def test_miller_array_datatype():
data_dir = os.path.dirname(os.path.abspath(__file__))
data_mtz = os.path.join(data_dir, 'data',
'insulin_unmerged_cutted_from_ccp4.mtz')
dm = DataManager(['miller_array', 'phil'])
dm.process_miller_array_file(data_mtz)
# test labels
labels = [
'M_ISYM', 'BATCH', 'I,SIGI,merged', 'IPR,SIGIPR,merged',
'FRACTIONCALC', 'XDET', 'YDET', 'ROT', 'WIDTH', 'LP', 'MPART', 'FLAG',
'BGPKRATIOS'
]
for label in dm.get_miller_array_labels():
assert label in labels
assert len(dm.get_miller_arrays()) == len(dm.get_miller_array_labels())
# test access by label
label = dm.get_miller_array_labels()[3]
new_label = dm.get_miller_arrays(labels=[label])[0].info().label_string()
assert label == new_label
# test custom PHIL
dm.write_phil_file(dm.export_phil_scope().as_str(),
filename='test.phil',
overwrite=True)
loaded_phil = iotbx.phil.parse(file_name='test.phil')
new_dm = DataManager(['miller_array', 'phil'])
new_dm.load_phil_scope(loaded_phil)
assert data_mtz == new_dm.get_default_miller_array_name()
for label in new_dm.get_miller_array_labels():
assert label in labels
os.remove('test.phil')
# test type
assert dm.get_miller_array_type() == 'x_ray'
label = labels[3]
dm.set_miller_array_type(data_mtz, label, 'electron')
assert dm.get_miller_array_type(label=label) == 'electron'
dm.write_phil_file(dm.export_phil_scope().as_str(),
filename='test_phil',
overwrite=True)
loaded_phil = iotbx.phil.parse(file_name='test_phil')
new_dm.load_phil_scope(loaded_phil)
assert new_dm.get_miller_array_type(label=label) == 'electron'
new_dm = DataManager(['miller_array'])
try:
new_dm.set_default_miller_array_type('q')
except Sorry:
pass
new_dm.set_default_miller_array_type('neutron')
new_dm.process_miller_array_file(data_mtz)
assert new_dm.get_miller_array_type(label=label) == 'neutron'
os.remove('test_phil')
# test writing file
arrays = dm.get_miller_arrays()
dataset = arrays[2].as_mtz_dataset(column_root_label='label1')
dataset.add_miller_array(miller_array=arrays[3],
column_root_label='label2')
mtz_object = dataset.mtz_object()
dm.write_miller_array_file(mtz_object, filename='test.mtz', overwrite=True)
dm.process_miller_array_file('test.mtz')
new_labels = dm.get_miller_array_labels('test.mtz')
assert 'label1,SIGlabel1' in new_labels
assert 'label2,SIGlabel2' in new_labels
os.remove('test.mtz')
# test file server
fs1 = dm.get_reflection_file_server()
fs2 = dm.get_reflection_file_server([data_mtz, data_mtz])
assert 2 * len(fs1.miller_arrays) == len(fs2.miller_arrays)
cs = crystal.symmetry(
unit_cell=dm.get_miller_arrays()[0].crystal_symmetry().unit_cell(),
space_group_symbol='P1')
fs = dm.get_reflection_file_server(crystal_symmetry=cs)
assert fs.crystal_symmetry.is_similar_symmetry(cs)
assert not fs.crystal_symmetry.is_similar_symmetry(
dm.get_miller_arrays()[0].crystal_symmetry())
fs = dm.get_reflection_file_server(labels=['I,SIGI,merged'])
assert len(fs.get_miller_arrays(None)) == 1
miller_array = fs.get_amplitudes(None, None, True, None, None)
assert miller_array.info().label_string() == 'I,as_amplitude_array,merged'
for label in dm.get_miller_array_labels():
dm.set_miller_array_type(label=label, array_type='electron')
fs = dm.get_reflection_file_server(array_type='x_ray')
assert len(fs.get_miller_arrays(None)) == 0
fs = dm.get_reflection_file_server(array_type='electron')
assert len(fs.get_miller_arrays(None)) == 13
fs = dm.get_reflection_file_server(
filenames=[data_mtz],
labels=[['I,SIGI,merged', 'IPR,SIGIPR,merged']],
array_type='neutron')
assert len(fs.get_miller_arrays(None)) == 0
for label in ['I,SIGI,merged', 'IPR,SIGIPR,merged']:
dm.set_miller_array_type(label=label, array_type='x_ray')
fs = dm.get_reflection_file_server(
filenames=[data_mtz],
labels=[['I,SIGI,merged', 'IPR,SIGIPR,merged']],
array_type='x_ray')
assert len(fs.get_miller_arrays(data_mtz)) == 2
fs = dm.get_reflection_file_server(filenames=[data_mtz],
array_type='x_ray')
assert len(fs.get_miller_arrays(data_mtz)) == 2
fs = dm.get_reflection_file_server(filenames=[data_mtz],
array_type='electron')
assert len(fs.get_miller_arrays(data_mtz)) == 11
# test subset of labels
label_subset = labels[3:8]
dm = DataManager(['miller_array', 'phil'])
dm.process_miller_array_file(data_mtz)
dm._miller_array_labels[data_mtz] = label_subset
