# -*- coding: utf-8 -*-
#GSASIIconstrGUI - constraint GUI routines
########### SVN repository information ###################
# $Date: 2024-03-17 12:50:24 -0500 (Sun, 17 Mar 2024) $
# $Author: toby $
# $Revision: 5767 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIconstrGUI.py $
# $Id: GSASIIconstrGUI.py 5767 2024-03-17 17:50:24Z toby $
########### SVN repository information ###################
'''
Constraints and rigid bodies GUI routines follow.
'''
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: 5767 $")
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 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
[docs]
def GetNumberRows(self):
return len(self.labels)
[docs]
def GetNumberCols(self):
return len(self.colLabels)
[docs]
def IsEmptyCell(self, row, col):
return False
[docs]
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])
[docs]
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
[docs]
def GetColLabelValue(self, col):
return self.colLabels[col]
[docs]
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 CheckConstraints(G2frame,Phases,Histograms,data,newcons=[],reqVaryList=None,seqhst=None,seqmode='use-all'):
'''Load constraints & check them for errors.
N.B. Equivalences based on symmetry (etc.)
are generated by running :func:`GSASIIstrIO.GetPhaseData`.
When reqVaryList is included (see WarnConstraintLimit) then
parameters with limits are checked against constraints and a
warning is shown.
'''
G2mv.InitVars()
#Find all constraints
constrDict = []
for key in data:
if key.startswith('_'): continue
constrDict += data[key]
if newcons:
constrDict = constrDict + newcons
constrDict, fixedList, ignored = G2mv.ProcessConstraints(constrDict, seqhst=seqhst, seqmode=seqmode)
parmDict = {}
# generate symmetry constraints to check for conflicts
rigidbodyDict = G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame, G2frame.root, 'Rigid bodies'))
rbIds = rigidbodyDict.get('RBIds', {'Vector': [], 'Residue': [],'Spin':[]})
rbVary, rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict, Print=False)
parmDict.update(rbDict)
(Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,EFtables,ORBtables,BLtables,MFtables,maxSSwave) = \
G2stIO.GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
parmDict.update(phaseDict)
# get Hist and HAP info
hapVary, hapDict, controlDict = G2stIO.GetHistogramPhaseData(Phases, Histograms, Print=False, resetRefList=False)
parmDict.update(hapDict)
histVary, histDict, controlDict = G2stIO.GetHistogramData(Histograms, Print=False)
parmDict.update(histDict)
# TODO: twining info needed?
#TwConstr,TwFixed = G2stIO.makeTwinFrConstr(Phases,Histograms,hapVary)
#constrDict += TwConstr
#fixedList += TwFixed
varyList = rbVary+phaseVary+hapVary+histVary
msg = G2mv.EvaluateMultipliers(constrDict,parmDict)
if msg:
return 'Unable to interpret multiplier(s): '+msg,''
if reqVaryList:
varyList = reqVaryList[:]
errmsg,warnmsg,groups,parmlist = G2mv.GenerateConstraints(varyList,constrDict,fixedList,parmDict) # changes varyList
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] = {}
G2mv.Map2Dict(parmDict,varyList) # changes parmDict & 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])
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')
else:
G2mv.Map2Dict(parmDict,varyList) # changes varyList
return errmsg,warnmsg
[docs]
def UpdateConstraints(G2frame, data, selectTab=None, Clear=False):
'''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 'Akappa' in name:
namelist = ['Akappa%d'%i for i in range(6)]
elif 'ANe' in name:
namelist = ['ANe0','ANe1']
elif 'AD(1' in name:
orb = name.split(':')[2][-1]
namelist = ['AD(1,0)'+orb,'AD(1,1)'+orb,'AD(1,-1)'+orb]
elif 'AD(2' in name:
orb = name.split(':')[2][-1]
namelist = ['AD(2,0)'+orb,'AD(2,1)'+orb,'AD(2,-1)'+orb,'AD(2,2)'+orb,'AD(2,-2)'+orb]
elif 'AD(4' in name:
orb = name.split(':')[2][-1]
namelist = ['AD(4,0)'+orb,'AD(4,1)'+orb,'AD(4,-1)'+orb,'AD(4,2)'+orb,'AD(4,-2)'+orb,
'AD(4,3)'+orb,'AD(4,-3)'+orb,'AD(4,4)'+orb,'AD(4,-4)'+orb]
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',]
if 'Tr' in name:
namelist = [rbfx+'Tr',]
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 or keys[2].split(';')[0] 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 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 = CheckConstraints(G2frame,Phases,Histograms,data,newcons,seqhst=seqhistnum,seqmode=seqmode)
if errmsg:
G2frame.ErrorDialog('Constraint Error',
'Error with newly added constraint:\n'+errmsg+
'\nIgnoring newly added constraint',parent=G2frame)
# reset error status
errmsg,warnmsg = CheckConstraints(G2frame,Phases,Histograms,data,seqhst=seqhistnum,seqmode=seqmode)
if errmsg:
print (errmsg)
print (G2mv.VarRemapShow([],True))
return False
elif warnmsg:
print ('Warning after constraint addition:\n'+warnmsg)
ans = G2G.ShowScrolledInfo(header='Constraint Warning',
txt='Warning noted after adding constraint:\n'+warnmsg+
'\n\nKeep this addition?',
buttonlist=[wx.ID_YES,wx.ID_NO],parent=G2frame,height=250)
if ans == wx.ID_NO: return False
return True
def WarnConstraintLimit():
'''Check if constraints reference variables with limits.
