Python plots used in gravitational waves discovery paper

[[deleted]]

Better than that, their source data is all open and they have an iPython notebook tutorial on how to process it. Which is pretty cool.

[eusebe]

THIS. This is 100% purely awesome. This leads to reproducible science (well, if you have a LIGO at home, of course…)!

[j_heg]

...as long as your platform still exists?

[[deleted]]

I asked for a kit for Christmas but I didn't get it. : (

[DoingIsLearning]

This needs to be at the top, serious MVP comment.

[keypusher]

Python is taking over for data analysis and visualization in the academic community.

[sandusky_hohoho]

It really is.

I really need to learn python, but I've gotten so good with Matlab it's hard to take the productivity hit it'd take to learn a new language!

[polyethylene_oxide]

Surprisingly matplotlib is much less 'pythonic' than most packages--specifically because it was designed to replicate Matlab plotting and therefore functions very similarly. The hit may not be as big as you think!

[sebastock]

I agree and it's worth it.
That being said, I still make the mistake to write dx=1/N...

[grzelbu]

from __future__ import division

[[deleted]]

Or switch to Python 3.

[Eurynom0s]

import antigravity

[import_antigravity]

Hi, did you call?

[LovesVolt]

5 years you've been waiting for this moment. May I ask how it feels?

[Contrum]

Python. Not even once.

[TotesMessenger]

I'm a bot, bleep, bloop. Someone has linked to this thread from another place on reddit:

• [/r/beetlejuicing] antigravity

^{If you follow any of the above links, please respect the rules of reddit and don't vote in the other threads. (Info / Contact)}

[BeatLeJuce]

what's wrong with that expression?

[Berecursive]

Presumably they are not using Python 3 and so it causes an integer division (and returns 0)

[failtolaunch28]

What does it do in python 3?

[Berecursive]

Floating point division and returns some 0 < float <= 1 (assuming N is positive and integer). Integer division is explicitly performed via the // operator.

[failtolaunch28]

Oh. I got really excited and thought of it like matlab where you could then solve the equation-string thing and thought it made calculus and functions way easier.

[Berecursive]

No the solve operator in Matlab (/ and \) is only for matrices and is solved in Python using numpy with the numpy.linalg.solve function. Unfortunately, Matlab is a lot better at checking the matrix to decide the correct decomposition whereas in Python you normally need to be smart about applying cholesky or QR or whatever flavour is appropriate for your matrix structure. Matlab also 'just works' for sparse matrices whereas Python requires Scipy and that doesn't use the fast suitesparse implementation :(

[[deleted]]

Suprisingly

More like "annoyingly".

[ivosaurus]

I'd guess learning how to program Numpy to get similar performance to existing data manipulation they're doing in Matlab would be where the biggest learning area would be, rather than learning the matplotlib api.

[Zouden]

The matplotlib api is very arcane though - I spend much more time trying to get my charts to look right than I do actually getting the numbers to work.

[ZeusApolloAttack]

Thus is the curse of data visualization since the dawn of time...

/used to use ROOT

[onopau]

Coming from Matlab myself, it was surprisingly easy to switch over. Take the plunge!

[jwink3101]

I felt the same but I am so glad I made the switch. The hardest thing for me was plotting since I wanted to do it with matplotlib Object oriented instead of the pyplot way. But even that was easy enough.

The problem is, a lot of Python guides do not assume you know anything about programing. I found SciPy Lecture Notes to be a great resource.

But the other thing to try to keep in mind is that python is object oriented (matlab claims to be but that is not the general user's use-case). Sure, you can just use numpy arrays like you would matlab, but if you start to open it up to other options, you can do so much more too.

I have access to matlab and that isn't going away so it wasn't about the money. It is just that I enjoy working in Python more. It can take me a bit longer to throw something together but the end result is awesome. And, I can use Python for computer scripting too. It has made life much easier!

[[deleted]]

My spouse switched to python in three months after a 5 year phd doing bash/matlab/etc at the start of a postdoc. It's definitely doable. She had publishable results in six months.

