Package 'Toothnroll' reference manual

Title:	Dental Tissues Landmarking Measuring and Mapping
Description:	Two- and three-dimensional morphometric maps of enamel and dentine thickness and multivariate analysis. Volume calculation of dental materials. Principal component analysis of thickness maps with associated morphometric map variations.
Authors:	Antonio Profico [cre, aut], Mathilde Augoyard [aut]
Maintainer:	Antonio Profico <[email protected]>
License:	GPL-2
Version:	1.11
Built:	2024-11-21 06:22:16 UTC
Source:	https://github.com/cran/Toothnroll

Tooth2Dmap

Description

Create 2D morphometric maps of enamel/dentin thickness

Usage

Tooth2Dmap(
  tooth.shape,
  input,
  rem.out = FALSE,
  fac.out = 0.5,
  smooth = FALSE,
  scale = TRUE,
  smooth.iter = 5,
  gamMap = FALSE,
  nrow = 120,
  ncol = 80,
  gdl = 250,
  method = "equiangular",
  plot = TRUE,
  pal = blue2green2red(101),
  aspect = 0.6,
  labels = c("Li", "Mes", "Bu", "D", "Li"),
  ylab = ""
)
Tooth2Dmap(
  tooth.shape,
  input,
  rem.out = FALSE,
  fac.out = 0.5,
  smooth = FALSE,
  scale = TRUE,
  smooth.iter = 5,
  gamMap = FALSE,
  nrow = 120,
  ncol = 80,
  gdl = 250,
  method = "equiangular",
  plot = TRUE,
  pal = blue2green2red(101),
  aspect = 0.6,
  labels = c("Li", "Mes", "Bu", "D", "Li"),
  ylab = ""
)

Arguments

`tooth.shape`	list: output from the function ToothShape
`input`	list: output from the function ToothAlignment
`rem.out`	logical: if TRUE outliers will be removed
`fac.out`	numeric: parameter to set the threshold in outlier detection
`smooth`	logical: if TRUE a smoothing filter is applied
`scale`	logical: if TRUE the thichkness matrix is scaled from 0 to 1
`smooth.iter`	numeric: number of smoothing iterations
`gamMap`	logical: if TRUE gam smoothing is applied
`nrow`	numeric: number of rows for gam smoothing matrix
`ncol`	numeric: number of columns for gam smoothing matrix
`gdl`	numeric: number of degree of freedom for gam smoothing matrix
`method`	character: if set on "equiangular" the dentine or enamel 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 dentine or enamel thickness is calculated at each point as the closest distance between external and internal outlines
`plot`	logical: if TRUE the 2D morphometric map is plotted
`pal`	character vector: colors to be used in the map production
`aspect`	numeric: axis ratio for 2D morphometric map
`labels`	character vector: names for x labels in the morphometric map
`ylab`	character vector: label for y axis in the morphometric map

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; Mathilde Augoyard

Examples


data("URI1_tooth")
require(morphomap)
Enamel<-URI1_tooth$mesh1
Dentin<-URI1_tooth$mesh2
Pulp<-URI1_tooth$mesh3
outline<-URI1_tooth$outline
set<-URI1_tooth$set
#Map of the crown
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "c")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh1$mesh
Internal<-AlignMeshes$almesh2$mesh
#Define 16 cross-sections from the 30% to the 90% along the crown
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                    bio.len = AlignMeshes$length,start=0.3,end=0.9)
#Extract 25 equiangular semilandmarks from each cross-section (anticlockwise)
Shape<-ToothShape(Core,25,sects_vector = NULL,cent.out = "E",direction="a")
Tooth2Dmap(Shape,AlignMeshes,rem.out =TRUE,scale=FALSE,smooth = FALSE,aspect = 0.5,gamMap = FALSE,
           nrow = 100,ncol = 100,gdl = 250,method="equiangular")

#Map of the root
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "r")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh2$mesh
Internal<-AlignMeshes$almesh3$mesh
#Define 16 cross-sections from the 10% to the 50% along the root
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                    bio.len = AlignMeshes$length,start=0.1,end=0.5)
#Extract 25 equiangular semilandmarks from each cross-section (anticlockwise)
Shape<-ToothShape(Core,25,sects_vector = NULL,cent.out = "E",direction="a")
Tooth2Dmap(Shape,AlignMeshes,rem.out =FALSE,scale=FALSE,smooth = FALSE,aspect = 0.5,gamMap = FALSE,
           nrow = 100,ncol = 100,gdl = 250,method="equiangular")

data("URI1_tooth")
require(morphomap)
Enamel<-URI1_tooth$mesh1
Dentin<-URI1_tooth$mesh2
Pulp<-URI1_tooth$mesh3
outline<-URI1_tooth$outline
set<-URI1_tooth$set
#Map of the crown
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "c")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh1$mesh
Internal<-AlignMeshes$almesh2$mesh
#Define 16 cross-sections from the 30% to the 90% along the crown
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                    bio.len = AlignMeshes$length,start=0.3,end=0.9)
#Extract 25 equiangular semilandmarks from each cross-section (anticlockwise)
Shape<-ToothShape(Core,25,sects_vector = NULL,cent.out = "E",direction="a")
Tooth2Dmap(Shape,AlignMeshes,rem.out =TRUE,scale=FALSE,smooth = FALSE,aspect = 0.5,gamMap = FALSE,
           nrow = 100,ncol = 100,gdl = 250,method="equiangular")

#Map of the root
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "r")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh2$mesh
Internal<-AlignMeshes$almesh3$mesh
#Define 16 cross-sections from the 10% to the 50% along the root
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                    bio.len = AlignMeshes$length,start=0.1,end=0.5)
#Extract 25 equiangular semilandmarks from each cross-section (anticlockwise)
Shape<-ToothShape(Core,25,sects_vector = NULL,cent.out = "E",direction="a")
Tooth2Dmap(Shape,AlignMeshes,rem.out =FALSE,scale=FALSE,smooth = FALSE,aspect = 0.5,gamMap = FALSE,
           nrow = 100,ncol = 100,gdl = 250,method="equiangular")

ToothAlignment

Description

Align dental meshes using as reference the cervical outline and five landmarks

Usage

ToothAlignment(mesh1, mesh2, mesh3 = NULL, set, outline, analyse = c("r", "c"))
ToothAlignment(mesh1, mesh2, mesh3 = NULL, set, outline, analyse = c("r", "c"))

Arguments

`mesh1`	3D mesh: dental mesh (enamel)
`mesh2`	3D mesh: dental mesh (dentin)
`mesh3`	3D mesh: dental mesh (dental pulp)
`set`	matrix: 5 landmarks acquired on the mesh (see details)
`outline`	matrix: set of coordinates along the cerical outline
`analyse`	character: "r" for root, "c" for crown

Details

The function needs five landmarks to align the dental meshes. Usually landmarks from 1 to 4 define the Lingual, Mesial, Buccal and Distal margins. The fifth landmark defines the end of the z axis (biomechanical length). The centroid of the cervical outline defines the origin of axes.

