2D and 3D cortical thickness maps and cross sectional geometry

Description

Tool to process long bone meshes (shape data, morphometric maps and cross-sectional geometry)

Author(s)

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

example dataset

Description

morphomapShape objects from 5 femora

Usage

data(Ex_mpShapeList)

Author(s)

Antonio Profico

example dataset

Description

3D mesh of a human femur bone

Usage

data(HomFem38023)

Author(s)

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

example dataset

Description

3D mesh of a chimpanzee femur bone

Usage

data(PanFem27713)

Author(s)

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

morphomap2Dmap

Description

Create a 2D cortical thickness map

Usage

morphomap2Dmap(
  morphomap.shape,
  rem.out = FALSE,
  fac.out = 0.5,
  smooth = FALSE,
  scale = TRUE,
  smooth.iter = 5,
  gamMap = FALSE,
  nrow = 90,
  ncol = 100,
  gdl = 250,
  method = "equiangular",
  unwrap = "A",
  plot = TRUE,
  pal = blue2green2red(101),
  aspect = 2
)

Arguments

Value

dataframe dataframe for colormap production

2Dmap thickness color map

gamoutput output from GAM

data input used to build the GAM map

Author(s)

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

Examples

if (interactive()){
library(colorRamps)
#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, start = 0.2,end=0.8)
shapeSections<-morphomapShape(rawSections,24,sects_vector=NULL,cent.out="CCA",
delta=0.1, side="left")

#built 2D morphometric map without GAM smoothing
bone2Dmap<-morphomap2Dmap(morphomap.shape=shapeSections,
                          plot = TRUE, rem.out = TRUE,fac.out = 1.0, pal = blue2green2red(101),
                          aspect=2)
#built 2D morphometric map with GAM smoothing
bone2Dmap<-morphomap2Dmap(morphomap.shape=shapeSections,gam=TRUE,
                          plot = TRUE, rem.out = TRUE,fac.out = 1.0, pal = blue2green2red(101),
                          aspect=2)

#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 2D morphometric map without GAM smoothing
bone2Dmap<-morphomap2Dmap(morphomap.shape=shapeSections,plot = TRUE, 
rem.out = TRUE,fac.out = 1.0,pal = blue2green2red(101),aspect=2)
#built 2D morphometric map with GAM smoothing
bone2Dmap<-morphomap2Dmap(morphomap.shape=shapeSections,gam=TRUE,
                          plot = TRUE, rem.out = TRUE,fac.out = 1.0,pal = blue2green2red(101),
                          aspect=2)
}

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

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")
}

morphomapAlignment

Description

Align a femur bone following the protocol proposed by Ruff (2002)

Usage

morphomapAlignment(
  mesh,
  set,
  side = c("left", "right"),
  param1 = 4,
  iter1 = 2000,
  iter2 = 2000,
  iter3 = 2000,
  from1 = 180,
  to1 = 360,
  from2 = -5,
  to2 = 5,
  from3 = -5,
  to3 = 5,
  tol = 0.5
)

Arguments

Details

The function 'morphomapAlignment' is designed to align a femur bone. I did not tested on other long bones. The function requires 7 anatomical landmarks samples as follow: 1-the point at the center of the diaphysis in posterior view after the less trochanter, 2- the most posterior point on the lateral epicondyle, 3-the most posterior point on the medial epicondyle, 4- the most inferior point on the intercondilar fossa, 5- neck of the femur, 6- the most inferior point on the medial epicondyle and 7-the most inferior point on the lateral epicondyle. If the function in a short time does not complete the alignement, please stop the R session, check your landmark configuration or try to increase the value of the argument 'tol'.

Value

sur: mesh of the aligned femur bone

coo: coordinates of the landmark used in the alignment (plus two added automatically)

mech_length: mechanical length of the aligned femur bone

Author(s)

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

morphomapArea

Description

Shoelace formula to calculate the area of a closed outline

Usage

morphomapArea(p, delta = 0.1, method = "shoelace")

Arguments

Value

ar numeric: area

Author(s)

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

Examples

extsec<-morphomapCircle(10,100)
#shoelace method
area<-morphomapArea(extsec, method="shoelace")
#delta method
area<-morphomapArea(extsec, method="delta",delta=0.01)

morphomapArray2matrix

Description

Convert an array into a matrix

Usage

morphomapArray2matrix(array)

