How to get pixel data from an image using R

Question

Can anyone help me on how to get the RGB pixel data from an image in R?

I need this information to compare differences in bird plumage to aid in the understanding of a speciation event.

My photos are taken by a digital camera and are now as a NEF-file. It doesn't matter which type of file that's needed, I have the possibility to convert the file to whatever I want. However, I would prefer to maintain as much information as possible in the file (i. e. PNG-files are good).

I have tried many packages in R: Pixmap, Raster, ImageMetrics and browsed the internet, tested methods, asked co-students etc. for several weeks trying to solve this problem. Here at Stackoverflow I've tried this: How to extract the pixel data Use R's pixmap package?, with no luck. My files are also too big for the R window (the entire array doesn't show), and I have difficulties understanding the array produced. The best thing for me would be to get the data as a matrix or in another way that makes it easier to understand what is what. I have found loads of similar questions, but in other programs (such as Java, C++, IOS, Matlab, Python etc) which I unfortunately don't know how to use.

My problems might be due to my low skills with this type of work, but I am trying as hard as I can with the background that I have. If anyone can help me or give me som tips, I will be very grateful.

Answer 1

First I generate an example png image :

png("/tmp/test.png")
plot(rnorm(100))
dev.off()

Then I convert it to a format readable by pixmap : here I convert the png to a ppm file as I want to keep colors information. I use ImageMagick from the command line, but you can use whatever program you want :

$ convert /tmp/test.png /tmp/test.ppm

Next, you can read the image with the read.pnm function from the pixmap package :

x <- read.pnm("/tmp/test.ppm")

And then, you can use the x@red, x@blue, x@green slots (or x@grey for a greyscale image) to get the pixels value for each channel as a matrix. You can check that the dimensions of the matrices are the same as the size of your picture :

dim(x@red)
[1] 480 480

Answer 2

Take this tiny sample 3x3 pixel png image:

Then:

library('png')
download.file('http://i.stack.imgur.com/hakvE.png', 'sample.png')
img <- readPNG('sample.png')
pix.top.left <- img[1,1,]     # row 1, column 1
pix.bottom.left <- img[3,1,]  # row 3, column 1
pix.top.right <- img[1,3,]    # row 1, column 3

If you're reading a PNG image with alpha channel (as the sample image above), then each of the pix. variables is a vector with four entries, each entry corresponding to Red ,Green, Blue and Alpha values of the pixel.

> pix.top.left
[1] 1 0 0 1