Source code for GSASIIdataGUI

# -*- coding: utf-8 -*-
#GSASIIdataGUI - Main GUI routines
#========== SVN repository information ###################
# $Date: 2024-03-17 12:50:24 -0500 (Sun, 17 Mar 2024) $
# $Author: toby $
# $Revision: 5767 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIdataGUI.py $
# $Id: GSASIIdataGUI.py 5767 2024-03-17 17:50:24Z toby $
#=========- SVN repository information ###################
'''
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 os
import inspect
if '2' in platform.python_version_tuple()[0]:
    import cPickle
else:
    try:
        import _pickle as cPickle
    except:
        print('Warning: failed to import the optimized Py3 pickle (_pickle)')
        import pickle as cPickle
import re
import numpy as np
import numpy.ma as ma
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
import GSASIIpath
GSASIIpath.SetVersionNumber("$Revision: 5767 $")
import GSASIImath as G2mth
import GSASIIIO as G2IO
import GSASIIfiles as G2fil
import GSASIIstrIO as G2stIO
import GSASIIlattice as G2lat
import GSASIIplot as G2plt
import GSASIIpwdGUI as G2pdG
import GSASIIimgGUI as G2imG
import GSASIIphsGUI as G2phG
import GSASIIspc as G2spc
import GSASIImapvars as G2mv
import GSASIIconstrGUI as G2cnstG
import GSASIIrestrGUI as G2restG
import GSASIIobj as G2obj
import GSASIIlog as log
import GSASIIctrlGUI as G2G
import GSASIIElem as G2elem
import GSASIIpwd as G2pwd
import GSASIIstrMain as G2stMn
#import GSASIIstrMath as G2stMth
import defaultIparms as dI
import GSASIIfpaGUI as G2fpa
import GSASIIseqGUI as G2seq
import GSASIIddataGUI as G2ddG
#import GSASIIspc as G2spc

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)

# define Ids for wx menu items
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 SetDefaultDData(dType,histoName,NShkl=0,NDij=0): ''' Sets default values for various histogram parameters param: str dType: 3 letter histogram type, e.g. 'PNT' param: str histoName: histogram name as it aoears in tree param: NShkl int: number of generalized mustrain coefficients - depends on symmetry param: NDij int: number of hydrostatic strain coefficients - depends on symmetry returns dict: default data for histogram - found in data tab for phase/histogram ''' if dType in ['SXC','SNC','SEC']: return {'Histogram':histoName,'Show':False,'Scale':[1.0,True],'Type':dType, 'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}, 'Extinction':['Lorentzian','None', {'Tbar':0.1,'Cos2TM':0.955, 'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]}], 'Flack':[0.0,False]} elif dType == 'SNT': return {'Histogram':histoName,'Show':False,'Scale':[1.0,True],'Type':dType, 'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}, 'Extinction':['Lorentzian','None', { 'Eg':[1.e-10,False],'Es':[1.e-10,False],'Ep':[1.e-10,False]}]} elif 'P' in dType: return {'Histogram':histoName,'Show':False,'Scale':[1.0,False],'Type':dType, 'Pref.Ori.':['MD',1.0,False,[0,0,1],0,{},[],0.1], 'Size':['isotropic',[1.,1.,1.],[False,False,False],[0,0,1], [1.,1.,1.,0.,0.,0.],6*[False,]], 'Mustrain':['isotropic',[1000.0,1000.0,1.0],[False,False,False],[0,0,1], NShkl*[0.01,],NShkl*[False,]], 'HStrain':[NDij*[0.0,],NDij*[False,]], 'Extinction':[0.0,False],'Babinet':{'BabA':[0.0,False],'BabU':[0.0,False]}}
[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.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) 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) 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. * 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'] = {} 'module versions newer than what we have tested & where problems are suspected' versionDict['tooNewUntested'] = {'Python':'3.12','wx': '4.2.2'} 'module versions newer than what we have tested but no problems are suspected'
[docs] def ShowVersions(): '''Show the versions all of required Python packages, etc. ''' import numpy as np import scipy as sp import wx import matplotlib as mpl import OpenGL as ogl import GSASIIpath 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") 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 print(GSASIIpath.getG2VersionInfo()) if not GSASIIpath.TestSPG(GSASIIpath.binaryPath): versionDict['errors'] += 'Error accessing GSAS-II binary files. Only limited functionality available.' else: prog = 'convcell' if sys.platform.startswith('win'): prog += '.exe' if not os.path.exists(os.path.join(GSASIIpath.binaryPath,prog)): versionDict['errors'] += 'Installed binary files need an update. If you built them, rerun scons' 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://bit.ly/G2install). 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')
[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 platform.python_version()[:3] == '2.7': msg = '''The end-of-life for python 2.7 was January 1, 2020. We strongly recommend reinstalling GSAS-II from a new installation kit as we may not be able to offer support for operation of GSAS-II in python 2.7. See instructions for details. ''' download = '' cmds = [] instructions = 'https://subversion.xray.aps.anl.gov/trac/pyGSAS' if sys.platform == "win32": download = 'https://subversion.xray.aps.anl.gov/admin_pyGSAS/downloads/gsas2full-Latest-Windows-x86_64.exe' instructions = 'https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/SingleStepWindowsIllustrated' elif sys.platform == "darwin": cmds = ['echo starting download, please wait...', '''echo 'curl "https://subversion.xray.aps.anl.gov/admin_pyGSAS/downloads/gsas2full-Latest-MacOSX-x86_64.sh" > /tmp/g2.sh; bash /tmp/g2.sh' ''', 'curl "https://subversion.xray.aps.anl.gov/admin_pyGSAS/downloads/gsas2full-Latest-MacOSX-x86_64.sh" > /tmp/g2.sh; bash /tmp/g2.sh' ] instructions = 'https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/MacSingleStepInstallerFigs' elif sys.platform.startswith("linux"): download = 'https://subversion.xray.aps.anl.gov/admin_pyGSAS/downloads/gsas2full-Latest-Linux-x86_64.sh' instructions = 'https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/LinuxSingleStepInstaller' else: print(u'Unknown platform: '+sys.platform) if platform.architecture()[0] != '64bit' and sys.platform == "win32": msg += '''\nYou are currently using 32-bit Python. Please check if you are running 32-bit windows or 64-bit windows (use Start/Settings/System/About & look for "System type". We recommend using the 64-bit installer if you have 64-bit windows.''' download = '' elif platform.architecture()[0] != '64bit' and sys.platform.startswith("linux"): msg += '''\nYou are using 32-bit Python. We now only package for 64-bit linux. If you are running 32-bit linux you will need to install Python yourself. See instructions at https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/InstallLinux''' instructions = 'https://subversion.xray.aps.anl.gov/trac/pyGSAS/wiki/InstallLinux' dlg = wx.Dialog(None,wx.ID_ANY,'End-Of-Life warning for Python 2.7', style=wx.DEFAULT_DIALOG_STYLE|wx.RESIZE_BORDER) mainSizer = wx.BoxSizer(wx.VERTICAL) txt = wx.StaticText(dlg,wx.ID_ANY,G2G.StripIndents(msg)) mainSizer.Add(txt) txt.Wrap(400) dlg.SetSizer(mainSizer) btnsizer = wx.BoxSizer(wx.HORIZONTAL) btnsizer.Add((1,1),1,wx.EXPAND,1) OKbtn = wx.Button(dlg, wx.ID_OK,'Continue') OKbtn.SetDefault() OKbtn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_OK)) btnsizer.Add(OKbtn) btn = wx.Button(dlg, wx.ID_ANY,'Show Instructions') def openInstructions(event): G2G.ShowWebPage(instructions,None) btn.Bind(wx.EVT_BUTTON, openInstructions) btnsizer.Add(btn) if download: btn = wx.Button(dlg, wx.ID_ANY,'Start Download') btn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_YES)) btnsizer.Add(btn) elif cmds: btn = wx.Button(dlg, wx.ID_ANY,'Start Install') btn.Bind(wx.EVT_BUTTON,lambda event: dlg.EndModal(wx.ID_CANCEL)) btnsizer.Add(btn) #btn = wx.Button(dlg, wx.ID_CANCEL) #btnsizer.AddButton(btn) btnsizer.Add((1,1),1,wx.EXPAND,1) #btnsizer.Realize() mainSizer.Add((-1,5),1,wx.EXPAND,1) mainSizer.Add(btnsizer,0,wx.ALIGN_CENTER,0) mainSizer.Add((-1,10)) res = 0 try: res = dlg.ShowModal() finally: dlg.Destroy() if res == wx.ID_YES: G2G.ShowWebPage(download,None) G2G.ShowWebPage(instructions,None) wx.Sleep(1) dlg = wx.MessageDialog(None,G2G.StripIndents( '''Download has been started in your browser; installation instructions will also be shown in a web page\n\nPress OK to exit GSAS-II, Cancel to continue.'''), 'start install',wx.OK|wx.CANCEL) if dlg.ShowModal() == wx.ID_OK: sys.exit() elif res == wx.ID_CANCEL: dlg = wx.MessageDialog(None,G2G.StripIndents( '''Press OK to continue. Instructions will be shown in a web page. Download and installation will start in the terminal window after you press OK. Respond to questions there.'''), 'start install',wx.OK|wx.CANCEL) if dlg.ShowModal() == wx.ID_OK: G2G.ShowWebPage(instructions,None) GSASIIpath.runScript(cmds, wait=True) sys.exit() 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://bit.ly/G2install') 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]) if GSASIIpath.GetConfigValue('wxInspector'): import wx.lib.inspection as wxeye wxeye.InspectionTool().Show() try: application.SetAppDisplayName('GSAS-II') except: pass #application.GetTopWindow().SendSizeEvent() application.GetTopWindow().Show(True) application.main.UpdateTask = GSASIIpath.GetRepoUpdatesInBackground()
#### 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 '''
[docs] def MenuBinding(self,event): '''Called when a menu is clicked upon; looks up the binding in table ''' log.InvokeMenuCommand(event.GetId(),self,event)
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.HowIsG2Installed() == 'svn': item = parent.Append(wx.ID_ANY,'Edit proxy...','Edit proxy internet information (used for updates)') self.Bind(wx.EVT_MENU, self.EditProxyInfo, id=item.GetId()) if GSASIIpath.GetConfigValue('debug'): try: import 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()) 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 ''' 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,'Save partials as csv','Save the computed partials as a csv file') self.Refine.append(item) item.Enable(state) # disabled during sequential fits self.Bind(wx.EVT_MENU, self.OnSavePartials, 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 = {}
[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): '''Used for all imports, including Phases, datasets, images... 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. :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 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+')' 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 zip file? if os.path.splitext(filename)[1].lower() == '.zip': extractedfiles = G2IO.ExtractFileFromZip( filename,parent=self, multipleselect=True) if extractedfiles is None: continue # error or Cancel if extractedfiles != filename: self.zipfile = filename # save zip name filelist1 += extractedfiles continue filelist1.append(filename) filelist = filelist1 Start = True #1st time read - clear selections below for filename in filelist: # is this a zip file? if os.path.splitext(filename)[1].lower() == '.zip': extractedfile = G2IO.ExtractFileFromZip(filename,parent=self) if extractedfile is None: continue # error or Cancel if extractedfile != filename: filename,self.zipfile = extractedfile,filename # now use the file that was created # 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) return [] elif len(secondaryReaders) + len(primaryReaders) == 0: self.ErrorDialog('No Format','No matching format for file '+filename) return [] fp = None msg = '' if len(filelist) == 1 and Preview: if self.PreviewFile(filename): 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 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 a warning message:\n\n'+rd.warnings) 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() 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,u'from '+reader.formatName+u' file',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. ''' # 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.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) 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 generalData = data['General'] SGData = generalData['SGData'] Super = generalData.get('Super',0) SuperVec = [] if Super: SuperVec = np.array(generalData['SuperVec'][0]) UseList = data['Histograms'] NShkl = len(G2spc.MustrainNames(SGData)) NDij = len(G2spc.HStrainNames(SGData)) for i in result: histoName = TextList[i] if histoName in HKLFlist: #redo UpdateHKLFdata(histoName) here: Id = GetGPXtreeItemId(self,self.root,histoName) refDict,reflData = self.GPXtree.GetItemPyData(Id) G,g = G2lat.cell2Gmat(generalData['Cell'][1:7]) Super = reflData.get('Super',0) for iref,ref in enumerate(reflData['RefList']): hkl = ref[:3] if Super: H = list(hkl+SuperVec*ref[3]) else: H = hkl ref[4+Super] = np.sqrt(1./G2lat.calc_rDsq2(H,G)) iabsnt = G2spc.GenHKLf(H,SGData)[0] if iabsnt: #flag space gp. absences if Super: if not ref[2+Super]: ref[3+Super] = 0 else: ref[3+Super] = 1 #twin id else: ref[3] = 0 UseList[histoName] = SetDefaultDData(reflData['Type'],histoName) 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[generalData['Name']] = {} UseList[histoName] = SetDefaultDData(Inst['Type'][0],histoName,NShkl=NShkl,NDij=NDij) else: raise Exception('Unexpected histogram '+histoName) Histograms,Phases = self.GetUsedHistogramsAndPhasesfromTree() # reindex 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,u'from '+reader.formatName+u' file',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. ''' 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,u'from '+reader.formatName+u' file',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. ''' # 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 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'] Super = generalData.get('Super',0) SuperVec = [] if Super: SuperVec = np.array(generalData['SuperVec'][0]) UseList = data['Histograms'] for histoName in newHistList: #redo UpdateHKLFdata(histoName) here: Id = GetGPXtreeItemId(self,self.root,histoName) refDict,reflData = self.GPXtree.GetItemPyData(Id) UseList[histoName] = SetDefaultDData(reflData['Type'],histoName) G,g = G2lat.cell2Gmat(generalData['Cell'][1:7]) if 'TwMax' in reflData: #nonmerohedral twins present UseList[histoName]['Twins'] = [] for iT in range(reflData['TwMax'][0]+1): if iT in reflData['TwMax'][1]: UseList[histoName]['Twins'].append([False,0.0]) else: UseList[histoName]['Twins'].append([np.array([[1,0,0],[0,1,0],[0,0,1]]),[1.0,False,reflData['TwMax'][0]]]) else: #no nonmerohedral twins UseList[histoName]['Twins'] = [[np.array([[1,0,0],[0,1,0],[0,0,1]]),[1.0,False,0]],] for iref,ref in enumerate(reflData['RefList']): hkl = ref[:3] if Super: H = list(hkl+SuperVec*ref[3]) else: H = hkl ref[4+Super] = np.sqrt(1./G2lat.calc_rDsq2(H,G)) iabsnt,mul,Uniq,phi = G2spc.GenHKLf(H,SGData) if iabsnt: #flag space gp. absences if Super: if not ref[2+Super]: ref[3+Super] = 0 else: ref[3+Super] = 1 #twin id? else: ref[3] = 0 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,u'from '+reader.formatName+u' file',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,databanks,rd): '''Read lines from a GSAS-II (new) instrument parameter file similar to G2pwdGUI.OnLoad If instprm file has multiple banks each with header #Bank n: ..., this finds matching bank no. to load - problem with nonmatches? Note that this routine performs a similar role to :func:`GSASIIfiles.ReadPowderInstprm`, but this will call a GUI routine for selection when needed. TODO: refactor to combine :param list instLines: strings from GSAS-II parameter file; can be concatenated with ';' :param int bank: bank number to check when instprm file has '#BANK n:...' strings when bank = n then use parameters; otherwise skip that set. Ignored if BANK n: not present. NB: this kind of instprm file