You cannot select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.

503 lines
19 KiB
R

# 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, charge.df)
#
### 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 = s, cycle = as.integer(ceiling(s/2)),
matrix(scan(zz, what = numeric(), sep = ","),
ncol = 3, byrow = T)))
close(zz)
}
# Column names after initial assignment
names(ff) <- c("sampleid", "segment", "cycle", "potential", "current", "charge")
# Calculate current density
currentdensity <- ff$current / wearea
ff <- cbind(ff[, 1:5], currentdensity = currentdensity, charge = ff[, 6])
## Collect attributes of this experiment
# InitE (volt)
position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
ff$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) {
# 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)
}