def display_file_info(file_name, parent=None): from iotbx import reflection_file_editor from iotbx import file_reader from iotbx import data_plots hkl_in = file_reader.any_file(file_name, force_type="hkl") hkl_in.check_file_type("hkl") labels = [] tables = [] stats = [] arrays_and_flags = hkl_in.file_server.get_r_free_flags( file_name=hkl_in.file_name, label=None, test_flag_value=None, disable_suitability_test=False, parameter_scope=None, return_all_valid_arrays=True, ) for array, test_flag_value in arrays_and_flags: labels.append(array.info().label_string()) (n_bins, n_free, sse, accu) = reflection_file_editor.get_r_free_stats( miller_array=array, test_flag_value=test_flag_value ) table = data_plots.table_data( title="Distribution of R-free test set", column_labels=["Reflection #", "Fraction counted"], graph_names=["Fraction free vs. resolution"], graph_labels=[["Reflection #", "ntest/total"]], graph_columns=[[0, 1]], data=[accu.reflection_counts, accu.free_fractions], ) tables.append(table) stats.append( group_args( n_free=n_free, n_all=array.indices().size(), percent_free=n_free / array.indices().size(), completeness=array.completeness(), ) ) if len(labels) == 0: raise Sorry("No recognizable R-free flags found in this file.") frame = wx.Frame(parent, -1, "R-free flags info", style=wx.DEFAULT_FRAME_STYLE) szr = wx.BoxSizer(wx.VERTICAL) frame.SetSizer(szr) panel = RfreeInspector(frame, -1) panel.set_data( file_name=file_name, labels=labels, tables=tables, stats=stats, flags_and_values=[(a.data(), f) for (a, f) in arrays_and_flags], ) szr.Add(panel, 1, wx.ALL | wx.EXPAND) szr.Fit(panel) frame.Fit() frame.Show()
def display_file_info(file_name, parent=None): from iotbx import reflection_file_editor from iotbx import file_reader from iotbx import data_plots hkl_in = file_reader.any_file(file_name, force_type="hkl") hkl_in.check_file_type("hkl") labels = [] tables = [] stats = [] arrays_and_flags = hkl_in.file_server.get_r_free_flags( file_name=hkl_in.file_name, label=None, test_flag_value=None, disable_suitability_test=False, parameter_scope=None, return_all_valid_arrays=True) for array, test_flag_value in arrays_and_flags: labels.append(array.info().label_string()) (n_bins, n_free, sse, accu) = reflection_file_editor.get_r_free_stats( miller_array=array, test_flag_value=test_flag_value) table = data_plots.table_data( title="Distribution of R-free test set", column_labels=["Reflection #", "Fraction counted"], graph_names=["Fraction free vs. resolution"], graph_labels=[["Reflection #", "ntest/total"]], graph_columns=[[0, 1]], data=[accu.reflection_counts, accu.free_fractions]) tables.append(table) stats.append( group_args(n_free=n_free, n_all=array.indices().size(), percent_free=n_free / array.indices().size(), completeness=array.completeness())) if (len(labels) == 0): raise Sorry("No recognizable R-free flags found in this file.") frame = wx.Frame(parent, -1, "R-free flags info", style=wx.DEFAULT_FRAME_STYLE) szr = wx.BoxSizer(wx.VERTICAL) frame.SetSizer(szr) panel = RfreeInspector(frame, -1) panel.set_data(file_name=file_name, labels=labels, tables=tables, stats=stats, flags_and_values=[(a.data(), f) for (a, f) in arrays_and_flags]) szr.Add(panel, 1, wx.ALL | wx.EXPAND) szr.Fit(panel) frame.Fit() frame.Show()
def run(args=(), params=None, out=None): if (out is None): out = sys.stdout validate_params(params) from iotbx import reflection_file_editor from iotbx import reflection_file_utils from iotbx import file_reader data_in = file_reader.any_file(params.import_data.data_file, force_type="hkl") data_in.check_file_type("hkl") miller_arrays = data_in.file_server.miller_arrays new_arrays = [] labels = ["H","K","L"] warnings = [] have_r_free = False for array in miller_arrays : if (reflection_file_editor.is_rfree_array(array, array.info())): have_r_free = True if (params.import_data.flags_file is not None): raise Sorry("The