[R-sig-Geo] How to reduce the buffering time with the function "buffer" (package raster)

Mon May 9 19:36:52 CEST 2016

I have tried the following code to compute distances from raster pixels of 5 via the function "gdal_proximity":

    pypath <- Sys.which("C:\\OSGeo4W64\\bin\\gdal_proximity")
    owd <- getwd()
    on.exit(setwd(owd))
    setwd(dirname(pypath))
    rastpath <- "H:\\Project\\grassland.tif"
    outpath <- "H:\\Project\\distance.shp"
    maxDist <- 50
    system2("C:\\OSGeo4W64\\OSGeo4W.bat", args=c(pypath,rastpath,outpath,maxDist))

But I obtain the error message:

    gdal_proximity.py srcfile dstfile [-srcband n] [-dstband n]
                      [-of format] [-co name=value]*
                      [-ot Byte/Int16/Int32/Float32/etc]
                      [-values n,n,n] [-distunits PIXEL/GEO]
                      [-maxdist n] [-nodata n] [-fixed-buf-val n] [-q]
    Warning message:
    running command '"C:\OSGeo4W64\OSGeo4W.bat" C:\OSGEO4~1\bin\GDAL_P~2.BAT H:\Project\grassland.tif H:\Project\distance.shp 50' had status 1

Here are some details about the raster "grassland.tif"

    > grassland
    class       : RasterLayer
    dimensions  : 9887, 30532, 301869884  (nrow, ncol, ncell)
    resolution  : 10, 10  (x, y)
    extent      : -515893.7, -210573.7, 110739.6, 209609.6  (xmin, xmax, ymin, ymax)
    coord. ref. : +proj=lcc +lat_1=46 +lat_2=60 +lat_0=44 +lon_0=-68.5 +x_0=0 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs
    values      : 5, 5  (min, max)

Thanks a lot for your time.
Have a nice day
Nell

________________________________
De : Nelly Reduan
Envoyé : vendredi 6 mai 2016 12:00:36
À : Forrest Stevens; Michael Sumner; r-sig-geo at r-project.org
Objet : RE: [R-sig-Geo] How to reduce the buffering time with the function "buffer" (package raster)

Thank you very much Forrest for your answer. How can I call the function "gdal_proximity" in R via system() ?

Thanks a lot for your time.

Nell

________________________________
De : Forrest Stevens <r-sig-geo at forreststevens.com>
Envoyé : mercredi 13 avril 2016 22:37:01
À : Nelly Reduan; Michael Sumner; Forrest Stevens; r-sig-geo at r-project.org
Objet : Re: [R-sig-Geo] How to reduce the buffering time with the function "buffer" (package raster)

So you're correct, the buffer() and distance() functions you're using will take a long period of time.  The code below illustrates the shortcut that I've used in the past when buffering only by the limit of one pixel, since it uses queens-case connectance and distance between cell-centers based on that connectance rule. This uses the gridDistance() function which is much faster than calculating straight line distances. You can see that the distance-based calculation takes under 40 seconds. But do notice that the buffer it creates by setting the threshold is around both classes and is indiscriminate of the nearest class:

library(raster)

clip_buff <- raster("clip_study_area_2010.tif")

system.time(d <- gridDistance(clip_buff, c(2,3)))
#   user  system elapsed
#  37.36   11.00   48.41

rf[(rf != 2 & rf != 3)] <- NA

## Set buffer to 10m just for fun and assign
## value of 4 to that buffered region:
rf[ d > 0 & d <= 10 ] <- 4
plot(rf)

If you want to buffer by more than one pixel dimension then you'll probably want straight line distances and I'd suggest using GDAL and using the gdal_proximity utility via a system() call. Alternatively, you could look into other utilities that have better-optimized raster-based distance tools. Hopefully this gives you some ideas on how to proceed?

Sincerely,
Forrest

On Wed, Apr 13, 2016 at 9:18 PM Nelly Reduan <nell.redu at hotmail.fr<mailto:nell.redu at hotmail.fr>> wrote:

I put a cropped raster with 3581676 cells in the link below:

https://www.dropbox.com/sh/ewaz4yncdqt7kxj/AAAEHyuWyHzBE7gSINA1oayTa?dl=0

Here is my code to built the buffers:

rf <- clip_buff

rf [(rf != 2 & rf != 3)] <- NA

plot(rf)

system.time(corr <- buffer(rf, 10))

system.time(dist_rf <- distance(rf))

I stopped the code with the functions "buffer" and "distance" after two hours.

Thanks a lot for your time.

Have a nice day.

Nell

________________________________
De : Michael Sumner <mdsumner at gmail.com<mailto:mdsumner at gmail.com>>
Envoyé : mardi 12 avril 2016 20:36

À : Nelly Reduan; Forrest Stevens; r-sig-geo at r-project.org<mailto:r-sig-geo at r-project.org>
Objet : Re: [R-sig-Geo] How to reduce the buffering time with the function "buffer" (package raster)

I think we still haven't seen a print of the raster object?

