def test_check_and_fix(tc):
n_det = tc.det_param.num_free()
n_beam = tc.s0_param.num_free()
n_xlo = tc.xlo_param.num_free()
n_xluc = tc.xluc_param.num_free()
# Similar to test_check_and_fail, setting 137 reflections as the minimum
# should leave all parameters free
options = ar_phil_scope.extract()
options.min_nref_per_parameter = 137
ar = AutoReduce(
options,
[tc.det_param],
[tc.s0_param],
[tc.xlo_param],
[tc.xluc_param],
gon_params=[],
reflection_manager=tc.refman,
)
ar.check_and_fix()
assert ar.det_params[0].num_free() == n_det == 6
assert ar.beam_params[0].num_free() == n_beam == 3
assert ar.xl_ori_params[0].num_free() == n_xlo == 3
assert ar.xl_uc_params[0].num_free() == n_xluc == 6
# Setting 138 reflections as the minimum should fix all the detector
# parameters and remove that parameterisation. The crystal unit cell also
# has 6 parameters, but each parameter is considered separately, so the
# critical minimum number of reflections is 138*1 not 138*6 in that case
options = ar_phil_scope.extract()
options.min_nref_per_parameter = 138
ar = AutoReduce(
options,
[tc.det_param],
[tc.s0_param],
[tc.xlo_param],
[tc.xluc_param],
gon_params=[],
reflection_manager=tc.refman,
)
ar.check_and_fix()
assert not ar.det_params
assert ar.xl_uc_params[0].num_free() == n_xluc
assert ar.beam_params[0].num_free() == n_beam
assert ar.xl_ori_params[0].num_free() == n_xlo
def test_check_and_fix(tc):
n_det = tc.det_param.num_free()
n_beam = tc.s0_param.num_free()
n_xlo = tc.xlo_param.num_free()
n_xluc = tc.xluc_param.num_free()
# Similar to test_check_and_fail, setting 792 reflections as the minimum
# should leave all parameters free
options = ar_phil_scope.extract()
options.min_nref_per_parameter = 792
ar = AutoReduce(options,
pred_param=tc.pred_param,
reflection_manager=tc.refman)
ar.check_and_fix()
det_params = tc.pred_param.get_detector_parameterisations()
beam_params = tc.pred_param.get_beam_parameterisations()
xl_ori_params = tc.pred_param.get_crystal_orientation_parameterisations()
xl_uc_params = tc.pred_param.get_crystal_unit_cell_parameterisations()
assert det_params[0].num_free() == n_det == 6
assert beam_params[0].num_free() == n_beam == 3
assert xl_ori_params[0].num_free() == n_xlo == 3
assert xl_uc_params[0].num_free() == n_xluc == 6
# Setting 793 reflections as the minimum should fix crystal unit cell
# parameters g_param_0, g_param_3 and g_param_4
options = ar_phil_scope.extract()
options.min_nref_per_parameter = 793
ar = AutoReduce(options,
pred_param=tc.pred_param,
reflection_manager=tc.refman)
ar.check_and_fix()
det_params = tc.pred_param.get_detector_parameterisations()
beam_params = tc.pred_param.get_beam_parameterisations()
xl_ori_params = tc.pred_param.get_crystal_orientation_parameterisations()
xl_uc_params = tc.pred_param.get_crystal_unit_cell_parameterisations()
assert det_params[0].num_free() == n_det
assert xl_uc_params[0].num_free() == 3
assert xl_uc_params[0].get_param_names() == [
"g_param_1", "g_param_2", "g_param_5"
]
assert beam_params[0].num_free() == n_beam
assert xl_ori_params[0].num_free() == n_xlo
def test_check_and_fail(tc):
# There are 823 reflections
assert len(tc.refman.get_matches()) == 823
# The parameters affecting the smallest number of reflections are
# g_param_0, g_param_3 and g_param_4, all of which have gradients for
# 792 reflections. Setting 792 reflections as the minimum should pass.
options = ar_phil_scope.extract()
options.min_nref_per_parameter = 792
ar = AutoReduce(options, pred_param=tc.pred_param, reflection_manager=tc.refman)
ar.check_and_fail()
# Setting 793 reflections as the minimum should fail
options.min_nref_per_parameter = 793
ar = AutoReduce(options, pred_param=tc.pred_param, reflection_manager=tc.refman)
with pytest.raises(DialsRefineConfigError):
ar.check_and_fail()
def test_check_and_fail(tc):
# There are 823 reflections and the detector parameterisation has 6 free
# parameters
assert len(tc.refman.get_matches()) == 823
assert tc.det_param.num_free() == 6
# Setting 137 reflections as the minimum should pass (137*6<823)
options = ar_phil_scope.extract()
options.min_nref_per_parameter = 137
ar = AutoReduce(
options,
[tc.det_param],
[tc.s0_param],
[tc.xlo_param],
[tc.xluc_param],
gon_params=[],
reflection_manager=tc.refman,
)
ar.check_and_fail()
# Setting 138 reflections as the minimum should fail (138*6>823)
options.min_nref_per_parameter = 138
ar = AutoReduce(
options,
[tc.det_param],
[tc.s0_param],
[tc.xlo_param],
[tc.xluc_param],
gon_params=[],
reflection_manager=tc.refman,
)
with pytest.raises(DialsRefineConfigError):
ar.check_and_fail()
def test_check_and_remove():
test = _Test()
# Override the single panel model and parameterisation. This test function
# exercises the code for non-hierarchical multi-panel detectors. The
# hierarchical detector version is tested via test_cspad_refinement.py
multi_panel_detector = Detector()
for x in range(3):
for y in range(3):
new_panel = make_panel_in_array((x, y), test.detector[0])
multi_panel_detector.add_panel(new_panel)
test.detector = multi_panel_detector
test.stills_experiments[0].detector = multi_panel_detector
test.det_param = DetectorParameterisationMultiPanel(multi_panel_detector, test.beam)
# update the generated reflections
test.generate_reflections()
# Predict the reflections in place and put in a reflection manager
ref_predictor = StillsExperimentsPredictor(test.stills_experiments)
ref_predictor(test.reflections)
test.refman = ReflectionManagerFactory.from_parameters_reflections_experiments(
refman_phil_scope.extract(),
test.reflections,
test.stills_experiments,
do_stills=True,
)
test.refman.finalise()
# Build a prediction parameterisation for the stills experiment
test.pred_param = StillsPredictionParameterisation(
test.stills_experiments,
detector_parameterisations=[test.det_param],
beam_parameterisations=[test.s0_param],
xl_orientation_parameterisations=[test.xlo_param],
xl_unit_cell_parameterisations=[test.xluc_param],
)
