source: trunk/GSASIIIO.py

Last change on this file was 4968, checked in by toby, 3 months ago

finish hist/phase tree entry; create new help file for it(incomplete)

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1# -*- coding: utf-8 -*-
2########### SVN repository information ###################
3# $Date: 2021-06-21 22:58:24 +0000 (Mon, 21 Jun 2021) $
4# $Author: vondreele $
5# $Revision: 4968 $
6# $URL: trunk/GSASIIIO.py $
7# $Id: GSASIIIO.py 4968 2021-06-21 22:58:24Z vondreele $
8########### SVN repository information ###################
9'''
10*GSASIIIO: Misc I/O routines*
11=============================
12
13Module with miscellaneous routines for input and output. Many
14are GUI routines to interact with user.
15
16Includes support for image reading.
17
18Also includes base class for data export routines (TODO: should move)
19
20TODO: This module needs some work to separate wx from non-wx routines. GUI
21routines should probably move to GSASIIctrlGUI.
22'''
23
24from __future__ import division, print_function
25
26# Allow this to be imported without wx present. Was needed for G2scriptable, but is
27# likely not needed anymore
28try:
29    import wx
30except ImportError:
31    # was needed by sphinx, but probably not anymore
32    class Placeholder(object):
33        def __init__(self):
34            self.Dialog = object
35    wx = Placeholder()
36import math
37import numpy as np
38import numpy.ma as ma
39
40import copy
41import platform
42if '2' in platform.python_version_tuple()[0]:
43    import cPickle
44else:
45    import pickle as cPickle
46import sys
47import re
48import random as ran
49import GSASIIpath
50GSASIIpath.SetVersionNumber("$Revision: 4968 $")
51try:
52    import GSASIIdataGUI as G2gd
53except ImportError:
54    pass
55import GSASIIobj as G2obj
56import GSASIIlattice as G2lat
57try:
58    import GSASIIpwdGUI as G2pdG
59    import GSASIIimgGUI as G2imG
60except ImportError:
61    pass
62import GSASIIElem as G2el
63import GSASIIstrIO as G2stIO
64import GSASIImapvars as G2mv
65import GSASIIfiles as G2fil
66try:
67    import GSASIIctrlGUI as G2G
68except ImportError:
69    pass
70import os
71import os.path as ospath
72
73DEBUG = False       #=True for various prints
74TRANSP = False      #=true to transpose images for testing
75if GSASIIpath.GetConfigValue('Transpose'): TRANSP = True
76npsind = lambda x: np.sin(x*np.pi/180.)
77
78def sfloat(S):
79    'Convert a string to float. An empty field or a unconvertable value is treated as zero'
80    if S.strip():
81        try:
82            return float(S)
83        except ValueError:
84            pass
85    return 0.0
86
87def sint(S):
88    'Convert a string to int. An empty field is treated as zero'
89    if S.strip():
90        return int(S)
91    else:
92        return 0
93
94def trim(val):
95    '''Simplify a string containing leading and trailing spaces
96    as well as newlines, tabs, repeated spaces etc. into a shorter and
97    more simple string, by replacing all ranges of whitespace
98    characters with a single space.
99
100    :param str val: the string to be simplified
101
102    :returns: the (usually) shortened version of the string
103    '''
104    return re.sub('\\s+', ' ', val).strip()
105
106def FileDlgFixExt(dlg,file):
107    'this is needed to fix a problem in linux wx.FileDialog'
108    ext = dlg.GetWildcard().split('|')[2*dlg.GetFilterIndex()+1].strip('*')
109    if ext not in file:
110        file += ext
111    return file
112       
113def GetPowderPeaks(fileName):
114    'Read powder peaks from a file'
115    sind = lambda x: math.sin(x*math.pi/180.)
116    asind = lambda x: 180.*math.asin(x)/math.pi
117    wave = 1.54052
118    File = open(fileName,'r')
119    Comments = []
120    peaks = []
121    S = File.readline()
122    while S:
123        if S[:1] == '#':
124            Comments.append(S[:-1])
125        else:
126            item = S.split()
127            if len(item) == 1:
128                peaks.append([float(item[0]),1.0])
129            elif len(item) > 1:
130                peaks.append([float(item[0]),float(item[0])])
131        S = File.readline()
132    File.close()
133    if Comments:
134       print ('Comments on file:')
135       for Comment in Comments: 
136            print (Comment)
137            if 'wavelength' in Comment:
138                wave = float(Comment.split('=')[1])
139    Peaks = []
140    if peaks[0][0] > peaks[-1][0]:          # d-spacings - assume CuKa
141        for peak in peaks:
142            dsp = peak[0]
143            sth = wave/(2.0*dsp)
144            if sth < 1.0:
145                tth = 2.0*asind(sth)
146            else:
147                break
148            Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
149    else:                                   #2-thetas - assume Cuka (for now)
150        for peak in peaks:
151            tth = peak[0]
152            dsp = wave/(2.0*sind(tth/2.0))
153            Peaks.append([tth,peak[1],True,False,0,0,0,dsp,0.0])
154    limits = [1000.,0.]
155    for peak in Peaks:
156        limits[0] = min(limits[0],peak[0])
157        limits[1] = max(limits[1],peak[0])
158    limits[0] = max(1.,(int(limits[0]-1.)/5)*5.)
159    limits[1] = min(170.,(int(limits[1]+1.)/5)*5.)
160    return Comments,Peaks,limits,wave
161
162def GetCheckImageFile(G2frame,treeId):
163    '''Try to locate an image file if the project and image have been moved
164    together. If the image file cannot be found, request the location from
165    the user.
166
167    :param wx.Frame G2frame: main GSAS-II Frame and data object
168    :param wx.Id treeId: Id for the main tree item for the image
169    :returns: Npix,imagefile,imagetag with (Npix) number of pixels,
170       imagefile, if it exists, or the name of a file that does exist or False if the user presses Cancel
171       and (imagetag) an optional image number
172
173    '''
174    Npix,Imagefile,imagetag = G2frame.GPXtree.GetImageLoc(treeId)
175    if isinstance(Imagefile,list):
176        imagefile,imagetag = Imagefile
177    else:
178        imagefile = Imagefile
179    if not os.path.exists(imagefile):
180        print ('Image file '+imagefile+' not found')
181        fil = imagefile.replace('\\','/') # windows?!
182        # see if we can find a file with same name or in a similarly named sub-dir
183        pth,fil = os.path.split(fil)
184        prevpth = None
185        while pth and pth != prevpth:
186            prevpth = pth
187            if os.path.exists(os.path.join(G2frame.dirname,fil)):
188                print ('found image file '+os.path.join(G2frame.dirname,fil))
189                imagefile = os.path.join(G2frame.dirname,fil)
190                G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
191                return Npix,imagefile,imagetag
192            pth,enddir = os.path.split(pth)
193            fil = os.path.join(enddir,fil)
194        # not found as a subdirectory, drop common parts of path for last saved & image file names
195        #    if image was .../A/B/C/imgs/ima.ge
196        #      & GPX was  .../A/B/C/refs/fil.gpx but is now .../NEW/TEST/TEST1
197        #    will look for .../NEW/TEST/TEST1/imgs/ima.ge, .../NEW/TEST/imgs/ima.ge, .../NEW/imgs/ima.ge and so on
198        Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
199        gpxPath = Controls.get('LastSavedAs','').replace('\\','/').split('/') # blank in older .GPX files
200        imgPath = imagefile.replace('\\','/').split('/')
201        for p1,p2 in zip(gpxPath,imgPath):
202            if p1 == p2:
203                gpxPath.pop(0),imgPath.pop(0)
204            else:
205                break
206        fil = os.path.join(*imgPath) # file with non-common prefix elements
207        prevpth = None
208        pth = os.path.abspath(G2frame.dirname)
209        while pth and pth != prevpth:
210            prevpth = pth
211            if os.path.exists(os.path.join(pth,fil)):
212                print ('found image file '+os.path.join(pth,fil))
213                imagefile = os.path.join(pth,fil)
214                G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
215                return Npix,imagefile,imagetag
216            pth,enddir = os.path.split(pth)
217        #GSASIIpath.IPyBreak()
218
219    if not os.path.exists(imagefile):
220        # note that this fails (at least on Mac) to get an image during the GUI initialization
221        prevnam = os.path.split(imagefile)[1]
222        prevext = os.path.splitext(imagefile)[1]
223        wildcard = 'Image format (*'+prevext+')|*'+prevext
224        dlg = wx.FileDialog(G2frame, 'Previous image file ('+prevnam+') not found; open here', '.', prevnam,
225                            wildcard,wx.FD_OPEN)
226        try:
227            dlg.SetFilename(''+ospath.split(imagefile)[1])
228            if dlg.ShowModal() == wx.ID_OK:
229                imagefile = dlg.GetPath()
230                G2frame.GPXtree.UpdateImageLoc(treeId,imagefile)
231            else:
232                imagefile = None # was False
233        finally:
234            dlg.Destroy()
235    return Npix,imagefile,imagetag
236
237def EditImageParms(parent,Data,Comments,Image,filename):
238    dlg = wx.Dialog(parent, wx.ID_ANY, 'Edit image parameters',
239                    style=wx.DEFAULT_DIALOG_STYLE | wx.RESIZE_BORDER)
240    def onClose(event):
241        dlg.EndModal(wx.ID_OK)
242    mainsizer = wx.BoxSizer(wx.VERTICAL)
243    h,w = Image.size[:2]
244    mainsizer.Add(wx.StaticText(dlg,wx.ID_ANY,'File '+str(filename)+'\nImage size: '+str(h)+' x '+str(w)),
245        0,wx.ALIGN_LEFT|wx.ALL, 2)
246   
247    vsizer = wx.BoxSizer(wx.HORIZONTAL)
248    vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Wavelength (\xC5) '),
249        0,wx.ALIGN_LEFT|wx.ALL, 2)
250    wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'wavelength')
251    vsizer.Add(wdgt)
252    mainsizer.Add(vsizer,0,wx.ALIGN_LEFT|wx.ALL, 2)
253
254    vsizer = wx.BoxSizer(wx.HORIZONTAL)
255    vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Pixel size (\xb5m). Width '),
256        0,wx.ALIGN_LEFT|wx.ALL, 2)
257    wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],0,size=(50,-1))
258    vsizer.Add(wdgt)
259    vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'  Height '),wx.ALIGN_LEFT|wx.ALL, 2)
260    wdgt = G2G.ValidatedTxtCtrl(dlg,Data['pixelSize'],1,size=(50,-1))
261    vsizer.Add(wdgt)
262    mainsizer.Add(vsizer,0,wx.ALIGN_LEFT|wx.ALL, 2)
263
264    vsizer = wx.BoxSizer(wx.HORIZONTAL)
265    vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Sample to detector (mm) '),
266        0,wx.ALIGN_LEFT|wx.ALL, 2)
267    wdgt = G2G.ValidatedTxtCtrl(dlg,Data,'distance')
268    vsizer.Add(wdgt)
269    mainsizer.Add(vsizer,0,wx.ALIGN_LEFT|wx.ALL, 2)
270
271    vsizer = wx.BoxSizer(wx.HORIZONTAL)
272    vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Beam center (pixels). X = '),
273        0,wx.ALIGN_LEFT|wx.ALL, 2)
274    wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],0,size=(75,-1))
275    vsizer.Add(wdgt)
276    vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'  Y = '),wx.ALIGN_LEFT|wx.ALL, 2)
277    wdgt = G2G.ValidatedTxtCtrl(dlg,Data['center'],1,size=(75,-1))
278    vsizer.Add(wdgt)
279    mainsizer.Add(vsizer,0,wx.ALIGN_LEFT|wx.ALL, 2)
280
281    vsizer = wx.BoxSizer(wx.HORIZONTAL)
282    vsizer.Add(wx.StaticText(dlg,wx.ID_ANY,u'Comments '),
283        0,wx.ALIGN_LEFT|wx.ALL, 2)
284    wdgt = G2G.ValidatedTxtCtrl(dlg,Comments,0,size=(250,-1))
285    vsizer.Add(wdgt)
286    mainsizer.Add(vsizer,0,wx.ALIGN_LEFT|wx.ALL, 2)
287
288    btnsizer = wx.StdDialogButtonSizer()
289    OKbtn = wx.Button(dlg, wx.ID_OK, 'Continue')
290    OKbtn.SetDefault()
291    OKbtn.Bind(wx.EVT_BUTTON,onClose)
292    btnsizer.AddButton(OKbtn) # not sure why this is needed
293    btnsizer.Realize()
294    mainsizer.Add(btnsizer, 1, wx.ALL|wx.EXPAND, 5)
295    dlg.SetSizer(mainsizer)
296    dlg.CenterOnParent()
297    dlg.ShowModal()
298   
299def LoadImage2Tree(imagefile,G2frame,Comments,Data,Npix,Image):
300    '''Load an image into the tree. Saves the location of the image, as well as the