Value

almesh1: mesh of the aligned mesh1

almesh2: mesh of the aligned mesh2

almesh3: mesh of the aligned mesh3

alset: coordinates of the aligned landmark configuration

length: biomechanical length of the root (see details)

margins: coordinates of the landmarks in correspondence of the four margins

margins_sel: position of the margin along the outline

aloutline: coordinates of the aligned cervical outline

diamBL: bucco-lingual diameter

diamMD: mesio-distal diameter

Author(s)

Antonio Profico; Mathilde Augoyard

Examples


data("URI1_tooth")
Enamel<-URI1_tooth$mesh1
Dentin<-URI1_tooth$mesh2
Pulp<-URI1_tooth$mesh3
outline<-URI1_tooth$outline
set<-URI1_tooth$set

#Example on the root
AlignMeshesR<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "r")
  require(rgl)
  open3d()
  shade3d(AlignMeshesR$almesh1$mesh,col="white",alpha=0.5)
  shade3d(AlignMeshesR$almesh2$mesh,col="pink",alpha=0.5,add=TRUE)
  shade3d(AlignMeshesR$almesh3$mesh,col="orange",alpha=0.5,add=TRUE)
  spheres3d(AlignMeshesR$alset,radius=0.25)
  spheres3d(AlignMeshesR$outline,radius=0.1,col="blue")
  lines3d(AlignMeshesR$outline)
  text3d(rbind(AlignMeshesR$outline[AlignMeshesR$margins_sel,],AlignMeshesR$alset[4,]),
  texts=1:5,cex=4)
  spheres3d(AlignMeshesR$alset[2,],radius=0.3,col="red")
  arrow3d(colMeans(AlignMeshesR$aloutline),AlignMeshesR$alset[4,],lwd=3,col="green",
  type="lines",s=1/10)
  lines3d(rbind(AlignMeshesR$alset[2,],AlignMeshesR$alset[1,]),lwd=3,col="green")
  axes3d()

#Example on the crown

AlignMeshesC<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,
analyse = "c")
  require(rgl)
  open3d()
  shade3d(AlignMeshesC$almesh1$mesh,col="white",alpha=0.5)
  shade3d(AlignMeshesC$almesh2$mesh,col="pink",alpha=0.5,add=TRUE)
  shade3d(AlignMeshesC$almesh3$mesh,col="orange",alpha=0.5,add=TRUE)
  spheres3d(AlignMeshesC$alset,radius=0.25)
  spheres3d(AlignMeshesC$outline,radius=0.1,col="blue")
  lines3d(AlignMeshesC$outline)
  text3d(rbind(AlignMeshesC$outline[AlignMeshesC$margins_sel,],AlignMeshesC$alset[4,]),
  texts=1:5,cex=4)
  spheres3d(AlignMeshesC$alset[2,],radius=0.3,col="red")
  arrow3d(colMeans(AlignMeshesC$aloutline),AlignMeshesC$alset[4,],lwd=3,col="green",
  type="lines",s=1/10)
  lines3d(rbind(AlignMeshesC$alset[2,],AlignMeshesC$alset[1,]),lwd=3,col="green")
  lines3d(rbind(AlignMeshesC$alset[2,],AlignMeshesC$alset[1,]),lwd=3,col="green")
  
  axes3d()

data("URI1_tooth")
Enamel<-URI1_tooth$mesh1
Dentin<-URI1_tooth$mesh2
Pulp<-URI1_tooth$mesh3
outline<-URI1_tooth$outline
set<-URI1_tooth$set

#Example on the root
AlignMeshesR<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "r")
  require(rgl)
  open3d()
  shade3d(AlignMeshesR$almesh1$mesh,col="white",alpha=0.5)
  shade3d(AlignMeshesR$almesh2$mesh,col="pink",alpha=0.5,add=TRUE)
  shade3d(AlignMeshesR$almesh3$mesh,col="orange",alpha=0.5,add=TRUE)
  spheres3d(AlignMeshesR$alset,radius=0.25)
  spheres3d(AlignMeshesR$outline,radius=0.1,col="blue")
  lines3d(AlignMeshesR$outline)
  text3d(rbind(AlignMeshesR$outline[AlignMeshesR$margins_sel,],AlignMeshesR$alset[4,]),
  texts=1:5,cex=4)
  spheres3d(AlignMeshesR$alset[2,],radius=0.3,col="red")
  arrow3d(colMeans(AlignMeshesR$aloutline),AlignMeshesR$alset[4,],lwd=3,col="green",
  type="lines",s=1/10)
  lines3d(rbind(AlignMeshesR$alset[2,],AlignMeshesR$alset[1,]),lwd=3,col="green")
  axes3d()

#Example on the crown

AlignMeshesC<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,
analyse = "c")
  require(rgl)
  open3d()
  shade3d(AlignMeshesC$almesh1$mesh,col="white",alpha=0.5)
  shade3d(AlignMeshesC$almesh2$mesh,col="pink",alpha=0.5,add=TRUE)
  shade3d(AlignMeshesC$almesh3$mesh,col="orange",alpha=0.5,add=TRUE)
  spheres3d(AlignMeshesC$alset,radius=0.25)
  spheres3d(AlignMeshesC$outline,radius=0.1,col="blue")
  lines3d(AlignMeshesC$outline)
  text3d(rbind(AlignMeshesC$outline[AlignMeshesC$margins_sel,],AlignMeshesC$alset[4,]),
  texts=1:5,cex=4)
  spheres3d(AlignMeshesC$alset[2,],radius=0.3,col="red")
  arrow3d(colMeans(AlignMeshesC$aloutline),AlignMeshesC$alset[4,],lwd=3,col="green",
  type="lines",s=1/10)
  lines3d(rbind(AlignMeshesC$alset[2,],AlignMeshesC$alset[1,]),lwd=3,col="green")
  lines3d(rbind(AlignMeshesC$alset[2,],AlignMeshesC$alset[1,]),lwd=3,col="green")
  
  axes3d()

ToothCore

Description

Tool to build 3D and 2D cross sections

Usage

ToothCore(
  out.sur = out.sur,
  inn.sur = inn.sur,
  num.sect = 61,
  bio.len,
  clean_int_out_O = TRUE,
  clean_int_out_I = TRUE,
  param1_out = 0.5,
  radius.fact_out = 2.5,
  param1_inn = 0.5,
  radius.fact_inn = 2.5,
  npovs = 100,
  num.points = 500,
  start = 0.2,
  end = 0.8,
  curved = FALSE,
  print.progress = TRUE
)
ToothCore(
  out.sur = out.sur,
  inn.sur = inn.sur,
  num.sect = 61,
  bio.len,
  clean_int_out_O = TRUE,
  clean_int_out_I = TRUE,
  param1_out = 0.5,
  radius.fact_out = 2.5,
  param1_inn = 0.5,
  radius.fact_inn = 2.5,
  npovs = 100,
  num.points = 500,
  start = 0.2,
  end = 0.8,
  curved = FALSE,
  print.progress = TRUE
)

