def test_renumber_table_id_columns():
"""Test the correct handling of duplicate table id values.
Note that this function does not have the ability to update the
experiment string identifier, only ensure that the table id values
do not clash.
"""
# Test the case of two single reflection tables.
rs = [
mock_reflection_file_object(id_=0).data,
mock_reflection_file_object(id_=0).data,
]
rs = renumber_table_id_columns(rs)
assert list(rs[0]["id"]) == [-1, 0, 0]
assert list(rs[0].experiment_identifiers().keys()) == [0]
assert list(rs[0].experiment_identifiers().values()) == ["0"]
assert list(rs[1]["id"]) == [-1, 1, 1]
assert list(rs[1].experiment_identifiers().keys()) == [1]
assert list(rs[1].experiment_identifiers().values()) == ["0"]
# Now test the case where one reflection table contains two experiments
rs = [
mock_two_reflection_file_object().data,
mock_reflection_file_object(id_=0).data,
]
rs = renumber_table_id_columns(rs)
assert list(rs[0]["id"]) == [-1, 0, 0, 1, 1]
assert list(rs[0].experiment_identifiers().keys()) == [0, 1]
assert list(rs[0].experiment_identifiers().values()) == ["0", "2"]
assert list(rs[1]["id"]) == [-1, 2, 2]
assert list(rs[1].experiment_identifiers().keys()) == [2]
assert list(rs[1].experiment_identifiers().values()) == ["0"]
rs = [
mock_reflection_file_object(id_=0).data,
mock_two_reflection_file_object(ids=[1, 2]).data,
]
rs = renumber_table_id_columns(rs)
assert list(rs[0]["id"]) == [-1, 0, 0]
assert list(rs[0].experiment_identifiers().keys()) == [0]
assert list(rs[0].experiment_identifiers().values()) == ["0"]
assert list(rs[1]["id"]) == [-1, 1, 1, 2, 2]
assert list(rs[1].experiment_identifiers().keys()) == [1, 2]
assert list(rs[1].experiment_identifiers().values()) == ["1", "2"]
rs = [
mock_two_reflection_file_object(ids=[1, 2]).data,
mock_reflection_file_object(id_=0).data,
]
rs = renumber_table_id_columns(rs)
assert list(rs[0]["id"]) == [-1, 0, 0, 1, 1]
assert list(rs[0].experiment_identifiers().keys()) == [0, 1]
assert list(rs[0].experiment_identifiers().values()) == ["1", "2"]
assert list(rs[1]["id"]) == [-1, 2, 2]
assert list(rs[1].experiment_identifiers().keys()) == [2]
assert list(rs[1].experiment_identifiers().values()) == ["0"]
def test_flatten_experiments_updating_id_values():
"""Test the correct handling of duplicate table id values.
Note that this function does not have the ability to update the
experiment string identifier, only ensure that the table id values
do not clash (it is not possible even to load multiple experiments
with the same identifier).
"""
# Test the case of two single reflection tables.
file_list = [
mock_reflection_file_object(id_=0),
mock_reflection_file_object(id_=0)
]
rs = flatten_reflections(file_list)
assert rs[0] is file_list[0].data
assert list(rs[0]["id"]) == [-1, 0, 0]
assert list(rs[0].experiment_identifiers().keys()) == [0]
assert list(rs[0].experiment_identifiers().values()) == ["0"]
assert rs[1] is file_list[1].data
assert list(rs[1]["id"]) == [-1, 1, 1]
assert list(rs[1].experiment_identifiers().keys()) == [1]
assert list(rs[1].experiment_identifiers().values()) == ["0"]
# Now test the case where one reflection table contains two experiments
file_list = [
mock_two_reflection_file_object(),
mock_reflection_file_object(id_=0)
]
rs = flatten_reflections(file_list)
assert rs[0] is file_list[0].data
assert list(rs[0]["id"]) == [-1, 0, 0, 1, 1]
assert list(rs[0].experiment_identifiers().keys()) == [0, 1]
assert list(rs[0].experiment_identifiers().values()) == ["0", "2"]
assert rs[1] is file_list[1].data
assert list(rs[1]["id"]) == [-1, 2, 2]
assert list(rs[1].experiment_identifiers().keys()) == [2]
assert list(rs[1].experiment_identifiers().values()) == ["0"]
file_list = [
mock_reflection_file_object(id_=0),
mock_two_reflection_file_object(ids=[1, 2]),
]
rs = flatten_reflections(file_list)
assert rs[0] is file_list[0].data
assert list(rs[0]["id"]) == [-1, 0, 0]
assert list(rs[0].experiment_identifiers().keys()) == [0]
assert list(rs[0].experiment_identifiers().values()) == ["0"]
assert rs[1] is file_list[1].data
assert list(rs[1]["id"]) == [-1, 1, 1, 2, 2]
assert list(rs[1].experiment_identifiers().keys()) == [1, 2]
assert list(rs[1].experiment_identifiers().values()) == ["1", "2"]
def test_reflections_and_experiments_from_files():
"""Test correct extracting of reflections and experiments."""
# Test when input reflections order matches the experiments order
refl_file_list = [
mock_two_reflection_file_object(ids=[0, 1]),
mock_reflection_file_object(id_=2),
]
def mock_exp_obj(id_=0):
"""Make a mock experiments file object."""
exp = Mock()
exp.data = ExperimentList()
exp.data.append(Experiment(identifier=str(id_)))
return exp
exp_file_list = [mock_exp_obj(id_=i) for i in [0, 1, 2]]
refls, expts = reflections_and_experiments_from_files(
refl_file_list, exp_file_list)
assert refls[0] is refl_file_list[0].data
assert refls[1] is refl_file_list[1].data
assert expts[0].identifier == "0"
assert expts[1].identifier == "1"
assert expts[2].identifier == "2"
# Test when input reflections order does not match experiments order.
refl_file_list = [
mock_reflection_file_object(id_=2),
mock_two_reflection_file_object(ids=[0, 1]),
]
refls, expts = reflections_and_experiments_from_files(
refl_file_list, exp_file_list)
assert refls[0] is refl_file_list[1].data
assert refls[1] is refl_file_list[0].data
assert expts[0].identifier == "0"
assert expts[1].identifier == "1"
assert expts[2].identifier == "2"
def test_sort_tables_to_experiments_order_multi_dataset_files():
"""Test reflection table sorting when a table contains multiple datasets."""
# Reflection tables in the wrong order
reflection_tables = [
mock_two_reflection_file_object(ids=[1, 2]).data,
mock_reflection_file_object(id_=0).data,
]
experiments = ExperimentList()
experiments.append(Experiment(identifier=str(0)))
experiments.append(Experiment(identifier=str(1)))
experiments.append(Experiment(identifier=str(2)))
refls = sort_tables_to_experiments_order(reflection_tables, experiments)
# Check that reflection tables are rearranged
assert refls[0] is reflection_tables[1]
assert refls[1] is reflection_tables[0]
assert list(refls[0].experiment_identifiers().values()) == ["0"]
assert list(refls[1].experiment_identifiers().values()) == ["1", "2"]