd95_1 conda-forge tomli 2.0.1 pypi_0 pypi tomlkit 0.13.0 pypi_0 pypi tornado 6.4.1 pypi_0 pypi tqdm 4.66.4 pypi_0 pypi traitlets 5.14.3 pypi_0 pypi types-python-dateutil 2.9.0.20240316 pypi_0 pypi tzdata 2024a h04d1e81_0
ujson 5.10.0 pypi_0 pypi uri-template 1.3.0 pypi_0 pypi urllib3 2.2.2 pypi_0 pypi wake-t 0.8.0 pypi_0 pypi watchdog 4.0.1 pypi_0 pypi wcwidth 0.2.13 pypi_0 pypi webcolors 24.6.0 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi websocket-client 1.8.0 pypi_0 pypi whatthepatch 1.0.6 pypi_0 pypi wheel 0.43.0 py312hecd8cb5_0
widgetsnbextension 4.0.11 pypi_0 pypi wrapt 1.16.0 pypi_0 pypi wurlitzer 3.1.1 pypi_0 pypi xz 5.4.6 h6c40b1e_1
yapf 0.40.2 pypi_0 pypi zipp 3.19.2 pypi_0 pypi zlib 1.3.1 h87427d6_1 conda-forge zstd 1.5.6 h915ae27_0 conda-forge

ax3l commented 3 months ago

Thanks for the report.

That looks like an environment issue. Did you try to re-create your conda environment with a fresh version of Jupyter Lab, ipywidgets and openPMD-viewer?