def test_xds_scalerA(regression_test, ccp4, xds, dials_data, run_in_tmpdir,
nproc):
if nproc is not None:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
template = dials_data("insulin").join("insulin_1_###.img").strpath
tmpdir = run_in_tmpdir.strpath
from xia2.Modules.Indexer.XDSIndexer import XDSIndexer
from xia2.Modules.Integrater.XDSIntegrater import XDSIntegrater
from xia2.Modules.Scaler.XDSScalerA import XDSScalerA
indexer = XDSIndexer()
indexer.set_working_directory(tmpdir)
from dxtbx.model.experiment_list import ExperimentListTemplateImporter
importer = ExperimentListTemplateImporter([template])
experiments = importer.experiments
imageset = experiments.imagesets()[0]
indexer.add_indexer_imageset(imageset)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, imageset.get_beam().get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
with mock.patch.object(sys, "argv", []):
sweep = XSweep("SWEEP1", wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
from xia2.Modules.Refiner.XDSRefiner import XDSRefiner
refiner = XDSRefiner()
refiner.set_working_directory(tmpdir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
integrater = XDSIntegrater()
integrater.set_working_directory(tmpdir)
integrater.setup_from_image(imageset.get_path(1))
integrater.set_integrater_refiner(refiner)
# integrater.set_integrater_indexer(indexer)
integrater.set_integrater_sweep(sweep)
integrater.set_integrater_sweep_name("SWEEP1")
integrater.set_integrater_project_info("CRYST1", "WAVE1", "SWEEP1")
scaler = XDSScalerA(base_path=pathlib.Path(tmpdir))
scaler.add_scaler_integrater(integrater)
scaler.set_scaler_xcrystal(cryst)
scaler.set_scaler_project_info("CRYST1", "WAVE1")
check_scaler_files_exist(scaler)
# test serialization of scaler
json_str = scaler.as_json()
# print json_str
scaler2 = XDSScalerA.from_json(string=json_str)
scaler2.set_scaler_xcrystal(cryst)
check_scaler_files_exist(scaler2)
scaler2.set_scaler_done(False)
check_scaler_files_exist(scaler2)
scaler2._scalr_integraters = {} # XXX
scaler2.add_scaler_integrater(integrater)
scaler2.set_scaler_prepare_done(False)
check_scaler_files_exist(scaler2)
def exercise_dials_refiner(nproc=None):
if not have_xia2_regression:
print "Skipping exercise_dials_refiner(): xia2_regression not configured"
return
if nproc is not None:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
xia2_demo_data = os.path.join(xia2_regression, "test_data", "mad_example")
template = os.path.join(xia2_demo_data, "12287_1_E%i_%03i.img")
cwd = os.path.abspath(os.curdir)
tmp_dir = os.path.abspath(open_tmp_directory())
os.chdir(tmp_dir)
from xia2.Modules.Indexer.DialsIndexer import DialsIndexer
from xia2.Modules.Refiner.DialsRefiner import DialsRefiner
from xia2.Modules.Integrater.DialsIntegrater import DialsIntegrater
indexer1 = DialsIndexer()
indexer1.set_working_directory(tmp_dir)
indexer1.setup_from_image(template % (1, 1))
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav1 = XWavelength("WAVE1", cryst, indexer1.get_wavelength())
samp1 = XSample("X1", cryst)
directory, image = os.path.split(template % (1, 1))
sweep1 = XSweep('SWEEP1', wav1, samp1, directory=directory, image=image)
indexer1.set_indexer_sweep(sweep1)
indexer2 = DialsIndexer()
indexer2.set_working_directory(tmp_dir)
indexer2.setup_from_image(template % (2, 1))
wav2 = XWavelength("WAVE2", cryst, indexer2.get_wavelength())
samp2 = XSample("X2", cryst)
directory, image = os.path.split(template % (2, 1))
sweep2 = XSweep('SWEEP2', wav2, samp2, directory=directory, image=image)
indexer2.set_indexer_sweep(sweep2)
refiner = DialsRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(indexer1)
refiner.add_refiner_indexer(indexer2)
refined_experiment_list = refiner.get_refined_experiment_list()
assert refined_experiment_list is not None
assert len(refined_experiment_list.detectors()) == 1
refined_detector = refined_experiment_list[0].detector
# test serialization of refiner
json_str = refiner.as_json()
