Note to self… Firefox US dictionary

Sunday, 21 June, 2015

Installed teh UK dictionary, but by default the US one is selected? In the portable version, simply delete the files from:

FirefoxPortable\App\Firefox\dictionaries

Digitising in QGIS

Friday, 19 June, 2015

I’ve been spending a fair bit of time digitising in QGIS 2.8.1 lately so thought I’d list some of my top tips for those doing the same (and dont forget the QGIS Manual)!

  • make sure to put the “Digitizing” and “Digitizing Tools” on the toolbar
  • “Toggle Editing” allows you to edit the layer currently highlighted in the ToC
  • the appropriate geometry will be selected, allowing you to add/edit points, lines or polygons
  • click “Add Feature” then left-click in your layer to start digitising. If its a line or polygon, you right click to finish your feature
  • middle press (scroll wheel) to pan around the image and rotate the scroll wheel to zoom in/out. Alternatively press the spacebar to allow the mouse to pan. PgUp/Dn to zoom.
  • Settings->Snapping Options allows you to set the snapping options (doh!). This is important for digitising features with shared boundaries to stop sliver polygons. From the snapping mode drop-doown, select Advanced - for polygons you will now get an option to “Avoid Intersections”. This will allow any overlapping polygons to share the same boundary. For lines I “snap to segments” at a tolerance of 5 pixels
  • Settings->Options->Digitizing allows you to set other options. I tick “Suppress attribute form pop-up after feature creation” to allow me just to digitize features - if you want to enter attribute data then you might want to untick them.
  • you can edit vertices by clicking the Node Tool on the toolbar. Ctrl and left mouse click to select a vertex and double click to add a vertex. You can also delete a selected vertex (delete button) and move it (left click and drag)
  • don’t forget to click “Toggle editing” again when you’ve finished to turn it off and save your edits!

Journal of Maps 2014 Impact Factor

Friday, 19 June, 2015

It’s that time of year again, yes Impact Factors are out and whether we like it or not authors and journals, alongside all those who rank them, will be sifting through the data to see who’s up and who’s down!! So with that in mind, its very pleasing to report that the Journal of Maps has again seen its impact factor rise this time to 1.2. The 1.0 boundary seems like a watershed as that is the point at which there are more citations than articles published. This year’s editorial provides a summary of general performance last year and whilst the number of articles stayed largely the same, we are seeing increasing submissions and downloads (and are probably up about 10% on submissions so far this year). As a result of this we have introduced an extra issue for 2015 which will allow us to increase the amount we publish.

This not only illustrates the resurgence in cartography and so the importance that maps play in a range of academic disciplines, but also how relevant they are to contemporary research. And there is no better example than this year’s “Best Map” winner which is available for free download from Taylor and Francis.

Environment Agency LiDAR to become open data

Friday, 19 June, 2015

Great news over at the Environment Agency blog noting that their extensive LiDAR back catalog will (from September 2015) become open data available from Datashare. This is a a valuable data source and one of the most extensive LiDAR datasets available for the UK.

OPEN ACCESS EPRINT: Optimising UAV image quality using consumer cameras

Thursday, 18 June, 2015

O’Connor, J. and Smith, M.J. (2015)
Geomatics World

Surveys using UAVs and photogrammetry are becoming ubiquitous. It is in the community’s best interests to remember the fundamentals of image capture. James O’Connor and Mike J Smith of the School of Geography, Geology and the Environment, Kingston University review the main considerations for image capture when undertaking an aerial survey using consumer grade cameras and make recommendations for acquiring the best imagery.

Adding subtitles….

Tuesday, 16 June, 2015

Harking back to my earlier posts on transcoding DVDs for viewing on a Pico Projector, I have recently been trying to make sure (for one film) that subtitles transferred across. This proved to be both more complicated to sort out and relatively simple (in the end!) to achieve. Subtitles (as opposed to closed captions) on DVDs are (perhaps strangely!) images that are stored as a separate stream within the video file and when activated are overlaid on top (with transparency applied) of the video stream. In order to transcode these you actually need to extract the subtitle stream, use optical character recognition (OCR) to convert them to text and then enable subtitles on your encoding software to add them back in again. Quite a few steps… which was why it took a little why to fathom out.

