Split all files into their separate functions, put each former file in a directory.
The idea is to better expose each function, since some functions tended to drown in the larger files. Note that dependecies are are not resolved yet. Many functions are probably broken right now, especially those who point to common.R.master
Taha Ahmed
14 years ago
parent
f12fe6306c
commit
b976bd3fa4
@ -0,0 +1,7 @@
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# AUTOLAB.R
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# Functions to read and manipulate data from AUTOLAB potentiostats/galvanostats
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# Taha Ahmed, June 2011
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# CONTENTS
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# >>>> amp2df
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# >>>> ocp2df
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@ -0,0 +1,61 @@
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source("/home/taha/chepec/chetex/common/R/common.R")
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##################################################
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#################### ocp2df ######################
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##################################################
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ocp2df <- function(datafilename) {
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## Description:
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## Reads voltage-time data (from AUTOLAB potentiostat)
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## and returns a dataframe with the data.
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## Usage:
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## ocp2df(datafilename)
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## Arguments:
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## datafilename: text string with full path to experimental file
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## Value:
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## Dataframe with the following columns:
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## $ sampleid : chr
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## $ time : num
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## $ potential : num
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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+"
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# regexp that matches a decimal number at the beginning of the line.
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# Matches numbers _without_ a negative sign (hyphen),
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# followed by one or more digits before the decimal, a decimal point,
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# and an one or more digits after the decimal point.
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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,
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stringsAsFactors = FALSE,
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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", "time", "potential")
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#
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return(ff)
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}
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@ -1,785 +0,0 @@
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# 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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# >>>> mps2df
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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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################### 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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}
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##################################################
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################### ocp2df #######################
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##################################################
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ocp2df <- function(datafilename) {
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## Description:
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## Reads time vs potential 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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## ocp2df(datafilename)
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## Arguments:
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## datafilename: text string with full path to experimental file
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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", "potential")
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#
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### Collect attributes of this experiment
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# RunTime (sec)
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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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#
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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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## Description:
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## Reads current-time data (from CHI 760 potentiostat)
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## and returns a dataframe with the data and the
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## data attributes (experimental conditions).
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## Usage:
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## chronoamp2df(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 centimeters)
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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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## $ step : num
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## $ time : num
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## $ current : num
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## $ currentdensity : num
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## $ InitE : num
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## $ HighE : num
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## $ LowE : num
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## $ InitPN : chr
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## $ Step : num
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## $ Pulse width : num
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## $ Sample interval : num
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## $ Quiet Time : 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,
|
||||
## time in seconds, and so on.
|
||||
#
|
||||
datafile <- file(datafilename, "r")
|
||||
chifile <- readLines(datafile, n = -1) #read all lines of input file
|
||||
close(datafile)
|
||||
#
|
||||
sampleid <- ProvideSampleId(datafilename)
|
||||
#
|
||||
rgxp.number <- "^\\-?\\d\\.\\d+[e,]"