#print json_str
refiner2 = DialsRefiner.from_json(string=json_str)
refined_expts_2 = refiner2.get_refined_experiment_list()
assert refined_expts_2[0].detector == refined_detector
refiner2.set_refiner_finish_done(False)
refined_expts_2 = refiner2.get_refined_experiment_list()
assert refined_expts_2[0].detector == refined_detector
refiner2.set_refiner_done(False)
refined_expts_2 = refiner2.get_refined_experiment_list()
assert refined_expts_2[0].detector == refined_detector
refiner2.set_refiner_prepare_done(False)
refined_expts_2 = refiner2.get_refined_experiment_list()
assert refined_expts_2[0].detector == refined_detector
assert (indexer1.get_indexer_experiment_list()[0].detector !=
indexer2.get_indexer_experiment_list()[0].detector)
assert (indexer1.get_indexer_experiment_list()[0].beam !=
indexer2.get_indexer_experiment_list()[0].beam)
indexer1.set_indexer_experiment_list(refined_experiment_list[0:1])
indexer2.set_indexer_experiment_list(refined_experiment_list[1:2])
assert (indexer1.get_indexer_experiment_list()[0].detector ==
indexer2.get_indexer_experiment_list()[0].detector)
assert (indexer1.get_indexer_experiment_list()[0].goniometer ==
indexer2.get_indexer_experiment_list()[0].goniometer)
def exercise_dials_integrater(xia2_regression_build, tmp_dir, nproc=None):
if nproc:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
xia2_demo_data = os.path.join(xia2_regression_build, "test_data",
"insulin")
template = os.path.join(xia2_demo_data, "insulin_1_###.img")
from xia2.Modules.Indexer.DialsIndexer import DialsIndexer
from xia2.Modules.Integrater.DialsIntegrater import DialsIntegrater
from dxtbx.datablock import DataBlockTemplateImporter
indexer = DialsIndexer()
indexer.set_working_directory(tmp_dir)
importer = DataBlockTemplateImporter([template])
datablocks = importer.datablocks
imageset = datablocks[0].extract_imagesets()[0]
indexer.add_indexer_imageset(imageset)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, imageset.get_beam().get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
from xia2.Modules.Refiner.DialsRefiner import DialsRefiner
refiner = DialsRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
#refiner.refine()
integrater = DialsIntegrater()
integrater.set_working_directory(tmp_dir)
integrater.setup_from_image(imageset.get_path(1))
integrater.set_integrater_refiner(refiner)
#integrater.set_integrater_indexer(indexer)
integrater.set_integrater_sweep(sweep)
integrater.integrate()
integrater_intensities = integrater.get_integrater_intensities()
assert os.path.exists(integrater_intensities)
from iotbx.reflection_file_reader import any_reflection_file
reader = any_reflection_file(integrater_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
expected_reflections = 48456
assert abs(mtz_object.n_reflections() -
expected_reflections) < 300, mtz_object.n_reflections()
assert mtz_object.column_labels() == [
'H', 'K', 'L', 'M_ISYM', 'BATCH', 'IPR', 'SIGIPR', 'I', 'SIGI', 'BG',
'SIGBG', 'FRACTIONCALC', 'XDET', 'YDET', 'ROT', 'LP', 'QE'
]
assert integrater.get_integrater_wedge() == (1, 45)
assert approx_equal(integrater.get_integrater_cell(),
(78.14, 78.14, 78.14, 90, 90, 90),
eps=1e-1)
# test serialization of integrater
json_str = integrater.as_json()
#print(json_str)
integrater2 = DialsIntegrater.from_json(string=json_str)
integrater2.set_integrater_sweep(sweep, reset=False)
integrater2_intensities = integrater.get_integrater_intensities()
assert integrater2_intensities == integrater_intensities
integrater2.set_integrater_finish_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() -
expected_reflections) < 300, mtz_object.n_reflections()
integrater2.set_integrater_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() -
expected_reflections) < 300, mtz_object.n_reflections()
integrater2.set_integrater_prepare_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() -
expected_reflections) < 300, mtz_object.n_reflections()
