old_contents: #!/usr/bin/env python
  #########################################################################################
  #
  # Concatenate bval files in time.
  #
  # ---------------------------------------------------------------------------------------
  # Copyright (c) 2015 Polytechnique Montreal <www.neuro.polymtl.ca>
  # Author: Simon LEVY
  #
  # About the license: see the file LICENSE.TXT
  #########################################################################################
  
  import sys
  from msct_parser import Parser
  from sct_utils import extract_fname
  
  # PARSER
  # ==========================================================================================
  def get_parser():
  
      # Initialize the parser
      parser = Parser(__file__)
      parser.usage.set_description('Concatenate bval files in time.')
      parser.add_option(name="-i",
                        type_value=[[','], 'file'],
                        description="List of the bval files to concatenate.",
                        mandatory=True,
                        example="dmri_b700.bval,dmri_b2000.bval")
      parser.add_option(name="-o",
                        type_value="file_output",
                        description='Output file with bvals merged.',
                        mandatory=False,
                        example='dmri_b700_b2000_concat.bval')
      return parser
  
  
  # MAIN
  # ==========================================================================================
  def main():
  
      # Get parser info
      parser = get_parser()
      arguments = parser.parse(sys.argv[1:])
      fname_bval_list = arguments["-i"]
      fname_out = arguments["-o"]
  
      # Build fname_out
      if fname_out == '':
          path_in, file_in, ext_in = extract_fname(fname_bval_list[0])
          fname_out = path_in+'bvals_merged'+ext_in
  
      # Open bval files and concatenate
      bvals_concat = ''
      for i_file in range(0,len(fname_bval_list)):
          f = open(fname_bval_list[i_file],'r')
          for line in f:
              bvals_concat += line
          f.close()
  
      # Write new bval
      new_f = open(fname_out,'w')
      new_f.write(bvals_concat)
      new_f.close()
  
  
  # START PROGRAM
  # ==========================================================================================
  if __name__ == "__main__":
      # call main function
      main()
  
  
  
  
new_contents: #!/usr/bin/env python
  #########################################################################################
  #
  # Concatenate bval files in time.
  #
  # ---------------------------------------------------------------------------------------
  # Copyright (c) 2015 Polytechnique Montreal <www.neuro.polymtl.ca>
  # Author: Simon LEVY
  #
  # About the license: see the file LICENSE.TXT
  #########################################################################################
  
  import sys
  from msct_parser import Parser
  from sct_utils import extract_fname
  
  # PARSER
  # ==========================================================================================
  def get_parser():
  
      # Initialize the parser
      parser = Parser(__file__)
      parser.usage.set_description('Concatenate bval files in time.')
      parser.add_option(name="-i",
                        type_value=[[','], 'file'],
                        description="List of the bval files to concatenate.",
                        mandatory=True,
                        example="dmri_b700.bval,dmri_b2000.bval")
      parser.add_option(name="-o",
                        type_value="file_output",
                        description='Output file with bvals merged.',
                        mandatory=False,
                        example='dmri_b700_b2000_concat.bval')
      return parser
  
  
  # MAIN
  # ==========================================================================================
  def main():
  
      # Get parser info
      parser = get_parser()
      arguments = parser.parse(sys.argv[1:])
      fname_bval_list = arguments["-i"]
      # Build fname_out
      if "-o" in arguments:
          fname_out = arguments["-o"]
      else:
          path_in, file_in, ext_in = extract_fname(fname_bval_list[0])
          fname_out = path_in+'bvals_concat'+ext_in
  
      # Open bval files and concatenate
      bvals_concat = ''
      for i_file in range(0,len(fname_bval_list)):
          f = open(fname_bval_list[i_file],'r')
          for line in f:
              bvals_concat += line
          f.close()
  
      # Write new bval
      new_f = open(fname_out,'w')
      new_f.write(bvals_concat)
      new_f.close()
  
  
  # START PROGRAM
  # ==========================================================================================
  if __name__ == "__main__":
      # call main function
      main()
  
  
  
  
subject: allow no selection of output file name