November leaves

November has been so mild that many of the trees still have their leaves.

apple tree

maple

That's not to say there aren't many leaves on the ground, and in the water.

leaves in the rill

leaves surrounded

It's not all leaves.

this tiny mushroom in the path has caught a thread

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with just a hint mackerel

16:10 GMT, looking west

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autumn trees

Walking over to a meeting, I spotted the sun low on the magnificent tree in front of the library.

Magnificent autumn colour (and it looker oranger in real life than in the pic).  Then a few steps further on I saw another tree catching the light:

It was also brighter in real life than here.

Just, wow!

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afternoon sunset II

a little earlier than yesterday, and more spectacular

16:18 GMT, looking west

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afternoon sunset

The view at 4:30pm, and it’s still over a month to the shortest day!

16:30 GMT, looking west

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back from Lyon

More cathedral than train station?

I’m just back from a short trip to Lyon, attending the kick-off meeting of our new EU research project, EvoEvo (“Evolution of Evolution”), selected for the FET Proactive “Evolving Living Technologies” call.  It was an excellent meeting, promising lots of interesting and exciting research over the next three years.  Our task at York is to develop a novel bio-inspired algorithm for tackling open-ended problems, based on the biological experiments and computational modelling being done by the other partners.  It’s going to be great fun.

It was my first trip to Lyon.  A 90 minute EasyJet flight from Stansted arrived at Terminal 3 in Lyon Saint-Exupéry airport, which is a sort of temporary high tech cowshed with metal walls and a plastic roof.

blue sky!

Sights architectural improved rapidly at the adjacent railway station, with its gorgeous swooping roof.  From there is was a 30 minute shuttle-tram ride into Lyon itself, then a shorter tram ride to the hotel.

… amoeba-table

amoeba basin …

The hotel itself, although perfectly comfortable and fine, had clearly embraced some form of crazed design concept. The first clue there was something different about the place was its stealth lifts, entrances cunningly camouflaged with a garish mural.  Then there was the the shape and colour of the hand basin in the en suite, manifesting as some sort of fluorescent green amoeboid entity.  This was clearly deliberate, as its colour and shape were mirrored by the small table in the room proper.

I never actually
tried sitting on this

looks like steel;
feels like lino

The decor continued in a sort of industrial-chic flavour, with a tin chair, and faux riveted brushed steel flooring (actually a very pleasant-feeling warm lino).

This being France, the food was, of course, excellent.  Even a mere sandwich from an airport cafe on the return trip was delicious.  On the Monday we sat outside to eat lunch in glorious sunshine.  It was blustery (probably the edge of St Jude’s storm), but very warm: I was actually rather concerned about the possibility of sunburn!

Another short hop, back to Stansted.  The flight arrived 10 minutes ahead of schedule, due to a strong tail wind (yet more remnants of the storm).  By happy chance I ended up first in the queue at passport control, and was thinking about where I had to go to get the bus to the airport carpark.  I realised the guy looking at my passport had asked me a question. Uhh. Rewind.  Oh, he’d said: “where was your flight from today?”  I looked at him blankly.  I’m in Stansted.  That means I’ve just flown in from somewhere.  Where?  Taormina?  No.  Where then?  Uhh...  Oh.  “Lyon”, I said, after a long, suspicious pause.  He looked more closely at my passport, but then let me through.  Whew.

So, safely back home.  Now to get down to the research…

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90 minutes later

If you don't like the weather, wait 15 minutes.

Ah, that's better!  Lovely sunshine, warm breezes.  So, we now have a couple of bags full of apples, ready to take to work and inflict on our colleagues on Monday.

The sunshine is making the berries look gorgeous.

Cotoneaster berries shining in the sunlight

a contrast in colours: yellow berries of the berberis against purple heuchera leaves

Notice the mushrooms nestling in the bottom left of that picture?  Well, the whole crop has been growing well in the damp:

I just wish I knew if they were safe to eat.  I am very firmly assuming not.

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apple picking time

Prediction is very difficult, especially about the future. — Niels Bohr (attrib.)

Our apple glut is reaching fruition, so it’s time to start harvesting.  Shall we pick them today, or tomorrow?  Let’s have a look at the BBC weather forecast.  It says today will be dry up until this evening, then rain continuing for most of tomorrow.  Great, let’s harvest today, then.

Off out into the garden, picking apples.  We’d been out, ooh, must have been all of five minutes, when … you’ve guessed it, it started to rain!

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a sky full of shepherd's delight

Great sunset tonight.

Interestingly, this isn’t looking towards the setting sun, but about 90° west of it.

A different part of the sky:

This view is diametrically opposite the setting sun.

No photo of the setting sun itself – in that direction there’s just thick black cloud!

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October the First is Too Late

It’s turned chilly all of a sudden.  With maximum temperatures of 14°C today, and forecast for the next few days, I cracked, and the central heating is now on.  Goodbye summer.

