# -*- coding: utf-8 -*-
#GSASIIpwdGUI - powder data display routines
'''GUI routines for PWDR datadree subitems follow.
'''
from __future__ import division, print_function
import platform
import sys
import os.path
# Don't depend on graphics for scriptable
try:
import wx
import wx.grid as wg
except ImportError:
pass
import numpy as np
import numpy.linalg as nl
import numpy.ma as ma
import math
import copy
import random as ran
import pickle
import scipy.interpolate as si
from fractions import Fraction
from . import GSASIIpath
from . import GSASIImath as G2mth
from . import GSASIIpwd as G2pwd
from . import GSASIIfiles as G2fil
from . import GSASIIobj as G2obj
from . import GSASIIlattice as G2lat
from . import GSASIIspc as G2spc
from . import GSASIIindex as G2indx
from . import GSASIIplot as G2plt
from . import GSASIIpwdplot as G2pwpl
from . import GSASIIdataGUI as G2gd
from . import GSASIIphsGUI as G2phsG
from . import GSASIIctrlGUI as G2G
from . import GSASIIElemGUI as G2elemGUI
from . import GSASIIElem as G2elem
from . import GSASIIsasd as G2sasd
from . import G2shapes
from . import SUBGROUPS as kSUB
from GSASII.imports.G2phase_CIF import CIFPhaseReader as CIFpr
from . import GSASIIscriptable as G2sc
from . import GSASIImiscGUI as G2IO
try:
from sympy import symbols, nsimplify, Rational as SRational
except ImportError:
G2fil.NeededPackage({'ISODISTORT k-vector search':['sympy']})
symbols = None
try:
VERY_LIGHT_GREY = wx.SystemSettings.GetColour(wx.SYS_COLOUR_BTNFACE)
WACV = wx.ALIGN_CENTER_VERTICAL
except:
pass
if '2' not in platform.python_version_tuple()[0]:
unichr = chr
GkDelta = unichr(0x0394)
GkSigma = unichr(0x03a3)
GkTheta = unichr(0x03f4)
Gklambda = unichr(0x03bb)
Pwr10 = unichr(0x0b9)+unichr(0x2070)
Pwr20 = unichr(0x0b2)+unichr(0x2070)
Pwrm1 = unichr(0x207b)+unichr(0x0b9)
Pwrm2 = unichr(0x207b)+unichr(0x0b2)
Pwrm6 = unichr(0x207b)+unichr(0x2076)
Pwrm4 = unichr(0x207b)+unichr(0x2074)
Angstr = unichr(0x00c5)
superMinusOne = unichr(0xaf)+unichr(0xb9)
notEq0 = unichr(0x2260)+'0'
# trig functions in degrees
sind = lambda x: math.sin(x*math.pi/180.)
tand = lambda x: math.tan(x*math.pi/180.)
cosd = lambda x: math.cos(x*math.pi/180.)
asind = lambda x: 180.*math.asin(x)/math.pi
npsind = lambda x: np.sin(x*np.pi/180.)
npasind = lambda x: 180.*np.arcsin(x)/math.pi
npcosd = lambda x: np.cos(x*math.pi/180.)
cellDisplayOpts = {'showExtinct':False}
cellGUIlist = [
[[0,1,2],4,([" a = "," Vol = "],[(10,5),"%.3f"],[True,False],[0,0])],
[[3,4,5,6],6,([" a = "," c = "," Vol = "],[(10,5),(10,5),"%.3f"],[True,True,False],[0,2,0])],
[[7,8,9,10,11,12],8,([" a = "," b = "," c = "," Vol = "],[(10,5),(10,5),(10,5),"%.3f"],
[True,True,True,False],[0,1,2,0])],
[[13,14,15,16],10,([" a = "," b = "," c = ",'\u03B2 = '," Vol = "],
[(10,5),(10,5),(10,5),(10,3),"%.3f"],[True,True,True,True,False],[0,1,2,4,0])],
[[17,18],8,([" a = "," b = "," c = ",'\u03B1 = ','\u03B2 = ','\u03B3 = '," Vol = "],
[(10,5),(10,5),(10,5),(10,3),(10,3),(10,3),"%.3f"],
[True,True,True,True,True,True,False],[0,1,2,3,4,5,0])]]
bravaisSymb = ['Fm3m','Im3m','Pm3m','R3-H','P6/mmm','I4/mmm','P4/mmm',
'Fmmm','Immm','Ammm','Bmmm','Cmmm','Pmmm','I2/m','A2/m','C2/m',
'P2/m','P1','C1']
[docs]
def SetLattice(controls):
'''impose constraints on lattice constaints and determine the
Bravias lattice index (ibrav) as used in cellGUIlist
'''
ibrav = bravaisSymb.index(controls[5])
if controls[5] in ['Fm3m','Im3m','Pm3m']:
controls[7] = controls[8] = controls[6]
controls[9] = controls[10] = controls[11] = 90.
elif controls[5] in ['R3m','P6/mmm','I4/mmm','P4/mmm']:
controls[7] = controls[6]
controls[9] = controls[10] = controls[11] = 90.
if controls[5] in ['R3-H','P6/mmm']:
controls[11] = 120.
elif controls[5] in ['Fmmm','Immm','Ammm','Bmmm','Cmmm','Pmmm']:
controls[9] = controls[10] = controls[11] = 90.
elif controls[5] in ['A2/m','C2/m','P2/m','I2/m']:
controls[9] = controls[11] = 90. # b unique
controls[12] = G2lat.calc_V(G2lat.cell2A(controls[6:12]))
return ibrav
################################################################################
###### class definitions
################################################################################
[docs]
class SubCellsDialog(wx.Dialog):
'Display magnetic subcell space group information from selection in Unit Cells table of results from k-SUBGROUPSMAG'
def __init__(self,parent,title,controls,SGData,items,phaseDict,ifPick=False):
wx.Dialog.__init__(self,parent,-1,title,
pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
self.panel = None
self.controls = controls
self.SGData = SGData #for parent phase
self.items = items
self.phaseDict = phaseDict
self.Pick = 0
self.ifPick = ifPick
self.Draw()
def Draw(self):
def RefreshGrid(event):
r,c = event.GetRow(),event.GetCol()
br = self.items[r]
phase = self.phaseDict[br]
rLab = magDisplay.GetRowLabelValue(r)
pname = '(%s) %s'%(rLab,phase['Name'])
if c == 0:
mSGData = phase['SGData']
text,table = G2spc.SGPrint(mSGData,AddInv=True)
if 'magAtms' in phase:
msg = 'Magnetic space group information'
text[0] = ' Magnetic Space Group: '+mSGData['MagSpGrp']
text[3] = ' The magnetic lattice point group is '+mSGData['MagPtGp']
OprNames,SpnFlp = G2spc.GenMagOps(mSGData)
G2G.SGMagSpinBox(self.panel,msg,text,table,mSGData['SGCen'],OprNames,
mSGData['SpnFlp'],False).Show()
else:
msg = 'Space Group Information'
G2G.SGMessageBox(self.panel,msg,text,table).Show()
elif c == 1:
self.Pick = r
self.Draw()
elif c == 2:
maxequiv = phase['maxequiv']
mSGData = phase['SGData']
Uvec = phase['Uvec']
Trans = phase['Trans']
ifMag = False
if 'magAtms' in phase:
ifMag = True
allmom = phase.get('allmom',False)
magAtms = phase.get('magAtms','')
mAtoms = TestMagAtoms(phase,magAtms,self.SGData,Uvec,Trans,allmom,maxequiv)
else:
mAtoms = TestAtoms(phase,self.controls[15],self.SGData,Uvec,Trans,maxequiv)
Atms = []
AtCods = []
atMxyz = []
for ia,atom in enumerate(mAtoms):
atom[0] += '_%d'%ia
SytSym,Mul,Nop,dupDir = G2spc.SytSym(atom[2:5],mSGData)
Atms.append(atom[:2]+['',]+atom[2:5])
AtCods.append('1')
if 'magAtms' in phase:
MagSytSym = G2spc.MagSytSym(SytSym,dupDir,mSGData)
CSI = G2spc.GetCSpqinel(mSGData['SpnFlp'],dupDir)
atMxyz.append([MagSytSym,CSI[0]])
else:
CSI = G2spc.GetCSxinel(SytSym)
atMxyz.append([SytSym,CSI[0]])
G2phsG.UseMagAtomDialog(self.panel,pname,Atms,AtCods,atMxyz,ifMag=ifMag,ifOK=True).ShowModal()
elif c in [3,4]:
if c == 3:
title = 'Conjugacy list for '+pname
items = phase['altList']
elif c == 4:
title = 'Super groups list list for '+pname
items = phase['supList']
if not items[0]:
wx.MessageBox(pname+' is a maximal subgroup',caption='Super group is parent',style=wx.ICON_INFORMATION)
return
SubCellsDialog(self.panel,title,self.controls,self.SGData,items,self.phaseDict).Show()
if self.panel: self.panel.Destroy()
self.panel = wx.Panel(self)
rowLabels = [str(i+1) for i in range(len(self.items))]
if self.ifPick:
colLabels = ['Space Gp','Pick','Uniq','nConj','nSup','Trans','Vec','a','b','c','\u03B1','\u03B2','\u03B3','Volume']
Types = [wg.GRID_VALUE_STRING,]+[wg.GRID_VALUE_BOOL,]+3*[wg.GRID_VALUE_LONG,]+2*[wg.GRID_VALUE_STRING,]+ \
3*[wg.GRID_VALUE_FLOAT+':10,5',]+3*[wg.GRID_VALUE_FLOAT+':10,3',]+[wg.GRID_VALUE_FLOAT+':10,2']
else:
colLabels = ['Space Gp','Uniq','nConj','nSup','Trans','Vec','a','b','c','\u03B1','\u03B2','\u03B3','Volume']
Types = [wg.GRID_VALUE_STRING,]+3*[wg.GRID_VALUE_LONG,]+2*[wg.GRID_VALUE_STRING,]+ \
3*[wg.GRID_VALUE_FLOAT+':10,5',]+3*[wg.GRID_VALUE_FLOAT+':10,3',]+[wg.GRID_VALUE_FLOAT+':10,2']
table = []
for kp,ip in enumerate(self.items):
phase = self.phaseDict[ip]
natms = phase.get('nAtoms',1)
pick = False
if kp == self.Pick:
pick = True
try:
nConj = len(phase['altList'])
nSup = len(phase['supList'])
except KeyError:
nConj = 0
nSup = 0
cell = list(phase['Cell'])
trans = G2spc.Trans2Text(phase['Trans'])
vec = G2spc.Latt2text([phase['Uvec'],])
if self.ifPick:
row = [phase['Name'],pick,natms,nConj,nSup,trans,vec]+cell
else:
row = [phase['Name'],natms,nConj,nSup,trans,vec]+cell
table.append(row)
CellsTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
mainSizer = wx.BoxSizer(wx.VERTICAL)
magDisplay = G2G.GSGrid(self.panel)
magDisplay.SetTable(CellsTable, True)
magDisplay.Bind(wg.EVT_GRID_CELL_LEFT_CLICK,RefreshGrid)
magDisplay.AutoSizeColumns(False)
mainSizer.Add(magDisplay,0)
OkBtn = wx.Button(self.panel,-1,"Ok")
OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
btnSizer = wx.BoxSizer(wx.HORIZONTAL)
btnSizer.Add((20,20),1)
btnSizer.Add(OkBtn)
btnSizer.Add((20,20),1)
mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10)
self.panel.SetSizer(mainSizer)
self.panel.Fit()
self.Fit()
def GetSelection(self):
return self.Pick
def OnOk(self,event):
parent = self.GetParent()
parent.Raise()
self.EndModal(wx.ID_OK)
[docs]
class RDFDialog(wx.Dialog):
'Display controls for generating RDF plot in Background'
def __init__(self,parent):
wx.Dialog.__init__(self,parent,-1,'Background radial distribution function',
pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
self.panel = None
self.result = {'UseObsCalc':'obs-calc','maxR':20.0,'Smooth':'linear'}
self.Draw()
def Draw(self):
def OnUseOC(event):
self.result['UseObsCalc'] = useOC.GetValue()
def OnSmCombo(event):
self.result['Smooth'] = smCombo.GetValue()
if self.panel: self.panel.Destroy()
self.panel = wx.Panel(self)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(wx.StaticText(self.panel,label='Background RDF controls:'),0)
plotType = wx.BoxSizer(wx.HORIZONTAL)
plotType.Add(wx.StaticText(self.panel,label=' Select plot type:'),0,WACV)
Choices = ['obs-back','calc-back','obs-calc','auto-back']
useOC = wx.ComboBox(self.panel,value=Choices[2],choices=Choices,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
useOC.SetValue(self.result['UseObsCalc'])
useOC.Bind(wx.EVT_COMBOBOX,OnUseOC)
plotType.Add(useOC,0,WACV)
mainSizer.Add(plotType,0)
dataSizer = wx.BoxSizer(wx.HORIZONTAL)
dataSizer.Add(wx.StaticText(self.panel,label=' Smoothing type: '),0,WACV)
smChoice = ['linear','nearest',]
smCombo = wx.ComboBox(self.panel,value=self.result['Smooth'],choices=smChoice,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
smCombo.Bind(wx.EVT_COMBOBOX, OnSmCombo)
dataSizer.Add(smCombo,0,WACV)
dataSizer.Add(wx.StaticText(self.panel,label=' Maximum radial dist.: '),0,WACV)
maxR = G2G.ValidatedTxtCtrl(self.panel,self.result,'maxR',nDig=(10,1),xmin=10.,xmax=50.,
typeHint=float)
dataSizer.Add(maxR,0,WACV)
mainSizer.Add(dataSizer,0)
OkBtn = wx.Button(self.panel,-1,"Ok")
OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
cancelBtn = wx.Button(self.panel,-1,"Cancel")
cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
btnSizer = wx.BoxSizer(wx.HORIZONTAL)
btnSizer.Add((20,20),1)
btnSizer.Add(OkBtn)
btnSizer.Add((20,20),1)
btnSizer.Add(cancelBtn)
btnSizer.Add((20,20),1)
mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10)
self.panel.SetSizer(mainSizer)
self.panel.Fit()
self.Fit()
def GetSelection(self):
return self.result
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)
################################################################################
##### Setup routines
################################################################################
[docs]
def GetFileBackground(G2frame,xye,background,scale=True):
''' Select a background file to subtract from PWDR pattern
param: xye list [npts,6] of PWDR pattern
param: background PWDR file to be used as background
param: scale bool:=True if scale mult included in background & apply it
returns: list background to subtract
'''
bxye = np.zeros(len(xye[1]))
mult = 1.0
if 'background PWDR' in background[1]:
backfile,mult = background[1]['background PWDR'][:2]
if backfile:
bId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,backfile)
if bId:
bxye = G2frame.GPXtree.GetItemPyData(bId)[1][1]
else:
print('Error: background PWDR {} not found'.format(backfile))
background[1]['background PWDR'] = ['',1.0,False]
if scale:
return bxye*mult
else:
return bxye
[docs]
def IsHistogramInAnyPhase(G2frame,histoName):
'''Tests a Histogram to see if it is linked to any phases.
Returns the name of the first phase where the histogram is used.
'''
phases = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases')
if phases:
item, cookie = G2frame.GPXtree.GetFirstChild(phases)
while item:
data = G2frame.GPXtree.GetItemPyData(item)
histoList = data['Histograms'].keys()
if histoName in histoList:
return G2frame.GPXtree.GetItemText(item)
item, cookie = G2frame.GPXtree.GetNextChild(phases, cookie)
return False
else:
return False
[docs]
def GetPhasesforHistogram(G2frame,histoName):
'''Returns phases (if any) associated with provided Histogram
Returns a list of phase dicts
'''
phList = []
Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
for ph in Phases:
if histoName in Phases[ph]['Histograms']:
phList.append(Phases[ph])
return phList
[docs]
def SetupSampleLabels(histName,dataType,histType):
'''Setup a list of labels and number formatting for use in
labeling sample parameters.
:param str histName: Name of histogram, ("PWDR ...")
:param str dataType:
'''
parms = []
parms.append(['Scale','Histogram scale factor: ',[10,7]])
if histType[2] in ['A','B','C']:
parms.append(['Gonio. radius','Goniometer radius (mm): ',[10,3]])
if 'PWDR' in histName:
if dataType == 'Debye-Scherrer':
if 'T' in histType:
parms += [['Absorption','Sample absorption (\xb5r/'+Gklambda+'): ',[10,4]],]
else:
parms += [['DisplaceX','Sample X displ. perp. to beam (\xb5m): ',[10,3]],
['DisplaceY','Sample Y displ. || to beam (\xb5m): ',[10,3]],
['Absorption','Sample absorption (\xb5\xb7r): ',[10,4]],]
elif dataType == 'Bragg-Brentano':
parms += [['Shift','Sample displacement(\xb5m): ',[10,4]],
['Transparency','Sample transparency(1/\xb5eff, cm): ',[10,3]],
['SurfRoughA','Surface roughness A: ',[10,4]],
['SurfRoughB','Surface roughness B: ',[10,4]]]
elif 'SASD' in histName:
parms.append(['Thick','Sample thickness (mm)',[10,3]])
parms.append(['Trans','Transmission (meas)',[10,3]])
parms.append(['SlitLen','Slit length (Q,\xc5'+Pwrm1+')',[10,3]])
parms.append(['Omega','Goniometer omega:',[10,3]])
parms.append(['Chi','Goniometer chi:',[10,3]])
parms.append(['Phi','Goniometer phi:',[10,3]])
parms.append(['Azimuth','Detector azimuth:',[10,3]])
parms.append(['Time','Clock time (s):',[12,3]])
parms.append(['Temperature','Sample temperature (K): ',[10,3]])
parms.append(['Pressure','Sample pressure (MPa): ',[10,3]])
return parms
[docs]
def GetFileList(G2frame,fileType):
''' Get list of file names containing a particular string
param: fileType str: any string within a file name
returns: list of file names from GSAS-II tree
Note routine of same name in GSASIIdataGUI; it has a skip option
'''
fileList = []
Id, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
while Id:
name = G2frame.GPXtree.GetItemText(Id)
if fileType in name.split()[0]:
fileList.append(name)
Id, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
return fileList
[docs]
def GetHistsLikeSelected(G2frame):
'''Get the histograms that match the current selected one:
The histogram prefix and data type (PXC etc.), the number of
wavelengths and the instrument geometry (Debye-Scherrer etc.)
must all match. The current histogram is not included in the list.
:param wx.Frame G2frame: pointer to main GSAS-II data tree
'''
histList = []
inst,inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))
hType = inst['Type'][0]
if 'Lam1' in inst:
hLam = 2
elif 'Lam' in inst:
hLam = 1
else:
hLam = 0
# sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId,'Sample Parameters'))
# hGeom = sample.get('Type')
hstName = G2frame.GPXtree.GetItemText(G2frame.PatternId)
hPrefix = hstName.split()[0]+' '
# cycle through tree looking for items that match the above
item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
while item:
name = G2frame.GPXtree.GetItemText(item)
if name.startswith(hPrefix) and name != hstName:
cType,cLam, = '?',-1
subitem, subcookie = G2frame.GPXtree.GetFirstChild(item)
while subitem:
subname = G2frame.GPXtree.GetItemText(subitem)
if subname == 'Sample Parameters':
# sample = G2frame.GPXtree.GetItemPyData(subitem)
# cGeom = sample.get('Type')
pass
elif subname == 'Instrument Parameters':
inst,inst2 = G2frame.GPXtree.GetItemPyData(subitem)
cType = inst['Type'][0]
if 'Lam1' in inst:
cLam = 2
elif 'Lam' in inst:
cLam = 1
else:
cLam = 0
subitem, subcookie = G2frame.GPXtree.GetNextChild(item, subcookie)
if cLam == hLam and cType == hType: # and cGeom == hGeom:
if name not in histList: histList.append(name)
item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
return histList
[docs]
def SetCopyNames(histName,dataType,addNames=[]):
'''Determine the items in the sample parameters that should be copied,
depending on the histogram type and the instrument type.
'''
copyNames = ['Scale',]
histType = 'HKLF'
if 'PWDR' in histName:
histType = 'PWDR'
if 'Debye' in dataType:
copyNames += ['DisplaceX','DisplaceY','Absorption']
else: #Bragg-Brentano
copyNames += ['Shift','Transparency','SurfRoughA','SurfRoughB']
elif 'SASD' in histName:
histType = 'SASD'
copyNames += ['Materials','Thick',]
if len(addNames):
copyNames += addNames
return histType,copyNames
[docs]
def CopyPlotCtrls(G2frame):
'''Global copy: Copy plot controls from current histogram to others.
'''
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No other histograms match '+hst,G2frame)
return
sourceData = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)
if 'Offset' not in sourceData[0]: #patch for old data
sourceData[0].update({'Offset':[0.0,0.0],'delOffset':0.02,'refOffset':-1.0,
'refDelt':0.01,})
G2frame.GPXtree.SetItemPyData(G2frame.PatternId,sourceData)
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy plot controls from\n'+str(hst[5:])+' to...',
'Copy plot controls', histList)
results = []
try:
if dlg.ShowModal() == wx.ID_OK:
results = dlg.GetSelections()
finally:
dlg.Destroy()
copyList = []
for i in results:
copyList.append(histList[i])
keys = ['Offset','delOffset','refOffset','refDelt']
source = dict(zip(keys,[sourceData[0][item] for item in keys]))
for hist in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,hist)
data = G2frame.GPXtree.GetItemPyData(Id)
data[0].update(source)
G2frame.GPXtree.SetItemPyData(Id,data)
print ('Copy of plot controls successful')
[docs]
def CopySelectedHistItems(G2frame):
'''Global copy: Copy items from current histogram to others.
'''
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No other histograms match '+hst,G2frame)
return
choices = ['Limits','Background','Instrument Parameters','Sample Parameters']
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy which histogram sections from\n'+str(hst[5:]),
'Select copy sections', choices, filterBox=False)
dlg.SetSelections(range(len(choices)))
choiceList = []
if dlg.ShowModal() == wx.ID_OK:
choiceList = [choices[i] for i in dlg.GetSelections()]
if not choiceList: return
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy parameters from\n'+str(hst[5:])+' to...',
'Copy parameters', histList)
results = []
try:
if dlg.ShowModal() == wx.ID_OK:
results = dlg.GetSelections()
finally:
dlg.Destroy()
copyList = []
for i in results:
copyList.append(histList[i])
if 'Limits' in choiceList: # Limits
data = G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId,'Limits'))
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
G2frame.GPXtree.SetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,Id,'Limits'),
copy.deepcopy(data))
if 'Background' in choiceList: # Background
data = G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId,'Background'))
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
G2frame.GPXtree.SetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,Id,'Background'),
copy.deepcopy(data))
if 'Instrument Parameters' in choiceList: # Instrument Parameters
# for now all items in Inst. parms are copied
data,data1 = G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(
G2frame,G2frame.PatternId,'Instrument Parameters'))
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,Id,'Instrument Parameters')
)[0].update(copy.deepcopy(data))
G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,Id,'Instrument Parameters')
)[1].update(copy.deepcopy(data1))
if 'Sample Parameters' in choiceList: # Sample Parameters
data = G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(
G2frame,G2frame.PatternId,'Sample Parameters'))
# selects items to be copied
histType,copyNames = SetCopyNames(hst,data['Type'],
addNames = ['Omega','Chi','Phi','Gonio. radius','InstrName'])
copyDict = {parm:data[parm] for parm in copyNames}
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,Id,'Sample Parameters')
).update(copy.deepcopy(copyDict))
[docs]
def TestMagAtoms(phase,magAtms,SGData,Uvec,Trans,allmom,maxequiv=100,maximal=False):
''' Tests substructure magnetic atoms for magnetic site symmetry
param: phase GSAS-II phase object
param: magAtms list:magnetic atom objects
param: SGData dict: GSAS-II space group object
param: Uvec array: Translation U vector
param: Trans array: Transformation matrix
param: allmom bool: =True if all atoms must have moments allowed
params: maxequiv int:maximum number of atoms with moments to consider
param: maximal bool:=True if maximal subgroups only are allowed
returns: unique magnetic atoms (if any)
'''
found = False
anymom = False
phase['Keep'] = False
if not magAtms:
phase['Keep'] = True
return []
invTrans = nl.inv(Trans)
atCodes = []
Phase = {'General':{'AtomPtrs':[2,1],'SGData':copy.deepcopy(phase['SGData'])},'Atoms':[]}
for matm in magAtms:
XYZ = G2spc.GenAtom(matm[3:6],SGData,False,Move=True)
xyzs = [xyz[0] for xyz in XYZ]
atCodes += len(xyzs)*['1',]
xyzs,atCodes = G2lat.ExpandCell(xyzs,atCodes,0,Trans)
for ix,x in enumerate(xyzs):
xyz = G2lat.TransformXYZ(x-Uvec,invTrans.T,np.zeros(3))%1.
Phase['Atoms'].append(matm[:2]+list(xyz))
SytSym,Mul,Nop,dupDir = G2spc.SytSym(xyz,phase['SGData'])
CSI = G2spc.GetCSpqinel(phase['SGData']['SpnFlp'],dupDir)
if any(CSI[0]):
anymom = True
if allmom:
if not any(CSI[0]):
phase['Keep'] = False
found = True
uAtms = G2lat.GetUnique(Phase,atCodes)[0]
natm = len(uAtms)
if anymom and natm <= maxequiv and not found:
phase['Keep'] = True
if maximal and phase['supList'][0]:
phase['Keep'] = False
return uAtms
[docs]
def TestAtoms(phase,magAtms,SGData,Uvec,Trans,maxequiv=100,maximal=False):
'''Tests atoms for substructure equivalents
param: phase GSAS-II phase object
param: magAtms list: atom objects
param: SGData dict: GSAS-II space group object
param: Uvec array: Translation U vector
param: Trans array: Transformation matrix
params: maxequiv int:maximum number of atoms with moments to consider
param: maximal bool:=True if maximal subgroups only are allowed
returns: unique atoms (if any)
'''
phase['Keep'] = True
invTrans = nl.inv(Trans)
atCodes = []
Phase = {'General':{'AtomPtrs':[2,1],'SGData':copy.deepcopy(phase['SGData'])},'Atoms':[]}
for matm in magAtms:
XYZ = G2spc.GenAtom(matm[3:6],SGData,False,Move=True)
xyzs = [xyz[0] for xyz in XYZ]
atCodes += len(xyzs)*['1',]
xyzs,atCodes = G2lat.ExpandCell(xyzs,atCodes,0,Trans)
for ix,x in enumerate(xyzs):
xyz = G2lat.TransformXYZ(x-Uvec,invTrans.T,np.zeros(3))%1.
Phase['Atoms'].append(matm[:2]+list(xyz))
uAtms = G2lat.GetUnique(Phase,atCodes)[0]
natm = len(uAtms)
if natm > maxequiv: #too many allowed atoms found
phase['Keep'] = False
if maximal and phase['supList'][0]:
phase['Keep'] = False
return uAtms
[docs]
def RefineCell(G2frame):
'''Refine a unit cell, called by OnRefine'''
def cellPrint(ibrav,A):
cell = G2lat.A2cell(A)
Vol = G2lat.calc_V(A)
if ibrav in ['Fm3m','Im3m','Pm3m']:
print (" %s%10.6f" % ('a =',cell[0]))
elif ibrav in ['R3-H','P6/mmm','I4/mmm','P4/mmm']:
print (" %s%10.6f %s%10.6f %s%12.3f" % ('a =',cell[0],' c =',cell[2],' volume =',Vol))
elif ibrav in ['P4/mmm','Fmmm','Immm','Ammm','Bmmm','Cmmm','Pmmm']:
print (" %s%10.6f %s%10.6f %s%10.6f %s%12.3f" % ('a =',cell[0],'b =',cell[1],'c =',cell[2],' volume =',Vol))
elif ibrav in ['I2/m','A2/m','C2/m','P2/m']:
print (" %s%10.6f %s%10.6f %s%10.6f %s%8.3f %s%12.3f" % ('a =',cell[0],'b =',cell[1],'c =',cell[2],'beta =',cell[4],' volume =',Vol))
else:
print (" %s%10.6f %s%10.6f %s%10.6f" % ('a =',cell[0],'b =',cell[1],'c =',cell[2]))
print (" %s%8.3f %s%8.3f %s%8.3f %s%12.3f" % ('alpha =',cell[3],'beta =',cell[4],'gamma =',cell[5],' volume =',Vol))
def vecPrint(Vec):
print (' %s %10.5f %10.5f %10.5f'%('Modulation vector:',Vec[0],Vec[1],Vec[2]))
Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[0]
Limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Limits'))[1]
if 'T' in Inst['Type'][0]:
difC = Inst['difC'][1]
dmin = G2lat.Pos2dsp(Inst,Limits[0])
elif 'E' in Inst['Type'][0]:
TTh = Inst['2-theta'][1]
dmin = G2lat.Pos2dsp(Inst,Limits[1])
else: #'C', 'B', or 'PKS'
wave = G2mth.getWave(Inst)
dmin = G2lat.Pos2dsp(Inst,Limits[1])
PatternId = G2frame.PatternId
peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Index Peak List'))
controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Unit Cells List'))
cell = controls[6:12]
A = G2lat.cell2A(cell)
ibrav = bravaisSymb.index(controls[5])
SGData = G2spc.SpcGroup(controls[13])[1]
if 'T' in Inst['Type'][0]:
if ssopt.get('Use',False):
vecFlags = [True if x in ssopt['ssSymb'] else False for x in ['a','b','g']]
SSGData = G2spc.SSpcGroup(SGData,ssopt['ssSymb'])[1]
G2frame.HKL = G2pwd.getHKLMpeak(dmin,Inst,SGData,SSGData,ssopt['ModVec'],ssopt['maxH'],A)
peaks = [G2indx.IndexSSPeaks(peaks[0],G2frame.HKL)[1],peaks[1]] #put peak fit esds back in peaks
Lhkl,M20,X20,Aref,Vec,Zero = \
G2indx.refinePeaksTSS(peaks[0],difC,Inst,SGData,SSGData,ssopt['maxH'],ibrav,A,ssopt['ModVec'],vecFlags,controls[1],controls[0])
else:
G2frame.HKL = G2pwd.getHKLpeak(dmin,SGData,A,Inst)
peaks = [G2indx.IndexPeaks(peaks[0],G2frame.HKL)[1],peaks[1]] #put peak fit esds back in peaks
Lhkl,M20,X20,Aref,Zero = G2indx.refinePeaksT(peaks[0],difC,ibrav,A,controls[1],controls[0])
elif 'E' in Inst['Type'][0]: #no super lattice stuff for EDX data - resolution too low
G2frame.HKL = G2pwd.getHKLpeak(dmin,SGData,A,Inst)
peaks = [G2indx.IndexPeaks(peaks[0],G2frame.HKL)[1],peaks[1]] #put peak fit esds back in peaks
Lhkl,M20,X20,Aref = G2indx.refinePeaksE(peaks[0],TTh,ibrav,A)
Zero = 0.0
else:
if ssopt.get('Use',False):
vecFlags = [True if x in ssopt['ssSymb'] else False for x in ['a','b','g']]
SSGData = G2spc.SSpcGroup(SGData,ssopt['ssSymb'])[1]
G2frame.HKL = G2pwd.getHKLMpeak(dmin,Inst,SGData,SSGData,ssopt['ModVec'],ssopt['maxH'],A)
peaks = [G2indx.IndexSSPeaks(peaks[0],G2frame.HKL)[1],peaks[1]] #put peak fit esds back in peaks
Lhkl,M20,X20,Aref,Vec,Zero = \
G2indx.refinePeaksZSS(peaks[0],wave,Inst,SGData,SSGData,ssopt['maxH'],ibrav,A,ssopt['ModVec'],vecFlags,controls[1],controls[0])
else:
G2frame.HKL = G2pwd.getHKLpeak(dmin,SGData,A,Inst)
peaks = [G2indx.IndexPeaks(peaks[0],G2frame.HKL)[1],peaks[1]] #put peak fit esds back in peaks
Lhkl,M20,X20,Aref,Zero = G2indx.refinePeaksZ(peaks[0],wave,ibrav,A,controls[1],controls[0])
controls[1] = Zero
controls[6:12] = G2lat.A2cell(Aref)
controls[12] = G2lat.calc_V(Aref)
if ssopt.get('Use',False):
ssopt['ModVec'] = Vec
G2frame.HKL = G2pwd.getHKLMpeak(dmin,Inst,SGData,SSGData,ssopt['ModVec'],ssopt['maxH'],A)
else:
G2frame.HKL = G2pwd.getHKLpeak(dmin,SGData,A,Inst)
newcell = [M20,X20,ibrav]+controls[6:13]+[False,False]
cells.append(newcell)
cells = G2indx.sortM20(cells)
G2frame.HKL = np.array(G2frame.HKL)
data = [controls,bravais,cells,dmin,ssopt,magcells]
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Unit Cells List'),data)
print (" %s%10.3f" % ('refinement M20 = ',M20))
print (' unindexed lines = %d'%X20)
cellPrint(controls[5],Aref)
ip = 4
if ssopt.get('Use',False):
vecPrint(Vec)
ip = 5
for hkl in G2frame.HKL:
hkl[ip] = G2lat.Dsp2pos(Inst,hkl[ip-1])+controls[1]
if 'PKS' in G2frame.GPXtree.GetItemText(G2frame.PatternId):
G2plt.PlotPowderLines(G2frame,indexFrom='Indexing from refine cell, M20=%.3f'%M20)
else:
G2pwpl.PlotPatterns(G2frame,indexFrom='Indexing from refine cell, M20=%.3f'%M20)
return data
################################################################################
##### Powder Peaks
################################################################################
[docs]
def UpdatePeakGrid(G2frame, data):
'''respond to selection of PWDR powder peaks data tree item.
'''
def OnAutoSearch(event):
'Search pattern for possible peak positions'
PatternId = G2frame.PatternId
limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits'))[1]
background = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Background'))
inst,inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters'))
Pattern = G2frame.GPXtree.GetItemPyData(PatternId)
profile = Pattern[1]
bxye = GetFileBackground(G2frame,profile,background)
x0 = profile[0]
iBeg = np.searchsorted(x0,limits[0])
iFin = np.searchsorted(x0,limits[1])
x = x0[iBeg:iFin]
y0 = (profile[1]-bxye)[iBeg:iFin]
ysig = 1.0*np.std(y0)
offset = [-1,1]
ymask = ma.array(y0,mask=(y0<ysig))
for off in offset:
ymask = ma.array(ymask,mask=(ymask-np.roll(y0,off)<=0.))
indx = ymask.nonzero()
mags = ymask[indx]
poss = x[indx]
refs = list(zip(poss,mags))
if 'T' in Inst['Type'][0]:
refs = G2mth.sortArray(refs,0,reverse=True) #big TOFs first
else: #'C', 'E' or 'B'
refs = G2mth.sortArray(refs,0,reverse=False) #small 2-Thetas or energies first
for i,ref1 in enumerate(refs): #reject picks closer than 1 FWHM
for ref2 in refs[i+1:]:
if abs(ref2[0]-ref1[0]) < 2.*G2pwd.getFWHM(ref1[0],inst):
del(refs[i])
if 'T' in Inst['Type'][0]:
refs = G2mth.sortArray(refs,1,reverse=False)
else: #'C', 'E' or 'B'
refs = G2mth.sortArray(refs,1,reverse=True)
for pos,mag in refs:
data['peaks'].append(G2mth.setPeakparms(inst,inst2,pos,mag))
UpdatePeakGrid(G2frame,data)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
def OnCopyPeaks(event):
'Copy peaks to other histograms'
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
copyList = []
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy peak list from\n'+str(hst[5:])+' to...',
'Copy peaks', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
copyList.append(histList[i])
finally:
dlg.Destroy()
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
G2frame.GPXtree.SetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,Id,'Peak List'),copy.deepcopy(data))
def OnCopyPeakFlags(event):
'Copy peak refinement flags to other histograms'
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
copyList = []
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy peak refinement flags from\n'+str(hst[5:])+' to...',
'Copy peak ref flags', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
copyList.append(histList[i])
finally:
dlg.Destroy()
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
pksId = G2gd.GetGPXtreeItemId(G2frame,Id,'Peak List')
pksTbl = G2frame.GPXtree.GetItemPyData(pksId)
for i,pk in enumerate(data['peaks']):
for col in range(1,len(pk),2):
try:
pksTbl['peaks'][i][col] = pk[col]
except:
pass
def OnLoadPeaks(event):
'Load peak list from file'
pth = G2G.GetExportPath(G2frame)
dlg = wx.FileDialog(G2frame, 'Choose GSAS-II PWDR peaks list file', pth, '',
'PWDR peak list files (*.pkslst)|*.pkslst',wx.FD_OPEN)
try:
if dlg.ShowModal() == wx.ID_OK:
peaks = []
filename = dlg.GetPath()
File = open(filename,'r')
S = File.readline()
while S:
if '#' in S:
S = File.readline()
continue
try:
peaks.append(eval(S))
except:
break
S = File.readline()
File.close()
except Exception as msg:
G2G.G2MessageBox(G2frame,
'Error reading file. See console for more info',
'Read error')
print('File read error:\n',msg)
finally:
dlg.Destroy()
data = {'peaks':peaks,'sigDict':{}}
UpdatePeakGrid(G2frame,data)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
def OnSavePeaks(event):
'Save peak to file suitable for OnLoadPeaks'
pth = G2G.GetExportPath(G2frame)
dlg = wx.FileDialog(G2frame, 'Choose GSAS-II PWDR peaks list file', pth, '',
'PWDR peak list files (*.pkslst)|*.pkslst',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
try:
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
# make sure extension is .pkslst
filename = os.path.splitext(filename)[0]+'.pkslst'
File = open(filename,'w')
File.write("#GSAS-II PWDR peaks list file; do not add/delete items!\n")
for item in data:
if item == 'peaks':
for pk in data[item]:
pk = ', '.join([str(i) for i in pk]) # remove numpy data types from values
File.write(f'[{pk}]\n')
File.close()
print ('PWDR peaks list saved to: '+filename)
finally:
dlg.Destroy()
def OnUnDo(event):
'Undo a peak fit - reads a saved file from PeakFit'
file = open(G2frame.undofile,'rb')
PatternId = G2frame.PatternId
for item in ['Background','Instrument Parameters','Peak List']:
Id = G2gd.GetGPXtreeItemId(G2frame,PatternId, item)
oldvals = pickle.load(file)
G2frame.GPXtree.SetItemPyData(Id,oldvals)
if item == 'Peak List':
data.update(G2frame.GPXtree.GetItemPyData(Id))
print (item+' recovered')
file.close()
G2frame.dataWindow.UnDo.Enable(False)
wx.CallAfter(UpdatePeakGrid,G2frame,data)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
def SaveState():
'Saves result of a peaak fit for possible UnDo'
G2frame.undofile = os.path.join(G2frame.dirname,'GSASII.save')
file = open(G2frame.undofile,'wb')
PatternId = G2frame.PatternId
for item in ['Background','Instrument Parameters','Peak List']:
pickle.dump(G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId,item)),file,1)
file.close()
G2frame.dataWindow.UnDo.Enable(True)
def OnLSQPeakFit(event):
'Do a peak fit'
if reflGrid.IsCellEditControlEnabled(): # complete any grid edits in progress
reflGrid.HideCellEditControl()
reflGrid.DisableCellEditControl()
if not G2frame.GSASprojectfile: #force a save of the gpx file so SaveState can write in the same directory
G2frame.OnFileSaveas(event)
wx.CallAfter(OnPeakFit)
def OnOneCycle(event):
'Do a single cycle of peak fit'
if reflGrid.IsCellEditControlEnabled(): # complete any grid edits in progress
reflGrid.HideCellEditControl()
reflGrid.DisableCellEditControl()
wx.CallAfter(OnPeakFit,oneCycle=True)
def OnSeqPeakFit(event):
'''Do a sequential peak fit across multiple histograms - peaks must be present in all.
results saved in Sequential peak fit results'''
histList = G2gd.GetGPXtreeDataNames(G2frame,['PWDR',])
od = {'label_1':'Copy to next','value_1':False,'label_2':'Reverse order','value_2':False}
dlg = G2G.G2MultiChoiceDialog(G2frame, 'Sequential peak fits',
'Select dataset to include',histList,extraOpts=od)
names = []
if dlg.ShowModal() == wx.ID_OK:
for sel in dlg.GetSelections():
names.append(histList[sel])
dlg.Destroy()
if not names:
return
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Sequential peak fit results')
if Id:
SeqResult = G2frame.GPXtree.GetItemPyData(Id)
else:
SeqResult = {}
Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Sequential peak fit results')
SeqResult = {'SeqPseudoVars':{},'SeqParFitEqList':[]}
SeqResult['histNames'] = names
dlg = wx.ProgressDialog('Sequential peak fit','Data set name = '+names[0],len(names),
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME|wx.PD_CAN_ABORT)
controls = {'deriv type':'analytic','min dM/M':0.001,}
print ('Peak Fitting with '+controls['deriv type']+' derivatives:')
oneCycle = False
prevVaryList = []
peaks = None
varyList = None
if od['value_2']:
names.reverse()
try:
for i,name in enumerate(names):
print (' Sequential fit for '+name)
dlg.Raise()
GoOn = dlg.Update(i,newmsg='Data set name = '+name)[0]
if not GoOn:
dlg.Destroy()
break
PatternId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name)
if i and od['value_1']:
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Peak List'),copy.deepcopy(peaks))
prevVaryList = varyList[:]
peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Peak List'))
background = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Background'))
limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits'))[1]
inst,inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters'))
Pattern = G2frame.GPXtree.GetItemPyData(PatternId)
data = Pattern[1]
fixback = GetFileBackground(G2frame,data,background,scale=False)
peaks['sigDict'],result,sig,Rvals,varyList,parmDict,fullvaryList,badVary = G2pwd.DoPeakFit(None,peaks['peaks'],
background,limits,inst,inst2,data,fixback,prevVaryList,oneCycle,controls) #needs wtFactor after controls?
if len(result[0]) != len(fullvaryList):
dlg.Destroy()
print (' ***** Sequential peak fit stopped at '+name+' *****')
break
else:
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Peak List'),copy.deepcopy(peaks))
SeqResult[name] = {'variables':result[0],'varyList':varyList,'sig':sig,'Rvals':Rvals,
'covMatrix':np.eye(len(result[0])),'title':name,'parmDict':parmDict,
'fullVary':fullvaryList,'badVary':badVary}
print (' ***** Sequential peak fit successful *****')
finally:
dlg.Destroy()
SeqResult['histNames'] = histList
G2frame.GPXtree.SetItemPyData(Id,SeqResult)
G2frame.G2plotNB.Delete('Sequential refinement') #clear away probably invalid plot
G2frame.GPXtree.SelectItem(Id)
def OnDelPeaks(event):
'Delete selected peaks from the Peak fit table'
if G2frame.dataWindow.XtraPeakMode.IsChecked(): # which table?
tbl = data['xtraPeaks']
else:
tbl = data['peaks']
choices = [f"{i[0]:.2f}" for i in tbl]
if not choices: return
sel = []
dlg = G2G.G2MultiChoiceDialog(G2frame,'Select peaks to delete',
'Delete peaks',choices)
try:
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelections()
finally:
dlg.Destroy()
for i in sorted(sel,reverse=True):
del tbl[i]
UpdatePeakGrid(G2frame,data)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
def OnClearPeaks(event):
'Clear the Peak fit table'
dlg = wx.MessageDialog(G2frame,'Delete all peaks?','Clear peak list',wx.OK|wx.CANCEL)
try:
if dlg.ShowModal() == wx.ID_OK:
peaks = {'peaks':[],'sigDict':{}}
finally:
dlg.Destroy()
UpdatePeakGrid(G2frame,peaks)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
def OnPeakFit(oneCycle=False,noFit=False,noPlot=False):
'Do peak fitting by least squares'
SaveState()
controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
if not controls:
controls = {'deriv type':'analytic','min dM/M':0.001,} #fill in defaults if needed
#print ('Peak Fitting with '+controls['deriv type']+' derivatives:')
PatternId = G2frame.PatternId
peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Peak List'))
if not peaks:
G2frame.ErrorDialog('No peaks!','Nothing to fit!')
return
background = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Background'))
limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits'))[1]
inst,inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters'))
Pattern = G2frame.GPXtree.GetItemPyData(PatternId)
data = Pattern[1]
wtFactor = Pattern[0]['wtFactor']
overallInfo = {}
peaks['LaueFringe'] = peaks.get('LaueFringe',{})
peaks['LaueFringe']['satellites'] = []
lines = peaks['LaueFringe'].get('Show')
if 'LF' in inst['Type'][0]:
wave = G2mth.getWave(inst)
overallInfo = {'ncell':peaks['LaueFringe']['ncell'],
'clat': peaks['LaueFringe']['clat'],
'clat-ref': peaks['LaueFringe']['clat-ref'],
'fitRange': peaks['LaueFringe'].get('fitRange',8.0),
'fitPowerM': peaks['LaueFringe'].get('fitPowerM',2.0),
'fitPowerP': peaks['LaueFringe'].get('fitPowerP',2.0),
} # add overall info here
if lines:
for i in peaks['peaks']:
pks = list(range(-lines,0)) + list(range(1,lines+1))
peaks['LaueFringe']['satellites'].extend(
G2pwd.LaueSatellite(i[0],wave,peaks['LaueFringe']['clat'],peaks['LaueFringe']['ncell'],pks))
if G2frame.dataWindow.XtraPeakMode.IsChecked(): # adding peaks to computed pattern
histoName = G2frame.GPXtree.GetItemText(G2frame.PatternId)
# do zero cycle refinement
from . import GSASIIstrMain as G2stMn
# recompute current pattern for current histogram, set as fixed background
bxye = G2stMn.DoNoFit(G2frame.GSASprojectfile,histoName)
peaksplus = peaks['xtraPeaks'] + [{}]
# dummy out background parameters (are not used so can't be refined)
background = [['chebyschev-1', False, 1, 0.0], {
'nDebye': 0,'debyeTerms': [],'nPeaks': 0,'peaksList': [],
'background PWDR': ['', 1.0, False],
'FixedPoints': [],'autoPrms': {}}]
#breakpoint() ##################################################
else:
peaksplus = peaks['peaks'] + [overallInfo]
bxye = GetFileBackground(G2frame,data,background,scale=False)
if noFit:
results = G2pwd.DoPeakFit(None,peaksplus,background,limits,inst,inst2,data,bxye,[],oneCycle,controls,wtFactor,noFit=True)
if not noPlot:
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
return
# try:
dlg = wx.ProgressDialog('Residual','Peak fit Rwp = ',101,parent=G2frame,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME|wx.PD_CAN_ABORT)
results = G2pwd.DoPeakFit(None,peaksplus,background,limits,inst,inst2,data,bxye,[],oneCycle,controls,wtFactor,dlg)
# finally:
# dlg.Destroy()
if results is None:
return
peaks['sigDict'] = results[0]
if 'LF' in inst['Type'][0] and 'clat' in overallInfo:
peaks['LaueFringe']['clat'] = overallInfo['clat']
text = 'Peak fit: Rwp=%.2f%% Nobs= %d Nparm= %d Npeaks= %d'%(results[3]['Rwp'],results[1][2]['fjac'].shape[1],len(results[0]),len(peaks['peaks']))
newpeaks = copy.copy(peaks)
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Peak List'),newpeaks)
G2frame.AddToNotebook(text,'PF')
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
wx.CallAfter(UpdatePeakGrid,G2frame,newpeaks)
def OnResetSigGam(event):
'Reset sig & gam values to instrument parameter values'
PatternId = G2frame.PatternId
Inst,Inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters'))
peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Peak List'))
if not peaks['peaks']:
G2frame.ErrorDialog('No peaks!','Nothing to do!')
return
newpeaks = {'peaks':[],'sigDict':{}}
for peak in peaks['peaks']:
newpeaks['peaks'].append(G2mth.setPeakparms(Inst,Inst2,peak[0],peak[2]))
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Peak List'),newpeaks)
UpdatePeakGrid(G2frame,newpeaks)
def setBackgroundColors():
'Set background colors in peak list table; red if negative (nonsense), white if ok'
for r in range(reflGrid.GetNumberRows()):
for c in range(reflGrid.GetNumberCols()):
if reflGrid.GetColLabelValue(c) in ['position','intensity','alpha','beta','sigma\u00b2','gamma']:
try:
if float(reflGrid.GetCellValue(r,c)) < 0.:
reflGrid.SetCellBackgroundColour(r,c,wx.RED)
else:
reflGrid.SetCellBackgroundColour(r,c,wx.SystemSettings.GetColour(wx.SYS_COLOUR_WINDOW))
except:
pass
def KeyEditPeakGrid(event):
'''Respond to pressing a key to act on selection of a row, column or cell
in the Peak List table
'''
rowList = reflGrid.GetSelectedRows()
colList = reflGrid.GetSelectedCols()
selectList = reflGrid.GetSelectedCells()
data = G2frame.GPXtree.GetItemPyData(G2frame.PickId)
if event.GetKeyCode() == wx.WXK_RETURN:
event.Skip(True)
elif event.GetKeyCode() == wx.WXK_CONTROL:
event.Skip(True)
elif event.GetKeyCode() == wx.WXK_SHIFT:
event.Skip(True)
elif rowList and (event.GetKeyCode() == wx.WXK_DELETE or event.GetKeyCode() == 8):
# pressing the delete key or backspace deletes selected peak(s)
reflGrid.ClearSelection()
reflGrid.ClearGrid()
rowList.sort()
rowList.reverse()
nDel = 0
for row in rowList:
G2frame.PeakTable.DeleteRow(row)
nDel += 1
if nDel:
msg = wg.GridTableMessage(G2frame.PeakTable,
wg.GRIDTABLE_NOTIFY_ROWS_DELETED,0,nDel)
reflGrid.ProcessTableMessage(msg)
data['peaks'] = G2frame.PeakTable.GetData()[:-nDel]
G2frame.GPXtree.SetItemPyData(G2frame.PickId,data)
setBackgroundColors()
elif colList and (event.GetKeyCode() == 89 or event.GetKeyCode() == 78):
reflGrid.ClearSelection()
key = event.GetKeyCode()
for col in colList:
if G2frame.PeakTable.GetTypeName(0,col) == wg.GRID_VALUE_BOOL:
if key == 89: #'Y'
for row in range(G2frame.PeakTable.GetNumberRows()): data['peaks'][row][col]=True
elif key == 78: #'N'
for row in range(G2frame.PeakTable.GetNumberRows()): data['peaks'][row][col]=False
elif selectList and (event.GetKeyCode() == 89 or event.GetKeyCode() == 78):
reflGrid.ClearSelection()
key = event.GetKeyCode()
for row,col in selectList:
if G2frame.PeakTable.GetTypeName(row,col) == wg.GRID_VALUE_BOOL:
if key == 89: #'Y'
data['peaks'][row][col]=True
elif key == 78: #'N'
data['peaks'][row][col]=False
else:
event.Skip()
return
# G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
wx.CallAfter(UpdatePeakGrid,G2frame,data)
def SelectVars(rows):
'''Set or clear peak refinement variables for peaks listed in rows
'''
refOpts = {reflGrid.GetColLabelValue(i):i+1 for i in range(reflGrid.GetNumberCols()) if reflGrid.GetColLabelValue(i) != "refine"}
dlg = G2G.G2MultiChoiceDialog(G2frame,'Select columns to refine',
'Refinement Selection', sorted(refOpts.keys()),
filterBox=False,toggle=False)
sels = []
try:
if dlg.ShowModal() == wx.ID_OK:
sels = [sorted(refOpts.keys())[i] for i in dlg.GetSelections()]
else:
return
finally:
dlg.Destroy()
tbl = reflGrid.GetTable().data
for r in rows:
for lbl,c in refOpts.items():
tbl[r][c] = lbl in sels
UpdatePeakGrid(G2frame,data)
def OnRefineSelected(event):
'''set refinement flags for the selected peaks
'''
rows = list(set([row for row,col in reflGrid.GetSelectedCells()] +
reflGrid.GetSelectedRows()))
tbl = reflGrid.GetTable().data
if not rows:
choices = [f"{i[0]:.2f}" for i in tbl]
dlg = G2G.G2MultiChoiceDialog(G2frame,'Select peaks to refine',
'select peaks',choices)
try:
if dlg.ShowModal() == wx.ID_OK:
rows = dlg.GetSelections()
finally:
dlg.Destroy()
if not rows: return
SelectVars(rows)
def OnRefineAll(event):
'''set refinement flags for all peaks
'''
SelectVars(range(reflGrid.GetNumberRows()))
def onCellListDClick(event):
'''Called after a double-click on a row/column label'''
r,c = event.GetRow(),event.GetCol()
if r < 0 and c < 0:
for row in range(reflGrid.GetNumberRows()):
reflGrid.SelectRow(row,True)
for col in range(reflGrid.GetNumberCols()):
reflGrid.SelectCol(col,True)
elif r >= 0 and c < 0: #row label: select it and replot!
reflGrid.ClearSelection()
reflGrid.SelectRow(r,True)
wx.CallAfter(G2frame.reflGrid.ForceRefresh)
wx.CallAfter(G2pwpl.PlotPatterns,G2frame,plotType='PWDR')
elif c > 0: #column label: just select it (& redisplay)
reflGrid.ClearSelection()
reflGrid.SelectCol(c,True)
if reflGrid.GetColLabelValue(c) != 'refine': return
choice = ['Y - vary all','N - vary none',]
dlg = wx.SingleChoiceDialog(G2frame,'Select refinement option for '+reflGrid.GetColLabelValue(c-1),
'Refinement controls',choice)
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelection()
tbl = reflGrid.GetTable().data
if sel == 0:
for r in range(reflGrid.GetNumberRows()): tbl[r][c]=True
else:
for r in range(reflGrid.GetNumberRows()): tbl[r][c]=False
wx.CallAfter(UpdatePeakGrid,G2frame,data)
def RefreshPeakGrid(event):
'recompute & plot the peaks any time a value in the table is edited'
col = event.GetCol()
if 'LF' in Inst['Type'][0]:
for i in range(len(data['LFpeaks'])):
data['peaks'][i][2:] = data['LFpeaks'][i]
wx.CallAfter(UpdatePeakGrid,G2frame,data)
if data['peaks']:
OnPeakFit(noFit=True,noPlot=col%2)
def ToggleXtraMode(event):
'''Switch "Extra Peak" mode in response to button'''
G2frame.dataWindow.XtraPeakMode.Check(
not G2frame.dataWindow.XtraPeakMode.IsChecked())
OnXtraMode(event)
def OnXtraMode(event):
'''Respond to change in "Extra Peak" mode from menu command
or button via :func:`ToggleXtraMode`.
