def test_mosflm_indexer(regression_test, ccp4, dials_data, run_in_tmpdir):
template = dials_data("insulin").join("insulin_1_###.img").strpath
from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
indexer = MosflmIndexer()
indexer.set_working_directory(run_in_tmpdir.strpath)
from dxtbx.model.experiment_list import ExperimentListTemplateImporter
importer = ExperimentListTemplateImporter([template])
experiments = importer.experiments
imageset = experiments.imagesets()[0]
indexer.add_indexer_imageset(imageset)
with mock.patch.object(
sys, "argv",
[]): # otherwise indexing fails when running pytest with '--runslow'
indexer.index()
assert indexer.get_indexer_cell() == pytest.approx(
(78.6657, 78.6657, 78.6657, 90.0, 90.0, 90.0), abs=1e-3)
experiment = indexer.get_indexer_experiment_list()[0]
sgi = experiment.crystal.get_space_group().info()
assert sgi.type().number() == 197
beam_centre = indexer.get_indexer_beam_centre()
assert beam_centre == pytest.approx((94.34, 94.57), abs=1e-2)
assert indexer.get_indexer_images() == [(1, 1), (22, 22), (45, 45)]
print(indexer.get_indexer_experiment_list()[0].crystal)
print(indexer.get_indexer_experiment_list()[0].detector)
# test serialization of indexer
json_str = indexer.as_json()
print(json_str)
indexer2 = MosflmIndexer.from_json(string=json_str)
indexer2.index()
assert indexer.get_indexer_cell() == pytest.approx(
indexer2.get_indexer_cell(), abs=1e-6)
assert indexer.get_indexer_beam_centre() == pytest.approx(
indexer2.get_indexer_beam_centre(), abs=1e-6)
assert indexer2.get_indexer_images() == [
[1, 1],
[22, 22],
[45, 45],
] # coming from json these are now lists
indexer.eliminate()
indexer2.eliminate()
assert indexer.get_indexer_cell() == pytest.approx(
indexer2.get_indexer_cell(), abs=1e-6)
assert indexer.get_indexer_lattice() == "hR"
assert indexer2.get_indexer_lattice() == "hR"
def exercise_mosflm_indexer():
if not have_dials_regression:
print "Skipping exercise_mosflm_indexer(): dials_regression not configured"
return
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_###.img")
cwd = os.path.abspath(os.curdir)
tmp_dir = os.path.abspath(open_tmp_directory())
os.chdir(tmp_dir)
from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
indexer = MosflmIndexer()
indexer.set_working_directory(tmp_dir)
from dxtbx.datablock import DataBlockTemplateImporter
importer = DataBlockTemplateImporter([template])
datablocks = importer.datablocks
imageset = datablocks[0].extract_imagesets()[0]
indexer.add_indexer_imageset(imageset)
indexer.index()
assert approx_equal(indexer.get_indexer_cell(),
(78.6657, 78.6657, 78.6657, 90.0, 90.0, 90.0), eps=1e-3)
experiment = indexer.get_indexer_experiment_list()[0]
sgi = experiment.crystal.get_space_group().info()
assert sgi.type().number() == 197
beam_centre = indexer.get_indexer_beam_centre()
assert approx_equal(beam_centre, (94.34, 94.57), eps=1e-2)
assert indexer.get_indexer_images() == [(1, 1), (22, 22), (45, 45)]
print indexer.get_indexer_experiment_list()[0].crystal
print indexer.get_indexer_experiment_list()[0].detector
# test serialization of indexer
json_str = indexer.as_json()
print json_str
indexer2 = MosflmIndexer.from_json(string=json_str)
indexer2.index()
assert approx_equal(indexer.get_indexer_cell(), indexer2.get_indexer_cell())
assert approx_equal(
indexer.get_indexer_beam_centre(), indexer2.get_indexer_beam_centre())
assert approx_equal(
indexer.get_indexer_images(), indexer2.get_indexer_images())
indexer.eliminate()
indexer2.eliminate()
assert approx_equal(indexer.get_indexer_cell(), indexer2.get_indexer_cell())
assert indexer.get_indexer_lattice() == 'hR'
assert indexer2.get_indexer_lattice() == 'hR'
def test_mosflm_indexer(ccp4, xia2_regression_build, tmpdir):
template = os.path.join(xia2_regression_build, "test_data", "insulin",
"insulin_1_###.img")
tmpdir.chdir()
from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
indexer = MosflmIndexer()
indexer.set_working_directory(tmpdir.strpath)
from dxtbx.datablock import DataBlockTemplateImporter
importer = DataBlockTemplateImporter([template])
datablocks = importer.datablocks
imageset = datablocks[0].extract_imagesets()[0]
indexer.add_indexer_imageset(imageset)
with mock.patch.object(
sys, 'argv',
[]): # otherwise indexing fails when running pytest with '--runslow'
indexer.index()
assert indexer.get_indexer_cell() == pytest.approx(
(78.6657, 78.6657, 78.6657, 90.0, 90.0, 90.0), abs=1e-3)
experiment = indexer.get_indexer_experiment_list()[0]
