Pierre Roudier wrote:
I was wondering if it could be a solution to use RSAGA or spgrass6 to
do that. Feedback, anyone ?
PostGIS uses a spatial index; if you provide it with a bounding box, it
should be able to select features (points/lines/polygons) within it. I
don't know how this relates to grids, and haven't tried to exploit
this. rgdal with postgis support seems to be hard to get to work on
windows; another interface could be RODBC.
Cheers,
Pierre
2010/1/29 Edzer Pebesma <edzer.pebe...@uni-muenster.de>:
Pierre Roudier wrote:
Dear list,
I am processing gridded data like DEMs, imported in R from geotiff
files. Of course, such data is regularly gridded, but very often with
NA values. In the framwork of some tests, I have to generate a
neighbourhood of the DEM, so that to extract local extrema of the
layer. For this task, I wrote a function based on the knearneig()
function from the spdep package, with k=4 or k=8, to generate and
analyse the neighbourhood of each point.
Unfortunately, I often have to process big datasets (let's say grids
with between 50,000 and 350,000 points), and that's working but
knearneigh() takes *hours* to process.
Does anybody would have any suggestion to improve the efficiency of this
step ?
the algorithm (knn.c file in the spdep sources) seems to compute all
distances between all grid cells, and for each grid cell find the nearest k
by some kind of insertion sort. That makes it general for all kinds of
spatial data points, including irregularly spread ones, but makes it also
inefficient (because O(n^2) with n the number of grid cells) for large data
sets.
Suggestions to improve this would be to use an index structure (for the
generic case of possibly irregularly spread data) such as the PR-bucket
quadtree used in package gstat (nsearch.c), or specifically for gridded data
to write a special knearneigh() that exploits the grid indexing already
present: you can explicitly address the nearest 4/8/12/... neighbours by
using row/col indexes. In this latter case you'd probably want to rewrite
the test function for the full grid, instead of looping over the cells.
Thanks,
Pierre
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--
Edzer Pebesma
Institute for Geoinformatics (ifgi), University of Münster Weseler Straße
253, 48151 Münster, Germany. Phone: +49 251 8333081, Fax: +49 251 8339763
http://ifgi.uni-muenster.de http://www.52north.org/geostatistics
e.pebe...@wwu.de
--
Edzer Pebesma
Institute for Geoinformatics (ifgi), University of Münster
Weseler Straße 253, 48151 Münster, Germany. Phone: +49 251
8333081, Fax: +49 251 8339763 http://ifgi.uni-muenster.de
http://www.52north.org/geostatistics e.pebe...@wwu.de
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