# Plots generated with %matplotlib widget are not being saved when converting to HTML file **URL:** \ **Category:** Jupyter Notebooks\ **Created:** [February 12, 2024, 5:54pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742 "2024-02-12T17:54:32Z")\ **Posts on this page:** 13\ **Page:** 1
**Author:** ![smazenou](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/s/7cd45c/32.png) [@smazenou](https://swan-community.web.cern.ch/u/smazenou)\ **Post date:** [February 12, 2024, 5:54pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/1 "2024-02-12T17:54:32Z")
Hello, I am trying to create notebook reports for archiving purposes, but it seems that the widget output is not saved. Steps to reproduce: 102 with nxcals pro, in a notebook called Untitled: ```auto import matplotlib.pyplot as plt import os import getpass import sys %matplotlib widget plt.plot([0, 1, 2, 3, 4], [0, 3, 1, 2, 5]) plt.show() os.system(f'{sys.executable} -m jupyter nbconvert --to html Untitled.ipynb') os.system(f'mv Untitled.html /eos/user/s/{getpass.getuser()}/') ``` Thanks in advance for your precious help. ---
**Author:** ![pesteves](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/p/f19dbf/32.png) [@pesteves](https://swan-community.web.cern.ch/u/pesteves)\ **Post date:** [March 4, 2024, 1:24pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/2 "2024-03-04T13:24:43Z")
Dear Simon, You can save the plot by using the following code: ```auto import matplotlib.pyplot as plt import os import getpass import sys # Create the plot plt.plot([0, 1, 2, 3, 4], [0, 3, 1, 2, 5]) # Save the plot as an image plt.savefig('/eos/user/s/YOURUSER/plot.png') # Show the plot plt.show() # Convert notebook to HTML os.system(f'{sys.executable} -m jupyter nbconvert --to html Untitled.ipynb') os.system(f'mv Untitled.html /eos/user/s/{getpass.getuser()}/') ``` Let me know if this works for you. I tested it and I could see the plot in the html file. Best, Pedro ---
**Author:** ![smazenou](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/s/7cd45c/32.png) [@smazenou](https://swan-community.web.cern.ch/u/smazenou)\ **Post date:** [March 4, 2024, 1:54pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/3 "2024-03-04T13:54:54Z")
Dear Petro, Thank you for this answer. However, I might not have been clear explaining my problem. I am developing notebooks for the MP3 group, and they would like to have both interactive notebooks (created with the magic command `%matplotlib widget`) and html reports of the notebook (created with the `jupyter nbconvert` command). The problem I’m facing is that interactive plots are not being saved in the html report, even though this behaviour works in vscode or in a “classic” jupyter environment. My quick fix was to add this comment to every plot: ```python %matplotlib inline # To display plots dynamically run the following line (don't forget to put again inline and run the cell again for the plot to appear in the report) # %matplotlib widget ``` However, this solution is far for being ideal given that matplotlib widget is not the default and that one has to rerun the cell to be able to zoom, and that one need to remember to rerun the cell with matplotlib inline for the plot to appear in the report. I hope those explanations were clearer and that you will be able to solve this issue 🙂 ---
**Author:** ![etejedor](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/e/e79b87/32.png) [@etejedor](https://swan-community.web.cern.ch/u/etejedor)\ **Post date:** [March 6, 2024, 1:49pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/4 "2024-03-06T13:49:46Z")
Dear Simon, So if I understand correctly, you want the generated HTML to have interactive plots? Or just a static image would do? Cheers, Enric ---
**Author:** ![smazenou](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/s/7cd45c/32.png) [@smazenou](https://swan-community.web.cern.ch/u/smazenou)\ **Post date:** [March 6, 2024, 2:11pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/5 "2024-03-06T14:11:21Z")
Dear Enric, I would like to have the images being static in the generated report indeed. Having interactive plots in the generated HTML report would be a nice to have, but it’s out of the scope of the issue. Cheers, Simon ---
