# Atomic Force Microscope Image Analysis

## Documentation for package ‘AFM’ version 2.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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

## -- 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