morphomap3Dmap {morphomap}

morphomap3Dmap

Description

Plot a 3D thickness map in four different anatomical views

Usage

morphomap3Dmap(
  morphomap.shape,
  out.sur,
  method = "equiangular",
  scale = TRUE,
  rem.out = FALSE,
  fac.out = 0.5,
  smooth = FALSE,
  smooth.iter = 5,
  k = 5,
  plot = TRUE,
  pal = blue2green2red(101)
)

Arguments

morphomap.shape

list: output from morphomapShape function

out.sur

3D mesh: 3D mesh of the long bone

method

character: if set on "equiangular" the cortical thickness is meant as the distance of the segment intersecting the external and internal outline starting from the centroid of the section. If set on "closest" the cortical thickness is calculated at each point as the closest distance between external and internal outlines

scale

logical: if TRUE the cortical thickness matrix will be scaled from 0 to 1

rem.out

logical: if TRUE outliers are identified and removed from thickness matrix

fac.out

numeric: parameter to set the threshold in outliers detection

smooth

logical: if TRUE the smoothing filter is applied on the thickness matrix

smooth.iter

numeric: number of smoothing iterations

k

integer: neighbourhood of kd-tree to search the nearest semilandmarks to each vertex

plot

logical: if TRUE the 3D map is plotted

pal

character vector: colors to be used in the map production

Value

cols color associated at each vertex of 3D mesh

thickmat thickness matrix after smoothing and outliers removal

Author(s)

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

Examples

if(interactive()){
#morphomap 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,param1 = 0.5,
radius.fact = 2.5,npovs = 100,clean_int_out = TRUE,
num.points = 500, start = 0.2,end=0.8)
shapeSections<-morphomapShape(rawSections,24,sects_vector=NULL,cent.out="CCA",
delta=0.1, side="left")

#built 3D morphometric map 
bone3Dmap<-morphomap3Dmap(shapeSections, out.sur=perMesh,
                          plot = TRUE,rem.out=TRUE,
                          fac.out=1.5,smooth=TRUE,
                          smooth.iter=5)
#or
require(rgl)
rgl::open3d()
rgl::shade3d(perMesh,col=bone3Dmap$cols,specular="black")

#morphomap 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)
shapeSections<-morphomapShape(rawSections,24,sects_vector=NULL,cent.out="CCA",
delta=0.1, side="left")
#built 3D morphometric map 
bone3Dmap<-morphomap3Dmap(shapeSections, out.sur=perMesh,
                          plot = TRUE,rem.out=TRUE,
                          fac.out=1.5,smooth=TRUE,
                          smooth.iter=5)
#or
require(rgl)
rgl::open3d()
rgl::shade3d(perMesh,col=bone3Dmap$cols,specular="black")
}