mims-unit.R

args = commandArgs(trailingOnly = TRUE)

if(length(args) < 3){
  stop("Input arguments should be greater than 3")
}else{
  input_file = args[1]
  before_file = args[2]
  after_file = args[3]
  output_file_mims = args[4]
  output_file_orientation = args[5]
  if(before_file == 'NULL'){
    before_file = NULL
  }
  if(after_file == 'NULL'){
    after_file = NULL
  }
  print(paste("Input file is:", input_file))
  print(paste("Before file is:", before_file))
  print(paste("After file is:", after_file))
  print(paste("Output file is:", output_file_mims))
  print(paste("Output file is:", output_file_orientation))
  print(paste("Loading file..."))
  dat = MIMSunit::import_mhealth_csv(filepath = input_file)
  if(!is.null(before_file)){
    print("Get the last 2 minutes data for before file")
    before_dat = MIMSunit::import_mhealth_csv(filepath = before_file)
    before_dat = MIMSunit::clip_data(before_dat, start_time = dat[1,1] - 120, stop_time = dat[1,1])
  }else{
    before_dat = NULL
  }
  if(!is.null(after_file)){
    print("Get the first 2 minutes data for after file")
    after_dat = MIMSunit::import_mhealth_csv(filepath = after_file)
    after_dat = MIMSunit::clip_data(after_dat, start_time = dat[nrow(dat),1], stop_time = dat[nrow(dat),1] + 120)
  }else{
    after_dat = NULL
  }

  print(paste("Computing MIMS-unit..."))
  output_dat = MIMSunit::custom_mims_unit(df = dat, epoch = "1 min", dynamic_range = c(-6, 6), before_df = before_dat, after_df = after_dat, output_mims_per_axis = TRUE, output_orientation_estimation = TRUE, epoch_for_orientation_estimation = '5 sec')
  print(paste("Saving MIMS-unit..."))
  write.csv(x = output_dat[['mims']], file = output_file_mims, append = FALSE, quote = FALSE, row.names = FALSE)
  print(paste("Saving Orientation estimation..."))
  write.csv(x = output_dat[['orientation']], file = output_file_orientation, append = FALSE, quote = FALSE, row.names = FALSE)
  print(paste("Completed"))
}