<commit_before>def initParser(subparsers, base_parser):
  import argparse  
  parser = subparsers.add_parser('fa', parents=[base_parser], help='Use the old FA-threshold heuristic')
  argument = parser.add_argument_group('Positional argument specific to the \'fa\' algorithm')
  argument.add_argument('output', help='The output response function text file')
  options = parser.add_argument_group('Options specific to the \'fa\' algorithm')
  options.add_argument('-erode', type=int, default=3, help='Number of brain mask erosion steps to apply prior to threshold (not used if mask is provided manually)')
  thresholds = options.add_mutually_exclusive_group()
  thresholds.add_argument('-number', type=int, default=300, help='The number of highest-FA voxels to use')
  thresholds.add_argument('-threshold', type=float, help='Apply a hard FA threshold, rather than selecting the top voxels')
  parser.set_defaults(algorithm='fa')
  parser.set_defaults(single_shell=True)
  
  
  
def checkOutputFiles():
  import lib.app
  lib.app.checkOutputFile(lib.app.args.output)



def getInputFiles():
  pass



def execute():<commit_msg>dwi2response fa: Fix<commit_after>def initParser(subparsers, base_parser):
  import argparse  
  parser = subparsers.add_parser('fa', parents=[base_parser], help='Use the old FA-threshold heuristic')
  argument = parser.add_argument_group('Positional argument specific to the \'fa\' algorithm')
  argument.add_argument('output', help='The output response function text file')
  options = parser.add_argument_group('Options specific to the \'fa\' algorithm')
  options.add_argument('-erode', type=int, default=3, help='Number of brain mask erosion steps to apply prior to threshold (not used if mask is provided manually)')
  thresholds = options.add_mutually_exclusive_group()
  thresholds.add_argument('-number', type=int, default=300, help='The number of highest-FA voxels to use')
  thresholds.add_argument('-threshold', type=float, help='Apply a hard FA threshold, rather than selecting the top voxels')
  parser.set_defaults(algorithm='fa')
  parser.set_defaults(single_shell=False)
  
  
  
def checkOutputFiles():
  import lib.app
  lib.app.checkOutputFile(lib.app.args.output)



def getInputFiles():
  pass



def execute():
{'fraction_non_alphanumeric': 0.1120460584588131, 'fraction_numerical': 0.003985828166519044, 'mean_word_length': 5.7432835820895525, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1053888', 'n_tokens_mistral': 683, 'n_tokens_neox': 648, 'n_words': 187}