MATLAB Tip of the Day: Counting in the Command Window

This is actually a two-fer: padding a number with a variable number of leading zeros or spaces and updating text in the Command Window without creating a bunch of new lines.

Variable number padding

The sprintf function includes in its documentation the instructions for padding a number with leading zeros.

myNumber = 4
paddedNumber = sprintf('%02d', myNumber)

paddedNumber =
        04

But what do you do when you don't know how many zeros you'll want to use? You need another variable. The syntax looks like this:

paddedNumber = sprintf('%0*d', numDigits, myNumber)

If I specify numDigits, I can pad myNumber with any number of zeros I choose. Of course, I need to define numDigits somehow. In the FrameCounter function below, I want to have enough leading zeros that my last frame has no zeros out front. So if my last frame is 123, I should get two leading zeros for numbers less than 10, one leading zero for numbers up to 99, and then no leading zeros for the rest. Here's how I like to do it:

numDigits = length(sprintf('d', lastNumber));

This is to say, I write out the number as a string and calculate how many characters that is (i.e. the length of the string). That's how many digits I need to do the padding. Simple.

Updating text in the Command Window

I was using a program in MATLAB that took a long time to run and had an unfortunate tendency to crash¹. I wanted to know which frame it had been working on before it failed, and in general I wanted to have some idea how much progress it had made. At the time, I wasn't aware of the built-in progress bar, and then I learned that that can actually slow down whatever process it is you're trying to keep tabs on, so I wrote my own. It just printed the current frame number to the Command Window every ten frames or so, which was enough to narrow down the range of the failed frame. Every time a new frame was printed to the Command Window, though, it made a new line, and after thousands of successful frames, I had a Command Window full of numbers. What I wanted was a way to update the number in place, without printing a new line.

In 2011, I went to the CPLC Summer School at UIUC (which was pretty fun and enlightening) and I saw what I wanted in action in an analysis program. I didn't have a chance to look at the source, though, so I asked how it worked. The student I was working with said he didn't recall for sure, but he thought it had something to do with backspaces. That clue was enough for me to figure it out on my own.

Here's how it works:

1. Print the text you want to display to the Command Window using fprintf.
2. Print enough backspace characters (again, with fprintf) to delete each of the characters that need to change.
3. Print the new text.

Getting it to work as a separate function took a little thinking, but turned out to be pretty simple. The result is below. I hope you find it (or its components) as useful as I have over the years.

FrameCounter

function FrameCounter(first_num, last_num, current_num, show_text)
%%  Determine the number of digits in the number
num_digits = length(sprintf('%d',last_num));
text = 'Frame ';
if nargin < 4
    show_text = 0;
end
%%  Before displaying the first number
if current_num == first_num
    if show_text == 1
        %%
        % Display "Frame " before the numbers
        fprintf(text)
    end
    for aaa = 1:num_digits
        %% Prime the counter with spaces
        fprintf(' ')
    end
end
%% Remove the previous number
for bbb = 1:num_digits
    fprintf('\b')
end
%%  Display the current number
fprintf('%0*d', num_digits, current_num)
%%  Last number
if current_num == last_num
    if show_text == 1
        char_num = length(sprintf(text));
    else %if show_text == 0
        char_num = 0;
    end
    backspaces = char_num + num_digits;
    pause(.1) % Without this pause, the last number sometimes doesn't display properly.
    %% Remove last number and "Frame " text
    for ccc = 1:backspaces
        fprintf('\b')
    end
end
end

---

1: The source of the crash was a read/write conflict with the Windows 7 indexing system. More on that conflict here if you're interested.

The best scientist I know

Joe Palca asked me on Twitter this morning,¹

Who is the best scientist you know, and what qualities make her/him the best?

I had to think a moment about this. I'm sure many people who love science have a favorite historical scientist. My shortlist is mostly crystallographers: Kathleen Lonsdale, Dorothy Crowfoot Hodgkin, the Braggs (Sr. and Jr.), Linus Pauling,² and I am amused by the story of Alessandro Volta, who was such a great practitioner of the scientific method, that he felt the need to zap himself with his electro-motive apparatus over and over again on various parts of the body "where the skin is very delicate" to make sure it really worked.³

Who is the best scientist you know? It's a simple enough question, but it can be interpreted in several ways. For one, what sense of "know" are we considering?

• Who is the best scientist you know of?
• Who is the best scientist you have seen (at a conference, seminar, etc.)?
• Who is the best scientist you have met?
• Who is the best scientist who knows your name in return?
• Who is the best scientist you know personally?

