def test_grouped_observations():
# some dummy observations for one reflection
I1, I2, I3 = 101, 100, 99
w1, w2, w3 = 0.9, 1.0, 0.8
g1, g2, g3 = 1.01, 1.0, 0.99
# combine with observations from some other group to make a dataset
hkl = flex.miller_index([(0, 0, 1)] * 3 + [(0, 0, 2)] * 2)
intensity = flex.double([I1, I2, I3, 10, 10])
weight = flex.double([w1, w2, w3, 1.0, 1.0])
phi = flex.double(len(hkl), 0) # dummy
scale = flex.double([g1, g2, g3, 1.0, 1.0])
# group the observations by Miller index
go = GroupedObservations(hkl, intensity, weight, phi, scale)
# ensure there are two groups, the first of size 3, the second of size 2
assert list(go.get_group_size()) == [3, 2]
# the first group has an average intensity given by the HRS formula expanded:
avI = (w1 * g1 * I1 + w2 * g2 * I2 +
w3 * g3 * I3) / (w1 * g1 * g1 + w2 * g2 * g2 + w3 * g3 * g3)
assert approx_equal(avI, go.get_average_intensity()[0])
print "OK"
def test_grouped_observations():
# some dummy observations for one reflection
I1, I2, I3 = 101, 100, 99
w1, w2, w3 = 0.9, 1.0, 0.8
g1, g2, g3 = 1.01, 1.0, 0.99
# combine with observations from some other group to make a dataset
hkl = flex.miller_index([(0,0,1)] * 3 + [(0,0,2)] * 2)
intensity = flex.double([I1, I2, I3, 10, 10])
weight = flex.double([w1, w2, w3, 1.0, 1.0])
phi = flex.double(len(hkl), 0) # dummy
scale = flex.double([g1, g2, g3, 1.0, 1.0])
# group the observations by Miller index
go = GroupedObservations(hkl,
intensity,
weight,
phi,
scale)
# ensure there are two groups, the first of size 3, the second of size 2
assert list(go.get_group_size()) == [3,2]
# the first group has an average intensity given by the HRS formula expanded:
avI = (w1*g1*I1 + w2*g2*I2 + w3*g3*I3) / (w1*g1*g1 + w2*g2*g2 + w3*g3*g3)
assert approx_equal(avI, go.get_average_intensity()[0])
print "OK"
def __init__(self, reflections, experiment, params=None):
if params is None:
params = om_scope.extract()
# initial filter
reflections = reflections.select(
reflections.get_flags(reflections.flags.integrated)
)
# create new column containing the reduced Miller index
xl = experiment.crystal
symm = cctbx.crystal.symmetry(
xl.get_unit_cell(), space_group=xl.get_space_group()
)
hkl_set = cctbx.miller.set(symm, reflections["miller_index"])
asu_set = hkl_set.map_to_asu()
reflections["asu_miller_index"] = asu_set.indices()
# sort table by reduced hkl
reflections.sort("asu_miller_index")
if params.observations.integration_type == "mix":
raise Sorry("integration_type=mix is not supported yet")
else:
ikey = "intensity." + params.observations.integration_type + ".value"
vkey = "intensity." + params.observations.integration_type + ".variance"
# filters
sel = reflections[vkey] > 0
reflections = reflections.select(sel)
if params.observations.i_over_sigma_cutoff > 0:
ios = reflections[ikey] / flex.sqrt(reflections[vkey])
sel = ios >= params.observations.i_over_sigma_cutoff
reflections = reflections.select(sel)
if params.observations.min_multiplicity > 0:
sel = minimum_multiplicity_selection(
reflections["asu_miller_index"], params.observations.min_multiplicity
)
reflections = reflections.select(sel)
# extract columns of interest
gp_idx = reflections["asu_miller_index"]
intensity = reflections[ikey]
weight = 1.0 / reflections[vkey]
phi = reflections["xyzcal.mm"].parts()[2]
scale = flex.double(len(reflections), 1.0)
# set up reflection grouping object
self._go = GroupedObservations(gp_idx, intensity, weight, phi, scale)
return
def __init__(self, reflections, experiment, params=None):
if params is None: params = om_scope.extract()
# initial filter
reflections = reflections.select(reflections.get_flags(
reflections.flags.integrated))
# create new column containing the reduced Miller index
xl = experiment.crystal
symm = cctbx.crystal.symmetry(xl.get_unit_cell(),
space_group=xl.get_space_group())
hkl_set = cctbx.miller.set(symm, reflections['miller_index'])
asu_set = hkl_set.map_to_asu()
reflections['asu_miller_index'] = asu_set.indices()
# sort table by reduced hkl
reflections.sort('asu_miller_index')
if params.observations.integration_type == 'mix':
raise Sorry('integration_type=mix is not supported yet')
else:
ikey = 'intensity.' + params.observations.integration_type + '.value'
vkey = 'intensity.' + params.observations.integration_type + '.variance'
# filters
sel = reflections[vkey] > 0
reflections = reflections.select(sel)
if params.observations.i_over_sigma_cutoff > 0:
ios = reflections[ikey] / flex.sqrt(reflections[vkey])
sel = ios >= params.observations.i_over_sigma_cutoff
reflections = reflections.select(sel)
if params.observations.min_multiplicity > 0:
sel = minimum_multiplicity_selection(reflections['asu_miller_index'],
params.observations.min_multiplicity)
reflections = reflections.select(sel)
# extract columns of interest
gp_idx = reflections['asu_miller_index']
intensity = reflections[ikey]
weight = 1. / reflections[vkey]
phi = reflections['xyzcal.mm'].parts()[2]
scale = flex.double(len(reflections), 1.0)
# set up reflection grouping object
self._go = GroupedObservations(gp_idx, intensity, weight, phi, scale)
return
class ObservationManager(object):
"""A class to maintain information about the reflections during
optimisation of their scale factors."""