def exercise_xds_indexer(dials_regression, tmp_dir, nproc=None):
if nproc is not None:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_###.img")
from xia2.Modules.Indexer.XDSIndexer import XDSIndexer
indexer = XDSIndexer()
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)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, indexer.get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
indexer.index()
assert approx_equal(indexer.get_indexer_cell(),
(78.076, 78.076, 78.076, 90, 90, 90),
eps=1), indexer.get_indexer_cell()
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, (94.4221, 94.5096), eps=1e-1)
assert indexer.get_indexer_images() == [(1, 5), (20, 24), (41, 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 = XDSIndexer.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 exercise_mosflm_integrater(xia2_regression_build, tmp_dir, nproc):
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
xia2_demo_data = os.path.join(xia2_regression_build, "test_data",
"insulin")
template = os.path.join(xia2_demo_data, "insulin_1_###.img")
# otherwise if this test is running multiple times simultaneously two mosflm
# processes try to write to the same genfile
os.environ['CCP4_SCR'] = tmp_dir
from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
from xia2.Modules.Integrater.MosflmIntegrater import MosflmIntegrater
from dxtbx.datablock import DataBlockTemplateImporter
indexer = MosflmIndexer()
indexer.set_working_directory(tmp_dir)
importer = DataBlockTemplateImporter([template])
datablocks = importer.datablocks
imageset = datablocks[0].extract_imagesets()[0]
indexer.add_indexer_imageset(imageset)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, indexer.get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
from xia2.Modules.Refiner.MosflmRefiner import MosflmRefiner
refiner = MosflmRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
nref_error = 500
integrater = MosflmIntegrater()
integrater.set_working_directory(tmp_dir)
integrater.setup_from_image(imageset.get_path(1))
integrater.set_integrater_refiner(refiner)
#integrater.set_integrater_indexer(indexer)
integrater.set_integrater_sweep(sweep)
integrater.integrate()
integrater_intensities = integrater.get_integrater_intensities()
assert os.path.exists(integrater_intensities)
from iotbx.reflection_file_reader import any_reflection_file
reader = any_reflection_file(integrater_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() - 81116) < nref_error, \
mtz_object.n_reflections()
assert mtz_object.column_labels() == [
'H', 'K', 'L', 'M_ISYM', 'BATCH', 'I', 'SIGI', 'IPR', 'SIGIPR',
'FRACTIONCALC', 'XDET', 'YDET', 'ROT', 'WIDTH', 'LP', 'MPART', 'FLAG',
'BGPKRATIOS'
]
assert integrater.get_integrater_wedge() == (1, 45)
assert approx_equal(integrater.get_integrater_cell(),
(78.014, 78.014, 78.014, 90.0, 90.0, 90.0),
eps=1e-2)
# test serialization of integrater
json_str = integrater.as_json()
#print json_str
integrater2 = MosflmIntegrater.from_json(string=json_str)
integrater2.set_integrater_sweep(sweep, reset=False)
integrater2_intensities = integrater.get_integrater_intensities()
assert integrater2_intensities == integrater_intensities
integrater2.set_integrater_finish_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() - 81116) < nref_error, \
mtz_object.n_reflections()
integrater2.set_integrater_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() - 81116) < nref_error, \
mtz_object.n_reflections()
integrater2.set_integrater_prepare_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert abs(mtz_object.n_reflections() - 81116) < nref_error, \
mtz_object.n_reflections()
self.integrate()
from xia2.Wrappers.Dials.ExportXDSASCII import ExportXDSASCII
exporter = ExportXDSASCII()
exporter.set_experiments_filename(self.get_integrated_experiments())
exporter.set_reflections_filename(self.get_integrated_reflections())
exporter.set_working_directory(self.get_working_directory())
auto_logfiler(exporter)
