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478 lines
18 KiB
R
478 lines
18 KiB
R
# CHI.R
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# Functions to read and manipulate data from the CHI760 potentiostat/galvanostat
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# Taha Ahmed, Jan 2011 - Feb 2011
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# CONTENTS
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# >>>> ocp2df
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# >>>> chronocm2df
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# >>>> chronoamp2df
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# >>>> amperometry2df
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# >>>> cv2df
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# >>>> lsv2df
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##################################################
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################### ocp2df #######################
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##################################################
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ocp2df <- function(datafilename) {
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# Function description: for recorded amperometric i-T curves
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# CH Instruments potentiostat records all data using standard SI units,
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# so all potential values are in volts, currents are in amperes,
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# charges in Coulombs, time in seconds, etc.
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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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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(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("time", "potential")
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#
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### Collect attributes of this experiment
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# These attributes are specific for each kind of experiment,
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# be careful when adapting to other electrochemical data
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rgxp.attr <- c("^Run\\sTime\\s\\(sec\\)")
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names.attr <- c("RunTime")
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for (n in 1:length(rgxp.attr)) {
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attrow.idx <- regexpr(rgxp.attr[n], chifile)
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attrow.len <- attr(attrow.idx, "match.length")
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attr(attrow.idx, "match.length") <- NULL
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# attrow.idx should now contain only one matching row
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attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)],
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"\\s=\\s")[[1]][2]
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}
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#
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return(ff)
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}
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##################################################
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################# chronocm2df ####################
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##################################################
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chronocm2df <- function(datafilename) {
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# Function description: chronocoulometry data
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# CH Instruments potentiostat records all data using standard SI units,
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# so all potential values are in volts, currents are in amperes,
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# charges in Coulombs, time in seconds, etc.
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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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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.
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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(step = factor(s),
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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("step", "time", "charge")
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#
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### Collect attributes of this experiment
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# These attributes are specific for each kind of experiment,
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# be careful when adapting to other electrochemical data
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rgxp.attr <- c("^Init\\sE\\s\\(V\\)",
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"^Final\\sE\\s\\(V\\)",
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"^Step\\s",
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"^Pulse\\sWidth\\s\\(sec\\)",
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"^Sample\\sInterval\\s\\(s\\)",
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"^Quiet\\sTime\\s\\(sec\\)",
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"^Sensitivity\\s\\(A/V\\)")
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names.attr <- c("InitE",
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"FinalE",
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"Steps",
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"PulseWidth",
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"SamplingInterval",
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"QuietTime",
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"Sensitivity")
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for (n in 1:length(rgxp.attr)) {
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attrow.idx <- regexpr(rgxp.attr[n], chifile)
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attrow.len <- attr(attrow.idx, "match.length")
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attr(attrow.idx, "match.length") <- NULL
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attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)],
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"\\s=\\s")[[1]][2]
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}
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#
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return(ff)
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}
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##################################################
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################# chronoamp2df ###################
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##################################################
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chronoamp2df <- function(datafilename, wearea = 1) {
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# Function description: chronoamperometry data
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# CH Instruments potentiostat records all data using standard SI units,
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# so all potential values are in volts, currents are in amperes,
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# charges in Coulombs, time in seconds, etc.
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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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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.
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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(step = factor(s),
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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("step", "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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#
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### Collect attributes of this experiment
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# These attributes are specific for each kind of experiment,
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# be careful when adapting to other electrochemical data
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rgxp.attr <- c("^Init\\sE\\s\\(V\\)",
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"^High\\sE\\s\\(V\\)",
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"^Low\\sE\\s\\(V\\)",
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"^Init\\sP/N",
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"^Step\\s",
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"^Pulse\\sWidth\\s\\(sec\\)",
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"^Sample\\sInterval\\s\\(s\\)",
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"^Quiet\\sTime\\s\\(sec\\)",
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"^Sensitivity\\s\\(A/V\\)")
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names.attr <- c("InitE",
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"HighE",
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"LowE",
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"InitPN",
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"Steps",
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"PulseWidth",
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"SamplingInterval",
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"QuietTime",
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"Sensitivity")
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for (n in 1:length(rgxp.attr)) {
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attrow.idx <- regexpr(rgxp.attr[n], chifile)
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attrow.len <- attr(attrow.idx, "match.length")
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attr(attrow.idx, "match.length") <- NULL
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attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)],
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"\\s=\\s")[[1]][2]
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}
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#
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return(ff)
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}
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##################################################
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############### amperometry2df ###################
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##################################################
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amperometry2df <- function(datafilename, wearea = 1) {
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# Function description: for recorded amperometric i-T curves
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# CH Instruments potentiostat records all data using standard SI units,
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# so all potential values are in volts, currents are in amperes,
