integrater = XDSIntegrater()
Debug.write('Using XDS Integrater in new resolution mode')
except NotAvailableError, e:
if preselection == 'xdsr':
raise RuntimeError, \
'preselected integrater xdsr not available: ' + \
'xds not installed?'
pass
if not integrater:
raise RuntimeError, 'no integrater implementations found'
# check to see if resolution limits were passed in through the
# command line...
dmin = Flags.get_resolution_high()
dmax = Flags.get_resolution_low()
if dmin:
Debug.write('Adding user-assigned resolution limits:')
if dmax:
Debug.write('dmin: %.3f dmax: %.2f' % (dmin, dmax))
integrater.set_integrater_resolution(dmin, dmax, user = True)
else:
Debug.write('dmin: %.3f' % dmin)
integrater.set_integrater_high_resolution(dmin, user = True)
def setup_from_xinfo_file(self, xinfo_file):
'''Set up this object & all subobjects based on the .xinfo
file contents.'''
settings = PhilIndex.params.xia2.settings
sweep_ids = [sweep.id for sweep in settings.sweep]
sweep_ranges = [sweep.range for sweep in settings.sweep]
if len(sweep_ids) == 0:
sweep_ids = None
sweep_ranges = None
xinfo = XInfo(xinfo_file, sweep_ids=sweep_ids, sweep_ranges=sweep_ranges)
self._name = xinfo.get_project()
crystals = xinfo.get_crystals()
for crystal in crystals.keys():
xc = XCrystal(crystal, self)
if crystals[crystal].has_key('sequence'):
xc.set_aa_sequence(crystals[crystal]['sequence'])
if crystals[crystal].has_key('ha_info'):
if crystals[crystal]['ha_info'] != { }:
xc.set_ha_info(crystals[crystal]['ha_info'])
if crystals[crystal].has_key('scaled_merged_reflection_file'):
xc.set_scaled_merged_reflections(
crystals[crystal]['scaled_merged_reflections'])
if crystals[crystal].has_key('reference_reflection_file'):
xc.set_reference_reflection_file(
crystals[crystal]['reference_reflection_file'])
if crystals[crystal].has_key('freer_file'):
xc.set_freer_file(crystals[crystal]['freer_file'])
# user assigned spacegroup
if crystals[crystal].has_key('user_spacegroup'):
xc.set_user_spacegroup(crystals[crystal]['user_spacegroup'])
elif settings.space_group is not None:
# XXX do we ever actually get here?
xc.set_user_spacegroup(settings.space_group.type().lookup_symbol())
# add a default sample if none present in xinfo file
if len(crystals[crystal]['samples']) == 0:
crystals[crystal]['samples']['X1'] = {}
for sample in crystals[crystal]['samples'].keys():
sample_info = crystals[crystal]['samples'][sample]
xsample = XSample(sample, xc)
xc.add_sample(xsample)
for wavelength in crystals[crystal]['wavelengths'].keys():
# FIXME 29/NOV/06 in here need to be able to cope with
# no wavelength information - this should default to the
# information in the image header (John Cowan pointed
# out that this was untidy - requiring that it agrees
# with the value in the header makes this almost
# useless.)
wave_info = crystals[crystal]['wavelengths'][wavelength]
if not wave_info.has_key('wavelength'):
Debug.write(
'No wavelength value given for wavelength %s' % wavelength)
else:
Debug.write(
'Overriding value for wavelength %s to %8.6f' % \
(wavelength, float(wave_info['wavelength'])))
# handle case where user writes f" in place of f''
if wave_info.has_key('f"') and not \
wave_info.has_key('f\'\''):
wave_info['f\'\''] = wave_info['f"']
xw = XWavelength(wavelength, xc,
wavelength = wave_info.get('wavelength', 0.0),
f_pr = wave_info.get('f\'', 0.0),
f_prpr = wave_info.get('f\'\'', 0.0),
dmin = wave_info.get('dmin', 0.0),
dmax = wave_info.get('dmax', 0.0))
# in here I also need to look and see if we have
# been given any scaled reflection files...
# check to see if we have a user supplied lattice...
if crystals[crystal].has_key('user_spacegroup'):
lattice = Syminfo.get_lattice(
crystals[crystal]['user_spacegroup'])
elif settings.space_group is not None:
# XXX do we ever actually get here?
lattice = Syminfo.get_lattice(
settings.space_group.type().lookup_symbol())
elif Flags.get_lattice():
lattice = Flags.get_lattice()
else:
lattice = None
# and also user supplied cell constants - from either
# the xinfo file (the first port of call) or the
# command-line.
if crystals[crystal].has_key('user_cell'):
cell = crystals[crystal]['user_cell']
elif settings.unit_cell is not None:
# XXX do we ever actually get here?
cell = settings.unit_cell.parameters()
else:
cell = None
dmin = wave_info.get('dmin', 0.0)
dmax = wave_info.get('dmax', 0.0)
if dmin == 0.0 and dmax == 0.0:
dmin = Flags.get_resolution_high()
dmax = Flags.get_resolution_low()
# want to be able to locally override the resolution limits
# for this sweep while leaving the rest for the data set
# intact...
for sweep_name in crystals[crystal]['sweeps'].keys():
sweep_info = crystals[crystal]['sweeps'][sweep_name]
sample_name = sweep_info.get('sample')
if sample_name is None:
if len(crystals[crystal]['samples']) == 1:
sample_name = crystals[crystal]['samples'].keys()[0]
else:
raise RuntimeError('No sample given for sweep %s' %sweep_name)
xsample = xc.get_xsample(sample_name)
assert xsample is not None
dmin_old = dmin
dmax_old = dmax
replace = False
if 'RESOLUTION' in sweep_info:
values = map(float, sweep_info['RESOLUTION'].split())
if len(values) == 1:
dmin = values[0]
elif len(values) == 2:
dmin = min(values)
dmax = max(values)
else:
raise RuntimeError, \
'bad resolution for sweep %s' % sweep_name
replace = True
# FIXME: AJP to implement
if 'ice' in sweep_info:
pass
if 'excluded_regions' in sweep_info:
pass
if sweep_info['wavelength'] == wavelength:
frames_to_process = sweep_info.get('start_end')
if not frames_to_process and Flags.get_start_end():
frames_to_process = Flags.get_start_end()
xsweep = xw.add_sweep(
sweep_name,
sample=xsample,
directory = sweep_info.get('DIRECTORY'),
image = sweep_info.get('IMAGE'),
beam = sweep_info.get('beam'),
reversephi = sweep_info.get('reversephi', False),
distance = sweep_info.get('distance'),
gain = float(sweep_info.get('GAIN', 0.0)),
dmin = dmin, dmax = dmax,
polarization = float(sweep_info.get(
'POLARIZATION', 0.0)),
frames_to_process = frames_to_process,
user_lattice = lattice,
user_cell = cell,
epoch = sweep_info.get('epoch', 0),
ice = sweep_info.get('ice', False),
excluded_regions = sweep_info.get(
'excluded_regions', []),
)
xsample.add_sweep(xsweep)
dmin = dmin_old
dmax = dmax_old
xc.add_wavelength(xw)
self.add_crystal(xc)
return
