diff --git a/CHI.R b/CHI.R index f8fd9ed..a6bd2bd 100644 --- a/CHI.R +++ b/CHI.R @@ -1,14 +1,249 @@ # CHI.R # Functions to read and manipulate data from the CHI760 potentiostat/galvanostat -# Taha Ahmed, Jan 2011 +# Taha Ahmed, Jan 2011 - Feb 2011 # CONTENTS +# >>>> chronocm2df +# >>>> chronoamp2df +# >>>> amperometry2df # >>>> cv2df # >>>> lsv2df + +################################################## +################# 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) + # + 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(step = factor(s), + matrix(scan(zz, what = numeric(), sep = ","), + ncol = 2, byrow = T))) + close(zz) + } + names(ff) <- c("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) +} + + + +################################################## +################# chronoamp2df ################### +################################################## +chronoamp2df <- function(datafilename) { + # Function description: chronoamperometry 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) + # + 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(step = factor(s), + matrix(scan(zz, what = numeric(), sep = ","), + ncol = 2, byrow = T))) + close(zz) + } + names(ff) <- c("step", "time", "current") + # + ### 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\\)", + "^High\\sE\\s\\(V\\)", + "^Low\\sE\\s\\(V\\)", + "^Init\\sP/N", + "^Step\\s", + "^Pulse\\sWidth\\s\\(sec\\)", + "^Sample\\sInterval\\s\\(s\\)", + "^Quiet\\sTime\\s\\(sec\\)", + "^Sensitivity\\s\\(A/V\\)") + names.attr <- c("InitE", + "HighE", + "LowE", + "InitPN", + "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) +} + + + +################################################## +############### amperometry2df ################### +################################################## +amperometry2df <- function(datafilename) { + # Function description: for recorded amperometric i-T curves + # 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) + # + 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(matrix(scan(zz, what = numeric(), sep = ","), + ncol = 2, byrow = T))) + close(zz) + } + names(ff) <- c("time", "current") + # + ### 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\\)", + "^Sample\\sInterval\\s\\(s\\)", + "^Run\\sTime\\s\\(sec\\)", + "^Quiet\\sTime\\s\\(sec\\)", + "^Sensitivity\\s\\(A/V\\)") + names.attr <- c("InitE", + "SamplingInterval", + "RunTime", + "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 + # attrow.idx should now contain only one matching row + attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)], + "\\s=\\s")[[1]][2] + } + # + return(ff) +} + + + ################################################## #################### cv2df ####################### ##################################################