morphomapShape | R Documentation |
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" )
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)
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