filter the heights of an AFMImage with a minimun and a maximum value
has the AFM Image heights of 0 or 1
calculate statistics about holes in a binary image
make a binary AFMImage setting all the heights different to 0 to 1.
AFMImage3DModelAnalysis-class
AFM image Power Spectrum Density analysis class
AFM image class
Extract a portion of an AFM image.
Import data from nanoscope analysis(tm) tool
initialize,AFMImageAnalyser-method
Constructor method of AFMImageAnalyser Class.
invert a binary AFMImage
AFM image sample
AFM image analyser class
AFMImageFractalDimensionMethod-class
AFM image fractal dimension method class
AFMImageFractalDimensionsAnalysis-class
AFM image fractal dimensions analysis class
AFM image sample
AFM image sample
AFMImageVariogramModel-class
AFM Image Variogram Model class
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
Calculate the 2D Power Spectral Density
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 Check visualy of the normality of the sample
calculateOmnidirectionalVariogram
Calculate experimental omnidirectional semi-variogram
getDTModelSillRange method
create the igraph weighted graph from the nodes and edges
Does an edge exist ?
updateProgress
Calculate iGraph from AFMImage
existsSegment checks if a segment exists in an AFMImage; check if all the heights at the segment coordinates are different to zero.
getAllPointsToRemove
simplify an AFM image.
Save an AFM image on disk.
calculate the angle between two vectors
Calculate topology image (TBC)
Atomic Force Microscopy images tools
Calculate Gaussian Mixture with two components from the AFM Image.
Calculate 2D fractal dimensions and scales of an AFM Image
AFMImageOfNormallyDistributedHeights
AFM image sample
AFMImageOfAluminiumInterface
AFM image sample
Save on disk an AFMImage as a Lattice (trellis) plot
get a triangle starting from center, two segments of length r with angles deg1 and deg2
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.
Calculate the roughness of the sample against length scale
calculatePhysicalDistanceFromPath
calculate the physical distances between nodes
Display a 3D image of an AFMImage and store it on disk.
addNode
calculate the shortest path between adjacent nodes
multiply the heights of an AFMImage
Get a sample of an AFM image.
calculateHolesCharacteristics
get the networks parameters
get a segment of points thanks to Bresenham line algorithm
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
get the spatial points on the circle including the center of the circle
display the network of nodes and edges
getMaxCircleMatrix
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
Display a 3D image of the holes in an AFMImage and store it on disk.
getIntersectionPointWithBorder
getIntersectionPointWithBorder to be described
getListOfDiameters
Generate a check report for one AFMImage
Generate an analysis report from an AFMImageAnalyser object
omniVariogramSlopeAnalysis-class
AFM Image log-log experimental variogram slope analysis
Perform all the calculation for PSD exploitation
Calculate the total Root Mean Square Roughness (Rrms total)
thin an Image in matrix format
AFMImageGaussianMixAnalysis-class
AFM image Gaussian Mix analysis class
Launch the AFM shiny application
removeNode
pnormmix distribution of a mixture of normals
canBeRemoved
putImagesFromAnalysisOnDisk
Put the images from all analysis on disk
AFMImageNetworksAnalysis-class
AFM image networks analysis class
evaluateVariogramModels method to evaluate the basic variogram models
getDTModelEvaluation method
Check the isotropy of a sample
generatePolygonEnvelope
removeLonguestEdge
calculateNetworkSkeleton
Calculate networks on the surface
Calculate the 3D model for 3D printing
Export an AFM Image as a STL format file.
Analyse an AFMImage
fusion the nodes that are intersecting
Generate an analysis report for one AFMImage
Get a zero padded AFMImage
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
Get Roughness parameters
displaygridIgraphPlotFromEdges
display the network of nodes and edges
dnormalmix density of a mixture of normals
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
identify largest circles in binary image
identifyNodesAndEdges
isAdjacentToBetterVertex
#' @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
Export all data from an analysis of an AFM Image as rdata file
Get Network parameters
saveOnDiskIntersectionForRoughnessAgainstLengthscale
save an image of the roughness against lenghtscale calculations
gridIgraphPlot
Get vertex id from x,y coordinates
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.
Shift the quadrants of the FFT 2D
Calculate the shifted PSD matrix
simplifyNetwork
transformAFMImageForNetworkAnalysis
Multiply, filter the heights and make a binary AFMImage from the transformed AFMImage