'''
data['xtraMode'] = G2frame.dataWindow.XtraPeakMode.IsChecked()
wx.CallAfter(UpdatePeakGrid,G2frame,data)
wx.CallAfter(G2pwpl.PlotPatterns,G2frame,plotType='PWDR')
def OnSetPeakWidMode(event):
'''Toggle G2pwd.peakInstPrmMode mode; determines if unvaried
sigma and gamma values are set from UVW & XY
'''
state = G2frame.dataWindow.setPeakMode.IsChecked()
G2pwd.setPeakInstPrmMode(state)
def ShiftLFc(event):
'''Shift the Laue Fringe lattice parameter
'''
Obj = event.GetEventObject()
move = Obj.GetValue()
Obj.SetValue(0)
data['LaueFringe']['clat'] *= 1. + move/2000.
wx.CallAfter(RefreshPeakGrid,None)
#### beginning of UpdatePeakGrid =================================
G2frame.GetStatusBar().SetStatusText('Global refine: select refine column & press Y or N',1)
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.PeakMenu)
G2frame.Bind(wx.EVT_MENU, OnAutoSearch, id=G2G.wxID_AUTOSEARCH)
G2frame.Bind(wx.EVT_MENU, OnCopyPeaks, id=G2G.wxID_PEAKSCOPY)
G2frame.Bind(wx.EVT_MENU, OnCopyPeakFlags, id=G2G.wxID_PEAKSCOPYFLAG)
G2frame.Bind(wx.EVT_MENU, OnSavePeaks, id=G2G.wxID_PEAKSAVE)
G2frame.Bind(wx.EVT_MENU, OnLoadPeaks, id=G2G.wxID_PEAKLOAD)
G2frame.Bind(wx.EVT_MENU, OnUnDo, id=G2G.wxID_UNDO)
G2frame.Bind(wx.EVT_MENU, OnRefineSelected, id=G2frame.dataWindow.peaksSel.GetId())
G2frame.Bind(wx.EVT_MENU, OnRefineAll, id=G2frame.dataWindow.peaksAll.GetId())
G2frame.Bind(wx.EVT_MENU, OnLSQPeakFit, id=G2G.wxID_LSQPEAKFIT)
G2frame.Bind(wx.EVT_MENU, OnOneCycle, id=G2G.wxID_LSQONECYCLE)
G2frame.Bind(wx.EVT_MENU, OnSeqPeakFit, id=G2G.wxID_SEQPEAKFIT)
G2frame.Bind(wx.EVT_MENU, OnDelPeaks, id=G2G.wxID_DELPEAKS)
G2frame.Bind(wx.EVT_MENU, OnClearPeaks, id=G2G.wxID_CLEARPEAKS)
G2frame.Bind(wx.EVT_MENU, OnResetSigGam, id=G2G.wxID_RESETSIGGAM)
G2frame.Bind(wx.EVT_MENU, OnSetPeakWidMode, id=G2G.wxID_SETUNVARIEDWIDTHS)
# get info in phases associated with current histogram
data['xtraPeaks'] = data.get('xtraPeaks',[])
histoName = G2frame.GPXtree.GetItemText(G2frame.PatternId)
phCount = 0
# isHistMag = False
for ph in GetPhasesforHistogram(G2frame,histoName):
phCount += 1
# if ph['General']['Type'] == 'magnetic':
# isHistMag = True
# break
if phCount == 0: # no phases for this histogram
G2frame.dataWindow.XtraPeakMode.Enable(False)
else:
G2frame.dataWindow.XtraPeakMode.Enable(True)
data['xtraMode'] = data.get('xtraMode',False)
G2frame.dataWindow.XtraPeakMode.Check(data['xtraMode'])
G2frame.Bind(wx.EVT_MENU, OnXtraMode, id=G2G.wxID_XTRAPEAKMODE)
OnSetPeakWidMode(None)
# can peaks be refined?
pkmode = False
if G2frame.dataWindow.XtraPeakMode.IsChecked():
if data['xtraPeaks']: pkmode = True
elif data['peaks']:
pkmode = True
for item in (G2frame.dataWindow.PeakCopy,
G2frame.dataWindow.PeakFit,
G2frame.dataWindow.PFOneCycle,
G2frame.dataWindow.SeqPeakFit):
item.Enable(pkmode)
G2frame.dataWindow.AutoSearch.Enable(not pkmode)
G2frame.PickTable = []
rowLabels = []
PatternId = G2frame.PatternId
Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters'))[0]
if G2frame.dataWindow.XtraPeakMode.IsChecked():
G2frame.dataWindow.ClearData()
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
if 'N' in Inst['Type'][0]:
lbl = 'List of k-vector/impurity or subgroup defining peaks'
else:
lbl = 'List of impurity or subgroup peaks'
topSizer.Add(wx.StaticText(parent,label=lbl),0,WACV)
btn = wx.Button(parent, wx.ID_ANY, 'Switch to Normal peak mode')
topSizer.Add(btn,0,wx.LEFT,8)
btn.Bind(wx.EVT_BUTTON,ToggleXtraMode)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
krowLabels = [str(i+1) for i,j in enumerate(data['xtraPeaks'])]
kcolLabels = []
Types = []
for _,f,l in zip(*G2pwd.getHeaderInfo(Inst['Type'][0])):
kcolLabels.append(l)
Types.append(wg.GRID_VALUE_FLOAT + f.replace('%',':').replace('f','').replace('.',','))
kcolLabels.append('refine')
Types.append(wg.GRID_VALUE_BOOL)
T = []
# put k-vecs in order
for peak in data['xtraPeaks']:
T.append(peak[0])
D = dict(zip(T,data['xtraPeaks']))
T.sort()
if 'T' in Inst['Type'][0]: #want big TOF's first
T.reverse()
X = []
for key in T: X.append(D[key])
data['xtraPeaks'] = X
G2frame.GPXtree.SetItemPyData(G2frame.PickId,data)
kPeakTable = G2G.Table(data['xtraPeaks'],rowLabels=krowLabels,
colLabels=kcolLabels,types=Types)
G2frame.dataWindow.currentGrids = []
reflGrid = G2G.GSGrid(parent=G2frame.dataWindow)
reflGrid.SetRowLabelSize(45)
reflGrid.SetTable(kPeakTable, True)
setBackgroundColors()
reflGrid.Bind(wg.EVT_GRID_CELL_CHANGED, RefreshPeakGrid)
reflGrid.Bind(wx.EVT_KEY_DOWN, KeyEditPeakGrid)
reflGrid.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, onCellListDClick)
reflGrid.AutoSizeColumns(False)
G2frame.reflGrid = reflGrid
mainSizer.Add(reflGrid,1,wx.ALL|wx.EXPAND,3)
G2frame.dataWindow.SetDataSize()
return
# Create the header on the Peak Table
for i in range(len(data['peaks'])): rowLabels.append(str(i+1))
colLabels = []
Types = []
for _,f,l in zip(*G2pwd.getHeaderInfo(Inst['Type'][0])):
colLabels.append(l)
if l.startswith('2'):
Types.append(wg.GRID_VALUE_FLOAT + ':7,3')
elif l == '00l':
Types.append(wg.GRID_VALUE_NUMBER)
else:
Types.append(wg.GRID_VALUE_FLOAT + f.replace('%',':').replace('f','').replace('.',','))
colLabels.append('refine')
Types.append(wg.GRID_VALUE_BOOL)
# sort peaks & save into tree
T = []
for peak in data['peaks']:
T.append(peak[0])
D = dict(zip(T,data['peaks']))
T.sort()
if 'T' in Inst['Type'][0]: #want big TOF's first
T.reverse()
X = []
for key in T: X.append(D[key])
data['peaks'] = X
G2frame.GPXtree.SetItemPyData(G2frame.PickId,data)
G2frame.dataWindow.ClearData()
if 'LF' in Inst['Type'][0]:
data['LFpeaks'] = []
for i in range(len(data['peaks'])):
if len(data['peaks'][i]) == 8: # need to extend the entry
if 'Lam' in Inst:
lam = Inst['Lam'][0]
else:
lam = (Inst['Lam1'][0] +
Inst['I(L2)/I(L1)'][0] * Inst['Lam2'][0]) / (
1 + Inst['I(L2)/I(L1)'][0])
if i == 0:
pos = data['peaks'][i][0]
data['LaueFringe']['clat'] = data['LaueFringe']['lmin'] * 0.5 * lam / np.sin(pos*np.pi/360)
l = data['LaueFringe']['lmin']
else:
l = data['LaueFringe']['clat'] / (0.5 * lam / np.sin(data['peaks'][i][0]*np.pi/360))
l = int(l + 0.5)
data['peaks'][i][0] = 360 * np.arcsin(0.5 * lam / (data['LaueFringe']['clat']/l)) / np.pi
data['peaks'][i] += [0., False, 0., False, l, None]
peakline = copy.deepcopy(data['peaks'][i][2:])
peakline[-1] = data['peaks'][i][0]
peakline[-2] = int(peakline[-2]+.5)
data['LFpeaks'].append(peakline)
G2frame.PeakTable = G2G.Table(data['LFpeaks'],rowLabels=rowLabels,colLabels=colLabels,types=Types)
else:
G2frame.PeakTable = G2G.Table(data['peaks'],rowLabels=rowLabels,colLabels=colLabels,types=Types)
#G2frame.SetLabel(G2frame.GetLabel().split('||')[0]+' || '+'Peak List')
G2frame.dataWindow.currentGrids = []
reflGrid = G2G.GSGrid(parent=G2frame.dataWindow)
reflGrid.SetRowLabelSize(45)
reflGrid.SetTable(G2frame.PeakTable, True)
setBackgroundColors()
reflGrid.Bind(wg.EVT_GRID_CELL_CHANGED, RefreshPeakGrid)
reflGrid.Bind(wx.EVT_KEY_DOWN, KeyEditPeakGrid)
reflGrid.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, onCellListDClick)
reflGrid.AutoSizeColumns(False)
G2frame.reflGrid = reflGrid
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,label='List of peaks to fit individually'),0,WACV)
btn = wx.Button(parent, wx.ID_ANY, 'Switch to Extra Peak mode')
topSizer.Add(btn,0,wx.LEFT,8)
btn.Bind(wx.EVT_BUTTON,ToggleXtraMode)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
if 'LF' in Inst['Type'][0]:
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Laue Fringe fitting'))
topSizer = wx.BoxSizer(wx.HORIZONTAL)
topSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Overall parms: '),0,WACV)
data['LaueFringe'] = data.get('LaueFringe',{})
data['LaueFringe']['ncell'] = data['LaueFringe'].get('ncell',20)
data['LaueFringe']['clat'] = data['LaueFringe'].get('clat',9.0)
data['LaueFringe']['lmin'] = data['LaueFringe'].get('lmin',1)
data['LaueFringe']['clat-ref'] = data['LaueFringe'].get('clat-ref',False)
data['LaueFringe']['Show'] = data['LaueFringe'].get('Show',0)
data['LaueFringe']['fitRange'] = data['LaueFringe'].get('fitRange',8.0)
data['LaueFringe']['fitPowerM'] = data['LaueFringe'].get('fitPowerM',2.0)
data['LaueFringe']['fitPowerP'] = data['LaueFringe'].get('fitPowerP',2.0)
prmVSizer = wx.BoxSizer(wx.VERTICAL)
prmSizer = wx.BoxSizer(wx.HORIZONTAL)
prmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' c='),0,WACV)
cVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['LaueFringe'],'clat',
typeHint=float,nDig=(10,4),size=(80,-1),
OnLeave=lambda *arg,**kw:RefreshPeakGrid(None))
prmSizer.Add(cVal,0,WACV)
cellSpin = wx.SpinButton(G2frame.dataWindow,style=wx.SP_VERTICAL,size=wx.Size(20,20))
cellSpin.SetValue(0)
cellSpin.SetRange(-1,1)
cellSpin.Bind(wx.EVT_SPIN, ShiftLFc)
prmSizer.Add(cellSpin,0,WACV)
cRef = G2G.G2CheckBox(G2frame.dataWindow,'ref',data['LaueFringe'],'clat-ref')
prmSizer.Add(cRef,0,WACV)
prmSizer.Add((15,-1))
siz = G2G.G2SpinWidget(G2frame.dataWindow,data['LaueFringe'] ,'lmin','l min')
prmSizer.Add(siz,0,WACV)
prmSizer.Add((15,-1))
siz = G2G.G2SpinWidget(G2frame.dataWindow,data['LaueFringe'] ,'ncell','Laue ncell',
onChange=RefreshPeakGrid,onChangeArgs=[None])
prmSizer.Add(siz,0,WACV)
# prmSizer.Add((15,-1))
# prmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Show '),0,WACV)
# ch = G2G.EnumSelector(G2frame.dataWindow,data['LaueFringe'],'Show',
# ['None','1','2','3','4','5','6'],list(range(7)),
# OnChange=RefreshPeakGrid)
# prmSizer.Add(ch,0,WACV)
# prmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' satellites'),0,WACV)
prmVSizer.Add(prmSizer)
prmSizer = wx.BoxSizer(wx.HORIZONTAL)
prmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' fit width'),0,WACV)
cVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['LaueFringe'],'fitRange',typeHint=float,
nDig=(6,1),size=(60,-1),xmin=1., xmax=20.,OnLeave=lambda *arg,**kw:RefreshPeakGrid(None))
prmSizer.Add(cVal,0,WACV)
prmSizer.Add((15,-1))
prmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' fit exponent, minus side'),0,WACV)
cVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['LaueFringe'],'fitPowerM',typeHint=float,
nDig=(6,1),size=(60,-1),xmin=0.5, xmax=10.,OnLeave=lambda *arg,**kw:RefreshPeakGrid(None))
prmSizer.Add(cVal,0,WACV)
prmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' plus side'),0,WACV)
cVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['LaueFringe'],'fitPowerP',typeHint=float,
nDig=(6,1),size=(60,-1),xmin=0.5, xmax=10.,OnLeave=lambda *arg,**kw:RefreshPeakGrid(None))
prmSizer.Add(cVal,0,WACV)
prmVSizer.Add(prmSizer)
prmSizer = wx.BoxSizer(wx.HORIZONTAL)
prmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Show '),0,WACV)
ch = G2G.EnumSelector(G2frame.dataWindow,data['LaueFringe'],'Show',
['None','1','2','3','4','5','6'],list(range(7)),OnChange=RefreshPeakGrid)
prmSizer.Add(ch,0,WACV)
prmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' satellites'),0,WACV)
prmVSizer.Add(prmSizer)
topSizer.Add(prmVSizer,0,WACV)
mainSizer.Add(topSizer)
mainSizer.Add(reflGrid,1,wx.EXPAND,1)
G2frame.dataWindow.SetDataSize()
#RefreshPeakGrid(None)
################################################################################
##### Background
################################################################################
[docs]
def UpdateBackground(G2frame,data):
'''respond to selection of PWDR background data tree item.
'''
def OnBackFlagCopy(event):
'Copy background refonement flags to other similar histograms'
flag = data[0][1]
backDict = data[-1]
if backDict['nDebye']:
DBflags = []
for term in backDict['debyeTerms']:
DBflags.append(term[1::2])
if backDict['nPeaks']:
PKflags = []
for term in backDict['peaksList']:
PKflags.append(term[1::2])
FBflag = bool(backDict['background PWDR'][2])
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy bkg ref. flags from\n'+str(hst[5:])+' to...',
'Copy bkg flags', histList)
copyList = []
try:
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
copyList.append(histList[i])
finally:
dlg.Destroy()
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
backData = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Background'))
backData[0][1] = copy.copy(flag)
bkDict = backData[-1]
if bkDict['nDebye'] == backDict['nDebye']:
for i,term in enumerate(bkDict['debyeTerms']):
term[1::2] = copy.copy(DBflags[i])
if bkDict['nPeaks'] == backDict['nPeaks']:
for i,term in enumerate(bkDict['peaksList']):
term[1::2] = copy.copy(PKflags[i])
try:
backData[1]['background PWDR'][2] = FBflag
except:
backData[1]['background PWDR'] = ['',-1.,False]
def OnBackCopy(event):
'Copy background functions/values to other similar histograms'
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
copyList = []
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy bkg params from\n'+str(hst[5:])+' to...',
'Copy parameters', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
copyList.append(histList[i])
finally:
dlg.Destroy()
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
G2frame.GPXtree.SetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,Id,'Background'),copy.deepcopy(data))
CalcBack(Id)
def OnBackSave(event):
'Save background values to file'
pth = G2G.GetExportPath(G2frame)
dlg = wx.FileDialog(G2frame, 'Set name to save GSAS-II background parameters file', pth, '',
'background parameter files (*.pwdrbck)|*.pwdrbck',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
try:
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
# make sure extension is .pwdrbck
filename = os.path.splitext(filename)[0]+'.pwdrbck'
File = open(filename,'w')
File.write("#GSAS-II background parameter file; do not add/delete items!\n")
out_tmp = list()
for item in data[0]:
if isinstance(item, np.float64) or isinstance(item, float):
out_tmp.append(float(item))
else:
out_tmp.append(item)
File.write(str(out_tmp)+'\n')
for item in data[1]:
if item in ['nPeaks','background PWDR','nDebye'] or not len(data[1][item]):
File.write(item+':'+str(data[1][item])+'\n')
else:
File.write(item+':\n')
for term in data[1][item]:
File.write(str(term)+'\n')
File.close()
print ('Background parameters saved to: '+filename)
finally:
dlg.Destroy()
def OnBackLoad(event):
'load background values from file'
pth = G2G.GetImportPath(G2frame)
if not pth: pth = '.'
dlg = wx.FileDialog(G2frame, 'Choose GSAS-II background parameters file', pth, '',
'background parameter files (*.pwdrbck)|*.pwdrbck',wx.FD_OPEN)
try:
if dlg.ShowModal() == wx.ID_OK:
newback = [[],{}]
filename = dlg.GetPath()
File = open(filename,'r')
S = File.readline()
if S[0] == '#': #skip the heading
S = File.readline() #should contain the std. bck fxn
newback[0] = eval(S.strip())
S = File.readline()
while S and ':' in S:
item,vals = S.strip().split(':')
if item in ['nPeaks','nDebye']:
newback[1][item] = int(vals)
elif 'PWDR' in item:
newback[1][item] = eval(vals)
elif item in ['FixedPoints','debyeTerms','peaksList']:
newback[1][item] = []
S = File.readline()
while S and ':' not in S:
newback[1][item].append(eval(S.strip()))
S = File.readline()
else:
continue
S = File.readline()
File.close()
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId,'Background'),newback)
finally:
dlg.Destroy()
CalcBack(G2frame.PatternId)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
wx.CallLater(100,UpdateBackground,G2frame,newback)
def OnBkgFit(event):
'Fit background functions to fixed set of background points'
def SetInstParms(Inst):
dataType = Inst['Type'][0]
insVary = []
insNames = []
insVals = []
for parm in Inst:
insNames.append(parm)
insVals.append(Inst[parm][1])
if parm in ['U','V','W','X','Y','Z','SH/L','I(L2)/I(L1)','alpha','A','B','C',
'beta-0','beta-1','beta-q','sig-0','sig-1','sig-2','sig-q',] and Inst[parm][2]:
Inst[parm][2] = False
# insVary.append(parm)
instDict = dict(zip(insNames,insVals))
if 'E' not in dataType: #exclude EDX
instDict['X'] = max(instDict['X'],0.01)
instDict['Y'] = max(instDict['Y'],0.01)
if 'SH/L' in instDict:
instDict['SH/L'] = max(instDict['SH/L'],0.002)
return dataType,instDict,insVary
PatternId = G2frame.PatternId
controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
background = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Background'))
limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits'))[1]
inst,inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters'))
# sort the points for convenience and then separate them; extend the range if needed
if 'FixedPoints' not in background[1] or not len(background[1]['FixedPoints']):
msg = ("You have not defined any fixed background points. "+
"Use the Fixed Points/Add menu item to define points that will be fit."+
'\n\nSee the "Fitting the Starting Background using Fixed Points" tutorial for more details.')
print (msg)
G2frame.ErrorDialog('No points',msg)
return
background[1]['FixedPoints'] = sorted(background[1]['FixedPoints'],key=lambda pair:pair[0])
X = [x for x,y in background[1]['FixedPoints']]
Y = [y for x,y in background[1]['FixedPoints']]
if X[0] > limits[0]:
X = [limits[0]] + X
Y = [Y[0]] + Y
if X[-1] < limits[1]:
X += [limits[1]]
Y += [Y[-1]]
# interpolate the fixed points onto the grid of data points within limits
pwddata = G2frame.GPXtree.GetItemPyData(PatternId)[1]
xBeg = np.searchsorted(pwddata[0],limits[0])
xFin = np.searchsorted(pwddata[0],limits[1])
xdata = pwddata[0][xBeg:xFin]
ydata = si.interp1d(X,Y)(ma.getdata(xdata))
W = [1]*len(xdata)
Z = [0]*len(xdata)
bxye = GetFileBackground(G2frame,data,background,scale=False)[xBeg:xFin]
if not np.any(bxye):
bxye = None
# load instrument and background params
print (' NB: Any instrument parameter refinement flags will be cleared')
dataType,insDict,insVary = SetInstParms(inst)
bakType,bakDict,bakVary = G2pwd.SetBackgroundParms(background)
# how many background parameters are refined?
if len(bakVary)*1.5 > len(X):
msg = ("You are attempting to vary "+str(len(bakVary))+
" background terms with only "+str(len(X))+" background points"+
"\nAdd more points or reduce the number of terms")
print (msg)
G2frame.ErrorDialog('Too few points',msg)
return
wx.BeginBusyCursor()
try:
G2pwd.DoPeakFit('LSQ',[],background,limits,inst,inst2,
np.array((xdata,ydata,W,Z,Z,Z)),bxye,prevVaryList=bakVary,controls=controls)
finally:
wx.EndBusyCursor()
# compute the background values and plot them
parmDict = {}
bakType,bakDict,bakVary = G2pwd.SetBackgroundParms(background)
parmDict.update(bakDict)
parmDict.update(insDict)
# Note that this generates a MaskedArrayFutureWarning, but these items are not always masked
pwddata[3][xBeg:xFin] *= 0.
pwddata[5][xBeg:xFin] *= 0.
pwddata[4][xBeg:xFin] = G2pwd.getBackground('',parmDict,bakType,dataType,xdata,bxye)[0]
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
# show the updated background values
wx.CallLater(100,UpdateBackground,G2frame,data)
def OnBkgCh(event):
'Change in Background mode, display it'
wx.CallAfter(G2pwpl.PlotPatterns,G2frame,plotType='PWDR')
def OnBkgClear(event):
'Clear fixed points from background'
if 'FixedPoints' not in data[1]:
return
else:
data[1]['FixedPoints'] = []
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
def OnPeaksMove(event):
'Move a background peak'
if not data[1]['nPeaks']:
G2frame.ErrorDialog('Error','No peaks to move')
return
Peaks = {'peaks':[],'sigDict':{}}
for peak in data[1]['peaksList']:
Peaks['peaks'].append([peak[0],0,peak[2],0,peak[4],0,peak[6],0])
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Peak List'),Peaks)
def OnMakeRDF(event):
'Make a Radial Distribution Function from the background - useful for selecting Debye background positions'
dlg = RDFDialog(G2frame)
try:
if dlg.ShowModal() == wx.ID_OK:
RDFcontrols = dlg.GetSelection()
else:
return
finally:
dlg.Destroy()
PatternId = G2frame.PatternId
background = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Background'))
inst,inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters'))
limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits'))[1]
pwddata = G2frame.GPXtree.GetItemPyData(PatternId)[1]
xmin = np.searchsorted(pwddata[0,:],limits[0])
xmax = np.searchsorted(pwddata[0,:],limits[1])
if pwddata[0,xmin] > 0:
auxPlot = G2pwd.MakeRDF(RDFcontrols,background,inst,pwddata[:,xmin:xmax])
for plot in auxPlot:
XY = np.array(plot[:2])
if 'D(R)' in plot[2]:
xlabel = r'$R, \AA$'
ylabel = r'$D(R), arb. units$'
else:
xlabel = r'$Q,\AA$'+superMinusOne
ylabel = r'$I(Q)$'
G2plt.PlotXY(G2frame,[XY,],Title=plot[2],labelX=xlabel,labelY=ylabel,lines=True)
else:
G2frame.ErrorDialog('RDF calculation failure','Negative 2-thetas/TOF; choose better limits')
def BackSizer():
def OnNewType(event):
data[0][0] = bakType.GetValue()
def OnBakRef(event):
data[0][1] = bakRef.GetValue()
def OnBakTerms(event):
data[0][2] = int(bakTerms.GetValue())
M = len(data[0])
N = data[0][2]+3
item = data[0]
if N > M: #add terms
for i in range(M,N):
item.append(0.0)
elif N < M: #delete terms
for i in range(N,M):
del(item[-1])
G2frame.GPXtree.SetItemPyData(BackId,data)
wx.CallLater(100,UpdateBackground,G2frame,data)
def AfterChange(invalid,value,tc):
if invalid: return
CalcBack(G2frame.PatternId)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
backSizer = wx.BoxSizer(wx.VERTICAL)
topSizer = wx.BoxSizer(wx.HORIZONTAL)
topSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Background function: '),0,WACV)
bakType = wx.ComboBox(G2frame.dataWindow,value=data[0][0],
choices=Choices,style=wx.CB_READONLY|wx.CB_DROPDOWN)
bakType.Bind(wx.EVT_COMBOBOX, OnNewType)
topSizer.Add(bakType)
topSizer.Add((5,0),0)
bakRef = wx.CheckBox(G2frame.dataWindow,label=' Refine?')
bakRef.SetValue(bool(data[0][1]))
bakRef.Bind(wx.EVT_CHECKBOX, OnBakRef)
topSizer.Add(bakRef,0,WACV)
backSizer.Add(topSizer)
topSizer = wx.BoxSizer(wx.HORIZONTAL)
topSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Number of coeff.: '),0,WACV)
bakTerms = wx.ComboBox(G2frame.dataWindow,-1,value=str(data[0][2]),choices=[str(i+1) for i in range(36)],
style=wx.CB_READONLY|wx.CB_DROPDOWN)
bakTerms.Bind(wx.EVT_COMBOBOX,OnBakTerms)
topSizer.Add(bakTerms,0,WACV)
topSizer.Add((5,0),0)
backSizer.Add(topSizer)
backSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Background coefficients:'),0)
bakSizer = wx.FlexGridSizer(0,5,5,5)
for i,value in enumerate(data[0][3:]):
bakVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data[0],i+3,nDig=(10,4),OnLeave=AfterChange)
bakSizer.Add(bakVal,0,WACV)
backSizer.Add(bakSizer)
return backSizer
def DebyeSizer():
def OnDebTerms(event):
data[1]['nDebye'] = int(debTerms.GetValue())
M = len(data[1]['debyeTerms'])
N = data[1]['nDebye']
if N > M: #add terms
for i in range(M,N):
data[1]['debyeTerms'].append([1.0,False,1.0,False,0.010,False])
elif N < M: #delete terms
for i in range(N,M):
del(data[1]['debyeTerms'][-1])
if N == 0:
CalcBack(G2frame.PatternId)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
wx.CallAfter(UpdateBackground,G2frame,data)
def KeyEditPeakGrid(event):
colList = debyeGrid.GetSelectedCols()
if event.GetKeyCode() == wx.WXK_RETURN:
event.Skip(True)
elif event.GetKeyCode() == wx.WXK_CONTROL:
event.Skip(True)
elif event.GetKeyCode() == wx.WXK_SHIFT:
event.Skip(True)
elif colList:
debyeGrid.ClearSelection()
key = event.GetKeyCode()
for col in colList:
if debyeTable.GetTypeName(0,col) == wg.GRID_VALUE_BOOL:
if key == 89: #'Y'
for row in range(debyeGrid.GetNumberRows()): data[1]['debyeTerms'][row][col]=True
elif key == 78: #'N'
for row in range(debyeGrid.GetNumberRows()): data[1]['debyeTerms'][row][col]=False
def OnCellChange(event):
CalcBack(G2frame.PatternId)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
debSizer = wx.BoxSizer(wx.VERTICAL)
topSizer = wx.BoxSizer(wx.HORIZONTAL)
topSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Debye scattering: '),0,WACV)
topSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Number of terms: '),0,WACV)
debTerms = wx.ComboBox(G2frame.dataWindow,-1,value=str(data[1]['nDebye']),choices=[str(i) for i in range(21)],
style=wx.CB_READONLY|wx.CB_DROPDOWN)
debTerms.Bind(wx.EVT_COMBOBOX,OnDebTerms)
topSizer.Add(debTerms,0,WACV)
topSizer.Add((5,0),0)
debSizer.Add(topSizer)
if data[1]['nDebye']:
debSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Debye diffuse terms:'),0)
rowLabels = []
for i in range(len(data[1]['debyeTerms'])): rowLabels.append(str(i))
colLabels = ['A','refine','R','refine','U','refine']
Types = [wg.GRID_VALUE_FLOAT+':10,2',wg.GRID_VALUE_BOOL,
wg.GRID_VALUE_FLOAT+':10,3',wg.GRID_VALUE_BOOL,
wg.GRID_VALUE_FLOAT+':10,5',wg.GRID_VALUE_BOOL]
debyeTable = G2G.Table(data[1]['debyeTerms'],rowLabels=rowLabels,colLabels=colLabels,types=Types)
debyeGrid = G2G.GSGrid(parent=G2frame.dataWindow)
debyeGrid.SetTable(debyeTable, True)
debyeGrid.Bind(wx.EVT_KEY_DOWN, KeyEditPeakGrid)
debyeGrid.Bind(wg.EVT_GRID_CELL_CHANGED,OnCellChange)
debyeGrid.AutoSizeColumns(False)
debSizer.Add(debyeGrid)
return debSizer
def PeaksSizer():
def OnPeaks(event):
'Respond to a change in the number of background peaks'
data[1]['nPeaks'] = int(peaks.GetValue())
M = len(data[1]['peaksList'])
N = data[1]['nPeaks']
if N > M: #add terms
for i in range(M,N):
data[1]['peaksList'].append([1.0,False,1.0,False,0.10,False,0.10,False])
elif N < M: #delete terms
for i in range(N,M):
del(data[1]['peaksList'][-1])
if N == 0:
CalcBack(G2frame.PatternId)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
# this callback is crashing wx when there is an open
# peaksGrid cell editor, at least on Mac. Code below
# should fix this, but it does not.
# https://stackoverflow.com/questions/64082199/wxpython-grid-destroy-with-open-celleditor-crashes-python-even-with-disablece
if peaksGrid and peaksGrid.IsCellEditControlEnabled():
# complete any grid edits in progress
#print('closing')
peaksGrid.HideCellEditControl()
peaksGrid.DisableCellEditControl()
#wx.CallLater(100,peaksGrid.Destroy) # crashes python
wx.CallAfter(UpdateBackground,G2frame,data)
def KeyEditPeakGrid(event):
colList = peaksGrid.GetSelectedCols()
if event.GetKeyCode() == wx.WXK_RETURN:
event.Skip(True)
elif event.GetKeyCode() == wx.WXK_CONTROL:
event.Skip(True)
elif event.GetKeyCode() == wx.WXK_SHIFT:
event.Skip(True)
elif colList:
peaksGrid.ClearSelection()
key = event.GetKeyCode()
for col in colList:
if peaksTable.GetTypeName(0,col) == wg.GRID_VALUE_BOOL:
if key == 89: #'Y'
for row in range(peaksGrid.GetNumberRows()): data[1]['peaksList'][row][col]=True
elif key == 78: #'N'
for row in range(peaksGrid.GetNumberRows()): data[1]['peaksList'][row][col]=False
def OnCellChange(event):
CalcBack(G2frame.PatternId)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
peaksSizer = wx.BoxSizer(wx.VERTICAL)
topSizer = wx.BoxSizer(wx.HORIZONTAL)
topSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Peaks in background: '),0,WACV)
topSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Number of peaks: '),0,WACV)
peaks = wx.ComboBox(G2frame.dataWindow,-1,value=str(data[1]['nPeaks']),choices=[str(i) for i in range(30)],
style=wx.CB_READONLY|wx.CB_DROPDOWN)
peaks.Bind(wx.EVT_COMBOBOX,OnPeaks)
topSizer.Add(peaks,0,WACV)
topSizer.Add((5,0),0)
peaksSizer.Add(topSizer)
G2frame.dataWindow.currentGrids = []
peaksGrid = None
if data[1]['nPeaks']:
peaksSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Peak list:'),0)
rowLabels = []
for i in range(len(data[1]['peaksList'])): rowLabels.append(str(i))
colLabels = ['pos','refine','int','refine','sig','refine','gam','refine']
Types = [wg.GRID_VALUE_FLOAT+':10,2',wg.GRID_VALUE_BOOL,
wg.GRID_VALUE_FLOAT+':12,5,g',wg.GRID_VALUE_BOOL,
wg.GRID_VALUE_FLOAT+':12,3,g',wg.GRID_VALUE_BOOL,
wg.GRID_VALUE_FLOAT+':12,3,g',wg.GRID_VALUE_BOOL]
peaksTable = G2G.Table(data[1]['peaksList'],rowLabels=rowLabels,colLabels=colLabels,types=Types)
peaksGrid = G2G.GSGrid(parent=G2frame.dataWindow)
peaksGrid.SetRowLabelSize(45)
peaksGrid.SetTable(peaksTable, True)
peaksGrid.Bind(wx.EVT_KEY_DOWN, KeyEditPeakGrid)
peaksGrid.Bind(wg.EVT_GRID_CELL_CHANGED,OnCellChange)
peaksGrid.AutoSizeColumns(False)
peaksSizer.Add(peaksGrid,0,wx.EXPAND)
return peaksSizer
def BackFileSizer():
def OnBackPWDR(event):
data[1]['background PWDR'][0] = back.GetValue()
if len(data[1]['background PWDR'][0]):
curHist = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,data[1]['background PWDR'][0])
if not Id:
G2G.G2MessageBox(G2frame,'Histogram not found -- how did this happen?','Missing histogram')
back.SetValue('')
data[1]['background PWDR'][0] = back.GetValue()
return
bkgHist = G2frame.GPXtree.GetItemPyData(Id)
if len(bkgHist[1][0]) != len(curHist[1][0]):
G2G.G2MessageBox(G2frame,'Histogram have different lengths','Mismatched histograms')
back.SetValue('')
data[1]['background PWDR'][0] = back.GetValue()
return
else:
data[1]['background PWDR'][2] = False
CalcBack()
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
wx.CallLater(100,UpdateBackground,G2frame,data)
def AfterChange(invalid,value,tc):
if invalid: return
CalcBack()
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
def OnBackFit(event):
data[1]['background PWDR'][2] = not data[1]['background PWDR'][2]
fileSizer = wx.BoxSizer(wx.VERTICAL)
fileSizer.Add((-1,5))
backSizer = wx.BoxSizer(wx.HORIZONTAL)
btn = wx.Button(G2frame.dataWindow, wx.ID_ANY,'Fit to fixed bkg')
backSizer.Add(btn,0,wx.RIGHT,3)
btn.Enable(len(data[1].get('FixedPoints',[])) > 5)
btn.Bind(wx.EVT_BUTTON,OnBkgFit)
btn = wx.Button(G2frame.dataWindow, wx.ID_ANY,'Compute auto background')
backSizer.Add(btn,0,wx.RIGHT,3)
btn.Bind(wx.EVT_BUTTON,onAutoBack)
btn = wx.Button(G2frame.dataWindow, wx.ID_ANY,'Copy auto background')
backSizer.Add(btn,0,wx.RIGHT,3)
data[1]['autoPrms'] = data[1].get('autoPrms',{})
btn.Enable(bool(data[1]['autoPrms'].get('Mode')))
btn.Bind(wx.EVT_BUTTON,copyAutoBack)
fileSizer.Add(backSizer)
fileSizer.Add((-1,5))
fileSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Fixed background histogram (for point-by-point subtraction):'),0)
if 'background PWDR' not in data[1]:
data[1]['background PWDR'] = ['',-1.,False]
backSizer = wx.BoxSizer(wx.HORIZONTAL)
Choices = ['',]+G2gd.GetGPXtreeDataNames(G2frame,['PWDR',])
Source = G2frame.GPXtree.GetItemText(G2frame.PatternId)
Choices.pop(Choices.index(Source))
back = wx.ComboBox(parent=G2frame.dataWindow,value=data[1]['background PWDR'][0],choices=Choices,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
back.Bind(wx.EVT_COMBOBOX,OnBackPWDR)
back.SetMaxSize((450,-1))
backSizer.Add(back)
backSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' multiplier'),0,WACV)
backMult = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data[1]['background PWDR'],1,nDig=(10,3),OnLeave=AfterChange)
backSizer.Add(backMult,0,WACV)
if len(data[1]['background PWDR'][0]):
backFit = wx.CheckBox(G2frame.dataWindow,label=' Refine?')
backFit.SetValue(data[1]['background PWDR'][2])
backFit.Bind(wx.EVT_CHECKBOX, OnBackFit)
backSizer.Add(backFit,0,WACV)
fileSizer.Add(backSizer)
return fileSizer
def onAutoBack(event):
'''Open a window for auto background computation
'''
bkgdict = data[1]
xydata = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[1]
autoBackground(G2frame)
if bkgdict['autoPrms']['Mode'] == 'fixed':
xydata[4] = G2pwd.autoBkgCalc(bkgdict,xydata[1])
addAutoBack(G2frame,data,xydata)
wx.CallAfter(UpdateBackground,G2frame,data)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
elif bkgdict['autoPrms']['Mode'] == 'fit':
xydata[4] = G2pwd.autoBkgCalc(bkgdict,xydata[1])
npts = len(xydata[0])
bkgdict['FixedPoints'] = [i for i in zip(
xydata[0].data[::npts//100],
xydata[4].data[::npts//100])]
OnBkgFit(event)
else:
wx.CallAfter(UpdateBackground,G2frame,data)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
def copyAutoBack(event):
'''reproduce the auto background computation on selected
other histograms
'''
savePatternId = G2frame.PatternId
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
autoBkgDict = data[1].get('autoPrms')
if not autoBkgDict.get('Mode'):
G2frame.ErrorDialog('No auto bkg setting','This is unexpected, no auto bkg parms for histogram '+hst,G2frame)
return
elif autoBkgDict['Mode'] == 'fit':
txt = 'set fixed points from auto bkg calc'
else:
txt = 'use auto bkg calc to define Fixed Bkg histogram'
histList = [i for i in GetHistsLikeSelected(G2frame)
if 'Autobkg for' not in i]
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
dlg = G2G.G2MultiChoiceDialog(G2frame,
f'Select histogram(s) to {txt} based on {hst}',
'Compute auto bkg for...', histList)
try:
copyList = []
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
copyList.append(histList[i])
finally:
dlg.Destroy()
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
G2frame.PatternId = Id
xydata = G2frame.GPXtree.GetItemPyData(Id)[1]
G2frame.GPXtree.SetItemPyData
bkgId = G2gd.GetGPXtreeItemId(G2frame,Id,'Background')
G2frame.GPXtree.SetItemPyData(bkgId,copy.deepcopy(data))
itemData = G2frame.GPXtree.GetItemPyData(bkgId)
if autoBkgDict['Mode'] == 'fixed':
xydata[4] = G2pwd.autoBkgCalc(itemData[1],xydata[1])
addAutoBack(G2frame,itemData,xydata)
elif autoBkgDict['Mode'] == 'fit':
xydata[4] = G2pwd.autoBkgCalc(itemData[1],xydata[1])
npts = len(xydata[0])
itemData[1]['FixedPoints'] = [i for i in zip(
xydata[0].data[::npts//100],
xydata[4].data[::npts//100])]
OnBkgFit(event)
G2frame.PatternId = savePatternId
wx.CallAfter(UpdateBackground,G2frame,data)
def CalcBack(PatternId=G2frame.PatternId):
limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits'))[1]
inst,inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters'))
backData = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Background'))
dataType = inst['Type'][0]
insDict = {inskey:inst[inskey][1] for inskey in inst}
parmDict = {}
bakType,bakDict,bakVary = G2pwd.SetBackgroundParms(data)
parmDict.update(bakDict)
parmDict.update(insDict)
pwddata = G2frame.GPXtree.GetItemPyData(PatternId)
xBeg = np.searchsorted(pwddata[1][0],limits[0])
xFin = np.searchsorted(pwddata[1][0],limits[1])
fixBack = GetFileBackground(G2frame,pwddata[1],backData,scale=False)
pwddata[1][4][xBeg:xFin] = G2pwd.getBackground('',parmDict,bakType,dataType,pwddata[1][0][xBeg:xFin],fixBack[xBeg:xFin])[0]
# UpdateBackground execution starts here
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.PeakMenu) # needed below
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.BackMenu)
if len(data) < 2: #add Debye diffuse & peaks scattering here
data.append({'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[],'background PWDR':['',1.0,False]})
if 'nPeaks' not in data[1]:
data[1].update({'nPeaks':0,'peaksList':[],'background PWDR':['',1.0,False]})
if 'background PWDR' not in data[1]:
data[1].update({'background PWDR':['',1.0,False]})
elif len(data[1]['background PWDR']) < 3:
data[1]['background PWDR'].append(False)
G2frame.dataWindow.currentGrids = []
G2frame.Bind(wx.EVT_MENU,OnBackCopy,id=G2G.wxID_BACKCOPY)
G2frame.Bind(wx.EVT_MENU,OnBackFlagCopy,id=G2G.wxID_BACKFLAGCOPY)
G2frame.Bind(wx.EVT_MENU,OnBackSave,id=G2G.wxID_BACKSAVE)
G2frame.Bind(wx.EVT_MENU,OnBackLoad,id=G2G.wxID_BACKLOAD)
G2frame.Bind(wx.EVT_MENU,OnPeaksMove,id=G2G.wxID_BACKPEAKSMOVE)
G2frame.Bind(wx.EVT_MENU,OnMakeRDF,id=G2G.wxID_MAKEBACKRDF)
for k in 'Add', 'Move', 'Delete':
G2frame.Bind(wx.EVT_MENU,OnBkgCh,id=G2frame.dataWindow.wxID_BackPts[k])
G2frame.Bind(wx.EVT_MENU,OnBkgFit,id=G2frame.dataWindow.wxID_BackPts['Fit'])
G2frame.Bind(wx.EVT_MENU,OnBkgClear,id=G2frame.dataWindow.wxID_BackPts['Clear'])
BackId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Background')
Choices = ['chebyschev','chebyschev-1','cosine','Q^2 power series','Q^-2 power series','lin interpolate','inv interpolate','log interpolate']
G2frame.dataWindow.ClearData()
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,label='Background used in refinement'),0,WACV)
# add help button to bring up help web page - at right side of window
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add(BackSizer())
mainSizer.Add((0,5),0)
mainSizer.Add(DebyeSizer())
mainSizer.Add((0,5),0)
mainSizer.Add(PeaksSizer(),0,wx.EXPAND)
mainSizer.Add((0,5),0)
mainSizer.Add(BackFileSizer())
G2frame.dataWindow.SetDataSize()
[docs]
def addAutoBack(G2frame,data,xydata):
'''Create a new histogram for the computed auto background and place
as the fixed background histogram
'''
bkgHistName = 'PWDR Autobkg for '+G2frame.GPXtree.GetItemText(G2frame.PatternId)[5:]
# if histogram exists we should probably reuse it, but for now, just create a new one
bkgHistName = G2obj.MakeUniqueLabel(bkgHistName,G2frame.GetHistogramNames('PWDR'))
Ymin = min(xydata[4])
Ymax = max(xydata[4])
d = copy.deepcopy(G2frame.GPXtree.GetItemPyData(G2frame.PatternId))
d[0] = {'wtFactor': 1.0, 'Dummy': False,
'ranId': ran.randint(0, sys.maxsize),
'Offset': [0.0, 0.0], 'delOffset': 0.02*Ymax,
'refOffset': -0.1*Ymax, 'refDelt': 0.1*Ymax,
'Yminmax': [Ymin, Ymax]}
d[1][1] = xydata[4]
d[1][2] = np.ones_like(xydata[4])
d[1][3] = np.zeros_like(xydata[4])
d[1][4] = np.zeros_like(xydata[4])
d[1][5] = np.zeros_like(xydata[4])
NewId = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=bkgHistName)
G2frame.GPXtree.SetItemPyData(NewId,d)
item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.PatternId)
while item:
nam = G2frame.GPXtree.GetItemText(item)
if nam == 'Comments':
d = [' # background generated with Autobkg']
elif nam == 'Background':
d = [['chebyschev-1',True,3,1.0,0.0,0.0],
{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[],
'background PWDR':['',1.0,False],'FixedPoints':[]}]
elif nam == 'Peak List':
d = {'sigDict':{},'peaks':[]}
elif nam == 'Index Peak List':
d = [[], []]
elif nam == 'Unit Cells List':
d = []
elif nam == 'Reflection Lists':
d = {}
else:
d = copy.deepcopy(G2frame.GPXtree.GetItemPyData(item))
G2frame.GPXtree.SetItemPyData(
G2frame.GPXtree.AppendItem(parent=NewId,text=nam),d)
item, cookie = G2frame.GPXtree.GetNextChild(G2frame.PatternId, cookie)
bId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId,'Background')
data = G2frame.GPXtree.GetItemPyData(bId)
# set fixed bkg & turn off computed background
data[1]['background PWDR'] = [bkgHistName, 1.0, False]
data[0][1] = False
data[0][3:] = data[0][2]*[0.]
for p in data[1]['peaksList']:
p[2] = 0.
p[1::2] = 4*[False]
for p in data[1]['debyeTerms']:
p[0] = 0
p[1::2] = 3*[False]
G2frame.GetUsedHistogramsAndPhasesfromTree() # reindex
# Autobackground Dialog
[docs]
class autoBackground(wx.Dialog):
'''Create a file selection widget for setting background with
pybaselines, as requested by James Feng.
:param wx.Frame G2frame: reference to the main GSAS-II frame.
'''
def __init__(self,G2frame,*args,**kwargs):
self.G2frame = G2frame
bId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId,'Background')
data = G2frame.GPXtree.GetItemPyData(bId)
self.bkgdict = data[1]
self.xydata = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[1]
npts = len(self.xydata[0])
# add auto bkg to background prms dict
self.bkgdict['autoPrms'] = self.bkgdict.get('autoPrms',{})
self.bkgdict['autoPrms']['opt'] = self.bkgdict['autoPrms'].get('opt',0)
logLam = min(10,float(int(10*np.log10(npts)**1.5)-9.5)/10.)
self.bkgdict['autoPrms']['logLam'] = self.bkgdict['autoPrms'].get('logLam',logLam)
self.bkgdict['autoPrms']['Mode'] = None
maxLam = min(15.,1.*int(3*self.bkgdict['autoPrms']['logLam']+0.9))
# save starting point info
self.startingBackground = copy.deepcopy(self.xydata[4])
# start process
wx.Dialog.__init__(self, parent=G2frame,
style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER)
self.CenterOnParent()
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(wx.StaticText(self,label=' Compute autobackground'),0)
choices = ['arpls','iarpls']
subSiz = wx.BoxSizer(wx.HORIZONTAL)
subSiz.Add(wx.StaticText(self,label='Computation option'))
for w in G2G.G2RadioButtons(self,self.bkgdict['autoPrms'],'opt',choices,
OnChange=self._calcBkg):
subSiz.Add(w,0,wx.ALIGN_CENTER_VERTICAL,0)
mainSizer.Add(subSiz)
siz = G2G.G2SliderWidget(self,self.bkgdict['autoPrms'],
'logLam','log(Lambda)',
1.,maxLam,100,self._calcBkg)
mainSizer.Add(siz)
subSiz = wx.BoxSizer(wx.HORIZONTAL)
subSiz.Add((-1,-1),1,wx.EXPAND,1)
btn = wx.Button(self, wx.ID_CLOSE, label='Set Fixed\nPoints && Fit')
btn.Bind(wx.EVT_BUTTON,lambda event: self.EndModal(wx.ID_CLOSE))
subSiz.Add(btn)
subSiz.Add((5,-1))
btn = wx.Button(self, wx.ID_OK, label='Define Fixed\nBkg histogram')
btn.Bind(wx.EVT_BUTTON,lambda event: self.EndModal(wx.ID_OK))
subSiz.Add(btn)
btn = wx.Button(self, wx.ID_CANCEL)
subSiz.Add((5,-1))
subSiz.Add(btn,0,wx.CENTER)
subSiz.Add((-1,-1),1,wx.EXPAND,1)
mainSizer.Add((-1,5))
mainSizer.Add(subSiz,0,wx.EXPAND)
mainSizer.Add((-1,5))
self.SetSizer(mainSizer)
mainSizer.Fit(self)
self._calcBkg()
res = self.ShowModal()
if res == wx.ID_CLOSE:
self.bkgdict['autoPrms']['Mode'] = 'fit'
elif res == wx.ID_OK:
self.bkgdict['autoPrms']['Mode'] = 'fixed'
else:
# restore the background to the starting values
self.xydata[4] = self.startingBackground
self.bkgdict['autoPrms']['Mode'] = None
def _calcBkg(self,event=None):
'''respond to a change in the background parameters by recomputing
the auto background
'''
self.xydata[4] = G2pwd.autoBkgCalc(self.bkgdict,self.xydata[1].data)
G2pwpl.PlotPatterns(self.G2frame,plotType='PWDR')
################################################################################
##### Limits
################################################################################
[docs]
def UpdateLimitsGrid(G2frame, data,datatype):
'''respond to selection of PWDR Limits data tree item.
Allows setting of limits and excluded regions in a PWDR data set
'''
def AfterChange(invalid,value,tc):
if invalid: return
datatype = G2frame.GPXtree.GetItemText(G2frame.PatternId)[:4]
wx.CallAfter(G2pwpl.PlotPatterns,G2frame,newPlot=False,plotType=datatype) #unfortunately this resets the plot width
def LimitSizer():
limits = wx.FlexGridSizer(0,3,0,5)
labels = ['Tmin','Tmax']
for i in [0,1]:
limits.Add(wx.StaticText(G2frame.dataWindow,
label=' Original {} {:.4f}'.format(labels[i],data[0][i])),0,WACV)
limits.Add(wx.StaticText(G2frame.dataWindow,label=' New: '),0,WACV)
limits.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data[1],i, \
xmin=data[0][0],xmax=data[0][1],nDig=(10,4),typeHint=float,OnLeave=AfterChange))
return limits
def ExclSizer():
def OnDelExcl(event):
Obj = event.GetEventObject()
item = Indx[Obj.GetId()]
del(data[item+2])
G2pwpl.PlotPatterns(G2frame,newPlot=False,plotType=datatype)
wx.CallAfter(UpdateLimitsGrid,G2frame,data,datatype)
Indx = {}
excl = wx.FlexGridSizer(0,3,0,5)
excl.Add(wx.StaticText(G2frame.dataWindow,label=' From: '),0,WACV)
excl.Add(wx.StaticText(G2frame.dataWindow,label=' To: '),0,WACV)
excl.Add(wx.StaticText(G2frame.dataWindow,label=' Delete?: '),0,WACV)
for Id,item in enumerate(data[2:]):
for i in [0,1]:
excl.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,item,i, \
xmin=data[0][0],xmax=data[0][1],nDig=(10,4),typeHint=float,OnLeave=AfterChange))
delExcl = wx.CheckBox(G2frame.dataWindow,label='')
Indx[delExcl.GetId()] = Id
delExcl.Bind(wx.EVT_CHECKBOX,OnDelExcl)
excl.Add(delExcl,0,WACV)
return excl
def onSetLimExcl(event):
txt = event.EventObject.FindItemById(event.GetId()).GetItemLabel() # gets menu command text
if 'lower' in txt:
G2frame.ifSetLimitsMode = 1
G2frame.CancelSetLimitsMode.Enable(True)
elif 'upper' in txt:
G2frame.ifSetLimitsMode = 2
G2frame.CancelSetLimitsMode.Enable(True)
elif 'excl' in txt:
G2frame.ifSetLimitsMode = 3
G2frame.CancelSetLimitsMode.Enable(True)
else:
G2frame.ifSetLimitsMode = 0
G2frame.CancelSetLimitsMode.Enable(False)
G2frame.plotFrame.Raise()
G2pwpl.PlotPatterns(G2frame,newPlot=False,plotType=datatype)
def OnLimitCopy(event):
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy limits from\n'+str(hst[5:])+' to...',
'Copy limits', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
item = histList[i]
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
G2frame.GPXtree.SetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,Id,'Limits'),copy.deepcopy(data))
finally:
dlg.Destroy()
def Draw():
G2frame.dataWindow.ClearData()
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,label=' Data range to be used in fits'),0,WACV)
# add help button to bring up help web page - at right side of window
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add((5,5))
mainSizer.Add(LimitSizer())
if len(data)>2:
mainSizer.Add((0,5),0)
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Excluded regions:'))
mainSizer.Add(ExclSizer())
G2frame.dataWindow.SetDataSize()
# start of UpdateLimitsGrid
G2frame.ifSetLimitsMode = 0
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.PeakMenu) # needed below
if 'P' in datatype: #powder data menu commands
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.LimitMenu)
G2frame.CancelSetLimitsMode.Enable(False)
G2frame.Bind(wx.EVT_MENU,OnLimitCopy,id=G2G.wxID_LIMITCOPY)
for n in (G2G.wxID_ADDEXCLREGION, G2G.wxID_SETLOWLIMIT,
G2G.wxID_SETTOPLIMIT, G2G.wxID_STOPSETLIMIT):
G2frame.Bind(wx.EVT_MENU,onSetLimExcl,id=n)
elif 'A' in datatype or 'R' in datatype: #SASD & REFD data menu commands
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.SASDLimitMenu)
G2frame.CancelSetLimitsMode.Enable(False)
G2frame.Bind(wx.EVT_MENU,OnLimitCopy,id=G2G.wxID_SASDLIMITCOPY)
Draw()
################################################################################
##### Instrument parameters
################################################################################
[docs]
def UpdateInstrumentGrid(G2frame,data):
'''respond to selection of PWDR/SASD/REFD/HKLF Instrument Parameters
data tree item.
'''
if 'Bank' not in data: #get it from name; absent for default parms selection
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
if 'Bank' in hst:
bank = int(hst.split('Bank')[1].split('_')[0])
data['Bank'] = [bank,bank,0]
else:
data['Bank'] = [1,1,0]
def keycheck(keys):
good = []
for key in keys:
if key in ['Type','Bank','U','V','W','X','Y','Z','SH/L','I(L2)/I(L1)','alpha','A','B','C',
'beta-0','beta-1','beta-q','sig-0','sig-1','sig-2','sig-q','Polariz.','alpha-0','alpha-1',
'Lam','Azimuth','2-theta','fltPath','difC','difA','difB','Zero','Lam1','Lam2','XE','YE','ZE','WE']:
good.append(key)
return good
def updateData(inst,ref):
Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,
G2frame.PatternId,'Instrument Parameters'))[0]
for item in Data:
try:
Data[item] = [Data[item][0],inst[item],ref[item]]
except KeyError:
try:
Data[item] = [Data[item][0],inst[item]]
except KeyError:
pass #skip 'Polariz.' for N-data
def RefreshInstrumentGrid(event,doAnyway=False):
if doAnyway or event.GetRow() == 1:
peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Peak List'))
newpeaks = []
for peak in peaks['peaks']:
newpeaks.append(G2mth.setPeakparms(data,Inst2,peak[0],peak[2]))
peaks['peaks'] = newpeaks
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Peak List'),peaks)
def OnCalibrate(event):
Pattern = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)
xye = ma.array(ma.getdata(Pattern[1]))
cw = np.diff(xye[0])
fitPeaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Peak List'))
IndexPeaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Index Peak List'))
Sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Sample Parameters'))
if not len(IndexPeaks[0]):
G2frame.ErrorDialog('Cannot calibrate','Index Peak List empty')
return
if not np.any(IndexPeaks[1]):
G2frame.ErrorDialog('Cannot calibrate','Peak positions not refined')
return False
Ok = False
for peak in IndexPeaks[0]:
if peak[2] and peak[3]:
Ok = True
if not Ok:
G2frame.ErrorDialog('Cannot calibrate','Index Peak List not indexed')
return
if G2pwd.DoCalibInst(IndexPeaks,fitPeaks,data,Sample):
UpdateInstrumentGrid(G2frame,data)
G2plt.PlotPeakWidths(G2frame)
else:
G2frame.ErrorDialog('Cannot calibrate','Nothing selected for refinement or refinement failed')
const = 0.0
if data['Type'][0][2] in ['A','B','C']:
const = 0.18/(np.pi*Sample['Gonio. radius'])
XY = []
Sigs = []
for ip,peak in enumerate(IndexPeaks[0]):
calcPos = G2lat.Dsp2pos(data,peak[-1])
shft = 0.0
if peak[2] and peak[3]:
binwid = cw[np.searchsorted(xye[0],peak[0])]
if const:
if 'Debye' in Sample['Type']:
shft -= const*(Sample['DisplaceX'][0]*npcosd(calcPos)+Sample['DisplaceY'][0]*npsind(calcPos))
else:
shft -= 2.0*const*Sample['Shift'][0]*npcosd(calcPos/2.0)
XY.append([peak[-1],peak[0]-shft,binwid])
Sigs.append(IndexPeaks[1][ip])
if len(XY):
XY = np.array(XY)
G2plt.PlotCalib(G2frame,data,XY,Sigs,newPlot=True)
def OnLoad(event):
'''Loads instrument parameters from a G2 .instprm file
in response to the Instrument Parameters-Operations/Load Profile menu
If instprm file has multiple banks each with header #Bank n: ..., this
finds matching bank no. to load - rejects nonmatches.
Note uses ReadPowderInstprm (GSASIIdataGUI.py) to read .instprm fil
'''
def GetDefaultParms(rd):
'''Solicits from user a default set of parameters & returns Inst parm dict
param: rd: importer data structure
returns: dict: Instrument parameter dictionary
'''
import defaultIparms as dI
sind = lambda x: math.sin(x*math.pi/180.)
tand = lambda x: math.tan(x*math.pi/180.)
while True: # loop until we get a choice
choices = []
head = 'Select from default instrument parameters'
for l in dI.defaultIparm_lbl:
choices.append('Defaults for '+l)
res = G2G.BlockSelector(choices,ParentFrame=G2frame,title=head,
header='Select default inst parms',useCancel=True)
if res is None: return None
if 'Generic TOF' in choices[res]:
dlg = G2G.MultiDataDialog(G2frame,title='Generic TOF detector bank',
prompts=['Total FP','2-theta',],values=[25.0,150.,],
limits=[[6.,200.],[5.,175.],],formats=['%6.2f','%6.1f',])
if dlg.ShowModal() == wx.ID_OK: #strictly empirical approx.
