# -*- coding: utf-8 -*-
#GSASIIdataGUI - Main GUI routines
'''
Routines for main GUI wx.Frame follow.
'''
from __future__ import division, print_function
import platform
import pickle
import time
import math
import random as ran
import copy
import sys
import shutil
import os
import inspect
import re
import numpy as np
import numpy.ma as ma
import numpy.linalg as nl
import matplotlib as mpl
try:
import OpenGL as ogl
try:
import OpenGL.GL # this fails in <=2020 versions of Python on OS X 11.x
except ImportError:
print('Drat, patching for Big Sur')
from ctypes import util
orig_util_find_library = util.find_library
def new_util_find_library( name ):
res = orig_util_find_library( name )
if res: return res
return '/System/Library/Frameworks/'+name+'.framework/'+name
util.find_library = new_util_find_library
except ImportError:
pass
import scipy as sp
import struct as st
try:
import wx
import wx.grid as wg
#import wx.wizard as wz
#import wx.aui
import wx.lib.scrolledpanel as wxscroll
except ImportError:
pass
from . import GSASIIpath
from . import GSASIImath as G2mth
from . import GSASIImiscGUI as G2IO
from . import GSASIIfiles as G2fil
from . import GSASIIstrIO as G2stIO
from . import GSASIIlattice as G2lat
from . import GSASIIplot as G2plt
from . import GSASIIpwdplot as G2pwpl
from . import GSASIIpwdGUI as G2pdG
from . import GSASIIimgGUI as G2imG
from . import GSASIIphsGUI as G2phG
from . import GSASIIspc as G2spc
from . import GSASIImapvars as G2mv
from . import GSASIIconstrGUI as G2cnstG
from . import GSASIIrestrGUI as G2restG
from . import GSASIIobj as G2obj
from . import GSASIIctrlGUI as G2G
from . import GSASIIElem as G2elem
from . import GSASIIpwd as G2pwd
from . import GSASIIstrMain as G2stMn
from . import defaultIparms as dI
from . import GSASIIfpaGUI as G2fpa
from . import GSASIIseqGUI as G2seq
from . import GSASIIddataGUI as G2ddG
try:
wx.NewIdRef
wx.NewId = wx.NewIdRef
except AttributeError:
pass
# trig functions in degrees
sind = lambda x: np.sin(x*np.pi/180.)
tand = lambda x: np.tan(x*np.pi/180.)
cosd = lambda x: np.cos(x*np.pi/180.)
# Define short names for convenience
WACV = wx.ALIGN_CENTER_VERTICAL
VERY_LIGHT_GREY = wx.Colour(240,240,240)
DULL_YELLOW = (230,230,190)
GkDelta = chr(0x0394)
# transformation matrices
commonTrans = {'abc':np.eye(3),'a-cb':np.array([[1.,0.,0.],[0.,0.,-1.],[0.,1.,0.]]),
'ba-c':np.array([[0.,1.,0.],[1.,0.,0.],[0.,0.,-1.]]),'-cba':np.array([[0.,0.,-1.],[0.,1.,0.],[1.,0.,0.]]),
'bca':np.array([[0.,1.,0.],[0.,0.,1.],[1.,0.,0.]]),'cab':np.array([[0.,0.,1.],[1.,0.,0.],[0.,1.,0.]]),
'R->H':np.array([[1.,-1.,0.],[0.,1.,-1.],[1.,1.,1.]]),'H->R':np.array([[2./3,1./3,1./3],[-1./3,1./3,1./3],[-1./3,-2./3,1./3]]),
'P->A':np.array([[-1.,0.,0.],[0.,-1.,1.],[0.,1.,1.]]),'R->O':np.array([[-1.,0.,0.],[0.,-1.,0.],[0.,0.,1.]]),
'P->B':np.array([[-1.,0.,1.],[0.,-1.,0.],[1.,0.,1.]]),'B->P':np.array([[-.5,0.,.5],[0.,-1.,0.],[.5,0.,.5]]),
'P->C':np.array([[1.,1.,0.],[1.,-1.,0.],[0.,0.,-1.]]),'C->P':np.array([[.5,.5,0.],[.5,-.5,0.],[0.,0.,-1.]]),
'P->F':np.array([[-1.,1.,1.],[1.,-1.,1.],[1.,1.,-1.]]),'F->P':np.array([[0.,.5,.5],[.5,0.,.5],[.5,.5,0.]]),
'P->I':np.array([[0.,1.,1.],[1.,0.,1.],[1.,1.,0.]]),'I->P':np.array([[-.5,.5,.5],[.5,-.5,.5],[.5,.5,-.5]]),
'A->P':np.array([[-1.,0.,0.],[0.,-.5,.5],[0.,.5,.5]]),'O->R':np.array([[-1.,0.,0.],[0.,-1.,0.],[0.,0.,1.]]),
'abc*':np.eye(3), }
commonNames = ['abc','bca','cab','a-cb','ba-c','-cba','P->A','A->P','P->B','B->P','P->C','C->P',
'P->I','I->P','P->F','F->P','H->R','R->H','R->O','O->R','abc*','setting 1->2'] #don't put any new ones after the setting one!
[docs]
def GetDisplay(pos):
'''Gets display number (0=main display) for window position (pos). If pos outside all displays
returns None
'''
displays = np.array([list(wx.Display(i).GetGeometry()) for i in range(wx.Display.GetCount())])
for ip,display in enumerate(displays):
display[2:3] += display[0:1]
if (display[0] < pos[0] < display[2]) and (display[1] < pos[1] < display[3]):
return ip
return None
#### class definitions used for main GUI ######################################
[docs]
class MergeDialog(wx.Dialog):
''' HKL transformation & merge dialog
:param wx.Frame parent: reference to parent frame (or None)
:param data: HKLF data
'''
def __init__(self,parent,data):
wx.Dialog.__init__(self,parent,wx.ID_ANY,'Setup HKLF merge',
pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw!
self.data = data
self.Super = data[1]['Super']
if self.Super:
self.Trans = np.eye(4)
else:
self.Trans = np.eye(3)
self.Type = data[0]['Type']
self.Cent = 'noncentrosymmetric'
self.Laue = '1'
self.Class = 'triclinic'
self.Common = 'abc'
self.Smart = False
self.Draw()
def Draw(self):
def OnCent(event):
Obj = event.GetEventObject()
self.Cent = Obj.GetValue()
self.Laue = ''
wx.CallAfter(self.Draw)
def OnLaue(event):
Obj = event.GetEventObject()
self.Laue = Obj.GetValue()
wx.CallAfter(self.Draw)
def OnClass(event):
Obj = event.GetEventObject()
self.Class = Obj.GetValue()
self.Laue = ''
wx.CallAfter(self.Draw)
def OnCommon(event):
Obj = event.GetEventObject()
self.Common = Obj.GetValue()
self.Trans = commonTrans[self.Common]
wx.CallAfter(self.Draw)
def OnSmart(event):
self.Smart = not self.Smart
self.panel.Destroy()
self.panel = wx.Panel(self)
mainSizer = wx.BoxSizer(wx.VERTICAL)
MatSizer = wx.BoxSizer(wx.HORIZONTAL)
transSizer = wx.BoxSizer(wx.VERTICAL)
transSizer.Add(wx.StaticText(self.panel,label=" HKL Transformation matrix: M*H = H'"))
if self.Super:
Trmat = wx.FlexGridSizer(4,4,0,0)
else:
commonSizer = wx.BoxSizer(wx.HORIZONTAL)
commonSizer.Add(wx.StaticText(self.panel,label=' Common transformations: '),0,WACV)
common = wx.ComboBox(self.panel,value=self.Common,choices=commonNames[:-2], #not the last two!
style=wx.CB_READONLY|wx.CB_DROPDOWN)
common.Bind(wx.EVT_COMBOBOX,OnCommon)
commonSizer.Add(common,0,WACV)
transSizer.Add(commonSizer)
Trmat = wx.FlexGridSizer(3,3,0,0)
for iy,line in enumerate(self.Trans):
for ix,val in enumerate(line):
item = G2G.ValidatedTxtCtrl(self.panel,self.Trans[iy],ix,nDig=(10,3),size=(65,25))
Trmat.Add(item)
transSizer.Add(Trmat)
MatSizer.Add((10,0),0)
MatSizer.Add(transSizer)
mainSizer.Add(MatSizer)
laueClass = ['triclinic','monoclinic','orthorhombic','trigonal(H)','trigonal(R)','tetragonal','hexagonal','cubic']
centroLaue = {'triclinic':['-1',],'monoclinic':['2/m','1 1 2/m','2/m 1 1',],
'orthorhombic':['m m m',],'trigonal(H)':['-3','-3 m 1','-3 1 m',],'trigonal(R)':['-3','-3 m'],\
'tetragonal':['4/m','4/m m m',],'hexagonal':['6/m','6/m m m',],'cubic':['m 3','m 3 m']}
noncentroLaue = {'triclinic':['1',],'monoclinic':['2','2 1 1','1 1 2','m','m 1 1','1 1 m',],
'orthorhombic':['2 2 2','m m 2','m 2 m','2 m m',],
'trigonal(H)':['3','3 1 2','3 2 1','3 m 1','3 1 m',],'trigonal(R)':['3','3 m'],
'tetragonal':['4','-4','4 2 2','4 m m','-4 2 m','-4 m 2',], \
'hexagonal':['6','-6','6 2 2','6 m m','-6 m 2','-6 2 m',],'cubic':['2 3','4 3 2','-4 3 m']}
centChoice = ['noncentrosymmetric','centrosymmetric']
mainSizer.Add(wx.StaticText(self.panel,label=' Select Laue class for new lattice:'),0)
Class = wx.ComboBox(self.panel,value=self.Class,choices=laueClass,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Class.Bind(wx.EVT_COMBOBOX,OnClass)
mainSizer.Add(Class,0)
mainSizer.Add(wx.StaticText(self.panel,label=' Target Laue symmetry:'),0)
Cent = wx.ComboBox(self.panel,value=self.Cent,choices=centChoice,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Cent.Bind(wx.EVT_COMBOBOX,OnCent)
mergeSizer = wx.BoxSizer(wx.HORIZONTAL)
mergeSizer.Add(Cent,0,WACV)
mergeSizer.Add((10,0),0)
Choice = centroLaue[self.Class]
if 'non' in self.Cent:
Choice = noncentroLaue[self.Class]
Laue = wx.ComboBox(self.panel,value=self.Laue,choices=Choice,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Laue.Bind(wx.EVT_COMBOBOX,OnLaue)
mergeSizer.Add(Laue,0,WACV)
mainSizer.Add(mergeSizer)
if self.Type == 'SEC':
Smart = wx.CheckBox(self.panel,label=' Do smart merge for microED?')
Smart.Bind(wx.EVT_CHECKBOX,OnSmart)
mainSizer.Add(Smart,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)
if self.Laue:
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.Trans,self.Cent,self.Laue,self.Smart
def OnOk(self,event):
parent = self.GetParent()
if parent is not None: parent.Raise()
self.EndModal(wx.ID_OK)
def OnCancel(self,event):
parent = self.GetParent()
if parent is not None: parent.Raise()
self.EndModal(wx.ID_CANCEL)
[docs]
class HKLSortDialog(wx.Dialog):
''' HKL transformation & sort dialog - no merge
:param wx.Frame parent: reference to parent frame (or None)
:param data: HKLF data
'''
def __init__(self,parent,data):
wx.Dialog.__init__(self,parent,wx.ID_ANY,'Setup HKLF sort',
pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE)
self.panel = wx.Panel(self) #just a dummy - gets destroyed in Draw!
self.data = data
self.Super = data[1]['Super']
if self.Super:
self.Trans = np.eye(4)
else:
self.Trans = np.eye(3)
self.Type = data[0]['Type']
self.Cent = 'noncentrosymmetric'
self.Laue = '1'
self.Class = 'triclinic'
self.Common = 'abc'
self.Draw()
def Draw(self):
def OnCent(event):
Obj = event.GetEventObject()
self.Cent = Obj.GetValue()
self.Laue = ''
wx.CallAfter(self.Draw)
def OnLaue(event):
Obj = event.GetEventObject()
self.Laue = Obj.GetValue()
wx.CallAfter(self.Draw)
def OnClass(event):
Obj = event.GetEventObject()
self.Class = Obj.GetValue()
self.Laue = ''
wx.CallAfter(self.Draw)
def OnCommon(event):
Obj = event.GetEventObject()
self.Common = Obj.GetValue()
self.Trans = commonTrans[self.Common]
wx.CallAfter(self.Draw)
def OnSmart(event):
self.Smart = not self.Smart
self.panel.Destroy()
self.panel = wx.Panel(self)
mainSizer = wx.BoxSizer(wx.VERTICAL)
MatSizer = wx.BoxSizer(wx.HORIZONTAL)
transSizer = wx.BoxSizer(wx.VERTICAL)
transSizer.Add(wx.StaticText(self.panel,label=" HKL Transformation matrix: M*H = H'"))
if self.Super:
Trmat = wx.FlexGridSizer(4,4,0,0)
else:
commonSizer = wx.BoxSizer(wx.HORIZONTAL)
commonSizer.Add(wx.StaticText(self.panel,label=' Common transformations: '),0,WACV)
common = wx.ComboBox(self.panel,value=self.Common,choices=commonNames[:-2], #not the last two!
style=wx.CB_READONLY|wx.CB_DROPDOWN)
common.Bind(wx.EVT_COMBOBOX,OnCommon)
commonSizer.Add(common,0,WACV)
transSizer.Add(commonSizer)
Trmat = wx.FlexGridSizer(3,3,0,0)
for iy,line in enumerate(self.Trans):
for ix,val in enumerate(line):
item = G2G.ValidatedTxtCtrl(self.panel,self.Trans[iy],ix,nDig=(10,3),size=(65,25))
Trmat.Add(item)
transSizer.Add(Trmat)
MatSizer.Add((10,0),0)
MatSizer.Add(transSizer)
mainSizer.Add(MatSizer)
laueClass = ['triclinic','monoclinic','orthorhombic','trigonal(H)','trigonal(R)','tetragonal','hexagonal','cubic']
centroLaue = {'triclinic':['-1',],'monoclinic':['2/m','1 1 2/m','2/m 1 1',],
'orthorhombic':['m m m',],'trigonal(H)':['-3','-3 m 1','-3 1 m',],'trigonal(R)':['-3','-3 m'],\
'tetragonal':['4/m','4/m m m',],'hexagonal':['6/m','6/m m m',],'cubic':['m 3','m 3 m']}
noncentroLaue = {'triclinic':['1',],'monoclinic':['2','2 1 1','1 1 2','m','m 1 1','1 1 m',],
'orthorhombic':['2 2 2','m m 2','m 2 m','2 m m',],
'trigonal(H)':['3','3 1 2','3 2 1','3 m 1','3 1 m',],'trigonal(R)':['3','3 m'],
'tetragonal':['4','-4','4 2 2','4 m m','-4 2 m','-4 m 2',], \
'hexagonal':['6','-6','6 2 2','6 m m','-6 m 2','-6 2 m',],'cubic':['2 3','4 3 2','-4 3 m']}
centChoice = ['noncentrosymmetric','centrosymmetric']
mainSizer.Add(wx.StaticText(self.panel,label=' Select Laue class for new lattice:'),0)
Class = wx.ComboBox(self.panel,value=self.Class,choices=laueClass,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Class.Bind(wx.EVT_COMBOBOX,OnClass)
mainSizer.Add(Class,0)
mainSizer.Add(wx.StaticText(self.panel,label=' Target Laue symmetry:'),0)
Cent = wx.ComboBox(self.panel,value=self.Cent,choices=centChoice,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Cent.Bind(wx.EVT_COMBOBOX,OnCent)
sortSizer = wx.BoxSizer(wx.HORIZONTAL)
sortSizer.Add(Cent,0,WACV)
sortSizer.Add((10,0),0)
Choice = centroLaue[self.Class]
if 'non' in self.Cent:
Choice = noncentroLaue[self.Class]
Laue = wx.ComboBox(self.panel,value=self.Laue,choices=Choice,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
Laue.Bind(wx.EVT_COMBOBOX,OnLaue)
sortSizer.Add(Laue,0,WACV)
mainSizer.Add(sortSizer)
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)
if self.Laue:
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.Trans,self.Cent,self.Laue
def OnOk(self,event):
parent = self.GetParent()
if parent is not None: parent.Raise()
self.EndModal(wx.ID_OK)
def OnCancel(self,event):
parent = self.GetParent()
if parent is not None: parent.Raise()
self.EndModal(wx.ID_CANCEL)
[docs]
def GUIpatches():
'Misc fixes that only needs to be done when running a GUI'
try: # patch for LANG environment var problem on occasional OSX machines
import locale
locale.getdefaultlocale()
except ValueError:
print('Fixing location (see https://github.com/matplotlib/matplotlib/issues/5420.)')
os.environ['LC_ALL'] = 'en_US.UTF-8'
locale.getdefaultlocale()
# PATCH: for Mavericks (OS X 10.9.x), wx produces an annoying warning about LucidaGrandeUI.
# In case stderr has been suppressed there, redirect python error output to stdout. Nobody
# else should care much about this.
sys.stderr = sys.stdout
[docs]
def convVersion(version):
'''Convert a version string ("x", "x.y", "x.y.z") into a series of ints.
:returns: [i0, i1, i2] where None is used if a value is not specified
and 0 is used if a field cannot be parsed.
'''
vIntList = [None,None,None]
for i,v in enumerate(version.split('.')):
if i >= 3: break
if len(v) == 0: break
v = list(filter(None,re.split('(\\d+)',v)))[0] # conv '1b2' to '1'
try:
vIntList[i] = int(v)
except:
vIntList[i] = 0
return vIntList
[docs]
def compareVersions(version1,version2):
'''Compare two version strings ("x", "x.y", "x.y.z")
Note that '3.' matches '3.1', and '3.0' matches '3.0.1'
but '3.0.0' does not match '3.0.1'
:returns: 0 if the versions match, -1 if version1 < version2,
or 1 if version1 > version2
'''
for v1,v2 in zip(convVersion(version1),convVersion(version2)):
if v1 is None or v2 is None:
return 0
if v1 < v2: return -1
if v1 > v2: return 1
return 0
# tabulate package versions that users should be warned about
versionDict = {}
'''Variable versionDict is used to designate versions of packages that
should generate warnings or error messages.
* ``versionDict['tooOld']`` is a dict with module versions that are too old and are
known to cause serious errors
* ``versionDict['tooOldWarn']`` is a dict with module versions that are
significantly out of date and should be updated, but will probably function OK.
* ``versionDict['badVersionWarn']`` is a dict of with lists of package
versions that are known to have bugs. One should select an older or
newer version of the package.
* ``versionDict['tooNewUntested']`` is a dict with module versions that have
not been tested but there is no reason to expect problems
* ``versionDict['tooNewWarn']`` is a dict with module versions that have not
been tested but there are concerns that problems may occur.
**Packages/versions to be avoided**
* Python:
* We are no longer supporting Python <=2.7 and <=3.6. Jan. 2023: We will soon start
removing code that is specific to Python 2.7.
* A problem has been noted with wx4.0.7.post2 with Python 3.10 that we can't
yet duplicate (2/4/22).
* We anticipate that Python 3.10+ will flag code that previously worked fine,
because it reports errors where we pass a floating point number to a
wxpython routine that expects a int value. We are fixing these as we learn about them.
* wxPython:
* <=2.x.x: while most of GSAS-II has been written to be
compatible with older versions of wxpython, we are now testing with
version 4.0+ only.
* wxpython 3.0 is pretty similar to 4.0, but we did see
some issues with Python 3.x.
* wxpython 4.1 has some serious internal bugs with Python 3.10+ so we recommend
4.2+ for compatibility with newer Python versions.
* 4.2.0 has a problem on MacOS where buttons w/default size are not displayed properly.
(see https://github.com/wxWidgets/Phoenix/issues/2319). Worked around (mostly?) in our code.
* 4.2.5 has a problem on MacOS where FileDialog is failing in SaveAs.
* Matplotlib:
* 1.x: there have been significant API changes since these versions and
significant graphics errors will occur.
* 3.1.x and 3.2.x: these versions have a known bug for plotting
3-D surfaces, such as microstrain vs crystal axes. The plots may appear
distorted as the lengths of x, y & z will not be constrained as equal.
Preferably use 3.0.x as 3.3.x is not fully tested.
* between 3.3.x vs 3.6.x there seems to be a change in how 3d graphics
are handled; we seem to have this fixed, but not sure how <3.3 will work.
Since 3.1 & 3.2 have problems; warn w/mpl <3.3.0
* numpy:
* 1.16.0: produces .gpx files that are not compatible with older
version numpy versions. This is a pretty outmoded version; upgrade.
'''
# add comments above when changing anything below
versionDict['tooOld'] = {'matplotlib': '2.', 'Python':'2.7'}
'modules that will certainly fail'
versionDict['tooOldWarn'] = {'wx': '3.99','Python':'3.6','matplotlib': '3.2.99'}
'modules that may fail and should be updated'
versionDict['badVersionWarn'] = {'numpy':['1.16.0'],
'matplotlib': ['3.1','3.2'],
'wx':['4.1']}
'versions of modules that are known to have bugs'
versionDict['tooNewWarn'] = {'wx':'4.2.5'}
'module versions newer than what we have tested & where problems are suspected'
versionDict['tooNewUntested'] = {'Python':'3.14','wx': '4.3'}
'module versions newer than what we have tested but no problems are suspected'
[docs]
def ShowVersions():
'''Show the versions of all GUI-required Python packages, etc.
'''
import numpy as np
import scipy as sp
import wx
import matplotlib as mpl
import OpenGL as ogl
pkgList = [('Python',None), ('wx',wx), ('matplotlib', mpl), ('numpy',np),
('scipy',sp), ('OpenGL',ogl)]
if GSASIIpath.GetConfigValue('debug'):
try:
import IPython
pkgList.append(('IPython',IPython))
except:
pass
print ("Python/module versions loaded:")
version = '?'
versionDict['errors'] = ''
warn = False
for s,m in pkgList:
msg = ''
if s == 'Python':
pkgver = platform.python_version()
prefix = ''
msg = "from {}. ".format(sys.executable)
else:
pkgver = m.__version__
prefix = 'Package '
if s in versionDict['tooOld']:
match = compareVersions(pkgver,versionDict['tooOld'][s])
if match <= 0:
if msg: msg += ' -- '
msg += "Too old, problems are likely"
warn = True
if versionDict['errors']: versionDict['errors'] += '\n'
versionDict['errors'] += prefix + '{} version {} is too old for GSAS-II. An update is required. '.format(s,pkgver)
if s in versionDict['tooOldWarn']:
match = compareVersions(pkgver,versionDict['tooOldWarn'][s])
if match <= 0:
msg += "Version can cause problems"
warn = True
if s in versionDict['badVersionWarn']:
for v in versionDict['badVersionWarn'][s]:
if compareVersions(pkgver,v) == 0:
msg += "Version is known to be buggy"
warn = True
break
if s in versionDict['tooNewUntested'] and not warn:
match = compareVersions(pkgver,versionDict['tooNewUntested'][s])
if match >= 0:
msg += "\n "
msg += "New untested version; please keep us posted"
warn = True
if s in versionDict['tooNewWarn'] and not warn:
match = compareVersions(pkgver,versionDict['tooNewWarn'][s])
if match >= 0:
msg += "Tests incomplete w/suspected bugs; Please report problems"
print(" {:12s}{} {}".format(s+':',pkgver,msg))
Image = None
try:
from PIL import Image
except ImportError:
try:
import Image
except ImportError:
pass
if Image is None:
print ("Image module not present; Note that PIL (Python Imaging Library) or pillow is needed for some image operations")
G2fil.NeededPackage({'Saving plot images':['pillow']})
else:
# version # can be in various places, try standard dunderscore first
for ver in '__version__','VERSION','PILLOW_VERSION':
if hasattr(Image,ver):
try:
version = eval('Image.'+ver)
break
except:
pass
print (" Image: %s (PIL or Pillow)"%version)
print (" Platform: %s %s %s"%(sys.platform,platform.architecture()[0],platform.machine()))
try:
import mkl
print (" Max threads:%s"%mkl.get_max_threads())
except:
pass
# warn if problems with Git
if GSASIIpath.HowIsG2Installed().startswith('git'):
try:
import git
git
except ImportError as msg:
if 'Failed to initialize' in msg.msg:
print('The gitpython package is unable to locate a git installation.')
print('See https://gsas-ii.readthedocs.io/en/latest/packages.html for more information.')
elif 'No module' in msg.msg:
print('Warning: Python gitpython module not installed')
else:
print(f'gitpython failed to import, but why? Error:\n{msg}')
print('Note: git and gitpython are required for GSAS-II to self-update')
except Exception as msg:
print(f'git import failed with unexpected error:\n{msg}')
print('Note: git and gitpython are required for GSAS-II to self-update')
# warn if problems with requests package
try:
import requests
requests
except:
print('Warning: Python requests package not installed (required for\n'+
' GSAS-II to access web pages or self-install binary modules)')
G2fil.NeededPackage({'Accessing web resources':['requests']})
try:
import pybaselines.whittaker
pybaselines.whittaker
except:
G2fil.NeededPackage({'Auto background capability':['pybaselines']})
if not GSASIIpath.TestSPG():
path2repo = os.path.dirname(GSASIIpath.path2GSAS2)
installLoc = os.path.join(path2repo,'GSASII-bin')
# TODO: note new code in gitstrap.py that avoids use of getGitBinaryLoc
# when the desired binary exists. Better to do lookup with
# getGitBinaryLoc only when an exact match is not available
binarydir = GSASIIpath.getGitBinaryLoc(verbose=True)
if not binarydir:
versionDict['errors'] += 'GSAS-II does not have a binaries built for this version of Python. You will need to install a supported Python version or build binaries yourself. See https://gsas-ii.readthedocs.io/en/latest/packages.html#python-requirements\n\n'
else:
msg = 'You do not have binaries installed for GSAS-II. Do you want to have them installed now?'
dlg = wx.MessageDialog(None, msg,'Install GSAS-II binaries?',
wx.YES_NO|wx.ICON_QUESTION)
result = wx.ID_NO
try:
result = dlg.ShowModal()
finally:
dlg.Destroy()
if result != wx.ID_NO:
try:
GSASIIpath.InstallGitBinary(binarydir, installLoc,
nameByVersion=True)
msg = f'Binaries installed from {binarydir} to {installLoc}\n'
print(msg)
GSASIIpath.BinaryPathFailed = False
GSASIIpath.SetBinaryPath(True)
except:
print('Download failed, sorry')
if not GSASIIpath.pathhack_TestSPG(GSASIIpath.binaryPath):
versionDict['errors'] += 'Error accessing GSAS-II binary files. Only limited functionality available.'
else:
# TODO: use GSASIIversion.txt (in binary directory) to see
# if version is recent enough rather than use presence of convcell[.exe]
if GSASIIpath.binaryPath:
prog = os.path.join(GSASIIpath.binaryPath,"convcell")
else:
prog = 'convcell'
if sys.platform.startswith('win'):
prog += '.exe'
if not shutil.which(prog):
versionDict['errors'] += 'NIST*LATTICE binaries not found. You may have old binaries or an installation problem. If you built these binaries, rerun scons or meson'
if warn:
print(70*'=')
print('''You are running GSAS-II in a Python environment with either untested
or known to be problematic packages, as noted above. If you are seeing
problems in running GSAS-II you are suggested to install an additional
copy of GSAS-II from one of the gsas2full installers (see
https://GSASII.github.io/). This will provide a working Python
environment as well as the latest GSAS-II version.
For information on GSAS-II package requirements see
https://gsas-ii.readthedocs.io/en/latest/packages.html''')
print(70*'=','\n')
print(GSASIIpath.getG2VersionInfo())
[docs]
def TestOldVersions():
'''Test the versions of required Python packages, etc.
Returns a non-empty text string if there are problems.
'''
import numpy as np
import scipy as sp
import wx
import matplotlib as mpl
import OpenGL as ogl
warnmsg = ''
errmsg = ''
for s,m in [('Python',None), ('wx',wx), ('matplotlib', mpl), ('numpy',np),
('scipy',sp), ('OpenGL',ogl)]:
if s == 'Python':
pkgver = platform.python_version()
prefix = ''
else:
pkgver = m.__version__
prefix = 'Package '+s
if s in versionDict['tooOld']:
match = compareVersions(pkgver,versionDict['tooOld'][s])
if match <= 0:
if errmsg: errmsg += '\n'
errmsg += prefix + '{} version {} is too old to run GSAS-II.'.format(s,pkgver)
if s in versionDict['tooOldWarn']:
match = compareVersions(pkgver,versionDict['tooOldWarn'][s])
if match <= 0:
if warnmsg: warnmsg += '\n'
warnmsg += prefix + '{} version {} is likely too old for GSAS-II.'.format(s,pkgver)
if s in versionDict['badVersionWarn']:
for v in versionDict['badVersionWarn'][s]:
if compareVersions(pkgver,v) == 0:
if errmsg: errmsg += '\n'
errmsg += prefix + '{} version {} causes problems with GSAS-II.'.format(s,pkgver)
break
return errmsg,warnmsg
#### GUI creation #############################################################
[docs]
def GSASIImain(application):
'''Start up the GSAS-II GUI'''
ShowVersions()
GUIpatches()
if versionDict['errors']:
msg = (
'\n\nGSAS-II will attempt to start, but this problem needs '+
'to be fixed for proper operation. Usually, the simplest solution '+
'will be to reinstall GSAS-II.'+
'\nSee https://GSASII.github.io')
dlg = wx.MessageDialog(None, versionDict['errors']+msg,
'GSAS-II Installation Problem', wx.OK)
try:
dlg.ShowModal()
finally:
dlg.Destroy()
msg = ''
#sys.exit()
elif platform.python_version_tuple()[0] == '2' and int(platform.python_version_tuple()[1]) < 7:
msg = 'GSAS-II works best with Python version 3.7 or later.\nThis version is way too old: '+sys.version.split()[0]
elif platform.python_version_tuple()[0] == '3' and int(platform.python_version_tuple()[1]) < 6:
msg = 'GSAS-II works best with Python version 3.7 or later.\nThis version is too old: '+sys.version.split()[0]
else:
msg = ''
if msg:
dlg = wx.MessageDialog(None, msg, 'Python version error', wx.OK)
try:
dlg.ShowModal()
finally:
dlg.Destroy()
sys.exit()
application.main = GSASII(None) # application.main is the main wx.Frame (G2frame in most places)
application.SetTopWindow(application.main)
# save the current package versions
application.main.PackageVersions = G2fil.get_python_versions([wx, mpl, np, sp, ogl])
try:
application.SetAppDisplayName('GSAS-II')
except:
pass
#application.GetTopWindow().SendSizeEvent()
application.GetTopWindow().Show(True)
application.main.UpdateTask = GSASIIpath.GetRepoUpdatesInBackground()
if GSASIIpath.GetConfigValue('debug'):
cmdfile = os.path.join(GSASIIpath.path2GSAS2,'debug_startup.py')
if os.path.exists(cmdfile):
print(f'executing debug commands from {cmdfile}')
txt = open(cmdfile,'r').read()
def exectxt():
# print(txt)
exec(txt)
wx.CallLater(100,exectxt)
#### Create main frame (window) for GUI; main menu items here #######################################
[docs]
class GSASII(wx.Frame):
'''Define the main GSAS-II frame and its associated menu items.
:param parent: reference to parent application
'''
def _Add_FileMenuItems(self, parent):
'''Add items to File menu
'''
item = parent.Append(wx.ID_ANY,'&Open project...\tCtrl+O','Open a GSAS-II project (.gpx) file')
self.Bind(wx.EVT_MENU, self.OnFileOpen, id=item.GetId())
# if sys.platform == "darwin":
item = parent.Append(wx.ID_ANY,'&Open in new window...','Open a GSAS-II project (.gpx) file in a separate process')
self.Bind(wx.EVT_MENU, self.OnNewGSASII, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Reopen recent...\tCtrl+E','Reopen a previously used GSAS-II project (.gpx) file')
self.Bind(wx.EVT_MENU, self.OnFileReopen, id=item.GetId())
item = parent.Append(wx.ID_ANY,'&Open w/project browser\tCtrl+B','Use project browser to a GSAS-II project (.gpx) file')
self.Bind(wx.EVT_MENU, self.OnFileBrowse, id=item.GetId())
item = parent.Append(wx.ID_ANY,'&Save project\tCtrl+S','Save project under current name')
self.Bind(wx.EVT_MENU, self.OnFileSave, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Save project as...','Save current project to new file')
self.Bind(wx.EVT_MENU, self.OnFileSaveas, id=item.GetId())
item = parent.Append(wx.ID_ANY,'&New project','Create empty new project, saving current is optional')
self.Bind(wx.EVT_MENU, self.OnFileClose, id=item.GetId())
item = parent.Append(wx.ID_PREFERENCES,"&Preferences",'')
self.Bind(wx.EVT_MENU, self.OnPreferences, item)
if GSASIIpath.GetConfigValue('debug'):
try:
import IPython
IPython
item = parent.Append(wx.ID_ANY,"IPython Console",'')
self.Bind(wx.EVT_MENU,
lambda event:GSASIIpath.IPyBreak(),
item)
except ImportError:
pass
def OnwxInspect(event):
import wx.lib.inspection as wxeye
wxeye.InspectionTool().Show()
item = parent.Append(wx.ID_ANY,"wx inspection tool",'')
self.Bind(wx.EVT_MENU, OnwxInspect, item)
item = parent.Append(wx.ID_ANY,'Reopen current\tCtrl+0','Reread the current GSAS-II project (.gpx) file')
self.Bind(wx.EVT_MENU, self.OnFileReread, id=item.GetId())
# if Git install assume GSAS-II was not installed into Python
if GSASIIpath.HowIsG2Installed().startswith('git'):
item = parent.Append(wx.ID_ANY,"Install GSASIIscriptable shortcut",'')
self.Bind(wx.EVT_MENU,
lambda event: GSASIIpath.makeScriptShortcut(),
item)
item = parent.Append(wx.ID_EXIT,'Exit\tALT+F4','Exit from GSAS-II')
self.Bind(wx.EVT_MENU, self.ExitMain, id=item.GetId())
def _Add_DataMenuItems(self,parent):
'''Add items to Data menu
'''
#(7/2025) next duplicated in Import menu; patch: remove this someday
item = parent.Append(wx.ID_ANY,'Read Powder Pattern Peaks...','')
self.Bind(wx.EVT_MENU, self.OnReadPowderPeaks, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Sum or Average powder data','')
self.Bind(wx.EVT_MENU, self.OnPwdrSum, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Sum image data','')
self.Bind(wx.EVT_MENU, self.OnImageSum, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Add new phase','')
self.Bind(wx.EVT_MENU, self.OnAddPhase, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Delete phase entries','')
self.Bind(wx.EVT_MENU, self.OnDeletePhase, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Rename data entry',
'Rename the selected data tree item (PWDR, HKLF or IMG)')
self.Bind(wx.EVT_MENU, self.OnRenameData, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Delete data entries',
'Delete selected data items from data tree')
self.Bind(wx.EVT_MENU, self.OnDataDelete, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Delete plots','Delete selected plots')
self.Bind(wx.EVT_MENU, self.OnPlotDelete, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Delete sequential result entries','')
self.Bind(wx.EVT_MENU, self.OnDeleteSequential, id=item.GetId())
expandmenu = wx.Menu()
item = parent.AppendSubMenu(expandmenu,'Expand tree items',
'Expand items of type in GSAS-II data tree')
for s in 'all','IMG','PWDR','PDF','HKLF','SASD','REFD':
if s == 'all':
help = 'Expand all items in GSAS-II data tree'
else:
help = 'Expand '+s+' type items in GSAS-II data tree'
item = expandmenu.Append(wx.ID_ANY,s,help)
self.Bind(wx.EVT_MENU,self.ExpandAll,id=item.GetId())
movemenu = wx.Menu()
item = parent.AppendSubMenu(movemenu,'Move tree items',
'Move items of type items to end of GSAS-II data tree')
for s in 'IMG','PWDR','PDF','HKLF','SASD','REFD','Phase':
help = 'Move '+s+' type items to end of GSAS-II data tree'
item = movemenu.Append(wx.ID_ANY,s,help)
self.Bind(wx.EVT_MENU,self.MoveTreeItems,id=item.GetId())
def _Add_CalculateMenuItems(self,parent):
'''Add items to the Calculate menu
'''
item = parent.Append(wx.ID_ANY,'Setup PDFs','Create PDF tree entries for selected powder patterns')
self.MakePDF.append(item)
self.Bind(wx.EVT_MENU, self.OnMakePDFs, id=item.GetId())
item = parent.Append(wx.ID_ANY,'&View LS parms\tCTRL+L','View least squares parameters')
self.Bind(wx.EVT_MENU, self.OnShowLSParms, id=item.GetId())
item = parent.Append(wx.ID_ANY,'&Refine\tCTRL+R','Perform a refinement')
if len(self.Refine): # extend state for new menus to match main
state = self.Refine[0].IsEnabled()
else:
state = False
item.Enable(state)
self.Refine.append(item)
self.Bind(wx.EVT_MENU, self.OnRefine, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Compute partials','Record the contribution from each phase')
self.Refine.append(item)
item.Enable(state) # disabled during sequential fits
self.Bind(wx.EVT_MENU, self.OnRefinePartials, id=item.GetId())
item = parent.Append(wx.ID_ANY,'&Parameter Impact\tCTRL+I','Perform a derivative calculation')
self.Bind(wx.EVT_MENU, self.OnDerivCalc, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Evaluate expression and s.u.','Perform uncertainty analysis on an expression of GSAS-II parameters')
self.Bind(wx.EVT_MENU, self.OnExpressionCalc, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Setup Cluster Analysis','Setup Cluster Analysis')
self.Bind(wx.EVT_MENU, self.OnClusterAnalysis, id=item.GetId())
item = parent.Append(wx.ID_ANY,'&Run Fprime','X-ray resonant scattering')
self.Bind(wx.EVT_MENU, self.OnRunFprime, id=item.GetId())
item = parent.Append(wx.ID_ANY,'&Run Absorb','x-ray absorption')
self.Bind(wx.EVT_MENU, self.OnRunAbsorb, id=item.GetId())
item = parent.Append(wx.ID_ANY,'&Run PlotXNFF','Plot X-ray, neutron & magnetic form factors')
self.Bind(wx.EVT_MENU, self.OnRunPlotXNFF, id=item.GetId())
# if GSASIIpath.GetConfigValue('debug'): # allow exceptions for debugging
# item = parent.Append(help='', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,
# text='tree test')
# self.Bind(wx.EVT_MENU, self.TreeTest, id=item.GetId())
def _init_Imports(self):
'''import all the G2phase*.py & G2sfact*.py & G2pwd*.py files that
are found in the path
'''
self.ImportPhaseReaderlist = G2fil.LoadImportRoutines('phase','Phase')
self.ImportSfactReaderlist = G2fil.LoadImportRoutines('sfact','Struct_Factor')
self.ImportPowderReaderlist = G2fil.LoadImportRoutines('pwd','Powder_Data')
self.ImportSmallAngleReaderlist = G2fil.LoadImportRoutines('sad','SmallAngle_Data')
self.ImportReflectometryReaderlist = G2fil.LoadImportRoutines('rfd','Reflectometry_Data')
self.ImportPDFReaderlist = G2fil.LoadImportRoutines('pdf','PDF_Data')
self.ImportImageReaderlist = G2fil.LoadImportRoutines('img','Images')
self.ImportMenuId = {}
msgs = G2fil.ImportErrorMsg()
if msgs:
print(f'Note: {len(msgs)} importer(s) could not be installed. See the'+
'\n "Import->Show importer error(s)" menu command for more information')
[docs]
def testSeqRefineMode(self):
'''Returns the list of histograms included in a sequential refinement or
an empty list if a standard (non-sequential) refinement.
Also sets Menu item status depending on mode
'''
cId = GetGPXtreeItemId(self,self.root, 'Controls')
if cId:
controls = self.GPXtree.GetItemPyData(cId)
seqSetting = controls.get('Seq Data',[])
else:
seqSetting = None
for item in self.Refine:
if 'Le Bail' in item.GetItemLabel() or 'partials' in item.GetItemLabel() :
item.Enable(not seqSetting)
elif seqSetting:
item.SetItemLabel('Se&quential refine\tCtrl+R') #might fail on old wx
else:
item.SetItemLabel('&Refine\tCtrl+R') #might fail on old wx
if seqSetting:
seqMode = True
else:
seqMode = False
for menu,Id in self.ExportSeq:
menu.Enable(Id,seqMode)
for menu,Id in self.ExportNonSeq:
menu.Enable(Id,not seqMode)
return seqSetting
[docs]
def PreviewFile(self,filename):
'utility to confirm we have the right file'
fp = open(filename,'r')
rdmsg = u'File '+ filename +u' begins:\n\n'
try:
rdmsg += fp.read(80)
rdmsg += '\n\nDo you want to read this file?'
except UnicodeDecodeError:
rdmsg = None
fp.close()
if rdmsg is None or not all([ord(c) < 128 and ord(c) != 0 for c in rdmsg]): # show only if ASCII
rdmsg = u'File '+ filename +u' is a binary file. Do you want to read this file?'
# it would be better to use something that
# would resize better, but this will do for now
dlg = wx.MessageDialog(self, rdmsg,'Is this the file you want?',wx.YES_NO|wx.ICON_QUESTION)
dlg.SetSize((700,300)) # does not resize on Mac
result = wx.ID_NO
try:
result = dlg.ShowModal()
finally:
dlg.Destroy()
if result == wx.ID_NO: return True
return False
[docs]
def OnImportGeneric(self,reader,readerlist,label,multiple=False,
usedRanIdList=[],Preview=True,load2Tree=False,filename=None):
'''Used for all imports from GUI, including Phases, datasets, images...
N.B. The code here is largely duplicated in
:func:`GSASIIscriptable:import_generic` so any changes made here
need to be duplicated there, too.
Called from :meth:`GSASII.OnImportPhase`, :meth:`GSASII.OnImportImage`,
:meth:`GSASII.OnImportSfact`, :meth:`GSASII.OnImportPowder`,
:meth:`GSASII.OnImportSmallAngle` and :meth:'GSASII.OnImportReflectometry`
Uses reader_objects subclassed from :class:`GSASIIobj.ImportPhase`,
:class:`GSASIIobj.ImportStructFactor`,
:class:`GSASIIobj.ImportPowderData`,
:class:`GSASIIobj.ImportSmallAngleData`
:class:`GSASIIobj.ImportReflectometryData` or
:class:`GSASIIobj.ImportImage`.
If a specific reader is specified, only that method will be called,
but if no reader is specified, every one that is potentially
compatible (by file extension) will be tried on the file(s)
selected in the Open File dialog.
:param reader_object reader: This will be a reference to
a particular object to be used to read a file or None,
if every appropriate reader should be used.
:param list readerlist: a list of reader objects appropriate for
the current read attempt. At present, this will be either
self.ImportPhaseReaderlist, self.ImportSfactReaderlist
self.ImportPowderReaderlist or self.ImportImageReaderlist
(defined in _init_Imports from the files found in the path),
but in theory this list could be tailored.
Used only when reader is None.
:param str label: string to place on the open file dialog:
Open `label` input file
:param bool multiple: True if multiple files can be selected
in the file dialog. False is default. At present True is used
only for reading of powder data.
:param list usedRanIdList: an optional list of random Ids that
have been used and should not be reused
:param bool Preview: indicates if a preview of the file should
be shown. Default is True, but set to False for image files
which are all binary.
:param bool load2Tree: indicates if the file should be loaded
into the data tree immediately (used for images only). True
only when called from :meth:`OnImportImage`; causes return
value to change to a list of True values rather than
reader objects.
:param str filename: a filename, used only for debugging
:returns: a list of reader objects (rd_list) that were able
to read the specified file(s). This list may be empty.
'''
self.lastimport = ''
self.zipfile = None
singlereader = True
cleanupList = []
if reader is None:
singlereader = False
multiple = False
#print "use all formats"
choices = "any file (*.*)|*.*"
choices += "|zip archive (.zip)|*.zip"
extdict = {}
# compile a list of allowed extensions
for rd in readerlist:
fmt = rd.formatName
for extn in rd.extensionlist:
if not extdict.get(extn): extdict[extn] = []
extdict[extn] += [fmt,]
for extn in sorted(extdict.keys(),key=lambda k: k.lower()):
fmt = ''
for f in extdict[extn]:
if fmt != "": fmt += ', '
fmt += f
choices += "|" + fmt + " file (*" + extn + ")|*" + extn
else:
readerlist = [reader,]
# compile a list of allowed extensions
choices = reader.formatName + " file ("
w = ""
for extn in reader.extensionlist:
if w != "": w += ";"
w += "*" + extn
choices += w + ")|" + w
choices += "|zip archive (.zip)|*.zip"
if not reader.strictExtension:
choices += "|any file (*.*)|*.*"
# get the file(s)
if multiple:
mode = wx.FD_OPEN|wx.FD_MULTIPLE
else:
mode = wx.FD_OPEN
if len(readerlist) > 1:
typ = ' (type to be guessed)'
else:
typ = ' (type '+readerlist[0].formatName+')'
if filename:
filelist = [filename,]
else:
filelist = G2G.GetImportFile(self,message="Choose "+label+" input file"+typ,
defaultFile="",wildcard=choices,style=mode)
rd_list = []
filelist1 = []
for filename in filelist:
# is this a non-zarr zip file?
ext = os.path.splitext(filename)[1].lower()
if ext == '.zip' and '.zarr.zip' not in filename.lower():
extractedfiles = G2G.ExtractFileFromZip(
filename,parent=self,msg=f'Reading {label} file(s)\n\n',
multipleselect=True)
if extractedfiles is None: continue # error or Cancel
if extractedfiles != filename:
self.zipfile = filename # save zip name
filelist1 += extractedfiles
txt = '\n\t'.join(extractedfiles)
print(f"Created temporary files\n\t{txt}")
cleanupList += extractedfiles
continue
filelist1.append(filename)
filelist = filelist1
Start = True #1st time read - clear selections below
for filename in filelist:
# is this a zip file?
ext = os.path.splitext(filename)[1].lower()
if ext == '.zip' and '.zarr.zip' not in filename.lower():
# if os.path.splitext(filename)[1].lower() == '.zip':
extractedfile = G2G.ExtractFileFromZip(filename,parent=self,
msg=f'Reading a {label} file\n\n')
if extractedfile is None: continue # error or Cancel
if extractedfile != filename:
filename,self.zipfile = extractedfile,filename # now use the file that was created
print(f"Created temporary file {extractedfile}")
cleanupList += [extractedfile]
# determine which formats are compatible with this file
primaryReaders = []
secondaryReaders = []
for rd in readerlist:
flag = rd.ExtensionValidator(filename)
if flag is None:
secondaryReaders.append(rd)
elif flag:
primaryReaders.append(rd)
if len(secondaryReaders) + len(primaryReaders) == 0 and reader:
self.ErrorDialog('Not supported','The selected reader cannot read file '+filename)
continue
elif len(secondaryReaders) + len(primaryReaders) == 0:
self.ErrorDialog('No Format','No matching format for file '+filename)
continue
fp = None
msg = ''
if len(filelist) == 1 and Preview:
if self.PreviewFile(filename):
G2fil.CleanupFromZip(label,cleanupList)
return []
self.lastimport = filename # this is probably not what I want to do -- it saves only the
# last name in a series. See rd.readfilename for a better name.
# try the file first with Readers that specify the
# file's extension and later with ones that merely allow it
errorReport = ''
for rd in primaryReaders+secondaryReaders:
if Start: #clear old bank selections to allow new ones to be selected by user
rd.selections = []
rd.dnames = []
rd.ReInitialize() # purge anything from a previous read
rd.errors = "" # clear out any old errors
if not rd.ContentsValidator(filename): # rejected on cursory check
errorReport += "\n "+rd.formatName + ' validator error'
if rd.errors:
errorReport += ': '+rd.errors
continue
if len(rd.selections)>1 and Start:
dlg = G2G.G2MultiChoiceDialog(self,'Dataset Selector','Select data to read from the list below',rd.dnames)
if dlg.ShowModal() == wx.ID_OK:
rd.selections = dlg.GetSelections()
Start = False
dlg.Destroy()
repeat = True
rdbuffer = {} # create temporary storage for file reader
block = 0
while repeat: # loop if the reader asks for another pass on the file
block += 1
repeat = False
rd.objname = os.path.basename(filename)
flag = False
if GSASIIpath.GetConfigValue('debug'): # allow exceptions for debugging
flag = rd.Reader(filename,self,buffer=rdbuffer,blocknum=block,
usedRanIdList=usedRanIdList,)
else:
try:
flag = rd.Reader(filename,self,buffer=rdbuffer,
blocknum=block,usedRanIdList=usedRanIdList,)
except rd.ImportException as detail:
rd.errors += "\n Read exception: "+str(detail)
except Exception as detail:
import traceback
rd.errors += "\n Unhandled read exception: "+str(detail)
rd.errors += "\n Traceback info:\n"+str(traceback.format_exc())
if flag: # this read succeeded
if rd.SciPy: #was default read by scipy; needs 1 time fixes
G2IO.EditImageParms(self,rd.Data,rd.Comments,rd.Image,filename)
rd.SciPy = False
rd.readfilename = filename
if load2Tree: #images only
if rd.repeatcount == 1 and not rd.repeat: # skip image number if only one in set
rd.Data['ImageTag'] = None
elif 'imagemap' in rdbuffer:
# if there is an image map, save the entry there rather than
# a simple number (HDF5 only at present)
rd.Data['ImageTag'] = rdbuffer['imagemap'][rd.imageEntry]
else:
rd.Data['ImageTag'] = rd.repeatcount
rd.Data['formatName'] = rd.formatName
if rd.sumfile:
rd.readfilename = rd.sumfile
# Load generic metadata, as configured
G2fil.GetColumnMetadata(rd)
G2IO.LoadImage2Tree(rd.readfilename,self,rd.Comments,rd.Data,rd.Npix,rd.Image)
rd_list.append(True) # save a stub the result before it is written over
del rd.Image
else:
rd_list.append(copy.deepcopy(rd)) # save the result before it is written over
if rd.repeat:
repeat = True
continue
errorReport += '\n'+rd.formatName + ' read error'
if rd.errors:
errorReport += ': '+rd.errors
if rd_list: # read succeeded, was there a warning or any errors?
if rd.warnings:
# self.ErrorDialog('Read Warning','The '+ rd.formatName+
# ' reader reported warning message(s):\n\n'+rd.warnings)
msg = f'The {rd.formatName} reader reported warning message(s):\n\n{rd.warnings}'
print(msg)
G2G.ShowScrolledInfo(self,msg,header='Read Warning')
break # success in reading, try no further
else:
if singlereader:
msg += '\n'+rd.warnings
print(u'The '+ rd.formatName+u' reader was not able to read file '+filename+msg)
try:
print(u'\n\nError message(s):\n\t'+errorReport)
except:
pass
self.ErrorDialog('Read Error','The '+ rd.formatName+
' reader was not able to read file '+filename+msg)
else:
print('No reader was able to read file '+filename+msg)
try:
print('\n\nError message(s):\n\t'+errorReport)
except:
pass
self.ErrorDialog('Read Error','No reader was able to read file '+filename+msg)
if fp: fp.close()
G2fil.CleanupFromZip(label,cleanupList)
return rd_list
def _Add_ImportMenu_Phase(self,parent):
'''configure the Import Phase menus accord to the readers found in _init_Imports
'''
submenu = wx.Menu()
item = parent.AppendSubMenu(submenu,'Phase','Import phase data')
for reader in self.ImportPhaseReaderlist:
item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
self.ImportMenuId[item.GetId()] = reader
self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId())
item = submenu.Append(wx.ID_ANY,'guess format from file','Import phase data, use file to try to determine format')
self.Bind(wx.EVT_MENU, self.OnImportPhase, id=item.GetId())
[docs]
def OnImportPhase(self,event):
'''Called in response to an Import/Phase/... menu item
to read phase information.
dict self.ImportMenuId is used to look up the specific
reader item associated with the menu item, which will be
None for the last menu item, which is the "guess" option
where all appropriate formats will be tried.
N.B. The code here is largely duplicated in
:mod:`GSASIIscriptable` so any changes made here
need to be duplicated there, too.
'''
# look up which format was requested
reqrdr = self.ImportMenuId.get(event.GetId())
# make a list of phase names, ranId's and the histograms used in those phases
phaseRIdList,usedHistograms = self.GetPhaseInfofromTree()
phaseNameList = list(usedHistograms.keys()) # phase names in use
usedHKLFhists = [] # used single-crystal histograms
for p in usedHistograms:
for h in usedHistograms[p]:
if h.startswith('HKLF ') and h not in usedHKLFhists:
usedHKLFhists.append(h)
rdlist = self.OnImportGeneric(reqrdr,self.ImportPhaseReaderlist,
'phase',usedRanIdList=phaseRIdList)
if len(rdlist) == 0: return
# for now rdlist is only expected to have one element
# but below will allow multiple phases to be imported
# if ever the import routines ever implement multiple phase reads.
self.CheckNotebook()
newPhaseList = []
for rd in rdlist:
PhaseName = ''
dlg = wx.TextEntryDialog(self, 'Enter the name for the new phase',
'Edit phase name', rd.Phase['General']['Name'],style=wx.OK)
while PhaseName == '':
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
PhaseName = dlg.GetValue().strip()
else:
dlg.Destroy()
return
dlg.Destroy()
# make new phase names unique
rd.Phase['General']['Name'] = G2obj.MakeUniqueLabel(PhaseName,phaseNameList)
if rd.SymOps.get('xyz',[]): # did the phase supply symmetry operations?
# check if they agree with GSAS-II's setting
OK = G2spc.CompareSym(rd.SymOps['xyz'],
SGData=rd.Phase['General']['SGData'])
# TODO: perhaps someday we could write a CIF with symmetry
# ops and use that to get try to get standard settings
if not OK and rd.Phase['General']['SGData']['SpGrp'] in G2spc.spg2origins:
# hope that a origin change will fix things
choice = G2G.ChooseOrigin(self,rd)
if choice is None: return # dialog cancelled
rd.Phase = choice
elif not OK:
# This user is in trouble
msg = '''Based on symmetry operations supplied in the input, it appears this structure uses a space group setting not compatible with GSAS-II.
