def exercise_dials_indexer(dials_data, tmp_dir, nproc=None):
if nproc is not None:
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)
indexer.index()
assert indexer.get_indexer_cell() == pytest.approx(
(78.14, 78.14, 78.14, 90, 90, 90), rel=1e-3)
solution = indexer.get_solution()
assert solution["rmsd"] == pytest.approx(0.03545, abs=1e-3)
assert solution["metric"] == pytest.approx(0.02517, abs=5e-3)
assert solution["number"] == 22
assert solution["lattice"] == "cI"
beam_centre = indexer.get_indexer_beam_centre()
assert beam_centre == pytest.approx((94.41567208118963, 94.51337522659865),
abs=1e-3)
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()
indexer2 = DialsIndexer.from_json(string=json_str)
indexer2.index()
assert indexer.get_indexer_cell() == pytest.approx(
indexer2.get_indexer_cell())
assert indexer.get_indexer_beam_centre() == pytest.approx(
indexer2.get_indexer_beam_centre())
indexer.eliminate()
indexer2.eliminate()
assert indexer.get_indexer_cell() == pytest.approx(
indexer2.get_indexer_cell())
assert indexer.get_indexer_lattice() == "hR"
assert indexer2.get_indexer_lattice() == "hR"
def exercise_dials_indexer(xia2_regression_build, 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(xia2_regression_build, "test_data",
"insulin")
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_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_indexer(dials_data, tmp_dir, nproc=None):
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
from xia2.Modules.Indexer.DialsIndexer import DialsIndexer
indexer = DialsIndexer()
indexer.set_working_directory(tmp_dir)
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))
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_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_indexer(nproc=None):
if not have_dials_regression:
print "Skipping exercise_dials_indexer(): dials_regression not configured"
return
if nproc is not None:
from xia2.Handlers.Flags import Flags
Flags.set_parallel(nproc)
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.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'
