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AFM (version 1.2.0)

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

1.2.0

License

AGPL-3

Maintainer

Mathieu Beauvais

Last Published

February 26th, 2016

Functions in AFM (1.2.0)

AFMImageFractalDimensionsAnalysis-class

AFM image fractal dimensions analysis class
getVertexId

Get vertex id from x,y coordinates
saveSpplotFromAFMImage

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

getListOfDiameters
putAnalysisOnDisk

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

evaluateVariogramModels method to evaluate the basic variogram models
AFMImage3DModelAnalysis-class

AFM image Power Spectrum Density analysis class
updateProgress

updateProgress
extractAFMImage

Extract a portion of an AFM image.
getCoordinatesFromVertexId

Get x,y coordinates from vertex id
generateCheckReport

Generate a check report for one AFMImage
AFMImageOfRegularPeaks

AFM image sample
checkNormality

Check visualy of the normality of the sample
importFromNanoscope

Import data from nanoscope analysis(tm) tool
calculateNetworkSkeleton

calculateNetworkSkeleton
generateReport

Generate an analysis report for one AFMImage
AFMImagePSDAnalysis-class

AFM image Power Spectrum Density analysis class
calculateNetworks

Calculate networks on the surface
shiftedPSDuv

Calculate the shifted PSD matrix
exportToSTL

Export an AFM Image as a STL format file.
getTopologyAFMImage

Calculate topology image (TBC)
getNetworkGridLayout

Get getNetworkGridLayout
AFMImage-class

AFM image class
AFM

Atomic Force Microscopy images tools
PSD2DAgainstFrequency

Calculate the 2D Power Spectral Density
isAdjacentToBetterVertex

isAdjacentToBetterVertex
AFMImageFractalDimensionMethod-class

AFM image fractal dimension method class
AFMImageAnalyser-class

AFM image analyser class
simplifyAFMImage

simplify an AFM image.
getSurroundingVertexesList

Get surrounding vertices from x,y coordinates
AFMImageOfNormallyDistributedHeights

AFM image sample
calculateOmnidirectionalVariogram

Calculate experimental omnidirectional semi-variogram
checkIsotropy

Check the isotropy of a sample
getAutomaticWidthForVariogramCalculation

calculate a width to be used for experimental variogram calculation
getDTModelEvaluation

getDTModelEvaluation method
saveOnDisk

Save an AFM image on disk.
runAFMApp

Launch the AFM shiny application
generateAFMImageReport

Generate an analysis report from an AFMImageAnalyser object
getFractalDimensions

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

Get an AFMImage as a Lattice (trellis) plot
calculateDirectionalVariograms

Calculate experimental directional semi-variograms
displayIn3D

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

AFM Image Variogram Model class
AFMImageOfAluminiumInterface

AFM image sample
initialize,AFMImageAnalyser-method

Constructor method of AFMImageAnalyser Class.
gridIgraphPlot

gridIgraphPlot
getDTModelSillRange

getDTModelSillRange method
RoughnessByLengthScale

Calculate the roughness of the sample against length scale
generateReportFromNanoscopeImageDirectory

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

Calculate iGraph from AFMImage
calculate3DModel

Calculate the 3D model for 3D printing
shiftFFT2D

Shift the quadrants of the FFT 2D
printVariogramModelEvaluations

printVariogramModelEvaluations
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.
existsEdge

Does an edge exist ?
AFMImageVariogramAnalysis-class

AFM image variogram analysis class
totalRMSRoughness

Calculate the total Root Mean Square Roughness (Rrms total)
AFMImageNetworksAnalysis-class

AFM image networks analysis class
getPaddedAFMImage

Get a zero padded AFMImage
AFMImageOfOnePeak

AFM image sample
sampleAFMImage

Get a sample of an AFM image.
getNyquistSpatialFrequency

Get the Nyquist spatial frequency
canBeRemoved

canBeRemoved
putImagesFromAnalysisOnDisk

Put the images from all analysis on disk
performAllPSDCalculation

Perform all the calculation for PSD exploitation
getRoughnessParameters

Get Roughness parameters
analyse

Analyse an AFMImage