pomodoro technique

Umesh recently discussed the Pomodoro Technique (slides), a time management method that uses a timer to break down tasks into 25-minute intervals called ‘pomodori’ (PDF book on PT, book on PT). The work intervals are separated by brief breaks, usually five minutes each. The name comes from the tomato-shaped kitchen timer that was used by Francesco Cirillo, the inventor of the method, when he was a university student. Why care? Because you have a lot to get done and using your time effectively is crucial to getting it done.

Related concepts that Umesh mentioned include Stephen Covey with The 7 Habits of Highly Effective People and David Allen with Getting Things Done (GTD). Covey makes four quadrants from the combinations of urgent and not urgent with important and not important. This framework, in the least, seems like a useful thing to have in the back of your mind, like which of the four quadrants is this activity in, if it’s in the wrong quadrant consider switching to other activities. GTD is based on ‘making it easy to store, track and retrieve all information related to the things that need to get done’. It uses things like a weekly review to, among other things, determine the priority of the individual tasks and commitments gathered during the workflow process. Another tool is mind maps, which you can use to ‘represent words, ideas, tasks, or other items linked to and arranged around a central key word or idea’. Other stuff that Umesh mentioned are the Unschedule and GQueues.

Next point was some reminders of why these tools are important. First, Parkinson’s Law: Work expands so as to fill the time available for its completion. Second, mistaking activity for accomplishment. Umesh gave some examples of non-accomplishment activity: Gmail, Rotten Tomatoes, Cat Melon Head, YouTube, Roger Federer, Engadget, Facebook, OMG! Ubuntu!, etc.

You need a timer (and there are many software timers, see below); an Activity Inventory, where you’ll make estimates of the number of pomodori needed for each task; and To Do Today. For example Activity Inventory, ‘Answer questions on thermodynamics in Ch. 4, 3’. For To Do Today, you’ll allocate, essentially making blanks for each of the tasks that you’ll do. Normal thing is to use a fixed number of pomodori. Pick a task from the To Do Today. Set timer to 25 minutes and work on it until the timer rings. Then mark it done. Take a five minute break and continue with the next pomodoro. After four pomodori, take a 30 minute break. Continue until the task is done.

Pomodoro rules include 1 pomodoro = 25 minutes work + 5 minutes break. Long break (30 minutes) after four pomodori. If you think a task will take more than 7 pomodori, break it down. Once a pomodoro begins, it has to ring. Further, protect the pomodoro. For example, void it if interrupted often. Consider internal interruptions (self) and external interruptions (others).

Mark internal interruptions, such as with an apostrophe in your To Do Today. If not urgent add it to your Activity Inventory (perhaps marking it as not urgent). If urgent, add to To Do Today, such as under Unplanned & Urgent. External interruptions, inform, negotiate and call back. Last thing is to plan, track and record. Look at what you’ve wanted to accomplish and compare to what you did accomplish. Pros of Pomodoro Technique include that it’s easy to concentrate for 25 minutes, you have frequent breaks and it helps track productivity (and postpone interruptions). Cons include that it focuses on efforts and does not tell you how to prioritize.

Pomodoro tools include: Focus Booster; Pomodoro Crate; Pomodoro Pro; Pomodairo, Tomatoi.st, TimeBoxed, Menubar Countdown, Keep Focused, MaToMaTo, Pomodoro Windows 7 gadget.

adding publications to your cv

Umesh recently discussed how to automate the ‘Publications’ section of LaTeX-based CVs (associated files, example CV). His desiderata for Publications: reverse chronological order; organization by type (e.g., for journals, conferences, abstracts and talks); and his name in bold. He doesn’t want to enter this stuff manually and he’d like it to match what shows up on his website.

For those who know Umesh, I’m not sure it really needs to be explained, but why LaTeX for this and not some other WYSIWYG option like Microsoft Word. Well, for one thing it’s WYSIWYG, which means it can be challenging to keep the formatting consistent. I want to say that using styles in most WYSIWYG makes consistent formatting relatively easy, although maybe not as straightforward as in LaTeX. Anyway, separation of content and style is a good idea and it’s something LaTeX is good at. And, though he didn’t mention it, there are lots of free tools for writing with it, absolving you of a lifetime of Office purchases.

One thing you might consider, though, is that some places require that you submit these kinds of documents as a .doc. Once upon a time, we worked really hard to convert a .tex, either directly or through the .pdf, into a .doc. Our conclusion then: if it can be done it’s highly non-trivial.