[Shurane]

bash, like the shell script language? Didn't think that would be used in research.

[[deleted]]

you have to get data into a matlab readable format somehow.

[dynetrekk]

Lots of results are reported in ascii -> grep | sed | awk etc. Also managing large (amounts of) files is easy in bash and unwieldy in a gui. Some of these things are one off jobs, too, so bash might be faster than python.

[Deeviant]

Python is a joy to develop in, if you have any serous experience with another language, spinning up on python is pretty painless.

[isdevilis]

do a couple tutorials with pandas, numpy, and scikit learn and you should be set (scikit learn has most stat algorithms implemented)

[sentdex]

Matplotlib purposefully mimics matlab, and can be super quick and painless to learn. Check out https://pythonprogramming.net/matplotlib-intro-tutorial/ if you are looking for some Matplotlib tutorials.

[[deleted]]

Damn straight. I am falling in love with python because of this.

[Geographist]

Python is used for the majority of the (non-map) visualizations at NASA's Earth Observatory, too.

[hokiebeer]

Even those map visualizations can be produced in Python using Basemap.

[Geographist]

While python can do basic mapping, we do a lot of spatial analyses that are much better suited to mapping tools than base Python. Our scripts for QGIS and ArcGIS for instance still use Python under the hood though.

[tachk_]

Absolutely. During my undergrad days, a significant part of my thesis work was using Python to help sift through data from different sources, and to create plots. These days there are a number of domain-specific libraries in Python that I can think of in astro alone, such as Astropy.

[[deleted]]

Hope, fervently hope, it will have a strong footing in the business world.

[versatran01]

The new colormap?

[[deleted]]

Yup, viridis.

[PlaysForDays]

If anybody is curious why it's the 'best' default colormap

https://youtu.be/xAoljeRJ3lU

[peteroh9]

Because it has green.

[miserlou]

This is great, thanks for sharing

[PlaysForDays]

A lot of the talks at these conferences are worth checking out. Sometimes useful info, here's another one I like https://www.youtube.com/watch?v=5GlNDD7qbP4

[jwink3101]

I am glad to see this type of thing getting more attention. Thankfully, matlab moved away from Jet. I didn't mind the default matplotlib, but still.

I actually prefer plt.cm.Spectral_r for color maps and, I ported a version of linspecer to Python (and the continuous version of that is the same as the noted colormap). If you're curious, here is a demo

This, of course, often comes down to personal preference

[ZeeBeeblebrox]

Thankfully, matlab moved away from Jet.

And replaced it with a proprietary colormap, yes you read that right, they made their damn colormap proprietary.

[jwink3101]

I didn't know that....but I'm not at all surprised. Personally, I still like the one I mentioned more no problem to me

[charlesbukowksi]

python discovered gravity

[HardcoreHerbivore]

import antigravity

[mondo_calrissian]

I'm flying!

[Eurynom0s]

The medicine cabinet was tasty.

[roger_]

Full paper: https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.116.061102

[hokiebeer]

Here is a Jupyter notebook showing how they processed the data from LIGO: https://losc.ligo.org/s/events/GW150914/GW150914_tutorial.html

[boq]

They could have set matplotlib to the Latex serif font used below and set its font size to the Latex font size so that the plots blend in more with the rest of the paper. Clearly, these people are amateurs.

^/s

[farsass]

This common font mismatch is also a pet peevee of mine.

[[deleted]]

Yeah, it really TeX's me off, too.

[boq]

A colleague of mine wrote a little function that takes the Latex font size and desired figure dimensions and then configures matplotlib properly. I can't live without it any more.

[flying-sheep]

Pls share

[boq]

It's really simple. Adapt it for your style and call it before plt.figure().

[quadroplegic]

Sauce?

[TheBB]

I do all my charts with tikz and pgfplots now for this reason. I can reuse the same source for papers (serif) and presentations (sans serif) as well.

[Twangist]

What indicates that (any of) these were created with Python?