301    ImageTag (where there is more than one image in the file), if defined.
302    '''
303    ImgNames = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
304    TreeLbl = 'IMG '+os.path.basename(imagefile)
305    ImageTag = Data.get('ImageTag')
306    if ImageTag:
307        TreeLbl += ' #'+'%04d'%(ImageTag)
308        imageInfo = (imagefile,ImageTag)
309    else:
310        imageInfo = imagefile
311    TreeName = G2obj.MakeUniqueLabel(TreeLbl,ImgNames)
312    Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=TreeName)
313    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)
314    Imax = np.amax(Image)
315    if G2frame.imageDefault:
316        Data.update(copy.deepcopy(G2frame.imageDefault))
317        Data['showLines'] = True
318        Data['ring'] = []
319        Data['rings'] = []
320        Data['cutoff'] = 10.
321        Data['pixLimit'] = 20
322        Data['edgemin'] = 100000000
323        Data['calibdmin'] = 0.5
324        Data['calibskip'] = 0
325        Data['ellipses'] = []
326        Data['calibrant'] = ''
327        Data['GonioAngles'] = [0.,0.,0.]
328        Data['DetDepthRef'] = False
329    else:
330        Data['type'] = 'PWDR'
331        Data['color'] = GSASIIpath.GetConfigValue('Contour_color','Paired')
332        if 'tilt' not in Data:          #defaults if not preset in e.g. Bruker importer
333            Data['tilt'] = 0.0
334            Data['rotation'] = 0.0
335            Data['pixLimit'] = 20
336            Data['calibdmin'] = 0.5
337            Data['cutoff'] = 10.
338        Data['showLines'] = False
339        Data['calibskip'] = 0
340        Data['ring'] = []
341        Data['rings'] = []
342        Data['edgemin'] = 100000000
343        Data['ellipses'] = []
344        Data['GonioAngles'] = [0.,0.,0.]
345        Data['DetDepth'] = 0.
346        Data['DetDepthRef'] = False
347        Data['calibrant'] = ''
348        Data['IOtth'] = [5.0,50.0]
349        if GSASIIpath.GetConfigValue('Image_2theta_min'):
350            try:
351                Data['IOtth'][0] = float(GSASIIpath.GetConfigValue('Image_2theta_min'))
352            except:
353                pass
354        if GSASIIpath.GetConfigValue('Image_2theta_max'):
355            try:
356                Data['IOtth'][1] = float(GSASIIpath.GetConfigValue('Image_2theta_max'))
357            except:
358                pass
359        Data['LRazimuth'] = [0.,180.]
360        Data['azmthOff'] = 0.0
361        Data['outChannels'] = 2500
362        Data['outAzimuths'] = 1
363        Data['centerAzm'] = False
364        Data['fullIntegrate'] = GSASIIpath.GetConfigValue('fullIntegrate',True)
365        Data['setRings'] = False
366        Data['background image'] = ['',-1.0]                           
367        Data['dark image'] = ['',-1.0]
368        Data['Flat Bkg'] = 0.0
369        Data['Oblique'] = [0.5,False]
370    Data['setDefault'] = False
371    Data['range'] = [(0,Imax),[0,Imax]]
372    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Image Controls'),Data)
373    Masks = {'Points':[],'Rings':[],'Arcs':[],'Polygons':[],'Frames':[],
374                 'Thresholds':[(0,Imax),[0,Imax]],
375                 'SpotMask':{'esdMul':3.,'spotMask':None}}
376    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Masks'),Masks)
377    G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Stress/Strain'),
378        {'Type':'True','d-zero':[],'Sample phi':0.0,'Sample z':0.0,'Sample load':0.0})
379    G2frame.GPXtree.SetItemPyData(Id,[Npix,imageInfo])
380    G2frame.PickId = Id
381    G2frame.PickIdText = G2frame.GetTreeItemsList(G2frame.PickId)
382    G2frame.Image = Id
383
384def GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None,FormatName=''):
385    '''Read a single image with an image importer. This is called to reread an image
386    after it has already been imported with :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
387    (or :func:`ReadImages` in Auto Integration) so it is not necessary to reload metadata.
388
389    :param wx.Frame G2frame: main GSAS-II Frame and data object.
390    :param str imagefile: name of image file
391    :param bool imageOnly: If True return only the image,
392      otherwise  (default) return more (see below)
393    :param int/str ImageTag: specifies a particular image to be read from a file.
394      First image is read if None (default).
395    :param str formatName: the image reader formatName
396
397    :returns: an image as a numpy array or a list of four items:
398      Comments, Data, Npix and the Image, as selected by imageOnly
399
400    '''
401    # determine which formats are compatible with this file
402    primaryReaders = []
403    secondaryReaders = []
404    for rd in G2frame.ImportImageReaderlist:
405        flag = rd.ExtensionValidator(imagefile)
406        if flag is None: 
407            secondaryReaders.append(rd)
408        elif flag:
409            if not FormatName:
410                primaryReaders.append(rd)
411            elif FormatName in rd.formatName:       #This is a kluge because the rd.formatName was changed!
412                primaryReaders.append(rd)
413    if len(secondaryReaders) + len(primaryReaders) == 0:
414        print('Error: No matching format for file '+imagefile)
415        raise Exception('No image read')
416    errorReport = ''
417    if not imagefile:
418        return
419    for rd in primaryReaders+secondaryReaders:
420        rd.ReInitialize() # purge anything from a previous read
421        rd.errors = "" # clear out any old errors
422        if not rd.ContentsValidator(imagefile): # rejected on cursory check
423            errorReport += "\n  "+rd.formatName + ' validator error'
424            if rd.errors: 
425                errorReport += ': '+rd.errors
426                continue
427        if imageOnly:
428            ParentFrame = None # prevent GUI access on reread
429        else:
430            ParentFrame = G2frame
431        if GSASIIpath.GetConfigValue('debug'):
432            flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
433        else:
434            flag = False
435            try:
436                flag = rd.Reader(imagefile,ParentFrame,blocknum=ImageTag)
437            except rd.ImportException as detail:
438                rd.errors += "\n  Read exception: "+str(detail)
439            except Exception as detail:
440                import traceback
441                rd.errors += "\n  Unhandled read exception: "+str(detail)
442                rd.errors += "\n  Traceback info:\n"+str(traceback.format_exc())
443        if flag: # this read succeeded
444            if rd.Image is None:
445                raise Exception('No image read. Strange!')
446            if GSASIIpath.GetConfigValue('Transpose'):
447                print ('Transposing Image!')
448                rd.Image = rd.Image.T
449            #rd.readfilename = imagefile
450            if imageOnly:
451                return rd.Image
452            else:
453                return rd.Comments,rd.Data,rd.Npix,rd.Image
454    else:
455        print('Error reading file '+imagefile)
456        print('Error messages(s)\n'+errorReport)
457        raise Exception('No image read')   
458
459def ReadImages(G2frame,imagefile):
460    '''Read one or more images from a file and put them into the Tree
461    using image importers. Called only in :meth:`AutoIntFrame.OnTimerLoop`.
462
463    ToDo: Images are most commonly read in :meth:`GSASIIdataGUI.GSASII.OnImportGeneric`
464    which is called from :meth:`GSASIIdataGUI.GSASII.OnImportImage`
465    it would be good if these routines used a common code core so that changes need to
466    be made in only one place.
467
468    :param wx.Frame G2frame: main GSAS-II Frame and data object.
469    :param str imagefile: name of image file
470
471    :returns: a list of the id's of the IMG tree items created
472    '''
473    # determine which formats are compatible with this file
474    primaryReaders = []
475    secondaryReaders = []
476    for rd in G2frame.ImportImageReaderlist:
477        flag = rd.ExtensionValidator(imagefile)
478        if flag is None:
479            secondaryReaders.append(rd)
480        elif flag:
481            primaryReaders.append(rd)
482    if len(secondaryReaders) + len(primaryReaders) == 0:
483        print('Error: No matching format for file '+imagefile)
484        raise Exception('No image read')
485    errorReport = ''
486    rdbuffer = {} # create temporary storage for file reader
487    for rd in primaryReaders+secondaryReaders:
488        rd.ReInitialize() # purge anything from a previous read
489        rd.errors = "" # clear out any old errors
490        if not rd.ContentsValidator(imagefile): # rejected on cursory check
491            errorReport += "\n  "+rd.formatName + ' validator error'
492            if rd.errors: 
493                errorReport += ': '+rd.errors
494                continue
495        ParentFrame = G2frame
496        block = 0
497        repeat = True
498        CreatedIMGitems = []
499        while repeat: # loop if the reader asks for another pass on the file
500            block += 1
501            repeat = False
502            if GSASIIpath.GetConfigValue('debug'):
503                flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
504            else:
505                flag = False
506                try:
507                    flag = rd.Reader(imagefile,ParentFrame,blocknum=block,Buffer=rdbuffer)
508                except rd.ImportException as detail:
509                    rd.errors += "\n  Read exception: "+str(detail)
510                except Exception as detail:
511                    import traceback
512                    rd.errors += "\n  Unhandled read exception: "+str(detail)
513                    rd.errors += "\n  Traceback info:\n"+str(traceback.format_exc())
514            if flag: # this read succeeded
515                if rd.Image is None:
516                    raise Exception('No image read. Strange!')