So BibTeX (what we use for references in LaTeX). It’s good for citing in papers, but getting it to do what we want (see list above) is tricky. Not to worry, it can be done with the datatool package. What follows is the version-by-version. Check the associated files for this post to see how this is done. You should be able to modify those files to make this stuff happen.

Version 1 looks ok, meaning it works, but the first thing is it’s not in reverse chronological (2008, 2009, 2003..).

Version 2 has the sorting worked out, starts with 2010, but isn’t grouped by type. It’s just a big list.

Version 3 gets grouping, and is only lacking (with respect to our list) in that names aren’t highlighted.

Version 4 has the name highlighting.

In summary, use BibTex and Datatool. Also, Rob’s bib2php (which I wrote about here) can use the same BibTex to add your references to your webpage. Other uses of Datatool include creating a list of papers since a particular year, creating a list of 10 most recent publications and managing multiple bibliographies. Problems include that output styles are limited and it may be slow to compile for many references.

making figures

Umesh recently discussed making figures with Inkscape (video tutorials), whose motto is ‘Draw Freely’, which we’ll get to (associated files). Inkscape is another vector graphics editor. It’s free and open source (information about open source alternatives). You can use it to edit figures generated using MATLAB and can also use it to make posters for conferences.

Umesh started his presentation by reviewing the differences between vector graphics (VGs) and raster graphics (RGs), which include that VGs are composed of fonts, line art and illustrations, whereas RGs are images. VG formats include EPS, PDF, AI and SVG, whereas those for RG are JPG, BMP, PNG and TIFF.

He also reviewed what we’d covered before: MATLAB, use code to generate your figures, try to do as much as possible in it (so before export), and what you see on the screen does not map to what prints in a straightforward way (meaning you need to do work to get it right); Adobe Illustrator, powerful vector graphics editor, but expensive (in Umesh’s view); Intaglio, simple interface, but Mac only. This gets us to Inkscape. Well, how did he get to Inkscape?

He had been using Microsoft PowerPoint which he thought of as convenient, but constrained in having a max page size (bad for posters). That size constraint was fixed, meaning there was nothing you could do in the case of conferences for which you needed to go bigger. From there, to Adobe Illustrator, which he used and liked, but found to be too expensive to install on his personal machines. He started to use Inkscape. Everything looks pretty simple, with a single bar of tools, similar to those in Adobe Illustrator and Intaglio.

Here is his first real Inkscape project, which was to make this greeting card for Prof. Al Bovik. The background is text from his work (papers, etc.).

Here is Umesh’s first poster with Inkscape. He notes that it was very easy to add images, it takes EPS and PDF files. You can also use LaTeX equations (no problems with that). Probably made this poster on a Mac. On running on Mac, we believe it is possible to run Inkscape natively and found a video that seemed to support that, but we’re not really sure.

Stepping back and reviewing, things Umesh likes about it are: that it’s free, so you can use it anywhere (on any machine and for any purpose); it provides the features that he used in Adobe Illustrator; it has useful extensions, such as for equations (built-in LaTeX engine with editing), function plotters and replace font. Adobe Illustrator is $200 and works on Microsoft Windows and Mac OS X. Inkscape is free and works on the three major operating systems. More feature comparison is available from Inkscape. In some sense, these application wars are a variant of ‘Get a Mac’.

Here are links to a couple things made in Inkscape, in case you’re of the belief that it’s impossible to use it to make professional looking things: a yellow Ferrari by Gilles Pinard and a lady named Megan by Luciano Lourenço.

Final thoughts from Umesh were to give Inkscape a shot. It’s free! You might find it ‘professional enough’. Current users in LCV are Umesh, Yan, Rich and Rob. Also, remember that there is proprietary software and there are proprietary formats. So don’t send things as DOC or AI, but as something that everyone can open and edit. Umesh also wanted me to mention plot2svg.m, which converts 3D and 2D MATLAB plots to SVG.

exporting figures

Rich recently discussed creating and exporting figures from MATLAB (associated files). He started by listing the things he wants: to produce a figure for a paper (e.g., for LaTeX); for fonts, line widths, etc. within the figure to be a specified size (e.g., 12 pts); for fonts and symbols in the figure to be identical in the text; to automate the process as much as possible since regenerating the figure is common {collect additional data; tweak simulations; reuse the figure in a new publication, talk or grant; make minor cosmetic alterations}; and to reuse the visualization code.

