Monday, October 5, 2020

Three Years in Melbourne

I'm a few days late to the exact date, but this week marks three years since I came to Melbourne. The weather is finally starting to show signs of spring, though being Melbourne it continues to oscillate wildly—I had to laugh a few days ago when I saw this prediction on my weather app:

Note the Monday high lower than the Sunday low.

Saturday and Sunday were indeed beautiful; I took a walk in shorts, T-shirt, and even sandals (for the first time in something like half a year) on Sunday and felt perfectly comfortable the entire time. Today, on the other hand, due to a cold front dumping lots of cold rain overnight, it's felt like right back into the depths of winter. I'm not too surprised, at least, as in my experience it takes till at least mid-November and some years even into December to really warm up in a sustained fashion.

Other than that, not much is going on here; we're all hoping for COVID-19 cases to drop enough to be able to ease some of the lockdown restrictions by the 19th, and I'm just recuperating from the last month or so of hard work for my final review. With the Daylight Savings Time change this weekend I've also got an hour's worth of jet-lag, so I should probably finish this up and get a good night's sleep. A hui hou!

Sunday, September 27, 2020

Finishing My Draft Thesis Review: Some Thoughts

This past Wednesday (the 23rd) I had my Draft Thesis Review, the final of the three annual reviews for PhD students at Swinburne. This review is for students to show off the culmination of their efforts to date, and also where students who still need some time to finish up can request an extension of six months, which is what I've done. (It's also what the vast majority of students do, at least in astrophysics; while Australian PhDs are nominally three years, in practice most people end up going over that time.) My project is progressing well, I just need a few more months to finish up the analysis of my results and publish; at this point the plan is to publish two papers together covering pretty much everything I've done for the past three years.

It's been pretty hectic the past month, writing the report for my panel along with work on the aforementioned papers, which will constitute most of the science chapters for my thesis as well. This is the first weekend I haven't worked in at least that long, and it was sorely needed. At least now I have a chance to catch my breath slightly before the final push over the next few months.

Now that the review is past, it's also time to start looking to the future. I'm still sorting out what I want to do after this at this point; my first preference would be to get a job back in Hawaii (probably with an observatory, given my prior experiences there), but after this past year I'm finding myself more amenable to the possibility of putting my skills to work in the medical industry somehow, perhaps for a few years, to do some good in the world. Maybe. Who knows! I've learned an absolute ton about programming over the past few years, so I've got some very broadly applicable skills, it just remains to see what's out there. But for now, I've got a timeline to write for my Finalization Plan to submit to the university, and then some analysis to get into! A hui hou!

Saturday, September 12, 2020

Drinking through Grass: Plant-Based Disposable Straws

Plastic is an incredible material which the vast majority of our ancestors would've gone to great lengths to obtain; imagine being able to store your grain for the winter in water, air, and vermin-proof containers which neither rust nor rot! Unfortunately, that extreme durability becomes a liability when used for products which are intended to be disposable, specifically drinking straws (as the increasing amounts of them ending up in the ocean show). Multiple different types of reusable straws are coming out on the market (and that's an admirable initiative), but they often have issues of their own, such as straws being difficult to wash out and possibly prone to mold.

Looking for another solution, a new company called Equo has created a range of disposable, plant-based straws which biodegrade over a few months or so. They had a Kickstarter campaign earlier this year, I backed it, and yesterday I finally got a chance to try some of their straw out!

The packaging got a little dented in transport, but the straws were all fine.

They offer four different kinds of straws, but I only got two, as I don't really use straws at home much. Or at all, really, I just thought they'd be fun to try out. They offer straws made from rice, coconut, sugarcane, and grass, as seen here. They're each made in slightly different ways, but it basically involves soaking or steaming the plant material into an elastic mush, then forming into straws as it dries. Except for the grass straws, which are simply stems from the grass Lepironia articulata, or grey sedge. They naturally form these hollow tubes, so they just need to be cut to size, sterilized, and packaged! Because they're natural grass stems, they don't go soggy in liquid—I used one yesterday, left it to dry overnight, and used it again today. They're all even edible (with maybe the exception of the grass ones), with Equo noting that you can cook the rice straws down into porridge after use, if you want, and simply eat the others.