|
||||
# regexp that matches a decimal number at the beginning of the line.
|
||||
# Matches numbers with or without a negative sign (hyphen),
|
||||
# followed by one digit before the decimal, a decimal point,
|
||||
# and an arbitrary number of digits after the decimal point,
|
||||
# immediately followed by either the letter 'e' or a comma.
|
||||
# Note that backslashes are escaped.
|
||||
#
|
||||
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, step.current = s,
|
||||
matrix(scan(zz, what = numeric(), sep = ","),
|
||||
ncol = 2, byrow = T)))
|
||||
close(zz)
|
||||
}
|
||||
names(ff) <- c("sampleid", "step.current", "time", "current")
|
||||
# Calculate current density
|
||||
currentdensity <- ff$current / wearea
|
||||
ff <- cbind(ff, currentdensity = currentdensity)
|
||||
#
|
||||
|
||||
### Collect attributes of this experiment
|
||||
# InitE (volt)
|
||||
position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
|
||||
InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$InitE <- InitE
|
||||
# HighE (volt)
|
||||
position.HighE <- regexpr("^High\\sE\\s\\(V\\)", chifile)
|
||||
HighE <- as.numeric(strsplit(chifile[which(position.HighE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$HighE <- HighE
|
||||
# LowE (volt)
|
||||
position.LowE <- regexpr("^Low\\sE\\s\\(V\\)", chifile)
|
||||
LowE <- as.numeric(strsplit(chifile[which(position.LowE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$LowE <- LowE
|
||||
# InitPN
|
||||
position.InitPN <- regexpr("^Init\\sP/N", chifile)
|
||||
InitPN <- strsplit(chifile[which(position.InitPN == 1)], "\\s=\\s")[[1]][2]
|
||||
ff$InitPN <- InitPN
|
||||
# Steps (total number of steps)
|
||||
position.Steps <- regexpr("^Step\\s", chifile)
|
||||
Steps <- as.numeric(strsplit(chifile[which(position.Steps == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$Steps <- Steps
|
||||
# Pulse width (s)
|
||||
position.PulseWidth <- regexpr("^Pulse\\sWidth\\s\\(sec\\)", chifile)
|
||||
PulseWidth <- as.numeric(strsplit(chifile[which(position.PulseWidth == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$PulseWidth <- PulseWidth
|
||||
# Sample interval (s)
|
||||
position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(s\\)", chifile)
|
||||
SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$SampleInterval <- SampleInterval
|
||||
# Quiet Time (s)
|
||||
position.QuietTime <- regexpr("^Quiet\\sTime\\s\\(sec\\)", chifile)
|
||||
QuietTime <- as.numeric(strsplit(chifile[which(position.QuietTime == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$QuietTime <- QuietTime
|
||||
# Sensitivity (A/V)
|
||||
position.Sensitivity <- regexpr("^Sensitivity\\s\\(A/V\\)", chifile)
|
||||
Sensitivity <- as.numeric(strsplit(chifile[which(position.Sensitivity == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$Sensitivity <- Sensitivity
|
||||
#
|
||||
return(ff)
|
||||
}
|
||||
|
||||
|
||||
|
||||
##################################################
|
||||
############### amperometry2df ###################
|
||||
##################################################
|
||||
amperometry2df <- function(datafilename, wearea = 1) {
|
||||
## Description:
|
||||
## Reads current-time data (from CHI 760 potentiostat)
|
||||
## and returns a dataframe with the data,
|
||||
## the data attributes (experimental conditions),
|
||||
## and some calculated parameters (charge, didt, etc.)
|
||||
## Usage:
|
||||
## amperometry2df(datafilename, wearea)
|
||||
## Arguments:
|
||||
## datafilename: text string with full path to experimental file
|
||||
## wearea: (optional) area of working electrode (in square centimeter)
|
||||
## Value:
|
||||
## Dataframe with the following columns (and no extra attributes):
|
||||
## $ sampleid : chr
|
||||
## $ time : num
|
||||
## $ current : num
|
||||
## $ currentdensity : num
|
||||
## $ timediff : num
|
||||
## $ dIdt : num
|
||||
## $ didt : num
|
||||
## $ charge : num
|
||||
## $ chargedensity : num
|
||||
## $ InitE : num
|
||||
## $ SampleInterval : num
|
||||
## $ RunTime : num
|
||||
## $ QuietTime : num
|
||||
## $ Sensitivity : num
|
||||
## Note:
|
||||
## The CH Instruments 760 potentiostat records all data
|
||||
## using standard SI units, therefore this function
|
||||
## assumes all potential values to be in volts,
|
||||
## currents to be in amperes, charges in Coulombs,
|
||||
## time in seconds, and so on.
|
||||
#
|
||||
datafile <- file(datafilename, "r")
|
||||
chifile <- readLines(datafile, n = -1) #read all lines of input file
|
||||
close(datafile)
|
||||
#
|
||||
sampleid <- ProvideSampleId(datafilename)
|
||||
#
|
||||
rgxp.number <- "^\\-?\\d\\.\\d+[e,]"
|
||||
# regexp that matches a decimal number at the beginning of the line.
|
||||
# Matches numbers with or without a negative sign (hyphen),
|
||||
# followed by one digit before the decimal, a decimal point,
|
||||
# and an arbitrary number of digits after the decimal point,
|
||||
# immediately followed by either the letter 'e' or a comma.
|
||||
# Note that backslashes are escaped due to the way R handles strings.
|
||||
#
|
||||
numrow.idx <- regexpr(rgxp.number, chifile)
|
||||
# Save the match length attribute to another variable,
|
||||
numrow.len <- attr(numrow.idx, "match.length")