His thoughts on how to make these happen include: not to export figures using the ‘export’ menu function; not to modify figure properties using the mouse; to avoid using third party graphics manipulation programs where possible; to use functions and scripts to generate plots (allows for reusability); to specify fonts, line styles, axis positions and figure sizes as variables (allows for modifiability); and to export using the print command (allows for controllability).

He also listed the differences between vector graphics and raster graphics. In vector graphics or line art, the format is the object properties, whereas in raster graphics or bitmap it is the pixel values. The file size for line art in vector graphics is small, whereas it’s large for raster graphics. Conversely, the file size for images is massive in vector graphics, whereas it’s merely large for raster graphics. Tools for editing vector graphics include Adobe Illustrator, Inkscape and Intaglio. Those for raster graphics include Adobe Photoshop and GIMP. In most cases, you should export your MATLAB figures as EPS or PDF (vector graphics).

Here is some other useful stuff that Rich mentioned:

• patch.m - 2D polygon plotting, useful for plotting error bars
• plotyy.m - different y axes on each side of the plot
• annotation.m - add arrows, textboxes etc. to your figure
• legend.m, nudgeLegend.m - add legend to a plot, and tweak its appearance (my code)
• set(gca,’box’,’off’) - turns the figure bounding box off
• set(gca,’layer’,’top’) - bring the axis to the top to stop stuff being plotted over the black edges and tick marks
• set(gca,’TickDir’,’out’) - set the direction of the tick marks to point outwards
• pu = get(gcf,’PaperUnits’); pp = get(gcf,’PaperPosition’); set(gcf,’Units’,pu,’Position’,pp) To set the screen size to be the same as the papersize - more WYSIWYG
• for mixtures of vector and bitmaped graphics - export each part separately and overlay e.g. within latex itself
• transparent background in eps file - comment out lines in the eps file that read: “X X X PR” or “X X X X MP”, where X is some number.
• LaTeX trick: use the layout package to find out how wide the page is for setting figure dimensions.

To get a better sense for how to actually do this stuff, here is some snippet’s of his demoFigs.m as well as the associated images from demoFig.pdf. The idea of demoFigs is to progressively improve a figure. I’m including only the good parts. I suggest you mess around with the script yourself.

Version 1—nothing special, just exported with MATLAB’s Figure menu.

Version 2—automated export, using print.

filename = ‘demo2.eps’;

print(gcf,’-depsc’,filename);

Note his use of the bang command (‘!’), which steps out of MATLAB and calls some OS commands.

! epstopdf demo2.eps 

! acroread demo2.pdf&

Version 3—set size of EPS/PDF, by specifying the paper size.

PS = [14,10]; % paper size (in centimeters)

PP = [0,0,PS]; % paper position on the printed page (in centimeters)

set(gcf,’paperpositionmode’,’manual’,’paperposition’, …

        PP,’papersize’,PS, ‘paperunits’,’centimeters’);

filename = ‘demo3.eps’;

print(gcf,’-depsc’,filename,’-painters’,’-loose’); % loose option stops matlab cropping white space automatically

Version 4—make better axes with less white space, by setting their position and using axes to create them.

left = 0.12;  % space on LHS of figure, normalised units

right = 0.02; % space on RHS of figure

top = 0.05;   % space above figure

bottom = 0.1; % space below figure

hspace = 0.07;% horizontal space between axes

height = (1-top-bottom); % height of axis

width = (1-left-right-hspace)/2; % width of axis

across = [hspace+width,0,0,0];

pos1 = [left,1-top-height,width,height]; % position of axis

pos2 = pos1+across;

figure

ax1 = axes(‘position’,pos1); % produce axis replaces subplot(1,2,1)

plot(t,s1,’-‘)

ylabel(‘y’)

xlabel(‘\omega = 2 \pi c/\lambda’)

ax2 = axes(‘position’,pos2); % produce second axis replace subplot(1,2,2)

plot(t,s2,’-‘)

xlabel(‘\omega = 2 \pi c/\lambda’)

Version 5—make better font sizes and linewidths, by setting them.

% Fonts

FontName = ‘Times’;

FSsm = 7; % small font size

FSmed = 10; % medium font size

% Line widths

LWthin = 1; % thin lines

% Colors

col1 = [0,0,1];

——>

ax1 = axes(‘position’,pos1); % produce axis replaces subplot(1,2,1)

plot(t,s1,’-‘,’linewidth’,LWthin)

ylabel(‘y’,’fontname’,FontName,’FontSize’,FSmed)

xlabel(‘\omega = 2 \pi c/\lambda’,’fontname’,FontName,’FontSize’,FSmed)

set(ax1,’FontName’,FontName,’FontSize’,FSsm)

ax2 = axes(‘position’,pos2); % produce second axis replace subplot(1,2,2)

plot(t,s2,’-‘,’linewidth’,LWthin)

xlabel(‘\omega = 2 \pi c/\lambda’,’fontname’,FontName,’FontSize’,FSmed)

set(ax2,’FontName’,FontName,’FontSize’,FSsm)

Version 6—make better xlabel on second plot using PSfrag.

