# CHI.R # Functions to read and manipulate data from the CHI760 potentiostat/galvanostat # Taha Ahmed, Jan 2011 - Feb 2011 # CONTENTS source("/home/taha/chepec/chetex/common/R/common.R") # >>>> ocp2df # >>>> chronocm2df # >>>> chronoamp2df # >>>> amperometry2df # >>>> cv2df # >>>> lsv2df ################################################## ################### ocp2df ####################### ################################################## ocp2df <- 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) # 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(sampleid, matrix(scan(zz, what = numeric(), sep = ","), ncol = 2, byrow = T))) close(zz) } names(ff) <- c("sampleid", "time", "potential") # ### 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("^Run\\sTime\\s\\(sec\\)") names.attr <- c("RunTime") 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) } ################################################## ################# 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) } ################################################## ################# chronoamp2df ################### ################################################## chronoamp2df <- function(datafilename, wearea = 1) { # 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) # 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", "current") # Calculate current density currentdensity <- ff$current / wearea ff <- cbind(ff, currentdensity = currentdensity) # ### 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, wearea = 1) { # 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) # 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(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 charge densities and differentials charge.df <- It2charge(ff$currentdensity, ff$time) ff <- cbind(ff, timediff = charge.df$timediff, chargedensity = charge$charge, sumchargedensity = charge$sumcharge, dQdt = charge$dQdt) # ### 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 ####################### ################################################## 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, segment = factor(s), cycle = factor(ceiling(s/2)), matrix(scan(zz, what = numeric(), sep = ","), ncol = 3, byrow = T))) close(zz) } names(ff) <- c("sampleid", "segment", "cycle", "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 # 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", "^Scan\\sRate\\s\\(V/s\\)", "^Segment\\s=", "^Sample\\sInterval\\s\\(V\\)", "^Quiet\\sTime\\s\\(sec\\)", "^Sensitivity\\s\\(A/V\\)") names.attr <- c("InitE", "HighE", "LowE", "InitPN", "ScanRate", "Segments", "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) } ################################################## ################### lsv2df ####################### ################################################## lsv2df <- function(datafilename, wearea = 1) { # Function description: # CH Instruments potentiostat records all data using standard SI units, # so all potential values are in volts, currents are in amperes, # charges in Coulombs, time in seconds, etc. # lsvfile <- file(datafilename, "r") chifile <- readLines(lsvfile, n = -1) #read all lines of input file close(lsvfile) # sampleid <- ProvideSampleId(datafilename) # rgxp.number <- "^\\-?\\d\\.\\d+," # regexp that matches a decimal number at the beginning of the line. # Matches numbers with or without a negative sign (hyphen), # followed by one digit before the decimal, a decimal point, # and an arbitrary number of digits after the decimal point, # immediately followed by a comma. # Note that backslashes are escaped. # numrow.idx <- regexpr(rgxp.number, chifile) # Save the match length attribute to another variable, numrow.len <- attr(numrow.idx, "match.length") # then scrap the attribute of the original variable. attr(numrow.idx, "match.length") <- NULL # i <- seq(1, length(numrow.idx) - 1, 1) j <- seq(2, length(numrow.idx), 1) # Start indices of data ranges starts <- which(numrow.idx[i] != 1 & numrow.idx[j] == 1) + 1 # End indices, except for the last ends <- which(numrow.idx[i] == 1 & numrow.idx[j] != 1) # Fix the last index of end indices ends <- c(ends, length(numrow.idx)) # ff <- data.frame(NULL) for (s in 1:length(starts)) { zz <- textConnection(chifile[starts[s]:ends[s]], "r") ff <- rbind(ff, data.frame(sampleid, segment = factor(s), matrix(scan(zz, what = numeric(), sep = ","), ncol = 3, byrow = T))) close(zz) } names(ff) <- c("sampleid", "segment", "potential", "current", "charge") # Calculate current density currentdensity <- ff$current / wearea ff <- cbind(ff[, 1:4], currentdensity = currentdensity, charge = ff[, 5]) # ### Collect attributes of this experiment # These attributes are specific for each kind of experiment, # be careful when adapting to other electrochemical data rgxp.attr <- c("^Init\\sE\\s\\(V\\)", "^Final\\sE\\s\\(V\\)", "^Scan\\sRate\\s\\(V/s\\)", "^Sample\\sInterval\\s\\(V\\)", "^Quiet\\sTime\\s\\(sec\\)", "^Sensitivity\\s\\(A/V\\)") names.attr <- c("InitE", "FinalE", "ScanRate", "SamplingInterval", "QuietTime", "Sensitivity") for (n in 1:length(rgxp.attr)) { attrow.idx <- regexpr(rgxp.attr[n], chifile) attrow.len <- attr(attrow.idx, "match.length") attr(attrow.idx, "match.length") <- NULL attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)], "\\s=\\s")[[1]][2] } # return(ff) }