FP,tth = dlg.GetValues()
difC = 505.632*FP*sind(tth/2.)
sig1 = 50.+2.5e-6*(difC/tand(tth/2.))**2
bet1 = .00226+7.76e+11/difC**4
Inst = G2frame.ReadPowderInstprm(dI.defaultIparms[res],bank,rd)
Inst[0]['difC'] = [difC,difC,0]
Inst[0]['sig-1'] = [sig1,sig1,0]
Inst[0]['beta-1'] = [bet1,bet1,0]
return Inst #this is [Inst1,Inst2] a pair of dicts
dlg.Destroy()
else:
inst1,inst2 = G2frame.ReadPowderInstprm(dI.defaultIparms[res],bank,rd)
return [inst1,inst2]
if 'lab data' in choices[res]:
rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False],
'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]})
else:
rd.Sample.update({'Type':'Debye-Scherrer','Absorption':[0.,False],'DisplaceX':[0.,False],
'DisplaceY':[0.,False]})
data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,
G2frame.PatternId,'Instrument Parameters'))[0]
bank = data['Bank'][0]
pth = G2G.GetImportPath(G2frame)
if not pth: pth = '.'
dlg = wx.FileDialog(G2frame, 'Choose GSAS-II instrument parameters file', pth, '',
'instrument parameter files (*.instprm)|*.instprm',wx.FD_OPEN)
try:
if dlg.ShowModal() == wx.ID_OK:
Found = False
filename = dlg.GetPath()
try:
File = open(dlg.GetPath(),'r')
instLines = File.readlines()
File.close()
rd = G2obj.ImportPowderData('Dummy')
rd.Sample = G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(
G2frame,G2frame.PatternId,'Sample Parameters'))
instvals = G2frame.ReadPowderInstprm(instLines, bank, rd)
Found = True
except:
print('instprm read failed')
if Found:
Inst,Inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId,'Instrument Parameters'))
if 'Bank' not in Inst: #patch for old .instprm files - may cause faults for TOF data
Inst['Bank'] = [1,1,0]
Inst.update(instvals[0])
if 'B' in Inst['Type'][1] and 'SH/L' in Inst:
del Inst['SH/L']
RefreshInstrumentGrid(event,doAnyway=True) #to get peaks updated
UpdateInstrumentGrid(G2frame,data)
else:
G2frame.ErrorDialog('No match','Bank %d not in %s'%(bank,filename),G2frame)
else:
rd = G2obj.ImportPowderData('Dummy')
rd.Sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId,'Sample Parameters'))
try:
data = GetDefaultParms(rd)[0]
except TypeError: #Cancel - got None
pass
UpdateInstrumentGrid(G2frame,data)
G2plt.PlotPeakWidths(G2frame)
finally:
dlg.Destroy()
def OnSave(event):
'''Respond to the Instrument Parameters Operations/Save Profile menu
item: writes current parameters to a .instprm file
It does not write Bank n: on # line & thus can be used any time w/o clash of bank nos.
note: doesn't currently write extended instrument parameters i.e. pdabc dictionary
'''
pth = G2G.GetExportPath(G2frame)
dlg = wx.FileDialog(G2frame, 'Set name to save GSAS-II instrument parameters file', pth, '',
'instrument parameter files (*.instprm)|*.instprm',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
try:
if dlg.ShowModal() == wx.ID_OK:
Sample = G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame, G2frame.PatternId,'Sample Parameters'))
filename = dlg.GetPath()
# make sure extension is .instprm
filename = os.path.splitext(filename)[0]+'.instprm'
File = open(filename,'w')
G2fil.WriteInstprm(File, data, Sample)
File.close()
print ('Instrument parameters saved to: '+filename)
finally:
dlg.Destroy()
def OnSaveAll(event):
'''Respond to the Instrument Parameters Operations/Save all Profile menu & writes
selected inst parms. across multiple banks into a single file
Each block starts with #Bank n: GSAS-II instrument... where n is bank no.
item: writes parameters from selected PWDR entries to a .instprm file
'''
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
histList.insert(0,hst)
saveList = []
dlg = G2G.G2MultiChoiceDialog(G2frame,'Save instrument parameters from',
'Save instrument parameters', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
saveList = [histList[i] for i in dlg.GetSelections()]
finally:
dlg.Destroy()
pth = G2G.GetExportPath(G2frame)
dlg = wx.FileDialog(G2frame, 'Choose GSAS-II instrument parameters file', pth, '',
'instrument parameter files (*.instprm)|*.instprm',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
try:
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
# make sure extension is .instprm
filename = os.path.splitext(filename)[0]+'.instprm'
File = open(filename,'w')
for hist in saveList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,hist)
inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Instrument Parameters'))[0]
inst1 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Instrument Parameters'))[1] #pdabc dictionary
Sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Sample Parameters'))
if 'Bank' not in inst: #patch
bank = 1
if 'Bank' in hist:
bank = int(hist.split('Bank')[1])
inst['Bank'] = [bank,bank,0]
G2fil.WriteInstprm(File, inst, inst1, Sample, inst['Bank'][0])
File.close()
finally:
dlg.Destroy()
def OnReset(event):
insVal.update(insDef)
updateData(insVal,insRef)
RefreshInstrumentGrid(event,doAnyway=True) #to get peaks updated
UpdateInstrumentGrid(G2frame,data)
G2plt.PlotPeakWidths(G2frame)
def OnInstFlagCopy(event):
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
keys = list(data.keys())
try:
keys.remove('Source')
except ValueError:
pass
flags = dict(zip(keys,[data[key][2] for key in keys]))
instType = data['Type'][0]
copyList = []
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy inst ref. flags from\n'+hst[5:],
'Copy refinement flags', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
copyList.append(histList[i])
finally:
dlg.Destroy()
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
instData = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Instrument Parameters'))[0]
if 'Bank' not in instData:
instData['Bank'] = [1,1,0]
if len(data) == len(instData) and instType == instData['Type'][0]: #don't mix data types or lam & lam1/lam2 parms!
for item in instData:
if item not in ['Source',]:
instData[item][2] = copy.copy(flags[item])
else:
print (item+' not copied - instrument parameters not commensurate')
def OnInstCopy(event):
#need fix for dictionary
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
copyList = []
copyData = copy.deepcopy(data)
if 'E' not in data['Type'][0]:
del copyData['Azimuth'] #not to be copied!
instType = data['Type'][0]
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy inst params from\n'+hst,
'Copy parameters', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
copyList.append(histList[i])
finally:
dlg.Destroy()
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
instData = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Instrument Parameters'))[0]
if 'Bank' not in data:
data['Bank'] = [1,1,0]
if 'Source' not in data:
data['Source'] = ['','']
if 'Bank' not in instData:
instData['Bank'] = [1,1,0]
if 'Source' not in instData:
instData['Source'] = ['','']
if 'Z' not in instData:
instData['Z'] = [0.,0.,False]
if len(data) == len(instData) and instType == instData['Type'][0]: #don't mix data types or lam & lam1/lam2 parms!
instData.update(copyData)
else:
if len(data) != len(instData):
print (item+' not copied - %d instrument parameters do not match source # %d'%(len(instData),len(data)))
else:
print (item+' not copied - instrument type %s does not match source type %s'%(instData['Type'][0],instType))
def AfterChange(invalid,value,tc):
if invalid: return
updateData(insVal,insRef)
G2plt.PlotPeakWidths(G2frame)
def AfterChangeEC(invalid,value,tc):
'''for SEC data only; converts electron energy in keV to wavelength
'''
if invalid: return
if value > 10.:
value *= 1000. #keV -> eV
value = 12.2639/np.sqrt(value+value**2*0.97845e-6)
tc.SetValue(value)
insVal.update({'Lam':value})
updateData(insVal,insRef)
def NewProfile(invalid,value,tc):
if invalid: return
G2plt.PlotPeakWidths(G2frame)
updateData(insVal,insRef)
def OnItemRef(event):
Obj = event.GetEventObject()
item = RefObj[Obj.GetId()]
insRef[item] = Obj.GetValue()
updateData(insVal,insRef)
def OnCopy1Val(event):
'''Select one instrument parameter value to edit and copy to many histograms.
Optionally allow values to be edited in a table.
'''
updateData(insVal,insRef)
G2G.SelectEdit1Var(G2frame,data,labelLst,elemKeysLst,dspLst,refFlgElem)
# change the values in the edit widgets to match data array
insVal.update({key:data[key][1] for key in instkeys})
insRef.update({key:data[key][2] for key in instkeys})
wx.CallAfter(UpdateInstrumentGrid,G2frame,data)
def OnInstMult(event):
'If checked or unchecked, redisplay window'
wx.CallAfter(UpdateInstrumentGrid,G2frame,data)
def lblWdef(lbl,dec,val):
'Label parameter showing the default value'
fmt = "%15."+str(dec)+"f"
return " " + lbl + " (" + (fmt % val).strip() + "): "
def RefineBox(item):
'Define a refine checkbox with binding'
wid = wx.CheckBox(G2frame.dataWindow,label='')
wid.SetValue(bool(insRef[item]))
RefObj[wid.GetId()] = item
wid.Bind(wx.EVT_CHECKBOX, OnItemRef)
return wid
def OnLamPick(event):
'After selection of lab. x-ray source type'
data['Source'][1] = lamType = event.GetEventObject().GetValue()
if 'P' in insVal['Type']:
insVal['Lam1'] = G2elem.waves[lamType][0]
insVal['Lam2'] = G2elem.waves[lamType][1]
elif 'S' in insVal['Type']: #and
try:
insVal['Lam'] = G2elem.meanwaves[lamType]
data['Type'][0] = 'SXC'
insVal['Type'] = 'SXC'
except KeyError:
if 'synch' in lamType:
insVal['Lam'] = 1.0 #obvious incorrect default
data['Type'][0] = 'SXC'
insVal['Type'] = 'SXC'
elif 'micro' in lamType:
insVal['Lam'] = insVal.get('Lam',0.025079) # @200keV
data['Type'][0] = 'SEC' #change to electron diffraction
insVal['Type'] = 'SEC' # in 3 places!
Pattern = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)
Pattern[0]['Type'] = 'SEC'
Pattern[1]['Type'] = 'SEC' #Here, too!
updateData(insVal,insRef)
wx.CallAfter(UpdateInstrumentGrid,G2frame,data)
def MakeParameterWindow():
'Displays the Instrument parameters in the dataWindow frame'
def MakeLamSizer():
if 'Lam1' in insVal:
subSizer = wx.BoxSizer(wx.HORIZONTAL)
subSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Azimuth: '),0,WACV)
txt = '%7.2f'%(insVal['Azimuth'])
subSizer.Add(wx.StaticText(G2frame.dataWindow,-1,txt.strip()),0,WACV)
subSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Ka1/Ka2: '),0,WACV)
txt = ' %8.6f/%8.6f\xc5'%(insVal['Lam1'],insVal['Lam2'])
subSizer.Add(wx.StaticText(G2frame.dataWindow,-1,txt.strip()),0,WACV)
waveSizer = wx.BoxSizer(wx.HORIZONTAL)
waveSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Source type: '),0,WACV)
# PATCH?: for now at least, Source is not saved anywhere before here
if 'Source' not in data: data['Source'] = ['CuKa','?']
choice = list(G2elem.waves.keys())
# ['TiKa','CrKa','FeKa','CoKa','CuKa','GaKa','MoKa','AgKa','InKa']
# patch if Lam1/2 & only element is specified
if 'Lam1' in data and data['Source'][1] not in choice:
indxs = [i for i,t in enumerate(choice) if
t.lower().startswith(data['Source'][1].lower())]
if len(indxs) == 1: data['Source'][1] = choice[indxs[0]]
lamPick = wx.ComboBox(G2frame.dataWindow,value=data['Source'][1],choices=choice,style=wx.CB_READONLY|wx.CB_DROPDOWN)
lamPick.Bind(wx.EVT_COMBOBOX, OnLamPick)
waveSizer.Add(lamPick,0)
subSizer.Add(waveSizer,0)
mainSizer.Add(subSizer)
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,lblWdef('I(L2)/I(L1)',4,insDef['I(L2)/I(L1)'])),0,WACV)
key = 'I(L2)/I(L1)'
labelLst.append(key)
elemKeysLst.append([key,1])
dspLst.append([10,4])
refFlgElem.append([key,2])
ratVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,key,nDig=(10,4),typeHint=float,OnLeave=AfterChange)
instSizer.Add(ratVal,0)
instSizer.Add(RefineBox(key),0,WACV)
else: # single wavelength
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Azimuth: '),0,WACV)
txt = '%7.2f'%(insVal['Azimuth'])
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,txt.strip()),0,WACV)
instSizer.Add((5,5),0)
key = 'Lam'
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Lam (\xc5): (%10.6f)'%(insDef[key])),0,WACV)
waveVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,key,nDig=(10,6),typeHint=float,OnLeave=AfterChange)
labelLst.append('Lam (\xc5)')
elemKeysLst.append([key,1])
dspLst.append([10,6])
instSizer.Add(waveVal,0,WACV)
refFlgElem.append([key,2])
instSizer.Add(RefineBox(key),0,WACV)
G2frame.dataWindow.ClearData()
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,label=' Instrument settings'),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
if insVal['Bank'] == None: #patch
insVal['Bank'] = 1
text = ' Histogram Type: %s Bank: %d'%(insVal['Type'],insVal['Bank'])
if 'SEC' in insVal['Type']:
text += ' (NB: Enter microscope voltage in keV to get wavelength)'
mainSizer.Add(wx.StaticText(G2frame.dataWindow,-1,text))
instSizer = wx.FlexGridSizer(0,3,5,5)
labelLst[:],elemKeysLst[:],dspLst[:],refFlgElem[:] = [],[],[],[]
if 'P' in insVal['Type']: #powder data
[instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,txt),0,WACV) for txt in [' Name (default)',' Value','Refine?']]
Reference = "Reference?"
if insVal['Type'][2] in ['A','B','C']: #constant wavelength
labelLst.append('Azimuth angle')
elemKeysLst.append(['Azimuth',1])
dspLst.append([10,2])
refFlgElem.append(None)
MakeLamSizer()
for item in ['Zero','Polariz.']:
if item in insDef:
labelLst.append(item)
elemKeysLst.append([item,1])
dspLst.append([10,4])
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,lblWdef(item,4,insDef[item])),0,WACV)
itemVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,item,nDig=(10,4),typeHint=float,OnLeave=AfterChange)
instSizer.Add(itemVal,0,WACV)
refFlgElem.append([item,2])
instSizer.Add(RefineBox(item),0,WACV)
if 'C' in insVal['Type']:
itemList = ['U','V','W','X','Y','Z','SH/L']
Reference = """References:
Thompson, P., Cox, D.E. & Hastings, J.B. (1987). J. Appl. Cryst. 20,79-83.
Finger, L. W., Cox, D. E. & Jephcoat, A. P. (1994). J. Appl. Cryst. 27, 892-900.
"""
elif 'B' in insVal['Type']:
itemList = ['U','V','W','X','Y','Z','alpha-0','alpha-1','beta-0','beta-1']
if 'X' in data['Type']:
Reference = "Reference: Von Dreele, R.B., Clarke, S.M. & Walsh, J.P.S. (2021). J. Appl. Cryst., 54, 3-6."
else:
Reference = "Reference: R.B. Von Dreele (2024). J. Appl. Cryst. 57, 1588-1597."
else: #'A'
itemList = ['U','V','W','X','Y','Z','alpha-0','alpha-1','beta-0','beta-1','SH/L']
Reference = """References:
Thompson, P., Cox, D.E. & Hastings, J.B. (1987). J. Appl. Cryst. 20,79-83.
Finger, L. W., Cox, D. E. & Jephcoat, A. P. (1994). J. Appl. Cryst. 27, 892-900.
Von Dreele, R.B., Clarke, S.M. & Walsh, J.P.S. (2021). J. Appl. Cryst., 54, 3-6.
"""
for item in itemList:
nDig = (10,3)
if item == 'SH/L':
nDig = (10,5)
labelLst.append(item)
elemKeysLst.append([item,1])
dspLst.append(nDig)
refFlgElem.append([item,2])
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,lblWdef(item,nDig[1],insDef[item])),0,WACV)
if item == 'SH/L':
itemVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,item,nDig=nDig,typeHint=float,OnLeave=NewProfile,xmin=0.002)
else:
itemVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,item,nDig=nDig,typeHint=float,OnLeave=NewProfile)
instSizer.Add(itemVal,0,WACV)
instSizer.Add(RefineBox(item),0,WACV)
elif 'E' in insVal['Type']:
key = '2-theta'
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' 2-theta (%10.6f):'%(insDef[key])),0,WACV)
tthVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,key,nDig=(10,6),typeHint=float,OnLeave=AfterChange)
labelLst.append('2-theta')
elemKeysLst.append([key,1])
dspLst.append([10,3])
instSizer.Add(tthVal,0,WACV)
refFlgElem.append([key,2])
instSizer.Add(RefineBox(key),0,WACV)
for item in ['XE','YE','ZE','WE','A','B','C','X','Y','Z']:
nDig = (10,6,'g')
labelLst.append(item)
elemKeysLst.append([item,1])
dspLst.append(nDig)
refFlgElem.append([item,2])
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,lblWdef(item,nDig[1],insDef[item])),0,WACV)
if item in ['XE','YE','ZE','WE']:
instSizer.Add(wx.StaticText(G2frame.dataWindow,label='%10.6g'%insVal[item]))
instSizer.Add((5,5),0)
else:
itemVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,item,nDig=nDig,typeHint=float,OnLeave=NewProfile)
instSizer.Add(itemVal,0,WACV)
instSizer.Add(RefineBox(item),0,WACV)
elif 'T' in insVal['Type']: #time of flight (neutrons)
Reference = """References:
Von Dreele, R., Jorgensen, J. D. & Windsor, C. G. (1982) J. Appl. Cryst. 15, 581-589.
Huq, A., Kirkham, M., Peterson, P.F., Hodges, J.P. Whitfield, P.S., Page, K., Hugle, T.,
Iverson, E.B., Parizzia, A. & Rennich, G. (2019). J. Appl. Cryst. 52, 1189–1201.
"""
subSizer = wx.BoxSizer(wx.HORIZONTAL)
subSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Flight path: '),0,WACV)
txt = '%8.3f'%(insVal['fltPath'])
subSizer.Add(wx.StaticText(G2frame.dataWindow,-1,txt.strip()),0,WACV)
labelLst.append('flight path')
elemKeysLst.append(['fltPath',1])
dspLst.append([10,2])
refFlgElem.append(None)
subSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' 2-theta: '),0,WACV)
txt = '%7.2f'%(insVal['2-theta'])
subSizer.Add(wx.StaticText(G2frame.dataWindow,-1,txt.strip()),0,WACV)
labelLst.append('2-theta')
elemKeysLst.append(['2-theta',1])
dspLst.append([10,2])
refFlgElem.append(None)
#note: this if statement is commented out as current implementation of pdabc is not
# intended to exclude diffing difC, difA, difB, etc. from refinement.
# TODO: check this is OK with other applications (work around is "show multiple" in GUI: which exposes everything")
# if 'pdabc' in Inst2:
# Items = ['sig-0','sig-1','sig-2','sig-q','X','Y','Z']
# subSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' difC: '),0,WACV)
# txt = '%8.2f'%(insVal['difC'])
# subSizer.Add(wx.StaticText(G2frame.dataWindow,-1,txt.strip()),0,WACV)
# labelLst.append('difC')
# elemKeysLst.append(['difC',1])
# dspLst.append([10,2])
# refFlgElem.append(None)
# subSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' alpha, beta: fixed by table'),0,WACV)
# else:
Items = ['difC','difA','difB','Zero','alpha','beta-0','beta-1','beta-q','sig-0','sig-1','sig-2','sig-q','X','Y','Z']
mainSizer.Add((5,5),0)
mainSizer.Add(subSizer)
mainSizer.Add((5,5),0)
for item in Items:
if item == '':
instSizer.Add((5,5),0)
instSizer.Add((5,5),0)
instSizer.Add((5,5),0)
continue
nDig = (10,3)
if 'beta' in item:
nDig = (12,6)
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,lblWdef(item,nDig[1],insDef[item])),0,WACV)
itemVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,item,nDig=nDig,typeHint=float,OnLeave=AfterChange)
instSizer.Add(itemVal,0,WACV)
labelLst.append(item)
elemKeysLst.append([item,1])
dspLst.append(nDig)
refFlgElem.append([item,2])
instSizer.Add(RefineBox(item),0,WACV)
elif 'PKS' in insVal['Type']: #peak positions only
Reference = ''
key = 'Lam'
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Lam (\xc5): (%10.6f)'%(insDef[key])),0,WACV)
waveVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,key,nDig=(10,6),typeHint=float,OnLeave=AfterChange)
labelLst.append('Lam (\xc5)')
elemKeysLst.append([key,1])
dspLst.append([10,6])
instSizer.Add(waveVal,0,WACV)
refFlgElem.append([key,2])
instSizer.Add((5,5),0)
for item in ['Zero',]:
if item in insDef:
labelLst.append(item)
elemKeysLst.append([item,1])
dspLst.append([10,4])
instSizer.Add(
wx.StaticText(G2frame.dataWindow,-1,lblWdef(item,4,insDef[item])),
0,WACV)
itemVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,item,nDig=(10,4),typeHint=float,OnLeave=AfterChange)
instSizer.Add(itemVal,0,WACV)
refFlgElem.append([item,2])
instSizer.Add((5,5),0)
elif 'S' in insVal['Type']: #single crystal data
Reference = ''
if 'C' in insVal['Type']: #constant wavelength
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Lam (\xc5): (%10.6f)'%(insDef['Lam'])),0,WACV)
if 'EC' in insVal['Type']:
waveVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,'Lam',nDig=(10,6),typeHint=float,OnLeave=AfterChangeEC)
else:
waveVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,'Lam',nDig=(10,6),typeHint=float,OnLeave=AfterChange)
instSizer.Add(waveVal,0,WACV)
labelLst.append('Lam (\xc5)')
waveSizer = wx.BoxSizer(wx.HORIZONTAL)
waveSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Source type: '),0,WACV)
# PATCH?: for now at least, Source is not saved anywhere before here
if 'Source' not in data: data['Source'] = ['CuKa','?']
choice = ['synchrotron','TiKa','CrKa','FeKa','CoKa','CuKa','MoKa','AgKa','micro-ED']
lamPick = wx.ComboBox(G2frame.dataWindow,value=data['Source'][1],choices=choice,style=wx.CB_READONLY|wx.CB_DROPDOWN)
lamPick.Bind(wx.EVT_COMBOBOX, OnLamPick)
waveSizer.Add(lamPick,0,WACV)
instSizer.Add(waveSizer,0,WACV)
elemKeysLst.append(['Lam',1])
dspLst.append([10,6])
refFlgElem.append(None)
else: #time of flight (neutrons)
pass #for now
elif insVal['Type'][0] in ['L','R',]:
Reference = ''
if 'C' in insVal['Type']:
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Lam (\xc5): (%10.6f)'%(insDef['Lam'])),0,WACV)
waveVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,insVal,'Lam',nDig=(10,6),typeHint=float,OnLeave=AfterChange)
instSizer.Add(waveVal,0,WACV)
labelLst.append('Lam (\xc5)')
elemKeysLst.append(['Lam',1])
dspLst.append([10,6])
refFlgElem.append(None)
instSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Azimuth: %7.2f'%(insVal['Azimuth'])),0,WACV)
labelLst.append('Azimuth angle')
elemKeysLst.append(['Azimuth',1])
dspLst.append([10,2])
refFlgElem.append(None)
else: #time of flight (neutrons)
pass #for now
mainSizer.Add(instSizer,0)
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=Reference))
G2frame.dataWindow.SetDataSize()
# end of MakeParameterWindow
plotYsel = {} # selected Y items
def MakeMultiParameterWindow(selected=None):
'''Displays the Instrument parameters for multiple histograms
in the dataWindow panel
'''
plotIndex = {'plotX':0} # index for param name => plotTbl index
# plotX is selected X axis
plotTbl = [] # table of values for each param
plotLabel = [] # table of values for each param
def onSelectHists(event):
'select histograms to show'
dlg = G2G.G2MultiChoiceDialog(G2frame,
'Select histograms to show of type '+data['Type'][1],
'Select histograms',hlist)
dlg.CenterOnParent()
try:
if dlg.ShowModal() == wx.ID_OK:
selected = dlg.GetSelections()
else:
return
finally:
dlg.Destroy()
wx.CallAfter(MakeMultiParameterWindow,selected)
return
def onSelectX(event):
'respond to change in plotting x axis; save and plot (if y selected)'
plotIndex['plotX'] = event.GetEventObject().rbindex
onPrmPlot(event)
def onCopySelRow(event):
row = event.GetEventObject().row
for i,h in enumerate(histnames):
if i == 0:
val = histdict[h][row][2]
else:
histdict[h][row][2] = val
wx.CallAfter(MakeMultiParameterWindow,selected)
def onPrmPlot(event):
'''Callback after a change to X or Y plot contents
plots multiple instrument param values vs selected X value.
If no Y values are selected, any previous plot is deleted.
'''
xvals = plotTbl[plotIndex['plotX']]
xlbl = plotLabel[plotIndex['plotX']]
XY = []
keys = ''
for k in plotYsel:
if k == 'plotX': continue
if not plotYsel[k]: continue
yvals = plotTbl[plotIndex[k]]
if keys: keys += ', '
keys += plotLabel[plotIndex[k]]
XY.append((xvals,yvals))
if not XY:
G2frame.G2plotNB.Delete('Parameter values')
return
G2plt.PlotXY(G2frame,XY,labelX=xlbl,labelY=keys,Title='Parameter values',newPlot=True)
# gather histograms matching the currently selected histogram
histoList,histIdList = G2frame.GetHistogramNamesID(['PWDR',])
hlist = GetHistsLikeSelected(G2frame)
if selected is None and len(hlist) > 10: # on initial call this is none
onSelectHists(None) # lots of histograms, give user a chance to choose
return
elif selected is None: # select all, not so many
selected = range(len(hlist))
lbl = 'Instrument parameters for all matching histograms'
else:
lbl = 'Instrument parameters for selected histograms'
wx.BeginBusyCursor()
h = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histnames = [h]
histdict = {h:data}
if 'hId' in G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[0]:
histnum = {h:G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[0]['hId']}
elif h in histoList: # how could this not be true?
histnum = {h:histoList.index(h)}
for i in selected:
h = hlist[i]
if h not in histoList: # unexpected
print('hist from GetHistsLikeSelected not in GetHistogramNamesID',h)
continue
hid = histIdList[h]
inst,inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,hid, 'Instrument Parameters'))
histnames.append(h)
histdict[h] = inst
histnum[h] = G2frame.GPXtree.GetItemPyData(hid)[0].get('hId',i)
# start posting info into window
G2frame.dataWindow.ClearData()
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,wx.ID_ANY,lbl))
if hlist:
btn = wx.Button(parent, wx.ID_ANY,'Select Histograms')
topSizer.Add(btn,0,wx.LEFT|wx.RIGHT,15)
btn.Bind(wx.EVT_BUTTON,onSelectHists)
topSizer.Add((20,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
# create table w/headers
sdlg = G2frame.dataWindow
fgs = wx.FlexGridSizer(0,len(histnames)+4,0,0)
fgs.Add(wx.StaticText(sdlg,wx.ID_ANY,'plot\nas X'),0,wx.LEFT|wx.RIGHT,1)
fgs.Add(wx.StaticText(sdlg,wx.ID_ANY,'plot\nas Y'),0,wx.LEFT|wx.RIGHT,1)
fgs.Add(wx.StaticText(sdlg,wx.ID_ANY,'Histogram '),0,WACV|wx.LEFT,14)
for i,h in enumerate(histnames):
if len(h[5:].strip()) > 15:
fgs.Add(G2G.ScrolledStaticText(sdlg,label=h[5:],dots=False,lbllen=15),
0,WACV|wx.LEFT|wx.RIGHT,5)
else:
fgs.Add(wx.StaticText(sdlg,wx.ID_ANY,h[5:]),0,WACV|wx.LEFT|wx.RIGHT,5)
if i == 0: fgs.Add(wx.StaticText(sdlg,wx.ID_ANY,'copy\nright'),0,wx.LEFT|wx.RIGHT,1)
firstRadio = wx.RB_GROUP
# put non-editable values at top of table (plot as x but not y)
keylist = ['num']
lbllist = ['#']
if 'T' in data['Type'][1]:
keylist += ['2-theta']
lbllist += ['2-theta']
for key,lbl in zip(keylist,lbllist):
rb = wx.RadioButton(sdlg,wx.ID_ANY,'',style=firstRadio)
rb.rbindex = len(plotTbl)
rb.Bind(wx.EVT_RADIOBUTTON,onSelectX)
plotLabel.append(lbl)
fgs.Add(rb,0,wx.ALIGN_CENTER|WACV)
if firstRadio:
rb.SetValue(True)
firstRadio = 0
fgs.Add((-1,-1)) # skip y checkbutton
fgs.Add(wx.StaticText(sdlg,wx.ID_ANY,lbl),0,WACV|wx.LEFT,14)
plotvals = []
for i,h in enumerate(histnames):
if key == 'num':
val = histnum[h]
else:
val = histdict[h][key][1]
fgs.Add(wx.StaticText(sdlg,wx.ID_ANY,str(val)),
0,wx.ALIGN_CENTER|WACV,0)
plotvals.append(val)
if i == 0: fgs.Add((-1,-1)) # skip copy row button
plotTbl.append(plotvals)
# determine what items will be shown based on histogram type
Items = []
if data['Type'][1][2] in ['A','B','C']: #constant wavelength
if 'Lam1' in data:
Items = ['Lam1','Lam2','I(L2)/I(L1)']
else:
Items = ['Lam','Zero','Polariz.']
if 'C' in data['Type'][1]:
Items += ['Azimuth','U','V','W','X','Y','Z','SH/L']
elif 'B' in data['Type'][1]:
Items += ['Azimuth','U','V','W','X','Y','Z','alpha-0','alpha-1','beta-0','beta-1']
else: #'A'
Items += ['Azimuth','U','V','W','X','Y','Z','alpha-0','alpha-1','beta-0','beta-1','SH/L']
elif 'E' in data['Type'][1]:
Items = ['2-theta','XE','YE','ZE','WE','A','B','C','X','Y','Z']
elif 'T' in data['Type'][1]: # TOF
Items = ['difC','difA','difB','Zero','alpha','beta-0','beta-1','beta-q','sig-0','sig-1','sig-2','sig-q','X','Y','Z']
# display the items in the table
for k in Items:
plotYsel[k] = plotYsel.get(k,False)
#if not l: l = k
l = k
rb = wx.RadioButton(sdlg,wx.ID_ANY,'',style=firstRadio)
rb.rbindex = len(plotTbl)
rb.Bind(wx.EVT_RADIOBUTTON,onSelectX)
plotLabel.append(l)
fgs.Add(rb,0,wx.ALIGN_CENTER|WACV)
if firstRadio:
rb.SetValue(True)
firstRadio = 0
fgs.Add(G2G.G2CheckBox(sdlg,'',plotYsel,k,OnChange=onPrmPlot),0,wx.ALIGN_CENTER|WACV)
plotIndex[k] = rb.rbindex
fgs.Add(wx.StaticText(sdlg,wx.ID_ANY,l),0,WACV|wx.LEFT,14)
plotvals = []
for i,h in enumerate(histnames):
miniSizer = wx.BoxSizer(wx.HORIZONTAL)
itemVal = G2G.ValidatedTxtCtrl(sdlg,histdict[h][k],1,nDig=(10,4),typeHint=float)
plotvals.append(histdict[h][k][1])
miniSizer.Add(itemVal)
miniSizer.Add((2,-1))
if i == 0:
miniSizer.Add(G2G.G2CheckBox(sdlg,'',histdict[h][k],2),0,WACV|wx.RIGHT,3)
fgs.Add(miniSizer,0,wx.ALIGN_RIGHT)
# copy row button
but = wx.Button(sdlg,wx.ID_ANY,'\u2192',style=wx.BU_EXACTFIT)
#but.SetBackgroundColour('yellow')
fgs.Add(but,0,wx.RIGHT,15)
but.Bind(wx.EVT_BUTTON, onCopySelRow)
but.row = k
else:
miniSizer.Add(G2G.G2CheckBox(sdlg,'',histdict[h][k],2),0,WACV|wx.RIGHT,15)
fgs.Add(miniSizer,0,wx.ALIGN_CENTER)
plotTbl.append(plotvals)
mainSizer.Add(fgs)
G2frame.dataWindow.SetDataSize()
wx.EndBusyCursor()
# end of MakeMultiParameterWindow
#### beginning of UpdateInstrumentGrid code
#patch: make sure all parameter items are lists
patched = 0
for key in data:
if type(data[key]) is tuple:
data[key] = list(data[key])
patched += 1
if patched: print (patched,' instrument parameters changed from tuples')
if 'E' not in data['Type'][0] and 'Z' not in data:
data['Z'] = [0.0,0.0,False]
#end of patch
labelLst,elemKeysLst,dspLst,refFlgElem = [],[],[],[]
instkeys = keycheck(data.keys())
if 'P' in data['Type'][0]: #powder data
insVal = dict(zip(instkeys,[data[key][1] for key in instkeys]))
insDef = dict(zip(instkeys,[data[key][0] for key in instkeys]))
insRef = dict(zip(instkeys,[data[key][2] for key in instkeys]))
if 'NC' in data['Type'][0]:
del(insDef['Polariz.'])
del(insVal['Polariz.'])
del(insRef['Polariz.'])
elif 'S' in data['Type'][0]: #single crystal data
insVal = dict(zip(instkeys,[data[key][1] for key in instkeys]))
insDef = dict(zip(instkeys,[data[key][0] for key in instkeys]))
insRef = {}
elif 'L' in data['Type'][0]: #low angle data
insVal = dict(zip(instkeys,[data[key][1] for key in instkeys]))
insDef = dict(zip(instkeys,[data[key][0] for key in instkeys]))
insRef = {}
elif 'R' in data['Type'][0]: #Reflectometry data
insVal = dict(zip(instkeys,[data[key][1] for key in instkeys]))
insDef = dict(zip(instkeys,[data[key][0] for key in instkeys]))
insRef = {}
RefObj = {}
Inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,
G2frame.PatternId,'Instrument Parameters'))[1]
G2gd.SetDataMenuBar(G2frame) # this was removed in 12ec78f Why? (BHT)
#RefData = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[1]
#RefData['Type'] = data['Type'][0]
# The above was added but RefData would need to be ...PatternId)[0]
# for this to work. Not sure what is going on, so I am commenting the new code (BHT)
#patch
if 'P' in insVal['Type']: #powder data
if 'C' in insVal['Type']: #constant wavelength
if 'Azimuth' not in insVal:
insVal['Azimuth'] = 0.0
insDef['Azimuth'] = 0.0
insRef['Azimuth'] = False
elif 'E' in insVal['Type']:
if 'WE' not in insVal:
insVal['WE'] = 0.0
insDef['WE'] = 0.0
insRef['WE'] = False
if 'X' not in insVal:
for item in ['X','Y','Z']:
insVal[item] = 0.0
insDef[item] = 0.0
insRef[item] = False
#end of patch
if 'P' in insVal['Type']: #powder data menu commands
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.InstMenu)
G2frame.GetStatusBar().SetStatusText('NB: Azimuth is used for polarization only',1)
G2frame.Bind(wx.EVT_MENU,OnCalibrate,id=G2G.wxID_INSTCALIB)
G2frame.Bind(wx.EVT_MENU,OnLoad,id=G2G.wxID_INSTLOAD)
G2frame.Bind(wx.EVT_MENU,OnSave,id=G2G.wxID_INSTSAVE)
G2frame.Bind(wx.EVT_MENU,OnSaveAll,id=G2G.wxID_INSTSAVEALL)
G2frame.Bind(wx.EVT_MENU,OnReset,id=G2G.wxID_INSTPRMRESET)
G2frame.Bind(wx.EVT_MENU,OnInstCopy,id=G2G.wxID_INSTCOPY)
G2frame.Bind(wx.EVT_MENU,OnInstFlagCopy,id=G2G.wxID_INSTFLAGCOPY)
G2frame.Bind(wx.EVT_MENU,OnCopy1Val,id=G2G.wxID_INST1VAL)
G2frame.Bind(wx.EVT_MENU,OnInstMult,id=G2G.wxID_INSTSHOWMULT)
menuitem = G2frame.dataWindow.InstMenu.FindItemById(G2G.wxID_INSTSHOWMULT)
if menuitem.IsChecked():
MakeMultiParameterWindow()
else:
MakeParameterWindow()
elif 'L' in insVal['Type'] or 'R' in insVal['Type'] or 'S' in insVal['Type']: #HKLF, SASD & REFD data menu commands
MakeParameterWindow()
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.SASDInstMenu)
G2frame.Bind(wx.EVT_MENU,OnInstCopy,id=G2G.wxID_SASDINSTCOPY)
G2frame.dataWindow.SetDataSize()
################################################################################
##### Sample parameters
################################################################################
[docs]
def UpdateSampleGrid(G2frame,data):
'''respond to selection of PWDR/SASD Sample Parameters
data tree item.
'''
def OnSampleSave(event):
'''Respond to the Sample Parameters Operations/Save menu
item: writes current parameters to a .samprm file
'''
pth = G2G.GetExportPath(G2frame)
dlg = wx.FileDialog(G2frame, 'Choose GSAS-II sample parameters file', pth, '',
'sample parameter files (*.samprm)|*.samprm',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
try:
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
# make sure extension is .samprm
filename = os.path.splitext(filename)[0]+'.samprm'
File = open(filename,'w')
File.write("#GSAS-II sample parameter file\n")
File.write("'Type':'"+str(data['Type'])+"'\n")
File.write("'Gonio. radius':"+str(data['Gonio. radius'])+"\n")
if data.get('InstrName'):
File.write("'InstrName':'"+str(data['InstrName'])+"'\n")
File.close()
finally:
dlg.Destroy()
def OnSampleLoad(event):
'''Loads sample parameters from a G2 .samprm file
in response to the Sample Parameters-Operations/Load menu
'''
pth = G2G.GetImportPath(G2frame)
if not pth: pth = '.'
dlg = wx.FileDialog(G2frame, 'Choose GSAS-II sample parameters file', pth, '',
'sample parameter files (*.samprm)|*.samprm',wx.FD_OPEN)
try:
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
File = open(filename,'r')
S = File.readline()
newItems = {}
while S:
if S[0] == '#':
S = File.readline()
continue
[item,val] = S[:-1].split(':')
newItems[item.strip("'")] = eval(val)
S = File.readline()
File.close()
data.update(newItems)
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId,'Sample Parameters'),data)
UpdateSampleGrid(G2frame,data)
finally:
dlg.Destroy()
def OnAllSampleLoad(event):
filename = ''
pth = G2G.GetImportPath(G2frame)
if not pth: pth = '.'
dlg = wx.FileDialog(G2frame, 'Choose multihistogram metadata text file', pth, '',
'metadata file (*.*)|*.*',wx.FD_OPEN)
try:
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
File = open(filename,'r')
S = File.readline()
newItems = []
itemNames = []
Comments = []
while S:
if S[0] == '#':
Comments.append(S)
S = File.readline()
continue
S = S.replace(',',' ').replace('\t',' ')
Stuff = S[:-1].split()
itemNames.append(Stuff[0])
newItems.append(Stuff[1:])
S = File.readline()
File.close()
finally:
dlg.Destroy()
if not filename:
G2frame.ErrorDialog('Nothing to do','No file selected')
return
dataDict = dict(zip(itemNames,newItems))
ifany = False
Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Controls'))
Names = [' ','Phi','Chi','Omega','Time','Temperature','Pressure']
freeNames = {}
for name in ['FreePrm1','FreePrm2','FreePrm3']:
freeNames[Controls[name]] = name
Names.append(Controls[name])
dlg = G2G.G2ColumnIDDialog( G2frame,' Choose multihistogram metadata columns:',
'Select columns',Comments,Names,np.array(newItems).T)
try:
if dlg.ShowModal() == wx.ID_OK:
colNames,newData = dlg.GetSelection()
dataDict = dict(zip(itemNames,newData.T))
for item in colNames:
if item != ' ':
ifany = True
finally:
dlg.Destroy()
if not ifany:
G2frame.ErrorDialog('Nothing to do','No columns identified')
return
histList = [G2frame.GPXtree.GetItemText(G2frame.PatternId),]
histList += GetHistsLikeSelected(G2frame)
colIds = {}
for i,name in enumerate(colNames):
if name != ' ':
colIds[name] = i
for ih,hist in enumerate(histList):
name = hist.split()[1] #this is file name
newItems = {}
for item in colIds:
key = freeNames.get(item,item)
try:
newItems[key] = float(dataDict[name][colIds[item]])
except KeyError:
try:
newItems[key] = float(dataDict['{:}'.format(ih+1)])
except KeyError:
break
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,hist)
sampleData = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Sample Parameters'))
sampleData.update(newItems)
UpdateSampleGrid(G2frame,data)
def OnSetScale(event):
if histName[:4] in ['REFD','PWDR']:
Scale = data['Scale'][0]
dlg = wx.MessageDialog(G2frame,'Rescale data by %.2f?'%(Scale),'Rescale data',wx.OK|wx.CANCEL)
try:
if dlg.ShowModal() == wx.ID_OK:
pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,histName)
y,w = G2frame.GPXtree.GetItemPyData(pId)[1][1:3]
y *= Scale
w /= Scale**2
data['Scale'][0] = 1.0
finally:
dlg.Destroy()
G2pwpl.PlotPatterns(G2frame,plotType=histName[:4],newPlot=True)
UpdateSampleGrid(G2frame,data)
return
#SASD rescaliing
histList = []
item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
while item:
name = G2frame.GPXtree.GetItemText(item)
if 'SASD' in name and name != histName:
histList.append(name)
item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
if not len(histList): #nothing to copy to!
return
dlg = wx.SingleChoiceDialog(G2frame,'Select reference histogram for scaling',
'Reference histogram',histList)
try:
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelection()
refHist = histList[sel]
finally:
dlg.Destroy()
Limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Limits'))
Profile = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[1]
Data = [Profile,Limits,data]
refId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,refHist)
refSample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,refId, 'Sample Parameters'))
refLimits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,refId, 'Limits'))
refProfile = G2frame.GPXtree.GetItemPyData(refId)[1]
refData = [refProfile,refLimits,refSample]
G2sasd.SetScale(Data,refData)
G2pwpl.PlotPatterns(G2frame,plotType='SASD',newPlot=True)
UpdateSampleGrid(G2frame,data)
def OnRescaleAll(event):
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
x0,y0,w0 = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[1][:3]
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
od = {'label_1':'Scaling range min','value_1':0.0,'label_2':'Scaling range max','value_2':10.}
dlg = G2G.G2MultiChoiceDialog(G2frame,
'Do scaling from\n'+str(hst[5:])+' to...','Rescale histograms', histList,extraOpts=od)
try:
if dlg.ShowModal() == wx.ID_OK:
Xmin = od['value_1']
Xmax = od['value_2']
iBeg = np.searchsorted(x0,Xmin)
iFin = np.searchsorted(x0,Xmax)
if iBeg > iFin:
wx.MessageBox('Wrong order for Xmin, Xmax','Error',style=wx.ICON_EXCLAMATION)
else:
sum0 = np.sum(y0[iBeg:iFin])
result = dlg.GetSelections()
for i in result:
item = histList[i]
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
xi,yi,wi = G2frame.GPXtree.GetItemPyData(Id)[1][:3]
sumi = np.sum(yi[iBeg:iFin])
if sumi:
Scale = sum0/sumi
yi *= Scale
wi /= Scale**2
finally:
dlg.Destroy()
G2pwpl.PlotPatterns(G2frame,plotType=histName[:4],newPlot=True)
def OnSampleCopy(event):
histType,copyNames = SetCopyNames(histName,data['Type'],
addNames = ['Omega','Chi','Phi','Gonio. radius','InstrName'])
copyDict = {}
for parm in copyNames:
copyDict[parm] = data[parm]
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy sample params from\n'+str(hst[5:])+' to...',
'Copy sample parameters', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelections()
for i in result:
item = histList[i]
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
sampleData = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Sample Parameters'))
sampleData.update(copy.deepcopy(copyDict))
finally:
dlg.Destroy()
def OnSampleCopySelected(event):
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
Controls = G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
# Assemble a list of item labels
TextTable = {key:label for key,label,dig in
SetupSampleLabels(hst,data.get('Type'),Inst['Type'][0])}
# get flexible labels
TextTable.update({key:Controls[key] for key in Controls if key.startswith('FreePrm')})
# add a few extra
TextTable.update({'Type':'Diffractometer type','InstrName':'Instrument Name',})
if 'SASD' in histList[0] or 'REFD' in histList[0]:
TextTable.update({'Materials':'Materials',})
# Assemble a list of dict entries that would be labeled in the Sample
# params data window (drop ranId and items not used).
keyList = [i for i in data.keys() if i in TextTable]
keyText = [TextTable[i] for i in keyList]
# sort both lists together, ordered by keyText
keyText, keyList = zip(*sorted(list(zip(keyText,keyList)))) # sort lists
selectedKeys = []
dlg = G2G.G2MultiChoiceDialog(G2frame,'Select which sample parameters\nto copy',
'Select sample parameters', keyText)
try:
if dlg.ShowModal() == wx.ID_OK:
selectedKeys = [keyList[i] for i in dlg.GetSelections()]
finally:
dlg.Destroy()
if not selectedKeys: return # nothing to copy
copyDict = {}
for parm in selectedKeys:
copyDict[parm] = copy.deepcopy(data[parm])
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy sample params from\n'+str(hst[5:])+' to...',
'Copy sample parameters', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelections()
for i in result:
item = histList[i]
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
sampleData = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Sample Parameters'))
sampleData.update(copyDict)
finally:
dlg.Destroy()
G2pwpl.PlotPatterns(G2frame,plotType=hst[:4],newPlot=False)
def OnSampleFlagCopy(event):
histType,copyNames = SetCopyNames(histName,data['Type'])
flagDict = {}
for parm in copyNames:
flagDict[parm] = data[parm][1]
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy sample ref. flags from\n'+str(hst[5:])+' to...',
'Copy sample flags', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelections()
for i in result:
item = histList[i]
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
sampleData = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Sample Parameters'))
for name in copyNames:
if name not in sampleData:
sampleData[name] = [0.0,False]
sampleData[name][1] = copy.copy(flagDict[name])
finally:
dlg.Destroy()
def OnHistoChange():
'''Called when the histogram type is changed to refresh the window
'''
#wx.CallAfter(UpdateSampleGrid,G2frame,data)
wx.CallLater(100,UpdateSampleGrid,G2frame,data)
def SetNameVal():
inst = instNameVal.GetValue()
data['InstrName'] = inst.strip()
def OnNameVal(event):
event.Skip()
wx.CallAfter(SetNameVal)
def AfterChange(invalid,value,tc):
if invalid:
return
if tc.key == 0 and 'SASD' in histName: #a kluge for Scale!
G2pwpl.PlotPatterns(G2frame,plotType='SASD',newPlot=True)
elif tc.key == 'Thick':
wx.CallAfter(UpdateSampleGrid,G2frame,data)
def OnMaterial(event):
Obj = event.GetEventObject()
Id = Info[Obj.GetId()]
data['Materials'][Id]['Name'] = Obj.GetValue()
wx.CallAfter(UpdateSampleGrid,G2frame,data)
def OnVolFrac(invalid,value,tc):
Id = Info[tc.GetId()]
data['Materials'][not Id]['VolFrac'] = 1.-value
wx.CallAfter(UpdateSampleGrid,G2frame,data)
def OnCopy1Val(event):
'Select one value to copy to many histograms and optionally allow values to be edited in a table'
G2G.SelectEdit1Var(G2frame,data,labelLst,elemKeysLst,dspLst,refFlgElem)
# TODO: check if values need to be copied to editing widgets
wx.CallAfter(UpdateSampleGrid,G2frame,data)
def OnSearchComments(event):
'''Set a selected Sample parameter from a selected entry in the comments
for a selected set of histograms
'''
def commentDict(G2frame,Id):
Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(
G2frame, Id, 'Comments'))
keyDict = {}
for line in Comments:
if ':' in line:
key,val = line.split(':')[0:2]
elif '=' in line:
key,val = line.split('=')[0:2]
else:
continue
try:
#keyList.append(key.strip())
keyDict[key.strip()] = float(val)
except:
pass
return keyDict
# get possible keys from current histogram's comments
keyDict = commentDict(G2frame, G2frame.PatternId)
# if GSASIIpath.GetConfigValue('debug'):
# from importlib import reload
# reload(G2G)
# print(f'reloading {G2G}')
sampleVar,commentKey = G2G.SelectSearchVars(G2frame,labelLst,keyDict)
if sampleVar is None or commentKey is None: return
# find the array element tied to the sample var
if sampleVar not in labelLst:
print(f'OnSearchComments: how did we get {sampleVar} not in {labelLst}?')
return
i = labelLst.index(sampleVar)
sampleArrKeys = elemKeysLst[i]
# need to select histograms to search/set
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
histList.insert(0,hst)
if len(histList) == 1: # only current histogram present -- don't ask
selection = [0]
else:
dlg = G2G.G2MultiChoiceDialog(G2frame,f'Set "{sampleVar}" value in histograms...',
'Set value from comments', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
selection = dlg.GetSelections()
else:
return
finally:
dlg.Destroy()
# cycle through selected histograms, get comments & values
count = 0
for i in selection:
hist = histList[i]
hId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root, hist)
if not hId:
print(f'{hist} not found! strange')
continue
keyDict = commentDict(G2frame, hId)
if hasattr(commentKey,'EvalExpression'):
commentKey.SetupCalc(keyDict)
value = commentKey.EvalExpression()
elif commentKey in keyDict:
value = keyDict[commentKey]
else:
print(f'"{commentKey}" not in Comments for {hist}')
continue
Sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,hId, 'Sample Parameters'))
# set the value in the selected entry in Sample Parameters
try:
d = Sample
for k in sampleArrKeys[:-1]:
d = d[k]
d[sampleArrKeys[-1]]
except KeyError:
print(f'Strange: "keys {sampleArrKeys}" not in Sample Parameters for {hist}')
continue
count += 1
d[sampleArrKeys[-1]] = value
print(f'Set from comments done. Set "{sampleVar}" in {count} of {len(selection)} histograms')
wx.CallAfter(UpdateSampleGrid,G2frame,data)
def SearchAllComments(value,tc,*args,**kwargs):
'''Called when the label for a FreePrm is changed: the comments
for all PWDR histograms are searched for a "label=value" or
"label:value" pair that matches the label (case is ignored) and
the values are then set to this value, if it can be converted
to a float. Stop after the first item that matches.
'''
Id, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
count = 0
while Id:
name = G2frame.GPXtree.GetItemText(Id)
if 'PWDR' in name:
Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Comments'))
Sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Sample Parameters'))
for i,item in enumerate(Comments):
if '=' in item:
itemSp = item.split('=')
elif ':' in item:
itemSp = item.split(':')
else:
continue
if value.lower() in itemSp[0].lower():
try:
Sample[tc.key] = float(itemSp[1])
count += 1
break
except:
print('"{item.strip()}" has an invalid value in Comments from {name}')
Id, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
print(f'{count} values were found in the histogram comments')
wx.CallLater(100,UpdateSampleGrid,G2frame,data)
# start of UpdateSampleGrid
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.PeakMenu) # needed below
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.SampleMenu)
Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(
G2frame,G2frame.PatternId, 'Instrument Parameters'))[0]
histName = G2frame.GPXtree.GetItemText(G2frame.PatternId)
#G2frame.SetLabel(G2frame.GetLabel().split('||')[0]+' || '+'Sample Parameters')
G2frame.Bind(wx.EVT_MENU, OnSetScale, id=G2G.wxID_SETSCALE)
G2frame.Bind(wx.EVT_MENU, OnSampleCopy, id=G2G.wxID_SAMPLECOPY)
G2frame.Bind(wx.EVT_MENU, OnSampleCopySelected, id=G2G.wxID_SAMPLECOPYSOME)
G2frame.Bind(wx.EVT_MENU, OnSampleFlagCopy, id=G2G.wxID_SAMPLEFLAGCOPY)
G2frame.Bind(wx.EVT_MENU, OnSampleSave, id=G2G.wxID_SAMPLESAVE)
G2frame.Bind(wx.EVT_MENU, OnSampleLoad, id=G2G.wxID_SAMPLELOAD)
G2frame.Bind(wx.EVT_MENU, OnCopy1Val, id=G2G.wxID_SAMPLE1VAL)
G2frame.Bind(wx.EVT_MENU, OnSearchComments, id=G2G.wxID_SEARCHVAL)
G2frame.Bind(wx.EVT_MENU, OnAllSampleLoad, id=G2G.wxID_ALLSAMPLELOAD)
G2frame.Bind(wx.EVT_MENU, OnRescaleAll, id=G2G.wxID_RESCALEALL)
if histName[:4] in ['SASD','REFD','PWDR']:
G2frame.dataWindow.SetScale.Enable(True)
Controls = G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
#patch
if 'ranId' not in data:
data['ranId'] = ran.randint(0,sys.maxsize)
if not 'Gonio. radius' in data:
data['Gonio. radius'] = 200.0
if not 'Omega' in data:
data.update({'Omega':0.0,'Chi':0.0,'Phi':0.0})
if 'Azimuth' not in data:
data['Azimuth'] = 0.0
if type(data['Temperature']) is int:
data['Temperature'] = float(data['Temperature'])
if 'Time' not in data:
data['Time'] = 0.0
if 'FreePrm1' not in Controls:
Controls['FreePrm1'] = 'Sample humidity (%)'
if 'FreePrm2' not in Controls:
Controls['FreePrm2'] = 'Sample voltage (V)'
if 'FreePrm3' not in Controls:
Controls['FreePrm3'] = 'Applied load (MN)'
if 'FreePrm1' not in data:
data['FreePrm1'] = 0.
if 'FreePrm2' not in data:
data['FreePrm2'] = 0.
if 'FreePrm3' not in data:
data['FreePrm3'] = 0.
if 'SurfRoughA' not in data and 'PWDR' in histName:
data['SurfRoughA'] = [0.,False]
data['SurfRoughB'] = [0.,False]
if 'Trans' not in data and 'SASD' in histName:
data['Trans'] = 1.0
if 'SlitLen' not in data and 'SASD' in histName:
data['SlitLen'] = 0.0
if 'Shift' not in data:
data['Shift'] = [0.0,False]
if 'Transparency' not in data:
data['Transparency'] = [0.0,False]
data['InstrName'] = data.get('InstrName','')
#patch end
labelLst,elemKeysLst,dspLst,refFlgElem = [],[],[],[]
parms = SetupSampleLabels(histName,data.get('Type'),Inst['Type'][0])
G2frame.dataWindow.ClearData()
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,label=' Sample and Experimental Parameters'),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
nameSizer = wx.BoxSizer(wx.HORIZONTAL)
nameSizer.Add(wx.StaticText(G2frame.dataWindow,wx.ID_ANY,' Instrument Name '),0,WACV)
nameSizer.Add((-1,-1),1,WACV)
instNameVal = wx.TextCtrl(G2frame.dataWindow,wx.ID_ANY,data['InstrName'],
size=(200,-1),style=wx.TE_PROCESS_ENTER)
nameSizer.Add(instNameVal)
instNameVal.Bind(wx.EVT_CHAR,OnNameVal)
mainSizer.Add(nameSizer,0)
mainSizer.Add((5,5),0)
labelLst.append('Instrument Name')
elemKeysLst.append(['InstrName'])
dspLst.append(None)
refFlgElem.append(None)
if 'PWDR' in histName:
nameSizer = wx.BoxSizer(wx.HORIZONTAL)
nameSizer.Add(wx.StaticText(G2frame.dataWindow,wx.ID_ANY,' Diffractometer type: '),0,WACV)
if 'T' in Inst['Type'][0] or 'E' in Inst['Type'][0]:
choices = ['Debye-Scherrer',]
else: #'[A','B','C']
choices = ['Debye-Scherrer','Bragg-Brentano',]
histoType = G2G.G2ChoiceButton(G2frame.dataWindow,choices,strLoc=data,strKey='Type',
onChoice=OnHistoChange)
nameSizer.Add(histoType)
mainSizer.Add(nameSizer,0)
mainSizer.Add((5,5),0)
parmSizer = wx.FlexGridSizer(0,2,5,0)
for key,lbl,nDig in parms:
if 'E' in Inst['Type'][0] and key in ['DisplaceX','DisplaceY','Absorption']:
continue
labelLst.append(lbl.strip().strip(':').strip())
dspLst.append(nDig)
if 'list' in str(type(data[key])):
parmRef = G2G.G2CheckBox(G2frame.dataWindow,' '+lbl,data[key],1)
parmSizer.Add(parmRef,0,wx.EXPAND)
parmVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data[key],0,
nDig=nDig,typeHint=float,OnLeave=AfterChange)
elemKeysLst.append([key,0])
refFlgElem.append([key,1])
else:
parmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' '+lbl),
0,wx.EXPAND)
parmVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,key,
typeHint=float,OnLeave=AfterChange)
elemKeysLst.append([key])
refFlgElem.append(None)
parmSizer.Add(parmVal,0,WACV)
Info = {}
for key in ('FreePrm1','FreePrm2','FreePrm3'):
parmVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,Controls,key,typeHint=str,
notBlank=False,OnLeave=SearchAllComments)
parmSizer.Add(parmVal,1,wx.EXPAND)
parmVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,key,typeHint=float)
parmSizer.Add(parmVal,0,WACV)
labelLst.append(Controls[key])
dspLst.append(None)
elemKeysLst.append([key])
refFlgElem.append(None)
mainSizer.Add(parmSizer,0)
mainSizer.Add((0,5),0)
if histName[:4] in ['SASD',]:
rho = [0.,0.]
anomrho = [0.,0.]
mu = 0.
subSizer = wx.FlexGridSizer(0,4,5,5)
Substances = G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Substances'))
for Id,item in enumerate(data['Materials']):
subSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Material: '),0,WACV)
matsel = wx.ComboBox(G2frame.dataWindow,value=item['Name'],choices=list(Substances['Substances'].keys()),
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Info[matsel.GetId()] = Id
matsel.Bind(wx.EVT_COMBOBOX,OnMaterial)
subSizer.Add(matsel,0,WACV)
subSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Volume fraction: '),0,WACV)
volfrac = G2G.ValidatedTxtCtrl(G2frame.dataWindow,item,'VolFrac',
xmin=0.,xmax=1.,nDig=(10,3),typeHint=float,OnLeave=OnVolFrac)
Info[volfrac.GetId()] = Id
subSizer.Add(volfrac,0,WACV)
try:
material = Substances['Substances'][item['Name']]
except KeyError:
print('ERROR - missing substance: '+item['Name'])
material = Substances['Substances']['vacuum']
mu += item['VolFrac']*material.get('XAbsorption',0.)
rho[Id] = material['Scatt density']
anomrho[Id] = material.get('XAnom density',0.)
data['Contrast'] = [(rho[1]-rho[0])**2,(anomrho[1]-anomrho[0])**2]
mainSizer.Add(subSizer,0)
conSizer = wx.BoxSizer(wx.HORIZONTAL)
conSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Contrast: %10.2f '%(data['Contrast'][0])),0,WACV)
conSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Anom. Contrast: %10.2f '%(data['Contrast'][1])),0,WACV)
mut = mu*data['Thick']
conSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Transmission (calc): %10.3f '%(np.exp(-mut))),0,WACV)
mainSizer.Add(conSizer,0)
G2frame.dataWindow.SetDataSize()
################################################################################
##### Indexing Peaks
################################################################################
[docs]
def UpdateIndexPeaksGrid(G2frame, data):
'''respond to selection of PWDR Index Peak List data
tree item.
'''
IndexId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Index Peak List')
Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[0]
limitId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Limits')
Limits = G2frame.GPXtree.GetItemPyData(limitId)
def RefreshIndexPeaksGrid(event):
r,c = event.GetRow(),event.GetCol()
peaks = G2frame.IndexPeaksTable.GetData()
if c == 2:
peaks[r][c] = not peaks[r][c]
G2frame.IndexPeaksTable.SetData(peaks)
G2frame.indxPeaks.ForceRefresh()
if 'PKS' in G2frame.GPXtree.GetItemText(G2frame.PatternId):
G2plt.PlotPowderLines(G2frame)
else:
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
def onCellListDClick(event):
'''Called after a double-click on a row/column label'''
r,c = event.GetRow(),event.GetCol()
if r >= 0 and c < 0: #row label: select it and replot!
