nel-lab / mesmerize-core

High level pandas-based API for batch analysis of Calcium Imaging data using CaImAn
Other
58 stars 15 forks source link

widget wont load #278

Closed blogeman closed 6 months ago

blogeman commented 6 months ago

The visualization widget won't load and I'm having a difficult time tracking down the source of the problem. When using the "mcorr_cnmy.ipynb" demo notebook I always get the following errors (see attached photo). Any ideas on what I can try to fix this? Capture Capture1

kushalkolar commented 6 months ago

Did you install mesmerize-viz? The JavaScript errors show that jupyter_rfb and ipydatagrid aren't installed. They get installed when you install mesmerize-viz.

blogeman commented 6 months ago

The following output won't show the version of mesmerize-viz, but the attached picture from the output of conda list shows that it is version 0.1.0b1

In [8]: mesmerize_core.version Out[8]: '0.3.0'

In [9]: mesmerize_viz.version

AttributeError Traceback (most recent call last) Cell In[9], line 1 ----> 1 mesmerize_viz.version

AttributeError: module 'mesmerize_viz' has no attribute 'version'

Capture

blogeman commented 6 months ago

Also it appears that jupyter-rfb is installed at version 0.4.2 and ipydatagrid is installed at version 1.2.1

kushalkolar commented 6 months ago

Do you launch jupyterlab from one env and then launch a kernel using Python in another env? If so see this https://github.com/vispy/jupyter_rfb/issues/86

On Mon, Feb 19, 2024, 13:25 Brandon Logeman @.***> wrote:

Also it appears that jupyter-rfb is installed at version 0.4.2 and ipydatagrid is installed at version 1.2.1

— Reply to this email directly, view it on GitHub https://github.com/nel-lab/mesmerize-core/issues/278#issuecomment-1952990240, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACHXXRHZFXHJF5F4XGU7MD3YUOKJLAVCNFSM6AAAAABDPYKLQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJSHE4TAMRUGA . You are receiving this because you commented.Message ID: @.***>

blogeman commented 6 months ago

That is exactly what I have been doing, launching jupyterlab from a base environment and then switching to a kernel for a different conda environment. Installing jupyter-rfb and ipydatagrid in the base environment seems to have done the trick. Many thanks!

kushalkolar commented 6 months ago

My recommendation would be to launch jupyterlab directly from the env with mesmerize-core, mesmerize-viz, jupyter_rfb, and all other ipywidget libs. Otherwise you have to worry about versions matching between your base env and the other envs: https://github.com/Anaconda-Platform/nb_conda_kernels/issues/201#issuecomment-901068937