Arguments

Value

mat a matrix

Author(s)

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

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
)

Arguments

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

Author(s)

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

Examples

#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")

morphomapCentroid

Description

Calculate the barycenter of the cortical area

Usage

morphomapCentroid(cp, mp, delta = 0.1)

Arguments

Value

centroid numeric vector: coordinates of the cortical area

Author(s)

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

Examples

extsec<-morphomapCircle(10,100)
intsec<-morphomapCircle(8,100)
plot(extsec,asp=1,type="l")
points(intsec,col=2,type="l")
cent<-morphomapCentroid(extsec,intsec,delta = 0.1)  
points(cent[1],cent[2],pch=19,col=3)

morphomapCheck

Description

Plot the long bone mesh to check the orientation of the long bone

Usage

morphomapCheck(mesh, col = "white")

Arguments

Author(s)

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

Examples

library(morphomap)
data(HomFem38023)
morphomapCheck(HomFem38023)

morphomapCircle

Description

Define a circular outline

Usage

morphomapCircle(r = 1, n = 1000)

Arguments

Value

mat matrix with coordinates

Author(s)

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

Examples

extsec<-morphomapCircle(10,100)
intsec<-morphomapCircle(8,100)
plot(extsec,asp=1,type="l")
points(intsec,type="l",col=2)

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

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)
}

morphomapDF

Description

Tool to build a data.frame suitable for morphometric maps

Usage

morphomapDF(
  morphomap.thickness,
  rem.out = TRUE,
  fac.out = 0.5,
  smooth = TRUE,
  scale = TRUE,
  smooth.iter = 5,
  method = "equiangular",
  unwrap = "A"
)

Arguments

Value

XYZ data.frame for morphometric map

labels character vector for x labels in the morphometric map

Author(s)

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

Examples

library(lattice)
library(colorRamps)
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,21,sects_vector=NULL,cent.out="CCA",delta=0.1)
femthick<-morphomapThickness(shapeSections)
dataDF<-morphomapDF(femthick)$XYZ
contourplot(dataDF[, 3] ~ dataDF[, 1] + dataDF[, 2],
            col.regions=blue2green2red(101),region=TRUE,
            colorkey=list(at=seq(0,1,length.out = 100)),
            scales = list(x = list(at = seq(0,100,length.out = 5), c("A","M","P","L","A"), 
            alternating = 1)),asp=1.5,cuts=20,xlab="femur margin",ylab="biomechanical length")

morphomapExport

Description

Export the output from ToothAlignement

Usage

morphomapExport(mpShapeObject, id, file)

Arguments

Author(s)

Antonio Profico

morphomapFlip

Description

Spherical flipping operator for bi-dimensional configuration

Usage

morphomapFlip(mat, param1 = 0.8, param2 = 10, radius.fact = 1.5, npovs = 100)

Arguments

Value

mat matrix after spherical flipping

Author(s)

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

Examples

#create a section
extsec<-morphomapCircle(10,1000)
intsec<-morphomapCircle(8,1000)
#simulate noise 
noiseX<-rnorm(1000,mean = 0,sd = 0.2)
noiseY<-rnorm(1000,mean = 0,sd = 0.2)
noise<-cbind(noiseX,noiseY)
noisect<-intsec+noise
#spherical flipping
flipsect<-morphomapFlip(noisect,param1 = 2,radius.fact = 2)
sortsect<-morphomapSort(flipsect)
#original section
plot(extsec,asp=1,type="l",xlim=c(-15,15),ylim=c(-15,15))
points(intsec,asp=1,type="l",xlim=c(-15,15),ylim=c(-15,15))
#noise
points(noisect,col=2)
#new section after spherical flipping
points(sortsect,type="l",col=3,asp=1,lwd=2)

morphomapImport

Description

Import a morphomapShape object exported with morphomapExport

Usage

morphomapImport(file)

Arguments

Value

3D_out num.pointsx3xnum.sect array in which the external outlines are stored

3D_inn num.pointsx3xnum.sect array in which the internal outlines are stored

2D_out num.pointsx2xnum.sect array in which the external outlines are stored

2D_inn num.pointsx2xnum.sect array in which the interal outlines are stored

ALPM_inn array with the coordinates of ALPM coordinates on the external outline

ALPM_out array with the coordinates of ALPM coordinates on the internal outline

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

morphomapMatrix2array

Description

Convert a matrix into an array

Usage

morphomapMatrix2array(matrix, nsects)

