def process_input_array(self, arr):
#array = self.miller_array.deep_copy()
array = arr.deep_copy()
multiplicities = None
if self.merge_equivalents:
if self.settings.show_anomalous_pairs:
merge = array.merge_equivalents()
multiplicities = merge.redundancies()
asu, matches = multiplicities.match_bijvoet_mates()
mult_plus, mult_minus = multiplicities.hemispheres_acentrics()
anom_mult = flex.int(
min(p, m)
for (p, m) in zip(mult_plus.data(), mult_minus.data()))
#flex.min_max_mean_double(anom_mult.as_double()).show()
anomalous_multiplicities = miller.array(
miller.set(asu.crystal_symmetry(),
mult_plus.indices(),
anomalous_flag=False), anom_mult)
anomalous_multiplicities = anomalous_multiplicities.select(
anomalous_multiplicities.data() > 0)
array = anomalous_multiplicities
multiplicities = anomalous_multiplicities
else:
merge = array.merge_equivalents()
array = merge.array()
multiplicities = merge.redundancies()
settings = self.settings
data = array.data()
self.missing_set = oop.null()
#if (array.is_xray_intensity_array()):
# data.set_selected(data < 0, flex.double(data.size(), 0.))
if (array.is_unique_set_under_symmetry()) and (settings.map_to_asu):
array = array.map_to_asu()
if (multiplicities is not None):
multiplicities = multiplicities.map_to_asu()
if (settings.d_min is not None):
array = array.resolution_filter(d_min=settings.d_min)
if (multiplicities is not None):
multiplicities = multiplicities.resolution_filter(
d_min=settings.d_min)
self.filtered_array = array.deep_copy()
if (settings.expand_anomalous):
array = array.generate_bijvoet_mates()
original_symmetry = array.crystal_symmetry()
if (multiplicities is not None):
multiplicities = multiplicities.generate_bijvoet_mates()
if (self.settings.show_missing):
self.missing_set = array.complete_set().lone_set(array)
if self.settings.show_anomalous_pairs:
self.missing_set = self.missing_set.select(
self.missing_set.centric_flags().data(), negate=True)
if (settings.expand_to_p1):
original_symmetry = array.crystal_symmetry()
array = array.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
#array = array.niggli_cell().expand_to_p1()
#self.missing_set = self.missing_set.niggli_cell().expand_to_p1()
self.missing_set = self.missing_set.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
if (multiplicities is not None):
multiplicities = multiplicities.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
data = array.data()
self.r_free_mode = False
self.phases = flex.double(data.size(), float('nan'))
self.radians = flex.double(data.size(), float('nan'))
self.ampl = flex.double(data.size(), float('nan'))
#if not self.foms:
# self.foms = flex.double(data.size(), float('nan'))
self.sigmas = None
#self.sigmas = flex.double(data.size(), float('nan'))
if isinstance(data, flex.bool):
self.r_free_mode = True
data_as_float = flex.double(data.size(), 0.0)
data_as_float.set_selected(data == True,
flex.double(data.size(), 1.0))
data = data_as_float
self.data = data.deep_copy()
else:
if isinstance(data, flex.double):
self.data = data.deep_copy()
elif isinstance(data, flex.complex_double):
self.data = data.deep_copy()
self.ampl = flex.abs(data)
self.phases = flex.arg(data) * 180.0 / math.pi
# purge nan values from array to avoid crash in fmod_positive()
b = flex.bool([bool(math.isnan(e)) for e in self.phases])
# replace the nan values with an arbitrary float value
self.phases = self.phases.set_selected(b, 42.4242)
# indicate the coresponding phase/radian is completely undetermnined
#self.foms = self.foms.set_selected(b, 0.0)
# Now cast negative degrees to equivalent positive degrees
self.phases = flex.fmod_positive(self.phases, 360.0)
self.radians = flex.arg(data)
# replace the nan values with an arbitrary float value
self.radians = self.radians.set_selected(b, 0.424242)
elif hasattr(array.data(), "as_double"):
self.data = array.data().as_double()
else:
raise RuntimeError("Unexpected data type: %r" % data)
if (settings.show_data_over_sigma):
if (array.sigmas() is None):
raise Sorry("sigmas not defined.")
