R/Plate.R

In ome/rOMERO-gateway: OMERO R Gateway

#' Plate 
#' @slot server Reference to the server
#' @slot dataobject The Java data object
#' @export Plate
#' @exportClass Plate
#' @seealso \linkS4class{OMERO}
#' @import rJava
Plate <- setClass( 
  'Plate',
  contains = 'OMERO',
  
  slots = c(
    server = "OMEROServer",
    dataobject = "jobjRef"
  ),
  
  validity=function(object)
  {
    if(is.null(object@server)) {
      return("OMEROserver is missing!")
    }
    if(is.null(object@dataobject)) {
      return("OMERO object is missing!")
    }
    if(!.jinstanceof(object@dataobject, J("omero.gateway.model.PlateData"))) {
      return("OMERO object is not an instance of PlateData!")
    }
    return(TRUE)
  }
)

#' Get the wells of the specific plate
#'
#' @param plate The plate
#' @return The wells @seealso \linkS4class{Well}
#' @export
#' @exportMethod getWells
#' @examples
#' \dontrun{
#' wells <- getWells(plate)
#' }
setGeneric(
  name = "getWells",
  def = function(plate)
  {
    standardGeneric("getWells")
  }
)

#' Get the wells of the specific plate
#'
#' @param plate The plate
#' @return The wells @seealso \linkS4class{Well}
#' @export
#' @exportMethod getWells
setMethod(
  f = "getWells",
  signature = "Plate",
  definition = function(plate)
  {
    server <- plate@server
    gateway <- getGateway(server)
    ctx <- getContext(server)
    browse <- gateway$getFacility(J("omero.gateway.facility.BrowseFacility")$class)
    jwells <- browse$getWells(ctx, .jlong(getOMEROID(plate)))
    
    wells <- c()
    jwellslist <- as.list(jwells)
    for (jwell in jwellslist) {
      if (jwell$asWell()$sizeOfWellSamples() > 0) {
        well <- Well(server=server, dataobject=jwell)
        wells <- c(wells, well)
      }
    }
    return(wells)
  }
)

#' Get all images of a plate
#'
#' @param omero The plate
#' @param fieldIndex Optional field index (only take the 
#'            specific field into account)
#' @return The images as array [[i, j]] where
#'        i is the well index and j is the field index;
#'        unless fieldIndex was specified, then a list of
#'        images is returned. @seealso \linkS4class{Image}
#' @export
#' @import rJava
#' @examples
#' \dontrun{
#' images <- getImages(plate)
#' }
setMethod(
  f = "getImages",
  signature = "Plate",
  definition = function(omero, fieldIndex)
  {
    wells <- getWells(omero)
    well <- wells[[1]]
    
    n <- length(getImages(well))
    
    if (missing(fieldIndex)) {
      result <- array(dim = c(0, n));
      for(w in wells) {
        fields <- getImages(w)
        result <- rbind(result, unlist(fields))
      }
    }
    else {
      result <- c()
      for(w in wells) {
        img <- getImages(w, fieldIndex)
        result <- c(result, img)
      }
    }
    return(result)
  }
)