Sea Ice Thoughts

Making single eps file from latex figure

2011-11-04T12:41:00.002+13:00

Journals, being the cash-strapped money-printing machines that they are, like to have submissions written in LaTeX, but only in the simplest LaTeX possible.

I like to use LaTeX as much as possible when annotating figures produced by other programs, as then the fonts in my document match those in my figures. This makes it sensible to compose figures within the LateX figure environment. A simple example which collects some sub-figures then labels them would be:

\begin{figure}
\begin{picture}(86,175)(0,0)
  \put(0,140){\includegraphics[width=86mm]{figures-a}}%
  \put(80,144){a}
  \put(0,75){\includegraphics[width=86mm]{figures-b}}%
  \put(80,78){b}
  \put(0,108){\includegraphics[width=86mm]{figures-c}}%
  \put(80,111){c}
\end{picture}
\caption{A multi-figure figure}
\label{f-FigureLabel}
\end{figure}

For final submission, journals like to have single eps files for each figure, so we need a way to make a single eps file from this. The trick is to use the preview and standalone environments. Create a file for the figure (e.g. fig-01.tex) with contents:

\documentclass{standalone}
\usepackage[dvips]{graphicx}
\usepackage[T1]{fontenc}
\usepackage[active,tightpage]{preview}

\begin{document}%
\begin{preview}%
%
\resizebox{86mm}{!}{%
% put \picture{} here
}%
%
\end{preview}%
\end{document}

do not include the \caption or \label, just the code for the figure itself.

Now run:

latex fig-01.tex --output-format=dvi
dvips -E -I 3c -o fig-01.eps fig-01.dvi

to produce a single eps file with cropped boundaries. This can then be included in the main document's figure directly.

Review: The Longest Winter: Scott's other Heroes (Meredith Hooper)

2011-09-14T15:10:00.002+12:00

I've just finished reading: The Longest Winter: Scott's Other Heroes by Meredith Cooper.

The Longest Winter concerns the activities of the member's of Scott's expedition that were tagged on to make it look like some serious science and exploration was included in his plans. Initially the group of six were to be deposited on the Ross Ice Shelf to explore to the East, but this was foiled by the lack of a suitable landing site at the Eastern edge of the ice shelf, and the subsequent occupation of the Bay of Whales by Amundsen's expedition.

Instead, the party was sent West, initially spending a comfortable winter at Cape Adare, far to the North of Ross Island, at the same site occupied by Borchgrevink in 1899, and where a small ruined hut remains to this day. This was a disappointment for the party as they had hoped to be installed mid-way along the Victoria land coast from which they could explore routes to the plateau and collect useful geological information. The Cape Adare site was unsuited to exploration as the sea ice was uncertain (being affected by frequent storms, and having few points on which to be pinned), and rocky mountains prevented sledging access to the interior.

At the end of this first winter, the party was collected by the Discovery and moved to a site at Terra Nova bay, close to the Drygalski ice tongue, to spend a few weeks exploring before being picked up and returned to the main expedition at the end of the summer. Instead, the ship was unable to access their landing site on its return, and the six men were left with no choice but to make do. This is where the real story starts, but also where the least information is available from the men, and, in fact, where very little actually happens.

The party found that winter brings terrible katabatic winds, similar to those that would be experienced by Mawson during his first winter. Terra Nova bay, in fact, is now known to be one of the windiest, and least hospitable places to be outside of the short sunny months of summer. Lacking in supplies and shelter, a snow cave was excavated, a seal-blubber stove constructed, and as much meat hunted as possible. Survival was slight, and the winter passed with little activity and much suffering. At its end, the men resolved to make their own way out of their situation, and begun to sledge back over the uncertain terrain of the Drygalski ice tongue, and along the sea ice of the Victoria Land coast to safety at Ross Island. Somehow, mainly through the good leadership of Campbell and the wise planning of Priestley, supplies were made to last, and sufficient strength was obtained for the men to struggle back to the main party, only to meet the sad news that Scott was dead.

The book has its good parts. For the reader experienced in the literature much will not be new, as the story Campbell's party is interleaved with that of the other portions of the expedition, and it was not always easy to skip over the parts I'd read many times before elsewhere. The parts concentrating on the men stuck out near Inexpressible island are good, well researched, and tied together to make a strong story. I would have been happier had the book been shorter, and concentrated only on this strong material, but I can see the use of the wider context to those not already steeped in the story. Hooper also uses the same names as the expedition used to place the action. This is a shame as it misses much of the later lore lain over the land, and makes it harder for me to know where anyone ever is, but then I am very familiar with the modern geography.

Finally, some parts of the book will make you feel very cold, so I'd suggest reading it while in a warm bath...

Where to go in Antarctica?

2011-09-06T19:37:00.001+12:00

Well, where to go if you can only go to Scott Base or McMurdo. Sounds obvious, right?

Maybe not... if you're a sun lover (and who isn't), you'll soak up slightly more rays at McMurdo than at Scott Base (assuming that you even go outside).

The following plot was generated by taking the sunshine energy arriving at Arrival Heights (just above McMurdo) and subtracting the sunshine energy arriving at Scott Base. Positive numbers (blue) correspond to McMurdo being sunnier, negative (green) mean SB was best. The red running line shows the 5 times exaggerated 7 day average of all years from 2000 to the present.

So, if you want to sunbathe, McMurdo's the place to pick, especially while the light is going or coming.

The Earthquake that killed Twitter?

2011-06-13T18:17:00.005+12:00

[For New Zealand visitors, the quick solution is probably to use geographical searching, although sometimes Twitter cannot keep up with the work that it needs to do: (eqnz near:"new zealand"). Or use a filter you'll have to keep updating.]

There was another earthquake in Christchurch today, strong enough that I felt long period shaking four hours' drive away in Dunedin, which made me very worried about my many friends up the coast. I did what everyone does in these situations, popped #eqnz into Twitter, and found myself connected to the stream of reports and rumours.

Initially I was a little concerned as most of the reports were from outside Christchurch, with few from the city itself, but this cleared up as networks, phones and power quickly came back to life. For about twenty minutes I, and the world, had a great source of news on the happenings, and a great sense of relief that, basically, everything was fine.

