AFM (version 2.0)

getNetworkParameters: Get Network parameters

Description

Get basic network parameters : Total root mean square Roughness or Total Rrms or totalRMSRoughness_TotalRrms Mean roughness or Ra or MeanRoughness_Ra

Usage

getNetworkParameters(AFMImageNetworksAnalysis, AFMImage)
# S4 method for AFMImageNetworksAnalysis
getNetworkParameters(AFMImageNetworksAnalysis, AFMImage)

Arguments

AFMImageNetworksAnalysis

an AFMImageNetworksAnalysis

AFMImage

an AFMImage

Value

a data.table of network parameters:

• totalNumberOfNodes the total number of nodes with degree different of 2

• totalNumberOfNodesWithDegreeTwoOrMore the total number of nodes with degree 2 or more

• totalNumberOfNodesWithDegreeOne the total number of nodes with degree one

• numberOfNodesPerArea the total number of nodes with degree diffrent of 2 per area

• numberOfNodesPerSurfaceArea the total number of nodes with degree diffrent of 2 per surface area

• MeanPhysicalDistanceBetweenNodes the mean physical distance between nodes of degree different of two

Details

getNetworkParameters returns a data.table of network parameters

Examples

# NOT RUN {
library(AFM)
library(parallel)

data(AFMImageCollagenNetwork)
AFMImage<-AFMImageCollagenNetwork
AFMIA = new("AFMImageNetworksAnalysis")
AFMIA@heightNetworksslider=10
AFMIA@filterNetworkssliderMin=150
AFMIA@filterNetworkssliderMax=300
AFMIA@smallBranchesTreatment=TRUE
clExist<-TRUE
cl <- makeCluster(2,outfile="")
AFMIA<-transformAFMImageForNetworkAnalysis(AFMImageNetworksAnalysis=AFMIA,AFMImage= AFMImage)
AFMIA<-identifyNodesAndEdges(cl=cl,AFMImageNetworksAnalysis= AFMIA,maxHeight= 300)
AFMIA<-identifyEdgesFromCircles(cl=cl,AFMImageNetworksAnalysis= AFMIA, MAX_DISTANCE = 75)
AFMIA<-identifyIsolatedNodes(AFMIA)
AFMIA<-createGraph(AFMIA)
AFMIA<-calculateShortestPaths(cl=cl, AFMImageNetworksAnalysis=AFMIA)
AFMIA<-calculateNetworkParameters(AFMImageNetworksAnalysis=AFMIA, AFMImage=AFMImage)
AFMIA<-calculateHolesCharacteristics(AFMImageNetworksAnalysis=AFMIA)
stopCluster(cl)
# }