self._intgr_corrected_hklout = os.path.join(
self.get_working_directory(), '%i_DIALS.HKL' % exporter.get_xpid())
exporter.set_hkl_filename(self._intgr_corrected_hklout)
exporter.run()
assert os.path.exists(self._intgr_corrected_hklout)
return self._intgr_corrected_hklout
if __name__ == '__main__':
# run a demo test
di = DialsIntegrater()
di.setup_from_image(sys.argv[1])
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, di.get_wavelength())
directory, image = os.path.split(sys.argv[1])
sweep = XSweep('SWEEP1', wav, directory=directory, image=image)
di.set_integrater_sweep(sweep)
di.integrate()
exporter = ExportXDSASCII()
exporter.set_experiments_filename(self.get_integrated_experiments())
exporter.set_reflections_filename(self.get_integrated_reflections())
exporter.set_working_directory(self.get_working_directory())
auto_logfiler(exporter)
self._intgr_corrected_hklout = os.path.join(
self.get_working_directory(), "%i_DIALS.HKL" % exporter.get_xpid())
exporter.set_hkl_filename(self._intgr_corrected_hklout)
exporter.run()
assert os.path.exists(self._intgr_corrected_hklout)
return self._intgr_corrected_hklout
if __name__ == "__main__":
# run a demo test
di = DialsIntegrater()
di.setup_from_image(sys.argv[1])
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, di.get_wavelength())
directory, image = os.path.split(sys.argv[1])
sweep = XSweep("SWEEP1", wav, directory=directory, image=image)
di.set_integrater_sweep(sweep)
di.integrate()
def exercise_dials_integrater(dials_data, tmp_dir, nproc=None):
if nproc:
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
template = dials_data("insulin").join("insulin_1_###.img").strpath
indexer = DialsIndexer()
indexer.set_working_directory(tmp_dir)
importer = ExperimentListTemplateImporter([template])
experiments = importer.experiments
imageset = experiments.imagesets()[0]
indexer.add_indexer_imageset(imageset)
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, imageset.get_beam().get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
sweep = XSweep("SWEEP1", wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
refiner = DialsRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
# refiner.refine()
integrater = DialsIntegrater()
integrater.set_output_format("hkl")
integrater.set_working_directory(tmp_dir)
integrater.setup_from_image(imageset.get_path(1))
integrater.set_integrater_refiner(refiner)
# integrater.set_integrater_indexer(indexer)
integrater.set_integrater_sweep(sweep)
integrater.integrate()
integrater_intensities = integrater.get_integrater_intensities()
assert os.path.exists(integrater_intensities)
reader = any_reflection_file(integrater_intensities)
assert reader.file_type() == "ccp4_mtz", repr(integrater_intensities)
mtz_object = reader.file_content()
expected_reflections = 47623
assert (abs(mtz_object.n_reflections() - expected_reflections) <
300), mtz_object.n_reflections()
assert mtz_object.column_labels() == [
"H",
"K",
"L",
"M_ISYM",
"BATCH",
"IPR",
"SIGIPR",
"I",
"SIGI",
"BG",
"SIGBG",
"FRACTIONCALC",
"XDET",
"YDET",
"ROT",
"LP",
"QE",
]
assert integrater.get_integrater_wedge() == (1, 45)
assert integrater.get_integrater_cell() == pytest.approx(
(78.14, 78.14, 78.14, 90, 90, 90), abs=1e-1)
# test serialization of integrater
json_str = integrater.as_json()
# print(json_str)
integrater2 = DialsIntegrater.from_json(string=json_str)
integrater2.set_integrater_sweep(sweep, reset=False)
integrater2_intensities = integrater.get_integrater_intensities()
assert integrater2_intensities == integrater_intensities
integrater2.set_integrater_finish_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - expected_reflections) <
300), mtz_object.n_reflections()
integrater2.set_integrater_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - expected_reflections) <
300), mtz_object.n_reflections()
integrater2.set_integrater_prepare_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - expected_reflections) <
300), mtz_object.n_reflections()