sgi = experiment.crystal.get_space_group().info()
assert sgi.type().number() == 197
beam_centre = indexer.get_indexer_beam_centre()
assert beam_centre == pytest.approx((94.34, 94.57), abs=1e-2)
assert indexer.get_indexer_images() == [(1, 1), (22, 22), (45, 45)]
print(indexer.get_indexer_experiment_list()[0].crystal)
print(indexer.get_indexer_experiment_list()[0].detector)
# test serialization of indexer
json_str = indexer.as_json()
print(json_str)
indexer2 = MosflmIndexer.from_json(string=json_str)
indexer2.index()
assert indexer.get_indexer_cell() == pytest.approx(
indexer2.get_indexer_cell(), abs=1e-6)
assert indexer.get_indexer_beam_centre() == pytest.approx(
indexer2.get_indexer_beam_centre(), abs=1e-6)
assert indexer2.get_indexer_images() == [[1, 1], [22, 22], [
45, 45
]] # coming from json these are now lists
indexer.eliminate()
indexer2.eliminate()
assert indexer.get_indexer_cell() == pytest.approx(
indexer2.get_indexer_cell(), abs=1e-6)
assert indexer.get_indexer_lattice() == 'hR'
assert indexer2.get_indexer_lattice() == 'hR'
def exercise_mosflm_index():
if not have_dials_regression:
print 'SKIP: dials_regression not configured'
exit(0)
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
cwd = os.path.abspath(os.curdir)
tmp_dir1 = os.path.abspath(open_tmp_directory())
os.chdir(tmp_dir1)
from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
m1 = MosflmIndexer()
m1.set_working_directory(tmp_dir1)
m1.setup_from_image(template % 1)
m1.index()
os.chdir(cwd)
tmp_dir2 = os.path.abspath(open_tmp_directory())
os.chdir(tmp_dir2)
from Original import Mosflm
m2 = Mosflm()
m2.set_working_directory(tmp_dir2)
m2.setup_from_image(template % 1)
m2.index()
assert m1.get_indexer_beam_centre() == m2.get_indexer_beam_centre()
assert m1.get_indexer_distance() == m2.get_indexer_distance()
assert m1.get_indexer_cell() == m2.get_indexer_cell()
assert m1.get_indexer_lattice() == m2.get_indexer_lattice()
assert m1.get_indexer_mosaic() == m2.get_indexer_mosaic()
os.chdir(cwd)
return
def exercise_mosflm_integrate(nproc):
if not have_dials_regression:
raise RuntimeError, 'dials_regression not available'
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
from xia2.Handlers.Flags import Flags
Flags.set_parallel(nproc)
cwd = os.path.abspath(os.curdir)
tmp_dir1 = os.path.abspath(open_tmp_directory())
os.chdir(tmp_dir1)
from xia2.Modules.Integrater.MosflmIntegrater import MosflmIntegrater
from xia2.Modules.Refiner.MosflmRefiner import MosflmRefiner
from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
indexer = MosflmIndexer()
indexer.set_working_directory(tmp_dir1)
indexer.setup_from_image(template % 1)
refiner = MosflmRefiner()
refiner.add_refiner_indexer(1, indexer)
m1 = MosflmIntegrater()
m1.set_working_directory(tmp_dir1)
m1.setup_from_image(template % 1)
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, m1.get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(template %1)
sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
m1.set_integrater_sweep(sweep)
m1.set_integrater_refiner(refiner)
m1.set_frame_wedge(1, 45)
m1.set_integrater_wedge(1, 45)
m1.integrate()
os.chdir(cwd)
tmp_dir2 = os.path.abspath(open_tmp_directory())
os.chdir(tmp_dir2)
from Original import Mosflm
m2 = Mosflm()
m2.set_working_directory(tmp_dir2)
m2.setup_from_image(template % 1)
m2.set_integrater_indexer(m2)
m2.set_integrater_sweep(sweep)
m2.set_frame_wedge(1, 45)
m2.set_integrater_wedge(1, 45)
m2.integrate()
from libtbx.test_utils import approx_equal
assert approx_equal(m1.get_integrater_cell(), m2.get_integrater_cell(),
eps=0.02)
assert approx_equal(indexer.get_indexer_distance(), m2.get_indexer_distance(),
eps=0.2)
assert approx_equal(m1.get_integrater_cell(),
m2.get_integrater_cell(), eps=0.02)
assert indexer.get_indexer_lattice() == m2.get_indexer_lattice()
assert approx_equal(indexer.get_indexer_mosaic(), m2.get_indexer_mosaic(),
eps=0.01)
m1_mtz = m1.get_integrater_intensities()
m2_mtz = m2.get_integrater_intensities()
from iotbx.reflection_file_reader import any_reflection_file
mas_1 = any_reflection_file(m1_mtz).as_miller_arrays()
mas_2 = any_reflection_file(m2_mtz).as_miller_arrays()
assert len(mas_1) == len(mas_2)
for ma1, ma2 in zip(mas_1, mas_2):
assert ma1.size() == ma2.size()
assert ma1.space_group() == ma2.space_group()
assert ma1.unit_cell().parameters() == ma2.unit_cell().parameters()
assert ma1.indices() == ma2.indices()
assert ma1.data() == ma2.data()
assert ma1.sigmas() == ma2.sigmas()
return