AFM: Atomic Force Microscope Image Analysis

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.

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

View on CRAN

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
AFMImage Man page
AFMImage3DModelAnalysis Man page
AFMImage3DModelAnalysis-class Man page
AFMImageAnalyser Man page
AFMImageAnalyser-class Man page
AFMImage-class Man page
AFMImageFractalDimensionMethod Man page
AFMImageFractalDimensionMethod-class Man page
AFMImageFractalDimensionsAnalysis Man page
AFMImageFractalDimensionsAnalysis-class Man page
AFMImageNetworksAnalysis Man page
AFMImageNetworksAnalysis-class Man page
AFMImageOfAluminiumInterface Man page
AFMImageOfNormallyDistributedHeights Man page
AFMImageOfOnePeak Man page
AFMImageOfRegularPeaks Man page
AFMImagePSDAnalysis Man page
AFMImagePSDAnalysis-class Man page
AFMImagePSDSlopesAnalysis Man page
AFMImagePSDSlopesAnalysis-class Man page
AFMImageVariogramAnalysis Man page
AFMImageVariogramAnalysis-class Man page
AFMImageVariogramModel Man page
AFMImageVariogramModel-class Man page
AFMImageVariogramSlopesAnalysis Man page
AFMImageVariogramSlopesAnalysis-class Man page
AFM-package Man page
analyse Man page
AreNodesConnected Man page
calculate3DModel Man page
calculate3DModel,AFMImage3DModelAnalysis-method Man page
calculate3DModel,AFMImage-method Man page
calculateDirectionalVariograms Man page
calculateIgraph Man page
calculateNetworks Man page
calculateNetworks,AFMImage-method Man page
calculateNetworks,AFMImageNetworksAnalysis-method Man page
calculateNetworkSkeleton Man page
calculateOmnidirectionalVariogram Man page
calculatePhysicalDistanceFromPath Man page
calculateShortestPaths Man page
canBeRemoved Man page
checkIsotropy Man page
checkNormality Man page
createGraph Man page
directionalVariograms Man page
directionalVariograms,AFMImageVariogramAnalysis-method Man page
displaygridIgraphPlot Man page
displaygridIgraphPlotFromEdges Man page
displayIn3D Man page
evaluateVariogramModels Man page
evaluateVariogramModels,AFMImageVariogramAnalysis-method Man page
existsEdge Man page
existsSegment Man page
exportToSTL Man page
extractAFMImage Man page
filterAFMImage Man page
fractalDimensionMethods Man page
fractalDimensionMethods,AFMImageFractalDimensionsAnalysis-method Man page
fusionCloseNodes Man page
generateAFMImageReport Man page
generateCheckReport Man page
generateReport Man page
generateReportFromNanoscopeImageDirectory Man page
getAngle Man page
getAutoIntersectionForOmnidirectionalVariogram Man page
getAutoIntersectionForRoughnessAgainstLengthscale Man page
getAutomaticWidthForVariogramCalculation Man page
getBresenham2DSegment Man page
getCircleSpatialPoints Man page
getCoordinatesFromVertexId Man page
getDTModelEvaluation Man page
getDTModelEvaluation,AFMImageVariogramAnalysis-method Man page
getDTModelSillRange Man page
getDTModelSillRange,AFMImageVariogramAnalysis-method Man page
getFractalDimensions Man page
getIntersectionPointWithBorder Man page
getListOfDiameters Man page
getLogLogOmnidirectionalSlopeGraph Man page
getNetworkGridLayout Man page
getNyquistSpatialFrequency Man page
getNyquistSpatialFrequency,AFMImage-method Man page
getPaddedAFMImage Man page
getRoughnessParameters Man page
getRoughnessParameters,AFMImage-method Man page
getSpplotFromAFMImage Man page
getSurroundingVertexesList Man page
getTopologyAFMImage Man page
getTriangle Man page
getVertexId Man page
gridIgraphPlot Man page
identifyEdgesFromCircles Man page
identifyIsolatedNodes Man page
identifyNodesWithCircles Man page
importFromNanoscope Man page
initialize,AFMImageAnalyser-method Man page
initialize,AFMImageFractalDimensionMethod-method Man page
initialize,AFMImageFractalDimensionsAnalysis-method Man page
initialize,AFMImage-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
isAngleBetweenEdgesAlwaysSuperiorToMinAngle Man page
makeBinaryAFMImage Man page
multiplyHeightsAFMImage Man page
omnidirectionalVariogram Man page
omnidirectionalVariogram,AFMImageVariogramAnalysis-method Man page
performAllPSDCalculation Man page
printVariogramModelEvaluations Man page
psd1d Man page
psd1d,AFMImagePSDAnalysis-method Man page
PSD1DAgainstFrequency Man page
PSD1DAgainstFrequency,AFMImage-method Man page
psd1d_breaks Man page
psd1d_breaks,AFMImagePSDAnalysis-method Man page
psd2d Man page
psd2d,AFMImagePSDAnalysis-method Man page
PSD2DAgainstFrequency Man page
PSD2DAgainstFrequency,AFMImage-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
roughnessAgainstLengthscale Man page
roughnessAgainstLengthscale,AFMImagePSDAnalysis-method Man page
RoughnessByLengthScale Man page
RoughnessByLengthScale,AFMImage-method Man page
runAFMApp Man page
sampleAFMImage Man page
saveOnDisk Man page
saveOnDiskIntersectionForRoughnessAgainstLengthscale Man page
saveSpplotFromAFMImage Man page
shiftedPSDuv Man page
shiftFFT2D Man page
simplifyAFMImage Man page
totalRMSRoughness Man page
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

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

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