Arguments

`out.sur`	object of class mesh3d
`inn.sur`	object of class mesh3d
`num.sect`	number of sections
`bio.len`	length of the selected region of interest along with extracting the digital section
`clean_int_out_O`	logical if TRUE the outer section will be cleaned by using spherical flipping
`clean_int_out_I`	logical if TRUE the inner section will be cleaned by using spherical flipping
`param1_out`	numeric parameter for clean_int_out_O spherical flipping operator (how much the section will be deformed)
`radius.fact_out`	logical if TRUE the inner section will be cleaned by using spherical flipping
`param1_inn`	numeric parameter for clean_int_out_I spherical flipping operator (how much the section will be deformed)
`radius.fact_inn`	logical if TRUE the inner section will be cleaned by using spherical flipping
`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
`curved`	logical: if TRUE the cutting planes will follow the mesh curvature (beta version)
`print.progress`	logical: if TRUE a progress bar is printed to the screen

Value

out3D num.pointsx3xnum.sect array of the external outlines

inn3D num.pointsx3xnum.sect array of the internal outlines

out3D num.pointsx2xnum.sect array of the external outlines

inn3D 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; Mathilde Augoyard

Examples


data("URI1_tooth")
require(morphomap)
require(Morpho)
require(rgl)
Enamel<-URI1_tooth$mesh1
Dentin<-URI1_tooth$mesh2
Pulp<-URI1_tooth$mesh3
outline<-URI1_tooth$outline
set<-URI1_tooth$set

#Unrolling the crown
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "c")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh1$mesh
Internal<-AlignMeshes$almesh2$mesh
#Define 16 cross-sections from the 30% to the 90% along the crown
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                bio.len = AlignMeshes$length,start=0.3,end=0.9)

plot3d(morphomapArray2matrix(Core$"out3D"),aspect=FALSE,xlab="x",ylab="y",zlab="z")
plot3d(morphomapArray2matrix(Core$"inn3D"),aspect=FALSE,add=TRUE)
wire3d(AlignMeshes$almesh2$mesh,col="white")
wire3d(AlignMeshes$almesh1$mesh,col="violet")

#Unrolling the rooth
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "r")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh2$mesh
Internal<-AlignMeshes$almesh3$mesh
#Define 16 cross-sections from the 10% to the 50% along the root
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                bio.len = AlignMeshes$length,start=0.1,end=0.5)

plot3d(morphomapArray2matrix(Core$"out3D"),aspect=FALSE,xlab="x",ylab="y",zlab="z")
plot3d(morphomapArray2matrix(Core$"inn3D"),aspect=FALSE,add=TRUE)
wire3d(AlignMeshes$almesh3$mesh,col="red")
wire3d(AlignMeshes$almesh2$mesh,col="lightblue")
wire3d(AlignMeshes$almesh1$mesh,col="white")

data("URI1_tooth")
require(morphomap)
require(Morpho)
require(rgl)
Enamel<-URI1_tooth$mesh1
Dentin<-URI1_tooth$mesh2
Pulp<-URI1_tooth$mesh3
outline<-URI1_tooth$outline
set<-URI1_tooth$set

#Unrolling the crown
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "c")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh1$mesh
Internal<-AlignMeshes$almesh2$mesh
#Define 16 cross-sections from the 30% to the 90% along the crown
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                bio.len = AlignMeshes$length,start=0.3,end=0.9)

plot3d(morphomapArray2matrix(Core$"out3D"),aspect=FALSE,xlab="x",ylab="y",zlab="z")
plot3d(morphomapArray2matrix(Core$"inn3D"),aspect=FALSE,add=TRUE)
wire3d(AlignMeshes$almesh2$mesh,col="white")
wire3d(AlignMeshes$almesh1$mesh,col="violet")

#Unrolling the rooth
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "r")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh2$mesh
Internal<-AlignMeshes$almesh3$mesh
#Define 16 cross-sections from the 10% to the 50% along the root
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                bio.len = AlignMeshes$length,start=0.1,end=0.5)

plot3d(morphomapArray2matrix(Core$"out3D"),aspect=FALSE,xlab="x",ylab="y",zlab="z")
plot3d(morphomapArray2matrix(Core$"inn3D"),aspect=FALSE,add=TRUE)
wire3d(AlignMeshes$almesh3$mesh,col="red")
wire3d(AlignMeshes$almesh2$mesh,col="lightblue")
wire3d(AlignMeshes$almesh1$mesh,col="white")

ToothDF

Description

Tool to build a data.frame suitable for morphometric maps

Usage

ToothDF(
  tooth.thickness,
  rem.out = TRUE,
  fac.out = 0.5,
  smooth = TRUE,
  scale = TRUE,
  smooth.iter = 5,
  method = "equiangular",
  labels = c("Li", "Mes", "Bu", "D", "Li"),
  relThick = FALSE
)
ToothDF(
  tooth.thickness,
  rem.out = TRUE,
  fac.out = 0.5,
  smooth = TRUE,
  scale = TRUE,
  smooth.iter = 5,
  method = "equiangular",
  labels = c("Li", "Mes", "Bu", "D", "Li"),
  relThick = FALSE
)

Arguments

`tooth.thickness`	list: tooth.Thickness object
`rem.out`	logical: if TRUE the outlier will be removed
`fac.out`	numeric: parameter to set the threshold in outliers detection
`smooth`	logical: if TRUE the smooth algorithm is applied
`scale`	logical: if TRUE the thichkness matrix is scaled from 0 to 1
`smooth.iter`	numeric: number of smoothing iterations
`method`	character: if set on "equiangular" the dental 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 dental thickness is calculated at each point as the closest distance between external and internal outlines
`labels`	character vector: names for x labels in the morphometric map
`relThick`	logical: if TRUE the dental thickness is converted into relative dental thickness

Value

XYZ data.frame for morphometric map

labels character vector for x labels in the morphometric map

Author(s)

Antonio Profico; Mathilde Augoyard

ToothExport

Description

Export the output from ToothAlignement

Usage

ToothExport(input, id, file)
ToothExport(input, id, file)

Arguments

`input`	list: output from ToothAlignement
`id`	character: label name
`file`	character: name the output file

Value

no return value, called for side effects (see description)

Author(s)

Antonio Profico; Mathilde Augoyard

ToothImport

Description

Import the output from ToothAlignement

Usage

ToothImport(file)
ToothImport(file)

Arguments

file

character: name of input file

Value

Mesh1: mesh of the aligned mesh1

Mesh2: mesh of the aligned mesh2

Mesh3: mesh of the aligned mesh3

B.Length: length of the region of interest

Landmarks: landmark coordinates

Outline: outline coordinates

Margins: position of the margins along the outline

diamBL: bucco-lingual diameter

diamMD: mesio-distal diameter

Author(s)