made by a Save all profile command in Instrument Parameters :return dict: Inst instrument parameter dict if OK, or str: Error message if failed ''' if 'GSAS-II' not in instLines[0]: # not a valid file return 'Not a valid GSAS-II instprm file' newItems = [] newVals = [] Found = False il = 0 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 while il < len(instLines): S = instLines[il] if S[0] == '#': if Found: break if 'Bank' in S: if bank == int(S.split(':')[0].split()[1]): il += 1 S = instLines[il] else: il += 1 S = instLines[il] while il < len(instLines) and '#Bank' not in S: il += 1 if il == len(instLines): return 'Bank %d not found in instprm file'%(bank) S = instLines[il] continue else: #a non #Bank file il += 1 S = instLines[il] Found = True if '"""' in S: delim = '"""' elif "'''" in S: delim = "'''" else: S = S.replace(' ','') SS = S.strip().split(';') for s in SS: [item,val] = s.split(':',1) newItems.append(item) try: newVals.append(float(val)) except ValueError: newVals.append(val) il += 1 continue # read multiline values, delimited by ''' or """ item,val = S.strip().split(':',1) val = val.replace(delim,'').rstrip() val += '\n' while True: il += 1 if il >= len(instLines): break S = instLines[il] if delim in S: val += S.replace(delim,'').rstrip() val += '\n' break else: val += S.rstrip() val += '\n' newItems.append(item) newVals.append(val) il += 1 if 'Lam1' in newItems: 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]}) return [G2fil.makeInstDict(newItems,newVals,len(newVals)*[False,]),{}]
[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]: 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 rd.instmsg = 'default: '+dI.defaultIparm_lbl[res] Inst = self.ReadPowderInstprm(dI.defaultIparms[res],bank,numbanks,rd) Inst[0]['difC'] = [difC,difC,0] Inst[0]['sig-1'] = [sig1,sig1,0] Inst[0]['beta-1'] = [bet1,bet1,0] return Inst #this is [Inst1,Inst2] a pair of dicts dlg.Destroy() else: rd.instmsg = 'default: '+dI.defaultIparm_lbl[res] inst1,inst2 = self.ReadPowderInstprm(dI.defaultIparms[res],bank,numbanks,rd) if rd.instdict.get('wave'): 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] for ext in '.prm','.inst','.ins','.instprm': if self.zipfile: instfile = G2IO.ExtractFileFromZip(self.zipfile, selection=os.path.split(basename + ext)[1],parent=self) if instfile == None: continue else: instfile = basename + ext if not os.path.exists(instfile): continue if 'instprm' in instfile: Lines = self.OpenPowderInstprm(instfile) instParmList = self.ReadPowderInstprm(Lines,bank,numbanks,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 #2nd priority: is there an instrument parameter file defined for the current data set? # or if this is a read on a set of set of files, use the last one again #if rd.instparm as found in data file header or (lastdatafile == filename and 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 self.zipfile: # instfile = G2IO.ExtractFileFromZip(self.zipfile, # selection=os.path.split(instfile)[1],parent=self) if instfile != None and os.path.exists(instfile): #print 'debug: try read',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,numbanks,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)) #Finally - ask user for Instrument parametrs file - seems it can't be in a zip file while True: # loop until we get a file that works or we get a cancel instfile = '' pth = os.path.dirname(filename) #look in same place data was found # pth = G2G.GetImportPath(self) 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|','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,numbanks,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 Refine is enabled ''' 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 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. ''' # 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 = {} for rd in rdlist: if 'Instrument Parameters' in rd.pwdparms: Iparm1,Iparm2 = rd.pwdparms['Instrument Parameters'] elif Iparms and not lastIparmfile: 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])) # 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] if 'phoenix' in wx.version(): HistName = 'PWDR '+rd.idstring else: HistName = 'PWDR '+G2obj.StripUnicode(rd.idstring,'_') # make new histogram names unique if 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() 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(rd.instmsg)) 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]) 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'), [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: self.EnablePlot = True if Id: self.GPXtree.Expand(Id) self.GPXtree.SelectItem(Id) 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] = 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 ''' # 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 while (N < 3): # insist on a dataset with a few points if 'TOF' in rd.idstring: names = ('dataset name', 'start TOF(ms)', 'end TOF(ms)', 'DT/T') inp = [rd.idstring, 10.,80.,0.0005] # see names for what's what dlg = G2G.ScrolledMultiEditor( self,[inp] * len(inp),range(len(inp)),names, header='Enter simulation name and range', minvals=(None,.5,1.0,0.0001), maxvals=(None,500.,500.,.01), sizevals=((225,-1),) ) else: names = ('dataset name', 'start angle', 'end angle', 'step size') if not wave or wave < 1.0: inp = [rd.idstring, 10.,40.,0.005] # see names for what's what else: inp = [rd.idstring, 10.,80.,0.01] # see names for what's what dlg = G2G.ScrolledMultiEditor( self,[inp] * len(inp),range(len(inp)),names, header='Enter simulation name and range', minvals=(None,0.001,0.001,0.0001), maxvals=(None,180.,180.,.1), sizevals=((225,-1),) ) 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) else: N = int((end-start)/step)+1 x = np.linspace(start,end,N,True) N = len(x) 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,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\npowder simulation (dummy) dataset to:' 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)) UseList[HistName] = 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 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]}) Iparm1, Iparm2 = G2fil.ReadPowderInstprm(dI.defaultIparms[0],1,1,rd) 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) dlg.ShowModal() == wx.ID_OK dlg.Destroy()
[docs] def EditProxyInfo(self,event): '''Edit the proxy information used by subversion (svn only, not used with git) ''' h,p,e = host,port,etc = GSASIIpath.getsvnProxy() labels = ['Proxy address','proxy port'] values = [host,port] i = 1 for item in etc: i += 1 labels.append('extra svn arg #'+str(i)) values.append(item) msg = '''This dialog allows customization of the subversion (svn) command. If a proxy server is needed, the address/host and port can be added supplied here. This will generate command-line options %t% --config-option servers:global:http-proxy-host=*host* %t% --config-option servers:global:http-proxy-port=*port* %% where *host* will be a network name (proxy.subnet.org) or IP address (102.3.123.23) and *port* will be a port number (integer such as 80, 8080, etc) or will be blank. %% Additional subversion command line options can be supplied here by pressing the '+' button. Two lines are needed for each option where the first svn option name (starting with two dashes) and the second line will be the value. As examples of options that might be of value, use two extra lines to add: %t% --config-dir %t% DIR %% to specify an alternate configuration location. %% Or, use four extra lines to add %t% --config-option %t% servers:global:http-proxy-username=*account* %t% --config-option %t% servers:global:http-proxy-password=*password* %% to specify a proxy user name (*account*) and password (*password*). Note that this information will be stored in a plain-text file. %% See http://svnbook.red-bean.com for more information on subversion. ''' dlg = G2G.MultiStringDialog(self,'Enter proxy values', labels,values,size=300,addRows=True,hlp=msg) if dlg.Show(): values = dlg.GetValues() h,p = values[:2] e = values[2:] dlg.Destroy() if h != host or p != port or etc != e: localproxy = proxyinfo = os.path.join( os.path.expanduser('~/.G2local/'), "proxyinfo.txt") if not os.path.exists(proxyinfo): proxyinfo = os.path.join(GSASIIpath.path2GSAS2,"proxyinfo.txt") GSASIIpath.setsvnProxy(h,p,e) if not h.strip() and not e: if os.path.exists(localproxy): os.remove(localproxy) if os.path.exists(proxyinfo): os.remove(proxyinfo) return try: fp = open(proxyinfo,'w') except: fp = open(localproxy,'w') proxyinfo = localproxy try: fp.write(h.strip()+'\n') fp.write(p.strip()+'\n') for i in e: if i.strip(): fp.write(i.strip()+'\n') fp.close() except Exception as err: print('Error writing file {}:\n{}'.format(proxyinfo,err)) print('File {} written'.format(proxyinfo))