Displays a warning message, but does nothing
'''
parmDict,reqVaryList = G2frame.MakeLSParmDict()
try:
errmsg,warnmsg = CheckConstraints(G2frame,Phases,Histograms,data,[],reqVaryList,seqhst=seqhistnum,seqmode=seqmode)
except Exception as msg:
if GSASIIpath.GetConfigValue('debug'):
import traceback
print (traceback.format_exc())
return 'CheckConstraints error retrieving parameter\nError='+str(msg),''
return errmsg,warnmsg
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 = CheckConstraints(G2frame,Phases,Histograms,data,seqhst=seqhistnum,seqmode=seqmode)
if errmsg:
G2frame.ErrorDialog('Constraint Error',
'Error after editing constraint:\n'+errmsg+
'\nDiscarding last constraint edit',parent=G2frame)
# reset error status
errmsg,warnmsg = CheckConstraints(G2frame,Phases,Histograms,data,seqhst=seqhistnum,seqmode=seqmode)
if errmsg:
print (errmsg)
print (G2mv.VarRemapShow([],True))
return False
elif warnmsg:
print ('Warning after constraint edit:\n'+warnmsg)
ans = G2G.ShowScrolledInfo(header='Constraint Warning',
txt='Warning noted after last constraint edit:\n'+warnmsg+
'\n\nKeep this change?',
buttonlist=[wx.ID_YES,wx.ID_NO],parent=G2frame,height=250)
if ans == wx.ID_NO: return False
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)
wx.CallAfter(UpdateConstraints, G2frame, data, G2frame.constr.GetSelection(), True)
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)
wx.CallAfter(UpdateConstraints, G2frame, data, G2frame.constr.GetSelection(), True)
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)
wx.CallAfter(UpdateConstraints, G2frame, data, G2frame.constr.GetSelection(), True)
def MakeConstraintsSizer(name,panel):
'''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 panel: 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(panel,wx.ID_ANY,
'Position variables fixed by space group symmetry'))
Sizer1.Add((-1,5))
Sizer = wx.FlexGridSizer(0,3,0,0)
Sizer1.Add(Sizer)
for var in symHolds:
varMean = G2obj.fmtVarDescr(var)
helptext = "Prevents variable: "+ var + " ("+ varMean + ")\nfrom being changed"
ch = G2G.HelpButton(panel,helptext)
Sizer.Add(ch)
Sizer.Add(wx.StaticText(panel,label='FIXED'),0,WACV|wx.ALIGN_CENTER|wx.RIGHT|wx.LEFT,2)
Sizer.Add(wx.StaticText(panel,label=var),0,WACV|wx.ALIGN_CENTER|wx.RIGHT|wx.LEFT)
else:
Sizer1.Add(wx.StaticText(panel,label='No holds generated'))
Sizer1.Add((-1,10))
symGen,SymErr,SymHelp = G2mv.GetSymEquiv(seqmode,seqhistnum)
symGenD,SymErrD,SymHelpD = G2mv.GetDroppedSym(seqmode,seqhistnum)
if len(symGen) == 0:
Sizer1.Add(wx.StaticText(panel,label='No equivalences generated'))
return Sizer1
Sizer1.Add(wx.StaticText(panel,label='Equivalences generated based on cell/space group input'))
Sizer1.Add((-1,5))
Sizer = wx.FlexGridSizer(0,5,0,0)
Sizer1.Add(Sizer)
helptext = ''
for sym,(warnmsg,note),helptext in zip(symGen,SymErr,SymHelp):
if warnmsg:
if helptext: helptext += '\n\n'
helptext += warnmsg
if helptext:
ch = G2G.HelpButton(panel,helptext)
Sizer.Add(ch,0,wx.LEFT|wx.RIGHT|WACV|wx.ALIGN_CENTER,1)
else:
Sizer.Add((-1,-1))
Sizer.Add(wx.StaticText(panel,wx.ID_ANY,'EQUIV'),
0,WACV|wx.ALIGN_CENTER|wx.RIGHT|wx.LEFT,2)
Sizer.Add(wx.StaticText(panel,wx.ID_ANY,sym),0,WACV|wx.ALIGN_LEFT|wx.RIGHT|wx.LEFT,2)
if note:
Sizer.Add(wx.StaticText(panel,wx.ID_ANY,note),0,WACV|wx.ALIGN_LEFT|wx.RIGHT|wx.LEFT,2)
else:
Sizer.Add((-1,-1))
Sizer.Add((-1,-1))
for sym,(warnmsg,note),helptext in zip(symGenD,SymErrD,SymHelpD):
if warnmsg:
if helptext: helptext += '\n\n'
helptext += warnmsg
if helptext:
ch = G2G.HelpButton(panel,helptext)
Sizer.Add(ch,0,wx.LEFT|wx.RIGHT|WACV|wx.ALIGN_CENTER,1)
else:
Sizer.Add((-1,-1))
Sizer.Add(wx.StaticText(panel,wx.ID_ANY,'EQUIV'),
0,WACV|wx.ALIGN_CENTER|wx.RIGHT|wx.LEFT,2)
Sizer.Add(wx.StaticText(panel,wx.ID_ANY,sym),0,WACV|wx.ALIGN_LEFT|wx.RIGHT|wx.LEFT,2)
if note:
Sizer.Add(wx.StaticText(panel,wx.ID_ANY,note),0,WACV|wx.ALIGN_LEFT|wx.RIGHT|wx.LEFT,2)
else:
Sizer.Add((-1,-1))
Sizer.Add((-1,-1))
return Sizer1
constSizer = wx.FlexGridSizer(0,8,0,0)
maxlen = 50 # characters before wrapping a constraint
for Id,item in enumerate(data[name]):
refineflag = False
helptext = ""
eqString = ['',]
problemItem, warnmsg, note = G2mv.getConstrError(item,seqmode,seqhistnum)
#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])
var,explain,note,warnmsg = item[0][1].fmtVarByMode(seqmode,note,warnmsg)
#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(panel,label='Edit',style=wx.BU_EXACTFIT)
constEdit.Bind(wx.EVT_BUTTON,OnConstEdit)
constSizer.Add(constEdit) # 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]:
m = term[0]
if np.isclose(m,0): continue
#var = str(term[1])
var,explain,note,warnmsg = term[1].fmtVarByMode(seqmode,note,warnmsg)
