# Ken Kompass. Provided AS IS with absolutely no warranty expressed or implied.
#
# This is an R program for randomizing files. Copy all of your image files from one experiment into a folder
# named "RandomizeFiles". Files can have any name EXCEPT a simple numeric name like "1", "2", "10", etc.

# The program will rename your files randomly as "1", "2", "3", etc., and provide you with a text file
# containing the code, which you can use to unblind your files after quantification.
# R can be downloaded for free: https://www.r-project.org/

# After downloading this program and R onto your computer, do the following steps to randomize your files:
# launch terminal (eg applications/utilities)
# type in:  R --vanilla
# type in: source('InsertPathForWhereProgramIsLocatedHere/randomize.filenames.r')
# eg for TIF files, type in: rename.files.randomly('InsertPathForWhereFolderContainingFilesIsLocatedHere/RandomizeFiles/', '.tif')
# eg for JPG files, type in: rename.files.randomly('InsertPathForWhereFolderContainingFilesIsLocatedHere/RandomizeFiles/', '.jpg')
# type in: q()



# created 9.11.12(?)
# modified 10.28.12, 
rename.files.randomly <- function(wdir=NA, file.ext=NA)
                                  # specify directory with files to randomize
                                           # specify the extension (only one permitted) for the files
{
  if( is.na(wdir) | is.na(file.ext) ) { stop("Missing parameter(s)") }

  all.files <- list.files(wdir, pattern=paste(file.ext, "$", sep=""))

  af.df <- data.frame(all.files, stringsAsFactors=FALSE)
  file.ext <- gsub("^.", "", file.ext)   # for consistency (replaced in next line)
  af.df["new.ID"] <- paste( sample(1:nrow(af.df), replace=FALSE), file.ext, sep="." )  # use 'sample' w/o replace to shuffle

  write.table(af.df, file=paste(wdir, "/", unlist(strsplit(wdir, "/"))[length(unlist(strsplit(wdir, "/")))], "_key.txt", sep=""), row.names=FALSE)

  for(i in 1:nrow(af.df))
  {
    file.rename(from=paste(wdir, "/", af.df$all.files[i], sep=""), to=paste(wdir, "/", af.df$new.ID[i], sep=""))
  }
}