I'm a huge sucker for more innovative use of our God-given natural resources, and from personal use I can give these the seal of approval, so I really hope these catch on. They're not yet available for sale generally, but now that they've started production hopefully we'll be seeing them ‘in the wild’ soon. A hui hou!

There's no way to look dignified while sipping through a straw, so I offer this photo of me trying out a sugarcane straw purely from a sense of scientific integrity.

Sunday, September 6, 2020

Some useful Unix utility replacements written in Rust

As I continue hurtling towards my Draft Thesis Review on the 23rd, frantically working on papers and my thesis to have ready for review, I thought I'd take a little time to show off some nifty command line utilities I came across recently. I learned about them from this useful blog post, and I'm only going to cover a few of the things listed there so be sure to check it out for yourself. I mentioned nearly a year ago that I was trying out the Xonsh shell ("konsh", like the snail), and it turns out I'm still using it (it's got some really helpful features like suggesting commands based on what you're typing and have used in the past), but these work just as well in Bash, and presumably other shells as well.

All of these utilities are written in Rust, a programming language which has been out for a decade at this point but which I only heard about for the first time in the early part of this year. It's a compiled, statically-typed language which bills itself as being like the venerable C language, but with a bunch of features which involve memory-safety built directly into it. It's not exactly widespread in use at this point, but the people who use it apparently love it, and I've been somewhat interested in learning it for a while time (maybe when I have time again). Anyway, let's get to the cool new utilities, which tend to be advertised as smarter, updated replacement for traditional Unix utilities you might be familiar with already. Today I'll briefly review two of them: fd, an updated find, and sd, an updated sed.

fd is first because it's the one I've found most useful personally so far. If I were to sum it up in one sentence, it'd be: "A utility that works like I always expect find to." find is an incredibly powerful utility, there's no doubt about that, but that comes at a cost of complexity. Let's say I'm in a directory, and I know that somewhere in the directories contained within this one is a file named “add_actions.lua”. I don't remember where, though, so I try to use find to locate it:

$ find add_actions.lua
find: ‘add_actions.lua’: No such file or directory

Well, that's not very helpful. The correct way to do what I want it to do it to add a -name flag before the name of the file I want; this finds the file correctly:

$ find -name add_actions.lua

I never remember this, however; just figuring this out for this example took me a few minutes of trying and reading the manual for find. I thought maybe you need to specify that you want to start searching in the directory you're currently in, by adding a period after find; this, it turns out, is unnecessary as that's the default action (so now I've wasted time remembering something superfluous). I also thought maybe I needed to specify that I was searching for things of type ‘file’ (and not, say, ‘directory’), which ultimately also turned out to be unnecessary but took me extra time to verify that that was the case. Now, the fact that the correct version doesn't require those additions does make the comparison slightly less impressive, but let's see how you would do this using fd:

$ fd add_actions.lua

Boom. No needing to add additional flags, it just intelligently assumes I'm giving the file name (or technically a regular expression to search against) if there are no flags or other arguments, and finds what I'm looking for by searching recursively starting from the current working directory. No looking up manuals or reading help files needed. Now, you might argue that this is a very simple example, and that's the point. I just want my computer to do what I want to do quickly so I can get back to doing whatever it was that caused me to need to find this file in the first place: fast, simple, easy, done. Much like find, fd comes with a host of options and flags which you can use to modify and specify your finding operation. I haven't looked into them deeply, and it's possible there are some use cases which find can handle which fd can't. And that's perfectly fine, computer have enough storage these days to hold both of them at once.

You might also say—in fact, I'll say it—if I used find more frequently I'd memorize its idiosyncrasies and not have this problem. And that's true, if I used it a few times per day I'd probably memorize in in a few days at most. But the fact is, I don't—I use find sporadically, perhaps every few weeks or even months, at just long enough intervals that I forget how to use it in between. (Especially if I were actually trying to perform a more complicated operation, such as only searching for files between two and four levels down created more than three weeks ago larger than 5 MB in size, for example. find can do all of that. I definitely don't remember how.)

