Source code for GSASIIconstrGUI

# -*- coding: utf-8 -*-
#GSASIIconstrGUI - constraint GUI routines
########### SVN repository information ###################
# $Date: 2021-07-28 14:36:42 +0000 (Wed, 28 Jul 2021) $
# $Author: vondreele $
# $Revision: 5002 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIconstrGUI.py $
# $Id: GSASIIconstrGUI.py 5002 2021-07-28 14:36:42Z vondreele $
########### SVN repository information ###################
'''
*GSASIIconstrGUI: Constraint GUI routines*
------------------------------------------

Used to define constraints and rigid bodies.

'''
from __future__ import division, print_function
import platform
import sys
import copy
import os.path
import wx
import wx.grid as wg
import wx.lib.scrolledpanel as wxscroll
import wx.lib.gridmovers as gridmovers
import random as ran
import numpy as np
import numpy.ma as ma
import numpy.linalg as nl
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 5002 $")
import GSASIIElem as G2elem
import GSASIIElemGUI as G2elemGUI
import GSASIIstrIO as G2stIO
import GSASIImapvars as G2mv
import GSASIImath as G2mth
import GSASIIlattice as G2lat
import GSASIIdataGUI as G2gd
import GSASIIctrlGUI as G2G
import GSASIIfiles as G2fl
import GSASIIplot as G2plt
import GSASIIobj as G2obj
import GSASIIspc as G2spc
import GSASIIpy3 as G2py3
import GSASIIphsGUI as G2phG
import GSASIIIO as G2IO
import GSASIIscriptable as G2sc
VERY_LIGHT_GREY = wx.Colour(235,235,235)
WACV = wx.ALIGN_CENTER_VERTICAL

[docs]class G2BoolEditor(wg.GridCellBoolEditor): '''Substitute for wx.grid.GridCellBoolEditor except toggles grid items immediately when opened, updates grid & table contents after every item change ''' def __init__(self): self.saveVals = None wx.grid.GridCellBoolEditor.__init__(self)
[docs] def Create(self, parent, id, evtHandler): '''Create the editing control (wx.CheckBox) when cell is opened for edit ''' self._tc = wx.CheckBox(parent, -1, "") self._tc.Bind(wx.EVT_CHECKBOX, self.onCheckSet) self.SetControl(self._tc) if evtHandler: self._tc.PushEventHandler(evtHandler)
[docs] def onCheckSet(self, event): '''Callback used when checkbox is toggled. Makes change to table immediately (creating event) ''' if self.saveVals: self.ApplyEdit(*self.saveVals)
[docs] def SetSize(self, rect): '''Set position/size the edit control within the cell's rectangle. ''' # self._tc.SetDimensions(rect.x, rect.y, rect.width+2, rect.height+2, # older self._tc.SetSize(rect.x, rect.y, rect.width+2, rect.height+2, wx.SIZE_ALLOW_MINUS_ONE)
[docs] def BeginEdit(self, row, col, grid): '''Prepares the edit control by loading the initial value from the table (toggles it since you would not click on it if you were not planning to change it), buts saves the original, pre-change value. Makes change to table immediately. Saves the info needed to make updates in self.saveVals. Sets the focus. ''' if grid.GetTable().GetValue(row,col) not in [True,False]: return self.startValue = int(grid.GetTable().GetValue(row, col)) self.saveVals = row, col, grid # invert state and set in editor if self.startValue: grid.GetTable().SetValue(row, col, 0) self._tc.SetValue(0) else: grid.GetTable().SetValue(row, col, 1) self._tc.SetValue(1) self._tc.SetFocus() self.ApplyEdit(*self.saveVals)
[docs] def EndEdit(self, row, col, grid, oldVal=None): '''End editing the cell. This is supposed to return None if the value has not changed, but I am not sure that actually works. ''' val = int(self._tc.GetValue()) if val != oldVal: #self.startValue:? return val else: return None
[docs] def ApplyEdit(self, row, col, grid): '''Save the value into the table, and create event. Called after EndEdit(), BeginEdit and onCheckSet. ''' val = int(self._tc.GetValue()) grid.GetTable().SetValue(row, col, val) # update the table
[docs] def Reset(self): '''Reset the value in the control back to its starting value. ''' self._tc.SetValue(self.startValue)
[docs] def StartingClick(self): '''This seems to be needed for BeginEdit to work properly''' pass
[docs] def Destroy(self): "final cleanup" super(G2BoolEditor, self).Destroy()
[docs] def Clone(self): 'required' return G2BoolEditor()
[docs]class DragableRBGrid(wg.Grid): '''Simple grid implentation for display of rigid body positions. :param parent: frame or panel where grid will be placed :param dict rb: dict with atom labels, types and positions :param function onChange: a callback used every time a value in rb is changed. ''' def __init__(self, parent, rb, onChange=None): #wg.Grid.__init__(self, parent, wx.ID_ANY,size=(-1,200)) wg.Grid.__init__(self, parent, wx.ID_ANY) self.SetTable(RBDataTable(rb,onChange), True) # Enable Row moving gridmovers.GridRowMover(self) self.Bind(gridmovers.EVT_GRID_ROW_MOVE, self.OnRowMove, self) self.SetColSize(0, 60) self.SetColSize(1, 40) self.SetColSize(2, 35) for r in range(len(rb['RBlbls'])): self.SetReadOnly(r,0,isReadOnly=True) self.SetCellEditor(r, 1, G2BoolEditor()) self.SetCellRenderer(r, 1, wg.GridCellBoolRenderer()) self.SetReadOnly(r,2,isReadOnly=True) self.SetCellEditor(r,3, wg.GridCellFloatEditor()) self.SetCellEditor(r,4, wg.GridCellFloatEditor()) self.SetCellEditor(r,6, wg.GridCellFloatEditor())
[docs] def OnRowMove(self,evt): 'called when a row move needs to take place' frm = evt.GetMoveRow() # Row being moved to = evt.GetBeforeRow() # Before which row to insert self.GetTable().MoveRow(frm,to)
[docs] def completeEdits(self): 'complete any outstanding edits' if self.IsCellEditControlEnabled(): # complete any grid edits in progress #if GSASIIpath.GetConfigValue('debug'): print ('Completing grid edit') self.SaveEditControlValue() self.HideCellEditControl() self.DisableCellEditControl()
[docs]class RBDataTable(wg.GridTableBase): '''A Table to support :class:`DragableRBGrid` ''' def __init__(self,rb,onChange): wg.GridTableBase.__init__(self) self.colLabels = ['Label','Select','Type','x','y','z'] self.coords = rb['RBcoords'] self.labels = rb['RBlbls'] self.types = rb['RBtypes'] self.index = rb['RBindex'] self.select = rb['RBselection'] self.onChange = onChange # required methods def GetNumberRows(self): return len(self.labels) def GetNumberCols(self): return len(self.colLabels) def IsEmptyCell(self, row, col): return False def GetValue(self, row, col): row = self.index[row] if col == 0: return self.labels[row] elif col == 1: if self.select[row]: return '1' else: return '' elif col == 2: return self.types[row] else: return '{:.5f}'.format(self.coords[row][col-3]) def SetValue(self, row, col, value): row = self.index[row] try: if col == 0: self.labels[row] = value elif col == 1: self.select[row] = bool(value) elif col == 2: self.types[row] = value else: self.coords[row][col-3] = float(value) except: pass if self.onChange: self.onChange() # Display column & row labels def GetColLabelValue(self, col): return self.colLabels[col] def GetRowLabelValue(self,row): return str(row) # Implement "row movement" by updating the pointer array def MoveRow(self,frm,to): grid = self.GetView() if grid: move = self.index[frm] del self.index[frm] if frm > to: self.index.insert(to,move) else: self.index.insert(to-1,move) # Notify the grid grid.BeginBatch() msg = wg.GridTableMessage( self, wg.GRIDTABLE_NOTIFY_ROWS_DELETED, frm, 1 ) grid.ProcessTableMessage(msg) msg = wg.GridTableMessage( self, wg.GRIDTABLE_NOTIFY_ROWS_INSERTED, to, 1 ) grid.ProcessTableMessage(msg) grid.EndBatch() if self.onChange: self.onChange()
# def MakeDrawAtom(data,atom): # 'Convert atom to format needed to draw it' # generalData = data['General'] # deftype = G2obj.validateAtomDrawType( # GSASIIpath.GetConfigValue('DrawAtoms_default'),generalData) # if generalData['Type'] in ['nuclear','faulted',]: # atomInfo = [atom[:2]+atom[3:6]+['1']+[deftype]+ # ['']+[[255,255,255]]+atom[9:]+[[],[]]][0] # ct,cs = [1,8] #type & color # atNum = generalData['AtomTypes'].index(atom[ct]) # atomInfo[cs] = list(generalData['Color'][atNum]) # return atomInfo
[docs]class ConstraintDialog(wx.Dialog): '''Window to edit Constraint values ''' def __init__(self,parent,title,text,data,separator='*',varname="",varyflag=False): wx.Dialog.__init__(self,parent,-1,'Edit '+title, pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) self.data = data[:] self.newvar = [varname,varyflag] panel = wx.Panel(self) mainSizer = wx.BoxSizer(wx.VERTICAL) topLabl = wx.StaticText(panel,-1,text) mainSizer.Add((10,10),1) mainSizer.Add(topLabl,0,wx.LEFT,10) mainSizer.Add((10,10),1) dataGridSizer = wx.FlexGridSizer(cols=3,hgap=2,vgap=2) self.OkBtn = wx.Button(panel,wx.ID_OK) for id in range(len(self.data)): lbl1 = lbl = str(self.data[id][1]) if lbl[-1] != '=': lbl1 = lbl + ' ' + separator + ' ' name = wx.StaticText(panel,wx.ID_ANY,lbl1,style=wx.ALIGN_RIGHT) scale = G2G.ValidatedTxtCtrl(panel,self.data[id],0,OKcontrol=self.DisableOK) dataGridSizer.Add(name,0,wx.LEFT|wx.RIGHT|WACV,5) dataGridSizer.Add(scale,0,wx.RIGHT,3) if ':' in lbl: dataGridSizer.Add( wx.StaticText(panel,-1,G2obj.fmtVarDescr(lbl)), 0,wx.RIGHT|WACV,3) else: dataGridSizer.Add((-1,-1)) if title == 'New Variable': name = wx.StaticText(panel,wx.ID_ANY,"New variable's\nname (optional)", style=wx.ALIGN_CENTER) scale = G2G.ValidatedTxtCtrl(panel,self.newvar,0,notBlank=False) dataGridSizer.Add(name,0,wx.LEFT|wx.RIGHT|WACV,5) dataGridSizer.Add(scale,0,wx.RIGHT|WACV,3) self.refine = wx.CheckBox(panel,label='Refine?') self.refine.SetValue(self.newvar[1]==True) self.refine.Bind(wx.EVT_CHECKBOX, self.OnCheckBox) dataGridSizer.Add(self.refine,0,wx.RIGHT|WACV,3) mainSizer.Add(dataGridSizer,0,wx.EXPAND) self.OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) self.OkBtn.SetDefault() cancelBtn = wx.Button(panel,wx.ID_CANCEL) cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) btnSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer.Add((20,20),1) btnSizer.Add(self.OkBtn) btnSizer.Add((20,20),1) btnSizer.Add(cancelBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.EXPAND, 10) panel.SetSizer(mainSizer) panel.Fit() self.Fit() self.CenterOnParent() def DisableOK(self,setting): for id in range(len(self.data)): # coefficient cannot be zero try: if abs(self.data[id][0]) < 1.e-20: setting = False break except: pass if setting: self.OkBtn.Enable() else: self.OkBtn.Disable() def OnCheckBox(self,event): self.newvar[1] = self.refine.GetValue() def OnOk(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_OK) def OnCancel(self,event): parent = self.GetParent() parent.Raise() self.EndModal(wx.ID_CANCEL) def GetData(self): return self.data
##### Constraints ################################################################################
[docs]def UpdateConstraints(G2frame,data): '''Called when Constraints tree item is selected. Displays the constraints in the data window ''' def FindEquivVarb(name,nameList): 'Creates a list of variables appropriate to constrain with name' outList = [] #phlist = [] items = name.split(':') namelist = [items[2],] if 'dA' in name: namelist = ['dAx','dAy','dAz'] elif 'AU' in name: namelist = ['AUiso','AU11','AU22','AU33','AU12','AU13','AU23'] elif 'AM' in name: namelist = ['AMx','AMy','AMz'] elif items[-1] in ['A0','A1','A2','A3','A4','A5']: namelist = ['A0','A1','A2','A3','A4','A5'] elif items[-1] in ['D11','D22','D33','D12','D13','D23']: namelist = ['D11','D22','D33','D12','D13','D23'] elif 'Tm' in name: namelist = ['Tmin','Tmax'] elif 'MX' in name or 'MY' in name or 'MZ' in name: namelist = ['MXcos','MYcos','MZcos','MXsin','MYsin','MZsin'] elif 'mV' in name: namelist = ['mV0','mV1','mV2'] elif 'Debye' in name or 'BkPk' in name: #special cases for Background fxns dbname = name.split(';')[0].split(':')[2] return [item for item in nameList if dbname in item] elif 'RB' in name: rbfx = 'RB'+items[2][2] if 'T' in name and 'Tr' not in name: namelist = [rbfx+'T11',rbfx+'T22',rbfx+'T33',rbfx+'T12',rbfx+'T13',rbfx+'T23'] if 'L' in name: namelist = [rbfx+'L11',rbfx+'L22',rbfx+'L33',rbfx+'L12',rbfx+'L13',rbfx+'L23'] if 'S' in name: namelist = [rbfx+'S12',rbfx+'S13',rbfx+'S21',rbfx+'S23',rbfx+'S31',rbfx+'S32',rbfx+'SAA',rbfx+'SBB'] if 'U' in name: namelist = [rbfx+'U',] for item in nameList: keys = item.split(':') #if keys[0] not in phlist: # phlist.append(keys[0]) if items[1] == '*' and keys[2] in namelist: # wildcard -- select only sequential options keys[1] = '*' mitem = ':'.join(keys) if mitem == name: continue if mitem not in outList: outList.append(mitem) elif keys[2] in namelist and item != name: outList.append(item) return outList def SelectVarbs(page,FrstVarb,varList,legend,constType): '''Select variables used in constraints after one variable has been selected. This routine determines the appropriate variables to be used based on the one that has been selected and asks for more to be added. It then creates the constraint and adds it to the constraints list. Called from OnAddEquivalence, OnAddFunction & OnAddConstraint (all but OnAddHold) :param list page: defines calling page -- type of variables to be used :parm GSASIIobj.G2VarObj FrstVarb: reference to first selected variable :param list varList: list of other appropriate variables to select from :param str legend: header for selection dialog :param str constType: type of constraint to be generated :returns: a constraint, as defined in :ref:`GSASIIobj <Constraint_definitions_table>` ''' choices = [[i]+list(G2obj.VarDescr(i)) for i in varList] meaning = G2obj.getDescr(FrstVarb.name) if not meaning: meaning = "(no definition found!)" l = str(FrstVarb).split(':') # make lists of phases & histograms to iterate over phaselist = [l[0]] if l[0]: phaselbl = ['phase #'+l[0]] if len(Phases) > 1: phaselist += ['all'] phaselbl += ['all phases'] else: phaselbl = [''] histlist = [l[1]] if l[1] == '*': pass elif l[1]: histlbl = ['histogram #'+l[1]] if len(Histograms) > 1: histlist += ['all'] histlbl += ['all histograms'] typ = Histograms[G2obj.LookupHistName(l[1])[0]]['Instrument Parameters'][0]['Type'][1] i = 0 for hist in Histograms: if Histograms[hist]['Instrument Parameters'][0]['Type'][1] == typ: i += 1 if i > 1: histlist += ['all='+typ] histlbl += ['all '+typ+' histograms'] else: histlbl = [''] # make a list of equivalent parameter names nameList = [FrstVarb.name] for var in varList: nam = var.split(":")[2] if nam not in nameList: nameList += [nam] # add "wild-card" names to the list of variables if l[1] == '*': pass elif page[1] == 'phs': if 'RB' in FrstVarb.name: pass elif FrstVarb.atom is None: for nam in nameList: for ph,plbl in zip(phaselist,phaselbl): if plbl: plbl = 'For ' + plbl var = ph+"::"+nam if var == str(FrstVarb) or var in varList: continue varList += [var] choices.append([var,plbl,meaning]) else: for nam in nameList: for ph,plbl in zip(phaselist,phaselbl): if plbl: plbl = ' in ' + plbl for atype in ['']+TypeList: if atype: albl = "For "+atype+" atoms" akey = "all="+atype else: albl = "For all atoms" akey = "all" var = ph+"::"+nam+":"+akey if var == str(FrstVarb) or var in varList: continue varList += [var] choices.append([var,albl+plbl,meaning]) elif page[1] == 'hap': if FrstVarb.name == "Scale": meaning = "Phase fraction" for nam in nameList: for ph,plbl in zip(phaselist,phaselbl): if plbl: plbl = 'For ' + plbl for hst,hlbl in zip(histlist,histlbl): if hlbl: if plbl: hlbl = ' in ' + hlbl else: hlbl = 'For ' + hlbl var = ph+":"+hst+":"+nam if var == str(FrstVarb) or var in varList: continue varList += [var] choices.append([var,plbl+hlbl,meaning]) elif