R/amperometry2df.R

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

#' Read amperometry data from CHI760
#'
#' Reads current-time data (from CHI 760 potentiostat)
#' and returns a dataframe with the data,
#' the data attributes (experimental conditions),
#' and some calculated parameters (charge, didt, etc.)
#'
#' @param datafilename text string with full path to experimental file
#' @param wearea       (optional) area of working electrode (in square centimeter)
#'
#' @details The CH Instruments 760 potentiostat records all data using
#'    standard SI units, therefore this function assumes all potentials
#'    to be in volts, currents to be in amperes, charges in Coulombs,
#'    time in seconds, and so on.
#'
#' @return Dataframe with the following columns (and no extra attributes):
#'    $ sampleid        : chr
#'    $ time            : num [seconds]
#'    $ current         : num [ampere]
#'    $ currentdensity  : num [ampere per square cm]
#'    $ timediff        : num [seconds]
#'    $ dIdt            : num
#'    $ didt            : num
#'    $ charge          : num [coulomb]
#'    $ chargedensity   : num [coulomb per square cm]
#'    $ InitE           : num
#'    $ SampleInterval  : num
#'    $ RunTime         : num
#'    $ QuietTime       : num
#'    $ Sensitivity     : num
#' @export
amperometry2df <- function(datafilename, wearea = 1) {
   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", "current")
   # Calculate current density
   currentdensity <- ff$current / wearea
   ff <- cbind(ff, currentdensity = currentdensity)
   # Calculate time and current diffs
   timediff <- c(ff$time[1], diff(ff$time))
   currentdiff <- c(ff$current[1], diff(ff$current))
   currentdensitydiff <- c(ff$currentdensity[1], diff(ff$currentdensity))
   # Calculate differential of current and current density
   dIdt <- currentdiff / timediff
   didt <- currentdensitydiff / timediff
   # Calculate charge and charge density
   charge <- cumsum(ff$current * timediff)
   chargedensity <- cumsum(ff$currentdensity * timediff)
   # Update ff dataframe
   ff <- cbind(ff,
            timediff = timediff,
            dIdt = dIdt,
            didt = didt,
            charge = charge,
            chargedensity = chargedensity)
   #
   ### Collect attributes of this experiment
   # InitE (volt)
   position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
   InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
   ff$InitE <- InitE
   # SampleInterval (volt)
   position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(s\\)", chifile)
   SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
   ff$SampleInterval <- SampleInterval
   # Run time (seconds)
   position.RunTime <- regexpr("^Run\\sTime\\s\\(sec\\)", chifile)
   RunTime <- as.numeric(strsplit(chifile[which(position.RunTime == 1)], "\\s=\\s")[[1]][2])
   ff$RunTime <- RunTime
   # Quiet time (seconds)
   position.QuietTime <- regexpr("^Quiet\\sTime\\s\\(sec\\)", chifile)
   QuietTime <- as.numeric(strsplit(chifile[which(position.QuietTime == 1)], "\\s=\\s")[[1]][2])
   ff$QuietTime <- QuietTime
   # Sensitivity (ampere per volt)
   position.Sensitivity <- regexpr("^Sensitivity\\s\\(A/V\\)", chifile)
   Sensitivity <- as.numeric(strsplit(chifile[which(position.Sensitivity == 1)], "\\s=\\s")[[1]][2])
   ff$Sensitivity <- Sensitivity
   #
   return(ff)
}