Then, just as we wondered why this thing wasn't trending, even in New Zealand, the #eqnz tag finally got noticed by Twitter and the inevitable happened.

Spam.

Rapidly created accounts with nonsense but early in the alphabet names flooded the tag, and those for popular movies and memes, with links to modestly disgusting porn and SEO sites. Fine, try to scam some movie or the latest tween obsession, but an Earthquake? Please.

Anyway, these people, we already know, have no compunction about their activities, and merrily waste bits and oxygen as they usually waste our time, but when they instead clobber a useful utility in a time of crisis, well, that utility is less useful.

And this is where this is Twitter's problem. Me, and a hoard of well-meaning Kiwis did our best to block these bloodsucking scum from the feed, but, and this amazes me, it takes four clicks to get from the search feed to finally reporting an account, and then, of course, it's too late anyway, as the spammer's gone and made ten or twenty more.

Twitter could do something useful here. First, they can fix the reporting for spam by adding a single big button to press, right there in with the search results.

Second, while people found they could get better news by using geographical filtering (eqnz near:"new zealand"), this still hides a lot of useful information. Twitter need to provide a way to search based on the reputation and activity of users, allowing and making it easy to only see tweets from the trusted, from accounts that have existed for more than three minutes, and which have activity profiles consistent with their belonging to real people.

If Twitter can fix that, they might survive, but if they cannot, the whole service is going down the drain...

Update: It gets much better once the tag isn't trending globally. I really hope twitter can sort something out for the next big distaster.

Tramp: Roaring Meg Hut

2011-06-13T16:52:00.002+12:00

So I was thinking to myself that there aren't enough tramps available on the internet, so there will be summaries of my tramps on here from now on.

Roaring Meg Hut

Target: Roaring Meg Hut
Start: Roaring Meg Picnic area / lookout on Cromwell-Queenstown road.
Time (Doc): 6-7 hours each way
Time (Me): 4.5 hours in, 3.5 hours out.
GPX (approx): http://the.earth.li/~alex/tmp/roaring-meg.gpx

Basically, you start at the Roaring Meg lookout, where there is plenty of parking and you can probably sneak in an overnight stay if you're tidy, walk past the sign in the picnic area and through the forest for fifteen minutes. You pop out on the 4WD track to the Roaring Meg dam/hydro scheme and follow this up the side of the Roaring Meg for about an hour, climbing gradually. After a couple of switchbacks to gain height in a small block of forest, the 4WD track descends to the dam, but you stay high and follow a thin trail above the true left of the Roaring Meg.

This trail is pretty easy to follow and has poles every couple of hundred meters. After another hour, you descend to the stream where you must cross the stream. I couldn't find anywhere to jump over the stream without getting my feet wet, and on the way out after some rain was wading to my knees. You now leave the stream and head a short distance along the side-gorge then turn right, climbing steeply for a little way to exit the gorge. A trail runs roughly parallel to the Roaring Meg, but a few hundred meters to its right, over rolling tussock covered hills. After about fourty minutes you descend slightly back to the Roaring Meg and a flat with a small musterers hut.

From here you have two choices. You can follow the poled route, which climbs an old farm track to the crest of the range, or you can leave the poled route and simply sidle along the gorge of the Roaring Meg.

If you chose to stick to the poled route, you ascend fairly steeply, following the course of a wee burn. At the crest of the ridge, you turn right and leave the roaring meg pack track (which continues down to Cardrona), and follow along the ridge for about a hundred meters before turning east and dropping down a track, reaching the flat with the roaring meg hut after about twenty minutes.

If you chose to follow the gorge, there is a faint track but you may sometimes find it easier to wade up the stream. The best route is usually about twenty meters above the level of the stream, on its right. After about fourty minutes you'll get to a flat and may need to cross the stream once or twice to avoid steep sides or miss out curves. The hut in on the left of the stream just above the old gold tailings.

The hut itself has 12 sleeping spaces, including a sort of double-bed type space. There is a fire and nearby poisoned pine trees for fuel. If you are lucky someone will have left you some dry wood, if not, you can get chopping.

I imagine this trip might have some hairy moments if there was a covering of snow between 800 and 1000 meters. From the hut you can go back to the Roaring Meg carpark, continue to Cardrona via Touhey's Gulley (the continuation of the Roaring Meg pack track) or follow a poled route away from the hut which goes over the tops to Lowburn.

Crossing the Roaring Meg

See also: http://www.smiths.net.nz/meg.html.

Saving me from myself

2011-06-03T18:33:00.001+12:00

The great thing about using Perl to schedule the generation of your LaTeX documents, is that you can also use the Perl to catch a bunch of little mistakes that make life unpleasant in non-obvious ways. One of my favourites is to put the \label before the \caption in the figure environment, because, of course, in any sane world you could do that, but not in LaTeX. Thus, Perl to the rescue:

method check_figure_labels {
    my $file = $self->src;
    my ($in_figure, $seen_caption) = 0;
    foreach my $line (read_file($file)) {
      $line =~ s/%.*$//; # strip comments
      given ($line) {
        when (/\\end{document}/) {
          last;
        }
        when (/\\begin{figure}/) {
          $in_figure = 1;
        }
        when (/\\end{figure}/) {
          $seen_caption = 0;
          $in_figure = 0;
        }
        next unless $in_figure;
        when (/\\caption/) {
          $seen_caption = 1;
        }
        when (/\\label{(.*?)}/) {
          die "Label for LATEX figure $1 comes before the \\caption you will hate yourself later\n"
            unless $seen_caption;
        }
      }
    }
}

Also, sometimes I cannot spell the names of famous (and awesome) physicists:

method check_rayleigh {
    my $file = $self->src;
    my $latex = read_file($file);
    if ($latex =~ /raleigh/i) {
       die "YOU ARE A MORON! RAYLEIGH HAS A Y IN IT!";
    }
    return;
}

Perl needs another compile/run cycle hook

2011-05-31T17:29:00.000+12:00

In my ongoing interest in Moose I see that you can make a class, thus;

use Moose;
has attr => (is => 'rw', isa => 'Str');
1;

and having made a class, you can make it be much faster by inlining a lot of the things that Moose makes, by declaring that the class is immutable:

__PACKAGE__->meta->make_immutable;

You can also use

namespace::autoclean

to remove the sugar that Moose provides so that your users can't call the sugar as useless methods. This is all a bit ugly, so I wanted a way to hide these in something you put at the top of your code, together, a bit like this:

package MooseX::autoclean;
use Check::UnitCheck;
sub import {
    my $caller = caller();
    Check::UnitCheck::unitcheckify(sub {
 "$importer"->meta->make_immutable;
 });
}

which would push a UNITCHECK block into my caller's UNITCHECK queue and have it be executed once the caller's code was compiled.