#if '?' in var: badVar = True
if len(eqString[-1]) > maxlen:
eqString.append(' ')
if eqString[-1] != '':
if m >= 0:
eqString[-1] += ' + '
else:
eqString[-1] += ' - '
m = abs(m)
if m == 1:
eqString[-1] += '{:} '.format(var)
else:
eqString[-1] += '{:.3g}*{:} '.format(m,var)
varMean = G2obj.fmtVarDescr(var)
helptext += '\n {:.5g} * {:} '.format(m,var) + " ("+ varMean + ")"
# Add extra notes about this constraint (such as from ISODISTORT)
if '_Explain' in data:
hlptxt = None
try:
hlptxt = data['_Explain'].get(item[-3])
except TypeError:
# Patch fixed Nov 2021. Older projects have phase RanId in
# item[-3].phase rather than a properly formed G2VarObj
hlptxt = data['_Explain'].get(str(item[-3].phase)+item[-3].name)
if hlptxt:
helptext += '\n\n'+ hlptxt
if item[-3]:
typeString = str(item[-3]) + ' ='
if note: note += ', '
note += '(NEW VAR)'
else:
typeString = 'New Variable = '
#print 'refine',item[-2]
refineflag = True
elif item[-1] == 'c':
helptext = "The following variables are constrained to equal a constant:"
for term in item[:-3]:
#var = str(term[1])
var,explain,note,warnmsg = term[1].fmtVarByMode(seqmode,note,warnmsg)
#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] += '{:.3g}*{:} '.format(m,var)
varMean = G2obj.fmtVarDescr(var)
helptext += '\n {:.5g} * {:} '.format(m,var) + " ("+ varMean + ")"
helptext += explain
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])
var,explain,note,warnmsg = item[0][1].fmtVarByMode(seqmode,note,warnmsg)
#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])
var1,explain,note,warnmsg = item[1][1].fmtVarByMode(seqmode,note,warnmsg)
helptext += '\n {:.5g} * {:} '.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])
var,explain,note,warnmsg = term[1].fmtVarByMode(seqmode,note,warnmsg)
#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] += '{:.3g}*{:} '.format(m,var)
helptext += '\n {:.5g} * {:} '.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
if warnmsg:
if helptext: helptext += '\n\nNote warning:\n'
helptext += warnmsg
if helptext:
ch = G2G.HelpButton(panel,helptext)
constSizer.Add(ch)
else:
constSizer.Add((-1,-1))
constDel = wx.CheckBox(panel,label='sel ')
constSizer.Add(constDel) # delete selection
panel.delBtn.checkboxList.append([constDel,Id,name])
if refineflag:
refresh = lambda event: wx.CallAfter(UpdateConstraints, G2frame, data, G2frame.constr.GetSelection(), True)
ch = G2G.G2CheckBox(panel,'vary ',item,-2,OnChange=refresh)
constSizer.Add(ch)
else:
constSizer.Add((-1,-1))
if typeString.strip().endswith('='):
constSizer.Add(wx.StaticText(panel,label=typeString),0,wx.EXPAND,1)
else:
constSizer.Add(wx.StaticText(panel,label=typeString),0,wx.EXPAND,1)
#if badVar: eqString[-1] += ' -- Error: variable removed'
#if note: eqString[-1] += ' (' + note + ')'
if len(eqString) > 1:
Eq = wx.BoxSizer(wx.VERTICAL)
for s in eqString:
line = wx.StaticText(panel,label=s)
if problemItem:
line.SetForegroundColour(wx.BLACK)
line.SetBackgroundColour(wx.YELLOW)
Eq.Add(line,0)
Eq.Add((-1,4))
else:
Eq = wx.StaticText(panel,label=eqString[0])
if problemItem:
Eq.SetForegroundColour(wx.BLACK)
Eq.SetBackgroundColour(wx.YELLOW)
constSizer.Add(Eq)
constSizer.Add((3,3))
if note:
Eq = wx.StaticText(panel,label=note,style=WACV)
if problemItem:
Eq.SetForegroundColour(wx.BLACK)
Eq.SetBackgroundColour(wx.YELLOW)
else:
Eq = (-1,-1)
constSizer.Add(Eq,1,wx.EXPAND,3)
if panel.delBtn.checkboxList:
panel.delBtn.Enable(True)
else:
panel.delBtn.Enable(False)
return constSizer
def OnConstDel(event):
'Delete selected constraints'
sel = G2frame.constr.GetSelection()
selList = event.GetEventObject().checkboxList
selList.reverse()
for obj,Id,name in event.GetEventObject().checkboxList:
if obj.GetValue(): del data[name][Id]
wx.CallAfter(UpdateConstraints,G2frame,data,sel,True)
def OnConstEdit(event):
'''Called to edit an individual contraint in response to a
click on its Edit button
'''
Obj = event.GetEventObject()
sel = G2frame.constr.GetSelection()
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 multiplier for each parameter in the New Var expression'
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)
G2frame.dataWindow.ClearData()
wx.CallAfter(UpdateConstraints,G2frame,data,sel,True)
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)
if typ != 'Sym-Generated':
butSizer = wx.BoxSizer(wx.HORIZONTAL)
btn = wx.Button(panel, wx.ID_ANY, 'Show Errors')
btn.Bind(wx.EVT_BUTTON,lambda event: G2G.ShowScrolledInfo(panel,errmsg,header='Error info'))
butSizer.Add(btn,0,wx.ALIGN_CENTER_VERTICAL)
btn.Enable(len(errmsg) > 0)
btn = wx.Button(panel, wx.ID_ANY, 'Show Warnings')
butSizer.Add(btn,0,wx.ALIGN_CENTER_VERTICAL)
