Added the functions chronocm2df(), chronoamp2df(), and amperometry2df().

All of them based on the previous functions. Note: Changed regexp to match
also numbers in scientific notation.

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 #######################
 ##################################################