Antonio Profico; Mathilde Augoyard

ToothPCA

Description

Perform the Principal Component Analysis on a list of tooth.shape objects

Usage

ToothPCA(
  mpShapeList,
  gamMap = FALSE,
  nrow = 120,
  ncol = 80,
  gdl = 250,
  rem.out = TRUE,
  scaleThick = FALSE,
  relThick = FALSE,
  fac.out = 1.5,
  method = "equiangular",
  scalePCA = TRUE
)
ToothPCA(
  mpShapeList,
  gamMap = FALSE,
  nrow = 120,
  ncol = 80,
  gdl = 250,
  rem.out = TRUE,
  scaleThick = FALSE,
  relThick = FALSE,
  fac.out = 1.5,
  method = "equiangular",
  scalePCA = TRUE
)

Arguments

`mpShapeList`	list: tooth.shape objects
`gamMap`	logical: if TRUE gamMap spline method is applied
`nrow`	numeric: number of rows if gamMap is TRUE
`ncol`	numeric: number of columns if gamMap is TRUE
`gdl`	numeric: degree of freedom (if gamMap is TRUE)
`rem.out`	logical: if TRUE outliers are removed
`scaleThick`	logical: if TRUE thickness values are scaled from 0 to 1
`relThick`	logical: if TRUE the thickness values are scaled by the diameter from the centroid to the external outline
`fac.out`	numeric: threshold to define an outlier observation
`method`	character: "equiangular" or "closest" to define the thickness from evenly spaced or closest semilandmarks between the external and internal outline
`scalePCA`	logical: indicate whether the variables should be scaled to have unit variance

Value

PCscores matrix of PC scores

PCs principal components

variance table of the explained Variance by the PCs

meanMap mean map

CorMaps maps of thickness used as input in the PCA

Author(s)

Antonio Profico; Mathilde Augoyard

Examples

### Example on the canine crown
data("UCcrown")
require(morphomap)
shapeList<-UCcrown
PCA<-ToothPCA(shapeList,gamMap = FALSE,scaleThick = TRUE,scalePCA = TRUE ,relThick = FALSE)
 
#gamMap set on TRUE
PCA<-ToothPCA(shapeList,gamMap = TRUE,scaleThick = TRUE,scalePCA = TRUE,relThick = FALSE)

otu<-substr(names(shapeList),1,2)
pchs <- ifelse(otu == "MH", 16, 17)
cols <- ifelse(otu == "MH", "orange", "darkblue")

plot(PCA$PCscores,col=cols,cex=1, pch = pchs,
     xlab=paste("PC1 (",round(PCA$Variance[1,2],2),"%)"),
     ylab=paste("PC2 (",round(PCA$Variance[2,2],2),"%)"),
     cex.lab=1,cex.axis=1)
title (main="UC (radicular dentine)", font.main= 1,adj = 0, cex.main = 1.2)
legend("topright", legend = c("MH", "NE"), col = c("orange", "darkblue"), pch = c(16,17), cex = 0.8)
abline(v=0,h=0,col="black",lwd=2,lty=3)

hpts1 <- chull(PCA$PCscores[which(otu=="MH"),1:2])
hpts1 <- c(hpts1, hpts1[1])
polygon(PCA$PCscores[which(otu=="MH")[hpts1],1:2 ], col = adjustcolor("orange", 0.3), border = NA)

hpts2 <- chull(PCA$PCscores[which(otu=="NE"),c(1:2)])
hpts2 <- c(hpts2, hpts2[1])
polygon(PCA$PCscores[which(otu=="NE")[hpts2], ], col = adjustcolor("darkblue", 0.3), border = NA)

PC1min<-ToothVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
PC1max<-ToothVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)

### Example on the canine root
data("UCroot")
require(morphomap)
shapeList<-UCroot
PCA<-ToothPCA(shapeList,gamMap = FALSE,scaleThick = TRUE,scalePCA = TRUE,relThick = FALSE)
otu<-substr(names(shapeList),1,2)
pchs <- ifelse(otu == "MH", 16, 17)
cols <- ifelse(otu == "MH", "orange", "darkblue")

plot(PCA$PCscores,col=cols,cex=1, pch = pchs,
     xlab=paste("PC1 (",round(PCA$Variance[1,2],2),"%)"),
     ylab=paste("PC2 (",round(PCA$Variance[2,2],2),"%)"),
     cex.lab=1,cex.axis=1)
title (main="UC (radicular dentine)", font.main= 1,adj = 0, cex.main = 1.2)
legend("topright", legend = c("MH", "NE"), col = c("orange", "darkblue"), pch = c(16,17), cex = 0.8)
abline(v=0,h=0,col="black",lwd=2,lty=3)

hpts1 <- chull(PCA$PCscores[which(otu=="MH"),1:2])
hpts1 <- c(hpts1, hpts1[1])
polygon(PCA$PCscores[which(otu=="MH")[hpts1],1:2 ], col = adjustcolor("orange", 0.3), border = NA)

hpts2 <- chull(PCA$PCscores[which(otu=="NE"),c(1:2)])
hpts2 <- c(hpts2, hpts2[1])
polygon(PCA$PCscores[which(otu=="NE")[hpts2], ], col = adjustcolor("darkblue", 0.3), border = NA)

PC1min<-ToothVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
PC1max<-ToothVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)

### Example on the central upper incisor (crown)
data("UI1crown")
require(morphomap)
shapeList<-UI1crown
PCA<-ToothPCA(shapeList,gamMap = FALSE,scaleThick = TRUE,scalePCA = TRUE ,relThick = FALSE)
otu<-substr(names(shapeList),1,2)
pchs <- ifelse(otu == "MH", 16, 17)
cols <- ifelse(otu == "MH", "orange", "darkblue")

plot(PCA$PCscores,col=cols,cex=1, pch = pchs,
     xlab=paste("PC1 (",round(PCA$Variance[1,2],2),"%)"),
     ylab=paste("PC2 (",round(PCA$Variance[2,2],2),"%)"),
     cex.lab=1,cex.axis=1)
title (main="UC (radicular dentine)", font.main= 1,adj = 0, cex.main = 1.2)
legend("topright", legend = c("MH", "NE"), col = c("orange", "darkblue"), pch = c(16,17), cex = 0.8)
abline(v=0,h=0,col="black",lwd=2,lty=3)

hpts1 <- chull(PCA$PCscores[which(otu=="MH"),1:2])
hpts1 <- c(hpts1, hpts1[1])
polygon(PCA$PCscores[which(otu=="MH")[hpts1],1:2 ], col = adjustcolor("orange", 0.3), border = NA)

hpts2 <- chull(PCA$PCscores[which(otu=="NE"),c(1:2)])
hpts2 <- c(hpts2, hpts2[1])
polygon(PCA$PCscores[which(otu=="NE")[hpts2], ], col = adjustcolor("darkblue", 0.3), border = NA)

PC1min<-ToothVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
PC1max<-ToothVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)

