def run_scaling(params, experiments, reflections):
"""Run scaling algorithms; stats only, cross validation or standard."""
if params.stats_only:
Script.stats_only(reflections, experiments, params)
sys.exit()
if params.export_mtz_only:
Script.export_mtz_only(reflections, experiments, params)
sys.exit()
if params.output.delete_integration_shoeboxes:
for r in reflections:
del r["shoebox"]
if params.cross_validation.cross_validation_mode:
from dials.algorithms.scaling.cross_validation.cross_validate import (
cross_validate,
)
from dials.algorithms.scaling.cross_validation.crossvalidator import (
DialsScaleCrossValidator,
)
cross_validator = DialsScaleCrossValidator(experiments, reflections)
try:
cross_validate(params, cross_validator)
except ValueError as e:
raise Sorry(e)
logger.info(
"Cross validation analysis does not produce scaling output files, rather\n"
"it gives insight into the dataset. Choose an appropriate parameterisation\n"
"and rerun scaling without cross_validation_mode.\n"
)
else:
script = Script(params, experiments, reflections)
# Register the observers at the highest level
if params.output.html:
register_default_scaling_observers(script)
else:
register_merging_stats_observers(script)
if params.filtering.method:
if script.scaler.id_ != "multi":
raise Sorry(
"""
Scaling and filtering can only be performed in multi-dataset scaling mode
(not single dataset or scaling against a reference)"""
)
register_scale_and_filter_observers(script)
script.run_scale_and_filter()
with open(params.filtering.output.scale_and_filter_results, "w") as f:
json.dump(script.filtering_results.to_dict(), f, indent=2)
else:
script.run()
script.export()
def run_scaling(params, experiments, reflections):
"""Run scaling algorithms; cross validation, scaling + filtering or standard.
Returns:
experiments: an experiment list with scaled data (if created)
joint_table: a single reflection table containing scaled data (if created).
"""
if params.output.delete_integration_shoeboxes:
for r in reflections:
del r["shoebox"]
if params.cross_validation.cross_validation_mode:
from dials.algorithms.scaling.cross_validation.cross_validate import (
cross_validate, )
from dials.algorithms.scaling.cross_validation.crossvalidator import (
DialsScaleCrossValidator, )
cross_validator = DialsScaleCrossValidator(experiments, reflections)
cross_validate(params, cross_validator)
logger.info(
"Cross validation analysis does not produce scaling output files, rather\n"
"it gives insight into the dataset. Choose an appropriate parameterisation\n"
"and rerun scaling without cross_validation_mode.\n")
return (None, None)
else:
# Register the observers at the highest level
if params.filtering.method:
algorithm = ScaleAndFilterAlgorithm(params, experiments,
reflections)
register_scale_and_filter_observers(algorithm)
else:
algorithm = ScalingAlgorithm(params, experiments, reflections)
if params.output.html:
register_default_scaling_observers(algorithm)
else:
register_merging_stats_observers(algorithm)
algorithm.run()
experiments, joint_table = algorithm.finish()
return experiments, joint_table
def test_dialsscalecrossvalidator():
"""Test the methods of the dials.scale cross validator"""
experiments = []
reflections = []
def mock_script():
script = mock.MagicMock()
script.scaler.work_free_stats = [1.0, 2.0, 3.0, 4.0]
return script
# test get results from script
crossvalidator = DialsScaleCrossValidator(experiments, reflections)
script = mock_script()
results = crossvalidator.get_results_from_script(script)
assert results == [1.0, 2.0, 3.0, 4.0]
params = generated_param()
params.scaling_options.free_set_percentage = 20.0
# test get free set offset
fsp = crossvalidator.get_free_set_percentage(params)
assert fsp == 20.0
# test set free set offset
params = crossvalidator.set_free_set_offset(params, 5)
assert params.scaling_options.free_set_offset == 5
# test get/set parameters
assert crossvalidator.get_parameter_type("model") == "choice"
assert crossvalidator.get_parameter_type(
"physical.absorption_correction") == "bool"
assert crossvalidator.get_parameter_type("physical.lmax") == "int"
assert crossvalidator.get_parameter_type(
"physical.decay_interval") == "float"
params = crossvalidator.set_parameter(params, "model", "physical")
assert params.model == "physical"
params = crossvalidator.set_parameter(params, "physical.decay_interval",
50.0)
assert params.physical.decay_interval == 50.0
params = crossvalidator.set_parameter(params, "physical.lmax", 10)
assert params.physical.lmax == 10
params = crossvalidator.set_parameter(params,
"weighting.error_model.error_model",
None)
assert params.weighting.error_model.error_model is None
params = crossvalidator.set_parameter(params, "cut_data.d_min", 1.8)
assert params.cut_data.d_min == 1.8
params = crossvalidator.set_parameter(params,
"scaling_options.outlier_zmax", 7.53)
assert params.scaling_options.outlier_zmax == 7.53
with pytest.raises(ValueError):
_ = crossvalidator.set_parameter(params, "bad_parameter", 7.53)
def test_crossvalidator():
"""Use the dials.scale cross validator to test the general methods of the
parent class."""
