Re: [R-sig-Geo] Help: Individual plots all raster in a raster stack in loop

[Andrew Vitale]

I was about to give up when I looked at your original email again.  Looks
like you just need to wrap it with print():

lapply(1:length(s), function(x){x11(); print(spplot(s[[x]], main =
names(s[[x]])))})

Does anyone on the list know why?


On Tue, Jul 2, 2013 at 1:38 PM, Zia Uddin Ahmed <z...@cornell.edu> wrote:

>  Hi Andrew,****
>
> It works fine with plot function. But like  to use “spplot” function.
> Because like to customize plot following ways to create animated gif plot.
>     ****
>
> However, when  I use spplot function in your code,  I have got plots with
> NULL values. Thanks Zia****
>
> ** **
>
> > lapply(1:nlayers(s), function(x){spplot(s[[x]], main =
> names(s[[x]]));x11()})****
>
> [[1]]****
>
> NULL****
>
> ** **
>
> [[2]]****
>
> NULL****
>
> ** **
>
> [[3]]****
>
> NULL****
>
> ** **
>
> [[4]]****
>
> NULL****
>
> ** **
>
> # ****
>
> bd<-readShapePoly("BD_boundary.shp")****
>
> thana <- list("sp.lines", as(bd, "SpatialLines"), col="grey", lwd=.7,lty=3)
> ****
>
> at.NDVI <- seq(-3, +3, by = 0.5)****
>
> rgb.palette <- colorRampPalette(c("firebrick4","khaki1","green4"))****
>
> ** **
>
> # Plot****
>
> ** **
>
> spplot(s$May_2012, main = "",****
>
>    sp.layout=list(thana),at=at.NDVI,****
>
>    par.settings=list(axis.line=list(col="grey60",lwd=0.5)),****
>
>
> colorkey=list(space="right",width=1.8,at=1:13,labels=list(cex=1.2,at=1:13,
> ****
>
>    labels=c("-3.0","","","-1.5","","", "0.0", "", "", "1.5", "", "",
> "3.0"))),****
>
>    col.regions=rgb.palette(60))****
>
> ** **
>
> # Animated GIF (This function did not work!)****
>
> saveGIF(****
>
> for (i in 1:ns){****
>
>    print(spplot(s[], main = list(label=paste("May_",i),cex=1.5),****
>
>    sp.layout=list(thana), at=at.NDVI,****
>
>    par.settings=list(axis.line=list(col="grey25",lwd=0.5)),****
>
>
> colorkey=list(space="right",width=1.8,at=1:21,labels=list(cex=1.2,at=1:21,
> ****
>
>    labels=c("-3.0","","","-1.5","","", "0.0", "", "", "1.5", "", "",
> "3.0"))),****
>
>    col.regions=rgb.palette(60)))}, ****
>
> height = 500, width = 350, interval = .3, outdir = getwd())****
>
> }****
>
> ** **
>
> *From:* Andrew Vitale [mailto:vitale...@gmail.com]
> *Sent:* Tuesday, July 02, 2013 4:24 PM
>
> *To:* Zia Uddin Ahmed
> *Cc:* r-sig-geo@r-project.org
> *Subject:* Re: [R-sig-Geo] Help: Individual plots all raster in a raster
> stack in loop****
>
> ** **
>
> Zia,****
>
> ** **
>
> I like to use the plot function from the raster package.****
>
> ** **
>
> ?raster:::plot****
>
> ** **
>
> To continue your example, I'm able to plot the individual layers of a
> stack using the lapply() function.  I'm not sure if there is a simpler way
> to do it, but this way works for me:****
>
> ** **
>
> library(raster)****
>
> library(sp)****
>
> library(gstat)****
>
> ** **
>
> fn <- system.file("external/test.grd", package="raster")****
>
> r <- raster(fn)****
>
> r2 <- raster(fn)+runif(ncell(r))****
>
> r3 <- raster(fn)+runif(ncell(r))****
>
> r4 <- raster(fn)+runif(ncell(r))****
>
> s <- stack(r, r2,r3, r4)****
>
> ** **
>
> # Plot all rasters in a raster stack****
>
> ** **
>
> lapply(1:nlayers(s), function(x){plot(s[[x]], main = names(s[[x]]));x11()})
> ****
>
> ** **
>
> ** **
>
> ####And if you want the layers all in one plot, just use****
>
> ** **
>
> plot(s)****
>
> ** **
>
> ** **
>
> ** **
>
> ** **
>
> ** **
>
> ** **
>
> On Tue, Jul 2, 2013 at 10:47 AM, Zia Uddin Ahmed <z...@cornell.edu> wrote:
> ****
>