|
||||
# then scrap the attribute of the original variable.
|
||||
attr(numrow.idx, "match.length") <- NULL
|
||||
#
|
||||
i <- seq(1, length(numrow.idx) - 1, 1)
|
||||
j <- seq(2, length(numrow.idx), 1)
|
||||
# Start indices of data ranges
|
||||
starts <- which(numrow.idx[i] != 1 & numrow.idx[j] == 1) + 1
|
||||
# End indices, except for the last
|
||||
ends <- which(numrow.idx[i] == 1 & numrow.idx[j] != 1)
|
||||
# Fix the last index of end indices
|
||||
ends <- c(ends, length(numrow.idx))
|
||||
#
|
||||
ff <- data.frame(NULL)
|
||||
for (s in 1:length(starts)) {
|
||||
zz <- textConnection(chifile[starts[s]:ends[s]], "r")
|
||||
ff <- rbind(ff,
|
||||
data.frame(stringsAsFactors = FALSE,
|
||||
sampleid, matrix(scan(zz, what = numeric(), sep = ","),
|
||||
ncol = 2, byrow = T)))
|
||||
close(zz)
|
||||
}
|
||||
names(ff) <- c("sampleid", "time", "current")
|
||||
# Calculate current density
|
||||
currentdensity <- ff$current / wearea
|
||||
ff <- cbind(ff, currentdensity = currentdensity)
|
||||
# Calculate time and current diffs
|
||||
timediff <- c(ff$time[1], diff(ff$time))
|
||||
currentdiff <- c(ff$current[1], diff(ff$current))
|
||||
currentdensitydiff <- c(ff$currentdensity[1], diff(ff$currentdensity))
|
||||
# Calculate differential of current and current density
|
||||
dIdt <- currentdiff / timediff
|
||||
didt <- currentdensitydiff / timediff
|
||||
# Calculate charge and charge density
|
||||
charge <- cumsum(ff$current)
|
||||
chargedensity <- cumsum(ff$currentdensity)
|
||||
# Update ff dataframe
|
||||
ff <- cbind(ff,
|
||||
timediff = timediff,
|
||||
dIdt = dIdt,
|
||||
didt = didt,
|
||||
charge = charge,
|
||||
chargedensity = chargedensity)
|
||||
#
|
||||
### Collect attributes of this experiment
|
||||
# InitE (volt)
|
||||
position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
|
||||
InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$InitE <- InitE
|
||||
# SampleInterval (volt)
|
||||
position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(s\\)", chifile)
|
||||
SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$SampleInterval <- SampleInterval
|
||||
# Run time (seconds)
|
||||
position.RunTime <- regexpr("^Run\\sTime\\s\\(sec\\)", chifile)
|
||||
RunTime <- as.numeric(strsplit(chifile[which(position.RunTime == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$RunTime <- RunTime
|
||||
# Quiet time (seconds)
|
||||
position.QuietTime <- regexpr("^Quiet\\sTime\\s\\(sec\\)", chifile)
|
||||
QuietTime <- as.numeric(strsplit(chifile[which(position.QuietTime == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$QuietTime <- QuietTime
|
||||
# Sensitivity (ampere per volt)
|
||||
position.Sensitivity <- regexpr("^Sensitivity\\s\\(A/V\\)", chifile)
|
||||
Sensitivity <- as.numeric(strsplit(chifile[which(position.Sensitivity == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$Sensitivity <- Sensitivity
|
||||
#
|
||||
return(ff)
|
||||
}
|
||||
|
||||
|
||||
|
||||
##################################################
|
||||
#################### cv2df #######################
|
||||
##################################################
|
||||
cv2df <- 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.
