VArrayViewer not displaying video, but a frozen frame.

[anna-teruel]

Hey! I've been using minian for a while and always worked perfectly. However, I've been trying to install it in a macos M1 with arm64 architecture, and although I can install it correctly, when I open my jupyter notebook and try to visualize raw data, it looks like my video is "frozen" and VArrayViewer shows only one frame. My 'varr' frame: 3000height: 600width: 600.

For installation, I cloned repository and run "pip install .", then I installed "pip install markupsafe==2.0" because it was desplying an error when tried to run "jupyter notebook". Although my mac has arm64, miniconda I have installed is 'macOS-10.16-x86_64-i386-64bit', which is compatible with minian.

In my environment, I have following packages installed. Perhaps it's an incompatibility issue? anyio 4.0.0 appnope 0.1.3 argon2-cffi 23.1.0 argon2-cffi-bindings 21.2.0 arrow 1.3.0 asciitree 0.3.3 asttokens 2.4.0 attrs 23.1.0 backcall 0.2.0 beautifulsoup4 4.12.2 bleach 6.0.0 bokeh 1.4.0 certifi 2023.7.22 cffi 1.16.0 cftime 1.6.2 click 8.1.7 cloudpickle 2.2.1 colorcet 3.0.1 comm 0.1.4 contourpy 1.1.1 cvxpy 1.3.2 cycler 0.12.0 dask 2021.2.0 datashader 0.12.1 datashape 0.5.2 debugpy 1.8.0 decorator 5.1.1 defusedxml 0.7.1 distributed 2021.2.0 ecos 2.0.12 entrypoints 0.4 exceptiongroup 1.1.3 executing 2.0.0 fasteners 0.19 fastjsonschema 2.18.1 ffmpeg-python 0.2.0 fonttools 4.43.0 fqdn 1.5.1 fsspec 2023.9.2 future 0.18.3 holoviews 1.12.7 idna 3.4 imageio 2.31.5 importlib-metadata 6.8.0 importlib-resources 6.1.0 ipykernel 6.25.2 ipython 8.12.3 ipython-genutils 0.2.0 ipywidgets 8.1.1 isoduration 20.11.0 jedi 0.19.1 Jinja2 2.11.3 joblib 1.3.2 jsonpointer 2.4 jsonschema 4.19.1 jsonschema-specifications 2023.7.1 jupyter 1.0.0 jupyter_client 7.4.9 jupyter-console 6.6.3 jupyter_core 5.3.2 jupyter-events 0.7.0 jupyter_server 2.7.3 jupyter_server_terminals 0.4.4 jupyterlab-pygments 0.2.2 jupyterlab-widgets 3.0.9 kiwisolver 1.4.5 llvmlite 0.35.0 locket 1.0.0 Markdown 3.4.4 MarkupSafe 2.0.0 matplotlib 3.7.3 matplotlib-inline 0.1.6 MedPy 0.4.0 minian 1.2.1 mistune 0.8.4 msgpack 1.0.7 multipledispatch 1.0.0 natsort 8.4.0 nbclassic 1.0.0 nbclient 0.5.13 nbconvert 6.4.5 nbformat 5.9.2 nest-asyncio 1.5.8 netCDF4 1.6.4 networkx 2.4 notebook 6.5.6 notebook_shim 0.2.3 numba 0.52.0 numcodecs 0.11.0 numpy 1.20.2 opencv-python 4.2.0.34 osqp 0.6.3 overrides 7.4.0 packaging 23.2 pandas 1.2.3 pandocfilters 1.5.0 panel 0.8.0 param 1.13.0 parso 0.8.3 partd 1.4.1 patsy 0.5.3 pexpect 4.8.0 pickleshare 0.7.5 Pillow 10.0.1 pip 23.2.1 pkgutil_resolve_name 1.3.10 platformdirs 3.10.0 prometheus-client 0.17.1 prompt-toolkit 3.0.39 psutil 5.9.5 ptyprocess 0.7.0 pure-eval 0.2.2 pycparser 2.21 pyct 0.5.0 pyFFTW 0.12.0 Pygments 2.16.1 PyMetis 2020.1 pyparsing 3.1.1 python-dateutil 2.8.2 python-json-logger 2.0.7 pytz 2023.3.post1 pyviz_comms 3.0.0 PyWavelets 1.4.1 PyYAML 6.0.1 pyzmq 24.0.1 qdldl 0.1.7.post0 qtconsole 5.4.4 QtPy 2.4.0 rechunker 0.3.3 referencing 0.30.2 rfc3339-validator 0.1.4 rfc3986-validator 0.1.1 rpds-py 0.10.3 scikit-image 0.18.1 scikit-learn 0.22.1 scipy 1.10.1 scs 3.2.3 Send2Trash 1.8.2 setuptools 68.2.2 SimpleITK 2.0.2 six 1.16.0 sk-video 1.1.10 sniffio 1.3.0 sortedcontainers 2.4.0 soupsieve 2.5 sparse 0.11.2 stack-data 0.6.3 statsmodels 0.14.0 tblib 2.0.0 terminado 0.17.1 testpath 0.6.0 tifffile 2023.7.10 toolz 0.12.0 tornado 6.3.3 tqdm 4.66.1 traitlets 5.10.1 types-python-dateutil 2.8.19.14 typing_extensions 4.8.0 uri-template 1.3.0 wcwidth 0.2.8 webcolors 1.13 webencodings 0.5.1 websocket-client 1.6.3 wheel 0.41.2 widgetsnbextension 4.0.9 xarray 0.17.0 zarr 2.16.1 zict 3.0.0 zipp 3.17.0

Please, find attached a video of what I see on my jupyter notebook. I have also tried to open jupyter with different browsers (safari and crhome), but error persist.

https://github.com/denisecailab/minian/assets/78961609/2393ebd1-06bd-4866-ad99-1ebc68b52985

I have tried with several videos. The one I am attaching is a video I analyzed a while ago, so I know the file is correct.

I don't know how to solve this issue, because I don't understand what's wrong. If anybody knows and could help, I would appreciate it.

Thanks!!

[Owenxz]

Hi, I had the same issue on linux, and downgrading pyviz_comms solved it as suggested by this post https://github.com/denisecailab/minian/issues/249#issue-1849967897

[anna-teruel]

Great! It was that. I downgraded it to pyviz_comms==2.0.2 and solved the problem. Thanks @Owenxz !!!!