from __future__ import absolute_import, division, print_function

from libtbx.math_utils import ifloor, iceil
from libtbx import adopt_init_args
import os
from six.moves import zip

MAP_TYPE_F_OBS = 1
MAP_TYPE_DIFF = 2
MAP_TYPE_ANOMALOUS = 4
MAP_TYPE_ISO_DIFF = 8
MAP_TYPE_NEUTRON = 16
MAP_TYPE_F_CALC = 32
MAP_TYPE_FILLED = 64

standard_map_names = {
  '2FOFCWT' : '2mFo-DFc',
  '2FOFCWT_no_fill' : '2mFo-DFc_no_fill',
  'FOFCWT' : 'mFo-DFc',
  'ANOM' : 'anomalous',
}

class MapNotFound(RuntimeError):
  pass

class server(object):
  """
  Manager for files containing map coefficients (either as complex arrays or
  separate F, PHI, and optional FOM).  Once an MTZ file or collection of
  Miller arrays is loaded, individual maps can be quickly retrieved, and it
  includes built-in recognition of standard map labels used in PHENIX (and
  CCP4).
  """
  def __init__(self, file_name=None, miller_arrays=()):
    assert (file_name is not None) or (len(miller_arrays) > 0)
    self.file_name = file_name
    self.miller_arrays = miller_arrays
    if (len(self.miller_arrays) == 0):
      from iotbx import file_reader
      f = file_reader.any_file(file_name, force_type="hkl")
      f.assert_file_type("hkl")
      self.miller_arrays = f.file_server.miller_arrays
    assert (len(self.miller_arrays) > 0)
    self.map_coeffs = []
    self.array_labels = []
    self.data_arrays = []
    self.phase_arrays = []
    self.weight_arrays = []
    self.rfree_arrays = []
    self.fcalc_arrays = []
    self._pdb_cache = {}
    from iotbx.reflection_file_utils import looks_like_r_free_flags_info
    for array in self.miller_arrays :
      labels = array.info().label_string()
      self.array_labels.append(labels)
      if (array.is_xray_amplitude_array() or array.is_xray_intensity_array()):
        if (labels.startswith("FC")):
          self.fcalc_arrays.append(array)
        else :
          self.data_arrays.append(array)
      elif (array.is_complex_array()):
        if (labels.startswith("FC") or labels.startswith("FMODEL") or
            labels.startswith("F-model")):
          self.fcalc_arrays.append(array)
        else :
          self.map_coeffs.append(array)
      elif (array.is_real_array()):
        if (labels.startswith("PH")):
          self.phase_arrays.append(array)
        elif (labels.startswith("FOM")):
          self.weight_arrays.append(array)
      elif (array.is_bool_array()):
        self.rfree_arrays.append(array)
      elif (array.is_integer_array()):
        if (looks_like_r_free_flags_info(array.info())):
          self.rfree_arrays.append(array)

  def is_phenix_refine_maps(self):
    return "2FOFCWT,PH2FOFCWT" in self.array_labels

  def is_cctbx_maps(self):
    return "2mFoDFc,P2mFoDFc" in self.array_labels

  def is_resolve_map(self):
    return ((("FP" in self.array_labels) or ("FP,SIGFP" in self.array_labels))
          and ("PHIM" in self.array_labels) and ("FOMM" in self.array_labels))

  def is_ccp4_style_map(self):
    return (("FWT,PHWT" in self.array_labels) or
            ("FWT,PHIFWT" in self.array_labels))

  def is_ccp4_style_difference_map(self):
    return ("DELFWT,PHDELWT" in self.array_labels)

  def is_solve_map(self):
    return ((("FP" in self.array_labels) or ("FP,SIGFP" in self.array_labels))
          and ("PHIB" in self.array_labels) and ("FOM" in self.array_labels))

  def is_anomalous_map(self):
    for array in self.map_coeffs :
      if array.info().label_string().startswith("ANOM"):
        return True
    return False