page[1] == 'hst': if FrstVarb.name == "Scale": meaning = "Scale factor" for nam in nameList: for hst,hlbl in zip(histlist,histlbl): if hlbl: hlbl = 'For ' + hlbl var = ":"+hst+":"+nam if var == str(FrstVarb) or var in varList: continue varList += [var] choices.append([var,hlbl,meaning]) elif page[1] == 'glb' or page[1] == 'sym': pass else: raise Exception('Unknown constraint page '+ page[1]) if len(choices): l1 = l2 = 1 for i1,i2,i3 in choices: l1 = max(l1,len(i1)) l2 = max(l2,len(i2)) fmt = "{:"+str(l1)+"s} {:"+str(l2)+"s} {:s}" atchoices = [fmt.format(*i1) for i1 in choices] # reformat list as str with columns dlg = G2G.G2MultiChoiceDialog( G2frame,legend, 'Constrain '+str(FrstVarb)+' with...',atchoices, toggle=False,size=(625,400),monoFont=True) dlg.CenterOnParent() res = dlg.ShowModal() Selections = dlg.GetSelections()[:] dlg.Destroy() if res != wx.ID_OK: return [] if len(Selections) == 0: dlg = wx.MessageDialog( G2frame, 'No variables were selected to include with '+str(FrstVarb), 'No variables') dlg.CenterOnParent() dlg.ShowModal() dlg.Destroy() return [] else: dlg = wx.MessageDialog( G2frame, 'There are no appropriate variables to include with '+str(FrstVarb), 'No variables') dlg.CenterOnParent() dlg.ShowModal() dlg.Destroy() return [] # now process the variables provided by the user varbs = [str(FrstVarb),] # list of selected variables for sel in Selections: var = varList[sel] # phase(s) included l = var.split(':') if l[0] == "all": phlist = [str(Phases[phase]['pId']) for phase in Phases] else: phlist = [l[0]] # histogram(s) included if l[1] == "all": hstlist = [str(Histograms[hist]['hId']) for hist in Histograms] elif '=' in l[1]: htyp = l[1].split('=')[1] hstlist = [str(Histograms[hist]['hId']) for hist in Histograms if Histograms[hist]['Instrument Parameters'][0]['Type'][1] == htyp] else: hstlist = [l[1]] if len(l) == 3: for ph in phlist: for hst in hstlist: var = ph + ":" + hst + ":" + l[2] if var in varbs: continue varbs.append(var) else: # constraints with atoms or rigid bodies if len(l) == 5: # rigid body parameter var = ':'.join(l) if var in varbs: continue varbs.append(var) elif l[3] == "all": for ph in phlist: key = G2obj.LookupPhaseName(ph)[0] for hst in hstlist: # should be blank for iatm,at in enumerate(Phases[key]['Atoms']): var = ph + ":" + hst + ":" + l[2] + ":" + str(iatm) if var in varbs: continue varbs.append(var) elif '=' in l[3]: for ph in phlist: key = G2obj.LookupPhaseName(ph)[0] cx,ct,cs,cia = Phases[key]['General']['AtomPtrs'] for hst in hstlist: # should be blank atyp = l[3].split('=')[1] for iatm,at in enumerate(Phases[key]['Atoms']): if at[ct] != atyp: continue var = ph + ":" + hst + ":" + l[2] + ":" + str(iatm) if var in varbs: continue varbs.append(var) else: for ph in phlist: key = G2obj.LookupPhaseName(ph)[0] for hst in hstlist: # should be blank var = ph + ":" + hst + ":" + l[2] + ":" + l[3] if var in varbs: continue varbs.append(var) if len(varbs) >= 1 or 'constraint' in constType: constr = [[1.0,FrstVarb]] for item in varbs[1:]: constr += [[1.0,G2obj.G2VarObj(item)]] if 'equivalence' in constType: return [constr+[None,None,'e']] elif 'function' in constType: return [constr+[None,False,'f']] elif 'constraint' in constType: return [constr+[1.0,None,'c']] else: raise Exception('Unknown constraint type: '+str(constType)) else: dlg = wx.MessageDialog( G2frame, 'There are no selected variables to include with '+str(FrstVarb), 'No variables') dlg.CenterOnParent() dlg.ShowModal() dlg.Destroy() return [] def ConstraintsLoad(data,newcons=[]): '''Load all constraints. Constraints based on symmetry (etc.) are generated by running :func:`GSASIIstrIO.GetPhaseData`. ''' G2mv.InitVars() #Find all constraints constraintSet = [] for key in data: if key.startswith('_'): continue constraintSet += data[key] if newcons: constraintSet = constraintSet + newcons constDictList,fixedList,ignored = G2stIO.ProcessConstraints(constraintSet) # generate symmetry constraints to check for conflicts rigidbodyDict = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies')) rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False) (Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables, BLtables,MFtables,maxSSwave) = G2stIO.GetPhaseData( Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints return constDictList,phaseDict,fixedList def ConstraintsCheck(data,newcons=[],reqVaryList=None): '''Load constraints & check them for errors. Since error checking can cause changes in constraints in case of repairable conflicts between equivalences, reload the constraints again after the check. This could probably be done more effectively, but only reloading when needed, but the reload should be quick. When reqVaryList is included (see WarnConstraintLimit) then parameters with limits are checked against constraints and a warning is shown. ''' constDictList,phaseDict,fixedList = ConstraintsLoad(data,newcons) msg = G2mv.EvaluateMultipliers(constDictList,phaseDict) if msg: return 'Unable to interpret multiplier(s): '+msg,'' res = G2mv.CheckConstraints('',constDictList,fixedList) # reload constraints in case any were merged in MoveConfEquiv constDictList,phaseDict,fixedList = ConstraintsLoad(data,newcons) impossible = [] if reqVaryList: Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls')) for key in ('parmMinDict','parmMaxDict','parmFrozen'): if key not in Controls: Controls[key] = {} varyList = reqVaryList[:] try: G2mv.GenerateConstraints(varyList,constDictList,fixedList,phaseDict) G2mv.Map2Dict(phaseDict,varyList) # check for limits on dependent vars consVars = [i for i in reqVaryList if i not in varyList] impossible = set( [str(i) for i in Controls['parmMinDict'] if i in consVars] + [str(i) for i in Controls['parmMaxDict'] if i in consVars]) except G2mv.ConstraintException: pass if impossible: msg = '' for i in sorted(impossible): if msg: msg += ', ' msg += i msg = ' &'.join(msg.rsplit(',',1)) msg = ('Note: limits on variable(s) '+msg+ ' will be ignored because they are constrained.') G2G.G2MessageBox(G2frame,msg,'Limits ignored for constrained vars') return res def CheckAddedConstraint(newcons): '''Check a new constraint that has just been input. If there is an error display a message and discard the last entry Since the varylist is not available, no warning messages should be generated here :returns: True if constraint should be added ''' errmsg,warnmsg = ConstraintsCheck(data,newcons) if errmsg: G2frame.ErrorDialog('Constraint Error', 'Error with newly added constraint:\n'+errmsg+ '\nIgnoring newly added constraint',parent=G2frame) # reset error status errmsg,warnmsg = ConstraintsCheck(data) if errmsg: print (errmsg) print (G2mv.VarRemapShow([],True)) return False elif warnmsg: print ('Unexpected contraint warning:\n'+warnmsg) return True def WarnConstraintLimit(): '''Check if constraints reference variables with limits. Displays a warning message, but does nothing ''' try: parmDict,reqVaryList = G2frame.MakeLSParmDict() errmsg,warnmsg = ConstraintsCheck(data,[],reqVaryList) except: print('Error retrieving parameters') def CheckChangedConstraint(): '''Check all constraints after an edit has been made. If there is an error display a message and reject the change. Since the varylist is not available, no warning messages should be generated. :returns: True if the edit should be retained ''' errmsg,warnmsg = ConstraintsCheck(data) if errmsg: G2frame.ErrorDialog('Constraint Error', 'Error after editing constraint:\n'+errmsg+ '\nDiscarding last constraint edit',parent=G2frame) # reset error status errmsg,warnmsg = ConstraintsCheck(data) if errmsg: print (errmsg) print (G2mv.VarRemapShow([],True)) return False elif warnmsg: print ('Unexpected contraint warning:\n'+warnmsg) return True def PageSelection(page): 'Decode page reference' if page[1] == "phs": vartype = "phase" varList = G2obj.removeNonRefined(phaseList) # remove any non-refinable prms from list constrDictEnt = 'Phase' elif page[1] == "hap": vartype = "Histogram*Phase" varList = G2obj.removeNonRefined(hapList) # remove any non-refinable prms from list constrDictEnt = 'HAP' elif page[1] == "hst": vartype = "Histogram" varList = G2obj.removeNonRefined(histList) # remove any non-refinable prms from list constrDictEnt = 'Hist' elif page[1] == "glb": vartype = "Global" varList = G2obj.removeNonRefined(globalList) # remove any non-refinable prms from list constrDictEnt = 'Global' elif page[1] == "sym": return None,None,None else: raise Exception('Should not happen!') return vartype,varList,constrDictEnt def OnAddHold(event): '''Create a new Hold constraint Hold constraints allows the user to select one variable (the list of available variables depends on which tab is currently active). ''' page = G2frame.Page vartype,varList,constrDictEnt = PageSelection(page) if vartype is None: return varList = G2obj.SortVariables(varList) title1 = "Hold "+vartype+" variable" if not varList: G2frame.ErrorDialog('No variables','There are no variables of type '+vartype, parent=G2frame) return l2 = l1 = 1 for i in varList: l1 = max(l1,len(i)) loc,desc = G2obj.VarDescr(i) l2 = max(l2,len(loc)) fmt = "{:"+str(l1)+"s} {:"+str(l2)+"s} {:s}" varListlbl = [fmt.format(i,*G2obj.VarDescr(i)) for i in varList] #varListlbl = ["("+i+") "+G2obj.fmtVarDescr(i) for i in varList] legend = "Select variables to hold (Will not be varied, even if vary flag is set)" dlg = G2G.G2MultiChoiceDialog(G2frame, legend,title1,varListlbl,toggle=False,size=(625,400),monoFont=True) dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: for sel in dlg.GetSelections(): Varb = varList[sel] VarObj = G2obj.G2VarObj(Varb) newcons = [[[0.0,VarObj],None,None,'h']] if CheckAddedConstraint(newcons): data[constrDictEnt] += newcons dlg.Destroy() wx.CallAfter(OnPageChanged,None) def OnAddEquivalence(event): '''add an Equivalence constraint''' page = G2frame.Page vartype,varList,constrDictEnt = PageSelection(page) if vartype is None: return title1 = "Create equivalence constraint between "+vartype+" variables" title2 = "Select additional "+vartype+" variable(s) to be equivalent with " if not varList: G2frame.ErrorDialog('No variables','There are no variables of type '+vartype, parent=G2frame) return # legend = "Select variables to make equivalent (only one of the variables will be varied when all are set to be varied)" GetAddVars(page,title1,title2,varList,constrDictEnt,'equivalence') def OnAddAtomEquiv(event): ''' Add equivalences between all parameters on atoms ''' page = G2frame.Page vartype,varList,constrDictEnt = PageSelection(page) if vartype is None: return title1 = "Setup equivalent atom variables" title2 = "Select additional atoms(s) to be equivalent with " if not varList: G2frame.ErrorDialog('No variables','There are no variables of type '+vartype, parent=G2frame) return # legend = "Select atoms to make equivalent (only one of the atom variables will be varied when all are set to be varied)" GetAddAtomVars(page,title1,title2,varList,constrDictEnt,'equivalence') def OnAddRiding(event): ''' Add riding equivalences between all parameters on atoms - not currently used''' page = G2frame.Page vartype,varList,constrDictEnt = PageSelection(page) if vartype is None: return title1 = "Setup riding atoms " title2 = "Select additional atoms(s) to ride on " if not varList: G2frame.ErrorDialog('No variables','There are no variables of type '+vartype, parent=G2frame) return # legend = "Select atoms to ride (only one of the atom variables will be varied when all are set to be varied)" GetAddAtomVars(page,title1,title2,varList,constrDictEnt,'riding') def OnAddFunction(event): '''add a Function (new variable) constraint''' page = G2frame.Page vartype,varList,constrDictEnt = PageSelection(page) if vartype is None: return title1 = "Setup new variable based on "+vartype+" variables" title2 = "Include additional "+vartype+" variable(s) to be included with " if not varList: G2frame.ErrorDialog('No variables','There are no variables of type '+vartype, parent=G2frame) return # legend = "Select variables to include in a new variable (the new variable will be varied when all included variables are varied)" GetAddVars(page,title1,title2,varList,constrDictEnt,'function') def OnAddConstraint(event): '''add a constraint equation to the constraints list''' page = G2frame.Page vartype,varList,constrDictEnt = PageSelection(page) if vartype is None: return title1 = "Creating constraint on "+vartype+" variables" title2 = "Select additional "+vartype+" variable(s) to include in constraint with " if not varList: G2frame.ErrorDialog('No variables','There are no variables of type '+vartype, parent=G2frame) return # legend = "Select variables to include in a constraint equation (the values will be constrainted to equal a specified constant)" GetAddVars(page,title1,title2,varList,constrDictEnt,'constraint') def GetAddVars(page,title1,title2,varList,constrDictEnt,constType): '''Get the variables to be added for OnAddEquivalence, OnAddFunction, and OnAddConstraint. Then create and check the constraint. ''' #varListlbl = ["("+i+") "+G2obj.fmtVarDescr(i) for i in varList] if constType == 'equivalence': omitVars = G2mv.GetDependentVars() else: omitVars = [] varList = G2obj.SortVariables([i for i in varList if i not in omitVars]) l2 = l1 = 1 for i in varList: l1 = max(l1,len(i)) loc,desc = G2obj.VarDescr(i) l2 = max(l2,len(loc)) fmt = "{:"+str(l1)+"s} {:"+str(l2)+"s} {:s}" varListlbl = [fmt.format(i,*G2obj.VarDescr(i)) for i in varList] dlg = G2G.G2SingleChoiceDialog(G2frame,'Select 1st variable:', title1,varListlbl,monoFont=True,size=(625,400)) dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: if constType == 'equivalence': omitVars = G2mv.GetDependentVars() + G2mv.GetIndependentVars() sel = dlg.GetSelection() FrstVarb = varList[sel] VarObj = G2obj.G2VarObj(FrstVarb) moreVarb = G2obj.SortVariables(FindEquivVarb(FrstVarb,[i for i in varList if i not in omitVars])) newcons = SelectVarbs(page,VarObj,moreVarb,title2+FrstVarb,constType) if len(newcons) > 0: if CheckAddedConstraint(newcons): data[constrDictEnt] += newcons dlg.Destroy() WarnConstraintLimit() wx.CallAfter(OnPageChanged,None) def FindNeighbors(phase,FrstName,AtNames): General = phase['General'] cx,ct,cs,cia = General['AtomPtrs'] Atoms = phase['Atoms'] atNames = [atom[ct-1] for atom in Atoms] Cell = General['Cell'][1:7] Amat,Bmat = G2lat.cell2AB(Cell) atTypes = General['AtomTypes'] Radii = np.array(General['BondRadii']) AtInfo = dict(zip(atTypes,Radii)) #or General['BondRadii'] Orig = atNames.index(FrstName.split()[1]) OType = Atoms[Orig][ct] XYZ = G2mth.getAtomXYZ(Atoms,cx) Neigh = [] Dx = np.inner(Amat,XYZ-XYZ[Orig]).T dist = np.sqrt(np.sum(Dx**2,axis=1)) sumR = AtInfo[OType]+0.5 #H-atoms only! IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.)) for j in IndB[0]: if j != Orig: Neigh.append(AtNames[j]) return Neigh def GetAddAtomVars(page,title1,title2,varList,constrDictEnt,constType): '''Get the atom variables to be added for OnAddAtomEquiv. Then create and check the constraints. Riding for H atoms only. ''' Atoms = {G2obj.VarDescr(i)[0]:[] for i in varList if 'Atom' in G2obj.VarDescr(i)[0]} for item in varList: atName = G2obj.VarDescr(item)[0] if atName in Atoms: Atoms[atName].append(item) AtNames = list(Atoms.keys()) AtNames.sort() dlg = G2G.G2SingleChoiceDialog(G2frame,'Select 1st