morphomapCore: morphomapCore

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

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)
}

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