AFM: Atomic Force Microscope Image Analysis
Version 1.2.2

Provides Atomic Force Microscope images analysis such as Power Spectral Density, roughness against lengthscale, experimental variogram and variogram models, fractal dimension and scale. The AFM images can be exported to STL format for 3D printing.

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AuthorMathieu Beauvais [aut, cre], Irma Liascukiene [aut], Jessem Landoulsi [aut]
Date of publication2016-09-01 01:33:25
MaintainerMathieu Beauvais <beauvais.escp@gmail.com>
LicenseAGPL-3
Version1.2.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("AFM")

Man pages

AFM: Atomic Force Microscopy images tools
AFMFractalDimensionAnalyser-getFractalDimensions: Calculate 2D fractal dimensions and scales of an AFM Image
AFMImage3DModelAnalysis-class: AFM image Power Spectrum Density analysis class
AFMImageAnalyser-class: AFM image analyser class
AFMImageAnalyser-class-initialize: Constructor method of AFMImageAnalyser Class.
AFMImage-class: AFM image class
AFMImage-extractAFMImage: Extract a portion of an AFM image.
AFMImage-filterAFMImage: filter the heights of an AFMImage with a minimun and a...
AFMImageFractalDimensionMethod-class: AFM image fractal dimension method class
AFMImageFractalDimensionsAnalysis-class: AFM image fractal dimensions analysis class
AFMImage-importFromNanoscope: Import data from nanoscope analysis(tm) tool
AFMImage-makeBinaryAFMImage: make a binary AFMImage setting all the heights different to 0...
AFMImage-multiplyHeightsAFMImage: multiply the heights of an AFMImage
AFMImageNetworksAnalysis-class: AFM image networks analysis class
AFMImageOfAluminiumInterface: AFM image sample
AFMImageOfNormallyDistributedHeights: AFM image sample
AFMImageOfOnePeak: AFM image sample
AFMImageOfRegularPeaks: AFM image sample
AFMImagePSDAnalysis-class: AFM image Power Spectrum Density analysis class
AFMImagePSDSlopesAnalysis-class: AFM Image psd slope analysis
AFMImage-sampleAFMImage: Get a sample of an AFM image.
AFMImage-saveOnDisk: Save an AFM image on disk.
AFMImage-simplifyAFMImage: simplify an AFM image.
AFMImageVariogramAnalyser-calculateDirectionalVariograms: Calculate experimental directional semi-variograms
AFMImageVariogramAnalyser-calculateOmnidirectionalVariogram: Calculate experimental omnidirectional semi-variogram
AFMImageVariogramAnalyser-getAutomaticWidthForVariogramCalculation: calculate a width to be used for experimental variogram...
AFMImageVariogramAnalysis-class: AFM image variogram analysis class
AFMImageVariogramAnalysis-evaluateVariogramModels-method: evaluateVariogramModels method to evaluate the basic...
AFMImageVariogramAnalysis-getDTModelEvaluation-method: getDTModelEvaluation method
AFMImageVariogramAnalysis-getDTModelSillRange-method: getDTModelSillRange method
AFMImageVariogramAnalysis-updateProgress-method: updateProgress
AFMImageVariogramModel-class: AFM Image Variogram Model class
AFMImageVariogramSlopesAnalysis-class: AFM Image psd slope analysis
AFMVariogramAnalyser-getSpplotFromAFMImage: Get an AFMImage as a Lattice (trellis) plot
AFMVariogramAnalyser-saveSpplotFromAFMImage: Save on disk an AFMImage as a Lattice (trellis) plot
analyse: Analyse an AFMImage
AreNodesConnected: check if nodes represented by circles are connected. The...
calculate3DModel-methods: Calculate the 3D model for 3D printing
calculateIgraph: Calculate iGraph from AFMImage
calculateNetworkSkeleton: calculateNetworkSkeleton
calculateNetworks-methods: Calculate networks on the surface
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 graph from the fusionned nodes and the...
displaygridIgraphPlot: display the network of nodes and edges
displaygridIgraphPlotFromEdges: display the network of nodes and edges
displayIn3D: Display a 3D image of an AFMImage and store it on disk.
existsEdge: Does an edge exist ?
existsSegment: existsSegment checks if a segment exists in an AFMImage;...
exportToSTL: Export an AFM Image as a STL format file.
