R/nitrc_scandata.R

In nitrcbot: Download Image Files from the 'NeuroImaging Tools and Resources Collaboratory'

#' @title Get/list scan data
#' @description Retrieves NITRC scan data info
#' @param project is the project for which we request demographics data, if project is NULL, we return all available subjects
#' @param nitrc_projects data.frame with all available NITRC projects
#' @param jsessionID value for the JSESSIONID cookie
#'
#' @return Dataframe of scan data
#' @importFrom httr content GET
#' @importFrom dplyr bind_rows
#' @importFrom jsonlite fromJSON
#' @examples
#' ## Get scan data for the ixi project
#' \dontrun{nitrc_scandata('ixi')}
#'
#' ## Get scan data for all accessible NITRC projects
#' \dontrun{nitrc_scandata()}
#' @export
nitrc_scandata = function(project = NULL,
                          nitrc_projects = NULL,
                          jsessionID = NULL) {

  if(is.null(nitrc_projects)) {
    nitrc_projects <- list_image_sets(project)
  }

  if(!is.null(project)) {
    scan_content = NULL
    if(project %in% nitrc_projects$ID){
      url = paste0("https://www.nitrc.org/ir/data/experiments?project=",project,"&columns=xnat:mrSessionData/ID,xnat:imageScanData/type,xnat:imageScanData/ID,subject_ID,xnat:mrSessionData/age ")
      scan_content = fromJSON(query_nitrc(url,jsessionID))
    }
    else {
      message(paste0('Could not find project ',project,' in NITRC'))
      return(NULL)
    }
  }
  else {
    message('Aquiring scan data for all projects')
    url = paste0("https://www.nitrc.org/ir/data/experiments?columns=xnat:mrSessionData/ID,xnat:imageScanData/type,xnat:imageScanData/ID,subject_ID,xnat:mrSessionData/age ")
    scan_content = fromJSON(query_nitrc(url,jsessionID))
  }
  if(scan_content$ResultSet$totalRecords > 0) {
    scandata = scan_content$ResultSet$Result
    colnames(scandata) <- c("ID","type","session_ID","age","scan_ID","URI")
    scandata = scandata[c("ID","type","session_ID","age","scan_ID")]
    return(scandata)
  }
  else {
    message("No scan data results found")
    return(NULL)
  }
}