#put all files in one folder, note that / in directories gets \\#
#you need the package "Morpho" up and running to make this script work#
		##### The next commands change all the inputs to YOUR filename as long as you adjust the names to your specific directory on your computer ####
		##### all four #FILENAME#s have to be changed #####
YOURFILE <- "FILE LOCATION"
YOURFILEMORPH <- "FILE LOCATION_Morph.tps"

#####Trying to import TPS File#####
#this is a variation of the function "readallTPS" in Morpho
#the outline stuff has been removed, for IDs it takes the IMAGE= information
#### get ID infos: with the function gsub the image information string has been removed 
#to show only the original filename to compare them later in tps.dig (nice visualization)
### extract Landmarks: by using gsub to mark missing values as NA quotation marks appear and the numerics are returned to characters
#as.numeric is therefore repeated
readallTPSimages <- function(file)
  {
    out=list()
    input <- readLines(file)
### get Landmark infos
    LM <- grep("LM=",input)
    LMstring <- input[LM]
    nLM <- sapply(LMstring,strsplit,split="=")
    nLM <- unlist(nLM)
    nLM <- as.integer(nLM[-which(nLM == "LM")])
    nobs <- length(nLM)
### get ID infos
    ID <- grep("IMAGE=",input)
    IDstring <- input[ID]
    nID <- sapply(IDstring,function(x){x <- gsub("=","",x)})
    nID <- gsub("IMAGE","",unlist(nID))
                                        #nID <- nID[-which(nID == "ID")]
    ##nobs <- length(nID)
    out$ID <- nID
    
### extract Landmarks
    LMdata <- list()
    for ( i in 1:nobs)
      {
        if (nLM[i] > 0)
          {
            LMdata[[i]] <- as.numeric(unlist(strsplit(unlist(input[c((LM[i]+1):(LM[i]+nLM[i]))]),split=" ")))
            LMdata[[i]] <- gsub("-1", "NA", LMdata[[i]])
	    LMdata[[i]] <- as.numeric(LMdata[[i]])
	    LMdata[[i]] <- matrix(LMdata[[i]],nLM[i],2,byrow = TRUE)
          }
        else
          LMdata[[i]] <- NA
      }
    names(LMdata) <- nID
    out$LM <- LMdata
  }
data <- list2array(readallTPSimages(YOURFILE))

#This may be a more comfortable way using geomorph functions
#data <- readland.tps(YOURFILE, specID = "imageID", readcurves = FALSE, warnmsg = T)

print(data)

#####Estimate missing Landmarks with Morpho#####
estimate <- fixLMtps(data,comp=5)
#####Export as .tps#####
writeland.tps(estimate$out, YOURFILEMORPH, scale = NULL, specID = TRUE)