예제 #1
0
def _prepare_pointless_hklin(working_directory,
                             hklin,
                             phi_width):
  '''Prepare some data for pointless - this will take only 180 degrees
  of data if there is more than this (through a "rebatch" command) else
  will simply return hklin.'''

  # also remove blank images?

  if not Flags.get_microcrystal() and not Flags.get_small_molecule():

    Debug.write('Excluding blank images')

    hklout = os.path.join(
        working_directory,
        '%s_noblank.mtz' % (os.path.split(hklin)[-1][:-4]))

    FileHandler.record_temporary_file(hklout)

    hklin = remove_blank(hklin, hklout)

  # find the number of batches

  md = Mtzdump()
  md.set_working_directory(working_directory)
  auto_logfiler(md)
  md.set_hklin(hklin)
  md.dump()

  batches = max(md.get_batches()) - min(md.get_batches())

  phi_limit = 180

  if batches * phi_width < phi_limit or Flags.get_small_molecule():
    return hklin

  hklout = os.path.join(
      working_directory,
      '%s_prepointless.mtz' % (os.path.split(hklin)[-1][:-4]))

  rb = Rebatch()
  rb.set_working_directory(working_directory)
  auto_logfiler(rb)
  rb.set_hklin(hklin)
  rb.set_hklout(hklout)

  first = min(md.get_batches())
  last = first + int(phi_limit / phi_width)

  Debug.write('Preparing data for pointless - %d batches (%d degrees)' % \
              ((last - first), phi_limit))

  rb.limit_batches(first, last)

  # we will want to delete this one exit
  FileHandler.record_temporary_file(hklout)

  return hklout
예제 #2
0
def remove_blank(hklin, hklout):
  '''Find and remove blank batches from the file. Returns hklin if no
  blanks.'''

  blanks, goods = find_blank(hklin)

  if not blanks:
    return hklin

  # if mostly blank return hklin too...
  if len(blanks) > len(goods):
    Debug.write('%d blank vs. %d good: ignore' % (len(blanks), len(goods)))
    return hklin

  rb = Rebatch()
  rb.set_hklin(hklin)
  rb.set_hklout(hklout)

  for b in blanks:
    rb.exclude_batch(b)

  rb.exclude_batches()

  return hklout