Atomic Force Microscope Image Analysis
Calculate networks on the surface
calculateNetworkSkeleton
calculate the physical distances between nodes
calculate the shortest path between adjacent nodes
canBeRemoved
existsSegment checks if a segment exists in an AFMImage; check if all ...
Get an AFMImage as a Lattice (trellis) plot
Check the isotropy of a sample
Check visualy of the normality of the sample
create the igraph weighted graph from the nodes and edges
Save on disk an AFMImage as a Lattice (trellis) plot
displayColoredNetworkWithVerticesSize
display the network of nodes and edges
display the network of nodes and edges
Display a 3D image of the holes in an AFMImage and store it on disk.
Display a 3D image of an AFMImage and store it on disk.
dnormalmix density of a mixture of normals
Does an edge exist ?
Analyse an AFMImage
check if nodes represented by circles are connected. The function defi...
Calculate the 3D model for 3D printing
addNode
Atomic Force Microscopy images tools
Calculate 2D fractal dimensions and scales of an AFM Image
AFM image class
Extract a portion of an AFM image.
filter the heights of an AFMImage with a minimun and a maximum value
calculate statistics about holes in a binary image
Import data from nanoscope analysis(tm) tool
invert a binary AFMImage
has the AFM Image heights of 0 or 1
make a binary AFMImage setting all the heights different to 0 to 1.
multiply the heights of an AFMImage
Get a sample of an AFM image.
Save an AFM image on disk.
simplify an AFM image.
AFM image Power Spectrum Density analysis class
Constructor method of AFMImageAnalyser Class.
AFM image analyser class
AFM image fractal dimension method class
AFM image fractal dimensions analysis class
AFM image Gaussian Mix analysis class
Calculate Gaussian Mixture with two components from the AFM Image.
get the networks parameters
AFM image networks analysis class
AFM image Power Spectrum Density analysis class
AFM Image psd slope analysis
Calculate experimental directional semi-variograms
Calculate experimental omnidirectional semi-variogram
calculate a width to be used for experimental variogram calculation
AFM image variogram analysis class
evaluateVariogramModels method to evaluate the basic variogram models
getDTModelEvaluation method
getDTModelSillRange method
updateProgress
AFM Image Variogram Model class
Calculate iGraph from AFMImage
get the networks parameters
Export an AFM Image as a STL format file.
fusion the nodes that are intersecting
Generate an analysis report from an AFMImageAnalyser object
Generate a check report for one AFMImage
generatePolygonEnvelope
Generate an analysis report for one AFMImage
Generate a pdf report for all AFM images in a directory
get 3D image full filename
getAllPointsToRemove
calculate the angle between two vectors
Calculate slopes and intersections in variogram `getAutoIntersectionFo...
get the intersection between tangente and plateau
get a segment of points thanks to Bresenham line algorithm
get the spatial points on the circle including the center of the circl...
Get x,y coordinates from vertex id
get the intersection between tangente and plateau
getIntersectionPointWithBorder to be described
getListOfDiameters
Get the graph of the Log Log omnidiretction variogram `getLogLogOmnidi...
getMaxCircleMatrix
#' @export getCoordinatesFromVertexId2<-function(AFMImage, vId) vertex...
Get Network parameters
Get the Nyquist spatial frequency
Get a zero padded AFMImage
Get Roughness parameters
Get surrounding vertices from x,y coordinates
Calculate topology image (TBC)
get a triangle starting from center, two segments of length r with ang...
Get vertex id from x,y coordinates
gridIgraphPlot
display the network of nodes and edges
identify isolated nodes comparing the list of edges and the list of no...
identifyMaxCircleRadius
identifyNodesAndEdges
identify largest circles in binary image
isAdjacentToBetterVertex
check if all the angles between one edge and a list of edges is superi...
loglike sum of density of a mixture of normals
AFM Image log-log experimental variogram slope analysis
Perform all the calculation for PSD exploitation
Perform the calculation for the Gaussian mixes
pnormmix distribution of a mixture of normals
printVariogramModelEvaluations
Calculate the 1D Power Spectral Density; returns a data table of PSD 1...
Calculate the 2D Power Spectral Density
Export all data from an analysis of an AFM Image as rdata file
Put the images from all analysis on disk
removeLonguestEdge
removeNode
Calculate the roughness of the sample against length scale
Launch the AFM shiny application
save an image of the roughness against lenghtscale calculations
Calculate the shifted PSD matrix
Shift the quadrants of the FFT 2D
simplifyNetwork
thin an Image in matrix format
Calculate the total Root Mean Square Roughness (Rrms total)
Multiply, filter the heights and make a binary AFMImage from the trans...
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.