1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
|
from __future__ import annotations
import pytest
from dxtbx.model import Detector
from dials.algorithms.refinement import DialsRefineConfigError
from dials.algorithms.refinement.parameterisation.autoreduce import AutoReduce
from dials.algorithms.refinement.parameterisation.autoreduce import (
phil_scope as ar_phil_scope,
)
from dials.algorithms.refinement.parameterisation.detector_parameters import (
DetectorParameterisationMultiPanel,
)
from dials.algorithms.refinement.parameterisation.prediction_parameters_stills import (
StillsPredictionParameterisation,
)
from dials.algorithms.refinement.prediction.managed_predictors import (
StillsExperimentsPredictor,
)
from dials.algorithms.refinement.reflection_manager import ReflectionManagerFactory
from dials.algorithms.refinement.reflection_manager import (
phil_scope as refman_phil_scope,
)
from .test_multi_panel_detector_parameterisation import make_panel_in_array
from .test_stills_prediction_parameters import _Test
@pytest.fixture(scope="session")
def tc():
test = _Test()
# 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],
)
return test
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_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_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_ignore(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()
options = ar_phil_scope.extract()
options.ignore = True
ar = AutoReduce(options, pred_param=tc.pred_param, reflection_manager=tc.refman)
ar()
# All parameters should remain free, and all reflections still present
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 beam_params[0].num_free() == n_beam
assert xl_ori_params[0].num_free() == n_xlo
assert xl_uc_params[0].num_free() == n_xluc
assert len(tc.refman.get_matches()) == 823
|
