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I am using a combine command in EBImage in R. My images files are upto 100 images I have also set expression with following command

options(expressions=500000)

While I use combine function from EBImage package with following code

combine(Images_0)

I get a error command as Error: C stack usage 15925536 is too close to the limit

What am I doing wrong?

Vikram R S
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1 Answers1

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This assumes the Bioconductor package EBImage is available.

This many not exactly answer your question but I hope it is helpful. I am not certain of where the code is having problems but I find that combine() can be very inefficient. There may be a do.call() call buried in the call to combine, which can consume significant memory.

I find that abind() of the abind package is often a very effective solution. Without knowing more about the images you are trying to combine (it does help to provide minimal reproducible examples), let me suggest the following possibility.

# load library and read example color image
  library(EBImage)
  img <- readImage(system.file("images", "sample-color.png", package="EBImage"))
  dim(img)
> [1] 768 512   3

# create a list of 48 images differing in lightness
  images <- lapply(runif(48, 0.4, 1/0.4), function(x) img/x)

This is a reasonably sized list of color images. You can view the first image with print(img). The last command created 48 copies of the image that vary in lightness.

Now compare the time required to combine the images in that list with combine() versus abind(). Incidentally, abind() has been slightly modified by EBImage to handle dimnames differently. 

# First with combine()
  system.time(x <- combine(images)) # rather fast AMD Ryzen 12-Core CPU 
>  user  system elapsed 
> 12.21    3.68   15.90

# Now with abind() where along = 4 adds a fourth dimension needed for the combination 
  system.time(y <- abind(images, along = 4)) # but much faster here
>  user  system elapsed 
>  0.53    0.02    0.55 

# The combined images are the same
    identical(x, y)
> [1] TRUE

The timing would likely vary with machines and the need for disk access but it seems like a pretty big difference to me. With many images, abind is really helpful. You can examine the combination with print(y, nx = 8, all = TRUE).

By the way, I would be curious to know if this fixed the "stack usage error."

David O
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