source: trunk/GSASIIIO.py @ 4654

Last change on this file since 4654 was 4654, checked in by toby, 2 years ago

new video tutorial; misc minor RB GUI fixes for Windows; option to show GPX sizes; remove use of deprecated imp module

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1# -*- coding: utf-8 -*-
2########### SVN repository information ###################
3# $Date: 2020-11-10 17:24:39 +0000 (Tue, 10 Nov 2020) $
4# $Author: toby $
5# $Revision: 4654 $
6# $URL: trunk/GSASIIIO.py $
7# $Id: GSASIIIO.py 4654 2020-11-10 17:24:39Z toby $
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: 4654 $")
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.shape[: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.ALIGN_CENTER|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 = copy.copy(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 == rd.formatName:
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 updateFromSeq and datum[0] == 'Phases':
701                for pdata in data[1:]:
702                    if pdata[0] in Phases:
703                        pdata[1].update(Phases[pdata[0]])
704            elif updateFromSeq and datum[0] == 'Covariance':
705                data[0][1] = CovData
706            elif updateFromSeq and datum[0] == 'Rigid bodies':
707                data[0][1] = RigidBodies
708            elif updateFromSeq and datum[0] in tmpHistIndex:
709                hist.seek(tmpHistIndex[datum[0]])
710                hdata = cPickleLoad(hist)
711                if data[0][0] != hdata[0][0]:
712                    print('Error! Updating {} with {}'.format(data[0][0],hdata[0][0]))
713                datum = hdata[0]
714                xferItems = ['Background','Instrument Parameters','Sample Parameters','Reflection Lists']
715                hItems = {name:j+1 for j,(name,val) in enumerate(hdata[1:]) if name in xferItems}
716                for j,(name,val) in enumerate(data[1:]):
717                    if name not in xferItems: continue
718                    data[j+1][1] = hdata[hItems[name]][1]
719            if datum[0].startswith('PWDR'):               
720                if 'ranId' not in datum[1][0]: # patch: add random Id if not present
721                    datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
722                G2frame.GPXtree.SetItemPyData(Id,datum[1][:3])  #temp. trim off junk (patch?)
723            elif datum[0].startswith('HKLF'): 
724                if 'ranId' not in datum[1][0]: # patch: add random Id if not present
725                    datum[1][0]['ranId'] = ran.randint(0,sys.maxsize)
726                G2frame.GPXtree.SetItemPyData(Id,datum[1])
727            else:
728                G2frame.GPXtree.SetItemPyData(Id,datum[1])             
729                if datum[0] == 'Controls' and 'LastSavedUsing' in datum[1]:
730                    LastSavedUsing = datum[1]['LastSavedUsing']
731                if datum[0] == 'Controls' and 'PythonVersions' in datum[1] and GSASIIpath.GetConfigValue('debug') and showProvenance:
732                    print('DBG_Packages used to create .GPX file:')
733                    if 'dict' in str(type(datum[1]['PythonVersions'])):  #patch
734                        for p in sorted(datum[1]['PythonVersions'],key=lambda s: s.lower()):
735                            print({:<14s}: {:s}".format(p[0],p[1]))
736                    else:
737                        for p in datum[1]['PythonVersions']:
738                            print({:<12s} {:s}".format(p[0]+':',p[1]))
739            oldPDF = False
740            for datus in data[1:]:
741#patch - 1/23/17 PDF cleanup
742                if datus[0][:4] in ['I(Q)','S(Q)','F(Q)','G(R)']:
743                    oldPDF = True
744                    data[1][1][datus[0][:4]] = copy.deepcopy(datus[1][:2])
745                    continue
746#end PDF cleanup
747                sub = G2frame.GPXtree.AppendItem(Id,datus[0])
748#patch
749                if datus[0] == 'Instrument Parameters' and len(datus[1]) == 1:
750                    if datum[0].startswith('PWDR'):
751                        datus[1] = [dict(zip(datus[1][3],zip(datus[1][0],datus[1][1],datus[1][2]))),{}]
752                    else:
753                        datus[1] = [dict(zip(datus[1][2],zip(datus[1][0],datus[1][1]))),{}]
754                    for item in datus[1][0]:               #zip makes tuples - now make lists!
755                        datus[1][0][item] = list(datus[1][0][item])
756#end patch
757                G2frame.GPXtree.SetItemPyData(sub,datus[1])
758            if 'PDF ' in datum[0][:4] and oldPDF:
759                sub = G2frame.GPXtree.AppendItem(Id,'PDF Peaks')
760                G2frame.GPXtree.SetItemPyData(sub,{'Limits':[1.,5.],'Background':[2,[0.,-0.2*np.pi],False],'Peaks':[]})
761            if datum [0].startswith('IMG'):                   #retrieve image default flag & data if set
762                Data = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id,'Image Controls'))
763                if Data['setDefault']:
764                    G2frame.imageDefault = Data               
765        if LastSavedUsing:
766            print('GPX load successful. Last saved with GSAS-II revision '+LastSavedUsing)
767        else:
768            print('project load successful')
769        if GSASIIpath.GetConfigValue('show_gpxSize'):
770            print(50*'=')
771            print('File section sizes (Kb)')
772            for item in sizeList:
773                print({:20s} {:10.3f}'.format(
774                    item[:20],sizeList[item]/1024.))
775            print(50*'=')
776        G2frame.NewPlot = True
777    except Exception as errmsg:
778        if GSASIIpath.GetConfigValue('debug'):
779            print('\nError reading GPX file:',errmsg)
780            import traceback
781            print (traceback.format_exc())
782        msg = wx.MessageDialog(G2frame,message="Error reading file "+
783            str(G2frame.GSASprojectfile)+". This is not a current GSAS-II .gpx file",
784            caption="Load Error",style=wx.ICON_ERROR | wx.OK | wx.STAY_ON_TOP)
785        msg.ShowModal()
786    finally:
787        filep.close()
788        wx.EndBusyCursor()
789        G2frame.Status.SetStatusText('Mouse RB drag/drop to reorder',0)
790    if deleteSeq:
791        if hist: hist.close()
792        try:
793            os.remove(GPXphase)
794        except:
795            print('Warning: unable to delete {}'.format(GPXphase))
796        try:
797            os.remove(GPXhist)
798        except:
799            print('Warning: unable to delete {}'.format(GPXhist))
800    G2frame.SetTitleByGPX()
801   
802def ProjFileSave(G2frame):
803    'Save a GSAS-II project file'
804    if not G2frame.GPXtree.IsEmpty():
805        file = open(G2frame.GSASprojectfile,'wb')
806        print ('save to file: '+G2frame.GSASprojectfile)
807        # stick the file name into the tree and version info into tree so they are saved.
808        # (Controls should always be created at this point)
809        try:
810            Controls = G2frame.GPXtree.GetItemPyData(
811                G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
812            Controls['LastSavedAs'] = os.path.abspath(G2frame.GSASprojectfile)
813            Controls['LastSavedUsing'] = str(GSASIIpath.GetVersionNumber())
814            Controls['PythonVersions'] = G2frame.PackageVersions
815        except:
816            pass
817        wx.BeginBusyCursor()
818        try:
819            item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
820            while item:
821                data = []
822                name = G2frame.GPXtree.GetItemText(item)
823                data.append([name,G2frame.GPXtree.GetItemPyData(item)])
824                item2, cookie2 = G2frame.GPXtree.GetFirstChild(item)
825                while item2:
826                    name = G2frame.GPXtree.GetItemText(item2)
827                    data.append([name,G2frame.GPXtree.GetItemPyData(item2)])
828                    item2, cookie2 = G2frame.GPXtree.GetNextChild(item, cookie2)                           
829                item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)                           
830                cPickle.dump(data,file,2)
831            file.close()
832            pth = os.path.split(os.path.abspath(G2frame.GSASprojectfile))[0]
833            if GSASIIpath.GetConfigValue('Save_paths'): G2G.SaveGPXdirectory(pth)
834            G2frame.LastGPXdir = pth
835        finally:
836            wx.EndBusyCursor()
837        print('project save successful')
838
839def SaveIntegration(G2frame,PickId,data,Overwrite=False):
840    'Save image integration results as powder pattern(s)'
841    waves = {'Cu':[1.54051,1.54433],'Ti':[2.74841,2.75207],'Cr':[2.28962,2.29351],
842        'Fe':[1.93597,1.93991],'Co':[1.78892,1.79278],'Mo':[0.70926,0.713543],
843        'Ag':[0.559363,0.563775]}
844    azms = G2frame.Integrate[1]
845    X = G2frame.Integrate[2][:-1]
846    N = len(X)
847    Id = G2frame.GPXtree.GetItemParent(PickId)
848    name = G2frame.GPXtree.GetItemText(Id)
849    name = name.replace('IMG ',data['type']+' ')
850    Comments = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,Id, 'Comments'))
851    Controls = G2frame.GPXtree.GetItemPyData(G2gd.GetGPXtreeItemId(G2frame,G2frame.root, 'Controls'))
852    if 'PWDR' in name:
853        if 'target' in data:
854            names = ['Type','Lam1','Lam2','I(L2)/I(L1)','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth'] 
855            codes = [0 for i in range(14)]
856        else:
857            if data.get('IfPink',False):
858                names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','alpha-0','alpha-1','beta-0','beta-1','Azimuth']
859                codes = [0 for i in range(15)]
860            else:
861                names = ['Type','Lam','Zero','Polariz.','U','V','W','X','Y','Z','SH/L','Azimuth'] 
862                codes = [0 for i in range(12)]
863    elif 'SASD' in name:
864        names = ['Type','Lam','Zero','Azimuth'] 
865        codes = [0 for i in range(4)]
866        X = 4.*np.pi*npsind(X/2.)/data['wavelength']    #convert to q
867    Xminmax = [X[0],X[-1]]
868    Azms = np.zeros(data['outAzimuths'])
869    dazm = 0.