> I like to plot (individual plot all raster objects in raster stack in a
> loop. Help will be appreciated.
> Thanks
> Zia
>
> library(raster)
> library(sp)
> library(gstat)
> fn <- system.file("external/test.grd", package="raster")
> r <- raster(fn)
> r2 <- raster(fn)+runif(ncell(r))
> r3 <- raster(fn)+runif(ncell(r))
> r4 <- raster(fn)+runif(ncell(r))
> s <- stack(r, r2,r3, r4)
> names(s)
> # [1] "test.1" "test.2" "test.3" "test.4"
>
> # Plot all rasters in a raster stack
> print(spplot(s$test.1))
> print(spplot(s$test.2))
> print(spplot(s$test.3))
> print(spplot(s$test.4))
>
> From: Andrew Vitale [mailto:vitale...@gmail.com]
> Sent: Monday, July 01, 2013 3:13 PM
> To: Zia Uddin Ahmed
> Cc: Roman Luštrik; r-sig-geo@r-project.org
> Subject: Re: [R-sig-Geo] Error creating a standard deviation map from
> raster stack
>
> Did the sample code I sent not run on your system?  That's strange.
>
>
> On my machine:
>
>
> library(raster)
> fn <- system.file("external/test.grd", package="raster")
> r <- raster(fn)
> r2 <- raster(fn)+runif(ncell(r))
> s <- stack(r, r2)
> nlayers(s)
> m<-mean(s)
>
> std<-calc(s, fun = sd)
>
> fun = function(x)
> { sqrt(var(x))
> }
> sd <- calc(s, fun)
>
> par(mfrow=c(1,2));plot(sd,main = 'sd'); plot(std, main = 'std')
>
> identical(sd, std)
> #[1] TRUE
>
> > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] raster_2.1-37 sp_1.0-9
>
> loaded via a namespace (and not attached):
> [1] grid_3.0.1      lattice_0.20-15
>
> On Mon, Jul 1, 2013 at 10:14 AM, Zia Uddin Ahmed <z...@cornell.edu<mailto:
> z...@cornell.edu>> wrote:
> Thanks you so much it works with following code. Zia
>
> fun = function(x)
> { sqrt(var(x))
> }
> sd <- calc(s, fun)
> plot(sd)
>
> From: Andrew Vitale [mailto:vitale...@gmail.com<mailto:vitale...@gmail.com
> >]
> Sent: Monday, July 01, 2013 12:45 PM
> To: Zia Uddin Ahmed
> Cc: Roman Luštrik; r-sig-geo@r-project.org<mailto:r-sig-geo@r-project.org>
>
> Subject: Re: [R-sig-Geo] Error creating a standard deviation map from
> raster stack
>
> Check out ?calc
>
> library(raster)
> fn <- system.file("external/test.grd", package="raster")
> r <- raster(fn)
> r2 <- raster(fn)+runif(ncell(r))
> s <- stack(r, r2)
> nlayers(s)
> m<-mean(s)
> std<-calc(s, fun = sd)
>
>
> On Mon, Jul 1, 2013 at 9:30 AM, Zia Uddin Ahmed <z...@cornell.edu<mailto:
> z...@cornell.edu>> wrote:
> In my case, object “s” is a set of 22 geo-tif files.
> Thanks
> zia
>
> From: romu...@gmail.com<mailto:romu...@gmail.com> [mailto:
> romu...@gmail.com<mailto:romu...@gmail.com>] On Behalf Of Roman Luštrik
> Sent: Monday, July 01, 2013 12:09 PM
> To: Zia Uddin Ahmed
> Cc: r-sig-geo@r-project.org<mailto:r-sig-geo@r-project.org>
> Subject: Re: [R-sig-Geo] Error creating a standard deviation map from
> raster stack
>
> What's the class/structure of object `s`?
>
> Cheers,
> Roman
> On Mon, Jul 1, 2013 at 4:38 PM, Zia Uddin Ahmed <z...@cornell.edu<mailto:
> z...@cornell.edu><mailto:z...@cornell.edu<mailto:z...@cornell.edu>>>
> wrote:
> I am trying to calculate standard deviation map from a raster stack. I
> have got following error . Any  suggestion?
> > std<-sd(s)
> Error in as.double(x) :
>   cannot coerce type 'S4' to vector of type 'double'
>
> Thanks
> Zia
>
> fn <- system.file("external/test.grd", package="raster")
> s <- stack(fn, fn)
> r <- raster(fn)
> s <- stack(r, fn)
> nlayers(s)
> m<-mean(s)
> std<-sd(s)
>
> > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] gstat_1.0-16  rgdal_0.8-10  raster_2.1-37 sp_1.0-9
>
> loaded via a namespace (and not attached):
> [1] grid_3.0.1       intervals_0.14.0 lattice_0.20-15  spacetime_1.0-4