dm.set_miller_array_type(label=label_subset[2], array_type='electron')
assert dm.get_miller_array_type(label=label_subset[2]) == 'electron'
dm.write_phil_file(dm.export_phil_scope().as_str(),
filename='test.phil',
overwrite=True)
loaded_phil = iotbx.phil.parse(file_name='test.phil')
new_dm = DataManager(['miller_array', 'phil'])
new_dm.load_phil_scope(loaded_phil)
assert new_dm.get_miller_array_type(label=label_subset[2]) == 'electron'
fs = new_dm.get_reflection_file_server(array_type='x_ray')
assert len(fs.get_miller_arrays(None)) == 4
fs = new_dm.get_reflection_file_server(array_type='electron')
assert len(fs.get_miller_arrays(None)) == 1
os.remove('test.phil')
label_subset = list()
dm = DataManager(['miller_array', 'phil'])
dm.process_miller_array_file(data_mtz)
dm._miller_array_labels[data_mtz] = label_subset
dm.write_phil_file(dm.export_phil_scope().as_str(),
filename='test.phil',
overwrite=True)
loaded_phil = iotbx.phil.parse(file_name='test.phil')
new_dm = DataManager(['miller_array', 'phil'])
new_dm.load_phil_scope(loaded_phil)
fs = new_dm.get_reflection_file_server(array_type='x_ray')
assert len(fs.get_miller_arrays(None)) == 13
fs = new_dm.get_reflection_file_server(array_type='electron')
assert len(fs.get_miller_arrays(None)) == 0
os.remove('test.phil')
def test_miller_array_datatype():
data_dir = os.path.dirname(os.path.abspath(__file__))
data_mtz = os.path.join(data_dir, 'data',
'insulin_unmerged_cutted_from_ccp4.mtz')
dm = DataManager(['miller_array', 'phil'])
dm.process_miller_array_file(data_mtz)
# test labels
labels = ['M_ISYM', 'BATCH', 'I,SIGI,merged', 'IPR,SIGIPR,merged',
'FRACTIONCALC', 'XDET', 'YDET', 'ROT', 'WIDTH', 'LP', 'MPART',
'FLAG', 'BGPKRATIOS']
for label in dm.get_miller_array_labels():
assert(label in labels)
assert(len(dm.get_miller_arrays()) == len(dm.get_miller_array_labels()))
# test access by label
label = dm.get_miller_array_labels()[3]
new_label = dm.get_miller_arrays(labels=[label])[0].info().label_string()
assert(label == new_label)
# test custom PHIL
dm.write_phil_file('test.phil', dm.export_phil_scope().as_str(), True)
loaded_phil = iotbx.phil.parse(file_name='test.phil')
new_dm = DataManager(['miller_array', 'phil'])
new_dm.load_phil_scope(loaded_phil)
assert(data_mtz == new_dm.get_default_miller_array_name())
for label in new_dm.get_miller_array_labels():
assert(label in labels)
os.remove('test.phil')
# test type
assert(dm.get_miller_array_type() == 'x_ray')
dm.set_miller_array_type(data_mtz, 'electron')
assert(dm.get_miller_array_type() == 'electron')
dm.write_phil_file('test_phil', dm.export_phil_scope().as_str(), True)
loaded_phil = iotbx.phil.parse(file_name='test_phil')
new_dm.load_phil_scope(loaded_phil)
assert(new_dm.get_miller_array_type() == 'electron')
new_dm = DataManager(['miller_array'])
try:
new_dm.set_default_miller_array_type('q')
except Sorry:
pass
new_dm.set_default_miller_array_type('neutron')
new_dm.process_miller_array_file(data_mtz)
assert(new_dm.get_miller_array_type() == 'neutron')
# test file server
fs1 = dm.get_reflection_file_server()
fs2 = dm.get_reflection_file_server([data_mtz, data_mtz])
assert(2*len(fs1.miller_arrays) == len(fs2.miller_arrays))
cs = crystal.symmetry(
unit_cell=dm.get_miller_arrays()[0].crystal_symmetry().unit_cell(),
space_group_symbol='P1')
fs = dm.get_reflection_file_server(crystal_symmetry=cs)
assert(fs.crystal_symmetry.is_similar_symmetry(cs))
assert(not fs.crystal_symmetry.is_similar_symmetry(
dm.get_miller_arrays()[0].crystal_symmetry()))
fs = dm.get_reflection_file_server(labels=['I,SIGI,merged'])
assert(len(fs.get_miller_arrays(None)) == 1)
miller_array = fs.get_amplitudes(None,None,True,None,None)
assert(miller_array.info().label_string() == 'I,as_amplitude_array,merged')
fs = dm.get_reflection_file_server(array_type='x_ray')
assert(len(fs.get_miller_arrays(None)) == 0)
fs = dm.get_reflection_file_server(array_type='electron')
assert(len(fs.get_miller_arrays(None)) == 13)
fs = dm.get_reflection_file_server(filenames=[data_mtz],
labels=[['I,SIGI,merged', 'IPR,SIGIPR,merged']], array_type='neutron')
assert(len(fs.get_miller_arrays(None)) == 0)
dm.set_miller_array_type(data_mtz, 'x_ray')
fs = dm.get_reflection_file_server(filenames=[data_mtz],
labels=[['I,SIGI,merged', 'IPR,SIGIPR,merged']], array_type='x_ray')
assert(len(fs.get_miller_arrays(data_mtz)) == 2)