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a week in Taormina

I’ve had a glorious week in Taormina, Sicily, at the European Conference on Artificial Life (ECAL).  Great weather (apart from a rain storm on Monday), superb food, and a marvelously stimulating, thought-provoking set of keynotes and presentations.  My head is buzzing with all the stuff I’ve been hearing about.

a complex fungus, spotted
halfway down one staircase

The town, the gardens, and the scenery were excellent, too.  The town is built on the side of a mountain, which makes for an interesting geography.  On the Monday morning, the hotel provided a map to help us find our way to the conference venue. Unfortunately the map had a tenuous relationship with reality. The geography mostly comprises a parallel bunch of roads running along contours, linked by an amazing array of staircases, of all widths and types.  The hotel map didn’t distinguish these, and everything from a main street to a three foot wide staircase had the same representation.  I got a better map, and navigation became rather easier.

Tuesday evening: a view down to the middle road from part way up one of the many staircases...

... and the view up the rest of the staircase.
There was another flight like this to get to the top road, then a shorter flight up to the hotel, then more stairs once inside up to my 4th floor room: I took the lift by this stage.

Evenings were spent in a variety of great restaurants, squeezed into little gap, some even laid out on the staircases.  Eating marvellous Italian food outdoors on a warm summer evening, having stimulating conversations with colleagues, is a great way to end each conference day. There were also wandering bands of musicians, who would play a few tunes, then send a collection jug round.  I’m not sure what the message was supposed to be the evening they played the jug around to the theme from The Godfather...

The walk down from the hotel to the conference each day was through the splendid public gardens.

Wednesday morning : the pagoda

Magnificent displays, from bougainvillea hedges...

... to cacti collections

Although the weather was warm and sunny, the skies were rather hazy at the start.  They cleared enough later in the week to see Etna, the summit obscured not by clouds, but by a faint trickle of smoke:

Thursday: the view at breakfast

Thursday: Taormina by night

A great conference, at a great venue.  Now it’s time to go home to cooler, cloudier England. Next year’s ALife conference is in New York, which will have a somewhat different vibe, I suspect.

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the nights are pulling in

Yet it seems like only yesterday that sunset was around 9:30pm

sunset, 7:45pm

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suddenly, apples! thousands of them!

The earlier predicted apple glut is well on its way, having been helped by sunshine and rain:

the young apple tree: crunchy Coxes

the old apple tree: tasty cookers

Soon...

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time to go home

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waspish caterpillar

I read recently, in the "Last Word" section of New Scientist, a piece asking for help to identify an Italian butterfly-like creature.  The questioner couldn't identify it because "it doesn't seem like any butterfly I've seen, nor is it in any of my insect books".  What caught my eye was the implication of ownership of at least three insect books.  We have only the one insect book.  And two butterfly books.  Oh, and a dragonfly book.

Yet none of our books could help us to identify this splendid caterpillar we found in the garden today.

at least it's on a weed

The reason I know that none could have helped is that I looked it up in them, after I had identified it using the web.  To identify it in the first place, I googled "caterpillar black yellow stripes", and got

it seems there are rather a lot of caterpillars using a yellow and black colour palette

Looking through the results identified several promising candidates.  The respective source pages all identified it as the caterpillar of the Cinnibar moth.  The wikipedia page has more details, confirming the identification.  But our insect book doesn't have it.  Neither do our butterfly books (well, it is a moth, I suppose).

Back in the garden, the spiders (which will obviously not be in our insect book) have been busy wrapping up the plants in a dense web.

And the patio roses we bought back in early May are now blooming their hearts out.

The labels must have lied about the colours.  I think we are going to have to separate these!

The weeds are growing apace, but it's way too hot at the moment (28°C) to garden.  So I'm blogging about the garden instead.

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rainfall statistics in d3

My explorations of the d3 data visualisation library for JavaScript continue apace.  I have now added "box-and-whisker" plots to the 2012 rainfall, helping demonstrate the anomalously wet April and July, and dry August, last year.  This required calculating the various means, medians and quartiles, which wasn't particularly difficult, and has given me a feel for working with arrays.

Box and whisker plots show minimum, lower quartile, median, upper quartile, and maximum.
The mean value is overlayed as a blob.

This latest version replicates the previous chart displaying this information, which I did in Excel. (The bars are slightly different, because here I have included the 2012 data in the statistics, whereas I excluded it in the previous version.)

I think this d3 version looks much cleaner.  It certainly lets me fiddle with things at the programmatic level I prefer!

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interaction with d3

My explorations of the d3 data visualisation library for JavaScript continue.  Last weekend I dipped my toe in the water, and drew some simple rainfall charts.  The code was clunky, and the data was hardwired, but the charts were pretty enough to convince me to continue.

And so this weekend I've explored some more.  I've modified the code to read in the data from a csv file, and then refactored like mad to make it more elegant.  The result of half a day's work was a web page indistinguishable (on the surface) from before: but now the charts, and the headings, are generated from the csv file data, so I can add more data each month, and the page will update without any code having to change.  So, a success.

