from __future__ import absolute_import, division, print_function # TODO: # - prompt user for missing symmetry # - cached scenes from crys3d.hklview import view_2d, view_3d from cctbx.miller.display import settings from wxtbx.phil_controls import simple_dialogs from wxtbx import misc_dialogs from wxtbx import icons from wxtbx import bitmaps import wxtbx.symmetry_dialog import wxtbx.utils import wx.glcanvas from wx.lib.agw import floatspin import wx from libtbx import object_oriented_patterns as oop from libtbx.str_utils import format_value from libtbx.utils import Sorry, Abort, to_str import libtbx.load_env from libtbx import group_args from math import sqrt import copy import os class settings_window (wxtbx.utils.SettingsPanel) : is_3d_view = True def __init__ (self, *args, **kwds) : wxtbx.utils.SettingsPanel.__init__(self, *args, **kwds) self.Bind(wx.EVT_CHAR, self.OnChar) def OnChar (self, event) : self.GetParent().viewer.OnChar(event) def add_controls (self) : ''' All the buttoms on the lef hand panel is defined here ''' self._index_span = None self._last_sg_sel = None # # d_min control self.d_min_ctrl = floatspin.FloatSpin(parent=self, increment=0.05, digits=2) self.d_min_ctrl.Bind(wx.EVT_SET_FOCUS, lambda evt: None) if (wx.VERSION >= (2,9)) : # XXX FloatSpin bug in 2.9.2/wxOSX_Cocoa self.d_min_ctrl.SetBackgroundColour(self.GetBackgroundColour()) box = wx.BoxSizer(wx.HORIZONTAL) self.panel_sizer.Add(box) label = wx.StaticText(self,-1,"High resolution:") box.Add(label, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) box.Add(self.d_min_ctrl, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.Bind(floatspin.EVT_FLOATSPIN, self.OnChangeResolution, self.d_min_ctrl) ##Kau added start self.column_ctrl = oop.null() self.column_ctrl = wx.Choice(self.panel, -1, # choices=["jinga","manga","linga","some lable", "ranga"], choices=[], size=(160,-1)) # self.Bind(wx.EVT_CHOICE, self.OnChangeSpaceGroup, self.array_ctrl) self.Bind(wx.EVT_CHOICE, self.OnChangeColumn, self.column_ctrl) # example_file=os.path.join("combine_4zg3.mtz") box = wx.BoxSizer(wx.HORIZONTAL) self.panel_sizer.Add(box) box.Add(wx.StaticText(self.panel, -1, "labels :"), 0, wx.ALL, 5) box.Add(self.column_ctrl, 0, wx.ALL, 5) ##This is to include I/SigI column details self.IoverSigI_ctrl = floatspin.FloatSpin(parent=self, increment=0.25, digits=2) self.IoverSigI_ctrl.Bind(wx.EVT_SET_FOCUS, lambda evt: None) if (wx.VERSION >= (2,9)) : # XXX FloatSpin bug in 2.9.2/wxOSX_Cocoa self.IoverSigI_ctrl.SetBackgroundColour(self.GetBackgroundColour()) box = wx.BoxSizer(wx.HORIZONTAL) self.panel_sizer.Add(box) label = wx.StaticText(self,-1,"I/SigI:") box.Add(label, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) box.Add(self.IoverSigI_ctrl, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.Bind(floatspin.EVT_FLOATSPIN, self.OnChangeIoverSigI, self.IoverSigI_ctrl) ##Kau added ends # # scale control # box = wx.BoxSizer(wx.HORIZONTAL) # self.panel_sizer.Add(box) # label = wx.StaticText(self, -1, "Scale:") # box.Add(label, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) # self.scale_ctrl = wx.Slider(self, size=(120,-1), style=wx.SL_AUTOTICKS) # self.scale_ctrl.SetMin(0) # self.scale_ctrl.SetMax(16) # self.scale_ctrl.SetTickFreq(4, 1) # self.Bind(wx.EVT_SLIDER, self.OnSetScale, self.scale_ctrl) # for x in [0, 4, 8, 12, 16] : # self.scale_ctrl.SetTick(x) # self.scale_ctrl.SetValue((self.settings.scale * 4) - 4) # box.Add(self.scale_ctrl, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) # # ###Kau added starts here # # information control # box = wx.BoxSizer(wx.HORIZONTAL) # self.panel_sizer.Add(box) # label = wx.StaticText(self, -1, "Information