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,u'from '+reader.formatName+u' file',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 ''' 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'),G2pdG.SetDefaultSubstances()) self.GPXtree.SetItemPyData( self.GPXtree.AppendItem(Id,text='Sample Parameters'), rd.Sample) self.GPXtree.SetItemPyData( self.GPXtree.AppendItem(Id,text='Models'),G2pdG.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,u'from '+reader.formatName+u' file',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 ''' 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'),G2pdG.SetDefaultSubstances()) self.GPXtree.SetItemPyData( self.GPXtree.AppendItem(Id,text='Sample Parameters'), rd.Sample) self.GPXtree.SetItemPyData( self.GPXtree.AppendItem(Id,text='Models'),G2pdG.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,u'from '+reader.formatName+u' file',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. ''' # 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): '''Add entry to Notebook tree item ''' Id = GetGPXtreeItemId(self,self.root,'Notebook') data = self.GPXtree.GetItemPyData(Id) data.append('Notebook entry @ %s: %s'%(time.ctime(),text))
### Command logging ###########################################################
[docs] def OnMacroRecordStatus(self,event,setvalue=None): '''Called when the record macro menu item is used which toggles the value. Alternately a value to be set can be provided. Note that this routine is made more complex because on the Mac there are lots of menu items (listed in self.MacroStatusList) and this loops over all of them. ''' nextvalue = log.ShowLogStatus() != True if setvalue is not None: nextvalue = setvalue if nextvalue: log.LogOn() set2 = True else: log.LogOff() set2 = False for menuitem in self.MacroStatusList: menuitem.Check(set2)
def _init_Macro(self): '''Define the items in the macro menu. ''' menu = self.MacroMenu item = menu.Append( help='Start or stop recording of menu actions, etc.', id=wx.ID_ANY, kind=wx.ITEM_CHECK,text='Record actions') self.MacroStatusList.append(item) item.Check(log.ShowLogStatus()) self.Bind(wx.EVT_MENU, self.OnMacroRecordStatus, item) # this may only be of value for development work item = menu.Append( help='Show logged commands', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='Show log') def OnShowLog(event): print (70*'=') print ('List of logged actions') for i,line in enumerate(log.G2logList): if line: print ('%d %s'%(i,line)) print (70*'=') self.Bind(wx.EVT_MENU, OnShowLog, item) item = menu.Append( help='Clear logged commands', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='Clear log') def OnClearLog(event): log.G2logList=[None] self.Bind(wx.EVT_MENU, OnClearLog, item) item = menu.Append( help='Save logged commands to file', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='Save log') def OnSaveLog(event): defnam = os.path.splitext(os.path.split(self.GSASprojectfile)[1])[0]+'.gcmd' dlg = wx.FileDialog(self, 'Choose a file to save past actions', '.', defnam, 'GSAS-II cmd output (*.gcmd)|*.gcmd', wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT) dlg.CenterOnParent() try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() # make sure extension is correct filename = os.path.splitext(filename)[0]+'.gcmd' else: filename = None finally: dlg.Destroy() if filename: fp = open(filename,'wb') fp.write(str(len(log.G2logList)-1)+'\n') for item in log.G2logList: if item: cPickle.dump(item,fp) fp.close() self.Bind(wx.EVT_MENU, OnSaveLog, item) item = menu.Append( help='Load logged commands from file', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='Load log') def OnLoadLog(event): # this appends. Perhaps we should ask to clear? defnam = os.path.splitext( os.path.split(self.GSASprojectfile)[1])[0]+'.gcmd' dlg = wx.FileDialog(self, 'Choose an file to read saved actions', '.', defnam, 'GSAS-II cmd output (*.gcmd)|*.gcmd', wx.FD_OPEN) dlg.CenterOnParent() try: if dlg.ShowModal() == wx.ID_OK: filename = dlg.GetPath() # make sure extension is correct filename = os.path.splitext(filename)[0]+'.gcmd' else: filename = None finally: dlg.Destroy() if filename and os.path.exists(filename): fp = open(filename,'rb') lines = fp.readline() for i in range(int(lines)): log.G2logList.append(cPickle.load(fp)) fp.close() self.Bind(wx.EVT_MENU, OnLoadLog, item) item = menu.Append( help='Replay saved commands', id=wx.ID_ANY, kind=wx.ITEM_NORMAL,text='Replay log') self.Bind(wx.EVT_MENU, log.ReplayLog, item) # End of logging ############################################################## 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,'Column metadata test','Test Column (.par) metadata import') self.Bind(wx.EVT_MENU, self.OnColMetaTest, 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 GSASIIpath.GetConfigValue('Enable_logging'): self.MacroMenu = wx.Menu(title='') menubar.Append(menu=self.MacroMenu, title='Macro') self._init_Macro() 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') 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) self.mainPanel.SplitVertically(self.treePanel, self.dataWindow, 200) self.Status.SetStatusWidths([200,-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() #### init_vars ################################################################
[docs] def init_vars(self): ''' initialize default values for GSAS-II "global" variables (saved in main Frame) ''' 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 = [] 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.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'
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]: try: self.GSASprojectfile = os.path.splitext(arg[1])[0]+u'.gpx' except: 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 OnColMetaTest(self,event): 'Test the .par/.*lbls pair for contents' G2imG.testColumnMetadata(self)
[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 = [] 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 CopyDialog(wx.Dialog): '''Creates a dialog for copying control settings between data tree items''' def __init__(self,parent,title,text,data): wx.Dialog.__init__(self,parent,-1,title, pos=wx.DefaultPosition,style=wx.DEFAULT_DIALOG_STYLE) self.data = data panel = wx.Panel(self) mainSizer = wx.BoxSizer(wx.VERTICAL) topLabl = wx.StaticText(panel,-1,text) mainSizer.Add((10,10),1) mainSizer.Add(topLabl,0,wx.ALIGN_CENTER_VERTICAL|wx.LEFT,10) mainSizer.Add((10,10),1) ncols = len(data)/40+1 dataGridSizer = wx.FlexGridSizer(cols=ncols,hgap=2,vgap=2) for Id,item in enumerate(self.data): ckbox = wx.CheckBox(panel,Id,item[1]) ckbox.Bind(wx.EVT_CHECKBOX,self.OnCopyChange) dataGridSizer.Add(ckbox,0,wx.LEFT,10) mainSizer.Add(dataGridSizer,0,wx.EXPAND) OkBtn = wx.Button(panel,-1,"Ok") OkBtn.Bind(wx.EVT_BUTTON, self.OnOk) cancelBtn = wx.Button(panel,-1,"Cancel") cancelBtn.Bind(wx.EVT_BUTTON, self.OnCancel) btnSizer = wx.BoxSizer(wx.HORIZONTAL) btnSizer.Add((20,20),1) btnSizer.Add(OkBtn) btnSizer.Add((20,20),1) btnSizer.Add(cancelBtn) btnSizer.Add((20,20),1) mainSizer.Add(btnSizer,0,wx.EXPAND|wx.BOTTOM|wx.TOP, 10) panel.SetSizer(mainSizer) panel.Fit() self.Fit() def OnCopyChange(self,event): Id = event.GetId() self.data[Id][0] = self.FindWindowById(Id).GetValue() 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) def GetData(self): return self.data