# Test that diamond anvil cell attenuation correction does something.
# That it does the right thing is left as a matter for the DIALS tests.
integrater3 = DialsIntegrater.from_json(string=json_str)
integrater3.set_integrater_sweep(sweep, reset=False)
integrater3.set_integrater_done(False)
integrater3.high_pressure = True
# Don't get .hkl output because we're applying the attenuation correction to data
# that weren't actually collected with a diamond anvil cell and some integrated
# intensities will be rather nonsensical, which causes an error
# 'cctbx Error: Inconsistent observation/sigma pair in columns: IPR, SIGIPR',
# when some internal .hkl consistency checks are run, which is not meaningful here.
integrater3.set_output_format("pickle")
# Compare the first ten profile-fitted integrated intensities without correction.
control_reflections = flex.reflection_table.from_file(
integrater2.get_integrated_reflections())
valid = control_reflections.get_flags(
control_reflections.flags.integrated_prf)
valid = valid.iselection()[:10]
control_reflections = control_reflections.select(valid)
# Get the first ten profile-fitted integrated intensities with DAC correction.
corrected_reflections = flex.reflection_table.from_file(
integrater3.get_integrated_reflections())
valid = corrected_reflections.get_flags(
corrected_reflections.flags.integrated_prf)
valid = valid.iselection()[:10]
corrected_reflections = corrected_reflections.select(valid)
# Check that we're comparing equivalent reflections.
assert control_reflections["miller_index"] == corrected_reflections[
"miller_index"]
control_intensities = control_reflections["intensity.prf.value"]
corrected_intensities = corrected_reflections["intensity.prf.value"]
# Check that the reflection intensities are not the same.
assert pytest.approx(control_intensities) != corrected_intensities
def exercise_dials_indexer(dials_regression, tmp_dir, nproc=None):
if nproc is not None:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_###.img")
from xia2.Modules.Indexer.DialsIndexer import DialsIndexer
indexer = DialsIndexer()
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)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, imageset.get_beam().get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
indexer.index()
assert approx_equal(indexer.get_indexer_cell(),
(78.14, 78.14, 78.14, 90, 90, 90),
eps=1e-1)
solution = indexer.get_solution()
assert approx_equal(solution['rmsd'], 0.041, eps=1e-2)
assert approx_equal(solution['metric'], 0.027, eps=1e-2)
assert solution['number'] == 22
assert solution['lattice'] == 'cI'
beam_centre = indexer.get_indexer_beam_centre()
assert approx_equal(beam_centre, (94.4223, 94.5097), eps=1e-2)
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 = DialsIndexer.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())
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 exercise_xds_integrater(dials_regression, tmp_dir, nproc=None):
if nproc:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_###.img")
from xia2.Modules.Indexer.XDSIndexer import XDSIndexer
from xia2.Modules.Integrater.XDSIntegrater import XDSIntegrater
indexer = XDSIndexer()
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)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, indexer.get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
sweep = XSweep('SWEEP1', wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
from xia2.Modules.Refiner.XDSRefiner import XDSRefiner
refiner = XDSRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
#refiner.refine()
integrater = XDSIntegrater()
integrater.set_working_directory(tmp_dir)
integrater.setup_from_image(imageset.get_path(1))
integrater.set_integrater_refiner(refiner)
integrater.set_integrater_sweep(sweep)
integrater.integrate()
from iotbx.reflection_file_reader import any_reflection_file
integrater_intensities = integrater.get_integrater_intensities()
assert os.path.exists(integrater_intensities)
reader = any_reflection_file(integrater_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert approx_equal(mtz_object.n_reflections(), 50000, eps=400)
assert mtz_object.column_labels() == [
'H', 'K', 'L', 'M_ISYM', 'BATCH', 'I', 'SIGI', 'FRACTIONCALC', 'XDET',
'YDET', 'ROT', 'LP', 'FLAG'
]
corrected_intensities = integrater.get_integrater_corrected_intensities()
assert os.path.exists(corrected_intensities)
reader = any_reflection_file(corrected_intensities)
assert reader.file_type() == "xds_ascii"
