Man pages for AFM
Atomic Force Microscope Image Analysis
| addNode | addNode |
| 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 |
| AFMImageCollagenNetwork | AFM image sample |
| 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 |
| AFMImageGaussianMixAnalysis-class | AFM image Gaussian Mix analysis class |
| AFMImage-getHolesStatistics | calculate statistics about holes in a binary image |
| AFMImage-importFromNanoscope | Import data from nanoscope analysis(tm) tool |
| AFMImage-invertBinaryAFMImage | invert a binary AFMImage |
| AFMImage-isBinary | has the AFM Image heights of 0 or 1 |
| 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 |
| 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 |
| calculateGaussianMixture | Calculate Gaussian Mixture with two components from the AFM... |
| calculateHolesCharacteristics | get the networks parameters |
| calculateIgraph | Calculate iGraph from AFMImage |
| calculateNetworkParameters | get the networks parameters |
| 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 weighted graph from the nodes and edges |
| displayColoredNetworkWithVerticesSize | displayColoredNetworkWithVerticesSize |
| displaygridIgraphPlot | display the network of nodes and edges |
| displaygridIgraphPlotFromEdges | display the network of nodes and edges |
| displayHolesIn3D | Display a 3D image of the holes in an AFMImage and store it... |
| displayIn3D | Display a 3D image of an AFMImage and store it on disk. |
| dnormalmix | dnormalmix density of a mixture of normals |
| 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 |
| 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... |
| 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 |
| 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... |
| getMaxCircleMatrix | getMaxCircleMatrix |
| getNetworkGridLayout | #' @export getCoordinatesFromVertexId2<-function(AFMImage,... |
| getNetworkParameters-methods | Get Network parameters |
| 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... |
| identifyMaxCircleRadius | identifyMaxCircleRadius |
| identifyNodesAndEdges | identifyNodesAndEdges |
| identifyNodesWithCircles | identify largest circles in binary image |
| isAdjacentToBetterVertex | isAdjacentToBetterVertex |
| isAngleBetweenEdgesAlwaysSuperiorToMinAngle | check if all the angles between one edge and a list of edges... |
| loglike.normalmix | loglike sum of density of a mixture of normals |
| 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 |
| 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 |
| removeLonguestEdge | removeLonguestEdge |
| removeNode | removeNode |
| 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 |
| simplifyNetwork | simplifyNetwork |
| thinImage | thin an Image in matrix format |
| totalRMSRoughness | Calculate the total Root Mean Square Roughness (Rrms total) |
| transformAFMImageForNetworkAnalysis-methods | Multiply, filter the heights and make a binary AFMImage from... |