fusionCloseNodes: fusion the nodes that are intersecting
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
getAngle: calculate the angle between two vectors
getAutoIntersectionForOmnidirectionalVariogram: Calculate slopes and intersections in variogram...
getAutoIntersectionForRoughnessAgainstLengthscale: get the intersection between tangente and plateau
getBresenham2DSegment: get a segment of points thanks to Bresenham line algorithm
getCircleSpatialPoints: get the spatial points on the circle including the center of...
getCoordinatesFromVertexId: Get x,y coordinates from vertex id
getIntersectionPointWithBorder: getIntersectionPointWithBorder to be described
getListOfDiameters: getListOfDiameters
getLogLogOmnidirectionalSlopeGraph: Get the graph of the Log Log omnidiretction variogram...
getNetworkGridLayout: #' @export getCoordinatesFromVertexId2<-function(AFMImage,...
getNyquistSpatialFrequency-methods: Get the Nyquist spatial frequency
getPaddedAFMImage: Get a zero padded AFMImage
getRoughnessParameters-methods: Get Roughness parameters
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...
getVertexId: Get vertex id from x,y coordinates
gridIgraphPlot: gridIgraphPlot
identifyEdgesFromCircles: display the network of nodes and edges
identifyIsolatedNodes: identify isolated nodes comparing the list of edges and the...
identifyNodesWithCircles: identify largest circles in binary image
isAdjacentToBetterVertex: isAdjacentToBetterVertex
isAngleBetweenEdgesAlwaysSuperiorToMinAngle: check if all the angles between one edge and a list of edges...
performAllPSDCalculation: Perform all the calculation for PSD exploitation
printVariogramModelEvaluations: printVariogramModelEvaluations
PSD1DAgainstFrequency-methods: Calculate the 1D Power Spectral Density; returns a data table...
PSD2DAgainstFrequency-methods: Calculate the 2D Power Spectral Density
putAnalysisOnDisk-methods: Export all data from an analysis of an AFM Image as rdata...
putImagesFromAnalysisOnDisk: Put the images from all analysis on disk
RoughnessByLengthScale-methods: Calculate the roughness of the sample against length scale
runAFMApp: Launch the AFM shiny application
saveOnDiskIntersectionForRoughnessAgainstLengthscale: save an image of the roughness against lenghtscale...
shiftedPSDuv: Calculate the shifted PSD matrix
shiftFFT2D: Shift the quadrants of the FFT 2D
totalRMSRoughness: Calculate the total Root Mean Square Roughness (Rrms total)
transformAFMImageForNetworkAnalysis-methods: Multiply, filter the heights and make a binary AFMImage from...

Functions

AFM Man page
AFM-package Man page
AFMImage Man page Source code
AFMImage-class Man page
AFMImage3DModelAnalysis Man page
AFMImage3DModelAnalysis-class Man page
AFMImageAnalyser Man page Source code
AFMImageAnalyser-class Man page
AFMImageFractalDimensionMethod Man page Source code
AFMImageFractalDimensionMethod-class Man page
AFMImageFractalDimensionsAnalysis Man page Source code
AFMImageFractalDimensionsAnalysis-class Man page
AFMImageNetworksAnalysis Man page Source code
AFMImageNetworksAnalysis-class Man page
AFMImageOfAluminiumInterface Man page
AFMImageOfNormallyDistributedHeights Man page
AFMImageOfOnePeak Man page
AFMImageOfRegularPeaks Man page
AFMImagePSDAnalysis Man page Source code
AFMImagePSDAnalysis-class Man page
AFMImagePSDSlopesAnalysis Man page Source code
AFMImagePSDSlopesAnalysis-class Man page
AFMImageVariogramAnalysis Man page Source code
AFMImageVariogramAnalysis-class Man page
AFMImageVariogramModel Man page Source code
AFMImageVariogramModel-class Man page
AFMImageVariogramSlopesAnalysis Man page Source code