This does not work, of course (in fact sometimes it segfaults, which is a whole different problem), because the caller (the Moose class you are declaring as you do this) has only been compiled by Perl at UNITCHECK stage. The compiled unit has not yet been executed to generate the class. Some other means is required to cause a block of code to be executed once your importing unit has finished executing, this might require the addition of another hook to Perl (er, UNITEND, I suppose) or some other tomfoolery.

Moose the revenge

2011-05-29T20:00:00.001+12:00

19:56 I continued my immersion in things Moose and dived past MooseX::Method::Signatures which was quite the groovy and on into MooseX::Declare. MooseX::Declare seemed like such a wonderful thing, until I wrapped it around my otherwise perfectly functioning class and BOOM! four thousand lines of errors and no idea why or where. Long story short, I'd coincidentally deleted the leading { in "$ENV{HOME}/blah" so the code inside the class was invalid. Fine, don't compile, but please DON'T JUST EXPLODE perhaps say why you've decided to explode and provide a useful error. I like Moose a lot, I'll be using it, but I'll be very cautious of any programming language (for that is what Moose is) which won't tell me where I've gone wrong.

20:00 Right, so now I'm going to go home and eat.

In which Alex learns Moose

2011-05-29T15:13:00.026+12:00

Today I have decided to learn Moose. I shall do this by converting my spider-web latex generation master script, now existing in four different incarnations, into an application class. It will be easy! Or will it? I liveblog myself, thus:

15:00 Finally decide to be productive (it is Sunday).
15:01 Decide to re-write generate.pl
15:02 type 'perl -MCPAN -e shell' 'install MooseX::Getopt'
15:12 While waiting for Moose to install, decide to liveblog myself. The install is taking a whole long while...
15:16 Meanwhile, I have written this, which I hope will work:

package MyApp::Generate;
use Moose;
with 'MooseX::Getopt';

has small => (is => 'rw', isa => 'Int', default => 0);

1;

15:23 Still waiting for Moose to build and test and install. I'd like to at least run perl -c on my snippet to see if I'm a fool or not, but as yet, I'm ignorant even of my foolishness.

15:29 Oh, there we are, installed. Time to try the very basic:

use 5.12.0;
use lib "$ENV{HOME}/alexwork/perl/";
use MyApp::Generate;

my $app = MyApp::Generate->new_from_opts();

15:33 Well, that works at least. Now, to make things work. (This might take a while).
15:38 So, I want a list of somethings, but not have it be commandline-able, this can be done using an attribute with a leading underscore:

has '_lib' => (accessor => 'lib', isa => 'ArrayRef[Str]', default => ['lib']);

15:47 Well, that didn't work, an enormous error (can I stop these enormous traces?) tells me I can't have a reference as a default, but I can have a sub to wrap it, so I do that.
16:12 Importing the crufty methods and changing the million script-local my variables into attributes of the class. How do I get a the entries of a HashRef attribute?
16:15 By which I mean, get in a tidy manner. For now I'll just grab it and use it.
16:28 still bashing in methods. Wondering what the output of an 'ArrayRef' attribute will be, a list or a reference. Not immediately clear.
16:35 well, it runs, but I want to have my options just as '--nopdf'. Maybe I can't do this, that would be sad.
16:39 Ah, I need to make the attributes be 'Bool' then MooseX::Getopt figures it out fine. Not all sad, happy even.
16:41 Now having trouble with a builder method. It's getting called, I'm going to find out what with.
16:45 As expected, I'm now in a confused state where I'm not quite sure why this method is being called.
16:46 so it looks like it's being called as part of the ->new_with_options during object construction, so maybe the builder is called when a default value is created...
16:48 Yes, this is so. I've added a guard for the default case.
16:50 I've constructed my object, now I fail to access an ArrayRef attribute correctly. What should it be?
16:51 It is indeed an array reference.
16:53 Now it seems I don't understand what a builder is for. Perhaps I really just need to write my own set_foo which then sets other things (I have an option which sets lots of things).
17:03 Well, I didn't. A builder is a different way to set a default, but to be able to override this in subclasses. I really want a trigger which will then go and set the other attributes.
17:06 Hmm, I can't suggest a trigger to be a method. For now this isn't a problem.

has src => (is => 'rw', isa => 'Str', default => '', trigger => \&_src_set);
sub _src_set {
    my $self = shift;
    my $val = shift;
    return unless defined($val);
    $val =~ s/\.tex$//;
    $self->out($val);
}

17:14 This now works for the first script, let's see if I can impose the class on the other generation routines without too much crying...
17:25 Different journals have their quirks, so it's time for a subclass instead of a slightly different but otherwise the same script.
17:35 Well, that was nice and easy.

Moral of the story: That was really very easy.

Next is to use more than just Moose. I think I like MooseX::Method::Signatures; One trouble, with picking all this up, it's that it's not clear what's worth picking up.

Putting comments next to paragraphs in latex and emacs (fix fill-paragraph)

2011-05-04T16:38:00.001+12:00

Again, this is just to save this for the edification of my future self. For the rest of you, do avoid using 30 year old technology if you value achieving anything on a Wednesday.

