Dear Edouard,
Following is my way to collect landmark coordinate using ImageJ and R (for
*R* user)
1. to set scale: Analyze/set Scale (record the distance in px and adding
known distance)
2. Collecting the coordinate of landmark point:
2.1 Analyze/Set Measurements -> check on Display label (to record image
name as specimen code)
2.2 Open image, then using multi-point Tools to mark your landmark points
2.3 Click m or Analyze Measure to print the result to Results window
(repeat step 2.2 and 2.3 for all specimen you have)
2.4 (save your results) On Results window: File/Save As --> save result to
an *.txt file.
2.5 Using R code which I wrote below to import landmark coordinate into R
(PLEASE check attach file): (with *readtps(filename, nland = number of
landmark points)*)
On Mon, Jun 15, 2015 at 7:59 PM, Edouard Masson-MacLean <
[email protected]> wrote:
> Hello,
>
> Is there a guide for the complete beginner on how to use ImageJ instead of
> tpsdig, especially on how to set the scale before digitizing?
>
> Many thanks
>
> Edouard
>
>
> -----------------------------------------------------
> Edouard Masson-MacLean
> PhD Candidate
> Room 119
> Department of Archaeology
> School of Geosciences
> University of Aberdeen
> St. Mary's, Elphinstone Road
> Aberdeen, AB24 3UF
> Scotland, UK
>
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#### read tps data from imageJ ####
readtps<-function(filepath, nland = 12){
tempdata<-read.table(filepath)
##### get lable and check correspond nlandmark point to all specimen
label <- tempdata["Label"]
l.table<-table(label)
if(length(l.table[l.table!=nland])!=0){
err<-l.table[l.table!=nland]
print(err)
stop("The number of landmark not equal to all specimen")
}
### get x and y coordinate
X<-round(tempdata["X"], 0)
Y<-round(tempdata["Y"],0)
XY<-cbind(X, Y)
XY<-as.vector(t(XY))
n = nland
m = 2
k = nrow(tempdata)/nland
coords<-aperm(array(XY, c(m, n, k)), c(2,1,3))
v.names<-names(l.table)
dimnames(coords)<-list(paste("LM", 1:nland, sep=""),c("X", "Y"), v.names)
return(coords)
}