Arguments

Value

array an array

Author(s)

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

morphomapMirror

Description

Mirror a long bone mesh along the yz plane

Usage

morphomapMirror(mesh)

Arguments

Value

mesh: object of class mesh3d

Author(s)

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

Examples

if(interactive()){
#a left human femur bone
require(rgl)
data(HomFem38023)
lfem<-HomFem38023
rfem<-morphomapMirror(lfem)
rgl::open3d()
rgl::wire3d(lfem,col="green")
rgl::ire3d(rfem,col="red")
}

morphomapMoment

Description

Calculate the moment of inertia around the x and y axes and the product of inertia

Usage

morphomapMoment(cp, mp, delta = 0.1)

Arguments

Value

Ix numeric: moment of inertia around the x axis

Iy numeric: moment of inertia around the y axis

Ixy numeric: product of inertia around the x and y axis

Author(s)

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

Examples

#create a section
extsec<-morphomapCircle(10,1000)
intsec<-morphomapCircle(8,1000)
InMs<-morphomapMoment(extsec,intsec,delta=0.1)

morphomapPCA

Description

Calculate maps of cortical thickness and perform a Principal Component Analysis

Usage

morphomapPCA(
  mpShapeList,
  gamMap = TRUE,
  nrow = 61,
  ncol = 24,
  rem.out = TRUE,
  scaleThick = FALSE,
  fac.out = 1.5,
  method = "equiangular",
  scalePCA = TRUE,
  unwrap = "A"
)

Arguments

Value

PCscores PC scores

PCs loadings

Variance Table of the explained Variance by the PCs

meanMap mean morphometric map

CorMaps morphometric maps

Author(s)

Antonio Profico

Examples

data(Ex_mpShapeList)
PCA<-morphomapPCA(Ex_mpShapeList)
plot(PCA$PCscores)
barplot(PCA$Variance[,2])

morphomapPic

Description

Save the sections defined via morphomapShape or morphomapCore

Usage

morphomapPic(
  morphomap.core,
  morphomap.shape,
  vector = NULL,
  full = TRUE,
  width = 1500,
  height = 1500,
  pointsize = 12,
  res = 300,
  colthk = "red",
  collbs = "blue",
  dirpath = tempdir()
)

Arguments

Author(s)

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

Examples

#export picture from 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=11,mech.len = mech_length, 
                           start = 0.2,end=0.8)
shapeSections<-morphomapShape(rawSections,250,sects_vector=NULL,cent.out="CCA",
delta=0.5, side="left")
morphomapPic(rawSections,shapeSections,full=TRUE,dirpath=tempdir(),
            width=2500,height=2500)

#export picture from 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=11,mech.len = mech_length, 
                           start = 0.2,end=0.8)
shapeSections<-morphomapShape(rawSections,250,sects_vector=NULL,cent.out="CCA",delta=0.5,
 side="left")
morphomapPic(rawSections,shapeSections,full=TRUE,dirpath=tempdir(),
             width=2500,height=2500)

morphomapPlotShape

Description

Visualize 2D and 3D cross sections

Usage

morphomapPlotShape(
  Shape,
  dims = 3,
  col1 = "red",
  col2 = "green",
  colc = "orange",
  colr = "violet",
  coll1 = "darkred",
  coll2 = "darkgreen",
  size = 1.5,
  lwd = 0.7,
  colmesh1 = "red",
  colmesh2 = "green",
  alpha = 0.3,
  tri = TRUE,
  outlines = TRUE,
  points = TRUE,
  lines = FALSE,
  centroid = FALSE,
  cent.out = "CCA",
  delta = 0.1,
  vecs = NULL
)

Arguments

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)
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,21,sects_vector=NULL,cent.out="CCA",
delta=0.1, side="left")
#Plot the object morphomapShape in three dimensions
morphomapPlotShape(shapeSections,dims=3, size=0.5)
#Plot a 2D cross-section 
morphomapPlotShape(shapeSections,dims=2,lines=TRUE,vecs=31)
}

morphomapReadMorphologika

Description

Import an array stored in a morphologika file

Usage

morphomapReadMorphologika(file)

Arguments

Value

out list containing an array, labels, groups and variables

Author(s)

