Duncan Golicher’s weblog

While backing up some old information on my hard drive I rediscovered a document I produced for Pronatura at the end of November 2003. It lies somewhere between the status of informal field notes and a formal technical report. I presented it to Pronatura a week after a field trip in a light plane. The idea of the document was to record the discussion during the flight.

This was very much at the end of the “pre-google earth” era. Spatial analysis was still rather more of a specialised activity than it is today and I had only begun to become interested in the subject myself. My previous research was generally non-spatial.

Now a “fly over” of the region can be achieved rather more comfortably and safely with a laptop than a four seater plane. The experience was stomach churning at times with a few moments of sheer terror as the turbulence caused by thermals rising from the central depression hit.

Despite the fact that some of the analytical methods used were hurriedly applied and could certainly be refined, I still generally agree with most of the conclusions in the document.So I have placed it here in case it could be useful as a general introduction to the region. It is not directly citable, but similar statements to those included in the document have been made in peer reviewed work I have published together with Luis Cayuela, although there have been very slight differences in emphasis between my interpretation of patterns and causes of deforestation in the region and those adopted by Luis Cayuela and some other colleagues.

Here is the document in PDF form ….

reflections-after-a-flight-over-the-altos-of-chiapas

Ecosur will soon be providing students and researchers with a networked data base for storing and visualising public domain spatial layers. This database should also store results from ongoing research. I am convinced that the advantages of providing a fully functional geographical data base at zero cost by using PostGIS/Postgresql are compelling. The release of a stable Postgresql 8.3 and Qgis 0.10 have made the task even simpler.

Postgresql 8.3 is now notably faster when running spatial queries than the version I had been using (8.1). It also has very advanced features.  These move PostgreSQL up to the power of the premium  proprietary enterprise data base, Oracle. They clearly go beyond those found in MySQL.

The only practical challenge I faced with PostgreSQL 8.1 involved a very simple issue of scalability when the database was viewed with Qgis 0.9. Despite some issues with the stability of Qgis (that did worry me, but appear to have been largely resolved) Qgis is a suitable visualisation tool for PostGIS. I have used it extensively since I started experimenting with PostGIS a few months ago and am generally satisfied. However a simple practical issue concerned me.

How could users easily be given access to the parts of a potentially very large database in such a way that they see only the part they need or are allowed to see?

The answer had clearly to be through the use of Postgresql schemas, but the Qgis interface didn’t show them in a user friendly way that matched the need.

This problem is now largely resolved by the new version of Qgis. Schemas now show up in an unfoldable tree structure. As groups of users and individual users can be given access to a subset of schemas it should now be feasible to design a database that hides all the complexity from users and allows them to quickly find the layers  they need.

Algunos estudiantes llevaron discos de Ubuntu Heron despues de mi presentación. Si han probado instalarlo estoy seguro que van a querer usarlo para ver videos. Para conseguir Flash para You Tube la mejor forma es abrir synaptics (sistema-administración-synaptics) y buscar “flashplugin-nonfree”. Luego los codecs se instalan cuando se necesitan.

Para tener Medibuntu (el repositorio para algunos codecs comerciales) la forma mas rapida es con comandos. Abre un terminal y pega este para abrir el archivo de los repositorios.
sudo gedit /etc/apt/sources.list

Luego pega este en el documento al fondo y guardarlo.

deb http://packages.medibuntu.org/ hardy free non-free

Para añadir la clave para activarlo pega este en un terminal.
wget -q http://packages.medibuntu.org/medibuntu-key.gpg -O- | sudo apt-key add - && sudo apt-get update

sudo apt-get update

Y luego nada mas añade los libs.

sudo apt-get install libdvdcss2 libdvdread3

No te asustas con el uso del terminal. Se puede conseguir lo mismo con el GUI, pero es mas facil comunicar la información como comandos.

I am impressed by Ubuntu Heron. The most important difference is  ease of installation. Both Feisty and Gutsy were simple enough to get running, given a reasonable degree of patience. However there were always a few problems to fix. These involved  screen resolution sound and video. Getting everything right needed  a search which produced multiple answers on the users forums.

A single issue that needs to be resolved by editing a config file is more than enough to get most Windows users, acustomed to  preinstalled operating systems, to give up and go strait back to what they know. Thus despite the clear merit of the underlying operating system, uptake remained much slower than it could have been among academic colleagues here.

In contrast my  experience installing Heron on a Toshiba Tecra was effortless. It all worked out of the box. What was more impressive was the short amount of time it took to get everything, including a large number of R packages, GRASS, QGis, Google Earth, MySQL, Apache, Postgresql etc all back together. I already knew what I wanted and where to get it, but even so the short time line is worth stressing.

3:15 Open Laptop and remove old hard disk (It was time to go from 80GB to 250GB and this is a great way to make the change without any fear of losing time)

3:20 New hard disk in place.