AFMImageVariogramSlopesAnalysis-class Man page
AreNodesConnected Man page Source code
PSD1DAgainstFrequency Man page
PSD1DAgainstFrequency,AFMImage-method Man page
PSD2DAgainstFrequency Man page
PSD2DAgainstFrequency,AFMImage-method Man page
RoughnessByLengthScale Man page
RoughnessByLengthScale,AFMImage-method Man page
analyse Man page Source code
calculate3DModel Man page
calculate3DModel,AFMImage-method Man page
calculate3DModel,AFMImage3DModelAnalysis-method Man page
calculateDirectionalVariograms Man page Source code
calculateIgraph Man page Source code
calculateNetworkSkeleton Man page Source code
calculateNetworks Man page
calculateNetworks,AFMImage-method Man page
calculateNetworks,AFMImageNetworksAnalysis-method Man page
calculateOmnidirectionalVariogram Man page Source code
calculatePhysicalDistanceFromPath Man page Source code
calculateShortestPaths Man page Source code
calculateWavModelExpectedRange Source code
calculateWavModelExpectedSill Source code
canBeRemoved Man page Source code
checkIsotropy Man page Source code
checkNormality Man page Source code
checkNormalityDensity Source code
checkNormalityQQ Source code
createGraph Man page Source code
createReportDirectory Source code
directionalVariograms Man page
directionalVariograms,AFMImageVariogramAnalysis-method Man page
displayIn3D Man page Source code
displaygridIgraphPlot Man page Source code
displaygridIgraphPlotFromEdges Man page Source code
evaluateVariogramModels Man page
evaluateVariogramModels,AFMImageVariogramAnalysis-method Man page
existsEdge Man page Source code
existsSegment Man page Source code
export3DImageForReport Source code
exportFractalDimImagesForReport Source code
exportPSDImagesForReport Source code
exportToSTL Man page Source code
exportVariogramImagesForReport Source code
extractAFMImage Man page Source code
filterAFMImage Man page Source code
fractalDimensionMethods Man page
fractalDimensionMethods,AFMImageFractalDimensionsAnalysis-method Man page
fusionCloseNodes Man page Source code
generateAFMImageReport Man page Source code
generateCheckReport Man page Source code
generateReport Man page Source code
generateReportFromNanoscopeImageDirectory Man page Source code
get3DImageFullfilename Source code
getAFMImageFromKrige Source code
getAngle Man page Source code
getAutoIntersectionForOmnidirectionalVariogram Man page Source code
getAutoIntersectionForRoughnessAgainstLengthscale Man page Source code
getAutomaticWidthForVariogramCalculation Man page Source code
getBresenham2DSegment Man page Source code
getCircleSpatialPoints Man page Source code
getCoordinatesFromVertexId Man page Source code
getCutsOfSpplotFromAFMImage Source code
getDTModelEvaluation Man page
getDTModelEvaluation,AFMImageVariogramAnalysis-method Man page
getDTModelSillRange Man page
getDTModelSillRange,AFMImageVariogramAnalysis-method Man page
getDirectionalVarioCsvFullfilename Source code
getDirectionalVarioPngFullfilename Source code
getFractalDimensions Man page Source code
getFractalDimensionsPngFullfilename Source code
getGgplotFromDataTable Source code
getHorizontalSlice Source code
getIntersectionPointWithBorder Man page Source code
getLibrariesVersions Source code
getListOfDiameters Man page Source code
getLogLogOmnidirectionalSlopeGraph Man page Source code
getNetworkGridLayout Man page Source code
getNyquistSpatialFrequency Man page
getNyquistSpatialFrequency,AFMImage-method Man page
getOmnidirectionalVarioCsvFullfilename Source code
getOmnidirectionalVarioPngFullfilename Source code
getPaddedAFMImage Man page Source code
getRoughnessAgainstLengthscale Source code
