from __future__ import absolute_import, division, print_function import libtbx.load_env from six.moves import range from six.moves import zip if (libtbx.env.has_module("ccp4io")): from iotbx import mtz else: mtz = None from iotbx.option_parser import option_parser from cctbx import sgtbx from cctbx import uctbx from cctbx.array_family import flex from libtbx.test_utils import Exception_expected, approx_equal, show_diff from itertools import count from six.moves import cStringIO as StringIO import sys, os def exercise_read_corrupt(): for i_trial in range(5): f = open("tmp_iotbx_mtz_ext.mtz", "w") if (i_trial > 0): f.write("\0"*(40*i_trial)) f.close() try: mtz.object(file_name="tmp_iotbx_mtz_ext.mtz") except RuntimeError as e: assert str(e) == "cctbx Error: MTZ file read error: tmp_iotbx_mtz_ext.mtz" else: raise Exception_expected def exercise_setting_nref_etc(): m = mtz.object() assert m.n_reflections() == 0 m.adjust_column_array_sizes(10) m.set_n_reflections(10) assert m.n_reflections() == 10 def exercise_basic(): assert mtz.ccp4_liberr_verbosity(-1) == 0 assert mtz.ccp4_liberr_verbosity(1) == 1 assert mtz.ccp4_liberr_verbosity(-1) == 1 assert mtz.ccp4_liberr_verbosity(0) == 0 assert mtz.ccp4_liberr_verbosity(-1) == 0 mtz_object = mtz.object() assert mtz_object.title() == "" assert mtz_object.history().size() == 0 assert mtz_object.space_group_name() == "" assert mtz_object.space_group_number() == 0 assert mtz_object.n_symmetry_matrices() == 0 assert mtz_object.space_group_confidence() == "\x00" assert mtz_object.space_group().order_z() == 1 assert mtz_object.point_group_name() == "" assert mtz_object.lattice_centring_type() == "\0" assert mtz_object.n_batches() == 0 assert mtz_object.batches().size() == 0 assert mtz_object.n_reflections() == 0 assert mtz_object.max_min_resolution() == (-1, -1) assert mtz_object.n_crystals() == 0 assert mtz_object.n_active_crystals() == 0 file_name = libtbx.env.find_in_repositories( relative_path="phenix_regression/reflection_files/dano.mtz", test=os.path.isfile) if (file_name is None): print("Skipping dano.mtz test: input file not available") else: mtz_object = mtz.object(file_name=file_name) assert mtz_object.title() == "......" assert mtz_object.history().size() == 17 assert mtz_object.space_group_name() == "P212121" assert mtz_object.space_group_number() == 19 assert mtz_object.point_group_name() == "PG222" assert mtz_object.lattice_centring_type() == "P" assert mtz_object.n_symmetry_matrices() == 4 assert mtz_object.space_group().type().lookup_symbol() == "P 21 21 21" assert mtz_object.n_batches() == 0 assert mtz_object.batches().size() == 0 assert mtz_object.n_reflections() == 165 assert approx_equal(mtz_object.max_min_resolution(), (19.869975507347792, 15.001543055390009)) assert mtz_object.n_crystals() == 4 assert mtz_object.n_active_crystals() == 3 assert mtz_object.has_crystal("unknown") assert not mtz_object.has_crystal("abc") assert mtz_object.has_column("H") assert not mtz_object.has_column("abc") crystal = mtz.crystal(mtz_object=mtz_object, i_crystal=1) assert crystal.mtz_object().n_reflections() == 165 assert crystal.i_crystal() == 1 assert mtz_object.crystals().size() == mtz_object.n_crystals() assert crystal.id() == 2 assert crystal.name() == "unknown" assert crystal.set_name(new_name="abc") is crystal assert crystal.name() == "abc" assert crystal.set_name("abc") is crystal assert crystal.name() == "abc" try: crystal.set_name("unknown3") except RuntimeError as e: assert str(e) == 'mtz::crystal::set_name(new_name="unknown3"):' \ ' new_name is used already for another crystal.' else: raise Exception_expected assert crystal.name() == "abc" assert crystal.set_name("unknown") is crystal assert crystal.name() == "unknown" assert crystal.project_name() == "unknown" assert crystal.set_project_name(new_project_name="abc") is crystal assert crystal.project_name() == "abc" assert crystal.set_project_name(new_project_name="unknown") is crystal assert crystal.project_name() == "unknown" assert approx_equal(crystal.unit_cell_parameters(), (84.511, 104.308, 174.103, 90, 90, 90)) assert approx_equal(crystal.unit_cell().parameters(), (84.511, 104.308, 174.103, 90, 90, 90)) assert crystal.n_datasets() == 1 dataset = mtz.dataset(mtz_crystal=crystal, i_dataset=0) assert dataset.mtz_crystal().i_crystal() == 1 assert dataset.i_dataset() == 0 assert dataset.mtz_object().n_crystals() == mtz_object.n_crystals() assert dataset.id() == 1 assert dataset.name() == "unknown230103:23:14:49" assert dataset.set_name(new_name="abc") is dataset assert dataset.name() == "abc" assert dataset.set_name(new_name="abc") is dataset assert dataset.name() == "abc" assert dataset.set_name("unknown230103:23:14:49") is dataset assert dataset.name() == "unknown230103:23:14:49" assert dataset.wavelength() == 0 assert dataset.set_wavelength(new_wavelength=0.12) is dataset assert approx_equal(dataset.wavelength(), 0.12) assert dataset.set_wavelength(0) is dataset assert dataset.wavelength() == 0 column = mtz.column(mtz_dataset=dataset, i_column=0) assert column.mtz_dataset().mtz_crystal().i_crystal() == 1 assert column.i_column() == 0 assert column.mtz_crystal().i_crystal() == 1 assert column.mtz_object().n_reflections() == 165 assert column.label() == "H" assert column.set_label(new_label="New") is column assert column.label() == "New" try: column.set_label("a,b,c") except RuntimeError as e: assert str(e) == 'mtz::column::set_label(new_label="a,b,c"):' \ ' new_label must not include commas.' else: raise Exception_expected assert column.label() == "New" assert column.set_label(new_label="New") is column assert column.label() == "New" try: column.set_label(new_label="K") except RuntimeError as e: assert str(e) == 'mtz::column::set_label(new_label="K"):' \ ' new_label is used already for another column.' else: raise Exception_expected assert column.set_label("H") is column assert column.label() == "H" assert