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|
# charges in Coulombs, time in seconds, etc.
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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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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(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("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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#
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### Collect attributes of this experiment
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# These attributes are specific for each kind of experiment,
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# be careful when adapting to other electrochemical data
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rgxp.attr <- c("^Init\\sE\\s\\(V\\)",
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"^Sample\\sInterval\\s\\(s\\)",
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"^Run\\sTime\\s\\(sec\\)",
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"^Quiet\\sTime\\s\\(sec\\)",
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"^Sensitivity\\s\\(A/V\\)")
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names.attr <- c("InitE",
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"SamplingInterval",
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"RunTime",
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"QuietTime",
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"Sensitivity")
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for (n in 1:length(rgxp.attr)) {
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attrow.idx <- regexpr(rgxp.attr[n], chifile)
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attrow.len <- attr(attrow.idx, "match.length")
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attr(attrow.idx, "match.length") <- NULL
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# attrow.idx should now contain only one matching row
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attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)],
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"\\s=\\s")[[1]][2]
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}
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#
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return(ff)
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}
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##################################################
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#################### cv2df #######################
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##################################################
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cv2df <- function(cvfilename, wearea = 1) {
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# Function description:
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# CH Instruments potentiostat records all data using standard SI units,
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# so all potential values are in volts, currents are in amperes,
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# charges in Coulombs, time in seconds, etc.
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#
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cvfile <- file(cvfilename, "r")
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chifile <- readLines(cvfile, n = -1) #read all lines of input file
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close(cvfile)
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#
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rgxp.number <- "^\\-?\\d\\.\\d+,"
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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 a comma.
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# Note that backslashes are escaped.
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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(segment = factor(s), cycle = factor(ceiling(s/2)),
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matrix(scan(zz, what = numeric(), sep = ","),
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ncol = 3, byrow = T)))
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close(zz)
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}
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names(ff) <- c("segment", "cycle", "potential", "current", "charge")
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# Calculate current density
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currentdensity <- ff$current / wearea
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ff <- cbind(ff[, 1:4], currentdensity = currentdensity, ff[, 5])
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#
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### Collect attributes of this experiment
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|
# These attributes are specific for each kind of experiment,
|
|
# be careful when adapting to other electrochemical data
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|
rgxp.attr <- c("^Init\\sE\\s\\(V\\)",
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"^High\\sE\\s\\(V\\)",
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"^Low\\sE\\s\\(V\\)",
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"^Init\\sP/N",
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"^Scan\\sRate\\s\\(V/s\\)",
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"^Segment\\s=",
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"^Sample\\sInterval\\s\\(V\\)",
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"^Quiet\\sTime\\s\\(sec\\)",
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"^Sensitivity\\s\\(A/V\\)")
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names.attr <- c("InitE",
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"HighE",
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"LowE",
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"InitPN",
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"ScanRate",
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"Segments",
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"SamplingInterval",
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"QuietTime",
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"Sensitivity")
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for (n in 1:length(rgxp.attr)) {
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attrow.idx <- regexpr(rgxp.attr[n], chifile)
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attrow.len <- attr(attrow.idx, "match.length")
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attr(attrow.idx, "match.length") <- NULL
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attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)],
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"\\s=\\s")[[1]][2]
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}
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#
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return(ff)
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}
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##################################################
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################### lsv2df #######################
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##################################################
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lsv2df <- function(lsvfilename, wearea = 1) {
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# Function description:
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# CH Instruments potentiostat records all data using standard SI units,
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|
# so all potential values are in volts, currents are in amperes,
|
|
# charges in Coulombs, time in seconds, etc.
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#
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lsvfile <- file(lsvfilename, "r")
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chifile <- readLines(lsvfile, n = -1) #read all lines of input file
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close(lsvfile)
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#
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rgxp.number <- "^\\-?\\d\\.\\d+,"
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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),
|
|
# followed by one digit before the decimal, a decimal point,
|
|
# and an arbitrary number of digits after the decimal point,
|
|
# immediately followed by a comma.
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|
# Note that backslashes are escaped.
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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(segment = factor(s),
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matrix(scan(zz, what = numeric(), sep = ","),
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ncol = 3, byrow = T)))
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close(zz)
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}
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names(ff) <- c("segment", "potential", "current", "charge")
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# Calculate current density
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currentdensity <- ff$current / wearea
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ff <- cbind(ff[, 1:3], currentdensity = currentdensity, ff[, 4])
|
|
#
|
|
### Collect attributes of this experiment
|
|
# These attributes are specific for each kind of experiment,
|
|
# be careful when adapting to other electrochemical data
|
|
rgxp.attr <- c("^Init\\sE\\s\\(V\\)",
|
|
"^Final\\sE\\s\\(V\\)",
|
|
"^Scan\\sRate\\s\\(V/s\\)",
|
|
"^Sample\\sInterval\\s\\(V\\)",
|
|
"^Quiet\\sTime\\s\\(sec\\)",
|
|
"^Sensitivity\\s\\(A/V\\)")
|
|
names.attr <- c("InitE",
|
|
"FinalE",
|
|
"ScanRate",
|
|
"SamplingInterval",
|
|
"QuietTime",
|
|
"Sensitivity")
|
|
for (n in 1:length(rgxp.attr)) {
|
|
attrow.idx <- regexpr(rgxp.attr[n], chifile)
|
|
attrow.len <- attr(attrow.idx, "match.length")
|
|
attr(attrow.idx, "match.length") <- NULL
|
|
attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)],
|
|
"\\s=\\s")[[1]][2]
|
|
}
|
|
#
|
|
return(ff)
|
|
}
|