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AFM (version 1.1.0)

Atomic Force Microscope Image Analysis

Description

Provides Atomic Force Microscope images analysis such as Power Spectrum Density, roughness against lengthscale, variogram and variance, fractal dimension and scale. The AFM images can be exported to STL format for 3D printing.

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Version

Install

install.packages('AFM')

Monthly Downloads

79

Version

1.1.0

License

AGPL-3

Maintainer

Mathieu Beauvais

Last Published

December 1st, 2015

Functions in AFM (1.1.0)

getDTModelEvaluation

getDTModelEvaluation method
AFMImageVariogramAnalysis-class

AFM image variogram analysis class
sampleAFMImage

Get a sample of an AFM image.
AFM

Atomic Force Microscopy images tools
analyse

Analyse an AFMImage
evaluateVariogramModels

evaluateVariogramModels method to evaluate the basic variogram models
getFractalDimensions

Calculate 2D fractal dimensions and scales of an AFM Image
saveOnDisk

Save an AFM image on disk.
getAutomaticWidthForVariogramCalculation

calculate a width to be used for experimental variogram calculation
AFMImageAnalyser-class

AFM image analyser class
generateAFMImageReport

Generate an analysis report from an AFMImageAnalyser object
putAnalysisOnDisk

Export all data from an analysis of an AFM Image as rdata file
checkNormality

Check visualy of the normality of the sample
PSD1DAgainstFrequency

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.
PSD2DAgainstFrequency

Calculate the 2D Power Spectral Density
AFMImageOfOnePeak

AFM image sample
extractAFMImage

Extract a portion of an AFM image.
initialize,AFMImageAnalyser-method

Constructor method of AFMImageAnalyser Class.
AFMImage-class

AFM image class
AFMImageFractalDimensionMethod-class

AFM image fractal dimension method class
calculateDirectionalVariograms

Calculate experimental directional semi-variograms
putImagesFromAnalysisOnDisk

Put the images from all analysis on disk
AFMImageVariogramModel-class

AFM Image Variogram Model class
calculateOmnidirectionalVariogram

Calculate experimental omnidirectional semi-variogram
exportToSTL

Export an AFM Image as a STL format file.
updateProgress

updateProgress
saveSpplotFromAFMImage

Save on disk an AFMImage as a Lattice (trellis) plot
shiftedPSDuv

Calculate the shifted PSD matrix
AFMImagePSDAnalysis-class

AFM image Power Spectrum Density analysis class
getNyquistSpatialFrequency

Get the Nyquist spatial frequency
generateReportFromNanoscopeImageDirectory

Generate a pdf report for all AFM images in a directory
getDTModelSillRange

getDTModelSillRange method
checkIsotropy

Check the isotropy of a sample
shiftFFT2D

Shift the quadrants of the FFT 2D
printVariogramModelEvaluations

printVariogramModelEvaluations
generateCheckReport

Generate a check report for one AFMImage
AFMImageOfRegularPeaks

AFM image sample
AFMImageFractalDimensionsAnalysis-class

AFM image fractal dimensions analysis class
totalRMSRoughness

Calculate the total Root Mean Square Roughness (Rrms total)
importFromNanoscope

Import data from nanoscope analysis(tm) tool
generateReport

Generate an analysis report for one AFMImage
AFMImageOfAluminiumInterface

AFM image sample
displayIn3D

Display a 3D image of an AFMImage and store it on disk.
getRoughnessParameters

Get Roughness parameters
performAllPSDCalculation

Perform all the calculation for PSD exploitation
getPaddedAFMImage

Get a zero padded AFMImage
getSpplotFromAFMImage

Get an AFMImage as a Lattice (trellis) plot
RoughnessByLengthScale

Calculate the roughness of the sample against length scale
AFMImageOfNormallyDistributedHeights

AFM image sample