filnam<-"jgk080730_clamshell035scansWed.csv"
obslevels<-5
XX<-readLines(filnam)
gstart<-grep("Change Buffer.", XX)
cat(length(gstart),"starts identified\n")
nstarts<-length(gstart)
print(Xstarts<-XX[gstart])
writeLines(Xstarts, "Xstarts.csv")
SS<-read.csv("Xstarts.csv", header=FALSE)
pHs<-SS[,4]
buffchange<-SS[,1]
gstart<-c(gstart,length(XX))
for(j in 1:nstarts){
	
istart<-gstart[j]
iend<- gstart[j+1]
writeLines(XX[istart:iend],"junk.txt")
YY<-readLines("junk.txt")
idata<- grep("pH Ca ScanGradient", YY)
YY<-YY[idata]
iheaders<-grep("Hrs_From", YY)
nheaders<-length(iheaders)
ZZ<-rep(" ",1+obslevels*nheaders)
ZZ[1]<- YY[iheaders[1]]
index<-1
for(i in 1:nheaders) {ZZ[index+1:obslevels]<- YY[iheaders[i]+1:obslevels]
	                  index<-index+obslevels
	                  }
writeLines(ZZ,"junk.csv")
WW<-read.csv("junk.csv")
attach(WW)
ni<-length(X_microns)
minHr<-min(Hrs_From)
maxHr<-max(Hrs_From)
minX<-min(X_microns)
maxX<-max(X_microns)
minYloc<-min(Y_microns)
maxYloc<-max(Y_microns)
minZloc<-min(Z_microns)
maxZloc<-max(Z_microns)
leng<- length(X_microns)
medCauV<-medHuV<- rep(0,leng)
for (i in 1:leng) {medHuV[i]<- median(c(gradH_8_uV[i],gradH_9_uV[i],gradH_10_uV[i]))
	                medCauV[i]<- median(c(gradCa_8_uV[i],gradCa_9_uV[i],gradCa_10_uV[i]))}

quartz(width=15, height=7)
layout(matrix(1:2, 1, 2, byrow = TRUE))
par(mar=c(5, 5, 4, 4.5) + 0.1)


buf0<- buffchange[j]
HmV<- (NagelSamp0H_10_mV+NagelSampZH_10_mV)/2
minY<- floor(min(HmV));  maxY<- ceiling(max(HmV))
CamV<- (NagelRead0Ca_10_mV+NagelReadZCa_10_mV)/2
plot(60*(c(minHr, maxHr)-buf0),c(minY, maxY),typ='n',
main=paste(filnam,"mV vs Time at pH",pHs[j]), ylab='[H] mV', xlab='minutes after buffer change', cex.lab=2, cex.axis=1.5)
lines(60*(Hrs_From[Z_microns == Z_microns[1]]-buf0),HmV[Z_microns == Z_microns[1]], typ='b', col='red', cex=2, lwd=4, lty=2)
lines(60*(Hrs_From[Z_microns == Z_microns[2]]-buf0),HmV[Z_microns == Z_microns[2]], typ='b', col='green', cex=2, lwd=3, lty=3)
lines(60*(Hrs_From[Z_microns == Z_microns[3]]-buf0),HmV[Z_microns == Z_microns[3]], typ='b', col='blue', cex=2, lwd=2, lty=4)
lines(60*(Hrs_From[Z_microns == Z_microns[4]]-buf0),HmV[Z_microns == Z_microns[4]], typ='b', col='orange', cex=2, lwd=2, lty=5)
lines(60*(Hrs_From[Z_microns == Z_microns[5]]-buf0),HmV[Z_microns == Z_microns[5]], typ='b', col='purple', cex=2, lwd=2, lty=6)

# par(new=TRUE, ann=FALSE)

minY<- floor(min(CamV));  maxY<- ceiling(max(CamV))
plot(60*(c(minHr, maxHr)-buf0),c(minY, maxY),typ='n', yaxt='n', xaxt='n')
lines(60*(Hrs_From[Z_microns == Z_microns[1]]-buf0),CamV[Z_microns == Z_microns[1]], typ='b', col='black', cex=2, lwd=4, lty=2)
lines(60*(Hrs_From[Z_microns == Z_microns[2]]-buf0),CamV[Z_microns == Z_microns[2]], typ='b', col='brown', cex=2, lwd=3, lty=3)
lines(60*(Hrs_From[Z_microns == Z_microns[3]]-buf0),CamV[Z_microns == Z_microns[3]], typ='b', col='grey', cex=2, lwd=2, lty=4)
lines(60*(Hrs_From[Z_microns == Z_microns[4]]-buf0),CamV[Z_microns == Z_microns[4]], typ='b', col='purple', cex=2, lwd=1, lty=5)
lines(60*(Hrs_From[Z_microns == Z_microns[5]]-buf0),CamV[Z_microns == Z_microns[5]], typ='b', col='purple', cex=2, lwd=1, lty=6)
axis(side=4, cex.axis=1.5)
mtext("[Ca] mV", side=4, line=2.5, cex=1.25)

par(ann=TRUE)
detach(WW)
browser()
              }
rm(list=ls())