  def contains_map_coefficients(self):
    return (len(self.map_coeffs) > 0)

  def contains_amplitude_and_phase(self):
    return (len(self.data_arrays) > 0) and (len(self.phase_arrays) > 0)

  def get_amplitudes_and_phases(self,
                                 f_label=None,
                                 phi_label=None,
                                 fom_label=None):
    f_array, phi_array, fom_array = None, None, None
    allowed_arrays = self.data_arrays + self.map_coeffs
    if (f_label in ["FC", "FMODEL", "F-model"]):
      allowed_arrays += self.fcalc_arrays
    for array in allowed_arrays :
      if (f_array is None):
        labels = array.info().labels
        label_string = array.info().label_string()
        if (f_label is not None):
          if (label_string == f_label) or (labels[0] == f_label):
            f_array = array
        elif (labels[0] == "FP"):
          f_array = array
        elif (labels[0] == "F"):
          f_array = array
    for array in self.phase_arrays :
      if (phi_array is None):
        labels = array.info().label_string()
        if (phi_label is not None):
          if (labels == phi_label):
            phi_array = array
            continue
        elif (labels == "PHIM"):
          phi_array = array
        elif (labels == "PHIB") and (not "PHIM" in self.array_labels):
          phi_array = array
        elif (labels == "PHIC") and not (("PHIM" in self.array_labels) or
                                         ("PHIB" in self.array_labels)):
          phi_array = array
        elif (labels == "PHI"):
          phi_array = array
    for array in self.weight_arrays :
      if (fom_array is None):
        labels = array.info().label_string()
        if (fom_label is not None):
          if (labels == fom_label):
            fom_array = array
        elif (labels == "FOMM"):
          fom_array = array
        elif (labels == "FOM"):
          fom_array = array
    return (f_array, phi_array, fom_array)

  def get_phenix_maps(self, keep_column_labels=False):
    f_maps = []
    diff_maps = []
    default_is_filled = None
    all_maps = []
    unknown_maps = []
    have_names = []
    for array in self.map_coeffs :
      labels = array.info().label_string()
      if (labels.endswith("_no_fill")):
        default_is_filled = True
      elif (labels.endswith("_fill")):
        default_is_filled = False
      if labels.startswith("2FOFCWT") or labels.startswith("2mFoDFc"):
        f_maps.append(array)
      elif labels.startswith("FOFCWT") or labels.startswith("mFoDFc"):
        diff_maps.append(array)
      elif labels.startswith("ANOM"):
        map_type = MAP_TYPE_ANOMALOUS
        map_name = "anomalous"
        if ("neutron" in labels):
          map_type |= MAP_TYPE_NEUTRON
          map_name += "_neutron"
        if (keep_column_labels):
          map_name = labels.split(",")[0]
        elif (map_name in have_names):
          map_name += "_%d" % (have_names.count(map_name) + 1)
        have_names.append(map_name)
        all_maps.append(map_info(map_coeffs=array,
          map_type=map_type,
          map_name=map_name))
      elif (labels.startswith("F-model")) or (labels.startswith("FC")):
        continue
      else :
        unknown_maps.append(array)
    unfilled_maps = []
    filled_maps = []
    for array in diff_maps :
      labels = array.info().label_string()
      map_type = MAP_TYPE_DIFF
      map_name = "mFo-DFc"
      if ("neutron" in labels):
        map_type |= MAP_TYPE_NEUTRON
        map_name += "_neutron"
      if (keep_column_labels):
        map_name = labels.split(",")[0]
      elif (map_name in have_names):
       map_name += "_%d" % (have_names.count(map_name) + 1)
      have_names.append(map_name)
      all_maps.append(map_info(map_coeffs=array,
        map_type=map_type,
        map_name=map_name))
    for array in f_maps :
      labels = array.info().label_string()
      map_name = "2mFo-DFc"
      map_type = MAP_TYPE_F_OBS
      if ("neutron" in labels):
        map_name += "_neutron"
        map_type |= MAP_TYPE_NEUTRON
      if labels.endswith("_no_fill"):
        map_name += "_no_fill"
      elif labels.endswith("_fill") or labels.endswith("_filled"):
        map_type |= MAP_TYPE_FILLED
      elif (default_is_filled):
        map_type |= MAP_TYPE_FILLED
      else :
        map_name += "_no_fill"
      if (keep_column_labels):
        map_name = labels.split(",")[0]
      elif (map_name in have_names):
       map_name += "_%d" % (have_names.count(map_name) + 1)
      have_names.append(map_name)
      all_maps.append(map_info(map_coeffs=array,
        map_type=map_type,
        map_name=map_name))
    return all_maps