DVDSubEdit was used to read the subtitles (subpic stream as its known) - load the file, clock “Run OCR” and then “Save as .srt”. For some strange reason (possibly linked to 4:3 and 16:9 subtitles mixed together) all the lines were duplicated which would mean they would appear twice…. so Subtitle Edit was used to remove these duplicate lines (Tools -> Merge lines with same text). Make sure the SRT file has the same name as the VOB file extracted from the DVD and is in the same directory…. in TEncode then simply select “Enable subtitles” (making sure the Mencoder encoder is being used) and then encode!!

The subtitling works well, although bear in mind that the OCR may not always be perfect.

Overcoming jet lag….

Monday, 15 June, 2015

After my trip to Argentina over Easter I’d thought I’d briefly blog about jet lag, the bane of all travellers. Wikipedia has a useful succinct definition

“Jet lag, medically referred to as desynchronosis, is a physiological condition which results from alterations to the body’s circadian rhythms resulting from rapid long-distance transmeridian (east-west or west-east) travel on high-speed aircraft.”

Or, more plainly, if you travel east or west rapidly your body clock becomes out-of-sync with local time. So what’s to be done about desynchronosis? My brother recommended Overcoming Jet Lag, a short book which is primarily filled with schedules to follow depending upon the number of time zones you are jumping. However the basis of it is relatively simple - your wakefulness and hunger become desynchronised to local time and the trick is to find rapid ways of resynchronising them. Here, for example, is the timetable for a 3-4 hour westward time zone change:

Travel Day - 3: STOP consuming caffeine (tea, coffee, choclate etc).
Travel Day - 1: FAST day (max 800 calories) with high-protein breakfast/lunch and high carb dinner.
Travel Day: drink 2-3 cups of strong coffee BEFORE 11am. Consume no more caffeine. Set watch to destination time and eat breakfast at destination time, making sure you are physically awake/active. Its a FEAST day so high-protein breakfast/lunch and high carb dinner. Sleep by around 8/9pm destination time.

The basis is to rapidly change the biological cues caused by wakefulness and eating, which can be assisted by taking caffeine. For my trip to Argentina (4 hours behind), my flight left at 7.30am - I stayed close to Heathrow and got a flight to Madrid. I woke at 5.30am and as I was still sleepy, went back to sleep on the plane, but managed to sneak two breakfasts just before arrival (high protein!). I switched on to the flight to Buenos Aires where they served coffee at 12 allowing me to (slightly late) take on board the caffeine. This was followed by “lunch” at around 3pm which was now closely synchronised to Argentinian time. The plane landed 7.30pm local time which allowed me to get to the hotel for 8.30pm, a rapid high carb dinner before crashing at 9.30pm (1.30am UK time). I slept through until 8am when I had a full breakfast.

What was amazing was that other than occasional hunger pangs over a few days I suffered no other jet lag symptoms and was virtually fully functional. Clearly the routine is highly dependent upon the timings of the flights. In this instance, travelling through the day and arriving in the evening was beneficial, far more so than travelling overnight. However it was notable that the airline (Iberia), after lunch, closed all the windows to get people to sleep. This is exactly what you DON’T want to do - it was imperative to stay awake so that you aligned to local time as soon as possible. Airlines are clearly interested in having sober, manageable, people rather than minimising jet lag. The timing and style of food is also critical, something you don’t have any control over in economy!!

Coming back was more complicated due to the timing of the flight and the (harder) eastward time zone shift. Here the recommendation is:

Travel Day - 3: STOP consuming caffeine (tea, coffee, choclate etc).
Travel Day - 1: FEAST day with high-protein breakfast/lunch and high carb dinner.
Travel Day: get out of bed earlier than usual. Its a FAST day so high-protein breakfast/lunch and high carb dinner (max 800 calories). Drink 2-3 cups of strong coffee BEFORE 6pm. Consume no more caffeine. Sleep by around 8pm local time (12pm destination time).
On Arrival: Its a FEAST day so high-protein breakfast/lunch and high carb dinner. No caffeine and stay awake!!

