morphomap (version 1.5)

morphomapCSG: 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
)

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

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

Author

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

Examples

# \donttest{
#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")
# }