I'm running into an unusual issue with the cover function in R. We are trying to fill cloudy pixels with values from another layer. I can make it work just fine with stacks as follows -
library(raster)
r1 <- raster(ncols=36, nrows=18)
r1[] <- 1:ncell(r1)
r1b <- r1a <- r1
r1_stack <- stack(r1, r1a, r1b)
r2 <- setValues(r1, runif(ncell(r1)))
r2b <- r2a <- r2
r_stack <- stack(r2, r2a, r2b)
r_stack[r_stack < 0.5] <- NA
r3 <- cover(r_stack, r1_stack)
But then i try to do the same thing with a raster stack and i get the error:
Error in as.character(x) :
cannot coerce type 'closure' to vector of type 'character'
The code:
# get all tifs
LS5_032_032_2008_09_21 <- list.files("LT050340302008090301T1-SC20170526100900/",
pattern = glob2rx("*band*.tif$"), full.names = T)
# stack bands
cloudy_scene <- stack(LS5_032_032_2008_09_21)
# import cloud mask
cloud_mask <- raster('LT050340302008090301T1-SC20170526100900/LT05_L1TP_034030_20080903_20160905_01_T1_sr_cloud_qa.tif')
# mask data
masked_data <- mask(cloudy_scene, mask = cloud_mask, maskvalue=0, inverse=TRUE)
####### get cloud free data
# get files
LS5_2008_09_19 <- list.files("LT050340302008091901T1-SC20170526101124/",
pattern = glob2rx("*band*.tif$"), full.names = T)
# subset and stack cloud free bands
cloud_free_data <- stack(LS5_2008_09_19)
# use cover function to assign NA pixels to corresponding pixels in other scene
cover <- cover(masked_data, cloud_free_data)
TRACEBACK() output:
9: toupper(format)
8: .defaultExtension(format)
7: .getExtension(filename, filetype)
6: .local(x, filename, ...)
5: writeStart(outRaster, filename = filename, format = format, datatype = datatype,
overwrite = overwrite)
4: writeStart(outRaster, filename = filename, format = format, datatype = datatype,
overwrite = overwrite)
3: .local(x, y, ...)
2: cover(masked_data, cloud_free_data)
1: cover(masked_data, cloud_free_data)
UPDATE: I tried to resample the data - still doesn't work
cloud_free_resam <- resample(cloud_free_data, masked_data)
cover <- cover(masked_data, cloud_free_resam)
ERROR:
Error in as.character(x) :
cannot coerce type 'closure' to vector of type 'character'
I also tried to crop both layers - same error
# find intersection boundary
crop_extent <- intersect(extent(cloud_free_data), extent(masked_data))
cloud_free_data <- crop(cloud_free_data, crop_extent)
masked_data <- crop(masked_data, crop_extent)
# use cover function to assign NA pixels to corresponding pixels in other scene
cover <- cover(masked_data, cloud_free_data)
GET THE DATA: (WARNING: 317mb download - unpacks to ~1gb) https://ndownloader.figshare.com/files/8561230
Any ideas what might be causing this error with this particular dataset? I'm sure we're missing something quite basic but...what? Thank you in advance.
Leah
This is a bug. Cover with two multi-layered Raster* objects cannot write to disk. This can be seen in the simple example by setting
rasterOptions(todisk=TRUE)
I have fixed this in version 2-6.1 (forthcoming)