So, I like to put little comments by my paragraphs in papers I'm writing:

% this is rubbish
blah blah blah

% this is just plain wrong
blah blah blah

% I have checked this and it is ok
dobedobedo bedadadada

Which is very useful, because this is the way to annotate the latex source so that I can understand why I've written what I did. Now, the annoying thing is that I also like to bounce on M-q when I can't think of anything else to say, so my lovely paragraphs get turned into comments by the default emacs fill-paragraph command:

% I have checked this and it is ok debedobedo
% bedadadada

At which point the text disappears from my output, and I get cranky.

The solution is, of course, very simple but impossible to actually find (get it together google, you are now officially beyond being useless):

Get filladapt.el

Put it into site_lisp

And put this into ~/.emacs:

(require 'filladapt)
(add-hook 'text-mode-hook 'turn-on-filladapt-mode)

Also useful, discovered in an aside, is to associate files not with 'runemacs.exe', but with 'emacsclientw.exe' but then you have to set the environment variable to 'ALTERNATE_EDITOR' to 'path\to\runemacs.exe' OR IT WILL LAUGH AT YOU.

Sea ice breakup in McMurdo Sound, 2011

2011-03-11T23:02:00.002+13:00

Our group installed an ice tethered profiler in the sea ice by Scott Base, close to where we spent much of the winter of 2009 working on the sea ice. If we'd been down there now, we'd have quite wet feet as the sea ice which had been in place since about 1998 has finally succumbed to a well-timed storm and has broken out. This is bad news for our ITP, as it has drifted to a position where the ocean depth is too shallow for the length of cable, so the poor unit is spending a lot of time acting as an anchor in the mud. Hopefully it will clear the coast and start working again...

Here are a series of satellite images taken around the time of the breakout, with the path of the ITP superimposed on them.

2011-02-20 (a big storm makes lots of waves, you can see the road from McMurdo to Pegasus as a white line near the profiler, with a tongue of water crossing it...)

2011-02-22 (the ice edge moves towards the profiler)

2011-02-23 (moved, stuck by the ice shelf)

2011-02-24

2011-02-25 (escapes from the ice shelf edge)

2011-03-03 (a few days later)

Antarctic exploration eBooks

2011-01-10T12:24:00.001+13:00

Being a geek of all things Antarctic, and most things Arctic, I've dug out a number of out of copyright accounts of the early exploration, some of which are really quite good:

Worth actually reading:

Roald AMUNDSEN

The South Pole; an account of the Norwegian antarctic expedition in the 'Fram', 1910 to 1912

Apsley CHERRY-GARRARD

The worst journey in the world

Ernest SHACKLETON

South: The Story of Shackleton's Last Expedition 1914-1917

Robert Falcon SCOTT

Scott's last expedition (vol I)

Worth reading if you obsess:

Sir Douglass MAWSON

The home of the blizzard

James COOK

Charles TURLEY

The voyages of Captain Scott

What to do with your shiny Kindle

2011-01-09T13:58:00.000+13:00

I have a Kindle, it hasn't changed my life, but it has changed how I'm reading.

After a couple of months of use and some experimenting, I've settled on a few useful things related to the Kindle which extend what it can do.

Calibre

Calibre organises eBooks and can download and format news to put on the Kindle. This lets you add content without paying Amazon to do it through one of their subscription packages.

Instapaper

Instapaper collects together long articles from the web and will send them to the Kindle as a newspaper. This works as a 'read it later' service. It cannot deal with articles on subscription sites (eg. Nature.com) but otherwise does a good job of moving this type of reading off the web and onto a suitable device.

Economist print subscription

The cheapest way to read the economist in New Zealand is to get a UK print subscription. This also gives you a web access code which, combined with Calibre, gets you a weekly delivery of the Economist to the Kindle. Amazon's Kindle subscription is somewhat more expensive.

Make an eBook

If you want to understand the Kindle's insides, it's useful to make a book. Sigil is the best software I have found for this.

US/UK registration

Amazon restricts content available depending on your region, but does not know when you've gone on holiday. If you're not in the UK or US you probably still want to have your Kindle registered to an address there, so that you can access the whole of the catalog.

The main pleasure of using the Kindle, instead of a bright PC screen, to read magazines and books, is that I can fall asleep while reading from the Kindle. The passive screen and almost-book feel put my mind into night mode, while a bright PC screen with distractions keeps me awake. You can also leave it out in the wind and not lose your page, very important in Dunedin.

Next crazy project is to use publicly available mapping data to generate custom map pages to take tramping with me. Combined with some sort of waterproofing, this could be very useful...

You know you're not a real programming language when...

2011-01-03T13:52:00.002+13:00

So, you want to do this:

myf = @(key, dir) if (ls('dir')) do_store(key, dir) end;

But you can't, as the syntax is only:

myf = @(args) expr

And expr can't be a conditional.

What you can do, to fake this, and display to the world that you are covered with infectious language lice, is hide the if statement inside an eval() call.

myf = @(key,dir) eval('if (ls(dir)); do_store(key, dir); end');

This, of course, only works for some use cases.

Now, most real languages have a ? : operator, so this isn't even an issue, but most languages with anonymous functions (lambdas, whatever) let you specify a whole code block, and even let you run it over multiple lines.

my $func = sub { ... };

If matlab let you define script local functions, this would also be less of a problem, as you could put the function body in the script file and reference its name, but you can't. Nor can you access private/ functions from a script file. Madness! And people wonder why scientists write disturbing code. We really have no choice, sometimes.

Everyone in New Zealand should get a Kindle

2010-11-11T16:05:00.004+13:00

Yes, yes, I know, you could get a Kobo from Whitcoulis, but, you see, Whitcoulis are the problem. You pay far too much for books in New Zealand. So much, in fact, that in living here for two and a half years I've only purchased one full price book, and that was a present for someone. It's not that I don't read, back in a sensible country I'd spend the cost of a New Zealand book every couple of weeks, but I'd get three or four books for that. I just feel that by buying a book here I'm being screwed. No longer, though, a Kindle, or another foreign e-reader, lets me get something worth reading, right now, for less.