Nothing really to say about the MATLAB code here, since it’s done in LaTeX. Only thing would be to keep the text simple so that you can locate it in the LaTeX.

Version 7—make everything with a ‘shell’ function.

filename = ‘demo7’;

Plot1By2Demo(t,s1,s2,filename)

managing references

Umesh recently discussed reference management using Zotero (slides). One should hardly need to be convinced that it’s better to use any reference management tool than to print everything you read. It might be like considering whether it’s better to write emails or handwritten letters for everyday communication. In one case, there is no search, no ordering and no easy way for grouping, with the exception of making stacks. More, there is an ever increasing blob that physically holds the information, the creation of which involves contributing to unseen deforestation. The paper blob is comparatively much more difficult to copy, to backup, to transmit and to carry.

The paper method for papers also involves various never-ending—and mostly unachievable—chores, such as sorting, stapling, ordering, grouping and filing everything. It also doesn’t set you up to do a number of things that any reference management tool can do, none of which I’ll list. One might counter that at least paper papers are easily and permanently disposed of, such as by transforming them into ash, assuming you live in a place where that’s allowed, or shredding them, if you could be bothered to, or—more likely—by dumping them in a recycling bin, never to be see again.

The evolution of methods that Umesh described, from printing to EndNote and then to JabRef, was likely a reaction to these and other functional advantages, as well as to changing interactions with other tools, such as those for word processing. Switching from Microsoft Word to LaTeX in a sense meant switching from EndNote to JabRef. But even JabRef has become among his non-preferred considering his most recent requirements: free; cross-platform; taggable; open source; and noteable. With these requirements, his reference management tool of choice is Zotero, “a free, easy-to-use tool to help you collect, organize, cite, and share your research sources.”

Cool things about Zotero include that it “lives” in Firefox and will eventually live in other browsers. Support for other browsers, part of their Zotero Everywhere project, is in alpha. Zotero allows you to capture lots of different kinds of stuff, including books, journals, and other resources, directly. This means you don’t have to move stuff from folder to folder. You can link stuff, such as files for supplemental information, with a given entry by drag and drop. You can tag anything. Zotero has integration with Microsoft Word and OpenOffice, and, like other tools, can format bibliographies in many different styles. It also allows syncing, sharing of your library, and some usage with mobile devices. Multi-user functionality is supposedly there.

I’m assuming you know this already, but Zotero isn’t the only tool in the game. Buried in our cloud-based notes on the future of ETS are Mendeley, Connotea and colwiz. Reference management tools, like so many things, may have that memetic self-reinforcing “I’m this and not that” quality so beautifully captured in the Get a Mac campaign. But then, does Zotero wear the suit or does it wear the button-up?

inception

Four of us from the Laboratory of Computational Vision (LCV) at NYU are starting a small meeting to discuss essential tools for scientists. Our focus is largely technical and the list of topics we plan to discuss includes many about programming, software, and computing. Besides technical stuff, we intend cover other topics that we consider to be important to our lives as scientists, such as time management. We’ll meet soon to discuss unit testing (docTest and xUnit for MATLAB). We believe that our discussions will be quite useful for other people who do the kinds of things we do. If you have any questions or posts to contribute, please send them via the links at the top. We’ll update this blog after every meeting, and we may add other stuff here as followup.

The 2011 ICC Cricket World Cup had a subset of us meeting in the morning before lab at one of two Manhattan bars that had a pixelated feed. At one point the more proximal option was so crowded we agreed to look for a different place. We walked around in circles for a while, missing a few wickets, as we waited for someone’s Droid to bring up the names of Irish bars in the area, none of which were showing the match. Just after India won the final two of us we went to Saravanaa Bhavan, only to see that they too were showing the match. Unlike the place we ran away from, they had plenty of space and their required minimum expenditure went towards delectable South Indian food, rather than runny eggs and sausages. Moral of the story might be that knowledge is power. Or meeting to share knowledge about essential things is essential, but then are there people who’d be willing to “meet” to discuss where to watch cricket. More to the point of this, blogging about essential meetings covering essential knowledge is also quite essential.