atom:', title1,AtNames,monoFont=True,size=(625,400)) dlg.CenterOnParent() FrstAtom = '' if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() FrstAtom = AtNames[sel] if 'riding' in constType: phaseName = (FrstAtom.split(' in ')[1]).strip() phase = Phases[phaseName] AtNames = FindNeighbors(phase,FrstAtom,AtNames) else: AtNames.remove(FrstAtom) dlg.Destroy() if FrstAtom == '': print ('no atom selected') return dlg = G2G.G2MultiChoiceDialog( G2frame,title2+FrstAtom, 'Constrain '+str(FrstAtom)+' with...',AtNames, toggle=False,size=(625,400),monoFont=True) if dlg.ShowModal() == wx.ID_OK: Selections = dlg.GetSelections()[:] else: print ('no target atom selected') dlg.Destroy() return dlg.Destroy() for name in Atoms[FrstAtom]: newcons = [] constr = [] if 'riding' in constType: if 'AUiso' in name: constr = [[1.0,G2obj.G2VarObj(name)]] elif 'AU11' in name: pass elif 'AU' not in name: constr = [[1.0,G2obj.G2VarObj(name)]] else: constr = [[1.0,G2obj.G2VarObj(name)]] pref = ':'+name.rsplit(':',1)[0].split(':',1)[1] #get stuff between phase id & atom id for sel in Selections: name2 = Atoms[AtNames[sel]][0] pid = name2.split(':',1)[0] #get phase id for 2nd atom id = name2.rsplit(':',1)[-1] #get atom no. for 2nd atom if 'riding' in constType: pref = pid+pref if 'AUiso' in pref: parts = pref.split('AUiso') constr += [[1.2,G2obj.G2VarObj('%s:%s'%(parts[0]+'AUiso',id))]] elif 'AU' not in pref: constr += [[1.0,G2obj.G2VarObj('%s:%s'%(pref,id))]] else: constr += [[1.0,G2obj.G2VarObj('%s:%s'%(pid+pref,id))]] if not constr: continue if 'frac' in pref and 'riding' not in constType: newcons = [constr+[1.0,None,'c']] else: newcons = [constr+[None,None,'e']] if len(newcons) > 0: if CheckAddedConstraint(newcons): data[constrDictEnt] += newcons WarnConstraintLimit() wx.CallAfter(OnPageChanged,None) def MakeConstraintsSizer(name,pageDisplay): '''Creates a sizer displaying all of the constraints entered of the specified type. :param str name: the type of constraints to be displayed ('HAP', 'Hist', 'Phase', 'Global', 'Sym-Generated') :param wx.Panel pageDisplay: parent panel for sizer :returns: wx.Sizer created by method ''' if name == 'Sym-Generated': #show symmetry generated constraints Sizer1 = wx.BoxSizer(wx.VERTICAL) if symHolds: Sizer1.Add(wx.StaticText(pageDisplay,wx.ID_ANY, 'Position variables fixed by space group symmetry')) Sizer1.Add((-1,5)) Sizer = wx.FlexGridSizer(0,2,0,0) Sizer1.Add(Sizer) for var in symHolds: Sizer.Add(wx.StaticText(pageDisplay,wx.ID_ANY,' FIXED'), 0,WACV|wx.ALIGN_CENTER|wx.RIGHT|wx.LEFT,3) Sizer.Add(wx.StaticText(pageDisplay,wx.ID_ANY,var)) Sizer.Add((-1,-1)) Sizer.Add((-1,2)) else: Sizer1.Add(wx.StaticText(pageDisplay,wx.ID_ANY, 'No holds generated')) Sizer1.Add((-1,10)) symGen = G2mv.GetSymEquiv() if len(symGen) == 0: Sizer1.Add(wx.StaticText(pageDisplay,wx.ID_ANY, 'No equvalences generated')) return Sizer1 Sizer1.Add(wx.StaticText(pageDisplay,wx.ID_ANY, 'Equivalences generated based on cell/space group input')) Sizer1.Add((-1,5)) Sizer = wx.FlexGridSizer(0,2,0,0) Sizer1.Add(Sizer) for sym in symGen: Sizer.Add(wx.StaticText(pageDisplay,wx.ID_ANY,' EQUIV'), 0,WACV|wx.ALIGN_CENTER|wx.RIGHT|wx.LEFT,3) Sizer.Add(wx.StaticText(pageDisplay,wx.ID_ANY,sym)) Sizer.Add((-1,-1)) Sizer.Add((-1,2)) return Sizer1 constSizer = wx.FlexGridSizer(0,6,0,0) maxlen = 50 # characters before wrapping a constraint for Id,item in enumerate(data[name]): refineflag = False helptext = "" eqString = ['',] problemItem = False badVar = False for term in item[:-3]: if str(term[1]) in G2mv.problemVars: problemItem = True if item[-1] == 'h': # Hold on variable constSizer.Add((-1,-1),0) # blank space for edit button typeString = 'FIXED' var = str(item[0][1]) if '?' in var: badVar = True varMean = G2obj.fmtVarDescr(var) eqString[-1] = var +' ' helptext = "Prevents variable:\n"+ var + " ("+ varMean + ")\nfrom being changed" elif item[-1] == 'f' or item[-1] == 'e' or item[-1] == 'c': # not true on original-style (2011?) constraints constEdit = wx.Button(pageDisplay,wx.ID_ANY,'Edit',style=wx.BU_EXACTFIT) constEdit.Bind(wx.EVT_BUTTON,OnConstEdit) constSizer.Add(constEdit,0,wx.LEFT|wx.RIGHT|WACV|wx.ALIGN_CENTER,1) # edit button Indx[constEdit.GetId()] = [Id,name] if item[-1] == 'f': helptext = "A new variable" if item[-3]: helptext += " named "+str(item[-3]) helptext += " is created from a linear combination of the following variables:\n" for term in item[:-3]: var = str(term[1]) if '?' in var: badVar = True if len(eqString[-1]) > maxlen: eqString.append(' ') m = term[0] if eqString[-1] != '': if m >= 0: eqString[-1] += ' + ' else: eqString[-1] += ' - ' m = abs(m) if m == 1: eqString[-1] += '{:} '.format(var) else: eqString[-1] += '{:g}*{:} '.format(m,var) varMean = G2obj.fmtVarDescr(var) helptext += '\n{:3g} * {:} '.format(m,var) + " ("+ varMean + ")" # Add ISODISTORT help items if '_Explain' in data: # this ignores the phase number. TODO: refactor that in hlptxt = None try: hlptxt = data['_Explain'].get(item[-3]) except TypeError: # note that phase RanId is item[-3].phase hlptxt = data['_Explain'].get(str(item[-3].phase)+item[-3].name) if hlptxt: helptext += '\n\n' helptext += hlptxt if item[-3]: typeString = '(NEWVAR) ' + str(item[-3]) + ' = ' else: typeString = 'New Variable = ' #print 'refine',item[-2] refineflag = True elif item[-1] == 'c': helptext = "The following variables constrained to equal a constant:" for term in item[:-3]: var = str(term[1]) if '?' in var: badVar = True if len(eqString[-1]) > maxlen: eqString.append(' ') m = term[0] if eqString[-1] != '': if term[0] > 0: eqString[-1] += ' + ' else: eqString[-1] += ' - ' m = -term[0] if m == 1: eqString[-1] += '{:} '.format(var) else: eqString[-1] += '{:g}*{:} '.format(m,var) varMean = G2obj.fmtVarDescr(var) helptext += '\n{:3g} * {:} '.format(m,var) + " ("+ varMean + ")" typeString = 'CONST' eqString[-1] += ' = '+str(item[-3]) elif item[-1] == 'e' and len(item[:-3]) == 2: if item[0][0] == 0: item[0][0] = 1.0 if item[1][0] == 0: item[1][0] = 1.0 var = str(item[0][1]) if '?' in var: badVar = True helptext = 'Variable {:} '.format(var) + " ("+ G2obj.fmtVarDescr(var) + ")" helptext += "\n\nis equivalent to " m = item[0][0]/item[1][0] var1 = str(item[1][1]) helptext += '\n{:3g} * {:} '.format(m,var1) + " ("+ G2obj.fmtVarDescr(var1) + ")" eqString[-1] += '{:} = {:}'.format(var1,var) if m != 1: eqString[-1] += ' / ' + str(m) typeString = 'EQUIV' elif item[-1] == 'e': helptext = "The following variable:" normval = item[0][0] indepterm = item[0][1] for i,term in enumerate(item[:-3]): var = str(term[1]) if '?' in var: badVar = True if term[0] == 0: term[0] = 1.0 if len(eqString[-1]) > maxlen: eqString.append(' ') varMean = G2obj.fmtVarDescr(var) if i == 0: # move independent variable to end, as requested by Bob helptext += '\n{:} '.format(var) + " ("+ varMean + ")" helptext += "\n\nis equivalent to the following, noting multipliers:" continue elif eqString[-1] != '': eqString[-1] += ' = ' #m = normval/term[0] m = term[0]/normval if m == 1: eqString[-1] += '{:}'.format(var) else: eqString[-1] += '{:g}*{:} '.format(m,var) helptext += '\n{:3g} * {:} '.format(m,var) + " ("+ varMean + ")" eqString[-1] += ' = {:} '.format(indepterm) typeString = 'EQUIV' else: print ('Unexpected constraint'+item) else: print ('Removing old-style constraints') data[name] = [] return constSizer constDel = wx.Button(pageDisplay,wx.ID_ANY,'Delete',style=wx.BU_EXACTFIT) constDel.Bind(wx.EVT_BUTTON,OnConstDel) Indx[constDel.GetId()] = [Id,name] constSizer.Add(constDel,0,wx.LEFT|wx.RIGHT|WACV|wx.ALIGN_CENTER,1) # delete button if helptext: ch = G2G.HelpButton(pageDisplay,helptext) constSizer.Add(ch,0,wx.LEFT|wx.RIGHT|WACV|wx.ALIGN_CENTER,1) else: constSizer.Add((-1,-1)) if refineflag: ch = G2G.G2CheckBox(pageDisplay,'',item,-2) constSizer.Add(ch,0,wx.LEFT|wx.RIGHT|WACV|wx.ALIGN_CENTER,1) else: constSizer.Add((-1,-1)) constSizer.Add(wx.StaticText(pageDisplay,wx.ID_ANY,typeString), 0,WACV|wx.ALIGN_CENTER|wx.RIGHT|wx.LEFT,3) if badVar: eqString[-1] += ' -- Error: variable removed' if problemItem: eqString[-1] += ' -- Conflict: see console' if len(eqString) > 1: Eq = wx.BoxSizer(wx.VERTICAL) for s in eqString: line = wx.StaticText(pageDisplay,wx.ID_ANY,s) if problemItem: line.SetBackgroundColour(wx.YELLOW) Eq.Add(line,0) Eq.Add((-1,4)) else: Eq = wx.StaticText(pageDisplay,wx.ID_ANY,eqString[0]) if problemItem or badVar: Eq.SetBackgroundColour(wx.YELLOW) constSizer.Add(Eq,1,WACV) return constSizer def OnConstDel(event): 'Delete a constraint' Obj = event.GetEventObject() Id,name = Indx[Obj.GetId()] del data[name][Id] ConstraintsLoad(data) wx.CallAfter(OnPageChanged,None) def OnConstEdit(event): '''Called to edit an individual contraint in response to a click on its Edit button ''' Obj = event.GetEventObject() Id,name = Indx[Obj.GetId()] if data[name][Id][-1] == 'f': items = data[name][Id][:-3] constType = 'New Variable' if data[name][Id][-3]: varname = str(data[name][Id][-3]) else: varname = "" lbl = 'Enter value for each term in constraint; sum = new variable' dlg = ConstraintDialog(G2frame,constType,lbl,items, varname=varname,varyflag=data[name][Id][-2]) elif data[name][Id][-1] == 'c': items = data[name][Id][:-3]+[ [str(data[name][Id][-3]),'fixed value =']] constType = 'Constraint' lbl = 'Edit value for each term in constant constraint sum' dlg = ConstraintDialog(G2frame,constType,lbl,items) elif data[name][Id][-1] == 'e': items = data[name][Id][:-3] constType = 'Equivalence' lbl = 'The following terms are set to be equal:' dlg = ConstraintDialog(G2frame,constType,lbl,items,'*') else: return try: prev = copy.deepcopy(data[name][Id]) if dlg.ShowModal() == wx.ID_OK: result = dlg.GetData() for i in range(len(data[name][Id][:-3])): if type(data[name][Id][i]) is tuple: # fix non-mutable construct data[name][Id][i] = list(data[name][Id][i]) data[name][Id][i][0] = result[i][0] if data[name][Id][-1] == 'c': data[name][Id][-3] = str(result[-1][0]) elif data[name][Id][-1] == 'f': data[name][Id][-2] = dlg.newvar[1] if dlg.newvar[0]: # process the variable name to put in global form (::var) varname = str(dlg.newvar[0]).strip().replace(' ','_') if varname.startswith('::'): varname = varname[2:] varname = varname.replace(':',';') if varname: data[name][Id][-3] = varname else: data[name][Id][-3] = '' if not CheckChangedConstraint(): data[name][Id] = prev else: data[name][Id] = prev except: import traceback print (traceback.format_exc()) finally: dlg.Destroy() wx.CallAfter(OnPageChanged,None) def UpdateConstraintPanel(panel,typ): '''Update the contents of the selected Constraint notebook tab. Called in :func:`OnPageChanged` ''' if panel.GetSizer(): panel.GetSizer().Clear(True) Siz = wx.BoxSizer(wx.VERTICAL) Siz.Add((5,5),0) Siz.Add(MakeConstraintsSizer(typ,panel),1,wx.EXPAND) panel.SetSizer(Siz,True) Size = Siz.GetMinSize() Size[0] += 40 Size[1] = max(Size[1],450) + 20 panel.SetSize(Size) panel.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1) panel.Show() def OnPageChanged(event): '''Called when a tab is pressed or when a "select tab" menu button is used (see RaisePage), or to refresh the current tab contents (event=None) ''' if event: #page change event! page = event.GetSelection() else: # called directly, get current page try: page = G2frame.constr.GetSelection() except: if GSASIIpath.GetConfigValue('debug'): print('DBG_gpx open error:C++ Run time error - skipped') return G2frame.constr.ChangeSelection(page) text = G2frame.constr.GetPageText(page) G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_EQUIVALANCEATOMS,False) # G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_ADDRIDING,False) if text == 'Histogram/Phase': enableEditCons = [False]+4*[True] G2frame.Page = [page,'hap'] UpdateConstraintPanel(HAPConstr,'HAP') elif text == 'Histogram': enableEditCons = [False]+4*[True] G2frame.Page = [page,'hst'] UpdateConstraintPanel(HistConstr,'Hist') elif text == 'Phase': enableEditCons = 5*[True] G2frame.Page = [page,'phs'] G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_EQUIVALANCEATOMS,True) # G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_ADDRIDING,True) if 'DELETED' in str(PhaseConstr): #seems to be no other way to do this (wx bug) if GSASIIpath.GetConfigValue('debug'): print ('DBG_wx error: PhaseConstr not cleanly deleted after Refine') return UpdateConstraintPanel(PhaseConstr,'Phase') elif text == 'Global': enableEditCons = [False]+4*[True] G2frame.Page = [page,'glb'] UpdateConstraintPanel(GlobalConstr,'Global') else: enableEditCons = 5*[False] G2frame.Page = [page,'sym'] UpdateConstraintPanel(SymConstr,'Sym-Generated') # remove menu items when not allowed for obj,flag in zip(G2frame.dataWindow.ConstraintEdit.GetMenuItems(),enableEditCons): obj.Enable(flag) G2frame.dataWindow.SetDataSize() def RaisePage(event): 'Respond to a "select tab" menu button' try: i = (G2G.wxID_CONSPHASE, G2G.wxID_CONSHAP, G2G.wxID_CONSHIST, G2G.wxID_CONSGLOBAL, G2G.wxID_CONSSYM, ).index(event.GetId()) G2frame.constr.SetSelection(i) wx.CallAfter(OnPageChanged,None) except ValueError: print('Unexpected event in RaisePage') def SetStatusLine(text): G2frame.GetStatusBar().SetStatusText(text,1) def OnShowISODISTORT(event): ShowIsoDistortCalc(G2frame) #### UpdateConstraints execution starts here ############################## if not data: data.update({'Hist':[],'HAP':[],'Phase':[],'Global':[]}) #empty dict - fill it if 'Global' not in data: #patch data['Global'] = [] # DEBUG code #===================================== #import GSASIIconstrGUI #reload(GSASIIconstrGUI) #reload(G2obj) #reload(G2stIO) #import GSASIIstrMain #reload(GSASIIstrMain) #reload(G2mv) #reload(G2gd) #=================================================== Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree() if not len(Phases) or not len(Histograms): dlg = wx.MessageDialog(G2frame,'You need both phases and histograms to see Constraints', 'No phases or histograms') dlg.CenterOnParent() dlg.ShowModal() dlg.Destroy() return G2obj.IndexAllIds(Histograms,Phases) for p in Phases: if 'ISODISTORT' in Phases[p]: G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_SHOWISO,True) break ###### patch: convert old-style (str) variables in constraints to G2VarObj objects ##### for key,value in data.items(): if key.startswith('_'): continue j = 0 for cons in value: #print cons # DEBUG for i in range(len(cons[:-3])): if type(cons[i][1]) is str: cons[i][1] = G2obj.G2VarObj(cons[i][1]) j += 1 if j: print (str(key) + ': '+str(j)+' variable(s) as strings converted to objects') ##### end patch ############################################################################# rigidbodyDict = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Rigid bodies')) rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]}) rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False) badPhaseParms = ['Ax','Ay','Az','Amul','AI/A','Atype','SHorder','AwaveType','FwaveType','PwaveType','MwaveType','Vol','isMag',] globalList = list(rbDict.keys()) globalList.sort() try: AtomDict = dict([Phases[phase]['pId'],Phases[phase]['Atoms']] for phase in Phases) except KeyError: G2frame.ErrorDialog('Constraint Error','Constraints cannot be set until a cycle of least squares'+ ' has been run.