def exercise_xds_integrater(dials_data, tmp_dir, nproc=None): if nproc: 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.XDSIndexer import XDSIndexer from xia2.Modules.Integrater.XDSIntegrater import XDSIntegrater indexer = XDSIndexer() 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, 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_xds_integrater(nproc=None): if not have_dials_regression: print "Skipping exercise_xds_integrater(): 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.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_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 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) from iotbx.reflection_file_reader import any_reflection_file 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_reindex_operator() == 'x,z,-y' assert integrater.get_integrater_wedge() == (1, 45) assert approx_equal(integrater.get_integrater_cell(), [78.066, 78.066, 78.066, 90, 90, 90], eps=3e-2) assert approx_equal(integrater.get_integrater_mosaic_min_mean_max(), (0.181, 0.181, 0.181), eps=1e-3) # 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=350) 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(), 50000, eps=300)
def exercise_xds_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.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)