R/jfids.R

In jefferis/flylight: Functions for working with Janelia FlyLight confocal images

#' Return the janelia image name for a path (excluding any file extension)
#'
#' @param file Path to file(s) to test
#' @param checkExists Check that calculated image stem exists (TODO)
#' @return Character vector of image names (or NA if checkExists fails)
#' @export
#' @seealso \code{\link{jfshortname_forfile}}
#' @examples
#' stopifnot(jfimagestem_forfile("Registration.GHT/affine/JFRC2_GMR_10A06_AE_01_08-fA01b_C100709_20100709225242046_01_ght.list")=="GMR_10A06_AE_01_08-fA01b_C100709_20100709225242046")
jfimagestem_forfile<-function(file,checkExists=FALSE){
  # get rid of any leading directories
  if(is.factor(file)) file=as.character(file)
  jfi=basename(file)
  # GMR_9G09_AE_01_41-fA01b_C100120_20100120131426046
  regex="GMR_[0-9]{1,2}[A-H][0-9]{2}_[A-Z]{2}_[0-9]{2}_[0-9]{2}-fA0[1-2](b|v)_C[0-9]{6}_[0-9]{17}"
  #trim off template brain
  jfi=sub(sprintf(".*(%s).*",regex),"\\1",jfi)
  if(checkExists){
    message("This option is not yet implemented!")
    # load_fcdb("neuron")
    # missing=!gn%in%neuron$gene_name
    # if(any(missing)){
    #		warning("gene_name:",gn[missing]," for file:",file[missing]," not present in neuron table")
    #		gn[missing]=NA_character_
    # }
  }
  jfi
}
#' Return a shortened (but unique) janelia image name for a path
#'
#' NB Does not include file extension
#' @param file Path to file(s) to test
#' @param checkExists Check that calculated image stem exists (TODO)
#' @return Character vector of image names (or NA if checkExists fails)
#' @export
#' @seealso \code{\link{jfimagestem_forfile}}
jfshortname_forfile<-function(file,checkExists=FALSE){
  image_stem=jfimagestem_forfile(file,checkExists=checkExists)
  uniquebit=sub("GMR_([^\\-]+).*","\\1",image_stem)
  gsub("_","",uniquebit)
}

#' Return the GMR code (ie plate row column) for a file
#'
#' @param f one or more paths
#' @return character vector GMR code
#' @export
#' @seealso \code{\link{jfimagestem_forfile}}
gmr_forfile<-function(f){
  sub("GMR_([^_]+)_.*","\\1",jfimagestem_forfile(f))
}