Then I decided to add a little bit of interaction: changing the colour of a bar or spot on mouse-over, and showing the actual data value.  The d3 library is powerful enough that it was very easy to do.

in May 2007 we had 76mm of rain

in July 2009 we had 63mm of rain

So that's some tasks completed off my to-do list.  I've still got a long way to go.  But, as when I was learning Python, I'm finding StackOverflow an invaluable resource.

The actual web page is here, but it may change over time as I add more functionality.

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my first d3

Way back when I was an undergraduate, I stumbled across a book called Curve Tracing, by Percival Frost.  The college library had a first edition, published in 1872.  Several years later, I came across a newer edition in a bookshop, and grabbed at it.

This beautiful little book has tons of curves defined by equations, and shown as graphs.

Plate IV from Curve Tracing

This was all originally done in the days before computers.  It's been a goal of mine to reimplement some of this work, in an interactive form, because many of these curves have parameters that affect their detailed shape.  So, I've been looking for a suitable tool.

Also, I'm interested in data visualisation (and have long been a disciple of Tufte).  I've tried to follow the "no chartjunk" ethos in my own work.  For example, to plot our rainfall statistics, I had to struggle with Excel charts to remove most of the garish "ink" provided by default. But it's still not perfect.  Additionally, I have some specific work I want to do with modified parallel coordinates, for which there is no existing library.  So, I've been looking for a suitable tool.

Last week a colleague of mine mentioned d3, a JavaScript library for Data-Driven Documents. I browsed the gallery for a while, and fell in love.  I spent yesterday playing around with evaluating it, on simple charts, to see what it could do.  This meant reading Scott Murray's d3 tutorial, and implementing a few simple charts to show the rainfall data. (Oh, and learning my first JavaScript.)

First off, I tried a simple bar chart, starting from Murray's tutorial example (when learning a new language, I usually find it easier to modify existing code than start from an empty file). After fiddling around to get the ordinal x-axis working, I got:

d3 chart of 2012 rainfall in mm

I think that looks suitably chartjunk-free and minimal.  It also has the nice feature of combining the actual numerical values into the bars, giving what Tufte calls both a macro-reading (the bars: gosh, July was wet!) and a micro-reading (the numbers: July had 113mm of rain) in one chart.

What's nice about d3 is the way the axes scale automatically.  Exactly the same code produced these charts (the only difference is the July data value: 13, 113, 233):

automatic axis scaling with changing data values

But, of course, we have several years of rainfall data.  A little more hacking coding gave me a grouped bar chart:

rainfall, June 2005 -- May 2013

Now it's possible to see how wet April 2012 was, compared to normal Aprils, even if it wasn't as wet as that July!  My implementation of this is a little kludgy, with too much hard-wiring, since my goal was to evaluate the capability, not (yet) learn the entire language; my next task is to code it more elegantly.

I've always found grouped bar charts rather cluttered, and so I wondered if there was a better way to show the data.  Rather than use some sort of surface plot, I decide to try a projection where the size of a spot is related to the amount of rainfall.  With a surprisingly small change to the code, the grouped bar chart metamorphosed into a "blob" chart:

(left): blob area proportional to monthly rainfall; (right) blob radius proportional to monthly rainfall

This enables comparisons in both dimensions (years, or months), depending on whether you view rows or columns.

So, based on a day's work, I'm very impressed with d3.  However, there are a lot more d3 facilities I need to get up to speed with before I can start my reFrost project in earnest:

• csv data import -- currently the data is hard-wired into the scripts (ugh)
• data manipulation -- to calculate medians and quartiles for box and whisker plots
• lines -- to draw graphs rather than charts
• maths -- to calculate the functions: and, presumably I'll need a lot more JavaScript
• interaction -- so parameter values can be chosen by the user
• transitions -- so the graphs will smoothly change as parameters are varied
• more -- stuff I don't know about yet, but will need

So, a way to go, but I think I might have identified the tools I need.

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sun pillars and ducks

Another glorious sunset tonight, with super colours and delicate cloud patterns.

Just how good it was wasn't clear until we moved so that the tree was no longer in the way, though.  Then we could see a glorious sun pillar -- much clearer than the previous one we saw. (And again, it was much brighter in reality than it appears in the photo.)

sun pillar, Sat 25 May 2013, 21:14 BST

After a day of relatively warm sunlight on the patio stones, the ducklings, now down to 10 in number, have decided to roost immediately outside our French windows.  They are oblivious to us inside, standing a foot away from them, taking photographs.

the one on the left is some sort of rugged individualist

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paint the sky with clouds

Walking down to work from the car park this morning, I was greeted by a marvelous sky -- and what appeared to be the cause.

a power station paints the clouds?

Zoom in on the "source", and you can see individual columns of vapour from the several cooling towers of a nearby power station.  The juxtaposition with the clouds makes for a great optical illusion: from this angle, the plume appears to be the source of the entire sky of clouds.

Down the bottom of the path, the view opened out, allowing sight of two more power stations, apparently also painting the sky with clouds.

well, the one on the right hasn't started painting yet, obviously...

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