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.

Author
Mathieu Beauvais [aut, cre], Irma Liascukiene [aut], Jessem Landoulsi [aut]
Date of publication
2016-09-01 01:33:25
Maintainer
Mathieu Beauvais <beauvais.escp@gmail.com>
License
AGPL-3
Version
1.2.2

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...

Files in this package

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