R/amiralandmarks-io.R
Generic functions to read/write landmarks in any supported format
read.landmarks(f, ...) write.landmarks(x, file, format = "amiralandmarks", ext = NULL, Force = FALSE, MakeDir = TRUE, ...)
f | Path to a file (can also be a URL) |
---|---|
... | Additional arguments passed on to format specific functions |
x | The landmarks object to write. Can also be a plain |
file | The path to the output file. If this does not end in an extension
like |
format | Character vector specifying output format. Defaults to
|
ext | Optional character vector specifying a new or non-standard
extension to use for output file, including the period (e.g.
|
Force | Whether to overwrite an existing file |
MakeDir | Whether to create directory implied by |
for read.landmarks
a matrix or list of additional class
landmarks, where the rownames specify the names of each landmark if
available.
For write.landmarks
the path to the written file, invisibly.
Presently the supported formats are
Amira
CMTK
Fiji (see http://fiji.sc/Name_Landmarks_and_Register)
See examples section for how to produce a listing of all currently
available formats with fileformats
.
Only the amiralandmarks format supports the use of paired landmarks
#> format class ext read write magic #> 1 amiralandmarks landmarks .landmarkAscii TRUE TRUE TRUE #> 2 amiralandmarks landmarks .landmarkBin TRUE TRUE TRUE #> 3 amiralandmarks landmarks .am TRUE TRUE TRUE #> 4 amiralandmarks landmarks .amiramesh TRUE TRUE TRUE #> 5 cmtklandmarks landmarks .landmarks TRUE TRUE TRUE #> 6 fijilandmarks landmarks .points TRUE TRUE TRUE## round trip tests m=matrix(rnorm(6), ncol=3) rownames(m)=c("nose", "ear") f=write.landmarks(m, file='knee', format='cmtk') read.landmarks(f)#> [,1] [,2] [,3] #> nose -1.117033 -0.4420909 -0.7190785 #> ear -2.339310 0.1766739 1.7054692 #> attr(,"class") #> [1] "landmarks" "matrix"# write in amira format which does not support named landmarks f2=write.landmarks(m, file='knee', format='amira') read.landmarks(f2)#> [,1] [,2] [,3] #> [1,] -1.117033 -0.4420909 -0.7190785 #> [2,] -2.339310 0.1766739 1.7054692 #> attr(,"class") #> [1] "landmarks" "matrix"# clean up unlink(c(f,f2))