AFM (version 1.2.0)

shiftedPSDuv: Calculate the shifted PSD matrix

Description

shiftedPSDuv returns the Power Spectral Density matrix in the frequency space from shifted FFT 2D

Usage

shiftedPSDuv(AFMImage)

Arguments

AFMImage

an AFMImage from Atomic Force Microscopy

Value

• (1/NM^2) * abs(shiftedFFT2Ddata)^2) with N the number of lines of the sample and M the number of samples per line of the sample

Examples

library(AFM)
library(ggplot2)

data(AFMImageOfRegularPeaks)
AFMImage<-AFMImageOfRegularPeaks
nMheightsData= matrix(AFMImage@data$h, nrow=AFMImage@samplesperline)
shiftedPSDuv<-shiftedPSDuv(AFMImage)
a=AFMImage@scansize
b=AFMImage@scansize

M=AFMImage@sampsline
N=AFMImage@lines
NM=N*M # pixels^2
MN = M*N 
A=a*b
ab=a*b

dx=a/M
dy=b/N

um = seq( (1-(M+1)/2)/(M*dx), (M-(M+1)/2)/(M*dx), by=1/(M*dx))
vn = seq( (1-(N+1)/2)/(N*dy), (N-(N+1)/2)/(N*dy), by=1/(N*dy))
x = rep(um, times = AFMImage@lines)
y = rep(vn, each = AFMImage@sampsline)
z = as.vector(shiftedPSDuv)

data<-data.frame(x=x, y=y, z=z)

p5 <- qplot(x, y, data=data, colour=log10(z))
p5 <- p5 + scale_colour_gradientn(colours = rainbow(7))
p5 <- p5 + ylab("v")
p5 <- p5 + xlab("u")
title<-paste("shifted PSD of", basename(AFMImage@fullfilename))
p5 <- p5 + ggtitle(title)
# Hide all the horizontal gridlines
p5 <- p5 + theme(panel.grid.minor.x=element_blank(), panel.grid.major.x=element_blank())
# Hide all the vertical gridlines
p5 <- p5 + theme(panel.grid.minor.y=element_blank(), panel.grid.major.y=element_blank())
p5 <- p5 + theme(panel.background = element_rect(fill = 'white', colour = 'black'))
p5