A way to project the 3D set into 2D:
If you have acquired only the outline of the articular surface area, you can
use the package morphomap for PCA, sorting points on the curve, and calculating
the area using the Shoelace formula:
library(morphomap)
PCA<-prcomp(yourset,scale=F)
plot(PCA$x,asp=1)
morphomapArea(morphomapSort(PCA$x))
If you have acquired a sparse set of points on the surface area, you can use
PCA combined with a convex hull to calculate the area:
library(sp)
PCA<-prcomp(yourset,scale=F)
box.hpts <- chull(PCA$x)
box.hpts <- c(box.hpts, box.hpts[1])
box.chull.coords <- PCA$x[box.hpts,]
chull.poly <- Polygon(box.chull.coords[,c(1,2)], hole=F)
chull.area <- chull.poly@area
________________________________
Da: morphmet2@googlegroups.com <morphmet2@googlegroups.com> per conto di
Antonio Profico <antonio.prof...@unipi.it>
Inviato: venerdì 10 gennaio 2025 00:58:53
A: Jordan Guerra; Morphmet
Oggetto: Re: [MORPHMET2] Re: Calculating surface areas from 3D landmarks
Dear Jordan,
try this code:
library(Arothron)
library(Rvcg)
library(Morpho)
library(rgl)
set<-read.amira.set("insertherethepath","auto")[,,1]
sur<-vcgBallPivoting(set)
open3d()
wire3d(sur,col="blue")
spheres3d(set,radius=1)
vcgArea(sur) #calculate the area
mesh2ply(sur,"mysur") #export the triangulated set
#Since you mentioned Amira
right click on the set-> pointWrap #it's similar to the R function
vcgBallPivoting
or
right click on the set -> Delaunay2D
on the surface
right click -> measure -> surfaceArea -> apply -> show
Best,
Antonio
________________________________
Da: morphmet2@googlegroups.com <morphmet2@googlegroups.com> per conto di Jordan
Guerra <jordansgue...@gmail.com>
Inviato: giovedì 9 gennaio 2025 23:18:54
A: Morphmet
Oggetto: [MORPHMET2] Re: Calculating surface areas from 3D landmarks
Correction to my original message: My surfaces were not aligned to orthogonal
planes when I collected the data
On Thursday, January 9, 2025 at 4:21:07 PM UTC-5 Jordan Guerra wrote:
Dear all,
Happy new year to everyone! I'm looking for some advice on how to
best/efficiently calculate the area of an articular surface using R.
I have 3D landmark data (collected in Amira) that I want to use to calculate
the area of different articular surfaces. I want my surfaces were not aligned
to orthogonal planes when I collected the data
What I've tried so far is to re-align the landmarks of the surfaces I'm
interested to one of the orthogonal planes (using 3 points) and then removing
one of the dimensions so that I have a 2D polygon that I can use Gauss's area
formula. However, because I am only using 3 points to determine the 'new'
orthogonal plane, I have doubts that this is the best way to do this since not
all of other landmarks fall on this plane.
Does anyone have any suggestions on how to do this better or is there an
R-package that does this already?
All the best,
Jordan
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