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546 lines
21 KiB
R
546 lines
21 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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source("/home/taha/chepec/chetex/common/R/common.R")
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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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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(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", "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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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.
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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(sampleid, 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("sampleid", "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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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.
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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(sampleid, 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("sampleid", "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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## Description:
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## Reads current-time data (from CHI 760 potentiostat)
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## and returns a dataframe with the data,
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## the data attributes (experimental conditions),
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## and some calculated parameters (charge, didt, etc.)
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## Usage:
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## amperometry2df(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: (optional) area of working electrode (in square centimeter)
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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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## $ InitE : num
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## $ SampleInterval : num
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## $ RunTime : 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$current / wearea
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ff <- cbind(ff, currentdensity = currentdensity)
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# Calculate time and current diffs
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timediff <- c(ff$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$currentdensity)
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# Update ff dataframe
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ff <- cbind(ff,
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timediff = timediff,
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dIdt = dIdt,
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didt = didt,
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charge = charge,
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chargedensity = chargedensity)
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#
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### Collect attributes of this experiment
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# InitE (volt)
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position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
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InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
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ff$InitE <- InitE
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# SampleInterval (volt)
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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$SampleInterval <- SampleInterval
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# Run time (seconds)
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position.RunTime <- regexpr("^Run\\sTime\\s\\(sec\\)", chifile)
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RunTime <- as.numeric(strsplit(chifile[which(position.RunTime == 1)], "\\s=\\s")[[1]][2])
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ff$RunTime <- RunTime
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# Quiet time (seconds)
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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$QuietTime <- QuietTime
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# Sensitivity (ampere per volt)
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position.Sensitivity <- regexpr("^Sensitivity\\s\\(A/V\\)", chifile)
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Sensitivity <- as.numeric(strsplit(chifile[which(position.Sensitivity == 1)], "\\s=\\s")[[1]][2])
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ff$Sensitivity <- Sensitivity
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#
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return(ff)
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}
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##################################################
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#################### cv2df #######################
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##################################################
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cv2df <- function(datafilename, 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(datafilename, "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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sampleid <- ProvideSampleId(datafilename)
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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(sampleid, cycle = as.integer(ceiling(s/2)), segment = 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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# Column names after initial assignment
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names(ff) <- c("sampleid", "cycle", "segment", "potential", "current", "charge")
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# Calculate current density
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currentdensity <- ff$current / wearea
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ff <- cbind(ff[, 1:5], currentdensity = currentdensity, charge = ff[, 6])
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## Collect attributes of this experiment
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# InitE (volt)
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position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
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InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
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ff$InitE <- InitE
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# HighE (volt)
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position.HighE <- regexpr("^High\\sE\\s\\(V\\)", chifile)
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HighE <- as.numeric(strsplit(chifile[which(position.HighE == 1)], "\\s=\\s")[[1]][2])
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ff$HighE <- HighE
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# LowE (volt)
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position.LowE <- regexpr("^Low\\sE\\s\\(V\\)", chifile)
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LowE <- as.numeric(strsplit(chifile[which(position.LowE == 1)], "\\s=\\s")[[1]][2])
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ff$LowE <- LowE
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# InitPN (positive or negative)
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position.InitPN <- regexpr("^Init\\sP/N", chifile)
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InitPN <- strsplit(chifile[which(position.InitPN == 1)], "\\s=\\s")[[1]][2]
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ff$InitPN <- InitPN
|
|
# ScanRate (volt per second)
|
|
position.ScanRate <- regexpr("^Scan\\sRate\\s\\(V/s\\)", chifile)
|
|
ScanRate <- as.numeric(strsplit(chifile[which(position.ScanRate == 1)], "\\s=\\s")[[1]][2])
|
|
ff$ScanRate <- ScanRate
|
|
# Segments, number of
|
|
position.Segments <- regexpr("^Segment\\s=", chifile)
|
|
Segments <- as.numeric(strsplit(chifile[which(position.Segments == 1)], "\\s=\\s")[[1]][2])
|
|
ff$Segments <- Segments
|
|
# SampleInterval (volt)
|
|
position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(V\\)", chifile)
|
|
SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
|
|
ff$SampleInterval <- SampleInterval
|
|
# 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)
|
|
}
|
|
|
|
|
|
|
|
|
|
##################################################
|
|
################### lsv2df #######################
|
|
##################################################
|
|
lsv2df <- function(datafilename, wearea = 1) {
|
|
# Function description:
|
|
# CH Instruments potentiostat records all data using standard SI units,
|
|
# so all potential values are in volts, currents are in amperes,
|
|
# charges in Coulombs, time in seconds, etc.
|
|
#
|
|
lsvfile <- file(datafilename, "r")
|
|
chifile <- readLines(lsvfile, n = -1) #read all lines of input file
|
|
close(lsvfile)
|
|
#
|
|
sampleid <- ProvideSampleId(datafilename)
|
|
#
|
|
rgxp.number <- "^\\-?\\d\\.\\d+,"
|
|
# 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 a comma.
|
|
# Note that backslashes are escaped.
|
|
#
|
|
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(sampleid, segment = factor(s),
|
|
matrix(scan(zz, what = numeric(), sep = ","),
|
|
ncol = 3, byrow = T)))
|
|
close(zz)
|
|
}
|
|
names(ff) <- c("sampleid", "segment", "potential", "current", "charge")
|
|
# Calculate current density
|
|
currentdensity <- ff$current / wearea
|
|
ff <- cbind(ff[, 1:4], currentdensity = currentdensity, charge = ff[, 5])
|
|
#
|
|
### 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)
|
|
}
|