With this in mind, I make the following prediction: all middlemen in New Zealand selling something I could just as easily download, should get themselves a new job. Bookshops, music shops, DVD shops, computer games shops: you're all doomed. Second hand bookshops, second hand CD sellers, second hand DVD and second hand computer games shops: you're even more doomed. Convert your premises to sell fluffy sheep keyrings to tourists, set up something better than the 4-D trout experience, or morph into a coffee shop and you might just have a livelihood. Continue to sell things in a cold shop with no natural light and surly attitude that I can get more cheaply without even getting out of bed, and you're doomed.

And don't even get me started on supermarkets and the price of cheese.

(Update: 2011-02-18: NZ Herald - Whitcoulls in Administration)

proj4 and Perl for windows

2010-10-29T19:44:00.003+13:00

All amazing people the world over use Perl to get stuff done. Sometimes the world conspires to make this a tiny bit harder than it should be. Today I want to convert coordinates using the proj4 library, but could not because the geo::proj4 library doesn't build nicely under windows. But, ugly to the rescue:

1) Install proj4 from http://trac.osgeo.org/proj/wiki/WikiStart#Download

2) Do the ugly:

# this works, would you adam and eve it

sub coords2pols {

my ($lat, $lon) = @_;

if ($lon > -50) {

($lon, $lat) = ($lat, $lon);

}

open my $fhi, '>tmp.txt' or die "tmp file $!";

print $fhi "$lon $lat\n";

close $fhi;

system('cs2cs +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs +to +proj=stere +lat_0=-90 +lat_ts=-71 +lon_0=0 +k=1 +x_0=0 +y_0=0 +ellps=WGS84 +datum=WGS84 +units=m +no_defs tmp.txt > tmp.out.txt') and die "$@";

open my $fh, '

my $line = <$fh>;

close($fh);

chomp($line);

my ($x, $y) = split(/\s+/, $line);

unlink('tmp.txt');

unlink('tmp.out.txt');

($x, $y);

}

LaTeX and windows

2010-10-05T12:49:00.003+13:00

Oh yes we hate it we do. LaTeX + Windows = Pain. Well, actually, writing large documents anywhere = pain. Here, though, a trick to make some of the pain go away! (Posted for my future reference.)

First: Perl! Emacs! (If not, this will be senseless...)

Use a perl script to generate your pdf. Easier than a makefile, better than a punch in the face.

When running pdflatex, use the '-synctex=-1' option.

Then, at the end of the generate script, use SumatraPDF to view the file:

exec($pdfview,

'-reuse-instance',

'-inverse-search',

'"c:\\Program Files (x86)\\Emacs\\emacs-23.1\\bin\\emacsclientw.exe +%l %f"',

"$out.pdf"

);

This is fantastic, as it will reopen the pdf where you last looked at it (which is what you probably want) and you get to clicky on bits of the file and get them come up in emacs (which is also what you want to do).

Oh yes.

Version Control for Scientists

2010-08-26T14:05:00.002+12:00

So, here I am, working very hard, writing code, making figures, assembling presentations, writing papers, thinking about three different things at once, calibrating my data, recording observations and generally trying to do science. The result of three years' work will be three or four artifacts: a dataset of observations, a couple of papers with a definite view on what that means, and the rest of my thoughts bundled into a big book of a PhD.

Now, the data I collect is hopefully fixed. The ice was 1.25 meters thick. The voltage measured by my logger was 0.027 V, the temperature of the air was -25C. Once I've collected the data and entered it into a handy digital format it shouldn't change - I won't be able to collect it again. It's important then for this data to be well structured, to be annotated with how I collected it, and for it to be safely stored for ever. This means it must be backed up safely and in lots of places, and that any processing I do doesn't alter any of the raw data - all I can do is read it in for further processing.

That data needs to be processed though. Raw readings need to be turned into temperatures through some calibration code, calculations turn these temperatures into ice growth rates and heat fluxes, eventually I want an output of pictures of what this means, and hard numbers to compare with other people. I also want to be able to prove to someone that I arrived at these hard numbers through an honest method, and to be able to recreate any figures I make today at some point in the future.

I achieve this by using code to transform my data and to produce all figures, and can in principle do this directly from the raw data (usually I save intermediate stages of the calculations to save time, but I could make these again too). This means I can easily redo a figure if someone points out a mistake, or if it might tell a better story if coupled with other information, or if it just needs to have a different format because last time I put it in a presentation and this time it's going into a paper.

Now, it's all well and good having the code to make the figure today, but what if I modify or add to my code in the future? How can I know exactly what I did today, if I might have added something to my code for something else tomorrow? Partly we can avoid this being a problem by designing the code well, to always operate as it used to even as we improve it, (but that's a whole different story). Mostly we need to make sure we can somehow get back to older versions of the code we're using, or the paper we're writing. This is the only way we can prove to someone else exactly what we did to produce our final, polished and published paper.

I think it's essential for a scientist to be using a version control system, not because it offers a way to safely make and remove changes when developing code, but because it offers proof of our methods, even in the future. While I don't expect my work to generate the controversy of climategate, by using version control it should always be both possible and very easy to defend work I've done, even once I've moved on.

And how do I do this? I use mercurial with TortoiseHg and Kiln, for which there is a very good tutorial, but more adventurous people might like git with github which also fits the bill very nicely. As well as a fix of honesty, I get a easy way to backup my work, to recover deleted paragraphs I realise I liked after all, and a simple way to synchronize my work between three different computers and an online backup (thoughtfully provided by Kiln).

(This post was spurred on by an interesting discussion on the merits or not (I'm with not, if you didn't notice above) on version control of data at http://sunlightlabs.com/blog/2010/we-dont-need-a-github-for-data/.)

LaTeX doom

2010-08-18T17:02:00.002+12:00

Having passed through the part of my PhD where I put everything into a powerpoint and yammer about it to intensely interested audiences, I find myself instead in the part where I have to put things into papers. This means wrestling with LaTeX and spending the bulk of my time fiddling figures into the right format, dimensions, resolution, font and, possibly, the right data. I officially hate type-setting because it's entirely distracting busywork but it's busywork you've just got to do.

Still, some people have hit their heads on this wall before, so I'm extending my sincere thanks to the following things, made by real people, that have made my life a little less stressful recently. Maybe they will help you too...

