I have a very specific script I am trying to make which computes image flatfields. Basically, I am computing a Master Dark Frame (MD) by averaging a set of Dark Photos.

I have a set of light photos as well. I want to take the averaged dark photo and subtract that average from each light photo within a directory. After this, a Master Flat (MF) is made by averaging all the light photos which had been subject to dark frame subtractions.

Here is my script so far:

##Takes all dark frame images from within working directory and stacks them   into a single object 
darkrastdat<- list.files()
darkstack<- stack(darkrastdat)
##computes the mean of all dark layers/pixels within the object, omits no- data values 
masterdark <- mean(darkstack, na.rm=TRUE)

##loads each light frame into an object 
lightrastdat<- list.files()

##subtracts master dark from each light frame 

##stacks and averages light frames 

##writes master flat as 16-bit into original working directory
writeRaster(mrast, filename= "MF.tif", datatype='INT2U', overwrite=TRUE)

I am able to get an master dark frame (MD) from within a directory of photos. I am having trouble coming up with a way to subtract that MD from each light frame individually.

Can anyone give me some advice?

  • Are you just trying to subtract one raster from another? r3 = r2 - r1 works if r1 etc are raster objects. – Spacedman Feb 26 '17 at 21:33
  • Hey Spacedman - I want to do just that - but I'd like to subract one raster from 20 files in a directory. i.e the Raster1 - MasterFlat1, Raster2-MasterFlat1, Raster3-MasterFlat1, Raster4-MasterFlat1, etc. – Alexander Feb 27 '17 at 19:42
  • Do you know how to write loops in R? Loop over the raster files, read each one in, subtract your masterflat, save it (or whatever). – Spacedman Feb 27 '17 at 20:42
  • That's exactly what I am having issues with actually - is writing the loop for it. I haven't had much experience with loops for loading files in within a directory and assigning each a unique object.... quite tricky! haha – Alexander Feb 27 '17 at 23:31
  • something like allrasters = lapply(list.files(), function(f){raster(f)}) or a for loop... – Spacedman Feb 27 '17 at 23:44

You seem to want to do something like this:

lightrastdat<- list.files()
corrected_rasters = lapply(
     r = raster(file)
     return(r - masterdark)

# this is how you do mean(r[[1]], r[[2]], r[[3]],... etc) when you don't 
# know how many rasters are in your list:

corrected_mean = do.call(mean, corrected_rasters)

Then save corrected_mean as a raster file.

The lapply gets the file names and for each one applies a function that reads in a raster from that file and subtracts the correction. The end result of lapply here is a list of raster objects.

To compute the mean of a list of objects, you need to use do.call, which applies a function as if the second argument to do.call was in the arguments. This lets you do foo(a[[1]],a[[2]],a[[3]],...) up to however many things are in a.

  • Thanks Spacedman- looks like this does just what I was wanting to do. And looks like I learned a thing or two about the lapply function and do.call - which are definitely extremely valuable. I should be able to adapt these into some other variations of scripts I have in mind. Thanks so much! – Alexander Mar 2 '17 at 3:07

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