870    if data['outAzimuths'] > 1:
871        dazm = np.min(np.abs(np.diff(azms)))/2.
872    G2frame.IntgOutList = []
873    for i,azm in enumerate(azms[:-1]):
874        Aname = name+" Azm= %.2f"%((azm+dazm)%360.)
875        item, cookie = G2frame.GPXtree.GetFirstChild(G2frame.root)
876        # if Overwrite delete any duplicate
877        if Overwrite and G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname):
878            print('Replacing '+Aname)
879            item = G2gd.GetGPXtreeItemId(G2frame,G2frame.root,Aname)
880            G2frame.GPXtree.Delete(item)
881        else:
882            nOcc = 0
883            while item:
884                Name = G2frame.GPXtree.GetItemText(item)
885                if Aname in Name:
886                    nOcc += 1
887                item, cookie = G2frame.GPXtree.GetNextChild(G2frame.root, cookie)
888            if nOcc:
889                Aname += '(%d)'%(nOcc)
890        Sample = G2obj.SetDefaultSample()       #set as Debye-Scherrer
891        Sample['Gonio. radius'] = data['distance']
892        Sample['Omega'] = data['GonioAngles'][0]
893        Sample['Chi'] = data['GonioAngles'][1]
894        Sample['Phi'] = data['GonioAngles'][2]
895        Sample['Azimuth'] = (azm+dazm)%360.    #put here as bin center
896        polariz = data['PolaVal'][0]
897        for item in Comments:
898            for key in ('Temperature','Pressure','Time','FreePrm1','FreePrm2','FreePrm3','Omega',
899                'Chi','Phi'):
900                if key.lower() in item.lower():
901                    try:
902                        Sample[key] = float(item.split('=')[1])
903                    except:
904                        pass
905            if 'label_prm' in item.lower():
906                for num in ('1','2','3'):
907                    if 'label_prm'+num in item.lower():
908                        Controls['FreePrm'+num] = item.split('=')[1].strip()
909        if 'PWDR' in Aname:
910            if 'target' in data:    #from lab x-ray 2D imaging data
911                wave1,wave2 = waves[data['target']]
912                parms = ['PXC',wave1,wave2,0.5,0.0,polariz,290.,-40.,30.,6.,-14.,0.0,0.0001,Azms[i]]
913            else:
914                if data.get('IfPink',False):
915                    parms = ['PXB',data['wavelength'],0.0,polariz,0.,8000.,-150.,-24.,0.,0.,0.,13.,-1300.,3.,-7.,Azms[i]]   #from Sect 35 LSS
916                else:
917                    parms = ['PXC',data['wavelength'],0.0,polariz,1.0,-0.10,0.4,0.30,1.0,0.0,0.0001,Azms[i]]
918        elif 'SASD' in Aname:
919            Sample['Trans'] = data['SampleAbs'][0]
920            parms = ['LXC',data['wavelength'],0.0,Azms[i]]
921        Y = G2frame.Integrate[0][i]
922        Ymin = np.min(Y)
923        Ymax = np.max(Y)
924        W = np.where(Y>0.,1./Y,1.e-6)                    #probably not true
925        Id = G2frame.GPXtree.AppendItem(parent=G2frame.root,text=Aname)
926        G2frame.IntgOutList.append(Id)
927        G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Comments'),Comments)                   
928        G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Limits'),copy.deepcopy([tuple(Xminmax),Xminmax]))
929        if 'PWDR' in Aname:
930            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Background'),[['chebyschev-1',1,3,1.0,0.0,0.0],
931                {'nDebye':0,'debyeTerms':[],'nPeaks':0,'peaksList':[]}])
932        inst = [dict(zip(names,zip(parms,parms,codes))),{}]
933        for item in inst[0]:
934            inst[0][item] = list(inst[0][item])
935        G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Instrument Parameters'),inst)
936        if 'PWDR' in Aname:
937            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
938            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Peak List'),{'sigDict':{},'peaks':[]})
939            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Index Peak List'),[[],[]])
940            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Unit Cells List'),[])
941            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Reflection Lists'),{})
942        elif 'SASD' in Aname:             
943            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Substances'),G2pdG.SetDefaultSubstances())
944            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Sample Parameters'),Sample)
945            G2frame.GPXtree.SetItemPyData(G2frame.GPXtree.AppendItem(Id,text='Models'),G2pdG.SetDefaultSASDModel())
946        valuesdict = {
947            'wtFactor':1.0,'Dummy':False,'ranId':ran.randint(0,sys.maxsize),'Offset':[0.0,0.0],'delOffset':0.02*Ymax,
948            'refOffset':-0.1*Ymax,'refDelt':0.1*Ymax,'Yminmax':[Ymin,Ymax]}
949        G2frame.GPXtree.SetItemPyData(Id,[valuesdict,
950            [np.array(X),np.array(Y),np.array(W),np.zeros(N),np.zeros(N),np.zeros(N)]])
951    return Id       #last powder pattern generated
952   
953def XYsave(G2frame,XY,labelX='X',labelY='Y',names=[]):
954    'Save XY table data'
955    pth = G2G.GetExportPath(G2frame)
956    dlg = wx.FileDialog(
957        G2frame, 'Enter csv filename for XY table', pth, '',
958        'XY table file (*.csv)|*.csv',wx.FD_SAVE|wx.FD_OVERWRITE_PROMPT)
959    try:
960        if dlg.ShowModal() == wx.ID_OK:
961            filename = dlg.GetPath()
962            filename = os.path.splitext(filename)[0]+'.csv'
963            File = open(filename,'w')
964        else:
965            filename = None
966    finally:
967        dlg.Destroy()
968    if not filename:
969        return
970    for i in range(len(XY)):
971        if len(names):
972            header = '%s,%s(%s)\n'%(labelX,labelY,names[i])
973        else:
974            header = '%s,%s(%d)\n'%(labelX,labelY,i)
975        File.write(header)
976        for x,y in XY[i].T:
977            File.write('%.3f,%.3f\n'%(x,y))   
978    File.close()
979    print (' XY data saved to: '+filename)                       
980   
981def PeakListSave(G2frame,file,peaks):
982    'Save powder peaks to a data file'
983    print ('save peak list to file: '+G2frame.peaklistfile)
984    if not peaks:
985        dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
986        try:
987            dlg.ShowModal()
988        finally:
989            dlg.Destroy()
990        return
991    for peak in peaks:
992        file.write("%10.4f %12.2f %10.3f %10.3f \n" % \
993            (peak[0],peak[2],peak[4],peak[6]))
994    print ('peak list saved')
995             
996def IndexPeakListSave(G2frame,peaks):
997    'Save powder peaks from the indexing list'
998    file = open(G2frame.peaklistfile,'wa')
999    print ('save index peak list to file: '+G2frame.peaklistfile)
1000    wx.BeginBusyCursor()
1001    try:
1002        if not peaks:
1003            dlg = wx.MessageDialog(G2frame, 'No peaks!', 'Nothing to save!', wx.OK)
1004            try:
1005                dlg.ShowModal()
1006            finally:
1007                dlg.Destroy()
1008            return
1009        for peak in peaks:
1010            file.write("%12.6f\n" % (peak[7]))
1011        file.close()
1012    finally:
1013        wx.EndBusyCursor()
1014    print ('index peak list saved')
1015               
1016def ExtractFileFromZip(filename, selection=None, confirmread=True,
1017                       confirmoverwrite=True, parent=None,
1018                       multipleselect=False):
1019    '''If the filename is a zip file, extract a file from that
1020    archive.
