Atomic Force Microscope Image Analysis

Documentation for package ‘AFM’ version 1.2.1

DESCRIPTION file.

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A C D E F G I O P R S T U V

AFM-package

Atomic Force Microscopy images tools

-- A --

AFM	Atomic Force Microscopy images tools
AFMImage	AFM image class
AFMImage-class	AFM image class
AFMImage3DModelAnalysis	AFM image Power Spectrum Density analysis class
AFMImage3DModelAnalysis-class	AFM image Power Spectrum Density analysis class
AFMImageAnalyser	AFM image analyser class
AFMImageAnalyser-class	AFM image analyser class
AFMImageFractalDimensionMethod	AFM image fractal dimension method class
AFMImageFractalDimensionMethod-class	AFM image fractal dimension method class
AFMImageFractalDimensionsAnalysis	AFM image fractal dimensions analysis class
AFMImageFractalDimensionsAnalysis-class	AFM image fractal dimensions analysis class
AFMImageNetworksAnalysis	AFM image networks analysis class
AFMImageNetworksAnalysis-class	AFM image networks analysis class
AFMImageOfAluminiumInterface	AFM image sample
AFMImageOfNormallyDistributedHeights	AFM image sample
AFMImageOfOnePeak	AFM image sample
AFMImageOfRegularPeaks	AFM image sample
AFMImagePSDAnalysis	AFM image Power Spectrum Density analysis class
AFMImagePSDAnalysis-class	AFM image Power Spectrum Density analysis class
AFMImageVariogramAnalysis	AFM image variogram analysis class
AFMImageVariogramAnalysis-class	AFM image variogram analysis class
AFMImageVariogramModel	AFM Image Variogram Model class
AFMImageVariogramModel-class	AFM Image Variogram Model class
analyse	Analyse an AFMImage

-- C --

calculate3DModel	Calculate the 3D model for 3D printing
calculate3DModel-method	Calculate the 3D model for 3D printing
calculateDirectionalVariograms	Calculate experimental directional semi-variograms
calculateIgraph	Calculate iGraph from AFMImage
calculateNetworks	Calculate networks on the surface
calculateNetworks-method	Calculate networks on the surface
calculateNetworkSkeleton	calculateNetworkSkeleton
calculateOmnidirectionalVariogram	Calculate experimental omnidirectional semi-variogram
canBeRemoved	canBeRemoved
checkIsotropy	Check the isotropy of a sample
checkNormality	Check visualy of the normality of the sample

-- D --

directionalVariograms	AFM image variogram analysis class
directionalVariograms-method	AFM image variogram analysis class
displayIn3D	Display a 3D image of an AFMImage and store it on disk.

-- E --

evaluateVariogramModels	evaluateVariogramModels method to evaluate the basic variogram models
evaluateVariogramModels-method	evaluateVariogramModels method to evaluate the basic variogram models
existsEdge	Does an edge exist ?
exportToSTL	Export an AFM Image as a STL format file.
extractAFMImage	Extract a portion of an AFM image.

-- F --

fractalDimensionMethods	AFM image fractal dimensions analysis class
fractalDimensionMethods-method	AFM image fractal dimensions analysis class

-- G --

generateAFMImageReport	Generate an analysis report from an AFMImageAnalyser object
generateCheckReport	Generate a check report for one AFMImage
generateReport	Generate an analysis report for one AFMImage
generateReportFromNanoscopeImageDirectory	Generate a pdf report for all AFM images in a directory
getAutomaticWidthForVariogramCalculation	calculate a width to be used for experimental variogram calculation
getBresenham2DSegment	get a segment of points thanks to Bresenham line algorithm
getCoordinatesFromVertexId	Get x,y coordinates from vertex id
getDTModelEvaluation	getDTModelEvaluation method
getDTModelEvaluation-method	getDTModelEvaluation method
getDTModelSillRange	getDTModelSillRange method
getDTModelSillRange-method	getDTModelSillRange method
getFractalDimensions	Calculate 2D fractal dimensions and scales of an AFM Image
getListOfDiameters	getListOfDiameters
getNetworkGridLayout	Get getNetworkGridLayout
getNyquistSpatialFrequency	Get the Nyquist spatial frequency
getNyquistSpatialFrequency-method	Get the Nyquist spatial frequency
getPaddedAFMImage	Get a zero padded AFMImage
getRoughnessParameters	Get Roughness parameters
getRoughnessParameters-method	Get Roughness parameters
getSpplotFromAFMImage	Get an AFMImage as a Lattice (trellis) plot
getSurroundingVertexesList	Get surrounding vertices from x,y coordinates
getTopologyAFMImage	Calculate topology image (TBC)
getVertexId	Get vertex id from x,y coordinates
gridIgraphPlot	gridIgraphPlot

