| 1 | #!/usr/bin/env python |
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| 2 | # -*- coding: utf-8 -*- |
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| 3 | #G2cif |
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| 4 | ########### SVN repository information ################### |
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| 5 | # $Date: 2013-07-22 20:57:37 -0500 (Mon, 22 Jul 2013) $ |
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| 6 | # $Author: toby $ |
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| 7 | # $Revision: 1006 $ |
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| 8 | # $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/exports/G2cif.py $ |
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| 9 | # $Id: G2cif.py 1006 2013-07-23 01:57:37Z toby $ |
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| 10 | ########### SVN repository information ################### |
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| 11 | '''Code to export a GSAS-II project as a CIF |
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| 12 | The heavy lifting is done in method export |
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| 13 | ''' |
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| 14 | |
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| 15 | # TODO: set def names for phase/hist save & load, bond pub flags,... |
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| 16 | |
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| 17 | import datetime as dt |
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| 18 | import os.path |
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| 19 | import sys |
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| 20 | import numpy as np |
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| 21 | import cPickle |
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| 22 | import copy |
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| 23 | import wx |
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| 24 | import wx.lib.scrolledpanel as wxscroll |
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| 25 | import wx.lib.resizewidget as rw |
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| 26 | import GSASIIpath |
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| 27 | GSASIIpath.SetVersionNumber("$Revision: 1006 $") |
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| 28 | import GSASIIIO as G2IO |
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| 29 | #reload(G2IO) |
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| 30 | import GSASIIgrid as G2gd |
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| 31 | reload(G2gd) |
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| 32 | import GSASIIstrIO as G2stIO |
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| 33 | #reload(G2stIO) |
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| 34 | #import GSASIImapvars as G2mv |
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| 35 | import GSASIImath as G2mth |
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| 36 | #reload(G2mth) |
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| 37 | import GSASIIlattice as G2lat |
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| 38 | import GSASIIspc as G2spc |
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| 39 | #reload(G2spc) |
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| 40 | import GSASIIphsGUI as G2pg |
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| 41 | #reload(G2pg) |
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| 42 | import GSASIIstrMain as G2stMn |
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| 43 | #reload(G2stMn) |
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| 44 | |
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| 45 | DEBUG = False #True to skip printing of reflection/powder profile lists |
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| 46 | |
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| 47 | CIFdic = None |
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| 48 | |
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| 49 | def getCallerDocString(): # for development |
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| 50 | "Return the calling function's doc string" |
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| 51 | import inspect as ins |
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| 52 | for item in ins.stack()[1][0].f_code.co_consts: |
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| 53 | if type(item) is str: |
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| 54 | return item |
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| 55 | else: |
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| 56 | return '?' |
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| 57 | |
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| 58 | #=============================================================================== |
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| 59 | # misc CIF utilities |
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| 60 | #=============================================================================== |
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| 61 | def PickleCIFdict(fil): |
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| 62 | '''Loads a CIF dictionary, cherry picks out the items needed |
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| 63 | by local code and sticks them into a python dict and writes |
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| 64 | that dict out as a cPickle file for later reuse. |
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| 65 | If the write fails a warning message is printed, |
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| 66 | but no exception occurs. |
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| 67 | |
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| 68 | :param str fil: file name of CIF dictionary, will usually end |
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| 69 | in .dic |
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| 70 | :returns: the dict with the definitions |
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| 71 | ''' |
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| 72 | import CifFile as cif # PyCifRW from James Hester |
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| 73 | cifdic = {} |
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| 74 | dictobj = cif.CifDic(fil) |
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| 75 | if DEBUG: print('loaded '+str(fil)) |
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| 76 | for item in dictobj.keys(): |
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| 77 | cifdic[item] = {} |
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| 78 | for j in ( |
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| 79 | '_definition','_type', |
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| 80 | '_enumeration', |
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| 81 | '_enumeration_detail', |
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| 82 | '_enumeration_range'): |
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| 83 | if dictobj[item].get(j): |
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| 84 | cifdic[item][j] = dictobj[item][j] |
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| 85 | try: |
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| 86 | fil = os.path.splitext(fil)[0]+'.cpickle' |
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| 87 | fp = open(fil,'w') |
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| 88 | cPickle.dump(cifdic,fp) |
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| 89 | fp.close() |
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| 90 | if DEBUG: print('wrote '+str(fil)) |
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| 91 | except: |
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| 92 | print ('Unable to write '+str(fil)) |
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| 93 | return cifdic |
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| 94 | |
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| 95 | def LoadCIFdic(): |
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| 96 | '''Create a composite core+powder CIF lookup dict containing |
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| 97 | information about all items in the CIF dictionaries, loading |
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| 98 | pickled files if possible. The routine looks for files |
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| 99 | named cif_core.cpickle and cif_pd.cpickle in every |
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| 100 | directory in the path and if they are not found, files |
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| 101 | cif_core.dic and/or cif_pd.dic are read. |
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| 102 | |
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| 103 | :returns: the dict with the definitions |
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| 104 | ''' |
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| 105 | cifdic = {} |
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| 106 | for ftyp in "cif_core","cif_pd": |
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| 107 | for loc in sys.path: |
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| 108 | fil = os.path.join(loc,ftyp+".cpickle") |
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| 109 | if not os.path.exists(fil): continue |
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| 110 | fp = open(fil,'r') |
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| 111 | try: |
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| 112 | cifdic.update(cPickle.load(fp)) |
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| 113 | if DEBUG: print('reloaded '+str(fil)) |
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| 114 | break |
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| 115 | finally: |
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| 116 | fp.close() |
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| 117 | else: |
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| 118 | for loc in sys.path: |
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| 119 | fil = os.path.join(loc,ftyp+".dic") |
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| 120 | if not os.path.exists(fil): continue |
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| 121 | #try: |
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| 122 | if True: |
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| 123 | cifdic.update(PickleCIFdict(fil)) |
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| 124 | break |
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| 125 | #except: |
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| 126 | # pass |
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| 127 | else: |
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| 128 | print('Could not load '+ftyp+' dictionary') |
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| 129 | return cifdic |
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| 130 | |
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| 131 | class CIFdefHelp(wx.Button): |
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| 132 | '''Create a help button that displays help information on |
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| 133 | the current data item |
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| 134 | |
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| 135 | :param parent: the panel which will be the parent of the button |
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| 136 | :param str msg: the help text to be displayed |
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| 137 | :param wx.Dialog helpwin: Frame for CIF editing dialog |
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| 138 | :param wx.TextCtrl helptxt: TextCtrl where help text is placed |
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| 139 | ''' |
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| 140 | def __init__(self,parent,msg,helpwin,helptxt): |
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| 141 | wx.Button.__init__(self,parent,wx.ID_HELP) |
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| 142 | self.Bind(wx.EVT_BUTTON,self._onPress) |
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| 143 | self.msg=msg |
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| 144 | self.parent = parent |
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| 145 | #self.helpwin = self.parent.helpwin |
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| 146 | self.helpwin = helpwin |
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| 147 | self.helptxt = helptxt |
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| 148 | def _onPress(self,event): |
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| 149 | 'Respond to a button press by displaying the requested text' |
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| 150 | try: |
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| 151 | #helptxt = self.helptxt |
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| 152 | ow,oh = self.helptxt.GetSize() |
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| 153 | self.helptxt.SetLabel(self.msg) |
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| 154 | w,h = self.helptxt.GetSize() |
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| 155 | if h > oh: |
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| 156 | self.helpwin.GetSizer().Fit(self.helpwin) |
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| 157 | except: # error posting help, ignore |
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| 158 | return |
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| 159 | |
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| 160 | def CIF2dict(cf): |
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| 161 | '''copy the contents of a CIF out from a PyCifRW block object |
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| 162 | into a dict |
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| 163 | |
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| 164 | :returns: cifblk, loopstructure where cifblk is a dict with |
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| 165 | CIF items and loopstructure is a list of lists that defines |
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| 166 | which items are in which loops. |
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| 167 | ''' |
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| 168 | blk = cf.keys()[0] # assume templates are a single CIF block, use the 1st |
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| 169 | loopstructure = cf[blk].loopnames()[:] # copy over the list of loop contents |
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| 170 | dblk = {} |