1021
1022    :param list Selection: used to predefine the name of the file
1023      to be extracted. Filename case and zip directory name are
1024      ignored in selection; the first matching file is used.
1025
1026    :param bool confirmread: if True asks the user to confirm before expanding
1027      the only file in a zip
1028
1029    :param bool confirmoverwrite: if True asks the user to confirm
1030      before overwriting if the extracted file already exists
1031
1032    :param bool multipleselect: if True allows more than one zip
1033      file to be extracted, a list of file(s) is returned.
1034      If only one file is present, do not ask which one, otherwise
1035      offer a list of choices (unless selection is used).
1036   
1037    :returns: the name of the file that has been created or a
1038      list of files (see multipleselect)
1039
1040    If the file is not a zipfile, return the name of the input file.
1041    If the zipfile is empty or no file has been selected, return None
1042    '''
1043    import zipfile # do this now, since we can save startup time by doing this only on need
1044    import shutil
1045    zloc = os.path.split(filename)[0]
1046    if not zipfile.is_zipfile(filename):
1047        #print("not zip")
1048        return filename
1049
1050    z = zipfile.ZipFile(filename,'r')
1051    zinfo = z.infolist()
1052
1053    if len(zinfo) == 0:
1054        #print('Zip has no files!')
1055        zlist = [-1]
1056    if selection:
1057        choices = [os.path.split(i.filename)[1].lower() for i in zinfo]
1058        if selection.lower() in choices:
1059            zlist = [choices.index(selection.lower())]
1060        else:
1061            print('debug: file '+str(selection)+' was not found in '+str(filename))
1062            zlist = [-1]
1063    elif len(zinfo) == 1 and confirmread:
1064        result = wx.ID_NO
1065        dlg = wx.MessageDialog(
1066            parent,
1067            'Is file '+str(zinfo[0].filename)+
1068            ' what you want to extract from '+
1069            str(os.path.split(filename)[1])+'?',
1070            'Confirm file', 
1071            wx.YES_NO | wx.ICON_QUESTION)
1072        try:
1073            result = dlg.ShowModal()
1074        finally:
1075            dlg.Destroy()
1076        if result == wx.ID_NO:
1077            zlist = [-1]
1078        else:
1079            zlist = [0]
1080    elif len(zinfo) == 1:
1081        zlist = [0]
1082    elif multipleselect:
1083        # select one or more from a from list
1084        choices = [i.filename for i in zinfo]
1085        dlg = G2G.G2MultiChoiceDialog(parent,'Select file(s) to extract from zip file '+str(filename),
1086            'Choose file(s)',choices)
1087        if dlg.ShowModal() == wx.ID_OK:
1088            zlist = dlg.GetSelections()
1089        else:
1090            zlist = []
1091        dlg.Destroy()
1092    else:
1093        # select one from a from list
1094        choices = [i.filename for i in zinfo]
1095        dlg = wx.SingleChoiceDialog(parent,
1096            'Select file to extract from zip file'+str(filename),'Choose file',
1097            choices,)
1098        if dlg.ShowModal() == wx.ID_OK:
1099            zlist = [dlg.GetSelection()]
1100        else:
1101            zlist = [-1]
1102        dlg.Destroy()
1103       
1104    outlist = []
1105    for zindex in zlist:
1106        if zindex >= 0:
1107            efil = os.path.join(zloc, os.path.split(zinfo[zindex].filename)[1])
1108            if os.path.exists(efil) and confirmoverwrite:
1109                result = wx.ID_NO
1110                dlg = wx.MessageDialog(parent,
1111                    'File '+str(efil)+' already exists. OK to overwrite it?',
1112                    'Confirm overwrite',wx.YES_NO | wx.ICON_QUESTION)
1113                try:
1114                    result = dlg.ShowModal()
1115                finally:
1116                    dlg.Destroy()
1117                if result == wx.ID_NO:
1118                    zindex = -1
1119        if zindex >= 0:
1120            # extract the file to the current directory, regardless of it's original path
1121            #z.extract(zinfo[zindex],zloc)
1122            eloc,efil = os.path.split(zinfo[zindex].filename)
1123            outfile = os.path.join(zloc, efil)
1124            fpin = z.open(zinfo[zindex])
1125            fpout = open(outfile, "wb")
1126            shutil.copyfileobj(fpin, fpout)
1127            fpin.close()
1128            fpout.close()
1129            outlist.append(outfile)
1130    z.close()
1131    if multipleselect and len(outlist) >= 1:
1132        return outlist
1133    elif len(outlist) == 1:
1134        return outlist[0]
1135    else:
1136        return None
1137
1138def striphist(var,insChar=''):
1139    'strip a histogram number from a var name'
1140    sv = var.split(':')
1141    if len(sv) <= 1: return var
1142    if sv[1]:
1143        sv[1] = insChar
1144    return ':'.join(sv)
1145
1146######################################################################
1147# base classes for reading various types of data files
1148#   not used directly, only by subclassing
1149######################################################################
1150class ExportBaseclass(object):
1151    '''Defines a base class for the exporting of GSAS-II results.
1152
1153    This class is subclassed in the various exports/G2export_*.py files. Those files
1154    are imported in :meth:`GSASIIdataGUI.GSASII._init_Exports` which defines the
1155    appropriate menu items for each one and the .Exporter method is called
1156    directly from the menu item.
1157
1158    Routines may also define a .Writer method, which is used to write a single
1159    file without invoking any GUI objects.
1160    '''
1161    # TODO: review exporters producing exceptions where .Writer can't be used where G2frame is None (see CIF)
1162    # TODO: review conflicting uses of .Writer with mode (SeqRef) & elsewhere
1163    # TODO: move this class to G2fil
1164    def __init__(self,G2frame,formatName,extension,longFormatName=None,):
1165        self.G2frame = G2frame
1166        self.formatName = formatName # short string naming file type
1167        self.extension = extension
1168        if longFormatName: # longer string naming file type
1169            self.longFormatName = longFormatName
1170        else:
1171            self.longFormatName = formatName
1172        self.OverallParms = {}
1173        self.Phases = {}
1174        self.Histograms = {}
1175        self.powderDict = {}
1176        self.sasdDict = {}
1177        self.refdDict = {}
1178        self.xtalDict = {}
1179        self.parmDict = {}
1180        self.sigDict = {}
1181        self.fp = None
1182        # updated in InitExport:
1183        self.currentExportType = None # type of export that has been requested
1184        # updated in ExportSelect (when used):
1185        self.phasenam = None # a list of selected phases
1186        self.histnam = None # a list of selected histograms
1187        self.filename = None # name of file to be written (single export) or template (multiple files)
1188        self.dirname = '' # name of directory where file(s) will be written
1189        self.fullpath = '' # name of file being written -- full path
1190       
1191        # items that should be defined in a subclass of this class
1192        self.exporttype = []  # defines the type(s) of exports that the class can handle.
1193        # The following types are defined: 'project', "phase", "powder", "single"
1194        self.multiple = False # set as True if the class can export multiple phases or histograms
1195        # self.multiple is ignored for "project" exports
1196
1197    def InitExport(self,event):
1198        '''Determines the type of menu that called the Exporter and
1199        misc initialization.
1200        '''
1201        self.filename = None # name of file to be written (single export)
1202        self.dirname = '' # name of file to be written (multiple export)
1203        if event:
1204            self.currentExportType = self.G2frame.ExportLookup.get(event.Id)
1205
1206    def MakePWDRfilename(self,hist):
1207        '''Make a filename root (no extension) from a PWDR histogram name
1208
1209        :param str hist: the histogram name in data tree (starts with "PWDR ")
1210        '''
1211        file0 = ''
1212        file1 = hist[5:]
1213        # replace repeated blanks
1214        while file1 != file0:
1215            file0 = file1
1216            file1 = file0.replace('  ',' ').strip()
1217        file0 = file1.replace('Azm= ','A')
1218        # if angle has unneeded decimal places on aziumuth, remove them
1219        if file0[-3:] == '.00': file0 = file0[:-3]
1220        file0 = file0.replace('.','_')
1221        file0 = file0.replace(' ','_')
1222        return file0
1223
1224    def ExportSelect(self,AskFile='ask'):
1225        '''Selects histograms or phases when needed. Sets a default file name when
1226        requested into self.filename; always sets a default directory in self.dirname.
