filnam="SD04SmExuLesionGrid.csv"
ZZ<- read.csv(filnam, skip=25)
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_3_uV
Caz<-AvggradCauV
Caz2<-gradCa_3_uV

quartz(width=18, height=6)
plot(c(min(Min_From),max(Min_From)), c(min(Y_microns),max(Y_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()
quartz(width=18, height=6)
plot(c(min(Min_From),max(Min_From)), c(-200,500),     
     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()
Nrows<-33
Ncols<-25
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
for (j in 1:Ncols) { 
		         Hzm[Nrows:1,j]<-Hzm[,j]
		         Hzm2[Nrows:1,j]<-Hzm2[,j]
		         Cazm[Nrows:1,j]<-Cazm[,j]
		         Cazm2[Nrows:1,j]<-Cazm2[,j]
		         }
		         
for (i in seq(1,Nrows,2)) {
              Hzm[i,Ncols:1]<- Hzm[i,]
              Hzm2[i,Ncols:1]<- Hzm2[i,]
              Cazm[i,Ncols:1]<- Cazm[i,]
              Cazm2[i,Ncols:1]<- Cazm2[i,]
              }
for (i in seq(1,Ncols,1)) {
              Hzm[Nrows:1,i]<- Hzm[,i]
              Hzm2[Nrows:1,i]<- Hzm2[,i]
              Cazm[Nrows:1,i]<- Cazm[,i]
              Cazm2[Nrows: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)