filnam="Jun20CalciteC.csv"
ZZ<- read.csv(filnam, skip=15)
attach(ZZ)
print(names(ZZ))
Min_From<-ZZ[,1]
X_microns<-ZZ[,2]
Y_microns<-ZZ[,3]
Z_microns<-ZZ[,4]

Hz<-AvggradHuV
Hz2<-gradH_2_uV
Caz<-AvggradCauV
Caz2<-gradCa_2_uV

quartz(width=18, height=6)
plot(c(min(Min_From),max(Min_From)), c(min(X_microns),max(X_microns)), 
     typ='n', 
     main=paste(filnam,"Position, X=red, Y=green, Z=blue"),
     xlab="time (min)",
     ylab="position um")
points(Min_From, Z_microns, col='blue', pch=20)
points(Min_From, Y_microns, col='green', pch=20)
points(Min_From, X_microns, col='red', pch=20)

browser()

Caz[147]<-Caz2[147]
Caz[148]<-(Caz[147]+Caz[149])/2
Caz2[148]<-(Caz2[147]+Caz2[149])/2
Caz[47]<-(Caz[46]+Caz[48])/2
Caz2[47]<-(Caz2[46]+Caz2[48])/2
Nrows<-17
Ncols<-9
quartz(width=18, height=6)
plot(c(min(Min_From),max(Min_From)), c(-120,700),     
     typ='n', 
     col='blue',
     main=paste(filnam,"uvDiff, Hz=red, Hz2=green, Caz=blue, Caz2=purple"),
     xlab="time (min)",
     ylab="uVolts")                                       ##c(min(Hz),max(Caz)
points(Min_From, Hz,  col='red' , pch=20, typ='b')   
points(Min_From, Hz2,  col='green' , pch=20, typ='b')   
points(Min_From, Caz,  col='blue' , pch=20, typ='b')   
points(Min_From, Caz2,  col='purple' , pch=20, typ='b')
for (i in seq(Nrows, Nrows*Ncols, Nrows)){ lines(c(Min_From[i], Min_From[i]),c(-120,700))}

browser()
quartz(width=18, height=6)
## AvggradHuV,AvggradCauV 

plot(c(min(Min_From),max(Min_From)), c(min(AvggradHuV),max(AvggradHuV)), 
     typ='n', 
     col='blue',
     main=paste(filnam,"uvDiff, HzAvg=red, CazAvg=green, Hz3=blue, Caz3=purple"),
     xlab="time (min)",
     ylab="uVolts")
points(Min_From, AvggradHuV,  col='red' , pch=20, typ='b',cex=1)   
points(Min_From, AvggradCauV,  col='green' , pch=20, typ='b',cex=1)   
points(Min_From, gradH_2_uV,  col='blue' , pch=20, typ='l',cex=1)   
points(Min_From, gradCa_2_uV,  col='purple' , pch=20, typ='l',cex=1)   

browser()
Hzm<-Hzm2<-Cazm<-Cazm2<- matrix(0,Nrows,Ncols)

for (i in 1:Nrows) { 
	for (j in 1:Ncols) { 
		         index<- (i-1)*Ncols + j
		         Hzm[i,j]<-Hz[index]
		         Hzm2[i,j]<-Hz2[index]
		         Cazm[i,j]<-Caz[index]
		         Cazm2[i,j]<-Caz2[index]
		         } }
		         
#reverse long axis
		         Hzm[Nrows:1,]<-Hzm[,]
		         Hzm2[Nrows:1,]<-Hzm2[,]
		         Cazm[Nrows:1,]<-Cazm[,]
		         Cazm2[Nrows:1,]<-Cazm2[,]
		         
altseq<- seq(2,Nrows,2)
              Hzm[altseq,Ncols:1]<- Hzm[altseq,]
              Hzm2[altseq,Ncols:1]<- Hzm2[altseq,]
              Cazm[altseq,Ncols:1]<- Cazm[altseq,]
              Cazm2[altseq,Ncols:1]<- Cazm2[altseq,]
      

              Hzm[Nrows:1, ]<- Hzm
              Hzm2[Nrows:1, ]<- Hzm2
              Cazm[Nrows:1, ]<- Cazm
              Cazm2[Nrows:1, ]<- Cazm2
        
              
quartz(width=14, height=7)
layout(matrix(c(1,2,3,4), 1, 4, byrow = TRUE))              
contour(t(Hzm), main= paste(filnam,'AvgHzm'), col=rainbow(13)[3:13], lwd=2, labcex = 0.8)            #heat.colors was col=rainbow(10)
#quartz(width=3.5, height=7)
contour(t(Hzm2), main=paste(filnam,'Hzm2'), col=rainbow(13)[3:13], lwd=2, labcex = 0.8)            
#quartz(width=3.5, height=7)
contour(t(Cazm), main=paste(filnam,'AvgCazm'), col=rainbow(13)[3:13], lwd=2, labcex = 0.8) 
#quartz(width=3.5, height=7)
contour(t(Cazm2), main=paste(filnam,'Cazm2'), col=rainbow(13)[3:13], lwd=2, labcex = 0.8)             
              
detach(ZZ)