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| 171 | for item in cf[blk].keys(): # make a copy of all the items in the block |
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| 172 | dblk[item] = cf[blk][item] |
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| 173 | return dblk,loopstructure |
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| 174 | |
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| 175 | def dict2CIF(dblk,loopstructure,blockname='Template'): |
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| 176 | '''Create a PyCifRW CIF object containing a single CIF |
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| 177 | block object from a dict and loop structure list. |
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| 178 | |
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| 179 | :param dblk: a dict containing values for each CIF item |
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| 180 | :param list loopstructure: a list of lists containing the contents of |
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| 181 | each loop, as an example:: |
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| 182 | |
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| 183 | [ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]] |
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| 184 | |
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| 185 | this describes a CIF with this type of structure:: |
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| 186 | |
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| 187 | loop_ _a _b <a1> <b1> <a2> ... |
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| 188 | loop_ _c <c1> <c2>... |
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| 189 | loop _d_1 _d_2 _d_3 ... |
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| 190 | |
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| 191 | Note that the values for each looped CIF item, such as _a, |
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| 192 | are contained in a list, for example as cifblk["_a"] |
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| 193 | |
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| 194 | :param str blockname: an optional name for the CIF block. |
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| 195 | Defaults to 'Template' |
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| 196 | |
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| 197 | :returns: the newly created PyCifRW CIF object |
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| 198 | ''' |
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| 199 | |
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| 200 | import CifFile as cif # PyCifRW from James Hester |
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| 201 | # compile a 'list' of items in loops |
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| 202 | loopnames = set() |
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| 203 | for i in loopstructure: |
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| 204 | loopnames |= set(i) |
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| 205 | # create a new block |
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| 206 | newblk = cif.CifBlock() |
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| 207 | # add the looped items |
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| 208 | for keys in loopstructure: |
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| 209 | vals = [] |
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| 210 | for key in keys: |
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| 211 | vals.append(dblk[key]) |
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| 212 | newblk.AddCifItem(([keys],[vals])) |
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| 213 | # add the non-looped items |
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| 214 | for item in dblk: |
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| 215 | if item in loopnames: continue |
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| 216 | newblk[item] = dblk[item] |
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| 217 | # create a CIF and add the block |
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| 218 | newcf = cif.CifFile() |
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| 219 | newcf[blockname] = newblk |
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| 220 | return newcf |
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| 221 | |
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| 222 | |
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| 223 | class EditCIFtemplate(wx.Dialog): |
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| 224 | '''Create a dialog for editing a CIF template |
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| 225 | |
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| 226 | :param wx.Frame parent: parent frame or None |
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| 227 | :param cifblk: dict or PyCifRW block containing values for each CIF item |
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| 228 | :param list loopstructure: a list of lists containing the contents of |
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| 229 | each loop, as an example:: |
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| 230 | |
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| 231 | [ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]] |
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| 232 | |
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| 233 | this describes a CIF with this type of structure:: |
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| 234 | |
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| 235 | loop_ _a _b <a1> <b1> <a2> ... |
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| 236 | loop_ _c <c1> <c2>... |
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| 237 | loop _d_1 _d_2 _d_3 ... |
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| 238 | |
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| 239 | Note that the values for each looped CIF item, such as _a, |
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| 240 | are contained in a list, for example as cifblk["_a"] |
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| 241 | ''' |
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| 242 | def __init__(self,parent,cifblk,loopstructure): |
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| 243 | OKbuttons = [] |
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| 244 | self.cifblk = cifblk |
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| 245 | self.loopstructure = loopstructure |
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| 246 | self.newfile = None |
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| 247 | global CIFdic # once this is loaded, keep it around |
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| 248 | if CIFdic is None: |
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| 249 | CIFdic = LoadCIFdic() |
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| 250 | wx.Dialog.__init__(self,parent,style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER) |
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| 251 | |
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| 252 | # define widgets that will be needed during panel creation |
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| 253 | self.helptxt = wx.StaticText(self,wx.ID_ANY,"") |
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| 254 | savebtn = wx.Button(self, wx.ID_CLOSE, "Save as template") |
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| 255 | OKbuttons.append(savebtn) |
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| 256 | savebtn.Bind(wx.EVT_BUTTON,self._onClose) |
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| 257 | OKbtn = wx.Button(self, wx.ID_OK, "Use") |
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| 258 | OKbtn.SetDefault() |
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| 259 | OKbuttons.append(OKbtn) |
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| 260 | |
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| 261 | self.SetTitle('Edit items in CIF template') |
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| 262 | vbox = wx.BoxSizer(wx.VERTICAL) |
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| 263 | cpnl = EditCIFpanel(self,cifblk,loopstructure,CIFdic,OKbuttons,size=(300,300)) |
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| 264 | vbox.Add(cpnl, 1, wx.ALIGN_LEFT|wx.ALL|wx.EXPAND, 0) |
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| 265 | G2gd.HorizontalLine(vbox,self) |
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| 266 | vbox.Add(self.helptxt, 0, wx.EXPAND|wx.ALL, 5) |
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| 267 | G2gd.HorizontalLine(vbox,self) |
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| 268 | btnsizer = wx.BoxSizer(wx.HORIZONTAL) |
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| 269 | btn = wx.Button(self, wx.ID_CANCEL) |
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| 270 | btnsizer.Add(btn,0,wx.ALIGN_CENTER|wx.ALL) |
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| 271 | btnsizer.Add(savebtn,0,wx.ALIGN_CENTER|wx.ALL) |
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| 272 | btnsizer.Add(OKbtn,0,wx.ALIGN_CENTER|wx.ALL) |
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| 273 | vbox.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5) |
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| 274 | self.SetSizer(vbox) |
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| 275 | vbox.Fit(self) |
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| 276 | def Post(self): |
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| 277 | '''Display the dialog |
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| 278 | |
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| 279 | :returns: True, unless Cancel has been pressed. |
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| 280 | ''' |
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| 281 | return (self.ShowModal() == wx.ID_OK) |
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| 282 | def _onClose(self,event): |
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| 283 | 'Save CIF entries in a template file' |
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| 284 | dlg = wx.FileDialog( |
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| 285 | self, message="Save as CIF template", |
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| 286 | defaultDir=os.getcwd(), |
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| 287 | defaultFile="", |
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| 288 | wildcard="CIF (*.cif)|*.cif", |
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| 289 | style=wx.SAVE | wx.CHANGE_DIR |
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| 290 | ) |
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| 291 | val = (dlg.ShowModal() == wx.ID_OK) |
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| 292 | fil = dlg.GetPath() |
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| 293 | dlg.Destroy() |
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| 294 | if val: # ignore a Cancel button |
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| 295 | fil = os.path.splitext(fil)[0]+'.cif' # force extension |
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| 296 | fp = open(fil,'w') |
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| 297 | newcf = dict2CIF(self.cifblk,self.loopstructure) |
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| 298 | fp.write(newcf.WriteOut()) |
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| 299 | fp.close() |
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| 300 | self.newfile = fil |
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| 301 | self.EndModal(wx.ID_OK) |
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| 302 | |
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| 303 | class EditCIFpanel(wxscroll.ScrolledPanel): |
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| 304 | '''Creates a scrolled panel for editing CIF template items |
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| 305 | |
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| 306 | :param wx.Frame parent: parent frame where panel will be placed |
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| 307 | :param cifblk: dict or PyCifRW block containing values for each CIF item |
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| 308 | :param list loopstructure: a list of lists containing the contents of |
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| 309 | each loop, as an example:: |
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| 310 | |
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| 311 | [ ["_a","_b"], ["_c"], ["_d_1","_d_2","_d_3"]] |
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| 312 | |
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| 313 | this describes a CIF with this type of structure:: |
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| 314 | |
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| 315 | loop_ _a _b <a1> <b1> <a2> ... |
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| 316 | loop_ _c <c1> <c2>... |
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| 317 | loop _d_1 _d_2 _d_3 ... |
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| 318 | |
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| 319 | Note that the values for each looped CIF item, such as _a, |
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| 320 | are contained in a list, for example as cifblk["_a"] |
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| 321 | |
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| 322 | :param dict cifdic: optional CIF dictionary definitions |
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| 323 | :param (other): optional keyword parameters for wx.ScrolledPanel |
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| 324 | ''' |
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| 325 | def __init__(self, parent, cifblk, loopstructure, cifdic={}, OKbuttons=[], **kw): |
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| 326 | self.parent = parent |
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| 327 | wxscroll.ScrolledPanel.__init__(self, parent, wx.ID_ANY, **kw) |
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| 328 | self.vbox = None |
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| 329 | self.AddDict = None |
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| 330 | self.cifdic = cifdic |
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| 331 | self.cifblk = cifblk |
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| 332 | self.loops = loopstructure |
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| 333 | self.parent = parent |
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| 334 | self.LayoutCalled = False |