1227
1228        :param bool AskFile: Determines how this routine processes getting a
1229          location to store the current export(s).
1230         
1231          * if AskFile is 'ask' (default option), get the name of the file to be written;
1232            self.filename and self.dirname are always set. In the case where
1233            multiple files must be generated, the export routine should do this
1234            based on self.filename as a template.
1235          * if AskFile is 'dir', get the name of the directory to be used;
1236            self.filename is not used, but self.dirname is always set. The export routine
1237            will always generate the file name.
1238          * if AskFile is 'single', get only the name of the directory to be used when
1239            multiple items will be written (as multiple files) are used
1240            *or* a complete file name is requested when a single file
1241            name is selected. self.dirname is always set and self.filename used
1242            only when a single file is selected. 
1243          * if AskFile is 'default', creates a name of the file to be used from
1244            the name of the project (.gpx) file. If the project has not been saved,
1245            then the name of file is requested.
1246            self.filename and self.dirname are always set. In the case where
1247            multiple file names must be generated, the export routine should do this
1248            based on self.filename.
1249          * if AskFile is 'default-dir', sets self.dirname from the project (.gpx)
1250            file. If the project has not been saved, then a directory is requested.
1251            self.filename is not used.
1252
1253        :returns: True in case of an error
1254        '''
1255       
1256        numselected = 1
1257        if self.currentExportType == 'phase':
1258            if len(self.Phases) == 0:
1259                self.G2frame.ErrorDialog(
1260                    'Empty project',
1261                    'Project does not contain any phases.')
1262                return True
1263            elif len(self.Phases) == 1:
1264                self.phasenam = list(self.Phases.keys())
1265            elif self.multiple: 
1266                choices = sorted(self.Phases.keys())
1267                phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1268                if phasenum is None: return True
1269                self.phasenam = [choices[i] for i in phasenum]
1270                if not self.phasenam: return True
1271                numselected = len(self.phasenam)
1272            else:
1273                choices = sorted(self.Phases.keys())
1274                phasenum = G2G.ItemSelector(choices,self.G2frame)
1275                if phasenum is None: return True
1276                self.phasenam = [choices[phasenum]]
1277                numselected = len(self.phasenam)
1278        elif self.currentExportType == 'single':
1279            if len(self.xtalDict) == 0:
1280                self.G2frame.ErrorDialog(
1281                    'Empty project',
1282                    'Project does not contain any single crystal data.')
1283                return True
1284            elif len(self.xtalDict) == 1:
1285                self.histnam = self.xtalDict.values()
1286            elif self.multiple:
1287                choices = sorted(self.xtalDict.values())
1288                hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1289                if not hnum: return True
1290                self.histnam = [choices[i] for i in hnum]
1291                numselected = len(self.histnam)
1292            else:
1293                choices = sorted(self.xtalDict.values())
1294                hnum = G2G.ItemSelector(choices,self.G2frame)
1295                if hnum is None: return True
1296                self.histnam = [choices[hnum]]
1297                numselected = len(self.histnam)
1298        elif self.currentExportType == 'powder':
1299            if len(self.powderDict) == 0:
1300                self.G2frame.ErrorDialog(
1301                    'Empty project',
1302                    'Project does not contain any powder data.')
1303                return True
1304            elif len(self.powderDict) == 1:
1305                self.histnam = list(self.powderDict.values())
1306            elif self.multiple:
1307                choices = sorted(self.powderDict.values())
1308                hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1309                if not hnum: return True
1310                self.histnam = [choices[i] for i in hnum]
1311                numselected = len(self.histnam)
1312            else:
1313                choices = sorted(self.powderDict.values())
1314                hnum = G2G.ItemSelector(choices,self.G2frame)
1315                if hnum is None: return True
1316                self.histnam = [choices[hnum]]
1317                numselected = len(self.histnam)
1318        elif self.currentExportType == 'sasd':
1319            if len(self.sasdDict) == 0:
1320                self.G2frame.ErrorDialog(
1321                    'Empty project',
1322                    'Project does not contain any small angle data.')
1323                return True
1324            elif len(self.sasdDict) == 1:
1325                self.histnam = self.sasdDict.values()
1326            elif self.multiple:
1327                choices = sorted(self.sasdDict.values())
1328                hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1329                if not hnum: return True
1330                self.histnam = [choices[i] for i in hnum]
1331                numselected = len(self.histnam)
1332            else:
1333                choices = sorted(self.sasdDict.values())
1334                hnum = G2G.ItemSelector(choices,self.G2frame)
1335                if hnum is None: return True
1336                self.histnam = [choices[hnum]]
1337                numselected = len(self.histnam)
1338        elif self.currentExportType == 'refd':
1339            if len(self.refdDict) == 0:
1340                self.G2frame.ErrorDialog(
1341                    'Empty project',
1342                    'Project does not contain any reflectivity data.')
1343                return True
1344            elif len(self.refdDict) == 1:
1345                self.histnam = self.refdDict.values()
1346            elif self.multiple:
1347                choices = sorted(self.refdDict.values())
1348                hnum = G2G.ItemSelector(choices,self.G2frame,multiple=True)
1349                if not hnum: return True
1350                self.histnam = [choices[i] for i in hnum]
1351                numselected = len(self.histnam)
1352            else:
1353                choices = sorted(self.refdDict.values())
1354                hnum = G2G.ItemSelector(choices,self.G2frame)
1355                if hnum is None: return True
1356                self.histnam = [choices[hnum]]
1357                numselected = len(self.histnam)
1358        elif self.currentExportType == 'image':
1359            if len(self.Histograms) == 0:
1360                self.G2frame.ErrorDialog(
1361                    'Empty project',
1362                    'Project does not contain any images.')
1363                return True
1364            elif len(self.Histograms) == 1:
1365                self.histnam = list(self.Histograms.keys())
1366            else:
1367                choices = sorted(self.Histograms.keys())
1368                hnum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1369                if self.multiple:
1370                    if not hnum: return True
1371                    self.histnam = [choices[i] for i in hnum]
1372                else:
1373                    if hnum is None: return True
1374                    self.histnam = [choices[hnum]]
1375                numselected = len(self.histnam)
1376        if self.currentExportType == 'map':
1377            # search for phases with maps
1378            mapPhases = []
1379            choices = []
1380            for phasenam in sorted(self.Phases):
1381                phasedict = self.Phases[phasenam] # pointer to current phase info           
1382                if len(phasedict['General']['Map'].get('rho',[])):
1383                    mapPhases.append(phasenam)
1384                    if phasedict['General']['Map'].get('Flip'):
1385                        choices.append('Charge flip map: '+str(phasenam))
1386                    elif phasedict['General']['Map'].get('MapType'):
1387                        choices.append(
1388                            str(phasedict['General']['Map'].get('MapType'))
1389                            + ' map: ' + str(phasenam))
1390                    else:
1391                        choices.append('unknown map: '+str(phasenam))
1392            # select a map if needed
1393            if len(mapPhases) == 0:
1394                self.G2frame.ErrorDialog(
1395                    'Empty project',
1396                    'Project does not contain any maps.')
1397                return True
1398            elif len(mapPhases) == 1:
1399                self.phasenam = mapPhases
1400            else: 
1401                phasenum = G2G.ItemSelector(choices,self.G2frame,multiple=self.multiple)
1402                if self.multiple:
1403                    if not phasenum: return True
1404                    self.phasenam = [mapPhases[i] for i in phasenum]
1405                else:
1406                    if phasenum is None: return True
1407                    self.phasenam = [mapPhases[phasenum]]
1408            numselected = len(self.phasenam)
1409
1410        # items selected, now set self.dirname and usually self.filename
1411        if AskFile == 'ask' or (AskFile == 'single' and numselected == 1) or (
1412            AskFile == 'default' and not self.G2frame.GSASprojectfile
1413            ):
1414            filename = self.askSaveFile()
1415            if not filename: return True
1416            self.dirname,self.filename = os.path.split(filename)
1417        elif AskFile == 'dir' or AskFile == 'single' or (
1418            AskFile == 'default-dir' and not self.G2frame.GSASprojectfile
1419            ):
1420            self.dirname = self.askSaveDirectory()
1421            if not self.dirname: return True
1422        elif AskFile == 'default-dir' or AskFile == 'default':
1423            self.dirname,self.filename = os.path.split(
1424                os.path.splitext(self.G2frame.GSASprojectfile)[0] + self.extension
1425                )
1426        else:
1427            raise Exception('This should not happen!')
1428
1429    def loadParmDict(self):
1430        '''Load the GSAS-II refinable parameters from the tree into a dict (self.parmDict). Update
1431        refined values to those from the last cycle and set the uncertainties for the
1432        refined parameters in another dict (self.sigDict).