  def get_resolve_map(self):
    map_coeffs, null_value = self.get_ccp4_maps()
    if (map_coeffs is None):
      map_coeffs = self._convert_amplitudes_and_phases(f_label="FP",
        phi_label="PHIM", fom_label="FOMM", weighted=True)
    from cctbx.miller import array_info
    info = array_info(labels=["FWT","PHWT"])
    return map_coeffs.set_info(info)

  def get_solve_map(self):
    map_coeffs = self._convert_amplitudes_and_phases(f_label="FP",
      phi_label="PHIB", fom_label="FOM", weighted=True)
    from cctbx.miller import array_info
    info = array_info(labels=["FWT","PHWT"])
    return map_coeffs.set_info(info)

  def get_ccp4_maps(self):
    f_map = diff_map = None
    for array in self.map_coeffs :
      labels = array.info().label_string()
      if (labels.startswith("FWT,")):
        f_map = array
      elif (labels.startswith("DELFWT,")):
        diff_map = array
    return (f_map, diff_map)

  def get_anomalous_map(self):
    for array in self.map_coeffs :
      labels = array.info().label_string()
      if (labels.upper().startswith("ANOM")):
        return array
    return None

  def _convert_amplitudes_and_phases(self, f_label=None, phi_label=None,
      fom_label=None, weighted=True):
    f, phi, fom = self.get_amplitudes_and_phases(f_label, phi_label, fom_label)
    if (f is None) or ((not f.is_complex_array()) and (phi is None)):
      raise MapNotFound(("Couldn't find amplitude or phase arrays in %s.\n"+
        "File contents:\n%s\nExpected labels: F=%s PHI=%s FOM=%s") %
        (self.file_name, "\n".join(self.array_labels), str(f_label),
         str(phi_label), str(fom_label)))
    return combine_f_phi_and_fom(f=f, phi=phi, fom=fom, weighted=weighted)

  def convert_any_map(self, f_label, phi_label, fom_label, **kwds):
    map_coeffs = self._convert_amplitudes_and_phases(f_label, phi_label,
      fom_label)
    return self._write_ccp4_map(map_coeffs, **kwds)

  def convert_complex_map(self, map_label, **kwds):
    map_coeffs = self._convert_amplitudes_and_phases(f_label=map_label)
    return self._write_ccp4_map(map_coeffs, **kwds)

  def convert_resolve_map(self, **kwds):
    map_coeffs = self.get_resolve_map()
    kwds['map_coeffs'] = map_coeffs
    kwds['simple_file_name'] = True
    return self._write_ccp4_map(**kwds)

  def convert_solve_map(self, **kwds):
    map_coeffs = self.get_solve_map()
    kwds['map_coeffs'] = map_coeffs
    kwds['simple_file_name'] = True
    return self._write_ccp4_map(**kwds)

  def convert_ccp4_map(self, **kwds):
    map_coeffs_list = list(self.get_ccp4_maps())
    files = []
    #kwds['simple_file_name'] = True
    for map_coeffs in map_coeffs_list :
      if (map_coeffs is None) : continue
      kwds['map_coeffs'] = map_coeffs
      output_file = self._write_ccp4_map(**kwds)
      files.append(os.path.abspath(output_file))
    return files

