Package: AFM 2.0
AFM: Atomic Force Microscope Image Analysis
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.
Authors:
AFM_2.0.tar.gz
AFM_2.0.zip(r-4.5)AFM_2.0.zip(r-4.4)AFM_2.0.zip(r-4.3)
AFM_2.0.tgz(r-4.4-any)AFM_2.0.tgz(r-4.3-any)
AFM_2.0.tar.gz(r-4.5-noble)AFM_2.0.tar.gz(r-4.4-noble)
AFM_2.0.tgz(r-4.4-emscripten)AFM_2.0.tgz(r-4.3-emscripten)
AFM.pdf |AFM.html✨
AFM/json (API)
NEWS
| # Install 'AFM' in R: |
| install.packages('AFM', repos = c('https://mbeauvai.r-universe.dev', 'https://cloud.r-project.org')) |
- AFMImageCollagenNetwork - AFM image sample
- AFMImageOfAluminiumInterface - AFM image sample
- AFMImageOfNormallyDistributedHeights - AFM image sample
- AFMImageOfOnePeak - AFM image sample
- AFMImageOfRegularPeaks - AFM image sample
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 years agofrom:98e8b5222e. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 19 2024 |
| R-4.5-win | NOTE | Nov 19 2024 |
| R-4.5-linux | NOTE | Nov 19 2024 |
| R-4.4-win | NOTE | Nov 19 2024 |
| R-4.4-mac | NOTE | Nov 19 2024 |
| R-4.3-win | OK | Nov 19 2024 |
| R-4.3-mac | OK | Nov 19 2024 |
Exports:AFMImageAFMImageAnalyserAFMImageFractalDimensionMethodAFMImageFractalDimensionsAnalysisAFMImageGaussianMixAnalysisAFMImageNetworksAnalysisAFMImagePSDAnalysisAFMImagePSDSlopesAnalysisAFMImageVariogramAnalysisAFMImageVariogramModelanalyseAreNodesConnectedcalculate3DModelcalculateDirectionalVariogramscalculateGaussianMixturecalculateHolesCharacteristicscalculateIgraphcalculateNetworkParameterscalculateNetworkscalculateNetworkSkeletoncalculateOmnidirectionalVariogramcalculatePhysicalDistanceFromPathcalculateShortestPathscanBeRemovedcheckIsotropycheckNormalitycreateGraphdisplayColoredNetworkWithVerticesSizedisplaygridIgraphPlotdisplaygridIgraphPlotFromEdgesdisplayHolesIn3DdisplayIn3DdnormalmixevaluateVariogramModelsexistsEdgeexistsSegmentexportToSTLextractAFMImagefilterAFMImagefusionCloseNodesgenerateAFMImageReportgenerateCheckReportgeneratePolygonEnvelopegenerateReportgenerateReportFromNanoscopeImageDirectoryget3DImageFullfilenamegetAllPointsToRemovegetAnglegetAutoIntersectionForOmnidirectionalVariogramgetAutoIntersectionForRoughnessAgainstLengthscalegetAutomaticWidthForVariogramCalculationgetBresenham2DSegmentgetCircleSpatialPointsgetCoordinatesFromVertexIdgetDTModelEvaluationgetDTModelSillRangegetFractalDimensionsgetHolesStatisticsgetIntersectionForRoughnessAgainstLengthscalegetIntersectionPointWithBordergetListOfDiametersgetLogLogOmnidirectionalSlopeGraphgetMaxCircleMatrixgetNetworkGridLayoutgetNetworkParametersgetNyquistSpatialFrequencygetPaddedAFMImagegetRoughnessParametersgetSpplotFromAFMImagegetSurroundingVertexesListgetTopologyAFMImagegetTrianglegetVertexIdgridIgraphPlotidentifyEdgesFromCirclesidentifyIsolatedNodesidentifyNodesAndEdgesidentifyNodesWithCirclesimportFromNanoscopeinitializeinvertBinaryAFMImageisAdjacentToBetterVertexisAngleBetweenEdgesAlwaysSuperiorToMinAngleisBinaryloglike.normalmixmakeBinaryAFMImagemultiplyHeightsAFMImageomniVariogramSlopeAnalysisperformAllPSDCalculationperformGaussianMixCalculationpnormmixprintVariogramModelEvaluationsPSD1DAgainstFrequencyPSD2DAgainstFrequencyputAnalysisOnDiskputImagesFromAnalysisOnDiskRoughnessByLengthScalerunAFMAppsampleAFMImagesaveOnDisksaveOnDiskIntersectionForRoughnessAgainstLengthscalesaveSpplotFromAFMImageshiftedPSDuvshiftFFT2DsimplifyAFMImagesimplifyNetworkthinImagetotalRMSRoughnesstransformAFMImageForNetworkAnalysisupdateProgress
Dependencies:abindaskpassbase64encbslibcachemclassclassIntclicolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbscandigestdplyre1071evaluatefansifarverfastmapfftwtoolsFNNfontawesomefractaldimfsgenericsggplot2gluegridExtragstatgtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphintervalsisobandjquerylibjsonlitekernlabKernSmoothknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemixtoolsmomentsmunsellnlmeopensslpillarpkgconfigplotlyplyrpngpracmapromisesproxypurrrR6rappdirsRColorBrewerRcpprglrlangrmarkdowns2sassscalessegmentedsfsftimeshinyshinyjssourcetoolsspspacetimestarsstringistringrsurvivalsystibbletidyrtidyselecttinytexunitsutf8vctrsviridisLitewithrwkxfunxtablextsyamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| addNode | addNode |