# A non-hierarchical detector does not have panel groups, thus panels are
# not treated independently wrt which reflections affect their parameters.
# As before, setting 792 reflections as the minimum should leave all
# parameters free, and should not remove any reflections
options = ar_phil_scope.extract()
options.min_nref_per_parameter = 792
ar = AutoReduce(options, pred_param=test.pred_param, reflection_manager=test.refman)
ar.check_and_remove()
det_params = test.pred_param.get_detector_parameterisations()
beam_params = test.pred_param.get_beam_parameterisations()
xl_ori_params = test.pred_param.get_crystal_orientation_parameterisations()
xl_uc_params = test.pred_param.get_crystal_unit_cell_parameterisations()
assert det_params[0].num_free() == 6
assert beam_params[0].num_free() == 3
assert xl_ori_params[0].num_free() == 3
assert xl_uc_params[0].num_free() == 6
assert len(test.refman.get_obs()) == 823
# Setting 793 reflections as the minimum fixes 3 unit cell parameters,
# and removes all those reflections. There are then too few reflections
# for any parameterisation and all will be fixed, leaving no free
# parameters for refinement. This fails within PredictionParameterisation,
# during update so the final 31 reflections are not removed.
options = ar_phil_scope.extract()
options.min_nref_per_parameter = 793
ar = AutoReduce(options, pred_param=test.pred_param, reflection_manager=test.refman)
with pytest.raises(
DialsRefineConfigError, match="There are no free parameters for refinement"
):
ar.check_and_remove()
det_params = test.pred_param.get_detector_parameterisations()
beam_params = test.pred_param.get_beam_parameterisations()
xl_ori_params = test.pred_param.get_crystal_orientation_parameterisations()
xl_uc_params = test.pred_param.get_crystal_unit_cell_parameterisations()
assert det_params[0].num_free() == 0
assert beam_params[0].num_free() == 0
assert xl_ori_params[0].num_free() == 0
assert xl_uc_params[0].num_free() == 0
assert len(test.refman.get_obs()) == 823 - 792
def test_check_and_remove():
test = _Test()
# Override the single panel model and parameterisation. This test function
# exercises the code for non-hierarchical multi-panel detectors. The
# hierarchical detector version is tested via test_cspad_refinement.py
from dxtbx.model import Detector
from dials.algorithms.refinement.parameterisation.detector_parameters import (
DetectorParameterisationMultiPanel, )
from dials.test.algorithms.refinement.test_multi_panel_detector_parameterisation import (
make_panel_in_array, )
multi_panel_detector = Detector()
for x in range(3):
for y in range(3):
new_panel = make_panel_in_array((x, y), test.detector[0])
multi_panel_detector.add_panel(new_panel)
test.detector = multi_panel_detector
test.stills_experiments[0].detector = multi_panel_detector
test.det_param = DetectorParameterisationMultiPanel(
multi_panel_detector, test.beam)
# update the generated reflections
test.generate_reflections()
# Predict the reflections in place and put in a reflection manager
ref_predictor = StillsExperimentsPredictor(test.stills_experiments)
ref_predictor(test.reflections)
test.refman = ReflectionManagerFactory.from_parameters_reflections_experiments(
refman_phil_scope.extract(),
test.reflections,
test.stills_experiments,
do_stills=True,
)
test.refman.finalise()
# A non-hierarchical detector does not have panel groups, thus panels are
# not treated independently wrt which reflections affect their parameters.
# As before, setting 137 reflections as the minimum should leave all
# parameters free, and should not remove any reflections
options = ar_phil_scope.extract()
options.min_nref_per_parameter = 137
ar = AutoReduce(
options,
[test.det_param],
[test.s0_param],
[test.xlo_param],
[test.xluc_param],
gon_params=[],
reflection_manager=test.refman,
)
ar.check_and_remove()
assert ar.det_params[0].num_free() == 6
assert ar.beam_params[0].num_free() == 3
assert ar.xl_ori_params[0].num_free() == 3
assert ar.xl_uc_params[0].num_free() == 6
assert len(ar.reflection_manager.get_obs()) == 823
# Setting reflections as the minimum should fix the detector parameters,
# which removes that parameterisation. Because all reflections are recorded
# on that detector, they will all be removed as well. This then affects all
# other parameterisations, which will be removed.
options = ar_phil_scope.extract()
options.min_nref_per_parameter = 138
ar = AutoReduce(
options,
[test.det_param],
[test.s0_param],
[test.xlo_param],
[test.xluc_param],
gon_params=[],
reflection_manager=test.refman,
)
ar.check_and_remove()
assert not ar.det_params
assert not ar.beam_params
assert not ar.xl_ori_params
assert not ar.xl_uc_params
assert len(ar.reflection_manager.get_obs()) == 0