**Author:** ![etejedor](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/e/e79b87/32.png) [@etejedor](https://swan-community.web.cern.ch/u/etejedor)\ **Post date:** [March 6, 2024, 2:16pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/6 "2024-03-06T14:16:20Z")
Dear Simon, It might be an issue with the nbconvert version that is in SWAN, I see this issue: > > > \# exporting matplotlib plots to html when using \`%matplotlib widget\` or \`noteboo…k\` > > I am sorry if this is a duplicate, but I have read a bunch of other issues and still don't understand if this should work or if it is correct behaviour. > > \# Problem: > > I am trying to export a notebook that contains matplotlib plots and using the magic command \`%matplotlib widget\` to get interactive plots. > See example: > > \`\`\`python > %matplotlib widget > > from matplotlib import pyplot as plt > from math import sin > > x = list(range(100)) > y = \[sin(x) for x in x\] > > plt.plot(x,y) > \`\`\` > > Reading \[this\](https://github.com/jupyter/nbclient/pull/75#issue-627213467), this way should work and be the desierd way. > > Now when exporting to html no images appear in the resulting file. I have tried these commands: > \`\`\`bash > jupyter-nbconvert --to html notebook.ipynb > jupyter-nbconvert --to html --execute notebook.ipynb > \`\`\` > > Using \`--execute\` I get parts of the widget (the buttons), but still not visible image. > > This also causes an issue downstream, where the pdf-exporter relies on the html exporter and there for \[has the same problem\](https://github.com/betatim/notebook-as-pdf/issues/34). > > \## Possible workarounds: > > One could just search and replace all magic commands and rerun. This will produce static images which will export just fine. But I feel like this is an unnecessary step and could be added as a feature. > > I personally don't care about the interactive features and could live with just a static image export. > > \## Some more analysis: > > The behaviour differs a lot depending on the tools used and in which order, which is part of why I am so confused. It seems like some temporary data > is stored somewhere, and a reboot is needed to get rid of it sometimes. Here are some attempts of untangling this: > > \- Running \`%matplotlob widget\` in VScode, then using \`jupyter-nbconvert --to html notebook.ipynb\` > \- Running \`%matplotlob widget\` in Jupyter Lab and than using \`jupyter-nbconvert --to html notebook.ipynb\` > \- Running \`%matplotlob widget\` with \`jupyter-nbconvert --execute notebook.ipynb --inplace & jupyter-nbconvert notebook.ipynb --to html\` > > With all of this the output datatype is set to \`"application/vnd.jupyter.widget-view+json"\`, which seems to be required \[as described here\](https://github.com/jupyter/nbconvert/issues/1081#issuecomment-528087715). > \`\`\`json > { > "output\_type": "display\_data", > "data": { > "application/vnd.jupyter.widget-view+json": { > "version\_major": 2, > "version\_minor": 0, > "model\_id": "c4687722682d4bbbb1fad0aa8e6e0d26" > }, > "image/png": "loads of base64....", > "text/plain": \[ > "Canvas(toolbar=Toolbar(toolitems=\[('Home', 'Reset original view', 'home', 'home'), ('Back', 'Back to previous …" > \] > }, > \`\`\` > > Most of the times this gets some javascript generated and displayes the wiget buttons, but no image. But the image is present as base64, which I assume should work, but doesn't? > Acationally this just doesn't work and has no javascript inside the resulting html file. > > > \- Running \`%matplotlob notebook\` in VScode, then using \`jupyter-nbconvert --to html notebook.ipynb\`: > not supported, doesn't work > \- Running \`%matplotlob notebook\` in Jupyter Lab and than using \`jupyter-nbconvert --to html notebook.ipynb\`: > This is the only instance that works!! A static image gets displayed. This seems to be because there is a \`\\` tag with base64 present that is used as a fallback: > \`\`\`json > "outputs": \[ > { > "data": { > "application/javascript": \[ > "so much JS......." > \], > "text/plain": \[ > "\" > \] > }, > "metadata": {}, > "output\_type": "display\_data" > }, > { > "data": { > "text/html": \[ > "\" //this seems to be what works > \], > "text/plain": \[ > "\" > \] > }, > "metadata": {}, > "output\_type": "display\_data" > }, > { > "data": { > "text/plain": \[ > "\[\\]" > \] > }, > "execution\_count": 1, > "metadata": {}, > "output\_type": "execute\_result" > } > \] > \`\`\` > > \- Running \`%matplotlob notebook\` with \`jupyter-nbconvert --execute notebook.ipynb --inplace\` and \`jupyter-nbconvert --execute notebook.ipynb --to html\`: > No result is shown. Once again a bunch of JS is generated, but doesn't seem to work inside the html. > \`\`\`json > "outputs": \[ > { > "data": { > "application/javascript": \[ > "loads of JS, once again...." > \], > "text/plain": \[ > "\" > \] > }, > "metadata": {}, > "output\_type": "display\_data" > }, > { > "data": { > "text/html": \[ > "\