[docs] class SumDialog(wx.Dialog): '''Allows user to supply scale factor(s) when summing data ''' 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 = [] 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: 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) try: if dlg.ShowModal() == wx.ID_OK: imSize = 0 result,scales = dlg.GetData() First = True Found = False for name,scale in zip(result,scales): if scale: 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 = G2IO.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 = np.amax(newImage) Imin = 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(None,'Enter a name for this phase','Phase Name Entry','New phase', style=wx.OK) 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(G2plt.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() 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 = [] 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: try: self.GSASprojectfile = os.path.splitext(filename)[0]+u'.gpx' except: 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 = [] 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) G2G.SaveConfigVars(config) self.LastGPXdir = pth
[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.GPXtree.SetItemText(self.root,'Project: ') self.GPXtree.DeleteChildren(self.root) self.dataWindow.ClearData() if len(self.HKL): self.HKL = [] self.Extinct = [] if self.G2plotNB.plotList: self.G2plotNB.clear() self.SetTitleByGPX() self.EnableRefineCommand() self.init_vars() G2obj.IndexAllIds({},{}) # clear old index info finally: dlg.Destroy()
[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. Runs only on Mac. ''' 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() G2script = os.path.join(os.path.split(__file__)[0],'GSASII.py') #GSASIIpath.MacStartGSASII(G2script,GSASprojectfile) G2G.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) 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 rescord last position of data & plot windows; saved to config.py file 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: 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.SetConfigValue(FrameInfo) 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\n'%('pos','dsp','esd','int','esd','sig','gam','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 \n" % \ (peak[0],dsp,esddsp,peak[2],esds['int'],np.sqrt(max(0.0001,peak[4]))/100.,peak[6]/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 'C' in Parms['Type'][0]: wave = G2mth.getWave(Parms) qMax = tth2q(fullLimits[1],wave) else: #'T'of qMax = tof2q(fullLimits[0],Parms['difC'][1]) 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:`GSASIIIO.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,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') # cPickle.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): Controls = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root, 'Controls')) 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=' Cite: B.H. Toby, IUCrJ, to be published')
[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 Controls = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root, 'Controls')) 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 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 = G2plt.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 = 'Detailed results are in ' + lst + '.lst\n' if 'GOF0' in Rvals and 'GOF' in Rvals: text += '\nFinal Reduced Chi^2: {:.3f} (before ref: {:.3f})\n'.format( Rvals['GOF']**2,Rvals['GOF0']**2) 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: Steepest descents dominates;'+ \ ' minimum may not have been reached or result may be false minimum.'+ \ ' You should reconsider which parameters you refine. Check covariance matrix.\n' text += '\nLoad new result?' dlg2 = wx.MessageDialog(self,text,'Refinement results, Rw =%.3f'%(Rw),wx.OK|wx.CANCEL) dlg2.CenterOnParent() try: if dlg2.ShowModal() == wx.ID_OK: if refPlotUpdate: refPlotUpdate({},restore=True) self.reloadFromGPX(rtext) else: if refPlotUpdate: refPlotUpdate({},restore=True) finally: dlg2.Destroy() 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'])
[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'): # Controls = self.GPXtree.GetItemPyData(GetGPXtreeItemId(self,self.root, 'Controls')) 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 = G2plt.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 fit: Rwp={:.3f}'.format(Rwp),wx.OK|wx.CANCEL) dlg2.CenterOnParent() try: if dlg2.ShowModal() == wx.ID_OK: if refPlotUpdate: refPlotUpdate({},restore=True) self.reloadFromGPX(rtext) else: if refPlotUpdate: refPlotUpdate({},restore=True) 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,newLeBail=False) 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['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 = 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): '''Deletes current data tree & reloads it from GPX file (after a refinemnt.) Done after events are completed to avoid crashes. :param rtext str: string info from caller to be put in Notebook after reload ''' self.GPXtree.DeleteChildren(self.root) self.HKL = [] 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) self.ResetPlots()
[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 self.OnFileSave(event) allerrors = {} allwarnings = {} 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 = G2plt.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: if refPlotUpdate: refPlotUpdate({},restore=True) self.PickIdText = None #force reload of PickId contents self.GPXtree.DeleteChildren(self.root) if len(self.HKL): self.HKL = [] 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) else: if refPlotUpdate: refPlotUpdate({},restore=True) finally: dlg.Destroy() else: self.ErrorDialog('Sequential refinement error',Msg)
[docs] def OnRunFprime(self,event): '''Run Fprime''' import fprime self.fprime = fprime.Fprime(self) self.fprime.Show()
[docs] def OnRunAbsorb(self,event): '''Run Absorb''' import Absorb self.absorb = Absorb.Absorb(self) self.absorb.Show()
[docs] def OnRunPlotXNFF(self,evnt): '''Run PlotXNFF''' 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' 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 data item window as well as the menu. Note that the same core menu items are used in all menus, but different items may be added depending on what data tree item (and for phases, the phase tab). Note that while the menus are created here, the binding for the menus is done later in various GSASII*GUI modules, where the functions to be called are defined. Use of the dataWindow scrolled panel: dataWindow has a “master” vertical BoxSizer: find it with G2frame.dataWindow.GetSizer() and always use it. A call to dataWindow.SetSizer() should not be needed. When placing a widget in the sizer that has its own scrolling (e.g. G2G.GSNoteBook, anything else?) that one widget should be placed in the sizer as G2frame.dataWindow.GetSizer().Add(G2frame.<obj>,1,wx.ALL|wx.EXPAND) [is wx.ALL superfluous here?] 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. Initial GUI draws to dataWindow will go through GSASIIdataGUI.SelectDataTreeItem(), which is called after any changes to data tree selection. SelectDataTreeItem places items in dataWindow or calls that do that. Before it calls those routines, it calls G2frame.dataWindow.ClearData() which deletes the contents of the master sizer. After the contents are posted a call is made to G2frame.dataWindow.SetDataSize() which repaints the window. For routines [such as GSASIIpwdGUI.UpdatePeakGrid()] that are called repeatedly to update the entire contents of dataWindow themselves, it is important to add calls to G2frame.dataWindow.ClearData() and G2frame.dataWindow.SetDataSize() at the beginning and end respectively to clear and refresh. This is not needed for GSNoteBook repaints, which seem to be working mostly automatically. If there is a problem, a call like wx.CallAfter(G2frame.phaseDisplay.SendSizeEvent) might be needed. There are some calls to G2frame.dataWindow.SendSizeEvent() that may be doing the same thing. ''' def __init__(self,parent): wx.ScrolledWindow.__init__(self,parent,wx.ID_ANY,size=parent.GetSize()) self.parent = parent 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.Unbind(wx.EVT_SIZE) #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