G2frame.indxPeaks.ClearSelection()
G2frame.indxPeaks.SelectRow(r,True)
G2pwpl.PlotPatterns(G2frame,plotType='PWDR')
wx.CallAfter(G2frame.indxPeaks.ForceRefresh)
def OnReload(event):
peaks = []
sigs = []
Peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Peak List'))
for ip,peak in enumerate(Peaks['peaks']):
dsp = G2lat.Pos2dsp(Inst,peak[0])
peaks.append([peak[0],peak[2],True,False,0,0,0,dsp,0.0]) #SS?
try:
sig = Peaks['sigDict']['pos'+str(ip)]
except KeyError:
sig = 0.
sigs.append(sig)
data = [peaks,sigs]
G2frame.GPXtree.SetItemPyData(IndexId,data)
UpdateIndexPeaksGrid(G2frame,data)
def OnSave(event):
pth = G2G.GetExportPath(G2frame)
dlg = wx.FileDialog(G2frame, 'Choose Index peaks csv file', pth, '',
'indexing peaks file (*.csv)|*.csv',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
try:
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
filename = os.path.splitext(filename)[0]+'.csv'
File = open(filename,'w')
names = 'h,k,l,position,intensity,d-Obs,d-calc\n'
File.write(names)
fmt = '%d,%d,%d,%.4f,%.1f,%.5f,%.5f\n'
for refl in data[0]:
if refl[3]:
File.write(fmt%(refl[4],refl[5],refl[6],refl[0],refl[1],refl[7],refl[8]))
File.close()
finally:
dlg.Destroy()
def OnExportPreDICT(event):
'Place 2theta positions from Index Peak List into clipboard for cut-&-paste'
if wx.TheClipboard.Open():
txt = ''
c = 0
for refl in data[0]:
if refl[2]:
c += 1
txt += '{}\n'.format(refl[0])
wx.TheClipboard.SetData(wx.TextDataObject(txt))
wx.TheClipboard.Close()
else:
G2frame.ErrorDialog('Clipboard locked','Sorry, unable to access the clipboard, try again later. You might need to restart GSAS-II or reboot')
return
G2G.G2MessageBox(G2frame,
'{} reflection positions placed in clipboard. '.format(c)+
'In PreDICT open the DICVOL input. Update the number of '
'reflections (& wavelength if needed) in GUI. Then'
' use paste to replace the reflections '
'(starting at line 6...) in the DICVOL input.',
'DICVOL input generated')
def KeyEditPickGrid(event):
colList = G2frame.indxPeaks.GetSelectedCols()
data = G2frame.GPXtree.GetItemPyData(IndexId)
if event.GetKeyCode() == wx.WXK_RETURN:
event.Skip(True)
elif event.GetKeyCode() == wx.WXK_CONTROL:
event.Skip(True)
elif event.GetKeyCode() == wx.WXK_SHIFT:
event.Skip(True)
elif colList:
G2frame.indxPeaks.ClearSelection()
key = event.GetKeyCode()
for col in colList:
if G2frame.IndexPeaksTable.GetColLabelValue(col) in ['use',]:
if key == 89: #'Y'
for row in range(G2frame.IndexPeaksTable.GetNumberRows()): data[0][row][col]=True
elif key == 78: #'N'
for row in range(G2frame.IndexPeaksTable.GetNumberRows()): data[0][row][col]=False
elif key == 83: # 'S'
for row in range(G2frame.IndexPeaksTable.GetNumberRows()): data[0][row][col] = not data[0][row][col]
def onRefineCell(event):
RefineCell(G2frame)
UpdateIndexPeaksGrid(G2frame,data)
# start of UpdateIndexPeaksGrid
controls = None
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.IndexMenu) # needed below
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.PeakMenu) # needed below
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.IndPeaksMenu)
if 'PWD' in G2frame.GPXtree.GetItemText(G2frame.PatternId):
G2frame.Bind(wx.EVT_MENU, OnReload, id=G2G.wxID_INDXRELOAD)
G2frame.Bind(wx.EVT_MENU, OnSave, id=G2G.wxID_INDEXSAVE)
G2frame.Bind(wx.EVT_MENU, OnExportPreDICT, id=G2G.wxID_INDEXEXPORTDICVOL)
G2frame.Bind(wx.EVT_MENU, onRefineCell, id=G2G.wxID_REFINECELL2)
G2frame.dataWindow.IndexPeaks.Enable(False)
G2frame.IndexPeaksTable = []
if len(data[0]):
G2frame.dataWindow.IndexPeaks.Enable(True)
Unit = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Unit Cells List'))
if Unit:
if len(Unit) == 4: #patch
Unit.append({})
if len(Unit) == 5: #patch
Unit.append({})
controls,bravais,cellist,dmin,ssopt,magcells = Unit
if 'T' in Inst['Type'][0]: #TOF - use other limit!
dmin = G2lat.Pos2dsp(Inst,Limits[1][0])
else:
dmin = G2lat.Pos2dsp(Inst,Limits[1][1])
G2frame.HKL = np.array([])
G2frame.Extinct = []
if ssopt.get('Use',False):
cell = controls[6:12]
A = G2lat.cell2A(cell)
spc = controls[13]
SGData = G2spc.SpcGroup(spc)[1]
SSGData = G2spc.SSpcGroup(SGData,ssopt['ssSymb'])[1]
Vec = ssopt['ModVec']
maxH = ssopt['maxH']
G2frame.HKL = np.array(G2pwd.getHKLMpeak(dmin,Inst,SGData,SSGData,Vec,maxH,A))
data[0] = G2indx.IndexSSPeaks(data[0],G2frame.HKL)[1]
else: #select cell from table - no SS
for i,cell in enumerate(cellist):
if cell[-2]:
ibrav = cell[2]
A = G2lat.cell2A(cell[3:9])
G2frame.HKL = G2lat.GenHBravais(dmin,ibrav,A,ifList=True)
for hkl in G2frame.HKL:
hkl.insert(4,G2lat.Dsp2pos(Inst,hkl[3]))
G2frame.HKL = np.array(G2frame.HKL)
data[0] = G2indx.IndexPeaks(data[0],G2frame.HKL)[1]
break
rowLabels = []
for i in range(len(data[0])): rowLabels.append(str(i+1))
colLabels = ['position','intensity','use','indexed','h','k','l','d-obs','d-calc']
Types = [wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_FLOAT+':10,1',]+2*[wg.GRID_VALUE_BOOL,]+ \
3*[wg.GRID_VALUE_LONG,]+2*[wg.GRID_VALUE_FLOAT+':10,5',]
if len(data[0]) and len(data[0][0]) > 9:
colLabels = ['position','intensity','use','indexed','h','k','l','m','d-obs','d-calc']
Types = [wg.GRID_VALUE_FLOAT+':10,4',wg.GRID_VALUE_FLOAT+':10,1',]+2*[wg.GRID_VALUE_BOOL,]+ \
4*[wg.GRID_VALUE_LONG,]+2*[wg.GRID_VALUE_FLOAT+':10,5',]
G2frame.GPXtree.SetItemPyData(IndexId,data)
G2frame.IndexPeaksTable = G2G.Table(data[0],rowLabels=rowLabels,colLabels=colLabels,types=Types)
G2frame.dataWindow.currentGrids = []
G2frame.indxPeaks = G2G.GSGrid(parent=G2frame.dataWindow)
G2frame.indxPeaks.SetRowLabelSize(45)
G2frame.indxPeaks.SetTable(G2frame.IndexPeaksTable, True)
XY = []
Sigs = []
for r in range(G2frame.indxPeaks.GetNumberRows()):
for c in range(G2frame.indxPeaks.GetNumberCols()):
if c == 2:
G2frame.indxPeaks.SetReadOnly(r,c,isReadOnly=False)
else:
G2frame.indxPeaks.SetReadOnly(r,c,isReadOnly=True)
if data[0][r][2] and data[0][r][3]:
XY.append([data[0][r][-1],data[0][r][0]])
try:
sig = data[1][r]
except IndexError:
sig = 0.
Sigs.append(sig)
G2frame.indxPeaks.Bind(wg.EVT_GRID_CELL_LEFT_CLICK, RefreshIndexPeaksGrid)
G2frame.indxPeaks.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, onCellListDClick)
G2frame.indxPeaks.Bind(wx.EVT_KEY_DOWN, KeyEditPickGrid)
G2frame.indxPeaks.AutoSizeColumns(False)
if len(XY):
XY = np.array(XY)
G2plt.PlotCalib(G2frame,Inst,XY,Sigs,newPlot=True)
G2frame.dataWindow.ClearData()
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,label='Index peaks list'),0,WACV)
# add help button to bring up help web page - at right side of window
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add(G2frame.indxPeaks,1,wx.EXPAND,1)
botSizer = G2frame.dataWindow.bottomBox
parent = G2frame.dataWindow.bottomPanel
if controls:
ibrav = SetLattice(controls)
for cellGUI in cellGUIlist:
if ibrav in cellGUI[0]:
useGUI = cellGUI
botSizer.Add(wx.StaticText(parent,label='Cell: ',style=wx.ALIGN_RIGHT),0,WACV)
cellSizer = wx.FlexGridSizer(0,min(6,useGUI[1]),3,3)
botSizer.Add(cellSizer,0,WACV)
for txt,fmt,ifEdit,Id in zip(*useGUI[2]):
if 'Vol' in txt:
val = fmt % controls[12]
botSizer.Add(wx.StaticText(parent,label=txt,style=wx.ALIGN_RIGHT),0,WACV)
volVal = wx.TextCtrl(parent,value=val,style=wx.TE_READONLY,size=(65,-1))
botSizer.Add(volVal,0,WACV)
else:
val = f'%.{fmt[1]}f' % controls[6+Id]
cellSizer.Add(wx.StaticText(parent,label=txt,style=wx.ALIGN_RIGHT),0,wx.ALIGN_RIGHT|WACV)
volVal = wx.TextCtrl(parent,value=val,style=wx.TE_READONLY,size=(65,-1))
cellSizer.Add(volVal,0,WACV)
volVal.SetBackgroundColour(VERY_LIGHT_GREY)
if not ssopt.get('Use',False): #zero for super lattice doesn't work!
botSizer.Add((15,-1))
vcSizer = wx.BoxSizer(wx.VERTICAL)
vcSizer.Add(wx.StaticText(parent,label="Zero offset",
style=wx.ALIGN_CENTER),0,wx.EXPAND)
hcSizer = wx.BoxSizer(wx.HORIZONTAL)
zero = G2G.ValidatedTxtCtrl(parent,controls,1,nDig=(10,4),typeHint=float,
xmin=-5.,xmax=5.,size=(50,-1))
hcSizer.Add(zero,0,WACV)
zeroVar = G2G.G2CheckBox(parent,'Ref?',controls,0)
hcSizer.Add(zeroVar,0,WACV|wx.LEFT,3)
vcSizer.Add(hcSizer)
botSizer.Add(vcSizer,0,WACV)
# TODO: get SUs from cell refinement
# TODO: implement Enable on G2frame.dataWindow.RefineCell2 to match G2frame.dataWindow.RefineCell
G2frame.dataWindow.SetDataSize()
################################################################################
##### Unit cells
################################################################################
[docs]
def UpdateUnitCellsGrid(G2frame, data, callSeaResSelected=False,New=False,showUse=False):
'''respond to selection of PWDR Unit Cells data tree item.
:param wx.Frame G2frame: Main GSAS-II window
:param dict data: contents of "Unit Cells List" data tree item
:param bool callSeaResSelected: when True, selects first entry in
UnitCellsTable search results table
:param bool New:
:param bool showUse: when showUse is False (default) the Show flag
is cleared in all search tables. When True, and there is a True value
for Show, the flag is set for that in the grid and the row is scrolled
into view. This is currently implemented for indexing (Cell Search
Results) only.
'''
global KeyList
KeyList = []
def OnExportCells(event):
pth = G2G.GetExportPath(G2frame)
dlg = wx.FileDialog(G2frame, 'Choose Indexing Result csv file', pth, '',
'indexing result file (*.csv)|*.csv',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
try:
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
filename = os.path.splitext(filename)[0]+'.csv'
File = open(filename,'w')
names = 'M20,X20,Bravais,a,b,c,alpha,beta,gamma,volume\n'
File.write(names)
fmt = '%.2f,%d,%s,%.4f,%.4f,%.4f,%.2f,%.2f,%.2f,%.3f\n'
for cell in cells:
File.write(fmt%(cell[0],cell[1],bravaisSymb[cell[2]], cell[3],cell[4],cell[5], cell[6],cell[7],cell[8],cell[9]))
File.close()
finally:
dlg.Destroy()
def OnShowGenRefls(event):
'''Generate the reflections from the unit cell and
display them in the console window
'''
OnHklShow(None,indexFrom=' Indexing from unit cell & symmetry settings')
for r in G2frame.HKL:
print("{0:.0f},{1:.0f},{2:.0f} 2\u03B8={4:7.3f} d={3:8.4f}".format(*r))
def OnHklShow(event=None,Print=True,Plot=True,indexFrom=''):
'''Compute the location of powder diffraction peaks from the
cell in controls[6:12]. If the structure is modulated (ssopt['Use']
is True), then the space group in ssopt['SGData'] if defined.
Otherwise, the space group is taken from controls[13].
Magnetic space group information is placed separately into SGData,
so space group information is added to this dict to not replace that.
Reflections are placed in G2frame.HKL
If cellDisplayOpts['showExtinct'] is True, all reflections are computed
and reflections that are not present in the G2frame.HKL array are
placed in G2frame.Extinct
:params Print: if True, the M20 value, etc. is printed on the console
:returns: None or [Symb,False,M20,X20,Nhkl,frfnd] where
* Symb: Space group symbol
* M20: line position fit metric
* X20: number of indexed lines fit metric
* Nhkl: number of generated reflections below dmin
* frfnd: fraction of lines indexed
'''
result = None
PatternId = G2frame.PatternId
peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Index Peak List'))
if 'T' in Inst['Type'][0]:
dmin = G2lat.Pos2dsp(Inst,Limits[0])
else:
dmin = G2lat.Pos2dsp(Inst,Limits[1])
cell = controls[6:12]
A = G2lat.cell2A(cell)
spc = controls[13]
if ssopt.get('Use',False): #modulated
SGData.update(ssopt.get('SGData',G2spc.SpcGroup(spc)[1]))
else: #not modulated
SGData.update(G2spc.SpcGroup(spc)[1])
Symb = SGData['SpGrp']
M20 = X20 = 0.
if ssopt.get('Use',False) and ssopt.get('ssSymb',''):
# modulated is set -- and a super-space group symbol is provided
SSGData = G2spc.SSpcGroup(SGData,ssopt['ssSymb'])[1]
if SSGData is None:
SSGData = G2spc.SSpcGroup(SGData,ssopt['ssSymb'][:-1])[1] #skip trailing 's' for mag.
Symb = SSGData['SSpGrp']
Vec = ssopt['ModVec']
maxH = ssopt['maxH']
G2frame.HKL = G2pwd.getHKLMpeak(dmin,Inst,SGData,SSGData,Vec,maxH,A)
if len(peaks[0]):
peaks = [G2indx.IndexSSPeaks(peaks[0],G2frame.HKL)[1],peaks[1]] #keep esds from peak fit
M20,X20 = G2indx.calc_M20SS(peaks[0],G2frame.HKL)
else:
G2frame.HKL = G2pwd.getHKLpeak(dmin,SGData,A,Inst)
G2frame.Extinct = []
if cellDisplayOpts['showExtinct']:
# generate a table of extinct reflections -- not all, just those not
# close to a allowed peak
allpeaks = G2pwd.getHKLpeak(dmin,G2spc.SpcGroup('P 1')[1],A,Inst)
alreadyShown = G2frame.HKL[:,4].round(3)
for peak in allpeaks: # show one reflection only if in a region with no others
pos = peak[4].round(3)
if pos in alreadyShown: continue
alreadyShown = np.append(alreadyShown,pos)
G2frame.Extinct.append(peak)
if len(peaks[0]): # put hkl values into the Index Peak List
peaks = [G2indx.IndexPeaks(peaks[0],G2frame.HKL)[1],peaks[1]] #keep esds from peak fit
M20,X20 = G2indx.calc_M20(peaks[0],G2frame.HKL)
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Index Peak List'),peaks)
G2frame.HKL = np.array(G2frame.HKL)
frfnd = 0.0
Nhkl = len(G2frame.HKL)
if Nhkl:
frfnd = min(1.0,float(len(peaks[0]))/Nhkl)
if Print:
print (' new M20,X20: %.2f %d, fraction found: %.3f for %s'%(M20,X20,frfnd,Symb))
result = [Symb,False,M20,X20,Nhkl,frfnd]
if not Plot: return result
if 'PKS' in G2frame.GPXtree.GetItemText(G2frame.PatternId):
G2plt.PlotPowderLines(G2frame,indexFrom=indexFrom)
else:
G2pwpl.PlotPatterns(G2frame,indexFrom=indexFrom)
return result
def OnSortCells(event):
'''Sort the display of found unit cells
'''
controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(UnitCellsId)
c = event.GetCol()
if colLabels[c] == 'M20':
cells = G2indx.sortM20(cells)
elif colLabels[c] in ['X20','Bravais','a','b','c','alpha','beta','gamma','Volume']:
if c == 1:
c += 1 #X20 before Use
cells = G2indx.sortCells(cells,c-1) #an extra column (Use) not in cells
else:
return
data = [controls,bravais,cells,dmin,ssopt,magcells]
G2frame.GPXtree.SetItemPyData(UnitCellsId,data)
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data,showUse=True)
def CopyUnitCell(event):
controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(UnitCellsId)
controls = controls[:5]+10*[0.,]
if len(cells):
for Cell in cells:
if Cell[-2]:
break
cell = Cell[2:10]
controls[4] = 1
controls[5] = bravaisSymb[cell[0]]
controls[6:13] = cell[1:8]
controls[13] = spaceGroups[bravaisSymb.index(controls[5])]
ssopt['SgResults'] = []
# G2frame.dataWindow.RefineCell.Enable(True) # set in UpdateUnitCellsGrid
elif magcells:
for phase in magcells:
if phase['Use']:
break
SGData = phase['SGData']
controls[4] = 1
controls[5] = (SGData['SGLatt']+SGData['SGLaue']).replace('-','')
if controls[5][1:] == 'm3': controls[5] += 'm'
if 'P3' in controls[5] or 'P-3' in controls[5]: controls[5] = 'P6/mmm'
if 'R' in controls[5]: controls[5] = 'R3-H'
controls[6:13] = phase['Cell']
controls[13] = SGData['SpGrp']
ssopt['SGData'] = SGData
data = [controls,bravais,cells,dminx,ssopt,magcells]
G2frame.dataWindow.RunSubGroups.Enable(True)
G2frame.GPXtree.SetItemPyData(UnitCellsId,data)
OnHklShow(None,indexFrom=' Indexing from new unit cell & symmetry settings')
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def LoadUnitCell(event):
'''Called in response to a Load Phase menu command'''
UnitCellsId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Unit Cells List')
#data = G2frame.GPXtree.GetItemPyData(UnitCellsId)
#if len(data) < 5:
# data.append({})
#controls,bravais,cells,dminx,ssopt = data[:5]
magcells = [] #clear away old mag cells list (if any)
controls[15:] = [['0','0','0',' ',' ',' '],[],]
data = controls,bravais,cells,dminx,ssopt,magcells
G2frame.GPXtree.SetItemPyData(UnitCellsId,data)
pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Phases')
if not pId: return
Phases = []
item, cookie = G2frame.GPXtree.GetFirstChild(pId)
while item:
pName = G2frame.GPXtree.GetItemText(item)
Phase = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,pId,pName))
if not Phase['General']['SGData'].get('SGFixed',False):
Phases.append(G2frame.GPXtree.GetItemText(item))
item, cookie = G2frame.GPXtree.GetNextChild(pId, cookie)
if not len(Phases):
wx.MessageBox('NB: Magnetic phases from mcif files are not suitable for this purpose,\n because of space group symbol - operators mismatches',
caption='No usable space groups',style=wx.ICON_EXCLAMATION)
return
elif len(Phases) == 1: # don't ask questions when there is only 1 answer
pNum = 0
else:
pNum = G2G.ItemSelector(Phases,G2frame,'Select phase',header='Phase')
if pNum is None: return
Phase = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,pId,Phases[pNum]))
Phase['magPhases'] = G2frame.GPXtree.GetItemText(G2frame.PatternId) #use as reference for recovering possible phases
Cell = Phase['General']['Cell']
SGData.update(Phase['General']['SGData'])
if 'SGGray' not in SGData:
SGData['SGGray'] = False
if Phase['General']['Type'] == 'nuclear' and 'MagSpGrp' in SGData:
SGData.update(G2spc.SpcGroup(SGData['SpGrp'])[1])
G2frame.dataWindow.RunSubGroups.Enable(True)
ssopt.update({'Use':False,'ssSymb':'(abg)','ModVec':[0.1,0.1,0.1],'maxH':1,'SgResults':[],})
if 'SuperSg' in Phase['General'] or SGData.get('SGGray',False):
ssopt.update({'SGData':SGData,'ssSymb':Phase['General']['SuperSg'],'ModVec':Phase['General']['SuperVec'][0],'Use':True,'maxH':1})
ssopt['ssSymb'] = ssopt['ssSymb'].replace(',','')
ssSym = ssopt['ssSymb']
if SGData.get('SGGray',False):
ssSym = ssSym[:-1]
if ssSym not in G2spc.SSChoice(SGData):
ssSym = ssSym.split(')')[0]+')000'
ssopt['ssSymb'] = ssSym
wx.MessageBox('Super space group '+SGData['SpGrp']+ssopt['ssSymb']+' not valid;\n It is set to '+ssSym,
caption='Unusable super space group',style=wx.ICON_EXCLAMATION)
G2frame.dataWindow.RunSubGroups.Enable(False)
SpGrp = SGData['SpGrp']
if 'mono' in SGData['SGSys']:
SpGrp = G2spc.fixMono(SpGrp)
if SpGrp == None:
wx.MessageBox('Monoclinic '+SGData['SpGrp']+' not usable here',caption='Unusable space group',style=wx.ICON_EXCLAMATION)
return
controls[13] = SpGrp
controls[4] = 1
controls[5] = (SGData['SGLatt']+SGData['SGLaue']).replace('-','')
if controls[5][1:] == 'm3': controls[5] += 'm'
if controls[5] in ['P3','P3m1','P31m','P6/m']: controls[5] = 'P6/mmm'
if controls[5] in ['P4/m',]: controls[5] = 'P4/mmm'
if 'R' in controls[5]: controls[5] = 'R3-H'
controls[6:13] = Cell[1:8]
cx,ct,cs,cia = Phase['General']['AtomPtrs']
controls[15] = [atom[:cx+3] for atom in Phase['Atoms']]
if 'N' in Inst['Type'][0]:
if not ssopt.get('Use',False):
G2frame.dataWindow.RunSubGroupsMag.Enable(True)
data = controls,bravais,cells,dminx,ssopt,magcells
G2frame.GPXtree.SetItemPyData(UnitCellsId,data)
G2frame.dataWindow.RefineCell.Enable(True)
OnHklShow(None,indexFrom=' Indexing from loaded unit cell & symmetry settings')
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
# TODO: I think this used to work, but this needs to be revisited due to
# AttributeError: 'G2DataWindow' object has no attribute 'ReImportMenuId'
# from:
# reqrdr = G2frame.dataWindow.ReImportMenuId.get(event.GetId())
#
# def ImportUnitCell(event):
# controls,bravais,cells,dminx,ssopt = G2frame.GPXtree.GetItemPyData(UnitCellsId)[:5]
# reqrdr = G2frame.dataWindow.ReImportMenuId.get(event.GetId())
# rdlist = G2frame.OnImportGeneric(reqrdr,
# G2frame.ImportPhaseReaderlist,'phase')
# if len(rdlist) == 0: return
# rd = rdlist[0]
# Cell = rd.Phase['General']['Cell']
# SGData = rd.Phase['General']['SGData']
# if '1 1' in SGData['SpGrp']:
# wx.MessageBox('Unusable space group',caption='Monoclinic '+SGData['SpGrp']+' not usable here',style=wx.ICON_EXCLAMATION)
# return
# controls[4] = 1
# controls[5] = (SGData['SGLatt']+SGData['SGLaue']).replace('-','')
# if controls[5][1:] == 'm3': controls[5] += 'm'
# if 'P3' in controls[5] or 'P-3' in controls[5]: controls[5] = 'P6/mmm'
# if 'R' in controls[5]: controls[5] = 'R3-H'
# controls[6:13] = Cell[1:8]
# controls[13] = SGData['SpGrp']
# ssopt['SgResults'] = []
# G2frame.dataWindow.RefineCell.Enable(True)
# OnHklShow(None,indexFrom=' Indexing from imported unit cell & symmetry settings')
# wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def onRefineCell(event):
data = RefineCell(G2frame)
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnIndexPeaks(event):
PatternId = G2frame.PatternId
#print ('Peak Indexing')
keepcells = []
try:
controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Unit Cells List'))
ssopt['SgResults'] = []
for cell in cells:
if cell[11]:
cell[10] = False #clear selection flag on keepers
keepcells.append(cell)
except IndexError:
pass
except ValueError:
G2frame.ErrorDialog('Error','Need to set controls in Unit Cell List first')
return
if ssopt.get('Use',False):
G2frame.ErrorDialog('Super lattice error','Indexing not available for super lattices')
return
if True not in bravais:
G2frame.ErrorDialog('Error','No Bravais lattices selected')
return
else:
ibrav = bravais.index(True)
if not len(peaks[0]):
G2frame.ErrorDialog('Error','Index Peak List is empty')
return
if len(peaks[0][0]) > 9:
G2frame.ErrorDialog('Error','You need to reload Index Peaks List first')
return
G2frame.dataWindow.CopyCell.Enable(False)
G2frame.dataWindow.RefineCell.Enable(False)
dlg = wx.ProgressDialog("Generated reflections",'0 '+" cell search for "+bravaisNames[ibrav],101,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME|wx.PD_CAN_SKIP|wx.PD_CAN_ABORT) #desn't work in 32 bit versions
# style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME|wx.PD_CAN_ABORT)
try:
OK,dmin,newcells = G2indx.DoIndexPeaks(peaks[0],controls,bravais,dlg,G2frame.ifX20)
finally:
dlg.Destroy()
cells = keepcells+newcells
cells = G2indx.sortM20(cells)
if OK:
cells[0][10] = True #select best M20
data = [controls,bravais,cells,dmin,ssopt,magcells]
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Unit Cells List'),data)
bestCell = cells[0]
if bestCell[0] > 10.:
G2frame.HKL = G2lat.GenHBravais(dmin,bestCell[2],G2lat.cell2A(bestCell[3:9]),ifList=True)
for hkl in G2frame.HKL:
hkl.insert(4,G2lat.Dsp2pos(Inst,hkl[3])+controls[1])
G2frame.HKL = np.array(G2frame.HKL)
if 'PKS' in G2frame.GPXtree.GetItemText(G2frame.PatternId):
G2plt.PlotPowderLines(G2frame,indexFrom=' Indexing from result #0, M20= %.3f'%cells[0][0])
else:
G2pwpl.PlotPatterns(G2frame,indexFrom=' Indexing from result #0, M20= %.3f'%cells[0][0])
G2frame.dataWindow.CopyCell.Enable(True)
G2frame.dataWindow.IndexPeaks.Enable(True)
G2frame.dataWindow.MakeNewPhase.Enable(True)
G2frame.ifX20 = True
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def SeaResSelected(event=None):
'''Responds when "show" is pressed in the UnitCellsTable (search results table)
or at end of UpdateUnitCellsGrid (When callSeaResSelected==True; event==None).
Generates & plots reflections
'''
from . import k_vector_search as kvs
data = G2frame.GPXtree.GetItemPyData(UnitCellsId)
cells,dminx = data[2:4]
if event is None:
r,c = 0,0
colLabel = 'show'
else:
r,c = event.GetRow(),event.GetCol()
colLabel = event.GetEventObject().GetColLabelValue(c)
if cells:
clearShowFlags()
disableCellEntries()
Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(
G2frame,G2frame.PatternId,'Instrument Parameters'))[0]
if cells[0][0] == '?': # k-vector table
# uncheck all rows then check only the one used row
for i in range(len(cells)):
UnitCellsTable.SetValue(i,c,False)
UnitCellsTable.SetValue(r,c,True)
if G2frame.kvecSearch['mode']:
phase_sel = G2frame.kvecSearch['phase']
_, Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
Phase = Phases[phase_sel]
lat_type = Phase["General"]["SGData"]["SGLatt"]
lat_sym = Phase["General"]["SGData"]["SGSys"]
if lat_sym == "trigonal":
brav_sym = "hR"
else:
brav_sym = lat_sym[0] + lat_type
Trans = np.eye(3)
Uvec = np.zeros(3)
Vvec = np.zeros(3)
newPhase = copy.deepcopy(Phase)
newPhase['ranId'] = ran.randint(0, sys.maxsize)
newPhase['General']['SGData'] = G2spc.SpcGroup('P 1')[1]
newPhase, _ = G2lat.TransformPhase(Phase, newPhase, Trans,
Uvec, Vvec, False)
atoms_pointer = newPhase['General']['AtomPtrs']
atom_coords = list()
atom_types = list()
for atom in newPhase["Atoms"]:
coord_tmp = atom[atoms_pointer[0]:atoms_pointer[0] + 3]
atom_coords.append(coord_tmp)
type_tmp = atom[atoms_pointer[1]]
atom_types.append(type_tmp)
atom_ids = kvs.unique_id_gen(atom_types)
cell_params = newPhase["General"]["Cell"][1:7]
lat_vectors = kvs.lat_params_to_vec(cell_params)
# Generate (hkl) coordinate in primitive reciprocal space.
# 0-5 for each direction should be generating enough
# satellite peaks for users to check.
hkl_refls = list()
for i in range(6):
for j in range(6):
for k in range(6):
hkl_refls.append([i, j, k])
k_search = kvs.kVector(brav_sym, lat_vectors,
atom_coords, atom_ids,hkl_refls, [0.], 0.)
kpoint = cells[r][3:6]
kpoint = k_search.hklConvToPrim(kpoint)
rep_prim_latt = k_search.kpathFinder()["reciprocal_primitive_lattice"]
satellite_peaks = list()
for nucp in k_search.nucPeaks:
all_zero_nuc = all(v == 0 for v in nucp)
all_zero_k = all(v == 0 for v in kpoint)
if all_zero_nuc and all_zero_k:
continue
hkl_prim = np.array(nucp)
hkl_p_k = hkl_prim + kpoint
k_cart = np.matmul(hkl_p_k,rep_prim_latt)
d_hkl_p_k = 2. * np.pi / np.linalg.norm(k_cart)
satellite_peaks.append(d_hkl_p_k)
hkl_m_k = hkl_prim - kpoint
k_cart = np.matmul(hkl_m_k,rep_prim_latt)
d_hkl_m_k = 2. * np.pi / np.linalg.norm(k_cart)
satellite_peaks.append(d_hkl_m_k)
satellite_peaks = sorted(list(set(satellite_peaks)),reverse=True)
# Here we are generating a dummy HKL list to host the
# satellite peak positions for the selected k vector. We
# set (hkl) for all the peaks to (000).
G2frame.HKL = list()
for d in satellite_peaks:
list_tmp = [0, 0, 0,d, G2lat.Dsp2pos(Inst, d),-1]
G2frame.HKL.append(list_tmp)
G2frame.HKL = np.array(G2frame.HKL)
G2pwpl.PlotPatterns(G2frame)
if colLabel == 'show':
for i in range(len(cells)):
cells[i][-2] = False
UnitCellsTable.SetValue(i,c,False)
UnitCellsTable.SetValue(r,c,True)
gridDisplay.ForceRefresh()
cells[r][-2] = True
ibrav = cells[r][2]
try:
A = G2lat.cell2A(cells[r][3:9])
G2frame.HKL = G2lat.GenHBravais(dmin,ibrav,A,ifList=True)
for hkl in G2frame.HKL:
hkl.insert(4,G2lat.Dsp2pos(Inst,hkl[3])+controls[1])
G2frame.HKL = np.array(G2frame.HKL)
if 'PKS' in G2frame.GPXtree.GetItemText(G2frame.PatternId):
G2plt.PlotPowderLines(G2frame,indexFrom=' Indexing selection #%d M20= %.3f'%(r,cells[r][0]))
else:
G2pwpl.PlotPatterns(G2frame,indexFrom=' Indexing selection #%d M20= %.3f'%(r,cells[r][0]))
except:
pass
elif colLabel == 'Keep':
if UnitCellsTable.GetValue(r,c):
UnitCellsTable.SetValue(r,c,False)
cells[r][c] = False
else:
cells[r][c] = True
UnitCellsTable.SetValue(r,c,True)
gridDisplay.ForceRefresh()
G2frame.GPXtree.SetItemPyData(UnitCellsId,data)
def MakeNewPhase(event):
PhaseName = ''
dlg = wx.TextEntryDialog(None,'Enter a name for this phase','Phase Name Entry','New phase',
style=wx.OK)
try:
if dlg.ShowModal() == wx.ID_OK:
PhaseName = dlg.GetValue()
cells = G2frame.GPXtree.GetItemPyData(UnitCellsId)[2]
for Cell in cells:
if Cell[-2]:
break
cell = Cell[2:10]
sub = G2gd.FindPhaseItem(G2frame)
sub = G2frame.GPXtree.AppendItem(parent=sub,text=PhaseName)
E,SGData = G2spc.SpcGroup(controls[13])
G2frame.GPXtree.SetItemPyData(sub, \
G2obj.SetNewPhase(Name=PhaseName,SGData=SGData,cell=cell[1:],Super=ssopt))
G2frame.GetStatusBar().SetStatusText('Change space group from '+str(controls[13])+' if needed',1)
finally:
dlg.Destroy()
def TransformUnitCell(event):
Trans = np.eye(3)
Uvec = np.zeros(3)
Vvec = np.zeros(3)
ifMag = False
Type = 'nuclear'
BNSlatt = ''
E,SGData = G2spc.SpcGroup(controls[13])
phase = {'General':{'Name':'','Type':Type,'Cell':['',]+controls[6:13],'SGData':SGData}}
dlg = G2phsG.TransformDialog(G2frame,phase,Trans,Uvec,Vvec,ifMag,BNSlatt)
try:
if dlg.ShowModal() == wx.ID_OK:
newPhase,Trans,Uvec,Vvec,ifMag,ifConstr,Common = dlg.GetSelection()
sgData = newPhase['General']['SGData']
controls[5] = sgData['SGLatt']+sgData['SGLaue']
controls[13] = sgData['SpGrp']
ssopt['SGData'] = sgData
controls[6:13] = newPhase['General']['Cell'][1:8]
else:
return
finally:
dlg.Destroy()
OnHklShow(None,indexFrom=' Indexing from transformed unit cell & symmetry settings')
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
# def OnLatSym(event):
# 'Run Bilbao PseudoLattice cell search'
# # look up a space group matching Bravais lattice (should not matter which one)
# bravaisSPG = {'Fm3m':225,'Im3m':229,'Pm3m':221,'R3-H':146,'P6/mmm':191,
# 'I4/mmm':139,'P4/mmm':123,'Fmmm':69,'Immm':71,
# 'Cmmm':65,'Pmmm':47,'C2/m':12,'P2/m':10,'P1':2}
# pUCid = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Unit Cells List')
# controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(pUCid)
# sgNum = bravaisSPG.get(controls[5],0)
# if sgNum < 1:
# wx.MessageBox('Sorry, only standard cell settings are allowed, please transform axes',caption='Bilbao requires standard settings',style=wx.ICON_EXCLAMATION)
# return
# cell = controls[6:12]
# tolerance = 5.
# dlg = G2G.SingleFloatDialog(G2frame,'Tolerance',
# 'Enter angular tolerance for search',5.0,[.1,30.],"%.1f")
# if dlg.ShowModal() == wx.ID_OK:
# tolerance = dlg.GetValue()
# dlg.Destroy()
# else:
# dlg.Destroy()
# return
# wx.MessageBox(' For use of PSEUDOLATTICE, please cite:\n\n'+
# G2G.GetCite('Bilbao: PSEUDOLATTICE'),
# caption='Bilbao PSEUDOLATTICE',
# style=wx.ICON_INFORMATION)
# wx.BeginBusyCursor()
# page = kSUB.subBilbaoCheckLattice(sgNum,cell,tolerance)
# wx.EndBusyCursor()
# if not page: return
# cells.clear()
# for i,(cell,mat) in enumerate(kSUB.parseBilbaoCheckLattice(page)):
# cells.append([])
# cells[-1] += [mat,0,16]
# cells[-1] += cell
# cells[-1] += [G2lat.calc_V(G2lat.cell2A(cell)),False,False]
# G2frame.GPXtree.SetItemPyData(pUCid,data)
# G2frame.OnFileSave(event)
# wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnNISTLatSym(event):
'Run NIST*LATTICE cell search'
pUCid = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Unit Cells List')
controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(pUCid)
nistInput=[0.2,1.,2,3]
msg = G2G.NISTlatUse(True)
dlg = wx.Dialog(G2frame,style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER)
sizer = wx.BoxSizer(wx.VERTICAL)
sizer.Add(wx.StaticText(dlg,label='NIST*LATTICE Cell Symmetry Search Settings'),
0,wx.ALIGN_CENTER_HORIZONTAL,0)
sizer.Add((-1,15))
sizer.Add(wx.StaticText(dlg,label=msg))
sizer.Add((-1,15))
sizer.Add(wx.StaticText(dlg,label=(
('Starting cell: '+3*'{:.3f}, '+3*'{:.2f}, ').format(
*controls[6:12]))))
sizer.Add((-1,15))
tableSizer = wx.FlexGridSizer(0,2,0,0)
tableSizer.Add(wx.StaticText(dlg,label='Cell length tolerance (A) '),
0,WACV|wx.ALIGN_LEFT)
w = G2G.ValidatedTxtCtrl(dlg,nistInput,0,nDig=(6,2))
tableSizer.Add(w)
tableSizer.Add(wx.StaticText(dlg,label='Cell angle tolerance (deg) '),
0,WACV|wx.ALIGN_LEFT)
w = G2G.ValidatedTxtCtrl(dlg,nistInput,1,nDig=(6,1))
tableSizer.Add(w)
#
# next option makes it too easy to create a really
# long-running (infinite?) computation. Removed for now.
#
#tableSizer.Add(wx.StaticText(dlg,label='Cell volume range (ratio) '),
# 0,WACV|wx.ALIGN_LEFT)
#w = G2G.ValidatedTxtCtrl(dlg,nistInput,2)
#tableSizer.Add(w)
tableSizer.Add(wx.StaticText(dlg,label='Search mode: Generate '),
0,WACV|wx.ALIGN_LEFT)
tableSizer.Add(G2G.EnumSelector(dlg,nistInput,3,
['supercells', 'subcells', 'sub- and supercells'],[1,2,3]))
sizer.Add(tableSizer,1,wx.EXPAND)
btnsizer = wx.StdDialogButtonSizer()
btn = wx.Button(dlg, wx.ID_OK)
btn.SetDefault()
btn.Bind(wx.EVT_BUTTON, lambda x: dlg.EndModal(wx.ID_OK))
btnsizer.AddButton(btn)
btn = wx.Button(dlg, wx.ID_CANCEL)
btn.Bind(wx.EVT_BUTTON, lambda x: dlg.EndModal(wx.ID_CANCEL))
btnsizer.AddButton(btn)
btnsizer.Realize()
sizer.Add(btnsizer, 0, wx.EXPAND|wx.ALL, 5)
dlg.SetSizer(sizer)
sizer.Fit(dlg)
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
dlg.Destroy()
else:
dlg.Destroy()
return
tol = 3*[nistInput[0]]+3*[nistInput[1]]
cell = controls[6:12]
center = controls[13].strip()[0]
delta = nistInput[2]
mode = nistInput[3]
wx.BeginBusyCursor()
import nistlat
out = nistlat.CellSymSearch(cell, center, tolerance=tol, mode=mode,deltaV=delta)
wx.EndBusyCursor()
if not out: return
cells.clear()
for o in out:
cells.append([])
c = o[2][0]
# assign a Laue class
laue = 16 # P1
if c[0] == c[1] == c[2] and c[3] == c[4] == c[5] == 90:
if o[2][1] == 'F':
laue = 0 # Fm3m
elif o[2][1] == 'I':
laue = 1 # Im3m
else:
laue = 2 # Pm3m
elif o[2][1] == 'R':
laue = 3 # R3
elif c[0] == c[1] and c[5] == 120:
laue = 4 # P6/mmm
elif c[0] == c[1] and c[3] == c[4] == c[5] == 90 and o[2][1] == 'I':
laue = 5 # I4/mmm
elif c[0] == c[1] and c[3] == c[4] == c[5] == 90 and o[2][1] == 'P':
laue = 6 # P4/mmm
elif c[3] == c[4] == c[5] == 90 and o[2][1] == 'F':
laue = 7 # 'Fmmm'
elif c[3] == c[4] == c[5] == 90 and o[2][1] == 'I':
laue = 8 # 'Immm'
elif c[3] == c[4] == c[5] == 90 and o[2][1] == 'A':
laue = 9 # 'Ammm'
elif c[3] == c[4] == c[5] == 90 and o[2][1] == 'B':
laue = 10 # 'Bmmm'
elif c[3] == c[4] == c[5] == 90 and o[2][1] == 'C':
laue = 11 # 'Cmmm'
elif c[3] == c[4] == c[5] == 90 and o[2][1] == 'P':
laue = 12 # 'Pmmm'
elif c[3] == c[5] == 90 and o[2][1] == 'C':
laue = 13 # 'C2/m'
elif c[3] == c[5] == 90 and o[2][1] == 'P':
laue = 14 # 'P2/m'
elif o[2][1] == 'C':
laue = 15 # 'C1'
cells[-1] += [o[4],0,laue]
cells[-1] += c
cells[-1] += [G2lat.calc_V(G2lat.cell2A(c)),False,False]
G2frame.GPXtree.SetItemPyData(pUCid,data)
G2frame.OnFileSave(event)
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnRunSubs(event):
G2frame.dataWindow.RunSubGroupsMag.Enable(False)
pUCid = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Unit Cells List')
controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(pUCid)
E,SGData = G2spc.SpcGroup(controls[13])
Kx = [' ','0','1/2','-1/2','1/3','-1/3','2/3','1']
Ky = [' ','0','1/2','1/3','2/3','1']
Kz = [' ','0','1/2','3/2','1/3','2/3','1']
kvec = [['0','0','0'],[' ',' ',' '],[' ',' ',' ',' ']]
dlg = G2G.MultiDataDialog(G2frame,title='SUBGROUPS options',
prompts=[' k-vector 1', \
' Use whole star',' Filter by','preserve axes','max unique'],
values=kvec[0:1]+[False,'',True,100],
limits=[[Kx[1:],Ky[1:],Kz[1:]],[True,False],['',' Landau transition',' Only maximal subgroups',],
[True,False],[1,100]],
formats=[['choice','choice','choice'],'bool','choice',
'bool','%d',])
dlg.CenterOnParent()
if dlg.ShowModal() != wx.ID_OK: return
magcells = []
newVals = dlg.GetValues()
kvec = newVals[0]+7*[' ']
star = newVals[1]
filterby = newVals[2]
keepaxes = newVals[3]
maxequiv = newVals[4]
nkvec = kvec.index(' ')
if 'maximal' in filterby:
maximal = True
Landau = False
elif 'Landau' in filterby:
maximal = False
Landau = True
else:
maximal = False
Landau = False
if nkvec not in [0,3,6,9]:
wx.MessageBox('Error: check your propagation vector(s)',
caption='Bilbao SUBGROUPS setup error',style=wx.ICON_EXCLAMATION)
return
if nkvec in [6,9] and Landau:
wx.MessageBox('Error, multi k-vectors & Landau not compatible',
caption='Bilbao SUBGROUPS setup error',style=wx.ICON_EXCLAMATION)
return
dlg = wx.ProgressDialog('SUBGROUPS results',
'Searching for subgroups',11,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE)
if kSUB.RegisterProgressDialog(dlg):
dlg.Destroy()
return
wx.MessageBox(' For use of SUBGROUPS, please cite:\n\n'+
G2G.GetCite('Bilbao: k-SUBGROUPSMAG'),
caption='Bilbao SUBGROUPS',
style=wx.ICON_INFORMATION)
try:
wx.BeginBusyCursor()
SubGroups,baseList = kSUB.GetNonStdSubgroups(SGData,kvec[:9],star,Landau)
wx.EndBusyCursor()
if SubGroups is None:
wx.MessageBox('Internet connection problem? Check console output.',
caption='Bilbao SUBGROUPS error',
style=wx.ICON_EXCLAMATION)
return
if not SubGroups:
if Landau:
wx.MessageBox('No results from SUBGROUPS, multi k-vectors & Landau not compatible',
caption='Bilbao SUBGROUPS error',style=wx.ICON_EXCLAMATION)
else:
wx.MessageBox('No results from SUBGROUPS, check your propagation vector(s)',
caption='Bilbao SUBGROUPS error',style=wx.ICON_EXCLAMATION)
return
controls[14] = kvec[:9]
try:
controls[16] = baseList
except IndexError:
controls.append(baseList)
for ir,result in enumerate(SubGroups):
dlg.Update(ir%10,newmsg=f'Processing {result[0]}')
Trans = np.array(eval(result[1][0]))
Uvec = np.array(eval(result[1][1]))
phase = G2lat.makeBilbaoPhase(result,Uvec,Trans)
phase['gid'] = result[2]
phase['altList'] = result[3]
phase['supList'] = eval(result[4])
RVT = None
if keepaxes:
RVT = G2lat.FindNonstandard(controls,phase)
if RVT is not None:
result,Uvec,Trans = RVT
phase.update(G2lat.makeBilbaoPhase(result,Uvec,Trans))
phase['Cell'] = G2lat.TransformCell(controls[6:12],Trans)
phase['maxequiv'] = maxequiv
phase['nAtoms'] = len(TestAtoms(phase,controls[15],SGData,Uvec,Trans,maxequiv,maximal))
magcells.append(phase)
finally:
dlg.Destroy()
kSUB.RegisterProgressDialog()
magcells[0]['Use'] = True
SGData = magcells[0]['SGData']
A = G2lat.cell2A(magcells[0]['Cell'][:6])
G2frame.HKL = np.array(G2pwd.getHKLpeak(1.0,SGData,A,Inst))
G2pwpl.PlotPatterns(G2frame,extraKeys=KeyList)
data = [controls,bravais,cells,dmin,ssopt,magcells]
G2frame.GPXtree.SetItemPyData(pUCid,data)
G2frame.OnFileSave(event)
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnRunSubsMag(event,kvec1=None):
def strTest(text):
if '.' in text: # no decimals
return False
elif text.strip() in [' ','0','1','-1','3/2']: # specials
return True
elif '/' in text: #process fraction
nums = text.split('/')
return (0 < int(nums[1]) < 10) and (0 < abs(int(nums[0])) < int(nums[1]))
return False
G2frame.dataWindow.RunSubGroups.Enable(False)
pUCid = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Unit Cells List')
controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(pUCid)
E,SGData = G2spc.SpcGroup(controls[13])
try:
atoms = list(set([atom[1] for atom in controls[15]]))
except:
wx.MessageBox('Error: Problem with phase. Use Load Phase 1st.',
caption='k-SUBGROUPSMAG setup error: Phase loaded?',style=wx.ICON_EXCLAMATION)
return
testAtoms = ['',]+[atom for atom in atoms if (len(G2elem.GetMFtable([atom,],[2.0,])) and atom != 'O')] #skip "magnetic" O atoms
kvec = [['0','0','0'],[' ',' ',' '],[' ',' ',' ',' ']]
msg = f"Run k-SUBGROUPSMAG on space group {SGData['SpGrp']}\n"+'For k-vectors, enter rational fraction, 0, -1 or 1; no decimals'
dlg = G2G.MultiDataDialog(G2frame,title='k-SUBGROUPSMAG options',
prompts=[' k-vector 1',' k-vector 2',' k-vector 3',
' Use whole star',' Filter by','preserve axes',
'test for mag. atoms','all have moment','max unique'],
values=kvec+[False,'',True,'',False,100],
limits=[['0','0','0'],['0','0','0'],['0','0','0'],
[True,False],['',' Landau transition',' Only maximal subgroups',],
[True,False],testAtoms,[True,False],[1,100]],
testfxns = [[strTest,strTest,strTest],
[strTest,strTest,strTest],
[strTest,strTest,strTest],
None,None,None,None,None,None],
formats=[['testfxn','testfxn','testfxn'],
['testfxn','testfxn','testfxn'],
['testfxn','testfxn','testfxn'],
'bool','choice','bool','choice','bool','%d',],
header=msg)
if dlg.ShowModal() != wx.ID_OK: return
magcells = []
newVals = dlg.GetValues()
kvec[:9] = newVals[0]+newVals[1]+newVals[2]+[' ',]
nkvec = kvec.index(' ')
star = newVals[3]
filterby = newVals[4]
keepaxes = newVals[5]
atype = newVals[6]
allmom = newVals[7]
maxequiv = newVals[8]
if 'maximal' in filterby:
maximal = True
Landau = False
elif 'Landau' in filterby:
maximal = False
Landau = True
else:
maximal = False
Landau = False
if nkvec not in [0,3,6,9]:
wx.MessageBox('Error: check your propagation vector(s)',
caption='Bilbao k-SUBGROUPSMAG setup error',style=wx.ICON_EXCLAMATION)
return
if nkvec in [6,9] and Landau:
wx.MessageBox('Error, multi k-vectors & Landau not compatible',
caption='Bilbao k-SUBGROUPSMAG setup error',style=wx.ICON_EXCLAMATION)
return
magAtms = [atom for atom in controls[15] if atom[1] == atype]
try:
dlg = wx.ProgressDialog('k-SUBGROUPSMAG results',
'Searching for magnetic subgroups',11,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE)
if kSUB.RegisterProgressDialog(dlg):
dlg.Destroy()
return
wx.MessageBox(
' For use of k-SUBGROUPSMAG in GSAS-II, please cite:\n\n'+
G2G.GetCite('Bilbao: k-SUBGROUPSMAG')+
'\nand\n'+
G2G.GetCite('Bilbao+GSAS-II magnetism'),
caption='Bilbao/GSAS-II Magnetism',
style=wx.ICON_INFORMATION)
MAXMAGN,baseList = kSUB.GetNonStdSubgroupsmag(SGData,kvec[:9],star,Landau)
if MAXMAGN is None:
wx.MessageBox('Check your internet connection?',caption='Bilbao k-SUBGROUPSMAG error',style=wx.ICON_EXCLAMATION)
return
if not MAXMAGN:
if Landau:
wx.MessageBox('No results from k-SUBGROUPSMAG, multi k-vectors & Landau not compatible',
caption='Bilbao k-SUBGROUPSMAG error',style=wx.ICON_EXCLAMATION)
else:
wx.MessageBox('No results from k-SUBGROUPSMAG, check your propagation vector(s)',
caption='Bilbao k-SUBGROUPSMAG error',style=wx.ICON_EXCLAMATION)
return
controls[14] = kvec[:9]
try:
controls[16] = baseList
except IndexError:
controls.append(baseList)
for ir,result in enumerate(MAXMAGN):
# result is SPGP,BNS,MV,itemList,altList,superList
dlg.Update(ir%10,newmsg=f'Processing {result[0]}')
Trans = np.array(eval(result[2][0]))
Uvec = np.array(eval(result[2][1]))
phase = G2lat.makeBilbaoPhase(result[:2],Uvec,Trans,True)
phase['gid'] = result[3]
phase['altList'] = result[4]
phase['supList'] = eval(result[5])
RVT = None
if keepaxes:
RVT = G2lat.FindNonstandard(controls,phase)
if RVT is not None:
result,Uvec,Trans = RVT
phase.update(G2lat.makeBilbaoPhase(result,Uvec,Trans,True))
phase['Cell'] = G2lat.TransformCell(controls[6:12],Trans)
phase['aType'] = atype
phase['allmom'] = allmom
phase['magAtms'] = magAtms
phase['maxequiv'] = maxequiv
phase['nAtoms'] = len(TestMagAtoms(phase,magAtms,SGData,Uvec,Trans,allmom,maxequiv,maximal))
magcells.append(phase)
finally:
dlg.Destroy()
kSUB.RegisterProgressDialog()
magcells[0]['Use'] = True
SGData = magcells[0]['SGData']
A = G2lat.cell2A(magcells[0]['Cell'][:6])
G2frame.HKL = np.array(G2pwd.getHKLpeak(1.0,SGData,A,Inst))
G2pwpl.PlotPatterns(G2frame,extraKeys=KeyList)
data = [controls,bravais,cells,dmin,ssopt,magcells]
G2frame.GPXtree.SetItemPyData(pUCid,data)
G2frame.OnFileSave(event)
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnISODISTORT_kvec(event):
'''Search for k-vector using the ISODISTORT web service.
Developed by Yuanpeng Zhang with help from Branton Campbell.
'''
if symbols is None:
G2G.G2MessageBox(G2frame,
'Unable to perform ISODISTORT kvec search without the sympy module. Use Help/Add packages... to address','No sympy')
return
# symbolic "variables" needed below for routine to_fraction_strs()
a, b, g = symbols('a b g')
def _showWebPage(event):
'Show a web page when the user presses the "show" button'
import tempfile
txt = event.GetEventObject().page
tmp = tempfile.NamedTemporaryFile(suffix='.html',delete=False)
with open(tmp.name,'w') as fp:
fp.write(txt.replace('<HEAD>','<head><base href="https://iso.byu.edu/">',))
fileList.append(tmp.name)
G2G.ShowWebPage('file://'+tmp.name,G2frame)
def showWebtext(txt):
import tempfile
tmp = tempfile.NamedTemporaryFile(suffix='.html',delete=False)
with open(tmp.name,'w') as fp:
fp.write(txt.replace('<HEAD>','<head><base href="https://iso.byu.edu/">',))
fileList.append(tmp.name)
G2G.ShowWebPage('file://'+tmp.name,G2frame)
def _get_opt_val(opt_name, out):
opt_pattern = rf'NAME="{opt_name}" VALUE="(.*?)"'
opt_match = re.search(opt_pattern, out)
return opt_match.group(1)
def grab_all_kvecs(out_html):
"""Extract all k-vectors from the ISODISTORT output HTML."""
import re
from k_vec_solve import k_vec_solve as kvsolve
kvec1_pattern = r'<SELECT NAME="kvec1">(.*?)</SELECT>'
kvec1_match = re.search(kvec1_pattern, out_html, re.DOTALL)
if kvec1_match:
select_content = kvec1_match.group(1)
# Extract option values
option_pattern = r'<OPTION VALUE="([^"]*)"[^>]*>([^<]*)</OPTION>'
options = re.findall(option_pattern, select_content)
final_kvec_keys = []
for value, _ in options:
final_kvec_keys.append(value)
all_kvecs = {}
for key in final_kvec_keys:
pattern_str = f"({key.split('(')[1]}"
k_form = kvsolve.parse_expression_string(pattern_str)
all_kvecs[key] = k_form
return all_kvecs
else:
return None
def frac_str(value, max_den=1000):
# Try to get a rational exactly; if huge, fall back to bounded approximation
try:
rat = nsimplify(value, rational=True, maxsteps=50)
if isinstance(rat, SRational):
num, den = rat.as_numer_denom()
num, den = int(num), int(den)
if den <= max_den:
return f"{num}/{den}" if den != 1 else str(num)
except Exception:
pass
# Best rational with denominator <= max_den
try:
f = Fraction(value).limit_denominator(max_den)
except TypeError:
f = Fraction(float(value)).limit_denominator(max_den)
return f"{f.numerator}/{f.denominator}" if f.denominator != 1 else str(f.numerator)
def to_fraction_strs(d, keys=(a, b, g), max_den=1000):
out = {}
for k in keys:
if k in d:
out[str(k)] = frac_str(d[k], max_den)
return out
def setup_kvec_input(k_vec, k_vec_dict, isocif_cif):
"""Set up the input for isodistort post request
Args:
k_vec (str): The k-vector to use for the isodistort request.
k_vec_dict (dict): The dictionary containing the k-vector
form extracted from isodistort.
isocif_cif (str): The CIF file content exported from ISOCIF.
Returns:
dict: New entries and those need to be corrected in the data
to be used in the post request.
"""
from k_vec_solve import k_vec_solve as kvsolve
k_forms = k_vec_dict.items()
all_keys = list(k_forms)
spg_num = kvsolve.grab_spg_num(isocif_cif)
k_vec_sol = kvsolve.find_kvec_form_param(spg_num, isocif_cif, k_vec, k_forms)
k_vec_form = all_keys[k_vec_sol[0]]
data_update = dict()
data_update['kvec1'] = k_vec_form[0]
k_vec_params = to_fraction_strs(k_vec_sol[1], max_den=1000)
if "a" in k_vec_params:
data_update['kparam11'] = k_vec_params["a"]
if "b" in k_vec_params:
data_update['kparam21'] = k_vec_params["b"]
if "g" in k_vec_params:
data_update['kparam31'] = k_vec_params["g"]
return data_update
# start of OnISODISTORT_kvec computations
try:
import requests
except:
G2G.G2MessageBox(G2frame,
'Unable to perform ISODISTORT kvec search without the requests module. Use Help/Add packages... to address','No requests')
return
import tempfile
import re
from GSASII.exports import G2export_CIF
from . import ISODISTORT as ISO
isoformsite = 'https://iso.byu.edu/isodistortform.php'
isocifformsite = 'https://iso.byu.edu/isocifform.php'
isocifuploadsite = 'https://iso.byu.edu/isocifuploadfile.php'
if not G2frame.kvecSearch['mode']:
return
k_table = G2frame.GPXtree.GetItemPyData(UnitCellsId)
k_cells, _ = k_table[2:4]
kpoint = None
for row in range(len(k_cells)):
if UnitCellsTable.GetValue(row, 0):
kpoint = cells[row][3:6]
break
if kpoint is None:
wx.MessageBox(
"Please select a k-vector from the table.",
style=wx.ICON_INFORMATION,
caption='Isotropic Subgroup Generation'
)
return
isoCite = G2G.GetCite('ISOTROPY, ISODISTORT, ISOCIF...',wrap=60,indent=5) # reuse saved citation
info_str = '''CIF files of the isotropic subgroups associated with the
selected k-vector will be created.
Generated CIF files will be saved in the same directory as the
current project file.
This can take up to a few minutes. Check the terminal for progress.
