Cannot seem to get place patch code working. please help

[k-moff]

Hi,
I am trying to get the placePatch code working to semiautomatically place patch landmarks on my specimens.

I am receiving the following error:

patchtest <- placePatch(pseudatlas, testdata, path = "C:/Users/katem/OneDrive/Documents/pseudlm/meshes", prefix = '', fileext=".ply", inflate=5)

Removed 0 duplicate 73 unreferenced vertices and 4 duplicate faces
Removed 0 duplicate 73 unreferenced vertices and 4 duplicate faces
Warning messages:
1: In place.patch(dat.array, path, atlas.mesh = atlas$mesh, atlas.lm = atlas$landmarks, :
matching for specimen 1 failed with: Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE): index larger than maximal 0

2: In place.patch(dat.array, path, atlas.mesh = atlas$mesh, atlas.lm = atlas$landmarks, :
matching for specimen 2 failed with: Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE): index larger than maximal 0

Could you please help? Below is the code and is working up until this point...

Thank you very much, Any help would be greatly appreciated.

library(Morpho)
library(geomorph)
library(Rvcg)
library(rgl)
library(devtools)

####import 3D surface as a mesh file - my template 3d mesh#####

template.mesh <- file2mesh("C:/Users/katem/OneDrive/Documents/pseudlm/pseudlmtesttemp.ply", clean = TRUE, readcol = FALSE)

####import landmarks and the patch defined on the template###

template.pts <- read.pts("C:/Users/katem/OneDrive/Documents/pseudlm/pseudlmtesttemp.pts")

###create atlas####

###extract info about fixed landmarks, curves, patches from an atlas created by idav checkpoint####
cExtract (template.pts)

###create atlas needed for placing patch semilandmarks####

pseudatlas <- createAtlas(template.mesh, landmarks = template.pts[c(1:56,57:64,65:69,70:74,75:79,80:84,85:92),], patch = template.pts[-c(1:56,57:64,65:69,70:74,75:79,80:84,85:92),], corrCurves = list(c(57:64),c(65:69),c(70:74),c(75:79),c(80:84),c(85:92)))

plotAtlas(pseudatlas)

####read pts files from landmarks on specimens i want to place patch on####

testpts1 <- read.pts("C:/Users/katem/OneDrive/Documents/pseudlm/pseudlmtest.pts")

testpts2 <- read.pts("C:/Users/katem/OneDrive/Documents/pseudlm/pseudlmtest2.pts")

cExtract(testpts1)

cExtract(testpts2)

####create landmark array for fixed landmarks ####

testdata <- bindArr(testpts1, testpts2, along=3)
dimnames(testdata)[[3]] <- c("pseudlmtest", "pseudlmtest2")

testpts1.mesh <- file2mesh("C:/Users/katem/OneDrive/Documents/pseudlm/meshes/pseudlmtest.ply", clean = TRUE, readcol = FALSE)
testpts2.mesh <- file2mesh("C:/Users/katem/OneDrive/Documents/pseudlm/meshes/pseudlmtest2.ply", clean = TRUE, readcol = FALSE)

checkLM(testdata)

####writemeshtodisk####

mesh2ply(testpts1.mesh, filename="pseudlmtest")
mesh2ply(testpts2.mesh, filename="pseudlmtest2")

place patch####

patchtest <- placePatch(pseudatlas, testdata, path = "C:/Users/katem/OneDrive/Documents/pseudlm/meshes", prefix = '', fileext=".ply", inflate=5)

RECEIVE ERROR PLEASE SEE ABOVE. THANKS