morphomap3Dmap: morphomap3Dmap

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

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")
}

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