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

morphomapRectangle

Description

Define a rectangular outline

Usage

morphomapRectangle(l = 1, h = 1, n = 1000)

Arguments

Value

mat matrix with coordinates

Author(s)

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

Examples

extsec<-morphomapRectangle(10,6,100)
intsec<-morphomapRectangle(8,4,100)
plot(extsec,asp=1,type="l")
points(intsec,type="l",col=2)

morphomapRegradius

Description

Wrapper of the function regularradius written by Julien Claude (Morphometrics with R)

Usage

morphomapRegradius(mat, center, n)

Arguments

Value

V2 position of landmarks equi angular spaced

Author(s)

Julien Claude, Antonio Profico

References

Claude, J. (2008). Morphometrics with R. Springer Science & Business Media.

Examples

extsec<-morphomapCircle(10,1000)
sel<-morphomapRegradius(extsec,center = c(0,0),n=11)
selcoo<-extsec[sel,]
plot(extsec,type="l",asp=1)
points(selcoo,col="red",pch=19)

morphomapSegm

Description

Separate a mesh from its visible and not visible components by using CA-LSE method

Usage

morphomapSegm(mesh, views = 30, param1 = 4, num.cores = NULL)

Arguments

Details

The result could be affected by the value set in the param1 argument. Before running morphomapCore please the periosteal and endosteal surfaces.

Value

external mesh3d of the visible facets from the points of view

internal mesh3d of the not visible facets from the points of view

Author(s)

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

References

Profico A., Schlager S., Valoriani V., Buzi C., Melchionna M., Veneziano A., Raia P., Moggi-Cecchi J. and Manzi G., 2018. Reproducing the internal and external anatomy of fossil bones: Two new automatic digital tools. American Journal of Physical Anthropology 166(4): 979-986.

Examples

if(interactive()){
#automatic separation of external and medullar femur components
require(rgl)
data(HomFem38023)
meshes<-morphomapSegm(HomFem38023,param1=4)
perMesh<-meshes$external
endMesh<-meshes$internal
rgl::open3d()
rgl::wire3d(perMesh,col="grey")
rgl::wire3d(endMesh,col="red")
}

morphomapShape

Description

Tool for the extraction of equiangular landmarks on the entire diaphysis

Usage

morphomapShape(
  morphomap.core,
  num.land,
  sects_vector,
  cent.out = "CCA",
  delta = 0.1,
  side = "left"
)

Arguments

Value

3D_out num.pointsx3xnum.sect array in which the external outlines are stored

3D_inn num.pointsx3xnum.sect array in which the internal outlines are stored

2D_out num.pointsx2xnum.sect array in which the external outlines are stored

2D_inn num.pointsx2xnum.sect array in which the interal outlines are stored

ALPM_inn array with the coordinates of ALPM coordinates on the external outline

ALPM_out array with the coordinates of ALPM coordinates on the internal outline

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

library(morphomap)
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,num.points = 500)
# Shape coordinates defining as center the barycenter of the cortical area
shapeSections_CCA<-morphomapShape(rawSections,21,sects_vector=NULL, cent.out="CCA",
delta=0.1,side="left")
# First the first cross section (2D)
morphomapPlotShape(shapeSections_CCA,dims=2,cent.out="CCA",vecs=1)
# First the first cross section (3D)
morphomapPlotShape(shapeSections_CCA,dims=3,size=0.5,lwd=2,cent.out="I",vecs=1)
# The entire diaphysis (3D)
morphomapPlotShape(shapeSections_CCA,dims=3,size=0.5,lwd=2,cent.out="I",vecs=NULL)
# Shape coordinates defining as center the barycenter of the external perimeter
shapeSections_E<-morphomapShape(rawSections, 21, sects_vector=NULL, cent.out="E", 
delta=0.1, side="left")
# First the first cross section (2D)
morphomapPlotShape(shapeSections_E,dims=2,cent.out="E",vecs=1)
# First the first cross section (3D)
morphomapPlotShape(shapeSections_E,dims=3,size=0.5,lwd=2,cent.out="I",vecs=1)
# The entire diaphysis (3D)
morphomapPlotShape(shapeSections_E,dims=3,size=0.5,lwd=2,cent.out="I",vecs=NULL)

