Python Flags.Flags類代碼示例

  def _updated_aimless(self):
    '''Generate a correctly configured Aimless...'''

    aimless = None

    if not self._scalr_corrections:
      aimless = self._factory.Aimless()
    else:

      aimless = self._factory.Aimless(
          partiality_correction = self._scalr_correct_partiality,
          absorption_correction = self._scalr_correct_absorption,
          decay_correction = self._scalr_correct_decay)

    if Flags.get_microcrystal():

      # fiddly little data sets - allow more rapid scaling...

      aimless.set_scaling_parameters('rotation', 2.0)
      if self._scalr_correct_decay:
        aimless.set_bfactor(bfactor=True, brotation = 2.0)

    if Flags.get_small_molecule():
      aimless.set_scaling_parameters('rotation', 15.0)
      aimless.set_bfactor(bfactor=False)

    aimless.set_surface_tie(PhilIndex.params.ccp4.aimless.surface_tie)
    aimless.set_surface_link(PhilIndex.params.ccp4.aimless.surface_link)

    return aimless

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 merge(self):
      '''Actually merge the already scaled reflections.'''

      self.check_hklin()
      self.check_hklout()

      if not self._onlymerge:
        raise RuntimeError, 'for scaling use scale()'

      if not self._scalepack:
        self.set_task('Merging scaled reflections from %s => %s' % \
                     (os.path.split(self.get_hklin())[-1],
                      os.path.split(self.get_hklout())[-1]))
      else:
        self.set_task('Merging reflections from %s => scalepack %s' % \
                     (os.path.split(self.get_hklin())[-1],
                      os.path.split(self.get_hklout())[-1]))

      self._xmlout = os.path.join(self.get_working_directory(),
                                  '%d_aimless.xml' % self.get_xpid())

      self.start()
      self.input('xmlout %d_aimless.xml' % self.get_xpid())
      if not Flags.get_small_molecule():
        self.input('bins 20')
      self.input('run 1 all')
      self.input('scales constant')
      self.input('initial unity')
      self.input('sdcorrection both noadjust 1.0 0.0 0.0')

      if self._anomalous:
        self.input('anomalous on')
      else:
        self.input('anomalous off')

      if self._scalepack:
        self.input('output polish unmerged')
      self.input('output unmerged')

      self.close_wait()

      # check for errors

      try:
        self.check_for_errors()
        self.check_ccp4_errors()
        self.check_aimless_errors()

        status = self.get_ccp4_status()

        if 'Error' in status:
          raise RuntimeError, '[AIMLESS] %s' % status

      except RuntimeError, e:
        try:
          os.remove(self.get_hklout())
        except:
          pass

        raise e

    def run(self):
      from xia2.Handlers.Streams import Debug
      Debug.write('Running %s' %self.get_executable())

      self.clear_command_line()
      self.add_command_line(self._sweep_filename)
      self.add_command_line(self._spot_filename)
      nproc = Flags.get_parallel()
      self.set_cpu_threads(nproc)
      self.add_command_line('nproc=%i' % nproc)
      for scan_range in self._scan_ranges:
        self.add_command_line('scan_range=%d,%d' % scan_range)

      if self._phil_file is not None:
        self.add_command_line("%s" %self._phil_file)

      self._optimized_filename = os.path.join(
        self.get_working_directory(), '%d_optimized_datablock.json' %self.get_xpid())
      self.add_command_line("output.datablock=%s" %self._optimized_filename)

      self.start()
      self.close_wait()
      self.check_for_errors()

      records = self.get_all_output()

      assert os.path.exists(self._optimized_filename), self._optimized_filename

      return

  def resolution_merged_isigma(self, limit = None, log = None):
    '''Compute a resolution limit where either Mn(I/sigma) = 1.0 (limit if
    set) or the full extent of the data.'''