### Example on the upper central incisor (root)
data("UI1root")
require(morphomap)
shapeList<-UI1root
PCA<-ToothPCA(shapeList,gamMap = FALSE,scaleThick = TRUE,scalePCA = TRUE,relThick = FALSE)
otu<-substr(names(UI1root),1,2)
pchs <- ifelse(otu == "MH", 16, 17)
cols <- ifelse(otu == "MH", "orange", "darkblue")

plot(PCA$PCscores,col=cols,cex=1, pch = pchs,
     xlab=paste("PC1 (",round(PCA$Variance[1,2],2),"%)"),
     ylab=paste("PC2 (",round(PCA$Variance[2,2],2),"%)"),
     cex.lab=1,cex.axis=1)
title (main="UC (radicular dentine)", font.main= 1,adj = 0, cex.main = 1.2)
legend("topright", legend = c("MH", "NE"), col = c("orange", "darkblue"), pch = c(16,17), cex = 0.8)
abline(v=0,h=0,col="black",lwd=2,lty=3)

hpts1 <- chull(PCA$PCscores[which(otu=="MH"),1:2])
hpts1 <- c(hpts1, hpts1[1])
polygon(PCA$PCscores[which(otu=="MH")[hpts1],1:2 ], col = adjustcolor("orange", 0.3), border = NA)

hpts2 <- chull(PCA$PCscores[which(otu=="NE"),c(1:2)])
hpts2 <- c(hpts2, hpts2[1])
polygon(PCA$PCscores[which(otu=="NE")[hpts2], ], col = adjustcolor("darkblue", 0.3), border = NA)

PC1min<-ToothVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
PC1max<-ToothVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)

### Example on the lateral upper incisor (crown)
data("UI2crown")
require(morphomap)
shapeList<-UI2crown
PCA<-ToothPCA(shapeList,gamMap = FALSE,scaleThick = TRUE,scalePCA = TRUE ,relThick = FALSE)
otu<-substr(names(shapeList),1,2)
pchs <- ifelse(otu == "MH", 16, 17)
cols <- ifelse(otu == "MH", "orange", "darkblue")

plot(PCA$PCscores,col=cols,cex=1, pch = pchs,
     xlab=paste("PC1 (",round(PCA$Variance[1,2],2),"%)"),
     ylab=paste("PC2 (",round(PCA$Variance[2,2],2),"%)"),
     cex.lab=1,cex.axis=1)
title (main="UC (radicular dentine)", font.main= 1,adj = 0, cex.main = 1.2)
legend("topright", legend = c("MH", "NE"), col = c("orange", "darkblue"), pch = c(16,17), cex = 0.8)
abline(v=0,h=0,col="black",lwd=2,lty=3)

hpts1 <- chull(PCA$PCscores[which(otu=="MH"),1:2])
hpts1 <- c(hpts1, hpts1[1])
polygon(PCA$PCscores[which(otu=="MH")[hpts1],1:2 ], col = adjustcolor("orange", 0.3), border = NA)

hpts2 <- chull(PCA$PCscores[which(otu=="NE"),c(1:2)])
hpts2 <- c(hpts2, hpts2[1])
polygon(PCA$PCscores[which(otu=="NE")[hpts2], ], col = adjustcolor("darkblue", 0.3), border = NA)

PC1min<-ToothVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
PC1max<-ToothVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)

### Example on the upper lateral incisor (root)
data("UI2root")
require(morphomap)
shapeList<-UI2root
PCA<-ToothPCA(shapeList,gamMap = FALSE,scaleThick = TRUE,scalePCA = TRUE,relThick = FALSE)
otu<-substr(names(UI2root),1,2)
pchs <- ifelse(otu == "MH", 16, 17)
cols <- ifelse(otu == "MH", "orange", "darkblue")

plot(PCA$PCscores,col=cols,cex=1, pch = pchs,
     xlab=paste("PC1 (",round(PCA$Variance[1,2],2),"%)"),
     ylab=paste("PC2 (",round(PCA$Variance[2,2],2),"%)"),
     cex.lab=1,cex.axis=1)
title (main="UC (radicular dentine)", font.main= 1,adj = 0, cex.main = 1.2)
legend("topright", legend = c("MH", "NE"), col = c("orange", "darkblue"), pch = c(16,17), cex = 0.8)
abline(v=0,h=0,col="black",lwd=2,lty=3)

hpts1 <- chull(PCA$PCscores[which(otu=="MH"),1:2])
hpts1 <- c(hpts1, hpts1[1])
polygon(PCA$PCscores[which(otu=="MH")[hpts1],1:2 ], col = adjustcolor("orange", 0.3), border = NA)

hpts2 <- chull(PCA$PCscores[which(otu=="NE"),c(1:2)])
hpts2 <- c(hpts2, hpts2[1])
polygon(PCA$PCscores[which(otu=="NE")[hpts2], ], col = adjustcolor("darkblue", 0.3), border = NA)

PC1min<-ToothVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
PC1max<-ToothVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
### Example on the canine crown
data("UCcrown")
require(morphomap)
shapeList<-UCcrown
PCA<-ToothPCA(shapeList,gamMap = FALSE,scaleThick = TRUE,scalePCA = TRUE ,relThick = FALSE)
 
#gamMap set on TRUE
PCA<-ToothPCA(shapeList,gamMap = TRUE,scaleThick = TRUE,scalePCA = TRUE,relThick = FALSE)

otu<-substr(names(shapeList),1,2)
pchs <- ifelse(otu == "MH", 16, 17)
cols <- ifelse(otu == "MH", "orange", "darkblue")

plot(PCA$PCscores,col=cols,cex=1, pch = pchs,
     xlab=paste("PC1 (",round(PCA$Variance[1,2],2),"%)"),
     ylab=paste("PC2 (",round(PCA$Variance[2,2],2),"%)"),
     cex.lab=1,cex.axis=1)
title (main="UC (radicular dentine)", font.main= 1,adj = 0, cex.main = 1.2)
legend("topright", legend = c("MH", "NE"), col = c("orange", "darkblue"), pch = c(16,17), cex = 0.8)
abline(v=0,h=0,col="black",lwd=2,lty=3)

hpts1 <- chull(PCA$PCscores[which(otu=="MH"),1:2])
hpts1 <- c(hpts1, hpts1[1])
polygon(PCA$PCscores[which(otu=="MH")[hpts1],1:2 ], col = adjustcolor("orange", 0.3), border = NA)

hpts2 <- chull(PCA$PCscores[which(otu=="NE"),c(1:2)])
hpts2 <- c(hpts2, hpts2[1])
polygon(PCA$PCscores[which(otu=="NE")[hpts2], ], col = adjustcolor("darkblue", 0.3), border = NA)

PC1min<-ToothVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
PC1max<-ToothVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)