\nWe suggest you refine a scale factor.') return # create a list of the phase variables symHolds = [] (Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtable,BLtable, MFtable,maxSSwave) = G2stIO.GetPhaseData( Phases,rbIds=rbIds,Print=False,symHold=symHolds) phaseList = [] for item in phaseDict: if item.split(':')[2] not in badPhaseParms: phaseList.append(item) phaseList.sort() phaseAtNames = {} phaseAtTypes = {} TypeList = [] for item in phaseList: Split = item.split(':') if Split[2][:2] in ['AU','Af','dA','AM']: Id = int(Split[0]) phaseAtNames[item] = AtomDict[Id][int(Split[3])][0] phaseAtTypes[item] = AtomDict[Id][int(Split[3])][1] if phaseAtTypes[item] not in TypeList: TypeList.append(phaseAtTypes[item]) else: phaseAtNames[item] = '' phaseAtTypes[item] = '' # create a list of the hist*phase variables seqList = G2frame.testSeqRefineMode() if seqList: # for sequential refinement, only process 1st histgram in list histDict = {seqList[0]:Histograms[seqList[0]]} else: histDict = Histograms hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,histDict,Print=False,resetRefList=False) hapList = sorted([i for i in hapDict.keys() if i.split(':')[2] not in ('Type',)]) if seqList: # convert histogram # to wildcard wildList = [] # list of variables with "*" for histogram number for i in hapList: s = i.split(':') if s[1] == "": continue s[1] = '*' sj = ':'.join(s) if sj not in wildList: wildList.append(sj) hapList = wildList histVary,histDict,controlDict = G2stIO.GetHistogramData(histDict,Print=False) histList = list(histDict.keys()) histList.sort() if seqList: # convert histogram # to wildcard wildList = [] # list of variables with "*" for histogram number for i in histList: s = i.split(':') if s[1] == "": continue s[1] = '*' sj = ':'.join(s) if sj not in wildList: wildList.append(sj) histList = wildList Indx = {} G2frame.Page = [0,'phs'] G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.ConstraintMenu) SetStatusLine('') G2frame.Bind(wx.EVT_MENU, OnAddConstraint, id=G2G.wxID_CONSTRAINTADD) G2frame.Bind(wx.EVT_MENU, OnAddFunction, id=G2G.wxID_FUNCTADD) G2frame.Bind(wx.EVT_MENU, OnAddEquivalence, id=G2G.wxID_EQUIVADD) G2frame.Bind(wx.EVT_MENU, OnAddHold, id=G2G.wxID_HOLDADD) G2frame.Bind(wx.EVT_MENU, OnAddAtomEquiv, id=G2G.wxID_EQUIVALANCEATOMS) # G2frame.Bind(wx.EVT_MENU, OnAddRiding, id=G2G.wxID_ADDRIDING) G2frame.Bind(wx.EVT_MENU, OnShowISODISTORT, id=G2G.wxID_SHOWISO) # tab commands for id in (G2G.wxID_CONSPHASE, G2G.wxID_CONSHAP, G2G.wxID_CONSHIST, G2G.wxID_CONSGLOBAL, G2G.wxID_CONSSYM, ): G2frame.Bind(wx.EVT_MENU, RaisePage,id=id) #G2frame.constr = G2G.GSNoteBook(parent=G2frame.dataWindow,size=G2frame.dataWindow.GetClientSize()) G2frame.constr = G2G.GSNoteBook(parent=G2frame.dataWindow) G2frame.dataWindow.GetSizer().Add(G2frame.constr,1,wx.ALL|wx.EXPAND) # note that order of pages is hard-coded in RaisePage PhaseConstr = wx.ScrolledWindow(G2frame.constr) G2frame.constr.AddPage(PhaseConstr,'Phase') HAPConstr = wx.ScrolledWindow(G2frame.constr) G2frame.constr.AddPage(HAPConstr,'Histogram/Phase') HistConstr = wx.ScrolledWindow(G2frame.constr) G2frame.constr.AddPage(HistConstr,'Histogram') GlobalConstr = wx.ScrolledWindow(G2frame.constr) G2frame.constr.AddPage(GlobalConstr,'Global') SymConstr = wx.ScrolledWindow(G2frame.constr) G2frame.constr.AddPage(SymConstr,'Sym-Generated') wx.CallAfter(OnPageChanged,None) G2frame.constr.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged) # validate all the constrants -- should not see any errors here normally errmsg,warnmsg = ConstraintsCheck(data) if errmsg: G2frame.ErrorDialog('Constraint Error', 'Error in constraints:\n'+errmsg+'\nCheck console output for more information', parent=G2frame) print (errmsg) print (G2mv.VarRemapShow([],True)) return elif warnmsg: print ('Unexpected contraint warning:\n'+warnmsg) WarnConstraintLimit()
###### check scale & phase fractions, create constraint if needed #############
[docs]def CheckAllScalePhaseFractions(G2frame): '''Check if scale factor and all phase fractions are refined without a constraint for all used histograms, if so, offer the user a chance to create a constraint on the sum of phase fractions ''' histograms, phases = G2frame.GetUsedHistogramsAndPhasesfromTree() for i,hist in enumerate(histograms): CheckScalePhaseFractions(G2frame,hist,histograms,phases)
[docs]def CheckScalePhaseFractions(G2frame,hist,histograms,phases): '''Check if scale factor and all phase fractions are refined without a constraint for histogram hist, if so, offer the user a chance to create a constraint on the sum of phase fractions ''' if G2frame.testSeqRefineMode(): histStr = '*' else: histStr = str(histograms[hist]['hId']) # Is this powder? if not hist.startswith('PWDR '): return # do this only if the scale factor is varied if not histograms[hist]['Sample Parameters']['Scale'][1]: return # are all phase fractions varied in all used histograms? phaseCount = 0 for p in phases: if hist not in phases[p]['Histograms']: continue if phases[p]['Histograms'][hist]['Use'] and not phases[p]['Histograms'][hist]['Scale'][1]: return else: phaseCount += 1 # all phase fractions and scale factor varied, now scan through constraints sub = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Constraints') Constraints = G2frame.GPXtree.GetItemPyData(sub) for c in Constraints.get('HAP',[]): if c[-1] != 'c': continue if not c[-3]: continue if len(c[:-3]) != phaseCount: continue # got a constraint equation with right number of terms, is it on phase fractions for # the correct histogram? if all([(i[1].name == 'Scale' and i[1].varname().split(':')[1] == histStr) for i in c[:-3]]): # got a constraint, this is OK return dlg = wx.MessageDialog(G2frame,'You are refining the scale factor and all phase fractions for histogram #'+ histStr+'. This will produce an unstable refinement. '+ 'Do you want to constrain the sum of phase fractions?','Create constraint?',wx.OK|wx.CANCEL) if dlg.ShowModal() != wx.ID_OK: dlg.Destroy() return dlg.Destroy() constr = [] for p in phases: if hist not in phases[p]['Histograms']: continue if not phases[p]['Histograms'][hist]['Use']: continue constr += [[1.0,G2obj.G2VarObj(':'.join((str(phases[p]['pId']),histStr,'Scale')))]] constr += [1.0,None,'c'] Constraints['HAP'] += [constr]
#### Make nuclear/magnetic phase transition constraints - called by OnTransform in G2phsGUI ##########
[docs]def TransConstraints(G2frame,oldPhase,newPhase,Trans,Vec,atCodes): '''Add constraints for new magnetic phase created via transformation of old nuclear one NB: A = [G11,G22,G33,2*G12,2*G13,2*G23] ''' def SetUniqAj(pId,iA,SGData): SGLaue = SGData['SGLaue'] SGUniq = SGData['SGUniq'] if SGLaue in ['m3','m3m']: if iA in [0,1,2]: parm = '%d::%s'%(pId,'A0') else: parm = None elif SGLaue in ['4/m','4/mmm']: if iA in [0,1]: parm = '%d::%s'%(pId,'A0') elif iA == 2: parm = '%d::%s'%(pId,'A2') else: parm = None elif SGLaue in ['6/m','6/mmm','3m1', '31m', '3']: if iA in [0,1,3]: parm = '%d::%s'%(pId,'A0') elif iA == 2: parm = '%d::%s'%(pId,'A2') else: parm = None elif SGLaue in ['3R', '3mR']: if ia in [0,1,2]: parm = '%d::%s'%(pId,'A0') else: parm = '%d::%s'%(pId,'A3') elif SGLaue in ['mmm',]: if iA in [0,1,2]: parm = '%d::A%s'%(pId,iA) else: parm = None elif SGLaue == '2/m': if iA in [0,1,2]: parm = '%d::A%s'%(pId,iA) elif iA == 3 and SGUniq == 'c': parm = '%d::A%s'%(pId,iA) elif iA == 4 and SGUniq == 'b': parm = '%d::A%s'%(pId,iA) elif iA == 5 and SGUniq == 'a': parm = '%d::A%s'%(pId,iA) else: parm = None else: parm = '%d::A%s'%(pId,iA) return parm Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree() UseList = newPhase['Histograms'] detTrans = np.abs(nl.det(Trans)) opId = oldPhase['pId'] npId = newPhase['pId'] cx,ct,cs,cia = newPhase['General']['AtomPtrs'] nAtoms = newPhase['Atoms'] nSGData = newPhase['General']['SGData'] #oAcof = G2lat.cell2A(oldPhase['General']['Cell'][1:7]) #nAcof = G2lat.cell2A(newPhase['General']['Cell'][1:7]) item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Constraints') if not item: print('Error: no constraints in Data Tree') return constraints = G2frame.GPXtree.GetItemPyData(item) xnames = ['dAx','dAy','dAz'] # constraints on matching atom params between phases for ia,code in enumerate(atCodes): atom = nAtoms[ia] if not ia and atom[cia] == 'A': wx.MessageDialog(G2frame, 'Anisotropic thermal motion constraints are not developed at the present time', 'Anisotropic thermal constraint?',style=wx.ICON_INFORMATION).ShowModal() siteSym = G2spc.SytSym(atom[cx:cx+3],nSGData)[0] CSX = G2spc.GetCSxinel(siteSym) # CSU = G2spc.GetCSuinel(siteSym) item = code.split('+')[0] iat,opr = item.split(':') Nop = abs(int(opr))%100-1 if '-' in opr: Nop *= -1 Opr = oldPhase['General']['SGData']['SGOps'][abs(Nop)][0] if Nop < 0: #inversion Opr *= -1 XOpr = np.inner(Opr,Trans) invOpr = nl.inv(XOpr) for i,ix in enumerate(list(CSX[0])): if not ix: continue name = xnames[i] IndpCon = [1.0,G2obj.G2VarObj('%d::%s:%d'%(npId,name,ia))] DepCons = [] for iop,opval in enumerate(invOpr[i]): if abs(opval) > 1e-6: DepCons.append([opval,G2obj.G2VarObj('%d::%s:%s'%(opId,xnames[iop],iat))]) if len(DepCons) == 1: constraints['Phase'].append([DepCons[0],IndpCon,None,None,'e']) elif len(DepCons) > 1: IndpCon[0] = -1. constraints['Phase'].append([IndpCon]+DepCons+[0.0,None,'c']) for name in ['Afrac','AUiso']: IndpCon = [1.0,G2obj.G2VarObj('%d::%s:%d'%(npId,name,ia))] DepCons = [1.0,G2obj.G2VarObj('%d::%s:%s'%(opId,name,iat))] constraints['Phase'].append([DepCons,IndpCon,None,None,'e']) # unfinished Anisotropic constraint generation # Uids = [[0,0,'AU11'],[1,1,'AU22'],[2,2,'AU33'],[0,1,'AU12'],[0,2,'AU13'],[1,2,'AU23']] # DepConsDict = dict(zip(Us,[[],[],[],[],[],[]])) # for iu,Uid in enumerate(Uids): # UMT = np.zeros((3,3)) # UMT[Uid[0],Uid[1]] = 1 # nUMT = G2lat.prodMGMT(UMT,invTrans) # nUT = G2lat.UijtoU6(nUMT) # for iu,nU in enumerate(nUT): # if abs(nU) > 1.e-8: # parm = '%d::%s;%s'%(opId,Us[iu],iat) # DepConsDict[Uid[2]].append([abs(nU%1.),G2obj.G2VarObj(parm)]) # nUcof = atom[iu:iu+6] # conStrings = [] # for iU,Usi in enumerate(Us): # parm = '%d::%s;%d'%(npId,Usi,ia) # parmDict[parm] = nUcof[iU] # varyList.append(parm) # IndpCon = [1.0,G2obj.G2VarObj(parm)] # conStr = str([IndpCon,DepConsDict[Usi]]) # if conStr in conStrings: # continue # conStrings.append(conStr) # if len(DepConsDict[Usi]) == 1: # if DepConsDict[Usi][0]: # constraints['Phase'].append([IndpCon,DepConsDict[Usi][0],None,None,'e']) # elif len(DepConsDict[Usi]) > 1: # for Dep in DepConsDict[Usi]: # Dep[0] *= -1 # constraints['Phase'].append([IndpCon]+DepConsDict[Usi]+[0.0,None,'c']) #how do I do Uij's for most Trans? # constraints on lattice parameters between phases Aold = G2lat.cell2A(oldPhase['General']['Cell'][1:7]) if True: # debug constraints['Phase'] += G2lat.GenCellConstraints(Trans,opId,npId,Aold,True) print('old A*',G2lat.cell2A(oldPhase['General']['Cell'][1:7])) print('new A*',G2lat.cell2A(newPhase['General']['Cell'][1:7])) print('old cell',oldPhase['General']['Cell'][1:7]) print('new cell',newPhase['General']['Cell'][1:7]) else: constraints['Phase'] += G2lat.GenCellConstraints(Trans,opId,npId,Aold) # constraints on HAP Scale, etc. for hId,hist in enumerate(UseList): #HAP - seems OK ohapkey = '%d:%d:'%(opId,hId) nhapkey = '%d:%d:'%(npId,hId) IndpCon = [1.0,G2obj.G2VarObj(ohapkey+'Scale')] DepCons = [detTrans,G2obj.G2VarObj(nhapkey+'Scale')] constraints['HAP'].append([DepCons,IndpCon,None,None,'e']) for name in ['Size;i','Mustrain;i']: IndpCon = [1.0,G2obj.G2VarObj(ohapkey+name)] DepCons = [1.0,G2obj.G2VarObj(nhapkey+name)] constraints['HAP'].append([IndpCon,DepCons,None,None,'e'])
#### Rigid bodies ############################################################# resRBsel = None
[docs]def UpdateRigidBodies(G2frame,data): '''Called when Rigid bodies tree item is selected. Displays the rigid bodies in the data window ''' def OnPageChanged(event): global resList resList = [] if event: #page change event! page = event.GetSelection() else: try: page = G2frame.rbBook.GetSelection() except: if GSASIIpath.GetConfigValue('debug'): print('DBG_gpx open error:C++ Run time error - skipped') return G2frame.rbBook.ChangeSelection(page) text = G2frame.rbBook.GetPageText(page) if text == 'Vector rigid bodies': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.VectorBodyMenu) G2frame.Bind(wx.EVT_MENU, AddVectorRB, id=G2G.wxID_VECTORBODYADD) G2frame.Bind(wx.EVT_MENU, ExtractPhaseRB, id=G2G.wxID_VECTORBODYIMP) G2frame.Bind(wx.EVT_MENU, AddVectTrans, id=G2G.wxID_VECTORBODYEXTD) G2frame.Bind(wx.EVT_MENU, SaveVectorRB, id=G2G.wxID_VECTORBODYSAV) G2frame.Bind(wx.EVT_MENU, ReadVectorRB, id=G2G.wxID_VECTORBODYRD) G2frame.Page = [page,'vrb'] UpdateVectorRB() elif text == 'Residue rigid bodies': G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RigidBodyMenu) G2frame.Bind(wx.EVT_MENU, AddResidueRB, id=G2G.wxID_RIGIDBODYADD) G2frame.Bind(wx.EVT_MENU, ExtractPhaseRB, id=G2G.wxID_RIGIDBODYIMP) G2frame.Bind(wx.EVT_MENU, OnImportRigidBody, id=G2G.wxID_RIGIDBODYIMPORT) G2frame.Bind(wx.EVT_MENU, OnSaveRigidBody, id=G2G.wxID_RIGIDBODYSAVE) G2frame.Bind(wx.EVT_MENU, OnDefineTorsSeq, id=G2G.wxID_RESIDUETORSSEQ) #enable only if residue RBs exist? G2frame.Bind(wx.EVT_MENU, DumpVectorRB, id=G2G.wxID_RESBODYSAV) G2frame.Bind(wx.EVT_MENU, LoadVectorRB, id=G2G.wxID_RESBODYRD) G2frame.Page = [page,'rrb'] UpdateResidueRB() else: G2gd.SetDataMenuBar(G2frame) #G2frame.Page = [page,'rrb'] def getMacroFile(macName): defDir = os.path.join(os.path.split(__file__)[0],'GSASIImacros') dlg = wx.FileDialog(G2frame,message='Choose '+macName+' rigid body macro file', defaultDir=defDir,defaultFile="",wildcard="GSAS-II macro file (*.mac)|*.mac", style=wx.FD_OPEN | wx.FD_CHANGE_DIR) try: if dlg.ShowModal() == wx.ID_OK: macfile = dlg.GetPath() macro = open(macfile,'r') head = macro.readline() if macName not in head: print (head) print ('**** ERROR - wrong restraint macro file selected, try again ****') macro = [] else: # cancel was pressed macro = [] finally: dlg.Destroy() return macro #advanced past 1st line def getTextFile(): dlg = wx.FileDialog(G2frame,'Choose rigid body text file', G2frame.LastGPXdir, '', "GSAS-II text file (*.txt)|*.txt|XYZ file (*.xyz)|*.xyz|" "Sybyl mol2 file (*.mol2)|*.mol2|PDB file (*.pdb;*.ent)|*.pdb;*.ent", wx.FD_OPEN | wx.FD_CHANGE_DIR) try: if dlg.ShowModal() == wx.ID_OK: txtfile = dlg.GetPath() ext = os.path.splitext(txtfile)[1] text = open(txtfile,'r') else: # cancel was pressed ext = '' text = [] finally: dlg.Destroy() if 'ent' in ext: ext = '.pdb' return text,ext.lower() def OnImportRigidBody(event): page = G2frame.rbBook.GetSelection() if 'Vector' in G2frame.rbBook.GetPageText(page): pass elif 'Residue' in G2frame.rbBook.GetPageText(page): ImportResidueRB() def OnSaveRigidBody(event): page = G2frame.rbBook.GetSelection() if 'Vector' in G2frame.rbBook.GetPageText(page): pass elif 'Residue' in G2frame.rbBook.GetPageText(page): SaveResidueRB() def DumpVectorRB(event): global resRBsel if resRBsel not in data['Residue']: return rbData = data['Residue'][resRBsel] pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose file to save residue rigid body', pth, '', 'RRB files (*.resbody)|*.resbody', wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() filename = os.path.splitext(filename)[0]+'.resbody' # set extension fp = open(filename,'w') fp.write('Name: '+rbData['RBname']+'\n') fp.write('atNames: ') for i in rbData['atNames']: fp.write(str(i)+" ") fp.write('\n') for item in rbData['rbSeq']: fp.write('rbSeq: ') fp.write('{:d} {:d} {:.1f}: '.format(*item[:3])) for num in item[3]: fp.write('{:d} '.format(num)) fp.write('\n') for i,sym in enumerate(rbData['rbTypes']): fp.write("{:3s}".format(sym)) fp.write('{:8.5f}{:9.5f}{:9.5f} ' .format(*rbData['rbXYZ'][i])) fp.write('\n') fp.close() print ('Vector rigid body saved to: '+filename) finally: dlg.Destroy() def LoadVectorRB(event): AtInfo = data['Residue']['AtInfo'] pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose file to read vector rigid body', pth, '', 'RRB files (*.resbody)|*.resbody', wx.FD_OPEN) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() filename = os.path.splitext(filename)[0]+'.resbody' # set extension fp = open(filename,'r') l = fp.readline().strip() if 'Name' not in l: fp.close() G2frame.ErrorDialog('Read Error', 'File '+filename+' does not start with Name\nFirst line =' +l+'\ninvalid file',parent=G2frame) return name = l.split(':')[1].strip() line = fp.readline().strip().split(':')[1].split() atNames = [i for i in line] types = [] coords = [] l = fp.readline().strip() rbSeq = [] while 'rbSeq' in l: tag,vals,lst = l.split(':') seq = [] for t,v in zip((int,int,float),vals.split()): seq.append(t(v)) seq.append([]) for num in lst.split(): seq[-1].append(int(num)) rbSeq.append(seq) l = fp.readline().strip() while l: nums = l.strip().split() types.append(nums.pop(0)) t = types[-1] if t not in AtInfo: Info = G2elem.GetAtomInfo(t) AtInfo[t] = [Info['Drad'],Info['Color']] coords.append([float(nums.pop(0)) for j in range(3)]) l = fp.readline().strip() fp.close() else: return finally: dlg.Destroy() coords = np.array(coords) rbid = ran.randint(0,sys.maxsize) namelist = [data['Residue'][key]['RBname'] for key in data['Residue'] if 'RBname' in data['Residue'][key]] name = G2obj.MakeUniqueLabel(name,namelist) data['Residue'][rbid] = {'RBname':name, 'rbXYZ': coords, 'rbRef':[0,1,2,False], 'rbTypes':types, 'atNames':atNames, 'useCount':0, 'rbSeq':rbSeq, 'SelSeq':[0,0],} data['RBIds']['Residue'].append(rbid) UpdateResidueRB() def AddVectorRB(event): 'Create a new vector rigid body' AtInfo = data['Vector']['AtInfo'] dlg = G2G.MultiIntegerDialog(G2frame,'New Rigid Body',['No. atoms','No. translations'],[3,1]) if dlg.ShowModal() == wx.ID_OK: nAtoms,nTrans = dlg.GetValues() if nAtoms < 3: dlg.Destroy() G2G.G2MessageBox(G2frame,'A vector rigid body must have 3 or more atoms') return rbid = ran.randint(0,sys.maxsize) vecMag = [1.0 for i in range(nTrans)] vecRef = [False for i in range(nTrans)] vecVal = [np.zeros((nAtoms,3)) for j in range(nTrans)] rbTypes = ['C' for i in range(nAtoms)] Info = G2elem.GetAtomInfo('C') AtInfo['C'] = [Info['Drad'],Info['Color']] name = 'UNKRB' namelist = [data['Vector'][key]['RBname'] for key in data['Vector'] if 'RBname' in data['Vector'][key]] name = G2obj.MakeUniqueLabel(name,namelist) data['Vector'][rbid] = {'RBname':name,'VectMag':vecMag,'rbXYZ':np.zeros((nAtoms,3)), 'rbRef':[0,1,2,False],'VectRef':vecRef,'rbTypes':rbTypes,'rbVect':vecVal,'useCount':0} data['RBIds']['Vector'].append(rbid) dlg.Destroy() UpdateVectorRB() def ExtractPhaseRB(event): 'Extract a rigid body from a file with a phase' def SetupDrawing(atmData): '''Add the dicts needed for G2plt.PlotStructure to work to the reader .Phase object ''' generalData = atmData['General'] generalData['BondRadii'] = [] G2phG.SetDrawingDefaults(atmData['Drawing']) atmData['Drawing'].update( {'oldxy':[0.,0.],'Quaternion':[0.,0.,0.,1.],'cameraPos':150., 'viewDir':[0,0,1],'atomPtrs': [2, 1, 6, 17], }) atmData['Drawing']['showRigidBodies'] = False generalData['Map'] = {'MapType':False, 'rho':[]} generalData['AtomTypes'] = [] generalData['BondRadii'] = [] generalData['AngleRadii'] = [] generalData['vdWRadii'] = [] generalData['Color'] = [] generalData['Isotopes'] = {} generalData['Isotope'] = {} cx,ct,cs,cia = generalData['AtomPtrs'] generalData['Mydir'] = G2frame.dirname for iat,atom in enumerate(atmData['Atoms']): atom[ct] = atom[ct].lower().capitalize() #force elem symbol to standard form if atom[ct] not in generalData['AtomTypes'] and atom[ct] != 'UNK': Info = G2elem.GetAtomInfo(atom[ct]) if not Info: atom[ct] = 'UNK' continue atom[ct] = Info['Symbol'] # N.B. symbol might be changed by GetAtomInfo generalData['AtomTypes'].append(atom[ct]) generalData['Z'] = Info['Z'] generalData['Isotopes'][atom[ct]] = Info['Isotopes'] generalData['BondRadii'].append(Info['Drad']) generalData['AngleRadii'].append(Info['Arad']) generalData['vdWRadii'].append(Info['Vdrad']) if atom[ct] in generalData['Isotope']: if generalData['Isotope'][atom[ct]] not in generalData['Isotopes'][atom[ct]]: isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1] generalData['Isotope'][atom[ct]] = isotope else: generalData['Isotope'][atom[ct]] = 'Nat. Abund.' if 'Nat. Abund.' not in generalData['Isotopes'][atom[ct]]: isotope = list(generalData['Isotopes'][atom[ct]].keys())[-1] generalData['Isotope'][atom[ct]] = isotope generalData['Color'].append(Info['Color']) # if generalData['Type'] == 'magnetic': # if len(landeg) < len(generalData['AtomTypes']): # landeg.append(2.0) atmData['Drawing']['Atoms'] = [] for atom in atmData['Atoms']: atmData['Drawing']['Atoms'].append(G2mth.MakeDrawAtom(atmData,atom)) def onCancel(event,page=0): 'complete or bail out from RB define, cleaning up' G2frame.rbBook.DeletePage(G2frame.rbBook.FindPage(pagename)) G2frame.rbBook.SetSelection(page) def Page1(): '''Show the GUI for first stage of the rigid body with all atoms in phase in crystal coordinates. Select the atoms to go onto the next stage ''' def ShowSelection(selections): 'respond to change in atom selections' ct,cs = [1,8] generalData = rd.Phase['General'] for i,atom in enumerate(rd.Phase['Drawing']['Atoms']): if i in selections: factor = 1 else: factor = 2.5 atNum = generalData['AtomTypes'].index(atom[ct]) atom[cs] = list(np.array(generalData['Color'][atNum])//factor) draw(*drawArgs) def onPage1OK(event): '1st section has been completed, move onto next' G2frame.G2plotNB.Delete(rd.Phase['General']['Name']) GetCoords(atmsel) Page2() if 'macromolecular' == rd.Phase['General']['Type']: # for PDB imports, lets see if a quick reformat of atoms list will work rd.Phase['Atoms'] = [a[3:] for a in rd.Phase['Atoms']] rd.Phase['General']['AtomPtrs'] = [i-3 for i in rd.Phase['General']['AtomPtrs']] rd.Phase['General']['Type'] = 'nuclear' SetupDrawing(rd.Phase) # add information to reader object to allow plotting atomlist = [atom[0] for atom in rd.Phase['Atoms']] atmsel = list(range(len(rd.Phase['Atoms']))) # broken -- # why no bonds? #for atm in rd.Phase['Drawing']['Atoms']: # atm[6] = 'balls & sticks' draw,drawArgs = G2plt.PlotStructure(G2frame,rd.Phase,True) ShowSelection(atmsel) if G2frame.rbBook.FindPage(pagename) is not None: G2frame.rbBook.DeletePage(G2frame.rbBook.FindPage(pagename)) RBImp = wx.ScrolledWindow(G2frame.rbBook) RBImpPnl = wx.Panel(RBImp) G2frame.rbBook.AddPage(RBImp,pagename) G2frame.rbBook.SetSelection(G2frame.rbBook.FindPage(pagename)) HelpInfo = ''' This window shows all the atoms that were read from the selected phase file. Select the atoms that will be used in the rigid body processing (this may include atoms needed to define an axis or origin that will not be included in the eventual rigid body.) Note that in the plot window, unselected atoms appear much darker than selected atoms. ''' mainSizer = G2G.G2MultiChoiceWindow(RBImpPnl, 'Select atoms to import', atomlist,atmsel,OnChange=ShowSelection, helpText=HelpInfo) # OK/Cancel buttons btnsizer = wx.StdDialogButtonSizer() OKbtn = wx.Button(RBImpPnl, wx.ID_OK, 'Continue') OKbtn.SetDefault() btnsizer.AddButton(OKbtn) OKbtn.Bind(wx.EVT_BUTTON,onPage1OK) btn = wx.Button(RBImpPnl, wx.ID_CANCEL) btn.Bind(wx.EVT_BUTTON,onCancel) btnsizer.AddButton(btn) btnsizer.Realize() mainSizer.Add(btnsizer,0,wx.ALIGN_CENTER,50) RBImpPnl.SetSizer(mainSizer,True) mainSizer.Layout() Size = mainSizer.GetMinSize() Size[0] += 40 Size[1] = max(Size[1],G2frame.GetSize()[1]-200) + 20 RBImpPnl.SetSize(Size) RBImp.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1) RBImp.Scroll(0,0) def Page2(): '''Show the GUI for the second stage, where selected atoms are now in Cartesian space, manipulate the axes and export selected atoms to a vector or residue rigid body. ''' def UpdateDraw(event=None): 'Called when info changes in grid, replots' UpdateVectorBody(rbData) DrawCallback() def onSetAll(event): 'Set all atoms as selected' grid.completeEdits() for i in range(len(rd.Phase['RBselection'])): rd.Phase['RBselection'][i] = 1 # table needs 0/1 for T/F grid.ForceRefresh() UpdateDraw() def onToggle(event): 'Toggles selection state for all atoms' grid.completeEdits() for i in range(len(rd.Phase['RBselection'])): rd.Phase['RBselection'][i] = int(not rd.Phase['RBselection'][i]) grid.ForceRefresh() UpdateDraw() def onSetOrigin(event): 'Resets origin to midpoint between all selected atoms' grid.completeEdits() center = np.array([0.,0.,0.]) count = 0 for i in range(len(rd.Phase['RBselection'])): if rd.Phase['RBselection'][i]: count += 1 center += rd.Phase['RBcoords'][i] if count: rd.Phase['RBcoords'] -= center/count grid.ForceRefresh() UpdateDraw() def onSetX(event): grid.completeEdits() center = np.array([0.,0.,0.]) count = 0 for i in range(len(rd.Phase['RBselection'])): if rd.Phase['RBselection'][i]: count += 1 center += rd.Phase['RBcoords'][i] if not count: G2G.G2MessageBox(G2frame,'No atoms selected', 'Selection required') return XYZP = center/count if np.sqrt(sum(XYZP**2)) < 0.1: G2G.G2MessageBox(G2frame, 'The selected atom(s) are too close to the origin', 'near origin') return if bntOpts['direction'] == 'y': YP = XYZP / np.sqrt(np.sum(XYZP**2)) ZP = np.cross((1,0,0),YP) if sum(ZP*ZP) < .1: # pathological condition: Y' along X ZP = np.cross((0,0,1),YP) XP = np.cross(YP,ZP) elif bntOpts['direction'] == 'z': ZP = XYZP / np.sqrt(np.sum(XYZP**2)) XP = np.cross((0,1,0),ZP) if sum(XP*XP) < .1: # pathological condition: X' along Y XP = np.cross((0,0,1),ZP) YP = np.cross(ZP,XP) else: XP = XYZP / np.sqrt(np.sum(XYZP**2)) YP = np.cross((0,0,1),XP) if sum(YP*YP) < .1: # pathological condition: X' along Z YP = np.cross((0,1,0),XP) ZP = np.cross(XP,YP) trans = np.array((XP,YP,ZP)) # update atoms in place rd.Phase['RBcoords'][:] = np.inner(trans,rd.Phase['RBcoords']).T grid.ForceRefresh() UpdateDraw() def onSetPlane(event): '''Finds eigen vector/matrix for best "ellipsoid" about atoms; rotate atoms so that smallest axis is along choice. ''' grid.completeEdits() selList = [i==1 for i in rd.Phase['RBselection']] XYZ = rd.Phase['RBcoords'][selList] Natoms = len(XYZ) if Natoms < 3: G2G.G2MessageBox(G2frame,'A plane requires three or more atoms','Need more atoms') return Zmat = np.zeros((3,3)) for xyz in XYZ: Zmat += np.outer(xyz.T,xyz) Evec,Emat = nl.eig(Zmat) Order = np.argsort(np.nan_to_num(Evec)) #short-long order if bntOpts['plane'] == 'xy': #short along z trans = np.array([Emat[Order[2]],Emat[Order[1]],Emat[Order[0]]]) elif bntOpts['plane'] == 'yz': #short along x trans = np.array([Emat[Order[0]],Emat[Order[2]],Emat[Order[1]]]) elif bntOpts['plane'] == 'xz': #short along y trans = np.array([Emat[Order[1]],Emat[Order[0]],Emat[Order[2]]]) else: print('unexpected plane',bntOpts['plane']) return # update atoms in place rd.Phase['RBcoords'][:] = np.inner(trans,rd.Phase['RBcoords']).T grid.ForceRefresh() UpdateDraw() def onWriteXYZ(event): '''Writes selected atoms in a .xyz file for use in Avogadro, etc. ''' grid.completeEdits() center = np.array([0.,0.,0.]) count = 0 for i in range(len(rd.Phase['RBselection'])): if rd.Phase['RBselection'][i]: count += 1 center += rd.Phase['RBcoords'][i] if count: center /= count else: print('nothing selected') return obj = G2IO.ExportBaseclass(G2frame,'XYZ','.xyz') #obj.InitExport(None) if obj.ExportSelect(): # set export parameters; ask for file name return obj.OpenFile() obj.Write(str(count)) obj.Write('') for i in range(len(rd.Phase['RBselection'])): if rd.Phase['RBselection'][i]: line = ' ' + rd.Phase['RBtypes'][i] for xyz in rd.Phase['RBcoords'][i]: line += ' ' + str(xyz) obj.Write(line) obj.CloseFile() #GSASIIpath.IPyBreak() def onAddVector(event): '''Adds selected atoms as a new vector rigid body. Closes out the importer tab when done. ''' grid.completeEdits() name = os.path.splitext(os.path.split(filename)[1])[0] namelist = [data['Vector'][key]['RBname'] for key in data['Vector'] if 'RBname' in data['Vector'][key]] name = G2obj.MakeUniqueLabel(name,namelist) rb = MakeVectorBody(name) UpdateVectorBody(rb,True) if len(rb['rbTypes']) < 3: return # must have at least 3 atoms rbid = ran.randint(0,sys.maxsize) data['Vector'][rbid] = rb data['RBIds']['Vector'].append(rbid) for t in rb['rbTypes']: if t in data['Vector']['AtInfo']: continue Info = G2elem.GetAtomInfo(t) data['Vector']['AtInfo'][t] = [Info['Drad'],Info['Color']] G2frame.G2plotNB.Delete('Rigid body') onCancel(event,0) def onAddResidue(event): '''Adds selected atoms as a new residue rigid body. Closes out the importer tab when done. ''' grid.completeEdits() name = os.path.split(filename)[1] rbXYZ = [] rbTypes = [] atNames = [] for i in rd.Phase['RBindex']: if rd.Phase['RBselection'][i]: rbXYZ.append(rd.Phase['RBcoords'][i]) rbTypes.append(rd.Phase['RBtypes'][i]) atNames.append(rd.Phase['RBlbls'][i]) if len(rbTypes) < 3: return # must have at least 3 atoms rbXYZ = np.array(rbXYZ) rbid = ran.randint(0,sys.maxsize) namelist = [data['Residue'][key]['RBname'] for key in data['Residue'] if 'RBname' in data['Residue'][key]] name = G2obj.MakeUniqueLabel(name,namelist) data['Residue'][rbid] = {'RBname':name,'rbXYZ':rbXYZ, 'rbTypes':rbTypes,'atNames':atNames,'rbRef':[0,1,2,False], 'rbSeq':[],'SelSeq':[0,0],'useCount':0} data['RBIds']['Residue'].append(rbid) for t in rbTypes: if t in data['Residue']['AtInfo']: continue Info = G2elem.GetAtomInfo(t) data['Residue']['AtInfo'][t] = [Info['Drad'],Info['Color']] print ('Rigid body added') G2frame.G2plotNB.Delete('Rigid body') onCancel(event,1) if G2frame.rbBook.FindPage(pagename) is not None: G2frame.rbBook.DeletePage(G2frame.rbBook.FindPage(pagename)) RBImp = wx.ScrolledWindow(G2frame.rbBook) RBImpPnl = wx.Panel(RBImp) G2frame.rbBook.AddPage(RBImp,pagename) G2frame.rbBook.SetSelection(G2frame.rbBook.FindPage(pagename)) AtInfo = {} for t in rd.Phase['RBtypes']: if t in AtInfo: continue Info = G2elem.GetAtomInfo(t) AtInfo[t] = [Info['Drad'],Info['Color']] plotDefaults = {'oldxy':[0.,0.],'Quaternion':[0.,0.,0.,1.],'cameraPos':30.,'viewDir':[0,0,1],} rd.Phase['RBindex'] = list(range(len(rd.Phase['RBtypes']))) rd.Phase['RBselection'] = len(rd.Phase['RBtypes']) * [1] name = 'UNKRB' namelist = [data['Vector'][key]['RBname'] for key in data['Vector'] if 'RBname' in data['Vector'][key]] name = G2obj.MakeUniqueLabel(name,namelist) rbData = MakeVectorBody() DrawCallback = G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,rbData,plotDefaults) mainSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer = wx.BoxSizer(wx.VERTICAL) helpText = ''' In this window, if wanted, one can select one or more atoms and use them to define an origin, a specified axis or place the selected atoms into a selected plane. (Different sets of atoms can be used for each operation.) %%Once that is done, atoms can be selected and can be exported in a "XYZ" file for use in a program such as Avogadro or can be used to create a Vector or Residue rigid body. ''' btnSizer.Add(G2G.HelpButton(RBImpPnl,helpText,wrap=400), 0,wx.ALIGN_RIGHT) btnSizer.Add(wx.StaticText(RBImpPnl,wx.ID_ANY,'Reorder atoms by dragging'),0,wx.ALL) btnSizer.Add((-1,15)) btn = wx.Button(RBImpPnl, wx.ID_ANY, 'Set All') btn.Bind(wx.EVT_BUTTON,onSetAll) btnSizer.Add(btn,0,wx.ALIGN_CENTER) btn = wx.Button(RBImpPnl, wx.ID_ANY, 'Toggle') btn.Bind(wx.EVT_BUTTON,onToggle) btnSizer.Add(btn,0,wx.ALIGN_CENTER) btnSizer.Add((-1,15)) btnSizer.Add(wx.StaticText(RBImpPnl,wx.ID_ANY,'Reorient using selected\natoms...'),0,wx.ALL) btnSizer.Add((-1,5)) btn = wx.Button(RBImpPnl, wx.ID_ANY, 'Set origin') btn.Bind(wx.EVT_BUTTON,onSetOrigin) btnSizer.Add(btn,0,wx.ALIGN_CENTER) bntOpts = {'plane':'xy','direction':'x'} inSizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(RBImpPnl, wx.ID_ANY, 'Place in plane') btn.Bind(wx.EVT_BUTTON,onSetPlane) inSizer.Add(btn) inSizer.Add(G2G.G2ChoiceButton(RBImpPnl,('xy','yz','xz'),None,None,bntOpts,'plane')) btnSizer.Add(inSizer,0,wx.ALIGN_CENTER) inSizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(RBImpPnl, wx.ID_ANY, 'Define as') btn.Bind(wx.EVT_BUTTON,onSetX) inSizer.Add(btn) inSizer.Add(G2G.G2ChoiceButton(RBImpPnl,('x','y','z'),None,None,bntOpts,'direction')) btnSizer.Add(inSizer,0,wx.ALIGN_CENTER) btnSizer.Add((-1,15)) btnSizer.Add(wx.StaticText(RBImpPnl,wx.ID_ANY,'Use selected atoms to\ncreate...'),0,wx.ALL) btnSizer.Add((-1,5)) btn = wx.Button(RBImpPnl, wx.ID_ANY, 'export as xyz') btn.Bind(wx.EVT_BUTTON,onWriteXYZ) btnSizer.Add(btn,0,wx.ALIGN_CENTER) btnSizer.Add((-1,10)) btn = wx.Button(RBImpPnl, wx.ID_ANY, 'a Vector Body') btn.Bind(wx.EVT_BUTTON,onAddVector) btnSizer.Add(btn,0,wx.ALIGN_CENTER) btn = wx.Button(RBImpPnl, wx.ID_ANY, 'a Residue Body') btn.Bind(wx.EVT_BUTTON,onAddResidue) btnSizer.Add(btn,0,wx.ALIGN_CENTER) btn = wx.Button(RBImpPnl, wx.ID_CANCEL) btn.Bind(wx.EVT_BUTTON,onCancel) btnSizer.Add((-1,10)) btnSizer.Add(btn,0,wx.ALIGN_CENTER) mainSizer.Add(btnSizer) mainSizer.Add((5,5)) grid = DragableRBGrid(RBImpPnl,rd.Phase,UpdateDraw) mainSizer.Add(grid) RBImpPnl.SetSizer(mainSizer,True) mainSizer.Layout() Size = mainSizer.GetMinSize() Size[0] += 40 Size[1] = max(Size[1],G2frame.GetSize()[1]-200) + 20 RBImpPnl.SetSize(Size) RBImp.