experiments = []
reflections = []
# test the create_results_dict method
crossvalidator = DialsScaleCrossValidator(experiments, reflections)
crossvalidator.create_results_dict(1)
assert len(crossvalidator.results_dict) == 1
assert (len(crossvalidator.results_dict[0]) == len(
crossvalidator.results_metadata["names"]) + 1)
crossvalidator = DialsScaleCrossValidator(experiments, reflections)
crossvalidator.create_results_dict(2)
assert len(crossvalidator.results_dict) == 2
assert (len(crossvalidator.results_dict[0]) == len(
crossvalidator.results_metadata["names"]) + 1)
assert (len(crossvalidator.results_dict[1]) == len(
crossvalidator.results_metadata["names"]) + 1)
# now test the add configuration
keys = ("model", )
values = (["a", "b"], )
crossvalidator.set_results_dict_configuration(keys, values)
assert crossvalidator.results_dict[0]["configuration"][0] == "model=a"
assert crossvalidator.results_dict[1]["configuration"][0] == "model=b"
# now try adding results to dict
results_1 = [1.0, 1.5, 0.5, 3.0, 4.0, 1.0]
results_2 = [1.0, 2.0, 1.0, 3.0, 2.0, 2.0]
results_3 = [1.0, 2.0, 1.0, 3.0, 3.0, 0.0]
results_4 = [1.0, 2.0, 1.0, 3.0, 3.5, 0.5]
crossvalidator.add_results_to_results_dict(0, results_1)
assert crossvalidator.results_dict[0]["work Rmeas"] == [1.0]
assert crossvalidator.results_dict[0]["free Rmeas"] == [1.5]
assert crossvalidator.results_dict[0]["work CC1/2"] == [3.0]
assert crossvalidator.results_dict[0]["free CC1/2"] == [4.0]
# add some more so that can test interpreting results
crossvalidator.add_results_to_results_dict(0, results_2)
crossvalidator.add_results_to_results_dict(1, results_3)
crossvalidator.add_results_to_results_dict(1, results_4)
# Now try interpreting results - check that values are calculated correctly
st = crossvalidator.interpret_results()
r1 = ["model=a", "mean", "1.0", "1.75*", "0.75*", "3.0", "3.0", "1.5"]
r2 = ["", "std dev", "0.0", "0.25", "0.25", "0.0", "1.0", "0.5"]
r3 = ["model=b", "mean", "1.0", "2.0", "1.0", "3.0", "3.25*", "0.25*"]
r4 = ["", "std dev", "0.0", "0.0", "0.0", "0.0", "0.25", "0.25"]
assert st._rows[0] == r1
assert st._rows[1] == r2
assert st._rows[2] == r3
assert st._rows[3] == r4
def test_cross_validate_script():
"""Test the script, mocking the run_script and interpret results calls"""
param = generated_param()
crossvalidator = DialsScaleCrossValidator([], [])
# test expected error raise due to unspecified parameter
param.cross_validation.cross_validation_mode = "multi"
with pytest.raises(ValueError):
cross_validate(param, crossvalidator)
# test single mode
param.cross_validation.cross_validation_mode = "single"
param.cross_validation.nfolds = 2
fpath = "dials.algorithms.scaling.cross_validation."