|
||||
#
|
||||
cvfile <- file(datafilename, "r")
|
||||
chifile <- readLines(cvfile, n = -1) #read all lines of input file
|
||||
close(cvfile)
|
||||
#
|
||||
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, cycle = as.integer(ceiling(s/2)), segment = s,
|
||||
matrix(scan(zz, what = numeric(), sep = ","),
|
||||
ncol = 3, byrow = T)))
|
||||
close(zz)
|
||||
}
|
||||
# Column names after initial assignment
|
||||
names(ff) <- c("sampleid", "cycle", "segment", "potential", "current", "charge")
|
||||
# Calculate current density
|
||||
currentdensity <- ff$current / wearea
|
||||
ff <- cbind(ff[, 1:5], currentdensity = currentdensity, charge = ff[, 6])
|
||||
## Collect attributes of this experiment
|
||||
# InitE (volt)
|
||||
position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
|
||||
InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$InitE <- InitE
|
||||
# HighE (volt)
|
||||
position.HighE <- regexpr("^High\\sE\\s\\(V\\)", chifile)
|
||||
HighE <- as.numeric(strsplit(chifile[which(position.HighE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$HighE <- HighE
|
||||
# LowE (volt)
|
||||
position.LowE <- regexpr("^Low\\sE\\s\\(V\\)", chifile)
|
||||
LowE <- as.numeric(strsplit(chifile[which(position.LowE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$LowE <- LowE
|
||||
# InitPN (positive or negative)
|
||||
position.InitPN <- regexpr("^Init\\sP/N", chifile)
|
||||
InitPN <- strsplit(chifile[which(position.InitPN == 1)], "\\s=\\s")[[1]][2]
|
||||
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) {
|
||||
## Description:
|
||||
## Reads LSV datafiles from CHI 760 potentiostat
|
||||
## (potential, current, and charge)
|
||||
## and returns a dataframe with the data,
|
||||
## the data attributes (experimental conditions),
|
||||
## and calculated current density and charge density.
|
||||
## Usage:
|
||||
## lsv2df(datafilename, wearea)
|
||||
## Arguments:
|
||||
## datafilename: text string with full path to experimental file
|
||||
## wearea: (optional) area of working electrode (in square centimeter)
|
||||
## Value:
|
||||
## Dataframe with the following columns (and no extra attributes):
|
||||
## $ sampleid : chr (id)
|
||||
## $ segment : num (id)
|
||||
## $ potential : num (measure)
|
||||
## $ current : num (measure)
|
||||
## $ charge : num (measure)
|
||||
## $ currentdensity : num (measure)
|
||||
## $ chargedensity : num (measure)
|
||||
## $ InitE : num (id)
|
||||
## $ FinalE : num (id)
|
||||
## $ ScanRate : num (id)
|
||||
## $ SampleInterval : num (id)
|
||||
## $ QuietTime : num (id)
|
||||
## $ Sensitivity : num (id)
|
||||
## Note:
|
||||
## The CH Instruments 760 potentiostat records all data
|
||||
## using standard SI units, therefore this function
|
||||
## assumes all potential values to be in volts,
|
||||
## currents to be in amperes, charges in Coulombs,
|
||||
## time in seconds, and so on.
|
||||
#
|
||||
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(stringsAsFactors = FALSE,
|
||||
sampleid, segment = 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$current / wearea
|
||||
ff <- cbind(ff, currentdensity = currentdensity)
|
||||
# Calculate charge density
|
||||
chargedensity <- ff$charge / wearea
|
||||
ff <- cbind(ff, chargedensity = chargedensity)
|
||||
#
|
||||
### Collect attributes of this experiment
|
||||
# InitE (volt)
|
||||
position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
|
||||
InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$InitE <- InitE
|
||||
# FinalE (volt)
|
||||
position.FinalE <- regexpr("^Final\\sE\\s\\(V\\)", chifile)
|
||||
FinalE <- as.numeric(strsplit(chifile[which(position.FinalE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$FinalE <- FinalE
|
||||
# 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$ScanRate <- ScanRate
|
||||
# SampleInterval (volt)
|
||||
position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(V\\)", chifile)
|
||||
SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$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)
|
||||
}
|
||||
@ -0,0 +1,12 @@
|
||||
# CHI.R
|
||||
# Functions to read and manipulate data from the CHI760 potentiostat/galvanostat
|
||||
# Taha Ahmed, Jan 2011 - Feb 2011
|
||||
|
||||
# CONTENTS
|
||||
# >>>> mps2df
|
||||
# >>>> ocp2df
|
||||
# >>>> chronocm2df
|
||||
# >>>> chronoamp2df
|
||||
# >>>> amperometry2df
|
||||
# >>>> cv2df
|
||||
# >>>> lsv2df
|
||||
@ -0,0 +1,123 @@
|
||||
source("/home/taha/chepec/chetex/common/R/common.R")