    if limit is None:
      limit = Flags.get_misigma()

    bins, ranges = self.get_resolution_bins()

    misigma_s = get_positive_values(
        [self.calculate_merged_isigma(bin) for bin in bins])
    s_s = [1.0 / (r[0] * r[0]) for r in ranges][:len(misigma_s)]

    if min(misigma_s) > limit:
      return 1.0 / math.sqrt(max(s_s))

    misigma_f = log_fit(s_s, misigma_s, 6)

    if log:
      fout = open(log, 'w')
      for j, s in enumerate(s_s):
        d = 1.0 / math.sqrt(s)
        o = misigma_s[j]
        m = misigma_f[j]
        fout.write('%f %f %f %f\n' % (s, d, o, m))
      fout.close()

    try:
      r_misigma = 1.0 / math.sqrt(
          interpolate_value(s_s, misigma_f, limit))
    except:
      r_misigma = 1.0 / math.sqrt(max(s_s))

    return r_misigma

  def update(self):
    '''Check to see if any more frames have appeared - if they
    have update myself and reset.'''

    images = find_matching_images(self._template,
                                  self._directory)

    if len(images) > len(self._images):

      self._images = images

      from xia2.Schema import load_imagesets
      imagesets = load_imagesets(
        self._template, self._directory, id_image=self._id_image,
        use_cache=False, reversephi=Flags.get_reversephi())

      max_images = 0
      best_sweep = None
      for imageset in imagesets:
        scan = imageset.get_scan()
        if scan is None: continue
        if imageset.get_scan().get_num_images() > max_images:
          best_sweep = imageset

      self._imageset = best_sweep

    return

    def reindex(self):
      '''Actually perform the reindexing.'''

      if PhilIndex.params.ccp4.reindex.program == 'reindex':
        return self.reindex_old()

      self.check_hklin()
      self.check_hklout()

      if not self._spacegroup and not self._operator:
        raise RuntimeError, 'reindex requires spacegroup or operator'

      if self._operator:
        self._operator = self._operator.replace('[', '').replace(']', '')

      Debug.write('Reindex... %s %s' % (self._spacegroup, self._operator))

      if self._spacegroup and Flags.get_small_molecule() and False:
        if not self._operator or self._operator.replace(' ', '') == 'h,k,l':
          return self.cctbx_reindex()

      self.start()

      if self._spacegroup:

        if type(self._spacegroup) == type(0):
          spacegroup = Syminfo.spacegroup_number_to_name(
              self._spacegroup)
        elif self._spacegroup[0] in '0123456789':
          spacegroup = Syminfo.spacegroup_number_to_name(
              int(self._spacegroup))
        else:
          spacegroup = self._spacegroup

        self.input('spacegroup \'%s\'' % spacegroup)

      if self._operator:
        # likewise
        self.input('reindex \'%s\'' % self._operator)
      else:
        self.input('reindex \'h,k,l\'')

      self.close_wait()

      # check for errors

      try:
        self.check_for_errors()

      except RuntimeError, e:
        try:
          os.remove(self.get_hklout())
        except:
          pass

        raise e

    def __init__(self):

      # set up the object ancestors...
      DriverInstance.__class__.__init__(self)

      # now set myself up...
      self._parallel = Flags.get_parallel()
      if self._parallel <= 1:
        self.set_executable('xscale')
      else:
        self.set_executable('xscale_par')

      self._version = 'new'

      # overall information
      self._resolution_shells = ''
      self._cell = None
      self._spacegroup_number = None
      self._reindex_matrix = None

      # corrections to apply - N.B. default values come from the
      # factory function default arguments...
      self._correct_decay = correct_decay
      self._correct_absorption = correct_absorption
      self._correct_modulation = correct_modulation

      # input reflections information - including grouping information
      # in the same way as the .xinfo files - through the wavelength
      # names, which will be used for the output files.
      self._input_reflection_files = []
      self._input_reflection_wavelength_names = []
      self._input_resolution_ranges = []

      # these are generated at the run time
      self._transposed_input = { }
      self._transposed_input_keys = []

      # output
      self._output_reflection_files = { }
      self._remove = []

      # decisions about the scaling
      self._crystal = None
      self._zero_dose = False
      self._anomalous = True
      self._merge = False