  def convert_anomalous_map(self, **kwds):
    map_coeffs = self.get_anomalous_map()
    if (map_coeffs is not None):
      kwds['map_coeffs'] = map_coeffs
      return self._write_ccp4_map(**kwds)
    return None

  def convert_phenix_maps(self, file_base, **kwds):
    all_maps = self.get_phenix_maps()
    files = []
    for map in all_maps :
      file_name = "%s_%s.ccp4" % (file_base, map.map_name)
      kwds['output_file'] = file_name
      self._write_ccp4_map(map.map_coeffs, **kwds)
      files.append(os.path.abspath(file_name))
    return files

  def convert_all_map_coefficients(self, **kwds):
    for map_coeffs in self.map_coeffs :
      labels = map_coeffs.info().label_string()
      map_file = self.convert_complex_map(labels, **kwds)
      yield map_file, labels

  def get_pdb_file(self, file_name):
    pdb_in, mtime = self._pdb_cache.get(file_name, (None, 0))
    if (pdb_in is None) or (os.path.getmtime(file_name) > mtime):
      from iotbx import file_reader
      f = file_reader.any_file(file_name, force_type="pdb",
        raise_sorry_if_errors=True)
      f.assert_file_type("pdb")
      pdb_in = f.file_object
      self._pdb_cache[file_name] = (pdb_in, os.path.getmtime(file_name))
    return pdb_in

  def _write_ccp4_map(self,
                       map_coeffs,
                       pdb_file=None,
                       output_file=None,
                       simple_file_name=False,
                       resolution_factor=0.25,
                       sigma_scaling=True,
                       force=False,
                       use_standard_map_names=False):
    sites_cart = None
    if (pdb_file is not None):
      pdb_in = self.get_pdb_file(pdb_file)
      sites_cart = pdb_in.hierarchy.atoms().extract_xyz()
    if (output_file is None):
      if (simple_file_name):
        output_file = os.path.splitext(self.file_name)[0] + ".ccp4"
      elif (use_standard_map_names):
        lab1 = map_coeffs.info().labels[0]
        map_name = standard_map_names.get(lab1, lab1)
        output_file = os.path.splitext(self.file_name)[0] + "_%s.ccp4" % \
          map_name
      else :
        lab1 = map_coeffs.info().labels[0]
        output_file = os.path.splitext(self.file_name)[0] + "_%s.ccp4" % lab1
    if (not force) and (os.path.exists(output_file) and
        os.path.getmtime(output_file) < os.path.getmtime(self.file_name)):
      return output_file
    fft_map = map_coeffs.fft_map(resolution_factor=resolution_factor)
    if (sigma_scaling):
      fft_map.apply_sigma_scaling()
    else :
      fft_map.apply_volume_scaling()
    map_data = fft_map.real_map()
    write_ccp4_map(
      sites_cart=sites_cart,
      unit_cell=map_coeffs.unit_cell(),
      map_data=map_data,
      n_real=fft_map.n_real(),
      file_name=output_file)
    return output_file

  def auto_open_maps(self, use_filled=True):
    maps = []
    if (self.is_phenix_refine_maps()) or (self.is_cctbx_maps()):
      maps = self.get_phenix_maps()
    elif (self.is_ccp4_style_map()):
      f_map, diff_map = self.get_ccp4_maps()
      if (f_map is not None):
        maps.append(map_info(f_map, MAP_TYPE_F_OBS, "2mFo-DFc"))
      if (diff_map is not None):
        maps.append(map_info(diff_map, MAP_TYPE_DIFF, "mFo-DFc"))
    elif (self.is_solve_map()):
      f_map = self.get_solve_map()
      maps.append(map_info(f_map, MAP_TYPE_F_OBS, "FP,PHIB,FOM"))
    elif (self.is_resolve_map()):
      f_map = self.get_resolve_map()
      maps.append(map_info(f_map, MAP_TYPE_F_OBS, "FP,PHIM,FOMM"))
    elif (self.is_anomalous_map()):
      anom_map = self.get_anomalous_map()
      maps.append(map_info(anom_map, MAP_TYPE_ANOMALOUS, "anomalous"))
    return maps