column.type() == "H" assert column.set_type(new_type="Nw") is column assert column.type() == "Nw" assert column.set_type("H") is column assert column.type() == "H" assert column.is_active() if (column.source() is None): assert column.group_name() is None assert column.group_type() is None assert column.group_position() == -1 else: assert column.source() == "" assert column.set_source(new_source="NsRc") is column assert column.source() == "NsRc" assert column.set_source(new_source="") is column assert column.source() == "" assert column.group_name() == "" assert column.set_group_name(new_group_name="NgN") is column assert column.group_name() == "NgN" assert column.set_group_name(new_group_name="") is column assert column.group_name() == "" assert column.group_type() == "" assert column.set_group_type(new_group_type="NgT") is column assert column.group_type() == "NgT" assert column.set_group_type(new_group_type="") is column assert column.group_type() == "" assert column.group_position() == -1 assert column.set_group_position(new_group_position=23) is column assert column.group_position() == 23 assert column.set_group_position(new_group_position=-1) is column assert column.group_position() == -1 assert column.array_size() == 165 assert column.array_capacity() == 200 assert column.path() == "/unknown/unknown230103:23:14:49/H" assert column.get_other("H").i_column() == 0 assert column.get_other("K").i_column() == 1 assert column.get_other("L").i_column() == 2 assert column.n_valid_values() == 165 valid_values = column.extract_valid_values() assert valid_values.size() == 165 assert approx_equal(flex.min(valid_values), 0) assert approx_equal(flex.max(valid_values), 5) assert approx_equal(flex.mean(valid_values), 2.41818189621) assert column.selection_valid().count(True) == 165 assert approx_equal(flex.mean(column.extract_values()), 2.41818189621) assert approx_equal(flex.mean(column.extract_values( not_a_number_substitute=10)), 2.41818189621) column = mtz_object.get_column("F*") assert column.label() == "Frem" assert column.n_valid_values() == 163 valid_values = column.extract_valid_values() assert valid_values.size() == 163 assert approx_equal(flex.min(valid_values), 32.5101776123) assert approx_equal(flex.max(valid_values), 2711.84350586) assert approx_equal(flex.mean(valid_values), 615.060852051) assert column.selection_valid().count(True) == 163 assert approx_equal(flex.mean(column.extract_values()), 615.060852051*163/165) assert approx_equal(flex.mean(column.extract_values(13)), (615.060852051*163+2*13)/165) v,s = column.extract_values_and_selection_valid( not_a_number_substitute=-97).as_tuple() assert v.size() == 165 assert s.count(True) == 163 assert approx_equal(v.select(~s), [-97]*2) expected_dataset_ids = iter(range(4)) expected_dataset_names = iter([ "HKL_base", "unknown230103:23:14:49", "unknown230103:23:14:21", "unknown230103:23:13:49"]) expected_n_columns = iter([0,8,5,5]) expected_column_labels = iter([ "H", "K", "L", "Frem", "SIGFrem", "DANOrem", "SIGDANOrem", "ISYMrem", "Finf", "SIGFinf", "DANOinf", "SIGDANOinf", "ISYMinf", "Fabs", "SIGFabs", "DANOabs", "SIGDANOabs", "ISYMabs"]) expected_column_types = iter("HHHFQDQYFQDQYFQDQY") for i_crystal,crystal in enumerate(mtz_object.crystals()): assert crystal.mtz_object().n_reflections() == 165 assert crystal.i_crystal() == i_crystal assert crystal.n_datasets() == 1 for i_dataset,dataset in enumerate(crystal.datasets()): assert dataset.mtz_crystal().i_crystal() == i_crystal assert dataset.i_dataset() == i_dataset assert dataset.id() == next(expected_dataset_ids) assert dataset.name() == next(expected_dataset_names) assert dataset.wavelength() == 0 assert dataset.n_columns() == next(expected_n_columns) for i_column,column in enumerate(dataset.columns()): assert column.mtz_dataset().i_dataset() == i_dataset assert column.i_column() == i_column assert column.label() == next(expected_column_labels) assert column.type() == next(expected_column_types) assert column.is_active() assert column.array_size() == 165 assert column.array_capacity() == 200 assert column.path().endswith(column.label()) get_column = mtz_object.get_column(column.label()) assert get_column.label() == column.label() group = mtz_object.extract_integers( column_label="ISYMabs") assert not group.anomalous_flag assert group.mtz_reflection_indices.size() == 165 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() data = mtz_object.extract_integers( mtz_reflection_indices=group.mtz_reflection_indices, column_label="ISYMabs") assert data.all_eq(group.data) group = mtz_object.extract_integers_anomalous( column_label_plus="ISYMabs", column_label_minus="ISYMabs") assert group.anomalous_flag assert group.mtz_reflection_indices.size() == 330 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() group = mtz_object.extract_reals( column_label="Frem") assert not group.anomalous_flag assert group.mtz_reflection_indices.size() == 163 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() data = mtz_object.extract_reals( mtz_reflection_indices=group.mtz_reflection_indices, column_label="Frem") assert data.all_eq(group.data) group = mtz_object.extract_reals_anomalous( column_label_plus="Frem", column_label_minus="DANOrem") assert group.anomalous_flag assert group.mtz_reflection_indices.size() == 326 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() group = mtz_object.extract_hendrickson_lattman( column_label_a="Frem", column_label_b="DANOrem", column_label_c="Frem", column_label_d="DANOrem") assert not group.anomalous_flag assert group.mtz_reflection_indices.size() == 163 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() group = mtz_object.extract_hendrickson_lattman_ab_only( column_label_a="Frem", column_label_b="DANOrem") assert not group.anomalous_flag assert group.mtz_reflection_indices.size() == 163 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() group = mtz_object.extract_hendrickson_lattman_anomalous( column_label_a_plus="Frem", column_label_b_plus="DANOrem", column_label_c_plus="Frem", column_label_d_plus="DANOrem", column_label_a_minus="Frem", column_label_b_minus="DANOrem", column_label_c_minus="Frem", column_label_d_minus="DANOrem") assert group.anomalous_flag assert group.mtz_reflection_indices.size() == 326 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() group = mtz_object.extract_hendrickson_lattman_anomalous_ab_only( column_label_a_plus="Frem", column_label_b_plus="DANOrem", column_label_a_minus="Frem", column_label_b_minus="DANOrem") assert group.anomalous_flag assert group.mtz_reflection_indices.size() == 326 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() group = mtz_object.extract_observations( column_label_data="Frem", column_label_sigmas="SIGFrem") assert not group.anomalous_flag assert group.mtz_reflection_indices.size() == 163 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() assert group.sigmas.size() == group.indices.size() group = mtz_object.extract_observations_anomalous( column_label_data_plus="Frem", column_label_sigmas_plus="SIGFrem", column_label_data_minus="DANOrem", column_label_sigmas_minus="SIGDANOrem") assert group.anomalous_flag assert group.mtz_reflection_indices.size() == 272 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() assert group.sigmas.size() == group.indices.size() group = mtz_object.extract_delta_anomalous( column_label_f_data="Frem", column_label_f_sigmas="SIGFrem", column_label_d_data="DANOrem", column_label_d_sigmas="SIGDANOrem", column_label_isym="ISYMrem") assert group.anomalous_flag assert group.mtz_reflection_indices.size() == 272 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() assert group.sigmas.size() == group.indices.size() group = mtz_object.extract_complex( column_label_ampl="Frem", column_label_phi="SIGFrem") assert not group.anomalous_flag assert group.mtz_reflection_indices.size() == 163 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() group = mtz_object.extract_complex_anomalous( column_label_ampl_plus="Frem", column_label_phi_plus="SIGFrem", column_label_ampl_minus="DANOrem", column_label_phi_minus="SIGDANOrem") assert group.anomalous_flag assert group.mtz_reflection_indices.size() == 326 assert group.indices.size() == group.mtz_reflection_indices.size() assert group.data.size() == group.mtz_reflection_indices.size() class QuickStop(Exception): pass class exercise_extract_any(object): def __init__(self, full=True): self.full = full self.counters = { "extract_integers": 0, "extract_reals": 0, "extract_reals_anomalous": 0, "extract_hendrickson_lattman": 0, "extract_observations": 0, "extract_observations_anomalous": 0, "extract_delta_anomalous": 0, "extract_complex": 0, "extract_complex_anomalous": 0} def all_tests_ran_at_least_once(self): return min(self.counters.values()) > 0 def raise_if_all_tests_ran_at_least_once(self): if (self.full): return if (self.all_tests_ran_at_least_once()): raise QuickStop def __call__(self, file_name, out): mtz_object = mtz.object(file_name=file_name) mtz_object.show_summary(out=out) types = "".join(mtz_object.column_types()) for type_group in ["B", "H", "I", "Y"]: i = types.find(type_group) if (i >= 0): label = mtz_object.column_labels()[i] group = mtz_object.extract_integers( column_label=label) assert group.data.size() == group.indices.size() self.counters["extract_integers"] += 1 for type_group in ["FQ", "JQ"]: i = types.find(type_group) if (i >= 0): labels = mtz_object.column_labels()[i:i+2] group = mtz_object.extract_reals( column_label=labels[0]) assert group.data.size() == group.indices.size() self.counters["extract_reals"] += 1 group = mtz_object.extract_observations( column_label_data=labels[0], column_label_sigmas=labels[1]) assert group.data.size() == group.indices.size() assert group.sigmas.size() == group.indices.size() self.counters["extract_observations"] += 1 for type_group in ["FQFQ", "JQJQ"]: i = types.find(type_group) if (i >= 0): labels = mtz_object.column_labels()[i:i+4] group = mtz_object.extract_observations_anomalous( column_label_data_plus=labels[0], column_label_sigmas_plus=labels[1], column_label_data_minus=labels[2], column_label_sigmas_minus=labels[3]) assert group.data.size() == group.indices.size() assert group.sigmas.size() == group.indices.size() self.counters["extract_observations_anomalous"] += 1 i = types.find("FQDQ") if (i >= 0): labels = mtz_object.column_labels()[i:i+4] group = mtz_object.extract_delta_anomalous( column_label_f_data=labels[0], column_label_f_sigmas=labels[1], column_label_d_data=labels[2], column_label_d_sigmas=labels[3], column_label_isym=mtz_object.next_isym_column_starting_at( i_column=i+4, return_label=True)) assert group.data.size() == group.indices.size() self.counters["extract_delta_anomalous"] += 1 i = types.find("FP") if (i >= 0): labels = mtz_object.column_labels()[i:i+2] group = mtz_object.extract_complex( column_label_ampl=labels[0], column_label_phi=labels[1]) assert group.data.size() == group.indices.size() self.counters["extract_complex"] += 1 for type_group in ["GLGL", "KMKM"]: i = types.find(type_group) if (i >= 0): labels = mtz_object.column_labels()[i:i+4] group = mtz_object.extract_reals_anomalous( column_label_plus=labels[0], column_label_minus=labels[2]) assert group.data.size() == group.indices.size() self.counters["extract_reals_anomalous"] += 1 group = mtz_object.extract_observations_anomalous( column_label_data_plus=labels[0], column_label_sigmas_plus=labels[1], column_label_data_minus=labels[2], column_label_sigmas_minus=labels[3]) assert group.data.size() == group.indices.size() assert group.sigmas.size() == group.indices.size() self.counters["extract_observations_anomalous"] += 1 # work around lack of FPFP in MTZ files available group = mtz_object.extract_complex_anomalous( column_label_ampl_plus=labels[0], column_label_phi_plus=labels[1], column_label_ampl_minus=labels[2], column_label_phi_minus=labels[3]) assert