      # scale factor output
      self._scale_factor = 1.0

      # Rmerge values - for the scale model analysis - N.B. get
      # one for each data set, obviously...
      self._rmerges = { }


      return

  def _index_prepare(self):

    if self._indxr_images == []:
      self._index_select_images()

    if self._mosflm_autoindex_thresh is None and \
           Flags.get_microcrystal():
      self._mosflm_autoindex_thresh = 5

    return

    def __init__(self, params=None):
      super(XDSIntegrateWrapper, self).__init__()

      # phil parameters

      if not params:
        from xia2.Handlers.Phil import master_phil
        params = master_phil.extract().xds.integrate
      self._params = params

      # now set myself up...

      self._parallel = Flags.get_parallel()
      self.set_cpu_threads(self._parallel)

      if self._parallel <= 1:
        self.set_executable('xds')
      else:
        self.set_executable('xds_par')

      # generic bits

      self._data_range = (0, 0)

      self._input_data_files = { }
      self._output_data_files = { }

      self._input_data_files_list = ['X-CORRECTIONS.cbf',
                                     'Y-CORRECTIONS.cbf',
                                     'BLANK.cbf',
                                     'BKGPIX.cbf',
                                     'GAIN.cbf',
                                     'XPARM.XDS']

      self._output_data_files_list = ['FRAME.cbf']

      self._refined_xparm = False

      self._updates = { }

      # note well - INTEGRATE.HKL is not included in this list
      # because it is likely to be very large - this is treated
      # separately...

      self._integrate_hkl = None

      # FIXME these will also be wanted by the full integrater
      # interface I guess?

      self._mean_mosaic = None
      self._min_mosaic = None
      self._max_mosaic = None

      return

    def get_cell(self):
      '''Compute an average cell.'''

      if len(self._cells) < 1:
        raise RuntimeError, 'no input unit cell parameters'

      # check that the input cells are reasonably uniform -
      # be really relaxed and allow 5% variation!

      average_cell = [self._cells[0][j] for j in range(6)]
      number_cells = 1

      for j in range(1, len(self._cells)):
        cell = self._cells[j]
        for k in range(6):
          average = average_cell[k] / number_cells
          if math.fabs((cell[k] - average) / average) > 0.05 \
                 and not Flags.get_relax():
            raise RuntimeError, 'incompatible unit cells'
          average = average_cell[k] / number_cells
          if math.fabs((cell[k] - average) / average) > 0.2:
            raise RuntimeError, 'very incompatible unit cells'

        # it was ok to remember for later on..
        for k in range(6):
          average_cell[k] += cell[k]
        number_cells += 1

      cellparm_inp = open(os.path.join(
          self.get_working_directory(), 'CELLPARM.INP'), 'w')

      for j in range(len(self._cells)):
        cell = self._cells[j]
        n_ref = self._n_refs[j]
        cellparm_inp.write('UNIT_CELL_CONSTANTS=')
        cellparm_inp.write(
            '%.3f %.3f %.3f %.3f %.3f %.3f WEIGHT=%d\n' % \
            (cell[0], cell[1], cell[2], cell[3], cell[4], cell[5],
             n_ref))

      cellparm_inp.close()

      self.start()

      self.close_wait()

      # FIXME need to look for errors in here

      cellparm_lp = open(os.path.join(
          self.get_working_directory(), 'CELLPARM.LP'), 'r')
      data = cellparm_lp.readlines()

      return map(float, data[-1].split()[:6])

  def new_resolution_unmerged_isigma(self, limit = None, log = None):
    '''Compute a resolution limit where either I/sigma = 1.0 (limit if
    set) or the full extent of the data.'''

    if limit is None:
      limit = Flags.get_isigma()

    bins, ranges = self.get_resolution_bins()

    isigma_s = get_positive_values(
        [self.calculate_unmerged_isigma(bin) for bin in bins])

    s_s = [1.0 / (r[0] * r[0]) for r in ranges][:len(isigma_s)]

    if min(isigma_s) > limit:
      return 1.0 / math.sqrt(max(s_s))

    for _l, s in enumerate(isigma_s):
      if s < limit:
        break

    if _l > 10 and _l < (len(isigma_s) - 10):
      start = _l - 10
      end = _l + 10
    elif _l <= 10:
      start = 0
      end = 20
    elif _l >= (len(isigma_s) - 10):
      start = -20
      end = -1

