#Data Electron Microprobe from Nov3, 2005 (1103)
h1<-w1<-9
h2<-0.5; w2<-6

quartz(wi=10.8, he=7.9)
opar<-par(mar=c(0,0,0,0)+0.1, ann=FALSE)
filnam<-"BL9LL_4"
xy<-read.table(paste(filnam,"_bse.size",sep=''), skip=2)
attach(xy)
xi<-V1; yi<-V2
detach(xy)
xy<-read.table(paste(filnam,"_bse.pgm",sep=''), skip=4)
attach(xy)
XX<-V1;
detach(xy)
XX<-matrix(XX,xi,yi)
XX[1025:1080,1:790]<-XX[1025:1080,790:1]
XX[1:1024,790:770]<-XX[1:1024,770:790]
image(XX, col=gray(1:255/255),xlab='', ylab='')

quartz(wi=w1, he=h1)
opar<-par(mar=c(0,0,0,0)+0.1, ann=FALSE)
xy<-read.table(paste(filnam,"_2_Ca.txt",sep=''), skip=33)
attach(xy)
YY<-t(as.matrix(xy))
# print(names(xy))
image(YY, col=gray(1:255/255),xlab='', ylab='')
quartz(wi=w2, he=h2)
# lx = left x; ly = lower y
lx<-10; ux<-490; ly<-70; uy<-110
opar<-par(mar=c(0,0,0,0)+0.1, ann=FALSE)
image(YY[lx:ux,ly:uy], col=gray(1:255/255),xlab='', ylab='')
yy<-YY[lx:ux,ly:uy]
detach(xy)



quartz(wi=w1, he=h1)
npar<-par(mar=c(0,0,0,0)+0.1, ann=FALSE)
xy<-read.table(paste(filnam,"_3_P.txt",sep=''), skip=33)
attach(xy)
ZZ<-t(as.matrix(xy))
# print(names(xy))
image(ZZ, col=gray(1:255/255),xlab='', ylab='')
quartz(wi=w2, he=h2)
opar<-par(mar=c(0,0,0,0)+0.1, ann=FALSE)
image(ZZ[lx:ux,ly:uy], col=gray(1:255/255),xlab='', ylab='')
zz<-ZZ[lx:ux,ly:uy]
detach(xy)

quartz(wi=w1, he=h1)
npar<-par(mar=c(0,0,0,0)+0.1, ann=FALSE)
plot(zz[1:3000], yy[1:3000], main=paste(filnam,"_2_Ca.txt",sep=''))

# Narrow down Na & K to surface examples
cat("Na and K is interesting in this example! \n")
# lx = left x; ly = lower y
lx<-10; ux<-490; ly<-385; uy<-425

quartz(wi=w1, he=h1)
opar<-par(mar=c(0,0,0,0)+0.1, ann=FALSE)
xy<-read.table(paste(filnam,"_1_Na.txt",sep=''), skip=33)
attach(xy)
WW<-t(as.matrix(xy))
# print(names(xy))
image(WW, col=gray(1:255/255),xlab='', ylab='')
quartz(wi=w2, he=h2)
opar<-par(mar=c(0,0,0,0)+0.1, ann=FALSE)
image(WW[lx:ux,ly:uy], col=gray(1:255/255),xlab='', ylab='')
ww<-WW[lx:ux,ly:uy]
detach(xy)

quartz(wi=w1, he=h1)
opar<-par(mar=c(0,0,0,0)+0.1, ann=FALSE)
xy<-read.table(paste(filnam,"_4_K.txt",sep=''), skip=33)
attach(xy)
UU<-t(as.matrix(xy))
# print(names(xy))
image(UU, col=gray(1:255/255),xlab='', ylab='')
quartz(wi=w2, he=h2)
opar<-par(mar=c(0,0,0,0)+0.1, ann=FALSE)
image(UU[lx:ux,ly:uy], col=gray(1:255/255),xlab='', ylab='')
uu<-UU[lx:ux,ly:uy]
detach(xy)

quartz(wi=w1, he=h1)
dens<-matrix(0,100,100)
for (i in 1:2500) {dens[uu[i]+1,ww[i]+1]<- dens[uu[i]+1,ww[i]+1] +1}
contour(dens^0.25, main=paste(filnam,"surface Na vs K",sep=' '))
mtext(paste("Focus:", "(lx,ux)=(10,490); (ly,uy)=(385,425)"), line= -2)

#lx<-25; ux<-275; ly<-300; uy<-350 surface area


# Control area:
lx<-10; ux<-490; ly<-250; uy<-290
w3<-w2; h3<- h2
quartz(wi=w3, he=h3)
opar<-par(mar=c(0,0,0,0)+0.1, ann=FALSE)
image(WW[lx:ux,ly:uy], col=gray(1:255/255),xlab='', ylab='')
ww<-WW[lx:ux,ly:uy]
quartz(wi=w3, he=h3)
opar<-par(mar=c(0,0,0,0)+0.1, ann=FALSE)
image(UU[lx:ux,ly:uy], col=gray(1:255/255),xlab='', ylab='')
uu<-UU[lx:ux,ly:uy]

quartz(wi=w1, he=h1)
dens<-matrix(0,100,100)
for (i in 1:2500) {dens[uu[i]+1,ww[i]+1]<- dens[uu[i]+1,ww[i]+1] +1}
contour(dens^0.25, main=paste(filnam,"Control (interior) Na vs K",sep=' '))
mtext(paste("Control:", "(lx,ux)=(10,490); (ly,uy)=(250,290)"), line= -2)


par(opar)