'''
wx.MessageBox(
f"{isoCite}\n\n{info_str}",
style=wx.ICON_INFORMATION,
caption='Isotropic Subgroup Generation'
)
wx.GetApp().Yield()
info_msg = "Processing IRREPs for the selected k-vector. "
info_msg += "This can take up to a few minutes."
print(info_msg)
# find tree item for current phase
phaseID = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases')
phase_nam = G2frame.kvecSearch['phase']
phaseTreeId = G2gd.GetGPXtreeItemId(G2frame, phaseID, phase_nam) # save reference
Phase = G2frame.GPXtree.GetItemPyData(phaseTreeId)
fileList = []
# write a CIF as a scratch file
obj = G2export_CIF.ExportPhaseCIF(G2frame)
obj.InitExport(None)
obj.currentExportType='phase'
obj.loadTree()
tmp = tempfile.NamedTemporaryFile(suffix='.cif', delete=False)
obj.dirname,obj.filename = os.path.split(tmp.name)
obj.phasenam = Phase['General']['Name']
obj.Writer('', Phase['General']['Name'])
parentcif = tmp.name
ISOparentcif = ISO.UploadCIF(parentcif)
up2 = {'filename': ISOparentcif, 'input': 'uploadparentcif'}
out2 = requests.post(isoformsite, up2).text
try:
pos = out2.index('<p><FORM')
except ValueError:
ISO.HandleError(out2)
return [], []
data = {}
while True:
try:
posB = out2[pos:].index('INPUT TYPE') + pos
posF = out2[posB:].index('>') + posB
items = out2[posB:posF].split('=',3)
name = items[2].split()[0].replace('"', '')
if 'isosystem' in name:
break
vals = items[3].replace('"', '')
data[name] = vals
pos = posF
except ValueError:
break
phase_sel = G2frame.kvecSearch['phase']
_, Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
Phase = Phases[phase_sel]
data['input'] = 'kvector'
data['irrepcount'] = '1'
# We need to upload the CIF file to ISOCIF and export from there, since
# some of the routines for k vector form solving only works with the
# CIF coming out from ISOCIF.
init_cif = ISO.UploadCIF(parentcif, upload_site=isocifuploadsite)
isocif_up = {'submit': 'OK', 'input': 'uploadcif', 'filename': init_cif}
isocif_out_1 = requests.post(isocifformsite, data=isocif_up).text
isocif_form = re.split(
'</form',
next(
i for i in re.split('<form', isocif_out_1, flags=re.IGNORECASE)
if 'Detect higher' in i
),
flags=re.IGNORECASE
)[0]
isocif_formDict = {}
for f in isocif_form.split('<'):
try:
name = re.split('name=',f,flags=re.IGNORECASE)[1].split('"')[1]
value = re.split('value=',f,flags=re.IGNORECASE)[1].split('"')[1]
isocif_formDict[name] = value
except IndexError:
pass
isocif_formDict['input'] = 'savecif'
isocif_out_cif = requests.post(isocifformsite, data=isocif_formDict).text
kvec_dict = grab_all_kvecs(out2)
#lat_sym = Phase['General']['SGData']
data_update = setup_kvec_input(kpoint, kvec_dict, isocif_out_cif)
for key, value in data_update.items():
data[key] = value
data['nmodstar1'] = '0'
out3 = requests.post(isoformsite, data=data).text
try:
pos = out3.index('irrep1')
except ValueError:
ISO.HandleError(out3)
return [],[]
kvec1 = _get_opt_val('kvec1', out3)
kvecnumber1 = _get_opt_val('kvecnumber1', out3)
kparam1 = _get_opt_val('kparam1', out3)
nmodstar1 = _get_opt_val('nmodstar1', out3)
data["kvec1"] = kvec1
data["kvecnumber1"] = kvecnumber1
data["kparam1"] = kparam1
data["nmodstar1"] = nmodstar1
pos = out3.index("irrep1")
pos1 = out3[pos:].index("</SELECT>")
str_tmp = out3[pos:][:pos1]
ir_options = re.findall(
r'<OPTION VALUE="([^"]+)">([^<]+)</OPTION>',str_tmp
)
proj_pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
G2frame.OnFileSave(None)
orgFilName = G2frame.GSASprojectfile
phsnam = phase_sel
# get restraints & clear geometrical restraints
resId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, 'Restraints')
Restraints = G2frame.GPXtree.GetItemPyData(resId)
resId = G2gd.GetGPXtreeItemId(G2frame, resId, phsnam)
#savedRestraints = None
if phsnam in Restraints:
Restraints[phsnam]['Bond']['Bonds'] = []
Restraints[phsnam]['Angle']['Angles'] = []
#savedRestraints = Restraints[phsnam]
del Restraints[phsnam]
#orgData = copy.deepcopy(data)
for ir_opt, _ in ir_options:
print("Processing irrep:", ir_opt)
data["input"] = "irrep"
data['irrep1'] = ir_opt
out4 = requests.post(isoformsite, data=data).text
irrep1 = _get_opt_val('irrep1', out4)
irrpointer1 = _get_opt_val('irrpointer1', out4)
data["irrep1"] = irrep1
data["irrpointer1"] = irrpointer1
r_pattern = r'<input\s+type=["\']?radio["\']?\s+name=["\']?'
r_pattern += r'orderparam["\']?\s+value=["\']?([^"\']+)["\']?'
radio_val_pattern = re.compile(r_pattern, re.IGNORECASE)
radio_vals = radio_val_pattern.findall(out4)
cleaned_radio_vals = [value.strip() for value in radio_vals]
iso_fn = _get_opt_val('isofilename', out4).strip()
data["isofilename"] = iso_fn
for radio_val in cleaned_radio_vals:
print("Processing mode:", radio_val)
data["input"] = "distort"
data["origintype"] = "method2"
data["orderparam"] = radio_val + '" CHECKED'
out5 = requests.post(isoformsite, data=data).text
out_cif = ISO.GetISOcif(out5, 2)
cif_fn_part1 = radio_val.split()[0]
cif_fn_part2_tmp = radio_val.split(")")[1].split(",")[0]
cif_fn_part2 = cif_fn_part2_tmp.split()[-1]
cif_fn_part1 = cif_fn_part1.replace('/', '_')
cif_fn_part2 = cif_fn_part2.replace('/', '_')
cif_fn = f"{phase_nam}_{cif_fn_part1}_{cif_fn_part2}.cif"
cif_fn = os.path.join(proj_pth, cif_fn)
with open(cif_fn, 'wb') as fl:
fl.write(out_cif.encode("utf-8"))
try:
rdlist = G2sc.import_generic(
cif_fn, [CIFpr()], fmthint='CIF'
)
except Exception:
continue
rd = rdlist[0]
key_list = [
'General', 'Atoms', 'Drawing',
'Histograms', 'Pawley ref', 'RBModels'
]
for key in key_list:
Phase[key] = rd.Phase[key]
newname = rd.Phase['General']['Name']
Phase['General']['Name'] = phsnam
# rename the phase in the data tree
G2phsG.renamePhaseName(G2frame,Phase,phaseTreeId,Phase['General'],newname)
G2frame.GSASprojectfile = os.path.splitext(
orgFilName
)[0] + '_' f"{phase_nam}_{cif_fn_part1}_{cif_fn_part2}.gpx"
G2IO.ProjFileSave(G2frame)
# restore the original saved project
G2frame.OnFileOpen(None, filename=orgFilName, askSave=False)
# reopen tree to the original phase
def _ShowPhase():
phId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, 'Phases')
G2frame.GPXtree.Expand(phId)
phId = G2gd.GetGPXtreeItemId(G2frame, phId, phsnam)
G2frame.GPXtree.SelectItem(phId)
wx.CallLater(100, _ShowPhase)
info_msg = f'''Done with subgroup output for the selected k-vector.
Please check output files in the following directory,
{os.getcwd()}
'''
wx.MessageBox(
info_msg,
style=wx.ICON_INFORMATION,
caption='Isotropic Subgroup Generation'
)
try:
os.unlink(tmp.name)
except PermissionError:
pass
return
def updateCellsWindow(event):
'called when k-vec mode is selected'
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnClearCells(event):
'remove previous search results'
data[2] = []
data[5] = []
ssopt['SgResults'] = []
wx.CallAfter(UpdateUnitCellsGrid, G2frame, data)
def OnISODIST(event):
phase_sel = G2frame.kvecSearch['phase']
if len(phase_sel.strip()) == 0:
err_title = "Missing parent phase"
err_msg = "Please select the parent phase from "
err_msg += "the drop-down list."
G2G.G2MessageBox(G2frame, err_msg, err_title)
def _setupResultsGrid(grid):
'''Turn on scrolling for grid and register the grid in resizeGrids so that it will be
adjusted when the window is resized (also when first created).
This ensure that Search Results tables display nicely
with scrollbars internal to the table (plays nicely with table
headers). See _onResizeUnitCellsList for more.
'''
grid.SetScrollRate(10,10)
resizeGrids.append(grid)
def clearShowFlags():
'''resets all the "Use" flags in all search tables
'''
for i,grid in enumerate(resizeGrids):
try:
for c in range(grid.GetNumberCols()):
if grid.GetColLabelValue(c) == 'show':
for r in range(grid.GetNumberRows()):
grid.GetTable().SetValue(r,c,False)
grid.ForceRefresh()
except:
pass
def disableCellEntries(mode=False):
'''Called to disable (or enable with mode==True) the widgets
associated with entering a unit cell into the 2nd Box
'''
for item in unitSizerWidgetList:
try:
item.Enable(mode)
except:
pass
def _onResizeUnitCellsList(event):
'''This is called to adjust the sizes of objects in
the dataWindow display if that window is resized.
The only task at present is to adjust the size of the
GSGrid tables (search results) to be at most the new
width of the window (less 15 pt to leave room for a
scrollbar) but if the grid is smaller than that width
add 15 pt for the scroll bar (might not be needed). For
the table height, make sure that each results table takes
less than 1/2 of the available vertical space.
'''
try:
G2frame.dataWindow.Layout()
wid,hgt = G2frame.dataWindow.GetSize()
for i,grid in enumerate(resizeGrids):
# save the initial value for BestSize, as it increases as SetMinSize
# gets changed
try:
gwid,ghgt = grid.initialGetBestSize
except:
grid.initialGetBestSize = grid.GetBestSize()
gwid,ghgt = grid.initialGetBestSize
grid.SetMaxSize((wid-15,int(hgt/2.5))) # leave inside on right room for scrollbar
# add a bit to the minimum width for the scroll bar (if there is room)
grid.SetMinSize((min(wid-15,gwid+15),min(int(hgt/2.5),ghgt)))
event.Skip()
except: # can fail after window is destroyed
pass
# Display of Autoindexing controls
def firstSizer():
def OnNcNo(event):
controls[2] = NcNo.GetValue()
def OnIfX20(event):
G2frame.ifX20 = x20.GetValue()
def OnBravais(event):
Obj = event.GetEventObject()
bravais[bravList.index(Obj.GetId())] = Obj.GetValue()
firstSizer = wx.BoxSizer(wx.VERTICAL)
firstSizer.Add(wx.StaticText(parent=G2frame.dataWindow,
label='Autoindexing of "Index Peak List" contents',style=wx.ALIGN_CENTER),0,wx.EXPAND)
firstSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Bravais Lattice(s) for autoindexing trials:'),0)
firstSizer.Add((5,5),0)
indentSizer = wx.BoxSizer(wx.HORIZONTAL)
indentSizer.Add((20,-1))
littleSizer = wx.FlexGridSizer(0,4,5,5)
bravList = []
bravs = zip(bravais,bravaisNames)
for brav,bravName in bravs:
bravCk = wx.CheckBox(G2frame.dataWindow,label=bravName)
bravList.append(bravCk.GetId())
bravCk.SetValue(brav)
bravCk.Bind(wx.EVT_CHECKBOX,OnBravais)
littleSizer.Add(bravCk,0,WACV)
indentSizer.Add(littleSizer,0)
firstSizer.Add(indentSizer,0)
littleSizer = wx.FlexGridSizer(0,5,5,5)
littleSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Max Nc/Nobs '),0,WACV)
NcNo = wx.SpinCtrl(G2frame.dataWindow)
NcNo.SetRange(2,8)
NcNo.SetValue(controls[2])
NcNo.Bind(wx.EVT_SPINCTRL,OnNcNo)
littleSizer.Add(NcNo,0,WACV)
littleSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Start Volume '),0,WACV)
startVol = G2G.ValidatedTxtCtrl(G2frame.dataWindow,controls,3,typeHint=int,xmin=25)
littleSizer.Add(startVol,0,WACV)
x20 = wx.CheckBox(G2frame.dataWindow,label='Use M20/(X20+1)?')
x20.SetValue(G2frame.ifX20)
x20.Bind(wx.EVT_CHECKBOX,OnIfX20)
littleSizer.Add(x20,0,WACV)
firstSizer.Add(littleSizer,0)
firstSizer.Add((5,5),0)
return firstSizer
# Display of k-vector search controls
def kvecSizer():
def OnKvecSearch(event):
'Run the k-vector search'
from . import k_vector_search as kvs
try:
import seekpath
seekpath
except:
G2fil.NeededPackage({'magnetic k-vector search':['seekpath']})
msg = 'Performing a k-vector search requires installation of the Python seekpath package. Use the Help/Add Package... to install that package.'
dlg = wx.MessageDialog(G2frame, msg,'Install seekpath package')
try:
dlg.ShowModal()
finally:
dlg.Destroy()
return
# msg = G2G.NISTlatUse(True)
_, _, cells, _, _, _ = data
wx.BeginBusyCursor()
# grab the satellite peaks. here, gsas-ii will only grab the data
# for the histogram under selection.
hist_name = G2frame.GPXtree.GetItemText(G2frame.PatternId)
Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, hist_name)
peakId = G2gd.GetGPXtreeItemId(G2frame, Id, 'Peak List')
peakdata = G2frame.GPXtree.GetItemPyData(peakId)
if len(peakdata["xtraPeaks"]) == 0:
err_title = "Empty satellite peak list"
err_msg = "The satellite peak list is empty. Please select the "
err_msg += "extra peak positions before executing the k vector "
err_msg += "search."
G2G.G2MessageBox(G2frame, err_msg, err_title)
wx.EndBusyCursor()
return
# we need to grab the instrument parameter and call gsas ii routine
# to convert the satellite peaks into d-spacing.
Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.PatternId, 'Instrument Parameters')
Parms, _ = G2frame.GPXtree.GetItemPyData(Id)
xtra_peaks_d = list()
for extra_peak in peakdata["xtraPeaks"]:
dsp_tmp = G2lat.Pos2dsp(Parms, extra_peak[0])
xtra_peaks_d.append(dsp_tmp)
# select a parent phase. error message will be presented in a pop-up
# window if an invalid selection is made.
phase_sel = G2frame.kvecSearch['phase']
if len(phase_sel.strip()) == 0:
err_title = "Missing parent phase"
err_msg = "Please select the parent phase from the dropdown."
G2G.G2MessageBox(G2frame, err_msg, err_title)
wx.EndBusyCursor()
return
# again, gsas ii will only grab the reflection lists for the
# histogram under selection. also, only those phases that are being
# used for the selected histogram will be included in the
# `refDict` variable.
refDict = G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame, G2frame.PatternId, 'Reflection Lists'))
if phase_sel not in refDict.keys():
err_title = "Phase selection error"
err_msg = "The parent phase selected is not used in "
err_msg += "current histogram. "
err_msg += "Please select from one of the followings, "
err_msg += f"{list(refDict.keys())}"
G2G.G2MessageBox(G2frame, err_msg, err_title)
wx.EndBusyCursor()
return
# grab the search option. By default, we would search over those
# high symmetry points only.
kvs_option_map = {"HighSymPts": 0,"HighSymPts & HighSymPaths": 1,"General": 2}
kvs_option = G2frame.kvecSearch['soption']
kvs_option = kvs_option_map[kvs_option]
if kvs_option == 2:
# grab the search range, which will be used for the option of
# 'General' only -- see the part below for user selection of the
# search option.
try:
kx_s = float(G2frame.kvecSearch['kx_step'])
ky_s = float(G2frame.kvecSearch['ky_step'])
kz_s = float(G2frame.kvecSearch['kz_step'])
num_procs = int(G2frame.kvecSearch['num_procs'])
except ValueError:
err_title = "Invalid k grid input"
err_msg = "The k gird values should all be float numbers"
G2G.G2MessageBox(G2frame, err_msg, err_title)
wx.EndBusyCursor()
return
if kx_s <= 0 or ky_s <= 0 or kz_s <= 0:
err_title = "Invalid k grid input"
err_msg = "The k step is less than or equal to 0. "
err_msg += "Please check the input values."
G2G.G2MessageBox(G2frame, err_msg, err_title)
wx.EndBusyCursor()
return
else:
warn_title = "Long execution time expected"
warn_msg = "Searching over general k points may take a while, "
warn_msg += "usually on the level of serveral hours. "
warn_msg += "Do you want to proceed?"
dialog = wx.MessageDialog(G2frame,warn_msg,warn_title,
wx.OK | wx.CANCEL | wx.ICON_INFORMATION)
result = dialog.ShowModal()
if result == wx.ID_OK:
pass
else:
dialog.Destroy()
wx.EndBusyCursor()
return
kstep = [kx_s, ky_s, kz_s]
else:
num_procs = None
kstep = None
# grab the user defined tolerance for determining the optimal k vector.
# refer to the following link for more detailed explanation about this,
#
# https://yr.iris-home.net/kvectordoc
#
try:
tol_val = float(G2frame.kvecSearch['tolerance'])
except ValueError:
err_title = "Invalid tolerance input"
err_msg = "The tolerance value should be a float number, "
err_msg += "representing the instrument resolution "
err_msg += ("level \u03B4d/d.")
G2G.G2MessageBox(G2frame, err_msg, err_title)
wx.EndBusyCursor()
return
_, Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
Phase = Phases[phase_sel]
# grab the Bravais lattice type
#
# given the lattice type and lattice system, the Bravais lattice type
# can be determined. see the comparison table in the Wikipedia link
# below for the correspondence,
#
# https://en.wikipedia.org/wiki/Crystal_system
#
# here, we need to assign the Bravais lattice with specific names as
# inputs for the `seekpath` routine.
lat_type = Phase["General"]["SGData"]["SGLatt"]
lat_sym = Phase["General"]["SGData"]["SGSys"]
if lat_sym == "trigonal":
brav_sym = "hR"
else:
brav_sym = lat_sym[0] + lat_type
# grab all atomic coordinates in the P1 symmetry
#
# define some matrix as necessary inputs for generating the P1
# structure.
Trans = np.eye(3)
Uvec = np.zeros(3)
Vvec = np.zeros(3)
# expand the structure to P1 symmetry
newPhase = copy.deepcopy(Phase)
newPhase['ranId'] = ran.randint(0, sys.maxsize)
newPhase['General']['SGData'] = G2spc.SpcGroup('P 1')[1]
newPhase, _ = G2lat.TransformPhase(Phase,newPhase,Trans,Uvec,Vvec,False)
atoms_pointer = newPhase['General']['AtomPtrs']
atom_coords = list()
atom_types = list()
for atom in newPhase["Atoms"]:
coord_tmp = atom[atoms_pointer[0]:atoms_pointer[0] + 3]
atom_coords.append(coord_tmp)
type_tmp = atom[atoms_pointer[1]]
atom_types.append(type_tmp)
# this will turn each of the atom types into a unique integer number,
# which is required by the `seekpath` routine
atom_ids = kvs.unique_id_gen(atom_types)
# grab the parent unit cell and construct the lattice vectors
cell_params = newPhase["General"]["Cell"][1:7]
lat_vectors = kvs.lat_params_to_vec(cell_params)
hkl_refls = list()
for i in range(6):
for j in range(6):
for k in range(6):
hkl_refls.append([i, j, k])
try:
# if we choose option-2, we need to use the `kvec_general` module
# Otherwise, the computation time would be unacceptably long.
k_search = kvs.kVector(brav_sym,lat_vectors,atom_coords,atom_ids,
hkl_refls,xtra_peaks_d,tol_val,option=kvs_option,
kstep=kstep,processes=num_procs)
except ModuleNotFoundError:
err_title = "Module not found"
err_msg = "The `kvec_general` module is not found. Please install "
err_msg += "the module before running the k-vector search with "
err_msg += "option-2."
G2G.G2MessageBox(G2frame, err_msg, err_title)
wx.EndBusyCursor()
return
k_opt = k_search.kOptFinder()
k_opt_dist = k_opt[1]
ave_dd = k_opt[2]
max_dd = k_opt[3]
k_opt = [list(k_search.kVecPrimToConv(k)) for k in k_opt[0]]
wx.EndBusyCursor()
cells.clear()
# display the result
select = False
for i, k_v in enumerate(k_opt):
select = True
cells.append([])
laue = 'P1'
cells[-1] += ['?', 0, laue]
c = k_v + [k_opt_dist[i], ave_dd[i], max_dd[i]]
cells[-1] += c
cells[-1] += [0, False, False]
# G2frame.OnFileSave(event) # forces save of project
wx.CallAfter(UpdateUnitCellsGrid, G2frame, data, select) # refresh & select 1st result
kvecSizer = wx.BoxSizer(wx.VERTICAL)
kvecSizer.Add(wx.StaticText(
parent=G2frame.dataWindow,label='k-Vector Search Mode',style=wx.ALIGN_CENTER),0,wx.EXPAND)
Histograms, Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
littleSizer = wx.BoxSizer(wx.HORIZONTAL)
littleSizer1x = wx.BoxSizer(wx.HORIZONTAL)
littleSizer2 = wx.BoxSizer(wx.HORIZONTAL)
G2frame.kvecSearch['phase'] = G2frame.kvecSearch.get('phase', '')
G2frame.kvecSearch['tolerance'] = G2frame.kvecSearch.get('tolerance', 0.0)
G2frame.kvecSearch['kx_step'] = G2frame.kvecSearch.get('kx_step', 0.01)
G2frame.kvecSearch['ky_step'] = G2frame.kvecSearch.get('ky_step', 0.01)
G2frame.kvecSearch['kz_step'] = G2frame.kvecSearch.get('k_step', 0.01)
G2frame.kvecSearch['num_procs'] = G2frame.kvecSearch.get('num_procs', 8)
G2frame.kvecSearch['soption'] = G2frame.kvecSearch.get('soption', "HighSymPts")
if len(Phases) == 0:
littleSizer.Add(wx.StaticText(G2frame.dataWindow,
label=' You need to define a phase to use k-vector searching'),0,WACV)
elif len(Phases) == 1:
G2frame.kvecSearch['phase'] = list(Phases.keys())[0]
else:
littleSizer.Add(wx.StaticText(G2frame.dataWindow, label='Select phase'), 0, WACV)
ch = G2G.EnumSelector(G2frame.dataWindow, G2frame.kvecSearch, 'phase',
[''] + list(Phases.keys()))
littleSizer.Add(ch, 10, WACV | wx.RIGHT, 0)
littleSizer1x.Add(wx.StaticText(G2frame.dataWindow, label='kx step'),0,WACV)
kx_s = G2G.ValidatedTxtCtrl(G2frame.dataWindow,G2frame.kvecSearch,'kx_step',
nDig=[6, 3],typeHint=float,size=(50, -1))
littleSizer1x.Add(kx_s, 0, WACV | wx.RIGHT, 10)
littleSizer1x.Add((10, -1))
littleSizer1x.Add(wx.StaticText(G2frame.dataWindow, label='ky step'),0,WACV)
ky_s = G2G.ValidatedTxtCtrl(G2frame.dataWindow,G2frame.kvecSearch,'ky_step',
nDig=[6, 3],typeHint=float,size=(50, -1))
littleSizer1x.Add(ky_s, 0, WACV | wx.RIGHT, 10)
littleSizer1x.Add((10, -1))
littleSizer1x.Add(wx.StaticText(G2frame.dataWindow, label='kz step'),0,WACV)
kz_s = G2G.ValidatedTxtCtrl(G2frame.dataWindow,G2frame.kvecSearch,'kz_step',
nDig=[6, 3],typeHint=float,size=(50, -1))
littleSizer1x.Add(kz_s, 0, WACV | wx.RIGHT, 10)
littleSizer1x.Add((10, -1))
littleSizer1x.Add(wx.StaticText(G2frame.dataWindow, label='Number of processors'),0,WACV)
num_procs = G2G.ValidatedTxtCtrl(G2frame.dataWindow,G2frame.kvecSearch,'num_procs',
nDig=[6, 2],typeHint=int,size=(50, -1))
littleSizer1x.Add(num_procs, 0, WACV | wx.RIGHT, 10)
littleSizer2.Add(wx.StaticText(G2frame.dataWindow, label='Search tolerance'),0,WACV)
tolVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,G2frame.kvecSearch,'tolerance',
nDig=[10, 6],typeHint=float,size=(70, -1))
littleSizer2.Add(tolVal, 0, WACV | wx.RIGHT, 20)
littleSizer2.Add(wx.StaticText(G2frame.dataWindow, label='Search option'), 0, WACV)
search_opts = ["HighSymPts", "HighSymPts & HighSymPaths", "General"]
ch1 = G2G.EnumSelector(G2frame.dataWindow,G2frame.kvecSearch,'soption',search_opts)
littleSizer2.Add(ch1, 10, WACV | wx.RIGHT, 0)
kvecSizer.Add(littleSizer, 0)
kvecSizer.Add((-1, 5), 0)
kvecSizer.Add(littleSizer1x, 0)
kvecSizer.Add((-1, 5), 0)
kvecSizer.Add(littleSizer2, 0)
kvecSizer.Add((-1, 5), 0)
btn = wx.Button(G2frame.dataWindow,wx.ID_ANY,'Start Search')
btn.Bind(wx.EVT_BUTTON,OnKvecSearch)
kvecSizer.Add(btn)
return kvecSizer
# Unit cell display controls
def unitSizer():
def OnSSselect(event):
if controls[5] in ['Fm3m','Im3m','Pm3m']:
SSselect.SetValue(False)
G2frame.ErrorDialog('Cubic lattice','Incommensurate superlattice not possible with a cubic lattice')
return
ssopt['Use'] = SSselect.GetValue()
if 'ssSymb' not in ssopt:
ssopt.update({'ssSymb':'(abg)','ModVec':[0.1,0.1,0.1],'maxH':1})
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnSelMG(event):
ssopt['ssSymb'] = selMG.GetValue()
Vec = ssopt['ModVec']
modS = G2spc.splitSSsym(ssopt['ssSymb'])[0]
ssopt['ModVec'] = G2spc.SSGModCheck(Vec,modS)[0]
print (' Selecting: '+controls[13]+ssopt['ssSymb']+ 'maxH:'+str(ssopt['maxH']))
OnHklShow(event,indexFrom=' Indexing from new super group %s'%(controls[13]+ssopt['ssSymb']))
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnModVal(invalid,value,tc):
OnHklShow(tc.event,indexFrom=' Indexing from new modulation vector')
def OnMoveMod(event):
Obj = event.GetEventObject()
ObjId = Obj.GetId()
Id,valObj = Indx[ObjId]
inc = float(shiftChoices[shiftSel.GetSelection()][:-1])
move = Obj.GetValue()*inc/100.
Obj.SetValue(0)
value = min(0.98,max(-0.98,float(valObj.GetValue())+move))
valObj.SetValue('%.4f'%(value))
ssopt['ModVec'][Id] = value
OnHklShow(event,indexFrom=' Indexing from changed modulation vector')
def OnMaxMH(event):
ssopt['maxH'] = int(maxMH.GetValue())
print (' Selecting: '+controls[13]+ssopt['ssSymb']+'maxH:'+str(ssopt['maxH']))
OnHklShow(event,indexFrom=' Indexing from new max. M')
def OnButton(xpos,ypos):
modSym = ssopt['ssSymb'].split(')')[0]+')'
if modSym in ['(a0g)','(a1/2g)']:
ssopt['ModVec'][0] = xpos
ssopt['ModVec'][2] = ypos
elif modSym in ['(0bg)','(1/2bg)']:
ssopt['ModVec'][1] = xpos
ssopt['ModVec'][2] = ypos
elif modSym in ['(ab0)','(ab1/2)']:
ssopt['ModVec'][0] = xpos
ssopt['ModVec'][1] = ypos
vec = ssopt['ModVec']
print(' Trying: %s %s modulation vector = %.3f %.3f %.3f'%(controls[13],ssopt['ssSymb'],vec[0],vec[1],vec[2]))
OnHklShow(None,indexFrom=' Indexing from selected modulation vector')
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnFindOneMV(event):
Peaks = np.copy(peaks[0])
print (' Trying: '+controls[13],ssopt['ssSymb']+' maxH: 1')
dlg = wx.ProgressDialog('Elapsed time','Modulation vector search',
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE)
try:
ssopt['ModVec'],result = G2indx.findMV(Peaks,controls,ssopt,Inst,deltM,dlg)
if len(result[0]) == 2:
G2plt.PlotXYZ(G2frame,result[2],1./result[3],labelX='a',labelY='g',newPlot=True,
Title='Modulation vector search for %s%s'%(controls[13],ssopt['ssSymb']),
buttonHandler=OnButton)
elif len(result[0]) == 1:
G2plt.PlotXY(G2frame,[[result[2],1./result[3]],],labelX='k',labelY='fit',newPlot=True,
Title='Modulation vector search for %s%s'%(controls[13],ssopt['ssSymb']))
finally:
dlg.Destroy()
OnHklShow(event,indexFrom=' Indexing from best modulation vector')
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnFindMV(event):
best = 1.
bestSS = ''
ssopt['SSgResults'] = []
for ssSym in ssChoice:
Vref = [x for x in ['a','b','g'] if x in ssSym]
if len(Vref) > 1:
print(' %s skipped - too many variables to search this way'%ssSym)
continue
ssopt['ssSymb'] = ssSym
Peaks = np.copy(peaks[0])
ssopt['ModVec'] = G2spc.SSGModCheck(ssopt['ModVec'],G2spc.splitSSsym(ssSym)[0],True)[0]
print (' Trying: '+controls[13]+ssSym+' maxH: 1')
dlg = wx.ProgressDialog('Elapsed time','Modulation vector search with %s'%ssSym,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT)
try:
ssopt['ModVec'],result = G2indx.findMV(Peaks,controls,ssopt,Inst,deltM,dlg)
M20,X20 = OnHklShow(event,indexFrom=' Indexing from best modulation vector')[2:4]
Ma,Mb,Mg = ssopt['ModVec']
ssopt['SSgResults'].append([ssSym,False,M20,X20,Ma,Mb,Mg,])
finally:
dlg.Destroy()
if result[1] < best:
bestSS = ssSym
best = result[1]
if bestSS != '':
ssopt['ssSymb'] = bestSS
ssopt['ModVec'],result = G2indx.findMV(Peaks,controls,ssopt,Inst,deltM,dlg=None)
G2plt.PlotXY(G2frame,[[result[2],1./result[3]],],labelX='k',labelY='fit',
newPlot=True,Title='Modulation vector search for %s'%bestSS)
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnBravSel(event):
brav = bravSel.GetString(bravSel.GetSelection())
controls[5] = brav
controls[13] = SPGlist[brav][0]
ssopt['Use'] = False
OnHklShow(event,indexFrom=' Indexing from Bravais lattice %s'%brav)
wx.CallLater(100,UpdateUnitCellsGrid,G2frame,data)
def OnSpcSel(event):
controls[13] = spcSel.GetString(spcSel.GetSelection())
ssopt['SGData'] = G2spc.SpcGroup(controls[13])[1]
# ssopt['Use'] = False
G2frame.dataWindow.RefineCell.Enable(True)
OnHklShow(event,indexFrom=' Indexing from space group %s'%controls[13])
wx.CallLater(100,UpdateUnitCellsGrid,G2frame,data)
def OnTryAllSG(event):
'''Computes extinctions for all possible space groups
creates data for a table that is displayed in the subsequent
UpdateUnitCellsGrid call.
'''
ssopt['SgResults'] = []
ssopt['SgSettings'] = ''
for controls[13] in SPGlist[controls[5]]:
ssopt['SGData'] = G2spc.SpcGroup(controls[13])[1]
ssopt['Use'] = False
G2frame.dataWindow.RefineCell.Enable(True)
res = OnHklShow(event,False,False,indexFrom=' ')
if res:
ssopt['SgResults'].append(res)
if ssopt['SgResults']:
ssopt['SgResults'] = G2mth.sortArray(ssopt['SgResults'],2,reverse=True)
controls[13] = ssopt['SgResults'][0][0]
ssopt['SGData'] = G2spc.SpcGroup(controls[13])[1]
G2frame.dataWindow.RefineCell.Enable(True)
ssopt['SgResults'][0][1] = True # select the first entry
ssopt['SgSettings'] = 'Brav. Lat.: {}, cell: {:.3f} {:.3f} {:.3f} {:.2f} {:.2f} {:.2f}'.format(*controls[5:12])
OnHklShow(event,False,False,indexFrom=' Indexing from space group %s'%controls[13])
wx.CallLater(100,UpdateUnitCellsGrid,G2frame,data)
def SetCellValue(Obj,ObjId,value):
if hasattr(Obj,'ChangeValue'):
setval = Obj.ChangeValue
else:
setval = Obj.SetValue
if controls[5] in ['Fm3m','Im3m','Pm3m']:
controls[6] = controls[7] = controls[8] = value
controls[9] = controls[10] = controls[11] = 90.0
setval(controls[6])
elif controls[5] in ['R3-H','P6/mmm','I4/mmm','P4/mmm']:
if ObjId == 0:
controls[6] = controls[7] = value
setval(controls[6])
else:
controls[8] = value
setval(controls[8])
controls[9] = controls[10] = controls[11] = 90.0
if controls[5] in ['R3-H','P6/mmm']:
controls[11] = 120.
elif controls[5] in ['Fmmm','Immm','Cmmm','Pmmm']:
controls[6+ObjId] = value
setval(controls[6+ObjId])
controls[9] = controls[10] = controls[11] = 90.0
elif controls[5] in ['I2/m','A2/m','C2/m','P2/m']:
controls[9] = controls[11] = 90.0
if ObjId != 3:
controls[6+ObjId] = value
setval(controls[6+ObjId])
else:
controls[10] = value
setval(controls[10])
else:
controls[6+ObjId] = value
if ObjId < 3:
setval(controls[6+ObjId])
else:
setval(controls[6+ObjId])
controls[12] = G2lat.calc_V(G2lat.cell2A(controls[6:12]))
volVal.SetValue("%.3f"%(controls[12]))
def OnMoveCell(event):
Obj = event.GetEventObject()
ObjId = cellList.index(Obj.GetId())
valObj = valDict[Obj.GetId()]
inc = float(shiftChoices[shiftSel.GetSelection()][:-1])
move = Obj.GetValue() # +1 or -1
Obj.SetValue(0)
value = float(valObj.GetValue()) * (1. + move*inc/100.)
SetCellValue(valObj,ObjId//2,value)
OnHklShow(event,indexFrom=' Indexing from new cell')
def OnCellChange(invalid,value,tc):
if invalid:
return
try: # fails when zero is updated
SetCellValue(tc,Info[tc.GetId()],value)
except:
pass
OnHklShow(tc.event,indexFrom=' Indexing from new cell ')
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnMagSel(event):
Obj = event.GetEventObject()
if Obj.GetValue():
SGData['SGSpin'] = [1,]*len(SGData['SGSpin'])
GenSym,GenFlg,BNSsym = G2spc.GetGenSym(SGData)
SGData['GenSym'] = GenSym
SGData['GenFlg'] = GenFlg
OprNames,SpnFlp = G2spc.GenMagOps(SGData)
SGData['SpnFlp'] = SpnFlp
SGData['MagSpGrp'] = G2spc.MagSGSym(SGData)
else:
del SGData['MagSpGrp']
ssopt['SGData'] = SGData
OnHklShow(event,indexFrom=' Indexing from new spin selection')
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnSpinOp(event):
Obj = event.GetEventObject()
isym = Indx[Obj.GetId()]+1
spCode = {'red':-1,'black':1}
SGData['SGSpin'][isym] = spCode[Obj.GetValue()]
G2spc.CheckSpin(isym,SGData)
GenSym,GenFlg,BNSsym = G2spc.GetGenSym(SGData)
SGData['GenSym'] = GenSym
SGData['GenFlg'] = GenFlg
OprNames,SpnFlp = G2spc.GenMagOps(SGData)
SGData['SpnFlp'] = SpnFlp
SGData['MagSpGrp'] = G2spc.MagSGSym(SGData)
OnHklShow(event,indexFrom=' Indexing from new spin operators')
def OnBNSlatt(event):
Obj = event.GetEventObject()
SGData.update(G2spc.SpcGroup(SGData['SpGrp'])[1])
BNSlatt = Obj.GetValue()
if '_' in BNSlatt:
SGData['BNSlattsym'] = [BNSlatt,BNSsym[BNSlatt]]
else:
SGData['BNSlattsym'] = [SGData['SGLatt'],[0.,0.,0.]]
SGData['SGSpin'] = [1,]*len(SGData['SGSpin'])
GenSym,GenFlg = G2spc.GetGenSym(SGData)[:2]
SGData['GenSym'] = GenSym
SGData['GenFlg'] = GenFlg
SGData['MagSpGrp'] = G2spc.MagSGSym(SGData)
G2spc.ApplyBNSlatt(SGData,SGData['BNSlattsym'])
OprNames,SpnFlp = G2spc.GenMagOps(SGData)
SGData['SpnFlp'] = SpnFlp
OnHklShow(event,indexFrom=' Indexing from new BNS centering')
def OnShowSpins(event):
msg = 'Magnetic space group information'
text,table = G2spc.SGPrint(SGData,AddInv=True)
text[0] = ' Magnetic Space Group: '+SGData['MagSpGrp']
text[3] = ' The magnetic lattice point group is '+SGData['MagPtGp']
G2G.SGMagSpinBox(G2frame.dataWindow,msg,text,table,SGData['SGCen'],OprNames,
SGData['SpnFlp'],False).Show()
def OnMakePks(event):
msg = ('This will replace the current contents of the Peaks List'+
' with peak positions generated from the current cell.'+
' Are you sure you want to delete the previous Peak List'+
' contents?')
dlg = wx.MessageDialog(G2frame, msg,'Replace peaks?',wx.YES_NO|wx.ICON_QUESTION)
try:
result = dlg.ShowModal()
finally:
dlg.Destroy()
if result != wx.ID_YES: return
hkl = G2frame.HKL
PatternId = G2frame.PatternId
limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Limits'))[1]
background = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Background'))
inst,inst2 = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Instrument Parameters'))
peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Peak List'))
Pattern = G2frame.GPXtree.GetItemPyData(PatternId)
peaks = []
profile = Pattern[1]
bxye = GetFileBackground(G2frame,profile,background)
x0 = profile[0]
iBeg = np.searchsorted(x0,limits[0])
iFin = np.searchsorted(x0,limits[1])
x = x0[iBeg:iFin]
y = (profile[1]-bxye)[iBeg:iFin]
# ysig = 1.0*np.std(y0)
poss = [p for p in hkl[:,4] if (x[0] <= p <= x[-1])]
mags = y[np.searchsorted(x,poss)]
refs = list(zip(poss,mags))
if 'T' in Inst['Type'][0]:
refs = G2mth.sortArray(refs,0,reverse=True) #big TOFs first
else: #'C', 'E' or 'B'
refs = G2mth.sortArray(refs,0,reverse=False) #small 2-Thetas or energies first
for i,ref1 in enumerate(refs): #reject picks closer than 1 FWHM
for ref2 in refs[i+1:]:
if abs(ref2[0]-ref1[0]) < 2.*G2pwd.getFWHM(ref1[0],inst):
del(refs[i])
if 'T' in Inst['Type'][0]:
refs = G2mth.sortArray(refs,1,reverse=False)
else: #'C', 'E' or 'B'
refs = G2mth.sortArray(refs,1,reverse=True)
for pos,mag in refs:
peaks.append(G2mth.setPeakparms(inst,inst2,pos,mag))
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Peak List'),peaks)
def OnNewHklShow(event):
disableCellEntries(True)
clearShowFlags()
OnHklShow(event,indexFrom=' Indexing from unit cell & symmetry settings')
def OnExtHklShow(event):
Obj = event.GetEventObject()
if Obj.GetValue():
OnHklShow(event,indexFrom=' Indexing including extinct hkls')
else:
OnHklShow(event,indexFrom=' Indexing from unit cell & symmetry settings')
def OnAxHklShow():
mode = Sel.GetStringSelection()
if 'None' not in mode:
OnHklShow(None,indexFrom=' Indexing showing only %s hkls'%mode)
else:
OnHklShow(None,indexFrom=' Indexing from unit cell & symmetry settings')
unitSizer = wx.BoxSizer(wx.VERTICAL)
unitSizer.Add(wx.StaticText(parent=G2frame.dataWindow,style=wx.ALIGN_CENTER,
label='Unit Cell && Symmetry Settings for Reflection Display'),0,wx.EXPAND)
ibrav = SetLattice(controls)
for cellGUI in cellGUIlist:
if ibrav in cellGUI[0]:
useGUI = cellGUI
cellList = []
valDict = {}
Info = {}
bravSizer = wx.BoxSizer(wx.HORIZONTAL)
bravSizer.Add(wx.StaticText(G2frame.dataWindow,label=" Bravais \n lattice ",style=wx.ALIGN_CENTER),0,WACV,5)
bravSel = wx.Choice(G2frame.dataWindow,choices=bravaisSymb,size=(75,-1))
unitSizerWidgetList.append(bravSel)
bravSel.SetSelection(bravaisSymb.index(controls[5]))
bravSel.Bind(wx.EVT_CHOICE,OnBravSel)
bravSizer.Add(bravSel,0,WACV)
bravSizer.Add(wx.StaticText(G2frame.dataWindow,label=" Space \n group ",style=wx.ALIGN_CENTER),0,WACV,5)
spcSel = wx.Choice(G2frame.dataWindow,choices=SPGlist[controls[5]],size=(100,-1))
unitSizerWidgetList.append(spcSel)
try:
spcSel.SetSelection(SPGlist[controls[5]].index(controls[13]))
except ValueError:
pass
spcSel.Bind(wx.EVT_CHOICE,OnSpcSel)
bravSizer.Add(spcSel,0,WACV)
bravSizer.Add((5,-1))
tryAll = wx.Button(G2frame.dataWindow,label='Try all?')
unitSizerWidgetList.append(tryAll)
tryAll.Bind(wx.EVT_BUTTON,OnTryAllSG)
bravSizer.Add(tryAll,0,WACV)
if 'E' not in Inst['Type'][0]:
SSselect = wx.CheckBox(G2frame.dataWindow,label="Modulated?")
unitSizerWidgetList.append(SSselect)
SSselect.SetValue(ssopt.get('Use',False))
SSselect.Bind(wx.EVT_CHECKBOX,OnSSselect)
bravSizer.Add(SSselect,0,WACV)
if ssopt.get('Use',False): #zero for super lattice doesn't work!
controls[0] = False
unitSizer.Add(bravSizer,0)
hSizer = wx.BoxSizer(wx.HORIZONTAL)
cellSizer = wx.FlexGridSizer(0,min(6,useGUI[1]),3,3)
for txt,fmt,ifEdit,Id in zip(*useGUI[2]):
cellSizer.Add(wx.StaticText(G2frame.dataWindow,label=txt,style=wx.ALIGN_RIGHT),0,wx.ALIGN_RIGHT|WACV)
if ifEdit: #a,b,c,etc.
cellVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,controls,6+Id,nDig=fmt,OnLeave=OnCellChange,size=(65,-1))
unitSizerWidgetList.append(cellVal)
Info[cellVal.GetId()] = Id
valSizer = wx.BoxSizer(wx.HORIZONTAL)
valSizer.Add(cellVal,0,WACV)
cellSpin = wx.SpinButton(G2frame.dataWindow,style=wx.SP_VERTICAL,size=wx.Size(20,20))
unitSizerWidgetList.append(cellSpin)
cellSpin.SetValue(0)
cellSpin.SetRange(-1,1)
cellSpin.Bind(wx.EVT_SPIN, OnMoveCell)
valSizer.Add(cellSpin,0,WACV)
cellSizer.Add(valSizer,0,WACV)
cellList.append(cellVal.GetId())
cellList.append(cellSpin.GetId())
valDict[cellSpin.GetId()] = cellVal
else: #volume
volVal = wx.TextCtrl(G2frame.dataWindow,value=(fmt%(controls[12])),style=wx.TE_READONLY,size=(65,-1))
volVal.SetBackgroundColour(VERY_LIGHT_GREY)
cellSizer.Add(volVal,0,WACV)
hSizer.Add(cellSizer,0,WACV)
hSizer.Add((10,-1))
vcSizer = wx.BoxSizer(wx.VERTICAL)
vcSizer.Add(wx.StaticText(G2frame.dataWindow,label='cell step',
style=wx.ALIGN_CENTER),0,wx.EXPAND)
shiftChoices = [ '0.01%','0.05%','0.1%','0.5%', '1.0%','2.5%','5.0%']
shiftSel = wx.Choice(G2frame.dataWindow,choices=shiftChoices)
unitSizerWidgetList.append(shiftSel)
shiftSel.SetSelection(3)
deltM = float(shiftChoices[shiftSel.GetSelection()][:-1])/100.
vcSizer.Add(shiftSel)
hSizer.Add(vcSizer,0,WACV)
if not ssopt.get('Use',False): #zero for super lattice doesn't work!
hSizer.Add((15,-1))
vcSizer = wx.BoxSizer(wx.VERTICAL)
vcSizer.Add(wx.StaticText(G2frame.dataWindow,label="Zero offset",
style=wx.ALIGN_CENTER),0,wx.EXPAND)
hcSizer = wx.BoxSizer(wx.HORIZONTAL)
zero = G2G.ValidatedTxtCtrl(G2frame.dataWindow,controls,1,nDig=(10,4),typeHint=float,
xmin=-5.,xmax=5.,size=(50,-1),OnLeave=OnCellChange)
unitSizerWidgetList.append(zero)
hcSizer.Add(zero,0,WACV)
zeroVar = G2G.G2CheckBox(G2frame.dataWindow,'Ref?',controls,0)
unitSizerWidgetList.append(zeroVar)
hcSizer.Add(zeroVar,0,WACV|wx.LEFT,3)
vcSizer.Add(hcSizer)
hSizer.Add(vcSizer,0,WACV)
unitSizer.Add(hSizer,0)
if ssopt.get('Use',False): #super lattice display
indChoice = ['1','2','3','4',]
SpSg = SGData['SpGrp']
if 'MagSpGrp' in SGData: #limit to one for magnetic SS for now
indChoice = ['1',]
SpSg = SGData['MagSpGrp']
ssChoice = G2spc.SSChoice(SGData)
if ssopt['ssSymb'] not in ssChoice:
ssopt['ssSymb'] = ssopt['ssSymb'][:-1]
ssSizer = wx.BoxSizer(wx.HORIZONTAL)
ssSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Supersymmetry space group: '+SpSg+' '),0,WACV)
selMG = wx.ComboBox(G2frame.dataWindow,value=ssopt['ssSymb'],
choices=ssChoice,style=wx.CB_READONLY|wx.CB_DROPDOWN)
unitSizerWidgetList.append(selMG)
selMG.Bind(wx.EVT_COMBOBOX, OnSelMG)
ssSizer.Add(selMG,0,WACV)
unitSizer.Add(ssSizer,0)
ssSizer = wx.BoxSizer(wx.HORIZONTAL)
ssSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Mod. vector: '),0,WACV)
modS = G2spc.splitSSsym(ssopt['ssSymb'])[0]
ssopt['ModVec'],ifShow = G2spc.SSGModCheck(ssopt['ModVec'],modS)
for i,[val,show] in enumerate(zip(ssopt['ModVec'],ifShow)):
if show:
valSizer = wx.BoxSizer(wx.HORIZONTAL)
modVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,ssopt['ModVec'],i,
xmin=-.98,xmax=.98,nDig=(10,4),typeHint=float,
OnLeave=OnModVal,size=wx.Size(50,-1))
unitSizerWidgetList.append(modVal)
valSizer.Add(modVal,0,WACV)
modSpin = wx.SpinButton(G2frame.dataWindow,style=wx.SP_VERTICAL,size=wx.Size(20,20))
unitSizerWidgetList.append(modSpin)
modSpin.SetValue(0)
modSpin.SetRange(-1,1)
modSpin.Bind(wx.EVT_SPIN, OnMoveMod)
valSizer.Add(modSpin,0,WACV)
ssSizer.Add(valSizer,0,WACV)
Indx[modVal.GetId()] = i
Indx[modSpin.GetId()] = [i,modVal]
else:
modVal = wx.TextCtrl(G2frame.dataWindow,value=('%.3f'%(val)),
size=wx.Size(50,20),style=wx.TE_READONLY)
modVal.SetBackgroundColour(VERY_LIGHT_GREY)
ssSizer.Add(modVal,0,WACV)
ssSizer.Add(wx.StaticText(G2frame.dataWindow,label=' in steps of cell step above'),0,WACV)
unitSizer.Add(ssSizer,0)
ssSizer = wx.BoxSizer(wx.HORIZONTAL)
ssSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Max. M: '),0,WACV)
maxMH = wx.ComboBox(G2frame.dataWindow,value=str(ssopt['maxH']),
choices=indChoice,style=wx.CB_READONLY|wx.CB_DROPDOWN)
unitSizerWidgetList.append(maxMH)
maxMH.Bind(wx.EVT_COMBOBOX, OnMaxMH)
ssSizer.Add(maxMH,0,WACV)
if len(peaks[0]):
findMV = wx.Button(G2frame.dataWindow,label="Find mod. vec.?")
findMV.Bind(wx.EVT_BUTTON,OnFindOneMV)
ssSizer.Add(findMV,0,WACV)
findallMV = wx.Button(G2frame.dataWindow,label="Try all?")
unitSizerWidgetList.append(findallMV)
findallMV.Bind(wx.EVT_BUTTON,OnFindMV)
ssSizer.Add(findallMV,0,WACV)
unitSizer.Add(ssSizer,0)
# cell display options
littleSizer = wx.BoxSizer(wx.HORIZONTAL)
cellDisplayOpts['Show'] = True
hklShow = wx.Button(G2frame.dataWindow,label="show HKL from cell")
hklShow.Bind(wx.EVT_BUTTON,OnNewHklShow)
littleSizer.Add(hklShow,0,WACV)
if 'E' not in Inst['Type'][0]:
littleSizer.Add((5,-1))
if not ssopt.get('Use',False): # Show Extinct not available for super lattice
showExt = G2G.G2CheckBox(G2frame.dataWindow,'Show Extinct',
cellDisplayOpts,'showExtinct',OnChange=OnExtHklShow)
unitSizerWidgetList.append(showExt)
littleSizer.Add(showExt,0,WACV)
littleSizer.Add(wx.StaticText(G2frame.dataWindow,label=' highlight ',style=wx.ALIGN_RIGHT),0,WACV)
G2frame.PlotOpts['hklHighlight'] = G2frame.PlotOpts.get('hklHighlight',0)
Sel = G2G.G2ChoiceButton(G2frame.dataWindow,[ 'None',] + [c+notEq0 for c in ('h','k','l')],
indLoc=G2frame.PlotOpts,indKey='hklHighlight',onChoice=OnAxHklShow)
unitSizerWidgetList.append(Sel)
littleSizer.Add(Sel,0,WACV)
if 'E' not in Inst['Type'][0]:
if 'N' in Inst['Type'][0]:
littleSizer.Add((5,-1))
MagSel = wx.CheckBox(G2frame.dataWindow,label="Magnetic?")
unitSizerWidgetList.append(MagSel)
MagSel.SetValue('MagSpGrp' in SGData)
MagSel.Bind(wx.EVT_CHECKBOX,OnMagSel)
littleSizer.Add(MagSel,0,WACV)
if len(G2frame.HKL) and 'PKS' not in G2frame.GPXtree.GetItemText(G2frame.PatternId):
littleSizer.Add((5,-1))
makePks = wx.Button(G2frame.dataWindow,label='Make new Peak list')
unitSizerWidgetList.append(makePks)
makePks.Bind(wx.EVT_BUTTON,OnMakePks)
littleSizer.Add(makePks,0,WACV)
unitSizer.Add(littleSizer,0)
# magnetic cell options
if 'N' in Inst['Type'][0] and 'MagSpGrp' in SGData:
neutSizer = wx.BoxSizer(wx.HORIZONTAL)
GenSym,GenFlg,BNSsym = G2spc.GetGenSym(SGData)
SGData['GenSym'] = GenSym
SGData['SGGray'] = False
neutSizer.Add(wx.StaticText(G2frame.dataWindow,label=' BNS lattice: '),0,WACV)
BNSkeys = [SGData['SGLatt'],]+list(BNSsym.keys())
BNSkeys.sort()
try: #this is an ugly kluge - bug in wx.ComboBox
if SGData['BNSlattsym'][0][2] in ['a','b','c']:
BNSkeys.reverse()
except:
pass
BNS = wx.ComboBox(G2frame.dataWindow,value=SGData['BNSlattsym'][0],
choices=BNSkeys,style=wx.CB_READONLY|wx.CB_DROPDOWN)
BNS.Bind(wx.EVT_COMBOBOX,OnBNSlatt)
neutSizer.Add(BNS,0,WACV)
spinColor = ['black','red']
spCode = {-1:'red',1:'black'}
for isym,sym in enumerate(GenSym[1:]):
neutSizer.Add(wx.StaticText(G2frame.dataWindow,label=' %s: '%(sym.strip())),0,WACV)
spinOp = wx.ComboBox(G2frame.dataWindow,value=spCode[SGData['SGSpin'][isym+1]],choices=spinColor,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[spinOp.GetId()] = isym
spinOp.Bind(wx.EVT_COMBOBOX,OnSpinOp)
neutSizer.Add(spinOp,0,WACV)
OprNames,SpnFlp = G2spc.GenMagOps(SGData)
SGData['SpnFlp'] = SpnFlp
showSpins = wx.Button(G2frame.dataWindow,label=' Show spins?')
