| Title: | Morphometric Maps, Bone Landmarking and Cross Sectional Geometry |
|---|---|
| Description: | Extract cross sections from long bone meshes at specified intervals along the diaphysis. Calculate two and three-dimensional morphometric maps, cross-sectional geometric parameters, and semilandmarks on the periosteal and endosteal contours of each cross section. |
| Authors: | Antonio Profico [aut, cre], Luca Bondioli [aut], Pasquale Raia [aut], Julien Claude [ctb], Paul O'Higgins [aut], Damiano Marchi [aut] |
| Maintainer: | Antonio Profico <[email protected]> |
| License: | GPL-2 |
| Version: | 1.5 |
| Built: | 2025-01-31 03:54:53 UTC |
| Source: | https://github.com/cran/morphomap |
Tool to process long bone meshes (shape data, morphometric maps and cross-sectional geometry)
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
morphomapShape objects from 5 femora
data(Ex_mpShapeList)data(Ex_mpShapeList)
Antonio Profico
3D mesh of a human femur bone
data(HomFem38023)data(HomFem38023)
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
Create a 2D cortical thickness map
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 )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 )
morphomap.shape |
list: output from morphomapShape function |
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 a smooth 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 |
ncol |
numeric: number of columns for gam smoothing |
gdl |
numeric: number of degree of freedom for gam smoothing |
method |
character: if set on "equiangular" the cortical thickness is meant as the distance of the segment intersecting the external and internal outline starting from the centroid of the section. If set on "closest" the cortical thickness is calculated at each point as the closest distance between external and internal outlines |
unwrap |
character: starting qaudrant to unwrap the diaphysis ("A"=anterior, "L"=lateral, "P"=posterior, "M"=mesial) |
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 |
dataframe dataframe for colormap production
2Dmap thickness color map
gamoutput output from GAM
data input used to build the GAM map
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
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) }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) }
Plot a 3D thickness map in four different anatomical views
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) )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) )
morphomap.shape |
list: output from morphomapShape function |
out.sur |
3D mesh: 3D mesh of the long bone |
method |
character: if set on "equiangular" the cortical thickness is meant as the distance of the segment intersecting the external and internal outline starting from the centroid of the section. If set on "closest" the cortical thickness is calculated at each point as the closest distance between external and internal outlines |
scale |
logical: if TRUE the cortical thickness matrix will be scaled from 0 to 1 |
rem.out |
logical: if TRUE outliers are identified and removed from thickness matrix |
fac.out |
numeric: parameter to set the threshold in outliers detection |
smooth |
logical: if TRUE the smoothing filter is applied on the thickness matrix |
smooth.iter |
numeric: number of smoothing iterations |
k |
integer: neighbourhood of kd-tree to search the nearest semilandmarks to each vertex |
plot |
logical: if TRUE the 3D map is plotted |
pal |
character vector: colors to be used in the map production |
cols color associated at each vertex of 3D mesh
thickmat thickness matrix after smoothing and outliers removal
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
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") }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") }
Align a femur bone following the protocol proposed by Ruff (2002)
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 )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 )
mesh |
3D mesh: femur long bone mesh |
set |
matrix: 7 landmarks acquired on the mesh (see details) |
side |
character: specify if the femur bone is "left" or "right" side |
param1 |
numeric: parameter for spherical flipping (usually ranged between 3 and 4) |
iter1 |
numeric: number of iterations first alignment |
iter2 |
numeric: number of iterations second alignment |
iter3 |
numeric: number of iterations third alignment |
from1 |
numeric: inferior range of the allowed rotation in the first alignment |
to1 |
numeric: superior range of the allowed rotation in the first alignment |
from2 |
numeric: inferior range of the allowed rotation in the second alignment |
to2 |
numeric: superior range of the allowed rotation in the second alignment |
from3 |
numeric: inferior range of the allowed rotation in the third alignment |
to3 |
numeric: superior range of the allowed rotation in the third alignment |
tol |
numeric: maximum allowed error in the alignment expressed in mm |
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'.
