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AFM (version 2.0)

Atomic Force Microscope Image Analysis

Description

Provides Atomic Force Microscope images analysis such as Gaussian mixes identification, Power Spectral Density, roughness against lengthscale, experimental variogram and variogram models, fractal dimension and scale, 2D network analysis. The AFM images can be exported to STL format for 3D printing.

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Version

Install

install.packages('AFM')

Monthly Downloads

367

Version

2.0

License

AGPL-3

Maintainer

Mathieu Beauvais

Last Published

October 7th, 2020

Functions in AFM (2.0)

filterAFMImage

filter the heights of an AFMImage with a minimun and a maximum value
isBinary

has the AFM Image heights of 0 or 1
getHolesStatistics

calculate statistics about holes in a binary image
makeBinaryAFMImage

make a binary AFMImage setting all the heights different to 0 to 1.
AFMImage3DModelAnalysis-class

AFM image Power Spectrum Density analysis class
AFMImage-class

AFM image class
extractAFMImage

Extract a portion of an AFM image.
importFromNanoscope

Import data from nanoscope analysis(tm) tool
initialize,AFMImageAnalyser-method

Constructor method of AFMImageAnalyser Class.
invertBinaryAFMImage

invert a binary AFMImage
AFMImageCollagenNetwork

AFM image sample
AFMImageAnalyser-class

AFM image analyser class
AFMImageFractalDimensionMethod-class

AFM image fractal dimension method class
AFMImageFractalDimensionsAnalysis-class

AFM image fractal dimensions analysis class
AFMImageOfOnePeak

AFM image sample
AFMImageOfRegularPeaks

AFM image sample
AFMImageVariogramModel-class

AFM Image Variogram Model class
getSpplotFromAFMImage

Get an AFMImage as a Lattice (trellis) plot
AFMImagePSDAnalysis-class

AFM image Power Spectrum Density analysis class
AFMImagePSDSlopesAnalysis-class

AFM Image psd slope analysis
getAutomaticWidthForVariogramCalculation

calculate a width to be used for experimental variogram calculation
AFMImageVariogramAnalysis-class

AFM image variogram analysis class
calculateDirectionalVariograms

Calculate experimental directional semi-variograms
PSD2DAgainstFrequency

Calculate the 2D Power Spectral Density
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.
checkNormality

Check visualy of the normality of the sample
calculateOmnidirectionalVariogram

Calculate experimental omnidirectional semi-variogram
getDTModelSillRange

getDTModelSillRange method
createGraph

create the igraph weighted graph from the nodes and edges
existsEdge

Does an edge exist ?
updateProgress

updateProgress
calculateIgraph

Calculate iGraph from AFMImage
existsSegment

existsSegment checks if a segment exists in an AFMImage; check if all the heights at the segment coordinates are different to zero.
getAllPointsToRemove

getAllPointsToRemove
simplifyAFMImage

simplify an AFM image.
saveOnDisk

Save an AFM image on disk.
getAngle

calculate the angle between two vectors
getTopologyAFMImage

Calculate topology image (TBC)
AFM

Atomic Force Microscopy images tools
calculateGaussianMixture

Calculate Gaussian Mixture with two components from the AFM Image.
getFractalDimensions

Calculate 2D fractal dimensions and scales of an AFM Image
AFMImageOfNormallyDistributedHeights

AFM image sample
AFMImageOfAluminiumInterface

AFM image sample
saveSpplotFromAFMImage

Save on disk an AFMImage as a Lattice (trellis) plot
getTriangle

get a triangle starting from center, two segments of length r with angles deg1 and deg2
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.
RoughnessByLengthScale

Calculate the roughness of the sample against length scale
calculatePhysicalDistanceFromPath

calculate the physical distances between nodes
displayIn3D

Display a 3D image of an AFMImage and store it on disk.
addNode

addNode
calculateShortestPaths

calculate the shortest path between adjacent nodes
multiplyHeightsAFMImage

multiply the heights of an AFMImage
sampleAFMImage

Get a sample of an AFM image.
calculateHolesCharacteristics

get the networks parameters
getBresenham2DSegment

get a segment of points thanks to Bresenham line algorithm
identifyEdgesFromCircles

display the network of nodes and edges
getLogLogOmnidirectionalSlopeGraph

Get the graph of the Log Log omnidiretction variogram getLogLogOmnidirectionalSlopeGraph returns Get the graph of the Log Log omnidirectional variogram
getCircleSpatialPoints

get the spatial points on the circle including the center of the circle
displaygridIgraphPlot

display the network of nodes and edges
getMaxCircleMatrix

getMaxCircleMatrix
identifyIsolatedNodes

identify isolated nodes comparing the list of edges and the list of nodes
performGaussianMixCalculation