ma = reader.as_miller_arrays(merge_equivalents=False)[0]
assert approx_equal(ma.size(), 50000, eps=400)
assert integrater.get_integrater_wedge() == (1, 45)
assert approx_equal(integrater.get_integrater_cell(),
[78.066, 78.066, 78.066, 90, 90, 90],
eps=1)
assert approx_equal(integrater.get_integrater_mosaic_min_mean_max(),
(0.180, 0.180, 0.180),
eps=1e-1)
# test serialization of integrater
json_str = integrater.as_json()
#print(json_str)
integrater2 = XDSIntegrater.from_json(string=json_str)
integrater2.set_integrater_sweep(sweep, reset=False)
integrater2_intensities = integrater.get_integrater_intensities()
assert integrater2_intensities == integrater_intensities
integrater2.set_integrater_finish_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert approx_equal(mtz_object.n_reflections(), 50000, eps=400)
integrater2.set_integrater_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert approx_equal(mtz_object.n_reflections(), 50000, eps=450)
integrater2.set_integrater_prepare_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert approx_equal(mtz_object.n_reflections(), 50100, eps=400)
def exercise_mosflm_integrater(dials_data, tmp_dir, nproc):
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
template = dials_data("insulin").join("insulin_1_###.img").strpath
# otherwise if this test is running multiple times simultaneously two mosflm
# processes try to write to the same genfile
os.environ["CCP4_SCR"] = tmp_dir
from xia2.Modules.Indexer.MosflmIndexer import MosflmIndexer
from xia2.Modules.Integrater.MosflmIntegrater import MosflmIntegrater
from dxtbx.model.experiment_list import ExperimentListTemplateImporter
indexer = MosflmIndexer()
indexer.set_working_directory(tmp_dir)
importer = ExperimentListTemplateImporter([template])
experiments = importer.experiments
imageset = experiments.imagesets()[0]
indexer.add_indexer_imageset(imageset)
from xia2.Schema.XCrystal import XCrystal
from xia2.Schema.XWavelength import XWavelength
from xia2.Schema.XSweep import XSweep
from xia2.Schema.XSample import XSample
cryst = XCrystal("CRYST1", None)
wav = XWavelength("WAVE1", cryst, indexer.get_wavelength())
samp = XSample("X1", cryst)
directory, image = os.path.split(imageset.get_path(1))
sweep = XSweep("SWEEP1", wav, samp, directory=directory, image=image)
indexer.set_indexer_sweep(sweep)
from xia2.Modules.Refiner.MosflmRefiner import MosflmRefiner
refiner = MosflmRefiner()
refiner.set_working_directory(tmp_dir)
refiner.add_refiner_indexer(sweep.get_epoch(1), indexer)
nref_error = 500
integrater = MosflmIntegrater()
integrater.set_working_directory(tmp_dir)
integrater.setup_from_image(imageset.get_path(1))
integrater.set_integrater_refiner(refiner)
# integrater.set_integrater_indexer(indexer)
integrater.set_integrater_sweep(sweep)
integrater.integrate()
integrater_intensities = integrater.get_integrater_intensities()
assert os.path.exists(integrater_intensities)
from iotbx.reflection_file_reader import any_reflection_file
reader = any_reflection_file(integrater_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - 81116) <
nref_error), mtz_object.n_reflections()
assert mtz_object.column_labels() == [
"H",
"K",
"L",
"M_ISYM",
"BATCH",
"I",
"SIGI",
"IPR",
"SIGIPR",
"FRACTIONCALC",
"XDET",
"YDET",
"ROT",
"WIDTH",
"LP",
"MPART",
"FLAG",
"BGPKRATIOS",
]
assert integrater.get_integrater_wedge() == (1, 45)
assert approx_equal(
integrater.get_integrater_cell(),
(78.014, 78.014, 78.014, 90.0, 90.0, 90.0),
eps=1e-2,
)
# test serialization of integrater
json_str = integrater.as_json()
# print json_str
integrater2 = MosflmIntegrater.from_json(string=json_str)
integrater2.set_integrater_sweep(sweep, reset=False)
integrater2_intensities = integrater.get_integrater_intensities()
assert integrater2_intensities == integrater_intensities
integrater2.set_integrater_finish_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - 81116) <
nref_error), mtz_object.n_reflections()
integrater2.set_integrater_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - 81116) <
nref_error), mtz_object.n_reflections()
integrater2.set_integrater_prepare_done(False)
integrater2_intensities = integrater2.get_integrater_intensities()
assert os.path.exists(integrater2_intensities)
reader = any_reflection_file(integrater2_intensities)
assert reader.file_type() == "ccp4_mtz"
mtz_object = reader.file_content()
assert (abs(mtz_object.n_reflections() - 81116) <
nref_error), mtz_object.n_reflections()