| Atomic Force Microscopy images tools | AFM |
| AFM image class | AFMImage AFMImage-class initialize,AFMImage-method |
| AFM image Power Spectrum Density analysis class | AFMImage3DModelAnalysis AFMImage3DModelAnalysis-class |
| AFM image analyser class | AFMImageAnalyser AFMImageAnalyser-class |
| AFM image sample | AFMImageCollagenNetwork |
| AFM image fractal dimension method class | AFMImageFractalDimensionMethod AFMImageFractalDimensionMethod-class initialize,AFMImageFractalDimensionMethod-method |
| AFM image fractal dimensions analysis class | AFMImageFractalDimensionsAnalysis AFMImageFractalDimensionsAnalysis-class fractalDimensionMethods fractalDimensionMethods,AFMImageFractalDimensionsAnalysis-method initialize,AFMImageFractalDimensionsAnalysis-method |
| AFM image Gaussian Mix analysis class | AFMImageGaussianMixAnalysis AFMImageGaussianMixAnalysis-class densityCurvesAllHeights densityCurvesAllHeights,AFMImageGaussianMixAnalysis-method eachComponentsCounts eachComponentsCounts,AFMImageGaussianMixAnalysis-method epsilonGaussianMix epsilonGaussianMix,AFMImageGaussianMixAnalysis-method gaussianMix gaussianMix,AFMImageGaussianMixAnalysis-method initialize,AFMImageGaussianMixAnalysis-method maxGaussianMix maxGaussianMix,AFMImageGaussianMixAnalysis-method minGaussianMix minGaussianMix,AFMImageGaussianMixAnalysis-method summaryMixture summaryMixture,AFMImageGaussianMixAnalysis-method tcdfsEcdfsCheck tcdfsEcdfsCheck,AFMImageGaussianMixAnalysis-method |
| AFM image networks analysis class | AFMImageNetworksAnalysis AFMImageNetworksAnalysis-class initialize,AFMImageNetworksAnalysis-method |
| AFM image sample | AFMImageOfAluminiumInterface |
| AFM image sample | AFMImageOfNormallyDistributedHeights |
| AFM image sample | AFMImageOfOnePeak |
| AFM image sample | AFMImageOfRegularPeaks |
| AFM image Power Spectrum Density analysis class | AFMImagePSDAnalysis AFMImagePSDAnalysis-class initialize,AFMImagePSDAnalysis-method intersections intersections,AFMImagePSDAnalysis-method psd1d psd1d,AFMImagePSDAnalysis-method psd1d_breaks psd1d_breaks,AFMImagePSDAnalysis-method psd2d psd2d,AFMImagePSDAnalysis-method psd2d_maxHighLengthScale psd2d_maxHighLengthScale,AFMImagePSDAnalysis-method psd2d_truncHighLengthScale psd2d_truncHighLengthScale,AFMImagePSDAnalysis-method roughnessAgainstLengthscale roughnessAgainstLengthscale,AFMImagePSDAnalysis-method |
| AFM Image psd slope analysis | AFMImagePSDSlopesAnalysis AFMImagePSDSlopesAnalysis-class initialize,AFMImagePSDSlopesAnalysis-method |
| AFM image variogram analysis class | AFMImageVariogramAnalysis AFMImageVariogramAnalysis-class directionalVariograms directionalVariograms,AFMImageVariogramAnalysis-method initialize,AFMImageVariogramAnalysis-method omnidirectionalVariogram omnidirectionalVariogram,AFMImageVariogramAnalysis-method variogramModels variogramModels,AFMImageVariogramAnalysis-method variogramSlopeAnalysis variogramSlopeAnalysis,AFMImageVariogramAnalysis-method |
| AFM Image Variogram Model class | AFMImageVariogramModel AFMImageVariogramModel-class initialize,AFMImageVariogramModel-method |
| Analyse an AFMImage | analyse |
| 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. | AreNodesConnected |
| Calculate the 3D model for 3D printing | calculate3DModel calculate3DModel,AFMImage-method calculate3DModel,AFMImage3DModelAnalysis-method |
| Calculate experimental directional semi-variograms | calculateDirectionalVariograms |
| Calculate Gaussian Mixture with two components from the AFM Image. | calculateGaussianMixture |
| get the networks parameters | calculateHolesCharacteristics |
| Calculate iGraph from AFMImage | calculateIgraph |
| get the networks parameters | calculateNetworkParameters |
