morphomapCore {morphomap}

morphomapCore

Description

Tool to build 3D and 2D cross sections

Usage

morphomapCore(
  out.sur = out.sur,
  inn.sur = inn.sur,
  num.sect = 61,
  mech.len,
  clean_int_out = TRUE,
  param1 = 0.5,
  radius.fact = 2.5,
  npovs = 100,
  num.points = 500,
  start = 0.2,
  end = 0.8,
  print.progress = TRUE
)

Arguments

out.sur

object of class mesh3d

inn.sur

object of class mesh3d

num.sect

number of sections

mech.len

mechanical length of the long bone

clean_int_out

logical if TRUE the inner section will be cleaned by using spherical flipping

param1

numeric parameter for spherical flipping operator (how much the section will be deformed)

radius.fact

numeric parameter for spherical flipping operator (distance from the center of the outline at which the povs are defined)

npovs

numeric: number of points of view defined around the section

num.points

number of equiengular points to be defined on each section

start

percentage of the mechanical length from which the first section is defined

end

percentage of the mechanical length from which the last section is defined

print.progress

logical: if TRUE a progress bar is printed to the screen

Value

3D_out num.pointsx3xnum.sect array of the external outlines

3D_inn num.pointsx3xnum.sect array of the internal outlines

2D_out num.pointsx2xnum.sect array of the external outlines

2D_inn num.pointsx2xnum.sect array of the internal outlines

mech_length mechanical length of the long bone

start percentage of the mechanical length from which the first section is defined

end percentage of the mechanical length from which the last section is defined

Author(s)

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

Examples

if(interactive()){
#raw section on a human femur bone
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)
#2D plot of the first section
plot(rawSections$`2D_out`[,,1],col="grey",asp=1,xlab="x",ylab="y",type="l")
points(rawSections$`2D_inn`[,,1],col="red",type="l")
#3D plot of the first section
require(rgl)
rgl::open3d()
rgl::plot3d(rawSections$`3D_out`[,,1],aspect=FALSE,col="grey",
type="l",lwd=5,xlab="x",ylab="y",zlab="z")
rgl::plot3d(rawSections$`3D_inn`[,,1],aspect=FALSE,col="red",
type="l",lwd=5,add=TRUE)

#raw section on a chimpanzee femur bone
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)
#2D plot of the first section
plot(rawSections$`2D_out`[,,1],col="grey",asp=1,xlab="x",ylab="y",type="l")
points(rawSections$`2D_inn`[,,1],col="red",type="l")
#3D plot of the first section
require(rgl)
rgl::open3d()
rgl::plot3d(rawSections$`3D_out`[,,1],aspect=FALSE,col="grey",
type="l",lwd=5,xlab="x",ylab="y",zlab="z")
rgl::plot3d(rawSections$`3D_inn`[,,1],aspect=FALSE,col="red",
type="l",lwd=5,add=TRUE)
}