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1) RBImp.Scroll(0,0) def GetCoords(atmsel): '''Create orthogonal coordinates for selected atoms. Place the origin at the center of the body ''' atms = rd.Phase['Atoms'] cell = rd.Phase['General']['Cell'][1:7] Amat,Bmat = G2lat.cell2AB(cell) rd.Phase['RBcoords'] = np.array([np.inner(Amat,atms[i][3:6]) for i in atmsel]) rd.Phase['RBcoords'] -= rd.Phase['RBcoords'].mean(axis=0) # origin to middle rd.Phase['RBtypes'] = [atms[i][1] for i in atmsel] rd.Phase['RBlbls'] = [atms[i][0] for i in atmsel] def UpdateVectorBody(rb,useSelection=False): '''Put the atoms in order to pass for plotting or for storage as a vector rigid body. :param dict rb: rigid body contents created in :func:`MakeVectorBody` :param bool useSelection: True if the rd.Phase['RBselection'] values will be used to select which atoms are included in the rigid body. If False (default) they are included in rb and are used for plotting. ''' coordlist = [] typeslist = [] sellist = [] for i in rd.Phase['RBindex']: use = True if useSelection and not rd.Phase['RBselection'][i]: use = False if use: coordlist.append(rd.Phase['RBcoords'][i]) typeslist.append(rd.Phase['RBtypes'][i]) sellist.append(rd.Phase['RBselection'][i]) coordlist = np.array(coordlist) rb['rbXYZ'] = coordlist rb['rbVect'] = [coordlist] rb['rbTypes'] = typeslist if not useSelection: rb['Selection'] = sellist elif 'Selection' in rb: del rb['Selection'] def MakeVectorBody(name=''): '''Make the basic vector rigid body dict (w/o coordinates) used for export and for plotting ''' vecMag = [1.0] vecRef = [False] rb = {'RBname':name,'VectMag':vecMag, 'rbRef':[0,1,2,False],'VectRef':vecRef, 'useCount':0} UpdateVectorBody(rb) return rb # too lazy to figure out why wx crashes if wx.__version__.split('.')[0] != '4': wx.MessageBox('Sorry, wxPython 4.x is required to run this command', caption='Update Python', style=wx.ICON_EXCLAMATION) return if platform.python_version()[:1] == '2': wx.MessageBox('Sorry, Python >=3.x is required to run this command', caption='Update Python', style=wx.ICON_EXCLAMATION) return # get importer type and a phase file of that type G2sc.LoadG2fil() choices = [rd.formatName for rd in G2sc.Readers['Phase']] dlg = G2G.G2SingleChoiceDialog(G2frame,'Select the format of the file', 'select format',choices) dlg.CenterOnParent() try: if dlg.ShowModal() == wx.ID_OK: col = dlg.GetSelection() else: col = None return finally: dlg.Destroy() reader = G2sc.Readers['Phase'][col] choices = reader.formatName + " file (" w = "" for extn in reader.extensionlist: if w != "": w += ";" w += "*" + extn choices += w + ")|" + w #choices += "|zip archive (.zip)|*.zip" if not reader.strictExtension: choices += "|any file (*.*)|*.*" typ = '( type '+reader.formatName+')' filelist = G2G.GetImportFile(G2frame, message="Choose phase input file"+typ, defaultFile="",wildcard=choices,style=wx.FD_OPEN) if len(filelist) != 1: return # read in the phase file filename = filelist[0] rd = reader with open(filename, 'r'): rd.ReInitialize() rd.errors = "" if not rd.ContentsValidator(filename): # Report error G2fl.G2Print("Warning: File {} has a validation error".format(filename)) return if len(rd.selections) > 1: print("File {} has {} phases. This is unexpected." .format(filename,len(rd.selections))) return rd.objname = os.path.basename(filename) try: rd.Reader(filename) except Exception as msg: G2fl.G2Print("Warning: read of file {} failed\n{}".format( filename,rd.errors)) if GSASIIpath.GetConfigValue('debug'): print(msg) import traceback print (traceback.format_exc()) GSASIIpath.IPyBreak() return pagename = 'Rigid body importer' Page1() return def AddVectTrans(event): 'Add a translation to an existing vector rigid body' choices = [] rbIdlist = [] for rbid in data['RBIds']['Vector']: if rbid != 'AtInfo': rbIdlist.append(rbid) choices.append(data['Vector'][rbid]['RBname']) if len(choices) == 0: G2G.G2MessageBox(G2frame,'No Vector Rigid Bodies found', 'No VR Bodies') return elif len(choices) == 1: rbid = rbIdlist[0] else: dlg = G2G.G2SingleChoiceDialog(G2frame,'Select the rigid body to save', 'select format',choices) try: if dlg.ShowModal() == wx.ID_OK: rbid = rbIdlist[dlg.GetSelection()] else: return finally: dlg.Destroy() data['Vector'][rbid]['VectMag'] += [1.0] data['Vector'][rbid]['VectRef'] += [False] nAtoms = len(data['Vector'][rbid]['rbXYZ']) data['Vector'][rbid]['rbVect'] += [np.zeros((nAtoms,3))] UpdateVectorRB() def SaveVectorRB(event): choices = [] rbIdlist = [] for rbid in data['RBIds']['Vector']: if rbid != 'AtInfo': rbIdlist.append(rbid) choices.append(data['Vector'][rbid]['RBname']) if len(choices) == 0: G2G.G2MessageBox(G2frame,'No Vector Rigid Bodies found', 'No VR Bodies') return elif len(choices) == 1: rbid = rbIdlist[0] else: dlg = G2G.G2SingleChoiceDialog(G2frame,'Select the rigid body to save', 'select format',choices) try: if dlg.ShowModal() == wx.ID_OK: rbid = rbIdlist[dlg.GetSelection()] else: return finally: dlg.Destroy() pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose file to save vector rigid body', pth, '', 'VRB files (*.vecbody)|*.vecbody', wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() filename = os.path.splitext(filename)[0]+'.vecbody' # set extension fp = open(filename,'w') fp.write('Name: '+data['Vector'][rbid]['RBname']+'\n') fp.write('Trans: ') for i in data['Vector'][rbid]['VectMag']: fp.write(str(i)+" ") fp.write('\n') ntrans = len(data['Vector'][rbid]['VectMag']) for i,sym in enumerate(data['Vector'][rbid]['rbTypes']): fp.write("{:3s}".format(sym)) for j in range(ntrans): fp.write('{:8.5f}{:9.5f}{:9.5f} ' .format(*data['Vector'][rbid]['rbVect'][j][i])) fp.write('\n') fp.close() print ('Vector rigid body saved to: '+filename) finally: dlg.Destroy() def ReadVectorRB(event): AtInfo = data['Vector']['AtInfo'] pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose file to read vector rigid body', pth, '', 'VRB files (*.vecbody)|*.vecbody', wx.FD_OPEN) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() filename = os.path.splitext(filename)[0]+'.vecbody' # set extension fp = open(filename,'r') l = fp.readline().strip() if 'Name' not in l: fp.close() G2frame.ErrorDialog('Read Error', 'File '+filename+' does not start with Name\nFirst line =' +l+'\ninvalid file',parent=G2frame) return name = l.split(':')[1].strip() trans = fp.readline().strip().split(':')[1].split() vecMag = [float(i) for i in trans] ntrans = len(trans) vecs = [[] for i in range(ntrans)] types = [] l = fp.readline().strip() while l: nums = l.strip().split() types.append(nums.pop(0)) t = types[-1] if t not in AtInfo: Info = G2elem.GetAtomInfo(t) AtInfo[t] = [Info['Drad'],Info['Color']] for i in range(ntrans): vecs[i].append([float(nums.pop(0)) for j in range(3)]) l = fp.readline().strip() fp.close() else: return finally: dlg.Destroy() natoms = len(types) vecs = [np.array(vecs[i]) for i in range(ntrans)] rbid = ran.randint(0,sys.maxsize) namelist = [data['Vector'][key]['RBname'] for key in data['Vector'] if 'RBname' in data['Vector'][key]] name = G2obj.MakeUniqueLabel(name,namelist) data['Vector'][rbid] = {'RBname':name,'VectMag':vecMag, 'rbXYZ':np.zeros((natoms,3)), 'rbRef':[0,1,2,False],'VectRef':ntrans*[False], 'rbTypes':types, 'rbVect':vecs,'useCount':0} data['RBIds']['Vector'].append(rbid) UpdateVectorRB() def AddResidueRB(event): global resRBsel AtInfo = data['Residue']['AtInfo'] macro = getMacroFile('rigid body') if not macro: return macStr = macro.readline() while macStr: items = macStr.split() if 'I' == items[0]: resRBsel = ran.randint(0,sys.maxsize) rbName = items[1] rbTypes = [] rbXYZ = [] rbSeq = [] atNames = [] nAtms,nSeq,nOrig,mRef,nRef = [int(items[i]) for i in [2,3,4,5,6]] for iAtm in range(nAtms): macStr = macro.readline().split() atName = macStr[0] atType = macStr[1] atNames.append(atName) rbXYZ.append([float(macStr[i]) for i in [2,3,4]]) rbTypes.append(atType) if atType not in AtInfo: Info = G2elem.GetAtomInfo(atType) AtInfo[atType] = [Info['Drad'],Info['Color']] rbXYZ = np.array(rbXYZ)-np.array(rbXYZ[nOrig-1]) for iSeq in range(nSeq): macStr = macro.readline().split() mSeq = int(macStr[0]) for jSeq in range(mSeq): macStr = macro.readline().split() iBeg = int(macStr[0])-1 iFin = int(macStr[1])-1 angle = 0.0 nMove = int(macStr[2]) iMove = [int(macStr[i])-1 for i in range(3,nMove+3)] rbSeq.append([iBeg,iFin,angle,iMove]) namelist = [data['Residue'][key]['RBname'] for key in data['Residue'] if 'RBname' in data['Residue'][key]] rbName = G2obj.MakeUniqueLabel(rbName,namelist) data['Residue'][resRBsel] = {'RBname':rbName,'rbXYZ':rbXYZ,'rbTypes':rbTypes, 'atNames':atNames,'rbRef':[nOrig-1,mRef-1,nRef-1,True],'rbSeq':rbSeq, 'SelSeq':[0,0],'useCount':0,'molCent':None} data['RBIds']['Residue'].append(resRBsel) print ('Rigid body '+rbName+' added') macStr = macro.readline() macro.close() UpdateResidueRB() def ImportResidueRB(): global resRBsel AtInfo = data['Residue']['AtInfo'] text,ext = getTextFile() if not text: return resRBsel = ran.randint(0,sys.maxsize) rbTypes = [] rbXYZ = [] atNames = [] txtStr = text.readline() if 'xyz' in ext: txtStr = text.readline() txtStr = text.readline() elif 'mol2' in ext: while 'ATOM' not in txtStr: txtStr = text.readline() txtStr = text.readline() elif 'pdb' in ext: while 'ATOM' not in txtStr[:6] and 'HETATM' not in txtStr[:6]: txtStr = text.readline() items = txtStr.split() nat = 1 while len(items): if 'txt' in ext: atName = items[0] atType = items[1] rbXYZ.append([float(items[i]) for i in [2,3,4]]) elif 'xyz' in ext: atType = items[0] rbXYZ.append([float(items[i]) for i in [1,2,3]]) atName = '%s%d'%(atType,nat) elif 'mol2' in ext: atType = items[1] atName = items[1]+items[0] rbXYZ.append([float(items[i]) for i in [2,3,4]]) elif 'pdb' in ext: atType = items[-1] if not items[2][-1].isnumeric(): atName = '%s%d'%(items[2],nat) else: atName = '5s'%items[2] xyz = txtStr[30:55].split() rbXYZ.append([float(x) for x in xyz]) atNames.append(atName) rbTypes.append(atType) if atType not in AtInfo: Info = G2elem.GetAtomInfo(atType) AtInfo[atType] = [Info['Drad'],Info['Color']] txtStr = text.readline() if 'mol2' in ext and 'BOND' in txtStr: break if 'pdb' in ext and ('ATOM' not in txtStr[:6] and 'HETATM' not in txtStr[:6]): break items = txtStr.split() nat += 1 if len(atNames) < 3: G2G.G2MessageBox(G2frame,'Not enough atoms in rigid body; must be 3 or more') else: rbXYZ = np.array(rbXYZ)-np.array(rbXYZ[0]) Xxyz = rbXYZ[1] X = Xxyz/np.sqrt(np.sum(Xxyz**2)) Yxyz = rbXYZ[2] Y = Yxyz/np.sqrt(np.sum(Yxyz**2)) Mat = G2mth.getRBTransMat(X,Y) rbXYZ = np.inner(Mat,rbXYZ).T name = 'UNKRB' namelist = [data['Residue'][key]['RBname'] for key in data['Residue'] if 'RBname' in data['Residue'][key]] name = G2obj.MakeUniqueLabel(name,namelist) data['Residue'][resRBsel] = {'RBname':name,'rbXYZ':rbXYZ,'rbTypes':rbTypes, 'atNames':atNames,'rbRef':[0,1,2,False],'rbSeq':[],'SelSeq':[0,0],'useCount':0,'molCent':False} data['RBIds']['Residue'].append(resRBsel) print ('Rigid body UNKRB added') text.close() UpdateResidueRB() def SaveResidueRB(): global resRBsel pth = G2G.GetExportPath(G2frame) dlg = wx.FileDialog(G2frame, 'Choose PDB file for Atom XYZ', pth, '', 'PDB files (*.pdb)|*.pdb',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() filename = os.path.splitext(filename)[0]+'.pdb' # make extension .pdb File = open(filename,'w') rbData = data['Residue'][resRBsel] for iat,xyz in enumerate(rbData['rbXYZ']): File.write('ATOM %6d %-4s%3s 1 %8.3f%8.3f%8.3f 1.00 0.00 %2s\n'%( iat,rbData['atNames'][iat],rbData['RBname'][:3],xyz[0],xyz[1],xyz[2],rbData['rbTypes'][iat])) File.close() print ('Atom XYZ saved to: '+filename) finally: dlg.Destroy() def FindNeighbors(Orig,XYZ,atTypes,atNames,AtInfo): Radii = [] for Atype in atTypes: Radii.append(AtInfo[Atype][0]) Radii = np.array(Radii) Neigh = [] Dx = XYZ-XYZ[Orig] dist = np.sqrt(np.sum(Dx**2,axis=1)) sumR = Radii[Orig]+Radii IndB = ma.nonzero(ma.masked_greater(dist-0.85*sumR,0.)) for j in IndB[0]: if j != Orig and atTypes[j] != 'H': Neigh.append(atNames[j]) return Neigh def FindAllNeighbors(XYZ,atTypes,atNames,AtInfo): NeighDict = {} for iat,xyz in enumerate(atNames): NeighDict[atNames[iat]] = FindNeighbors(iat,XYZ,atTypes,atNames,AtInfo) return NeighDict def FindRiding(Orig,Pivot,NeighDict): riding = [Orig,Pivot] iAdd = 1 new = True while new: newAtms = NeighDict[riding[iAdd]] for At in newAtms: new = False if At not in riding: riding.append(At) new = True iAdd += 1 if iAdd < len(riding): new = True return riding[2:] def OnDefineTorsSeq(event): global resRBsel rbData = data['Residue'][resRBsel] if not len(rbData): return atNames = rbData['atNames'] AtInfo = data['Residue']['AtInfo'] atTypes = rbData['rbTypes'] XYZ = rbData['rbXYZ'] neighDict = FindAllNeighbors(XYZ,atTypes,atNames,AtInfo) TargList = [] dlg = wx.SingleChoiceDialog(G2frame,'Select origin atom for torsion sequence','Origin atom',rbData['atNames']) if dlg.ShowModal() == wx.ID_OK: Orig = dlg.GetSelection() TargList = neighDict[atNames[Orig]] dlg.Destroy() if not len(TargList): return dlg = wx.SingleChoiceDialog(G2frame,'Select pivot atom for torsion sequence','Pivot atom',TargList) if dlg.ShowModal() == wx.ID_OK: Piv = atNames.index(TargList[dlg.GetSelection()]) riding = FindRiding(atNames[Orig],atNames[Piv],neighDict) Riding = [] for atm in riding: Riding.append(atNames.index(atm)) rbData['rbSeq'].append([Orig,Piv,0.0,Riding]) dlg.Destroy() UpdateResidueRB() def UpdateVectorRB(Scroll=0): '''Display & edit a selected Vector RB ''' global resRBsel def rbNameSizer(rbid,rbData): def OnRBName(event): event.Skip() Obj = event.GetEventObject() name = Obj.GetValue() if name == rbData['RBname']: return # no change namelist = [data['Vector'][key]['RBname'] for key in data['Vector'] if 'RBname' in data['Vector'][key]] name = G2obj.MakeUniqueLabel(name,namelist) rbData['RBname'] = name wx.CallAfter(UpdateVectorRB) def OnDelRB(event): Obj = event.GetEventObject() rbid = Indx[Obj.GetId()] if rbid in data['Vector']: del data['Vector'][rbid] data['RBIds']['Vector'].remove(rbid) rbData['useCount'] -= 1 wx.CallAfter(UpdateVectorRB) def OnPlotRB(event): G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,rbData,plotDefaults) # start of rbNameSizer nameSizer = wx.BoxSizer(wx.HORIZONTAL) nameSizer.Add(wx.StaticText(VectorRBDisplay,-1,'Rigid body name: '),0,WACV) RBname = wx.TextCtrl(VectorRBDisplay,-1,rbData['RBname'], style=wx.TE_PROCESS_ENTER) RBname.Bind(wx.EVT_LEAVE_WINDOW, OnRBName) RBname.Bind(wx.EVT_TEXT_ENTER,OnRBName) RBname.Bind(wx.EVT_KILL_FOCUS,OnRBName) nameSizer.Add(RBname,0,WACV) nameSizer.Add((5,0),) plotRB = wx.Button(VectorRBDisplay,wx.ID_ANY,'Plot',style=wx.BU_EXACTFIT) plotRB.Bind(wx.EVT_BUTTON, OnPlotRB) Indx[plotRB.GetId()] = rbid nameSizer.Add(plotRB,0,WACV) nameSizer.Add((5,0),) if not rbData['useCount']: delRB = wx.Button(VectorRBDisplay,wx.ID_ANY,"Delete",style=wx.BU_EXACTFIT) delRB.Bind(wx.EVT_BUTTON, OnDelRB) Indx[delRB.GetId()] = rbid nameSizer.Add(delRB,0,WACV) return nameSizer def rbRefAtmSizer(rbid,rbData): def OnRefSel(event): Obj = event.GetEventObject() iref = Indx[Obj.GetId()] sel = Obj.GetValue() rbData['rbRef'][iref] = atNames.index(sel) FillRefChoice(rbid,rbData) refAtmSizer = wx.BoxSizer(wx.HORIZONTAL) atNames = [name+str(i) for i,name in enumerate(rbData['rbTypes'])] rbRef = rbData.get('rbRef',[0,1,2,False]) rbData['rbRef'] = rbRef if rbData['useCount']: refAtmSizer.Add(wx.StaticText(VectorRBDisplay,-1, 'Orientation reference atoms A-B-C: %s, %s, %s'%(atNames[rbRef[0]], \ atNames[rbRef[1]],atNames[rbRef[2]])),0) else: refAtmSizer.Add(wx.StaticText(VectorRBDisplay,-1, 'Orientation reference atoms A-B-C: '),0,WACV) for i in range(3): choices = [atNames[j] for j in refChoice[rbid][i]] refSel = wx.ComboBox(VectorRBDisplay,-1,value='', choices=choices,style=wx.CB_READONLY|wx.CB_DROPDOWN) refSel.SetValue(atNames[rbRef[i]]) refSel.Bind(wx.EVT_COMBOBOX, OnRefSel) Indx[refSel.GetId()] = i refAtmSizer.Add(refSel,0,WACV) refHelpInfo = ''' * The "Orientation Reference" control defines the Cartesian axes for rigid bodies with the three atoms, A, B and C. The vector from B to A defines the x-axis and the y axis is placed in the plane defined by B to A and C to A. A,B,C must not be collinear. ''' hlp = G2G.HelpButton(VectorRBDisplay,refHelpInfo,wrap=400) refAtmSizer.Add(hlp,0,wx.LEFT|wx.RIGHT|wx.ALIGN_CENTER_VERTICAL,2) return refAtmSizer def rbVectMag(rbid,imag,rbData): def OnRBVectorMag(event): event.Skip() Obj = event.GetEventObject() rbid,imag = Indx[Obj.GetId()] try: val = float(Obj.GetValue()) if val <= 0.: raise ValueError rbData['VectMag'][imag] = val except ValueError: pass Obj.SetValue('%8.4f'%(val)) wx.CallAfter(UpdateVectorRB,VectorRB.GetScrollPos(wx.VERTICAL)) G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,data['Vector'][rbid],plotDefaults) def OnRBVectorRef(event): Obj = event.GetEventObject() rbid,imag = Indx[Obj.GetId()] rbData['VectRef'][imag] = Obj.GetValue() magSizer = wx.BoxSizer(wx.HORIZONTAL) magSizer.Add(wx.StaticText(VectorRBDisplay,-1,'Translation magnitude: '),0,WACV) magValue = wx.TextCtrl(VectorRBDisplay,-1,'%8.4f'%(rbData['VectMag'][imag])) Indx[magValue.GetId()] = [rbid,imag] magValue.Bind(wx.EVT_TEXT_ENTER,OnRBVectorMag) magValue.Bind(wx.EVT_KILL_FOCUS,OnRBVectorMag) magSizer.Add(magValue,0,WACV) magSizer.Add((5,0),) magref = wx.CheckBox(VectorRBDisplay,label=' Refine?') magref.SetValue(rbData['VectRef'][imag]) magref.Bind(wx.EVT_CHECKBOX,OnRBVectorRef) Indx[magref.GetId()] = [rbid,imag] magSizer.Add(magref,0,WACV) return magSizer def rbVectors(rbid,imag,mag,XYZ,rbData): def TypeSelect(event): AtInfo = data['Vector']['AtInfo'] r,c = event.GetRow(),event.GetCol() if vecGrid.GetColLabelValue(c) == 'Type': PE = G2elemGUI.PickElement(G2frame,oneOnly=True) if PE.ShowModal() == wx.ID_OK: if PE.Elem != 'None': El = PE.Elem.strip().lower().capitalize() if El not in AtInfo: Info = G2elem.GetAtomInfo(El) AtInfo[El] = [Info['Drad'],Info['Color']] rbData['rbTypes'][r] = El vecGrid.SetCellValue(r,c,El) PE.Destroy() wx.CallAfter(UpdateVectorRB,VectorRB.GetScrollPos(wx.VERTICAL)) def ChangeCell(event): r,c = event.GetRow(),event.GetCol() if r >= 0 and (0 <= c < 3): try: val = float(vecGrid.GetCellValue(r,c)) rbData['rbVect'][imag][r][c] = val except ValueError: pass G2plt.PlotRigidBody(G2frame,'Vector',AtInfo,data['Vector'][rbid],plotDefaults) wx.CallAfter(UpdateVectorRB,VectorRB.GetScrollPos(wx.VERTICAL)) vecSizer = wx.BoxSizer() Types = 3*[wg.GRID_VALUE_FLOAT+':10,5',]+[wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',] colLabels = ['Vector x','Vector y','Vector z','Type','Cart x','Cart y','Cart z'] table = [] rowLabels = [] atNames = [] for ivec,xyz in enumerate(rbData['rbVect'][imag]): table.append(list(xyz)+[rbData['rbTypes'][ivec],]+list(XYZ[ivec])) rowLabels.append(str(ivec)) atNames.append(rbData['rbTypes'][ivec]+str(ivec)) rbData['atNames'] = atNames vecTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) vecGrid = G2G.GSGrid(VectorRBDisplay) vecGrid.SetTable(vecTable, True) if 'phoenix' in wx.version(): vecGrid.Bind(wg.EVT_GRID_CELL_CHANGED, ChangeCell) else: vecGrid.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeCell) if not imag: vecGrid.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, TypeSelect) attr = wx.grid.GridCellAttr() attr.IncRef() attr.SetEditor(G2G.GridFractionEditor(vecGrid)) for c in range(3): attr.IncRef() vecGrid.SetColAttr(c, attr) for row in range(vecTable.GetNumberRows()): if imag: vecGrid.SetCellStyle(row,3,VERY_LIGHT_GREY,True) for col in [4,5,6]: vecGrid.SetCellStyle(row,col,VERY_LIGHT_GREY,True) # vecGrid.SetScrollRate(0,0) vecGrid.AutoSizeColumns(False) vecSizer.Add(vecGrid) return vecSizer def FillRefChoice(rbid,rbData): choiceIds = [i for i in range(len(rbData['rbTypes']))] rbRef = rbData.get('rbRef',[-1,-1,-1,False]) for i in range(3): if rbRef[i] in choiceIds: choiceIds.remove(rbRef[i]) refChoice[rbid] = [choiceIds[:],choiceIds[:],choiceIds[:]] for i in range(3): refChoice[rbid][i].append(rbRef[i]) refChoice[rbid][i].sort() def OnRBSelect(event): global resRBsel sel = rbSelect.GetSelection() if sel == 0: return # 1st entry is blank rbname = rbchoice[sel-1] resRBsel = RBnames[rbname] wx.CallLater(100,UpdateVectorRB) # beginning of UpdateVectorRB AtInfo = data['Vector']['AtInfo'] refChoice = {} RefObjs = [] GS = VectorRBDisplay.GetSizer() if GS: try: #get around a c++ error in wx 4.0; doing is again seems to be OK GS.Clear(True) except: GS.Clear(True) RBnames = {} for rbid in data['RBIds']['Vector']: RBnames.update({data['Vector'][rbid]['RBname']:rbid,}) if not RBnames: return rbchoice = list(RBnames.keys()) rbchoice.sort() if GS: VectorRBSizer = GS else: VectorRBSizer = wx.BoxSizer(wx.VERTICAL) if resRBsel not in data['RBIds']['Vector']: resRBsel = RBnames[rbchoice[0]] if len(RBnames) > 1: selSizer = wx.BoxSizer(wx.HORIZONTAL) selSizer.Add(wx.StaticText(VectorRBDisplay,label=' Select rigid body to view:'),0) rbSelect = wx.ComboBox(VectorRBDisplay,choices=['']+rbchoice) name = data['Vector'][resRBsel]['RBname'] rbSelect.SetSelection(1+rbchoice.index(name)) rbSelect.Bind(wx.EVT_COMBOBOX,OnRBSelect) selSizer.Add(rbSelect,0) VectorRBSizer.Add(selSizer,0) rbData = data['Vector'][resRBsel] if 'DELETED' in str(G2frame.GetStatusBar()): #seems to be no other way to do this (wx bug) if GSASIIpath.GetConfigValue('debug'): print ('DBG_wx error: Rigid Body/Status not cleanly deleted after Refine') return SetStatusLine(' You may use e.g. "c60" or "s60" for a vector entry') FillRefChoice(resRBsel,rbData) VectorRBSizer.Add(rbNameSizer(resRBsel,rbData),0) VectorRBSizer.Add(rbRefAtmSizer(resRBsel,rbData),0) XYZ = np.array([[0.,0.,0.] for Ty in rbData['rbTypes']]) for imag,mag in enumerate(rbData['VectMag']): XYZ += mag*rbData['rbVect'][imag] VectorRBSizer.Add(rbVectMag(rbid,imag,rbData),0) VectorRBSizer.Add(rbVectors(rbid,imag,mag,XYZ,rbData),0) VectorRBSizer.Add((5,5),0) data['Vector'][rbid]['rbXYZ'] = XYZ VectorRBSizer.Add((5,25),) VectorRBSizer.Layout() VectorRBDisplay.SetSizer(VectorRBSizer,True) VectorRBDisplay.SetAutoLayout(True) Size = VectorRBSizer.GetMinSize() VectorRBDisplay.SetSize(Size) Size[0] += 40 Size[1] = max(Size[1],450) + 20 VectorRB.SetSize(Size) VectorRB.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1) G2frame.dataWindow.SendSizeEvent() VectorRBDisplay.Show() def UpdateResidueRB(): '''Draw the contents of the Residue Rigid Body tab for Rigid Bodies tree entry ''' global resRBsel def rbNameSizer(rbid,rbData): def OnRBName(event): event.Skip() Obj = event.GetEventObject() name = Obj.GetValue() if name == rbData['RBname']: return # no change namelist = [data['Residue'][key]['RBname'] for key in data['Residue'] if 'RBname' in data['Residue'][key]] name = G2obj.MakeUniqueLabel(name,namelist) rbData['RBname'] = name wx.CallAfter(UpdateResidueRB) def OnDelRB(event): Obj = event.GetEventObject() rbid = Indx[Obj.GetId()] if rbid in data['Residue']: del data['Residue'][rbid] data['RBIds']['Residue'].remove(rbid) wx.CallAfter(UpdateResidueRB) def OnStripH(event): Obj = event.GetEventObject() rbid = Indx[Obj.GetId()] if rbid in data['Residue']: newNames = [] newTypes = [] newXYZ = [] for i,atype in enumerate(rbData['rbTypes']): if atype != 'H': newNames.append(rbData['atNames'][i]) newTypes.append(rbData['rbTypes'][i]) newXYZ.append(rbData['rbXYZ'][i]) rbData['atNames'] = newNames rbData['rbTypes'] = newTypes rbData['rbXYZ'] = newXYZ G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults) wx.CallAfter(UpdateResidueRB) def OnPlotRB(event): G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults) # start of rbNameSizer nameSizer = wx.BoxSizer(wx.HORIZONTAL) nameSizer.Add(wx.StaticText(ResidueRBDisplay,-1,'Residue name: '),0,WACV) RBname = wx.TextCtrl(ResidueRBDisplay,-1,rbData['RBname'], style=wx.TE_PROCESS_ENTER) RBname.Bind(wx.EVT_LEAVE_WINDOW, OnRBName) RBname.Bind(wx.EVT_TEXT_ENTER,OnRBName) RBname.Bind(wx.EVT_KILL_FOCUS,OnRBName) nameSizer.Add(RBname,0,WACV) nameSizer.Add((5,0),) plotRB = wx.Button(ResidueRBDisplay,wx.ID_ANY,'Plot',style=wx.BU_EXACTFIT) plotRB.Bind(wx.EVT_BUTTON, OnPlotRB) Indx[plotRB.GetId()] = rbid nameSizer.Add(plotRB,0,WACV) nameSizer.Add((5,0),) if not rbData['useCount']: delRB = wx.Button(ResidueRBDisplay,wx.ID_ANY,"Delete",style=wx.BU_EXACTFIT) delRB.Bind(wx.EVT_BUTTON, OnDelRB) Indx[delRB.GetId()] = rbid nameSizer.Add(delRB,0,WACV) if 'H' in rbData['rbTypes']: stripH = wx.Button(ResidueRBDisplay,wx.ID_ANY,"Strip H-atoms",style=wx.BU_EXACTFIT) stripH.Bind(wx.EVT_BUTTON, OnStripH) Indx[stripH.GetId()] = rbid nameSizer.Add(stripH,0,WACV) nameSizer.Add(wx.StaticText(ResidueRBDisplay,-1,' body type #'+ str(data['RBIds']['Residue'].index(rbid))),0,WACV) return nameSizer def rbResidues(rbid,rbData): def TypeSelect(event): AtInfo = data['Residue']['AtInfo'] r,c = event.GetRow(),event.GetCol() if resGrid.GetColLabelValue(c) == 'Type': PE = G2elemGUI.PickElement(G2frame,oneOnly=True) if PE.ShowModal() == wx.ID_OK: if PE.Elem != 'None': El = PE.Elem.strip().lower().capitalize() if El not in AtInfo: Info = G2elem.GetAtomInfo(El) AtInfo[El] = [Info['Drad'],Info['Color']] rbData['rbTypes'][r] = El resGrid.SetCellValue(r,c,El) PE.Destroy() def ChangeCell(event): r,c = event.GetRow(),event.GetCol() if c == 0: rbData['atNames'][r] = resGrid.GetCellValue(r,c) if r >= 0 and (2 <= c <= 4): try: val = float(resGrid.GetCellValue(r,c)) rbData['rbXYZ'][r][c-2] = val except ValueError: pass G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults) def OnRefSel(event): Obj = event.GetEventObject() iref,res,jref = Indx[Obj.GetId()] sel = Obj.GetValue() ind = atNames.index(sel) if rbData['rbTypes'][ind] == 'H': G2G.G2MessageBox(G2frame,'You should not select an H-atom for rigid body orientation') rbData['rbRef'][iref] = ind FillRefChoice(rbid,rbData) for i,ref in enumerate(RefObjs[jref]): ref.SetItems([atNames[j] for j in refChoice[rbid][i]]) ref.SetValue(atNames[rbData['rbRef'][i]]) rbXYZ = rbData['rbXYZ'] if not iref: #origin change rbXYZ -= rbXYZ[ind] Xxyz = rbXYZ[rbData['rbRef'][1]] X = Xxyz/np.sqrt(np.sum(Xxyz**2)) Yxyz = rbXYZ[rbData['rbRef'][2]] Y = Yxyz/np.sqrt(np.sum(Yxyz**2)) Mat = G2mth.getRBTransMat(X,Y) rbXYZ = np.inner(Mat,rbXYZ).T rbData['rbXYZ'] = rbXYZ rbData['molCent'] = False res.ClearSelection() resTable = res.GetTable() for r in range(res.GetNumberRows()): row = resTable.GetRowValues(r) row[2:4] = rbXYZ[r] resTable.SetRowValues(r,row) res.ForceRefresh() G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults) def OnMolCent(event): rbData['molCent'] = not rbData['molCent'] if rbData['molCent']: Obj = event.GetEventObject() res = Indx[Obj.GetId()] rbXYZ = rbData['rbXYZ'] rbCent = np.array([np.sum(rbXYZ[:,0]),np.sum(rbXYZ[:,1]),np.sum(rbXYZ[:,2])])/rbXYZ.shape[0] rbXYZ -= rbCent rbData['rbXYZ'] = rbXYZ res.ClearSelection() resTable = res.GetTable() for r in range(res.GetNumberRows()): row = resTable.GetRowValues(r) row[2:4] = rbXYZ[r] resTable.SetRowValues(r,row) res.ForceRefresh() G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults) def OnCycleXYZ(event): Obj = event.GetEventObject() res = Indx[Obj.GetId()] rbXYZ = rbData['rbXYZ'] resTable = res.GetTable() for r in range(res.GetNumberRows()): rbXYZ[r] = np.roll(rbXYZ[r],1) row = resTable.GetRowValues(r) row[2:4] = rbXYZ[r] resTable.SetRowValues(r,row) res.ForceRefresh() G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults) Types = 2*[wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_FLOAT+':10,5',] colLabels = ['Name','Type','Cart x','Cart y','Cart z'] table = [] rowLabels = [] for ivec,xyz in enumerate(rbData['rbXYZ']): table.append([rbData['atNames'][ivec],]+[rbData['rbTypes'][ivec],]+list(xyz)) rowLabels.append(str(ivec)) vecTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types) resGrid = G2G.GSGrid(ResidueRBDisplay) Indx[resGrid.GetId()] = rbid resList.append(resGrid) resGrid.SetTable(vecTable, True) if 'phoenix' in wx.version(): resGrid.Bind(wg.EVT_GRID_CELL_CHANGED, ChangeCell) else: resGrid.Bind(wg.EVT_GRID_CELL_CHANGE, ChangeCell) resGrid.