### Example on the canine root
data("UCroot")
require(morphomap)
shapeList<-UCroot
PCA<-ToothPCA(shapeList,gamMap = FALSE,scaleThick = TRUE,scalePCA = TRUE,relThick = FALSE)
otu<-substr(names(shapeList),1,2)
pchs <- ifelse(otu == "MH", 16, 17)
cols <- ifelse(otu == "MH", "orange", "darkblue")

plot(PCA$PCscores,col=cols,cex=1, pch = pchs,
     xlab=paste("PC1 (",round(PCA$Variance[1,2],2),"%)"),
     ylab=paste("PC2 (",round(PCA$Variance[2,2],2),"%)"),
     cex.lab=1,cex.axis=1)
title (main="UC (radicular dentine)", font.main= 1,adj = 0, cex.main = 1.2)
legend("topright", legend = c("MH", "NE"), col = c("orange", "darkblue"), pch = c(16,17), cex = 0.8)
abline(v=0,h=0,col="black",lwd=2,lty=3)

hpts1 <- chull(PCA$PCscores[which(otu=="MH"),1:2])
hpts1 <- c(hpts1, hpts1[1])
polygon(PCA$PCscores[which(otu=="MH")[hpts1],1:2 ], col = adjustcolor("orange", 0.3), border = NA)

hpts2 <- chull(PCA$PCscores[which(otu=="NE"),c(1:2)])
hpts2 <- c(hpts2, hpts2[1])
polygon(PCA$PCscores[which(otu=="NE")[hpts2], ], col = adjustcolor("darkblue", 0.3), border = NA)

PC1min<-ToothVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
PC1max<-ToothVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)

### Example on the central upper incisor (crown)
data("UI1crown")
require(morphomap)
shapeList<-UI1crown
PCA<-ToothPCA(shapeList,gamMap = FALSE,scaleThick = TRUE,scalePCA = TRUE ,relThick = FALSE)
otu<-substr(names(shapeList),1,2)
pchs <- ifelse(otu == "MH", 16, 17)
cols <- ifelse(otu == "MH", "orange", "darkblue")

plot(PCA$PCscores,col=cols,cex=1, pch = pchs,
     xlab=paste("PC1 (",round(PCA$Variance[1,2],2),"%)"),
     ylab=paste("PC2 (",round(PCA$Variance[2,2],2),"%)"),
     cex.lab=1,cex.axis=1)
title (main="UC (radicular dentine)", font.main= 1,adj = 0, cex.main = 1.2)
legend("topright", legend = c("MH", "NE"), col = c("orange", "darkblue"), pch = c(16,17), cex = 0.8)
abline(v=0,h=0,col="black",lwd=2,lty=3)

hpts1 <- chull(PCA$PCscores[which(otu=="MH"),1:2])
hpts1 <- c(hpts1, hpts1[1])
polygon(PCA$PCscores[which(otu=="MH")[hpts1],1:2 ], col = adjustcolor("orange", 0.3), border = NA)

hpts2 <- chull(PCA$PCscores[which(otu=="NE"),c(1:2)])
hpts2 <- c(hpts2, hpts2[1])
polygon(PCA$PCscores[which(otu=="NE")[hpts2], ], col = adjustcolor("darkblue", 0.3), border = NA)

PC1min<-ToothVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
PC1max<-ToothVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)

### Example on the upper central incisor (root)
data("UI1root")
require(morphomap)
shapeList<-UI1root
PCA<-ToothPCA(shapeList,gamMap = FALSE,scaleThick = TRUE,scalePCA = TRUE,relThick = FALSE)
otu<-substr(names(UI1root),1,2)
pchs <- ifelse(otu == "MH", 16, 17)
cols <- ifelse(otu == "MH", "orange", "darkblue")

plot(PCA$PCscores,col=cols,cex=1, pch = pchs,
     xlab=paste("PC1 (",round(PCA$Variance[1,2],2),"%)"),
     ylab=paste("PC2 (",round(PCA$Variance[2,2],2),"%)"),
     cex.lab=1,cex.axis=1)
title (main="UC (radicular dentine)", font.main= 1,adj = 0, cex.main = 1.2)
legend("topright", legend = c("MH", "NE"), col = c("orange", "darkblue"), pch = c(16,17), cex = 0.8)
abline(v=0,h=0,col="black",lwd=2,lty=3)

hpts1 <- chull(PCA$PCscores[which(otu=="MH"),1:2])
hpts1 <- c(hpts1, hpts1[1])
polygon(PCA$PCscores[which(otu=="MH")[hpts1],1:2 ], col = adjustcolor("orange", 0.3), border = NA)

hpts2 <- chull(PCA$PCscores[which(otu=="NE"),c(1:2)])
hpts2 <- c(hpts2, hpts2[1])
polygon(PCA$PCscores[which(otu=="NE")[hpts2], ], col = adjustcolor("darkblue", 0.3), border = NA)

PC1min<-ToothVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
PC1max<-ToothVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)

### Example on the lateral upper incisor (crown)
data("UI2crown")
require(morphomap)
shapeList<-UI2crown
PCA<-ToothPCA(shapeList,gamMap = FALSE,scaleThick = TRUE,scalePCA = TRUE ,relThick = FALSE)
otu<-substr(names(shapeList),1,2)
pchs <- ifelse(otu == "MH", 16, 17)
cols <- ifelse(otu == "MH", "orange", "darkblue")

plot(PCA$PCscores,col=cols,cex=1, pch = pchs,
     xlab=paste("PC1 (",round(PCA$Variance[1,2],2),"%)"),
     ylab=paste("PC2 (",round(PCA$Variance[2,2],2),"%)"),
     cex.lab=1,cex.axis=1)
title (main="UC (radicular dentine)", font.main= 1,adj = 0, cex.main = 1.2)
legend("topright", legend = c("MH", "NE"), col = c("orange", "darkblue"), pch = c(16,17), cex = 0.8)
abline(v=0,h=0,col="black",lwd=2,lty=3)

hpts1 <- chull(PCA$PCscores[which(otu=="MH"),1:2])
hpts1 <- c(hpts1, hpts1[1])
polygon(PCA$PCscores[which(otu=="MH")[hpts1],1:2 ], col = adjustcolor("orange", 0.3), border = NA)

hpts2 <- chull(PCA$PCscores[which(otu=="NE"),c(1:2)])
hpts2 <- c(hpts2, hpts2[1])
polygon(PCA$PCscores[which(otu=="NE")[hpts2], ], col = adjustcolor("darkblue", 0.3), border = NA)

PC1min<-ToothVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
PC1max<-ToothVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)