Then we should consider what we mean by "best scientist"? The follow-up question (what qualities…?) allows us to define our own criteria for best, but who gets to be a scientist? Must we consider only professional scientists?

Because this question has so many variations, I have several answers. Here are two scientists I aspire to be more like.

W.E. Moerner is one of the best scientists I know. I have heard him speak on a few occasions, and I have read a fair number of his papers. My advisor was a postdoctoral fellow in his laboratory, and from comments she has made over the course of my PhD, I believe that experience has significantly influenced her approach to science and advising.

Dr. Moerner gave a seminar at UM once, and I was among the students and post-docs who ate lunch with him. We had sandwiches and chips in the Biophysics conference room, and he chatted with each and all of us about a variety of topics. Someone asked him about his work with Kador on single-molecule spectroscopy, and he jumped up to the white board and started sketching out diagrams and explaining the story. He did so clearly and carefully, and seemed to have all the patience in the world when someone didn't understand. He has a reputation for being brilliant, and that made me a bit intimidated at first, but that feeling wore off quickly. He was approachable and just plain excited to tell us about the neat things he'd learned. And he didn't just talk to us, he conversed with us.

Krishanthi Karunatilaka is one of the best scientists I know personally. She was a post-doc in our lab until last fall. She is absolutely meticulous; I have some real notebook-envy for her tidy, organized notes in clear and even handwriting. She is driven and dedicated without any of the pushiness that I have come to associate with those terms. She has worked some long, hard days because she wants to know the answers to the questions she has. She also finds balance. I know that her Saturday mornings in Ann Arbor were set aside for a peaceful cup of coffee on her apartment balcony. She doesn't get knocked down by failures. If an experiment doesn't work (or gives unexpected answers), she has another idea, she keeps rolling on. When someone else is struggling, she's the first person to say "Don't worry, you can try something else. Keep going." She has a talent for presenting even brand-new data in a way that makes it sound like she's considered their implications for weeks.

Other names come to mind as well,⁴ but you'd find they follow the same pattern: the best scientists I know do good, thoughtful, careful scientific work, and are also excellent teachers, communicators, and just generally nice people.

So those are my "best scientists." Who are the best scientists you know? What makes them the best?

---

1: I admit, I had a complete fan-girl moment.

2: I admire Marie Curie, too, but she is used so often as The Token Female Scientist, that I think of the words of Mr. Bennet: “That will do extremely well… You have delighted us long enough. Let the other young ladies have time to exhibit.”

3: From Volta's letter to the Royal Society:

If, by means of an ample contact of the hand (well moistened) I establish on one side a good communication with one of the extremities of my electro-motive apparatus … and on the other I apply the forehead, eye-lid, tip of the nose, also well moistened, or any other part of the body where the skin is very delicate: if I apply, I say, with a little pressure, any one of these delicate parts, well moistened, to the point of a metallic wire, communicating properly with the other extremity of the said apparatus, I experience, at the moment that the conducting circle is completed, at the place of the skin touched, and a little beyond it, a blow and a prick, which suddenly passes, and is repeated as many times as the circle is interrupted and restored.

4: For example, my introduction to Jenny Glusker was similar in many respects to my lunch with Dr. Moerner.

Victor DiRita, a collaborator and dissertation committee member of mine, is another one of the best scientists I know. He teaches me something every time time we meet, even if only for a few minutes.

The best amateur scientist I know is probably my uncle Tom, for lots of the same reasons. He is also the only person I know who gets really excited about moss.

Swift

I got an iPod Touch in 2009¹ and wished from the start that I could write my own apps for it.² I knew approximately nothing about coding, though, so it was a rather far-away sort of wish.

In grad school I learned to code in Matlab. It was a sink-or-swim kind of thing. With the help of another grad student, two books, the wonders of Matlab Central (and later StackExchange), and lots of practice, I learned how to write and debug programs.

My brother is a programmer, and by his standards I'm a hobbyist at best, but I can make the computer do what I need, and I've gotten better as I've gone. Still, he teases me about how I should learn a "real" language, and I kind of agree. So about a year ago, after listening to a Mac Power Users episode about learning to code, I bought a book about learning Objective-C.³ I got a little better than halfway through it before other things got in the way; it's one of the things I was planning to come back to this summer between grad school and job.⁴

Those summer plans may have just changed, though. A week or two ago at the WWDC Keynote, Apple announced a new programming language called Swift and I think I'm in love. I watched the demo and thought "I can definitely do this." I may finally be able to write the apps I wished for. There's an eBook about the language, which I've already started reading. Though it starts from "Hello world," I don't think it would be much help if you had no familiarity with programming whatsoever,⁵ but it does look promising for someone (like me) who has at least dipped their toes into the programming pool before.