If you continue from this point, it is quite likely that all intensity computations will be wrong. At a minimum view the structure and check site multiplicities to confirm they are correct. The Bilbao web site may help you convert this.'''
wx.MessageBox(msg,caption='Symmetry problem likely',style=wx.ICON_EXCLAMATION)
elif rd.Phase['General']['SGData']['SpGrp'] in G2spc.spg2origins:
try:
choice = G2G.ChooseOrigin(self,rd)
if choice is None: return # dialog cancelled
rd.Phase = choice
except:
print('ChooseOrigin failed. Check your atom types')
PhaseName = rd.Phase['General']['Name'][:]
newPhaseList.append(PhaseName)
print(u'Read phase {} from file {}'.format(PhaseName,self.lastimport))
sub = FindPhaseItem(self)
psub = self.GPXtree.AppendItem(parent=sub,text=PhaseName)
self.GPXtree.SetItemPyData(psub,rd.Phase)
wx.CallAfter(self.GPXtree.SelectItem,psub) # should call SelectDataTreeItem
try:
rd.MPhase['General']['Name'] = G2obj.MakeUniqueLabel(PhaseName+' mag',phaseNameList)
PhaseName = rd.MPhase['General']['Name'][:]
newPhaseList.append(PhaseName)
psub = self.GPXtree.AppendItem(parent=sub,text=PhaseName)
self.GPXtree.SetItemPyData(psub,rd.MPhase)
wx.CallAfter(self.GPXtree.SelectItem,psub) # should call SelectDataTreeItem
except (AttributeError,TypeError):
pass
self.GPXtree.Expand(self.root) # make sure phases are seen
self.GPXtree.Expand(sub)
self.GPXtree.Expand(psub)
self.PickIdText = None
# add constraints imported with phase to tree
# at present, constraints are generated only in ISODISTORT_proc in the
# CIF import
if rd.Constraints:
sub = GetGPXtreeItemId(self,self.root,'Constraints') # was created in CheckNotebook if needed
Constraints = self.GPXtree.GetItemPyData(sub)
for i in rd.Constraints:
if type(i) is dict:
if '_Explain' not in Constraints: Constraints['_Explain'] = {}
Constraints['_Explain'].update(i)
else:
Constraints['Phase'].append(i)
# make ISODISTORT magnetic phase constraints here
Phases = self.GetPhaseData()
prevPhases = list(Phases.keys())
parentPhase = None
Vratio = None
if ('ISODISTORT' in rd.Phase and
'XformInfo' in rd.Phase['ISODISTORT'] and
PhaseName in prevPhases and len(prevPhases) > 1):
Trans = rd.Phase['ISODISTORT']['XformInfo'].get('Trans',np.eye(3))
Vec = rd.Phase['ISODISTORT']['XformInfo'].get('offset',[0,0,0])
prevPhases.pop(prevPhases.index(PhaseName))
if len(prevPhases) == 1:
parentPhase = prevPhases[0]
else:
dlg = G2G.G2SingleChoiceDialog(self,
f'Select parent phase to {PhaseName}',
'Select phase',prevPhases)
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelection()
parentPhase = prevPhases[sel]
dlg.Destroy()
else:
dlg.Destroy()
if parentPhase:
oldPhase = Phases[parentPhase]
newPhase = Phases[PhaseName]
oRanId = oldPhase['ranId']
nRanId = newPhase['ranId']
Vratio = np.abs(nl.det(Trans)) # volume ratio
#Vratio = newPhase['General']['Cell'][7]/oldPhase['General']['Cell'][7]
debug = True
# create constraints relating two unit cells
Constraints['Phase'] += G2lat.GenCellConstraints(Trans,oRanId,nRanId,
G2lat.cell2A(oldPhase['General']['Cell'][1:7]),
oldPhase['General']['SGData'],
newPhase['General']['SGData'],debug)
# create constraints relating the atoms in newPhase to their positions in the chemical cell
constr,message = G2lat.MatchGenAtomConstraints(
oldPhase,newPhase,Trans,[0,0,0],Vec)
if message:
wx.MessageDialog(self,message,
'Constraint Gen. Problem',style=wx.ICON_INFORMATION).ShowModal()
Constraints['Phase'] += constr
if not newPhaseList: return # somehow, no new phases
# get a list of existing histograms
PWDRlist = []
HKLFlist = []
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name.startswith('PWDR ') and name not in PWDRlist:
PWDRlist.append(name)
if name.startswith('HKLF ') and name not in HKLFlist:
HKLFlist.append(name)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
TextList = PWDRlist + HKLFlist
if not TextList:
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree() # reindex
return #no histograms
header = 'Select histogram(s) to add to new phase(s):'
for phaseName in newPhaseList:
header += '\n '+phaseName
notOK = True
while notOK:
result = G2G.ItemSelector(TextList,self,header,header='Add histogram(s)',multiple=True)
if not result:
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree() # reindex
return
# check that selected single crystal histograms are not already in use!
used = [TextList[i] for i in result if TextList[i] in usedHKLFhists]
#for i in result:
# if TextList[i] in usedHKLFhists: used.append(TextList[i])
if used:
msg = 'The following single crystal histogram(s) are already in use'
for i in used:
msg += '\n '+str(i)
msg += '\nAre you sure you want to add them to this phase? '
msg += 'Associating a single crystal dataset to >1 histogram is usually an error, '
msg += 'so No is suggested here.'
if self.ErrorDialog('Likely error',msg,self,wtype=wx.YES_NO) == wx.ID_YES: notOK = False
else:
notOK = False
# connect new phases to histograms
sub = GetGPXtreeItemId(self,self.root,'Phases')
if not sub:
raise Exception('ERROR -- why are there no phases here?')
wx.BeginBusyCursor()
item, cookie = self.GPXtree.GetFirstChild(sub)
while item: # loop over (new) phases
phaseName = self.GPXtree.GetItemText(item)
data = self.GPXtree.GetItemPyData(item)
item, cookie = self.GPXtree.GetNextChild(sub, cookie)
if phaseName not in newPhaseList: continue
SGData = data['General']['SGData']
NShkl = len(G2spc.MustrainNames(SGData))
NDij = len(G2spc.HStrainNames(SGData))
#====> This is where histograms are linked to a newly-read Phase
for i in result:
histoName = TextList[i]
if histoName in HKLFlist:
Id = GetGPXtreeItemId(self,self.root,histoName)
refDict,reflData = self.GPXtree.GetItemPyData(Id)
G2mth.UpdateHKLFvals(histoName, data, reflData)
elif histoName in PWDRlist:
Id = GetGPXtreeItemId(self,self.root,histoName)
Inst = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,Id,'Instrument Parameters'))[0]
refList = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,Id,'Reflection Lists'))
refList[data['General']['Name']] = {}
data['Histograms'][histoName] = G2mth.SetDefaultDData(Inst['Type'][0],histoName,NShkl=NShkl,NDij=NDij)
else:
raise Exception('Unexpected histogram '+histoName)
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree() # reindex
if Vratio: # make HAP constraints for ISODISTORT mag phase
for hist in data['Histograms']:
hRanId = Histograms[hist]['ranId']
Constraints['HAP'] += G2lat.GenHAPConstraints(Vratio,oRanId,nRanId,hRanId)
wx.EndBusyCursor()
self.EnableRefineCommand()
return # success
def _Add_ImportMenu_Image(self,parent):
'''configure the Import Image menus accord to the readers found in _init_Imports
'''
submenu = wx.Menu()
item = parent.AppendSubMenu(submenu, 'Image','Import image file')
for reader in self.ImportImageReaderlist:
item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
self.ImportMenuId[item.GetId()] = reader
self.Bind(wx.EVT_MENU, self.OnImportImage, id=item.GetId())
item = submenu.Append(wx.ID_ANY,'guess format from file','Import image data, use file to try to determine format')
self.Bind(wx.EVT_MENU, self.OnImportImage, id=item.GetId())
[docs]
def OnImportImage(self,event):
'''Called in response to an Import/Image/... menu item
to read an image from a file. Like all the other imports,
dict self.ImportMenuId is used to look up the specific
reader item associated with the menu item, which will be
None for the last menu item, which is the "guess" option
where all appropriate formats will be tried.
A reader object is filled each time an image is read.
N.B. The code here is largely duplicated in
:mod:`GSASIIscriptable` so any changes made here
need to be duplicated there, too.
'''
self.CheckNotebook()
# look up which format was requested
reqrdr = self.ImportMenuId.get(event.GetId())
rdlist = self.OnImportGeneric(reqrdr,self.ImportImageReaderlist,
'image',multiple=True,Preview=False,load2Tree=True)
if rdlist:
self.GPXtree.SelectItem(GetGPXtreeItemId(self,self.Image,'Image Controls')) #show last image to have beeen read
def _Add_ImportMenu_Sfact(self,parent):
'''configure the Import Structure Factor menus accord to the readers found in _init_Imports
'''
submenu = wx.Menu()
item = parent.AppendSubMenu(submenu,'Structure Factor','Import Structure Factor data')
for reader in self.ImportSfactReaderlist:
item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
self.ImportMenuId[item.GetId()] = reader
self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId())
item = submenu.Append(wx.ID_ANY,'guess format from file','Import Structure Factor, use file to try to determine format')
self.Bind(wx.EVT_MENU, self.OnImportSfact, id=item.GetId())
[docs]
def OnImportSfact(self,event):
'''Called in response to an Import/Structure Factor/... menu item
to read single crystal datasets.
dict self.ImportMenuId is used to look up the specific
reader item associated with the menu item, which will be
None for the last menu item, which is the "guess" option
where all appropriate formats will be tried.
N.B. The code here is largely duplicated in
:mod:`GSASIIscriptable` so any changes made here
need to be duplicated there, too.
'''
# get a list of existing histograms
HKLFlist = []
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name.startswith('HKLF ') and name not in HKLFlist:
HKLFlist.append(name)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
# look up which format was requested
reqrdr = self.ImportMenuId.get(event.GetId())
rdlist = self.OnImportGeneric(reqrdr,self.ImportSfactReaderlist,
'Structure Factor',multiple=True)
if len(rdlist) == 0: return
self.CheckNotebook()
newHistList = []
for rd in rdlist:
HistName = rd.objname
if len(rdlist) <= 2:
dlg = wx.TextEntryDialog( # allow editing of Structure Factor name
self, 'Enter the name for the new Structure Factor',
'Edit Structure Factor name', HistName,
style=wx.OK)
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
HistName = dlg.GetValue()
dlg.Destroy()
HistName = 'HKLF '+G2obj.StripUnicode(HistName,'_')
# make new histogram names unique
if len(rd.Banks):
for Bank in rd.Banks:
valuesdict = {'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),}
HistName = G2obj.MakeUniqueLabel(HistName,HKLFlist)
print (u'Read structure factor table '+HistName+u' from file '+self.lastimport)
Id = self.GPXtree.AppendItem(parent=self.root,text=HistName)
if not Bank['RefDict'].get('FF'):
Bank['RefDict']['FF'] = {}
self.GPXtree.SetItemPyData(Id,[valuesdict,Bank['RefDict']])
Sub = self.GPXtree.AppendItem(Id,text='Instrument Parameters')
self.GPXtree.SetItemPyData(Sub,copy.copy(rd.Parameters))
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Reflection List'),{}) #dummy entry for GUI use
newHistList.append(HistName)
else:
valuesdict = {'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),}
HistName = G2obj.MakeUniqueLabel(HistName,HKLFlist)
print (u'Read structure factor table '+HistName+u' from file '+self.lastimport)
if not rd.RefDict.get('FF'):
rd.RefDict['FF'] = {}
Id = self.GPXtree.AppendItem(parent=self.root,text=HistName)
self.GPXtree.SetItemPyData(Id,[valuesdict,rd.RefDict])
Sub = self.GPXtree.AppendItem(Id,text='Instrument Parameters')
self.GPXtree.SetItemPyData(Sub,rd.Parameters)
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Reflection List'),{}) #dummy entry for GUI use
newHistList.append(HistName)
self.GPXtree.SelectItem(Id)
self.GPXtree.Expand(Id)
self.Sngl = True
if not newHistList: return # somehow, no new histograms
# make a list of phase names
phaseRIdList,usedHistograms = self.GetPhaseInfofromTree()
phaseNameList = list(usedHistograms.keys()) # phase names in use
if not phaseNameList: return # no phases yet, nothing to do
header = 'Select phase(s) to add the new\nsingle crystal dataset(s) to:'
for Name in newHistList:
header += '\n '+str(Name)
result = G2G.ItemSelector(phaseNameList,self,header,header='Add to phase(s)',multiple=True)
if not result: return
# connect new phases to histograms
sub = GetGPXtreeItemId(self,self.root,'Phases')
if not sub:
raise Exception('ERROR -- why are there no phases here?')
wx.BeginBusyCursor()
item, cookie = self.GPXtree.GetFirstChild(sub)
iph = -1
#====> This is where phase(s) are linked to a newly-read HKLF histogram
while item: # loop over (new) phases
iph += 1
data = self.GPXtree.GetItemPyData(item)
item, cookie = self.GPXtree.GetNextChild(sub, cookie)
if iph not in result: continue
for histoName in newHistList:
Id = GetGPXtreeItemId(self,self.root,histoName)
refDict,reflData = self.GPXtree.GetItemPyData(Id)
G2mth.UpdateHKLFvals(histoName, data, reflData)
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree() # reindex
wx.EndBusyCursor()
self.EnableRefineCommand()
return # success
def _Add_ImportMenu_powder(self,parent):
'''configure the Powder Data menus accord to the readers found in _init_Imports
'''
def OnAutoImport(event):
G2G.AutoLoadFiles(self,FileTyp='pwd')
submenu = wx.Menu()
item = parent.AppendSubMenu(submenu,'Powder Data','Import Powder data')
for reader in self.ImportPowderReaderlist:
item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
self.ImportMenuId[item.GetId()] = reader
self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId())
item = submenu.Append(wx.ID_ANY,'guess format from file','Import powder data, use file to try to determine format')
self.Bind(wx.EVT_MENU, self.OnImportPowder, id=item.GetId())
submenu.AppendSeparator()
item = submenu.Append(wx.ID_ANY,'Simulate a dataset','Create a powder data set entry that will be simulated')
self.Bind(wx.EVT_MENU, self.OnDummyPowder, id=item.GetId())
item = submenu.Append(wx.ID_ANY,'Auto Import','Import data files as found')
self.Bind(wx.EVT_MENU, OnAutoImport, id=item.GetId())
item = submenu.Append(wx.ID_ANY,'Fit instr. profile from fundamental parms...','')
self.Bind(wx.EVT_MENU, self.OnPowderFPA, id=item.GetId())
[docs]
def OpenPowderInstprm(self,instfile):
'''Read a GSAS-II (new) instrument parameter file
:param str instfile: name of instrument parameter file
'''
File = open(instfile,'r')
lines = File.readlines()
File.close()
return lines
[docs]
def ReadPowderInstprm(self, instLines, bank, rd):
'''Read contents of a GSAS-II (new) .instprm instrument parameter file
similar to G2pwdGUI.OnLoad. Uses :func:`GSASIIfiles.ReadInstprm`
to actually read the file.
If instprm file has multiple banks (where each has header #Bank n: ...,
and bank is supplied as None here, this routine (in GUI) uses a
dialog for selection. Note that multibank .instprm files are made by
a "Save all profile" command in Instrument Parameters.
:param list instLines: contents of GSAS-II parameter file as a
list of str; N.B. lines can be concatenated with ';'
:param int bank: bank number to use when instprm file has values
for multiple banks (noted by headers of '#BANK n:...'.). This
is ignored for instprm files without those headers.
If bank is None with multiple banks, a selection window is shown.
:param GSASIIobj.ImportPowder rd: The reader object that
will be read from. Sample parameters are placed here.
:returns: Either an instrument parameter dict if OK, or
an Error message (str) if read failed
'''
if 'GSAS-II' not in instLines[0]: # not a valid file
return 'Not a valid GSAS-II instprm file'
if bank is None: # no bank was specified in the input file, is more than one present in file?
banklist = set([])
for S in instLines:
if S[0] == '#' and 'Bank' in S:
banklist.add(int(S.split(':')[0].split()[1]))
if len(banklist) > 1: # yes, the user must make a selection
choices = [str(i) for i in banklist]
bank = int(G2G.ItemSelector(choices,self,multiple=False))
else:
bank = 1
rd.powderentry[2] = bank
nbank,instdict = G2fil.ReadInstprm(instLines, bank, rd.Sample)
return instdict
[docs]
def ReadPowderIparm(self,instfile,bank,databanks,rd):
'''Read a GSAS (old) instrument parameter file
:param str instfile: name of instrument parameter file
:param int bank: the bank number read in the raw data file
:param int databanks: the number of banks in the raw data file.
If the number of banks in the data and instrument parameter files
agree, then the sets of banks are assumed to match up and bank
is used to select the instrument parameter file. If not and not TOF,
the user is asked to make a selection.
:param obj rd: the raw data (histogram) data object. This
sets rd.instbank.
'''
if not os.path.exists(instfile): # no such file
return {}
fp = 0
try:
fp = open(instfile,'r')
Iparm = {}
for S in fp:
if '#' in S[0]:
continue
Iparm[S[:12]] = S[12:-1]
except IOError:
print(u'Error reading file: {}'.format(instfile))
if fp:
fp.close()
ibanks = int(Iparm.get('INS BANK ','1').strip())
if ibanks == 1: # there is only one bank here, return it
rd.instbank = 1
rd.powderentry[2] = 1
return Iparm
if 'PNT' in Iparm['INS HTYPE ']: #allow mismatch between banks in data iparm file for TOF
rd.instbank = bank
elif ibanks != databanks or bank is None:
choices = []
for i in range(1,1+ibanks):
choices.append('Bank '+str(i))
bank = 1 + G2G.BlockSelector(
choices, self,
title=u'Select an instrument parameter bank for '+
os.path.split(rd.powderentry[0])[1]+u' BANK '+str(bank)+
u'\nOr use Cancel to select from the default parameter sets',
header='Block Selector')
if bank is None: return {}
# pull out requested bank # bank from the data, and change the bank to 1
IparmS = {}
for key in Iparm:
if 'INS' in key[:3]: #skip around rubbish lines in some old iparm files
if key[4:6] == " ":
IparmS[key] = Iparm[key]
elif int(key[4:6].strip()) == bank:
IparmS[key[:4]+' 1'+key[6:]] = Iparm[key]
rd.instbank = bank
return IparmS
[docs]
def GetPowderIparm(self,rd, prevIparm, lastIparmfile, lastdatafile):
'''Open and read an instrument parameter file for a data file
Returns the list of parameters used in the data tree
:param obj rd: the raw data (histogram) data object.
:param str prevIparm: not used
:param str lastIparmfile: Name of last instrument parameter
file that was read, or a empty string.
:param str lastdatafile: Name of last data file that was read.
:returns: a list of two dicts, the first containing instrument parameters
and the second used for TOF lookup tables for profile coeff.
'''
def GetDefaultParms(self,rd):
'''Solicits from user a default set of parameters & returns Inst parm dict
param: self: refers to the GSASII main class
param: rd: importer data structure
returns: dict: Instrument parameter dictionary
'''
#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 '+rd.idstring
for l in dI.defaultIparm_lbl:
choices.append('Defaults for '+l)
res = G2G.BlockSelector(choices,ParentFrame=self,title=head,
header='Select default inst parms',useCancel=True)
if res is None: return None
rd.instfile = ''
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]})
if 'Generic' in choices[res]:
rd.instmsg = 'default: '+dI.defaultIparm_lbl[res]
Inst = self.ReadPowderInstprm(dI.defaultIparms[res],bank,rd)
return Inst #this is [Inst1,Inst2] a pair of dicts
# The input below is now requested for each bank in OnImportPowder
# dlg = G2G.MultiDataDialog(self,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[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:
rd.instmsg = 'default: '+dI.defaultIparm_lbl[res]
inst1,inst2 = self.ReadPowderInstprm(dI.defaultIparms[res],bank,rd)
if rd.instdict.get('wave') and 'Lam' in inst1:
inst1['Lam'][0] = rd.instdict.get('wave')
inst1['Lam'][1] = rd.instdict.get('wave')
return [inst1,inst2]
# stuff we might need from the reader
filename = rd.powderentry[0]
bank = rd.powderentry[2]
numbanks = rd.numbanks
#1st priority: is there an instrument parameter file matching the current file
# with extension .instprm, .prm, .inst, or .ins? If so read it
basename = os.path.splitext(filename)[0]
if basename:
#-- look for an instrument file matching the name of the data file -------------
print('looking for default instrument parameter file named\n\t',
os.path.split(basename)[1],
'with extensions .prm, .inst, .ins or .instprm')
for ext in '.prm','.inst','.ins','.instprm':
if self.zipfile:
instfile = G2G.ExtractFileFromZip(self.zipfile,
selection=os.path.split(basename + ext)[1],parent=self)
if instfile == None:
continue
print(f'created {instfile} from {self.zipfile}')
self.cleanupList.append(instfile)
else:
instfile = basename + ext
if not os.path.exists(instfile):
continue
if 'instprm' in instfile:
Lines = self.OpenPowderInstprm(instfile)
instParmList = self.ReadPowderInstprm(Lines,bank,rd) #this is [Inst1,Inst2] a pair of dicts
if 'list' in str(type(instParmList)):
rd.instfile = instfile
rd.instmsg = 'GSAS-II file '+instfile
return instParmList
else:
#print 'debug: open/read failed',instfile
pass # fail silently
else:
Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
if Iparm:
#print 'debug: success'
rd.instfile = instfile
rd.instmsg = instfile + ' bank ' + str(rd.instbank)
return G2fil.SetPowderInstParms(Iparm,rd)
else:
#print 'debug: open/read failed',instfile
pass # fail silently
#-- look for an instrument file matching the name of the data file -------------
# 2nd choice: is there an instrument parameter file defined in the
# current data set? (rd.instparm as found in data file header)
# Alternately, if reading a set of files, reuse the last one again
# (lastIparmfile)
if rd.instparm or lastIparmfile:
if rd.instparm:
instfile = os.path.join(os.path.split(filename)[0],rd.instparm)
else:
# for multiple reads of one data file, reuse the inst parm file
instfile = lastIparmfile
if instfile != None and os.path.exists(instfile):
if 'instprm' in instfile: #GSAS-II file must have .instprm as extension
Lines = self.OpenPowderInstprm(instfile)
if Lines is not None:
instParmList = self.ReadPowderInstprm(Lines,bank,rd) #this is [Inst1,Inst2] a pair of dicts
else: #old GSAS style iparm file - could be named anything!
Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
if Iparm:
#print 'debug: success'
rd.instfile = instfile
rd.instmsg = instfile + ' bank ' + str(rd.instbank)
instParmList = G2fil.SetPowderInstParms(Iparm,rd) #this is [Inst1,Inst2] a pair of dicts
if 'list' in str(type(instParmList)): #record stuff & return stuff
rd.instfile = instfile
rd.instmsg = 'GSAS-II file '+instfile
return instParmList
else: #bad iparms - try default
rd.instmsg = instParmList #an error message
return GetDefaultParms(self,rd)
else:
self.ErrorDialog('Open Error',u'Error opening instrument parameter file '
+u'{} requested by file {}'.format(instfile,filename))
#-- No other choice: ask the User for an instrument file -----------------------
while True: # loop until we get a file that works or we get a cancel
instfile = ''
if self.zipfile:
instfile = G2G.ExtractFileFromZip(self.zipfile,parent=self,
msg='Reading an instrument parameter file\n\n')
if instfile == None:
self.zipfile = None
continue
print(f'created {instfile} from {self.zipfile}')
self.cleanupList.append(instfile)
else:
pth = os.path.dirname(filename) #look in same place data was found
if not pth: pth = '.'
extOrd = [0,1]
if GSASIIpath.GetConfigValue('Instprm_default',False):
extOrd = [1,0]
extList = ['GSAS iparm file (*.prm,*.inst,*.ins)|*.prm;*.inst;*.ins;*.PRM|','GSAS-II iparm file (*.instprm)|*.instprm|']
dlg = wx.FileDialog(self,
u'Choose inst. param file for "'+rd.idstring+u'" (or Cancel for default)',
pth, '',extList[extOrd[0]]+extList[extOrd[1]]+'All files (*.*)|*.*', wx.FD_OPEN)
if os.path.exists(lastIparmfile):
dlg.SetFilename(os.path.split(lastIparmfile)[-1])
if dlg.ShowModal() == wx.ID_OK:
instfile = dlg.GetPath()
dlg.Destroy()
if not instfile:
return GetDefaultParms(self,rd) #on Cancel/break
if 'instprm' in instfile:
Lines = self.OpenPowderInstprm(instfile)
if Lines is not None:
instParmList = self.ReadPowderInstprm(Lines,bank,rd) #this is [Inst1,Inst2] a pair of dicts
if 'list' in str(type(instParmList)):
rd.instfile = instfile
rd.instmsg = 'GSAS-II file '+instfile
return instParmList
else:
rd.instmsg = instParmList #an error message
return GetDefaultParms(self,rd)
else:
Iparm = self.ReadPowderIparm(instfile,bank,numbanks,rd)
if Iparm:
#print 'debug: success with',instfile
rd.instfile = instfile
rd.instmsg = instfile + ' bank ' + str(rd.instbank)
return G2fil.SetPowderInstParms(Iparm,rd)
else:
self.ErrorDialog('Read Error',
u'Error opening/reading file {}'.format(instfile))
[docs]
def EnableRefineCommand(self):
'''Check that phases are connected to histograms - if so then
Data/Remove Histogram is enabled
'''
if callable(self.dataWindow.DataGeneral): # will fail w/o Phase menus
self.dataWindow.DataGeneral()
haveData = False
sub = GetGPXtreeItemId(self,self.root,'Phases')
if sub:
item, cookie = self.GPXtree.GetFirstChild(sub)
while item: # loop over phases
data = self.GPXtree.GetItemPyData(item)
item, cookie = self.GPXtree.GetNextChild(sub, cookie)
UseList = data['Histograms']
if UseList:
haveData = True
break
if haveData:
self.dataWindow.DataMenu.Enable(G2G.wxID_DATADELETE,True)
for item in self.Refine: item.Enable(True)
else:
self.dataWindow.DataMenu.Enable(G2G.wxID_DATADELETE,False)
for item in self.Refine: item.Enable(False)
[docs]
def OnImportPowder(self,event):
'''Called in response to an Import/Powder Data/... menu item
to read a powder diffraction data set.
dict self.ImportMenuId is used to look up the specific
reader item associated with the menu item, which will be
None for the last menu item, which is the "guess" option
where all appropriate formats will be tried.
Also reads an instrument parameter file for each dataset.
N.B. The code here is largely duplicated in
:mod:`GSASIIscriptable` so any changes made here
need to be duplicated there, too.
'''
FP,tth = 25.0,150.
# get a list of existing histograms
PWDRlist = []
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name.startswith('PWDR ') and name not in PWDRlist:
PWDRlist.append(name)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
# look up which format was requested
reqrdr = self.ImportMenuId.get(event.GetId())
rdlist = self.OnImportGeneric(
reqrdr,self.ImportPowderReaderlist,'Powder Data',multiple=True)
if len(rdlist) == 0: return
self.CheckNotebook()
Iparm = None
lastIparmfile = ''
lastdatafile = ''
newHistList = []
# lastVals = []
self.EnablePlot = False
Iparms = {}
self.cleanupList = [] # inst parms created in GetPowderIparm
iSource = '?'
for ihst,rd in enumerate(rdlist):
if 'Instrument Parameters' in rd.pwdparms: # reader supplies InstPrms
Iparm1,Iparm2 = rd.pwdparms['Instrument Parameters']
iSource = rd.instmsg
elif Iparms and not lastIparmfile: # have vals from previous loop
Iparm1,Iparm2 = Iparms
else:
# get instrument parameters for each dataset, unless already set
# if lastIparmfile: # is this histogram like previous?
# if lastVals != (rd.powderdata[0].min(),rd.powderdata[0].max(),len(rd.powderdata[0])):
# lastIparmfile = ''
Iparms = self.GetPowderIparm(rd, Iparm, lastIparmfile, lastdatafile)
if not Iparms: #may have bailed out
Id = 0
continue
Iparm1,Iparm2 = Iparms
if rd.repeat_instparm:
lastIparmfile = rd.instfile
else:
Iparms = {}
# lastVals = (rd.powderdata[0].min(),rd.powderdata[0].max(),len(rd.powderdata[0]))
iSource = rd.instmsg
# for defaulted TOF data, reset the default bank number & for generic get FP/2Th
if iSource.startswith('default:') and 'Bank' in Iparm1 and 'T' in Iparm1['Type'][0]:
if 'Generic' in iSource:
dlg = G2G.MultiDataDialog(self,title='Generic TOF detector bank',
prompts=['Total flight path','2-theta',],values=[FP,tth],
limits=[[6.,200.],[5.,175.],],formats=['%6.2f','%6.1f',],
header=f'Set detector info for\n{rd.idstring}')
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
Iparm1['difC'] = [difC,difC,0]
Iparm1['sig-1'] = [sig1,sig1,0]
Iparm1['beta-1'] = [bet1,bet1,0]
dlg.Destroy()
Iparm1['Bank'][0] = Iparm1['Bank'][1] = ihst+1
# override any keys in read instrument parameters with ones set in import
for key in Iparm1:
if key in rd.instdict:
Iparm1[key] = rd.instdict[key]
#
lastdatafile = rd.powderentry[0]
HistName = 'PWDR '+rd.idstring
# do some error checking
if len(rd.powderdata[0]) == 0 or len(rd.powderdata[1]) == 0:
G2G.G2MessageBox(self,
f'No data in file {rd.powderentry[0]} skipping',
'Invalid file')
Id = 0
continue
elif len(rd.powderdata[0]) != len(rd.powderdata[1]):
G2G.G2MessageBox(self,
f'Unequal X and Y lengths in file {rd.powderentry[0]} skipping',
'Invalid file')
Id = 0
continue
elif HistName in PWDRlist:
dlg = wx.MessageDialog(self,'Skip %s?'%(HistName),'Duplicate data name',wx.YES_NO)
try:
if dlg.ShowModal() == wx.ID_YES:
Id = 0
continue
finally:
dlg.Destroy()
# make new histogram names unique
HistName = G2obj.MakeUniqueLabel(HistName,PWDRlist)
try:
print('Read powder data '+HistName+
' from file '+G2obj.StripUnicode(rd.readfilename) +
' (format: '+ rd.formatName +
'). Inst parameters from '+G2obj.StripUnicode(iSource))
except:
print('Read powder data')
# data are read, now store them in the tree
Id = self.GPXtree.AppendItem(parent=self.root,text=HistName)
if 'T' in Iparm1['Type'][0]:
if not rd.clockWd and rd.GSAS:
rd.powderdata[0] *= 100. #put back the CW centideg correction
cw = np.diff(rd.powderdata[0])
rd.powderdata[0] = rd.powderdata[0][:-1]+cw/2.
if rd.GSAS: #NB: old GSAS wanted intensities*CW even if normalized!
npts = min(len(rd.powderdata[0]),len(rd.powderdata[1]),len(cw))
rd.powderdata[1] = rd.powderdata[1][:npts]/cw[:npts]
rd.powderdata[2] = rd.powderdata[2][:npts]*cw[:npts]**2 #1/var=w at this point
else: #NB: from topas/fullprof type files
rd.powderdata[1] = rd.powderdata[1][:-1]
rd.powderdata[2] = rd.powderdata[2][:-1]
if 'Itype' in Iparm2:
Ibeg = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][0])
Ifin = np.searchsorted(rd.powderdata[0],Iparm2['Tminmax'][1])
rd.powderdata[0] = rd.powderdata[0][Ibeg:Ifin]
YI,WYI = G2pwd.calcIncident(Iparm2,rd.powderdata[0])
rd.powderdata[1] = rd.powderdata[1][Ibeg:Ifin]/YI
var = 1./rd.powderdata[2][Ibeg:Ifin]
var += WYI*rd.powderdata[1]**2
var /= YI**2
rd.powderdata[2] = 1./var
rd.powderdata[1] = np.where(np.isinf(rd.powderdata[1]),0.,rd.powderdata[1])
rd.powderdata[3] = np.zeros_like(rd.powderdata[0])
rd.powderdata[4] = np.zeros_like(rd.powderdata[0])
rd.powderdata[5] = np.zeros_like(rd.powderdata[0])
elif 'PNB' in Iparm1['Type'][0]:
Iparm1['Lam'][1] = rd.Wave
Ymin = np.min(rd.powderdata[1])
Ymax = np.max(rd.powderdata[1])
valuesdict = {
'wtFactor':1.0,
'Dummy':False,
'ranId':ran.randint(0,sys.maxsize),
'Offset':[0.0,0.0],'delOffset':0.02*Ymax,'refOffset':-.1*Ymax,'refDelt':0.1*Ymax,
'Yminmax':[Ymin,Ymax]
}
# apply user-supplied corrections to powder data
if 'CorrectionCode' in Iparm1:
print('Applying corrections from instprm file')
corr = Iparm1['CorrectionCode'][0]
try:
exec(corr)
print('done')
except Exception as err:
print(u'error: {}'.format(err))
print('with commands -------------------')
print(corr)
print('---------------------------------')
finally:
del Iparm1['CorrectionCode']
rd.Sample['ranId'] = valuesdict['ranId'] # this should be removed someday
self.GPXtree.SetItemPyData(Id,[valuesdict,rd.powderdata])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Comments'),rd.comments)
Tmin = min(rd.powderdata[0])
Tmax = max(rd.powderdata[0])
Tmin1 = Tmin
if 'NT' in Iparm1['Type'][0] and G2lat.Pos2dsp(Iparm1,Tmin) < 0.4:
Tmin1 = G2lat.Dsp2pos(Iparm1,0.4)
if 'PXE' in Iparm1['Type'][0]:
Iparm1.update(rd.Inst)
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Limits'),
rd.pwdparms.get('Limits',[(Tmin,Tmax),[Tmin1,Tmax]])
)
self.PatternId = GetGPXtreeItemId(self,Id,'Limits')
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Background'),
rd.pwdparms.get('Background',
[['chebyschev-1',True,3,1.0,0.0,0.0],{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[],
'background PWDR':['',1.0,False]}]))
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Instrument Parameters'),
copy.deepcopy([Iparm1,Iparm2]))
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Sample Parameters'),
rd.Sample)
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Peak List')
,{'peaks':[],'sigDict':{}})
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Index Peak List'),
[[],[]])
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Unit Cells List'),
[])
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Reflection Lists'),
{})
# if any Control values have been set, move them into tree
Controls = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root, 'Controls'))
Controls.update(rd.Controls)
newHistList.append(HistName)
rd.repeat_instparm = False #clear the iparm reuse flag
else:
# there are no break statements in this while loop so these are always run:
self.EnablePlot = True
if Id:
self.GPXtree.Expand(Id)
self.GPXtree.SelectItem(Id) # perhaps this is better as a CallAfter (See #282)
G2fil.CleanupFromZip('instprm',self.cleanupList)
if not newHistList: return # somehow, no new histograms
# make a list of phase names
phaseRIdList,usedHistograms = self.GetPhaseInfofromTree()
phaseNameList = list(usedHistograms.keys()) # phase names in use
if not phaseNameList: return # no phases yet, nothing to do
header = 'Select phase(s) to link\nto the newly-read data:'
for Name in newHistList:
header += '\n '+str(Name)
result = G2G.ItemSelector(phaseNameList,self,header,header='Add to phase(s)',multiple=True)
if not result: return
# connect new phases to histograms
sub = GetGPXtreeItemId(self,self.root,'Phases')
if not sub:
raise Exception('ERROR -- why are there no phases here?')
item, cookie = self.GPXtree.GetFirstChild(sub)
iph = -1
while item: # loop over (new) phases
iph += 1
data = self.GPXtree.GetItemPyData(item)
item, cookie = self.GPXtree.GetNextChild(sub, cookie)
if iph not in result: continue
generalData = data['General']
SGData = generalData['SGData']
UseList = data['Histograms']
NShkl = len(G2spc.MustrainNames(SGData))
NDij = len(G2spc.HStrainNames(SGData))
for histoName in newHistList:
UseList[histoName] = G2mth.SetDefaultDData(Iparm1['Type'][0],histoName,NShkl=NShkl,NDij=NDij)
Id = GetGPXtreeItemId(self,self.root,histoName)
refList = self.GPXtree.GetItemPyData(
GetGPXtreeItemId(self,Id,'Reflection Lists'))
refList[generalData['Name']] = []
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree() # reindex
self.EnableRefineCommand()
return # success
[docs]
def OnDummyPowder(self,event):
'''Called in response to Import/Powder Data/Simulate menu item
to create a Dummy powder diffraction data set.
Reads an instrument parameter file and then gets input from the user
'''
# make a list of phase names
phaseRIdList,defPhases = self.GetPhaseInfofromTree()
phaseNameList = list(defPhases.keys()) # phase names in use
if not phaseNameList: # no phases yet, nothing to do
G2G.G2MessageBox(self,
'You must have phases defined to simulate a pattern',
'No phase')
return
# get a list of existing histograms
PWDRlist = []
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name.startswith('PWDR ') and name not in PWDRlist:
PWDRlist.append(name)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
# Initialize a base class reader
rd = G2obj.ImportPowderData(
extensionlist=tuple(),
strictExtension=False,
formatName = 'Simulate dataset',
longFormatName = 'Compute a simulated pattern')
rd.powderentry[0] = '' # no filename
# #self.powderentry[1] = pos # bank offset (N/A here)
rd.powderentry[2] = 1 # only one bank
rd.comments.append('This is a dummy dataset for powder pattern simulation')
self.CheckNotebook()
Iparm = None
lastdatafile = ''
self.zipfile = None
# get instrument parameters for it
Iparm = self.GetPowderIparm(rd, Iparm, '', lastdatafile)
if Iparm is None:
return
Iparm1, Iparm2 = Iparm
if 'T' in Iparm1['Type'][0]:
rd.idstring = 'TOF neutron simulation'
simType = 'TOF'
else:
# need to get name, 2theta start, end, step
rd.idstring = ' CW'
simType = 'CW'
if 'X' in Iparm1['Type'][0]:
rd.idstring = 'CW x-ray simulation'
else:
rd.idstring = 'CW neutron simulation'
# base initial range on wavelength
wave = Iparm1.get('Lam')
if wave:
wave = wave[0]
else:
wave = Iparm1.get('Lam1')
if wave:
wave = wave[0]
N = 0
inp = None
while (N < 3): # insist on a dataset with a few points
if 'TOF' in rd.idstring:
names = ('dataset name', 'T start (ms)', 'T end (ms)', 'DT/T')
if inp is None:
inp = [rd.idstring, 10.,80.,0.0005] # see names for what's what
minvals = (None,.5,1.0,0.0001)
maxvals = (None,500.,500.,.01)
else:
names = ('dataset name', 'start angle', 'end angle', 'step size')
if not wave or wave < 1.0 and inp is None:
inp = [rd.idstring, 10.,40.,0.005] # see names for what's what
elif inp is None:
inp = [rd.idstring, 10.,80.,0.01] # see names for what's what
minvals=(None,0.001,0.001,0.0001),
maxvals=(None,180.,180.,.1),
dlg = G2G.ScrolledMultiEditor(
self,[inp] * len(inp),range(len(inp)),names,
header='Enter range for simulation and histogram name',
minvals=minvals,
maxvals=maxvals,
sizevals=((250,-1),None,None,None),
size=(400,150))
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
if inp[1] > inp[2]:
end,start,step = inp[1:]
else:
start,end,step = inp[1:]
step = abs(step)
else:
return False
if 'TOF' in rd.idstring:
N = (np.log(end)-np.log(start))/step
x = np.exp((np.arange(0,N))*step+np.log(start*1000.))
N = len(x)
rd.Sample['Scale'][0] = 5000. # default (1) is way too low for "counts"
# compute TOF peak widths: are there any negative values?
wids = G2mth.setPeakparms(Iparm1,Iparm2,x,np.ones_like(x))
allPos = ((wids[4] >= 0) & (wids[6] >= 0) &
(wids[8] >= 0) & (wids[10] >= 0))
conv = 1000.
else:
N = int((end-start)/step)+1
x = np.linspace(start,end,N,True)
N = len(x)
# compute CW peak widths: are there any negative values?
wids = G2mth.setPeakparms(Iparm1,Iparm2,x,np.ones_like(x))
allPos = ((wids[4] >= 0) & (wids[6] >= 0))
conv = 1.
# test for any areas w/negative peak wids
good,bad = G2mth.FindTrue(allPos) # get TOF/2th ranges as indices
if bad:
s = f"Found {len(bad)} region(s) with negative peak widths: "
for b in bad:
s += f"{x[b][0]/conv:.1f}-{x[b][1]/conv:.1f}, "
s = s[:-2]
N = 0
G2G.G2MessageBox(self,s,'Bad range')
if good: # reset simulation range to use good range
longestgood = good[np.argmax([i2-i1+1 for i1,i2 in good])]
inp[1] = float(max(inp[1],min(x[longestgood[0]],x[longestgood[1]])/conv))
inp[2] = float(min(inp[2],max(x[longestgood[0]],x[longestgood[1]])/conv))
else:
return False
continue
rd.powderdata = [
np.array(x), # x-axis values
np.zeros_like(x), # powder pattern intensities
np.ones_like(x), # 1/sig(intensity)^2 values (weights)
np.zeros_like(x), # calc. intensities (zero)
np.zeros_like(x), # calc. background (zero)
np.zeros_like(x), # obs-calc profiles
]
Tmin = rd.powderdata[0][0]
Tmax = rd.powderdata[0][-1]
# data are read, now store them in the tree
HistName = inp[0]
HistName = 'PWDR '+HistName
HistName = G2obj.MakeUniqueLabel(HistName,PWDRlist) # make new histogram names unique
Id = self.GPXtree.AppendItem(parent=self.root,text=HistName)
Ymin = np.min(rd.powderdata[1])
Ymax = np.max(rd.powderdata[1])
valuesdict = {
'wtFactor':1.0,
'Dummy':True,'simType':simType,
'ranId':ran.randint(0,sys.maxsize),
'Offset':[0.0,0.0],'delOffset':0.02*Ymax,'refOffset':-.1*Ymax,'refDelt':0.1*Ymax,
'Yminmax':[Ymin,Ymax]
}
self.GPXtree.SetItemPyData(Id,[valuesdict,rd.powderdata])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Comments'),rd.comments)
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Limits'),
[(Tmin,Tmax),[Tmin,Tmax]])
self.PatternId = GetGPXtreeItemId(self,Id,'Limits')
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Background'),
[['chebyschev-1',True,3,1.0,0.0,0.0],
{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[],'background PWDR':['',1.0,False]}])
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Instrument Parameters'),
[Iparm1,Iparm2])
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Sample Parameters'),
rd.Sample)
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Peak List')
,{'peaks':[],'sigDict':{}})
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Index Peak List'),
[[],[]])
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Unit Cells List'),
[])
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Reflection Lists'),
{})
self.GPXtree.Expand(Id)
self.GPXtree.SelectItem(Id)
print(u'Added simulation powder data {}'.format(HistName)+
' with parameters from {}'.format(rd.instmsg))
# make a list of phase names
phaseRIdList,defPhases = self.GetPhaseInfofromTree()
phaseNameList = list(defPhases.keys()) # phase names in use
if not phaseNameList: return # no phases yet, nothing to do
if len(phaseNameList) == 1:
result = [0]
else:
header = 'Select phase(s) to add the new\npowder simulation (dummy) dataset to:'
result = G2G.ItemSelector(phaseNameList,self,header,header='Phases to simulate',multiple=True)
if not result: return
# connect new phases to histograms
sub = GetGPXtreeItemId(self,self.root,'Phases')
if not sub:
raise Exception('ERROR -- why are there no phases here?')
item, cookie = self.GPXtree.GetFirstChild(sub)
iph = -1
while item: # loop over (new) phases
iph += 1
data = self.GPXtree.GetItemPyData(item)
item, cookie = self.GPXtree.GetNextChild(sub, cookie)
if iph not in result: continue
generalData = data['General']
SGData = generalData['SGData']
UseList = data['Histograms']
NShkl = len(G2spc.MustrainNames(SGData))
NDij = len(G2spc.HStrainNames(SGData))
UseList[HistName] = G2mth.SetDefaultDData('PWDR',HistName,NShkl=NShkl,NDij=NDij)
Id = GetGPXtreeItemId(self,self.root,HistName)
refList = self.GPXtree.GetItemPyData(
GetGPXtreeItemId(self,Id,'Reflection Lists'))
refList[generalData['Name']] = []
cId = GetGPXtreeItemId(self,self.root, 'Controls')
Controls = self.GPXtree.GetItemPyData(cId)
Controls['max cyc'] = 0
self.EnableRefineCommand()
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree() # reindex
# perhaps at some point this should be changed to run the refinement
# directly, for now provide a reminder
G2G.G2MessageBox(self,
'Now use Calculate/Refine to compute the simulation result',
'Use "Refine"')
return # success
[docs]
def AddSimulatedPowder(self,ttArr,intArr,HistName,Lam1,Lam2):
'''Create a PWDR entry for a computed powder pattern
'''
# get a list of existing histograms
PWDRlist = []
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name.startswith('PWDR ') and name not in PWDRlist:
PWDRlist.append(name)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
# Initialize a base class reader
rd = G2obj.ImportPowderData(
extensionlist=tuple(),
strictExtension=False,
formatName = 'FPA Simulated dataset',
longFormatName = 'Fundamental Parameters simulated pattern')
rd.powderentry[0] = '' # no filename
# #self.powderentry[1] = pos # bank offset (N/A here)
rd.powderentry[2] = 1 # only one bank
rd.comments.append('This is a powder pattern simulated with Fundamental Parameters')
self.CheckNotebook()
#self.zipfile = None
# get instrument parameters for it
rd.Sample.update({'Type':'Bragg-Brentano','Shift':[0.,False],'Transparency':[0.,False],
'SurfRoughA':[0.,False],'SurfRoughB':[0.,False]})
nbank, (Iparm1, Iparm2) = G2fil.ReadInstprm(dI.defaultIparms[0],1,rd.Sample)
rd.idstring = ' CW'
simType = 'CW'
# set wavelength
if Lam2:
Iparm1['Lam1'][0] = Lam1
Iparm1['Lam2'][0] = Lam2
Iparm1['Lam1'][1] = Lam1
Iparm1['Lam2'][1] = Lam2
else:
Iparm1['Lam'] = Iparm1['Lam1']
del Iparm1['Lam1'],Iparm1['Lam2']
Iparm1['Lam'][0] = Lam1
Iparm1['Lam'][1] = Lam1
rd.powderdata = [
np.array(ttArr), # x-axis values
np.array(intArr), # powder pattern intensities
np.ones_like(ttArr), # 1/sig(intensity)^2 values (weights)
np.zeros_like(intArr), # calc. intensities (zero)
np.zeros_like(ttArr), # calc. background (zero)
np.zeros_like(ttArr), # obs-calc profiles
]
Tmin = rd.powderdata[0][0]
Tmax = rd.powderdata[0][-1]
# data are read, now store them in the tree
HistName = 'PWDR '+HistName
HistName = G2obj.MakeUniqueLabel(HistName,PWDRlist) # make new histogram names unique
Id = self.GPXtree.AppendItem(parent=self.root,text=HistName)
Ymin = np.min(rd.powderdata[1])
Ymax = np.max(rd.powderdata[1])
valuesdict = {
'wtFactor':1.0,
'Dummy':True,'simType':simType,
'ranId':ran.randint(0,sys.maxsize),
'Offset':[0.0,0.0],'delOffset':0.02*Ymax,'refOffset':-.1*Ymax,'refDelt':0.1*Ymax,
'Yminmax':[Ymin,Ymax]
}
self.GPXtree.SetItemPyData(Id,[valuesdict,rd.powderdata])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Comments'),rd.comments)
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Limits'),
[(Tmin,Tmax),[Tmin,Tmax]])
self.PatternId = GetGPXtreeItemId(self,Id,'Limits')
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Background'),
[['chebyschev-1',True,3,1.0,0.0,0.0],
{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[],'background PWDR':['',1.0,False]}])
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Instrument Parameters'),
[Iparm1,Iparm2])
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Sample Parameters'),
rd.Sample)
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Peak List')
,{'peaks':[],'sigDict':{}})
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Index Peak List'),
[[],[]])
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Unit Cells List'),
[])
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Reflection Lists'),
{})
self.GPXtree.Expand(Id)
self.GPXtree.SelectItem(Id)
print(u'Added simulation powder data {}'.format(HistName))
return Id
[docs]
def OnPreferences(self,event):
'Edit the GSAS-II configuration variables'
dlg = G2G.SelectConfigSetting(self)
restart = False
try:
dlg.ShowModal() == wx.ID_OK
restart = dlg.restart
reload = dlg.reload
finally:
dlg.Destroy()
# trigger a restart if the var description asks for that
if restart:
ans = G2G.askQuestion(self,"A restart of GSAS-II is needed for your change to take effect. OK to restart?",'Restart?')
if not ans: return
msg = ('Before restarting, do you want to save your project? '+
'Select "Yes" to save, "No" to skip the save, or "Cancel"'+
' to discontinue the restart process.\n\n'+
'If "Yes", GSAS-II will reopen the project after the update. '+
'The restart will now begin unless Cancel is pressed.')
dlg = wx.MessageDialog(self, msg,'Save Project and Restart?',
wx.YES_NO|wx.CANCEL|wx.YES_DEFAULT|wx.CENTRE|wx.ICON_QUESTION)
ans = dlg.ShowModal()
dlg.Destroy()
if ans == wx.ID_CANCEL:
return
elif ans == wx.ID_YES:
ans = self.OnFileSave(None)
if not ans: return
project = os.path.abspath(self.GSASprojectfile)
print(f"Restarting GSAS-II with project file {project!r}")
else:
print("Restarting GSAS-II without a project file ")
project = None
G2fil.openInNewTerm(project)
print ('exiting GSAS-II')
sys.exit()
if reload:
ans = self.OnFileSave(None)
if not ans: return
self.clearProject() # clear out data tree
self.StartProject()
def _Add_ImportMenu_smallangle(self,parent):
'''configure the Small Angle Data menus accord to the readers found in _init_Imports
'''
submenu = wx.Menu()
item = parent.AppendSubMenu(submenu,'Small Angle Data','Import small angle data')
for reader in self.ImportSmallAngleReaderlist:
item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
self.ImportMenuId[item.GetId()] = reader
self.Bind(wx.EVT_MENU, self.OnImportSmallAngle, id=item.GetId())
# item = submenu.Append(wx.ID_ANY,
# help='Import small angle data, use file to try to determine format',
# kind=wx.ITEM_NORMAL,text='guess format from file')
# self.Bind(wx.EVT_MENU, self.OnImportSmallAngle, id=item.GetId())
[docs]
def OnImportSmallAngle(self,event):
'''Called in response to an Import/Small Angle Data/... menu item
to read a small angle diffraction data set.
dict self.ImportMenuId is used to look up the specific
reader item associated with the menu item, which will be
None for the last menu item, which is the "guess" option
where all appropriate formats will be tried.
Small angle data is presumed to be as QIE form for either x-rays or neutrons
N.B. This code is not yet duplicated in :mod:`GSASIIscriptable`.
'''
def GetSASDIparm(reader):
''' Setup instrument parameters for small ang scattering data
'''
parm = reader.instdict
Iparm = {'Type':[parm['type'],parm['type'],0],'Lam':[parm['wave'],
parm['wave'],0],'Azimuth':[0.,0.,0]}
return Iparm,{}
# get a list of existing histograms
SASDlist = []
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name.startswith('SASD ') and name not in SASDlist:
SASDlist.append(name)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
# look up which format was requested
reqrdr = self.ImportMenuId.get(event.GetId())
rdlist = self.OnImportGeneric(
reqrdr,self.ImportSmallAngleReaderlist,'Small Angle Data',multiple=True)
if len(rdlist) == 0: return
self.CheckNotebook()
newHistList = []
self.EnablePlot = False
for rd in rdlist:
HistName = rd.idstring
HistName = 'SASD '+HistName
# make new histogram names unique
HistName = G2obj.MakeUniqueLabel(HistName,SASDlist)
print ('Read small angle data '+HistName+ \
' from file '+self.lastimport)
# data are read, now store them in the tree
Id = self.GPXtree.AppendItem(parent=self.root,text=HistName)
Iparm1,Iparm2 = GetSASDIparm(rd)
Tmin = min(rd.smallangledata[0])
Tmax = max(rd.smallangledata[0])
valuesdict = {
'wtFactor':1.0,
'Dummy':False,
'ranId':ran.randint(0,sys.maxsize),
'Offset':[0.0,0.0],
}
rd.Sample['ranId'] = valuesdict['ranId'] # this should be removed someday
self.GPXtree.SetItemPyData(Id,[valuesdict,rd.smallangledata])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Comments'),rd.comments)
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Limits'),
[(Tmin,Tmax),[Tmin,Tmax]])
self.PatternId = GetGPXtreeItemId(self,Id,'Limits')
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Instrument Parameters'),
[Iparm1,Iparm2])
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Substances'),G2pwd.SetDefaultSubstances())
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Sample Parameters'),
rd.Sample)
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Models'),G2pwd.SetDefaultSASDModel())
newHistList.append(HistName)
else:
self.EnablePlot = True
self.GPXtree.Expand(Id)
self.GPXtree.SelectItem(Id)
if not newHistList: return # somehow, no new histograms
return # success
def _Add_ImportMenu_reflectometry(self,parent):
'''configure the reflectometry Data menus accord to the readers found in _init_Imports
'''
submenu = wx.Menu()
item = parent.AppendSubMenu(submenu,'Reflectometry Data','Import reflectometry data')
for reader in self.ImportReflectometryReaderlist:
item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
self.ImportMenuId[item.GetId()] = reader
self.Bind(wx.EVT_MENU, self.OnImportReflectometry, id=item.GetId())
# item = submenu.Append(wx.ID_ANY,
# help='Import reflectometry data, use file to try to determine format',
# kind=wx.ITEM_NORMAL,text='guess format from file')
# self.Bind(wx.EVT_MENU, self.OnImportReflectometry, id=item.GetId())
[docs]
def OnImportReflectometry(self,event):
'''Called in response to an Import/Reflectometry Data/... menu item
to read a reflectometry data set.
dict self.ImportMenuId is used to look up the specific
reader item associated with the menu item, which will be
None for the last menu item, which is the "guess" option
where all appropriate formats will be tried.
Reflectometry data is presumed to be in QIE form for x-rays of neutrons
N.B. This code is not yet duplicated in :mod:`GSASIIscriptable`.
