From 2790047c3a029f487b907db6ecd3d22f23f81293 Mon Sep 17 00:00:00 2001
From: Taha Ahmed <taha@mkem150>
Date: Fri, 18 Mar 2011 17:44:20 +0100
Subject: [PATCH] Major update to cv2df(). Removed df attributes, built-into df
 instead.

Be advised: This change will break all old reports that used the cv2df() function.
Experimental information (potential limits, scanspeeds, etc.) are now added to the
return dataframe as columns instead of attributes.
With this information built-in to the dataframe, analysis is simplified using melt
and cast and other grouping functions.
---
 CHI.R | 69 +++++++++++++++++++++++++++++++++--------------------------
 1 file changed, 39 insertions(+), 30 deletions(-)

diff --git a/CHI.R b/CHI.R
index 82a187f..9fe3e6e 100644
--- a/CHI.R
+++ b/CHI.R
@@ -369,44 +369,53 @@ cv2df <- function(datafilename, wearea = 1) {
    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)),
+               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$current / wearea
    ff <- cbind(ff[, 1:5], currentdensity = currentdensity, charge = ff[, 6])
-   #
-   ### Collect attributes of this experiment
-   # These attributes are specific for each kind of experiment,
-   # be careful when adapting to other electrochemical data
-   rgxp.attr <- c("^Init\\sE\\s\\(V\\)",
-                  "^High\\sE\\s\\(V\\)",
-                  "^Low\\sE\\s\\(V\\)",
-                  "^Init\\sP/N",
-                  "^Scan\\sRate\\s\\(V/s\\)",
-                  "^Segment\\s=",
-                  "^Sample\\sInterval\\s\\(V\\)",
-                  "^Quiet\\sTime\\s\\(sec\\)",
-                  "^Sensitivity\\s\\(A/V\\)")
-   names.attr <- c("InitE",
-                   "HighE",
-                   "LowE",
-                   "InitPN",
-                   "ScanRate",
-                   "Segments",
-                   "SamplingInterval",
-                   "QuietTime",
-                   "Sensitivity")
-   for (n in 1:length(rgxp.attr)) {
-      attrow.idx <- regexpr(rgxp.attr[n], chifile)
-      attrow.len <- attr(attrow.idx, "match.length")
-      attr(attrow.idx, "match.length") <- NULL
-      attr(ff, names.attr[n]) <- strsplit(chifile[which(attrow.idx == 1)],
-         "\\s=\\s")[[1]][2]
-   }
+   ## Collect attributes of this experiment
+   # InitE (volt)
+   position.InitE <- regexpr("^Init\\sE\\s\\(V\\)", chifile)
+   InitE <- as.numeric(strsplit(chifile[which(position.InitE == 1)], "\\s=\\s")[[1]][2])
+   ff$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.Segment <- regexpr("^Segment\\s=", chifile)
+   Segment <- as.numeric(strsplit(chifile[which(position.Segment == 1)], "\\s=\\s")[[1]][2])
+   ff$Segment <- Segment
+   # SampleInterval (volt)
+   position.SampleInterval <- regexpr("^Sample\\sInterval\\s\\(V\\)", chifile)
+   SampleInterval <- as.numeric(strsplit(chifile[which(position.SampleInterval == 1)], "\\s=\\s")[[1]][2])
+   ff$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)
 }