group.data.size() == group.indices.size() self.counters["extract_complex_anomalous"] += 1 i = types.find("AAAA") if (i >= 0): labels = mtz_object.column_labels()[i:i+4] group = mtz_object.extract_hendrickson_lattman( column_label_a=labels[0], column_label_b=labels[1], column_label_c=labels[2], column_label_d=labels[3]) assert group.data.size() == group.indices.size() self.counters["extract_hendrickson_lattman"] += 1 def walk_callback(arg, top, names): exercise_function, out = arg for name in names: if (not name.lower().endswith(".mtz")): continue file_name = os.path.normpath(os.path.join(top, name)) print("Processing:", file_name, file=out) exercise_function(file_name=file_name, out=out) exercise_function.raise_if_all_tests_ran_at_least_once() def exercise_walk(root_dir, full, verbose=False): if (verbose): out = sys.stdout else: out = StringIO() exercise_function = exercise_extract_any(full=full) try: if sys.version_info.major == 3: for root, dirs, files in os.walk(root_dir): walk_callback( arg=(exercise_function, out), top=root, names=files) else: os.path.walk( top=root_dir, func=walk_callback, arg=(exercise_function, out)) except QuickStop: pass if (verbose): print(exercise_function.counters) def exercise_modifiers(verbose=0): if (verbose): out = sys.stdout mtz_object = mtz.object() mtz_object.set_title(title="012345678") assert mtz_object.title() == "012345678" mtz_object.set_title(title="012345678", append=True) assert mtz_object.title() == "012345678 012345678" mtz_object.set_title(title="0123456789"*10+"012345678", append=True) assert mtz_object.title() == "012345678 "*2 + "0123456789"*5 mtz_object.set_title("0123456789"*100) assert mtz_object.title() == "0123456789"*7 mtz_object.set_title(title="") assert mtz_object.title() == "" mtz_object.set_title(title="abc", append=True) assert mtz_object.title() == "abc" mtz_object.set_title(title="def", append=True) assert mtz_object.title() == "abc def" mtz_object.set_title(title="a") assert mtz_object.title() == "a" mtz_object.set_title(title="bc", append=True) assert mtz_object.title() == "a bc" mtz_object.set_title(title=" "*70) mtz_object.set_title(title="abc", append=True) assert mtz_object.title() == "abc" mtz_object.set_title(title="z"*70) mtz_object.set_title(title="abc", append=True) assert mtz_object.title() == "z"*70 mtz_object.set_title(title="z"*69) mtz_object.set_title(title="abc", append=True) assert mtz_object.title() == "z"*69 mtz_object.set_title(title="z"*68) mtz_object.set_title(title="abc", append=True) assert mtz_object.title() == "z"*68 + " a" mtz_object.set_title(title="z"*67) mtz_object.set_title(title="abc", append=True) assert mtz_object.title() == "z"*67 + " ab" mtz_object.add_history(lines=flex.std_string(["a1", "a2"])) assert list(mtz_object.history()) == ["a1", "a2"] mtz_object.add_history(lines=flex.std_string(["b1", "b2"])) assert list(mtz_object.history()) == ["b1", "b2", "a1", "a2"] mtz_object.add_history(line="c1") assert list(mtz_object.history()) == ["c1", "b1", "b2", "a1", "a2"] mtz_object.set_space_group_name(name="sg"*100) assert mtz_object.space_group_name() == "sgsgsgsgsgsgsgsgsgsg" mtz_object.set_space_group_number(number=12) assert mtz_object.space_group_number() == 12 mtz_object.set_point_group_name(name="pg"*100) assert mtz_object.point_group_name() == "pgpgpgpgpg" mtz_object.set_lattice_centring_type(symbol="C") assert mtz_object.lattice_centring_type() == "C" for space_group_symbols in sgtbx.space_group_symbol_iterator(): space_group = sgtbx.space_group(space_group_symbols) mtz_object.set_space_group(space_group) assert mtz_object.space_group() == space_group assert mtz_object.n_symmetry_matrices() == space_group.order_z() assert mtz_object.xml() is None assert mtz_object.unknown_headers() is None assert mtz_object.number_of_unknown_headers() == 0 mtz_object = mtz.object() \ .set_title(title="exercise") \ .add_history(lines=flex.std_string(["h2"])) \ .add_history(line="h1") \ .set_space_group_name("sg") \ .set_space_group_number(123) \ .set_point_group_name("pg") \ .set_space_group(sgtbx.space_group_info(number=123).group()) assert mtz_object.title() == "exercise" assert list(mtz_object.history()) == ["h1", "h2"] for stage in [0,1]: for i_crystal in range(3): if (stage == 0): if (i_crystal % 2 == 0): crystal = mtz_object.add_crystal( name="crystal_%d"%i_crystal, project_name="project_%d"%i_crystal, unit_cell_parameters=(10+i_crystal,20,20,90,90,120)) else: crystal = mtz_object.add_crystal( name="crystal_%d"%i_crystal, project_name="project_%d"%i_crystal, unit_cell=uctbx.unit_cell((10+i_crystal,20,20,90,90,120))) else: crystal = mtz_object.crystals()[i_crystal] assert crystal.i_crystal() == i_crystal assert crystal.name() == "crystal_%d"%i_crystal assert crystal.project_name() == "project_%d"%i_crystal assert approx_equal(crystal.unit_cell_parameters(), (10+i_crystal,20,20,90,90,120)) if (not verbose): out = StringIO() assert mtz_object.show_summary(out=out) is mtz_object if (not verbose): assert not show_diff(out.getvalue(), """\ Title: exercise Space group symbol from file: sg Space group number from file: 123 Space group from matrices: P 4/m m m (No. 123) Point group symbol from file: pg Number of crystals: 3 Number of Miller indices: 0 History: h1 h2 Crystal 1: Name: crystal_0 Project: project_0 Id: 1 Unit cell: (10, 20, 20, 90, 90, 120) Number of datasets: 0 Crystal 2: Name: crystal_1 Project: project_1 Id: 2 Unit cell: (11, 20, 20, 90, 90, 120) Number of datasets: 0 Crystal 3: Name: crystal_2 Project: project_2 Id: 3 Unit cell: (12, 20, 20, 90, 90, 120) Number of datasets: 0 """) mtz_object.crystals()[1].set_unit_cell_parameters([13,21,23,81,82,83]) assert approx_equal(mtz_object.crystals()[1].unit_cell_parameters(), [13,21,23,81,82,83]) mtz_object.crystals()[1].set_unit_cell_parameters([11,20,20,90,90,120]) assert approx_equal(mtz_object.crystals()[1].unit_cell_parameters(), [11,20,20,90,90,120]) for