btn.Bind(wx.EVT_BUTTON,lambda event: G2G.ShowScrolledInfo(panel,warnmsg.replace('&','&&')))
btn.Enable(len(warnmsg) > 0)
btn = wx.Button(panel, wx.ID_ANY, 'Show generated constraints')
butSizer.Add(btn,0,wx.ALIGN_CENTER_VERTICAL)
txt = G2mv.VarRemapShow(linelen=999).replace('&','&&')
btn.Bind(wx.EVT_BUTTON,lambda event:
G2G.ShowScrolledColText(panel,
'*** Constraints after processing ***'+txt,
header='Generated constraints',col1len=80))
panel.delBtn = wx.Button(panel, wx.ID_ANY, 'Delete selected')
butSizer.Add(panel.delBtn,0,wx.ALIGN_CENTER_VERTICAL)
panel.delBtn.Bind(wx.EVT_BUTTON,OnConstDel)
panel.delBtn.checkboxList = []
butSizer.Add((-1,-1),1,wx.EXPAND,1)
butSizer.Add(G2G.HelpButton(panel,helpIndex='Constraints'))
Siz.Add(butSizer,0,wx.EXPAND)
if G2frame.testSeqRefineMode():
butSizer = wx.BoxSizer(wx.HORIZONTAL)
butSizer.Add(wx.StaticText(panel,wx.ID_ANY,' Sequential Ref. Settings. Wildcard use: '),0,WACV)
btn = G2G.EnumSelector(panel, data, '_seqmode',
['Set hist # to *', 'Ignore unless hist=*', 'Use as supplied'],
['auto-wildcard', 'wildcards-only', 'use-all'],
lambda x: wx.CallAfter(UpdateConstraints, G2frame, data, G2frame.constr.GetSelection(), True))
butSizer.Add(btn,0,wx.ALIGN_CENTER_VERTICAL)
butSizer.Add(G2G.HelpButton(panel,helpIndex='Constraints-SeqRef'))
butSizer.Add(wx.StaticText(panel,wx.ID_ANY,' Selected histogram: '),0,WACV)
btn = G2G.EnumSelector(panel, data, '_seqhist',
list(seqHistList),list(range(len(seqHistList))),
lambda x: wx.CallAfter(UpdateConstraints, G2frame, data, G2frame.constr.GetSelection(), True))
butSizer.Add(btn,0,wx.ALIGN_CENTER_VERTICAL)
Siz.Add(butSizer,0)
G2G.HorizontalLine(Siz,panel)
# 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,int(Size[0]/10-4),int(Size[1]/10-1))
panel.Show()
def OnPageChanged(event,selectTab=None):
'''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()
elif selectTab: #reload previous
page = selectTab
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 Clear:
G2frame.dataWindow.ClearData()
if not data: # usually created in CheckNotebook
data.update({'Hist':[],'HAP':[],'Phase':[],'Global':[],
'_seqmode':'auto-wildcard', '_seqhist':0}) #empty dict - fill it
if 'Global' not in data: #patch
data['Global'] = []
seqHistList = G2frame.testSeqRefineMode()
# patch: added ~version 5030 -- new mode for wild-card use in seq refs
# note that default for older sequential fits is 'wildcards-only' but in new GPX is 'auto-wildcard'
if seqHistList:
data['_seqmode'] = data.get('_seqmode','wildcards-only')
else:
data['_seqmode'] = data.get('_seqmode','auto-wildcard')
data['_seqhist'] = data.get('_seqhist',0)
# end patch
# DEBUG code #=====================================
#import GSASIIconstrGUI
#reload(GSASIIconstrGUI)
#reload(G2obj)
#reload(G2stIO)
#import GSASIIstrMain
#reload(GSASIIstrMain)
#reload(G2mv)
#reload(G2gd)
#===================================================
seqmode = 'use-all'
seqhistnum = None
if seqHistList: # Selections used with sequential refinements
seqmode = data.get('_seqmode','wildcards-only')
seqhistnum = min(data.get('_seqhist',0),len(seqHistList)-1)
Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
G2frame.dataWindow.ConstraintEdit.Enable(G2G.wxID_SHOWISO,True)
#removed this check as it prevents examination of ISODISTORT constraints without data
# 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
# for p in Phases:
# if 'ISODISTORT' in Phases[p] and 'G2VarList' in Phases[p]['ISODISTORT']:
# 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':[],'Spin':[]})
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,EFtable,ORBtables,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
if seqHistList: # for sequential refinement, only process selected histgram in list
histDict = {seqHistList[seqhistnum]:Histograms[seqHistList[seqhistnum]]}
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',)])
# derive list of variables
if seqHistList: # 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)
if seqmode == 'use-all':
hapList += wildList
else:
hapList = wildList
histVary,histDict,controlDict = G2stIO.GetHistogramData(histDict,Print=False)
histList = list(histDict.keys())
histList.sort()
if seqHistList: # 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)
if seqmode == 'use-all':
histList += wildList
else:
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,selectTab)
G2frame.constr.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged)
errmsg,warnmsg = WarnConstraintLimit() # check limits & constraints
if errmsg:
G2frame.ErrorDialog('Constraint Error',
'Error in constraints.\nCheck console output for more information'+
' or press "Show Errors" & "Show Warnings" buttons',
parent=G2frame)
