patojo potoo

Spyder (python IDE) on OSX Snow Leopard and Lion

pete_ — Sat, 24 Mar 2012 17:57:34 +0000

After noticing a theme in the spyder dev email list of difficulties getting spyder running on OSX i have decided to post some lessons learned from (semi* — mind the asterisk) successfully installing it on both snow leopard and lion.

Snow Leopard

* A disclaimer: I did not get matplotlib to work on Snow Leopard. I was able to get spyder running though, it just threw some gripy error messages on startup in the Ipython shell.

Its a bit tricky because you can get off on the wrong foot early in the process if you don’t get python working properly. I hodge-podged it on Snow Leopard and it took a while and lots trial and error. Generally I followed the guidelines for installing python on OSX from python. brilliant.

Once you have the latest (non-mac) version of python blinking stupidly at you when you type:
$ python
you should be off on the right track.

I recommend installing PIP for python package management, it has uninstall going for it, which is nice.

At this stage shift over to following the install instructions for spyder. I used the development version.

The main issue now is getting QT and PyQT working. I found that the best approach was to build QT from source tarball, not the OSX binary package.

Then SIP and PyQT from source as well.

Now install the other spyder dependencies using PIP.

Finally!
$ sudo python setup.py install

in /Users//src/spyderlib

Now, go home (~) and
$ spyder
Should get you off and running.

Lion

On Lion I decided I’d try the enthought method and got the full (academic) EPD 7.2.2 package and installed QT, PyQT, and SIP as in Snow Leopard. Mind you, EPD is a whole-kit-and-kaboodle approach: it bundles python and a BUNCH of packages including numpy and scipy. I was a little wary of this but it actually worked out well and was much quicker than the Snow Leopard saga.

Also installed PIP to make sure I had dependencies for spyder.

Then grabbed the spyder development version and installed as above.

Next time I’ve got to do this im going to just go for the EPD version. Up and running quick is the bottom line.

Compiling PostGIS 2.0 on Mint 12 (ubuntu oneric)

pete_ — Sat, 24 Mar 2012 17:15:49 +0000

Compiling PostGIS 2.0 on a fresh Mint12 install has been a little tricky mostly because of the geos version dependencies (>3.3.2). Initially, I thought I could use the ubuntu gdal package and a source compiled geos. However make check for postgis failed in the raster segment on a bunch of geos calls from gdal. Thus I devised to package the unstable geos (3.3.2) so that aptitude could build gdal against it. I was able to package and install the unstable geos but this didn’t solve the problem as the aptitude version of gdal is fixed to geos 3.2.3.

Sooooo. This was going to be a triumphant post about compiling postgis 2 but it has turned out to be a little less grandiose: How to package up a development version of geos (or any other development version of a package designed to be compiled from source) and install it via the package management system. BORING. Useful to know though. I relied heavily on IntroToDebianPackaging for conceptual guidance, though it uses a different package creation tool.

To create the .deb package I used dpkg-buildpackage but had to create a /debian directory and a few files. dpkg-buildpackage needs a directory called debian:
geos-3.3.2/debian/

First got the geos development package and unpacked using:
$ tar -jxvz geos-3.3.2.tar.bz2

Created a debian directory in it using guidelines from DebianWiki in the new
geos-3.3.2 source directory:
$ mkdir geos-3.3.2/debian

Then grabbed the ubuntu .deb package using:
$ aptitude download geos-3.2.2

Copied DEBIAN/control from the ubuntu package and modified it accordingly. Also copied copyright from the downloaded deb. and added changelog, rules, and compat to geos-3.3.2/debian/ per DebianPackagingWiki.

The key here was to use the same name when running:
# dch --create -v 1.0-1 --package libgeos

As is in the “Package” field in the control file.

After the above command you can cd to the root of the package and run dpkg-buildpackage which will create a .debi file in the parent directory which can be installed using dpkg -i .


Hope it works for ya!!



SilviLaser 2011
pete_ — Thu, 27 Oct 2011 21:36:22 +0000





The Tahune Airwalk  From Silvilaser2011


Just returned from SilviLaser 2011 at the University of Tasmania in Hobart. It is an excellent conference attended by academics and professionals in forestry and remote sensing from around the globe. The conference is unique in my experience as it has a comparatively narrow focus: active remote sensing, mostly laser and some radar, of biophysical forest metrics. It addresses this topic in great depth. There were no concurrent sessions which was refreshing and kept us all on the same page. As a young researcher in the field it was great to see the current work and put faces to the names that I cited in my dissertation and the paper  Sohail Shafii and I presented . Our presentation was in the Emerging Technologies session with several other excellent presentations.
Terrestrial laser scanning (TLS), regional/national inventory applications, and operationaization of LiDAR inventory in a forest management context seemed to be emerging topics that were well represented, along with a few satellite (ICESat/GLAS) studies, and several papers focusing on statistical methods for imputing area-based stand metrics from point distributions. There seems to be a great deal of interest in this at the moment. I have some reservations about it, mostly because I don’t understand RandomForest that well. 
I’ve posted the abstracts, and all the papers. The program is below:
 



Graduated
pete_ — Thu, 08 Sep 2011 23:01:31 +0000
As of June, I have graduated. I’m relieved and grateful for the support of family, friends, and advisors. Bruce Hartsough and Debbie Elliott-Fisk have been indispensable, thanks so much Bruce and Debbie!
I’ve posted my dissertation and will be updating the site with publications, etc. soon.
As of August I have taken a position as a postdoctoral researcher at the UC Davis Institute for Transportation Studies/Energy Institute. 



LibLAS to GRASS r.in.xyz
pete_ — Fri, 04 Mar 2011 21:27:10 +0000
I wrote some python to  pipe las2txt to  GRASS’s r.in.xyz on using subprocess which is what most of the GRASS python scripts use. Its not very sophisticated at all but seems to work decently well however I suspect Howard’s point about it not being much better than the text file approach is true. Its based on the GRASS LIDAR wiki page(GRASS Wiki): Heres an example:
from liblas import file, header
import subprocess as sub
import grass.script as grass

def run(cmd, **kwargs):
    grass.run_command(cmd, quiet = True, **kwargs)

path='../data/las/ucd_01.las'
dbname='ucd_01.las'
h=file.File(path).header
run("g.region", e=h.max[0], w=h.min[0], s=h.min[1], n=h.max[1])
pts=sub.Popen('las2txt -i %s --parse xyz --delimiter "|" --keep-classes 2 --stdout'%path, shell=True, stdout=sub.PIPE)
mkInRast=grass.feed_command("r.in.xyz", input="-", output=dbname, method='mean')
mkInRast.stdin.write(pts.communicate()[0])
mkInRast.stdin.close()
mkInRast.wait()

#this stuff is based on the wiki page for interpolating/filtering the resulting GRASS dataset

run("r.to.vect", flags='z', input=dbname, output=dbname+'_pt', feature='point')
run("v.surf.rst", layer='0', input=dbname+'_pt', elev= dbname+'_rst')
run("g.remove", vect='%s_pt'%dbname)
run("g.remove", rast=dbname)

DEM from LIDAR


Hillshade from LiDAR using GRASS and LibLAS from python