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| 335 | self.parentOKbuttons = OKbuttons |
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| 336 | self.ValidatedControlsList = [] |
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| 337 | self._fill() |
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| 338 | def _fill(self): |
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| 339 | 'Fill the scrolled panel with widgets for each CIF item' |
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| 340 | wx.BeginBusyCursor() |
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| 341 | self.AddDict = {} |
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| 342 | self.ValidatedControlsList = [] |
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| 343 | # delete any only contents |
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| 344 | if self.vbox: |
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| 345 | self.vbox.DeleteWindows() |
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| 346 | self.vbox = None |
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| 347 | self.Update() |
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| 348 | vbox = wx.BoxSizer(wx.VERTICAL) |
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| 349 | self.vbox = vbox |
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| 350 | # compile a 'list' of items in loops |
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| 351 | loopnames = set() |
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| 352 | for i in self.loops: |
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| 353 | loopnames |= set(i) |
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| 354 | # post the looped CIF items |
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| 355 | for lnum,lp in enumerate(self.loops): |
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| 356 | hbox = wx.BoxSizer(wx.HORIZONTAL) |
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| 357 | hbox.Add(wx.StaticText(self,wx.ID_ANY,'Loop '+str(lnum+1))) |
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| 358 | vbox.Add(hbox) |
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| 359 | but = wx.Button(self,wx.ID_ANY,"Add row") |
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| 360 | self.AddDict[but]=lnum |
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| 361 | |
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| 362 | hbox.Add(but) |
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| 363 | but.Bind(wx.EVT_BUTTON,self.OnAddRow) |
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| 364 | fbox = wx.GridBagSizer(0, 0) |
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| 365 | vbox.Add(fbox) |
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| 366 | rows = 0 |
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| 367 | for i,item in enumerate(lp): |
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| 368 | txt = wx.StaticText(self,wx.ID_ANY,item+" ") |
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| 369 | fbox.Add(txt,(0,i+1)) |
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| 370 | if self.cifdic.get(item): |
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| 371 | df = self.cifdic[item].get('_definition') |
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| 372 | if df: |
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| 373 | txt.SetToolTipString(G2IO.trim(df)) |
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| 374 | but = CIFdefHelp(self, |
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| 375 | "Definition for "+item+":\n\n"+G2IO.trim(df), |
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| 376 | self.parent, |
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| 377 | self.parent.helptxt) |
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| 378 | fbox.Add(but,(1,i+1),flag=wx.ALIGN_CENTER) |
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| 379 | for j,val in enumerate(self.cifblk[item]): |
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| 380 | ent = self.CIFEntryWidget(self.cifblk[item],j,item) |
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| 381 | fbox.Add(ent,(j+2,i+1),flag=wx.EXPAND|wx.ALL) |
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| 382 | rows = max(rows,len(self.cifblk[item])) |
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| 383 | for i in range(rows): |
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| 384 | txt = wx.StaticText(self,wx.ID_ANY,str(i+1)) |
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| 385 | fbox.Add(txt,(i+2,0)) |
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| 386 | line = wx.StaticLine(self,wx.ID_ANY, size=(-1,3), style=wx.LI_HORIZONTAL) |
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| 387 | vbox.Add(line, 0, wx.EXPAND|wx.ALIGN_CENTER|wx.ALL, 10) |
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| 388 | |
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| 389 | # post the non-looped CIF items |
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| 390 | for item in sorted(self.cifblk.keys()): |
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| 391 | if item not in loopnames: |
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| 392 | hbox = wx.BoxSizer(wx.HORIZONTAL) |
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| 393 | vbox.Add(hbox) |
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| 394 | txt = wx.StaticText(self,wx.ID_ANY,item) |
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| 395 | hbox.Add(txt) |
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| 396 | if self.cifdic.get(item): |
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| 397 | df = self.cifdic[item].get('_definition') |
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| 398 | if df: |
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| 399 | txt.SetToolTipString(G2IO.trim(df)) |
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| 400 | but = CIFdefHelp(self, |
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| 401 | "Definition for "+item+":\n\n"+G2IO.trim(df), |
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| 402 | self.parent, |
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| 403 | self.parent.helptxt) |
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| 404 | hbox.Add(but,0,wx.ALL,2) |
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| 405 | ent = self.CIFEntryWidget(self.cifblk,item,item) |
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| 406 | hbox.Add(ent) |
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| 407 | self.SetSizer(vbox) |
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| 408 | #vbox.Fit(self.parent) |
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| 409 | self.SetAutoLayout(1) |
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| 410 | self.SetupScrolling() |
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| 411 | self.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded) |
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| 412 | self.Layout() |
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| 413 | wx.EndBusyCursor() |
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| 414 | def OnLayoutNeeded(self,event): |
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| 415 | '''Called when an update of the panel layout is needed. Calls |
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| 416 | self.DoLayout after the current operations are complete using |
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| 417 | CallAfter. This is called only once, according to flag |
|---|
| 418 | self.LayoutCalled, which is cleared in self.DoLayout. |
|---|
| 419 | ''' |
|---|
| 420 | if self.LayoutCalled: return # call already queued |
|---|
| 421 | wx.CallAfter(self.DoLayout) # queue a call |
|---|
| 422 | self.LayoutCalled = True |
|---|
| 423 | def DoLayout(self): |
|---|
| 424 | '''Update the Layout and scroll bars for the Panel. Clears |
|---|
| 425 | self.LayoutCalled so that next change to panel can |
|---|
| 426 | request a new update |
|---|
| 427 | ''' |
|---|
| 428 | wx.BeginBusyCursor() |
|---|
| 429 | self.Layout() |
|---|
| 430 | self.SetupScrolling() |
|---|
| 431 | wx.EndBusyCursor() |
|---|
| 432 | self.LayoutCalled = False |
|---|
| 433 | def OnAddRow(self,event): |
|---|
| 434 | 'add a row to a loop' |
|---|
| 435 | lnum = self.AddDict.get(event.GetEventObject()) |
|---|
| 436 | if lnum is None: return |
|---|
| 437 | for item in self.loops[lnum]: |
|---|
| 438 | self.cifblk[item].append('?') |
|---|
| 439 | self._fill() |
|---|
| 440 | |
|---|
| 441 | def ControlOKButton(self,setvalue): |
|---|
| 442 | '''Enable or Disable the OK button(s) for the dialog. Note that this is |
|---|
| 443 | passed into the ValidatedTxtCtrl for use by validators. |
|---|
| 444 | |
|---|
| 445 | :param bool setvalue: if True, all entries in the dialog are |
|---|
| 446 | checked for validity. The first invalid control triggers |
|---|
| 447 | disabling of buttons. |
|---|
| 448 | If False then the OK button(s) are disabled with no checking |
|---|
| 449 | of the invalid flag for each control. |
|---|
| 450 | ''' |
|---|
| 451 | if setvalue: # turn button on, do only if all controls show as valid |
|---|
| 452 | for ctrl in self.ValidatedControlsList: |
|---|
| 453 | if ctrl.invalid: |
|---|
| 454 | for btn in self.parentOKbuttons: |
|---|
| 455 | btn.Disable() |
|---|
| 456 | return |
|---|
| 457 | else: |
|---|
| 458 | for btn in self.parentOKbuttons: |
|---|
| 459 | btn.Enable() |
|---|
| 460 | else: |
|---|
| 461 | for btn in self.parentOKbuttons: |
|---|
| 462 | btn.Disable() |
|---|
| 463 | |
|---|
| 464 | def CIFEntryWidget(self,dct,item,dataname): |
|---|
| 465 | '''Create an entry widget for a CIF item. Use a validated entry for numb values |
|---|
| 466 | where int is required when limits are integers and floats otherwise. |
|---|
| 467 | At present this does not allow entry of the special CIF values of "." and "?" for |
|---|
| 468 | numerical values and highlights them as invalid. |
|---|
| 469 | Use a selection widget when there are specific enumerated values for a string. |
|---|
| 470 | ''' |
|---|
| 471 | if self.cifdic.get(dataname): |
|---|
| 472 | if self.cifdic[dataname].get('_enumeration'): |
|---|
| 473 | values = ['?']+self.cifdic[dataname]['_enumeration'] |
|---|
| 474 | choices = ['undefined'] |
|---|
| 475 | for i in self.cifdic[dataname].get('_enumeration_detail',values): |
|---|
| 476 | choices.append(G2IO.trim(i)) |
|---|
| 477 | ent = G2gd.EnumSelector(self, dct, item, choices, values, size=(200, -1)) |
|---|
| 478 | return ent |
|---|
| 479 | if self.cifdic[dataname].get('_type') == 'numb': |
|---|
| 480 | mn = None |
|---|
| 481 | mx = None |
|---|
| 482 | hint = int |
|---|
| 483 | if self.cifdic[dataname].get('_enumeration_range'): |
|---|
| 484 | rng = self.cifdic[dataname]['_enumeration_range'].split(':') |
|---|
| 485 | if '.' in rng[0] or '.' in rng[1]: hint = float |
|---|
| 486 | if rng[0]: mn = hint(rng[0]) |
|---|
| 487 | if rng[1]: mx = hint(rng[1]) |
|---|
| 488 | ent = G2gd.ValidatedTxtCtrl( |
|---|
| 489 | self,dct,item,typeHint=hint,min=mn,max=mx, |
|---|
| 490 | CIFinput=True, |
|---|
| 491 | OKcontrol=self.ControlOKButton) |
|---|
| 492 | self.ValidatedControlsList.append(ent) |
|---|
| 493 | return ent |
|---|
| 494 | rw1 = rw.ResizeWidget(self) |
|---|
| 495 | #print item |
|---|
| 496 | #print dct[item] |
|---|
| 497 | ent = G2gd.ValidatedTxtCtrl( |
|---|
| 498 | rw1,dct,item,size=(100, 20), |
|---|
| 499 | style=wx.TE_MULTILINE|wx.TE_PROCESS_ENTER, |
|---|
| 500 | CIFinput=True, |
|---|
| 501 | OKcontrol=self.ControlOKButton) |
|---|
| 502 | self.ValidatedControlsList.append(ent) |
|---|
| 503 | return rw1 |
|---|
| 504 | |
|---|
| 505 | class CIFtemplateSelect(wx.BoxSizer): |
|---|
| 506 | '''Create a set of buttons to show, select and edit a CIF template |
|---|
| 507 | |
|---|
| 508 | :param str tmplate: one of 'publ', 'phase', or 'instrument' to determine |
|---|
| 509 | the type of template |
|---|
| 510 | ''' |
|---|
| 511 | def __init__(self,frame,panel,tmplate,G2dict, repaint, title): |
|---|
| 512 | wx.BoxSizer.__init__(self,wx.VERTICAL) |
|---|
| 513 | self.cifdefs = frame |
|---|
| 514 | self.dict = G2dict |
|---|
| 515 | self.repaint = repaint |
|---|
| 516 | self.fil = 'template_'+tmplate+'.cif' |
|---|
| 517 | self.CIF = G2dict.get("CIF_template") |
|---|
| 518 | txt = wx.StaticText(panel,wx.ID_ANY,title) |
|---|
| 519 | self.Add(txt,0,wx.ALIGN_CENTER) |
|---|
| 520 | # change font on title |
|---|
| 521 | txtfnt = txt.GetFont() |
|---|
| 522 | txtfnt.SetWeight(wx.BOLD) |
|---|
| 523 | txtfnt.SetPointSize(2+txtfnt.GetPointSize()) |
|---|
| 524 | txt.SetFont(txtfnt) |
|---|
| 525 | self.Add((-1,3)) |
|---|
| 526 | |
|---|
| 527 | if not self.CIF: # empty or None |
|---|
| 528 | for pth in sys.path: |
|---|
| 529 | if os.path.exists(os.path.join(pth,self.fil)): |
|---|
| 530 | self.CIF = os.path.join(pth,self.fil) |
|---|
| 531 | CIFtxt = "Template: "+self.fil |
|---|
| 532 | break |
|---|
| 533 | else: |
|---|
| 534 | print CIF+' not found in path!' |
|---|
| 535 | self.CIF = None |
|---|
| 536 | CIFtxt = "none! (No template found)" |
|---|
| 537 | elif type(self.CIF) is not list and type(self.CIF) is not tuple: |
|---|
| 538 | if not os.path.exists(self.CIF): |
|---|
| 539 | print("Error: template file has disappeared:"+self.CIF) |
|---|
| 540 | self.CIF = None |
|---|
| 541 | CIFtxt = "none! (file not found)" |
|---|
| 542 | else: |
|---|
| 543 | if len(self.CIF) < 40: |
|---|
| 544 | CIFtxt = "File: "+self.CIF |
|---|
| 545 | else: |
|---|
| 546 | CIFtxt = "File: ..."+self.CIF[-40:] |
|---|
| 547 | else: |
|---|
| 548 | CIFtxt = "Template is customized" |
|---|
| 549 | # show template source |
|---|
| 550 | self.Add(wx.StaticText(panel,wx.ID_ANY,CIFtxt)) |
|---|
| 551 | # show str, button to select file; button to edit (if CIF defined) |
|---|
| 552 | but = wx.Button(panel,wx.ID_ANY,"Select Template File") |
|---|
| 553 | but.Bind(wx.EVT_BUTTON,self.onGetTemplateFile) |
|---|
| 554 | hbox = wx.BoxSizer(wx.HORIZONTAL) |
|---|
| 555 | hbox.Add(but,0,0,2) |
|---|
| 556 | but = wx.Button(panel,wx.ID_ANY,"Edit Template") |
|---|
| 557 | but.Bind(wx.EVT_BUTTON,self.onEditTemplateContents) |
|---|
| 558 | hbox.Add(but,0,0,2) |
|---|
| 559 | #self.Add(hbox,0,wx.ALIGN_CENTER) |
|---|
| 560 | self.Add(hbox) |
|---|
| 561 | def onGetTemplateFile(self,event): |
|---|
| 562 | dlg = wx.FileDialog( |
|---|
| 563 | self.cifdefs, message="Save as CIF template", |
|---|
| 564 | defaultDir=os.getcwd(), |
|---|
| 565 | defaultFile="", |
|---|
| 566 | wildcard="CIF (*.cif)|*.cif", |
|---|
| 567 | style=wx.OPEN | wx.CHANGE_DIR |
|---|
| 568 | ) |
|---|
| 569 | if dlg.ShowModal() == wx.ID_OK: |
|---|
| 570 | self.dict["CIF_template"] = dlg.GetPath() |
|---|
| 571 | dlg.Destroy() |
|---|
| 572 | self.repaint() #EditCIFDefaults() |
|---|
| 573 | else: |
|---|
| 574 | dlg.Destroy() |
|---|
| 575 | |
|---|
| 576 | def onEditTemplateContents(self,event): |
|---|
| 577 | import CifFile as cif # PyCifRW from James Hester |
|---|
| 578 | if type(self.CIF) is list or type(self.CIF) is tuple: |