So that's my next side project: learn another language, try to make an app (I have several ideas), and see how it goes. I'm excited to get started.

---

1: Nearly 5 years later, it's a bit sluggish but still kicking.

2: I was also bowled over by the idea that the device playing podcasts in my pocket had a bigger hard drive than my laptop's original drive: 64 vs 60 GB. When I stop to think about it, it still amazes me how powerful the gadgets in my pockets and bags are. And then I start feeling old…

3: It's a really good book, too: The Big Nerd Ranch Guide. My inability to finish it has much more to do with being an overwhelmed graduate student in need of "off" time for my brain than the quality of the book. I highly recommend it, and I think it's an excellent example of instructional writing.

4: Oh yeah, I accepted a job about the same time I was completely overloaded with dissertation and defense stuff. The defense is done, the dissertation is submitted, and though I wrote about the stresses and thrills of job-hunting, I guess never did mention here that I did accept an offer. More on that another time. Short version: I have a job starting in August and I'm excited about it!

5: This is actually the same gripe I have about the Matlab Getting Started Guide and books for "beginners." All of these say that you can start from scratch, but they usually assume knowledge and vocabulary that a first-time programmer may not have. (I'm looking at you, floating-point array.)

Consider these programming languages like human languages: the Getting Started Guide might tell me how a verb is conjugated, but if I don't know what "conjugation" is, I don't know what to do with that information. If you've learned another language before, you've probably learned the meta-terminology already, and have some kind of structure for understanding this new set of words, sounds, and grammar rules.

Many kinds of good scientist

I saw this article by Adam Ruben make the rounds on Twitter a few days ago. Then I saw the article spreading on Facebook, with friends from grad school saying things like "So true!" and "That's totally me!" so I took a look.

He had me until the grants ("I dread writing grants…") but then I realized I wasn't even a third of the way through his list. It just went on and on, with an increasing tone of whininess. The post spirals out into a humble brag. By the time I got to the mice he's killed, I just grumbled, "Okay, dude, we get it. Poor you."

If you can sift through it, though, he makes some points about the culture of academic science that are worth expanding on.

I am not a priestess of Science

• I don’t sit at home reading journals on the weekend.
• I have skipped talks at scientific conferences for social purposes.
• Sometimes I see sunshine on the lawn outside the lab window and realize that I’d rather be outside in the sun.
• I have gone home at 5 p.m.

I love being a scientist, but I have a mighty big problem with the idea that as a scientist (or more broadly, as an academic) I'm supposed to "devote my life" to my work. That's not called Science, that's called Workaholism. If that’s what you enjoy, then by all means do it, but don’t expect me to have the same desires.

Here's my own confession: I worked roughly 8:30-5:30 five days a week through grad school. Sometimes I would keep working when I got home, but that didn't happen every week, much less every day. I came in to work or worked at home a few weekends, but I never made it a routine thing.

It's not that I wasn't dedicated to science or my research project. It's not that I didn't care, or that I was lazy. It's that I needed balance. For the most part, I leave work at work, and I am home at home. Balance for me means lunchtime chatter with friends, Friday date nights with my husband, and brunch with the in-laws. It means taking holidays and coming to work focused. We talk and talk about "work–life balance," but the cultural incentives are heavily on the side of more work and not at all balanced.

The summer after my freshman year, I spent about three months as an REU-type student at Duquesne University. It was awesome, and I learned so very much. An important part of what I learned, though, was that I needed to Stop. I lived in a dorm, worked in the lab, and knew almost no one besides the people I worked with. I ate breakfast in the dorm room, lunch in the lab break room, and dinner back in the dorm room. I had a crappy-to-okay Internet connection, I didn't know my way around Pittsburgh (and was honestly a little frightened of wandering the city alone), and I was too shy to get to know the other girls on my floor, so I stayed in and read research papers. I read a lot of articles that summer. I still have them all, in a cardboard box tucked at the back of a closet. I didn't understand half of what they said on the first read-through, so I read them over and over, looked up terms online, asked questions in the lab, and just tried to work it all out through context. At the end of the summer, I was praised for my efforts, but I was also teetering towards burn-out. I hadn’t spent enough time away from science.

I have been very careful since then to take breaks and disconnect from work. I have sought balance. And I have advised newer students to be mindful of their own balance. I love my science very much, but I refuse to pass on the idea that the only way to succeed in science is as part of a monastic order.

