Open only part of an image (JPEG/TIFF etc.) in R - r

Question

I am analysing very large images in R, in the order of tens of thousands of pixels square. Unfortunately, even with 64 GB RAM, these images sometimes fail to fit into memory, and when they do I can only open one at a time, precluding parallelisation.
My current strategy is to load them using the JPEG or TIFF packages. e.g.:
image <- readJPEG('image.jpg')
However, as I am only performing simple mathematical manipulations (summing, thresholding etc.) that could be performed piece-by-piece, is it possible to only open part of an image at a time by specifying the dimensions to load? If so, I could write a loop to open 1024 x 1024 sized tiles. The JPEG and TIFF packages do not offer an option to do this.

Answer 1

If you are working with very large images, libvips is probably your best bet. You can shell out to it from R using system().
Your question is not very specific, but let's make a 10,000x10,000 pixel TIFF with ImageMagick and it is a black-white gradient:
convert -size 10000x10000 gradient: -depth 8 a.tif
Now threshold that at 50% with vips and check memory required:
vips im_thresh a.tif b.tif 128 --vips-leak
memory: high-water mark 292.21 MB
Pretty frugal, no? By comparison, the equivalent ImageMagick command requires 1.6GB of RAM:
/usr/bin/time -l convert a.tif -threshold 50% b.tif
Sample Output
...
1603895296 maximum resident set size
...
How about adding 64 to every pixel using im_gadd which does:
usage: vips im_gadd a in1 b in2 c out
where:
a is of type "double"
in1 is of type "image"
b is of type "double"
in2 is of type "image"
c is of type "double"
out is of type "image"
calculate a*in1 + b*in2 + c = outfile
So we use:
vips im_gadd 1 a.tif 0 b.tif 64 c.tif --vips-leak
memory: high-water mark 584.41 MB
Need to do some statistics?
vips im_stats c.tif
band minimum maximum sum sum^2 mean deviation
all 64 319 1.915e+10 4.20922e+12 191.5 73.6206
1 64 319 1.915e+10 4.20922e+12 191.5 73.6206

Answer 2

As it turns out, there is an R package - RBioFormats - that allows you to specify part of an image being opened (though it is not available on CRAN). It can be installed from Git as follows:
source("https://bioconductor.org/biocLite.R")
biocLite("aoles/RBioFormats") # You might need to first run `install.packages("devtools")`
library(RBioFormats)
The dimensions of the image can be read from the metadata without having to open the image:
metadata <- read.metadata('image.tiff')
xdim <- metadata#.Data[[1]]$sizeX
ydim <- metadata#.Data[[1]]$sizeY
Suppose that we want to load the top-left 512 x 512 pixels, we use the subset function:
image <- read.image('image.tiff', subset = list(X = 1:512, y = 1:512))
From this it is trivial to write a loop to iteratively process a whole large image. RBioFormats is an R interface into the Java BioFormats library and will open Tiffs, PNGs, JPEGs as well as many proprietary imaging formats.