stage in [0,1]: for i_crystal,crystal in enumerate(mtz_object.crystals()): for i_dataset in range(5-i_crystal): if (stage == 0): new_name = "dataset_%d" % i_dataset assert not crystal.has_dataset(name=new_name) dataset = crystal.add_dataset(name=new_name, wavelength=10-i_dataset) assert crystal.has_dataset(name=new_name) else: dataset = crystal.datasets()[i_dataset] assert dataset.name() == "dataset_%d"%i_dataset assert approx_equal(dataset.wavelength(), 10-i_dataset) if (not verbose): out = StringIO() mtz_object.show_summary(out=out) if (not verbose): assert not show_diff(out.getvalue(), """\ Title: exercise Space group symbol from file: sg Space group number from file: 123 Space group from matrices: P 4/m m m (No. 123) Point group symbol from file: pg Number of crystals: 3 Number of Miller indices: 0 History: h1 h2 Crystal 1: Name: crystal_0 Project: project_0 Id: 1 Unit cell: (10, 20, 20, 90, 90, 120) Number of datasets: 5 Dataset 1: Name: dataset_0 Id: 1 Wavelength: 10 Number of columns: 0 Dataset 2: Name: dataset_1 Id: 2 Wavelength: 9 Number of columns: 0 Dataset 3: Name: dataset_2 Id: 3 Wavelength: 8 Number of columns: 0 Dataset 4: Name: dataset_3 Id: 4 Wavelength: 7 Number of columns: 0 Dataset 5: Name: dataset_4 Id: 5 Wavelength: 6 Number of columns: 0 Crystal 2: Name: crystal_1 Project: project_1 Id: 2 Unit cell: (11, 20, 20, 90, 90, 120) Number of datasets: 4 Dataset 1: Name: dataset_0 Id: 6 Wavelength: 10 Number of columns: 0 Dataset 2: Name: dataset_1 Id: 7 Wavelength: 9 Number of columns: 0 Dataset 3: Name: dataset_2 Id: 8 Wavelength: 8 Number of columns: 0 Dataset 4: Name: dataset_3 Id: 9 Wavelength: 7 Number of columns: 0 Crystal 3: Name: crystal_2 Project: project_2 Id: 3 Unit cell: (12, 20, 20, 90, 90, 120) Number of datasets: 3 Dataset 1: Name: dataset_0 Id: 10 Wavelength: 10 Number of columns: 0 Dataset 2: Name: dataset_1 Id: 11 Wavelength: 9 Number of columns: 0 Dataset 3: Name: dataset_2 Id: 12 Wavelength: 8 Number of columns: 0 """) # dataset_0_0 = mtz_object.crystals()[0].datasets()[0] assert dataset_0_0.name() == "dataset_0" assert dataset_0_0.set_name(new_name="dataset_x") is dataset_0_0 assert dataset_0_0.name() == "dataset_x" assert dataset_0_0.set_name(new_name="dataset_0") is dataset_0_0 assert dataset_0_0.name() == "dataset_0" try: dataset_0_0.set_name(new_name="dataset_1") except RuntimeError as e: assert str(e) == 'mtz::dataset::set_name(new_name="dataset_1"):' \ ' new_name is used already for another dataset.' else: raise Exception_expected assert dataset_0_0.name() == "dataset_0" # for stage in [0,1]: i_seq_iter = count() for i_crystal,crystal in enumerate(mtz_object.crystals()): for i_dataset,dataset in enumerate(crystal.datasets()): for i_column in range((i_crystal+i_dataset) % 3 + 1): i_seq = next(i_seq_iter) col_label = "column_%d"%i_seq col_type = "FB?"[(i_crystal-i_dataset+i_column) % 3] if (stage == 0): column = dataset.add_column(label=col_label, type=col_type) else: column = dataset.columns()[i_column] assert column.label() == col_label assert column.type() == col_type if (not verbose): out = StringIO() mtz_object.show_summary(out=out) if (not verbose): assert not show_diff(out.getvalue(), """\ Title: exercise Space group symbol from file: sg Space group number from file: 123 Space group from matrices: P 4/m m m (No. 123) Point group symbol from file: pg Number of crystals: 3 Number of Miller indices: 0 History: h1 h2 Crystal 1: Name: crystal_0 Project: project_0 Id: 1 Unit cell: (10, 20, 20, 90, 90, 120) Number of datasets: 5 Dataset 1: Name: dataset_0 Id: 1 Wavelength: 10 Number of columns: 1 label #valid %valid min max type column_0 0 0.00% None None F: amplitude Dataset 2: Name: dataset_1 Id: 2 Wavelength: 9 Number of columns: 2 label #valid %valid min max type column_1 0 0.00% None None ?: *** UNDEFINED column type *** column_2 0 0.00% None None F: amplitude Dataset 3: Name: dataset_2 Id: 3 Wavelength: 8 Number of columns: 3 label #valid %valid min max type column_3 0 0.00% None None B: BATCH number column_4 0 0.00% None None ?: *** UNDEFINED column type *** column_5 0 0.00% None None F: amplitude Dataset 4: Name: dataset_3 Id: 4 Wavelength: 7 Number of columns: 1 label #valid %valid min max type column_6 0 0.00% None None F: amplitude Dataset 5: Name: dataset_4 Id: 5 Wavelength: 6 Number of columns: 2 label #valid %valid min max type column_7 0 0.00% None None ?: *** UNDEFINED column type *** column_8 0 0.00% None None F: amplitude Crystal 2: Name: crystal_1 Project: project_1 Id: 2 Unit cell: (11, 20, 20, 90, 90, 120) Number of datasets: 4 Dataset 1: Name: dataset_0 Id: 6 Wavelength: 10 Number of columns: 2 label #valid %valid min max type column_9 0 0.00% None None B: BATCH number column_10 0 0.00% None None ?: *** UNDEFINED column type *** Dataset 2: Name: dataset_1 Id: 7 Wavelength: 9 Number of columns: 3 label #valid %valid min max type column_11 0 0.00% None None F: amplitude column_12 0 0.00% None None B: BATCH number column_13 0 0.00% None None ?: *** UNDEFINED column type *** Dataset 3: Name: dataset_2 Id: 8 Wavelength: 8 Number of columns: 1 label #valid %valid min max type column_14 0 0.00% None None ?: *** UNDEFINED column type *** Dataset 4: Name: dataset_3 Id: 9 Wavelength: 7 Number of columns: 2 label #valid %valid min max type column_15 0 0.00% None None B: BATCH number column_16 0 0.00% None None ?: *** UNDEFINED column type *** Crystal 3: Name: crystal_2 Project: project_2 Id: 3 Unit cell: (12, 20, 20, 90, 90, 120) Number of datasets: 3 Dataset 1: Name: dataset_0 Id: 10 Wavelength: 10 Number of columns: 3 label #valid %valid min max type column_17 0 0.00% None None ?: *** UNDEFINED column type *** column_18 0 0.00% None None F: amplitude column_19 0 0.00% None None B: BATCH number Dataset 2: Name: dataset_1 Id: 11 Wavelength: 9 Number of columns: 1 label #valid %valid min max type column_20 0 0.00% None