1433
1434        Expands the parm & sig dicts to include values derived from constraints.
1435
1436        This could be made faster for sequential fits by reducing the histogram list to only
1437        the active histogram being exported.
1438        '''
1439        self.G2frame.CheckNotebook()
1440        self.parmDict = {}
1441        self.sigDict = {}
1442        rigidbodyDict = {}
1443        covDict = {}
1444        consDict = {}
1445        Histograms,Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1446        if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1447        item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1448        while item:
1449            name = self.G2frame.GPXtree.GetItemText(item)
1450            if name == 'Rigid bodies':
1451                 rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(item)
1452            elif name == 'Covariance':
1453                 covDict = self.G2frame.GPXtree.GetItemPyData(item)
1454            elif name == 'Constraints':
1455                 consDict = self.G2frame.GPXtree.GetItemPyData(item)
1456            item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1457        rbVary,rbDict =  G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1458        self.parmDict.update(rbDict)
1459        rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1460        Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave =  G2stIO.GetPhaseData(
1461            Phases,RestraintDict=None,rbIds=rbIds,Print=False)
1462        self.parmDict.update(phaseDict)
1463        hapVary,hapDict,controlDict =  G2stIO.GetHistogramPhaseData(
1464            Phases,Histograms,Print=False,resetRefList=False)
1465        self.parmDict.update(hapDict)
1466        histVary,histDict,controlDict =  G2stIO.GetHistogramData(Histograms,Print=False)
1467        self.parmDict.update(histDict)
1468        self.parmDict.update(zip(
1469            covDict.get('varyList',[]),
1470            covDict.get('variables',[])))
1471        self.sigDict = dict(zip(
1472            covDict.get('varyList',[]),
1473            covDict.get('sig',[])))
1474        # expand to include constraints: first compile a list of constraints
1475        constList = []
1476        for item in consDict:
1477            if item.startswith('_'): continue
1478            constList += consDict[item]
1479        # now process the constraints
1480        G2mv.InitVars()
1481        constDict,fixedList,ignored = G2stIO.ProcessConstraints(constList)
1482        varyList = covDict.get('varyListStart')
1483        if varyList is None and len(constDict) == 0:
1484            # no constraints can use varyList
1485            varyList = covDict.get('varyList')
1486        elif varyList is None:
1487            # old GPX file from before pre-constraint varyList is saved
1488            print (' *** Old refinement: Please use Calculate/Refine to redo  ***')
1489            raise Exception(' *** Export aborted ***')
1490        else:
1491            varyList = list(varyList)
1492        # add symmetry-generated constraints
1493        rigidbodyDict = self.G2frame.GPXtree.GetItemPyData(   
1494            G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Rigid bodies'))
1495        rbIds = rigidbodyDict.get('RBIds',{'Vector':[],'Residue':[]})
1496        rbVary,rbDict = G2stIO.GetRigidBodyModels(rigidbodyDict,Print=False)
1497        Natoms,atomIndx,phaseVary,phaseDict,pawleyLookup,FFtables,BLtables,MFtables,maxSSwave = G2stIO.GetPhaseData(
1498            Phases,RestraintDict=None,rbIds=rbIds,Print=False) # generates atom symmetry constraints
1499        msg = G2mv.EvaluateMultipliers(constDict,phaseDict)
1500        if msg:
1501            print('Unable to interpret multiplier(s): '+msg)
1502            raise Exception(' *** CIF creation aborted ***')
1503        try:
1504            G2mv.GenerateConstraints(varyList,constDict,fixedList,self.parmDict)
1505            #print(G2mv.VarRemapShow(varyList))
1506        except:
1507            # this really should not happen
1508            print (' *** ERROR - constraints are internally inconsistent ***')
1509            errmsg, warnmsg = G2mv.CheckConstraints(varyList,constDict,fixedList)
1510            print ('Errors'+errmsg)
1511            if warnmsg: print ('Warnings'+warnmsg)
1512            raise Exception(' *** CIF creation aborted ***')
1513        # add the constrained values to the parameter dictionary
1514        G2mv.Dict2Map(self.parmDict,varyList)
1515        # and add their uncertainties into the esd dictionary (sigDict)
1516        if covDict.get('covMatrix') is not None:
1517            self.sigDict.update(G2mv.ComputeDepESD(covDict['covMatrix'],covDict['varyList'],self.parmDict))
1518
1519    def loadTree(self):
1520        '''Load the contents of the data tree into a set of dicts
1521        (self.OverallParms, self.Phases and self.Histogram as well as self.powderDict
1522        & self.xtalDict)
1523       
1524        * The childrenless data tree items are overall parameters/controls for the
1525          entire project and are placed in self.OverallParms
1526        * Phase items are placed in self.Phases
1527        * Data items are placed in self.Histogram. The key for these data items
1528          begin with a keyword, such as PWDR, IMG, HKLF,... that identifies the data type.
1529        '''
1530        self.OverallParms = {}
1531        self.powderDict = {}
1532        self.sasdDict = {}
1533        self.refdDict = {}
1534        self.xtalDict = {}
1535        self.Phases = {}
1536        self.Histograms = {}
1537        self.SeqRefdata = None
1538        self.SeqRefhist = None
1539        if self.G2frame.GPXtree.IsEmpty(): return # nothing to do
1540        histType = None       
1541        if self.currentExportType == 'phase':
1542            # if exporting phases load them here
1543            sub = G2gd.GetGPXtreeItemId(self.G2frame,self.G2frame.root,'Phases')
1544            if not sub:
1545                print ('no phases found')
1546                return True
1547            item, cookie = self.G2frame.GPXtree.GetFirstChild(sub)
1548            while item:
1549                phaseName = self.G2frame.GPXtree.GetItemText(item)
1550                self.Phases[phaseName] =  self.G2frame.GPXtree.GetItemPyData(item)
1551                item, cookie = self.G2frame.GPXtree.GetNextChild(sub, cookie)
1552            return
1553        elif self.currentExportType == 'single':
1554            histType = 'HKLF'
1555        elif self.currentExportType == 'powder':
1556            histType = 'PWDR'
1557        elif self.currentExportType == 'image':
1558            histType = 'IMG'
1559        elif self.currentExportType == 'sasd':
1560            histType = 'SASD'
1561        elif self.currentExportType == 'refd':
1562            histType = 'REFD'
1563
1564        if histType: # Loading just one kind of tree entry
1565            item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1566            while item:
1567                name = self.G2frame.GPXtree.GetItemText(item)
1568                if name.startswith(histType):
1569                    if self.Histograms.get(name): # there is already an item with this name
1570                        print('Histogram name '+str(name)+' is repeated. Renaming')
1571                        if name[-1] == '9':
1572                            name = name[:-1] + '10'
1573                        elif name[-1] in '012345678':
1574                            name = name[:-1] + str(int(name[-1])+1)
1575                        else:                           
1576                            name += '-1'
1577                    self.Histograms[name] = {}
1578                    # the main info goes into Data, but the 0th
1579                    # element contains refinement results, carry
1580                    # that over too now.
1581                    self.Histograms[name]['Data'] = self.G2frame.GPXtree.GetItemPyData(item)[1]
1582                    self.Histograms[name][0] = self.G2frame.GPXtree.GetItemPyData(item)[0]
1583                    item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1584                    while item2: 
1585                        child = self.G2frame.GPXtree.GetItemText(item2)
1586                        self.Histograms[name][child] = self.G2frame.GPXtree.GetItemPyData(item2)
1587                        item2, cookie2 = self.G2frame.GPXtree.GetNextChild(item, cookie2)
1588                item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1589            # index powder and single crystal histograms by number
1590            for hist in self.Histograms:
1591                if hist.startswith("PWDR"): 
1592                    d = self.powderDict
1593                elif hist.startswith("HKLF"): 
1594                    d = self.xtalDict
1595                elif hist.startswith("SASD"):
1596                    d = self.sasdDict
1597                elif hist.startswith("REFD"):
1598                    d = self.refdDict
1599                else:
1600                    return                   
1601                i = self.Histograms[hist].get('hId')
1602                if i is None and not d.keys():
1603                    i = 0
1604                elif i is None or i in d.keys():
1605                    i = max(d.keys())+1
1606                d[i] = hist
1607            return
1608        # else standard load: using all interlinked phases and histograms
1609        self.Histograms,self.Phases = self.G2frame.GetUsedHistogramsAndPhasesfromTree()
1610        item, cookie = self.G2frame.GPXtree.GetFirstChild(self.G2frame.root)
1611        while item:
1612            name = self.G2frame.GPXtree.GetItemText(item)
1613            item2, cookie2 = self.G2frame.GPXtree.GetFirstChild(item)
1614            if not item2: 
1615                self.OverallParms[name] = self.G2frame.GPXtree.GetItemPyData(item)
1616            item, cookie = self.G2frame.GPXtree.GetNextChild(self.G2frame.root, cookie)
1617        # index powder and single crystal histograms
1618        for hist in self.Histograms:
1619            i = self.Histograms[hist]['hId']
1620            if hist.startswith("PWDR"): 
1621                self.powderDict[i] = hist
1622            elif hist.startswith("HKLF"): 
1623                self.xtalDict[i] = hist
1624            elif hist.startswith("SASD"):
1625                self.sasdDict[i] = hist
1626            elif hist.startswith("REFD"):
1627                self.refdDict[i] = hist
1628
1629    def dumpTree(self,mode='type'):
1630        '''Print out information on the data tree dicts loaded in loadTree.
