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ENH: Point cloud function and plotting function #16
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I'm rerunning all notebooks from scratch (the cyclo-octane one takes very long) so we can verify that the barcodes remain the same as in the paper. Will post screenshots here. |
Cyclo-octane: @ammedmar please could you check that these and the ones for Klein look good, I've run out of time for now. |
@ammedmar I have pushed a plotting function, You can test it on the Klein bottle notebook by adding the import line from steenroder.plotting import plot_diagrams and then e.g. by plotting the result of the last computation (R=1.3, absolute cohomology) via plot_diagrams(barcode[:3], st_barcode[:3], k=1, kind="A") |
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Lgtm! Just a small comment.
Thanks @gtauzin! I realized I forgot to document |
Testing on @ammedmar's machine shows that the plotting function does not work well in all systems. I think this is a MathJax-related issue because the function tries to produce LaTeX legend labels. The simplest way to fix this would be to agree on default legend label names that do not require LaTeX, and still allow LaTeX rendering as an option in case people want to try that and it works. @ammedmar what do you think? What would be suitable names to replace |
Yes, we can drop the LaTeX labels then. How about the following? |
@ammedmar I have now implemented your suggestion. Could you please check that the diagrams in the Klein bottle notebook (in this branch) display as expected for you? They display well at my end. |
I also tested it on the rpn an cp2 notebooks and it looks good. You were right about tex being the issue.
I don't think either of these needs to be address in this PR though. |
Thanks @ammedmar!
This is a good idea and would be one easy commit, I'll do it today.
This is harder and I'd indeed leave it to another PR -- I just note that one can make the whole figure bigger as a temporary fix. |
@ammedmar I've made the change. Let me know if happy to merge! |
Yes, it looks good! |
Fixes #14 and (partly) #13 and refactors notebooks accordingly.
Important: introduces
GUDHI
andplotly
requirements at installation time.Removes
check_agreement_with_gudhi
function which had been once used for debugging.Plotting is achieved in Plotly and it creates a 2D persistence diagram containing the regular bars and the Steenrod bars simultaneously.