[R-sig-Geo] Needing to speed up a process involving calc() and cover() raster functions

[Benjamin Leutner]

Hi Mathieu,

your question is rather difficult to understand. From the context I 
gather that you are referring to the results of the sam() function from 
RStoolbox.
Further, I assume you want to threshold each layer for a maximum 
spectral angle  and then find the class with the minimum spectral angle 
per pixel, right?

In this case you could do:

out   <- stack(lapply(1:nlayers(classified), function(i) 
clamp(classified[[i]], upper = threshs[[i]], useValues = FALSE)))
class <- which.min(out)

Cheers,
Benjamin

On 22.12.2015 10:57, Mathieu Rajerison wrote:
> Hi,
>
>
> I use RSToolBox to classify a RGB raster.
>
> I have a resulting RasterBrick which has as many layer as end members, in
> my case 3 for different tones of blue.
>
> I reclassify each band with calc to extract the pixels which have a small
> angle mapping value. The threshold used is different depending on the
> endmember layer.
>
> I finally assembly all the bands with the cover function.
>
> I needed to increase the memory limit assigned to R to have it worked. I
> suspect that my code could be optimized, but I don't know in which way.
>
> Here is the part of my code, that I think, could be optilmized, if you want
> to have a look and give some advice :
>
> # RECLASSIFY
> # classified is the classified RasterStack
> # here I change the values of each band to 1 or NA depending on the
> spectral angle mapping value.
> # Is calc() slower than reclassify() for this purpose as I have only one
> threshold value ?
>
> threshs = c(.1,.2,.1)
> for (i in 1:nlayers(classified )) {
>
>      clas = classified[[i]]
>      thresh=threshs[i]
>
>      out[[i]] = calc(clas, function(x) {x[x >= thresh] = NA;
>                                         x[x < thresh] = 1;
>                                         return(x)})
>    }
>
> # COVERING
>    r = out[[1]]
>    for(i in 2:length(out)) {
>      r = cover(out[[i]], r)   ## I cover by iteration
>    }
>
> plot(r) # r is the final combined raster
>
> ================================================================
> My sessionInfo() :
>> sessionInfo()
> R version 3.1.2 (2014-10-31)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252
>   LC_MONETARY=French_France.1252
> [4] LC_NUMERIC=C                   LC_TIME=French_France.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] R.utils_2.1.0        R.oo_1.19.0          R.methodsS3_1.7.0
>   igraph_1.0.1         scatterplot3d_0.3-36
>   [6] gdalUtils_2.0.1.7    spdep_0.5-88         Matrix_1.2-2
> maptools_0.8-34      spgrass6_0.8-8
> [11] XML_3.98-1.3         rgeos_0.3-8          FNN_1.1
>   rgdal_0.9-2          RStoolbox_0.1.1
> [16] raster_2.3-40        sp_1.0-17
>
> loaded via a namespace (and not attached):
>   [1] boot_1.3-13        car_2.0-25         caret_6.0-57       coda_0.18-1
>       codetools_0.2-9    colorspace_1.2-6
>   [7] deldir_0.1-9       digest_0.6.8       doParallel_1.0.8   foreach_1.4.2
>       foreign_0.8-61     geosphere_1.4-3
> [13] ggplot2_1.0.1      grid_3.1.2         gtable_0.1.2
> iterators_1.0.7    lattice_0.20-29    LearnBayes_2.15
> [19] lme4_1.1-10        magrittr_1.5       MASS_7.3-35
>   MatrixModels_0.4-1 mgcv_1.8-3         minqa_1.2.4
> [25] munsell_0.4.2      nlme_3.1-118       nloptr_1.0.4       nnet_7.3-8
>        parallel_3.1.2     pbkrtest_0.4-2
> [31] plyr_1.8.3         proto_0.3-10       quantreg_5.19      Rcpp_0.12.0
>       reshape2_1.4.1     scales_0.2.5
> [37] SparseM_1.7        splines_3.1.2      stats4_3.1.2       stringi_0.5-5
>       stringr_1.0.0      tools_3.1.2
>
> ============================================================
> Best,
>
> Mathieu
>
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>
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-- 
Benjamin Leutner M.Sc.

Department of Remote Sensing
University of Wuerzburg
Campus Hubland Nord 86
97074 Wuerzburg, Germany

Tel: +49-(0)931-31 89594
Fax: +49-(0)931-31 89594-0
Email: benjamin.leutner at uni-wuerzburg.de
Web: http://www.fernerkundung.uni-wuerzburg.de