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
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
Shoelace formula to calculate the area of a closed outline
morphomapArea(p, delta = 0.1, method = "shoelace")morphomapArea(p, delta = 0.1, method = "shoelace")
p |
matrix: kx2 matrix |
delta |
numeric: picture elements of adjustable side length |
method |
character: the user can choice to calculate the area applying the "shoelace" formula or discretizing the cross sections in dA areas (method = "delta") |
ar numeric: area
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
extsec<-morphomapCircle(10,100) #shoelace method area<-morphomapArea(extsec, method="shoelace") #delta method area<-morphomapArea(extsec, method="delta",delta=0.01)extsec<-morphomapCircle(10,100) #shoelace method area<-morphomapArea(extsec, method="shoelace") #delta method area<-morphomapArea(extsec, method="delta",delta=0.01)
Convert an array into a matrix
morphomapArray2matrix(array)morphomapArray2matrix(array)
array |
an array |
mat a matrix
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
Calculate the barycenter of the cortical area
morphomapCentroid(cp, mp, delta = 0.1)morphomapCentroid(cp, mp, delta = 0.1)
cp |
matrix: coordinates of the external outline of the section |
mp |
matrix: coordinates of the internal outline of the section |
delta |
numeric: picture elements of adjustable side length |
centroid numeric vector: coordinates of the cortical area
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
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)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)
Plot the long bone mesh to check the orientation of the long bone
morphomapCheck(mesh, col = "white")morphomapCheck(mesh, col = "white")
mesh |
3D mesh: long bone 3D model |
col |
character: color mesh |
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
library(morphomap) data(HomFem38023) morphomapCheck(HomFem38023)library(morphomap) data(HomFem38023) morphomapCheck(HomFem38023)
Define a circular outline
morphomapCircle(r = 1, n = 1000)morphomapCircle(r = 1, n = 1000)
r |
numeric: radius of the outline |
n |
numeric: number of points along the outline |
mat matrix with coordinates
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
extsec<-morphomapCircle(10,100) intsec<-morphomapCircle(8,100) plot(extsec,asp=1,type="l") points(intsec,type="l",col=2)extsec<-morphomapCircle(10,100) intsec<-morphomapCircle(8,100) plot(extsec,asp=1,type="l") points(intsec,type="l",col=2)
Tool to build 3D and 2D cross sections
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 )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 )
out.sur |
object of class mesh3d |
inn.sur |
object of class mesh3d |
num.sect |
number of sections |
mech.len |
mechanical length of the long bone |
clean_int_out |
logical if TRUE the inner section will be cleaned by using spherical flipping |
param1 |
numeric parameter for spherical flipping operator (how much the section will be deformed) |
radius.fact |
numeric parameter for spherical flipping operator (distance from the center of the outline at which the povs are defined) |
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 |
print.progress |
logical: if TRUE a progress bar is printed to the screen |
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
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
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) }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) }
Tool for Cross-sectional geometry
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 )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 )
cp |
matrix: coordinates of the external outline |
mp |
matrix: coordinates of the internal outline |
translate |
logical: if TRUE the section will be centered |
center |
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 |
numeric: picture elements of adjustable side length |
Cx |
numeric: new x center coordinate |
Cy |
numeric: new y center coordinate |
I_xy |
logical: if TRUE the product of inertia around the x and y axis is calculated |
I_minmax |
logical: if TRUE the Imin and Imax will be calculated |
Zxy |
logical: if TRUE the polar moment of inertia will be calculated |
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
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
#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")#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")
Tool to build a data.frame suitable for morphometric maps
morphomapDF( morphomap.thickness, rem.out = TRUE, fac.out = 0.5, smooth = TRUE, scale = TRUE, smooth.iter = 5, method = "equiangular", unwrap = "A" )morphomapDF( morphomap.thickness, rem.out = TRUE, fac.out = 0.5, smooth = TRUE, scale = TRUE, smooth.iter = 5, method = "equiangular", unwrap = "A" )
morphomap.thickness |
