r raster cover function - error with landsat stacks

Question

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

Answer 1

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)