7 ms·

An open access book on scientific visualization using Python and Matplotlib

309 points by sebg 5y ago

joelbondurant 5y ago
All pre-science must be registered with the Science Ministry to be ordained Fact-Check within 90 days or drone strikes will melt your mother's tombstone.
pmdulaney 5y ago
This is beautiful!
mistermann 5y ago
Does anyone know of a site where people submit visualizations, where one might find these tools pushed to the extremes of what they can do in novel ways?
- webmaven 5y ago
  Perhaps the Information is Beautiful site?: https://informationisbeautiful.net https://informationisbeautiful.net There is also the Data is Beautiful reddit: https://www.reddit.com/r/dataisbeautiful/ https://www.reddit.com/r/dataisbeautiful/
  - mindcrime 5y ago
    Perhaps also https://www.reddit.com/r/dataviz/ https://www.reddit.com/r/dataviz/
- wswope 5y ago
  Apologies if it’s not what you had in mind, but the examples in the MPL docs are exceptionally thorough when it comes to showing off advanced features (though they can be quite hard to parse). https://matplotlib.org/stable/gallery/index.html https://matplotlib.org/stable/gallery/index.html
- nefitty 5y ago
  My friend, if you have not heard of it already, I am proud to introduce you to the magic that is Observable: https://observablehq.com/collection/@observablehq/visualization https://observablehq.com/collection/@observablehq/visualizat... I'm a full stack web dev, not a data scientist, but Observable has dramatically changed my relationship to code. The last time I felt this excited by programming was about 20 years ago when I was in middle school and discovered Game Maker's scripting language...
- DataCrayon 5y ago
  some examples on https://plotapi.com/gallery/ https://plotapi.com/gallery/ and https://datacrayon.com https://datacrayon.com
jointpdf 5y ago
This person is prolific and has a ton of great tutorials, free books, and more in their repo (I like the numpy book: https://www.labri.fr/perso/nrougier/from-python-to-numpy/ https://www.labri.fr/perso/nrougier/from-python-to-numpy/). Major thanks to the author for sharing all this knowledge.
- rougier 5y ago
  Thanks!
  - belter 5y ago
    Thank you for this: https://rougier.github.io/python-visualization-landscape/landscape-colors.html https://rougier.github.io/python-visualization-landscape/lan... and your other interesting projects.
  - bloqs 5y ago
    Fantastic work!
abetusk 5y ago
This book is distributed under a non commercial license (CC-BY-NC-SA 4.0) [0]. While I understand that language is evolving and that only under a "strict definition" of open access does it mean removing barriers to copying and reuse [1], it's seems pretty duplicitous to say it's "open" while putting it under a non-commercial license. [0] https://github.com/rougier/scientific-visualization-book/blob/master/LICENSE.txt https://github.com/rougier/scientific-visualization-book/blo... [1] https://en.wikipedia.org/w/index.php?title=Open_access&oldid=1053544406 https://en.wikipedia.org/w/index.php?title=Open_access&oldid...
- deleted 5y ago
  [deleted]
- marmaduke 5y ago
  Maybe you could explain why a non commercial license would not be open, for anyone not looking to turn a profit off of the author’s work?
- jjnoakes 5y ago
  To expand upon this a little, it's worth noting that the book and the code are licensed separately and differently.
  - rougier 5y ago
    Yes, code is BSD licensed.
- mindcrime 5y ago
  it's seems pretty duplicitous to say it's "open" while putting it under a non-commercial license. I can't really agree with that. For open source, yes, the OSD does make it clear that the definition does not permit licenses that prevent commercial resale. But "open access" for scientific works, or just technical documentation in general, does not seem - in vernacular use - to entail such a strict requirement. Of course as an advocate of "free culture" in the most general sense, I might say I would prefer a book, paper, article, etc. to be published under something less restrictive. But I see nothing "duplicitious"[1] about this particular usage. Consider that the corresponding Wikipedia entry on Open Access[2] contains this blurb, which supports the idea that both "gratis open access" and "libre open access" would be considered sub-types of the more general idea of "open access." Similar to the free content definition, the terms 'gratis' and 'libre' were used in the BOAI definition to distinguish between free to read versus free to reuse.[38] Gratis open access (Free to read) refers to online access free of charge, and libre open access (open access) refers to online access free of charge plus some additional re-use rights [1]: https://www.vocabulary.com/dictionary/duplicitous https://www.vocabulary.com/dictionary/duplicitous [2]: https://en.wikipedia.org/wiki/Open_access https://en.wikipedia.org/wiki/Open_access