'''
def GetREFDIparm(reader):
''' Setup reflectometry data instrument parameters
'''
parm = reader.instdict
Iparm = {'Type':[parm['type'],parm['type'],0],'Lam':[parm['wave'],
parm['wave'],0],'Azimuth':[0.,0.,0]}
return Iparm,{}
# get a list of existing histograms
REFDlist = []
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name.startswith('REFD ') and name not in REFDlist:
REFDlist.append(name)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
# look up which format was requested
reqrdr = self.ImportMenuId.get(event.GetId())
rdlist = self.OnImportGeneric(
reqrdr,self.ImportReflectometryReaderlist,'Reflectometry Data',multiple=True)
if len(rdlist) == 0: return
self.CheckNotebook()
newHistList = []
self.EnablePlot = False
for rd in rdlist:
HistName = rd.idstring
HistName = 'REFD '+HistName
# make new histogram names unique
HistName = G2obj.MakeUniqueLabel(HistName,REFDlist)
print ('Read reflectometry data '+HistName+ \
' from file '+self.lastimport)
# data are read, now store them in the tree
Id = self.GPXtree.AppendItem(parent=self.root,text=HistName)
Iparm1,Iparm2 = GetREFDIparm(rd)
Tmin = min(rd.reflectometrydata[0])
Tmax = max(rd.reflectometrydata[0])
ifDQ = np.any(rd.reflectometrydata[5])
valuesdict = {
'wtFactor':1.0,
'Dummy':False,
'ranId':ran.randint(0,sys.maxsize),
'Offset':[0.0,0.0],
'ifDQ':ifDQ
}
rd.Sample['ranId'] = valuesdict['ranId'] # this should be removed someday
self.GPXtree.SetItemPyData(Id,[valuesdict,rd.reflectometrydata])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Comments'),rd.comments)
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Limits'),
[(Tmin,Tmax),[Tmin,Tmax]])
self.PatternId = GetGPXtreeItemId(self,Id,'Limits')
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Instrument Parameters'),
[Iparm1,Iparm2])
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Substances'),G2pwd.SetDefaultSubstances())
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Sample Parameters'),
rd.Sample)
self.GPXtree.SetItemPyData(
self.GPXtree.AppendItem(Id,text='Models'),G2pwd.SetDefaultREFDModel())
newHistList.append(HistName)
else:
self.EnablePlot = True
self.GPXtree.Expand(Id)
self.GPXtree.SelectItem(Id)
if not newHistList: return # somehow, no new histograms
return # success
def _Add_ImportMenu_PDF(self,parent):
'''configure the PDF Data menus accord to the readers found in _init_Imports
'''
submenu = wx.Menu()
item = parent.AppendSubMenu(submenu,'PDF G(R) Data','Import PDF G(R) data')
for reader in self.ImportPDFReaderlist:
item = submenu.Append(wx.ID_ANY,readFromFile(reader),reader.longFormatName)
self.ImportMenuId[item.GetId()] = reader
self.Bind(wx.EVT_MENU, self.OnImportPDF, id=item.GetId())
submenu.AppendSeparator()
item = submenu.Append(wx.ID_ANY,'Auto Import','Import PDF files as found')
def OnAutoImport(event):
G2G.AutoLoadFiles(self,FileTyp='gr')
self.Bind(wx.EVT_MENU, OnAutoImport, id=item.GetId())
# item = submenu.Append(wx.ID_ANY,
# help='Import reflectometry data, use file to try to determine format',
# kind=wx.ITEM_NORMAL,text='guess format from file')
# self.Bind(wx.EVT_MENU, self.OnImportReflectometry, id=item.GetId())
[docs]
def OnImportPDF(self,event):
'''Called in response to an Import/PDF G(R) Data/... menu item
to read a PDF G(R) data set.
dict self.ImportMenuId is used to look up the specific
reader item associated with the menu item, which will be
None for the last menu item, which is the "guess" option
where all appropriate formats will be tried.
N.B. The code here is largely duplicated in
:mod:`GSASIIscriptable` so any changes made here
need to be duplicated there, too.
'''
# get a list of existing histograms
PDFlist = []
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name.startswith('PDF ') and name not in PDFlist:
PDFlist.append(name)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
# look up which format was requested
reqrdr = self.ImportMenuId.get(event.GetId())
rdlist = self.OnImportGeneric(
reqrdr,self.ImportPDFReaderlist,'PDF G(R) Data',multiple=True)
if len(rdlist) == 0: return
self.CheckNotebook()
newHistList = []
self.EnablePlot = False
for rd in rdlist:
HistName = rd.idstring
HistName = 'PDF '+HistName
# make new histogram names unique
HistName = G2obj.MakeUniqueLabel(HistName,PDFlist)
print ('Read PDF G(R) data '+HistName+ \
' from file '+self.lastimport)
# data are read, now store them in the tree
Id = self.GPXtree.AppendItem(self.root,text=HistName)
Ymin = np.min(rd.pdfdata[1])
Ymax = np.max(rd.pdfdata[1])
Rmin = np.min(rd.pdfdata[0])
Rmax = np.max(rd.pdfdata[0])
valuesdict = {
'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),
'Offset':[0.0,0.0],'delOffset':0.02*Ymax,
'Yminmax':[Ymin,Ymax],
}
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Comments'),rd.comments)
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='PDF Controls'),
{'G(R)':[valuesdict,rd.pdfdata,HistName],'diffGRname':'','diffMult':1.0,'Rmax':Ymax,'Type':rd.Type,
'dscale':[1.0,False],'Fitrange':[Rmin,Rmax],'qdamp':[0.03,False],'qbroad':[0,False],'Temp':300.})
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='PDF Peaks'),
{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
else:
self.EnablePlot = True
self.GPXtree.Expand(Id)
self.GPXtree.SelectItem(Id)
if not newHistList: return # somehow, no new histograms
return # success
[docs]
def AddToNotebook(self,text,typ=None, TimeStamp=True):
'''Add entry to Notebook tree item
'''
Id = GetGPXtreeItemId(self,self.root,'Notebook')
data = self.GPXtree.GetItemPyData(Id)
if TimeStamp:
data.append(f'[TS] Notebook entry @ {time.ctime()}')
if typ:
data.append(f'[{typ}] {text}')
else:
data.append(f'{text}')
def _init_Exports(self,menu):
'''Find exporter routines and add them into menus
'''
# set up the top-level menus
projectmenu = wx.Menu()
item = menu.AppendSubMenu(projectmenu,'Entire project as','Export entire project')
self.ExportNonSeq.append([menu,item.Id])
phasemenu = wx.Menu()
item = menu.AppendSubMenu(phasemenu,'Phase as','Export phase or sometimes phases')
self.ExportNonSeq.append([menu,item.Id])
powdermenu = wx.Menu()
item = menu.AppendSubMenu(powdermenu,'Powder data as','Export powder diffraction histogram(s)')
self.ExportNonSeq.append([menu,item.Id])
sasdmenu = wx.Menu()
item = menu.AppendSubMenu(sasdmenu,'Small angle data as','Export small angle histogram(s)')
refdmenu = wx.Menu()
item = menu.AppendSubMenu(refdmenu,'Reflectometry data as','Export reflectometry histogram(s)')
singlemenu = wx.Menu()
item = menu.AppendSubMenu(singlemenu,'Single crystal data as','Export single crystal histogram(s)')
imagemenu = wx.Menu()
item = menu.AppendSubMenu(imagemenu,'Image data as','Export powder image(s) data')
mapmenu = wx.Menu()
item = menu.AppendSubMenu(mapmenu,'Maps as','Export density map(s)')
# sequential exports are handled differently; N.B. en-/disabled in testSeqRefineMode
item = menu.Append(wx.ID_ANY,'Sequential project as CIF',
'Export project from sequential fit as a full CIF')
self.Bind(wx.EVT_MENU, self.DoSequentialProjExport, item)
self.ExportSeq.append([menu,item.Id])
seqPhasemenu = wx.Menu()
item = menu.AppendSubMenu(seqPhasemenu,'Sequential phases','Export phases from sequential fit')
self.ExportSeq.append([menu,item.Id])
seqHistmenu = wx.Menu()
item = menu.AppendSubMenu(seqHistmenu,'Sequential histograms','Export histograms from sequential fit')
self.ExportSeq.append([menu,item.Id])
# find all the exporter files
if not self.exporterlist: # this only needs to be done once
self.exporterlist = G2fil.LoadExportRoutines(self)
# Add submenu item(s) for each Exporter by its self-declared type (can be more than one)
for obj in self.exporterlist:
#print 'exporter',obj
for typ in obj.exporttype:
if typ == "project":
submenu = projectmenu
elif typ == "phase":
submenu = phasemenu
elif typ == "powder":
submenu = powdermenu
elif typ == "single":
submenu = singlemenu
elif typ == "image":
submenu = imagemenu
elif typ == "map":
submenu = mapmenu
elif typ == "sasd":
submenu = sasdmenu
elif typ == "refd":
submenu = refdmenu
# elif typ == "pdf":
# submenu = pdfmenu
else:
print("Error, unknown type in "+str(obj))
break
item = submenu.Append(wx.ID_ANY,obj.formatName,obj.longFormatName)
self.Bind(wx.EVT_MENU, obj.Exporter, id=item.GetId())
self.ExportLookup[item.GetId()] = typ # lookup table for submenu item
for lbl,submenu in (('Phase',seqPhasemenu),('Powder',seqHistmenu),):
if lbl.lower() in obj.exporttype:
try:
obj.Writer
except AttributeError:
continue
# define a unique event handler for this menu item
def seqMenuItemEventHandler(event,obj=obj,typ=lbl):
'This handler has the needed exporter/type embedded'
# lookup sequential table
Id = GetGPXtreeItemId(self,self.root,'Sequential results')
if not Id:
print('Error in Seq seqMenuItemEventHandler for ',typ,'without Seq Res table')
return
data = self.GPXtree.GetItemPyData(Id)
G2IO.ExportSequential(self,data,obj,typ)
if '2' in platform.python_version_tuple()[0]:
if 'mode' in inspect.getargspec(obj.Writer)[0]:
item = submenu.Append(wx.ID_ANY,obj.formatName,obj.longFormatName)
self.Bind(wx.EVT_MENU, seqMenuItemEventHandler, item)
else:
if 'mode' in inspect.getfullargspec(obj.Writer)[0]:
item = submenu.Append(wx.ID_ANY,obj.formatName,obj.longFormatName)
self.Bind(wx.EVT_MENU, seqMenuItemEventHandler, item)
item = imagemenu.Append(wx.ID_ANY,'Multiple image controls and masks',
'Export image controls and masks for multiple images')
self.Bind(wx.EVT_MENU, self.OnSaveMultipleImg, id=item.GetId())
#code to debug an Exporter. hard-code the routine below, to allow a reload before use
# def DebugExport(event):
# print 'start reload'
# reload(G2IO)
# import G2export_pwdr as dev
# reload(dev)
# dev.ExportPowderFXYE(self).Exporter(event)
# item = menu.Append(
# wx.ID_ANY,kind=wx.ITEM_NORMAL,
# help="debug exporter",text="test Export FXYE")
# self.Bind(wx.EVT_MENU, DebugExport, id=item.GetId())
# # #self.ExportLookup[item.GetId()] = 'image'
# self.ExportLookup[item.GetId()] = 'powder'
# Exporters ###################################################################
def _Add_ExportMenuItems(self,parent):
# item = parent.Append(
# help='Select PWDR item to enable',id=wx.ID_ANY,
# kind=wx.ITEM_NORMAL,
# text='Export Powder Patterns...')
# self.ExportPattern.append(item)
# item.Enable(False)
# self.Bind(wx.EVT_MENU, self.OnExportPatterns, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Export All Peak Lists...','')
self.ExportPeakList.append(item)
item.Enable(True)
self.Bind(wx.EVT_MENU, self.OnExportPeakList, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Export HKLs...','')
self.ExportHKL.append(item)
self.Bind(wx.EVT_MENU, self.OnExportHKL, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Export MTZ file...','')
self.ExportMTZ.append(item)
self.Bind(wx.EVT_MENU, self.OnExportMTZ, id=item.GetId())
item = parent.Append(wx.ID_ANY,'Export PDF...','Select PDF item to enable')
self.ExportPDF.append(item)
item.Enable(False)
self.Bind(wx.EVT_MENU, self.OnExportPDF, id=item.GetId())
[docs]
def FillMainMenu(self,menubar,addhelp=True):
'''Define contents of the main GSAS-II menu for the (main) data tree window.
For the mac, this is also called for the data item windows as well so that
the main menu items are data menu as well.
'''
File = wx.Menu(title='')
menubar.Append(menu=File, title='&File')
self._Add_FileMenuItems(File)
Data = wx.Menu(title='')
menubar.Append(menu=Data, title='Data')
self._Add_DataMenuItems(Data)
Calculate = wx.Menu(title='')
menubar.Append(menu=Calculate, title='&Calculate')
self._Add_CalculateMenuItems(Calculate)
Import = wx.Menu(title='')
menubar.Append(menu=Import, title='Import')
self._Add_ImportMenu_Image(Import)
self._Add_ImportMenu_Phase(Import)
self._Add_ImportMenu_powder(Import)
self._Add_ImportMenu_Sfact(Import)
self._Add_ImportMenu_smallangle(Import)
self._Add_ImportMenu_reflectometry(Import)
self._Add_ImportMenu_PDF(Import)
item = Import.Append(wx.ID_ANY,'Read Powder Pattern Peaks...','')
self.Bind(wx.EVT_MENU, self.OnReadPowderPeaks, id=item.GetId())
item = Import.Append(wx.ID_ANY,'Column metadata test','Test Column (.par) metadata import')
self.Bind(wx.EVT_MENU, self.OnColMetaTest, id=item.GetId())
msgs = G2fil.ImportErrorMsg()
if msgs:
item = Import.Append(wx.ID_ANY,
'Show importer error(s)',
'Show the error message explaining why importers could not be loaded')
self.Bind(wx.EVT_MENU, lambda e: G2G.ImportMsg(self,msgs),
id=item.GetId())
#======================================================================
# Code to help develop/debug an importer, much is hard-coded below
# but module is reloaded before each use, allowing faster testing
# def DebugImport(event):
# print 'start reload'
# import G2phase_ISO as dev
# reload(dev)
# rd = dev.ISODISTORTPhaseReader()
# self.ImportMenuId[event.GetId()] = rd
# self.OnImportPhase(event)
# or ----------------------------------------------------------------------
#self.OnImportGeneric(rd,[],'test of ISODISTORTPhaseReader')
# special debug code
# or ----------------------------------------------------------------------
# filename = '/Users/toby/projects/branton/subgroup_cif.txt'
# if not rd.ContentsValidator(filename):
# print 'not validated'
# # make a list of used phase ranId's
# phaseRIdList = []
# sub = GetGPXtreeItemId(self,self.root,'Phases')
# if sub:
# item, cookie = self.GPXtree.GetFirstChild(sub)
# while item:
# phaseName = self.GPXtree.GetItemText(item)
# ranId = self.GPXtree.GetItemPyData(item).get('ranId')
# if ranId: phaseRIdList.append(ranId)
# item, cookie = self.GPXtree.GetNextChild(sub, cookie)
# if rd.Reader(filename,usedRanIdList=phaseRIdList):
# print 'read OK'
# item = Import.Append(
# wx.ID_ANY,kind=wx.ITEM_NORMAL,
# help="debug importer",text="test importer")
# self.Bind(wx.EVT_MENU, DebugImport, id=item.GetId())
#======================================================================
self.ExportMenu = wx.Menu(title='')
menubar.Append(menu=self.ExportMenu, title='Export')
self._init_Exports(self.ExportMenu)
self._Add_ExportMenuItems(self.ExportMenu)
if addhelp:
HelpMenu=G2G.MyHelp(self,includeTree=True,
morehelpitems=[('&Tutorials\tCtrl+T','Tutorials'),])
menubar.Append(menu=HelpMenu,title='&Help')
def _init_ctrls(self, parent):
try:
size = GSASIIpath.GetConfigValue('Main_Size')
if type(size) is tuple:
pass
elif type(size) is str:
size = eval(size)
else:
raise Exception
except:
size = wx.Size(700,450)
wx.Frame.__init__(self, name='GSASII', parent=parent,
size=size,style=wx.DEFAULT_FRAME_STYLE, title='GSAS-II main window')
fontIncr = GSASIIpath.GetConfigValue('FontSize_incr')
if fontIncr is not None and fontIncr != 0:
f = wx.Font(self.GetFont())
f.SetPointSize(f.PointSize+fontIncr)
self.SetFont(f)
self._init_Imports()
#initialize Menu item objects (these contain lists of menu items that are enabled or disabled)
self.MakePDF = []
self.Refine = []
self.ExportSeq = []
self.ExportNonSeq = []
#self.ExportPattern = []
self.ExportPeakList = []
self.ExportHKL = []
self.ExportPDF = []
self.ExportPhase = []
self.ExportCIF = []
self.ExportMTZ = []
#
self.MacroStatusList = [] # logging
self.Status = self.CreateStatusBar()
self.Status.SetFieldsCount(2)
# Bob: note different ways to display the SplitterWindow. I like the 3d effect on the Mac
# as it makes the splitter bar a bit easier to "grab" -- this might need to be platform selected.
#self.mainPanel = wx.SplitterWindow(self, wx.ID_ANY, style=wx.SP_BORDER|wx.SP_LIVE_UPDATE)
#self.mainPanel = wx.SplitterWindow(self, wx.ID_ANY, style=wx.SP_BORDER|wx.SP_LIVE_UPDATE|wx.SP_3DSASH)
self.mainPanel = wx.SplitterWindow(self, wx.ID_ANY, style=wx.SP_LIVE_UPDATE|wx.SP_3D)
self.mainPanel.SetMinimumPaneSize(100)
self.treePanel = wx.Panel(self.mainPanel, wx.ID_ANY,
style = wx.TAB_TRAVERSAL|wx.SUNKEN_BORDER)
self.dataWindow = G2DataWindow(self.mainPanel)
dataSizer = wx.BoxSizer(wx.VERTICAL)
self.dataWindow.SetSizer(dataSizer)
sash = min(max(100,GSASIIpath.GetConfigValue('Split_Loc',250)),500)
# if GSASIIpath.GetConfigValue('debug'):
# print('SplitterWindow sash=',sash,GSASIIpath.GetConfigValue('Split_Loc'))
self.mainPanel.SplitVertically(self.treePanel, self.dataWindow.outer, sash)
self.Status.SetStatusWidths([sash,-1]) # make these match?
G2G.wxID_GPXTREE = wx.NewId()
treeSizer = wx.BoxSizer(wx.VERTICAL)
self.treePanel.SetSizer(treeSizer)
self.GPXtree = G2G.G2TreeCtrl(id=G2G.wxID_GPXTREE,
parent=self.treePanel, size=self.treePanel.GetClientSize(),style=wx.TR_DEFAULT_STYLE )
treeSizer.Add(self.GPXtree,1,wx.EXPAND|wx.ALL,0)
self.GPXtree.Bind(wx.EVT_TREE_SEL_CHANGED,self.OnDataTreeSelChanged)
self.GPXtree.Bind(wx.EVT_TREE_ITEM_RIGHT_CLICK,self.OnDataTreeSelChanged)
self.GPXtree.Bind(wx.EVT_TREE_ITEM_COLLAPSED,
self.OnGPXtreeItemCollapsed, id=G2G.wxID_GPXTREE)
self.GPXtree.Bind(wx.EVT_TREE_ITEM_EXPANDED,
self.OnGPXtreeItemExpanded, id=G2G.wxID_GPXTREE)
self.GPXtree.Bind(wx.EVT_TREE_DELETE_ITEM,
self.OnGPXtreeItemDelete, id=G2G.wxID_GPXTREE)
self.GPXtree.Bind(wx.EVT_TREE_KEY_DOWN,
self.OnGPXtreeKeyDown, id=G2G.wxID_GPXTREE)
self.GPXtree.Bind(wx.EVT_TREE_BEGIN_RDRAG,
self.OnGPXtreeBeginRDrag, id=G2G.wxID_GPXTREE)
self.GPXtree.Bind(wx.EVT_TREE_END_DRAG,
self.OnGPXtreeEndDrag, id=G2G.wxID_GPXTREE)
self.root = self.GPXtree.root
try:
size = GSASIIpath.GetConfigValue('Plot_Size')
if type(size) is tuple:
pass
elif type(size) is str:
size = eval(size)
else:
raise Exception
except:
size = wx.Size(700,600)
self.plotFrame = wx.Frame(None,-1,'GSASII Plots',size=size,
style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX)
self.G2plotNB = G2plt.G2PlotNoteBook(self.plotFrame,G2frame=self)
self.plotFrame.Show()
for win,var in ((self,'Main_Pos'),(self.plotFrame,'Plot_Pos')):
try:
pos = GSASIIpath.GetConfigValue(var)
if type(pos) is str: pos = eval(pos)
win.SetPosition(pos)
if GetDisplay(pos) is None: win.Center()
except:
if GSASIIpath.GetConfigValue(var):
print('Value for config {} {} is invalid'.format(var,GSASIIpath.GetConfigValue(var)))
win.Center()
# create a stand-in for a menu until it is created
class dummymenu(object):
def Enable(*args, **kwargs): pass
self.CancelSetLimitsMode = dummymenu()
#### init_vars ################################################################
[docs]
def init_vars(self):
''' initialize default values for GSAS-II "global" variables (saved in main Frame, G2frame)
'''
self.oldFocus = None
self.undofile = ''
self.TreeItemDelete = False
self.Weight = False
self.IfPlot = False
self.DDShowAll = False
self.atmSel = ''
self.PatternId = 0
self.PickId = 0
self.PickIdText = None
self.PeakTable = []
self.LimitsTable = []
self.ifX20 = True #use M20 /= (1+X20) in powder indexing, etc.
self.HKL = np.array([])
self.Extinct = []
self.PlotOpts = {} # new place to put plotting options
self.Lines = [] # lines used for data limits & excluded regions
self.MagLines = [] # lines used for plot magnification
self.itemPicked = None
self.Interpolate = 'nearest'
self.ContourColor = GSASIIpath.GetConfigValue('Contour_color','GSPaired')
self.VcovColor = 'RdYlGn'
self.RamaColor = 'Blues'
self.Projection = 'equal area'
self.logPlot = False
self.plusPlot = True
self.ErrorBars = False
self.CumeChi = False
self.Contour = False
self.TforYaxis = False
self.Legend = False
self.SinglePlot = True
self.Waterfall = False
self.selections= None
self.PDFselections = None
self.SubBack = False
self.seqReverse = False
self.seqLines = True #draw lines between points
self.plotView = 0
self.Image = 0
self.oldImagefile = '' # the name of the last image file read
self.oldImageTag = None # the name of the tag for multi-image files
self.PauseIntegration = False
self.ImageZ = []
self.Integrate = 0
self.imageDefault = {}
self.IntgOutList = [] # list of integration tree item Ids created in G2IO.SaveIntegration
self.AutointPWDRnames = [] # list of autoint created PWDR tree item names (to be deleted on a reset)
self.autoIntFrame = None
self.IntegratedList = [] # list of already integrated IMG tree items
self.Sngl = False
self.ifGetRing = False
self.MaskKey = '' #trigger for making image masks
self.MskDelete = False #trigger for mask delete
self.StrainKey = '' #ditto for new strain d-zeros
self.EnablePlot = True
self.hist = '' # selected histogram in Phase/Data tab
self.dataDisplayPhaseText = ''
self.lastTreeSetting = [] # used to track the selected Tree item before a refinement
self.ExpandingAll = False
self.SeqTblHideList = None
self.newGPXfile = ''
self.lastSelectedPhaseTab = None # track the last tab pressed on a phase window
self.testRBObjSizers = {} #rigid body sizer datafile contents
self.RMCchoice = 'RMCProfile'
self.ifSetLimitsMode = 0
def __init__(self, parent):
self.ExportLookup = {}
self.exporterlist = []
self._init_ctrls(parent)
self.Image = wx.Image(GSASIIpath.getIconFile('gsas2.ico'),
wx.BITMAP_TYPE_ICO)
if "wxMSW" in wx.PlatformInfo:
img = self.Image.Scale(16, 16).ConvertToBitmap()
elif "wxGTK" in wx.PlatformInfo:
img = self.Image.Scale(22, 22).ConvertToBitmap()
else:
img = self.Image.ConvertToBitmap()
if 'phoenix' in wx.version():
self.SetIcon(wx.Icon(img))
else:
self.SetIcon(wx.IconFromBitmap(img))
self.Bind(wx.EVT_CLOSE, self.ExitMain)
self.GSASprojectfile = ''
self.dirname = os.path.abspath(os.path.expanduser('~')) #start in the users home directory by default; may be meaningless
self.TutorialImportDir = None # location to read tutorial files, set when a tutorial is viewed
self.LastImportDir = None # last-used directory where an import was done
self.LastGPXdir = '' # directory where a GPX file was last or saved
self.LastExportDir = None # the last directory used for exports, if any.
self.dataDisplay = None
self.init_vars()
if GSASIIpath.GetConfigValue('Starting_directory'):
try:
pth = GSASIIpath.GetConfigValue('Starting_directory')
pth = os.path.expanduser(pth)
os.chdir(pth)
self.LastGPXdir = pth
except:
print('Ignoring Config Starting_directory value: '+
GSASIIpath.GetConfigValue('Starting_directory'))
arg = sys.argv
if len(arg) > 1 and arg[1]:
self.GSASprojectfile = os.path.splitext(arg[1])[0]+'.gpx'
self.dirname = os.path.abspath(os.path.dirname(arg[1]))
if self.dirname:
self.GSASprojectfile = os.path.split(self.GSASprojectfile)[1]
os.chdir(self.dirname)
self.LastGPXdir = self.dirname
try:
#open the file if possible
if sys.platform == "darwin": # on Mac delay a bit so GUI can open
wx.CallAfter(self.StartProject)
else:
self.StartProject()
return
except Exception:
print ('Error opening or reading file'+arg[1])
import traceback
print (traceback.format_exc())
elif any('SPYDER' in name for name in os.environ):
self.OnFileReopen(None)
[docs]
def GetTreeItemsList(self,item):
''' returns a list of all GSAS-II tree items
'''
return self.GPXtree._getTreeItemsList(item)
# def OnSize(self,event):
# 'Called to make GPXtree fill mainPanel'
# print 'OnSize'
# event.Skip()
# w,h = self.GetClientSizeTuple()
# self.dataWindow.SetupScrolling()
# self.mainPanel.SetSize(wx.Size(w,h))
# self.GPXtree.SetSize(wx.Size(w,h))
# self.dataWindow.SetSize(self.dataPanel.GetClientSize())
[docs]
def SetDataSize(self):
'''this routine is a placeholder until all G2frame.SetDataSize calls are replaced
by G2frame.dataWindow.SetDataSize
'''
# TOTO: diagnostic patch
print ('G2frame.SetDataSize called rather than dataWindow.SetDataSize')
G2obj.HowDidIgetHere(True)
self.dataWindow.SetDataSize()
[docs]
def OnDataTreeSelChanged(self, event):
'''Called when a data tree item is selected. May be called on item deletion as well.
'''
if self.TreeItemDelete:
self.TreeItemDelete = False
else:
if self.ExpandingAll:
if GSASIIpath.GetConfigValue('debug'): print('Skipping Tree selection due to ExpandAll')
return
pltNum = self.G2plotNB.nb.GetSelection()
if pltNum >= 0: #to avoid the startup with no plot!
self.G2plotNB.nb.GetPage(pltNum)
item = event.GetItem()
wx.CallAfter(SelectDataTreeItem,self,item,self.oldFocus)
#if self.oldFocus: # now done via last parameter on SelectDataTreeItem
# wx.CallAfter(self.oldFocus.SetFocus)
[docs]
def OnGPXtreeItemCollapsed(self, event):
'Called when a tree item is collapsed - all children will be collapsed'
self.GPXtree.CollapseAllChildren(event.GetItem())
[docs]
def OnGPXtreeItemExpanded(self, event):
'Called when a tree item is expanded'
event.Skip()
[docs]
def OnGPXtreeItemDelete(self, event):
'Called when a tree item is deleted, inhibit the next tree item selection action'
self.TreeItemDelete = True
[docs]
def OnGPXtreeItemActivated(self, event):
'Called when a tree item is activated'
event.Skip()
def OnGPXtreeBeginRDrag(self,event):
event.Allow()
self.BeginDragId = event.GetItem()
self.ParentId = self.GPXtree.GetItemParent(self.BeginDragId)
DragText = self.GPXtree.GetItemText(self.BeginDragId)
self.DragData = [[DragText,self.GPXtree.GetItemPyData(self.BeginDragId)],]
item, cookie = self.GPXtree.GetFirstChild(self.BeginDragId)
while item: #G2 data tree has no sub children under a child of a tree item
name = self.GPXtree.GetItemText(item)
self.DragData.append([name,self.GPXtree.GetItemPyData(item)])
item, cookie = self.GPXtree.GetNextChild(self.BeginDragId, cookie)
def OnGPXtreeEndDrag(self,event):
event.Allow()
self.EndDragId = event.GetItem()
try:
NewParent = self.GPXtree.GetItemParent(self.EndDragId)
except:
self.EndDragId = self.GPXtree.GetLastChild(self.root)
NewParent = self.root
if self.ParentId != NewParent:
self.ErrorDialog('Drag not allowed','Wrong parent for item dragged')
else:
Name,Item = self.DragData[0]
NewId = self.GPXtree.InsertItem(self.ParentId,self.EndDragId,Name,data=None)
self.GPXtree.SetItemPyData(NewId,Item)
for name,item in self.DragData[1:]: #loop over children
Id = self.GPXtree.AppendItem(parent=NewId,text=name)
self.GPXtree.SetItemPyData(Id,item)
self.GPXtree.Delete(self.BeginDragId)
SelectDataTreeItem(self,NewId)
[docs]
def OnGPXtreeKeyDown(self,event): #doesn't exactly work right with Shift key down
'Allows stepping through the tree with the up/down arrow keys'
self.oldFocus = wx.Window.FindFocus()
keyevt = event.GetKeyEvent()
key = event.GetKeyCode()
item = self.GPXtree.GetSelection()
if type(item) is int: return # is this the toplevel in tree?
name = self.GPXtree.GetItemText(item)
parent = self.GPXtree.GetItemParent(item)
if key == wx.WXK_UP:
if keyevt.GetModifiers() == wx.MOD_SHIFT and parent != self.root:
if type(parent) is int: return # is this the toplevel in tree?
prev = self.GPXtree.GetPrevSibling(parent)
NewId = GetGPXtreeItemId(self,prev,name)
if NewId:
self.GPXtree.Collapse(parent)
self.GPXtree.Expand(prev)
self.oldFocus = wx.Window.FindFocus()
wx.CallAfter(self.GPXtree.SelectItem,NewId)
else:
wx.CallAfter(self.GPXtree.SelectItem,item)
elif sys.platform == "win32":
self.GPXtree.GetPrevSibling(item)
self.GPXtree.SelectItem(item)
else:
item = self.GPXtree.GetPrevSibling(item)
if item.IsOk(): self.GPXtree.SelectItem(item)
elif key == wx.WXK_DOWN:
if keyevt.GetModifiers() == wx.MOD_SHIFT and parent != self.root:
prev = self.GPXtree.GetNextSibling(parent)
NewId = GetGPXtreeItemId(self,prev,name)
if NewId:
self.GPXtree.Collapse(parent)
self.GPXtree.Expand(prev)
self.oldFocus = wx.Window.FindFocus()
wx.CallAfter(self.GPXtree.SelectItem,NewId)
else:
wx.CallAfter(self.GPXtree.SelectItem,item)
elif sys.platform == "win32":
self.GPXtree.GetNextSibling(item)
self.GPXtree.SelectItem(item)
else:
item = self.GPXtree.GetNextSibling(item)
if item.IsOk(): self.GPXtree.SelectItem(item)
[docs]
def OnPowderFPA(self,event):
'Perform FPA simulation/peak fitting'
# if GSASIIpath.GetConfigValue('debug'):
# print('Debug: reloading G2fpa')
# import imp
# imp.reload(G2fpa)
G2fpa.GetFPAInput(self)
[docs]
def OnReadPowderPeaks(self,event):
'Bound to menu Data/Read Powder Peaks'
self.CheckNotebook()
pth = G2G.GetImportPath(self)
if not pth: pth = '.'
dlg = wx.FileDialog(self, 'Choose file with peak list', pth, '',
'peak files (*.txt)|*.txt|All files (*.*)|*.*',wx.FD_MULTIPLE)
try:
if dlg.ShowModal() == wx.ID_OK:
for file_ajk in dlg.GetPaths():
self.HKL = np.array([])
self.Extinct = []
self.powderfile = file_ajk
comments,peaks,limits,wave = G2IO.GetPowderPeaks(self.powderfile)
Id = self.GPXtree.AppendItem(parent=self.root,text='PKS '+os.path.basename(self.powderfile))
data = ['PKS',wave,0.0]
names = ['Type','Lam','Zero']
codes = [0,0,0]
inst = [G2fil.makeInstDict(names,data,codes),{}]
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Comments'),comments)
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Limits'),[tuple(limits),limits])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Index Peak List'),[peaks,[]])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
self.GPXtree.Expand(Id)
self.GPXtree.SelectItem(Id)
os.chdir(dlg.GetDirectory()) # to get Mac/Linux to change directory!
finally:
dlg.Destroy()
[docs]
def CheckNotebook(self):
'''Make sure the data tree has the minimally expected controls.
'''
new = False
if not GetGPXtreeItemId(self,self.root,'Notebook'):
new = True
sub = self.GPXtree.AppendItem(parent=self.root,text='Notebook')
self.GPXtree.SetItemPyData(sub,[''])
if not GetGPXtreeItemId(self,self.root,'Controls'):
new = True
sub = self.GPXtree.AppendItem(parent=self.root,text='Controls')
self.GPXtree.SetItemPyData(sub,copy.copy(G2obj.DefaultControls))
if not GetGPXtreeItemId(self,self.root,'Covariance'):
new = True
sub = self.GPXtree.AppendItem(parent=self.root,text='Covariance')
self.GPXtree.SetItemPyData(sub,{})
if not GetGPXtreeItemId(self,self.root,'Constraints'):
new = True
sub = self.GPXtree.AppendItem(parent=self.root,text='Constraints')
self.GPXtree.SetItemPyData(sub,{'Hist':[],'HAP':[],'Phase':[],
'Global':[],'_seqmode':'auto-wildcard', '_seqhist':0})
if not GetGPXtreeItemId(self,self.root,'Restraints'):
new = True
sub = self.GPXtree.AppendItem(parent=self.root,text='Restraints')
self.GPXtree.SetItemPyData(sub,{})
if not GetGPXtreeItemId(self,self.root,'Rigid bodies'):
new = True
sub = self.GPXtree.AppendItem(parent=self.root,text='Rigid bodies')
self.GPXtree.SetItemPyData(sub,{'Vector':{'AtInfo':{}},'Residue':{'AtInfo':{}},
'Spin':{},'RBIds':{'Vector':[],'Residue':[],'Spin':[]}})
if new:
self.GPXtree.Expand(self.GPXtree.root)
[docs]
class SumDialog(wx.Dialog):
'''Used to sum images or powder patterns. Allows user to supply
scale factor(s) when summing data.
TODO: clean up the scrolling & resize on this dialog. Can we use the copy down button from CIF?
TODO: move it to GSASIIctrlGUI? (BHT) this class should not be in
the middle of the (already too complex) GSASIImain class.
'''
def __init__(self,parent,title,text,dataType,data,dataList,Limits=None):
wx.Dialog.__init__(self,parent,-1,title,size=(400,250),
pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER)
self.plotFrame = wx.Frame(self,-1,'Sum Plots',size=wx.Size(700,600), \
style=wx.DEFAULT_FRAME_STYLE ^ wx.CLOSE_BOX)
self.G2plotNB = G2plt.G2PlotNoteBook(self.plotFrame,G2frame=self)
self.text = text
self.data = data
self.average = False
self.selectData = copy.copy(data[:-1])
self.selectVals = len(data)*[0.0,]
self.dataList = dataList
self.Limits = Limits
self.filterlist = range(len(self.dataList)) # list of the choice numbers that have been filtered (list of int indices)
self.dataType = dataType
self.filterVal = ''
self.panel = None
self.Draw()
def Draw(self):
if self.panel:
self.panel.DestroyChildren() #safe: wx.Panel
self.panel.Destroy()
size = (480,350)
self.panel = wxscroll.ScrolledPanel(self, wx.ID_ANY,size=size,
style = wx.TAB_TRAVERSAL|wx.SUNKEN_BORDER)
mainSizer = wx.BoxSizer(wx.VERTICAL)
mainSizer.Add(wx.StaticText(self.panel,label=self.text),0)
mainSizer.Add((10,10))
self.dataGridSizer = wx.FlexGridSizer(cols=2,hgap=2,vgap=2)
self.dataGridSizer.Add((-1,-1))
topSizer = wx.BoxSizer(wx.HORIZONTAL)
topSizer.Add((-1,-1),1,wx.EXPAND,1)
topSizer.Add(wx.StaticText(self.panel,label='Filter: '),0,WACV)
self.timer = wx.Timer()
self.timer.Bind(wx.EVT_TIMER,self.OnFilter)
self.filterBox = wx.TextCtrl(self.panel, wx.ID_ANY, self.filterVal,
size=(80,-1),style=wx.TE_PROCESS_ENTER)
self.filterBox.Bind(wx.EVT_TEXT,self.onChar)
self.filterBox.Bind(wx.EVT_TEXT_ENTER,self.OnFilter)
topSizer.Add(self.filterBox,0,WACV)
self.dataGridSizer.Add(topSizer,1,wx.RIGHT|wx.BOTTOM|wx.EXPAND,1)
self.dataGridSizer.Add((-1,10))
self.dataGridSizer.Add((-1,10))
for Id,item in enumerate(self.selectData):
name = wx.TextCtrl(self.panel,-1,item,size=wx.Size(300,20))
name.SetEditable(False)
scale = G2G.ValidatedTxtCtrl(self.panel,self.selectVals,Id,nDig=(10,3),typeHint=float)
self.dataGridSizer.Add(scale,0,wx.LEFT,10)
self.dataGridSizer.Add(name,0,wx.RIGHT,10)
if self.dataType:
ScaleAll = wx.Button(self.panel,wx.ID_ANY,'Set all above')
ScaleAll.Bind(wx.EVT_BUTTON, self.OnAllScale)
if self.dataType == 'PWDR':
self.Avg = wx.CheckBox(self.panel,label=' Make average?')
self.Avg.Bind(wx.EVT_CHECKBOX,self.OnAve)
self.dataGridSizer.Add(ScaleAll,0,wx.LEFT,10)
if self.dataType == 'PWDR':
self.dataGridSizer.Add(self.Avg,0,wx.RIGHT,10)
self.dataGridSizer.Add(wx.StaticText(self.panel,-1,' Result type: '+self.dataType),1,
wx.LEFT|wx.ALIGN_CENTER_VERTICAL,1)
mainSizer.Add(self.dataGridSizer,0,wx.EXPAND)
self.name = G2G.ValidatedTxtCtrl(self.panel,self.data,-1,size=wx.Size(300,20))
mainSizer.Add(self.name,0,wx.RIGHT|wx.TOP,10)
self.OkBtn = wx.Button(self.panel,-1,"Ok")
self.OkBtn.Bind(wx.EVT_BUTTON, self.OnOk)
cancelBtn = wx.Button(self.panel,-1,"Cancel")
cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel)
btnSizer = wx.FlexGridSizer(0,3,10,20)
if self.dataType =='PWDR':
TestBtn = wx.Button(self.panel,-1,"Test")
TestBtn.Bind(wx.EVT_BUTTON, self.OnTest)
btnSizer.Add(TestBtn)
btnSizer.Add(self.OkBtn)
btnSizer.Add(cancelBtn)
btnSizer.Add((5,5))
self.panel.SetSizer(mainSizer)
self.panel.SetAutoLayout(1)
self.panel.SetupScrolling()
mainSizer.Add((10,10),1)
mainSizer.Add(btnSizer,0,wx.CENTER)
self.panel.SetSizer(mainSizer)
self.panel.Fit()
self.Fit()
def OnAve(self,event):
self.average = self.Avg.GetValue()
[docs]
def OnFilter(self,event):
'''Read text from filter control and select entries that match.
'''
if self.timer.IsRunning():
self.timer.Stop()
self.filterVal = txt = self.filterBox.GetValue()
if txt:
txt = txt.lower()
ChoiceList = []
ChoiceVals = []
for i,item in enumerate(self.selectData):
if item.lower().find(txt) != -1:
ChoiceList.append(item)
ChoiceVals.append(self.selectVals[i])
self.selectData = ChoiceList
self.selectVals = ChoiceVals
else:
# self.selectData = copy.copy(self.data[:-1])
self.selectVals = len(self.data)*[0.0,]
wx.CallAfter(self.Draw)
def GetData(self):
if self.dataType == 'PWDR':
return self.selectData+[self.data[-1],],self.result
else:
return self.selectData+[self.data[-1],],self.selectVals
[docs]
def onChar(self,event):
'Respond to keyboard events in the Filter box'
self.filterVal = self.filterBox.GetValue()
if self.timer.IsRunning():
self.timer.Stop()
self.timer.Start(1000,oneShot=True)
if event: event.Skip()
def OnAllScale(self,event):
dlg = G2G.SingleFloatDialog(self,'New scale',
'Enter new value for all scale factors',1.)
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
val = dlg.GetValue()
dlg.Destroy()
else:
dlg.Destroy()
return
for Id,item in enumerate(self.selectData):
self.selectVals[Id] = val
wx.CallAfter(self.Draw)
def OnTest(self,event):
lenX = 0
Xminmax = [0,0]
XY = []
Xsum = []
Ysum = []
Vsum = []
for i,item in enumerate(self.selectData):
name = item
scale = self.selectVals[i]
Id = self.data.index(name)
data = self.dataList[Id]
if scale:
x,y,w,yc,yb,yd = data #numpy arrays!
if self.Limits is not None:
xMin = np.searchsorted(x,self.Limits[1][0])
xMax = np.searchsorted(x,self.Limits[1][1])
x = x[xMin:xMax+1]
y = y[xMin:xMax+1]
lenX = xMax-xMin+1
XY.append([x,scale*y])
v = 1./w[xMin:xMax+1]
if lenX:
if lenX != len(x):
self.GetParent().ErrorDialog('Data length error','Data to be summed must have same number of points'+
'\nExpected:'+str(lenX)+
'\nFound: '+str(len(x))+'\nfor '+name)
return
# self.OnCancel(event)
else:
lenX = len(x)
if Xminmax[1]:
if Xminmax != [x[0],x[-1]]:
self.GetParent().ErrorDialog('Data range error','Data to be summed must span same range'+
'\nExpected:'+str(Xminmax[0])+' '+str(Xminmax[1])+
'\nFound: '+str(x[0])+' '+str(x[-1])+'\nfor '+name)
return
# self.OnCancel(event)
else:
Xminmax = [x[0],x[-1]]
Xsum = x
if self.dataType == 'PWDR' and self.average:
Ysum.append(scale*y)
Vsum.append(abs(scale)*v)
else:
try:
Ysum += scale*y
Vsum += abs(scale)*v
except ValueError:
Ysum = scale*y
Vsum = abs(scale)*v
if self.dataType =='PWDR' and self.average:
maYsum = ma.masked_equal(Ysum,0)
Ysum = ma.mean(maYsum,axis=0)
Wsum = 1./np.array(Ysum)
else:
Wsum = 1./Vsum
YCsum = np.zeros(lenX)
YBsum = np.zeros(lenX)
YDsum = np.zeros(lenX)
XY.append([Xsum,Ysum])
self.result = [Xsum,Ysum,Wsum,YCsum,YBsum,YDsum]
# N.B. PlotXY expects the first arg to point to G2frame. In this case, we
# create a duplicate (temporary) Plot notebook window that is a child of the
# modal SumDialog dialog (self). This nicely gets deleted when the dialog is destroyed,
# but the plot window is not fully functional, at least on the Mac.
if len(XY[0][0]):
G2plt.PlotXY(self,XY,lines=True,Title='Sum:'+self.data[-1],labelY='Intensity',)
self.plotFrame.Show()
return True
def OnOk(self,event):
if self.dataType == 'PWDR':
if not self.OnTest(event): return
parent = self.GetParent()
if parent is not None: parent.Raise()
self.EndModal(wx.ID_OK)
def OnCancel(self,event):
parent = self.GetParent()
if parent is not None: parent.Raise()
self.EndModal(wx.ID_CANCEL)
[docs]
def OnPwdrSum(self,event):
'Sum or Average together powder data(?)'
TextList = []
DataList = []
Limits = []
Names = []
Inst = None
Comments = ['Sum/Average equals: \n']
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
Names.append(name)
if 'PWDR' in name:
TextList.append(name)
DataList.append(self.GPXtree.GetItemPyData(item)[1]) # (x,y,w,yc,yb,yd)
if not Inst:
Inst = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,item, 'Instrument Parameters'))
if not Limits:
Limits = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,item, 'Limits'))
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
if len(TextList) < 2:
self.ErrorDialog('Not enough data to sum/average','There must be more than one "PWDR" pattern')
return
TextList.append('default_ave_name')
dlg = self.SumDialog(self,'Sum/Average data','''
Enter scale for each pattern to be summed/averaged
Limits for first pattern used sets range for the sum
All patterns used must extend over this range
''','PWDR',
TextList,DataList,Limits)
try:
if dlg.ShowModal() == wx.ID_OK:
result,sumData = dlg.GetData()
Xsum,Ysum,Wsum,YCsum,YBsum,YDsum = sumData
Xminmax = [Xsum[0],Xsum[-1]]
outname = 'PWDR '+result[-1]
Id = 0
if outname in Names:
dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK|wx.CANCEL)
try:
if dlg2.ShowModal() == wx.ID_OK:
Id = GetGPXtreeItemId(self,self.root,name)
self.GPXtree.Delete(Id)
finally:
dlg2.Destroy()
Id = self.GPXtree.AppendItem(parent=self.root,text=outname)
if Id:
Sample = G2obj.SetDefaultSample()
Ymin = np.min(Ysum)
Ymax = np.max(Ysum)
valuesdict = {
'wtFactor':1.0,
'Dummy':False,
'ranId':ran.randint(0,sys.maxsize),
'Offset':[0.0,0.0],'delOffset':0.02*Ymax,'refOffset':-.1*Ymax,'refDelt':0.1*Ymax,
'Yminmax':[Ymin,Ymax]
}
self.GPXtree.SetItemPyData(Id,[valuesdict,[np.array(Xsum),np.array(Ysum),np.array(Wsum),
np.array(YCsum),np.array(YBsum),np.array(YDsum)]])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Comments'),Comments)
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Limits'),[tuple(Xminmax),Xminmax])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Background'),[['chebyschev-1',True,3,1.0,0.0,0.0],
{'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[],'background PWDR':['',1.0,False]}])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Instrument Parameters'),Inst)
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Peak List'),{'peaks':[],'sigDict':{}})
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
self.GPXtree.SelectItem(Id)
self.GPXtree.Expand(Id)
finally:
dlg.Destroy()
[docs]
def OnImageSum(self,event):
'Sum together image data'
TextList = []
DataList = []
IdList = []
Names = []
Items = []
Comments = ['Sum equals: \n']
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
Names.append(name)
if 'IMG' in name:
Items.append(item)
TextList.append(name)
DataList.append(self.GPXtree.GetImageLoc(item)) #Size,Image,Tag
IdList.append(item)
Data = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,item,'Image Controls'))
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
if len(TextList) < 2:
self.ErrorDialog('Not enough data to sum','There must be more than one "IMG" pattern')
return
TextList.append('default_sum_name')
dlg = self.SumDialog(self,'Sum data',' Enter scale for each image to be summed','IMG',
TextList,DataList)
chkItems = ['pixelSize','wavelength','distance','center','size','tilt','rotation']
try:
if dlg.ShowModal() == wx.ID_OK:
imSize = 0
result,scales = dlg.GetData()
First = True
Found = False
for item,name,scale in zip(Items,result,scales):
if scale:
if not Found:
Data = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,item,'Image Controls'))
chkData = {Id:Data[Id] for Id in chkItems}
else:
data = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,item,'Image Controls'))
chkdata = {Id:data[Id] for Id in chkItems}
if str(chkdata) != str(chkData):
self.ErrorDialog('Image Controls error','Images to be summed must have same Image Controls - see Console for list')
chkDiff = [[iD,chkData[iD],chkdata[iD]] for iD in chkData if str(chkData[iD]) != str(chkdata[iD])]
print('Differences: ')
for diff in chkDiff:
print('%s: %s %s'%(diff[0],str(diff[1]),str(diff[2])))
return
Found = True
Comments.append("%10.3f %s" % (scale,' * '+name))
i = TextList.index(name)
Npix,imagefile,imagetag = DataList[i]
imagefile = G2IO.GetCheckImageFile(self,IdList[i])[1]
image = G2fil.GetImageData(self,imagefile,imageOnly=True,ImageTag=imagetag)
if First:
newImage = np.zeros_like(image)
First = False
if imSize:
if imSize != Npix:
self.ErrorDialog('Image size error','Images to be summed must be same size'+ \
'\nExpected:'+str(imSize)+ \
'\nFound: '+str(Npix)+'\nfor '+name)
return
newImage = newImage+scale*image
else:
imSize = Npix
newImage = newImage+scale*image
del(image)
if not Found:
self.ErrorDialog('Image sum error','No nonzero image multipliers found')
return
newImage = np.array(newImage,dtype=np.int32)
outname = 'IMG '+result[-1]
Id = 0
if outname in Names:
dlg2 = wx.MessageDialog(self,'Overwrite data?','Duplicate data name',wx.OK|wx.CANCEL)
try:
if dlg2.ShowModal() == wx.ID_OK:
Id = GetGPXtreeItemId(self,self.root,name)
finally:
dlg2.Destroy()
else:
Id = self.GPXtree.AppendItem(parent=self.root,text=outname)
if Id:
pth = os.path.split(os.path.abspath(imagefile))[0]
# pth = G2G.GetExportPath(self)
dlg = wx.FileDialog(self, 'Choose sum image filename', pth,outname.split('IMG ')[1],
'G2img files (*.G2img)|*.G2img',
wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
if dlg.ShowModal() == wx.ID_OK:
newimagefile = dlg.GetPath()
newimagefile = G2IO.FileDlgFixExt(dlg,newimagefile)
G2IO.PutG2Image(newimagefile,Comments,Data,Npix,newImage)
Imax = int(np.amax(newImage))
Imin = int(np.amin(newImage))
newImage = []
self.GPXtree.SetItemPyData(Id,[imSize,newimagefile])
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Comments'),Comments)
del(newImage)
if self.imageDefault:
Data.update(copy.deepcopy(self.imageDefault))
Data['formatName'] = 'GSAS-II image'
Data['showLines'] = True
Data['ring'] = []
Data['rings'] = []
Data['cutoff'] = 10
Data['pixLimit'] = 20
Data['ellipses'] = []
Data['calibrant'] = ''
Data['range'] = [(Imin,Imax),[Imin,Imax]]
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Image Controls'),Data)
Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],
'Frames':[],'Thresholds':[(Imin,Imax),[Imin,Imax]],
'SpotMask':{'esdMul':2.,'spotMask':None}}
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Masks'),Masks)
self.GPXtree.SetItemPyData(self.GPXtree.AppendItem(Id,text='Stress/Strain'),
{'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
self.GPXtree.SelectItem(Id)
self.GPXtree.Expand(Id)
self.PickId = GetGPXtreeItemId(self,self.root,outname)
self.Image = self.PickId
finally:
dlg.Destroy()
[docs]
def OnAddPhase(self,event):
'Add a new, empty phase to the tree. Called by Data/Add Phase menu'
PhaseName = ''
dlg = wx.TextEntryDialog(self,'Enter a name for this phase','Phase Name Entry','New phase',
style=wx.OK)
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
PhaseName = dlg.GetValue()
self.CheckNotebook()
sub = FindPhaseItem(self)
dlg.Destroy()
else:
dlg.Destroy()
return
if not GetGPXtreeItemId(self,self.root,'Restraints'):
subr = self.GPXtree.AppendItem(parent=self.root,text='Restraints')
self.GPXtree.SetItemPyData(subr,{PhaseName:{}})
else:
subr = GetGPXtreeItemId(self,self.root,'Restraints')
self.GPXtree.GetItemPyData(subr).update({PhaseName:{}})
self.GPXtree.AppendItem(parent=subr,text=PhaseName)
newphase = self.GPXtree.AppendItem(parent=sub,text=PhaseName)
E,SGData = G2spc.SpcGroup('P 1')
self.GPXtree.SetItemPyData(newphase,G2obj.SetNewPhase(Name=PhaseName,SGData=SGData))
self.GPXtree.Expand(sub)
SelectDataTreeItem(self,newphase) #bring up new phase General tab
[docs]
def OnDeletePhase(self,event):
'''Delete one or more phases from the tree. Called by Data/Delete Phase menu.
Also delete this phase from Reflection Lists for each PWDR histogram;
removes the phase from restraints and deletes any constraints
with variables from the phase.
