R/T1SegData.r

In neuroconductor/MriCloudR: R wrapper for MriCloud API

sliceType <- objectProperties::setSingleEnum(
  "slice",
  levels =
    c("Axial", "Sagittal", "SagittalToAxial"))
atlasName <- objectProperties::setSingleEnum(
  "atlas",
  levels = c("Adult_286labels_10atlases_V5L",
             "Pediatric_286labels_11atlases_V5L",
             "Cortical_13Labels_30atlases_V1",
             "ADNI_297labels_9atlases_non_bifurcated_V1",
             "ADNI_297labels_9atlases_non_bifurcated_M2_V1",
             "Connectome_297labels_10atlases_V1",
             "Connectome_297labels_10atlases_M2_V1"))
gender <- objectProperties::setSingleEnum(
  "gender", levels = c("", "Male", "Female"))


#' T1 Segmentation Data Payload Class
#'
#' This class is used to create an object payload for T1 segmentation processing.
#'
#' @import objectProperties
#' @export
#' @export T1SegData
#'
#' @field processingServer processing server to use for segmentation processing
#' @field hdr hdr data filename
#' @field img imd data filename
#' @field sliceType "Axial", "Sagital", or "SagittalToAxial". Defaults to "Sagital".
#' @field atlas "Adult_286labels_10atlases_V5L", "Pediatric_286labels_11atlases_V5L",
#' "Cortical_13Labels_30atlases_V1", "ADNI_297labels_9atlases_non_bifurcated_V1",
#' "ADNI_297labels_9atlases_non_bifurcated_M2_V1",
#' "Connectome_297labels_10atlases_V1", "Connectome_297labels_10atlases_M2_V1".
#' Defaults to "Adult_286labels_10atlases_V5L".
#' @field gender "Male", or "Female" (OPTIONAL)
#' @field age Age of subject (OPTIONAL)
#' @field description Any description of the dataset (OPTIONAL)

T1SegData <- setRefClass(
  "T1SegData",
  properties(
    fields = list(
      processingServer = "character",
      hdr = "character",
      img = "character",
      age = "numeric",
      gender = "genderSingleEnum",
      sliceType = "sliceSingleEnum",
      atlas = "atlasSingleEnum",
      description = "character")
  )
)


T1SegData$methods(
  initialize =
    function(
      st = sliceType("Sagittal"),
      atl = atlasName("Adult_286labels_10atlases_V5L"),
      procserv = "remoteprocessstatus@anatomyworks.com",
      ...
    )
    {

      processingServer <<- procserv
      sliceType <<- st
      atlas <<- atl
      callSuper( ...)

    }
)