GLCM function for RasterStack using FOR loop in R

Question

I would like to calculate glcm function in R for all (52) bands in my RasterStack. Using this code:

LS<-stack(img1,img2,img3,img4,img5,img6,img7,img8,img9,img10,img11,img12,img13)
names(LS) <- paste0("B", c(1:52))
band<-brick()
for (i in 1:52){ 
 band[i]<-glcm(LS$B1,window = c(3, 3),na_opt = 'center')
 }

I get 1 layer RasterBrick with NA values and an error message: 1: In x@data@values[i] <- value : number of items to replace is not a multiple of replacement length

Do you know how to get the result for all the bands in my RasterStack?

• JPD: Does the loop successfully run through all 52 iterations? Or does it exit on a certain value of i?
• roubalma: It goes through all the iterations but I got this message for 52 times: 1: In x@data@values[i] <- value : number of items to replace is not a multiple of replacement length
• JPD: Ok, have you tried running glcm on img1 before stacking it with anything else? If so, do you get the same error message?
• roubalma: Yes, I tried to do that and it worked for one selected band. It works for one band using RasterStack as well with this code: glcm(LS$B1,window = c(3, 3),na_opt = 'center')
• JPD: Does it make a difference if band is a stack instead of a brick?

Answer 1

The glcm function outputs a stack, with each band containing values for each of the statistics calculated. By default, all available statistics are computed.

You won't be able to put this stack into a single band within the brick as you are trying with band[i]<-. This is probably what is giving you the error message.

One solution would be to output each stack to a list and then look at stacking them together once the loop has completed.

Something like this should work:

out <- list()
for(i in 1:dim(LS)[3]) {
 out[i] <- glcm::glcm(LS[[i]], window = c(3, 3), na_opt = 'center')
}

• roubalma: Thank you, I tried to use list instead of brick usign this code LS<-stack(img1,img2,img3,img4,img5,img6,img7,img8,img9,img10,img11,img12,img13) names(LS) <- paste0("B", c(1:52)) band<-list() for (i in 1:52){ band[i]<-glcm(LS$B1,window = c(3, 3),na_opt = 'center') } and it went through 52 iterations but they were all calculated for the band B1. And I also get this warning implicit list embedding of S4 objects is deprecated
• JPD: I'm not sure how to deal with the deprecated warning, but I have added suggested code to my answer to ensure the list contains the unique stacks.
• roubalma: Thank you very much for your help! The code you suggested works. It helped me a lot.
• JPD: @roubalma Happy to help. Please mark the answer with the green tick if you feel it has helped with your issue.