I am not a priestess of Science. I got a PhD all the same.

A PhD is not proof of knowing everything

• I remember about 1% of the organic chemistry I learned in college. Multivariable calculus? Even less.
• I have felt certain that the 22-year-old intern knows more about certain subjects than I do.
• I have pretended to know what I’m talking about.
• I find science difficult.
• I have worked as a teaching assistant for classes in which I did not understand the material.
• I have taught facts and techniques to students that I only myself learned the day before.
• I have feigned familiarity with scientific publications I haven’t read. ¹

A PhD is not proof of knowing anything. It's rewarded for "Persistence to a high Degree" as much as anything. It's not about facts you've memorized, or stuff you can recall on demand–no matter what certain committee members may say. It's about learning something new. And that new stuff wasn't in the classes you took. (As I've discussed with some friends and labmates before: course material covers stuff someone already knows; research is stuff we don't know yet.)

The work you do in a PhD is, as a rule, highly specialized and focused. I spent most of 5 years watching one protein in one pathway in one kind of bacteria. I am the world's expert on the motion of that protein. Yippee. I don't have equal expertise for other bacteria, or even other proteins in the same bacteria, much less other aspects of microbiology, microscopy and the rest. But I do have some expertise, and I have much more in these particular fields than a friend who has studied the thermodynamics of two dimensional structures, or another friend who has studied the surface chemistry of semiconductors. The three of us have each spent 5 years studying chemistry, and we have each earned a PhD for doing so, but we would not be able to pick up each other's projects on a whim. It would take more time and more learning. The need to learn something new doesn't make us bad scientists.

We have got to get over the idea that we must know everything, that everyone around us knows everything and expects the same of us. It's just not true, and it sets unrealistic expectations.

Academics posture too much

• I have asked questions at seminars not because I wanted to know the answers but because I wanted to demonstrate that I was paying attention.
• I have worried more about accolades than about content.

I don't understand why seminars start with the speaker's professional biography. It's not like it'll convince me to come see the talk: I'm already there, sitting in a seat. And if you were to tell me the speaker is from Nowhere State and has done absolutely nothing of note, I'm still not about to get up and leave. Will the talk be better because I now know that Dr. I-Never-Heard-Of worked with Dr. Famous? Fame, publication record and grant money are no guarantees for talk quality, yet those are the things chosen for introductions.²

With fame so highly valued, I suppose it's no surprise that people (in my experience, mostly men) feel the need to show off. Asking a question brings you to the attention of the seminar speaker and the audience. If you don't care about the answer, please don't ask the question; you're just wasting everyone else's time with your ego-stroking. Let someone else ask the question they care about. This counts double for "questions" that don't ask anything. Those are called statements. Keep them to yourself during the open Q&A.

Most scientists don't communicate well

• I can’t read most scientific papers unless I devote my full attention, usually with a browser window open to look up terms on Wikipedia.
• When a visiting scientist gives a colloquium, more often than not I don’t understand what he or she is saying. This even happens sometimes with research I really should be familiar with.
• When I ask scientists to tell me about their research, I nod and tell them it’s interesting even if I don’t understand it at all.
• I have used big science words to sound important to colleagues.

I like words. I like big, fancy words and unusual words and old words hardly anyone uses, but if you study too long for words of four syllables,³ I lose patience. Tell me how you rowed the boat gently down the stream, but not how you 'propelled the craft placidly through the liquid solution.’⁴ I'll know you're smart by the clarity of your point, not the frills in your sentences or the jargon you use. You don't have to emulate Newton and hide your knowledge in nonsense sentences.

Scientists are people

• Sometimes science feels like it’s made of the same politics, pettiness, and ridiculousness that underlie any other job.

Sorry to break it to you, fella, but science is like any other job. There are politics and pettiness, rudeness and ridiculousness. There are easily bruised egos. There are liars and cheats. There are people doing this job, flaws, fears and all. We scientists aren't a special case.

This is what a scientist looks like

As a counter to Ruben's concept of a scientist, here is my own list:

• Science is my job, not my life.
• I do not know everything.
• I do not need to know everything.
• I do not learn by pretending to know.
• My knowledge is not spoiled by sharing it with others.
• I am not perfect.
• I am a scientist anyway.

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1: Another article I read this week was on feigning cultural literacy. It's worth a read. There's a lot of overlap here.

2: Possibly the worst scientific talk I have ever sat through was given by a Nobel laureate; it was absolutely dreadful.

