nandb (version 0.2.1)

ForceChannels: Fix an image that didn't recognise channels while reading

Description

Sometimes, when you open an image in ImageJ, it displays the channels as you would like, but when you read it into R, it has just mashed all the channels (which you would like to be separated somehow) into a stack. In my expreience, it always does so in a way that, say you have a stack of 3 channels and 5 z positions, then the red images would occupy [, , 1], [, , 6] and [, , 11]. This function fixes this kind of confusion. So, in that example it would have a 3d array as input and a 4d as output with dimensions (assuming our images are 256x256 pixels) 256, 256, 3, 5.

Usage

ForceChannels(img.arr, n.ch)

Arguments

img.arr

An array, the read image.

n.ch

The number of channels that you want the read image to have.

Value

An array, channel indices in the third slot, slice indices in the fourth.

Examples

# NOT RUN {
library(magrittr)
x <- lapply(1:300, function(x) matrix(runif(4), nrow = 2)) %>%
  Reduce(function(x, y) abind::abind(x, y, along = 3), .)
str(x)
ForceChannels(x, 6) %>% str

# }