def process_new_dicom_orthanc()

in python/de-identifier/research_pacs/de_identifier/main.py [0:0]

• 52 lines of code
• 19 McCabe index (conditional complexity)

def process_new_dicom_orthanc(src_instance_id, msg):
  """
  Process new DICOM instances stored in the source Orthanc server as follows:
  - Download the configuration file how original DICOM files are processed
  - De-identify the DICOM file uing the function `deidentify_dicom_orthanc`
  - Write the de-identified DICOM file to the destination (destination Orthanc server, S3 or local)
  - Write detailed logs to S3 or file, if needed
  
  Args:
    src_instance_id (str): Instance ID in the source Orthanc server
    msg (dict): Content of the SQS message
    
  """
  err = None
  logs = {'Message': msg}
  try:
  
    # Load the config file, either from the custom location passed in the message or from the 
    # default location, and create a DicomDeidentifier object
    try:
      if 'ConfigFile' in msg:
        config_location = msg['ConfigFile']
        logger.info(f'Using a custom config file "{config_location}"')
      else:
        config_location = env.config_file
      logger.debug(f'Loading the config file at "{config_location}"')
      logs['ConfigFile'] = config_location
      config = rpacs_util.load_file(config_location, env.region, 'yaml')
    except Exception as e:
      raise Exception(f'Failed to download the config file - {e}')
    
    # Download the original DICOM file
    try:
      logger.debug('Loading the original DICOM file from Orthanc')
      src_dicom = client.src_orthanc.download_instance_dicom(src_instance_id)
    except Exception as e:
      raise Exception(f'Failed to download the original DICOM file from Orthanc - {e}')
    
    # De-identify the DICOM file
    logger.debug('De-identifying the original DICOM file from Orthanc')
    dst_dicom = deidentify_dicom_orthanc(src_instance_id, src_dicom, config, logs)
    
    # Send the de-identified DICOM file to the destination, if the call is `deidentify_dicom` 
    # returned a DICOM file (the file might be skipped based on its labels)
    try:
      if dst_dicom != None:
        if 'Destination' in msg:
          rpacs_util.write_file(dst_dicom, msg['Destination'], env.region, 'bytes')
          logger.info(f"Uploaded the de-identified DICOM file to \"{msg['Destination']}\"")
        else:
          dst_instance_id = client.dst_orthanc.upload_instance(dst_dicom)
          logger.info(f"Uploaded the de-identified DICOM file to Orthanc - ID={dst_instance_id}")
    except Exception as e:
      raise Exception(f'Failed the write the de-identified DICOM file - {e}')
    
  except Exception as e:
    logger.error(f'Failed to process the DICOM file - {e}')
    logs.update({'Error': str(e)})
    err = e
  
  # Print the result logs to the screen
  for key, value in logs.items():
    if key == 'Message':
      continue
    elif key == 'TransformationsApplied':
      for t_key, t_value in value.items():
        logger.info(f'Result: {key} {t_key}={json.dumps(t_value)}')
    else:  
      logger.info(f'Result: {key}={json.dumps(value)}')
  
  # Upload the detailed logs
  if 'LogFile' in msg:
    try:
      rpacs_util.write_file(logs, msg['LogFile'], env.region, 'json')
      logger.info(f"Uploaded the detailed logs to \"{msg['LogFile']}\"")
    except Exception as e:
      logger.error(f'Failed to upload the log file - {e}')

  # Raise the exception err if it was catched earlier
  if err != None:
    raise err