It may be a tiled file on disk? Try readAll to pull into memory, if it is tiled and read in on demand via gdal tools like extract will be very slow since access is done line by line.

But just guessing, please give full details and ideally a reproducible example.

Cheers, Mije

On Wed, 13 Apr 2016, 02:33 Nelly Reduan <nell.redu at hotmail.fr<mailto:nell.redu at hotmail.fr>> wrote:
Yes, I tested the functions "distance" and "buffer" by using a cropped raster with around 5 million cells. But my original raster has 48096864 cells. Ideally, I would like to build the buffers from my original raster. Here are some characteristics of the original raster:

class       : RasterLayer

dimensions  : 4876, 9864, 48096864  (nrow, ncol, ncell)

extent      : 188384.5, 484304.5, 4914481, 5060761  (xmin, xmax, ymin, ymax)

coord. ref. : +proj=tmerc +lat_0=0 +lon_0=-73.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs

Thanks a lot for your help.

Have a nice day.

Nell

________________________________
De : Forrest Stevens <r-sig-geo at forreststevens.com<mailto:r-sig-geo at forreststevens.com>>
Envoyé : lundi 11 avril 2016 18:55
À : Nelly Reduan; Forrest Stevens; r-sig-geo at r-project.org<mailto:r-sig-geo at r-project.org>
Objet : Re: [R-sig-Geo] How to reduce the buffering time with the function "buffer" (package raster)

And this is for a raster with around 5 milliion cells? Your results surprise me a bit, especially if the bottleneck is at the call to buffer()/distance().  Your best bet is to wait for a response from Robert Hijmans or someone else working on the package, they might have some other tricks up their sleeves. In any case, I agree, 5+ hours is extremely excessive.

Sincerely,
Forrest

On Mon, Apr 11, 2016 at 6:57 PM Nelly Reduan <nell.redu at hotmail.fr<mailto:nell.redu at hotmail.fr><mailto:nell.redu at hotmail.fr<mailto:nell.redu at hotmail.fr>>> wrote:

Thank you very much Forrest for your answer. I don't think I have memory problems (my computer has a 32 GB memory).

Here is my code to draw the 100-m buffers with the function "buffer" (package raster):

r1 <- r ## r is the original raster and has a resolution of 10m
r1[(r1[]!=2 & r1[]!=5)]=NA
plot(r1)
r2 <- buffer(r1, 10)

I also tested the function distance (package raster):

r1 <- r ## r is the original raster and has a resolution of 10m
r1[(r1[]!=2 & r1[]!=5)]=NA
plot(r1)
r3 <- distance(r1)

In the two cases, I stopped the functions afer 5 hours as this was too long ! For the moment, I haven't find solutions.

Thanks a lot for your time.

Have a nice day.

Nell

________________________________
De : Forrest Stevens <r-sig-geo at forreststevens.com<mailto:r-sig-geo at forreststevens.com><mailto:r-sig-geo at forreststevens.com<mailto:r-sig-geo at forreststevens.com>>>
Envoyé : lundi 11 avril 2016 09:09
À : Nelly Reduan; r-sig-geo at r-project.org<mailto:r-sig-geo at r-project.org><mailto:r-sig-geo at r-project.org<mailto:r-sig-geo at r-project.org>>
Objet : Re: [R-sig-Geo] How to reduce the buffering time with the function "buffer" (package raster)

Five million cells isn't all that many, how slow is too slow? Buffering a raster of about 10 million cells on my laptop takes on the order of 20 seconds or so for a binary raster. Is it possible that you're fighting memory problems?

In the past when doing multiple ring buffers I've found it faster to calculate a distance-to raster first, and then apply multiple logical comparisons on the distance raster.  I don't know if this applies to your situation or not but it's one trick that might help.

Sincerely,
Forrest

On Mon, Apr 11, 2016 at 10:58 AM Nelly Reduan <nell.redu at hotmail.fr<mailto:nell.redu at hotmail.fr><mailto:nell.redu at hotmail.fr<mailto:nell.redu at hotmail.fr>>> wrote:

Hello,

I would like to build 100-m buffers (representing ecological corridors) around land cover attributes in a raster layer and to assign a given value (i.e., value of 13) to buffer cells.

To do this, I'm using the function "buffer" (package raster) to draw the buffers around particular raster cells (i.e., cell values of 2 and 5). For example, in the image below, the buffers are represented in blue (cell values of 13) and the particular raster cells are represented in yellow (cell values of 2).

The problem is that the time to run the function "buffer" is very low because I have a raster of 5000000 cells. Does anyone know how I can reduce the buffering time ?

Thanks a lot for your time.

Have a nice day.

Nell

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