Atomic Force Microscope Image Analysis

Documentation for package ‘AFM’ version 2.0

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-- A --

addNode	addNode
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
AFMImageCollagenNetwork	AFM image sample
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
AFMImageGaussianMixAnalysis	AFM image Gaussian Mix analysis class
AFMImageGaussianMixAnalysis-class	AFM image Gaussian Mix 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
AFMImagePSDSlopesAnalysis	AFM Image psd slope analysis
AFMImagePSDSlopesAnalysis-class	AFM Image psd slope analysis
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
AreNodesConnected	check if nodes represented by circles are connected. The function defines all the possible segments between the circles and check if at least one segment exists.

-- C --

calculate3DModel	Calculate the 3D model for 3D printing
calculate3DModel-method	Calculate the 3D model for 3D printing
calculateDirectionalVariograms	Calculate experimental directional semi-variograms
calculateGaussianMixture	Calculate Gaussian Mixture with two components from the AFM Image.
calculateHolesCharacteristics	get the networks parameters
calculateIgraph	Calculate iGraph from AFMImage
calculateNetworkParameters	get the networks parameters
calculateNetworks	Calculate networks on the surface
calculateNetworks-method	Calculate networks on the surface
calculateNetworkSkeleton	calculateNetworkSkeleton
calculateOmnidirectionalVariogram	Calculate experimental omnidirectional semi-variogram
calculatePhysicalDistanceFromPath	calculate the physical distances between nodes
calculateShortestPaths	calculate the shortest path between adjacent nodes
canBeRemoved	canBeRemoved
checkIsotropy	Check the isotropy of a sample
checkNormality	Check visualy of the normality of the sample
createGraph	create the igraph weighted graph from the nodes and edges

-- D --

densityCurvesAllHeights	AFM image Gaussian Mix analysis class
densityCurvesAllHeights-method	AFM image Gaussian Mix analysis class
directionalVariograms	AFM image variogram analysis class
directionalVariograms-method	AFM image variogram analysis class
displayColoredNetworkWithVerticesSize	displayColoredNetworkWithVerticesSize
displaygridIgraphPlot	display the network of nodes and edges
displaygridIgraphPlotFromEdges	display the network of nodes and edges
displayHolesIn3D	Display a 3D image of the holes in an AFMImage and store it on disk.
displayIn3D	Display a 3D image of an AFMImage and store it on disk.
dnormalmix	dnormalmix density of a mixture of normals

-- E --

eachComponentsCounts	AFM image Gaussian Mix analysis class
eachComponentsCounts-method	AFM image Gaussian Mix analysis class
epsilonGaussianMix	AFM image Gaussian Mix analysis class
epsilonGaussianMix-method	AFM image Gaussian Mix analysis class
evaluateVariogramModels	evaluateVariogramModels method to evaluate the basic variogram models
evaluateVariogramModels-method	evaluateVariogramModels method to evaluate the basic variogram models
existsEdge	Does an edge exist ?
existsSegment	existsSegment checks if a segment exists in an AFMImage; check if all the heights at the segment coordinates are different to zero.
exportToSTL	Export an AFM Image as a STL format file.
extractAFMImage	Extract a portion of an AFM image.

-- F --

filterAFMImage	filter the heights of an AFMImage with a minimun and a maximum value
fractalDimensionMethods	AFM image fractal dimensions analysis class
fractalDimensionMethods-method	AFM image fractal dimensions analysis class
fusionCloseNodes	fusion the nodes that are intersecting