content:") # box.Add(label, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) # self.scale_ctrl = wx.Slider(self, size=(120,-1), style=wx.SL_AUTOTICKS) # self.scale_ctrl.SetMin(0) # self.scale_ctrl.SetMax(16) # self.scale_ctrl.SetTickFreq(4, 1) # self.Bind(wx.EVT_SLIDER, self.OnSetScale, self.scale_ctrl) # for x in [0, 4, 8, 12, 16] : # self.scale_ctrl.SetTick(x) # self.scale_ctrl.SetValue((self.settings.scale * 4) - 4) # box.Add(self.scale_ctrl, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) # # ###Kau added ends here ctrls = self.create_controls( setting="black_background", label="Black background") self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5) ctrls = self.create_controls( setting="show_axes", label="Show h,k,l axes") self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5) # ctrls = self.create_controls( # setting="show_data_over_sigma", # label="Use I or F over sigma") # self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5) if (not self.is_3d_view) : # ctrls = self.create_controls( # setting="uniform_size", # label="Use same radius for all points") # self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5) # ctrls = self.create_controls( # setting="sqrt_scale_radii", # label="Scale radii to sqrt(value)") # self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5) # ctrls = self.create_controls( # setting="sqrt_scale_colors", # label="Scale colors to sqrt(value)") # self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5) self.sg_ctrl = oop.null() if (self.is_3d_view) : self.sg_ctrl = wx.Choice(self.panel, -1, choices=[], size=(160,-1)) self.Bind(wx.EVT_CHOICE, self.OnChangeSpaceGroup, self.sg_ctrl) box = wx.BoxSizer(wx.HORIZONTAL) self.panel_sizer.Add(box) box.Add(wx.StaticText(self.panel, -1, "Space group:"), 0, wx.ALL, 5) box.Add(self.sg_ctrl, 0, wx.ALL, 5) ctrls = self.create_controls( setting="expand_to_p1", label="Expand data to P1") ctrls2 = self.create_controls( setting="expand_anomalous", label="show Friedel pairs") box = wx.BoxSizer(wx.HORIZONTAL) self.panel_sizer.Add(box) box.Add(ctrls[0], 0, wx.ALL, 5) box.Add(ctrls2[0], 0, wx.ALL, 5) ctrls = self.create_controls( setting="spheres", label="Display reflections as spheres") self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5) self.spheres_ctrl = ctrls[0] else : self.spheres_ctrl = oop.null() ###Kau added start # d_min control # self.d_min_ctrl = floatspin.FloatSpin(parent=self, increment=0.05, digits=2) # self.d_min_ctrl.Bind(wx.EVT_SET_FOCUS, lambda evt: None) # if (wx.VERSION >= (2,9)) : # XXX FloatSpin bug in 2.9.2/wxOSX_Cocoa # self.d_min_ctrl.SetBackgroundColour(self.GetBackgroundColour()) # box = wx.BoxSizer(wx.HORIZONTAL) # self.panel_sizer.Add(box) # label = wx.StaticText(self,-1,"High resolution:") # box.Add(label, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) # box.Add(self.d_min_ctrl, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) # self.Bind(floatspin.EVT_FLOATSPIN, self.OnChangeResolution, self.d_min_ctrl) ##kau added end box = wx.BoxSizer(wx.HORIZONTAL) self.panel_sizer.Add(box) txt = wx.StaticText(self.panel, -1, "Color scheme:") box.Add(txt, 0, wx.TOP|wx.BOTTOM|wx.LEFT|wx.ALIGN_CENTER_VERTICAL, 5) self.color_ctrl = wx.Choice(self.panel, -1, choices=["rainbow","heatmap","redblue","grayscale","monochrome"]) self.color_ctrl.SetStringSelection(self.settings.color_scheme) box.Add(self.color_ctrl, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.Bind(wx.EVT_CHOICE, self.OnChangeColor, self.color_ctrl) ctrls = self.create_controls( setting="show_missing", label="Show missing reflections") ctrls2 = self.create_controls( setting="show_only_missing", label="only") box = wx.BoxSizer(wx.HORIZONTAL) self.panel_sizer.Add(box) box.Add(ctrls[0], 0, wx.ALL, 5) box.Add(ctrls2[0], 0, wx.ALL, 5) ctrls = self.create_controls( setting="show_systematic_absences", label="Show systematic absences") self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5) if (self.is_3d_view) : ctrls = self.create_controls( setting="sphere_detail", label="Sphere detail level", min=4, max=20) box = wx.BoxSizer(wx.HORIZONTAL) box.Add(ctrls[0], 0, wx.TOP|wx.BOTTOM|wx.LEFT|wx.ALIGN_CENTER_VERTICAL, 5) box.Add(ctrls[1], 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.panel_sizer.Add(box) ctrls = self.create_controls( setting="slice_mode", label="Show only a slice through reciprocal space") self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5) self.slice_ctrl = ctrls[0] ctrls = self.create_controls( setting="keep_constant_scale", label="Keep scale constant across all slices") self.panel_sizer.Add(ctrls[0], 0, wx.ALL, 5) box2 = wx.BoxSizer(wx.HORIZONTAL) box2.Add(wx.StaticText(self.panel, -1, "View slice:"), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) ctrls = self.create_controls self.hkl_choice = wx.Choice(self.panel, -1, choices=["h","k","l"]) self.hkl_choice.SetStringSelection(self.settings.slice_axis) box2.Add(self.hkl_choice, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) box2.Add(wx.StaticText(self.panel, -1, "="), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.slice_index = wx.SpinCtrl(self.panel, -1) self.slice_index.SetValue(self.settings.slice_index) box2.Add(self.slice_index, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.panel_sizer.Add(box2) self.Bind(wx.EVT_CHOICE, self.OnSetSlice, self.hkl_choice) self.Bind(wx.EVT_SPINCTRL, self.OnSetSlice, self.slice_index) # reflection info box box = wx.StaticBox(self.panel, -1, "Reflection info") box_szr = wx.StaticBoxSizer(box, wx.VERTICAL) self.panel_sizer.Add((1,10)) self.panel_sizer.Add(box_szr, 0, wx.EXPAND|wx.ALL) grid_szr = wx.FlexGridSizer(rows=3, cols=2) box_szr.Add(grid_szr, 0, wx.EXPAND|wx.ALL) grid_szr.Add(wx.StaticText(self.panel, -1, "Clicked:"), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.hkl_info = wx.TextCtrl(self.panel, -1, size=(80,-1), style=wx.TE_READONLY) grid_szr.Add(self.hkl_info, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) grid_szr.Add(wx.StaticText(self.panel, -1, "Resolution:"), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.d_min_info = wx.TextCtrl(self.panel, -1, size=(80,-1), style=wx.TE_READONLY) grid_szr.Add(self.d_min_info, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.add_value_widgets(grid_szr) def add_value_widgets (self, sizer) : sizer.Add(wx.StaticText(self.panel, -1, "Value:"), 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) self.value_info = wx.TextCtrl(self.panel, -1, size=(80,-1), style=wx.TE_READONLY) sizer.Add(self.value_info, 0, wx.ALL|wx.ALIGN_CENTER_VERTICAL, 5) def set_index_span (self, index_span) : self._index_span = index_span def update_reflection_info (self, hkl, d_min, value) : print(hkl, value) if (hkl is None) : self.hkl_info.SetValue("") self.d_min_info.SetValue("") self.value_info.SetValue("") else : self.hkl_info.SetValue("%d, %d, %d" % hkl) d_min_str = format_value("%.3g", d_min) self.d_min_info.SetValue(d_min_str) value_str = format_value("%.3g", value, replace_none_with="---") self.value_info.SetValue(value_str) def clear_reflection_info (self) : self.update_reflection_info(None, None, None) def update_space_group_choices (self, miller_array) : from cctbx.sgtbx.subgroups import subgroups from cctbx import sgtbx sg_info = miller_array.space_group_info() subgrs = subgroups(sg_info).groups_parent_setting() choices = [] for subgroup in subgrs : subgroup_info = sgtbx.space_group_info(group=subgroup) choices.append(str(subgroup_info)) if (str(sg_info) in choices) : current = choices.index(str(sg_info)) else : choices.insert(0, str(sg_info)) current = 0 self.sg_ctrl.SetItems(choices) self.sg_ctrl.SetSelection(current) self._last_sg_sel = str(sg_info) # XXXXXXXXXXXXXXXXXXXXXX # Kau added starts here # def update_column_choices (self, array_info,valid_arrays,sel) : def update_column_choices (self,array_info,arrays,sel) : choices=[] # print("Kau printing array_info from within function", array_info) for labels in array_info: choices.append(str(labels)) self.column_ctrl.SetItems(choices) # for f in valid_arrays: # print("Kau last array selected is ", valid_arrays) current=sel self.column_ctrl.SetItems(choices) self.column_ctrl.SetSelection(current) self._last_column_sel = str(sel) # Kau added ends here # XXXXXXXXXXXXXXXXXXXXXX def OnSetSlice (self, event) : if (self._index_span is None) : self.slice_index.SetValue(0) return self.settings.slice_axis = str(self.hkl_choice.GetStringSelection()) axis_index = ["h","k","l"].index(self.settings.slice_axis) min_value = self._index_span.min()[axis_index] max_value = self._index_span.max()[axis_index] self.settings.slice_index = self.slice_index.GetValue() self.slice_index.SetRange(min_value, max_value) if (self.settings.slice_index > max_value) : self.settings.slice_index = max_value self.slice_index.SetValue(max_value) elif (self.settings.slice_index < min_value) : self.settings.slice_index = min_value self.slice_index.SetValue(min_value) if (not self.is_3d_view) or (self.slice_ctrl.GetValue()) : try : self.parent.update_settings() except ValueError as e : # TODO set limits raise Sorry(str(e)) def OnChangeSpaceGroup (self, event) : sg_sel = str(self.sg_ctrl.GetStringSelection()) if (sg_sel != self._last_sg_sel) : from cctbx import sgtbx sg_info = sgtbx.space_group_info(sg_sel) self.parent.set_space_group(sg_info) ####Kau added starts here def OnChangeColumn (self, event) : column_sel = self.column_ctrl.GetSelection() if (column_sel != self._last_column_sel) : self.parent.set_column(column_sel) # ####Kau added ends here def OnChangeResolution (self, event) : self.settings.d_min = self.d_min_ctrl.GetValue() self.parent.update_settings() ####Kau added starts here def OnChangeIoverSigI (self, event) : i_on_sig_i = self.IoverSigI_ctrl.GetValue() self.settings.d_min = self.parent.miller_array.sigma_filter(i_on_sig_i).d_min() self.parent.update_settings() # ####Kau added ends here def OnChangeColor (self, event) : self.settings.color_scheme = str(self.color_ctrl.GetStringSelection()) self.parent.update_settings() def OnSetScale (self, event) : self.settings.scale = (self.scale_ctrl.GetValue() + 4) / 4 self.parent.update_settings() ##kau added starts here # def OnInformationColorChange(self,event): # self.settings.color_scheme = (self.color_ctrl.GetValue()+4) / 4 # set.parent.update_settings() ##Kau added ends here class HKLViewFrame (wx.Frame) : def __init__ (self, *args, **kwds) : wx.Frame.__init__(self, *args, **kwds) self.parent = self.GetParent() self.view_2d = None self.view_3d = None # used by 2D subclass self.statusbar = self.CreateStatusBar() self.sizer = wx.BoxSizer(wx.HORIZONTAL) self.miller_array = None app = wx.GetApp() if (getattr(app, "hklview_settings", None) is not None) : # XXX copying the initial settings avoids awkward interactions when # multiple viewer windows are opened self.settings = copy.deepcopy(app.hklview_settings) else : self.settings = settings() self.create_settings_panel() self.sizer.Add(self.settings_panel, 0, wx.EXPAND) self.create_viewer_panel() self.sizer.Add(self.viewer, 