if seqhistnum is None:
print ('\nError message(s):\n',errmsg)
else:
print ('\nError message(s) for histogram #{}:\n{}'.format(seqhistnum,errmsg))
if warnmsg: print ('\nAlso note these constraint warning(s):\n'+warnmsg)
#elif GSASIIpath.GetConfigValue('debug'):
# print ('Generated constraints\n',G2mv.VarRemapShow())
###### check scale & phase fractions, create constraint if needed #############
[docs]
def CheckAllScalePhaseFractions(G2frame,refine=True):
'''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
:returns: False if refinement should be continued
'''
histograms, phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
cId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Constraints')
Constraints = G2frame.GPXtree.GetItemPyData(cId)
problems = []
for h,hist in enumerate(histograms):
if CheckScalePhaseFractions(G2frame,hist,histograms,phases,Constraints):
problems.append((h,hist))
if len(problems) == 0: return
msg = 'You are refining the scale factor and all phase fractions for histogram(s) #'
for i,(h,hist) in enumerate(problems):
if i: msg += ', '
msg += str(h)
msg += '. This is not recommended as it will produce an unstable refinement. Do you want to create constrain(s) on the sum of phase fractions to address this?'
if refine:
msg += '\n\nRefinement may cause a significant shift in scaling, so it may be best to refine only a few other parameters (Press "No" to continue refinement without, "Cancel" to stop.)'
opts = wx.YES|wx.NO|wx.CANCEL
else:
opts = wx.YES|wx.NO
dlg = wx.MessageDialog(G2frame,msg,'Warning: Constraint Needed',opts)
ans = dlg.ShowModal()
dlg.Destroy()
if ans == wx.ID_YES:
for h,hist in problems:
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']),
str(histograms[hist]['hId']),
'Scale')
))]]
Constraints['HAP'].append(constr+[1.0,None,'c'])
wx.CallAfter(G2frame.GPXtree.SelectItem,cId) # should call SelectDataTreeItem
UpdateConstraints(G2frame,Constraints,1,True) # repaint with HAP tab
return False
elif ans == wx.ID_NO:
return False
return True
[docs]
def CheckScalePhaseFractions(G2frame,hist,histograms,phases,Constraints):
'''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(): # more work needed due to seqmode
return False
# histStr = '*'
else:
histStr = str(histograms[hist]['hId'])
# Is this powder?
if not hist.startswith('PWDR '): return False
# do this only if the scale factor is varied
if not histograms[hist]['Sample Parameters']['Scale'][1]: return False
# 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 False
else:
phaseCount += 1
# all phase fractions and scale factor varied, now scan for a constraint
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 False
return True
#### 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,
oldPhase['General']['SGData'],nSGData,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,
oldPhase['General']['SGData'],nSGData,True)
# 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()
elif text == 'Spinning rigid bodies':
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.SpinBodyMenu)
G2frame.Bind(wx.EVT_MENU, AddSpinRB, id=G2G.wxID_SPINBODYADD)
G2frame.Page = [page,'srb']
UpdateSpinRB()
else:
G2gd.SetDataMenuBar(G2frame)
#G2frame.Page = [page,'rrb']
def getMacroFile(macName):
defDir = os.path.join(GSASIIpath.path2GSAS2,'inputs','GSASIImacros')
if not os.path.exists(defDir): # patch 3/2024 for svn dir organization
defDir = os.path.join(GSASIIpath.path2GSAS2,'GSASIImacros')
if not os.path.exists(defDir):
print('Warning: GSASIImacros directory not found')
return []
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):
try:
ImportResidueRB()
except Exception as msg:
print('Error reading .xyz file\n Error msg:',msg)
if GSASIIpath.GetConfigValue('debug'):
import traceback
print (traceback.format_exc())
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,int(Size[0]/10-4),int(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,int(Size[0]/10-4),int(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 AddSpinRB(event):
rbid = ran.randint(0,sys.maxsize)
atType = 'C'
rbType = 'Q'
Natoms = 1
name = 'UNKRB'
namelist = [data['Spin'][key]['RBname'] for key in data['Spin']]
name = G2obj.MakeUniqueLabel(name,namelist)
atColor = G2elem.GetAtomInfo(atType)['Color']
data['Spin'][rbid] = {'RBname':name,'Natoms':Natoms,'atType':atType,'rbType':rbType,'atColor':atColor,
'useCount':0,'nSH':0,'SHC':[{},],'Radius':[1.0,False],'Matrix':np.eye(3),'rbPos':np.zeros(3)}
data['RBIds']['Spin'].append(rbid)
UpdateSpinRB()
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)
nameSizer.Add((-1,-1),1,wx.EXPAND,1)
nameSizer.Add(G2G.HelpButton(VectorRBDisplay,helpIndex=G2frame.dataWindow.helpKey))