showSpins.Bind(wx.EVT_BUTTON,OnShowSpins)
neutSizer.Add(showSpins,0,WACV)
unitSizer.Add(neutSizer,0)
unitSizer.Add((5,5),0)
return unitSizer
# The various grids for Unilt Cells List
def SpGrpGrid():
def OnSelectSgrp(event):
'Called when the Space Group Search Results show column is checked'
if event is not None:
clearShowFlags()
r = event.GetRow()
for i in range(len(ssopt['SgResults'])):
ssopt['SgResults'][i][1] = False
SgTable.SetValue(i,1,False)
SgTable.SetValue(r,1,True)
controls[13] = ssopt['SgResults'][r][0]
else:
for r in range(len(ssopt['SgResults'])):
if ssopt['SgResults'][r][1]:
controls[13] = ssopt['SgResults'][r][0]
break
SgDisplay.ForceRefresh()
ssopt['SGData'] = G2spc.SpcGroup(controls[13])[1]
G2frame.dataWindow.RefineCell.Enable(True)
OnHklShow(event,True,indexFrom=' Space group selection %s #%d'%(controls[13],r))
SpGrpGrid = wx.BoxSizer(wx.VERTICAL)
lbl = (' Space group search results from "Try all"'+ssopt.get('SgSettings',''))
SpGrpGrid.Add(wx.StaticText(parent=G2frame.dataWindow,label=lbl))
colLabels = ['Sp Grp','show','M20','X20','Nhkl','fr. found']
Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_BOOL,wg.GRID_VALUE_FLOAT+':10,2',wg.GRID_VALUE_NUMBER,
wg.GRID_VALUE_NUMBER,wg.GRID_VALUE_FLOAT+':10,3']
rowLabels = []
table = []
for result in ssopt['SgResults']:
rowLabels.append('')
row = result
table.append(row)
SgTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
SgDisplay = G2G.GSGrid(G2frame.dataWindow)
SgDisplay.SetTable(SgTable, True)
SgDisplay.Bind(wg.EVT_GRID_CELL_LEFT_CLICK,OnSelectSgrp)
SgDisplay.SetRowLabelSize(0)
SgDisplay.AutoSizeColumns(False)
for r in range(SgDisplay.GetNumberRows()):
for c in range(SgDisplay.GetNumberCols()):
if c == 1:
SgDisplay.SetReadOnly(r,c,isReadOnly=False)
else:
SgDisplay.SetReadOnly(r,c,isReadOnly=True)
SpGrpGrid.Add(SgDisplay)
_setupResultsGrid(SgDisplay)
OnSelectSgrp(None)
return SpGrpGrid
def SSGrid():
def OnSelectSSG(event):
'Called when the Super Space Group Search Results show column is checked'
if event is not None:
if event.GetCol() != 1:
return
clearShowFlags()
r = event.GetRow()
for i in range(len(ssopt['SSgResults'])):
results[i][1] = False
SSgTable.SetValue(r,1,True)
ssopt['ModVec'] = results[r][4:]
ssopt['ssSymb'] = results[r][0]
result = results[r]
# else:
# for r,result in enumerate(results):
# try:
# if result[1]:
# ssopt['ModVec'] = result[4:]
# ssopt['ssSymb'] = result[0]
# break
# except ValueError: #old style!
SSDisplay.ForceRefresh() #repaints the grids only
OnHklShow(event,True,indexFrom=' Super Space group selection %s #%d'%(controls[13]+result[0],r))
results = ssopt['SSgResults']
if type(results[0][1]) != bool:
return None
SSGrpGrid = wx.BoxSizer(wx.VERTICAL)
lbl = (' Super Space group search results for '+controls[5])
SSGrpGrid.Add(wx.StaticText(parent=G2frame.dataWindow,label=lbl))
if len(results[0]) == 6:
colLabels = ['SSp Grp','show','M20','X20','Nhkl','fr. found']
Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_BOOL,wg.GRID_VALUE_FLOAT+':10,2',wg.GRID_VALUE_NUMBER,
wg.GRID_VALUE_NUMBER,wg.GRID_VALUE_FLOAT+':10,3']
else:
colLabels = ['SSp Grp','show','M20','X20','\u03B1','\u03B2','\u03B3']
Types = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_BOOL,wg.GRID_VALUE_FLOAT+':10,2',wg.GRID_VALUE_NUMBER,
wg.GRID_VALUE_FLOAT+':10,3',wg.GRID_VALUE_FLOAT+':10,3',wg.GRID_VALUE_FLOAT+':10,3']
rowLabels = []
table = []
for result in results:
rowLabels.append('')
row = result
table.append(row)
SSgTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
SSDisplay = G2G.GSGrid(G2frame.dataWindow)
SSDisplay.SetTable(SSgTable, True)
SSDisplay.Bind(wg.EVT_GRID_CELL_LEFT_CLICK,OnSelectSSG)
SSDisplay.SetRowLabelSize(0)
SSDisplay.AutoSizeColumns(False)
for r in range(SSDisplay.GetNumberRows()):
for c in range(SSDisplay.GetNumberCols()):
if c == 1:
SSDisplay.SetReadOnly(r,c,isReadOnly=False)
else:
SSDisplay.SetReadOnly(r,c,isReadOnly=True)
SSGrpGrid.Add(SSDisplay)
_setupResultsGrid(SSDisplay)
OnSelectSSG(None)
return SSGrpGrid
def MagSubGrid():
global KeyList
def ClearCurrentShowNext():
KeepShowNext(False)
KeyList += [['j',ClearCurrentShowNext,'Show next Mag. Spc. Group, clear keep flag on current']]
def KeepCurrentShowNext():
KeepShowNext(True)
KeyList += [['k',KeepCurrentShowNext,'Show next Mag. Spc. Group, keep current']]
def KeepShowNext(KeepCurrent=True):
'''Show next "keep" item in Magnetic Space Group list, possibly resetting the
keep flag for the current displayed cell
'''
for i in range(len(magcells)): # find plotted setting
if magcells[i]['Use']: break
else:
return # no Try is set
if not KeepCurrent: # clear current
magcells[i]['Keep'] = False
MagCellsTable.SetValue(i,2,False)
keeps = [j for j in range(i+1,len(magcells)) if magcells[j]['Keep']]
if not keeps:
if not KeepCurrent: magDisplay.ForceRefresh()
return # no remaining Keep-flagged entries
next = keeps[0]
# update table
magcells[i]['Use'] = False
MagCellsTable.SetValue(i,1,False)
magcells[next]['Use'] = True
MagCellsTable.SetValue(next,1,True)
# get SG info and plot
SGData = magcells[next]['SGData']
A = G2lat.cell2A(magcells[next]['Cell'][:6])
G2frame.HKL = G2pwd.getHKLpeak(1.0,SGData,A,Inst)
G2pwpl.PlotPatterns(G2frame,extraKeys=KeyList)
magDisplay.ForceRefresh()
# change Scroll to display new setting
xscroll = G2frame.dataWindow.GetScrollPos(wx.HORIZONTAL)
yscroll = magDisplay.CellToRect(next,1)[1]/G2frame.dataWindow.GetScrollPixelsPerUnit()[1]
G2frame.dataWindow.Scroll(xscroll,yscroll)
def RefreshMagCellsGrid(event):
'Display results from k-SUBGROUPSMAG in the Unit Cells tab & allow inspection of results'
controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(UnitCellsId)
r,c = event.GetRow(),event.GetCol()
rLab = magDisplay.GetRowLabelValue(r)
br = baseList[r]
phase = phaseDict[br]
pname = '(%s) %s'%(rLab,phase['Name'])
if magcells:
if c == 0:
mSGData = phase['SGData']
text,table = G2spc.SGPrint(mSGData,AddInv=True)
if 'magAtms' in phase:
msg = 'Magnetic space group information'
text[0] = ' Magnetic Space Group: '+mSGData['MagSpGrp']
text[3] = ' The magnetic lattice point group is '+mSGData['MagPtGp']
OprNames,SpnFlp = G2spc.GenMagOps(mSGData)
G2G.SGMagSpinBox(G2frame.dataWindow,msg,text,table,mSGData['SGCen'],OprNames,
mSGData['SpnFlp'],False).Show()
else:
msg = 'Space Group Information'
G2G.SGMessageBox(G2frame.dataWindow,msg,text,table).Show()
elif c == 1:
for i in range(len(magcells)):
magcells[i]['Use'] = False
for i in range(len(baseList)):
MagCellsTable.SetValue(i,c,False)
MagCellsTable.SetValue(r,c,True)
magDisplay.ForceRefresh()
phase['Use'] = True
mSGData = phase['SGData']
A = G2lat.cell2A(phase['Cell'][:6])
G2frame.HKL = np.array(G2pwd.getHKLpeak(1.0,mSGData,A,Inst))
G2pwpl.PlotPatterns(G2frame,extraKeys=KeyList)
elif c == 2:
if MagCellsTable.GetValue(r,c):
MagCellsTable.SetValue(r,c,False)
phase['Keep'] = False
else:
phase['Keep'] = True
MagCellsTable.SetValue(r,c,True)
magDisplay.ForceRefresh()
elif c ==3:
maxequiv = magcells[0].get('maxequiv',100)
mSGData = phase['SGData']
Uvec = phase['Uvec']
Trans = phase['Trans']
ifMag = False
if 'magAtms' in phase:
ifMag = True
allmom = phase.get('allmom',False)
magAtms = phase.get('magAtms','')
mAtoms = TestMagAtoms(phase,magAtms,SGData,Uvec,Trans,allmom,maxequiv)
else:
mAtoms = TestAtoms(phase,controls[15],SGData,Uvec,Trans,maxequiv)
Atms = []
AtCods = []
atMxyz = []
for ia,atom in enumerate(mAtoms):
atom[0] += '_%d'%ia
SytSym,Mul,Nop,dupDir = G2spc.SytSym(atom[2:5],mSGData)
Atms.append(atom[:2]+['',]+atom[2:5])
AtCods.append('1')
if 'magAtms' in phase:
MagSytSym = G2spc.MagSytSym(SytSym,dupDir,mSGData)
CSI = G2spc.GetCSpqinel(mSGData['SpnFlp'],dupDir)
atMxyz.append([MagSytSym,CSI[0]])
else:
CSI = G2spc.GetCSxinel(SytSym)
atMxyz.append([SytSym,CSI[0]])
G2phsG.UseMagAtomDialog(G2frame,pname,Atms,AtCods,atMxyz,ifMag=ifMag,ifOK=True).ShowModal()
elif c in [4,5]:
if 'altList' not in phase: return
if c == 4:
title = 'Conjugacy list for '+pname
items = phase['altList']
ifPick = True
elif c == 5:
title = 'Super groups list for '+pname
items = phase['supList']
if not items[0]:
wx.MessageBox(pname+' is a maximal subgroup',caption='Super group is parent',style=wx.ICON_INFORMATION)
return
ifPick = False
Pick = -1
dlg = SubCellsDialog(G2frame,title,controls,SGData,items,phaseDict,ifPick)
try:
if dlg.ShowModal() == wx.ID_OK:
altList = copy.copy(phase['altList'])
Pick = dlg.GetSelection()
pickPhase = phaseDict[altList[Pick]]
pickPhase['altList'] = altList
pickPhase['Use'] = phase['Use']
baseList[r] = altList[Pick]
finally:
dlg.Destroy()
if Pick >= 0:
data = [controls,bravais,cells,dminx,ssopt,magcells]
G2frame.GPXtree.SetItemPyData(UnitCellsId,data)
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
def OnRefreshKeep(event):
controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(UnitCellsId)
c = event.GetCol()
E,SGData = G2spc.SpcGroup(controls[13])
if c == 2:
testAtoms = ['',]+list(set([atom[1] for atom in controls[15]]))
ifMag = False
maxequiv = magcells[0]['maxequiv']
maximal = False
if 'magAtms' in magcells[0]:
ifMag = True
allmom = magcells[0]['allmom']
magAtms = magcells[0]['magAtms']
dlg = G2G.MultiDataDialog(G2frame,title='Keep options',
prompts=['max unique','test for mag. atoms','all have moment','only maximal subgroups',],
values=[maxequiv,'',allmom,False],limits=[[1,100],testAtoms,[True,False],[True,False]],
formats=['%d','choice','bool','bool'])
else:
dlg = G2G.MultiDataDialog(G2frame,title='Keep options',
prompts=['max unique','only maximal subgroups',],
values=[maxequiv,False],limits=[[1,100],[True,False],],
formats=['%d','bool',])
if dlg.ShowModal() == wx.ID_OK:
if ifMag:
maxequiv,atype,allmom,maximal = dlg.GetValues()
magAtms = [atom for atom in controls[15] if atom[1] == atype]
else:
maxequiv,maximal = dlg.GetValues()
dlg = wx.ProgressDialog('Setting Keep flags','Processing '+magcells[0]['Name'],len(magcells),
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME)
for ip,phase in enumerate(magcells):
dlg.Update(ip,newmsg='Processing '+phase['Name'])
Uvec = phase['Uvec']
Trans = phase['Trans']
if ifMag:
phase['nAtoms'] = len(TestMagAtoms(phase,magAtms,SGData,Uvec,Trans,allmom,maxequiv,maximal))
else:
phase['nAtoms'] = len(TestAtoms(phase,controls[15],SGData,Uvec,Trans,maxequiv,maximal))
dlg.Destroy()
data = controls,bravais,cells,dminx,ssopt,magcells
G2frame.GPXtree.SetItemPyData(UnitCellsId,data)
wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
MagSubGrid = wx.BoxSizer(wx.VERTICAL)
itemList = [phase.get('gid',ip+1) for ip,phase in enumerate(magcells)]
phaseDict = dict(zip(itemList,magcells))
G2frame.dataWindow.CopyCell.Enable(False)
kvec1 = ','.join(controls[14][:3])
kvec2 = ','.join(controls[14][3:6])
kvec3 = ','.join(controls[14][6:])
baseList = controls[16]
if 'magAtms' in magcells[0]:
G2frame.dataWindow.RunSubGroupsMag.Enable(True)
Label = '\n Magnetic subgroup cells from Bilbao k-SUBGROUPSMAG for %s; kvec1=(%s)'%(controls[13],kvec1)
else:
G2frame.dataWindow.RunSubGroups.Enable(True)
Label = '\n Subgroup cells from Bilbao SUBGROUPS for %s; kvec1=(%s)'%(controls[13],kvec1)
if ' ' not in kvec2:
Label += ', kvec2=(%s)' % kvec2
if ' ' not in kvec3:
Label += ', kvec3=(%s)' % kvec3
Label += ':'
MagSubGrid.Add(wx.StaticText(parent=G2frame.dataWindow,label=Label))
rowLabels = [str(i+1) for i in range(len(baseList))]
colLabels = ['Space Gp','Try','Keep','Uniq','nConj','nSup','Trans','Vec','a','b','c','\u03B1','\u03B2','\u03B3','Volume']
Types = [wg.GRID_VALUE_STRING,]+2*[wg.GRID_VALUE_BOOL,]+3*[wg.GRID_VALUE_LONG,]+2*[wg.GRID_VALUE_STRING,]+ \
3*[wg.GRID_VALUE_FLOAT+':10,5',]+3*[wg.GRID_VALUE_FLOAT+':10,3',]+[wg.GRID_VALUE_FLOAT+':10,2']
table = []
for ip in baseList:
phase = phaseDict[ip]
natms = phase.get('nAtoms',1)
try:
nConj = len(phase['altList'])
nSup = len(phase['supList'])
except KeyError:
nConj = 0
nSup = 0
cell = list(phase['Cell'])
trans = G2spc.Trans2Text(phase['Trans'])
vec = G2spc.Latt2text([phase['Uvec'],])
row = [phase['Name'],phase['Use'],phase['Keep'],natms,nConj,nSup,trans,vec]+cell
table.append(row)
MagCellsTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
G2frame.GetStatusBar().SetStatusText(
'Double click Keep to refresh Keep flags; click Space Gp to see sym. ops., Uniq to see unique atoms list; Try to trigger K & J keys on plot',1)
magDisplay = G2G.GSGrid(G2frame.dataWindow)
magDisplay.SetRowLabelSize(45)
magDisplay.SetTable(MagCellsTable, True)
magDisplay.Bind(wg.EVT_GRID_CELL_LEFT_CLICK,RefreshMagCellsGrid)
magDisplay.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK,OnRefreshKeep)
magDisplay.AutoSizeColumns(False)
for r in range(magDisplay.GetNumberRows()):
for c in range(magDisplay.GetNumberCols()):
if c in [1,2]:
magDisplay.SetReadOnly(r,c,isReadOnly=False)
else:
magDisplay.SetReadOnly(r,c,isReadOnly=True)
MagSubGrid.Add(magDisplay)
_setupResultsGrid(magDisplay)
return MagSubGrid
#### UpdateUnitCellsGrid code starts here
# create all menubars accessed here
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.LimitMenu) # Needed below
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.PeakMenu) # Needed below
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.IndexMenu)
resizeGrids = [] # track Grids to resize
Indx = {}
G2frame.ifSetLimitsMode = 0
G2frame.CancelSetLimitsMode.Enable(False)
UnitCellsId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Unit Cells List')
SPGlist = G2spc.spglist
spaceGroups = ['F m 3 m','I m 3 m','P m 3 m','R 3 m','P 6/m m m','I 4/m m m',
'P 4/m m m','F m m m','I m m m','A m m m','B m m m','C m m m','P m m m','I 2/m','A 2/m','C 2/m','P 2/m','P -1','C -1']
Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[0]
Limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Limits'))[1]
if 'T' in Inst['Type'][0]:
#difC = Inst['difC'][1]
dmin = G2lat.Pos2dsp(Inst,Limits[0])
elif 'E' in Inst['Type'][0]:
#TTh = Inst['2-theta'][1]
dmin = G2lat.Pos2dsp(Inst,Limits[1])
else: #'C', 'B', or 'PKS'
#wave = G2mth.getWave(Inst)
dmin = G2lat.Pos2dsp(Inst,Limits[1])
G2frame.GetStatusBar().SetStatusText('')
G2frame.Bind(wx.EVT_MENU, OnIndexPeaks, id=G2G.wxID_INDEXPEAKS)
G2frame.Bind(wx.EVT_MENU, OnRunSubs, id=G2G.wxID_RUNSUB)
G2frame.Bind(wx.EVT_MENU, OnRunSubsMag, id=G2G.wxID_RUNSUBMAG)
#G2frame.Bind(wx.EVT_MENU, OnLatSym, id=G2G.wxID_LATSYM) # removed from site
G2frame.Bind(wx.EVT_MENU, OnNISTLatSym, id=G2G.wxID_NISTLATSYM)
G2frame.Bind(wx.EVT_MENU, CopyUnitCell, id=G2G.wxID_COPYCELL)
G2frame.Bind(wx.EVT_MENU, LoadUnitCell, id=G2G.wxID_LOADCELL)
#G2frame.Bind(wx.EVT_MENU, ImportUnitCell, id=G2G.wxID_IMPORTCELL)
G2frame.Bind(wx.EVT_MENU, TransformUnitCell, id=G2G.wxID_TRANSFORMCELL)
G2frame.Bind(wx.EVT_MENU, onRefineCell, id=G2G.wxID_REFINECELL)
G2frame.Bind(wx.EVT_MENU, MakeNewPhase, id=G2G.wxID_MAKENEWPHASE)
G2frame.Bind(wx.EVT_MENU, OnExportCells, id=G2G.wxID_EXPORTCELLS)
G2frame.Bind(wx.EVT_MENU, OnShowGenRefls, id=G2G.wxID_SHOWGENHKLS)
G2frame.Bind(wx.EVT_MENU, OnClearCells, id=G2G.wxID_CLEARCELLS)
if len(data) < 6:
data.append([])
controls,bravais,cells,dminx,ssopt,magcells = data
if len(controls) < 13: #add cell volume if missing
controls.append(G2lat.calc_V(G2lat.cell2A(controls[6:12])))
if len(controls) < 14: #add space group if missing
controls.append(spaceGroups[bravaisSymb.index(controls[5])])
if len(controls) < 15:
controls.append(list(range(1,len(magcells)+1)))
while len(bravais) < 18:
bravais += [0,]
SGData = ssopt.get('SGData',G2spc.SpcGroup(controls[13])[1])
G2frame.GPXtree.SetItemPyData(UnitCellsId,data) #update with volume
bravaisNames = ['Cubic-F','Cubic-I','Cubic-P','Trigonal-R','Trigonal/Hexagonal-P',
'Tetragonal-I','Tetragonal-P','Orthorhombic-F','Orthorhombic-I','Orthorhombic-A',
'Orthorhombic-B','Orthorhombic-C','Orthorhombic-P',
'Monoclinic-I','Monoclinic-A','Monoclinic-C','Monoclinic-P','Triclinic','Triclinic',]
G2frame.dataWindow.IndexPeaks.Enable(False)
peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Index Peak List'))
if peaks:
G2frame.dataWindow.IndexPeaks.Enable(True)
G2frame.dataWindow.RefineCell.Enable(False)
if controls[12] > 1.0 and len(peaks[0]): #if a "real" volume (i.e. not default) and peaks
G2frame.dataWindow.RefineCell.Enable(True)
G2frame.dataWindow.CopyCell.Enable(False)
G2frame.dataWindow.MakeNewPhase.Enable(False)
G2frame.dataWindow.ExportCells.Enable(False)
if cells:
G2frame.dataWindow.CopyCell.Enable(True)
G2frame.dataWindow.MakeNewPhase.Enable(True)
G2frame.dataWindow.ExportCells.Enable(True)
elif magcells:
G2frame.dataWindow.CopyCell.Enable(True)
if G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Phases'):
G2frame.dataWindow.LoadCell.Enable(True)
pkId = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Peak List')
if pkId:
peakList = G2frame.GPXtree.GetItemPyData(pkId)
# in case we are loading this without visiting the Peak List first, initialize
peakList['xtraMode'] = peakList.get('xtraMode',False)
G2frame.dataWindow.XtraPeakMode.Check(peakList['xtraMode'])
# GUI code
setRow = None
G2frame.dataWindow.ClearData()
# setup for resizing
G2frame.dataWindow.customResize = _onResizeUnitCellsList
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,label='Indexing tools'),0,WACV)
if not hasattr(G2frame,'kvecSearch'):
G2frame.kvecSearch = {'mode':False}
if G2frame.dataWindow.XtraPeakMode.IsChecked():
cb = G2G.G2CheckBox(parent,'Search for k-vector',G2frame.kvecSearch,'mode',OnChange=updateCellsWindow)
topSizer.Add(cb,0,WACV|wx.LEFT,15)
else:
G2frame.kvecSearch['mode'] = False
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add((-1,3),0)
if not G2frame.kvecSearch['mode']:
# autoindexing GUI
mainSizer.Add(firstSizer())
else:
# k-vector GUI
mainSizer.Add(kvecSizer())
# 2nd "box": unit cell/sym info
mainSizer.Add((-1,3),0)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add((-1, 3), 0)
unitSizerWidgetList = [] # entries in unitSizer to disable/enable
mainSizer.Add(unitSizer())
# 3rd "box" search results
mainSizer.Add((-1,3),0)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add(wx.StaticText(parent=G2frame.dataWindow,
label='Cell Search Results',style=wx.ALIGN_CENTER),0,wx.EXPAND,3)
G2frame.dataWindow.currentGrids = []
# space group search results
if len(ssopt.get('SgResults',[])):
mainSizer.Add(SpGrpGrid())
# cell search results
if cells:
mode = 0
try: # for Cell sym, 1st entry is cell xform matrix;
# for kvector search, 1st item is a question mark
len(cells[0][0])
mode = 1
if cells[0][0] == '?': mode = 2
except:
pass
# k-vector search results table
if mode == 2:
G2frame.kvecSearch['mode'] == True
colLabels = ['show']
Types = [wg.GRID_VALUE_BOOL]
colLabels += [
'kx', 'ky', 'kz',
'Ave. \u03B4d/d',
'Ave. \u03B4d',
'Max. \u03B4d'
]
Types += (6 * [wg.GRID_VALUE_FLOAT + ':10, 5'])
mainSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label='\n k-vector search results:'))
elif mode == 1:
mainSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label='\n Cell symmetry search:'))
colLabels = ['show']
Types = [wg.GRID_VALUE_BOOL]
colLabels += ['a','b','c','\u03B1','\u03B2','\u03B3','Volume','Keep']
Types += (3*[wg.GRID_VALUE_FLOAT+':10,5',]+
3*[wg.GRID_VALUE_FLOAT+':10,3',]+
[wg.GRID_VALUE_FLOAT+':10,2',wg.GRID_VALUE_BOOL])
else:
# indexing search results table
mainSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label='\n Indexing Result:'))
colLabels = ['M20','X20','show','Bravais']
Types = [wg.GRID_VALUE_FLOAT+':10,2',wg.GRID_VALUE_NUMBER,
wg.GRID_VALUE_BOOL,wg.GRID_VALUE_STRING]
colLabels += ['a','b','c','\u03B1','\u03B2','\u03B3','Volume','Keep']
Types += (3*[wg.GRID_VALUE_FLOAT+':10,5',]+
3*[wg.GRID_VALUE_FLOAT+':10,3',]+
[wg.GRID_VALUE_FLOAT+':10,2',wg.GRID_VALUE_BOOL])
rowLabels = []
table = []
# are we going to keep a current "Show" flag?
isUseSet = any([cell[-2] for cell in cells]) and showUse and mode == 0
setRow = None
for i,cell in enumerate(cells):
# reset all "show" flags when table is first created, unless
# we are going to set the Show flag in a row
if not isUseSet:
cell[-2] = False
elif cell[-2]:
setRow = i
rowLabels.append('')
if mode:
row = [cell[-2]]+cell[3:10]+[cell[11],]
else:
row = cell[0:2]+[cell[-2]]+[bravaisSymb[cell[2]]]+cell[3:10]+[cell[11],]
# if cell[-2]:
# if mode != 2:
# A = G2lat.cell2A(cell[3:9])
# G2frame.HKL = G2lat.GenHBravais(dmin,cell[2],A)
# for hkl in G2frame.HKL:
# hkl.insert(4,G2lat.Dsp2pos(Inst,hkl[3])+controls[1])
# G2frame.HKL = np.array(G2frame.HKL)
# else:
# # We need to fill in the todos when the mode is 2, i.e.,
# # the k-vector search.
# pass
table.append(row)
UnitCellsTable = G2G.Table(table,rowLabels=rowLabels,colLabels=colLabels,types=Types)
gridDisplay = G2G.GSGrid(G2frame.dataWindow)
gridDisplay.SetTable(UnitCellsTable, True)
G2frame.dataWindow.CopyCell.Enable(True)
gridDisplay.Bind(wg.EVT_GRID_CELL_LEFT_CLICK,SeaResSelected)
gridDisplay.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK,OnSortCells)
gridDisplay.SetRowLabelSize(0)
gridDisplay.AutoSizeColumns(False)
for r in range(gridDisplay.GetNumberRows()):
for c in range(gridDisplay.GetNumberCols()):
if c == 2:
gridDisplay.SetReadOnly(r,c,isReadOnly=False)
else:
gridDisplay.SetReadOnly(r,c,isReadOnly=True)
if mode == 2:
hSizer = wx.BoxSizer(wx.HORIZONTAL)
hSizer.Add(gridDisplay)
ISObut = wx.Button(G2frame.dataWindow,label='Call ISODISTORT')
ISObut.Bind(wx.EVT_BUTTON, OnISODISTORT_kvec)
hSizer.Add(ISObut)
mainSizer.Add(hSizer)
else:
mainSizer.Add(gridDisplay)
_setupResultsGrid(gridDisplay)
if setRow: # we have a "Show" flag to set
setGrid = gridDisplay
gridDisplay.SetCellValue(setRow,2,'True') # set flag in grid
disableCellEntries()
# G@ Modulation vector results list
if ssopt and 'SSgResults' in ssopt and len(ssopt['SSgResults']) > 1:
ssgrid = SSGrid()
if ssgrid: mainSizer.Add(ssgrid)
# Subgroup/magnetic s.g. search results
if magcells and len(controls) > 16:
mainSizer.Add(MagSubGrid())
# GUI creation done -- finally
G2frame.Contour = False
if New:
OnHklShow(None,indexFrom=' Indexing from unit cell & symmetry settings')
New = False
G2frame.dataWindow.SetDataSize()
if callSeaResSelected:
SeaResSelected(None) # select 1st item in table
elif setRow:
wx.CallAfter(setGrid.MakeCellVisible,setRow,0) # scroll to line setRow
################################################################################
##### Reflection list
################################################################################
[docs]
def UpdateReflectionGrid(G2frame,data,HKLF=False,Name=''):
'''respond to selection of PWDR or HKLF Reflections data tree
item by displaying a table of reflections in the data window.
Note that this is used for Single Xtal even though in pwdGUI.
'''
Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
dMin = 0.05
if not isinstance(G2frame.Hide, bool):
G2frame.Hide = False
if 'UsrReject' in Controls:
dMin = Controls['UsrReject'].get('MinD',0.05)
def OnPlot1DHKL(event):
phaseName = G2frame.RefList
if phaseName not in ['Unknown',]:
pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases')
phaseId = G2gd.GetGPXtreeItemId(G2frame,pId,phaseName)
General = G2frame.GPXtree.GetItemPyData(phaseId)['General']
Super = General.get('Super',0)
else:
Super = 0
if 'list' in str(type(data)): #single crystal data is 2 dict in list
refList = data[1]['RefList']
else: #powder data is a dict of dicts; each same structure as SC 2nd dict
if 'RefList' in data[phaseName]:
refList = np.array(data[phaseName]['RefList'])
else:
wx.MessageBox('No reflection list - do Refine first',caption='Reflection plotting')
return
G2plt.Plot1DSngl(G2frame,newPlot=True,hklRef=refList,Super=Super,Title=phaseName)
def OnPlotHKL(event):
'''Plots a layer of reflections
'''
phaseName = G2frame.RefList
if phaseName not in ['Unknown',]:
pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases')
phaseId = G2gd.GetGPXtreeItemId(G2frame,pId,phaseName)
General = G2frame.GPXtree.GetItemPyData(phaseId)['General']
Super = General.get('Super',0)
SuperVec = General.get('SuperVec',[])
else:
Super = 0
SuperVec = []
if 'list' in str(type(data)): #single crystal data is 2 dict in list
refList = data[1]['RefList']
else: #powder data is a dict of dicts; each same structure as SC 2nd dict
if 'RefList' in data[phaseName]:
refList = np.array(data[phaseName]['RefList'])
else:
wx.MessageBox('No reflection list - do Refine first',caption='Reflection plotting')
return
FoMax = np.max(refList.T[8+Super])
Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
controls = {'Type' : 'Fo','ifFc' : True,'HKLmax' : Hmax,'HKLmin' : Hmin,
'FoMax' : FoMax,'Zone' : '001','Layer' : 0,'Scale' : 1.0,'Super':Super,'SuperVec':SuperVec}
G2plt.PlotSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
def OnPlot3DHKL(event):
'''Plots the reflections in 3D
'''
phaseName = G2frame.RefList
Super = 0
SuperVec = []
if phaseName not in ['Unknown',]:
pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases')
phaseId = G2gd.GetGPXtreeItemId(G2frame,pId,phaseName)
General = G2frame.GPXtree.GetItemPyData(phaseId)['General']
if General.get('Modulated',False):
Super = 1
SuperVec = General['SuperVec']
if 'list' in str(type(data)): #single crystal data is 2 dict in list
refList = data[1]['RefList']
else: #powder data is a dict of dicts; each same structure as SC 2nd dict
if 'RefList' in data[phaseName]:
refList = np.array(data[phaseName]['RefList'])
else:
wx.MessageBox('No reflection list - do Refine first',caption='Reflection plotting')
return
refList.T[3+Super] = np.where(refList.T[4+Super]<dMin,-refList.T[3+Super],refList.T[3+Super])
FoMax = np.max(refList.T[8+Super])
Hmin = np.array([int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))])
Hmax = np.array([int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))])
Vpoint = np.array([int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))])
if len(data) > 1: #single crystal data
controls = {'Type':'Fosq','Iscale':False,'HKLmax':Hmax,'HKLmin':Hmin,'Zone':False,'viewKey':'L',
'microED':{'Nexp':[False,0],'Ztilt':[False,0]},'dType':data[1]['Type'],
'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
'backColor':[0,0,0],'depthFog':False,'Zclip':10.0,'cameraPos':10.,'Zstep':0.05,'viewUp':[0,1,0],
'Scale':1.0,'oldxy':[],'viewDir':[0,0,1]},'Super':Super,'SuperVec':SuperVec}
else: #powder data
controls = {'Type':'Fosq','Iscale':False,'HKLmax':Hmax,'HKLmin':Hmin,'Zone':False,'viewKey':'L',
'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
'backColor':[0,0,0],'depthFog':False,'Zclip':10.0,'cameraPos':10.,'Zstep':0.05,'viewUp':[0,1,0],
'Scale':1.0,'oldxy':[],'viewDir':[0,0,1]},'Super':Super,'SuperVec':SuperVec}
G2plt.Plot3DSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
def OnWilsonStat(event):
''' Show Wilson plot for PWDR and HKLF & return Wilson statistics <<E>, <E^2> & <E^2-1> to console
'''
phaseName = G2frame.RefList
if phaseName not in ['Unknown',]:
pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases')
phaseId = G2gd.GetGPXtreeItemId(G2frame,pId,phaseName)
General = G2frame.GPXtree.GetItemPyData(phaseId)['General']
Super = General.get('Super',0)
else:
Super = 0
if 'list' in str(type(data)): #single crystal data is 2 dict in list
refList = data[1]['RefList']
else: #powder data is a dict of dicts; each same structure as SC 2nd dict
if 'RefList' in data[phaseName]:
refList = np.array(data[phaseName]['RefList'])
else:
wx.MessageBox('No reflection list - do Refine first',caption='Reflection plotting')
return
PE = G2elemGUI.PickElement(G2frame,ifNone=False)
if PE.ShowModal() == wx.ID_OK:
normEle = PE.Elem.strip()
PE.Destroy()
Estat,Ehist = G2mth.DoWilsonStat(refList,Super,normEle,Inst)
print(' Wilson statistics : <|E|>: %.3f, <|E^2|>: %.3f, <|E^2-1|>: %.3f'%(Estat[0]/Estat[1],1.,Estat[2]/Estat[1]))
print(' Expected: random P-1: <|E|>: 0.798, <|E^2|>: 1.000, <|E^2-1|>: 0.968')
print(' random P1 : <|E|>: 0.886, <|E^2|>: 1.000, <|E^2-1|>: 0.736')
XY = [[Ehist[0],Ehist[1]],[Ehist[0],Ehist[2]]]
G2plt.PlotXY(G2frame,XY,labelX='sin$^2$%s/%s$^2$'%(GkTheta,Gklambda),
labelY=r'ln(<|F$_o$|$^2$>/%sf$^2$)'%GkSigma,newPlot=True,Title='Wilson plot')
def OnMakeCSV(event):
'''Make csv file from displayed ref table.
'''
phaseName = G2frame.RefList
pth = G2G.GetExportPath(G2frame)
dlg = wx.FileDialog(G2frame, 'Choose Reflection List csv file', pth, '',
'Reflection List (*.csv)|*.csv',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
try:
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
filename = os.path.splitext(filename)[0]+'.csv'
File = open(filename,'w')
File.write('%s\n'%phaseName)
colLabels = [G2frame.PeakTable.GetColLabelValue(i) for i in range(G2frame.PeakTable.GetNumberCols())]
File.write('%s\n'%(','.join(colLabels)))
nRows = G2frame.PeakTable.GetNumberRows()
for i in range(nRows):
refLine = G2frame.PeakTable.GetRowValues(i)
strLine = ','.join([str(item) for item in refLine])
File.write('%s\n'%strLine)
File.close()
finally:
dlg.Destroy()
def MakeReflectionTable(phaseName):
'''Returns a wx.grid table (G2G.Table) containing a list of all reflections
for a phase.
'''
Super = 0
if phaseName not in ['Unknown',]:
pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Phases')
if pId: # phase section missing from file (unusual)
phaseId = G2gd.GetGPXtreeItemId(G2frame,pId,phaseName)
if phaseId: #is phase deleted?
General = G2frame.GPXtree.GetItemPyData(phaseId)['General']
G,g = G2lat.cell2Gmat(General['Cell'][1:7])
GA,GB = G2lat.Gmat2AB(G) #Orthogonalization matricies
SGData = General['SGData']
if General.get('Modulated',False):
Super = 1
try:
Histograms = G2frame.GPXtree.GetItemPyData(phaseId)['Histograms']
histName = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histData = Histograms[histName]
except:
if GSASIIpath.GetConfigValue('debug'):
print('Reflection table problem: histogram {} not found in phase {}'.format(histName,phaseName))
return
rowLabels = []
if HKLF:
if G2frame.Hide:
refList = np.array([refl for refl in data[1]['RefList'] if refl[3]])
else:
refList = data[1]['RefList']
refs = refList
else:
muStrData = histData['Mustrain']
sizeData = histData['Size']
if len(data) > 1:
G2frame.dataWindow.SelectPhase.Enable(True)
try: #patch for old reflection lists
if not len(data[phaseName]):
return None
refList = np.array(data[phaseName]['RefList'])
I100 = refList.T[8+Super]*refList.T[11+Super]
except TypeError:
refList = np.array([refl[:11+Super] for refl in data[phaseName]])
I100 = refList.T[8+Super]*np.array([refl[11+Super] for refl in data[phaseName]])
MuStr = G2pwd.getMustrain(refList.T[:3],G,SGData,muStrData)
CrSize = G2pwd.getCrSize(refList.T[:3],G,GB,sizeData)
Imax = np.max(I100)
if Imax:
I100 *= 100.0/Imax
if 'C' in Inst['Type'][0]:
refs = np.vstack((refList.T[:15+Super],I100,MuStr,CrSize)).T
elif 'T' in Inst['Type'][0]:
refs = np.vstack((refList.T[:18+Super],I100,MuStr,CrSize)).T
elif Inst['Type'][0][2] in ['A','B']:
refs = np.vstack((refList.T[:17+Super],I100,MuStr,CrSize)).T
elif 'E' in Inst['Type'][0]:
refs = np.vstack((refList.T[:12+Super],I100,MuStr,CrSize)).T #last two not shown for now
rowLabels = [str(i) for i in range(len(refs))]
Types = (4+Super)*[wg.GRID_VALUE_LONG,]+4*[wg.GRID_VALUE_FLOAT+':10,4',]+ \
2*[wg.GRID_VALUE_FLOAT+':10,2',]+[wg.GRID_VALUE_FLOAT+':10,3',]+ \
[wg.GRID_VALUE_FLOAT+':10,3',]
if HKLF:
colLabels = ['H','K','L','flag','d','Fosq','sig','Fcsq','FoTsq','FcTsq','phase','ExtC',]
if 'T' in Inst['Type'][0]:
colLabels = ['H','K','L','flag','d','Fosq','sig','Fcsq','FoTsq','FcTsq','phase','ExtC','wave','tbar']
Types += 2*[wg.GRID_VALUE_FLOAT+':10,3',]
elif 'E' in Inst['Type'][0]:
colLabels = ['H','K','L','flag','d','Fosq','sig','Fcsq','FoTsq','FcTsq','phase','ExtC']
if refs.shape[1] > 12:
colLabels += ['Nexp','Zpos']
Types += [wg.GRID_VALUE_LONG,wg.GRID_VALUE_FLOAT+':10,3',]
if Super:
colLabels.insert(3,'M')
else:
if 'C' in Inst['Type'][0]:
colLabels = ['H','K','L','mul','d','pos','sig\u00b2','gam','Fo\u00b2','Fc\u00b2','phase','Icorr','Prfo','Trans','ExtP','I100','\u03bcstrain','Size']
Types += 6*[wg.GRID_VALUE_FLOAT+':10,3',]
elif 'T' in Inst['Type'][0]:
colLabels = ['H','K','L','mul','d','pos','sig\u00b2','gam','Fo\u00b2','Fc\u00b2','phase','Icorr','alp','bet','wave','Prfo','Abs','Ext','I100','\u03bcstrain','Size']
Types += 9*[wg.GRID_VALUE_FLOAT+':10,3',]
elif Inst['Type'][0][2] in ['A','B']:
colLabels = ['H','K','L','mul','d','pos','sig\u00b2','gam','Fo\u00b2','Fc\u00b2','phase','Icorr','alp','bet','Prfo','Abs','Ext','I100','\u03bcstrain','Size']
Types += 8*[wg.GRID_VALUE_FLOAT+':10,3',]
elif 'E' in Inst['Type'][0]:
colLabels = ['H','K','L','mul','d','pos','sig\u00b2','gam','Fo\u00b2','Fc\u00b2','phase','Icorr','I100']
Types += [wg.GRID_VALUE_FLOAT+':10,3',]
if Super:
colLabels.insert(3,'M')
refs.T[3+Super] = np.where(refs.T[4+Super]<dMin,-refs.T[3+Super],refs.T[3+Super])
return G2G.Table(refs,rowLabels=rowLabels,colLabels=colLabels,types=Types)
def ShowReflTable(phaseName):
'''Posts a table of reflections for a phase, creating the table
if needed using MakeReflectionTable
'''
def setBackgroundColors(im,it):
for r in range(G2frame.refTable[phaseName].GetNumberRows()):
if HKLF:
if float(G2frame.refTable[phaseName].GetCellValue(r,3+im)) <= 0.:
G2frame.refTable[phaseName].SetCellBackgroundColour(r,3+im,wx.RED)
Fosq = float(G2frame.refTable[phaseName].GetCellValue(r,5+im))
Fcsq = float(G2frame.refTable[phaseName].GetCellValue(r,7+im))
sig = float(G2frame.refTable[phaseName].GetCellValue(r,6+im))
rat = 11.
if sig:
rat = abs(Fosq-Fcsq)/sig
if rat > 10.:
G2frame.refTable[phaseName].SetCellBackgroundColour(r,7+im,wx.RED)
elif rat > 3.0:
G2frame.refTable[phaseName].SetCellBackgroundColour(r,7+im,wx.Colour(255,255,0))
else: #PWDR
if float(G2frame.refTable[phaseName].GetCellValue(r,12+im+itof)) < 0.:
G2frame.refTable[phaseName].SetCellBackgroundColour(r,12+im+itof,wx.RED)
if float(G2frame.refTable[phaseName].GetCellValue(r,3+im)) < 0:
G2frame.refTable[phaseName].SetCellBackgroundColour(r,8+im,wx.RED)
if not HKLF and not len(data[phaseName]):
return #deleted phase?
G2frame.RefList = phaseName
if HKLF:
G2frame.GetStatusBar().SetStatusText('abs(DF)/sig > 10 red; > 3 yellow; flag:>0 twin no., 0 sp.gp absent, -1 user rejected, -2 Rfree',1)
else:
G2frame.GetStatusBar().SetStatusText('Prfo < 0. in red; if excluded Fosq in red & mul < 0',1)
itof = 0
if HKLF:
im = data[1].get('Super',0)
else:
if 'T' in data[phaseName].get('Type',''):
itof = 3
im = data[phaseName].get('Super',0)
# has this table already been displayed?
if G2frame.refTable[phaseName].GetTable() is None:
G2frame.PeakTable = MakeReflectionTable(phaseName)
if not G2frame.PeakTable: return
G2frame.refTable[phaseName].SetTable(G2frame.PeakTable, True)
G2frame.refTable[phaseName].EnableEditing(False)
G2frame.refTable[phaseName].SetMargins(0,0)
G2frame.refTable[phaseName].AutoSizeColumns(False)
setBackgroundColors(im,itof)
if HKLF:
if G2frame.Hide:
refList = np.array([refl[:6+im] for refl in data[1]['RefList'] if refl[3]])
else:
refList = np.array([refl[:6+im] for refl in data[1]['RefList']])
else:
refList = np.array([refl[:6+im] for refl in data[phaseName]['RefList']])
G2frame.HKL = np.vstack((refList.T)).T #build for plots
# raise the tab (needed for 1st use and from OnSelectPhase)
for PageNum in range(G2frame.refBook.GetPageCount()):
if phaseName == G2frame.refBook.GetPageText(PageNum):
G2frame.refBook.SetSelection(PageNum)
break
else:
print (phaseName)
print (phases)
raise Exception("how did we not find a phase name?")
def OnToggleExt(event):
G2frame.Hide = not G2frame.Hide
UpdateReflectionGrid(G2frame,data,HKLF=True,Name=Name)
def OnPageChanged(event):
'''Respond to a press on a phase tab by displaying the reflections. This
routine is needed because the reflection table may not have been created yet.
'''
G2frame.refBook.SetSize(G2frame.dataWindow.GetClientSize()) #TODO -almost right
page = event.GetSelection()
phaseName = G2frame.refBook.GetPageText(page)
ShowReflTable(phaseName)
def OnSelectPhase(event):
'''For PWDR, selects a phase with a selection box. Called from menu.
'''
if len(phases) < 2: return
dlg = wx.SingleChoiceDialog(G2frame,'Select','Phase',phases)
try:
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelection()
ShowReflTable(phases[sel])
finally:
dlg.Destroy()
# start of UpdateReflectionGrid
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.ReflMenu)
if not data:
print ('No phases, no reflections')
lbl = 'No phases, no reflections'
elif HKLF:
lbl = 'Single crystal reflections'
else:
lbl = 'Powder reflections, selected by phase'
G2frame.dataWindow.ClearData()
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,wx.ID_ANY,lbl),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
if not data:
return
if HKLF:
G2frame.RefList = 1
phaseName = IsHistogramInAnyPhase(G2frame,Name)
if not phaseName:
phaseName = 'Unknown'
phases = [phaseName]
else:
phaseName = G2frame.RefList
phases = list(data.keys())
Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[0]
if HKLF:
G2frame.Bind(wx.EVT_MENU, OnPlotHKL, id=G2G.wxID_PWDHKLPLOT)
G2frame.Bind(wx.EVT_MENU, OnPlot1DHKL, id=G2G.wxID_1DHKLSTICKPLOT)
G2frame.Bind(wx.EVT_MENU, OnPlot3DHKL, id=G2G.wxID_PWD3DHKLPLOT)
G2frame.Bind(wx.EVT_MENU, OnWilsonStat, id=G2G.wxID_WILSONSTAT)
G2frame.Bind(wx.EVT_MENU, OnToggleExt, id=G2G.wxID_SHOWHIDEEXTINCT)
G2frame.dataWindow.SelectPhase.Enable(False)
else:
G2frame.Bind(wx.EVT_MENU, OnSelectPhase, id=G2G.wxID_SELECTPHASE)
G2frame.Bind(wx.EVT_MENU, OnPlot1DHKL, id=G2G.wxID_1DHKLSTICKPLOT)
G2frame.Bind(wx.EVT_MENU, OnPlotHKL, id=G2G.wxID_PWDHKLPLOT)
G2frame.Bind(wx.EVT_MENU, OnPlot3DHKL, id=G2G.wxID_PWD3DHKLPLOT)
G2frame.Bind(wx.EVT_MENU, OnMakeCSV, id=G2G.wxID_CSVFROMTABLE)
G2frame.Bind(wx.EVT_MENU, OnWilsonStat, id=G2G.wxID_WILSONSTAT)
G2frame.dataWindow.SelectPhase.Enable(False)
G2frame.refBook = G2G.GSNoteBook(parent=G2frame.dataWindow)
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
mainSizer.Add(G2frame.refBook,1,wx.ALL|wx.EXPAND,1)
G2frame.refTable = {}
G2frame.dataWindow.currentGrids = []
for tabnum,phase in enumerate(phases):
if isinstance(data,list): #single crystal HKLF
G2frame.refTable[phase] = G2G.GSGrid(parent=G2frame.refBook)
G2frame.refTable[phase].SetRowLabelSize(60) # leave room for big numbers
G2frame.refBook.AddPage(G2frame.refTable[phase],phase)
G2frame.refTable[phase].SetScrollRate(10,10) # reflection grids (inside tab) need scroll bars
elif len(data[phase]): #else dict for PWDR
G2frame.refTable[phase] = G2G.GSGrid(parent=G2frame.refBook)
G2frame.refTable[phase].SetRowLabelSize(60)
G2frame.refBook.AddPage(G2frame.refTable[phase],phase)
G2frame.refTable[phase].SetScrollRate(10,10) # as above
else: #cleanup deleted phase reflection lists
del data[phase]
if len(data):
G2frame.RefList = list(data.keys())[0]
phaseName = G2frame.RefList
else:
G2frame.RefList = ''
phaseName = ''
if phaseName: ShowReflTable(phaseName)
G2frame.refBook.Bind(wx.aui.EVT_AUINOTEBOOK_PAGE_CHANGED, OnPageChanged)
G2frame.dataWindow.SetDataSize()
################################################################################
##### SASD/REFD Substances
################################################################################
[docs]
def UpdateSubstanceGrid(G2frame,data):
'''respond to selection of SASD/REFD Substance data tree item.
'''
import Substances as substFile
def LoadSubstance(name):
subst = substFile.Substances[name]
ElList = subst['Elements'].keys()
for El in ElList:
Info = G2elem.GetAtomInfo(El.strip().capitalize())
Info.update(subst['Elements'][El])
data['Substances'][name]['Elements'][El] = Info
if 'Volume' in subst:
data['Substances'][name]['Volume'] = subst['Volume']
data['Substances'][name]['Density'] = \
G2mth.Vol2Den(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])
elif 'Density' in subst:
data['Substances'][name]['Density'] = subst['Density']
data['Substances'][name]['Volume'] = \
G2mth.Den2Vol(data['Substances'][name]['Elements'],data['Substances'][name]['Density'])
else:
data['Substances'][name]['Volume'] = G2mth.El2EstVol(data['Substances'][name]['Elements'])
data['Substances'][name]['Density'] = \
G2mth.Vol2Den(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])
if 'X' in Inst['Type'][0]:
data['Substances'][name]['Scatt density'] = \
G2mth.XScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])[0]
recontrst,absorb,imcontrst = G2mth.XScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
elif 'NC' in Inst['Type'][0]:
isotopes = list(Info['Isotopes'].keys())
isotopes.sort()
data['Substances'][name]['Elements'][El]['Isotope'] = isotopes[-1]
data['Substances'][name]['Scatt density'] = \
G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])[0]
recontrst,absorb,imcontrst = G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
data['Substances'][name]['XAnom density'] = recontrst
data['Substances'][name]['XAbsorption'] = absorb
data['Substances'][name]['XImag density'] = imcontrst
def OnReloadSubstances(event):
for name in data['Substances'].keys():
if name not in ['vacuum','unit scatter']:
if 'X' in Inst['Type'][0]:
data['Substances'][name]['Scatt density'] = \
G2mth.XScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])[0]
recontrst,absorb,imcontrst = G2mth.XScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
elif 'NC' in Inst['Type'][0]:
data['Substances'][name]['Scatt density'] = \
G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])[0]
recontrst,absorb,imcontrst = G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
data['Substances'][name]['XAnom density'] = recontrst
data['Substances'][name]['XAbsorption'] = absorb
data['Substances'][name]['XImag density'] = imcontrst
UpdateSubstanceGrid(G2frame,data)
def OnLoadSubstance(event):
names = list(substFile.Substances.keys())
names.sort()
dlg = wx.SingleChoiceDialog(G2frame, 'Which substance?', 'Select substance', names, wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
name = names[dlg.GetSelection()]
else:
return
finally:
dlg.Destroy()
data['Substances'][name] = {'Elements':{},'Volume':1.0,'Density':1.0,
'Scatt density':0.0,'Real density':0.0,'XAbsorption':0.0,'XImag density':0.0}
LoadSubstance(name)
UpdateSubstanceGrid(G2frame,data)
def OnCopySubstance(event):
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
copyList = []
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy substances from\n'+hst[5:]+' to...',
'Copy substances', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
copyList.append(histList[i])
finally:
dlg.Destroy()
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Instrument Parameters'))[0]
wave = G2mth.getWave(Inst)
ndata = copy.deepcopy(data)
for name in ndata['Substances'].keys():
if name not in ['vacuum','unit scatter']:
if 'X' in Inst['Type'][0]:
recontrst,absorb,imcontrst = G2mth.XScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
elif 'NC' in Inst['Type'][0]:
recontrst,absorb,imcontrst = G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
ndata['Substances'][name]['XAnom density'] = recontrst
ndata['Substances'][name]['XAbsorption'] = absorb
ndata['Substances'][name]['XImag density'] = imcontrst
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Substances'),ndata)
def OnAddSubstance(event):
dlg = wx.TextEntryDialog(None,'Enter a name for this substance','Substance Name Entry','New substance',
style=wx.OK|wx.CANCEL)
if dlg.ShowModal() == wx.ID_OK:
Name = dlg.GetValue()
data['Substances'][Name] = {'Elements':{},'Volume':1.0,'Density':1.0,
'Scatt density':0.0,'XAnom density':0.,'XAbsorption':0.,'XImag density':0.}
AddElement(Name)
else:
return
dlg.Destroy()
if not data['Substances'][Name]['XAbsorption']:
del data['Substances'][Name]
UpdateSubstanceGrid(G2frame,data)
def OnDeleteSubstance(event):
TextList = []
for name in data['Substances']:
if name not in ['vacuum','unit scatter']:
TextList += [name,]
if not TextList:
return
dlg = wx.SingleChoiceDialog(G2frame, 'Which substance?', 'Select substance to delete', TextList, wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
name = TextList[dlg.GetSelection()]
else:
return
finally:
dlg.Destroy()
del(data['Substances'][name])
UpdateSubstanceGrid(G2frame,data)
def OnAddElement(event):
TextList = []
for name in data['Substances']:
if name not in ['vacuum','unit scatter']:
TextList += [name,]
if not TextList:
return
dlg = wx.SingleChoiceDialog(G2frame, 'Which substance?', 'Select substance', TextList, wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
name = TextList[dlg.GetSelection()]
AddElement(name)
else:
return
finally:
dlg.Destroy()
UpdateSubstanceGrid(G2frame,data)
def AddElement(name):
ElList = list(data['Substances'][name]['Elements'].keys())
dlg = G2elemGUI.PickElements(G2frame,ElList)
if dlg.ShowModal() == wx.ID_OK:
for El in dlg.Elem:
El = El.strip().capitalize()
Info = G2elem.GetAtomInfo(El)
Info.update({'Num':1.})
data['Substances'][name]['Elements'][El] = Info
isotopes = list(Info['Isotopes'].keys())
isotopes.sort()
data['Substances'][name]['Elements'][El]['Isotope'] = isotopes[-1]
data['Substances'][name]['Volume'] = G2mth.El2EstVol(data['Substances'][name]['Elements'])
data['Substances'][name]['Density'] = \
G2mth.Vol2Den(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])
if 'X' in Inst['Type'][0]:
data['Substances'][name]['Scatt density'] = \
G2mth.XScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])[0]
recontrst,absorb,imcontrst = G2mth.XScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
elif 'NC' in Inst['Type'][0]:
data['Substances'][name]['Scatt density'] = \
G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])[0]
recontrst,absorb,imcontrst = G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
data['Substances'][name]['XAnom density'] = recontrst
data['Substances'][name]['XAbsorption'] = absorb
data['Substances'][name]['XImag density'] = imcontrst
else:
return
dlg.Destroy()
def OnDeleteElement(event):
TextList = []
for name in data['Substances']:
if name not in ['vacuum','unit scatter']:
TextList += [name,]
if not TextList:
return
dlg = wx.SingleChoiceDialog(G2frame, 'Which substance?', 'Select substance', TextList, wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
name = TextList[dlg.GetSelection()]
else:
return
finally:
dlg.Destroy()
ElList = list(data['Substances'][name]['Elements'].keys())
if len(ElList):
DE = G2elemGUI.DeleteElement(G2frame,ElList)
if DE.ShowModal() == wx.ID_OK:
El = DE.GetDeleteElement().strip().upper()
del(data['Substances'][name]['Elements'][El])
data['Substances'][name]['Volume'] = G2mth.El2EstVol(data['Substances'][name]['Elements'])
data['Substances'][name]['Density'] = \
G2mth.Vol2Den(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])
if 'X' in Inst['Type'][0]:
data['Substances'][name]['Scatt density'] = \
G2mth.XScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])[0]
recontrst,absorb,imcontrst = G2mth.XScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
elif 'NC' in Inst['Type'][0]:
data['Substances'][name]['Scatt density'] = \
G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])[0]
recontrst,absorb,imcontrst = G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
data['Substances'][name]['XAnom density'] = recontrst
data['Substances'][name]['XAbsorption'] = absorb
data['Substances'][name]['XImag density'] = imcontrst
UpdateSubstanceGrid(G2frame,data)
def SubstSizer():
def OnNum(invalid,value,tc):
if invalid: return
name,El,keyId = Indx[tc.GetId()]
data['Substances'][name]['Volume'] = G2mth.El2EstVol(data['Substances'][name]['Elements'])
data['Substances'][name]['Density'] = \
G2mth.Vol2Den(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])
if 'X' in Inst['Type'][0]:
recontrst,absorb,imcontrst = G2mth.XScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
elif 'NC' in Inst['Type'][0]:
recontrst,absorb,imcontrst = G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
data['Substances'][name]['XAnom density'] = recontrst
data['Substances'][name]['XAbsorption'] = absorb
data['Substances'][name]['XImag density'] = imcontrst
wx.CallAfter(UpdateSubstanceGrid,G2frame,data)
def OnVolDen(invalid,value,tc):
if invalid: return
name,keyId = Indx[tc.GetId()]
if keyId in 'Volume':
data['Substances'][name]['Density'] = \
G2mth.Vol2Den(data['Substances'][name]['Elements'],value)
elif keyId in 'Density':
data['Substances'][name]['Volume'] = \
G2mth.Den2Vol(data['Substances'][name]['Elements'],value)
if 'X' in Inst['Type'][0]:
data['Substances'][name]['Scatt density'] = \
G2mth.XScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])[0]
recontrst,absorb,imcontrst = G2mth.XScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
elif 'NC' in Inst['Type'][0]:
data['Substances'][name]['Scatt density'] = \
G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'])[0]
recontrst,absorb,imcontrst = G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
data['Substances'][name]['XAnom density'] = recontrst
data['Substances'][name]['XAbsorption'] = absorb
data['Substances'][name]['XImag density'] = imcontrst
wx.CallAfter(UpdateSubstanceGrid,G2frame,data)
def OnIsotope(event):
Obj = event.GetEventObject()
El,name = Indx[Obj.GetId()]
data['Substances'][name]['Elements'][El]['Isotope'] = Obj.GetValue()
recontrst,absorb,imcontrst = G2mth.NCScattDen(data['Substances'][name]['Elements'],data['Substances'][name]['Volume'],wave)
data['Substances'][name]['XAnom density'] = recontrst
data['Substances'][name]['XAbsorption'] = absorb
data['Substances'][name]['XImag density'] = imcontrst
wx.CallAfter(UpdateSubstanceGrid,G2frame,data)
Indx = {}
substSizer = wx.BoxSizer(wx.VERTICAL)
substSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Substance list: wavelength: %.5fA'%(wave)))
for name in data['Substances']:
G2G.HorizontalLine(substSizer,G2frame.dataWindow)
substSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Data for '+name+':'),0)
if name == 'vacuum':
substSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Not applicable'),0)
elif name == 'unit scatter':
substSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Scattering density,f: %.3f *10%scm%s'%(data['Substances'][name]['Scatt density'],Pwr10,Pwrm2)),0)
else:
elSizer = wx.FlexGridSizer(0,8,5,5)
Substance = data['Substances'][name]
Elems = Substance['Elements']
for El in Elems: #do elements as pull downs for isotopes for neutrons
elSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' '+El+': '),
0,WACV)
num = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Substances'][name]['Elements'][El],'Num',
nDig=(10,2,'f'),typeHint=float,OnLeave=OnNum)
Indx[num.GetId()] = [name,El,'Num']
elSizer.Add(num,0,WACV)
if 'N' in Inst['Type'][0]:
elSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Isotope: '),0,WACV)
isotopes = list(Elems[El]['Isotopes'].keys())
isotope = wx.ComboBox(G2frame.dataWindow,choices=isotopes,value=Elems[El].get('Isotope','Nat. Abund.'),
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[isotope.GetId()] = [El,name]
isotope.Bind(wx.EVT_COMBOBOX,OnIsotope)
elSizer.Add(isotope,0,WACV)
substSizer.Add(elSizer,0)
vdsSizer = wx.FlexGridSizer(0,4,5,5)
vdsSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Volume: '),
0,WACV)
vol = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Substances'][name],'Volume',nDig=(10,2),typeHint=float,OnLeave=OnVolDen)
Indx[vol.GetId()] = [name,'Volume']
vdsSizer.Add(vol,0,WACV)
vdsSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' Density: '),
0,WACV)
den = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Substances'][name],'Density',nDig=(10,2),typeHint=float,OnLeave=OnVolDen)
Indx[den.GetId()] = [name,'Density']
vdsSizer.Add(den,0,WACV)
substSizer.Add(vdsSizer,0)
denSizer = wx.FlexGridSizer(0,2,0,0)
denSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Scattering density,f'),0,WACV)
denSizer.Add(wx.StaticText(G2frame.dataWindow,label=': %.3f *10%scm%s'%(Substance['Scatt density'],Pwr10,Pwrm2)),0,WACV)
denSizer.Add(wx.StaticText(G2frame.dataWindow,label=" Real density,f+f'"),0,WACV)
denSizer.Add(wx.StaticText(G2frame.dataWindow,label=': %.3f *10%scm%s'%(Substance['XAnom density'],Pwr10,Pwrm2)),0,WACV)
denSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Imaginary density,f"'),0,WACV)
denSizer.Add(wx.StaticText(G2frame.dataWindow,label=': %.3g *10%scm%s'%(Substance['XImag density'],Pwr10,Pwrm2)),0,WACV)
denSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Absorption'),0,WACV)
denSizer.Add(wx.StaticText(G2frame.dataWindow,label=': %.3g cm%s'%(Substance['XAbsorption'],Pwrm1)),0,WACV)
substSizer.Add(denSizer)
return substSizer
# start of UpdateSubstanceGrid
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.SubstanceMenu)
Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[0]
Name = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[2]
wave = G2mth.getWave(Inst)
G2frame.Bind(wx.EVT_MENU, OnLoadSubstance, id=G2G.wxID_LOADSUBSTANCE)
G2frame.Bind(wx.EVT_MENU, OnReloadSubstances, id=G2G.wxID_RELOADSUBSTANCES)
G2frame.Bind(wx.EVT_MENU, OnAddSubstance, id=G2G.wxID_ADDSUBSTANCE)
G2frame.Bind(wx.EVT_MENU, OnCopySubstance, id=G2G.wxID_COPYSUBSTANCE)
G2frame.Bind(wx.EVT_MENU, OnDeleteSubstance, id=G2G.wxID_DELETESUBSTANCE)
G2frame.Bind(wx.EVT_MENU, OnAddElement, id=G2G.wxID_ELEMENTADD)
G2frame.Bind(wx.EVT_MENU, OnDeleteElement, id=G2G.wxID_ELEMENTDELETE)
G2frame.dataWindow.ClearData()
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,label='Sample substances for %s:'%Name),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
#print('Substance ',G2frame.dataWindow.helpKey)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
mainSizer.Add(SubstSizer(),0)
G2frame.dataWindow.SetDataSize()
################################################################################
##### SASD Models
################################################################################
[docs]
def UpdateModelsGrid(G2frame,data):
'''respond to selection of SASD Models data tree item.