earthscienceman 5y ago
Does anyone know if M. Rougier has posted his emacs config for python? I'm heavy on the emacs/python/science and I'm curious if he uses any of the more extensive packages, like elpy.
- rougier 5y ago
  I'm using default python mode actually (no elpy, no lsp) and emacs python configuration is maybe 3 or 4 lines.
  - earthscienceman 5y ago
    Make sense, cheers from an American scientist ! I purchased the hard copy despite it being from Amazon, although I understand the logistics at play there. J'étais à Polytechnique à Paris pendant deux ans, j'aimerais que les Américains soient aussi au logiciel "Open Source" que les Français
    - kergonath 5y ago
      One of the reasons why we do it is that we don’t have the same funding lying around. And also a different attitude towards intellectual property and a strong dislike of being effectively hostage of a for-profit software company. At least that’s the feeling around here (not X, but close enough to meet people there for lunch :) ). It is still more difficult than we’d like to get funded for Open Source development (as a non-CS scientist), but there have been some encouraging noise recently, and some political will to reduce our reliance on black-box commercial software.
    - rougier 5y ago
      I tried to avoid Amazon and even found a French printers but the mailing costs were too high outside Europe.
andersource 5y ago
This is the most visually aesthetic book I've ever seen, and seems to be amazingly thorough in material. Thanks for this!
newtwilly 5y ago
Anyone have experience with both MatPlotLib and Vega / Vega-lite? I like working in Clojure and am just about to do a bunch of data-viz. I've only done a simple line chart so far, and I used this oz library for interfacing with Clojure and displaying results in the browser. [1] One of the problems was lack of error messages. Not sure what part of the tooling was failing me there. [1]. https://github.com/metasoarous/oz https://github.com/metasoarous/oz
- gimagon 5y ago
  I can't speak to oz's error messages, but for the vega-lite + python integration, I've found altair pretty usable. In particular, simple scatter plots with tooltips were easy to get up and running. https://altair-viz.github.io/ https://altair-viz.github.io/ https://altair-viz.github.io/gallery/scatter_tooltips.html?highlight=tooltips https://altair-viz.github.io/gallery/scatter_tooltips.html?h...
- geokon 5y ago
  if you need simple output you can just run clojure in orgmode and output svg https://geokon-gh.github.io/literate-clojure.html https://geokon-gh.github.io/literate-clojure.html
  - newtwilly 5y ago
    Thanks for sharing. I may do this if I ever decide to do some 'notebook' style work. Oz mentions integrating with jupyter and whatever else, but I love org-mode and wouldn't really want to start using a tool other than Emacs if I could avoid it :)
    - geokon 5y ago
      To be clear, there isn't really any org magic going on. You can also do the same identical stuff directly from a REPL and just spit the SVGs to file. I've also used the same stuff in a GUI - where the SVGs are rendered directly in the UI (I just parse the SVG elements and draw to the Canvas) Oz/Vega/etc. innately have this blackbox JS layout/rendering layer which I'm weary of. Here you are just manipulating SVG hiccup directly in Clojure. And then at the very last stage it's exported to SVG's XML syntax.
RyEgswuCsn 5y ago
Both the book and the organisation of the sources for the book are very impressive. Thanks for the marvellous work!
oolonthegreat 5y ago
looks very nice and thorough! can't wait to have some free time in my hands to dive into it, thanks for the work.
totetsu 5y ago
I'm looking for a Library that can make timed message sequence diagrams. I.e message flows with timeouts and windows, for presenting radio protocols. Anyone know of one?
- kejaed 5y ago
  Some scripting and PlantUML might work.