### Example on the upper lateral incisor (root)
data("UI2root")
require(morphomap)
shapeList<-UI2root
PCA<-ToothPCA(shapeList,gamMap = FALSE,scaleThick = TRUE,scalePCA = TRUE,relThick = FALSE)
otu<-substr(names(UI2root),1,2)
pchs <- ifelse(otu == "MH", 16, 17)
cols <- ifelse(otu == "MH", "orange", "darkblue")

plot(PCA$PCscores,col=cols,cex=1, pch = pchs,
     xlab=paste("PC1 (",round(PCA$Variance[1,2],2),"%)"),
     ylab=paste("PC2 (",round(PCA$Variance[2,2],2),"%)"),
     cex.lab=1,cex.axis=1)
title (main="UC (radicular dentine)", font.main= 1,adj = 0, cex.main = 1.2)
legend("topright", legend = c("MH", "NE"), col = c("orange", "darkblue"), pch = c(16,17), cex = 0.8)
abline(v=0,h=0,col="black",lwd=2,lty=3)

hpts1 <- chull(PCA$PCscores[which(otu=="MH"),1:2])
hpts1 <- c(hpts1, hpts1[1])
polygon(PCA$PCscores[which(otu=="MH")[hpts1],1:2 ], col = adjustcolor("orange", 0.3), border = NA)

hpts2 <- chull(PCA$PCscores[which(otu=="NE"),c(1:2)])
hpts2 <- c(hpts2, hpts2[1])
polygon(PCA$PCscores[which(otu=="NE")[hpts2], ], col = adjustcolor("darkblue", 0.3), border = NA)

PC1min<-ToothVariations(PCA,min(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)
PC1max<-ToothVariations(PCA,max(PCA$PCscores[,1]),PCA$PCs[,1],asp=0.5,meanmap = FALSE)

ToothRegradius

Description

Finds equiangular landmarks

Usage

ToothRegradius(mat, center, n, direction = c("c", "a"))
ToothRegradius(mat, center, n, direction = c("c", "a"))

Arguments

`mat`	a kx2 matrix
`center`	coordinates of the center from which the calculation of regular radius started
`n`	number of points
`direction`	specify direction: "c"=clockwise; "a"=anticlockwise

Value

V2 position of landmarks equiangular spaced

Author(s)

Antonio Profico; Mathilde Augoyard

ToothShape

Description

Tool for the extraction of equiangular landmarks on the entire dental region of interest

Usage

ToothShape(
  tooth.core,
  num.land,
  sects_vector,
  cent.out = "E",
  delta = 0.1,
  direction = "c",
  out.sur = NULL,
  inn.sur = NULL
)
ToothShape(
  tooth.core,
  num.land,
  sects_vector,
  cent.out = "E",
  delta = 0.1,
  direction = "c",
  out.sur = NULL,
  inn.sur = NULL
)

Arguments

`tooth.core`	list: tooth.core object
`num.land`	numeric: number of landmarks defining each section
`sects_vector`	numeric: number of sections
`cent.out`	how to define the center of each section. The method allowed are "CCA" (center of cortical area), "E" (barycenter of the external outline) and "I" (barycenter of the internal outline)
`delta`	pixel size used to calculate the CCA
`direction`	clockwise if "c", anticlockwise if"a"
`out.sur`	mesh: if provided, the external outlines will be projected back on the surface
`inn.sur`	mesh: if provided, the internal outlines will be projected back on the surface

Value

out3D num.pointsx3xnum.sect array in which the external outlines are stored

inn3D num.pointsx3xnum.sect array in which the internal outlines are stored

out2D num.pointsx2xnum.sect array in which the external outlines are stored

inn2D 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 length of the selected region of interest

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

centroids of the cross-sections

Author(s)

Antonio Profico; Mathilde Augoyard

Examples


data("URI1_tooth")
require(morphomap)
require(rgl)
Enamel<-URI1_tooth$mesh1
Dentin<-URI1_tooth$mesh2
Pulp<-URI1_tooth$mesh3
outline<-URI1_tooth$outline
set<-URI1_tooth$set

#Unrolling the crown
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "c")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh1$mesh
Internal<-AlignMeshes$almesh2$mesh
#Define 16 cross-sections from the 30% to the 90% along the crown
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                bio.len = AlignMeshes$length,start=0.3,end=0.9)
Shape<-ToothShape(Core,num.land = 21,sects_vector = NULL,direction = "a")

plot3d(morphomapArray2matrix(Shape$"out3D"),type="s",radius = 0.1,aspect=FALSE,
xlab="x",ylab="y",zlab="z")
plot3d(morphomapArray2matrix(Shape$"inn3D"),type="s",radius = 0.1,aspect=FALSE,
add=TRUE)
wire3d(AlignMeshes$almesh2$mesh,col="white")
wire3d(AlignMeshes$almesh1$mesh,col="violet")

#Unrolling the rooth
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,
analyse = "r")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh2$mesh
Internal<-AlignMeshes$almesh3$mesh
#Define 16 cross-sections from the 10% to the 50% along the root
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                bio.len = AlignMeshes$length,start=0.1,end=0.5)
Shape<-ToothShape(Core,num.land = 21,sects_vector = NULL,direction = "a")

plot3d(morphomapArray2matrix(Shape$"out3D"),type="s",radius = 0.1,aspect=FALSE,
xlab="x",ylab="y",zlab="z")
plot3d(morphomapArray2matrix(Shape$"inn3D"),type="s",radius = 0.1,aspect=FALSE,
add=TRUE)
wire3d(AlignMeshes$almesh3$mesh,col="red")
wire3d(AlignMeshes$almesh2$mesh,col="lightblue")
wire3d(AlignMeshes$almesh1$mesh,col="white")

data("URI1_tooth")
require(morphomap)
require(rgl)
Enamel<-URI1_tooth$mesh1
Dentin<-URI1_tooth$mesh2
Pulp<-URI1_tooth$mesh3
outline<-URI1_tooth$outline
set<-URI1_tooth$set

#Unrolling the crown
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "c")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh1$mesh
Internal<-AlignMeshes$almesh2$mesh
#Define 16 cross-sections from the 30% to the 90% along the crown
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                bio.len = AlignMeshes$length,start=0.3,end=0.9)
Shape<-ToothShape(Core,num.land = 21,sects_vector = NULL,direction = "a")

plot3d(morphomapArray2matrix(Shape$"out3D"),type="s",radius = 0.1,aspect=FALSE,
xlab="x",ylab="y",zlab="z")
plot3d(morphomapArray2matrix(Shape$"inn3D"),type="s",radius = 0.1,aspect=FALSE,
add=TRUE)
wire3d(AlignMeshes$almesh2$mesh,col="white")
wire3d(AlignMeshes$almesh1$mesh,col="violet")

#Unrolling the rooth
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,
analyse = "r")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh2$mesh
Internal<-AlignMeshes$almesh3$mesh
#Define 16 cross-sections from the 10% to the 50% along the root
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                bio.len = AlignMeshes$length,start=0.1,end=0.5)
Shape<-ToothShape(Core,num.land = 21,sects_vector = NULL,direction = "a")

plot3d(morphomapArray2matrix(Shape$"out3D"),type="s",radius = 0.1,aspect=FALSE,
xlab="x",ylab="y",zlab="z")
plot3d(morphomapArray2matrix(Shape$"inn3D"),type="s",radius = 0.1,aspect=FALSE,
add=TRUE)
wire3d(AlignMeshes$almesh3$mesh,col="red")
wire3d(AlignMeshes$almesh2$mesh,col="lightblue")
wire3d(AlignMeshes$almesh1$mesh,col="white")