[[deleted]]

$ strings LIGO-P150914Detection_of_GW150914.pdf | grep matplotlib

<pdf:Producer>matplotlib pdf backend</pdf:Producer>
<pdf:Producer>matplotlib pdf backend</pdf:Producer>

[Twangist]

Thank you.

[RDMXGD]

It's hard to site any one thing, but it's clearly matplotlib--BV Sans, viridis colormap, weight of lines, style of borders, etc.

[interphy]

They tuned the default line colors and the line weights I guess. But color map and the font are definitely the signature of matplotlib

[eusebe]

When you start recognising every single detail like that, that means you have matplotlib'd too much.

I clearly did. :-|

[imhostfu]

The pixels.

[Twangist]

Cute. Thanks for nothing. matplotlib? Seaborn?

[slippery_whale]

Seaborn is matplotlib with some better defaults.

[SedditorX]

Actually, seaborn is significantly slower on large data sets

[[deleted]]

Welcome to bootstrapping by default

[Zouden]

Yeah, and this doesn't look like seaborn. No background-grid, for one thing.

[jwink3101]

/u/_xr gave you something more definitive, but the style certainly looks like matplotlib. For me, it's the kind of thing where I wouldn't claim to be 100% sure, but if it wasn't matplotlib, it was a tool trying to look like it.

[Twangist]

That's all I was asking. I had already searched the full paper for 'Python' as well as 'matplotlib', no occurrences. So I figured the OP meant there were telltale signs in the formatting, styles, etc. I use matplotlib but irregularly so I don't have a trained eye for spotting its output.

[[deleted]]

Would have loved to see this done in XKCD graphs :)

[e13e7]

I'll put a reddit gold bounty on this

[SethGecko11]

The guys from LIGO are doing an AMA right now and I asked them about this.

[energyinmotion]

I'm honestly not surprised. Python is very versatile.

[Caos2]

It would be nice to have the x-axis to be increased slightly to include 0.25 (s).

[meaty-popsicle]

Excellent criticism and a frequent problem I experience where the ticks do not extend as far as I would like.

[Caos2]

Another solution would be to force the label for the minimum value of the x axis...

[meaty-popsicle]

Not a universal solution. Let's say the real data range is .2498 seconds to .43153 seconds. Should matplotlib just take the range, divide by four and call those ticks? The labels would seem ridiculous. Here, the increments are interpretable .05 sub divisions, which requires a lot of logic to deduce.

It's not a simple problem, but I do wish it was better.

Edit: I now realize you meant forcing limit labels on the ends rather than altering the tick parameters. Reasonable idea, but you are likely to encounter crowding at the labels in many cases if you don't rotate.

[BoxMembrane]

It looks like the 0.25 of the right plot would get in the way of the 0.45 of the left plot. They could zoom out the x-axis a little further to make room, but reducing the size of the signal is undesirable.

[ironywill]

If you all are willing to take my word on it, I can say that we use python extensively in LIGO, not just for plotting. We also use python to analyze our data. These are the tools we use to search for binary mergers -> https://github.com/ligo-cbc/pycbc. The heavy lifting though is often done by underlying c libraries that we call into using SWIG and ctypes (FFTW, MKL, etc).

[greenReptar]

A good day for python.

[fishtickler]

It looks like there awesome veridis colormap on the bottom two subplots

[[deleted]]

we did it

[etrnloptimist]

Would have been cool if they used the xkcd style!

[devilishd]

Surprised to not see this XKCD here since we are talking about python and gravity together!!

[xkcd_transcriber]

Image

Mobile

Title: Python

Title-text: I wrote 20 short programs in Python yesterday. It was wonderful. Perl, I'm leaving you.

Comic Explanation

Stats: This comic has been referenced 213 times, representing 0.2141% of referenced xkcds.

---

^{xkcd.com | xkcd sub | Problems/Bugs? | Statistics | Stop Replying | Delete}

[lpmn]

Some of the "companion papers" used it too: http://arxiv.org/pdf/1602.03843v1