Now that I've written it, I'm not quite sure whom this slightly long-winded apologia is directed against; die-hard find users who oppose making computer usage “too easy” for other people? (I mean, I know such people exist, but I doubt many of them read this blog.) Anyway, the basic point is that fd uses intelligent defaults to simplify your ability to find files using the command line and keep you from having to memorize specific details which serve to slow you down if you haven't. Let's look at a slightly more complicated example, using sd. Suppose I have a text file, ‘test.txt’, with the phrase “The rine in Spine falls minely on the pline,” and I'd like to correct it to a more Received English pronunciation. With sed, you could do:

sed -i s/ine/ain/g test.txt

This will change the text in the file to “The rain in Spain falls mainly on the plain.” (Which seems hydrologically unlikely if there are mountains nearby due to the rain-shadow effect, but I digress.) There are a few things of note in this command: the -i flag causes the substitutions to happen in the file, rather than merely printing the changed output to the terminal. The ‘s’ at the beginning tells sed this is a substitution. The ‘g’ at the end makes the substitution happen everywhere the pattern ‘ine’ is found, instead of just at the first location per line in the file. And the slashes work because there aren't any slashes in the text, but if there were I'd have to get creative with the symbols used to separate the before and after patterns. Contrast this with the equivalent command using sd:

sd ine ain test.txt

No flag to remember to add to make it have an actual effect on disk. No need to tell it yes, you want to change this in all locations rather than just the first one per line. And no arcane symbols separating patterns, making the whole thing much more readable, especially when you start using more complicated regular expressions with symbols in them. Now, sd is even less of a replacement for sed than fd was for find, because sed can actually do a lot more than just simple substitution; but sd acknowledges this on its GitHub page and says that it's just intended to focus on doing one thing, and doing it well (which is the Unix way, at heart!).

Anyway, that's enough to give you a taste of what these utilities can do and how they do it. I definitely suggest you check out the post I found these from and see which ones you might want to use for yourself, as there are quite a few covering a lot of different use cases. I've only actually used a few of them so far, but I've really enjoyed the ones I have, so hopefully you find something here to spice up your command line usage. (If nothing else, fd makes me actually eager to search for files using the command line, instead of reluctant like find does.) Happy computing! A hui hou!

Sunday, August 30, 2020

Painting Solar Twins (Quintuplets?)

Back in late February or early March, approximately 217 years ago before the lockdown started, I picked up a pack of five small artist's canvas boards. I didn't have a plan in mind for them at the time, but one of my fellow-students Christian, who's working on another aspect of the same problem for his PhD as I am, was having his first annual review soon, so we decided it would be fun if I painted all the panels to look like solar twin stars so he could put photos of them in his talk (as his research is focused on discovering new solar twins further away than the ones we know of now).

Solar twins, if you don't know, are simply stars that are very similar to our Sun, in temperature, mass, luminosity, etc.. They're the basis of my PhD project, which revolves around using solar twins to be able to get the first constraints on variation in the fine-structure constant from main-sequence stars. (I actually just made some plots representing the culmination of almost three years' of PhD work this past week, so perhaps I'll write some more about that when I have time; my final annual review, the Draft Thesis Review, is coming up on September 23 so I'm going to be insanely busy preparing for that the next few weeks.)

I quickly got the panels painted in time for them to be added to Christian's talk (see the picture below for what they looked like then), but I wasn't completely satisfied with them, and kept going back to play with them some more.

“Solar Quintuplets,” acrylic pentaptych on canvas, 10×10 cm.

I actually quite like the effect of these with the peaks of transparent yellow oxide, a color I really learned a lot about the nuances of while making these. I mixed it quite thinly with some transparent medium, giving it an almost honey-like color and consistency here. However, I felt the stars didn't quite have enough limb-darkening around the edges, so I decided to darken those ever so slightly. This, unfortunately, set me down a long trail of darkening the limbs too much, attempting to lighten the center by thin transparent glazes, overdoing it and lightening everything too much, etc., etc., until I've finally got them to something resembling what I imagined (though honestly, at this point I'm inclined to just accept that not every project works out and be done with them).