309 points by sebg 5y ago

All pre-science must be registered with the Science Ministry to be ordained Fact-Check within 90 days or drone strikes will melt your mother's tombstone.

pmdulaney 5y ago

This is beautiful!

mistermann 5y ago

Does anyone know of a site where people submit visualizations, where one might find these tools pushed to the extremes of what they can do in novel ways?

webmaven 5y ago
Perhaps the Information is Beautiful site?: https://informationisbeautiful.net https://informationisbeautiful.net There is also the Data is Beautiful reddit: https://www.reddit.com/r/dataisbeautiful/ https://www.reddit.com/r/dataisbeautiful/
- mindcrime 5y ago
  Perhaps also https://www.reddit.com/r/dataviz/ https://www.reddit.com/r/dataviz/
wswope 5y ago
Apologies if it’s not what you had in mind, but the examples in the MPL docs are exceptionally thorough when it comes to showing off advanced features (though they can be quite hard to parse). https://matplotlib.org/stable/gallery/index.html https://matplotlib.org/stable/gallery/index.html
nefitty 5y ago
My friend, if you have not heard of it already, I am proud to introduce you to the magic that is Observable: https://observablehq.com/collection/@observablehq/visualization https://observablehq.com/collection/@observablehq/visualizat... I'm a full stack web dev, not a data scientist, but Observable has dramatically changed my relationship to code. The last time I felt this excited by programming was about 20 years ago when I was in middle school and discovered Game Maker's scripting language...
DataCrayon 5y ago
some examples on https://plotapi.com/gallery/ https://plotapi.com/gallery/ and https://datacrayon.com https://datacrayon.com

jointpdf 5y ago

This person is prolific and has a ton of great tutorials, free books, and more in their repo (I like the numpy book: https://www.labri.fr/perso/nrougier/from-python-to-numpy/ https://www.labri.fr/perso/nrougier/from-python-to-numpy/). Major thanks to the author for sharing all this knowledge.

rougier 5y ago
Thanks!
- belter 5y ago
  Thank you for this: https://rougier.github.io/python-visualization-landscape/landscape-colors.html https://rougier.github.io/python-visualization-landscape/lan... and your other interesting projects.
- bloqs 5y ago
  Fantastic work!

abetusk 5y ago

This book is distributed under a non commercial license (CC-BY-NC-SA 4.0) [0]. While I understand that language is evolving and that only under a "strict definition" of open access does it mean removing barriers to copying and reuse [1], it's seems pretty duplicitous to say it's "open" while putting it under a non-commercial license. [0] https://github.com/rougier/scientific-visualization-book/blob/master/LICENSE.txt https://github.com/rougier/scientific-visualization-book/blo... [1] https://en.wikipedia.org/w/index.php?title=Open_access&oldid=1053544406 https://en.wikipedia.org/w/index.php?title=Open_access&oldid...

deleted 5y ago
[deleted]
marmaduke 5y ago
Maybe you could explain why a non commercial license would not be open, for anyone not looking to turn a profit off of the author’s work?
jjnoakes 5y ago
To expand upon this a little, it's worth noting that the book and the code are licensed separately and differently.
- rougier 5y ago
  Yes, code is BSD licensed.
mindcrime 5y ago
it's seems pretty duplicitous to say it's "open" while putting it under a non-commercial license. I can't really agree with that. For open source, yes, the OSD does make it clear that the definition does not permit licenses that prevent commercial resale. But "open access" for scientific works, or just technical documentation in general, does not seem - in vernacular use - to entail such a strict requirement. Of course as an advocate of "free culture" in the most general sense, I might say I would prefer a book, paper, article, etc. to be published under something less restrictive. But I see nothing "duplicitious"[1] about this particular usage. Consider that the corresponding Wikipedia entry on Open Access[2] contains this blurb, which supports the idea that both "gratis open access" and "libre open access" would be considered sub-types of the more general idea of "open access." Similar to the free content definition, the terms 'gratis' and 'libre' were used in the BOAI definition to distinguish between free to read versus free to reuse.[38] Gratis open access (Free to read) refers to online access free of charge, and libre open access (open access) refers to online access free of charge plus some additional re-use rights [1]: https://www.vocabulary.com/dictionary/duplicitous https://www.vocabulary.com/dictionary/duplicitous [2]: https://en.wikipedia.org/wiki/Open_access https://en.wikipedia.org/wiki/Open_access

