def DialsSpotfinder(self):
from xia2.Wrappers.Dials.Spotfinder import Spotfinder
spotfinder = Spotfinder(params=PhilIndex.params.dials.find_spots)
spotfinder.set_working_directory(self.get_working_directory())
spotfinder.setup_from_imageset(self.get_imageset())
auto_logfiler(spotfinder, 'SPOTFINDER')
return spotfinder
def DialsSpotfinder(self):
spotfinder = Spotfinder(params=PhilIndex.params.dials.find_spots)
spotfinder.set_working_directory(self.get_working_directory())
spotfinder.setup_from_imageset(self.get_imageset())
auto_logfiler(spotfinder, "SPOTFINDER")
return spotfinder
def DialsSpotfinder(self):
from xia2.Wrappers.Dials.Spotfinder import Spotfinder
spotfinder = Spotfinder(params=PhilIndex.params.dials.find_spots)
spotfinder.set_working_directory(self.get_working_directory())
spotfinder.setup_from_imageset(self.get_imageset())
auto_logfiler(spotfinder, 'SPOTFINDER')
return spotfinder
def exercise_dials_wrappers(template, nproc=None):
if nproc is not None:
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
scan_ranges = [(1, 45)]
image_range = (1, 45)
print("Begin importing")
importer = Import()
importer.setup_from_image(template % 1)
importer.set_image_range(image_range)
importer.run()
print("".join(importer.get_all_output()))
print("Done importing")
print("Begin spotfinding")
spotfinder = Spotfinder()
spotfinder.set_input_sweep_filename(importer.get_sweep_filename())
spotfinder.set_scan_ranges(scan_ranges)
spotfinder.run()
print("".join(spotfinder.get_all_output()))
print("Done spotfinding")
print("Begin indexing")
indexer = Index()
indexer.add_spot_filename(spotfinder.get_spot_filename())
indexer.add_sweep_filename(importer.get_sweep_filename())
indexer.run("fft3d")
print("".join(indexer.get_all_output()))
print("Done indexing")
print("Begin refining")
rbs = RefineBravaisSettings()
rbs.set_experiments_filename(indexer.get_experiments_filename())
rbs.set_indexed_filename(indexer.get_indexed_filename())
rbs.run()
print("".join(rbs.get_all_output()))
print("Done refining")
bravais_setting_22 = rbs.get_bravais_summary()[22]
assert bravais_setting_22["bravais"] == "cI"
assert bravais_setting_22["cb_op"] == "b+c,a+c,a+b"
assert bravais_setting_22["unit_cell"] == pytest.approx(
(78.14, 78.14, 78.14, 90, 90, 90), abs=1e-1
)
bravais_setting_22_json = bravais_setting_22["experiments_file"]
assert os.path.exists(bravais_setting_22_json)
print("Begin reindexing")
reindexer = Reindex()
reindexer.set_experiments_filename(indexer.get_experiments_filename())
reindexer.set_indexed_filename(indexer.get_indexed_filename())
reindexer.set_cb_op(bravais_setting_22["cb_op"])
reindexer.run()
assert os.path.exists(reindexer.get_reindexed_experiments_filename())
assert os.path.exists(reindexer.get_reindexed_reflections_filename())
print("".join(reindexer.get_all_output()))
print("Done reindexing")
print("Begin refining")
refiner = Refine()
refiner.set_experiments_filename(bravais_setting_22_json)
refiner.set_indexed_filename(reindexer.get_reindexed_reflections_filename())
refiner.set_scan_varying(True)
refiner.run()
assert os.path.exists(refiner.get_refined_experiments_filename())
print("".join(refiner.get_all_output()))
print("Done refining")
print("Begin integrating")
integrater = Integrate()
integrater.set_experiments_filename(refiner.get_refined_experiments_filename())
integrater.set_reflections_filename(reindexer.get_reindexed_reflections_filename())
integrater.run()
print("".join(integrater.get_all_output()))
print("Done integrating")
print("Begin exporting")
exporter = ExportMtz()
exporter.set_experiments_filename(integrater.get_integrated_experiments())
exporter.set_reflections_filename(integrater.get_integrated_reflections())
exporter.run()
print("".join(exporter.get_all_output()))
print("Done exporting")
assert os.path.exists(exporter.get_mtz_filename())
print("Begin exporting xds_ascii")
exporter = ExportXDSASCII()
exporter.set_experiments_filename(integrater.get_integrated_experiments())
exporter.set_reflections_filename(integrater.get_integrated_reflections())
exporter.run()
print("".join(exporter.get_all_output()))
print("Done exporting")
assert os.path.exists(exporter.get_hkl_filename())