If any deleted phase is marked as Used in a histogram, a more rigorous
"deep clean" is done and histogram refinement results are cleared, as well as
the covariance information and all plots are deleted
'''
selItem = self.GPXtree.GetSelection()
if self.dataWindow:
self.dataWindow.ClearData()
TextList = []
DelList = []
DelItemList = []
consDeleted = 0
usedPhase = False
if GetGPXtreeItemId(self,self.root,'Phases'):
sub = GetGPXtreeItemId(self,self.root,'Phases')
else:
return
if GetGPXtreeItemId(self,self.root,'Restraints'):
subr = GetGPXtreeItemId(self,self.root,'Restraints')
else:
subr = 0
if GetGPXtreeItemId(self,self.root,'Constraints'):
id = GetGPXtreeItemId(self,self.root,'Constraints')
constr = self.GPXtree.GetItemPyData(id)
else:
constr = {}
item, cookie = self.GPXtree.GetFirstChild(sub)
while item:
TextList.append(self.GPXtree.GetItemText(item))
item, cookie = self.GPXtree.GetNextChild(sub, cookie)
dlg = wx.MultiChoiceDialog(self, 'Which phase(s) to delete?', 'Delete phase', TextList, wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelections()
for i in result: DelList.append([i,TextList[i]])
item, cookie = self.GPXtree.GetFirstChild(sub)
i = 0
while item:
if [i,self.GPXtree.GetItemText(item)] in DelList: DelItemList.append(item)
item, cookie = self.GPXtree.GetNextChild(sub, cookie)
i += 1
for item in DelItemList:
phase = self.GPXtree.GetItemPyData(item)
for h in phase['Histograms']:
if 'Use' not in phase['Histograms'][h]: continue
if phase['Histograms'][h]['Use']:
usedPhase = True
break
if 'pId' in phase:
p = phase['pId']
else:
p = '?'
self.GPXtree.Delete(item)
if item == selItem: selItem = self.root
# look for constraints to remove
for key in constr:
delThis = []
if key.startswith('_'): continue
for i,cons in enumerate(constr[key]):
for var in cons[0:-3]:
if str(var[1]).startswith(str(p)):
delThis.append(i)
break
for i in reversed(delThis):
consDeleted += 1
del constr[key][i]
# delete refinement results from histograms
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if 'PWDR' in name:
data = self.GPXtree.GetItemPyData(item)
if usedPhase: # remove r-factors
dellist = [value for value in data[0] if ':' in value]
for v in dellist+['Durbin-Watson', 'R', 'wR', 'Rb',
'wRb', 'wRmin','Nobs']:
if v in data[0]: del data[0][v]
# could wipe out computed & difference patterns, but does not work
#data[1][3] = np.zeros_like(data[1][3])
#data[1][5] = np.zeros_like(data[1][5])
# always get rid of reflection lists
Id = GetGPXtreeItemId(self,item, 'Reflection Lists')
refList = self.GPXtree.GetItemPyData(Id)
if len(refList):
for i,item in DelList:
if item in refList:
del(refList[item])
elif 'HKLF' in name and usedPhase: # probably not needed if phase is not used
data = self.GPXtree.GetItemPyData(item)
data[0] = {}
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
finally:
dlg.Destroy()
if usedPhase: # clear info from last refinement for "deep clean" if a used phase is deleted
id = GetGPXtreeItemId(self,self.root,'Covariance')
if DelItemList and id:
self.GPXtree.SetItemPyData(id,{})
id = GetGPXtreeItemId(self,self.root,'Sequential results')
if DelItemList and id:
self.GPXtree.Delete(id)
if id == selItem: selItem = self.root
# delete all plots
for lbl in self.G2plotNB.plotList:
self.G2plotNB.Delete(lbl)
if subr and DelList: #remove restraints for deleted phase
DelList = [itm[1] for itm in DelList]
item, cookie = self.GPXtree.GetFirstChild(subr)
while item:
name = self.GPXtree.GetItemText(item)
if name in DelList:
self.GPXtree.Delete(item)
if item == selItem: selItem = self.root
item, cookie = self.GPXtree.GetNextChild(subr, cookie)
# force redisplay of current tree item if it was not deleted
self.PickId = 0
self.PatternId = 0
self.PickIdText = None
SelectDataTreeItem(self,selItem)
wx.CallAfter(self.GPXtree.SelectItem,selItem)
if consDeleted:
print('\n',consDeleted,'constraints were deleted')
[docs]
def OnRenameData(self,event):
'''Renames an existing histogram. Called by Data/Rename Phase menu.
Must be used before a histogram is used in a phase.
'''
name = self.GPXtree.GetItemText(self.PickId)
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree()
if name in Histograms:
G2G.G2MessageBox(self,
'Histogram is used. You must remove it from all phases before it can be renamed',
'Rename not allowed')
return
if 'PWDR' in name or 'HKLF' in name or 'IMG' in name:
if 'Bank' in name:
names = name.split('Bank')
names[1] = ' Bank'+names[1]
elif 'Azm' in name:
names = name.split('Azm')
names[1] = ' Azm'+names[1]
else:
names = [name,'']
dataType = names[0][:names[0].index(' ')+1] #includes the ' '
dlg = G2G.SingleStringDialog(self,'Change tree name',
'Data name: '+name,names[0][names[0].index(' ')+1:])
#if dlg.ShowModal() == wx.ID_OK:
if dlg.Show():
name = dataType+dlg.GetValue().strip()+names[1]
self.GPXtree.SetItemText(self.PickId,name)
if 'PWDR' in name:
self.GPXtree.GetItemPyData(self.PickId)[2] = name
dlg.Destroy()
[docs]
def GetFileList(self,fileType,skip=None):
''' Get list of file names containing a particular string; can skip one of known GSAS-II id
param: fileType str: any string within a file name
param: skip int:default=None, a GSAS-II assigned id of a data item to skip in collecting the names
returns: list of file names from GSAS-II tree
returns: str name of file optionally skipped
Appears unused, but potentially useful.
Note routine of same name in GSASIIpwdGUI; it does not have the skip option
'''
fileList = []
Source = ''
Id, cookie = self.GPXtree.GetFirstChild(self.root)
while Id:
name = self.GPXtree.GetItemText(Id)
if fileType in name:
if Id == skip:
Source = name
else:
fileList.append([False,name,Id])
Id, cookie = self.GPXtree.GetNextChild(self.root, cookie)
if skip:
return fileList,Source
else:
return fileList
[docs]
def OnDataDelete(self, event):
'''Delete one or more histograms from data tree. Called by the
Data/DeleteData menu
'''
TextList = []
DelList = []
DelItemList = []
nItems = {'PWDR':0,'SASD':0,'REFD':0,'IMG':0,'HKLF':0,'PDF':0}
PDFnames = []
selItem = self.GPXtree.GetSelection()
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree()
if not self.GPXtree.GetCount():
G2G.G2MessageBox(self,'No tree items to be deleted','Nothing to delete')
return
item, cookie = self.GPXtree.GetFirstChild(self.root)
used = False
seqUse = False
while item:
name = self.GPXtree.GetItemText(item)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
if name in ['Notebook','Controls','Covariance','Constraints',
'Restraints','Phases','Rigid bodies','Hist/Phase']:
continue
if 'Sequential' in name:
continue
if name in self.testSeqRefineMode():
seqUse = True
continue
if 'PWDR' in name[:4]:
nItems['PWDR'] += 1
if name in Histograms:
used = True
continue
if 'SASD' in name[:4]: nItems['SASD'] += 1
if 'REFD' in name[:4]: nItems['REFD'] += 1
if 'IMG' in name[:3]: nItems['IMG'] += 1
if 'HKLF' in name[:4]:
nItems['HKLF'] += 1
if name in Histograms:
used = True
continue
if 'PDF' in name[:3]:
PDFnames.append(name)
nItems['PDF'] += 1
TextList.append(name)
for pdfName in PDFnames:
try:
TextList.remove('PWDR'+pdfName[4:])
except ValueError:
print (u'PWDR'+pdfName[4:]+u' for '+pdfName+u' not found')
if len(TextList) == 0:
if used:
msg = 'All histograms are associated with at least one phase. You must unset a histogram "use" flag in all phase(s) where it is referenced before it can be deleted'
elif seqUse:
msg = 'All histograms are in used in the sequential list. You must remove it from the list (in Controls) before it can be deleted'
else:
msg = 'No data items found in tree to delete'
G2G.G2MessageBox(self,msg,'Nothing to delete')
return
dlg = G2G.G2MultiChoiceDialog(self, 'Which data to delete?', 'Delete data', TextList, wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelections()
for i in result: DelList.append(TextList[i])
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
itemName = self.GPXtree.GetItemText(item)
if itemName in DelList:
if 'PWDR' in itemName[:4]: nItems['PWDR'] -= 1
elif 'SASD' in itemName[:4]: nItems['SASD'] -= 1
elif 'REFD' in itemName[:4]: nItems['REFD'] -= 1
elif 'IMG' in itemName[:3]: nItems['IMG'] -= 1
elif 'HKLF' in itemName[:4]: nItems['HKLF'] -= 1
elif 'PDF' in itemName[:3]: nItems['PDF'] -= 1
DelItemList.append(item)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
for item in DelItemList:
self.GPXtree.Delete(item)
if item == selItem: selItem = self.root
if DelList:
self.PickId = 0
self.PickIdText = None
self.PatternId = 0
if nItems['PWDR']:
wx.CallAfter(G2pwpl.PlotPatterns,self,True)
else:
self.G2plotNB.Delete('Powder Patterns')
self.lastPlotType = None
if not nItems['IMG']:
self.G2plotNB.Delete('2D Powder Image')
if not nItems['HKLF']:
self.G2plotNB.Delete('Structure Factors')
if '3D Structure Factors' in self.G2plotNB.plotList:
self.G2plotNB.Delete('3D Structure Factors')
finally:
dlg.Destroy()
if DelList:
SelectDataTreeItem(self,selItem)
try: # fails if previously selected item is deleted
self.GPXtree.UpdateSelection()
except:
self.GPXtree.SelectItem(self.root)
[docs]
def OnPlotDelete(self,event):
'''Delete one or more plots from plot window. Called by the
Data/DeletePlots menu
'''
plotNames = self.G2plotNB.plotList
if len(plotNames):
dlg = G2G.G2MultiChoiceDialog(self, 'Which plots to delete?', 'Delete plots', plotNames, wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelections()
result.sort(reverse=True)
for i in result:
self.G2plotNB.Delete(plotNames[i])
finally:
dlg.Destroy()
[docs]
def OnDeleteSequential(self,event):
''' Delete any sequential results table. Called by the Data/Delete sequential results menu
'''
selItem = self.GPXtree.GetSelection()
SeqList = []
DelList = []
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if 'Sequential' in name:
SeqList.append(name)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
if not len(SeqList):
G2G.G2MessageBox(self,'No tree items to be deleted','Nothing to delete')
return
dlg = G2G.G2MultiChoiceDialog(self, 'Which sequential results to delete?', 'Delete seq resulta', SeqList, wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelections()
finally:
dlg.Destroy()
DelList = [SeqList[i] for i in result]
if not len(DelList):
G2G.G2MessageBox(self,'No tree items selected','Nothing deleted')
return
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
itemName = self.GPXtree.GetItemText(item)
if itemName in DelList:
self.GPXtree.Delete(item)
if item == selItem: selItem = self.root
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
SelectDataTreeItem(self,selItem)
self.GPXtree.UpdateSelection()
[docs]
def OnFileReopen(self, event):
''' Creates a dialog box showing previously opened GSAS-II projects & offers to open one
called by File/Reopen recent... menu item
'''
files = GSASIIpath.GetConfigValue('previous_GPX_files')
if not files:
print('no previous projects found')
return
sellist = []
keeplist = []
try:
for f in files:
dirname,filroot = os.path.split(f)
if os.path.exists(f) and '.gpx' in f:
sellist.append("{} from {}".format(filroot,dirname))
keeplist.append(f)
except:
print('Error processing previous project list:',files)
if len(keeplist) == 0:
GSASIIpath.SetConfigValue({'previous_GPX_files':tuple([])})
return
dlg = G2G.G2SingleChoiceDialog(self,'Select previous project to open',
'Select project',sellist)
dlg.CenterOnParent()
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelection()
dlg.Destroy()
else:
dlg.Destroy()
return
filroot,dirname = sellist[sel].split(' from ')
f = os.path.join(dirname,filroot)
if os.path.exists(f):
self.OnFileOpen(event, filename=f)
self.LastGPXdir = dirname
else:
print('file not found',f)
[docs]
def OnFileReread(self, event):
'''reread the current GPX file; no questions asked -- no save
for development purposes.
'''
def _setStart(nameParent,name):
'''Reload the last selected tree item by name'''
start = self.root
if GetGPXtreeItemId(self,self.root,nameParent):
start = GetGPXtreeItemId(self,self.root,nameParent)
Id = GetGPXtreeItemId(self,start,name)
#breakpoint()
if Id:
self.GPXtree.SelectItem(Id)
SelectDataTreeItem(self,Id)
Id = self.GPXtree.GetSelection()
parent = self.GPXtree.GetItemParent(Id)
name = self.GPXtree.GetItemText(Id)
nameParent = self.GPXtree.GetItemText(parent)
f = os.path.join(self.LastGPXdir,self.GSASprojectfile)
if os.path.exists(f):
self.OnFileOpen(event, filename=f, askSave=False)
else:
print('file not found',f)
wx.CallLater(100,_setStart,nameParent,name)
def _SaveOld(self,askSave=True):
'''See if we should save current project and continue
to read another.
returns True if the project load should continue
'''
if self.dataWindow:
self.dataWindow.ClearData()
if self.dataWindow and askSave:
dlg = wx.MessageDialog(self,
'Do you want to save and replace the current project?\n'
'(Use No to read without saving or Cancel to continue '
'with current project)',
'Save & Overwrite?',
wx.YES|wx.NO|wx.CANCEL)
try:
result = dlg.ShowModal()
finally:
dlg.Destroy()
if result == wx.ID_NO:
result = True
elif result == wx.ID_CANCEL:
return False
else:
if not self.OnFileSave(None):
return False
self.GPXtree.DeleteChildren(self.root)
self.GSASprojectfile = ''
self.HKL = np.array([])
self.Extinct = []
if self.G2plotNB.plotList:
self.G2plotNB.clear()
return True
[docs]
def OnFileOpen(self, event, filename=None, askSave=True):
'''Gets a GSAS-II .gpx project file in response to the
File/Open Project menu button
'''
def GetGPX():
if self.LastGPXdir:
pth = self.LastGPXdir
else:
pth = '.'
#if GSASIIpath.GetConfigValue('debug'): print('debug: open from '+pth)
dlg = wx.FileDialog(self, 'Choose GSAS-II project file', pth,
wildcard='GSAS-II project file (*.gpx)|*.gpx',style=wx.FD_OPEN)
try:
if dlg.ShowModal() != wx.ID_OK: return
self.GSASprojectfile = dlg.GetPath()
self.GSASprojectfile = G2IO.FileDlgFixExt(dlg,self.GSASprojectfile)
self.LastGPXdir = dlg.GetDirectory()
finally:
dlg.Destroy()
self.EnablePlot = False
if self.GPXtree.GetChildrenCount(self.root,False):
if not self._SaveOld(askSave=askSave): return
if not filename:
GetGPX()
filename = self.GSASprojectfile
else:
self.GSASprojectfile = os.path.splitext(filename)[0]+'.gpx'
self.dirname = os.path.split(filename)[0]
# if self.G2plotNB.plotList:
# self.G2plotNB.clear()
self.init_vars()
try:
self.StartProject() #open the file if possible
except:
print ('\nError opening file '+filename)
import traceback
print (traceback.format_exc())
[docs]
def OnFileBrowse(self, event):
'''Gets a GSAS-II .gpx project using the GPX browser, in response
to the File/"Open Project browser" menu button
'''
self.EnablePlot = False
if self.LastGPXdir:
pth = self.LastGPXdir
else:
pth = '.'
try:
dlg = G2G.gpxFileSelector(parent=self,startdir=pth)
if wx.ID_OK == dlg.ShowModal():
filename = dlg.Selection
else:
return
finally:
dlg.Destroy()
if self.GPXtree.GetChildrenCount(self.root,False):
if not self._SaveOld(): return # cancel was entered; nothing changed
self.GSASprojectfile = filename
self.LastGPXdir = os.path.split(os.path.abspath(filename))[0]
self.init_vars()
try:
self.StartProject() #open the file if possible
except:
print ('\nError opening file '+filename)
import traceback
print (traceback.format_exc())
[docs]
def StartProject(self):
'''Opens a GSAS-II project file & selects the 1st available data set to
display (PWDR, HKLF, REFD or SASD)
'''
Id = 0
phaseId = None
seqId = None
G2IO.ProjFileOpen(self)
self.GPXtree.SetItemText(self.root,'Project: '+self.GSASprojectfile)
self.GPXtree.Expand(self.root)
self.HKL = np.array([])
self.Extinct = []
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name[:4] in ['PWDR','HKLF','IMG ','PDF ','SASD','REFD']:
if not Id:
if name[:4] == 'IMG ':
Id = GetGPXtreeItemId(self,item,'Image Controls')
else:
Id = item
elif name.startswith("Sequential") and self.testSeqRefineMode():
seqId = item
elif name == "Phases":
phaseId = item
elif name == 'Controls':
data = self.GPXtree.GetItemPyData(item)
if data:
for item in self.Refine: item.Enable(True)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
if phaseId: # show all phases
self.GPXtree.Expand(phaseId)
if seqId:
self.EnablePlot = True
SelectDataTreeItem(self,seqId)
self.GPXtree.SelectItem(seqId) # needed on OSX or item is not selected in tree; perhaps not needed elsewhere
elif Id:
self.EnablePlot = True
self.GPXtree.Expand(Id)
SelectDataTreeItem(self,Id)
self.GPXtree.SelectItem(Id) # needed on OSX or item is not selected in tree; perhaps not needed elsewhere
elif phaseId:
Id = phaseId
# open 1st phase
Id, unused = self.GPXtree.GetFirstChild(phaseId)
SelectDataTreeItem(self,Id)
self.GPXtree.SelectItem(Id) # as before for OSX
self.CheckNotebook()
if self.dirname: os.chdir(self.dirname) # to get Mac/Linux to change directory!
pth = os.path.split(os.path.abspath(self.GSASprojectfile))[0]
if GSASIIpath.GetConfigValue('Save_paths'):
G2G.SaveGPXdirectory(pth,write=False)
config = G2G.GetConfigValsDocs()
GSASIIpath.addPrevGPX(self.GSASprojectfile,config) # add new proj
G2G.SaveConfigVars(config)
self.LastGPXdir = pth
if GSASIIpath.GetConfigValue('debug'):
cmdfile = os.path.join(GSASIIpath.path2GSAS2,'debug_setup.py')
if os.path.exists(cmdfile):
print(f'executing debug commands from {cmdfile}')
txt = open(cmdfile,'r').read()
def exectxt():
# print(txt)
exec(txt)
wx.CallLater(100,exectxt)
[docs]
def OnFileClose(self, event):
'''Clears the data tree in response to the
File/New Project menu button. User is given option to save
the project.
'''
dlg = wx.MessageDialog(self,
'Do you want to save the current project and start with an empty one?\n(Use No to clear without saving or Cancel to continue with current project)',
'Save & Clear?',
wx.YES | wx.NO | wx.CANCEL)
try:
result = dlg.ShowModal()
if result == wx.ID_OK:
self.OnFileSaveMenu(event)
if result != wx.ID_CANCEL:
self.GSASprojectfile = ''
self.clearProject()
finally:
dlg.Destroy()
[docs]
def clearProject(self):
'Initializes the data tree etc.'
self.GPXtree.SetItemText(self.root,'Project: ')
self.GPXtree.DeleteChildren(self.root)
self.dataWindow.ClearData()
if len(self.HKL):
self.HKL = np.array([])
self.Extinct = []
if self.G2plotNB.plotList:
self.G2plotNB.clear()
self.SetTitleByGPX()
self.EnableRefineCommand()
self.init_vars()
G2obj.IndexAllIds({},{}) # clear old index info
[docs]
def OnFileSave(self, event):
'''Save the current project in response to the
File/Save Project menu button
'''
if self.GSASprojectfile:
self.GPXtree.SetItemText(self.root,'Project: '+self.GSASprojectfile)
self.CheckNotebook()
G2IO.ProjFileSave(self)
return True
else:
return self.OnFileSaveas(event)
[docs]
def OnNewGSASII(self, event):
'''Gets a GSAS-II .gpx project file in response to the
File/Open new window menu button.
'''
if self.LastGPXdir:
pth = self.LastGPXdir
else:
pth = '.'
GSASprojectfile = ''
dlg = wx.FileDialog(self, 'Choose GSAS-II project file', pth,
wildcard='GSAS-II project file (*.gpx)|*.gpx',style=wx.FD_OPEN)
try:
if dlg.ShowModal() == wx.ID_OK:
GSASprojectfile = dlg.GetPath()
if not os.path.exists(GSASprojectfile):
print(f'File not found {GSASprojectfile}')
dlg.Destroy()
return
self.LastGPXdir = dlg.GetDirectory()
finally:
dlg.Destroy()
G2fil.openInNewTerm(GSASprojectfile)
[docs]
def SetTitleByGPX(self):
'''Set the title for the two window frames
'''
projName = os.path.split(self.GSASprojectfile)[1]
if not projName: projName = "<unnamed project>"
if self.testSeqRefineMode():
s = u' (sequential refinement)'
else:
s = u''
self.SetTitle("GSAS-II project: "+projName + s)
self.plotFrame.SetTitle("GSAS-II plots: "+projName)
[docs]
def OnFileSaveas(self, event):
'''Save the current project with a new name in response to the
File/Save as menu button. The current project then has this new name
'''
if GSASIIpath.GetConfigValue('Starting_directory'):
pth = GSASIIpath.GetConfigValue('Starting_directory')
pth = os.path.expanduser(pth)
elif self.LastGPXdir:
pth = self.LastGPXdir
else:
pth = '.'
dlg = wx.FileDialog(self, 'Choose GSAS-II project file name', pth, self.newGPXfile,
'GSAS-II project file (*.gpx)|*.gpx',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
try:
if dlg.ShowModal() == wx.ID_OK: #TODO: what about Cancel?
self.GSASprojectfile = dlg.GetPath()
self.GSASprojectfile = G2IO.FileDlgFixExt(dlg,self.GSASprojectfile)
self.GPXtree.SetItemText(self.root,'Project: '+self.GSASprojectfile)
self.CheckNotebook()
G2IO.ProjFileSave(self)
self.SetTitleByGPX()
self.LastGPXdir = dlg.GetDirectory()
os.chdir(self.LastGPXdir)
config = G2G.GetConfigValsDocs()
GSASIIpath.addPrevGPX(self.GSASprojectfile,config) # add new name
G2G.SaveConfigVars(config)
return True
else:
return False
finally:
dlg.Destroy()
[docs]
def ExpandAll(self,event):
'''Expand all tree items or those of a single type
'''
txt = self.GetMenuBar().GetLabel(event.Id)
if txt == 'all':
self.ExpandingAll = True
try:
self.GPXtree.ExpandAll()
finally:
self.ExpandingAll = False
else:
self.ExpandingAll = True
try:
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name.startswith(txt+' '): self.GPXtree.Expand(item)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
finally:
self.ExpandingAll = False
[docs]
def MoveTreeItems(self,event):
'''Move tree items of a single type to the end of the tree
'''
txt = self.GetMenuBar().GetLabel(event.Id)
# make a list of items to copy
copyList = []
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
if self.GPXtree.GetItemText(item).startswith(txt+' '):
copyList.append(item)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
self.ExpandingAll = True
try:
for item in copyList:
name = self.GPXtree.GetItemText(item)
newId = self.GPXtree.AppendItem(self.root,name)
self.GPXtree.SetItemPyData(newId,self.GPXtree.GetItemPyData(item))
chld, chldcookie = self.GPXtree.GetFirstChild(item)
while chld:
chname = self.GPXtree.GetItemText(chld)
newCh = self.GPXtree.AppendItem(newId,chname)
self.GPXtree.SetItemPyData(newCh,self.GPXtree.GetItemPyData(chld))
chld, chldcookie = self.GPXtree.GetNextChild(item, chldcookie)
self.GPXtree.Delete(item)
finally:
self.ExpandingAll = False
SelectDataTreeItem(self,self.root)
[docs]
def ExitMain(self, event):
'''Called if exit selected or the main window is closed
record last position of data & plot windows to config
NB: not called if console window closed
'''
if self.GPXtree.GetCount() > 1:
dlg = wx.MessageDialog(self,
'Do you want to save and exit?\n(Use No to exit without save or Cancel to prevent exiting)',
'Confirm exit/save?',
wx.YES|wx.NO|wx.CANCEL)
try:
dlg.CenterOnParent()
result = dlg.ShowModal()
finally:
dlg.Destroy()
else:
result = wx.ID_NO
if result == wx.ID_NO:
pass
elif result == wx.ID_CANCEL:
return
else:
# add a version number to Notebook before exiting
try:
gv = GSASIIpath.getSavedVersionInfo()
if gv is not None:
for item in gv.git_tags+gv.git_prevtags:
if item.isnumeric(): ver = int(item)
if '?' not in gv.git_versiontag: tag = gv.git_versiontag
rtext = f'version {gv.git_version[:8]} {ver}/{tag}'
self.AddToNotebook(rtext,'VER')
except:
pass
if not self.OnFileSave(event): return
try:
FrameInfo = {'Main_Pos':tuple(self.GetPosition()),
'Main_Size':tuple(self.GetSize()),
'Plot_Pos':tuple(self.plotFrame.GetPosition()),
'Plot_Size':tuple(self.plotFrame.GetSize())}
GSASIIpath.AddConfigValue(FrameInfo)
GSASIIpath.AddConfigValue({'Split_Loc':self.mainPanel.GetSashPosition()})
config = G2G.GetConfigValsDocs()
G2G.SaveConfigVars(config)
except:
print('Config save failed')
if self.G2plotNB:
self.G2plotNB.Destroy()
if self.undofile and os.path.exists(self.undofile):
os.remove(self.undofile)
sys.exit()
[docs]
def OnExportMTZ(self,event):
''' exports MTZ file from macromoleculat Reflection Lists in multiple histograms
'''
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree()
MTZok = False
for phase in Phases:
Phase = Phases[phase]
General = Phase['General']
if 'macro' in General['Type']: #really ought to be just one
SGData = General['SGData']
Cell = General['Cell'][1:7]
MTZok = True
break
if not MTZok:
wx.MessageBox('No macromolecular phase found; no MTZ file created',caption='No macromolecular phase',
style=wx.ICON_EXCLAMATION)
return
header = 'Select histograms for MTZ file:'
histList = [item for item in Histograms]
od = {'label_1':'Export Fo^2','value_1':False,}
dlg = G2G.G2MultiChoiceDialog(self,header,'Add to MTZ',histList,extraOpts=od)
result = None
if dlg.ShowModal() == wx.ID_OK:
result = dlg.GetSelections()
dlg.Destroy()
if not result: return
useHist = [histList[item] for item in result]
useFo = not od['value_1']
nDif = len(useHist)
nCol = 4*nDif+3
refDict = {}
Hrange = [1000,-1000]
Krange = [1000,-1000]
Lrange = [1000,-1000]
dRange = [10000.,0.0]
IoRange = [[10000.0,0.0] for i in range(nDif)]
IcRange = [[10000.0,0.0] for i in range(nDif)]
SigRange = [[10000.0,0.0] for i in range(nDif)]
for ih,hist in enumerate(useHist):
Refset = Histograms[hist]['Reflection Lists'][General['Name']]['RefList']
for ref in Refset:
Hrange[0] = min(ref[0],Hrange[0])
Hrange[1] = max(ref[0],Hrange[1])
Krange[0] = min(ref[1],Krange[0])
Krange[1] = max(ref[1],Krange[1])
Lrange[0] = min(ref[2],Lrange[0])
Lrange[1] = max(ref[2],Lrange[1])
dRange[0] = min(ref[4],dRange[0])
dRange[1] = max(ref[4],dRange[1])
if useFo:
IoRange[ih][0] = min(np.sqrt(ref[8]),IoRange[ih][0])
IoRange[ih][1] = max(np.sqrt(ref[8]),IoRange[ih][1])
SigRange[ih][0] = min(np.sqrt(ref[8])/2.,SigRange[ih][0])
SigRange[ih][1] = max(np.sqrt(ref[8])/2.,SigRange[ih][1])
IcRange[ih][0] = min(np.sqrt(ref[9]),IcRange[ih][0])
IcRange[ih][1] = max(np.sqrt(ref[9]),IcRange[ih][1])
else:
IoRange[ih][0] = min(ref[8],IoRange[ih][0])
IoRange[ih][1] = max(ref[8],IoRange[ih][1])
SigRange[ih][0] = min(np.sqrt(ref[8]),SigRange[ih][0])
SigRange[ih][1] = max(np.sqrt(ref[8]),SigRange[ih][1])
IcRange[ih][0] = min(ref[9],IcRange[ih][0])
IcRange[ih][1] = max(ref[9],IcRange[ih][1])
hklStr = '%5d%5d%5d'%(ref[0],ref[1],ref[2])
if useFo:
rec = {ih:np.array([np.sqrt(ref[8]),np.sqrt(ref[8])/2.,np.sqrt(ref[9]),ref[10]],dtype=np.float32)}
else:
rec = {ih:np.array([ref[8],np.sqrt(ref[8]),ref[9],ref[10]],dtype=np.float32)}
if hklStr in refDict:
refDict[hklStr].update(rec)
else:
refDict[hklStr] = rec
nRef = len(refDict)
#set up header stuff
Header = '%s'%('VERS MTZ:V1.1'.ljust(80))
Header += ('TITLE %s'%(General['Name'])).ljust(80)
Header += ('NCOL %10d%10d%10d'%(nCol,nRef,0)).ljust(80)
Header += ('CELL %9.4f%9.4f%9.4f%9.4f%9.4f%9.4f'%(Cell[0],Cell[1],Cell[2],Cell[3],Cell[4],Cell[5])).ljust(80)
Header += 'SORT 1 2 3 0 0'.ljust(80)
Nops = len(SGData['SGOps'])
Ncent = len(SGData['SGCen'])
SGSym = SGData['SpGrp']
SGnum = G2spc.SpaceGroupNumber(SGSym)
Header += ("SYMINF %6d%6d %s %6d '%s' PG%s"%(Nops*Ncent,Nops,SGSym[0],SGnum,SGSym,SGData['SGPtGrp'])).ljust(80)
SGtext,SGTable = G2spc.SGPrint(SGData)
textOps = G2spc.TextOps(SGtext,SGTable,reverse=True)
for ops in textOps:
Header += ('SYMM %s'%ops.upper()).ljust(80)
Header += ('RESO %.8f %.8f '%(1./dRange[1]**2,1./dRange[0]**2)).ljust(80)
Header += 'VALM NAN'.ljust(80)
Header += ('COLUMN %s H%18d%18d'%('H'.ljust(30),Hrange[0],Hrange[1])).ljust(79)+'0'
Header += ('COLUMN %s H%18d%18d'%('K'.ljust(30),Krange[0],Krange[1])).ljust(79)+'0'
Header += ('COLUMN %s H%18d%18d'%('L'.ljust(30),Lrange[0],Lrange[1])).ljust(79)+'0'
for ih,hist in enumerate(useHist):
hname = hist.split()[1].split('.')[0]
if useFo:
Header += ('COLUMN %s F%18.4f%18.4f'%(('F_'+hname).ljust(30),IoRange[ih][0],IoRange[ih][1])).ljust(78)+'%2d'%(ih+1)
Header += ('COLUMN %s Q%18.8f%18.8f'%(('SIGFP_'+hname).ljust(30),SigRange[ih][0],SigRange[ih][1])).ljust(78)+'%2d'%(ih+1)
Header += ('COLUMN %s F%18.4f%18.4f'%(('FC_'+hname).ljust(30),IcRange[ih][0],IcRange[ih][1])).ljust(78)+'%2d'%(ih+1)
else:
Header += ('COLUMN %s J%18.4f%18.4f'%(('I_'+hname).ljust(30),IoRange[ih][0],IoRange[ih][1])).ljust(78)+'%2d'%(ih+1)
Header += ('COLUMN %s Q%18.8f%18.8f'%(('SIGI_'+hname).ljust(30),SigRange[ih][0],SigRange[ih][1])).ljust(78)+'%2d'%(ih+1)
Header += ('COLUMN %s J%18.4f%18.4f'%(('IC_'+hname).ljust(30),IcRange[ih][0],IcRange[ih][1])).ljust(78)+'%2d'%(ih+1)
Header += ('COLUMN %s P%18.4f%18.4f'%(('PHIC_'+hname).ljust(30),-180.0,180.)).ljust(78)+'%2d'%(ih+1)
Header += ('NDIF %10d'%nDif).ljust(80)
projName = os.path.split(self.GSASprojectfile)[1]
for iH,hist in enumerate(useHist):
hname = hist.split()[1].split('.')[0]
Iparm = Histograms[hist]['Instrument Parameters'][0]
wave = G2mth.getWave(Iparm)
cell = G2lat.CellDijCorr(Cell,SGData,Phase['Histograms'],hist)
Header += ('PROJECT %7d %s'%(iH+1,projName)).ljust(80)
Header += ('CRYSTAL %7d %s'%(iH+1,General['Name'])).ljust(80)
Header += ('DATASET %7d %s'%(iH+1,hname)).ljust(80)
Header += ('DCELL %7d %10.4f%10.4f%10.4f%10.4f%10.4f%10.4f' \
%(iH+1,cell[0],cell[1],cell[2],cell[3],cell[4],cell[5])).ljust(80) # not correct- sholud include Dijs
Header += ('DWAVE %7d %10.5f'%(iH+1,wave)).ljust(80)
Header += ('END'.ljust(80))
Header += ('Created by GSAS-II on %s'%time.ctime()).ljust(80)
Header += ('MTZENDOFHEADER'.ljust(80))
if useFo:
fName = General['Name'].replace(' ','_')+'F.mtz'
else:
fName = General['Name'].replace(' ','_')+'F2.mtz'
MTZ = open(fName,'wb')
MTZ.write(st.pack('4sl2s70x',b'MTZ ',21+nCol*nRef,b'DA'))
for ref in refDict:
rec = [float(i) for i in ref.split()]
refData = refDict[ref]
for i in range(nDif):
if i in refData:
rec += list(refData[i])
else:
rec += [np.nan,np.nan,np.nan,np.nan]
string = b''
for item in rec:
string += st.pack('f',item)
MTZ.write(string)
MTZ.write(Header.encode())
MTZ.close()
print('MTZ file %s written'%fName)
[docs]
def OnExportPeakList(self,event):
'''Exports a PWDR peak list as a text file
'''
pth = G2G.GetExportPath(self)
dlg = wx.FileDialog(self, 'Choose output peak list file name', pth, '',
'(*.*)|*.*',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
try:
if dlg.ShowModal() == wx.ID_OK:
self.peaklistfile = dlg.GetPath()
self.peaklistfile = G2IO.FileDlgFixExt(dlg,self.peaklistfile)
file = open(self.peaklistfile,'w')
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if 'PWDR' in name:
item2, cookie2 = self.GPXtree.GetFirstChild(item)
wave = 0.0
while item2:
name2 = self.GPXtree.GetItemText(item2)
if name2 == 'Instrument Parameters':
Inst = self.GPXtree.GetItemPyData(item2)[0]
Type = Inst['Type'][0]
if 'T' not in Type:
wave = G2mth.getWave(Inst)
elif name2 == 'Peak List':
pkdata = self.GPXtree.GetItemPyData(item2)
peaks = pkdata['peaks']
sigDict = pkdata['sigDict']
item2, cookie2 = self.GPXtree.GetNextChild(item, cookie2)
file.write("#%s \n" % (name+' Peak List'))
if wave:
file.write('#wavelength = %10.6f\n'%(wave))
if 'T' in Type:
file.write('#%9s %10s %10s %12s %10s %10s %10s %10s %10s %10s\n'%('pos','dsp','esd','int','esd','alp','bet','sig','gam','FWHM'))
else:
file.write('#%9s %10s %10s %12s %10s %10s %10s %10s %10s %10s\n'%('pos','dsp','esd','int','esd','sig','esd','gam','esd','FWHM'))
for ip,peak in enumerate(peaks):
dsp = G2lat.Pos2dsp(Inst,peak[0])
if 'T' in Type: #TOF - more cols
esds = {'pos':0.,'int':0.,'alp':0.,'bet':0.,'sig':0.,'gam':0.}
for name in list(esds.keys()):
esds[name] = sigDict.get('%s%d'%(name,ip),0.)
sig = np.sqrt(peak[8])
gam = peak[10]
esddsp = abs(G2lat.Pos2dsp(Inst,peak[0]-esds['pos'])-G2lat.Pos2dsp(Inst,peak[0]+esds['pos']))/2.
FWHM = G2pwd.getgamFW(gam,sig) +(peak[4]+peak[6])*np.log(2.)/(peak[4]*peak[6]) #to get delta-TOF from Gam(peak)
file.write("%10.2f %10.5f %10.5f %12.2f%10.2f %10.3f %10.3f %10.3f %10.3f %10.3f\n" % \
(peak[0],dsp,esddsp,peak[2],esds['int'],peak[4],peak[6],peak[8],peak[10],FWHM))
else: #CW
#get esds from sigDict for each peak & put in output - esds for sig & gam from UVWXY?
esds = {'pos':0.,'int':0.,'sig':0.,'gam':0.}
for name in list(esds.keys()):
esds[name] = sigDict.get('%s%d'%(name,ip),0.)
sig = np.sqrt(peak[4]) #var -> sig
gam = peak[6]
esddsp = abs(G2lat.Pos2dsp(Inst,peak[0]-esds['pos'])-G2lat.Pos2dsp(Inst,peak[0]+esds['pos']))/2.
FWHM = G2pwd.getgamFW(gam,sig) #to get delta-2-theta in deg. from Gam(peak)
file.write("%10.4f %10.5f %10.5f %12.2f %10.2f %10.5f %10.5f %10.5f %10.5f %10.5f \n" % \
(peak[0],dsp,esddsp,peak[2],esds['int'],np.sqrt(max(0.0001,peak[4]))/100.,esds['sig']/100.,peak[6]/100.,esds['gam']/100,FWHM/100.)) #convert to deg
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
file.close()
finally:
dlg.Destroy()
[docs]
def OnExportHKL(self,event):
'''Exports a PWDR reflection list as a text file
'''
pth = G2G.GetExportPath(self)
dlg = wx.FileDialog(self, 'Choose output reflection list file name', pth, '',
'(*.*)|*.*',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
try:
if dlg.ShowModal() == wx.ID_OK:
self.peaklistfile = dlg.GetPath()
self.peaklistfile = G2IO.FileDlgFixExt(dlg,self.peaklistfile)
file = open(self.peaklistfile,'w')
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if 'PWDR' in name:
item2, cookie2 = self.GPXtree.GetFirstChild(item)
while item2:
name2 = self.GPXtree.GetItemText(item2)
if name2 == 'Reflection Lists':
data = self.GPXtree.GetItemPyData(item2)
phases = data.keys()
for phase in phases:
peaks = data[phase]
I100 = peaks['RefList'].T[8]*np.array([refl[11] for refl in peaks['RefList']])
Imax = np.max(I100)
if Imax:
I100 *= 100.0/Imax
file.write("%s %s %s \n" % (name,phase,' Reflection List'))
if 'T' in peaks.get('Type','PXC'):
file.write('%s \n'%(' h k l m d-space TOF wid Fo**2 Fc**2 Icorr Prfo Trans ExtP I100'))
else:
file.write('%s \n'%(' h k l m d-space 2-theta wid Fo**2 Fc**2 Icorr Prfo Trans ExtP I100'))
for ipk,peak in enumerate(peaks['RefList']):
if 'T' in peaks.get('Type','PXC'):
sig = np.sqrt(peak[6])
gam = peak[7]
FWHM = G2pwd.getgamFW(gam,sig)
file.write(" %3d %3d %3d %3d%10.5f%10.2f%10.5f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" % \
(int(peak[0]),int(peak[1]),int(peak[2]),int(peak[3]),peak[4],peak[5],FWHM,peak[8],
peak[9],peak[11],peak[12],peak[13],peak[14],I100[ipk]))
else:
sig = np.sqrt(peak[6])
gam = peak[7]
FWHM = G2pwd.getgamFW(gam,sig)
file.write(" %3d %3d %3d %3d%10.5f%10.5f%10.5f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" % \
(int(peak[0]),int(peak[1]),int(peak[2]),int(peak[3]),peak[4],peak[5],FWHM/100.,
peak[8],peak[9],peak[11],peak[12],peak[13],peak[14],I100[ipk]))
item2, cookie2 = self.GPXtree.GetNextChild(item, cookie2)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
file.close()
finally:
dlg.Destroy()
[docs]
def OnExportPDF(self,event):
'Save S(Q), G(R),... as selected by user'
def PDFSave(G2frame,exports,PDFsaves):
'Save a PDF I(Q), S(Q), F(Q), G(r) and g(r) in column formats'
if len(exports) > 1:
dirname = G2G.askSaveDirectory(G2frame)
if not dirname: return
else:
defnam = exports[0].replace(' ','_')[5:]
filename = G2G.askSaveFile(G2frame,defnam,'.gr','G(r) file, etc.')
if not filename: return
dirname,filename = os.path.split(filename)
filename = os.path.splitext(filename)[0]
Inst = None
Limits = None
for export in exports:
if len(exports) > 1:
filename = export.replace(' ','_')[5:]
PickId = GetGPXtreeItemId(G2frame, G2frame.root, export)
PDFControls = G2frame.GPXtree.GetItemPyData(
GetGPXtreeItemId(G2frame, PickId,'PDF Controls'))
if PDFsaves[4]: #pdfGUI file for G(R)
pId = GetGPXtreeItemId(G2frame, G2frame.root, 'PWDR'+export[4:])
Inst = G2frame.GPXtree.GetItemPyData(
GetGPXtreeItemId(G2frame, pId,'Instrument Parameters'))[0]
Limits = G2frame.GPXtree.GetItemPyData(
GetGPXtreeItemId(G2frame, pId,'Limits'))
G2fil.PDFWrite(export,os.path.join(dirname,filename),
PDFsaves,PDFControls,Inst,Limits)
names = G2pdG.GetFileList(self,'PDF')
exports = []
if names:
od = {'label_1':'Export I(Q)','value_1':False,'label_2':'Export S(Q)','value_2':False,
'label_3':'Export F(Q)','value_3':False,'label_4':'Export G(R)','value_4':True,
'label_5':'Make G(R) for pdfGUI','value_5':False,
'label_6':'Make F(Q) & g(r) for RMCProfile','value_6':False}
dlg = G2G.G2MultiChoiceDialog(self,'Select','PDF patterns to export',names,extraOpts=od)
if dlg.ShowModal() == wx.ID_OK:
sel = dlg.GetSelections()
for x in sel:
exports.append(names[x])
dlg.Destroy()
if exports:
PDFsaves = [od['value_1'],od['value_2'],od['value_3'],od['value_4'],od['value_5'],od['value_6']]
PDFSave(self,exports,PDFsaves)
[docs]
def OnMakePDFs(self,event):
'''Sets up PDF data structure filled with defaults; if found chemical formula is inserted
so a default PDF can be made.
'''
sind = lambda x: math.sin(x*math.pi/180.)
tth2q = lambda t,w:4.0*math.pi*sind(t/2.0)/w
tof2q = lambda t,C:2.0*math.pi*C/t
TextList = []
ElLists = []
Qlimits = []
Names = []
if self.GPXtree.GetCount():
Id, cookie = self.GPXtree.GetFirstChild(self.root)
while Id:
name = self.GPXtree.GetItemText(Id)
Names.append(name)
if 'PWDR' in name:
TextList.append(name)
Data = self.GPXtree.GetItemPyData(Id)[1]
pwdrMin = np.min(Data[1])
Comments = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,Id,'Comments'))
Parms = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,Id,'Instrument Parameters'))[0]
fullLimits = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,Id,'Limits'))[0]
if 'T' in Parms['Type'][0]:
qMax = tof2q(fullLimits[0],Parms['difC'][1])
else: #'A', 'B' or 'C'
wave = G2mth.getWave(Parms)
qMax = tth2q(fullLimits[1],wave)
Qlimits.append([0.9*qMax,qMax])
ElList = {}
sumnum = 1.
for item in Comments: #grab chemical formula from Comments
if 'formula' in item[:15].lower():
formula = item.split('=')[1].strip('"\n').split()
try:
if len(formula) < 2:
raise ValueError
elems = formula[::2]
nums = formula[1::2]
Formula = zip(elems,nums)
sumnum = 0.
for [elem,num] in Formula:
ElData = copy.deepcopy(G2elem.GetElInfo(elem,Parms))
ElData['FormulaNo'] = float(num)
sumnum += float(num)
ElList[elem] = ElData
except ValueError:
G2G.G2MessageBox(self,'Carbon-based (and wrong) PDF will be generated','Missing chemical formula')
ElData = copy.deepcopy(G2elem.GetElInfo('C',Parms))
sumnum = 1.0
ElData['FormulaNo'] = 1.0
ElList['C'] = ElData
ElLists.append(ElList)
Id, cookie = self.GPXtree.GetNextChild(self.root, cookie)
if len(TextList) < 1:
self.ErrorDialog('Nothing to make PDFs for','There must be at least one "PWDR" pattern')
return
dlg = G2G.G2MultiChoiceDialog(self,'Make PDF controls','Make PDF controls for:',TextList, wx.CHOICEDLG_STYLE)
try:
if dlg.ShowModal() == wx.ID_OK:
for i in dlg.GetSelections():
PDFnames = GetGPXtreeDataNames(self,['PDF ',])
G2obj.CreatePDFitems(self,TextList[i],ElLists[i],Qlimits[i],sumnum,pwdrMin,PDFnames)
for item in self.ExportPDF: item.Enable(True)
finally:
dlg.Destroy()
[docs]
def GetPWDRdatafromTree(self,PWDRname):
''' Returns powder data from GSASII tree
:param str PWDRname: a powder histogram name as obtained from
:meth:`GSASIIstruct.GetHistogramNames`
:returns: PWDRdata = powder data dictionary with
Powder data arrays, Limits, Instrument Parameters,
Sample Parameters
'''
PWDRdata = {}
try:
PWDRdata.update(self.GPXtree.GetItemPyData(PWDRname)[0]) #wtFactor + ?
except ValueError:
PWDRdata['wtFactor'] = 1.0
PWDRdata['Data'] = self.GPXtree.GetItemPyData(PWDRname)[1] #powder data arrays
PWDRdata['Limits'] = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,PWDRname,'Limits'))
PWDRdata['Background'] = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,PWDRname,'Background'))
PWDRdata['Instrument Parameters'] = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,PWDRname,'Instrument Parameters'))
PWDRdata['Sample Parameters'] = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,PWDRname,'Sample Parameters'))
PWDRdata['Reflection Lists'] = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,PWDRname,'Reflection Lists'))
if 'ranId' not in PWDRdata: # patch, add a random Id
PWDRdata['ranId'] = ran.randint(0,sys.maxsize)
if 'ranId' not in PWDRdata['Sample Parameters']: # I hope this becomes obsolete at some point
PWDRdata['Sample Parameters']['ranId'] = PWDRdata['ranId']
return PWDRdata
[docs]
def GetHKLFdatafromTree(self,HKLFname):
''' Returns single crystal data from GSASII tree
:param str HKLFname: a single crystal histogram name as obtained
from
:meth:`GSASIIstruct.GetHistogramNames`
:returns: HKLFdata = single crystal data list of reflections
'''
HKLFdata = {}
HKLFdata.update(self.GPXtree.GetItemPyData(HKLFname)[0]) #wtFactor + ?
# try:
# HKLFdata.update(self.GPXtree.GetItemPyData(HKLFname)[0]) #wtFactor + ?
# except ValueError:
# HKLFdata['wtFactor'] = 1.0
HKLFdata['Data'] = self.GPXtree.GetItemPyData(HKLFname)[1]
HKLFdata['Instrument Parameters'] = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,HKLFname,'Instrument Parameters'))
return HKLFdata
[docs]
def GetPhaseData(self):
'''Returns a dict with defined phases.
Note routine :func:`GSASIIstrIO.GetPhaseData` also exists to
get same kind of info from GPX file & put in a list of 9 items.
'''
phaseData = {}
if GetGPXtreeItemId(self,self.root,'Phases'):
sub = GetGPXtreeItemId(self,self.root,'Phases')
else:
# print 'no phases found in GetPhaseData'
sub = None
if sub:
item, cookie = self.GPXtree.GetFirstChild(sub)
while item:
phaseName = self.GPXtree.GetItemText(item)
phaseData[phaseName] = self.GPXtree.GetItemPyData(item)
if 'ranId' not in phaseData[phaseName]:
phaseData[phaseName]['ranId'] = ran.randint(0,sys.maxsize)
item, cookie = self.GPXtree.GetNextChild(sub, cookie)
return phaseData
[docs]
def GetPhaseInfofromTree(self, Used=False):
'''Get the phase names and their rId values,
also the histograms referenced in each phase.
:param bool Used: if Used is True, only histograms that are
referenced in the histogram are returned
:returns: (phaseRIdList, usedHistograms) where
* phaseRIdList is a list of random Id values for each phase
* usedHistograms is a dict where the keys are the phase names
and the values for each key are a list of the histogram names
used in each phase.
'''
phaseRIdList = []
usedHistograms = {}
sub = GetGPXtreeItemId(self,self.root,'Phases')
if sub:
item, cookie = self.GPXtree.GetFirstChild(sub)
while item:
phaseName = self.GPXtree.GetItemText(item)
ranId = self.GPXtree.GetItemPyData(item).get('ranId')
if ranId: phaseRIdList.append(ranId)
data = self.GPXtree.GetItemPyData(item)
UseList = data['Histograms']
if Used:
usedHistograms[phaseName] = [h for h in UseList if UseList[h].get('Use',True)]
else:
usedHistograms[phaseName] = list(UseList.keys())
item, cookie = self.GPXtree.GetNextChild(sub, cookie)
return phaseRIdList,usedHistograms
[docs]
def GetPhaseNames(self):
'''Returns a list of defined phases.
Note routine :func:`GSASIIstrIO.GetPhaseNames` also exists to
get same info from GPX file.
'''
phaseNames = []
if GetGPXtreeItemId(self,self.root,'Phases'):
sub = GetGPXtreeItemId(self,self.root,'Phases')
else:
# print 'no phases found in GetPhaseNames'
sub = None
if sub:
item, cookie = self.GPXtree.GetFirstChild(sub)
while item:
phase = self.GPXtree.GetItemText(item)
phaseNames.append(phase)
item, cookie = self.GPXtree.GetNextChild(sub, cookie)
return phaseNames
[docs]
def GetHistogramTypes(self):
""" Returns a list of histogram types found in the GSASII data tree
:return: list of histogram types
"""
HistogramTypes = []
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name[:4] in ['PWDR','HKLF']:
Inst = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,item,'Instrument Parameters'))
HistogramTypes.append(Inst[0]['Type'][0])
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
return HistogramTypes
[docs]
def GetHistogramNames(self,hType):
""" Returns a list of histogram names found in the GSASII data tree
Note routine :func:`GSASIIstrIO.GetHistogramNames` also exists to
get same info from GPX file.
:param str hType: list of histogram types
:return: list of histogram names
"""
HistogramNames = []
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name[:4] in hType:
HistogramNames.append(name)
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
return HistogramNames
[docs]
def GetHistogramNamesID(self,hType):
""" Returns a list of histogram names found in the GSASII data tree
and a lookup table of their Id values. Should replace GetHistogramNames
since that will not be much faster (and there may be real speed gains from
caching the Ids rather than keep searching for them).
N.B routine :func:`GSASIIstrIO.GetHistogramNames` also exists to
get same info, but from GPX file.
:param str hType: list of histogram types
:return: list of histogram names and a dict of histogram Ids
keyed by histogram name.
"""
HistogramNames = []
HistogramIds = {}
if self.GPXtree.GetCount():
item, cookie = self.GPXtree.GetFirstChild(self.root)
while item:
name = self.GPXtree.GetItemText(item)
if name[:4] in hType:
HistogramNames.append(name)
HistogramIds[name] = item
item, cookie = self.GPXtree.GetNextChild(self.root, cookie)
return HistogramNames,HistogramIds
[docs]
def GetUsedHistogramsAndPhasesfromTree(self):
''' Returns all histograms that are found in any phase
and any phase that uses a histogram.
This also assigns numbers to used phases and histograms by the
order they appear in the file.
Note routine :func:`GSASIIstrIO.GetUsedHistogramsAndPhases` also exists to
get same info from GPX file.
:returns: (Histograms,Phases)
* Histograms = dictionary of histograms as {name:data,...}
* Phases = dictionary of phases that use histograms
'''
Histograms = {}
Phases = {}
phaseNames = self.GetPhaseNames()
phaseData = self.GetPhaseData()
histoList,histIdList = self.GetHistogramNamesID(['PWDR','HKLF'])
badnum = 0
for phase in phaseData:
Phase = phaseData[phase]
pId = phaseNames.index(phase)
Phase['pId'] = pId
if Phase['Histograms']:
for hist in Phase['Histograms']:
if 'Use' not in Phase['Histograms'][hist]: #patch: add Use flag as True
Phase['Histograms'][hist]['Use'] = True
if Phase['Histograms'][hist]['Use'] and phase not in Phases:
Phases[phase] = Phase
if (hist not in Histograms) and Phase['Histograms'][hist]['Use']:
if hist not in histIdList:
if badnum == 0:
print('Error: hist {} not found in histIdList. Deleted?'.format(hist))
badnum += 1
continue
item = histIdList[hist]
if item:
if 'PWDR' in hist[:4]:
Histograms[hist] = self.GetPWDRdatafromTree(item)
elif 'HKLF' in hist[:4]:
Histograms[hist] = self.GetHKLFdatafromTree(item)
hId = histoList.index(hist)
Histograms[hist]['hId'] = hId
else: # would happen if a referenced histogram were renamed or deleted
print(u'For phase "'+phase+
u'" unresolved reference to histogram "'+hist+u'"')
if badnum > 1: print(' ...hist not in histIdList error occured {} times'.format(badnum))
G2obj.IndexAllIds(Histograms=Histograms,Phases=phaseData)
return Histograms,Phases
[docs]
def MakeLSParmDict(self,seqHist=None):
'''Load all parameters used for computation from the tree into a
dict of paired values [value, refine flag]. Note that this is
different than the parmDict used in the refinement, which only has
values.
Note that similar things are done in
:meth:`GSASIIfiles.ExportBaseclass.loadParmDict` (from the tree) and
:func:`GSASIIstrMain.Refine` and :func:`GSASIIstrMain.SeqRefine` (from
a GPX file).
:param dict seqHist: defines a specific histogram to be loaded for a sequential
refinement, if None (default) all are loaded.
Note: at present this parameter is not used anywhere.
:returns: (parmDict,varyList) where:
* parmDict is a dict with values and refinement flags
for each parameter and
* varyList is a list of variables (refined parameters).
'''
parmDict = {}
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree()
if seqHist:
histDict = {seqHist:Histograms[seqHist]}
else:
histDict = Histograms
for phase in Phases:
if 'pId' not in Phases[phase]:
self.ErrorDialog('View parameter error','You must run least squares at least once')
raise Exception('No pId for phase '+phase)
rigidbodyDict = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root,'Rigid bodies'))
rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[],'Spin':[]})
Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtable,EFtable,ORBtables,BLtable,MFtable,maxSSwave = \
G2stIO.GetPhaseData(Phases,RestraintDict=None,rbIds=rbIds,Print=False)
hapVary,hapDict,controlDict = G2stIO.GetHistogramPhaseData(Phases,histDict,Print=False,resetRefList=False)
histVary,histDict,histDict1, controlDict = G2stIO.GetHistogramData(histDict,Print=False)
varyList = rbVary+phaseVary+hapVary+histVary
parmDict.update(rbDict)
parmDict.update(phaseDict)
parmDict.update(hapDict)
parmDict.update(histDict)
for parm in parmDict:
if parm.split(':')[-1] in ['Azimuth','Gonio. radius','Lam1','Lam2',
'Omega','Chi','Phi','nDebye','nPeaks']:
parmDict[parm] = [parmDict[parm],'-']
elif parm.split(':')[-2] in ['Ax','Ay','Az','SHmodel','SHord']:
parmDict[parm] = [parmDict[parm],'-']
elif parm in varyList:
parmDict[parm] = [parmDict[parm],'T']
else:
parmDict[parm] = [parmDict[parm],'F']
# for i in parmDict: print i,'\t',parmDict[i]
# fl = open('parmDict.dat','wb')
# pickle.dump(parmDict,fl,1)
# fl.close()
return parmDict,varyList
[docs]
def OnShowLSParms(self,event):
'''Displays a window showing all parameters in the refinement.