|
||||
|
||||
##################################################
|
||||
############### amperometry2df ###################
|
||||
##################################################
|
||||
amperometry2df <- function(datafilename, wearea = 1) {
|
||||
## Description:
|
||||
## Reads current-time data (from CHI 760 potentiostat)
|
||||
## and returns a dataframe with the data,
|
||||
## the data attributes (experimental conditions),
|
||||
## and some calculated parameters (charge, didt, etc.)
|
||||
## Usage:
|
||||
## amperometry2df(datafilename, wearea)
|
||||
## Arguments:
|
||||
## datafilename: text string with full path to experimental file
|
||||
## wearea: (optional) area of working electrode (in square centimeter)
|
||||
## Value:
|
||||
## Dataframe with the following columns (and no extra attributes):
|
||||
## $ sampleid : chr
|
||||
## $ time : num
|
||||
## $ current : num
|
||||
## $ currentdensity : num
|
||||
## $ timediff : num
|
||||
## $ dIdt : num
|
||||
## $ didt : num
|
||||
## $ charge : num
|
||||
## $ chargedensity : num
|
||||
## $ InitE : num
|
||||
## $ SampleInterval : num
|
||||
## $ RunTime : num
|
||||
## $ QuietTime : num
|
||||
## $ Sensitivity : num
|
||||
## Note:
|
||||
## The CH Instruments 760 potentiostat records all data
|
||||
## using standard SI units, therefore this function
|
||||
## assumes all potential values to be in volts,
|
||||
## currents to be in amperes, charges in Coulombs,
|
||||
## time in seconds, and so on.
|
||||
#
|
||||
datafile <- file(datafilename, "r")
|
||||
chifile <- readLines(datafile, n = -1) #read all lines of input file
|
||||
close(datafile)
|
||||
#
|
||||
sampleid <- ProvideSampleId(datafilename)
|
||||
#
|
||||
rgxp.number <- "^\\-?\\d\\.\\d+[e,]"
|
||||
# regexp that matches a decimal number at the beginning of the line.
|
||||
# Matches numbers with or without a negative sign (hyphen),
|
||||
# followed by one digit before the decimal, a decimal point,
|
||||
# and an arbitrary number of digits after the decimal point,
|
||||
# immediately followed by either the letter 'e' or a comma.
|
||||
# Note that backslashes are escaped due to the way R handles strings.
|
||||
#
|
||||
numrow.idx <- regexpr(rgxp.number, chifile)
|
||||
# Save the match length attribute to another variable,
|
||||
numrow.len <- attr(numrow.idx, "match.length")
|
||||
# then scrap the attribute of the original variable.
|
||||
attr(numrow.idx, "match.length") <- NULL
|
||||
#
|
||||
i <- seq(1, length(numrow.idx) - 1, 1)
|
||||
j <- seq(2, length(numrow.idx), 1)
|
||||
# Start indices of data ranges
|
||||
starts <- which(numrow.idx[i] != 1 & numrow.idx[j] == 1) + 1
|
||||
# End indices, except for the last
|
||||
ends <- which(numrow.idx[i] == 1 & numrow.idx[j] != 1)
|
||||
# Fix the last index of end indices
|
||||
ends <- c(ends, length(numrow.idx))
|
||||
#
|
||||
ff <- data.frame(NULL)
|
||||
for (s in 1:length(starts)) {
|
||||
zz <- textConnection(chifile[starts[s]:ends[s]], "r")
|
||||
ff <- rbind(ff,
|
||||
data.frame(stringsAsFactors = FALSE,
|
||||
sampleid, matrix(scan(zz, what = numeric(), sep = ","),
|
||||
ncol = 2, byrow = T)))
|
||||
close(zz)
|
||||
}
|
||||
names(ff) <- c("sampleid", "time", "current")
|
||||
# Calculate current density
|
||||
currentdensity <- ff$current / wearea
|
||||
ff <- cbind(ff, currentdensity = currentdensity)
|
||||
# Calculate time and current diffs
|
||||
timediff <- c(ff$time[1], diff(ff$time))
|
||||
currentdiff <- c(ff$current[1], diff(ff$current))
|
||||