> [5] xts_0.9-3        zoo_1.7-9
> >
>
> -----Original Message-----
> From: r-sig-geo-boun...@r-project.org<mailto:
> r-sig-geo-boun...@r-project.org><mailto:r-sig-geo-boun...@r-project.org
> <mailto:r-sig-geo-boun...@r-project.org>> [mailto:
> r-sig-geo-boun...@r-project.org<mailto:r-sig-geo-boun...@r-project.org
> ><mailto:r-sig-geo-boun...@r-project.org<mailto:
> r-sig-geo-boun...@r-project.org>>] On Behalf Of ASANTOS
> Sent: Sunday, June 23, 2013 4:08 PM
> To: Sarah Goslee; r-sig-geo@r-project.org<mailto:r-sig-geo@r-project.org
> ><mailto:r-sig-geo@r-project.org<mailto:r-sig-geo@r-project.org>>
> Subject: Re: [R-sig-Geo] Problem with NDVI difference with subset image
>
> Hi Dra. Goslee,
>
>              I work in OS linux and I like very much your lssub function,
> despites your notice. I think that the problems are in linux system,
> because:
>
>  > landc<- stack(c("stackIm1.sample.tif","tackIm2.sample.tif"))
> Error in .local(.Object, ...) :
>    `/home/asantos/Documentos/Sensoriamento remoto percevejo
> bronzeador/Contornos/tackIm2.sample.tif' does not exist in the file system,
> and is not recognised as a supported dataset name.
>
> Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",
>  :
>    Cannot create a RasterLayer object from this file. (file does not exist)
>
>
>               When I try to look the geotiff created
> (stackIm1.sample.tif) there are something wrong, because the pictures
> doesn't open (complete example below).
>
> Thanks for your attention,
>
> Alexandre
>
> require(raster)
> require(sp)
> require(rgdal)
> require(landsat)
> #
> #Create raster
> r <- raster(nc=1000, nr=1000)
> set.seed(20130622)
> stackIm1 <- stack(lapply(1, function(x) setValues(r,
> round(runif(ncell(r))* 255))))## Simulation red band
> stackIm2 <- stack(lapply(1, function(x) setValues(r,
> round(runif(ncell(r))* 255))))## Simulation nir
>
> # define projection system
> r.geo <- CRS("+proj=utm +zone=23 +south +datum=WGS84 +units=m +no_defs")
>  # geographical datum WGS84
> proj4string(stackIm1) <- r.geo
> proj4string(stackIm2) <- r.geo
> #
>
> #Create geotiff
> writeRaster(stackIm1, filename="stackIm1.tif",
> format="GTiff",overwrite=TRUE)
> writeRaster(stackIm2, filename="stackIm2.tif",
> format="GTiff",overwrite=TRUE)
> #
>
> #Subset a geotiff image 50 x 50 pixels
> stackIm1.sample<-lssub("stackIm1.tif", "stackIm1.sample.tif", centerx = 0,
> centery = 0, widthx = 50, widthy = 50)
> stackIm2.sample<-lssub("stackIm1.tif", "sstackIm2.sample.tif", centerx =
> 0, centery = 0, widthx = 50, widthy = 50)
> #
> landc<- stack(c("stackIm1.sample.tif","tackIm2.sample.tif"))
>
>
>
>
>
> Em 23/06/2013 12:59, Sarah Goslee escreveu:
> > Hi,
> >
> > What happens?
> >
> > Do you get an error? Where?
> >
> > What is your sessionInfo()?
> >
> > As it says in the lssub() help, this function was written for a
> > particular purpose, is only known to work on linux, and may not be
> > widely applicable.
> >
> > It's a "use at your own risk" kind of function, and you may well be
> > better off using one of the many other methods available for
> > subsetting raster data, which would save you the whole "export as
> > GeoTIFF, subset, reimport" sequence.
> >
> > Sarah
> >
> > On Sun, Jun 23, 2013 at 11:36 AM, Alexandre Santos
> > <alexandresanto...@yahoo.com.br<mailto:alexandresanto...@yahoo.com.br
> ><mailto:alexandresanto...@yahoo.com.br<mailto:
> alexandresanto...@yahoo.com.br>>> wrote:
> >> Dear Members,
> >>
> >>
> >> I'm having trouble calculating NDVI difference, first the images
