filnam="Wolfram0612_006.csv"
ZZ<- read.csv(filnam, skip=13)
attach(ZZ)
print(names(ZZ))
Min_From<-ZZ[,1]
X_microns<-ZZ[,2]
Y_microns<-ZZ[,3]
Z_microns<-ZZ[,4]

quartz(width=18, height=6)
plot(c(min(Min_From),max(Min_From)), c(min(Y_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)

Hz<-1000*(ZZ[,11]- ZZ[,13]);Hz[30]<-(Hz[29]+Hz[32])/2;Hz[31]<-(Hz[29]+Hz[32])/2;  Hz[322]<-(Hz[321]+Hz[324])/2;Hz[323]<-(Hz[321]+Hz[324])/2
Caz<-1000*(ZZ[,12]-ZZ[,14]);Caz[30]<-(Caz[29]+Caz[32])/2;Caz[31]<-(Caz[29]+Caz[32])/2;Caz[322]<-(Caz[321]+Caz[324])/2;Caz[323]<- (Caz[321]+Caz[324])/2


#2nd rep
Hz2<-1000*(ZZ[,15]- ZZ[,17]) ; Hz2[30]<- (Hz2[29]+Hz2[32])/2;  Hz2[31]<- (Hz2[29]+Hz2[32])/2;  Hz2[322]<-(Hz2[321]+Hz2[324])/2;Hz2[323]<-(Hz2[321]+Hz2[324])/2
Caz2<-1000*(ZZ[,16]- ZZ[,18]) ; Caz2[30]<- (Caz2[29]+Caz2[32])/2;  Caz2[31]<- (Caz2[29]+Caz2[32])/2;Caz2[322]<-(Caz2[321]+Caz2[324])/2;Caz2[323]<- (Caz2[321]+Caz2[324])/2


browser()
quartz(width=18, height=6)
plot(c(min(Min_From),max(Min_From)), c(-1400,500),     
     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')
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, Hz=red, Hz2=green, Caz=blue, Caz2=purple"),
     xlab="time (min)",
     ylab="uVolts")
points(Min_From, AvggradHuV,  col='red' , pch=20, typ='b',cex=2)   
points(Min_From, AvggradCauV,  col='red' , pch=20, typ='b',cex=2)   

browser()

Hzm<-Hzm2<-Cazm<-Cazm2<- matrix(0,25,21)

for (i in 1:25) { 
	for (j in 1:21) { 
		         index<- (i-1)*21 + j
		         Hzm[i,j]<-Hz[index]
		         Hzm2[i,j]<-Hz2[index]
		         Cazm[i,j]<-Caz[index]
		         Cazm2[i,j]<-Caz2[index]
		         } }
		         
#reverse long axis
for (j in 1:21) { 
		         Hzm[25:1,j]<-Hzm[,j]
		         Hzm2[25:1,j]<-Hzm2[,j]
		         Cazm[25:1,j]<-Cazm[,j]
		         Cazm2[25:1,j]<-Cazm2[,j]
		         }
		         
for (i in seq(1,25,2)) {
              Hzm[i,21:1]<- Hzm[i,]
              Hzm2[i,21:1]<- Hzm2[i,]
              Cazm[i,21:1]<- Cazm[i,]
              Cazm2[i,21:1]<- Cazm2[i,]
              }
for (i in seq(1,21,1)) {
              Hzm[25:1,i]<- Hzm[,i]
              Hzm2[25:1,i]<- Hzm2[,i]
              Cazm[25:1,i]<- Cazm[,i]
              Cazm2[25:1,i]<- Cazm2[,i]
              }
              
              
quartz(width=7, height=7)
contour(t(Hzm), main='Hzm', col=rainbow(13)[3:13], lwd=3, labcex = 0.8)            #heat.colors was col=rainbow(10)
quartz(width=7, height=7)
contour(t(Hzm2), main='Hzm2', col=rainbow(13)[3:13], lwd=3, labcex = 0.8)            
quartz(width=7, height=7)
contour(t(Cazm), main='Cazm', col=rainbow(13)[3:13], lwd=3, labcex = 0.8) 
quartz(width=7, height=7)
contour(t(Cazm2), main='Cazm2', col=rainbow(13)[3:13], lwd=3, labcex = 0.8)             
              
detach(ZZ)