| Calculate networks on the surface | calculateNetworks calculateNetworks,AFMImage-method calculateNetworks,AFMImageNetworksAnalysis-method |
| calculateNetworkSkeleton | calculateNetworkSkeleton |
| Calculate experimental omnidirectional semi-variogram | calculateOmnidirectionalVariogram |
| calculate the physical distances between nodes | calculatePhysicalDistanceFromPath |
| calculate the shortest path between adjacent nodes | calculateShortestPaths |
| canBeRemoved | canBeRemoved |
| Check the isotropy of a sample | checkIsotropy |
| Check visualy of the normality of the sample | checkNormality |
| create the igraph weighted graph from the nodes and edges | createGraph |
| displayColoredNetworkWithVerticesSize | displayColoredNetworkWithVerticesSize |
| display the network of nodes and edges | displaygridIgraphPlot |
| display the network of nodes and edges | displaygridIgraphPlotFromEdges |
| Display a 3D image of the holes in an AFMImage and store it on disk. | displayHolesIn3D |
| Display a 3D image of an AFMImage and store it on disk. | displayIn3D |
| dnormalmix density of a mixture of normals | dnormalmix |
| evaluateVariogramModels method to evaluate the basic variogram models | evaluateVariogramModels evaluateVariogramModels,AFMImageVariogramAnalysis-method |
| Does an edge exist ? | existsEdge |
| existsSegment checks if a segment exists in an AFMImage; check if all the heights at the segment coordinates are different to zero. | existsSegment |
| Export an AFM Image as a STL format file. | exportToSTL |
| Extract a portion of an AFM image. | extractAFMImage |
| filter the heights of an AFMImage with a minimun and a maximum value | filterAFMImage |
| fusion the nodes that are intersecting | fusionCloseNodes |
| Generate an analysis report from an AFMImageAnalyser object | generateAFMImageReport |
| Generate a check report for one AFMImage | generateCheckReport |
| generatePolygonEnvelope | generatePolygonEnvelope |
| Generate an analysis report for one AFMImage | generateReport |
| Generate a pdf report for all AFM images in a directory | generateReportFromNanoscopeImageDirectory |
| get 3D image full filename | get3DImageFullfilename |
| getAllPointsToRemove | getAllPointsToRemove |
| calculate the angle between two vectors | getAngle |
| Calculate slopes and intersections in variogram 'getAutoIntersectionForOmnidirectionalVariogram' returns the slope in the omnidirectional variograms | getAutoIntersectionForOmnidirectionalVariogram |
| get the intersection between tangente and plateau | getAutoIntersectionForRoughnessAgainstLengthscale |
| calculate a width to be used for experimental variogram calculation | getAutomaticWidthForVariogramCalculation |
| get a segment of points thanks to Bresenham line algorithm | getBresenham2DSegment |
| get the spatial points on the circle including the center of the circle | getCircleSpatialPoints |
| Get x,y coordinates from vertex id | getCoordinatesFromVertexId |
| getDTModelEvaluation method | getDTModelEvaluation getDTModelEvaluation,AFMImageVariogramAnalysis-method |
| getDTModelSillRange method | getDTModelSillRange getDTModelSillRange,AFMImageVariogramAnalysis-method |
| Calculate 2D fractal dimensions and scales of an AFM Image | getFractalDimensions |
| calculate statistics about holes in a binary image | getHolesStatistics |
| get the intersection between tangente and plateau | getIntersectionForRoughnessAgainstLengthscale |
| getIntersectionPointWithBorder to be described | getIntersectionPointWithBorder |
| getListOfDiameters | getListOfDiameters |
| Get the graph of the Log Log omnidiretction variogram 'getLogLogOmnidirectionalSlopeGraph' returns Get the graph of the Log Log omnidirectional variogram | getLogLogOmnidirectionalSlopeGraph |
| getMaxCircleMatrix | getMaxCircleMatrix |
| #' @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 | getNetworkGridLayout |