Called from the Calculate/View LS Parms menu.
This could potentially be sped up by loading only the histogram that is needed
for a sequential fit.
'''
if G2cnstG.CheckAllScalePhaseFractions(self,refine=False): return
try:
parmDict,varyList = self.MakeLSParmDict()
except:
print('Error retrieving parameters')
return
parmValDict = {}
for i in parmDict:
parmValDict[i] = parmDict[i][0]
reqVaryList = copy.copy(varyList) # save requested variables
wx.BeginBusyCursor()
try:
# process constraints
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree()
if not len(Phases) or not len(Histograms):
print('No constraints processing without phases and histograms defined')
raise G2mv.ConstraintException
sub = GetGPXtreeItemId(self,self.root,'Constraints')
Constraints = self.GPXtree.GetItemPyData(sub)
errmsg,warnmsg = G2cnstG.CheckConstraints(self,Phases,Histograms,Constraints,[],reqVaryList)
except G2mv.ConstraintException:
print('Error in Constraint Processing')
pass
Controls = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root, 'Controls'))
for key in ('parmMinDict','parmMaxDict','parmFrozen'):
if key not in Controls: Controls[key] = {}
G2mv.Map2Dict(parmValDict,G2mv.saveVaryList)
wx.EndBusyCursor()
# # check for limits on dependent vars
# consVars = [i for i in reqVaryList if i not in varyList]
# impossible = set(
# [str(i) for i in Controls['parmMinDict'] if i in consVars] +
# [str(i) for i in Controls['parmMaxDict'] if i in consVars])
# if impossible:
# msg = ''
# for i in sorted(impossible):
# if msg: msg += ', '
# msg += i
# msg = ' &'.join(msg.rsplit(',',1))
# msg = ('Note: limits on variable(s) '+msg+
# ' will be ignored because they are constrained.')
# G2G.G2MessageBox(self,msg,'Limits ignored for constrained vars')
# debug stuff
#if GSASIIpath.GetConfigValue('debug'):
# print('reloading',G2G)
# import imp
# imp.reload(G2G)
# end debug stuff
dlg = G2G.ShowLSParms(self,'Least Squares Parameters',parmValDict,G2mv.saveVaryList,reqVaryList,Controls)
dlg.CenterOnParent()
dlg.ShowModal()
dlg.Destroy()
def OnDerivCalc(self,event):
controlId = GetGPXtreeItemId(self,self.root, 'Controls')
if not controlId:
self.ErrorDialog('Computation error','No refinement information present')
return
Controls = self.GPXtree.GetItemPyData(controlId)
self._cleanPartials(Controls) # set phase partials as invalid
self.OnFileSave(event)
errmsg, warnmsg = G2stIO.ReadCheckConstraints(self.GSASprojectfile) # check constraints are OK
if errmsg:
print ('\nError message(s):\n',errmsg)
self.ErrorDialog('Error in constraints',errmsg)
return
Controls = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root, 'Controls'))
wx.BeginBusyCursor()
pdlg = wx.ProgressDialog('Computing derivatives','Impact computation in progress',100,
parent=self,style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE|wx.PD_CAN_ABORT)
pdlg.CenterOnParent()
derivCalcs,varyList = G2stMn.Refine(self.GSASprojectfile,pdlg,allDerivs=True)
pdlg.Destroy()
wx.EndBusyCursor()
if derivCalcs is None:
print('Calculation aborted')
return
# prepare table contents & display
colTypes = [wg.GRID_VALUE_STRING,wg.GRID_VALUE_STRING,wg.GRID_VALUE_FLOAT+':8,4',wg.GRID_VALUE_STRING]
colLbls = ['variable name','varied','Derivative','Definition']
tbl = []
for x in sorted(derivCalcs,key=lambda x:abs(derivCalcs[x][1]),reverse=True):
if derivCalcs[x][1] == 0.0 : continue
if np.sign(derivCalcs[x][2]) != np.sign(derivCalcs[x][0]): continue
txt = G2obj.fmtVarDescr(x)
txt = txt.replace('Ph=','Phase: ')
txt = txt.replace('Pwd=','Histogram: ')
tbl.append([x,(' T' if x in varyList else ' '),derivCalcs[x][1],txt])
G2G.G2ScrolledGrid(self,'Parameter Impact Results','Impact Results',tbl,colLbls,colTypes,
maxSize=(700,400),comment=f' Cite: {G2G.GetCite("Parameter Impact")}')
[docs]
def OnExpressionCalc(self,event):
'''Compute an arbitrary expression (supplied by user) as well as the
(statistical) standard uncertainty on that expression.
Uses the :class:`GSASIIexprGUI.ExpressionDialog` to obtain
an expression which is evaluated using the
:class:`GSASIIobj.ExpressionObj` capability. Then the derivative of
the expression is computed numerically for every parameter in the
covariance matrix. Finally the derivative list is used to find
the s.u. on the expression using Ted Prince's method.
'''
from . import GSASIIexprGUI as G2exG
from . import GSASIIstrMath as G2stMth
def extendChanges():
'''Propagate changes due to constraint and rigid bodies
from varied parameters to dependent parameters
'''
# apply constraints
G2mv.Dict2Map(prms)
# apply rigid body constraints
G2stMth.ApplyRBModels(prms,Phases,rigidbodyDict)
# apply shifts to atoms
for dk in prms:
if not '::dA' in dk: continue
if prms[dk] == 0: continue
k = dk.replace('::dA','::A')
prms[k] += prms[dk]
prms[dk] = 0
# TODO: debug: find what has changed
#print(var,[k for k in prms if prms[k] != parmValDict[k]])
#print(var,[prms[k] for k in prms if prms[k] != parmValDict[k]])
# end debug
def striphist(var,insChar=''):
'strip a histogram number from a var name'
sv = var.split(':')
if len(sv) <= 1: return var
if sv[1]:
sv[1] = insChar
return ':'.join(sv)
parmDict,varyList = self.MakeLSParmDict()
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree()
if not len(Phases) or not len(Histograms):
print('Expression computation not possible without definition of phases and histograms')
return
Constraints = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root,'Constraints'))
errmsg,warnmsg = G2cnstG.CheckConstraints(self,Phases,Histograms,
Constraints,[],copy.copy(varyList))
item = GetGPXtreeItemId(self,self.root,'Covariance')
covData = self.GPXtree.GetItemPyData(item)
covData['covMatrix'] = covData.get('covMatrix',[])
parmValDict = {i:parmDict[i][0] for i in parmDict} # dict w/parm values only
G2mv.Map2Dict(parmValDict,G2mv.saveVaryList)
rigidbodyDict = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root,'Rigid bodies'))
if self.testSeqRefineMode():
seqDict = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root,'Sequential results'))
histNames = [h for h in self.testSeqRefineMode() if h in seqDict]
if len(histNames) == 0:
print('no histograms')
return
# wildcard the histogram values
for k in sorted(parmValDict,reverse=True):
ks = striphist(k,'*')
if ks != k:
parmValDict[ks] = parmValDict[k]
del parmValDict[k]
dlg = G2exG.ExpressionDialog(self,parmValDict,
header="Evaluate an expression of GSAS-II parameters",
VarLabel = "Expression",
fit=False,wildCard=self.testSeqRefineMode())
exprobj = dlg.Show(True)
if not exprobj: return
if not self.testSeqRefineMode():
histNames = [0]
for h in histNames:
prfx = ''
if self.testSeqRefineMode():
parmValDict = seqDict[h]['parmDict']
covMatrix = seqDict[h]['covMatrix']
CvaryList = seqDict[h]['varyList']
Csig = seqDict[h]['sig']
prfx = h+': '
else:
covMatrix = covData['covMatrix']
CvaryList = covData['varyList']
Csig = covData['sig']
# evaluate the expression
try:
calcobj = G2obj.ExpressionCalcObj(exprobj)
calcobj.SetupCalc(parmValDict)
value = calcobj.EvalExpression()
except:
continue
# evaluate the derivatives of the expression with respect to
# the varied parameters
if len(covMatrix) > 0:
derivs = []
for var,sig in zip(CvaryList,Csig):
prms = copy.copy(parmValDict)
if sig == 0:
derivs.append(0.0)
continue
prms[var] += sig
extendChanges()
calcobj.SetupCalc(prms)
valP = calcobj.EvalExpression()
prms[var] -= 2*sig
extendChanges()
calcobj.SetupCalc(prms)
valM = calcobj.EvalExpression()
derivs.append((valP-valM)/(2*sig))
Avec = np.array(derivs)
sig = np.sqrt(np.inner(Avec.T,np.inner(covMatrix,Avec)))
else:
sig = -1
if sig > 0:
print(f'{prfx}{exprobj.expression!r} value = {G2mth.ValEsd(value,sig)}')
elif sig == 0:
print(f'{prfx}{exprobj.expression!r} value = {G2mth.ValEsd(value,-abs(value)/10000)} (0 uncertainty)')
else:
print(f'{prfx}{exprobj.expression!r} value = {G2mth.ValEsd(value,-abs(value)/10000)} (no s.u.: no covariance available')
[docs]
def OnRefine(self,event):
'''Perform a single refinement or a sequential refinement (depending on controls setting)
Called from the Calculate/Refine menu.
'''
Controls = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root, 'Controls'))
self._cleanPartials(Controls) # phase partials invalid after a refinement
if self.testSeqRefineMode():
self.OnSeqRefine(event)
return
if G2cnstG.CheckAllScalePhaseFractions(self):
return # can be slow for sequential fits, skip
self.OnFileSave(event)
errmsg, warnmsg = G2stIO.ReadCheckConstraints(self.GSASprojectfile) # check constraints are OK
if warnmsg:
print ('\nNote these constraint warning(s):\n'+warnmsg)
print ('Generated constraints\n',G2mv.VarRemapShow([],True))
if errmsg:
print ('\nError message(s):\n',errmsg)
self.ErrorDialog('Error in constraints',errmsg)
return
if Controls.get('newLeBail',False):
dlgtxt = '''Reset Le Bail structure factors?
Yes: all structure factors are reset to start at unity; Le Bail-only fitting will be applied before any least-squares cycles.\n
No: least-squares fitting starts with previously fit structure factors.'''
#dlgb = wx.MessageDialog(self,dlgtxt,'Le Bail Mode',style=wx.YES_NO)
#result = wx.ID_NO
# try:
# result = dlgb.ShowModal()
# finally:
# dlgb.Destroy()
result = G2G.ShowScrolledInfo(self,dlgtxt,header='Le Bail Mode',
width=400,height=200,
buttonlist=[
('Yes', lambda event: event.GetEventObject().GetParent().EndModal(wx.ID_YES)),
('No', lambda event: event.GetEventObject().GetParent().EndModal(wx.ID_NO))
])
if result == wx.ID_YES:
res = self.OnLeBail(event)
if res: return
Controls['newLeBail'] = False
if GSASIIpath.GetConfigValue('G2RefinementWindow'):
trialMode = 'analytic Hessian' in Controls['deriv type']
dlg = G2G.G2RefinementProgress(parent=self,trialMode=trialMode)
dlg.SetMaxCycle(Controls['max cyc'])
else:
dlg = G2G.RefinementProgress(parent=self)
Rw = 100.00
self.SaveTreeSetting() # save the current tree selection
self.GPXtree.SaveExposedItems() # save the exposed/hidden tree items
if self.PatternId and self.GPXtree.GetItemText(self.PatternId).startswith('PWDR '):
refPlotUpdate = G2pwpl.PlotPatterns(self,refineMode=True) # prepare for plot updating
else:
refPlotUpdate = None
try:
OK,Rvals = G2stMn.Refine(self.GSASprojectfile,dlg,refPlotUpdate=refPlotUpdate,newLeBail=Controls.get('newLeBail',False))
finally:
dlg.Update(101.) # forces the Auto_Hide; needed after move w/Win & wx3.0
dlg.Destroy()
if OK:
Rw = Rvals['Rwp']
rtext = 'LS Refinement: Rw = %.3f%%, GOF = %.2f, Nobs = %d, Nvar = %d'%(Rvals['Rwp'],Rvals['GOF'],Rvals['Nobs'],Rvals['Nvars'])
lamMax = Rvals.get('lamMax',0.001)
lst = os.path.splitext(os.path.abspath(self.GSASprojectfile))[0]
text = f'Detailed results are in file {os.path.split(lst)[1]}.lst in directory {os.path.split(lst)[0]}\n'
if 'GOF0' in Rvals and 'GOF' in Rvals:
text += f"\nFinal Reduced Chi^2: {Rvals['GOF']**2:.3f}"
text += f"\n (before refinement: {Rvals['GOF0']**2:.3f})\n"
if Rvals.get('Max shft/sig') is not None:
rtext += ', Max delt/sig = {:.3f}'.format(Rvals['Max shft/sig'])
text += '\nMax shift/sigma={:.3f}\n'.format(Rvals['Max shft/sig'])
if 'msg' in Rvals: text += '\n' + Rvals['msg'] + '\n'
if 'Aborted' in Rvals:
text += '\nWARNING: Minimizer halted because chi**2 increased\n'
if lamMax >= 10.:
text += ('\nWARNING: Marquardt factor raised to point where steepest descents dominates fitting;'+
' minimum may not have been reached or your result may be a false minimum.'+
' You should reconsider which parameters you refine: check covariance matrix.\n')
#breakpoint()
tbl = [] # assemble a list of varied parameters
for i in Rvals.get('parmDictAfterFit',{}):
if i not in Rvals['parmDictBeforeFit']: continue
if i not in Rvals['parmDictSigDict']: continue
try: # make ure we have valid numbers
diff = ((Rvals['parmDictAfterFit'][i]-
Rvals['parmDictBeforeFit'][i])
/ Rvals['parmDictSigDict'][i])
diff
except:
continue
txt = '?'
v = G2obj.getVarDescr(i)
if v is not None and v[-1] is not None:
txt = G2obj.fmtVarDescr(i)
tbl.append((i,Rvals['parmDictBeforeFit'][i],Rvals['parmDictAfterFit'][i],
Rvals['parmDictSigDict'].get(i),txt))
lbl = f'Refinement results, Rw={Rw:.3f}'
ans = G2G.G2AfterFit(self,text,lbl,tbl) # this replaces the next 8 lines
if ans == wx.ID_OK: # refinement has been accepted save, log & display
self.reloadFromGPX(rtext,Rvals)
G2IO.LogCellChanges(self)
# log parameters into notebook
txt = ''
if Controls.get('LoggedVars') and 'parmDictAfterFit' in Rvals:
txt = ''
for i in sorted(Controls['LoggedVars']):
if i not in Rvals['parmDictAfterFit']: continue
if txt: txt += ', '
txt += (f'{i} : {Rvals["parmDictAfterFit"][i]:.7g}')
elif GSASIIpath.GetConfigValue('LogAllVars') and 'parmDictAfterFit' in Rvals:
txt = ''
for c,i in enumerate(Rvals['parmDictSigDict']):
if i not in Rvals['parmDictAfterFit']: continue
if txt: txt += ', '
txt += (f'{i} : {Rvals["parmDictAfterFit"][i]:.7g}')
if txt: self.AddToNotebook(txt,'VALS',False)
if refPlotUpdate: # restore plot if liveplot in use
refPlotUpdate({},restore=True)
refPlotUpdate = None
self.ResetPlots() # delete any plots that have not been updated
elif 'psing' in Rvals:
if 'msg' in Rvals:
msg = 'Refinement results:\n\n'
msg += Rvals['msg']
msg += '\n\n'
else:
msg = ''
try:
dlg = wx.MessageDialog(self, msg,'Note singularities',wx.OK)
dlg.CenterOnParent()
dlg.SetSize((700,300)) # does not resize on Mac
dlg.ShowModal()
finally:
dlg.Destroy()
else:
self.ErrorDialog('Refinement error',Rvals['msg']+'''
\nNote that when GSAS-II fails in a refinement, this is often
because parameters are varied in incompatible ways. You are
suggested to use Calculate/"View LS params" to review what
is being refined.
''')
[docs]
def OnLeBail(self,event):
'''Do a 1 cycle LeBail refinement with no other variables; usually done upon initialization of a LeBail refinement
either single or sequentially
'''
Controls = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root, 'Controls'))
self._cleanPartials(Controls) # phase partials invalid after a refinement
self.OnFileSave(event)
item = GetGPXtreeItemId(self,self.root,'Covariance')
covData = self.GPXtree.GetItemPyData(item)
try:
rChi2initial = 'GOF: {:.3f}'.format(covData['Rvals']['GOF']**2)
except:
rChi2initial = '?'
if GSASIIpath.GetConfigValue('G2RefinementWindow'):
if (self.testSeqRefineMode()):
l = len(self.testSeqRefineMode())
else:
l = 0
dlg = G2G.G2RefinementProgress(parent=self,trialMode=False,
seqLen=l,seqShow=10)
else:
dlg = G2G.RefinementProgress(parent=self)
self.SaveTreeSetting() # save the current tree selection
self.GPXtree.SaveExposedItems() # save the exposed/hidden tree items
if self.PatternId and self.GPXtree.GetItemText(self.PatternId).startswith('PWDR '):
refPlotUpdate = G2pwpl.PlotPatterns(self,refineMode=True) # prepare for plot updating
else:
refPlotUpdate = None
seqList = self.testSeqRefineMode()
try:
OK,Rvals = G2stMn.DoLeBail(self.GSASprojectfile,dlg,cycles=1,refPlotUpdate=refPlotUpdate,seqList=seqList)
finally:
dlg.Update(101.) # forces the Auto_Hide; needed after move w/Win & wx3.0
dlg.Destroy()
if OK and seqList:
print('continuing with sequential fit')
elif OK:
text = ''
rtext = 'LeBail-only fit done. '
Rwp = Rvals.get('Rwp')
if 'GOF' in Rvals:
txt = 'Final Reduced Chi^2: {:.3g}\n'.format(Rvals['GOF']**2)+rChi2initial
text += txt
rtext += txt
text += '\nLoad new result & continue refinement?'
dlg2 = wx.MessageDialog(self,text,'LeBail-only fit: Rwp={:.3f}'.format(Rwp),wx.OK|wx.CANCEL)
dlg2.CenterOnParent()
try:
if dlg2.ShowModal() == wx.ID_OK:
self.reloadFromGPX(rtext)
if refPlotUpdate:
refPlotUpdate({},restore=True)
refPlotUpdate = None
self.ResetPlots()
else:
if refPlotUpdate:
refPlotUpdate({},restore=True)
refPlotUpdate = None
self.ResetPlots()
return True
finally:
dlg2.Destroy()
else:
self.ErrorDialog('Le Bail error',Rvals['msg'])
return True
return False
def _cleanPartials(self,Controls):
'''Delete any partials created with :meth:`OnRefinePartials`; used
in GUI-based refinements, as the partials are no longer correct after
any fit.
Also clears the PhasePartials name from Controls
'''
PhasePartials = os.path.abspath(os.path.splitext(self.GSASprojectfile)[0]+'.partials')
if os.path.exists(PhasePartials):
os.remove(PhasePartials)
print('file deleted:',PhasePartials)
Controls['PhasePartials'] = None
def LoadPartial(self,target_hId):
PhasePartials = os.path.abspath(os.path.splitext(self.GSASprojectfile)[0]+'.partials')
if not os.path.exists(PhasePartials): return None,None,[]
fp = open(PhasePartials,'rb')
pickle.load(fp) # skip over initial None
while True: # loop until we find target histogram or hit end of file
yDict = {}
try:
hId = pickle.load(fp) # get histogram number
if hId == target_hId:
# found the target, read until we get a None or EOF
x = pickle.load(fp)
yb = pickle.load(fp)
while True:
phase = pickle.load(fp)
if phase is None:
fp.close()
return x, yb, yDict
yDict[phase] = pickle.load(fp)
else:
while pickle.load(fp) is not None:
pass
except EOFError:
if yDict:
fp.close()
return x, yb, yDict
# did not find the right histogram -- unexpected!
return None,None,[]
[docs]
def OnRefinePartials(self,event):
'''Computes and saves the intensities from each phase for each powder
histogram. Do a 0 cycle fit with no variables to pickle intensities for each
phase into a file. Not for sequential fits.
Sets Controls['PhasePartials'] to a file name to trigger save of
info in :meth:`GSASIIstrMath.getPowderProfile` and then clear that.
'''
if self.testSeqRefineMode(): # should not happen, as should not be enabled
G2G.G2MessageBox(self,
'Phase partials cannot be computed for sequential fits',
'Sequential not allowed')
return
Controls = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root, 'Controls'))
savCyc,Controls['max cyc'] = Controls['max cyc'],0
saveDervtype,Controls['deriv type'] = Controls['deriv type'],'analytic Hessian'
Controls['PhasePartials'] = os.path.abspath(os.path.splitext(self.GSASprojectfile)[0]+'.partials')
self.OnFileSave(event)
dlg = G2G.RefinementProgress(parent=self)
self.SaveTreeSetting() # save the current tree selection
self.GPXtree.SaveExposedItems() # save the exposed/hidden tree items
try:
OK,Rvals = G2stMn.Refine(self.GSASprojectfile,dlg,refPlotUpdate=None)
except Exception as msg:
print('Refinement failed with message',msg)
Controls['deriv type'] = saveDervtype
Controls['max cyc'] = savCyc
Controls['PhasePartials'] = None
self.OnFileSave(event)
return True
finally:
dlg.Update(101.) # forces the Auto_Hide; needed after move w/Win & wx3.0
dlg.Destroy()
if OK:
G2G.G2MessageBox(self,'Phase partials computed; if necessary, press "P" on multiphase PWDR plot to view',
'Partials complete')
Controls['deriv type'] = saveDervtype
Controls['max cyc'] = savCyc
self.OnFileSave(event)
[docs]
def OnSavePartials(self,event):
''' Saves partials as a csv file
'''
Controls = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root, 'Controls'))
phPartialFile = Controls.get('PhasePartials','')
try:
fp = open(phPartialFile,'rb')
except:
G2G.G2MessageBox(self,
'Phase partials cannot be saved - partials file does not exist',
'No partials file')
return
# savCyc,Controls['max cyc'] = Controls['max cyc'],0
# saveDervtype,Controls['deriv type'] = Controls['deriv type'],'analytic Hessian'
while True: # loop until we get a name or the user says no to export
filename = None
defpath,defnam = os.path.split(os.path.abspath(
os.path.splitext(self.GSASprojectfile)[0]+'_part_N.csv'))
dlg = wx.FileDialog(self,
'Choose a file prefix to save the partials', defpath, defnam,
'spreadsheet input (*.csv)|*.csv',wx.FD_SAVE)
dlg.CenterOnParent()
try:
if dlg.ShowModal() == wx.ID_OK:
filename = os.path.splitext(dlg.GetPath())[0] # drop extension
if not filename.endswith('_part_N'):
filename += '_part_N'
break
else:
return False
finally:
dlg.Destroy()
# write the .csv file(s)
histograms,phases = self.GetUsedHistogramsAndPhasesfromTree()
pickle.load(fp) # skip over initial None
done = False
while not done: # looping over histograms
valList = None
lblList = ['x','obs','wgt','calc','background']
try:
hId = pickle.load(fp) # get histogram number
pickle.load(fp) # skip over x values
pickle.load(fp) # skip over bkg values
for h in histograms:
if 'PWDR' not in h[:4]: continue
if hId == histograms[h]['hId']: break
else:
print('Error histogram',hId,'not found. This should not happen!')
fp.close()
# Controls['deriv type'] = saveDervtype
# Controls['max cyc'] = savCyc
Controls['PhasePartials'] = None
self.OnFileSave(event)
return
Limits = histograms[h]['Limits'][1]
x = histograms[h]['Data'][0]
xB = np.searchsorted(x,Limits[0])
xF = np.searchsorted(x,Limits[1])+1
valList = [x,histograms[h]['Data'][1],
histograms[h]['Data'][2],histograms[h]['Data'][3],
histograms[h]['Data'][4]]
while True: # read until we hit an EOF or a None
phase = pickle.load(fp) # get phase & then y vals
if phase is None: break
lblList.append(phase)
ypartial = np.zeros_like(x)
yp = pickle.load(fp)
if len(yp):
ypartial[xB:xF] = yp
valList.append(ypartial)
else:
valList = None
continue
except EOFError:
done = True
if valList:
phPartialFile = filename.replace('_part_N','_part_'+str(hId)+'.csv')
fp1 = open(phPartialFile,'w')
fp1.write(', '.join(lblList))
fp1.write('\n')
for l in zip(*valList):
fp1.write(', '.join([str(i) for i in l])+'\n')
fp1.close()
print('File',phPartialFile,'written')
fp.close()
print('Saving partials as csv files finished')
[docs]
def OnClusterAnalysis(self,event):
''' Setsup cluster analysis & make tree entry
'''
try:
SKLearn = False
import sklearn.cluster
sklearn.cluster
SKLearn = True
except:
res = GSASIIpath.condaInstall('scikit-learn')
if res:
msg = 'Installation of the sklearn package failed with error:\n' + str(res)
G2G.G2MessageBox(self,msg,'Install sklearn Error')
else:
SKLearn = True
Id = GetGPXtreeItemId(self,self.root,'Cluster Analysis')
if not Id:
Id = self.GPXtree.AppendItem(self.root,text='Cluster Analysis')
ClustDict = {'Files':[],'Method':'correlation','Limits':[0.,100.],'DataMatrix':[],'plots':'All',
'LinkMethod':'average','Opt Order':False,'ConDistMat':[],'NumClust':2,'codes':None,'Scikit':'K-Means'}
self.GPXtree.SetItemPyData(Id,ClustDict)
else:
ClustDict = self.GPXtree.GetItemPyData(Id)
print('Cluster Analysis exists - nothing done')
ClustDict['SKLearn'] = SKLearn
self.GPXtree.SelectItem(Id)
[docs]
def reloadFromGPX(self,rtext=None,Rvals={}):
'''Deletes current data tree & reloads it from GPX file (after a
refinement.) Done after events are completed to avoid crashes.
:param str rtext: string info from caller to be put in Notebook after reload
'''
self.GPXtree.DeleteChildren(self.root)
self.HKL = np.array([])
self.Extinct = []
G2IO.ProjFileOpen(self,False)
self.TreeItemDelete = False # tree has been repopulated; ignore previous deletions
self.GPXtree.RestoreExposedItems() # reset exposed/hidden tree items
if rtext is not None:
self.AddToNotebook(rtext,'REF')
for tag,entry in (['VARS','varyList'],['CNSTR','contrSumm'],
['RSTR','restrSumm'],['RB','RBsumm']):
if entry in Rvals and Rvals[entry]:
self.AddToNotebook(Rvals[entry],tag,TimeStamp=False)
[docs]
def SaveTreeSetting(self):
'Save the current selected tree item by name (since the id will change)'
oldId = self.GPXtree.GetSelection() #retain current selection
oldPath = self.GetTreeItemsList(oldId)
self.lastTreeSetting = oldPath
[docs]
def ResetPlots(self):
'''This reloads the current tree item, often drawing a plot. It
also refreshes any plots that have registered a refresh routine
(see G2plotNB.RegisterRedrawRoutine) and deletes all plots that
have not been refreshed and require one (see G2plotNB.SetNoDelete).
'''
for lbl,win in zip(self.G2plotNB.plotList,self.G2plotNB.panelList):
win.plotInvalid = True # mark all current plots as invalid so we can tell what has been updated
oldPath = self.lastTreeSetting # reload last selected tree item, triggers window and possibly plot redraw
Id = self.root
for txt in oldPath:
Id = GetGPXtreeItemId(self, Id, txt)
pltText = None
self.PickIdText = None # forces reload of page when selected
if Id:
self.PickId = Id
self.GPXtree.SelectItem(Id)
# selection above appears to trigger a tree event (all platforms?),
# but if not call SelectDataTreeItem(self,Id)
# wx.Yield()
time.sleep(0.1)
pltNumber = self.G2plotNB.nb.GetSelection()
if pltNumber >= 0:
pltText = self.G2plotNB.nb.GetPageText(pltNumber)
else:
pltText = None
# update plots where a routine is supplied
for lbl,win in zip(self.G2plotNB.plotList,self.G2plotNB.panelList):
if win.plotInvalid and win.replotFunction:
if GSASIIpath.GetConfigValue('debug'):
print('updating',lbl,'by calling',str(win.replotFunction))
try:
win.replotFunction(*win.replotArgs,**win.replotKWargs)
except Exception as msg:
if GSASIIpath.GetConfigValue('debug'):
print('Error calling',win.replotFunction,'with args',
win.replotArgs,win.replotKWargs)
if GSASIIpath.GetConfigValue('debug'):
print(msg)
GSASIIpath.IPyBreak()
# delete any remaining plots unless they have been
# updated (win.plotInvalid is False) or are tagged as not
# needing a refresh (win.plotRequiresRedraw is False)
for lbl,win in zip(self.G2plotNB.plotList,self.G2plotNB.panelList):
if win.plotInvalid and win.plotRequiresRedraw:
if GSASIIpath.GetConfigValue('debug'):
print('Closing out-of-date plot',lbl)
if lbl == 'Powder Patterns':
self.lastPlotType = None
self.G2plotNB.Delete(lbl)
# put the previously last-raised plot tab on top, if present.
# Search by label text, since tab number may have changed
for i in range(self.G2plotNB.nb.GetPageCount()):
if self.G2plotNB.nb.GetPageText(i) == pltText:
self.G2plotNB.nb.SetSelection(i)
break
[docs]
def OnSeqRefine(self,event):
'''Perform a sequential refinement.
Called from self.OnRefine (Which is called from the Calculate/Refine menu)
'''
Controls = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root, 'Controls'))
seqList = self.testSeqRefineMode()
Id = GetGPXtreeItemId(self,self.root,'Sequential results')
if not Id:
Id = self.GPXtree.AppendItem(self.root,text='Sequential results')
self.GPXtree.SetItemPyData(Id,{})
self.G2plotNB.Delete('Sequential refinement') #clear away probably invalid plot
Controls['ShowCell'] = True
for key in ('parmMinDict','parmMaxDict','parmFrozen'):
if key not in Controls: Controls[key] = {}
# check for deleted or unused histograms in refine list
phaseRIdList,histdict = self.GetPhaseInfofromTree(Used=True)
usedHistograms = []
for k in histdict:
usedHistograms += histdict[k]
usedHistograms = list(set(usedHistograms))
newseqList = [i for i in seqList if i in usedHistograms]
if len(newseqList) != len(seqList):
G2G.G2MessageBox(self,
str(len(seqList)-len(newseqList))+
' histograms that are not used have been removed from the sequential list.',
'Histograms removed')
seqList = Controls['Seq Data'] = newseqList
allerrors = {}
allwarnings = {}
Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree()
#
# Check if a phase lattice parameter refinement flag is set, if so transfer it to the Dij terms
cellFit = 0
for key in Phases:
if Phases[key]['General']['Cell'][0]: cellFit += 1
if cellFit:
msg = f'''You are refining the unit cell parameter for {cellFit} phase(s).
In sequential fits the Dij (hydrostatic strain) terms, which provide offsets to the reciprocal cell tensor, must be refined rather than the cell parameters.
Do you want to transfer the cell refinement flag to the Dij terms?
(Select Yes to continue the refinement)'''
dlg = wx.MessageDialog(None, msg,'xfer cell flag to Dij?',
wx.YES_NO|wx.ICON_QUESTION)
result = wx.ID_NO
try:
result = dlg.ShowModal()
finally:
dlg.Destroy()
if result == wx.ID_NO:
return
for p in Phases:
count = 0
if Phases[p]['General']['Cell'][0]:
for h in Phases[p]['Histograms']:
if not Phases[p]['Histograms'][h]['Use']: continue
Phases[p]['Histograms'][h]['HStrain'][1] = len(
Phases[p]['Histograms'][h]['HStrain'][1]) * [True]
count += 1
if count > 0: print(f'{count} hydrostratic strain refinement flags were set for phase {p}')
Phases[p]['General']['Cell'][0] = False
# save Tree to file and from here forward, work from the .gpx file not from the data tree
self.OnFileSave(event)
Histograms,Phases = G2stIO.GetUsedHistogramsAndPhases(self.GSASprojectfile)
for h in seqList: # check constraints are OK for each histogram to be processed
errmsg, warnmsg = G2stIO.ReadCheckConstraints(self.GSASprojectfile,
h,Histograms,Phases)
if warnmsg or errmsg:
print ('\nConstraint warnings/errors for histogram "{}":'.format(h))
if warnmsg:
allwarnings[h] = warnmsg
print ('warning:',warnmsg)
if errmsg:
allerrors[h] = errmsg
print ('Error message: ',errmsg)
if allerrors:
if len(allerrors) == len(seqList):
l = 'all histograms'
elif len(allerrors) == 1:
l = 'one histogram'
else:
l = str(len(allerrors)) + ' histograms'
self.ErrorDialog('Error in Constraints',
'There were constraint errors in {}. Refinement is not possible. See console output or visit Constraints data tree item for more details.'.format(l))
return
elif allwarnings:
if len(allwarnings) == len(seqList):
l = 'all histograms'
elif len(allwarnings) == 1:
l = 'one histogram'
else:
l = str(len(allwarnings)) + ' histograms'
msg = 'There were constraint warnings generated in {}. See console output or visit the Constraints data tree item for more details. Continue with refinement?'.format(l)
dlg = wx.MessageDialog(self,msg,caption='Constraint warnings',style=wx.YES_NO)
dlg.CenterOnParent()
result = wx.ID_NO
try:
result = dlg.ShowModal()
finally:
dlg.Destroy()
if result == wx.ID_NO: return
self.GPXtree.SaveExposedItems()
# find 1st histogram to be refined
if 'Seq Data' in Controls:
histNames = Controls['Seq Data']
else: # patch from before Controls['Seq Data'] was implemented
histNames = G2stIO.GetHistogramNames(self.GSASprojectfile,['PWDR',])
if Controls.get('Reverse Seq'):
histNames.reverse()
if Controls.get('newLeBail',False):
dlgtxt = '''Do Le Bail refinement of intensities first?
If Yes, resets starting structure factors; recommended after major parameter changes.
If No, then previous structure factors are used.'''
dlgb = wx.MessageDialog(self,dlgtxt,'Le Bail Refinement',style=wx.YES_NO)
result = wx.ID_NO
try:
result = dlgb.ShowModal()
finally:
dlgb.Destroy()
if result == wx.ID_YES:
res = self.OnLeBail(event)
if res: return
# select it
if GSASIIpath.GetConfigValue('G2RefinementWindow'):
trialMode = 'analytic Hessian' in Controls['deriv type']
dlgp = G2G.G2RefinementProgress(parent=self,trialMode=trialMode,
seqLen=len(histNames))
else:
dlgp = G2G.RefinementProgress('Residual for histogram 0','Powder profile Rwp =',parent=self)
self.PatternId = GetGPXtreeItemId(self,self.root,histNames[0])
if self.PatternId and self.GPXtree.GetItemText(self.PatternId).startswith('PWDR '):
refPlotUpdate = G2pwpl.PlotPatterns(self,refineMode=True) # prepare for plot updating
else:
refPlotUpdate = None
try:
OK,Msg = G2stMn.SeqRefine(self.GSASprojectfile,dlgp,refPlotUpdate) #Msg is Rvals dict if Ok=True
finally:
dlgp.Update(101.) # forces the Auto_Hide; needed after move w/Win & wx3.0
dlgp.Destroy()
if OK:
lst = os.path.splitext(os.path.abspath(self.GSASprojectfile))[0]
text = 'Detailed results are in ' + lst + '.lst\n'
if Msg.get('Frozen'):
text += '\n' + Msg['Frozen']
if Msg.get('steepestNum',0) > 0:
text += '\nNote that {} histograms had extreme correlations where steepest descents dominates\n'.format(Msg['steepestNum'])
if len(Msg.get('maxshift/sigma',[])) > 0:
avg = np.average(Msg['maxshift/sigma'])
mx = np.max(Msg['maxshift/sigma'])
text += '\nBiggest Max shft/sig was {:.3f} (average across histograms {:.3f})\n'.format(mx,avg)
text += '\nLoad new result?'
dlg = wx.MessageDialog(self,text,'Refinement results',wx.OK|wx.CANCEL)
dlg.CenterOnParent()
try:
if dlg.ShowModal() == wx.ID_OK:
self.PickIdText = None #force reload of PickId contents
self.GPXtree.DeleteChildren(self.root)
if len(self.HKL):
self.HKL = np.array([])
self.Extinct = []
G2IO.ProjFileOpen(self,False)
self.GPXtree.RestoreExposedItems()
self.ResetPlots()
sId = GetGPXtreeItemId(self,self.root,'Sequential results')
SelectDataTreeItem(self,sId)
self.GPXtree.SelectItem(sId)
if refPlotUpdate:
refPlotUpdate({},restore=True)
refPlotUpdate = None
else:
if refPlotUpdate:
refPlotUpdate({},restore=True)
refPlotUpdate = None
finally:
dlg.Destroy()
else:
self.ErrorDialog('Sequential refinement error',Msg)
[docs]
def OnRunFprime(self,event):
'''Run Fprime'''
from . import fprime
self.fprime = fprime.Fprime(self)
self.fprime.Show()
[docs]
def OnRunAbsorb(self,event):
'''Run Absorb'''
from . import Absorb
self.absorb = Absorb.Absorb(self)
self.absorb.Show()
[docs]
def OnRunPlotXNFF(self,evnt):
'''Run PlotXNFF'''
from . import PlotXNFF
self.plotXNFF = PlotXNFF.PlotXNFF(self)
self.plotXNFF.Show()
[docs]
def ErrorDialog(self,title,message,parent=None, wtype=wx.OK):
'Display an error message'
# TODO: really would be better to have something customized for this
result = None
if parent is None:
dlg = wx.MessageDialog(self, message, title, wtype)
else:
dlg = wx.MessageDialog(parent, message, title, wtype)
dlg.CenterOnParent() # not working on Mac
try:
result = dlg.ShowModal()
finally:
dlg.Destroy()
return result
[docs]
def OnSaveMultipleImg(self,event):
'''Select and save multiple image parameter and mask files
'''
G2IO.SaveMultipleImg(self)
[docs]
def DoSequentialProjExport(self,event):
'''Export a sequential project
duplicates part of GSASIIseqGUI.DoSequentialExport
'''
Id = GetGPXtreeItemId(self,self.root,'Sequential results')
if not Id:
print('Error in DoSequentialProjExport: no Seq Res table. How did this happen?')
return
data = self.GPXtree.GetItemPyData(Id)
Controls = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root, 'Controls'))
G2IO.ExportSequentialFullCIF(self,data,Controls)
#### Data window side of main GUI; menu definitions here #########################
[docs]
class G2DataWindow(wx.ScrolledWindow): #wxscroll.ScrolledPanel):
'''Create the GSAS-II data window as well as sets up the menus for each
window. There will be one instance of this in the GSAS-II app named as
``G2frame.dataWindow``.
This creates two panels, where the inner one is the data object in
this class, which is scrolled. The outer one
(:data:`G2frame.dataWindow.outer`) uses all space in
the appropriate part of the window, but defines a sizer at the
top and bottom of the window that can be used to place information
that will not be scrolled. The inner one is the ``G2frame.dataWindow``
object.
Note that before any items are to be placed in either of these panels,
one should call::
G2frame.dataWindow.ClearData()
This deletes the contents of the three main sizers used in the
panels. Do not delete the sizers for the unscrolled regions at the
top and bottom of the outer panel, as they cannot be [easily?]
regenerated if deleted.
The sizer for the scrolled panel should be not be reused,
though some earlier code may do that.
After the contents of the data window have been created,
a call is made to::
G2frame.dataWindow.SetDataSize()
this ensures that the window's scroll bars are placed properly.
Initial GUI creation for the contents of dataWindow is done in
:func:`SelectDataTreeItem`, which is invoked when a selection
is made in the data tree selection. This may places items into
the dataWindow, but more commonly calls other routines tht call
that.
Routines that are called multiple times to redraw the contents
of the data window should call :meth:`ClearData()` and
:meth:`SetDataSize` at the beginning and end of the GUI code,
respectively, to clear contents and complete the layout.
When placing a widget in the sizer that has its own scrolling
e.g. :class:`GSASIIctrlGUI.GSNoteBook` (anything else?) that
one widget should be placed in the scrolledpanel sizer using::
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
mainSizer.Add(G2frame.<obj>,1,wx.EXPAND)
so that it consumes the full size of the panel and so that
the NoteBook widget does the scrolling.
For other uses, one will likely place a bunch of widgets and (other
[sub-]sizers) into the master sizer. In this case, DO NOT use wx.EXPAND,
as this will result in the widget resizing/repositioning as the window
resizes. Possible exceptions might be for widgets going into a fixed-size
panel that is inside the dataWindow (probably not being done). A call to
Sizer.Fit(dataWindow) will do bad things, though a call to
SubSizer.Fit(dataWindow.subpanel) could make sense.
Use of the unscrolled top sizer:
:data:`G2DataWindow.topBox` provides access to a Horizontal
wx.BoxSizer, where GUI objects can be placed. The parent for these
objects should be :data:`G2DataWindow.topPanel`. For the unscrolled
bottom region of the window, use :data:`G2DataWindow.bottomBox`
and :data:`G2DataWindow.bottomPanel` as parent.
Sample code::
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,label='Indexing tools'),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
Menus: The same core menu items are used in all menu bars (defined in
:meth:`PrefillDataMenu` and :meth:`PostfillDataMenu, but
different items may be added, depending on what data tree item and
in some cases (phases +?) window tab. Menu definitions are
performed in :meth:`_initMenus`. Menus that are needed at all
times in GSAS-II are created there with a call sich as::
self.ConstraintMenu = wx.MenuBar()
but to reduce the time needed to start GSAS-II initially, most menus
are created "on demand". This is done by defining a routine (named
here as :func:`_makemenu`) and the above definition is replaced with::
self.ConstraintMenu = _makemenu
The code that causes a menubar to be displayed (:func:`SetDataMenuBar`)
checks to see if the menubar has been already been created, if so it
is displayed, if not the function (the appropriate one of many
:func:`_makemenu` routines) is called. This creates and displays the
menu.
Note, if there is a problem, a call like
wx.CallAfter(G2frame.phaseDisplay.SendSizeEvent)
might be needed. There are some calls to G2frame.dataWindow.SendSizeEvent()
or G2frame.dataWindow.outer.SendSizeEvent()
that may be doing the same thing.
'''
def __init__(self,parent):
self.parent = parent
# create an outer unscrolled panel
self.outer = wx.Panel(parent,size=parent.GetSize(),name='Outer data window')
mainSizer = wx.BoxSizer(wx.VERTICAL)
self.outer.SetSizer(mainSizer)
# three things in unscrolled panel, topBox, self (ScrolledWindow) and bottomBox
# topBox
self.topBox = wx.BoxSizer(wx.HORIZONTAL)
self.topPanel = self.outer
mainSizer.Add(self.topBox,0,wx.EXPAND)
# scrolled area
wx.ScrolledWindow.__init__(self,self.outer,wx.ID_ANY,size=parent.GetSize(),
name="inner scrolled data window")
mainSizer.Add(self,1,wx.EXPAND,0)
scrollSizer = wx.BoxSizer(wx.VERTICAL) # this should be replaced when panel is used
self.SetSizer(scrollSizer)
# bottomBox
self.bottomBox = wx.BoxSizer(wx.HORIZONTAL)
self.bottomPanel = self.outer
mainSizer.Add(self.bottomBox)
self._initMenus()
self.currentGrids = []
self.helpKey = '' # defines help entry for current item selected in data tree
[docs]
def ClearData(self):
'''Initializes the contents of the dataWindow panel
'''
self.customResize = None # allows a dataWindow to define a routine used for a resize
self.Unbind(wx.EVT_SIZE)
self.topBox.Clear(True)
self.bottomBox.Clear(True)
#self.SetBackgroundColour(wx.WHITE) # this screws up dark mode
#self.SetBackgroundColour(VERY_LIGHT_GREY) # BHT: I prefer a gray background. Makes TextCtrls stand out, but
# a bit lighter than the splitter bar
Sizer = self.GetSizer()
if Sizer:
try:
Sizer.Clear(True)
except:
pass
else:
print ('No sizer in dataWindow')
if GSASIIpath.GetConfigValue('debug'): raise Exception
Sizer.Add((-1,3)) # small space on top of scrolled window
[docs]
def SetStatusWidth(self):
'Make the left-side of the status bar track the size of the data tree'
G2frame = self.GetTopLevelParent()
wid,hgt = G2frame.GPXtree.GetSize()
G2frame.GetStatusBar().SetStatusWidths([wid+10, -1])
[docs]
def SetDataSize(self):
'''Sizes the contents of the dataWindow panel and sets up
for response to change in size of window.
'''
def _onResizeGd(event):
'''Called when a Window containing only 1 grid is resized'''
self.Layout()
self.SetVirtualSize(self.GetSize())
self.SetStatusWidth()
event.Skip()
def _onResizeNB(event):
'''Called when a Window containing only a notebook is resized'''
self.Layout()
self.SetVirtualSize(self.GetSize())
self.SetStatusWidth()
event.Skip()
def _onResize(event):
'''Called when any other type of window is resized'''
self.SetStatusWidth()
Sizer = self.GetSizer()
if not Sizer:
print ('No sizer in dataWindow')
if GSASIIpath.GetConfigValue('debug'): raise Exception
return
# find out more about what is in the scrolled window
numChild = len(self.GetChildren())
haveGrid = None # is there a single grid in this panel?
haveNotebook = None # is there a single notebook in this panel?
for child in self.GetChildren():
if isinstance(child,G2G.GSGrid) or isinstance(child,G2G.GSNoteBook):
if haveGrid or haveNotebook:
haveGrid = None
haveNotebook = None
break
if isinstance(child,G2G.GSGrid):
haveGrid = child
elif isinstance(child,G2G.GSNoteBook):
haveNotebook = child
extra = 0
if sys.platform == "darwin": extra = 3 # N.B. 3 extra items in MacOS (Linux?)
if self.customResize:
# use resize routine defined specific for current data tree item
self.Bind(wx.EVT_SIZE,self.customResize)
self.SetAutoLayout(True)
self.SetScrollRate(10,10)
# for simple windows with only a GSNotebook or GSGrid, turn off
# scrolling in the scrolled window and let the notebook or grid
# handle the scaling
elif numChild <= 2+extra and haveGrid:
self.Bind(wx.EVT_SIZE,_onResizeGd)
self.SetVirtualSize(self.GetSize())
self.SetAutoLayout(False)
self.SetScrollRate(0,0)
if isinstance(haveGrid,G2G.GSGrid):
haveGrid.SetScrollRate(10,10)
elif numChild <= 2+extra and haveNotebook:
self.Bind(wx.EVT_SIZE,_onResizeNB)
self.SetVirtualSize(self.GetSize())
self.SetAutoLayout(False)
self.SetScrollRate(0,0)
else:
# otherwise turn on autolayout and scrolling for the scrolled window
self.Bind(wx.EVT_SIZE,_onResize)
self.SetAutoLayout(True)
self.SetScrollRate(10,10)
self.outer.SendSizeEvent()
#### Menu definitions here
def _initMenus(self):
'''define all GSAS-II data window menus.
NB: argument order conforms to both classic & phoenix variants for wx.
