old_contents: #!/bin/env python
  """
  write_ARFI_index_IOS.py
  
  Write individual ARFI index lesion IOS files in each patient directory to do
  additional analysis instead of Zach's spreadsheets that challenges plot
  generation, etc.
  
  This should be a one-time-use script, with a follow-on script to collect all of
  the data for downstream analysis.
  """
  
  __author__ = "Mark Palmeri"
  __email__ = "mlp6@duke.edu"
  __date__ = "2014-11-18"
  
  import csv
  
  invivo_root = '/luscinia/ProstateStudy/invivo'
  
  f = open('ARFI_27_Regions.csv')
  reader = csv.reader(f)
  
  regions27 = ['1p', '2p', '3p', '4p', '5p', '6p', '7p', '8p', '9p', '10p',
               '11p', '12p', '1a', '2a', '3a', '4a', '5a', '6a', '7a', '8a',
               '9a', '10a', '11a', '12a', '13as', '14as', '15as']
  
  # skip the header
  next(reader, None)
  
  for r in reader:
      # leave off P# and Matlab index
      ios = r[2::]
      lesion_indices = [a for a, b in enumerate(ios) if b != '0']
  
      arfi_path = '%s/Patient%s' % (invivo_root, r[0])
  
      try:
          f = open('%s/ARFI_Index_Lesion_IOS.txt' % arfi_path, 'w')
          if len(lesion_indices) == 0:
              f.write('None')
          else:
              for les in lesion_indices:
                  f.write('%s, %s\n' % (regions27[les], ios[les]))
                  print "%s, %s" % (regions27[les], ios[les])
      except IOError:
          print "Cannot create file to save ARFI IOS data"
      else:
          print "Successfully wrote Patient%s ARFI index lesion IOS data." % r[0]
          f.close()
  
new_contents: #!/bin/env python
  """
  write_ARFI_index_IOS.py
  
  Write individual ARFI index lesion IOS files in each patient directory to do
  additional analysis instead of Zach's spreadsheets that challenges plot
  generation, etc.
  
  This should be a one-time-use script, with a follow-on script to collect all of
  the data for downstream analysis.
  """
  
  __author__ = "Mark Palmeri"
  __email__ = "mlp6@duke.edu"
  __date__ = "2014-11-18"
  
  import csv
  
  invivo_root = '/luscinia/ProstateStudy/invivo'
  
  f = open('ARFI_27_Regions.csv')
  reader = csv.reader(f)
  
  regions27 = ['1p', '2p', '3p', '4p', '5p', '6p', '7p', '8p', '9p', '10p',
               '11p', '12p', '1a', '2a', '3a', '4a', '5a', '6a', '7a', '8a',
               '9a', '10a', '11a', '12a', '13as', '14as', '15as']
  
  # skip the header
  next(reader, None)
  
  for r in reader:
      # leave off P# and Matlab index
      ios = r[2::]
      lesion_indices = [a for a, b in enumerate(ios) if b != '0']
  
      arfi_path = '%s/Patient%s' % (invivo_root, r[0])
  
      try:
          f = open('%s/ARFI_Index_Lesion_IOS.txt' % arfi_path, 'a')
          if len(lesion_indices) == 0:
              f.write('None')
          else:
              for les in lesion_indices:
                  f.write('%s, %s\n' % (regions27[les], ios[les]))
                  print "%s, %s" % (regions27[les], ios[les])
      except IOError:
          print "Cannot create file to save ARFI IOS data"
      else:
          print "Successfully wrote Patient%s ARFI index lesion IOS data." % r[0]
          f.close()
  
subject: append txt file for multiple lesions