class map_info(object):
  def __init__(self, map_coeffs, map_type, map_name=None):
    self.map_coeffs = map_coeffs
    self.map_type = map_type
    self.map_name = map_name

  def is_fobs_map(self):
    return (self.map_type & MAP_TYPE_F_OBS)

  def is_difference_map(self):
    return (self.map_type & MAP_TYPE_DIFF)

  def is_anomalous_map(self):
    return (self.map_type & MAP_TYPE_ANOMALOUS)

  def is_neutron_map(self):
    return (self.map_type & MAP_TYPE_NEUTRON)

  def is_filled_map(self):
    return (self.map_type & MAP_TYPE_FILLED)

  def fft_map(self, resolution_factor):
    map_coeffs = self.map_coeffs.unique_under_symmetry()
    map = map_coeffs.fft_map(resolution_factor=resolution_factor)
    map.apply_sigma_scaling()
    return map

  def __getattr__(self, name):
    return getattr(self.map_coeffs, name)

def write_ccp4_map(sites_cart, unit_cell, map_data, n_real, file_name,
    buffer=10):
  import iotbx.mrcfile
  from cctbx import sgtbx
  from scitbx.array_family import flex
  if sites_cart is not None :
    frac_min, frac_max = unit_cell.box_frac_around_sites(
      sites_cart=sites_cart,
      buffer=buffer)
  else :
    frac_min, frac_max = (0.0, 0.0, 0.0), (1.0, 1.0, 1.0)
  gridding_first = tuple([ifloor(f*n) for f,n in zip(frac_min,n_real)])
  gridding_last = tuple([iceil(f*n) for f,n in zip(frac_max,n_real)])
  space_group = sgtbx.space_group_info("P1").group()
  iotbx.mrcfile.write_ccp4_map(
    file_name=file_name,
    unit_cell=unit_cell,
    space_group=space_group,
    gridding_first=gridding_first,
    gridding_last=gridding_last,
    map_data=map_data,
    labels=flex.std_string(["iotbx.map_conversion.write_ccp4_map_box"]))

def write_dsn6_map(sites_cart, unit_cell, map_data, n_real, file_name,
    buffer=10):
  import iotbx.dsn6
  from cctbx import sgtbx
  from scitbx.array_family import flex
  if sites_cart is not None :
    frac_min, frac_max = unit_cell.box_frac_around_sites(
      sites_cart=sites_cart,
      buffer=buffer)
  else :
    frac_min, frac_max = (0.0, 0.0, 0.0), (1.0, 1.0, 1.0)
  gridding_first = tuple([ifloor(f*n) for f,n in zip(frac_min,n_real)])
  gridding_last = tuple([iceil(f*n) for f,n in zip(frac_max,n_real)])
  print("n_real:", n_real)
  print("gridding start:", gridding_first)
  print("gridding end:", gridding_last)
  iotbx.dsn6.write_dsn6_map(
    file_name=file_name,
    unit_cell=unit_cell,
    gridding_first=gridding_first,
    gridding_last=gridding_last,
    map_data=map_data)

