nandb (version 0.2.1)

WriteImageTxt: Read/write an image array to/from disk as text file(s).

Description

If (as with brightness) you wish for the pixel values in an image to be represented by real numbers that aren't necessarily integers, the tiff format won't work. As a workaround we represent images (arrays) as comma-separated value (csv) files on disk, where for image stacks (3-dimensional arrays), we write one file for each slice, numbering it with the slice number.

Usage

WriteImageTxt(img.arr, file.name)
ReadImageTxt(file.name)

Arguments

img.arr

An image, represented by a 2- or 3-dimensional array.

file.name

The name of the input/output output file(s), without a file extension.

Details

The image slices are transposed prior to being written to disk to ensure that displaying an image with EBImage::display() in R will yield the same result (as opposed to a transposed image) as displaying the written text file in ImageJ (i.e. I've made a modification to ensure the files display correctly in ImageJ). These functions do not work for 4-dimensional arrays (e.g. a z stack with several channels).

Examples

# NOT RUN {
setwd(tempdir())
img <- ReadImageData(system.file('extdata', '50.tif', package = 'nandb'))
WriteImageTxt(img, 'temp')

img <- ReadImageTxt('temp_01.csv')
file.remove(list.files())  # cleanup
# }