1631        Used for testing only.
1632        '''
1633        if self.SeqRefdata and self.SeqRefhist:
1634            print('Note that dumpTree does not show sequential results')
1635        print ('\nOverall')
1636        if mode == 'type':
1637            def Show(arg): return type(arg)
1638        else:
1639            def Show(arg): return arg
1640        for key in self.OverallParms:
1641            print ('  '+key+Show(self.OverallParms[key]))
1642        print ('Phases')
1643        for key1 in self.Phases:
1644            print ('    '+key1+Show(self.Phases[key1]))
1645        print ('Histogram')
1646        for key1 in self.Histograms:
1647            print ('    '+key1+Show(self.Histograms[key1]))
1648            for key2 in self.Histograms[key1]:
1649                print ('      '+key2+Show(self.Histograms[key1][key2]))
1650
1651    def defaultSaveFile(self):
1652        return os.path.abspath(
1653            os.path.splitext(self.G2frame.GSASprojectfile
1654                             )[0]+self.extension)
1655       
1656    def askSaveFile(self):
1657        '''Ask the user to supply a file name
1658
1659        :returns: a file name (str) or None if Cancel is pressed
1660
1661        '''
1662        #pth = G2G.GetExportPath(self.G2frame)
1663        if self.G2frame.GSASprojectfile:
1664            defnam = os.path.splitext(
1665                os.path.split(self.G2frame.GSASprojectfile)[1]
1666                )[0]+self.extension
1667        else:
1668            defnam = 'default' + self.extension
1669        return G2G.askSaveFile(self.G2frame,defnam,self.extension,self.longFormatName)
1670
1671    def askSaveDirectory(self):
1672        '''Ask the user to supply a directory name. Path name is used as the
1673        starting point for the next export path search.
1674
1675        :returns: a directory name (str) or None if Cancel is pressed
1676
1677        TODO: Can this be replaced with G2G.askSaveDirectory?
1678        '''
1679        pth = G2G.GetExportPath(self.G2frame)
1680        dlg = wx.DirDialog(
1681            self.G2frame, 'Input directory where file(s) will be written', pth,
1682            wx.DD_DEFAULT_STYLE)
1683        dlg.CenterOnParent()
1684        try:
1685            if dlg.ShowModal() == wx.ID_OK:
1686                filename = dlg.GetPath()
1687                self.G2frame.LastExportDir = filename
1688            else:
1689                filename = None
1690        finally:
1691            dlg.Destroy()
1692        return filename
1693
1694    # Tools for file writing.
1695    def OpenFile(self,fil=None,mode='w'):
1696        '''Open the output file
1697
1698        :param str fil: The name of the file to open. If None (default)
1699          the name defaults to self.dirname + self.filename.
1700          If an extension is supplied, it is not overridded,
1701          but if not, the default extension is used.
1702        :returns: the file object opened by the routine which is also
1703          saved as self.fp
1704        '''
1705        if mode == 'd': # debug mode
1706            self.fullpath = '(stdout)'
1707            self.fp = sys.stdout
1708            return
1709        if not fil:
1710            if not os.path.splitext(self.filename)[1]:
1711                self.filename += self.extension
1712            fil = os.path.join(self.dirname,self.filename)
1713        self.fullpath = os.path.abspath(fil)
1714        self.fp = open(self.fullpath,mode)
1715        return self.fp
1716
1717    def Write(self,line):
1718        '''write a line of output, attaching a line-end character
1719
1720        :param str line: the text to be written.
1721        '''
1722        if self.fp is None:
1723            raise Exception('Attempt to Write without use of OpenFile')
1724        self.fp.write(line+'\n')
1725       
1726    def CloseFile(self,fp=None):
1727        '''Close a file opened in OpenFile
1728
1729        :param file fp: the file object to be closed. If None (default)
1730          file object self.fp is closed.
1731        '''
1732        if self.fp is None:
1733            raise Exception('Attempt to CloseFile without use of OpenFile')
1734        if self.fp == sys.stdout: return # debug mode
1735        if fp is None:
1736            fp = self.fp
1737            self.fp = None
1738        if fp is not None: fp.close()
1739       
1740    def SetSeqRef(self,data,hist):
1741        '''Set the exporter to retrieve results from a sequential refinement
1742        rather than the main tree
1743        '''
1744        self.SeqRefdata = data
1745        self.SeqRefhist = hist
1746        data_name = data[hist]
1747        for i,val in zip(data_name['varyList'],data_name['sig']):
1748            self.sigDict[i] = val
1749            self.sigDict[striphist(i)] = val
1750        for i in data_name['parmDict']:
1751            self.parmDict[striphist(i)] = data_name['parmDict'][i]
1752            self.parmDict[i] = data_name['parmDict'][i]
1753            # zero out the dA[xyz] terms, they would only bring confusion
1754            key = i.split(':')
1755            if len(key) < 3: continue
1756            if key[2].startswith('dA'):
1757                self.parmDict[i] = 0.0
1758        for i,(val,sig) in data_name.get('depParmDict',{}).items():
1759            self.parmDict[i] = val
1760            self.sigDict[i] = sig
1761        #GSASIIpath.IPyBreak()
1762
1763    # Tools to pull information out of the data arrays
1764    def GetCell(self,phasenam):
1765        """Gets the unit cell parameters and their s.u.'s for a selected phase
1766
1767        :param str phasenam: the name for the selected phase
1768        :returns: `cellList,cellSig` where each is a 7 element list corresponding
1769          to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1770          cell values and `cellSig` has their uncertainties.
1771        """
1772        if self.SeqRefdata and self.SeqRefhist:
1773            return self.GetSeqCell(phasenam,self.SeqRefdata[self.SeqRefhist])
1774        phasedict = self.Phases[phasenam] # pointer to current phase info
1775        try:
1776            pfx = str(phasedict['pId'])+'::'
1777            A,sigA = G2stIO.cellFill(pfx,phasedict['General']['SGData'],self.parmDict,self.sigDict)
1778            cellSig = G2stIO.getCellEsd(pfx,phasedict['General']['SGData'],A,
1779                self.OverallParms['Covariance'])  # returns 7 vals, includes sigVol
1780            cellList = G2lat.A2cell(A) + (G2lat.calc_V(A),)
1781            return cellList,cellSig
1782        except KeyError:
1783            cell = phasedict['General']['Cell'][1:]
1784            return cell,7*[0]
1785           
1786    def GetSeqCell(self,phasenam,data_name):
1787        """Gets the unit cell parameters and their s.u.'s for a selected phase
1788        and histogram in a sequential fit
1789
1790        :param str phasenam: the name for the selected phase
1791        :param dict data_name: the sequential refinement parameters for the selected histogram
1792        :returns: `cellList,cellSig` where each is a 7 element list corresponding
1793          to a, b, c, alpha, beta, gamma, volume where `cellList` has the
1794          cell values and `cellSig` has their uncertainties.