Do not use argument= for these as the argument names are different for classic & phoenix
'''
#### GSAS-II Menu items
# Main menu
G2frame = self.GetTopLevelParent()
G2frame.GSASIIMenu = wx.MenuBar()
G2frame.dataMenuBars = [G2frame.GSASIIMenu] # list of all menus (added to in PrefillDataMenu)
G2frame.FillMainMenu(G2frame.GSASIIMenu)
G2frame.SetMenuBar(G2frame.GSASIIMenu)
# Controls
self.ControlsMenu = G2frame.GSASIIMenu
# Notebook
self.DataNotebookMenu = G2frame.GSASIIMenu
# Comments
self.DataCommentsMenu = G2frame.GSASIIMenu
# Constraints
G2G.Define_wxId('wxID_CONSTRAINTADD', 'wxID_EQUIVADD', 'wxID_HOLDADD', 'wxID_FUNCTADD',
'wxID_ADDRIDING', 'wxID_CONSPHASE', 'wxID_CONSHIST', 'wxID_CONSHAP',
'wxID_CONSGLOBAL', 'wxID_CONSSYM', 'wxID_EQUIVALANCEATOMS',)
G2G.Define_wxId('wxID_SHOWISO')
def _makemenu(): # routine to create menu when first used
self.ConstraintMenu = wx.MenuBar()
self.PrefillDataMenu(self.ConstraintMenu)
self.ConstraintTab = wx.Menu(title='')
self.ConstraintMenu.Append(menu=self.ConstraintTab, title='Select tab')
for Id,txt in (
(G2G.wxID_CONSPHASE,'Phase'),
(G2G.wxID_CONSHAP,'Histogram/Phase'),
(G2G.wxID_CONSHIST,'Histogram'),
(G2G.wxID_CONSGLOBAL,'Global'),
(G2G.wxID_CONSSYM,'Sym-Generated'),
):
self.ConstraintTab.Append(Id,txt,'Select '+txt+' constraint editing tab')
self.ConstraintEdit = wx.Menu(title='')
self.ConstraintMenu.Append(menu=self.ConstraintEdit, title='Edit Constr.') # renamed from Edit due to Mac adding extra items to menu
self.ConstraintEdit.Append(G2G.wxID_HOLDADD,'Add hold','Prevent refinement of parameter values')
self.ConstraintEdit.Append(G2G.wxID_EQUIVADD,'Add equivalence','Force parameter values to be equivalent')
self.ConstraintEdit.Append(G2G.wxID_CONSTRAINTADD,'Add constraint equation',
'Add a constraint equation to apply to parameter values')
self.ConstraintEdit.Append(G2G.wxID_FUNCTADD,'Add New Var',
'Create a variable composed of existing parameters')
self.ConstraintEdit.Append(G2G.wxID_EQUIVALANCEATOMS,'Make atoms equivalent',
'Force atom parameter values to be equivalent')
self.ConstraintEdit.Enable(G2G.wxID_EQUIVALANCEATOMS,False)
# self.ConstraintEdit.Append(id=G2G.wxID_ADDRIDING, kind=wx.ITEM_NORMAL,text='Add H riding constraints',
# help='Add H atom riding constraints between atom parameter values')
# self.ConstraintEdit.Enable(G2G.wxID_ADDRIDING,False)
self.ConstraintEdit.Append(G2G.wxID_SHOWISO,'Show New Var modes',
'Show New Var constraints and dependent vars')
self.ConstraintEdit.Enable(G2G.wxID_SHOWISO,False)
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.ConstraintMenu)
self.ConstraintMenu = _makemenu
# Rigid bodies
G2G.Define_wxId('wxID_RIGIDBODYADD', 'wxID_RIGIDBODYIMPORT', 'wxID_RESIDUETORSSEQ',
'wxID_VECTORBODYADD', 'wxID_RIGIDBODYSAVE','wxID_RIGIDBODYIMP','wxID_RESBODYSAV','wxID_RESBODYRD',
'wxID_VECTORBODYIMP','wxID_VECTORBODYSAV','wxID_VECTORBODYRD','wxID_VECTORBODYEXTD','wxID_SPINBODYADD')
def _makemenu(): # routine to create menu when first used
self.RigidBodyMenu = wx.MenuBar()
self.PrefillDataMenu(self.RigidBodyMenu)
self.ResidueRBMenu = wx.Menu(title='')
self.ResidueRBMenu.Append(G2G.wxID_RIGIDBODYIMPORT,'Import XYZ','Import rigid body XYZ from file')
self.ResidueRBMenu.Append(G2G.wxID_RIGIDBODYIMP,'Extract from file','Extract rigid body from phase file')
self.ResidueRBMenu.Append(G2G.wxID_RIGIDBODYSAVE,'Save as PDB','Save rigid body to PDB file')
self.ResidueRBMenu.Append(G2G.wxID_RESIDUETORSSEQ,'Define torsion','Define torsion sequence')
self.ResidueRBMenu.Append(G2G.wxID_RIGIDBODYADD,'Import residues','Import residue rigid bodies from macro file')
self.ResidueRBMenu.Append(G2G.wxID_RESBODYSAV,'Save rigid body','Write a rigid body to a file')
self.ResidueRBMenu.Append(G2G.wxID_RESBODYRD,'Read rigid body','Read a rigid body from a file')
self.RigidBodyMenu.Append(menu=self.ResidueRBMenu, title='Edit Residue Body')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.RigidBodyMenu)
self.RigidBodyMenu = _makemenu
def _makemenu(): # routine to create menu when first used
self.VectorBodyMenu = wx.MenuBar()
self.PrefillDataMenu(self.VectorBodyMenu)
self.VectorRBEdit = wx.Menu(title='')
self.VectorRBEdit.Append(G2G.wxID_VECTORBODYADD,'Add rigid body','Add vector rigid body')
self.VectorBodyMenu.Append(menu=self.VectorRBEdit, title='Edit Vector Body')
self.VectorRBEdit.Append(G2G.wxID_VECTORBODYIMP,'Extract from file','Extract rigid body from phase file')
self.VectorRBEdit.Append(G2G.wxID_VECTORBODYSAV,'Save rigid body','Write a rigid body to a file')
self.VectorRBEdit.Append(G2G.wxID_VECTORBODYRD,'Read rigid body','Read a rigid body from a file')
self.VectorRBEdit.Append(G2G.wxID_VECTORBODYEXTD,'Add translation','Add translation to existing rigid body')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.VectorBodyMenu)
self.VectorBodyMenu = _makemenu
def _makemenu(): # routine to create menu when first used
self.SpinBodyMenu = wx.MenuBar()
self.PrefillDataMenu(self.SpinBodyMenu)
self.SpinRBEdit = wx.Menu(title='')
self.SpinRBEdit.Append(G2G.wxID_SPINBODYADD,'Add rigid body','Add spinning rigid body')
self.SpinBodyMenu.Append(menu=self.SpinRBEdit, title='Edit Spinning Body')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.SpinBodyMenu)
self.SpinBodyMenu = _makemenu
# Restraints
G2G.Define_wxId('wxID_RESTRAINTADD', 'wxID_RESTDELETE', 'wxID_RESRCHANGEVAL',
'wxID_RESTCHANGEESD', 'wxID_AARESTRAINTADD', 'wxID_AARESTRAINTPLOT','wxID_USEMOGUL')
def _makemenu(): # routine to create menu when first used
self.RestraintTab = wx.Menu(title='')
self.RestraintEdit = wx.Menu(title='')
self.RestraintEdit.Append(G2G.wxID_RESTRAINTADD,'Add restraints','Add restraints')
self.RestraintEdit.Enable(G2G.wxID_RESTRAINTADD,True) #gets disabled if macromolecule phase
self.RestraintEdit.Append(G2G.wxID_AARESTRAINTADD,'Add residue restraints',
'Add residue based restraints for macromolecules from macro file')
self.RestraintEdit.Enable(G2G.wxID_AARESTRAINTADD,False) #gets enabled if macromolecule phase
self.RestraintEdit.Append(G2G.wxID_USEMOGUL,'Add MOGUL restraints',
'Add restraints from MOGUL csv file')
self.RestraintEdit.Enable(G2G.wxID_USEMOGUL,False) #gets enabled if bonds or angles
self.RestraintEdit.Append(G2G.wxID_AARESTRAINTPLOT,'Plot residue restraints',
'Plot selected residue based restraints for macromolecules from macro file')
self.RestraintEdit.Enable(G2G.wxID_AARESTRAINTPLOT,False) #gets enabled if macromolecule phase
self.RestraintEdit.Append(G2G.wxID_RESRCHANGEVAL,'Change value','Change observed value')
self.RestraintEdit.Append(G2G.wxID_RESTCHANGEESD,'Change esd','Change esd in observed value')
self.RestraintEdit.Append(G2G.wxID_RESTDELETE,'Delete restraints','Delete selected restraints')
self.RestraintMenu = wx.MenuBar()
self.PrefillDataMenu(self.RestraintMenu)
self.RestraintMenu.Append(menu=self.RestraintTab, title='Select tab')
self.RestraintMenu.Append(menu=self.RestraintEdit, title='Edit Restr.')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.RestraintMenu)
self.RestraintMenu = _makemenu
# Sequential results
G2G.Define_wxId('wxID_RENAMESEQSEL', 'wxID_SAVESEQSEL', 'wxID_SAVESEQCSV', 'wxID_SAVESEQSELCSV', 'wxID_PLOTSEQSEL',
'wxID_ADDSEQVAR', 'wxID_DELSEQVAR', 'wxID_EDITSEQVAR', 'wxID_COPYPARFIT', 'wxID_AVESEQSEL','wxID_SELECTUSE',
'wxID_ADDPARFIT', 'wxID_DELPARFIT', 'wxID_EDITPARFIT', 'wxID_DOPARFIT', 'wxID_ADDSEQDIST', 'wxID_ADDSEQANGLE', 'wxID_ORGSEQINC',)
G2G.Define_wxId('wxID_UPDATESEQSEL')
G2G.Define_wxId('wxID_EDITSEQSELPHASE')
G2G.Define_wxId('wxID_XPORTSEQFCIF')
G2G.Define_wxId('wxID_XPORTSEQCSV')
def _makemenu(): # routine to create menu when first used
self.SequentialMenu = wx.MenuBar()
self.PrefillDataMenu(self.SequentialMenu)
self.SequentialFile = wx.Menu(title='')
self.SequentialMenu.Append(menu=self.SequentialFile, title='Columns/Rows')
self.SequentialFile.Append(G2G.wxID_SELECTUSE,'Set used...',
'Dialog to select rows for plots/equation fitting')
self.SequentialFile.Append(G2G.wxID_UPDATESEQSEL,'Update phase from row',
'Update phase information from selected row')
self.SequentialFile.Append(G2G.wxID_EDITSEQSELPHASE,'Set phase vals',
'Edit phase parameter vals in selected rows')
self.SequentialFile.AppendSeparator()
self.SequentialFile.Append(G2G.wxID_PLOTSEQSEL,'Plot selected cols',
'Plot selected sequential refinement columns')
self.SequentialFile.Append(G2G.wxID_RENAMESEQSEL,'Rename selected cols',
'Rename selected sequential refinement columns')
self.SequentialFile.Append(G2G.wxID_SAVESEQSEL,'Save selected as text',
'Save selected sequential refinement results as a text file')
self.SequentialFile.Append(G2G.wxID_SAVESEQSELCSV,'Save selected as CSV',
'Save selected sequential refinement columns as a CSV spreadsheet file')
self.SequentialFile.Append(G2G.wxID_AVESEQSEL,'Compute average',
'Compute average for selected parameter')
self.SequentialFile.Append(G2G.wxID_ORGSEQINC,'Hide columns...',
'Select columns to remove from displayed table')
self.SequentialFile.AppendSeparator()
self.SequentialFile.Append(G2G.wxID_SAVESEQCSV,'Save all as CSV',
'Save all sequential refinement results as a CSV spreadsheet file')
self.SequentialPvars = wx.Menu(title='')
self.SequentialMenu.Append(menu=self.SequentialPvars, title='Pseudo Vars')
self.SequentialPvars.Append(G2G.wxID_ADDSEQVAR,'Add Formula','Add a new custom pseudo-variable')
self.SequentialPvars.Append(G2G.wxID_ADDSEQDIST,'Add Distance','Add a new bond distance pseudo-variable')
self.SequentialPvars.Append(G2G.wxID_ADDSEQANGLE,'Add Angle','Add a new bond angle pseudo-variable')
self.SequentialPvars.Append(G2G.wxID_DELSEQVAR,'Delete','Delete an existing pseudo-variable')
self.SequentialPvars.Append(G2G.wxID_EDITSEQVAR,'Edit','Edit an existing pseudo-variable')
self.SequentialPfit = wx.Menu(title='')
self.SequentialMenu.Append(menu=self.SequentialPfit, title='Parametric Fit')
self.SequentialPfit.Append(G2G.wxID_ADDPARFIT,'Add equation','Add a new equation to minimize')
self.SequentialPfit.Append(G2G.wxID_COPYPARFIT,'Copy equation','Copy an equation to minimize - edit it next')
self.SequentialPfit.Append(G2G.wxID_DELPARFIT,'Delete equation','Delete an equation for parametric minimization')
self.SequentialPfit.Append(G2G.wxID_EDITPARFIT,'Edit equation','Edit an existing parametric minimization equation')
self.SequentialPfit.Append(G2G.wxID_DOPARFIT,'Fit to equation(s)','Perform a parametric minimization')
# fill sequential Export menu
# for an exporter to be used for sequential exports, it must have a Writer method and
# that Writer method must offer a mode argument.
#============================================================
# N.B. this largely duplicates menu items now in Export
#============================================================
self.SeqExportLookup = {}
self.SequentialEx = wx.Menu(title='')
self.SequentialMenu.Append(menu=self.SequentialEx, title='Seq Export')
for lbl,txt in (
('Project','Export entire sequential fit'),
('Phase','Export selected phase(s)'),
('Powder','Export selected powder histogram(s)'),
('sasd','Export selected small angle histogram(s)')):
objlist = []
for obj in self.parent.GetTopLevelParent().exporterlist:
if lbl.lower() in obj.exporttype:
try:
obj.Writer
except AttributeError:
continue
if '2' in platform.python_version_tuple()[0]:
if 'mode' in inspect.getargspec(obj.Writer)[0]:
objlist.append(obj)
else:
if 'mode' in inspect.getfullargspec(obj.Writer)[0]:
objlist.append(obj)
if objlist or lbl == 'Project':
submenu = wx.Menu()
item = self.SequentialEx.AppendSubMenu(submenu,lbl+' as',txt)
if lbl == 'Project':
submenu.Append(G2G.wxID_XPORTSEQFCIF,'... as full CIF',
'Save all sequential refinement results as a CIF file')
G2G.Define_wxId('wxID_XPORTCINEMA')
submenu.Append(G2G.wxID_XPORTCINEMA,'... to CINEMA: Debye-Scherrer',
'Pass sequential refinement results for plotting in CINEMA: Debye-Scherrer')
for obj in objlist:
item = submenu.Append(wx.ID_ANY,obj.formatName,obj.longFormatName)
self.SeqExportLookup[item.GetId()] = (obj,lbl) # lookup table for submenu item
# Bind is in UpdateSeqResults
self.SequentialEx.Append(G2G.wxID_XPORTSEQCSV,'Save table as CSV',
'Save all sequential refinement results as a CSV spreadsheet file')
G2G.Define_wxId('wxID_XPORTSEQIMG')
self.SequentialEx.Append(G2G.wxID_XPORTSEQIMG,'Save histogram images',
'Save all sequential refinements as a series of images')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.SequentialMenu)
self.SequentialMenu = _makemenu
#Cluster analysis - what do I need here?
self.ClusterAnalysisMenu = G2frame.GSASIIMenu
# self.ClusterAnalysisMenu = wx.MenuBar()
# self.PrefillDataMenu(self.ClusterAnalysisMenu,empty=True)
# self.PostfillDataMenu(empty=True)
# PWDR & SASD
G2G.Define_wxId('wxID_PWDANALYSIS','wxID_PWDCOPY','wxID_PLOTCTRLCOPY',
'wxID_PWDHKLPLOT', 'wxID_PWD3DHKLPLOT','wxID_1DHKLSTICKPLOT')
G2G.Define_wxId('wxID_CHHKLLBLS')
G2G.Define_wxId('wxID_CHPHPARTIAL')
G2G.Define_wxId('wxID_PHPARTIALCSV')
def _makemenu(): # routine to create menu when first used
self.PWDRMenu = wx.MenuBar()
self.PrefillDataMenu(self.PWDRMenu)
self.ErrorAnal = wx.Menu(title='')
self.PWDRMenu.Append(menu=self.ErrorAnal,title='Commands')
self.ErrorAnal.Append(G2G.wxID_PWDANALYSIS,'Error Analysis','Error analysis on powder pattern')
self.ErrorAnal.Append(G2G.wxID_PWDCOPY,'Copy params','Copy of PWDR parameters')
self.ErrorAnal.Append(G2G.wxID_PLOTCTRLCOPY,'Copy plot controls','Copy of PWDR plot controls')
self.moveDiffCurve = self.ErrorAnal.Append(wx.ID_ANY,'Move diff. curve',
'Click on position where difference curve is placed')
self.moveTickLoc = self.ErrorAnal.Append(wx.ID_ANY,'Move ticks','Move mouse to where tick marks should be positioned')
self.moveTickSpc = self.ErrorAnal.Append(wx.ID_ANY,'Set tick space','Click to set spacing between phase tick marks')
self.setPlotLim = self.ErrorAnal.Append(wx.ID_ANY,'Set plot limits...','Allows entry of plot min & max values')
self.setPlotFmt = self.ErrorAnal.Append(wx.ID_ANY,'Set plot formatting...','Allows changes to text size and line widths, etc.')
self.ErrorAnal.Append(G2G.wxID_CHHKLLBLS,'hkl label config...','Configure labels on reflections or delete them')
G2frame.PartialConfig = self.ErrorAnal.Append(G2G.wxID_CHPHPARTIAL,'Phase partial config...','Configure how individual phase profiles are shown')
G2frame.PartialCSV = self.ErrorAnal.Append(G2G.wxID_PHPARTIALCSV,'Save partials as csv','Save the computed partials as a csv file')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.PWDRMenu)
self.PWDRMenu = _makemenu
# HKLF - many wxIDs defined in PWDR & SASD above
G2G.Define_wxId('wxID_3DALLHKLPLOT','wxID_SORTHKL','wxID_MERGEHKL','wxID_FIXFSQSQDATA')
def _makemenu(): # routine to create menu when first used
self.HKLFMenu = wx.MenuBar()
self.PrefillDataMenu(self.HKLFMenu)
self.ErrorAnal = wx.Menu(title='')
self.HKLFMenu.Append(menu=self.ErrorAnal,title='Commands')
self.ErrorAnal.Append(G2G.wxID_PWDANALYSIS,'Error Analysis','Error analysis on single crystal data')
self.ErrorAnal.Append(G2G.wxID_SORTHKL,'Sort HKLs','Transform & sort HKLF data to new histogram')
self.ErrorAnal.Append(G2G.wxID_MERGEHKL,'Merge HKLs','Transform & merge HKLF data to new histogram')
self.ErrorAnal.Append(G2G.wxID_1DHKLSTICKPLOT,'Plot 1D HKLs','Plot of HKLs from single crystal data in 1D')
self.ErrorAnal.Append(G2G.wxID_3DALLHKLPLOT,'Plot all 3D HKLs','Plot HKLs from all single crystal data in 3D')
self.ErrorAnal.Append(G2G.wxID_FIXFSQSQDATA,'Fix (F^2)^2 data','Fix F^2 data imported as F')
# self.ErrorAnal.Append(G2G.wxID_PWDCOPY,'Copy params','Copy of HKLF parameters') #unused
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.HKLFMenu)
self.HKLFMenu = _makemenu
# PWDR / Limits
G2G.Define_wxId('wxID_LIMITCOPY', 'wxID_ADDEXCLREGION',)
G2G.Define_wxId('wxID_SETLOWLIMIT')
G2G.Define_wxId('wxID_SETTOPLIMIT')
G2G.Define_wxId('wxID_STOPSETLIMIT')
def _makemenu(): # routine to create menu when first used
self.LimitMenu = wx.MenuBar()
self.PrefillDataMenu(self.LimitMenu)
self.LimitEdit = wx.Menu(title='')
self.LimitMenu.Append(menu=self.LimitEdit, title='Edit Limits')
self.LimitEdit.Append(G2G.wxID_LIMITCOPY,'Copy','Copy limits to other histograms')
self.LimitEdit.Append(G2G.wxID_SETLOWLIMIT,'Set lower limit',
'Click on a data point to set the lower limit location')
self.LimitEdit.Append(G2G.wxID_SETTOPLIMIT,'Set upper limit',
'Click on a data point to set the upper limit location')
self.LimitEdit.Append(G2G.wxID_ADDEXCLREGION,'Add excluded region',
'Add excluded region - select a point on plot; drag later to adjust')
G2frame.CancelSetLimitsMode = self.LimitEdit.Append(
G2G.wxID_STOPSETLIMIT,'Cancel set',
'Clears a previous Set limits/add excluded region')
G2frame.CancelSetLimitsMode.Enable(False)
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.LimitMenu)
self.LimitMenu = _makemenu
# PWDR / Background
G2G.Define_wxId('wxID_BACKCOPY', 'wxID_BACKFLAGCOPY','wxID_MAKEBACKRDF',
'wxID_RESCALEALL','wxID_BACKPEAKSMOVE','wxID_BACKSAVE','wxID_BACKLOAD')
def _makemenu(): # routine to create menu when first used
self.BackMenu = wx.MenuBar()
self.PrefillDataMenu(self.BackMenu)
self.BackEdit = wx.Menu(title='')
self.BackMenu.Append(menu=self.BackEdit, title='Background')
self.BackEdit.Append(G2G.wxID_BACKCOPY,'Copy','Copy background parameters to other histograms')
self.BackEdit.Append(G2G.wxID_BACKFLAGCOPY,'Copy flags',
'Copy background refinement flags to other histograms')
self.BackEdit.Append(G2G.wxID_BACKSAVE,'Save ...','Save background parameters to file')
self.BackEdit.Append(G2G.wxID_BACKLOAD,'Load ...','Load background parameters from file')
self.BackEdit.Append(G2G.wxID_BACKPEAKSMOVE,'Move peaks','Move background peaks to Peak List')
self.BackEdit.Append(G2G.wxID_MAKEBACKRDF,'Plot RDF','Plot radial distribution from differences')
self.BackFixed = wx.Menu(title='') # fixed background point menu
self.BackMenu.Append(menu=self.BackFixed, title='Fixed Points')
self.wxID_BackPts = {}
self.wxID_BackPts['Add'] = wx.NewId() # N.B. not using wxID_ global as for other menu items
self.BackFixed.AppendRadioItem(self.wxID_BackPts['Add'],'Add','Add fixed background points with mouse clicks')
self.wxID_BackPts['Move'] = wx.NewId()
item = self.BackFixed.AppendRadioItem(self.wxID_BackPts['Move'],'Move','Move selected fixed background points with mouse drags')
item.Check(True)
self.wxID_BackPts['Delete'] = wx.NewId()
self.BackFixed.AppendRadioItem(self.wxID_BackPts['Delete'],'Delete','Delete fixed background points with mouse clicks')
self.wxID_BackPts['Clear'] = wx.NewId()
self.BackFixed.Append(self.wxID_BackPts['Clear'],'Clear','Clear fixed background points')
self.wxID_BackPts['Fit'] = wx.NewId()
self.BackFixed.Append(self.wxID_BackPts['Fit'],'Fit background',
'Fit background function to fixed background points')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.BackMenu)
self.BackMenu = _makemenu
# PWDR / Instrument Parameters
G2G.Define_wxId('wxID_INSTPRMRESET','wxID_INSTCOPY','wxID_INSTFLAGCOPY','wxID_INSTLOAD',
'wxID_INSTSAVE', 'wxID_INST1VAL', 'wxID_INSTCALIB', 'wxID_INSTSAVEALL',
'wxID_INSTSHOWMULT',)
def _makemenu(): # routine to create menu when first used
self.InstMenu = wx.MenuBar()
self.PrefillDataMenu(self.InstMenu)
self.InstEdit = wx.Menu(title='')
self.InstMenu.Append(menu=self.InstEdit, title='Operations')
self.InstEdit.Append(G2G.wxID_INSTCALIB,'Calibrate','Calibrate from indexed peaks')
self.InstEdit.Append(G2G.wxID_INSTPRMRESET,'Reset profile','Reset instrument profile parameters to default')
self.InstEdit.Append(G2G.wxID_INSTLOAD,'Load profile...','Load instrument profile parameters from file')
self.InstEdit.Append(G2G.wxID_INSTSAVE,'Save profile...','Save instrument profile parameters to file')
self.InstEdit.Append(G2G.wxID_INSTSAVEALL,'Save all profile...','Save all instrument profile parameters to one file')
self.InstEdit.Append(G2G.wxID_INSTCOPY,'Copy','Copy instrument profile parameters to other histograms')
self.InstEdit.Append(G2G.wxID_INSTFLAGCOPY,'Copy flags','Copy instrument parameter refinement flags to other histograms')
self.InstEdit.Append(G2G.wxID_INST1VAL,'Set one value','Set one instrument parameter value across multiple histograms')
self.InstEdit.AppendCheckItem(G2G.wxID_INSTSHOWMULT,'Show multiple','Show multiple histograms of same type as current')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.InstMenu)
self.InstMenu = _makemenu
# PWDR / Sample Parameters
G2G.Define_wxId('wxID_SAMPLECOPY', 'wxID_SAMPLECOPYSOME', 'wxID_SAMPLEFLAGCOPY','wxID_SAMPLESAVE',
'wxID_SAMPLELOAD', 'wxID_SETSCALE', 'wxID_SAMPLE1VAL', 'wxID_ALLSAMPLELOAD','wxID_SEARCHVAL',)
def _makemenu(): # routine to create menu when first used
self.SampleMenu = wx.MenuBar()
self.PrefillDataMenu(self.SampleMenu)
self.SampleEdit = wx.Menu(title='')
self.SampleMenu.Append(menu=self.SampleEdit, title='Command')
self.SetScale = self.SampleEdit.Append(G2G.wxID_SETSCALE,'Set scale','Set scale by matching to another histogram')
self.SampleEdit.Append(G2G.wxID_SAMPLELOAD,'Load','Load sample parameters from file')
self.SampleEdit.Append(G2G.wxID_SAMPLESAVE,'Save','Save sample parameters to file')
self.SampleEdit.Append(G2G.wxID_SAMPLECOPY,'Copy','Copy refinable and most other sample parameters to other histograms')
self.SampleEdit.Append(G2G.wxID_SAMPLECOPYSOME,'Copy selected...','Copy selected sample parameters to other histograms')
self.SampleEdit.Append(G2G.wxID_SAMPLEFLAGCOPY,'Copy flags','Copy sample parameter refinement flags to other histograms')
self.SampleEdit.Append(G2G.wxID_SAMPLE1VAL,'Set one value','Set one sample parameter value across multiple histograms')
self.SampleEdit.Append(G2G.wxID_ALLSAMPLELOAD,'Load all','Load sample parameters over multiple histograms')
self.SampleEdit.Append(G2G.wxID_RESCALEALL,'Rescale all','Rescale all data with selected range')
self.SampleEdit.Append(G2G.wxID_SEARCHVAL,'Set from comments','Search the comments to set a parameter value')
self.PostfillDataMenu()
self.SetScale.Enable(False)
SetDataMenuBar(G2frame,self.SampleMenu)
self.SampleMenu = _makemenu
# PWDR / Peak List
G2G.Define_wxId('wxID_UNDO', 'wxID_LSQPEAKFIT', 'wxID_LSQONECYCLE', 'wxID_RESETSIGGAM',
'wxID_CLEARPEAKS', 'wxID_AUTOSEARCH','wxID_PEAKSCOPY', 'wxID_SEQPEAKFIT','wxID_PEAKLOAD','wxID_PEAKSAVE')
G2G.Define_wxId('wxID_DELPEAKS')
G2G.Define_wxId('wxID_SETUNVARIEDWIDTHS')
G2G.Define_wxId('wxID_XTRAPEAKMODE')
G2G.Define_wxId('wxID_PEAKSCOPYFLAG')
def _makemenu(): # routine to create menu when first used
self.PeakMenu = wx.MenuBar()
self.PrefillDataMenu(self.PeakMenu)
self.PeakEdit = wx.Menu(title='')
self.PeakMenu.Append(menu=self.PeakEdit, title='Peak Fitting')
self.peaksSel = self.PeakEdit.Append(wx.ID_ANY,'Set sel. ref flags...','Set refinement flags for selected peaks')
self.peaksAll = self.PeakEdit.Append(wx.ID_ANY,'Set all ref flags...','Set refinement flags for all peaks')
self.AutoSearch = self.PeakEdit.Append(G2G.wxID_AUTOSEARCH,'Auto search','Automatic peak search')
self.UnDo = self.PeakEdit.Append(G2G.wxID_UNDO,'UnDo','Undo last least squares refinement')
self.PeakFit = self.PeakEdit.Append(G2G.wxID_LSQPEAKFIT,'Peakfit\tCtrl+P','Peak fitting' )
self.PFOneCycle = self.PeakEdit.Append(G2G.wxID_LSQONECYCLE,'Peakfit one cycle','One cycle of Peak fitting' )
self.PeakEdit.Append(G2G.wxID_RESETSIGGAM,'Reset sig and gam','Reset sigma and gamma to global fit' )
self.PeakCopy = self.PeakEdit.Append(G2G.wxID_PEAKSCOPY,'Peak copy','Copy peaks to other histograms')
self.PeakCopyFlag = self.PeakEdit.Append(G2G.wxID_PEAKSCOPYFLAG,'Peak flags copy','Copy peak refinement flags to other histograms')
self.PeakEdit.Append(G2G.wxID_PEAKLOAD,'Load peaks...','Load peak list from file')
self.PeakEdit.Append(G2G.wxID_PEAKSAVE,'Save peaks...','Save peak list to file')
self.SeqPeakFit = self.PeakEdit.Append(G2G.wxID_SEQPEAKFIT,'Seq PeakFit',
'Sequential Peak fitting for all histograms' )
self.PeakEdit.Append(G2G.wxID_DELPEAKS,'Delete peaks','Delete selected peaks from the list' )
self.PeakEdit.Append(G2G.wxID_CLEARPEAKS,'Clear peaks','Clear the peak list' )
self.movePeak = self.PeakEdit.Append(wx.ID_ANY,'Move selected peak',
'Select a peak in the table, then use this to move it with the mouse.')
self.setPeakMode = self.PeakEdit.Append(G2G.wxID_SETUNVARIEDWIDTHS,
'Gen unvaried widths',
'When unvaried, Generate sigma & gamma from UVWXY...',
kind=wx.ITEM_CHECK)
self.setPeakMode.Check(True)
self.XtraPeakMode = self.PeakEdit.Append(G2G.wxID_XTRAPEAKMODE,
'Add impurity/subgrp/magnetic peaks',
'Set positions of magnetic, impurity or subgroup peaks',
kind=wx.ITEM_CHECK)
self.XtraPeakMode.Check(False)
self.PostfillDataMenu()
self.UnDo.Enable(False)
self.PeakFit.Enable(False)
self.PFOneCycle.Enable(False)
self.AutoSearch.Enable(True)
SetDataMenuBar(G2frame,self.PeakMenu)
self.PeakMenu = _makemenu
# PWDR / Index Peak List
G2G.Define_wxId('wxID_INDXRELOAD','wxID_INDEXSAVE','wxID_INDEXEXPORTDICVOL','wxID_REFINECELL2')
def _makemenu(): # routine to create menu when first used
self.IndPeaksMenu = wx.MenuBar()
self.PrefillDataMenu(self.IndPeaksMenu)
self.IndPeaksEdit = wx.Menu(title='')
self.IndPeaksMenu.Append(menu=self.IndPeaksEdit,title='Operations')
self.IndPeaksEdit.Append(G2G.wxID_INDXRELOAD,'Load/Reload','Load/Reload index peaks from peak list')
self.IndPeaksEdit.Append(G2G.wxID_INDEXSAVE,'Save','Save index peaks to CSV file')
self.IndPeaksEdit.Append(G2G.wxID_INDEXEXPORTDICVOL,'Export to PreDICT','Export index peaks to PreDICT (.csv)')
self.RefineCell2 = self.IndPeaksEdit.Append(G2G.wxID_REFINECELL2,'Refine Cell',
'Refine unit cell parameters from indexed peaks')
self.PostfillDataMenu()
#self.RefineCell2.Enable(False)
SetDataMenuBar(G2frame,self.IndPeaksMenu)
self.IndPeaksMenu = _makemenu
# PWDR / Unit Cells List
G2G.Define_wxId('wxID_INDEXPEAKS', 'wxID_REFINECELL', 'wxID_COPYCELL', 'wxID_MAKENEWPHASE',
'wxID_EXPORTCELLS','wxID_LOADCELL','wxID_IMPORTCELL','wxID_TRANSFORMCELL',
'wxID_RUNSUB','wxID_RUNSUBMAG')
#G2G.Define_wxId('wxID_LATSYM')
G2G.Define_wxId('wxID_NISTLATSYM')
G2G.Define_wxId('wxID_SHOWGENHKLS')
G2G.Define_wxId('wxID_CLEARCELLS')
def _makemenu(): # routine to create menu when first used
self.IndexMenu = wx.MenuBar()
self.PrefillDataMenu(self.IndexMenu)
self.IndexEdit = wx.Menu(title='')
self.IndexMenu.Append(menu=self.IndexEdit, title='Cell Index/Refine')
self.IndexPeaks = self.IndexEdit.Append(G2G.wxID_INDEXPEAKS,'Index Cell',
'Find cells that index fitted peaks')
# self.IndexEdit.Append(G2G.wxID_LATSYM,'Cell Symmetry Search-Bilbao',
# 'Run Bilbao "Lattice Symmetry" to find higher symmetry cells')
self.IndexEdit.Append(G2G.wxID_NISTLATSYM,'Cell Symmetry Search',
'Run NIST*LATTICE to find higher symmetry cells')
self.RunSubGroups = self.IndexEdit.Append(G2G.wxID_RUNSUB,'Run SUBGROUPS',
'If disabled, do Load Phase first')
self.RunSubGroupsMag = self.IndexEdit.Append(G2G.wxID_RUNSUBMAG,'Run k-SUBGROUPMAG',
'If disabled, do Load Phase first')
self.CopyCell = self.IndexEdit.Append(G2G.wxID_COPYCELL,'Copy Cell',
'Copy selected unit cell from indexing to cell refinement fields')
self.LoadCell = self.IndexEdit.Append(G2G.wxID_LOADCELL,'Load Phase',
'Load unit cell from a phase tree entry')
# TODO: broken. Needs to be a cascade menu as per ReImportMenuId?
# self.ImportCell = self.IndexEdit.Append(G2G.wxID_IMPORTCELL,'Import Cell',
# 'Import unit cell from file')
self.TransposeCell = self.IndexEdit.Append(G2G.wxID_TRANSFORMCELL,'Transform Cell',
'Transform unit cell')
self.RefineCell = self.IndexEdit.Append(G2G.wxID_REFINECELL,'Refine Cell',
'Refine unit cell parameters from indexed peaks')
self.MakeNewPhase = self.IndexEdit.Append(G2G.wxID_MAKENEWPHASE,'Make new phase',
'Make new phase from selected unit cell')
self.ExportCells = self.IndexEdit.Append(G2G.wxID_EXPORTCELLS,'Export cell list','Export cell list to csv file')
self.IndexEdit.Append(G2G.wxID_SHOWGENHKLS,'Show reflections','Show generated reflection positions on console')
self.IndexEdit.Append(
G2G.wxID_CLEARCELLS,'Clear search results',
'Clear cell/k-vector/magnetic cell search results'
)
self.PostfillDataMenu()
self.LoadCell.Enable(False)
self.IndexPeaks.Enable(False)
self.RunSubGroups.Enable(False)
self.RunSubGroupsMag.Enable(False)
self.CopyCell.Enable(False)
self.RefineCell.Enable(False)
self.MakeNewPhase.Enable(False)
SetDataMenuBar(G2frame,self.IndexMenu)
self.IndexMenu = _makemenu
# PWDR / Reflection Lists
G2G.Define_wxId('wxID_SELECTPHASE','wxID_SHOWHIDEEXTINCT','wxID_WILSONSTAT','wxID_CSVFROMTABLE' ) #some wxIDs defined above in PWDR & SASD
def _makemenu(): # routine to create menu when first used
self.ReflMenu = wx.MenuBar()
self.PrefillDataMenu(self.ReflMenu)
self.ReflEdit = wx.Menu(title='')
self.ReflMenu.Append(menu=self.ReflEdit, title='Reflection List')
self.SelectPhase = self.ReflEdit.Append(G2G.wxID_SELECTPHASE,'Select phase','Select phase for reflection list')
self.ReflEdit.Append(G2G.wxID_1DHKLSTICKPLOT,'Plot 1D HKLs','Plot of HKLs in 1D')
self.ReflEdit.Append(G2G.wxID_PWDHKLPLOT,'Plot HKLs','Plot HKLs in 2D')
self.ReflEdit.Append(G2G.wxID_PWD3DHKLPLOT,'Plot 3D HKLs','Plot HKLs in 3D')
self.ReflEdit.Append(G2G.wxID_CSVFROMTABLE,'Make csv file from table','Make csv file from table')
self.ReflEdit.Append(G2G.wxID_WILSONSTAT,'Wilson statistics')
self.HideShow = self.ReflEdit.Append(G2G.wxID_SHOWHIDEEXTINCT,'Show/hide extinct reflections')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.ReflMenu)
self.ReflMenu = _makemenu
# SASD & REFD / Limits
G2G.Define_wxId('wxID_SASDLIMITCOPY', )
def _makemenu(): # routine to create menu when first used
self.SASDLimitMenu = wx.MenuBar()
self.PrefillDataMenu(self.SASDLimitMenu)
self.SASDLimitEdit = wx.Menu(title='')
self.SASDLimitMenu.Append(menu=self.SASDLimitEdit, title='Edit Limits')
self.SASDLimitEdit.Append(G2G.wxID_SASDLIMITCOPY,'Copy','Copy limits to other histograms')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.SASDLimitMenu)
self.SASDLimitMenu = _makemenu
# SASD / Instrument Parameters
G2G.Define_wxId('wxID_SASDINSTCOPY',)
def _makemenu(): # routine to create menu when first used
self.SASDInstMenu = wx.MenuBar()
self.PrefillDataMenu(self.SASDInstMenu)
self.SASDInstEdit = wx.Menu(title='')
self.SASDInstMenu.Append(menu=self.SASDInstEdit, title='Operations')
self.SASDInstEdit.Append(G2G.wxID_SASDINSTCOPY,'Copy','Copy instrument profile parameters to other histograms')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.SASDInstMenu)
self.SASDInstMenu = _makemenu
#SASD & REFL/ Substance editor
G2G.Define_wxId('wxID_LOADSUBSTANCE','wxID_RELOADSUBSTANCES','wxID_ADDSUBSTANCE','wxID_COPYSUBSTANCE',
'wxID_DELETESUBSTANCE','wxID_ELEMENTADD', 'wxID_ELEMENTDELETE',)
def _makemenu(): # routine to create menu when first used
self.SubstanceMenu = wx.MenuBar()
self.PrefillDataMenu(self.SubstanceMenu)
self.SubstanceEdit = wx.Menu(title='')
self.SubstanceMenu.Append(menu=self.SubstanceEdit, title='Edit substance')
self.SubstanceEdit.Append(G2G.wxID_LOADSUBSTANCE,'Load substance','Load substance from file')
self.SubstanceEdit.Append(G2G.wxID_RELOADSUBSTANCES,'Reload substances','Reload all substances from file')
self.SubstanceEdit.Append(G2G.wxID_ADDSUBSTANCE,'Add substance','Add new substance to list')
self.SubstanceEdit.Append(G2G.wxID_COPYSUBSTANCE,'Copy substances','Copy substances')
self.SubstanceEdit.Append(G2G.wxID_DELETESUBSTANCE,'Delete substance','Delete substance from list')
self.SubstanceEdit.Append(G2G.wxID_ELEMENTADD,'Add elements','Add elements to substance')
self.SubstanceEdit.Append(G2G.wxID_ELEMENTDELETE,'Delete elements','Delete elements from substance')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.SubstanceMenu)
self.SubstanceMenu = _makemenu
# SASD/ Models
G2G.Define_wxId('wxID_MODELCOPY', 'wxID_MODELFIT', 'wxID_MODELADD','wxID_MODELUNDO',
'wxID_MODELFITALL', 'wxID_MODELCOPYFLAGS','wxID_MODELPLOT',)
def _makemenu(): # routine to create menu when first used
self.ModelMenu = wx.MenuBar()
self.PrefillDataMenu(self.ModelMenu)
self.ModelEdit = wx.Menu(title='')
self.ModelMenu.Append(menu=self.ModelEdit, title='Models')
self.ModelEdit.Append(G2G.wxID_MODELADD,'Add','Add new term to model')
self.ModelEdit.Append(G2G.wxID_MODELFIT,'Fit','Fit model parameters to data')
self.SasdUndo = self.ModelEdit.Append(G2G.wxID_MODELUNDO,'Undo','Undo model fit')
self.SasdUndo.Enable(False)
self.SasSeqFit = self.ModelEdit.Append(G2G.wxID_MODELFITALL,'Sequential fit','Sequential fit of model parameters to all SASD data')
self.SasSeqFit.Enable(False)
self.ModelEdit.Append(G2G.wxID_MODELCOPY,'Copy','Copy model parameters to other histograms')
self.ModelEdit.Append(G2G.wxID_MODELCOPYFLAGS,'Copy flags','Copy model refinement flags to other histograms')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.ModelMenu)
self.ModelMenu = _makemenu
# REFD/ Models - wxIDs as for SASD/Models
def _makemenu(): # routine to create menu when first used
self.REFDModelMenu = wx.MenuBar()
self.PrefillDataMenu(self.REFDModelMenu)
self.REFDModelEdit = wx.Menu(title='')
self.REFDModelMenu.Append(menu=self.REFDModelEdit, title='Models')
self.REFDModelEdit.Append(G2G.wxID_MODELFIT,'Fit','Fit model parameters to data')
self.REFDUndo = self.REFDModelEdit.Append(G2G.wxID_MODELUNDO,'Undo','Undo model fit')
self.REFDUndo.Enable(False)
self.REFDModelEdit.Append(G2G.wxID_MODELFITALL,'Sequential fit','Sequential fit of model parameters to all REFD data')
self.REFDModelEdit.Append(G2G.wxID_MODELCOPY,'Copy','Copy model parameters to other histograms')
self.REFDModelEdit.Append(G2G.wxID_MODELPLOT,'Plot','Plot model SDL for selected histograms')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.REFDModelMenu)
self.REFDModelMenu = _makemenu
# IMG / Image Controls
G2G.Define_wxId('wxID_IMCALIBRATE', 'wxID_IMRECALIBRATE', 'wxID_IMINTEGRATE', 'wxID_IMCLEARCALIB', 'wxID_IMRECALIBALL',
'wxID_IMCOPYCONTROLS', 'wxID_INTEGRATEALL', 'wxID_IMSAVECONTROLS', 'wxID_IMLOADCONTROLS', 'wxID_IMAUTOINTEG',
'wxID_IMCOPYSELECTED', 'wxID_SAVESELECTEDCONTROLS', 'wxID_IMXFERCONTROLS', 'wxID_IMRESETDIST', 'wxID_CALCRINGS',
'wxID_LOADELECTEDCONTROLS','wxID_IMDISTRECALIB', 'wxID_IMINTEGPDFTOOL','wxID_IMMULTGAINMAP')
G2G.Define_wxId('wxID_IMDRWPHS')
def _makemenu(): # routine to create menu when first used
self.ImageMenu = wx.MenuBar()
self.PrefillDataMenu(self.ImageMenu)
self.ImageEdit = wx.Menu(title='')
self.ImageMenu.Append(menu=self.ImageEdit, title='Calibration')
self.ImageEdit.Append(G2G.wxID_IMCALIBRATE,'Calibrate','Calibrate detector by fitting to calibrant lines')
self.ImageEdit.Append(G2G.wxID_IMRECALIBRATE,'Recalibrate','Recalibrate detector by fitting to calibrant lines')
self.ImageEdit.Append(G2G.wxID_IMRECALIBALL,'Recalibrate all','Recalibrate all images by fitting to calibrant lines')
self.ImageEdit.Append(G2G.wxID_CALCRINGS,'Calculate rings','Calculate rings from calibration parameters')
self.ImageEdit.Append(G2G.wxID_IMDISTRECALIB,'Multi-distance Recalibrate','Recalibrate all images varying delta-distance and fitting wavelength')
self.ImageEdit.Append(G2G.wxID_IMCLEARCALIB,'Clear calibration','Clear calibration data points and rings')
self.ImageEdit.Append(G2G.wxID_IMMULTGAINMAP,'Multiimage Gain map','Make gain map from multiple images')
ImageIntegrate = wx.Menu(title='')
self.ImageMenu.Append(menu=ImageIntegrate, title='Integration')
ImageIntegrate.Append(G2G.wxID_IMINTEGRATE,'Integrate','Integrate selected image')
ImageIntegrate.Append(G2G.wxID_INTEGRATEALL,'Integrate all','Integrate all images selected from list')
ImageIntegrate.Append(G2G.wxID_IMAUTOINTEG,'Auto Integrate','Open Auto-integration window to integrate a series of images')
ImageIntegrate.Append(G2G.wxID_IMINTEGPDFTOOL,'Integrate/PDF app (in dev)','Start Integration/PDF task (in development)')
ImageParams = wx.Menu(title='')
self.ImageMenu.Append(menu=ImageParams, title='Parms')
ImageParams.Append(G2G.wxID_IMCOPYCONTROLS,'Copy Controls','Copy image controls to other images')
ImageParams.Append(G2G.wxID_IMCOPYSELECTED,'Copy Selected','Copy selected image controls to other images')
ImageParams.Append(G2G.wxID_IMSAVECONTROLS,'Save Controls','Save image controls to file')
ImageParams.Append(G2G.wxID_SAVESELECTEDCONTROLS,'Save Multiple Controls','Save controls from selected images to file')
ImageParams.Append(G2G.wxID_IMLOADCONTROLS,'Load Controls','Load image controls from file')
ImageParams.Append(G2G.wxID_LOADELECTEDCONTROLS,'Load Multiple Controls','Load multiple image controls from multiple files')
ImageParams.Append(G2G.wxID_IMXFERCONTROLS,'Xfer controls','Transfer integration controls to other detector distances')
ImageParams.Append(G2G.wxID_IMRESETDIST,'Reset dist','Reset all detector dist to set dist')
ImageParams.Append(G2G.wxID_IMDRWPHS,'Superimpose phase','Display the rings from selected phase(s) on image')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.ImageMenu)
self.ImageMenu = _makemenu
# IMG / Masks
G2G.Define_wxId('wxID_MASKCOPY', 'wxID_MASKSAVE', 'wxID_MASKLOAD', 'wxID_NEWMASKSPOT', 'wxID_NEWMASKARC', 'wxID_NEWMASKRING',
'wxID_NEWMASKFRAME', 'wxID_NEWMASKPOLY','wxID_NEWMASKXLINE','wxID_NEWMASKYLINE','wxID_MASKLOADNOT',
'wxID_FINDSPOTS', 'wxID_AUTOFINDSPOTS', 'wxID_DELETESPOTS','wxID_MASKCOPYSELECTED', 'wxID_LOADSPOTS')
def _makemenu(): # routine to create menu when first used
self.MaskMenu = wx.MenuBar()
self.PrefillDataMenu(self.MaskMenu)
self.MaskEdit = wx.Menu(title='')
self.MaskMenu.Append(menu=self.MaskEdit, title='Operations')
submenu = wx.Menu()
self.MaskEdit.AppendSubMenu( submenu,'Create new','')
self.MaskEdit.Append(G2G.wxID_MASKCOPY,'Copy mask','Copy mask to other images')
self.MaskEdit.Append(G2G.wxID_MASKCOPYSELECTED,'Copy Selected','Copy selected masks to other images')
self.MaskEdit.Append(G2G.wxID_MASKSAVE,'Save mask','Save mask to file')
self.MaskEdit.Append(G2G.wxID_MASKLOADNOT,'Load mask','Load mask from file; ignoring threshold')
self.MaskEdit.Append(G2G.wxID_MASKLOAD,'Load mask w/threshold','Load mask from file keeping the threshold value')
self.MaskEdit.Append(G2G.wxID_FINDSPOTS,'Pixel mask search','Search for pixels to mask')
self.MaskEdit.Append(G2G.wxID_LOADSPOTS,'Load pixel mask','Use non-zero pixels in an image to mask')
self.MaskEdit.Append(G2G.wxID_AUTOFINDSPOTS,'Multi-IMG pixel mask search','Search multiple images for pixels to mask; NB: slow')
self.MaskEdit.Append(G2G.wxID_DELETESPOTS,'Delete spot masks','Delete all spot masks')
submenu.Append(G2G.wxID_NEWMASKARC,'Arc mask','Create an arc mask with mouse input')
submenu.Append(G2G.wxID_NEWMASKFRAME,'Frame mask','Create a frame mask with mouse input')
submenu.Append(G2G.wxID_NEWMASKPOLY,'Polygon mask','Create a polygon mask with mouse input')
submenu.Append(G2G.wxID_NEWMASKRING,'Ring mask','Create a ring mask with mouse input')
submenu.Append(G2G.wxID_NEWMASKSPOT,'Spot mask','Create spot masks with mouse input')
submenu.Append(G2G.wxID_NEWMASKXLINE,'X line mask','Create line masks with mouse input')
submenu.Append(G2G.wxID_NEWMASKYLINE,'Y line mask','Create line masks with mouse input')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.MaskMenu)
self.MaskMenu = _makemenu
# IMG / Stress/Strain
G2G.Define_wxId('wxID_STRSTACOPY', 'wxID_STRSTAFIT', 'wxID_STRSTASAVE', 'wxID_STRSTALOAD', 'wxID_STRSTSAMPLE',
'wxID_APPENDDZERO', 'wxID_STRSTAALLFIT', 'wxID_UPDATEDZERO', 'wxID_STRSTAPLOT', 'wxID_STRRINGSAVE',)
def _makemenu(): # routine to create menu when first used
self.StrStaMenu = wx.MenuBar()
self.PrefillDataMenu(self.StrStaMenu)
self.StrStaEdit = wx.Menu(title='')
self.StrStaMenu.Append(menu=self.StrStaEdit, title='Operations')
self.StrStaEdit.Append(G2G.wxID_APPENDDZERO,'Append d-zero','Append d-zero for one ring')
self.StrStaEdit.Append(G2G.wxID_STRSTAFIT,'Fit stress/strain','Fit stress/strain data')
self.StrStaEdit.Append(G2G.wxID_STRSTAPLOT,'Plot intensity distribution','Plot intensity distribution')
self.StrStaEdit.Append(G2G.wxID_STRRINGSAVE,'Save intensity distribution','Save intensity distribution')
self.StrStaEdit.Append(G2G.wxID_UPDATEDZERO,'Update d-zero','Update d-zero from ave d-zero')
self.StrStaEdit.Append(G2G.wxID_STRSTAALLFIT,'All image fit','Fit stress/strain data for all images')
self.StrStaEdit.Append(G2G.wxID_STRSTACOPY,'Copy stress/strain','Copy stress/strain data to other images')
self.StrStaEdit.Append(G2G.wxID_STRSTASAVE,'Save stress/strain','Save stress/strain data to file')
self.StrStaEdit.Append(G2G.wxID_STRSTALOAD,'Load stress/strain','Load stress/strain data from file')
self.StrStaEdit.Append(G2G.wxID_STRSTSAMPLE,'Load sample data','Load sample data from file')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.StrStaMenu)
self.StrStaMenu = _makemenu
# PDF / PDF Controls
G2G.Define_wxId('wxID_PDFCOPYCONTROLS', 'wxID_PDFSAVECONTROLS', 'wxID_PDFLOADCONTROLS', 'wxID_PDFCOMPUTE',
'wxID_PDFCOMPUTEALL', 'wxID_PDFADDELEMENT', 'wxID_PDFDELELEMENT',)
def _makemenu(): # routine to create menu when first used
self.PDFMenu = wx.MenuBar()
self.PrefillDataMenu(self.PDFMenu)
self.PDFEdit = wx.Menu(title='')
self.PDFMenu.Append(menu=self.PDFEdit, title='PDF Controls')
self.PDFEdit.Append(G2G.wxID_PDFADDELEMENT,'Add elements','Add one or more elements to sample composition')
self.PDFEdit.Append(G2G.wxID_PDFDELELEMENT,'Delete element','Delete element from sample composition')
self.PDFEdit.Append(G2G.wxID_PDFCOPYCONTROLS,'Copy controls','Copy PDF controls')
self.PDFEdit.Append(G2G.wxID_PDFLOADCONTROLS,'Load Controls','Load PDF controls from file')
self.PDFEdit.Append(G2G.wxID_PDFSAVECONTROLS,'Save controls','Save PDF controls to file')
self.PDFEdit.Append(G2G.wxID_PDFCOMPUTE,'Compute PDF','Compute PDF')
self.PDFEdit.Append(G2G.wxID_PDFCOMPUTEALL,'Compute all PDFs','Compute all PDFs with or w/o optimization')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.PDFMenu)
self.PDFMenu = _makemenu
# PDF / PDF Peaks
G2G.Define_wxId('wxID_PDFPKSFIT','wxID_PDFPKSFITALL', 'wxID_PDFCOPYPEAKS', 'wxID_CLEARPDFPEAKS',)
def _makemenu(): # routine to create menu when first used
self.PDFPksMenu = wx.MenuBar()
self.PrefillDataMenu(self.PDFPksMenu)
self.PDFPksEdit = wx.Menu(title='')
self.PDFPksMenu.Append(menu=self.PDFPksEdit, title='PDF Peaks')
self.PDFPksEdit.Append(G2G.wxID_PDFPKSFIT,'PDF peak fit','Fit PDF peaks')
self.PDFPksEdit.Append(G2G.wxID_PDFPKSFITALL,'Seq PDF peak fit','Sequential Peak fitting for all PDFs')
self.PDFPksEdit.Append(G2G.wxID_PDFCOPYPEAKS,'Copy peaks','Copy PDF peaks')
self.PDFPksEdit.Append(G2G.wxID_CLEARPDFPEAKS,'Clear peaks','Clear PDF peaks')
self.PostfillDataMenu()
SetDataMenuBar(G2frame,self.PDFPksMenu)
self.PDFPksMenu = _makemenu
# Phase / General tab
G2G.Define_wxId('wxID_FOURCALC', 'wxID_FOURSEARCH', 'wxID_FOURCLEAR','wxID_CHARGEFLIP','wxID_VALIDPROTEIN',
'wxID_MULTIMCSA','wxID_SINGLEMCSA', 'wxID_4DCHARGEFLIP', 'wxID_TRANSFORMSTRUCTURE','wxID_USEBILBAOMAG',
'wxID_COMPARESTRUCTURE','wxID_COMPARECELLS','wxID_USEBILBAOSUB')
