R/ocp2df.R

In chepec/ec-chi: Collection of scripts for reading data from CHI760 potentiostat/ galvanostat

#' Read time vs potential data from CHI760
#'
#' Reads time vs potential data from CHI760
#'
#' @param datafilename string with full path to experimental file
#'#'
#' @return Dataframe with the following columns (and no extra attributes):
#'    $ sampleid        : chr
#'    $ time            : num
#'    $ potential       : num
#'    $ RunTime         : num
#' @export
ocp2df <- function(datafilename) {
   datafile <- file(datafilename, "r")
   chifile <- readLines(datafile, n = -1) #read all lines of input file
   close(datafile)
   #
   sampleid <- common::ProvideSampleId(datafilename)
   #
   rgxp.number <- "^\\-?\\d\\.\\d+[e,]"
   # regexp that matches a decimal number at the beginning of the line.
   # Matches numbers with or without a negative sign (hyphen),
   # followed by one digit before the decimal, a decimal point,
   # and an arbitrary number of digits after the decimal point,
   # immediately followed by either the letter 'e' or a comma.
   # Note that backslashes are escaped due to the way R handles strings.
   #
   numrow.idx <- regexpr(rgxp.number, chifile)
   # Save the match length attribute to another variable,
   numrow.len <- attr(numrow.idx, "match.length")
   # then scrap the attribute of the original variable.
   attr(numrow.idx, "match.length") <- NULL
   #
   i <- seq(1, length(numrow.idx) - 1, 1)
   j <- seq(2, length(numrow.idx), 1)
   # Start indices of data ranges
   starts <- which(numrow.idx[i] != 1 & numrow.idx[j] == 1) + 1
   # End indices, except for the last
   ends <- which(numrow.idx[i] == 1 & numrow.idx[j] != 1)
   # Fix the last index of end indices
   ends <- c(ends, length(numrow.idx))
   #
   ff <- data.frame(NULL)
   for (s in 1:length(starts)) {
      zz <- textConnection(chifile[starts[s]:ends[s]], "r")
      ff <- rbind(ff,
               data.frame(stringsAsFactors = FALSE,
               sampleid, matrix(scan(zz, what = numeric(), sep = ","),
               ncol = 2, byrow = T)))
      close(zz)
   }
   names(ff) <- c("sampleid", "time", "potential")
   #
   ### Collect attributes of this experiment
   # RunTime (sec)
   position.RunTime <- regexpr("^Run\\sTime\\s\\(sec\\)", chifile)
   RunTime <- as.numeric(strsplit(chifile[which(position.RunTime == 1)], "\\s=\\s")[[1]][2])
   ff$RunTime <- RunTime
   #
   return(ff)
}