| getNetworkParameters {AFM} | R Documentation |
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 signature 'AFMImageNetworksAnalysis'
getNetworkParameters(AFMImageNetworksAnalysis, AFMImage)
Arguments
AFMImageNetworksAnalysis |
|
AFMImage |
an |
Details
getNetworkParameters returns a data.table of network parameters
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
Author(s)
M.Beauvais
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)
## End(Not run)