# Shape coordinates defining as center the barycenter of the internal perimeter 
shapeSections_I<-morphomapShape(rawSections, 21, sects_vector=NULL, cent.out="I", 
delta=0.1, side="left")
# First the first cross section (2D)
morphomapPlotShape(shapeSections_I,dims=2,lines=TRUE,cent.out="I",vecs=1)
# First the first cross section (3D)
morphomapPlotShape(shapeSections_I,dims=3,lines=TRUE,centroid=TRUE, size=0.5,
lwd=2,cent.out="I",vecs=1)
# The entire diaphysis (3D)
morphomapPlotShape(shapeSections_I,dims=3,size=0.5,lwd=2,cent.out="I",vecs=NULL)

morphomapSort

Description

Sort a series of points stored as a 2D matrix

Usage

morphomapSort(mat)

Arguments

Value

mat sorted kx2 matrix

Author(s)

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

Examples

rand<-sample(100)
extsec<-morphomapCircle(10,100)[rand,]
plot(extsec,type="l",asp=1)
sorted<-morphomapSort(extsec)
plot(sorted,type="l",asp=1)

morphomapThickness

Description

Tool for the extraction of equiangular landmarks on the entire diaphysis

Usage

morphomapThickness(morphomap.shape)

Arguments

Value

sect_thickness cortical thickness at each pair of landmarks on the external and internal outlines

ALPM_thickness cortical thickness at ALPM quadrants

Author(s)

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

Examples

#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, 
                           start = 0.2,end=0.8)
shapeSections<-morphomapShape(rawSections,21,sects_vector=NULL,cent.out="CCA",delta=0.1)
femthick<-morphomapThickness(shapeSections)
plot(femthick$ALPM_thickness[1,,],type="l",
     main="LAMP thickness",xlab="section",ylab="thickness")
points(femthick$ALPM_thickness[2,,],type="l",col=2)
points(femthick$ALPM_thickness[3,,],type="l",col=3)
points(femthick$ALPM_thickness[4,,],type="l",col=4)

morphomapTranslate

Description

Translate a section to a new center defined by the user

Usage

morphomapTranslate(corA, medA, Cx, Cy)

Arguments

Value

cortical new centered coordinates of the external outline

medullar new centered coordinates of the internal outline

Author(s)

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

Examples

extsec<-morphomapCircle(10,1000)
intsec<-morphomapCircle(8,1000)
plot(extsec,asp=1,type="l",xlim=c(-11,11),ylim=c(-11,11))
points(intsec,type="l")
traSect<-morphomapTranslate(extsec,intsec,1,1)
points(traSect$cortical,type="l",col="red")
points(traSect$medullar,type="l",col="red")

morphomapTri2sects

Description

Triangulate the external and internal outlines of a 3D cross section

Usage

morphomapTri2sects(cp, mp)

Arguments

Value

matrix coordinates of the triangulated mesh

tri triangulations of the triangulated mesh

Author(s)

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

morphomapTriangulate

Description

Build a mesh starting from the coordinates of the diaphysis

Usage

morphomapTriangulate(set, n, close = FALSE)

Arguments

Value

mesh a mesh of the triangulated semilandark configuration

Author(s)

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

morphomapVariations

Description

Calculate cortical map variation from PCA

Usage

morphomapVariations(PCA, scores, PC, pal = blue2green2red(101), asp = 2)

Arguments

Value

mapvar: matrix containing values of cortical thickness

Author(s)

Antonio Profico

Examples

data(Ex_mpShapeList)
PCA<-morphomapPCA(Ex_mpShapeList)
plot(PCA$PCscores)
barplot(PCA$Variance[,2])
morphomapVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1])
morphomapVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1])

morphomapWriteMorphologika

Description

Export an array in the morphologika format file

Usage

morphomapWriteMorphologika(array, groups = NULL, variables = NULL, file)

Arguments

Author(s)

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

morphomapZmoment

Description

Calculate the polar moment of inertia around the x and y axes and the polar section module

Usage

morphomapZmoment(cp, mp, Cx = 0, Cy = 0, delta = 0.1)

Arguments

Value

Zx numeric: moment of inertia around the x axis

Zy numeric: moment of inertia around the y axis

dx numeric: maximum chord length from y axis

dy numeric: maximum chord length from x axis

Zpol numeric: polar moment of inertia

Author(s)

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

Examples

extsec<-morphomapCircle(10,1000)
intsec<-morphomapCircle(8,1000)
ZMs<-morphomapZmoment(extsec,intsec,delta=0.1)