currentdensitydiff <- c(ff$currentdensity[1], diff(ff$currentdensity))
|
||||
# Calculate differential of current and current density
|
||||
dIdt <- currentdiff / timediff
|
||||
didt <- currentdensitydiff / timediff
|
||||
# Calculate charge and charge density
|
||||
charge <- cumsum(ff$current)
|
||||
chargedensity <- cumsum(ff$currentdensity)
|
||||
# Update ff dataframe
|
||||
ff <- cbind(ff,
|
||||
timediff = timediff,
|
||||
dIdt = dIdt,
|
||||
didt = didt,
|
||||
charge = charge,
|
||||
chargedensity = chargedensity)
|
||||
#
|
||||
### Collect attributes of this experiment
|
||||
# InitE (volt)
|
||||
position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
|
||||
InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$InitE <- InitE
|
||||
# SampleInterval (volt)
|
||||
position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(s\\)", chifile)
|
||||
SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$SampleInterval <- SampleInterval
|
||||
# Run time (seconds)
|
||||
position.RunTime <- regexpr("^Run\\sTime\\s\\(sec\\)", chifile)
|
||||
RunTime <- as.numeric(strsplit(chifile[which(position.RunTime == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$RunTime <- RunTime
|
||||
# Quiet time (seconds)
|
||||
position.QuietTime <- regexpr("^Quiet\\sTime\\s\\(sec\\)", chifile)
|
||||
QuietTime <- as.numeric(strsplit(chifile[which(position.QuietTime == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$QuietTime <- QuietTime
|
||||
# Sensitivity (ampere per volt)
|
||||
position.Sensitivity <- regexpr("^Sensitivity\\s\\(A/V\\)", chifile)
|
||||
Sensitivity <- as.numeric(strsplit(chifile[which(position.Sensitivity == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$Sensitivity <- Sensitivity
|
||||
#
|
||||
return(ff)
|
||||
}
|
||||
@ -0,0 +1,122 @@
|
||||
source("/home/taha/chepec/chetex/common/R/common.R")
|
||||
|
||||
##################################################
|
||||
################# chronoamp2df ###################
|
||||
##################################################
|
||||
chronoamp2df <- function(datafilename, wearea = 1) {
|
||||
## Description:
|
||||
## Reads current-time data (from CHI 760 potentiostat)
|
||||
## and returns a dataframe with the data and the
|
||||
## data attributes (experimental conditions).
|
||||
## Usage:
|
||||
## chronoamp2df(datafilename, wearea)
|
||||
## Arguments:
|
||||
## datafilename: text string with full path to experimental file
|
||||
## wearea: (optional) area of working electrode (in square centimeters)
|
||||
## Value:
|
||||
## Dataframe with the following columns (and no extra attributes):
|
||||
## $ sampleid : chr
|
||||
## $ step : num
|
||||
## $ time : num
|
||||
## $ current : num
|
||||
## $ currentdensity : num
|
||||
## $ InitE : num
|
||||
## $ HighE : num
|
||||
## $ LowE : num
|
||||
## $ InitPN : chr
|
||||
## $ Step : num
|
||||
## $ Pulse width : num
|
||||
## $ Sample interval : num
|
||||
## $ Quiet Time : num
|
||||
## $ Sensitivity : num
|
||||
## Note:
|
||||
## The CH Instruments 760 potentiostat records all data
|
||||
## using standard SI units, therefore this function
|
||||
## assumes all potential values to be in volts,
|
||||
## currents to be in amperes, charges in Coulombs,
|
||||
## time in seconds, and so on.
|
||||
#
|
||||
datafile <- file(datafilename, "r")
|
||||
chifile <- readLines(datafile, n = -1) #read all lines of input file
|
||||
close(datafile)
|
||||
#
|
||||
sampleid <- ProvideSampleId(datafilename)
|
||||
#
|
||||
rgxp.number <- "^\\-?\\d\\.\\d+[e,]"