None B: BATCH number Dataset 3: Name: dataset_2 Id: 12 Wavelength: 8 Number of columns: 2 label #valid %valid min max type column_21 0 0.00% None None F: amplitude column_22 0 0.00% None None B: BATCH number """) for column in mtz_object.columns(): assert column.array_size() == 2000 assert column.array_capacity() == 2402 mtz_object.reserve(5000) for column in mtz_object.columns(): assert column.array_size() == 2000 assert column.array_capacity() == 5000 mtz_object.reserve(100) for column in mtz_object.columns(): assert column.array_size() == 2000 assert column.array_capacity() == 5000 # mtz_object = mtz.object() \ .set_title(title="exercise") \ .set_space_group_name("sg") \ .set_space_group_number(123) \ .set_point_group_name("pg") \ .set_lattice_centring_type("pg") \ .set_space_group(sgtbx.space_group_info(number=123).group()) unit_cell = uctbx.unit_cell((10,10,10,90,90,90)) mtz_object.set_hkl_base(unit_cell=unit_cell) dataset = mtz_object.add_crystal( name="crystal_1", project_name="crystal_1", unit_cell=unit_cell).add_dataset( name="crystal_1", wavelength=0) try: dataset.add_column(label="a,b,c", type="H") except RuntimeError as e: assert str(e) == 'mtz::dataset::add_column(label="a,b,c", ...):' \ ' label must not include commas.' else: raise Exception_expected for label in "HKL": dataset.add_column(label=label, type="H") column = dataset.add_column(label="F", type="F") mtz_reflection_indices = column.set_reals( miller_indices=flex.miller_index([(1,2,3),(2,3,4),(3,4,5)]), data=flex.double([10,20,30])) assert list(mtz_reflection_indices) == [0,1,2] column = dataset.add_column(label="SigF", type="Q") column.set_reals( mtz_reflection_indices=mtz_reflection_indices, data=flex.double([1,2,3])) group = mtz_object.extract_observations( column_label_data="F", column_label_sigmas="SigF") assert list(group.indices) == [(1, 2, 3), (2, 3, 4), (3, 4, 5)] assert approx_equal(group.data, [10, 20, 30]) assert approx_equal(group.sigmas, [1, 2, 3]) column = dataset.add_column(label="I", type="F") mtz_reflection_indices = column.set_reals( miller_indices=flex.miller_index([(2,3,5),(1,2,3),(3,4,5)]), data=flex.double([11,21,31])) assert list(mtz_reflection_indices) == [3, 0, 2] column = dataset.add_column(label="SigI", type="Q") column.set_reals( mtz_reflection_indices=mtz_reflection_indices, data=flex.double([4,5,6])) group = mtz_object.extract_observations( column_label_data="I", column_label_sigmas="SigI") assert list(group.indices) == [(1, 2, 3), (3, 4, 5), (2, 3, 5)] assert approx_equal(group.data, [21, 31, 11]) assert approx_equal(group.sigmas, [5, 6, 4]) if (not verbose): out = StringIO() mtz_object.show_summary(out=out) if (not verbose): assert not show_diff(out.getvalue(), """\ Title: exercise Space group symbol from file: sg Space group number from file: 123 Space group from matrices: P 4/m m m (No. 123) Point group symbol from file: pg Number of crystals: 2 Number of Miller indices: 4 Resolution range: 2.67261 1.41421 History: Crystal 1: Name: HKL_base Project: HKL_base Id: 0 Unit cell: (10, 10, 10, 90, 90, 90) Number of datasets: 1 Dataset 1: Name: HKL_base Id: 0 Wavelength: 0 Number of columns: 0 Crystal 2: Name: crystal_1 Project: crystal_1 Id: 1 Unit cell: (10, 10, 10, 90, 90, 90) Number of datasets: 1 Dataset 1: Name: crystal_1 Id: 1 Wavelength: 0 Number of columns: 7 label #valid %valid min max type H 4 100.00% 1.00 3.00 H: index h,k,l K 4 100.00% 2.00 4.00 H: index h,k,l L 4 100.00% 3.00 5.00 H: index h,k,l F 3 75.00% 10.00 30.00 F: amplitude SigF 3 75.00% 1.00 3.00 Q: standard deviation I 3 75.00% 11.00 31.00 F: amplitude SigI 3 75.00% 4.00 6.00 Q: standard deviation """) if (not verbose): out = StringIO() assert mtz_object.show_column_data(out=out) is mtz_object if (not verbose): assert not show_diff(out.getvalue(), """\ Column data: ------------------------------------------------------------------------------- F SigF I SigI 1 2 3 10 1 21 5 2 3 4 20 2 None None 3 4 5 30 3 31 6 2 3 5 None None 11 4 ------------------------------------------------------------------------------- """) mtz_object.write(file_name="tmp_iotbx_mtz_ext.mtz") if (not verbose): out = StringIO() mtz.object(file_name="tmp_iotbx_mtz_ext.mtz").show_summary(out=out) if (not verbose): assert not show_diff(out.getvalue(), """\ Title: exercise Space group symbol from file: sg Space group number from file: 123 Space group from matrices: P 4/m m m (No. 123) Point group symbol from file: pg Number of crystals: 2 Number of Miller indices: 4 Resolution range: 2.67261 1.41421 History: Crystal 1: Name: HKL_base Project: HKL_base Id: 0 Unit cell: (10, 10, 10, 90, 90, 90) Number of datasets: 1 Dataset 1: Name: HKL_base Id: 0 Wavelength: 0 Number of columns: 0 Crystal 2: Name: crystal_1 Project: crystal_1 Id: 2 Unit cell: (10, 10, 10, 90, 90, 90) Number of datasets: 1 Dataset 1: Name: crystal_1 Id: 1 Wavelength: 0 Number of columns: 7 label #valid %valid min max type H 4 100.00% 1.00 3.00 H: index h,k,l K 4 100.00% 2.00 4.00 H: index h,k,l L 4 100.00% 3.00 5.00 H: index h,k,l F 3 75.00% 10.00 30.00 F: amplitude SigF 3 75.00% 1.00 3.00 Q: standard deviation I 3 75.00% 11.00 31.00 F: amplitude SigI 3 75.00% 4.00 6.00 Q: standard deviation """) # original_miller_indices = mtz_object.extract_miller_indices() assert list(original_miller_indices) \ == [(1, 2, 3), (2, 3, 4), (3, 4, 5), (2, 3, 5)] new_miller_indices = flex.miller_index( [(3, -1, 2), (-4, 2, -3), (5, -3, 4), (-5, 2, -3)]) assert not mtz_object.extract_miller_indices().all_eq(new_miller_indices) mtz_object.replace_miller_indices(miller_indices=new_miller_indices) assert mtz_object.extract_miller_indices().all_eq(new_miller_indices) mtz_object.replace_miller_indices(miller_indices=original_miller_indices) assert not mtz_object.extract_miller_indices().all_eq(new_miller_indices) assert mtz_object.extract_miller_indices().all_eq(original_miller_indices) # c = mtz_object.get_column(label="F") s = c.selection_valid() v = c.extract_values(not_a_number_substitute=-1) assert list(s) == [True, True, True, False] assert approx_equal(v, [10.0, 20.0, 30.0, -1.0]) c.set_values(values=flex.float([5,9,3,7]), selection_valid=None) v = c.extract_values(not_a_number_substitute=-1) assert approx_equal(v, [5.0, 9.0, 3.0, 7.0]) c.set_values(values=flex.float([7,8,2,0])) v = c.extract_values(not_a_number_substitute=-1) assert approx_equal(v, [7.0, 8.0, 2.0, 0.0]) c.set_values( values=flex.float([5,9,3,7]), selection_valid=flex.bool([False]*4)) v = c.extract_values(not_a_number_substitute=-1) assert approx_equal(v, [-1]*4) for i_trial in range(10): s = flex.random_bool(size=4, threshold=0.5) v = flex.float(list(flex.random_double(size=4)*10-5)) c.set_values(values=v, selection_valid=s) sx = c.selection_valid() vx = c.extract_values(not_a_number_substitute=99) assert list(s) == list(sx) assert vx.select(s).all_eq(v.select(s)) assert vx.select(~s).all_ne(v.select(~s)) assert vx.select(~s).all_eq(99) # values_in = count() values_out = count() for i_batch in range(10): batch = mtz_object.add_batch() assert batch.num() == i_batch+1 assert batch.set_num(value=next(values_in)) is batch assert batch.num() == next(values_out) assert batch.set_num(value=i_batch+1) is batch assert batch.title() == " " assert batch.set_title("Hello MTZ") is batch assert batch.title() == "Hello MTZ" assert batch.set_title("Hello MTZ"*10) is batch assert len(batch.title()) == 70 assert list(batch.gonlab()) == ["", "", ""] assert batch.set_gonlab( flex.std_string(["what", "ever", "this_is....."])) is batch assert list(batch.gonlab()) == ["what", "ever", "this_is"] assert batch.iortyp() == 0 assert batch.set_iortyp(value=next(values_in)) is batch assert batch.iortyp() == next(values_out) assert list(batch.lbcell()) == [0, 0, 0, 0, 0, 0] assert batch.set_lbcell(flex.int(range(3,9))) is batch assert list(batch.lbcell()) == list(range(3,9)) assert batch.misflg() == 0 assert batch.set_misflg(value=next(values_in)) is batch assert batch.misflg() == next(values_out) assert batch.jumpax() == 0 assert batch.set_jumpax(value=next(values_in)) is batch assert batch.jumpax() == next(values_out) assert batch.ncryst() == 0 assert batch.set_ncryst(value=next(values_in)) is batch assert batch.ncryst() == next(values_out) assert batch.lcrflg() == 0 assert batch.set_lcrflg(value=next(values_in)) is batch assert batch.lcrflg() == next(values_out) assert batch.ldtype() == 0 assert batch.set_ldtype(value=next(values_in)) is batch assert batch.ldtype() == next(values_out) assert batch.jsaxs() == 0 assert batch.set_jsaxs(value=next(values_in)) is batch assert batch.jsaxs() == next(values_out) assert batch.nbscal() == 0 assert batch.set_nbscal(value=next(values_in)) is batch assert batch.nbscal() == next(values_out) assert batch.ngonax() == 0 assert batch.set_ngonax(value=next(values_in)) is batch assert batch.ngonax() == next(values_out) assert batch.lbmflg() == 0 assert batch.set_lbmflg(value=next(values_in)) is batch assert batch.lbmflg() == next(values_out) assert batch.ndet() == 0 assert batch.set_ndet(value=next(values_in) % 3) is batch assert batch.ndet() == next(values_out) % 3 assert batch.nbsetid() == 0 assert batch.set_nbsetid(value=next(values_in)) is batch assert batch.nbsetid() == next(values_out) assert list(batch.cell()) == [0]*6 assert batch.set_cell(flex.float(range(18,24))) is batch assert list(batch.cell()) == list(range(18,24)) assert list(batch.umat()) == [0]*9 assert batch.set_umat(flex.float(range(16,25))) is batch assert list(batch.umat()) == list(range(16,25)) assert list(batch.phixyz()) == [0]*6 assert batch.set_phixyz(flex.float(range(28,34))) is batch assert list(batch.phixyz()) == list(range(28,34)) assert list(batch.crydat()) == [0]*12 assert batch.set_crydat(flex.float(range(26,38))) is batch assert list(batch.crydat()) == list(range(26,38)) assert list(batch.datum()) == [0]*3 assert batch.set_datum(flex.float(range(26,29))) is batch assert list(batch.datum()) == list(range(26,29)) assert batch.phistt() == 0 assert batch.set_phistt(value=next(values_in)) is batch assert batch.phistt() == next(values_out) assert batch.phiend() == 0 assert batch.set_phiend(value=next(values_in)) is batch assert batch.phiend() == next(values_out) assert list(batch.scanax()) == [0]*3 assert batch.set_scanax(flex.float(range(62,65))) is batch assert list(batch.scanax()) == list(range(62,65)) assert batch.time1() == 0 assert batch.set_time1(value=next(values_in)) is batch assert batch.time1() == next(values_out) assert batch.time2() == 0 assert batch.set_time2(value=next(values_in)) is batch assert batch.time2() == next(values_out) assert batch.bscale() == 0 assert batch.set_bscale(value=next(values_in)) is batch assert batch.bscale() == next(values_out) assert batch.bbfac() == 0 assert batch.set_bbfac(value=next(values_in)) is batch assert batch.bbfac() == next(values_out) assert batch.sdbscale() == 0 assert batch.set_sdbscale(value=next(values_in)) is batch assert batch.sdbscale() == next(values_out) assert batch.sdbfac() == 0 assert batch.set_sdbfac(value=next(values_in)) is batch assert batch.sdbfac() == next(values_out) assert batch.phirange() == 0 assert batch.set_phirange(value=next(values_in)) is batch assert batch.phirange() == next(values_out) assert list(batch.e1()) == [0]*3 assert batch.set_e1(flex.float(range(71,74))) is batch assert list(batch.e1()) == list(range(71,74)) assert list(batch.e2()) == [0]*3 assert batch.set_e2(flex.float(range(72,75))) is batch assert list(batch.e2()) == list(range(72,75)) assert list(batch.e3()) == [0]*3 assert batch.set_e3(flex.float(range(73,76))) is batch assert list(batch.e3()) == list(range(73,76)) assert list(batch.source()) == [0]*3 assert batch.set_source(flex.float(range(74,77))) is batch assert list(batch.source()) == list(range(74,77)) assert list(batch.so()) == [0]*3 assert batch.set_so(flex.float(range(75,78))) is