[R-sig-Geo] Lidar data classification

[Tomislav Hengl]

Op 17-3-2011 11:38, Ervan Rutishauser schreef:
> Dear all,
>
> I would like to perform a classification of a large lidar data points
> acquired over a tropical forest plot network (500 km2).
> I computed the mean canopy(tree) height by 5m x 5m cell (pixel) and 3 others
> parameters (max height, height variation over 2 years, mean height in a 50m
> x 50 m neighborhood)
> I did most of this using the raster package.
> Now, I have a kind of multispectral image with 4 layers and I would like to
> perform a large-scale classification of the data based on these 4
> parameters. My aim is to find out "homogeneous" canopy regions, for
> instance: high canopy with low change over the 2 years, canopy gaps, areas
> of recruitment, etc.
>
> I tried to perfom a standard cluster analysis (hclust), but I could not
> compute the dissimilarity matrix (dist) on such a big data set (80'000 rows
> and 4 variables), even with a 64-bits PC.
> The k-means (kmeans{}) classification works, but return me strange results
> (4 main clusters north/south/east/west). I have seen that the biOps package
> allowed to do isodata classification. However isodata{} required an image
> and I don't know how to compute a 4-layer image (if possible).
>
> Does anyone have any suggestion? Shall I turn me to GIS software?
> I am trying to do it with SAGA at the moment, but find it difficult too :)

Are you referring to 
[http://www.saga-gis.org/saga_modules_doc/grid_discretisation/index.html]? 
Which problems did you experience exactly?

I have been processing large grids using SAGA for years now. I am not a 
computer scientists, but if I test the same operation in SAGA and R, I 
usually discover that (a) SAGA is faster, (b) there are usually much 
less problems with memory consumption etc (see e.g. sec 5.5.2 in 
[http://spatial-analyst.net/book/]).

SAGA has a fairly simply module development system 
[http://www.saga-gis.org/saga_modules_doc/lectures_introduction/index.html] 
and there is also an API functionality 
[http://www.saga-gis.org/saga_api_doc/html/] so you can access SAGA 
grids and libraries from python. As far as I know, linking of R and SAGA 
also goes pretty smooth.

The drawback

T. Hengl
http://www.wewur.wur.nl/popups/vcard.aspx?id=HENGL001

>
> Thank you for any help. Best regards,
> Ervan