|
||||
# regexp that matches a decimal number at the beginning of the line.
|
||||
# Matches numbers with or without a negative sign (hyphen),
|
||||
# followed by one digit before the decimal, a decimal point,
|
||||
# and an arbitrary number of digits after the decimal point,
|
||||
# immediately followed by either the letter 'e' or a comma.
|
||||
# Note that backslashes are escaped.
|
||||
#
|
||||
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, step.current = s,
|
||||
matrix(scan(zz, what = numeric(), sep = ","),
|
||||
ncol = 2, byrow = T)))
|
||||
close(zz)
|
||||
}
|
||||
names(ff) <- c("sampleid", "step.current", "time", "current")
|
||||
# Calculate current density
|
||||
currentdensity <- ff$current / wearea
|
||||
ff <- cbind(ff, currentdensity = currentdensity)
|
||||
#
|
||||
|
||||
### Collect attributes of this experiment
|
||||
# InitE (volt)
|
||||
position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
|
||||
InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$InitE <- InitE
|
||||
# HighE (volt)
|
||||
position.HighE <- regexpr("^High\\sE\\s\\(V\\)", chifile)
|
||||
HighE <- as.numeric(strsplit(chifile[which(position.HighE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$HighE <- HighE
|
||||
# LowE (volt)
|
||||
position.LowE <- regexpr("^Low\\sE\\s\\(V\\)", chifile)
|
||||
LowE <- as.numeric(strsplit(chifile[which(position.LowE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$LowE <- LowE
|
||||
# InitPN
|
||||
position.InitPN <- regexpr("^Init\\sP/N", chifile)
|
||||
InitPN <- strsplit(chifile[which(position.InitPN == 1)], "\\s=\\s")[[1]][2]
|
||||
ff$InitPN <- InitPN
|
||||
# Steps (total number of steps)
|
||||
position.Steps <- regexpr("^Step\\s", chifile)
|
||||
Steps <- as.numeric(strsplit(chifile[which(position.Steps == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$Steps <- Steps
|
||||
# Pulse width (s)
|
||||
position.PulseWidth <- regexpr("^Pulse\\sWidth\\s\\(sec\\)", chifile)
|
||||
PulseWidth <- as.numeric(strsplit(chifile[which(position.PulseWidth == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$PulseWidth <- PulseWidth
|
||||
# Sample interval (s)
|
||||
position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(s\\)", chifile)
|
||||
SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$SampleInterval <- SampleInterval
|
||||
# Quiet Time (s)
|
||||
position.QuietTime <- regexpr("^Quiet\\sTime\\s\\(sec\\)", chifile)
|
||||
QuietTime <- as.numeric(strsplit(chifile[which(position.QuietTime == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$QuietTime <- QuietTime
|
||||
# Sensitivity (A/V)
|
||||
position.Sensitivity <- regexpr("^Sensitivity\\s\\(A/V\\)", chifile)
|
||||
Sensitivity <- as.numeric(strsplit(chifile[which(position.Sensitivity == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$Sensitivity <- Sensitivity
|
||||
#
|
||||
return(ff)
|
||||
}
|
||||
@ -0,0 +1,78 @@
|
||||
source("/home/taha/chepec/chetex/common/R/common.R")
|
||||
|
||||
##################################################
|
||||
################# chronocm2df ####################
|
||||
##################################################
|
||||
chronocm2df <- function(datafilename) {
|
||||
# Function description: chronocoulometry data
|
||||
# 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.
|
||||
#
|
||||
datafile <- file(datafilename, "r")
|
||||
chifile <- readLines(datafile, n = -1) #read all lines of input file
|
||||
close(datafile)
|
||||
#
|
||||
sampleid <- ProvideSampleId(datafilename)
|
||||
#
|
||||
rgxp.number <- "^\\-?\\d\\.\\d+[e,]"
|
||||
# regexp that matches a decimal number at the beginning of the line.
|
||||
# Matches numbers with or without a negative sign (hyphen),
|
||||
# followed by one digit before the decimal, a decimal point,
|
||||
# and an arbitrary number of digits after the decimal point,
|
||||
# immediately followed by either the letter 'e' or a comma.
|
||||
# Note that backslashes are escaped.
|
||||
#
|
||||
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, step = factor(s),
|
||||
matrix(scan(zz, what = numeric(), sep = ","),
|
||||
ncol = 2, byrow = T)))
|
||||
close(zz)
|
||||
}
|
||||
names(ff) <- c("sampleid", "step", "time", "charge")
|
||||
#
|
||||
### 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\\)",
|
||||
"^Step\\s",
|
||||
"^Pulse\\sWidth\\s\\(sec\\)",
|
||||
"^Sample\\sInterval\\s\\(s\\)",
|
||||
"^Quiet\\sTime\\s\\(sec\\)",
|
||||
"^Sensitivity\\s\\(A/V\\)")
|
||||
names.attr <- c("InitE",
|
||||
"FinalE",
|
||||
"Steps",
|
||||
"PulseWidth",
|
||||
"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)
|
||||
}
|
||||
@ -0,0 +1,94 @@
|
||||
source("/home/taha/chepec/chetex/common/R/common.R")
|
||||
|
||||
##################################################
|
||||
#################### cv2df #######################
|
||||
##################################################
|
||||
cv2df <- 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.
