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AFM (version 1.0.0)

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.

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Version

Install

install.packages('AFM')

Monthly Downloads

79

Version

1.0.0

License

AGPL-3

Maintainer

Mathieu Beauvais

Last Published

October 29th, 2015

Functions in AFM (1.0.0)

getDTModelSillRange

getDTModelSillRange method
saveOnDisk

Save an AFM image on disk.
AFMImageVariogramAnalysis-class

AFM image variogram analysis class
AFMImagePSDAnalysis-class

AFM image Power Spectrum Density analysis class
getFractalDimensions

Calculate 2D fractal dimensions and scales of an AFM Image
PSD2DAgainstFrequency

Calculate the 2D Power Spectral Density
AFM

Atomic Force Microscopy images tools
AFMImageOfOnePeak

AFM image sample
extractAFMImage

Extract a portion of an AFM image.
shiftFFT2D

Shift the quadrants of the FFT 2D
AFMImage-class

AFM image class
evaluateVariogramModels

evaluateVariogramModels method to evaluate the basic variogram models
exportToSTL

Export an AFM Image as a STL format file.
putAnalysisOnDisk

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

Save on disk an AFMImage as a Lattice (trellis) plot
displayIn3D

Display a 3D image of an AFMImage and store it on disk.
AFMImageFractalDimensionMethod-class

AFM image fractal dimension method class
putImagesFromAnalysisOnDisk

Put the images from all analysis on disk
getAutomaticWidthForVariogramCalculation

calculate a width to be used for experimental variogram calculation
generateReport

Generate an analysis report for one AFMImage
calculateOmnidirectionalVariogram

Calculate experimental omnidirectional semi-variogram
checkIsotropy

Check the isotropy of a sample
getPaddedAFMImage

Get a zero padded AFMImage
AFMImageFractalDimensionsAnalysis-class

AFM image fractal dimensions analysis class
generateReportFromNanoscopeImageDirectory

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

AFM image 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.
calculateDirectionalVariograms

Calculate experimental directional semi-variograms
AFMImageOfNormallyDistributedHeights

AFM image sample
RoughnessByLengthScale

Calculate the roughness of the sample against length scale
generateAFMImageReport

Generate an analysis report from an AFMImageAnalyser object
generateCheckReport

Generate a check report for one AFMImage
checkNormality

Check visualy of the normality of the sample
importFromNanoscope

Import data from nanoscope analysis(tm) tool
AFMImageOfRegularPeaks

AFM image sample
getNyquistSpatialFrequency

Get the Nyquist spatial frequency
analyse

Analyse an AFMImage
shiftedPSDuv

Calculate the shifted PSD matrix
AFMImageAnalyser-class

AFM image analyser class
sampleAFMImage

Get a sample of an AFM image.
totalRMSRoughness

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

Get Roughness parameters
initialize,AFMImageAnalyser-method

Constructor method of AFMImageAnalyser Class.
getDTModelEvaluation

getDTModelEvaluation method
AFMImageVariogramModel-class

AFM Image Variogram Model class