517                if GSASIIpath.GetConfigValue('Transpose'):
518                    print ('Transposing Image!')
519                    rd.Image = rd.Image.T
520                rd.Data['ImageTag'] = rd.repeatcount
521                rd.readfilename = imagefile
522                # Load generic metadata, as configured
523                G2fil.GetColumnMetadata(rd)
524                LoadImage2Tree(imagefile,G2frame,rd.Comments,rd.Data,rd.Npix,rd.Image)
525                repeat = rd.repeat
526            CreatedIMGitems.append(G2frame.Image)
527        if CreatedIMGitems: return CreatedIMGitems
528    else:
529        print('Error reading file '+imagefile)
530        print('Error messages(s)\n'+errorReport)
531        return []
532        #raise Exception('No image read')   
533
534def SaveMultipleImg(G2frame):
535    if not G2frame.GPXtree.GetCount():
536        print ('no images!')
537        return
538    choices = G2gd.GetGPXtreeDataNames(G2frame,['IMG ',])
539    if len(choices) == 1:
540        names = choices
541    else:
542        dlg = G2G.G2MultiChoiceDialog(G2frame,'Stress/Strain fitting','Select images to fit:',choices)
543        dlg.SetSelections([])
544        names = []
545        if dlg.ShowModal() == wx.ID_OK:
546            names = [choices[sel] for sel in dlg.GetSelections()]
547        dlg.Destroy()
548    if not names: return
549    for name in names:
550        Id = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, name)
551        Npix,imagefile,imagetag = G2frame.GPXtree.GetImageLoc(Id)
552        imroot = os.path.splitext(imagefile)[0]
553        if imagetag:
554            imroot += '_' + str(imagetag)
555        Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Image Controls'))
556        print('Writing '+imroot+'.imctrl')
557        File = open(imroot+'.imctrl','w')
558        keys = ['type','wavelength','calibrant','distance','center',
559                    'tilt','rotation','azmthOff','fullIntegrate','LRazimuth',
560                    'IOtth','outChannels','outAzimuths','invert_x','invert_y','DetDepth',
561                    'calibskip','pixLimit','cutoff','calibdmin','chisq','Flat Bkg',
562                    'binType','SampleShape','PolaVal','SampleAbs','dark image','background image']
563        for key in keys:
564            if key not in Data: continue    #uncalibrated!
565            File.write(key+':'+str(Data[key])+'\n')
566        File.close()
567        mask = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Masks'))
568        G2imG.CleanupMasks(mask)
569        print('Writing '+imroot+'.immask')
570        File = open(imroot+'.immask','w')
571        for key in ['Points','Rings','Arcs','Polygons','Frames','Thresholds']:
572            File.write(key+':'+str(mask[key])+'\n')
573        File.close()
574       
575def PutG2Image(filename,Comments,Data,Npix,image):
576    'Write an image as a python pickle - might be better as an .edf file?'
577    File = open(filename,'wb')
578    cPickle.dump([Comments,Data,Npix,image],File,2)
579    File.close()
580    return
581
582objectScanIgnore = [int,bool,float,str,np.float64,np.float32,np.int32,np.int64,np.ndarray,G2obj.G2VarObj,G2obj.ExpressionObj]
583try:
584    objectScanIgnore += [ma.MaskedArray] # fails in doc builds
585except AttributeError:
586    pass
587   
588if '2' in platform.python_version_tuple()[0]:
589    objectScanIgnore += [unicode,long,]
590   
591def objectScan(data,tag,indexStack=[]):
592    '''Recursively scan an object looking for unexpected data types.
593    This is used in debug mode to scan .gpx files for objects we did not
594    intend to be there.
595    '''
596    if type(data) is list or type(data) is tuple:
597        for i in range(len(data)):
598            val = objectScan(data[i],tag,indexStack+[i])
599            if val:
600                data[i] = val
601                print('...fixed')
602    elif type(data) is dict:
603        for key in data:
604            val = objectScan(data[key],tag,indexStack+[key])
605            if val:
606                data[key] = val
607                print('...fixed')
608    elif data is None:
609        return None
610    elif type(data) in objectScanIgnore:
611        return None
612    else:
613        s = 'unexpected object in '+tag
614        for i in indexStack:
615            s += "[{}]".format(i)
616        #print(s,data.__class__.__name__) # loses full name of class
617        print(s,type(data))
618        global unexpectedObject
619        unexpectedObject = True
620        # fix bad objects
621        if "gdi.Colour" in str(type(data)):
622            return tuple(data)
623        return
624   
625def cPickleLoad(fp):
626    if '2' in platform.python_version_tuple()[0]:
627        return cPickle.load(fp)
628    else:
629       return cPickle.load(fp,encoding='latin-1')
630
631def ProjFileOpen(G2frame,showProvenance=True):
632    'Read a GSAS-II project file and load into the G2 data tree'
633    if not os.path.exists(G2frame.GSASprojectfile):
634        print ('\n*** Error attempt to open project file that does not exist:\n   '+
635               str(G2frame.GSASprojectfile))
636        return
637    LastSavedUsing = None
638    filep = open(G2frame.GSASprojectfile,'rb')
639    if showProvenance: print ('loading from file: '+G2frame.GSASprojectfile)
640    GPXphase = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqPhase'
641    GPXhist = os.path.splitext(G2frame.GSASprojectfile)[0]+'.seqHist'
642    deleteSeq = False
643    hist = None
644    tmpHistIndex = {}
645    updateFromSeq = False
646    if os.path.exists(GPXphase) and os.path.exists(GPXhist):
647        dlg = wx.MessageDialog(G2frame,
648            'Load results from crashed sequential fit?\nNo deletes the files!', 'Recover partial sequential fit?', wx.YES | wx.NO | wx.CANCEL)
649        dlg.CenterOnParent()
650        try:
651            result = dlg.ShowModal()
652            deleteSeq = result != wx.ID_CANCEL
653            if result == wx.ID_YES:
654                updateFromSeq = True
655                fp = open(GPXphase,'rb')
656                data = cPickleLoad(fp) # first block in file should be Phases
657                if data[0][0] != 'Phases':
658                    raise Exception('Unexpected block in {} file. How did this happen?'
659                            .format(GPXphase))
660                Phases = {}
661                for name,vals in data[1:]:
662                    Phases[name] = vals
663                name,CovData = cPickleLoad(fp)[0] # 2nd block in file should be Covariance
664                name,RigidBodies = cPickleLoad(fp)[0] # 3rd block in file should be Rigid Bodies
665                fp.close()
666                # index the histogram updates
667                hist = open(GPXhist,'rb')
668                try:
669                    while True:
670                        loc = hist.tell()
671                        datum = cPickleLoad(hist)[0]
672                        tmpHistIndex[datum[0]] = loc
673                except EOFError:
674                    pass
675        finally:
676            dlg.Destroy()
677    wx.BeginBusyCursor()
678    try:
679        if GSASIIpath.GetConfigValue('show_gpxSize'):
680            posPrev = 0
681            sizeList = {}
682        while True:
683            try:
684                data = cPickleLoad(filep)
685            except EOFError:
686                break
687            datum = data[0]
688            if GSASIIpath.GetConfigValue('show_gpxSize'):
689                sizeList[datum[0]] = filep.tell()-posPrev
690                posPrev = filep.tell()
691            # scan the GPX file for unexpected objects
692            if GSASIIpath.GetConfigValue('debug'):
693                global unexpectedObject
694                unexpectedObject = False               
695                objectScan(data,'tree item "{}" entry '.format(datum[0]))
696                #if unexpectedObject:
697                #    print(datum[0])
698                #    GSASIIpath.IPyBreak()
699            Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=datum[0])
700            if datum[0] == 'Phases' and GSASIIpath.GetConfigValue('SeparateHistPhaseTreeItem',False):
701                G2frame.GPXtree.AppendItem(parent=G2frame.root,text='Hist/Phase')
702            if updateFromSeq and datum[0] == 'Phases':
703                for pdata in data[1:]:
704                    if pdata[0] in Phases:
705                        pdata[1].update(Phases[pdata[0]])
706            elif updateFromSeq and datum[0] == 'Covariance':
707                data[0][1] = CovData
708            elif updateFromSeq and datum[0] == 'Rigid bodies':
709                data[0][1] = RigidBodies
710            elif updateFromSeq and datum[0] in tmpHistIndex:
711                hist.seek(tmpHistIndex[datum[0]])
712                hdata = cPickleLoad(hist)
713                if data[0][0] != hdata[0][0]:
714                    print('Error! Updating {} with {}'.format(data[0][0],hdata[0][0]))
715                datum = hdata[0]
716                xferItems = ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']
717                hItems = {name:j+1 for j,(name,val) in enumerate(hdata[1:]) if name in xferItems}
718                for j,(name,val) in enumerate(data[1:]):
719                    if name not in xferItems: continue
720                    data[j+1][1] = hdata[hItems[name]][1]
721            if datum[0].startswith('PWDR'):               
722                if 'ranId' not in datum[1][0]: # patch: add random Id if not present
723                    datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
724                G2frame.GPXtree.SetItemPyData(Id,datum[1][:3])  #temp. trim off junk (patch?)
725            elif datum[0].startswith('HKLF'): 
726                if 'ranId' not in datum[1][0]: # patch: add random Id if not present
727                    datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
728                G2frame.GPXtree.SetItemPyData(Id,datum[1])
729            else:
730                G2frame.GPXtree.SetItemPyData(Id,datum[1])             
731                if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
732                    LastSavedUsing = datum[1]['LastSavedUsing']
733                if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
734                    print('DBG_Packages used to create .GPX file:')
735                    if 'dict' in str(type(datum[1]['PythonVersions'])):  #patch
736                        for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
737                            print({:<14s}: {:s}".format(p[0],p[1]))
738                    else:
739                        for p in datum[1]['PythonVersions']:
740                            print({:<12s} {:s}".format(p[0]+':',p[1]))
741            oldPDF = False
742            for datus in data[1:]:
743#patch - 1/23/17 PDF cleanup
744                if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
745                    oldPDF = True
746                    data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
747                    continue
748#end PDF cleanup
749                sub = G2frame.GPXtree.AppendItem(Id,datus[0])
750#patch
751                if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
752                    if datum[0].startswith('PWDR'):
753                        datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
754                    else:
755                        datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
756                    for item in datus[1][0]:               #zip makes tuples - now make lists!