data file (%s) already contains R-free flags." % params.import_data.data_file) if (array.is_xray_reconstructed_amplitude_array()): if ("F(+)" in labels): labels.extend(["F_rec(+)", "SIGF_rec(+)", "F_rec(-)", "SIGF_rec(-)"]) else : labels.extend(["F(+)", "SIGF(+)", "F(-)", "SIGF(-)"]) else : labels.extend(array.info().labels) array = array.map_to_asu() if (not array.is_unique_set_under_symmetry()): array = array.merge_equivalents().array() new_arrays.append(array) complete_set = reflection_file_utils.make_joined_set( new_arrays).complete_set() if (not have_r_free): if (params.import_data.flags_file is not None): flags_in = file_reader.any_file(params.import_data.flags_file, force_type="hkl") flags_in.check_file_type("hkl") flags_and_values = flags_in.file_server.get_r_free_flags( file_name=flags_in.file_name, label=None, test_flag_value=None, disable_suitability_test=False, parameter_scope=None, return_all_valid_arrays=True) if (len(flags_and_values) == 0): raise Sorry("No R-free flags were found in the file %s." % params.import_data.flags_file) elif (len(flags_and_values) > 1): raise Sorry(("Multiple valid sets of R-free flags were found in the "+ "file %s. Please use the reflection file editor to select a "+ "single set of flags.") % params.import_data.flags_file) old_flags, test_flag_value = flags_and_values[0] labels.extend(old_flags.info().labels) old_flags = old_flags.map_to_asu().merge_equivalents().array() old_flags = old_flags.customized_copy( data=old_flags.data()==test_flag_value) missing_set = complete_set.lone_set(old_flags) n_missing = missing_set.indices().size() fraction_free = old_flags.data().count(True) / old_flags.data().size() if (n_missing != 0): (n_bins, n_free, sse, accu) = reflection_file_editor.get_r_free_stats( miller_array=old_flags, test_flag_value=True) min_bins = int(old_flags.indices().size() * 0.005) if (n_bins < (n_free / 100)) or (sse > 0.005) or (n_bins < min_bins): if (not params.import_data.ignore_shells): raise Sorry(("The R-free flags in %s appear to have been "+ "assigned in thin resolution shells. PHENIX is unable to "+ "properly extend flags created in this manner. If you "+ "prefer to ignore this check and want to create new flags using "+ "random assignment, or if you think this message is in error, "+ "you can use the reflection file editor instead. "+ "(To view the distribution of R-free flags, click the "+ "toolbar button \"Other tools\" and select \"Inspect R-free "+ "flags\".)") % params.import_data.flags_file) else : print >> out, "WARNING: ignoring thin shells" if (n_missing <= 20) : # XXX hack from scitbx.array_family import flex missing_flags = missing_set.array(data=flex.bool(n_missing, False)) else : missing_flags = missing_set.generate_r_free_flags( fraction_free=fraction_free, max_free=None, use_lattice_symmetry=True) new_flags = old_flags.concatenate(other=missing_flags) else : new_flags = old_flags new_arrays.append(new_flags) mtz_out = new_arrays[0].as_mtz_dataset( column_root_label="A") for i, array in enumerate(new_arrays[1:]): mtz_out.add_miller_array( miller_array=array, column_root_label="%s" % string.uppercase[i+1]) mtz_obj = mtz_out.mtz_object() for i, column in enumerate(mtz_obj.columns()): column.set_label(labels[i]) if (params.import_data.output_file is None): base,ext = os.path.splitext(params.import_data.data_file) params.import_data.output_file = base + "_flags.mtz" mtz_obj.write(file_name=params.import_data.output_file) print >> out, "Data and flags written to %s" % params.import_data.output_file return params.import_data.output_file
