################################################################################
############# function to transform an array in a tps file #####################
################################################################################

write.tps=function(array.file,name.file=NA,scale.val=F,picture=F,type.pic="TIF",images.lab=F,comment=F) {

# calculate the numbers of landmarks
p=length(array.file$coordinates[,1,1])
# find the number of specimen
n=length(array.file$coordinates[1,1,])
###########
if (scale.val==F & picture==F & comment==F & images.lab==F) aux=2
if (scale.val==T | picture==T | comment==T | images.lab==T) aux=3
if (scale.val==T & picture==T | scale.val==T & images.lab==T | scale.val==T & comment==T | picture==T & comment==T | images.lab==T & comment==T) aux=4
if (scale.val==T & picture==T & comment==T | scale.val==T & images.lab==T & comment==T) aux=5

# create a vector with the names of the first line
landmarks=vector(length=n)
landmarks[]=paste(c("lm=",p),collapse="")

# create a vecotor with the vector with the scale
if (any(array.file$scales!=0)) {
scales=vector(length=n)
for (i in 1:n) {scales[i]=paste(c("scale=",array.file$scales[i]),collapse="")}
}

# create a vecotor with the vector with the picture
if (any(array.file$pictures!=0)) {
pictures=vector(length=n)
for (i in 1:n) {pictures[i]=paste(c("image=",array.file$pictures[i],".",type.pic),collapse="")}
}

# create a vector with the vector images
if (any(array.file$images!=0)) {
images=vector(length=n)
for (i in 1:n) {images[i]=paste(c("image=",array.file$images[i]),collapse="")}
}


# create a vecotor with the vector with the scale
if (any(array.file$comments!=0)) {
comments=vector(length=n)
for (i in 1:n) {comments[i]=paste(c("comment=",array.file$comments[i]),collapse="")}
}

# create a vector with the ID
ID=vector(length=n)
for (i in 1:n) {ID[i]=paste(c("id=",c(0:(n-1))[i]),collapse="")}

# create a matrix with the paired coordinate of every landmarks
coordinates=matrix(NA,n,p)
# fill this matrix
for (i in 1:n) {
    for (j in 1:p) {
    coordinates[i,j]=paste(array.file$coordinates[j,,i],collapse=" ")
    }
}

# create a matrix with all the info that will go in the tps depending on what is available
if (picture==F & scale.val==F & comment==F & images.lab==F) {
    tpsmtr=matrix(NA,n,(p+aux))
    for (i in 1:n) {
          tpsmtr[i,]=c(landmarks[i],coordinates[i,],ID[i])
    }
}
if (picture==T & scale.val==F & comment==F & images.lab==F) {
    tpsmtr=matrix(NA,n,(p+aux))
    for (i in 1:n) {
          tpsmtr[i,]=c(landmarks[i],coordinates[i,],pictures[i],ID[i])
    }
}
if (images.lab==T & scale.val==F & comment==F & picture==F) {
    tpsmtr=matrix(NA,n,(p+aux))
    for (i in 1:n) {
          tpsmtr[i,]=c(landmarks[i],coordinates[i,],images[i],ID[i])
    }
}
if (picture==F & scale.val==T & comment==F & images.lab==F) {
    tpsmtr=matrix(NA,n,(p+aux))
    for (i in 1:n) {
          tpsmtr[i,]=c(landmarks[i],coordinates[i,],ID[i],scales[i])
    }
}
if (picture==F & scale.val==F & comment==T & images.lab==F) {
    tpsmtr=matrix(NA,n,(p+aux))
    for (i in 1:n) {
          tpsmtr[i,]=c(landmarks[i],coordinates[i,],ID[i],comments[i])
    }
}
if (picture==T & scale.val==T & comment==F & images.lab==F) {
    tpsmtr=matrix(NA,n,(p+aux))
    for (i in 1:n) {
          tpsmtr[i,]=c(landmarks[i],coordinates[i,],pictures[i],ID[i],scales[i])
    }
}
if (images.lab==T & scale.val==T & comment==F & picture==F) {
    tpsmtr=matrix(NA,n,(p+aux))
    for (i in 1:n) {
          tpsmtr[i,]=c(landmarks[i],coordinates[i,],images[i],ID[i],scales[i])
    }
}
if (picture==F & scale.val==T & comment==T & images.lab==F) {
    tpsmtr=matrix(NA,n,(p+aux))
    for (i in 1:n) {
          tpsmtr[i,]=c(landmarks[i],coordinates[i,],ID[i],scales[i],comments[i])
    }
}
if (picture==T & scale.val==F & comment==T & images.lab==F) {
    tpsmtr=matrix(NA,n,(p+aux))
    for (i in 1:n) {
          tpsmtr[i,]=c(landmarks[i],coordinates[i,],pictures[i],ID[i],comments[i])
    }
}
if (scale.val==T & picture==T & comment==T & images.lab==F) {
    tpsmtr=matrix(NA,n,(p+aux))
    for (i in 1:n) {
          tpsmtr[i,]=c(landmarks[i],coordinates[i,],pictures[i],ID[i],scales[i],comments[i])
    }
}
if (scale.val==T & images.lab==T & comment==T & picture==F) {
    tpsmtr=matrix(NA,n,(p+aux))
    for (i in 1:n) {
          tpsmtr[i,]=c(landmarks[i],coordinates[i,],images[i],ID[i],scales[i],comments[i])
    }
}


# save this matrix in a file
cat(paste(t(tpsmtr)),sep="\n",file=name.file)
}