| Get Network parameters | getNetworkParameters getNetworkParameters,AFMImage-method getNetworkParameters,AFMImageNetworksAnalysis-method |
| Get the Nyquist spatial frequency | getNyquistSpatialFrequency getNyquistSpatialFrequency,AFMImage-method |
| Get a zero padded AFMImage | getPaddedAFMImage |
| Get Roughness parameters | getRoughnessParameters getRoughnessParameters,AFMImage-method |
| Get an AFMImage as a Lattice (trellis) plot | getSpplotFromAFMImage |
| Get surrounding vertices from x,y coordinates | getSurroundingVertexesList |
| Calculate topology image (TBC) | getTopologyAFMImage |
| get a triangle starting from center, two segments of length r with angles deg1 and deg2 | getTriangle |
| Get vertex id from x,y coordinates | getVertexId |
| gridIgraphPlot | gridIgraphPlot |
| display the network of nodes and edges | identifyEdgesFromCircles |
| identify isolated nodes comparing the list of edges and the list of nodes | identifyIsolatedNodes |
| identifyMaxCircleRadius | identifyMaxCircleRadius |
| identifyNodesAndEdges | identifyNodesAndEdges |
| identify largest circles in binary image | identifyNodesWithCircles |
| Import data from nanoscope analysis(tm) tool | importFromNanoscope |
| Constructor method of AFMImageAnalyser Class. | initialize,AFMImageAnalyser-method |
| invert a binary AFMImage | invertBinaryAFMImage |
| isAdjacentToBetterVertex | isAdjacentToBetterVertex |
| check if all the angles between one edge and a list of edges is superior to a specified value. | isAngleBetweenEdgesAlwaysSuperiorToMinAngle |
| has the AFM Image heights of 0 or 1 | isBinary |
| loglike sum of density of a mixture of normals | loglike.normalmix |
| make a binary AFMImage setting all the heights different to 0 to 1. | makeBinaryAFMImage |
| multiply the heights of an AFMImage | multiplyHeightsAFMImage |
| AFM Image log-log experimental variogram slope analysis | initialize,omniVariogramSlopeAnalysis-method omniVariogramSlopeAnalysis omniVariogramSlopeAnalysis-class |
| Perform all the calculation for PSD exploitation | performAllPSDCalculation |
| Perform the calculation for the Gaussian mixes | performGaussianMixCalculation |
| pnormmix distribution of a mixture of normals | pnormmix |
| printVariogramModelEvaluations | printVariogramModelEvaluations |
| 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. | PSD1DAgainstFrequency PSD1DAgainstFrequency,AFMImage-method |
| Calculate the 2D Power Spectral Density | PSD2DAgainstFrequency PSD2DAgainstFrequency,AFMImage,AFMImagePSDAnalysis-method PSD2DAgainstFrequency,AFMImage-method |
| Export all data from an analysis of an AFM Image as rdata file | putAnalysisOnDisk putAnalysisOnDisk,AFMImageAnalyser-method |
| Put the images from all analysis on disk | putImagesFromAnalysisOnDisk |
| removeLonguestEdge | removeLonguestEdge |
| removeNode | removeNode |
| Calculate the roughness of the sample against length scale | RoughnessByLengthScale RoughnessByLengthScale,AFMImage-method |
| Launch the AFM shiny application | runAFMApp |
| Get a sample of an AFM image. | sampleAFMImage |
| Save an AFM image on disk. | saveOnDisk |
| save an image of the roughness against lenghtscale calculations | saveOnDiskIntersectionForRoughnessAgainstLengthscale |
| Save on disk an AFMImage as a Lattice (trellis) plot | saveSpplotFromAFMImage |
| Calculate the shifted PSD matrix | shiftedPSDuv |
| Shift the quadrants of the FFT 2D | shiftFFT2D |
| simplify an AFM image. | simplifyAFMImage |
| simplifyNetwork | simplifyNetwork |
| thin an Image in matrix format | thinImage |
| Calculate the total Root Mean Square Roughness (Rrms total) | totalRMSRoughness |
| Multiply, filter the heights and make a binary AFMImage from the transformed AFMImage | transformAFMImageForNetworkAnalysis transformAFMImageForNetworkAnalysis,AFMImage-method transformAFMImageForNetworkAnalysis,AFMImageNetworksAnalysis-method |
| updateProgress | updateProgress updateProgress,AFMImageVariogramAnalysis-method |