|---|
| 579 | dblk,loopstructure = copy.deepcopy(self.CIF) # don't modify original |
|---|
| 580 | else: |
|---|
| 581 | dblk,loopstructure = CIF2dict(cif.ReadCif(self.CIF)) |
|---|
| 582 | dlg = EditCIFtemplate(self.cifdefs,dblk,loopstructure) |
|---|
| 583 | val = dlg.Post() |
|---|
| 584 | if val: |
|---|
| 585 | if dlg.newfile: # results saved in file |
|---|
| 586 | self.dict["CIF_template"] = dlg.newfile |
|---|
| 587 | print 'saved' |
|---|
| 588 | else: |
|---|
| 589 | self.dict["CIF_template"] = [dlg.cifblk,dlg.loopstructure] |
|---|
| 590 | print 'edited' |
|---|
| 591 | self.repaint() #EditCIFDefaults() # note that this does a dlg.Destroy() |
|---|
| 592 | else: |
|---|
| 593 | print 'cancelled' |
|---|
| 594 | dlg.Destroy() |
|---|
| 595 | |
|---|
| 596 | #=============================================================================== |
|---|
| 597 | # end of misc CIF utilities |
|---|
| 598 | #=============================================================================== |
|---|
| 599 | |
|---|
| 600 | class ExportCIF(G2IO.ExportBaseclass): |
|---|
| 601 | def __init__(self,G2frame): |
|---|
| 602 | super(self.__class__,self).__init__( # fancy way to say <parentclass>.__init__ |
|---|
| 603 | G2frame=G2frame, |
|---|
| 604 | formatName = 'full CIF', |
|---|
| 605 | extension='.cif', |
|---|
| 606 | longFormatName = 'Export project as CIF' |
|---|
| 607 | ) |
|---|
| 608 | self.author = '' |
|---|
| 609 | |
|---|
| 610 | def export(self,mode='full'): |
|---|
| 611 | '''Export a CIF |
|---|
| 612 | |
|---|
| 613 | :param str mode: "full" (default) to create a complete CIF of project, |
|---|
| 614 | "simple" for a simple CIF with only coordinates |
|---|
| 615 | ''' |
|---|
| 616 | |
|---|
| 617 | # ===== define functions for export method ======================================= |
|---|
| 618 | def openCIF(filnam): |
|---|
| 619 | if DEBUG: |
|---|
| 620 | self.fp = sys.stdout |
|---|
| 621 | else: |
|---|
| 622 | self.fp = open(filnam,'w') |
|---|
| 623 | |
|---|
| 624 | def closeCIF(): |
|---|
| 625 | if not DEBUG: |
|---|
| 626 | self.fp.close() |
|---|
| 627 | |
|---|
| 628 | def WriteCIFitem(name,value=''): |
|---|
| 629 | if value: |
|---|
| 630 | if "\n" in value or len(value)> 70: |
|---|
| 631 | if name.strip(): self.fp.write(name+'\n') |
|---|
| 632 | self.fp.write('; '+value+'\n') |
|---|
| 633 | self.fp.write('; '+'\n') |
|---|
| 634 | elif " " in value: |
|---|
| 635 | if len(name)+len(value) > 65: |
|---|
| 636 | self.fp.write(name + '\n ' + '"' + str(value) + '"'+'\n') |
|---|
| 637 | else: |
|---|
| 638 | self.fp.write(name + ' ' + '"' + str(value) + '"'+'\n') |
|---|
| 639 | else: |
|---|
| 640 | if len(name)+len(value) > 65: |
|---|
| 641 | self.fp.write(name+'\n ' + value+'\n') |
|---|
| 642 | else: |
|---|
| 643 | self.fp.write(name+' ' + value+'\n') |
|---|
| 644 | else: |
|---|
| 645 | self.fp.write(name+'\n') |
|---|
| 646 | |
|---|
| 647 | def WriteAudit(): |
|---|
| 648 | WriteCIFitem('_audit_creation_method', |
|---|
| 649 | 'created in GSAS-II') |
|---|
| 650 | WriteCIFitem('_audit_creation_date',self.CIFdate) |
|---|
| 651 | if self.author: |
|---|
| 652 | WriteCIFitem('_audit_author_name',self.author) |
|---|
| 653 | WriteCIFitem('_audit_update_record', |
|---|
| 654 | self.CIFdate+' Initial software-generated CIF') |
|---|
| 655 | |
|---|
| 656 | def WriteOverall(): |
|---|
| 657 | '''Write out overall refinement information. |
|---|
| 658 | |
|---|
| 659 | More could be done here, but this is a good start. |
|---|
| 660 | ''' |
|---|
| 661 | WriteCIFitem('_pd_proc_info_datetime', self.CIFdate) |
|---|
| 662 | WriteCIFitem('_pd_calc_method', 'Rietveld Refinement') |
|---|
| 663 | #WriteCIFitem('_refine_ls_shift/su_max',DAT1) |
|---|
| 664 | #WriteCIFitem('_refine_ls_shift/su_mean',DAT2) |
|---|
| 665 | #WriteCIFitem('_refine_diff_density_max',rhomax) #these need to be defined for each phase! |
|---|
| 666 | #WriteCIFitem('_refine_diff_density_min',rhomin) |
|---|
| 667 | WriteCIFitem('_computing_structure_refinement','GSAS-II (Toby & Von Dreele, J. Appl. Cryst. 46, 544-549, 2013)') |
|---|
| 668 | try: |
|---|
| 669 | vars = str(len(self.OverallParms['Covariance']['varyList'])) |
|---|
| 670 | except: |
|---|
| 671 | vars = '?' |
|---|
| 672 | WriteCIFitem('_refine_ls_number_parameters',vars) |
|---|
| 673 | try: |
|---|
| 674 | GOF = G2mth.ValEsd(self.OverallParms['Covariance']['Rvals']['GOF'],-0.009) |
|---|
| 675 | except: |
|---|
| 676 | GOF = '?' |
|---|
| 677 | WriteCIFitem('_refine_ls_goodness_of_fit_all',GOF) |
|---|
| 678 | |
|---|
| 679 | # get restraint info |
|---|
| 680 | # restraintDict = self.OverallParms.get('Restraints',{}) |
|---|
| 681 | # for i in self.OverallParms['Constraints']: |
|---|
| 682 | # print i |
|---|
| 683 | # for j in self.OverallParms['Constraints'][i]: |
|---|
| 684 | # print j |
|---|
| 685 | #WriteCIFitem('_refine_ls_number_restraints',TEXT) |
|---|
| 686 | # other things to consider reporting |
|---|
| 687 | # _refine_ls_number_reflns |
|---|
| 688 | # _refine_ls_goodness_of_fit_obs |
|---|
| 689 | # _refine_ls_wR_factor_obs |
|---|
| 690 | # _refine_ls_restrained_S_all |
|---|
| 691 | # _refine_ls_restrained_S_obs |
|---|
| 692 | |
|---|
| 693 | # include an overall profile r-factor, if there is more than one powder histogram |
|---|
| 694 | R = '%.5f'%(self.OverallParms['Covariance']['Rvals']['Rwp']/100.) |
|---|
| 695 | WriteCIFitem('\n# OVERALL WEIGHTED R-FACTOR') |
|---|
| 696 | WriteCIFitem('_refine_ls_wR_factor_obs',R) |
|---|
| 697 | # _refine_ls_R_factor_all |
|---|
| 698 | # _refine_ls_R_factor_obs |
|---|
| 699 | WriteCIFitem('_refine_ls_matrix_type','full') |
|---|
| 700 | #WriteCIFitem('_refine_ls_matrix_type','userblocks') |
|---|
| 701 | |
|---|
| 702 | def WritePubTemplate(): |
|---|
| 703 | '''TODO: insert the publication template ``template_publ.cif`` or some modified |
|---|
| 704 | version for this project. Store this in the GPX file? |
|---|
| 705 | ''' |
|---|
| 706 | print getCallerDocString() |
|---|
| 707 | |
|---|
| 708 | def WritePhaseTemplate(): |
|---|
| 709 | '''TODO: insert the phase template ``template_phase.cif`` or some modified |
|---|
| 710 | version for this project |
|---|
| 711 | ''' |
|---|
| 712 | print getCallerDocString() |
|---|
| 713 | |
|---|
| 714 | def WritePowderTemplate(): |
|---|
| 715 | '''TODO: insert the phase template ``template_instrument.cif`` or some modified |
|---|
| 716 | version for this project |
|---|
| 717 | ''' |
|---|
| 718 | print getCallerDocString() |
|---|
| 719 | |
|---|
| 720 | def WriteSnglXtalTemplate(): |
|---|
| 721 | '''TODO: insert the single-crystal histogram template |
|---|
| 722 | for this project |
|---|
| 723 | ''' |
|---|
| 724 | print getCallerDocString() |
|---|
| 725 | |
|---|
| 726 | def FormatSH(phasenam): |
|---|
| 727 | 'Format a full spherical harmonics texture description as a string' |
|---|
| 728 | phasedict = self.Phases[phasenam] # pointer to current phase info |
|---|
| 729 | pfx = str(phasedict['pId'])+'::' |
|---|
| 730 | s = "" |
|---|
| 731 | textureData = phasedict['General']['SH Texture'] |
|---|
| 732 | if textureData.get('Order'): |
|---|
| 733 | s += "Spherical Harmonics correction. Order = "+str(textureData['Order']) |
|---|
| 734 | s += " Model: " + str(textureData['Model']) + "\n Orientation angles: " |
|---|
| 735 | for name in ['omega','chi','phi']: |
|---|
| 736 | aname = pfx+'SH '+name |
|---|
| 737 | s += name + " = " |
|---|
| 738 | sig = self.sigDict.get(aname,-0.09) |
|---|
| 739 | s += G2mth.ValEsd(self.parmDict[aname],sig) |
|---|
| 740 | s += "; " |
|---|
| 741 | s += "\n" |
|---|
| 742 | s1 = " Coefficients: " |
|---|
| 743 | for name in textureData['SH Coeff'][1]: |
|---|
| 744 | aname = pfx+name |
|---|
| 745 | if len(s1) > 60: |
|---|
| 746 | s += s1 + "\n" |
|---|
| 747 | s1 = " " |
|---|
| 748 | s1 += aname + ' = ' |
|---|
| 749 | sig = self.sigDict.get(aname,-0.0009) |
|---|
| 750 | s1 += G2mth.ValEsd(self.parmDict[aname],sig) |
|---|
| 751 | s1 += "; " |
|---|
| 752 | s += s1 |
|---|
| 753 | return s |
|---|
| 754 | |
|---|
| 755 | def FormatHAPpo(phasenam): |
|---|
| 756 | '''return the March-Dollase/SH correction for every |
|---|
| 757 | histogram in the current phase formatted into a |
|---|
| 758 | character string |
|---|
| 759 | ''' |
|---|
| 760 | phasedict = self.Phases[phasenam] # pointer to current phase info |
|---|
| 761 | s = '' |
|---|
| 762 | for histogram in sorted(phasedict['Histograms']): |
|---|
| 763 | if histogram.startswith("HKLF"): continue # powder only |
|---|
| 764 | Histogram = self.Histograms.get(histogram) |
|---|
| 765 | if not Histogram: continue |
|---|
| 766 | hapData = phasedict['Histograms'][histogram] |
|---|
| 767 | if hapData['Pref.Ori.'][0] == 'MD': |
|---|
| 768 | aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':MD' |
|---|
| 769 | if self.parmDict.get(aname,1.0) != 1.0: continue |
|---|
| 770 | sig = self.sigDict.get(aname,-0.009) |
|---|
| 771 | if s != "": s += '\n' |
|---|
| 772 | s += 'March-Dollase correction' |
|---|
| 773 | if len(self.powderDict) > 1: |
|---|
| 774 | s += ', histogram '+str(Histogram['hId']+1) |
|---|
| 775 | s += ' coef. = ' + G2mth.ValEsd(self.parmDict[aname],sig) |
|---|
| 776 | s += ' axis = ' + str(hapData['Pref.Ori.'][3]) |
|---|
| 777 | else: # must be SH |
|---|
| 778 | if s != "": s += '\n' |
|---|
| 779 | s += 'Simple spherical harmonic correction' |
|---|
| 780 | if len(self.powderDict) > 1: |
|---|
| 781 | s += ', histogram '+str(Histogram['hId']+1) |
|---|
| 782 | s += ' Order = '+str(hapData['Pref.Ori.'][4])+'\n' |
|---|
| 783 | s1 = " Coefficients: " |
|---|
| 784 | for item in hapData['Pref.Ori.'][5]: |
|---|
| 785 | aname = str(phasedict['pId'])+':'+str(Histogram['hId'])+':'+item |
|---|
| 786 | if len(s1) > 60: |
|---|
| 787 | s += s1 + "\n" |
|---|
| 788 | s1 = " " |
|---|
| 789 | s1 += aname + ' = ' |
|---|
| 790 | sig = self.sigDict.get(aname,-0.0009) |
|---|
| 791 | s1 += G2mth.ValEsd(self.parmDict[aname],sig) |
|---|
| 792 | s1 += "; " |
|---|
| 793 | s += s1 |
|---|
| 794 | return s |
|---|
| 795 | def FormatBackground(bkg,hId): |
|---|
| 796 | '''Display the Background information as a descriptive text string. |
|---|
| 797 | |
|---|
| 798 | TODO: this needs to be expanded to show the diffuse peak and |
|---|
| 799 | Debye term information as well. (Bob) |
|---|
| 800 | |
|---|
| 801 | :returns: the text description (str) |
|---|
| 802 | ''' |
|---|
| 803 | hfx = ':'+str(hId)+':' |
|---|
| 804 | fxn, bkgdict = bkg |
|---|
| 805 | terms = fxn[2] |
|---|
| 806 | txt = 'Background function: "'+fxn[0]+'" function with '+str(terms)+' terms:\n' |
|---|
| 807 | l = " " |
|---|
| 808 | for i,v in enumerate(fxn[3:]): |
|---|
| 809 | name = '%sBack:%d'%(hfx,i) |
|---|
| 810 | sig = self.sigDict.get(name,-0.009) |
|---|
| 811 | if len(l) > 60: |
|---|
| 812 | txt += l + '\n' |
|---|
| 813 | l = ' ' |
|---|
| 814 | l += G2mth.ValEsd(v,sig)+', ' |
|---|
| 815 | txt += l |
|---|
| 816 | if bkgdict['nDebye']: |
|---|
| 817 | txt += '\n Background Debye function parameters: A, R, U:' |
|---|
| 818 | names = ['A:','R:','U:'] |
|---|
| 819 | for i in range(bkgdict['nDebye']): |
|---|
| 820 | txt += '\n ' |
|---|
| 821 | for j in range(3): |
|---|
| 822 | name = hfx+'Debye'+names[j]+str(i) |
|---|
| 823 | sig = self.sigDict.get(name,-0.009) |
|---|
| 824 | txt += G2mth.ValEsd(bkgdict['debyeTerms'][i][2*j],sig)+', ' |
|---|
| 825 | if bkgdict['nPeaks']: |
|---|
| 826 | txt += '\n Background peak parameters: pos, int, sig, gam:' |
|---|
| 827 | names = ['pos:','int:','sig:','gam:'] |
|---|
| 828 | for i in range(bkgdict['nPeaks']): |
|---|
| 829 | txt += '\n ' |
|---|
| 830 | for j in range(4): |
|---|
| 831 | name = hfx+'BkPk'+names[j]+str(i) |
|---|
| 832 | sig = self.sigDict.get(name,-0.009) |
|---|
| 833 | txt += G2mth.ValEsd(bkgdict['peaksList'][i][2*j],sig)+', ' |
|---|
| 834 | return txt |
|---|
| 835 | |
|---|
| 836 | def FormatInstProfile(instparmdict,hId): |
|---|
| 837 | '''Format the instrumental profile parameters with a |
|---|
| 838 | string description. Will only be called on PWDR histograms |
|---|
| 839 | ''' |
|---|
| 840 | s = '' |
|---|
| 841 | inst = instparmdict[0] |
|---|
| 842 | hfx = ':'+str(hId)+':' |
|---|
| 843 | if 'C' in inst['Type'][0]: |
|---|
| 844 | s = 'Finger-Cox-Jephcoat function parameters U, V, W, X, Y, SH/L:\n' |
|---|
| 845 | s += ' peak variance(Gauss) = Utan(Th)^2^+Vtan(Th)+W:\n' |
|---|
| 846 | s += ' peak HW(Lorentz) = X/cos(Th)+Ytan(Th); SH/L = S/L+H/L\n' |
|---|
| 847 | s += ' U, V, W in (centideg)^2^, X & Y in centideg\n ' |
|---|
| 848 | for item in ['U','V','W','X','Y','SH/L']: |
|---|
| 849 | name = hfx+item |
|---|
| 850 | sig = self.sigDict.get(name,-0.009) |
|---|
| 851 | s += G2mth.ValEsd(inst[item][1],sig)+', ' |
|---|
| 852 | elif 'T' in inst['Type'][0]: #to be tested after TOF Rietveld done |
|---|
| 853 | s = 'Von Dreele-Jorgenson-Windsor function parameters\n'+ \ |
|---|
| 854 | ' alpha, beta-0, beta-1, beta-q, sig-0, sig-1, sig-q, X, Y:\n ' |
|---|
| 855 | for item in ['alpha','bet-0','bet-1','bet-q','sig-0','sig-1','sig-q','X','Y']: |
|---|
| 856 | name = hfx+item |
|---|
| 857 | sig = self.sigDict.get(name,-0.009) |
|---|
| 858 | s += G2mth.ValEsd(inst[item][1],sig)+', ' |
|---|
| 859 | return s |
|---|
| 860 | |
|---|
| 861 | def FormatPhaseProfile(phasenam): |
|---|
| 862 | '''Format the phase-related profile parameters (size/strain) |
|---|
| 863 | with a string description. |
|---|
| 864 | return an empty string or None if there are no |
|---|
| 865 | powder histograms for this phase. |
|---|
| 866 | ''' |
|---|
| 867 | s = '' |
|---|
| 868 | phasedict = self.Phases[phasenam] # pointer to current phase info |
|---|
| 869 | SGData = phasedict['General'] ['SGData'] |
|---|
| 870 | for histogram in sorted(phasedict['Histograms']): |
|---|
| 871 | if histogram.startswith("HKLF"): continue # powder only |
|---|
| 872 | Histogram = self.Histograms.get(histogram) |
|---|
| 873 | if not Histogram: continue |
|---|
| 874 | hapData = phasedict['Histograms'][histogram] |
|---|
| 875 | pId = phasedict['pId'] |
|---|
| 876 | hId = Histogram['hId'] |
|---|
| 877 | phfx = '%d:%d:'%(pId,hId) |
|---|
| 878 | size = hapData['Size'] |
|---|
| 879 | mustrain = hapData['Mustrain'] |
|---|
| 880 | hstrain = hapData['HStrain'] |
|---|
| 881 | s = ' Crystallite size model "%s" for %s (microns)\n '%(size[0],phasenam) |
|---|
| 882 | names = ['Size;i','Size;mx'] |
|---|
| 883 | if 'uniax' in size[0]: |
|---|
| 884 | names = ['Size;i','Size;a','Size;mx'] |
|---|
| 885 | s += 'anisotropic axis is %s\n '%(str(size[3])) |
|---|
| 886 | s += 'parameters: equatorial size, axial size, G/L mix\n ' |
|---|
| 887 | for i,item in enumerate(names): |
|---|
| 888 | name = phfx+item |
|---|
| 889 | sig = self.sigDict.get(name,-0.009) |
|---|
| 890 | s += G2mth.ValEsd(size[1][i],sig)+', ' |
|---|
| 891 | elif 'ellip' in size[0]: |
|---|
| 892 | s += 'parameters: S11, S22, S33, S12, S13, S23, G/L mix\n ' |
|---|
| 893 | for i in range(6): |
|---|
| 894 | name = phfx+'Size:'+str(i) |
|---|
| 895 | sig = self.sigDict.get(name,-0.009) |
|---|
| 896 | s += G2mth.ValEsd(size[4][i],sig)+', ' |
|---|
| 897 | sig = self.sigDict.get(phfx+'Size;mx',-0.009) |
