def calculate_cc_int(self, odd_reflections, even_reflections):
odd_reflections_merged = reflection_table_utils.merge_reflections(
odd_reflections, self.params.merging.minimum_multiplicity)
even_reflections_merged = reflection_table_utils.merge_reflections(
even_reflections, self.params.merging.minimum_multiplicity)
# Create target symmetry
if self.params.merging.set_average_unit_cell:
assert 'average_unit_cell' in (self.params.statistics).__dict__
unit_cell = self.params.statistics.__phil_get__(
'average_unit_cell')
else:
unit_cell = self.params.scaling.unit_cell
target_symm = symmetry(
unit_cell=unit_cell,
space_group_info=self.params.scaling.space_group)
# Build miller arrays
miller_indices_odd = miller.set(target_symm,
odd_reflections_merged['miller_index'],
True)
intensities_odd = miller.array(
miller_indices_odd, odd_reflections_merged['intensity'],
flex.double(odd_reflections_merged.size(), 1.0))
miller_indices_even = miller.set(
target_symm, even_reflections_merged['miller_index'], True)
intensities_even = miller.array(
miller_indices_even, even_reflections_merged['intensity'],
flex.double(even_reflections_merged.size(), 1.0))
# Calculate crosss-correlation
self.Total_CC_OneHalf_Table = self.calculate_cross_correlation(
intensities_odd, intensities_even)
def calculate_cc_iso(self, reflections):
if self.params.statistics.cciso.mtz_file == None:
self.Total_CC_Iso_Table = None
return
reflections_merged = reflection_table_utils.merge_reflections(
reflections, self.params.merging.minimum_multiplicity)
# Create target symmetry
if self.params.merging.set_average_unit_cell:
assert 'average_unit_cell' in (self.params.statistics).__dict__
unit_cell = self.params.statistics.__phil_get__(
'average_unit_cell')
else:
unit_cell = self.params.scaling.unit_cell
target_symm = symmetry(
unit_cell=unit_cell,
space_group_info=self.params.scaling.space_group)
# Build miller array for experimental data
miller_indices = miller.set(target_symm,
reflections_merged['miller_index'], True)
exp_intensities = miller.array(
miller_indices, reflections_merged['intensity'],
flex.double(reflections_merged.size(), 1.0))
self.Total_CC_Iso_Table = self.calculate_cross_correlation(
self.params.scaling.i_model, exp_intensities)
def run(self, experiments, reflections):
# select, merge and output odd reflections
odd_reflections = reflection_table_utils.select_odd_experiment_reflections(reflections)
odd_reflections_merged = reflection_table_utils.merge_reflections(odd_reflections, self.params.merging.minimum_multiplicity)
self.gather_and_output_reflections(odd_reflections_merged, 'odd')
# select, merge and output even reflections
even_reflections = reflection_table_utils.select_even_experiment_reflections(reflections)
even_reflections_merged = reflection_table_utils.merge_reflections(even_reflections, self.params.merging.minimum_multiplicity)
self.gather_and_output_reflections(even_reflections_merged, 'even')
# merge and output all reflections
all_reflections_merged = reflection_table_utils.merge_reflections(reflections, self.params.merging.minimum_multiplicity)
self.gather_and_output_reflections(all_reflections_merged, 'all')
return None, reflections