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, TypeSelect) for c in range(2,5): attr = wx.grid.GridCellAttr() attr.IncRef() attr.SetEditor(G2G.GridFractionEditor(resGrid)) resGrid.SetColAttr(c, attr) for row in range(vecTable.GetNumberRows()): resGrid.SetReadOnly(row,1,True) resGrid.AutoSizeColumns(False) vecSizer = wx.BoxSizer() vecSizer.Add(resGrid) refAtmSizer = wx.BoxSizer(wx.HORIZONTAL) atNames = rbData['atNames'] rbRef = rbData['rbRef'] if rbData['rbRef'][3] or rbData['useCount']: refAtmSizer.Add(wx.StaticText(ResidueRBDisplay,-1, 'Orientation reference non-H atoms A-B-C: %s, %s, %s'%(atNames[rbRef[0]], \ atNames[rbRef[1]],atNames[rbRef[2]])),0) else: refAtmSizer.Add(wx.StaticText(ResidueRBDisplay,-1, 'Orientation reference non-H atoms A-B-C: '),0,WACV) refObj = [0,0,0] for i in range(3): choices = [atNames[j] for j in refChoice[rbid][i]] refSel = wx.ComboBox(ResidueRBDisplay,-1,value='', choices=choices,style=wx.CB_READONLY|wx.CB_DROPDOWN) refSel.SetValue(atNames[rbRef[i]]) refSel.Bind(wx.EVT_COMBOBOX, OnRefSel) Indx[refSel.GetId()] = [i,resGrid,len(RefObjs)] refObj[i] = refSel refAtmSizer.Add(refSel,0,WACV) RefObjs.append(refObj) cycleXYZ = wx.Button(ResidueRBDisplay,label=' Cycle XYZ?') cycleXYZ.Bind(wx.EVT_BUTTON,OnCycleXYZ) Indx[cycleXYZ.GetId()] = resGrid refAtmSizer.Add(cycleXYZ,0,WACV) if 'molCent' not in rbData: rbData['molCent'] = False #patch molcent = wx.Button(ResidueRBDisplay,label=' Center RB?') molcent.Bind(wx.EVT_BUTTON,OnMolCent) Indx[molcent.GetId()] = resGrid refAtmSizer.Add(molcent,0,WACV) refHelpInfo = ''' * The "Orientation Reference" control defines the Cartesian axes for rigid bodies with the three atoms, A, B and C. The vector from B to A defines the x-axis and the y axis is placed in the plane defined by B to A and C to A. A,B,C must not be collinear. %%* The origin is at A unless the "Center RB?" button is pressed. %%* The 'Cycle XYZ' button will permute the rigid body XYZ coordinates so XYZ --> ZXY. Repeat if needed. %%* The "Center RB?" button will shift the origin of the rigid body to be the midpoint of all atoms in the body (not mass weighted). ''' hlp = G2G.HelpButton(ResidueRBDisplay,refHelpInfo,wrap=400) refAtmSizer.Add(hlp,0,wx.LEFT|wx.RIGHT|wx.ALIGN_CENTER_VERTICAL,2) mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add(refAtmSizer) mainSizer.Add(vecSizer) return mainSizer def Add2SeqSizer(seqSizer,angSlide,rbid,iSeq,Seq,atNames): def ChangeAngle(event): event.Skip() Obj = event.GetEventObject() rbid,Seq = Indx[Obj.GetId()][:2] val = Seq[2] try: val = float(Obj.GetValue()) Seq[2] = val except ValueError: pass Obj.SetValue('%8.2f'%(val)) G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,data['Residue'][rbid],plotDefaults) def OnRadBtn(event): Obj = event.GetEventObject() Seq,iSeq,angId = Indx[Obj.GetId()] data['Residue'][rbid]['SelSeq'] = [iSeq,angId] angSlide.SetValue(int(100*Seq[2])) def OnDelBtn(event): Obj = event.GetEventObject() rbid,Seq = Indx[Obj.GetId()] data['Residue'][rbid]['rbSeq'].remove(Seq) wx.CallAfter(UpdateResidueRB) iBeg,iFin,angle,iMove = Seq ang = wx.TextCtrl(ResidueRBDisplay,wx.ID_ANY, '%8.2f'%(angle),size=(70,-1),style=wx.TE_PROCESS_ENTER) if not iSeq: radBt = wx.RadioButton(ResidueRBDisplay,wx.ID_ANY, '',style=wx.RB_GROUP) data['Residue'][rbid]['SelSeq'] = [iSeq,ang.GetId()] radBt.SetValue(True) else: radBt = wx.RadioButton(ResidueRBDisplay,wx.ID_ANY,'') radBt.Bind(wx.EVT_RADIOBUTTON,OnRadBtn) seqSizer.Add(radBt) delBt = wx.Button(ResidueRBDisplay,wx.ID_ANY,'Del', style=wx.BU_EXACTFIT) delBt.Bind(wx.EVT_BUTTON,OnDelBtn) seqSizer.Add(delBt) bond = wx.StaticText(ResidueRBDisplay,wx.ID_ANY, '%s %s'%(atNames[iBeg],atNames[iFin]),size=(50,20)) seqSizer.Add(bond,0,WACV) Indx[radBt.GetId()] = [Seq,iSeq,ang.GetId()] Indx[delBt.GetId()] = [rbid,Seq] Indx[ang.GetId()] = [rbid,Seq,ang] ang.Bind(wx.EVT_TEXT_ENTER,ChangeAngle) ang.Bind(wx.EVT_KILL_FOCUS,ChangeAngle) seqSizer.Add(ang,0,WACV) atms = '' for i in iMove: atms += ' %s,'%(atNames[i]) moves = wx.StaticText(ResidueRBDisplay,wx.ID_ANY, atms[:-1],size=(200,20)) seqSizer.Add(moves,1,wx.EXPAND|wx.RIGHT) return seqSizer def SlideSizer(): def OnSlider(event): Obj = event.GetEventObject() rbData = Indx[Obj.GetId()] iSeq,angId = rbData['SelSeq'] val = float(Obj.GetValue())/100. rbData['rbSeq'][iSeq][2] = val Indx[angId][2].SetValue('%8.2f'%(val)) G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults) slideSizer = wx.BoxSizer(wx.HORIZONTAL) slideSizer.Add(wx.StaticText(ResidueRBDisplay,-1,'Selected torsion angle:'),0) iSeq,angId = rbData['SelSeq'] angSlide = wx.Slider(ResidueRBDisplay,-1, int(100*rbData['rbSeq'][iSeq][2]),0,36000,size=(200,20), style=wx.SL_HORIZONTAL) angSlide.Bind(wx.EVT_SLIDER, OnSlider) Indx[angSlide.GetId()] = rbData slideSizer.Add(angSlide,0) return slideSizer,angSlide def FillRefChoice(rbid,rbData): choiceIds = [i for i in range(len(rbData['atNames']))] for seq in rbData['rbSeq']: for i in seq[3]: try: choiceIds.remove(i) except ValueError: pass rbRef = rbData['rbRef'] for i in range(3): try: choiceIds.remove(rbRef[i]) except ValueError: pass refChoice[rbid] = [choiceIds[:],choiceIds[:],choiceIds[:]] for i in range(3): refChoice[rbid][i].append(rbRef[i]) refChoice[rbid][i].sort() def OnRBSelect(event): global resRBsel sel = rbSelect.GetSelection() if sel == 0: return # 1st entry is blank rbname = rbchoice[sel-1] resRBsel = RBnames[rbname] G2plt.PlotRigidBody(G2frame,'Residue',AtInfo,rbData,plotDefaults) wx.CallLater(100,UpdateResidueRB) #----- beginning of UpdateResidueRB ----------------------------------------------- AtInfo = data['Residue']['AtInfo'] refChoice = {} RefObjs = [] GS = ResidueRBDisplay.GetSizer() if GS: try: #get around a c++ error in wx 4.0; doing is again seems to be OK GS.Clear(True) except: GS.Clear(True) RBnames = {} for rbid in data['RBIds']['Residue']: RBnames.update({data['Residue'][rbid]['RBname']:rbid,}) if not RBnames: return rbchoice = list(RBnames.keys()) rbchoice.sort() if GS: ResidueRBSizer = GS else: ResidueRBSizer = wx.BoxSizer(wx.VERTICAL) if resRBsel not in data['RBIds']['Residue']: resRBsel = RBnames[rbchoice[0]] if len(RBnames) > 1: selSizer = wx.BoxSizer(wx.HORIZONTAL) selSizer.Add(wx.StaticText(ResidueRBDisplay, label=' Select residue to view:'),0) rbSelect = wx.ComboBox(ResidueRBDisplay,choices=['']+rbchoice) name = data['Residue'][resRBsel]['RBname'] rbSelect.SetSelection(1+rbchoice.index(name)) rbSelect.Bind(wx.EVT_COMBOBOX,OnRBSelect) selSizer.Add(rbSelect,0) ResidueRBSizer.Add(selSizer,0) rbData = data['Residue'][resRBsel] FillRefChoice(resRBsel,rbData) ResidueRBSizer.Add(rbNameSizer(resRBsel,rbData),0) ResidueRBSizer.Add(rbResidues(resRBsel,rbData),0) if len(rbData['rbSeq']): ResidueRBSizer.Add((-1,15),0) slideSizer,angSlide = SlideSizer() seqSizer = wx.FlexGridSizer(0,5,4,8) for lbl in 'Sel','','Bond','Angle','Riding atoms': seqSizer.Add(wx.StaticText(ResidueRBDisplay,wx.ID_ANY,lbl)) ResidueRBSizer.Add(seqSizer) # for iSeq,Seq in enumerate(rbData['rbSeq']): # ResidueRBSizer.Add(SeqSizer(angSlide,resRBsel,iSeq,Seq,rbData['atNames'])) for iSeq,Seq in enumerate(rbData['rbSeq']): Add2SeqSizer(seqSizer,angSlide,resRBsel,iSeq,Seq,rbData['atNames']) ResidueRBSizer.Add(slideSizer,) ResidueRBSizer.Add((5,25),) ResidueRBSizer.Layout() ResidueRBDisplay.SetSizer(ResidueRBSizer,True) ResidueRBDisplay.SetAutoLayout(True) Size = ResidueRBSizer.GetMinSize() ResidueRBDisplay.SetSize(Size) Size[0] += 40 Size[1] = max(Size[1],450) + 20 ResidueRB.SetSize(Size) ResidueRB.SetScrollbars(10,10,Size[0]/10-4,Size[1]/10-1) G2frame.dataWindow.SendSizeEvent() ResidueRBDisplay.Show() def SetStatusLine(text): G2frame.GetStatusBar().SetStatusText(text,1) #### UpdateRigidBodies starts here ========= global resList,resRBsel if not data.get('RBIds') or not data: data.update({'Vector':{'AtInfo':{}},'Residue':{'AtInfo':{}}, 'RBIds':{'Vector':[],'Residue':[]}}) #empty/bad dict - fill it Indx = {} resList = [] plotDefaults = {'oldxy':[0.,0.],'Quaternion':[0.,0.,0.,1.],'cameraPos':30.,'viewDir':[0,0,1],} G2frame.rbBook = G2G.GSNoteBook(parent=G2frame.dataWindow) G2frame.dataWindow.GetSizer().Add(G2frame.rbBook,1,wx.ALL|wx.EXPAND) VectorRB = wx.ScrolledWindow(G2frame.rbBook) VectorRBDisplay = wx.Panel(VectorRB) G2frame.rbBook.AddPage(VectorRB,'Vector rigid bodies') ResidueRB = wx.ScrolledWindow(G2frame.rbBook) ResidueRBDisplay = wx.Panel(ResidueRB) G2frame.rbBook.AddPage(ResidueRB,'Residue rigid bodies') # vector RBs are not too common, so select Residue as the default when one is present if len(data['RBIds']['Residue']) > 0 and len(data['RBIds']['Vector']) == 0: G2frame.rbBook.ChangeSelection(1) OnPageChanged(None) G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.RigidBodyMenu) SetStatusLine('') UpdateVectorRB() G2frame.rbBook.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged) wx.CallAfter(OnPageChanged,None)
[docs]def ShowIsoDistortCalc(G2frame,phase=None): '''Compute the ISODISTORT mode values from the current coordinates. Called in response to the (Phase/Atoms tab) AtomCompute or Constraints/Edit Constr. "Show ISODISTORT modes" menu item, which should be enabled only when Phase['ISODISTORT'] is defined. ''' def _onClose(event): dlg.EndModal(wx.ID_CANCEL) def fmtHelp(item,fullname): helptext = "A new variable" if item[-3]: helptext += " named "+str(item[-3]) helptext += " is a linear combination of the following parameters:\n" first = True for term in item[:-3]: line = '' var = str(term[1]) m = term[0] if first: first = False line += ' = ' else: if m >= 0: line += ' + ' else: line += ' - ' m = abs(m) line += '%.3f*%s '%(m,var) varMean = G2obj.fmtVarDescr(var) helptext += "\n" + line + " ("+ varMean + ")" helptext += '\n\nISODISTORT full name: '+str(fullname) return helptext Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree() # init for constraint isophases = [p for p in Phases if 'ISODISTORT' in Phases[p]] if not isophases: G2frame.ErrorDialog('no ISODISTORT phases', 'Unexpected error: no ISODISTORT phases') return if phase and phase not in isophases: G2frame.ErrorDialog('not ISODISTORT phase', 'Unexpected error: selected phase is not an ISODISTORT phase') print('Unexpected error: selected phase is not an ISODISTORT phase', phase,isophases) elif not phase and len(isophases) == 1: phase = isophases[0] elif not phase: dlg = wx.SingleChoiceDialog(G2frame,'Select phase from ISODISTORT phases', 'Select Phase',isophases) if dlg.ShowModal() == wx.ID_OK: sel = dlg.GetSelection() phase = isophases[sel] else: return # if len(data.get('Histograms',[])) == 0: # G2frame.ErrorDialog( # 'No data', # 'Sorry, this computation requires that a histogram first be added to the phase' # ) # return covdata = G2frame.GPXtree.GetItemPyData( G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Covariance')) # make a lookup table for named NewVar Phase constraints sub = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Constraints') Constraints = G2frame.GPXtree.GetItemPyData(sub) constDict = {} for c in Constraints['Phase']: if c[-1] != 'f' or not c[-3]: continue constDict[str(c[-3])] = c parmDict,varyList = G2frame.MakeLSParmDict() dlg = wx.Dialog(G2frame,wx.ID_ANY,'ISODISTORT mode values',#size=(630,400), style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) mainSizer = wx.BoxSizer(wx.VERTICAL) if 'ISODISTORT' not in Phases[phase]: G2frame.ErrorDialog('not ISODISTORT phase', 'Unexpected error: selected phase is not an ISODISTORT phase') return data = Phases[phase] ISO = data['ISODISTORT'] mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY, 'ISODISTORT mode computation for cordinates in phase '+ str(data['General'].get('Name')))) aSizer = wx.BoxSizer(wx.HORIZONTAL) panel1 = wxscroll.ScrolledPanel( dlg, wx.ID_ANY,#size=(100,200), style = wx.TAB_TRAVERSAL|wx.SUNKEN_BORDER) subSizer1 = wx.FlexGridSizer(cols=2,hgap=5,vgap=2) panel2 = wxscroll.ScrolledPanel( dlg, wx.ID_ANY,#size=(100,200), style = wx.TAB_TRAVERSAL|wx.SUNKEN_BORDER) subSizer2 = wx.FlexGridSizer(cols=3,hgap=5,vgap=2) subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,'Parameter name ')) subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT) subSizer2.Add((-1,-1)) subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,'Mode name ')) subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT) # ISODISTORT displacive modes if 'G2VarList' in ISO: deltaList = [] for gv,Ilbl in zip(ISO['G2VarList'],ISO['IsoVarList']): dvar = gv.varname() var = dvar.replace('::dA','::A') albl = Ilbl[:Ilbl.rfind('_')] v = Ilbl[Ilbl.rfind('_')+1:] pval = ISO['ParentStructure'][albl][['dx','dy','dz'].index(v)] if var in parmDict: cval = parmDict[var][0] else: dlg.EndModal(wx.ID_CANCEL) G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var)) return deltaList.append(cval-pval) modeVals = np.inner(ISO['Var2ModeMatrix'],deltaList) for lbl,xyz,var,val,norm,G2mode in zip( ISO['IsoVarList'],deltaList, ISO['IsoModeList'],modeVals,ISO['NormList'],ISO['G2ModeList'] ): #GSASIIpath.IPyBreak() if str(G2mode) in constDict: ch = G2G.HelpButton(panel2,fmtHelp(constDict[str(G2mode)],var)) subSizer2.Add(ch,0,wx.LEFT|wx.RIGHT|WACV|wx.ALIGN_CENTER,1) else: subSizer2.Add((-1,-1)) subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl))) try: value = G2py3.FormatSigFigs(xyz) except TypeError: value = str(xyz) subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT) subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var))) try: value = G2py3.FormatSigFigs(val/norm) if 'varyList' in covdata: if str(G2mode) in covdata['varyList']: sig = covdata['sig'][covdata['varyList'].index(str(G2mode))] value = G2mth.ValEsd(val/norm,sig/norm) except TypeError: value = '?' subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT) #GSASIIpath.IPyBreak() # ISODISTORT occupancy modes if 'G2OccVarList' in ISO: deltaList = [] for gv,Ilbl in zip(ISO['G2OccVarList'],ISO['OccVarList']): var = gv.varname() albl = Ilbl[:Ilbl.rfind('_')] pval = ISO['BaseOcc'][albl] if var in parmDict: cval = parmDict[var][0] else: dlg.EndModal(wx.ID_CANCEL) G2frame.ErrorDialog('Atom not found',"No value found for parameter "+str(var)) return deltaList.append(cval-pval) modeVals = np.inner(ISO['Var2OccMatrix'],deltaList) for lbl,delocc,var,val,norm,G2mode in zip( ISO['OccVarList'],deltaList, ISO['OccModeList'],modeVals,ISO['OccNormList'],ISO['G2OccModeList']): if str(G2mode) in constDict: ch = G2G.HelpButton(panel2,fmtHelp(constDict[str(G2mode)],var)) subSizer2.Add(ch,0,wx.LEFT|wx.RIGHT|WACV|wx.ALIGN_CENTER,1) else: subSizer2.Add((-1,-1)) subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl))) try: value = G2py3.FormatSigFigs(delocc) except TypeError: value = str(delocc) subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,value),0,wx.ALIGN_RIGHT) #subSizer.Add((10,-1)) subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(var))) try: value = G2py3.FormatSigFigs(val/norm) if 'varyList' in covdata: if str(G2mode) in covdata['varyList']: sig = covdata['sig'][covdata['varyList'].index(str(G2mode))] value = G2mth.ValEsd(val/norm,sig/norm) except TypeError: value = '?' subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,value),0,wx.ALIGN_RIGHT) # finish up ScrolledPanel panel1.SetSizer(subSizer1) panel2.SetSizer(subSizer2) panel1.SetAutoLayout(1) panel1.SetupScrolling() panel2.SetAutoLayout(1) panel2.SetupScrolling() # Allow window to be enlarged but not made smaller dlg.SetSizer(mainSizer) w1,l1 = subSizer1.GetSize() w2,l2 = subSizer2.GetSize() panel1.SetMinSize((w1+10,200)) panel2.SetMinSize((w2+20,200)) aSizer.Add(panel1,1, wx.ALL|wx.EXPAND,1) aSizer.Add(panel2,2, wx.ALL|wx.EXPAND,1) mainSizer.Add(aSizer,1, wx.ALL|wx.EXPAND,1) # make OK button btnsizer = wx.BoxSizer(wx.HORIZONTAL) btn = wx.Button(dlg, wx.ID_CLOSE) btn.Bind(wx.EVT_BUTTON,_onClose) btnsizer.Add(btn) mainSizer.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5) mainSizer.Fit(dlg) dlg.SetMinSize(dlg.GetSize()) dlg.ShowModal() dlg.Destroy()