getRoughnessAgainstLengthscale10nm Source code
getRoughnessAgainstLengthscaleIntersection Source code
getRoughnessParameters Man page
getRoughnessParameters,AFMImage-method Man page
getSimplifiedRoughnessAgainstLenghscale Source code
getSpplotColors Source code
getSpplotFromAFMImage Man page Source code
getSpplotImagefullfilename Source code
getSpplotPredictedImageFullfilename Source code
getSurroundingVertexesList Man page Source code
getTopologyAFMImage Man page Source code
getTriangle Man page Source code
getVarioPngchosenFitSample Source code
getVertexId Man page Source code
gridIgraphPlot Man page Source code
identifyEdgesFromCircles Man page Source code
identifyIsolatedNodes Man page Source code
identifyNodesWithCircles Man page Source code
importFromNanoscope Man page Source code
initialize,AFMImage-method Man page
initialize,AFMImageAnalyser-method Man page
initialize,AFMImageFractalDimensionMethod-method Man page
initialize,AFMImageFractalDimensionsAnalysis-method Man page
initialize,AFMImageNetworksAnalysis-method Man page
initialize,AFMImagePSDAnalysis-method Man page
initialize,AFMImagePSDSlopesAnalysis-method Man page
initialize,AFMImageVariogramAnalysis-method Man page
initialize,AFMImageVariogramModel-method Man page
initialize,AFMImageVariogramSlopesAnalysis-method Man page
intersections Man page
intersections,AFMImagePSDAnalysis-method Man page
isAdjacentToBetterVertex Man page Source code
isAngleBetweenEdgesAlwaysSuperiorToMinAngle Man page Source code
isReportDirectoryWritePermissionCorrect Source code
makeBinaryAFMImage Man page Source code
multiplyHeightsAFMImage Man page Source code
mykrigefunction Source code
omnidirectionalVariogram Man page
omnidirectionalVariogram,AFMImageVariogramAnalysis-method Man page
performAllPSDCalculation Man page Source code
printVariogramModelEvaluations Man page Source code
psd1d Man page
psd1d,AFMImagePSDAnalysis-method Man page
psd1d_breaks Man page
psd1d_breaks,AFMImagePSDAnalysis-method Man page
psd2d Man page
psd2d,AFMImagePSDAnalysis-method Man page
psd2d_maxHighLengthScale Man page
psd2d_maxHighLengthScale,AFMImagePSDAnalysis-method Man page
psd2d_truncHighLengthScale Man page
psd2d_truncHighLengthScale,AFMImagePSDAnalysis-method Man page
putAnalysisOnDisk Man page
putAnalysisOnDisk,AFMImageAnalyser-method Man page
putImagesFromAnalysisOnDisk Man page Source code
roughnessAgainstLengthscale Man page
roughnessAgainstLengthscale,AFMImagePSDAnalysis-method Man page
runAFMApp Man page Source code
sampleAFMImage Man page Source code
saveHorizontalSlices Source code
saveOnDisk Man page Source code
saveOnDiskIntersectionForRoughnessAgainstLengthscale Man page Source code
saveSpplotFromAFMImage Man page Source code
saveSpplotFromKrige Source code
shiftFFT2D Man page Source code
shiftedPSDuv Man page Source code
simplifyAFMImage Man page Source code
statsFromKrige Source code
totalRMSRoughness Man page Source code
transformAFMImageForNetworkAnalysis Man page
transformAFMImageForNetworkAnalysis,AFMImage-method Man page
transformAFMImageForNetworkAnalysis,AFMImageNetworksAnalysis-met Man page
updateProgress Man page
updateProgress,AFMImageVariogramAnalysis-method Man page
variogramModels Man page
variogramModels,AFMImageVariogramAnalysis-method Man page

Files

inst
inst/shiny
inst/shiny/AFM-desktop
inst/shiny/AFM-desktop/ui.R
inst/shiny/AFM-desktop/server.R
inst/shiny/AFM-desktop/www
inst/shiny/AFM-desktop/www/index.html
tests
tests/testthat
tests/testthat/configuration.R
tests/testthat/testAFMReportMaker.R
NAMESPACE
NEWS
data
data/AFMImageOfNormallyDistributedHeights.rda
data/AFMImageOfRegularPeaks.rda