with mock.patch(fpath +
"crossvalidator.DialsScaleCrossValidator.run_script"
) as mock_run_script:
with mock.patch(
fpath +
"crossvalidator.DialsScaleCrossValidator.interpret_results"
) as mock_interpret:
cross_validate(param, crossvalidator)
assert mock_run_script.call_count == 2
assert mock_interpret.call_count == 1
# test multi mode
param = generated_param()
param.cross_validation.cross_validation_mode = "multi"
param.cross_validation.nfolds = 2
fpath = "dials.algorithms.scaling.cross_validation."
with mock.patch(fpath +
"crossvalidator.DialsScaleCrossValidator.run_script"
) as mock_run_script:
with mock.patch(
fpath +
"crossvalidator.DialsScaleCrossValidator.interpret_results"
) as mock_interpret:
param.cross_validation.parameter = "physical.absorption_correction"
cross_validate(param, crossvalidator)
assert mock_run_script.call_count == 4
assert mock_interpret.call_count == 1
param.cross_validation.parameter = "physical.decay_interval"
with pytest.raises(ValueError):
cross_validate(param, crossvalidator)
param.cross_validation.parameter = "physical.absorption_correction"
param.cross_validation.parameter_values = ["True", "False"]
cross_validate(param, crossvalidator)
assert mock_run_script.call_count == 8
assert mock_interpret.call_count == 2
param.cross_validation.parameter = "physical.decay_interval"
param.cross_validation.parameter_values = ["5.0", "10.0"]
cross_validate(param, crossvalidator)
assert mock_run_script.call_count == 12
assert mock_interpret.call_count == 3
param.cross_validation.parameter = "model"
param.cross_validation.parameter_values = ["array", "physical"]
cross_validate(param, crossvalidator)
assert mock_run_script.call_count == 16
assert mock_interpret.call_count == 4
param.cross_validation.parameter = "physical.lmax"
param.cross_validation.parameter_values = ["4", "6"]
cross_validate(param, crossvalidator)
assert mock_run_script.call_count == 20
assert mock_interpret.call_count == 5
param.cross_validation.parameter = "bad_interval"
with pytest.raises(ValueError):
cross_validate(param, crossvalidator)
param.cross_validation.cross_validation_mode = "bad"
with pytest.raises(ValueError):
cross_validate(param, crossvalidator)
def test_dialsscalecrossvalidator():
"""Test the methods of the dials.scale cross validator"""
experiments = []
reflections = []
def mock_script():
script = mock.MagicMock()
script.scaler.final_rmsds = [1.0, 2.0, 3.0, 4.0]
return script
# test get results from script
crossvalidator = DialsScaleCrossValidator(experiments, reflections)
script = mock_script()
results = crossvalidator.get_results_from_script(script)
assert results == [1.0, 2.0, 3.0, 4.0]
params = generated_param()
params.scaling_options.free_set_percentage = 20.0
# test get free set offset
fsp = crossvalidator.get_free_set_percentage(params)
assert fsp == 20.0
# test set free set offset
params = crossvalidator.set_free_set_offset(params, 5)
assert params.scaling_options.free_set_offset == 5
# test get/set parameters
assert crossvalidator.get_parameter_type("model") == "choice"
assert crossvalidator.get_parameter_type("absorption_term") == "bool"
assert crossvalidator.get_parameter_type("lmax") == "int"
assert crossvalidator.get_parameter_type("decay_interval") == "float"
params = crossvalidator.set_parameter(params, "model", "KB")
assert params.model == "KB"
params = crossvalidator.set_parameter(params, "decay_interval", 50.0)
assert params.parameterisation.decay_interval == 50.0
params = crossvalidator.set_parameter(params, "lmax", 10)
assert params.parameterisation.lmax == 10
params = crossvalidator.set_parameter(params, "optimise_errors", False)
assert params.weighting.optimise_errors is False
params = crossvalidator.set_parameter(params, "d_min", 1.8)
assert params.cut_data.d_min == 1.8
params = crossvalidator.set_parameter(params, "outlier_zmax", 7.53)
assert params.scaling_options.outlier_zmax == 7.53
with pytest.raises(AssertionError):
_ = crossvalidator.set_parameter(params, "bad_parameter", 7.53)