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
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