757                        datus[1][0][item] = list(datus[1][0][item])
758#end patch
759                G2frame.GPXtree.SetItemPyData(sub,datus[1])
760            if 'PDF ' in datum[0][:4] and oldPDF:
761                sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks')
762                G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
763            if datum [0].startswith('IMG'):                   #retrieve image default flag & data if set
764                Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'))
765                if Data['setDefault']:
766                    G2frame.imageDefault = Data
767                    G2frame.imageDefault['setDefault'] = False
768                    if 'formatName' in G2frame.imageDefault: del G2frame.imageDefault['formatName']
769        if LastSavedUsing:
770            print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
771        else:
772            print('project load successful')
773        if GSASIIpath.GetConfigValue('show_gpxSize'):
774            print(50*'=')
775            print('File section sizes (Kb)')
776            for item in sizeList:
777                print({:20s} {:10.3f}'.format(
778                    item[:20],sizeList[item]/1024.))
779            print(50*'=')
780        G2frame.NewPlot = True
781    except Exception as errmsg:
782        if GSASIIpath.GetConfigValue('debug'):
783            print('\nError reading GPX file:',errmsg)
784            import traceback
785            print (traceback.format_exc())
786        msg = wx.MessageDialog(G2frame,message="Error reading file "+
787            str(G2frame.GSASprojectfile)+". This is not a current GSAS-II .gpx file",
788            caption="Load Error",style=wx.ICON_ERROR | wx.OK | wx.STAY_ON_TOP)
789        msg.ShowModal()
790    finally:
791        filep.close()
792        wx.EndBusyCursor()
793        G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
794    if deleteSeq:
795        if hist: hist.close()
796        try:
797            os.remove(GPXphase)
798        except:
799            print('Warning: unable to delete {}'.format(GPXphase))
800        try:
801            os.remove(GPXhist)
802        except:
803            print('Warning: unable to delete {}'.format(GPXhist))
804    G2frame.SetTitleByGPX()
805    if LastSavedUsing:
806        try:
807            G2G.updateNotifier(G2frame,int(LastSavedUsing))
808        except:
809            pass
810   
811def ProjFileSave(G2frame):
812    'Save a GSAS-II project file'
813    if not G2frame.GPXtree.IsEmpty():
814        file = open(G2frame.GSASprojectfile,'wb')
815        print ('save to file: '+G2frame.GSASprojectfile)
816        # stick the file name into the tree and version info into tree so they are saved.
817        # (Controls should always be created at this point)
818        try:
819            Controls = G2frame.GPXtree.GetItemPyData(
820                G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
821            Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
822            Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
823            Controls['PythonVersions'] = G2frame.PackageVersions
824        except:
825            pass
826        wx.BeginBusyCursor()
827        try:
828            item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
829            while item:
830                data = []
831                name = G2frame.GPXtree.GetItemText(item)
832                if name.startswith('Hist/Phase'):  # skip over this
833                    item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)                           
834                    continue
835                data.append([name,G2frame.GPXtree.GetItemPyData(item)])
836                item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
837                while item2:
838                    name = G2frame.GPXtree.GetItemText(item2)
839                    data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
840                    item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)                           
841                item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)                           
842                cPickle.dump(data,file,2)
843            file.close()
844            pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
845            if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
846            G2frame.LastGPXdir = pth
847        finally:
848            wx.EndBusyCursor()
849        print('project save successful')
850
851def SaveIntegration(G2frame,PickId,data,Overwrite=False):
852    'Save image integration results as powder pattern(s)'
853    waves = {'Cu':[1.54051,1.54433],'Ti':[2.74841,2.75207],'Cr':[2.28962,2.29351],
854        'Fe':[1.93597,1.93991],'Co':[1.78892,1.79278],'Mo':[0.70926,0.713543],
855        'Ag':[0.559363,0.563775]}
856    azms = G2frame.Integrate[1]
857    X = G2frame.Integrate[2][:-1]
858    N = len(X)
859    Id = G2frame.GPXtree.GetItemParent(PickId)
860    name = G2frame.GPXtree.GetItemText(Id)
861    name = name.replace('IMG ',data['type']+' ')
862    Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
863    Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
864    Comments.append('Dark image = %s\n'%str(data['dark image']))
865    Comments.append('Background image = %s\n'%str(data['background image']))
866    Comments.append('Gain map = %s\n'%str(data['Gain map']))
867   
868    if 'PWDR' in name:
869        if 'target' in data:
870            names = ['Type','Lam1','Lam2','I(L2)/I(L1)','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth'] 
871            codes = [0 for i in range(14)]
872        else:
873            if data.get('IfPink',False):
874                names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','alpha-0','alpha-1','beta-0','beta-1','Azimuth']
875                codes = [0 for i in range(15)]
876            else:
877                names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth'] 
878                codes = [0 for i in range(12)]
879    elif 'SASD' in name:
880        names = ['Type','Lam','Zero','Azimuth'] 
881        codes = [0 for i in range(4)]
882        X = 4.*np.pi*npsind(X/2.)/data['wavelength']    #convert to q
883    Xminmax = [X[0],X[-1]]
884    Azms = np.zeros(data['outAzimuths'])
885    dazm = 0.
886    if data['outAzimuths'] > 1:
887        dazm = np.min(np.abs(np.diff(azms)))/2.
888    G2frame.IntgOutList = []
889    for i,azm in enumerate(azms[:-1]):
890        Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
891        item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
892        # if Overwrite delete any duplicate
893        if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
894            print('Replacing '+Aname)
895            item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
896            G2frame.GPXtree.Delete(item)
897        else:
898            nOcc = 0
899            while item:
900                Name = G2frame.GPXtree.GetItemText(item)
901                if Aname in Name:
902                    nOcc += 1
903                item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
904            if nOcc:
905                Aname += '(%d)'%(nOcc)
906        Sample = G2obj.SetDefaultSample()       #set as Debye-Scherrer
907        Sample['Gonio. radius'] = data['distance']
908        Sample['Omega'] = data['GonioAngles'][0]
909        Sample['Chi'] = data['GonioAngles'][1]
910        Sample['Phi'] = data['GonioAngles'][2]
911        Sample['Azimuth'] = (azm+dazm)%360.    #put here as bin center
912        polariz = data['PolaVal'][0]
913        for item in Comments:
914            for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
915                'Chi','Phi'):
916                if key.lower() in item.lower():
917                    try:
918                        Sample[key] = float(item.split('=')[1])
919                    except:
920                        pass
921            if 'label_prm' in item.lower():
922                for num in ('1','2','3'):
923                    if 'label_prm'+num in item.lower():
924                        Controls['FreePrm'+num] = item.split('=')[1].strip()
925        if 'PWDR' in Aname:
926            if 'target' in data:    #from lab x-ray 2D imaging data
927                wave1,wave2 = waves[data['target']]
928                parms = ['PXC',wave1,wave2,0.5,0.0,polariz,290.,-40.,30.,6.,-14.,0.0,0.0001,Azms[i]]
929            else:
930                if data.get('IfPink',False):
931                    parms = ['PXB',data['wavelength'],0.0,polariz,0.,8000.,-150.,-24.,0.,0.,0.,13.,-1300.,3.,-7.,Azms[i]]   #from Sect 35 LSS
932                else:
933                    parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
934        elif 'SASD' in Aname:
935            Sample['Trans'] = data['SampleAbs'][0]
936            parms = ['LXC',data['wavelength'],0.0,Azms[i]]
937        Y = G2frame.Integrate[0][i]
938        Ymin = np.min(Y)
939        Ymax = np.max(Y)
940        W = np.where(Y>0.,1./Y,1.e-6)                    #probably not true
941        Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
942        G2frame.IntgOutList.append(Id)
943        G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)                   
944        G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
945        if 'PWDR' in Aname:
946            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev-1',1,3,1.0,0.0,0.0],
947                {'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[],'background PWDR':['',1.0,False]}])
948        inst = [dict(zip(names,zip(parms,parms,codes))),{}]
949        for item in inst[0]:
950            inst[0][item] = list(inst[0][item])
951        G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
952        if 'PWDR' in Aname:
953            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
954            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
955            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
956            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
957            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
958        elif 'SASD' in Aname:             
959            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
960            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
961            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
962        valuesdict = {
963            'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),'Offset':[0.0,0.0],'delOffset':0.02*Ymax,
964            'refOffset':-0.1*Ymax,'refDelt':0.1*Ymax,'Yminmax':[Ymin,Ymax]}
965        G2frame.GPXtree.SetItemPyData(Id,[valuesdict,
966            [np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
967    return Id       #last powder pattern generated
968   
969def XYsave(G2frame,XY,labelX='X',labelY='Y',names=[]):
970    'Save XY table data'
971    pth = G2G.GetExportPath(G2frame)
972    dlg = wx.FileDialog(
973        G2frame, 'Enter csv filename for XY table', pth, '',
974        'XY table file (*.csv)|*.csv',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
975    try:
976        if dlg.ShowModal() == wx.ID_OK:
977            filename = dlg.GetPath()
978            filename = os.path.splitext(filename)[0]+'.csv'
979            File = open(filename,'w')
980        else:
981            filename = None
982    finally:
983        dlg.Destroy()
984    if not filename:
985        return
986    for i in range(len(XY)):
987        if len(names):
988            header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
989        else:
990            header = '%s,%s(%d)\n'%(labelX,labelY,i)
991        File.write(header)
992        for x,y in XY[i].T:
993            File.write('%.3f,%.3f\n'%(x,y))   
994    File.close()
995    print (' XY data saved to: '+filename)                       
996   
997def PeakListSave(G2frame,file,peaks):
998    'Save powder peaks to a data file'
999    print ('save peak list to file: '+G2frame.peaklistfile)
1000    if not peaks:
1001        dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1002        try:
1003            dlg.ShowModal()
1004        finally:
1005            dlg.Destroy()
1006        return
1007    for peak in peaks:
1008        file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
1009            (peak[0],peak[2],peak[4],peak[6]))
1010    print ('peak list saved')
1011             
1012def IndexPeakListSave(G2frame,peaks):
1013    'Save powder peaks from the indexing list'
1014    file = open(G2frame.peaklistfile,'wa')
1015    print ('save index peak list to file: '+G2frame.peaklistfile)
1016    wx.BeginBusyCursor()
1017    try:
1018        if not peaks:
1019            dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1020            try:
1021                dlg.ShowModal()
1022            finally:
1023                dlg.Destroy()
1024            return
1025        for peak in peaks:
1026            file.write("%12.6f\n" % (peak[7]))
1027        file.close()
1028    finally:
1029        wx.EndBusyCursor()
1030    print ('index peak list saved')
1031               
1032def ExtractFileFromZip(filename, selection=None, confirmread=True,
1033                       confirmoverwrite=True, parent=None,
1034                       multipleselect=False):
1035    '''If the filename is a zip file, extract a file from that
1036    archive.
1037
1038    :param list Selection: used to predefine the name of the file
1039      to be extracted. Filename case and zip directory name are
1040      ignored in selection; the first matching file is used.
1041
1042    :param bool confirmread: if True asks the user to confirm before expanding
1043      the only file in a zip
1044
1045    :param bool confirmoverwrite: if True asks the user to confirm
1046      before overwriting if the extracted file already exists
1047
1048    :param bool multipleselect: if True allows more than one zip
1049      file to be extracted, a list of file(s) is returned.