    _s_s = s_s[start:end]
    _isigma_s = isigma_s[start:end]

    _isigma_f = log_fit(_s_s, _isigma_s, 3)

    if log:
      fout = open(log, 'w')
      for j, s in enumerate(_s_s):
        d = 1.0 / math.sqrt(s)
        o = _isigma_s[j]
        m = _isigma_f[j]
        fout.write('%f %f %f %f\n' % (s, d, o, m))
      fout.close()

    try:
      r_isigma = 1.0 / math.sqrt(interpolate_value(_s_s, _isigma_f,
                                                   limit))
    except:
      r_isigma = 1.0 / math.sqrt(max(_s_s))

    return r_isigma

  def _index_select_images(self):
    '''Select correct images based on image headers.'''

    if Flags.get_small_molecule():
      return self._index_select_images_small_molecule()

    if Flags.get_microcrystal():
      return self._index_select_images_microcrystal()

    phi_width = self.get_phi_width()
    images = self.get_matching_images()

    if Flags.get_interactive():
      selected_images = index_select_images_user(phi_width, images,
                                                 Chatter)
    else:
      selected_images = index_select_images_lone(phi_width, images)

    for image in selected_images:
      Debug.write('Selected image %s' % image)
      self.add_indexer_image_wedge(image)

    return

  def __init__(self):
    super(XDSScalerA, self).__init__()

    self._sweep_information = { }

    self._reference = None

    # spacegroup and unit cell information - these will be
    # derived from an average of all of the sweeps which are
    # passed in

    self._xds_spacegroup = None
    self._factory = CCP4Factory()

    self._chef_analysis_groups = { }
    self._chef_analysis_times = { }
    self._chef_analysis_resolutions = { }

    self._user_resolution_limits = { }

    # scaling correction choices - may be set one on the command line...

    if Flags.get_scale_model():
      self._scalr_correct_absorption = Flags.get_scale_model_absorption()
      self._scalr_correct_modulation = Flags.get_scale_model_modulation()
      self._scalr_correct_decay = Flags.get_scale_model_decay()

      self._scalr_corrections = True

    else:

      self._scalr_correct_decay = True
      self._scalr_correct_modulation = True
      self._scalr_correct_absorption = True
      self._scalr_corrections = True

    return

  def migrate(self, directory):
    '''Migrate (or not) data to a local directory.'''

    if not Flags.get_migrate_data():
      # we will not migrate this data
      return directory

    if directory in self._data_migrate.keys():
      # we have already migrated this data
      return self._data_migrate[directory]

    # create a directory to move data to...
    self._data_migrate[directory] = tempfile.mkdtemp()

    # copy all files in source directory to new directory
    # retaining timestamps etc.

    start_time = time.time()

    migrated = 0
    migrated_dir = 0
    for f in os.listdir(directory):
      # copy over only files....
      if os.path.isfile(os.path.join(directory, f)):
        shutil.copy2(os.path.join(directory, f),
                     self._data_migrate[directory])
        migrated += 1
      elif os.path.isdir(os.path.join(directory, f)):
        shutil.copytree(os.path.join(directory, f),
                        os.path.join(self._data_migrate[directory],
                                     f))
        migrated_dir += 1


    Debug.write('Migrated %d files from %s to %s' % \
                (migrated, directory, self._data_migrate[directory]))

    if migrated_dir > 0:
      Debug.write('Migrated %d directories from %s to %s' % \
                  (migrated_dir, directory,
                   self._data_migrate[directory]))

    end_time = time.time()
    duration = end_time - start_time

    Debug.write('Migration took %s' % \
                time.strftime("%Hh %Mm %Ss", time.gmtime(duration)))

    return self._data_migrate[directory]