text: #!/usr/bin/env python3
  
  """
  
  Copyright (c) 2017-2020 Vanessa Sochat
  
  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restriction, including without limitation the rights
  to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  copies of the Software, and to permit persons to whom the Software is
  furnished to do so, subject to the following conditions:
  
  The above copyright notice and this permission notice shall be included in all
  copies or substantial portions of the Software.
  
  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  SOFTWARE.
  
  """
  
  from deid.logger import bot
  from deid.dicom import get_files
  from deid.data import get_dataset
  from deid.config import load_deid
  from deid.dicom import has_burned_pixels
  
  import datetime
  import os
  
  
  def main(args, parser):
      """inspect currently serves to inspect the header fields of a set
         of dicom files against a standard, and flag images that don't
         pass the different levels of criteria
      """
  
      # If a deid is given, check against format
      deid = args.deid
      if deid is not None:
          params = load_deid(deid)
          if params["format"] != args.format:
              bot.error(
                  "Format in deid (%s) doesn't match choice here (%s) exiting."
                  % (params["format"], args.format)
              )
      # Get list of dicom files
      base = args.folder
      if base is None:
          bot.info("No input folder specified, will use demo dicom-cookies.")
          base = get_dataset("dicom-cookies")
  
      dicom_files = list(
          get_files(base, pattern=args.pattern)
      )  # todo : consider using generator functionality
      result = has_burned_pixels(dicom_files, deid=deid)
  
      print("\nSUMMARY ================================\n")
      if result["clean"]:
          bot.custom(
              prefix="CLEAN", message="%s files" % len(result["clean"]), color="CYAN"
          )
  
      if result["flagged"]:
          for group, files in result["flagged"].items():
              bot.flag("%s %s files" % (group, len(files)))
  
      if args.save:
          folders = "-".join([os.path.basename(folder) for folder in base])
          outfile = "pixel-flag-results-%s-%s.tsv" % (
              folders,
              datetime.datetime.now().strftime("%y-%m-%d"),
          )
  
          with open(outfile, "w") as filey:
              filey.writelines("dicom_file\tpixels_flagged\tflag_list\treason\n")
  
              for clean in result["clean"]:
                  filey.writelines("%s\tCLEAN\t\t\n" % clean)
  
              for flagged, details in result["flagged"].items():
                  if details["flagged"] is True:
                      for result in details["results"]:
                          group = result["group"]
                          reason = result["reason"]
                          filey.writelines(
                              "%s\tFLAGGED\t%s\t%s\n" % (flagged, group, reason)
                          )
  
              print("Result written to %s" % outfile)
  