function to convert xrdml to R data frame

This is a specialist thing -- the xrdml format is a common way of storing the results of X-Ray Diffraction scans (we use a Panalytical Aeris).

Probably these could be combined in a later version, with the type of output specified by the function options . You need to bring your own xrdml file(s)!

1. xrdml to data frame

xrdml2df <- function(xfile,
                     xdir = "wd"
                     ) {
  if(xdir == "wd") {
    xdir <- getwd()
    }
  xrdmlRaw <- readLines(paste0(xdir, xfile))
  twothet0 <- grep("2Theta", xrdmlRaw)
  beg0 <- xrdmlRaw[twothet0 + 1]
  beg0 <- gsub("\t\t\t\t\t<startPosition>", "", beg0)
  beg0 <- gsub("</startPosition>", "", beg0)
  beg0 <- as.numeric(beg0)
  end0 <- xrdmlRaw[twothet0 + 2]
  end0 <- gsub("\t\t\t\t\t<endPosition>", "", end0)
  end0 <- gsub("</endPosition>", "", end0)
  end0 <- as.numeric(end0)
  c0 <- grep("<counts", xrdmlRaw)
  xrdmlRaw[c0] <- gsub('\t\t\t\t<counts unit="counts">', "", xrdmlRaw[c0])
  xrdmlRaw[c0] <- gsub("</counts>", "", xrdmlRaw[c0])
  counts <- as.numeric(unlist(strsplit(xrdmlRaw[c0], " ")))
  counts2theta <-
    data.frame(Angle = seq(beg0, end0, ((end0 - beg0) / (length(counts) - 1))),
    Counts = counts)
  rm(list = c("xrdmlRaw","twothet0","beg0","end0","c0","counts"))
  return(counts2theta)
}

2. xrdml to csv

xrdml2csv <- function(xfile,
                     xdir = "wd",
                     toscreen = FALSE
                     ) {
  if(xdir == "wd") {
    xdir <- getwd()
    }
  xrdmlRaw <- readLines(paste0(xdir, xfile))
  twothet0 <- grep("2Theta", xrdmlRaw)
  beg0 <- xrdmlRaw[twothet0 + 1]
  beg0 <- gsub("\t\t\t\t\t<startPosition>", "", beg0)
  beg0 <- gsub("</startPosition>", "", beg0)
  beg0 <- as.numeric(beg0)
  end0 <- xrdmlRaw[twothet0 + 2]
  end0 <- gsub("\t\t\t\t\t<endPosition>", "", end0)
  end0 <- gsub("</endPosition>", "", end0)
  end0 <- as.numeric(end0)
  c0 <- grep("<counts", xrdmlRaw)
  xrdmlRaw[c0] <- gsub('\t\t\t\t<counts unit="counts">', "", xrdmlRaw[c0])
  xrdmlRaw[c0] <- gsub("</counts>", "", xrdmlRaw[c0])
  counts <- as.numeric(unlist(strsplit(xrdmlRaw[c0], " ")))
  counts2theta <-
    data.frame(Angle = seq(beg0, end0, ((end0 - beg0) / (length(counts) - 1))),
    Counts = counts)
  cfile <- paste0(substr(xfile,1,str_locate(xfile,".xrdml")[1]),"csv")
  write.csv(counts2theta, file = cfile, row.names = FALSE)
  rm(list = c("xrdmlRaw","twothet0","beg0","end0","c0","counts"))
  if(toscreen==TRUE) return(counts2theta)
}