def run (args=(), params=None, out=None) : if (out is None) : out = sys.stdout validate_params(params) from iotbx import reflection_file_editor from iotbx import reflection_file_utils from iotbx import file_reader data_in = file_reader.any_file(params.import_data.data_file, force_type="hkl") data_in.check_file_type("hkl") miller_arrays = data_in.file_server.miller_arrays new_arrays = [] labels = ["H","K","L"] warnings = [] have_r_free = False for array in miller_arrays : if (reflection_file_editor.is_rfree_array(array, array.info())) : have_r_free = True if (params.import_data.flags_file is not None) : raise Sorry("The data file (%s) already contains R-free flags." % params.import_data.data_file) if (array.is_xray_reconstructed_amplitude_array()) : if ("F(+)" in labels) : labels.extend(["F_rec(+)", "SIGF_rec(+)", "F_rec(-)", "SIGF_rec(-)"]) else : labels.extend(["F(+)", "SIGF(+)", "F(-)", "SIGF(-)"]) else : labels.extend(array.info().labels) array = array.map_to_asu() if (not array.is_unique_set_under_symmetry()) : array = array.merge_equivalents().array() new_arrays.append(array) complete_set = reflection_file_utils.make_joined_set( new_arrays).complete_set() if (not have_r_free) : if (params.import_data.flags_file is not None) : flags_in = file_reader.any_file(params.import_data.flags_file, force_type="hkl") flags_in.check_file_type("hkl") flags_and_values = flags_in.file_server.get_r_free_flags( file_name=flags_in.file_name, label=None, test_flag_value=None, disable_suitability_test=False, parameter_scope=None, return_all_valid_arrays=True) if (len(flags_and_values) == 0) : raise Sorry("No R-free flags were found in the file %s." % params.import_data.flags_file) elif (len(flags_and_values) > 1) : raise Sorry(("Multiple valid sets of R-free flags were found in the "+ "file %s. Please use the reflection file editor to select a "+ "single set of flags.") % params.import_data.flags_file) old_flags, test_flag_value = flags_and_values[0] labels.extend(old_flags.info().labels) old_flags = old_flags.map_to_asu().merge_equivalents().array() old_flags = old_flags.customized_copy( data=old_flags.data()==test_flag_value) missing_set = complete_set.lone_set(old_flags) n_missing = missing_set.indices().size() fraction_free = old_flags.data().count(True) / old_flags.data().size() if (n_missing != 0) : (n_bins, n_free, sse, accu) = reflection_file_editor.get_r_free_stats( miller_array=old_flags, test_flag_value=True) min_bins = int(old_flags.indices().size() * 0.005) if (n_bins < (n_free / 100)) or (sse > 0.005) or (n_bins < min_bins) : if (not params.import_data.ignore_shells) : raise Sorry(("The R-free flags in %s appear to have been "+ "assigned in thin resolution shells. PHENIX is unable to "+ "properly extend flags created in this manner. If you "+ "prefer to ignore this check and want to create new flags using "+ "random assignment, or if you think this message is in error, "+ "you can use the reflection file editor instead. "+ "(To view the distribution of R-free flags, click the "+ "toolbar button \"Other tools\" and select \"Inspect R-free "+ "flags\".)") % params.import_data.flags_file) else : print >> out, "WARNING: ignoring thin shells" if (n_missing <= 20) : # XXX hack from scitbx.array_family import flex missing_flags = missing_set.array(data=flex.bool(n_missing, False)) else : missing_flags = missing_set.generate_r_free_flags( fraction_free=fraction_free, max_free=None, use_lattice_symmetry=True) new_flags = old_flags.concatenate(other=missing_flags) else : new_flags = old_flags new_arrays.append(new_flags) mtz_out = new_arrays[0].as_mtz_dataset( column_root_label="A") for i, array in enumerate(new_arrays[1:]) : mtz_out.add_miller_array( miller_array=array, column_root_label="%s" % string.uppercase[i+1]) mtz_obj = mtz_out.mtz_object() for i, column in enumerate(mtz_obj.columns()) : column.set_label(labels[i]) if (params.import_data.output_file is None) : base,ext = os.path.splitext(params.import_data.data_file) params.import_data.output_file = base + "_flags.mtz" mtz_obj.write(file_name=params.import_data.output_file) print >> out, "Data and flags written to %s" % params.import_data.output_file return params.import_data.output_file