1050      If only one file is present, do not ask which one, otherwise
1051      offer a list of choices (unless selection is used).
1052   
1053    :returns: the name of the file that has been created or a
1054      list of files (see multipleselect)
1055
1056    If the file is not a zipfile, return the name of the input file.
1057    If the zipfile is empty or no file has been selected, return None
1058    '''
1059    import zipfile # do this now, since we can save startup time by doing this only on need
1060    import shutil
1061    zloc = os.path.split(filename)[0]
1062    if not zipfile.is_zipfile(filename):
1063        #print("not zip")
1064        return filename
1065
1066    z = zipfile.ZipFile(filename,'r')
1067    zinfo = z.infolist()
1068
1069    if len(zinfo) == 0:
1070        #print('Zip has no files!')
1071        zlist = [-1]
1072    if selection:
1073        choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1074        if selection.lower() in choices:
1075            zlist = [choices.index(selection.lower())]
1076        else:
1077            print('debug: file '+str(selection)+' was not found in '+str(filename))
1078            zlist = [-1]
1079    elif len(zinfo) == 1 and confirmread:
1080        result = wx.ID_NO
1081        dlg = wx.MessageDialog(
1082            parent,
1083            'Is file '+str(zinfo[0].filename)+
1084            ' what you want to extract from '+
1085            str(os.path.split(filename)[1])+'?',
1086            'Confirm file', 
1087            wx.YES_NO | wx.ICON_QUESTION)
1088        try:
1089            result = dlg.ShowModal()
1090        finally:
1091            dlg.Destroy()
1092        if result == wx.ID_NO:
1093            zlist = [-1]
1094        else:
1095            zlist = [0]
1096    elif len(zinfo) == 1:
1097        zlist = [0]
1098    elif multipleselect:
1099        # select one or more from a from list
1100        choices = [i.filename for i in zinfo]
1101        dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1102            'Choose file(s)',choices)
1103        if dlg.ShowModal() == wx.ID_OK:
1104            zlist = dlg.GetSelections()
1105        else:
1106            zlist = []
1107        dlg.Destroy()
1108    else:
1109        # select one from a from list
1110        choices = [i.filename for i in zinfo]
1111        dlg = wx.SingleChoiceDialog(parent,
1112            'Select file to extract from zip file'+str(filename),'Choose file',
1113            choices,)
1114        if dlg.ShowModal() == wx.ID_OK:
1115            zlist = [dlg.GetSelection()]
1116        else:
1117            zlist = [-1]
1118        dlg.Destroy()
1119       
1120    outlist = []
1121    for zindex in zlist:
1122        if zindex >= 0:
1123            efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1124            if os.path.exists(efil) and confirmoverwrite:
1125                result = wx.ID_NO
1126                dlg = wx.MessageDialog(parent,
1127                    'File '+str(efil)+' already exists. OK to overwrite it?',
1128                    'Confirm overwrite',wx.YES_NO | wx.ICON_QUESTION)
1129                try:
1130                    result = dlg.ShowModal()
1131                finally:
1132                    dlg.Destroy()
1133                if result == wx.ID_NO:
1134                    zindex = -1
1135        if zindex >= 0:
1136            # extract the file to the current directory, regardless of it's original path
1137            #z.extract(zinfo[zindex],zloc)
1138            eloc,efil = os.path.split(zinfo[zindex].filename)
1139            outfile = os.path.join(zloc, efil)
1140            fpin = z.open(zinfo[zindex])
1141            fpout = open(outfile, "wb")
1142            shutil.copyfileobj(fpin, fpout)
1143            fpin.close()
1144            fpout.close()
1145            outlist.append(outfile)
1146    z.close()
1147    if multipleselect and len(outlist) >= 1:
1148        return outlist
1149    elif len(outlist) == 1:
1150        return outlist[0]
1151    else:
1152        return None
1153
1154def striphist(var,insChar=''):
1155    'strip a histogram number from a var name'
1156    sv = var.split(':')
1157    if len(sv) <= 1: return var
1158    if sv[1]:
1159        sv[1] = insChar
1160    return ':'.join(sv)
1161
1162######################################################################
1163# base classes for reading various types of data files
1164#   not used directly, only by subclassing
1165######################################################################
1166class ExportBaseclass(object):
1167    '''Defines a base class for the exporting of GSAS-II results.
1168
1169    This class is subclassed in the various exports/G2export_*.py files. Those files
1170    are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1171    appropriate menu items for each one and the .Exporter method is called
1172    directly from the menu item.
1173
1174    Routines may also define a .Writer method, which is used to write a single
1175    file without invoking any GUI objects.
1176    '''
1177    # TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1178    # TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1179    # TODO: move this class to G2fil
1180    def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1181        self.G2frame = G2frame
1182        self.formatName = formatName # short string naming file type
1183        self.extension = extension
1184        if longFormatName: # longer string naming file type
1185            self.longFormatName = longFormatName
1186        else:
1187            self.longFormatName = formatName
1188        self.OverallParms = {}
1189        self.Phases = {}
1190        self.Histograms = {}
1191        self.powderDict = {}
1192        self.sasdDict = {}
1193        self.refdDict = {}
1194        self.xtalDict = {}
1195        self.parmDict = {}
1196        self.sigDict = {}
1197        self.fp = None
1198        # updated in InitExport:
1199        self.currentExportType = None # type of export that has been requested
1200        # updated in ExportSelect (when used):
1201        self.phasenam = None # a list of selected phases
1202        self.histnam = None # a list of selected histograms
1203        self.filename = None # name of file to be written (single export) or template (multiple files)
1204        self.dirname = '' # name of directory where file(s) will be written
1205        self.fullpath = '' # name of file being written -- full path
1206       
1207        # items that should be defined in a subclass of this class
1208        self.exporttype = []  # defines the type(s) of exports that the class can handle.
1209        # The following types are defined: 'project', "phase", "powder", "single"
1210        self.multiple = False # set as True if the class can export multiple phases or histograms
1211        # self.multiple is ignored for "project" exports
1212
1213    def InitExport(self,event):
1214        '''Determines the type of menu that called the Exporter and
1215        misc initialization.
1216        '''
1217        self.filename = None # name of file to be written (single export)
1218        self.dirname = '' # name of file to be written (multiple export)
1219        if event:
1220            self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1221
1222    def MakePWDRfilename(self,hist):
1223        '''Make a filename root (no extension) from a PWDR histogram name
1224
1225        :param str hist: the histogram name in data tree (starts with "PWDR ")
1226        '''
1227        file0 = ''
1228        file1 = hist[5:]
1229        # replace repeated blanks
1230        while file1 != file0:
1231            file0 = file1
1232            file1 = file0.replace('  ',' ').strip()
1233        file0 = file1.replace('Azm= ','A')
1234        # if angle has unneeded decimal places on aziumuth, remove them
1235        if file0[-3:] == '.00': file0 = file0[:-3]
1236        file0 = file0.replace('.','_')
1237        file0 = file0.replace(' ','_')
1238        return file0
1239
1240    def ExportSelect(self,AskFile='ask'):
1241        '''Selects histograms or phases when needed. Sets a default file name when
1242        requested into self.filename; always sets a default directory in self.dirname.
1243
1244        :param bool AskFile: Determines how this routine processes getting a
1245          location to store the current export(s).
1246         
1247          * if AskFile is 'ask' (default option), get the name of the file to be written;
1248            self.filename and self.dirname are always set. In the case where
1249            multiple files must be generated, the export routine should do this
1250            based on self.filename as a template.
1251          * if AskFile is 'dir', get the name of the directory to be used;
1252            self.filename is not used, but self.dirname is always set. The export routine
1253            will always generate the file name.
1254          * if AskFile is 'single', get only the name of the directory to be used when
1255            multiple items will be written (as multiple files) are used
1256            *or* a complete file name is requested when a single file
1257            name is selected. self.dirname is always set and self.filename used
1258            only when a single file is selected. 
1259          * if AskFile is 'default', creates a name of the file to be used from
1260            the name of the project (.gpx) file. If the project has not been saved,
1261            then the name of file is requested.
1262            self.filename and self.dirname are always set. In the case where
1263            multiple file names must be generated, the export routine should do this
1264            based on self.filename.
1265          * if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1266            file. If the project has not been saved, then a directory is requested.
1267            self.filename is not used.
1268
1269        :returns: True in case of an error
1270        '''
1271       
1272        numselected = 1
1273        if self.currentExportType == 'phase':
1274            if len(self.Phases) == 0:
1275                self.G2frame.ErrorDialog(
1276                    'Empty project',
1277                    'Project does not contain any phases.')
1278                return True
1279            elif len(self.Phases) == 1:
1280                self.phasenam = list(self.Phases.keys())
1281            elif self.multiple: 
1282                choices = sorted(self.Phases.keys())
1283                phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1284                if phasenum is None: return True
1285                self.phasenam = [choices[i] for i in phasenum]
1286                if not self.phasenam: return True
1287                numselected = len(self.phasenam)
1288            else:
1289                choices = sorted(self.Phases.keys())
1290                phasenum = G2G.ItemSelector(choices,self.G2frame)
1291                if phasenum is None: return True
1292                self.phasenam = [choices[phasenum]]
1293                numselected = len(self.phasenam)
1294        elif self.currentExportType == 'single':
1295            if len(self.xtalDict) == 0:
1296                self.G2frame.ErrorDialog(
1297                    'Empty project',
1298                    'Project does not contain any single crystal data.')
1299                return True
1300            elif len(self.xtalDict) == 1:
1301                self.histnam = self.xtalDict.values()
1302            elif self.multiple:
1303                choices = sorted(self.xtalDict.values())
1304                hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1305                if not hnum: return True
1306                self.histnam = [choices[i] for i in hnum]
1307                numselected = len(self.histnam)
1308            else:
1309                choices = sorted(self.xtalDict.values())
1310                hnum = G2G.ItemSelector(choices,self.G2frame)
1311                if hnum is None: return True
1312                self.histnam = [choices[hnum]]
1313                numselected = len(self.histnam)
1314        elif self.currentExportType == 'powder':
1315            if len(self.powderDict) == 0:
1316                self.G2frame.ErrorDialog(
1317                    'Empty project',
1318                    'Project does not contain any powder data.')
1319                return True
1320            elif len(self.powderDict) == 1:
1321                self.histnam = list(self.powderDict.values())
1322            elif self.multiple:
1323                choices = sorted(self.powderDict.values())
1324                hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1325                if not hnum: return True
1326                self.histnam = [choices[i] for i in hnum]
1327                numselected = len(self.histnam)
1328            else:
1329                choices = sorted(self.powderDict.values())
1330                hnum = G2G.ItemSelector(choices,self.G2frame)
1331                if hnum is None: return True
1332                self.histnam = [choices[hnum]]
1333                numselected = len(self.histnam)
1334        elif self.currentExportType == 'sasd':
1335            if len(self.sasdDict) == 0:
1336                self.G2frame.ErrorDialog(
1337                    'Empty project',
1338                    'Project does not contain any small angle data.')
