Applying a System Call for ImageJ over a List in R

Question

I am working with a large number of image files within several subdirectories of one parent folder.

I am attempting to run an ImageJ macro to batch-process the images (specifically, I am trying to stitch together a series of images taken on the microscope into single images). Unfortunately, I don't think I can't run this as an ImageJ Macro because the images were taken with varying grid sizes, ie some are 2x3, some are 3x3, some are 3x2, etc.

I've written an R script that is able to evaluate the image folders and determine the grid size, now I am trying to feed that information to my ImageJ macro to batch process the folder.

The issue I am running into seems like it should be easy to solve, but I haven't had any luck figuring it out: in R, I have a data.frame that I need to pass to the system command line-by-line with the columns concatenated into a single character string delimited by *'s.

Here's an example from the data.frame I have in R:

                       X xcoord ycoord input
1 4_10249_XY01_Fused_CH2      2      3 /XY01
2 4_10249_XY02_Fused_CH2      2      2 /XY02
3 4_10249_XY03_Fused_CH2      3      3 /XY03
4 4_10249_XY04_Fused_CH2      2      2 /XY04
5 4_10249_XY05_Fused_CH2      2      2 /XY05
6 4_10249_XY06_Fused_CH2      2      3 /XY06

Here's what each row needs to be transformed into so that ImageJ can understand it:

4_10249_XY01_Fused_CH2*2*3*/XY01
4_10249_XY02_Fused_CH2*2*2*/XY02
4_10249_XY03_Fused_CH2*3*3*/XY03
4_10249_XY04_Fused_CH2*2*2*/XY04
4_10249_XY05_Fused_CH2*2*2*/XY05
4_10249_XY06_Fused_CH2*2*3*/XY06

I tried achieving this with a for loop inside of a function that I thought would pass each row into the system command, but the macro only runs for the first line, none of the others.

macro <- function(i) {
  for (row in 1:nrow(i)) {
    df<-paste(i$X, i$xcoord, i$ycoord, i$input, sep='*')
  }
  system2('/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx', args=c('-batch "/Users/All Stitched CH2.ijm"', df))
}
macro(table)

I think this is because the for loop is not maintaining the list-form of the data.frame. How do I concatenate the table by row and maintain the list-structure? I don't know if I'm asking the right question, but hopefully I'm close enough that someone here understands what I'm trying to do.

I appreciate any help or tips you can provide!

Answer 1

Turns out taking a break helps a lot!

I came back to this after lunch and came up with an easy solution (duh!)- I thought I would post it in case anyone comes along later with a similar issue.

I used stringr to combine my datatable by columns, then put them back into list form using as.list. Finally, for feeding the list into my macro, I edited the macro to only contain the system command and then used lapply to apply the macro to my list of inputs. Here is what my code looks like in the end:

library(stringr)
tablecombined<- str_c(table$X, table$xcoord, table$ycoord, table$input, sep = "*")


listylist<-as.list(tablecombined)


macro <- function(i) {
  system2('/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx', args=c('-batch "/Users/All Stitched CH2.ijm"', i))
}

runme<- lapply(listylist, macro)

Note: I am using the system2 command because it can take arguments, which is necessary for me to be able to feed it a series of images to iterate over. I started with the solution posted here: How can I call/execute an imageJ macro with R? but needed additional flexibility for my specific situation. Hopefully someone may find this useful in the future when running ImageJ Macros from R!