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]),
style=wx.TE_PROCESS_ENTER)
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,wx.EXPAND)
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,int(Size[0]/10-4),int(Size[1]/10-1))
G2frame.dataWindow.SendSizeEvent()
VectorRBDisplay.Show()
def UpdateSpinRB():
def OnTypeSel(event):
Obj = event.GetEventObject()
ObjId = event.GetId()
data['Spin'][Indx[ObjId]]['rbType'] = Obj.GetValue()
def OnAtSel(event):
Obj = event.GetEventObject()
ObjId = event.GetId()
PE = G2elemGUI.PickElement(G2frame,oneOnly=False)
if PE.ShowModal() == wx.ID_OK:
if PE.Elem != 'None':
El = PE.Elem.strip().lower().capitalize()
data['Spin'][Indx[ObjId]]['atType'] = El
data['Spin'][Indx[ObjId]]['Color'] = G2elem.GetAtomInfo(El)['Color']
Obj.ChangeValue(El)
if 'Q' in El:
wx.CallAfter(UpdateSpinRB)
def OnElSel(event):
Obj = event.GetEventObject()
ObjId = event.GetId()
PE = G2elemGUI.PickElement(G2frame,oneOnly=False,ifOrbs=True)
if PE.ShowModal() == wx.ID_OK:
if PE.Elem != 'None':
El = PE.Elem.strip().lower().capitalize()
data['Spin'][Indx[ObjId]]['elType'] = El
Obj.ChangeValue(El)
def OnSymSel(event):
ObjId = event.GetId()
data['Spin'][Indx[ObjId]]['RBsym'] = simsel.GetValue()
#patch
if 'Spin' not in data:
data['Spin'] = {}
data['RBIds'].update({'Spin':[]})
# end patch
if not len(data['Spin']):
return
GS = SpinRBDisplay.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)
SetStatusLine(' ')
if GS:
SpinRBSizer = GS
else:
SpinRBSizer = wx.BoxSizer(wx.VERTICAL)
Indx = {}
SpinRBSizer.Add(wx.StaticText(SpinRBDisplay,label=' Spinning rigid body shells/nonspherical atoms (Atom=Q & select Orbitals):'))
nQ = 0
for spinID in data['Spin']:
if 'Q' in data['Spin'][spinID]['atType']:
nQ += 1
if nQ:
bodSizer = wx.FlexGridSizer(0,6,5,5)
else:
bodSizer = wx.FlexGridSizer(0,5,5,5)
for item in ['Name','Type','RB sym','Atom','Number']:
bodSizer.Add(wx.StaticText(SpinRBDisplay,label=item))
for ibod,spinID in enumerate(data['Spin']):
if nQ:
bodSizer.Add(wx.StaticText(SpinRBDisplay,label='Orbitals from'))
bodSizer.Add(G2G.ValidatedTxtCtrl(SpinRBDisplay,data['Spin'][spinID],'RBname'))
bodSizer.Add(wx.StaticText(SpinRBDisplay,label='Q'),0)
data['Spin'][spinID]['rbType'] = 'Q' #patch
symchoice = ['53m','m3m','-43m','6/mmm','-6m2','-3m','3m','32','4/mmm','-42m','mmm','2/m','-1','1']
data['Spin'][spinID]['RBsym'] = data['Spin'][spinID].get('RBsym','53m')
simsel = wx.ComboBox(SpinRBDisplay,choices=symchoice,value=data['Spin'][spinID]['RBsym'],
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[simsel.GetId()] = spinID
simsel.Bind(wx.EVT_COMBOBOX,OnSymSel)
bodSizer.Add(simsel)
atSel = wx.TextCtrl(SpinRBDisplay,value=data['Spin'][spinID]['atType'],style=wx.TE_PROCESS_ENTER)
atSel.Bind(wx.EVT_TEXT_ENTER,OnAtSel)
Indx[atSel.GetId()] = spinID
bodSizer.Add(atSel,0)
bodSizer.Add(G2G.ValidatedTxtCtrl(SpinRBDisplay,data['Spin'][spinID],'Natoms'))
if 'Q' in data['Spin'][spinID]['atType']:
data['Spin'][spinID]['elType'] = data['Spin'][spinID].get('elType','C')
elSel = wx.TextCtrl(SpinRBDisplay,value=data['Spin'][spinID]['elType'],style=wx.TE_PROCESS_ENTER)
elSel.Bind(wx.EVT_TEXT_ENTER,OnElSel)
Indx[elSel.GetId()] = spinID
bodSizer.Add(elSel,0)
elif nQ:
bodSizer.Add((5,5))
SpinRBSizer.Add(bodSizer)
SpinRBSizer.Add((5,25),)
SpinRBSizer.Layout()
SpinRBDisplay.SetSizer(SpinRBSizer,True)
SpinRBDisplay.SetAutoLayout(True)
Size = SpinRBSizer.GetMinSize()
SpinRBDisplay.SetSize(Size)
Size[0] += 40
Size[1] = max(Size[1],450) + 20
SpinRB.SetSize(Size)
SpinRB.SetScrollbars(10,10,int(Size[0]/10-4),int(Size[1]/10-1))
G2frame.dataWindow.SendSizeEvent()
SpinRBDisplay.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)
nameSizer.Add((-1,-1),1,wx.EXPAND,1)
nameSizer.Add(G2G.HelpButton(ResidueRBDisplay,helpIndex=G2frame.dataWindow.helpKey))
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 OnHDswitch(event):
Obj = event.GetEventObject()
res = Indx[Obj.GetId()]
resTable = res.GetTable()
AtInfo = data['Residue']['AtInfo']
for r in range(res.GetNumberRows()):
row = resTable.GetRowValues(r)
if row[1] == 'H':
row[0] = 'D'+row[0][1:]
row[1] = 'D'
elif row[1] == 'D':
row[0] = 'H'+row[0][1:]
row[1] = 'H'
rbData['atNames'][r] = row[0]
rbData['rbTypes'][r] = row[1]
Info = G2elem.GetAtomInfo(row[1])
AtInfo[row[1]] = [Info['Drad'],Info['Color']]
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']
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)
refAtmSizer2 = None
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)
refAtmSizer.Add((50,-1)) # moves the help button out a bit
RefObjs.append(refObj)
refAtmSizer2 = wx.BoxSizer(wx.HORIZONTAL)
cycleXYZ = wx.Button(ResidueRBDisplay,label=' Cycle XYZ?')