list: morphomap.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 cortical thickness is meant as the distance of the segment intersecting the external and internal outline starting from the centroid of the section. If set on "closest" the cortical thickness is calculated at each point as the closest distance between external and internal outlines |
unwrap |
character: starting qaudrant to unwrap the diaphysis ("A"=anterior, "L"=lateral, "P"=posterior, "M"=mesial) |
XYZ data.frame for morphometric map
labels character vector for x labels in the morphometric map
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
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)$XYZ contourplot(dataDF[, 3] ~ dataDF[, 1] + dataDF[, 2], col.regions=blue2green2red(101),region=TRUE, colorkey=list(at=seq(0,1,length.out = 100)), scales = list(x = list(at = seq(0,100,length.out = 5), c("A","M","P","L","A"), alternating = 1)),asp=1.5,cuts=20,xlab="femur margin",ylab="biomechanical length")library(lattice) library(colorRamps) data(HomFem38023) meshes<-morphomapSegm(HomFem38023, param1=4) perMesh<-meshes$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")
Export the output from ToothAlignement
morphomapExport(mpShapeObject, id, file)morphomapExport(mpShapeObject, id, file)
mpShapeObject |
list: list containing morphomapShape objects |
id |
character: label name |
file |
character: name the output file |
Antonio Profico
Spherical flipping operator for bi-dimensional configuration
morphomapFlip(mat, param1 = 0.8, param2 = 10, radius.fact = 1.5, npovs = 100)morphomapFlip(mat, param1 = 0.8, param2 = 10, radius.fact = 1.5, npovs = 100)
mat |
numeric matrix: coordinates of the bi-dimensional configuration |
param1 |
numeric: first parameter for spherical flipping |
param2 |
numeric: second parameter for spherical flipping |
radius.fact |
mechanical length of the long bone |
npovs |
number of evenly spaced points to be defined on each section |
mat matrix after spherical flipping
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
#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)#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)
Import a morphomapShape object exported with morphomapExport
morphomapImport(file)morphomapImport(file)
file |
character: name of input file |
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
Antonio Profico
Convert a matrix into an array
morphomapMatrix2array(matrix, nsects)morphomapMatrix2array(matrix, nsects)
matrix |
an array |
nsects |
number of cross sections |
array an array
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
Mirror a long bone mesh along the yz plane
morphomapMirror(mesh)morphomapMirror(mesh)
mesh |
object of class mesh3d |
mesh: object of class mesh3d
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
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") }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") }
Calculate the moment of inertia around the x and y axes and the product of inertia
morphomapMoment(cp, mp, delta = 0.1)morphomapMoment(cp, mp, delta = 0.1)
cp |
matrix: coordinates of the external outline |
mp |
matrix: coordinates of the internal outline |
delta |
numeric: picture elements of adjustable side length |
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
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
#create a section extsec<-morphomapCircle(10,1000) intsec<-morphomapCircle(8,1000) InMs<-morphomapMoment(extsec,intsec,delta=0.1)#create a section extsec<-morphomapCircle(10,1000) intsec<-morphomapCircle(8,1000) InMs<-morphomapMoment(extsec,intsec,delta=0.1)
Calculate maps of cortical thickness and perform a Principal Component Analysis
morphomapPCA( mpShapeList, gamMap = TRUE, nrow = 61, ncol = 24, rem.out = TRUE, scaleThick = FALSE, fac.out = 1.5, method = "equiangular", scalePCA = TRUE, unwrap = "A" )morphomapPCA( mpShapeList, gamMap = TRUE, nrow = 61, ncol = 24, rem.out = TRUE, scaleThick = FALSE, fac.out = 1.5, method = "equiangular", scalePCA = TRUE, unwrap = "A" )
mpShapeList |
list: list containing morphomapShape objects |
gamMap |
list: list containing morphomapShape objects |
nrow |
list: list containing morphomapShape objects |
ncol |
list: list containing morphomapShape objects |
rem.out |
list: list containing morphomapShape objects |
scaleThick |
list: list containing morphomapShape objects |
fac.out |
list: list containing morphomapShape objects |
method |
list: list containing morphomapShape objects |
scalePCA |
list: list containing morphomapShape objects |
unwrap |
list: list containing morphomapShape objects |
PCscores PC scores
PCs loadings
Variance Table of the explained Variance by the PCs
meanMap mean morphometric map
CorMaps morphometric maps
Antonio Profico
data(Ex_mpShapeList) PCA<-morphomapPCA(Ex_mpShapeList) plot(PCA$PCscores) barplot(PCA$Variance[,2])data(Ex_mpShapeList) PCA<-morphomapPCA(Ex_mpShapeList) plot(PCA$PCscores) barplot(PCA$Variance[,2])