Anyway, here they are, taken outside in the full light of day, which almost doesn't work as well as taking them indoors with the flash on. Even the jet-blackness of Black 2.0 is overwhelmed by the Sun's light, making them look a bit washed out. They really do look better in person (and indoors), trust me! I do at least kind of like how the surface texture came out, though again it doesn't really display well here. Pretty much all my cool and fun gel mediums are sitting at my desk at Swinburne, so I had to get creative with the two jars of matte and gloss finish thick viscosity medium I had on hand to get that texture. 

As I said, I'm inclined to accept these as just not really working out and move on. They can't all be winners, and frankly I've had—what is to my mind—an almost surreal level of success in translating ideas from my head to canvas so far, so I'm fine with an occasional dud. I've discovered I don't particularly enjoy painting on these canvas panels, for whatever reason—I vastly prefer a stretched canvas or wooden surface, so I probably won't get these again. A good learning experience, I suppose. With that I'm down to the last piece of stretched canvas I have on had (which does have a picture in progress), so I'm really looking forward to the end of the lockdown (whenever that happens) and the opportunity to pick up some more of my paints and mediums and some more surfaces to paint on. There's a round wooden artist's board that's been sitting around at Swinburne since early this year that I can't wait to get back to working on; I've got a fun mixed-media idea that's been percolating in my head for most of a year now. Soon, hopefully! A hui hou!

Saturday, August 15, 2020

Order-of-magnitude Calculation, Or: How Many Numbers Am I Keeping Track Of?

I haven't talked about it much on here, but I'm coming to the end of my original three-year PhD period at the end of September, a week prior to which I've got my final annual review. I'll be applying for a six-month extension to finish writing the two papers which will contain the majority of my original contributions to the sum total of human knowledge, and which will make up the bulk of my thesis. I'm currently in the process of trying to get some results from all the measurements I've spent the past almost-three-years collecting, correcting, collating, and calibrating.

I got to thinking on Friday about just how many numbers I actually have to keep track of. I'm just going to do a quick order-of magnitude estimate here, as it'll get us close enough that it won't really matter. For starters, I have around 11,000 different observations (divvied up between 144 stars, but that's not really relevant here). In each observation, I've attempted to make ~150 measurements of the wavelength of specific absorption features corresponding to particular atomic transitions. Now, these ~150 measurements get several corrections applied to them, and I keep all those corrections and corrected measurements around too so I can go back and check them. This adds up to a total of 9 different arrays.

From those ~150 transition measurements I also construct ~200 pairs of transitions and collect measurements for them (which are the real results of my research), and that comprises (currently) another 3 arrays. There are a few more numbers I keep track of per-observation, but few enough that I'll leave them out for now. Doing the math here:


Yes, that's “billion” with a b. I'm actually surprised by this, because when I first tried doing this on Friday I got an answer an order-of-magnitude lower (22.5 million). I've done the math here several times, however, and it all checks out. Huh. That's…a lot of numbers. Well, technically, a lot of those are not numbers; specifically, they're Not-A-Numbers, or NaNs—essentially a computer-understandable way of saying N/A for cases were a measurement does not exist for some reason or another. Perhaps it would be better to call them “data points,” as I still need to keep track of which data points are numbers and which aren't, so it's still important for me to have ways to organize and keep tabs on all of them.

That's all for tonight, I just wanted to get that out of my head and down somewhere. Perhaps in a few months when I'm quite certain I won't be adding more arrays of numbers—I added several just this past week, actually—I'll do a more careful calculation and get an exact number, but for now, a hui hou!

Edit (September 8, 202): Argh, I knew there must be a mistake somewhere! I multiplied when I should've added and didn't parenthesize well; the correct calculation should've been:


I'm still planning to revisit this and do a post with a more accurate number a bit later on, so keep an eye out for that one.