def _makemenu(): # routine to create menu when first used
# note that the phase menus are all interconnected, so they all get created at once.
self.DataGeneral = wx.MenuBar()
self.PrefillDataMenu(self.DataGeneral)
self.DataGeneral.Append(menu=wx.Menu(title=''),title='Select tab')
self.GeneralCalc = wx.Menu(title='')
self.DataGeneral.Append(menu=self.GeneralCalc,title='Compute')
self.GeneralCalc.Append(G2G.wxID_FOURCALC,'Fourier map','Compute Fourier map',)
self.GeneralCalc.Append(G2G.wxID_FOURSEARCH,'Search map','Search Fourier map')
self.GeneralCalc.Append(G2G.wxID_CHARGEFLIP,'Charge flipping','Run charge flipping')
self.GeneralCalc.Append(G2G.wxID_4DCHARGEFLIP,'4D Charge flipping','Run 4D charge flipping')
self.GeneralCalc.Enable(G2G.wxID_4DCHARGEFLIP,False)
self.GeneralCalc.Append(G2G.wxID_FOURCLEAR,'Clear map','Clear map')
self.GeneralCalc.Append(G2G.wxID_SINGLEMCSA,'MC/SA','Run Monte Carlo - Simulated Annealing')
self.GeneralCalc.Append(G2G.wxID_MULTIMCSA,'Multi MC/SA','Run Monte Carlo - Simulated Annealing on multiprocessors')
self.GeneralCalc.Append(G2G.wxID_TRANSFORMSTRUCTURE,'Transform','Transform crystal structure')
G2G.Define_wxId('wxID_TRANSFORMSTD')
self.GeneralCalc.Append(G2G.wxID_TRANSFORMSTD,'Std setting','Create a copy of this phase transformed into the standard setting')
self.GeneralCalc.Append(G2G.wxID_COMPARECELLS,'Compare Cells','Compare Unit Cells using NIST*LATTICE')
self.GeneralCalc.Append(G2G.wxID_COMPARESTRUCTURE,'Compare polyhedra','Compare polyhedra to ideal octahedra/tetrahedra')
self.GeneralCalc.Enable(G2G.wxID_COMPARESTRUCTURE,False)
G2G.Define_wxId('wxID_SUBSRCH')
self.GeneralCalc.Append(G2G.wxID_SUBSRCH,'SUBGROUPS search','Search for settings of this phase in higher symmetry')
self.GeneralCalc.Append(G2G.wxID_USEBILBAOMAG,'Select magnetic/subgroup phase','If disabled, make in PWDR/Unit Cells')
self.GeneralCalc.Append(G2G.wxID_USEBILBAOSUB,'Make subgroup project file(s)','Requires subcell search in PWDR/Unit Cells')
G2G.Define_wxId('wxID_SUPERSRCH')
self.GeneralCalc.Append(G2G.wxID_SUPERSRCH,'Bilbao Supergroup search','Search for settings of this phase in higher symmetry')
G2G.Define_wxId('wxID_ISOSRCH')
self.GeneralCalc.Append(G2G.wxID_ISOSRCH,'ISOCIF Supergroup search','Search for settings of this phase in higher symmetry')
# G2G.Define_wxId('wxID_NISTLATCELL')
# self.GeneralCalc.Append(G2G.wxID_NISTLATCELL,'Cell Symmetry Search',
# 'Run NIST*LATTICE to find higher symmetry cells')
self.GeneralCalc.Append(G2G.wxID_VALIDPROTEIN,'Protein quality','Protein quality analysis')
G2G.Define_wxId('wxID_TESTBCS')
self.GeneralCalc.Append(G2G.wxID_TESTBCS,'Test Bilbao access',
'Check if Bilbao key works')
submenu = wx.Menu()
self.GeneralCalc.AppendSubMenu(submenu,'Replace phase','Replace phase from file')
# setup a cascade menu for the formats that have been defined
self.ReplaceMenuId = {} # points to readers for each menu entry
for reader in self.parent.GetTopLevelParent().ImportPhaseReaderlist:
item = submenu.Append(wx.ID_ANY,'Replace phase from '+reader.formatName+' file',reader.longFormatName)
self.ReplaceMenuId[item.GetId()] = reader
item = submenu.Append(wx.ID_ANY,'guess format from file','Replace phase, try to determine format from file')
self.ReplaceMenuId[item.GetId()] = None # try all readers
self.PostfillDataMenu()
#self.DataGeneral = _makemenu
# Phase / Data tab or Hist/Phase menu (used in one place or other)
G2G.Define_wxId('wxID_DATACOPY', 'wxID_DATACOPYFLAGS', 'wxID_DATASELCOPY', 'wxID_DATAUSE',
'wxID_PWDRADD', 'wxID_HKLFADD','wxID_DATADELETE',
'wxID_DATASELREAD', )
self.DataMenu = wx.MenuBar()
self.PrefillDataMenu(self.DataMenu)
self.DataMenu.Append(menu=wx.Menu(title=''),title='Select tab')
self.DataEdit = wx.Menu(title='')
self.DataMenu.Append(menu=self.DataEdit, title='Edit Phase')
self.DataEdit.Append(G2G.wxID_DATACOPY,'Copy data','Copy phase data to other histograms')
self.DataEdit.Append(G2G.wxID_DATACOPYFLAGS,'Copy flags','Copy phase data flags to other histograms')
self.DataEdit.Append(G2G.wxID_DATASELCOPY,'Copy selected data','Copy selected phase data to other histograms')
self.DataEdit.Append(G2G.wxID_DATAUSE,'Select used data','Select all histograms to use')
self.DataEdit.Append(G2G.wxID_PWDRADD,'Add powder histograms','Select new powder histograms to be used for this phase')
self.DataEdit.Append(G2G.wxID_HKLFADD,'Add single crystal histograms','Select new single crystal histograms to be used for this phase')
self.DataEdit.Append(G2G.wxID_DATADELETE,'Remove histograms','Remove histograms from use for this phase')
G2G.Define_wxId('wxID_DATADIJ')
self.DataEdit.Append(G2G.wxID_DATADIJ,'Apply Strain to Lattice Constants',
'Shift cell by Dij of selected histogram')
self.DataEdit.Append(G2G.wxID_DATASELREAD,'Read selected data from .gpx','Read selected phase/hist data from a saved GSAS-II project')
self.PostfillDataMenu()
# Phase / Atoms tab
G2G.Define_wxId('wxID_ATOMSEDITADD', 'wxID_ATOMSEDITINSERT', 'wxID_ATOMSEDITDELETE',
'wxID_ATOMSMODIFY', 'wxID_ATOMSTRANSFORM', 'wxID_ATOMSVIEWADD', #'wxID_ATOMVIEWINSERT',
'wxID_RELOADDRAWATOMS', 'wxID_ATOMSDISAGL', 'wxID_ATOMMOVE', 'wxID_MAKEMOLECULE',
'wxID_ATOMSPDISAGL', 'wxID_ISODISP', 'wxID_ADDHATOM', 'wxID_UPDATEHATOM','wxID_ATOMSCLEARHIST',
'wxID_ATOMSROTATE', 'wxID_ATOMSDENSITY','wxID_ATOMSBNDANGLHIST','wxID_ATOMSSAVEHIST',
'wxID_ATOMSSETALL', 'wxID_ATOMSSETSEL','wxID_ATOMFRACSPLIT','wxID_COLLECTATOMS',
'wxID_ATOMSSETVP', 'wxID_ATOMSSETLST')
self.AtomsMenu = wx.MenuBar()
self.PrefillDataMenu(self.AtomsMenu)
self.AtomsMenu.Append(menu=wx.Menu(title=''),title='Select tab')
self.AtomEdit = wx.Menu(title='')
self.AtomCompute = wx.Menu(title='')
self.AtomsMenu.Append(menu=self.AtomEdit, title='Edit Atoms')
self.AtomsMenu.Append(menu=self.AtomCompute, title='Compute')
submenu = wx.Menu()
self.AtomEdit.AppendSubMenu(submenu,'On selected atoms...','Set/Act on selected atoms')
submenu.Append(G2G.wxID_ATOMSSETSEL,'Refine selected','Set refinement flags for selected atoms')
submenu.Append(G2G.wxID_ATOMSMODIFY,'Modify parameters','Modify parameters values for all selected atoms')
submenu.Append(G2G.wxID_ATOMSSETVP,'Set view point','Set the view point to be position of 1st selected atom')
submenu.Append(G2G.wxID_ATOMMOVE,'Move atom to view point','Move a single atom to view point in plot')
submenu.Append(G2G.wxID_ATOMSEDITINSERT,'Insert atom','Inserts an H atom before all selected atoms')
#submenu.Append(G2G.wxID_ATOMVIEWINSERT,'Insert view point','Select atom row to insert before; inserted as an H atom')
submenu.Append(G2G.wxID_ADDHATOM,'Calc H atoms','Insert H atoms in expected bonding positions for selected atoms')
submenu.Append(G2G.wxID_ATOMSEDITDELETE,'Delete atom','Delete selected atoms')
submenu.Append(G2G.wxID_ATOMSTRANSFORM,'Transform atoms','Symmetry transform selected atoms')
submenu.Append(G2G.wxID_ATOMSSETALL,'Select All','Select all atoms')
submenu.Append(G2G.wxID_ATOMSSETLST,'Select from list','Select atoms from a filtered listbox')
self.AtomEdit.Append(G2G.wxID_ATOMSEDITADD,'Append atom','Appended as an H atom')
self.AtomEdit.Append(G2G.wxID_ATOMSVIEWADD,'Append atom at view point','Appended as an H atom')
self.AtomEdit.Append(G2G.wxID_UPDATEHATOM,'Update H atoms','Update H atoms in standard positions')
self.AtomEdit.Append(G2G.wxID_MAKEMOLECULE,'Assemble molecule','Select a single atom to assemble as a molecule from scattered atom positions')
self.AtomEdit.Append(G2G.wxID_COLLECTATOMS,'Collect atoms','Collect selected atoms to specified unit cell location')
self.AtomEdit.Append(G2G.wxID_RELOADDRAWATOMS,'Update draw atoms','Update atom drawing list')
submenu = wx.Menu()
self.AtomEdit.AppendSubMenu(submenu,'Reimport atoms','Reimport atoms from file; sequence must match')
# setup a cascade menu for the formats that have been defined
self.ReImportMenuId = {} # points to readers for each menu entry
for reader in self.parent.GetTopLevelParent().ImportPhaseReaderlist:
item = submenu.Append(wx.ID_ANY,'reimport coordinates from '+reader.formatName+' file',reader.longFormatName)
self.ReImportMenuId[item.GetId()] = reader
item = submenu.Append(wx.ID_ANY,'guess format from file','Reimport coordinates, try to determine format from file')
self.ReImportMenuId[item.GetId()] = None # try all readers
self.AtomCompute.Append(G2G.wxID_ATOMSDISAGL,'Show Distances && Angles','Compute distances & angles for selected atoms')
self.AtomCompute.Append(G2G.wxID_ATOMSPDISAGL,'Save Distances && Angles','Compute distances & angles for selected atoms')
self.AtomCompute.Append(G2G.wxID_ATOMSBNDANGLHIST,'Histogram Bonds && Angles','Histogram bonds & angles for selected atoms')
self.AtomCompute.Append(G2G.wxID_ATOMSSAVEHIST,'Save all B&&A histograms','Save all bond & angle histograms')
self.AtomCompute.Append(G2G.wxID_ATOMSCLEARHIST,'Clear all B&&A histograms','Clear all bond & angle histograms')
self.AtomCompute.Append(G2G.wxID_ATOMFRACSPLIT,'Apportion atom frac','2 atom type site fraction apportion')
self.AtomCompute.Append(G2G.wxID_ATOMSDENSITY,'Density','Compute density for current phase')
self.AtomCompute.ISOcalc = self.AtomCompute.Append(G2G.wxID_ISODISP,
'Show New Var modes',
'Show New Var constraints and dependent vars')
self.PostfillDataMenu()
# Phase / Imcommensurate "waves" tab
G2G.Define_wxId('wxID_WAVEVARY',)
self.WavesData = wx.MenuBar()
self.PrefillDataMenu(self.WavesData)
self.WavesData.Append(menu=wx.Menu(title=''),title='Select tab')
self.WavesDataEdit = wx.Menu(title='')
self.WavesData.Append(menu=self.WavesDataEdit, title='Edit Wave')
self.WavesDataEdit.Append(G2G.wxID_WAVEVARY,'Global wave vary','Global setting of wave vary flags')
self.PostfillDataMenu()
#Phase / Dysnomia (Maximum Entropy Method) tab
G2G.Define_wxId('wxID_LOADDYSNOMIA', 'wxID_SAVEDYSNOMIA', 'wxID_RUNDYSNOMIA', )
self.MEMMenu = wx.MenuBar()
self.PrefillDataMenu(self.MEMMenu)
self.MEMMenu.Append(menu=wx.Menu(title=''),title='Select tab')
self.MEMDataEdit = wx.Menu(title='')
self.MEMMenu.Append(menu=self.MEMDataEdit, title='Operations')
#self.MEMDataEdit.Append(G2G.wxID_LOADDYSNOMIA,'Load from Dysnomia file','Load MEM info from Dysnomia file')
#self.MEMDataEdit.Append(G2G.wxID_SAVEDYSNOMIA,'Save Dysnomia file','Save MEM info in Dysnomia file')
self.MEMDataEdit.Append(G2G.wxID_RUNDYSNOMIA,'Run Dysnomia','Run Dysnomia to make new Fobs map')
self.PostfillDataMenu()
#Phase / fullrmc & RMCprofile (Reverse Monte Carlo method) tab
G2G.Define_wxId('wxID_SETUPRMC','wxID_RUNRMC','wxID_VIEWRMC','wxID_STOPRMC',
'wxID_ATOMSRMC', 'wxID_SUPERRMC')
self.FRMCMenu = wx.MenuBar()
self.PrefillDataMenu(self.FRMCMenu)
self.FRMCMenu.Append(menu=wx.Menu(title=''),title='Select tab')
self.FRMCDataEdit = wx.Menu(title='')
self.FRMCMenu.Append(menu=self.FRMCDataEdit, title='Operations')
self.FRMCDataEdit.Append(G2G.wxID_SETUPRMC,'Setup RMC','Setup new fullrmc or RMCprofile file')
self.FRMCDataEdit.Append(G2G.wxID_RUNRMC,'Execute','Run fullrmc or RMCprofile file')
#self.FRMCDataEdit.Append(G2G.wxID_STOPRMC,'Stop run','Stop fullrmc run')
self.FRMCDataEdit.Append(G2G.wxID_VIEWRMC,'Plot','View fullrmc or RMCprofile results')
self.FRMCDataEdit.Append(G2G.wxID_SUPERRMC,'Load Supercell','Load fullrmc results as a supercell')
self.FRMCDataEdit.Append(G2G.wxID_ATOMSRMC,'Superimpose into cell','Load fullrmc results folded into original cell')
self.PostfillDataMenu()
# Phase/ ISODISTORT tab
G2G.Define_wxId('wxID_ISODISTORT','wxID_ISODNEWPHASE','wxID_SHOWISO1','wxID_SHOWISOMODES','wxID_ISOPDFFIT')
self.ISODData = wx.MenuBar()
self.PrefillDataMenu(self.ISODData)
self.ISODData.Append(menu=wx.Menu(title=''),title='Select tab')
self.ISODDataEdit = wx.Menu(title='')
self.ISODData.Append(menu=self.ISODDataEdit, title='Operations')
self.ISODDataEdit.Append(G2G.wxID_ISODISTORT,'Run ISODISTORT','To find displacement modes')
self.ISODDataEdit.Append(G2G.wxID_ISODNEWPHASE,'Make CIF file','From ISODISTORT selection')
self.ISODDataEdit.Append(G2G.wxID_ISOPDFFIT,'Make PDFfit phase','From current ISODISTORT phase')
self.ISODDataEdit.Append(G2G.wxID_SHOWISO1,'Show modes','And values From ISODISTORT')
self.ISODDataEdit.Append(G2G.wxID_SHOWISOMODES,'Show relationships','For ISODISTORT')
self.PostfillDataMenu()
# Phase / Layer tab
G2G.Define_wxId('wxID_LOADDIFFAX', 'wxID_LAYERSIMULATE', 'wxID_SEQUENCESIMULATE', 'wxID_LAYERSFIT', 'wxID_COPYPHASE',)
self.LayerData = wx.MenuBar()
self.PrefillDataMenu(self.LayerData)
self.LayerData.Append(menu=wx.Menu(title=''),title='Select tab')
self.LayerDataEdit = wx.Menu(title='')
self.LayerData.Append(menu=self.LayerDataEdit, title='Operations')
self.LayerDataEdit.Append(G2G.wxID_LOADDIFFAX,'Load from DIFFaX file','Load layer info from DIFFaX file')
self.LayerDataEdit.Append(G2G.wxID_COPYPHASE,'Copy phase cell','Copy phase cell from another project')
self.LayerDataEdit.Append(G2G.wxID_LAYERSIMULATE,'Simulate pattern','Simulate diffraction pattern from layer stacking')
self.LayerDataEdit.Append(G2G.wxID_LAYERSFIT,'Fit pattern','Fit diffraction pattern with layer stacking model')
self.LayerDataEdit.Append(G2G.wxID_SEQUENCESIMULATE,'Sequence simulations','Sequence simulation changing one parameter')
self.PostfillDataMenu()
# Phase / Draw Options tab
self.DataDrawOptions = wx.MenuBar()
self.PrefillDataMenu(self.DataDrawOptions)
self.DataDrawOptions.Append(menu=wx.Menu(title=''),title='Select tab')
self.PostfillDataMenu()
# Phase / Deformation tab
G2G.Define_wxId('wxID_DEFORMSETSEL','wxID_DEFORMDISTSET')
self.DeformationMenu = wx.MenuBar()
self.PrefillDataMenu(self.DeformationMenu)
self.DeformationMenu.Append(menu=wx.Menu(title=''),title='Select tab')
self.DeformationEdit = wx.Menu(title='')
self.DeformationMenu.Append(menu=self.DeformationEdit, title='Edit Deformations')
self.DeformationEdit.Append(G2G.wxID_DEFORMSETSEL,'Add atoms','Add atoms for deformation study, neutral atoms only')
self.DeformationEdit.Append(G2G.wxID_DEFORMDISTSET,'Set bond parms','Set bond selection parameters')
self.PostfillDataMenu()
# Phase / Draw Atoms tab
G2G.Define_wxId('wxID_DRAWATOMSTYLE', 'wxID_DRAWATOMLABEL', 'wxID_DRAWATOMCOLOR', 'wxID_DRAWATOMRESETCOLOR',
'wxID_DRAWVIEWPOINT', 'wxID_DRAWTRANSFORM', 'wxID_DRAWDELETE', 'wxID_DRAWFILLCELL',
'wxID_DRAWADDEQUIV', 'wxID_DRAWFILLCOORD', 'wxID_DRAWDISAGLTOR', 'wxID_DRAWPLANE',
'wxID_DRAWDISTVP', 'wxID_DRAWADDSPHERE', 'wxID_DRWAEDITRADII',
'wxID_DRAWSETSEL', 'wxID_DRAWLOADSEL', 'wxID_DRAWADDBOX'
)
G2G.Define_wxId('wxID_DRAWRESTRBOND', 'wxID_DRAWRESTRANGLE', 'wxID_DRAWRESTRPLANE', 'wxID_DRAWRESTRCHIRAL',)
self.DrawAtomsMenu = wx.MenuBar()
self.PrefillDataMenu(self.DrawAtomsMenu)
self.DrawAtomsMenu.Append(menu=wx.Menu(title=''),title='Select tab')
self.DrawAtomEdit = wx.Menu(title='')
self.DrawAtomCompute = wx.Menu(title='')
self.DrawAtomRestraint = wx.Menu(title='')
self.DrawAtomRigidBody = wx.Menu(title='')
self.DrawAtomsMenu.Append(menu=self.DrawAtomEdit, title='Edit Figure')
self.DrawAtomsMenu.Append(menu=self.DrawAtomCompute,title='Compute')
self.DrawAtomsMenu.Append(menu=self.DrawAtomRestraint, title='Restraints')
self.DrawAtomsMenu.Append(menu=self.DrawAtomRigidBody, title='Rigid body')
self.DrawAtomEdit.Append(G2G.wxID_DRAWATOMSTYLE,'Atom style','Select atoms first')
self.DrawAtomEdit.Append(G2G.wxID_DRAWATOMLABEL,'Atom label','Select atoms first')
self.DrawAtomEdit.Append(G2G.wxID_DRAWATOMCOLOR,'Atom color','Select atoms first')
self.DrawAtomEdit.Append(G2G.wxID_DRAWATOMRESETCOLOR,'Reset atom colors','Resets all atom colors to defaults')
self.DrawAtomEdit.Append(G2G.wxID_DRWAEDITRADII,'Edit atom radii','Edit drawing atom radii')
self.DrawAtomEdit.Append(G2G.wxID_DRAWVIEWPOINT,'Set view point','View point is 1st atom selected')
self.DrawAtomEdit.Append(G2G.wxID_DRAWSETSEL,'Select from list','Select atoms from a filtered listbox')
self.DrawAtomEdit.Append(G2G.wxID_DRAWADDEQUIV,'Add atoms','Add symmetry & cell equivalents to drawing set from selected atoms')
self.DrawAtomEdit.Append(G2G.wxID_DRAWADDSPHERE,'Add sphere of atoms','Add atoms within sphere of enclosure')
# self.DrawAtomEdit.Append(G2G.wxID_DRAWADDBOX,'Add box of atoms','Add atoms within box of enclosure')
self.DrawAtomEdit.Append(G2G.wxID_DRAWTRANSFORM,'Transform draw atoms','Transform selected atoms by symmetry & cell translations')
self.DrawAtomEdit.Append(G2G.wxID_DRAWFILLCOORD,'Fill CN-sphere','Fill coordination sphere for selected atoms')
self.DrawAtomEdit.Append(G2G.wxID_DRAWFILLCELL,'Fill unit cell','Fill unit cell with selected atoms')
G2G.Define_wxId('wxID_DRAWADDMOLECULE')
self.DrawAtomEdit.Append(G2G.wxID_DRAWADDMOLECULE,'Complete molecule','Cyclicly add atoms bonded to selected atoms')
self.DrawAtomEdit.Append(G2G.wxID_DRAWDELETE,'Delete atoms','Delete selected atoms from drawing set')
G2G.Define_wxId('wxID_RELOADATOMS')
self.DrawAtomEdit.Append(G2G.wxID_RELOADATOMS,'Update draw atoms','Update atom drawing list')
self.DrawAtomEdit.Append(G2G.wxID_DRAWLOADSEL,'Load selected atoms','Copy selected atoms into draw atoms')
G2G.Define_wxId('wxID_DRAWRANDOM')
self.DrawAtomEdit.Append(G2G.wxID_DRAWRANDOM,'Randomized action','Perform an action in randomized order')
self.DrawAtomCompute.Append(G2G.wxID_DRAWDISTVP,'View pt. dist.','Compute distance of selected atoms from view point')
self.DrawAtomCompute.Append(G2G.wxID_DRAWDISAGLTOR,'Dist. Ang. Tors.',
'Compute distance, angle or torsion for 2-4 selected atoms')
self.DrawAtomCompute.Append(G2G.wxID_DRAWPLANE,'Best plane','Compute best plane for 4+ selected atoms')
G2G.Define_wxId('wxID_DRAWISO')
self.DrawAtomCompute.Append(G2G.wxID_DRAWISO,'Show New Var modes',
'Show New Var constraints and dependent vars')
G2G.Define_wxId('wxID_DRAWVOIDMAP')
self.DrawAtomCompute.Append(G2G.wxID_DRAWVOIDMAP,'Create void map','Create a map of locations outside of any VDW radius')
self.DrawAtomRestraint.Append(G2G.wxID_DRAWRESTRBOND,'Add bond restraint','Add bond restraint for selected atoms (2)')
self.DrawAtomRestraint.Append(G2G.wxID_DRAWRESTRANGLE,'Add angle restraint',
'Add angle restraint for selected atoms (3: one end 1st)')
self.DrawAtomRestraint.Append(G2G.wxID_DRAWRESTRPLANE,'Add plane restraint',
'Add plane restraint for selected atoms (4+)')
self.DrawAtomRestraint.Append(G2G.wxID_DRAWRESTRCHIRAL,'Add chiral restraint',
'Add chiral restraint for selected atoms (4: center atom 1st)')
G2G.Define_wxId('wxID_DRAWDEFINERB')
self.DrawAtomRigidBody.Append(G2G.wxID_DRAWDEFINERB,'Define rigid body','Define rigid body with selected atoms')
self.PostfillDataMenu()
# Phase / MCSA tab
G2G.Define_wxId('wxID_ADDMCSAATOM', 'wxID_ADDMCSARB', 'wxID_CLEARMCSARB', 'wxID_MOVEMCSA', 'wxID_MCSACLEARRESULTS',)
self.MCSAMenu = wx.MenuBar()
self.PrefillDataMenu(self.MCSAMenu)
self.MCSAMenu.Append(menu=wx.Menu(title=''),title='Select tab')
self.MCSAEdit = wx.Menu(title='')
self.MCSAMenu.Append(menu=self.MCSAEdit, title='MC/SA')
self.MCSAEdit.Append(G2G.wxID_ADDMCSAATOM,'Add atom','Add single atom to MC/SA model')
self.MCSAEdit.Append(G2G.wxID_ADDMCSARB,'Add rigid body','Add rigid body to MC/SA model' )
self.MCSAEdit.Append(G2G.wxID_CLEARMCSARB,'Clear rigid bodies','Clear all atoms & rigid bodies from MC/SA model' )
self.MCSAEdit.Append(G2G.wxID_MOVEMCSA,'Move MC/SA solution','Move MC/SA solution to atom list' )
self.MCSAEdit.Append(G2G.wxID_MCSACLEARRESULTS,'Clear results','Clear table of MC/SA results' )
self.PostfillDataMenu()
# Phase / Texture tab
G2G.Define_wxId('wxID_CLEARTEXTURE', 'wxID_REFINETEXTURE',)
self.TextureMenu = wx.MenuBar()
self.PrefillDataMenu(self.TextureMenu)
self.TextureMenu.Append(menu=wx.Menu(title=''),title='Select tab')
self.TextureEdit = wx.Menu(title='')
self.TextureMenu.Append(menu=self.TextureEdit, title='Texture')
self.TextureEdit.Append(G2G.wxID_REFINETEXTURE,'Refine texture','Refine the texture coefficients from sequential results')
self.PostfillDataMenu()
# Phase / Pawley tab
G2G.Define_wxId('wxID_PAWLEYLOAD', 'wxID_PAWLEYESTIMATE', 'wxID_PAWLEYUPDATE', 'wxID_PAWLEYSELALL',
'wxID_PAWLEYSELNONE','wxID_PAWLEYSELTOGGLE', 'wxID_PAWLEYSET',)
self.PawleyMenu = wx.MenuBar()
self.PrefillDataMenu(self.PawleyMenu)
self.PawleyMenu.Append(menu=wx.Menu(title=''),title='Select tab')
self.PawleyEdit = wx.Menu(title='')
self.PawleyMenu.Append(menu=self.PawleyEdit,title='Operations')
self.PawleyEdit.Append(G2G.wxID_PAWLEYSET,'Pawley settings','Change Pawley refinement settings')
self.PawleyEdit.Append(G2G.wxID_PAWLEYLOAD,'Pawley create','Initialize Pawley reflection list')
self.PawleyEdit.Append(G2G.wxID_PAWLEYESTIMATE,'Pawley estimate','Estimate initial Pawley intensities')
self.PawleyEdit.Append(G2G.wxID_PAWLEYUPDATE,'Pawley update','Update negative Pawley intensities with -0.5*Fobs and turn off refinement')
self.PawleyEdit.Append(G2G.wxID_PAWLEYSELALL,'Refine all','Refine Fsq of all reflections')
self.PawleyEdit.Append(G2G.wxID_PAWLEYSELNONE,'Refine none','No reflection Fsq refinement')
self.PawleyEdit.Append(G2G.wxID_PAWLEYSELTOGGLE,'Toggle Selection','Toggle Selection flag for all reflections to opposite setting')
self.PostfillDataMenu()
# Phase / Map peaks tab
G2G.Define_wxId('wxID_PEAKSMOVE', 'wxID_PEAKSCLEAR','wxID_PEAKSUNIQUE', 'wxID_PEAKSDELETE','wxID_PEAKSSAVE','wxID_PEAKSDA',
'wxID_PEAKSDISTVP', 'wxID_PEAKSVIEWPT', 'wxID_FINDEQVPEAKS', 'wxID_SHOWBONDS','wxID_INVERTPEAKS','wxID_ROLLMAP')
self.MapPeaksMenu = wx.MenuBar()
self.PrefillDataMenu(self.MapPeaksMenu)
self.MapPeaksMenu.Append(menu=wx.Menu(title=''),title='Select tab')
self.MapPeaksEdit = wx.Menu(title='')
self.MapPeaksMenu.Append(menu=self.MapPeaksEdit, title='Map peaks')
self.MapPeaksEdit.Append(G2G.wxID_PEAKSMOVE,'Move peaks','Move selected peaks to atom list')
self.MapPeaksEdit.Append(G2G.wxID_PEAKSVIEWPT,'View point','View point is 1st peak selected')
self.MapPeaksEdit.Append(G2G.wxID_PEAKSDISTVP,'View pt. dist.','Compute distance of selected peaks from view point')
self.MapPeaksEdit.Append(G2G.wxID_SHOWBONDS,'Hide bonds','Hide or show bonds between peak positions')
self.MapPeaksEdit.Append(G2G.wxID_PEAKSDA,'Calc dist/ang','Calculate distance or angle for selection')
self.MapPeaksEdit.Append(G2G.wxID_FINDEQVPEAKS,'Equivalent peaks','Find equivalent peaks')
self.MapPeaksEdit.Append(G2G.wxID_INVERTPEAKS,'Invert peak positions','Inverts map & peak positions')
self.MapPeaksEdit.Append(G2G.wxID_ROLLMAP,'Roll charge flip map','Roll charge flip map by specified steps')
self.MapPeaksEdit.Append(G2G.wxID_PEAKSUNIQUE,'Unique peaks','Select unique set')
self.MapPeaksEdit.Append(G2G.wxID_PEAKSSAVE,'Save peaks','Save peaks to csv file')
self.MapPeaksEdit.Append(G2G.wxID_PEAKSDELETE,'Delete peaks','Delete selected peaks')
self.MapPeaksEdit.Append(G2G.wxID_PEAKSCLEAR,'Clear peaks','Clear the map peak list')
self.PostfillDataMenu()
# Phase / Rigid bodies tab
G2G.Define_wxId(
'wxID_ASSIGNATMS2RB','wxID_GLOBALRESREFINE','wxID_RBREMOVEALL','wxID_AUTOFINDRESRB',
'wxID_COPYRBPARMS','wxID_GLOBALTHERM',)
self.RigidBodiesMenu = wx.MenuBar()
self.PrefillDataMenu(self.RigidBodiesMenu)
self.RigidBodiesMenu.Append(menu=wx.Menu(title=''),title='Select tab')
self.RigidBodiesEdit = wx.Menu(title='')
self.RigidBodiesMenu.Append(menu=self.RigidBodiesEdit, title='Edit Body')
self.RigidBodiesEdit.Append(G2G.wxID_ASSIGNATMS2RB,'Locate && Insert Rigid Body',
'Locate rigid body in structure mapping to existing atoms')
self.RigidBodiesEdit.Append(G2G.wxID_AUTOFINDRESRB,'Auto find residues',
'Auto find of residue RBs in macromolecule')
self.RigidBodiesEdit.Append(G2G.wxID_COPYRBPARMS,'Duplicate rigid body parms',
'Duplicate rigid body location & TLS parameters')
self.RigidBodiesEdit.Append(G2G.wxID_GLOBALTHERM,'Global thermal motion',
'Global setting of residue thermal motion models')
self.RigidBodiesEdit.Append(G2G.wxID_GLOBALRESREFINE,'Global residue refine',
'Global setting of residue RB refinement flags')
self.RigidBodiesEdit.Append(G2G.wxID_RBREMOVEALL,'Remove all rigid bodies',
'Remove all rigid body assignment for atoms')
self.PostfillDataMenu()
# don't know which menu was selected, but should be General on first phase use
SetDataMenuBar(G2frame,self.DataGeneral)
self.DataGeneral = _makemenu
# end of GSAS-II menu definitions
[docs]
def readFromFile(reader):
'''Define a caption for a file import menu item'''
nam = reader.formatName
if nam.startswith('(user'):
return nam.replace('(user)','(user) from')+' file'
else:
return f'from {reader.formatName} file'
#### Notebook Tree Item editor ##############################################
[docs]
def UpdateNotebook(G2frame,data):
'''Called when the data tree notebook entry is selected. Allows for
editing of the text in that tree entry
'''
def onUpdateWindow(event=None):
'redraw the window'
wx.CallAfter(UpdateNotebook,G2frame,data)
def OnAddNotebook(event):
'add comment text to notebook and redisplay'
dlg = G2G.SingleStringDialog(G2frame.dataWindow,'Enter Comment',
'','',(600,50),
'''Enter a string here that will be included in the Notebook
This can contain any text you wish. It will have no effect on GSAS-II
other than being included in the Notebook section of the project file.''')
if dlg.Show():
data.append(f'[TS] Notebook entry @ {time.ctime()}')
data.append(f'[CM] {dlg.GetValue().strip()}')
dlg.Destroy()
wx.CallAfter(UpdateNotebook,G2frame,data)
def OnSaveNotebook(event):
filename = os.path.splitext(G2frame.GSASprojectfile)[0]+'_notebook.txt'
filename = os.path.join(G2frame.dirname,filename)
with open(filename,'w') as fp:
fp.write(textBox.GetText())
G2G.G2MessageBox(G2frame,
f'Displayed notebook contents written into {filename}',
'file written')
def onPlotNotebook():
'Locate values from the Notebook and plot them'
if NBplotLbl['GOF'] or NBplotLbl['Rw']:
if NBplotLbl['GOF']:
target = 'GOF'
elif NBplotLbl['Rw']:
target = 'Rw'
vals = []
for i,l in enumerate(data):
ls = l.split()
if len(ls) < 1: # empty line
continue
elif '[' not in ls[0] or '[REF]' in ls[0]:
if target not in l: continue
try:
vals.append(float(l.split(target)[1].split(',')[0].replace('=','').replace('%','')))
except:
continue
X = np.arange(len(vals))
Y = np.array(vals)
else:
# find what we are plotting if not Rw or GOF
for i,j in NBplotLbl.items():
if j:
target = i
break
else:
target = 'none'
if target == 'none':
G2frame.G2plotNB.Delete('fit results')
return
pos,vals = G2G.findValsInNotebook(data,target)
X = np.array(pos)
Y = np.array(vals)
if len(Y) == 0:
G2G.G2MessageBox(G2frame,'There are no values to plot','No points')
return
elif len(Y) == 1:
G2G.G2MessageBox(G2frame,'There is only one value to plot','One point')
return
XY = [X,Y]
G2plt.PlotXY(G2frame,[XY,],Title='fit results',newPlot=True,
labelX='seq',labelY=target,lines=True)
##### === UpdateNotebook starts here
filterLbls = ['all', # must be 1st
'Timestamps','Refinement results','Variables',
'Comments','Charge flip','Fourier','Peak fit',
'Constraints','Restraints','Rigid Bodies',
'Cell params','GSAS-II version #','Logged vars',
'(clear)' # must be last
]
filterPrefix = ['', # should match filterLbls
'TS', 'REF','VARS',
'CM', 'CF', 'FM', 'PF',
'CNSTR','RSTR','RB',
'CEL','VER','VALS',
' ']
G2frame.G2plotNB.Delete('fit results') # clear any old plot since we
# start out with None selected
cId = GetGPXtreeItemId(G2frame,G2frame.root, 'Controls')
if cId:
controls = G2frame.GPXtree.GetItemPyData(cId)
else: # unexpected: Notebook w/o Controls tree entries
G2frame.CheckNotebook()
cId = GetGPXtreeItemId(G2frame,G2frame.root, 'Controls')
controls = G2frame.GPXtree.GetItemPyData(cId)
controls['Notebook'] = controls.get('Notebook',{}) # filter & order settings get saved here, plot settings do not
G2frame.dataWindow.ClearData()
topSizer = G2frame.dataWindow.topBox
topSizer.Clear(True)
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,-1,'Notes/results for current project'),0,WACV)
topSizer.Add((20,-1))
addBtn = wx.Button(parent,label='Add comment')
topSizer.Add(addBtn,0,WACV)
addBtn.Bind(wx.EVT_BUTTON,OnAddNotebook)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex=G2frame.dataWindow.helpKey))
wx.CallAfter(G2frame.dataWindow.SetDataSize)
botSizer = G2frame.dataWindow.bottomBox
botSizer.Clear(True)
parent = G2frame.dataWindow.bottomPanel
botSizer.Add((20,-1))
controls['Notebook']['order'] = controls['Notebook'].get('order',True)
botSizer.Add(wx.StaticText(parent,wx.ID_ANY,' order: '),0,WACV)
botSizer.Add(G2G.EnumSelector(parent,controls['Notebook'],
'order',['oldest-1st','newest-1st'],[False,True],
OnChange=onUpdateWindow))
# initize filter settings on 1st use
controls['Notebook']['filterSel'] = controls['Notebook'].get('filterSel',[])
# initialize if list has changed or this is new
if len(controls['Notebook']['filterSel']) != len(filterLbls):
controls['Notebook']['filterSel'] = [False]+(len(filterLbls)-1)*[True]
controls['Notebook']['filterSel'][filterPrefix.index('VER')] = False
controls['Notebook']['filterSel'][filterPrefix.index('VALS')] = False
controls['Notebook']['filterSel'][filterPrefix.index(' ')] = False
# set all if all selected
if controls['Notebook']['filterSel'][0]:
controls['Notebook']['filterSel'] = [True for i in controls['Notebook']['filterSel']]
controls['Notebook']['filterSel'][0] = False
controls['Notebook']['filterSel'][-1] = False
# reset all if (clear) selected
elif controls['Notebook']['filterSel'][-1]:
controls['Notebook']['filterSel'] = [False for i in controls['Notebook']['filterSel']]
# find recorded parameters
v = []
for l in data:
if '[VALS]' in l:
v += [i.split(' : ')[0].strip() for i in l[6:].split(',') if i.strip()]
if '[CEL]' in l:
ph = l.split('Phase')[1].split()[0]
hst = l.split('Hist')[1].split(':')[0].strip()
vars = [i.split('=')[0] for i in l.split(':')[1].split()]
v += [f'{v}[p{ph}_h{hst}]' for v in vars]
plotable = ['Rw','GOF']
plotable += sorted(list(set(v)))
NBplotLbl = {'none':True}
NBplotLbl.update(dict.fromkeys(plotable,False))
botSizer.Add((20,-1))
fBtn = G2G.popupSelectorButton(parent,'Set filters',
filterLbls,
controls['Notebook']['filterSel'],
OnChange=onUpdateWindow)
botSizer.Add(fBtn,0,WACV)
fBtn = G2G.popupSelectorButton(parent,'Plot',choiceDict=NBplotLbl,
OnChange=onPlotNotebook)
botSizer.Add((20,-1))
botSizer.Add(fBtn,0,WACV)
botSizer.Add((20,-1),1,wx.EXPAND,1)
Btn = wx.Button(parent,label='Save')
botSizer.Add(Btn,0,WACV)
Btn.Bind(wx.EVT_BUTTON,OnSaveNotebook)
import wx.stc as stc
textBox = stc.StyledTextCtrl(G2frame.dataWindow,wx.ID_ANY)
textBox.SetScrollWidthTracking(True) # does not seem to do anything
if controls['Notebook']['order']:
# reverse entries in blocks, so that lines stay after their timestamp
order = []
pos = -1
for i,l in enumerate(data):
pos += 1
ls = l.split()
if len(ls) < 1: # empty line
continue
elif '[' not in ls[0]:
pos = 0 # old untagged NB entry
elif '[TS]' in ls[0]:
pos = 0 # Move time stamp to top
order.insert(pos,i)
else:
order = range(len(data))
# get prefixes to be shown
selLbl = [l for i,l in enumerate(filterPrefix)
if controls['Notebook']['filterSel'][i]]
first = True
for i in order:
line = data[i]
if not line.strip(): continue # empty line
prefix = ''
if line[0] == '[' and ']' in line:
prefix, line = line[1:].split(']',1)
show = False
if controls['Notebook']['filterSel'][0] or prefix == '':
show = True
elif prefix in selLbl:
show = True
if show:
if prefix == 'TS':
if not first: textBox.AppendText("\n")
textBox.AppendText(line.strip())
elif prefix and (controls['Notebook']['filterSel'][0]
or controls['Notebook']['filterSel'][1]):
# indent all but timestamps
for l in line.strip().split('\n'):
if not first: textBox.AppendText("\n")
if prefix == 'VALS':
l = 'Values: '+l.replace(' : ','=')
textBox.AppendText(' '+l.strip())
first = False
else:
if not first: textBox.AppendText("\n")
textBox.AppendText(line.strip())
first = False
bigSizer = wx.BoxSizer(wx.VERTICAL)
bigSizer.Add(textBox,1,wx.EXPAND)
textBox.SetReadOnly(True)
bigSizer.Layout()
bigSizer.FitInside(G2frame.dataWindow)
G2frame.dataWindow.SetSizer(bigSizer)
G2frame.dataWindow.SetDataSize()
G2frame.SendSizeEvent()
#### Comments ###############################################################
#### Controls Tree Item editor ##############################################
[docs]
def UpdateControls(G2frame,data):
'''Edit overall GSAS-II controls in main Controls data tree entry
'''
#patch
if 'deriv type' not in data:
data = {}
data['deriv type'] = 'analytic Hessian'
data['min dM/M'] = 0.001
data['shift factor'] = 1.
data['max cyc'] = 3
data['F**2'] = False
if 'SVDtol' not in data:
data['SVDtol'] = 1.e-6
if 'shift factor' not in data:
data['shift factor'] = 1.
if 'max cyc' not in data:
data['max cyc'] = 3
if 'F**2' not in data:
data['F**2'] = False
if 'Author' not in data:
data['Author'] = 'no name'
if 'FreePrm1' not in data:
data['FreePrm1'] = 'Sample humidity (%)'
if 'FreePrm2' not in data:
data['FreePrm2'] = 'Sample voltage (V)'
if 'FreePrm3' not in data:
data['FreePrm3'] = 'Applied load (MN)'
if 'Copy2Next' not in data:
data['Copy2Next'] = False
if 'Reverse Seq' not in data:
data['Reverse Seq'] = False
if 'UsrReject' not in data:
data['UsrReject'] = {'minF/sig':0.,'MinExt':0.01,'MaxDF/F':20.,'MaxD':500.,'MinD':0.10}
if 'HatomFix' not in data:
data['HatomFix'] = False
if 'Marquardt' not in data:
data['Marquardt'] = -3
if 'newLeBail' not in data:
data['newLeBail'] = False
#end patch
def SeqSizer():
def OnSelectData(event):
choices = GetGPXtreeDataNames(G2frame,['PWDR','HKLF',])
phaseRIdList,histdict = G2frame.GetPhaseInfofromTree(Used=True)
usedHistograms = []
for k in histdict:
usedHistograms += histdict[k]
usedHistograms = list(set(usedHistograms))
choices = [i for i in choices if i in usedHistograms]
if len(choices) == 0:
G2G.G2MessageBox(G2frame,'No histograms in use found for a sequential fit.','No Histograms')
return
sel = []
try:
if 'Seq Data' in data:
sel = [choices.index(item) for item in data['Seq Data']]
except ValueError: #data changed somehow - start fresh
sel = []
dlg = G2G.G2MultiChoiceDialog(G2frame,
'Select datasets to include. Select no datasets to end sequential refinements.',
'Sequential refinement selection',choices)
dlg.SetSelections(sel)
names = []
if dlg.ShowModal() == wx.ID_OK:
for sel in dlg.GetSelections():
names.append(choices[sel])
data['Seq Data'] = names
dlg.Destroy()
G2frame.SetTitleByGPX()
if names: # probably not needed (should be set previously)
item = GetGPXtreeItemId(G2frame,G2frame.root,'Constraints')
constraints = G2frame.GPXtree.GetItemPyData(item)
constraints['_seqmode'] = constraints.get('_seqmode','auto-wildcard')
wx.CallAfter(UpdateControls,G2frame,data)
def OnReverse(event):
data['Reverse Seq'] = reverseSel.GetValue()
def OnCopySel(event):
data['Copy2Next'] = copySel.GetValue()
def OnClrSeq(event):
sId = GetGPXtreeItemId(G2frame,G2frame.root,'Sequential results')
if sId:
dlg = wx.MessageDialog(G2frame,'Are you sure?','Delete sequential results table',wx.OK|wx.CANCEL)
try:
if dlg.ShowModal() == wx.ID_OK:
G2frame.GPXtree.Delete(sId)
finally:
dlg.Destroy()
seqSizer = wx.BoxSizer(wx.VERTICAL)
dataSizer = wx.BoxSizer(wx.HORIZONTAL)
SeqData = data.get('Seq Data',[])
if not SeqData:
dataSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Select datasets to switch to sequential refinement: '),0,WACV)
selSeqData = wx.Button(G2frame.dataWindow,label='Select datasets')
else:
lbl = 'Sequential Refinement with '+str(len(SeqData))+' dataset(s) selected'
dataSizer.Add(wx.StaticText(G2frame.dataWindow,label=lbl),0,WACV)
selSeqData = wx.Button(G2frame.dataWindow,label=' Reselect datasets')
selSeqData.Bind(wx.EVT_BUTTON,OnSelectData)
dataSizer.Add(selSeqData,0,WACV)
seqSizer.Add(dataSizer)
if SeqData:
selSizer = wx.BoxSizer(wx.HORIZONTAL)
reverseSel = wx.CheckBox(G2frame.dataWindow,-1,label=' Reverse order?')
reverseSel.Bind(wx.EVT_CHECKBOX,OnReverse)
reverseSel.SetValue(data['Reverse Seq'])
selSizer.Add(reverseSel,0,WACV)
copySel = wx.CheckBox(G2frame.dataWindow,-1,label=' Copy results to next histogram?')
copySel.Bind(wx.EVT_CHECKBOX,OnCopySel)
copySel.SetValue(data['Copy2Next'])
selSizer.Add(copySel,0,WACV)
clrSeq = wx.Button(G2frame.dataWindow,label='Clear previous seq. results')
clrSeq.Bind(wx.EVT_BUTTON,OnClrSeq)
selSizer.Add(clrSeq,0,WACV)
seqSizer.Add(selSizer,0)
return seqSizer
def LSSizer():
def OnDerivType(event):
data['deriv type'] = derivSel.GetValue()
derivSel.SetValue(data['deriv type'])
wx.CallAfter(UpdateControls,G2frame,data)
def OnMaxCycles(event):
data['max cyc'] = int(maxCyc.GetValue())
maxCyc.SetValue(str(data['max cyc']))
def OnMarqLam(event):
data['Marquardt'] = int(marqLam.GetValue())
marqLam.SetValue(str(data['Marquardt']))
def OnFactor(event):
event.Skip()
try:
value = min(max(float(Factr.GetValue()),0.00001),100.)
except ValueError:
value = 1.0
data['shift factor'] = value
Factr.SetValue('%.5f'%(value))
def OnFsqRef(event):
data['F**2'] = fsqRef.GetValue()
LSSizer = wx.FlexGridSizer(cols=4,vgap=5,hgap=5)
tmpSizer=wx.BoxSizer(wx.HORIZONTAL)
tmpSizer.Add(wx.StaticText(G2frame.dataWindow,label='Refinement\ntype: '),0,WACV)
tmpSizer.Add(G2G.HelpButton(G2frame.dataWindow,helpIndex='RefineType'))
LSSizer.Add(tmpSizer,0,WACV)
Choice=['analytic Jacobian','numeric','analytic Hessian','Hessian SVD']
derivSel = wx.ComboBox(parent=G2frame.dataWindow,value=data['deriv type'],choices=Choice,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
derivSel.SetValue(data['deriv type'])
derivSel.Bind(wx.EVT_COMBOBOX, OnDerivType)
LSSizer.Add(derivSel,0,WACV)
LSSizer.Add(wx.StaticText(G2frame.dataWindow,label='Min delta-M/M: '),0,WACV)
LSSizer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'min dM/M',nDig=(10,2,'g'),xmin=1.e-9,xmax=1.),0,WACV)
if 'Hessian' in data['deriv type']:
LSSizer.Add(wx.StaticText(G2frame.dataWindow,label='Max cycles: '),0,WACV)
Choice = ['0','1','2','3','5','10','15','20']
maxCyc = wx.ComboBox(parent=G2frame.dataWindow,value=str(data['max cyc']),choices=Choice,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
maxCyc.Bind(wx.EVT_COMBOBOX, OnMaxCycles)
LSSizer.Add(maxCyc,0,WACV)
if 'SVD' not in data['deriv type']:
LSSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Initial lambda = 10**'),0,WACV)
MarqChoice = ['-3','-2','-1','0','1','2','3','4']
marqLam = wx.ComboBox(parent=G2frame.dataWindow,value=str(data['Marquardt']),choices=MarqChoice,
style=wx.CB_READONLY|wx.CB_DROPDOWN)
marqLam.Bind(wx.EVT_COMBOBOX,OnMarqLam)
LSSizer.Add(marqLam,0,WACV)
LSSizer.Add(wx.StaticText(G2frame.dataWindow,label='SVD zero\ntolerance:'),0,WACV)
LSSizer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'SVDtol',nDig=(10,1,'g'),xmin=1.e-9,xmax=.01),0,WACV)
else:
LSSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Initial shift factor: '),0,WACV)
Factr = G2G.ValidatedTxtCtrl(G2frame.dataWindow,data,'shift factor',nDig=(10,5),xmin=1.e-5,xmax=100.)
LSSizer.Add(Factr,0,WACV)
ShklSizer = None
if G2frame.Sngl:
ShklSizer = wx.FlexGridSizer(cols=4,vgap=5,hgap=5)
userReject = data['UsrReject']
usrRej = {'minF/sig':[' Min obs/sig (0-5): ',[0.,5.], ],'MinExt':[' Min extinct. (0-.9): ',[0.,.9],],
'MaxDF/F':[' Max delt-F/sig (3-1000): ',[3.,1000.],],'MaxD':[' Max d-spacing (3-500): ',[3.,500.],],
'MinD':[' Min d-spacing (0.1-2.0): ',[0.1,2.0],]}
fsqRef = wx.CheckBox(G2frame.dataWindow,-1,label='Refine HKLF as F^2? ')
fsqRef.SetValue(data['F**2'])
fsqRef.Bind(wx.EVT_CHECKBOX,OnFsqRef)
ShklSizer.Add(fsqRef,0,WACV)
ShklSizer.Add((1,0),)
for item in usrRej:
ShklSizer.Add(wx.StaticText(G2frame.dataWindow,-1,label=usrRej[item][0]),0,WACV)
usrrej = G2G.ValidatedTxtCtrl(G2frame.dataWindow,userReject,item,nDig=(10,2),
xmin=usrRej[item][1][0],xmax=usrRej[item][1][1])
ShklSizer.Add(usrrej,0,WACV)
return LSSizer,ShklSizer
def AuthSizer():
def OnAuthor(event):
event.Skip()
data['Author'] = auth.GetValue()
Author = data['Author']
authSizer = wx.BoxSizer(wx.HORIZONTAL)
authSizer.Add(wx.StaticText(G2frame.dataWindow,label=' CIF Author (last, first):'),0,WACV)
auth = wx.TextCtrl(G2frame.dataWindow,-1,value=Author,style=wx.TE_PROCESS_ENTER)
auth.Bind(wx.EVT_TEXT_ENTER,OnAuthor)
auth.Bind(wx.EVT_KILL_FOCUS,OnAuthor)
authSizer.Add(auth,0,WACV)
return authSizer
def ClearFrozen(event):
'Removes all frozen parameters by clearing the entire dict'
Controls['parmFrozen'] = {}
wx.CallAfter(UpdateControls,G2frame,data)
# start of UpdateControls
if 'SVD' in data['deriv type']:
G2frame.GetStatusBar().SetStatusText('Hessian SVD not recommended for initial refinements; use analytic Hessian or Jacobian',1)
else:
G2frame.GetStatusBar().SetStatusText('',1)
G2frame.dataWindow.ClearData()
SetDataMenuBar(G2frame,G2frame.dataWindow.ControlsMenu)
topSizer = G2frame.dataWindow.topBox
parent = G2frame.dataWindow.topPanel
topSizer.Add(wx.StaticText(parent,wx.ID_ANY,'Refinement Controls'),0,WACV)
topSizer.Add((-1,-1),1,wx.EXPAND)
topSizer.Add(G2G.HelpButton(parent,helpIndex='Controls'))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add((5,5),0)
LSSizer,ShklSizer = LSSizer()
mainSizer.Add(LSSizer)
if ShklSizer:
mainSizer.Add((5,15),0)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
subSizer = wx.BoxSizer(wx.HORIZONTAL)
subSizer.Add((-1,-1),1,wx.EXPAND)
subSizer.Add(wx.StaticText(G2frame.dataWindow,label='Single Crystal Refinement Settings'),0,WACV)
subSizer.Add((-1,-1),1,wx.EXPAND)
mainSizer.Add(subSizer,0,wx.EXPAND)
mainSizer.Add(ShklSizer)
mainSizer.Add((5,15),0)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
subSizer = wx.BoxSizer(wx.HORIZONTAL)
subSizer.Add((-1,-1),1,wx.EXPAND)
subSizer.Add(wx.StaticText(G2frame.dataWindow,label='Sequential Settings'),0,WACV)
subSizer.Add((-1,-1),1,wx.EXPAND)
mainSizer.Add(subSizer,0,wx.EXPAND)
mainSizer.Add(SeqSizer())
mainSizer.Add((5,15),0)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
subSizer = wx.BoxSizer(wx.HORIZONTAL)
subSizer.Add((-1,-1),1,wx.EXPAND)
subSizer.Add(wx.StaticText(G2frame.dataWindow,label='Global Settings'),0,WACV)
subSizer.Add((-1,-1),1,wx.EXPAND)
mainSizer.Add(subSizer,0,wx.EXPAND)
mainSizer.Add(AuthSizer())
mainSizer.Add((5,5),0)
Controls = data
# count frozen variables (in appropriate place)
for key in ('parmMinDict','parmMaxDict','parmFrozen'):
if key not in Controls: Controls[key] = {}
parmFrozen = Controls['parmFrozen']
if G2frame.testSeqRefineMode():
frozenList = set()
for h in parmFrozen:
if h == 'FrozenList': continue
frozenList = frozenList.union(parmFrozen[h])
count = len(frozenList)
elif 'FrozenList' in parmFrozen:
count = len(parmFrozen['FrozenList'])
else:
count = 0
if count > 0:
subSizer = wx.BoxSizer(wx.HORIZONTAL)
subSizer.Add(wx.StaticText(G2frame.dataWindow,
label='There are {} frozen variables (values refined outside limits)'.format(count)),0,WACV)
subSizer.Add((5,-1))
btn = wx.Button(G2frame.dataWindow, wx.ID_ANY,'Clear All Frozen')
btn.Bind(wx.EVT_BUTTON,ClearFrozen)
subSizer.Add(btn)
mainSizer.Add(subSizer)
G2frame.dataWindow.SetDataSize()
# G2frame.SendSizeEvent()
#### Main PWDR & HKLF panel ########################################################
[docs]
def UpdatePWHKPlot(G2frame,kind,item):
'''Called when the PWDR & HKLF histogram main tree entry is called. Displays the
histogram weight factor, refinement statistics for the histogram
and the range of data for a simulation.
Also invokes a plot of the histogram.
'''
def onEditSimRange(event):
'Edit simulation range'
if 'TOF' in data[0].get('simType','CW'):
inp = [
min(data[1][0])/1000.,
max(data[1][0])/1000.,
None
]
inp[2] = (np.log(inp[1]) - np.log(inp[0]))/(len(data[1][0])-1.)
names = ('start TOF(ms)', 'end TOF(ms)', 'DT/T')
dlg = G2G.ScrolledMultiEditor(
G2frame,[inp] * len(inp), range(len(inp)), names,
header='Edit simulation range',
minvals=(0.5,1.0,0.0001),
maxvals=(500.,500.,.01),
)
else:
inp = [
min(data[1][0]),
max(data[1][0]),
None
]
inp[2] = (inp[1] - inp[0])/(len(data[1][0])-1.)
names = ('start angle', 'end angle', 'step size')
dlg = G2G.ScrolledMultiEditor(
G2frame,[inp] * len(inp), range(len(inp)), names,
header='Edit simulation range',
minvals=(0.001,0.001,0.0001),
maxvals=(180.,180.,.1),
)
dlg.CenterOnParent()
val = dlg.ShowModal()
dlg.Destroy()
if val != wx.ID_OK: return
if inp[0] > inp[1]:
end,start,step = inp
else:
start,end,step = inp
step = abs(step)
if 'TOF' in data[0].get('simType','CW'):
N = (np.log(end)-np.log(start))/step
newdata = np.exp((np.arange(0,N))*step+np.log(start*1000.))
else:
N = int((end-start)/step)+1
newdata = np.linspace(start,end,N,True)
if len(newdata) < 2: return # too small a range - reject
data[1] = [newdata,np.zeros_like(newdata),np.ones_like(newdata),
np.zeros_like(newdata),np.zeros_like(newdata),np.zeros_like(newdata)]
Tmin = newdata[0]
Tmax = newdata[-1]
G2frame.GPXtree.SetItemPyData(GetGPXtreeItemId(G2frame,item,'Limits'),
[(Tmin,Tmax),[Tmin,Tmax]])
wx.CallAfter(UpdatePWHKPlot,G2frame,kind,item) # redisplay data screen
def OnPlot1DHKL(event):
'''Plots a 1D stick diagram of reflection intensities'''
data = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)
refList = data[1]['RefList']
G2plt.Plot1DSngl(G2frame,newPlot=True,hklRef=refList,Super=Super,Title=phaseName)
# def OnPlot3DHKL(event):
# '''Plots in 3D reciprocal space with green dots proportional to F^2, etc. from single histogram'''
# refList = data[1]['RefList']
# 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]))])
# controls = {'Type' : 'Fosq','Iscale' : False,'HKLmax' : Hmax,'HKLmin' : Hmin,'Zone':False,'viewKey':'L',
# 'FoMax' : FoMax,'Scale' : 1.0,'Drawing':{'viewPoint':[Vpoint,[]],'default':Vpoint[:],
# 'microED':{'Nexp':[False,0],'Ztilt':[False,0]},
# '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 OnPlotAll3DHKL(event):
'''Plots in 3D reciprocal space with green dots proportional to F^2, etc. from all SHKL histograms'''
choices = GetGPXtreeDataNames(G2frame,['HKLF',])
dlg = G2G.G2MultiChoiceDialog(G2frame, 'Select reflection sets to plot',
'Use data',choices)
try:
if dlg.ShowModal() == wx.ID_OK:
refNames = [choices[i] for i in dlg.GetSelections()]
else:
return
finally:
dlg.Destroy()
refList = np.zeros(0)
for name in refNames:
Id = GetGPXtreeItemId(G2frame,G2frame.root, name)
reflData = G2frame.GPXtree.GetItemPyData(Id)[1]
if len(refList):
refList = np.concatenate((refList,reflData['RefList']))
else:
refList = reflData['RefList']
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 = [int(np.mean(refList.T[0])),int(np.mean(refList.T[1])),int(np.mean(refList.T[2]))]
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':[1,0,0]},'Super':Super,'SuperVec':SuperVec}
G2plt.Plot3DSngl(G2frame,newPlot=True,Data=controls,hklRef=refList,Title=phaseName)
def OnMergeHKL(event):
'''Merge HKLF data sets to unique set according to Laue symmetry'''
data = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)
Name = G2frame.GPXtree.GetItemText(G2frame.PatternId)
Inst = G2frame.GPXtree.GetItemPyData(GetGPXtreeItemId(G2frame,
G2frame.PatternId,'Instrument Parameters'))
CId = GetGPXtreeItemId(G2frame,G2frame.PatternId,'Comments')
if CId:
Comments = G2frame.GPXtree.GetItemPyData(CId)
else:
Comments = []
refList = np.copy(data[1]['RefList'])
Comments.append(' Merging %d reflections from %s'%(len(refList),Name))
data[0]['Type'] = Inst[0]['Type'][1][:]
dlg = MergeDialog(G2frame,data)
try:
if dlg.ShowModal() == wx.ID_OK:
Trans,Cent,Laue,Smart = dlg.GetSelection()
else:
return
finally:
dlg.Destroy()
Super = data[1]['Super']
isup = 0
if Super:
isup = 1
refList,badRefs = G2lat.transposeHKLF(Trans,isup,refList)
if len(badRefs): #do I want to list badRefs?
