def exercise_refine_bravais_settings():
if not have_dials_regression:
print "Skipping exercise_refine_bravais_settings(): dials_regression not available."
return
data_dir = os.path.join(dials_regression, "indexing_test_data", "i04_weak_data")
pickle_path = os.path.join(data_dir, "indexed.pickle")
experiments_path = os.path.join(data_dir, "experiments.json")
commands = ["dials.refine_bravais_settings",
pickle_path,
experiments_path,
"reflections_per_degree=5",
"minimum_sample_size=500",
"beam.fix=all",
"detector.fix=all",
"prefix=tst_"]
command = " ".join(commands)
print command
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
result = easy_run.fully_buffered(command=command).raise_if_errors()
for i in range(1, 10):
assert os.path.exists("tst_bravais_setting_%i.json" %i)
from dxtbx.serialize import load
experiments_list = load.experiment_list(
"tst_bravais_setting_9.json", check_format=False)
assert len(experiments_list) == 1
assert experiments_list[0].crystal.get_unit_cell().is_similar_to(
uctbx.unit_cell((57.782, 57.782, 150.011, 90, 90, 90)))
assert experiments_list[0].crystal.get_space_group().type().hall_symbol() \
== ' P 4'
assert os.path.exists("tst_bravais_summary.json")
from json import load
bravais_summary = load(open("tst_bravais_summary.json", "rb"))
assert bravais_summary.keys() == [
'1', '3', '2', '5', '4', '7', '6', '9', '8']
bravais_summary['9'].keys() == [
'bravais', 'max_angular_difference', 'unit_cell', 'rmsd', 'nspots']
assert approx_equal(
bravais_summary['9']['unit_cell'],
[57.78, 57.78, 150.0, 90.0, 90.0, 90.0], eps=1e-1)
assert bravais_summary['9']['bravais'] == 'tP'
assert bravais_summary['9']['recommended'] == True
assert approx_equal(bravais_summary['9']['rmsd'], 0.047, eps=1e-2)
os.chdir(cwd)
def exercise_refine_bravais_settings():
if not have_dials_regression:
print "Skipping exercise_refine_bravais_settings(): dials_regression not available."
return
data_dir = os.path.join(dials_regression, "indexing_test_data", "i04_weak_data")
pickle_path = os.path.join(data_dir, "indexed.pickle")
experiments_path = os.path.join(data_dir, "experiments.json")
commands = ["dials.refine_bravais_settings",
pickle_path,
experiments_path,
"reflections_per_degree=5",
"minimum_sample_size=500",
"beam.fix=all",
"detector.fix=all"]
command = " ".join(commands)
print command
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
result = easy_run.fully_buffered(command=command).raise_if_errors()
for i in range(1, 10):
assert os.path.exists("bravais_setting_%i.json" %i)
from dxtbx.serialize import load
experiments_list = load.experiment_list(
"bravais_setting_9.json", check_format=False)
assert len(experiments_list) == 1
assert experiments_list[0].crystal.get_unit_cell().is_similar_to(
uctbx.unit_cell((57.782, 57.782, 150.011, 90, 90, 90)))
assert experiments_list[0].crystal.get_space_group().type().hall_symbol() \
== ' P 4'
assert os.path.exists("bravais_summary.json")
from json import load
bravais_summary = load(open("bravais_summary.json", "rb"))
assert bravais_summary.keys() == [
'1', '3', '2', '5', '4', '7', '6', '9', '8']
bravais_summary['9'].keys() == [
'bravais', 'max_angular_difference', 'unit_cell', 'rmsd', 'nspots']
assert approx_equal(
bravais_summary['9']['unit_cell'],
[57.78, 57.78, 150.0, 90.0, 90.0, 90.0], eps=1e-1)
assert bravais_summary['9']['bravais'] == 'tP'
assert bravais_summary['9']['recommended'] == True
assert approx_equal(bravais_summary['9']['rmsd'], 0.047, eps=1e-2)
os.chdir(cwd)
def exercise_refine_bravais_settings_3():
if not have_dials_regression:
print "Skipping exercise_refine_bravais_settings(): dials_regression not available."
return
data_dir = os.path.join(dials_regression, "indexing_test_data", "trypsin")
pickle_path = os.path.join(data_dir, "indexed.pickle")
experiments_path = os.path.join(data_dir, "experiments.json")
commands = ["dials.refine_bravais_settings",
pickle_path,
experiments_path,
"crystal_id=1"]
command = " ".join(commands)
print command
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
result = easy_run.fully_buffered(command=command).raise_if_errors()
for i in range(1, 10):
assert os.path.exists("bravais_setting_%i.json" %i)
from dxtbx.serialize import load
experiments_list = load.experiment_list(
"bravais_setting_5.json", check_format=False)
assert len(experiments_list) == 1
assert experiments_list[0].crystal.get_unit_cell().is_similar_to(
uctbx.unit_cell((54.37, 58.29, 66.51, 90.00, 90.00, 90.00)))
assert experiments_list[0].crystal.get_space_group().type().hall_symbol() \
== ' P 2 2'
assert os.path.exists("bravais_summary.json")
from json import load
bravais_summary = load(open("bravais_summary.json", "rb"))
assert bravais_summary.keys() == [
'1', '3', '2', '5', '4', '7', '6', '9', '8']
assert approx_equal(
bravais_summary['5']['unit_cell'],
[54.37, 58.29, 66.51, 90.00, 90.00, 90.00], eps=1e-1)
assert bravais_summary['5']['bravais'] == 'oP'
assert approx_equal(bravais_summary['5']['rmsd'], 0.1200, eps=1e-2)
assert bravais_summary['5']['recommended'] == True
assert bravais_summary['9']['recommended'] == False
os.chdir(cwd)
def exercise_refine_bravais_settings_2():
if not have_dials_regression:
print "Skipping exercise_refine_bravais_settings(): dials_regression not available."
return
data_dir = os.path.join(dials_regression, "indexing_test_data", "multi_sweep")
pickle_path = os.path.join(data_dir, "indexed.pickle")
experiments_path = os.path.join(data_dir, "experiments.json")
commands = ["dials.refine_bravais_settings", pickle_path, experiments_path]
command = " ".join(commands)
print command
cwd = os.path.abspath(os.curdir)
tmp_dir = open_tmp_directory()
os.chdir(tmp_dir)
result = easy_run.fully_buffered(command=command).raise_if_errors()
for i in range(1, 10):
assert os.path.exists("bravais_setting_%i.json" %i)
from dxtbx.serialize import load
experiments_list = load.experiment_list(
"bravais_setting_9.json", check_format=False)
assert len(experiments_list) == 4
assert len(experiments_list.crystals()) == 1
assert experiments_list[0].crystal.get_unit_cell().is_similar_to(
uctbx.unit_cell((7.31, 7.31, 6.82, 90.00, 90.00, 90.00)))
assert experiments_list[0].crystal.get_space_group().type().hall_symbol() \
== ' I 4'
assert os.path.exists("bravais_summary.json")
from json import load
bravais_summary = load(open("bravais_summary.json", "rb"))
for i in range(1, 23): assert str(i) in bravais_summary.keys()
assert approx_equal(
bravais_summary['9']['unit_cell'],
[7.31, 7.31, 6.82, 90.00, 90.00, 90.00], eps=1e-1)
assert bravais_summary['9']['bravais'] == 'tI'
assert approx_equal(bravais_summary['9']['rmsd'], 0.103, eps=1e-2)
assert bravais_summary['9']['recommended'] == True
os.chdir(cwd)
