read.landmarks {nat}

Generic functions to read/write landmarks in any supported format

Description

Generic functions to read/write landmarks in any supported format

Usage

read.landmarks(f, ...)

write.landmarks(
  x,
  file,
  format = "amiralandmarks",
  ext = NULL,
  Force = FALSE,
  MakeDir = TRUE,
  ...
)

Arguments

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 matrix or data.frame.

file

The path to the output file. If this does not end in an extension like .landmarksAscii, then one will be added based on the value of the ext argument.

format

Character vector specifying output format. Defaults to "amiralandmarks". Partial matching is used (e.g. amira is sufficient).

ext

Optional character vector specifying a new or non-standard extension to use for output file, including the period (e.g. ext='.am'). When ext=NULL, the default, the default extension for the selected format will be added if f does not have an extension. When ext=NA, the extension will not be modified and no extension will be appended if f does not have one.

Force

Whether to overwrite an existing file

MakeDir

Whether to create directory implied by file argument.

Details

Presently the supported formats are

• Amira

• CMTK

• Fiji (see https://imagej.net/plugins/name-landmarks-and-register)

See examples section for how to produce a listing of all currently available formats with fileformats.

Value

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.

Paired landmarks

Only the amiralandmarks format supports the use of paired landmarks

See Also

fileformats

Examples

## Listing of supported fileformats for landmarks
fileformats(class = 'landmarks', rval = "info")

## 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)

# write in amira format which does not support named landmarks
f2=write.landmarks(m, file='knee', format='amira')
read.landmarks(f2)

# clean up
unlink(c(f,f2))