1795        """
1796        phasedict = self.Phases[phasenam]
1797        SGdata = phasedict['General']['SGData']
1798        pId = phasedict['pId']
1799        RecpCellTerms = G2lat.cell2A(phasedict['General']['Cell'][1:7])
1800        ESDlookup = {}
1801        Dlookup = {}
1802        varied = [striphist(i) for i in data_name['varyList']]
1803        for item,val in data_name['newCellDict'].items():
1804            if item in varied:
1805                ESDlookup[val[0]] = item
1806                Dlookup[item] = val[0]
1807        A = RecpCellTerms[:]
1808        for i in range(6):
1809            var = str(pId)+'::A'+str(i)
1810            if var in ESDlookup:
1811                A[i] = data_name['newCellDict'][ESDlookup[var]][1] # override with refined value
1812        cellDict = dict(zip([str(pId)+'::A'+str(i) for i in range(6)],A))
1813        zeroDict = {i:0.0 for i in cellDict}
1814        A,zeros = G2stIO.cellFill(str(pId)+'::',SGdata,cellDict,zeroDict)
1815        covData = {
1816            'varyList': [Dlookup.get(striphist(v),v) for v in data_name['varyList']],
1817            'covMatrix': data_name['covMatrix']
1818            }
1819        return list(G2lat.A2cell(A)) + [G2lat.calc_V(A)], G2stIO.getCellEsd(str(pId)+'::',SGdata,A,covData)
1820               
1821    def GetAtoms(self,phasenam):
1822        """Gets the atoms associated with a phase. Can be used with standard
1823        or macromolecular phases
1824
1825        :param str phasenam: the name for the selected phase
1826        :returns: a list of items for eac atom where each item is a list containing:
1827          label, typ, mult, xyz, and td, where
1828
1829          * label and typ are the atom label and the scattering factor type (str)
1830          * mult is the site multiplicity (int)
1831          * xyz is contains a list with four pairs of numbers:
1832            x, y, z and fractional occupancy and
1833            their standard uncertainty (or a negative value)
1834          * td is contains a list with either one or six pairs of numbers:
1835            if one number it is U\\ :sub:`iso` and with six numbers it is
1836            U\\ :sub:`11`, U\\ :sub:`22`, U\\ :sub:`33`, U\\ :sub:`12`, U\\ :sub:`13` & U\\ :sub:`23`
1837            paired with their standard uncertainty (or a negative value)
1838        """
1839        phasedict = self.Phases[phasenam] # pointer to current phase info           
1840        cx,ct,cs,cia = phasedict['General']['AtomPtrs']
1841        cfrac = cx+3
1842        fpfx = str(phasedict['pId'])+'::Afrac:'       
1843        atomslist = []
1844        for i,at in enumerate(phasedict['Atoms']):
1845            if phasedict['General']['Type'] == 'macromolecular':
1846                label = '%s_%s_%s_%s'%(at[ct-1],at[ct-3],at[ct-4],at[ct-2])
1847            else:
1848                label = at[ct-1]
1849            fval = self.parmDict.get(fpfx+str(i),at[cfrac])
1850            fsig = self.sigDict.get(fpfx+str(i),-0.009)
1851            mult = at[cs+1]
1852            typ = at[ct]
1853            xyz = []
1854            for j,v in enumerate(('x','y','z')):
1855                val = at[cx+j]
1856                pfx = str(phasedict['pId']) + '::A' + v + ':' + str(i)
1857                val = self.parmDict.get(pfx, val)
1858                dpfx = str(phasedict['pId'])+'::dA'+v+':'+str(i)
1859                sig = self.sigDict.get(dpfx,-0.000009)
1860                xyz.append((val,sig))
1861            xyz.append((fval,fsig))
1862            td = []
1863            if at[cia] == 'I':
1864                pfx = str(phasedict['pId'])+'::AUiso:'+str(i)
1865                val = self.parmDict.get(pfx,at[cia+1])
1866                sig = self.sigDict.get(pfx,-0.0009)
1867                td.append((val,sig))
1868            else:
1869                for i,var in enumerate(('AU11','AU22','AU33','AU12','AU13','AU23')):
1870                    pfx = str(phasedict['pId'])+'::'+var+':'+str(i)
1871                    val = self.parmDict.get(pfx,at[cia+2+i])
1872                    sig = self.sigDict.get(pfx,-0.0009)
1873                    td.append((val,sig))
1874            atomslist.append((label,typ,mult,xyz,td))
1875        return atomslist
1876######################################################################
1877def ExportPowderList(G2frame):
1878    '''Returns a list of extensions supported by :func:`GSASIIIO:ExportPowder`
1879    along with their descriptions (note that a extension may be repeated
1880    but descriptions are unique).
1881    This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1882   
1883    :param wx.Frame G2frame: the GSAS-II main data tree window
1884    '''
1885    extList = []
1886    extLabel = []
1887    for obj in G2frame.exporterlist:
1888        if 'powder' in obj.exporttype:
1889            try:
1890                obj.Writer
1891                extList.append(obj.extension)
1892                extLabel.append(obj.formatName)
1893            except AttributeError:
1894                pass
1895    return extList,extLabel
1896
1897def ExportPowder(G2frame,TreeName,fileroot,extension,hint=''):
1898    '''Writes a single powder histogram using the Export routines.
1899    This is used in :meth:`GSASIIimgGUI.AutoIntFrame` only.
1900
1901    :param wx.Frame G2frame: the GSAS-II main data tree window
1902    :param str TreeName: the name of the histogram (PWDR ...) in the data tree
1903    :param str fileroot: name for file to be written, extension ignored
1904    :param str extension: extension for file to be written (start with '.'). Must
1905      match a powder export routine that has a Writer object.
1906    :param str hint: a string that must match the export's format
1907    '''
1908    filename = os.path.abspath(os.path.splitext(fileroot)[0]+extension)
1909    for obj in G2frame.exporterlist:
1910        if obj.extension == extension and 'powder' in obj.exporttype:
1911            if hint and hint not in obj.formatName: continue
1912            obj.currentExportType = 'powder'
1913            obj.InitExport(None)
1914            obj.loadTree() # load all histograms in tree into dicts
1915            if TreeName not in obj.Histograms:
1916                raise Exception('Histogram not found: '+str(TreeName))
1917            try:
1918                obj.Writer
1919            except AttributeError:
1920                continue
1921            try:
1922                obj.Writer(TreeName,filename)
1923                print('wrote file '+filename)
1924                return
1925            except Exception:
1926                print('Export Routine for '+extension+' failed.')
1927    else:
1928        print('No Export routine supports extension '+extension)
1929
1930def ExportSequential(G2frame,data,obj,exporttype):
1931    '''
1932    Used to export from every phase/dataset in a sequential refinement using
1933    a .Writer method for either projects or phases. Prompts to select histograms
1934    and for phase exports, which phase(s).
1935
1936    :param wx.Frame G2frame: the GSAS-II main data tree window
1937    :param dict data: the sequential refinement data object
1938    :param str exporttype: indicates the type of export ('project' or 'phase')
1939    '''
1940    if len(data['histNames']) == 0:
1941        G2G.G2MessageBox(G2frame,'There are no sequential histograms','Warning')
1942    obj.InitExport(None)
1943    obj.loadTree()
1944    obj.loadParmDict()
1945    if len(data['histNames']) == 1:
1946        histlist = data['histNames']
1947    else:
1948        dlg = G2G.G2MultiChoiceDialog(G2frame,'Select histograms to export from list',
1949                                 'Select histograms',data['histNames'])
1950        if dlg.ShowModal() == wx.ID_OK:
1951            histlist = [data['histNames'][l] for l in dlg.GetSelections()]
1952            dlg.Destroy()
1953        else:
1954            dlg.Destroy()
1955            return
1956    if exporttype == 'Phase':
1957        phaselist = list(obj.Phases.keys())
1958        if len(obj.Phases) == 0:
1959            G2G.G2MessageBox(G2frame,'There are no phases in sequential ref.','Warning')
1960            return
1961        elif len(obj.Phases) > 1:
1962            dlg = G2G.G2MultiChoiceDialog(G2frame,'Select phases to export from list',
1963                                    'Select phases', phaselist)
1964            if dlg.ShowModal() == wx.ID_OK:
1965                phaselist = [phaselist[l] for l in dlg.GetSelections()]
1966                dlg.Destroy()
1967            else:
1968                dlg.Destroy()
1969                return
1970        filename = obj.askSaveFile()
1971        if not filename: return True
1972        obj.dirname,obj.filename = os.path.split(filename)
1973        print('Writing output to file '+str(obj.filename)+"...")
1974        mode = 'w'
1975        for p in phaselist:
1976            for h in histlist:
1977                obj.SetSeqRef(data,h)
1978                #GSASIIpath.IPyBreak()
1979                obj.Writer(h,phasenam=p,mode=mode)
1980                mode = 'a'
1981        print('...done')
1982    elif exporttype == 'Project':  # note that the CIF exporter is not yet ready for this
1983        filename = obj.askSaveFile()
1984        if not filename: return True
1985        obj.dirname,obj.filename = os.path.split(filename)
1986        print('Writing output to file '+str(obj.filename)+"...")