earthscienceman 5y ago

Does anyone know if M. Rougier has posted his emacs config for python? I'm heavy on the emacs/python/science and I'm curious if he uses any of the more extensive packages, like elpy.

rougier 5y ago
I'm using default python mode actually (no elpy, no lsp) and emacs python configuration is maybe 3 or 4 lines.
- earthscienceman 5y ago
  Make sense, cheers from an American scientist ! I purchased the hard copy despite it being from Amazon, although I understand the logistics at play there. J'étais à Polytechnique à Paris pendant deux ans, j'aimerais que les Américains soient aussi au logiciel "Open Source" que les Français
  - kergonath 5y ago
    One of the reasons why we do it is that we don’t have the same funding lying around. And also a different attitude towards intellectual property and a strong dislike of being effectively hostage of a for-profit software company. At least that’s the feeling around here (not X, but close enough to meet people there for lunch :) ). It is still more difficult than we’d like to get funded for Open Source development (as a non-CS scientist), but there have been some encouraging noise recently, and some political will to reduce our reliance on black-box commercial software.
  - rougier 5y ago
    I tried to avoid Amazon and even found a French printers but the mailing costs were too high outside Europe.

andersource 5y ago

This is the most visually aesthetic book I've ever seen, and seems to be amazingly thorough in material. Thanks for this!

newtwilly 5y ago

Anyone have experience with both MatPlotLib and Vega / Vega-lite? I like working in Clojure and am just about to do a bunch of data-viz. I've only done a simple line chart so far, and I used this oz library for interfacing with Clojure and displaying results in the browser. [1] One of the problems was lack of error messages. Not sure what part of the tooling was failing me there. [1]. https://github.com/metasoarous/oz https://github.com/metasoarous/oz

gimagon 5y ago
I can't speak to oz's error messages, but for the vega-lite + python integration, I've found altair pretty usable. In particular, simple scatter plots with tooltips were easy to get up and running. https://altair-viz.github.io/ https://altair-viz.github.io/ https://altair-viz.github.io/gallery/scatter_tooltips.html?highlight=tooltips https://altair-viz.github.io/gallery/scatter_tooltips.html?h...
geokon 5y ago
if you need simple output you can just run clojure in orgmode and output svg https://geokon-gh.github.io/literate-clojure.html https://geokon-gh.github.io/literate-clojure.html
- newtwilly 5y ago
  Thanks for sharing. I may do this if I ever decide to do some 'notebook' style work. Oz mentions integrating with jupyter and whatever else, but I love org-mode and wouldn't really want to start using a tool other than Emacs if I could avoid it :)
  - geokon 5y ago
    To be clear, there isn't really any org magic going on. You can also do the same identical stuff directly from a REPL and just spit the SVGs to file. I've also used the same stuff in a GUI - where the SVGs are rendered directly in the UI (I just parse the SVG elements and draw to the Canvas) Oz/Vega/etc. innately have this blackbox JS layout/rendering layer which I'm weary of. Here you are just manipulating SVG hiccup directly in Clojure. And then at the very last stage it's exported to SVG's XML syntax.

RyEgswuCsn 5y ago

Both the book and the organisation of the sources for the book are very impressive. Thanks for the marvellous work!

oolonthegreat 5y ago

looks very nice and thorough! can't wait to have some free time in my hands to dive into it, thanks for the work.

totetsu 5y ago

I'm looking for a Library that can make timed message sequence diagrams. I.e message flows with timeouts and windows, for presenting radio protocols. Anyone know of one?

kejaed 5y ago
Some scripting and PlantUML might work.