\" // this has no imagedata attached > \], > "text/plain": \[ > "\" > \] > }, > "metadata": {}, > "output\_type": "display\_data" > }, > { > "data": { > "text/plain": \[ > "\[\\]" > \] > }, > "execution\_count": 1, > "metadata": {}, > "output\_type": "execute\_result" > } > \], > \`\`\` Are you running this from the SWAN Classic UI or from the new JupyterLab (Alma9)? I believe it’s worth trying in JupyterLab since there we have newer versions of all Jupyter packages. Cheers, Enric ---
**Author:** ![smazenou](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/s/7cd45c/32.png) [@smazenou](https://swan-community.web.cern.ch/u/smazenou)\ **Post date:** [March 6, 2024, 2:31pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/7 "2024-03-06T14:31:47Z")
Given that our notebooks requires NXCALS accees, we are stuck using 102b and CC7. ---
**Author:** ![etejedor](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/e/e79b87/32.png) [@etejedor](https://swan-community.web.cern.ch/u/etejedor)\ **Post date:** [March 6, 2024, 2:35pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/8 "2024-03-06T14:35:18Z")
Can you check if it works with %matplotlib notebook + jupyter nbconvert as suggested in the issue linked above? ---
**Author:** ![smazenou](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/s/7cd45c/32.png) [@smazenou](https://swan-community.web.cern.ch/u/smazenou)\ **Post date:** [March 6, 2024, 2:42pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/9 "2024-03-06T14:42:22Z")
%matplotlib notebook used to be working, but we had to pin it to version matplotlib==3.1.3 due to another bug (see [Bug in interactive matplotlib plots in SWAN notebooks](https://swan-community.web.cern.ch/t/bug-in-interactive-matplotlib-plots-in-swan-notebooks/419)) The problem is that we wanted to remove that old dependancy, so we switched to the notebook backend, created new plots in our notebook and now it would be a great effort to migrate everything back. ---
**Author:** ![smazenou](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/s/7cd45c/32.png) [@smazenou](https://swan-community.web.cern.ch/u/smazenou)\ **Post date:** [March 6, 2024, 2:44pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/10 "2024-03-06T14:44:44Z")
Also, fyi, the `ipympl` package (i.e. the one responsable for the %matplotlib widget magic command) is not installed on the JupyterLab environment. ---
**Author:** ![etejedor](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/e/e79b87/32.png) [@etejedor](https://swan-community.web.cern.ch/u/etejedor)\ **Post date:** [March 6, 2024, 2:48pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/11 "2024-03-06T14:48:19Z")
Can you please check if the conversion to HTML itself works well (with matplotlib widget) if you select LCG 105a (not NXCALS), CentOS7? If that is so, we are now in the process of creating a new NXCALS software stack that will be based on LCG 105a, so we would just wait until that is available and the problem would be solved. ---
**Author:** ![smazenou](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/s/7cd45c/32.png) [@smazenou](https://swan-community.web.cern.ch/u/smazenou)\ **Post date:** [March 6, 2024, 3:03pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/12 "2024-03-06T15:03:59Z")
It looks like I’m unable to generate %matplotlib widget plots with 105b somehow. However, if I update `ipympl` to latest and I restart the kernel, then it looks like everything is working as espected. Therefore, I think nxcals LCG 105a would be solving my issue. ---
**Author:** ![etejedor](https://swan-community.web.cern.ch/letter_avatar_proxy/v4/letter/e/e79b87/32.png) [@etejedor](https://swan-community.web.cern.ch/u/etejedor)\ **Post date:** [March 6, 2024, 3:18pm UTC](https://swan-community.web.cern.ch/t/plots-generated-with-matplotlib-widget-are-not-being-saved-when-converting-to-html-file/742/13 "2024-03-06T15:18:06Z")
Ok, good to hear. You can also request the SPI librarians ([https://its.cern.ch/jira/projects/SPI/issues](https://its.cern.ch/jira/projects/SPI/issues)) to update ipympl in the LCG releases. That won’t make it into 105a, but it will be there from 106 on (and therefore in the next NXCALS stack, whenever it’s created).