| Title: | Dental Tissues Landmarking Measuring and Mapping |
| Version: | 1.11 |
| 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. |
| Imports: | Arothron (≥ 1.0), alphashape3d (≥ 1.0), compositions(≥ 2.0), morphomap (≥ 1.0), stringr (≥ 1.0), vegan,lattice (≥ 0.2), mgcv (≥ 1.8), Rvcg (≥ 0.18), Morpho (≥ 2.0), oce (≥ 1.1), rgl (≥ 0.1), geometry (≥ 0.4.0), colorRamps (≥ 2.3), DescTools (≥ 0.99), grDevices (≥ 3.5), graphics (≥ 3.5) |
| License: | GPL-2 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| NeedsCompilation: | no |
| Packaged: | 2024-04-12 09:27:42 UTC; anton |
| Author: | Antonio Profico [cre, aut], Mathilde Augoyard [aut] |
| Maintainer: | Antonio Profico <antonio.profico@gmail.com> |
| Depends: | R (≥ 3.5.0) |
| Repository: | CRAN |
| Date/Publication: | 2024-04-12 15:20:22 UTC |
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 = ""
)
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$length,start=0.1,end=0.5)
#Extract 25 equiangular semilandmarks from each cross-section (anticlockwise)
Shape<-ToothShape(Core,25,sects_vector = NULL,cent.out = "E",direction="a")
Tooth2Dmap(Shape,AlignMeshes,rem.out =FALSE,scale=FALSE,smooth = FALSE,aspect = 0.5,gamMap = FALSE,
nrow = 100,ncol = 100,gdl = 250,method="equiangular")
ToothAlignment
Description
Align dental meshes using as reference the cervical outline and five landmarks
Usage
ToothAlignment(mesh1, mesh2, mesh3 = NULL, set, outline, analyse = c("r", "c"))
Arguments
mesh1 |
3D mesh: dental mesh (enamel) |
mesh2 |
3D mesh: dental mesh (dentin) |
mesh3 |
3D mesh: dental mesh (dental pulp) |
set |
matrix: 5 landmarks acquired on the mesh (see details) |
outline |
matrix: set of coordinates along the cerical outline |
analyse |
character: "r" for root, "c" for crown |
Details
The function needs five landmarks to align the dental meshes. Usually landmarks from 1 to 4 define the Lingual, Mesial, Buccal and Distal margins. The fifth landmark defines the end of the z axis (biomechanical length). The centroid of the cervical outline defines the origin of axes.
Value
almesh1: mesh of the aligned mesh1
almesh2: mesh of the aligned mesh2
almesh3: mesh of the aligned mesh3
alset: coordinates of the aligned landmark configuration
length: biomechanical length of the root (see details)
margins: coordinates of the landmarks in correspondence of the four margins
margins_sel: position of the margin along the outline
aloutline: coordinates of the aligned cervical outline
diamBL: bucco-lingual diameter
diamMD: mesio-distal diameter
Author(s)
Antonio Profico; Mathilde Augoyard
Examples
data("URI1_tooth")
Enamel<-URI1_tooth$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()
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
)
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")
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
)
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)
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)
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
)
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)
ToothRegradius
Description
Finds equiangular landmarks
Usage
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
)
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")
ToothThickness
Description
Tool for the extraction of equiangular landmarks on the selected dental mesh
Usage
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
)
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
)
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])
example dataset
Description
list of ToothShape (modern human and neanderthal upper canines)
Usage
data(UCcrown)
Author(s)
Antonio Profico, Mathilde Augoyard
example dataset
Description
list of ToothShape (modern human and neanderthal upper canines)
Usage
data(UCroot)
Author(s)
Antonio Profico, Mathilde Augoyard
example dataset
Description
list of ToothShape (modern human and neanderthal upper central incisors)
Usage
data(UI1crown)
Author(s)
Antonio Profico, Mathilde Augoyard
example dataset
Description
list of ToothShape (modern human and neanderthal upper central incisors)
Usage
data(UI1root)
Author(s)
Antonio Profico, Mathilde Augoyard
example dataset
Description
list of ToothShape (modern human and neanderthal upper lateral incisors)
Usage
data(UI2crown)
Author(s)
Antonio Profico, Mathilde Augoyard
example dataset
Description
list of ToothShape (modern human and neanderthal upper lateral incisors)
Usage
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)
Author(s)
Antonio Profico, Mathilde Augoyard