1, wx.EXPAND|wx.ALL) self.SetupToolbar() self.SetupMenus() self.add_view_specific_functions() self.SetMenuBar(self.menubar) self.toolbar.Realize() self.SetSizerAndFit(self.sizer) self.SetMinSize(self.settings_panel.GetSize()) self.Bind(wx.EVT_CLOSE, self.OnClose, self) self.Bind(wx.EVT_WINDOW_DESTROY, self.OnDestroy, self) self.Bind(wx.EVT_ACTIVATE, self.OnActive) self.viewer.SetFocus() def SetupToolbar (self) : self.toolbar = self.CreateToolBar(style=wx.TB_TEXT) if wx.VERSION < (4,0): self.toolbar.AddTool = self.toolbar.AddLabelTool self.toolbar.SetToolBitmapSize((32,32)) btn = self.toolbar.AddTool(-1, label="Load file", bitmap=icons.hkl_file.GetBitmap(), shortHelp="Load file", kind=wx.ITEM_NORMAL) self.Bind(wx.EVT_MENU, self.OnLoadFile, btn) btn = self.toolbar.AddTool(-1, label="Save image", bitmap=icons.save_all.GetBitmap(), shortHelp="Save image", kind=wx.ITEM_NORMAL) self.Bind(wx.EVT_MENU, self.OnSave, btn) btn = self.toolbar.AddTool(-1, label="Delete reflection", bitmap=bitmaps.fetch_icon_bitmap("actions","editdelete"), # FIXME shortHelp="Delete reflection", kind=wx.ITEM_NORMAL) self.Bind(wx.EVT_MENU, self.OnDeleteReflection, btn) def SetupMenus (self) : self.menubar = wx.MenuBar(-1) self.file_menu = wx.Menu() if wx.VERSION < (4,0): self.file_menu.Append = self.file_menu.AppendItem self.menubar.Append(self.file_menu, "File") item = wx.MenuItem(self.file_menu, -1, "Load data...\tCtrl-O") self.Bind(wx.EVT_MENU, self.OnLoadFile, item) self.file_menu.Append(item) if (libtbx.env.has_module("phenix")) : phenix_dir = os.path.dirname(libtbx.env.dist_path("phenix")) examples_dir = os.path.join(phenix_dir, "phenix_examples") if (os.path.isdir(examples_dir)) : submenu = wx.Menu() if wx.VERSION < (4,0): submenu.Append = self.file_menu.AppendItem self.file_menu.AppendSubMenu(submenu, "Load example data") examples_and_data = [ ("p9-sad", "p9.sca"), ("sec17-sad", "sec17.sca"), ("rnase-s", "rnase25.mtz"), ("porin-twin", "porin.mtz"), ] for subdir, data in examples_and_data : example_file = os.path.join(examples_dir, subdir, data) item = wx.MenuItem(submenu, -1, subdir) submenu.Append(item) self.Bind(wx.EVT_MENU, lambda evt, f=example_file: self.load_reflections_file(f), item) def OnActive (self, event) : if (self.IsShown()) and (type(self.viewer).__name__ != "_wxPyDeadObject") : self.viewer.Refresh() def create_viewer_panel (self) : self.viewer = view_3d.hklview_3d(parent=self, size=(800,600), style=wx.glcanvas.WX_GL_DOUBLEBUFFER) def create_settings_panel (self) : self.settings_panel = settings_window(self, -1, style=wx.RAISED_BORDER) # print("I am printing type", type(self.settings_panel)) def add_view_specific_functions (self) : item = wx.MenuItem(self.file_menu, -1, "Show 2D view") self.file_menu.Append(item) self.Bind(wx.EVT_MENU, self.OnShow2D, item) btn = self.toolbar.AddTool(-1, label="Show 2D view", bitmap=icons.hklview_2d.GetBitmap(), shortHelp="Show 2D view", kind=wx.ITEM_NORMAL) self.Bind(wx.EVT_MENU, self.OnShow2D, btn) btn = self.toolbar.AddTool(-1, label="Clear labels", bitmap=icons.clear_left.GetBitmap(), shortHelp="Clear labels", kind=wx.ITEM_NORMAL) self.Bind(wx.EVT_MENU, self.OnClearLabels, btn) def update_clicked (self, index) :#hkl, d_min=None, value=None) : if (index is None) : self.settings_panel.clear_reflection_info() else : hkl, d_min, value = self.viewer.scene.get_reflection_info(index) self.settings_panel.update_reflection_info(hkl, d_min, value) def update_settings_for_unmerged (self) : self.settings.expand_to_p1 = False self.settings.expand_anomalous = False self.settings_panel.get_control("expand_to_p1").SetValue(False) self.settings_panel.get_control("expand_to_p1").Enable(False) self.settings_panel.get_control("expand_anomalous").SetValue(False) self.settings_panel.get_control("expand_anomalous").Enable(False) self.settings_panel.get_control("scale_radii_multiplicity").Enable(False) def