My problem was that this was an overnight flight that arrived at 5am local time! The fasting aspect, coffee and sleep worked very well. The book is quite clear that you should do everything you would normally do to go to sleep even if you feel you aren’t fully asleep. Your body will still rest and start the process of resetting itself. In order to maximise this (on a small uncomfortable seat!) I used a neck pillow and sleep mask (critical to supporting the head and reducing the stimulus of light), along with getting in a down sleeping bag I had brought. Yup - I got in a sleeping bag!! This all worked amazing well - however the poor seat, located opposite the toilet, made for a poor nights rest which was only 5 hours long! The rest of the day went fine, but by the end I was just sleep deprived and it took a few days to recover that. Lesson… choose your flights and seat location carefully!

Peer Review (event summary)

Thursday, 11 June, 2015

I was recently on a panel discussion organised by Sense About Science on peer review specifically targeted at PhD and early career researchers. This series has been running 4 or 5 years now and has slowly evolved over time in to its current format of 2 group discussion sessions followed by brief panel member presentations and then a long Q&A (a good review of the event by my PhD student James O’Connor). Elizabeth Moylan of BioMed Central spoke about how the system currently operates commenting upon single/double blind and open review, the cycle of review, potential biases and the problem of reviewer fatigue. This is particularly a problem where journals seek fast review times and if papers get cycled between different journals. She noted new developments that uncouple review from the journal (Peerage of Science and Axios Review), as well as ideas for collaborative review and receiving credit for review. All important discussions and developments in the peer review process.

I spoke next (see my slides) covering why people choose to publish before moving on to the process (and emotions!) of submitting a paper, receiving a review and (hopefully) seeing it in print before concluding on why people review.

Irene Hames spoke on some of the developments in peer review and how we can and should be making the most of these. They included (in no particular order) retraction watch, PubPeer, PeerJ, Faculty1000 and Rubriq. She also highlighted how journals are now competing for peer reviews and that this is an area ripe for credit (dont forget to get your ORCID ID and list them there) as well as abuse!! See this story over at Retraction Watch for example. She also briefly talked about what you can do with a review - this is actually a piece of work by the reviewer and being able to use these reviews is potentially a valuable output. Check with the journal!

The discussion was really thought provoking and highlighted, first and foremost, the strong biomedical interest in the attendees. Questions relating to supervisors taking credit for reviews students had undertaken, unhelpful reviews, rude reviews, why rejections happen, how reviewers are selected, differences between subjects, journal funding models…. all really pertinent topics. It’s also worth noting that authors compete for space where journals have page budgets - so whilst a paper may well be publishable, that doesn’t necessarily mean it will be accepted. And that writing well goes a long way to helping a paper along in the review process - you can never practice enough at writing!!

A hugely valuable day and well worth being a part of the debate.

GeoBig

Friday, 5 June, 2015

Its a bit twee in its connotations, but “big data” keeps popping up all over the place. My brother sent me the link to this story: “5 Ways Big Geospatial Data Is Driving Analytics In the Real World“. There is nothing overly new or exciting in the actual research itself, however what is interesting is how “geo” is now overtly mainstream. A lot of the benefits and issues associated with geodata are now more widely understood and appreciated meaning that more people want to use it. Definitely boom times…

Be bold, Be Blad

Friday, 5 June, 2015

DPReview report on the latest aerial camera range from Hasselblad, the A5D. These are medium format cameras that compete directly with the Phase Range range I reported on earlier (the 80MP iXU180). Three models at 40, 50 and 60 MP, with up to 14 stops dynamic range with a 53×40 or 44×33mm sensor (technical specs here). Weighting in at 1.3kg (body only) its slightly heavier as well.

Clearly the medium format aerial imaging space is heating up a lot - sales are likely much higher than bespoke large format cameras and used across a range of platforms including UAVs. Expect this to get better and cheaper with the competitive drive. Exciting times!