# Test combine experiments wrapper. Duplicate the file and adjust the
# identifier to allow combination.
shutil.copy(indexer.get_experiments_filename(), "copy.expt")
shutil.copy(indexer.get_indexed_filename(), "copy.refl")
expts = load.experiment_list("copy.expt")
expts[0].identifier = "0"
expts.as_file("copy.expt")
refls = flex.reflection_table.from_file("copy.refl")
refls.experiment_identifiers()[0] = "0"
refls.as_file("copy.refl")
exporter = CombineExperiments()
exporter.add_experiments(indexer.get_experiments_filename())
exporter.add_experiments("copy.expt")
exporter.add_reflections(indexer.get_indexed_filename())
exporter.add_reflections("copy.refl")
exporter.run()
print("".join(exporter.get_all_output()))
print("Done combining")
assert os.path.exists(exporter.get_combined_experiments_filename())
assert os.path.exists(exporter.get_combined_reflections_filename())
def exercise_dials_wrappers(nproc=None):
if not have_dials_regression:
print "Skipping exercise_dials_wrappers(): dials_regression not configured"
return
if nproc is not None:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
from xia2.Wrappers.Dials.Import import Import
from xia2.Wrappers.Dials.Spotfinder import Spotfinder
from xia2.Wrappers.Dials.Index import Index
from xia2.Wrappers.Dials.Integrate import Integrate
from xia2.Wrappers.Dials.RefineBravaisSettings import RefineBravaisSettings
from xia2.Wrappers.Dials.Refine import Refine
from xia2.Wrappers.Dials.Reindex import Reindex
from xia2.Wrappers.Dials.ExportMtz import ExportMtz
from xia2.Wrappers.Dials.ExportXDSASCII import ExportXDSASCII
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
scan_ranges = [(1, 45)]
image_range = (1, 45)
cwd = os.path.abspath(os.curdir)
tmp_dir = os.path.abspath(open_tmp_directory())
os.chdir(tmp_dir)
print "Begin importing"
importer = Import()
importer.setup_from_image(template %1)
importer.set_image_range(image_range)
importer.run()
print ''.join(importer.get_all_output())
print "Done importing"
print "Begin spotfinding"
spotfinder = Spotfinder()
spotfinder.set_input_sweep_filename(importer.get_sweep_filename())
spotfinder.set_scan_ranges(scan_ranges)
spotfinder.run()
print ''.join(spotfinder.get_all_output())
print "Done spotfinding"
print "Begin indexing"
indexer = Index()
indexer.add_spot_filename(spotfinder.get_spot_filename())
indexer.add_sweep_filename(importer.get_sweep_filename())
indexer.run('fft3d')
print ''.join(indexer.get_all_output())
print "Done indexing"
print "Begin refining"
rbs = RefineBravaisSettings()
rbs.set_experiments_filename(indexer.get_experiments_filename())
rbs.set_indexed_filename(indexer.get_indexed_filename())
rbs.run()
print ''.join(rbs.get_all_output())
print "Done refining"
bravais_setting_22 = rbs.get_bravais_summary()[22]
assert bravais_setting_22['bravais'] == 'cI'
assert bravais_setting_22['cb_op'] == 'b+c,a+c,a+b'
assert approx_equal(bravais_setting_22['unit_cell'],
(78.14,78.14,78.14,90,90,90), eps=1e-1)
bravais_setting_22_json = bravais_setting_22['experiments_file']
assert os.path.exists(bravais_setting_22_json)
print "Begin reindexing"
reindexer = Reindex()
reindexer.set_experiments_filename(indexer.get_experiments_filename())
reindexer.set_indexed_filename(indexer.get_indexed_filename())
reindexer.set_cb_op(bravais_setting_22['cb_op'])
reindexer.run()
assert os.path.exists(reindexer.get_reindexed_experiments_filename())