1339                return True
1340            elif len(self.sasdDict) == 1:
1341                self.histnam = self.sasdDict.values()
1342            elif self.multiple:
1343                choices = sorted(self.sasdDict.values())
1344                hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1345                if not hnum: return True
1346                self.histnam = [choices[i] for i in hnum]
1347                numselected = len(self.histnam)
1348            else:
1349                choices = sorted(self.sasdDict.values())
1350                hnum = G2G.ItemSelector(choices,self.G2frame)
1351                if hnum is None: return True
1352                self.histnam = [choices[hnum]]
1353                numselected = len(self.histnam)
1354        elif self.currentExportType == 'refd':
1355            if len(self.refdDict) == 0:
1356                self.G2frame.ErrorDialog(
1357                    'Empty project',
1358                    'Project does not contain any reflectivity data.')
1359                return True
1360            elif len(self.refdDict) == 1:
1361                self.histnam = self.refdDict.values()
1362            elif self.multiple:
1363                choices = sorted(self.refdDict.values())
1364                hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1365                if not hnum: return True
1366                self.histnam = [choices[i] for i in hnum]
1367                numselected = len(self.histnam)
1368            else:
1369                choices = sorted(self.refdDict.values())
1370                hnum = G2G.ItemSelector(choices,self.G2frame)
1371                if hnum is None: return True
1372                self.histnam = [choices[hnum]]
1373                numselected = len(self.histnam)
1374        elif self.currentExportType == 'image':
1375            if len(self.Histograms) == 0:
1376                self.G2frame.ErrorDialog(
1377                    'Empty project',
1378                    'Project does not contain any images.')
1379                return True
1380            elif len(self.Histograms) == 1:
1381                self.histnam = list(self.Histograms.keys())
1382            else:
1383                choices = sorted(self.Histograms.keys())
1384                hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1385                if self.multiple:
1386                    if not hnum: return True
1387                    self.histnam = [choices[i] for i in hnum]
1388                else:
1389                    if hnum is None: return True
1390                    self.histnam = [choices[hnum]]
1391                numselected = len(self.histnam)
1392        if self.currentExportType == 'map':
1393            # search for phases with maps
1394            mapPhases = []
1395            choices = []
1396            for phasenam in sorted(self.Phases):
1397                phasedict = self.Phases[phasenam] # pointer to current phase info           
1398                if len(phasedict['General']['Map'].get('rho',[])):
1399                    mapPhases.append(phasenam)
1400                    if phasedict['General']['Map'].get('Flip'):
1401                        choices.append('Charge flip map: '+str(phasenam))
1402                    elif phasedict['General']['Map'].get('MapType'):
1403                        choices.append(
1404                            str(phasedict['General']['Map'].get('MapType'))
1405                            + ' map: ' + str(phasenam))
1406                    else:
1407                        choices.append('unknown map: '+str(phasenam))
1408            # select a map if needed
1409            if len(mapPhases) == 0:
1410                self.G2frame.ErrorDialog(
1411                    'Empty project',
1412                    'Project does not contain any maps.')
1413                return True
1414            elif len(mapPhases) == 1:
1415                self.phasenam = mapPhases
1416            else: 
1417                phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1418                if self.multiple:
1419                    if not phasenum: return True
1420                    self.phasenam = [mapPhases[i] for i in phasenum]
1421                else:
1422                    if phasenum is None: return True
1423                    self.phasenam = [mapPhases[phasenum]]
1424            numselected = len(self.phasenam)
1425
1426        # items selected, now set self.dirname and usually self.filename
1427        if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1428            AskFile == 'default' and not self.G2frame.GSASprojectfile
1429            ):
1430            filename = self.askSaveFile()
1431            if not filename: return True
1432            self.dirname,self.filename = os.path.split(filename)
1433        elif AskFile == 'dir' or AskFile == 'single' or (
1434            AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1435            ):
1436            self.dirname = self.askSaveDirectory()
1437            if not self.dirname: return True
1438        elif AskFile == 'default-dir' or AskFile == 'default':
1439            self.dirname,self.filename = os.path.split(
1440                os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1441                )
1442        else:
1443            raise Exception('This should not happen!')
1444
1445    def loadParmDict(self):
1446        '''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1447        refined values to those from the last cycle and set the uncertainties for the
1448        refined parameters in another dict (self.sigDict).
1449
1450        Expands the parm & sig dicts to include values derived from constraints.
1451
1452        This could be made faster for sequential fits by reducing the histogram list to only
1453        the active histogram being exported.
1454        '''
1455        self.G2frame.CheckNotebook()
1456        self.parmDict = {}
1457        self.sigDict = {}
1458        rigidbodyDict = {}
1459        covDict = {}
1460        consDict = {}
1461        Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1462        if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1463        item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1464        while item:
1465            name = self.G2frame.GPXtree.GetItemText(item)
1466            if name == 'Rigid bodies':
1467                 rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1468            elif name == 'Covariance':
1469                 covDict = self.G2frame.GPXtree.GetItemPyData(item)
1470            elif name == 'Constraints':
1471                 consDict = self.G2frame.GPXtree.GetItemPyData(item)
1472            item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1473        rbVary,rbDict =  G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1474        self.parmDict.update(rbDict)
1475        rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1476        Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave =  G2stIO.GetPhaseData(
1477            Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1478        self.parmDict.update(phaseDict)
1479        hapVary,hapDict,controlDict =  G2stIO.GetHistogramPhaseData(
1480            Phases,Histograms,Print=False,resetRefList=False)
1481        self.parmDict.update(hapDict)
1482        histVary,histDict,controlDict =  G2stIO.GetHistogramData(Histograms,Print=False)
1483        self.parmDict.update(histDict)
1484        self.parmDict.update(zip(
1485            covDict.get('varyList',[]),
1486            covDict.get('variables',[])))
1487        self.sigDict = dict(zip(
1488            covDict.get('varyList',[]),
1489            covDict.get('sig',[])))
1490        # expand to include constraints: first compile a list of constraints
1491        constList = []
1492        for item in consDict:
1493            if item.startswith('_'): continue
1494            constList += consDict[item]
1495        # now process the constraints
1496        G2mv.InitVars()
1497        constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1498        varyList = covDict.get('varyListStart')
1499        if varyList is None and len(constDict) == 0:
1500            # no constraints can use varyList
1501            varyList = covDict.get('varyList')
1502        elif varyList is None:
1503            # old GPX file from before pre-constraint varyList is saved
1504            print (' *** Old refinement: Please use Calculate/Refine to redo  ***')
1505            raise Exception(' *** Export aborted ***')
1506        else:
1507            varyList = list(varyList)
1508        # add symmetry-generated constraints
1509        rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(   
1510            G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies'))
1511        rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1512        rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1513        Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1514            Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
1515        msg = G2mv.EvaluateMultipliers(constDict,phaseDict)
1516        if msg:
1517            print('Unable to interpret multiplier(s): '+msg)
1518            raise Exception(' *** CIF creation aborted ***')
1519        try:
1520            G2mv.GenerateConstraints(varyList,constDict,fixedList,self.parmDict)
1521            #print(G2mv.VarRemapShow(varyList))
1522        except:
1523            # this really should not happen
1524            print (' *** ERROR - constraints are internally inconsistent ***')
1525            errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1526            print ('Errors'+errmsg)
1527            if warnmsg: print ('Warnings'+warnmsg)
1528            raise Exception(' *** CIF creation aborted ***')
1529        # add the constrained values to the parameter dictionary
1530        G2mv.Dict2Map(self.parmDict,varyList)
1531        # and add their uncertainties into the esd dictionary (sigDict)
1532        if covDict.get('covMatrix') is not None:
1533            self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1534
1535    def loadTree(self):
1536        '''Load the contents of the data tree into a set of dicts
1537        (self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1538        & self.xtalDict)
1539       
1540        * The childrenless data tree items are overall parameters/controls for the
1541          entire project and are placed in self.OverallParms
1542        * Phase items are placed in self.Phases
1543        * Data items are placed in self.Histogram. The key for these data items
1544          begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1545        '''
1546        self.OverallParms = {}
1547        self.powderDict = {}
1548        self.sasdDict = {}
1549        self.refdDict = {}
1550        self.xtalDict = {}
1551        self.Phases = {}
1552        self.Histograms = {}
1553        self.SeqRefdata = None
1554        self.SeqRefhist = None
1555        if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1556        histType = None       
1557        if self.currentExportType == 'phase':
1558            # if exporting phases load them here
1559            sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1560            if not sub:
1561                print ('no phases found')
1562                return True
1563            item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1564            while item:
1565                phaseName = self.G2frame.GPXtree.GetItemText(item)
1566                self.Phases[phaseName] =  self.G2frame.GPXtree.GetItemPyData(item)
1567                item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1568            # Get rigid body info into self.OverallParms
1569            for key in ('Rigid bodies','Covariance'):
1570                item = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,key)
1571                if item:
1572                    self.OverallParms[key] = self.G2frame.GPXtree.GetItemPyData(item)
1573                item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1574            return
1575        elif self.currentExportType == 'single':
1576            histType = 'HKLF'
1577        elif self.currentExportType == 'powder':
1578            histType = 'PWDR'
1579        elif self.currentExportType == 'image':
1580            histType = 'IMG'
1581        elif self.currentExportType == 'sasd':
1582            histType = 'SASD'
1583        elif self.currentExportType == 'refd':
1584            histType = 'REFD'
1585
1586        if histType: # Loading just one kind of tree entry
1587            item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1588            while item:
1589                name = self.G2frame.GPXtree.GetItemText(item)
1590                if name.startswith(histType):
1591                    if self.Histograms.get(name): # there is already an item with this name
1592                        print('Histogram name '+str(name)+' is repeated. Renaming')
1593                        if name[-1] == '9':
1594                            name = name[:-1] + '10'
1595                        elif name[-1] in '012345678':
1596                            name = name[:-1] + str(int(name[-1])+1)
1597                        else:                           
1598                            name += '-1'
1599                    self.Histograms[name] = {}
1600                    # the main info goes into Data, but the 0th
1601                    # element contains refinement results, carry
1602                    # that over too now.
