source("/home/taha/chepec/chetex/common/R/common/ProvideSampleId.R") ################################################## ################### ocp2df ####################### ################################################## ocp2df <- function(datafilename) { ## Description: ## Reads time vs potential data (from CHI 760 potentiostat) ## and returns a dataframe with the data and ## the data attributes (experimental conditions). ## Usage: ## ocp2df(datafilename) ## Arguments: ## datafilename: text string with full path to experimental file ## 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", "potential") # ### Collect attributes of this experiment # RunTime (sec) position.RunTime <- regexpr("^Run\\sTime\\s\\(sec\\)", chifile) RunTime <- as.numeric(strsplit(chifile[which(position.RunTime == 1)], "\\s=\\s")[[1]][2]) ff$RunTime <- RunTime # return(ff) }