morphomapCSG: morphomapCSG

In morphomap: Morphometric Maps, Bone Landmarking and Cross Sectional Geometry

morphomapCSG

Description

Tool for Cross-sectional geometry

Usage

morphomapCSG(
  cp,
  mp,
  translate = FALSE,
  center = c("I", "E", "CCA"),
  delta = 0.1,
  Cx = NULL,
  Cy = NULL,
  I_xy = TRUE,
  I_minmax = TRUE,
  Zxy = TRUE
)

Arguments

cp	matrix: coordinates of the external outline
mp	matrix: coordinates of the internal outline
translate	logical: if TRUE the section will be centered
center	how to define the center of each section. The method allowed are "CCA" (center of cortical area), "E" (barycenter of the external outline) and "I" (barycenter of the internal outline)
delta	numeric: picture elements of adjustable side length
Cx	numeric: new x center coordinate
Cy	numeric: new y center coordinate
I_xy	logical: if TRUE the product of inertia around the x and y axis is calculated
I_minmax	logical: if TRUE the Imin and Imax will be calculated
Zxy	logical: if TRUE the polar moment of inertia will be calculated

Value

Cx x coordinate of the centered section

Cy y coordinate of the centered section

T_area total area

M_area medullar area

CA cortical area

Ext_perim external perimeter

Med_perim medullar perimiter

Mean_thick mean thickness of the section

Sd_thick thickness standard deviation

Min_thick minimum thickness

Max_thick maximum thickness

Ix numeric: moment of inertia around the x axis

Iy numeric: moment of inertia around the y axis

Zx numeric: moment of inertia around the x axis

Zy numeric: moment of inertia around the y axis

Zpol numeric: polar moment of inertia

dx new centered coordinates of the internal outline

dy new centered coordinates of the internal outline

Imin numeric: minimum moment of inertia

Imax numeric: maximum moment of inertia

J numeric: polar moment of inertia

Zmax numeric: the maximum polar section

Zmin numeric: the minimum polar section

theta numeric: theta angle

Author(s)

Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi

Examples

#calculation of csg parameter on a human femur cross section
data(HomFem38023)
meshes<-morphomapSegm(HomFem38023, param1=4)
perMesh<-meshes$external
endMesh<-meshes$internal
mech_length<-380.23
rawSections<-morphomapCore(out.sur=perMesh,
                           inn.sur=endMesh,num.sect=61,mech.len = mech_length, 
                           start = 0.2,end=0.8)
shapeSections<-morphomapShape(rawSections,250,sects_vector=NULL,cent.out="CCA",
delta=0.1, side="left")
csgSect31<-morphomapCSG(cp = shapeSections$`2D_out`[,,31],
                        mp=shapeSections$`2D_inn`[,,31],
                        translate = FALSE,center="CCA")

#Cross sectional geometry along the entire femur bone
results<-matrix(NA,ncol=24,nrow=61)
rownames(results)<-paste("section",c(1:61))
colnames(results)<-c("Cx","Cy","T_area","M_area","CA",
                     "Ext_perim","Med_perim","Mean_thick","Sd_thick" ,
                     "Min_thick","Max_thick","Ix","Iy","Zx" ,"Zy","Zpol" ,
                     "dx","dy","Imin","Imax","J","Zmax","Zmin","theta")

for(i in 1:61){
  results[i,]<-unlist(morphomapCSG(cp = shapeSections$`2D_out`[,,i],
                                     mp=shapeSections$`2D_inn`[,,i],
                                   translate = FALSE,center="CCA",delta = 0.5))
}

plot(c(1:61),results[,24],type="b",main="Theta",cex=1,
     xlab="section",ylab="radians")


#calculation of csg parameter on a chimpanzee femur cross section
data(PanFem27713)
meshes<-morphomapSegm(PanFem27713, param1=3)
perMesh<-meshes$external
endMesh<-meshes$internal
mech_length<-277.13
rawSections<-morphomapCore(out.sur=perMesh,
                           inn.sur=endMesh,num.sect=61,mech.len = mech_length, 
                           start = 0.2,end=0.8)
shapeSections<-morphomapShape(rawSections,250,sects_vector=NULL,cent.out="CCA",
delta=0.1, side="left")
csgSect31<-morphomapCSG(cp = shapeSections$`2D_out`[,,31],
                        mp=shapeSections$`2D_inn`[,,31],
                        translate = FALSE,center="CCA")

#Cross sectional geometry along the entire femur bone
results<-matrix(NA,ncol=24,nrow=61)
rownames(results)<-paste("section",c(1:61))
colnames(results)<-c("Cx","Cy","T_area","M_area","CA",
                     "Ext_perim","Med_perim","Mean_thick","Sd_thick" ,
                     "Min_thick","Max_thick","Ix","Iy","Zx" ,"Zy","Zpol" ,
                     "dx","dy","Imin","Imax","J","Zmax","Zmin","theta")

for(i in 1:61){
  results[i,]<-unlist(morphomapCSG(cp = shapeSections$`2D_out`[,,i],
                                   mp=shapeSections$`2D_inn`[,,i],
                                   translate = FALSE,center="CCA",delta = 0.5))
  }

plot(c(1:61),results[,24],type="b",main="Theta",cex=1,
     xlab="section",ylab="radians")

morphomap documentation built on Oct. 10, 2023, 1:08 a.m.