-- I --

importFromNanoscope	Import data from nanoscope analysis(tm) tool
initialize-method	AFM image class
initialize-method	Constructor method of AFMImageAnalyser Class.
initialize-method	AFM image fractal dimension method class
initialize-method	AFM image fractal dimensions analysis class
initialize-method	AFM image networks analysis class
initialize-method	AFM image Power Spectrum Density analysis class
initialize-method	AFM image variogram analysis class
initialize-method	AFM Image Variogram Model class
intersections	AFM image Power Spectrum Density analysis class
intersections-method	AFM image Power Spectrum Density analysis class
isAdjacentToBetterVertex	isAdjacentToBetterVertex

-- O --

omnidirectionalVariogram	AFM image variogram analysis class
omnidirectionalVariogram-method	AFM image variogram analysis class

-- P --

performAllPSDCalculation	Perform all the calculation for PSD exploitation
printVariogramModelEvaluations	printVariogramModelEvaluations
psd1d	AFM image Power Spectrum Density analysis class
psd1d-method	AFM image Power Spectrum Density analysis class
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.
PSD1DAgainstFrequency-method	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.
psd1d_breaks	AFM image Power Spectrum Density analysis class
psd1d_breaks-method	AFM image Power Spectrum Density analysis class
psd2d	AFM image Power Spectrum Density analysis class
psd2d-method	AFM image Power Spectrum Density analysis class
PSD2DAgainstFrequency	Calculate the 2D Power Spectral Density
PSD2DAgainstFrequency-method	Calculate the 2D Power Spectral Density
psd2d_maxHighLengthScale	AFM image Power Spectrum Density analysis class
psd2d_maxHighLengthScale-method	AFM image Power Spectrum Density analysis class
psd2d_truncHighLengthScale	AFM image Power Spectrum Density analysis class
psd2d_truncHighLengthScale-method	AFM image Power Spectrum Density analysis class
putAnalysisOnDisk	Export all data from an analysis of an AFM Image as rdata file
putAnalysisOnDisk-method	Export all data from an analysis of an AFM Image as rdata file
putImagesFromAnalysisOnDisk	Put the images from all analysis on disk

-- R --

roughnessAgainstLengthscale	AFM image Power Spectrum Density analysis class
roughnessAgainstLengthscale-method	AFM image Power Spectrum Density analysis class
RoughnessByLengthScale	Calculate the roughness of the sample against length scale
RoughnessByLengthScale-method	Calculate the roughness of the sample against length scale
runAFMApp	Launch the AFM shiny application

-- S --

sampleAFMImage	Get a sample of an AFM image.
saveOnDisk	Save an AFM image on disk.
saveSpplotFromAFMImage	Save on disk an AFMImage as a Lattice (trellis) plot
shiftedPSDuv	Calculate the shifted PSD matrix
shiftFFT2D	Shift the quadrants of the FFT 2D
simplifyAFMImage	simplify an AFM image.

-- T --

totalRMSRoughness

Calculate the total Root Mean Square Roughness (Rrms total)

-- U --

updateProgress	updateProgress
updateProgress-method	updateProgress

-- V --

variogramModels	AFM image variogram analysis class
variogramModels-method	AFM image variogram analysis class