assert os.path.exists(reindexer.get_reindexed_reflections_filename())
print ''.join(reindexer.get_all_output())
print "Done reindexing"
print "Begin refining"
refiner = Refine()
refiner.set_experiments_filename(bravais_setting_22_json)
refiner.set_indexed_filename(reindexer.get_reindexed_reflections_filename())
refiner.set_scan_varying(True)
refiner.run()
assert os.path.exists(refiner.get_refined_experiments_filename())
print ''.join(refiner.get_all_output())
print "Done refining"
print "Begin integrating"
integrater = Integrate()
integrater.set_experiments_filename(refiner.get_refined_experiments_filename())
integrater.set_reflections_filename(reindexer.get_reindexed_reflections_filename())
integrater.run()
print ''.join(integrater.get_all_output())
print "Done integrating"
print "Begin exporting"
exporter = ExportMtz()
exporter.set_experiments_filename(integrater.get_integrated_experiments())
exporter.set_reflections_filename(integrater.get_integrated_reflections())
exporter.run()
print ''.join(exporter.get_all_output())
print "Done exporting"
assert os.path.exists(exporter.get_mtz_filename())
print "Begin exporting xds_ascii"
exporter = ExportXDSASCII()
exporter.set_experiments_filename(integrater.get_integrated_experiments())
exporter.set_reflections_filename(integrater.get_integrated_reflections())
exporter.run()
print ''.join(exporter.get_all_output())
print "Done exporting"
assert os.path.exists(exporter.get_hkl_filename())
import shutil
shutil.copy(indexer.get_experiments_filename(), "copy.json")
shutil.copy(indexer.get_indexed_filename(), "copy.pickle")
print "Begin combining"
from xia2.Wrappers.Dials.CombineExperiments import CombineExperiments
exporter = CombineExperiments()
exporter.add_experiments(indexer.get_experiments_filename())
exporter.add_experiments("copy.json")
exporter.add_reflections(indexer.get_indexed_filename())
exporter.add_reflections("copy.pickle")
exporter.run()
print ''.join(exporter.get_all_output())
print "Done combining"
assert os.path.exists(exporter.get_combined_experiments_filename())
assert os.path.exists(exporter.get_combined_reflections_filename())
def exercise_dials_wrappers(dials_regression, nproc=None):
if nproc is not None:
from xia2.Handlers.Phil import PhilIndex
PhilIndex.params.xia2.settings.multiprocessing.nproc = nproc
from xia2.Wrappers.Dials.Import import Import
from xia2.Wrappers.Dials.Spotfinder import Spotfinder
from xia2.Wrappers.Dials.Index import Index
from xia2.Wrappers.Dials.Integrate import Integrate
from xia2.Wrappers.Dials.RefineBravaisSettings import RefineBravaisSettings
from xia2.Wrappers.Dials.Refine import Refine
from xia2.Wrappers.Dials.Reindex import Reindex
from xia2.Wrappers.Dials.ExportMtz import ExportMtz
from xia2.Wrappers.Dials.ExportXDSASCII import ExportXDSASCII
xia2_demo_data = os.path.join(dials_regression, "xia2_demo_data")
template = os.path.join(xia2_demo_data, "insulin_1_%03i.img")
scan_ranges = [(1, 45)]
image_range = (1, 45)
print("Begin importing")
importer = Import()
importer.setup_from_image(template % 1)
importer.set_image_range(image_range)
importer.run()
print(''.join(importer.get_all_output()))
print("Done importing")
print("Begin spotfinding")
spotfinder = Spotfinder()
spotfinder.set_input_sweep_filename(importer.get_sweep_filename())
spotfinder.set_scan_ranges(scan_ranges)
spotfinder.run()