|---|
| 898 | s += G2mth.ValEsd(size[1][2],sig)+', ' |
|---|
| 899 | else: #isotropic |
|---|
| 900 | s += 'parameters: Size, G/L mix\n ' |
|---|
| 901 | i = 0 |
|---|
| 902 | for item in names: |
|---|
| 903 | name = phfx+item |
|---|
| 904 | sig = self.sigDict.get(name,-0.009) |
|---|
| 905 | s += G2mth.ValEsd(size[1][i],sig)+', ' |
|---|
| 906 | i = 2 #skip the aniso value |
|---|
| 907 | s += '\n Mustrain model "%s" for %s (10^6^)\n '%(mustrain[0],phasenam) |
|---|
| 908 | names = ['Mustrain;i','Mustrain;mx'] |
|---|
| 909 | if 'uniax' in mustrain[0]: |
|---|
| 910 | names = ['Mustrain;i','Mustrain;a','Mustrain;mx'] |
|---|
| 911 | s += 'anisotropic axis is %s\n '%(str(size[3])) |
|---|
| 912 | s += 'parameters: equatorial mustrain, axial mustrain, G/L mix\n ' |
|---|
| 913 | for i,item in enumerate(names): |
|---|
| 914 | name = phfx+item |
|---|
| 915 | sig = self.sigDict.get(name,-0.009) |
|---|
| 916 | s += G2mth.ValEsd(mustrain[1][i],sig)+', ' |
|---|
| 917 | elif 'general' in mustrain[0]: |
|---|
| 918 | names = 'parameters: ' |
|---|
| 919 | for i,name in enumerate(G2spc.MustrainNames(SGData)): |
|---|
| 920 | names += name+', ' |
|---|
| 921 | if i == 9: |
|---|
| 922 | names += '\n ' |
|---|
| 923 | names += 'G/L mix\n ' |
|---|
| 924 | s += names |
|---|
| 925 | txt = '' |
|---|
| 926 | for i in range(len(mustrain[4])): |
|---|
| 927 | name = phfx+'Mustrain:'+str(i) |
|---|
| 928 | sig = self.sigDict.get(name,-0.009) |
|---|
| 929 | if len(txt) > 60: |
|---|
| 930 | s += txt+'\n ' |
|---|
| 931 | txt = '' |
|---|
| 932 | txt += G2mth.ValEsd(mustrain[4][i],sig)+', ' |
|---|
| 933 | s += txt |
|---|
| 934 | sig = self.sigDict.get(phfx+'Mustrain;mx',-0.009) |
|---|
| 935 | s += G2mth.ValEsd(mustrain[1][2],sig)+', ' |
|---|
| 936 | |
|---|
| 937 | else: #isotropic |
|---|
| 938 | s += ' parameters: Mustrain, G/L mix\n ' |
|---|
| 939 | i = 0 |
|---|
| 940 | for item in names: |
|---|
| 941 | name = phfx+item |
|---|
| 942 | sig = self.sigDict.get(name,-0.009) |
|---|
| 943 | s += G2mth.ValEsd(mustrain[1][i],sig)+', ' |
|---|
| 944 | i = 2 #skip the aniso value |
|---|
| 945 | s += '\n Macrostrain for %s\n'%(phasenam) |
|---|
| 946 | txt = ' parameters: ' |
|---|
| 947 | names = G2spc.HStrainNames(SGData) |
|---|
| 948 | for name in names: |
|---|
| 949 | txt += name+', ' |
|---|
| 950 | s += txt+'\n ' |
|---|
| 951 | for i in range(len(names)): |
|---|
| 952 | name = phfx+name[i] |
|---|
| 953 | sig = self.sigDict.get(name,-0.009) |
|---|
| 954 | s += G2mth.ValEsd(hstrain[0][i],sig)+', ' |
|---|
| 955 | return s |
|---|
| 956 | |
|---|
| 957 | def FmtAtomType(sym): |
|---|
| 958 | 'Reformat a GSAS-II atom type symbol to match CIF rules' |
|---|
| 959 | sym = sym.replace('_','') # underscores are not allowed: no isotope designation? |
|---|
| 960 | # in CIF, oxidation state sign symbols come after, not before |
|---|
| 961 | if '+' in sym: |
|---|
| 962 | sym = sym.replace('+','') + '+' |
|---|
| 963 | elif '-' in sym: |
|---|
| 964 | sym = sym.replace('-','') + '-' |
|---|
| 965 | return sym |
|---|
| 966 | |
|---|
| 967 | def PutInCol(val,wid): |
|---|
| 968 | '''Pad a value to >=wid+1 columns by adding spaces at the end. Always |
|---|
| 969 | adds at least one space |
|---|
| 970 | ''' |
|---|
| 971 | val = str(val).replace(' ','') |
|---|
| 972 | if not val: val = '?' |
|---|
| 973 | fmt = '{:' + str(wid) + '} ' |
|---|
| 974 | return fmt.format(val) |
|---|
| 975 | |
|---|
| 976 | def MakeUniqueLabel(lbl,labellist): |
|---|
| 977 | 'Make sure that every atom label is unique' |
|---|
| 978 | lbl = lbl.strip() |
|---|
| 979 | if not lbl: # deal with a blank label |
|---|
| 980 | lbl = 'A_1' |
|---|
| 981 | if lbl not in labellist: |
|---|
| 982 | labellist.append(lbl) |
|---|
| 983 | return lbl |
|---|
| 984 | i = 1 |
|---|
| 985 | prefix = lbl |
|---|
| 986 | if '_' in lbl: |
|---|
| 987 | prefix = lbl[:lbl.rfind('_')] |
|---|
| 988 | suffix = lbl[lbl.rfind('_')+1:] |
|---|
| 989 | try: |
|---|
| 990 | i = int(suffix)+1 |
|---|
| 991 | except: |
|---|
| 992 | pass |
|---|
| 993 | while prefix+'_'+str(i) in labellist: |
|---|
| 994 | i += 1 |
|---|
| 995 | else: |
|---|
| 996 | lbl = prefix+'_'+str(i) |
|---|
| 997 | labellist.append(lbl) |
|---|
| 998 | |
|---|
| 999 | def WriteAtomsNuclear(phasenam): |
|---|
| 1000 | 'Write atom positions to CIF' |
|---|
| 1001 | phasedict = self.Phases[phasenam] # pointer to current phase info |
|---|
| 1002 | General = phasedict['General'] |
|---|
| 1003 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1004 | Atoms = phasedict['Atoms'] |
|---|
| 1005 | cfrac = cx+3 |
|---|
| 1006 | fpfx = str(phasedict['pId'])+'::Afrac:' |
|---|
| 1007 | for i,at in enumerate(Atoms): |
|---|
| 1008 | fval = self.parmDict.get(fpfx+str(i),at[cfrac]) |
|---|
| 1009 | if fval != 0.0: |
|---|
| 1010 | break |
|---|
| 1011 | else: |
|---|
| 1012 | WriteCIFitem('\n# PHASE HAS NO ATOMS!') |
|---|
| 1013 | return |
|---|
| 1014 | |
|---|
| 1015 | WriteCIFitem('\n# ATOMIC COORDINATES AND DISPLACEMENT PARAMETERS') |
|---|
| 1016 | WriteCIFitem('loop_ '+ |
|---|
| 1017 | '\n\t_atom_site_label'+ |
|---|
| 1018 | '\n\t_atom_site_type_symbol'+ |
|---|
| 1019 | '\n\t_atom_site_fract_x'+ |
|---|
| 1020 | '\n\t_atom_site_fract_y'+ |
|---|
| 1021 | '\n\t_atom_site_fract_z'+ |
|---|
| 1022 | '\n\t_atom_site_occupancy'+ |
|---|
| 1023 | '\n\t_atom_site_adp_type'+ |
|---|
| 1024 | '\n\t_atom_site_U_iso_or_equiv'+ |
|---|
| 1025 | '\n\t_atom_site_symmetry_multiplicity') |
|---|
| 1026 | |
|---|
| 1027 | varnames = {cx:'Ax',cx+1:'Ay',cx+2:'Az',cx+3:'Afrac', |
|---|
| 1028 | cia+1:'AUiso',cia+2:'AU11',cia+3:'AU22',cia+4:'AU33', |
|---|
| 1029 | cia+5:'AU12',cia+6:'AU13',cia+7:'AU23'} |
|---|
| 1030 | self.labellist = [] |
|---|
| 1031 | |
|---|
| 1032 | pfx = str(phasedict['pId'])+'::' |
|---|
| 1033 | # loop over all atoms |
|---|
| 1034 | naniso = 0 |
|---|
| 1035 | for i,at in enumerate(Atoms): |
|---|
| 1036 | s = PutInCol(MakeUniqueLabel(at[ct-1],self.labellist),6) # label |
|---|
| 1037 | fval = self.parmDict.get(fpfx+str(i),at[cfrac]) |
|---|
| 1038 | if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact) |
|---|
| 1039 | s += PutInCol(FmtAtomType(at[ct]),4) # type |
|---|
| 1040 | if at[cia] == 'I': |
|---|
| 1041 | adp = 'Uiso ' |
|---|
| 1042 | else: |
|---|
| 1043 | adp = 'Uani ' |
|---|
| 1044 | naniso += 1 |
|---|
| 1045 | # compute Uequiv crudely |
|---|
| 1046 | # correct: Defined as "1/3 trace of diagonalized U matrix". |
|---|
| 1047 | # SEE cell2GS & Uij2Ueqv to GSASIIlattice. Former is needed to make the GS matrix used by the latter. |
|---|
| 1048 | t = 0.0 |
|---|
| 1049 | for j in (2,3,4): |
|---|
| 1050 | var = pfx+varnames[cia+j]+":"+str(i) |
|---|
| 1051 | t += self.parmDict.get(var,at[cia+j]) |
|---|
| 1052 | for j in (cx,cx+1,cx+2,cx+3,cia,cia+1): |
|---|
| 1053 | if j in (cx,cx+1,cx+2): |
|---|
| 1054 | dig = 11 |
|---|
| 1055 | sigdig = -0.00009 |
|---|
| 1056 | else: |
|---|
| 1057 | dig = 10 |
|---|
| 1058 | sigdig = -0.009 |
|---|
| 1059 | if j == cia: |
|---|
| 1060 | s += adp |
|---|
| 1061 | else: |
|---|
| 1062 | var = pfx+varnames[j]+":"+str(i) |
|---|
| 1063 | dvar = pfx+"d"+varnames[j]+":"+str(i) |
|---|
| 1064 | if dvar not in self.sigDict: |
|---|
| 1065 | dvar = var |
|---|
| 1066 | if j == cia+1 and adp == 'Uani ': |
|---|
| 1067 | val = t/3. |
|---|
| 1068 | sig = sigdig |
|---|
| 1069 | else: |
|---|
| 1070 | #print var,(var in self.parmDict),(var in self.sigDict) |
|---|
| 1071 | val = self.parmDict.get(var,at[j]) |
|---|
| 1072 | sig = self.sigDict.get(dvar,sigdig) |
|---|
| 1073 | s += PutInCol(G2mth.ValEsd(val,sig),dig) |
|---|
| 1074 | s += PutInCol(at[cs+1],3) |
|---|
| 1075 | WriteCIFitem(s) |
|---|
| 1076 | if naniso == 0: return |
|---|
| 1077 | # now loop over aniso atoms |
|---|
| 1078 | WriteCIFitem('\nloop_' + '\n\t_atom_site_aniso_label' + |
|---|
| 1079 | '\n\t_atom_site_aniso_U_11' + '\n\t_atom_site_aniso_U_12' + |
|---|
| 1080 | '\n\t_atom_site_aniso_U_13' + '\n\t_atom_site_aniso_U_22' + |
|---|
| 1081 | '\n\t_atom_site_aniso_U_23' + '\n\t_atom_site_aniso_U_33') |
|---|
| 1082 | for i,at in enumerate(Atoms): |
|---|
| 1083 | fval = self.parmDict.get(fpfx+str(i),at[cfrac]) |
|---|
| 1084 | if fval == 0.0: continue # ignore any atoms that have a occupancy set to 0 (exact) |
|---|
| 1085 | if at[cia] == 'I': continue |
|---|
| 1086 | s = PutInCol(self.labellist[i],6) # label |
|---|
| 1087 | for j in (2,3,4,5,6,7): |
|---|
| 1088 | sigdig = -0.0009 |
|---|
| 1089 | var = pfx+varnames[cia+j]+":"+str(i) |
|---|
| 1090 | val = self.parmDict.get(var,at[cia+j]) |
|---|
| 1091 | sig = self.sigDict.get(var,sigdig) |
|---|
| 1092 | s += PutInCol(G2mth.ValEsd(val,sig),11) |
|---|
| 1093 | WriteCIFitem(s) |
|---|
| 1094 | |
|---|
| 1095 | def HillSortElements(elmlist): |
|---|
| 1096 | '''Sort elements in "Hill" order: C, H, others, (where others |
|---|
| 1097 | are alphabetical). |
|---|
| 1098 | |
|---|
| 1099 | :params list elmlist: a list of element strings |
|---|
| 1100 | |
|---|
| 1101 | :returns: a sorted list of element strings |
|---|
| 1102 | ''' |
|---|
| 1103 | newlist = [] |
|---|
| 1104 | oldlist = elmlist[:] |
|---|
| 1105 | for elm in ('C','H'): |
|---|
| 1106 | if elm in elmlist: |
|---|
| 1107 | newlist.append(elm) |
|---|
| 1108 | oldlist.pop(oldlist.index(elm)) |
|---|
| 1109 | return newlist+sorted(oldlist) |
|---|
| 1110 | |
|---|
| 1111 | def WriteComposition(phasenam): |
|---|
| 1112 | '''determine the composition for the unit cell, crudely determine Z and |
|---|
| 1113 | then compute the composition in formula units |
|---|
| 1114 | ''' |
|---|
| 1115 | phasedict = self.Phases[phasenam] # pointer to current phase info |
|---|
| 1116 | General = phasedict['General'] |
|---|
| 1117 | Z = General.get('cellZ',0.0) |
|---|
| 1118 | cx,ct,cs,cia = General['AtomPtrs'] |
|---|
| 1119 | Atoms = phasedict['Atoms'] |
|---|
| 1120 | fpfx = str(phasedict['pId'])+'::Afrac:' |
|---|
| 1121 | cfrac = cx+3 |
|---|
| 1122 | cmult = cs+1 |
|---|
| 1123 | compDict = {} # combines H,D & T |
|---|
| 1124 | sitemultlist = [] |
|---|
| 1125 | massDict = dict(zip(General['AtomTypes'],General['AtomMass'])) |
|---|
| 1126 | cellmass = 0 |
|---|
| 1127 | for i,at in enumerate(Atoms): |
|---|
| 1128 | atype = at[ct].strip() |
|---|
| 1129 | if atype.find('-') != -1: atype = atype.split('-')[0] |
|---|
| 1130 | if atype.find('+') != -1: atype = atype.split('+')[0] |
|---|
| 1131 | atype = atype[0].upper()+atype[1:2].lower() # force case conversion |
|---|
| 1132 | if atype == "D" or atype == "D": atype = "H" |
|---|
| 1133 | fvar = fpfx+str(i) |
|---|
| 1134 | fval = self.parmDict.get(fvar,at[cfrac]) |
|---|
| 1135 | mult = at[cmult] |
|---|
| 1136 | if not massDict.get(at[ct]): |
|---|
| 1137 | print 'No mass found for atom type '+at[ct] |
|---|
| 1138 | print 'Will not compute cell contents for phase '+phasenam |
|---|
| 1139 | return |
|---|
| 1140 | cellmass += massDict[at[ct]]*mult*fval |
|---|
| 1141 | compDict[atype] = compDict.get(atype,0.0) + mult*fval |
|---|
| 1142 | if fval == 1: sitemultlist.append(mult) |
|---|
| 1143 | if len(compDict.keys()) == 0: return # no elements! |
|---|
| 1144 | if Z < 1: # Z has not been computed or set by user |
|---|
| 1145 | Z = 1 |
|---|
| 1146 | for i in range(2,min(sitemultlist)+1): |
|---|
| 1147 | for m in sitemultlist: |
|---|
| 1148 | if m % i != 0: |
|---|
| 1149 | break |
|---|
| 1150 | else: |
|---|
| 1151 | Z = i |
|---|
| 1152 | General['cellZ'] = Z # save it |
|---|
| 1153 | |
|---|
| 1154 | # when scattering factors are included in the CIF, this needs to be |
|---|
| 1155 | # added to the loop here but only in the one-block case. |
|---|
| 1156 | # For multiblock CIFs, scattering factors go in the histogram |
|---|
| 1157 | # blocks (for all atoms in all appropriate phases) - an example?: |
|---|
| 1158 | #loop_ |
|---|
| 1159 | # _atom_type_symbol |
|---|
| 1160 | # _atom_type_description |
|---|
| 1161 | # _atom_type_scat_dispersion_real |
|---|
| 1162 | # _atom_type_scat_dispersion_imag |
|---|
| 1163 | # _atom_type_scat_source |
|---|
| 1164 | # 'C' 'C' 0.0033 0.0016 |
|---|
| 1165 | # 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' |
|---|
| 1166 | # 'H' 'H' 0.0000 0.0000 |
|---|
| 1167 | # 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' |
|---|
| 1168 | # 'P' 'P' 0.1023 0.0942 |
|---|
| 1169 | # 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' |
|---|
| 1170 | # 'Cl' 'Cl' 0.1484 0.1585 |
|---|
| 1171 | # 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' |
|---|
| 1172 | # 'Cu' 'Cu' 0.3201 1.2651 |
|---|
| 1173 | # 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4' |
|---|
| 1174 | |
|---|
| 1175 | #if oneblock: # add scattering factors for current phase here |
|---|
| 1176 | WriteCIFitem('\nloop_ _atom_type_symbol _atom_type_number_in_cell') |
|---|
| 1177 | formula = '' |
|---|
| 1178 | reload(G2mth) |
|---|
| 1179 | for elem in HillSortElements(compDict.keys()): |
|---|
| 1180 | WriteCIFitem(' ' + PutInCol(elem,4) + |
|---|
| 1181 | G2mth.ValEsd(compDict[elem],-0.009,True)) |
|---|
| 1182 | if formula: formula += " " |
|---|
| 1183 | formula += elem |
|---|
| 1184 | if compDict[elem] == Z: continue |
|---|
| 1185 | formula += G2mth.ValEsd(compDict[elem]/Z,-0.009,True) |
|---|
| 1186 | WriteCIFitem( '\n# Note that Z affects _cell_formula_sum and _weight') |
|---|
| 1187 | WriteCIFitem( '_cell_formula_units_Z',str(Z)) |
|---|
| 1188 | WriteCIFitem( '_chemical_formula_sum',formula) |
|---|
| 1189 | WriteCIFitem( '_chemical_formula_weight', |
|---|
| 1190 | G2mth.ValEsd(cellmass/Z,-0.09,True)) |
|---|
| 1191 | |
|---|
| 1192 | def WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList): |
|---|
| 1193 | '''Report bond distances and angles for the CIF |
|---|
| 1194 | |
|---|
| 1195 | Note that _geom_*_symmetry_* fields are values of form |
|---|
| 1196 | n_klm where n is the symmetry operation in SymOpList (counted |
|---|
| 1197 | starting with 1) and (k-5, l-5, m-5) are translations to add |
|---|
| 1198 | to (x,y,z). See |
|---|
| 1199 | http://www.iucr.org/__data/iucr/cifdic_html/1/cif_core.dic/Igeom_angle_site_symmetry_.html |
|---|
| 1200 | |
|---|
| 1201 | TODO: need a method to select publication flags for distances/angles |
|---|
| 1202 | ''' |
|---|
| 1203 | phasedict = self.Phases[phasenam] # pointer to current phase info |
|---|
| 1204 | Atoms = phasedict['Atoms'] |
|---|
| 1205 | generalData = phasedict['General'] |
|---|
| 1206 | cx,ct,cs,cia = phasedict['General']['AtomPtrs'] |
|---|
| 1207 | cn = ct-1 |
|---|
| 1208 | fpfx = str(phasedict['pId'])+'::Afrac:' |
|---|
| 1209 | cfrac = cx+3 |
|---|
| 1210 | DisAglData = {} |
|---|
| 1211 | DisAglCtls = {} |
|---|
| 1212 | # create a list of atoms, but skip atoms with zero occupancy |
|---|
| 1213 | xyz = [] |
|---|
| 1214 | fpfx = str(phasedict['pId'])+'::Afrac:' |
|---|
| 1215 | for i,atom in enumerate(Atoms): |
|---|
| 1216 | if self.parmDict.get(fpfx+str(i),atom[cfrac]) == 0.0: continue |
|---|
| 1217 | xyz.append([i,]+atom[cn:cn+2]+atom[cx:cx+3]) |
|---|
| 1218 | if 'DisAglCtls' in generalData: |
|---|
| 1219 | DisAglCtls = generalData['DisAglCtls'] |
|---|
| 1220 | else: |
|---|
| 1221 | dlg = G2gd.DisAglDialog(self.G2frame,DisAglCtls,generalData) |
|---|
