AFMImageVariogramAnalyser-calculateOmnidirectionalVariogram: Calculate experimental omnidirectional semi-variogram

In AFM: Atomic Force Microscope Image Analysis

Description

calculateOmnidirectionalVariogram returns the semivariance calculated for all the directions calculate the experimental omnidirectional variogram of an AFMImage with the variogram function of the gstat package. The experimental semi-variogram is used to fit (find the best sill and range) the theoretical variogram models. With 512*512 images, it takes several minutes to calculate.

Usage

calculateOmnidirectionalVariogram(AFMImageVariogramAnalysis, AFMImage)

Arguments

AFMImageVariogramAnalysis	an AFMImageVariogramAnalysis to manage and store the result of variogram analysis
AFMImage	an AFMImage from Atomic Force Microscopy

Value

the semivariance calculated in all the directions

Author(s)

M.Beauvais

Examples

## Not run: 
library(AFM)
library(ggplot2)

data(AFMImageOfRegularPeaks)
variogramAnalysis<-AFMImageVariogramAnalysis(sampleFitPercentage=3.43/100)
avario<-AFM::calculateOmnidirectionalVariogram(AFMImageVariogramAnalysis= variogramAnalysis, 
                                               AFMImage= AFMImageOfRegularPeaks)
dist<-gamma<-NULL
p <- ggplot(avario, aes(x=dist, y=gamma))
p <- p + geom_point()
p <- p + geom_line()
p <- p + ylab("semivariance")
p <- p + xlab("distance (nm)")
p <- p + ggtitle("Experimental semivariogram")
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 
[1] "using automatic width of 1"
[1] "calculating omnidirectional variogram using width of 1 ..."

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