> Geotiff can not view using Ubuntu 4.12 64-bit and therefore can not get to
> the NDVI, follow an example:
> >>
> >> require(raster)
> >> require(sp)
> >> require(rgdal)
> >> require(landsat)
> >> #
> >> #Create raster
> >> r <- raster(nc=1000, nr=1000)
> >> set.seed(20130622)
> >> stackIm1 <- stack(lapply(1, function(x) setValues(r,
> round(runif(ncell(r))* 255))))## Simulation red band
> >> stackIm2 <- stack(lapply(1, function(x) setValues(r,
> round(runif(ncell(r))* 255))))## Simulation nir
> >>
> >> # define projection system
> >> r.geo <- CRS("+proj=utm +zone=23 +south +datum=WGS84 +units=m
> +no_defs")    # geographical datum WGS84
> >> proj4string(stackIm1) <- r.geo
> >> proj4string(stackIm2) <- r.geo
> >> #
> >>
> >> #Create geotiff
> >> writeRaster(stackIm1, filename="stackIm1.tif",
> format="GTiff",overwrite=TRUE)
> >> writeRaster(stackIm2, filename="stackIm2.tif",
> format="GTiff",overwrite=TRUE)
> >> #
> >>
> >> #Subset a geotiff image 50 x 50 pixels
> >> stackIm1.sample<-lssub("stackIm1.tif", "stackIm1.sample.tif", centerx =
> 0, centery = 0, widthx = 50, widthy = 50)
> >> stackIm2.sample<-lssub("stackIm1.tif", "sstackIm2.sample.tif", centerx
> = 0, centery = 0, widthx = 50, widthy = 50)
> >> #
> >>
> >> #Calculate NDVI difference
> >>
> >> multi.espc<-stack(c("stackIm1.sample.tif","stackIm2.sample.tif"))
> >>
> >> band3<-raster(multi.espc,1)
> >> band4<-raster(multi.espc,2)
> >>
> >> ndvi<-(band4-band3)/(band4+band3)
> >>
> >> #
> >>
> >>
> >>
>
> --
> ======================================================================
> Alexandre dos Santos
> Proteção Florestal
> Coordenador do curso Técnico em Florestas
> Vice Coordenador do curso de Engenharia Florestal
> IFMT - Instituto Federal de Educação, Ciência e Tecnologia de Mato Grosso
> Campus Cáceres
> Caixa Postal 244
> Avenida dos Ramires, s/n
> Bairro: Distrito Industrial
> Cáceres - MT                      CEP: 78.200-000
> Fone: (+55) 65 
> 8132-8112<tel:%28%2B55%29%2065%208132-8112<%28%2B55%29%2065%208132-8112>>
> (TIM)   (+55) 65 
> 9686-6970<tel:%28%2B55%29%2065%209686-6970<%28%2B55%29%2065%209686-6970>>
> (VIVO)
>          alexandre.san...@cas.ifmt.edu.br<mailto:
> alexandre.san...@cas.ifmt.edu.br><mailto:alexandre.san...@cas.ifmt.edu.br
> <mailto:alexandre.san...@cas.ifmt.edu.br>>
>
> _______________________________________________
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>
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>
>
>
> --
> In God we trust, all others bring data.
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
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> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
>
>
> --
> Andrew P. Vitale
> Masters Student
> Department of Geography
> University of Nevada, Reno
> (412) 915-3632<tel:%28412%29%20915-3632 <%28412%29%20915-3632>>
> vitale...@gmail.com<mailto:vitale...@gmail.com>
>
>
>
> --
> Andrew P. Vitale
> Masters Student
> Department of Geography
> University of Nevada, Reno
> (412) 915-3632
> vitale...@gmail.com<mailto:vitale...@gmail.com>
>
>         [[alternative HTML version deleted]]
>
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo****
>
>
>
> ****
>
> ** **
>
> -- ****
>
> *Andrew P. Vitale*****
>
> Masters Student****
>
> Department of Geography****
>
> University of Nevada, Reno****
>
> (412) 915-3632****
>
> vitale...@gmail.com****
>



-- 
*Andrew P. Vitale*
Masters Student
Department of Geography
University of Nevada, Reno
(412) 915-3632
vitale...@gmail.com

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