| 1222 | if dlg.ShowModal() == wx.ID_OK: |
|---|
| 1223 | DisAglCtls = dlg.GetData() |
|---|
| 1224 | generalData['DisAglCtls'] = DisAglCtls |
|---|
| 1225 | else: |
|---|
| 1226 | dlg.Destroy() |
|---|
| 1227 | return |
|---|
| 1228 | dlg.Destroy() |
|---|
| 1229 | DisAglData['OrigAtoms'] = xyz |
|---|
| 1230 | DisAglData['TargAtoms'] = xyz |
|---|
| 1231 | SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps( |
|---|
| 1232 | generalData['SGData']) |
|---|
| 1233 | |
|---|
| 1234 | xpandSGdata = generalData['SGData'].copy() |
|---|
| 1235 | xpandSGdata.update({'SGOps':symOpList, |
|---|
| 1236 | 'SGInv':False, |
|---|
| 1237 | 'SGLatt':'P', |
|---|
| 1238 | 'SGCen':np.array([[0, 0, 0]]),}) |
|---|
| 1239 | DisAglData['SGData'] = xpandSGdata |
|---|
| 1240 | |
|---|
| 1241 | DisAglData['Cell'] = generalData['Cell'][1:] #+ volume |
|---|
| 1242 | if 'pId' in phasedict: |
|---|
| 1243 | DisAglData['pId'] = phasedict['pId'] |
|---|
| 1244 | DisAglData['covData'] = self.OverallParms['Covariance'] |
|---|
| 1245 | try: |
|---|
| 1246 | AtomLabels,DistArray,AngArray = G2stMn.RetDistAngle(DisAglCtls,DisAglData) |
|---|
| 1247 | except KeyError: # inside DistAngle for missing atom types in DisAglCtls |
|---|
| 1248 | print '**** ERROR - try again but do "Reset" to fill in missing atom types ****' |
|---|
| 1249 | |
|---|
| 1250 | # loop over interatomic distances for this phase |
|---|
| 1251 | WriteCIFitem('\n# MOLECULAR GEOMETRY') |
|---|
| 1252 | WriteCIFitem('loop_' + |
|---|
| 1253 | '\n\t_geom_bond_atom_site_label_1' + |
|---|
| 1254 | '\n\t_geom_bond_atom_site_label_2' + |
|---|
| 1255 | '\n\t_geom_bond_distance' + |
|---|
| 1256 | '\n\t_geom_bond_site_symmetry_1' + |
|---|
| 1257 | '\n\t_geom_bond_site_symmetry_2' + |
|---|
| 1258 | '\n\t_geom_bond_publ_flag') |
|---|
| 1259 | |
|---|
| 1260 | for i in sorted(AtomLabels.keys()): |
|---|
| 1261 | Dist = DistArray[i] |
|---|
| 1262 | for D in Dist: |
|---|
| 1263 | line = ' '+PutInCol(AtomLabels[i],6)+PutInCol(AtomLabels[D[0]],6) |
|---|
| 1264 | sig = D[4] |
|---|
| 1265 | if sig == 0: sig = -0.00009 |
|---|
| 1266 | line += PutInCol(G2mth.ValEsd(D[3],sig,True),10) |
|---|
| 1267 | line += " 1_555 " |
|---|
| 1268 | line += " {:3d}_".format(D[2]) |
|---|
| 1269 | for d in D[1]: |
|---|
| 1270 | line += "{:1d}".format(d+5) |
|---|
| 1271 | line += " yes" |
|---|
| 1272 | WriteCIFitem(line) |
|---|
| 1273 | |
|---|
| 1274 | # loop over interatomic angles for this phase |
|---|
| 1275 | WriteCIFitem('\nloop_' + |
|---|
| 1276 | '\n\t_geom_angle_atom_site_label_1' + |
|---|
| 1277 | '\n\t_geom_angle_atom_site_label_2' + |
|---|
| 1278 | '\n\t_geom_angle_atom_site_label_3' + |
|---|
| 1279 | '\n\t_geom_angle' + |
|---|
| 1280 | '\n\t_geom_angle_site_symmetry_1' + |
|---|
| 1281 | '\n\t_geom_angle_site_symmetry_2' + |
|---|
| 1282 | '\n\t_geom_angle_site_symmetry_3' + |
|---|
| 1283 | '\n\t_geom_angle_publ_flag') |
|---|
| 1284 | |
|---|
| 1285 | for i in sorted(AtomLabels.keys()): |
|---|
| 1286 | Dist = DistArray[i] |
|---|
| 1287 | for k,j,tup in AngArray[i]: |
|---|
| 1288 | Dj = Dist[j] |
|---|
| 1289 | Dk = Dist[k] |
|---|
| 1290 | line = ' '+PutInCol(AtomLabels[Dj[0]],6)+PutInCol(AtomLabels[i],6)+PutInCol(AtomLabels[Dk[0]],6) |
|---|
| 1291 | sig = tup[1] |
|---|
| 1292 | if sig == 0: sig = -0.009 |
|---|
| 1293 | line += PutInCol(G2mth.ValEsd(tup[0],sig,True),10) |
|---|
| 1294 | line += " {:3d}_".format(Dj[2]) |
|---|
| 1295 | for d in Dj[1]: |
|---|
| 1296 | line += "{:1d}".format(d+5) |
|---|
| 1297 | line += " 1_555 " |
|---|
| 1298 | line += " {:3d}_".format(Dk[2]) |
|---|
| 1299 | for d in Dk[1]: |
|---|
| 1300 | line += "{:1d}".format(d+5) |
|---|
| 1301 | line += " yes" |
|---|
| 1302 | WriteCIFitem(line) |
|---|
| 1303 | |
|---|
| 1304 | def WritePhaseInfo(phasenam): |
|---|
| 1305 | WriteCIFitem('\n# phase info for '+str(phasenam) + ' follows') |
|---|
| 1306 | phasedict = self.Phases[phasenam] # pointer to current phase info |
|---|
| 1307 | WriteCIFitem('_pd_phase_name', phasenam) |
|---|
| 1308 | pfx = str(phasedict['pId'])+'::' |
|---|
| 1309 | A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict) |
|---|
| 1310 | cellSig = G2stIO.getCellEsd(pfx, |
|---|
| 1311 | phasedict['General']['SGData'],A, |
|---|
| 1312 | self.OverallParms['Covariance']) # returns 7 vals, includes sigVol |
|---|
| 1313 | cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),) |
|---|
| 1314 | defsigL = 3*[-0.00001] + 3*[-0.001] + [-0.01] # significance to use when no sigma |
|---|
| 1315 | names = ['length_a','length_b','length_c', |
|---|
| 1316 | 'angle_alpha','angle_beta ','angle_gamma', |
|---|
| 1317 | 'volume'] |
|---|
| 1318 | prevsig = 0 |
|---|
| 1319 | for lbl,defsig,val,sig in zip(names,defsigL,cellList,cellSig): |
|---|
| 1320 | if sig: |
|---|
| 1321 | txt = G2mth.ValEsd(val,sig) |
|---|
| 1322 | prevsig = -sig # use this as the significance for next value |
|---|
| 1323 | else: |
|---|
| 1324 | txt = G2mth.ValEsd(val,min(defsig,prevsig),True) |
|---|
| 1325 | WriteCIFitem('_cell_'+lbl,txt) |
|---|
| 1326 | |
|---|
| 1327 | WriteCIFitem('_symmetry_cell_setting', |
|---|
| 1328 | phasedict['General']['SGData']['SGSys']) |
|---|
| 1329 | |
|---|
| 1330 | spacegroup = phasedict['General']['SGData']['SpGrp'].strip() |
|---|
| 1331 | # regularize capitalization and remove trailing H/R |
|---|
| 1332 | spacegroup = spacegroup[0].upper() + spacegroup[1:].lower().rstrip('rh ') |
|---|
| 1333 | WriteCIFitem('_symmetry_space_group_name_H-M',spacegroup) |
|---|
| 1334 | |
|---|
| 1335 | # generate symmetry operations including centering and center of symmetry |
|---|
| 1336 | SymOpList,offsetList,symOpList,G2oprList = G2spc.AllOps( |
|---|
| 1337 | phasedict['General']['SGData']) |
|---|
| 1338 | WriteCIFitem('loop_\n _space_group_symop_id\n _space_group_symop_operation_xyz') |
|---|
| 1339 | for i,op in enumerate(SymOpList,start=1): |
|---|
| 1340 | WriteCIFitem(' {:3d} {:}'.format(i,op.lower())) |
|---|
| 1341 | |
|---|
| 1342 | # loop over histogram(s) used in this phase |
|---|
| 1343 | if not oneblock and not self.quickmode: |
|---|
| 1344 | # report pointers to the histograms used in this phase |
|---|
| 1345 | histlist = [] |
|---|
| 1346 | for hist in self.Phases[phasenam]['Histograms']: |
|---|
| 1347 | if self.Phases[phasenam]['Histograms'][hist]['Use']: |
|---|
| 1348 | if phasebyhistDict.get(hist): |
|---|
| 1349 | phasebyhistDict[hist].append(phasenam) |
|---|
| 1350 | else: |
|---|
| 1351 | phasebyhistDict[hist] = [phasenam,] |
|---|
| 1352 | blockid = datablockidDict.get(hist) |
|---|
| 1353 | if not blockid: |
|---|
| 1354 | print "Internal error: no block for data. Phase "+str( |
|---|
| 1355 | phasenam)+" histogram "+str(hist) |
|---|
| 1356 | histlist = [] |
|---|
| 1357 | break |
|---|
| 1358 | histlist.append(blockid) |
|---|
| 1359 | |
|---|
| 1360 | if len(histlist) == 0: |
|---|
| 1361 | WriteCIFitem('# Note: phase has no associated data') |
|---|
| 1362 | |
|---|
| 1363 | # report atom params |
|---|
| 1364 | if phasedict['General']['Type'] == 'nuclear': #this needs macromolecular variant, etc! |
|---|
| 1365 | WriteAtomsNuclear(phasenam) |
|---|
| 1366 | else: |
|---|
| 1367 | raise Exception,"no export for mm coordinates implemented" |
|---|
| 1368 | # report cell contents |
|---|
| 1369 | WriteComposition(phasenam) |
|---|
| 1370 | if not self.quickmode: # report distances and angles |
|---|
| 1371 | WriteDistances(phasenam,SymOpList,offsetList,symOpList,G2oprList) |
|---|
| 1372 | |
|---|
| 1373 | def Yfmt(ndec,val): |
|---|
| 1374 | 'Format intensity values' |
|---|
| 1375 | out = ("{:."+str(ndec)+"f}").format(val) |
|---|
| 1376 | out = out.rstrip('0') # strip zeros to right of decimal |
|---|
| 1377 | return out.rstrip('.') # and decimal place when not needed |
|---|
| 1378 | |
|---|
| 1379 | def WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,nRefSets=1): |
|---|
| 1380 | WriteCIFitem('_reflns_number_total', str(refcount)) |
|---|
| 1381 | if hklmin is not None and nRefSets == 1: # hkl range has no meaning with multiple phases |
|---|
| 1382 | WriteCIFitem('_reflns_limit_h_min', str(int(hklmin[0]))) |
|---|
| 1383 | WriteCIFitem('_reflns_limit_h_max', str(int(hklmax[0]))) |
|---|
| 1384 | WriteCIFitem('_reflns_limit_k_min', str(int(hklmin[1]))) |
|---|
| 1385 | WriteCIFitem('_reflns_limit_k_max', str(int(hklmax[1]))) |
|---|
| 1386 | WriteCIFitem('_reflns_limit_l_min', str(int(hklmin[2]))) |
|---|
| 1387 | WriteCIFitem('_reflns_limit_l_max', str(int(hklmax[2]))) |
|---|
| 1388 | if hklmin is not None: |
|---|
| 1389 | WriteCIFitem('_reflns_d_resolution_low ', G2mth.ValEsd(dmax,-0.009)) |
|---|
| 1390 | WriteCIFitem('_reflns_d_resolution_high ', G2mth.ValEsd(dmin,-0.009)) |
|---|
| 1391 | |
|---|
| 1392 | def WritePowderData(histlbl): |
|---|
| 1393 | histblk = self.Histograms[histlbl] |
|---|
| 1394 | inst = histblk['Instrument Parameters'][0] |
|---|
| 1395 | hId = histblk['hId'] |
|---|
| 1396 | pfx = ':' + str(hId) + ':' |
|---|
| 1397 | |
|---|
| 1398 | if 'Lam1' in inst: |
|---|
| 1399 | ratio = self.parmDict.get('I(L2)/I(L1)',inst['I(L2)/I(L1)'][1]) |
|---|
| 1400 | sratio = self.sigDict.get('I(L2)/I(L1)',-0.0009) |
|---|
| 1401 | lam1 = self.parmDict.get('Lam1',inst['Lam1'][1]) |
|---|
| 1402 | slam1 = self.sigDict.get('Lam1',-0.00009) |
|---|
| 1403 | lam2 = self.parmDict.get('Lam2',inst['Lam2'][1]) |
|---|
| 1404 | slam2 = self.sigDict.get('Lam2',-0.00009) |
|---|
| 1405 | # always assume Ka1 & Ka2 if two wavelengths are present |
|---|
| 1406 | WriteCIFitem('_diffrn_radiation_type','K\\a~1,2~') |
|---|
| 1407 | WriteCIFitem('loop_' + |
|---|
| 1408 | '\n\t_diffrn_radiation_wavelength' + |
|---|
| 1409 | '\n\t_diffrn_radiation_wavelength_wt' + |
|---|
| 1410 | '\n\t_diffrn_radiation_wavelength_id') |
|---|
| 1411 | WriteCIFitem(' ' + PutInCol(G2mth.ValEsd(lam1,slam1),15)+ |
|---|
| 1412 | PutInCol('1.0',15) + |
|---|
| 1413 | PutInCol('1',5)) |
|---|
| 1414 | WriteCIFitem(' ' + PutInCol(G2mth.ValEsd(lam2,slam2),15)+ |
|---|
| 1415 | PutInCol(G2mth.ValEsd(ratio,sratio),15)+ |
|---|
| 1416 | PutInCol('2',5)) |
|---|
| 1417 | else: |
|---|
| 1418 | lam1 = self.parmDict.get('Lam',inst['Lam'][1]) |
|---|
| 1419 | slam1 = self.sigDict.get('Lam',-0.00009) |
|---|
| 1420 | WriteCIFitem('_diffrn_radiation_wavelength',G2mth.ValEsd(lam1,slam1)) |
|---|
| 1421 | |
|---|
| 1422 | if not oneblock: |
|---|
| 1423 | if not phasebyhistDict.get(histlbl): |
|---|
| 1424 | WriteCIFitem('\n# No phases associated with this data set') |
|---|
| 1425 | else: |
|---|
| 1426 | WriteCIFitem('\n# PHASE TABLE') |
|---|
| 1427 | WriteCIFitem('loop_' + |
|---|
| 1428 | '\n\t_pd_phase_id' + |
|---|
| 1429 | '\n\t_pd_phase_block_id' + |
|---|
| 1430 | '\n\t_pd_phase_mass_%') |
|---|
| 1431 | wtFrSum = 0. |
|---|
| 1432 | for phasenam in phasebyhistDict.get(histlbl): |
|---|
| 1433 | hapData = self.Phases[phasenam]['Histograms'][histlbl] |
|---|
| 1434 | General = self.Phases[phasenam]['General'] |
|---|
| 1435 | wtFrSum += hapData['Scale'][0]*General['Mass'] |
|---|
| 1436 | |
|---|
| 1437 | for phasenam in phasebyhistDict.get(histlbl): |
|---|
| 1438 | hapData = self.Phases[phasenam]['Histograms'][histlbl] |
|---|
| 1439 | General = self.Phases[phasenam]['General'] |
|---|
| 1440 | wtFr = hapData['Scale'][0]*General['Mass']/wtFrSum |
|---|
| 1441 | pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':' |
|---|
| 1442 | if pfx+'Scale' in self.sigDict: |
|---|
| 1443 | sig = self.sigDict[pfx+'Scale']*wtFr/hapData['Scale'][0] |
|---|
| 1444 | else: |
|---|
| 1445 | sig = -0.0001 |
|---|
| 1446 | WriteCIFitem( |
|---|
| 1447 | ' '+ |
|---|
| 1448 | str(self.Phases[phasenam]['pId']) + |
|---|
| 1449 | ' '+datablockidDict[phasenam]+ |
|---|
| 1450 | ' '+G2mth.ValEsd(wtFr,sig) |
|---|
| 1451 | ) |
|---|
| 1452 | WriteCIFitem('loop_' + |
|---|
| 1453 | '\n\t_gsas_proc_phase_R_F_factor' + |
|---|
| 1454 | '\n\t_gsas_proc_phase_R_Fsqd_factor' + |
|---|
| 1455 | '\n\t_gsas_proc_phase_id' + |
|---|
| 1456 | '\n\t_gsas_proc_phase_block_id') |
|---|
| 1457 | for phasenam in phasebyhistDict.get(histlbl): |
|---|
| 1458 | pfx = str(self.Phases[phasenam]['pId'])+':'+str(hId)+':' |
|---|
| 1459 | WriteCIFitem( |
|---|
| 1460 | ' '+ |
|---|
| 1461 | ' '+G2mth.ValEsd(histblk[pfx+'Rf']/100.,-.00009) + |
|---|
| 1462 | ' '+G2mth.ValEsd(histblk[pfx+'Rf^2']/100.,-.00009)+ |
|---|
| 1463 | ' '+str(self.Phases[phasenam]['pId'])+ |
|---|
| 1464 | ' '+datablockidDict[phasenam] |
|---|
| 1465 | ) |
|---|
| 1466 | else: |
|---|
| 1467 | # single phase in this histogram |
|---|
| 1468 | pfx = '0:'+str(hId)+':' |
|---|
| 1469 | WriteCIFitem('_refine_ls_R_F_factor ','%.5f'%(histblk[pfx+'Rf']/100.)) |
|---|
| 1470 | WriteCIFitem('_refine_ls_R_Fsqd_factor ','%.5f'%(histblk[pfx+'Rf^2']/100.)) |
|---|
| 1471 | |
|---|
| 1472 | WriteCIFitem('_pd_proc_ls_prof_R_factor ','%.5f'%(histblk['R']/100.)) |
|---|
| 1473 | WriteCIFitem('_pd_proc_ls_prof_wR_factor ','%.5f'%(histblk['wR']/100.)) |
|---|
| 1474 | WriteCIFitem('_gsas_proc_ls_prof_R_B_factor ','%.5f'%(histblk['Rb']/100.)) |
|---|
| 1475 | WriteCIFitem('_gsas_proc_ls_prof_wR_B_factor','%.5f'%(histblk['wRb']/100.)) |
|---|
| 1476 | WriteCIFitem('_pd_proc_ls_prof_wR_expected','%.5f'%(histblk['wRmin']/100.)) |
|---|
| 1477 | |
|---|
| 1478 | if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X': |
|---|
| 1479 | WriteCIFitem('_diffrn_radiation_probe','x-ray') |
|---|
| 1480 | pola = histblk['Instrument Parameters'][0].get('Polariz.') |
|---|
| 1481 | if pola: |
|---|
| 1482 | pfx = ':' + str(hId) + ':' |
|---|
| 1483 | sig = self.sigDict.get(pfx+'Polariz.',-0.0009) |
|---|
| 1484 | txt = G2mth.ValEsd(pola[1],sig) |
|---|
| 1485 | WriteCIFitem('_diffrn_radiation_polarisn_ratio',txt) |
|---|
| 1486 | elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N': |
|---|
| 1487 | WriteCIFitem('_diffrn_radiation_probe','neutron') |
|---|
| 1488 | # TOF (note that this may not be defined) |
|---|
| 1489 | #if histblk['Instrument Parameters'][0]['Type'][1][2] == 'T': |
|---|
| 1490 | # WriteCIFitem('_pd_meas_2theta_fixed',text) |
|---|
| 1491 | |
|---|
| 1492 | |
|---|
| 1493 | # TODO: this will need help from Bob |
|---|
| 1494 | #if not oneblock: |
|---|
| 1495 | #WriteCIFitem('\n# SCATTERING FACTOR INFO') |
|---|
| 1496 | #WriteCIFitem('loop_ _atom_type_symbol') |
|---|
| 1497 | #if histblk['Instrument Parameters'][0]['Type'][1][1] == 'X': |
|---|
| 1498 | # WriteCIFitem(' _atom_type_scat_dispersion_real') |
|---|
| 1499 | # WriteCIFitem(' _atom_type_scat_dispersion_imag') |
|---|
| 1500 | # for lbl in ('a1','a2','a3', 'a4', 'b1', 'b2', 'b3', 'b4', 'c'): |
|---|
| 1501 | # WriteCIFitem(' _atom_type_scat_Cromer_Mann_'+lbl) |
|---|
| 1502 | #elif histblk['Instrument Parameters'][0]['Type'][1][1] == 'N': |
|---|
| 1503 | # WriteCIFitem(' _atom_type_scat_length_neutron') |
|---|
| 1504 | #WriteCIFitem(' _atom_type_scat_source') |
|---|
| 1505 | |
|---|
| 1506 | WriteCIFitem('_pd_proc_ls_background_function',FormatBackground(histblk['Background'],histblk['hId'])) |
|---|
| 1507 | |
|---|
| 1508 | # TODO: this will need help from Bob |
|---|
| 1509 | #WriteCIFitem('_exptl_absorpt_process_details','?') |
|---|
| 1510 | #WriteCIFitem('_exptl_absorpt_correction_T_min','?') |
|---|