G2frame.ErrorDialog('Failed transformation','Matrix yields fractional hkl indices')
return
Comments.append(" Transformation M*H = H' applied; M=")
Comments.append(str(Trans))
refList = G2lat.LaueUnique(Laue,refList)
dlg = wx.ProgressDialog('Build HKL dictonary','',len(refList)+1,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE)
HKLdict = {}
lenhkl = len(refList[0])
if lenhkl == 14+Super: #remove extra columns from extended microED data
lenhkl -= 2
sumExt = 0.
Next = 0
for ih,hkl in enumerate(refList):
if hkl[3+Super] == 0:
sumExt += hkl[5+Super]
Next += 1
if not hkl[5+Super]: #skip Fo == 0
continue
if str(hkl[:3+Super]) not in HKLdict:
HKLdict[str(hkl[:3+Super])] = [hkl[:3+Super],[hkl[3+Super:lenhkl],]]
else:
HKLdict[str(hkl[:3+Super])][1].append(hkl[3+Super:lenhkl])
dlg.Update(ih)
dlg.Destroy()
mergeRef = []
aveExt = 0.0
if Next:
aveExt = sumExt/Next
print('Ave extinct Fo^2: %f.2'%(aveExt))
dlg = wx.ProgressDialog('Processing merge','',len(HKLdict)+1,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE)
sumDf = 0.
sumFo = 0.
Nmerge = {1:[0,0],}
MaxN = 1
for ih,hkl in enumerate(HKLdict):
HKL = HKLdict[hkl]
Nhkl = len(HKL[1])
if Nhkl not in Nmerge:
Nmerge.update({Nhkl:[1,0],})
MaxN = max(MaxN,Nhkl)
else:
Nmerge[Nhkl][0] += 1
newHKL = list(HKL[0])+list(HKL[1][0])
if len(HKL[1]) > 1:
fos = np.array(HKL[1])
wFo = 1/fos[:,3]**2
Fo = np.average(fos[:,2],weights=wFo)
std = np.std(fos[:,2])
sig = np.sqrt(np.mean(fos[:,3])**2+std**2)
if Smart:
test = np.abs(fos[:,2]-Fo)/std
Nmerge[Nhkl][1] += len(fos[:,2][test >2.0])
fos[:,2] = np.where(test > 2.0,Fo,fos[:,2])
Fo = np.average(fos[:,2],weights=wFo)
std = np.std(fos[:,2])
sig = np.sqrt(np.mean(fos[:,3])**2+std**2)
sumFo += np.sum(fos[:,2])
sumDf += np.sum(np.abs(fos[:,2]-Fo))
dlg.Update(ih)
newHKL[5+Super] = Fo
newHKL[6+Super] = sig
newHKL[8+Super] = Fo
if newHKL[5+Super] > 0.:
mergeRef.append(list(newHKL))
dlg.Destroy()
mtext = ' Duplicate reflection statistics:'
print(mtext)
Comments.append(mtext)
for ihkl in range(MaxN):
try:
mtext = 'Ndup hkl: %d Number: %d Rej: %d'%(ihkl+1,Nmerge[ihkl+1][0],Nmerge[ihkl+1][1])
except KeyError:
mtext = 'Ndup hkl: %d Number: 0'%(ihkl+1)
print(mtext)
Comments.append(mtext)
if Super:
mergeRef = G2mth.sortArray(G2mth.sortArray(G2mth.sortArray(G2mth.sortArray(mergeRef,3),2),1),0)
else:
mergeRef = G2mth.sortArray(G2mth.sortArray(G2mth.sortArray(mergeRef,2),1),0)
mergeRef = np.array(mergeRef)
if sumFo:
mtext = ' merge R = %6.2f%s for %d reflections in %s'%(100.*sumDf/sumFo,'%',mergeRef.shape[0],Laue)
print (mtext)
Comments.append(mtext)
else:
print( 'nothing to merge for %s reflections'%(mergeRef.shape[0]))
HKLFlist = []
newName = Name+u' '+Laue
if G2frame.GPXtree.GetCount():
item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
while item:
name = G2frame.GPXtree.GetItemText(item)
if name.startswith('HKLF ') and name not in HKLFlist:
HKLFlist.append(name)
item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
newName = G2obj.MakeUniqueLabel(newName,HKLFlist)
newData = copy.deepcopy(data)
newData[0]['ranId'] = ran.randint(0,sys.maxsize)
newData[1]['RefList'] = mergeRef
newData[0]['Nobs'] = mergeRef.shape[0]
newData[0]['wR'] = 0.0
keys = list(newData[0].keys())
for item in keys:
if ':' in item:
del newData[0][item]
Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=newName)
G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),Inst)
G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection List'),{}) #dummy entry for GUI use
G2frame.GPXtree.SetItemPyData(Id,newData)
def OnSortHKL(event):
'''Sort HKLF data sets to unique set according to Laue symmetry - no merge'''
data = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)
Name = G2frame.GPXtree.GetItemText(G2frame.PatternId)
Inst = G2frame.GPXtree.GetItemPyData(GetGPXtreeItemId(G2frame,
G2frame.PatternId,'Instrument Parameters'))
CId = GetGPXtreeItemId(G2frame,G2frame.PatternId,'Comments')
if CId:
Comments = G2frame.GPXtree.GetItemPyData(CId)
else:
Comments = []
refList = np.copy(data[1]['RefList'])
Comments.append(' Sorting %d reflections from %s'%(len(refList),Name))
data[0]['Type'] = Inst[0]['Type'][1][:]
dlg = HKLSortDialog(G2frame,data)
try:
if dlg.ShowModal() == wx.ID_OK:
Trans,Cent,Laue = dlg.GetSelection()
else:
return
finally:
dlg.Destroy()
Super = data[1]['Super']
isup = 0
if Super:
isup = 1
refList,badRefs = G2lat.transposeHKLF(Trans,isup,refList)
if len(badRefs): #do I want to list badRefs?
G2frame.ErrorDialog('Failed transformation','Matrix yields fractional hkl indices')
return
Comments.append(" Transformation M*H = H' applied; M=")
Comments.append(str(Trans))
refList = G2lat.LaueUnique(Laue,refList)
dlg = wx.ProgressDialog('Build HKL dictonary','',len(refList)+1,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE)
HKLdict = {}
lenhkl = len(refList[0])
sumExt = 0.
Next = 0
for ih,hkl in enumerate(refList):
if hkl[3+Super] == 0:
sumExt += hkl[5+Super]
Next += 1
if str(hkl[:3+Super]) not in HKLdict:
HKLdict[str(hkl[:3+Super])] = [hkl[:3+Super],[hkl[3+Super:lenhkl],]]
else:
HKLdict[str(hkl[:3+Super])][1].append(hkl[3+Super:lenhkl])
dlg.Update(ih)
dlg.Destroy()
sortRef = []
aveExt = 0.0
if Next:
aveExt = sumExt/Next
print('Ave extinct Fo^2: %f.2'%(aveExt))
dlg = wx.ProgressDialog('Processing sort','',len(HKLdict)+1,
style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE)
HKLs = list(HKLdict)
HKLs.sort()
for ih,hkl in enumerate(HKLs):
HKL = HKLdict[hkl]
for Hdata in HKL[1]:
sortRef.append(np.hstack((HKL[0],Hdata)))
dlg.Destroy()
sortRef = np.array(sortRef)
HKLFlist = []
newName = Name+u' '+Laue+'_Sort'
if G2frame.GPXtree.GetCount():
item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
while item:
name = G2frame.GPXtree.GetItemText(item)
if name.startswith('HKLF ') and name not in HKLFlist:
HKLFlist.append(name)
item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
newName = G2obj.MakeUniqueLabel(newName,HKLFlist)
newData = copy.deepcopy(data)
newData[0]['ranId'] = ran.randint(0,sys.maxsize)
newData[1]['RefList'] = sortRef
newData[0]['Nobs'] = sortRef.shape[0]
newData[0]['wR'] = 0.0
keys = list(newData[0].keys())
for item in keys:
if ':' in item:
del newData[0][item]
Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=newName)
G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),Inst)
G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection List'),{}) #dummy entry for GUI use
G2frame.GPXtree.SetItemPyData(Id,newData)
def OnFixFsqFsq(event):
''' Fix HKLF data that had been misimported as F instead of F^2'''
Name = G2frame.GPXtree.GetItemText(G2frame.PatternId)
Inst = G2frame.GPXtree.GetItemPyData(GetGPXtreeItemId(G2frame,
G2frame.PatternId,'Instrument Parameters'))
CId = GetGPXtreeItemId(G2frame,G2frame.PatternId,'Comments')
if CId:
Comments = G2frame.GPXtree.GetItemPyData(CId)
else:
Comments = []
Super = data[1]['Super']
refList = np.copy(data[1]['RefList'])
Comments.append(' Changing %d reflection F^2^2 to F^2 from %s'%(len(refList),Name))
for ih,hkl in enumerate(refList): #undo F--> F^2
hkl[5+Super] = np.sqrt(hkl[5+Super])
hkl[6+Super] = hkl[6+Super]/(2.0*hkl[5+Super])
hkl[7+Super] = np.sqrt(hkl[7+Super])
HKLFlist = []
if G2frame.GPXtree.GetCount():
item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
while item:
name = G2frame.GPXtree.GetItemText(item)
if name.startswith('HKLF ') and name not in HKLFlist:
HKLFlist.append(name)
item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
newName = G2obj.MakeUniqueLabel(Name,HKLFlist)
newData = copy.deepcopy(data)
newData[0]['ranId'] = ran.randint(0,sys.maxsize)
newData[1]['RefList'] = refList
newData[0]['Nobs'] = refList.shape[0]
newData[0]['wR'] = 0.0
keys = list(newData[0].keys())
for item in keys:
if ':' in item:
del newData[0][item]
Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=newName)
G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),Inst)
G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection List'),{}) #dummy entry for GUI use
G2frame.GPXtree.SetItemPyData(Id,newData)
def OnErrorAnalysis(event):
'''Plots an "Abrams" plot - sorted delta/sig across data set.
Should be straight line of slope 1 - never is'''
def OnPlotFoFcVsFc():
''' Extinction check, plots Fo-Fc & 1/ExtC vs Fo for single crystal data '''
test = lambda xy:(xy[iFlg+Super]>0 and xy[iFo+Super]>0)
iFlg,iFo,iSig,iFc,iFcT,iExt = 3,5,6,7,9,11
refList = data[1]['RefList']
wtFctr = data[0]['wtFactor']
Fo = np.sqrt(np.array([xy[iFo+Super] for xy in refList if test(xy)]))
Fc = np.sqrt(np.array([xy[iFc+Super] for xy in refList if test(xy)]))
FcT = np.sqrt(np.array([xy[iFcT+Super] for xy in refList if test(xy)]))
Sig = np.array([xy[iSig+Super] for xy in refList if test(xy)])/wtFctr #sig(fo^2)/wtFactor (1/GOF)
XE = [[xy[iFcT+Super],xy[iExt+Super]] for xy in refList if test(xy)]
XE = np.array([[np.sqrt(xe[0]),xe[1]] for xe in XE]).T
XE[1] = np.where(XE[1]>0.,XE[1],1.0)
G2plt.PlotXY(G2frame,[[FcT,2.*Fo*(Fo-Fc)/Sig],],XY2=[XE,],labelX='Fc',labelY=GkDelta+'F/sig, ExtC',newPlot=False,
Title='Extinction check',lines=False,points2=True,names=[GkDelta+'F/sig',],names2=['ExtC',])
G2plt.PlotDeltSig(G2frame,kind)
if kind in ['HKLF',]:
OnPlotFoFcVsFc()
# def OnCompression(event):
# data[0] = int(comp.GetValue())
def onCopyPlotCtrls(event):
'''Respond to menu item to copy multiple sections from a histogram.
Need this here to pass on the G2frame object.
'''
G2pdG.CopyPlotCtrls(G2frame)
def onCopySelectedItems(event):
'''Respond to menu item to copy multiple sections from a histogram.
Need this here to pass on the G2frame object.
'''
G2pdG.CopySelectedHistItems(G2frame)
def OnAddMag(event):
'Respond to the request to create a magnification region'
if not data[0]['Magnification']: data[0]['Magnification'] = [[None,1.0]]
data[0]['Magnification'] += [[(data[1][0][0]+data[1][0][-1])/2,2.]]
wx.CallAfter(UpdatePWHKPlot,G2frame,kind,G2frame.PatternId)
def OnDelMag(event):
'Respond to the request to delete a magnification region'
del data[0]['Magnification'][event.EventObject.row]
if len(data[0]['Magnification']) == 1: data[0]['Magnification'] = []
wx.CallAfter(UpdatePWHKPlot,G2frame,kind,G2frame.PatternId)
def OnEditMag(**args):
'Update to show edits to mag factors in window and plot'
wx.CallAfter(UpdatePWHKPlot,G2frame,kind,G2frame.PatternId)
#### Start of UpdatePWHKPlot
data = G2frame.GPXtree.GetItemPyData(item)
if kind == 'PWDR': # Compute a "data entropy" factor?
Limits = G2frame.GPXtree.GetItemPyData(GetGPXtreeItemId(G2frame,item,'Limits'))
iBeg = np.searchsorted(data[1][0],Limits[1][0])
iFin = np.searchsorted(data[1][0],Limits[1][1])+1
meanI = np.mean(data[1][1][iBeg:iFin])
S = None
if meanI != 0:
S = -1.0+np.sum(np.log(meanI**2/(data[1][1][iBeg:iFin]-meanI)**2))/(iFin-iBeg)
#patches
if not data:
return
if 'wtFactor' not in data[0]:
data[0] = {'wtFactor':1.0}
# if kind == 'PWDR' and 'Compression' not in data[0]:
# data[0]['Compression'] = 1
if 'list' in str(type(data[1])) and kind == 'HKLF':
RefData = {'RefList':[],'FF':[]}
for ref in data[1]:
RefData['RefList'].append(ref[:11]+[ref[13],])
RefData['FF'].append(ref[14])
data[1] = RefData
G2frame.GPXtree.SetItemPyData(item,data)
#end patches
if kind in ['PWDR','SASD','REFD']:
SetDataMenuBar(G2frame,G2frame.dataWindow.PWDRMenu)
if kind in ['PWDR',]:
G2frame.Bind(wx.EVT_MENU, OnErrorAnalysis, id=G2G.wxID_PWDANALYSIS)
G2frame.Bind(wx.EVT_MENU, onCopySelectedItems, id=G2G.wxID_PWDCOPY)
G2frame.Bind(wx.EVT_MENU, onCopyPlotCtrls, id=G2G.wxID_PLOTCTRLCOPY)
elif kind in ['HKLF',]:
SetDataMenuBar(G2frame,G2frame.dataWindow.HKLFMenu)
G2frame.Bind(wx.EVT_MENU, OnErrorAnalysis, id=G2G.wxID_PWDANALYSIS)
G2frame.Bind(wx.EVT_MENU, OnSortHKL, id=G2G.wxID_SORTHKL)
G2frame.Bind(wx.EVT_MENU, OnMergeHKL, id=G2G.wxID_MERGEHKL)
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, OnPlotAll3DHKL, id=G2G.wxID_3DALLHKLPLOT)
# G2frame.Bind(wx.EVT_MENU, OnPlotFoVsFc, id=G2G.wxID_FOVSFCPLOT)
G2frame.Bind(wx.EVT_MENU, OnFixFsqFsq, id=G2G.wxID_FIXFSQSQDATA)
if kind == 'PWDR':
lbl = 'Powder'
elif kind == 'SASD':
lbl = 'Small-angle'
elif kind == 'REFD':
lbl = 'Reflectometry'
elif kind == 'HKLF':
lbl = 'Single crystal'
else:
lbl = '?'
lbl += ' histogram: ' + G2frame.GPXtree.GetItemText(item)[:60]
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))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
mainSizer.Add((5,5),)
wtSizer = wx.BoxSizer(wx.HORIZONTAL)
wtSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Weight factor: '),0,WACV)
wtSizer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data[0],'wtFactor',nDig=(10,3),xmin=1.e-9),0,WACV)
# if kind == 'PWDR': #possible future compression feature; NB above patch as well
# wtSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Compression factor: '),0,WACV)
# choice = ['1','2','3','4','5','6']
# comp = wx.ComboBox(parent=G2frame.dataWindow,choices=choice,
# style=wx.CB_READONLY|wx.CB_DROPDOWN)
# comp.SetValue(str(data[0]['Compression']))
# comp.Bind(wx.EVT_COMBOBOX, OnCompression)
# wtSizer.Add(comp,0,WACV)
if kind == 'PWDR' and S is not None:
wtSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Data "Surprise" factor: %.3f'%S))
mainSizer.Add(wtSizer,0,wx.EXPAND)
wtSizer = wx.BoxSizer(wx.HORIZONTAL)
wtSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Histogram label: '),0,WACV)
if 'histTitle' not in data[0]: data[0]['histTitle'] = ''
wtSizer.Add(G2G.ValidatedTxtCtrl(G2frame.dataWindow,data[0],'histTitle',typeHint=str,
notBlank=False,size=(300,-1)),1,WACV)
mainSizer.Add(wtSizer,0)
if data[0].get('Dummy',False):
simSizer = wx.BoxSizer(wx.HORIZONTAL)
Tmin = min(data[1][0])
Tmax = max(data[1][0])
num = len(data[1][0])
if 'TOF' in data[0].get('simType','CW'):
step = (np.log(Tmax) - np.log(Tmin))/(num-1.)
t = u'\u00b5s'
lbl = u'Simulation range: {:.2f} to {:.2f} {:s} with {:.4f} resolution ({:d} points)'
else:
step = (Tmax - Tmin)/(num-1)
t = u'2\u03b8' # 2theta
lbl = u'Simulation range: {:.2f} to {:.2f} {:s} with {:.4f} steps ({:d} points)'
lbl += u'\n(Edit range resets observed intensities).'
lbl = lbl.format(Tmin,Tmax,t,step,num)
simSizer.Add(wx.StaticText(G2frame.dataWindow,wx.ID_ANY,lbl),0,WACV)
but = wx.Button(G2frame.dataWindow,wx.ID_ANY,"Edit range")
but.Bind(wx.EVT_BUTTON,onEditSimRange)
mainSizer.Add(simSizer)
mainSizer.Add(but,0)
if 'Nobs' in data[0]:
Rmsg = f" Data residual wR: {data[0]['wR']:.3f}% on {data[0]['Nobs']} observations"
covdata = G2frame.GPXtree.GetItemPyData(GetGPXtreeItemId(G2frame,G2frame.root,'Covariance'))
if 'Rvals' in covdata:
Rvals = covdata['Rvals']
if 'chisq' in Rvals and 'sumwYo' in data[0]:
# compute Chi**2 contribution from Rwp
chisq = (data[0]['wR']/100)**2 * data[0]['sumwYo']
frac = f"{100 * chisq / Rvals['chisq']:.1f}"
Rmsg += f". Contributes {frac}% of total \u03C7\u00b2"
mainSizer.Add(wx.StaticText(G2frame.dataWindow,wx.ID_ANY,Rmsg))
if kind == 'PWDR':
try: #old gpx file
DBW = ma.getdata(data[0]['Durbin-Watson'])
except KeyError:
DBW = 1.0
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Durbin-Watson statistic: %.3f'%DBW))
for value in data[0]:
if 'Nref' in value:
pfx = value.split('Nref')[0]
if str(data[0].get('hId',0)) != pfx.split(':')[1]:
continue
name = data[0].get(pfx.split(':')[0]+'::Name','?')
if 'SS' in value:
mainSizer.Add((5,5),)
mainSizer.Add(wx.StaticText(G2frame.dataWindow,-1,u' For incommensurate phase '+name+u':'))
for m,(Rf2,Rf,Nobs) in enumerate(zip(data[0][pfx+'Rf^2'],data[0][pfx+'Rf'],data[0][value])):
mainSizer.Add(wx.StaticText(G2frame.dataWindow,-1,
u' m = +/- %d: RF\u00b2: %.3f%%, RF: %.3f%% on %d reflections '%(m,Rf2,Rf,Nobs)))
else:
mainSizer.Add((5,5),)
mainSizer.Add(wx.StaticText(G2frame.dataWindow,-1,u' For phase '+name+u':'))
mainSizer.Add(wx.StaticText(G2frame.dataWindow,-1,
u' Unweighted phase residuals RF\u00b2: %.3f%%, RF: %.3f%% on %d reflections '% \
(data[0][pfx+'Rf^2'],data[0][pfx+'Rf'],data[0][value])))
# Draw edit box for Magnification factors/positions
if kind == 'PWDR':
if 'Magnification' not in data[0]:
data[0]['Magnification'] = []
mainSizer.Add((-1,10))
lenmag = len(data[0]['Magnification'])
data[0]['Magnification'][1:] = sorted(data[0]['Magnification'][1:],key=lambda x: x[0])
if lenmag > 1:
panel = wx.StaticBox(G2frame.dataWindow, wx.ID_ANY, 'Magnification regions',style=wx.ALIGN_CENTER)
mSizer = wx.StaticBoxSizer(panel,wx.VERTICAL)
magSizer = wx.FlexGridSizer(lenmag+1,3,0,0)
Name = G2frame.GPXtree.GetItemText(G2frame.PatternId)
Inst = G2frame.GPXtree.GetItemPyData(GetGPXtreeItemId(G2frame,
G2frame.PatternId,'Instrument Parameters'))
if 'C' in Inst[0]['Type'][0]:
magSizer.Add(wx.StaticText(panel,-1,'2Theta'),1,wx.ALIGN_CENTER,1)
else:
magSizer.Add(wx.StaticText(panel,-1,'TOF'),1,wx.ALIGN_CENTER,1)
magSizer.Add(wx.StaticText(panel,-1,'Magnification\nfactor',
style=wx.ALIGN_CENTRE_HORIZONTAL),1,wx.ALIGN_CENTER,1)
magSizer.Add(wx.StaticText(panel,-1,'Delete\nbutton',
style=wx.ALIGN_CENTRE_HORIZONTAL),1,wx.ALIGN_CENTER,1)
magSizer.Add(wx.StaticText(panel,-1,'(start)'),1,wx.ALIGN_CENTER,1)
edit = G2G.ValidatedTxtCtrl(panel,data[0]['Magnification'][0],1,
nDig=(7,2),xmin=0.01,xmax=1000.,OnLeave=OnEditMag,size=(65,-1))
magSizer.Add(edit,1,wx.ALIGN_CENTER,5)
magSizer.Add((1,1))
for i in range(1,lenmag):
edit = G2G.ValidatedTxtCtrl(panel,data[0]['Magnification'][i],0,nDig=(10,3),
xmin=data[1][0][0],xmax=data[1][0][-1],OnLeave=OnEditMag)
magSizer.Add(edit)
edit = G2G.ValidatedTxtCtrl(panel,data[0]['Magnification'][i],1,
nDig=(7,2),xmin=0.01,xmax=1000.,OnLeave=OnEditMag,size=(65,-1))
magSizer.Add(edit,1,wx.ALIGN_CENTER,5)
delmag = wx.Button(panel,wx.ID_ANY,label='Del',size=(40,-1))
delmag.Bind(wx.EVT_BUTTON,OnDelMag)
delmag.row = i
magSizer.Add(delmag,1,wx.ALIGN_CENTER,5)
mSizer.Add(magSizer)
else:
panel = G2frame.dataWindow
mSizer = wx.BoxSizer(wx.VERTICAL)
addmag = wx.Button(panel,wx.ID_ANY,label='Add a magnification region')
addmag.Bind(wx.EVT_BUTTON,OnAddMag)
mSizer.Add(addmag,1,wx.ALIGN_CENTER,1)
mainSizer.Add(mSizer)
G2frame.GPXtree.SetItemPyData(item,data)
G2frame.PatternId = item
if kind in ['PWDR','SASD','REFD',]:
# When I added code to allow for contour plots from unequally spaced data
# I forced all contour plots to replot with newPlot=True. I'm not sure if
# this is actually needed and for autointegration we really don't want
# plots to rescale.
# NewPlot = True
# if getattr(G2frame,'Contour',False):
# pass
# if hasattr(G2frame,'xylim'):
# NewPlot = False
# now only rescale when needed
if hasattr(G2frame,'xylim'):
NewPlot = False
else:
NewPlot = True
# if GSASIIpath.GetConfigValue('debug'):
# from importlib import reload
# reload(G2pwpl)
# print('reloading G2pwpl and closing all plots')
# for lbl in G2frame.G2plotNB.plotList:
# G2frame.G2plotNB.Delete(lbl)
# G2frame.lastPlotType = None
G2pwpl.PlotPatterns(G2frame,plotType=kind,newPlot=NewPlot,fromTree=True)
elif kind == 'HKLF':
Name = G2frame.GPXtree.GetItemText(item)
phaseName = G2pdG.IsHistogramInAnyPhase(G2frame,Name)
if phaseName:
pId = GetGPXtreeItemId(G2frame,G2frame.root,'Phases')
phaseId = GetGPXtreeItemId(G2frame,pId,phaseName)
General = G2frame.GPXtree.GetItemPyData(phaseId)['General']
Super = General.get('Super',0)
SuperVec = General.get('SuperVec',[])
else:
Super = 0
SuperVec = []
refList = data[1]['RefList']
nRef = refList.shape[0]
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Total Nref: %d'%nRef))
FoMax = np.max(refList.T[5+data[1].get('Super',0)])
page = G2frame.G2plotNB.nb.GetSelection()
tab = ''
if page >= 0:
tab = G2frame.G2plotNB.nb.GetPageText(page)
if '3D' in tab:
Page = G2frame.G2plotNB.nb.GetPage(page)
controls = Page.controls
G2plt.Plot3DSngl(G2frame,newPlot=False,Data=controls,hklRef=refList,Title=phaseName)
else:
controls = {'Type' : 'Fo','ifFc' : True,'dType':data[1]['Type'],
'HKLmax' : [int(np.max(refList.T[0])),int(np.max(refList.T[1])),int(np.max(refList.T[2]))],
'HKLmin' : [int(np.min(refList.T[0])),int(np.min(refList.T[1])),int(np.min(refList.T[2]))],
'microED':{'Nexp':[False,0],'Ztilt':[False,0]},
'FoMax' : FoMax,'Zone' : '001','Layer' : 0,'Scale' : 1.0,'Super':Super,'SuperVec':SuperVec}
G2plt.PlotSngl(G2frame,newPlot=True,Data=controls,hklRef=refList)
G2frame.dataWindow.SetDataSize()
# make sure parent histogram item is displayed
if item != G2frame.GPXtree.GetSelection():
wx.CallAfter(G2frame.GPXtree.SelectItem,item)
##### Data (GPX) tree routines ###############################################
[docs]
def GetGPXtreeDataNames(G2frame,dataTypes):
'''Finds all items in tree that match a 4 character prefix
:param wx.Frame G2frame: Data tree frame object
:param list dataTypes: Contains one or more data tree item types to be matched
such as ['IMG '] or ['PWDR','HKLF']
:returns: a list of tree item names for the matching items
'''
names = []
item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
while item:
name = G2frame.GPXtree.GetItemText(item)
if name[:4] in dataTypes:
names.append(name)
item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
return names
[docs]
def GetGPXtreeItemId(G2frame, parentId, itemText):
'''Find the tree item that matches the text in itemText starting with parentId
:param wx.Frame G2frame: Data tree frame object
:param wx.TreeItemId parentId: tree item to start search with
:param str itemText: text for tree item
'''
try:
item, cookie = G2frame.GPXtree.GetFirstChild(parentId)
while item:
if G2frame.GPXtree.GetItemText(item) == itemText:
return item
item, cookie = G2frame.GPXtree.GetNextChild(parentId, cookie)
return 0
except: #trap C++ error?
return 0
[docs]
def SelectDataTreeItem(G2frame,item,oldFocus=None):
'''Called from :meth:`GSASIIdataGUI.GSASII.OnDataTreeSelChanged` when a item is selected on the tree.
Also called from GSASII.OnGPXtreeEndDrag, OnAddPhase -- might be better to select item, triggering
the the bind to SelectDataTreeItem
Also Called in GSASIIphsGUI.UpdatePhaseData by OnTransform callback.
'''
def OnShowShift(event):
if 'cycle' in event.EventObject.GetLabel():
shftesd = [data['Rvals']['lastShifts'].get(k,0)/s for k,s in
zip(data['varyList'],data['sig'])]
lbl = 'Total shift/esd for last refinement cycle'
else:
if 'Lastshft' not in data:
return
if data['Lastshft'] is None:
return
shftesd = data['Lastshft']/data['sig']
lbl = 'Total shift/esd over last refinement run'
G2plt.PlotNamedFloatHBarGraph(G2frame,shftesd,data['varyList'],Xlabel='Total shift/esd',
Ylabel='Variables',Title=lbl,PlotName='Shift/esd')
if G2frame.PickIdText == G2frame.GetTreeItemsList(item): # don't redo the current data tree item
if GSASIIpath.GetConfigValue('debug'): print('Skipping SelectDataTreeItem as G2frame.PickIdText unchanged')
return
# save or finish processing of outstanding events
for grid in G2frame.dataWindow.currentGrids: # complete any open wx.Grid edits
#if GSASIIpath.GetConfigValue('debug'): print 'Testing grid edit in',grid
try:
if grid.IsCellEditControlEnabled(): # complete any grid edits in progress
if GSASIIpath.GetConfigValue('debug'): print ('Completing grid edit in%s'%str(grid))
grid.SaveEditControlValue()
# not sure if the next two things do anything
grid.HideCellEditControl()
grid.DisableCellEditControl()
except:
pass
if G2frame.dataWindow.GetLabel() == 'Comments': # save any recently entered comments
try:
data = [G2frame.dataDisplay.GetValue()]
G2frame.dataDisplay.ClearData()
Id = GetGPXtreeItemId(G2frame,G2frame.root, 'Comments')
if Id: G2frame.GPXtree.SetItemPyData(Id,data)
except: #clumsy but avoids dead window problem when opening another project
pass
elif G2frame.dataWindow.GetLabel() == 'Notebook': # save any recent notebook entries
try:
data = [G2frame.dataDisplay.GetValue()]
G2frame.dataDisplay.ClearData()
Id = GetGPXtreeItemId(G2frame,G2frame.root, 'Notebook')
if Id: G2frame.GPXtree.SetItemPyData(Id,data)
except: #clumsy but avoids dead window problem when opening another project
pass
# elif 'Phase Data for' in G2frame.dataWindow.GetLabel():
# if G2frame.dataDisplay:
# oldPage = G2frame.dataDisplay.GetSelection()
G2frame.GetStatusBar().SetStatusText('',1)
SetDataMenuBar(G2frame)
G2frame.SetTitleByGPX()
G2frame.PickId = item
G2frame.PickIdText = None
parentID = G2frame.root
if item == G2frame.root:
G2frame.dataWindow.ClearData()
G2frame.dataWindow.helpKey = "Data tree"
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
mainSizer.Add(wx.StaticText(G2frame.dataWindow, wx.ID_ANY,
'Select an item from the tree to see/edit parameters'))
G2frame.dataWindow.SetDataSize()
return
else:
# Set up the help entry for the current selected tree item
try: #don't know why we get here when opening new project
parentID = G2frame.GPXtree.GetItemParent(item)
# save name of calling tree item for help. N.B. may want to override this later
prfx = G2frame.GPXtree.GetItemText(item)
if prfx:
prfx = prfx.split()[0].upper()
else: #just deleted item - escape!!
return
prfx1 = G2frame.GPXtree.GetItemText(parentID).split()[0]
if prfx in ('IMG','PKS','PWDR','SASD','HKLF','PDF','REFD',):
G2frame.dataWindow.helpKey = prfx
elif prfx1 == 'Phases':
G2frame.dataWindow.helpKey = 'Phases'
elif prfx1 in ('IMG','PKS','PWDR','SASD','HKLF','PDF','REFD',):
suffix = G2frame.GPXtree.GetItemText(item)
suffix1 = suffix.split()[0]
if '(Q)' in suffix1 or '(R)' in suffix1: suffix = suffix1
G2frame.dataWindow.helpKey = prfx1 + '_' + suffix
else:
G2frame.dataWindow.helpKey = G2frame.GPXtree.GetItemText(item) # save name of calling tree item for help
except IndexError:
G2frame.dataWindow.helpKey = ''
if GSASIIpath.GetConfigValue('debug'):
print ('bug: why here? prfx=%s prfx1=%s'%(prfx,prfx1))
G2obj.HowDidIgetHere()
# clear out the old panel contents
if G2frame.dataWindow:
G2frame.dataWindow.ClearData()
# process first-level entries in tree
if G2frame.GPXtree.GetItemParent(item) == G2frame.root:
G2frame.PatternId = 0
if G2frame.GPXtree.GetItemText(item) == 'Notebook':
SetDataMenuBar(G2frame,G2frame.dataWindow.DataNotebookMenu)
data = G2frame.GPXtree.GetItemPyData(item)
UpdateNotebook(G2frame,data)
elif G2frame.GPXtree.GetItemText(item) == 'Controls':
data = G2frame.GPXtree.GetItemPyData(item)
if not data: #fill in defaults
data = copy.copy(G2obj.DefaultControls) #least squares controls
G2frame.GPXtree.SetItemPyData(item,data)
UpdateControls(G2frame,data)
for i in G2frame.Refine: i.Enable(True)
elif G2frame.GPXtree.GetItemText(item).startswith('Sequential '):
G2frame.dataWindow.helpKey = 'Sequential' # for now all sequential refinements are documented in one place
data = G2frame.GPXtree.GetItemPyData(item)
G2seq.UpdateSeqResults(G2frame,data)
elif G2frame.GPXtree.GetItemText(item) == 'Covariance':
data = G2frame.GPXtree.GetItemPyData(item)
text = ''
if 'Rvals' in data:
lbl = 'Refinement results'
else:
lbl = '*** No refinement results ***'
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='Covariance'))
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
G2G.HorizontalLine(mainSizer,G2frame.dataWindow)
if 'Rvals' in data:
Nvars = len(data['varyList'])
Rvals = data['Rvals']
text = ('\nTotal residuals after last refinement: \n'+
'\twR = {:.3f}\n\tχ**2 = {:.1f}\n\tGOF = {:.2f}').format(
Rvals['Rwp'],Rvals['chisq'],Rvals['GOF'])
text += '\n\tNobs = {}\n\tNvals = {}\n\tSVD zeros = {}'.format(
Rvals['Nobs'],Nvars,Rvals.get('SVD0',0.))
if Rvals.get('Max shft/sig') is not None:
text += '\n\tmax shift/esd = {:.3f} (over all cycles)'.format(Rvals['Max shft/sig'])
if 'lamMax' in Rvals:
text += '\n\tlog10 MaxLambda = {:.1f}'.format(np.log10(Rvals['lamMax']))
if '2' not in platform.python_version_tuple()[0]: # greek OK in Py2?
text += '\n\tReduced χ**2 = {:.2f}'.format(Rvals['GOF']**2)
mainSizer.Add(wx.StaticText(G2frame.dataWindow,wx.ID_ANY,text))
if Rvals.get('RestraintSum',0) > 0:
diffr_chisq = (Rvals['chisq']-Rvals['RestraintSum'])
chisq_data = (diffr_chisq)/(Rvals['Nobs']-Rvals['Nvars'])
lbl = '\nData-only residuals (without restraints)'
lbl += f'\n\tχ**2 = {diffr_chisq:.1f}'
lbl += f'\n\tGOF = {np.sqrt(chisq_data):.2f}'
lbl += f'\n\tReduced χ**2 = {chisq_data:.2f}'
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=lbl))
Restraints = Rvals.get('Restraints',{})
if len(Restraints):
nRestraints = Rvals['nRestraints']
lbl = '\nRestraint residuals:'
for name in Restraints:
if nRestraints[name]:
lbl += '\n %s: N = %d, χ**2 = %.1f'%(name,nRestraints[name],Restraints[name])
mainSizer.Add(wx.StaticText(G2frame.dataWindow,label=lbl))
plotSizer = wx.BoxSizer(wx.HORIZONTAL)
if 'Lastshft' in data and not data['Lastshft'] is None:
showShift = wx.Button(G2frame.dataWindow,label='Plot shift/esd -- last refinement')
showShift.Bind(wx.EVT_BUTTON,OnShowShift)
plotSizer.Add(showShift)
if 'lastShifts' in data['Rvals']:
showShift = wx.Button(G2frame.dataWindow,label='Plot shift/esd -- last cycle')
showShift.Bind(wx.EVT_BUTTON,OnShowShift)
plotSizer.Add((10,-1))
plotSizer.Add(showShift)
mainSizer.Add((-1,10))
mainSizer.Add(plotSizer)
G2frame.dataWindow.SetDataSize()
G2plt.PlotCovariance(G2frame,data)
#try:
# if True:
# import imp
# import phfrac
# imp.reload(phfrac)
# Histograms,Phases = G2frame.GetUsedHistogramsAndPhasesfromTree()
# for histo in Histograms:
# hId = Histograms[histo]['hId']
# #phfrac.massFracs(data,Phases,histo,hId)
# vDict,sDict = phfrac.calcMassFracs(
# data['varyList'],data['covMatrix'],Phases,histo,hId)
# for key in vDict:
# print(key,vDict[key],sDict[key])
#except:
# pass
elif G2frame.GPXtree.GetItemText(item) == 'Constraints':
data = G2frame.GPXtree.GetItemPyData(item)
#import imp
#imp.reload(G2cnstG) # for testing changes to GSASIIconstrGUI
G2cnstG.UpdateConstraints(G2frame,data)
elif G2frame.GPXtree.GetItemText(item) == 'Rigid bodies':
data = G2frame.GPXtree.GetItemPyData(item)
# import imp
# imp.reload(G2cnstG) # for testing changes to GSASIIconstrGUI
# print('debug: reloaded',G2cnstG)
G2cnstG.UpdateRigidBodies(G2frame,data)
elif G2frame.GPXtree.GetItemText(item).startswith('IMG '):
G2frame.Image = item
data = G2frame.GPXtree.GetItemPyData(GetGPXtreeItemId(
G2frame,item,'Image Controls'))
G2imG.UpdateImageData(G2frame,data)
G2plt.PlotImage(G2frame,newPlot=True)
elif G2frame.GPXtree.GetItemText(item).startswith('PKS '):
G2frame.PatternId = item
G2plt.PlotPowderLines(G2frame)
elif G2frame.GPXtree.GetItemText(item).startswith('PWDR '):
G2frame.PatternId = item
#for i in G2frame.ExportPattern: i.Enable(True)
if G2frame.EnablePlot:
UpdatePWHKPlot(G2frame,'PWDR',item)
elif G2frame.GPXtree.GetItemText(item).startswith('SASD '):
G2frame.PatternId = item
#for i in G2frame.ExportPattern: i.Enable(True)
if G2frame.EnablePlot:
UpdatePWHKPlot(G2frame,'SASD',item)
elif G2frame.GPXtree.GetItemText(item).startswith('REFD '):
G2frame.PatternId = item
#for i in G2frame.ExportPattern: i.Enable(True)
if G2frame.EnablePlot:
UpdatePWHKPlot(G2frame,'REFD',item)
elif G2frame.GPXtree.GetItemText(item).startswith('HKLF '):
G2frame.Sngl = True
if G2frame.EnablePlot:
UpdatePWHKPlot(G2frame,'HKLF',item)
elif G2frame.GPXtree.GetItemText(item).startswith('PDF '):
G2frame.PatternId = item
data = G2frame.GPXtree.GetItemPyData(GetGPXtreeItemId(G2frame,item,'PDF Controls'))
G2pdG.UpdatePDFGrid(G2frame,data)
for i in G2frame.ExportPDF: i.Enable(True) # this should be done on .gpx load; is done on OnMakePDFs
if len(data['G(R)']):
G2plt.PlotISFG(G2frame,data,plotType='G(R)')
elif G2frame.GPXtree.GetItemText(item) == 'Phases':
if len(G2frame.GetPhaseNames()) == 0:
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
mainSizer.Add(wx.StaticText(G2frame.dataWindow,
wx.ID_ANY,'Create phases first'))
elif len(G2frame.GetPhaseNames()) == 1: # if there is only one phase, select it
item, cookie = G2frame.GPXtree.GetFirstChild(item)
data = G2frame.GPXtree.GetItemPyData(item)
G2phG.UpdatePhaseData(G2frame,item,data)
wx.CallAfter(G2frame.GPXtree.SelectItem,item)
else:
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
mainSizer.Add(wx.StaticText(G2frame.dataWindow,
wx.ID_ANY,'Select one phase to see its parameters'))
elif G2frame.GPXtree.GetItemText(item) == 'Cluster Analysis':
data = G2frame.GPXtree.GetItemPyData(item)
G2frame.dataWindow.helpKey = 'Cluster Analysis'
G2seq.UpdateClusterAnalysis(G2frame,data)
elif G2frame.GPXtree.GetItemText(item) == 'Restraints':
data = G2frame.GPXtree.GetItemPyData(item)
#patch - put phases in restraint tree
names = G2frame.GetPhaseNames()
for name in names:
if not GetGPXtreeItemId(G2frame,item,name):
G2frame.GPXtree.AppendItem(parent=item,text=name)
if name not in data:
data[name] = {}
#end patch
if len(G2frame.GetPhaseNames()) == 0:
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
mainSizer.Add(wx.StaticText(G2frame.dataWindow,
wx.ID_ANY,'Create phases first'))
elif len(G2frame.GetPhaseNames()) == 1: # why force choice of a phase if there is only one?
item, cookie = G2frame.GPXtree.GetFirstChild(item)
phaseName = G2frame.GPXtree.GetItemText(item)
if phaseName not in data:
data[phaseName] = {}
G2frame.dataWindow.helpKey = 'Restraints'
G2restG.UpdateRestraints(G2frame,data,phaseName)
else:
G2frame.GPXtree.Expand(item)
mainSizer = wx.BoxSizer(wx.VERTICAL)
G2frame.dataWindow.SetSizer(mainSizer)
mainSizer.Add(
wx.StaticText(G2frame.dataWindow,wx.ID_ANY,'Select one phase to see its restraints'))
elif G2frame.GPXtree.GetItemText(item).startswith('Hist/Phase'):
#import imp
#imp.reload(G2ddG)
G2ddG.MakeHistPhaseWin(G2frame)
elif GSASIIpath.GetConfigValue('debug'):
print('Unknown tree item',G2frame.GPXtree.GetItemText(item))
############################################################################
# process second-level entries in tree
elif G2frame.GPXtree.GetItemText(item) == 'PDF Peaks':
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
peaks = G2frame.GPXtree.GetItemPyData(GetGPXtreeItemId(G2frame,G2frame.PatternId,'PDF Peaks'))
data = G2frame.GPXtree.GetItemPyData(GetGPXtreeItemId(G2frame,G2frame.PatternId,'PDF Controls'))
G2pdG.UpdatePDFPeaks(G2frame,peaks,data)
if len(data['G(R)']):
G2plt.PlotISFG(G2frame,data,plotType='G(R)',newPlot=True,peaks=peaks)
elif G2frame.GPXtree.GetItemText(item) == 'PDF Controls':
G2frame.dataWindow.helpKey = G2frame.GPXtree.GetItemText(item) # special treatment to avoid PDF_PDF Controls
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
data = G2frame.GPXtree.GetItemPyData(item)
G2pdG.UpdatePDFGrid(G2frame,data)
for i in G2frame.ExportPDF: i.Enable(True) # this should be done on .gpx load; is done on OnMakePDFs
if len(data['G(R)']):
if 'I(Q)' in data: G2plt.PlotISFG(G2frame,data,plotType='I(Q)')
if 'S(Q)' in data: G2plt.PlotISFG(G2frame,data,plotType='S(Q)')
if 'F(Q)' in data: G2plt.PlotISFG(G2frame,data,plotType='F(Q)')
G2plt.PlotISFG(G2frame,data,plotType='G(R)')
elif G2frame.GPXtree.GetItemText(parentID) == 'Phases':
data = G2frame.GPXtree.GetItemPyData(item)
# debug stuff
# if GSASIIpath.GetConfigValue('debug'):
# print('Debug: reloading G2phG')
# from importlib import reload
# reload(G2phG)
# end debug stuff
G2phG.UpdatePhaseData(G2frame,item,data)
elif G2frame.GPXtree.GetItemText(parentID) == 'Restraints':
data = G2frame.GPXtree.GetItemPyData(parentID)
G2frame.dataWindow.helpKey = 'Restraints'
phaseName = G2frame.GPXtree.GetItemText(item)
if phaseName not in data:
data[phaseName] = {}
G2restG.UpdateRestraints(G2frame,data,phaseName)
elif G2frame.GPXtree.GetItemText(item) == 'Comments':
SetDataMenuBar(G2frame,G2frame.dataWindow.DataCommentsMenu)
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
data = G2frame.GPXtree.GetItemPyData(item)
UpdateComments(G2frame,data)
elif G2frame.GPXtree.GetItemText(item) == 'Image Controls':
G2frame.Image = G2frame.GPXtree.GetItemParent(item)
masks = G2frame.GPXtree.GetItemPyData(
GetGPXtreeItemId(G2frame,G2frame.Image, 'Masks'))
data = G2frame.GPXtree.GetItemPyData(item)
G2frame.ImageZ = G2imG.GetImageZ(G2frame,data)
G2imG.UpdateImageControls(G2frame,data,masks)
G2plt.PlotImage(G2frame,newPlot=False)
elif G2frame.GPXtree.GetItemText(item) == 'Masks':
G2frame.Image = G2frame.GPXtree.GetItemParent(item)
masks = G2frame.GPXtree.GetItemPyData(item)
data = G2frame.GPXtree.GetItemPyData(
GetGPXtreeItemId(G2frame,G2frame.Image, 'Image Controls'))
G2frame.ImageZ = G2imG.GetImageZ(G2frame,data)
G2imG.UpdateMasks(G2frame,masks)
G2plt.PlotImage(G2frame,newPlot=False)
elif G2frame.GPXtree.GetItemText(item) == 'Stress/Strain':
G2frame.Image = G2frame.GPXtree.GetItemParent(item)
data = G2frame.GPXtree.GetItemPyData(
GetGPXtreeItemId(G2frame,G2frame.Image, 'Image Controls'))
G2frame.ImageZ = G2imG.GetImageZ(G2frame,data,newRange=False)
strsta = G2frame.GPXtree.GetItemPyData(item)
G2plt.PlotStrain(G2frame,strsta,newPlot=True)
G2plt.PlotImage(G2frame,newPlot=False)
G2imG.UpdateStressStrain(G2frame,strsta)
elif G2frame.GPXtree.GetItemText(item) == 'Peak List':
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
data = G2frame.GPXtree.GetItemPyData(item)
#patch
if 'list' in str(type(data)):
data = {'peaks':data,'sigDict':{}}
G2frame.GPXtree.SetItemPyData(item,data)
#end patch
# if GSASIIpath.GetConfigValue('debug'):
# from importlib import reload
# reload(G2pdG)
# imp.reload(G2pwd)
# reload(G2plt)
# print('reloading G2pwdGUI & G2plt')
G2pdG.UpdatePeakGrid(G2frame,data)
for i in G2frame.ExportPeakList: i.Enable(True)
newPlot = False
if getattr(G2frame,'Contour','False'):
G2frame.Contour = False
newPlot = True
G2pwpl.PlotPatterns(G2frame,newPlot,fromTree=True)
elif G2frame.GPXtree.GetItemText(item) == 'Background':
NewPlot = False # plot using previous limits
if getattr(G2frame,'Contour',False): # except if contour plot
G2frame.Contour = False
NewPlot = True
elif not hasattr(G2frame,'xylim'): # or no limits present
NewPlot = True
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
data = G2frame.GPXtree.GetItemPyData(item)
G2pdG.UpdateBackground(G2frame,data)
G2pwpl.PlotPatterns(G2frame,newPlot=NewPlot,fromTree=True)
elif G2frame.GPXtree.GetItemText(item) == 'Limits':
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
datatype = G2frame.GPXtree.GetItemText(G2frame.PatternId)[:4]
data = G2frame.GPXtree.GetItemPyData(item)
G2pdG.UpdateLimitsGrid(G2frame,data,datatype)
G2pwpl.PlotPatterns(G2frame,plotType=datatype,newPlot=True,fromTree=True)
elif G2frame.GPXtree.GetItemText(item) == 'Instrument Parameters':
# if GSASIIpath.GetConfigValue('debug'):
# from importlib import reload
# reload(G2pdG)
# print('reloading G2pwdGUI')
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
data = G2frame.GPXtree.GetItemPyData(item)[0]
G2pdG.UpdateInstrumentGrid(G2frame,data)
if 'P' in data['Type'][0]: #powder data only
G2plt.PlotPeakWidths(G2frame)
elif G2frame.GPXtree.GetItemText(item) == 'Models':
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
data = G2frame.GPXtree.GetItemPyData(item)
if prfx1 == 'SASD':
G2pdG.UpdateModelsGrid(G2frame,data)
elif prfx1 == 'REFD':
G2pdG.UpdateREFDModelsGrid(G2frame,data)
G2pwpl.PlotPatterns(G2frame,plotType=prfx1,fromTree=True)
if prfx1 == 'SASD':
if len(data['Size']['Distribution']):
G2plt.PlotSASDSizeDist(G2frame)
if len(data['Pair']['Distribution']):
G2plt.PlotSASDPairDist(G2frame)
elif G2frame.GPXtree.GetItemText(item) == 'Substances':
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
data = G2frame.GPXtree.GetItemPyData(item)
G2pdG.UpdateSubstanceGrid(G2frame,data)
elif G2frame.GPXtree.GetItemText(item) == 'Sample Parameters':
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
data = G2frame.GPXtree.GetItemPyData(item)
datatype = G2frame.GPXtree.GetItemText(G2frame.PatternId)[:4]
if 'Temperature' not in data: #temp fix for old gpx files
data = {'Scale':[1.0,True],'Type':'Debye-Scherrer','Absorption':[0.0,False],'DisplaceX':[0.0,False],
'DisplaceY':[0.0,False],'Temperature':300.,'Pressure':1.0,
'FreePrm1':0.,'FreePrm2':0.,'FreePrm3':0.,
'Gonio. radius':200.0}
G2frame.GPXtree.SetItemPyData(item,data)
G2pdG.UpdateSampleGrid(G2frame,data)
G2pwpl.PlotPatterns(G2frame,True,plotType=datatype,fromTree=True)
elif G2frame.GPXtree.GetItemText(item) == 'Index Peak List':
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
data = G2frame.GPXtree.GetItemPyData(item)
#patch
if len(data) != 2:
data = [data,[]]
G2frame.GPXtree.SetItemPyData(item,data)
#end patch
G2pdG.UpdateIndexPeaksGrid(G2frame,data)
for i in G2frame.ExportPeakList: i.Enable(True)
if 'PKS' in G2frame.GPXtree.GetItemText(G2frame.PatternId):
G2plt.PlotPowderLines(G2frame)
else:
newPlot = False
if getattr(G2frame,'Contour','False'):
G2frame.Contour = False
newPlot = True
G2pwpl.PlotPatterns(G2frame,newPlot,fromTree=True)
elif G2frame.GPXtree.GetItemText(item) == 'Unit Cells List':
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
data = G2frame.GPXtree.GetItemPyData(item)
if not data:
data.append([0,0.0,4,25.0,0,'P1',1.,1.,1.,90.,90.,90.,1.,'P 1']) #zero error flag, zero value, max Nc/No, start volume
data.append([0,0,0,0,0, 0,0,0,0,0, 0,0,0,0,0, 0,0]) #Bravais lattice flags
data.append([]) #empty cell list
data.append([]) #empty dmin
data.append({}) #empty superlattice stuff
data.append([]) #empty mag cells list
G2frame.GPXtree.SetItemPyData(item,data)
#patch
if len(data) < 5:
data.append({'Use':False,'ModVec':[0,0,0.1],'maxH':1,'ssSymb':''}) #empty superlattice stuff
G2frame.GPXtree.SetItemPyData(item,data)
#end patch
G2pdG.UpdateUnitCellsGrid(G2frame,data,New=True)
elif G2frame.GPXtree.GetItemText(item) == 'Reflection Lists': #powder reflections
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
data = G2frame.GPXtree.GetItemPyData(item)
G2frame.RefList = ''
if len(data):
G2frame.RefList = list(data.keys())[0]
G2pdG.UpdateReflectionGrid(G2frame,data)
G2frame.dataWindow.HideShow.Enable(False)
newPlot = False
if getattr(G2frame,'Contour','False'):
G2frame.Contour = False
newPlot = True
G2pwpl.PlotPatterns(G2frame,newPlot,fromTree=True)
elif G2frame.GPXtree.GetItemText(item) == 'Reflection List': #HKLF reflections
G2frame.PatternId = G2frame.GPXtree.GetItemParent(item)
name = G2frame.GPXtree.GetItemText(G2frame.PatternId)
data = G2frame.GPXtree.GetItemPyData(G2frame.PatternId)
G2pdG.UpdateReflectionGrid(G2frame,data,HKLF=True,Name=name)
G2frame.dataWindow.HideShow.Enable(True)
if G2frame.PickId:
G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
# window has been filled, now resize scroll bars
G2frame.dataWindow.SetDataSize()
G2frame.Raise()
if oldFocus:
oldFocus.GetTopLevelParent().Raise()
oldFocus.SetFocus()
#debug code
# print 'Got here!'
# def FillWindow(panel,size=1.):
# sizer = panel.GetSizer()
# sizer.Add(wx.StaticText(panel, wx.ID_ANY, "Panel Two: long line "+int(size*40)*'*', (5,5)))
# for i in range(int(size*15)): sizer.Add(wx.StaticText(panel, wx.ID_ANY, "Line "+str(2+i), (5,5)))
# panel.Layout()
# panel.SendSizeEvent()
# G2frame.dataWindow.ClearData()
# FillWindow(G2frame.dataWindow)
# N.B. it does not appear that MakePDF, ExportMTZ or ExportHKL are ever disabled
[docs]
def FindPhaseItem(G2frame):
'''Finds the Phase item in the tree. If not present it adds one
also adding 'Hist/Phase' if config var SeparateHistPhaseTreeItem
is set as True.
'''
if not GetGPXtreeItemId(G2frame,G2frame.root,'Phases'):
sub = G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Phases')
if GSASIIpath.GetConfigValue('SeparateHistPhaseTreeItem',False):
G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Hist/Phase')
else:
sub = GetGPXtreeItemId(G2frame,G2frame.root,'Phases')
return sub
if __name__ == '__main__':
ShowVersions()