-- G --

gaussianMix	AFM image Gaussian Mix analysis class
gaussianMix-method	AFM image Gaussian Mix analysis class
generateAFMImageReport	Generate an analysis report from an AFMImageAnalyser object
generateCheckReport	Generate a check report for one AFMImage
generatePolygonEnvelope	generatePolygonEnvelope
generateReport	Generate an analysis report for one AFMImage
generateReportFromNanoscopeImageDirectory	Generate a pdf report for all AFM images in a directory
get3DImageFullfilename	get 3D image full filename
getAllPointsToRemove	getAllPointsToRemove
getAngle	calculate the angle between two vectors
getAutoIntersectionForOmnidirectionalVariogram	Calculate slopes and intersections in variogram 'getAutoIntersectionForOmnidirectionalVariogram' returns the slope in the omnidirectional variograms
getAutoIntersectionForRoughnessAgainstLengthscale	get the intersection between tangente and plateau
getAutomaticWidthForVariogramCalculation	calculate a width to be used for experimental variogram calculation
getBresenham2DSegment	get a segment of points thanks to Bresenham line algorithm
getCircleSpatialPoints	get the spatial points on the circle including the center of the circle
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
getHolesStatistics	calculate statistics about holes in a binary image
getIntersectionForRoughnessAgainstLengthscale	get the intersection between tangente and plateau
getIntersectionPointWithBorder	getIntersectionPointWithBorder to be described
getListOfDiameters	getListOfDiameters
getLogLogOmnidirectionalSlopeGraph	Get the graph of the Log Log omnidiretction variogram 'getLogLogOmnidirectionalSlopeGraph' returns Get the graph of the Log Log omnidirectional variogram
getMaxCircleMatrix	getMaxCircleMatrix
getNetworkGridLayout	#' @export getCoordinatesFromVertexId2<-function(AFMImage, vId) vertexId<-as.numeric(vId) y<-floor(vertexId/HASHSIZE) x<-vertexId-y*HASHSIZE return(data.table(vId=vId, coords.x1=x,coords.x2=y)) Get getNetworkGridLayout
getNetworkParameters	Get Network parameters
getNetworkParameters-method	Get Network parameters
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)
getTriangle	get a triangle starting from center, two segments of length r with angles deg1 and deg2
getVertexId	Get vertex id from x,y coordinates
gridIgraphPlot	gridIgraphPlot

-- I --

identifyEdgesFromCircles	display the network of nodes and edges
identifyIsolatedNodes	identify isolated nodes comparing the list of edges and the list of nodes
identifyMaxCircleRadius	identifyMaxCircleRadius
identifyNodesAndEdges	identifyNodesAndEdges
identifyNodesWithCircles	identify largest circles in binary image
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 Gaussian Mix analysis class
initialize-method	AFM image networks analysis class
initialize-method	AFM image Power Spectrum Density analysis class
initialize-method	AFM Image psd slope analysis
initialize-method	AFM image variogram analysis class
initialize-method	AFM Image Variogram Model class
initialize-method	AFM Image log-log experimental variogram slope analysis
intersections	AFM image Power Spectrum Density analysis class
intersections-method	AFM image Power Spectrum Density analysis class
invertBinaryAFMImage	invert a binary AFMImage
isAdjacentToBetterVertex	isAdjacentToBetterVertex
isAngleBetweenEdgesAlwaysSuperiorToMinAngle	check if all the angles between one edge and a list of edges is superior to a specified value.
isBinary	has the AFM Image heights of 0 or 1

-- L --

loglike.normalmix

loglike sum of density of a mixture of normals

-- M --

makeBinaryAFMImage	make a binary AFMImage setting all the heights different to 0 to 1.
maxGaussianMix	AFM image Gaussian Mix analysis class
maxGaussianMix-method	AFM image Gaussian Mix analysis class
minGaussianMix	AFM image Gaussian Mix analysis class
minGaussianMix-method	AFM image Gaussian Mix analysis class
multiplyHeightsAFMImage	multiply the heights of an AFMImage

-- O --

omnidirectionalVariogram	AFM image variogram analysis class
omnidirectionalVariogram-method	AFM image variogram analysis class
omniVariogramSlopeAnalysis	AFM Image log-log experimental variogram slope analysis
omniVariogramSlopeAnalysis-class	AFM Image log-log experimental variogram slope analysis

-- P --

performAllPSDCalculation	Perform all the calculation for PSD exploitation
performGaussianMixCalculation	Perform the calculation for the Gaussian mixes
pnormmix	pnormmix distribution of a mixture of normals
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 --

removeLonguestEdge	removeLonguestEdge
removeNode	removeNode
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.
saveOnDiskIntersectionForRoughnessAgainstLengthscale	save an image of the roughness against lenghtscale calculations
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.
simplifyNetwork	simplifyNetwork
summaryMixture	AFM image Gaussian Mix analysis class
summaryMixture-method	AFM image Gaussian Mix analysis class

-- T --

tcdfsEcdfsCheck	AFM image Gaussian Mix analysis class
tcdfsEcdfsCheck-method	AFM image Gaussian Mix analysis class
thinImage	thin an Image in matrix format
totalRMSRoughness	Calculate the total Root Mean Square Roughness (Rrms total)
transformAFMImageForNetworkAnalysis	Multiply, filter the heights and make a binary AFMImage from the transformed AFMImage
transformAFMImageForNetworkAnalysis-method	Multiply, filter the heights and make a binary AFMImage from the transformed AFMImage

-- U --

updateProgress	updateProgress
updateProgress-method	updateProgress

-- V --

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