data/AFMImageOfAluminiumInterface.rda
data/AFMImageOfOnePeak.rda
R
R/runAFMApp.R
R/AFMPSDAnalyser.R
R/AFMNetworksAnalyser.R
R/AFMImage.R
R/AFMVariogramAnalyser.R
R/AFMReportMaker.R
R/AFM3DPrinter.R
R/AFMImageAnalyser.R
R/pkgname.R
R/AFMFractalDimensionAnalyser.R
MD5
DESCRIPTION
man
man/checkIsotropy.Rd
man/existsEdge.Rd
man/generateCheckReport.Rd
man/displaygridIgraphPlot.Rd
man/AFMImageVariogramSlopesAnalysis-class.Rd
man/AFMImageVariogramAnalyser-calculateOmnidirectionalVariogram.Rd
man/getVertexId.Rd
man/AFMImageOfOnePeak.Rd
man/shiftedPSDuv.Rd
man/saveOnDiskIntersectionForRoughnessAgainstLengthscale.Rd
man/PSD1DAgainstFrequency-methods.Rd
man/getLogLogOmnidirectionalSlopeGraph.Rd
man/AFMImageOfNormallyDistributedHeights.Rd
man/getNyquistSpatialFrequency-methods.Rd
man/analyse.Rd
man/existsSegment.Rd
man/AFMImage-filterAFMImage.Rd
man/AFMImageVariogramAnalysis-evaluateVariogramModels-method.Rd
man/createGraph.Rd
man/AFMImageVariogramAnalyser-getAutomaticWidthForVariogramCalculation.Rd
man/shiftFFT2D.Rd
man/getAutoIntersectionForRoughnessAgainstLengthscale.Rd
man/AFMImageFractalDimensionsAnalysis-class.Rd
man/getPaddedAFMImage.Rd
man/displaygridIgraphPlotFromEdges.Rd
man/AFMImage-extractAFMImage.Rd
man/generateReportFromNanoscopeImageDirectory.Rd
man/RoughnessByLengthScale-methods.Rd
man/AreNodesConnected.Rd
man/canBeRemoved.Rd
man/AFMImage-saveOnDisk.Rd
man/calculateShortestPaths.Rd
man/getCircleSpatialPoints.Rd
man/getListOfDiameters.Rd
man/AFMImageVariogramAnalysis-getDTModelSillRange-method.Rd
man/PSD2DAgainstFrequency-methods.Rd
man/AFMImageOfRegularPeaks.Rd
man/calculateNetworks-methods.Rd
man/AFMImageVariogramAnalysis-class.Rd
man/isAdjacentToBetterVertex.Rd
man/getAutoIntersectionForOmnidirectionalVariogram.Rd
man/getBresenham2DSegment.Rd
man/AFMImageOfAluminiumInterface.Rd
man/AFMImageAnalyser-class-initialize.Rd
man/getRoughnessParameters-methods.Rd
man/identifyIsolatedNodes.Rd
man/AFMImageVariogramAnalysis-updateProgress-method.Rd
man/AFMImageVariogramAnalyser-calculateDirectionalVariograms.Rd
man/putImagesFromAnalysisOnDisk.Rd
man/identifyEdgesFromCircles.Rd
man/putAnalysisOnDisk-methods.Rd
man/AFMImage3DModelAnalysis-class.Rd
man/getIntersectionPointWithBorder.Rd
man/getTopologyAFMImage.Rd
man/generateAFMImageReport.Rd
man/AFMImageVariogramModel-class.Rd
man/isAngleBetweenEdgesAlwaysSuperiorToMinAngle.Rd
man/AFMImagePSDSlopesAnalysis-class.Rd
man/getCoordinatesFromVertexId.Rd
man/AFMVariogramAnalyser-getSpplotFromAFMImage.Rd
man/AFMImagePSDAnalysis-class.Rd
man/AFMImage-importFromNanoscope.Rd
man/getNetworkGridLayout.Rd
man/AFM.Rd
man/runAFMApp.Rd
man/fusionCloseNodes.Rd
man/AFMImageFractalDimensionMethod-class.Rd
man/checkNormality.Rd
man/AFMImageVariogramAnalysis-getDTModelEvaluation-method.Rd
man/printVariogramModelEvaluations.Rd
man/getAngle.Rd
man/calculate3DModel-methods.Rd
man/AFMImage-simplifyAFMImage.Rd
man/identifyNodesWithCircles.Rd
man/AFMImageAnalyser-class.Rd
man/totalRMSRoughness.Rd
man/getSurroundingVertexesList.Rd
man/AFMImage-class.Rd
man/AFMImage-makeBinaryAFMImage.Rd
man/AFMImage-sampleAFMImage.Rd
man/getTriangle.Rd
man/displayIn3D.Rd
man/calculatePhysicalDistanceFromPath.Rd
man/performAllPSDCalculation.Rd
man/exportToSTL.Rd
man/transformAFMImageForNetworkAnalysis-methods.Rd
man/AFMImage-multiplyHeightsAFMImage.Rd
man/AFMImageNetworksAnalysis-class.Rd
man/gridIgraphPlot.Rd
man/AFMFractalDimensionAnalyser-getFractalDimensions.Rd
man/calculateNetworkSkeleton.Rd
man/generateReport.Rd
man/calculateIgraph.Rd
man/AFMVariogramAnalyser-saveSpplotFromAFMImage.Rd
CHANGES
AFM documentation built on May 29, 2017, 11:29 a.m.