Save the sections defined via morphomapShape or morphomapCore
morphomapPic( morphomap.core, morphomap.shape, vector = NULL, full = TRUE, width = 1500, height = 1500, pointsize = 12, res = 300, colthk = "red", collbs = "blue", dirpath = tempdir() )morphomapPic( morphomap.core, morphomap.shape, vector = NULL, full = TRUE, width = 1500, height = 1500, pointsize = 12, res = 300, colthk = "red", collbs = "blue", dirpath = tempdir() )
morphomap.core |
list: morphomap.core object |
morphomap.shape |
list: morphomap.shape object |
vector |
numeric: define which sections will be saved |
full |
logical: if TRUE the thickness at ALPM is reported |
width |
numeric: width of the picture |
height |
numeric: height of the picture |
pointsize |
numeric: pointsize of plotted text |
res |
numeric: the nominal resolution in ppi which will be recorded |
colthk |
specify the color for the numbers |
collbs |
specify the color for the labels |
dirpath |
character: path of the directory where the pictures will be saved |
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
#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)#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)
Visualize 2D and 3D cross sections
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 )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 )
Shape |
list: output from morphomapShape function |
dims |
numeric: 2 = bi-dimensional cross sections, 3 = three-dimensional cross sections |
col1 |
color of the external outline |
col2 |
color of the internal outline |
colc |
color of the centroid of the cross section |
colr |
color of the radii |
coll1 |
color of the lines on the enternal outline |
coll2 |
color of the lines on the internal outline |
size |
numeric: points and spheres size |
lwd |
numeric: line width in pixels |
colmesh1 |
color of the periosteal mesh |
colmesh2 |
color of the endosteal mesh |
alpha |
numeric: alpha value between 0(fully transparent) and 1 (opaque) |
tri |
logical: if TRUE the semilandmarks configuration is triangulated |
outlines |
logical: if TRUE the 2D and 3D outlines are plotted |
points |
logical: if TRUE points (2D) and spheres (3D) are plotted |
lines |
logical: if TRUE 2D and 3D lines are plotted |
centroid |
logical: if TRUE 2D and 3D centroids are plotted |
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 |
vecs |
numeric: which sections will be plotted. If dims is set on 2 only the first element of the vector vecs is considered |
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
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) }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) }
Import an array stored in a morphologika file
morphomapReadMorphologika(file)morphomapReadMorphologika(file)
file |
path of the file to be read |
out list containing an array, labels, groups and variables
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
Define a rectangular outline
morphomapRectangle(l = 1, h = 1, n = 1000)morphomapRectangle(l = 1, h = 1, n = 1000)
l |
numeric: length of the rectangle |
h |
numeric: height of the rectangle |
n |
numeric: number of points along the outline |
mat matrix with coordinates
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
extsec<-morphomapRectangle(10,6,100) intsec<-morphomapRectangle(8,4,100) plot(extsec,asp=1,type="l") points(intsec,type="l",col=2)extsec<-morphomapRectangle(10,6,100) intsec<-morphomapRectangle(8,4,100) plot(extsec,asp=1,type="l") points(intsec,type="l",col=2)
Wrapper of the function regularradius written by Julien Claude (Morphometrics with R)
morphomapRegradius(mat, center, n)morphomapRegradius(mat, center, n)
mat |
a kx2 matrix |
center |
coordinates of the center from which the calculation of regular radius started |
n |
number of points |
V2 position of landmarks equi angular spaced
Julien Claude, Antonio Profico
Claude, J. (2008). Morphometrics with R. Springer Science & Business Media.
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)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)
Separate a mesh from its visible and not visible components by using CA-LSE method
morphomapSegm(mesh, views = 30, param1 = 4, num.cores = NULL)morphomapSegm(mesh, views = 30, param1 = 4, num.cores = NULL)
mesh |
object of class mesh3d |
views |
numeric: number of points of view |
param1 |
numeric: first parameter for spherical flipping (usually ranged between 3 and 4) |
num.cores |
numeric: number of cores |
The result could be affected by the value set in the param1 argument. Before running morphomapCore please the periosteal and endosteal surfaces.
external mesh3d of the visible facets from the points of view
internal mesh3d of the not visible facets from the points of view
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
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.
