Fwd: function to open tps files with landmarks in R

[morphmet]

-------- Original Message --------
Subject:        function to open tps files with landmarks in R
Date:   Fri, 23 Jul 2010 15:32:50 +0100
From:   marta rufino <marta.m.ruf...@gmail.com>
To:     morphmet_modera...@morphometrics.org

Just did a function to open tps landmarks in R. Maybe it would be useful 
to someone, so I am publishing it.

It produces the results in two formats: a data frame and a array. The
array is arranged to be used with Claude's book examples/functions.
You only need to introduce the path to your file in 'fil'.
Cheers, M

open.tps.landmark=function(fil){
   # to test: 
fil="D:\\MARTA\\PosDoc\\navalha\\originais\\nav_ordered_11LM_b.TPS"
   # fil is the file name, with respective extension and path
   # note the file is better to not include the path for each image.
   # X and Y are outline coordinates, ind is the individual number and
facto the fcator (i.e. image name)
   # note that facto should then be arranged accordingly

     # open the file
     kk=scan(fil, what="char", quote="",sep="\n", strip.white=T, quiet=T)
     kk=casefold(kk, upper=F)

     #detect landmarks, number of points, etc.
         sp=grep("lm=",kk) # landmark points
         n=length(sp) # number of configurations
         p=as.numeric(sub("lm=","",kk[sp])) #number of landmarks in each
animal
         sp.start=sp+1 #starting location of the
         sp.end=sp+p #ending position of each curve
         im=kk[grep("image=", kk)]#list of images
         im=sub("image=","",im)
         im=sub(".tif","",im); im=sub(".jpg","",im)


   # extract landmark coordinates
   # this would be much better, if done with a apply function... :(
   newd=array(NA, c(1,4))
   colnames(newd)= c("X","Y","ind","facto")
   for(ii in 1:n){

kk1=data.frame(X=as.numeric(unlist(strsplit(kk[sp.start[ii]:sp.end[ii]],
" ")))[seq(1,p[ii]*2,2)],

Y=as.numeric(unlist(strsplit(kk[sp.start[ii]:sp.end[ii]], "
")))[seq(2,p[ii]*2,2)],
                    ind=ii, facto=im[ii])
       newd=rbind(newd, kk1)
               }
       newd=newd[-1,]

   ## to create the array that is used on Claude's
   newd1=array(NA, dim=c(p[1],2,n))
   newd1[,1,]=matrix(newd[,1], ncol=n)
   newd1[,2,]=matrix(newd[,2], ncol=n)

   # plot(Y~X, newd[newd$N==1,], typ="o", asp=1) #Check plotting
   xyplot(Y~X, newd, groups=facto, typ="l", aspect="iso") #Check plotting
   print("in $dt the landmarks are organized in a data frame")
   print("in $arr these are organized in an array, ready to go through
Claude's book")
   list(dt=newd, arr=newd1)
       }