print(''.join(spotfinder.get_all_output()))
print("Done spotfinding")
print("Begin indexing")
indexer = Index()
indexer.add_spot_filename(spotfinder.get_spot_filename())
indexer.add_sweep_filename(importer.get_sweep_filename())
indexer.run('fft3d')
print(''.join(indexer.get_all_output()))
print("Done indexing")
print("Begin refining")
rbs = RefineBravaisSettings()
rbs.set_experiments_filename(indexer.get_experiments_filename())
rbs.set_indexed_filename(indexer.get_indexed_filename())
rbs.run()
print(''.join(rbs.get_all_output()))
print("Done refining")
bravais_setting_22 = rbs.get_bravais_summary()[22]
assert bravais_setting_22['bravais'] == 'cI'
assert bravais_setting_22['cb_op'] == 'b+c,a+c,a+b'
assert approx_equal(bravais_setting_22['unit_cell'],
(78.14, 78.14, 78.14, 90, 90, 90),
eps=1e-1)
bravais_setting_22_json = bravais_setting_22['experiments_file']
assert os.path.exists(bravais_setting_22_json)
print("Begin reindexing")
reindexer = Reindex()
reindexer.set_experiments_filename(indexer.get_experiments_filename())
reindexer.set_indexed_filename(indexer.get_indexed_filename())
reindexer.set_cb_op(bravais_setting_22['cb_op'])
reindexer.run()
assert os.path.exists(reindexer.get_reindexed_experiments_filename())
assert os.path.exists(reindexer.get_reindexed_reflections_filename())
print(''.join(reindexer.get_all_output()))
print("Done reindexing")
print("Begin refining")
refiner = Refine()
refiner.set_experiments_filename(bravais_setting_22_json)
refiner.set_indexed_filename(
reindexer.get_reindexed_reflections_filename())
refiner.set_scan_varying(True)
refiner.run()
assert os.path.exists(refiner.get_refined_experiments_filename())
print(''.join(refiner.get_all_output()))
print("Done refining")
print("Begin integrating")
integrater = Integrate()
integrater.set_experiments_filename(
refiner.get_refined_experiments_filename())
integrater.set_reflections_filename(
reindexer.get_reindexed_reflections_filename())
integrater.run()
print(''.join(integrater.get_all_output()))
print("Done integrating")
print("Begin exporting")
exporter = ExportMtz()
exporter.set_experiments_filename(integrater.get_integrated_experiments())
exporter.set_reflections_filename(integrater.get_integrated_reflections())
exporter.run()
print(''.join(exporter.get_all_output()))
print("Done exporting")
assert os.path.exists(exporter.get_mtz_filename())
print("Begin exporting xds_ascii")
exporter = ExportXDSASCII()
exporter.set_experiments_filename(integrater.get_integrated_experiments())
exporter.set_reflections_filename(integrater.get_integrated_reflections())
exporter.run()
print(''.join(exporter.get_all_output()))
print("Done exporting")
assert os.path.exists(exporter.get_hkl_filename())
import shutil
shutil.copy(indexer.get_experiments_filename(), "copy.json")
shutil.copy(indexer.get_indexed_filename(), "copy.pickle")
print("Begin combining")
from xia2.Wrappers.Dials.CombineExperiments import CombineExperiments
exporter = CombineExperiments()
exporter.add_experiments(indexer.get_experiments_filename())
exporter.add_experiments("copy.json")
exporter.add_reflections(indexer.get_indexed_filename())
exporter.add_reflections("copy.pickle")
exporter.run()
print(''.join(exporter.get_all_output()))
print("Done combining")
assert os.path.exists(exporter.get_combined_experiments_filename())
assert os.path.exists(exporter.get_combined_reflections_filename())