new_contents: #!/usr/bin/python
  
  # This script renames the directories in a CATMAID stack's image root
  # to take into account missing layers corresponding to particular
  # z-values.  This can occur when exporting the data from TrakEM2.
  
  import glob, os, re, sys, subprocess
  
  layers_missing_z = [
    4950.0,
    9450.0,
    17500.0,
    17550.0,
    17600.0
  ]
  
  layers_missing = [ int(round(z/50)) for z in layers_missing_z ]
  
  layers_missing.sort()
  
  layers_to_insert = layers_missing[:]
  
  # Find the layers we already have:
  
  directories = filter(lambda x: re.match('\d+$', x), os.listdir('.'))
  directories = [int(x, 10) for x in directories]
  directories.sort()
  
  directory_mapping = zip(directories, directories)
  
  while layers_to_insert:
      missing_layer = layers_to_insert.pop(0)
      for i, t in enumerate(directory_mapping):
          if t[1] >= missing_layer:
              directory_mapping[i] = (t[0], t[1] + 1)
  
  directory_mapping.reverse()
  
  for t in directory_mapping:
      if t[0] != t[1]:
          print "Will rename", t[0], "to", t[1]
          subprocess.check_call(["mv", str(t[0]), str(t[1])])
  
  for l in layers_missing:
      print "Will create directory for missing layer", l
      os.mkdir(str(l))
  
subject: Add a script to rename CATMAID image directories to take account of missing layers