data-raw/landmarks.R

In jefferis/elmr: Support for working with light and electron microscopy fly brain data

# download elm landmarks (or use local version)
elm_landmarks_ <- function(u="https://raw.githubusercontent.com/saalfeldlab/elm/master/lm-em-landmarks.csv") {
  hu=try(HEAD(u, timeout(1)), silent = TRUE)
  internet.ok=!inherits(hu, 'try-error')
  if(internet.ok){
    tf=tempfile(fileext = '.csv')
    on.exit(unlink(tf))
    downloader::download(u, destfile=tf, quiet=!interactive())
  } else {
    tf=system.file("elm/lm-em-landmarks.csv", package = 'elmr')
  }
  x=read.csv(tf, col.names = c("Label", "Use", "X","Y","Z", "X1","Y1","Z1"), header = FALSE)
  x$Use=as.logical(x$Use)
  x
}
if(FALSE) {
elm.landmarks <- elm_landmarks_()
elm.landmarks.12=elm.landmarks
# NB only transform landmarks in use.
elm.landmarks[elm.landmarks$Use,6:8]=xform_brain(elm.landmarks[elm.landmarks$Use,6:8], sample =FAFB12, reference = FAFB13, method='single')
# alternatively try to transform all
# elm.landmarks[,6:8]=xform_brain(elm.landmarks[,6:8], sample =FAFB12, reference = FAFB13, method='single')
elm.landmarks=subset(elm.landmarks, Use)
devtools::use_data(elm.landmarks, overwrite = T)
devtools::use_data(elm.landmarks.12, overwrite = T)
}

read_elm_csv <- function(x) {
  y = read.csv(
    x,
    col.names = c("Label", "Use", "X", "Y", "Z", "X1", "Y1", "Z1"),
    header = FALSE
  )
  y$Use = as.logical(y$Use)
  y
}
# elm.landmarks.feb17=read_elm_csv('data-raw/170211_new_ELM_landmarks_v7.csv')
elm.landmarks.mar17=read_elm_csv('data-raw/170303_ELM_landmarks_v14.csv')
elm.landmarks.13=elm.landmarks.mar17
devtools::use_data(elm.landmarks.13, overwrite = T)

# Skeleton for FAFB14 landmarks
stopifnot(all(elm.landmarks.mar17$Use))
elm.landmarks=elm.landmarks.mar17
elm.landmarks[, 6:8]=
  xform_brain(
    elm.landmarks[, 6:8],
    sample = FAFB13,
    reference = FAFB14,
    method ='single'
  )

devtools::use_data(elm.landmarks, overwrite = T)