AFM                     Atomic Force Microscopy images tools
AFMImage-class          AFM image class
AFMImage3DModelAnalysis-class
                        AFM image Power Spectrum Density analysis class
AFMImageAnalyser-class
                        AFM image analyser class
AFMImageCollagenNetwork
                        AFM image sample
AFMImageFractalDimensionMethod-class
                        AFM image fractal dimension method class
AFMImageFractalDimensionsAnalysis-class
                        AFM image fractal dimensions analysis class
AFMImageGaussianMixAnalysis-class
                        AFM image Gaussian Mix 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-class
                        AFM image Power Spectrum Density analysis class
AFMImagePSDSlopesAnalysis-class
                        AFM Image psd slope analysis
AFMImageVariogramAnalysis-class
                        AFM image variogram analysis class
AFMImageVariogramModel-class
                        AFM Image Variogram Model class
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.
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.
PSD2DAgainstFrequency   Calculate the 2D Power Spectral Density
RoughnessByLengthScale
                        Calculate the roughness of the sample against
                        length scale
addNode                 addNode
analyse                 Analyse an AFMImage
calculate3DModel        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
calculateNetworkSkeleton
                        calculateNetworkSkeleton
calculateNetworks       Calculate networks on the surface
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
displayColoredNetworkWithVerticesSize
                        displayColoredNetworkWithVerticesSize
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.
displaygridIgraphPlot   display the network of nodes and edges
displaygridIgraphPlotFromEdges
                        display the network of nodes and edges
dnormalmix              dnormalmix density of a mixture of normals
evaluateVariogramModels
                        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.
filterAFMImage          filter the heights of an AFMImage with a
                        minimun and a maximum value
fusionCloseNodes        fusion the nodes that are intersecting
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
getDTModelSillRange     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
getNyquistSpatialFrequency
                        Get the Nyquist spatial frequency
getPaddedAFMImage       Get a zero padded AFMImage
getRoughnessParameters
                        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
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,AFMImageAnalyser-method
                        Constructor method of AFMImageAnalyser 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
loglike.normalmix       loglike sum of density of a mixture of normals
makeBinaryAFMImage      make a binary AFMImage setting all the heights
                        different to 0 to 1.
multiplyHeightsAFMImage
                        multiply the heights of an AFMImage
omniVariogramSlopeAnalysis-class
                        AFM Image log-log experimental variogram slope
                        analysis
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
putAnalysisOnDisk       Export all data from an analysis of an AFM
                        Image as rdata file
putImagesFromAnalysisOnDisk
                        Put the images from all analysis on disk
removeLonguestEdge      removeLonguestEdge
removeNode              removeNode
runAFMApp               Launch the AFM shiny application
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
shiftFFT2D              Shift the quadrants of the FFT 2D
shiftedPSDuv            Calculate the shifted PSD matrix
simplifyAFMImage        simplify an AFM image.
simplifyNetwork         simplifyNetwork
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
updateProgress          updateProgress