cycleXYZ.Bind(wx.EVT_BUTTON,OnCycleXYZ)
Indx[cycleXYZ.GetId()] = resGrid
refAtmSizer2.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
refAtmSizer2.Add(molcent,0,WACV)
HDbut = wx.Button(ResidueRBDisplay,label='H <-> D?')
HDbut.Bind(wx.EVT_BUTTON,OnHDswitch)
Indx[HDbut.GetId()] = resGrid
refAtmSizer2.Add(HDbut,0,WACV)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(refAtmSizer,0,wx.EXPAND)
if refAtmSizer2: mainSizer.Add(refAtmSizer2)
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 = G2G.G2Slider(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,wx.EXPAND)
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,int(Size[0]/10-4),int(Size[1]/10-1)) # dataframe already scrolls
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
SpinRB = wx.ScrolledWindow(G2frame.rbBook)
SpinRBDisplay = wx.Panel(SpinRB)
G2frame.rbBook.AddPage(SpinRB,'Spinning rigid bodies')
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)
Phases = G2frame.GetPhaseData()
isophases = [p for p in Phases if 'G2VarList' in Phases[p]['ISODISTORT']]
if not isophases:
G2G.G2MessageBox(G2frame,'no ISODISTORT mode data for any phase')
return
if phase and phase not in isophases:
G2G.G2MessageBox(G2frame,'no ISODISTORT mode data for this phase')
return
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
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)
constrDict = {}
for c in Constraints['Phase']:
if c[-1] != 'f' or not c[-3]: continue
constrDict[str(c[-3])] = c
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)
data = Phases[phase]
ISO = data['ISODISTORT']
mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY,
'ISODISTORT mode computation for coordinates 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=3,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=4,hgap=5,vgap=2)
subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,'ISODISTORT\nname'))
subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,'GSAS-II\nname'))
subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT)
for i in range(3): subSizer1.Add((-1,5)) # spacer
subSizer2.Add((-1,-1))
subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,'ISODISTORT\nMode name'))
subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,'GSAS-II\nname'))
subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,' value'),0,wx.ALIGN_RIGHT)
for i in range(4): subSizer2.Add((-1,5))
# ISODISTORT displacive modes
if 'G2VarList' in ISO:
dispVals,dispSUs,modeVals,modeSUs = G2mth.CalcIsoDisp(Phases[phase],covdata=covdata)
for (lbl,xyz,xyzsig,G2var,
var,mval,msig,G2mode) in zip(
ISO['IsoVarList'],dispVals,dispSUs,ISO['G2VarList'],
ISO['IsoModeList'],modeVals,modeSUs,ISO['G2ModeList'] ):
if str(G2mode) in constrDict:
ch = G2G.HelpButton(panel2,fmtHelp(constrDict[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,label=str(lbl)))
subSizer1.Add(wx.StaticText(panel1,label=str(G2var)))
try:
value = G2mth.ValEsd(xyz,xyzsig)
except TypeError:
value = str(xyz)
subSizer1.Add(wx.StaticText(panel1,label=value),0,wx.ALIGN_RIGHT)
subSizer2.Add(wx.StaticText(panel2,label=str(var)))
subSizer2.Add(wx.StaticText(panel2,label=str(G2mode)))
try:
# value = G2mth.ValEsd(mval,msig)
value = '%.5f'%(mval/2.) #why /2.0
except TypeError:
value = str(mval)
subSizer2.Add(wx.StaticText(panel2,label=value),0,wx.ALIGN_RIGHT)
# ISODISTORT occupancy modes
if 'G2OccVarList' in ISO:
deltaList = []
parmDict,varyList = G2frame.MakeLSParmDict()
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 constrDict:
ch = G2G.HelpButton(panel2,fmtHelp(constrDict[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 = G2fl.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 = G2fl.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.CenterOnParent()
dlg.ShowModal()
dlg.Destroy()
[docs]
def ShowIsoModes(G2frame,phase):
'''Show details about the ISODISTORT mode and the displacements they
translate to.