3: “…he does not write with ease. He studies too much for words of four syllables. Do not you, Darcy?” – Mr. Bingley, Pride & Prejudice

4: In case you're not familiar with the “sophisticated version" of "Row Your Boat"

Propel, propel, propel your craft
Placidly down the liquid solution.
Ecstatically, ecstatically, ecstatically, ecstatically,
Existence is but an illusion.

They call me Dr. Haas

Good morning. How are you? I'm Dr. Worm Haas.
I'm interested in things.

---

As of today, I've officially completed all the requirements for my PhD.

So I'm not a real worm, but I am a real doctor.¹

Dr. Worm has been stuck in my head for a few days. Now you too can share in my joy/misery.

---

1: As my grandmother joked: I'm not a "real" doctor, either because I'm not "the kind that helps people." (She agrees that a PhD is helpful, too.)

Some things I've enjoyed recently

• Type:Rider, a game about the history of typography. It's beautiful and fun.
• This post at Wandering Scientist. I love the two quotes at the end.
• This post at the Chronicle of Higher Education blog. I'm bothered whenever I hear someone preaching about the "real world" and how students aren't prepared for it. The "real" world is full of real people who should be treated with respect and kindness. We gain nothing by dismissing our students.
• Forbidden Island, my new favorite puzzle (it's a digitized board game, but I've been playing the local multiplayer solo)
• 2048, which has usurped sudoku as my go-to time-waster. (Thanks a lot, @chemjobber)
• iThoughts, an iOS/Mac mind-mapping app I've used for a year or two that was recently updated with some nice improvements.
• This post at Penny Arcade on the use and purpose of Twitter was amusing. I also worry at times that my tweets aren't "good enough." Plus, I have a soft spot for Austen references.
• This Periodic Table by Compound Interest is pretty cool.
• It's not nearly as recent as the rest of this list, but I've really been enjoying the Points of Significance column at Nature Methods, and the Points of View column before it. My statistics background is much weaker than I'd like, so it's nice to have a primer. Points of View is similarly helpful for tips on designing figures.

Thanks

I want to take a small break from my thesis-writing to thank some folks for the very kind things they've said about me and done for me lately. First, thanks to you, reader, for stopping by my little corner of the big wide Internet. And thanks to those of you who have enjoyed it enough to pass it on elsewhere. It's pretty exciting (and honestly a teensy bit scary) to see your words quoted and linked on somebody else's blog, recommended on Twitter, and highlighted as a thing worth reading. There are only so many hours in a day, and I am delighted that there are people who find my words worthwhile enough to spend some of that precious time on.

Attention

More thoughts from my trip to San Francisco. This really happened, and though you may think it's "not so bad," it still shook me.

---

We waited for the light to change. A fire truck rolled past, and one of the firefighters caught my eye and waved to me. I smiled. It seemed friendly. Yes, potentially flirtatious, but certainly benign.

I left the group as they entered the dance club. Tired feet took me downhill to the hotel. Four men hiked the hill in the other direction. As they approached, one called "Hey." It wasn't a greeting; it was an invitation to a conversation. I pretended not to hear and kept walking.

Another intersection. Another crosswalk. Another light slow to change. A man carrying a shopping bag neared the same stop. He skipped right to "What are you doing out tonight? You're a sweet little thing. You want to get something to eat?"

My training in politeness kicked in, even though he stepped closer, approaching my shoulder, step by step. "No thank you. Have a good night," I said, glad the light had finally turned.

I realized then that those four men walking uphill had triggered something in me. I had weighed them as a possible threat and found them unlikely to be trouble. It was unconsciously done. But the lone man on the corner tripped my alarms and reminded me that those alarms even exist, that out on the street I am always judging men–and occasionally women– for their potential to cause me harm. And that fact scared me.

Someone looking at me would see I was wearing a black pea coat, jeans, and sneakers. Not exactly dressed for attention. It was 1 am. But it doesn't matter what I was wearing, and it doesn't matter what time of day it was. I shouldn't have to spend my energy shielding myself from unwanted attention.

An important read about quitting vs staying in STEM

Choosing to end any phase of your life is never easy. As a woman, choosing to leave science is harder still. Although there are support groups and professional associations for women in science, there is little day-to-day support for staying. There is even less support for leaving.

This article by Frances Hocutt spoke to me. I know many people (especially women) who have stood at that same threshold and thought "Do I dare quit?" I'm glad she had the courage to choose self-respect.

When a pipeline leaks, we don't blame the water.

Go read it.

via @shanley