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