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 not sweep_ids:
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:
xc = XCrystal(crystal, self)
if "sequence" in crystals[crystal]:
xc.set_aa_sequence(crystals[crystal]["sequence"])
if "ha_info" in crystals[crystal]:
if crystals[crystal]["ha_info"] != {}:
xc.set_ha_info(crystals[crystal]["ha_info"])
if "scaled_merged_reflection_file" in crystals[crystal]:
xc.set_scaled_merged_reflections(
crystals[crystal]["scaled_merged_reflections"])
if "reference_reflection_file" in crystals[crystal]:
xc.set_reference_reflection_file(
crystals[crystal]["reference_reflection_file"])
if "freer_file" in crystals[crystal]:
xc.set_freer_file(crystals[crystal]["freer_file"])
# user assigned spacegroup
if "user_spacegroup" in crystals[crystal]:
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 not crystals[crystal]["samples"]:
crystals[crystal]["samples"]["X1"] = {}
for sample in crystals[crystal]["samples"]:
xsample = XSample(sample, xc)
xc.add_sample(xsample)
if not crystals[crystal]["wavelengths"]:
raise RuntimeError("No wavelengths specified in xinfo file")
for wavelength, wave_info in crystals[crystal][
"wavelengths"].items():
# 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.)
if "wavelength" not in wave_info:
logger.debug("No wavelength value given for wavelength %s",
wavelength)
else:
logger.debug(
"Overriding value for wavelength %s to %8.6f",
wavelength,
float(wave_info["wavelength"]),
)
# handle case where user writes f" in place of f''
if 'f"' in wave_info and "f''" not in wave_info:
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 "user_spacegroup" in crystals[crystal]:
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())
else:
lattice = None
# and also user supplied cell constants - from either
# the xinfo file (the first port of call) or the
# command-line.
if "user_cell" in crystals[crystal]:
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 = PhilIndex.params.xia2.settings.resolution.d_min
dmax = PhilIndex.params.xia2.settings.resolution.d_max
# 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, sweep_info in crystals[crystal][
"sweeps"].items():
sample_name = sweep_info.get("sample")
if sample_name is None:
if len(crystals[crystal]["samples"]) == 1:
sample_name = list(crystals[crystal]["samples"])[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
if "RESOLUTION" in sweep_info:
values = [
float(x) for x in 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)
if sweep_info["wavelength"] == wavelength:
frames_to_process = sweep_info.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)
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 not sweep_ids:
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 'sequence' in crystals[crystal]:
xc.set_aa_sequence(crystals[crystal]['sequence'])
if 'ha_info' in crystals[crystal]:
if crystals[crystal]['ha_info'] != { }:
xc.set_ha_info(crystals[crystal]['ha_info'])
if 'scaled_merged_reflection_file' in crystals[crystal]:
xc.set_scaled_merged_reflections(
crystals[crystal]['scaled_merged_reflections'])
if 'reference_reflection_file' in crystals[crystal]:
xc.set_reference_reflection_file(
crystals[crystal]['reference_reflection_file'])
if 'freer_file' in crystals[crystal]:
xc.set_freer_file(crystals[crystal]['freer_file'])
# user assigned spacegroup
if 'user_spacegroup' in crystals[crystal]:
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 not crystals[crystal]['samples']:
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)
if not crystals[crystal]['wavelengths']:
raise RuntimeError('No wavelengths specified in xinfo file')
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 'wavelength' not in wave_info:
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 'f"' in wave_info and not \
'f\'\'' in wave_info:
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 'user_spacegroup' in crystals[crystal]:
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())
else:
lattice = None
# and also user supplied cell constants - from either
# the xinfo file (the first port of call) or the
# command-line.
if 'user_cell' in crystals[crystal]:
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 = PhilIndex.params.xia2.settings.resolution.d_min
dmax = PhilIndex.params.xia2.settings.resolution.d_max
# 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
# FIXME ticket number here please
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')
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
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 not sweep_ids:
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 'sequence' in crystals[crystal]:
xc.set_aa_sequence(crystals[crystal]['sequence'])
if 'ha_info' in crystals[crystal]:
if crystals[crystal]['ha_info'] != {}:
xc.set_ha_info(crystals[crystal]['ha_info'])
if 'scaled_merged_reflection_file' in crystals[crystal]:
xc.set_scaled_merged_reflections(
crystals[crystal]['scaled_merged_reflections'])
if 'reference_reflection_file' in crystals[crystal]:
xc.set_reference_reflection_file(
crystals[crystal]['reference_reflection_file'])
if 'freer_file' in crystals[crystal]:
xc.set_freer_file(crystals[crystal]['freer_file'])
# user assigned spacegroup
if 'user_spacegroup' in crystals[crystal]:
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 not crystals[crystal]['samples']:
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)
if not crystals[crystal]['wavelengths']:
raise RuntimeError('No wavelengths specified in xinfo file')
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 'wavelength' not in wave_info:
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 'f"' in wave_info and not \
'f\'\'' in wave_info:
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 'user_spacegroup' in crystals[crystal]:
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())
else:
lattice = None
# and also user supplied cell constants - from either
# the xinfo file (the first port of call) or the
# command-line.
if 'user_cell' in crystals[crystal]:
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 = PhilIndex.params.xia2.settings.resolution.d_min
dmax = PhilIndex.params.xia2.settings.resolution.d_max
# 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
if sweep_info['wavelength'] == wavelength:
frames_to_process = sweep_info.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)