ToothThickness

Description

Tool for the extraction of equiangular landmarks on the selected dental mesh

Usage

ToothThickness(tooth.shape)
ToothThickness(tooth.shape)

Arguments

tooth.shape

list: tooth.shape object

Value

sect_thickness_eq dental thickness (equiangular method)

sect_thickness_cp dental thickness (closest point method)

sect_Rthickness_eq relative dental thickness (equiangular method)

sect_Rthickness_cp relative dental thickness (closest point method)

ALPM_thickness dental thickness at ALPM quadrants

tooth.shape tooth.shape object

Author(s)

Antonio Profico; Mathilde Augoyard

ToothVariations

Description

Calculate and return morphometric map variation

Usage

ToothVariations(
  PCA,
  scores,
  PC,
  asp = 2,
  pal = blue2green2red(101),
  meanmap = TRUE
)
ToothVariations(
  PCA,
  scores,
  PC,
  asp = 2,
  pal = blue2green2red(101),
  meanmap = TRUE
)

Arguments

`PCA`	list: output from ToothPCA
`scores`	numeric: principal component value
`PC`	numeric: principal component eigenvalue
`asp`	numeric: x,y ratio of the morphometric map
`pal`	character vector: vector of colors
`meanmap`	logical: if TRUE the mean map corresponds to the real mean morphometric maps, otherwise the mean map is 0

Value

XYZ data.frame of morphometric map variation

Author(s)

Antonio Profico; Mathilde Augoyard

ToothVolumes

Description

Extract volumes from the object ToothShape

Usage

ToothVolumes(
  ShapeExt,
  ShapeInn,
  col1 = "gray",
  col2 = "red",
  col3 = "green",
  alpha1 = 1,
  alpha2 = 1,
  alpha3 = 1,
  plot = FALSE
)
ToothVolumes(
  ShapeExt,
  ShapeInn,
  col1 = "gray",
  col2 = "red",
  col3 = "green",
  alpha1 = 1,
  alpha2 = 1,
  alpha3 = 1,
  plot = FALSE
)

Arguments

`ShapeExt`	3D mesh: external mesh
`ShapeInn`	3D mesh: internal mesh
`col1`	color of the ShapeExt
`col2`	color of the ShapeInn
`col3`	color of the boolean operation between ShapeExt and ShapeInn
`alpha1`	value to set trasparancy of col1
`alpha2`	value to set trasparancy of col1
`alpha3`	value to set trasparancy of col1
`plot`	logical: if TRUE the volumes are shown

Value

meshOut: external selected mesh

meshInnT: internal selected mesh

meshDiff: differences between selected meshes

volumeT: volume of the external mesh

volInn:volume of the internal mesh

volDiff: difference between volumeT and volInn

Author(s)

Antonio Profico; Mathilde Augoyard

Examples


data("URI1_tooth")
require(morphomap)
Enamel<-URI1_tooth$mesh1
Dentin<-URI1_tooth$mesh2
Pulp<-URI1_tooth$mesh3
outline<-URI1_tooth$outline
set<-URI1_tooth$set

#Unrolling the crown
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "c")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh1$mesh
Internal<-AlignMeshes$almesh2$mesh
#Define 16 cross-sections from the 30% to the 90% along the crown
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                bio.len = AlignMeshes$length,start=0.3,end=0.9)
Shape<-ToothShape(Core,num.land = 100,sects_vector = NULL,direction = "a")
volumes<-ToothVolumes(Shape$"out3D",Shape$"inn3D",plot=TRUE)
unlist(volumes[4:6])

data("URI1_tooth")
require(morphomap)
Enamel<-URI1_tooth$mesh1
Dentin<-URI1_tooth$mesh2
Pulp<-URI1_tooth$mesh3
outline<-URI1_tooth$outline
set<-URI1_tooth$set

#Unrolling the crown
AlignMeshes<-ToothAlignment(mesh1=Enamel,mesh2=Dentin,mesh3=Pulp,set,outline,analyse = "c")
#Virtual sectioning dentine-pulp
External<-AlignMeshes$almesh1$mesh
Internal<-AlignMeshes$almesh2$mesh
#Define 16 cross-sections from the 30% to the 90% along the crown
Core<-ToothCore(External,Internal,num.points = 1000,num.sect =16,
                bio.len = AlignMeshes$length,start=0.3,end=0.9)
Shape<-ToothShape(Core,num.land = 100,sects_vector = NULL,direction = "a")
volumes<-ToothVolumes(Shape$"out3D",Shape$"inn3D",plot=TRUE)
unlist(volumes[4:6])

example dataset

Description

list of ToothShape (modern human and neanderthal upper canines)

Usage

data(UCcrown)
data(UCcrown)

Author(s)

Antonio Profico, Mathilde Augoyard

example dataset

Description

list of ToothShape (modern human and neanderthal upper canines)

Usage

data(UCroot)
data(UCroot)

Author(s)

Antonio Profico, Mathilde Augoyard

example dataset

Description

list of ToothShape (modern human and neanderthal upper central incisors)

Usage

data(UI1crown)
data(UI1crown)

Author(s)

Antonio Profico, Mathilde Augoyard

example dataset

Description

list of ToothShape (modern human and neanderthal upper central incisors)

Usage

data(UI1root)
data(UI1root)

Author(s)

Antonio Profico, Mathilde Augoyard

example dataset

Description

list of ToothShape (modern human and neanderthal upper lateral incisors)

Usage

data(UI2crown)
data(UI2crown)

Author(s)

Antonio Profico, Mathilde Augoyard

example dataset

Description

list of ToothShape (modern human and neanderthal upper lateral incisors)

Usage

data(UI2root)
data(UI2root)

Author(s)

Antonio Profico, Mathilde Augoyard

example dataset

Description

3D dental meshes of a modern human upper right central incisor

Usage

data(URI1_tooth)
data(URI1_tooth)

Author(s)

Antonio Profico, Mathilde Augoyard

Package 'Toothnroll'

Help Index

Tooth2Dmap

Description

Usage

Arguments

Value

Author(s)

Examples

ToothAlignment

Description

Usage

Arguments

Details

Value

Author(s)

Examples

ToothCore

Description

Usage

Arguments

Value

Author(s)

Examples

ToothDF

Description

Usage

Arguments

Value

Author(s)

ToothExport

Description

Usage

Arguments

Value

Author(s)

ToothImport

Description

Usage

Arguments

Value

Author(s)

ToothPCA

Description

Usage

Arguments

Value

Author(s)

Examples

ToothRegradius

Description

Usage

Arguments

Value

Author(s)

ToothShape

Description

Usage

Arguments

Value

Author(s)

Examples

ToothThickness

Description

Usage

Arguments

Value

Author(s)

ToothVariations

Description

Usage

Arguments

Value

Author(s)

ToothVolumes

Description

Usage

Arguments

Value

Author(s)