########################################################################
# convenience functions
def convert_resolve_map(mtz_file, **kwds):
  server_ = server(file_name=mtz_file)
  return server_.convert_resolve_map(**kwds)

def convert_solve_map(mtz_file, **kwds):
  server_ = server(file_name=mtz_file)
  return server_.convert_solve_map(**kwds)

def convert_ccp4_map(mtz_file, **kwds):
  server_ = server(file_name=mtz_file)
  return server_.convert_ccp4_map(**kwds)

def convert_any_map_coeffs(mtz_file, **kwds):
  server_ = server(file_name=mtz_file)
  return server_.convert_any_map(**kwds)

def convert_phenix_maps(file_base, **kwds):
  server_ = server(file_name=file_base+".mtz")
  return server_.convert_phenix_maps(file_base, **kwds)

def convert_map_coefficients(map_coefficients,
                              mtz_file,
                              **kwds):
  """
  Convert the map coefficients in an MTZ file created by phenix.maps or
  phenix.refine (and related applications).  The parameter block expected in
  map_coefficients is actually in mmtbx/maps/__init__.py, but the I/O belongs
  here.
  """
  outputs = []
  server_ = server(file_name=mtz_file)
  for map in map_coefficients :
    array_label = map.mtz_label_amplitudes + "," + map.mtz_label_phases
    try :
      map_file = server_.convert_any_map(array_label, None, None, **kwds)
    except MapNotFound :
      continue
    outputs.append((map_file, map.map_type))
  return outputs

class write_ccp4_maps_wrapper(object):
  """
  Callable object for running map conversions in parallel (probably overkill,
  but anything we can do to take advantage of multiple CPUs is worth trying).
  """
  def __init__(self, pdb_hierarchy, map_coeffs, output_files,
      resolution_factor):
    adopt_init_args(self, locals())

  def run(self):
    sites_cart = self.pdb_hierarchy.atoms().extract_xyz()
    for map_coeffs, file_name in zip(self.map_coeffs, self.output_files):
      if (map_coeffs is None):
        continue
      fft_map = map_coeffs.fft_map(resolution_factor=self.resolution_factor)
      write_ccp4_map(
        sites_cart=sites_cart,
        unit_cell=map_coeffs.unit_cell(),
        map_data=fft_map.real_map(),
        n_real=fft_map.n_real(),
        file_name=file_name)

def write_map_coeffs(fwt_coeffs, delfwt_coeffs, file_name, anom_coeffs=None,
    fmodel_coeffs=None):
  """
  Convenience function for writing out 2mFo-DFc and mFo-DFc (and, optionally,
  anomalous difference) map coefficients with predefined labels, which will
  be recognized by the auto-open function in Coot.
  """
  import iotbx.mtz
  decorator = iotbx.mtz.label_decorator(phases_prefix="PH")
  mtz_dataset = fwt_coeffs.as_mtz_dataset(
    column_root_label="2FOFCWT",
    label_decorator=decorator)
  mtz_dataset.add_miller_array(
    miller_array=delfwt_coeffs,
    column_root_label="FOFCWT",
    label_decorator=decorator)
  if (anom_coeffs is not None):
    mtz_dataset.add_miller_array(
      miller_array=anom_coeffs,
      column_root_label="ANOM",
      label_decorator=decorator)
  if (fmodel_coeffs is not None):
    mtz_dataset.add_miller_array(
      miller_array=fmodel_coeffs,
      column_root_label="F-model",
      label_decorator=decorator)
  mtz_object = mtz_dataset.mtz_object()
  mtz_object.write(file_name=file_name)
  del mtz_object

# FIXME this is probably too much code duplication...
# used by phenix.composite_omit_map, etc.
def write_map_coefficients_generic(map_coeffs, map_types, file_name):
  import iotbx.mtz
  mtz_dataset = None
  for map_type, map_coeffs in zip(map_types, map_coeffs):
    if map_coeffs.anomalous_flag():
      map_coeffs = map_coeffs.average_bijvoet_mates()
    dec = iotbx.mtz.label_decorator(phases_prefix="PH")
    if (map_type == "2mFo-DFc"):
      label = "2FOFCWT"
    elif (map_type == "mFo-DFc"):
      label = "FOFCWT"
    elif (map_type == "mFo"):
      label = "FWT"
      dec = iotbx.mtz.ccp4_label_decorator()
    elif (map_type in ["anom", "anomalous"]):
      label = "ANOM"
    else :
      label = map_type
    if (mtz_dataset is None):
      mtz_dataset = map_coeffs.as_mtz_dataset(
        column_root_label=label,
        label_decorator=dec)
    else :
      mtz_dataset.add_miller_array(
        miller_array=map_coeffs,
        column_root_label=label,
        label_decorator=dec)
  mtz_dataset.mtz_object().write(file_name)