3: 25 Heron install CD is asking me for details of location, keyboard and partitioning.

3:41 Heron installed and running.

3:45 Reboot in order to use NVidia, this was recognised as necessary after activating advanced visual effects. No manual configuration needed at all.

5:03 R, GRASS, QGis, Google Earth, Flash plugin + codecs, Apache MySQL, Postgresql all installed.

So I will never worry about a hard disk crash again. Providing I have my personally generated data safe somewhere, all the rest is easy. Perhaps it is not so simple on all laptops, but it is just so encouraging to see that Ubuntu is getting within a hair of the grandma friendly Linux.

I occasionally do have need of Windows XP. So this morning I moved the .virtualbox directory over from my old home directory to the new one, after a quick install of virtual box and adding my usename to the virtualbox group. It worked exactly as it had before. The advantage of virtualising windows is so glaringly obvious I am constantly surprised by my colleagues reluctance to protect themselves against virus attack that way. It is understandable to want to continue using what you are used to (Windows XP). However it is very strange not to want to make sure that you can get back to work quickly after a disaster. Virtualising XP gives the confidence that you can be back up and running in less than an hour. As desktop PCs are more or less generic virtual machines can be backed up and moved freely between them even if an IT department hasn’t done what it should and provided a sensible networked option of virtual machines for Windows XP users.

It is worth being aware that Heron comes with Firefox 3 beta preinstalled, which is fine, as it will soon be the official version. However in the meantime you can install Firefox 2 in order to use  plugins that don’t yet work with the new version. Be aware that  you must  close down Firefox 3 in order to run firefox-2 (type firefox-2 on a command line or set up a launcher).

I also noticed that the Heron repositories has up to date versions of other programs that I didn’t realise had progressed. The most important development for me at the moment was that Postgresql8.3 is now the stable version and that QGis is 0.10.0 instead of 0.9.1. Despite still not getting to version 1.0, QGis  does look as if it has improved greatly in terms of both stability and appearance. This is encouraging after my recent presentations. QGis 0.9 did have a few uncomfortable issues that I didn’t mention. Also Open Office is better. The most notable improvement is when you try to change the language setting. Anyone who knows the frustrating illogicality of being presented with “thesaurus” when you want to check the spelling of a Spanish document will know what I mean. The options are now in much more sensible places.

Despite recent posts, I admit to being a long term Windows user myself. I therefore share many of the characteristics of Windows users. The most important of these is that I am naturally extremely conservative and very reluctant to change a laptop when I have things working the way I am used to. I have been using Ubuntu Feisty since late July 2007 without ever  bothering to upgrade to Gutsy (although I installed it for my son).

However I decided that the release of Heron really deserved my attention. I was becoming increasingly  frustrated with the limited disk space on my duel boot Toshiba Tecra with its original 80 GB HD (40 GB still in an XP partition that I now never use). So today I treated myself to a 250GB external Simpletech ATA hardrive. On getting it home I  invalidated the warranty by opening the case, taking out the drive and swopping it for my 80GB ATA drive. I mention the fact that it is ATA as older (my Toshiba was bought in October 2006) or cheaper laptops are likely to have IDE drives. Always check first and be aware that this simple trick will not work if your machine uses IDE. But if you need a new hard drive, and can afford one, simply switching the drives saves all worries about upgrading. If it goes wrong just put the old drive back in.

In went the Heron CD (I decided not to bother with any native windows install this time) and 15 minutes later all the basics were installed without any tweaking at all. I turned on the advanced visual effects. Ubuntu realised I needed an Nvidia driver and installed it. After rebooting I then had all the  wobbly windows and spinning cubes if might ever want, if I ever feel like using them. A completely painless, risk free upgrade in no time at all. Now all I need to do is copy the parts of my home director I want to keep back over from the external drive and it is all back where it was, with extras. Two hours maximum for the whole process, including putting back R, GRASS, Qgis MYSQL etc. PostGis is just a little bit more difficult in my case due to the fact that I previously used Postgreql 8.1 and it is time for 8.2. But that detail is fairly tecnical.  Contrast the basic experience with a complete re- install of Vista. It would be a nightmare that could last the best part of a  week.

Last night I read this very useful and sympathetic account of the install experience from a novices’ perspective http://www.bspcn.com/2008/04/28/the-great-ubuntu-girlfriend-experiment/

As I had handed out several disks of the Heron after the Ecosur seminar I thought I should be aware of these sort of problems.  I am quite likely to have a few students coming into my office in the next few days asking for help. The girlfriend gotchas really are all very minor. My  experience with the new Heron install was simple to the point of being disappointingly trivial. I missed all the thrills of fixing screen resolution and sound. The only important detail worth mentioning is to make sure that the flash plugin is installed from symantics before going to watch a you tube video. There are then no problems. You simply get a polite message asking for permission to install codecs and there is no need to try to install a gzipped file from adobe. Done.