|
||||
#
|
||||
cvfile <- file(datafilename, "r")
|
||||
chifile <- readLines(cvfile, n = -1) #read all lines of input file
|
||||
close(cvfile)
|
||||
#
|
||||
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, cycle = as.integer(ceiling(s/2)), segment = s,
|
||||
matrix(scan(zz, what = numeric(), sep = ","),
|
||||
ncol = 3, byrow = T)))
|
||||
close(zz)
|
||||
}
|
||||
# Column names after initial assignment
|
||||
names(ff) <- c("sampleid", "cycle", "segment", "potential", "current", "charge")
|
||||
# Calculate current density
|
||||
currentdensity <- ff$current / wearea
|
||||
ff <- cbind(ff[, 1:5], currentdensity = currentdensity, charge = ff[, 6])
|
||||
## Collect attributes of this experiment
|
||||
# InitE (volt)
|
||||
position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
|
||||
InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$InitE <- InitE
|
||||
# HighE (volt)
|
||||
position.HighE <- regexpr("^High\\sE\\s\\(V\\)", chifile)
|
||||
HighE <- as.numeric(strsplit(chifile[which(position.HighE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$HighE <- HighE
|
||||
# LowE (volt)
|
||||
position.LowE <- regexpr("^Low\\sE\\s\\(V\\)", chifile)
|
||||
LowE <- as.numeric(strsplit(chifile[which(position.LowE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$LowE <- LowE
|
||||
# InitPN (positive or negative)
|
||||
position.InitPN <- regexpr("^Init\\sP/N", chifile)
|
||||
InitPN <- strsplit(chifile[which(position.InitPN == 1)], "\\s=\\s")[[1]][2]
|
||||
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)
|
||||
}
|
||||
@ -0,0 +1,114 @@
|
||||
source("/home/taha/chepec/chetex/common/R/common.R")
|
||||
|
||||
##################################################
|
||||
################### lsv2df #######################
|
||||
##################################################
|
||||
lsv2df <- function(datafilename, wearea = 1) {
|
||||
## Description:
|
||||
## Reads LSV datafiles from CHI 760 potentiostat
|
||||
## (potential, current, and charge)
|
||||
## and returns a dataframe with the data,
|
||||
## the data attributes (experimental conditions),
|
||||
## and calculated current density and charge density.
|
||||
## Usage:
|
||||
## lsv2df(datafilename, wearea)
|
||||
## Arguments:
|
||||
## datafilename: text string with full path to experimental file
|
||||
## wearea: (optional) area of working electrode (in square centimeter)
|
||||
## Value:
|
||||
## Dataframe with the following columns (and no extra attributes):
|
||||
## $ sampleid : chr (id)
|
||||
## $ segment : num (id)
|
||||
## $ potential : num (measure)
|
||||
## $ current : num (measure)
|
||||
## $ charge : num (measure)
|
||||
## $ currentdensity : num (measure)
|
||||
## $ chargedensity : num (measure)
|
||||
## $ InitE : num (id)
|
||||
## $ FinalE : num (id)
|
||||
## $ ScanRate : num (id)
|
||||
## $ SampleInterval : num (id)
|
||||
## $ QuietTime : num (id)
|
||||
## $ Sensitivity : num (id)
|
||||
## Note:
|
||||
## The CH Instruments 760 potentiostat records all data
|
||||
## using standard SI units, therefore this function
|
||||
## assumes all potential values to be in volts,
|
||||
## currents to be in amperes, charges in Coulombs,
|
||||
## time in seconds, and so on.
|
||||
#
|
||||
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(stringsAsFactors = FALSE,
|
||||
sampleid, segment = 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$current / wearea
|
||||
ff <- cbind(ff, currentdensity = currentdensity)
|
||||
# Calculate charge density
|
||||
chargedensity <- ff$charge / wearea
|
||||
ff <- cbind(ff, chargedensity = chargedensity)
|
||||
#
|
||||
### Collect attributes of this experiment
|
||||
# InitE (volt)
|
||||
position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
|
||||
InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$InitE <- InitE
|
||||
# FinalE (volt)
|
||||
position.FinalE <- regexpr("^Final\\sE\\s\\(V\\)", chifile)
|
||||
FinalE <- as.numeric(strsplit(chifile[which(position.FinalE == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$FinalE <- FinalE
|
||||
# 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$ScanRate <- ScanRate
|
||||
# SampleInterval (volt)
|
||||
position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(V\\)", chifile)
|
||||
SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
|
||||
ff$SampleInterval <- SampleInterval
|
||||
# Quiet time (seconds)
|
||||