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147 lines
5.9 KiB
R
147 lines
5.9 KiB
R
source("/home/taha/chepec/chetex/common/R/common.R")
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##################################################
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################### mps2df #######################
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##################################################
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mps2df <- function(datafilename, wearea = 1) {
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## Description:
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## Reads time vs current data (from CHI 760 potentiostat)
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## and returns a dataframe with the data and
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## the data attributes (experimental conditions).
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## Usage:
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## mps2df(datafilename, wearea)
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## Arguments:
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## datafilename: text string with full path to experimental file
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## wearea: working electrode area in square centimeters (optional)
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## Value:
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## Dataframe with the following columns (and no extra attributes):
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## $ sampleid : chr
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## $ time : num
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## $ current : num
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## $ currentdensity : num
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## $ timediff : num
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## $ dIdt : num
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## $ didt : num
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## $ charge : num
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## $ chargedensity : num
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## $ PotentialSteps : num
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## $ TimeSteps : num
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## $ Cycle : num
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## $ SampleInterval : num
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## $ QuietTime : num
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## $ Sensitivity : num
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## Note:
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## The CH Instruments 760 potentiostat records all data
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## using standard SI units, therefore this function
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## assumes all potential values to be in volts,
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## currents to be in amperes, charges in Coulombs,
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## time in seconds, and so on.
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#
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datafile <- file(datafilename, "r")
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chifile <- readLines(datafile, n = -1) #read all lines of input file
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close(datafile)
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#
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sampleid <- ProvideSampleId(datafilename)
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#
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rgxp.number <- "^\\-?\\d+\\.\\d+[e,]"
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# regexp that matches a decimal number at the beginning of the line.
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# Matches numbers with or without a negative sign (hyphen),
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# followed by one digit before the decimal, a decimal point,
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# and an arbitrary number of digits after the decimal point,
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# immediately followed by either the letter 'e' or a comma.
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# Note that backslashes are escaped due to the way R handles strings.
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#
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numrow.idx <- regexpr(rgxp.number, chifile)
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# Save the match length attribute to another variable,
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numrow.len <- attr(numrow.idx, "match.length")
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# then scrap the attribute of the original variable.
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attr(numrow.idx, "match.length") <- NULL
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#
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i <- seq(1, length(numrow.idx) - 1, 1)
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j <- seq(2, length(numrow.idx), 1)
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# Start indices of data ranges
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starts <- which(numrow.idx[i] != 1 & numrow.idx[j] == 1) + 1
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# End indices, except for the last
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ends <- which(numrow.idx[i] == 1 & numrow.idx[j] != 1)
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# Fix the last index of end indices
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ends <- c(ends, length(numrow.idx))
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#
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ff <- data.frame(NULL)
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for (s in 1:length(starts)) {
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zz <- textConnection(chifile[starts[s]:ends[s]], "r")
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ff <- rbind(ff,
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data.frame(stringsAsFactors = FALSE,
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sampleid, matrix(scan(zz, what = numeric(), sep = ","),
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ncol = 2, byrow = T)))
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close(zz)
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}
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names(ff) <- c("sampleid", "time", "current")
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# Calculate current density
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currentdensity <- ff$current / wearea
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ff <- cbind(ff, currentdensity = currentdensity)
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# Calculate time diff and current diff
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timediff <- c(ff$time[1], diff(ff$time))
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currentdiff <- c(ff$current[1], diff(ff$current))
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currentdensitydiff <- c(ff$currentdensity[1], diff(ff$currentdensity))
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# Calculate differential of current and current density
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dIdt <- currentdiff / timediff
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didt <- currentdensitydiff / timediff
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# Calculate charge and charge density
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charge <- cumsum(ff$current)
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chargedensity <- cumsum(ff$currentdensity)
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# Update ff dataframe
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ff <- cbind(ff,
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timediff = timediff,
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dIdt = dIdt,
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didt = didt,
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charge = charge,
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chargedensity = chargedensity)
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#
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### Collect attributes of this experiment
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# Potential steps
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PotentialSteps <- ""
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positions.PotentialSteps <- regexpr("^E\\d+\\s\\(V\\)", chifile)
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PotentialSteps <- paste("\\num{", strsplit(chifile[which(positions.PotentialSteps == 1)],
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"\\s=\\s")[[1]][2], "}", sep = "")
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if (length(which(positions.PotentialSteps == 1)) > 1) {
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for (i in 2:length(which(positions.PotentialSteps == 1))) {
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PotentialSteps <-
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paste(PotentialSteps,
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paste("\\num{", strsplit(chifile[which(positions.PotentialSteps == 1)],
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"\\s=\\s")[[i]][2], "}", sep = ""), sep = ", ")
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}
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}
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ff$PotentialSteps <- PotentialSteps
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# Time steps
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TimeSteps <- ""
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positions.TimeSteps <- regexpr("^T\\d+\\s\\(s\\)", chifile)
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TimeSteps <- paste("\\num{", strsplit(chifile[which(positions.TimeSteps == 1)],
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"\\s=\\s")[[1]][2], "}", sep = "")
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if (length(which(positions.TimeSteps == 1)) > 1) {
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for (i in 2:length(which(positions.TimeSteps == 1))) {
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TimeSteps <-
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paste(TimeSteps,
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paste("\\num{", strsplit(chifile[which(positions.TimeSteps == 1)],
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"\\s=\\s")[[i]][2], "}", sep = ""), sep = ", ")
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}
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}
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ff$TimeSteps <- TimeSteps
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# Cycles
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position.Cycles <- regexpr("^Cycle", chifile)
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Cycles <- as.numeric(strsplit(chifile[which(position.Cycles == 1)], "\\s=\\s")[[1]][2])
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ff$Cycles <- Cycles
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# Sample interval (s)
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position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(s\\)", chifile)
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SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
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ff$SampleInterval <- SampleInterval
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# Quiet Time (s)
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position.QuietTime <- regexpr("^Quiet\\sTime\\s\\(sec\\)", chifile)
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QuietTime <- as.numeric(strsplit(chifile[which(position.QuietTime == 1)], "\\s=\\s")[[1]][2])
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ff$QuietTime <- QuietTime
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# Sensitivity (A/V)
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position.Sensitivity <- regexpr("^Sensitivity\\s\\(A/V\\)", chifile)
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Sensitivity <- as.numeric(strsplit(chifile[which(position.Sensitivity == 1)], "\\s=\\s")[[1]][2])
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ff$Sensitivity <- Sensitivity
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#
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return(ff)
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} |