| 1511 | #WriteCIFitem('_exptl_absorpt_correction_T_max','?') |
|---|
| 1512 | #C extinction |
|---|
| 1513 | #WRITE(IUCIF,'(A)') '# Extinction correction' |
|---|
| 1514 | #CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_min',TEXT(1:10)) |
|---|
| 1515 | #CALL WRVAL(IUCIF,'_gsas_exptl_extinct_corr_T_max',TEXT(11:20)) |
|---|
| 1516 | |
|---|
| 1517 | if not oneblock: # instrumental profile terms go here |
|---|
| 1518 | WriteCIFitem('_pd_proc_ls_profile_function', |
|---|
| 1519 | FormatInstProfile(histblk["Instrument Parameters"],histblk['hId'])) |
|---|
| 1520 | |
|---|
| 1521 | #refprx = '_refln.' # mm |
|---|
| 1522 | refprx = '_refln_' # normal |
|---|
| 1523 | WriteCIFitem('\n# STRUCTURE FACTOR TABLE') |
|---|
| 1524 | # compute maximum intensity reflection |
|---|
| 1525 | Imax = 0 |
|---|
| 1526 | for phasenam in histblk['Reflection Lists']: |
|---|
| 1527 | scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0] |
|---|
| 1528 | Icorr = np.array([refl[13] for refl in histblk['Reflection Lists'][phasenam]])[0] |
|---|
| 1529 | FO2 = np.array([refl[8] for refl in histblk['Reflection Lists'][phasenam]]) |
|---|
| 1530 | I100 = scale*FO2*Icorr |
|---|
| 1531 | Imax = max(Imax,max(I100)) |
|---|
| 1532 | |
|---|
| 1533 | WriteCIFitem('loop_') |
|---|
| 1534 | if len(histblk['Reflection Lists'].keys()) > 1: |
|---|
| 1535 | WriteCIFitem('\t_pd_refln_phase_id') |
|---|
| 1536 | WriteCIFitem('\t' + refprx + 'index_h' + |
|---|
| 1537 | '\n\t' + refprx + 'index_k' + |
|---|
| 1538 | '\n\t' + refprx + 'index_l' + |
|---|
| 1539 | '\n\t' + refprx + 'F_squared_meas' + |
|---|
| 1540 | '\n\t' + refprx + 'F_squared_calc' + |
|---|
| 1541 | '\n\t' + refprx + 'phase_calc' + |
|---|
| 1542 | '\n\t_pd_refln_d_spacing') |
|---|
| 1543 | if Imax > 0: |
|---|
| 1544 | WriteCIFitem('\t_gsas_i100_meas') |
|---|
| 1545 | |
|---|
| 1546 | refcount = 0 |
|---|
| 1547 | hklmin = None |
|---|
| 1548 | hklmax = None |
|---|
| 1549 | dmax = None |
|---|
| 1550 | dmin = None |
|---|
| 1551 | for phasenam in histblk['Reflection Lists']: |
|---|
| 1552 | scale = self.Phases[phasenam]['Histograms'][histlbl]['Scale'][0] |
|---|
| 1553 | phaseid = self.Phases[phasenam]['pId'] |
|---|
| 1554 | refcount += len(histblk['Reflection Lists'][phasenam]) |
|---|
| 1555 | for ref in histblk['Reflection Lists'][phasenam]: |
|---|
| 1556 | if DEBUG: |
|---|
| 1557 | print 'DEBUG: skip reflection list' |
|---|
| 1558 | break |
|---|
| 1559 | if hklmin is None: |
|---|
| 1560 | hklmin = ref[0:3] |
|---|
| 1561 | hklmax = ref[0:3] |
|---|
| 1562 | dmax = dmin = ref[4] |
|---|
| 1563 | if len(histblk['Reflection Lists'].keys()) > 1: |
|---|
| 1564 | s = PutInCol(phaseid,2) |
|---|
| 1565 | else: |
|---|
| 1566 | s = "" |
|---|
| 1567 | for i,hkl in enumerate(ref[0:3]): |
|---|
| 1568 | hklmax[i] = max(hkl,hklmax[i]) |
|---|
| 1569 | hklmin[i] = min(hkl,hklmin[i]) |
|---|
| 1570 | s += PutInCol(int(hkl),4) |
|---|
| 1571 | for I in ref[8:10]: |
|---|
| 1572 | s += PutInCol(G2mth.ValEsd(I,-0.0009),10) |
|---|
| 1573 | s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7) |
|---|
| 1574 | dmax = max(dmax,ref[4]) |
|---|
| 1575 | dmin = min(dmin,ref[4]) |
|---|
| 1576 | s += PutInCol(G2mth.ValEsd(ref[4],-0.009),8) |
|---|
| 1577 | if Imax > 0: |
|---|
| 1578 | I100 = 100.*scale*ref[8]*ref[13]/Imax |
|---|
| 1579 | s += PutInCol(G2mth.ValEsd(I100,-0.09),6) |
|---|
| 1580 | WriteCIFitem(" "+s) |
|---|
| 1581 | |
|---|
| 1582 | WriteReflStat(refcount,hklmin,hklmax,dmin,dmax,len(histblk['Reflection Lists'])) |
|---|
| 1583 | WriteCIFitem('\n# POWDER DATA TABLE') |
|---|
| 1584 | # is data fixed step? If the step varies by <0.01% treat as fixed step |
|---|
| 1585 | steps = histblk['Data'][0][1:] - histblk['Data'][0][:-1] |
|---|
| 1586 | if abs(max(steps)-min(steps)) > abs(max(steps))/10000.: |
|---|
| 1587 | fixedstep = False |
|---|
| 1588 | else: |
|---|
| 1589 | fixedstep = True |
|---|
| 1590 | |
|---|
| 1591 | if fixedstep: # and not TOF |
|---|
| 1592 | WriteCIFitem('_pd_meas_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0],-0.00009)) |
|---|
| 1593 | WriteCIFitem('_pd_meas_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1],-0.00009)) |
|---|
| 1594 | WriteCIFitem('_pd_meas_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009)) |
|---|
| 1595 | # zero correct, if defined |
|---|
| 1596 | zero = None |
|---|
| 1597 | zerolst = histblk['Instrument Parameters'][0].get('Zero') |
|---|
| 1598 | if zerolst: zero = zerolst[1] |
|---|
| 1599 | zero = self.parmDict.get('Zero',zero) |
|---|
| 1600 | if zero: |
|---|
| 1601 | WriteCIFitem('_pd_proc_2theta_range_min', G2mth.ValEsd(histblk['Data'][0][0]-zero,-0.00009)) |
|---|
| 1602 | WriteCIFitem('_pd_proc_2theta_range_max', G2mth.ValEsd(histblk['Data'][0][-1]-zero,-0.00009)) |
|---|
| 1603 | WriteCIFitem('_pd_proc_2theta_range_inc', G2mth.ValEsd(steps.sum()/len(steps),-0.00009)) |
|---|
| 1604 | |
|---|
| 1605 | if zero: |
|---|
| 1606 | WriteCIFitem('_pd_proc_number_of_points', str(len(histblk['Data'][0]))) |
|---|
| 1607 | else: |
|---|
| 1608 | WriteCIFitem('_pd_meas_number_of_points', str(len(histblk['Data'][0]))) |
|---|
| 1609 | WriteCIFitem('\nloop_') |
|---|
| 1610 | # WriteCIFitem('\t_pd_proc_d_spacing') # need easy way to get this |
|---|
| 1611 | if not fixedstep: |
|---|
| 1612 | if zero: |
|---|
| 1613 | WriteCIFitem('\t_pd_proc_2theta_corrected') |
|---|
| 1614 | else: |
|---|
| 1615 | WriteCIFitem('\t_pd_meas_2theta_scan') |
|---|
| 1616 | # at least for now, always report weights. |
|---|
| 1617 | #if countsdata: |
|---|
| 1618 | # WriteCIFitem('\t_pd_meas_counts_total') |
|---|
| 1619 | #else: |
|---|
| 1620 | WriteCIFitem('\t_pd_meas_intensity_total') |
|---|
| 1621 | WriteCIFitem('\t_pd_calc_intensity_total') |
|---|
| 1622 | WriteCIFitem('\t_pd_proc_intensity_bkg_calc') |
|---|
| 1623 | WriteCIFitem('\t_pd_proc_ls_weight') |
|---|
| 1624 | maxY = max(histblk['Data'][1].max(),histblk['Data'][3].max()) |
|---|
| 1625 | if maxY < 0: maxY *= -10 # this should never happen, but... |
|---|
| 1626 | ndec = max(0,10-int(np.log10(maxY))-1) # 10 sig figs should be enough |
|---|
| 1627 | maxSU = histblk['Data'][2].max() |
|---|
| 1628 | if maxSU < 0: maxSU *= -1 # this should never happen, but... |
|---|
| 1629 | ndecSU = max(0,8-int(np.log10(maxSU))-1) # 8 sig figs should be enough |
|---|
| 1630 | lowlim,highlim = histblk['Limits'][1] |
|---|
| 1631 | |
|---|
| 1632 | if DEBUG: |
|---|
| 1633 | print 'DEBUG: skip profile list' |
|---|
| 1634 | else: |
|---|
| 1635 | for x,yobs,yw,ycalc,ybkg in zip(histblk['Data'][0], |
|---|
| 1636 | histblk['Data'][1], |
|---|
| 1637 | histblk['Data'][2], |
|---|
| 1638 | histblk['Data'][3], |
|---|
| 1639 | histblk['Data'][4]): |
|---|
| 1640 | if lowlim <= x <= highlim: |
|---|
| 1641 | pass |
|---|
| 1642 | else: |
|---|
| 1643 | yw = 0.0 # show the point is not in use |
|---|
| 1644 | |
|---|
| 1645 | if fixedstep: |
|---|
| 1646 | s = "" |
|---|
| 1647 | else: |
|---|
| 1648 | s = PutInCol(G2mth.ValEsd(x-zero,-0.00009),10) |
|---|
| 1649 | s += PutInCol(Yfmt(ndec,yobs),12) |
|---|
| 1650 | s += PutInCol(Yfmt(ndec,ycalc),12) |
|---|
| 1651 | s += PutInCol(Yfmt(ndec,ybkg),11) |
|---|
| 1652 | s += PutInCol(Yfmt(ndecSU,yw),9) |
|---|
| 1653 | WriteCIFitem(" "+s) |
|---|
| 1654 | |
|---|
| 1655 | def WriteSingleXtalData(histlbl): |
|---|
| 1656 | histblk = self.Histograms[histlbl] |
|---|
| 1657 | #refprx = '_refln.' # mm |
|---|
| 1658 | refprx = '_refln_' # normal |
|---|
| 1659 | |
|---|
| 1660 | WriteCIFitem('\n# STRUCTURE FACTOR TABLE') |
|---|
| 1661 | WriteCIFitem('loop_' + |
|---|
| 1662 | '\n\t' + refprx + 'index_h' + |
|---|
| 1663 | '\n\t' + refprx + 'index_k' + |
|---|
| 1664 | '\n\t' + refprx + 'index_l' + |
|---|
| 1665 | '\n\t' + refprx + 'F_squared_meas' + |
|---|
| 1666 | '\n\t' + refprx + 'F_squared_sigma' + |
|---|
| 1667 | '\n\t' + refprx + 'F_squared_calc' + |
|---|
| 1668 | '\n\t' + refprx + 'phase_calc' |
|---|
| 1669 | ) |
|---|
| 1670 | |
|---|
| 1671 | hklmin = None |
|---|
| 1672 | hklmax = None |
|---|
| 1673 | dmax = None |
|---|
| 1674 | dmin = None |
|---|
| 1675 | refcount = len(histblk['Data']) |
|---|
| 1676 | for ref in histblk['Data']: |
|---|
| 1677 | s = " " |
|---|
| 1678 | if hklmin is None: |
|---|
| 1679 | hklmin = ref[0:3] |
|---|
| 1680 | hklmax = ref[0:3] |
|---|
| 1681 | dmax = dmin = ref[4] |
|---|
| 1682 | for i,hkl in enumerate(ref[0:3]): |
|---|
| 1683 | hklmax[i] = max(hkl,hklmax[i]) |
|---|
| 1684 | hklmin[i] = min(hkl,hklmin[i]) |
|---|
| 1685 | s += PutInCol(int(hkl),4) |
|---|
| 1686 | sig = ref[6] * ref[8] / ref[5] |
|---|
| 1687 | s += PutInCol(G2mth.ValEsd(ref[8],-abs(sig/10)),12) |
|---|
| 1688 | s += PutInCol(G2mth.ValEsd(sig,-abs(sig)/10.),10) |
|---|
| 1689 | s += PutInCol(G2mth.ValEsd(ref[9],-abs(sig/10)),12) |
|---|
| 1690 | s += PutInCol(G2mth.ValEsd(ref[10],-0.9),7) |
|---|
| 1691 | dmax = max(dmax,ref[4]) |
|---|
| 1692 | dmin = min(dmin,ref[4]) |
|---|
| 1693 | WriteCIFitem(s) |
|---|
| 1694 | WriteReflStat(refcount,hklmin,hklmax,dmin,dmax) |
|---|
| 1695 | hId = histblk['hId'] |
|---|
| 1696 | pfx = '0:'+str(hId)+':' |
|---|
| 1697 | WriteCIFitem('_reflns_wR_factor_obs ','%.4f'%(histblk['wR']/100.)) |
|---|
| 1698 | WriteCIFitem('_reflns_R_F_factor_obs ','%.4f'%(histblk[pfx+'Rf']/100.)) |
|---|
| 1699 | WriteCIFitem('_reflns_R_Fsqd_factor_obs','%.4f'%(histblk[pfx+'Rf^2']/100.)) |
|---|
| 1700 | def EditAuthor(event=None): |
|---|
| 1701 | 'Edit the CIF author name' |
|---|
| 1702 | dlg = G2gd.SingleStringDialog(self.G2frame, |
|---|
| 1703 | 'Get CIF Author', |
|---|
| 1704 | 'Provide CIF Author name (Last, First)', |
|---|
| 1705 | value=self.author) |
|---|
| 1706 | if not dlg.Show(): |
|---|
| 1707 | dlg.Destroy() |
|---|
| 1708 | return False # cancel was pressed |
|---|
| 1709 | self.author = dlg.GetValue() |
|---|
| 1710 | dlg.Destroy() |
|---|
| 1711 | try: |
|---|
| 1712 | self.OverallParms['Controls']["Author"] = self.author # save for future |
|---|
| 1713 | except KeyError: |
|---|
| 1714 | pass |
|---|
| 1715 | return True |
|---|
| 1716 | def EditInstNames(event=None): |
|---|
| 1717 | 'Provide a dialog for editing instrument names' |
|---|
| 1718 | dictlist = [] |
|---|
| 1719 | keylist = [] |
|---|
| 1720 | lbllist = [] |
|---|
| 1721 | for hist in self.Histograms: |
|---|
| 1722 | if hist.startswith("PWDR"): |
|---|
| 1723 | key2 = "Sample Parameters" |
|---|
| 1724 | d = self.Histograms[hist][key2] |
|---|
| 1725 | elif hist.startswith("HKLF"): |
|---|
| 1726 | key2 = "Instrument Parameters" |
|---|
| 1727 | d = self.Histograms[hist][key2][0] |
|---|
| 1728 | |
|---|
| 1729 | lbllist.append(hist) |
|---|
| 1730 | dictlist.append(d) |
|---|
| 1731 | keylist.append('InstrName') |
|---|
| 1732 | instrname = d.get('InstrName') |
|---|
| 1733 | if instrname is None: |
|---|
| 1734 | d['InstrName'] = '' |
|---|
| 1735 | return G2gd.CallScrolledMultiEditor( |
|---|
| 1736 | self.G2frame,dictlist,keylist, |
|---|
| 1737 | prelbl=range(1,len(dictlist)+1), |
|---|
| 1738 | postlbl=lbllist, |
|---|
| 1739 | title='Instrument names', |
|---|
| 1740 | header="Edit instrument names. Note that a non-blank\nname is required for all histograms", |
|---|
| 1741 | CopyButton=True) |
|---|
| 1742 | |
|---|
| 1743 | def EditRanges(event): |
|---|
| 1744 | but = event.GetEventObject() |
|---|
| 1745 | phasedict = but.phasedict |
|---|
| 1746 | dlg = G2gd.DisAglDialog(self.G2frame,{},phasedict['General']) |
|---|
| 1747 | if dlg.ShowModal() == wx.ID_OK: |
|---|
| 1748 | phasedict['General']['DisAglCtls'] = dlg.GetData() |
|---|
| 1749 | dlg.Destroy() |
|---|
| 1750 | |
|---|
| 1751 | def EditCIFDefaults(): |
|---|
| 1752 | 'Fills the CIF Defaults window' |
|---|
| 1753 | import wx.lib.scrolledpanel as wxscroll |
|---|
| 1754 | self.cifdefs.DestroyChildren() |
|---|
| 1755 | self.cifdefs.SetTitle('Edit CIF settings') |
|---|
| 1756 | vbox = wx.BoxSizer(wx.VERTICAL) |
|---|
| 1757 | cpnl = wxscroll.ScrolledPanel(self.cifdefs,size=(300,300)) |
|---|
| 1758 | cbox = wx.BoxSizer(wx.VERTICAL) |
|---|
| 1759 | but = wx.Button(cpnl, wx.ID_ANY,'Edit CIF Author') |
|---|
| 1760 | but.Bind(wx.EVT_BUTTON,EditAuthor) |
|---|
| 1761 | cbox.Add(but,0,wx.ALIGN_CENTER,3) |
|---|
| 1762 | but = wx.Button(cpnl, wx.ID_ANY,'Edit Instrument Name(s)') |
|---|
| 1763 | but.Bind(wx.EVT_BUTTON,EditInstNames) |
|---|
| 1764 | cbox.Add(but,0,wx.ALIGN_CENTER,3) |
|---|
| 1765 | G2gd.HorizontalLine(cbox,cpnl) |
|---|
| 1766 | cbox.Add( |
|---|
| 1767 | CIFtemplateSelect(self.cifdefs, |
|---|
| 1768 | cpnl,'publ',self.OverallParms['Controls'], |
|---|
| 1769 | EditCIFDefaults, |
|---|
| 1770 | "Publication (overall) template", |
|---|
| 1771 | ), |
|---|
| 1772 | 0,wx.EXPAND|wx.ALIGN_LEFT|wx.ALL) |
|---|
| 1773 | for phasenam in sorted(self.Phases.keys()): |
|---|
| 1774 | G2gd.HorizontalLine(cbox,cpnl) |
|---|
| 1775 | title = 'Phase '+phasenam |
|---|
| 1776 | phasedict = self.Phases[phasenam] # pointer to current phase info |
|---|
| 1777 | cbox.Add( |
|---|
| 1778 | CIFtemplateSelect(self.cifdefs, |
|---|
| 1779 | cpnl,'phase',phasedict['General'], |
|---|
| 1780 | EditCIFDefaults, |
|---|
| 1781 | title), |
|---|
| 1782 | 0,wx.EXPAND|wx.ALIGN_LEFT|wx.ALL) |
|---|
| 1783 | cpnl.SetSizer(cbox) |
|---|
| 1784 | but = wx.Button(cpnl, wx.ID_ANY,'Edit distance/angle ranges') |
|---|
| 1785 | #cbox.Add(but,0,wx.ALIGN_CENTER,3) |
|---|
| 1786 | cbox.Add((-1,2)) |
|---|
| 1787 | cbox.Add(but,0,wx.ALIGN_LEFT,0) |
|---|
| 1788 | but.phasedict = self.Phases[phasenam] # set a pointer to current phase info |
|---|
| 1789 | but.Bind(wx.EVT_BUTTON,EditRanges) # phase bond/angle ranges |
|---|
| 1790 | for i in sorted(self.powderDict.keys()): |
|---|
| 1791 | G2gd.HorizontalLine(cbox,cpnl) |
|---|
| 1792 | hist = self.powderDict[i] |
|---|
| 1793 | histblk = self.Histograms[hist] |
|---|
| 1794 | title = 'Powder dataset '+hist[5:] |
|---|
| 1795 | cbox.Add( |
|---|
| 1796 | CIFtemplateSelect(self.cifdefs, |
|---|
| 1797 | cpnl,'powder',histblk["Sample Parameters"], |
|---|
| 1798 | EditCIFDefaults, |
|---|
| 1799 | title), |
|---|
| 1800 | 0,wx.EXPAND|wx.ALIGN_LEFT|wx.ALL) |
|---|
| 1801 | cpnl.SetSizer(cbox) |
|---|
| 1802 | for i in sorted(self.xtalDict.keys()): |
|---|
| 1803 | G2gd.HorizontalLine(cbox,cpnl) |
|---|
| 1804 | hist = self.xtalDict[i] |
|---|
| 1805 | histblk = self.Histograms[hist] |
|---|
| 1806 | title = 'Single Xtal dataset '+hist[5:] |
|---|
| 1807 | cbox.Add( |
|---|
| 1808 | CIFtemplateSelect(self.cifdefs, |
|---|
| 1809 | cpnl,'single',histblk["Instrument Parameters"][0], |
|---|
| 1810 | EditCIFDefaults, |
|---|
| 1811 | title), |
|---|
| 1812 | 0,wx.EXPAND|wx.ALIGN_LEFT|wx.ALL) |
|---|
| 1813 | cpnl.SetSizer(cbox) |
|---|
| 1814 | |
|---|
| 1815 | cpnl.SetAutoLayout(1) |
|---|
| 1816 | cpnl.SetupScrolling() |
|---|
| 1817 | #cpnl.Bind(rw.EVT_RW_LAYOUT_NEEDED, self.OnLayoutNeeded) # needed if sizes change |
|---|
| 1818 | cpnl.Layout() |
|---|
| 1819 | |
|---|
| 1820 | vbox.Add(cpnl, 1, wx.ALIGN_LEFT|wx.ALL|wx.EXPAND, 0) |
|---|
| 1821 | btnsizer = wx.StdDialogButtonSizer() |
|---|
| 1822 | btn = wx.Button(self.cifdefs, wx.ID_OK, "Create CIF") |
|---|
| 1823 | btn.SetDefault() |
|---|
| 1824 | btnsizer.AddButton(btn) |
|---|
| 1825 | btn = wx.Button(self.cifdefs, wx.ID_CANCEL) |
|---|