'''
#patches
if 'Current' not in data:
data['Current'] = 'Size dist.'
if 'logBins' not in data['Size']:
data['Size']['logBins'] = True
if 'MinMaxDiam' in data['Size']:
data['Size']['MinDiam'] = 50.
data['Size']['MaxDiam'] = 10000.
del data['Size']['MinMaxDiam']
if isinstance(data['Size']['MaxEnt']['Sky'],float):
data['Size']['MaxEnt']['Sky'] = -3
if 'Power' not in data['Size']['IPG']:
data['Size']['IPG']['Power'] = -1
if 'Matrix' not in data['Particle']:
data['Particle']['Matrix'] = {'Name':'vacuum','VolFrac':[0.0,False]}
if 'BackFile' not in data:
data['BackFile'] = ''
if 'Pair' not in data:
data['Pair'] = {'Method':'Moore','MaxRadius':100.,'NBins':100,'Errors':'User','Result':[],
'Percent error':2.5,'Background':[0,False],'Distribution':[],'Moore':10,'Dist G':100.,}
if 'Shapes' not in data:
data['Shapes'] = {'outName':'run','NumAA':100,'Niter':1,'AAscale':1.0,'Symm':1,'bias-z':0.0,
'inflateV':1.0,'AAglue':0.0,'pdbOut':False,'boxStep':4.0}
if 'boxStep' not in data['Shapes']:
data['Shapes']['boxStep'] = 4.0
plotDefaults = {'oldxy':[0.,0.],'Quaternion':[0.,0.,0.,1.],'cameraPos':150.,'viewDir':[0,0,1],}
#end patches
def RefreshPlots(newPlot=False):
PlotText = G2frame.G2plotNB.nb.GetPageText(G2frame.G2plotNB.nb.GetSelection())
if 'Powder' in PlotText:
G2pwpl.PlotPatterns(G2frame,plotType='SASD',newPlot=newPlot)
elif 'Size' in PlotText:
G2plt.PlotSASDSizeDist(G2frame)
elif 'Pair' in PlotText:
G2plt.PlotSASDPairDist(G2frame)
def OnAddModel(event):
if data['Current'] == 'Particle fit':
material = 'vacuum'
if len(data['Particle']['Levels']):
material = data['Particle']['Levels'][-1]['Controls']['Material']
data['Particle']['Levels'].append({
'Controls':{'FormFact':'Sphere','DistType':'LogNormal','Material':material,
'FFargs':{},'SFargs':{},'NumPoints':50,'Cutoff':0.01,'Contrast':0.0,
'SlitSmear':[0.0,False],'StrFact':'Dilute'}, #last 2 not used - future?
'LogNormal':{'Volume':[0.05,False],'Mean':[1000.,False],'StdDev':[0.5,False],'MinSize':[10.,False],},
'Gaussian':{'Volume':[0.05,False],'Mean':[1000.,False],'StdDev':[300.,False],},
'LSW':{'Volume':[0.05,False],'Mean':[1000.0,False],},
'Schulz-Zimm':{'Volume':[0.05,False],'Mean':[1000.,False],'StdDev':[300.,False],},
'Unified':{'G':[1.e3,False],'Rg':[100.,False],'B':[1.e-5,False],'P':[4.,False],'Cutoff':[1.e-5,False],},
'Porod':{'B':[1.e-4,False],'P':[4.,False],'Cutoff':[1.e-5,False],},
'Monodisperse':{'Volume':[0.05,False],'Radius':[100.,False],}, #OK for spheres
'Bragg':{'PkInt':[100.,False],'PkPos':[0.2,False],
'PkSig':[10.,False],'PkGam':[10.,False],}, #reasonable 31A peak
})
G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
RefreshPlots(True)
wx.CallAfter(UpdateModelsGrid,G2frame,data)
def OnCopyModel(event):
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
wtFactor = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[0]['wtFactor']
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
copyList = []
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy models from\n'+hst[5:]+' to...',
'Copy models', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
copyList.append(histList[i])
finally:
dlg.Destroy()
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
ProfDict = G2frame.GPXtree.GetItemPyData(Id)[0]
ProfDict['wtFactor'] = wtFactor
newdata = copy.deepcopy(data)
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Models'),newdata)
if newdata['BackFile']:
Profile = G2frame.GPXtree.GetItemPyData(Id)[1]
BackId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,newdata['BackFile'])
BackSample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,BackId, 'Sample Parameters'))
Profile[5] = BackSample['Scale'][0]*G2frame.GPXtree.GetItemPyData(BackId)[1][1]
UpdateModelsGrid(G2frame,newdata)
wx.CallAfter(UpdateModelsGrid,G2frame,data)
RefreshPlots(True)
def OnCopyFlags(event):
thisModel = copy.deepcopy(data)
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy sample ref. flags from\n'+str(hst[5:])+' to...',
'Copy sample flags', histList)
distChoice = ['LogNormal','Gaussian','LSW','Schulz-Zimm','Bragg','Unified',
'Porod','Monodisperse',]
parmOrder = ['Volume','Radius','Mean','StdDev','G','Rg','B','P',
'Cutoff','PkInt','PkPos','PkSig','PkGam','VolFr','Dist',]
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelections()
for i in result:
item = histList[i]
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
newModel = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Models'))
newModel['Back'][1] = copy.copy(thisModel['Back'][1])
for ilev,level in enumerate(newModel['Particle']['Levels']):
for form in level:
if form in distChoice:
thisForm = thisModel['Particle']['Levels'][ilev][form]
for item in parmOrder:
if item in thisForm:
level[form][item][1] = copy.copy(thisForm[item][1])
elif form == 'Controls':
thisForm = thisModel['Particle']['Levels'][ilev][form]['SFargs']
for item in parmOrder:
if item in thisForm:
level[form]['SFargs'][item][1] = copy.copy(thisForm[item][1])
finally:
dlg.Destroy()
def OnFitModelAll(event):
choices = G2gd.GetGPXtreeDataNames(G2frame,['SASD',])
od = {'label_1':'Copy to next','value_1':False,'label_2':'Reverse order','value_2':False}
dlg = G2G.G2MultiChoiceDialog(G2frame, 'Sequential SASD refinement',
'Select dataset to include',choices,extraOpts=od)
names = []
if dlg.ShowModal() == wx.ID_OK:
for sel in dlg.GetSelections():
names.append(choices[sel])
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Sequential SASD results')
if Id:
SeqResult = G2frame.GPXtree.GetItemPyData(Id)
else:
SeqResult = {}
Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Sequential SASD results')
SeqResult = {'SeqPseudoVars':{},'SeqParFitEqList':[]}
SeqResult['histNames'] = names
else:
dlg.Destroy()
return
dlg.Destroy()
dlg = wx.ProgressDialog('SASD Sequential fit','Data set name = '+names[0],len(names),
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME|wx.PD_CAN_ABORT)
wx.BeginBusyCursor()
if od['value_2']:
names.reverse()
JModel = None
try:
for i,name in enumerate(names):
print (' Sequential fit for '+name)
GoOn = dlg.Update(i,newmsg='Data set name = '+name)[0]
if not GoOn:
break
sId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name)
if i and od['value_1']:
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,sId, 'Models'),JModel)
IProfDict,IProfile = G2frame.GPXtree.GetItemPyData(sId)[:2]
IModel = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,sId, 'Models'))
ISample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,sId, 'Sample Parameters'))
ILimits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,sId, 'Limits'))
IfOK,result,varyList,sig,Rvals,covMatrix,parmDict,Msg = G2sasd.ModelFit(IProfile,IProfDict,ILimits,ISample,IModel)
JModel = copy.deepcopy(IModel)
if not IfOK:
G2frame.ErrorDialog('Failed sequential refinement for data '+name,
' Msg: '+Msg+'\nYou need to rethink your selection of parameters\n'+ \
' Model restored to previous version for'+name)
SeqResult['histNames'] = names[:i]
dlg.Destroy()
break
else:
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,sId, 'Models'),copy.deepcopy(IModel))
G2sasd.ModelFxn(IProfile,IProfDict,ILimits,ISample,IModel)
saveDict = {}
for item in parmDict:
if ';' in item:
trm = item.split(';')[1]
if trm in ['FFVolume','StrFact','FormFact']:
continue
saveDict.update({item:parmDict[item]})
SeqResult[name] = {'variables':result[0],'varyList':varyList,'sig':sig,'Rvals':Rvals,
'covMatrix':covMatrix,'title':name,'parmDict':saveDict}
else:
dlg.Destroy()
print (' ***** Small angle sequential refinement successful *****')
finally:
wx.EndBusyCursor()
G2frame.GPXtree.SetItemPyData(Id,SeqResult)
G2frame.GPXtree.SelectItem(Id)
def OnFitModel(event):
if data['Current'] == 'Size dist.':
if not any(Sample['Contrast']):
G2frame.ErrorDialog('No contrast; your sample is a vacuum!',
'You need to define a scattering substance!\n'+ \
' Do Substances and then Sample parameters')
return
G2sasd.SizeDistribution(Profile,ProfDict,Limits,Sample,data)
G2plt.PlotSASDSizeDist(G2frame)
RefreshPlots(True)
elif data['Current'] == 'Particle fit':
SaveState()
Results = G2sasd.ModelFit(Profile,ProfDict,Limits,Sample,data)
if not Results[0]:
G2frame.ErrorDialog('Failed refinement',
' Msg: '+Results[-1]+'\nYou need to rethink your selection of parameters\n'+ \
' Model restored to previous version')
G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
RefreshPlots(True)
wx.CallAfter(UpdateModelsGrid,G2frame,data)
elif data['Current'] == 'Pair distance':
SaveState()
G2sasd.PairDistFxn(Profile,ProfDict,Limits,Sample,data)
RefreshPlots(True)
G2plt.PlotSASDPairDist(G2frame)
wx.CallAfter(UpdateModelsGrid,G2frame,data)
elif data['Current'] == 'Shapes':
SaveState()
wx.MessageBox(' For use of SHAPES, please cite:\n\n'+
G2G.GetCite('SHAPES'),
caption='Program Shapes',style=wx.ICON_INFORMATION)
dlg = wx.ProgressDialog('Running SHAPES','Cycle no.: 0 of 160',161,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME)
data['Pair']['Result'] = [] #clear old results (if any) for now
data['Pair']['Result'] = G2shapes.G2shapes(Profile,ProfDict,Limits,data,dlg)
wx.CallAfter(UpdateModelsGrid,G2frame,data)
def OnUnDo(event):
DoUnDo()
data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,
G2frame.PatternId,'Models'))
G2frame.dataWindow.SasdUndo.Enable(False)
UpdateModelsGrid(G2frame,data)
G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
RefreshPlots(True)
def DoUnDo():
print ('Undo last refinement')
file = open(G2frame.undosasd,'rb')
PatternId = G2frame.PatternId
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Models'),pickle.load(file))
print (' Models recovered')
file.close()
def SaveState():
G2frame.undosasd = os.path.join(G2frame.dirname,'GSASIIsasd.save')
file = open(G2frame.undosasd,'wb')
PatternId = G2frame.PatternId
for item in ['Models']:
pickle.dump(G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId,item)),file,1)
file.close()
G2frame.dataWindow.SasdUndo.Enable(True)
def OnSelectFit(event):
data['Current'] = fitSel.GetValue()
wx.CallAfter(UpdateModelsGrid,G2frame,data)
def OnCheckBox(event):
Obj = event.GetEventObject()
item,ind = Indx[Obj.GetId()]
item[ind] = Obj.GetValue()
def OnIntVal(event):
event.Skip()
Obj = event.GetEventObject()
item,ind,minVal = Indx[Obj.GetId()]
try:
value = int(Obj.GetValue())
if value <= minVal:
raise ValueError
except ValueError:
value = item[ind]
Obj.SetValue(str(value))
item[ind] = value
def SizeSizer():
def OnShape(event):
data['Size']['Shape'][0] = partsh.GetValue()
wx.CallAfter(UpdateModelsGrid,G2frame,data)
def OnMethod(event):
data['Size']['Method'] = method.GetValue()
wx.CallAfter(UpdateModelsGrid,G2frame,data)
sizeSizer = wx.BoxSizer(wx.VERTICAL)
sizeSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Size distribution parameters: '),0)
binSizer = wx.FlexGridSizer(0,7,5,5)
binSizer.Add(wx.StaticText(G2frame.dataWindow,label=' No. size bins: '),0,WACV)
bins = ['50','100','150','200']
nbins = wx.ComboBox(G2frame.dataWindow,value=str(data['Size']['Nbins']),choices=bins,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[nbins.GetId()] = [data['Size'],'Nbins',0]
nbins.Bind(wx.EVT_COMBOBOX,OnIntVal)
binSizer.Add(nbins,0,WACV)
binSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Min diam.: '),0,WACV)
minDias = ['10','25','50','100','150','200']
mindiam = wx.ComboBox(G2frame.dataWindow,value=str(data['Size']['MinDiam']),choices=minDias,
style=wx.CB_DROPDOWN)
mindiam.Bind(wx.EVT_LEAVE_WINDOW,OnIntVal)
mindiam.Bind(wx.EVT_TEXT_ENTER,OnIntVal)
mindiam.Bind(wx.EVT_KILL_FOCUS,OnIntVal)
Indx[mindiam.GetId()] = [data['Size'],'MinDiam',0]
binSizer.Add(mindiam,0,WACV)
binSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Max diam.: '),0,WACV)
maxDias = [str(1000*(i+1)) for i in range(10)]
maxdiam = wx.ComboBox(G2frame.dataWindow,value=str(data['Size']['MaxDiam']),choices=maxDias,
style=wx.CB_DROPDOWN)
maxdiam.Bind(wx.EVT_LEAVE_WINDOW,OnIntVal)
maxdiam.Bind(wx.EVT_TEXT_ENTER,OnIntVal)
maxdiam.Bind(wx.EVT_KILL_FOCUS,OnIntVal)
Indx[maxdiam.GetId()] = [data['Size'],'MaxDiam',0]
binSizer.Add(maxdiam,0,WACV)
logbins = wx.CheckBox(G2frame.dataWindow,label='Log bins?')
Indx[logbins.GetId()] = [data['Size'],'logBins']
logbins.SetValue(data['Size']['logBins'])
logbins.Bind(wx.EVT_CHECKBOX, OnCheckBox)
binSizer.Add(logbins,0,WACV)
sizeSizer.Add(binSizer,0)
sizeSizer.Add((5,5),0)
partSizer = wx.BoxSizer(wx.HORIZONTAL)
partSizer.Add(wx.StaticText(G2frame.dataWindow,label='Particle description: '),0,WACV)
shapes = {'Spheroid':' Aspect ratio: ','Cylinder':' Diameter ','Cylinder AR':' Aspect ratio: ',
'Unified sphere':'','Unified rod':' Diameter: ','Unified rod AR':' Aspect ratio: ',
'Unified disk':' Thickness: ', 'Spherical shell': ' Shell thickness'}
partsh = wx.ComboBox(G2frame.dataWindow,value=str(data['Size']['Shape'][0]),choices=list(shapes.keys()),
style=wx.CB_READONLY|wx.CB_DROPDOWN)
partsh.Bind(wx.EVT_COMBOBOX,OnShape)
partSizer.Add(partsh,0,WACV)
if data['Size']['Shape'][0] not in ['Unified sphere',]:
partSizer.Add(wx.StaticText(G2frame.dataWindow,label=shapes[data['Size']['Shape'][0]]),0,WACV)
partprm = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Size']['Shape'],1,
nDig=(10,3),typeHint=float,xmin=0.)
partSizer.Add(partprm,0,WACV)
sizeSizer.Add(partSizer,0)
sizeSizer.Add((5,5),0)
fitSizer = wx.BoxSizer(wx.HORIZONTAL)
methods = ['MaxEnt','IPG',]
fitSizer.Add(wx.StaticText(G2frame.dataWindow,label='Fitting method: '),0,WACV)
method = wx.ComboBox(G2frame.dataWindow,value=data['Size']['Method'],choices=methods,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
method.Bind(wx.EVT_COMBOBOX,OnMethod)
fitSizer.Add(method,0,WACV)
iters = ['10','25','50','100','150','200']
fitSizer.Add(wx.StaticText(G2frame.dataWindow,label=' No. iterations: '),0,WACV)
Method = data['Size']['Method']
iter = wx.ComboBox(G2frame.dataWindow,value=str(data['Size'][Method]['Niter']),choices=iters,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[iter.GetId()] = [data['Size'][Method],'Niter',0]
iter.Bind(wx.EVT_COMBOBOX,OnIntVal)
fitSizer.Add(iter,0,WACV)
if 'MaxEnt' in data['Size']['Method']:
fitSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Log floor factor: '),0,WACV)
floors = [str(-i) for i in range(9)]
floor = wx.ComboBox(G2frame.dataWindow,value=str(data['Size']['MaxEnt']['Sky']),choices=floors,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[floor.GetId()] = [data['Size']['MaxEnt'],'Sky',-10]
floor.Bind(wx.EVT_COMBOBOX,OnIntVal)
fitSizer.Add(floor,0,WACV)
elif 'IPG' in data['Size']['Method']:
fitSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Q power weight (-1 for sigma): '),0,WACV)
choices = ['-1','0','1','2','3','4']
power = wx.ComboBox(G2frame.dataWindow,value=str(data['Size']['IPG']['Power']),choices=choices,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[power.GetId()] = [data['Size']['IPG'],'Power',-2]
power.Bind(wx.EVT_COMBOBOX,OnIntVal)
fitSizer.Add(power,0,WACV)
sizeSizer.Add(fitSizer,0)
return sizeSizer
def PairSizer():
def OnMethod(event):
data['Pair']['Method'] = method.GetValue()
wx.CallAfter(UpdateModelsGrid,G2frame,data)
def OnError(event):
data['Pair']['Errors'] = error.GetValue()
wx.CallAfter(UpdateModelsGrid,G2frame,data)
def OnMaxRadEst(event):
Results = G2sasd.RgFit(Profile,ProfDict,Limits,Sample,data)
if not Results[0]:
G2frame.ErrorDialog('Failed refinement',
' Msg: '+Results[-1]+'\nYou need to rethink your selection of parameters\n'+ \
' Model restored to previous version')
RefreshPlots(True)
wx.CallAfter(UpdateModelsGrid,G2frame,data)
def OnMooreTerms(event):
data['Pair']['Moore'] = int(round(Limits[1][1]*data['Pair']['MaxRadius']/np.pi))-1
wx.CallAfter(UpdateModelsGrid,G2frame,data)
def OnNewVal(invalid,value,tc):
if invalid: return
parmDict = {'Rg':data['Pair']['MaxRadius']/2.5,'G':data['Pair']['Dist G'],
'B':data['Pair'].get('Dist B',Profile[1][-1]*Profile[0][-1]**4),
'Back':data['Back'][0]}
Profile[2] = G2sasd.getSASDRg(Profile[0],parmDict)
RefreshPlots(True)
pairSizer = wx.BoxSizer(wx.VERTICAL)
pairSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Pair distribution parameters: '),0)
binSizer = wx.FlexGridSizer(0,6,5,5)
binSizer.Add(wx.StaticText(G2frame.dataWindow,label=' No. R bins: '),0,WACV)
bins = ['50','100','150','200']
nbins = wx.ComboBox(G2frame.dataWindow,value=str(data['Pair']['NBins']),choices=bins,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[nbins.GetId()] = [data['Pair'],'NBins',0]
nbins.Bind(wx.EVT_COMBOBOX,OnIntVal)
binSizer.Add(nbins,0,WACV)
binSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Max diam.: '),0,WACV)
maxdiam = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Pair'],'MaxRadius',xmin=10.,nDig=(10,1),OnLeave=OnNewVal)
binSizer.Add(maxdiam,0,WACV)
maxest = wx.Button(G2frame.dataWindow,label='Make estimate')
maxest.Bind(wx.EVT_BUTTON,OnMaxRadEst)
binSizer.Add(maxest,0,WACV)
pairSizer.Add(binSizer,0)
pairSizer.Add((5,5),0)
fitSizer = wx.BoxSizer(wx.HORIZONTAL)
methods = ['Moore',] #'Regularization',
fitSizer.Add(wx.StaticText(G2frame.dataWindow,label='Fitting method: '),0,WACV)
method = wx.ComboBox(G2frame.dataWindow,value=data['Pair']['Method'],choices=methods,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
method.Bind(wx.EVT_COMBOBOX,OnMethod)
fitSizer.Add(method,0,WACV)
if data['Pair']['Method'] == 'Moore':
fitSizer.Add(wx.StaticText(G2frame.dataWindow,label=" P.B. Moore, J. Appl. Cryst., 13, 168-175 (1980)"),0,WACV)
else:
fitSizer.Add(wx.StaticText(G2frame.dataWindow,label=" D.I. Svergun, J. Appl. Cryst., 24, 485-492 (1991)"),0,WACV)
pairSizer.Add(fitSizer,0)
if 'Moore' in data['Pair']['Method']:
mooreSizer = wx.BoxSizer(wx.HORIZONTAL)
mooreSizer.Add(wx.StaticText(G2frame.dataWindow,label='Number of functions: '),0,WACV)
moore = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Pair'],'Moore',xmin=2,xmax=20)
mooreSizer.Add(moore,0,WACV)
mooreterms = wx.Button(G2frame.dataWindow,label = 'Auto determine?')
mooreterms.Bind(wx.EVT_BUTTON,OnMooreTerms)
mooreSizer.Add(mooreterms,0,WACV)
pairSizer.Add(mooreSizer,0)
errorSizer = wx.BoxSizer(wx.HORIZONTAL)
errorSizer.Add(wx.StaticText(G2frame.dataWindow,label='Error method: '),0,WACV)
errors = ['User','Sqrt','Percent']
error = wx.ComboBox(G2frame.dataWindow,value=data['Pair']['Errors'],choices=errors,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
error.Bind(wx.EVT_COMBOBOX,OnError)
if 'Percent' in data['Pair']['Errors']:
percent = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Pair'],'Percent error',xmin=0.5,nDig=(10,1))
errorSizer.Add(percent,0,WACV)
errorSizer.Add(error,0,WACV)
pairSizer.Add(errorSizer,0)
return pairSizer
def ShapesSizer():
# def OnPDBout(event):
# data['Shapes']['pdbOut'] = not data['Shapes']['pdbOut']
def OnShapeSelect(event):
r,c = event.GetRow(),event.GetCol()
for i in [1,2]:
for j in range(len(Patterns)):
shapeTable.SetValue(j,i,False)
shapeTable.SetValue(r,c,True)
ShapesResult.ForceRefresh()
Limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Limits'))[1]
ProfDict,Profile = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[:2]
iBeg = np.searchsorted(Profile[0],Limits[0])
iFin = np.searchsorted(Profile[0],Limits[1])
pattern = Patterns[r]
Profile[3][iBeg:iFin+1] = np.array(pattern[2])
selAtoms = Atoms[2*r+(c-1)]
prCalc = PRcalc[r][2]
prDelt= np.diff(PRcalc[r][0])[0]
prsum = np.sum(prCalc)
prCalc /= prsum*prDelt
data['Pair']['Pair Calc'] = np.array([PRcalc[r][0],prCalc]).T
print('%s %d'%('num. beads',len(selAtoms[1])))
print('%s %.3f'%('selected r value',pattern[-1]))
print('%s %.3f'%('selected Delta P(r)',PRcalc[r][-1]))
PDBtext = 'P(R) dif: %.3f r-value: %.3f Nbeads: %d'%(PRcalc[r][-1],pattern[-1],len(selAtoms[1]))
# RefreshPlots(True)
G2pwpl.PlotPatterns(G2frame,plotType='SASD',newPlot=True)
G2plt.PlotSASDPairDist(G2frame)
G2plt.PlotBeadModel(G2frame,selAtoms,plotDefaults,PDBtext)
shapeSizer = wx.BoxSizer(wx.VERTICAL)
shapeSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Shape parameters:'),0)
parmSizer = wx.FlexGridSizer(0,4,5,5)
#1st row
parmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' No. amino acids: '),0,WACV)
numAA = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Shapes'],'NumAA',xmin=10)
parmSizer.Add(numAA,0,WACV)
parmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Nballs=no. amino acids*'),0,WACV)
scaleAA = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Shapes'],'AAscale',xmin=0.01,xmax=10.,nDig=(10,2))
parmSizer.Add(scaleAA,0,WACV)
#2nd row
parmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Inflate by (1.-1.4): '),0,WACV)
inflate = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Shapes'],'inflateV',xmin=1.,xmax=1.4,nDig=(10,2))
parmSizer.Add(inflate,0,WACV)
parmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Axial symmetry (1-12): '),0,WACV)
symm = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Shapes'],'Symm',xmin=1,xmax=12)
parmSizer.Add(symm,0,WACV)
#3rd row
parmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' z-axis bias (-2 to 2): '),0,WACV)
zaxis = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Shapes'],'bias-z',xmin=-2.,xmax=2.,nDig=(10,2))
parmSizer.Add(zaxis,0,WACV)
parmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' elongation (0-20): '),0,WACV)
glue = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Shapes'],'AAglue',xmin=0.,xmax=20.,nDig=(10,2))
parmSizer.Add(glue,0,WACV)
#4th row
parmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' No. iterations (1-10): '),0,WACV)
niter = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Shapes'],'Niter',xmin=1,xmax=10)
parmSizer.Add(niter,0,WACV)
parmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Output name: '),0,WACV)
name = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Shapes'],'outName')
parmSizer.Add(name,0,WACV)
#last row
parmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Bead separation (3.5-5): '),0,WACV)
beadsep = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Shapes'],'boxStep',xmin=3.5,xmax=5,nDig=(10,1))
parmSizer.Add(beadsep,0,WACV)
# pdb = wx.CheckBox(G2frame.dataWindow,label=' Save as pdb files?: ')
# pdb.SetValue(data['Shapes']['pdbOut'])
# pdb.Bind(wx.EVT_CHECKBOX, OnPDBout)
# parmSizer.Add(pdb,0,WACV)
shapeSizer.Add(parmSizer)
if len(data['Pair'].get('Result',[])):
shapeSizer.Add(wx.StaticText(G2frame.dataWindow,label=' SHAPES run results:'),0)
Atoms,Patterns,PRcalc = data['Pair']['Result']
colLabels = ['name','show beads','show shape','Rvalue','P(r) dif','Nbeads','Nshape']
Types = [wg.GRID_VALUE_STRING,]+2*[wg.GRID_VALUE_BOOL,]+2*[wg.GRID_VALUE_FLOAT+':10,3',]+2*[wg.GRID_VALUE_LONG,]
rowLabels = [str(i) for i in range(len(Patterns))]
tableVals = []
for i in range(len(Patterns)):
tableVals.append([Atoms[2*i][0],False,False,Patterns[i][-1],PRcalc[i][-1],len(Atoms[2*i][1]),len(Atoms[2*i+1][1])])
shapeTable = G2G.Table(tableVals,rowLabels=rowLabels,colLabels=colLabels,types=Types)
ShapesResult = G2G.GSGrid(G2frame.dataWindow)
ShapesResult.SetRowLabelSize(45)
ShapesResult.SetTable(shapeTable,True)
ShapesResult.AutoSizeColumns(False)
ShapesResult.Bind(wg.EVT_GRID_CELL_LEFT_CLICK, OnShapeSelect)
for r in range(len(Patterns)):
for c in range(7):
if c in [1,2]:
ShapesResult.SetReadOnly(r,c,isReadOnly=False)
else:
ShapesResult.SetReadOnly(r,c,isReadOnly=True)
shapeSizer.Add(ShapesResult,0)
return shapeSizer
def PartSizer():
FormFactors = {'Sphere':{},'Spheroid':{'Aspect ratio':[1.0,False]},
'Cylinder':{'Length':[100.,False]},'Cylinder diam':{'Diameter':[100.,False]},
'Cylinder AR':{'Aspect ratio':[1.0,False]},'Unified sphere':{},
'Unified rod':{'Length':[100.,False]},'Unified rod AR':{'Aspect ratio':[1.0,False]},
'Unified disk':{'Thickness':[100.,False]},
'Unified tube':{'Length':[100.,False],'Thickness':[10.,False]},
'Spherical shell':{'Shell thickness':[1.5,False] }, }
StructureFactors = {'Dilute':{},'Hard sphere':{'VolFr':[0.1,False],'Dist':[100.,False]},
'Sticky hard sphere':{'VolFr':[0.1,False],'Dist':[100.,False],'epis':[0.05,False],'Sticky':[0.2,False]},
'Square well':{'VolFr':[0.1,False],'Dist':[100.,False],'Depth':[0.1,False],'Width':[1.,False]},
'InterPrecipitate':{'VolFr':[0.1,False],'Dist':[100.,False]},}
ffDistChoices = ['Sphere','Spheroid','Cylinder','Cylinder diam',
'Cylinder AR','Unified sphere','Unified rod','Unified rod AR',
'Unified disk','Unified tube','Spherical shell',]
ffMonoChoices = ['Sphere','Spheroid','Cylinder','Cylinder AR',]
sfChoices = ['Dilute','Hard sphere','Sticky hard sphere','Square well','InterPrecipitate',]
slMult = 1000.
def OnValue(event):
event.Skip()
Obj = event.GetEventObject()
item,key,sldrObj = Indx[Obj.GetId()]
try:
value = float(Obj.GetValue())
if value <= 0.:
raise ValueError
except ValueError:
value = item[key][0]
item[key][0] = value
Obj.SetValue('%.3g'%(value))
if key in ['P','epis','Sticky','Depth','Width','VolFr','Dist']:
sldrObj.SetValue(slMult*value)
else:
logv = np.log10(value)
valMinMax = [logv-1,logv+1]
sldrObj.SetScaledRange(slMult*valMinMax[0],slMult*valMinMax[1])
sldrObj.SetValue(slMult*logv)
G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
RefreshPlots(True)
def OnSelect(event):
Obj = event.GetEventObject()
item,key = Indx[Obj.GetId()]
if key in ['NumPoints',]:
item[key] = int(Obj.GetValue())
else:
item[key] = Obj.GetValue()
if 'Refine' not in Obj.GetLabel():
if 'FormFact' in key :
item['FFargs'] = FormFactors[Obj.GetValue()]
elif 'StrFact' in key:
item['SFargs'] = StructureFactors[Obj.GetValue()]
wx.CallAfter(UpdateModelsGrid,G2frame,data)
G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
RefreshPlots(True)
def OnDelLevel(event):
Obj = event.GetEventObject()
item = Indx[Obj.GetId()]
del data['Particle']['Levels'][item]
wx.CallAfter(UpdateModelsGrid,G2frame,data)
G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
RefreshPlots(True)
def OnParmSlider(event):
Obj = event.GetEventObject()
item,key,pvObj = Indx[Obj.GetId()]
slide = Obj.GetValue()
if key in ['P','epis','Sticky','Depth','Width','VolFr','Dist']:
value = float(slide/slMult)
else:
value = 10.**float(slide/slMult)
item[key][0] = value
pvObj.SetValue('%.3g'%(item[key][0]))
G2sasd.ModelFxn(Profile,ProfDict,Limits,Sample,data)
RefreshPlots(True)
def SizeSizer():
sizeSizer = wx.FlexGridSizer(0,4,5,5)
sizeSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Distribution: '),0,WACV)
Distchoice = ['LogNormal','Gaussian','LSW','Schulz-Zimm','Bragg','Unified','Porod','Monodisperse',]
distChoice = wx.ComboBox(G2frame.dataWindow,value=level['Controls']['DistType'],choices=Distchoice,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[distChoice.GetId()] = [level['Controls'],'DistType']
distChoice.Bind(wx.EVT_COMBOBOX,OnSelect)
sizeSizer.Add(distChoice,0,WACV) #put structure factor choices here
if level['Controls']['DistType'] not in ['Bragg','Unified','Porod',]:
sizeSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Form Factor: '),0,WACV)
if 'Mono' in level['Controls']['DistType']:
ffChoice = wx.ComboBox(G2frame.dataWindow,value=level['Controls']['FormFact'],choices=ffMonoChoices,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
else:
ffChoice = wx.ComboBox(G2frame.dataWindow,value=level['Controls']['FormFact'],choices=ffDistChoices,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[ffChoice.GetId()] = [level['Controls'],'FormFact']
ffChoice.Bind(wx.EVT_COMBOBOX,OnSelect)
sizeSizer.Add(ffChoice,0,WACV)
sizeSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Material: '),0,WACV)
matSel = wx.ComboBox(G2frame.dataWindow,value=level['Controls']['Material'],
choices=list(Substances['Substances'].keys()),style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[matSel.GetId()] = [level['Controls'],'Material']
matSel.Bind(wx.EVT_COMBOBOX,OnSelect)
sizeSizer.Add(matSel,0,WACV) #do neutron test here?
rho = Substances['Substances'][level['Controls']['Material']].get('XAnom density',0.0)
level['Controls']['Contrast'] = contrast = (rho-rhoMat)**2
sizeSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Resonant X-ray contrast: '),0,WACV)
sizeSizer.Add(wx.StaticText(G2frame.dataWindow,label=' %.2f 10%scm%s'%(contrast,Pwr20,Pwrm4)),0,WACV)
if 'Mono' not in level['Controls']['DistType']:
sizeSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Num. radii: '),0,WACV)
radii = ['25','50','75','100','200']
nRadii = wx.ComboBox(G2frame.dataWindow,value=str(level['Controls']['NumPoints']),choices=radii,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[nRadii.GetId()] = [level['Controls'],'NumPoints']
nRadii.Bind(wx.EVT_COMBOBOX,OnSelect)
sizeSizer.Add(nRadii,0,WACV)
sizeSizer.Add(wx.StaticText(G2frame.dataWindow,label=' R dist. cutoff: '),0,WACV)
rCutoff = G2G.ValidatedTxtCtrl(G2frame.dataWindow,level['Controls'],'Cutoff',
xmin=0.001,xmax=0.1,typeHint=float)
sizeSizer.Add(rCutoff,0,WACV)
elif level['Controls']['DistType'] in ['Unified',]:
Parms = level['Unified']
Best = G2sasd.Bestimate(Parms['G'][0],Parms['Rg'][0],Parms['P'][0])
sizeSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Estimated Dist B: %12.4g'%(Best)),0,WACV)
return sizeSizer
def ParmSizer():
parmSizer = wx.FlexGridSizer(0,3,5,5)
parmSizer.AddGrowableCol(2,1)
parmSizer.SetFlexibleDirection(wx.HORIZONTAL)
Parms = level[level['Controls']['DistType']]
FFargs = level['Controls']['FFargs']
SFargs = level['Controls'].get('SFargs',{})
parmOrder = ['Volume','Radius','Mean','StdDev','MinSize','G','Rg','B','P','Cutoff',
'PkInt','PkPos','PkSig','PkGam',]
for parm in parmOrder:
if parm in Parms:
if parm == 'MinSize':
parmSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Dist '+parm,style=wx.ALIGN_CENTER))
else:
parmVar = wx.CheckBox(G2frame.dataWindow,label='Refine? Dist '+parm)
parmVar.SetValue(Parms[parm][1])
parmVar.Bind(wx.EVT_CHECKBOX, OnSelect)
parmSizer.Add(parmVar,0,WACV)
Indx[parmVar.GetId()] = [Parms[parm],1]
# azmthOff = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'azmthOff',nDig=(10,2),typeHint=float,OnLeave=OnAzmthOff)
parmValue = wx.TextCtrl(G2frame.dataWindow,value='%.3g'%(Parms[parm][0]),
style=wx.TE_PROCESS_ENTER)
parmValue.Bind(wx.EVT_TEXT_ENTER,OnValue)
parmValue.Bind(wx.EVT_KILL_FOCUS,OnValue)
parmSizer.Add(parmValue,0,WACV)
if parm == 'P':
value = Parms[parm][0]
valMinMax = [0.1,4.2]
else:
value = np.log10(Parms[parm][0])
valMinMax = [value-1,value+1]
parmSldr = G2G.G2Slider(G2frame.dataWindow,minValue=slMult*valMinMax[0],
maxValue=slMult*valMinMax[1],value=slMult*value)
Indx[parmValue.GetId()] = [Parms,parm,parmSldr]
Indx[parmSldr.GetId()] = [Parms,parm,parmValue]
parmSldr.Bind(wx.EVT_SLIDER,OnParmSlider)
parmSizer.Add(parmSldr,1,wx.EXPAND)
if level['Controls']['DistType'] not in ['Bragg']:
parmOrder = ['Aspect ratio','Length','Diameter','Thickness','VolFr','Dist','epis','Sticky','Depth','Width','Shell thickness',]
fTypes = ['FF ','SF ']
for iarg,Args in enumerate([FFargs,SFargs]):
for parm in parmOrder:
if parm in Args:
parmVar = wx.CheckBox(G2frame.dataWindow,label='Refine? '+fTypes[iarg]+parm)
parmVar.SetValue(Args[parm][1])
Indx[parmVar.GetId()] = [Args[parm],1]
parmVar.Bind(wx.EVT_CHECKBOX, OnSelect)
parmSizer.Add(parmVar,0,WACV)
# azmthOff = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'azmthOff',nDig=(10,2),typeHint=float,OnLeave=OnAzmthOff)
parmValue = wx.TextCtrl(G2frame.dataWindow,value='%.3g'%(Args[parm][0]),
style=wx.TE_PROCESS_ENTER)
parmValue.Bind(wx.EVT_TEXT_ENTER,OnValue)
parmValue.Bind(wx.EVT_KILL_FOCUS,OnValue)
parmSizer.Add(parmValue,0,WACV)
value = Args[parm][0]
if parm == 'epis':
valMinMax = [0,.1]
elif parm in ['Sticky','Width',]:
valMinMax = [0,1.]
elif parm == 'Depth':
valMinMax = [-2.,2.]
elif parm == 'Dist':
valMinMax = [100.,1000.]
elif parm == 'VolFr':
valMinMax = [1.e-4,1.]
else:
value = np.log10(Args[parm][0])
valMinMax = [value-1,value+1]
parmSldr = G2G.G2Slider(G2frame.dataWindow,minValue=slMult*valMinMax[0],
maxValue=slMult*valMinMax[1],value=slMult*value)
Indx[parmVar.GetId()] = [Args[parm],1]
Indx[parmValue.GetId()] = [Args,parm,parmSldr]
Indx[parmSldr.GetId()] = [Args,parm,parmValue]
parmSldr.Bind(wx.EVT_SLIDER,OnParmSlider)
parmSizer.Add(parmSldr,1,wx.EXPAND)
return parmSizer
Indx = {}
partSizer = wx.BoxSizer(wx.VERTICAL)
topSizer = wx.BoxSizer(wx.HORIZONTAL)
topSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Particle fit parameters: '),0,WACV)
topSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Matrix: '),0,WACV)
matsel = wx.ComboBox(G2frame.dataWindow,value=data['Particle']['Matrix']['Name'],
choices=list(Substances['Substances'].keys()),style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[matsel.GetId()] = [data['Particle']['Matrix'],'Name']
matsel.Bind(wx.EVT_COMBOBOX,OnSelect) #Do neutron test here?
rhoMat = Substances['Substances'][data['Particle']['Matrix']['Name']].get('XAnom density',0.0)
topSizer.Add(matsel,0,WACV)
topSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Volume fraction: '),0,WACV)
volfrac = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Particle']['Matrix']['VolFrac'],0,typeHint=float)
topSizer.Add(volfrac,0,WACV)
volVar = wx.CheckBox(G2frame.dataWindow,label=' Refine?')
volVar.SetValue(data['Particle']['Matrix']['VolFrac'][1])
Indx[volVar.GetId()] = [data['Particle']['Matrix']['VolFrac'],1]
volVar.Bind(wx.EVT_CHECKBOX, OnSelect)
topSizer.Add(volVar,0,WACV)
partSizer.Add(topSizer,0,)
for ilev,level in enumerate(data['Particle']['Levels']):
G2G.HorizontalLine(partSizer,G2frame.dataWindow)
topLevel = wx.BoxSizer(wx.HORIZONTAL)
topLevel.Add(wx.StaticText(G2frame.dataWindow,label=' Model component %d: '%(ilev)),0,WACV)
delBtn = wx.Button(G2frame.dataWindow,label=' Delete?')
Indx[delBtn.GetId()] = ilev
delBtn.Bind(wx.EVT_BUTTON,OnDelLevel)
topLevel.Add(delBtn,0,WACV)
partSizer.Add(topLevel,0)
partSizer.Add(SizeSizer())
if level['Controls']['DistType'] not in ['Bragg','Unified','Porod',]:
topLevel.Add(wx.StaticText(G2frame.dataWindow,label=' Structure factor: '),0,WACV)
strfctr = wx.ComboBox(G2frame.dataWindow,value=level['Controls']['StrFact'],
choices=sfChoices,style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[strfctr.GetId()] = [level['Controls'],'StrFact']
strfctr.Bind(wx.EVT_COMBOBOX,OnSelect)
topLevel.Add(strfctr,0,WACV)
partSizer.Add(ParmSizer(),0,wx.EXPAND)
return partSizer
def OnEsdScale(event):
event.Skip()
try:
value = float(esdScale.GetValue())
if value <= 0.:
raise ValueError
except ValueError:
value = 1./np.sqrt(ProfDict['wtFactor'])
ProfDict['wtFactor'] = 1./value**2
esdScale.SetValue('%.3f'%(value))
RefreshPlots(True)
def OnBackChange(invalid,value,tc):
Profile[4][:] = value
RefreshPlots()
def OnBackFile(event): #multiple backgrounds?
data['BackFile'] = backFile.GetValue()
if data['BackFile']:
BackId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,data['BackFile'])
BackSample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,BackId, 'Sample Parameters'))
Profile[5] = BackSample['Scale'][0]*G2frame.GPXtree.GetItemPyData(BackId)[1][1]
else:
Profile[5] = np.zeros(len(Profile[5]))
RefreshPlots(True)
# start of UpdateModelsGrid
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.ModelMenu)
Sample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Sample Parameters'))
Limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Limits'))
Substances = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Substances'))
ProfDict,Profile = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[:2]
if data['BackFile']:
BackId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,data['BackFile'])
BackSample = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,BackId, 'Sample Parameters'))
Profile[5] = BackSample['Scale'][0]*G2frame.GPXtree.GetItemPyData(BackId)[1][1]
G2frame.dataWindow.ClearData()
G2frame.Bind(wx.EVT_MENU, OnCopyModel, id=G2G.wxID_MODELCOPY)
G2frame.Bind(wx.EVT_MENU, OnCopyFlags, id=G2G.wxID_MODELCOPYFLAGS)
G2frame.Bind(wx.EVT_MENU, OnFitModel, id=G2G.wxID_MODELFIT)
G2frame.Bind(wx.EVT_MENU, OnFitModelAll, id=G2G.wxID_MODELFITALL)
G2frame.Bind(wx.EVT_MENU, OnUnDo, id=G2G.wxID_MODELUNDO)
G2frame.Bind(wx.EVT_MENU, OnAddModel, id=G2G.wxID_MODELADD)
Indx = {}
G2frame.dataWindow.ClearData()
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
topSizer = wx.BoxSizer(wx.HORIZONTAL)
models = ['Size dist.','Particle fit','Pair distance',]
if len(data['Pair']['Distribution']):
models += ['Shapes',]
topSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Modeling by: '),0,WACV)
fitSel = wx.ComboBox(G2frame.dataWindow,value=data['Current'],choices=models,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
fitSel.Bind(wx.EVT_COMBOBOX,OnSelectFit)
topSizer.Add(fitSel,0,WACV)
topSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Error multiplier: '),0,WACV)
# azmthOff = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'azmthOff',nDig=(10,2),typeHint=float,OnLeave=OnAzmthOff)
esdScale = wx.TextCtrl(G2frame.dataWindow,value='%.3f'%(1./np.sqrt(ProfDict['wtFactor'])),style=wx.TE_PROCESS_ENTER)
esdScale.Bind(wx.EVT_TEXT_ENTER,OnEsdScale)
esdScale.Bind(wx.EVT_KILL_FOCUS,OnEsdScale)
topSizer.Add(esdScale,0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(G2frame.dataWindow,helpIndex=G2frame.dataWindow.helpKey))
mainSizer.Add(topSizer,0,wx.EXPAND)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
if 'Size' in data['Current']:
G2frame.dataWindow.SasSeqFit.Enable(False)
if 'MaxEnt' in data['Size']['Method']:
G2frame.GetStatusBar().SetStatusText('Size distribution by Maximum entropy',1)
elif 'IPG' in data['Size']['Method']:
G2frame.GetStatusBar().SetStatusText('Size distribution by Interior-Point Gradient',1)
mainSizer.Add(SizeSizer())
elif 'Particle' in data['Current']:
G2frame.dataWindow.SasSeqFit.Enable(True)
mainSizer.Add(PartSizer(),1,wx.EXPAND)
elif 'Pair' in data['Current']:
G2frame.dataWindow.SasSeqFit.Enable(False)
mainSizer.Add(PairSizer(),1,wx.EXPAND)
elif 'Shape' in data['Current']:
G2frame.dataWindow.SasSeqFit.Enable(False)
mainSizer.Add(ShapesSizer(),1,wx.EXPAND)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
backSizer = wx.BoxSizer(wx.HORIZONTAL)
backSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Background:'),0,WACV)
backVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Back'],0,
nDig=(10,3,'g'),OnLeave=OnBackChange)
backSizer.Add(backVal,0,WACV)
if 'Shape' not in data['Current']:
backVar = wx.CheckBox(G2frame.dataWindow,label='Refine?')
Indx[backVar.GetId()] = [data['Back'],1]
backVar.SetValue(data['Back'][1])
backVar.Bind(wx.EVT_CHECKBOX, OnCheckBox)
backSizer.Add(backVar,0,WACV)
#multiple background files?
backSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Background file: '),0,WACV)
Choices = ['',]+G2gd.GetGPXtreeDataNames(G2frame,['SASD',])
backFile = wx.ComboBox(parent=G2frame.dataWindow,value=data['BackFile'],choices=Choices,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
backFile.Bind(wx.EVT_COMBOBOX,OnBackFile)
backSizer.Add(backFile)
mainSizer.Add(backSizer)
G2frame.dataWindow.SetDataSize()
################################################################################
##### REFD Models
################################################################################
[docs]
def UpdateREFDModelsGrid(G2frame,data):
'''respond to selection of REFD Models data tree item.
'''
def OnCopyModel(event):
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
copyList = []
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy reflectivity models from\n'+str(hst[5:])+' to...',
'Copy parameters', histList)
try:
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
copyList.append(histList[i])
finally:
dlg.Destroy()
for item in copyList:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
G2frame.GPXtree.SetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,Id,'Models'),copy.deepcopy(data))
def OnFitModel(event):
SaveState()
G2pwd.REFDRefine(Profile,ProfDict,Inst,Limits,Substances,data)
x,xr,y = G2pwd.makeSLDprofile(data,Substances)
ModelPlot(data,x,xr,y)
G2pwpl.PlotPatterns(G2frame,plotType='REFD')
wx.CallAfter(UpdateREFDModelsGrid,G2frame,data)
def OnModelPlot(event):
hst = G2frame.GPXtree.GetItemText(G2frame.PatternId)
histList = GetFileList(G2frame,'REFD')
# histList = [hst,]
# histList += GetHistsLikeSelected(G2frame)
if not histList:
G2frame.ErrorDialog('No match','No histograms match '+hst,G2frame)
return
plotList = []
od = {'label_1':'Zero at substrate','value_1':False,'label_2':'Show layer transitions','value_2':True}
dlg = G2G.G2MultiChoiceDialog(G2frame,'Plot reflectivity models for:',
'Plot SLD models', histList,extraOpts=od)
try:
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
plotList.append(histList[i])
else:
dlg.Destroy()
return
finally:
dlg.Destroy()
XY = []
LinePos = []
for item in plotList:
mId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
model = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,mId,'Models'))
if len(model['Layers']) == 2: #see if any real layers defined; will be > 2
continue
Substances = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,mId,'Substances'))['Substances']
x,xr,y = G2pwd.makeSLDprofile(model,Substances)
if od['value_1']:
XY.append([xr,y])
disLabel = r'$Distance\ from\ substrate,\ \AA$'
else:
XY.append([x,y])
disLabel = r'$Distance\ from\ top\ surface,\ \AA$'
if od['value_2']:
laySeq = model['Layer Seq'].split()
nLines = len(laySeq)+1
linePos = np.zeros(nLines)
for ilay,lay in enumerate(np.fromstring(data['Layer Seq'],dtype=int,sep=' ')):
linePos[ilay+1:] += model['Layers'][lay].get('Thick',[0.,False])[0]
if od['value_1']:
linePos = linePos[-1]-linePos
LinePos.append(linePos)
G2plt.PlotXY(G2frame,XY,labelX=disLabel,labelY=r'$SLD,\ 10^{10}cm^{-2}$',newPlot=True,
Title='Scattering length density',lines=True,names=[],vertLines=LinePos)
def OnFitModelAll(event):
choices = G2gd.GetGPXtreeDataNames(G2frame,['REFD',])
od = {'label_1':'Copy to next','value_1':False,'label_2':'Reverse order','value_2':False}
dlg = G2G.G2MultiChoiceDialog(G2frame, 'Sequential REFD refinement',
'Select dataset to include',choices,extraOpts=od)
names = []
if dlg.ShowModal() == wx.ID_OK:
for sel in dlg.GetSelections():
names.append(choices[sel])
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Sequential REFD results')
if Id:
SeqResult = G2frame.GPXtree.GetItemPyData(Id)
else:
SeqResult = {}
Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Sequential REFD results')
SeqResult = {'SeqPseudoVars':{},'SeqParFitEqList':[]}
SeqResult['histNames'] = names
else:
dlg.Destroy()
return
dlg.Destroy()
dlg = wx.ProgressDialog('REFD Sequential fit','Data set name = '+names[0],len(names),
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_REMAINING_TIME|wx.PD_CAN_ABORT)
wx.BeginBusyCursor()
if od['value_2']:
names.reverse()
JModel = None
try:
for i,name in enumerate(names):
print (' Sequential fit for '+name)
GoOn = dlg.Update(i,newmsg='Data set name = '+name)[0]
if not GoOn:
break
sId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name)
if i and od['value_1']:
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,sId, 'Models'),JModel)
IProfDict,IProfile = G2frame.GPXtree.GetItemPyData(sId)[:2]
IModel = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,sId, 'Models'))
ISubstances = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,sId, 'Substances'))['Substances']
ILimits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,sId, 'Limits'))
IfOK,result,varyList,sig,Rvals,covMatrix,parmDict,Msg = G2pwd.REFDRefine(IProfile,IProfDict,Inst,ILimits,ISubstances,IModel)
JModel = copy.deepcopy(IModel)
if not IfOK:
G2frame.ErrorDialog('Failed sequential refinement for data '+name,
' Msg: '+Msg+'\nYou need to rethink your selection of parameters\n'+ \
' Model restored to previous version for'+name)
SeqResult['histNames'] = names[:i]
dlg.Destroy()
break
else:
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,sId, 'Models'),copy.deepcopy(IModel))
SeqResult[name] = {'variables':result[0],'varyList':varyList,'sig':sig,'Rvals':Rvals,
'covMatrix':covMatrix,'title':name,'parmDict':parmDict}
else:
dlg.Destroy()
print (' ***** Small angle sequential refinement successful *****')
finally:
wx.EndBusyCursor()
G2frame.GPXtree.SetItemPyData(Id,SeqResult)
G2frame.GPXtree.SelectItem(Id)
def ModelPlot(data,x,xr,y):
laySeq = data['Layer Seq'].split()
nLines = len(laySeq)+1
linePos = np.zeros(nLines)
for ilay,lay in enumerate(np.fromstring(data['Layer Seq'],dtype=int,sep=' ')):
linePos[ilay+1:] += data['Layers'][lay].get('Thick',[0.,False])[0]
if data['Zero'] == 'Top':
XY = [[x,y],]
disLabel = r'$Distance\ from\ top\ surface,\ \AA$'
else:
XY = [[xr,y],]
linePos = linePos[-1]-linePos
disLabel = r'$Distance\ from\ substrate,\ \AA$'
G2plt.PlotXY(G2frame,XY,labelX=disLabel,labelY=r'$SLD,\ 10^{10}cm^{-2}$',newPlot=True,
Title='Scattering length density',lines=True,names=[],vertLines=[linePos,])
def OnUnDo(event):
DoUnDo()
data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,
G2frame.PatternId,'Models'))
G2frame.dataWindow.REFDUndo.Enable(False)
G2pwd.REFDModelFxn(Profile,Inst,Limits,Substances,data)
x,xr,y = G2pwd.makeSLDprofile(data,Substances)
ModelPlot(data,x,xr,y)
G2pwpl.PlotPatterns(G2frame,plotType='REFD')
wx.CallLater(100,UpdateREFDModelsGrid,G2frame,data)
def DoUnDo():
print ('Undo last refinement')
file = open(G2frame.undorefd,'rb')
PatternId = G2frame.PatternId
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'Models'),pickle.load(file))
print (' Model recovered')
file.close()
def SaveState():
G2frame.undorefd = os.path.join(G2frame.dirname,'GSASIIrefd.save')
file = open(G2frame.undorefd,'wb')
PatternId = G2frame.PatternId
pickle.dump(G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId,'Models')),file,1)
file.close()
G2frame.dataWindow.REFDUndo.Enable(True)
def ControlSizer():
def OnRefPos(event):
data['Zero'] = refpos.GetValue()
x,xr,y = G2pwd.makeSLDprofile(data,Substances)
ModelPlot(data,x,xr,y)
def OnMinSel(event):
data['Minimizer'] = minSel.GetValue()
def OnWeight(event):
data['2% weight'] = weight.GetValue()
def OnSLDplot(event):
x,xr,y = G2pwd.makeSLDprofile(data,Substances)
ModelPlot(data,x,xr,y)
# def OnQ4fftplot(event):
# q4fft.SetValue(False)
# R,F = G2pwd.makeRefdFFT(Limits,Profile)
# XY = [[R[:2500],F[:2500]],]
# G2plt.PlotXY(G2frame,XY,labelX='thickness',labelY='F(R)',newPlot=True,
# Title='Fourier transform',lines=True)
def OndQSel(event):
data['dQ type'] = dQSel.GetStringSelection()
Recalculate()
def NewRes(invalid,value,tc):
Recalculate()
def Recalculate():
G2pwd.REFDModelFxn(Profile,Inst,Limits,Substances,data)
x,xr,y = G2pwd.makeSLDprofile(data,Substances)
ModelPlot(data,x,xr,y)
G2pwpl.PlotPatterns(G2frame,plotType='REFD')
controlSizer = wx.BoxSizer(wx.VERTICAL)
resol = wx.BoxSizer(wx.HORIZONTAL)
choice = ['None','const '+GkDelta+'Q/Q',]
if ProfDict['ifDQ']:
choice += [GkDelta+'Q/Q in data']
dQSel = wx.RadioBox(G2frame.dataWindow,wx.ID_ANY,'Instrument resolution type:',choices=choice,
majorDimension=0,style=wx.RA_SPECIFY_COLS)
dQSel.SetStringSelection(data['dQ type'])
dQSel.Bind(wx.EVT_RADIOBOX,OndQSel)
resol.Add(dQSel,0,WACV)
resol.Add(wx.StaticText(G2frame.dataWindow,label=' (FWHM %): '),0,WACV)
resol.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Resolution'],0,nDig=(10,3),xmin=0.,xmax=5.,OnLeave=NewRes),0,WACV)
controlSizer.Add(resol,0)
minimiz = wx.BoxSizer(wx.HORIZONTAL)
minimiz.Add(wx.StaticText(G2frame.dataWindow,label=' Minimizer: '),0,WACV)
minlist = ['LMLS','Basin Hopping','MC/SA Anneal','L-BFGS-B',]
minSel = wx.ComboBox(G2frame.dataWindow,value=data['Minimizer'],choices=minlist,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
minSel.Bind(wx.EVT_COMBOBOX, OnMinSel)
minimiz.Add(minSel,0,WACV)
minimiz.Add(wx.StaticText(G2frame.dataWindow,label=' Bounds factor: '),0,WACV)
minimiz.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Toler',nDig=(10,2),xmax=0.99,xmin=0.1),0,WACV)
weight = wx.CheckBox(G2frame.dataWindow,label='Use 2% sig. weights')
weight.SetValue(data.get('2% weight',False))
weight.Bind(wx.EVT_CHECKBOX, OnWeight)
minimiz.Add(weight,0,WACV)
controlSizer.Add(minimiz,0)
plotSizer = wx.BoxSizer(wx.HORIZONTAL)
plotSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Plot controls: '),0,WACV)
sld = wx.Button(G2frame.dataWindow,label='Plot SLD?')
sld.Bind(wx.EVT_BUTTON, OnSLDplot)
plotSizer.Add(sld,0,WACV)
plotSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Zero position location: '),0,WACV)
poslist = ['Top','Bottom']
refpos = wx.ComboBox(G2frame.dataWindow,value=data['Zero'],choices=poslist,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
refpos.Bind(wx.EVT_COMBOBOX, OnRefPos)
plotSizer.Add(refpos,0,WACV)
# q4fft = wx.CheckBox(G2frame.dataWindow,label='Plot fft?')
# q4fft.Bind(wx.EVT_CHECKBOX, OnQ4fftplot)
# plotSizer.Add(q4fft,0,WACV)
controlSizer.Add(plotSizer,0)
return controlSizer
def OverallSizer():
#'DualFitFile':'', 'DualFltBack':[0.0,False],'DualScale':[1.0,False] future for neutrons - more than one?
def OnScaleRef(event):
data['Scale'][1] = scaleref.GetValue()
def OnBackRef(event):
data['FltBack'][1] = backref.GetValue()
def OnSliderMax(event):
data['slider max'] = float(slidermax.GetValue())
wx.CallAfter(UpdateREFDModelsGrid,G2frame,data)
def Recalculate(invalid,value,tc):
if invalid:
return
G2pwd.REFDModelFxn(Profile,Inst,Limits,Substances,data)
x,xr,y = G2pwd.makeSLDprofile(data,Substances)
ModelPlot(data,x,xr,y)
G2pwpl.PlotPatterns(G2frame,plotType='REFD')
overall = wx.BoxSizer(wx.HORIZONTAL)
overall.Add(wx.StaticText(G2frame.dataWindow,label=' Scale: '),0,WACV)
overall.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Scale'],0,
nDig=(10,2),typeHint=float,OnLeave=Recalculate),0,WACV)
scaleref = wx.CheckBox(G2frame.dataWindow,label=' Refine? ')
scaleref.SetValue(data['Scale'][1])
scaleref.Bind(wx.EVT_CHECKBOX, OnScaleRef)
overall.Add(scaleref,0,WACV)
overall.Add(wx.StaticText(G2frame.dataWindow,label=' Flat bkg.: '),0,WACV)
overall.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['FltBack'],0,
nDig=(10,2,'g'),typeHint=float,OnLeave=Recalculate),0,WACV)
backref = wx.CheckBox(G2frame.dataWindow,label=' Refine? ')
backref.SetValue(data['FltBack'][1])
backref.Bind(wx.EVT_CHECKBOX, OnBackRef)
overall.Add(backref,0,WACV)
overall.Add(wx.StaticText(G2frame.dataWindow,label=' Select slider range 0-'),0,WACV)
choice = ['1000','2000','5000','10000']
slidermax = wx.ComboBox(G2frame.dataWindow,value='%d'%data['slider max'],choices=choice,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
slidermax.Bind(wx.EVT_COMBOBOX,OnSliderMax)
overall.Add(slidermax,0,WACV)
return overall
def LayerSizer():
#'Penetration':[0.,False]?
def OnSelect(event):
Obj = event.GetEventObject()
item = Indx[Obj.GetId()]
Name = Obj.GetValue()
data['Layers'][item]['Name'] = Name
if 'Rough' not in data['Layers'][item]:
data['Layers'][item]['Rough'] = [0.,False]
if 'Thick' not in data['Layers'][item]:
data['Layers'][item]['Thick'] = [10.,False]
if 'N' in Inst['Type'][0]:
data['Layers'][item]['Mag SLD'] = [0.,False]
if Name == 'unit scatter':
data['Layers'][item]['iDenMul'] = [0.,False]
G2pwd.REFDModelFxn(Profile,Inst,Limits,Substances,data)
G2pwpl.PlotPatterns(G2frame,plotType='REFD')
wx.CallAfter(UpdateREFDModelsGrid,G2frame,data)
def OnCheckBox(event):
Obj = event.GetEventObject()
item,parm = Indx[Obj.GetId()]
data['Layers'][item][parm][1] = Obj.GetValue()
def OnInsertLayer(event):
Obj = event.GetEventObject()
ind = Indx[Obj.GetId()]
data['Layers'].insert(ind+1,{'Name':'vacuum','DenMul':[1.0,False],})
data['Layer Seq'] = ' '.join([str(i+1) for i in range(len(data['Layers'])-2)])
G2pwd.REFDModelFxn(Profile,Inst,Limits,Substances,data)
G2pwpl.PlotPatterns(G2frame,plotType='REFD')
wx.CallAfter(UpdateREFDModelsGrid,G2frame,data)
def OnDeleteLayer(event):
Obj = event.GetEventObject()
ind = Indx[Obj.GetId()]
del data['Layers'][ind]
data['Layer Seq'] = ' '.join([str(i+1) for i in range(len(data['Layers'])-2)])
G2pwd.REFDModelFxn(Profile,Inst,Limits,Substances,data)
G2pwpl.PlotPatterns(G2frame,plotType='REFD')
wx.CallAfter(UpdateREFDModelsGrid,G2frame,data)
def Recalculate(invalid,value,tc):
if invalid:
return
if tc and tc.GetId() in Indx: #sets slider
Indx[tc.GetId()].SetValue(value)
G2pwd.REFDModelFxn(Profile,Inst,Limits,Substances,data)
x,xr,y = G2pwd.makeSLDprofile(data,Substances)
ModelPlot(data,x,xr,y)
G2pwpl.PlotPatterns(G2frame,plotType='REFD')
def OnMoveParm(event):
Obj = event.GetEventObject()
ilay,parm,parmObj = Indx[Obj.GetId()]
move = Obj.GetValue() # +1 or -1
Obj.SetValue(0)
data['Layers'][ilay][parm][0] += move
parmObj.SetValue(data['Layers'][ilay][parm][0])
Recalculate(False,1.0,None)
def OnParmSlider(event):
Obj = event.GetEventObject()
ilay,parmObj = Indx[Obj.GetId()]
value = Obj.GetValue()
data['Layers'][ilay]['Thick'][0] = value
parmObj.SetValue(data['Layers'][ilay]['Thick'][0])
Recalculate(False,1.0,None)
Indx = {}
layerSizer = wx.BoxSizer(wx.VERTICAL)
for ilay,layer in enumerate(data['Layers']):
if not ilay:
layerSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Top layer (superphase):'),0)
elif ilay < len(data['Layers'])-1:
layerSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Layer no. %d'%(ilay)),0)
else:
layerSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Bottom layer (substrate):'),0)
midlayer = wx.BoxSizer(wx.HORIZONTAL)
midlayer.Add(wx.StaticText(G2frame.dataWindow,label=' Substance: '),0,WACV)
midName = data['Layers'][ilay]['Name']
midSel = wx.ComboBox(G2frame.dataWindow,value=midName,
choices=list(Substances.keys()),style=wx.CB_READONLY|wx.CB_DROPDOWN)
Indx[midSel.GetId()] = ilay
midSel.Bind(wx.EVT_COMBOBOX,OnSelect)
midlayer.Add(midSel,0,WACV)
if midName != 'vacuum':
if midName != 'unit scatter':
midlayer.Add(wx.StaticText(G2frame.dataWindow,label=' Den. Mult.: '),0,WACV)
midlayer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Layers'][ilay]['DenMul'],0,
nDig=(10,4),OnLeave=Recalculate),0,WACV)
varBox = wx.CheckBox(G2frame.dataWindow,label='Refine?')