1603                    self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1604                    self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1605                    item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1606                    while item2: 
1607                        child = self.G2frame.GPXtree.GetItemText(item2)
1608                        self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1609                        item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1610                item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1611            # index powder and single crystal histograms by number
1612            for hist in self.Histograms:
1613                if hist.startswith("PWDR"): 
1614                    d = self.powderDict
1615                elif hist.startswith("HKLF"): 
1616                    d = self.xtalDict
1617                elif hist.startswith("SASD"):
1618                    d = self.sasdDict
1619                elif hist.startswith("REFD"):
1620                    d = self.refdDict
1621                else:
1622                    return                   
1623                i = self.Histograms[hist].get('hId')
1624                if i is None and not d.keys():
1625                    i = 0
1626                elif i is None or i in d.keys():
1627                    i = max(d.keys())+1
1628                d[i] = hist
1629            return
1630        # else standard load: using all interlinked phases and histograms
1631        self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1632        item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1633        while item:
1634            name = self.G2frame.GPXtree.GetItemText(item)
1635            item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1636            if not item2: 
1637                self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1638            item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1639        # index powder and single crystal histograms
1640        for hist in self.Histograms:
1641            i = self.Histograms[hist]['hId']
1642            if hist.startswith("PWDR"): 
1643                self.powderDict[i] = hist
1644            elif hist.startswith("HKLF"): 
1645                self.xtalDict[i] = hist
1646            elif hist.startswith("SASD"):
1647                self.sasdDict[i] = hist
1648            elif hist.startswith("REFD"):
1649                self.refdDict[i] = hist
1650
1651    def dumpTree(self,mode='type'):
1652        '''Print out information on the data tree dicts loaded in loadTree.
1653        Used for testing only.
1654        '''
1655        if self.SeqRefdata and self.SeqRefhist:
1656            print('Note that dumpTree does not show sequential results')
1657        print ('\nOverall')
1658        if mode == 'type':
1659            def Show(arg): return type(arg)
1660        else:
1661            def Show(arg): return arg
1662        for key in self.OverallParms:
1663            print ('  '+key+Show(self.OverallParms[key]))
1664        print ('Phases')
1665        for key1 in self.Phases:
1666            print ('    '+key1+Show(self.Phases[key1]))
1667        print ('Histogram')
1668        for key1 in self.Histograms:
1669            print ('    '+key1+Show(self.Histograms[key1]))
1670            for key2 in self.Histograms[key1]:
1671                print ('      '+key2+Show(self.Histograms[key1][key2]))
1672
1673    def defaultSaveFile(self):
1674        return os.path.abspath(
1675            os.path.splitext(self.G2frame.GSASprojectfile
1676                             )[0]+self.extension)
1677       
1678    def askSaveFile(self):
1679        '''Ask the user to supply a file name
1680
1681        :returns: a file name (str) or None if Cancel is pressed
1682
1683        '''
1684        #pth = G2G.GetExportPath(self.G2frame)
1685        if self.G2frame.GSASprojectfile:
1686            defnam = os.path.splitext(
1687                os.path.split(self.G2frame.GSASprojectfile)[1]
1688                )[0]+self.extension
1689        else:
1690            defnam = 'default' + self.extension
1691        return G2G.askSaveFile(self.G2frame,defnam,self.extension,self.longFormatName)
1692
1693    def askSaveDirectory(self):
1694        '''Ask the user to supply a directory name. Path name is used as the
1695        starting point for the next export path search.
1696
1697        :returns: a directory name (str) or None if Cancel is pressed
1698
1699        TODO: Can this be replaced with G2G.askSaveDirectory?
1700        '''
1701        pth = G2G.GetExportPath(self.G2frame)
1702        dlg = wx.DirDialog(
1703            self.G2frame, 'Input directory where file(s) will be written', pth,
1704            wx.DD_DEFAULT_STYLE)
1705        dlg.CenterOnParent()
1706        try:
1707            if dlg.ShowModal() == wx.ID_OK:
1708                filename = dlg.GetPath()
1709                self.G2frame.LastExportDir = filename
1710            else:
1711                filename = None
1712        finally:
1713            dlg.Destroy()
1714        return filename
1715
1716    # Tools for file writing.
1717    def OpenFile(self,fil=None,mode='w'):
1718        '''Open the output file
1719
1720        :param str fil: The name of the file to open. If None (default)
1721          the name defaults to self.dirname + self.filename.
1722          If an extension is supplied, it is not overridded,
1723          but if not, the default extension is used.
1724        :returns: the file object opened by the routine which is also
1725          saved as self.fp
1726        '''
1727        if mode == 'd': # debug mode
1728            self.fullpath = '(stdout)'
1729            self.fp = sys.stdout
1730            return
1731        if not fil:
1732            if not os.path.splitext(self.filename)[1]:
1733                self.filename += self.extension
1734            fil = os.path.join(self.dirname,self.filename)
1735        self.fullpath = os.path.abspath(fil)
1736        self.fp = open(self.fullpath,mode)
1737        return self.fp
1738
1739    def Write(self,line):
1740        '''write a line of output, attaching a line-end character
1741
1742        :param str line: the text to be written.
1743        '''
1744        if self.fp is None:
1745            raise Exception('Attempt to Write without use of OpenFile')
1746        self.fp.write(line+'\n')
1747       
1748    def CloseFile(self,fp=None):
1749        '''Close a file opened in OpenFile
1750
1751        :param file fp: the file object to be closed. If None (default)
1752          file object self.fp is closed.
1753        '''
1754        if self.fp is None:
1755            raise Exception('Attempt to CloseFile without use of OpenFile')
1756        if self.fp == sys.stdout: return # debug mode
1757        if fp is None:
1758            fp = self.fp
1759            self.fp = None
1760        if fp is not None: fp.close()
1761       
1762    def SetSeqRef(self,data,hist):
1763        '''Set the exporter to retrieve results from a sequential refinement
1764        rather than the main tree
1765        '''
1766        self.SeqRefdata = data
1767        self.SeqRefhist = hist
1768        data_name = data[hist]
1769        for i,val in zip(data_name['varyList'],data_name['sig']):
1770            self.sigDict[i] = val
1771            self.sigDict[striphist(i)] = val
1772        for i in data_name['parmDict']:
1773            self.parmDict[striphist(i)] = data_name['parmDict'][i]
1774            self.parmDict[i] = data_name['parmDict'][i]
1775            # zero out the dA[xyz] terms, they would only bring confusion
1776            key = i.split(':')
1777            if len(key) < 3: continue
1778            if key[2].startswith('dA'):
1779                self.parmDict[i] = 0.0
1780        for i,(val,sig) in data_name.get('depParmDict',{}).items():
1781            self.parmDict[i] = val
1782            self.sigDict[i] = sig
1783        #GSASIIpath.IPyBreak()
1784
1785    # Tools to pull information out of the data arrays
1786    def GetCell(self,phasenam):
1787        """Gets the unit cell parameters and their s.u.'s for a selected phase
1788
1789        :param str phasenam: the name for the selected phase
1790        :returns: `cellList,cellSig` where each is a 7 element list corresponding
1791          to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1792          cell values and `cellSig` has their uncertainties.
1793        """
1794        if self.SeqRefdata and self.SeqRefhist:
1795            return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1796        phasedict = self.Phases[phasenam] # pointer to current phase info
1797        try:
1798            pfx = str(phasedict['pId'])+'::'
1799            A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1800            cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1801                self.OverallParms['Covariance'])  # returns 7 vals, includes sigVol
1802            cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1803            return cellList,cellSig
1804        except KeyError:
1805            cell = phasedict['General']['Cell'][1:]
1806            return cell,7*[0]
1807           
1808    def GetSeqCell(self,phasenam,data_name):
1809        """Gets the unit cell parameters and their s.u.'s for a selected phase
1810        and histogram in a sequential fit
1811
1812        :param str phasenam: the name for the selected phase
1813        :param dict data_name: the sequential refinement parameters for the selected histogram
1814        :returns: `cellList,cellSig` where each is a 7 element list corresponding
1815          to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1816          cell values and `cellSig` has their uncertainties.
1817        """
1818        phasedict = self.Phases[phasenam]
1819        SGdata = phasedict['General']['SGData']
1820        pId = phasedict['pId']
1821        RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1822        ESDlookup = {}
1823        Dlookup = {}
1824        varied = [striphist(i) for i in data_name['varyList']]
1825        for item,val in data_name['newCellDict'].items():
1826            if item in varied:
1827                ESDlookup[val[0]] = item
1828                Dlookup[item] = val[0]
1829        A = RecpCellTerms[:]
1830        for i in range(6):
1831            var = str(pId)+'::A'+str(i)
1832            if var in ESDlookup:
1833                A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1834        cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1835        zeroDict = {i:0.0 for i in cellDict}
1836        A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1837        covData = {
1838            'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1839            'covMatrix': data_name['covMatrix']
1840            }
1841        return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1842               
1843    def GetAtoms(self,phasenam):
1844        """Gets the atoms associated with a phase. Can be used with standard
1845        or macromolecular phases
1846
1847        :param str phasenam: the name for the selected phase
1848        :returns: a list of items for eac atom where each item is a list containing:
1849          label, typ, mult, xyz, and td, where
1850
1851          * label and typ are the atom label and the scattering factor type (str)
1852          * mult is the site multiplicity (int)
1853          * xyz is contains a list with four pairs of numbers:
1854            x, y, z and fractional occupancy and
1855            their standard uncertainty (or a negative value)
1856          * td is contains a list with either one or six pairs of numbers:
1857            if one number it is U\\ :sub:`iso` and with six numbers it is
1858            U\\ :sub:`11`, U\\ :sub:`22`, U\\ :sub:`33`, U\\ :sub:`12`, U\\ :sub:`13` & U\\ :sub:`23`
1859            paired with their standard uncertainty (or a negative value)
1860        """
1861        phasedict = self.Phases[phasenam] # pointer to current phase info           
1862        cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1863        cfrac = cx+3
1864        fpfx = str(phasedict['pId'])+'::Afrac:'       
1865        atomslist = []
1866        for i,at in enumerate(phasedict['Atoms']):
1867            if phasedict['General']['Type'] == 'macromolecular':
1868                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1869            else:
1870                label = at[ct-1]
1871            fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1872            fsig = self.sigDict.get(fpfx+str(i),-0.009)
1873            mult = at[cs+1]
1874            typ = at[ct]
1875            xyz = []
1876            for j,v in enumerate(('x','y','z')):
1877                val = at[cx+j]
1878                pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1879                val = self.parmDict.get(pfx, val)
1880                dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1881                sig = self.sigDict.get(dpfx,-0.000009)
1882                xyz.append((val,sig))
1883            xyz.append((fval,fsig))
1884            td = []
1885            if at[cia] == 'I':
1886                pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1887                val = self.parmDict.get(pfx,at[cia+1])
1888                sig = self.sigDict.get(pfx,-0.0009)
1889                td.append((val,sig))
1890            else:
1891                for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1892                    pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1893                    val = self.parmDict.get(pfx,at[cia+2+i])
1894                    sig = self.sigDict.get(pfx,-0.0009)
1895                    td.append((val,sig))
1896            atomslist.append((label,typ,mult,xyz,td))
1897        return atomslist
1898######################################################################
1899def ExportPowderList(G2frame):
1900    '''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1901    along with their descriptions (note that a extension may be repeated
1902    but descriptions are unique).
1903    This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1904   
1905    :param wx.Frame G2frame: the GSAS-II main data tree window
1906    '''
1907    extList = []
1908    extLabel = []
1909    for obj in G2frame.exporterlist:
1910        if 'powder' in obj.exporttype:
1911            try:
1912                obj.Writer
1913                extList.append(obj.extension)
1914                extLabel.append(obj.formatName)
1915            except AttributeError:
1916                pass
1917    return extList,extLabel
1918
1919def ExportPowder(G2frame,TreeName,fileroot,extension,hint=''):
1920    '''Writes a single powder histogram using the Export routines.