sigmas = array.sigmas()
non_zero_sel = sigmas != 0
array = array.select(non_zero_sel)
array = array.customized_copy(data=array.data() /
array.sigmas())
self.data = array.data()
if (multiplicities is not None):
multiplicities = multiplicities.select(non_zero_sel)
if array.sigmas() is not None:
self.sigmas = array.sigmas()
else:
self.sigmas = None
work_array = array
work_array.set_info(arr.info())
multiplicities = multiplicities
return work_array, multiplicities
def process_input_array(self, arr):
array = arr.deep_copy()
work_array = arr
multiplicities = None
try:
if self.merge_equivalents:
array, multiplicities, merge = MergeData(
array, self.settings.show_anomalous_pairs)
settings = self.settings
data = array.data()
#import code, traceback; code.interact(local=locals(), banner="".join( traceback.format_stack(limit=10) ) )
self.missing_set = oop.null()
#if (array.is_xray_intensity_array()):
# data.set_selected(data < 0, flex.double(data.size(), 0.))
if (array.is_unique_set_under_symmetry()) and (
settings.map_to_asu):
array = array.map_to_asu()
if (multiplicities is not None):
multiplicities = multiplicities.map_to_asu()
if (settings.d_min is not None):
array = array.resolution_filter(d_min=settings.d_min)
if (multiplicities is not None):
multiplicities = multiplicities.resolution_filter(
d_min=settings.d_min)
self.filtered_array = array.deep_copy()
if (settings.expand_anomalous):
if not array.is_unique_set_under_symmetry():
raise Sorry(
"Error! Cannot generate bijvoet mates of unmerged reflections."
)
array = array.generate_bijvoet_mates()
original_symmetry = array.crystal_symmetry()
if (multiplicities is not None):
multiplicities = multiplicities.generate_bijvoet_mates()
if (self.settings.show_missing):
self.missing_set = array.complete_set().lone_set(array)
if self.settings.show_anomalous_pairs:
self.missing_set = self.missing_set.select(
self.missing_set.centric_flags().data(), negate=True)
if (settings.expand_to_p1):
if not array.is_unique_set_under_symmetry():
raise Sorry(
"Error! Cannot expand unmerged reflections to P1.")
original_symmetry = array.crystal_symmetry()
array = array.expand_to_p1().customized_copy(
crystal_symmetry=original_symmetry)
#array = array.niggli_cell().expand_to_p1()
#self.missing_set = self.missing_set.niggli_cell().expand_to_p1()
self.missing_set = self.missing_set.expand_to_p1(
).customized_copy(crystal_symmetry=original_symmetry)
if (multiplicities is not None):
multiplicities = multiplicities.expand_to_p1(
).customized_copy(crystal_symmetry=original_symmetry)
data = array.data()
self.r_free_mode = False
self.phases = flex.double(data.size(), float('nan'))
self.radians = flex.double(data.size(), float('nan'))
self.ampl = flex.double(data.size(), float('nan'))
self.sigmas = None
if isinstance(data, flex.bool):
self.r_free_mode = True
data_as_float = flex.double(data.size(), 0.0)
data_as_float.set_selected(data == True,
flex.double(data.size(), 1.0))
data = data_as_float
self.data = data #.deep_copy()
else:
if isinstance(data, flex.double):
self.data = data #.deep_copy()
elif isinstance(data, flex.complex_double):
self.data = data #.deep_copy()
self.ampl = flex.abs(data)
self.phases = flex.arg(data) * 180.0 / math.pi
# purge nan values from array to avoid crash in fmod_positive()
#b = flex.bool([bool(math.isnan(e)) for e in self.phases])
b = graphics_utils.IsNansArray(self.phases)
# replace the nan values with an arbitrary float value
self.phases = self.phases.set_selected(b, 42.4242)
# Cast negative degrees to equivalent positive degrees
self.phases = flex.fmod_positive(self.phases, 360.0)
self.radians = flex.arg(data)
# replace the nan values with an arbitrary float value
self.radians = self.radians.set_selected(b, 0.424242)
elif hasattr(array.data(), "as_double"):
self.data = data
else:
raise RuntimeError("Unexpected data type: %r" % data)
if (settings.show_data_over_sigma):
if (array.sigmas() is None):
raise Sorry("sigmas not defined.")
sigmas = array.sigmas()
non_zero_sel = sigmas != 0
array = array.select(non_zero_sel)
array = array.customized_copy(data=array.data() /
array.sigmas())
self.data = array.data()
if (multiplicities is not None):
multiplicities = multiplicities.select(non_zero_sel)
if array.sigmas() is not None:
self.sigmas = array.sigmas()
else:
self.sigmas = None
work_array = array
except Exception as e:
print(to_str(e) + "".join(traceback.format_stack(limit=10)))
raise e
return None, None
work_array.set_info(arr.info())
multiplicities = multiplicities
return work_array, multiplicities