# AUTOLAB.R # Functions to read and manipulate data from AUTOLAB potentiostats/galvanostats # Taha Ahmed, June 2011 # CONTENTS source("/home/taha/chepec/chetex/common/R/common.R") # >>>> chronoamp2df ################################################## ################# chronoamp2df ################### ################################################## chronoamp2df <- function(datafilename, wearea = 1) { ## Description: ## Reads current-time data (from AUTOLAB potentiostat) ## and returns a dataframe with the data and some ## calculated quantities based on the data. ## 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: ## $ sampleid : chr ## $ time : num ## $ current : num ## $ currentdensity : num ## $ timediff : num ## $ dIdt : num ## $ didt : num ## $ charge : num ## $ chargedensity : num # datafile <- file(datafilename, "r") chifile <- readLines(datafile, n = -1) #read all lines of input file close(datafile) # sampleid <- ProvideSampleId(datafilename) # rgxp.number <- "^\\d+\\.\\d+" # regexp that matches a decimal number at the beginning of the line. # Matches numbers _without_ a negative sign (hyphen), # followed by one or more digits before the decimal, a decimal point, # and an one or more digits after the decimal point. # 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, matrix(scan(zz, what = numeric(), sep = ""), ncol = 2, byrow = T))) close(zz) } names(ff) <- c("sampleid", "time", "current") # Calculate current density currentdensity <- ff$current / wearea ff <- cbind(ff, currentdensity = currentdensity) # Calculate time diff and current diff timediff <- c(ff$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) # return(ff) }