[docs] def OnResize(self,event): 'Used for grids to match ScrolledWindow size' event.Skip() Sizer = self.GetSizer() if not Sizer: return #if Sizer.GetItemCount() == 1: # not wx 2.8 if len(Sizer.GetChildren()) == 1: # if there is a single grid, resize it if isinstance(Sizer.GetItem(0).GetWindow(), G2G.GSGrid): Sizer.GetItem(0).GetWindow().SetSize(self.GetSize())
[docs] def SetDataSize(self): '''Sizes the contents of the dataWindow panel ''' Sizer = self.GetSizer() if not Sizer: print ('No sizer in dataWindow') if GSASIIpath.GetConfigValue('debug'): raise Exception return #if Sizer.GetItemCount() == 1: # not wx 2.8 if len(Sizer.GetChildren()) == 1: # handle cases with a single grid in DataWindow differently # note that Grid's scroll bars must be turned on with .SetScrollRate(10,10) # just after the call to .GSGrid() if isinstance(Sizer.GetItem(0).GetWindow(), G2G.GSGrid): self.Bind(wx.EVT_SIZE,self.OnResize) Sizer.GetItem(0).GetWindow().SetSize(self.GetSize()) self.SetAutoLayout(False) self.SetScrollRate(0,0) self.SendSizeEvent() return elif len(Sizer.GetChildren()) == 2: # case where there is a NoteBook & help button if isinstance(Sizer.GetItem(0).GetWindow(), G2G.GSNoteBook): # with wx4.2 (& 4.1?) AutoLayout causes all inner windows # to be made large and scrolling is done at outer window # this messes things up for grids inside notebooks (Reflection lists) # for this case turn off AutoLayout on dataWindow, but # use a Bind to redo Layout. This works for expansion but not # contraction of the window. def _onResize(event): self.Layout() event.Skip() self.Bind(wx.EVT_SIZE,_onResize) self.SetScrollRate(0,0) self.Layout() self.SetAutoLayout(False) return self.SetAutoLayout(True) self.SetScrollRate(10,10) self.SendSizeEvent()
[docs] def PrefillDataMenu(self,menu,empty=False): '''Create the "standard" part of data frame menus & add the dataWindow menu headings This menu duplicates the tree menu, but adds an extra help command for the current data item and a separator. ''' self.datamenu = menu self.GetTopLevelParent().FillMainMenu(menu,addhelp=False) # add the data tree menu items to the main menu if not empty: menu.Append(wx.Menu(title=''),title='|') # add a separator
[docs] def PostfillDataMenu(self,empty=False): '''Add the help menu to the menus associated with data tree items. ''' menu = self.datamenu G2frame = self.GetTopLevelParent() if not empty: menu.Append(wx.Menu(title=''),title='|') # add another separator HelpMenu=G2G.MyHelp(G2frame,includeTree=True, morehelpitems=[('&Tutorials','Tutorials'),]) menu.Append(menu=HelpMenu,title='&Help')
#### 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 = wx.MenuBar() self.PrefillDataMenu(self.ControlsMenu,empty=True) self.PostfillDataMenu(empty=True) # Notebook self.DataNotebookMenu = wx.MenuBar() self.PrefillDataMenu(self.DataNotebookMenu,empty=True) self.PostfillDataMenu(empty=True) # Comments self.DataCommentsMenu = wx.MenuBar() self.PrefillDataMenu(self.DataCommentsMenu,empty=True) self.PostfillDataMenu(empty=True) # 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',) 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) G2G.Define_wxId('wxID_SHOWISO') self.ConstraintEdit.Append(G2G.wxID_SHOWISO,'Show ISODISTORT modes', 'Show ISODISTORT mode values for all phases') self.ConstraintEdit.Enable(G2G.wxID_SHOWISO,False) self.PostfillDataMenu() # Rigid bodies G2G.Define_wxId('wxID_RIGIDBODYADD', 'wxID_DRAWDEFINERB', 'wxID_RIGIDBODYIMPORT', 'wxID_RESIDUETORSSEQ', 'wxID_VECTORBODYADD', 'wxID_RIGIDBODYSAVE','wxID_RIGIDBODYIMP','wxID_RESBODYSAV','wxID_RESBODYRD', 'wxID_VECTORBODYIMP','wxID_VECTORBODYSAV','wxID_VECTORBODYRD','wxID_VECTORBODYEXTD','wxID_SPINBODYADD') 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() 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() 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() # Restraints G2G.Define_wxId('wxID_RESTRAINTADD', 'wxID_RESTDELETE', 'wxID_RESRCHANGEVAL', 'wxID_RESTCHANGEESD', 'wxID_AARESTRAINTADD', 'wxID_AARESTRAINTPLOT','wxID_USEMOGUL') 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() # 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',) 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') G2G.Define_wxId('wxID_UPDATESEQSEL') self.SequentialFile.Append(G2G.wxID_UPDATESEQSEL,'Update phase from row', 'Update phase information from selected row') G2G.Define_wxId('wxID_EDITSEQSELPHASE') 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': G2G.Define_wxId('wxID_XPORTSEQFCIF') submenu.Append(G2G.wxID_XPORTSEQFCIF,'... as full CIF', 'Save all sequential refinement results as a CIF file') 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 G2G.Define_wxId('wxID_XPORTSEQCSV') self.SequentialEx.Append(G2G.wxID_XPORTSEQCSV,'Save table as CSV', 'Save all sequential refinement results as a CSV spreadsheet file') self.PostfillDataMenu() #Cluster analysis - what do I need here? 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_MERGEHKL', 'wxID_PWDHKLPLOT', 'wxID_PWD3DHKLPLOT','wxID_3DALLHKLPLOT','wxID_1DHKLSTICKPLOT') 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.PostfillDataMenu() # HKLF - wxIDs defined in PWDR & SASD above 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_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_PWD3DHKLPLOT,'Plot 3D HKLs','Plot HKLs from single crystal data in 3D') self.ErrorAnal.Append(G2G.wxID_3DALLHKLPLOT,'Plot all 3D HKLs','Plot HKLs from all single crystal data in 3D') # self.ErrorAnal.Append(G2G.wxID_PWDCOPY,'Copy params','Copy of HKLF parameters') #unused self.PostfillDataMenu() # PWDR / Limits G2G.Define_wxId('wxID_LIMITCOPY', 'wxID_ADDEXCLREGION',) 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_ADDEXCLREGION,'Add exclude', 'Add excluded region - select a point on plot; drag to adjust') self.PostfillDataMenu() # PWDR / Background G2G.Define_wxId('wxID_BACKCOPY', 'wxID_BACKFLAGCOPY','wxID_MAKEBACKRDF', 'wxID_RESCALEALL','wxID_BACKPEAKSMOVE','wxID_BACKSAVE','wxID_BACKLOAD') 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['Del'] = wx.NewId() self.BackFixed.AppendRadioItem(self.wxID_BackPts['Del'],'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() # PWDR / Instrument Parameters G2G.Define_wxId('wxID_INSTPRMRESET','wxID_INSTCOPY','wxID_INSTFLAGCOPY','wxID_INSTLOAD', 'wxID_INSTSAVE', 'wxID_INST1VAL', 'wxID_INSTCALIB', 'wxID_INSTSAVEALL', 'wxID_INSTSHOWMULT',) 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() # PWDR / Sample Parameters G2G.Define_wxId('wxID_SAMPLECOPY', 'wxID_SAMPLECOPYSOME', 'wxID_SAMPLEFLAGCOPY','wxID_SAMPLESAVE', 'wxID_SAMPLELOAD', 'wxID_SETSCALE', 'wxID_SAMPLE1VAL', 'wxID_ALLSAMPLELOAD',) 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.PostfillDataMenu() self.SetScale.Enable(False) # 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') 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.