update_settings_for_merged (self, enable_multiplicity=False) : self.settings_panel.get_control("expand_to_p1").Enable(True) self.settings_panel.get_control("expand_anomalous").Enable(True) if (enable_multiplicity) : self.settings_panel.get_control("scale_radii_multiplicity").Enable(True) else : self.settings_panel.get_control("scale_radii_multiplicity").Enable(False) def process_miller_array (self, array) : if (array is None) : return if (array.is_hendrickson_lattman_array()) : raise Sorry("Hendrickson-Lattman coefficients are not supported.") info = array.info() if isinstance(info, str) : labels = "TEST DATA" else : labels = info.label_string() if (array.unit_cell() is None) or (array.space_group() is None) : dlg = wxtbx.symmetry_dialog.SymmetryDialog(self, -1, "Enter symmetry") dlg.SetUnitCell(array.unit_cell()) dlg.SetSpaceGroup(array.space_group_info()) if (dlg.ShowModal() == wx.ID_OK) : symm = dlg.GetSymmetry() array = array.customized_copy(crystal_symmetry=symm).set_info(info) wx.CallAfter(dlg.Destroy) details = [] merge = None if (not array.is_unique_set_under_symmetry()) : merge = wx.MessageBox("The data in the selected array are not symmetry-"+ "unique, which usually means they are unmerged (but could also be due "+ "to different indexing conventions). Do you want to merge equivalent "+ "observations (preserving anomalous data if present), or view the "+ "array unmodified? (Note that if you do not merge the array, the "+ "options to expand to P1 or generate Friedel pairs will be be disabled"+ ", and the 2D view will only show indices present in the file, rather "+ "than a full pseudo-precession view.)", style=wx.YES_NO) if (merge == wx.YES) : merge = True #array = array.merge_equivalents().array().set_info(info) details.append("merged") self.update_settings_for_merged(True) else : merge = False details.append("unmerged data") self.update_settings_for_unmerged() else : self.update_settings_for_merged() if array.is_complex_array() : array = array.amplitudes().set_info(info) details.append("as amplitudes") from iotbx.reflection_file_utils import looks_like_r_free_flags_info if (array.is_integer_array()) and (looks_like_r_free_flags_info(info)) : from iotbx.reflection_file_utils import get_r_free_flags_scores score_array = get_r_free_flags_scores([array], None) test_flag_value = score_array.test_flag_values[0] array = array.customized_copy(data=(array.data() == test_flag_value)) array.set_info(info) sg = "%s" % array.space_group_info() uc = "a=%g b=%g c=%g angles=%g,%g,%g" % array.unit_cell().parameters() details_str = "" if (len(details) > 0) : details_str = "(%s)" % ", ".join(details) array_info = group_args( labels=labels, details_str=details_str, merge=merge, sg=sg, uc=uc) return array, array_info def set_miller_array (self, array) : if (array is None) : return array, array_info = self.process_miller_array(array) self.statusbar.SetStatusText("Data: %s %s (Space group: %s Unit Cell: %s)" % (array_info.labels, array_info.details_str, array_info.sg, array_info.uc)) self.settings_panel.d_min_ctrl.SetValue(array.d_min()) self.settings_panel.d_min_ctrl.SetRange(array.d_min(), 20.0) ##kau added starts # self.settings_panel.IoverSigI_ctrl.SetValue(array.sigma_filter(0.0).d_min()) # self.settings_panel.IoverSigI_ctrl.SetRange(array.sigma_filter(0.5).d_min(), 100.0) self.settings_panel.IoverSigI_ctrl.SetValue(0.0) self.settings_panel.IoverSigI_ctrl.SetRange(0.0, 100.0) ##Kau added ends self.settings_panel.set_index_span(array.index_span()) self.settings_panel.update_space_group_choices(array) # self.settings_panel.update_column_choices(array) # kau added if (type(self).