1921    This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1922
1923    :param wx.Frame G2frame: the GSAS-II main data tree window
1924    :param str TreeName: the name of the histogram (PWDR ...) in the data tree
1925    :param str fileroot: name for file to be written, extension ignored
1926    :param str extension: extension for file to be written (start with '.'). Must
1927      match a powder export routine that has a Writer object.
1928    :param str hint: a string that must match the export's format
1929    '''
1930    filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1931    for obj in G2frame.exporterlist:
1932        if obj.extension == extension and 'powder' in obj.exporttype:
1933            if hint and hint not in obj.formatName: continue
1934            obj.currentExportType = 'powder'
1935            obj.InitExport(None)
1936            obj.loadTree() # load all histograms in tree into dicts
1937            if TreeName not in obj.Histograms:
1938                raise Exception('Histogram not found: '+str(TreeName))
1939            try:
1940                obj.Writer
1941            except AttributeError:
1942                continue
1943            try:
1944                obj.Writer(TreeName,filename)
1945                print('wrote file '+filename)
1946                return
1947            except Exception:
1948                print('Export Routine for '+extension+' failed.')
1949    else:
1950        print('No Export routine supports extension '+extension)
1951
1952def ExportSequential(G2frame,data,obj,exporttype):
1953    '''
1954    Used to export from every phase/dataset in a sequential refinement using
1955    a .Writer method for either projects or phases. Prompts to select histograms
1956    and for phase exports, which phase(s).
1957
1958    :param wx.Frame G2frame: the GSAS-II main data tree window
1959    :param dict data: the sequential refinement data object
1960    :param str exporttype: indicates the type of export ('project' or 'phase')
1961    '''
1962    if len(data['histNames']) == 0:
1963        G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1964    obj.InitExport(None)
1965    obj.loadTree()
1966    obj.loadParmDict()
1967    if len(data['histNames']) == 1:
1968        histlist = data['histNames']
1969    else:
1970        dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
1971                                 'Select histograms',data['histNames'])
1972        if dlg.ShowModal() == wx.ID_OK:
1973            histlist = [data['histNames'][l] for l in dlg.GetSelections()]
1974            dlg.Destroy()
1975        else:
1976            dlg.Destroy()
1977            return
1978    if exporttype == 'Phase':
1979        phaselist = list(obj.Phases.keys())
1980        if len(obj.Phases) == 0:
1981            G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
1982            return
1983        elif len(obj.Phases) > 1:
1984            dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
1985                                    'Select phases', phaselist)
1986            if dlg.ShowModal() == wx.ID_OK:
1987                phaselist = [phaselist[l] for l in dlg.GetSelections()]
1988                dlg.Destroy()
1989            else:
1990                dlg.Destroy()
1991                return
1992        filename = obj.askSaveFile()
1993        if not filename: return True
1994        obj.dirname,obj.filename = os.path.split(filename)
1995        print('Writing output to file '+str(obj.filename)+"...")
1996        mode = 'w'
1997        for p in phaselist:
1998            for h in histlist:
1999                obj.SetSeqRef(data,h)
2000                #GSASIIpath.IPyBreak()
2001                obj.Writer(h,phasenam=p,mode=mode)
2002                mode = 'a'
2003        print('...done')
2004    elif exporttype == 'Project':  # note that the CIF exporter is not yet ready for this
2005        filename = obj.askSaveFile()
2006        if not filename: return True
2007        obj.dirname,obj.filename = os.path.split(filename)
2008        print('Writing output to file '+str(obj.filename)+"...")
2009        mode = 'w'
2010        for h in histlist:
2011            obj.SetSeqRef(data,h)
2012            obj.Writer(h,mode=mode)
2013            print('\t'+str(h)+' written')
2014            mode = 'a'
2015        print('...done')
2016    elif exporttype == 'Powder':
2017        filename = obj.askSaveFile()
2018        if not filename: return True
2019        obj.dirname,obj.filename = os.path.split(filename)
2020        print('Writing output to file '+str(obj.filename)+"...")
2021        mode = 'w'
2022        for h in histlist:
2023            obj.SetSeqRef(data,h)
2024            obj.Writer(h,mode=mode)
2025            print('\t'+str(h)+' written')
2026            mode = 'a'
2027        print('...done')
2028
2029def ReadDIFFaX(DIFFaXfile):
2030    print ('read '+DIFFaXfile)
2031    Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2032        'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2033    df = open(DIFFaXfile,'r')
2034    lines = df.readlines()
2035    df.close()
2036    struct = False
2037    Struct = []
2038    stack = False
2039    Stack = []
2040    trans = False
2041    Trans = []
2042    for diff in lines:
2043        diff = diff[:-1].lower()
2044        if '!'  in diff:
2045            continue
2046        while '}' in diff: #strip comments
2047            iB = diff.index('{')
2048            iF = diff.index('}')+1
2049            if iB:
2050                diff = diff[:iB]
2051            else:
2052                diff = diff[iF:]
2053        if not diff:
2054            continue
2055        if diff.strip() == 'instrumental':
2056            continue
2057        if diff.strip() == 'structural':
2058            struct = True
2059            continue
2060        elif diff.strip() == 'stacking':
2061            struct = False
2062            stack = True
2063            continue
2064        elif diff.strip() == 'transitions':
2065            stack = False
2066            trans = True
2067            continue
2068        diff = diff.strip()
2069        if struct:
2070            if diff:
2071                Struct.append(diff)
2072        elif stack:
2073            if diff:
2074                Stack.append(diff)
2075        elif trans:
2076            if diff:
2077                Trans.append(diff)
2078   
2079#STRUCTURE records
2080    laueRec = Struct[1].split()
2081    Layer['Laue'] = laueRec[0]
2082    if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2083        Layer['Toler'] = float(laueRec[1])    #tolerance for 'unknown'?
2084    if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2085    if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2086    cell = Struct[0].split()
2087    Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2088    nLayers = int(Struct[2])
2089    N = 3
2090    if 'layer' not in Struct[3]:
2091        N = 4
2092        if Struct[3] != 'infinite':
2093            width = Struct[3].split()
2094            Layer['Width'][0] = [float(width[0]),float(width[1])]
2095    for nL in range(nLayers):
2096        if '=' in Struct[N]:
2097            name = Struct[N].split('=')
2098            sameas = int(name[1])-1
2099            Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2100            N += 1
2101            continue
2102        Symm = 'None'
2103        if 'centro' in Struct[N+1]: Symm = '-1'
2104        Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2105        N += 2
2106        while 'layer' not in Struct[N]:
2107            atom = Struct[N][4:].split()
2108            atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2109            if atomType not in Layer['AtInfo']:
2110                Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2111            atomName = '%s(%s)'%(atomType,atom[0])
2112            newVals = []
2113            for val in atom[1:6]:
2114                if '/' in val:
2115                    newVals.append(eval(val+'.'))
2116                else:
2117                    newVals.append(float(val))               
2118            atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2119            Layer['Layers'][-1]['Atoms'].append(atomRec)
2120            N += 1
2121            if N > len(Struct)-1:
2122                break
2123#TRANSITIONS records
2124    transArray = []
2125    N = 0
2126    for i in range(nLayers):
2127        transArray.append([])
2128        for j in range(nLayers):
2129            vals = Trans[N].split()
2130            newVals = []
2131            for val in vals[:4]:
2132                if '/' in val:
2133                    newVals.append(eval(val+'.'))
2134                else:
2135                    newVals.append(float(val))
2136            transArray[-1].append(newVals+['',False])
2137            N += 1
2138    Layer['Transitions'] = transArray
2139#STACKING records
2140    Layer['Stacking'] = [Stack[0],'']
2141    if Stack[0] == 'recursive':
2142        Layer['Stacking'][1] = Stack[1]
2143    elif Stack[0] == 'explicit':
2144        if Stack[1] == 'random':
2145            Layer['Stacking'][1] = Stack[1]
2146        else:
2147            Layer['Stacking'][1] = 'list'
2148            Layer['Stacking'].append('')
2149            for stack in Stack[2:]:
2150                Layer['Stacking'][2] += ' '+stack
2151    return Layer
2152
2153def postURL(URL,postdict):
2154    '''Posts a set of values as from a web form. If access fails to an https
2155    site the access is retried with http.
2156
2157    :param str URL: the URL to post; typically something
2158       like 'http://www.../dir/page?'
2159    :param dict postdict: contains keywords and values, such
2160       as {'centrosymmetry': '0', 'crystalsystem': '0', ...}
2161    :returns: a string with the response from the web server or None
2162       if access fails.
2163    '''
2164    try:
2165        import requests # delay this until now, since rarely needed
2166    except:
2167        # this import seems to fail with the Anaconda pythonw on
2168        # macs; it should not!
2169        print('Warning: failed to import requests. Python config error')
2170        return None
2171       
2172    repeat = True
2173    while repeat:
2174        r = None
2175        repeat = False
2176        try:
2177            r = requests.get(URL,params=postdict)
2178            if r.status_code == 200:
2179                print('request OK')
2180                page = r.text
2181                return page # success
2182            else:
2183                print('request to {} failed. Reason={}'.format(URL,r.reason))
2184        except Exception as msg:     #ConnectionError?
2185            print('connection error - not on internet?')
2186            if GSASIIpath.GetConfigValue('debug'): print(msg)
2187        finally:
2188            if r: r.close()
2189        if URL.startswith('https:'):
2190            repeat = True
2191            URL = URL.replace('https:','http:')
2192    else:
2193        return None
2194
2195if __name__ == '__main__':
2196    import GSASIIdataGUI
2197    application = GSASIIdataGUI.GSASIImain(0)
2198    G2frame = application.main
2199    #app = wx.PySimpleApp()
2200    #G2frame = wx.Frame(None) # create a frame
2201    #frm.Show(True)
2202    #filename = '/tmp/notzip.zip'
2203    #filename = '/tmp/all.zip'
2204    #filename = '/tmp/11bmb_7652.zip'
2205   
2206    #selection=None, confirmoverwrite=True, parent=None
2207    #print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2208    #print ExtractFileFromZip(filename,multipleselect=True)
2209    #                         #confirmread=False, confirmoverwrite=False)
2210
2211    # choicelist=[ ('a','b','c'),
2212    #              ('test1','test2'),('no choice',)]
2213    # titles = [ 'a, b or c', 'tests', 'No option here']
2214    # dlg = MultipleChoicesDialog(
2215    #     choicelist,titles,
2216    #     parent=frm)
2217    # if dlg.ShowModal() == wx.ID_OK:
2218    #     print 'Got OK'
2219    imagefile = '/tmp/NDC5_00237_3.ge3'
2220    Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2221
2222    print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2223
2224    GSASIIpath.IPyBreak_base()
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