Indx[varBox.GetId()] = [ilay,'DenMul']
varBox.SetValue(data['Layers'][ilay]['DenMul'][1])
varBox.Bind(wx.EVT_CHECKBOX, OnCheckBox)
midlayer.Add(varBox,0,WACV)
realScatt = data['Layers'][ilay]['DenMul'][0]*Substances[midName]['Scatt density']
midlayer.Add(wx.StaticText(G2frame.dataWindow,
label=' Real scat. den.: %.4g'%(realScatt)),0,WACV)
imagScatt = data['Layers'][ilay]['DenMul'][0]*Substances[midName]['XImag density']
midlayer.Add(wx.StaticText(G2frame.dataWindow,
label=' Imag scat. den.: %.4g'%(imagScatt)),0,WACV)
else:
realScatt = data['Layers'][ilay]['DenMul'][0]
midlayer.Add(wx.StaticText(G2frame.dataWindow,
label=' Real scat. den.: %.4g'%(realScatt)),0,WACV)
imagScatt = data['Layers'][ilay]['iDenMul'][0]
midlayer.Add(wx.StaticText(G2frame.dataWindow,
label=' Imag scat. den.: %.4g'%(imagScatt)),0,WACV)
else:
midlayer.Add(wx.StaticText(G2frame.dataWindow,label=', air or gas'),0,WACV)
layerSizer.Add(midlayer)
if midName == 'unit scatter':
nxtlayer = wx.BoxSizer(wx.HORIZONTAL)
nxtlayer.Add(wx.StaticText(G2frame.dataWindow,label=' Real Den. : '),0,WACV)
nxtlayer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Layers'][ilay]['DenMul'],0,
nDig=(10,4),OnLeave=Recalculate),0,WACV)
varBox = wx.CheckBox(G2frame.dataWindow,label='Refine?')
Indx[varBox.GetId()] = [ilay,'DenMul']
varBox.SetValue(data['Layers'][ilay]['DenMul'][1])
varBox.Bind(wx.EVT_CHECKBOX, OnCheckBox)
nxtlayer.Add(varBox,0,WACV)
nxtlayer.Add(wx.StaticText(G2frame.dataWindow,label=' Imag Den. : '),0,WACV)
nxtlayer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Layers'][ilay]['iDenMul'],0,
nDig=(10,4),OnLeave=Recalculate),0,WACV)
varBox = wx.CheckBox(G2frame.dataWindow,label='Refine?')
Indx[varBox.GetId()] = [ilay,'iDenMul']
varBox.SetValue(data['Layers'][ilay]['iDenMul'][1])
varBox.Bind(wx.EVT_CHECKBOX, OnCheckBox)
nxtlayer.Add(varBox,0,WACV)
layerSizer.Add(nxtlayer)
if midName != 'vacuum':
if 'N' in Inst['Type'][0] and midName not in ['vacuum','unit scatter']:
magLayer = wx.BoxSizer(wx.HORIZONTAL)
magLayer.Add(wx.StaticText(G2frame.dataWindow,label=' Magnetic SLD: '),0,WACV)
magLayer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Layers'][ilay]['Mag SLD'],0,
nDig=(10,4),OnLeave=Recalculate),0,WACV)
varBox = wx.CheckBox(G2frame.dataWindow,label='Refine?')
Indx[varBox.GetId()] = [ilay,'Mag SLD']
varBox.SetValue(data['Layers'][ilay]['Mag SLD'][1])
varBox.Bind(wx.EVT_CHECKBOX, OnCheckBox)
magLayer.Add(varBox,0,WACV)
magLayer.Add(wx.StaticText(G2frame.dataWindow,
label=' Real+mag scat. den.: %.4g'%(realScatt+data['Layers'][ilay]['Mag SLD'][0])),0,WACV)
layerSizer.Add(magLayer)
if ilay:
names = {'Rough':'Upper surface Roughness, '+Angstr,'Thick':'Layer Thickness, '+Angstr}
parmsline = wx.BoxSizer(wx.HORIZONTAL)
parms= ['Rough','Thick']
if ilay == len(data['Layers'])-1:
parms = ['Rough',]
if len(parms) > 1:
slide = wx.BoxSizer(wx.HORIZONTAL)
slide.Add(wx.StaticText(G2frame.dataWindow,label=' Layer thickness: '),0,WACV)
parmSldr = G2G.G2Slider(G2frame.dataWindow,minValue=0,maxValue=data['slider max'],value=data['Layers'][ilay]['Thick'][0])
parmSldr.Bind(wx.EVT_SLIDER,OnParmSlider)
slide.Add(parmSldr,1,wx.EXPAND)
for parm in parms:
parmsline.Add(wx.StaticText(G2frame.dataWindow,label=' %s: '%(names[parm])),0,WACV)
parmval = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['Layers'][ilay][parm],0,nDig=(10,2),OnLeave=Recalculate)
if parm =='Thick':
Indx[parmval.GetId()] = parmSldr
parmsline.Add(parmval,0,WACV)
parmSpin = wx.SpinButton(G2frame.dataWindow,style=wx.SP_VERTICAL,size=wx.Size(25,25))
Indx[parmSpin.GetId()] = [ilay,parm,parmval]
parmSpin.SetValue(0)
parmSpin.SetRange(-1,1)
parmSpin.Bind(wx.EVT_SPIN, OnMoveParm)
parmsline.Add(parmSpin,0,WACV)
varBox = wx.CheckBox(G2frame.dataWindow,label='Refine?')
Indx[varBox.GetId()] = [ilay,parm]
varBox.SetValue(data['Layers'][ilay][parm][1])
varBox.Bind(wx.EVT_CHECKBOX, OnCheckBox)
parmsline.Add(varBox,0,WACV)
layerSizer.Add(parmsline)
if len(parms) > 1:
Indx[parmSldr.GetId()] = [ilay,parmval] #parmval is always for Thick
layerSizer.Add(slide,1,wx.EXPAND)
if ilay < len(data['Layers'])-1:
newlayer = wx.BoxSizer(wx.HORIZONTAL)
insert = wx.Button(G2frame.dataWindow,label='Insert')
Indx[insert.GetId()] = ilay
insert.Bind(wx.EVT_BUTTON,OnInsertLayer)
newlayer.Add(insert)
delet = wx.Button(G2frame.dataWindow,label='Delete')
Indx[delet.GetId()] = ilay
delet.Bind(wx.EVT_BUTTON,OnDeleteLayer)
newlayer.Add(delet)
layerSizer.Add(newlayer)
G2G.HorizontalLine(layerSizer,G2frame.dataWindow)
return layerSizer
def OnRepSeq(event):
event.Skip()
stack = repseq.GetValue()
nstar = stack.count('*')
if nstar:
try:
newstack = ''
Istar = 0
for star in range(nstar):
Istar = stack.index('*',Istar+1)
iB = stack[:Istar].rfind(' ')
if iB == -1:
mult = int(stack[:Istar])
else:
mult = int(stack[iB:Istar])
pattern = stack[Istar+2:stack.index(')',Istar)]+' '
newstack += mult*pattern
stack = newstack
except ValueError:
stack += ' Error in string'
wx.MessageBox(stack,'Error',style=wx.ICON_EXCLAMATION)
repseq.SetValue(data['Layer Seq'])
return
try:
Slist = np.array(stack.split(),dtype=int)
except ValueError:
stack += ' Error in string'
repseq.SetValue(data['Layer Seq'])
wx.MessageBox(stack,'Error',style=wx.ICON_EXCLAMATION)
return
if len(Slist) < 1:
stack += ' Error in sequence - too short!'
Stest = np.arange(1,Nlayers-1)
if not np.all(np.array([item in Stest for item in Slist])):
stack += ' Error: invalid layer selection'
elif not np.all(np.ediff1d(Slist)):
stack += ' Error: Improbable sequence or bad string'
if 'Error' in stack:
repseq.SetValue(data['Layer Seq'])
wx.MessageBox(stack,'Error',style=wx.ICON_EXCLAMATION)
return
else:
data['Layer Seq'] = stack
repseq.SetValue(stack)
G2pwd.REFDModelFxn(Profile,Inst,Limits,Substances,data)
x,xr,y = G2pwd.makeSLDprofile(data,Substances)
ModelPlot(data,x,xr,y)
G2pwpl.PlotPatterns(G2frame,plotType='REFD')
# start of UpdateREFDModelsGrid
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.REFDModelMenu)
Substances = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Substances'))['Substances']
ProfDict,Profile,Name = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)[:3]
#patch
if 'slider max' not in data:
data['slider max'] = 2000.
if 'ifDQ' not in ProfDict:
ProfDict['ifDQ'] = np.any(Profile[5])
data['dQ type'] = 'None'
Limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Limits'))
Inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Instrument Parameters'))[0]
G2frame.dataWindow.ClearData()
G2frame.Bind(wx.EVT_MENU, OnCopyModel, id=G2G.wxID_MODELCOPY)
G2frame.Bind(wx.EVT_MENU, OnModelPlot, id=G2G.wxID_MODELPLOT)
G2frame.Bind(wx.EVT_MENU, OnFitModel, id=G2G.wxID_MODELFIT)
G2frame.Bind(wx.EVT_MENU, OnFitModelAll, id=G2G.wxID_MODELFITALL)
G2frame.Bind(wx.EVT_MENU, OnUnDo, id=G2G.wxID_MODELUNDO)
G2frame.dataWindow.ClearData()
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,label=' Reflectometry fitting for: '+Name),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Controls:'))
mainSizer.Add(ControlSizer())
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Global parameters:'))
mainSizer.Add(OverallSizer())
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
Nlayers = len(data['Layers'])
if Nlayers > 2:
if 'Layer Seq' not in data:
data['Layer Seq'] = ' '.join([str(i+1) for i in range(Nlayers-2)])
lineSizer = wx.BoxSizer(wx.HORIZONTAL)
lineSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Layer sequence: '),0,WACV)
repseq = wx.TextCtrl(G2frame.dataWindow,value = data['Layer Seq'],style=wx.TE_PROCESS_ENTER,size=(500,25))
repseq.Bind(wx.EVT_TEXT_ENTER,OnRepSeq)
repseq.Bind(wx.EVT_KILL_FOCUS,OnRepSeq)
lineSizer.Add(repseq,0,WACV)
mainSizer.Add(lineSizer)
Str = ' Use sequence nos. from:'
for ilay,layer in enumerate(data['Layers'][1:-1]):
Str += ' %d: %s'%(ilay+1,layer['Name'])
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=Str))
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=' NB: Repeat sequence by e.g. 6*(1 2) '))
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Layers: scatt. densities are 10%scm%s = 10%s%s%s'%(Pwr10,Pwrm2,Pwrm6,Angstr,Pwrm2)))
mainSizer.Add(LayerSizer())
G2frame.dataWindow.SetDataSize()
################################################################################
##### PDF controls
################################################################################
[docs]
def computePDF(G2frame,data):
'''Calls :func:`GSASIIpwd.CalcPDF` to compute the PDF and put into the data tree array.
Called from OnComputePDF and OnComputeAllPDF and OnComputeAllPDF in
GSASIIimgGUI.py
'''
xydata = {}
problem = False
for key in ['Sample','Sample Bkg.','Container','Container Bkg.']:
name = data[key]['Name']
if name.strip():
pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name)
if not pId:
print(key,'Entry',name,'Not found.')
problem = True
continue
xydata[key] = G2frame.GPXtree.GetItemPyData(pId)
if problem:
print('PDF computation aborted')
return
powId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,data['Sample']['Name'])
limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,powId,'Limits'))
Xlimits = [limits[1][0],limits[0][1]] #use lower limit but ignore upper limit
inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,powId,'Instrument Parameters'))[0]
auxPlot = G2pwd.CalcPDF(data,inst,Xlimits,xydata)
try:
data['I(Q)'] = xydata['IofQ']
data['S(Q)'] = xydata['SofQ']
data['F(Q)'] = xydata['FofQ']
data['G(R)'] = xydata['GofR']
data['g(r)'] = xydata['gofr']
return auxPlot
except: # PDF Calc aborted
pass
[docs]
def OptimizePDF(G2frame,data,showFit=True,maxCycles=5):
'''Optimize the PDF to minimize the difference between G(r) and the expected value for
low r (-4 pi r #density).
'''
xydata = {}
for key in ['Sample','Sample Bkg.','Container','Container Bkg.']:
name = data[key]['Name']
if name:
xydata[key] = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name))
powName = data['Sample']['Name']
powId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,powName)
limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,powId,'Limits'))
Xlimits = [limits[1][0],limits[0][1]] #use lower limit but ignore upper limit
inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,powId,'Instrument Parameters'))[0]
res = G2pwd.OptimizePDF(data,xydata,Xlimits,inst,showFit,maxCycles)
return res['success']
[docs]
def UpdatePDFGrid(G2frame,data):
'''respond to selection of PWDR PDF data tree item.
'''
def PDFFileSizer():
def FillFileSizer(fileSizer,key):
#fileSizer is a FlexGridSizer(3,4)
def OnSelectFile(event):
Obj = event.GetEventObject()
fileKey,itemKey,fmt = itemDict[Obj.GetId()]
if itemKey == 'Name':
value = Obj.GetValue()
Obj.SetValue(fmt%(value))
data[fileKey][itemKey] = value
data[fileKey]['Mult'] = GetExposure(value)
mult.SetValue(data[fileKey]['Mult'])
ResetFlatBkg()
wx.CallAfter(OnComputePDF,None)
def OnMoveMult(event):
data[key]['Mult'] += multSpin.GetValue()*0.01
mult.SetValue(data[key]['Mult'])
multSpin.SetValue(0)
wx.CallAfter(OnComputePDF,None)
def OnMult(invalid,value,tc):
if invalid: return
ResetFlatBkg()
wx.CallAfter(OnComputePDF,None)
def OnRefMult(event):
item['Refine'] = refMult.GetValue()
if item['Refine']:
G2frame.GetStatusBar().SetStatusText('Be sure Mult is close to anticipated value. '+ \
'Suggest setting Flat Bkg. to 0 before Optimize Mult',1)
def GetExposure(backFile):
dataId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'PWDR'+dataFile[4:])
dataComments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,dataId,'Comments'))
if not backFile:
return -1.
backId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,backFile)
backComments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,backId,'Comments'))
expTime = 1.
sumExp = 1.
for item in dataComments:
if 'exposureTime' in item:
expTime = float(item.split('=')[1])
if 'summedExposures' in item:
sumExp = float(item.split('=')[1])
dataExp = expTime*sumExp
expTime = 1.
sumExp = 1.
for item in backComments:
if 'exposureTime' in item:
expTime = float(item.split('=')[1])
if 'summedExposures' in item:
sumExp = float(item.split('=')[1])
backExp = expTime*sumExp
return -dataExp/backExp
item = data[key]
fileList = [''] + GetFileList(G2frame,'PWDR')
fileSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' '+key+' file:'),0,WACV)
fileName = wx.ComboBox(G2frame.dataWindow,value=item['Name'],choices=fileList,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
itemDict[fileName.GetId()] = [key,'Name','%s']
fileName.Bind(wx.EVT_COMBOBOX,OnSelectFile)
fileSizer.Add(fileName,0,)
fileSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label='Multiplier:'),0,WACV)
mulBox = wx.BoxSizer(wx.HORIZONTAL)
mult = G2G.ValidatedTxtCtrl(G2frame.dataWindow,item,'Mult',nDig=(10,3),
typeHint=float,OnLeave=OnMult)
mulBox.Add(mult,0,)
multSpin = wx.SpinButton(G2frame.dataWindow,style=wx.SP_VERTICAL,size=wx.Size(20,25))
multSpin.SetRange(-1,1)
multSpin.SetValue(0)
multSpin.Bind(wx.EVT_SPIN, OnMoveMult)
mulBox.Add(multSpin,0,WACV)
fileSizer.Add(mulBox,0,WACV)
if 'Refine' in item and item['Name'] and 'Sample' in key:
refMult = wx.CheckBox(parent=G2frame.dataWindow,label='Refine?')
refMult.SetValue(item['Refine'])
refMult.Bind(wx.EVT_CHECKBOX, OnRefMult)
fileSizer.Add(refMult,0,WACV)
else:
fileSizer.Add((5,5),0)
def ResetFlatBkg():
Smin = np.min(G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'PWDR'+dataFile[4:]))[1][1])
Bmin = 0; Cmin = 0.; Cmul = 0.; CBmin = 0.
if data['Sample Bkg.']['Name']:
Bmin = np.min(G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,G2frame.root,data['Sample Bkg.']['Name']))[1][1])
Smin += Bmin*data['Sample Bkg.']['Mult']
if data['Container']['Name']:
Cmin = np.min(G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,G2frame.root,data['Container']['Name']))[1][1])
Cmul = data['Container']['Mult']
if data['Container Bkg.']['Name']:
CBmin = np.min(G2frame.GPXtree.GetItemPyData(
G2gd.GetGPXtreeItemId(G2frame,G2frame.root,data['Container Bkg.']['Name']))[1][1])
Cmin += CBmin*data['Container Bkg.']['Mult']
Smin += Cmul*Cmin
data['Flat Bkg'] = max(0,Smin)
G2frame.flatBkg.SetValue(data['Flat Bkg'])
PDFfileSizer = wx.BoxSizer(wx.VERTICAL)
PDFfileSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=' PDF data files: '),0)
PDFfileSizer.Add((5,5),0)
if 'C' in inst['Type'][0]:
str = ' Sample file: PWDR%s Wavelength, A: %.5f Energy, keV: %.3f Polariz.: %.2f '%(dataFile[4:],wave,keV,polariz)
PDFfileSizer.Add(wx.StaticText(parent=G2frame.dataWindow,label=str),0)
PDFfileSizer.Add((5,5),0)
fileSizer = wx.FlexGridSizer(0,5,5,1)
select = ['Sample Bkg.','Container']
if data['Container']['Name']:
select.append('Container Bkg.')
for key in select:
FillFileSizer(fileSizer,key)
PDFfileSizer.Add(fileSizer,0)
return PDFfileSizer
def SampleSizer():
def FillElemSizer(elemSizer,ElData):
def OnElemNum(invalid,value,tc):
if invalid: return
data['Form Vol'] = max(10.0,SumElementVolumes())
wx.CallAfter(UpdatePDFGrid,G2frame,data)
wx.CallAfter(OnComputePDF,tc.event)
elemSizer.Add(wx.StaticText(parent=G2frame.dataWindow,
label=' Element: '+'%2s'%(ElData['Symbol'])+' * '),0,WACV)
num = G2G.ValidatedTxtCtrl(G2frame.dataWindow,ElData,'FormulaNo',nDig=(10,3),xmin=0.0,
typeHint=float,OnLeave=OnElemNum)
elemSizer.Add(num,0,WACV)
elemSizer.Add(wx.StaticText(parent=G2frame.dataWindow,
label="f': %.3f"%(ElData['fp'])+' f": %.3f'%(ElData['fpp'])+' mu: %.2f barns'%(ElData['mu']) ),
0,WACV)
def AfterChange(invalid,value,tc):
if invalid: return
wx.CallAfter(UpdatePDFGrid,G2frame,data)
wx.CallAfter(OnComputePDF,tc.event)
def OnGeometry(event):
data['Geometry'] = geometry.GetValue()
wx.CallAfter(UpdatePDFGrid,G2frame,data)
#UpdatePDFGrid(G2frame,data)
wx.CallAfter(OnComputePDF,event)
sampleSizer = wx.BoxSizer(wx.VERTICAL)
if not ElList:
sampleSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Sample information: fill in this 1st'),0)
else:
sampleSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Sample information: '),0)
sampleSizer.Add((5,5),0)
Abs = G2lat.CellAbsorption(ElList,data['Form Vol'])
Trans = G2pwd.Transmission(data['Geometry'],Abs*data['Pack'],data['Diam'])
elemSizer = wx.FlexGridSizer(0,3,5,1)
for El in ElList:
FillElemSizer(elemSizer,ElList[El])
sampleSizer.Add(elemSizer,0)
sampleSizer.Add((5,5),0)
midSizer = wx.BoxSizer(wx.HORIZONTAL)
midSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Formula volume: '),0,WACV)
formVol = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Form Vol',nDig=(10,3),xmin=10.0,
typeHint=float,OnLeave=AfterChange)
midSizer.Add(formVol,0)
midSizer.Add(wx.StaticText(G2frame.dataWindow,
label=' Theoretical absorption: %.4f cm-1 Sample absorption: %.4f cm-1'%(Abs,Abs*data['Pack'])),
0,WACV)
sampleSizer.Add(midSizer,0)
sampleSizer.Add((5,5),0)
geoBox = wx.BoxSizer(wx.HORIZONTAL)
geoBox.Add(wx.StaticText(G2frame.dataWindow,label=' Sample geometry: '),0,WACV)
if 'C' in inst['Type'][0]:
choice = ['Cylinder','Bragg-Brentano','Tilting flat plate in transmission','Fixed flat plate']
else:
choice = ['Cylinder',]
geometry = wx.ComboBox(G2frame.dataWindow,value=data['Geometry'],choices=choice,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
geometry.Bind(wx.EVT_COMBOBOX, OnGeometry)
geoBox.Add(geometry,0)
geoBox.Add(wx.StaticText(G2frame.dataWindow,label=' Sample diameter/thickness, mm: '),0,WACV)
diam = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Diam',nDig=(10,3),xmin=0.01,
typeHint=float,OnLeave=AfterChange)
geoBox.Add(diam,0)
sampleSizer.Add(geoBox,0)
sampleSizer.Add((5,5),0)
geoBox = wx.BoxSizer(wx.HORIZONTAL)
geoBox.Add(wx.StaticText(G2frame.dataWindow,label=' Packing: '),0,WACV)
pack = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Pack',nDig=(10,2),xmin=0.01,
typeHint=float,OnLeave=AfterChange)
geoBox.Add(pack,0)
geoBox.Add(wx.StaticText(G2frame.dataWindow,label=' Sample transmission: %.3f %%'%(100.*Trans)),0,WACV)
sampleSizer.Add(geoBox,0)
return sampleSizer
def SFGctrlSizer():
def OnOptimizePDF(event):
'''Optimize Flat Bkg, BackRatio & Ruland corrections to remove spurious
"intensity" from portion of G(r) with r<Rmin.
Invoked by Optimize PDF button and from menu command.
'''
if not data['ElList']:
G2frame.ErrorDialog('PDF error','Chemical formula not defined')
return
G2frame.GetStatusBar().SetStatusText('',1)
wx.BeginBusyCursor()
try:
data['Ruland'] = 0.01 #always set small to start
OptimizePDF(G2frame,data)
finally:
wx.EndBusyCursor()
OnComputePDF(event)
wx.CallAfter(UpdatePDFGrid,G2frame,data)
def AfterChangeNoRefresh(invalid,value,tc):
if invalid: return
if tc.GetId() in Indx:
Indx[tc.GetId()][0].SetValue(int(value*Indx[tc.GetId()][1]))
wx.CallAfter(OnComputePDF,None)
def OnDetType(event):
#TODO: to be removed
data['DetType'] = detType.GetValue()
wx.CallAfter(UpdatePDFGrid,G2frame,data)
wx.CallAfter(OnComputePDF,None)
def OnFlatSpin(event):
data['Flat Bkg'] += flatSpin.GetValue()*0.01*data['IofQmin']
G2frame.flatBkg.ChangeValue(data['Flat Bkg'])
flatSpin.SetValue(0)
wx.CallAfter(OnComputePDF,None)
def OnBackSlider(event):
value = int(backSldr.GetValue())/100.
data['BackRatio'] = value
backVal.ChangeValue(data['BackRatio'])
wx.CallAfter(OnComputePDF,None)
def OnRulSlider(event):
value = int(rulandSldr.GetValue())/100.
data['Ruland'] = max(0.001,value)
rulandWdt.ChangeValue(data['Ruland'])
wx.CallAfter(OnComputePDF,None)
def OnGRscaleSlider(event):
value = int(gscaleSldr.GetValue())/50.
data['GR Scale'] = max(0.1,min(2.,value))
gscale.ChangeValue(data['GR Scale'])
wx.CallAfter(OnComputePDF,None)
def NewQmax(invalid,value,tc):
if invalid: return
data['QScaleLim'][0] = 0.9*value
SQmin.ChangeValue(data['QScaleLim'][0])
wx.CallAfter(OnComputePDF,None)
def OnResetQ(event):
data['QScaleLim'][1] = qLimits[1]
SQmax.ChangeValue(data['QScaleLim'][1])
data['QScaleLim'][0] = 0.9*qLimits[1]
SQmin.ChangeValue(data['QScaleLim'][0])
wx.CallAfter(OnComputePDF,None)
def OnLorch(event):
data['Lorch'] = lorch.GetValue()
wx.CallAfter(OnComputePDF,None)
def OnNoRing(event):
data['noRing'] = not data['noRing']
wx.CallAfter(OnComputePDF,None)
Indx = {}
sfgSizer = wx.BoxSizer(wx.VERTICAL)
sqBox = wx.BoxSizer(wx.HORIZONTAL)
sqBox.Add(wx.StaticText(G2frame.dataWindow,label=' S(Q)->F(Q)->G(r) controls: '),0,WACV)
sqBox.Add((1,1),1,wx.EXPAND,1)
optB = wx.Button(G2frame.dataWindow,label='Optimize PDF',style=wx.BU_EXACTFIT)
optB.Bind(wx.EVT_BUTTON, OnOptimizePDF)
sqBox.Add(optB,0,WACV)
sfgSizer.Add(sqBox,0,wx.EXPAND)
sfgSizer.Add((5,5),0)
sqBox = wx.BoxSizer(wx.HORIZONTAL)
#TODO: this should be removed
sqBox.Add(wx.StaticText(G2frame.dataWindow,label=' Detector type: '),0,WACV)
choice = ['Area detector','Point detector']
detType = wx.ComboBox(G2frame.dataWindow,value=data['DetType'],choices=choice,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
detType.Bind(wx.EVT_COMBOBOX, OnDetType)
sqBox.Add(detType,0)
if data['DetType'] == 'Area detector':
sqBox.Add(wx.StaticText(G2frame.dataWindow,label=' IP transmission coeff.: '),0,WACV)
obliqCoeff = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'ObliqCoeff',nDig=(10,3),xmin=0.0,xmax=1.0,
typeHint=float,OnLeave=AfterChangeNoRefresh)
sqBox.Add(obliqCoeff,0)
#TODO: end of proposed removal
sqBox.Add(wx.StaticText(G2frame.dataWindow,label=' Flat Bkg.: '),0,WACV)
G2frame.flatBkg = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Flat Bkg',nDig=(10,0),
typeHint=float,OnLeave=AfterChangeNoRefresh)
sqBox.Add(G2frame.flatBkg,0)
flatSpin = wx.SpinButton(G2frame.dataWindow,style=wx.SP_VERTICAL,size=wx.Size(20,25))
flatSpin.SetRange(-1,1)
flatSpin.SetValue(0)
flatSpin.Bind(wx.EVT_SPIN, OnFlatSpin)
sqBox.Add(flatSpin,0,WACV)
sqBox.Add((1,1),1,wx.EXPAND,1)
sqBox.Add(wx.StaticText(G2frame.dataWindow,label='Rmin: '),0,WACV)
rmin = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Rmin',nDig=(5,1),
xmin=0.01,typeHint=float,size=wx.Size(50,20))
sqBox.Add(rmin,0,WACV)
sfgSizer.Add(sqBox,0,wx.EXPAND)
if data['DetType'] == 'Area detector' and fullLimits[1] > 80.:
sfgSizer.Add(wx.StaticText(G2frame.dataWindow,label=' NB: Detector choice may be in error; use Point detector instead'))
bkBox = wx.BoxSizer(wx.HORIZONTAL)
bkBox.Add(wx.StaticText(G2frame.dataWindow,label=' Background ratio: '),0,WACV)
backSldr = G2G.G2Slider(parent=G2frame.dataWindow,style=wx.SL_HORIZONTAL,
value=int(100*data['BackRatio']))
bkBox.Add(backSldr,1,wx.EXPAND)
backSldr.Bind(wx.EVT_SLIDER, OnBackSlider)
backVal = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'BackRatio',nDig=(10,3),xmin=0.0,xmax=1.0,
typeHint=float,OnLeave=AfterChangeNoRefresh)
Indx[backVal.GetId()] = [backSldr,100]
bkBox.Add(backVal,0,WACV)
sfgSizer.Add(bkBox,0,wx.EXPAND)
if 'XC' in inst['Type'][0]:
sqBox = wx.BoxSizer(wx.HORIZONTAL)
sqBox.Add(wx.StaticText(G2frame.dataWindow,label=' Ruland width: '),0,WACV)
rulandSldr = G2G.G2Slider(parent=G2frame.dataWindow,style=wx.SL_HORIZONTAL,
value=int(100*data['Ruland']))
sqBox.Add(rulandSldr,1,wx.EXPAND)
rulandSldr.Bind(wx.EVT_SLIDER, OnRulSlider)
rulandWdt = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Ruland',nDig=(10,3),xmin=0.001,xmax=1.0,
typeHint=float,OnLeave=AfterChangeNoRefresh)
Indx[rulandWdt.GetId()] = [rulandSldr,100]
sqBox.Add(rulandWdt,0,WACV)
sfgSizer.Add(sqBox,0,wx.EXPAND)
gscaleBox = wx.BoxSizer(wx.HORIZONTAL)
gscaleBox.Add(wx.StaticText(G2frame.dataWindow,label=' G(R) scale: '),0,WACV)
gscaleSldr = G2G.G2Slider(parent=G2frame.dataWindow,style=wx.SL_HORIZONTAL,
value=int(50*data['GR Scale']))
gscaleBox.Add(gscaleSldr,1,wx.EXPAND)
gscaleSldr.Bind(wx.EVT_SLIDER, OnGRscaleSlider)
gscale = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'GR Scale',nDig=(10,3),xmin=0.1,xmax=2.,
typeHint=float,OnLeave=AfterChangeNoRefresh)
Indx[gscale.GetId()] = [gscaleSldr,50]
gscaleBox.Add(gscale,0,WACV)
sfgSizer.Add(gscaleBox,0,wx.EXPAND)
sqBox = wx.BoxSizer(wx.HORIZONTAL)
sqBox.Add(wx.StaticText(G2frame.dataWindow,label=' Scaling Q-range: '),0,WACV)
SQmin = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['QScaleLim'],0,nDig=(10,3),
xmin=qLimits[0],xmax=.95*data['QScaleLim'][1],
typeHint=float,OnLeave=AfterChangeNoRefresh)
sqBox.Add(SQmin,0,WACV)
sqBox.Add(wx.StaticText(G2frame.dataWindow,label=' to Qmax '),0,WACV)
SQmax = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data['QScaleLim'],1,nDig=(10,3),
xmin=qLimits[0],xmax=qLimits[1],typeHint=float,OnLeave=NewQmax)
sqBox.Add(SQmax,0,WACV)
resetQ = wx.Button(G2frame.dataWindow,label='Reset?',style=wx.BU_EXACTFIT)
sqBox.Add(resetQ,0,WACV)
resetQ.Bind(wx.EVT_BUTTON, OnResetQ)
sqBox.Add(wx.StaticText(G2frame.dataWindow,label=' Plot Rmax: '),0,WACV)
rmax = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'Rmax',nDig=(10,1),xmin=10.,xmax=200.,
typeHint=float,OnLeave=AfterChangeNoRefresh,size=wx.Size(50,20))
sqBox.Add(rmax,0,WACV)
lorch = wx.CheckBox(parent=G2frame.dataWindow,label='Lorch damping?')
lorch.SetValue(data['Lorch'])
lorch.Bind(wx.EVT_CHECKBOX, OnLorch)
sqBox.Add(lorch,0,WACV)
noRing = wx.CheckBox(parent=G2frame.dataWindow,label='Suppress G(0) ringing?')
noRing.SetValue(data['noRing'])
noRing.Bind(wx.EVT_CHECKBOX, OnNoRing)
sqBox.Add(noRing,0,WACV)
sfgSizer.Add(sqBox,0)
return sfgSizer
def DiffSizer():
def OnSelectGR(event):
newName = grName.GetValue()
if newName:
data['delt-G(R)'] = copy.deepcopy(data['G(R)'])
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,newName)
pId = G2gd.GetGPXtreeItemId(G2frame,Id,'PDF Controls')
subData = G2frame.GPXtree.GetItemPyData(pId)['G(R)']
if subData[1][0][-1] != data['G(R)'][1][0][-1]:
G2frame.ErrorDialog('delt-G(R) Error',' G(R) for '+newName+' not same R range')
grName.SetValue(data['diffGRname'])
return
data['diffGRname'] = newName
data['delt-G(R)'][1] = np.array([subData[1][0],data['G(R)'][1][1]-subData[1][1]])
data['delt-G(R)'][2] += ('-\n'+subData[2])
G2plt.PlotISFG(G2frame,data,newPlot=True,plotType='delt-G(R)')
wx.CallAfter(UpdatePDFGrid,G2frame,data)
def OnMult(invalid,value,tc):
if invalid: return
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,data['diffGRname'])
if Id == 0: return
pId = G2gd.GetGPXtreeItemId(G2frame,Id,'PDF Controls')
if pId == 0: return
subData = G2frame.GPXtree.GetItemPyData(pId)['G(R)']
data['delt-G(R)'][1] = np.array([subData[1][0],data['G(R)'][1][1]-data['diffMult']*subData[1][1]])
G2plt.PlotISFG(G2frame,data,newPlot=True,plotType='delt-G(R)')
diffSizer = wx.BoxSizer(wx.HORIZONTAL)
fileList = [''] + GetFileList(G2frame,'PDF')
diffSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Subtract G(R) for: '),0,WACV)
grName = wx.ComboBox(G2frame.dataWindow,value=data['diffGRname'],choices=fileList,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
grName.Bind(wx.EVT_COMBOBOX,OnSelectGR)
diffSizer.Add(grName,0,WACV)
if data['diffGRname']:
diffSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Mult: '),0,WACV)
mult = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'diffMult',nDig=(10,3),
typeHint=float,OnLeave=OnMult)
diffSizer.Add(mult,0,WACV)
OnMult(False,None,None)
return diffSizer
def SumElementVolumes():
sumVol = 0.
ElList = data['ElList']
for El in ElList:
Avol = (4.*math.pi/3.)*ElList[El]['Drad']**3
sumVol += Avol*ElList[El]['FormulaNo']
return sumVol
wx.CallAfter(OnComputePDF,None)
def OnCopyPDFControls(event):
TextList = GetFileList(G2frame,'PDF')
Source = G2frame.GPXtree.GetItemText(G2frame.PatternId)
if len(TextList) == 1:
G2frame.ErrorDialog('Nothing to copy controls to','There must be more than one "PDF" pattern')
return
od = {'label_1':'Only refine flag','value_1':False,'label_2':'Only Lorch flag','value_2':False}
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy PDF controls','Copy controls from '+Source+' to:',TextList,extraOpts=od)
try:
if dlg.ShowModal() == wx.ID_OK:
PDFlist = [TextList[i] for i in dlg.GetSelections()]
for item in PDFlist:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
olddata = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'PDF Controls'))
if od['value_1']:
olddata['Sample Bkg.']['Refine'] = data['Sample Bkg.']['Refine'] #only one flag
elif od['value_2']:
olddata['Lorch'] = data['Lorch'] #only one flag
else:
sample = olddata['Sample']
olddata.update(copy.deepcopy(data))
olddata['Sample'] = sample
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'PDF Controls'),olddata)
G2frame.GetStatusBar().SetStatusText('PDF controls copied',1)
finally:
dlg.Destroy()
def OnSavePDFControls(event):
pth = G2G.GetExportPath(G2frame)
dlg = wx.FileDialog(G2frame, 'Choose GSAS-II PDF controls file', pth, '',
'PDF controls files (*.pdfprm)|*.pdfprm',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
try:
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
# make sure extension is .pdfprm
filename = os.path.splitext(filename)[0]+'.pdfprm'
File = open(filename,'w')
File.write("#GSAS-II PDF controls file; do not add/delete items!\n")
for item in data:
if item[:] not in ['Sample','I(Q)','S(Q)','F(Q)','G(R)']:
File.write(item+':'+data[item]+'\n')
File.close()
print ('PDF controls saved to: '+filename)
finally:
dlg.Destroy()
def OnLoadPDFControls(event):
pth = G2G.GetExportPath(G2frame)
dlg = wx.FileDialog(G2frame, 'Choose GSAS-II PDF controls file', pth, '',
'PDF controls files (*.pdfprm)|*.pdfprm',wx.FD_OPEN)
try:
if dlg.ShowModal() == wx.ID_OK:
filename = dlg.GetPath()
File = open(filename,'r')
newdata = {}
S = File.readline()
while S:
if '#' in S:
S = File.readline()
continue
key,val = S.split(':',1)
try:
newdata[key] = eval(val)
#except SyntaxError:
except:
newdata[key] = val.strip()
S = File.readline()
File.close()
data.update(newdata)
finally:
dlg.Destroy()
OnComputePDF(event)
wx.CallAfter(UpdatePDFGrid,G2frame,data)
def OnAddElement(event):
ElList = data['ElList']
choice = list(ElList.keys())
PE = G2elemGUI.PickElements(G2frame,choice)
if PE.ShowModal() == wx.ID_OK:
for El in PE.Elem:
if El not in ElList:
try:
data['ElList'][El] = copy.deepcopy(G2elem.GetElInfo(El,inst))
data['ElList'][El]['FormulaNo'] = 1.0
except IndexError: # happens with element Q
pass
data['Form Vol'] = max(10.0,SumElementVolumes())
PE.Destroy()
wx.CallAfter(UpdatePDFGrid,G2frame,data)
def OnDeleteElement(event):
ElList = data['ElList']
choice = list(ElList.keys())
dlg = G2elemGUI.DeleteElement(G2frame,choice=choice)
if dlg.ShowModal() == wx.ID_OK:
del ElList[dlg.GetDeleteElement()]
dlg.Destroy()
wx.CallAfter(UpdatePDFGrid,G2frame,data)
def OnComputePDF(event):
'''Compute and plot PDF, in response to a menu command or a change to a
computation parameter.
'''
if not data['ElList']:
G2frame.ErrorDialog('PDF error','Chemical formula not defined')
OnAddElement(event)
auxPlot = computePDF(G2frame,data)
if auxPlot is None: return
G2frame.GetStatusBar().SetStatusText('PDF computed',1)
for plot in auxPlot:
XY = np.array(plot[:2])
G2plt.PlotXY(G2frame,[XY,],Title=plot[2])
if event is not None:
G2plt.PlotISFG(G2frame,data,newPlot=True,plotType='I(Q)')
G2plt.PlotISFG(G2frame,data,newPlot=True,plotType='S(Q)')
G2plt.PlotISFG(G2frame,data,newPlot=True,plotType='F(Q)')
G2plt.PlotISFG(G2frame,data,newPlot=True,plotType='g(r)')
G2plt.PlotISFG(G2frame,data,newPlot=True,plotType='G(R)')
else:
G2plt.PlotISFG(G2frame,data,newPlot=False)
def OnComputeAllPDF(event):
print('Calculating PDFs...')
choices = []
if G2frame.GPXtree.GetCount():
Id, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
while Id:
Name = G2frame.GPXtree.GetItemText(Id)
if Name.startswith('PDF '):
Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'PDF Controls'))
if not Data['ElList']:
print(' No chemical formula for {}'.format(Name))
else:
choices.append(Name)
Id, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
if not choices:
print(' No PDFs to compute\n')
return
od = {'label_1':'Optimize PDFs','value_1':True}
dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select PDFs to compute','Select PDFs',
choices,extraOpts=od)
try:
if dlg.ShowModal() == wx.ID_OK:
results = dlg.GetSelections()
else:
return
finally:
dlg.Destroy()
if not results:
print(' No PDFs to compute\n')
return
Names = [choices[i] for i in results]
pgbar = wx.ProgressDialog('Compute PDF','PDFs done: 0',len(Names)+1,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT)
notConverged = 0
Id, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
N = 0
try:
while Id:
Name = G2frame.GPXtree.GetItemText(Id)
if Name in Names:
N += 1
msg = 'PDFs done: {} of {}'.format(N-1,len(Names))
if not pgbar.Update(N,msg)[0]:
pgbar.Destroy()
break
pId = G2gd.GetGPXtreeItemId(G2frame,Id,'PDF Controls')
Data = G2frame.GPXtree.GetItemPyData(pId)
print(' Computing {}'.format(Name))
computePDF(G2frame,Data)
if od['value_1']:
notConverged += not OptimizePDF(G2frame,Data,maxCycles=10)
computePDF(G2frame,Data)
G2frame.GPXtree.SetItemPyData(pId,Data)
Id, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
finally:
pgbar.Destroy()
if od['value_1']:
msg = '{}/{} PDFs computed; {} unconverged'.format(N,len(Names),notConverged)
else:
msg = '{}/{} PDFs computed'.format(N,len(Names))
G2frame.GetStatusBar().SetStatusText(msg,1)
print(msg)
# what item is being plotted? -- might be better to select from tree
G2plt.PlotISFG(G2frame,data,newPlot=True,plotType='I(Q)')
G2plt.PlotISFG(G2frame,data,newPlot=True,plotType='S(Q)')
G2plt.PlotISFG(G2frame,data,newPlot=True,plotType='F(Q)')
G2plt.PlotISFG(G2frame,data,newPlot=True,plotType='G(R)')
G2plt.PlotISFG(G2frame,data,newPlot=True,plotType='g(r)')
#### Routine UpdatePDFGrid starts here
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.PDFMenu)
global inst
tth2q = lambda t,w:4.0*math.pi*sind(t/2.0)/w
tof2q = lambda t,C:2.0*math.pi*C/t
dataFile = G2frame.GPXtree.GetItemText(G2frame.PatternId)
powName = 'PWDR'+dataFile[4:]
powId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root, powName)
if powId: # skip if no matching PWDR entry
fullLimits,limits = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,powId, 'Limits'))[:2]
inst = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,powId, 'Instrument Parameters'))[0]
if 'C' in inst['Type'][0]:
wave = G2mth.getWave(inst)
keV = G2mth.wavekE(wave)
qLimits = [tth2q(fullLimits[0],wave),tth2q(fullLimits[1],wave)]
polariz = inst['Polariz.'][1]
else: #'T'of
qLimits = [tof2q(fullLimits[1],inst['difC'][1]),tof2q(fullLimits[0],inst['difC'][1])]
polariz = 1.0
data['QScaleLim'][1] = min(qLimits[1],data['QScaleLim'][1])
if data['QScaleLim'][0]:
data['QScaleLim'][0] = max(qLimits[0],data['QScaleLim'][0])
else: #initial setting at 90% of max Q
data['QScaleLim'][0] = 0.90*data['QScaleLim'][1]
itemDict = {}
#patch
if 'BackRatio' not in data:
data['BackRatio'] = 0.
if 'noRing' not in data:
data['noRing'] = False
if 'Rmax' not in data:
data['Rmax'] = 100.
if 'Flat Bkg' not in data:
data['Flat Bkg'] = 0.
if 'IofQmin' not in data:
data['IofQmin'] = 1.0
if 'Rmin' not in data:
data['Rmin'] = 1.5
if data['DetType'] == 'Image plate':
data['DetType'] = 'Area detector'
if 'Refine' not in data['Sample Bkg.']:
data['Sample Bkg.']['Refine'] = False
if 'diffGRname' not in data:
data['diffGRname'] = ''
if 'diffMult' not in data:
data['diffMult'] = 1.0
if 'GR Scale' not in data:
data['GR Scale'] = 1.0
if powId:
G2frame.dataWindow.PDFMenu.EnableTop(0,enable=True)
else:
G2frame.dataWindow.PDFMenu.EnableTop(0,enable=False)
G2frame.Bind(wx.EVT_MENU, OnCopyPDFControls, id=G2G.wxID_PDFCOPYCONTROLS)
G2frame.Bind(wx.EVT_MENU, OnSavePDFControls, id=G2G.wxID_PDFSAVECONTROLS)
G2frame.Bind(wx.EVT_MENU, OnLoadPDFControls, id=G2G.wxID_PDFLOADCONTROLS)
G2frame.Bind(wx.EVT_MENU, OnAddElement, id=G2G.wxID_PDFADDELEMENT)
G2frame.Bind(wx.EVT_MENU, OnDeleteElement, id=G2G.wxID_PDFDELELEMENT)
G2frame.Bind(wx.EVT_MENU, OnComputePDF, id=G2G.wxID_PDFCOMPUTE)
G2frame.Bind(wx.EVT_MENU, OnComputeAllPDF, id=G2G.wxID_PDFCOMPUTEALL)
G2frame.dataWindow.ClearData()
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
if powId:
ElList = data['ElList']
mainSizer.Add(PDFFileSizer())
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add(SampleSizer())
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add(SFGctrlSizer())
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add(DiffSizer())
else:
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label='Controls for %s:\n'%powName))
mainSizer.Add(DiffSizer())
G2frame.dataWindow.SetDataSize()
###############################################################################################################
####UpdatePDFPeaks: peaks in G(r)
###############################################################################################################
def UpdatePDFPeaks(G2frame,peaks,data):
def limitSizer():
def NewLim(invalid,value,tc):
if invalid:
return
G2plt.PlotISFG(G2frame,data,newPlot=False,plotType='G(R)',peaks=peaks)
limitBox = wx.BoxSizer(wx.HORIZONTAL)
limitBox.Add(wx.StaticText(G2frame.dataWindow,label=' PDF Limits: '),0,WACV)
lowLim = G2G.ValidatedTxtCtrl(G2frame.dataWindow,peaks['Limits'],0,nDig=(10,3),
xmin=0.,xmax=10.,typeHint=float,OnLeave=NewLim)
limitBox.Add(lowLim,0,WACV)
highLim = G2G.ValidatedTxtCtrl(G2frame.dataWindow,peaks['Limits'],1,nDig=(10,3),
xmin=peaks['Limits'][0],xmax=10.,typeHint=float,OnLeave=NewLim)
limitBox.Add(highLim,0,WACV)
return limitBox
def backSizer():
def NewBack(invalid,value,tc):
if invalid:
return
G2plt.PlotISFG(G2frame,data,newPlot=False,plotType='G(R)',peaks=peaks)
def OnRefBack(event):
peaks['Background'][2] = refbk.GetValue()
backBox = wx.BoxSizer(wx.HORIZONTAL)
backBox.Add(wx.StaticText(G2frame.dataWindow,label=' Background slope: '),0,WACV)
slope = G2G.ValidatedTxtCtrl(G2frame.dataWindow,peaks['Background'][1],1,nDig=(10,3),
xmin=-4.*np.pi,xmax=0.,typeHint=float,OnLeave=NewBack)
backBox.Add(slope,0,WACV)
refbk = wx.CheckBox(parent=G2frame.dataWindow,label=' Refine?')
refbk.SetValue(peaks['Background'][2])
refbk.Bind(wx.EVT_CHECKBOX, OnRefBack)
backBox.Add(refbk,0,WACV)
return backBox
def peakSizer():
def PeaksRefine(event):
c = event.GetCol()
if PDFPeaks.GetColLabelValue(c) == 'refine':
choice = ['P - position','M - magnitude','S - standrd deviation']
dlg = wx.MultiChoiceDialog(G2frame,'Select','Refinement controls',choice)
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelections()
parms = ''
for x in sel:
parms += choice[x][0]
for peak in peaks['Peaks']:
peak[3] = parms
dlg.Destroy()
wx.CallAfter(UpdatePDFPeaks,G2frame,peaks,data)
def ElTypeSelect(event):
r,c = event.GetRow(),event.GetCol()
if 'Atom' in PDFPeaks.GetColLabelValue(c):
PE = G2elemGUI.PickElement(G2frame)
if PE.ShowModal() == wx.ID_OK:
el = PE.Elem.strip()
peaks['Peaks'][r][c] = el
PDFPeaks.SetCellValue(r,c,el)
PE.Destroy()
colLabels = ['position','magnitude','sig','refine','Atom A','Atom B','Bond No.']
Types = 3*[wg.GRID_VALUE_FLOAT+':10,3',]+[wg.GRID_VALUE_CHOICE+': ,P,M,S,PM,PS,MS,PMS',]+ \
2*[wg.GRID_VALUE_STRING,]+[wg.GRID_VALUE_FLOAT+':10,3',]
rowLabels = [str(i) for i in range(len(peaks['Peaks']))]
peakTable = G2G.Table(peaks['Peaks'],rowLabels=rowLabels,colLabels=colLabels,types=Types)
PDFPeaks = G2G.GSGrid(G2frame.dataWindow)
PDFPeaks.SetRowLabelSize(45)
PDFPeaks.SetTable(peakTable,True)
PDFPeaks.AutoSizeColumns(False)
PDFPeaks.Bind(wg.EVT_GRID_LABEL_LEFT_DCLICK, PeaksRefine)
PDFPeaks.Bind(wg.EVT_GRID_CELL_LEFT_DCLICK, ElTypeSelect)
peakBox = wx.BoxSizer(wx.VERTICAL)
peakBox.Add(wx.StaticText(G2frame.dataWindow,label=' PDF Peaks:'),0)
peakBox.Add(PDFPeaks,0)
return peakBox
def OnCopyPDFPeaks(event):
TextList = GetFileList(G2frame,'PDF')
Source = G2frame.GPXtree.GetItemText(G2frame.PatternId)
if len(TextList) == 1:
G2frame.ErrorDialog('Nothing to copy PDF peaks to','There must be more than one "PDF" pattern')
return
od = {'label_1':'Only refine flags','value_1':False}
dlg = G2G.G2MultiChoiceDialog(G2frame,'Copy PDF peaks','Copy peaks from '+Source+' to:',TextList,extraOpts=od)
try:
if dlg.ShowModal() == wx.ID_OK:
PDFlist = [TextList[i] for i in dlg.GetSelections()]
for item in PDFlist:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,item)
olddata = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'PDF Peaks'))
if od['value_1']:
olddata['Background'][2] = peaks['Background'][2]
for ip,peak in enumerate(olddata['Peaks']):
peak[3] = peaks['Peaks'][ip][3]
else:
olddata.update(copy.deepcopy(peaks))
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'PDF Peaks'),olddata)
G2frame.GetStatusBar().SetStatusText('PDF peaks copied',1)
finally:
dlg.Destroy()
def OnFitPDFpeaks(event):
PatternId = G2frame.PatternId
data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'PDF Controls'))
peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'PDF Peaks'))
if not peaks:
G2frame.ErrorDialog('No peaks!','Nothing to fit!')
return
newpeaks = G2pwd.PDFPeakFit(peaks,data['G(R)'])[0]
print ('PDF peak fit finished')
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,PatternId, 'PDF Peaks'),newpeaks)
G2plt.PlotISFG(G2frame,data,peaks=newpeaks,newPlot=False)
wx.CallAfter(UpdatePDFPeaks,G2frame,newpeaks,data)
def OnFitAllPDFpeaks(event):
Names = G2gd.GetGPXtreeDataNames(G2frame,['PDF ',])
od = {'label_1':'Copy to next','value_1':False,'label_2':'Reverse order','value_2':False}
dlg = G2G.G2MultiChoiceDialog(G2frame,'PDF peak fitting','Select PDFs to fit:',Names,extraOpts=od)
try:
if dlg.ShowModal() == wx.ID_OK:
Id = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,'Sequential PDF peak fit results')
if Id:
SeqResult = G2frame.GPXtree.GetItemPyData(Id)
else:
SeqResult = {}
Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Sequential PDF peak fit results')
SeqResult = {'SeqPseudoVars':{},'SeqParFitEqList':[]}
items = dlg.GetSelections()
if od['value_2']:
items.reverse()
newpeaks = None
G2frame.EnablePlot = False
for item in items:
name = Names[item]
pId = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,name)
data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,pId, 'PDF Controls'))
if od['value_1'] and newpeaks is not None:
peaks = copy.deepcopy(newpeaks)
else:
peaks = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,pId,'PDF Peaks'))
newpeaks,vals,varyList,sigList,parmDict,Rvals = G2pwd.PDFPeakFit(peaks,data['G(R)'])
if vals is None:
print ('Nothing varied!')
dlg.Destroy()
return
SeqResult[name] = {'variables':vals,'varyList':varyList,'sig':sigList,'Rvals':Rvals,
'covMatrix':np.eye(len(varyList)),'title':name,'parmDict':parmDict}
G2frame.GPXtree.SetItemPyData(G2gd.GetGPXtreeItemId(G2frame,pId, 'PDF Peaks'),newpeaks)
SeqResult['histNames'] = Names
G2frame.G2plotNB.Delete('Sequential refinement') #clear away probably invalid plot
G2plt.PlotISFG(G2frame,data,peaks=newpeaks,newPlot=False)
G2frame.GPXtree.SetItemPyData(Id,SeqResult)
G2frame.GPXtree.SelectItem(Id)
print ('All PDFs peak fitted - results in Sequential PDF peak fit results')
else:
print ('Sequential fit cancelled')
finally:
dlg.Destroy()
def OnClearPDFpeaks(event):
peaks['Peaks'] = []
G2plt.PlotISFG(G2frame,data,peaks=peaks,newPlot=False)
wx.CallAfter(UpdatePDFPeaks,G2frame,peaks,data)
# start of UpdatePDFPeaks
G2gd.SetDataMenuBar(G2frame,G2frame.dataWindow.PDFPksMenu)
G2frame.Bind(wx.EVT_MENU, OnCopyPDFPeaks, id=G2G.wxID_PDFCOPYPEAKS)
G2frame.Bind(wx.EVT_MENU, OnFitPDFpeaks, id=G2G.wxID_PDFPKSFIT)
G2frame.Bind(wx.EVT_MENU, OnFitAllPDFpeaks, id=G2G.wxID_PDFPKSFITALL)
G2frame.Bind(wx.EVT_MENU, OnClearPDFpeaks, id=G2G.wxID_CLEARPDFPEAKS)
G2frame.dataWindow.ClearData()
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
mainSizer.Add((5,5),0)
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=' PDF peak fit controls:'))
mainSizer.Add((5,5),0)
mainSizer.Add(limitSizer())
mainSizer.Add((5,5),0)
mainSizer.Add(backSizer())
if len(peaks['Peaks']):
mainSizer.Add((5,5),0)
mainSizer.Add(peakSizer())
G2frame.dataWindow.SetDataSize()