| 1826 | btnsizer.AddButton(btn) |
|---|
| 1827 | btnsizer.Realize() |
|---|
| 1828 | vbox.Add(btnsizer, 0, wx.ALIGN_CENTER|wx.ALL, 5) |
|---|
| 1829 | self.cifdefs.SetSizer(vbox) |
|---|
| 1830 | vbox.Fit(self.cifdefs) |
|---|
| 1831 | self.cifdefs.Layout() |
|---|
| 1832 | |
|---|
| 1833 | # ===== end of functions for export method ======================================= |
|---|
| 1834 | #================================================================================= |
|---|
| 1835 | |
|---|
| 1836 | # the export process starts here |
|---|
| 1837 | # load all of the tree into a set of dicts |
|---|
| 1838 | self.loadTree() |
|---|
| 1839 | # create a dict with refined values and their uncertainties |
|---|
| 1840 | self.loadParmDict() |
|---|
| 1841 | |
|---|
| 1842 | # Someday: get restraint & constraint info |
|---|
| 1843 | #restraintDict = self.OverallParms.get('Restraints',{}) |
|---|
| 1844 | #for i in self.OverallParms['Constraints']: |
|---|
| 1845 | # print i |
|---|
| 1846 | # for j in self.OverallParms['Constraints'][i]: |
|---|
| 1847 | # print j |
|---|
| 1848 | |
|---|
| 1849 | self.CIFdate = dt.datetime.strftime(dt.datetime.now(),"%Y-%m-%dT%H:%M") |
|---|
| 1850 | # index powder and single crystal histograms |
|---|
| 1851 | self.powderDict = {} |
|---|
| 1852 | self.xtalDict = {} |
|---|
| 1853 | for hist in self.Histograms: |
|---|
| 1854 | i = self.Histograms[hist]['hId'] |
|---|
| 1855 | if hist.startswith("PWDR"): |
|---|
| 1856 | self.powderDict[i] = hist |
|---|
| 1857 | elif hist.startswith("HKLF"): |
|---|
| 1858 | self.xtalDict[i] = hist |
|---|
| 1859 | # is there anything to export? |
|---|
| 1860 | if len(self.Phases) == len(self.powderDict) == len(self.xtalDict) == 0: |
|---|
| 1861 | self.G2frame.ErrorDialog( |
|---|
| 1862 | 'Empty project', |
|---|
| 1863 | 'Project does not contain interconnected data & phase(s)') |
|---|
| 1864 | return |
|---|
| 1865 | # get the project file name |
|---|
| 1866 | self.CIFname = os.path.splitext( |
|---|
| 1867 | os.path.split(self.G2frame.GSASprojectfile)[1] |
|---|
| 1868 | )[0] |
|---|
| 1869 | self.CIFname = self.CIFname.replace(' ','') |
|---|
| 1870 | if not self.CIFname: # none defined & needed, save as GPX to get one |
|---|
| 1871 | self.G2frame.OnFileSaveas(None) |
|---|
| 1872 | if not self.G2frame.GSASprojectfile: return |
|---|
| 1873 | self.CIFname = os.path.splitext( |
|---|
| 1874 | os.path.split(self.G2frame.GSASprojectfile)[1] |
|---|
| 1875 | )[0] |
|---|
| 1876 | self.CIFname = self.CIFname.replace(' ','') |
|---|
| 1877 | # test for quick CIF mode or no data |
|---|
| 1878 | self.quickmode = False |
|---|
| 1879 | phasenam = phasenum = None # include all phases |
|---|
| 1880 | if mode != "full" or len(self.powderDict) + len(self.xtalDict) == 0: |
|---|
| 1881 | self.quickmode = True |
|---|
| 1882 | oneblock = True |
|---|
| 1883 | if len(self.Phases) == 0: |
|---|
| 1884 | self.G2frame.ErrorDialog( |
|---|
| 1885 | 'No phase present', |
|---|
| 1886 | 'Cannot create a coordinates CIF with no phases') |
|---|
| 1887 | return |
|---|
| 1888 | elif len(self.Phases) > 1: # quick mode: choose one phase |
|---|
| 1889 | choices = sorted(self.Phases.keys()) |
|---|
| 1890 | phasenum = G2gd.ItemSelector(choices,self.G2frame) |
|---|
| 1891 | if phasenum is None: return |
|---|
| 1892 | phasenam = choices[phasenum] |
|---|
| 1893 | # will this require a multiblock CIF? |
|---|
| 1894 | elif len(self.Phases) > 1: |
|---|
| 1895 | oneblock = False |
|---|
| 1896 | elif len(self.powderDict) + len(self.xtalDict) > 1: |
|---|
| 1897 | oneblock = False |
|---|
| 1898 | else: # one phase, one dataset, Full CIF |
|---|
| 1899 | oneblock = True |
|---|
| 1900 | |
|---|
| 1901 | # make sure needed infomation is present |
|---|
| 1902 | # get CIF author name -- required for full CIFs |
|---|
| 1903 | try: |
|---|
| 1904 | self.author = self.OverallParms['Controls'].get("Author",'').strip() |
|---|
| 1905 | except KeyError: |
|---|
| 1906 | pass |
|---|
| 1907 | while not (self.author or self.quickmode): |
|---|
| 1908 | if not EditAuthor(): return |
|---|
| 1909 | self.shortauthorname = self.author.replace(',','').replace(' ','')[:20] |
|---|
| 1910 | |
|---|
| 1911 | # check there is an instrument name for every histogram |
|---|
| 1912 | if not self.quickmode: |
|---|
| 1913 | invalid = 0 |
|---|
| 1914 | key3 = 'InstrName' |
|---|
| 1915 | for hist in self.Histograms: |
|---|
| 1916 | if hist.startswith("PWDR"): |
|---|
| 1917 | key2 = "Sample Parameters" |
|---|
| 1918 | d = self.Histograms[hist][key2] |
|---|
| 1919 | elif hist.startswith("HKLF"): |
|---|
| 1920 | key2 = "Instrument Parameters" |
|---|
| 1921 | d = self.Histograms[hist][key2][0] |
|---|
| 1922 | instrname = d.get(key3) |
|---|
| 1923 | if instrname is None: |
|---|
| 1924 | d[key3] = '' |
|---|
| 1925 | invalid += 1 |
|---|
| 1926 | elif instrname.strip() == '': |
|---|
| 1927 | invalid += 1 |
|---|
| 1928 | if invalid: |
|---|
| 1929 | msg = "" |
|---|
| 1930 | if invalid > 3: msg = ( |
|---|
| 1931 | "\n\nNote: it may be faster to set the name for\n" |
|---|
| 1932 | "one histogram for each instrument and use the\n" |
|---|
| 1933 | "File/Copy option to duplicate the name" |
|---|
| 1934 | ) |
|---|
| 1935 | if not EditInstNames(): return |
|---|
| 1936 | # check for a distance-angle range search range for each phase |
|---|
| 1937 | if not self.quickmode: |
|---|
| 1938 | for phasenam in sorted(self.Phases.keys()): |
|---|
| 1939 | #i = self.Phases[phasenam]['pId'] |
|---|
| 1940 | phasedict = self.Phases[phasenam] # pointer to current phase info |
|---|
| 1941 | if 'DisAglCtls' not in phasedict['General']: |
|---|
| 1942 | dlg = G2gd.DisAglDialog(self.G2frame,{},phasedict['General']) |
|---|
| 1943 | if dlg.ShowModal() == wx.ID_OK: |
|---|
| 1944 | phasedict['General']['DisAglCtls'] = dlg.GetData() |
|---|
| 1945 | else: |
|---|
| 1946 | dlg.Destroy() |
|---|
| 1947 | return |
|---|
| 1948 | dlg.Destroy() |
|---|
| 1949 | |
|---|
| 1950 | if oneblock and not self.quickmode: |
|---|
| 1951 | # select a dataset to use (there should only be one set in one block, |
|---|
| 1952 | # but take whatever comes 1st) |
|---|
| 1953 | for hist in self.Histograms: |
|---|
| 1954 | histblk = self.Histograms[hist] |
|---|
| 1955 | if hist.startswith("PWDR"): |
|---|
| 1956 | instnam = histblk["Sample Parameters"]['InstrName'] |
|---|
| 1957 | break # ignore all but 1st data histogram |
|---|
| 1958 | elif hist.startswith("HKLF"): |
|---|
| 1959 | instnam = histblk["Instrument Parameters"][0]['InstrName'] |
|---|
| 1960 | break # ignore all but 1st data histogram |
|---|
| 1961 | if self.quickmode: |
|---|
| 1962 | fil = self.askSaveFile() |
|---|
| 1963 | else: |
|---|
| 1964 | fil = self.defSaveFile() |
|---|
| 1965 | if not fil: return |
|---|
| 1966 | if not self.quickmode: # give the user a chance to edit all defaults |
|---|
| 1967 | self.cifdefs = wx.Dialog( |
|---|
| 1968 | self.G2frame,style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER) |
|---|
| 1969 | EditCIFDefaults() |
|---|
| 1970 | val = self.cifdefs.ShowModal() |
|---|
| 1971 | self.cifdefs.Destroy() |
|---|
| 1972 | if val != wx.ID_OK: |
|---|
| 1973 | return |
|---|
| 1974 | #====================================================================== |
|---|
| 1975 | # Start writing the CIF - single block |
|---|
| 1976 | #====================================================================== |
|---|
| 1977 | openCIF(fil) |
|---|
| 1978 | if oneblock: |
|---|
| 1979 | WriteCIFitem('data_'+self.CIFname) |
|---|
| 1980 | if phasenam is None: # if not already selected, select the first phase (should be one) |
|---|
| 1981 | phasenam = self.Phases.keys()[0] |
|---|
| 1982 | #print 'phasenam',phasenam |
|---|
| 1983 | phaseblk = self.Phases[phasenam] # pointer to current phase info |
|---|
| 1984 | if not self.quickmode: |
|---|
| 1985 | instnam = instnam.replace(' ','') |
|---|
| 1986 | WriteCIFitem('_pd_block_id', |
|---|
| 1987 | str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 1988 | str(self.shortauthorname) + "|" + instnam) |
|---|
| 1989 | WriteAudit() |
|---|
| 1990 | WritePubTemplate() |
|---|
| 1991 | WriteOverall() |
|---|
| 1992 | WritePhaseTemplate() |
|---|
| 1993 | # report the phase info |
|---|
| 1994 | WritePhaseInfo(phasenam) |
|---|
| 1995 | if hist.startswith("PWDR") and not self.quickmode: |
|---|
| 1996 | # preferred orientation |
|---|
| 1997 | SH = FormatSH(phasenam) |
|---|
| 1998 | MD = FormatHAPpo(phasenam) |
|---|
| 1999 | if SH and MD: |
|---|
| 2000 | WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + '\n' + MD) |
|---|
| 2001 | elif SH or MD: |
|---|
| 2002 | WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + MD) |
|---|
| 2003 | else: |
|---|
| 2004 | WriteCIFitem('_pd_proc_ls_pref_orient_corr', 'none') |
|---|
| 2005 | # report profile, since one-block: include both histogram and phase info |
|---|
| 2006 | WriteCIFitem('_pd_proc_ls_profile_function', |
|---|
| 2007 | FormatInstProfile(histblk["Instrument Parameters"],histblk['hId']) |
|---|
| 2008 | +'\n'+FormatPhaseProfile(phasenam)) |
|---|
| 2009 | WritePowderTemplate() |
|---|
| 2010 | WritePowderData(hist) |
|---|
| 2011 | elif hist.startswith("HKLF") and not self.quickmode: |
|---|
| 2012 | WriteSnglXtalTemplate() |
|---|
| 2013 | WriteSingleXtalData(hist) |
|---|
| 2014 | else: |
|---|
| 2015 | #====================================================================== |
|---|
| 2016 | # Start writing the CIF - multiblock |
|---|
| 2017 | #====================================================================== |
|---|
| 2018 | # publication info |
|---|
| 2019 | WriteCIFitem('\ndata_'+self.CIFname+'_publ') |
|---|
| 2020 | WriteAudit() |
|---|
| 2021 | WriteCIFitem('_pd_block_id', |
|---|
| 2022 | str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 2023 | str(self.shortauthorname) + "|Overall") |
|---|
| 2024 | WritePubTemplate() |
|---|
| 2025 | # overall info |
|---|
| 2026 | WriteCIFitem('data_'+str(self.CIFname)+'_overall') |
|---|
| 2027 | WriteOverall() |
|---|
| 2028 | #============================================================ |
|---|
| 2029 | WriteCIFitem('# POINTERS TO PHASE AND HISTOGRAM BLOCKS') |
|---|
| 2030 | datablockidDict = {} # save block names here -- N.B. check for conflicts between phase & hist names (unlikely!) |
|---|
| 2031 | # loop over phase blocks |
|---|
| 2032 | if len(self.Phases) > 1: |
|---|
| 2033 | loopprefix = '' |
|---|
| 2034 | WriteCIFitem('loop_ _pd_phase_block_id') |
|---|
| 2035 | else: |
|---|
| 2036 | loopprefix = '_pd_phase_block_id' |
|---|
| 2037 | |
|---|
| 2038 | for phasenam in sorted(self.Phases.keys()): |
|---|
| 2039 | i = self.Phases[phasenam]['pId'] |
|---|
| 2040 | datablockidDict[phasenam] = (str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 2041 | 'phase_'+ str(i) + '|' + str(self.shortauthorname)) |
|---|
| 2042 | WriteCIFitem(loopprefix,datablockidDict[phasenam]) |
|---|
| 2043 | # loop over data blocks |
|---|
| 2044 | if len(self.powderDict) + len(self.xtalDict) > 1: |
|---|
| 2045 | loopprefix = '' |
|---|
| 2046 | WriteCIFitem('loop_ _pd_block_diffractogram_id') |
|---|
| 2047 | else: |
|---|
| 2048 | loopprefix = '_pd_block_diffractogram_id' |
|---|
| 2049 | for i in sorted(self.powderDict.keys()): |
|---|
| 2050 | hist = self.powderDict[i] |
|---|
| 2051 | histblk = self.Histograms[hist] |
|---|
| 2052 | instnam = histblk["Sample Parameters"]['InstrName'] |
|---|
| 2053 | instnam = instnam.replace(' ','') |
|---|
| 2054 | i = histblk['hId'] |
|---|
| 2055 | datablockidDict[hist] = (str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 2056 | str(self.shortauthorname) + "|" + |
|---|
| 2057 | instnam + "_hist_"+str(i)) |
|---|
| 2058 | WriteCIFitem(loopprefix,datablockidDict[hist]) |
|---|
| 2059 | for i in sorted(self.xtalDict.keys()): |
|---|
| 2060 | hist = self.xtalDict[i] |
|---|
| 2061 | histblk = self.Histograms[hist] |
|---|
| 2062 | instnam = histblk["Instrument Parameters"][0]['InstrName'] |
|---|
| 2063 | instnam = instnam.replace(' ','') |
|---|
| 2064 | i = histblk['hId'] |
|---|
| 2065 | datablockidDict[hist] = (str(self.CIFdate) + "|" + str(self.CIFname) + "|" + |
|---|
| 2066 | str(self.shortauthorname) + "|" + |
|---|
| 2067 | instnam + "_hist_"+str(i)) |
|---|
| 2068 | WriteCIFitem(loopprefix,datablockidDict[hist]) |
|---|
| 2069 | #============================================================ |
|---|
| 2070 | # loop over phases, exporting them |
|---|
| 2071 | phasebyhistDict = {} # create a cross-reference to phases by histogram |
|---|
| 2072 | for j,phasenam in enumerate(sorted(self.Phases.keys())): |
|---|
| 2073 | i = self.Phases[phasenam]['pId'] |
|---|
| 2074 | WriteCIFitem('\ndata_'+self.CIFname+"_phase_"+str(i)) |
|---|
| 2075 | print "debug, processing ",phasenam |
|---|
| 2076 | WriteCIFitem('# Information for phase '+str(i)) |
|---|
| 2077 | WriteCIFitem('_pd_block_id',datablockidDict[phasenam]) |
|---|
| 2078 | # report the phase |
|---|
| 2079 | WritePhaseTemplate() |
|---|
| 2080 | WritePhaseInfo(phasenam) |
|---|
| 2081 | # preferred orientation |
|---|
| 2082 | SH = FormatSH(phasenam) |
|---|
| 2083 | MD = FormatHAPpo(phasenam) |
|---|
| 2084 | if SH and MD: |
|---|
| 2085 | WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + '\n' + MD) |
|---|
| 2086 | elif SH or MD: |
|---|
| 2087 | WriteCIFitem('_pd_proc_ls_pref_orient_corr', SH + MD) |
|---|
| 2088 | else: |
|---|
| 2089 | WriteCIFitem('_pd_proc_ls_pref_orient_corr', 'none') |
|---|
| 2090 | # report sample profile terms |
|---|
| 2091 | PP = FormatPhaseProfile(phasenam) |
|---|
| 2092 | if PP: |
|---|
| 2093 | WriteCIFitem('_pd_proc_ls_profile_function',PP) |
|---|
| 2094 | |
|---|
| 2095 | #============================================================ |
|---|
| 2096 | # loop over histograms, exporting them |
|---|
| 2097 | for i in sorted(self.powderDict.keys()): |
|---|
| 2098 | hist = self.powderDict[i] |
|---|
| 2099 | histblk = self.Histograms[hist] |
|---|
| 2100 | if hist.startswith("PWDR"): |
|---|
| 2101 | WriteCIFitem('\ndata_'+self.CIFname+"_pwd_"+str(i)) |
|---|
| 2102 | #instnam = histblk["Sample Parameters"]['InstrName'] |
|---|
| 2103 | # report instrumental profile terms |
|---|
| 2104 | WriteCIFitem('_pd_proc_ls_profile_function', |
|---|
| 2105 | FormatInstProfile(histblk["Instrument Parameters"],histblk['hId'])) |
|---|
| 2106 | WriteCIFitem('# Information for histogram '+str(i)+': '+hist) |
|---|
| 2107 | WriteCIFitem('_pd_block_id',datablockidDict[hist]) |
|---|
| 2108 | WritePowderTemplate() |
|---|
| 2109 | WritePowderData(hist) |
|---|
| 2110 | for i in sorted(self.xtalDict.keys()): |
|---|
| 2111 | hist = self.xtalDict[i] |
|---|
| 2112 | histblk = self.Histograms[hist] |
|---|
| 2113 | if hist.startswith("HKLF"): |
|---|
| 2114 | WriteCIFitem('\ndata_'+self.CIFname+"_sx_"+str(i)) |
|---|
| 2115 | #instnam = histblk["Instrument Parameters"][0]['InstrName'] |
|---|
| 2116 | WriteCIFitem('# Information for histogram '+str(i)+': '+hist) |
|---|
| 2117 | WriteCIFitem('_pd_block_id',datablockidDict[hist]) |
|---|
| 2118 | WriteSnglXtalTemplate() |
|---|
| 2119 | WriteSingleXtalData(hist) |
|---|
| 2120 | |
|---|
| 2121 | WriteCIFitem('#--' + 15*'eof--' + '#') |
|---|
| 2122 | closeCIF() |
|---|