def get_map_summary(map, resolution_factor=0.25):
  info = []
  real_map = map.real_map_unpadded()
  n_grid_points = real_map.size()
  map.apply_volume_scaling()
  stats_vol = map.statistics()
  info.append(("Grid points (with resolution_factor=%g)" % resolution_factor,
    str(n_grid_points)))
  info.append(("Min value (volume-scaled)", "%.2f" % stats_vol.min()))
  info.append(("Max value (volume-scaled)", "%.2f" % stats_vol.max()))
  info.append(("Mean value (volume-scaled)", "%.2f" % stats_vol.mean()))
  info.append(("Sigma (volume-scaled)", "%.2f" % stats_vol.sigma()))
  map.apply_sigma_scaling()
  stats_sigma = map.statistics()
  info.append(("Min value (sigma-scaled)", "%.2f" % stats_sigma.min()))
  info.append(("Max value (sigma-scaled)", "%.2f" % stats_sigma.max()))
  from cctbx import maptbx
  more_stats = maptbx.more_statistics(map.real_map(False))
  info.append(("Skewness", "%.2f" % more_stats.skewness()))
  return info

class auto_convert_map_coefficients(object):
  def __init__(self, mtz_file, pdb_file=None, resolution_factor=0.25):
    self.f_map = None
    self.diff_map = None
    self.anom_map = None
    self.f_map_type = None
    map_server = server(file_name=mtz_file)
    if (map_server.is_phenix_refine_maps()):
      self.f_map = map_server.convert_complex_map(
        map_label="2FOFCWT,PH2FOFCWT",
        pdb_file=pdb_file,
        use_standard_map_names=True,
        resolution_factor=resolution_factor)
      self.f_map_type = "2mFo-DFc"
      self.diff_map = map_server.convert_complex_map(
        map_label="FOFCWT,PHFOFCWT",
        pdb_file=pdb_file,
        use_standard_map_names=True,
        resolution_factor=resolution_factor)
    elif (map_server.is_ccp4_style_map()):
      self.f_map = map_server.convert_complex_map(
        map_label="FWT,PHWT",
        pdb_file=pdb_file,
        use_standard_map_names=True,
        resolution_factor=resolution_factor)
      self.f_map_type = "fwt" # could be 2mFo-DFc, or resolve Fobs map
      if (map_server.is_ccp4_style_difference_map()):
        self.f_map_type = "2mFo-DFc" # now we know it's definitely 2mFo-DFc
        self.diff_map = map_server.convert_complex_map(
          map_label="DELFWT,PHDELWT",
          pdb_file=pdb_file,
          use_standard_map_names=True,
          resolution_factor=resolution_factor)
    if (map_server.is_anomalous_map()):
      self.anom_map = map_server.convert_anomalous_map(
        pdb_file=pdb_file,
        use_standard_map_names=True,
        resolution_factor=resolution_factor)

def combine_f_phi_and_fom(f, phi, fom=None, weighted=True):
  info = f.info()
  if (f.anomalous_flag()):
    f = f.average_bijvoet_mates()
  f = f.map_to_asu().set_info(info)
  if (f.is_complex_array()):
    return f
  else :
    assert f.is_real_array()
    if (weighted) and (fom is not None):
      f, fom = f.common_sets(other=fom.map_to_asu())
      f = f * fom
    f, phi = f.common_sets(other=phi.map_to_asu())
    # XXX is deg always True?
    return f.phase_transfer(phi,
      deg=True).customized_copy(sigmas=None).set_info(info)