from __future__ import absolute_import, division, print_function # LIBTBX_PRE_DISPATCHER_INCLUDE_SH export PHENIX_GUI_ENVIRONMENT=1 # LIBTBX_PRE_DISPATCHER_INCLUDE_SH export BOOST_ADAPTBX_FPE_DEFAULT=1 import wxtbx.plots from libtbx.utils import Sorry, Abort, Usage from libtbx import group_args import wx import os import sys def run(args): app = wx.App(0) file_name = None if (len(args) == 0): ask_for_file_name() else : file_name = args[0] if (file_name is None) or (not os.path.isfile(file_name)): raise Usage("wxtbx.inspect_r_free_flags data.mtz") display_file_info(file_name) app.MainLoop() def ask_for_file_name(parent=None): import iotbx.file_reader file_name = wx.FileSelector( message="Select a reflections file", flags=wx.FD_OPEN, wildcard=iotbx.file_reader.get_wildcard_strings(["hkl"])) if (file_name == "") or (file_name is None): raise Abort() return file_name 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() class RfreeInspector(wx.Panel): def __init__(self, *args, **kwds): wx.Panel.__init__(self, *args, **kwds) self.sizer = wx.BoxSizer(wx.VERTICAL) grid = wx.FlexGridSizer(cols=2, rows=4) self.sizer.Add(grid, 0, wx.ALL, 5) grid.Add(wx.StaticText(self, -1, "File name:"), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.file_txt = wx.TextCtrl(self, -1, size=(400,-1), style=wx.TE_READONLY) grid.Add(self.file_txt, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) grid.Add(wx.StaticText(self, -1, "Column(s):"), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.labels_choice = wx.Choice(self, -1, size=(200,-1)) grid.Add(self.labels_choice, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) grid.Add(wx.StaticText(self, -1, "Completeness:"), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.comp_txt = wx.StaticText(self, -1, "", size=(100,-1)) grid.Add(self.comp_txt, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) grid.Add(wx.StaticText(self, -1, "Test set size:"), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.percent_txt = wx.StaticText(self, -1, "", size=(300,-1)) grid.Add(self.percent_txt, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) txt = wx.StaticText(self, -1, """The graph on the right shows the total number of test set \ reflections as a function of resolution. A set picked at random will have an \ approximately straight line; if the test set was picked in thin resolution \ shells to avoid bias caused by non-crystallographic symmetry, it will \ increase in sharp steps. CCTBX/PHENIX can not currently extend a set picked \ in shells; we suggest creating a new set in such cases.""") txt.Wrap(790) self.sizer.Add(txt, 0, wx.ALL, 5) plot_sizer = wx.BoxSizer(wx.HORIZONTAL) self.sizer.Add(plot_sizer, 1, wx.ALL|wx.EXPAND) self.plot1 = RfreeFlagsPlot(self, figure_size=(5,5)) plot_sizer.Add(self.plot1, 1, wx.ALL|wx.EXPAND) self.plot2 = wxtbx.plots.iotbx_data_plot_base( parent=self, tables=[], size=(400,400), show_data_points=False) plot_sizer.Add(self.plot2, 1, wx.ALL|wx.EXPAND) self.SetSizer(self.sizer) self.Bind(wx.EVT_CHOICE, self.OnChooseArray, self.labels_choice) self.stats = [] def set_data(self, file_name, labels, tables, stats, flags_and_values): self.stats = stats self.flags_and_values = flags_and_values self.file_txt.SetValue(file_name) self.labels_choice.SetItems(labels) self.labels_choice.SetSelection(0) self.plot2.set_tables(tables) self.OnChooseArray(None) def OnChooseArray(self, evt): array_selection = self.labels_choice.GetSelection() flags, value = self.flags_and_values[array_selection] self.plot1.show_pie(flags, value) self.plot2.set_plot(graph_name="Fraction free vs. resolution", table_index=array_selection) self.comp_txt.SetLabel("%.2f%%" % (100 * self.stats[array_selection].completeness)) self.percent_txt.SetLabel("%d / %d (%.2f%%)" % (self.stats[array_selection].n_free, self.stats[array_selection].n_all, 100 * self.stats[array_selection].percent_free)) self.Refresh() class RfreeFlagsPlot(wxtbx.plots.plot_container): def show_pie(self, flags, test_flag_value): values = sorted(list(set(flags))) n_values = len(values) labels = [] colors = [] counts = [] for i, value in enumerate(values): if (value == test_flag_value): colors.append((1.,0.,0.)) else : colors.append((0.5*(n_values-i)/n_values, 0.5*(n_values-i)/n_values, 1.)) labels.append(str(value)) counts.append(flags.count(value)) self.figure.clear() p = self.figure.add_subplot(111) p.set_position([0.1,0.1,0.8, 0.8]) p.pie(counts, labels=labels, colors=colors) p.set_title("Flag values") self.canvas.draw() if (__name__ == "__main__"): run(sys.argv[1:])