1987        mode = 'w'
1988        for h in histlist:
1989            obj.SetSeqRef(data,h)
1990            obj.Writer(h,mode=mode)
1991            print('\t'+str(h)+' written')
1992            mode = 'a'
1993        print('...done')
1994    elif exporttype == 'Powder':
1995        filename = obj.askSaveFile()
1996        if not filename: return True
1997        obj.dirname,obj.filename = os.path.split(filename)
1998        print('Writing output to file '+str(obj.filename)+"...")
1999        mode = 'w'
2000        for h in histlist:
2001            obj.SetSeqRef(data,h)
2002            obj.Writer(h,mode=mode)
2003            print('\t'+str(h)+' written')
2004            mode = 'a'
2005        print('...done')
2006
2007def ReadDIFFaX(DIFFaXfile):
2008    print ('read '+DIFFaXfile)
2009    Layer = {'Laue':'-1','Cell':[False,1.,1.,1.,90.,90.,90,1.],'Width':[[10.,10.],[False,False]],
2010        'Layers':[],'Stacking':[],'Transitions':[],'Toler':0.01,'AtInfo':{}}
2011    df = open(DIFFaXfile,'r')
2012    lines = df.readlines()
2013    df.close()
2014    struct = False
2015    Struct = []
2016    stack = False
2017    Stack = []
2018    trans = False
2019    Trans = []
2020    for diff in lines:
2021        diff = diff[:-1].lower()
2022        if '!'  in diff:
2023            continue
2024        while '}' in diff: #strip comments
2025            iB = diff.index('{')
2026            iF = diff.index('}')+1
2027            if iB:
2028                diff = diff[:iB]
2029            else:
2030                diff = diff[iF:]
2031        if not diff:
2032            continue
2033        if diff.strip() == 'instrumental':
2034            continue
2035        if diff.strip() == 'structural':
2036            struct = True
2037            continue
2038        elif diff.strip() == 'stacking':
2039            struct = False
2040            stack = True
2041            continue
2042        elif diff.strip() == 'transitions':
2043            stack = False
2044            trans = True
2045            continue
2046        diff = diff.strip()
2047        if struct:
2048            if diff:
2049                Struct.append(diff)
2050        elif stack:
2051            if diff:
2052                Stack.append(diff)
2053        elif trans:
2054            if diff:
2055                Trans.append(diff)
2056   
2057#STRUCTURE records
2058    laueRec = Struct[1].split()
2059    Layer['Laue'] = laueRec[0]
2060    if Layer['Laue'] == 'unknown' and len(laueRec) > 1:
2061        Layer['Toler'] = float(laueRec[1])    #tolerance for 'unknown'?
2062    if Layer['Laue'] == '2/m(1)': Layer['Laue'] = '2/m(c)'
2063    if Layer['Laue'] == '2/m(2)': Layer['Laue'] = '2/m(ab)'
2064    cell = Struct[0].split()
2065    Layer['Cell'] = [False,float(cell[0]),float(cell[1]),float(cell[2]),90.,90.,float(cell[3]),1.0]
2066    nLayers = int(Struct[2])
2067    N = 3
2068    if 'layer' not in Struct[3]:
2069        N = 4
2070        if Struct[3] != 'infinite':
2071            width = Struct[3].split()
2072            Layer['Width'][0] = [float(width[0]),float(width[1])]
2073    for nL in range(nLayers):
2074        if '=' in Struct[N]:
2075            name = Struct[N].split('=')
2076            sameas = int(name[1])-1
2077            Layer['Layers'].append({'Name':name[0],'SameAs':Layer['Layers'][sameas]['Name'],'Symm':'None','Atoms':[]})
2078            N += 1
2079            continue
2080        Symm = 'None'
2081        if 'centro' in Struct[N+1]: Symm = '-1'
2082        Layer['Layers'].append({'Name':Struct[N],'SameAs':'','Symm':Symm,'Atoms':[]})
2083        N += 2
2084        while 'layer' not in Struct[N]:
2085            atom = Struct[N][4:].split()
2086            atomType = G2el.FixValence(Struct[N][:4].replace(' ','').strip().capitalize())
2087            if atomType not in Layer['AtInfo']:
2088                Layer['AtInfo'][atomType] = G2el.GetAtomInfo(atomType)
2089            atomName = '%s(%s)'%(atomType,atom[0])
2090            newVals = []
2091            for val in atom[1:6]:
2092                if '/' in val:
2093                    newVals.append(eval(val+'.'))
2094                else:
2095                    newVals.append(float(val))               
2096            atomRec = [atomName,atomType,newVals[0],newVals[1],newVals[2],newVals[4],newVals[3]/78.9568]
2097            Layer['Layers'][-1]['Atoms'].append(atomRec)
2098            N += 1
2099            if N > len(Struct)-1:
2100                break
2101#TRANSITIONS records
2102    transArray = []
2103    N = 0
2104    for i in range(nLayers):
2105        transArray.append([])
2106        for j in range(nLayers):
2107            vals = Trans[N].split()
2108            newVals = []
2109            for val in vals[:4]:
2110                if '/' in val:
2111                    newVals.append(eval(val+'.'))
2112                else:
2113                    newVals.append(float(val))
2114            transArray[-1].append(newVals+['',False])
2115            N += 1
2116    Layer['Transitions'] = transArray
2117#STACKING records
2118    Layer['Stacking'] = [Stack[0],'']
2119    if Stack[0] == 'recursive':
2120        Layer['Stacking'][1] = Stack[1]
2121    elif Stack[0] == 'explicit':
2122        if Stack[1] == 'random':
2123            Layer['Stacking'][1] = Stack[1]
2124        else:
2125            Layer['Stacking'][1] = 'list'
2126            Layer['Stacking'].append('')
2127            for stack in Stack[2:]:
2128                Layer['Stacking'][2] += ' '+stack
2129    return Layer
2130
2131def postURL(URL,postdict):
2132    '''Posts a set of values as from a web form. If access fails to an https
2133    site the access is retried with http.
2134
2135    :param str URL: the URL to post; typically something
2136       like 'http://www.../dir/page?'
2137    :param dict postdict: contains keywords and values, such
2138       as {'centrosymmetry': '0', 'crystalsystem': '0', ...}
2139    :returns: a string with the response from the web server or None
2140       if access fails.
2141    '''
2142    try:
2143        import requests # delay this until now, since rarely needed
2144    except:
2145        # this import seems to fail with the Anaconda pythonw on
2146        # macs; it should not!
2147        print('Warning: failed to import requests. Python config error')
2148        return None
2149       
2150    repeat = True
2151    while repeat:
2152        r = None
2153        repeat = False
2154        try:
2155            r = requests.get(URL,params=postdict)
2156            if r.status_code == 200:
2157                print('request OK')
2158                page = r.text
2159                return page # success
2160            else:
2161                print('request to {} failed. Reason={}'.format(URL,r.reason))
2162        except Exception as msg:     #ConnectionError?
2163            print('connection error - not on internet?')
2164            if GSASIIpath.GetConfigValue('debug'): print(msg)
2165        finally:
2166            if r: r.close()
2167        if URL.startswith('https:'):
2168            repeat = True
2169            URL = URL.replace('https:','http:')
2170    else:
2171        return None
2172
2173if __name__ == '__main__':
2174    import GSASIIdataGUI
2175    application = GSASIIdataGUI.GSASIImain(0)
2176    G2frame = application.main
2177    #app = wx.PySimpleApp()
2178    #G2frame = wx.Frame(None) # create a frame
2179    #frm.Show(True)
2180    #filename = '/tmp/notzip.zip'
2181    #filename = '/tmp/all.zip'
2182    #filename = '/tmp/11bmb_7652.zip'
2183   
2184    #selection=None, confirmoverwrite=True, parent=None
2185    #print ExtractFileFromZip(filename, selection='11bmb_7652.fxye',parent=frm)
2186    #print ExtractFileFromZip(filename,multipleselect=True)
2187    #                         #confirmread=False, confirmoverwrite=False)
2188
2189    # choicelist=[ ('a','b','c'),
2190    #              ('test1','test2'),('no choice',)]
2191    # titles = [ 'a, b or c', 'tests', 'No option here']
2192    # dlg = MultipleChoicesDialog(
2193    #     choicelist,titles,
2194    #     parent=frm)
2195    # if dlg.ShowModal() == wx.ID_OK:
2196    #     print 'Got OK'
2197    imagefile = '/tmp/NDC5_00237_3.ge3'
2198    Comments, Data, Npix, Image = GetImageData(G2frame,imagefile,imageOnly=False,ImageTag=None)
2199
2200    print("\n\nResults loaded to Comments, Data, Npix and Image\n\n")
2201
2202    GSASIIpath.IPyBreak_base()
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