__name__ == "HKLViewFrame") : if (array.indices().size() > 100000) : if (self.settings.spheres) : cnf = wx.MessageBox(message="Warning: this is a lot of reflections; "+ "unless you have a very powerful graphics card, displaying "+ "spheres may be slow and/or unstable, especially if data are "+ "expanded to P1. Do you want to switch to a faster rendering "+ "style?", style=wx.YES|wx.NO) if (cnf == wx.YES) : self.settings.spheres = False self.settings_panel.spheres_ctrl.SetValue(False) self.miller_array = array # print("kau this is array ",type(array)) self.viewer.set_miller_array(array, zoom=True, merge=array_info.merge) self.viewer.Refresh() if (self.view_2d is not None) : self.view_2d.set_miller_array(array) def update_settings (self, *args, **kwds) : if (self.miller_array is None) : return False self.viewer.update_settings(*args, **kwds) def set_space_group (self, space_group_info) : # print("kau printing space_group_info ", space_group_info) if (self.miller_array is None) : raise Sorry("No data loaded!") from cctbx import crystal symm = crystal.symmetry( space_group_info=space_group_info, unit_cell=self.miller_array.unit_cell()) array = self.miller_array.expand_to_p1().customized_copy( crystal_symmetry=symm) print("MERGING 2") array = array.merge_equivalents().array().set_info(self.miller_array.info()) self.viewer.set_miller_array(array, zoom=False) self.viewer.Refresh() #kau added starts here def set_column (self, column_sel) : # print("kau printing column_sel ", column_sel) self.set_miller_array(self.valid_arrays[column_sel]) if (self.miller_array is None) : raise Sorry("No data loaded!") # from cctbx import crystal # symm = crystal.symmetry( # space_group_info=space_group_info, # unit_cell=self.miller_array.unit_cell()) # array = self.miller_array.expand_to_p1().customized_copy( # crystal_symmetry=symm) # print "MERGING 2" # array = array.merge_equivalents().array().set_info(self.miller_array.info()) # array=self.miller_array.column_root_label(column_sel) # print("Kau this is array from set_column ", array) # settings_panel.array_storage() # self.viewer.set_miller_array(array[column_sel], zoom=False) self.viewer.Refresh() ##kau added ends here def delete_miller_index (self, hkl) : if (self.miller_array is None) : raise Sorry("No data loaded!") info = self.miller_array.info() self.miller_array = self.miller_array.delete_index(hkl).set_info(info) self.viewer.set_miller_array(self.miller_array, zoom=True) self.viewer.Refresh() def load_reflections_file (self, file_name, set_array=True, data_only=False) : file_name = to_str(file_name) if (file_name != "") : from iotbx.reflection_file_reader import any_reflection_file from iotbx.gui_tools.reflections import get_array_description try : hkl_file = any_reflection_file(file_name) except Exception as e : raise Sorry(to_str(e)) arrays = hkl_file.as_miller_arrays(merge_equivalents=False, )#observation_type_callback=misc_dialogs.get_shelx_file_data_type) #arrays = f.file_server.miller_arrays valid_arrays = [] array_info = [] for array in arrays : if array.is_hendrickson_lattman_array() : continue elif (data_only) : if (not array.is_real_array()) and (not array.is_complex_array()) : continue labels = array.info().label_string() desc = get_array_description(array) array_info.append("%s (%s)" % (labels, desc)) valid_arrays.append(array) self.valid_arrays = valid_arrays if (len(valid_arrays) == 0) : msg = "No arrays of the supported types in this file." raise Sorry(msg) elif (len(valid_arrays) == 1) : if (set_array) : self.set_miller_array(valid_arrays[0]) return valid_arrays[0] else : #dlg = SelectArrayDialog(self, -1, "Select data") dlg = wx.SingleChoiceDialog(parent=None, message="Please select the data you wish to view:", caption="Select data", choices=array_info) # print("kau labels info is", array_info) #Kau added # print("Kau printing array_info from calling ", array_info) if (dlg.ShowModal() == wx.ID_OK) : sel = dlg.GetSelection() if (set_array) : self.set_miller_array(valid_arrays[sel]) wx.CallAfter(dlg.Destroy) self.settings_panel.update_column_choices(array_info, valid_arrays,sel) # kau added # self.settings_panel.update_column_choices(array_info,valid_arrays,sel) # kau added return valid_arrays[sel] wx.CallAfter(dlg.Destroy) raise Abort() def OnLoadFile (self, evt) : file_name = wx.FileSelector("Reflections file", wildcard="Reflection files (*.mtz, *.sca, *.hkl)|*.mtz;*.sca;*.hkl", default_path=os.getcwd(), flags=wx.FD_OPEN) self.load_reflections_file(to_str(file_name)) def OnSave (self, evt) : output_file = wx.FileSelector("Save image as:", default_path=os.getcwd(), default_filename="hklview.png", wildcard="PNG image (*.png)|*.png", flags=wx.FD_SAVE) if (output_file != "") : self.viewer.save_screen_shot(file_name=to_str(output_file), extensions=["png"]) def OnShow2D (self, evt) : if (self.view_2d is None) : self.view_2d = HKLViewFrame2D(self, -1, "2D data viewer") self.view_2d.set_miller_array(self.viewer.miller_array) self.view_2d.Show() if (wxtbx.MAC_OS_X_MAVERICKS) : wx.GetApp().SafeYield(self.view_2d, True) self.view_2d.Raise() def OnDeleteReflection (self, event) : hkl = simple_dialogs.get_miller_index( parent=self, title="Delete reflection", label="h,k,l", caption="Please specify the Miller index (h,k,l) of the reflection "+ "to delete. This will only delete a single value; Friedel mates "+ "and unmerged symmetry-related observations will not be affected.") if (hkl is not None) : self.delete_miller_index(hkl) def OnClearLabels (self, evt) : self.viewer.clear_labels() def OnClose (self, event) : self.Unbind(wx.EVT_ACTIVATE) self.Destroy() event.Skip() def OnDestroy (self, event) : if (self.parent is not None) : self.parent.view_3d = None event.Skip() class settings_window_2d (settings_window) : is_3d_view = False class HKLViewFrame2D (HKLViewFrame) : def create_viewer_panel (self) : self.viewer = view_2d.hklview_2d(parent=self, size=(640,640)) self.viewer.SetMinSize((640,640)) def create_settings_panel (self) : self.settings.expand_to_p1 = True self.settings.expand_anomalous = True self.settings.slice_mode = True #self.settings.black_background = False self.settings_panel = settings_window_2d(self, -1, style=wx.RAISED_BORDER) def add_view_specific_functions (self) : item = wx.MenuItem(self.file_menu, -1, "Show 3D view") self.file_menu.Append(item) self.Bind(wx.EVT_MENU, self.OnShow3D, item) btn = self.toolbar.AddTool(-1, label="Show 3D view", bitmap=icons.hklview_3d.GetBitmap(), shortHelp="Show 3D view", kind=wx.ITEM_NORMAL) self.Bind(wx.EVT_MENU, self.OnShow3D, btn) def update_settings_for_merged (self, enable_multiplicity=False) : self.settings.expand_to_p1 = True self.settings.expand_anomalous = True if (enable_multiplicity) : self.settings_panel.get_control("scale_radii_multiplicity").Enable(True) else : self.settings_panel.get_control("scale_radii_multiplicity").Enable(False) def OnClose (self, evt) : self.Destroy() evt.Skip() def OnDestroy (self, event) : if (self.parent is not None) : self.parent.view_2d = None event.Skip() def OnShow2D (self, evt) : pass def OnShow3D (self, evt) : if (self.view_3d is None) : self.view_3d = HKLViewFrame(self, -1, "3D data viewer") self.view_3d.Show() if (self.viewer.miller_array is not None) : self.view_3d.set_miller_array(self.viewer.miller_array) self.view_3d.Raise()