'''
def _onClose(event):
dlg.EndModal(wx.ID_CANCEL)
# make a lookup table for named NewVar Phase constraints
sub = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Constraints')
Constraints = G2frame.GPXtree.GetItemPyData(sub)
constrDict = {}
for c in Constraints['Phase']:
if c[-1] != 'f' or not c[-3]: continue
constrDict[str(c[-3])] = c
Phases = G2frame.GetPhaseData()
data = Phases[phase]
ISO = data['ISODISTORT']
if 'IsoVarList' in ISO:
modeExp = {}
for i,row in enumerate(ISO['Var2ModeMatrix']):
line = '('
l = 1
for j,k in enumerate(row):
var = ISO['IsoVarList'][j]
if np.isclose(k,0): continue
if l > 30:
line += '\n'
l = 0
l += 3
if k < 0 and j > 0:
line += ' - '
k = -k
elif j > 0:
line += ' + '
if np.isclose(k,1):
l1 = '%s ' % str(var)
else:
l1 = '%.3f * %s' % (k,str(var))
line += l1
l += len(l1)
line += ') / {:.3g}'.format(ISO['NormList'][i])
modeExp[str(ISO['G2ModeList'][i])] = line
crdExp = {}
for i,(lbl,row) in enumerate(zip(ISO['IsoVarList'],ISO['Mode2VarMatrix'])):
l = ''
for j,(k,n) in enumerate(zip(row,ISO['NormList'])):
if np.isclose(k,0): continue
l1 = ''
if j > 0 and k < 0:
k = -k
l1 = '-'
elif j > 0:
l1 += ' +'
if np.isclose(k,1):
l += '{:} {:4g} * {:}'.format(l1, n, ISO['G2ModeList'][j])
else:
l += '{:} {:3g} * {:4g} * {:}'.format(l1, k, n, ISO['G2ModeList'][j])
crdExp[lbl] = l
dlg = wx.Dialog(G2frame,wx.ID_ANY,'ISODISTORT modes and displacements',#size=(630,400),
style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(wx.StaticText(dlg,wx.ID_ANY,
'ISODISTORT modes and displacements in phase '+str(data['General'].get('Name','?'))))
# ISODISTORT displacive modes
if 'G2VarList' in ISO:
panel1 = wxscroll.ScrolledPanel(dlg, style = wx.TAB_TRAVERSAL|wx.SUNKEN_BORDER)
subSizer1 = wx.FlexGridSizer(cols=5,hgap=5,vgap=2)
panel2 = wxscroll.ScrolledPanel(dlg, style = wx.TAB_TRAVERSAL|wx.SUNKEN_BORDER)
subSizer2 = wx.FlexGridSizer(cols=6,hgap=5,vgap=2)
subSizer1.Add(wx.StaticText(panel1,label='ISODISTORT\nvariable'),0,wx.ALIGN_CENTER)
subSizer1.Add((8,-1)) # spacer
subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,'GSAS-II\nequiv.'),0,wx.ALIGN_CENTER)
subSizer1.Add((8,-1)) # spacer
subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,'expression'),0,wx.ALIGN_CENTER)
subSizer2.Add((-1,-1))
subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,'ISODISTORT\nMode name'),0,wx.ALIGN_CENTER)
subSizer2.Add((8,-1)) # spacer
subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,'GSAS-II\nequiv.'),0,wx.ALIGN_CENTER)
subSizer2.Add((8,-1)) # spacer
subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,'expression'),0,wx.ALIGN_CENTER)
for i in range(6): subSizer2.Add((-1,5))
for i,lbl in enumerate(ISO['IsoVarList']):
var = str(ISO['G2VarList'][i]).replace('::dA','::A')
if np.isclose(ISO['G2coordOffset'][i],0):
G2var = '{:}'.format(var)
elif ISO['G2coordOffset'][i] < 0:
G2var = '({:} + {:.3g})'.format(var,-ISO['G2coordOffset'][i])
else:
G2var = '({:} - {:.3g})'.format(var,ISO['G2coordOffset'][i])
subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(lbl)),0,WACV)
subSizer1.Add((-1,-1)) # spacer
subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,str(G2var)),0,WACV)
subSizer1.Add((-1,-1)) # spacer
subSizer1.Add(wx.StaticText(panel1,wx.ID_ANY,crdExp[lbl]),0,WACV)
for (isomode,G2mode) in zip(ISO['IsoModeList'],ISO['G2ModeList']):
if str(G2mode) in constrDict:
ch = G2G.HelpButton(panel2,fmtHelp(constrDict[str(G2mode)],isomode))
subSizer2.Add(ch,0,wx.LEFT|wx.RIGHT|WACV|wx.ALIGN_CENTER,1)
else:
subSizer2.Add((-1,-1))
subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(isomode)))
subSizer2.Add((-1,-1)) # spacer
subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,str(G2mode)))
subSizer2.Add((-1,-1)) # spacer
subSizer2.Add(wx.StaticText(panel2,wx.ID_ANY,modeExp[str(G2mode)]))
# 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
w1,l1 = subSizer1.GetSize()
w2,l2 = subSizer2.GetSize()
panel1.SetMinSize((min(700,w1+20),max(50,l1)))
panel2.SetMinSize((min(700,w2+20),max(50,l2)))
mainSizer.Add(panel1,1, wx.ALL|wx.EXPAND,1)
mainSizer.Add(panel2,1, 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)
dlg.SetSizer(mainSizer)
mainSizer.Fit(dlg)
dlg.SetMinSize(dlg.GetSize())
dlg.CenterOnParent()
dlg.ShowModal()
dlg.Destroy()
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