def filter_bad_reflections(cls,
reflections,
partiality_cutoff=0.4,
min_isigi=-5.0):
"""Initial filter to select integrated reflections."""
logger.info(
"Applying filter of min_isigi > %s, partiality > %s",
min_isigi,
partiality_cutoff,
)
logger.disabled = True
intensity_choice = []
if "intensity.sum.value" in reflections:
intensity_choice.append("sum")
if "intensity.prf.value" in reflections:
intensity_choice.append("profile")
if intensity_choice:
good = filter_reflection_table_selection(
reflections,
intensity_choice=intensity_choice,
combine_partials=False,
partiality_threshold=partiality_cutoff,
min_isigi=min_isigi,
)
logger.disabled = False
mask = ~good
reflections.set_flags(mask, reflections.flags.excluded_for_scaling)
return reflections
def filter_bad_reflections(reflections,
partiality_cutoff=0.4,
min_isigi=-5.0,
intensity_choice="combine"):
"""Initial filter to select integrated reflections."""
logger.info(
"Applying filter of min_isigi > %s, partiality > %s",
min_isigi,
partiality_cutoff,
)
logger.disabled = True
if intensity_choice == "combine":
if "intensity.sum.value" not in reflections:
if "intensity.prf.value" not in reflections:
intensity_choice = None
else:
intensity_choice = ["profile"]
elif "intensity.prf.value" not in reflections:
intensity_choice = ["sum"]
else:
intensity_choice = ["sum | profile"]
else:
intensity_choice = [intensity_choice]
if intensity_choice:
good = filter_reflection_table_selection(
reflections,
intensity_choice=intensity_choice,
combine_partials=False,
partiality_threshold=partiality_cutoff,
min_isigi=min_isigi,
)
mask = ~good
reflections.set_flags(mask, reflections.flags.excluded_for_scaling)
logger.disabled = False
return reflections