Tuesday, August 4, 2020

Baking Cinnamon Rolls

This weekend I made some cinnamon rolls using a recipe from a friend, and they turned out pretty good. I think this is the first time I've done some proper baking with proper dough and yeast for…three years, perhaps? I took some pictures during the process and thought I'd show 'em off.

Here's the dough after letting it rise for an hour.
It's been so long since I last mixed up a proper dough. It's funny how the smells come back to you, like the way the yeast smells. I also have a ton of yeast left over now since the smallest package of it I could find was a half-kilogram, so I guess I need to do some more baking soon. I had a hankering for runzas just the other day…

Cutting up the rolled-up log of dough with the cinnamon mix inside.
This part reminded me of watching videos during tours of the Jelly Belly factory about how they make those little taffies with the pictures inside, by rolling up logs of ingredients and cutting across them.

Putting the rolls in the pan…

…and a half-hour later, when they'd risen some more and filled up the space.

Finally, baked, frosted, and sampled!
The frosting didn't work out quite so well unfortunately, as the butter wasn't softened all the way through. Which left little lumps of butter which later melted once spread over the piping hot rolls, visible here as the yellowish regions. Thankfully it doesn't seem to have affected the taste, these do indeed taste delectable. I left them in the oven a few minutes too long so they came out a bit more “done” than they should be, but I'd say they're still a solid 6 or 7 out of 10. Not too bad for a first try! I'll have to do these again sometime. A hui hou!

Sunday, August 2, 2020

A Doily and a Scarf

Approximately three centuries of subjective time ago, back in October 2018, I mentioned that I had taken up knitting and begun work on a scarf. And a few months ago (I think in May), I finally finished it! Then, because I had some yarn left over, haven't crocheted anything in a while, and was bored, I used the leftover yarn to crochet a doily off the top of my head in a few hours.

And here they both are!

When I picked that scarf pattern I decided I wanted something more advanced that a real beginner's-level pattern, and boy did I get it. Doing that cabling turned out to be really annoying, though it does look cool when I didn't mess up and make either one too many or too few rows between crossing the cable over. A friend of mine at the JCMT used to tell me that knitting was simpler than crochet and I finally get what she meant now, though in a way knitting is actually harder for me. It's true that crochet has a large variety of different stitch types while knitting only has two, but knitting is about keeping track of numbers of stitches much more than crochet generally is (at least, the things I tend to crochet) and it turns out I am pretty rubbish at keeping track of numbers of stitches, so I have a long way to go in knitting. But I do enjoy it. As of this writing, I've just ordered a few skeins of yarn online to give me something else to do as Melbourne goes into Stage 4 lockdown for six weeks. (I've never lived under a curfew before, it's mildly exciting. [For, I'm sure, the next day or two.]) I'm planning on both knitting and crocheting something, though I have yet to pick out patterns for either. We'll see what I end up doing! And maybe it'll take me less than a year to do this time. A hui hou!

Sunday, July 19, 2020

Painting the JCMT

While at home these past few months, I've been a bit constrained in my painting by a lack of painting materials (namely, I don't have a very wide array of colors with me—most of my paint is still at my desk in Swinburne, and will be there for at least the next month-and-a-half—and I also didn't have much canvas with me when the first lockdown started). However, I did have a canvas in progress which I started near the end of last year, of the James Clerk Maxwell Telescope where I used to work from 2013–2016. Thankfully, it didn't require a wide variety of colors, and I'd already blocked in about half of it back in November (based on the only in-progress picture of it I could find), though I took a few months' break from it after that. I've been working on it slowly off and on over the course of the lockdown(s), and I finally finished it last week.

“James Clerk Maxwell Telescope,” acrylic on canvas, 14×18”.

I based this off a photo taken by a college friend of mine who was a telescope operator at the JCMT for a few years, contemporaneously with me. If you're not familiar with the JCMT, it's a telescope which detects light in the sub-millimeter wavelength range, between infrared and radio waves. The dish itself sits behind the large Gore-Tex membrane in the world, which is the area in the middle of the painting with the contour lines. (The Gore-Tex is essentially invisible at sub-millimeter wavelengths, so it doesn't block the observations.)