Perform the calculation for the Gaussian mixes
calculateNetworkParameters

get the networks parameters
displayColoredNetworkWithVerticesSize

displayColoredNetworkWithVerticesSize
displayHolesIn3D

Display a 3D image of the holes in an AFMImage and store it on disk.
getIntersectionPointWithBorder

getIntersectionPointWithBorder to be described
getListOfDiameters

getListOfDiameters
generateCheckReport

Generate a check report for one AFMImage
generateAFMImageReport

Generate an analysis report from an AFMImageAnalyser object
omniVariogramSlopeAnalysis-class

AFM Image log-log experimental variogram slope analysis
performAllPSDCalculation

Perform all the calculation for PSD exploitation
totalRMSRoughness

Calculate the total Root Mean Square Roughness (Rrms total)
thinImage

thin an Image in matrix format
AFMImageGaussianMixAnalysis-class

AFM image Gaussian Mix analysis class
runAFMApp

Launch the AFM shiny application
removeNode

removeNode
pnormmix

pnormmix distribution of a mixture of normals
canBeRemoved

canBeRemoved
putImagesFromAnalysisOnDisk

Put the images from all analysis on disk
AFMImageNetworksAnalysis-class

AFM image networks analysis class
evaluateVariogramModels

evaluateVariogramModels method to evaluate the basic variogram models
getDTModelEvaluation

getDTModelEvaluation method
checkIsotropy

Check the isotropy of a sample
generatePolygonEnvelope

generatePolygonEnvelope
removeLonguestEdge

removeLonguestEdge
calculateNetworkSkeleton

calculateNetworkSkeleton
calculateNetworks

Calculate networks on the surface
calculate3DModel

Calculate the 3D model for 3D printing
exportToSTL

Export an AFM Image as a STL format file.
analyse

Analyse an AFMImage
fusionCloseNodes

fusion the nodes that are intersecting
generateReport

Generate an analysis report for one AFMImage
getPaddedAFMImage

Get a zero padded AFMImage
get3DImageFullfilename

get 3D image full filename
getNyquistSpatialFrequency

Get the Nyquist spatial frequency
generateReportFromNanoscopeImageDirectory

Generate a pdf report for all AFM images in a directory
getCoordinatesFromVertexId

Get x,y coordinates from vertex id
getIntersectionForRoughnessAgainstLengthscale

get the intersection between tangente and plateau
getRoughnessParameters

Get Roughness parameters
displaygridIgraphPlotFromEdges

display the network of nodes and edges
dnormalmix

dnormalmix density of a mixture of normals
identifyMaxCircleRadius

identifyMaxCircleRadius
getAutoIntersectionForOmnidirectionalVariogram

Calculate slopes and intersections in variogram getAutoIntersectionForOmnidirectionalVariogram returns the slope in the omnidirectional variograms
printVariogramModelEvaluations

printVariogramModelEvaluations
getSurroundingVertexesList

Get surrounding vertices from x,y coordinates
identifyNodesWithCircles

identify largest circles in binary image
identifyNodesAndEdges

identifyNodesAndEdges
isAdjacentToBetterVertex

isAdjacentToBetterVertex
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
getAutoIntersectionForRoughnessAgainstLengthscale

get the intersection between tangente and plateau
putAnalysisOnDisk

Export all data from an analysis of an AFM Image as rdata file
getNetworkParameters

Get Network parameters
saveOnDiskIntersectionForRoughnessAgainstLengthscale

save an image of the roughness against lenghtscale calculations
gridIgraphPlot

gridIgraphPlot
getVertexId

Get vertex id from x,y coordinates
loglike.normalmix

loglike sum of density of a mixture of normals
isAngleBetweenEdgesAlwaysSuperiorToMinAngle

check if all the angles between one edge and a list of edges is superior to a specified value.
shiftFFT2D

Shift the quadrants of the FFT 2D
shiftedPSDuv

Calculate the shifted PSD matrix
simplifyNetwork

simplifyNetwork
transformAFMImageForNetworkAnalysis

Multiply, filter the heights and make a binary AFMImage from the transformed AFMImage