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' ) G2G.Define_wxId('wxID_DELPEAKS') 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.') G2G.Define_wxId('wxID_SETUNVARIEDWIDTHS') 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) G2G.Define_wxId('wxID_XTRAPEAKMODE') 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) # PWDR / Index Peak List G2G.Define_wxId('wxID_INDXRELOAD','wxID_INDEXSAVE','wxID_INDEXEXPORTDICVOL') 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.PostfillDataMenu() # 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','wxID_LATSYM') 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 Bilboa "Lattice Symmetry" to find higher symmetry cells') G2G.Define_wxId('wxID_NISTLATSYM') self.IndexEdit.Append(G2G.wxID_NISTLATSYM,'Cell Symmetry Search-NIST*LATTICE', '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') 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') G2G.Define_wxId('wxID_SHOWGENHKLS') self.IndexEdit.Append(G2G.wxID_SHOWGENHKLS,'Show reflections','Show generated reflection positions on console') 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) # PWDR / Reflection Lists G2G.Define_wxId('wxID_SELECTPHASE','wxID_SHOWHIDEEXTINCT','wxID_WILSONSTAT','wxID_CSVFROMTABLE' ) #some wxIDs defined above in PWDR & SASD 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() # SASD & REFD / Limits G2G.Define_wxId('wxID_SASDLIMITCOPY', ) 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() # SASD / Instrument Parameters G2G.Define_wxId('wxID_SASDINSTCOPY',) 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() #SASD & REFL/ Substance editor G2G.Define_wxId('wxID_LOADSUBSTANCE','wxID_RELOADSUBSTANCES','wxID_ADDSUBSTANCE','wxID_COPYSUBSTANCE', 'wxID_DELETESUBSTANCE','wxID_ELEMENTADD', 'wxID_ELEMENTDELETE',) 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() # SASD/ Models G2G.Define_wxId('wxID_MODELCOPY', 'wxID_MODELFIT', 'wxID_MODELADD','wxID_MODELUNDO', 'wxID_MODELFITALL', 'wxID_MODELCOPYFLAGS','wxID_MODELPLOT',) 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() # REFD/ Models - wxIDs as for SASD/Models 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() # 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') 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') 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') self.PostfillDataMenu() # 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',) 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_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; NB: slow') 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() # 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',) 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() # PDF / PDF Controls G2G.Define_wxId('wxID_PDFCOPYCONTROLS', 'wxID_PDFSAVECONTROLS', 'wxID_PDFLOADCONTROLS', 'wxID_PDFCOMPUTE', 'wxID_PDFCOMPUTEALL', 'wxID_PDFADDELEMENT', 'wxID_PDFDELELEMENT',) 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() # PDF / PDF Peaks G2G.Define_wxId('wxID_PDFPKSFIT','wxID_PDFPKSFITALL', 'wxID_PDFCOPYPEAKS', 'wxID_CLEARPDFPEAKS',) 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() # 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') 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) 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') self.GeneralCalc.Append(G2G.wxID_VALIDPROTEIN,'Protein quality','Protein quality analysis') self.PostfillDataMenu() # 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_ATOMSROTATE', 'wxID_ATOMSDENSITY','wxID_ATOMSBNDANGLHIST', '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 viewpoint','Set the viewpoint to be position of 1st selected atom') submenu.Append(G2G.wxID_ATOMMOVE,'Move atom to view point','Move a single atom to viewpoint in plot') submenu.Append(G2G.wxID_ATOMSEDITINSERT,'Insert atom','Inserts an H atom before all selected atoms') submenu.Append(G2G.wxID_ATOMVIEWINSERT,'Insert viewpoint','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 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_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,'ISODISTORT mode values', 'Compute values of ISODISTORT modes from atom parameters') 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 Dysonmia','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,'Select atoms','Select atoms for deformation study') 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', ) 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') # TODO: removed until it can be made to do something self.DrawAtomEdit.Append(G2G.wxID_DRAWVIEWPOINT,'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_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') G2G.Define_wxId('wxID_DRAWVOIDMAP') self.DrawAtomEdit.Append(G2G.wxID_DRAWVOIDMAP,'Create void map','Create a map of locations outside of any VDW radius') 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') 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') 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)') 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,'Copy rigid body parms', 'Copy 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()
# end of GSAS-II menu definitions #### 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 OnNoteBook(event): event.Skip() data = text.GetValue().split('\n') G2frame.GPXtree.SetItemPyData(GetGPXtreeItemId(G2frame,G2frame.root,'Notebook'),data) if 'nt' not in os.name: text.AppendText('\n') G2frame.dataWindow.ClearData() bigSizer = wx.BoxSizer(wx.VERTICAL) topSizer = wx.BoxSizer(wx.HORIZONTAL) topSizer.Add(wx.StaticText(G2frame.dataWindow,-1,' Add notes on project here: '),0) topSizer.Add((250,-1)) topSizer.Add(G2G.HelpButton(G2frame.dataWindow,helpIndex='Notebook')) bigSizer.Add(topSizer) text = wx.TextCtrl(G2frame.dataWindow,wx.ID_ANY, style=wx.TE_MULTILINE|wx.TE_PROCESS_ENTER | wx.TE_DONTWRAP) text.Bind(wx.EVT_TEXT_ENTER,OnNoteBook) text.Bind(wx.EVT_KILL_FOCUS,OnNoteBook) for line in data: text.AppendText(line+"\n") text.AppendText('Notebook entry @ '+time.ctime()+"\n") bigSizer.Add(text,1,wx.ALL|wx.EXPAND) bigSizer.Layout() bigSizer.FitInside(G2frame.dataWindow) G2frame.dataWindow.SetSizer(bigSizer) G2frame.dataWindow.SetDataSize() G2frame.SendSizeEvent()
#### Comments ###############################################################
[docs] def UpdateComments(G2frame,data): '''Place comments into the data window ''' lines = "" for line in data: if 'phoenix' in wx.version() and hasattr(line,'decode'): lines += line.decode('latin-1').rstrip()+'\n' else: lines += line.rstrip()+'\n' try: text = wx.StaticText(G2frame.dataWindow,wx.ID_ANY,lines) except: text = wx.StaticText(G2frame.dataWindow,wx.ID_ANY, G2obj.StripUnicode(lines)) G2frame.dataWindow.GetSizer().Add(text,1,wx.ALL|wx.EXPAND)
#### 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':0.05} 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) bigSizer = wx.BoxSizer(wx.HORIZONTAL) mainSizer = wx.BoxSizer(wx.VERTICAL) mainSizer.Add((5,5),0) subSizer = wx.BoxSizer(wx.HORIZONTAL) subSizer.Add((-1,-1),1,wx.EXPAND) subSizer.Add(wx.StaticText(G2frame.dataWindow,label='Refinement Controls'),0,WACV) subSizer.Add((-1,-1),1,wx.EXPAND) mainSizer.Add(subSizer,0,wx.EXPAND) 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) bigSizer.Add(mainSizer) bigSizer.Add(G2G.HelpButton(G2frame.dataWindow,helpIndex='Controls')) bigSizer.Layout() bigSizer.FitInside(G2frame.dataWindow) G2frame.dataWindow.SetSizer(bigSizer) G2frame.dataWindow.SetDataSize() G2frame.SendSizeEvent()
#### Main PWDR panel ########################################################
[docs] def UpdatePWHKPlot(G2frame,kind,item): '''Called when the 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''' 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[:], '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''' 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)) dlg = MergeDialog(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 = {} for ih,hkl in enumerate(refList): if str(hkl[:3+Super]) not in HKLdict: HKLdict[str(hkl[:3+Super])] = [hkl[:3+Super],[hkl[3+Super:],]] else: HKLdict[str(hkl[:3+Super])][1].append(hkl[3+Super:]) dlg.Update(ih) dlg.Destroy() mergeRef = [] dlg = wx.ProgressDialog('Processing