old_contents: import os
  import re
  from qidicom import meta
  from .sarcoma_config import sarcoma_location
  
  from qiutil.logging import logger
  
  
  def fix_dicom_headers(collection, subject, *dicom_files, **opts):
      """
      Fix the given input OHSU QIN AIRC DICOM files as follows:
  
      - Replace the ``Patient ID`` value with the subject number, e.g.
          ``Sarcoma001``
  
      - Add the ``Body Part Examined`` tag
  
      - Standardize the file name
  
      The ``Body Part Examined`` tag is set as follows:
  
      - If the collection is ``Sarcoma``, then the body part is the
          :meth:`qipipe.staging.sarcoma_config.sarcoma_location`.
      
      - Otherwise, the body part is the capitalized collection name, e.g.
          ``BREAST``.
          
      The output file name is standardized as follows:
  
      - The file name is lower-case
  
      - The file extension is ``.dcm``
      
      - The scan type is appended to the fie name, e.g. ``_t1``
  
      - Each non-word character is replaced by an underscore
      
      :param collection: the collection name
      :param subject: the input subject name
      :param opts: the following keyword arguments:
      :keyword dest: the location in which to write the modified files
          (default is the current directory)
      :return: the files which were created
      :raise StagingError: if the collection is not supported
      """
  
      # Make the tag name => value dictionary.
      if collection == 'Sarcoma':
          site = sarcoma_location(subject)
      else:
          site = collection.upper()
      tnv = dict(PatientID=subject, BodyPartExamined=site)
  
      # Set the tags in each image file.
      if 'dest' in opts:
          dest = opts['dest']
      else:
          dest = os.getcwd()
      edited = meta.edit(dest, *dicom_files, **tnv)
  
      # Rename the edited files as necessary.
      out_files = []
      for f in edited:
          std_name = _standardize_dicom_file_name(f)
          if f != std_name:
              os.rename(f, std_name)
              out_files.append(std_name)
          logger(__name__).debug(
              "The DICOM headers in %s were fixed and saved as %s." % (f, std_name))
  
      return out_files
  
  
  def _standardize_dicom_file_name(path):
      """
      Standardizes the given input file name.
      """
      fdir, fname = os.path.split(path)
      # Replace non-word characters.
      fname = re.sub('\W', '_', fname.lower())
      # Add a .dcm extension, if necessary.
      _, ext = os.path.splitext(fname)
      if not ext:
          fname = fname + '.dcm'
      return os.path.join(fdir, fname)
  
new_contents: import os
  import re
  from qidicom import meta
  from .sarcoma_config import sarcoma_location
  
  from qiutil.logging import logger
  
  
  def fix_dicom_headers(collection, subject, *dicom_files, **opts):
      """
      Fix the given input OHSU QIN AIRC DICOM files as follows:
  
      - Replace the ``Patient ID`` value with the subject number, e.g.
          ``Sarcoma001``
  
      - Add the ``Body Part Examined`` tag
  
      - Standardize the file name
  
      The ``Body Part Examined`` tag is set as follows:
  
      - If the collection is ``Sarcoma``, then the body part is the
          :meth:`qipipe.staging.sarcoma_config.sarcoma_location`.
      
      - Otherwise, the body part is the capitalized collection name, e.g.
          ``BREAST``.
          
      The output file name is standardized as follows:
  
      - The file name is lower-case
  
      - The file extension is ``.dcm``
  
      - Each non-word character is replaced by an underscore
      
      :param collection: the collection name
      :param subject: the input subject name
      :param opts: the following keyword arguments:
      :keyword dest: the location in which to write the modified files
          (default is the current directory)
      :return: the files which were created
      :raise StagingError: if the collection is not supported
      """
  
      # Make the tag name => value dictionary.
      if collection == 'Sarcoma':
          site = sarcoma_location(subject)
      else:
          site = collection.upper()
      tnv = dict(PatientID=subject, BodyPartExamined=site)
  
      # Set the tags in each image file.
      if 'dest' in opts:
          dest = opts['dest']
      else:
          dest = os.getcwd()
      edited = meta.edit(dest, *dicom_files, **tnv)
  
      # Rename the edited files as necessary.
      out_files = []
      for f in edited:
          std_name = _standardize_dicom_file_name(f)
          if f != std_name:
              os.rename(f, std_name)
              out_files.append(std_name)
          logger(__name__).debug(
              "The DICOM headers in %s were fixed and saved as %s." % (f, std_name))
  
      return out_files
  
  
  def _standardize_dicom_file_name(path):
      """
      Standardizes the given input file name.
      """
      fdir, fname = os.path.split(path)
      # Replace non-word characters.
      fname = re.sub('\W', '_', fname.lower())
      # Add a .dcm extension, if necessary.
      _, ext = os.path.splitext(fname)
      if not ext:
          fname = fname + '.dcm'
      return os.path.join(fdir, fname)
  
subject: Remove scan_type.