Mercurial: http://mercurial.selenic.com/

For making it possible to make mistakes and magically recover without a thousand files marked '-old', '-old-old', '-broken' and '-fixed'. If you don't use version control, you're already lost.

SIUnitx: http://tug.ctan.org/tex-archive/macros/latex/contrib/siunitx/siunitx.pdf

Because no one gets the spacing with units right, and typing $^\circ$ is just too much.

Detexify: http://detexify.kirelabs.org/classify.html

Because I can't remember the magic words.

JabRef: http://jabref.sourceforge.net/index.php

Because who needs EndNote anyway.

The LaTeX Visual FAQ: http://www.ctan.org/tex-archive/info/visualFAQ/visualFAQ.pdf

Because clicky and my headache is solved.

Antarctic-Arctic see-saw

2010-04-22T18:08:00.005+12:00

In recent years we've seen a large loss of sea ice in Arctic and a small increase in the Antarctic. This is a well established fact, but sometimes we are asked 'why don't they both decrease, if global warming is global?'. This is a reasonable question, and one explanation for this was found in an interesting analysis by Chylek et. al. in GRL, 'Twentieth century bipolar seesaw of the Arctic and Antarctic surface air temperatures': (http://www.agu.org/journals/gl/gl1008/2010GL042793/).

They show that over the 20th century when the Antarctic was a little warmer, the Arctic was a little cooler, and vice-versa, and explain this by suggesting that the Atlantic ocean couples the Antarctic and Arctic regions, with ocean currents sometimes sending warm water northwards away from the Antarctic (so cooling the Antarctic) through the equator and on to the Arctic (so warming the Arctic), and sometimes this not happening quite as much, making the Arctic a little cooler, and the Antarctic a little warmer.

This imposes a strong signal of warming and cooling on top of the signal from CO2 driven global warming, so we shouldn't be surprised if major changes driven by temperatures, such as the extent of summer sea ice cover, appear at one of the poles without showing up immediately at the other.

head hurty

2010-04-06T19:57:00.003+12:00

While working away at some temperature data, I made my head sore. Not just because I'm trying to figure out what's going on, but because the graph comes out all head-hurty. Those blue lines are vertical, but they're not, yet they are! ouch.

2010-03-15T20:21:00.002+13:00

Here's a quick look at some of the sea ice I'm studying at the moment. It grew over the winter of 2009 in McMurdo Sound (this year's batch is just getting going). We get the ice using a large hollow drill, or corer, giving us a solid cylinder of ice. By scratching an arrow on the top, and piecing the cylinders together carefully, we can work out which way was North and we mark that with a thin cut along the core. We then take the core back to Scott Base where I chop it up using a meat-saw in a frozen laboratory, then measure it with instruments, all at -20 degrees C.

This video shows thin slices of the ice (each one is about 9cm diameter, 1cm thick) photographed under crossed polarisers. The video starts 70cm into the ice and finishes around 148 cm in, representing growth for around 70 days. Individual crystal grains show up as different patches of dark or light, and you can follow them as they grow downwards. Currents below the ice, inputs of small seed crystals and growth of platelet crystals into the ocean change the crystal make up of the ice as it grows. Early on currents help to align the ice crystals, later small seeds appear and disrupt the existing crystals, finally the first stages of platelet ice appear.

A slight diservice

2010-02-26T17:40:00.003+13:00

Yet again the brave adventurers of the Catlin Arctic Survey are heading to the wilderness of the icy Arctic ocean to do things no one has done before. Or are they?

The expedition will also be the first to take water samples from the sea ice in winter, as all previous Arctic measurements have been taken from ships in open water in summer.

Starting with Nansen's nutjob voyage in the Fram, a specially designed oceanographic research ship. Once Nansen left for the pole this was lead by Sverdrup, who now has a unit named for him which battles with the Tesla for being really quite big. This research continued through the fifties with countless drifting ice stations (think Ice Station Zebra, without the excitement) and present day ice camps or research cruises along with visits by nuclear submarines and flown in scientific parties. A slightly shorter but still long history of investigations on winter sea ice and oceanography in Antarctica also exists, in which I'm playing my small part.

Now, I'm not saying we shouldn't be doing more research in the Arctic. There's no doubt that ocean acidification is one of the more pressing problems when it comes to understanding global changes, and our stock of winter measurements of the polar oceans is still incredibly small and very patchy. But it's quite wrong to suggest that no one has even started looking. While this might drum up interest in what is essentially a glorified holiday for Ann Daniels, it's important that a measured message finds its way to the media, and to the public. Science gets to say big things about climate change because those big things are based on over a hundred years of careful measurement by many thousands of people, it's important we don't forget them...

Cthuloid horrors: Matlab parameter variation

2010-02-10T04:37:00.002+13:00

When working out how much heat has flowed through the sea ice I've found a couple of good parameterisations (models) for the thermal conductivity of the ice. Now, I want to see if my choice of model seriously affects the results I'm getting, as I'm hoping that my conclusions will be robust to things I've haven't been able to measure directly myself.

To do this I could write several different scripts to run my heat flux calculations, or I can write one framework to handle the calculations then plug in different models and parameters from outside. Now, I'm using matlab, mostly because it makes very pretty graphs and makes doing maths very easy. It's not great, though, at making programming easy. Still, I've come up with the following fairly simple method for varying the parameters to a model while still making it easy to develop it with just one set to start with.