def __init__(self, reflections, experiment, params=None):
if params is None: params = om_scope.extract()
# initial filter
reflections = reflections.select(
reflections.get_flags(reflections.flags.integrated))
# create new column containing the reduced Miller index
xl = experiment.crystal
symm = cctbx.crystal.symmetry(xl.get_unit_cell(),
space_group=xl.get_space_group())
hkl_set = cctbx.miller.set(symm, reflections['miller_index'])
asu_set = hkl_set.map_to_asu()
reflections['asu_miller_index'] = asu_set.indices()
# sort table by reduced hkl
reflections.sort('asu_miller_index')
if params.observations.integration_type == 'mix':
raise Sorry('integration_type=mix is not supported yet')
else:
ikey = 'intensity.' + params.observations.integration_type + '.value'
vkey = 'intensity.' + params.observations.integration_type + '.variance'
# filters
sel = reflections[vkey] > 0
reflections = reflections.select(sel)
if params.observations.i_over_sigma_cutoff > 0:
ios = reflections[ikey] / flex.sqrt(reflections[vkey])
sel = ios >= params.observations.i_over_sigma_cutoff
reflections = reflections.select(sel)
if params.observations.min_multiplicity > 0:
sel = minimum_multiplicity_selection(
reflections['asu_miller_index'],
params.observations.min_multiplicity)
reflections = reflections.select(sel)
# extract columns of interest
gp_idx = reflections['asu_miller_index']
intensity = reflections[ikey]
weight = 1. / reflections[vkey]
phi = reflections['xyzcal.mm'].parts()[2]
scale = flex.double(len(reflections), 1.0)
# set up reflection grouping object
self._go = GroupedObservations(gp_idx, intensity, weight, phi, scale)
return
@property
def intensity(self):
return self._go.get_intensity()
@intensity.setter
def intensity(self, intensity):
self._go.set_intensity(intensity)
@property
def weight(self):
return self._go.get_weight()
@weight.setter
def weight(self, weight):
self._go.set_weight(weight)
@property
def scale(self):
return self._go.get_scale()
@scale.setter
def scale(self, scale):
self._go.set_scale(scale)
@property
def group_index(self):
return self._go.get_group_index()
@property
def phi(self):
return self._go.get_phi()
@property
def group_size(self):
return self._go.get_group_size()
def get_average_intensity(self):
'''Calculate the weighted average intensity in reflection groups at the
current scales using the formula of Hamilton, Rollett and Sparks (1965).
Return as a vector for each observation'''
# delegate to the GroupedObservations object
return self._go.get_average_intensity()
class ObservationManager(object):
"""A class to maintain information about the reflections during
optimisation of their scale factors."""
def __init__(self, reflections, experiment, params=None):
if params is None: params = om_scope.extract()
# initial filter
reflections = reflections.select(reflections.get_flags(
reflections.flags.integrated))
# create new column containing the reduced Miller index
xl = experiment.crystal
symm = cctbx.crystal.symmetry(xl.get_unit_cell(),
space_group=xl.get_space_group())
hkl_set = cctbx.miller.set(symm, reflections['miller_index'])
asu_set = hkl_set.map_to_asu()
reflections['asu_miller_index'] = asu_set.indices()
# sort table by reduced hkl
reflections.sort('asu_miller_index')
if params.observations.integration_type == 'mix':
raise Sorry('integration_type=mix is not supported yet')
else:
ikey = 'intensity.' + params.observations.integration_type + '.value'
vkey = 'intensity.' + params.observations.integration_type + '.variance'
# filters
sel = reflections[vkey] > 0
reflections = reflections.select(sel)
if params.observations.i_over_sigma_cutoff > 0:
ios = reflections[ikey] / flex.sqrt(reflections[vkey])
sel = ios >= params.observations.i_over_sigma_cutoff
reflections = reflections.select(sel)
if params.observations.min_multiplicity > 0:
sel = minimum_multiplicity_selection(reflections['asu_miller_index'],
params.observations.min_multiplicity)
reflections = reflections.select(sel)
# extract columns of interest
gp_idx = reflections['asu_miller_index']
intensity = reflections[ikey]
weight = 1. / reflections[vkey]
phi = reflections['xyzcal.mm'].parts()[2]
scale = flex.double(len(reflections), 1.0)
# set up reflection grouping object
self._go = GroupedObservations(gp_idx, intensity, weight, phi, scale)
return
@property
def intensity(self):
return self._go.get_intensity()
@intensity.setter
def intensity(self, intensity):
self._go.set_intensity(intensity)
@property
def weight(self):
return self._go.get_weight()
@weight.setter
def weight(self, weight):
self._go.set_weight(weight)
@property
def scale(self):
return self._go.get_scale()
@scale.setter
def scale(self, scale):
self._go.set_scale(scale)
@property
def group_index(self):
return self._go.get_group_index()
@property
def phi(self):
return self._go.get_phi()
@property
def group_size(self):
return self._go.get_group_size()
def get_average_intensity(self):
'''Calculate the weighted average intensity in reflection groups at the
current scales using the formula of Hamilton, Rollett and Sparks (1965).
Return as a vector for each observation'''
# delegate to the GroupedObservations object
return self._go.get_average_intensity()