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") }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") }
Tool for the extraction of equiangular landmarks on the entire diaphysis
morphomapShape( morphomap.core, num.land, sects_vector, cent.out = "CCA", delta = 0.1, side = "left" )morphomapShape( morphomap.core, num.land, sects_vector, cent.out = "CCA", delta = 0.1, side = "left" )
morphomap.core |
list: morphomap.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 |
side |
character: specify if the long bone is "left" or "right" side |
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
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
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)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)
Sort a series of points stored as a 2D matrix
morphomapSort(mat)morphomapSort(mat)
mat |
numeric matrix: a kx2 matrix |
mat sorted kx2 matrix
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
rand<-sample(100) extsec<-morphomapCircle(10,100)[rand,] plot(extsec,type="l",asp=1) sorted<-morphomapSort(extsec) plot(sorted,type="l",asp=1)rand<-sample(100) extsec<-morphomapCircle(10,100)[rand,] plot(extsec,type="l",asp=1) sorted<-morphomapSort(extsec) plot(sorted,type="l",asp=1)
Tool for the extraction of equiangular landmarks on the entire diaphysis
morphomapThickness(morphomap.shape)morphomapThickness(morphomap.shape)
morphomap.shape |
list: morphomap.shape object |
sect_thickness cortical thickness at each pair of landmarks on the external and internal outlines
ALPM_thickness cortical thickness at ALPM quadrants
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
#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)#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)
Translate a section to a new center defined by the user
morphomapTranslate(corA, medA, Cx, Cy)morphomapTranslate(corA, medA, Cx, Cy)
corA |
matrix: coordinates of the external outline |
medA |
matrix: coordinates of the internal outline |
Cx |
numeric: new x center coordinate |
Cy |
numeric: new y center coordinate |
cortical new centered coordinates of the external outline
medullar new centered coordinates of the internal outline
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
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")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")
Triangulate the external and internal outlines of a 3D cross section
morphomapTri2sects(cp, mp)morphomapTri2sects(cp, mp)
cp |
matrix: coordinates of the external outline of the section |
mp |
matrix: coordinates of the internal outline of the section |
matrix coordinates of the triangulated mesh
tri triangulations of the triangulated mesh
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
Build a mesh starting from the coordinates of the diaphysis
morphomapTriangulate(set, n, close = FALSE)morphomapTriangulate(set, n, close = FALSE)
set |
matrix: coordinates of the cross sections to be triangulated |
n |
numeric: number of cross sections |
close |
logical: if TRUE the two surfaces are closed |
mesh a mesh of the triangulated semilandark configuration
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
Calculate cortical map variation from PCA
morphomapVariations(PCA, scores, PC, pal = blue2green2red(101), asp = 2)morphomapVariations(PCA, scores, PC, pal = blue2green2red(101), asp = 2)
PCA |
list: list containing morphomapShape objects |
scores |
list: list containing morphomapShape objects |
PC |
list: list containing morphomapShape objects |
pal |
list: list containing morphomapShape objects |
asp |
numeric: aspect ratio of the morphometric map |
mapvar: matrix containing values of cortical thickness
Antonio Profico
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])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])
Export an array in the morphologika format file
morphomapWriteMorphologika(array, groups = NULL, variables = NULL, file)morphomapWriteMorphologika(array, groups = NULL, variables = NULL, file)
array |
an array |
groups |
a vector containing a classifier |
variables |
list containing further classifiers |
file |
path of the file to be saved |
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
Calculate the polar moment of inertia around the x and y axes and the polar section module
morphomapZmoment(cp, mp, Cx = 0, Cy = 0, delta = 0.1)morphomapZmoment(cp, mp, Cx = 0, Cy = 0, delta = 0.1)
cp |
matrix: coordinates of the external outline of the section |
mp |
matrix: coordinates of the internal outline of the section |
Cx |
numeric: x coordinate of the section center |
Cy |
numeric: y coordinate of the section center |
delta |
numeric: picture elements of adjustable side length |
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
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi
extsec<-morphomapCircle(10,1000) intsec<-morphomapCircle(8,1000) ZMs<-morphomapZmoment(extsec,intsec,delta=0.1)extsec<-morphomapCircle(10,1000) intsec<-morphomapCircle(8,1000) ZMs<-morphomapZmoment(extsec,intsec,delta=0.1)
3D mesh of a chimpanzee femur bone
data(PanFem27713)data(PanFem27713)
Antonio Profico, Luca Bondioli, Pasquale Raia, Paul O'Higgins, Damiano Marchi