First we define our model a bit like this:

function result = hf_heat_flux(temperatures, salinity, args)
% defaults
d.RHO_SEA_ICE = 935;
d.CONDF = @hf_conductivity_mu;

% replace defaults from args
d = ag_struct_args(d, args);

% do calculation
...
conductivity = d.CONDF(d.RHO_SEA_ICE, temperatures, salinity);
...
results = make_up_numbers(conductivity, temperatures);
end

Now, ag_struct_args simply replaces structure members in d with those present in args, and returns the modified structure. This lets us have default parameters but then replace them from args easily.

function r = ag_struct_args( s, defaults )
%AG_STRUCT_ARGS fill in optional arguments
r = defaults;

n = fieldnames(s);
for k = 1:(size(n, 2))
name = n{1,k};
r.(name) = s.(name);
end

end

Now we can use our heat flux calculation for single runs easily. To do multiple runs we need another couple of tricks. First we make a function to iterate over an unknown number of varying inputs, which finally sends these inputs to our initial function in the args structure:

function r = ag_do_vary( fun, flatten, args, varyargs )
%AG_DO_VARY Run a function with varying inputs (eg. models)
if (~isempty(varyargs))
if (size(varyargs, 2) > 1)
newargs = {varyargs{1, 2:end}};
else
newargs = {};
end
fname = varyargs{1}.field;
for k = 1:size(varyargs{1}.values, 2)
args.(fname) = varyargs{1}.values{k};
r{k} = ag_do_vary(fun, flatten, args, newargs);
end
if (~isempty(flatten))
r = flatten(r');
end
return;
end;

% got the whole set of args sorted out
r.data = fun(args);
r.params = args;
end

A good flatten function is @cell2mat.

This returns an array of structures, each member having a .params entry containing the input to our model, and a .data entry letting us know the result. We call it like this, first producing an anonymous function to eventually call our model, and then calling it multiple times:

rho.field = 'RHO_SEA_ICE';
rho.values = {930 935 940};
cond.field = 'CONDF';
cond.values = {@cond_mu @cond_old};

fun = @(params) hf_heat_flux(T, S, params);
ret = ag_do_vary(fun, @cell2mat, struct(), {rho cond});

Geophysics Conference Twitter Tags

2010-02-03T04:12:00.005+13:00

Scientific conferences are ideal happenings for the microblogging service Twitter, and probably reason enough for you to get a twitter account if you've not got one already. On the whole people use Twitter to follow the thoughts and musings of a few people that find interesting, but it can also be used to rapidly form groups of people into diffuse conversations around a #tag. By adding a short tag to your messages, prefixed by a # (hash or pound sign), then searching for that tag yourself, you can temporally become connected with other people. Essentially you advertise your interest in the topic so that people do not have to dig around to find you.

The advantages of this at a conference are enormous. Instead of putting up a couple of blog posts and turning up at an ice breaker, you can start very early on by announcing that you've had your abstract selected:

Abstract accepted: "Sea ice on a supercooled ocean: field measurements of ice growth and structure..." . #igstromso

When finding somewhere to stay, perhaps you'd like to share a room but don't know anyone else going, so ask on Twitter, and maybe you'll find someone who can help.

Looking for a roommate for IGS meeting in Tromso #igstromso

You get there a day early, and see that some other people have set up an impromptu social, so you go along and start the networking a day early.

A group of us will be in the igloo bar from 9pm. http://made.up/link. #igstromso

Finally you can comment on talks and interesting discussions, partly as a reminder to yourself for later, and to connect with others that might be at the other side of the room, not to mention a little bit of advertising for yourself just before your own talk.

Currently Twitter's not quite in the mainstream, so while it would be helpful if conference organisers could come up with and publish a twitter tag for people to use but in the mean time we'll have to guess what might end up being adopted.

Eventually people self-organise around a particular #tag, but this won't settle in until the conference is under way. A lot of the time some combination of the organisation and city hosting the meeting (eg. #igstromso) is the best thing to aim for. Most organisations have three or four letter abbreviations but these tend to be too general, and get swamped with other noise from twitter.

As an example I've been searching for the following from time to time to see what they turn up:

#apecs
For the association of polar early career scientists. A tag I'd hope to see used more frequently.

#ipyosc #ipyoslo (bad: #ipy, #oslo2010)
The IPY wrapup Oslo science conference. #oslo2010 is a great idea but gets mis-hits from the eurovision song contest which is likely to be much more popular with the rest of Europe.

#igstromso (bad: #igs)
IGS international symposium on sea ice in the physical and biogeochemical system.

#iahrlahti (bad: #iahr)
21st meeting of the IAHR in Lahti, Finland.

#egu #agu
For the AGU and EGU annual meetups. Suffer from conflicts as they're very short, so I just use these while the meetings are happening.

Of course, I also scan #seaice but keep clear of the noise of #climate, #physics and other more general tags - these provide a way to engage with the general public, but in such a diffuse way that I feel a blog or traditional media provide more reliable outreach. Twitter is best when used to create a manageable community tightly focused enough to want to read 50% of the posts that crop up. Unlike an email list it's less intrusive for the people that don't care right now, but might do later, and it quickly dissolves once the event is over.

10:23 Followup with Boots

2010-02-02T07:07:00.004+13:00

I've been following up on my overdose of Silicea by trying to find out exactly what is in the pills I took and how they are made. I've sent the following to Boots and my local trading standards office, who both politely sent me to the MHRA - the UK body that regulates medicines and healthcare products. I'm now sending off some FOI requests to them, and a simillar enquiry to Nelsons, who actually hold the authorisation to market the product.

I recently purchased a Boots branded 'Silicea C30 Homeopathic Remedy', expecting it to contain only sugar pills which had been laced with water forced to memorise the presence of silica after repeated dilutions. I did not expect there to be any silica in this product, though. I have since done deeper research into methods of homeopathic production, and believe that the pills provided do not meet the description on the label.

Initially I expected this product to contain no Silica as it would eventually be diluted so far as to be effectively not present and brought it under this impression. A homeopathic dilution of C30 implies that only 1 part in 10^60 could remain (10 with 60 zeros after it). I now know that even the most advanced water purification techniques cannot produce water with absolutely no silica in and that as a result it is unlikely that this product contains Silica at the C30 dilution level, but instead probably contains Silica at around the C4 or C5 dilution levels, plus extra Silica on the pills leached from the glass in which they are contained.

I believe this product is mislabeled. Please let me know what you will be doing about this.

Ten to the Twenty-Three

2010-01-30T10:30:00.003+13:00

I spent this Saturday overdosing on untested medicines. Not actual medicine, of course, in fact, nothing worse than a handful of sugar pressed into medical looking shapes and bottled up with specious claims to cure serious symptoms. Why? Well, along with the Sceptics in the Pub this mass overdose was organised to highlight the support Boots, a high street chemist, tacitly gives to the physically impossible claims of homeopaths.