batch assert list(batch.so()) == list(range(75,78)) assert batch.alambd() == 0 assert batch.set_alambd(value=next(values_in)) is batch assert batch.alambd() == next(values_out) assert batch.delamb() == 0 assert batch.set_delamb(value=next(values_in)) is batch assert batch.delamb() == next(values_out) assert batch.delcor() == 0 assert batch.set_delcor(value=next(values_in)) is batch assert batch.delcor() == next(values_out) assert batch.divhd() == 0 assert batch.set_divhd(value=next(values_in)) is batch assert batch.divhd() == next(values_out) assert batch.divvd() == 0 assert batch.set_divvd(value=next(values_in)) is batch assert batch.divvd() == next(values_out) assert list(batch.dx()) == [0]*2 assert batch.set_dx(flex.float(range(84,86))) is batch assert list(batch.dx()) == list(range(84,86)) assert list(batch.theta()) == [0]*2 assert batch.set_theta(flex.float(range(85,87))) is batch assert list(batch.theta()) == list(range(85,87)) assert list(batch.detlm()) == [0]*8 assert batch.set_detlm(flex.float(range(86,94))) is batch assert list(batch.detlm()) == list(range(86,94)) if (not verbose): out = StringIO() batch.show(out=out) if (not verbose and i_batch == 3): batch_3_show = out assert not show_diff(out.getvalue(), """\ batch number: 4 batch title: Hello MTZHello MTZHello MTZHello MTZHello MTZHello MTZHello MTZHello M names of the three axes: ['what', 'ever', 'this_is'] type of orientation block: 82 refinement flags for cell: [3, 4, 5, 6, 7, 8] number of phixyz used (0, 1, or 2): 83 reciprocal axis closest to rotation axis: 84 crystal number: 85 mosaicity model: 0 = isotropic, 1 = anisotropic: 86 type of data: 2D (1), 3D (2), or Laue (3): 87 goniostat scan axis number: 88 number of batch scales & Bfactors (0 if unset): 89 number of goniostat axes: 90 flag for type of beam info: 91 0: for alambd, delamb; 1: also delcor, divhd, divvd number of detectors (current maximum 2): 2 dataset id: 93 cell dimensions: [18.0, 19.0, 20.0, 21.0, 22.0, 23.0] orientation matrix U: [16.0, 17.0, 18.0, 19.0, 20.0, 21.0, 22.0, 23.0, 24.0] in Fortranic order, i.e. U(1,1), U(2,1) ... missetting angles at beginning and end of oscillation: [28.0, 29.0, 30.0, 31.0, 32.0, 33.0] mosaicity: [26.0, 27.0, 28.0, 29.0, 30.0, 31.0, 32.0, 33.0, 34.0, 35.0, 36.0, 37.0] datum values of goniostat axes: [26.0, 27.0, 28.0] start of phi relative to datum: 94.0 end of phi relative to datum: 95.0 rotation axis in lab frame: [62.0, 63.0, 64.0] start time: 96.0 stop time: 97.0 batch scale: 98.0 batch temperature factor: 99.0 sd bscale: 100.0 sd bbfac: 101.0 phi range: 102.0 vectors ("Cambridge" laboratory axes) defining ngonax goniostat axes: vector 1: [71.0, 72.0, 73.0] vector 2: [72.0, 73.0, 74.0] vector 3: [73.0, 74.0, 75.0] idealised source vector: [74.0, 75.0, 76.0] source vector: [75.0, 76.0, 77.0] wavelength (A): 103.0 dispersion (deltalambda / lambda): 104.0 correlated component: 105.0 horizontal beam divergence: 106.0 vertical beam divergence: 107.0 xtal to detector distance: [84.0, 85.0] detector tilt angle: [85.0, 86.0] min & max values of detector coords (pixels): [86.0, 87.0, 88.0, 89.0, 90.0, 91.0, 92.0, 93.0] """) mtz_object.write(file_name="tmp_iotbx_mtz_ext.mtz") restored = mtz.object(file_name="tmp_iotbx_mtz_ext.mtz") assert restored.n_batches() == 10 if (not verbose): out = StringIO() restored.batches()[3].show(out=out) if (not verbose): assert out.getvalue() == batch_3_show.getvalue() for i_trial in range(10): perm = flex.random_permutation(size=10) for batch,new_num in zip(mtz_object.batches(), perm): batch.set_num(value=new_num+1) mtz_object.sort_batches() assert [batch.num() for batch in mtz_object.batches()] \ == [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] for batch,nbsetid in zip(mtz_object.batches(), [0,0,1,0,1,1,1,0,1,1]): batch.set_nbsetid(value=nbsetid) for crystal in mtz_object.crystals(): for dataset in crystal.datasets(): assert dataset.id() in [0,1] assert dataset.n_batches() == [4,6][dataset.id()] assert dataset.batches().size() == dataset.n_batches() for batch in dataset.batches(): assert batch.nbsetid() == dataset.id() batch = dataset.add_batch() assert batch.nbsetid() == dataset.id() assert dataset.n_batches() == [5,7][dataset.id()] # quick test for delete_reflection assert mtz_object.n_reflections() > 3 mx = mtz_object.extract_miller_indices()[1] assert mx in mtz_object.extract_miller_indices() mtz_object.delete_reflection(1) assert mx not in mtz_object.extract_miller_indices() # test for delete_reflections isel = flex.size_t((1,0)) try: mtz_object.delete_reflections(isel) except RuntimeError: pass else: raise Exception_expected isel = flex.size_t((0,2)) mx = [mtz_object.extract_miller_indices()[i] for i in isel] for m in mx: assert m in mtz_object.extract_miller_indices() mtz_object.delete_reflections(isel) for m in mx: assert m not in mtz_object.extract_miller_indices() def exercise(): if (mtz is None): print("Skipping iotbx/mtz/tst_ext.py: ccp4io not available") return command_line = (option_parser() .option(None, "--verbose", action="store_true") .option(None, "--forever", action="store_true", help="Infinite loop, for detection of memory leaks") .option(None, "--walk", action="store", type="string", metavar="ROOT_DIR", help="Find and process all MTZ files under ROOT_DIR") .option(None, "--full", action="store_true", help="Visit all MTZ files") ).process(args=sys.argv[1:]) exercise_read_corrupt() exercise_basic() exercise_setting_nref_etc() exercise_modifiers(verbose=command_line.options.verbose) for file_name in command_line.args: exercise_extract_any()(file_name=file_name, out=sys.stdout) if (command_line.options.walk is not None): exercise_walk( root_dir=command_line.options.walk, full=command_line.options.full, verbose=command_line.options.verbose) while (command_line.options.forever): exercise_basic() exercise_modifiers() def run(): exercise() print("OK") if (__name__ == "__main__"): run()