Python Flags.get_reference_reflection_file方法代码示例

# 需要导入模块: from xia2.Handlers.Flags import Flags [as 别名]
# 或者: from xia2.Handlers.Flags.Flags import get_reference_reflection_file [as 别名]

#.........这里部分代码省略.........
        U = fixed.inverse() * sqr(u).transpose()
        B = sqr(b)

        if reference_U is None:
          reference_U = U
          continue

        results = []
        for op in s.all_ops():
          R = B * sqr(op.r().as_double()).transpose() * B.inverse()
          nearly_i3 = (U * R).inverse() * reference_U
          score = sum([abs(_n - _i) for (_n, _i) in zip(nearly_i3, i3)])
          results.append((score, op.r().as_hkl(), op))

        results.sort()
        best = results[0]
        Debug.write('Best reindex: %s %.3f' % (best[1], best[0]))
        intgr.set_integrater_reindex_operator(best[2].r().inverse().as_hkl(),
                                              reason='unifying [U] setting')
        si.set_reflections(intgr.get_integrater_intensities())

        # recalculate to verify
        u, b, s = get_umat_bmat_lattice_symmetry_from_mtz(si.get_reflections())
        U = fixed.inverse() * sqr(u).transpose()
        Debug.write('New reindex: %s' % (U.inverse() * reference_U))

        # FIXME I should probably raise an exception at this stage if this
        # is not about I3...

    if self.get_scaler_reference_reflection_file():
      self._reference = self.get_scaler_reference_reflection_file()
      Debug.write('Using HKLREF %s' % self._reference)

    elif Flags.get_reference_reflection_file():
      self._reference = Flags.get_reference_reflection_file()
      Debug.write('Using HKLREF %s' % self._reference)

    params = PhilIndex.params
    use_brehm_diederichs = params.xia2.settings.use_brehm_diederichs
    if len(self._sweep_handler.get_epochs()) > 1 and use_brehm_diederichs:

      brehm_diederichs_files_in = []
      for epoch in self._sweep_handler.get_epochs():

        si = self._sweep_handler.get_sweep_information(epoch)
        hklin = si.get_reflections()
        brehm_diederichs_files_in.append(hklin)

      # now run cctbx.brehm_diederichs to figure out the indexing hand for
      # each sweep
      from xia2.Wrappers.Cctbx.BrehmDiederichs import BrehmDiederichs
      from xia2.lib.bits import auto_logfiler
      brehm_diederichs = BrehmDiederichs()
      brehm_diederichs.set_working_directory(self.get_working_directory())
      auto_logfiler(brehm_diederichs)
      brehm_diederichs.set_input_filenames(brehm_diederichs_files_in)
      # 1 or 3? 1 seems to work better?
      brehm_diederichs.set_asymmetric(1)
      brehm_diederichs.run()
      reindexing_dict = brehm_diederichs.get_reindexing_dict()

      for epoch in self._sweep_handler.get_epochs():

        si = self._sweep_handler.get_sweep_information(epoch)
        intgr = si.get_integrater()
        hklin = si.get_reflections()

# 需要导入模块: from xia2.Handlers.Flags import Flags [as 别名]
# 或者: from xia2.Handlers.Flags.Flags import get_reference_reflection_file [as 别名]

#.........这里部分代码省略.........

    # if one or more of them was not in the lowest lattice,
    # need to return here to allow reprocessing

    if need_to_return:
      self.set_scaler_done(False)
      self.set_scaler_prepare_done(False)
      return

    # next if there is more than one sweep then generate
    # a merged reference reflection file to check that the
    # setting for all reflection files is the same...

    # if we get to here then all data was processed with the same
    # lattice

    # ----------------------------------------------------------
    # next ensure that all sweeps are set in the correct setting
    # ----------------------------------------------------------

    if self.get_scaler_reference_reflection_file():
      self._reference = self.get_scaler_reference_reflection_file()
      Debug.write('Using HKLREF %s' % self._reference)

      md = self._factory.Mtzdump()
      md.set_hklin(self.get_scaler_reference_reflection_file())
      md.dump()

      self._xds_spacegroup = Syminfo.spacegroup_name_to_number(
          md.get_spacegroup())

      Debug.write('Spacegroup %d' % self._xds_spacegroup)

    elif Flags.get_reference_reflection_file():
      self._reference = Flags.get_reference_reflection_file()

      Debug.write('Using HKLREF %s' % self._reference)

      md = self._factory.Mtzdump()
      md.set_hklin(Flags.get_reference_reflection_file())
      md.dump()

      self._xds_spacegroup = Syminfo.spacegroup_name_to_number(
          md.get_spacegroup())

      Debug.write('Spacegroup %d' % self._xds_spacegroup)

    params = PhilIndex.params
    use_brehm_diederichs = params.xia2.settings.use_brehm_diederichs
    if len(self._sweep_information.keys()) > 1 and use_brehm_diederichs:
      brehm_diederichs_files_in = []
      for epoch in self._sweep_information.keys():

        intgr = self._sweep_information[epoch]['integrater']
        hklin = self._sweep_information[epoch]['corrected_intensities']
        refiner = intgr.get_integrater_refiner()

        # in here need to consider what to do if the user has
        # assigned the pointgroup on the command line ...

        if not self._scalr_input_pointgroup:
          pointgroup, reindex_op, ntr = \
                      self._pointless_indexer_jiffy(hklin, refiner)

          if ntr: