PSD1DAgainstFrequency-methods: Calculate the 1D Power Spectral Density; returns a data table...

In AFM: Atomic Force Microscope Image Analysis

Description

Calculate the 1D Power Spectral Density; returns a data table of PSD 1D and PSD 2D values against spatial frequencies.
As mentionned in Sidick2009, this function calculates the PSD against spatial frequencies in 1D from PSD2DAgainstFrequency by using breaks in the log space to sum PSD 2D and frequency values.

Usage

PSD1DAgainstFrequency(AFMImage, AFMImagePSDAnalysis)

## S4 method for signature 'AFMImage'
PSD1DAgainstFrequency(AFMImage, AFMImagePSDAnalysis)

Arguments

AFMImage	an AFMImage to be analysed
AFMImagePSDAnalysis	n AFMImagePSDAnalysis to store the setup and results of PSD analysis

Value

PSD1DAgainstFrequency returns a data table of frequencies and PSD values

• freq: the considered frequency

• PSD: the considered PSD value

• type: PSD-1D

• fullfilename: directory and filename on the disk

Examples

## Not run: 
library(AFM)
library(ggplot2)
library(plyr)
library(scales)
data("AFMImageOfNormallyDistributedHeights")
 newAFMImage<-AFMImageOfNormallyDistributedHeights
newAFMImage@fullfilename<-"C:/Users/one/AFMImageOfNormallyDistributedHeights.txt"
psdAnalysis<-AFMImagePSDAnalysis()
# Create a closure to update progress
psdAnalysis@updateProgress<- function(value = NULL, detail = NULL, message = NULL) {
  if (exists("progressPSD")){
   if (!is.null(message)) {
     progressPSD$set(message = message, value = 0)
   }else{
     progressPSD$set(value = value, detail = detail)
   }
  }
}
psdAnalysis@psd1d_breaks<-2^3
psdAnalysis@psd2d_truncHighLengthScale<-TRUE
psdAnalysis<-performAllPSDCalculation(AFMImagePSDAnalysis= psdAnalysis, AFMImage= newAFMImage)
datap<-psdAnalysis@psd1d
p <- ggplot(data=datap)
p <- p + geom_point(aes(freq, PSD, color=type),data=datap[datap$type %in% c("PSD-2D")])
p <- p + geom_line(aes(freq, PSD, color=type),data=datap[datap$type %in% c("PSD-1D")],size=1.1)
p <- p + scale_x_log10()
p <- p + scale_y_log10()
p <- p + ylab("PSD (nm^4)")
p <- p + xlab("Frequency (nm^-1)")
p

## End(Not run)

Example output

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 

AFM documentation built on Oct. 23, 2020, 5:23 p.m.