Being made of nothing but sugar, these pills are entirely harmless, but the credibility that Boots and other high street chemists lend to these cures acts to confuse the public about the effectiveness of the tested and proven remedies available elsewhere in their shops. By promoting, even passively, these sham treatments, they are misdirecting their customers towards products which will not work, and allowing two very different standards of truth to be applied.

Using a homeopathic concoction to treat a bruise (which will heal itself given a little time) won't cause anyone any harm and will make Boots a little money. Elsewhere in the health system homeopathic practitioners push these impossible archaic ideas as cures for serious conditions where not receiving the proper, proven, treatment drastically decreases the quality of life of suffering people.

These non-treatments are not even labelled with suitable warnings, and in the Boots Reading Oracle branch at least are displayed prominently on the aisle where people queue to reach the counter where genuine prescriptions are dispensed. This can only add to the potential for the public to confuse a homeopathic remedy with real medicines.

Boots, and other licensed pharmacies, should restrict themselves to selling products which make claims of effectiveness that can be tested. They are given special rights by the government to act on the front line of healthcare, and are rightly seen by the public as a trusted source of information on medications. We should not let them endorse products as health treatments when there is no scientific basis for this.

Update: le canard noir has some parallel thoughts.

Silicea C30

2010-01-27T07:39:00.009+13:00

This Saturday I'll be heading to Oxford to overdose on homeopathic medicines as part of the 1032 campaign with the Oxford Sceptics in the Pub. The non-potion I brought yesterday and will be enjoying soon is marketed by Boots as Silicea C30 (it's not listed on their website). What do the homeopaths claim is in there, and what's really in there?

Silicea is a slightly made up name for what the rest of us call Silica, chemically SiO2, the most abundant compound on (well, in) the Earth. It turns up as sand, quartz, flint and other rocks and gems. Eating those would be harmless so long as they weren't too sharp. It's also used in silica gel as a desiccant, for instance packed in with new trainers, which you wouldn't want to swallow as there's often other stuff in there with the silica. You can obtain food grade silica gel, without the extra chemicals, and eat that, with no toxic effects (in fact it's available as a dietary supplement). The one thing you shouldn't do is grind up sand or quartz very fine and breath it in, as the teeny particles will stick to the walls of your lungs and irritate them for the rest of your life.

According to the homeopaths, though, whatever contact silica once had with the solution that was dripped onto the pills has been long washed away by 30 repeated 100:1 dilutions. This, they say, only makes it more powerful. As an aside, even if you buy the top of the range Millipore Milli-Q ultrapure water supplies you're specified to have no better than 3 ug / L of silica, or a concentration (by mass) of 3e-9. In homeopathic terms this is only a C4.5 dilution, so anyone advertising or selling something at C30 is clearly doing something misleading.

By the internal logic of homeopathy you treat a symptom with an overdilute solution of something that causes the same symptom. To me it seems that high doses of silica do nothing, so this C30 dilution of it should do nothing only better. According to http://abchomeopathy.com/r.php/Sil (which you really don't need to read), though, Silicea is active against a huge list of things, including, to my amusement, impaired thinking. So there you go.

What's really in there? Little balls of fructose and glucose. A double dose of woo, if you will.

(Flint from the Wikimedia commons.)

Degrees of Freedom : Minutes to Midnight

2010-01-26T06:30:00.004+13:00

I've always been intrigued by the Doomsday clock a device created by the Bulletin of the Atomic Scientists to represent the likelyhood of mankind bringing about its own destruction. It's currently at 6 minutes to midnight, and has ranged between 17 minutes (as the cold war wound down in 1991) and 2 minutes (the testing of the hydrogen bomb, and mounting global tensions in the early 50s). While mostly focussed on nuclear doom and political armageddon, they also take into account climate change and biosecurity. As an object it's easy to understand and provides a powerful image of our ticking towards our end. As a generator of news and public interest it's also powerful. It combines the views of concerned experts into a press-worthy event and allows a way for opinion to drive coverage.

Climate change will never provide a route to our immediate extinction, only a set of hardened circumstances for our older selves and our descendants, so metaphores of catastrophy don't match its effects. Nevertheless, some way could be found to deliver a punchy message about its impacts or likelyhood that can be modified to as changes in politics science or technology, drive us towards a solution or a worsening of our situation. Picking an actual impact would be problematical, as we're only just becomming able to predict these, and the science surrounding sea ice retreat, ocean acidification or species extinction would change the severity of the index and so, perhaps, remove its power as a public point of debate.

Perhaps something as simple as a thermostat would work, with the dial swinging in and out of our comfort zone, or the controls for an oven burning a pizza to a crisp.

(Thermostat from here)

Why we do fieldwork

2010-01-26T04:28:00.003+13:00

Since the 1970s satelites have been used to compile ice charts for the Arctic and Antarctic oceans. These work by monitoring the microwave emission of the ice or ocean or by firing microwaves down at the ice and listening for the faint returns. Microwaves are especially useful as they pass through clouds, and don't need light from the sun, so work in all weathers and all seasons. Different types of ice scatter and emit the microwaves differently, and ice is very different from open water. By following what happens year on year, and applying algorithms which seek to distinguish the various types of ice, it's possible to make maps of the extent, surface cover and (less well) the likely age of the ice and so some idea of its thickness.

In a recent GRL article "Perennial pack ice in the southern Beaufort Sea was not as it appeared in the summer of 2009" Barber et. al. went sailing through the ice in the sector of the Arctic near Canada early in Autumn, just as the ice was starting to form again. Charts produced from RADARSAT suggested they'd encounter thick multiyear ice but they found rotten ice, formed from ice that had almost disintegrated in the summer, to the point that it had a structure like Swiss cheese, and had since grown a thin cover of ice inside the holes. It turns out that this mix of ice looks like old ice, but is really better classified as weak young ice.

This shows in the most compelling way why we need to spend a lot of (your) money and (our) time and energy getting out and poking bits of the world to see how they work.