(Incidentally, getting the contour lines to look not-wrong may have been the hardest part of the painting, as I painted them on only to realize they looked wrong at least twice. The membrane has a somewhat complicated shape, so I ended up drawing them on with pencil so I could more easily change them, and after several weeks of adjusting them they're at least approximately correct.)

Another neat fact about the JCMT is that the SCUBA-2 sub-millmeter camera (which I worked with primarily, though on the quality assurance side) is the coldest place in the known universe: the detector is kept at a working temperature of just 70 millikelvins above absolute zero. This is because the detector has to be colder than what it's observing to prevent swamping the observation with thermal noise, and sub-millimeter light comes from extremely cold gas and dust, on the order of a few to tens of kelvins.

Anyway, that's one of the things I've been working on lately. I'd like to do another painting of the other telescope I've worked at (the Yuan-Tseh Lee Array) on the last canvas I have with me, but as I only just started that this week it probably won't be done anytime soon (though it's also a much smaller canvas, so we'll see). Maybe I can start a series of “Observatories I Have Worked At.” And maybe in the future, it'll contain more than two paintings! Who knows? A hui hou!

Saturday, July 11, 2020

The Lockdown Life

This past Wednesday, Melbourne (and one shire to the north) went back into Stage 3 lockdown for six weeks due to rising case number of COVID-19. This is after we'd gotten all the way down a few days in early June with zero new reported cases, then a few weeks of just single-digit new cases. Then, near the end of June, we started getting double-digit numbers, which stretched into two weeks, then eventually breached triple digits just within the last week or so. In contrast, most of the rest of Australia has been completely or almost completely free of reported new cases, other than New South Wales which is still getting a low number irregularly. Practically overnight Victoria has became a pariah state, with all the other states and territories closing their borders and politely but firmly making it known that Victorians aren't welcome 'round these parts, y’hear?

It's a bit of a disappointment, considering we seemed to have beaten the virus more-or-less and were starting to open back up again. Out of an abundance of caution I didn't go anywhere since the lockdown started to lift in late May except for a single visit to friends, but as June progressed I was starting to think about heading into my desk at Swinburne to pick some things up (especially some more paint and something to paint on, as I have a very limited selection of the former and have nearly run out of the latter).

It's odd that this second lockdown hit me harder than the first one, considering I hadn't even really come out of the first one to begin with; I know friends who were starting to get out and about in the interim where it seemed like we were on top of things. It just feels more unjust somehow—those of us who've been being good for months now are forced back into lockdown through no fault of our own due to the actions of a relatively tiny amount of people who took "lockdown being lifted" for "business as usual" and ignored social distancing guidelines put in place to prevent exactly this happening. Before the lockdown, someone could be excused for not knowing what was happening amidst the confusion and unwittingly spreading the virus before becoming symptomatic; it's a lot harder to justify such behavior afterwards when they should know better.

Then as I was preparing to lead our small group Bible study Thursday night, a verse in 1 Peter I'd been looking at all week jumped out at me:
For is it better, if the will of God, that you suffer for doing what is right rather than for doing what is wrong.
   —1 Peter 3:17
While it's still pretty annoying to have to forego any hope of taking a trip anywhere further than walking distance for another month and a half, I can at least agree with this in principle: I'm glad the lockdown isn't of my doing, and I don't have any lives on my conscience from spreading the virus to potential victims. It's just frustrating when the reward for doing good is the absence of a negative rather than a more tangible positive, but I suppose that's just the world we live in. And that I'd probably feel rather differently if I were in the other position.

In the meantime, it's not like I'm ever going to run out of things to do from my home: I've still got a Ph.D. to finish, papers and a thesis to write, plenty of games that won't play themselves, some art projects I should really get around to finishing and sharing, and I've started copying Brahm's absolutely fantastic “Variations and Fugue on a Theme by Handel,” which is of pleasantly maddening complexity. (I find myself needing to dive into the LilyPond documentation quite frequently to figure out how to represent the various intricacies and special cases of music notation that pop up.) And hey, at least it beats being in the hospital! A hui hou!