nef2Coe: Imports `.nef` files and creates `Coe` objects.

Description

nef2Coe converts .nef files to Coe objects. This function is intended to ease data exchange between Momocs and SHAPE suite (see Iwata in the References below).

Usage

nef2Coe(nef.path)

Arguments

nef.path

A character that indicates the path for the .nef file to convert.

Value

nef2Coe returns a Coe object.

References

Iwata H, Ukai Y. 2002. SHAPE: a computer program package for quantitative evaluation of biological shapes based on elliptic Fourier descriptors. The Journal of Heredity 93: 384-385. You can also have a look to the SHAPE's manual distributed with the program suite, that gives a description of the .nef format.

Examples

Run this code

# I (VB) just finished my post-doc in India and I wont have time for Momocs
# until mid march or maybe a bit after that.
# Ryan Felice found a bug in my own version. I provide hereafter the function
# he kindly sent to me and that worked fine for him.
# Hope this help. Thanks again to him.
NEF2COE<-function (nef.path){
  nef <- readLines(nef.path)
  HARMO.l <- grep(pattern = "HARMO", nef)
  nb.h <- as.numeric(substring(nef[HARMO.l], 8))
  nef <- nef[-(1:HARMO.l)]
  nb.coo <- length(nef)/(nb.h + 1)
  coo.i <- 1:nb.coo
  coo.beg <- (coo.i - 1) * (nb.h + 1) + 1
  coo.end <- coo.beg + nb.h
  res <- matrix(NA, nrow = nb.coo, ncol = nb.h * 4, dimnames = list(nef[coo.beg], paste(rep(LETTERS[1:4], each = nb.h), 1:nb.h, sep = "")))
  for (i in seq(along = coo.i)) {
    nef.i <- nef[(coo.beg[i]+1):coo.end[i]]
    x <- as.numeric(unlist(strsplit(nef.i, " ")))
    x1<-x[!is.na(x)]
    a.i<-x1[seq(1,length(x1),4)]
    b.i<-x1[seq(2,length(x1),4)]
    c.i<-x1[seq(3,length(x1),4)]
    d.i<-x1[seq(4,length(x1),4)]
    res[i, ]<-c(a.i,b.i,c.i,d.i)
  }
  return(Coe(res,method="eFourier"))}