merge','',len(HKLdict)+1, style = wx.PD_ELAPSED_TIME|wx.PD_AUTO_HIDE) sumDf = 0. sumFo = 0. for ih,hkl in enumerate(HKLdict): HKL = HKLdict[hkl] 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) 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() 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 OnErrorAnalysis(event): '''Plots an "Abrams" plot - sorted delta/sig across data set. Should be straight line of slope 1 - never is''' G2plt.PlotDeltSig(G2frame,kind) # 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 = -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) 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, 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) if G2frame.dataWindow: G2frame.dataWindow.ClearData() mainSizer = wx.BoxSizer(wx.VERTICAL) 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': wtSizer.Add(wx.StaticText(G2frame.dataWindow,label=' Data "Surprise" factor: %.3f'%S)) wtSizer.Add((-1,-1),1,wx.EXPAND) wtSizer.Add(G2G.HelpButton(G2frame.dataWindow,helpIndex=G2frame.dataWindow.helpKey)) 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}% to Chi**2" 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] 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.dataWindow.SetSizer(mainSizer) G2frame.GPXtree.SetItemPyData(item,data) G2frame.PatternId = item if kind in ['PWDR','SASD','REFD',]: NewPlot = True if 'Contour' in dir(G2frame) and G2frame.Contour: pass elif 'xylim' in dir(G2frame): NewPlot = False G2plt.PlotPatterns(G2frame,plotType=kind,newPlot=NewPlot) 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'] 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, '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]))], '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 'Lastshft' not in data: return if data['Lastshft'] is None: return shftesd = data['Lastshft']/data['sig'] G2plt.PlotNamedFloatHBarGraph(G2frame,shftesd,data['varyList'],Xlabel='Total shift/esd', Ylabel='Variables',Title='Total shift/esd',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() SetDataMenuBar(G2frame) G2frame.SetTitleByGPX() G2frame.PickId = item G2frame.PickIdText = None parentID = G2frame.root if item == G2frame.root: G2frame.dataWindow.ClearData() G2frame.helpKey = "Data tree" G2frame.dataWindow.GetSizer().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) for i in G2frame.Refine: i.Enable(True) UpdateControls(G2frame,data) 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 = '' mainSizer = wx.BoxSizer(wx.HORIZONTAL) subSizer = wx.BoxSizer(wx.VERTICAL) if 'Rvals' in data: lbl = 'Refinement results' else: lbl = 'No refinement results' + 50*' ' subSizer.Add(wx.StaticText(G2frame.dataWindow,label=lbl)) if 'Rvals' in data: Nvars = len(data['varyList']) Rvals = data['Rvals'] text = ('\nTotal residuals after last refinement: \n'+ '\twR = {:.3f}\n\tchi**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) subSizer.Add(wx.StaticText(G2frame.dataWindow,wx.ID_ANY,text)) if Rvals.get('RestraintSum',0) > 0: chisq_data = (Rvals['chisq']-Rvals['RestraintSum'])/(Rvals['Nobs']-Rvals['Nvars']) lbl = '\nData-only residuals (without restraints)' lbl += f'\n\tGOF = {np.sqrt(chisq_data):.2f}' lbl += f'\n\tReduced χ**2 = {chisq_data:.2f}' subSizer.Add(wx.StaticText(G2frame.dataWindow,label=lbl)) if 'Lastshft' in data and not data['Lastshft'] is None: showShift = wx.Button(G2frame.dataWindow,label='Show shift/esd plot') showShift.Bind(wx.EVT_BUTTON,OnShowShift) subSizer.Add((-1,10)) subSizer.Add(showShift) mainSizer.Add(subSizer) mainSizer.Add(G2G.HelpButton(G2frame.dataWindow,helpIndex='Covariance')) G2frame.dataWindow.GetSizer().Add(mainSizer) 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 UpdatePWHKPlot(G2frame,'HKLF',item) elif G2frame.GPXtree.GetItemText(item).startswith('PDF '): G2frame.PatternId = item for i in G2frame.ExportPDF: i.Enable(True) # this should be done on .gpx load; is done on OnMakePDFs (GSASII.py) data = G2frame.GPXtree.GetItemPyData(GetGPXtreeItemId(G2frame,item,'PDF Controls')) G2pdG.UpdatePDFGrid(G2frame,data) if len(data['G(R)']): G2plt.PlotISFG(G2frame,data,plotType='G(R)') elif G2frame.GPXtree.GetItemText(item) == 'Phases': if 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: G2frame.dataWindow.GetSizer().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()) == 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] = {} G2restG.UpdateRestraints(G2frame,data,phaseName) else: G2frame.GPXtree.Expand(item) G2frame.dataWindow.GetSizer().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': for i in G2frame.ExportPDF: i.Enable(True) # this should be done on .gpx load; is done on OnMakePDFs (GSASII.py) 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) 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') # import imp # imp.reload(G2phG) # end debug stuff G2phG.UpdatePhaseData(G2frame,item,data) elif G2frame.GPXtree.GetItemText(parentID) == 'Restraints': data = G2frame.GPXtree.GetItemPyData(parentID) 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) for i in G2frame.ExportPeakList: i.Enable(True) 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) newPlot = False if hasattr(G2frame,'Contour'): if G2frame.Contour: G2frame.Contour = False newPlot = True G2plt.PlotPatterns(G2frame,newPlot) elif G2frame.GPXtree.GetItemText(item) == 'Background': G2frame.PatternId = G2frame.GPXtree.GetItemParent(item) data = G2frame.GPXtree.GetItemPyData(item) G2pdG.UpdateBackground(G2frame,data) G2plt.PlotPatterns(G2frame,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) G2plt.PlotPatterns(G2frame,plotType=datatype,newPlot=True) elif G2frame.GPXtree.GetItemText(item) == 'Instrument Parameters': 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) G2plt.PlotPatterns(G2frame,plotType=prfx1) 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) G2plt.PlotPatterns(G2frame,True,plotType=datatype) elif G2frame.GPXtree.GetItemText(item) == 'Index Peak List': G2frame.PatternId = G2frame.GPXtree.GetItemParent(item) for i in G2frame.ExportPeakList: i.Enable(True) data = G2frame.GPXtree.GetItemPyData(item) #patch if len(data) != 2: data = [data,[]] G2frame.GPXtree.SetItemPyData(item,data) #end patch G2pdG.UpdateIndexPeaksGrid(G2frame,data) if 'PKS' in G2frame.GPXtree.GetItemText(G2frame.PatternId): G2plt.PlotPowderLines(G2frame) else: newPlot = False if hasattr(G2frame,'Contour'): if G2frame.Contour: G2frame.Contour = False newPlot = True G2plt.PlotPatterns(G2frame,newPlot) 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 # debug stuff #if GSASIIpath.GetConfigValue('debug'): # import imp # imp.reload(G2pdG) # for testing changes # print('debug: reloaded',G2pdG) # end debug stuff G2pdG.UpdateUnitCellsGrid(G2frame,data) if 'PKS' in G2frame.GPXtree.GetItemText(G2frame.PatternId): G2plt.PlotPowderLines(G2frame) else: newPlot = False if hasattr(G2frame,'Contour'): if G2frame.Contour: G2frame.Contour = False newPlot = True G2plt.PlotPatterns(G2frame,newPlot) G2plt.PlotPatterns(G2frame) elif G2frame.GPXtree.GetItemText(item) == 'Reflection Lists': #powder reflections G2frame.dataWindow.HideShow.Enable(False) 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) newPlot = False if hasattr(G2frame,'Contour'): if G2frame.Contour: G2frame.Contour = False newPlot = True G2plt.PlotPatterns(G2frame,newPlot) elif G2frame.GPXtree.GetItemText(item) == 'Reflection List': #HKLF reflections G2frame.dataWindow.HideShow.Enable(True) 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) 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)
[docs] def SetDataMenuBar(G2frame,menu=None): '''Set the menu for the data frame. Note that data frame items do not have menus, for these (menu=None) display the standard main menu for the data tree window. ''' if menu is None: G2frame.SetMenuBar(G2frame.GSASIIMenu) else: G2frame.SetMenuBar(menu)
[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()