Loop through clip tiff files and export to new folder

Question

I am using Bivand's book to try an figure out how to use R for spatial data but struggling.

I have folder with annual tiff files for the years 1950 through 2010 (name: tas_mean_C_cru_TS31_01_1950, columns 4762, rows 2557, source type continuous, pixel type floating point, pixel depth 32 bit, compression LZW).

I want to clip them with a polygon layer and then put the clipped rasters in a new folder with the same name as the original raster. I have code below that I have tried to manipulate from examples in the book and online, but it does not work. My problem comes at the loop section and I get an error at the end.

My two questions are: 1) What is wrong with my loop statement? I am trying to loop through the files in the folder defined in input.path. 2) If I take a step back and ignore the clipping, how can I get the files to be copied and placed in a new folder with the same name?

Thanks Jen

---

#load libraries
library (sp)
library (rgdal)
library (raster)
library (maps)
library (mapproj)

#SET THE WORKING DIRECTORY PATH
input.path  = "F:/Dropbox/GIS/SNAP/Temp/tas50_09/"
#SET THE OUTPUT DIRECTORY
out.file<-"F:/temp/"
#FIND THE SIZE OF THE MATRIX -- WILL NEED THESE TO PRE-ALLOCATE SUBSEQUENT MATRICES
nrow <- 2557
ncol <- 4762
# initial rasters are....
# xmn=-2173225.11814296,xmx= 1498276.88185705, ymn = 409671.150470569, 
# ymx = 2381118.15047057, crs = '+proj=aea +lat_1=55 +lat_2=65 +lat_0=50 +lon_0=-154 +x_0=0 +y_0=0 +ellps=GRS80 +datum=NAD83 +units=m +no_defs')
# polygon to clip rasters
poly<-readOGR("F:/Dropbox/GIS/AKCommunities","AleutianComm50mile")
#reads the path to the files with a tif extention
file.names <- dir(input.path, pattern =".tif")
# then a loop for reading each existing file of type ".tif" as table
for(j in 1:length(input.path)){
  v <- extract(input.path, poly, weights=TRUE, cellnumbers=TRUE)
#Write the data to a geotiff
out <- raster(v ,xmn=-1446037.8545397,xmx= -686037.854539692, ymn = 356262.979377343, ymx = 607262.979377344, crs = '+proj=aea +lat_1=55 +lat_2=65 +lat_0=50 +lon_0=-154 +x_0=0 +y_0=0 +ellps=GRS80 +datum=NAD83 +units=m +no_defs')
writeRaster(v,filename=paste(out.file,'file.names ',sep=''),format = 'GTiff',options='COMPRESS=LZW',datatype='FLT4S',overwrite=T)
}
# I get the following error
Error in (function (classes, fdef, mtable)  : 
unable to find an inherited method for function ‘extract’ for signature ‘"character", "SpatialPolygonsDataFrame"’

Answer 1

The following edit may help you find problems in your logic.

Consistent naming schemes are a good thing when you need to iterate:

ipath <- "F:/Dropbox/GIS/SNAP/Temp/tas50_09/"
opath <- "F:/temp/"

ppath <- "F:/Dropbox/GIS/AKCommunities"
pname <- "AleutianComm50mile"

Avoid object names which may have namespace clashes, including "poly", "nrow" and "ncol".

ppoly <- readOGR(ppath,pname)

Be apprised, you don't use these values anywhere:

m <- 2557
n <- 4762

Pulling complicated literal values out of your loop improves readability:

p1 <- '+proj=aea +lat_1=55 +lat_2=65 +lat_0=50 +lon_0=-154'
p2 <- '+x_0=0 +y_0=0 +ellps=GRS80 +datum=NAD83 +units=m +no_defs'
projargs <- paste(p1,p2)

## output raster limits
xmn <- -1446037.8545397
xmx <- -686037.854539692
ymn <- 356262.979377343
ymx <- 607262.979377344

Use $ to anchor pattern match end-of-string and avoid unintentional mismatches.

files <- list.files(ipath, pattern='[.]tif$')
stopifnot(length(files)>0)

Now the problem area is much easier to read.

1. Seems questionable whether you need weights and cellnumbers from extract().
2. You may want to use nrow=m and ncol=n arguments in raster(), if v is not a matrix object:

Should be close now, anyway.

for (f in files) {

    ifile <- file.path(ipath,f)
    ofile <- file.path(opath,f)

    v  <- extract(ifile, ppoly, weights=TRUE, cellnumbers=TRUE)

    rv <- raster(v, crs=CRS(projargs), xmn=xmn, xmx=xmx, ymn=ymn, ymx=ymx)

    writeRaster(rv, filename = ofile, format='GTiff',
                options='COMPRESS=LZW', datatype='FLT4S', overwrite=TRUE)
}

Answer 2

I realize this is almost two years old but I figured I can put my solution to whomever comes across this question. I'm ecstatic that I created my first for loop. I, too, had the same error messages. Using the naming convention of @goangit, I created something myself. Just slightly different. The convention is really organized, so I agree with @goangit and suggest this becomes a habit in the future. Its the shortest little thing. Anyway, below is the script for a generic raster clipping loop.

#Set your working directory
setwd("C:/Here_it_is/")
ipath <- "C:/Here_it_is/"   
#I know it repeats the above, but I noticed for me, it needed the wd set
opath <- "C:/Where_its_going/"

#Identify your polygon boundary
ppath <- "C:/GIS/" #directory where the .shp is 
pname <- "boundary" #filename of the actual .shp without the extension.

#Read your polygon boundary
ppoly <- readOGR(ppath,pname) #if this doesn't work theyn maybe you do not have the package loaded? 

#Identify spatial extent
e <- extent(ppoly)

#Projection type and datum, respectively
p1 <- "+proj=UTM"
p2 <- "+datum=WGS84"
projmap <- paste(p1,p2)

#Identify the list of images you wish to perform the loop
files <- list.files(ipath, pattern=".tif$", full.names=FALSE)
stopifnot(length(files)>0)

#add output directory
outfiles <- pasteO(opath, files) #paste0 forgoes any separator between the two vectors "opath" and "files". if you need to add a slash somewhere then you need to change it to the paste function or change your vectors above.

#Change extension
extension(outfiles) <- "tif" #if you want to make it .tif 

for (f in 1:length(files)){
r <- raster(files[f])
rc <- crop(r, e)
rm <- mask(rc, ppoly)
rw <- writeRaster(rm,outfiles[f],overwrite=TRUE)
}

#This should save where you designated the outfiles vector as.